Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 129 of 290
Found at i:43790293 original size:54 final size:53
Alignment explanation
Indices: 43790195--43790300 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 53
43790185 TAGGGTAACT
* *
43790195 CAGAGAGTTCACGGTCTAGCACATGGCTGAGAACACACCCGTGTGACCCAAAA
1 CAGAGAGTTCACGGTCTAGCACATCGCTCAGAACACACCCGTGTGACCCAAAA
* *
43790248 CAGAGAGTTACACGGTCTAGCACA-CGTTCA-AGCACACGCCAGTGTGACCCAAA
1 CAGAGAGTT-CACGGTCTAGCACATCGCTCAGAACACAC-CC-GTGTGACCCAAA
43790301 TTCAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
52 6 0.13
53 14 0.30
54 26 0.57
ACGTcount: A:0.32, C:0.29, G:0.24, T:0.15
Consensus pattern (53 bp):
CAGAGAGTTCACGGTCTAGCACATCGCTCAGAACACACCCGTGTGACCCAAAA
Found at i:43803080 original size:9 final size:10
Alignment explanation
Indices: 43803056--43803106 Score: 66
Period size: 11 Copynumber: 4.7 Consensus size: 10
43803046 CACAATAGTC
43803056 CTCTCACAATT
1 CTCTCA-AATT
43803067 CTCTCTAAATT
1 CTCTC-AAATT
43803078 CTCTCCAAATT
1 CTCT-CAAATT
43803089 CTCTCAAATTT
1 CTCTCAAA-TT
43803100 CTCTCAA
1 CTCTCAA
43803107 TTTTTGTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.11
11 31 0.84
12 2 0.05
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.39
Consensus pattern (10 bp):
CTCTCAAATT
Found at i:43803133 original size:22 final size:23
Alignment explanation
Indices: 43803097--43803139 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
43803087 TTCTCTCAAA
43803097 TTTCTCTCAATTTTTGTCAAAGC
1 TTTCTCTCAATTTTTGTCAAAGC
*
43803120 TTTCTCT-AATTTTTTTCAAA
1 TTTCTCTCAATTTTTGTCAAA
43803140 AAAATCTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.23, C:0.19, G:0.05, T:0.53
Consensus pattern (23 bp):
TTTCTCTCAATTTTTGTCAAAGC
Found at i:43803133 original size:23 final size:22
Alignment explanation
Indices: 43803097--43803139 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
43803087 TTCTCTCAAA
43803097 TTTCTCTCAATTTTTGTCAAAGC
1 TTTCTCTCAATTTTT-TCAAAGC
43803120 TTTCTCT-AATTTTTTTCAAA
1 TTTCTCTCAA-TTTTTTCAAA
43803140 AAAATCTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.23, C:0.19, G:0.05, T:0.53
Consensus pattern (22 bp):
TTTCTCTCAATTTTTTCAAAGC
Found at i:43804296 original size:7 final size:7
Alignment explanation
Indices: 43804284--43804309 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
43804274 TAGTCGTTTC
43804284 GTATTTA
1 GTATTTA
43804291 GTATTTA
1 GTATTTA
43804298 GTATTTA
1 GTATTTA
43804305 GTATT
1 GTATT
43804310 ACCTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:43805666 original size:127 final size:127
Alignment explanation
Indices: 43805351--43805976 Score: 1112
Period size: 127 Copynumber: 4.9 Consensus size: 127
43805341 GTAGAAACCT
* * *
43805351 TTTTTATATAG-TTTCATATAATAAAATAAAAGTTGTTTTTAATATTTAAATTGTACTTTACTTT
1 TTTTTATATAGTTTTAAT-TAAAAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTA-TTT
43805415 TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTTATTATTTTTATATTTA
64 TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATA-TTTTTATTATTTTTATATTT-
43805480 A
127 A
* *
43805481 TTTTTATATAGTTTCAATTAATAAAATAAAAGTT-TTTTTAATATTTTAATTGTACTTTATTTTT
1 TTTTTATATAGTTTTAATTAAAAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTATTTTT
43805545 TTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTTA
66 TTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTTA
43805607 TTTTTATATAGTTTTAATTAAAAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTATTTTT
1 TTTTTATATAGTTTTAATTAAAAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTATTTTT
43805672 TTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTTA
66 TTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTTA
43805734 TTTTTATATAGTTTTAATTAAAAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTATTTTT
1 TTTTTATATAGTTTTAATTAAAAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTATTTTT
43805799 TTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTTA
66 TTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTTA
*
43805861 TTTTTATATAGTTTTAATTAAAAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTTT
1 TTTTTATATAGTTTTAATTAAAAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTATTTTT
* * *
43805926 TTAATTTTAATATAATAAACGTTCTTTTAAATTAGCCAATAATTTTTATTA
66 TTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAAT-ATTTTTATTA
43805977 AAATAAATGT
Statistics
Matches: 484, Mismatches: 9, Indels: 8
0.97 0.02 0.02
Matches are distributed among these distances:
126 33 0.07
127 340 0.70
128 56 0.12
129 24 0.05
130 27 0.06
131 4 0.01
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.56
Consensus pattern (127 bp):
TTTTTATATAGTTTTAATTAAAAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTATTTTT
TTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTTA
Found at i:43809393 original size:24 final size:24
Alignment explanation
Indices: 43809358--43809407 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
43809348 TTTTTCCTTA
*
43809358 AAAAACACTAAAATCCTAAACCCT
1 AAAAACACTAAAATACTAAACCCT
*
43809382 AAAAAC-CTTAAACTACTAAACCCT
1 AAAAACAC-TAAAATACTAAACCCT
43809406 AA
1 AA
43809408 CCTTAAACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.54, C:0.28, G:0.00, T:0.18
Consensus pattern (24 bp):
AAAAACACTAAAATACTAAACCCT
Found at i:43809907 original size:30 final size:28
Alignment explanation
Indices: 43809871--43809937 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 28
43809861 AAATTATTTT
43809871 TAAAAAAATCTAAAAAATTCAAAAAAAAATA
1 TAAAAAAAT-T-AAAAATTC-AAAAAAAATA
* *
43809902 TAAAAATAATTTAAAATTCAAAAAATATA
1 TAAAAA-AATTAAAAATTCAAAAAAAATA
43809931 TAAAAAA
1 TAAAAAA
43809938 TAATAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 1 0.03
29 15 0.45
30 7 0.21
31 7 0.21
32 3 0.09
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (28 bp):
TAAAAAAATTAAAAATTCAAAAAAAATA
Found at i:43809938 original size:30 final size:30
Alignment explanation
Indices: 43809884--43809941 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
43809874 AAAAATCTAA
43809884 AAAATTCAAAAAAAAATATAAAAATAATTT
1 AAAATTCAAAAAAAAATATAAAAATAATTT
*
43809914 AAAATTC-AAAAAATATATAAAAAATAAT
1 AAAATTCAAAAAAAAATAT-AAAAATAAT
43809942 AATTTCTCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (30 bp):
AAAATTCAAAAAAAAATATAAAAATAATTT
Found at i:43810637 original size:11 final size:11
Alignment explanation
Indices: 43810610--43810652 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
43810600 TGACCTTTCC
43810610 AAGGTATGGG-
1 AAGGTATGGGA
*
43810620 TAGGTATGGGA
1 AAGGTATGGGA
*
43810631 AAGGTATGGGC
1 AAGGTATGGGA
43810642 AAGGTATGGGA
1 AAGGTATGGGA
43810653 TATATTCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:43810649 original size:22 final size:21
Alignment explanation
Indices: 43810610--43810652 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
43810600 TGACCTTTCC
*
43810610 AAGGTATGGGTAGGTATGGGA
1 AAGGTATGGGAAGGTATGGGA
43810631 AAGGTATGGGCAAGGTATGGGA
1 AAGGTATGGG-AAGGTATGGGA
43810653 TATATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (21 bp):
AAGGTATGGGAAGGTATGGGA
Found at i:43814722 original size:18 final size:18
Alignment explanation
Indices: 43814699--43814791 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
43814689 CCCAACTACT
*
43814699 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
43814717 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
43814735 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
*
43814753 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
43814771 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
43814789 GTA
1 GTA
43814792 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:43814751 original size:36 final size:36
Alignment explanation
Indices: 43814699--43814791 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
43814689 CCCAACTACT
*
43814699 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
43814735 GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
43814771 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
43814792 AACGGTCGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:43819084 original size:59 final size:59
Alignment explanation
Indices: 43819021--43819135 Score: 144
Period size: 57 Copynumber: 2.0 Consensus size: 59
43819011 AACTTGATAC
* * * * *
43819021 TTTTTATTAGTTTAGTATCTAAACTTTTTTTT-A-GCTCAATTTGATACATGAATTTAG
1 TTTTTTTTAATTTAATACCTAAACTTTTTTTTAAGGCTCAATTTGATACATAAATTTAG
* * *
43819078 TTTTTTTTAATTTAATACCTAAGCTTTTTTTTAAGGTTCAATTTGATACTTAAATTTA
1 TTTTTTTTAATTTAATACCTAAACTTTTTTTTAAGGCTCAATTTGATACATAAATTTA
43819136 TTAAATTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
57 27 0.56
58 1 0.02
59 20 0.42
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.54
Consensus pattern (59 bp):
TTTTTTTTAATTTAATACCTAAACTTTTTTTTAAGGCTCAATTTGATACATAAATTTAG
Found at i:43820506 original size:27 final size:27
Alignment explanation
Indices: 43820476--43820532 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
43820466 CAGGAGTTCC
43820476 TATAATAATCATAGGAATTTTTTATTT
1 TATAATAATCATAGGAATTTTTTATTT
43820503 TATAATAATCATAGGAATTTTTTATTT
1 TATAATAATCATAGGAATTTTTTATTT
43820530 TAT
1 TAT
43820533 CCTACTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.53
Consensus pattern (27 bp):
TATAATAATCATAGGAATTTTTTATTT
Found at i:43821284 original size:5 final size:5
Alignment explanation
Indices: 43821274--43821381 Score: 67
Period size: 5 Copynumber: 21.4 Consensus size: 5
43821264 TCTTAATATT
* * * * *
43821274 TCATA TCATA TCATA TCATA TTTCATA -CAAA TTATA TCCTA TCTTA TCCTA
1 TCATA TCATA TCATA TCATA --TCATA TCATA TCATA TCATA TCATA TCATA
* * * * * * *
43821325 TCATAA T-GTA TCATA TCATA TCAAA TCATA GCTTA TCATA TTATA TAAAA
1 TCAT-A TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
43821375 TCATA TC
1 TCATA TC
43821382 CTACCCCTAT
Statistics
Matches: 77, Mismatches: 21, Indels: 10
0.71 0.19 0.09
Matches are distributed among these distances:
4 5 0.06
5 65 0.84
6 2 0.03
7 5 0.06
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.41
Consensus pattern (5 bp):
TCATA
Found at i:43821929 original size:29 final size:29
Alignment explanation
Indices: 43821867--43821930 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
43821857 CCCACACTGT
* * **
43821867 CGTGTGCCCTACATAGCCTACCACACGGC
1 CGTGTGCCCTACACAACCTACCACAAAGC
*
43821896 TGTGTGCCCTACACAACCTACCACAAAGC
1 CGTGTGCCCTACACAACCTACCACAAAGC
43821925 CGTGTG
1 CGTGTG
43821931 GCAACACACA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.23, C:0.38, G:0.20, T:0.19
Consensus pattern (29 bp):
CGTGTGCCCTACACAACCTACCACAAAGC
Found at i:43827181 original size:16 final size:17
Alignment explanation
Indices: 43827150--43827183 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
43827140 AAAGGAAAAT
*
43827150 ATAGAGAACGTAAAGAA
1 ATAGAAAACGTAAAGAA
43827167 ATAGAAAAC-TAAAGAA
1 ATAGAAAACGTAAAGAA
43827183 A
1 A
43827184 AAATTGGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.65, C:0.06, G:0.18, T:0.12
Consensus pattern (17 bp):
ATAGAAAACGTAAAGAA
Found at i:43834973 original size:20 final size:19
Alignment explanation
Indices: 43834948--43835000 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
43834938 ATAGACCCAG
43834948 ATCATATTTAGATAGT-GCAA
1 ATCATA-TTAGATAGTAG-AA
* *
43834968 ATCATACTTATATAGTAGAT
1 ATCATA-TTAGATAGTAGAA
43834988 ATCATATTAGATA
1 ATCATATTAGATA
43835001 TACATACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 6 0.21
20 21 0.75
21 1 0.04
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (19 bp):
ATCATATTAGATAGTAGAA
Found at i:43835293 original size:42 final size:42
Alignment explanation
Indices: 43835234--43835318 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 42
43835224 TACCAGTACT
* * *
43835234 TCACACGGACTGGCACACGACCGTGTGAGC-CAAGTTAGAGAG
1 TCACACGGACTGACACACGACCATGTGA-CTCAAGTGAGAGAG
* *
43835276 TCACACGGCCTGACACACGTCCATGTGACTCAAGTGAGAGAG
1 TCACACGGACTGACACACGACCATGTGACTCAAGTGAGAGAG
43835318 T
1 T
43835319 TACATGGTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.03
42 36 0.97
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.16
Consensus pattern (42 bp):
TCACACGGACTGACACACGACCATGTGACTCAAGTGAGAGAG
Found at i:43843377 original size:31 final size:31
Alignment explanation
Indices: 43843339--43843402 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
43843329 GTATGCTGAG
* *
43843339 TAAAAACTCAGTGGTATTTTTATAATCCGAA
1 TAAAAACTCAGTGCTATTTCTATAATCCGAA
* *
43843370 TAAAAACTCAGTGCTATTTCTGTAATCTGAA
1 TAAAAACTCAGTGCTATTTCTATAATCCGAA
43843401 TA
1 TA
43843403 TTTAAAAACA
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:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (31 bp):
TAAAAACTCAGTGCTATTTCTATAATCCGAA
Found at i:43843775 original size:173 final size:174
Alignment explanation
Indices: 43843477--43843790 Score: 535
Period size: 173 Copynumber: 1.8 Consensus size: 174
43843467 TGACTATTAT
*
43843477 TTTTTTTATTTAAACAATATCCTAATTCACACAATTGTTATATAAATGATTATTCACATATCAAA
1 TTTTTTTATTTAAACAATATCCTAATTCACACAATTATTATATAAATGATTATTCACATATCAAA
* *
43843542 CCATATTATTCATACAATGGCATTAGTCATGCAATACTCAATTCATGGATACATCATTTCATACC
66 CCATATTATTCATACAATGGCATCAGTCATGCAATACTCAATTCATGAATACATCATTTCATACC
43843607 ATACTCAATTCTCATTAATGTCTAGTATCATATCATAACTATCA
131 ATACTCAATTCTCATTAATGTCTAGTATCATATCATAACTATCA
43843651 TTTTTTTA-TTAAACAATATCCTAATTCACACAATTATTATATAAAT-ATTTATTCACATATC-A
1 TTTTTTTATTTAAACAATATCCTAATTCACACAATTATTATATAAATGA-TTATTCACATATCAA
* * *
43843713 ACCATATTTATTCGTACAATGGCATCAGTCATGCAGTACTTAATTCATGAATACATCATTTCATA
65 ACCATA-TTATTCATACAATGGCATCAGTCATGCAATACTCAATTCATGAATACATCATTTCATA
43843778 CCATACTCAATTC
129 CCATACTCAATTC
43843791 ATGAGTATAT
Statistics
Matches: 132, Mismatches: 6, Indels: 5
0.92 0.04 0.03
Matches are distributed among these distances:
172 8 0.06
173 116 0.88
174 8 0.06
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.39
Consensus pattern (174 bp):
TTTTTTTATTTAAACAATATCCTAATTCACACAATTATTATATAAATGATTATTCACATATCAAA
CCATATTATTCATACAATGGCATCAGTCATGCAATACTCAATTCATGAATACATCATTTCATACC
ATACTCAATTCTCATTAATGTCTAGTATCATATCATAACTATCA
Found at i:43843898 original size:17 final size:18
Alignment explanation
Indices: 43843856--43843898 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
43843846 TCAATTTACT
* *
43843856 ATATCACTTTCATTTCTC
1 ATATCAATTTCATTTCTA
43843874 ATAT-AATTTCATTTC-A
1 ATATCAATTTCATTTCTA
43843890 ATATCAATT
1 ATATCAATT
43843899 GTAAGACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 4 0.18
17 14 0.64
18 4 0.18
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATCAATTTCATTTCTA
Found at i:43844985 original size:12 final size:13
Alignment explanation
Indices: 43844962--43845002 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
43844952 ACCCTAAGCT
43844962 TTTCTCCTTTTTC
1 TTTCTCCTTTTTC
43844975 TTTCT-CTTTTTC
1 TTTCTCCTTTTTC
43844987 TTTCTTTCCTTTTTC
1 TTTC--TCCTTTTTC
43845002 T
1 T
43845003 CCTCTATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 11 0.44
13 5 0.20
14 1 0.04
15 8 0.32
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTCTCCTTTTTC
Found at i:43845000 original size:15 final size:16
Alignment explanation
Indices: 43844971--43845055 Score: 59
Period size: 16 Copynumber: 5.2 Consensus size: 16
43844961 TTTTCTCCTT
43844971 TTTCTTTCTCTTTTTC
1 TTTCTTTCTCTTTTTC
43844987 TTTCTTTC-CTTTTTC
1 TTTCTTTCTCTTTTTC
* *
43845002 TCCTCTATT-TCGTTTTC
1 T-TTCT-TTCTCTTTTTC
* *
43845019 TATTCTGTTAT-TGTTTC
1 T-TTCT-TTCTCTTTTTC
* *
43845036 TTTCTTTTTCTTTTTG
1 TTTCTTTCTCTTTTTC
43845052 TTTC
1 TTTC
43845056 ATTTATTTGT
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
15 11 0.20
16 23 0.43
17 19 0.35
18 1 0.02
ACGTcount: A:0.04, C:0.21, G:0.05, T:0.71
Consensus pattern (16 bp):
TTTCTTTCTCTTTTTC
Found at i:43845560 original size:13 final size:13
Alignment explanation
Indices: 43845539--43845568 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
43845529 CAGTGTTTTC
*
43845539 TAGCTAAATAGCA
1 TAGCCAAATAGCA
43845552 TAGCCAAATAGCA
1 TAGCCAAATAGCA
43845565 TAGC
1 TAGC
43845569 TAAAGCAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (13 bp):
TAGCCAAATAGCA
Found at i:43846330 original size:255 final size:255
Alignment explanation
Indices: 43845879--43846385 Score: 935
Period size: 255 Copynumber: 2.0 Consensus size: 255
43845869 AACAACCTGA
43845879 AAAGTTTGCAAAAGTATAAAGCTAGAATAGAAATAATAGAAAGTCTAAATGGAATGATCGAACTC
1 AAAGTTTGCAAAAGTATAAAGCTAGAATAGAAATAATAGAAAGTCTAAATGGAATGATCGAACTC
* *
43845944 CTGAAATACCAACCCGCCTAAGCTTAAGGATTTCTTGAAATTTAAGCAAACAGACAAAATGAGGT
66 CTGAAATACCAACCCGCCTAAGCTTAAGGATTTCTTAAAATTCAAGCAAACAGACAAAATGAGGT
43846009 TACAAACTTAATGTGTAACCTATTAAATCAATTAAGCAGAATAATAACAAACATGCTTCAGGATA
131 TACAAACTTAATGTGTAACCTATTAAATCAATTAAGCAGAATAATAACAAACATGCTTCAGGATA
* *
43846074 TTATTATTCAGGCAGTTTTTTTATTCAGGAACGGAAACATAAACAAAGTATGTTAGAAAC
196 TTATTATTCAGGCAGTTTTTTGATTCAGGAACGGAAACAGAAACAAAGTATGTTAGAAAC
43846134 AAAGTTTGCAAAAGTATAAAGCTAGAATAGAAATAATAGAAAGTCTAAATGGAATGATCGAACTC
1 AAAGTTTGCAAAAGTATAAAGCTAGAATAGAAATAATAGAAAGTCTAAATGGAATGATCGAACTC
*
43846199 CTGAAATACCAACCCGCCTAAGCTTAAGGATTTCTTAAAATTCAAGCAAACAGACAAAATGAGTT
66 CTGAAATACCAACCCGCCTAAGCTTAAGGATTTCTTAAAATTCAAGCAAACAGACAAAATGAGGT
*
43846264 TACAAACTTAATGTGTAACCTATCT-AATCAATTAAGCGGAATAATAACAAACATGCTTCAGGAT
131 TACAAACTTAATGTGTAACCTAT-TAAATCAATTAAGCAGAATAATAACAAACATGCTTCAGGAT
*
43846328 ATTATTATTCAGGCAGTTTTTTGATTCAGGAACGGAAATAGAAACAAAGTATGTTAGA
195 ATTATTATTCAGGCAGTTTTTTGATTCAGGAACGGAAACAGAAACAAAGTATGTTAGA
43846386 GGCAGATATA
Statistics
Matches: 244, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
255 243 1.00
256 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (255 bp):
AAAGTTTGCAAAAGTATAAAGCTAGAATAGAAATAATAGAAAGTCTAAATGGAATGATCGAACTC
CTGAAATACCAACCCGCCTAAGCTTAAGGATTTCTTAAAATTCAAGCAAACAGACAAAATGAGGT
TACAAACTTAATGTGTAACCTATTAAATCAATTAAGCAGAATAATAACAAACATGCTTCAGGATA
TTATTATTCAGGCAGTTTTTTGATTCAGGAACGGAAACAGAAACAAAGTATGTTAGAAAC
Found at i:43846428 original size:28 final size:28
Alignment explanation
Indices: 43846388--43846459 Score: 117
Period size: 28 Copynumber: 2.6 Consensus size: 28
43846378 ATGTTAGAGG
43846388 CAGATATAAATACATATATAGAGCTTAT
1 CAGATATAAATACATATATAGAGCTTAT
*
43846416 CAGATATAAATACATATATAGAGGTTAT
1 CAGATATAAATACATATATAGAGCTTAT
* *
43846444 CAGATACAAATGCATA
1 CAGATATAAATACATA
43846460 AACCTACTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.29
Consensus pattern (28 bp):
CAGATATAAATACATATATAGAGCTTAT
Found at i:43846636 original size:2 final size:2
Alignment explanation
Indices: 43846631--43846700 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
43846621 CATATATATA
43846631 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
43846673 TG TG TA TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
43846701 GCTTAGCCAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.01, C:0.00, G:0.49, T:0.50
Consensus pattern (2 bp):
TG
Found at i:43848682 original size:43 final size:43
Alignment explanation
Indices: 43848596--43848710 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 43
43848586 AATGCCACTA
* * *
43848596 TCCCAGACAGGGTCTTACGCGAAATCACAATAAGATGTCAATG
1 TCCCAGACATGGTCTTACACGTAATCACAATAAGATGTCAATG
* *
43848639 TTCCAGACATGGTCTTACACGTAATCTCAATACA-ATG-CTAATG
1 TCCCAGACATGGTCTTACACGTAATCACAATA-AGATGTC-AATG
* *
43848682 TCCCAGACATGATCTTACATGTAATCACA
1 TCCCAGACATGGTCTTACACGTAATCACA
43848711 TCTCGATAAC
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
42 1 0.02
43 59 0.97
44 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGTAATCACAATAAGATGTCAATG
Found at i:43850749 original size:28 final size:28
Alignment explanation
Indices: 43850718--43850785 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
43850708 TCGATATTTT
*
43850718 GCACACTAAGTGCTATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
* * *
43850746 GCACATTAAGTTCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
43850774 GCACACTAAGTG
1 GCACACTAAGTG
43850786 TCATATTTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:43850869 original size:40 final size:40
Alignment explanation
Indices: 43850825--43850903 Score: 90
Period size: 40 Copynumber: 2.0 Consensus size: 40
43850815 TGTACATAGC
*
43850825 CGAAGCTAT-CTCAAA-TCACACATTAAGTGCCAAATTTAGA
1 CGAAGCTATAC-CAAACT-ACACACTAAGTGCCAAATTTAGA
* * *
43850865 CGAAGTTATACCAAACTACACACTAAGTGTCATATTTAG
1 CGAAGCTATACCAAACTACACACTAAGTGCCAAATTTAG
43850904 CCGATATGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
40 31 0.94
41 2 0.06
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.27
Consensus pattern (40 bp):
CGAAGCTATACCAAACTACACACTAAGTGCCAAATTTAGA
Found at i:43857507 original size:63 final size:63
Alignment explanation
Indices: 43857440--43857566 Score: 236
Period size: 63 Copynumber: 2.0 Consensus size: 63
43857430 ACATGAAATG
*
43857440 ATAGAAGAAACTTCAAGAAAACCTTTTTCATTGTCTGCAAAGTACAAAGAAACTTACAAACAT
1 ATAGAAGAAACCTCAAGAAAACCTTTTTCATTGTCTGCAAAGTACAAAGAAACTTACAAACAT
*
43857503 ATAGAAGAAACCTCAAGAAAACCTTTTTCTTTGTCTGCAAAGTACAAAGAAACTTACAAACAT
1 ATAGAAGAAACCTCAAGAAAACCTTTTTCATTGTCTGCAAAGTACAAAGAAACTTACAAACAT
43857566 A
1 A
43857567 CTGTCGTCGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.25
Consensus pattern (63 bp):
ATAGAAGAAACCTCAAGAAAACCTTTTTCATTGTCTGCAAAGTACAAAGAAACTTACAAACAT
Found at i:43865963 original size:29 final size:29
Alignment explanation
Indices: 43865878--43865964 Score: 156
Period size: 29 Copynumber: 3.0 Consensus size: 29
43865868 AAAAGCACTT
*
43865878 TCTAAATAACTTATAGCATTGCACATGAG
1 TCTAAATAACTTATAGCATTGCACATGGG
*
43865907 TCTAAATAACTTATAGCATCGCACATGGG
1 TCTAAATAACTTATAGCATTGCACATGGG
43865936 TCTAAATAACTTATAGCATTGCACATGGG
1 TCTAAATAACTTATAGCATTGCACATGGG
43865965 GGCCTCTGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (29 bp):
TCTAAATAACTTATAGCATTGCACATGGG
Found at i:43868450 original size:4 final size:4
Alignment explanation
Indices: 43868441--43868468 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
43868431 AAGTTTTATT
43868441 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
43868469 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:43873848 original size:38 final size:39
Alignment explanation
Indices: 43873774--43873853 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 39
43873764 TTTCAAATTA
* * *
43873774 TAAGCAAATATATATACTGTCAAGAAAGCCTCAT-AAAT
1 TAAGCAAATATATATACTGTAAACAAAGACTCATAAAAT
* *
43873812 TAAGCAAATATATATACATTTAAACAATGACT-ATAAAAT
1 TAAGCAAATATATATAC-TGTAAACAAAGACTCATAAAAT
43873851 TAA
1 TAA
43873854 ATTAAATTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
38 19 0.54
39 16 0.46
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.29
Consensus pattern (39 bp):
TAAGCAAATATATATACTGTAAACAAAGACTCATAAAAT
Found at i:43878143 original size:17 final size:18
Alignment explanation
Indices: 43878118--43878160 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
43878108 GAACTGCAAC
*
43878118 TCCTCAAAAACT-CGGTTT
1 TCCT-AAAAACTAAGGTTT
43878136 TCCTAAAAACTAAGGTTT
1 TCCTAAAAACTAAGGTTT
*
43878154 TCGTAAA
1 TCCTAAA
43878161 TAAAAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (18 bp):
TCCTAAAAACTAAGGTTT
Found at i:43879817 original size:24 final size:25
Alignment explanation
Indices: 43879779--43879827 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
43879769 TCCCTTTTCA
* *
43879779 TTTTCTTTCATTTTCATTTTTCTTC
1 TTTTCGTTCATTTTCACTTTTCTTC
*
43879804 TTTTCGTTC-TTTTCCCTTTTCTTC
1 TTTTCGTTCATTTTCACTTTTCTTC
43879828 CCTCATCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.04, C:0.24, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTTCGTTCATTTTCACTTTTCTTC
Found at i:43883159 original size:17 final size:18
Alignment explanation
Indices: 43883128--43883162 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
43883118 ATAAATTATT
43883128 AAAAAATTCATAAAAATA
1 AAAAAATTCATAAAAATA
*
43883146 AAAAAATTTA-AAAAATA
1 AAAAAATTCATAAAAATA
43883163 GAGAAAATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAAATTCATAAAAATA
Found at i:43883490 original size:23 final size:24
Alignment explanation
Indices: 43883434--43883482 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
43883424 ATTATAAAGG
*
43883434 AATA-AGAAAGAA-AAAGAGAGGA
1 AATATAGAAAAAATAAAGAGAGGA
43883456 AATATAGAAAAAATAAAGAGA-GA
1 AATATAGAAAAAATAAAGAGAGGA
43883479 AATA
1 AATA
43883483 ATGTAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 13 0.54
24 7 0.29
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.10
Consensus pattern (24 bp):
AATATAGAAAAAATAAAGAGAGGA
Found at i:43884966 original size:28 final size:28
Alignment explanation
Indices: 43884924--43885019 Score: 88
Period size: 28 Copynumber: 3.4 Consensus size: 28
43884914 TCGAACATGT
* * * *
43884924 GGGTTCACACTTTAGGGGTCACACCTAG
1 GGGTTCGCACATTAGGGATCACACCTAC
* *
43884952 GGGTTCGCTCATTAGGGATTACACCTAC
1 GGGTTCGCACATTAGGGATCACACCTAC
*
43884980 GGGTTTGCACATTA-GGATTTACACACCTA-
1 GGGTTCGCACATTAGGGA--T-CACACCTAC
43885009 GGGTTCGCACA
1 GGGTTCGCACA
43885020 CCTAGGGGTT
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
27 3 0.05
28 34 0.62
29 11 0.20
30 7 0.13
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (28 bp):
GGGTTCGCACATTAGGGATCACACCTAC
Found at i:43885273 original size:22 final size:23
Alignment explanation
Indices: 43885245--43885287 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
43885235 TGATGTAAGG
43885245 TTCACATAA-TAAACAAGTATGT
1 TTCACATAACTAAACAAGTATGT
*
43885267 TTCACATAACTAAACATGTAT
1 TTCACATAACTAAACAAGTAT
43885288 AGTTCGCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (23 bp):
TTCACATAACTAAACAAGTATGT
Found at i:43885297 original size:23 final size:21
Alignment explanation
Indices: 43885244--43885297 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
43885234 ATGATGTAAG
43885244 GTTCACATAATAAACAAGTAT
1 GTTCACATAATAAACAAGTAT
*
43885265 GTTTCACATAACTAAACATGTAT
1 G-TTCACATAA-TAAACAAGTAT
*
43885288 AGTTCGCATA
1 -GTTCACATA
43885298 CTATATAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 9 0.32
23 17 0.61
24 1 0.04
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (21 bp):
GTTCACATAATAAACAAGTAT
Found at i:43885501 original size:45 final size:45
Alignment explanation
Indices: 43885446--43885542 Score: 106
Period size: 45 Copynumber: 2.2 Consensus size: 45
43885436 CAATTTTTTA
* * * * *
43885446 AGGGTCCGCATAATATTT-CTATGGGGTTTGTATTATAATTCTTAT
1 AGGGTTCGCATAATATTTCCTAT-AGGTTTGTATAACAATTCTAAT
**
43885491 AGGGTTCGCATGTTATTTCCTATAGGTTTGTATAACAATTCTAAT
1 AGGGTTCGCATAATATTTCCTATAGGTTTGTATAACAATTCTAAT
*
43885536 GGGGTTC
1 AGGGTTC
43885543 ACCTATATTG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
45 39 0.91
46 4 0.09
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (45 bp):
AGGGTTCGCATAATATTTCCTATAGGTTTGTATAACAATTCTAAT
Found at i:43886057 original size:24 final size:25
Alignment explanation
Indices: 43886009--43886061 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
43885999 AAGCTCATTC
*
43886009 TTGACATCTTTTAACAAAAATTTTT
1 TTGACAACTTTTAACAAAAATTTTT
43886034 TTGACAACTTTTAAC-AAAATTTTT
1 TTGACAACTTTTAACAAAAATTTTT
43886058 TTGA
1 TTGA
43886062 AGGTATACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (25 bp):
TTGACAACTTTTAACAAAAATTTTT
Found at i:43888273 original size:50 final size:51
Alignment explanation
Indices: 43888192--43888296 Score: 140
Period size: 50 Copynumber: 2.1 Consensus size: 51
43888182 AATCTTAAAA
** * *
43888192 GATTTTCAATTAAATCTCTAATTTCTAAAAAGTGCTCCA-TTAACATTATT
1 GATTTTCAACCAAATCCCTAAATTCTAAAAAGTGCTCCATTTAACATTATT
* * *
43888242 GATTTTCAACCAAATCCCTAAATTCTCAAAAGTGCTCCATTTAATATTGTT
1 GATTTTCAACCAAATCCCTAAATTCTAAAAAGTGCTCCATTTAACATTATT
43888293 GATT
1 GATT
43888297 AAGATTCCCA
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
50 34 0.72
51 13 0.28
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.40
Consensus pattern (51 bp):
GATTTTCAACCAAATCCCTAAATTCTAAAAAGTGCTCCATTTAACATTATT
Found at i:43888371 original size:78 final size:76
Alignment explanation
Indices: 43888242--43888524 Score: 349
Period size: 78 Copynumber: 3.7 Consensus size: 76
43888232 TAACATTATT
*
43888242 GATTTTCAACCAAATCCCTAAATTCTCAAAAGTGCTCCATTTAATATTGTTGATTAAGATTCCCA
1 GATTTTCAACCAAAT-CCTAAATTCTCAAAAGTGCTCCATTTAACATTGTTGATTAAGATTCCCA
*
43888307 ATCGTATCTTAAA
65 ATC-AATCTTAAA
* * **
43888320 GATTTTTAACCAAATACCTAAATTCTCAAAAGTGCTCCATTTAACATTGTTGATTAAAATTTGCA
1 GATTTTCAACCAAAT-CCTAAATTCTCAAAAGTGCTCCATTTAACATTGTTGATTAAGATTCCCA
43888385 ATCAAATCTTAAA
65 ATC-AATCTTAAA
* ** * * *
43888398 GATTTTCGACC----CCTAAATTCTCAAAAGTAATCCATTTAACATTTTTTTATTAAGATTCTCA
1 GATTTTCAACCAAATCCTAAATTCTCAAAAGTGCTCCATTTAACA-TTGTTGATTAAGATTCCCA
43888459 ATCAATTCTTAAA
65 ATCAA-TCTTAAA
* *
43888472 GATTTTCAACCAAATTCTTAAATTCTCAAAACTGCTCCATTTAACATTGTTGA
1 GATTTTCAACCAAA-TCCTAAATTCTCAAAAGTGCTCCATTTAACATTGTTGA
43888525 CTAAAATCAA
Statistics
Matches: 174, Mismatches: 24, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
73 30 0.17
74 34 0.20
78 84 0.48
79 26 0.15
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.37
Consensus pattern (76 bp):
GATTTTCAACCAAATCCTAAATTCTCAAAAGTGCTCCATTTAACATTGTTGATTAAGATTCCCAA
TCAATCTTAAA
Found at i:43888473 original size:21 final size:21
Alignment explanation
Indices: 43888447--43888500 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
43888437 CATTTTTTTA
*
43888447 TTAAGATTCTCAATC-AATTC
1 TTAAGATTCTCAACCAAATTC
*
43888467 TTAAAGATTTTCAACCAAATTC
1 TT-AAGATTCTCAACCAAATTC
43888489 TTAA-ATTCTCAA
1 TTAAGATTCTCAA
43888501 AACTGCTCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 9 0.31
21 13 0.45
22 7 0.24
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
TTAAGATTCTCAACCAAATTC
Found at i:43897587 original size:40 final size:42
Alignment explanation
Indices: 43897507--43897587 Score: 98
Period size: 40 Copynumber: 2.0 Consensus size: 42
43897497 TACAATTTAT
43897507 ATTTAATATTTATAGTTATCTCCTTAATAATATCATTTTTAAA
1 ATTTAATATTTATAG-TATCTCCTTAATAATATCATTTTTAAA
*
43897550 ATTTAA-ATTTATA-TATTTCCTTTAA-AATA-CATATTTTA
1 ATTTAATATTTATAGTATCTCC-TTAATAATATCAT-TTTTA
43897588 TCATCACATT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
39 3 0.09
40 15 0.43
41 4 0.11
42 7 0.20
43 6 0.17
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.52
Consensus pattern (42 bp):
ATTTAATATTTATAGTATCTCCTTAATAATATCATTTTTAAA
Found at i:43898348 original size:22 final size:22
Alignment explanation
Indices: 43898323--43898380 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 22
43898313 ATATACAAAC
43898323 AATAACAATAAAATAGCAACAA
1 AATAACAATAAAATAGCAACAA
* * * * *
43898345 AATAATAATGAAATGGTAGCAA
1 AATAACAATAAAATAGCAACAA
*
43898367 AATAGCAA-AAAATA
1 AATAACAATAAAATA
43898381 AAAAAAAATA
Statistics
Matches: 27, Mismatches: 9, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.64, C:0.09, G:0.10, T:0.17
Consensus pattern (22 bp):
AATAACAATAAAATAGCAACAA
Found at i:43900662 original size:21 final size:21
Alignment explanation
Indices: 43900638--43900679 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
43900628 TTTTCCTAAG
*
43900638 ATATGAATTGGATTGAATTGA
1 ATATGAATTGGATTAAATTGA
*
43900659 ATATGAATTGTATTAAATTGA
1 ATATGAATTGGATTAAATTGA
43900680 GCTAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.40
Consensus pattern (21 bp):
ATATGAATTGGATTAAATTGA
Found at i:43901287 original size:25 final size:25
Alignment explanation
Indices: 43901228--43901289 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
43901218 TGGCTCACAT
* *
43901228 GAGCTTCCCATTATATGGCTCGAAA
1 GAGCTTCCCGTTATATAGCTCGAAA
*
43901253 GAGCTTCCCGTTATATAGTTCGAAA
1 GAGCTTCCCGTTATATAGCTCGAAA
43901278 GAGCTTCCCGTT
1 GAGCTTCCCGTT
43901290 TACATGTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCGAAA
Found at i:43906094 original size:6 final size:7
Alignment explanation
Indices: 43906064--43906096 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
43906054 TATCGACAAA
43906064 AAAATTT
1 AAAATTT
43906071 AAAATTT
1 AAAATTT
43906078 AAAATTT
1 AAAATTT
43906085 AAAA-TT
1 AAAATTT
43906091 AAAATT
1 AAAATT
43906097 GTAAGTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAAATTT
Found at i:43906651 original size:20 final size:19
Alignment explanation
Indices: 43906622--43906680 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 19
43906612 ATTTTAAAAT
*
43906622 CAAGTGAAAATAATTTTAAC
1 CAAGTCAAAAT-ATTTTAAC
**
43906642 CAAGTCAAAATATTCCAAC
1 CAAGTCAAAATATTTTAAC
* *
43906661 TAAGTTAAAATCATTTTAAC
1 CAAGTCAAAAT-ATTTTAAC
43906681 ACATCAAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (19 bp):
CAAGTCAAAATATTTTAAC
Found at i:43910060 original size:23 final size:23
Alignment explanation
Indices: 43910030--43910074 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
43910020 GGTGGAAAAC
*
43910030 AATATATTTTTGTGCTTGTTGAT
1 AATATATTTTTGTACTTGTTGAT
43910053 AATATATTTTTGTACTTGTTGA
1 AATATATTTTTGTACTTGTTGA
43910075 CGACTATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.04, G:0.16, T:0.56
Consensus pattern (23 bp):
AATATATTTTTGTACTTGTTGAT
Found at i:43922754 original size:14 final size:13
Alignment explanation
Indices: 43922735--43922768 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
43922725 CTTGTTCTTA
43922735 TTCTTAATTATATG
1 TTCTTAATTAT-TG
43922749 TTCTTAATTATTG
1 TTCTTAATTATTG
43922762 TT-TTAAT
1 TTCTTAAT
43922769 ATTTCAGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 4 0.20
14 11 0.55
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (13 bp):
TTCTTAATTATTG
Found at i:43925224 original size:20 final size:20
Alignment explanation
Indices: 43925199--43925247 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
43925189 CGCAAATTGG
*
43925199 TATCGATATCATTT-TGAAAA
1 TATCGATA-CATTTATAAAAA
*
43925219 TATCGATACTTTTATAAAAA
1 TATCGATACATTTATAAAAA
43925239 TATCGATAC
1 TATCGATAC
43925248 TCGTGAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (20 bp):
TATCGATACATTTATAAAAA
Found at i:43925256 original size:19 final size:20
Alignment explanation
Indices: 43925215--43925266 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
43925205 TATCATTTTG
** *
43925215 AAAATATCGATACTTTTATA
1 AAAATATCGATACTCGTAGA
43925235 AAAATATCGATACTCGT-GA
1 AAAATATCGATACTCGTAGA
*
43925254 AAAATATTGATAC
1 AAAATATCGATAC
43925267 CACAAGCTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.33
Consensus pattern (20 bp):
AAAATATCGATACTCGTAGA
Found at i:43925257 original size:20 final size:19
Alignment explanation
Indices: 43925215--43925266 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
43925205 TATCATTTTG
* *
43925215 AAAATATCGATACTTTTATA
1 AAAATATCGATAC-TGTGTA
43925235 AAAATATCGATACTCGTG-A
1 AAAATATCGATACT-GTGTA
*
43925254 AAAATATTGATAC
1 AAAATATCGATAC
43925267 CACAAGCTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.33
Consensus pattern (19 bp):
AAAATATCGATACTGTGTA
Found at i:43926046 original size:48 final size:48
Alignment explanation
Indices: 43925932--43926030 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
43925922 AAAATTAGGG
43925932 TTGGATGGGATTTTTAAATATTTCTTCGCCGACTTACCTTAATCTTTT
1 TTGGATGGGATTTTTAAATATTTCTTCGCCGACTTACCTTAATCTTTT
43925980 TTGGATGGGATTTTTAAATATTTCTTCGCCGACTTACCTTAATCTTTT
1 TTGGATGGGATTTTTAAATATTTCTTCGCCGACTTACCTTAATCTTTT
43926028 TTG
1 TTG
43926031 TGCTTTCTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.20, C:0.16, G:0.15, T:0.48
Consensus pattern (48 bp):
TTGGATGGGATTTTTAAATATTTCTTCGCCGACTTACCTTAATCTTTT
Found at i:43927379 original size:20 final size:20
Alignment explanation
Indices: 43927354--43927391 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
43927344 ACAATTTTAA
43927354 AACCAAGCGAAAATGATTTT
1 AACCAAGCGAAAATGATTTT
**
43927374 AACCAAGTTAAAATGATT
1 AACCAAGCGAAAATGATT
43927392 CCAATCAAGT
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:0.47, C:0.13, G:0.13, T:0.26
Consensus pattern (20 bp):
AACCAAGCGAAAATGATTTT
Found at i:43927400 original size:20 final size:20
Alignment explanation
Indices: 43927363--43927407 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
43927353 AAACCAAGCG
**
43927363 AAAATGATTTTAACCAAGTT
1 AAAATGATTCCAACCAAGTT
*
43927383 AAAATGATTCCAATCAAGTT
1 AAAATGATTCCAACCAAGTT
43927403 AAAAT
1 AAAAT
43927408 CATTTTAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.31
Consensus pattern (20 bp):
AAAATGATTCCAACCAAGTT
Found at i:43935939 original size:7 final size:7
Alignment explanation
Indices: 43935927--43935956 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
43935917 TTTCTTGGAT
43935927 TAACTCA
1 TAACTCA
43935934 TAACTCA
1 TAACTCA
43935941 TAACTCA
1 TAACTCA
43935948 TAACTCA
1 TAACTCA
43935955 TA
1 TA
43935957 TCTAAATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (7 bp):
TAACTCA
Found at i:43937653 original size:31 final size:31
Alignment explanation
Indices: 43937617--43937681 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
43937607 AAAGAAAAAA
* *
43937617 ACTTAAATAAAAACTTTCAAATAGTTGAATG
1 ACTTAAATAAAAACTTTCAAATAATTAAATG
*
43937648 ACTTAAATGAAAACTTTCAAATAATTAAATG
1 ACTTAAATAAAAACTTTCAAATAATTAAATG
43937679 ACT
1 ACT
43937682 ATTTTGTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAATTAAATG
Found at i:43938059 original size:31 final size:31
Alignment explanation
Indices: 43938021--43938079 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
43938011 AAAAAAAATT
*
43938021 TTAAACTCAAACACCCAGTTTTTGTTTTGAA
1 TTAAACTCAAACACCCAGATTTTGTTTTGAA
* *
43938052 TTAAACTCGAAGACCCAGATTTTGTTTT
1 TTAAACTCAAACACCCAGATTTTGTTTT
43938080 TGTGTTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.39
Consensus pattern (31 bp):
TTAAACTCAAACACCCAGATTTTGTTTTGAA
Found at i:43939463 original size:18 final size:18
Alignment explanation
Indices: 43939436--43939528 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
43939426 TACGACCGTT
43939436 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
43939454 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
43939472 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
43939490 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
43939508 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
43939526 TAC
1 TAC
43939529 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:43949649 original size:29 final size:30
Alignment explanation
Indices: 43949600--43949663 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
43949590 TAAAAATTTG
* *
43949600 GAATTTAGTTTTTATA-TTTTTATTTTTTA
1 GAATTTAGTTTTTATACTTTTCATATTTTA
43949629 GAATTTAGTTCTTT-TACTTTTCATATTTTA
1 GAATTTAGTT-TTTATACTTTTCATATTTTA
*
43949659 AAATT
1 GAATT
43949664 CAGGTCCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 12 0.40
30 18 0.60
ACGTcount: A:0.27, C:0.05, G:0.06, T:0.62
Consensus pattern (30 bp):
GAATTTAGTTTTTATACTTTTCATATTTTA
Found at i:43951485 original size:90 final size:90
Alignment explanation
Indices: 43951320--43951496 Score: 205
Period size: 90 Copynumber: 2.0 Consensus size: 90
43951310 AAATAAGCCC
* * *
43951320 TCAAACTTTTTCGAAAAAAAAACAATTAAGCCCTTACTTTTTTTTGCACTCAATTGGATACTTGA
1 TCAAACTTTTTC-AAAAAAAAACAATTAAGCCCATACTTTTTTTTACACTCAATTGGATACTTAA
* *
43951385 ACTTTTAAAAT-ACATCAAAAAGGCCA
65 ACTGTCAAAATGA-ATCAAAAAGGCCA
* ** * * * *
43951411 TCAAACTTTTTC-ACAAAAAGTAATTAAGCCCATGCTTTTTTTTAACATTTAATTGGGTACTTAA
1 TCAAACTTTTTCAAAAAAAAACAATTAAGCCCATACTTTTTTTT-ACACTCAATTGGATACTTAA
43951475 ACTGTCAAAATGAATCAAAAAG
65 ACTGTCAAAATGAATCAAAAAG
43951497 CTCCTTCGAC
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
89 26 0.36
90 33 0.46
91 13 0.18
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.34
Consensus pattern (90 bp):
TCAAACTTTTTCAAAAAAAAACAATTAAGCCCATACTTTTTTTTACACTCAATTGGATACTTAAA
CTGTCAAAATGAATCAAAAAGGCCA
Found at i:43951660 original size:28 final size:28
Alignment explanation
Indices: 43951634--43951687 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
43951624 AAATGAAATT
*
43951634 TATAAAAAA-A-TTAACTTTTAATAAAA
1 TATAAAAAATATTTAACATTTAATAAAA
*
43951660 TATAAAAAATATTTAACATTTATTAAAA
1 TATAAAAAATATTTAACATTTAATAAAA
43951688 ATCAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 9 0.38
27 1 0.04
28 14 0.58
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (28 bp):
TATAAAAAATATTTAACATTTAATAAAA
Found at i:43951918 original size:21 final size:20
Alignment explanation
Indices: 43951894--43951969 Score: 73
Period size: 21 Copynumber: 3.7 Consensus size: 20
43951884 GGTATGATAA
43951894 ATTTTATAAATTTTTTTACG
1 ATTTTATAAATTTTTTTACG
**
43951914 AATTTTATATTTTTTTTTAC-
1 -ATTTTATAAATTTTTTTACG
* *
43951934 ATTTTTTATAATTTTCTTACG
1 ATTTTATA-AATTTTTTTACG
*
43951955 ACTTTATAAAATTTT
1 ATTTTAT-AAATTTT
43951970 ATGTATTTCT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 7 0.16
20 8 0.18
21 28 0.64
22 1 0.02
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.62
Consensus pattern (20 bp):
ATTTTATAAATTTTTTTACG
Found at i:43952007 original size:19 final size:20
Alignment explanation
Indices: 43951985--43952036 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
43951975 TTTCTATATA
**
43951985 TTTTATAATTTTTTAC-GCT
1 TTTTATAATTTTTTACAAAT
* *
43952004 TTTTATAAATGTTTACAAAT
1 TTTTATAATTTTTTACAAAT
43952024 TTTTATAATTTTT
1 TTTTATAATTTTT
43952037 ATTAAAATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.62
Consensus pattern (20 bp):
TTTTATAATTTTTTACAAAT
Found at i:43952037 original size:48 final size:48
Alignment explanation
Indices: 43951927--43952038 Score: 113
Period size: 48 Copynumber: 2.3 Consensus size: 48
43951917 TTTATATTTT
* * ***
43951927 TTTTTACATTTTTTATAATTTTCTTACGACTTTATAAAATTTTATGTA
1 TTTTTATAATTTTTATAATTTTCTTACGACTTTATAAAATTTTACAAA
* *
43951975 TTTCTAT-ATATTTTATAATTTT-TTACG-CTTTTTATAAATGTTTACAAA
1 TTTTTATAAT-TTTTATAATTTTCTTACGACTTTATA-AAAT-TTTACAAA
43952023 TTTTTATAATTTTTAT
1 TTTTTATAATTTTTAT
43952039 TAAAATTTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
46 6 0.12
47 10 0.19
48 34 0.65
49 2 0.04
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (48 bp):
TTTTTATAATTTTTATAATTTTCTTACGACTTTATAAAATTTTACAAA
Found at i:43952385 original size:93 final size:89
Alignment explanation
Indices: 43952201--43952476 Score: 276
Period size: 93 Copynumber: 3.1 Consensus size: 89
43952191 TCAAATGATA
** * *
43952201 TTTTTGATGCATTTTGGCAATTCAAGTATCCAATTTAGTG---AAAAAAAAGTAGGGACTTAAAT
1 TTTTTGATGCATTTTGAAAATTCAAGTACCCAATTGAGTGAAAAAAAAAAAGTAGGG-CTT-AAT
** *
43952263 T-TTTTTTTTGTTTAAA-TTTGAGGCA
64 TCTTTTTTTTG-AAAAAGTTTGAGGCC
* * *
43952288 TTTTTTATTCATTTTGAAAATTCAAGTACTCAATTGAGTGTAAAAAAAAAAAAGTAGAGGCTTAA
1 TTTTTGATGCATTTTGAAAATTCAAGTACCCAATTGAGTG--AAAAAAAAAAAGTAG-GGCTTAA
43952353 TTGCTTTTTTTTGAAAAAGTTTGAGGCC
63 TT-CTTTTTTTTGAAAAAGTTTGAGGCC
* * *
43952381 TTTTTGATGCATTTTGAAAATTTAATTACCCAATTGAGTGAAAAAAAAAGAGTATGGGGCTTAAT
1 TTTTTGATGCATTTTGAAAATTCAAGTACCCAATTGAGTGAAAAAAAAAAAGTA--GGGCTTAAT
* * *
43952446 TAC-TTTTTTAGAAAAAGTTGGAGGAC
64 T-CTTTTTTTTGAAAAAGTTTGAGGCC
43952472 TTTTT
1 TTTTT
43952477 ATACCCTTAA
Statistics
Matches: 158, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
87 33 0.21
91 42 0.27
92 28 0.18
93 55 0.35
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (89 bp):
TTTTTGATGCATTTTGAAAATTCAAGTACCCAATTGAGTGAAAAAAAAAAAGTAGGGCTTAATTC
TTTTTTTTGAAAAAGTTTGAGGCC
Found at i:43954397 original size:9 final size:9
Alignment explanation
Indices: 43954375--43954428 Score: 63
Period size: 9 Copynumber: 5.6 Consensus size: 9
43954365 TTTTGTTTCT
43954375 TTATTAAATA
1 TTATT-AATA
*
43954385 TTATTAGTA
1 TTATTAATA
43954394 TTATTTCTAATA
1 TTA--T-TAATA
43954406 TTATTAATA
1 TTATTAATA
43954415 TTATTAATA
1 TTATTAATA
43954424 TTATT
1 TTATT
43954429 TTTTTTATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
9 25 0.64
10 6 0.15
11 1 0.03
12 7 0.18
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (9 bp):
TTATTAATA
Found at i:43954436 original size:18 final size:18
Alignment explanation
Indices: 43954375--43954428 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 18
43954365 TTTTGTTTCT
*
43954375 TTATTAAATATTATTAGTA
1 TTATT-AATATTATTAATA
43954394 TTATTTCTAATATTATTAATA
1 TTA--T-TAATATTATTAATA
43954415 TTATTAATATTATT
1 TTATTAATATTATT
43954429 TTTTTTATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 10 0.32
19 4 0.13
21 16 0.52
22 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
TTATTAATATTATTAATA
Found at i:43954556 original size:12 final size:12
Alignment explanation
Indices: 43954523--43954666 Score: 52
Period size: 12 Copynumber: 11.8 Consensus size: 12
43954513 TTTCATATTG
43954523 TTATTATTAGTAT
1 TTATTATTA-TAT
*
43954536 TATAATATTATAT
1 T-TATTATTATAT
43954549 TTATTATTA-AT
1 TTATTATTATAT
*
43954560 ATTAGTA-TATATT
1 -TTATTATTATA-T
43954573 TTATTA-TATAT
1 TTATTATTATAT
* *
43954584 GTA-CATATATACT
1 TTATTAT-TATA-T
43954597 TT-TTA-TATA-
1 TTATTATTATAT
* **
43954606 GTATTATCGT-T
1 TTATTATTATAT
43954617 TCTATTATTATAT
1 T-TATTATTATAT
*
43954630 TTATTATTTTCACT
1 TTATTATTAT-A-T
*
43954644 ATTATTATTATTT
1 -TTATTATTATAT
*
43954657 TTATCATTAT
1 TTATTATTAT
43954667 TATACGTATA
Statistics
Matches: 97, Mismatches: 18, Indels: 33
0.66 0.12 0.22
Matches are distributed among these distances:
9 1 0.01
10 4 0.04
11 12 0.12
12 50 0.52
13 13 0.13
14 8 0.08
15 9 0.09
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (12 bp):
TTATTATTATAT
Found at i:43954562 original size:26 final size:24
Alignment explanation
Indices: 43954517--43954579 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 24
43954507 CTTTAATTTC
*
43954517 ATATTGTTATTATTAGTATTA-TAAT
1 ATATT-TTATTATTAATATTAGT-AT
43954542 ATTATATTTATTATTAATATTAGTAT
1 A-TAT-TTTATTATTAATATTAGTAT
43954568 ATATTTTATTAT
1 ATATTTTATTAT
43954580 ATATGTACAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
24 8 0.24
25 4 0.12
26 20 0.59
27 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (24 bp):
ATATTTTATTATTAATATTAGTAT
Found at i:43954636 original size:24 final size:25
Alignment explanation
Indices: 43954607--43954661 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
43954597 TTTTATATAG
43954607 TATTATCGTTT-CTATTATTA-TATT
1 TATTATC-TTTACTATTATTATTATT
43954631 TATTAT-TTTCACTATTATTATTATT
1 TATTATCTTT-ACTATTATTATTATT
43954656 T-TTATC
1 TATTATC
43954662 ATTATTATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
22 3 0.11
24 19 0.70
25 5 0.19
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (25 bp):
TATTATCTTTACTATTATTATTATT
Found at i:43954828 original size:20 final size:18
Alignment explanation
Indices: 43954803--43954857 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 18
43954793 TTATATTATG
43954803 TATATTATTTTTTAAA-A
1 TATATTATTTTTTAAATA
*
43954820 TAT-TATATTTTTTATATA
1 TATAT-TATTTTTTAAATA
*
43954838 TTATATATATTTTTTTAATA
1 -TATAT-TATTTTTTAAATA
43954858 CCGTATTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 1 0.03
17 13 0.42
18 1 0.03
19 3 0.10
20 13 0.42
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TATATTATTTTTTAAATA
Found at i:43954835 original size:29 final size:32
Alignment explanation
Indices: 43954767--43954841 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 32
43954757 TCTTCATAAT
*
43954767 TTTTTTAT-TTATTATTTTAAATACTCTTATA
1 TTTTTTATATTATTATTTTAAATACTATTATA
* *
43954798 TTATGTATATTATT-TTTTAAA-A-TATTATA
1 TTTTTTATATTATTATTTTAAATACTATTATA
43954827 TTTTTTATA-TATTAT
1 TTTTTTATATTATTAT
43954842 ATATATTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
28 4 0.11
29 14 0.38
30 1 0.03
31 13 0.35
32 5 0.14
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (32 bp):
TTTTTTATATTATTATTTTAAATACTATTATA
Found at i:43954838 original size:16 final size:16
Alignment explanation
Indices: 43954803--43954843 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
43954793 TTATATTATG
43954803 TATATTAT-TTTTTAA
1 TATATTATATTTTTAA
* *
43954818 AATATTATATTTTTTA
1 TATATTATATTTTTAA
43954834 TATATTATAT
1 TATATTATAT
43954844 ATATTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATATTATATTTTTAA
Found at i:43954975 original size:84 final size:79
Alignment explanation
Indices: 43954820--43954978 Score: 178
Period size: 84 Copynumber: 1.9 Consensus size: 79
43954810 TTTTTTAAAA
* * * *
43954820 TATTATATTTTTTATATATTATATATATTTTTTTAATACCGTATTATGTACATGTTATTATTATA
1 TATTATATTTATTATATATTATATATATTTTATTAATACCGTATTATATACATGTTATTATAATA
43954885 TCTATTTTTACCCC
66 TCTATTTTTACCCC
* * *
43954899 TATTATATTTATTATTAATATTAGTATATATTTTATT-ATACGTGTATATGATATACTTTTTATA
1 TATTATATTTATTA-T-ATATTA-TATATATTTTATTAATAC-CGTAT-T-ATATACATGTTAT-
43954963 TATAATAT-TATTTTTA
59 TATAATATCTATTTTTA
43954979 TATATATCAT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
79 13 0.20
80 1 0.02
81 10 0.15
82 16 0.24
83 1 0.02
84 18 0.27
85 7 0.11
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57
Consensus pattern (79 bp):
TATTATATTTATTATATATTATATATATTTTATTAATACCGTATTATATACATGTTATTATAATA
TCTATTTTTACCCC
Found at i:43954994 original size:20 final size:17
Alignment explanation
Indices: 43954943--43954984 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
43954933 ATTATACGTG
*
43954943 TATATGATATACTTTTTA
1 TATATAATATA-TTTTTA
43954961 TATATAATATTATTTTTA
1 TATATAATA-TATTTTTA
43954979 TATATA
1 TATATA
43954985 TCATTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
TATATAATATATTTTTA
Found at i:43955220 original size:26 final size:27
Alignment explanation
Indices: 43955182--43955265 Score: 68
Period size: 26 Copynumber: 3.1 Consensus size: 27
43955172 TATGTATATA
* *
43955182 TATT-TTATGTATATAT-CGTTATTTT
1 TATTATTATGTATAAATACATTATTTT
43955207 CTATTATTAT-TATAAATACATTATTTT
1 -TATTATTATGTATAAATACATTATTTT
* * *
43955234 TCTTATTATAT-TAGTAGTACATTATTTT
1 TATTATTATGTATA--AATACATTATTTT
43955262 TATT
1 TATT
43955266 TTCTTGTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
26 20 0.42
27 13 0.27
28 15 0.31
ACGTcount: A:0.30, C:0.06, G:0.05, T:0.60
Consensus pattern (27 bp):
TATTATTATGTATAAATACATTATTTT
Found at i:43955245 original size:28 final size:28
Alignment explanation
Indices: 43955203--43955262 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
43955193 TATATCGTTA
43955203 TTTTCTATTATTATTA-TAAATACATTAT
1 TTTTCTATTATTATTAGT-AATACATTAT
*
43955231 TTTTCTTATTA-TATTAGTAGTACATTAT
1 TTTTC-TATTATTATTAGTAATACATTAT
43955259 TTTT
1 TTTT
43955263 ATTTTCTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (28 bp):
TTTTCTATTATTATTAGTAATACATTAT
Found at i:43956110 original size:15 final size:16
Alignment explanation
Indices: 43956079--43956111 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43956069 TATCTCGTTA
*
43956079 TTTTCTAGTTTTAAGT
1 TTTTATAGTTTTAAGT
43956095 TTTTATAGTTTT-AGT
1 TTTTATAGTTTTAAGT
43956110 TT
1 TT
43956112 AGTTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.18, C:0.03, G:0.12, T:0.67
Consensus pattern (16 bp):
TTTTATAGTTTTAAGT
Found at i:43967247 original size:14 final size:14
Alignment explanation
Indices: 43967228--43967257 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
43967218 TACCGAGATA
*
43967228 TTTTCAATTTCTGT
1 TTTTCAATTTATGT
43967242 TTTTCAATTTATGT
1 TTTTCAATTTATGT
43967256 TT
1 TT
43967258 CAAAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTTCAATTTATGT
Found at i:43967486 original size:88 final size:89
Alignment explanation
Indices: 43967093--43967502 Score: 489
Period size: 89 Copynumber: 4.7 Consensus size: 89
43967083 CTAATGTTTT
* *
43967093 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGTTGAGGTATTTTCAA----
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCACATGTCGAGGTATTTTCAATTTC
* * ***
43967151 TATTCTT-AATTTCTGTTTTTCAAA
65 TGTTCTTCAATTTATGTTTCAAAAA
* * ** *
43967175 AATCAACTCATATTGAGAGAGGTGAGTTGACCCTCGGGC-CACATACCGAGATATTTTCAATTTC
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCACATGTCGAGGTATTTTCAATTTC
*
43967239 TGTTTTTCAATTTATGTTTCAAAAA
65 TGTTCTTCAATTTATGTTTCAAAAA
* * * * *
43967264 AATAAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTTACATGTCGAGGTATTTTCAACTTAT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGTCGAGGTATTTTCAATTTCT
43967329 GTTCTTCAATTTATGTTTCAAAAA
66 GTTCTTCAATTTATGTTTCAAAAA
* * *
43967353 AATCAGCTCATATTGCAAGAGGTGAGTTGAGCCTCGGCTCACATGTTGAGGTATTTTCAATTTCT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGTCGAGGTATTTTCAATTTCT
*
43967418 GTTCTTCAATTTATGTTT-TAAAA
66 GTTCTTCAATTTATGTTTCAAAAA
* * * * *
43967441 AATCAGCTCATACTGCGAGAGGTGAGTTGAGTCTCGGCTCACATGTGGAGGTATTTTTAATT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGTCGAGGTATTTTCAATT
43967503 CTTGTTTTTT
Statistics
Matches: 281, Mismatches: 39, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
82 35 0.12
84 15 0.05
88 68 0.24
89 163 0.58
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (89 bp):
AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGTCGAGGTATTTTCAATTTCT
GTTCTTCAATTTATGTTTCAAAAA
Found at i:43967626 original size:78 final size:78
Alignment explanation
Indices: 43967515--43967733 Score: 219
Period size: 78 Copynumber: 2.8 Consensus size: 78
43967505 TGTTTTTTTT
* * * * * *
43967515 AAAAGTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGCTCACGCGCTGAGTTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGCGAATTGAGCCTCAGCTCACACGCTAAGGTATTTTCAATT
43967580 ACTATTTCAAAAA
66 ACTATTTCAAAAA
*
43967593 AAAAATCAACTCATATTGCGAGAGGTC-AATTGAGCCTCAGGTCACACGCTAAGGTATTTTCAAT
1 AAAAATCAACTCATATTGCGAGAGG-CGAATTGAGCCTCAGCTCACACGCTAAGGTATTTTCAAT
* ****
43967657 TCCTATTT--TTTT
65 TACTATTTCAAAAA
* * * * * * * * *
43967669 AAAAGTCAATTCGTATTGCAAGAGGCGAGTTGAGCCTCAGGTCACACGTTGAGGTATTCTCAATT
1 AAAAATCAACTCATATTGCGAGAGGCGAATTGAGCCTCAGCTCACACGCTAAGGTATTTTCAATT
43967734 TCTGTTTTTC
Statistics
Matches: 119, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
75 1 0.01
76 55 0.46
78 62 0.52
79 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (78 bp):
AAAAATCAACTCATATTGCGAGAGGCGAATTGAGCCTCAGCTCACACGCTAAGGTATTTTCAATT
ACTATTTCAAAAA
Found at i:43967710 original size:76 final size:76
Alignment explanation
Indices: 43967454--43967742 Score: 287
Period size: 76 Copynumber: 3.8 Consensus size: 76
43967444 CAGCTCATAC
* * * * * *
43967454 TGCGAGAGGTGAGTTGAGTCTC-GGCTCACATG-TGGAGGTATTTTTAATTCTTGTTTTTTTTAA
1 TGCGAGAGGCGAGTTGAGCCTCAGG-TCACACGCT-GAGGTATTTTCAATTCCT-ATTTTTTTAA
43967517 AAGTCAACTCGTAT
63 AAGTCAACTCGTAT
* * * * ****
43967531 TGCGAGAGGCGAGTTGAGCCTCAGCTCACGCGCTGAGTTATTTTCAATTACTATTTCAAAAAAAA
1 TGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATTCCTATTT--TTTTAAA
* *
43967596 AATCAACTCATAT
64 AGTCAACTCGTAT
* *
43967609 TGCGAGAGGTC-AATTGAGCCTCAGGTCACACGCTAAGGTATTTTCAATTCCTATTTTTTTAAAA
1 TGCGAGAGG-CGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATTCCTATTTTTTTAAAA
*
43967673 GTCAATTCGTAT
65 GTCAACTCGTAT
* * * * *
43967685 TGCAAGAGGCGAGTTGAGCCTCAGGTCACACGTTGAGGTATTCTCAATTTCTGTTTTT
1 TGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATTCCTATTTTT
43967743 CAATTTATGT
Statistics
Matches: 170, Mismatches: 36, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
75 1 0.01
76 65 0.38
77 39 0.23
78 64 0.38
79 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (76 bp):
TGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATTCCTATTTTTTTAAAAG
TCAACTCGTAT
Found at i:43967732 original size:154 final size:155
Alignment explanation
Indices: 43967437--43967733 Score: 402
Period size: 154 Copynumber: 1.9 Consensus size: 155
43967427 TTTATGTTTT
* * * * * * *
43967437 AAAAAATCAGCTCATACTGCGAGAGGTGAGTTGAGTCTCGGCTCACATGTGGAGGTATTTTTAAT
1 AAAAAATCAACTCATACTGCGAGAGGTCAATTGAGCCTCGGCTCACACGTGAAGGTATTTTCAAT
* * * *
43967502 TCTTGTTTTTTTTAAAAGTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGCTCACGCGCTGA
66 TCCTGATTTTTTTAAAAGTCAACTCGTATTGCAAGAGGCGAGTTGAGCCTCAGCTCACACGCTGA
* *
43967567 GTTATTTTCAATTACTATTTCAAAA
131 GGTATTCTCAATTACTATTTCAAAA
*
43967592 AAAAAATCAACTCATATTGCGAGAGGTCAATTGAGCCTCAGG-TCACACGCT-AAGGTATTTTCA
1 AAAAAATCAACTCATACTGCGAGAGGTCAATTGAGCCTC-GGCTCACACG-TGAAGGTATTTTCA
* * *
43967655 ATTCCT-ATTTTTTTAAAAGTCAATTCGTATTGCAAGAGGCGAGTTGAGCCTCAGGTCACACGTT
64 ATTCCTGATTTTTTTAAAAGTCAACTCGTATTGCAAGAGGCGAGTTGAGCCTCAGCTCACACGCT
43967719 GAGGTATTCTCAATT
129 GAGGTATTCTCAATT
43967734 TCTGTTTTTC
Statistics
Matches: 123, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
154 65 0.53
155 55 0.45
156 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (155 bp):
AAAAAATCAACTCATACTGCGAGAGGTCAATTGAGCCTCGGCTCACACGTGAAGGTATTTTCAAT
TCCTGATTTTTTTAAAAGTCAACTCGTATTGCAAGAGGCGAGTTGAGCCTCAGCTCACACGCTGA
GGTATTCTCAATTACTATTTCAAAA
Found at i:43967834 original size:29 final size:29
Alignment explanation
Indices: 43967782--43967839 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
43967772 TTGCGAGAGA
* *
43967782 TGAGTTGAGCTTCAGGTTATACGCTGAGG
1 TGAGTTGAGCTTCAGGTCACACGCTGAGG
*
43967811 TGAGTTGAGCTTCGGGTCACACGCTGAGG
1 TGAGTTGAGCTTCAGGTCACACGCTGAGG
43967840 ATAAAGATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.19, C:0.17, G:0.36, T:0.28
Consensus pattern (29 bp):
TGAGTTGAGCTTCAGGTCACACGCTGAGG
Found at i:43968831 original size:10 final size:10
Alignment explanation
Indices: 43968816--43968845 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
43968806 TTATTAAACT
43968816 AAAAAAATAC
1 AAAAAAATAC
43968826 AAAAAAATA-
1 AAAAAAATAC
43968835 AAAAAAATAC
1 AAAAAAATAC
43968845 A
1 A
43968846 TTTTTTCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.10
Consensus pattern (10 bp):
AAAAAAATAC
Found at i:43969435 original size:21 final size:18
Alignment explanation
Indices: 43969411--43969461 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 18
43969401 TTCTTTATTA
*
43969411 AATATTATTAGTATTATTTC
1 AATATTATTAATATTA--TC
43969431 TAATATTATTAATATTATC
1 -AATATTATTAATATTATC
43969450 AATATTATTAAT
1 AATATTATTAAT
43969462 TTTTTTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 12 0.41
19 2 0.07
21 15 0.52
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (18 bp):
AATATTATTAATATTATC
Found at i:43969594 original size:26 final size:24
Alignment explanation
Indices: 43969549--43969611 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 24
43969539 CTTTAATTTC
*
43969549 ATATTGTTATTATTAGTATTA-TAAT
1 ATATT-TTATTATTAATATTAGT-AT
43969574 ATTATATTTATTATTAATATTAGTAT
1 A-TAT-TTTATTATTAATATTAGTAT
43969600 ATATTTTATTAT
1 ATATTTTATTAT
43969612 ATATGTACAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
24 8 0.24
25 4 0.12
26 20 0.59
27 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (24 bp):
ATATTTTATTATTAATATTAGTAT
Found at i:43969668 original size:24 final size:23
Alignment explanation
Indices: 43969639--43969692 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
43969629 TTTTATATAG
43969639 TATTATCGTTT-CTATTATTATATT
1 TATTATC-TTTACTATTATTAT-TT
43969663 TATTAT-TTTCACTATTATTATTT
1 TATTATCTTT-ACTATTATTATTT
*
43969686 TTTTATC
1 TATTATC
43969693 ATTATTATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 3 0.12
23 7 0.27
24 16 0.62
ACGTcount: A:0.24, C:0.09, G:0.02, T:0.65
Consensus pattern (23 bp):
TATTATCTTTACTATTATTATTT
Found at i:43969859 original size:20 final size:19
Alignment explanation
Indices: 43969834--43969889 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
43969824 TTATATTATG
43969834 TATATTATTTTTTAAAATAT
1 TATATTATTTTTT-AAATAT
*
43969854 TATA-T-TTTTTTATATAT
1 TATATTATTTTTTAAATAT
*
43969871 TATATATATTTTTTTAATA
1 TATAT-TATTTTTTAAATA
43969890 CCGTATTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 9 0.30
18 6 0.20
19 2 0.07
20 13 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATATTATTTTTTAAATAT
Found at i:43969861 original size:17 final size:17
Alignment explanation
Indices: 43969839--43969875 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
43969829 TTATGTATAT
43969839 TATTTTTTAAAATATTA
1 TATTTTTTAAAATATTA
* *
43969856 TATTTTTTTATATATTA
1 TATTTTTTAAAATATTA
43969873 TAT
1 TAT
43969876 ATATTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTTTTTAAAATATTA
Found at i:43970010 original size:16 final size:18
Alignment explanation
Indices: 43969975--43970014 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
43969965 ATTATATGTG
43969975 TATAATATACTTTTTATA
1 TATAATATACTTTTTATA
43969993 TATAATATACTTTTTATA
1 TATAATATACTTTTTATA
43970011 TATA
1 TATA
43970015 TCATTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
TATAATATACTTTTTATA
Found at i:43970267 original size:28 final size:28
Alignment explanation
Indices: 43970225--43970284 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
43970215 TATATTGTTA
43970225 TTTTCTATTATTATTA-TAAATACATTAT
1 TTTTCTATTATTATTAGT-AATACATTAT
*
43970253 TTTTCTTATTA-TATTAGTAGTACATTAT
1 TTTTC-TATTATTATTAGTAATACATTAT
43970281 TTTT
1 TTTT
43970285 ATTTTCTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (28 bp):
TTTTCTATTATTATTAGTAATACATTAT
Found at i:43970512 original size:513 final size:517
Alignment explanation
Indices: 43969979--43971013 Score: 1936
Period size: 523 Copynumber: 2.0 Consensus size: 517
43969969 TATGTGTATA
43969979 ATATACTTTTTATATATAATA-TACTTTTTATATATATCATTATATTCATACTTATTATTTTCAC
1 ATATACTTTTTATATATAATATTA-TTTTTATATATATCATTATATTCATACTTATTATTTTCAC
43970043 TATTGTTGCTTATTATTTTATTTTAATATTATTATGTATACATATATCTTTTTGTACATACTTAT
65 TATTGTTGCTTATTATTTTATTTTAATATTATTATGTATACATATATCTTTTTGTACATACTTAT
*
43970108 ACTTACTTTATTACTCCTTGATCATCACCATTACCACTATTATTAGTATAATTATTATTCTTTTC
130 ACTTACTTTATTACTCCTTGATCATCACCATTACCACTATTATTAGTATAATTATGATTCTTTTC
*
43970173 ATCATTA-T-C-A-ACATATATATACATATATATATATTTTATGTATATATTGTTATTTTCTATT
195 ATCATTATTACTATACATATATATACATATATATATATTTTATGTATATATCGTTATTTTCTATT
43970234 ATTATTATAAATACATTATTTTTCTTATTATATTAGTAGTACATTATTTTTATTTTCTTGTAAAT
260 ATTATTATAAATACATTATTTTTCTTATTATATTAGTAGTACATTATTTTTATTTTCTTGTAAAT
43970299 ATTGTTATTGTTGTTTTAATATTCTCAGTTTTTAATATTTTTATTATTAATTGCATCATTTTTTG
325 ATTGTTATTGTTGTTTTAATATTCTCAGTTTTTAATATTTTTATTATTAATTGCATCATTTTTTG
43970364 CATTATTTACGAATTCTTATTATAATAATGTTTCACTCATACTTTTTAATTAATTTCAACAAATA
390 CATTATTTACGAATTCTTATTATAATAATGTTTCACTCATACTTTTTAATTAATTTCAACAAATA
43970429 AGGCAACGCACCGATTTAACATTAAGTCGTCGATTTCATCGCTATGTTGGGTGAATATTAATG
455 AGGCAACGCACCGATTTAACATTAAGTCGTCGATTTCATCGCTATGTTGGGTGAATATTAATG
43970492 ATATACTTTTTATATATAATATTATTTTTATATATATCATTATATTCATACTTATTATTTTCACT
1 ATATACTTTTTATATATAATATTATTTTTATATATATCATTATATTCATACTTATTATTTTCACT
43970557 ATTGTTGCTTATTATTTTATTTTAATATTATTATGTATACATATATCTTTTTGTACATACTTATA
66 ATTGTTGCTTATTATTTTATTTTAATATTATTATGTATACATATATCTTTTTGTACATACTTATA
43970622 CTTACTTTATTACTCCTTGATCATCACCATTACCACTATTATTAGTATAATTATGATTCTTTTCA
131 CTTACTTTATTACTCCTTGATCATCACCATTACCACTATTATTAGTATAATTATGATTCTTTTCA
**
43970687 TCATTATTAACATGTATATACATATATATATGTATATATATATTTTATGTATATATCGTTATTTT
196 TCATTATT-AC-----TATACATATATATACATATATATATATTTTATGTATATATCGTTATTTT
43970752 CTATTATTATTATAAATACATTATTTTTCTTATTATATTAGTAGTACATTATTTTTATTTTCTTG
255 CTATTATTATTATAAATACATTATTTTTCTTATTATATTAGTAGTACATTATTTTTATTTTCTTG
43970817 TAAATATTGTTATTGTTGTTTTAATATTCTCAGTTTTTAATATTTTTATTATTAATTGCATCATT
320 TAAATATTGTTATTGTTGTTTTAATATTCTCAGTTTTTAATATTTTTATTATTAATTGCATCATT
43970882 TTTTGCATTATTTACGAATTCTTATTATAATAATGTTTCACTCATACTTTTTAATTAATTTCAAC
385 TTTTGCATTATTTACGAATTCTTATTATAATAATGTTTCACTCATACTTTTTAATTAATTTCAAC
43970947 AAATAAGGCAACGCACCGATTTAACATTAAGTCGTCGATTTCATCGCTATGTTGGGTGAATATTA
450 AAATAAGGCAACGCACCGATTTAACATTAAGTCGTCGATTTCATCGCTATGTTGGGTGAATATTA
43971012 AT
515 AT
43971014 CGGCTCATGT
Statistics
Matches: 507, Mismatches: 4, Indels: 12
0.97 0.01 0.02
Matches are distributed among these distances:
513 197 0.39
514 3 0.01
516 1 0.00
522 1 0.00
523 305 0.60
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (517 bp):
ATATACTTTTTATATATAATATTATTTTTATATATATCATTATATTCATACTTATTATTTTCACT
ATTGTTGCTTATTATTTTATTTTAATATTATTATGTATACATATATCTTTTTGTACATACTTATA
CTTACTTTATTACTCCTTGATCATCACCATTACCACTATTATTAGTATAATTATGATTCTTTTCA
TCATTATTACTATACATATATATACATATATATATATTTTATGTATATATCGTTATTTTCTATTA
TTATTATAAATACATTATTTTTCTTATTATATTAGTAGTACATTATTTTTATTTTCTTGTAAATA
TTGTTATTGTTGTTTTAATATTCTCAGTTTTTAATATTTTTATTATTAATTGCATCATTTTTTGC
ATTATTTACGAATTCTTATTATAATAATGTTTCACTCATACTTTTTAATTAATTTCAACAAATAA
GGCAACGCACCGATTTAACATTAAGTCGTCGATTTCATCGCTATGTTGGGTGAATATTAATG
Found at i:43970537 original size:20 final size:17
Alignment explanation
Indices: 43970492--43970527 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 17
43970482 AATATTAATG
43970492 ATATACTTTTTATATATA
1 ATATA-TTTTTATATATA
43970510 ATATTATTTTTATATATA
1 ATA-TATTTTTATATATA
43970528 TCATTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATATTTTTATATATA
Found at i:43970765 original size:26 final size:27
Alignment explanation
Indices: 43970727--43970810 Score: 68
Period size: 26 Copynumber: 3.1 Consensus size: 27
43970717 TGTATATATA
* *
43970727 TATT-TTATGTATATAT-CGTTATTTT
1 TATTATTATGTATAAATACATTATTTT
43970752 CTATTATTAT-TATAAATACATTATTTT
1 -TATTATTATGTATAAATACATTATTTT
* * *
43970779 TCTTATTATAT-TAGTAGTACATTATTTT
1 TATTATTATGTATA--AATACATTATTTT
43970807 TATT
1 TATT
43970811 TTCTTGTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
26 20 0.42
27 13 0.27
28 15 0.31
ACGTcount: A:0.30, C:0.06, G:0.05, T:0.60
Consensus pattern (27 bp):
TATTATTATGTATAAATACATTATTTT
Found at i:43970790 original size:28 final size:28
Alignment explanation
Indices: 43970748--43970807 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
43970738 TATATCGTTA
43970748 TTTTCTATTATTATTA-TAAATACATTAT
1 TTTTCTATTATTATTAGT-AATACATTAT
*
43970776 TTTTCTTATTA-TATTAGTAGTACATTAT
1 TTTTC-TATTATTATTAGTAATACATTAT
43970804 TTTT
1 TTTT
43970808 ATTTTCTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (28 bp):
TTTTCTATTATTATTAGTAATACATTAT
Found at i:43971368 original size:26 final size:27
Alignment explanation
Indices: 43971330--43971413 Score: 68
Period size: 26 Copynumber: 3.1 Consensus size: 27
43971320 TGTATATATA
* *
43971330 TATT-TTATGTATATAT-CGTTATTTT
1 TATTATTATGTATAAATACATTATTTT
43971355 CTATTATTAT-TATAAATACATTATTTT
1 -TATTATTATGTATAAATACATTATTTT
* * *
43971382 TCTTATTATAT-TAGTAGTACATTATTTT
1 TATTATTATGTATA--AATACATTATTTT
43971410 TATT
1 TATT
43971414 TTCTTGTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
26 20 0.42
27 13 0.27
28 15 0.31
ACGTcount: A:0.30, C:0.06, G:0.05, T:0.60
Consensus pattern (27 bp):
TATTATTATGTATAAATACATTATTTT
Found at i:43971393 original size:28 final size:28
Alignment explanation
Indices: 43971351--43971410 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
43971341 TATATCGTTA
43971351 TTTTCTATTATTATTA-TAAATACATTAT
1 TTTTCTATTATTATTAGT-AATACATTAT
*
43971379 TTTTCTTATTA-TATTAGTAGTACATTAT
1 TTTTC-TATTATTATTAGTAATACATTAT
43971407 TTTT
1 TTTT
43971411 ATTTTCTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (28 bp):
TTTTCTATTATTATTAGTAATACATTAT
Found at i:43971544 original size:40 final size:40
Alignment explanation
Indices: 43971494--43971572 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
43971484 TGTTTGCATT
43971494 ATTTACGAATTCTTATTATAATAATGTTTTACTCATACTC
1 ATTTACGAATTCTTATTATAATAATGTTTTACTCATACTC
*
43971534 ATTTATGAATTCTTATTATAATAATGTTTTACTCATACT
1 ATTTACGAATTCTTATTATAATAATGTTTTACTCATACT
43971573 TTTTAATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.49
Consensus pattern (40 bp):
ATTTACGAATTCTTATTATAATAATGTTTTACTCATACTC
Found at i:43974700 original size:131 final size:130
Alignment explanation
Indices: 43974288--43974857 Score: 475
Period size: 131 Copynumber: 4.3 Consensus size: 130
43974278 ATGAAAAAGC
* * * * * * * * *
43974288 GCAACCCAGCACGATAGGGTACGATTCTCAAATAGCCAAACATCGAACATTGCCTTCATTTTGAG
1 GCAACCCAGCACGATAGGGCACGATTCCCGAATTGTCAAACACCGAATATTGCCTTCGTTTT-AA
* * * *** * * * *
43974353 AGGTTTTTA-ATAAACATGAGCGAAAACCTAAAGGAATATTCGATTGTTTTGAA-CAAACGAGAA
65 AGATTTTTAGA-AGACATGAGTGAAATTTTGAAGGGATATTCGATTATTTT-AAGCAAACAAGAA
*
43974416 ATC
128 ATT
* ** * * * * *
43974419 ACAACTTAGCACGATAGGGTATGACTCCCGAATTGTCAAACACCGAGTATTGCCTTCATTTTAAA
1 GCAACCCAGCACGATAGGGCACGATTCCCGAATTGTCAAACACCGAATATTGCCTTCGTTTTAAA
** * *
43974484 GGATTTTTAGAAGACATGAGTGAAATTTCAAAGGAATATTCGATTGTTTTGAA-CAAACAAGAAA
66 -GATTTTTAGAAGACATGAGTGAAATTTTGAAGGGATATTCGATTATTTT-AAGCAAACAAGAAA
43974548 TT
129 TT
*
43974550 GCAACCCAGCACGATAGGGCACGATTCCCGAATTGTCAAGCACCGAATATTGCCTTCGTTTTAAA
1 GCAACCCAGCACGATAGGGCACGATTCCCGAATTGTCAAACACCGAATATTGCCTTCGTTTTAAA
* * *
43974615 TGATTTTTAGAAGACGTGAATGAAATTTTGAAGGGATATTTGATTATTTTAAGCAAACAAGAAAT
66 -GATTTTTAGAAGACATGAGTGAAATTTTGAAGGGATATTCGATTATTTTAAGCAAACAAGAAAT
43974680 T
130 T
* * * * * * * * **
43974681 GCAACCCAGCACGTTAGGGCATGATTTCGCGAATTGCCAAATATCGCACATCACCTTCGTTTTAA
1 GCAACCCAGCACGATAGGGCACGA-TTCCCGAATTGTCAAACACCGAATATTGCCTTCGTTTTAA
* * *
43974746 AGAATTTTTTTTTAAAAGGA-ATGGGTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAACG
65 AG-A----TTTTTAGAA-GACATGAGTGAAATTTTGAAGGGATATTCGATTATTTTAAGCAAAC-
*
43974810 CA-AAATT
123 AAGAAATT
* * * * *
43974817 GCAACCCAACACGTTAAGGCACTATTCCGCGAATTGCCAAA
1 GCAACCCAGCACGATAGGGCACGATTCC-CGAATTGTCAAA
43974858 TATCGAATCT
Statistics
Matches: 365, Mismatches: 62, Indels: 19
0.82 0.14 0.04
Matches are distributed among these distances:
130 4 0.01
131 238 0.65
132 34 0.09
135 3 0.01
136 83 0.23
137 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (130 bp):
GCAACCCAGCACGATAGGGCACGATTCCCGAATTGTCAAACACCGAATATTGCCTTCGTTTTAAA
GATTTTTAGAAGACATGAGTGAAATTTTGAAGGGATATTCGATTATTTTAAGCAAACAAGAAATT
Found at i:43974798 original size:136 final size:132
Alignment explanation
Indices: 43974471--43974864 Score: 413
Period size: 136 Copynumber: 3.0 Consensus size: 132
43974461 CCGAGTATTG
* * * ** * *
43974471 CCTTCATTTTAAAGGATTTTTAGAAGACATGAGTGAAATTTCAAAGGAATATTCGATTGTTTTGA
1 CCTTCGTTTTAAATGATTTTTAAAAGACATGAGTGAAATTTTGAAGGGATATTCGATTATTTT-A
* * * * ** * *
43974536 A-CAAACAAGAAATTGCAACCCAGCACGATAGGGCACGA-TTCCCGAATTGTCAAGCACCGAATA
65 AGCAAACAAGAAATTGCAACCCAGCACGTTAGGGCATGATTTCGCGAATTGCCAAATATCGAACA
**
43974599 TTG
130 TCA
* * * *
43974602 CCTTCGTTTTAAATGATTTTTAGAAGACGTGAATGAAATTTTGAAGGGATATTTGATTATTTTAA
1 CCTTCGTTTTAAATGATTTTTAAAAGACATGAGTGAAATTTTGAAGGGATATTCGATTATTTTAA
*
43974667 GCAAACAAGAAATTGCAACCCAGCACGTTAGGGCATGATTTCGCGAATTGCCAAATATCGCACAT
66 GCAAACAAGAAATTGCAACCCAGCACGTTAGGGCATGATTTCGCGAATTGCCAAATATCGAACAT
43974732 CA
131 CA
*
43974734 CCTTCGTTTTAAA-GAATTTTTTTTTAAAAGGA-ATGGGTGAAATTTTGAAGGGATATTCGATTA
1 CCTTCGTTTTAAATG-A----TTTTTAAAA-GACATGAGTGAAATTTTGAAGGGATATTCGATTA
* * * * *
43974797 TTTTGAGCAAACGCA-AAATTGCAACCCAACACGTTAAGGCACT-ATTCCGCGAATTGCCAAATA
60 TTTTAAGCAAAC-AAGAAATTGCAACCCAGCACGTTAGGGCA-TGATTTCGCGAATTGCCAAATA
43974860 TCGAA
123 TCGAA
43974865 TCTCGTCTTC
Statistics
Matches: 222, Mismatches: 31, Indels: 15
0.83 0.12 0.06
Matches are distributed among these distances:
130 2 0.01
131 90 0.41
132 33 0.15
136 93 0.42
137 4 0.02
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (132 bp):
CCTTCGTTTTAAATGATTTTTAAAAGACATGAGTGAAATTTTGAAGGGATATTCGATTATTTTAA
GCAAACAAGAAATTGCAACCCAGCACGTTAGGGCATGATTTCGCGAATTGCCAAATATCGAACAT
CA
Found at i:43974875 original size:136 final size:136
Alignment explanation
Indices: 43974635--43974890 Score: 367
Period size: 136 Copynumber: 1.9 Consensus size: 136
43974625 AAGACGTGAA
* * *
43974635 TGAAATTTTGAAGGGATATTTGATTATTTTAAGCAAACAAGAAATTGCAACCCAGCACGTTAGGG
1 TGAAATTTTGAAGGGATATTCGATTATTTTAAGCAAACAAGAAATTGCAACCCAACACGTTAAGG
* *
43974700 CATGATTTCGCGAATTGCCAAATATCGCACATCACCTTCGTTTTAAAGAATTTTTTTTTAAAAGG
66 CATGATTCCGCGAATTGCCAAATATCGCACATCACCTTCGCTTTAAAGAATTTTTTTTTAAAAGG
43974765 AATGGG
131 AATGGG
* *
43974771 TGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAACGCA-AAATTGCAACCCAACACGTTAAG
1 TGAAATTTTGAAGGGATATTCGATTATTTTAAGCAAAC-AAGAAATTGCAACCCAACACGTTAAG
* *
43974835 GCACT-ATTCCGCGAATTGCCAAATATCG-A-ATCTCGTCTTCGCTTTAGAGAATTTTT
65 GCA-TGATTCCGCGAATTGCCAAATATCGCACATCAC--CTTCGCTTTAAAGAATTTTT
43974891 AAATGAATAC
Statistics
Matches: 107, Mismatches: 9, Indels: 8
0.86 0.07 0.06
Matches are distributed among these distances:
134 4 0.04
135 1 0.01
136 100 0.93
137 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (136 bp):
TGAAATTTTGAAGGGATATTCGATTATTTTAAGCAAACAAGAAATTGCAACCCAACACGTTAAGG
CATGATTCCGCGAATTGCCAAATATCGCACATCACCTTCGCTTTAAAGAATTTTTTTTTAAAAGG
AATGGG
Found at i:43978101 original size:45 final size:45
Alignment explanation
Indices: 43978051--43978248 Score: 158
Period size: 45 Copynumber: 4.5 Consensus size: 45
43978041 GGTGGCTTAA
43978051 ATCTGCTTCACTGCAACTTCAGGAAGCCAAGGTTCGTCGTCTTCG
1 ATCTGCTTCACTGCAACTTCAGGAAGCCAAGGTTCGTCGTCTTCG
* * **
43978096 ATCTGCTTCACTGCAACTTCAGGGAA-ACAA-GATC-TAAAAT-TTC-
1 ATCTGCTTCACTGCAACTTCA-GGAAGCCAAGGTTCGT--CGTCTTCG
* * * * * * * * * **
43978139 AGCCTACTCCACTACAACTTTAGGGAG-CTAGGTTGGT-GGCTTAA
1 A-TCTGCTTCACTGCAACTTCAGGAAGCCAAGGTTCGTCGTCTTCG
* *
43978183 ATCTGCTTCACTGCAACTTCAGGAAGCCAAGATTCGTCGTCTTTG
1 ATCTGCTTCACTGCAACTTCAGGAAGCCAAGGTTCGTCGTCTTCG
43978228 ATCTGCTTCACTGCAACTTCA
1 ATCTGCTTCACTGCAACTTCA
43978249 AGGGAACAGG
Statistics
Matches: 114, Mismatches: 28, Indels: 22
0.70 0.17 0.13
Matches are distributed among these distances:
43 28 0.25
44 31 0.27
45 51 0.45
46 4 0.04
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.29
Consensus pattern (45 bp):
ATCTGCTTCACTGCAACTTCAGGAAGCCAAGGTTCGTCGTCTTCG
Found at i:43978143 original size:132 final size:133
Alignment explanation
Indices: 43977876--43978263 Score: 572
Period size: 132 Copynumber: 2.9 Consensus size: 133
43977866 GTAATCTTCG
* * * **
43977876 GCCTACTCCACTACAACTTTAGGGAGCTAGGATAGTGGTTTGAATCTGCTTCACTGTGAC-TCAG
1 GCCTACTCCACTACAACTTTAGGGAGCTAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCAG
** *
43977940 GAAGACC-AGATTCACCGTCTTTGATCTGC-TCTACTGCAACTTCAGGGAGACAGGATCTACAGA
66 GAAG-CCAAGATTCGTCGTCTTTGATCTGCTTC-ACTGCAACTTCAGGGAAACAGGATCTACAGA
43978003 ATTTA
129 ATTTA
* *
43978008 GCCTACTCTACTACAACTTTAGAGAGCTAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCAG
1 GCCTACTCCACTACAACTTTAGGGAGCTAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCAG
* * *
43978073 GAAGCCAAGGTTCGTCGTCTTCGATCTGCTTCACTGCAACTTCAGGGAAACAAGATCTA-A-AAT
66 GAAGCCAAGATTCGTCGTCTTTGATCTGCTTCACTGCAACTTCAGGGAAACAGGATCTACAGAAT
43978136 TTCA
131 TT-A
*
43978140 GCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCTGCTTCACTGCAACTTCAG
1 GCCTACTCCACTACAACTTTAGGGAGCTAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCAG
43978205 GAAGCCAAGATTCGTCGTCTTTGATCTGCTTCACTGCAACTTCAAGGG-AACAGGATCTA
66 GAAGCCAAGATTCGTCGTCTTTGATCTGCTTCACTGCAACTTC-AGGGAAACAGGATCTA
43978264 TAGGATTCAC
Statistics
Matches: 232, Mismatches: 19, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
131 5 0.02
132 170 0.73
133 55 0.24
134 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (133 bp):
GCCTACTCCACTACAACTTTAGGGAGCTAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCAG
GAAGCCAAGATTCGTCGTCTTTGATCTGCTTCACTGCAACTTCAGGGAAACAGGATCTACAGAAT
TTA
Found at i:44005020 original size:26 final size:26
Alignment explanation
Indices: 44004990--44005065 Score: 107
Period size: 26 Copynumber: 2.9 Consensus size: 26
44004980 TCTCATCCCT
*
44004990 ATTTTACCCCTAGCAAAATTTTGACA
1 ATTTTACTCCTAGCAAAATTTTGACA
* *
44005016 ATTTTACTCTTAGTAAAATTTTGACA
1 ATTTTACTCCTAGCAAAATTTTGACA
* *
44005042 ATTTTGCTCCTTGCAAAATTTTGA
1 ATTTTACTCCTAGCAAAATTTTGA
44005066 GAAAATATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.42
Consensus pattern (26 bp):
ATTTTACTCCTAGCAAAATTTTGACA
Found at i:44005334 original size:9 final size:10
Alignment explanation
Indices: 44005316--44005344 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
44005306 CATTTCTTTT
44005316 TTTCTATTCA
1 TTTCTATTCA
44005326 TTT-TATTCA
1 TTTCTATTCA
44005335 TTTCTATTCA
1 TTTCTATTCA
44005345 AATACACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.21, C:0.17, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:44008099 original size:30 final size:30
Alignment explanation
Indices: 44008065--44008122 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
44008055 CACGGCCATG
* *
44008065 ACACACGGGCGTGTAG-TCTACCCGTGTGTC
1 ACACACAGGCATGTAGAT-TACCCGTGTGTC
*
44008095 ACACACAGGCATGTGGATTACCCGTGTG
1 ACACACAGGCATGTAGATTACCCGTGTG
44008123 AAAGTGCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.21, C:0.28, G:0.29, T:0.22
Consensus pattern (30 bp):
ACACACAGGCATGTAGATTACCCGTGTGTC
Found at i:44010849 original size:17 final size:18
Alignment explanation
Indices: 44010814--44010851 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
44010804 GTGTGCCAAA
*
44010814 AGAGCATGGAGATATCGC
1 AGAGCATGGAGATAGCGC
*
44010832 AGAGC-TGGAGCTAGCGC
1 AGAGCATGGAGATAGCGC
44010849 AGA
1 AGA
44010852 TGCCTTGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.32, C:0.18, G:0.37, T:0.13
Consensus pattern (18 bp):
AGAGCATGGAGATAGCGC
Found at i:44019694 original size:27 final size:27
Alignment explanation
Indices: 44019656--44019710 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
44019646 AGGTTGTGTG
*
44019656 CAATACTGAGTTGGTTCTTAGTCTACA
1 CAATACTGAGTTGGTTCTTAGTCGACA
*
44019683 CAATATTGAGTTGGTTCTTAGTCGACA
1 CAATACTGAGTTGGTTCTTAGTCGACA
44019710 C
1 C
44019711 GGCCACGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (27 bp):
CAATACTGAGTTGGTTCTTAGTCGACA
Found at i:44031247 original size:162 final size:163
Alignment explanation
Indices: 44030973--44031297 Score: 555
Period size: 162 Copynumber: 2.0 Consensus size: 163
44030963 TTGTATATTA
44030973 ATATCACTCAATTCGGGTCGAATGGTGGTGGCACTGAATTGTATATACCCATGTCTGTTGGTACT
1 ATATCACTCAATTCGGGTCGAATGGTGGTGGCACTGAATTGTATATACCCATGTCTGTTGGTACT
** * * *
44031038 GTATCGTGGTATCCAGACTCGAGTGCTAGCAATCATGTCTGTTGTGATGCGTCTGTACTGCATGA
66 ACATCGTGGTATCCAGACTCGAGTGCTAACAATCATGTCTATTGTGATGCGTCGGTACTGCATGA
*
44031103 CTCCACTCCGTATTTAGGTACGTCTTTT-TTTT
131 CTCCACTCCATATTTAGGTACGTCTTTTCTTTT
*
44031135 ATATCACTCAATTCGGGTCGAATGGTGGTGGCACTG-ATTCGTATATACCCATGTTTGTTGGTAC
1 ATATCACTCAATTCGGGTCGAATGGTGGTGGCACTGAATT-GTATATACCCATGTCTGTTGGTAC
*
44031199 TACATCGTGGTATCCAGACTCGGGTGCTAACAATCATGTCTATTGTGATGCGTCGGTACTGCATG
65 TACATCGTGGTATCCAGACTCGAGTGCTAACAATCATGTCTATTGTGATGCGTCGGTACTGCATG
44031264 ACTCCACTCCATATTTAGGTACGTCTTTTCTTTT
130 ACTCCACTCCATATTTAGGTACGTCTTTTCTTTT
44031298 GATGGGTGAT
Statistics
Matches: 153, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
161 3 0.02
162 146 0.95
163 4 0.03
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (163 bp):
ATATCACTCAATTCGGGTCGAATGGTGGTGGCACTGAATTGTATATACCCATGTCTGTTGGTACT
ACATCGTGGTATCCAGACTCGAGTGCTAACAATCATGTCTATTGTGATGCGTCGGTACTGCATGA
CTCCACTCCATATTTAGGTACGTCTTTTCTTTT
Found at i:44036749 original size:29 final size:30
Alignment explanation
Indices: 44036699--44036766 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
44036689 CGGCTCAAGA
* * *
44036699 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TCAAAAGTTAAAGGACTAATAGT
*
44036729 GTAAATATGAAAAGTTAAAGGACTAATAGT
1 GTAAATATCAAAAGTTAAAGGACTAATAGT
*
44036759 GCAAATAT
1 GTAAATAT
44036767 TTTAAGGGCG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.28
Consensus pattern (30 bp):
GTAAATATCAAAAGTTAAAGGACTAATAGT
Found at i:44038842 original size:46 final size:46
Alignment explanation
Indices: 44038790--44038929 Score: 183
Period size: 46 Copynumber: 3.0 Consensus size: 46
44038780 GTGTGCTCTC
* *
44038790 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* *
44038836 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCACGGCAACA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * * * *
44038882 TGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCA
1 TGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
44038928 TG
1 TG
44038930 TCAAAGATAA
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
45 1 0.01
46 81 0.99
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (46 bp):
TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
Done.