Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 62 of 205
Found at i:18584223 original size:26 final size:26
Alignment explanation
Indices: 18584193--18584288 Score: 156
Period size: 26 Copynumber: 3.7 Consensus size: 26
18584183 CACTAATATT
18584193 GCAGCAAAGCTGCCAGTAATAGTAAC
1 GCAGCAAAGCTGCCAGTAATAGTAAC
18584219 GCAGCAAAGCTGCCAGTAATAGTAAC
1 GCAGCAAAGCTGCCAGTAATAGTAAC
* * *
18584245 GCAGCAAAGTTGCCAGTAACAGTATC
1 GCAGCAAAGCTGCCAGTAATAGTAAC
*
18584271 GCAGCAAAGTTGCCAGTA
1 GCAGCAAAGCTGCCAGTA
18584289 TATTATACTT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 67 1.00
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAGTAATAGTAAC
Found at i:18594456 original size:22 final size:23
Alignment explanation
Indices: 18594430--18594482 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
18594420 TAAATGAATG
*
18594430 AATAAATATTAAGTAAAAC-AAT-
1 AATAAATATAAAG-AAAACAAATA
18594452 AATAACA-ATAAAGAAAACAAATA
1 AATAA-ATATAAAGAAAACAAATA
18594475 AATAAATA
1 AATAAATA
18594483 AATGAGATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 5 0.19
22 14 0.54
23 7 0.27
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.21
Consensus pattern (23 bp):
AATAAATATAAAGAAAACAAATA
Found at i:18594616 original size:20 final size:20
Alignment explanation
Indices: 18594553--18594616 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 20
18594543 TACTTAAAAA
* * *
18594553 AAAGTAAAAAATACAATAAT
1 AAAGAAAAAAAAATAATAAT
18594573 AAA-ATAAAACGAAAAT-ATATAT
1 AAAGA-AAAA--AAAATAATA-AT
18594595 AAAGAAAAAAAAATAATAAT
1 AAAGAAAAAAAAATAATAAT
18594615 AA
1 AA
18594617 CCTAAATAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
20 16 0.46
21 6 0.17
22 12 0.34
23 1 0.03
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (20 bp):
AAAGAAAAAAAAATAATAAT
Found at i:18597524 original size:21 final size:21
Alignment explanation
Indices: 18597498--18597540 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
18597488 AAACAAGTAG
18597498 CAACATTGTTTCATTTATTAT
1 CAACATTGTTTCATTTATTAT
18597519 CAACATTGTTTCATTTATTAT
1 CAACATTGTTTCATTTATTAT
18597540 C
1 C
18597541 TCTTCTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.16, G:0.05, T:0.51
Consensus pattern (21 bp):
CAACATTGTTTCATTTATTAT
Found at i:18601123 original size:54 final size:54
Alignment explanation
Indices: 18601037--18601151 Score: 194
Period size: 54 Copynumber: 2.1 Consensus size: 54
18601027 TCTGGGCCAC
* *
18601037 TGAGACCAGCTTTAGGCAGCAAAATTTCCATCACAGATTCACTGTCCAGCTCAT
1 TGAGACCAGCTTTAGGCAACAAAATTTCCATCACAGACTCACTGTCCAGCTCAT
* *
18601091 TGAGACCAGCTTTAGGCAACAAAATTTTCATCACGGACTCACTGTCCAGCTCAT
1 TGAGACCAGCTTTAGGCAACAAAATTTCCATCACAGACTCACTGTCCAGCTCAT
18601145 TGAGACC
1 TGAGACC
18601152 TTGATATTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (54 bp):
TGAGACCAGCTTTAGGCAACAAAATTTCCATCACAGACTCACTGTCCAGCTCAT
Found at i:18601476 original size:18 final size:17
Alignment explanation
Indices: 18601434--18601480 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
18601424 TCAAAATAGT
*
18601434 TTTAAAAAAT-ATTATA
1 TTTAAAAAATAATTAGA
18601450 TTTATAAAAATAATTCAGA
1 TTTA-AAAAATAATT-AGA
18601469 TTT-AAAAATAAT
1 TTTAAAAAATAAT
18601481 CACCAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 4 0.15
17 15 0.56
18 3 0.11
19 5 0.19
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TTTAAAAAATAATTAGA
Found at i:18601887 original size:108 final size:106
Alignment explanation
Indices: 18601774--18602548 Score: 1117
Period size: 109 Copynumber: 7.2 Consensus size: 106
18601764 GGCACCAGAG
* * *
18601774 TACGAAAAAAGTAAAAAAAAAAATTGGTGGTAGCTTGCCAATGGCCGGCACCACCATTTTTGGAG
1 TACGAAAAAAGTAAAAAAAAAAATTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGG-G
18601839 AATTTTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATCAGTA
65 AA-TTTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATCAGTA
* *
18601882 TACGAAAAAAGT-AAAAAAAAAATT-GTAGTGGCCTGCCAATGGCCGACACCACCTTTTTTGGGG
1 TACGAAAAAAGTAAAAAAAAAAATTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTT-GGG
* *
18601945 AAATTTTTTTTACTTTTTTCGTGTCAATAACAGGTATCAGTA
65 AATTTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATCAGTA
* * * *
18601987 TACGAAAAAAGTTAAAAAAAAAATTGATGGTGGCCTGCCAATAGCCGGCACCACCTTTTTTGGGG
1 TACGAAAAAAGTAAAAAAAAAAATTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGGGA
*
18602052 ATTTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATCAGTG
66 ATTTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATCAGTA
* **
18602093 TAAGAAAAAAGTAAAAAAAAAAAAATTTGACGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTG
1 TACGAAAAAAGT--AAAAAAAAAAA-TTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTG
* *
18602158 GGGATTTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATCAGTG
63 GGAATTTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATCAGTA
* **
18602202 TAAGAAAAAAGTAAAAAAAAAAAAATTTGACGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTG
1 TACGAAAAAAGT--AAAAAAAAAAA-TTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTG
*
18602267 GGAA-TTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATGAGTA
63 GGAATTTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATCAGTA
* * *
18602310 TACGAAAAAAGTAAAAAAAAAATTTGGTGGTGGCCTGCCGATGGCCGGCTCCACCTTTTTTGGGG
1 TACGAAAAAAGTAAAAAAAAAAATTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTT-GGG
18602375 AATTTTTTTTTTA-TTTTTTCGTGTCAATAGCAGGTATCAGTA
65 AA-TTTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATCAGTA
** * *
18602417 TACGAAAAAAAGTAAAAAAAAATTCTTTTGGTGGTGGCCTGCCAATGGCCAGCACCATCTTTTTT
1 TACG-AAAAAAGTAAAAAAAAA---AATTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTT
*
18602482 GGAAATTTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATCAGTA
62 GGGAATTTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATCAGTA
18602527 TACGAAAAAAAGTAAAAAAAAA
1 TACG-AAAAAAGTAAAAAAAAA
18602549 TTCTTTTGGT
Statistics
Matches: 618, Mismatches: 35, Indels: 26
0.91 0.05 0.04
Matches are distributed among these distances:
105 84 0.14
106 112 0.18
107 77 0.12
108 96 0.16
109 159 0.26
110 55 0.09
111 35 0.06
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (106 bp):
TACGAAAAAAGTAAAAAAAAAAATTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGGGA
ATTTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATCAGTA
Found at i:18602605 original size:110 final size:106
Alignment explanation
Indices: 18601842--18602652 Score: 482
Period size: 109 Copynumber: 7.6 Consensus size: 106
18601832 TTTGGAGAAT
18601842 TTTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATCAGTATACG-AAAAAAGTAAAAAAAAA---
1 TTTTTTTTTA-TTTTTTCGTGTCAATAGCAGGTATCAGTATACGAAAAAAAGTAAAAAAAAATTC
* * * ** **
18601903 -ATT-GTAGTGGCCTGCCAATGGCC-GACACCACCTTTTTTGGGGAAA
65 TTTTGGTGGTGG-C-GCCAATGGCCAG-CACCAACAGTAAT---GAAA
*
18601948 -TTTTTTTTACTTTTTTCGTGTCAATAACAGGTATCAGTATACG-AAAAAAGTTAAAAAAAAA--
1 TTTTTTTTTA-TTTTTTCGTGTCAATAGCAGGTATCAGTATACGAAAAAAAG-TAAAAAAAAATT
* * * * * ** ** **
18602009 --ATTGATGGTGGCCTGCCAATAGCCGGCACCACCTTTTTTGGGGA
64 CTTTTGGTGGTGG-C-GCCAATGGCCAGCACCAACAGTAAT-GAAA
* * ***
18602053 TTTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATCAGTGTAAG-AAAAAAGTAAAAAAAAAAAA
1 TTTTTTTTTA-TTTTTTCGTGTCAATAGCAGGTATCAGTATACGAAAAAAAGTAAAAAAAAATTC
* ** * * ** ** **
18602117 ATTTGACGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGGGGA
65 TTTTGGTGGTGG-C-GCCAATGGCCAGCACCAACAGTAAT-GAAA
* * ***
18602162 TTTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATCAGTGTAAG-AAAAAAGTAAAAAAAAAAAA
1 TTTTTTTTTA-TTTTTTCGTGTCAATAGCAGGTATCAGTATACGAAAAAAAGTAAAAAAAAATTC
* ** * * ** ** *
18602226 ATTTGACGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGGGAA
65 TTTTGGTGGTGG-C-GCCAATGGCCAGCACCAACAGTAAT-GAAA
*
18602271 -TTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATGAGTATACG-AAAAAAGTAAAAAAAAA---
1 TTTTTTTTTA-TTTTTTCGTGTCAATAGCAGGTATCAGTATACGAAAAAAAGTAAAAAAAAATTC
* * * * * ** ** *
18602331 ATTTGGTGGTGGCCTGCCGATGGCCGGCTCCACCTTTTTTGGGGAAT
65 TTTTGGTGGTGG-C-GCCAATGGCCAGCACCAACAGTAAT---GAAA
18602378 TTTTTTTTTATTTTTTCGTGTCAATAGCAGGTATCAGTATACGAAAAAAAGTAAAAAAAAATTCT
1 TTTTTTTTTATTTTTTCGTGTCAATAGCAGGTATCAGTATACGAAAAAAAGTAAAAAAAAATTCT
* ** **
18602443 TTTGGTGGTGGCCTGCCAATGGCCAGCACCATCTTTTTTGGAAA
66 TTTGGTGGTGG-C-GCCAATGGCCAGCACCAACAGTAAT-GAAA
18602487 TTTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATCAGTATACGAAAAAAAGTAAAAAAAAATTC
1 TTTTTTTTTA-TTTTTTCGTGTCAATAGCAGGTATCAGTATACGAAAAAAAGTAAAAAAAAATTC
* *
18602552 TTTTGGTGGT-G-GCCATTGGCCGGCACCCAACAGTAAT--AA
65 TTTTGGTGGTGGCGCCAATGGCCAGCA-CCAACAGTAATGAAA
* * * ** *
18602591 TTTTTTTTACTTTTTTTCTCGTGTTAAAATTAGGTATCAGTATACAAAAAAAAGTAAAAAAA
1 TTTTTTTT--TATTTTT-TCGTGTCAATAGCAGGTATCAGTATACGAAAAAAAGTAAAAAAA
18602653 CAAATTTTTG
Statistics
Matches: 643, Mismatches: 42, Indels: 40
0.89 0.06 0.06
Matches are distributed among these distances:
104 10 0.02
105 103 0.16
106 112 0.17
107 71 0.11
108 84 0.13
109 164 0.26
110 64 0.10
111 35 0.05
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (106 bp):
TTTTTTTTTATTTTTTCGTGTCAATAGCAGGTATCAGTATACGAAAAAAAGTAAAAAAAAATTCT
TTTGGTGGTGGCGCCAATGGCCAGCACCAACAGTAATGAAA
Found at i:18602892 original size:19 final size:19
Alignment explanation
Indices: 18602868--18602907 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
18602858 TTGTTTTTTT
18602868 TATTTTTTTAATTTTAAAA
1 TATTTTTTTAATTTTAAAA
*
18602887 TATTTTTTTATTTTTAAAA
1 TATTTTTTTAATTTTAAAA
18602906 TA
1 TA
18602908 AATTTTTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTTTTTAATTTTAAAA
Found at i:18602913 original size:19 final size:19
Alignment explanation
Indices: 18602872--18602915 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
18602862 TTTTTTTATT
**
18602872 TTTTTAATTTTAAAATATT
1 TTTTTAATTTTAAAATAAA
*
18602891 TTTTTATTTTTAAAATAAA
1 TTTTTAATTTTAAAATAAA
18602910 TTTTTA
1 TTTTTA
18602916 GTATTTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTAATTTTAAAATAAA
Found at i:18602931 original size:21 final size:19
Alignment explanation
Indices: 18602869--18602931 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
18602859 TGTTTTTTTT
* * *
18602869 ATTTTTTTAATTTTAAAAT
1 ATTTTTGTATTTTTAAAAA
*
18602888 ATTTTTTTATTTTTAAAATAA
1 ATTTTTGTATTTTT-AAA-AA
18602909 ATTTTTAGTATTTATTAAAAA
1 ATTTTT-GTATTT-TTAAAAA
18602930 AT
1 AT
18602932 GAGCTGGGCC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 13 0.35
20 3 0.08
21 11 0.30
22 8 0.22
23 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
ATTTTTGTATTTTTAAAAA
Found at i:18604095 original size:13 final size:13
Alignment explanation
Indices: 18604077--18604101 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18604067 CAAAAAGGGG
18604077 TTTTACTAAAATA
1 TTTTACTAAAATA
18604090 TTTTACTAAAAT
1 TTTTACTAAAAT
18604102 TATGATTTAG
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:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTACTAAAATA
Found at i:18611050 original size:15 final size:15
Alignment explanation
Indices: 18611030--18611064 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
18611020 CTGTACTATT
*
18611030 ATTATAATTATTATC
1 ATTATAACTATTATC
*
18611045 ATTATAACTATTGTC
1 ATTATAACTATTATC
18611060 ATTAT
1 ATTAT
18611065 TATATAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (15 bp):
ATTATAACTATTATC
Found at i:18620082 original size:20 final size:19
Alignment explanation
Indices: 18620057--18620119 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
18620047 ACAAATGTAC
18620057 AAACAGGGACACCGAAGTGT
1 AAACAGGG-CACCGAAGTGT
* *
18620077 ATACAGGGGCATCGAAGTGT
1 AAACA-GGGCACCGAAGTGT
*
18620097 AAATAGAGGCACCGAAGTGT
1 AAACAG-GGCACCGAAGTGT
18620117 AAA
1 AAA
18620120 TCTTGTACAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.03
20 32 0.89
21 3 0.08
ACGTcount: A:0.40, C:0.16, G:0.30, T:0.14
Consensus pattern (19 bp):
AAACAGGGCACCGAAGTGT
Found at i:18620120 original size:20 final size:20
Alignment explanation
Indices: 18620066--18620120 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
18620056 CAAACAGGGA
* * *
18620066 CACCGAAGTGTATACAGGGG
1 CACCGAAGTGTAAATAGAGG
*
18620086 CATCGAAGTGTAAATAGAGG
1 CACCGAAGTGTAAATAGAGG
18620106 CACCGAAGTGTAAAT
1 CACCGAAGTGTAAAT
18620121 CTTGTACAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.18
Consensus pattern (20 bp):
CACCGAAGTGTAAATAGAGG
Found at i:18625134 original size:23 final size:24
Alignment explanation
Indices: 18625075--18625129 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
18625065 CCAACCCTTA
*
18625075 TTCCTCCAAATACCTAACTTAGTTT
1 TTCC-CCAAATCCCTAACTTAGTTT
18625100 TTCCCCAAATCCCTAACTTAGTTT
1 TTCCCCAAATCCCTAACTTAGTTT
*
18625124 TCCCCC
1 TTCCCC
18625130 CATCCGTCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.24, C:0.36, G:0.04, T:0.36
Consensus pattern (24 bp):
TTCCCCAAATCCCTAACTTAGTTT
Found at i:18632891 original size:17 final size:17
Alignment explanation
Indices: 18632877--18632923 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
18632867 ATTAAATAGC
18632877 AAAAATAAATAAATAAG
1 AAAAATAAATAAATAAG
* * *
18632894 AAAAATAAACAAATGAT
1 AAAAATAAATAAATAAG
*
18632911 AAAAATCAATAAA
1 AAAAATAAATAAA
18632924 CCAATCCAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.17
Consensus pattern (17 bp):
AAAAATAAATAAATAAG
Found at i:18634172 original size:46 final size:46
Alignment explanation
Indices: 18634098--18634282 Score: 275
Period size: 46 Copynumber: 4.0 Consensus size: 46
18634088 ACAATGCTAT
*
18634098 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCAC
* *
18634144 AACTCTGTATGGTTTTCGTT-ACTAAAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTC-TTCACTGAAATACCATACCTACGTTTCAC
*
18634190 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTCCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCAC
* * *
18634236 AACTCAATATGGTTTTCTTTC-CTGAATTACCATACCTACGTTCCAC
1 AACTCAGTATGGTTTTC-TTCACTGAAATACCATACCTACGTTTCAC
18634282 A
1 A
18634283 CTTTGCCATG
Statistics
Matches: 128, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
45 2 0.02
46 121 0.95
47 5 0.04
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCAC
Found at i:18638722 original size:30 final size:29
Alignment explanation
Indices: 18638661--18638722 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
18638651 CTTAAATTAC
* *
18638661 TTATGTTTCTTTTACTGTTATATATAATA
1 TTATGTTTCTTTTACTGTAATATAAAATA
*
18638690 TTATGTTTCTTTT-TTGTAATATTAAAAATA
1 TTATGTTTCTTTTACTGTAATA-T-AAAATA
18638720 TTA
1 TTA
18638723 AATTTATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 14 0.50
30 8 0.29
ACGTcount: A:0.31, C:0.05, G:0.06, T:0.58
Consensus pattern (29 bp):
TTATGTTTCTTTTACTGTAATATAAAATA
Found at i:18646199 original size:13 final size:13
Alignment explanation
Indices: 18646181--18646205 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18646171 AAAATTCGTT
18646181 AATGGTACATTTA
1 AATGGTACATTTA
18646194 AATGGTACATTT
1 AATGGTACATTT
18646206 TCCCCTATAT
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:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (13 bp):
AATGGTACATTTA
Found at i:18647734 original size:5 final size:5
Alignment explanation
Indices: 18647724--18647780 Score: 71
Period size: 5 Copynumber: 11.2 Consensus size: 5
18647714 TGAAGTTTTC
* *
18647724 TCGAA TCGAA TCGAG T-GAGA TGGAA TTCGAA TCGAA TCGAA TCGAA TCGAA
1 TCGAA TCGAA TCGAA TCGA-A TCGAA -TCGAA TCGAA TCGAA TCGAA TCGAA
18647775 TCGAA T
1 TCGAA T
18647781 ATATTTATTC
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
4 2 0.04
5 38 0.83
6 6 0.13
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:18648160 original size:17 final size:17
Alignment explanation
Indices: 18648118--18648200 Score: 66
Period size: 17 Copynumber: 4.8 Consensus size: 17
18648108 AATTCAATTT
18648118 TAATATAAAT-ATTCAA
1 TAATATAAATAATTCAA
18648134 T-ATGACTAAATAATTCAA
1 TAAT-A-TAAATAATTCAA
18648152 TAATATAAATAATAT-AA
1 TAATATAAATAAT-TCAA
* *
18648169 -AATGTGAAATTTAATTTAA
1 TAATAT-AAA--TAATTCAA
18648188 TAATATAAATAAT
1 TAATATAAATAAT
18648201 AGATATAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 19
0.72 0.03 0.25
Matches are distributed among these distances:
15 2 0.04
16 6 0.11
17 22 0.40
18 10 0.18
19 11 0.20
20 4 0.07
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (17 bp):
TAATATAAATAATTCAA
Found at i:18648795 original size:9 final size:9
Alignment explanation
Indices: 18648778--18648808 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
18648768 TCGAGTTGAT
18648778 TCGAATAAC
1 TCGAATAAC
*
18648787 TCGATTAAC
1 TCGAATAAC
18648796 TCGAATAAC
1 TCGAATAAC
18648805 TCGA
1 TCGA
18648809 TTCGTTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:18650367 original size:17 final size:17
Alignment explanation
Indices: 18650344--18650388 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
18650334 TATCTTCAAT
18650344 AATTTAAATAATAAAAA
1 AATTTAAATAATAAAAA
* *
18650361 TATTTAAAATCATAAAAA
1 AATTT-AAATAATAAAAA
18650379 AATTATAAAT
1 AATT-TAAAT
18650389 TAAAATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 4 0.17
18 18 0.78
19 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTTAAATAATAAAAA
Found at i:18656268 original size:37 final size:37
Alignment explanation
Indices: 18656219--18656364 Score: 139
Period size: 37 Copynumber: 3.9 Consensus size: 37
18656209 AAAACTTTTA
* *
18656219 CAGAAAATCTTTACTATTGTTTTCCGTCTTTTCTTTG
1 CAGAGAATCTTTACTATTGTTCTCCGTCTTTTCTTTG
* * * * ** *
18656256 CATAGAACCTTTACTGTTGATCTATGTCTTTTTTTTTTTG
1 CAGAGAATCTTTACTATTGTTCTCCGTC---TTTTCTTTG
* * **
18656296 CAGAGAATCTTTATTACTAATCTCCGTCTTTTCTTTG
1 CAGAGAATCTTTACTATTGTTCTCCGTCTTTTCTTTG
*
18656333 CAGAGAATCTTTACTATTGTTCTCCATCTTTT
1 CAGAGAATCTTTACTATTGTTCTCCGTCTTTT
18656365 GCAGGGAATC
Statistics
Matches: 83, Mismatches: 23, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
37 55 0.66
40 28 0.34
ACGTcount: A:0.20, C:0.19, G:0.11, T:0.50
Consensus pattern (37 bp):
CAGAGAATCTTTACTATTGTTCTCCGTCTTTTCTTTG
Found at i:18659598 original size:3 final size:3
Alignment explanation
Indices: 18659573--18659615 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
18659563 GTTATTTTTG
*
18659573 TTA TTA -TA TTA TATA TTA CTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
18659616 ACATATATAC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:18659808 original size:26 final size:26
Alignment explanation
Indices: 18659760--18659809 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
18659750 TATAAATTTA
*
18659760 CATTTTATAATACATATACATTTTTC
1 CATTTTATAATACATACACATTTTTC
* *
18659786 CATTTTATAATTCATACATATTTT
1 CATTTTATAATACATACACATTTT
18659810 CACATACATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (26 bp):
CATTTTATAATACATACACATTTTTC
Found at i:18660197 original size:19 final size:20
Alignment explanation
Indices: 18660156--18660197 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
18660146 ACCATTCATC
* *
18660156 AAGGTTATTTTCTTGATTTA
1 AAGGTTATTTTCTTGAATAA
*
18660176 AAGGTT-TTTTTTTGAATAA
1 AAGGTTATTTTCTTGAATAA
18660195 AAG
1 AAG
18660198 CATTATTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.50
Consensus pattern (20 bp):
AAGGTTATTTTCTTGAATAA
Found at i:18666039 original size:44 final size:45
Alignment explanation
Indices: 18665989--18666340 Score: 223
Period size: 44 Copynumber: 8.0 Consensus size: 45
18665979 TGAATACAAA
* * * *
18665989 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATACC
1 AGATCTTGTCTTCATATACTGGTCGTGAAGTAGATCAAAGATAAC
** ** * * * *
18666033 AGATCTTGTCCCCCCATACTGGTGGTGGAGTAGGTCAAAGAAAAC
1 AGATCTTGTCTTCATATACTGGTCGTGAAGTAGATCAAAGATAAC
* * * **
18666078 AGACCGTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAGT
1 AGATCTTGTCTTCATATACTGGTCGTGAAGTAGATCAAAGATAAC
* * * * * * * * *
18666122 AGGTCATGTCTTCCTATATTGGTAGCGAAGTGGATCGAATAT-AC
1 AGATCTTGTCTTCATATACTGGTCGTGAAGTAGATCAAAGATAAC
* * ** * * *
18666166 ATATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGA-AAGC
1 AGATCTTGTCTTCATATACTGGTCGTGAAGTAGATCAAAGATAA-C
* *
18666211 AGATCTTGTCTTCATGTACTGG-CATGAAGTAGATCAAAGA-AAC
1 AGATCTTGTCTTCATATACTGGTCGTGAAGTAGATCAAAGATAAC
* ** * * * * *
18666254 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGGTCGAAGAAAAC
1 AGATCTTGTCTTCATATACTGGTCGTGAAGTAGATCAAAGATAAC
* * * *
18666299 AGACCGTGTCTTCATGTACT-GACGTGAAGTAGATCAAAGATA
1 AGATCTTGTCTTCATATACTGGTCGTGAAGTAGATCAAAGATA
18666341 GTAGGTCCTA
Statistics
Matches: 223, Mismatches: 79, Indels: 12
0.71 0.25 0.04
Matches are distributed among these distances:
43 19 0.09
44 124 0.56
45 80 0.36
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (45 bp):
AGATCTTGTCTTCATATACTGGTCGTGAAGTAGATCAAAGATAAC
Found at i:18666439 original size:221 final size:222
Alignment explanation
Indices: 18665989--18666421 Score: 733
Period size: 221 Copynumber: 2.0 Consensus size: 222
18665979 TGAATACAAA
* * * *
18665989 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATACCAGATCTTGTCCCCCCATACTG
1 AGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGATAACAGATCTTGTCCCCCCATACTG
*
18666054 GTGGTGGAGTAGGTCAAAGAAAACAGACCGTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAT
66 GTGGTGGAGTAGGTCAAAGAAAACAGACCGTGTCTTCATGTACTGACGTGAAGTAGATCAAAGAT
* *
18666119 AGTAGGTCATGTCTTCCTATATTGGTAGCGAAGTGGATCGAATATACATATCTTGCCTTCCCATA
131 AGTAGGTCATATCTTCCTATATTGGTAGCGAAGTGGATCGAATATACATATCTTACCTTCCCATA
*
18666184 CTGGTGGCGAAGCAGATCAAAGAAAGC
196 CTGGCGGCGAAGCAGATCAAAGAAAGC
*
18666211 AGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGA-AACAGATCTTGTCTCCCCATACTG
1 AGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGATAACAGATCTTGTCCCCCCATACTG
*
18666275 GTGGTGGAGTAGGTCGAAGAAAACAGACCGTGTCTTCATGTACTGACGTGAAGTAGATCAAAGAT
66 GTGGTGGAGTAGGTCAAAGAAAACAGACCGTGTCTTCATGTACTGACGTGAAGTAGATCAAAGAT
* * *
18666340 AGTAGGTCCTATCTTCCTATATTGGTAGCGAAGTGGATCGAATATACATATTTTATCTTCCCATA
131 AGTAGGTCATATCTTCCTATATTGGTAGCGAAGTGGATCGAATATACATATCTTACCTTCCCATA
*
18666405 CTGGCGGCGAAGTAGAT
196 CTGGCGGCGAAGCAGAT
18666422 TGAAGATTAT
Statistics
Matches: 197, Mismatches: 14, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
221 160 0.81
222 37 0.19
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (222 bp):
AGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGATAACAGATCTTGTCCCCCCATACTG
GTGGTGGAGTAGGTCAAAGAAAACAGACCGTGTCTTCATGTACTGACGTGAAGTAGATCAAAGAT
AGTAGGTCATATCTTCCTATATTGGTAGCGAAGTGGATCGAATATACATATCTTACCTTCCCATA
CTGGCGGCGAAGCAGATCAAAGAAAGC
Found at i:18666882 original size:132 final size:132
Alignment explanation
Indices: 18666614--18666891 Score: 333
Period size: 132 Copynumber: 2.1 Consensus size: 132
18666604 ATTGAAGTTT
* * *
18666614 ACAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGG
1 ACAGATCTTATCTCCCTAAACAGTAGTGGAGCAAATCAAAGATGGCAGATTTTACCTCCCTGAAG
* * ** * * *
18666679 TTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGTAGCAGTGGAATAGATTGAAAA
66 TTACAGTGGAGCACATTAAAGCCAACAATCCTATCTCCCTGAGTAGCAATGGAATAGATTGAAAA
**
18666744 TT
131 CC
* *
18666746 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGATGGCAGATTTTACCTCCCTGAAG
1 ACAGATCTTATCTCCCTAAACAGTAGTGGAGCAAATCAAAGATGGCAGATTTTACCTCCCTGAAG
* * * * * * * *
18666811 TTGCATTGGAGCAGATTAAAGTCAACAATCCTATCTCCTTGAAGTTGCAATGGAGTGGATT-AAA
66 TTACAGTGGAGCACATTAAAGCCAACAATCCTATCTCCCTG-AGTAGCAATGGAATAGATTGAAA
18666875 ACC
130 ACC
*
18666878 ACAGATCTCATCTC
1 ACAGATCTTATCTC
18666892 TTTGAAGTTG
Statistics
Matches: 122, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
132 108 0.89
133 14 0.11
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (132 bp):
ACAGATCTTATCTCCCTAAACAGTAGTGGAGCAAATCAAAGATGGCAGATTTTACCTCCCTGAAG
TTACAGTGGAGCACATTAAAGCCAACAATCCTATCTCCCTGAGTAGCAATGGAATAGATTGAAAA
CC
Found at i:18670805 original size:21 final size:21
Alignment explanation
Indices: 18670771--18670822 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
18670761 CATATCTTCT
18670771 AAGATTGC--ATATCATATCC
1 AAGATTGCATATATCATATCC
*
18670790 AAGATTGCATATATCATATCT
1 AAGATTGCATATATCATATCC
*
18670811 AAGATTACATAT
1 AAGATTGCATAT
18670823 CCTTGAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 8 0.28
21 21 0.72
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (21 bp):
AAGATTGCATATATCATATCC
Found at i:18671973 original size:44 final size:45
Alignment explanation
Indices: 18671923--18672088 Score: 200
Period size: 44 Copynumber: 3.8 Consensus size: 45
18671913 ATCTACTATT
* **
18671923 TTCAACCTACTCCACTATTG-CTCAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACTCAGGGAGATAGGATTCACAATC
*
18671967 TTCAACCTATTCCACTGCTGACT-AGGGAGATTA-GA-CCTACAATC
1 TTCAACCTATTCCACTGCTGACTCAGGGAGA-TAGGATTC-ACAATC
* * * *
18672011 TTCAATCTATTCCACTGCTG-CCCAGGGAGATAGAATTCTCAATC
1 TTCAACCTATTCCACTGCTGACTCAGGGAGATAGGATTCACAATC
18672055 TTCAACCTATTCCACTGCTGAC-CAGGGAGATAGG
1 TTCAACCTATTCCACTGCTGACTCAGGGAGATAGG
18672089 GTTGGGGTTA
Statistics
Matches: 104, Mismatches: 11, Indels: 14
0.81 0.09 0.11
Matches are distributed among these distances:
43 4 0.04
44 94 0.90
45 6 0.06
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.27
Consensus pattern (45 bp):
TTCAACCTATTCCACTGCTGACTCAGGGAGATAGGATTCACAATC
Found at i:18672196 original size:43 final size:43
Alignment explanation
Indices: 18672149--18672290 Score: 108
Period size: 43 Copynumber: 3.2 Consensus size: 43
18672139 TATTTTTAAC
18672149 CTGCTCCGCTACAACTCAGAGAGGCAAGGCTGGTGTCTTCGAT
1 CTGCTCCGCTACAACTCAGAGAGGCAAGGCTGGTGTCTTCGAT
* * ** * * * * * ** *
18672192 CTGCTTCGCTGTC-GGTGCA-AGAAGGCAAGATCCGCTATTTTTTAAC
1 CTGCTCCGCT-ACAACT-CAGAG-AGGCAAG-GCTGGT-GTCTTCGAT
18672238 CTGCTCCGCTACAACTCAGAGAGGCAAGGCTGGTGTCTTCGAT
1 CTGCTCCGCTACAACTCAGAGAGGCAAGGCTGGTGTCTTCGAT
*
18672281 CTGCTTCGCT
1 CTGCTCCGCT
18672291 GTCGGTGCAA
Statistics
Matches: 67, Mismatches: 25, Indels: 14
0.63 0.24 0.13
Matches are distributed among these distances:
43 25 0.37
44 13 0.19
45 13 0.19
46 16 0.24
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.27
Consensus pattern (43 bp):
CTGCTCCGCTACAACTCAGAGAGGCAAGGCTGGTGTCTTCGAT
Found at i:18672398 original size:44 final size:44
Alignment explanation
Indices: 18672170--18672485 Score: 126
Period size: 44 Copynumber: 7.1 Consensus size: 44
18672160 CAACTCAGAG
*
18672170 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAAGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
* * * * * ** * * * **
18672214 AGGCAAGATCCGCTATTTTTTAACCTGCTCCGCT-ACAACT-CA-GA
1 AGGCAAG-GCTGGT-GTCTTCGATCTGCTTCGCTGTC-GGTGCAGGA
*
18672258 GAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAAGA
1 -AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
* * * * * ** * * * * *
18672303 AGGCAAGATCCGCTATTTTTTAACCTGCTCCACTGTAAC-CT--AGGG
1 AGGCAAG-GCTGGT-GTCTTCGATCTGCTTCGCTGT--CGGTGCAGGA
*
18672348 AGGCAAGGCTGGTGTCTTCGATCTGTTTCGCTGTCGGTGCAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
* * * ** * * * **** *
18672392 AGGCAAGATCTGCTAT-TTATAGCCTGCTCCGCT-ACAACCCAGGG
1 AGGCAAG-GCTGGTGTCTTCGA-TCTGCTTCGCTGTCGGTGCAGGA
18672436 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
18672480 AGGCAA
1 AGGCAA
18672486 TATCTTCTAT
Statistics
Matches: 177, Mismatches: 77, Indels: 36
0.61 0.27 0.12
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 41 0.23
44 64 0.36
45 40 0.23
46 28 0.16
47 1 0.01
48 1 0.01
ACGTcount: A:0.20, C:0.25, G:0.29, T:0.27
Consensus pattern (44 bp):
AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
Found at i:18672422 original size:177 final size:175
Alignment explanation
Indices: 18672099--18672639 Score: 789
Period size: 177 Copynumber: 3.1 Consensus size: 175
18672089 GTTGGGGTTA
* *
18672099 TCGATCTGCTTCGCTGACGGTGCAGGAAAGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
* *
18672164 TCAGAGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCCGCTA
66 TCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTA
* *
18672229 TTTTTTAACCTGCTCCGCTACAACTCAGAGAGGCAAGGCTGGTGTCT
131 --TTTTAGCCTGCTCCGCTACAACCCAGAGAGGCAAGGCTGGTGTCT
* * * **
18672276 TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCCGCTATTTTTTAACCTGCTCCACTGTAA
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTA-TTTTTAACCTGCTCCGCTACAA
* *
18672341 C-CTAGGGAGGCAAGGCTGGTGTCTTCGATCTGTTTCGCTGTCGGTGCAGGAAGGCAAGATCTGC
65 CTC-AGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGC
*
18672405 TATTTATAGCCTGCTCCGCTACAACCCAGGGAGGCAAGGCTGGTGTCT
129 TATTT-TAGCCTGCTCCGCTACAACCCAGAGAGGCAAGGCTGGTGTCT
* * *
18672453 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAATATCTTCTATTTTTAGCCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
* * * * *
18672518 TCAGGGAGGCAAAGCTGGTGTCTTTGATCTACTTCGCTATCGGTGCAAGAAGGCAAGATTTGCTA
66 TCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTA
* *
18672583 TTTTAGCCTGCTCCGCTGCAACCCA-AGAAGACAAGGCTGGTGTCT
131 TTTTAGCCTGCTCCGCTACAACCCAGAG-AGGCAAGGCTGGTGTCT
*
18672628 TCGATCTACTTC
1 TCGATCTGCTTC
18672640 ACTCCAATAC
Statistics
Matches: 326, Mismatches: 33, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
174 1 0.00
175 48 0.15
176 81 0.25
177 117 0.36
178 79 0.24
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (175 bp):
TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
TCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTA
TTTTAGCCTGCTCCGCTACAACCCAGAGAGGCAAGGCTGGTGTCT
Found at i:18672503 original size:88 final size:88
Alignment explanation
Indices: 18672099--18672639 Score: 760
Period size: 88 Copynumber: 6.1 Consensus size: 88
18672089 GTTGGGGTTA
* * *
18672099 TCGATCTGCTTCGCTGACGGTGCAGGAAAGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
* *
18672164 TCAGAGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
*
18672187 TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCCGCTATTTTTTAACCTGCTCCGCTACAA
1 TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTA-TTTTTAACCTGCTCCGCTACAA
* *
18672252 CTCAGAGAGGCAAGGCTGGTGTCT
65 CCCAGGGAGGCAAGGCTGGTGTCT
* * **
18672276 TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCCGCTATTTTTTAACCTGCTCCACTGTAA
1 TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTA-TTTTTAACCTGCTCCGCTACAA
*
18672341 CCTAGGGAGGCAAGGCTGGTGTCT
65 CCCAGGGAGGCAAGGCTGGTGTCT
* * * *
18672365 TCGATCTGTTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTATAGCCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
18672430 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * *
18672453 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAATATCTTCTATTTTTAGCCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
* *
18672518 TCAGGGAGGCAAAGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * * * *
18672541 TTGATCTACTTCGCTATCGGTGCAAGAAGGCAAGATTTGCTA-TTTTAGCCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
* * *
18672605 CCAAGAAGACAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
*
18672628 TCGATCTACTTC
1 TCGATCTGCTTC
18672640 ACTCCAATAC
Statistics
Matches: 413, Mismatches: 39, Indels: 3
0.91 0.09 0.01
Matches are distributed among these distances:
87 50 0.12
88 195 0.47
89 168 0.41
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
CCAGGGAGGCAAGGCTGGTGTCT
Found at i:18672677 original size:44 final size:44
Alignment explanation
Indices: 18672625--18673026 Score: 300
Period size: 44 Copynumber: 9.1 Consensus size: 44
18672615 AAGGCTGGTG
* *
18672625 TCTTCGATCTACTTCACTCCAATACATGAAGACAAGTTCTGCTT
1 TCTTCGATCTACTTCACTCCAATACATGAAGACAAGATCTGCTA
* ***
18672669 TCTTCGATCTACTTCACCACCAATATGGGAAGACAAGATCTGC-A
1 TCTTCGATCTACTTCA-CTCCAATACATGAAGACAAGATCTGCTA
* * * * * * *
18672713 TCTTTGATCCACTTC-CTACCAATATAGGAAGACATGACCTACTA
1 TCTTCGATCTACTTCACT-CCAATACATGAAGACAAGATCTGCTA
* * * * *
18672757 TCTTCGATCTACTTCACGCCAATACATAAAGATAAGATCTGATT
1 TCTTCGATCTACTTCACTCCAATACATGAAGACAAGATCTGCTA
* * *
18672801 TCTTCGATCTACTTCGCCACCAGT--ATGGAAAGACAAGATCTGC-A
1 TCTTCGATCTACTTC-ACTCCAATACAT-G-AAGACAAGATCTGCTA
* * * * *
18672845 TCTTCGATCCACTTC-CTACCAATATAGGAAGACAAGACCCGCTA
1 TCTTCGATCTACTTCACT-CCAATACATGAAGACAAGATCTGCTA
* *
18672889 TCTTCGATCTACTTCA-TGCTAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACT-CCAATACATGAAGACAAGATCTGCTA
* * * *** *
18672933 TCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAGATCTGC-A
1 TCTTCGATCTACTTC-ACTCCAATACATGAAGACAAGATCTGCTA
* * * *
18672977 TCTTCGATCCACTTCGCTACCAATATA-GAAAGACAGGATCTGCTA
1 TCTTCGATCTACTTCACT-CCAATACATG-AAGACAAGATCTGCTA
18673022 TCTTC
1 TCTTC
18673027 ACTGATCTGC
Statistics
Matches: 279, Mismatches: 62, Indels: 33
0.75 0.17 0.09
Matches are distributed among these distances:
42 2 0.01
43 40 0.14
44 173 0.62
45 64 0.23
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (44 bp):
TCTTCGATCTACTTCACTCCAATACATGAAGACAAGATCTGCTA
Found at i:18672762 original size:88 final size:89
Alignment explanation
Indices: 18672625--18673026 Score: 388
Period size: 88 Copynumber: 4.6 Consensus size: 89
18672615 AAGGCTGGTG
* * * * * *
18672625 TCTTCGATCTACTTCACT-CCAATACATGAAGACAAGTTCTGCTTTCTTCGATCTACTTCACCAC
1 TCTTCGATCCACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACCAC
*
18672689 CAATATGGGAAGACAAGATCTGCA
66 CAATATAGGAAGACAAGATCTGCA
* * * * *
18672713 TCTTTGATCCACTTC-CTACCAATATAGGAAGACATGACCTACTATCTTCGATCTACTTCA-CGC
1 TCTTCGATCCACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACCAC
* ** *
18672776 CAATACATAAAGATAAGATCTG-A
66 CAATATAGGAAGACAAGATCTGCA
* * * *
18672799 TTTCTTCGATCTACTTCGCCACCAGTAT-GGAAAGACAAGATCTGC-ATCTTCGATCCACTTC-C
1 --TCTTCGATCCACTTCGCTACCAATATAGG-AAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * *
18672861 TACCAATATAGGAAGACAAGACCCGCTA
63 CACCAATATAGGAAGACAAGATCTGC-A
* * * * * * * *
18672889 TCTTCGATCTACTTC-ATGCTAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCAC
1 TCTTCGATCCACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACCAC
* * *
18672953 CAGTATGGGAAGATAAGATCTGCA
66 CAATATAGGAAGACAAGATCTGCA
* *
18672977 TCTTCGATCCACTTCGCTACCAATATAGAAAGACAGGATCTGCTATCTTC
1 TCTTCGATCCACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCTTC
18673027 ACTGATCTGC
Statistics
Matches: 247, Mismatches: 55, Indels: 23
0.76 0.17 0.07
Matches are distributed among these distances:
86 1 0.00
87 39 0.16
88 140 0.57
89 66 0.27
90 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (89 bp):
TCTTCGATCCACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACCAC
CAATATAGGAAGACAAGATCTGCA
Found at i:18672803 original size:132 final size:132
Alignment explanation
Indices: 18672625--18673026 Score: 633
Period size: 132 Copynumber: 3.0 Consensus size: 132
18672615 AAGGCTGGTG
* * *
18672625 TCTTCGATCTACTTCACTCCAATACATGAAGACAAGTTCTGCTTTCTTCGATCTACTTCACCACC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACC
* * * *
18672690 AATATGGGAAGACAAGATCTGCATCTTTGATCCACTTCCTACCAATATAGGAAGACATGACCTAC
66 AGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAAGACCTGC
18672755 TA
131 TA
* * *
18672757 TCTTCGATCTACTTCACGCCAATACATAAAGATAAGATCTGATTTCTTCGATCTACTTCGCCACC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACC
* *
18672822 AGTATGGAAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAAGACCCGC
66 AGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAAGACCTGC
18672887 TA
131 TA
* *
18672889 TCTTCGATCTACTTCATGCTAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACC
* * * *
18672954 AGTATGGGAAGATAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGAAAGACAGGATCTG
66 AGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTC-CTACCAATATAGGAAGACAAGACCTG
18673019 CTA
130 CTA
18673022 TCTTC
1 TCTTC
18673027 ACTGATCTGC
Statistics
Matches: 246, Mismatches: 23, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
132 216 0.88
133 30 0.12
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (132 bp):
TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACC
AGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAAGACCTGC
TA
Found at i:18674327 original size:14 final size:15
Alignment explanation
Indices: 18674304--18674336 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
18674294 TTCGACGTTT
18674304 TTCCAAATAAGGT-C
1 TTCCAAATAAGGTCC
*
18674318 TTCCACATAAGGTCC
1 TTCCAAATAAGGTCC
18674333 TTCC
1 TTCC
18674337 TCGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.30
Consensus pattern (15 bp):
TTCCAAATAAGGTCC
Found at i:18675208 original size:26 final size:26
Alignment explanation
Indices: 18675154--18675208 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
18675144 AAGAAAATCC
* **
18675154 AAAAGAATGAAAGAATAATTATTTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
18675180 AAAAGAATGAAAAAAT-ATTAGCTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
18675205 AAAA
1 AAAA
18675209 TGGATGCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.62, C:0.05, G:0.11, T:0.22
Consensus pattern (26 bp):
AAAAGAATGAAAAAATAATTAGCTCA
Found at i:18678130 original size:33 final size:33
Alignment explanation
Indices: 18678088--18678156 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
18678078 TTTAGGTTGT
**
18678088 AACACTATTACTGGCAAACTCCTATGCCTGGCG
1 AACACTATTACTGGCAAACTCCTATAACTGGCG
18678121 AACACTATTACTGGCAAACTCCTATAACTGGCG
1 AACACTATTACTGGCAAACTCCTATAACTGGCG
18678154 AAC
1 AAC
18678157 TTTTATGTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (33 bp):
AACACTATTACTGGCAAACTCCTATAACTGGCG
Found at i:18678134 original size:16 final size:17
Alignment explanation
Indices: 18678091--18678157 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 17
18678081 AGGTTGTAAC
18678091 ACTATTACTGGCAAACT
1 ACTATTACTGGCAAACT
* ** *
18678108 CCTATGCCTGGCGAAC-
1 ACTATTACTGGCAAACT
18678124 ACTATTACTGGCAAACT
1 ACTATTACTGGCAAACT
* * *
18678141 CCTATAACTGGCGAACT
1 ACTATTACTGGCAAACT
18678158 TTTATGTCTG
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
16 12 0.32
17 26 0.68
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.25
Consensus pattern (17 bp):
ACTATTACTGGCAAACT
Found at i:18680056 original size:17 final size:17
Alignment explanation
Indices: 18680014--18680084 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 17
18680004 GTATTACACT
18680014 TATGTCTGGCAAACCCC
1 TATGTCTGGCAAACCCC
* * *
18680031 TACT-ACTGGCGATCCCC
1 TA-TGTCTGGCAAACCCC
* *
18680048 TATGTCTGGCAAACACT
1 TATGTCTGGCAAACCCC
* * *
18680065 TGTGTTTGGCGAACCCC
1 TATGTCTGGCAAACCCC
18680082 TAT
1 TAT
18680085 AACTGATGAA
Statistics
Matches: 38, Mismatches: 14, Indels: 4
0.68 0.25 0.07
Matches are distributed among these distances:
16 1 0.03
17 36 0.95
18 1 0.03
ACGTcount: A:0.21, C:0.31, G:0.20, T:0.28
Consensus pattern (17 bp):
TATGTCTGGCAAACCCC
Found at i:18681930 original size:28 final size:28
Alignment explanation
Indices: 18681877--18681933 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
18681867 GCCCTTGTGT
**
18681877 GTGAGCCCTTGCATGTGGAACCCTATAG
1 GTGAGCCCTTGCATGCAGAACCCTATAG
*
18681905 GTGAGCCCTTGTATGCAG-ACCTCTATAG
1 GTGAGCCCTTGCATGCAGAACC-CTATAG
18681933 G
1 G
18681934 CGAACCCCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.26
Consensus pattern (28 bp):
GTGAGCCCTTGCATGCAGAACCCTATAG
Found at i:18682077 original size:25 final size:25
Alignment explanation
Indices: 18682043--18682098 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
18682033 TAATTTGTTG
*
18682043 TACATGCGAGTCACTTGTTGATTAT
1 TACATGCGAGTCACTTGTTGAGTAT
18682068 TACATGCGAGTCACTTGTTGAGTAT
1 TACATGCGAGTCACTTGTTGAGTAT
18682093 TACATG
1 TACATG
18682099 TGAACCACCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (25 bp):
TACATGCGAGTCACTTGTTGAGTAT
Found at i:18682223 original size:36 final size:36
Alignment explanation
Indices: 18682143--18682213 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
18682133 TATACACGAG
* *
18682143 TCATATGCATCATGCAAATCCTAGAAACTATGCGAT
1 TCATATGTATCATGCAAACCCTAGAAACTATGCGAT
* *
18682179 TCATATGTATCATGCAGACCCTAGGAACTATGCGA
1 TCATATGTATCATGCAAACCCTAGAAACTATGCGA
18682214 GTTGTATGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.27
Consensus pattern (36 bp):
TCATATGTATCATGCAAACCCTAGAAACTATGCGAT
Found at i:18685504 original size:15 final size:15
Alignment explanation
Indices: 18685484--18685514 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
18685474 AACATTAAAG
18685484 GAAATTAACTGAAAA
1 GAAATTAACTGAAAA
18685499 GAAATTAACTGAAAA
1 GAAATTAACTGAAAA
18685514 G
1 G
18685515 GAACCTGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.58, C:0.06, G:0.16, T:0.19
Consensus pattern (15 bp):
GAAATTAACTGAAAA
Found at i:18696152 original size:17 final size:17
Alignment explanation
Indices: 18696130--18696164 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
18696120 ACCCCTACAA
18696130 AACAATTAATTAATCAT
1 AACAATTAATTAATCAT
18696147 AACAATTAATTAATCAT
1 AACAATTAATTAATCAT
18696164 A
1 A
18696165 CTTCCACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (17 bp):
AACAATTAATTAATCAT
Found at i:18699966 original size:20 final size:20
Alignment explanation
Indices: 18699920--18699975 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
18699910 ACGGGAGTAG
* *
18699920 GACATGCTATGATATGATTC
1 GACATGATATGATATGAATC
*
18699940 GATATGATATGATATGACATC
1 GACATGATATGATATGA-ATC
*
18699961 -ACATGATATGTTATG
1 GACATGATATGATATG
18699976 TAACTATGCG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.36
Consensus pattern (20 bp):
GACATGATATGATATGAATC
Found at i:18706168 original size:110 final size:110
Alignment explanation
Indices: 18705975--18706412 Score: 831
Period size: 110 Copynumber: 4.0 Consensus size: 110
18705965 TTTTAATAAT
*
18705975 CTCATTATATGTTTTGATTATATCTGCTCTTTTTGACACAATGTCTAGAACTACTCATAGTTCCT
1 CTCATTATATGTTTTGATCATATCTGCTCTTTTTGACACAATGTCTAGAACTACTCATAGTTCCT
18706040 CCCCAACCCATAAATAGGAGGATAATGTGCTTTAGCGAACTAAGA
66 CCCCAACCCATAAATAGGAGGATAATGTGCTTTAGCGAACTAAGA
18706085 CTCATTATATGTTTTGATCATATCTGCTCTTTTTGACACAATGTCTAGAACTACTCATAGTTCCT
1 CTCATTATATGTTTTGATCATATCTGCTCTTTTTGACACAATGTCTAGAACTACTCATAGTTCCT
18706150 CCCCAACCCATAAATAGGAGGATAATGTGCTTTAGCGAACTAAGA
66 CCCCAACCCATAAATAGGAGGATAATGTGCTTTAGCGAACTAAGA
*
18706195 CTCATTATATGTTTTGATCATATCTGCTCTTTTTGACACAATGTCTAGAATTACTCATAGTTCCT
1 CTCATTATATGTTTTGATCATATCTGCTCTTTTTGACACAATGTCTAGAACTACTCATAGTTCCT
18706260 CCCCAACCCATAAATAGGAGGATAATGTGCTTTAGCGAACTAAGA
66 CCCCAACCCATAAATAGGAGGATAATGTGCTTTAGCGAACTAAGA
*
18706305 CTCATTATATGTTTTGATCATATCTGCTCTTTTTGACACAATGTCTAGAATTACTCATAGTTCCT
1 CTCATTATATGTTTTGATCATATCTGCTCTTTTTGACACAATGTCTAGAACTACTCATAGTTCCT
**
18706370 CCCCAACCCATAAATAGGAGGATAATACGCTTTAGCGAACTAA
66 CCCCAACCCATAAATAGGAGGATAATGTGCTTTAGCGAACTAA
18706413 TTGACTCAAT
Statistics
Matches: 324, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 324 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.34
Consensus pattern (110 bp):
CTCATTATATGTTTTGATCATATCTGCTCTTTTTGACACAATGTCTAGAACTACTCATAGTTCCT
CCCCAACCCATAAATAGGAGGATAATGTGCTTTAGCGAACTAAGA
Found at i:18706731 original size:13 final size:13
Alignment explanation
Indices: 18706713--18706737 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18706703 TGTATTCCTT
18706713 TTTTTTGTTTTTG
1 TTTTTTGTTTTTG
18706726 TTTTTTGTTTTT
1 TTTTTTGTTTTT
18706738 ATTACTCTTC
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:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
TTTTTTGTTTTTG
Found at i:18707019 original size:33 final size:33
Alignment explanation
Indices: 18706982--18707045 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
18706972 TATATTTACT
18706982 AAAATAATTAAAAACTAT-ATTTATATAAATAAC
1 AAAATAATTAAAAA-TATAATTTATATAAATAAC
* * *
18707015 AAAATATTTAAATATATAATTTATATTAATA
1 AAAATAATTAAAAATATAATTTATATAAATA
18707046 TATTAATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 3 0.11
33 24 0.89
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (33 bp):
AAAATAATTAAAAATATAATTTATATAAATAAC
Found at i:18715029 original size:44 final size:43
Alignment explanation
Indices: 18714955--18715713 Score: 350
Period size: 44 Copynumber: 17.4 Consensus size: 43
18714945 CTACTCTTTG
* * * *
18714955 CAACTTCAGAGAGATAAGATCTAAGGCTTTAATCCGCTCCACTA
1 CAACTTCAGGGAGATAAGAT-TACGACTTTAATCTGCTCCACTA
* * * *
18714999 CAACTTTAGGGAGATAGGATTATCGACTTTAATTTGCTCCACTG
1 CAACTTCAGGGAGATAAGATTA-CGACTTTAATCTGCTCCACTA
* * * * * *
18715043 CAACTTCAGGGAGATACGACTTGCCATCTTCAGTCTGCCCCACTA
1 CAACTTCAGGGAGATAAGA-TTACGA-CTTTAATCTGCTCCACTA
* * *
18715088 CAACTTCA-GGAGGATAAGACTTGCTTAC-TTAGTCTGCTCCACTA
1 CAACTTCAGGGA-GATAAGA-TTAC-GACTTTAATCTGCTCCACTA
* * *** * *
18715132 CAACTTCAGGGAGATAAAACTA-GA-TGCGATCTGCT-CTCTG
1 CAACTTCAGGGAGATAAGATTACGACTTTAATCTGCTCCACTA
* * ** * *
18715172 CAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTCCACTG
1 CAACTTCAGGGAGATAAGAT-TACGACTTTAATCTGCTCCACTA
* *
18715216 CAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTA
1 CAACTTCAGGGAGATAAGATTA-CGACTTTAATCTGCTCCACTA
* * * * * * *
18715260 CAGCTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTG
1 CAACTTCAGGGAGATAAGA-TTACGA-CTTTAATCTGCTCCACTA
* * * *
18715305 CAACTTCA-GGAGGATAAGACTTGCTTAC-TTATTCTGCTCCACTG
1 CAACTTCAGGGA-GATAAGA-TTAC-GACTTTAATCTGCTCCACTA
* * * *** * * * *
18715349 CAACTTCAGAGAGATAAAACTA-GA-TGCGATTTG-TTCTCTG
1 CAACTTCAGGGAGATAAGATTACGACTTTAATCTGCTCCACTA
* ** *
18715389 CAACTTCAGAGAGATAAGATCTGA-GGTTTTAATCTGCTCCACTG
1 CAACTTCAGGGAGATAAGAT-T-ACGACTTTAATCTGCTCCACTA
* * *
18715433 CAACTTTAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTA
1 CAACTTCAGGGAGATAAGATTA-CGACTTTAATCTGCTCCACTA
* * * * * * *
18715477 CAGCTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTG
1 CAACTTCAGGGAGATAAGA-TTACGA-CTTTAATCTGCTCCACTA
* * * * *
18715522 CAACTTCA-AGAGGATAAGACTTGCTTAC-TTAGTCTGCTCCACTG
1 CAACTTCAGGGA-GATAAGA-TTAC-GACTTTAATCTGCTCCACTA
* ** * *
18715566 CAACTTCAGGGAGATAAGACTA-G--TTGCGATCTGCT-CTCTG
1 CAACTTCAGGGAGATAAGATTACGACTT-TAATCTGCTCCACTA
* ** * *
18715606 CAACTTCAGAGAGATAAGATCTGA-GGTTTTAATCCGCTCCACTG
1 CAACTTCAGGGAGATAAGAT-T-ACGACTTTAATCTGCTCCACTA
* * * * *
18715650 CAACTTCAGGGAGATAGGATTAGCCATCTTCAGTCTGCCCCACTA
1 CAACTTCAGGGAGATAAGATTA-CGA-CTTTAATCTGCTCCACTA
18715695 CAACTTCA-GGAGGATAAGA
1 CAACTTCAGGGA-GATAAGA
18715714 CTTGCTTACT
Statistics
Matches: 549, Mismatches: 126, Indels: 79
0.73 0.17 0.10
Matches are distributed among these distances:
40 66 0.12
41 21 0.04
42 7 0.01
43 27 0.05
44 285 0.52
45 140 0.26
46 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (43 bp):
CAACTTCAGGGAGATAAGATTACGACTTTAATCTGCTCCACTA
Found at i:18715274 original size:217 final size:217
Alignment explanation
Indices: 18714899--18715718 Score: 1309
Period size: 217 Copynumber: 3.8 Consensus size: 217
18714889 ATTTGCTATT
* * * * * *
18714899 TTAGTCTGCTCCGCTGCAACTTCAAGGAGATAAGACTAAATGCGATCTACTCTTTGCAACTTCAG
1 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGATGCGATCTGCTCTCTGCAACTTCAG
* * * *
18714964 AGAGATAAGATCTAAGGCTTTAATCCGCTCCACTACAACTTTAGGGAGATAGGATTATCGACTTT
66 AGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTT
* * * * *
18715029 AATTTGCTCCACTGCAACTTCAGGGAGATACGACTTGCCATCTTCAGTCTGCCCCACTACAACTT
131 AATCTGCTCCACTACAGCTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTT
18715094 CAGGAGGATAAGACTTGCTTAC
196 CAGGAGGATAAGACTTGCTTAC
*
18715116 TTAGTCTGCTCCACTACAACTTCAGGGAGATAAAACTAGATGCGATCTGCTCTCTGCAACTTCAG
1 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGATGCGATCTGCTCTCTGCAACTTCAG
18715181 AGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTT
66 AGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTT
18715246 AATCTGCTCCACTACAGCTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTT
131 AATCTGCTCCACTACAGCTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTT
18715311 CAGGAGGATAAGACTTGCTTAC
196 CAGGAGGATAAGACTTGCTTAC
* * * *
18715333 TTATTCTGCTCCACTGCAACTTCAGAGAGATAAAACTAGATGCGATTTGTTCTCTGCAACTTCAG
1 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGATGCGATCTGCTCTCTGCAACTTCAG
* * *
18715398 AGAGATAAGATCTGAGGTTTTAATCTGCTCCACTGCAACTTTAGGGAGATAGGATTATCGGCTTT
66 AGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTT
18715463 AATCTGCTCCACTACAGCTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTT
131 AATCTGCTCCACTACAGCTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTT
*
18715528 CAAGAGGATAAGACTTGCTTAC
196 CAGGAGGATAAGACTTGCTTAC
* *
18715550 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGTTGCGATCTGCTCTCTGCAACTTCAG
1 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGATGCGATCTGCTCTCTGCAACTTCAG
* * **
18715615 AGAGATAAGATCTGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAGCCATCTT
66 AGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTA-TCGGCTT
* * * *
18715680 CAGTCTGCCCCACTACAACTTCA-GGAGGATAAGACTTGC
130 TAATCTGCTCCACTACAGCTTCAGGGA-GATAAGACTTGC
18715719 TTACTTAGGA
Statistics
Matches: 561, Mismatches: 40, Indels: 3
0.93 0.07 0.00
Matches are distributed among these distances:
217 526 0.94
218 35 0.06
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (217 bp):
TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGATGCGATCTGCTCTCTGCAACTTCAG
AGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTT
AATCTGCTCCACTACAGCTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTT
CAGGAGGATAAGACTTGCTTAC
Found at i:18715522 original size:173 final size:176
Alignment explanation
Indices: 18715207--18715711 Score: 484
Period size: 173 Copynumber: 2.9 Consensus size: 176
18715197 GTTTTAATCC
* * * *
18715207 GCTCCACTGCAACTTCAGGGAGATAGGAT-TATCGGCTTTAATCTGCTCCACTACAGCTTCAGGG
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTA--GGTTTTAATCTGCTCCACTGCAACTTCAGGG
* ** * * * *
18715271 AGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCA-GGAGGATAAGACTTG-CTTACT
64 AGATAAGA-TT-ACGGCTTTAATCTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCCAT-CT
* * * *
18715334 T-ATTCTGCTCCACTGCAACTTCAGAGA-GATAAAACTAG-ATGC-GA-TTT
125 TCAGTCTGCCCCACTGCAACTTCAGAGAGGATAAAACTAGCATACTGAGTCT
* * * *
18715381 G-TTCTCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCTGCTCCACTGCAACTTTAGGGA
1 GCTCCACTGCAACTTCAGGGAGATAAGATCT-AGGTTTTAATCTGCTCCACTGCAACTTCAGGGA
* * *
18715445 GATAGGATTATCGGCTTTAATCTGCTCCACTACAGCTTCAGGGAGATAAGACTTGCCATCTTCAG
65 GATAAGATTA-CGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAG
* * * *
18715510 TCTGCCCCACTGCAACTTCA-AGAGGATAAGACTTGCTTACTTAGTCT
129 TCTGCCCCACTGCAACTTCAGAGAGGATAAAACTAGCATACTGAGTCT
*** * *
18715557 GCTCCACTGCAACTTCAGGGAGATAAGA-CTA-GTTGCGATCTGCT-CTCTGCAACTTCAGAGAG
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTAGGTTTTAATCTGCTCCACTGCAACTTCAGGGAG
* * *
18715619 ATAAGATCTGA-GGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGA-TTAGCCATCTTCA
66 ATAAGAT-T-ACGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCCATCTTCA
*
18715682 GTCTGCCCCACTACAACTTCAG-GAGGATAA
128 GTCTGCCCCACTGCAACTTCAGAGAGGATAA
18715712 GACTTGCTTA
Statistics
Matches: 274, Mismatches: 42, Indels: 31
0.79 0.12 0.09
Matches are distributed among these distances:
172 43 0.16
173 184 0.67
174 15 0.05
175 4 0.01
176 5 0.02
177 23 0.08
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (176 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATCTAGGTTTTAATCTGCTCCACTGCAACTTCAGGGAG
ATAAGATTACGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAGTC
TGCCCCACTGCAACTTCAGAGAGGATAAAACTAGCATACTGAGTCT
Found at i:18716599 original size:26 final size:26
Alignment explanation
Indices: 18716570--18716622 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
18716560 AAAAAGGTCA
18716570 TAACAATGGATAAGAATAAAGTTGGT
1 TAACAATGGATAAGAATAAAGTTGGT
18716596 TAACAATGGATAAGAATAAAGTTGGT
1 TAACAATGGATAAGAATAAAGTTGGT
18716622 T
1 T
18716623 CTGAGCATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.45, C:0.04, G:0.23, T:0.28
Consensus pattern (26 bp):
TAACAATGGATAAGAATAAAGTTGGT
Found at i:18722814 original size:15 final size:15
Alignment explanation
Indices: 18722805--18722837 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
18722795 CAAATGCTAT
18722805 AATAATAAATACAAC
1 AATAATAAATACAAC
*
18722820 AATAATAAATACATC
1 AATAATAAATACAAC
18722835 AAT
1 AAT
18722838 GGCATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:18726164 original size:7 final size:7
Alignment explanation
Indices: 18726149--18726183 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
18726139 TGTTCTTTTT
18726149 CTAAACC
1 CTAAACC
*
18726156 CTGAACC
1 CTAAACC
18726163 CTAAACC
1 CTAAACC
18726170 CTAAACC
1 CTAAACC
18726177 CTAAACC
1 CTAAACC
18726184 ACACAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.40, C:0.43, G:0.03, T:0.14
Consensus pattern (7 bp):
CTAAACC
Found at i:18731777 original size:20 final size:20
Alignment explanation
Indices: 18731752--18731792 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
18731742 CAGGAGAAGA
18731752 TAGCTTCAAATTTACTTAGG
1 TAGCTTCAAATTTACTTAGG
18731772 TAGCTTCAAATTTACTTAGG
1 TAGCTTCAAATTTACTTAGG
18731792 T
1 T
18731793 TCATGCTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (20 bp):
TAGCTTCAAATTTACTTAGG
Found at i:18733784 original size:22 final size:22
Alignment explanation
Indices: 18733744--18733785 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
18733734 AAAAAACTAG
*
18733744 AAAATGAAAATTATTATTTTTA
1 AAAATGAAAATTATAATTTTTA
*
18733766 AAAATGAAAA-TATAAATTTT
1 AAAATGAAAATTATAATTTTT
18733786 CTCAAAAACC
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:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (22 bp):
AAAATGAAAATTATAATTTTTA
Found at i:18739928 original size:20 final size:18
Alignment explanation
Indices: 18739884--18739944 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 18
18739874 ATACTTTTTC
*
18739884 TTTATATATATTTTAAATT
1 TTTATATAT-TTTTAAATA
18739903 TATTATATATTTTTGAAAATA
1 T-TTATATATTTTT--AAATA
* *
18739924 TTTATGTATTTTTATATA
1 TTTATATATTTTTAAATA
18739942 TTT
1 TTT
18739945 CTTTGATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 7 0.19
19 5 0.14
20 19 0.53
21 5 0.14
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTATATATTTTTAAATA
Found at i:18740392 original size:18 final size:18
Alignment explanation
Indices: 18740358--18740393 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
18740348 TTTTATTACC
18740358 ATTAACATTAAAGTTTTT
1 ATTAACATTAAAGTTTTT
*
18740376 ATTAA-ATTAAAATTTTT
1 ATTAACATTAAAGTTTTT
18740393 A
1 A
18740394 ATATAACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
ATTAACATTAAAGTTTTT
Found at i:18745851 original size:14 final size:14
Alignment explanation
Indices: 18745820--18745862 Score: 68
Period size: 14 Copynumber: 3.0 Consensus size: 14
18745810 AAGAAAAACT
18745820 TAATAATAATATAAA
1 TAATAAT-ATATAAA
*
18745835 TAATAATATATACA
1 TAATAATATATAAA
18745849 TAATAATATATAAA
1 TAATAATATATAAA
18745863 AGTTGAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 19 0.73
15 7 0.27
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (14 bp):
TAATAATATATAAA
Found at i:18746121 original size:18 final size:18
Alignment explanation
Indices: 18746098--18746148 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 18
18746088 AATATGTAGA
18746098 TAAATATATAA-ACTAATG
1 TAAATA-ATAATACTAATG
18746116 TAAATAATAATACTAA--
1 TAAATAATAATACTAATG
*
18746132 T-AATAATAATTCTAATG
1 TAAATAATAATACTAATG
18746149 ATAATTGTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 13 0.45
16 1 0.03
17 4 0.14
18 11 0.38
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (18 bp):
TAAATAATAATACTAATG
Found at i:18746138 original size:15 final size:15
Alignment explanation
Indices: 18746118--18746153 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
18746108 AACTAATGTA
18746118 AATAATAATACTAAT
1 AATAATAATACTAAT
*
18746133 AATAATAATTCTAAT
1 AATAATAATACTAAT
*
18746148 GATAAT
1 AATAAT
18746154 TGTCGAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.36
Consensus pattern (15 bp):
AATAATAATACTAAT
Found at i:18746425 original size:69 final size:69
Alignment explanation
Indices: 18746314--18746459 Score: 267
Period size: 69 Copynumber: 2.1 Consensus size: 69
18746304 AGTCGGTTAC
*
18746314 ACACGAGGAAGGGTTAGCACCCTTGTAACGCCCAAAATTGGTACCGAATTGATTGTTTATTGTCT
1 ACACGAGGAAGGGTTAGCACCCTTGTAACGCCCAAAATTGGTACCGAATTGATTGTTTAATGTCT
18746379 TAGT
66 TAGT
18746383 ACACGAGGAAGGGTTAGCACCCTTGTAACGCCCAAAATTGGTACCGAATTGATTGTTTAATGTCT
1 ACACGAGGAAGGGTTAGCACCCTTGTAACGCCCAAAATTGGTACCGAATTGATTGTTTAATGTCT
18746448 TAGT
66 TAGT
*
18746452 GC-CGAGGA
1 ACACGAGGA
18746460 TTTGAAAAGA
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
68 6 0.08
69 69 0.92
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (69 bp):
ACACGAGGAAGGGTTAGCACCCTTGTAACGCCCAAAATTGGTACCGAATTGATTGTTTAATGTCT
TAGT
Found at i:18747517 original size:23 final size:22
Alignment explanation
Indices: 18747460--18747519 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
18747450 AAAACATGTG
*
18747460 AATAATAATTTAAAATAATAGT
1 AATAATAATTTAAAATAATAAT
* *
18747482 -ATATTACATTTTAAAATTATAAT
1 AATAATA-A-TTTAAAATAATAAT
18747505 AATAATAAGTTTAAA
1 AATAATAA-TTTAAA
18747520 GGTAATGTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 5 0.17
22 1 0.03
23 19 0.63
24 5 0.17
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (22 bp):
AATAATAATTTAAAATAATAAT
Found at i:18747737 original size:3 final size:3
Alignment explanation
Indices: 18747729--18747754 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
18747719 GTATATATGT
18747729 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
18747755 GGGATTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:18747799 original size:5 final size:6
Alignment explanation
Indices: 18747780--18747836 Score: 60
Period size: 6 Copynumber: 9.2 Consensus size: 6
18747770 ATTGGAATTC
* * *
18747780 AAATAA AAATAA AAATAA AACACTAC AAATAG AAATAA AAAGAA AAATAA
1 AAATAA AAATAA AAATAA AA-A-TAA AAATAA AAATAA AAATAA AAATAA
*
18747830 AGATAA A
1 AAATAA A
18747837 CTAAATTGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
6 37 0.86
7 2 0.05
8 4 0.09
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.14
Consensus pattern (6 bp):
AAATAA
Found at i:18749277 original size:50 final size:50
Alignment explanation
Indices: 18749212--18750080 Score: 434
Period size: 50 Copynumber: 17.5 Consensus size: 50
18749202 TTTGGAAAGT
* *
18749212 AAGATTCGCCATTGTGGCTTTAATCTTTTTAACTGCAATGTCGTGGAAGC
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGTGGAAGC
* * * *
18749262 AAGATTCACCGTTGTGGCTTTAATCTGCTTT-ACTGCACTG-CCTGGGAATGT
1 AAGATTCACCGTTGTGGCTTTAATCT-TTTTAACTGCAATGTCGT-GGAA-GC
* * * * * * *
18749313 AAGATTCGCCGTTATAGCTTTAATCATTTTAACTGCAATTTCATGGAGGC
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGTGGAAGC
* ** ** * * *
18749363 AAGATTCACCGTTGTGGCTTTAATCTGTTCCACTATACTGTC-TGGGAGGT
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGT-GGAAGC
* * * *** *
18749413 AAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAACACCGAGGAAGC
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGTGGAAGC
* ** ** * * *
18749463 AAGATTCACCGTTGTGGCTTTAATCTGTTCCACTATACTGTC-TGGGAGGT
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGT-GGAAGC
* * * *** *
18749513 AAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAACACCGAGGAAGC
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGTGGAAGC
* ** * * ** *
18749563 AAGATTCACCGTTGTGGCTTTAATCTGTTCCACGGC-ATCGCCAAGGAAGT
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAAT-GTCGTGGAAGC
* * * * *
18749613 AGGATTCGCCGCTGTGGCTTTAA------T--CTGTAATGTCGGGGAAGC
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGTGGAAGC
* ** ** ** * *
18749655 AAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCACCG-CTTGAGAAGT
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGTG-GAAGC
* * * * *
18749705 AAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTTAG-GGAGGC
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATG-TCGTGGAAGC
* * *** * * *
18749755 AAGATTCACCGATGTGGCTTTAATCTATTCCGCTGC-ATCG-CCTGGGGAGT
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAAT-GTCGT-GGAAGC
* * * *
18749805 AAGATTCACTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCAG-GGAGGC
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTC-GTGGAAGC
* * *** * * *
18749855 AAGATTCACCGATGTGGCTTTAATCTATTCCGCTGC-ATCG-CCTGGGGAGT
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAAT-GTCGT-GGAAGC
* * * *
18749905 AAGATTCACTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCAG-GGAGGC
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTC-GTGGAAGC
* * ** * ** * *
18749955 AAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACTACCAG-GGAGGT
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTC-GTGGAAGC
* * * * * *
18750005 AAGATTCGCTGCTGTAGCTTTAATCTTTTTAATTGCAATGTCAG-GGAGGC
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTC-GTGGAAGC
* *
18750055 AAAATTCATCGTTGTGGCTTTAATCT
1 AAGATTCACCGTTGTGGCTTTAATCT
18750081 GTTCCACTGC
Statistics
Matches: 593, Mismatches: 192, Indels: 68
0.70 0.23 0.08
Matches are distributed among these distances:
42 29 0.05
43 2 0.00
49 11 0.02
50 506 0.85
51 43 0.07
52 2 0.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (50 bp):
AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGTGGAAGC
Found at i:18749465 original size:100 final size:100
Alignment explanation
Indices: 18749210--18750088 Score: 943
Period size: 100 Copynumber: 8.9 Consensus size: 100
18749200 CATTTGGAAA
** * *
18749210 GTAAGATTCGCCATTGTGGCTTTAATCTTTTTAACTGCAATGTC-GTGGAAGCAAGATTCACCGT
1 GTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCAG-GGAGGCAAGATTCACCGT
* ** *
18749274 TGTGGCTTTAATCTGCTT-TACTGCACTGCCTGGGAAT
65 TGTGGCTTTAATCTG-TTCCACTATACTGCCTGGG-AG
* * * * *
18749311 GTAAGATTCGCCGTTATAGCTTTAATCATTTTAACTGCAATTTCATGGAGGCAAGATTCACCGTT
1 GTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGTT
*
18749376 GTGGCTTTAATCTGTTCCACTATACTGTCTGGGAG
66 GTGGCTTTAATCTGTTCCACTATACTGCCTGGGAG
** * *
18749411 GTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAA-CACCGAGGAAGCAAGATTCACCGT
1 GTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCAG-GGAGGCAAGATTCACCGT
*
18749475 TGTGGCTTTAATCTGTTCCACTATACTGTCTGGGAG
65 TGTGGCTTTAATCTGTTCCACTATACTGCCTGGGAG
** * *
18749511 GTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAA-CACCGAGGAAGCAAGATTCACCGT
1 GTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCAG-GGAGGCAAGATTCACCGT
* ** *
18749575 TGTGGCTTTAATCTGTTCCACGGCAT-C-GCCAAGGAA
65 TGTGGCTTTAATCTGTTCCAC--TATACTGCCTGGGAG
* * * * * * * *
18749611 GTAGGATTCGCCGCTGTGGCTTTAA------T--CTGTAATGTCGGGGAAGCAAGATTCACCGAT
1 GTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGTT
* ** * * * *
18749668 GTGGCTTTAATCTGCTCCACTGCACCGCTTGAGAA
66 GTGGCTTTAATCTGTTCCACTATACTGCCTGGGAG
* *
18749703 GTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTTAGGGAGGCAAGATTCACCGAT
1 GTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGTT
* *
18749768 GTGGCTTTAATCTATTCCGCTGCAT-C-GCCTGGG-G
66 GTGGCTTTAATCTGTTCCACT--ATACTGCCTGGGAG
* * *
18749802 AGTAAGATTCACTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGA
1 -GTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGT
* *
18749867 TGTGGCTTTAATCTATTCCGCTGCAT-C-GCCTGGG-G
65 TGTGGCTTTAATCTGTTCCACT--ATACTGCCTGGGAG
* * *
18749902 AGTAAGATTCACTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGA
1 -GTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGT
** * *
18749967 TGTGGCTTTAATCTGTTCCACTGCACTACCAGGGAG
65 TGTGGCTTTAATCTGTTCCACTATACTGCCTGGGAG
* * * *
18750003 GTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAATTGCAATGTCAGGGAGGCAAAATTCATCGTT
1 GTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGTT
18750068 GTGGCTTTAATCTGTTCCACT
66 GTGGCTTTAATCTGTTCCACT
18750089 GCACCGCCTA
Statistics
Matches: 684, Mismatches: 72, Indels: 45
0.85 0.09 0.06
Matches are distributed among these distances:
91 1 0.00
92 68 0.10
93 2 0.00
94 1 0.00
98 1 0.00
99 2 0.00
100 521 0.76
101 86 0.13
102 2 0.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (100 bp):
GTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGTT
GTGGCTTTAATCTGTTCCACTATACTGCCTGGGAG
Found at i:18750263 original size:44 final size:44
Alignment explanation
Indices: 18750214--18750589 Score: 181
Period size: 44 Copynumber: 8.1 Consensus size: 44
18750204 TTTAATCCAT
* *
18750214 TCCACTATAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGC
* *
18750258 TCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTAATGCGATC
1 TCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATC---T--G--C
* * * * ***
18750309 TACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTA-TTTTAATCCAT
1 T-C-C-ACTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTCAATCTGC
* * *
18750356 TCCACTATAATCTCAGGGAGATAGGATTACTAGCTTCAATCTAC
1 TCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGC
* * * *
18750400 TCCGCTGTAATCTCAGGGAGAT-AGATTTCTGGCTTGAATCTGATGTGATC
1 TCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATC-----TG--C
* * * * * *
18750450 TACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTA-TTTTAATCCGT
1 T-C-C-ACTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTCAATCTGC
* * *
18750497 TCCACTATAATCTCAGGGAGATAGGATTACTAGCTTCAATCTAC
1 TCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGC
* * * *
18750541 TCCGCTGTAATCTCAAGGAGATAAGATTTCTGGCTTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATTACTAGC-TTCAATCTGC
18750586 TCCA
1 TCCA
18750590 ACTTGAAGGT
Statistics
Matches: 246, Mismatches: 52, Indels: 67
0.67 0.14 0.18
Matches are distributed among these distances:
42 2 0.01
43 18 0.07
44 136 0.55
45 16 0.07
46 2 0.01
47 3 0.01
48 1 0.00
49 2 0.01
50 2 0.01
51 3 0.01
52 3 0.01
53 17 0.07
54 37 0.15
55 2 0.01
56 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.33
Consensus pattern (44 bp):
TCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGC
Found at i:18750535 original size:141 final size:142
Alignment explanation
Indices: 18750156--18750584 Score: 779
Period size: 141 Copynumber: 3.0 Consensus size: 142
18750146 GAGATAAGAC
18750156 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCATTCCACTA
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCATTCCACTA
* *
18750221 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATT
18750286 TCTGGCTTCAAT
131 TCTGGCTTCAAT
*
18750298 CTAATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCATTCCACTA
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCATTCCACTA
18750363 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGAT-AGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATT
*
18750427 TCTGGCTTGAAT
131 TCTGGCTTCAAT
* *
18750439 CTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTA
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCATTCCACTA
*
18750504 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAAGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATT
18750569 TCTGGCTTTCAAT
131 TCTGGC-TTCAAT
18750582 CTG
1 CTG
18750585 CTCCAACTTG
Statistics
Matches: 276, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
141 136 0.49
142 132 0.48
143 8 0.03
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.34
Consensus pattern (142 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCATTCCACTA
TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATT
TCTGGCTTCAAT
Found at i:18751925 original size:14 final size:15
Alignment explanation
Indices: 18751882--18751927 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
18751872 CCTTAGCCTC
*
18751882 TTCATTTTTAC-TTT
1 TTCATTTTTCCATTT
*
18751896 TTCATTTTTTCATTT
1 TTCATTTTTCCATTT
*
18751911 TT-ATTTTTCCGTTT
1 TTCATTTTTCCATTT
18751925 TTC
1 TTC
18751928 TCTTTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 22 0.81
15 5 0.19
ACGTcount: A:0.11, C:0.15, G:0.02, T:0.72
Consensus pattern (15 bp):
TTCATTTTTCCATTT
Found at i:18751925 original size:22 final size:21
Alignment explanation
Indices: 18751882--18751942 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 21
18751872 CCTTAGCCTC
18751882 TTCATTTTTACTTTTTCATTTT
1 TTCATTTTTA-TTTTTCATTTT
*
18751904 TTCATTTTTATTTTTCCGTTTT
1 TTCATTTTTATTTTT-CATTTT
*
18751926 TCTCTTTTTTTATTTTT
1 T-TC-ATTTTTATTTTT
18751943 TTTATTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 5 0.15
22 16 0.47
23 2 0.06
24 11 0.32
ACGTcount: A:0.10, C:0.13, G:0.02, T:0.75
Consensus pattern (21 bp):
TTCATTTTTATTTTTCATTTT
Found at i:18752776 original size:14 final size:15
Alignment explanation
Indices: 18752752--18752780 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
18752742 TTGCTTTGGC
18752752 CTCTCCTTTTTTCTT
1 CTCTCCTTTTTTCTT
18752767 CTCT-CTTTTTTCTT
1 CTCTCCTTTTTTCTT
18752781 TTTCATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
CTCTCCTTTTTTCTT
Found at i:18752794 original size:6 final size:6
Alignment explanation
Indices: 18752780--18752860 Score: 76
Period size: 6 Copynumber: 13.7 Consensus size: 6
18752770 TCTTTTTTCT
* **
18752780 TTTTCA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTTC TTCTT--
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TT-TTGA
* * * *
18752827 TTTTGT TTTTGA TTTGGA TTTGGA TTTGGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
18752861 TTTTTGAGCT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
4 2 0.03
5 2 0.03
6 60 0.91
7 2 0.03
ACGTcount: A:0.12, C:0.04, G:0.16, T:0.68
Consensus pattern (6 bp):
TTTTGA
Found at i:18752864 original size:35 final size:35
Alignment explanation
Indices: 18752792--18752867 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 35
18752782 TTCATTTTGA
* * ***
18752792 TTTTGATTTTGATTTTGATTTTGATTTTTCTTCTT
1 TTTTGATTTTGATTTGGATTTGGATTTGGATTCTT
* *
18752827 TTTTGTTTTTGATTTGGATTTGGATTTGGATTTTT
1 TTTTGATTTTGATTTGGATTTGGATTTGGATTCTT
18752862 TTTTGA
1 TTTTGA
18752868 GCTCATAGGG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.12, C:0.03, G:0.17, T:0.68
Consensus pattern (35 bp):
TTTTGATTTTGATTTGGATTTGGATTTGGATTCTT
Found at i:18756249 original size:18 final size:18
Alignment explanation
Indices: 18756226--18756276 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 18
18756216 AATATGTAGA
18756226 TAAATATATAA-ACTAATG
1 TAAATA-ATAATACTAATG
18756244 TAAATAATAATACTAA--
1 TAAATAATAATACTAATG
*
18756260 T-AATAATAATTCTAATG
1 TAAATAATAATACTAATG
18756277 ATAATTGTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 13 0.45
16 1 0.03
17 4 0.14
18 11 0.38
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (18 bp):
TAAATAATAATACTAATG
Found at i:18756266 original size:15 final size:15
Alignment explanation
Indices: 18756246--18756281 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
18756236 AACTAATGTA
18756246 AATAATAATACTAAT
1 AATAATAATACTAAT
*
18756261 AATAATAATTCTAAT
1 AATAATAATACTAAT
*
18756276 GATAAT
1 AATAAT
18756282 TGTCGAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.36
Consensus pattern (15 bp):
AATAATAATACTAAT
Found at i:18757576 original size:23 final size:22
Alignment explanation
Indices: 18757519--18757578 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
18757509 AAAACATGTG
*
18757519 AATAATAATTTAAAATAATAGT
1 AATAATAATTTAAAATAATAAT
* *
18757541 -ATATTACATTTTAAAATTATAAT
1 AATAATA-A-TTTAAAATAATAAT
18757564 AATAATAAGTTTAAA
1 AATAATAA-TTTAAA
18757579 GGTAATGTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 5 0.17
22 1 0.03
23 19 0.63
24 5 0.17
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (22 bp):
AATAATAATTTAAAATAATAAT
Found at i:18757673 original size:3 final size:3
Alignment explanation
Indices: 18757667--18757735 Score: 111
Period size: 3 Copynumber: 23.0 Consensus size: 3
18757657 ATAAAGAAGA
***
18757667 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GGG AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
18757715 AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
18757736 GGGATTAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:18757780 original size:5 final size:6
Alignment explanation
Indices: 18757761--18757817 Score: 60
Period size: 6 Copynumber: 9.2 Consensus size: 6
18757751 ATTGGAATTC
* * *
18757761 AAATAA AAATAA AAATAA AACACTAC AAATAG AAATAA AAAGAA AAATAA
1 AAATAA AAATAA AAATAA AA-A-TAA AAATAA AAATAA AAATAA AAATAA
*
18757811 AGATAA A
1 AAATAA A
18757818 CTAAATTGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
6 37 0.86
7 2 0.05
8 4 0.09
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.14
Consensus pattern (6 bp):
AAATAA
Found at i:18760664 original size:50 final size:49
Alignment explanation
Indices: 18760590--18761162 Score: 326
Period size: 50 Copynumber: 11.5 Consensus size: 49
18760580 AGATTCGTCA
* * *
18760590 TTGTGACTTTAATCCT-TTTAACTGCAATGTCGGGAAAGCAAGATTCACCG
1 TTGTGGCTTTAAT-CTGTTTCACTGCAATGCCGGG-AAGCAAGATTCACCG
* * ** * * * *
18760640 TTGTGGCTTTAGTCTGCTTCACTGCGTTGCCAGGGAAGTAACACTCGCCG
1 TTGTGGCTTTAATCTGTTTCACTGCAATGCC-GGGAAGCAAGATTCACCG
* * * * * * * * *
18760690 CTGTGGCTTTAGTATTTTTAACTACAATGTCGGGGAAGCAAGATTCAACA
1 TTGTGGCTTTAATCTGTTTCACTGCAATG-CCGGGAAGCAAGATTCACCG
* * ** * * * *
18760740 TTGTGGCTTTAGTCTGCTTCACTGCGTTGCCAGGGAAGTAACACTCGCCG
1 TTGTGGCTTTAATCTGTTTCACTGCAATGCC-GGGAAGCAAGATTCACCG
* * * *
18760790 ATGTGGCTTTAGTCTTTTTAACTGCAATGCCGGGGAAGCAAGATTCACCG
1 TTGTGGCTTTAATCTGTTTCACTGCAATGCC-GGGAAGCAAGATTCACCG
* * * * * * **
18760840 TTGTGGCTTTAATATGTTCCGCTAC-ATCGCCTGGGAAGTAAGATTCGCTA
1 TTGTGGCTTTAATCTGTTTCACTGCAAT-GCC-GGGAAGCAAGATTCACCG
* * * ** * *
18760890 TTGTAGCTTTAATCTTTTTAACTGCAATGTCATGGAGGCAAGATTCAACG
1 TTGTGGCTTTAATCTGTTTCACTGCAATG-CCGGGAAGCAAGATTCACCG
* ** * * * * * *
18760940 TTGTGGCTTTAATCT-ATTCTGTTGCACTGCCTGAGAGGTAAGATTCGCTG
1 TTGTGGCTTTAATCTGTTTC-ACTGCAATGCC-GGGAAGCAAGATTCACCG
* * * * * *
18760990 CTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAACAAGATTCACCG
1 TTGTGGCTTTAATCTGTTTCACTGCAATG-CCGGGAAGCAAGATTCACCG
* * * * * **
18761040 TTGTGGCTTTAATCTGTTTCGCTGC-ATCGCTTGGGGAGTAAGATTCGCTA
1 TTGTGGCTTTAATCTGTTTCACTGCAAT-GC-CGGGAAGCAAGATTCACCG
* * *
18761090 TTTTGGCTTTAATCTTTTTAACTGCAATGCCGGGGAAGCAAGATTCACCG
1 TTGTGGCTTTAATCTGTTTCACTGCAATGCC-GGGAAGCAAGATTCACCG
*
18761140 ATGTGGCTTTAATCTGTTTCACT
1 TTGTGGCTTTAATCTGTTTCACT
18761163 ACATCGCTTG
Statistics
Matches: 375, Mismatches: 133, Indels: 30
0.70 0.25 0.06
Matches are distributed among these distances:
49 11 0.03
50 352 0.94
51 12 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (49 bp):
TTGTGGCTTTAATCTGTTTCACTGCAATGCCGGGAAGCAAGATTCACCG
Found at i:18760722 original size:100 final size:100
Alignment explanation
Indices: 18760495--18761162 Score: 655
Period size: 100 Copynumber: 6.7 Consensus size: 100
18760485 TAACACGTTA
* ** * * * * *
18760495 CTTTAATCTGTTTAACTGTGATGTCGAGGAATCAAGATTCGCCGTTGTAGCTTCAATCTGC-TCT
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGCTTC-
* * * *
18760559 AGTGCACTAG-CTGAGAGAGTAAGATTCG-T-CATTGTGA
65 ACTGCA-TTGCCTGGGA-AGTAAGATTCGCTGC--TGTGG
* * *
18760596 CTTTAATCCTTTTAACTGCAATGTCGGGAAAGCAAGATTCACCGTTGTGGCTTTAGTCTGCTTCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGCTTCA
* * * * *
18760661 CTGCGTTGCCAGGGAAGTAACACTCGCCGCTGTGG
66 CTGCATTGCCTGGGAAGTAAGATTCGCTGCTGTGG
* * * * * *
18760696 CTTTAGTATTTTTAACTACAATGTCGGGGAAGCAAGATTCAACATTGTGGCTTTAGTCTGCTTCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGCTTCA
* * * * * *
18760761 CTGCGTTGCCAGGGAAGTAACACTCGCCGATGTGG
66 CTGCATTGCCTGGGAAGTAAGATTCGCTGCTGTGG
* * *
18760796 CTTTAGTCTTTTTAACTGCAATGCCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATATG-TTCC
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGCTT-C
* * * ** *
18760860 GCTACATCGCCTGGGAAGTAAGATTCGCTATTGTAG
65 ACTGCATTGCCTGGGAAGTAAGATTCGCTGCTGTGG
** * * *
18760896 CTTTAATCTTTTTAACTGCAATGTCATGGAGGCAAGATTCAACGTTGTGGCTTTAATCT-ATTCT
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGCTTC-
** * * * *
18760960 GTTGCACTGCCTGAGAGGTAAGATTCGCTGCTGTAG
65 ACTGCATTGCCTGGGAAGTAAGATTCGCTGCTGTGG
* * *
18760996 CTTTAATCTTTTTAACTGCAATGTCGGGGAAACAAGATTCACCGTTGTGGCTTTAATCTGTTTCG
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGCTTCA
* * * ** *
18761061 CTGCATCGCTTGGGGAGTAAGATTCGCTATTTTGG
66 CTGCATTGCCTGGGAAGTAAGATTCGCTGCTGTGG
* * *
18761096 CTTTAATCTTTTTAACTGCAATGCCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTTCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGCTTCA
18761161 CT
66 CT
18761163 ACATCGCTTG
Statistics
Matches: 477, Mismatches: 82, Indels: 17
0.83 0.14 0.03
Matches are distributed among these distances:
99 3 0.01
100 410 0.86
101 61 0.13
102 3 0.01
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (100 bp):
CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGCTTCA
CTGCATTGCCTGGGAAGTAAGATTCGCTGCTGTGG
Found at i:18763179 original size:30 final size:29
Alignment explanation
Indices: 18763139--18763207 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
18763129 CTTTTTCATA
*
18763139 TTTTTATTTTGAATTTAATTGATTTCTTTT
1 TTTTTCTTTTGAATTTAATT-ATTTCTTTT
* * *
18763169 TTTTTCTTTTGACTTTGATTTTTTCTTTT
1 TTTTTCTTTTGAATTTAATTATTTCTTTT
18763198 TTTTTCTTTT
1 TTTTTCTTTT
18763208 TGATTTGGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
29 18 0.51
30 17 0.49
ACGTcount: A:0.12, C:0.07, G:0.06, T:0.75
Consensus pattern (29 bp):
TTTTTCTTTTGAATTTAATTATTTCTTTT
Found at i:18773401 original size:16 final size:16
Alignment explanation
Indices: 18773380--18773413 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18773370 ACAATATCCA
* *
18773380 ATTATCATATTTGCAC
1 ATTATCACATTTACAC
18773396 ATTATCACATTTACAC
1 ATTATCACATTTACAC
18773412 AT
1 AT
18773414 ACATTCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (16 bp):
ATTATCACATTTACAC
Found at i:18778582 original size:79 final size:76
Alignment explanation
Indices: 18778333--18778617 Score: 346
Period size: 75 Copynumber: 3.8 Consensus size: 76
18778323 AAAAAGTTTA
*
18778333 TCTATTGTATTTTACATCAAT-A-ATATACTTATTTACAATCTAC-AAAAACAATAGAAAAATTA
1 TCTATTGTATTTTACATCAATAATATATACTTATTTACAATCTACGAAAAA-AATAAAAAAATTA
*
18778395 TTTGTATTGTAT
65 TTTGTATTATAT
* * * *
18778407 TCTATTGTATTTTATATCAATAATATATATTTATTTACAATCTACG-AAAAATTTAAAAAATTAT
1 TCTATTGTATTTTACATCAATAATATATACTTATTTACAATCTACGAAAAAAATAAAAAAATTAT
*
18778471 TTGTATTTTAT
66 TTGTATTATAT
* * *
18778482 TTTATTGTATTTTATATCAATAATATATACTTATTTACAATATACGAAAAAAATGAAAAAAAAAT
1 TCTATTGTATTTTACATCAATAATATATACTTATTTACAATCTACGAAAAAAAT---AAAAAAAT
* *
18778547 TGTTTATATTATAT
63 TATTTGTATTATAT
* * * * *
18778561 CCTACTATATTTTACATCAATAATATATACTTATTTACAATTTAC-CAAAAAATAAAA
1 TCTATTGTATTTTACATCAATAATATATACTTATTTACAATCTACGAAAAAAATAAAA
18778618 GCAATGAAAA
Statistics
Matches: 183, Mismatches: 21, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
74 20 0.11
75 69 0.38
76 30 0.16
78 7 0.04
79 57 0.31
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (76 bp):
TCTATTGTATTTTACATCAATAATATATACTTATTTACAATCTACGAAAAAAATAAAAAAATTAT
TTGTATTATAT
Found at i:18778582 original size:154 final size:149
Alignment explanation
Indices: 18778335--18778611 Score: 376
Period size: 154 Copynumber: 1.8 Consensus size: 149
18778325 AAAGTTTATC
* * *
18778335 TATTGTATTTTACATCAATAATATACTTATTTACAATCTACAAAAACAATAGAAAAATTATTTGT
1 TATTGTATTTTACATCAATAATATACTTATTTACAATATACAAAAACAATAAAAAAATTATTTAT
* * * * * * *
18778400 ATTGTATTCTATTGTATTTTATATCAATAATATATATTTATTTACAATCTACGAAAAATTTAAAA
66 ATTATATCCTACTATATTTTACATCAATAATATATACTTATTTACAATCTACCAAAAATTTAAAA
18778465 AATTATTTGTATTTTATTT
131 AATTATTTGTATTTTATTT
*
18778484 TATTGTATTTTATATCAATAATATATACTTATTTACAATATACGAAAAA-AATGAAAAAAAAATT
1 TATTGTATTTTACATCAAT-A-ATATACTTATTTACAATATAC-AAAAACAAT---AAAAAAATT
* *
18778548 GTTTATATTATATCCTACTATATTTTACATCAATAATATATACTTATTTACAATTTACCAAAAA
60 ATTTATATTATATCCTACTATATTTTACATCAATAATATATACTTATTTACAATCTACCAAAAA
18778612 ATAAAAGCAA
Statistics
Matches: 109, Mismatches: 13, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
149 18 0.17
150 1 0.01
151 23 0.21
152 5 0.05
154 62 0.57
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (149 bp):
TATTGTATTTTACATCAATAATATACTTATTTACAATATACAAAAACAATAAAAAAATTATTTAT
ATTATATCCTACTATATTTTACATCAATAATATATACTTATTTACAATCTACCAAAAATTTAAAA
AATTATTTGTATTTTATTT
Found at i:18780717 original size:25 final size:26
Alignment explanation
Indices: 18780682--18780730 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
18780672 TTTTCTTTTA
*
18780682 CTTTTCTTTTTTAGATTAGGTTTTCT
1 CTTTTCTTTTTTAGATTAGATTTTCT
*
18780708 CTTTTC-TTTTTAGGTTAGATTTT
1 CTTTTCTTTTTTAGATTAGATTTT
18780731 AGTTTTGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (26 bp):
CTTTTCTTTTTTAGATTAGATTTTCT
Found at i:18785056 original size:6 final size:6
Alignment explanation
Indices: 18785047--18785101 Score: 60
Period size: 6 Copynumber: 9.0 Consensus size: 6
18785037 AGGGTTAGGG
*
18785047 CTTTTT C-TTTT CTTTTCTT CTCTTCT CTTTTT CTTTTT CTTTTT C-TTTT
1 CTTTTT CTTTTT C-TTT-TT CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT
18785096 CTTTTT
1 CTTTTT
18785102 TAGATTAGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
5 10 0.24
6 21 0.50
7 6 0.14
8 5 0.12
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
CTTTTT
Found at i:18785057 original size:5 final size:5
Alignment explanation
Indices: 18785049--18785100 Score: 59
Period size: 5 Copynumber: 9.8 Consensus size: 5
18785039 GGTTAGGGCT
* *
18785049 TTTTC TTTTC TTTTC TTCTC TTCTC TTTTTC TTTTTC TTTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC -TTTTC -TTTTC TTTTC
18785097 TTTT
1 TTTT
18785101 TTAGATTAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
5 28 0.64
6 16 0.36
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:18797128 original size:133 final size:134
Alignment explanation
Indices: 18796884--18797145 Score: 312
Period size: 133 Copynumber: 2.0 Consensus size: 134
18796874 AGATGCATTC
* * ** * * * *
18796884 TCATGATTTATCTAGAGTGTGGATACCAAGAAGGCCAATATTTCCCAAATAAAAACTACACATGA
1 TCATGATTTATATACAGCATGGATACCAAAAAGGACAACATTTCCCAAATAAAAACTACACATCA
* ** * ** *
18796949 TCCTAATTACAAGGCTTGAAGTTTTACCACCTTGATGTCATCTTGATAGGT-TAGTAAGACAAGT
66 TCCTAAATACAAGGCTAAAAGTTGTACCACCTCAATGCCATCTTGATAGGTGTAGTAAGACAAGT
18797013 CATG
131 CATG
* *
18797017 TCATGATTTATATACAGCATGGATACCAAAAAGGAGAACATTTCCCAAATGAAAAA-TACACGTC
1 TCATGATTTATATACAGCATGGATACCAAAAAGGACAACATTTCCCAAAT-AAAAACTACACATC
* * * *
18797081 ATCCTAAATATATGGCTAAAAGTTGTACCATCTCAATGCCATTTTGATAGGTGTAGTAAGACAAG
65 ATCCTAAATACAAGGCTAAAAGTTGTACCACCTCAATGCCATCTTGATAGGTGTAGTAAGACAAG
18797146 AAGTAAACAC
Statistics
Matches: 106, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
133 89 0.84
134 17 0.16
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29
Consensus pattern (134 bp):
TCATGATTTATATACAGCATGGATACCAAAAAGGACAACATTTCCCAAATAAAAACTACACATCA
TCCTAAATACAAGGCTAAAAGTTGTACCACCTCAATGCCATCTTGATAGGTGTAGTAAGACAAGT
CATG
Found at i:18797212 original size:34 final size:34
Alignment explanation
Indices: 18797163--18797230 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
18797153 CACATCAGCA
18797163 GGAAATACAGAACTTTGAGGAAGAGTCTCATGTG
1 GGAAATACAGAACTTTGAGGAAGAGTCTCATGTG
* * *
18797197 GGAAATTCAGCACTTTGAGGAAGTGTCTCATGTG
1 GGAAATACAGAACTTTGAGGAAGAGTCTCATGTG
18797231 CTTCACATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.26
Consensus pattern (34 bp):
GGAAATACAGAACTTTGAGGAAGAGTCTCATGTG
Found at i:18800107 original size:9 final size:9
Alignment explanation
Indices: 18800062--18800110 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
18800052 AACGAGAGAA
*
18800062 GAAGAAGAA
1 GAAGAAGAG
18800071 GAAGAAGAG
1 GAAGAAGAG
* *
18800080 GAGGAGGAG
1 GAAGAAGAG
* *
18800089 GAGGAGGAG
1 GAAGAAGAG
18800098 GAAGAAGAG
1 GAAGAAGAG
18800107 GAAG
1 GAAG
18800111 TGATTTAATC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (9 bp):
GAAGAAGAG
Found at i:18801194 original size:20 final size:20
Alignment explanation
Indices: 18801169--18801213 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
18801159 ATAACCCACA
18801169 CAAAATTCTCTAAAAGCTTG
1 CAAAATTCTCTAAAAGCTTG
18801189 CAAAATTCTCTAAAAGCTTG
1 CAAAATTCTCTAAAAGCTTG
*
18801209 TAAAA
1 CAAAA
18801214 GCTAATACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (20 bp):
CAAAATTCTCTAAAAGCTTG
Found at i:18803243 original size:5 final size:5
Alignment explanation
Indices: 18803233--18803266 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
18803223 TTAATATAAA
18803233 TATAT TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATA
18803267 AAAATGTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:18811569 original size:26 final size:26
Alignment explanation
Indices: 18811531--18811602 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 26
18811521 TATTTTCTTG
* *
18811531 AAATTTTATCAGGGGT-AAATTCATCA
1 AAATTTTACCAGGGGTAAAACT-ATCA
18811557 AAATTTTACCAGGGGTAAAACTATCA
1 AAATTTTACCAGGGGTAAAACTATCA
**
18811583 AAATTTTACTGGGGGTAAAA
1 AAATTTTACCAGGGGTAAAA
18811603 TAAGGATGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 37 0.90
27 4 0.10
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (26 bp):
AAATTTTACCAGGGGTAAAACTATCA
Found at i:18811900 original size:82 final size:82
Alignment explanation
Indices: 18811755--18811916 Score: 252
Period size: 82 Copynumber: 2.0 Consensus size: 82
18811745 CCAAAACCCC
* * * * **
18811755 TCATATAACATAAAGGGGTAGTAACCCTAGTAGGAATACTAGGGTGTGCCATCCGCCTTACTCCC
1 TCATATAACATAAAGGGGCAGCAACCCTAGTAGGAATACTAGAGTGTGCCATCCACCCCACTCCC
18811820 ACTCTTAGTAAGAAGCT
66 ACTCTTAGTAAGAAGCT
* *
18811837 TCATATAACATAAAGGGGCAGCAACCCTAGTAGTAATACTAGAGTGTGCCATCCACCCCACTCCT
1 TCATATAACATAAAGGGGCAGCAACCCTAGTAGGAATACTAGAGTGTGCCATCCACCCCACTCCC
18811902 ACTCTTAGTAAGAAG
66 ACTCTTAGTAAGAAG
18811917 TTGTTTTTCT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 72 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (82 bp):
TCATATAACATAAAGGGGCAGCAACCCTAGTAGGAATACTAGAGTGTGCCATCCACCCCACTCCC
ACTCTTAGTAAGAAGCT
Found at i:18815728 original size:14 final size:14
Alignment explanation
Indices: 18815709--18815739 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
18815699 TGATTATTTT
*
18815709 TAATCTAAATTTAC
1 TAATCTAAATTAAC
18815723 TAATCTAAATTAAC
1 TAATCTAAATTAAC
18815737 TAA
1 TAA
18815740 GAACGCAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:18818423 original size:6 final size:6
Alignment explanation
Indices: 18818412--18818509 Score: 90
Period size: 6 Copynumber: 15.8 Consensus size: 6
18818402 GGAAACAACC
* * * * *
18818412 ATAAAA ATAAAA ATATAG TTCAAAAA ATAAAA A-CAAA ATAAAT ATAAGAAA
1 ATAAAA ATAAAA ATAAAA AT-A-AAA ATAAAA ATAAAA ATAAAA AT-A-AAA
* *
18818463 ATAACA ATAAAC ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAA
18818510 GAAATAAACT
Statistics
Matches: 73, Mismatches: 14, Indels: 10
0.75 0.14 0.10
Matches are distributed among these distances:
5 4 0.05
6 59 0.81
7 4 0.05
8 6 0.08
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:18820201 original size:15 final size:14
Alignment explanation
Indices: 18820160--18820207 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
18820150 GGAAAATGAA
* *
18820160 AAAAATAAGAACAAG
1 AAAAATAATAA-AAT
18820175 AAAAATAATAAAAAT
1 AAAAATAAT-AAAAT
*
18820190 AAAAATACTAAAAT
1 AAAAATAATAAAAT
18820204 AAAA
1 AAAA
18820208 GAATCTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 9 0.31
15 18 0.62
16 2 0.07
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (14 bp):
AAAAATAATAAAAT
Found at i:18824381 original size:17 final size:18
Alignment explanation
Indices: 18824356--18824389 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18824346 AAAAATTAGA
18824356 AAACAAAAA-CAAAAATT
1 AAACAAAAACCAAAAATT
*
18824373 AAACTAAAACCAAAAAT
1 AAACAAAAACCAAAAAT
18824390 AAAAAGCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.74, C:0.15, G:0.00, T:0.12
Consensus pattern (18 bp):
AAACAAAAACCAAAAATT
Found at i:18824392 original size:17 final size:17
Alignment explanation
Indices: 18824356--18824389 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
18824346 AAAAATTAGA
18824356 AAACAAAAACAAAAATT
1 AAACAAAAACAAAAATT
*
18824373 AAACTAAAACCAAAAAT
1 AAAC-AAAAACAAAAAT
18824390 AAAAAGCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.74, C:0.15, G:0.00, T:0.12
Consensus pattern (17 bp):
AAACAAAAACAAAAATT
Found at i:18825542 original size:13 final size:13
Alignment explanation
Indices: 18825526--18825557 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
18825516 TCACACGGGC
*
18825526 GTGTGGCCATTCT
1 GTGTGGCCATCCT
18825539 GTGTGGCCATCCT
1 GTGTGGCCATCCT
18825552 GTGTGG
1 GTGTGG
18825558 ATCCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.22, G:0.38, T:0.34
Consensus pattern (13 bp):
GTGTGGCCATCCT
Found at i:18826311 original size:84 final size:84
Alignment explanation
Indices: 18826209--18826365 Score: 278
Period size: 84 Copynumber: 1.9 Consensus size: 84
18826199 TCATGTCTAA
* *
18826209 TGTATTGTTAGTCTAGAAAATAACATTTATGTCTCTATCTTTTGGGAGTAAATCACTCTGATATC
1 TGTATTGTTAGTCTAGAAAATAACATTTATGTCTCTATCTTCTGGGAGTAAATCACTCTAATATC
18826274 CAAGATAATGCATCTCCCC
66 CAAGATAATGCATCTCCCC
* *
18826293 TGTATTGTTAGTCTAGAAAATAATATTTATGTCTCTATCTTCTGGGAGTAAATCATTCTAATATC
1 TGTATTGTTAGTCTAGAAAATAACATTTATGTCTCTATCTTCTGGGAGTAAATCACTCTAATATC
18826358 CAAGATAA
66 CAAGATAA
18826366 GGTATCCACC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 69 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (84 bp):
TGTATTGTTAGTCTAGAAAATAACATTTATGTCTCTATCTTCTGGGAGTAAATCACTCTAATATC
CAAGATAATGCATCTCCCC
Found at i:18826830 original size:296 final size:296
Alignment explanation
Indices: 18826293--18826875 Score: 1121
Period size: 296 Copynumber: 2.0 Consensus size: 296
18826283 GCATCTCCCC
18826293 TGTATTGTTAGTCTAGAAAATAATATTTATGTCTCTATCTTCTGGGAGTAAATCATTCTAATATC
1 TGTATTGTTAGTCTAGAAAATAATATTTATGTCTCTATCTTCTGGGAGTAAATCATTCTAATATC
18826358 CAAGATAAGGTATCCACCTATTTGGACTTGATAGACGACATAATAGTCCTTTTAGACTATAGACC
66 CAAGATAAGGTATCCACCTATTTGGACTTGATAGACGACATAATAGTCCTTTTAGACTATAGACC
*
18826423 TTTTAGATTACCTACTAATACAAGTTGTCTTCTTACATTTCGATCAGACAACGTAATACAACTTA
131 TTTTAGATTACCTACTAATACAAGTTGTCTTCTTACATTCCGATCAGACAACGTAATACAACTTA
* *
18826488 ATATTAGTTAAAATTTAGGTAATCAATGAGCAAATATTTTCTTACATTTTGTTTTGAGTGCAAAA
196 ATATCAGTTAAAATTTAGGTAATCAATGAGCAAATATTTGCTTACATTTTGTTTTGAGTGCAAAA
18826553 ACCATTAAGGACAAATACAAATGATATCATGTCTAA
261 ACCATTAAGGACAAATACAAATGATATCATGTCTAA
18826589 TGTATTGTTAGTCTAGAAAATAATATTTATGTCTCTATCTTCTGGGAGTAAATCATTCTAATATC
1 TGTATTGTTAGTCTAGAAAATAATATTTATGTCTCTATCTTCTGGGAGTAAATCATTCTAATATC
18826654 CAAGATAAGGTATCCACCTATTTGGACTTGATAGACGACATAATAGTCCTTTTAGACTATAGACC
66 CAAGATAAGGTATCCACCTATTTGGACTTGATAGACGACATAATAGTCCTTTTAGACTATAGACC
*
18826719 TTTTAGATTACCTACTAATACAAGTTGTCTTCTTACATTCCGATCCGACAACGTAATACAACTTA
131 TTTTAGATTACCTACTAATACAAGTTGTCTTCTTACATTCCGATCAGACAACGTAATACAACTTA
*
18826784 GTATCAGTTAAAATTTAGGTAATCAATGAGCAAATATTTGCTTACATTTTGTTTTGAGTGCAAAA
196 ATATCAGTTAAAATTTAGGTAATCAATGAGCAAATATTTGCTTACATTTTGTTTTGAGTGCAAAA
18826849 ACCATTAAGGACAAATACAAATGATAT
261 ACCATTAAGGACAAATACAAATGATAT
18826876 TAATGTGAAT
Statistics
Matches: 282, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
296 282 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.36
Consensus pattern (296 bp):
TGTATTGTTAGTCTAGAAAATAATATTTATGTCTCTATCTTCTGGGAGTAAATCATTCTAATATC
CAAGATAAGGTATCCACCTATTTGGACTTGATAGACGACATAATAGTCCTTTTAGACTATAGACC
TTTTAGATTACCTACTAATACAAGTTGTCTTCTTACATTCCGATCAGACAACGTAATACAACTTA
ATATCAGTTAAAATTTAGGTAATCAATGAGCAAATATTTGCTTACATTTTGTTTTGAGTGCAAAA
ACCATTAAGGACAAATACAAATGATATCATGTCTAA
Found at i:18832715 original size:17 final size:17
Alignment explanation
Indices: 18832665--18832772 Score: 99
Period size: 17 Copynumber: 6.2 Consensus size: 17
18832655 AGAATTATGA
*
18832665 GCCCACATGCCCGTGTGG
1 GCCCACATGCCCGTCT-G
* * *
18832683 GCCCACACGTCTGTCTG
1 GCCCACATGCCCGTCTG
*
18832700 GCCCACATACCCGTCTG
1 GCCCACATGCCCGTCTG
* * *
18832717 GCCCATATGCCTGTGTGG
1 GCCCACATGCCCGTCT-G
* *
18832735 GCCCACATGCCCTTGTG
1 GCCCACATGCCCGTCTG
18832752 GCCCACATGCCCGATCTG
1 GCCCACATGCCCG-TCTG
18832770 GCC
1 GCC
18832773 TAGCTCGTGT
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
17 39 0.55
18 32 0.45
ACGTcount: A:0.13, C:0.41, G:0.26, T:0.20
Consensus pattern (17 bp):
GCCCACATGCCCGTCTG
Found at i:18832727 original size:52 final size:53
Alignment explanation
Indices: 18832665--18832791 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 53
18832655 AGAATTATGA
* *
18832665 GCCCACATGCCCGTGTGGGCCCACACG-TCTGTCTGGCCCACATACCCG-TCTG
1 GCCCATATGCCCGTGTGGGCCCACACGCCCT-TCTGGCCCACATACCCGATCTG
* * * *
18832717 GCCCATATGCCTGTGTGGGCCCACATGCCCTTGTGGCCCACATGCCCGATCTG
1 GCCCATATGCCCGTGTGGGCCCACACGCCCTTCTGGCCCACATACCCGATCTG
*
18832770 G-CC-TA-GCTCGTGT-GGCCCACAC
1 GCCCATATGCCCGTGTGGGCCCACAC
18832792 AGCCACACTC
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
49 8 0.12
50 6 0.09
51 2 0.03
52 41 0.64
53 7 0.11
ACGTcount: A:0.13, C:0.40, G:0.26, T:0.20
Consensus pattern (53 bp):
GCCCATATGCCCGTGTGGGCCCACACGCCCTTCTGGCCCACATACCCGATCTG
Found at i:18832762 original size:35 final size:34
Alignment explanation
Indices: 18832665--18832772 Score: 117
Period size: 35 Copynumber: 3.1 Consensus size: 34
18832655 AGAATTATGA
* *
18832665 GCCCACATGCCCGTGTGGGCCCACACGTCTGTCTG
1 GCCCACATGCCCGTGT-GGCCCACATGCCTGTCTG
* * * *
18832700 GCCCACATACCCGTCTGGCCCATATGCCTGTGTGG
1 GCCCACATGCCCGTGTGGCCCACATGCCTGTCT-G
* *
18832735 GCCCACATGCCCTTGTGGCCCACATGCCCGATCTG
1 GCCCACATGCCCGTGTGGCCCACATGCCTG-TCTG
18832770 GCC
1 GCC
18832773 TAGCTCGTGT
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
34 13 0.22
35 44 0.75
36 2 0.03
ACGTcount: A:0.13, C:0.41, G:0.26, T:0.20
Consensus pattern (34 bp):
GCCCACATGCCCGTGTGGCCCACATGCCTGTCTG
Found at i:18834561 original size:14 final size:14
Alignment explanation
Indices: 18834542--18834577 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
18834532 AAATTTTTTA
18834542 TTTAATTTATATAC
1 TTTAATTTATATAC
18834556 TTTAATTTATATAC
1 TTTAATTTATATAC
18834570 TTTAATTT
1 TTTAATTT
18834578 CTAACGTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTAATTTATATAC
Found at i:18842987 original size:27 final size:26
Alignment explanation
Indices: 18842868--18843005 Score: 98
Period size: 27 Copynumber: 5.1 Consensus size: 26
18842858 GGTCACCGAG
*
18842868 ACCCTGAATTTGTGAAATTATCAAAAT
1 ACCCT-AATTTGTAAAATTATCAAAAT
*** *
18842895 ACCTCCGGTGTGTAAAATTA-CTAAAAT
1 ACC-CTAATTTGTAAAATTATC-AAAAT
* * *
18842922 ACCCTTAATTTGTAAAATTACCGAAAC
1 ACCC-TAATTTGTAAAATTATCAAAAT
18842949 ACCCCTAATTTGTAAAATTATCAAAAT
1 A-CCCTAATTTGTAAAATTATCAAAAT
** * **
18842976 AACCCTGGTTTGTGAAATTATTGAAAT
1 -ACCCTAATTTGTAAAATTATCAAAAT
18843003 ACC
1 ACC
18843006 TTTGTAGGGT
Statistics
Matches: 86, Mismatches: 19, Indels: 13
0.73 0.16 0.11
Matches are distributed among these distances:
26 5 0.06
27 75 0.87
28 6 0.07
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (26 bp):
ACCCTAATTTGTAAAATTATCAAAAT
Found at i:18843287 original size:27 final size:27
Alignment explanation
Indices: 18843246--18843319 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
18843236 ATGGAGGAAG
*
18843246 TACTGTTACGGGTGGCTCTGCCACATA
1 TACTGTTACTGGTGGCTCTGCCACATA
* *
18843273 TACTGTTACTCGTGGCTTTGCCACATA
1 TACTGTTACTGGTGGCTCTGCCACATA
*
18843300 TACTG-TACTGGTAGCTCTGC
1 TACTGTTACTGGTGGCTCTGC
18843320 TGCATTATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
26 12 0.29
27 29 0.71
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.34
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTCTGCCACATA
Found at i:18843527 original size:28 final size:28
Alignment explanation
Indices: 18843469--18843528 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
18843459 TACTGCATAC
*
18843469 TGTTTCTGTATTGGGCTAAGTCCCACCT
1 TGTTTCTGTATTGGGCTAAGTCCCACAT
*
18843497 TGTTTCTGTATTGGGCTAAAG-CCTACAT
1 TGTTTCTGTATTGGGCT-AAGTCCCACAT
18843525 TGTT
1 TGTT
18843529 CAGTTCTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 26 0.90
29 3 0.10
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.42
Consensus pattern (28 bp):
TGTTTCTGTATTGGGCTAAGTCCCACAT
Found at i:18855183 original size:53 final size:53
Alignment explanation
Indices: 18855116--18855232 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
18855106 CATCTTTCAA
* *
18855116 TCAAA-TTAAAAGATAATAGTATATTTTTAAATACATATTAACATATCAATAT
1 TCAAATTTAAAAGATAACAATATATTTTTAAATACATATTAACATATCAATAT
18855168 TCAAATTTAAAAGATAACAATATATTTTTAAATACATATTAACATATCAATAT
1 TCAAATTTAAAAGATAACAATATATTTTTAAATACATATTAACATATCAATAT
18855221 TCAAATTTAAAA
1 TCAAATTTAAAA
18855233 TTTAAAATTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 5 0.08
53 57 0.92
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.38
Consensus pattern (53 bp):
TCAAATTTAAAAGATAACAATATATTTTTAAATACATATTAACATATCAATAT
Found at i:18859266 original size:4 final size:4
Alignment explanation
Indices: 18859259--18859301 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
18859249 AGACCGACAT
*
18859259 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AAAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
18859302 TGATCGTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.23
Consensus pattern (4 bp):
ATAG
Found at i:18862048 original size:57 final size:52
Alignment explanation
Indices: 18861971--18862080 Score: 139
Period size: 57 Copynumber: 2.0 Consensus size: 52
18861961 TTAGGGTTCT
18861971 TTTGCAAGTGACTTGAAAGAGTGTAGTCTTTTTCTTATCTTAAGATCTCACA
1 TTTGCAAGTGACTTGAAAGAGTGTAGTCTTTTTCTTATCTTAAGATCTCACA
* * * *
18862023 TNNNNNTTGCAAGTGTCTTGTAAGAGTGTAGTCTTTTTCTTATTTTAATATCTCACA
1 T-----TTGCAAGTGACTTGAAAGAGTGTAGTCTTTTTCTTATCTTAAGATCTCACA
18862080 T
1 T
18862081 AGGTTAGCCA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
52 1 0.02
57 48 0.98
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.43
Consensus pattern (52 bp):
TTTGCAAGTGACTTGAAAGAGTGTAGTCTTTTTCTTATCTTAAGATCTCACA
Found at i:18862236 original size:61 final size:61
Alignment explanation
Indices: 18862133--18862250 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 61
18862123 TAATTTTAAT
* * * * * *
18862133 TTTTAGATTTAGGACTAAATTGATAGATTTTGTAAATTTTGAGGGCCAAATTTATTAAATA
1 TTTTAGAATTAGAACTAAAATGACAAATTTTGTAAATATTGAGGGCCAAATTTATTAAATA
** *
18862194 TTTTAGAATTAGAACTAAAATGACAAATTTTGTTTATATTGAGGGCTAAATTTATTA
1 TTTTAGAATTAGAACTAAAATGACAAATTTTGTAAATATTGAGGGCCAAATTTATTA
18862251 TTATTTTTTA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.42
Consensus pattern (61 bp):
TTTTAGAATTAGAACTAAAATGACAAATTTTGTAAATATTGAGGGCCAAATTTATTAAATA
Done.