Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 125 of 175
Found at i:39135232 original size:82 final size:82
Alignment explanation
Indices: 39135133--39135319 Score: 197
Period size: 82 Copynumber: 2.3 Consensus size: 82
39135123 GACTTTATGT
* * * *
39135133 CTAGCAGGCT-TGATGCCGGTGAAAC-ATTTC-GGACTATAAGTCTAGCAGGCTAAAAGCCGGTG
1 CTAGCAGGCTAAG-TGCCGGTGAAACTA-ATCAGG-CTATAAGCCTAGAAGGCTAAAAGCCGGTG
39135195 -TACTGAATCAGG-TTATAAGC
63 AT-CTGAATCAGGCTT-TAAGC
* * **
39135215 CTAGCAGGCTAAGTGCCGGTG-ATCTGAATCAGGTTATAAGCCTAGAAGGCTAAGTGCCGGTGAT
1 CTAGCAGGCTAAGTGCCGGTGAAACT-AATCAGGCTATAAGCCTAGAAGGCTAAAAGCCGGTGAT
39135279 CTGAATCAGGCTTTAAGC
65 CTGAATCAGGCTTTAAGC
*
39135297 CTAACAGGCTAAGTGCCGGTGAA
1 CTAGCAGGCTAAGTGCCGGTGAA
39135320 TCTGTTTAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
81 2 0.02
82 79 0.89
83 8 0.09
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (82 bp):
CTAGCAGGCTAAGTGCCGGTGAAACTAATCAGGCTATAAGCCTAGAAGGCTAAAAGCCGGTGATC
TGAATCAGGCTTTAAGC
Found at i:39139393 original size:19 final size:19
Alignment explanation
Indices: 39139369--39139415 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
39139359 CGACGTCTTT
*
39139369 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTACAT-CA
39139388 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
39139407 TATGCATTA
1 TTTGCATTA
39139416 AAGTCCACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:39146632 original size:51 final size:51
Alignment explanation
Indices: 39146555--39146683 Score: 177
Period size: 51 Copynumber: 2.5 Consensus size: 51
39146545 CTTCACCAGA
*
39146555 AGAGACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAAATGG
1 AGAGACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAATCCTAAAAAAATGG
* * **
39146606 AGAGACCAAGGTGAAAACCCGTAAAGGGCGCTTTGAATTCTAAAAAAAAAAAG
1 AGAGACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAATCCT--AAAAAAATGG
* *
39146659 AAAGGCCAAGGTGAAAACCCGCAAA
1 AGAGACCAAGGTGAAAACCCGCAAA
39146684 TGGCCCCTTG
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 38 0.56
53 30 0.44
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (51 bp):
AGAGACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAATCCTAAAAAAATGG
Found at i:39147989 original size:45 final size:44
Alignment explanation
Indices: 39147845--39148007 Score: 143
Period size: 44 Copynumber: 3.7 Consensus size: 44
39147835 AATCTTATTT
* * * * * *
39147845 CCCTGAAGTTGCAGTGGAGCAGATTAAAG-TCACTAATCTTATCC
1 CCCTGAAGTTGCAATGGAGCAGACTGAAGAT-ACGAGTCCTATCC
* * * * * *
39147889 CCTTGAAGTTGCAGTGGGGCAGA-TCGAAGTTACCAG-CCTTATCT
1 CCCTGAAGTTGCAATGGAGCAGACT-GAAGATACGAGTCC-TATCC
39147933 CCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCGAGTCCTATCC
1 CCCTGAAGTTGCAATGGAGCAGACTGAAGATA-CGAGTCCTATCC
**
39147978 CCCTGAAGTTGCAACAGAGCAGACTGAAGA
1 CCCTGAAGTTGCAATGGAGCAGACTGAAGA
39148008 CAGCGAATCT
Statistics
Matches: 98, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
43 2 0.02
44 57 0.58
45 37 0.38
46 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (44 bp):
CCCTGAAGTTGCAATGGAGCAGACTGAAGATACGAGTCCTATCC
Found at i:39148013 original size:45 final size:45
Alignment explanation
Indices: 39147928--39148013 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
39147918 TTACCAGCCT
* ** *
39147928 TATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCGAGTCC
1 TATCCCCCTGAAGTTGCAACAGAGCAGACTGAAGACAGCGAGTCC
39147973 TATCCCCCTGAAGTTGCAACAGAGCAGACTGAAGACAGCGA
1 TATCCCCCTGAAGTTGCAACAGAGCAGACTGAAGACAGCGA
39148014 ATCTTATTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (45 bp):
TATCCCCCTGAAGTTGCAACAGAGCAGACTGAAGACAGCGAGTCC
Found at i:39149770 original size:21 final size:22
Alignment explanation
Indices: 39149733--39149775 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
39149723 GTGATTTTTA
39149733 TGTTTAATTTTGC-TTTTATTT
1 TGTTTAATTTTGCTTTTTATTT
*
39149754 TGTTTTATTTT-CTTTTTTATTT
1 TGTTTAATTTTGC-TTTTTATTT
39149776 GTGAACTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.05
21 10 0.53
22 8 0.42
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.77
Consensus pattern (22 bp):
TGTTTAATTTTGCTTTTTATTT
Found at i:39149819 original size:15 final size:15
Alignment explanation
Indices: 39149801--39149835 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
39149791 GTTATTATAA
39149801 TTATTATTACTATTT
1 TTATTATTACTATTT
*
39149816 TTATTATTAGTATTT
1 TTATTATTACTATTT
39149831 TTATT
1 TTATT
39149836 TTGTTGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (15 bp):
TTATTATTACTATTT
Found at i:39151524 original size:17 final size:17
Alignment explanation
Indices: 39151471--39151524 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
39151461 AAGAATTCGT
*
39151471 CAAATCATAGATCTCGC
1 CAAAACATAGATCTCGC
* * *
39151488 TAAAACATAAATCTCAC
1 CAAAACATAGATCTCGC
*
39151505 CAAAACATAGATTTCGC
1 CAAAACATAGATCTCGC
39151522 CAA
1 CAA
39151525 TCAGCACATA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.22
Consensus pattern (17 bp):
CAAAACATAGATCTCGC
Found at i:39153369 original size:44 final size:44
Alignment explanation
Indices: 39153320--39153404 Score: 143
Period size: 44 Copynumber: 1.9 Consensus size: 44
39153310 GATTTTTTTC
*
39153320 TCCCACTTAAACTTTGATTAATGTAGATTATTTTAATATTAGTT
1 TCCCACTTAAACTCTGATTAATGTAGATTATTTTAATATTAGTT
* *
39153364 TCCCACTTAAACTCTGATTAGTGTAGGTTATTTTAATATTA
1 TCCCACTTAAACTCTGATTAATGTAGATTATTTTAATATTA
39153405 TTTGACCTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.46
Consensus pattern (44 bp):
TCCCACTTAAACTCTGATTAATGTAGATTATTTTAATATTAGTT
Found at i:39156151 original size:23 final size:22
Alignment explanation
Indices: 39156096--39156151 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
39156086 CTATTACGTA
*
39156096 GATATAACTGC-TTGGAGACAC
1 GATATAACTGCAGTGGAGACAC
***
39156117 GATATGTTTGCAAGTGGAGACAC
1 GATATAACTGC-AGTGGAGACAC
39156140 GATATAACTGCA
1 GATATAACTGCA
39156152 TAATTTGGCT
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
21 8 0.31
22 1 0.04
23 17 0.65
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (22 bp):
GATATAACTGCAGTGGAGACAC
Found at i:39161534 original size:17 final size:17
Alignment explanation
Indices: 39161512--39161545 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39161502 TACATCTTTA
39161512 ATTTTTCATGCTAAAAT
1 ATTTTTCATGCTAAAAT
*
39161529 ATTTTTCATGTTAAAAT
1 ATTTTTCATGCTAAAAT
39161546 GCTTGTAGCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (17 bp):
ATTTTTCATGCTAAAAT
Found at i:39161960 original size:17 final size:17
Alignment explanation
Indices: 39161938--39162261 Score: 197
Period size: 17 Copynumber: 18.4 Consensus size: 17
39161928 TTTTTAATGG
39161938 AATTTTTGAAACACGAA
1 AATTTTTGAAACACGAA
*
39161955 AATTTTTGAAACACGGA
1 AATTTTTGAAACACGAA
** * *
39161972 TTTTTTTTAAACACGAC
1 AATTTTTGAAACACGAA
* *
39161989 AATTTTTTAAACACGAG
1 AATTTTTGAAACACGAA
*
39162006 AATTTTTGCAAAACACAAA
1 AATTTTTG--AAACACGAA
*
39162025 AATTTTTTAAAACACGAA
1 AA-TTTTTGAAACACGAA
* * *
39162043 AATTTGTGAAACACTAG
1 AATTTTTGAAACACGAA
* ** *
39162060 AGTCGTTGAAAACACGGA
1 AATTTTTG-AAACACGAA
* *
39162078 AATTTGTGAAAACACAAA
1 AATTTTTG-AAACACGAA
* *
39162096 AATTTTTGAAACATGGA
1 AATTTTTGAAACACGAA
*
39162113 AATTTTTAGAAAACACAAA
1 AATTTTT-G-AAACACGAA
* * *
39162132 AATTTTTGGATCACCG-G
1 AATTTTTGAAACA-CGAA
39162149 AATTTTTGAAAACACGAA
1 AATTTTTG-AAACACGAA
* * *
39162167 AATTTTCT-AAACGCCAG
1 AATTTT-TGAAACACGAA
*
39162184 AATTTTTGAAAACACGAG
1 AATTTTTG-AAACACGAA
*
39162202 GATTTTTGAAACACGAA
1 AATTTTTGAAACACGAA
** *
39162219 TTTTTTTTTGAAAATACGAA
1 --AATTTTTG-AAACACGAA
39162239 AATTTTTGAAA-AC-ACA
1 AATTTTTGAAACACGA-A
39162255 AATTTTT
1 AATTTTT
39162262 TTTTTTGAAA
Statistics
Matches: 234, Mismatches: 57, Indels: 33
0.72 0.18 0.10
Matches are distributed among these distances:
15 1 0.00
16 11 0.05
17 113 0.48
18 67 0.29
19 29 0.12
20 13 0.06
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (17 bp):
AATTTTTGAAACACGAA
Found at i:39162199 original size:35 final size:35
Alignment explanation
Indices: 39161937--39162261 Score: 202
Period size: 35 Copynumber: 9.2 Consensus size: 35
39161927 TTTTTTAATG
*
39161937 GAATTTTTG-AAACACGAAAATTTTTGAAACA-CG
1 GAATTTTTGAAAACACGAAAATTTTTGAAACACCA
* ** * * *
39161970 GATTTTTTTTAAACACGACAATTTTTTAAACACGA
1 GAATTTTTGAAAACACGAAAATTTTTGAAACACCA
* * *
39162005 GAATTTTTGCAAAACACAAAAATTTTTTAAAACACGA
1 GAATTTTTG-AAAACACGAAAA-TTTTTGAAACACCA
* * * * * ** *
39162042 AAATTTGTG-AAACACTAGAGTCGTTGAAA-ACACG
1 GAATTTTTGAAAACACGAAAATTTTTGAAACAC-CA
* * **
39162076 GAAATTTGTGAAAACACAAAAATTTTTGAAACA-TG
1 G-AATTTTTGAAAACACGAAAATTTTTGAAACACCA
* * * *
39162111 GAAATTTTTAGAAAACACAAAAATTTTTGGATCACCG
1 G-AATTTTT-GAAAACACGAAAATTTTTGAAACACCA
*
39162148 GAATTTTTGAAAACACGAAAATTTTCT-AAACGCCA
1 GAATTTTTGAAAACACGAAAATTTT-TGAAACACCA
**
39162183 GAATTTTTGAAAACACGAGGATTTTTGAAACA-C-
1 GAATTTTTGAAAACACGAAAATTTTTGAAACACCA
*
39162216 GAATTTTTTTTTGAAAATACGAAAATTTTTGAAA-ACACA
1 GAA----TTTTTGAAAACACGAAAATTTTTGAAACAC-CA
39162255 -AATTTTT
1 GAATTTTT
39162262 TTTTTTGAAA
Statistics
Matches: 229, Mismatches: 44, Indels: 37
0.74 0.14 0.12
Matches are distributed among these distances:
33 12 0.05
34 33 0.14
35 79 0.34
36 55 0.24
37 47 0.21
38 3 0.01
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (35 bp):
GAATTTTTGAAAACACGAAAATTTTTGAAACACCA
Found at i:39162244 original size:37 final size:38
Alignment explanation
Indices: 39162186--39162288 Score: 120
Period size: 37 Copynumber: 2.7 Consensus size: 38
39162176 AACGCCAGAA
** *
39162186 TTTTTGAAAACACGAGGATTTTTG-AAACACGAATTTT
1 TTTTTGAAAACACGAAAATTTTTGAAAACACAAATTTT
*
39162223 TTTTTGAAAATACGAAAATTTTTGAAAACACAAATTTTTT
1 TTTTTGAAAACACGAAAATTTTTGAAAACACAAA--TTTT
* *
39162263 TTTTTGAAAACATGAGAA-TTTTGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAA
39162289 GACGAAATCT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
37 21 0.38
38 8 0.14
39 8 0.14
40 19 0.34
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.40
Consensus pattern (38 bp):
TTTTTGAAAACACGAAAATTTTTGAAAACACAAATTTT
Found at i:39162263 original size:18 final size:19
Alignment explanation
Indices: 39161940--39162263 Score: 80
Period size: 18 Copynumber: 18.3 Consensus size: 19
39161930 TTTAATGGAA
*
39161940 TTTTTG-AAACACGAAA-A
1 TTTTTGAAAACACGAAATT
*
39161957 TTTTTG-AAACACG-GATT
1 TTTTTGAAAACACGAAATT
*
39161974 TTTTT-TAAACACGACAA-T
1 TTTTTGAAAACACGA-AATT
39161992 TTTTT--AAACACGAGAA--
1 TTTTTGAAAACACGA-AATT
* *
39162008 TTTTTGCAAAACACAAAAAT
1 TTTTTG-AAAACACGAAATT
*
39162028 TTTTT-AAAACACGAAA-A
1 TTTTTGAAAACACGAAATT
* * * *
39162045 TTTGTG-AAACACTAGA-G
1 TTTTTGAAAACACGAAATT
**
39162062 TCGTTGAAAACACGGAAA--
1 TTTTTGAAAACAC-GAAATT
* **
39162080 TTTGTGAAAACAC-AAAAA
1 TTTTTGAAAACACGAAATT
*
39162098 TTTTTG-AAACATGGAAA-T
1 TTTTTGAAAACA-CGAAATT
* * *
39162116 TTTTAGAAAACACAAAAAT
1 TTTTTGAAAACACGAAATT
* ** *
39162135 TTTTGGATCAC-CGGAA--
1 TTTTTGAAAACACGAAATT
*
39162151 TTTTTGAAAACACGAAAAT
1 TTTTTGAAAACACGAAATT
* * *
39162170 TTTCT--AAACGCCAGAA--
1 TTTTTGAAAACACGA-AATT
*
39162186 TTTTTGAAAACACGAGGA--
1 TTTTTGAAAACACGA-AATT
*
39162204 TTTTTG-AAACACGAATTTT
1 TTTTTGAAAACACGAA-ATT
* *
39162223 TTTTTGAAAATACGAAA-A
1 TTTTTGAAAACACGAAATT
39162241 TTTTTGAAAACAC-AAATT
1 TTTTTGAAAACACGAAATT
39162259 TTTTT
1 TTTTT
39162264 TTTTGAAAAC
Statistics
Matches: 230, Mismatches: 48, Indels: 57
0.69 0.14 0.17
Matches are distributed among these distances:
16 21 0.09
17 76 0.33
18 83 0.36
19 37 0.16
20 13 0.06
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
TTTTTGAAAACACGAAATT
Found at i:39162302 original size:38 final size:36
Alignment explanation
Indices: 39162186--39162303 Score: 112
Period size: 37 Copynumber: 3.1 Consensus size: 36
39162176 AACGCCAGAA
*
39162186 TTTTTGAAAACACGAGGATTTTTGAAACACG-AATTTT
1 TTTTTGAAAACACGA-GAATTTTGAAA-ACGAAATTTT
* * *
39162223 TTTTTGAAAATACGAAAATTTTTGAAAACACAAATTTTTT
1 TTTTTGAAAACACGAGAA-TTTTGAAAAC-GAAA--TTTT
* *
39162263 TTTTTGAAAACATGAGAATTTTGAAAGACGAAATCTT
1 TTTTTGAAAACACGAGAATTTTGAAA-ACGAAATTTT
39162300 TTTT
1 TTTT
39162304 ATTTTTATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
36 3 0.05
37 29 0.44
38 2 0.03
39 11 0.17
40 21 0.32
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTTTGAAAACACGAGAATTTTGAAAACGAAATTTT
Found at i:39162923 original size:9 final size:9
Alignment explanation
Indices: 39162902--39162957 Score: 59
Period size: 8 Copynumber: 6.8 Consensus size: 9
39162892 AAACATTTTC
39162902 TTTTCTC-T
1 TTTTCTCTT
39162910 TTTTCTCTT
1 TTTTCTCTT
39162919 TTTTC-CTT
1 TTTTCTCTT
39162927 TTTTCT-TT
1 TTTTCTCTT
*
39162935 CTTT-T-TT
1 TTTTCTCTT
*
39162942 TTCTCTCTT
1 TTTTCTCTT
39162951 TTTTCTC
1 TTTTCTC
39162958 CTCTCTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
7 5 0.12
8 21 0.52
9 14 0.35
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTCTCTT
Found at i:39162931 original size:30 final size:32
Alignment explanation
Indices: 39162897--39162955 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
39162887 AAATTAAACA
39162897 TTTTCTTT-TCTCTTTT-TCTCTTTTTTCCTT
1 TTTTCTTTCTCTCTTTTCTCTCTTTTTTCCTT
* *
39162927 TTTTCTTTCTTTTTTTTCTCTCTTTTTTC
1 TTTTCTTTCTCTCTTTTCTCTCTTTTTTC
39162956 TCCTCTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 8 0.32
31 6 0.24
32 11 0.44
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (32 bp):
TTTTCTTTCTCTCTTTTCTCTCTTTTTTCCTT
Found at i:39162940 original size:12 final size:12
Alignment explanation
Indices: 39162925--39162970 Score: 56
Period size: 13 Copynumber: 3.6 Consensus size: 12
39162915 TCTTTTTTCC
*
39162925 TTTTTTCTTTCTT
1 TTTTTTCTCTC-T
39162938 TTTTTTCTCTCT
1 TTTTTTCTCTCT
39162950 TTTTTCTCCTCTCT
1 TTTTT-T-CTCTCT
39162964 TTTTTTC
1 TTTTTTC
39162971 GGCCTGCCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 7 0.23
13 12 0.40
14 11 0.37
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTTCTCTCT
Found at i:39162953 original size:14 final size:14
Alignment explanation
Indices: 39162925--39162969 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
39162915 TCTTTTTTCC
*
39162925 TTTTTTCTTTC-TT
1 TTTTTTCTCTCTTT
39162938 TTTTTTCTCTCTTT
1 TTTTTTCTCTCTTT
* *
39162952 TTTCTCCTCTCTTT
1 TTTTTTCTCTCTTT
39162966 TTTT
1 TTTT
39162970 CGGCCTGCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTTCTCTCTTT
Found at i:39162957 original size:11 final size:11
Alignment explanation
Indices: 39162909--39162967 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
39162899 TTCTTTTCTC
39162909 TTTT-TCTCTT
1 TTTTCTCTCTT
39162919 TTTTC-CT-TT
1 TTTTCTCTCTT
* *
39162928 TTTCTTTCTTTT
1 TTT-TCTCTCTT
39162940 TTTTCTCTCTT
1 TTTTCTCTCTT
39162951 TTTTCTCCTCTCT
1 TTTTCT-CTCT-T
39162964 TTTT
1 TTTT
39162968 TTCGGCCTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
9 5 0.12
10 7 0.17
11 14 0.35
12 9 0.22
13 5 0.12
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTCTCTCTT
Found at i:39163162 original size:8 final size:8
Alignment explanation
Indices: 39163149--39163178 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
39163139 GACTGAATTA
39163149 ATTTTTTT
1 ATTTTTTT
39163157 A-TTTTTT
1 ATTTTTTT
39163164 ATTTTTTT
1 ATTTTTTT
39163172 ATTTTTT
1 ATTTTTT
39163179 CTTTCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
ATTTTTTT
Found at i:39163169 original size:15 final size:15
Alignment explanation
Indices: 39163149--39163178 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39163139 GACTGAATTA
39163149 ATTTTTTTATTTTTT
1 ATTTTTTTATTTTTT
39163164 ATTTTTTTATTTTTT
1 ATTTTTTTATTTTTT
39163179 CTTTCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (15 bp):
ATTTTTTTATTTTTT
Found at i:39163185 original size:4 final size:4
Alignment explanation
Indices: 39163176--39163256 Score: 78
Period size: 4 Copynumber: 20.0 Consensus size: 4
39163166 TTTTTTATTT
* *
39163176 TTTC TTTC TTTT TCTTC -TTC CTTC -TTC TTTC -TTC TTTC TTTC TTTC
1 TTTC TTTC TTTC T-TTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
39163222 TTTC TTCTC TTTTC TTTC TCTTT TTTC TTTC TTTC
1 TTTC TT-TC -TTTC TTTC T-TTC TTTC TTTC TTTC
39163257 CCGATCAACC
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
3 9 0.14
4 46 0.70
5 9 0.14
6 2 0.03
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:39163210 original size:26 final size:27
Alignment explanation
Indices: 39163176--39163254 Score: 83
Period size: 26 Copynumber: 3.0 Consensus size: 27
39163166 TTTTTTATTT
*
39163176 TTTCTTTCTTTTTCTTC-TTCCTTCTTC
1 TTTC-TTCTTTCTCTTCTTTCCTTCTTC
*
39163203 TTTCTTCTTTCT-TTCTTTCTTTCTTC
1 TTTCTTCTTTCTCTTCTTTCCTTCTTC
* *
39163229 TCTT-TTCTTTCTCTTTTTTCTTTCTT
1 T-TTCTTCTTTCTCTTCTTTCCTTCTT
39163255 TCCCGATCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
25 3 0.07
26 25 0.54
27 18 0.39
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTCTTCTTTCTCTTCTTTCCTTCTTC
Found at i:39163250 original size:7 final size:7
Alignment explanation
Indices: 39163151--39163256 Score: 63
Period size: 7 Copynumber: 15.0 Consensus size: 7
39163141 CTGAATTAAT
*
39163151 TTTTTTA
1 TTTTTTC
*
39163158 TTTTTTAT
1 TTTTTT-C
*
39163166 TTTTTTA
1 TTTTTTC
39163173 TTTTTTC
1 TTTTTTC
*
39163180 TTTCTT-
1 TTTTTTC
*
39163186 TTTCTTC
1 TTTTTTC
**
39163193 TTCCTTC
1 TTTTTTC
*
39163200 TTCTTTC
1 TTTTTTC
*
39163207 TTCTTTC
1 TTTTTTC
39163214 TTTCTTTC
1 TTT-TTTC
*
39163222 TTTCTTC
1 TTTTTTC
*
39163229 TCTTTTC
1 TTTTTTC
*
39163236 -TTTCTC
1 TTTTTTC
39163242 TTTTTTC
1 TTTTTTC
39163249 TTTCTTTC
1 TTT-TTTC
39163257 CCGATCAACC
Statistics
Matches: 81, Mismatches: 13, Indels: 9
0.79 0.13 0.09
Matches are distributed among these distances:
6 10 0.12
7 54 0.67
8 17 0.21
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTTC
Found at i:39163394 original size:21 final size:21
Alignment explanation
Indices: 39163370--39163424 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
39163360 TCTTCTTTGC
39163370 TCTTTTCTTCTT-CTT-TTTCTT
1 TCTTTT-TTCTTGCTTGTTT-TT
*
39163391 TCTTTTTGCTTGCTTGTTTTT
1 TCTTTTTTCTTGCTTGTTTTT
39163412 TCTTTTTTCTTGC
1 TCTTTTTTCTTGC
39163425 CTCTTGGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 4 0.13
21 23 0.77
22 3 0.10
ACGTcount: A:0.00, C:0.20, G:0.07, T:0.73
Consensus pattern (21 bp):
TCTTTTTTCTTGCTTGTTTTT
Found at i:39163794 original size:29 final size:29
Alignment explanation
Indices: 39163752--39163856 Score: 113
Period size: 29 Copynumber: 3.6 Consensus size: 29
39163742 CAAAACCTCT
* *
39163752 AGGGTCAAAGTGTAATTTTGGAAAATTTA
1 AGGGTCAAAATGTAATTTTAGAAAATTTA
* *
39163781 AGGGTCAAAATGTAATTTCAAGAAAGTTT-
1 AGGGTCAAAATGTAATTT-TAGAAAATTTA
* *
39163810 AGGGTCAAAATATAATTTTAAAAAAATTTA
1 AGGGTCAAAATGTAATTTT-AGAAAATTTA
* *
39163840 GGGGTCAAAATGCAATT
1 AGGGTCAAAATGTAATT
39163857 GTGTAAAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
29 41 0.66
30 21 0.34
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (29 bp):
AGGGTCAAAATGTAATTTTAGAAAATTTA
Found at i:39164139 original size:68 final size:67
Alignment explanation
Indices: 39164066--39164192 Score: 200
Period size: 67 Copynumber: 1.9 Consensus size: 67
39164056 ATGAGTTTTT
* * * *
39164066 TTTTTTTAAAAATAGAAATTTCAAAAATACCTCAGTGTGTGACCCGAGGCTCAACTCACCTCTCG
1 TTTTTTGAAAAACAGAAA-TTAAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCG
39164131 TAA
65 TAA
*
39164134 TTTTTTGAAAAACAGAAATTAAAAAATACCTCAGCGTGTGATCCGAGGCTCAACTCACC
1 TTTTTTGAAAAACAGAAATTAAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACC
39164193 GTGTGACCCG
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
67 38 0.70
68 16 0.30
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.28
Consensus pattern (67 bp):
TTTTTTGAAAAACAGAAATTAAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGT
AA
Found at i:39164195 original size:24 final size:24
Alignment explanation
Indices: 39164163--39164216 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
39164153 TAAAAAATAC
* *
39164163 CTCAGCGTGTGATCCGAGGCTCAA
1 CTCACCGTGTGACCCGAGGCTCAA
39164187 CTCACCGTGTGACCCGAGGCTCAA
1 CTCACCGTGTGACCCGAGGCTCAA
39164211 CTCACC
1 CTCACC
39164217 TCTCGCAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.37, G:0.24, T:0.19
Consensus pattern (24 bp):
CTCACCGTGTGACCCGAGGCTCAA
Found at i:39164381 original size:77 final size:77
Alignment explanation
Indices: 39164187--39164495 Score: 417
Period size: 75 Copynumber: 4.0 Consensus size: 77
39164177 CGAGGCTCAA
* *
39164187 CTCACCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAACAAA
1 CTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT-TTGAAAAACAAA
39164252 AATTTAAAAGAAATAC
64 AA-TTAAAA-AAATAC
* * * * *
39164268 CTCAGCATGTG-TCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
1 CTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAA
39164332 TTAAAAAAATAC
66 TTAAAAAAATAC
* * * * * *
39164344 ATCAGCGTGCGACCCGAGACTCAACTCACCTCACGCAATATGAGCTGATTTTTGAAAAATAGAAA
1 CTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAA
*
39164409 TT--TAAAATAC
66 TTAAAAAAATAC
39164419 CTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGCAAAAACAAAA
1 CTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAACAAAA
*
39164484 ATTGAAAAAATA
65 ATTAAAAAAATA
39164496 ATTTTTGAAA
Statistics
Matches: 202, Mismatches: 22, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
75 57 0.28
76 25 0.12
77 55 0.27
78 19 0.09
79 3 0.01
80 34 0.17
81 9 0.04
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (77 bp):
CTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAA
TTAAAAAAATAC
Found at i:39164492 original size:152 final size:155
Alignment explanation
Indices: 39164192--39164495 Score: 436
Period size: 152 Copynumber: 2.0 Consensus size: 155
39164182 CTCAACTCAC
* * * *
39164192 CGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAACAAAAATTT
1 CGTGCGACCCGAGACTCAACTCACCTCACGCAATATGAGCTGATTTTCTTGAAAAACAAAAATTT
* * *
39164257 AAAAGAAATACCTCAGCATGTGTCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
66 --AAGAAATACCTCAGCATGCGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
*
39164322 AAAACAGAAATTAAAAAAATACATCAG
129 AAAACAAAAATTAAAAAAATACATCAG
* *
39164349 CGTGCGACCCGAGACTCAACTCACCTCACGCAATATGAGCTGA-TTT-TTGAAAAATAGAAATTT
1 CGTGCGACCCGAGACTCAACTCACCTCACGCAATATGAGCTGATTTTCTTGAAAAACAAAAATTT
*
39164412 -A-AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGCA
66 AAGAAATACCTCAGCATGCG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-A
*
39164475 AAAACAAAAATTGAAAAAATA
129 AAAACAAAAATTAAAAAAATA
39164496 ATTTTTGAAA
Statistics
Matches: 133, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
151 15 0.11
152 41 0.31
153 20 0.15
155 15 0.11
156 3 0.02
157 39 0.29
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (155 bp):
CGTGCGACCCGAGACTCAACTCACCTCACGCAATATGAGCTGATTTTCTTGAAAAACAAAAATTT
AAGAAATACCTCAGCATGCGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
AACAAAAATTAAAAAAATACATCAG
Found at i:39165373 original size:15 final size:14
Alignment explanation
Indices: 39165353--39165388 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
39165343 CTTTTTTCTT
39165353 TTTTTTTTGTTTTTG
1 TTTTTTTTG-TTTTG
39165368 TTTTTTTTGTTTTG
1 TTTTTTTTGTTTTG
39165382 TTTTTTT
1 TTTTTTT
39165389 AGGCATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (14 bp):
TTTTTTTTGTTTTG
Found at i:39172770 original size:17 final size:16
Alignment explanation
Indices: 39172748--39172844 Score: 68
Period size: 17 Copynumber: 5.6 Consensus size: 16
39172738 TTTTTTAAAT
39172748 GAAATTTTTCAAACAC
1 GAAATTTTTCAAACAC
**
39172764 GGAAATTTTAGAAACAC
1 -GAAATTTTTCAAACAC
* *
39172781 GAATTGTTTTTTAAACAC
1 GAA--ATTTTTCAAACAC
*
39172799 GACAATTTTTGAAACAC
1 GA-AATTTTTCAAACAC
39172816 GAGAATTTTTTCAAAACAC
1 GA-AA-TTTTTC-AAACAC
*
39172835 AAAAATTTTT
1 -GAAATTTTT
39172845 TAAAACACAA
Statistics
Matches: 64, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
16 3 0.05
17 29 0.45
18 22 0.34
19 9 0.14
20 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.34
Consensus pattern (16 bp):
GAAATTTTTCAAACAC
Found at i:39172826 original size:35 final size:34
Alignment explanation
Indices: 39172752--39172844 Score: 89
Period size: 35 Copynumber: 2.6 Consensus size: 34
39172742 TTAAATGAAA
* * *
39172752 TTTTTCAAACACGGAAATTTTAGAAACACGAATTG
1 TTTTTAAAACAC-GAAATTTTTGAAACACGAAATG
*
39172787 TTTTTTAAACACGACAATTTTTGAAACACGAGAAT-
1 TTTTTAAAACACGA-AATTTTTGAAACACGA-AATG
*
39172822 TTTTTCAAAACACAAAAATTTTT
1 TTTTT-AAAACAC-GAAATTTTT
39172845 TAAAACACAA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
34 2 0.04
35 31 0.63
36 15 0.31
37 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (34 bp):
TTTTTAAAACACGAAATTTTTGAAACACGAAATG
Found at i:39172856 original size:17 final size:18
Alignment explanation
Indices: 39172752--39172860 Score: 82
Period size: 18 Copynumber: 6.1 Consensus size: 18
39172742 TTAAATGAAA
* *
39172752 TTTTTCAAACACGGAAA-
1 TTTTTAAAACACGAAAAT
*
39172769 -TTTTAGAAACACG-AATT
1 TTTTTA-AAACACGAAAAT
* *
39172786 GTTTTTTAAACACGACAA-
1 -TTTTTAAAACACGAAAAT
* *
39172804 TTTTTGAAACACGAGAAT
1 TTTTTAAAACACGAAAAT
*
39172822 TTTTTCAAAACACAAAAAT
1 TTTTT-AAAACACGAAAAT
*
39172841 TTTTTAAAACACAAAAAT
1 TTTTTAAAACACGAAAAT
39172859 TT
1 TT
39172861 CTGAAACACT
Statistics
Matches: 75, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
16 6 0.08
17 22 0.29
18 27 0.36
19 20 0.27
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (18 bp):
TTTTTAAAACACGAAAAT
Found at i:39172867 original size:17 final size:18
Alignment explanation
Indices: 39172823--39172869 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
39172813 CACGAGAATT
39172823 TTTTC-AAAACACAAAAA
1 TTTTCTAAAACACAAAAA
*
39172840 TTTTTTAAAACACAAAAA
1 TTTTCTAAAACACAAAAA
*
39172858 -TTTCTGAAACAC
1 TTTTCTAAAACAC
39172870 TAGAGCTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.30
Consensus pattern (18 bp):
TTTTCTAAAACACAAAAA
Found at i:39172942 original size:18 final size:17
Alignment explanation
Indices: 39172921--39172996 Score: 66
Period size: 18 Copynumber: 4.4 Consensus size: 17
39172911 GGATCACCGG
39172921 AATTTTTGAAAACACGAA
1 AATTTTTG-AAACACGAA
* *
39172939 AATTTTCT-AAACACCAG
1 AATTTT-TGAAACACGAA
* *
39172956 AATTTTTGAAAACATGAG
1 AATTTTTG-AAACACGAA
*
39172974 GATTTTTGAAACAC-AA
1 AATTTTTGAAACACGAA
39172990 AATTTTT
1 AATTTTT
39172997 TTTTTTGAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
16 8 0.17
17 18 0.38
18 20 0.43
19 1 0.02
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (17 bp):
AATTTTTGAAACACGAA
Found at i:39172979 original size:35 final size:35
Alignment explanation
Indices: 39172888--39172996 Score: 114
Period size: 35 Copynumber: 3.1 Consensus size: 35
39172878 TTTTTTAAAT
* * * * *
39172888 TTTTTCAAAACACAAAAATTTTTGGATCACCGGAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCAGAA
39172923 TTTTTGAAAACACGAAAATTTTCT-AAACACCAGAA
1 TTTTTGAAAACACGAAAATTTT-TGAAACACCAGAA
* ** *
39172958 TTTTTGAAAACATGAGGATTTTTGAAACA-CAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCAGAA
39172992 TTTTT
1 TTTTT
39172997 TTTTTTGAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
34 10 0.16
35 52 0.83
36 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTGAAACACCAGAA
Found at i:39173019 original size:40 final size:40
Alignment explanation
Indices: 39172958--39173083 Score: 157
Period size: 40 Copynumber: 3.1 Consensus size: 40
39172948 AACACCAGAA
*
39172958 TTTTTGAAAACATGAGGATTTTTGAAACACAAAATTTTTT
1 TTTTTGAAAACATGAGAATTTTTGAAACACAAAATTTTTT
* * *
39172998 TTTTTGAAAATATGAAAATTTTTGAAAACACAGAA-TTTTT
1 TTTTTGAAAACATGAGAATTTTTG-AAACACAAAATTTTTT
* *
39173038 TTTTTGAAAACATGAGAA-TTTTGAAAGACGAAATCTTTTT
1 TTTTTGAAAACATGAGAATTTTTGAAACACAAAAT-TTTTT
39173078 TATTTT
1 T-TTTT
39173084 TATTTTGTTA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
38 7 0.10
39 5 0.07
40 48 0.66
41 13 0.18
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (40 bp):
TTTTTGAAAACATGAGAATTTTTGAAACACAAAATTTTTT
Found at i:39173042 original size:23 final size:23
Alignment explanation
Indices: 39173016--39173059 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
39173006 AATATGAAAA
39173016 TTTTTGAAAACA-CAGAATTTTT
1 TTTTTGAAAACATCAGAATTTTT
*
39173038 TTTTTGAAAACATGAGAATTTT
1 TTTTTGAAAACATCAGAATTTT
39173060 GAAAGACGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (23 bp):
TTTTTGAAAACATCAGAATTTTT
Found at i:39173505 original size:17 final size:17
Alignment explanation
Indices: 39173476--39173525 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
39173466 AAAATTATTT
*
39173476 AAAA-TAAAATAAAATA
1 AAAATTAAATTAAAATA
*
39173492 AAAATTAAATTAAATTA
1 AAAATTAAATTAAAATA
39173509 AAAATATAAATATAAAA
1 AAAAT-TAAAT-TAAAA
39173526 ATATAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 4 0.14
17 15 0.54
18 5 0.18
19 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATTAAATTAAAATA
Found at i:39173526 original size:14 final size:13
Alignment explanation
Indices: 39173486--39173532 Score: 55
Period size: 14 Copynumber: 3.8 Consensus size: 13
39173476 AAAATAAAAT
*
39173486 AAAATAAAAATT-
1 AAAATATAAATTA
39173498 -AAAT-TAAATTA
1 AAAATATAAATTA
39173509 AAAATATAAATATA
1 AAAATATAAAT-TA
39173523 AAAATATAAA
1 AAAATATAAA
39173533 AATGCATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 5 0.17
11 4 0.13
12 4 0.13
13 5 0.17
14 12 0.40
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATATAAATTA
Found at i:39173686 original size:7 final size:7
Alignment explanation
Indices: 39173670--39173720 Score: 59
Period size: 7 Copynumber: 7.1 Consensus size: 7
39173660 TTAAACCTTT
39173670 TTTTTCTC
1 TTTTT-TC
39173678 TTTTTTC
1 TTTTTTC
39173685 TTTTTTC
1 TTTTTTC
*
39173692 CTTTTTC
1 TTTTTTC
39173699 TTTTTT-
1 TTTTTTC
*
39173705 TTTCTCTC
1 TTT-TTTC
39173713 TTTTTTC
1 TTTTTTC
39173720 T
1 T
39173721 CCTCTCTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 3 0.08
7 26 0.70
8 8 0.22
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:39173725 original size:14 final size:14
Alignment explanation
Indices: 39173697--39173732 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
39173687 TTTTCCTTTT
* *
39173697 TCTTTTTTTTTCTC
1 TCTTTTTTCTCCTC
39173711 TCTTTTTTCTCCTC
1 TCTTTTTTCTCCTC
39173725 TCTTTTTT
1 TCTTTTTT
39173733 TTAACCTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (14 bp):
TCTTTTTTCTCCTC
Found at i:39173732 original size:35 final size:34
Alignment explanation
Indices: 39173667--39173732 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 34
39173657 AAATTAAACC
** *
39173667 TTTTTTTTCTCTTTTTTCTTTTTTCCTTTTTCTT
1 TTTTTTTTCTCTTTTTTCTCCTCTCCTTTTTCTT
*
39173701 TTTTTTTCTCTCTTTTTTCTCCTCTCTTTTTT
1 TTTTTTT-TCTCTTTTTTCTCCTCTCCTTTTT
39173733 TTAACCTGCC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 7 0.26
35 20 0.74
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (34 bp):
TTTTTTTTCTCTTTTTTCTCCTCTCCTTTTTCTT
Found at i:39174017 original size:29 final size:29
Alignment explanation
Indices: 39173974--39174078 Score: 106
Period size: 29 Copynumber: 3.6 Consensus size: 29
39173964 AAAACTTCTA
* * ** *
39173974 GGGTCAAAGTGTAATTTTGGAAATTTTAG
1 GGGTCAAAATATAATTTAAGAAAATTTAG
39174003 GGGTCAAAATATAATTTCAA-AAAAGTTTA-
1 GGGTCAAAATATAATTT-AAGAAAA-TTTAG
*
39174032 GAGTCAAAATATAAATTTAAGAAAATTTAG
1 GGGTCAAAATAT-AATTTAAGAAAATTTAG
*
39174062 GGGTCAAAATACAATTT
1 GGGTCAAAATATAATTT
39174079 TGTAAAAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
29 40 0.63
30 23 0.37
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (29 bp):
GGGTCAAAATATAATTTAAGAAAATTTAG
Found at i:39183827 original size:411 final size:411
Alignment explanation
Indices: 39183065--39183861 Score: 1522
Period size: 411 Copynumber: 1.9 Consensus size: 411
39183055 TTGGAATCGG
39183065 GCTATGTAAACTGGGTTAGAGTATTTTGGGCTCGGGTTTGATGTAATTCGGGTTATTGGGCTAGA
1 GCTATGTAAACTGGGTTAGAGTATTTTGGGCTCGGGTTTGATGTAATTCGGGTTATTGGGCTAGA
39183130 GTGTACTGAAATTGGGCCTATTATATTCGATTGTAGTTGGACTATTATTGGACCTTTATTTATTT
66 GTGTACTGAAATTGGGCCTATTATATTCGATTGTAGTTGGACTATTATTGGACCTTTATTTATTT
*
39183195 GATATTTTTTCATATTTGGGTTTTAATAGTTGGGCTCGGGTCGGGAAAAATTTGGGTATTACAGC
131 GATATTTTTTCATATTTGGGTTTTAATAGTTGGGCTCGGGTCGGGAAAAATTTGGGTATTACAAC
*
39183260 GATATTTCGCCTATTTTCTGGTAGCTTGACTGCATATTACCTGTAATGTGTCACATCGACACTAT
196 GACATTTCGCCTATTTTCTGGTAGCTTGACTGCATATTACCTGTAATGTGTCACATCGACACTAT
*
39183325 ATGGTGTGTAGGGATGGGTGGGTGTTTTTAACCTTACATGGTGTGATGGGATGGTCGGAGATGGT
261 ATGGTGTGTAGGGATGGGTGAGTGTTTTTAACCTTACATGGTGTGATGGGATGGTCGGAGATGGT
* * *
39183390 GTGTAGAGGATGGGGGTATGACTCGCTATCTCTGTTCTGTTTTTCTGATTCTGATAATTGTTCTC
326 GTGTAGAGGACGGAGGTAGGACTCGCTATCTCTGTTCTGTTTTTCTGATTCTGATAATTGTTCTC
39183455 GGAGATGGGTGCATATTACCT
391 GGAGATGGGTGCATATTACCT
39183476 GCTATGTAAACTGGGTTAGAGTATTTTGGGCTCGGGTTTGATGTAATTCGGGTTATTGGGCTAGA
1 GCTATGTAAACTGGGTTAGAGTATTTTGGGCTCGGGTTTGATGTAATTCGGGTTATTGGGCTAGA
* *
39183541 GTGTATTGAAATTGGGCCTCTTATATTCGATTGTAGTTGGACTATTATTGGACCTTTATTTATTT
66 GTGTACTGAAATTGGGCCTATTATATTCGATTGTAGTTGGACTATTATTGGACCTTTATTTATTT
39183606 GATATTTTTTCATATTTGGGTTTTAATAGTTGGGCTCGGGTCGGGAAAAATTTGGGTATTACAAC
131 GATATTTTTTCATATTTGGGTTTTAATAGTTGGGCTCGGGTCGGGAAAAATTTGGGTATTACAAC
39183671 GACATTTCGCCTATTTTCTGGTAGCTTGACTGCATATTACCTGTAATGTGTCACATCGACACTAT
196 GACATTTCGCCTATTTTCTGGTAGCTTGACTGCATATTACCTGTAATGTGTCACATCGACACTAT
39183736 ATGGTGTGTAGGGATGGGTGAGTGTTTTTAACCTTACATGGTGTGATGGGATGGTCGGAGATGGT
261 ATGGTGTGTAGGGATGGGTGAGTGTTTTTAACCTTACATGGTGTGATGGGATGGTCGGAGATGGT
39183801 GTGTAGAGGACGGAGGTAGGACTCGCTATCTCTGTTCTGTTTTTCTGATTCTGATAATTGT
326 GTGTAGAGGACGGAGGTAGGACTCGCTATCTCTGTTCTGTTTTTCTGATTCTGATAATTGT
39183862 ATCTATTATG
Statistics
Matches: 378, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
411 378 1.00
ACGTcount: A:0.21, C:0.12, G:0.28, T:0.39
Consensus pattern (411 bp):
GCTATGTAAACTGGGTTAGAGTATTTTGGGCTCGGGTTTGATGTAATTCGGGTTATTGGGCTAGA
GTGTACTGAAATTGGGCCTATTATATTCGATTGTAGTTGGACTATTATTGGACCTTTATTTATTT
GATATTTTTTCATATTTGGGTTTTAATAGTTGGGCTCGGGTCGGGAAAAATTTGGGTATTACAAC
GACATTTCGCCTATTTTCTGGTAGCTTGACTGCATATTACCTGTAATGTGTCACATCGACACTAT
ATGGTGTGTAGGGATGGGTGAGTGTTTTTAACCTTACATGGTGTGATGGGATGGTCGGAGATGGT
GTGTAGAGGACGGAGGTAGGACTCGCTATCTCTGTTCTGTTTTTCTGATTCTGATAATTGTTCTC
GGAGATGGGTGCATATTACCT
Found at i:39191585 original size:20 final size:20
Alignment explanation
Indices: 39191560--39191597 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39191550 TTGTACGGGA
39191560 TTGCAC-TTTAGTGCCTCTGT
1 TTGCACTTTTA-TGCCTCTGT
39191580 TTGCACTTTTATGCCTCT
1 TTGCACTTTTATGCCTCT
39191598 AATTACACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.11, C:0.26, G:0.16, T:0.47
Consensus pattern (20 bp):
TTGCACTTTTATGCCTCTGT
Found at i:39207272 original size:25 final size:24
Alignment explanation
Indices: 39207215--39207272 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 24
39207205 ATCCCTTCAC
* *
39207215 TTCCTCTTCTCTTCCTCTTTACAT
1 TTCCTCTTCTCTCCCACTTTACAT
39207239 TT-CTGCTTCTACTCCCACTTCT-CAT
1 TTCCT-CTTCT-CTCCCACTT-TACAT
39207264 TTCCTCTTC
1 TTCCTCTTC
39207273 CCCTGTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
23 2 0.07
24 7 0.25
25 16 0.57
26 3 0.11
ACGTcount: A:0.09, C:0.40, G:0.02, T:0.50
Consensus pattern (24 bp):
TTCCTCTTCTCTCCCACTTTACAT
Found at i:39209932 original size:23 final size:23
Alignment explanation
Indices: 39209892--39209937 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
39209882 TTTAGATTAT
** *
39209892 TTATTTTAATTTTTAAATTTTAA
1 TTATTTTAATTTAAAAATGTTAA
*
39209915 TTATTTTGATTTAAAAATGTTAA
1 TTATTTTAATTTAAAAATGTTAA
39209938 AAATTCCCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (23 bp):
TTATTTTAATTTAAAAATGTTAA
Found at i:39210209 original size:21 final size:21
Alignment explanation
Indices: 39210159--39210210 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
39210149 ACCGTTATTT
* *
39210159 TAATCTCACCACTACAGTATC
1 TAATATCACCACTACAGTAAC
* *
39210180 CAATATCACCACTACATTAAC
1 TAATATCACCACTACAGTAAC
*
39210201 TAATTTCACC
1 TAATATCACC
39210211 GCCACCATTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.33, G:0.02, T:0.29
Consensus pattern (21 bp):
TAATATCACCACTACAGTAAC
Found at i:39212336 original size:18 final size:18
Alignment explanation
Indices: 39212289--39212329 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
39212279 TTTTAAAATC
* *
39212289 ATAAAAAATTTAA-AAAA
1 ATAAAAAAATAAACAAAA
39212306 ATAAAAAAATAAACAAAA
1 ATAAAAAAATAAACAAAA
39212324 ATAAAA
1 ATAAAA
39212330 TTATAAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (18 bp):
ATAAAAAAATAAACAAAA
Found at i:39218584 original size:19 final size:19
Alignment explanation
Indices: 39218547--39218585 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
39218537 AAAATGAAAT
39218547 TATTAAAAATATTTATATTA
1 TATTAAAAATA-TTATATTA
39218567 TATTAAATAATA-TATATTA
1 TATTAAA-AATATTATATTA
39218586 AAATTATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 7 0.39
21 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTAAAAATATTATATTA
Found at i:39224940 original size:45 final size:45
Alignment explanation
Indices: 39224876--39224962 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
39224866 CAGATACTCG
* *
39224876 GTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCCA
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCA
*
39224921 GTGGAATCAGCACATAGCAACCACCTTACTAATTAATGATGT
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
39224963 TCGGTTCACA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.26
Consensus pattern (45 bp):
GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCA
Found at i:39225031 original size:51 final size:50
Alignment explanation
Indices: 39224964--39225157 Score: 203
Period size: 51 Copynumber: 3.8 Consensus size: 50
39224954 TAATGATGTT
* *
39224964 CGGTTCACATAGTAGCCTGCACATAGTACTATCA-ATGTGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTA-CACATGTGACCA-TACCATC
* * * * *
39225015 CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCATACCATC
* * * * * * *
39225066 CGGTACGCATAGTAGCCTGTACATAGCACTACACATGCGACC-TATCATTT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TC
*
39225116 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACC
39225158 GTCACTTTCA
Statistics
Matches: 115, Mismatches: 25, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
49 2 0.02
50 40 0.35
51 71 0.62
52 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACCATC
Found at i:39225179 original size:101 final size:99
Alignment explanation
Indices: 39224970--39225158 Score: 256
Period size: 101 Copynumber: 1.9 Consensus size: 99
39224960 TGTTCGGTTC
* *
39224970 ACATAGTAGCCTGCACATAGTACTATCAATGTGACCATTACCATCCGATACACGTAGTAGCCTGC
1 ACATAGTAGCCTGCACATAGCACTATCAATGCGACCA-TACCATCCGATACACGTAGTAGCCTGC
*
39225035 ACATAGTACTACACACGTGATCGAAACTATCCGGT
65 ACATAGTACTACACACGTGACCGAAACTATCCGGT
* * * *
39225070 ACGCATAGTAGCCTGTACATAGCACTA-CACATGCGACC-TATCATTTCGGTACACGTAGTAGCC
1 A--CATAGTAGCCTGCACATAGCACTATCA-ATGCGACCATACCA-TCCGATACACGTAGTAGCC
39225133 TGCACATAGTACTACACACGTGACCG
62 TGCACATAGTACTACACACGTGACCG
39225159 TCACTTTCAC
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
100 5 0.06
101 44 0.56
102 29 0.37
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (99 bp):
ACATAGTAGCCTGCACATAGCACTATCAATGCGACCATACCATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGACCGAAACTATCCGGT
Found at i:39227411 original size:17 final size:18
Alignment explanation
Indices: 39227373--39227411 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
39227363 TTGATTTTAT
*
39227373 TTATTGATAAAAATTGAA
1 TTATTGATAAAAATAGAA
39227391 -TATT-ATAAAAATAGAA
1 TTATTGATAAAAATAGAA
39227407 TTATT
1 TTATT
39227412 TCTTATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (18 bp):
TTATTGATAAAAATAGAA
Found at i:39230902 original size:30 final size:30
Alignment explanation
Indices: 39230868--39230927 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
39230858 TATTTTATTA
39230868 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
*
39230898 TTAATTTTGTTATTATTTTAGAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
39230928 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:39235311 original size:27 final size:25
Alignment explanation
Indices: 39235281--39235337 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 25
39235271 AAATTAACTT
*
39235281 AAATCAAGTTTAATATTATTATATTAA
1 AAATAAAGTTTAATATTATT-T-TTAA
* * *
39235308 AAATAAATTTTATTTTTATTTTTAA
1 AAATAAAGTTTAATATTATTTTTAA
39235333 AAATA
1 AAATA
39235338 TTTAAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 9 0.35
26 1 0.04
27 16 0.62
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (25 bp):
AAATAAAGTTTAATATTATTTTTAA
Found at i:39235472 original size:16 final size:19
Alignment explanation
Indices: 39235424--39235479 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 19
39235414 TTTAGTCCTA
39235424 TAATAAATTATTAATATAAT
1 TAATAAATTATTAATAT-AT
39235444 TAATATAATTTATT-AT-T-T
1 TAATA-AA-TTATTAATATAT
39235462 TAATAAATTATTTAATAT
1 TAATAAATTA-TTAATAT
39235480 TTCAAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
16 3 0.10
17 4 0.13
18 8 0.26
19 1 0.03
20 6 0.19
21 4 0.13
22 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATAAATTATTAATATAT
Found at i:39235514 original size:15 final size:13
Alignment explanation
Indices: 39235489--39235528 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
39235479 TTTCAAATTT
39235489 ATTTT-AATAATA
1 ATTTTAAATAATA
39235501 GATTTTAAAATAATA
1 -ATTTT-AAATAATA
39235516 ATTTTAAATAATA
1 ATTTTAAATAATA
39235529 TTCCTCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 13 0.52
14 5 0.20
15 7 0.28
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (13 bp):
ATTTTAAATAATA
Found at i:39236499 original size:19 final size:20
Alignment explanation
Indices: 39236455--39236519 Score: 57
Period size: 19 Copynumber: 3.3 Consensus size: 20
39236445 TTATAATATT
*
39236455 ATTTTAATAATAAAATTTAAC
1 ATTTTAATAAT-AATTTTAAC
39236476 A--TTAATAATAATTTTAA-
1 ATTTTAATAATAATTTTAAC
*
39236493 ATTTTAAATAAT-ATTCTTAAT
1 ATTTT-AATAATAATT-TTAAC
39236514 ATTTTA
1 ATTTTA
39236520 TTGAAAATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
17 1 0.03
18 7 0.18
19 13 0.34
20 11 0.29
21 6 0.16
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTTAATAATAATTTTAAC
Found at i:39236504 original size:20 final size:21
Alignment explanation
Indices: 39236479--39236519 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
39236469 ATTTAACATT
39236479 AATAATAATT-TTAA-ATTTTA
1 AATAAT-ATTCTTAATATTTTA
39236499 AATAATATTCTTAATATTTTA
1 AATAATATTCTTAATATTTTA
39236520 TTGAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 10 0.53
21 6 0.32
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AATAATATTCTTAATATTTTA
Found at i:39241145 original size:19 final size:19
Alignment explanation
Indices: 39241097--39241146 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
39241087 TTTTTATCAA
**
39241097 TATTTTGAAATTTAAAAAT
1 TATTTTGATTTTTAAAAAT
* *
39241116 TATTTTAATTTTTGAAAAT
1 TATTTTGATTTTTAAAAAT
39241135 TATTTTGATTTT
1 TATTTTGATTTT
39241147 CTTTTTGTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
TATTTTGATTTTTAAAAAT
Found at i:39241761 original size:4 final size:4
Alignment explanation
Indices: 39241717--39241742 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
39241707 TTATTGAACT
39241717 TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TT
39241743 GAAAAACCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAA
Found at i:39242114 original size:13 final size:13
Alignment explanation
Indices: 39242096--39242126 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
39242086 AGTGTATTAC
39242096 CCTTATGTGATAT
1 CCTTATGTGATAT
39242109 CCTTATGTGATAT
1 CCTTATGTGATAT
39242122 CCTTA
1 CCTTA
39242127 ATCTCTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (13 bp):
CCTTATGTGATAT
Found at i:39242893 original size:6 final size:6
Alignment explanation
Indices: 39242882--39242937 Score: 112
Period size: 6 Copynumber: 9.3 Consensus size: 6
39242872 AACCCATCAC
39242882 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
39242930 AAAAAG AA
1 AAAAAG AA
39242938 CATCGTATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:39257789 original size:60 final size:60
Alignment explanation
Indices: 39257696--39257818 Score: 228
Period size: 60 Copynumber: 2.0 Consensus size: 60
39257686 CTATTGAGTC
* *
39257696 TTCCATTATACAAGAATCTATTATCAAGAGTTCCATACCATTGCCTTTGGTAGCTAGGCA
1 TTCCATTAAACAAGAATCTATTATCAAGAGTTCCATACCATTGCCTTTGGTAGCAAGGCA
39257756 TTCCATTAAACAAGAATCTATTATCAAGAGTTCCATACCATTGCCTTTGGTAGCAAGGCA
1 TTCCATTAAACAAGAATCTATTATCAAGAGTTCCATACCATTGCCTTTGGTAGCAAGGCA
39257816 TTC
1 TTC
39257819 TTTCCACTCT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.33
Consensus pattern (60 bp):
TTCCATTAAACAAGAATCTATTATCAAGAGTTCCATACCATTGCCTTTGGTAGCAAGGCA
Found at i:39259859 original size:38 final size:38
Alignment explanation
Indices: 39259808--39259885 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
39259798 AGGATACAAT
*
39259808 TGGCATGTCAATAGGTTATATCGCGCTTTGTATGAGTC
1 TGGCATGTCAATAGGTTATATCGCGCTTTGTACGAGTC
*
39259846 TGGCATGTCAATAGGTTATATCGCGCTTTGTGCGAGTC
1 TGGCATGTCAATAGGTTATATCGCGCTTTGTACGAGTC
39259884 TG
1 TG
39259886 ACTTGAGATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.36
Consensus pattern (38 bp):
TGGCATGTCAATAGGTTATATCGCGCTTTGTACGAGTC
Found at i:39260769 original size:29 final size:29
Alignment explanation
Indices: 39260713--39260769 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
39260703 TTAAAATTAT
* * *
39260713 TAAAATTTTAAAAAATATATAATTATTTA
1 TAAAATTATAAAAAATATAAAATGATTTA
39260742 TAAAATTAT-AAAAATATAAAAATGATTT
1 TAAAATTATAAAAAATAT-AAAATGATTT
39260770 TTTAAAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
TAAAATTATAAAAAATATAAAATGATTTA
Found at i:39266431 original size:134 final size:133
Alignment explanation
Indices: 39266075--39266487 Score: 473
Period size: 133 Copynumber: 3.1 Consensus size: 133
39266065 GCGCTTCCCC
* * *
39266075 AAAAACGCCGCAAAAAAATTGGAATATAGCGGCGTTTTCTGAGAAACGCCGGTAACGATAA-CGA
1 AAAAACGCCGC--AAAAATTGGAATATAGCGGCGTTTTCGGAGAAACGCCGGTAAAGA-AATCTA
* *
39266139 ATTTGAGGAAAAAATCTGAGCAAAACAGTACTGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCG
63 ATTTGAGGAAAAAATTTGAGCAAAAC-GTACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCG
*
39266204 CATTTTA
127 CATTGTA
* * * *
39266211 AAAAACGCCAG-AAAAGAAT-GCAT-TAGCGGCGTTTTCAGG-GAAACGCCGATAAAGATATCTA
1 AAAAACGCC-GCAAAA-ATTGGAATATAGCGGCGTTTTC-GGAGAAACGCCGGTAAAGAAATCTA
* * *
39266272 ATTTGAGGAAAAAATTTG-GACAAAACGCTACCGTTTTATTGCTTCATTTTATTTCCTTAGTGGC
63 ATTTGAGGAAAAAATTTGAG-CAAAACG-TACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGC
39266336 GCATTGTA
126 GCATTGTA
* * *
39266344 AAAAACGCCGCAAATATTGGGATATAGTGGCGTTATT-GGAGAAACGCCGGTAAAGAAATCTAAT
1 AAAAACGCCGCAAAAATTGGAATATAGCGGCGTT-TTCGGAGAAACGCCGGTAAAGAAATCTAAT
* * * *
39266408 TTGAGGAAAAATTTTGAGCAAAACGGTACCGTTTTGTTGTTTCCTTTTA-TGCTTTAGTGGCGAA
65 TTGAGGAAAAAATTTGAGCAAAAC-GTACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCGCA
*
39266472 ATGTTA
129 TTG-TA
39266478 AAAAACGCCG
1 AAAAACGCCG
39266488 GAAACGGTTC
Statistics
Matches: 236, Mismatches: 27, Indels: 30
0.81 0.09 0.10
Matches are distributed among these distances:
132 6 0.03
133 122 0.52
134 92 0.39
135 6 0.03
136 9 0.04
137 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.30
Consensus pattern (133 bp):
AAAAACGCCGCAAAAATTGGAATATAGCGGCGTTTTCGGAGAAACGCCGGTAAAGAAATCTAATT
TGAGGAAAAAATTTGAGCAAAACGTACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCGCATT
GTA
Found at i:39266873 original size:21 final size:20
Alignment explanation
Indices: 39266834--39266886 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
39266824 TTTGTGATCT
*
39266834 GGGCTTAGAGTTTAGGTTTA
1 GGGCTTAGAGTTGAGGTTTA
*
39266854 GGGCTTGGAGATTGAGGTTTA
1 GGGCTTAGAG-TTGAGGTTTA
* *
39266875 AGGTTTAGAGTT
1 GGGCTTAGAGTT
39266887 TGCATTTCAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.21, C:0.04, G:0.38, T:0.38
Consensus pattern (20 bp):
GGGCTTAGAGTTGAGGTTTA
Found at i:39268761 original size:17 final size:18
Alignment explanation
Indices: 39268725--39268765 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
39268715 ATAATTTCGT
*
39268725 AATAATGCATCAATTTAA
1 AATAATGCATCAATTCAA
*
39268743 AATAATGTAT-AATTCAA
1 AATAATGCATCAATTCAA
39268760 AATAAT
1 AATAAT
39268766 AAAATACTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (18 bp):
AATAATGCATCAATTCAA
Found at i:39271290 original size:17 final size:17
Alignment explanation
Indices: 39271270--39271302 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
39271260 TTAATATCTA
*
39271270 TATAAGTTTTCTAAATT
1 TATAAGTTTTATAAATT
39271287 TATAAGTTTTATAAAT
1 TATAAGTTTTATAAAT
39271303 AAGTTTTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (17 bp):
TATAAGTTTTATAAATT
Found at i:39271341 original size:16 final size:16
Alignment explanation
Indices: 39271311--39271349 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
39271301 ATAAGTTTTC
*
39271311 TAAAA-TTATTTGTAT
1 TAAAATTTATTAGTAT
39271326 TAAAATTTATTAGTAT
1 TAAAATTTATTAGTAT
39271342 T-AAATTTA
1 TAAAATTTA
39271350 CTTCGTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (16 bp):
TAAAATTTATTAGTAT
Found at i:39271594 original size:21 final size:21
Alignment explanation
Indices: 39271568--39271646 Score: 97
Period size: 21 Copynumber: 3.8 Consensus size: 21
39271558 TGTTATAATA
*
39271568 CATAACTTGTATATAAGCTTG
1 CATAACTTATATATAAGCTTG
*
39271589 CATAACTTATATTTAAGCTTG
1 CATAACTTATATATAAGCTTG
* * *
39271610 CATAACTTACATAATAA-TTTA
1 CATAACTTATAT-ATAAGCTTG
39271631 CATAACTTATATATAA
1 CATAACTTATATATAA
39271647 TAGCATAATA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 4 0.08
21 43 0.86
22 3 0.06
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (21 bp):
CATAACTTATATATAAGCTTG
Found at i:39271600 original size:116 final size:116
Alignment explanation
Indices: 39271473--39271713 Score: 448
Period size: 116 Copynumber: 2.1 Consensus size: 116
39271463 TTATATAATA
39271473 CATAACTTATATTTAAGCTTGCATAACTTACATAATAATTTACAGAACTTATATATAATAACA-A
1 CATAACTTATATTTAAGCTTGCATAACTTACATAATAATTTACAGAACTTATATATAATAACATA
39271537 CATAAATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTG
66 -ATAAATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTG
* *
39271589 CATAACTTATATTTAAGCTTGCATAACTTACATAATAATTTACATAACTTATATATAATAGCATA
1 CATAACTTATATTTAAGCTTGCATAACTTACATAATAATTTACAGAACTTATATATAATAACATA
39271654 ATAAATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTG
66 ATAAATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTG
39271705 CATAACTTA
1 CATAACTTA
39271714 CATAAATTAA
Statistics
Matches: 122, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
116 121 0.99
117 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.39
Consensus pattern (116 bp):
CATAACTTATATTTAAGCTTGCATAACTTACATAATAATTTACAGAACTTATATATAATAACATA
ATAAATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTG
Found at i:39271727 original size:9 final size:9
Alignment explanation
Indices: 39271682--39271927 Score: 233
Period size: 9 Copynumber: 26.8 Consensus size: 9
39271672 TATGTTATAA
39271682 TACATAACTT
1 TACATAAC-T
*
39271692 GTATATAAGCT
1 -TACATAA-CT
*
39271703 TGCATAACT
1 TACATAACT
*
39271712 TACATAAAT
1 TACATAACT
*
39271721 TAAATAACT
1 TACATAACT
39271730 TACATAACT
1 TACATAACT
39271739 TACATAAGC-
1 TACATAA-CT
*
39271748 TACATAAAT
1 TACATAACT
*
39271757 TAAATAACT
1 TACATAACT
39271766 TACATAACT
1 TACATAACT
39271775 TACATAAACT
1 TACAT-AACT
* *
39271785 TGCATAAAT
1 TACATAACT
*
39271794 TAAATAACT
1 TACATAACT
*
39271803 TACATTACT
1 TACATAACT
*
39271812 TACATAACC
1 TACATAACT
*
39271821 TACATAAAT
1 TACATAACT
*
39271830 TAAATAACT
1 TACATAACT
39271839 TACATAACT
1 TACATAACT
*
39271848 TACATAAAT
1 TACATAACT
*
39271857 TAAATAACT
1 TACATAACT
39271866 TACATAACT
1 TACATAACT
*
39271875 TACATAAAT
1 TACATAACT
* *
39271884 TCCATGGACT
1 TACAT-AACT
* *
39271894 GACATAACC
1 TACATAACT
*
39271903 TACATAAAT
1 TACATAACT
*
39271912 TAAATAACT
1 TACATAACT
39271921 TACATAA
1 TACATAA
39271928 ATTAAATATT
Statistics
Matches: 186, Mismatches: 44, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
9 159 0.85
10 19 0.10
11 7 0.04
12 1 0.01
ACGTcount: A:0.48, C:0.17, G:0.03, T:0.32
Consensus pattern (9 bp):
TACATAACT
Found at i:39271738 original size:27 final size:27
Alignment explanation
Indices: 39271696--39271927 Score: 257
Period size: 27 Copynumber: 8.5 Consensus size: 27
39271686 TAACTTGTAT
*
39271696 ATAAGCTTGCATAACTTACATAAATTAA
1 ATAA-CTTACATAACTTACATAAATTAA
** *
39271724 ATAACTTACATAACTTACATAAGCTAC
1 ATAACTTACATAACTTACATAAATTAA
* * * *
39271751 ATAAATTAAATAACTTACATAACTTAC
1 ATAACTTACATAACTTACATAAATTAA
* * * * *
39271778 ATAAACTTGCATAAATTAAATAACTTAC
1 AT-AACTTACATAACTTACATAAATTAA
* *
39271806 ATTACTTACATAACCTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
39271833 ATAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
**
39271860 ATAACTTACATAACTTACATAAATTCC
1 ATAACTTACATAACTTACATAAATTAA
* * *
39271887 ATGGACTGACATAACCTACATAAATTAA
1 AT-AACTTACATAACTTACATAAATTAA
39271915 ATAACTTACATAA
1 ATAACTTACATAA
39271928 ATTAAATATT
Statistics
Matches: 171, Mismatches: 31, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
27 123 0.72
28 48 0.28
ACGTcount: A:0.48, C:0.17, G:0.03, T:0.31
Consensus pattern (27 bp):
ATAACTTACATAACTTACATAAATTAA
Found at i:39271752 original size:36 final size:36
Alignment explanation
Indices: 39271712--39271928 Score: 263
Period size: 36 Copynumber: 6.0 Consensus size: 36
39271702 TTGCATAACT
*
39271712 TACATAAATTAAATAACTTACATAACTTACATAAGC
1 TACATAAATTAAATAACTTACATAACTTACATAAAC
39271748 TACATAAATTAAATAACTTACATAACTTACATAAAC
1 TACATAAATTAAATAACTTACATAACTTACATAAAC
* * *
39271784 TTGCATAAATTAAATAACTTACATTACTTACATAACC
1 -TACATAAATTAAATAACTTACATAACTTACATAAAC
*
39271821 TACATAAATTAAATAACTTACATAACTTACATAAAT
1 TACATAAATTAAATAACTTACATAACTTACATAAAC
* * * * * **
39271857 TAAATAACTTACATAACTTACATAAATTCCATGGAC
1 TACATAAATTAAATAACTTACATAACTTACATAAAC
** * * *
39271893 TGACATAACCTACATAAATTAAATAACTTACATAAA
1 T-ACATAAATTAAATAACTTACATAACTTACATAAA
39271929 TTAAATATTT
Statistics
Matches: 155, Mismatches: 24, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
36 96 0.62
37 59 0.38
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.31
Consensus pattern (36 bp):
TACATAAATTAAATAACTTACATAACTTACATAAAC
Found at i:39275981 original size:14 final size:14
Alignment explanation
Indices: 39275964--39275993 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
39275954 AAATAAAACT
39275964 AAGAAAATAGTATA
1 AAGAAAATAGTATA
39275978 AAGAAAATAGTATA
1 AAGAAAATAGTATA
39275992 AA
1 AA
39275994 AGCTCTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (14 bp):
AAGAAAATAGTATA
Found at i:39288900 original size:12 final size:12
Alignment explanation
Indices: 39288882--39288914 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39288872 GGGGCCACAC
39288882 GCCCGTGTCCTTA
1 GCCCGTGTCC-TA
39288895 -CCCGTGTCCTA
1 GCCCGTGTCCTA
39288906 GCCCGTGTC
1 GCCCGTGTC
39288915 TAAACTAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 17 0.89
ACGTcount: A:0.06, C:0.42, G:0.24, T:0.27
Consensus pattern (12 bp):
GCCCGTGTCCTA
Found at i:39291652 original size:15 final size:16
Alignment explanation
Indices: 39291619--39291649 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
39291609 TAACATGTCT
39291619 TTATTAAGAAAAAAAA
1 TTATTAAGAAAAAAAA
39291635 TTATTAAGAAAAAAA
1 TTATTAAGAAAAAAA
39291650 TTAGTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (16 bp):
TTATTAAGAAAAAAAA
Found at i:39294041 original size:22 final size:22
Alignment explanation
Indices: 39294002--39294044 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39293992 TTTCGTTTTA
39294002 AAAACAAGGGAAAAAAAAGAAC
1 AAAACAAGGGAAAAAAAAGAAC
*
39294024 AAAAC-AGTGAAAAGAAAAGAA
1 AAAACAAGGGAAAA-AAAAGAA
39294045 AAATGGAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.72, C:0.07, G:0.19, T:0.02
Consensus pattern (22 bp):
AAAACAAGGGAAAAAAAAGAAC
Found at i:39294905 original size:50 final size:50
Alignment explanation
Indices: 39294755--39295032 Score: 205
Period size: 50 Copynumber: 5.7 Consensus size: 50
39294745 TCGAGGAAAC
* * *
39294755 AAGATTCGTCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGT
1 AAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
* * * * * **
39294805 AAGATCCGTCGTTGT-GCTTCAATCT-TTGCAATGTCA--G---GGAAACC
1 AAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTG-CACCGCCAGGGAAGT
*
39294849 AA-ATCCGCCGTCATAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
1 AAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
* * * * * ** * ** * **
39294898 AAGATCCGCCATTGTGGCTTCAATTTTTTTAATTGCAATGTC-GGAGAAAC
1 AAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAGG-GAAGT
* * * *
39294948 CAGATCTGCCGTTGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGT
1 AAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
* *
39294998 AAGATCCGCCGTCGTGGCTTCAATCTTTTCCACTG
1 AAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTG
39295033 TAATGCTAAA
Statistics
Matches: 166, Mismatches: 51, Indels: 22
0.69 0.21 0.09
Matches are distributed among these distances:
43 9 0.05
44 18 0.11
45 6 0.04
46 1 0.01
47 1 0.01
48 5 0.03
49 20 0.12
50 104 0.63
51 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (50 bp):
AAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
Found at i:39294974 original size:100 final size:98
Alignment explanation
Indices: 39294735--39295026 Score: 375
Period size: 100 Copynumber: 3.0 Consensus size: 98
39294725 TAATCCGACC
* *
39294735 TATTGCAATGTC-GAGGAAACAAGAT-TCGTCGTCGTAGCTTCAATCTGTTCCACTACACCGCCA
1 TATTGCAATGTCGGA-GAAACCAGATCT-GCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCA
* *
39294798 GGGAAGTAAGATCCGTCGTTGT-GCTTCAA---TC
64 GGGAAGTAAGATCCGCCGTTGTGGCTTCAATTTTT
* * * *
39294829 T-TTGCAATGTCAGG-GAAACCAAATCCGCCGTCATAGCTTCAATCTGTTCCACTGCACCGCCAG
1 TATTGCAATGTC-GGAGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAG
*
39294892 GGAAGTAAGATCCGCCATTGTGGCTTCAATTTTTT
65 GGAAGTAAGATCCGCCGTTGTGGCTTCAA-TTTTT
*
39294927 TAATTGCAATGTCGGAGAAACCAGATCTGCCGTTGTAGCTTCAATCTGTTCCACTACACCGCCAG
1 T-ATTGCAATGTCGGAGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAG
* *
39294992 GGAAGTAAGATCCGCCGTCGTGGCTTCAATCTTT
65 GGAAGTAAGATCCGCCGTTGTGGCTTCAATTTTT
39295026 T
1 T
39295027 CCACTGTAAT
Statistics
Matches: 170, Mismatches: 17, Indels: 17
0.83 0.08 0.08
Matches are distributed among these distances:
93 71 0.42
94 8 0.05
95 1 0.01
98 2 0.01
99 7 0.04
100 81 0.48
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.28
Consensus pattern (98 bp):
TATTGCAATGTCGGAGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGG
GAAGTAAGATCCGCCGTTGTGGCTTCAATTTTT
Found at i:39307555 original size:21 final size:21
Alignment explanation
Indices: 39307512--39307555 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
39307502 TACATAAATG
*
39307512 TAATAATAATATATATTACAA
1 TAATAATAATATATAATACAA
*
39307533 TAATAATAATGA-ATAATATAA
1 TAATAATAAT-ATATAATACAA
39307554 TA
1 TA
39307556 TAGCAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
TAATAATAATATATAATACAA
Found at i:39309569 original size:13 final size:13
Alignment explanation
Indices: 39309551--39309580 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39309541 TTTTACCTTT
*
39309551 TTAATTTTCTTAG
1 TTAATTTACTTAG
39309564 TTAATTTACTTAG
1 TTAATTTACTTAG
39309577 TTAA
1 TTAA
39309581 AATCTAGTTT
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:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (13 bp):
TTAATTTACTTAG
Found at i:39312151 original size:10 final size:10
Alignment explanation
Indices: 39312136--39312160 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
39312126 TGCCCAAAAA
39312136 AAGAAAAGGG
1 AAGAAAAGGG
39312146 AAGAAAAGGG
1 AAGAAAAGGG
39312156 AAGAA
1 AAGAA
39312161 TGAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (10 bp):
AAGAAAAGGG
Found at i:39312501 original size:26 final size:25
Alignment explanation
Indices: 39312420--39312507 Score: 95
Period size: 26 Copynumber: 3.4 Consensus size: 25
39312410 TATTTTATTT
39312420 TTATTAAATTATATTTAATAATGATA
1 TTATTAAATTATATTTAATAAT-ATA
* * * * *
39312446 ATATTAAAATATGATTAAATTATGTA
1 TTATTAAATTAT-ATTTAATAATATA
*
39312472 TTATTAAATTATATTTAATAATAATC
1 TTATTAAATTATATTTAATAAT-ATA
39312498 TTATTAAATT
1 TTATTAAATT
39312508 TTAATAGCAA
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
25 8 0.16
26 33 0.67
27 8 0.16
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (25 bp):
TTATTAAATTATATTTAATAATATA
Found at i:39313156 original size:9 final size:9
Alignment explanation
Indices: 39313126--39313177 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
39313116 ATTAATTTTT
*
39313126 AAATTTTAA
1 AAATTATAA
39313135 AAATTCATAA
1 AAATT-ATAA
*
39313145 AAATTATTA
1 AAATTATAA
*
39313154 AAATTATTTA
1 AAATTA-TAA
*
39313164 AAAGTATAA
1 AAATTATAA
39313173 AAATT
1 AAATT
39313178 TATTTTAGCA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 20 0.56
10 16 0.44
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (9 bp):
AAATTATAA
Found at i:39314728 original size:16 final size:16
Alignment explanation
Indices: 39314701--39314742 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
39314691 CATTTAATTT
39314701 TTTTTAATTTTTA-TAAA
1 TTTTTAA-TTTTAGT-AA
39314718 TTTTTAATTTTAGTAA
1 TTTTTAATTTTAGTAA
*
39314734 TTTTAAATT
1 TTTTTAATT
39314743 ATTTTTATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
TTTTTAATTTTAGTAA
Found at i:39317473 original size:17 final size:17
Alignment explanation
Indices: 39317437--39317471 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39317427 TTTGTTCTCA
*
39317437 TATTTCTTTTTTATTTT
1 TATTTCTTTGTTATTTT
39317454 TATTTACTTTGTTATTTT
1 TATTT-CTTTGTTATTTT
39317472 ATGAGTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.77
Consensus pattern (17 bp):
TATTTCTTTGTTATTTT
Found at i:39321427 original size:43 final size:43
Alignment explanation
Indices: 39321379--39321464 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
39321369 TCATATTTCA
39321379 TTTCTCATCTCATAATCATTTCTCAACTTTGCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCAACTTTGCCATTTCAATAT
* *
39321422 TTTCTCATCTCATATTCATTTCTCATCTTTGCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCAACTTTGCCATTTCAATAT
39321465 AAATCACATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.23, C:0.26, G:0.02, T:0.49
Consensus pattern (43 bp):
TTTCTCATCTCATAATCATTTCTCAACTTTGCCATTTCAATAT
Found at i:39323219 original size:29 final size:29
Alignment explanation
Indices: 39323186--39323301 Score: 112
Period size: 29 Copynumber: 4.0 Consensus size: 29
39323176 ATGCAGAGTT
*
39323186 GCACCAAAGTGCAATAACAGAACAAAGTG
1 GCACCGAAGTGCAATAACAGAACAAAGTG
* *
39323215 GCACCGAAGTGCAATATCCA-AACAGAA-TA
1 GCACCGAAGTGCAATA-ACAGAACA-AAGTG
** * * *
39323244 GCACCGAAGTGCTCTATCAGAATAGAGTG
1 GCACCGAAGTGCAATAACAGAACAAAGTG
39323273 GCACCGAAGTGC-ATAACAGAACAAGAGTG
1 GCACCGAAGTGCAATAACAGAACAA-AGTG
39323302 CGCTGAATGT
Statistics
Matches: 69, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
28 11 0.16
29 54 0.78
30 4 0.06
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.14
Consensus pattern (29 bp):
GCACCGAAGTGCAATAACAGAACAAAGTG
Found at i:39325527 original size:26 final size:24
Alignment explanation
Indices: 39325491--39325540 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
39325481 TTAGAAAATT
* *
39325491 TTAAAAAATTAATATTTTTTAAAA
1 TTAAAAAATTAAAATTATTTAAAA
39325515 TTAAAAATTATTAAAATTATTTAAAA
1 TTAAAAA--ATTAAAATTATTTAAAA
39325541 AGAATGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
26 15 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TTAAAAAATTAAAATTATTTAAAA
Found at i:39325528 original size:16 final size:16
Alignment explanation
Indices: 39325495--39325533 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
39325485 AAAATTTTAA
* * *
39325495 AAAATTAATATTTTTT
1 AAAATTAAAAATTATT
39325511 AAAATTAAAAATTATT
1 AAAATTAAAAATTATT
39325527 AAAATTA
1 AAAATTA
39325534 TTTAAAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAATTAAAAATTATT
Found at i:39328937 original size:46 final size:46
Alignment explanation
Indices: 39328919--39329075 Score: 140
Period size: 46 Copynumber: 3.3 Consensus size: 46
39328909 TGACAAGTGG
* * *
39328919 AAAGTGATAAGTAATAGCT-TCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
* *
39328965 AAAGTGATAAGTGATAGCT-TCGGCTACACATATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
* * *
39329011 AAGTGAAAAGTGATAAGTGATAGCT-TCGGCTATACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
39329063 AAAGTGATAAGTG
1 AAAGTGATAAGTG
39329076 GCTACACTTA
Statistics
Matches: 99, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
46 56 0.57
52 43 0.43
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.27
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTATAGCTACACTTATCTGATCAAGTGAC
Found at i:39328938 original size:52 final size:51
Alignment explanation
Indices: 39328867--39329075 Score: 275
Period size: 52 Copynumber: 4.1 Consensus size: 51
39328857 ATCAAGTGAC
* **
39328867 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-G
* *
39328919 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
*
39328965 AAAGTGATAAGTGATAGCTTCGGCTACACATATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
* *
39329016 AAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTG
1 -AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-AAGTG
39329069 ATAAGTG
1 A-AAGTG
39329076 GCTACACTTA
Statistics
Matches: 138, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
46 43 0.31
52 85 0.62
53 10 0.07
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:39328973 original size:98 final size:98
Alignment explanation
Indices: 39328853--39329076 Score: 385
Period size: 98 Copynumber: 2.3 Consensus size: 98
39328843 TTTGAGTACT
* *
39328853 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACATATCTGATCAAGTGACAAGTG
*
39328918 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
39328951 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACATATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACATATCTGATCAAGTGACAAGTG
*
39329016 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
*
39329049 TCTGATCAAGAGACAAAGTGATAAGTGG
1 TCTGATCAAGTGACAAAGTGATAAGTGG
39329077 CTACACTTAT
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 118 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACATATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:39329085 original size:37 final size:37
Alignment explanation
Indices: 39329038--39329258 Score: 365
Period size: 37 Copynumber: 6.0 Consensus size: 37
39329028 TGATAGCTTC
* *
39329038 GGCTATACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
39329075 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
39329112 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
*
39329149 GGCTGCACTTATCTGATCAAGAAACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
* *
39329186 GACTACACTTATCTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
**
39329223 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
39329258 G
1 G
39329259 ATCATACGTA
Statistics
Matches: 174, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
35 11 0.06
36 4 0.02
37 159 0.91
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
Found at i:39336513 original size:14 final size:14
Alignment explanation
Indices: 39336488--39336522 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
39336478 AATTATCCAC
39336488 TTAAAT-AAAATTA
1 TTAAATAAAAATTA
39336501 TTAAATAAAAATTA
1 TTAAATAAAAATTA
39336515 TTAAATAA
1 TTAAATAA
39336523 TAATATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAAATAAAAATTA
Found at i:39346836 original size:25 final size:25
Alignment explanation
Indices: 39346802--39346853 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
39346792 AACCCGATGT
*
39346802 GAATGATTCCACTTACTATCAGTGG
1 GAATGATTCCACTTACTATCAATGG
39346827 GAATGATTCCACTTACTATCAATGG
1 GAATGATTCCACTTACTATCAATGG
39346852 GA
1 GA
39346854 CTTTGATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (25 bp):
GAATGATTCCACTTACTATCAATGG
Found at i:39351127 original size:23 final size:23
Alignment explanation
Indices: 39351097--39351169 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 23
39351087 ATCTACCTTG
*
39351097 TTTGGACAGCTCTTATACATC-AA
1 TTTGGACAGCT-TTATACACCAAA
39351120 TTTGGACAGCATTTATACACCAAAA
1 TTTGGACAGC-TTTATACACC-AAA
*
39351145 TTTGGACAGCTTATATACAACAAA
1 TTTGGACAGCTT-TATACACCAAA
39351169 T
1 T
39351170 GGGCAGCATA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
23 18 0.41
24 7 0.16
25 19 0.43
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (23 bp):
TTTGGACAGCTTTATACACCAAA
Found at i:39351244 original size:69 final size:69
Alignment explanation
Indices: 39351125--39351529 Score: 586
Period size: 69 Copynumber: 5.9 Consensus size: 69
39351115 ATCAATTTGG
* * * *
39351125 ACAGCATTTATACACCAAAATTTGGACAGCTTATATACAACAAATGGGCAGCATATACATACCAA
1 ACAGCATTTTTACACCAAAATTT-AACAGCATATATACAACAAATAGGCAGCATATACATACC-A
39351190 AATT-A
64 AATTGA
* *
39351195 ACAGCACTTTTACACCAAAATTTAACAGCATATATACAGCAAATAGGCAGCATATACATACCAAA
1 ACAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCAAA
*
39351260 TTTA
66 TTGA
** * *
39351264 ACAGCACATTTACACAAAAATTTAACAGCATATATACAACAAATGGGCAGCATATACATACCAAA
1 ACAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCAAA
39351329 TTGA
66 TTGA
* * *
39351333 GCAGCATTTTTACACCAAAATTTAACAACATATATACAACAAATAGGCAACATATACATACCAAA
1 ACAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCAAA
39351398 TTGA
66 TTGA
* * *
39351402 GCAGCATTTTTATACCAAAATTTAATAGC----ATACAACAAATAGGCAGCATATACATACCAAA
1 ACAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCAAA
39351463 TTGA
66 TTGA
* *
39351467 GCAGCATTTTTATACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCA
1 ACAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCA
39351530 CATCATATAC
Statistics
Matches: 307, Mismatches: 23, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
65 63 0.21
68 5 0.02
69 218 0.71
70 21 0.07
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (69 bp):
ACAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCAAA
TTGA
Found at i:39351457 original size:24 final size:24
Alignment explanation
Indices: 39351430--39351527 Score: 73
Period size: 22 Copynumber: 4.2 Consensus size: 24
39351420 AATTTAATAG
39351430 CATACAACAAATAGGCAGCATATA
1 CATACAACAAATAGGCAGCATATA
* * *
39351454 CATAC--CAAATTGAGCAGCATTTT
1 CATACAACAAATAG-GCAGCATATA
* * *
39351477 TATACCAA-AATTTA-ACAGCATAT-
1 CATA-CAACAA-ATAGGCAGCATATA
39351500 -ATACAACAAATAGGCAGCATATA
1 CATACAACAAATAGGCAGCATATA
39351523 CATAC
1 CATAC
39351528 CACATCATAT
Statistics
Matches: 55, Mismatches: 10, Indels: 18
0.66 0.12 0.22
Matches are distributed among these distances:
21 5 0.09
22 19 0.35
23 11 0.20
24 17 0.31
25 2 0.04
26 1 0.02
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.23
Consensus pattern (24 bp):
CATACAACAAATAGGCAGCATATA
Found at i:39352452 original size:41 final size:41
Alignment explanation
Indices: 39352336--39352485 Score: 194
Period size: 41 Copynumber: 3.7 Consensus size: 41
39352326 ATAAAACGCT
* * * * *
39352336 GGCATAAAGCCTGCTAGGCACAAAGCCCGATACATTTCACC
1 GGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
* *
39352377 GGCACAAAGCCTGCTA-GAATAAAGTCTGATATAATTCACC
1 GGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
* *
39352417 GGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATTTACT
1 GGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
* *
39352458 GGCATAAAACCTGCTAGGCATAAAGCCT
1 GGCACAAAGCCTGCTAGGCATAAAGCCT
39352486 AAACTTACAG
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 34 0.36
41 61 0.64
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (41 bp):
GGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
Found at i:39353358 original size:28 final size:26
Alignment explanation
Indices: 39353327--39353378 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
39353317 TTTTTAATGT
*
39353327 TTATTATAATATAATAATATATTATACC
1 TTATTATAACAT-AT-ATATATTATACC
39353355 TTATTATAACATATATATATTATA
1 TTATTATAACATATATATATTATA
39353379 TTAATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 10 0.43
27 2 0.09
28 11 0.48
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (26 bp):
TTATTATAACATATATATATTATACC
Found at i:39360194 original size:29 final size:29
Alignment explanation
Indices: 39360152--39360234 Score: 130
Period size: 29 Copynumber: 2.9 Consensus size: 29
39360142 TCCACCATGA
39360152 CACGAACTCTCAATGAATAAGTTCTTTAC
1 CACGAACTCTCAATGAATAAGTTCTTTAC
* *
39360181 CACGAATTCTCAATGAATAAGCTCTTTAC
1 CACGAACTCTCAATGAATAAGTTCTTTAC
* *
39360210 CACGAACTCTCAACGAACAAGTTCT
1 CACGAACTCTCAATGAATAAGTTCT
39360235 CCACCTCTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.35, C:0.27, G:0.11, T:0.28
Consensus pattern (29 bp):
CACGAACTCTCAATGAATAAGTTCTTTAC
Found at i:39371251 original size:70 final size:70
Alignment explanation
Indices: 39371171--39371306 Score: 254
Period size: 70 Copynumber: 1.9 Consensus size: 70
39371161 CAACAAGCCA
* *
39371171 ATGCAAGAAATGAAATAAATATTTTGAACTCAAAATGACATAAGTAAAAACAAGAAGAAAGACAA
1 ATGCAAGAAATGAAATAAATAATTTGAACTCAAAATGAAATAAGTAAAAACAAGAAGAAAGACAA
39371236 CATTG
66 CATTG
39371241 ATGCAAGAAATGAAATAAATAATTTGAACTCAAAATGAAATAAGTAAAAACAAGAAGAAAGACAA
1 ATGCAAGAAATGAAATAAATAATTTGAACTCAAAATGAAATAAGTAAAAACAAGAAGAAAGACAA
39371306 C
66 C
39371307 GTTGGGCAAC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.58, C:0.10, G:0.14, T:0.18
Consensus pattern (70 bp):
ATGCAAGAAATGAAATAAATAATTTGAACTCAAAATGAAATAAGTAAAAACAAGAAGAAAGACAA
CATTG
Found at i:39377019 original size:19 final size:19
Alignment explanation
Indices: 39376985--39377034 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
39376975 TTGTAATAAG
*
39376985 TTGTGTAATTAAGTAAT-T
1 TTGTGTAATTGAGTAATGT
*
39377003 CTTGTGTAATTGGGTAATGT
1 -TTGTGTAATTGAGTAATGT
39377023 TATGTGTAATTG
1 T-TGTGTAATTG
39377035 TATAATTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (19 bp):
TTGTGTAATTGAGTAATGT
Found at i:39381414 original size:402 final size:402
Alignment explanation
Indices: 39380678--39381474 Score: 1350
Period size: 402 Copynumber: 2.0 Consensus size: 402
39380668 CAAAAAGAAA
39380678 TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCAGGAATTGGAGAAAGAGT
1 TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCAGGAATTGGAGAAAGAGT
39380743 TCGAAAACAATTCAGCAGTTAAGAGTAGGTAACAACACATGCTGCTTGGATGCAAATAAAGACCT
66 TCGAAAACAATTCAGCAGTTAAGAGTAGGTAACAACACATGCTGCTTGGATGCAAATAAAGACCT
*
39380808 TTGCATTTATTAGAAACACATTATATTTAAGAGATAAAGCTTGACACGGCTGGCATCAAGCAACT
131 TTGCATTTATTAGAAACACATTATATTTAAGAGATAAAGCTTGACACGCCTGGCATCAAGCAACT
*
39380873 AATCAGAATCGACAATAAGAATGTTAACAGCATGATTTTATCAAAATGCCTTCAGCATGTAATAC
196 AATC--AA-C-ACAATAAGAATGTTAACAGCATGATTTCATCAAAATGCCTTCAGCATGTAATAC
* *
39380938 TTTCCAACTTATAACCAGAATTCATCATACAAAAAGAGAAATACAGGAAATGTACTTTAAAGGGA
257 TTTCCAACTTAAAAACAGAATTCATCATACAAAAAGAGAAATACAGGAAATGTACTTTAAAGGGA
* * *
39381003 TGGAAAGGATGTAAGATAATTTGACTGGATAAGGTAAGAAGAGTAAGGTAAAGGTAAGGAAAATT
322 TGGAAAGGATGTAAGATAATTTGACTGGACAAGGTAAGAAGAGTAAGGTAAAGGGAAGGAAAATG
39381068 ATGCTACAAAACTGTC
387 ATGCTACAAAACTGTC
39381084 TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCCA-GAATTGGAGAAAGAG
1 TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGA-CCAGGAATTGGAGAAAGAG
*
39381148 TTCGAAAACAATTCAGCAGTTAAGAGTAGGTAGCAACACATATGCTGCTTGGATGCAAATAAAGA
65 TTCGAAAACAATTCAGCAGTTAAGAGTAGGTAACAACAC--ATGCTGCTTGGATGCAAATAAAGA
* *
39381213 CCTTTGCATTTATTAGAAACACATTATATTTAAGAGATAAAGGTTGACACGCCTGGCGTCAAGCA
128 CCTTTGCATTTATTAGAAACACATTATATTTAAGAGATAAAGCTTGACACGCCTGGCATCAAGCA
39381278 ACTAATC-A-ACAATAAGAATGTTAACAGCATGATTTCATCAAAATGCCTTCAGCATGTAATACT
193 ACTAATCAACACAATAAGAATGTTAACAGCATGATTTCATCAAAATGCCTTCAGCATGTAATACT
* * *
39381341 TTCCAACTTAAAAACAGTATTCATCATACATAGAA-AGATATACAGGAAATGTACTTTAAAGGGA
258 TTCCAACTTAAAAACAGAATTCATCATACA-AAAAGAGAAATACAGGAAATGTACTTTAAAGGGA
* * *
39381405 TGGAAAGGATGTACGTTAATTTGATTGGACAAGGTAAGAAGAGTAAGGTAAAGGGAAGGAAAATG
322 TGGAAAGGATGTAAGATAATTTGACTGGACAAGGTAAGAAGAGTAAGGTAAAGGGAAGGAAAATG
39381470 ATGCT
387 ATGCT
39381475 TTATTGTCTG
Statistics
Matches: 371, Mismatches: 16, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
402 173 0.47
403 3 0.01
405 1 0.00
406 98 0.26
407 3 0.01
408 93 0.25
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (402 bp):
TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCAGGAATTGGAGAAAGAGT
TCGAAAACAATTCAGCAGTTAAGAGTAGGTAACAACACATGCTGCTTGGATGCAAATAAAGACCT
TTGCATTTATTAGAAACACATTATATTTAAGAGATAAAGCTTGACACGCCTGGCATCAAGCAACT
AATCAACACAATAAGAATGTTAACAGCATGATTTCATCAAAATGCCTTCAGCATGTAATACTTTC
CAACTTAAAAACAGAATTCATCATACAAAAAGAGAAATACAGGAAATGTACTTTAAAGGGATGGA
AAGGATGTAAGATAATTTGACTGGACAAGGTAAGAAGAGTAAGGTAAAGGGAAGGAAAATGATGC
TACAAAACTGTC
Found at i:39381927 original size:15 final size:16
Alignment explanation
Indices: 39381900--39381929 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39381890 CTTTGATCCC
39381900 CTTTCCATCCACTTTT
1 CTTTCCATCCACTTTT
39381916 CTTTCC-TCCACTTT
1 CTTTCCATCCACTTT
39381930 GGGAAACAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.10, C:0.40, G:0.00, T:0.50
Consensus pattern (16 bp):
CTTTCCATCCACTTTT
Found at i:39395093 original size:22 final size:19
Alignment explanation
Indices: 39395049--39395094 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 19
39395039 TACAAATAAA
*
39395049 AGAAAGCAATTATGAGATG
1 AGAAAGCAATTATGAAATG
39395068 AGAAAGCAAATTAATTGAAATG
1 AGAAAGC-AATT-A-TGAAATG
39395090 AGAAA
1 AGAAA
39395095 ACAACAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 7 0.30
20 4 0.17
21 1 0.04
22 11 0.48
ACGTcount: A:0.54, C:0.04, G:0.22, T:0.20
Consensus pattern (19 bp):
AGAAAGCAATTATGAAATG
Found at i:39403471 original size:34 final size:34
Alignment explanation
Indices: 39403411--39403489 Score: 81
Period size: 34 Copynumber: 2.3 Consensus size: 34
39403401 TTAAGTTTAC
* *
39403411 ATATATATATATGGGTAGTATTGAATACGT-ACAA
1 ATATATATGTATAGGTAGTATTGAATACGTGA-AA
* * *
39403445 ATATATATGTATAGTTAGT-TTCGAATAGGTGAAT
1 ATATATATGTATAGGTAGTATT-GAATACGTGAAA
39403479 ATATATATGTA
1 ATATATATGTA
39403490 AAATTCTTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
33 2 0.05
34 35 0.92
35 1 0.03
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (34 bp):
ATATATATGTATAGGTAGTATTGAATACGTGAAA
Found at i:39403783 original size:41 final size:41
Alignment explanation
Indices: 39403738--39403841 Score: 174
Period size: 41 Copynumber: 2.5 Consensus size: 41
39403728 GACTTTAAGT
*
39403738 CTAGCAGGCTAAGTGCCGGTGATCT-GAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGAT-TGGAATCAGGCTATAAAC
*
39403779 CTAGCAGGCTAAGTGCCGGTGATTGGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATTGGAATCAGGCTATAAAC
39403820 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
39403842 ATATGTTAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
40 1 0.02
41 59 0.98
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATTGGAATCAGGCTATAAAC
Found at i:39413707 original size:20 final size:20
Alignment explanation
Indices: 39413682--39413757 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
39413672 AAGTTTATGC
*
39413682 TAAGTAAATGGAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
39413702 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
* *
39413722 TGAGTAAATGAAATAGAAAG
1 TAAGTAAATGAAATGGAAAG
*
39413742 TAAGTAAATGGAATGG
1 TAAGTAAATGAAATGG
39413758 TTAGAAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.51, C:0.00, G:0.28, T:0.21
Consensus pattern (20 bp):
TAAGTAAATGAAATGGAAAG
Found at i:39413770 original size:40 final size:40
Alignment explanation
Indices: 39413686--39413773 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
39413676 TTATGCTAAG
* * ** *
39413686 TAAATGGAATGGAAAGTAAGTAAATGAAATGGAAAGTGAG
1 TAAATGAAATAGAAAGTAAGTAAATGAAATGGAAAGAAAA
* **
39413726 TAAATGAAATAGAAAGTAAGTAAATGGAATGGTTAGAAAA
1 TAAATGAAATAGAAAGTAAGTAAATGAAATGGAAAGAAAA
39413766 TAAATGAA
1 TAAATGAA
39413774 GTGGTTCATA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.53, C:0.00, G:0.25, T:0.22
Consensus pattern (40 bp):
TAAATGAAATAGAAAGTAAGTAAATGAAATGGAAAGAAAA
Found at i:39416691 original size:16 final size:16
Alignment explanation
Indices: 39416672--39416706 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
39416662 AATAATGAGT
39416672 AAAT-AAAATAACAATG
1 AAATAAAAATAA-AATG
39416688 AAATAAAAATAAAATG
1 AAATAAAAATAAAATG
39416704 AAA
1 AAA
39416707 ACAAATAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.17
Consensus pattern (16 bp):
AAATAAAAATAAAATG
Done.