Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 166 of 235
Found at i:56012562 original size:16 final size:16
Alignment explanation
Indices: 56012541--56012571 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56012531 GCCTAGGATG
56012541 TGAATTGAATTAAATA
1 TGAATTGAATTAAATA
*
56012557 TGAATTGTATTAAAT
1 TGAATTGAATTAAAT
56012572 TGAGCTGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (16 bp):
TGAATTGAATTAAATA
Found at i:56012912 original size:24 final size:23
Alignment explanation
Indices: 56012885--56012966 Score: 65
Period size: 24 Copynumber: 3.4 Consensus size: 23
56012875 TAGCTCGAAA
*
56012885 GAGCGTCCCGTTATTAGCTCTCTT
1 GAGCTTCCCGTTATTAGCTCT-TT
* * *
56012909 GAGCTTCCTGTTATATGGTTCTTGT
1 GAGCTTCCCGTTAT-TAGCTCTT-T
* *
56012934 GAGCTTCCCATTAATAGCTCTTTT
1 GAGCTTCCCGTTATTAGCTC-TTT
*
56012958 GAGCATCCC
1 GAGCTTCCC
56012967 AATTGGTTGT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
24 26 0.58
25 19 0.42
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.39
Consensus pattern (23 bp):
GAGCTTCCCGTTATTAGCTCTTT
Found at i:56013059 original size:26 final size:26
Alignment explanation
Indices: 56013030--56013127 Score: 110
Period size: 26 Copynumber: 3.8 Consensus size: 26
56013020 TCTATTATAT
56013030 GGCTCTTCGTGAGCTTCCCGATTAAA
1 GGCTCTTCGTGAGCTTCCCGATTAAA
* *
56013056 GGCTTTTTGTGAGCTTCCCGATTAAA
1 GGCTCTTCGTGAGCTTCCCGATTAAA
*** * *
56013082 GGCTCTTTAAGAGCTTCCTGATTAAT
1 GGCTCTTCGTGAGCTTCCCGATTAAA
*
56013108 GGCTC-TC-TAAGCTTCCCGAT
1 GGCTCTTCGTGAGCTTCCCGAT
56013128 ATTGGCTCTC
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
24 10 0.16
25 1 0.02
26 50 0.82
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.35
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTCCCGATTAAA
Found at i:56013158 original size:25 final size:24
Alignment explanation
Indices: 56013106--56013172 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
56013096 TTCCTGATTA
*
56013106 ATGGCTCTCTAAGCTTCCCGATAT
1 ATGGCTCTCTAAGCTTCCCAATAT
56013130 -TGGCTCTCTTGAA-CTTCCCAATAT
1 ATGGCTCTC-T-AAGCTTCCCAATAT
*
56013154 ATGGCTATCTAAAGCTTCC
1 ATGGCTCTCT-AAGCTTCC
56013173 TGATTAATGG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
23 8 0.22
24 14 0.39
25 14 0.39
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.34
Consensus pattern (24 bp):
ATGGCTCTCTAAGCTTCCCAATAT
Found at i:56013182 original size:25 final size:25
Alignment explanation
Indices: 56013067--56013186 Score: 113
Period size: 26 Copynumber: 4.8 Consensus size: 25
56013057 GCTTTTTGTG
* *
56013067 AGCTTCCCGATTAAAGGCTCTTTAA
1 AGCTTCCCGATTAATGGCTCTCTAA
*
56013092 GAGCTTCCTGATTAATGGCTCTCT-A
1 -AGCTTCCCGATTAATGGCTCTCTAA
* *
56013117 AGCTTCCCGA-TATTGGCTCTCTTGA
1 AGCTTCCCGATTAATGGCTCTC-TAA
* *
56013142 A-CTTCCC-AATATATGGCTATCTAA
1 AGCTTCCCGATTA-ATGGCTCTCTAA
*
56013166 AGCTTCCTGATTAATGGCTCT
1 AGCTTCCCGATTAATGGCTCT
56013187 TCAGAGCTAC
Statistics
Matches: 77, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
23 11 0.14
24 21 0.27
25 22 0.29
26 23 0.30
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (25 bp):
AGCTTCCCGATTAATGGCTCTCTAA
Found at i:56013229 original size:73 final size:73
Alignment explanation
Indices: 56013093--56013234 Score: 189
Period size: 73 Copynumber: 1.9 Consensus size: 73
56013083 GCTCTTTAAG
* * *
56013093 AGCTTCCTGATTAATGGCTCTCTAAGCTTCCCGATATTGGCTCTCTTGAACTTCCCAATATATGG
1 AGCTTCCTGATTAATGGCTCTCTAAGCTACCCGATATTGGCTCGCATGAACTTCCCAATATATGG
56013158 CTATCTAA
66 CTATCTAA
* * **
56013166 AGCTTCCTGATTAATGGCTCT-TCAGAGCTACCCGTTATTGGCTCGCATGAGCTTCCTGA-ATAT
1 AGCTTCCTGATTAATGGCTCTCT-A-AGCTACCCGATATTGGCTCGCATGAACTTCCCAATATAT
56013229 GGCTAT
64 GGCTAT
56013235 TATGAGCTTC
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
72 1 0.02
73 32 0.53
74 27 0.45
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (73 bp):
AGCTTCCTGATTAATGGCTCTCTAAGCTACCCGATATTGGCTCGCATGAACTTCCCAATATATGG
CTATCTAA
Found at i:56016069 original size:46 final size:49
Alignment explanation
Indices: 56015936--56016069 Score: 152
Period size: 50 Copynumber: 2.8 Consensus size: 49
56015926 GGGGTAAGGT
* *
56015936 GCCGATGCCATGTCCTAGACATGGTCTTACAC-AGGCTTTAGCATATCTGA
1 GCCGATGCCATGTCCAAGACATGGTCTTACACTA-GCTCTA-CATATCTGA
* * * *
56015986 GTCGATGCCATGTCCCAGACATGGTCTTACATTAGCTCT-CATAATGTG-
1 GCCGATGCCATGTCCAAGACATGGTCTTACACTAGCTCTACAT-ATCTGA
56016034 GCCGATG-CATGTCCAAGACAT-GTCTTACACTAGCTC
1 GCCGATGCCATGTCCAAGACATGGTCTTACACTAGCTC
56016070 ACAATAGCCC
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
46 14 0.19
47 13 0.18
48 9 0.12
49 4 0.05
50 33 0.45
51 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (49 bp):
GCCGATGCCATGTCCAAGACATGGTCTTACACTAGCTCTACATATCTGA
Found at i:56017743 original size:28 final size:28
Alignment explanation
Indices: 56017693--56017783 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 28
56017683 GTGACAGAGT
* * *
56017693 CACCAGATATAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCAGGGC
*
56017722 TACCAGAACAGATAATTTGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCAGGGC
**
56017750 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAGGGC
56017778 CACCAG
1 CACCAG
56017784 GACGCTTCCT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 49 0.89
29 6 0.11
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCAGGGC
Found at i:56017936 original size:28 final size:28
Alignment explanation
Indices: 56017889--56017953 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
56017879 AAATTAACCC
*
56017889 TAGGGGTATAAAGGTCA-TTTAGCATACA
1 TAGGGGTATAAAGGTAATTTTA-CATACA
*
56017917 TAGGGGTATAATGGTAATTTTACATACA
1 TAGGGGTATAAAGGTAATTTTACATACA
56017945 TAGGGGTAT
1 TAGGGGTAT
56017954 TCTAGTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 30 0.88
29 4 0.12
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTACATACA
Found at i:56025614 original size:28 final size:28
Alignment explanation
Indices: 56025566--56025656 Score: 121
Period size: 28 Copynumber: 3.2 Consensus size: 28
56025556 GTGACAGAGT
*
56025566 CACCAGATACAGATATTTTGTGGCAATGC
1 CACCAGA-ACAGATAATTTGTGGCAATGC
**
56025595 CACCAGAACAGATAATTTGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCAATGC
*
56025623 CACCAGAATAGATAATTTGTGGC-ATAGC
1 CACCAGAACAGATAATTTGTGGCAAT-GC
56025651 CACCAG
1 CACCAG
56025657 GACGCTTCCT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
28 48 0.87
29 7 0.13
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCAATGC
Found at i:56025809 original size:28 final size:28
Alignment explanation
Indices: 56025762--56025826 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
56025752 AAATTAACCC
56025762 TAGGGGTATAAAGGTCATTTAGCATACA
1 TAGGGGTATAAAGGTCATTTAGCATACA
* * *
56025790 TAGGGGTATAATGGTTATTTTGCATACA
1 TAGGGGTATAAAGGTCATTTAGCATACA
56025818 TAGGGGTAT
1 TAGGGGTAT
56025827 TCTAGTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAAAGGTCATTTAGCATACA
Found at i:56028454 original size:17 final size:17
Alignment explanation
Indices: 56028432--56028508 Score: 74
Period size: 17 Copynumber: 4.7 Consensus size: 17
56028422 ATCTACAAGA
56028432 TAAATATTAAATTAAAT
1 TAAATATTAAATTAAAT
56028449 TAAATATTAAATT--AT
1 TAAATATTAAATTAAAT
*
56028464 TAAA-A-TACTATTAAGA-
1 TAAATATTA-AATTAA-AT
*
56028480 TAAGTATTAAATTAAAT
1 TAAATATTAAATTAAAT
*
56028497 TTAATATTAAAT
1 TAAATATTAAAT
56028509 CTATTAAAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
13 2 0.04
14 4 0.08
15 6 0.12
16 4 0.08
17 30 0.62
18 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.42
Consensus pattern (17 bp):
TAAATATTAAATTAAAT
Found at i:56030344 original size:39 final size:39
Alignment explanation
Indices: 56030279--56030378 Score: 114
Period size: 39 Copynumber: 2.6 Consensus size: 39
56030269 ATCCACTTTT
* * * **
56030279 AAGCATATATCA-ATTTACACATATAATCACCTAACATAC
1 AAGCATATATCACA-ATACTCAAATAATCAAATAACATAC
**
56030318 AAGCATATATCACAATACTCAAATAATCAAATAACATTT
1 AAGCATATATCACAATACTCAAATAATCAAATAACATAC
56030357 AAGCATATATC-CAATACTCAAA
1 AAGCATATATCACAATACTCAAA
56030379 AACATCTTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
38 11 0.21
39 41 0.77
40 1 0.02
ACGTcount: A:0.49, C:0.21, G:0.03, T:0.27
Consensus pattern (39 bp):
AAGCATATATCACAATACTCAAATAATCAAATAACATAC
Found at i:56038491 original size:23 final size:23
Alignment explanation
Indices: 56038462--56038583 Score: 113
Period size: 23 Copynumber: 5.3 Consensus size: 23
56038452 TGATGGACAA
* *
56038462 TAAGCTCTATTGAGTTGAATCAG
1 TAAGCTCTAATGAGCTGAATCAG
* *
56038485 TAAGCTCCAATGAGCTGAAACAG
1 TAAGCTCTAATGAGCTGAATCAG
* *
56038508 TAAGCT-TTATCGAGCTGAATCGG
1 TAAGCTCTAAT-GAGCTGAATCAG
* * *
56038531 TAAGCTCCAATGAGCTAAAACAG
1 TAAGCTCTAATGAGCTGAATCAG
* *
56038554 TAAGCTCTTACT-AGATGAATCAG
1 TAAGCTC-TAATGAGCTGAATCAG
56038577 TAAGCTC
1 TAAGCTC
56038584 ATACGAGTTG
Statistics
Matches: 78, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
22 2 0.03
23 72 0.92
24 4 0.05
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.26
Consensus pattern (23 bp):
TAAGCTCTAATGAGCTGAATCAG
Found at i:56038527 original size:46 final size:46
Alignment explanation
Indices: 56038462--56038583 Score: 165
Period size: 46 Copynumber: 2.7 Consensus size: 46
56038452 TGATGGACAA
* * * *
56038462 TAAGCTCTATTGAGTTGAATCAGTAAGCTCCAATGAGCTGAAACAG
1 TAAGCTTTATCGAGATGAATCAGTAAGCTCCAATGAGCTAAAACAG
* *
56038508 TAAGCTTTATCGAGCTGAATCGGTAAGCTCCAATGAGCTAAAACAG
1 TAAGCTTTATCGAGATGAATCAGTAAGCTCCAATGAGCTAAAACAG
*
56038554 TAAGCTCTTA-CTAGATGAATCAGTAAGCTC
1 TAAGCT-TTATCGAGATGAATCAGTAAGCTC
56038584 ATACGAGTTG
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
46 64 0.96
47 3 0.04
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.26
Consensus pattern (46 bp):
TAAGCTTTATCGAGATGAATCAGTAAGCTCCAATGAGCTAAAACAG
Found at i:56039873 original size:21 final size:21
Alignment explanation
Indices: 56039849--56039891 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
56039839 AGTCCAGTAA
56039849 TACATGAAATTTCATAACATG
1 TACATGAAATTTCATAACATG
56039870 TACATGAAATTTCATAACATG
1 TACATGAAATTTCATAACATG
56039891 T
1 T
56039892 GATAGTGTGA
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:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (21 bp):
TACATGAAATTTCATAACATG
Found at i:56065638 original size:20 final size:20
Alignment explanation
Indices: 56065613--56065661 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
56065603 TTGCATAAGT
56065613 TGTAAAATAGGTAATAAATG
1 TGTAAAATAGGTAATAAATG
*
56065633 TGTAAAATAGGTTATAAATG
1 TGTAAAATAGGTAATAAATG
*
56065653 TGTGAAATA
1 TGTAAAATA
56065662 TTGAGAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (20 bp):
TGTAAAATAGGTAATAAATG
Found at i:56066237 original size:47 final size:47
Alignment explanation
Indices: 56066133--56066447 Score: 172
Period size: 47 Copynumber: 6.8 Consensus size: 47
56066123 TTAATTGTGT
* *** * *
56066133 GCTAGTGTAAGA-CATGTCAGGGACAT-GCATCGGCCACATTATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGA-GACGAGA
* * *
56066179 GCCAATGTAAGA-CATGTCTAGGACATGGCATCGGCATTGAGACGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTGAGACGAGA
* * * * *
56066226 GCTAGTTTAAGA-CATGTTTGGGACAT-GCATCAGCCTCGAGATGTA-A
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-GGCTTGAGACG-AGA
* * * *
56066272 GCCAGTGTGAA-A-CATGTCTGGGACAT-GCATCGGC-T-ACAAGATGT
1 GCTAGTGT-AAGACCATGTCTGGGACATGGCATCGGCTTGAGACGA-GA
* * * * * *
56066316 GCCAGTATAAGACCATGTCTGGGACATGGCATTGGCCTCA-ATTTCGATA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGA---CGAGA
** * * *
56066365 G-TCAGTGTAAGACCATGTCCAGGACATGGCATCGACTTGATA-GATGT
1 GCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGACGA-GA
56066412 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
56066448 ATTACACCCT
Statistics
Matches: 207, Mismatches: 43, Indels: 37
0.72 0.15 0.13
Matches are distributed among these distances:
42 1 0.00
43 5 0.02
44 8 0.04
45 16 0.08
46 68 0.33
47 72 0.35
48 3 0.01
49 31 0.15
50 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (47 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGACGAGA
Found at i:56066294 original size:46 final size:44
Alignment explanation
Indices: 56066233--56066343 Score: 127
Period size: 46 Copynumber: 2.5 Consensus size: 44
56066223 AGAGCTAGTT
* * *
56066233 TAAGACATGTTTGGGACATGCATCAGCCT-CGAGATGTAAGCCAGTG
1 TAAGACATGTCTGGGACATGCATC-GCCTACAAGATGT--GCCAGTA
*
56066279 TGAA-ACATGTCTGGGACATGCATCGGCTACAAGATGTGCCAGTA
1 T-AAGACATGTCTGGGACATGCATCGCCTACAAGATGTGCCAGTA
56066323 TAAGACCATGTCTGGGACATG
1 TAAGA-CATGTCTGGGACATG
56066344 GCATTGGCCT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
43 2 0.04
44 8 0.14
45 18 0.32
46 27 0.47
47 2 0.04
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (44 bp):
TAAGACATGTCTGGGACATGCATCGCCTACAAGATGTGCCAGTA
Found at i:56066296 original size:93 final size:92
Alignment explanation
Indices: 56066133--56066305 Score: 217
Period size: 93 Copynumber: 1.9 Consensus size: 92
56066123 TTAATTGTGT
* *
56066133 GCTAGTGTAAGACATGTCAGGGACATGCATCGGCCACATTATGAGAGCCAATGTAAGACATGTCT
1 GCTAGTGTAAGACATGTCAGGGACATGCATCAGCCACATGATGAGAGCCAATGTAAGACATGTCT
56066198 AGGACATGGCATCGGCATTGAGACGAGA
66 AGGACAT-GCATCGGCATTGAGACGAGA
* ** * *
56066226 GCTAGTTTAAGACATGTTTGGGACATGCATCAGCCTCGA-GATGTA-AGCCAGTGTGAA-ACATG
1 GCTAGTGTAAGACATGTCAGGGACATGCATCAGCCAC-ATGATG-AGAGCCAATGT-AAGACATG
*
56066288 TCTGGGACATGCATCGGC
63 TCTAGGACATGCATCGGC
56066306 TACAAGATGT
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
92 8 0.12
93 57 0.83
94 4 0.06
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (92 bp):
GCTAGTGTAAGACATGTCAGGGACATGCATCAGCCACATGATGAGAGCCAATGTAAGACATGTCT
AGGACATGCATCGGCATTGAGACGAGA
Found at i:56066892 original size:41 final size:41
Alignment explanation
Indices: 56066844--56066928 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
56066834 GTTAGATCTC
56066844 TTATTTTGATTATGGCATGTATAGGACTCTTTGATCTTGTT
1 TTATTTTGATTATGGCATGTATAGGACTCTTTGATCTTGTT
56066885 TTATTTTGATTATGGCATGTATAGGACTCTTTGATCTTGTT
1 TTATTTTGATTATGGCATGTATAGGACTCTTTGATCTTGTT
56066926 TTA
1 TTA
56066929 GTGTCACATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.20, C:0.09, G:0.19, T:0.52
Consensus pattern (41 bp):
TTATTTTGATTATGGCATGTATAGGACTCTTTGATCTTGTT
Found at i:56073122 original size:13 final size:13
Alignment explanation
Indices: 56073104--56073128 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56073094 GTAAGTGATT
56073104 TTGATGATTTTTC
1 TTGATGATTTTTC
56073117 TTGATGATTTTT
1 TTGATGATTTTT
56073129 GCACTTTTAG
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:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (13 bp):
TTGATGATTTTTC
Found at i:56074013 original size:46 final size:46
Alignment explanation
Indices: 56073836--56074050 Score: 161
Period size: 46 Copynumber: 4.6 Consensus size: 46
56073826 TTTGTGCTAA
* * ** **
56073836 TGTAAGACATGTCTAGGACATGCATCGGCCACATTATGGGAGCCAG
1 TGTAAGACATGTCTGGGACATGCATCGGCTACAAGATGTAAGCCAG
** * * *
56073882 TGTAAGACCATGTCTGGGACATGGCATCGGC-ATTGAGACG-AGAGCTAC
1 TGTAAGA-CATGTCTGGGACAT-GCATCGGCTA-CAAGATGTA-AGCCAG
* * * * *
56073930 CGTAAGACATGTTTGGGACATGCATTAGTCT-CGAGATGTAAGCCAG
1 TGTAAGACATGTCTGGGACATGCA-TCGGCTACAAGATGTAAGCCAG
* *
56073976 TGTAAGACATGTCTGGGACATGCATCGGCTACAAGATGT--GTCAA
1 TGTAAGACATGTCTGGGACATGCATCGGCTACAAGATGTAAGCCAG
*
56074020 TGTAAGACCATGTCTAGGACATCGCATCGGC
1 TGTAAGA-CATGTCTGGGACAT-GCATCGGC
56074051 CTCAATTTTG
Statistics
Matches: 134, Mismatches: 25, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
44 10 0.07
45 17 0.13
46 56 0.42
47 31 0.23
48 20 0.15
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (46 bp):
TGTAAGACATGTCTGGGACATGCATCGGCTACAAGATGTAAGCCAG
Found at i:56076078 original size:24 final size:24
Alignment explanation
Indices: 56076046--56076092 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
56076036 CTGTCAGGAG
**
56076046 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGCAGATAAGGGAT
56076070 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGCAGATAAGGGA
56076093 GGAAATCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.38, T:0.23
Consensus pattern (24 bp):
AGGATTTAGGAGCAGATAAGGGAT
Found at i:56077333 original size:27 final size:27
Alignment explanation
Indices: 56077293--56077404 Score: 138
Period size: 27 Copynumber: 4.1 Consensus size: 27
56077283 AGGAAGCGTC
*
56077293 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
56077320 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
*
56077347 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
56077375 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
56077401 CTGG
1 CTGG
56077405 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.11
27 49 0.65
28 18 0.24
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:56077399 original size:54 final size:54
Alignment explanation
Indices: 56077293--56077404 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
56077283 AGGAAGCGTC
* *
56077293 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
56077347 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
56077401 CTGG
1 CTGG
56077405 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:56078521 original size:43 final size:43
Alignment explanation
Indices: 56078473--56078642 Score: 195
Period size: 43 Copynumber: 4.0 Consensus size: 43
56078463 ATTGCCAAGA
*
56078473 TGTGATTACATGTAAGACCATGTCTGGGACATTGACATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
*
56078516 TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCAT-TA-
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCAT--TGTAT
* * * * *
56078559 TATGATTTCGTGTAAGACCATGTCTGGGAAATTGGCATCG-AT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
* * *
56078601 ATGTGATAACATGTAAGACCATATCTGGGATA-TGGCATTGTA
1 -TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTA
56078643 CAAGCTATGT
Statistics
Matches: 108, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
41 1 0.01
42 7 0.06
43 97 0.90
44 2 0.02
45 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
Found at i:56082542 original size:42 final size:42
Alignment explanation
Indices: 56082472--56082565 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
56082462 GTAAGACGAT
* * * * * *
56082472 ATGGCGTTGATATGAGATTTCGTGTAAGACTACATCTAGGAC
1 ATGGCGTCGAAATGAGAATCCGTATAAGACCACATCTAGGAC
* *
56082514 ATGGCGTCGAAATGAGAATCCGTATAAGACCATATCTAGGAT
1 ATGGCGTCGAAATGAGAATCCGTATAAGACCACATCTAGGAC
*
56082556 ATGGCATCGA
1 ATGGCGTCGA
56082566 TGTGAAATCC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.27
Consensus pattern (42 bp):
ATGGCGTCGAAATGAGAATCCGTATAAGACCACATCTAGGAC
Found at i:56086596 original size:24 final size:26
Alignment explanation
Indices: 56086569--56086622 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 26
56086559 AATTTTAAAA
*
56086569 AATAGA-GTAATTAAATAAAATAA-T
1 AATAGATGTAATTAAATAAAAAAATT
56086593 AATA-ATGTAATTAAATAAAAAAATT
1 AATAGATGTAATTAAATAAAAAAATT
56086618 AATAG
1 AATAG
56086623 TTTAGTGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 1 0.04
24 20 0.77
25 5 0.19
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (26 bp):
AATAGATGTAATTAAATAAAAAAATT
Found at i:56088284 original size:17 final size:17
Alignment explanation
Indices: 56088262--56088295 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
56088252 ATGCATCTAG
56088262 GTGCTAAGATGCAGCTC
1 GTGCTAAGATGCAGCTC
56088279 GTGCTAAGATGCAGCTC
1 GTGCTAAGATGCAGCTC
56088296 ATATCAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (17 bp):
GTGCTAAGATGCAGCTC
Found at i:56102593 original size:18 final size:18
Alignment explanation
Indices: 56102572--56102615 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
56102562 ATTCTGGTGA
56102572 TTCTAATAAAAGCAACAG
1 TTCTAATAAAAGCAACAG
**
56102590 TTCTGAAT-TGAGCAACAG
1 TTCT-AATAAAAGCAACAG
56102608 TTCTAATA
1 TTCTAATA
56102616 GAATCCCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 3 0.14
18 16 0.73
19 3 0.14
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (18 bp):
TTCTAATAAAAGCAACAG
Found at i:56106644 original size:16 final size:17
Alignment explanation
Indices: 56106612--56106644 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
56106602 TTTTTGGGCT
56106612 TAATGGGCCAAAACGGGA
1 TAATGGGCC-AAACGGGA
56106630 TAATGGGCC-AACGGG
1 TAATGGGCCAAACGGG
56106645 TCCAAGTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.33, C:0.18, G:0.36, T:0.12
Consensus pattern (17 bp):
TAATGGGCCAAACGGGA
Found at i:56106955 original size:27 final size:26
Alignment explanation
Indices: 56106879--56106990 Score: 116
Period size: 27 Copynumber: 4.2 Consensus size: 26
56106869 AGGAAGCGTC
* * * *
56106879 CTGGTGGCTATGCCACAAATACCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
*
56106906 CTGGTGGCTTTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
56106933 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGT-T
* * *
56106961 CTAGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGTT
56106987 CTGG
1 CTGG
56106991 CAGTCATGCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 5 0.07
27 52 0.71
28 16 0.22
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:56106983 original size:54 final size:54
Alignment explanation
Indices: 56106879--56106990 Score: 136
Period size: 54 Copynumber: 2.1 Consensus size: 54
56106869 AGGAAGCGTC
* * *
56106879 CTGGTGGCTATGCCACAAATACCTGATCTGGTGGCTTTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAAATACCTGATCTAGTGACTCTGCCACATATATCTGTT
* * * * *
56106933 CTGGTGGCTCTGCCACGATTATCTGTATCTAGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAAATACCTG-ATCTAGTGACTCTGCCACATATATCTGTT
56106987 CTGG
1 CTGG
56106991 CAGTCATGCT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
54 33 0.67
55 16 0.33
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAAATACCTGATCTAGTGACTCTGCCACATATATCTGTT
Found at i:56110495 original size:42 final size:42
Alignment explanation
Indices: 56110371--56110495 Score: 144
Period size: 41 Copynumber: 3.0 Consensus size: 42
56110361 GGGATCACAT
* * * **
56110371 ATATCGATGCCGATAGCCCAGCTATGGTCTTACACGATATCTC
1 ATATCGATGCC-ATATCCCAGATATGGTCTTACACGAAATCAA
* * * *
56110414 GTATCGATG-CATGTCCCAGACATGGTCTTACACGTAATCAA
1 ATATCGATGCCATATCCCAGATATGGTCTTACACGAAATCAA
*
56110455 ATATCGATGCCATATCTCAGATATGGTCTTACACGAAATCA
1 ATATCGATGCCATATCCCAGATATGGTCTTACACGAAATCA
56110496 CACATAACCC
Statistics
Matches: 67, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
41 31 0.46
42 28 0.42
43 8 0.12
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (42 bp):
ATATCGATGCCATATCCCAGATATGGTCTTACACGAAATCAA
Found at i:56113373 original size:43 final size:43
Alignment explanation
Indices: 56113311--56113427 Score: 155
Period size: 43 Copynumber: 2.7 Consensus size: 43
56113301 ACGGTACTAT
*** *
56113311 TCAGGCCTTCGAGCCTAGCAGGCTATAATGCTGGTAAGTTAATA
1 TCAGG-CTTCGAGCCTAGCAGGCTATAATGCCAATAAGTCAATA
*
56113355 TCAGGCTTCGAGCCTAGCAGGCTATAATGCCAATGAGTCAATA
1 TCAGGCTTCGAGCCTAGCAGGCTATAATGCCAATAAGTCAATA
* *
56113398 TCGGGCTTCGAGCCTAGCAGGC-GTAATGCC
1 TCAGGCTTCGAGCCTAGCAGGCTATAATGCC
56113428 GGTGAATGAG
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 7 0.11
43 54 0.82
44 5 0.08
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (43 bp):
TCAGGCTTCGAGCCTAGCAGGCTATAATGCCAATAAGTCAATA
Found at i:56114027 original size:16 final size:18
Alignment explanation
Indices: 56113996--56114028 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
56113986 AACTCGTCAC
56113996 ACTATCTATCGTTTTGGT
1 ACTATCTATCGTTTTGGT
56114014 ACTAT-TAT-GTTTTGG
1 ACTATCTATCGTTTTGG
56114029 AATTCGTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (18 bp):
ACTATCTATCGTTTTGGT
Found at i:56115016 original size:17 final size:17
Alignment explanation
Indices: 56114994--56115043 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
56114984 CATTGATATG
56114994 CATATAATATATATACA
1 CATATAATATATATACA
*
56115011 CATATAATATATACACA
1 CATATAATATATATACA
56115028 CAATTATAATA-ATATA
1 C-A-TATAATATATATA
56115044 AAAATAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 17 0.59
18 5 0.17
19 7 0.24
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (17 bp):
CATATAATATATATACA
Found at i:56117925 original size:4 final size:4
Alignment explanation
Indices: 56117914--56117945 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
56117904 AATTAAAAAG
56117914 TAAA -AAA TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
56117946 TTGAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:56123406 original size:15 final size:15
Alignment explanation
Indices: 56123386--56123434 Score: 98
Period size: 15 Copynumber: 3.3 Consensus size: 15
56123376 TCGACTTCTT
56123386 GTTCTTCCCAAACTC
1 GTTCTTCCCAAACTC
56123401 GTTCTTCCCAAACTC
1 GTTCTTCCCAAACTC
56123416 GTTCTTCCCAAACTC
1 GTTCTTCCCAAACTC
56123431 GTTC
1 GTTC
56123435 CACGTAGCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.18, C:0.39, G:0.08, T:0.35
Consensus pattern (15 bp):
GTTCTTCCCAAACTC
Found at i:56127629 original size:36 final size:36
Alignment explanation
Indices: 56127560--56127643 Score: 98
Period size: 36 Copynumber: 2.3 Consensus size: 36
56127550 CTATTCCTTA
* * *
56127560 TTCCTCACCTGTATCTTCTTTATCGACTGCATCTTG
1 TTCCTCACCTGTATCTACTTTATCGACTACATCTTC
* *
56127596 TTCCTCACTTGTATCTACTTTATC-AGTCACATCTTC
1 TTCCTCACCTGTATCTACTTTATCGACT-ACATCTTC
*
56127632 TTCCTCATCTGT
1 TTCCTCACCTGT
56127644 GGTCTTATTG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 2 0.05
36 38 0.95
ACGTcount: A:0.15, C:0.31, G:0.08, T:0.45
Consensus pattern (36 bp):
TTCCTCACCTGTATCTACTTTATCGACTACATCTTC
Found at i:56130611 original size:40 final size:40
Alignment explanation
Indices: 56130549--56130766 Score: 262
Period size: 40 Copynumber: 5.5 Consensus size: 40
56130539 AAGCCAAGTA
* * * *
56130549 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
56130588 CCTTCGGGACATAGCCCGGATATAGTAACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
56130628 CCTTCGGAACTTAGCCCGGATATAGTAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
56130668 CCTTTGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * * * *
56130708 CCTTCGGGACTTAGCTCGGA-ACTAGTCATTAGCGCAAACG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
56130748 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
56130767 TTATCATCAA
Statistics
Matches: 155, Mismatches: 21, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
39 13 0.08
40 142 0.92
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:56137070 original size:53 final size:53
Alignment explanation
Indices: 56137013--56137115 Score: 138
Period size: 53 Copynumber: 1.9 Consensus size: 53
56137003 GATTTTCTTC
* *
56137013 TCTATTGATTCATTATGGTATTC-TCCCATGATTCTTTGTG-TTTTTCTTTCTCT
1 TCTATTGATTCATTATAGT-TTCTTCCC-TGATTCTCTGTGATTTTTCTTTCTCT
* *
56137066 TCTATTGGTTCCTTATAGTTTCTTCCCTGATTCTCTGTGATTTTTCTTTC
1 TCTATTGATTCATTATAGTTTCTTCCCTGATTCTCTGTGATTTTTCTTTC
56137116 CTACGTCAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
52 14 0.32
53 30 0.68
ACGTcount: A:0.12, C:0.20, G:0.12, T:0.56
Consensus pattern (53 bp):
TCTATTGATTCATTATAGTTTCTTCCCTGATTCTCTGTGATTTTTCTTTCTCT
Found at i:56141823 original size:26 final size:26
Alignment explanation
Indices: 56141787--56141838 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
56141777 CAGTTAGTCT
56141787 CGATTAAAGCTTTTGAAATATTCATA
1 CGATTAAAGCTTTTGAAATATTCATA
56141813 CGATTAAAGCTTTTGAAATATTCATA
1 CGATTAAAGCTTTTGAAATATTCATA
56141839 GTCCTTGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (26 bp):
CGATTAAAGCTTTTGAAATATTCATA
Found at i:56144856 original size:46 final size:45
Alignment explanation
Indices: 56144800--56144967 Score: 194
Period size: 46 Copynumber: 3.6 Consensus size: 45
56144790 ACTCGTAGTC
*
56144800 GATGCATGTCCCAGACATGTTTTACACTGGCTTATGTCTCGAGGCT
1 GATGCATGTCCCAGACATGTCTTACACTGGCTT-TGTCTCGAGGCT
* * *
56144846 GATGCATGTCCCAGACATGTCTTACACTAGCTCTTGTCTCAATGCT
1 GATGCATGTCCCAGACATGTCTTACACTGGCT-TTGTCTCGAGGCT
* * * *
56144892 GATGCCATGTCCCAGACATGGCCTTACACTGGTTCTTGTAAT-GTGGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TTGT-CTCGAGGCT
*
56144940 GATGCATGTCCAAGACATGTCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
56144968 AGCTCACAAT
Statistics
Matches: 105, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
46 53 0.50
47 28 0.27
48 23 0.22
49 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTTTGTCTCGAGGCT
Found at i:56151569 original size:40 final size:40
Alignment explanation
Indices: 56151524--56151604 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
56151514 AGCAGGCAAA
56151524 ATTTCCTTTTTATTTCGCAAGTAACCGAGGCTTCAGCAGG
1 ATTTCCTTTTTATTTCGCAAGTAACCGAGGCTTCAGCAGG
* *
56151564 ATTTCCTTTTTATTTCGTAAGTAACCGAGGCTTTAGCAGG
1 ATTTCCTTTTTATTTCGCAAGTAACCGAGGCTTCAGCAGG
56151604 A
1 A
56151605 ATAGATTAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (40 bp):
ATTTCCTTTTTATTTCGCAAGTAACCGAGGCTTCAGCAGG
Found at i:56151898 original size:94 final size:94
Alignment explanation
Indices: 56151789--56151977 Score: 378
Period size: 94 Copynumber: 2.0 Consensus size: 94
56151779 GGAATTTTTA
56151789 AGTGTTAGTCAATTTAGGTTGGGGCCATTCACATCTATTATTATTTTTGAGATCGACCTTCATTC
1 AGTGTTAGTCAATTTAGGTTGGGGCCATTCACATCTATTATTATTTTTGAGATCGACCTTCATTC
56151854 TTTTTGTTCATCTTTTCTTCACCAAGCTT
66 TTTTTGTTCATCTTTTCTTCACCAAGCTT
56151883 AGTGTTAGTCAATTTAGGTTGGGGCCATTCACATCTATTATTATTTTTGAGATCGACCTTCATTC
1 AGTGTTAGTCAATTTAGGTTGGGGCCATTCACATCTATTATTATTTTTGAGATCGACCTTCATTC
56151948 TTTTTGTTCATCTTTTCTTCACCAAGCTT
66 TTTTTGTTCATCTTTTCTTCACCAAGCTT
56151977 A
1 A
56151978 ATCTTCTACT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.46
Consensus pattern (94 bp):
AGTGTTAGTCAATTTAGGTTGGGGCCATTCACATCTATTATTATTTTTGAGATCGACCTTCATTC
TTTTTGTTCATCTTTTCTTCACCAAGCTT
Found at i:56153339 original size:20 final size:21
Alignment explanation
Indices: 56153296--56153341 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
56153286 ACTGTTTTGT
56153296 TATGGG-CCAACTGTATTGAA
1 TATGGGCCCAACTGTATTGAA
*
56153316 -ATGGGCCCAACTGTGTT-AA
1 TATGGGCCCAACTGTATTGAA
56153335 TATGGGC
1 TATGGGC
56153342 AAGGCCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGGGCCCAACTGTATTGAA
Found at i:56161050 original size:26 final size:26
Alignment explanation
Indices: 56161000--56161061 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
56160990 AACAAAAGTT
*
56161000 AGTATAAAAAAAGAAATAAAGAAAGATA
1 AGTAT-AAAAAAGAAAGAAAGAAAGA-A
*
56161028 AGTATAAAAAA-AAAGAAATAAAGAA
1 AGTATAAAAAAGAAAGAAAGAAAGAA
56161053 AG-ATAAAAA
1 AGTATAAAAA
56161062 CATAAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 7 0.22
25 3 0.09
26 11 0.34
27 6 0.19
28 5 0.16
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (26 bp):
AGTATAAAAAAGAAAGAAAGAAAGAA
Found at i:56161069 original size:30 final size:30
Alignment explanation
Indices: 56161003--56161069 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
56160993 AAAAGTTAGT
** *
56161003 ATAAAAAAAGAAATAAAGAAAGATAAGTAT
1 ATAAAAAAAGAAATAAAGAAAGATAAAAAC
*
56161033 AAAAAAAAAGAAATAAAGAAAGATAAAAAC
1 ATAAAAAAAGAAATAAAGAAAGATAAAAAC
56161063 ATAAAAA
1 ATAAAAA
56161070 TTAAGAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.76, C:0.01, G:0.10, T:0.12
Consensus pattern (30 bp):
ATAAAAAAAGAAATAAAGAAAGATAAAAAC
Found at i:56163386 original size:15 final size:15
Alignment explanation
Indices: 56163366--56163396 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
56163356 CTATTCAAAT
56163366 TCCATATACCATATA
1 TCCATATACCATATA
*
56163381 TCCATATATCATATA
1 TCCATATACCATATA
56163396 T
1 T
56163397 AAATCATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (15 bp):
TCCATATACCATATA
Found at i:56163616 original size:25 final size:26
Alignment explanation
Indices: 56163588--56163679 Score: 109
Period size: 25 Copynumber: 3.7 Consensus size: 26
56163578 GAATTAGTAT
*
56163588 GCTCTCATGAGCTGTA-AATCGGTAA
1 GCTCACATGAGCTGTAGAATCGGTAA
*
56163613 GCTCACATGAGCTG-AGAATCGATAA
1 GCTCACATGAGCTGTAGAATCGGTAA
* * *
56163638 GCTAACACGAGCT-AAGAATCGGTAA
1 GCTCACATGAGCTGTAGAATCGGTAA
*
56163663 GCTCATATGAGCTGTAG
1 GCTCACATGAGCTGTAG
56163680 TGTGTCTGCA
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
24 1 0.02
25 52 0.95
26 2 0.04
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.23
Consensus pattern (26 bp):
GCTCACATGAGCTGTAGAATCGGTAA
Found at i:56174191 original size:23 final size:23
Alignment explanation
Indices: 56174147--56174191 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
56174137 TTTATTATTA
*
56174147 TTAGCAGCTCTGCTACGTTACTT
1 TTAGCAGCTCTGCTACGATACTT
*
56174170 TTAGCAGC-CTCGCTGCGATACT
1 TTAGCAGCTCT-GCTACGATACT
56174192 AGTGTACTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.18, C:0.29, G:0.20, T:0.33
Consensus pattern (23 bp):
TTAGCAGCTCTGCTACGATACTT
Found at i:56184921 original size:21 final size:21
Alignment explanation
Indices: 56184859--56184914 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
56184849 ATCCCCACAT
56184859 GGTGAGATGGTTGGTACGGGA
1 GGTGAGATGGTTGGTACGGGA
56184880 GGTGAGATGGTTGGTACGGGA
1 GGTGAGATGGTTGGTACGGGA
*
56184901 GGTGAGACGGTTGG
1 GGTGAGATGGTTGG
56184915 ATTGGGATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.18, C:0.05, G:0.54, T:0.23
Consensus pattern (21 bp):
GGTGAGATGGTTGGTACGGGA
Found at i:56186634 original size:42 final size:46
Alignment explanation
Indices: 56186552--56186656 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 46
56186542 ATTGTATCAA
* * *
56186552 TCTCGCACACTAAGTGCATATATATATATAGCCGAAGCTATCTCG-T
1 TCTCACACACTAAGTGCATATATATATATA-CCAAAGCTATCCCGAT
56186598 TCTCACACACTAAGTGCA-A-ATATATAT-CCAAAGCTATCCCGAT
1 TCTCACACACTAAGTGCATATATATATATACCAAAGCTATCCCGAT
56186641 T-TCGA-ACACTAAGTGC
1 TCTC-ACACACTAAGTGC
56186657 CCATAATTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
42 25 0.46
43 3 0.06
44 8 0.15
45 1 0.02
46 17 0.31
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (46 bp):
TCTCACACACTAAGTGCATATATATATATACCAAAGCTATCCCGAT
Found at i:56191873 original size:48 final size:47
Alignment explanation
Indices: 56191751--56191911 Score: 159
Period size: 48 Copynumber: 3.4 Consensus size: 47
56191741 TATGTGTGCT
** * * *
56191751 AGTGTAAGACATGTCTAGGACATGCATTAGCCAC-A-TTATGA-GAGCC
1 AGTGTAAGACATGTC-AGGACATGCATCGGCCTCGAGATAT-ACAAGCC
* *
56191797 AGTGTAAGATATGTCAGGACATGCATCGGCCTTGAGATATACAAGCC
1 AGTGTAAGACATGTCAGGACATGCATCGGCCTCGAGATATACAAGCC
* *
56191844 AGTGTAAGACATGT-ATGGGACATGCATCGGCCTCGAGGTATACAAGCT
1 AGTGTAAGACATGTCA--GGACATGCATCGGCCTCGAGATATACAAGCC
*
56191892 AGTGTAAGACCTGTCTAGGA
1 AGTGTAAGACATGTC-AGGA
56191912 TATGGCATTA
Statistics
Matches: 96, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
45 14 0.15
46 17 0.18
47 20 0.21
48 44 0.46
50 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (47 bp):
AGTGTAAGACATGTCAGGACATGCATCGGCCTCGAGATATACAAGCC
Found at i:56191995 original size:49 final size:47
Alignment explanation
Indices: 56191751--56192104 Score: 162
Period size: 49 Copynumber: 7.5 Consensus size: 47
56191741 TATGTGTGCT
* * ** *
56191751 AGTGTAAGACATGTCTAGGACAT-GCAT-TAGCCACATTA-TGAGAGCC
1 AGTGTAAGACCTGTCTAGGACATGGCATCGA-CCTGA-TAGTGAAAGCC
** *
56191797 AGTGTAAGATATGTC-AGGACAT-GCATCGGCCTTGAGATA-T-ACAAGCC
1 AGTGTAAGACCTGTCTAGGACATGGCATCGACC-T--GATAGTGA-AAGCC
* * * * *
56191844 AGTGTAAGACATGTATGGGACAT-GCATCGGCCTCGAGGTA-T-ACAAGCT
1 AGTGTAAGACCTGTCTAGGACATGGCATCGACCT-GA--TAGTGA-AAGCC
* * * * * *
56191892 AGTGTAAGACCTGTCTAGGATATGGCAT-TAGCTTG-TTGTG--TGTC
1 AGTGTAAGACCTGTCTAGGACATGGCATCGA-CCTGATAGTGAAAGCC
* * *
56191936 AGTGTAAGACCTGTCTGGGACATGGCATCGACACTAATAGATGAGAGCC
1 AGTGTAAGACCTGTCTAGGACATGGCATCGAC-CTGATAG-TGAAAGCC
* **** * *
56191985 AGTGTAAGACCTGTCTAAGACACAATATCGGCCTCGATATGTGAAAGTC
1 AGTGTAAGACCTGTCTAGGACATGGCATCGACCT-GATA-GTGAAAGCC
* **
56192034 AGTGTAAGACCTGTCTAGGACATGGCATCGACTTTGAT-GTGTTAGCC
1 AGTGTAAGACCTGTCTAGGACATGGCATCGAC-CTGATAGTGAAAGCC
56192081 AGTGTAAGACCATGTCTAGGACAT
1 AGTGTAAGACC-TGTCTAGGACAT
56192105 AACGTTGGCA
Statistics
Matches: 236, Mismatches: 50, Indels: 42
0.72 0.15 0.13
Matches are distributed among these distances:
44 28 0.12
45 16 0.07
46 20 0.08
47 40 0.17
48 59 0.25
49 71 0.30
50 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (47 bp):
AGTGTAAGACCTGTCTAGGACATGGCATCGACCTGATAGTGAAAGCC
Found at i:56196946 original size:10 final size:10
Alignment explanation
Indices: 56196924--56196970 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
56196914 AAATCTATCG
*
56196924 AAAA-TAATC
1 AAAATTAATT
56196933 AAAATTAATT
1 AAAATTAATT
*
56196943 AAAATTTGATAT
1 AAAA-TTAAT-T
56196955 AAAATTAATT
1 AAAATTAATT
56196965 AAAATT
1 AAAATT
56196971 CAACATGTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 4 0.12
10 15 0.47
11 8 0.25
12 5 0.16
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (10 bp):
AAAATTAATT
Found at i:56198670 original size:27 final size:27
Alignment explanation
Indices: 56198653--56198914 Score: 326
Period size: 27 Copynumber: 9.6 Consensus size: 27
56198643 ATATTAAGTC
56198653 CGCACACTCAGTGCTATATAGTCAACT
1 CGCACACTCAGTGCTATATAGTCAACT
* *
56198680 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTCAGTGCTATATAGTC-AACT
* *
56198708 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAGTCAACT
* *
56198735 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTCAGTGCTATATAGTC-AACT
* *
56198763 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAGTCAACT
* *
56198790 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTCAGTGCTATATAGTC-AACT
* *
56198818 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAGTCAACT
* *
56198845 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTCAGTGCTATATAGTC-AACT
* * *
56198873 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTCAGTGCTATATAGTCAACT
*
56198900 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
56198915 GCACAATTTA
Statistics
Matches: 228, Mismatches: 3, Indels: 8
0.95 0.01 0.03
Matches are distributed among these distances:
27 120 0.53
28 108 0.47
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAGTCAACT
Found at i:56198737 original size:55 final size:55
Alignment explanation
Indices: 56198653--56198914 Score: 497
Period size: 55 Copynumber: 4.8 Consensus size: 55
56198643 ATATTAAGTC
* *
56198653 CGCACACTCAGTGCTATATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
56198708 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
56198763 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
56198818 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
*
56198873 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
56198915 GCACAATTTA
Statistics
Matches: 204, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
55 204 1.00
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
Found at i:56200930 original size:30 final size:30
Alignment explanation
Indices: 56200890--56200949 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
56200880 TCTTATCCTG
*
56200890 CAAAATTTGCAACACTAATCTCAGGTGCTC
1 CAAAATTTGCAACACCAATCTCAGGTGCTC
* *
56200920 CAAATTTTGCAACACCAGTCTCAGGTGCTC
1 CAAAATTTGCAACACCAATCTCAGGTGCTC
56200950 AGCATGTTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (30 bp):
CAAAATTTGCAACACCAATCTCAGGTGCTC
Found at i:56210235 original size:67 final size:67
Alignment explanation
Indices: 56210127--56210259 Score: 257
Period size: 67 Copynumber: 2.0 Consensus size: 67
56210117 TTGCAGGGGT
56210127 CGACTACACTGACCTTTGCCCATTACGACTTGGATATCTCCCTGCACGGGGCTTCAATACTAATG
1 CGACTACACTGACCTTTGCCCATTACGACTTGGATATCTCCCTGCACGGGGCTTCAATACTAATG
56210192 CC
66 CC
*
56210194 CGACTACACTGACCTTTGCCCATTACGACTTGGATATCTCCCTGCACGGGGCTTCAATACTGATG
1 CGACTACACTGACCTTTGCCCATTACGACTTGGATATCTCCCTGCACGGGGCTTCAATACTAATG
56210259 C
66 C
56210260 TGTTTGTTTC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.27
Consensus pattern (67 bp):
CGACTACACTGACCTTTGCCCATTACGACTTGGATATCTCCCTGCACGGGGCTTCAATACTAATG
CC
Found at i:56211305 original size:27 final size:27
Alignment explanation
Indices: 56211275--56211452 Score: 171
Period size: 27 Copynumber: 6.6 Consensus size: 27
56211265 ATATTGAGCC
* *
56211275 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
56211302 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
56211329 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
56211357 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
56211384 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
56211411 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
56211438 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
56211453 GTACAATTTA
Statistics
Matches: 127, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
27 102 0.80
28 25 0.20
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:56211414 original size:82 final size:81
Alignment explanation
Indices: 56211296--56211451 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
56211286 TGCTATATAA
* * *
56211296 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTC-GAATCGCA
56211361 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
56211378 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCA
56211442 CACTTAGTGC
65 CACTTAGTGC
56211452 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 19 0.29
82 47 0.71
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:56215170 original size:30 final size:31
Alignment explanation
Indices: 56215096--56215186 Score: 132
Period size: 31 Copynumber: 3.0 Consensus size: 31
56215086 AGCTGTTACA
*
56215096 CTATACTTTTTAAATTGGTCAAGTTTAG-CC
1 CTATACTTTTTGAATTGGTCAAGTTTAGTCC
*
56215126 CTTGTACTTTTTGAATTGGTCAAGTTTAGTCC
1 C-TATACTTTTTGAATTGGTCAAGTTTAGTCC
*
56215158 CTATAC-TTTTGAATTGGCCAAGTTTAGTC
1 CTATACTTTTTGAATTGGTCAAGTTTAGTC
56215187 TTGATCCAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
30 23 0.42
31 29 0.53
32 3 0.05
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.44
Consensus pattern (31 bp):
CTATACTTTTTGAATTGGTCAAGTTTAGTCC
Found at i:56220797 original size:8 final size:8
Alignment explanation
Indices: 56220784--56220808 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
56220774 GAAATAAACA
56220784 TGATAAAT
1 TGATAAAT
56220792 TGATAAAT
1 TGATAAAT
56220800 TGATAAAT
1 TGATAAAT
56220808 T
1 T
56220809 TTGACAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (8 bp):
TGATAAAT
Found at i:56222340 original size:31 final size:31
Alignment explanation
Indices: 56222305--56222369 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
56222295 TAATAAAATG
*
56222305 GTCATTGAACTATTCAAAAGATTTCACTTAA
1 GTCATTGAACTATTCAAAACATTTCACTTAA
*
56222336 GTCATTGAACTATTCAAAACATTTCATTTAA
1 GTCATTGAACTATTCAAAACATTTCACTTAA
56222367 GTC
1 GTC
56222370 CTTGGACAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (31 bp):
GTCATTGAACTATTCAAAACATTTCACTTAA
Found at i:56226491 original size:12 final size:12
Alignment explanation
Indices: 56226474--56226501 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
56226464 GTCTTTGTTT
56226474 ACACGGGCAGAC
1 ACACGGGCAGAC
56226486 ACACGGGCAGAC
1 ACACGGGCAGAC
56226498 ACAC
1 ACAC
56226502 TTTCAAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.36, G:0.29, T:0.00
Consensus pattern (12 bp):
ACACGGGCAGAC
Found at i:56236049 original size:22 final size:22
Alignment explanation
Indices: 56236019--56236068 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
56236009 GTTCTTCATT
*
56236019 GTCACCTTGTTTATTACCGATA
1 GTCAACTTGTTTATTACCGATA
56236041 GTCAACTTGTTTATTACCGATA
1 GTCAACTTGTTTATTACCGATA
56236063 GTCAAC
1 GTCAAC
56236069 ATACAATCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (22 bp):
GTCAACTTGTTTATTACCGATA
Found at i:56245169 original size:27 final size:26
Alignment explanation
Indices: 56245132--56245243 Score: 100
Period size: 27 Copynumber: 4.2 Consensus size: 26
56245122 AGCATGGCTG
* *
56245132 CCAGGACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGACAGAGCCA
*
56245158 CCAGATACAGATAATCGTGCCAGAGCCA
1 CCAGA-ACAGATAAT-GTGACAGAGCCA
*
56245186 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCA
* * * *
56245213 TCA-AATCAGATATTTGTGGCATAGCCA
1 CCAGAA-CAGATA-ATGTGACAGAGCCA
56245240 CCAG
1 CCAG
56245244 GACACTTCCT
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
26 6 0.08
27 50 0.68
28 17 0.23
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATAATGTGACAGAGCCA
Found at i:56245223 original size:54 final size:54
Alignment explanation
Indices: 56245132--56245243 Score: 127
Period size: 54 Copynumber: 2.1 Consensus size: 54
56245122 AGCATGGCTG
* * *
56245132 CCAGGACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGCCAGAGCCA
1 CCAGAACAGATAATGTGACAGAGCCACCAAATACAGATAATCGTGCCAGAGCCA
* * * * * *
56245186 CCAGAACAGATATATGTGGCAGAGCCATCAAAT-CAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCACCAAATACAGATAATCGTGCCAGAGCCA
56245240 CCAG
1 CCAG
56245244 GACACTTCCT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
54 32 0.67
55 16 0.33
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATAATGTGACAGAGCCACCAAATACAGATAATCGTGCCAGAGCCA
Found at i:56248897 original size:36 final size:36
Alignment explanation
Indices: 56248850--56248921 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
56248840 ATAAGCAAAT
*
56248850 AGTGCTTAGTAAGCTTGTATAATCTTAAACTTTAAC
1 AGTGCTTAGTAAGCTCGTATAATCTTAAACTTTAAC
56248886 AGTGCTTAGTAAGCTCGTATAATCTTAAACTTTAAC
1 AGTGCTTAGTAAGCTCGTATAATCTTAAACTTTAAC
56248922 TTCCTAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (36 bp):
AGTGCTTAGTAAGCTCGTATAATCTTAAACTTTAAC
Found at i:56249270 original size:26 final size:28
Alignment explanation
Indices: 56249207--56249270 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 28
56249197 TAAGTACTTC
56249207 ATAT-AACCA-TTCATATATCTATTTCT
1 ATATAAACCATTTCATATATCTATTTCT
*
56249233 ATATAAA-CATTTCGTATAGTC-ATTT-T
1 ATATAAACCATTTCATATA-TCTATTTCT
56249259 ATA-AAACCATTT
1 ATATAAACCATTT
56249271 ATCATGTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
25 3 0.09
26 15 0.45
27 13 0.39
28 2 0.06
ACGTcount: A:0.38, C:0.16, G:0.03, T:0.44
Consensus pattern (28 bp):
ATATAAACCATTTCATATATCTATTTCT
Found at i:56252665 original size:26 final size:26
Alignment explanation
Indices: 56252633--56252692 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
56252623 TTCACCAGCT
56252633 CAAAGCCTACTAAATAAACATCGGCC
1 CAAAGCCTACTAAATAAACATCGGCC
* * * *
56252659 CATAGCCTACTAAGTAATCATCGGCT
1 CAAAGCCTACTAAATAAACATCGGCC
56252685 CAAAGCCT
1 CAAAGCCT
56252693 GCTATTCAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.37, C:0.30, G:0.13, T:0.20
Consensus pattern (26 bp):
CAAAGCCTACTAAATAAACATCGGCC
Found at i:56254021 original size:50 final size:50
Alignment explanation
Indices: 56253915--56254114 Score: 321
Period size: 50 Copynumber: 4.0 Consensus size: 50
56253905 ATATGCAAGA
* * * *
56253915 TCAAGTATATCATCACATAAATACTTATC-ATATGGCCAAATATACAAGGT
1 TCAA-TATATCATCACATAAATACTTACCTACATGGCCGAATACACAAGGT
*
56253965 TCAATATATCATCACATGAATACTTACCTACATGGCCGAATACACAAGGT
1 TCAATATATCATCACATAAATACTTACCTACATGGCCGAATACACAAGGT
*
56254015 TCAATATATCATCACATAAATACTTACCTACATGGTCGAATACACAAGGT
1 TCAATATATCATCACATAAATACTTACCTACATGGCCGAATACACAAGGT
*
56254065 TCAATATATCATCGCATAAATACTTACCTACATGGCCGAATACACAAGGT
1 TCAATATATCATCACATAAATACTTACCTACATGGCCGAATACACAAGGT
56254115 CATTTAGCTC
Statistics
Matches: 140, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
49 22 0.16
50 118 0.84
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.28
Consensus pattern (50 bp):
TCAATATATCATCACATAAATACTTACCTACATGGCCGAATACACAAGGT
Found at i:56255363 original size:13 final size:14
Alignment explanation
Indices: 56255345--56255376 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
56255335 AATTTGCAAC
56255345 TTAAAGCCTCC-AA
1 TTAAAGCCTCCAAA
56255358 TTAAAGCCTCCAAA
1 TTAAAGCCTCCAAA
56255372 TTAAA
1 TTAAA
56255377 AGAACAACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (14 bp):
TTAAAGCCTCCAAA
Found at i:56256498 original size:21 final size:21
Alignment explanation
Indices: 56256474--56256514 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
56256464 CTTTTCTTTA
56256474 TTAAC-TAATAAAACATATATT
1 TTAACATAATAAAACA-ATATT
56256495 TTAACATAATAAAACAATAT
1 TTAACATAATAAAACAATAT
56256515 CAACCGTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (21 bp):
TTAACATAATAAAACAATATT
Found at i:56282066 original size:17 final size:17
Alignment explanation
Indices: 56282024--56282104 Score: 60
Period size: 17 Copynumber: 4.6 Consensus size: 17
56282014 AATTCAATTT
*
56282024 TAATATAAATAA-TCAA
1 TAATATAAATAATTTAA
56282040 T-ATGACTAAATAATTTAA
1 TAAT-A-TAAATAATTTAA
*
56282058 TAATATAAATAATATAA
1 TAATATAAATAATTTAA
* *
56282075 -AATGTGAAATTTAACTTAA
1 TAATAT-AAA--TAATTTAA
56282094 TAATATAAATA
1 TAATATAAATA
56282105 GTAGATATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
15 2 0.04
16 6 0.12
17 23 0.45
18 5 0.10
19 11 0.22
20 4 0.08
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (17 bp):
TAATATAAATAATTTAA
Found at i:56282368 original size:30 final size:30
Alignment explanation
Indices: 56282325--56282387 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
56282315 TGGGAGGTGG
*
56282325 AATGGGAAGGGAGTAAAAGTTTTAGGGAGAA
1 AATGGGAAGGGAGTAAAAATTTT-GGGAGAA
*
56282356 AATGGG-AGGGAGTAAAAATTTTGGGGGAA
1 AATGGGAAGGGAGTAAAAATTTTGGGAGAA
56282385 AAT
1 AAT
56282388 AAAAAGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 9 0.30
30 15 0.50
31 6 0.20
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (30 bp):
AATGGGAAGGGAGTAAAAATTTTGGGAGAA
Found at i:56283789 original size:31 final size:31
Alignment explanation
Indices: 56283754--56283817 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
56283744 CCTTTTCATA
*
56283754 TTTCATATTTCATAACACTGGGCCGAAGTCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
* ** *
56283785 TTTCATATTTTATATTATTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
56283816 TT
1 TT
56283818 ATTGTAAACG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:56284081 original size:25 final size:25
Alignment explanation
Indices: 56284026--56284108 Score: 125
Period size: 25 Copynumber: 3.4 Consensus size: 25
56284016 CTGGAGGCCT
*
56284026 AGCCTCTTTTAAT-AACTGGGG-TAA
1 AGCC-CTTTTAATAAACTGGGGCAAA
*
56284050 AGCCCTTTTGATAAACTGGGGCAAA
1 AGCCCTTTTAATAAACTGGGGCAAA
56284075 AGCCCTTTTAATAAACTGGGGCAAA
1 AGCCCTTTTAATAAACTGGGGCAAA
56284100 AGCCCTTTT
1 AGCCCTTTT
56284109 TGCACTTCCT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
23 7 0.13
24 12 0.22
25 35 0.65
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (25 bp):
AGCCCTTTTAATAAACTGGGGCAAA
Found at i:56284179 original size:20 final size:20
Alignment explanation
Indices: 56284156--56284222 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
56284146 TTATGAATAC
56284156 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
56284176 ATCATGTGCATATCATATAT
1 ATCATGTGCATATCATACAT
56284196 ATCATGTGCATATCATATCA-
1 ATCATGTGCATATCATA-CAT
56284216 ATCATGT
1 ATCATGT
56284223 ATATCAAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 43 0.98
21 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.37
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:56284187 original size:11 final size:11
Alignment explanation
Indices: 56284156--56284211 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
56284146 TTATGAATAC
56284156 ATCATGTGCAT
1 ATCATGTGCAT
*
56284167 ATCA--TACAT
1 ATCATGTGCAT
56284176 ATCATGTGCAT
1 ATCATGTGCAT
*
56284187 ATCATAT--AT
1 ATCATGTGCAT
56284196 ATCATGTGCAT
1 ATCATGTGCAT
56284207 ATCAT
1 ATCAT
56284212 ATCAATCATG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 16 0.43
11 21 0.57
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.38
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:56291842 original size:31 final size:31
Alignment explanation
Indices: 56291804--56291867 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
56291794 CCTTTTCATA
* *
56291804 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTCCATAACACTGAGCCGAAGCCT
**
56291835 TTTCATATTCCATATTACTGAGCCGAAGCCT
1 TTTCATATTCCATAACACTGAGCCGAAGCCT
56291866 TT
1 TT
56291868 ATTGTAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (31 bp):
TTTCATATTCCATAACACTGAGCCGAAGCCT
Found at i:56292130 original size:25 final size:25
Alignment explanation
Indices: 56292075--56292157 Score: 125
Period size: 25 Copynumber: 3.4 Consensus size: 25
56292065 CTGGAGGCCT
*
56292075 AGCCTCTTTTAAT-AACTGGGG-TAA
1 AGCC-CTTTTAATAAACTGGGGCAAA
*
56292099 AGCCCTTTTGATAAACTGGGGCAAA
1 AGCCCTTTTAATAAACTGGGGCAAA
56292124 AGCCCTTTTAATAAACTGGGGCAAA
1 AGCCCTTTTAATAAACTGGGGCAAA
56292149 AGCCCTTTT
1 AGCCCTTTT
56292158 TGCACTTCCT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
23 7 0.13
24 12 0.22
25 35 0.65
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (25 bp):
AGCCCTTTTAATAAACTGGGGCAAA
Found at i:56292228 original size:20 final size:20
Alignment explanation
Indices: 56292205--56292251 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
56292195 TTATGAATAC
56292205 ATCATGTGCATATCATA-CA
1 ATCATGTGCATATCATATCA
56292224 TATCATGTGCATATCATATCA
1 -ATCATGTGCATATCATATCA
56292245 ATCATGT
1 ATCATGT
56292252 ATATCAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATATCA
Found at i:56295436 original size:43 final size:42
Alignment explanation
Indices: 56295389--56295524 Score: 164
Period size: 43 Copynumber: 3.2 Consensus size: 42
56295379 AAAAAACGTT
* * *
56295389 GCTAAAGATCATGACCTTTAGTGGCACTTTTCTCACAAACGCC
1 GCTAAAG-TCATGACCTTTAGCGGCGCTTTTCACACAAACGCC
*
56295432 GCTAAAGGTCATGACCTTTAGCAGCGCTTTTCACACAAACGCC
1 GCTAAA-GTCATGACCTTTAGCGGCGCTTTTCACACAAACGCC
* * * * *
56295475 GCTAAATGTCAAGACCTTTAGCGGCGCTTTACCCAAAAACGTC
1 GCTAAA-GTCATGACCTTTAGCGGCGCTTTTCACACAAACGCC
56295518 GCTAAAG
1 GCTAAAG
56295525 GTAATGAAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
42 1 0.01
43 79 0.98
44 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.24
Consensus pattern (42 bp):
GCTAAAGTCATGACCTTTAGCGGCGCTTTTCACACAAACGCC
Found at i:56295586 original size:27 final size:28
Alignment explanation
Indices: 56295539--56295592 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
56295529 TGAAATTTAA
*
56295539 AAAAAAATAAAATATTATAAAAGTCATG
1 AAAAAAATAAAAAATTATAAAAGTCATG
* *
56295567 AAAAATATAAAAAATT-TAAAATTCAT
1 AAAAAAATAAAAAATTATAAAAGTCAT
56295593 TATTAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (28 bp):
AAAAAAATAAAAAATTATAAAAGTCATG
Found at i:56295727 original size:19 final size:21
Alignment explanation
Indices: 56295686--56295733 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
56295676 TTAAAATTTT
56295686 AACTAAAAATATTAAAATAAA
1 AACTAAAAATATTAAAATAAA
* *
56295707 AA-TAAAAAT-TTAGAATCAA
1 AACTAAAAATATTAAAATAAA
56295726 AACTAAAA
1 AACTAAAA
56295734 TAAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.23
Consensus pattern (21 bp):
AACTAAAAATATTAAAATAAA
Found at i:56297539 original size:44 final size:44
Alignment explanation
Indices: 56297476--56297564 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
56297466 ATATAGCAAC
*
56297476 ATATAAGGTATAACATCTGTTAAAATAAAGTTGACACCTAAATG
1 ATATAAGGCATAACATCTGTTAAAATAAAGTTGACACCTAAATG
56297520 ATATAAGGCATAACATCTGTTAAAATAAAGTTGACACCTAAATG
1 ATATAAGGCATAACATCTGTTAAAATAAAGTTGACACCTAAATG
56297564 A
1 A
56297565 AAGCGATAAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.28
Consensus pattern (44 bp):
ATATAAGGCATAACATCTGTTAAAATAAAGTTGACACCTAAATG
Found at i:56301259 original size:32 final size:32
Alignment explanation
Indices: 56301218--56301280 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
56301208 TAAGTAAACT
56301218 TTAAATCCTAAACCATTTAATATATATAAAGC
1 TTAAATCCTAAACCATTTAATATATATAAAGC
56301250 TTAAATCCTAAACCATTTAATATATATAAAG
1 TTAAATCCTAAACCATTTAATATATATAAAG
56301281 TCTAATCCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.48, C:0.14, G:0.03, T:0.35
Consensus pattern (32 bp):
TTAAATCCTAAACCATTTAATATATATAAAGC
Found at i:56301380 original size:22 final size:22
Alignment explanation
Indices: 56301336--56301381 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
56301326 CTTAAACCCC
* *
56301336 AACCCTTAAACCATAATCCTTA
1 AACCCATAAACCATAAACCTTA
* *
56301358 AACCCATAATCCATAAACTTTA
1 AACCCATAAACCATAAACCTTA
56301380 AA
1 AA
56301382 ATAGTAACTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (22 bp):
AACCCATAAACCATAAACCTTA
Found at i:56301434 original size:14 final size:14
Alignment explanation
Indices: 56301400--56301444 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
56301390 TCATACACTT
* *
56301400 TAAACTCTAAACCA
1 TAAACCCTAAACTA
* *
56301414 TATACCCTAAATTA
1 TAAACCCTAAACTA
56301428 TAAACCCTAAACTA
1 TAAACCCTAAACTA
56301442 TAA
1 TAA
56301445 TGATAATTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:56301580 original size:14 final size:14
Alignment explanation
Indices: 56301561--56301592 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
56301551 TCATAATCTT
*
56301561 TAAATCCTAAACCA
1 TAAATCCTAAAACA
56301575 TAAATCCTAAAACA
1 TAAATCCTAAAACA
56301589 TAAA
1 TAAA
56301593 CCCTGAACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAATCCTAAAACA
Found at i:56301660 original size:25 final size:25
Alignment explanation
Indices: 56301615--56301662 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
56301605 AACACTTAAA
*
56301615 CCTTAAATCACAACCCTTAAACCAC
1 CCTTAAACCACAACCCTTAAACCAC
*
56301640 CCTTAAACCATAATCCC-TAAACC
1 CCTTAAACCACAA-CCCTTAAACC
56301663 CATATCTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.21
Consensus pattern (25 bp):
CCTTAAACCACAACCCTTAAACCAC
Found at i:56301710 original size:28 final size:29
Alignment explanation
Indices: 56301643--56301711 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
56301633 AAACCACCCT
* *
56301643 TAAACCATAATCCCTAAACCCATATCTCA
1 TAAACCATAAACCCTAAACCCATATATCA
*
56301672 TAAA-CATTAAACCCTTAA-CCATATATCA
1 TAAACCA-TAAACCCTAAACCCATATATCA
*
56301700 TAAACCCTAAAC
1 TAAACCATAAAC
56301712 TATAATGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
28 20 0.59
29 14 0.41
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (29 bp):
TAAACCATAAACCCTAAACCCATATATCA
Found at i:56303017 original size:27 final size:27
Alignment explanation
Indices: 56302980--56303117 Score: 176
Period size: 27 Copynumber: 5.1 Consensus size: 27
56302970 AGCATGGCTG
* *
56302980 CCAGA-ACAGATAATGTGACAGAGTCA
1 CCAGATACAGATAATGTGGCAGAGCCA
56303006 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGATACAGATAAT-GTGGCAGAGCCA
*
56303034 CCAGA-ATAGATATATGTGGCAGAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
56303061 CCAGATA-AGATATATGTGGCAGAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
* *
56303088 CCAGAT-CAGATATTGTGGCATAGCCA
1 CCAGATACAGATAATGTGGCAGAGCCA
56303114 CCAG
1 CCAG
56303118 GACGCTTCCT
Statistics
Matches: 102, Mismatches: 5, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
26 21 0.21
27 63 0.62
28 18 0.18
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.17
Consensus pattern (27 bp):
CCAGATACAGATAATGTGGCAGAGCCA
Found at i:56305148 original size:39 final size:40
Alignment explanation
Indices: 56305064--56305188 Score: 144
Period size: 40 Copynumber: 3.1 Consensus size: 40
56305054 ACAAGTGGCG
* * * * * *
56305064 TTTTTTTAAAAGCGCCGCTAAAGGTGA-ACTTATAGCGGCG
1 TTTTTTAAAAAGCGCCGCTAATGCTCATTCTT-TAGCGGCA
* *
56305104 TTTTTTAAAAAGCGCCGCTAATGCTCGTTCTTTAGTGGCA
1 TTTTTTAAAAAGCGCCGCTAATGCTCATTCTTTAGCGGCA
* *
56305144 TTTTTTAAAAAGCGCCGCTAATGCTTATTCTTTGGCGGCA
1 TTTTTTAAAAAGCGCCGCTAATGCTCATTCTTTAGCGGCA
56305184 TTTTT
1 TTTTT
56305189 CATTCAAACG
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 69 0.96
41 3 0.04
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (40 bp):
TTTTTTAAAAAGCGCCGCTAATGCTCATTCTTTAGCGGCA
Found at i:56311467 original size:27 final size:27
Alignment explanation
Indices: 56311436--56311613 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
56311426 TGAATTGTAC
56311436 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
56311463 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
56311489 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
56311517 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
56311545 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
56311572 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
56311599 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
56311614 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:56311550 original size:82 final size:81
Alignment explanation
Indices: 56311437--56311592 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
56311427 GAATTGTACA
* *
56311437 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
56311501 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
56311518 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
56311583 TGCGAGTTGA
65 TGCGAATTGA
56311593 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:56311604 original size:82 final size:81
Alignment explanation
Indices: 56311433--56311613 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
56311423 GATTGAATTG
* *
56311433 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
56311498 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
56311514 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
56311578 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
56311596 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
56311614 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:56322813 original size:19 final size:18
Alignment explanation
Indices: 56322787--56322829 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
56322777 TTGAGTTTTG
56322787 TTTT-TTTATGTTATATA
1 TTTTATTTATGTTATATA
*
56322804 TATTTATTTATGTTATTTA
1 T-TTTATTTATGTTATATA
56322823 TTTTATT
1 TTTTATT
56322830 GTATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 9 0.39
19 13 0.57
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (18 bp):
TTTTATTTATGTTATATA
Found at i:56323518 original size:17 final size:17
Alignment explanation
Indices: 56323496--56323528 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
56323486 GGGTTTTTAG
56323496 GTGATTTTTGGTGCCAA
1 GTGATTTTTGGTGCCAA
56323513 GTGATTTTTGGTGCCA
1 GTGATTTTTGGTGCCA
56323529 CACACAGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.12, G:0.30, T:0.42
Consensus pattern (17 bp):
GTGATTTTTGGTGCCAA
Found at i:56323597 original size:21 final size:21
Alignment explanation
Indices: 56323573--56323612 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
56323563 GTTTTCACTC
56323573 GGGCATGTGAGATTTCTACAT
1 GGGCATGTGAGATTTCTACAT
*
56323594 GGGCGTGTGAGATTTCTAC
1 GGGCATGTGAGATTTCTAC
56323613 GTAGCCGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.15, G:0.33, T:0.33
Consensus pattern (21 bp):
GGGCATGTGAGATTTCTACAT
Found at i:56323621 original size:21 final size:21
Alignment explanation
Indices: 56323578--56323622 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
56323568 CACTCGGGCA
* *
56323578 TGTGAGATTTCTACATGGGCG
1 TGTGAGATTTCTACATAGCCG
*
56323599 TGTGAGATTTCTACGTAGCCG
1 TGTGAGATTTCTACATAGCCG
56323620 TGT
1 TGT
56323623 CTGCTTTGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.31, T:0.36
Consensus pattern (21 bp):
TGTGAGATTTCTACATAGCCG
Found at i:56330434 original size:40 final size:40
Alignment explanation
Indices: 56330374--56330555 Score: 217
Period size: 40 Copynumber: 4.5 Consensus size: 40
56330364 TATTCGAATG
* *
56330374 ATATCCAGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * * *
56330414 ATATCCGGACTAAGATCCGAAGGTATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* * *
56330454 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
*
56330494 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
*
56330534 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGATCCGAAG
56330556 TCCTTGTGCG
Statistics
Matches: 121, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 1 0.01
40 117 0.97
41 3 0.02
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:56330507 original size:80 final size:80
Alignment explanation
Indices: 56330374--56330555 Score: 242
Period size: 80 Copynumber: 2.3 Consensus size: 80
56330364 TATTCGAATG
* * * * *
56330374 ATATCCAGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAG-TCCCGAAGGC
* *
56330438 ATTTGTGCGAGTTG-CT
65 ATTTATGCGAG-TGACC
* *
56330454 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
*
56330519 TTTATGCTAGTGACC
66 TTTATGCGAGTGACC
56330534 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
56330556 TCCTTGTGCG
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
79 3 0.03
80 87 0.97
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
TTTATGCGAGTGACC
Found at i:56339260 original size:24 final size:24
Alignment explanation
Indices: 56339228--56339308 Score: 135
Period size: 24 Copynumber: 3.4 Consensus size: 24
56339218 CTATCCAGGG
*
56339228 CTTCCCGATATGATTCTTTGTGAA
1 CTTCCCGATATGGTTCTTTGTGAA
56339252 CTTCCCGATATGGTTCTTTGTGAA
1 CTTCCCGATATGGTTCTTTGTGAA
* *
56339276 CTTCCCAATTTGGTTCTTTGTGAA
1 CTTCCCGATATGGTTCTTTGTGAA
56339300 CTTCCCGAT
1 CTTCCCGAT
56339309 TATGTCTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (24 bp):
CTTCCCGATATGGTTCTTTGTGAA
Found at i:56341781 original size:13 final size:13
Alignment explanation
Indices: 56341763--56341788 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56341753 TTCAGGCAAA
56341763 TCTCTAATTTCTT
1 TCTCTAATTTCTT
56341776 TCTCTAATTTCTT
1 TCTCTAATTTCTT
56341789 CAACATTGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (13 bp):
TCTCTAATTTCTT
Found at i:56344212 original size:39 final size:39
Alignment explanation
Indices: 56344150--56344345 Score: 302
Period size: 39 Copynumber: 5.0 Consensus size: 39
56344140 AATTATATTA
* * *
56344150 CCAGCACAAAGCCTACGGGACTTTAGCTCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
*
56344189 CCAGTACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
*
56344228 CCAGCACGAAGCCAGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
* **
56344267 CTAGCATAAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
* *
56344306 CCAGTACGAAGCCTGCGGAACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
56344345 C
1 C
56344346 TAGTGTCTTG
Statistics
Matches: 142, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 142 1.00
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (39 bp):
CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
Found at i:56346639 original size:14 final size:17
Alignment explanation
Indices: 56346608--56346642 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
56346598 GTATGTCCAT
56346608 TTCTTATCTTCTTCTTC
1 TTCTTATCTTCTTCTTC
* *
56346625 TTCTTATTTTTTTCTTC
1 TTCTTATCTTCTTCTTC
56346642 T
1 T
56346643 CCTCTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (17 bp):
TTCTTATCTTCTTCTTC
Found at i:56346641 original size:20 final size:18
Alignment explanation
Indices: 56346616--56346654 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
56346606 ATTTCTTATC
*
56346616 TTCTTCTTCTTCTTATTTTT
1 TTCTTC-TCCTCTT-TTTTT
56346636 TTCTTCTCCTCTTTTTTT
1 TTCTTCTCCTCTTTTTTT
56346654 T
1 T
56346655 GTAACACCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 6 0.33
20 6 0.33
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (18 bp):
TTCTTCTCCTCTTTTTTT
Found at i:56350128 original size:39 final size:39
Alignment explanation
Indices: 56350095--56350198 Score: 172
Period size: 39 Copynumber: 2.7 Consensus size: 39
56350085 TTCCATCATG
* *
56350095 TAGCCTGCGGACCTTAAGTCCGGTTATAATTCCAGCACA
1 TAGCCTGCGGACCCTAAGTCCGGATATAATTCCAGCACA
* *
56350134 TAGCCTGCAGACCCTAAGTCTGGATATAATTCCAGCACA
1 TAGCCTGCGGACCCTAAGTCCGGATATAATTCCAGCACA
56350173 TAGCCTGCGGACCCTAAGTCCGGATA
1 TAGCCTGCGGACCCTAAGTCCGGATA
56350199 AACATCACTG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (39 bp):
TAGCCTGCGGACCCTAAGTCCGGATATAATTCCAGCACA
Found at i:56358750 original size:19 final size:19
Alignment explanation
Indices: 56358726--56358769 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
56358716 CTTTCCCTTC
56358726 TCTTTCTTTCCTT-CTCTTT
1 TCTTTCTTTCCTTCCTC-TT
*
56358745 TCTTTCTTTCTTTCCTCTT
1 TCTTTCTTTCCTTCCTCTT
56358764 TCTTTC
1 TCTTTC
56358770 ACTTTCTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (19 bp):
TCTTTCTTTCCTTCCTCTT
Found at i:56358755 original size:15 final size:15
Alignment explanation
Indices: 56358700--56358755 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
56358690 CCTCTCCTTG
*
56358700 CTTTCATTCTCTTGTT
1 CTTTCCTTCTCTT-TT
56358716 CTTTCCCTTCTC-TTT
1 CTTT-CCTTCTCTTTT
56358731 CTTTCCTTCTCTTTT
1 CTTTCCTTCTCTTTT
*
56358746 CTTTCTTTCT
1 CTTTCCTTCT
56358756 TTCCTCTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
14 7 0.19
15 18 0.50
16 5 0.14
17 6 0.17
ACGTcount: A:0.02, C:0.32, G:0.02, T:0.64
Consensus pattern (15 bp):
CTTTCCTTCTCTTTT
Found at i:56358779 original size:19 final size:18
Alignment explanation
Indices: 56358725--56358781 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
56358715 TCTTTCCCTT
56358725 CTCTTTCTTTCC-TTCT-
1 CTCTTTCTTTCCTTTCTC
56358741 CT-TTTCTTT-CTTTCTTTC
1 CTCTTTCTTTCCTTTC--TC
56358759 CTCTTTCTTTCACTTTCTC
1 CTCTTTCTTTC-CTTTCTC
56358778 CTCT
1 CTCT
56358782 CTCCTCTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
14 1 0.03
15 10 0.29
16 2 0.06
17 1 0.03
18 2 0.06
19 13 0.38
21 5 0.15
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (18 bp):
CTCTTTCTTTCCTTTCTC
Found at i:56359006 original size:3 final size:3
Alignment explanation
Indices: 56358998--56359040 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
56358988 TTTTAATTAA
* * *
56358998 ATT ATT ATT ATT TTT ATT AGT ATT AGT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
56359041 GTTCTTTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:56359016 original size:12 final size:12
Alignment explanation
Indices: 56358999--56359058 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 12
56358989 TTTAATTAAA
*
56358999 TTATTATTATTT
1 TTATTAGTATTT
*
56359011 TTATTAGTATTA
1 TTATTAGTATTT
* * *
56359023 GTATTATTATTA
1 TTATTAGTATTT
*
56359035 TTATTAGT-TCT
1 TTATTAGTATTT
*
56359046 TTATTACTATTT
1 TTATTAGTATTT
56359058 T
1 T
56359059 ATTTTACGTT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
11 8 0.22
12 29 0.78
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (12 bp):
TTATTAGTATTT
Found at i:56363260 original size:40 final size:40
Alignment explanation
Indices: 56363182--56363274 Score: 125
Period size: 40 Copynumber: 2.3 Consensus size: 40
56363172 ATTACCACAA
*
56363182 GCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACTC
1 GCACAATTGCCTTCGGGTCTTAACCCGGACATAGCAACTC
* * * *
56363222 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCAC-AATTGCCTTCGGGTCTTAACCCGGACATAGCAACTC
56363262 GCACAATTGCCTT
1 GCACAATTGCCTT
56363275 TACATTCATA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
39 2 0.04
40 42 0.91
41 2 0.04
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.26
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAACCCGGACATAGCAACTC
Found at i:56363389 original size:141 final size:141
Alignment explanation
Indices: 56363135--56363414 Score: 533
Period size: 141 Copynumber: 2.0 Consensus size: 141
56363125 CAAAACGCTC
56363135 ACATTCATACCCAAGTTTCTTCGGAATTTAGCCGGATATTACCACAAGCACAATTGCCTTCGGGT
1 ACATTCATACCCAAGTTTCTTCGGAATTTAGCCGGATATTACCACAAGCACAATTGCCTTCGGGT
* *
56363200 CTTAACCCGGGCATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCA
66 CTTAACCCGGGCATAGCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTTGCA
*
56363265 CAATTGCCTTT
131 CAAATGCCTTT
56363276 ACATTCATACCCAAGTTTCTTCGGAATTTAGCCGGATATTACCACAAGCACAATTGCCTTCGGGT
1 ACATTCATACCCAAGTTTCTTCGGAATTTAGCCGGATATTACCACAAGCACAATTGCCTTCGGGT
56363341 CTTAACCCGGGCATAGCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTTGCA
66 CTTAACCCGGGCATAGCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTTGCA
56363406 CAAATGCCT
131 CAAATGCCT
56363415 GCGGGTCTTA
Statistics
Matches: 136, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
141 136 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (141 bp):
ACATTCATACCCAAGTTTCTTCGGAATTTAGCCGGATATTACCACAAGCACAATTGCCTTCGGGT
CTTAACCCGGGCATAGCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTTGCA
CAAATGCCTTT
Done.