Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 151 of 182
Found at i:46538392 original size:29 final size:28
Alignment explanation
Indices: 46538357--46538430 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 28
46538347 CGAAGTTAAA
46538357 TTCAAATA-CTAAATTAAGATAATAAAAAT
1 TTCAAATATC-AAATTAA-ATAATAAAAAT
* *
46538386 TTCAAATATCAAATTAAATATTAAAACTAAA
1 TTCAAATATCAAATTAAATAAT-AAA--AAT
46538417 TTCAAATATCAAAT
1 TTCAAATATCAAAT
46538431 AATATATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 4 0.10
29 18 0.46
30 1 0.03
31 16 0.41
ACGTcount: A:0.57, C:0.09, G:0.01, T:0.32
Consensus pattern (28 bp):
TTCAAATATCAAATTAAATAATAAAAAT
Found at i:46538423 original size:31 final size:31
Alignment explanation
Indices: 46538353--46538440 Score: 96
Period size: 31 Copynumber: 2.9 Consensus size: 31
46538343 ATAACGAAGT
*
46538353 TAAATTCAAATA-CTAAATTAAGATAAT-AAA
1 TAAATTCAAATATC-AAATTAAGATATTAAAA
*
46538383 -AATTTCAAATATCAAATTAA-ATATTAAAA
1 TAAATTCAAATATCAAATTAAGATATTAAAA
*
46538412 CTAAATTCAAATATCAAA-TAATATATTAA
1 -TAAATTCAAATATCAAATTAAGATATTAA
46538441 CTCTTTTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
28 4 0.08
29 20 0.40
30 4 0.08
31 22 0.44
ACGTcount: A:0.58, C:0.08, G:0.01, T:0.33
Consensus pattern (31 bp):
TAAATTCAAATATCAAATTAAGATATTAAAA
Found at i:46543634 original size:29 final size:30
Alignment explanation
Indices: 46543594--46543663 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 30
46543584 GATCTTCATA
*
46543594 TTTTTTCGTTTTA-A-TCAATTTAATTTTTTT
1 TTTTTTC-TTTTATATTC-ATTTAACTTTTTT
*
46543624 TTTTTTCTTTTATATTCTTTTAACTTTTTT
1 TTTTTTCTTTTATATTCATTTAACTTTTTT
46543654 TTTTTTCTTT
1 TTTTTTCTTT
46543664 ATTTTTATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 5 0.14
30 29 0.81
31 2 0.06
ACGTcount: A:0.14, C:0.09, G:0.01, T:0.76
Consensus pattern (30 bp):
TTTTTTCTTTTATATTCATTTAACTTTTTT
Found at i:46547542 original size:23 final size:23
Alignment explanation
Indices: 46547484--46547543 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
46547474 GAGTAATAAG
* *
46547484 AGTTTGACTCAAACAAATAAATA
1 AGTTTAACTGAAACAAATAAATA
*
46547507 GAGTTTAATTGAAACAAATAAACT-
1 -AGTTTAACTGAAACAAATAAA-TA
46547531 AGTTTAACTGAAA
1 AGTTTAACTGAAA
46547544 GATTATTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 12 0.39
24 18 0.58
25 1 0.03
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (23 bp):
AGTTTAACTGAAACAAATAAATA
Found at i:46549054 original size:19 final size:18
Alignment explanation
Indices: 46549032--46549067 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
46549022 TATTTTTTTA
46549032 CTTAAATCTATTTTTCGAG
1 CTTAAAT-TATTTTTCGAG
*
46549051 CTTATATTATTTTTCGA
1 CTTAAATTATTTTTCGA
46549068 ACTTTTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.25, C:0.14, G:0.08, T:0.53
Consensus pattern (18 bp):
CTTAAATTATTTTTCGAG
Found at i:46550274 original size:20 final size:21
Alignment explanation
Indices: 46550241--46550281 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
46550231 CATCATATCC
*
46550241 TTCTATCAACAATAATAATAA
1 TTCTATCAAAAATAATAATAA
46550262 TTCT-TCAAAAATAATAATAA
1 TTCTATCAAAAATAATAATAA
46550282 ACAAACATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (21 bp):
TTCTATCAAAAATAATAATAA
Found at i:46563378 original size:13 final size:14
Alignment explanation
Indices: 46563362--46563393 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
46563352 GTAATGTGAT
46563362 TAGAGTATG-TTTA
1 TAGAGTATGTTTTA
46563375 TAGAGTATGTTTTA
1 TAGAGTATGTTTTA
46563389 TAGAG
1 TAGAG
46563394 GGAGCGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TAGAGTATGTTTTA
Found at i:46563769 original size:27 final size:27
Alignment explanation
Indices: 46563739--46563808 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
46563729 GAACTCAGGT
*
46563739 TTTAAGGTTCAAA-TTTGAGATTTGAGG
1 TTTAAGGTTCAAAGTTTGA-ATTTAAGG
* *
46563766 TTTAATGTTTAAAGTTTGAATTTAAGG
1 TTTAAGGTTCAAAGTTTGAATTTAAGG
* *
46563793 TTTGAGGTTTAAAGTT
1 TTTAAGGTTCAAAGTT
46563809 CAAGTTTGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 32 0.86
28 5 0.14
ACGTcount: A:0.30, C:0.01, G:0.23, T:0.46
Consensus pattern (27 bp):
TTTAAGGTTCAAAGTTTGAATTTAAGG
Found at i:46563777 original size:34 final size:34
Alignment explanation
Indices: 46563739--46563804 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
46563729 GAACTCAGGT
* *
46563739 TTTAAGGTTCAAATTTGAGATTTGAGGTTTAATG
1 TTTAAAGTTCAAATTTAAGATTTGAGGTTTAATG
** *
46563773 TTTAAAGTTTGAATTTAAGGTTTGAGGTTTAA
1 TTTAAAGTTCAAATTTAAGATTTGAGGTTTAA
46563805 AGTTCAAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.45
Consensus pattern (34 bp):
TTTAAAGTTCAAATTTAAGATTTGAGGTTTAATG
Found at i:46574835 original size:14 final size:14
Alignment explanation
Indices: 46574816--46574842 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
46574806 GATGCATTCG
46574816 TGTATATATATATA
1 TGTATATATATATA
46574830 TGTATATATATAT
1 TGTATATATATAT
46574843 CATTTAAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TGTATATATATATA
Found at i:46585796 original size:19 final size:20
Alignment explanation
Indices: 46585756--46585797 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
46585746 CAAATAATAT
*
46585756 TAAAAAAAATAGCGAAACAA
1 TAAAAAAAATAGCGAAAAAA
46585776 TAAAAAAAAT-GC-ATAAAAA
1 TAAAAAAAATAGCGA-AAAAA
46585795 TAA
1 TAA
46585798 CATCCGAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 9 0.45
20 10 0.50
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (20 bp):
TAAAAAAAATAGCGAAAAAA
Found at i:46585837 original size:12 final size:12
Alignment explanation
Indices: 46585804--46585870 Score: 66
Period size: 12 Copynumber: 5.8 Consensus size: 12
46585794 ATAACATCCG
46585804 AACAA-AAAAAT
1 AACAACAAAAAT
* *
46585815 AAGAACCAAAAT
1 AACAACAAAAAT
* *
46585827 AGCAGCAAAAAT
1 AACAACAAAAAT
*
46585839 AACAGC-AAAAT
1 AACAACAAAAAT
46585850 AACAACAAAAAT
1 AACAACAAAAAT
*
46585862 AGCAACAAA
1 AACAACAAA
46585871 GTAATAGCAA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
11 14 0.31
12 31 0.69
ACGTcount: A:0.69, C:0.16, G:0.07, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:46585847 original size:23 final size:23
Alignment explanation
Indices: 46585809--46585894 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
46585799 ATCCGAACAA
* *
46585809 AAAAATAAGAACCAAAATAGCAGC
1 AAAAATAACAA-CAAAATAACAGC
* *
46585833 AAAAATAACAGCAAAATAACAAC
1 AAAAATAACAACAAAATAACAGC
* * *
46585856 AAAAATAGCAACAAAGTAATAGC
1 AAAAATAACAACAAAATAACAGC
* *
46585879 AAAAACAACATCAAAA
1 AAAAATAACAACAAAA
46585895 CAGCAACCAA
Statistics
Matches: 49, Mismatches: 13, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
23 40 0.82
24 9 0.18
ACGTcount: A:0.66, C:0.16, G:0.08, T:0.09
Consensus pattern (23 bp):
AAAAATAACAACAAAATAACAGC
Found at i:46585848 original size:11 final size:11
Alignment explanation
Indices: 46585821--46585882 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
46585811 AAATAAGAAC
*
46585821 CAAAATAGCAG
1 CAAAATAACAG
46585832 CAAAAATAACAG
1 C-AAAATAACAG
*
46585844 CAAAATAACAA
1 CAAAATAACAG
* *
46585855 CAAAAATAGCAA
1 C-AAAATAACAG
* *
46585867 CAAAGTAATAG
1 CAAAATAACAG
46585878 CAAAA
1 CAAAA
46585883 ACAACATCAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
11 21 0.51
12 20 0.49
ACGTcount: A:0.65, C:0.16, G:0.10, T:0.10
Consensus pattern (11 bp):
CAAAATAACAG
Found at i:46585878 original size:14 final size:12
Alignment explanation
Indices: 46585809--46585880 Score: 58
Period size: 12 Copynumber: 5.9 Consensus size: 12
46585799 ATCCGAACAA
46585809 AAAAATAAG-AAC
1 AAAAAT-AGCAAC
* *
46585821 CAAAATAGCAGC
1 AAAAATAGCAAC
* *
46585833 AAAAATAACAGC
1 AAAAATAGCAAC
*
46585845 -AAAATAACAAC
1 AAAAATAGCAAC
46585856 AAAAATAGCAAC
1 AAAAATAGCAAC
46585868 AAAGTAATAGCAA
1 AAA--AATAGCAA
46585881 AAACAACATC
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
11 12 0.24
12 30 0.60
14 8 0.16
ACGTcount: A:0.65, C:0.15, G:0.10, T:0.10
Consensus pattern (12 bp):
AAAAATAGCAAC
Found at i:46585952 original size:24 final size:22
Alignment explanation
Indices: 46585891--46585962 Score: 90
Period size: 22 Copynumber: 3.1 Consensus size: 22
46585881 AAACAACATC
* *
46585891 AAAACAGCAACCAAAACAGTAAA
1 AAAACAAC-ACCAAAACAATAAA
*
46585914 AAAATAACACCAAAACAATAAA
1 AAAACAACACCAAAACAATAAA
46585936 AAAACAACACCAAAAAACAATAAA
1 AAAACAACACC--AAAACAATAAA
46585960 AAA
1 AAA
46585963 TAATAACAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
22 23 0.53
23 6 0.14
24 14 0.33
ACGTcount: A:0.72, C:0.19, G:0.03, T:0.06
Consensus pattern (22 bp):
AAAACAACACCAAAACAATAAA
Found at i:46585973 original size:22 final size:21
Alignment explanation
Indices: 46585903--46585973 Score: 56
Period size: 24 Copynumber: 3.1 Consensus size: 21
46585893 AACAGCAACC
*
46585903 AAAACAGT-AAAAAAATAACA
1 AAAACAATAAAAAAAATAACA
46585923 CCAAAACAATAAAAAAACA-ACACCAA
1 --AAAACAATAAAAAAA-ATA-A-C-A
46585949 AAAACAATAAAAAATAATAACA
1 AAAACAATAAAAAA-AATAACA
46585971 AAA
1 AAA
46585974 TAGTATCAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
22 11 0.27
23 8 0.20
24 18 0.44
25 3 0.07
26 1 0.02
ACGTcount: A:0.75, C:0.15, G:0.01, T:0.08
Consensus pattern (21 bp):
AAAACAATAAAAAAAATAACA
Found at i:46587297 original size:2 final size:2
Alignment explanation
Indices: 46587290--46587328 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
46587280 AAATATAGTG
46587290 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46587329 TACACCCAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46588040 original size:18 final size:17
Alignment explanation
Indices: 46588017--46588051 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
46588007 CAATTCATAG
46588017 CACTTTCAATTCCAATTT
1 CACTTTCAATT-CAATTT
*
46588035 CACTTTCACTTCAATTT
1 CACTTTCAATTCAATTT
46588052 TGATCACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.46
Consensus pattern (17 bp):
CACTTTCAATTCAATTT
Found at i:46588872 original size:2 final size:2
Alignment explanation
Indices: 46588865--46588893 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
46588855 TTATATCTTT
46588865 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46588894 TAGTTAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46589954 original size:36 final size:36
Alignment explanation
Indices: 46589906--46589977 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
46589896 ATCGACATAA
*
46589906 AATTTCTCTCTATCAAAGGCTACTTTTAATCTATCT
1 AATTTCTCTCTATCAAAGGCTACTTTTAATCCATCT
* * **
46589942 AATTTCTGTCTATTAAAGGCTGGTTTTAATCCATCT
1 AATTTCTCTCTATCAAAGGCTACTTTTAATCCATCT
46589978 TTAATCTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.44
Consensus pattern (36 bp):
AATTTCTCTCTATCAAAGGCTACTTTTAATCCATCT
Found at i:46597090 original size:120 final size:120
Alignment explanation
Indices: 46596877--46597114 Score: 449
Period size: 120 Copynumber: 2.0 Consensus size: 120
46596867 GTGGTGGAGT
* *
46596877 GTACAATTTATTAGTTTGATGGCTCGGGAATATACGATGCCTTGCGAGGCTATTAAAATTTTTTT
1 GTACAATTTATTAGTTTGATGGCTCAGGAATATACGATGCCTTGCGAGGCTATTAAAATTTTTTC
46596942 GTACCTATAATAGTGGATTGACAGATGGTGTTTCTATTCGTGGTTGGCTCGTAGG
66 GTACCTATAATAGTGGATTGACAGATGGTGTTTCTATTCGTGGTTGGCTCGTAGG
46596997 GTACAATTTATTAGTTTGATGGCTCAGGAATATACGATGCCTTGCGAGGCTATTAAAATTTTTTC
1 GTACAATTTATTAGTTTGATGGCTCAGGAATATACGATGCCTTGCGAGGCTATTAAAATTTTTTC
*
46597062 GTACCTATAATAGTGGATTGGCAGATGGTGTTTCTATTCGTGGTTGGCTCGTA
66 GTACCTATAATAGTGGATTGACAGATGGTGTTTCTATTCGTGGTTGGCTCGTA
46597115 TAAATTTCAC
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 115 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (120 bp):
GTACAATTTATTAGTTTGATGGCTCAGGAATATACGATGCCTTGCGAGGCTATTAAAATTTTTTC
GTACCTATAATAGTGGATTGACAGATGGTGTTTCTATTCGTGGTTGGCTCGTAGG
Found at i:46598753 original size:22 final size:22
Alignment explanation
Indices: 46598721--46598780 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
46598711 TTGTTATTGT
*
46598721 TATTTTGCTGTCATTTCGCTGC
1 TATTTTACTGTCATTTCGCTGC
46598743 TATTTTACTGTCATTTCGCTGC
1 TATTTTACTGTCATTTCGCTGC
*
46598765 TATTTTACTGTTATTT
1 TATTTTACTGTCATTT
46598781 TACAATAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.13, C:0.18, G:0.13, T:0.55
Consensus pattern (22 bp):
TATTTTACTGTCATTTCGCTGC
Found at i:46598779 original size:11 final size:11
Alignment explanation
Indices: 46598718--46598783 Score: 51
Period size: 11 Copynumber: 6.0 Consensus size: 11
46598708 TTTTTGTTAT
*
46598718 TGTTATTTTGC
1 TGTTATTTTAC
* **
46598729 TGTCATTTCGC
1 TGTTATTTTAC
*
46598740 TGCTATTTTAC
1 TGTTATTTTAC
* **
46598751 TGTCATTTCGC
1 TGTTATTTTAC
*
46598762 TGCTATTTTAC
1 TGTTATTTTAC
46598773 TGTTATTTTAC
1 TGTTATTTTAC
46598784 AATAGTATTG
Statistics
Matches: 40, Mismatches: 15, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
11 40 1.00
ACGTcount: A:0.14, C:0.18, G:0.14, T:0.55
Consensus pattern (11 bp):
TGTTATTTTAC
Found at i:46601552 original size:6 final size:6
Alignment explanation
Indices: 46601543--46601587 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
46601533 AAAAAAACAT
*
46601543 CATGTC CATGTG CATGTG CATGTG CATGTG CATGTG CATGTG CAT
1 CATGTG CATGTG CATGTG CATGTG CATGTG CATGTG CATGTG CAT
46601588 ACCAAGAAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (6 bp):
CATGTG
Found at i:46626897 original size:72 final size:73
Alignment explanation
Indices: 46626780--46626956 Score: 252
Period size: 72 Copynumber: 2.5 Consensus size: 73
46626770 CCGTCACTCG
*
46626780 AGCAGGTGGCT-ATAAATGAAAATACGGAGACGATCAGAATCAAAAAGCCTTTGAATGAGAAGAC
1 AGCAGGTGG-TGATAAACGAAAATACGGAGACGATCAGAATCAAAAAGCCTTTGAATGAGAAGAC
46626844 AATTC-TCA
65 AATTCTTCA
* * *
46626852 AGCAGGTGGTGATACACGAAAATACGGAGACGATGATAATCAAAAAGCCTTTGAATGAGAAGACA
1 AGCAGGTGGTGATAAACGAAAATACGGAGACGATCAGAATCAAAAAGCCTTTGAATGAGAAGACA
*
46626917 ATTCTTGA
66 ATTCTTCA
* * *
46626925 A-CATGTAGTGATAAACGAAAATTCGGAGACGA
1 AGCAGGTGGTGATAAACGAAAATACGGAGACGA
46626957 GATCTTTGAA
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
71 1 0.01
72 90 0.96
73 3 0.03
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (73 bp):
AGCAGGTGGTGATAAACGAAAATACGGAGACGATCAGAATCAAAAAGCCTTTGAATGAGAAGACA
ATTCTTCA
Found at i:46634789 original size:15 final size:16
Alignment explanation
Indices: 46634760--46634791 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
46634750 TTTTTGAATG
46634760 ATTTTAATATTTTTTA
1 ATTTTAATATTTTTTA
46634776 ATTTTAAT-TTTTTTA
1 ATTTTAATATTTTTTA
46634791 A
1 A
46634792 AAAATAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTTTAATATTTTTTA
Found at i:46637409 original size:8 final size:9
Alignment explanation
Indices: 46637389--46637417 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
46637379 TTACTAATCT
46637389 AAAATTTTA
1 AAAATTTTA
46637398 AAAATTTTA
1 AAAATTTTA
46637407 AAAATTTTA
1 AAAATTTTA
46637416 AA
1 AA
46637418 TGGCCTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AAAATTTTA
Found at i:46641960 original size:23 final size:22
Alignment explanation
Indices: 46641926--46641968 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
46641916 TTGACTTGGG
*
46641926 TTTTGTCTTACTTTTGGTTGTT
1 TTTTGTCTTACTTTTCGTTGTT
*
46641948 TTTTTTCTGTACTTTTCGTTG
1 TTTTGTCT-TACTTTTCGTTG
46641969 ATCACAATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.05, C:0.12, G:0.16, T:0.67
Consensus pattern (22 bp):
TTTTGTCTTACTTTTCGTTGTT
Found at i:46643485 original size:59 final size:59
Alignment explanation
Indices: 46643366--46643489 Score: 137
Period size: 59 Copynumber: 2.1 Consensus size: 59
46643356 AAATCAGAGA
* * * * * *
46643366 TTAACTTGACAAAAAAAAAGTTCAAGCTCTAATATAAGAGCAATTGTCTAGTTCATGGC
1 TTAACTTGACAAAAAAAAAGTTCAAGCACTAATATAAGAACAATTATCAAATTCAGGGC
*
46643425 TTAACTTGGACAAAAAAAAA-TTCAAGCACTAACT-TGAGAACAATTATCAAATAT-AGGGC
1 TTAACTT-GACAAAAAAAAAGTTCAAGCACTAA-TATAAGAACAATTATCAAAT-TCAGGGC
46643484 TTAACT
1 TTAACT
46643490 CCTAAAAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
59 41 0.75
60 14 0.25
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (59 bp):
TTAACTTGACAAAAAAAAAGTTCAAGCACTAATATAAGAACAATTATCAAATTCAGGGC
Found at i:46646290 original size:20 final size:22
Alignment explanation
Indices: 46646254--46646298 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
46646244 AATAACTCGA
46646254 TTAATTCGAATAATTTAAATAT
1 TTAATTCGAATAATTTAAATAT
*
46646276 TTAATTC-AA-AATTTAAATTT
1 TTAATTCGAATAATTTAAATAT
46646296 TTA
1 TTA
46646299 TGAAATTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.59
21 2 0.09
22 7 0.32
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAATTCGAATAATTTAAATAT
Found at i:46648362 original size:16 final size:15
Alignment explanation
Indices: 46648341--46648388 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
46648331 AGCTTAATAA
46648341 AAAAAATTAAAATTAT
1 AAAAAA-TAAAATTAT
46648357 AAAAAA-ATAAATTAT
1 AAAAAATA-AAATTAT
46648372 AAAATAATAAAATTAT
1 AAAA-AATAAAATTAT
46648388 A
1 A
46648389 TTTTTACTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.03
15 11 0.38
16 16 0.55
17 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAAATAAAATTAT
Found at i:46648368 original size:15 final size:16
Alignment explanation
Indices: 46648340--46648388 Score: 73
Period size: 15 Copynumber: 3.1 Consensus size: 16
46648330 GAGCTTAATA
46648340 AAAAAAATTAAAATTAT
1 AAAAAAA-TAAAATTAT
46648357 AAAAAAAT-AAATTAT
1 AAAAAAATAAAATTAT
*
46648372 AAAATAATAAAATTAT
1 AAAAAAATAAAATTAT
46648388 A
1 A
46648389 TTTTTACTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 14 0.47
16 9 0.30
17 7 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAAAATAAAATTAT
Found at i:46649165 original size:102 final size:102
Alignment explanation
Indices: 46649050--46649257 Score: 362
Period size: 102 Copynumber: 2.0 Consensus size: 102
46649040 GGATATGTTA
* *
46649050 TGTTACTATTCATCCCTGCACCATTGTCAACCATATTTGGACCTGCTAAAAGATTGCCTCCTCGA
1 TGTTACTATTCATCCCCGCACCATTGTCAACCATATTTGGACCTGCTAAAAGATTGCCTCCTAGA
*
46649115 GTCCTCATGCTATTTGGAAGCACAGTTTGTGAATTGT
66 GTCCTCATGCTATTTGGAAGCACAGTTCGTGAATTGT
* *
46649152 TGTTATTATTCATCCCCGCACCATTGTCAACCATATTTGGACCTGCTAAAAGATTGCCTCCTAGG
1 TGTTACTATTCATCCCCGCACCATTGTCAACCATATTTGGACCTGCTAAAAGATTGCCTCCTAGA
*
46649217 GTGCTCATGCTATTTGGAAGCACAGTTCGTGAATTGT
66 GTCCTCATGCTATTTGGAAGCACAGTTCGTGAATTGT
46649254 TGTT
1 TGTT
46649258 CAGGAGAATG
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 100 1.00
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (102 bp):
TGTTACTATTCATCCCCGCACCATTGTCAACCATATTTGGACCTGCTAAAAGATTGCCTCCTAGA
GTCCTCATGCTATTTGGAAGCACAGTTCGTGAATTGT
Found at i:46652469 original size:23 final size:23
Alignment explanation
Indices: 46652422--46652475 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
46652412 TCGAACATAA
**
46652422 AACTCGAATTATTTATTTAATTT
1 AACTCGAATTATCAATTTAATTT
46652445 AACTCGAATTACTCAATTTAA-TT
1 AACTCGAATTA-TCAATTTAATTT
*
46652468 AATTCGAA
1 AACTCGAA
46652476 ATTGAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.43
Consensus pattern (23 bp):
AACTCGAATTATCAATTTAATTT
Found at i:46655487 original size:6 final size:6
Alignment explanation
Indices: 46655470--46655507 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
46655460 TGATCAAAAT
*
46655470 TGAAAG TG-AAG TGAAAG TGAAAG TGAAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
46655508 TATGAATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.47, C:0.00, G:0.32, T:0.21
Consensus pattern (6 bp):
TGAAAG
Found at i:46656511 original size:29 final size:29
Alignment explanation
Indices: 46656477--46656533 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
46656467 TAAGAATTTC
* *
46656477 ATATTTTTGTTCATGTTCGTTTATTTAAA
1 ATATTTGTGTTCATGTTCATTTATTTAAA
* *
46656506 ATATTTGTGTTTATGTTCATTTGTTTAA
1 ATATTTGTGTTCATGTTCATTTATTTAA
46656534 TGTTCACGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.23, C:0.05, G:0.12, T:0.60
Consensus pattern (29 bp):
ATATTTGTGTTCATGTTCATTTATTTAAA
Found at i:46657118 original size:20 final size:19
Alignment explanation
Indices: 46657095--46657141 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
46657085 AATTTTAAAA
*
46657095 TTTTAAATTCTTTATATATT
1 TTTTAAATTCTTTAGA-ATT
*
46657115 TTTTAGAATTTTTTAGAATT
1 TTTTA-AATTCTTTAGAATT
46657135 TTTTAAA
1 TTTTAAA
46657142 AATAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 13 0.54
21 9 0.38
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (19 bp):
TTTTAAATTCTTTAGAATT
Found at i:46657127 original size:11 final size:10
Alignment explanation
Indices: 46657112--46657139 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
46657102 TTCTTTATAT
46657112 ATTTTTTAGA
1 ATTTTTTAGA
46657122 ATTTTTTAGA
1 ATTTTTTAGA
46657132 ATTTTTTA
1 ATTTTTTA
46657140 AAAATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (10 bp):
ATTTTTTAGA
Found at i:46660835 original size:22 final size:22
Alignment explanation
Indices: 46660810--46660852 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
46660800 AATCCAAACA
46660810 ATAACAATAAAAT-AGTAGCAAT
1 ATAACAATAAAATGA-TAGCAAT
* *
46660832 ATAATAATGAAATGATAGCAA
1 ATAACAATAAAATGATAGCAA
46660853 AATAGTGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.58, C:0.07, G:0.12, T:0.23
Consensus pattern (22 bp):
ATAACAATAAAATGATAGCAAT
Found at i:46673215 original size:23 final size:22
Alignment explanation
Indices: 46673173--46673220 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
46673163 AAATTAAAAA
*
46673173 AATTAAATTTCGAGTTAATT-G
1 AATTAAATTTCGAGTCAATTCG
46673194 AATTAAATTATTCGAGTCAATTCG
1 AATTAAA-T-TTCGAGTCAATTCG
46673218 AAT
1 AAT
46673221 AAAAAATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 1 0.04
23 11 0.48
24 4 0.17
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (22 bp):
AATTAAATTTCGAGTCAATTCG
Found at i:46673522 original size:12 final size:12
Alignment explanation
Indices: 46673505--46673535 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
46673495 ACTAAAGTAT
46673505 TTTTTTTTTAAA
1 TTTTTTTTTAAA
46673517 TTTTTTTTTAAA
1 TTTTTTTTTAAA
46673529 TTTTTTT
1 TTTTTTT
46673536 AATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTTTTTAAA
Found at i:46673930 original size:3 final size:3
Alignment explanation
Indices: 46673922--46673951 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
46673912 TGTTTAAAAT
*
46673922 TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
46673952 AGAAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:46673939 original size:12 final size:12
Alignment explanation
Indices: 46673922--46673986 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
46673912 TGTTTAAAAT
46673922 TAATAATAACAA
1 TAATAATAACAA
*
46673934 TAATAATAATAA
1 TAATAATAACAA
*
46673946 TAATAA-AGAAAA
1 TAATAATA-ACAA
*
46673958 AAATGTAATAAACAA
1 TAA--TAAT-AACAA
46673973 TAATAA-AACAA
1 TAATAATAACAA
46673984 TAA
1 TAA
46673987 AGTTTTTACG
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
11 9 0.21
12 22 0.51
13 3 0.07
14 3 0.07
15 5 0.12
16 1 0.02
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (12 bp):
TAATAATAACAA
Found at i:46674695 original size:2 final size:2
Alignment explanation
Indices: 46674688--46674731 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
46674678 ATCATTTATG
46674688 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46674729 TA T
1 TA T
46674732 GTATCGATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46675861 original size:208 final size:200
Alignment explanation
Indices: 46675234--46675933 Score: 812
Period size: 201 Copynumber: 3.5 Consensus size: 200
46675224 ATTTGACATA
* * * *
46675234 TAATCCGATTTCAAGTTTCTTTTTCATATCAACCGGCTAATTGAATTTTTAACGGTGTTAGTGAA
1 TAATCCAATTTCAAGTTTCTTTTT-ATATAAACCGGCTAATTGAATTTTTAACGGTATTAGTGAT
* * *
46675299 TTAGATTAA---G--ATATTGAT-A-TCGATTGGTAT-GATCATTCTTGATATATGTAAG-AGTA
65 TTAGATTAAGGTGTAATATTAATAAGTCGATTGGTATGGA-CATTCTTGCTA-ATGCAAGAAG-A
* * *
46675355 CT-TGGGTTTTATTTAT-GAAATATACATAATTTTTCTTAAATTTCTATTTCGATTTGACATAAT
127 -TGTGAGTCTTATTTATGGAAATATACATAATTTTTCTAAAATTTCTATTTCGATTTGACATAAT
*
46675418 CTTTAATTAC
191 CTTTAATTAG
*** * * *
46675428 TAATTTGATTTCAAGTTTCTTTTTATATAAACTGGATAATTGAATTTTTAATGGTATTAGTGATT
1 TAATCCAATTTCAAGTTTCTTTTTATATAAACCGGCTAATTGAATTTTTAACGGTATTAGTGATT
* * *
46675493 TAGATTAAGGTGTGATATTAATAAGTTGATTGGTTTGGACATTCTTGCTAATGCAAGAAGATGTG
66 TAGATTAAGGTGTAATATTAATAAGTCGATTGGTATGGACATTCTTGCTAATGCAAGAAGATGTG
* * * * * *
46675558 GGTCTTATTTATGAAAATGTACATAAATTTTTTTAAAATTTTTATTTCGATTTGACATATTCTTT
131 AGTCTTATTTATGGAAATATACAT-AATTTTTCTAAAATTTCTATTTCGATTTGACATAATCTTT
46675623 AATTAG
195 AATTAG
* *
46675629 TAATCCTATTTCAAGTTTCTTTTTATATAAACCGGCTAATTGAATTTTTAACAGTATTAGTGATT
1 TAATCCAATTTCAAGTTTCTTTTTATATAAACCGGCTAATTGAATTTTTAACGGTATTAGTGATT
* * * *
46675694 TAGATTAAGTTGTAATATTAACTTAGATCGATTGGTATGCG-CATTTTTGTTAATGCAAGAAGAT
66 TAGATTAAGGTGTAATATTAA-TAAG-TCGATTGGTATG-GACATTCTTGCTAATGCAAGAAGAT
*
46675758 GTGAGTCTTATTAATTTATATGGAAATATACATAATGTTTCTAAAATTTCTATTTCGATTTGACA
128 GTGAGTC---TT-A-TT-TATGGAAATATACATAATTTTTCTAAAATTTCTATTTCGATTTGACA
*
46675823 TAATCTTTAACTAG
187 TAATCTTTAATTAG
* * ** * *
46675837 TACTCCAATTTCAAGTTTCTTTTTATATCAACCAACTAATTGAATTTTTAACGGTGTTAATGATT
1 TAATCCAATTTCAAGTTTCTTTTTATATAAACCGGCTAATTGAATTTTTAACGGTATTAGTGATT
*
46675902 TAGATTAAGGTGTAATATTAATAAGTTGATTG
66 TAGATTAAGGTGTAATATTAATAAGTCGATTG
46675934 AGTTAATGTA
Statistics
Matches: 431, Mismatches: 54, Indels: 30
0.84 0.10 0.06
Matches are distributed among these distances:
193 43 0.10
194 22 0.05
196 1 0.00
198 8 0.02
199 21 0.05
200 30 0.07
201 120 0.28
202 3 0.01
203 37 0.09
204 1 0.00
206 8 0.02
207 4 0.01
208 120 0.28
209 13 0.03
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.45
Consensus pattern (200 bp):
TAATCCAATTTCAAGTTTCTTTTTATATAAACCGGCTAATTGAATTTTTAACGGTATTAGTGATT
TAGATTAAGGTGTAATATTAATAAGTCGATTGGTATGGACATTCTTGCTAATGCAAGAAGATGTG
AGTCTTATTTATGGAAATATACATAATTTTTCTAAAATTTCTATTTCGATTTGACATAATCTTTA
ATTAG
Found at i:46676947 original size:210 final size:210
Alignment explanation
Indices: 46676665--46677087 Score: 657
Period size: 210 Copynumber: 2.0 Consensus size: 210
46676655 CTAGACAATT
* * * * ** *
46676665 ACATACCATATCCAGAGAATGAACTCGGTGGAGTTGCCTCTTTGCAGCAGCAGCAACTATCAATG
1 ACATAACATATCCACAGAATGAACTCGGTGAACTTGCCTCTAAGCAGCAGCAGCAACCATCAATG
*
46676730 CTCCAAACACTCAATGATGAATACCAACAGAACATTCTCCTGAACAACAATTCACGAATTGTGCT
66 CTCCAAACACTCAATGATGAATACCAACAGAACATTCTCCTGAACAACAATTCACGAACTGTGCT
* *
46676795 TCCAAATAGCATGAGGACCCTAGGAGGCAATCTTTTAGCAGGTCCAAATATGGTTGACAATGGTG
131 TCCAAATAGCATGAGGACCCAAGGAGGCAATCTTTTAGCAGGTACAAATATGGTTGACAATGGTG
*
46676860 CAGGGATGAATAATA
196 CAGGGAGGAATAATA
* * *
46676875 ACATAACATATCCACAGGATGAACTTGGTGAACTTGCCTCTAAGCAGCAGCAGCAACCATCAGTG
1 ACATAACATATCCACAGAATGAACTCGGTGAACTTGCCTCTAAGCAGCAGCAGCAACCATCAATG
* * *
46676940 CTCCAAACATTCAATGATGAATACCATCAGAGCATTCTCCTGAACAACAATTCACGAACTGTGCT
66 CTCCAAACACTCAATGATGAATACCAACAGAACATTCTCCTGAACAACAATTCACGAACTGTGCT
* **
46677005 TCCAAATAGCATGATGACCCAAGGAGGCAATCTTTTAGCAGGTATGAATATGGTTGACAATGGTG
131 TCCAAATAGCATGAGGACCCAAGGAGGCAATCTTTTAGCAGGTACAAATATGGTTGACAATGGTG
*
46677070 CGGGGAGGAATAATA
196 CAGGGAGGAATAATA
46677085 ACA
1 ACA
46677088 ACAATATGTC
Statistics
Matches: 192, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
210 192 1.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (210 bp):
ACATAACATATCCACAGAATGAACTCGGTGAACTTGCCTCTAAGCAGCAGCAGCAACCATCAATG
CTCCAAACACTCAATGATGAATACCAACAGAACATTCTCCTGAACAACAATTCACGAACTGTGCT
TCCAAATAGCATGAGGACCCAAGGAGGCAATCTTTTAGCAGGTACAAATATGGTTGACAATGGTG
CAGGGAGGAATAATA
Found at i:46677826 original size:13 final size:14
Alignment explanation
Indices: 46677803--46677831 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
46677793 TAATCTAAAG
46677803 AAGTAAAAATTATA
1 AAGTAAAAATTATA
46677817 AAGT-AAAATTATA
1 AAGTAAAAATTATA
46677830 AA
1 AA
46677832 ATTATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (14 bp):
AAGTAAAAATTATA
Found at i:46679711 original size:10 final size:10
Alignment explanation
Indices: 46679696--46679755 Score: 61
Period size: 10 Copynumber: 6.0 Consensus size: 10
46679686 TTAGTTAAAA
46679696 TTAAAAATAT
1 TTAAAAATAT
46679706 TTAAAAATAT
1 TTAAAAATAT
*
46679716 TTCAAAATA-
1 TTAAAAATAT
46679725 -TAAAATATAT
1 TTAAAA-ATAT
46679735 TTCAAAAATAT
1 TT-AAAAATAT
**
46679746 AAAAAAATAT
1 TTAAAAATAT
46679756 AAGATTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 4 0.10
9 3 0.07
10 26 0.62
11 5 0.12
12 4 0.10
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (10 bp):
TTAAAAATAT
Found at i:46679722 original size:20 final size:19
Alignment explanation
Indices: 46679699--46679750 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
46679689 GTTAAAATTA
46679699 AAAATATTTAAAAATATTTC
1 AAAATA-TTAAAAATATTTC
46679719 AAAATA-TAAAATATATTTC
1 AAAATATTAAAA-ATATTTC
46679738 AAAA-ATATAAAAA
1 AAAATAT-TAAAAA
46679751 AATATAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 6 0.21
19 12 0.41
20 11 0.38
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATATTAAAAATATTTC
Found at i:46679794 original size:20 final size:20
Alignment explanation
Indices: 46679698--46679919 Score: 111
Period size: 20 Copynumber: 10.9 Consensus size: 20
46679688 AGTTAAAATT
*
46679698 AAAAATATTTAAAAATATTTC
1 AAAAATA-TAAAAAATATTTC
*
46679719 -AAAATATAAAATATATTTC
1 AAAAATATAAAAAATATTTC
*
46679738 AAAAATATAAAAAAATATAAGATTTT
1 AAAAATAT--AAAAA-AT---ATTTC
* ** *
46679764 TAATTTGTAAAAAATATTTC
1 AAAAATATAAAAAATATTTC
46679784 AAAAATATAAAAAAAATATTTC
1 AAAAATAT--AAAAAATATTTC
*
46679806 GAAAATAT-AAAAA-A--T-
1 AAAAATATAAAAAATATTTC
*
46679821 --AAATGTAAAAAATATTTC
1 AAAAATATAAAAAATATTTC
* *
46679839 GAAAATATAAAAAATATTTTTT
1 AAAAATATAAAAAATA--TTTC
* ***
46679861 AAAAAT-TCAAAAATATAAA
1 AAAAATATAAAAAATATTTC
**
46679880 AATAAACGTAAAAAATATTTC
1 AA-AAATATAAAAAATATTTC
*
46679901 AAAAATAAAAAAAATATTT
1 AAAAATATAAAAAATATTT
46679920 TTTAAAATTC
Statistics
Matches: 151, Mismatches: 30, Indels: 41
0.68 0.14 0.18
Matches are distributed among these distances:
13 5 0.03
14 5 0.03
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 19 0.13
20 51 0.34
21 19 0.13
22 31 0.21
23 4 0.03
24 5 0.03
26 8 0.05
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAAATATAAAAAATATTTC
Found at i:46679831 original size:33 final size:33
Alignment explanation
Indices: 46679794--46679916 Score: 146
Period size: 33 Copynumber: 3.8 Consensus size: 33
46679784 AAAAATATAA
*
46679794 AAAAAATATTTCGAAAATATAAAAAATAAATGT
1 AAAAAATATTTCAAAAATATAAAAAATAAATGT
* * *
46679827 AAAAAATATTTCGAAAATATAAAAAAT-ATTTT
1 AAAAAATATTTCAAAAATATAAAAAATAAATGT
** *
46679859 TTAAAA-A-TTCAAAAATAT-AAAAATAAACGT
1 AAAAAATATTTCAAAAATATAAAAAATAAATGT
*
46679889 AAAAAATATTTCAAAAATAAAAAAAATA
1 AAAAAATATTTCAAAAATATAAAAAATA
46679917 TTTTTTAAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
29 6 0.08
30 16 0.21
31 2 0.03
32 17 0.23
33 34 0.45
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.28
Consensus pattern (33 bp):
AAAAAATATTTCAAAAATATAAAAAATAAATGT
Found at i:46679832 original size:22 final size:22
Alignment explanation
Indices: 46679772--46679835 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
46679762 TTTAATTTGT
* *
46679772 AAAAAATATTTCAAAAATATAA
1 AAAAAATATGTAAAAAATATAA
* **
46679794 AAAAAATATTTCGAAAATATAA
1 AAAAAATATGTAAAAAATATAA
46679816 AAAATAA-ATGTAAAAAATAT
1 AAAA-AATATGTAAAAAATAT
46679836 TTCGAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 35 0.95
23 2 0.05
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (22 bp):
AAAAAATATGTAAAAAATATAA
Found at i:46679943 original size:62 final size:63
Alignment explanation
Indices: 46679807--46679945 Score: 237
Period size: 62 Copynumber: 2.2 Consensus size: 63
46679797 AAATATTTCG
* * *
46679807 AAAATATAAAAAATAAATGTAAAAAATATTTCGAAAATATAAAAAATATTTTTTAAAAATTCA
1 AAAATATAAAAAATAAACGTAAAAAATATTTCAAAAATAAAAAAAATATTTTTTAAAAATTCA
46679870 AAAATAT-AAAAATAAACGTAAAAAATATTTCAAAAATAAAAAAAATATTTTTT-AAAATTCA
1 AAAATATAAAAAATAAACGTAAAAAATATTTCAAAAATAAAAAAAATATTTTTTAAAAATTCA
46679931 AAAATATAAAAAATA
1 AAAATATAAAAAATA
46679946 TTTAAAAAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
61 15 0.21
62 50 0.69
63 7 0.10
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (63 bp):
AAAATATAAAAAATAAACGTAAAAAATATTTCAAAAATAAAAAAAATATTTTTTAAAAATTCA
Found at i:46679955 original size:29 final size:30
Alignment explanation
Indices: 46679784--46679955 Score: 118
Period size: 29 Copynumber: 5.6 Consensus size: 30
46679774 AAAATATTTC
**
46679784 AAAAATATAAAAAAAATATTTCGAAAATATAAA
1 AAAAATATTTAAAAAA-ATTTC-AAAA-ATAAA
* * *
46679817 AAATAA-ATGTAAAAAATATTTCGAAAATATA
1 AAA-AATATTTAAAAAA-ATTTCAAAAATAAA
**
46679848 AAAAATATTTTTTAAAAA-TTCAAAAATATAA
1 AAAAATA-TTTAAAAAAATTTCAAAAATA-AA
**
46679879 AAATAA-ACGTAAAAAATATTTCAAAAATAAA
1 AAA-AATATTTAAAAAA-ATTTCAAAAATAAA
*** *
46679910 AAAAATATTTTTTAAAA-TTCAAAAATATA
1 AAAAATATTTAAAAAAATTTCAAAAATAAA
46679939 AAAAATATTTAAAAAAA
1 AAAAATATTTAAAAAAA
46679956 ATTGGAAATA
Statistics
Matches: 109, Mismatches: 22, Indels: 20
0.72 0.15 0.13
Matches are distributed among these distances:
29 25 0.23
30 19 0.17
31 25 0.23
32 21 0.19
33 17 0.16
34 2 0.02
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.29
Consensus pattern (30 bp):
AAAAATATTTAAAAAAATTTCAAAAATAAA
Found at i:46681668 original size:22 final size:22
Alignment explanation
Indices: 46681653--46681700 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
46681643 TAATTTTAGT
46681653 TTCATTTGAATTTAATTTGAAA
1 TTCATTTGAATTTAATTTGAAA
* *
46681675 TTCATTTGAAATTAATTTGAAT
1 TTCATTTGAATTTAATTTGAAA
46681697 TTCA
1 TTCA
46681701 ATTTTAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.50
Consensus pattern (22 bp):
TTCATTTGAATTTAATTTGAAA
Found at i:46681670 original size:11 final size:11
Alignment explanation
Indices: 46681640--46681704 Score: 67
Period size: 11 Copynumber: 5.8 Consensus size: 11
46681630 CAAATTAAAT
*
46681640 ATTTAATTTTA
1 ATTTAATTTGA
* *
46681651 GTTTCATTTGA
1 ATTTAATTTGA
46681662 ATTTAATTTGA
1 ATTTAATTTGA
* *
46681673 AATTCATTTGA
1 ATTTAATTTGA
*
46681684 AATTAATTTGA
1 ATTTAATTTGA
46681695 ATTTCAATTT
1 ATTT-AATTT
46681705 TAACTTAGTG
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
11 39 0.89
12 5 0.11
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.54
Consensus pattern (11 bp):
ATTTAATTTGA
Found at i:46681782 original size:6 final size:6
Alignment explanation
Indices: 46681769--46681854 Score: 68
Period size: 6 Copynumber: 14.7 Consensus size: 6
46681759 TTTTTTATTT
* * * ** *
46681769 TTTTAA TTTCAA TTTCAA CTTCGA TTTTAA TTTGAA TTTTAA TTTTAA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA
* * * *
46681817 TTTGAA TTTT-A GTTTCA TTTTAA TTTGAA -TTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
46681855 TTAAGTTAAT
Statistics
Matches: 63, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
5 8 0.13
6 55 0.87
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (6 bp):
TTTTAA
Found at i:46681813 original size:18 final size:18
Alignment explanation
Indices: 46681769--46681853 Score: 75
Period size: 18 Copynumber: 4.8 Consensus size: 18
46681759 TTTTTTATTT
* *
46681769 TTTTAATTTCAATTTCAA
1 TTTTAATTTTAATTTGAA
* **
46681787 CTTCGATTTTAATTTGAA
1 TTTTAATTTTAATTTGAA
46681805 TTTTAATTTTAATTTGAA
1 TTTTAATTTTAATTTGAA
* * *
46681823 TTTT-AGTTTCATTTTAA
1 TTTTAATTTTAATTTGAA
*
46681840 TTTGAA-TTTAATTT
1 TTTTAATTTTAATTT
46681854 TTTAAGTTAA
Statistics
Matches: 53, Mismatches: 13, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
17 20 0.38
18 33 0.62
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (18 bp):
TTTTAATTTTAATTTGAA
Found at i:46681960 original size:27 final size:27
Alignment explanation
Indices: 46681863--46681976 Score: 113
Period size: 28 Copynumber: 4.1 Consensus size: 27
46681853 TTTTAAGTTA
* * *
46681863 ATTTTTAAAATTTTTATATTATAAATTT
1 ATTTTTGAAATTATT-TATTATATATTT
** * **
46681891 GAAATTTGAAATTATTTTTTAATATAAAT
1 -ATTTTTGAAATTATTTATT-ATATATTT
46681920 ATTTTTGAAATTATTTATTAT-TATTT
1 ATTTTTGAAATTATTTATTATATATTT
46681946 ATTTTTGAAATTTATTTATTATATATTT
1 ATTTTTGAAA-TTATTTATTATATATTT
46681974 ATT
1 ATT
46681977 ATTAATTTTT
Statistics
Matches: 69, Mismatches: 13, Indels: 7
0.78 0.15 0.08
Matches are distributed among these distances:
26 13 0.19
27 13 0.19
28 27 0.39
29 16 0.23
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (27 bp):
ATTTTTGAAATTATTTATTATATATTT
Found at i:46682479 original size:70 final size:70
Alignment explanation
Indices: 46682366--46682503 Score: 213
Period size: 70 Copynumber: 2.0 Consensus size: 70
46682356 ATTCACATAA
* * *
46682366 TGTGGTTAATTTGGCTTGATCGATGATAATGGTAGAAATGTCTAGAACAAGTCTTAGGTGGCTTG
1 TGTGGTTAATTTGGCTTGATCGATGACAATAGTAGAAATGTCTAGAACAAGCCTTAGGTGGCTTG
46682431 TTAAT
66 TTAAT
* * * *
46682436 TGTGGTTAATTTGGTTTGGTGGATGACAATAGTAGAATTGTCTAGAACAAGCCTTAGGTGGCTTG
1 TGTGGTTAATTTGGCTTGATCGATGACAATAGTAGAAATGTCTAGAACAAGCCTTAGGTGGCTTG
46682501 TTA
66 TTA
46682504 TGTAACATCC
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.26, C:0.09, G:0.28, T:0.37
Consensus pattern (70 bp):
TGTGGTTAATTTGGCTTGATCGATGACAATAGTAGAAATGTCTAGAACAAGCCTTAGGTGGCTTG
TTAAT
Found at i:46683625 original size:17 final size:17
Alignment explanation
Indices: 46683605--46683638 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
46683595 ATCACTCGCT
*
46683605 ATTTCAATATCATTTTC
1 ATTTCAATAACATTTTC
46683622 ATTTCAATAACATTTTC
1 ATTTCAATAACATTTTC
46683639 CATATCAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTCAATAACATTTTC
Found at i:46684809 original size:13 final size:13
Alignment explanation
Indices: 46684791--46684834 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
46684781 TTACTTTTTT
46684791 TTATTATAATATA
1 TTATTATAATATA
46684804 TTATTATAATACTA
1 TTATTATAATA-TA
*
46684818 TTATTTATCATATA
1 TTA-TTATAATATA
46684832 TTA
1 TTA
46684835 ACACCCATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 11 0.39
14 10 0.36
15 7 0.25
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (13 bp):
TTATTATAATATA
Found at i:46688970 original size:16 final size:16
Alignment explanation
Indices: 46688918--46688973 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
46688908 TATTTGGTTC
46688918 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
46688934 GCTATAATGTAATAGA
1 GCTGTAATGGAATAGA
46688950 GCTGTAATGGAATAG-
1 GCTGTAATGGAATAGA
46688965 GACTGTAAT
1 G-CTGTAAT
46688974 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 1 0.03
16 34 0.97
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.29
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:46689150 original size:56 final size:54
Alignment explanation
Indices: 46689085--46689241 Score: 192
Period size: 56 Copynumber: 2.8 Consensus size: 54
46689075 GATTATTGTT
46689085 ATTAATTTTAATA-AGATTATTATTAAATATAATTTAATAAAAAATAAATAATTTA
1 ATTAATTTTAATATA-ATTATTATTAAATATAATTTAATAAAAAA-AAATAATTTA
* * *
46689140 ATTATATTTTAACATAATTATTATTAAATACAATTTAATAAAATAAATATAATTTA
1 ATTA-ATTTTAATATAATTATTATTAAATATAATTTAATAAAA-AAAAATAATTTA
*
46689196 ATAACATTTTTAATATAATTATTATTAAAATATGAA-TTAATAAAAA
1 ATTA-A-TTTTAATATAATTATTATT-AAATAT-AATTTAATAAAAA
46689242 TTATAATATA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
55 4 0.04
56 47 0.53
57 22 0.25
58 14 0.16
59 2 0.02
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (54 bp):
ATTAATTTTAATATAATTATTATTAAATATAATTTAATAAAAAAAAATAATTTA
Found at i:46689227 original size:29 final size:29
Alignment explanation
Indices: 46689146--46689224 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 29
46689136 TTTAATTATA
*
46689146 TTTTAACATAATTATTATTAAAT-ACAAT
1 TTTTAAAATAATTATTATTAAATAACAAT
* * * *
46689174 TTAATAAAATAAATATAATTTAATAAC-AT
1 TT-TTAAAATAATTATTATTAAATAACAAT
*
46689203 TTTTAATATAATTATTATTAAA
1 TTTTAAAATAATTATTATTAAA
46689225 ATATGAATTA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
28 17 0.44
29 20 0.51
30 2 0.05
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (29 bp):
TTTTAAAATAATTATTATTAAATAACAAT
Found at i:46692013 original size:22 final size:23
Alignment explanation
Indices: 46691983--46692037 Score: 94
Period size: 22 Copynumber: 2.4 Consensus size: 23
46691973 ACGCTAGCGC
46691983 GCTTACTGTTCAGCACTGTGTGT
1 GCTTACTGTTCAGCACTGTGTGT
46692006 GCTT-CTGTTCAGCACTGTGTGT
1 GCTTACTGTTCAGCACTGTGTGT
*
46692028 GCATACTGTT
1 GCTTACTGTT
46692038 TCCCCAGCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 21 0.70
23 9 0.30
ACGTcount: A:0.13, C:0.22, G:0.25, T:0.40
Consensus pattern (23 bp):
GCTTACTGTTCAGCACTGTGTGT
Found at i:46692083 original size:25 final size:25
Alignment explanation
Indices: 46692036--46692084 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
46692026 GTGCATACTG
**
46692036 TTTCCCCAGCACTTATGTGCTTCTA
1 TTTCCCCAGCACTTATGCACTTCTA
46692061 TTTCCCCAGCACTTATGCACTTCT
1 TTTCCCCAGCACTTATGCACTTCT
46692085 GTTAAGTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.16, C:0.35, G:0.10, T:0.39
Consensus pattern (25 bp):
TTTCCCCAGCACTTATGCACTTCTA
Found at i:46693581 original size:85 final size:86
Alignment explanation
Indices: 46693407--46693582 Score: 327
Period size: 85 Copynumber: 2.1 Consensus size: 86
46693397 AACGCTACAA
*
46693407 ACAATAAATTCCTGAGTGGTTAAAGAGTTGAACCATAAAAAAAAAAAGAATGGTAATGGCTTATC
1 ACAATAAATTCCTGAGTGGTTAAAGAGTTGAACCATAAAAAAAAAAAGAATGGCAATGGCTTATC
*
46693472 GTCTTCAACAAAAAATAAAAT
66 GTCTTCAACAAAAAAGAAAAT
46693493 ACAATAAATTCCTGAGTGGTTAAAGAGTTGAACCAT-AAAAAAAAAAGAATGGCAATGGCTTATC
1 ACAATAAATTCCTGAGTGGTTAAAGAGTTGAACCATAAAAAAAAAAAGAATGGCAATGGCTTATC
46693557 GTCTTCAACAAAAAAGAAAAT
66 GTCTTCAACAAAAAAGAAAAT
46693578 ACAAT
1 ACAAT
46693583 CTATCGAATA
Statistics
Matches: 88, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
85 52 0.59
86 36 0.41
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.23
Consensus pattern (86 bp):
ACAATAAATTCCTGAGTGGTTAAAGAGTTGAACCATAAAAAAAAAAAGAATGGCAATGGCTTATC
GTCTTCAACAAAAAAGAAAAT
Found at i:46695300 original size:28 final size:24
Alignment explanation
Indices: 46695243--46695289 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
46695233 AGAAATAATC
46695243 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
46695267 TTTCAATTAAACTCTGTTTATTT
1 TTTCAATTAAACTCTGTTTATTT
46695290 ATTTGAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.06, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:46695302 original size:24 final size:24
Alignment explanation
Indices: 46695243--46695305 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
46695233 AGAAATAATC
* *
46695243 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATCAAACTCTGTTTATTTA
*
46695267 TTTCAATTAAACTCTGTTTATTTA
1 TTTCAATCAAACTCTGTTTATTTA
* *
46695291 TTTGAGTCAAACTCT
1 TTTCAATCAAACTCT
46695306 TATTACTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.51
Consensus pattern (24 bp):
TTTCAATCAAACTCTGTTTATTTA
Found at i:46697203 original size:21 final size:23
Alignment explanation
Indices: 46697179--46697221 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
46697169 AGAAATAATC
46697179 TTTCAATTAAACT-T-TTTATTG
1 TTTCAATTAAACTCTGTTTATTG
46697200 TTTCAATTAAACTCTGTTTATT
1 TTTCAATTAAACTCTGTTTATT
46697222 TATTTGAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 13 0.65
22 1 0.05
23 6 0.30
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (23 bp):
TTTCAATTAAACTCTGTTTATTG
Found at i:46714197 original size:10 final size:9
Alignment explanation
Indices: 46714174--46714210 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
46714164 TTATTAACTT
46714174 AAAATTTTA
1 AAAATTTTA
46714183 AAAATTTTA
1 AAAATTTTA
*
46714192 AAAAATTT-
1 AAAATTTTA
46714200 -AAATTTTA
1 AAAATTTTA
46714208 AAA
1 AAA
46714211 GGTCGGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
7 6 0.25
9 18 0.75
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AAAATTTTA
Found at i:46714918 original size:2 final size:2
Alignment explanation
Indices: 46714911--46714941 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
46714901 TAGCAAGTTC
46714911 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46714942 CACAGTGTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46715167 original size:13 final size:14
Alignment explanation
Indices: 46715149--46715177 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
46715139 TATAAATATC
46715149 TTTTTTTTTGT-TT
1 TTTTTTTTTGTATT
46715162 TTTTTTTTTGTATT
1 TTTTTTTTTGTATT
46715176 TT
1 TT
46715178 ACATTTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.03, C:0.00, G:0.07, T:0.90
Consensus pattern (14 bp):
TTTTTTTTTGTATT
Found at i:46718577 original size:19 final size:19
Alignment explanation
Indices: 46718555--46718599 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
46718545 TTATATTAGG
46718555 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
46718574 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
46718593 ATTTAAT
1 ATTTAAT
46718600 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:46719422 original size:15 final size:16
Alignment explanation
Indices: 46719402--46719431 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46719392 CTTCCCTATT
46719402 TTCTA-TTTCTTTTAG
1 TTCTATTTTCTTTTAG
46719417 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
46719432 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAG
Found at i:46719436 original size:22 final size:22
Alignment explanation
Indices: 46719397--46719457 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
46719387 TTTGACTTCC
* *
46719397 CTATTTTCTATTT-CTTTTAGTT
1 CTATTTTCT-TTTATTTTTAATT
46719419 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTATTTTTAATT
46719441 CTGA--TTCTTTTATTTTT
1 CT-ATTTTCTTTTATTTTT
46719458 TCTTAGATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 16 0.46
22 18 0.51
23 1 0.03
ACGTcount: A:0.15, C:0.11, G:0.03, T:0.70
Consensus pattern (22 bp):
CTATTTTCTTTTATTTTTAATT
Found at i:46720774 original size:12 final size:12
Alignment explanation
Indices: 46720723--46720774 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
46720713 GAATTATTTG
46720723 AAATATTAATAT
1 AAATATTAATAT
46720735 AATTATATTAAT-T
1 AA--ATATTAATAT
* *
46720748 TAATATTAATTT
1 AAATATTAATAT
*
46720760 AAATATTGATAT
1 AAATATTAATAT
46720772 AAA
1 AAA
46720775 GTTTAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 8 0.24
12 15 0.45
13 2 0.06
14 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (12 bp):
AAATATTAATAT
Found at i:46723211 original size:20 final size:20
Alignment explanation
Indices: 46723182--46723219 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
46723172 AAAAGCTCTT
*
46723182 CGATTAGTCTCGTCGGATCC
1 CGATTAGTCTCGACGGATCC
*
46723202 CGATTTGTCTCGACGGAT
1 CGATTAGTCTCGACGGAT
46723220 GTTCTTCCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.32
Consensus pattern (20 bp):
CGATTAGTCTCGACGGATCC
Found at i:46724524 original size:17 final size:17
Alignment explanation
Indices: 46724502--46724534 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
46724492 ATTGTTTGGA
46724502 TATTA-TAACTTTTGTTT
1 TATTATTAA-TTTTGTTT
46724519 TATTATTAATTTTGTT
1 TATTATTAATTTTGTT
46724535 ACTATTTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (17 bp):
TATTATTAATTTTGTTT
Found at i:46726470 original size:20 final size:21
Alignment explanation
Indices: 46726445--46726498 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
46726435 AACCTGAGAC
*
46726445 TTCTACCGATAGAACGTCA-G
1 TTCTACCGATACAACGTCAGG
*
46726465 TTCTACCGATACAACTTCAGG
1 TTCTACCGATACAACGTCAGG
46726486 TT-TACCGATACAA
1 TTCTACCGATACAA
46726499 GTATGCTTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 28 0.90
21 3 0.10
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (21 bp):
TTCTACCGATACAACGTCAGG
Found at i:46732533 original size:2 final size:2
Alignment explanation
Indices: 46732528--46732574 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
46732518 TGAGAGAAAA
46732528 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
46732570 AG AG A
1 AG AG A
46732575 ATGTTGGGTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:46736366 original size:17 final size:16
Alignment explanation
Indices: 46736345--46736406 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
46736335 AAAAATATAA
46736345 AAAAAATAAAATTATT
1 AAAAAATAAAATTATT
46736361 ACAAAATTATAATAATTATT
1 A-AAAA--ATAA-AATTATT
* **
46736381 AATAAATAAAAAAATT
1 AAAAAATAAAATTATT
*
46736397 AAAAATTAAA
1 AAAAAATAAA
46736407 CAAAATACAT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
16 14 0.38
17 8 0.22
19 7 0.19
20 8 0.22
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAAAATAAAATTATT
Found at i:46736410 original size:45 final size:44
Alignment explanation
Indices: 46736319--46736412 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 44
46736309 AAAATAATTT
* *
46736319 AAAATTTAAAATTGTTAAAAATATAAAAAAAATAAAATTATTAC
1 AAAATTTAAAATTATTAAAAATATAAAAAAAATAAAATTATAAC
* *
46736363 AAAATTATAATAATTATTAATAA-ATAAAAAAATTAAAAATTA-AAC
1 AAAATT-TAA-AATTATTAAAAATATAAAAAAAAT-AAAATTATAAC
46736408 AAAAT
1 AAAAT
46736413 ACATAACTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
44 6 0.14
45 20 0.47
46 17 0.40
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (44 bp):
AAAATTTAAAATTATTAAAAATATAAAAAAAATAAAATTATAAC
Found at i:46739572 original size:6 final size:6
Alignment explanation
Indices: 46739561--46739586 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
46739551 GTACATCAAA
46739561 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
46739587 GATGGATCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:46752842 original size:15 final size:15
Alignment explanation
Indices: 46752819--46752850 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
46752809 AATTTTGTTT
*
46752819 AAGAGAAAAAGAAAA
1 AAGAAAAAAAGAAAA
46752834 AAGAAAAAAAGAAAA
1 AAGAAAAAAAGAAAA
46752849 AA
1 AA
46752851 AACATAATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAGAAAA
Found at i:46752852 original size:9 final size:8
Alignment explanation
Indices: 46752819--46752851 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
46752809 AATTTTGTTT
*
46752819 AAGAGAAA
1 AAGAAAAA
46752827 AAG-AAAA
1 AAGAAAAA
46752834 AAGAAAAA
1 AAGAAAAA
46752842 AAGAAAAA
1 AAGAAAAA
46752850 AA
1 AA
46752852 ACATAATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:46760389 original size:61 final size:61
Alignment explanation
Indices: 46760153--46760950 Score: 875
Period size: 61 Copynumber: 13.2 Consensus size: 61
46760143 ATTTCGCTAG
* * * *
46760153 CAGTAGAATATCAGTGAGTCAATT-AGCTCCTTTCGTAGTTACATATCTGAA-TTGGCCCT
1 CAGTAGAATATCAGTGAGTCAATTCAGTTCCTTTCATAGTTACATAGCTGAATTTGGCTCT
* * * * * * **
46760212 CAGTAGCATATCAGTGAGCCAAGTCAGCTCCTTTCATAGTTAGATAGCTGAATTTTCGCTAG
1 CAGTAGAATATCAGTGAGTCAATTCAGTTCCTTTCATAGTTACATAGCTGAA-TTTGGCTCT
* * **
46760274 CAGTAGAATATCAGTGAGCCAATTCAGTTTTCTTTCATAGTTACATAGCTGAATTCAGCTCT
1 CAGTAGAATATCAGTGAGTCAATTCAG-TTCCTTTCATAGTTACATAGCTGAATTTGGCTCT
* *
46760336 CAGTAGAATATCAGTGAGTCAATTAAGTTCCTTTCATAGTTAGATAGCTGAATTTGGCTCT
1 CAGTAGAATATCAGTGAGTCAATTCAGTTCCTTTCATAGTTACATAGCTGAATTTGGCTCT
* * *
46760397 CAGTAGAATATCAGTGAGTCAATTCA-TCCCCTTTCATAGTCAGATAGCTGAATTTGGCTC-
1 CAGTAGAATATCAGTGAGTCAATTCAGT-TCCTTTCATAGTTACATAGCTGAATTTGGCTCT
* * * * * * *
46760457 GA-TAGCATAACAGTGAGCCAATTCAGCTCCTTTCATAG-TAGATAGCTGAATTTGGCTAT
1 CAGTAGAATATCAGTGAGTCAATTCAGTTCCTTTCATAGTTACATAGCTGAATTTGGCTCT
* * *
46760516 CAGTAGAATATCAGTGAGCCAATTCAGTTCCTTTCATAGTTACATAGCTAAATTCGGCTCT
1 CAGTAGAATATCAGTGAGTCAATTCAGTTCCTTTCATAGTTACATAGCTGAATTTGGCTCT
* * *
46760577 CAGTAGAATATCAGTGAGTCAATTAAGTTCCTTTCATAGTTAGAAAGCTGAATTTGGCTCT
1 CAGTAGAATATCAGTGAGTCAATTCAGTTCCTTTCATAGTTACATAGCTGAATTTGGCTCT
* * * * *
46760638 AAGTAGACTATCAGTGAGTCAATTCAGCTCCTTCCATAGATACATAGCTGAATTTGGCTCT
1 CAGTAGAATATCAGTGAGTCAATTCAGTTCCTTTCATAGTTACATAGCTGAATTTGGCTCT
* *
46760699 CAGTAGAATATCA---AGTCAATTCAG-CCTCTTTCATAGTTAGATAGCTGAATTTGGCTCT
1 CAGTAGAATATCAGTGAGTCAATTCAGTTC-CTTTCATAGTTACATAGCTGAATTTGGCTCT
* * * * * * * *
46760757 TAGTATAAAATCAATGAGCCAATTAAGTTCCTTTCAAAGTTACATAGCTGATTTTGGCTCT
1 CAGTAGAATATCAGTGAGTCAATTCAGTTCCTTTCATAGTTACATAGCTGAATTTGGCTCT
* * * * ** * *
46760818 AAGTA-ATACATAAGTCAACCAATTCCAGTTCCTTCCATAGTTACATA-CTGAATTCGGCTCT
1 CAGTAGA-ATATCAGTGAGTCAATT-CAGTTCCTTTCATAGTTACATAGCTGAATTTGGCTCT
* * * * *
46760879 CAGTACAA-ATCAGTGAATCAATTAAGTTCCTTTCCTAGTTTACATAGTTGAATTTGGCTCT
1 CAGTAGAATATCAGTGAGTCAATTCAGTTCCTTTCATAG-TTACATAGCTGAATTTGGCTCT
*
46760940 CAGTGGAATAT
1 CAGTAGAATAT
46760951 ATCAGAGAGA
Statistics
Matches: 624, Mismatches: 95, Indels: 37
0.83 0.13 0.05
Matches are distributed among these distances:
57 1 0.00
58 67 0.11
59 64 0.10
60 79 0.13
61 309 0.50
62 82 0.13
63 22 0.04
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (61 bp):
CAGTAGAATATCAGTGAGTCAATTCAGTTCCTTTCATAGTTACATAGCTGAATTTGGCTCT
Found at i:46760554 original size:180 final size:182
Alignment explanation
Indices: 46760153--46760950 Score: 893
Period size: 180 Copynumber: 4.4 Consensus size: 182
46760143 ATTTCGCTAG
* * * *
46760153 CAGTAGAATATCAGTGAGTCAATT-AGCTCCTTTCGTAGTTACATATCTGAA-TTGGCCCTCAGT
1 CAGTAGAATATCAGTGAGTCAATTAAGTTCCTTTCATAGTTACATAGCTGAATTTGGCTCTCAGT
* * * * * *
46760216 AGCATATCAGTGAGCCAAGTCAGCTCCTTTCATAGTTAGATAGCTGAATTTTCGCTAGCAGTAGA
66 AGAATATCAGTGAGCCAATTAAGTTCCTTTCATAGTTAGATAGCTGAA-TTTGGCTCG-AGTAGA
* * * * **
46760281 ATATCAGTGAGCCAATTCAGTTTTCTTTCATAGTTACATAGCTGAATTCAGCTCT
129 ATAACAGTGAGCCAATTCAG-CTCCTTCCATAGTTACATAGCTGAATTTGGCTCT
*
46760336 CAGTAGAATATCAGTGAGTCAATTAAGTTCCTTTCATAGTTAGATAGCTGAATTTGGCTCTCAGT
1 CAGTAGAATATCAGTGAGTCAATTAAGTTCCTTTCATAGTTACATAGCTGAATTTGGCTCTCAGT
* * * * *
46760401 AGAATATCAGTGAGTCAATTCA-TCCCCTTTCATAGTCAGATAGCTGAATTTGGCTCGA-TAGCA
66 AGAATATCAGTGAGCCAATTAAGT-TCCTTTCATAGTTAGATAGCTGAATTTGGCTCGAGTAGAA
* * *
46760464 TAACAGTGAGCCAATTCAGCTCCTTTCATAG-TAGATAGCTGAATTTGGCTAT
130 TAACAGTGAGCCAATTCAGCTCCTTCCATAGTTACATAGCTGAATTTGGCTCT
* * * *
46760516 CAGTAGAATATCAGTGAGCCAATTCAGTTCCTTTCATAGTTACATAGCTAAATTCGGCTCTCAGT
1 CAGTAGAATATCAGTGAGTCAATTAAGTTCCTTTCATAGTTACATAGCTGAATTTGGCTCTCAGT
* * * *
46760581 AGAATATCAGTGAGTCAATTAAGTTCCTTTCATAGTTAGAAAGCTGAATTTGGCTCTAAGTAGAC
66 AGAATATCAGTGAGCCAATTAAGTTCCTTTCATAGTTAGATAGCTGAATTTGGCTC-GAGTAGAA
* * *
46760646 TATCAGTGAGTCAATTCAGCTCCTTCCATAGATACATAGCTGAATTTGGCTCT
130 TAACAGTGAGCCAATTCAGCTCCTTCCATAGTTACATAGCTGAATTTGGCTCT
* * * *
46760699 CAGTAGAATATCA---AGTCAATTCAG-CCTCTTTCATAGTTAGATAGCTGAATTTGGCTCTTAG
1 CAGTAGAATATCAGTGAGTCAATTAAGTTC-CTTTCATAGTTACATAGCTGAATTTGGCTCTCAG
* * * * * * *
46760760 TATAAAATCAATGAGCCAATTAAGTTCCTTTCAAAGTTACATAGCTGATTTTGGCTCTA--AGTA
65 TAGAATATCAGTGAGCCAATTAAGTTCCTTTCATAGTTAGATAGCTGAATTTGGCTCGAGTAG-A
* * * * *
46760823 ATACATAAGTCAACCAATTCCAGTTCCTTCCATAGTTACATA-CTGAATTCGGCTCT
129 ATA-A-CAGTGAGCCAATT-CAGCTCCTTCCATAGTTACATAGCTGAATTTGGCTCT
* * * *
46760879 CAGTACAA-ATCAGTGAATCAATTAAGTTCCTTTCCTAGTTTACATAGTTGAATTTGGCTCTCAG
1 CAGTAGAATATCAGTGAGTCAATTAAGTTCCTTTCATAG-TTACATAGCTGAATTTGGCTCTCAG
*
46760943 TGGAATAT
65 TAGAATAT
46760951 ATCAGAGAGA
Statistics
Matches: 525, Mismatches: 73, Indels: 34
0.83 0.12 0.05
Matches are distributed among these distances:
177 2 0.00
178 3 0.01
179 6 0.01
180 245 0.47
181 32 0.06
182 70 0.13
183 85 0.16
184 30 0.06
185 52 0.10
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (182 bp):
CAGTAGAATATCAGTGAGTCAATTAAGTTCCTTTCATAGTTACATAGCTGAATTTGGCTCTCAGT
AGAATATCAGTGAGCCAATTAAGTTCCTTTCATAGTTAGATAGCTGAATTTGGCTCGAGTAGAAT
AACAGTGAGCCAATTCAGCTCCTTCCATAGTTACATAGCTGAATTTGGCTCT
Found at i:46760939 original size:241 final size:242
Alignment explanation
Indices: 46760153--46760950 Score: 988
Period size: 241 Copynumber: 3.3 Consensus size: 242
46760143 ATTTCGCTAG
* * *
46760153 CAGTAGAATATCAGTGAGTCAATT-AGCTCCTTTCGTAGTTACATATCTGAA-TTGGCCCTCAGT
1 CAGTAGAATATCAGTGAGTCAATTCAGCTCCTTTCCTAGTTACATAGCTGAATTTGGCTCTCAGT
* * * *
46760216 AGCATATCAGTGAGCCAAGTCAGCTCCTTTCATAGTTAGATAGCTGAATTTTCGCTAGCAGTAGA
66 AGAATATCA--GAGCCAATTCAGCTCCTTTCATAGTTAGATAGCTGAA-TTTGGCTATCAGTAGA
* *
46760281 ATATCAGTGAGCCAATTCAGTTTTCTTTCATAGTTACATAGCTGAATTCAGCTCTCAGTAGAATA
128 ATATCAGTGAGCCAATTCAG-TTCCTTTCATAGTTACATAGCTGAATTCGGCTCTCAGTAGAATA
46760346 TCAGTGAGTCAATTAAGTTCCTTTCATAGTTAGATAGCTGAATTTGGCTCT
192 TCAGTGAGTCAATTAAGTTCCTTTCATAGTTAGATAGCTGAATTTGGCTCT
* * * * * *
46760397 CAGTAGAATATCAGTGAGTCAATTCATCCCCTTTCATAGTCAGATAGCTGAATTTGGCTC-GA-T
1 CAGTAGAATATCAGTGAGTCAATTCAGCTCCTTTCCTAGTTACATAGCTGAATTTGGCTCTCAGT
* *
46760460 AGCATAACAGTGAGCCAATTCAGCTCCTTTCATAG-TAGATAGCTGAATTTGGCTATCAGTAGAA
66 AGAATATCA--GAGCCAATTCAGCTCCTTTCATAGTTAGATAGCTGAATTTGGCTATCAGTAGAA
*
46760524 TATCAGTGAGCCAATTCAGTTCCTTTCATAGTTACATAGCTAAATTCGGCTCTCAGTAGAATATC
129 TATCAGTGAGCCAATTCAGTTCCTTTCATAGTTACATAGCTGAATTCGGCTCTCAGTAGAATATC
*
46760589 AGTGAGTCAATTAAGTTCCTTTCATAGTTAGAAAGCTGAATTTGGCTCT
194 AGTGAGTCAATTAAGTTCCTTTCATAGTTAGATAGCTGAATTTGGCTCT
* * *
46760638 AAGTAGACTATCAGTGAGTCAATTCAGCTCC-TTCCATAGATACATAGCTGAATTTGGCTCTCAG
1 CAGTAGAATATCAGTGAGTCAATTCAGCTCCTTTCC-TAGTTACATAGCTGAATTTGGCTCTCAG
* * * *
46760702 TAGAATATCA-AGTCAATTCAGC-CTCTTTCATAGTTAGATAGCTGAATTTGGCTCTTAGTATAA
65 TAGAATATCAGAGCCAATTCAGCTC-CTTTCATAGTTAGATAGCTGAATTTGGCTATCAGTAGAA
* * * * * * * *
46760765 AATCAATGAGCCAATTAAGTTCCTTTCAAAGTTACATAGCTGATTTTGGCTCTAAGTA-ATACAT
129 TATCAGTGAGCCAATTCAGTTCCTTTCATAGTTACATAGCTGAATTCGGCTCTCAGTAGA-ATAT
* * ** * * * *
46760829 AAGTCAACCAATTCCAGTTCCTTCCATAGTTACATA-CTGAATTCGGCTCT
193 CAGTGAGTCAATT-AAGTTCCTTTCATAGTTAGATAGCTGAATTTGGCTCT
* * * * *
46760879 CAGTACAA-ATCAGTGAATCAATTAAGTTCCTTTCCTAGTTTACATAGTTGAATTTGGCTCTCAG
1 CAGTAGAATATCAGTGAGTCAATTCAGCTCCTTTCCTAG-TTACATAGCTGAATTTGGCTCTCAG
*
46760943 TGGAATAT
65 TAGAATAT
46760951 ATCAGAGAGA
Statistics
Matches: 485, Mismatches: 58, Indels: 25
0.85 0.10 0.04
Matches are distributed among these distances:
239 1 0.00
240 46 0.09
241 279 0.58
242 53 0.11
243 20 0.04
244 58 0.12
245 22 0.05
246 6 0.01
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (242 bp):
CAGTAGAATATCAGTGAGTCAATTCAGCTCCTTTCCTAGTTACATAGCTGAATTTGGCTCTCAGT
AGAATATCAGAGCCAATTCAGCTCCTTTCATAGTTAGATAGCTGAATTTGGCTATCAGTAGAATA
TCAGTGAGCCAATTCAGTTCCTTTCATAGTTACATAGCTGAATTCGGCTCTCAGTAGAATATCAG
TGAGTCAATTAAGTTCCTTTCATAGTTAGATAGCTGAATTTGGCTCT
Found at i:46778412 original size:15 final size:16
Alignment explanation
Indices: 46778381--46778414 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
46778371 TTAGTTTCGT
46778381 GTTCAGATCATTTTGG
1 GTTCAGATCATTTTGG
*
46778397 GTTCAGGTCA-TTTGG
1 GTTCAGATCATTTTGG
46778412 GTT
1 GTT
46778415 TGCCAGTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.15, C:0.12, G:0.29, T:0.44
Consensus pattern (16 bp):
GTTCAGATCATTTTGG
Found at i:46794103 original size:29 final size:29
Alignment explanation
Indices: 46794046--46794135 Score: 101
Period size: 31 Copynumber: 3.0 Consensus size: 29
46794036 AATAATAGTC
* **
46794046 ACTAAACTTTTATTAAAATAACATTTCAATT
1 ACTAAACTTTCA--AAAATAACAAATCAATT
46794077 ACTAAACTTTCAAAAATAACAAATCAATT
1 ACTAAACTTTCAAAAATAACAAATCAATT
46794106 ACT-AACGTTTTCAAAAAATAACAAATCAAT
1 ACTAAAC--TTTC-AAAAATAACAAATCAAT
46794136 CATCTAAGTA
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
28 3 0.06
29 18 0.34
30 4 0.08
31 28 0.53
ACGTcount: A:0.51, C:0.16, G:0.01, T:0.32
Consensus pattern (29 bp):
ACTAAACTTTCAAAAATAACAAATCAATT
Found at i:46796268 original size:28 final size:28
Alignment explanation
Indices: 46796237--46796325 Score: 85
Period size: 28 Copynumber: 3.1 Consensus size: 28
46796227 AAAACGGGAC
**
46796237 TTTTGGATACCCGGGGGTAAAATGGTAA
1 TTTTGGATAATCGGGGGTAAAATGGTAA
* *
46796265 TTTTGG-TGAAATTGGGGTTAAAATGG-AA
1 TTTTGGAT--AATCGGGGGTAAAATGGTAA
46796293 TTTTGGA-AAGTTCGGGGGTAAAATGGTAA
1 TTTTGGATAA--TCGGGGGTAAAATGGTAA
46796322 TTTT
1 TTTT
46796326 TAGTGAAATC
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
26 2 0.04
27 1 0.02
28 27 0.55
29 19 0.39
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.35
Consensus pattern (28 bp):
TTTTGGATAATCGGGGGTAAAATGGTAA
Found at i:46796286 original size:29 final size:28
Alignment explanation
Indices: 46796249--46796408 Score: 112
Period size: 29 Copynumber: 5.5 Consensus size: 28
46796239 TTGGATACCC
46796249 GGGGGTAAAATGGTAATTTTGGTGAAATT
1 GGGGGTAAAATGGTAATTTT-GTGAAATT
*
46796278 GGGGTTAAAATGG-AATTTTG-GAAAGTT
1 GGGGGTAAAATGGTAATTTTGTGAAA-TT
*
46796305 CGGGGGTAAAATGGTAATTTTTAGTGAAATC
1 -GGGGGTAAAATGGTAA-TTTT-GTGAAATT
* * * **
46796336 GAGGTTAAAAAT-GAAATTTT-AAAAGATT
1 GGGGGT-AAAATGGTAATTTTGTGAA-ATT
*
46796364 CGGGGGTAAAATGGTAATTTTCGGTGAAATC
1 -GGGGGTAAAATGGTAATTTT--GTGAAATT
*
46796395 GGGGTTGAAAATGG
1 GGGGGT-AAAATGG
46796409 GATTTAGGGA
Statistics
Matches: 101, Mismatches: 16, Indels: 26
0.71 0.11 0.18
Matches are distributed among these distances:
26 4 0.04
27 5 0.05
28 25 0.25
29 29 0.29
30 16 0.16
31 16 0.16
32 6 0.06
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.31
Consensus pattern (28 bp):
GGGGGTAAAATGGTAATTTTGTGAAATT
Found at i:46796428 original size:59 final size:57
Alignment explanation
Indices: 46796248--46796445 Score: 231
Period size: 59 Copynumber: 3.4 Consensus size: 57
46796238 TTTGGATACC
* *
46796248 CGGGGGTAAAATGGTAATTTTGGTGAAATTGGGGTTAAAATGGAATTTTGGAAAGTT
1 CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAATGGAATTTAGGAAAGTT
* * *
46796305 CGGGGGTAAAATGGTAATTTTTAGTGAAATCGAGGTTAAAAATGAAATTTTA--AAAGATT
1 CGGGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTT-AAAATGGAA-TTTAGGAAAG-TT
* *
46796364 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTGAAAATGGGATTTAGGGAAGTT
1 CGGGGGTAAAATGGTAATTTT-GGTGAAATCGGGGTT-AAAATGGAATTTAGGAAAGTT
* *
46796423 TGGGGGTCAAGAT-GTAATTTTGG
1 CGGGGGT-AAAATGGTAATTTTGG
46796446 AAAAGTTTTG
Statistics
Matches: 120, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
57 17 0.14
58 30 0.25
59 63 0.52
60 10 0.08
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.32
Consensus pattern (57 bp):
CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAATGGAATTTAGGAAAGTT
Found at i:46796669 original size:30 final size:30
Alignment explanation
Indices: 46796418--46796653 Score: 348
Period size: 30 Copynumber: 7.9 Consensus size: 30
46796408 GGATTTAGGG
* *
46796418 AAGTTTGGGGGTCAAGATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
*
46796448 AAGTTTTGGGGTCAAATTGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
* *
46796478 AAGTTTTAGGGCCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
* *
46796508 AAGTTTTGGGGCCAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
46796538 AAGTTTTGGGGTCAAAATGTAATTTTAGG-A
1 AAGTTTTGGGGTCAAAATGTAATTTT-GGAA
*
46796568 AAGTTTTGGGGTCAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
***
46796598 AAGTTTTGGGGTCAAAATGTAATTTCAAAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
*
46796628 AAGTTTTGGGGTCAAAATATAATTTT
1 AAGTTTTGGGGTCAAAATGTAATTTT
46796654 TGGATAATTT
Statistics
Matches: 187, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
29 2 0.01
30 183 0.98
31 2 0.01
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (30 bp):
AAGTTTTGGGGTCAAAATGTAATTTTGGAA
Found at i:46797636 original size:3 final size:3
Alignment explanation
Indices: 46797630--46797700 Score: 52
Period size: 3 Copynumber: 22.7 Consensus size: 3
46797620 GTTTTTTTTA
* * * * *
46797630 TAT TAT TAT TAT TAT TAT TAT TAAC TAT AAT CAT AAA TAT TAAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT T-AT TAT
* *
46797677 AAT TAT TAAT TAT TAT GAT TAT TA
1 TAT TAT T-AT TAT TAT TAT TAT TA
46797701 ATAATACTTT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
3 45 0.85
4 8 0.15
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (3 bp):
TAT
Found at i:46798263 original size:27 final size:29
Alignment explanation
Indices: 46798230--46798292 Score: 94
Period size: 27 Copynumber: 2.2 Consensus size: 29
46798220 GTATTGGGCC
46798230 TATTTGGGCCATTGTAATCGGGCC-TTTG
1 TATTTGGGCCATTGTAATCGGGCCTTTTG
* *
46798258 -ATTTGGGCCTTTGTAATTGGGCCTTTTG
1 TATTTGGGCCATTGTAATCGGGCCTTTTG
46798286 TATTTGG
1 TATTTGG
46798293 ACTCTGGACT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 21 0.68
28 4 0.13
29 6 0.19
ACGTcount: A:0.13, C:0.14, G:0.29, T:0.44
Consensus pattern (29 bp):
TATTTGGGCCATTGTAATCGGGCCTTTTG
Found at i:46798292 original size:15 final size:14
Alignment explanation
Indices: 46798230--46798292 Score: 74
Period size: 14 Copynumber: 4.5 Consensus size: 14
46798220 GTATTGGGCC
*
46798230 TATTTGGGCCATTG
1 TATTTGGGCCTTTG
* *
46798244 TAATCGGGCCTTTG
1 TATTTGGGCCTTTG
46798258 -ATTTGGGCCTTTG
1 TATTTGGGCCTTTG
*
46798271 TAATTGGGCCTTTTG
1 TATTTGGGCC-TTTG
46798286 TATTTGG
1 TATTTGG
46798293 ACTCTGGACT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
13 11 0.28
14 19 0.47
15 10 0.25
ACGTcount: A:0.13, C:0.14, G:0.29, T:0.44
Consensus pattern (14 bp):
TATTTGGGCCTTTG
Found at i:46798363 original size:17 final size:16
Alignment explanation
Indices: 46798333--46798372 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
46798323 AATTTATTCC
46798333 AAATTT-ACCAAATTT
1 AAATTTAACCAAATTT
46798348 AAATTTAACACAAATTT
1 AAATTTAAC-CAAATTT
46798365 AAATTTAA
1 AAATTTAA
46798373 AAATTGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 6 0.26
16 2 0.09
17 15 0.65
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTTAACCAAATTT
Found at i:46798403 original size:18 final size:18
Alignment explanation
Indices: 46798382--46798430 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
46798372 AAAATTGATT
46798382 TAAATTTAAATTT-TAAGA
1 TAAATTTAAATTTGTAA-A
**
46798400 TAAATCCAAATTTGTAAA
1 TAAATTTAAATTTGTAAA
46798418 TAAATTTAGAATT
1 TAAATTTA-AATT
46798431 AACTTAAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (18 bp):
TAAATTTAAATTTGTAAA
Found at i:46801332 original size:15 final size:16
Alignment explanation
Indices: 46801302--46801335 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
46801292 AAACATTAAT
46801302 TTTATCATTTTAATAA
1 TTTATCATTTTAATAA
*
46801318 TTTAT-ATTTTTATAA
1 TTTATCATTTTAATAA
46801333 TTT
1 TTT
46801336 TTAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATCATTTTAATAA
Found at i:46806668 original size:20 final size:20
Alignment explanation
Indices: 46806643--46806685 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
46806633 CTCATCCCCA
*
46806643 CCCGCCCCATCCTCGCACGC
1 CCCGCCCCATCCCCGCACGC
*
46806663 CCCGCCCCATCCCCGCTCGC
1 CCCGCCCCATCCCCGCACGC
46806683 CCC
1 CCC
46806686 TTTAAACTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.07, C:0.70, G:0.14, T:0.09
Consensus pattern (20 bp):
CCCGCCCCATCCCCGCACGC
Found at i:46808127 original size:16 final size:18
Alignment explanation
Indices: 46808101--46808133 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
46808091 AAAAAATATA
46808101 AAAATTATTTA-AAATTC
1 AAAATTATTTATAAATTC
46808118 AAAA-TATTTATAAATT
1 AAAATTATTTATAAATT
46808134 TTTTGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATTATTTATAAATTC
Found at i:46808181 original size:8 final size:8
Alignment explanation
Indices: 46808168--46808193 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
46808158 ATAAATAAAG
46808168 TTAAAATT
1 TTAAAATT
46808176 TTAAAATT
1 TTAAAATT
46808184 TTAAAATT
1 TTAAAATT
46808192 TT
1 TT
46808194 TCTAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TTAAAATT
Found at i:46808726 original size:22 final size:21
Alignment explanation
Indices: 46808700--46808740 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
46808690 TTTATTATTT
*
46808700 TTATTGTCAAAGTACAATTTCA
1 TTATTATCAAAGTA-AATTTCA
*
46808722 TTATTATCAATGTAAATTT
1 TTATTATCAAAGTAAATTT
46808741 TATAAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (21 bp):
TTATTATCAAAGTAAATTTCA
Found at i:46808853 original size:37 final size:37
Alignment explanation
Indices: 46808803--46808880 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
46808793 GCAGCCCCTG
46808803 CTCCACCATGGTAGATTGTCACAATAATAATGTATAA
1 CTCCACCATGGTAGATTGTCACAATAATAATGTATAA
46808840 CTCCACCATGGTAGATTGTCACAATAATAATGTATAA
1 CTCCACCATGGTAGATTGTCACAATAATAATGTATAA
46808877 CTCC
1 CTCC
46808881 TAGTTGTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (37 bp):
CTCCACCATGGTAGATTGTCACAATAATAATGTATAA
Found at i:46809240 original size:32 final size:32
Alignment explanation
Indices: 46809204--46809266 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
46809194 AATTAAATTA
* *
46809204 AATTAACATTTAATGTATAGTATTGTACATTG
1 AATTAAAAGTTAATGTATAGTATTGTACATTG
* * *
46809236 AATTAAAAGTTCATGTTTAGTTTTGTACATT
1 AATTAAAAGTTAATGTATAGTATTGTACATT
46809267 ATCCTTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (32 bp):
AATTAAAAGTTAATGTATAGTATTGTACATTG
Found at i:46809770 original size:32 final size:32
Alignment explanation
Indices: 46809700--46809777 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 32
46809690 AGTACCTTAA
* * * *
46809700 ATAATTTTTTTTGAATAGTTTAGTGACTTAAAT
1 ATAA-TTTTTTTAAATAATTTAATGACTCAAAT
46809733 A-AATTTTTTTAAATAATTTAATGA-TCAAATT
1 ATAATTTTTTTAAATAATTTAATGACTCAAA-T
46809764 ATAA-TTTTTTAAAT
1 ATAATTTTTTTAAAT
46809778 TAAGTGATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 4 0.10
31 30 0.77
32 4 0.10
33 1 0.03
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (32 bp):
ATAATTTTTTTAAATAATTTAATGACTCAAAT
Found at i:46817118 original size:15 final size:16
Alignment explanation
Indices: 46817088--46817121 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
46817078 AAAATGTAAT
46817088 TTTATCATTTTAATAA
1 TTTATCATTTTAATAA
*
46817104 TTTAT-ATTTTTATAA
1 TTTATCATTTTAATAA
46817119 TTT
1 TTT
46817122 TTATGGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATCATTTTAATAA
Found at i:46818828 original size:307 final size:308
Alignment explanation
Indices: 46818264--46818884 Score: 1149
Period size: 307 Copynumber: 2.0 Consensus size: 308
46818254 CAAGTGAGTA
46818264 TTTTG-TTTATTTCAAAATGTCATACTAATAAATTTAACAAAAGAAATTAACAGAGTTAATAATT
1 TTTTGTTTTATTTCAAAATGTCATACTAATAAATTTAACAAAAGAAATTAACAGAGTTAATAATT
46818328 AGATTTGAATTTTGAAATCTGAAAGTAAAGAGACTAATTTCTTAAAAATAAAAATAAATAACTAA
66 AGATTTGAATTTTGAAATCTGAAAGTAAAGAGACTAATTTCTTAAAAATAAAAATAAATAACTAA
*
46818393 ATTCTAAATTTATGAAGAGTGCATACATATTCAAGGTTGCGAATCAGGATTGTATGCAAAATAAA
131 ATTCTAAATTTATGAAGAGTGCATACATATTCAAGGTTGCGAATCAGGATCGTATGCAAAATAAA
*
46818458 AATGGACTGAATTTGACAAGATTTTCAATTTTGGAGCATGCATTATAATAAAAATTGCAGGTGTA
196 AATGGACTGAATTTGACAAGATTTTCAATTTTGGAGCATGCATTATAATAAAAATTACAGGTGTA
* *
46818523 GAATTGTAATTTTAATGATTTATAAGGGAGCTGATGTAATTTTTCAT-
261 GAATTGCAATTTTAATGATTTATAAGGGAGCTGATGTAATTTTCCATC
46818570 TTTTGTTTTATTTCAAAATGTCATACTAATAAATTTAACAAAAGAAATTAACAGAGTTAATAATT
1 TTTTGTTTTATTTCAAAATGTCATACTAATAAATTTAACAAAAGAAATTAACAGAGTTAATAATT
*
46818635 AGATTTGAATTTTGAAATCTGAAAGTAAAGAGACTAATTTCTTAAAAAT-AAAATATAATAATTA
66 AGATTTGAATTTTGAAATCTGAAAGTAAAGAGACTAATTTCTTAAAAATAAAAATA-AATAACTA
*
46818699 AATTCTAAATTTATGAAGAGTGCATACATTTTCAAGGTTGCGAATCAGGATCGTATGCAAAATAA
130 AATTCTAAATTTATGAAGAGTGCATACATATTCAAGGTTGCGAATCAGGATCGTATGCAAAATAA
*
46818764 AAATGGACTGAATTTGACAAGATTTTCAATTTTGGAGCATGCATTGTAATAAAAATTACAGGTGT
195 AAATGGACTGAATTTGACAAGATTTTCAATTTTGGAGCATGCATTATAATAAAAATTACAGGTGT
46818829 AGAATTGCAATTTTAATGATTTATAAGGGAGCTGATGTAATTTTCCATC
260 AGAATTGCAATTTTAATGATTTATAAGGGAGCTGATGTAATTTTCCATC
46818878 TTTTGTT
1 TTTTGTT
46818885 CCCTTGTATT
Statistics
Matches: 305, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
306 11 0.04
307 287 0.94
308 7 0.02
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (308 bp):
TTTTGTTTTATTTCAAAATGTCATACTAATAAATTTAACAAAAGAAATTAACAGAGTTAATAATT
AGATTTGAATTTTGAAATCTGAAAGTAAAGAGACTAATTTCTTAAAAATAAAAATAAATAACTAA
ATTCTAAATTTATGAAGAGTGCATACATATTCAAGGTTGCGAATCAGGATCGTATGCAAAATAAA
AATGGACTGAATTTGACAAGATTTTCAATTTTGGAGCATGCATTATAATAAAAATTACAGGTGTA
GAATTGCAATTTTAATGATTTATAAGGGAGCTGATGTAATTTTCCATC
Found at i:46819719 original size:42 final size:43
Alignment explanation
Indices: 46819656--46819751 Score: 149
Period size: 43 Copynumber: 2.3 Consensus size: 43
46819646 TCGCGGTGTT
* *
46819656 TATGGTCTTTAGCGGCGCTTTT-CCATAAACGCCGCTAAAGAA
1 TATGGTCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGAA
*
46819698 TATGGTCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGAC
1 TATGGTCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGAA
*
46819741 TATGTTCTTTA
1 TATGGTCTTTA
46819752 CTTTGTTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 21 0.43
43 28 0.57
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (43 bp):
TATGGTCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGAA
Found at i:46822002 original size:93 final size:89
Alignment explanation
Indices: 46821894--46822073 Score: 234
Period size: 93 Copynumber: 2.0 Consensus size: 89
46821884 TATCTGATAA
* **
46821894 AAAAATTCAATTTTTTTGTGTTGGCCATTGCATGTCCGACACCACCTTTTTATCTAATAAAAAAT
1 AAAAATTCAATTTTTTGGTGTTGGCCATTGCATAACCGACACCACCTTTTTATCTAATAAAAAAT
46821959 TTAAATTTTTCTTGTGTCGGCCATGC
66 TTAAA-TTTT-TTGTGTCGGCCATGC
* * * * *
46821985 AAAAATTCAAATCTTTTTGGTGTTGGCTATTGCATAACCGACATCACCTTTTTATTTGATAAGAA
1 AAAAATTC-AAT-TTTTTGGTGTTGGCCATTGCATAACCGACACCACCTTTTTATCTAATAAAAA
* *
46822050 TTTTAAATTTTTTGTGTTGGCCAT
64 ATTTAAATTTTTTGTGTCGGCCAT
46822074 TGCATGACCG
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
91 20 0.26
92 7 0.09
93 50 0.65
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (89 bp):
AAAAATTCAATTTTTTGGTGTTGGCCATTGCATAACCGACACCACCTTTTTATCTAATAAAAAAT
TTAAATTTTTTGTGTCGGCCATGC
Found at i:46822150 original size:62 final size:62
Alignment explanation
Indices: 46822056--46822328 Score: 315
Period size: 62 Copynumber: 4.4 Consensus size: 62
46822046 AGAATTTTAA
* * *
46822056 ATTTTTT-GTGTTGGCCATTGCA-TGACCGACACCACCTTTTTATCTAATAAAAAAATTCAAT
1 ATTTTTTCGTGTTGGTCA-TGCATTGGCCGACACCACCTATTTATCTAATAAAAAAATTCAAT
* * * *
46822117 TTTTTTTAGTGTTGATCATGCATTGGCCGACACCACCTATTTATCTGATAAAAAAA-TCAA-
1 ATTTTTTCGTGTTGGTCATGCATTGGCCGACACCACCTATTTATCTAATAAAAAAATTCAAT
* * * *
46822177 ATTTTTTCGTGTTGGTCATTGCA-TGGGCAACACCACCTTTTTATCTAATAAAAAAAATTCAAA
1 ATTTTTTCGTGTTGGTCA-TGCATTGGCCGACACCACCTATTTATCTAAT-AAAAAAATTCAAT
* * *
46822240 ATTTTTTCGTGTTGGCCATGCATTGGCTGACACCACCTATTTATCTGATAAAAAAATTCAA-
1 ATTTTTTCGTGTTGGTCATGCATTGGCCGACACCACCTATTTATCTAATAAAAAAATTCAAT
* * *
46822301 ATTTTTTTTGTGTTGGCCATGCAATGGC
1 A-TTTTTTCGTGTTGGTCATGCATTGGC
46822329 AGAGCCTGGA
Statistics
Matches: 183, Mismatches: 21, Indels: 15
0.84 0.10 0.07
Matches are distributed among these distances:
60 37 0.20
61 26 0.14
62 82 0.45
63 38 0.21
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (62 bp):
ATTTTTTCGTGTTGGTCATGCATTGGCCGACACCACCTATTTATCTAATAAAAAAATTCAAT
Found at i:46822285 original size:123 final size:122
Alignment explanation
Indices: 46822022--46822320 Score: 404
Period size: 123 Copynumber: 2.4 Consensus size: 122
46822012 TATTGCATAA
* * * * * * *
46822022 CCGACATCACCTTTTTATTTGAT-AAGAATTTTAAATTTTTTGTGTTGGCCATTGCATGACCGAC
1 CCGACACCACCTATTTATCTGATAAAAAAATTCAAATTTTTTGTGTTGGCCATTGCATGACCAAC
** *
46822086 ACCACCTTTTTATCTAATAAAAAAATTCAATTTTTTTTAGTGTTGATCATGCATTGG
66 ACCACCTTTTTATCTAATAAAAAAATTCAAAATTTTTTAGTGTTGACCATGCATTGG
* **
46822143 CCGACACCACCTATTTATCTGATAAAAAAA-TCAAATTTTTTCGTGTTGGTCATTGCATGGGCAA
1 CCGACACCACCTATTTATCTGATAAAAAAATTCAAATTTTTT-GTGTTGGCCATTGCATGACCAA
* *
46822207 CACCACCTTTTTATCTAATAAAAAAAATTCAAAATTTTTTCGTGTTGGCCATGCATTGG
65 CACCACCTTTTTATCTAAT-AAAAAAATTCAAAATTTTTTAGTGTTGACCATGCATTGG
*
46822266 CTGACACCACCTATTTATCTGATAAAAAAATTCAAATTTTTTTTGTGTTGGCCAT
1 CCGACACCACCTATTTATCTGATAAAAAAATTCAAA--TTTTTTGTGTTGGCCAT
46822321 GCAATGGCAG
Statistics
Matches: 155, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
121 30 0.19
122 41 0.26
123 63 0.41
124 5 0.03
125 10 0.06
126 6 0.04
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (122 bp):
CCGACACCACCTATTTATCTGATAAAAAAATTCAAATTTTTTGTGTTGGCCATTGCATGACCAAC
ACCACCTTTTTATCTAATAAAAAAATTCAAAATTTTTTAGTGTTGACCATGCATTGG
Found at i:46830351 original size:21 final size:20
Alignment explanation
Indices: 46830307--46830351 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
46830297 AGTTTTGAGT
*
46830307 TTTGGGTTTTGAATTATTGA
1 TTTGGGTTTTGAATTATCGA
46830327 TTTGGAGTTTTGAATT-TCGA
1 TTTGG-GTTTTGAATTATCGA
46830347 CTTTG
1 -TTTG
46830352 TATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.18, C:0.04, G:0.24, T:0.53
Consensus pattern (20 bp):
TTTGGGTTTTGAATTATCGA
Found at i:46831573 original size:26 final size:25
Alignment explanation
Indices: 46831518--46831573 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
46831508 ATATTAGTTT
*
46831518 TTAT-AAAATTAAATCAAATATATA
1 TTATAAAAATTAAATAAAATATATA
* *
46831542 TCATAAAAATTATAATAAAATATATG
1 TTATAAAAATTA-AATAAAATATATA
46831568 TTATAA
1 TTATAA
46831574 GTTATTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 3 0.12
25 7 0.27
26 16 0.62
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
TTATAAAAATTAAATAAAATATATA
Found at i:46832448 original size:30 final size:29
Alignment explanation
Indices: 46832388--46832450 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
46832378 ATAAATTTTC
*
46832388 AATTTATTATTAAAAAATTATGTATTTAT
1 AATTTATTATTAAAAAATTATGTATATAT
* *
46832417 AATTTATTTATTAACATAATTTTGT-TATAT
1 AATTTA-TTATTAA-AAAATTATGTATATAT
46832447 AATT
1 AATT
46832451 GTTTTAACAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 6 0.21
30 15 0.52
31 8 0.28
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (29 bp):
AATTTATTATTAAAAAATTATGTATATAT
Found at i:46834649 original size:432 final size:433
Alignment explanation
Indices: 46833820--46835123 Score: 2548
Period size: 432 Copynumber: 3.0 Consensus size: 433
46833810 CGTGTTTGAT
46833820 TTTTTAATTTAAAAATTATTTTAATGCATGAAAAAATAAAAGTGTCATCATAATAATCTTAATTA
1 TTTTTAATTTAAAAATTATTTTAATGCATGAAAAAATAAAAGTGTCATCATAATAATCTTAATTA
46833885 TAATGTAAAAGAAAGGGTAAATCTTTAATTTTATTTATGAATTAGTGACCTAATTAAAGTTGAGC
66 TAATGTAAAAGAAAGGGTAAATCTTTAATTTTATTTATGAATTAGTGACCTAATTAAAGTTGAGC
46833950 TAACTTAGTAAAAGACTTAAATAATAATATTAATTATAATTTGAAAGAAAAAAGATA-TTTTATA
131 TAACTTAGTAAAAGACTTAAATAATAATATTAATTATAATTTGAAAGAAAAAAGATATTTTTATA
46834014 ATTCTACTACTAAATTGCTAATTCGATTAAGAGTGACACCAACTCAATAAAAGACTTAAACATAA
196 ATTCTACTACTAAATTGCTAATTCGATTAAGAGTGACACCAACTCAATAAAAGACTTAAACATAA
46834079 GTATTTGAATTTATAAGAATAAGAGAGCAAAAGTTATATATTTGGTACTAAAAGGTAATGGTGTT
261 GTATTTGAATTTATAAGAATAAGAGAGCAAAAGTTATATATTTGGTACTAAAAGGTAATGGTGTT
46834144 AACTTTTTAGCATTTAATTTTATTTTTAGGGTTGATTTGATGAAAGTTAAA-TGTTAATATTATT
326 AACTTTTTAGCATTTAATTTTATTTTTAGGGTTGATTTGATGAAAGTTAAATTGTTAATATTATT
46834208 ATGTTTGATTTTTTCACAATTTTGTAATTGGTGGAATAAGTTTA
391 AT-TTTGATTTTTTCACAATTTTGTAATTGGTGGAATAAGTTTA
46834252 TTTTTAATTTAAAAATTATTTTAATGCATGAAAAAATAAAAGTGTCATCATAATAATCTTAATTA
1 TTTTTAATTTAAAAATTATTTTAATGCATGAAAAAATAAAAGTGTCATCATAATAATCTTAATTA
46834317 TAATGTAAAAGAAAGGGTAAATCTTTAATTTTATTTATGAATTAGTGACCTAATTAAAGTTGAGC
66 TAATGTAAAAGAAAGGGTAAATCTTTAATTTTATTTATGAATTAGTGACCTAATTAAAGTTGAGC
46834382 TAACTTAGTAAAAGACTTAAATAATAATATTAATTATAATTTGAAAGAAAAAAGATATTTTTATA
131 TAACTTAGTAAAAGACTTAAATAATAATATTAATTATAATTTGAAAGAAAAAAGATATTTTTATA
46834447 ATTCTACTACTAAATTGCTAATTCGATTAAGAGTGACACCAACTCAATAAAAGACTTAAACATAA
196 ATTCTACTACTAAATTGCTAATTCGATTAAGAGTGACACCAACTCAATAAAAGACTTAAACATAA
46834512 GTATTTGAATTTATAAGAATAAGAGAGCAAAAGTTATATATTTGGTACTAAAAGGTAATGGTGTT
261 GTATTTGAATTTATAAGAATAAGAGAGCAAAAGTTATATATTTGGTACTAAAAGGTAATGGTGTT
46834577 AACTTTTTAGCATTTAATTTTATTTTTAGGGTTGATTTGATGAAAGTTAAATTGTTAATATTATT
326 AACTTTTTAGCATTTAATTTTATTTTTAGGGTTGATTTGATGAAAGTTAAATTGTTAATATTATT
46834642 A-TTTGATTTTTTCACAATTTTGTAATTGGTGGAATAAGTTTA
391 ATTTTGATTTTTTCACAATTTTGTAATTGGTGGAATAAGTTTA
46834684 TTTTTAATTTAAAAATTATTTTAATGCATGAAAAAATAAAAGTGTCATCATAATAATCTTAATTA
1 TTTTTAATTTAAAAATTATTTTAATGCATGAAAAAATAAAAGTGTCATCATAATAATCTTAATTA
46834749 TAATGTAAAAGAAAGGGTAAATCTTTAATTTTATTTATGAATTAGTGACCTAATTAAAGTTGAGC
66 TAATGTAAAAGAAAGGGTAAATCTTTAATTTTATTTATGAATTAGTGACCTAATTAAAGTTGAGC
46834814 TAACTTAGTAAAAGACTTAAATAA-AATATTAATTAT-ATTTGAAAGAAAAAAGATATTTTTATA
131 TAACTTAGTAAAAGACTTAAATAATAATATTAATTATAATTTGAAAGAAAAAAGATATTTTTATA
46834877 ATTCTACTACTAAATTGCTAATTCGATTAAGAGTGACACCAACTCAATAAAAGACTTAAACATAA
196 ATTCTACTACTAAATTGCTAATTCGATTAAGAGTGACACCAACTCAATAAAAGACTTAAACATAA
46834942 GTATTTGAATTTATAAGAATAAGAGAGCAAAAGTTATATATTTGGTACTAAAAGGTAATGGTGTT
261 GTATTTGAATTTATAAGAATAAGAGAGCAAAAGTTATATATTTGGTACTAAAAGGTAATGGTGTT
46835007 AACTTTTTAGCATTTAATTTTA-TTTTAGGGTTGATTTGATGAAAGTTAAATTGTTTAATATTAT
326 AACTTTTTAGCATTTAATTTTATTTTTAGGGTTGATTTGATGAAAGTTAAATTG-TTAATATTAT
46835071 TATTTTGATTTTTTCACAATTTTGTAATTGGTGGAATAAGTTTA
390 TATTTTGATTTTTTCACAATTTTGTAATTGGTGGAATAAGTTTA
46835115 TTTTTAATT
1 TTTTTAATT
46835124 GCAAATTTGT
Statistics
Matches: 868, Mismatches: 0, Indels: 9
0.99 0.00 0.01
Matches are distributed among these distances:
429 31 0.04
430 191 0.22
431 62 0.07
432 382 0.44
433 188 0.22
434 14 0.02
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.40
Consensus pattern (433 bp):
TTTTTAATTTAAAAATTATTTTAATGCATGAAAAAATAAAAGTGTCATCATAATAATCTTAATTA
TAATGTAAAAGAAAGGGTAAATCTTTAATTTTATTTATGAATTAGTGACCTAATTAAAGTTGAGC
TAACTTAGTAAAAGACTTAAATAATAATATTAATTATAATTTGAAAGAAAAAAGATATTTTTATA
ATTCTACTACTAAATTGCTAATTCGATTAAGAGTGACACCAACTCAATAAAAGACTTAAACATAA
GTATTTGAATTTATAAGAATAAGAGAGCAAAAGTTATATATTTGGTACTAAAAGGTAATGGTGTT
AACTTTTTAGCATTTAATTTTATTTTTAGGGTTGATTTGATGAAAGTTAAATTGTTAATATTATT
ATTTTGATTTTTTCACAATTTTGTAATTGGTGGAATAAGTTTA
Done.