Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397257.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_95.0, whole genome shotgun sequence
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: 12062019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 103452 characters in sequence are not A, C, G, or T
File 6 of 26
Found at i:1963299 original size:17 final size:17
Alignment explanation
Indices: 1963279--1963324 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
1963269 TGAATCATTG
*
1963279 TATATATTTGTACGAAA
1 TATATATTTGTACAAAA
1963296 TATATATTTGTACAAAA
1 TATATATTTGTACAAAA
1963313 TATATATTTGTA
1 TATATATTTGTA
1963325 GTTTTAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (17 bp):
TATATATTTGTACAAAA
Found at i:1963529 original size:15 final size:14
Alignment explanation
Indices: 1963506--1963540 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1963496 GAAACTATTT
1963506 TTTTCTTTCTTCCC
1 TTTTCTTTCTTCCC
1963520 TTTTCGTTTCTTCCC
1 TTTTC-TTTCTTCCC
*
1963535 TATTCT
1 TTTTCT
1963541 CTTGCCCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.03, C:0.31, G:0.03, T:0.63
Consensus pattern (14 bp):
TTTTCTTTCTTCCC
Found at i:1964214 original size:27 final size:27
Alignment explanation
Indices: 1964088--1964393 Score: 226
Period size: 27 Copynumber: 11.1 Consensus size: 27
1964078 GCTATGTTTT
* * *
1964088 AAAATTTAATTATTGCACGTCATATTG
1 AAAATTTAATTGTTACACGTCATGTTG
*
1964115 AAAA--TAATTGTTACAC-ACTATGTTG
1 AAAATTTAATTGTTACACGTC-ATGTTG
* ** *
1964140 AAAAATGTAATTGTTATGCGTGATGTTG
1 -AAAATTTAATTGTTACACGTCATGTTG
* *
1964168 AAAATATAGTTATTGTTGTTACATGTCATGTTG
1 -AAA-AT--TTA--ATTGTTACACGTCATGTTG
* *
1964201 AAGATTTAATTGTTACACATCATGTTG
1 AAAATTTAATTGTTACACGTCATGTTG
* * *
1964228 AAAGTTTAATTGTTACATGTCATGTTA
1 AAAATTTAATTGTTACACGTCATGTTG
* *
1964255 AAAATATAATTATTACACGTCATGTTG
1 AAAATTTAATTGTTACACGTCATGTTG
*
1964282 AAAATTTAATTGTTACACGTCATGTTAA
1 AAAATTTAATTGTTACACGTCATGTT-G
* * * * **
1964310 AAAATATAATTATTACATGTCATATAA
1 AAAATTTAATTGTTACACGTCATGTTG
* * * *
1964337 AAAATTTTATCGTTACACGACATGTAG
1 AAAATTTAATTGTTACACGTCATGTTG
*
1964364 AAAATTTTAA-T-TTACACGTCATGATG
1 AAAA-TTTAATTGTTACACGTCATGTTG
1964390 AAAA
1 AAAA
1964394 AATTGTTAAA
Statistics
Matches: 218, Mismatches: 49, Indels: 25
0.75 0.17 0.09
Matches are distributed among these distances:
24 1 0.00
25 15 0.07
26 20 0.09
27 112 0.51
28 45 0.21
29 5 0.02
31 4 0.02
32 2 0.01
33 14 0.06
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.39
Consensus pattern (27 bp):
AAAATTTAATTGTTACACGTCATGTTG
Found at i:1971114 original size:15 final size:15
Alignment explanation
Indices: 1971094--1971129 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
1971084 ATTACTATTT
1971094 TATATATACTTTTAA
1 TATATATACTTTTAA
1971109 TATATATACTTTTAA
1 TATATATACTTTTAA
1971124 TATATA
1 TATATA
1971130 AATATATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATACTTTTAA
Found at i:1972395 original size:23 final size:22
Alignment explanation
Indices: 1972365--1972465 Score: 123
Period size: 23 Copynumber: 4.4 Consensus size: 22
1972355 GTTTAGAGTT
1972365 TGTGACACGCCATGG-GAGGAATG
1 TGTGACACG-CATGGTGA-GAATG
1972388 TGTGACACAGCATGGTGAGAATG
1 TGTGACAC-GCATGGTGAGAATG
* * *
1972411 TGTGACATGGTATGGTGAGAATT
1 TGTGACA-CGCATGGTGAGAATG
1972434 TGTGACACGACATGGTGAGAATG
1 TGTGACACG-CATGGTGAGAATG
1972457 TGTGACACG
1 TGTGACACG
1972466 GCTGTGACAC
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
22 1 0.01
23 64 0.94
24 3 0.04
ACGTcount: A:0.28, C:0.13, G:0.36, T:0.24
Consensus pattern (22 bp):
TGTGACACGCATGGTGAGAATG
Found at i:1972556 original size:127 final size:127
Alignment explanation
Indices: 1972327--1972601 Score: 309
Period size: 127 Copynumber: 2.2 Consensus size: 127
1972317 ACAACAAGCC
* * **
1972327 ATATGTGACATGGCTGTGACACGACAAGGTTTAGAGTTTGTGACACGCCATGGGAGGAATGTGTG
1 ATATGTGACACGGCTGTGACACGACAAGGTTTAGAGTTTGTGACACGCCATGGGAAGAACATGTG
* * * * * ** * *
1972392 ACACAGCATGGTGAGAATGTGTGACATGGTATGGTGAGAATTTGTGACACGACATGGTGAGA
66 ACACAGCATGATAAAAATCTGTGACACGACATGGTGAGAATGTGTGACACGACATCGTGAGA
* ** * * * *
1972454 ATGTGTGACACGGCTGTGACACGGTAGGGTTTAGAGTTTGT-ACCATGTCATGGTAAGAACATGT
1 ATATGTGACACGGCTGTGACACGACAAGGTTTAGAGTTTGTGA-CACGCCATGGGAAGAACATGT
* * * *
1972518 GACACCGCATGATAAAAATCTGTGACACGACATGGTGAGAATGTGTGACATGGCATCTTGAGA
65 GACACAGCATGATAAAAATCTGTGACACGACATGGTGAGAATGTGTGACACGACATCGTGAGA
*
1972581 ATATGTGACACGGTTGTGACA
1 ATATGTGACACGGCTGTGACA
1972602 TTATAGGTTT
Statistics
Matches: 121, Mismatches: 26, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
126 1 0.01
127 120 0.99
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.26
Consensus pattern (127 bp):
ATATGTGACACGGCTGTGACACGACAAGGTTTAGAGTTTGTGACACGCCATGGGAAGAACATGTG
ACACAGCATGATAAAAATCTGTGACACGACATGGTGAGAATGTGTGACACGACATCGTGAGA
Found at i:1972564 original size:23 final size:23
Alignment explanation
Indices: 1972538--1972592 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
1972528 GATAAAAATC
* *
1972538 TGTGACACGACATGGTGAGAATG
1 TGTGACACGACATCGTGAGAATA
* * *
1972561 TGTGACATGGCATCTTGAGAATA
1 TGTGACACGACATCGTGAGAATA
1972584 TGTGACACG
1 TGTGACACG
1972593 GTTGTGACAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (23 bp):
TGTGACACGACATCGTGAGAATA
Found at i:1972646 original size:23 final size:23
Alignment explanation
Indices: 1972620--1972687 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
1972610 TTATGACATG
*
1972620 GCATGGTGGGAATGTGTGACACA
1 GCATGGTGAGAATGTGTGACACA
* * *
1972643 GCATGATGAGAATGTGTGAGATA
1 GCATGGTGAGAATGTGTGACACA
* *
1972666 GCATGGTGAAAATGTTTGACAC
1 GCATGGTGAGAATGTGTGACAC
1972688 GGTTGTGACA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.31, C:0.10, G:0.34, T:0.25
Consensus pattern (23 bp):
GCATGGTGAGAATGTGTGACACA
Found at i:1972759 original size:23 final size:22
Alignment explanation
Indices: 1972733--1972792 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
1972723 TCCATGATGG
* * *
1972733 GAATGTGAAACACGACATTGTGA
1 GAATGTGTAACACG-CATGGTAA
*
1972756 GAATATGTAACACTGCATGGTAA
1 GAATGTGTAACAC-GCATGGTAA
1972779 GAATGTGTAACACG
1 GAATGTGTAACACG
1972793 GCTGTAACAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 1 0.03
23 29 0.94
24 1 0.03
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.23
Consensus pattern (22 bp):
GAATGTGTAACACGCATGGTAA
Found at i:1972878 original size:23 final size:23
Alignment explanation
Indices: 1972819--1972878 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
1972809 GTTTAGAGTT
* *
1972819 TGTGACATGGCATAATGGGAATA
1 TGTGACATGGCATGATGAGAATA
* *
1972842 TGTGACATGACATGATGAGAATG
1 TGTGACATGGCATGATGAGAATA
1972865 TGTGACATGGCATG
1 TGTGACATGGCATG
1972879 TCACGACAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.32, C:0.10, G:0.32, T:0.27
Consensus pattern (23 bp):
TGTGACATGGCATGATGAGAATA
Found at i:1972878 original size:104 final size:102
Alignment explanation
Indices: 1972608--1972878 Score: 278
Period size: 104 Copynumber: 2.6 Consensus size: 102
1972598 GACATTATAG
* * * *
1972608 GTTTATGACATGGCATGGTGGGAATGTGTGACACAGCATGATGAGAATGTGTGAGATAGCATGGT
1 GTTTGTGACATGGCATGATGGGAATGTGTGACAGA-CATGATGAGAATGTGTGACAT-GCATGGT
* * * * **
1972673 GAAAATGTTTGACACGGTTGTGACATGGTAAAGTTTAGA
64 GAAAATGTGTAACACGGCTGTAACATGACAAAGTTTAGA
* ** * *
1972712 GTTTGTGACACT-CCATGATGGGAATGTGAAACACGACATTG-TGAGAATATGTAACACTGCATG
1 GTTTGTGACA-TGGCATGATGGGAATGTGTGACA-GACA-TGATGAGAATGTGTGACA-TGCATG
*
1972775 GT-AAGAATGTGTAACACGGCTGTAACATGACAAGGTTTAGA
62 GTGAA-AATGTGTAACACGGCTGTAACATGACAAAGTTTAGA
* *
1972816 GTTTGTGACATGGCATAATGGGAATATGTGACATGACATGATGAGAATGTGTGACATGGCATG
1 GTTTGTGACATGGCATGATGGGAATGTGTGACA-GACATGATGAGAATGTGTGACAT-GCATG
1972879 TCACGACAAG
Statistics
Matches: 135, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
103 6 0.04
104 124 0.92
105 5 0.04
ACGTcount: A:0.31, C:0.11, G:0.30, T:0.28
Consensus pattern (102 bp):
GTTTGTGACATGGCATGATGGGAATGTGTGACAGACATGATGAGAATGTGTGACATGCATGGTGA
AAATGTGTAACACGGCTGTAACATGACAAAGTTTAGA
Found at i:1973184 original size:79 final size:78
Alignment explanation
Indices: 1973036--1973209 Score: 186
Period size: 79 Copynumber: 2.2 Consensus size: 78
1973026 AAGCATGGCG
* * * * * * * * **
1973036 TGTCACCTTATAATACTGCAACGATAGGTGTCTTGTCATGACAAGATGTCACTGACATCTAATCT
1 TGTCACCCTATAATACTACAACGACAGATGACATGTCACGACAAGATGTCAATGACATCTAATAA
* **
1973101 TTGGAGCGTGGTA
66 TTGGAGAGTGACA
* * *
1973114 TGTCACCCTATAATACTACAACGACATGATGACATGTCACGATAAGATGTCAATGCCATCTAGTA
1 TGTCACCCTATAATACTACAACGACA-GATGACATGTCACGACAAGATGTCAATGACATCTAATA
*
1973179 ATTGGAGAGTGACG
65 ATTGGAGAGTGACA
1973193 TGTCACCCTATAATACT
1 TGTCACCCTATAATACT
1973210 GCAATGACTT
Statistics
Matches: 78, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
78 23 0.29
79 55 0.71
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (78 bp):
TGTCACCCTATAATACTACAACGACAGATGACATGTCACGACAAGATGTCAATGACATCTAATAA
TTGGAGAGTGACA
Found at i:1973266 original size:70 final size:71
Alignment explanation
Indices: 1973180--1973452 Score: 216
Period size: 72 Copynumber: 3.8 Consensus size: 71
1973170 CATCTAGTAA
* * *
1973180 TTGGAGAGTGACGTGTCACCCTATAATACTGCAATGACTTG-TGTGTCACCACAAGATGT-TA-A
1 TTGGAGAGTGGCGTGTCACCCTATAATACTGCAATGACTCGACGTGTCACCACAAGATGTCTACA
1973242 TGACAT-T
66 --ACATCT
* * * * *
1973249 TTCGGAGAGTGGTGTGTCACTCTATAATACTGCAA-GACAAGGCGACGTGTCACGATAAGATGTC
1 TT-GGAGAGTGGCGTGTCACCCTATAATACTGCAATGAC---TCGACGTGTCACCACAAGATGTC
1973313 TACAACATCT
62 TACAACATCT
* * * *
1973323 TTGGAGAGTGGCATGTCACCCTATAATACTGCAATGACTCATACGTGTCACAACAAGATGTCAAC
1 TTGGAGAGTGGCGTGTCACCCTATAATACTGCAATGACTC-GACGTGTCACCACAAGATGTCTAC
* *
1973388 GATATCT
65 AACATCT
* * ** * ** * * *
1973395 TTAGAAAGCAGAGTGTCACTTTATAATACTACAATGACT-TAGCGTGTCACGACAAGAT
1 TTGGAGAGTGGCGTGTCACCCTATAATACTGCAATGACTCGA-CGTGTCACCACAAGAT
1973453 ACCAACGACA
Statistics
Matches: 165, Mismatches: 28, Indels: 20
0.77 0.13 0.09
Matches are distributed among these distances:
69 5 0.03
70 31 0.19
71 16 0.10
72 56 0.34
73 48 0.29
74 8 0.05
75 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (71 bp):
TTGGAGAGTGGCGTGTCACCCTATAATACTGCAATGACTCGACGTGTCACCACAAGATGTCTACA
ACATCT
Found at i:1973441 original size:143 final size:141
Alignment explanation
Indices: 1973180--1973452 Score: 309
Period size: 143 Copynumber: 1.9 Consensus size: 141
1973170 CATCTAGTAA
* ** * * *
1973180 TTGGAGAGTGACGTGTCACCCTATAATACTGCAATGACTTGTGTGTCACCACAAGATGTTAATGA
1 TTGGAGAGTGACATGTCACCCTATAATACTGCAATGACTTACGTGTCACAACAAGATGTCAACGA
* * ** * * *
1973245 CATTTTCGGAGAGTGGTGTGTCACTCTATAATACTGCAAGACAAGGCGACGTGTCACGATAAGAT
66 CATTTTCAGAAAGCAGAGTGTCACTCTATAATACTACAAGACAA-G-GACGTGTCACGACAAGAT
1973310 GTCTACAACATCT
129 GTCTACAACATCT
*
1973323 TTGGAGAGTGGCATGTCACCCTATAATACTGCAATGACTCATACGTGTCACAACAAGATGTCAAC
1 TTGGAGAGTGACATGTCACCCTATAATACTGCAATGACT--TACGTGTCACAACAAGATGTCAAC
* * *
1973388 GATATCTTT-AGAAAGCAGAGTGTCACTTTATAATACTACAATGACTTA-G-CGTGTCACGACAA
64 GACAT-TTTCAGAAAGCAGAGTGTCACTCTATAATACTACAA-GAC-AAGGACGTGTCACGACAA
1973450 GAT
126 GAT
1973453 ACCAACGACA
Statistics
Matches: 108, Mismatches: 17, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
143 52 0.48
144 1 0.01
145 48 0.44
146 6 0.06
147 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (141 bp):
TTGGAGAGTGACATGTCACCCTATAATACTGCAATGACTTACGTGTCACAACAAGATGTCAACGA
CATTTTCAGAAAGCAGAGTGTCACTCTATAATACTACAAGACAAGGACGTGTCACGACAAGATGT
CTACAACATCT
Found at i:1982345 original size:19 final size:19
Alignment explanation
Indices: 1982321--1982358 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1982311 ATTAAATTAG
1982321 ATAAAAATAAAAAATTTAA
1 ATAAAAATAAAAAATTTAA
**
1982340 ATAAAAATTTAAAATTTAA
1 ATAAAAATAAAAAATTTAA
1982359 TTTAAACACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAAAAATAAAAAATTTAA
Found at i:1983014 original size:33 final size:33
Alignment explanation
Indices: 1982967--1983032 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
1982957 TAATAAGTTG
*
1982967 ATTGGAGAACAACTAAGAAATAAGAAATAGTCT
1 ATTGAAGAACAACTAAGAAATAAGAAATAGTCT
1983000 ATTGAAGAACAACTAAGAAATAAGAAATAGTCT
1 ATTGAAGAACAACTAAGAAATAAGAAATAGTCT
1983033 CATGTATCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (33 bp):
ATTGAAGAACAACTAAGAAATAAGAAATAGTCT
Found at i:1987132 original size:30 final size:30
Alignment explanation
Indices: 1987096--1987184 Score: 124
Period size: 30 Copynumber: 3.0 Consensus size: 30
1987086 GTTAGTGCGT
* * * *
1987096 GTTTATGGTTGAGCTTGTTAGAAACCTTGG
1 GTTTATGGTTGAACTTGTTAAAAACCATGA
1987126 GTTTATGGTTGAACTTGTTAAAAACCATGA
1 GTTTATGGTTGAACTTGTTAAAAACCATGA
**
1987156 GTTTATGGTTGAACTCATTAAAAACCATG
1 GTTTATGGTTGAACTTGTTAAAAACCATG
1987185 GGATGGGTGT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.37
Consensus pattern (30 bp):
GTTTATGGTTGAACTTGTTAAAAACCATGA
Found at i:1988174 original size:16 final size:16
Alignment explanation
Indices: 1988144--1988173 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1988134 CTAAAATTTA
1988144 GATTTTGATTCTTTTC
1 GATTTTGATTCTTTTC
1988160 GATTTTGATT-TTTT
1 GATTTTGATTCTTTT
1988174 TGATATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (16 bp):
GATTTTGATTCTTTTC
Found at i:1989512 original size:42 final size:42
Alignment explanation
Indices: 1989422--1989584 Score: 202
Period size: 42 Copynumber: 3.9 Consensus size: 42
1989412 GTGTTGTGAT
* * *
1989422 GTGGATTGAGAAGGTCTCCACATTCCCATAATTTTGTCGTAAA
1 GTGGATTGAGTAGGTCTCCAC-TTCCCATGATTTTGTGGTAAA
* * *
1989465 GTGGATTGAGCATGTCTCCACTTCTCATGATTTTGTGGTAAA
1 GTGGATTGAGTAGGTCTCCACTTCCCATGATTTTGTGGTAAA
* * * *
1989507 ATGGATTGAGTAAGTCTCCAATTTCCATGATTTT-TGTGTAAA
1 GTGGATTGAGTAGGTCTCCACTTCCCATGATTTTGTG-GTAAA
*
1989549 GTGGATTGAGTAGGTCTCCATTTCCCATGATTTTGT
1 GTGGATTGAGTAGGTCTCCACTTCCCATGATTTTGT
1989585 ATATTGGCTC
Statistics
Matches: 103, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
41 2 0.02
42 81 0.79
43 20 0.19
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (42 bp):
GTGGATTGAGTAGGTCTCCACTTCCCATGATTTTGTGGTAAA
Found at i:1989566 original size:84 final size:85
Alignment explanation
Indices: 1989423--1989584 Score: 231
Period size: 84 Copynumber: 1.9 Consensus size: 85
1989413 TGTTGTGATG
*
1989423 TGGATTGAGAAGGTCTCCACATTCCCATAATTTTGTCGTAAAGTGGATTGAGCATGTCTCCACTT
1 TGGATTGAGAAGGTCTCCACATTCCCATAATTTTGTCGTAAAGTGGATTGAGCAGGTCTCCACTT
*
1989488 CTCATGATTTTGTGGTAAAA
66 CCCATGATTTTGTGGTAAAA
* * * *
1989508 TGGATTGAGTAA-GTCTCCA-ATTTCCATGATTTTTGT-GTAAAGTGGATTGAGTAGGTCTCCAT
1 TGGATTGAG-AAGGTCTCCACATTCCCAT-AATTTTGTCGTAAAGTGGATTGAGCAGGTCTCCAC
1989570 TTCCCATGATTTTGT
64 TTCCCATGATTTTGT
1989585 ATATTGGCTC
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
84 44 0.64
85 23 0.33
86 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (85 bp):
TGGATTGAGAAGGTCTCCACATTCCCATAATTTTGTCGTAAAGTGGATTGAGCAGGTCTCCACTT
CCCATGATTTTGTGGTAAAA
Found at i:1992556 original size:21 final size:21
Alignment explanation
Indices: 1992530--1992575 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1992520 TTCTTGGCAA
*
1992530 TGGTTAAGGACACATAAATGG
1 TGGTTAAGGACACACAAATGG
1992551 TGGTTAAGGACACACAAATGG
1 TGGTTAAGGACACACAAATGG
1992572 TGGT
1 TGGT
1992576 GAATGAGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.11, G:0.30, T:0.24
Consensus pattern (21 bp):
TGGTTAAGGACACACAAATGG
Found at i:1992587 original size:12 final size:12
Alignment explanation
Indices: 1992570--1992598 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1992560 ACACACAAAT
1992570 GGTGGTGAATGA
1 GGTGGTGAATGA
1992582 GGTGGTGAATGA
1 GGTGGTGAATGA
1992594 GGTGG
1 GGTGG
1992599 CTAATATGCC
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:0.21, C:0.00, G:0.55, T:0.24
Consensus pattern (12 bp):
GGTGGTGAATGA
Found at i:1995906 original size:31 final size:29
Alignment explanation
Indices: 1995871--1996005 Score: 116
Period size: 28 Copynumber: 4.6 Consensus size: 29
1995861 TTACGATAAC
1995871 TCTTGTCTTTAATTAAGAAAAAAATATTTT
1 TCTTGTC-TTAATTAAGAAAAAAATATTTT
* ***
1995901 ATCTTGTCTAAATT--GAGGTAAATATGTTT
1 -TCTTGTCTTAATTAAGAAAAAAATAT-TTT
1995930 TCTTGTC-TAGATTAAGACAAAAAATATTTT
1 TCTTGTCTTA-ATTAAGA-AAAAAATATTTT
* * *
1995960 TCTTATTTTAAATTAAGATAAAAATA-TTT
1 TCTTGTCTT-AATTAAGAAAAAAATATTTT
*
1995989 TCTTGTCTAAATTAAGA
1 TCTTGTCTTAATTAAGA
1996006 CTATACATGT
Statistics
Matches: 83, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
27 1 0.01
28 26 0.31
29 12 0.14
30 22 0.27
31 21 0.25
32 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (29 bp):
TCTTGTCTTAATTAAGAAAAAAATATTTT
Found at i:1995933 original size:28 final size:27
Alignment explanation
Indices: 1995892--1996034 Score: 124
Period size: 28 Copynumber: 5.0 Consensus size: 27
1995882 ATTAAGAAAA
* *
1995892 AAATATTTTATCTTGTCTAAATTGAGGT
1 AAATATTTT-TCTTGTCTAAATTAAGAT
* *
1995920 AAATATGTTTTCTTGTCTAGATTAAGACAAA
1 AAATAT-TTTTCTTGTCTAAATTAAG---AT
* *
1995951 AAATATTTTTCTTATTTTAAATTAAGAT
1 AAATATTTTTCTT-GTCTAAATTAAGAT
*
1995979 AAAAATATTTTCTTGTCTAAATTAAGACT
1 AAATAT-TTTTCTTGTCTAAATTAAGA-T
* *
1996008 ATACATGTTTTCTTGTCTAAATTAAGA
1 AAATAT-TTTTCTTGTCTAAATTAAGA
1996035 CAAACATGTT
Statistics
Matches: 94, Mismatches: 14, Indels: 13
0.78 0.12 0.11
Matches are distributed among these distances:
28 37 0.39
29 35 0.37
30 7 0.07
31 15 0.16
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (27 bp):
AAATATTTTTCTTGTCTAAATTAAGAT
Found at i:1995972 original size:59 final size:59
Alignment explanation
Indices: 1995871--1996034 Score: 174
Period size: 59 Copynumber: 2.8 Consensus size: 59
1995861 TTACGATAAC
* * * * *
1995871 TCTTGTCTTTAATTAAGA-AAAAAATATTTTATCTTGTCTAAATTGAGGTAAATATGTTT
1 TCTTGTC-TAAATTAAGACAAAAAATATTTTATCTTGTCTAAATTAAGATAAAAATATTT
* * *
1995930 TCTTGTCTAGATTAAGACAAAAAATATTTT-TCTTATTTTAAATTAAGATAAAAATATTT
1 TCTTGTCTAAATTAAGACAAAAAATATTTTATCTT-GTCTAAATTAAGATAAAAATATTT
* * * *
1995989 TCTTGTCTAAATTAAGACTATACAT-GTTT-TCTTGTCTAAATTAAGA
1 TCTTGTCTAAATTAAGACAAAAAATATTTTATCTTGTCTAAATTAAGA
1996035 CAAACATGTT
Statistics
Matches: 88, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
57 11 0.12
58 19 0.22
59 58 0.66
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.45
Consensus pattern (59 bp):
TCTTGTCTAAATTAAGACAAAAAATATTTTATCTTGTCTAAATTAAGATAAAAATATTT
Found at i:1996018 original size:29 final size:29
Alignment explanation
Indices: 1995871--1996044 Score: 140
Period size: 29 Copynumber: 6.0 Consensus size: 29
1995861 TTACGATAAC
* * *
1995871 TCTTGTCTTTAATTAAGA-AAAAAATATTTT
1 TCTTGTC-TAAATTAAGACTAAAAAT-GTTT
* * *
1995901 ATCTTGTCTAAATTGAG-GTAAATATGTTT
1 -TCTTGTCTAAATTAAGACTAAAAATGTTT
* * *
1995930 TCTTGTCTAGATTAAGACAAAAAATATTTT
1 TCTTGTCTAAATTAAGACTAAAAAT-GTTT
* * *
1995960 TCTTATTTTAAATTAAGA-TAAAAATATTT
1 TCTT-GTCTAAATTAAGACTAAAAATGTTT
* *
1995989 TCTTGTCTAAATTAAGACTATACATGTTT
1 TCTTGTCTAAATTAAGACTAAAAATGTTT
*
1996018 TCTTGTCTAAATTAAGAC-AAACATGTT
1 TCTTGTCTAAATTAAGACTAAAAATGTT
1996045 AAAGCTGCCA
Statistics
Matches: 116, Mismatches: 22, Indels: 13
0.77 0.15 0.09
Matches are distributed among these distances:
28 33 0.28
29 41 0.35
30 25 0.22
31 17 0.15
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (29 bp):
TCTTGTCTAAATTAAGACTAAAAATGTTT
Found at i:1998050 original size:16 final size:16
Alignment explanation
Indices: 1998029--1998061 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1998019 TATCTGCTTG
*
1998029 TTCTTATGATCCCTTA
1 TTCTTACGATCCCTTA
1998045 TTCTTACGATCCCTTA
1 TTCTTACGATCCCTTA
1998061 T
1 T
1998062 AAGTTTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.27, G:0.06, T:0.48
Consensus pattern (16 bp):
TTCTTACGATCCCTTA
Found at i:2002659 original size:33 final size:34
Alignment explanation
Indices: 2002617--2002682 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
2002607 TAGAATTTGA
2002617 ATATAAGAAAAAGTC-TTTTTCTTAAAAAAATTG
1 ATATAAGAAAAAGTCTTTTTTCTTAAAAAAATTG
*
2002650 ATATAAGAAAAATTCTTTTTTCTTAAAAAAATT
1 ATATAAGAAAAAGTCTTTTTTCTTAAAAAAATT
2002683 AACAATCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 14 0.45
34 17 0.55
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (34 bp):
ATATAAGAAAAAGTCTTTTTTCTTAAAAAAATTG
Found at i:2004029 original size:59 final size:58
Alignment explanation
Indices: 2003931--2004091 Score: 184
Period size: 59 Copynumber: 2.8 Consensus size: 58
2003921 TCTGGTCTTT
* *
2003931 GATTAAGATAAAAATATTTTATCTTGT-TTAAATTGAGACAAATATGTTTTATTGTCTA
1 GATTAAGATAAAAATATTTT-TCTTGTCTTAAATTAAGACAAATATATTTTATTGTCTA
* * * *
2003989 GATTAAAATAAAAAATATTTTTCTTGTCTTAAATTAAGACAAACATATTTTTTTGTTTA
1 GATTAAGAT-AAAAATATTTTTCTTGTCTTAAATTAAGACAAATATATTTTATTGTCTA
* * * *
2004048 AATTAAGACAAACAT-GTTTTCTTGTC-TAAATTAAGACAACATAT
1 GATTAAGATAAAAATATTTTTCTTGTCTTAAATTAAGACAA-ATAT
2004092 TAAAATTGTA
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
56 13 0.15
57 13 0.15
58 19 0.22
59 43 0.49
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.42
Consensus pattern (58 bp):
GATTAAGATAAAAATATTTTTCTTGTCTTAAATTAAGACAAATATATTTTATTGTCTA
Found at i:2004100 original size:28 final size:28
Alignment explanation
Indices: 2003932--2004092 Score: 135
Period size: 28 Copynumber: 5.6 Consensus size: 28
2003922 CTGGTCTTTG
* * *
2003932 ATTAAGATAAAAATATTTTATCTTGTTTAA
1 ATTAAGACAAACATATTTTA--TTGTCTAA
* * * *
2003962 ATTGAGACAAATATGTTTTATTGTCTAG
1 ATTAAGACAAACATATTTTATTGTCTAA
* * * *
2003990 ATTAAAATAAAAAATATTTTTCTTGTCTTAA
1 ATTAAGA-CAAACATA-TTTTATTGTC-TAA
* *
2004021 ATTAAGACAAACATATTTTTTTGTTTAA
1 ATTAAGACAAACATATTTTATTGTCTAA
* *
2004049 ATTAAGACAAACATGTTTTCTTGTCTAA
1 ATTAAGACAAACATATTTTATTGTCTAA
2004077 ATTAAGAC-AACATATT
1 ATTAAGACAAACATATT
2004093 AAAATTGTAT
Statistics
Matches: 106, Mismatches: 22, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
27 7 0.07
28 47 0.44
29 13 0.12
30 31 0.29
31 8 0.08
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (28 bp):
ATTAAGACAAACATATTTTATTGTCTAA
Found at i:2005626 original size:21 final size:23
Alignment explanation
Indices: 2005584--2005654 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 23
2005574 TAAAGATGCT
*
2005584 TTTCATGTAAAATGTATTGATACA
1 TTTCAT-TAAAAGGTATTGATACA
* *
2005608 TTTCATT-AAA-GTATCGATAGA
1 TTTCATTAAAAGGTATTGATACA
**
2005629 TTTTTTTAAAAGGTATTGATACA
1 TTTCATTAAAAGGTATTGATACA
2005652 TTT
1 TTT
2005655 TATCAATAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 14 0.36
22 6 0.15
23 13 0.33
24 6 0.15
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (23 bp):
TTTCATTAAAAGGTATTGATACA
Found at i:2005649 original size:23 final size:22
Alignment explanation
Indices: 2005591--2005657 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
2005581 GCTTTTCATG
*
2005591 TAAAATGTATTGATACATTTCAT
1 TAAAA-GTATTGATACATTTTAT
* * *
2005614 T-AAAGTATCGATAGATTTTTT
1 TAAAAGTATTGATACATTTTAT
2005635 TAAAAGGTATTGATACATTTTAT
1 TAAAA-GTATTGATACATTTTAT
2005658 CAATAGATTC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
21 14 0.40
22 6 0.17
23 15 0.43
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (22 bp):
TAAAAGTATTGATACATTTTAT
Found at i:2019137 original size:17 final size:17
Alignment explanation
Indices: 2019107--2019139 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2019097 TTCTTGATAA
2019107 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
2019124 AATAATAACT-CTTATT
1 AATAA-AACTCCTTATT
2019140 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:2019318 original size:31 final size:29
Alignment explanation
Indices: 2019280--2019389 Score: 98
Period size: 29 Copynumber: 3.8 Consensus size: 29
2019270 TTAAGAAAAA
* *
2019280 TCTTGTCTTTAACTACGACAAAAATATTTTT
1 TCTTGTCTTAAACTAAGACAAAAATA--TTT
* *
2019311 TCTTGTCTTAAATTAAGACAAACATATTT
1 TCTTGTCTTAAACTAAGACAAAAATATTT
* * *
2019340 TCTTGTC-TAAATTAAGACCAAACATGTTT
1 TCTTGTCTTAAACTAAGA-CAAAAATATTT
**
2019369 TCTTGTC-TAAGTTAAGACAAA
1 TCTTGTCTTAAACTAAGACAAA
2019390 TATGTTAAAG
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
28 14 0.19
29 36 0.50
31 22 0.31
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.40
Consensus pattern (29 bp):
TCTTGTCTTAAACTAAGACAAAAATATTT
Found at i:2019361 original size:29 final size:29
Alignment explanation
Indices: 2019308--2019386 Score: 124
Period size: 29 Copynumber: 2.7 Consensus size: 29
2019298 CAAAAATATT
2019308 TTTTCTTGTCTTAAATTAAGA-CAAACATA
1 TTTTCTTGTC-TAAATTAAGACCAAACATA
*
2019337 TTTTCTTGTCTAAATTAAGACCAAACATG
1 TTTTCTTGTCTAAATTAAGACCAAACATA
*
2019366 TTTTCTTGTCTAAGTTAAGAC
1 TTTTCTTGTCTAAATTAAGAC
2019387 AAATATGTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 10 0.21
29 37 0.79
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (29 bp):
TTTTCTTGTCTAAATTAAGACCAAACATA
Found at i:2024064 original size:22 final size:21
Alignment explanation
Indices: 2024024--2024065 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2024014 GTACTAGTCA
* *
2024024 AACATGGAGTCTCATTTTATC
1 AACATGGAGTCTAAATTTATC
2024045 AACATGGATGTCTAAATTTAT
1 AACATGGA-GTCTAAATTTAT
2024066 TTTGCAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (21 bp):
AACATGGAGTCTAAATTTATC
Found at i:2024155 original size:29 final size:28
Alignment explanation
Indices: 2024106--2024357 Score: 255
Period size: 29 Copynumber: 9.0 Consensus size: 28
2024096 TTTAAAACAA
* * *
2024106 CTTGTCTTTAATTAAGGCAAAGCATGTTAT
1 CTTGTC-TAAATTAAGACAAA-CATGTTTT
* *
2024136 CTTGTCTAAATTGAGACAAACCTGTTTT
1 CTTGTCTAAATTAAGACAAACATGTTTT
* *
2024164 CTTGTCTTAAATTAAGACAAATATATTTT
1 CTTGTC-TAAATTAAGACAAACATGTTTT
*
2024193 CTTATCTAAATTAAGACAAAACATGTTTT
1 CTTGTCTAAATTAAGAC-AAACATGTTTT
* * * *
2024222 CTTATCTAAATTAAGACAAATATATTTG
1 CTTGTCTAAATTAAGACAAACATGTTTT
*
2024250 CTTGTCTAAATTAAGACAAAACATTTTTT
1 CTTGTCTAAATTAAGAC-AAACATGTTTT
* *
2024279 CTTGTCTACATTAAG------ATATTTT
1 CTTGTCTAAATTAAGACAAACATGTTTT
*
2024301 CTTATCTAAATTAAGACATAACATGTTTT
1 CTTGTCTAAATTAAGACA-AACATGTTTT
2024330 CTTGTCTAAATTAAGACAAAACATGTTT
1 CTTGTCTAAATTAAGAC-AAACATGTTT
2024358 AAAGTTACTA
Statistics
Matches: 186, Mismatches: 25, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
22 19 0.10
28 47 0.25
29 113 0.61
30 7 0.04
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (28 bp):
CTTGTCTAAATTAAGACAAACATGTTTT
Found at i:2024212 original size:57 final size:57
Alignment explanation
Indices: 2024135--2024349 Score: 291
Period size: 57 Copynumber: 3.9 Consensus size: 57
2024125 AAGCATGTTA
* * *
2024135 TCTTGTCTAAATTGAGAC-AAACCTGTTTTCTTGTCTTAAATTAAGACAAATATATTT
1 TCTTATCTAAATTAAGACAAAACATGTTTTCTTGTC-TAAATTAAGACAAATATATTT
*
2024192 TCTTATCTAAATTAAGACAAAACATGTTTTCTTATCTAAATTAAGACAAATATATTT
1 TCTTATCTAAATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAATATATTT
* * * *
2024249 GCTTGTCTAAATTAAGACAAAACATTTTTTCTTGTCTACATTAAG------ATATTT
1 TCTTATCTAAATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAATATATTT
*
2024300 TCTTATCTAAATTAAGACATAACATGTTTTCTTGTCTAAATTAAGACAAA
1 TCTTATCTAAATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAA
2024350 ACATGTTTAA
Statistics
Matches: 138, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
51 46 0.33
57 77 0.56
58 15 0.11
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.41
Consensus pattern (57 bp):
TCTTATCTAAATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAATATATTT
Found at i:2024230 original size:86 final size:83
Alignment explanation
Indices: 2024115--2024349 Score: 264
Period size: 86 Copynumber: 2.8 Consensus size: 83
2024105 ACTTGTCTTT
* * * *
2024115 AATTAAGGCAAAGCATGTTATCTTGTCTAAATTGAGACAAACCTGTTTTCTTGTCTTAAATTAAG
1 AATTAA-GCAAA-CATGTTTTCTTATCTAAATTAAGACAAACATGTTTTCTTGTC-TAAATTAAG
*
2024180 ACAAATATATTTTCTTATCTA
63 ACAAACATATTTTCTTATCTA
* * *
2024201 AATTAAGACAAAACATGTTTTCTTATCTAAATTAAGACAAATATATTTGCTTGTCTAAATTAAGA
1 AATTAAG-C-AAACATGTTTTCTTATCTAAATTAAGACAAACATGTTTTCTTGTCTAAATTAAGA
* *
2024266 CAAAACATTTTTTCTTGTCTA
64 C-AAACATATTTTCTTATCTA
* *
2024287 CATTAAG-----ATATTTTCTTATCTAAATTAAGACATAACATGTTTTCTTGTCTAAATTAAGAC
1 AATTAAGCAAACATGTTTTCTTATCTAAATTAAGACA-AACATGTTTTCTTGTCTAAATTAAGAC
2024347 AAA
65 AAA
2024350 ACATGTTTAA
Statistics
Matches: 130, Mismatches: 15, Indels: 15
0.81 0.09 0.09
Matches are distributed among these distances:
79 27 0.21
80 24 0.18
85 12 0.09
86 64 0.49
87 3 0.02
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (83 bp):
AATTAAGCAAACATGTTTTCTTATCTAAATTAAGACAAACATGTTTTCTTGTCTAAATTAAGACA
AACATATTTTCTTATCTA
Found at i:2024302 original size:22 final size:22
Alignment explanation
Indices: 2024275--2024316 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2024265 ACAAAACATT
* *
2024275 TTTTCTTGTCTACATTAAGATA
1 TTTTCTTATCTAAATTAAGATA
2024297 TTTTCTTATCTAAATTAAGA
1 TTTTCTTATCTAAATTAAGA
2024317 CATAACATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (22 bp):
TTTTCTTATCTAAATTAAGATA
Found at i:2024324 original size:51 final size:51
Alignment explanation
Indices: 2024186--2024345 Score: 221
Period size: 51 Copynumber: 3.0 Consensus size: 51
2024176 TAAGACAAAT
*
2024186 ATATTTTCTTATCTAAATTAAGACAAAACATGTTTTCTTATCTAAATTAAG
1 ATATTTTCTTATCTAAATTAAGACAAAACATGTTTTCTTGTCTAAATTAAG
* * *
2024237 ACAAATATATTTGCTTGTCTAAATTAAGACAAAACATTTTTTCTTGTCTACATTAAG
1 ----ATAT-TTT-CTTATCTAAATTAAGACAAAACATGTTTTCTTGTCTAAATTAAG
*
2024294 ATATTTTCTTATCTAAATTAAGACATAACATGTTTTCTTGTCTAAATTAAG
1 ATATTTTCTTATCTAAATTAAGACAAAACATGTTTTCTTGTCTAAATTAAG
2024345 A
1 A
2024346 CAAAACATGT
Statistics
Matches: 95, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
51 41 0.43
52 3 0.03
53 4 0.04
55 4 0.04
56 3 0.03
57 40 0.42
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (51 bp):
ATATTTTCTTATCTAAATTAAGACAAAACATGTTTTCTTGTCTAAATTAAG
Found at i:2043163 original size:17 final size:16
Alignment explanation
Indices: 2043141--2043174 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2043131 GATGTTTCAC
*
2043141 TTTAAGTTTAGTTATTA
1 TTTAAGTTAAGTT-TTA
2043158 TTTAAGTTAAGTTTTA
1 TTTAAGTTAAGTTTTA
2043174 T
1 T
2043175 GTTTTTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (16 bp):
TTTAAGTTAAGTTTTA
Found at i:2045177 original size:35 final size:35
Alignment explanation
Indices: 2045043--2045181 Score: 145
Period size: 36 Copynumber: 3.9 Consensus size: 35
2045033 TTTTTACAAA
* *
2045043 ATCAGGCAATAACACTTACACTAGCTTTTTAACTAG
1 ATCAAGCAATAAC-CTTACACTAGCTTTTTAACGAG
* * * *
2045079 ATCAAGCAATAACCCTTATAAC-GGCTTTTTCATGAG
1 ATCAAGCAATAA-CCTTA-CACTAGCTTTTTAACGAG
* *
2045115 ATCAAGCAATAAACCTTACACTTGCTTTTTAACGGG
1 ATCAAGCAAT-AACCTTACACTAGCTTTTTAACGAG
**
2045151 ATCAAGTGATAACCTTACACTAGCTTTTTAA
1 ATCAAGCAATAACCTTACACTAGCTTTTTAA
2045182 TAGGATAAAC
Statistics
Matches: 85, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
35 22 0.26
36 58 0.68
37 5 0.06
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.32
Consensus pattern (35 bp):
ATCAAGCAATAACCTTACACTAGCTTTTTAACGAG
Found at i:2047936 original size:28 final size:28
Alignment explanation
Indices: 2047904--2047964 Score: 99
Period size: 26 Copynumber: 2.2 Consensus size: 28
2047894 AGAATTACGC
2047904 AAGTAAGAGATATGAATTCCATTAGTAA
1 AAGTAAGAGATATGAATTCCATTAGTAA
*
2047932 AAGT-A-AGATATGGATTCCATTAGTAA
1 AAGTAAGAGATATGAATTCCATTAGTAA
2047958 AAGTAAG
1 AAGTAAG
2047965 TCAAAATGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 24 0.80
27 2 0.07
28 4 0.13
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.28
Consensus pattern (28 bp):
AAGTAAGAGATATGAATTCCATTAGTAA
Found at i:2051022 original size:154 final size:151
Alignment explanation
Indices: 2050726--2051024 Score: 377
Period size: 154 Copynumber: 1.9 Consensus size: 151
2050716 AGCCAAATCT
* * * *
2050726 TCCAATACATATTAATAGTTATTTGGTTTGGAGAGGAAAAAAGAGAACAAAAATTTTTTATTTAT
1 TCCAATACATATTAATAGTTATTTGATTTGGAGAGGAAAAAAGAGAAAAAAAATTTTTGATTGAT
* * * * * * *
2050791 TCACGAGAAAAGAGAATAGTAGAAAAGGTTTTTCTAATTTGATAAATGATTATTGTTTGATTGAT
66 TCACAAAAAAAGAGAATAGGAGAAAAGGTTTTTCTAATTTAATAAATGATAATTATTTAATTGAT
2050856 TCTAAAAAAAAAAGGGTCAAATAC
131 TC---AAAAAAAAGGGTCAAATAC
*
2050880 TCCAATACATATTAATAGTTATTTGATTTTGAGA-GAAAAACAGAGAAAAAAAATTGTTTGATTG
1 TCCAATACATATTAATAGTTATTTGATTTGGAGAGGAAAAA-AGAGAAAAAAAATT-TTTGATTG
*
2050944 ATTCACAAAAAAAGAAAAGAATAGGAG-AAAGAGTTTTTCTAATTTAATGAATGATAATTATTTA
64 ATTCACAAAAAAAG---AGAATAGGAGAAAAG-GTTTTTCTAATTTAATAAATGATAATTATTTA
2051008 ATTGATTCACAAAAAAA
125 ATTGATTCA-AAAAAAA
2051025 AAAAGAAAAA
Statistics
Matches: 125, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
153 6 0.05
154 45 0.36
155 19 0.15
156 7 0.06
157 4 0.03
158 44 0.35
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.33
Consensus pattern (151 bp):
TCCAATACATATTAATAGTTATTTGATTTGGAGAGGAAAAAAGAGAAAAAAAATTTTTGATTGAT
TCACAAAAAAAGAGAATAGGAGAAAAGGTTTTTCTAATTTAATAAATGATAATTATTTAATTGAT
TCAAAAAAAAGGGTCAAATAC
Found at i:2051076 original size:60 final size:58
Alignment explanation
Indices: 2050978--2051099 Score: 136
Period size: 60 Copynumber: 2.1 Consensus size: 58
2050968 GAGAAAGAGT
***
2050978 TTTTCTAATTTAATGAATGATAATTATTTAATTGATTCACAAAAAAAAAAAGAAAAAGGG
1 TTTTCTAATTTAATGAATGATAATTATTTAACCAATT--CAAAAAAAAAAAGAAAAAGGG
** * * * * *
2051038 TTTTCTAATTTCTTTAATGATAATTGTTTAACCAATTCAGAAAAACAAAGAGAAAGGG
1 TTTTCTAATTTAATGAATGATAATTATTTAACCAATTCAAAAAAAAAAAGAAAAAGGG
2051096 TTTT
1 TTTT
2051100 TTGAATTTGA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
58 22 0.42
60 30 0.58
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.36
Consensus pattern (58 bp):
TTTTCTAATTTAATGAATGATAATTATTTAACCAATTCAAAAAAAAAAAGAAAAAGGG
Found at i:2051677 original size:3 final size:3
Alignment explanation
Indices: 2051671--2051700 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2051661 CCTCCTCCTC
*
2051671 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2051701 CTATACACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2054095 original size:25 final size:27
Alignment explanation
Indices: 2054077--2054128 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
2054067 AAAATAATGA
2054077 GAAAAAAGCAAACAAAAAA-AATAAAG
1 GAAAAAAGCAAACAAAAAATAATAAAG
* *
2054103 GAAGAAGGCAAACAAAAAAT-ATAAAG
1 GAAAAAAGCAAACAAAAAATAATAAAG
2054129 AAAGTTCTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.71, C:0.08, G:0.15, T:0.06
Consensus pattern (27 bp):
GAAAAAAGCAAACAAAAAATAATAAAG
Found at i:2064243 original size:17 final size:17
Alignment explanation
Indices: 2064221--2064258 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
2064211 TTTGGGAGCA
*
2064221 TGCTTACTTTATATTGT
1 TGCTTACTTTATATTAT
2064238 TGCTTACTTTATATTAT
1 TGCTTACTTTATATTAT
2064255 TGCT
1 TGCT
2064259 CACATTTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (17 bp):
TGCTTACTTTATATTAT
Found at i:2074318 original size:14 final size:14
Alignment explanation
Indices: 2074265--2074321 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
2074255 ATTTAACATC
2074265 TTAAGTTAAACT-TT
1 TTAAGTTAAA-TATT
2074279 TTAAGTTAAATATT
1 TTAAGTTAAATATT
**
2074293 AATT-TTTTAAATATT
1 --TTAAGTTAAATATT
2074308 TTAAGTTAAATATT
1 TTAAGTTAAATATT
2074322 AATATTCATC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 3 0.09
14 21 0.60
15 9 0.26
16 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (14 bp):
TTAAGTTAAATATT
Found at i:2075968 original size:21 final size:21
Alignment explanation
Indices: 2075935--2075975 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2075925 ATTTAAGTTT
*
2075935 AAAACTCAATCAAACAATTTC
1 AAAAATCAATCAAACAATTTC
* *
2075956 AAAAATCATTCAAGCAATTT
1 AAAAATCAATCAAACAATTT
2075976 TGATCATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.20, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAAATCAATCAAACAATTTC
Found at i:2081143 original size:34 final size:34
Alignment explanation
Indices: 2081105--2081207 Score: 140
Period size: 33 Copynumber: 3.1 Consensus size: 34
2081095 ATTGTAAGAA
*
2081105 TTTCACTTGATCCCATGAAAAAAC-ATTATGAGGG
1 TTTCACTTGATCTCAT-AAAAAACTATTATGAGGG
* * *
2081139 TTTCA-TTGATCTCGTAAAAAGCTATTATTAGGG
1 TTTCACTTGATCTCATAAAAAACTATTATGAGGG
2081172 TTTCACTTGATCTCAT-AAAAACTATTATGAGGG
1 TTTCACTTGATCTCATAAAAAACTATTATGAGGG
2081205 TTT
1 TTT
2081208 NNNNNNNNNN
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
32 6 0.10
33 40 0.67
34 14 0.23
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (34 bp):
TTTCACTTGATCTCATAAAAAACTATTATGAGGG
Found at i:2092487 original size:2 final size:2
Alignment explanation
Indices: 2092480--2092504 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2092470 TGATATAAGT
2092480 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2092505 TTGAATAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2094138 original size:31 final size:31
Alignment explanation
Indices: 2094092--2094154 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
2094082 AATTATTTCT
* * *
2094092 ATTTTTTATTATTTTATATTTTTTAATAATTA
1 ATTTTTAATTATTTTATAATTTCTAA-AATTA
2094124 ATTTTTAATT-TTTTATAATTTCTAAAATTA
1 ATTTTTAATTATTTTATAATTTCTAAAATTA
2094154 A
1 A
2094155 AAACTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 6 0.21
31 13 0.46
32 9 0.32
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (31 bp):
ATTTTTAATTATTTTATAATTTCTAAAATTA
Found at i:2094194 original size:30 final size:31
Alignment explanation
Indices: 2094142--2094203 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
2094132 TTTTTTATAA
* *
2094142 TTTCTAAAATTAAAAACTTATTTTTAATTTT
1 TTTCAAAAATTAAAAACGTATTTTTAATTTT
*
2094173 TTTCAAAAATTTAAAA-GTATTTTTAATTTT
1 TTTCAAAAATTAAAAACGTATTTTTAATTTT
2094203 T
1 T
2094204 AAAATTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (31 bp):
TTTCAAAAATTAAAAACGTATTTTTAATTTT
Found at i:2094213 original size:29 final size:29
Alignment explanation
Indices: 2094142--2094203 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 29
2094132 TTTTTTATAA
* * *
2094142 TTTCTAAAATTAAAAACTTATTTTTAATTTT
1 TTTCAAAAATTTAAAA-GTATTTTTAA-TTT
2094173 TTTCAAAAATTTAAAAGTATTTTTAATTT
1 TTTCAAAAATTTAAAAGTATTTTTAATTT
2094202 TT
1 TT
2094204 AAAATTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 5 0.18
30 9 0.32
31 14 0.50
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (29 bp):
TTTCAAAAATTTAAAAGTATTTTTAATTT
Found at i:2108100 original size:2 final size:2
Alignment explanation
Indices: 2108093--2108125 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2108083 TACTGATCCC
2108093 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2108126 GTTGTGTGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2124705 original size:21 final size:22
Alignment explanation
Indices: 2124680--2124723 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
2124670 AAGTGATTAA
2124680 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
2124701 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
2124723 T
1 T
2124724 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:2129045 original size:21 final size:21
Alignment explanation
Indices: 2129021--2129076 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
2129011 TTGAATGGAG
2129021 GCATCAGTCTTTGTCATAAAT
1 GCATCAGTCTTTGTCATAAAT
** * *
2129042 GCATTGGTCTTTGTTATGAAT
1 GCATCAGTCTTTGTCATAAAT
* *
2129063 GTATCATTCTTTGT
1 GCATCAGTCTTTGT
2129077 TGTGAATTGC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.46
Consensus pattern (21 bp):
GCATCAGTCTTTGTCATAAAT
Found at i:2131193 original size:17 final size:18
Alignment explanation
Indices: 2131171--2131217 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
2131161 AAGAGTTGAA
2131171 TTCTTGATCTTCAA-ATC
1 TTCTTGATCTTCAATATC
*
2131188 TTCTTGAATTCTTCAATTTC
1 TTCTTG-A-TCTTCAATATC
*
2131208 TTCTTTATCT
1 TTCTTGATCT
2131218 CTAATGAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 6 0.24
18 4 0.16
19 8 0.32
20 7 0.28
ACGTcount: A:0.19, C:0.21, G:0.04, T:0.55
Consensus pattern (18 bp):
TTCTTGATCTTCAATATC
Found at i:2134811 original size:170 final size:170
Alignment explanation
Indices: 2134611--2134980 Score: 388
Period size: 170 Copynumber: 2.2 Consensus size: 170
2134601 NNNNNNNNNN
* * *
2134611 TAGTCACCCATGCCTTCGAAAGCTTTATTACTCGCCTTAAATGATTTTATAATCTCATAATTAAT
1 TAGTCACCCAAGCCTTCAAAAGCCTTATTACTCGCCTTAAATGATTTTATAATCTCATAATTAAT
* * * *
2134676 TTT-AAGTTAATTTTCTTATATTTTT-AGTTAAAATATATTATAATTGAATGTCTGCTTC-AGAA
66 TTTCAA-TTAATTTTCTTACATTTTTGA-TAAAAATAGATTATAATTGAATGTCTGCCTCGAGAA
** * * ** *
2134738 A-ATGTGAAGCATAAGCCATCCATTGGTAAAAAAAGTTTGTTTA
129 ACA--TGAAAAAAAAGCCATCCATTGGCAAAAAAAGCATATTTA
** ********** *
2134781 TAGTCATTCAAGCCTTCAAAAGCCTTATTACTCGNNNNNNNNNNTTTTATAATCTCATAATTGAT
1 TAGTCACCCAAGCCTTCAAAAGCCTTATTACTCGCCTTAAATGATTTTATAATCTCATAATTAAT
* *
2134846 TTTCAATTAATTTTTTTACATTTTTGATAAAAATAGATTGTAATTGAATGTCTGCCTCGAGAAAC
66 TTTCAATTAATTTTCTTACATTTTTGATAAAAATAGATTATAATTGAATGTCTGCCTCGAGAAAC
* *
2134911 ATGAAAAAAAAGCCATTCATTGGCAAGAAAAGCATATTTA
131 ATGAAAAAAAAGCCATCCATTGGCAAAAAAAGCATATTTA
*
2134951 TAGTCACCCAAGCTTTCAAAAGCCTTATTA
1 TAGTCACCCAAGCCTTCAAAAGCCTTATTA
2134981 TTNNNNNNNN
Statistics
Matches: 162, Mismatches: 34, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
170 153 0.94
171 8 0.05
172 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.37
Consensus pattern (170 bp):
TAGTCACCCAAGCCTTCAAAAGCCTTATTACTCGCCTTAAATGATTTTATAATCTCATAATTAAT
TTTCAATTAATTTTCTTACATTTTTGATAAAAATAGATTATAATTGAATGTCTGCCTCGAGAAAC
ATGAAAAAAAAGCCATCCATTGGCAAAAAAAGCATATTTA
Found at i:2139890 original size:74 final size:74
Alignment explanation
Indices: 2139776--2139960 Score: 228
Period size: 74 Copynumber: 2.5 Consensus size: 74
2139766 GATAGAGAAG
* * * * * *
2139776 ACTTAGTCAACTAATAAGCATGGTTAGTCAACTAAGAGCTTACTGCTAGAAACTGCAGTCATAAA
1 ACTTAGTCGACTAAAAAGCATGGTTAGTCAACTAAGAGCTTACTACCAAAAACTGCAGTCACAAA
*
2139841 ACAGAGATA
66 ACAGAGACA
* * * * * * *
2139850 ACTTAGTTGACTAAGAAGAATGGTTACTCATCTAAGAGCTTACTACCAAAAACTGCAGTTACAAG
1 ACTTAGTCGACTAAAAAGCATGGTTAGTCAACTAAGAGCTTACTACCAAAAACTGCAGTCACAAA
2139915 ACAGAGACA
66 ACAGAGACA
*
2139924 ACTTAATCGACTAAAAAGCAT-GTTAGTCAACTAAGAG
1 ACTTAGTCGACTAAAAAGCATGGTTAGTCAACTAAGAG
2139961 TACTTTGTCT
Statistics
Matches: 92, Mismatches: 19, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
73 14 0.15
74 78 0.85
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (74 bp):
ACTTAGTCGACTAAAAAGCATGGTTAGTCAACTAAGAGCTTACTACCAAAAACTGCAGTCACAAA
ACAGAGACA
Found at i:2145711 original size:38 final size:38
Alignment explanation
Indices: 2145632--2145739 Score: 130
Period size: 38 Copynumber: 2.8 Consensus size: 38
2145622 AGCAAAAAAA
* * *
2145632 TTTTTAATATCAAAGACTATTAGTTTGTTTCAAAGAAT
1 TTTTTAATATCAAAGACTACTATTTTGTTTCAAACAAT
* *
2145670 TTTTTAATATCAAAGACTACTATTTTGTTTTAAACAGT
1 TTTTTAATATCAAAGACTACTATTTTGTTTCAAACAAT
*
2145708 TTTTGTACATA--AAAGATTACTATTTTGTTTCA
1 TTTT-TA-ATATCAAAGACTACTATTTTGTTTCA
2145740 GTATAGTTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
38 56 0.92
39 2 0.03
40 3 0.05
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.47
Consensus pattern (38 bp):
TTTTTAATATCAAAGACTACTATTTTGTTTCAAACAAT
Found at i:2146492 original size:34 final size:36
Alignment explanation
Indices: 2146435--2146515 Score: 105
Period size: 36 Copynumber: 2.3 Consensus size: 36
2146425 CATCATAATA
* * *
2146435 GCTTTTT-ATGAGATTAAGTGAAA-CCTTTA-CAAT
1 GCTTTTTCATGGGATCAAGCGAAACCCTTTAGCAAT
2146468 GCTTTTTCATGGGATCAAGCGAAACCCTTTAGCAAT
1 GCTTTTTCATGGGATCAAGCGAAACCCTTTAGCAAT
*
2146504 GGTTTTTCATGG
1 GCTTTTTCATGG
2146516 CTCAACCATA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
33 7 0.17
34 13 0.32
35 6 0.15
36 15 0.37
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (36 bp):
GCTTTTTCATGGGATCAAGCGAAACCCTTTAGCAAT
Found at i:2149396 original size:20 final size:19
Alignment explanation
Indices: 2149353--2149401 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
2149343 TGAGATGGAG
2149353 AGAGAAAAAAAAAAGGAAC
1 AGAGAAAAAAAAAAGGAAC
*
2149372 A-AGAAAAAAAACAGTTGAA-
1 AGAGAAAAAAAAAAG--GAAC
2149391 AGAGAAAAAAA
1 AGAGAAAAAAA
2149402 TTTATATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 12 0.46
19 2 0.08
20 12 0.46
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.04
Consensus pattern (19 bp):
AGAGAAAAAAAAAAGGAAC
Found at i:2150392 original size:13 final size:13
Alignment explanation
Indices: 2150376--2150408 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2150366 TGTGATATAC
2150376 TGATATAAT-ATGA
1 TGATATAATCAT-A
2150389 TGATATAATCATA
1 TGATATAATCATA
2150402 TGATATA
1 TGATATA
2150409 TTTCACCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 17 0.89
14 2 0.11
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.39
Consensus pattern (13 bp):
TGATATAATCATA
Found at i:2153512 original size:20 final size:18
Alignment explanation
Indices: 2153481--2153517 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
2153471 CCCTTTCTGT
2153481 TGTTTTTCTAAACTTTCA
1 TGTTTTTCTAAACTTTCA
2153499 TGTTATTTCTTAAACTTTC
1 TGTT-TTTC-TAAACTTTC
2153518 CTGATTCTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.22, C:0.16, G:0.05, T:0.57
Consensus pattern (18 bp):
TGTTTTTCTAAACTTTCA
Found at i:2155700 original size:29 final size:30
Alignment explanation
Indices: 2155654--2155725 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
2155644 ATAAAATTTA
*
2155654 AATAAATTTTTATTCTTTT-TTTTGTATTC
1 AATAAATTTTTATACTTTTATTTTGTATTC
* *
2155683 AATAAGTTTTTATACTTTTATTTTGTATTA
1 AATAAATTTTTATACTTTTATTTTGTATTC
* *
2155713 AACAAATCTTTAT
1 AATAAATTTTTAT
2155726 GACTAATAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 17 0.47
30 19 0.53
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.58
Consensus pattern (30 bp):
AATAAATTTTTATACTTTTATTTTGTATTC
Found at i:2158594 original size:14 final size:14
Alignment explanation
Indices: 2158575--2158601 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2158565 CAATAATTAA
2158575 AATTTAGAGATTTT
1 AATTTAGAGATTTT
2158589 AATTTAGAGATTT
1 AATTTAGAGATTT
2158602 CGAATTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (14 bp):
AATTTAGAGATTTT
Found at i:2162077 original size:28 final size:29
Alignment explanation
Indices: 2162046--2162101 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
2162036 TATTTTAAAT
* * *
2162046 TATTTAAT-AAATTTTTATTCTTTTATTA
1 TATTCAATCAAATTCTTATACTTTTATTA
*
2162074 TATTCAATCAAGTTCTTATACTTTTATT
1 TATTCAATCAAATTCTTATACTTTTATT
2162102 TGAAATTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (29 bp):
TATTCAATCAAATTCTTATACTTTTATTA
Found at i:2164709 original size:2 final size:2
Alignment explanation
Indices: 2164704--2164730 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2164694 GTGTGTGTGT
2164704 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
2164731 CAACCTGAGG
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2166534 original size:13 final size:14
Alignment explanation
Indices: 2166510--2166538 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2166500 GTGGGAATCC
2166510 TCAATGCTTTTGCT
1 TCAATGCTTTTGCT
2166524 TCAAT-CTTTTGCT
1 TCAATGCTTTTGCT
2166537 TC
1 TC
2166539 TAAAAGGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.14, C:0.24, G:0.10, T:0.52
Consensus pattern (14 bp):
TCAATGCTTTTGCT
Found at i:2174571 original size:15 final size:15
Alignment explanation
Indices: 2174537--2174570 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2174527 AGAGGTAAAG
2174537 TTTTTATTTATATTA
1 TTTTTATTTATATTA
2174552 TTTTTATTTAT-TTA
1 TTTTTATTTATATTA
2174566 TTTTT
1 TTTTT
2174571 TGAATTCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTATTTATATTA
Found at i:2175557 original size:35 final size:35
Alignment explanation
Indices: 2175491--2175557 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
2175481 TTTGTTGATT
* **
2175491 GTGTAAAGGTTATCGCTTGATCTTGTAAAAAACAA
1 GTGTAAAGGTTATCACTTGATCTCATAAAAAACAA
* *
2175526 GTGTAAAGGTTATCACTTTATCTCATTAAAAA
1 GTGTAAAGGTTATCACTTGATCTCATAAAAAA
2175558 GTAAGAATAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.34
Consensus pattern (35 bp):
GTGTAAAGGTTATCACTTGATCTCATAAAAAACAA
Found at i:2176862 original size:2 final size:2
Alignment explanation
Indices: 2176855--2176883 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2176845 TTTGGGCTAA
2176855 AT 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 AT A
2176884 GAATAAAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2177410 original size:24 final size:26
Alignment explanation
Indices: 2177342--2177399 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 26
2177332 CTAGTATCAA
*
2177342 TTTCTGAACAAAATTTTCGTTGGAAATGTT
1 TTTCT-AACAGAA-TTTCGTTGGAAA--TT
2177372 TTTCTAACAGAATTTCGTTGGAAATT
1 TTTCTAACAGAATTTCGTTGGAAATT
2177398 TT
1 TT
2177400 CAATAGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 4 0.15
28 12 0.44
29 6 0.22
30 5 0.19
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (26 bp):
TTTCTAACAGAATTTCGTTGGAAATT
Found at i:2179737 original size:23 final size:26
Alignment explanation
Indices: 2179688--2179742 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 26
2179678 NCAATAAGTA
*
2179688 ATATATTAATTTTATATAGTATATAT
1 ATATATTAACTTTATATAGTATATAT
2179714 ATATATT-ACTTTAT-TA-TATATAT
1 ATATATTAACTTTATATAGTATATAT
2179737 ATATAT
1 ATATAT
2179743 GAAATTAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 13 0.46
24 2 0.07
25 6 0.21
26 7 0.25
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (26 bp):
ATATATTAACTTTATATAGTATATAT
Found at i:2179896 original size:23 final size:23
Alignment explanation
Indices: 2179874--2179921 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
2179864 TAATCATATA
2179874 AATAAAACTTAT-TATAAGTTAT
1 AATAAAACTTATGTATAAGTTAT
* * *
2179896 AGTAATACTTATGTATAAATTA-
1 AATAAAACTTATGTATAAGTTAT
2179918 AATA
1 AATA
2179922 TATACATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (23 bp):
AATAAAACTTATGTATAAGTTAT
Found at i:2180565 original size:11 final size:11
Alignment explanation
Indices: 2180545--2180584 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
2180535 TTAAAATTAA
2180545 AAAATTTTTAT
1 AAAATTTTTAT
*
2180556 AAAATGTTTAT
1 AAAATTTTTAT
2180567 AAAATTTTTTAT
1 AAAA-TTTTTAT
2180579 AAAATT
1 AAAATT
2180585 AATAATATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (11 bp):
AAAATTTTTAT
Found at i:2180577 original size:12 final size:12
Alignment explanation
Indices: 2180544--2180584 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
2180534 TTTAAAATTA
*
2180544 AAAAATTTTTAT
1 AAAATTTTTTAT
*
2180556 AAAA-TGTTTAT
1 AAAATTTTTTAT
2180567 AAAATTTTTTAT
1 AAAATTTTTTAT
2180579 AAAATT
1 AAAATT
2180585 AATAATATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (12 bp):
AAAATTTTTTAT
Found at i:2180778 original size:24 final size:24
Alignment explanation
Indices: 2180751--2180802 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
2180741 AGCAAAAGGA
2180751 ATAAATA-TCTAA-ATGTTTAATATT
1 ATAAATACTC-AATATGTTT-ATATT
2180775 ATAAA-ACTCAATATGTTTATATT
1 ATAAATACTCAATATGTTTATATT
2180798 -TAAAT
1 ATAAAT
2180803 TTATTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
22 4 0.16
23 8 0.32
24 13 0.52
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (24 bp):
ATAAATACTCAATATGTTTATATT
Found at i:2180986 original size:26 final size:28
Alignment explanation
Indices: 2180957--2181008 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
2180947 TACGTCTTAA
2180957 ATTTTCTAACGG-ATTTT-CAACGGATT
1 ATTTTCTAACGGAATTTTCCAACGGATT
**
2180983 ATTTTCTATTGGAATTTTCCAACGGA
1 ATTTTCTAACGGAATTTTCCAACGGA
2181009 AATCTGATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 10 0.45
27 5 0.23
28 7 0.32
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (28 bp):
ATTTTCTAACGGAATTTTCCAACGGATT
Found at i:2181187 original size:23 final size:24
Alignment explanation
Indices: 2181153--2181205 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
2181143 AAGTTGAAAT
*
2181153 AAATTTCCGTTGGAA-TTCGTTGG
1 AAATTTCCGTTGGAATTTCGTTGA
*
2181176 AAATTTCTGTTGGAATTTCGTTGA
1 AAATTTCCGTTGGAATTTCGTTGA
2181200 AAATTT
1 AAATTT
2181206 TCAACGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.43
Consensus pattern (24 bp):
AAATTTCCGTTGGAATTTCGTTGA
Found at i:2181198 original size:11 final size:11
Alignment explanation
Indices: 2181154--2181198 Score: 56
Period size: 12 Copynumber: 3.9 Consensus size: 11
2181144 AGTTGAAATA
2181154 AATTTCCGTTGG
1 AATTT-CGTTGG
2181166 AA-TTCGTTGG
1 AATTTCGTTGG
2181176 AAATTTCTGTTGG
1 -AATTTC-GTTGG
2181189 AATTTCGTTG
1 AATTTCGTTG
2181199 AAAATTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 6 0.20
11 8 0.27
12 11 0.37
13 5 0.17
ACGTcount: A:0.20, C:0.11, G:0.24, T:0.44
Consensus pattern (11 bp):
AATTTCGTTGG
Found at i:2184707 original size:14 final size:14
Alignment explanation
Indices: 2184653--2184715 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 14
2184643 ATACGTCAAG
*
2184653 TAACATACATCCAT-
1 TAACATTCAT-CATC
* *
2184667 TAATATTCATCAAC
1 TAACATTCATCATC
*
2184681 TAACACTCATCATC
1 TAACATTCATCATC
*
2184695 TAACATTCATCATT
1 TAACATTCATCATC
2184709 TAACATT
1 TAACATT
2184716 TGTAACGAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
13 2 0.05
14 38 0.95
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (14 bp):
TAACATTCATCATC
Found at i:2199661 original size:13 final size:13
Alignment explanation
Indices: 2199643--2199667 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2199633 GACCTTTTAC
2199643 TAAAATTTTATCT
1 TAAAATTTTATCT
2199656 TAAAATTTTATC
1 TAAAATTTTATC
2199668 ACCAATTAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
TAAAATTTTATCT
Found at i:2211438 original size:19 final size:18
Alignment explanation
Indices: 2211414--2211458 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
2211404 ATGTAATATC
2211414 ATTTTTATAATAATTTTAT
1 ATTTTTATAATAATTTT-T
** *
2211433 ATTTTTATTTTTATTTTT
1 ATTTTTATAATAATTTTT
2211451 ATTTTTAT
1 ATTTTTAT
2211459 TTTTTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTTTATAATAATTTTT
Found at i:2211443 original size:6 final size:6
Alignment explanation
Indices: 2211426--2211462 Score: 65
Period size: 6 Copynumber: 6.0 Consensus size: 6
2211416 TTTTATAATA
2211426 ATTTTAT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTT-T ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
2211463 TTAATATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:2211494 original size:12 final size:12
Alignment explanation
Indices: 2211426--2211496 Score: 51
Period size: 12 Copynumber: 5.8 Consensus size: 12
2211416 TTTTATAATA
2211426 ATTTTATATTTTT
1 ATTTTAT-TTTTT
2211439 ATTTT-TATTTTT
1 ATTTTAT-TTTTT
2211451 ATTTTTATTTTTTT
1 A-TTTTA-TTTTTT
* *
2211465 AATATAATTTTTT
1 -ATTTTATTTTTT
2211478 A---TATTTTTT
1 ATTTTATTTTTT
2211487 ATTTTATTTT
1 ATTTTATTTT
2211497 AATTGTGAGT
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
9 8 0.17
12 15 0.31
13 15 0.31
14 8 0.17
15 2 0.04
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
ATTTTATTTTTT
Found at i:2221781 original size:5 final size:5
Alignment explanation
Indices: 2221763--2221823 Score: 86
Period size: 5 Copynumber: 12.0 Consensus size: 5
2221753 TTGTTAGAGG
* * *
2221763 TTTCG TTTCTT TTTCT TTTCT TTCCT TTCCT TTTCT TTTCT TTTCT TTTCT
1 TTTCT TTTC-T TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
2221814 TTTCT TTTCT
1 TTTCT TTTCT
2221824 CTTAGTTAGT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
5 48 0.92
6 4 0.08
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTCT
Found at i:2222101 original size:6 final size:7
Alignment explanation
Indices: 2222076--2222100 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2222066 ATTTACTTTT
2222076 AAAAATA
1 AAAAATA
2222083 AAAAATA
1 AAAAATA
2222090 AAAAATA
1 AAAAATA
2222097 AAAA
1 AAAA
2222101 TGGGTGTTGA
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:2227526 original size:54 final size:51
Alignment explanation
Indices: 2227466--2227594 Score: 118
Period size: 53 Copynumber: 2.4 Consensus size: 51
2227456 TATTTGTATG
*
2227466 TTATAAAAATTATAAAATAAGAGGTAAAATTATAAAATTATTATAA-AGACAAAT
1 TTATAAAAATTA-AAAATAAGAGGT-AAATTAT-AAATTATTATAAGA-ACAAAA
** * * *
2227520 TTATAAACTTTTTAAAAAATAA-AGGTACATTATAAATTATTGTGAGAACAAAA
1 TTATAAA--AATT-AAAAATAAGAGGTAAATTATAAATTATTATAAGAACAAAA
*
2227573 TTATAAAAATTAAAAAAAAGAG
1 TTATAAAAATTAAAAATAAGAG
2227595 TTATTATAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
50 7 0.11
51 4 0.07
53 22 0.36
54 14 0.23
55 4 0.07
56 9 0.15
57 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (51 bp):
TTATAAAAATTAAAAATAAGAGGTAAATTATAAATTATTATAAGAACAAAA
Found at i:2229104 original size:17 final size:18
Alignment explanation
Indices: 2229084--2229121 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
2229074 CAAGTTAAGA
2229084 TTAATTAAAAATATT-AT
1 TTAATTAAAAATATTAAT
*
2229101 TTAATTAAAATTATTAAT
1 TTAATTAAAAATATTAAT
2229119 TTA
1 TTA
2229122 TAAAAATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAATTAAAAATATTAAT
Found at i:2229127 original size:17 final size:17
Alignment explanation
Indices: 2229084--2229129 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
2229074 CAAGTTAAGA
2229084 TTAATTAAAAA-TATTAT
1 TTAA-TAAAAATTATTAT
*
2229101 TTAATTAAAATTATTAAT
1 TTAATAAAAATTATT-AT
2229119 TT-ATAAAAATT
1 TTAATAAAAATT
2229130 GTACTGAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 5 0.20
17 16 0.64
18 4 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAATAAAAATTATTAT
Found at i:2231462 original size:13 final size:13
Alignment explanation
Indices: 2231446--2231478 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2231436 AAATTATTTG
2231446 ATAAATTTTTTTT
1 ATAAATTTTTTTT
*
2231459 ATAAGTTTTTTTT
1 ATAAATTTTTTTT
2231472 ATAAATT
1 ATAAATT
2231479 ATAATTTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (13 bp):
ATAAATTTTTTTT
Found at i:2238494 original size:314 final size:302
Alignment explanation
Indices: 2237936--2238552 Score: 921
Period size: 314 Copynumber: 2.0 Consensus size: 302
2237926 AATATTGATG
* ** *
2237936 ATGCATATAATAGATGCACAATCTTAACTTTCCTTTTGGAAATCACTCATTGCTTGTGTTTGATG
1 ATGCATATAATAGATGCACAATCTTAACTTTCCTTTGGGAAATCACTCATAACTTATGTTTGATG
*
2238001 ACAAGCAGGACTGAGATTGTATTCAATATTTATATGCTGCTGCACAAAAAGTGCTAGCAACATTT
66 ACAAGCAGGACTGAGATTGTATTCAATATTTATATGCTGCTGCACAAAAACTGCTAGCAACATTT
2238066 AAAGAAGTGTCACTCTGGTTATCCCACACAAGGTAACTTAACAAATTCTGCACACTTCTAAAACA
131 AAAGAAGTGTCACTCTGGTTATCCCACACAAGGTAACTTAACAAATTCTGCACACTTCTAAAACA
*
2238131 CGAAACCATAAAAAGAGCTTCTCAATGAATTTTTAACAAACAAATCACCATTCTAAGAGTAAAAT
196 CAAAACCATAAAAAGAGCTTCTCAATGAATTTTTAACAAACAAATCACCATTCTAAGAGTAAAAT
* *
2238196 TAACCATCCCTGTTAGCAAACATTTTATGAGAAATTTGTTTTA
261 TAACCATCCCTATTAACAAACATTTTATGAGAAATTT-TTTTA
*
2238239 ATGCATATAATAGATGCACAATCTTAACTTTCCTTTGGGAAATCACACTCATCAATTTATGTTTG
1 ATGCATATAATAGATGCACAATCTTAACTTTCCTTTGGGAAAT--CACTCAT-AACTTATGTTTG
* * * *
2238304 ATGACAAGCAGGACTTG-GATTGTATTCGATATTTATATGCTGCTGCACAAAAACTGCTGGTATC
63 ATGACAAGCAGGAC-TGAGATTGTATTCAATATTTATATGCTGCTGCACAAAAACTGCTAGCAAC
* * * * *
2238368 ATTTAAGGATGTGTCACTGTGGTCAAATAATGGTCCCACGCAGGGTAACTTAACAAATTCTGCAC
127 ATTTAAAGAAGTGTCACTCTGGT----T-A---TCCCACACAAGGTAACTTAACAAATTCTGCAC
2238433 ACTTCTAAAACACAAAACCATAAAAAGAGCTTCTCAATGAATTTTTAACAAACAAATCACCATTC
184 ACTTCTAAAACACAAAACCATAAAAAGAGCTTCTCAATGAATTTTTAACAAACAAATCACCATTC
* **
2238498 TAAGATTAAAATTAGTCATCCCTATTAACAAACATTTTATGAGAAATTTTTTTA
249 TAAGAGTAAAATTAACCATCCCTATTAACAAACATTTTATGAGAAATTTTTTTA
2238552 A
1 A
2238553 ACTTAATAAC
Statistics
Matches: 281, Mismatches: 21, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
303 42 0.15
305 7 0.02
306 84 0.30
307 2 0.01
310 1 0.00
311 1 0.00
313 6 0.02
314 138 0.49
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.31
Consensus pattern (302 bp):
ATGCATATAATAGATGCACAATCTTAACTTTCCTTTGGGAAATCACTCATAACTTATGTTTGATG
ACAAGCAGGACTGAGATTGTATTCAATATTTATATGCTGCTGCACAAAAACTGCTAGCAACATTT
AAAGAAGTGTCACTCTGGTTATCCCACACAAGGTAACTTAACAAATTCTGCACACTTCTAAAACA
CAAAACCATAAAAAGAGCTTCTCAATGAATTTTTAACAAACAAATCACCATTCTAAGAGTAAAAT
TAACCATCCCTATTAACAAACATTTTATGAGAAATTTTTTTA
Found at i:2239685 original size:27 final size:27
Alignment explanation
Indices: 2239647--2239700 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2239637 TATATACCAT
2239647 TCAATCATGACAACTAAGATGAACCTA
1 TCAATCATGACAACTAAGATGAACCTA
2239674 TCAATCATGACAACTAAGATGAACCTA
1 TCAATCATGACAACTAAGATGAACCTA
2239701 ATGTCACAAG
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:0.44, C:0.22, G:0.11, T:0.22
Consensus pattern (27 bp):
TCAATCATGACAACTAAGATGAACCTA
Found at i:2240165 original size:12 final size:11
Alignment explanation
Indices: 2240142--2240179 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
2240132 AATTCCACAA
*
2240142 CCCCCGCCCAC
1 CCCCCCCCCAC
2240153 CCCCACCCCCAC
1 CCCC-CCCCCAC
2240165 CCCCCCCCC-C
1 CCCCCCCCCAC
2240175 CCCCC
1 CCCCC
2240180 GTCCCAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 6 0.24
11 9 0.36
12 10 0.40
ACGTcount: A:0.08, C:0.89, G:0.03, T:0.00
Consensus pattern (11 bp):
CCCCCCCCCAC
Found at i:2242439 original size:21 final size:21
Alignment explanation
Indices: 2242395--2242451 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
2242385 TTTGGTGTTC
*
2242395 ATCTATCGATAGATACCCCCG
1 ATCTATCGATAGATGCCCCCG
* **
2242416 ATCTATCGATAGATGCTCTTG
1 ATCTATCGATAGATGCCCCCG
*
2242437 ATCTTTCGATAGATG
1 ATCTATCGATAGATG
2242452 ATGTTGTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (21 bp):
ATCTATCGATAGATGCCCCCG
Found at i:2248127 original size:36 final size:36
Alignment explanation
Indices: 2248087--2248157 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
2248077 CATGGGAAAG
* *
2248087 TGATTTTAATCCAAGCTGCCTAGTGAATCTTCTTAA
1 TGATTTTAATCCAAGCCGCCAAGTGAATCTTCTTAA
2248123 TGATTTTAATCCAAGCCGCCAAGTGAATCTTCTTA
1 TGATTTTAATCCAAGCCGCCAAGTGAATCTTCTTA
2248158 CTTGCAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
TGATTTTAATCCAAGCCGCCAAGTGAATCTTCTTAA
Found at i:2257567 original size:6 final size:6
Alignment explanation
Indices: 2257542--2257583 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
2257532 GCATTGCCTT
*
2257542 TTTTTC -TTTTC TTTCCTC TTTTTC TTTTT- TTTTTC TTTTTC T
1 TTTTTC TTTTTC TTT-TTC TTTTTC TTTTTC TTTTTC TTTTTC T
2257584 CTCTTTTCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
5 10 0.32
6 16 0.52
7 5 0.16
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:2257578 original size:17 final size:18
Alignment explanation
Indices: 2257542--2257583 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
2257532 GCATTGCCTT
2257542 TTTTTCTTTTCTTTCCTC
1 TTTTTCTTTTCTTTCCTC
**
2257560 TTTTTCTTTT-TTTTTTC
1 TTTTTCTTTTCTTTCCTC
2257577 TTTTTCT
1 TTTTTCT
2257584 CTCTTTTCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTCTTTTCTTTCCTC
Found at i:2258440 original size:254 final size:253
Alignment explanation
Indices: 2257969--2258722 Score: 971
Period size: 254 Copynumber: 3.0 Consensus size: 253
2257959 CATGTAACAG
* * * *
2257969 GACGTGGACGAGTGCTGAAAGAAAGTGTGACATGTAGTGCCCT-TATTGACATGTCATGTGGCAT
1 GACGTGGACGGGTGCT-AAAGAAAGTGTGACATGTGGTGCCCTCT-TTGACATGCCACGTGGCAT
* * *
2258033 ATTTATATTAGTATTTAGTGCCACGTGGCATTGCTACATCAGCATG-CCAAAGTGATGTGGCACT
64 ATCTATATTAGTATTCAGTGCCACGTGGCATTGCTACATCAGCATGTCAAAAGTGATGTGGCACT
*
2258097 GCCACGTTAGCATTTTCAATCCATCTCACATGTCAC-TTCAGCAAACCATGTTATGTCAATGCCA
129 GCCACGTTAGCATTTTCAATCCATCTCACATGTCACGTT-AGCAAACGATGTTATGTCAATGCCA
*
2258161 CGTCAACAATAATATTAGCTTTGTGAAAGGTAATTTTGAAAGGAAAATATTAGAGGAGCAT
193 CGTCAACAATAATATTAGCTTTGTGAAAGGTAATTTTAAAAGGAAAATATTAGAGGAGCAT
* *
2258222 GACGTGGACGGGTGCTAAAGAAAAATGTGACATGTGGTGCCCTCTTTGACATGCCACGTGGTATA
1 GACGTGGACGGGTGCTAAAG-AAAGTGTGACATGTGGTGCCCTCTTTGACATGCCACGTGGCATA
*
2258287 TCTATATTAGTATTCAGTGCCACGTGGCATTGTTACATCAGCATGTCAAAAGTGATGTGGCACTG
65 TCTATATTAGTATTCAGTGCCACGTGGCATTGCTACATCAGCATGTCAAAAGTGATGTGGCACTG
* * * * * * *
2258352 CCACGATAGCATTTTCAATCTATCTTACATATGACGTTGGCAGACGATGTTATGTCAATGCCACG
130 CCACGTTAGCATTTTCAATCCATCTCACATGTCACGTTAGCAAACGATGTTATGTCAATGCCACG
* * * * *
2258417 TCAACAATAATATCAACTTTGTG-AAGAGTAATTTCAAAAGAAAAATATTAAAGGAGCAT
195 TCAACAATAATATTAGCTTTGTGAAAG-GTAATTTTAAAAGGAAAATATTAGAGGAGCAT
* * *
2258476 GACGTGGATGGGTGCTAAAGGAAAGTGTGACATGTGGTGCCCTCCTTGACATGCCACTTGGCATA
1 GACGTGGACGGGTGCTAAA-GAAAGTGTGACATGTGGTGCCCTCTTTGACATGCCACGTGGCATA
* * * * ** * * *
2258541 TCTATATTAGTATTGAGTACCATGTAGCATTGCTACATCAATATGTTAAAA-TGATGTGACATTG
65 TCTATATTAGTATTCAGTGCCACGTGGCATTGCTACATCAGCATGTCAAAAGTGATGTGGCACTG
* * * * * * * *
2258605 CCACGTTAACATTTTGAATCCACCTCACATGTCACGTCAGCAAATGATGTTATGTTAGTGCCATG
130 CCACGTTAGCATTTTCAATCCATCTCACATGTCACGTTAGCAAACGATGTTATGTCAATGCCACG
* * * *
2258670 TCAATAATAATATTAGCTCTGTAAAAGGTAA-TTTCAAAGGAAAAATATTAGAG
195 TCAACAATAATATTAGCTTTGTGAAAGGTAATTTTAAAAGG-AAAATATTAGAG
2258723 AGACTAAATT
Statistics
Matches: 430, Mismatches: 63, Indels: 16
0.84 0.12 0.03
Matches are distributed among these distances:
252 10 0.02
253 191 0.44
254 226 0.53
255 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (253 bp):
GACGTGGACGGGTGCTAAAGAAAGTGTGACATGTGGTGCCCTCTTTGACATGCCACGTGGCATAT
CTATATTAGTATTCAGTGCCACGTGGCATTGCTACATCAGCATGTCAAAAGTGATGTGGCACTGC
CACGTTAGCATTTTCAATCCATCTCACATGTCACGTTAGCAAACGATGTTATGTCAATGCCACGT
CAACAATAATATTAGCTTTGTGAAAGGTAATTTTAAAAGGAAAATATTAGAGGAGCAT
Found at i:2258964 original size:7 final size:7
Alignment explanation
Indices: 2258920--2258965 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
2258910 AAGAAGGAGC
*
2258920 AATAAGT
1 AATAAAT
2258927 AATAAAT
1 AATAAAT
2258934 AA-AAAT
1 AATAAAT
*
2258940 AATATAT
1 AATAAAT
*
2258947 AATATA-
1 AATAAAT
2258953 AATAAAT
1 AATAAAT
2258960 AATAAA
1 AATAAA
2258966 ACAAAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
6 11 0.32
7 23 0.68
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (7 bp):
AATAAAT
Found at i:2260434 original size:23 final size:22
Alignment explanation
Indices: 2260405--2260467 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
2260395 TTTTTTTGTT
2260405 AAAAAATATAATAATAATTAATA
1 AAAAAATATAATAATAATT-ATA
*
2260428 AAAAAATATAATAATAATTTTA
1 AAAAAATATAATAATAATTATA
2260450 AAAATTAATA-AATAATAA
1 AAAA--AATATAATAATAA
2260468 AATTATCATT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
22 6 0.16
23 27 0.73
24 4 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAAAATATAATAATAATTATA
Found at i:2260438 original size:20 final size:19
Alignment explanation
Indices: 2260404--2260469 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
2260394 TTTTTTTTGT
2260404 TAAAAAATATAATAATAATTAA
1 TAAAAAA-AT-ATAATAA-TAA
2260426 TAAAAAAATATAATAATAA
1 TAAAAAAATATAATAATAA
**
2260445 TTTTAAAAAT-TAATAAATAA
1 -TAAAAAAATATAAT-AATAA
2260465 TAAAA
1 TAAAA
2260470 TTATCATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 10 0.26
20 19 0.50
21 2 0.05
22 7 0.18
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAAAATATAATAATAA
Found at i:2281982 original size:20 final size:21
Alignment explanation
Indices: 2281957--2282002 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
2281947 AGATGAATGG
2281957 AAAGAAGC-TTCAATCAGTT-A
1 AAAGAAGCATT-AATCAGTTGA
*
2281977 AAAGAAGCATTAATCGGTTGA
1 AAAGAAGCATTAATCAGTTGA
2281998 AAAGA
1 AAAGA
2282003 GGCTAGCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.22
Consensus pattern (21 bp):
AAAGAAGCATTAATCAGTTGA
Found at i:2283089 original size:22 final size:22
Alignment explanation
Indices: 2283019--2283095 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
2283009 ATGATATGAA
* * *
2283019 AATATTCTTAATTATAAGTAAAT
1 AATATT-TTTATTATAATTTAAT
** * * *
2283042 AATATTTTTACCAAAATATAAA
1 AATATTTTTATTATAATTTAAT
2283064 AATATTTTTATTATAATTTAAT
1 AATATTTTTATTATAATTTAAT
2283086 AATATCTTTT
1 AATAT-TTTT
2283096 TTAAGCTGTC
Statistics
Matches: 40, Mismatches: 13, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
22 30 0.75
23 10 0.25
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.48
Consensus pattern (22 bp):
AATATTTTTATTATAATTTAAT
Found at i:2289075 original size:3 final size:3
Alignment explanation
Indices: 2289067--2289095 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2289057 TTACAATTTT
2289067 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2289096 CCATTTTTGC
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2300854 original size:11 final size:11
Alignment explanation
Indices: 2300838--2300868 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
2300828 TATAAAATGT
2300838 TATTATTTTAA
1 TATTATTTTAA
2300849 TATTATTTTAA
1 TATTATTTTAA
2300860 TATTATTTT
1 TATTATTTT
2300869 TTAACGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTATTTTAA
Found at i:2303044 original size:32 final size:32
Alignment explanation
Indices: 2303008--2303097 Score: 108
Period size: 36 Copynumber: 2.7 Consensus size: 32
2302998 ACCAATGGCC
** *
2303008 CTCCTCTTTACTGGTTCCCTTCTCTGTAATCT
1 CTCCTCTTTACTCTTTCCCTTCTCTATAATCT
*
2303040 CTCCTCTTTAGTCTTTCCCTTCCTTCTCTATAATCT
1 CTCCTCTTTACTCTTT--C--CCTTCTCTATAATCT
2303076 CTCCTCTTTACTCTTTCCCTTC
1 CTCCTCTTTACTCTTTCCCTTC
2303098 ATTCTACAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
32 18 0.37
34 2 0.04
36 29 0.59
ACGTcount: A:0.09, C:0.38, G:0.04, T:0.49
Consensus pattern (32 bp):
CTCCTCTTTACTCTTTCCCTTCTCTATAATCT
Found at i:2303074 original size:36 final size:36
Alignment explanation
Indices: 2303025--2303102 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 36
2303015 TTACTGGTTC
* *
2303025 CCTTCTCTGTAATCTCTCCTCTTTAGTCTTTCCCTT
1 CCTTCTCTATAATCTCTCCTCTTTACTCTTTCCCTT
2303061 CCTTCTCTATAATCTCTCCTCTTTACTCTTTCCCTT
1 CCTTCTCTATAATCTCTCCTCTTTACTCTTTCCCTT
*
2303097 CATTCT
1 CCTTCT
2303103 ACAACATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.10, C:0.37, G:0.03, T:0.50
Consensus pattern (36 bp):
CCTTCTCTATAATCTCTCCTCTTTACTCTTTCCCTT
Found at i:2314253 original size:14 final size:15
Alignment explanation
Indices: 2314210--2314255 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
2314200 TGTATCAAGG
*
2314210 TTTATCCTCCCTACA
1 TTTAGCCTCCCTACA
2314225 TTTAGCCTCCCTACA
1 TTTAGCCTCCCTACA
2314240 TTTAGCCT-CCTACA
1 TTTAGCCTCCCTACA
2314254 TT
1 TT
2314256 AGGAGTTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 8 0.27
15 22 0.73
ACGTcount: A:0.20, C:0.37, G:0.04, T:0.39
Consensus pattern (15 bp):
TTTAGCCTCCCTACA
Found at i:2317060 original size:28 final size:25
Alignment explanation
Indices: 2316991--2317045 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
2316981 CGCAACCATG
* *
2316991 TATATCAACTTGTGGCCTTGCCACA
1 TATAACAACCTGTGGCCTTGCCACA
*
2317016 TATAACAACCTGTGGCCTTGCCACG
1 TATAACAACCTGTGGCCTTGCCACA
2317041 TATAA
1 TATAA
2317046 TCACAAACCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.29
Consensus pattern (25 bp):
TATAACAACCTGTGGCCTTGCCACA
Found at i:2333905 original size:19 final size:19
Alignment explanation
Indices: 2333873--2333909 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2333863 TCAAATCTAG
2333873 ATATACATACAAAACATAT
1 ATATACATACAAAACATAT
* *
2333892 ATATATATATAAAACATA
1 ATATACATACAAAACATA
2333910 AATTGATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (19 bp):
ATATACATACAAAACATAT
Found at i:2337716 original size:34 final size:33
Alignment explanation
Indices: 2337648--2337720 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 33
2337638 GAGAATAGTG
2337648 AATATATAATTTATTAATAAAAACACATAGTAAA
1 AATATATAATTTA-TAATAAAAACACATAGTAAA
*
2337682 AATATATAATTTA-AATATAATAAGGACATA-TAAA
1 AATATATAATTTATAATA-AA-AA-CACATAGTAAA
2337716 AATAT
1 AATAT
2337721 CTTCATAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
32 4 0.11
33 2 0.06
34 24 0.69
35 5 0.14
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (33 bp):
AATATATAATTTATAATAAAAACACATAGTAAA
Found at i:2338184 original size:27 final size:27
Alignment explanation
Indices: 2338154--2338215 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
2338144 AAAAATATTC
*
2338154 ATCCACTTCTAATGGGTAAAGTTATAT
1 ATCCACTTCTAATAGGTAAAGTTATAT
* * **
2338181 ATCCTCTTTTGGTAGGTAAAGTTATAT
1 ATCCACTTCTAATAGGTAAAGTTATAT
2338208 ATCCACTT
1 ATCCACTT
2338216 TTGGGACATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (27 bp):
ATCCACTTCTAATAGGTAAAGTTATAT
Found at i:2338216 original size:27 final size:27
Alignment explanation
Indices: 2338168--2338219 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
2338158 ACTTCTAATG
*
2338168 GGTAAAGTTATATATCCTCTTTTGGTA
1 GGTAAAGTTATATATCCACTTTTGGTA
2338195 GGTAAAGTTATATATCCACTTTTGG
1 GGTAAAGTTATATATCCACTTTTGG
2338220 GACATTCACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (27 bp):
GGTAAAGTTATATATCCACTTTTGGTA
Found at i:2338749 original size:17 final size:18
Alignment explanation
Indices: 2338730--2338765 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2338720 AGTATAAGAG
2338730 AAAGTATTTAAAGGGAGAA
1 AAAGTATTTAAAGGGAG-A
*
2338749 AAAGTATTTAGAGGGAG
1 AAAGTATTTAAAGGGAG
2338766 TAAGAAGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (18 bp):
AAAGTATTTAAAGGGAGA
Found at i:2338946 original size:14 final size:14
Alignment explanation
Indices: 2338927--2338966 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2338917 ATATACATAA
2338927 CATAAATGAATATT
1 CATAAATGAATATT
2338941 CATAAA--AATATT
1 CATAAATGAATATT
2338953 CAT-AATAGAATATT
1 CATAAAT-GAATATT
2338967 AATTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 2 0.09
12 9 0.39
14 12 0.52
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (14 bp):
CATAAATGAATATT
Done.