Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 112 of 297
Found at i:40232833 original size:26 final size:26
Alignment explanation
Indices: 40232804--40232875 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 26
40232794 GAGGAAGTGC
**
40232804 AAAAGGGCTTATGCCCTAGTTTATTGA
1 AAAAGGGCTT-TGCCCTAGTTTACCGA
* *
40232831 AAAAGGGTTTTGCCCTGGTTTACCG-
1 AAAAGGGCTTTGCCCTAGTTTACCGA
* *
40232856 AAAATGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCTAGTT
40232876 ATTAAAGAGG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
25 16 0.43
26 12 0.32
27 9 0.24
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (26 bp):
AAAAGGGCTTTGCCCTAGTTTACCGA
Found at i:40240890 original size:20 final size:20
Alignment explanation
Indices: 40240865--40240931 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
40240855 ATTTTGATAT
40240865 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGATATGC
40240885 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
40240905 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
40240925 ACATGAT
1 ACATGAT
40240932 GTATTCATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:40240892 original size:11 final size:11
Alignment explanation
Indices: 40240876--40240931 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
40240866 CATGATTGAT
40240876 ATGATATGCAC
1 ATGATATGCAC
*
40240887 ATGATATG--T
1 ATGATATGCAC
40240896 ATGATATGCAC
1 ATGATATGCAC
* *
40240907 ATGGTATG--T
1 ATGATATGCAC
40240916 ATGATATGCAC
1 ATGATATGCAC
40240927 ATGAT
1 ATGAT
40240932 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:40241081 original size:25 final size:26
Alignment explanation
Indices: 40240981--40241104 Score: 189
Period size: 26 Copynumber: 4.8 Consensus size: 26
40240971 GAGGAAGTGC
40240981 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
40241007 AAAAAGGGCTTATGCCCCAGTTTATTG
1 -AAAAGGGCTTATGCCCCAGTTTATTG
*
40241034 AAAAGGGCTTATGCCCCAATTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
40241060 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
40241085 AAAAGGGCTT-TGCCCTAGTT
1 AAAAGGGCTTATGCCCCAGTT
40241105 ATTAAAGAGG
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
25 31 0.34
26 35 0.38
27 26 0.28
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:40248325 original size:27 final size:27
Alignment explanation
Indices: 40248280--40248381 Score: 82
Period size: 27 Copynumber: 3.8 Consensus size: 27
40248270 AAATCCCTAT
* * * * *
40248280 TACAGAATATACCATAAAGGCGATCCA
1 TACAGAGTATGCCACAAAGGCTATACA
*
40248307 TACAGAGTATGCCACAAAGGCTATATATA
1 TACAGAGTATGCCACAAAGGC--TATACA
* *
40248336 TACAGAGTATG-C-CATAGGCTATTCA
1 TACAGAGTATGCCACAAAGGCTATACA
* *
40248361 TTCAGAGTGTGCCACAAAGGC
1 TACAGAGTATGCCACAAAGGC
40248382 ATTTTTTAGC
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
25 13 0.22
26 1 0.02
27 30 0.51
28 1 0.02
29 14 0.24
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.23
Consensus pattern (27 bp):
TACAGAGTATGCCACAAAGGCTATACA
Found at i:40248340 original size:29 final size:29
Alignment explanation
Indices: 40248306--40248381 Score: 90
Period size: 27 Copynumber: 2.8 Consensus size: 29
40248296 AAGGCGATCC
40248306 ATACAGAGTATGCCACAAAGGCTATAT-AT
1 ATACAGAGTATGCCACAAAGGCTAT-TCAT
*
40248335 ATACAGAGTATG-C-CATAGGCTATTCAT
1 ATACAGAGTATGCCACAAAGGCTATTCAT
*
40248362 -T-CAGAGTGTGCCACAAAGGC
1 ATACAGAGTATGCCACAAAGGC
40248382 ATTTTTTAGC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
25 8 0.20
26 3 0.07
27 17 0.41
28 1 0.02
29 12 0.29
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (29 bp):
ATACAGAGTATGCCACAAAGGCTATTCAT
Found at i:40249999 original size:14 final size:15
Alignment explanation
Indices: 40249975--40250003 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40249965 GTCATCGTAC
40249975 CTCCACTCTTCTCAT
1 CTCCACTCTTCTCAT
40249990 CTCC-CTCTTCTCAT
1 CTCCACTCTTCTCAT
40250004 TGCAGTCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.10, C:0.48, G:0.00, T:0.41
Consensus pattern (15 bp):
CTCCACTCTTCTCAT
Found at i:40250084 original size:15 final size:16
Alignment explanation
Indices: 40250052--40250084 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40250042 TTATTCTAGT
40250052 TTTCTTCACCTACTCC
1 TTTCTTCACCTACTCC
*
40250068 TTTCTTCCCCT-CTCC
1 TTTCTTCACCTACTCC
40250083 TT
1 TT
40250085 AGTTTAACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.06, C:0.45, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTCTTCACCTACTCC
Found at i:40252845 original size:54 final size:53
Alignment explanation
Indices: 40252746--40253012 Score: 236
Period size: 54 Copynumber: 4.9 Consensus size: 53
40252736 TGGCATTTTC
* * * * *
40252746 ATAGCCTTTGTGGTGAACTCT-ATTAGGGTAGCCTTTGTGGAAAACTCTGTAAGG
1 ATAGACTTTGTGGTGAACTCTGA--AGGATAGTCTTTGTGGCAAACTCTGAAAGG
* *
40252800 ATAGACTTTGTGGTGAACTCTGTAAGGATAGTCTTCGTGGTAAACTCTGAAAGG
1 ATAGACTTTGTGGTGAACTCTG-AAGGATAGTCTTTGTGGCAAACTCTGAAAGG
* * * * *
40252854 ATAGCCTTTGTGGCT-AACTCTGAAAGGATAGCCTTTATGGCGAACTCTAAAAGG
1 ATAGACTTTGTGG-TGAACTCTG-AAGGATAGTCTTTGTGGCAAACTCTGAAAGG
* * * * *
40252908 ATA-ACCCTTATGGTGAACTCTGAAGGAATACTCTTTGTGGCGAACTTTG-AAGG
1 ATAGA-CTTTGTGGTGAACTCTGAAGG-ATAGTCTTTGTGGCAAACTCTGAAAGG
* * * *
40252961 AATAGTCTTTGTGGTGAACTTTGAAGGAATAGTCTTTGTGGTAAAATCTGAA
1 -ATAGACTTTGTGGTGAACTCTGAAGG-ATAGTCTTTGTGGCAAACTCTGAA
40253013 TGAACTGTCT
Statistics
Matches: 173, Mismatches: 31, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
53 9 0.05
54 161 0.93
55 2 0.01
56 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (53 bp):
ATAGACTTTGTGGTGAACTCTGAAGGATAGTCTTTGTGGCAAACTCTGAAAGG
Found at i:40253012 original size:27 final size:26
Alignment explanation
Indices: 40252746--40253012 Score: 214
Period size: 27 Copynumber: 9.9 Consensus size: 26
40252736 TGGCATTTTC
*
40252746 ATAGCCTTTGTGGTGAACTCT-ATTAGG
1 ATAGTCTTTGTGGTGAACTCTGA--AGG
* * **
40252773 GTAGCCTTTGTGGAAAACTCTGTAAGG
1 ATAGTCTTTGTGGTGAACTCTG-AAGG
*
40252800 ATAGACTTTGTGGTGAACTCTGTAAGG
1 ATAGTCTTTGTGGTGAACTCTG-AAGG
* *
40252827 ATAGTCTTCGTGGTAAACTCTGAAAGG
1 ATAGTCTTTGTGGTGAACTCTG-AAGG
*
40252854 ATAGCCTTTGTGGCT-AACTCTGAAAGG
1 ATAGTCTTTGTGG-TGAACTCTG-AAGG
* * * *
40252881 ATAGCCTTTATGGCGAACTCTAAAAGG
1 ATAGTCTTTGTGGTGAACTCT-GAAGG
** * *
40252908 ATAACCCTTATGGTGAACTCTGAAGG
1 ATAGTCTTTGTGGTGAACTCTGAAGG
* * *
40252934 AATACTCTTTGTGGCGAACTTTGAAGG
1 -ATAGTCTTTGTGGTGAACTCTGAAGG
*
40252961 AATAGTCTTTGTGGTGAACTTTGAAGG
1 -ATAGTCTTTGTGGTGAACTCTGAAGG
* *
40252988 AATAGTCTTTGTGGTAAAATCTGAA
1 -ATAGTCTTTGTGGTGAACTCTGAA
40253013 TGAACTGTCT
Statistics
Matches: 203, Mismatches: 31, Indels: 12
0.83 0.13 0.05
Matches are distributed among these distances:
26 4 0.02
27 197 0.97
28 1 0.00
29 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (26 bp):
ATAGTCTTTGTGGTGAACTCTGAAGG
Found at i:40258359 original size:15 final size:15
Alignment explanation
Indices: 40258333--40258369 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
40258323 TTAAATATGT
40258333 TTAATT-TTAATTAA
1 TTAATTATTAATTAA
40258347 TTAATTATTAATTAA
1 TTAATTATTAATTAA
40258362 TATAATTA
1 T-TAATTA
40258370 GGATTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.29
15 9 0.43
16 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTAATTATTAATTAA
Found at i:40260313 original size:21 final size:21
Alignment explanation
Indices: 40260287--40260332 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
40260277 AACAGTTTTT
40260287 CCTTCAAGTGGACGATTTGGG
1 CCTTCAAGTGGACGATTTGGG
* *
40260308 CCTTCAAGTGGATGGTTTGGG
1 CCTTCAAGTGGACGATTTGGG
40260329 CCTT
1 CCTT
40260333 TTCCTCCCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.20, G:0.33, T:0.33
Consensus pattern (21 bp):
CCTTCAAGTGGACGATTTGGG
Found at i:40267098 original size:15 final size:15
Alignment explanation
Indices: 40267072--40267108 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
40267062 TTAAATATGT
40267072 TTAATT-TTAATTAA
1 TTAATTATTAATTAA
40267086 TTAATTATTAATTAA
1 TTAATTATTAATTAA
40267101 TATAATTA
1 T-TAATTA
40267109 GGATTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.29
15 9 0.43
16 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTAATTATTAATTAA
Found at i:40269052 original size:21 final size:21
Alignment explanation
Indices: 40269026--40269071 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
40269016 AACAGTTTTT
40269026 CCTTCAAGTGGACGATTTGGG
1 CCTTCAAGTGGACGATTTGGG
* *
40269047 CCTTCAAGTGGATGGTTTGGG
1 CCTTCAAGTGGACGATTTGGG
40269068 CCTT
1 CCTT
40269072 TTCCTCCCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.20, G:0.33, T:0.33
Consensus pattern (21 bp):
CCTTCAAGTGGACGATTTGGG
Found at i:40273428 original size:47 final size:47
Alignment explanation
Indices: 40273357--40274251 Score: 1772
Period size: 47 Copynumber: 19.0 Consensus size: 47
40273347 ATAGATAAAT
*
40273357 TTTCAAAAATTAAGGCATGACCACTCTCTCTCGATTCACAAACCCGA
1 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
40273404 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
1 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
40273451 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
1 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
40273498 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
1 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
40273545 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
1 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
40273592 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
1 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
40273639 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
1 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
40273686 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
1 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
40273733 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
1 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
40273780 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
1 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
40273827 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
1 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
40273874 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
1 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
40273921 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
1 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
40273968 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
1 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
40274015 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
1 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
40274062 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
1 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
40274109 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
1 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
40274156 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
1 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
*
40274203 TTTTAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
1 TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
40274250 TT
1 TT
40274252 CTACTAACCC
Statistics
Matches: 846, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 846 1.00
ACGTcount: A:0.32, C:0.30, G:0.13, T:0.26
Consensus pattern (47 bp):
TTTCAAAAATTAAGGCATGGCCACTCTCTCTCGATTCACAAACCCGA
Found at i:40274708 original size:28 final size:28
Alignment explanation
Indices: 40274671--40274741 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
40274661 TATCATTATT
* *
40274671 GTTCGCCGCAAAGGTTTATTTTTTTGTA
1 GTTCACCGCAAAGGTTTATTTTTTCGTA
* *
40274699 GTTCATCGCAAAGGCTTATTTTTTCGTA
1 GTTCACCGCAAAGGTTTATTTTTTCGTA
*
40274727 GTTCACCACAAAGGT
1 GTTCACCGCAAAGGT
40274742 CTTTCATAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (28 bp):
GTTCACCGCAAAGGTTTATTTTTTCGTA
Found at i:40283757 original size:20 final size:20
Alignment explanation
Indices: 40283729--40283782 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
40283719 ACAGGCAAGG
40283729 CACACGGTCGTGTGTTCAGA
1 CACACGGTCGTGTGTTCAGA
*
40283749 CACATGGTCGTGTGTTCAGA
1 CACACGGTCGTGTGTTCAGA
*
40283769 CACACGGACGTGTG
1 CACACGGTCGTGTG
40283783 AGGTACCACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.24
Consensus pattern (20 bp):
CACACGGTCGTGTGTTCAGA
Found at i:40285929 original size:6 final size:6
Alignment explanation
Indices: 40285918--40285948 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
40285908 GTCCCTTTTA
40285918 TTATTT TTATTT TTATTT TTATTT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT TTATTT T
40285949 CCTTTATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:40289647 original size:23 final size:21
Alignment explanation
Indices: 40289595--40289649 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 21
40289585 TTTAGAAAGA
*
40289595 AAAAATTAAATTAATATAAGTT
1 AAAAA-TAAAATAATATAAGTT
40289617 AAATAATAAAATAATATAAGTGAT
1 AAA-AATAAAATAATATAAGT--T
40289641 AAAAATAAA
1 AAAAATAAA
40289650 GGAAAAGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 17 0.59
23 8 0.28
24 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (21 bp):
AAAAATAAAATAATATAAGTT
Found at i:40290839 original size:95 final size:95
Alignment explanation
Indices: 40290673--40290929 Score: 336
Period size: 95 Copynumber: 2.7 Consensus size: 95
40290663 TGTACTAGTG
* *
40290673 GTGGATACCTTACCGATGGCTAAGATCTTGCATATATTGCGGATTCTTCATAGCTCGTGTGAGCA
1 GTGGATACCTTACCGATGGCTAAGATCCTGCATATATTGCGGATTCTTCATAGCTCGTGTGAACA
40290738 GCATTGTGTAACAGTTAATGTCGCGATTTA
66 GCATTGTGTAACAGTTAATGTCGCGATTTA
* * * *
40290768 TTGGATACCTTATCGATGGCTAAGATCCTGCATATATTGCGGATTCTTCACAGCTCGTGTGAATA
1 GTGGATACCTTACCGATGGCTAAGATCCTGCATATATTGCGGATTCTTCATAGCTCGTGTGAACA
* * **
40290833 GTATTGTGTAACGGTTAATGTTTCGATTTA
66 GCATTGTGTAACAGTTAATGTCGCGATTTA
* * * * * * * * *
40290863 GTGGATACCTTGCCAATGGCTAAGATTCTGGATGTACTAC-GATTCTTCATAGCTTGTGTGAGCA
1 GTGGATACCTTACCGATGGCTAAGATCCTGCATATATTGCGGATTCTTCATAGCTCGTGTGAACA
40290927 GCA
66 GCA
40290930 CCATGTAATG
Statistics
Matches: 138, Mismatches: 24, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
94 22 0.16
95 116 0.84
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (95 bp):
GTGGATACCTTACCGATGGCTAAGATCCTGCATATATTGCGGATTCTTCATAGCTCGTGTGAACA
GCATTGTGTAACAGTTAATGTCGCGATTTA
Found at i:40292192 original size:20 final size:19
Alignment explanation
Indices: 40292152--40292193 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
40292142 TATGAATATG
*
40292152 TGATGATTTTGATATGTTT
1 TGATGATTTTGATATGGTT
40292171 TGATGAGTTTTGA-ATAGGTT
1 TGATGA-TTTTGATAT-GGTT
40292191 TGA
1 TGA
40292194 ACACAACACG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (19 bp):
TGATGATTTTGATATGGTT
Found at i:40292337 original size:17 final size:18
Alignment explanation
Indices: 40292312--40292346 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
40292302 ACTCTGCTTC
*
40292312 ATTTTTAAT-TGTTTTAT
1 ATTTATAATATGTTTTAT
40292329 ATTTATAATATGTTTTAT
1 ATTTATAATATGTTTTAT
40292347 TTAACACCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (18 bp):
ATTTATAATATGTTTTAT
Found at i:40293383 original size:17 final size:17
Alignment explanation
Indices: 40293363--40293398 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
40293353 AATATGAAAC
40293363 GTATAAATTAATGGAAT
1 GTATAAATTAATGGAAT
*
40293380 GTATAAATTAATGGCAT
1 GTATAAATTAATGGAAT
40293397 GT
1 GT
40293399 GAGTACATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.36
Consensus pattern (17 bp):
GTATAAATTAATGGAAT
Found at i:40300927 original size:16 final size:16
Alignment explanation
Indices: 40300904--40300976 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 16
40300894 GAAAAGATTA
40300904 GATGAAGAAGATGAGT
1 GATGAAGAAGATGAGT
* *
40300920 GGTTAAG-AG-TGA-T
1 GATGAAGAAGATGAGT
*
40300933 GATGAAGAAGATGAGAA
1 GATGAAGAAGATGAG-T
*
40300950 GA-GAA-AAGATTA--
1 GATGAAGAAGATGAGT
40300962 GATGAAGAAGATGAG
1 GATGAAGAAGATGAG
40300977 AGAGAGGGAC
Statistics
Matches: 43, Mismatches: 7, Indels: 15
0.66 0.11 0.23
Matches are distributed among these distances:
12 2 0.05
13 9 0.21
14 11 0.26
15 11 0.26
16 8 0.19
17 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.36, T:0.18
Consensus pattern (16 bp):
GATGAAGAAGATGAGT
Found at i:40300965 original size:29 final size:29
Alignment explanation
Indices: 40300890--40300982 Score: 109
Period size: 29 Copynumber: 3.2 Consensus size: 29
40300880 ATTTCATGTT
40300890 AAGAGAAAAGATTAGATGAAGAAGATGAG
1 AAGAGAAAAGATTAGATGAAGAAGATGAG
* ** *
40300919 -TG-GTTAAGAGTGATGATGAAGAAGATGAG
1 AAGAGAAAAGA-TTA-GATGAAGAAGATGAG
40300948 AAGAGAAAAGATTAGATGAAGAAGATGAG
1 AAGAGAAAAGATTAGATGAAGAAGATGAG
40300977 AGAGAG
1 A-AGAG
40300983 GGACAATAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
27 5 0.10
28 3 0.06
29 31 0.61
30 7 0.14
31 5 0.10
ACGTcount: A:0.49, C:0.00, G:0.34, T:0.16
Consensus pattern (29 bp):
AAGAGAAAAGATTAGATGAAGAAGATGAG
Found at i:40301359 original size:16 final size:16
Alignment explanation
Indices: 40301335--40301381 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
40301325 TGTTATTAAA
*
40301335 TTATATAATTTTATTT
1 TTATATAATTATATTT
*
40301351 TTATTTAATTATATTT
1 TTATATAATTATATTT
*
40301367 AGTA-ATAATTATATT
1 -TTATATAATTATATT
40301382 AAAACATGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 24 0.92
17 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TTATATAATTATATTT
Found at i:40314429 original size:20 final size:20
Alignment explanation
Indices: 40314404--40314443 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
40314394 CCACTTCATT
40314404 TTGCTTAAATTGAGTTAGGG
1 TTGCTTAAATTGAGTTAGGG
40314424 TTGCTTAAATTGAGTTAGGG
1 TTGCTTAAATTGAGTTAGGG
40314444 AAAATTGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.30, T:0.40
Consensus pattern (20 bp):
TTGCTTAAATTGAGTTAGGG
Found at i:40317184 original size:7 final size:7
Alignment explanation
Indices: 40317172--40317204 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
40317162 TTACTAATTT
40317172 AAATATA
1 AAATATA
40317179 AAATATA
1 AAATATA
*
40317186 AATTATA
1 AAATATA
40317193 AAATATA
1 AAATATA
40317200 AAATA
1 AAATA
40317205 ATTAAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AAATATA
Found at i:40327224 original size:21 final size:21
Alignment explanation
Indices: 40327198--40327238 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40327188 ATCTGCTCAA
* *
40327198 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
40327219 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
40327239 TTGCTCATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:40330157 original size:27 final size:27
Alignment explanation
Indices: 40330094--40330158 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
40330084 CTGCACACGG
* *
40330094 CAAACGTTTCGTGGGTTCCCCAAACCA
1 CAAACGTTTCATGGATTCCCCAAACCA
* * *
40330121 TAAACATTTCATGGATTCCCCAAACTA
1 CAAACGTTTCATGGATTCCCCAAACCA
*
40330148 CGAACGTTTCA
1 CAAACGTTTCA
40330159 ACTGATCAGA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CAAACGTTTCATGGATTCCCCAAACCA
Found at i:40334038 original size:42 final size:43
Alignment explanation
Indices: 40333991--40334103 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 43
40333981 TGTGTTTTCG
40333991 TGTAAGACCACATCTGGGACATTGGCATC-AT-TTGAGATTTA-A
1 TGTAAGACCACATCTGGGACATTGGCATCGATATT-AGA-TTACA
* * * *
40334033 TGTAAGACC-CTGTCTGGGACAGTGGCGTCGATATTTGATTACA
1 TGTAAGACCAC-ATCTGGGACATTGGCATCGATATTAGATTACA
40334076 TGTAAGACCACATCTGGGACATTGGCAT
1 TGTAAGACCACATCTGGGACATTGGCAT
40334104 TGTACGAGTT
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
41 1 0.02
42 27 0.46
43 28 0.47
44 3 0.05
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (43 bp):
TGTAAGACCACATCTGGGACATTGGCATCGATATTAGATTACA
Found at i:40338570 original size:43 final size:43
Alignment explanation
Indices: 40338509--40338590 Score: 155
Period size: 43 Copynumber: 1.9 Consensus size: 43
40338499 GTGAGAAATG
40338509 TCATGTTTATTCTGATCATAAAAGTTTGAAATATCTGATAATT
1 TCATGTTTATTCTGATCATAAAAGTTTGAAATATCTGATAATT
*
40338552 TCATGTTTATTCTGATCATAAAAGTTTGAAATATTTGAT
1 TCATGTTTATTCTGATCATAAAAGTTTGAAATATCTGAT
40338591 GACTGAGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (43 bp):
TCATGTTTATTCTGATCATAAAAGTTTGAAATATCTGATAATT
Found at i:40341375 original size:38 final size:38
Alignment explanation
Indices: 40341274--40341401 Score: 157
Period size: 38 Copynumber: 3.3 Consensus size: 38
40341264 AAACCAGAAC
* * * *
40341274 ATAACACCAGCACGAAGCCTACGGGACTTTAAACTCAGAT
1 ATAATACCAGCACGAAGCCTGCGGGA-TTT-AACCCGGAT
* *
40341314 ATAATACCAGCACTAGGCCTGCGGGATTTAACCCGGAT
1 ATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGAT
* *
40341352 ATAATACCAACACGAAGCATGCGGGATTTAACCCGGAT
1 ATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGAT
*
40341390 ATAATTCCAGCA
1 ATAATACCAGCA
40341402 TATAGCCTGC
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
38 51 0.67
39 3 0.04
40 22 0.29
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (38 bp):
ATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGAT
Found at i:40345078 original size:29 final size:30
Alignment explanation
Indices: 40345042--40345233 Score: 123
Period size: 29 Copynumber: 6.6 Consensus size: 30
40345032 GTTGAAGAAC
**
40345042 TCGCACACACAGTGCCTCAATTACCGGTCT
1 TCGCACACACAGTGCCTCAATTACCGGAAT
* ** **
40345072 T-GCACACATAGTG-CTCGGTTAAAGGAAT
1 TCGCACACACAGTGCCTCAATTACCGGAAT
40345100 TCGCACACACAGTGCCTCAATTACC--AAT
1 TCGCACACACAGTGCCTCAATTACCGGAAT
* * * ** *
40345128 CTCGAACACATAATG-CTCGGTTGA-AGGAAT
1 -TCGCACACACAGTGCCTCAATT-ACCGGAAT
40345158 TCGCACACACAGTGCCTCAATTACC-G-AT
1 TCGCACACACAGTGCCTCAATTACCGGAAT
* ** **
40345186 CTCGCACACATAGTG-CTCGGTTAAAGGAAT
1 -TCGCACACACAGTGCCTCAATTACCGGAAT
*
40345216 TTGCACACACAGTGCCTC
1 TCGCACACACAGTGCCTC
40345234 TAATCATTCG
Statistics
Matches: 119, Mismatches: 31, Indels: 24
0.68 0.18 0.14
Matches are distributed among these distances:
28 26 0.22
29 73 0.61
30 20 0.17
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (30 bp):
TCGCACACACAGTGCCTCAATTACCGGAAT
Found at i:40345118 original size:58 final size:58
Alignment explanation
Indices: 40345007--40345233 Score: 366
Period size: 58 Copynumber: 3.9 Consensus size: 58
40344997 GTGCCCACTG
* *
40345007 ACCGATCTCGCACACATAGTGCTCGGTTGAA-GAACTCGCACACACAGTGCCTCAATT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTCAATT
* *
40345064 ACCGGTCTTGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTCAATT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTCAATT
* * * *
40345122 ACCAATCTCGAACACATAATGCTCGGTTGAAGGAATTCGCACACACAGTGCCTCAATT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTCAATT
*
40345180 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTTGCACACACAGTGCCTC
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTC
40345234 TAATCATTCG
Statistics
Matches: 154, Mismatches: 15, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
57 28 0.18
58 126 0.82
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (58 bp):
ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTCAATT
Found at i:40345451 original size:43 final size:43
Alignment explanation
Indices: 40345387--40345488 Score: 150
Period size: 43 Copynumber: 2.3 Consensus size: 43
40345377 CCTTGCTCGA
** *
40345387 ATCACCGGCATTAAGCTTGCTAGGCACGAAGGCCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
*
40345430 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAT
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
*
40345473 ATCACTAGGCACGAAG
1 ATCAC-CGGCACGAAG
40345489 GCCCGAATAC
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
43 44 0.83
44 9 0.17
ACGTcount: A:0.31, C:0.30, G:0.25, T:0.14
Consensus pattern (43 bp):
ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
Found at i:40345489 original size:28 final size:28
Alignment explanation
Indices: 40345449--40345505 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
40345439 ACGAAGCCTG
*
40345449 CTAGGCACGAAGGCCCGAATACATATCA
1 CTAGGCACGAAGGCCCGAATACACATCA
40345477 CTAGGCACGAAGGCCCGAATACACATCA
1 CTAGGCACGAAGGCCCGAATACACATCA
40345505 C
1 C
40345506 CGGCATGAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.35, C:0.32, G:0.21, T:0.12
Consensus pattern (28 bp):
CTAGGCACGAAGGCCCGAATACACATCA
Found at i:40345522 original size:71 final size:71
Alignment explanation
Indices: 40345406--40345548 Score: 259
Period size: 71 Copynumber: 2.0 Consensus size: 71
40345396 ATTAAGCTTG
*
40345406 CTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATAC
1 CTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCAAATAC
*
40345471 ATATCA
66 ACATCA
*
40345477 CTAGGCACGAAGGCCCGAATACACATCACCGGCATGAAGCCTGCTAGGCACGAAGGCCCAAATAC
1 CTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCAAATAC
40345542 ACATCA
66 ACATCA
40345548 C
1 C
40345549 CGAGTTTCAT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.33, C:0.33, G:0.23, T:0.11
Consensus pattern (71 bp):
CTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCAAATAC
ACATCA
Found at i:40350976 original size:42 final size:43
Alignment explanation
Indices: 40350876--40351048 Score: 176
Period size: 43 Copynumber: 4.0 Consensus size: 43
40350866 AGCTCGTACA
* *
40350876 ATGCCAACGTCCCAGACGTGGTCTTAC-CTGTAATCAAATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACAC-GAAATCAAATATCG
*
40350919 ATGCC-ACTGTCCCAGACAAGGTCTTACACGAAATCAAATA-CG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGAAATCAAATATCG
* ** *
40350961 ATGCCAATGTCCCAGACATGGTCAAACACGTAAATCACAA-ATTG
1 ATGCCAACGTCCCAGACATGGTCTTACACG-AAATCA-AATATCG
* * *
40351005 ATGCCAACGTCCTAGACGTGGTCTTACACGATAA-CACATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGA-AATCAAATATCG
40351048 A
1 A
40351049 AATCCTATGT
Statistics
Matches: 107, Mismatches: 15, Indels: 16
0.78 0.11 0.12
Matches are distributed among these distances:
42 29 0.27
43 47 0.44
44 31 0.29
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGAAATCAAATATCG
Found at i:40352949 original size:15 final size:15
Alignment explanation
Indices: 40352911--40352956 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
40352901 AAAGATTATT
40352911 ATAAAGGTTAA-ATTA
1 ATAAAGGTTAATA-TA
*
40352926 GTAAA--TTAATATA
1 ATAAAGGTTAATATA
40352939 ATAAAGGTTAATATA
1 ATAAAGGTTAATATA
40352954 ATA
1 ATA
40352957 TAACAACATG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 10 0.38
14 1 0.04
15 15 0.58
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (15 bp):
ATAAAGGTTAATATA
Found at i:40362252 original size:12 final size:12
Alignment explanation
Indices: 40362235--40362264 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
40362225 GTTAGTTATG
40362235 TTTTGGTAATGA
1 TTTTGGTAATGA
40362247 TTTTGGTAATGA
1 TTTTGGTAATGA
40362259 TTTTGG
1 TTTTGG
40362265 CCATTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (12 bp):
TTTTGGTAATGA
Found at i:40368732 original size:46 final size:46
Alignment explanation
Indices: 40368674--40368940 Score: 279
Period size: 46 Copynumber: 5.8 Consensus size: 46
40368664 GATATTTGGG
40368674 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* * *** * * * *
40368720 TATCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGG
1 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGA-A
40368767 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* * *** * * * *
40368813 TATCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGG
1 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGA-A
*
40368860 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA
1 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* *
40368906 C-GCACGAGCTCGTTGAGTTGAGTCTGAGTTCACTT
1 CATC-CGAGCTCGTTGAGTTGAGTCCGAGTTCACTT
40368941 TTGAGTCTGA
Statistics
Matches: 175, Mismatches: 39, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
45 1 0.01
46 103 0.59
47 71 0.41
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
Found at i:40368831 original size:93 final size:93
Alignment explanation
Indices: 40368672--40368936 Score: 469
Period size: 93 Copynumber: 2.8 Consensus size: 93
40368662 AGGATATTTG
40368672 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATATCCGAACTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATATCCGAACTCGTTGAG
40368737 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
40368765 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATATCCGAACTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATATCCGAACTCGTTGAG
40368830 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* ** *
40368858 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA-CGCACGAGCTCGTTGA
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATATC-CGAACTCGTTGA
*
40368922 GTTGAGTCTGAGTTC
65 GTTGAGTCCGAGTTC
40368937 ACTTTTGAGT
Statistics
Matches: 166, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
92 1 0.01
93 165 0.99
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATATCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:40368946 original size:18 final size:18
Alignment explanation
Indices: 40368923--40368958 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
40368913 GCTCGTTGAG
40368923 TTGAGTCTGAGTTCACTT
1 TTGAGTCTGAGTTCACTT
40368941 TTGAGTCTGAGTTCACTT
1 TTGAGTCTGAGTTCACTT
40368959 ATGGATGCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (18 bp):
TTGAGTCTGAGTTCACTT
Found at i:40368978 original size:64 final size:64
Alignment explanation
Indices: 40368877--40369004 Score: 202
Period size: 64 Copynumber: 2.0 Consensus size: 64
40368867 GCTCGTTGAG
* * *
40368877 TTGAGTCCGAGTTCACTTATGGATGTGAACGCACGAGCTCGTTGAGTTGAGTCTGAGTTCACTT
1 TTGAGTCCGAGTTCACTTATGGATGCGAACGCACGAGCTCGTTCAGTTGAGTCCGAGTTCACTT
* * *
40368941 TTGAGTCTGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTCAGTTGAGTCCGAGTTCACTT
1 TTGAGTCCGAGTTCACTTATGGATGCGAACGCACGAGCTCGTTCAGTTGAGTCCGAGTTCACTT
40369005 AGGGGCGGGT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (64 bp):
TTGAGTCCGAGTTCACTTATGGATGCGAACGCACGAGCTCGTTCAGTTGAGTCCGAGTTCACTT
Found at i:40373483 original size:8 final size:8
Alignment explanation
Indices: 40373470--40373501 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
40373460 CTAGATCGGC
40373470 AAAAGCCG
1 AAAAGCCG
40373478 AAAAGCCG
1 AAAAGCCG
*
40373486 AAATGCCG
1 AAAAGCCG
40373494 AAAAGCCG
1 AAAAGCCG
40373502 GTATTTTGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.47, C:0.25, G:0.25, T:0.03
Consensus pattern (8 bp):
AAAAGCCG
Found at i:40373789 original size:28 final size:28
Alignment explanation
Indices: 40373745--40373812 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
40373735 TAGATGTACT
*
40373745 ATTATACCCCTACGTATGCAAAATTACC
1 ATTATACCCCTACGTATGCAAAATGACC
*
40373773 ATTATACCCCTATGTATGCAAAATGACC
1 ATTATACCCCTACGTATGCAAAATGACC
*
40373801 TTTATACCCCTA
1 ATTATACCCCTA
40373813 GGGTTAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.34, C:0.28, G:0.07, T:0.31
Consensus pattern (28 bp):
ATTATACCCCTACGTATGCAAAATGACC
Found at i:40373949 original size:28 final size:26
Alignment explanation
Indices: 40373918--40374007 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 26
40373908 AGGAAGCGTC
40373918 CTGGTGGCTATGCCACAAATTATCTGTT
1 CTGGTGGC-ATGCCACAAA-TATCTGTT
* * *
40373946 CTGGTGGCCCTGCCAGATATATCTGTT
1 CTGGTGG-CATGCCACAAATATCTGTT
40373973 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCA-TGCCAC-AAATATCTGT-T
40374002 CTGGTG
1 CTGGTG
40374008 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
26 1 0.02
27 20 0.38
28 23 0.44
29 8 0.15
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.32
Consensus pattern (26 bp):
CTGGTGGCATGCCACAAATATCTGTT
Found at i:40373976 original size:27 final size:28
Alignment explanation
Indices: 40373918--40374007 Score: 112
Period size: 27 Copynumber: 3.2 Consensus size: 28
40373908 AGGAAGCGTC
*
40373918 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* * *
40373946 CTGGTGGCCCTGCCA-GATATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
40373973 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
40374002 CTGGTG
1 CTGGTG
40374008 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:40376324 original size:48 final size:48
Alignment explanation
Indices: 40376220--40376395 Score: 257
Period size: 48 Copynumber: 3.7 Consensus size: 48
40376210 GTAGACTAAA
** * * *
40376220 TGCCAATATCATGGCCCAAAGCCAACTCAAT--ATCTCGCACCCAAAG
1 TGCCAATATCATGGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
*
40376266 TGCTAATATCATGGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
1 TGCCAATATCATGGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
* *
40376314 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCTGAAG
1 TGCCAATATCATGGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
*
40376362 TGCCAATATCATGGCCTGAAGCCAAATAAATGAA
1 TGCCAATATCATGGCCTGAAGCCAAATCAATGAA
40376396 TCCCCTAATG
Statistics
Matches: 117, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
46 27 0.23
48 90 0.77
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.19
Consensus pattern (48 bp):
TGCCAATATCATGGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
Found at i:40380645 original size:42 final size:43
Alignment explanation
Indices: 40380556--40380668 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 43
40380546 TGCGATAACA
*
40380556 TGTAAGACCATGTCTAGGACATTGGCATTGTATTGAGATTACG
1 TGTAAGACCATGTCTAGGACATTGGCATTCTATTGAGATTACG
* * * **
40380599 TGTAAGACCATGTTTGGGACATTGGCA-TCTATTGTGATTTTG
1 TGTAAGACCATGTCTAGGACATTGGCATTCTATTGAGATTACG
* * * *
40380641 TGTAAGACCCTATCTAGGATAGTGGCAT
1 TGTAAGACCATGTCTAGGACATTGGCAT
40380669 CGATATGTAT
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 32 0.56
43 25 0.44
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.35
Consensus pattern (43 bp):
TGTAAGACCATGTCTAGGACATTGGCATTCTATTGAGATTACG
Found at i:40389608 original size:18 final size:18
Alignment explanation
Indices: 40389585--40389641 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
40389575 CTGTTTGTAC
40389585 ACTGCACTGATTACTGTT
1 ACTGCACTGATTACTGTT
*
40389603 ACTGCATTGATTA-TGGTT
1 ACTGCACTGATTACT-GTT
40389621 ACTGCACTGATTACTGTT
1 ACTGCACTGATTACTGTT
40389639 ACT
1 ACT
40389642 AAAATGGGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 1 0.03
18 33 0.94
19 1 0.03
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (18 bp):
ACTGCACTGATTACTGTT
Found at i:40389681 original size:34 final size:34
Alignment explanation
Indices: 40389632--40389719 Score: 104
Period size: 34 Copynumber: 2.6 Consensus size: 34
40389622 CTGCACTGAT
*
40389632 TACTGTTACTAAAATGGGCTAAAACCCAGATTAC
1 TACTGTTACTGAAATGGGCTAAAACCCAGATTAC
* ** * *
40389666 TACTGTTATTGAAATGGGCTAAGGCTCAGATTGC
1 TACTGTTACTGAAATGGGCTAAAACCCAGATTAC
* *
40389700 CACTGTTACTGATATGGGCT
1 TACTGTTACTGAAATGGGCT
40389720 TAGGCCCCAC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (34 bp):
TACTGTTACTGAAATGGGCTAAAACCCAGATTAC
Found at i:40395155 original size:8 final size:8
Alignment explanation
Indices: 40395142--40395173 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
40395132 CTAGATCGGC
40395142 AAAAGCCG
1 AAAAGCCG
40395150 AAAAGCCG
1 AAAAGCCG
*
40395158 AAATGCCG
1 AAAAGCCG
40395166 AAAAGCCG
1 AAAAGCCG
40395174 GTATTTTGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.47, C:0.25, G:0.25, T:0.03
Consensus pattern (8 bp):
AAAAGCCG
Found at i:40395461 original size:28 final size:28
Alignment explanation
Indices: 40395417--40395484 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
40395407 TAGATGTACT
*
40395417 ATTATACCCCTACGTATGCAAAATTACC
1 ATTATACCCCTACGTATGCAAAATGACC
*
40395445 ATTATACCCCTATGTATGCAAAATGACC
1 ATTATACCCCTACGTATGCAAAATGACC
*
40395473 TTTATACCCCTA
1 ATTATACCCCTA
40395485 GGGTTAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.34, C:0.28, G:0.07, T:0.31
Consensus pattern (28 bp):
ATTATACCCCTACGTATGCAAAATGACC
Found at i:40395621 original size:28 final size:26
Alignment explanation
Indices: 40395590--40395679 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 26
40395580 AGGAAGCGTC
40395590 CTGGTGGCTATGCCACAAATTATCTGTT
1 CTGGTGGC-ATGCCACAAA-TATCTGTT
* * *
40395618 CTGGTGGCCCTGCCAGATATATCTGTT
1 CTGGTGG-CATGCCACAAATATCTGTT
40395645 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCA-TGCCAC-AAATATCTGT-T
40395674 CTGGTG
1 CTGGTG
40395680 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
26 1 0.02
27 20 0.38
28 23 0.44
29 8 0.15
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.32
Consensus pattern (26 bp):
CTGGTGGCATGCCACAAATATCTGTT
Found at i:40395648 original size:27 final size:28
Alignment explanation
Indices: 40395590--40395679 Score: 112
Period size: 27 Copynumber: 3.2 Consensus size: 28
40395580 AGGAAGCGTC
*
40395590 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* * *
40395618 CTGGTGGCCCTGCCA-GATATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
40395645 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
40395674 CTGGTG
1 CTGGTG
40395680 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:40397996 original size:48 final size:48
Alignment explanation
Indices: 40397892--40398787 Score: 1679
Period size: 48 Copynumber: 18.7 Consensus size: 48
40397882 GTAGACTAAA
* ** * * *
40397892 TGCCAATATCATGGCCCAAAGCCAACTCAAT--ATCTCGCACCCAAAG
1 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
* *
40397938 TGCTAATATCATGGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
1 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
40397986 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
1 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
40398034 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
1 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
40398082 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
1 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
40398130 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
1 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
40398178 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
1 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
40398226 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
1 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
40398274 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
1 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
40398322 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
1 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
40398370 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
1 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
40398418 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
1 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
40398466 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
1 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
40398514 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
1 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
40398562 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
1 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
40398610 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
1 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
40398658 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
1 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
*
40398706 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCTGAAG
1 TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
* *
40398754 TGCCAATATCATGGCCTGAAGCCAAATAAATGAA
1 TGCCAATATCATAGCCTGAAGCCAAATCAATGAA
40398788 TCCCCTAATG
Statistics
Matches: 837, Mismatches: 11, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
46 27 0.03
48 810 0.97
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.17
Consensus pattern (48 bp):
TGCCAATATCATAGCCTGAAGCCAAATCAATGAAGCTCGCACCCGAAG
Found at i:40403037 original size:42 final size:43
Alignment explanation
Indices: 40402948--40403060 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 43
40402938 TGCGATAACA
*
40402948 TGTAAGACCATGTCTAGGACATTGGCATTGTATTGAGATTACG
1 TGTAAGACCATGTCTAGGACATTGGCATTCTATTGAGATTACG
* * * **
40402991 TGTAAGACCATGTTTGGGACATTGGCA-TCTATTGTGATTTTG
1 TGTAAGACCATGTCTAGGACATTGGCATTCTATTGAGATTACG
* * * *
40403033 TGTAAGACCCTATCTAGGATAGTGGCAT
1 TGTAAGACCATGTCTAGGACATTGGCAT
40403061 CGATATGTAT
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 32 0.56
43 25 0.44
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.35
Consensus pattern (43 bp):
TGTAAGACCATGTCTAGGACATTGGCATTCTATTGAGATTACG
Found at i:40413319 original size:57 final size:55
Alignment explanation
Indices: 40413255--40413366 Score: 206
Period size: 57 Copynumber: 2.0 Consensus size: 55
40413245 GTTAAAGAAA
40413255 GGAATTAAACAATGAAAAGGAAGGGTGATGAAAAAAAAAAAATGGTCTCATCCATAC
1 GGAATTAAACAATGAAAAGGAAGGGTGATG--AAAAAAAAAATGGTCTCATCCATAC
40413312 GGAATTAAACAATGAAAAGGAAGGGTGATGAAAAAAAAAATGGTCTCATCCATAC
1 GGAATTAAACAATGAAAAGGAAGGGTGATGAAAAAAAAAATGGTCTCATCCATAC
40413367 CCCCCCTTGT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
55 25 0.45
57 30 0.55
ACGTcount: A:0.50, C:0.11, G:0.21, T:0.18
Consensus pattern (55 bp):
GGAATTAAACAATGAAAAGGAAGGGTGATGAAAAAAAAAATGGTCTCATCCATAC
Found at i:40415094 original size:27 final size:27
Alignment explanation
Indices: 40415063--40415240 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
40415053 TAAATTGTAC
40415063 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
40415090 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40415116 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* * *
40415144 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
40415172 AGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40415199 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
40415226 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40415241 GACTCGATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 106 0.83
28 21 0.17
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:40415180 original size:82 final size:81
Alignment explanation
Indices: 40415064--40415219 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
40415054 AAATTGTACA
* * *
40415064 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATATGTA-GCACTAAGTG
40415128 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
40415145 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TCTAACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTG
*
40415210 TGCGAGTTGA
65 TGCGAATTGA
40415220 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:40415231 original size:82 final size:81
Alignment explanation
Indices: 40415060--40415240 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
40415050 GATTAAATTG
* * *
40415060 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
40415125 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
40415141 TGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTATG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TCTAACTATGTAGCACTAAGTGTGCGAAATGAATATGAT-GCACT
* **
40415205 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
40415223 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
40415241 GACTCGATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:40423544 original size:40 final size:40
Alignment explanation
Indices: 40423485--40423662 Score: 252
Period size: 40 Copynumber: 4.5 Consensus size: 40
40423475 CGGATGATAA
*
40423485 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
40423525 CTGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
40423565 CCGGGCTAAGTCCCGAAGGCATTTGTCCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
40423605 CCGAGCTAAGTCTCGAAGGCAGTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
40423645 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
40423663 TACTTGGTTT
Statistics
Matches: 123, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 15 0.12
40 108 0.88
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:40433756 original size:43 final size:43
Alignment explanation
Indices: 40433709--40433803 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
40433699 TCATAGATAG
*
40433709 GGTCTTACACGAAATCAT-AATACGATCCCAATGTCCCAAACAT
1 GGTCTTACACGAAATC-TCAATACAATCCCAATGTCCCAAACAT
* * * * *
40433752 GGTCTTATATGCAATCTCAATACAATGCTAATGTCCCAAACAT
1 GGTCTTACACGAAATCTCAATACAATCCCAATGTCCCAAACAT
*
40433795 GATCTTACA
1 GGTCTTACA
40433804 TGTAATCACA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 1 0.02
43 42 0.98
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (43 bp):
GGTCTTACACGAAATCTCAATACAATCCCAATGTCCCAAACAT
Found at i:40446200 original size:56 final size:56
Alignment explanation
Indices: 40446114--40446233 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
40446104 ACAAGGGATG
40446114 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
40446170 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
40446226 ATGGGCAA
1 ATGGGCAA
40446234 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:40447447 original size:40 final size:39
Alignment explanation
Indices: 40447363--40447587 Score: 231
Period size: 40 Copynumber: 5.6 Consensus size: 39
40447353 TCGAATGATG
* * * *
40447363 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
40447403 TTCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40447443 TTCGGGCTAAG-CTCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTC-CGAAGGCATTTGTGCGAGTTACTAAA
*
40447482 TCCGGGTTAAGTTCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40447522 TCCGGGTTAAGTCCCGAATGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
40447563 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
40447588 AACGTAATCG
Statistics
Matches: 159, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
38 1 0.01
39 33 0.21
40 114 0.72
41 11 0.07
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40457603 original size:79 final size:80
Alignment explanation
Indices: 40457505--40457687 Score: 221
Period size: 79 Copynumber: 2.3 Consensus size: 80
40457495 TCCTCGTTCA
* *
40457505 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
40457568 ATTTAGTAAC-TCGCACC
64 ATATAGTAACTTAGCA-C
* **
40457585 AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
* *
40457649 ATGGTCACTTAGCAC
66 ATAGTAACTTAGCAC
*
40457664 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
40457688 CATCATTCAA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
ATAGTAACTTAGCAC
Found at i:40457687 original size:40 final size:40
Alignment explanation
Indices: 40457503--40457687 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
40457493 GCTCCTCGTT
* *
40457503 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
40457543 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
40457583 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
40457622 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
40457663 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40457688 CATCATTCAA
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.02
39 31 0.25
40 79 0.64
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:40471966 original size:30 final size:30
Alignment explanation
Indices: 40471910--40471967 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
40471900 CACGGCCATG
* *
40471910 ACACACGGGCATGTGGTCTACTCGTGTGTC
1 ACACACGGACATGTGGTCTACCCGTGTGTC
*
40471940 ACACACGGACGTGTGGATC-ACCCGTGTG
1 ACACACGGACATGTGG-TCTACCCGTGTG
40471968 GAAGTGCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.19, C:0.28, G:0.31, T:0.22
Consensus pattern (30 bp):
ACACACGGACATGTGGTCTACCCGTGTGTC
Found at i:40479986 original size:16 final size:15
Alignment explanation
Indices: 40479962--40479991 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40479952 AACTGTTTTA
40479962 TTACAAATTTCACTC
1 TTACAAATTTCACTC
40479977 TTACATAATTTCACT
1 TTACA-AATTTCACT
40479992 TACTCCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (15 bp):
TTACAAATTTCACTC
Found at i:40480250 original size:49 final size:49
Alignment explanation
Indices: 40480197--40480372 Score: 181
Period size: 51 Copynumber: 3.5 Consensus size: 49
40480187 CTGGTACGCA
40480197 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCCGGTACACG
* * ** * * * *
40480246 TAGTAGCCTGCACTTAGTACTACACACGTGATTGAAACTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGCGA--CCAACAATCCGGTACACG
* * * ** *
40480297 TAATAGCCTGTACTTAGTACTACACATGCGACCTAACCATTTGGTACATG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AACAATCCGGTACACG
* *
40480347 TAGTATCCTGCACTTAGAACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
40480373 CGTGACCTAA
Statistics
Matches: 100, Mismatches: 24, Indels: 5
0.78 0.19 0.04
Matches are distributed among these distances:
49 29 0.29
50 32 0.32
51 39 0.39
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCCGGTACACG
Found at i:40480314 original size:51 final size:50
Alignment explanation
Indices: 40480178--40480327 Score: 167
Period size: 49 Copynumber: 3.0 Consensus size: 50
40480168 TTACCACAAC
* * *
40480178 TGAAGCTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGA
1 TGAAACTATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGA
** * * * *
40480228 -CCAACAATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA
1 TGAAACTATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGA
* * * *
40480277 TTGAAACTATCGGGTACGCATAATAGCCTGTACTTAGTACTACACATGCGA
1 -TGAAACTATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGA
40480328 CCTAACCATT
Statistics
Matches: 79, Mismatches: 19, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
49 40 0.51
51 39 0.49
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (50 bp):
TGAAACTATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGA
Found at i:40480369 original size:50 final size:50
Alignment explanation
Indices: 40480197--40480382 Score: 187
Period size: 50 Copynumber: 3.7 Consensus size: 50
40480187 CTGGTACGCA
*
40480197 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AACAATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATCCGGTACACG
* * * * * *
40480246 TAGTAGCCTGCACTTAGTACTACACACGTGA-TTGAAACTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCT--AACAATCCGGTACACG
* * * * ** *
40480297 TAATAGCCTGTACTTAGTACTACACATGCGACCTAACCATTTGGTACATG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATCCGGTACACG
* * *
40480347 TAGTATCCTGCACTTAGAACTACACACGTGACCTAA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCTAA
40480383 AACCATTTTA
Statistics
Matches: 109, Mismatches: 24, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
49 29 0.27
50 40 0.37
51 39 0.36
52 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATCCGGTACACG
Found at i:40483428 original size:15 final size:15
Alignment explanation
Indices: 40483394--40483453 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 15
40483384 TATAGATAAC
* * *
40483394 AAGAAAACCAGGATT
1 AAGAAATCCAAGATA
*
40483409 AAGAAGTCCAAGATA
1 AAGAAATCCAAGATA
* *
40483424 GAGAAATCCAAAATA
1 AAGAAATCCAAGATA
40483439 AAGAAATCCAAGATA
1 AAGAAATCCAAGATA
40483454 CAATATCATA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.57, C:0.13, G:0.17, T:0.13
Consensus pattern (15 bp):
AAGAAATCCAAGATA
Found at i:40483429 original size:30 final size:30
Alignment explanation
Indices: 40483395--40483453 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
40483385 ATAGATAACA
** * *
40483395 AGAAAACCAGGATTAAGAAGTCCAAGATAG
1 AGAAAACCAAAATAAAGAAATCCAAGATAG
*
40483425 AGAAATCCAAAATAAAGAAATCCAAGATA
1 AGAAAACCAAAATAAAGAAATCCAAGATA
40483454 CAATATCATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.14
Consensus pattern (30 bp):
AGAAAACCAAAATAAAGAAATCCAAGATAG
Found at i:40487440 original size:56 final size:56
Alignment explanation
Indices: 40487349--40487491 Score: 250
Period size: 56 Copynumber: 2.6 Consensus size: 56
40487339 GATGACATGA
* * *
40487349 TACATGCTAGGTCTGAGAGCTTGTGTAGCCCCATTGAGAGACATGTAATTATGTGG
1 TACACGCTAGGTCTGGGAGCTTATGTAGCCCCATTGAGAGACATGTAATTATGTGG
*
40487405 TACACGCTAGGTCCGGGAGCTTATGTAGCCCCATTGAGAGACATGTAATTATGTGG
1 TACACGCTAGGTCTGGGAGCTTATGTAGCCCCATTGAGAGACATGTAATTATGTGG
40487461 TACACGCTAGGTCTGGGAGCTTATGTAGCCC
1 TACACGCTAGGTCTGGGAGCTTATGTAGCCC
40487492 TGTTAAGAGG
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 82 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.28
Consensus pattern (56 bp):
TACACGCTAGGTCTGGGAGCTTATGTAGCCCCATTGAGAGACATGTAATTATGTGG
Found at i:40487540 original size:56 final size:54
Alignment explanation
Indices: 40487397--40487561 Score: 177
Period size: 56 Copynumber: 3.0 Consensus size: 54
40487387 AGACATGTAA
* ** * * **
40487397 TTATGTGGTACACGCTAGGTCCGGGAGCTTATGTAGCCCCATTGAGAGACATGTAA
1 TTATGTGATACACGCTAGGTCCGGGAGCTTATGTAGCCCTGTTAAGAGGC--GTGG
* *
40487453 TTATGTGGTACACGCTAGGTCTGGGAGCTTATGTAGCCCTGTTAAGAGGCGTGG
1 TTATGTGATACACGCTAGGTCCGGGAGCTTATGTAGCCCTGTTAAGAGGCGTGG
* * * *
40487507 TTATGTGATACATGCTAGGTCCGGGTGTTCTTATGTAGCCTTGTTGAGAGGCGTG
1 TTATGTGATACACGCTAGGTCCGGGAG--CTTATGTAGCCCTGTTAAGAGGCGTG
40487562 CTATGTTATG
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
54 25 0.27
56 69 0.73
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.31
Consensus pattern (54 bp):
TTATGTGATACACGCTAGGTCCGGGAGCTTATGTAGCCCTGTTAAGAGGCGTGG
Found at i:40490939 original size:50 final size:50
Alignment explanation
Indices: 40490821--40491109 Score: 265
Period size: 50 Copynumber: 5.7 Consensus size: 50
40490811 AACCGAAGCT
* * * *
40490821 ATCTGGTACACATAGTAGCTTGCACTTAGTACTACACATGCGACC-AACA
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
* * *
40490870 ATCCGGTACACGTAGTAGCCTGCACTTAGTACTATACACGTGACCTAACC
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
* * ** *
40490920 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAACT
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-CCTAACC
* * * * * * * *
40490971 ACCCGGTACGCATAGAAGCTTGCACTTAGTACTATACATGCGACCTAACC
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
** * * * *
40491021 ATCTGGTACATGTAGTATCCTGCATTTTGTACTACACACGTGATCTAAAACC
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCT--AACC
* *** *
40491073 ATTTTAAACACATAGTAGCCTGCACATAGTACTACAC
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACAC
40491110 TTGTGTTTTC
Statistics
Matches: 186, Mismatches: 50, Indels: 5
0.77 0.21 0.02
Matches are distributed among these distances:
49 39 0.21
50 79 0.42
51 37 0.20
52 31 0.17
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (50 bp):
ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
Found at i:40491021 original size:101 final size:100
Alignment explanation
Indices: 40490821--40491065 Score: 312
Period size: 101 Copynumber: 2.5 Consensus size: 100
40490811 AACCGAAGCT
* * * * * * *
40490821 ATCTGGTACACATAGTAGCTTGCACTTAGTACTACACATGCGA-CCAACAATCCGGTACACGTAG
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAACAACCCGGTACACATAG
* *
40490885 TAGCCTGCACTTAGTACTATACACGTGACCTAACC
66 AAGCCTGCACTTAGTACTATACACGCGACCTAACC
* * *
40490920 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAACTACCCGGTACGCATA
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATC-AAACAACCCGGTACACATA
* *
40490985 GAAGCTTGCACTTAGTACTATACATGCGACCTAACC
65 GAAGCCTGCACTTAGTACTATACACGCGACCTAACC
* * * *
40491021 ATCTGGTACATGTAGTATCCTGCATTTTGTACTACACACGTGATC
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATC
40491066 TAAAACCATT
Statistics
Matches: 125, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
99 38 0.30
100 1 0.01
101 86 0.69
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (100 bp):
ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAACAACCCGGTACACATAG
AAGCCTGCACTTAGTACTATACACGCGACCTAACC
Found at i:40491892 original size:33 final size:33
Alignment explanation
Indices: 40491845--40491937 Score: 96
Period size: 33 Copynumber: 2.8 Consensus size: 33
40491835 CATGGCTAGC
* * *
40491845 CTATGGCATTCTGATGAGAAGATCATAGTTGGG
1 CTATGGCATCCTGATGAGAAGACCATAGCTGGG
* * *
40491878 CTATGGTATCCTGATTATAAGACCATAGCTGGG
1 CTATGGCATCCTGATGAGAAGACCATAGCTGGG
* * * *
40491911 GTATGGCATTCTGCTGATAAGACCATA
1 CTATGGCATCCTGATGAGAAGACCATA
40491938 ACCCGGTTAT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (33 bp):
CTATGGCATCCTGATGAGAAGACCATAGCTGGG
Found at i:40496179 original size:39 final size:39
Alignment explanation
Indices: 40496127--40496208 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 39
40496117 GTTTTCACAT
* *
40496127 TTAAAGAGATTGAATACAAGCATTTTTGTTATGTTTTAG
1 TTAAAGAGATTGAATACAAGCATTTATGTTATGGTTTAG
*
40496166 TTAAAGAGCTTGAATACAAGCATTTATGTTATGGTTTAG
1 TTAAAGAGATTGAATACAAGCATTTATGTTATGGTTTAG
40496205 TTAA
1 TTAA
40496209 GTTTTCACAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.41
Consensus pattern (39 bp):
TTAAAGAGATTGAATACAAGCATTTATGTTATGGTTTAG
Found at i:40497749 original size:26 final size:24
Alignment explanation
Indices: 40497711--40497795 Score: 73
Period size: 26 Copynumber: 3.4 Consensus size: 24
40497701 TGGCTATCCA
*
40497711 GAGC-TCCTGATTAAAGGCTCTTCGT
1 GAGCTTCCTAATTAAA-GCTCTT-GT
*
40497736 GAGCTTCCTAATTAAAAGTTCTTTGT
1 GAGCTTCCTAATT-AAAGCTC-TTGT
* * * *
40497762 GAACTTTCTAATTATAGCTCTTAT
1 GAGCTTCCTAATTAAAGCTCTTGT
40497786 GAGCTTCCTA
1 GAGCTTCCTA
40497796 TTATATAGCC
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
24 11 0.23
25 9 0.19
26 23 0.48
27 5 0.10
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (24 bp):
GAGCTTCCTAATTAAAGCTCTTGT
Found at i:40502398 original size:39 final size:39
Alignment explanation
Indices: 40502354--40502585 Score: 358
Period size: 39 Copynumber: 6.0 Consensus size: 39
40502344 ATTATATTAT
* * * *
40502354 CAGCACAAAGCCTGTGGGACTTTAACCCGGATACATCTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
40502393 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
**
40502432 CAGCACGAAGCCTGCGGGACTTTAGTTCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
40502471 CAGCACGAAGCCTGCGGAACTTT-GCCCGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
40502509 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATAAATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
40502548 CAGCACGAAGCCTGCGAGACTTTAGCCCGGATACATTT
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
40502586 TCAGTGTCTT
Statistics
Matches: 176, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
38 34 0.19
39 142 0.81
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.22
Consensus pattern (39 bp):
CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
Found at i:40502522 original size:116 final size:117
Alignment explanation
Indices: 40502354--40502585 Score: 358
Period size: 116 Copynumber: 2.0 Consensus size: 117
40502344 ATTATATTAT
* * *
40502354 CAGCACAAAGCCTGTGGGACTTTAACCCGGATACATCTCCAGCACGAAGCCTGCGGGACTTTGGC
1 CAGCACAAAGCCTGCGGAACTTTAACCCGGATACATCTCCAGCACGAAGCCTGCGGGACTTTAGC
* * **
40502419 CCGGATACATTTCCAGCACGAAGCCTGCGGGACTTTAGTTCGGATACATTTC
66 CCGGATAAATTTCCAGCACGAAGCCTGCGAGACTTTAGCCCGGATACATTTC
* * * *
40502471 CAGCACGAAGCCTGCGGAACTTT-GCCCGGATATATTTCCAGCACGAAGCCTGCGGGACTTTAGC
1 CAGCACAAAGCCTGCGGAACTTTAACCCGGATACATCTCCAGCACGAAGCCTGCGGGACTTTAGC
40502535 CCGGATAAATTTCCAGCACGAAGCCTGCGAGACTTTAGCCCGGATACATTT
66 CCGGATAAATTTCCAGCACGAAGCCTGCGAGACTTTAGCCCGGATACATTT
40502586 TCAGTGTCTT
Statistics
Matches: 104, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
116 84 0.81
117 20 0.19
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.22
Consensus pattern (117 bp):
CAGCACAAAGCCTGCGGAACTTTAACCCGGATACATCTCCAGCACGAAGCCTGCGGGACTTTAGC
CCGGATAAATTTCCAGCACGAAGCCTGCGAGACTTTAGCCCGGATACATTTC
Found at i:40502533 original size:77 final size:78
Alignment explanation
Indices: 40502354--40502585 Score: 351
Period size: 77 Copynumber: 3.0 Consensus size: 78
40502344 ATTATATTAT
* * * * * *
40502354 CAGCACAAAGCCTGTGGGACTTTAACCCGGATACATCTCCAGCACGAAGCCTGCGGGACTTTGGC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGAACTTTAGC
40502419 CCGGATACATTTC
66 CCGGATACATTTC
**
40502432 CAGCACGAAGCCTGCGGGACTTTAGTTCGGATACATTTCCAGCACGAAGCCTGCGGAACTTT-GC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGAACTTTAGC
*
40502496 CCGGATATATTTC
66 CCGGATACATTTC
*
40502509 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATAAATTTCCAGCACGAAGCCTGC-GAGACTTTAG
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGA-ACTTTAG
40502573 CCCGGATACATTT
65 CCCGGATACATTT
40502586 TCAGTGTCTT
Statistics
Matches: 140, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
76 2 0.01
77 70 0.50
78 68 0.49
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.22
Consensus pattern (78 bp):
CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGAACTTTAGC
CCGGATACATTTC
Found at i:40506249 original size:27 final size:26
Alignment explanation
Indices: 40506205--40506256 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
40506195 CTTGCTGTAA
*
40506205 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
40506232 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
40506257 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:40507788 original size:149 final size:149
Alignment explanation
Indices: 40507518--40507814 Score: 567
Period size: 149 Copynumber: 2.0 Consensus size: 149
40507508 TAGCTAAACA
*
40507518 GATAATTTCATATGCACAAATTTTCAGTATCATACTTACTTCACATTACCAACCCTTATATTCAT
1 GATAATTTCATATGCACAAATTTTCAATATCATACTTACTTCACATTACCAACCCTTATATTCAT
40507583 ACACAAAGATCAACTTAGCCAAAGGCCGGTAGCTCATTTATCAACTGAGCGAATACTTATTTGTA
66 ACACAAAGATCAACTTAGCCAAAGGCCGGTAGCTCATTTATCAACTGAGCGAATACTTATTTGTA
40507648 AGGGCTCAACTAATTCAAG
131 AGGGCTCAACTAATTCAAG
* *
40507667 GATAATTTCATATGCACAATTTTTCAATATCATACTTACTTCACATTACCAACCCTTTTATTCAT
1 GATAATTTCATATGCACAAATTTTCAATATCATACTTACTTCACATTACCAACCCTTATATTCAT
40507732 ACACAAAGATCAACTTAGCCAAAGGCCGGTAGCTCATTTATCAACTGAGCGAATACTTATTTGTA
66 ACACAAAGATCAACTTAGCCAAAGGCCGGTAGCTCATTTATCAACTGAGCGAATACTTATTTGTA
40507797 AGGGCTCAACTAATTCAA
131 AGGGCTCAACTAATTCAA
40507815 AGCACATACG
Statistics
Matches: 145, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 145 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (149 bp):
GATAATTTCATATGCACAAATTTTCAATATCATACTTACTTCACATTACCAACCCTTATATTCAT
ACACAAAGATCAACTTAGCCAAAGGCCGGTAGCTCATTTATCAACTGAGCGAATACTTATTTGTA
AGGGCTCAACTAATTCAAG
Found at i:40508049 original size:79 final size:82
Alignment explanation
Indices: 40507938--40508122 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
40507928 GCTACTCGTT
* *
40507938 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
40508001 GGATTTAGTAAC-TCGCA
65 GGATGTAGTAACTTAGCA
* **
40508018 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
40508081 GATGTGGTCACTTAGCA
66 GATGTAGTAACTTAGCA
40508098 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40508123 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATGTAGTAACTTAGCA
Found at i:40508122 original size:40 final size:39
Alignment explanation
Indices: 40507938--40508122 Score: 223
Period size: 40 Copynumber: 4.7 Consensus size: 39
40507928 GCTACTCGTT
* *
40507938 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAT-TAGTAACTCGCA
*
40507978 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGA-TTAGTAACTCGCA
*
40508018 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-ATTAGTAACTCGCA
* * * *
40508057 CAAATGCCTTC-GGATCTTAGTCCGGATGTGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TAGTAAC-TCGCA
40508098 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40508123 CATCATTCAA
Statistics
Matches: 127, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
38 2 0.02
39 34 0.27
40 79 0.62
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
Found at i:40510568 original size:293 final size:293
Alignment explanation
Indices: 40509710--40510589 Score: 1744
Period size: 293 Copynumber: 3.0 Consensus size: 293
40509700 ACACATGCAC
40509710 ATGTACATATAATGAGCATCAATTATGACGGTTAATTATTTTTATGACTCGGTTTAGTGGTCCCA
1 ATGTACATATAATGAGCATCAATTATGACGGTTAATTATTTTTATGACTCGGTTTAGTGGTCCCA
40509775 AAACCACTTCCCGACTAGGGTCAATTTTGGGCTGTCACATGCATTCATGATATATATTTTTTCTG
66 AAACCACTTCCCGACTAGGGTCAATTTTGGGCTGTCACATGCATTCATGATATATATTTTTTCTG
40509840 TATCTGCTATGGGCCTATGGGTTTCATTCTGATTTCTGTACTAGGCCAAGGCCCAGATAAGTCTG
131 TATCTGCTATGGGCCTATGGGTTTCATTCTGATTTCTGTACTAGGCCAAGGCCCAGATAAGTCTG
40509905 ACTCTGAGGTTTGATCTGTTTTGGGCTATGGTTGGGTTATGTTACACACTGAGTTTACCGAACTC
196 ACTCTGAGGTTTGATCTGTTTTGGGCTATGGTTGGGTTATGTTACACACTGAGTTTACCGAACTC
40509970 ACCCTTTATTTTCATCTTTGCAGGAAATCCCCA
261 ACCCTTTATTTTCATCTTTGCAGGAAATCCCCA
40510003 ATGTACATATAATGAGCATCAATTATGACGGTTAATTA-TTTTATGACTCGGTTTAGTGGTCCCA
1 ATGTACATATAATGAGCATCAATTATGACGGTTAATTATTTTTATGACTCGGTTTAGTGGTCCCA
*
40510067 AAACCACTTCCCGACTAGGGTCAATTTTGCGCTGTCACATGCATTCATGATATATATTTTTTCTG
66 AAACCACTTCCCGACTAGGGTCAATTTTGGGCTGTCACATGCATTCATGATATATATTTTTTCTG
40510132 TATCTGCTATGGGCCTATGGGTTTCATTCTGATTTCTGTACTAGGCCAAGGCCCAGATAAGTCTG
131 TATCTGCTATGGGCCTATGGGTTTCATTCTGATTTCTGTACTAGGCCAAGGCCCAGATAAGTCTG
40510197 ACTCTGAGGTTTGATCTGTTTTGGGCTATGGTTGGGTTATGTTACACACTGAGTTTACCGAACTC
196 ACTCTGAGGTTTGATCTGTTTTGGGCTATGGTTGGGTTATGTTACACACTGAGTTTACCGAACTC
40510262 ACCCTTTATTTTCATCTTTGCAGGAAATCCCCA
261 ACCCTTTATTTTCATCTTTGCAGGAAATCCCCA
40510295 ATGTACATATAATGAGCATCAATTATGACGGTTAATTATTTTTATGACTCGGTTTAGTGGTCCCA
1 ATGTACATATAATGAGCATCAATTATGACGGTTAATTATTTTTATGACTCGGTTTAGTGGTCCCA
40510360 AAACCACTTCCCGACTAGGGTCAATTTTGGGCTGTCACATGCATTCATGATATATATTTTTTCTG
66 AAACCACTTCCCGACTAGGGTCAATTTTGGGCTGTCACATGCATTCATGATATATATTTTTTCTG
40510425 TATCTGCTATGGGCCTATGGGTTTCATTCTGATTTCTGTACTAGGCCAAGGCCCAGATAAGTCTG
131 TATCTGCTATGGGCCTATGGGTTTCATTCTGATTTCTGTACTAGGCCAAGGCCCAGATAAGTCTG
40510490 ACTCTGAGGTTTGATCTGTTTTGGGCTATGGTTGGGTTATGTTACACACTGAGTTTACCGAACTC
196 ACTCTGAGGTTTGATCTGTTTTGGGCTATGGTTGGGTTATGTTACACACTGAGTTTACCGAACTC
40510555 ACCCTTTATTTTCATCTTTGCAGGAAATCCCCA
261 ACCCTTTATTTTCATCTTTGCAGGAAATCCCCA
40510588 AT
1 AT
40510590 CATAGCGGGC
Statistics
Matches: 584, Mismatches: 2, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
292 291 0.50
293 293 0.50
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (293 bp):
ATGTACATATAATGAGCATCAATTATGACGGTTAATTATTTTTATGACTCGGTTTAGTGGTCCCA
AAACCACTTCCCGACTAGGGTCAATTTTGGGCTGTCACATGCATTCATGATATATATTTTTTCTG
TATCTGCTATGGGCCTATGGGTTTCATTCTGATTTCTGTACTAGGCCAAGGCCCAGATAAGTCTG
ACTCTGAGGTTTGATCTGTTTTGGGCTATGGTTGGGTTATGTTACACACTGAGTTTACCGAACTC
ACCCTTTATTTTCATCTTTGCAGGAAATCCCCA
Found at i:40512217 original size:27 final size:27
Alignment explanation
Indices: 40512200--40512431 Score: 140
Period size: 27 Copynumber: 8.8 Consensus size: 27
40512190 ATATCGAGTC
40512200 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* * *
40512227 CGCACA--C--TG-TATAT--TGAGCC
1 CGCACACTCAGTGCTATATAATCAACT
40512247 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* ** *
40512274 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTCAGTGCTATATAATCAACT
* * *
40512301 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* *** * *
40512329 CGCACACTTAGTGCCGCATGATCAATT
1 CGCACACTCAGTGCTATATAATCAACT
* * **
40512356 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTCAGTGCTAT-ATAATCAACT
* * * *
40512383 CGCACACTTAGTGCAACATAGTCATA-T
1 CGCACACTCAGTGCTATATAATCA-ACT
* *
40512410 CGCACACTTAGTGCTGTATAAT
1 CGCACACTCAGTGCTATATAAT
40512432 TAAATCCCGC
Statistics
Matches: 164, Mismatches: 30, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
20 9 0.05
22 6 0.04
23 2 0.01
24 2 0.01
25 6 0.04
27 116 0.71
28 23 0.14
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:40512250 original size:47 final size:47
Alignment explanation
Indices: 40512189--40512281 Score: 168
Period size: 47 Copynumber: 2.0 Consensus size: 47
40512179 TTCACGAATA
*
40512189 TATATCGAGTCCGCACACTCAGTGCTATATAATCAACTCGCACACTG
1 TATATCGAGCCCGCACACTCAGTGCTATATAATCAACTCGCACACTG
*
40512236 TATATTGAGCCCGCACACTCAGTGCTATATAATCAACTCGCACACT
1 TATATCGAGCCCGCACACTCAGTGCTATATAATCAACTCGCACACT
40512282 TAGTGCTACG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (47 bp):
TATATCGAGCCCGCACACTCAGTGCTATATAATCAACTCGCACACTG
Found at i:40512386 original size:82 final size:81
Alignment explanation
Indices: 40512267--40512423 Score: 226
Period size: 82 Copynumber: 1.9 Consensus size: 81
40512257 GTGCTATATA
* *
40512267 ATCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGC
1 ATCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGC
40512332 ACACTTAGTGCCGCATG
65 ACACTTAGTGCCGCATG
* * ** *
40512349 ATCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCATATCGC
1 ATCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGC
40512413 ACACTTAGTGC
65 ACACTTAGTGC
40512424 TGTATAATTA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
ATCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATG
Found at i:40519723 original size:27 final size:27
Alignment explanation
Indices: 40519693--40519870 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40519683 ATATTGAGCC
* * * *
40519693 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
40519720 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40519747 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40519775 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40519802 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40519829 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40519856 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40519871 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40519832 original size:82 final size:81
Alignment explanation
Indices: 40519714--40519869 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40519704 TGCTATATAA
* *
40519714 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40519779 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40519796 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40519860 CACTTAGTGC
65 CACTTAGTGC
40519870 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40524778 original size:26 final size:26
Alignment explanation
Indices: 40524742--40524792 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
40524732 CTTTATACTG
* *
40524742 ATTACTAGCAGCTTTGCTGCGATACC
1 ATTACTAGCAGCTCTACTGCGATACC
*
40524768 ATTACTCGCAGCTCTACTGCGATAC
1 ATTACTAGCAGCTCTACTGCGATAC
40524793 TGATATTGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (26 bp):
ATTACTAGCAGCTCTACTGCGATACC
Found at i:40533857 original size:48 final size:47
Alignment explanation
Indices: 40533786--40534055 Score: 261
Period size: 48 Copynumber: 5.6 Consensus size: 47
40533776 ATTGAAATAC
* * *
40533786 GTGTAAGACCATGTTTGGGACATGGCATCAGCGTTGATATGTGTGCTA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGC-TTGATATGTGAGCTA
* *
40533834 GTGTAAGACCATGTCTGGGACATGGCATCGGTGTTGATATGTGTGCTA
1 GTGTAAGACCATGTCTGGGACATGGCATCGG-CTTGATATGTGAGCTA
* * *** * * *
40533882 GGGTAAGACCATGTCTGGGACATGGCATTGGCCACATTACGAGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCTTGA-TATGTGAGCTA
* * * * * * ***
40533930 CTATAAGACCATGCCTGGGACATGGAATCGGCAATGAGACAAGAGCTA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGC-TTGATATGTGAGCTA
* * * *
40533978 GTGTAAGACCATGTTTGGGACATGGCATCGACTTCAACATGTGAGCTA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCTT-GATATGTGAGCTA
40534026 GTGTAAGACCATGTCTGGGACATGGCATCG
1 GTGTAAGACCATGTCTGGGACATGGCATCG
40534056 ACATTTTACC
Statistics
Matches: 180, Mismatches: 38, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
47 2 0.01
48 177 0.98
49 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (47 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGGCTTGATATGTGAGCTA
Found at i:40534845 original size:15 final size:15
Alignment explanation
Indices: 40534825--40534854 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40534815 GTATAGTACC
40534825 GTATTTTGGATATTT
1 GTATTTTGGATATTT
40534840 GTATTTTGGATATTT
1 GTATTTTGGATATTT
40534855 CCTATCATTC
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:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (15 bp):
GTATTTTGGATATTT
Found at i:40537589 original size:40 final size:40
Alignment explanation
Indices: 40537499--40537592 Score: 143
Period size: 40 Copynumber: 2.4 Consensus size: 40
40537489 AGCTAAATGT
* * *
40537499 GGCATTTAGTATGCGGTTCGAGATAGCTTCAGCTATGTAC
1 GGCACTTAGTGTGCGATTCGAGATAGCTTCAGCTATGTAC
* *
40537539 GGCACTTAGTGTGCGATTTGAGATAGCTTCGGCTATGTAC
1 GGCACTTAGTGTGCGATTCGAGATAGCTTCAGCTATGTAC
40537579 GGCACTTAGTGTGC
1 GGCACTTAGTGTGC
40537593 AAGATATTGA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (40 bp):
GGCACTTAGTGTGCGATTCGAGATAGCTTCAGCTATGTAC
Found at i:40537629 original size:28 final size:28
Alignment explanation
Indices: 40537598--40537691 Score: 111
Period size: 28 Copynumber: 3.4 Consensus size: 28
40537588 TGTGCAAGAT
40537598 ATTGAGTATGGCACTTAGTGTACGGAAC
1 ATTGAGTATGGCACTTAGTGTACGGAAC
* *
40537626 ATTGAGAATGGCACTTAGTGT--GTGAGAT
1 ATTGAGTATGGCACTTAGTGTACG-GA-AC
* *
40537654 GTTGAGTATGGCACTTAGTGTACGGGAC
1 ATTGAGTATGGCACTTAGTGTACGGAAC
*
40537682 ATTGAATATG
1 ATTGAGTATG
40537692 CAGCAGTATT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
26 1 0.02
27 2 0.04
28 49 0.91
29 1 0.02
30 1 0.02
ACGTcount: A:0.28, C:0.11, G:0.31, T:0.31
Consensus pattern (28 bp):
ATTGAGTATGGCACTTAGTGTACGGAAC
Found at i:40537665 original size:56 final size:56
Alignment explanation
Indices: 40537579--40537686 Score: 180
Period size: 56 Copynumber: 1.9 Consensus size: 56
40537569 GGCTATGTAC
40537579 GGCACTTAGTGTGCAAGATATTGAGTATGGCACTTAGTGTACGGAACATTGAGAAT
1 GGCACTTAGTGTGCAAGATATTGAGTATGGCACTTAGTGTACGGAACATTGAGAAT
** * *
40537635 GGCACTTAGTGTGTGAGATGTTGAGTATGGCACTTAGTGTACGGGACATTGA
1 GGCACTTAGTGTGCAAGATATTGAGTATGGCACTTAGTGTACGGAACATTGA
40537687 ATATGCAGCA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.27, C:0.12, G:0.31, T:0.30
Consensus pattern (56 bp):
GGCACTTAGTGTGCAAGATATTGAGTATGGCACTTAGTGTACGGAACATTGAGAAT
Found at i:40551070 original size:45 final size:45
Alignment explanation
Indices: 40550986--40551147 Score: 204
Period size: 45 Copynumber: 3.6 Consensus size: 45
40550976 TTGGCATTTC
* * *
40550986 GCCTGCTAGGATCGAA-GCCCG-ATA-TCATTTCACCGGTATTATA
1 GCCTGCTAGGCTCAAAGGCCCGAATAGT-ATCTCACCGGTATTATA
* *
40551029 GCGTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCAGTATTATA
1 GCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGGTATTATA
* * * *
40551074 GCCTGTTAGGCTCAAACGCCCGAATAGTATCTCACCGGCATCATA
1 GCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGGTATTATA
*
40551119 GCCTGCTAGGCTCAAAGGCCCAAATAGTA
1 GCCTGCTAGGCTCAAAGGCCCGAATAGTA
40551148 CCGTACAATA
Statistics
Matches: 102, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
43 13 0.13
44 5 0.05
45 83 0.81
46 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (45 bp):
GCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGGTATTATA
Found at i:40555009 original size:27 final size:27
Alignment explanation
Indices: 40554947--40555027 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 27
40554937 AAGGGCGTTT
* * *
40554947 CAGTCATTTTACCAAATAGGGGGAAAA
1 CAGTCATTTTACCACATAAGGGAAAAA
* * * *
40554974 CTGTTATTTTTCCACATAAGGGCAAAA
1 CAGTCATTTTACCACATAAGGGAAAAA
* *
40555001 CAGTCATTTCACCTCATAAGGGAAAAA
1 CAGTCATTTTACCACATAAGGGAAAAA
40555028 TAGACATTCT
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (27 bp):
CAGTCATTTTACCACATAAGGGAAAAA
Found at i:40565028 original size:16 final size:15
Alignment explanation
Indices: 40565007--40565040 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
40564997 TTAAGTCACA
*
40565007 AAATTTTCACAAATAT
1 AAATTTACACAAA-AT
40565023 AAATTTACACAAAAT
1 AAATTTACACAAAAT
40565038 AAA
1 AAA
40565041 CACATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATTTACACAAAAT
Found at i:40568503 original size:28 final size:27
Alignment explanation
Indices: 40568440--40568591 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
40568430 ATATTAAGTC
* * *
40568440 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
40568467 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
40568495 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
40568522 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
40568550 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
40568577 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40568592 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:40568524 original size:55 final size:55
Alignment explanation
Indices: 40568440--40568591 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
40568430 ATATTAAGTC
* * *
40568440 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
40568495 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
40568550 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
40568592 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:40572604 original size:28 final size:26
Alignment explanation
Indices: 40572548--40572605 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
40572538 AAAATTATAT
* *
40572548 TTAATAATTTATTTTAAAATATTTCA
1 TTAATAATTTATTTTAAAATAATTAA
*
40572574 TTAATAATTTAGGTTTTAAATTAATTAA
1 TTAATAATTTA--TTTTAAAATAATTAA
40572602 TTAA
1 TTAA
40572606 ATTAGATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 11 0.41
28 16 0.59
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (26 bp):
TTAATAATTTATTTTAAAATAATTAA
Found at i:40579470 original size:26 final size:26
Alignment explanation
Indices: 40579416--40579498 Score: 87
Period size: 26 Copynumber: 3.2 Consensus size: 26
40579406 GGTTGTTAAG
* * * *
40579416 ACCCCGATTTGTATAATTATCAAAAT
1 ACCCTGATTTGTAAAATTACCGAAAT
*
40579442 ACCCTGATTTGTAAAATTACCGAATT
1 ACCCTGATTTGTAAAATTACCGAAAT
*
40579468 ACCCTTG-TAGTGTAAAATTACCGAAAT
1 ACCC-TGAT-TTGTAAAATTACCGAAAT
40579495 ACCC
1 ACCC
40579499 CAATAGGGTA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
26 26 0.54
27 22 0.46
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (26 bp):
ACCCTGATTTGTAAAATTACCGAAAT
Found at i:40579509 original size:27 final size:27
Alignment explanation
Indices: 40579452--40579512 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
40579442 ACCCTGATTT
* *** *
40579452 GTAAAATTACCGAATTACCCTTGTAGT
1 GTAAAATTACCGAAATACCCCAATAGG
40579479 GTAAAATTACCGAAATACCCCAATAGG
1 GTAAAATTACCGAAATACCCCAATAGG
40579506 GTAAAAT
1 GTAAAAT
40579513 GACTATTTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (27 bp):
GTAAAATTACCGAAATACCCCAATAGG
Found at i:40580007 original size:44 final size:41
Alignment explanation
Indices: 40579932--40580094 Score: 137
Period size: 43 Copynumber: 3.8 Consensus size: 41
40579922 CCAATATGTG
* * *
40579932 ATTTCATGTAAGACCAAGTCAAGGACGTTGGCATCGATTTGA
1 ATTTCGTGTAAGACCATGTCTAGGACGTTGGCATCGATTT-A
* *
40579974 TATTTACGTGTAAGACCATGTCTTGGACATTGGCATCGTATTTA
1 -ATTT-CGTGTAAGACCATGTCTAGGACGTTGGCATCG-ATTTA
* * * * *
40580018 ATTTCGTATAAGACCCTGTCTGGGACGGTGGCATCGATATTTG
1 ATTTCGTGTAAGACCATGTCTAGGACGTTGGCATCG--ATTTA
* ** * *
40580061 ATTACAAGTAAGACCAAGTCTAGGAGGTTGGCAT
1 ATTTCGTGTAAGACCATGTCTAGGACGTTGGCAT
40580095 TGTACAAGCT
Statistics
Matches: 97, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
42 27 0.28
43 38 0.39
44 28 0.29
45 4 0.04
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (41 bp):
ATTTCGTGTAAGACCATGTCTAGGACGTTGGCATCGATTTA
Found at i:40580038 original size:42 final size:45
Alignment explanation
Indices: 40579940--40580062 Score: 137
Period size: 42 Copynumber: 2.8 Consensus size: 45
40579930 TGATTTCATG
* ** *
40579940 TAAGACCAAGTCAAGGACGTTGGCATCG-ATTTGATATTTACGTG
1 TAAGACCATGTCTGGGACGTTGGCATCGTATTTGATATTTACGTA
* *
40579984 TAAGACCATGTCTTGGACATTGGCATCGTATTT-A-ATTT-CGTA
1 TAAGACCATGTCTGGGACGTTGGCATCGTATTTGATATTTACGTA
* *
40580026 TAAGACCCTGTCTGGGACGGTGGCATCGATATTTGAT
1 TAAGACCATGTCTGGGACGTTGGCATCG-TATTTGAT
40580063 TACAAGTAAG
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
42 27 0.41
43 9 0.14
44 26 0.39
45 4 0.06
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (45 bp):
TAAGACCATGTCTGGGACGTTGGCATCGTATTTGATATTTACGTA
Found at i:40580074 original size:43 final size:43
Alignment explanation
Indices: 40579983--40580081 Score: 103
Period size: 42 Copynumber: 2.3 Consensus size: 43
40579973 ATATTTACGT
* * * *
40579983 GTAAGACCATGTCTTGGACATTGGCATCGTATTTAATTTCGTA
1 GTAAGACCATGTCTGGGACAGTGGCATCGTATTTAATTACGAA
* * *
40580026 -TAAGACCCTGTCTGGGACGGTGGCATCGATATTTGATTAC-AA
1 GTAAGACCATGTCTGGGACAGTGGCATCG-TATTTAATTACGAA
*
40580068 GTAAGACCAAGTCT
1 GTAAGACCATGTCT
40580082 AGGAGGTTGG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
42 25 0.56
43 20 0.44
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (43 bp):
GTAAGACCATGTCTGGGACAGTGGCATCGTATTTAATTACGAA
Found at i:40581004 original size:26 final size:25
Alignment explanation
Indices: 40580947--40581005 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
40580937 GCTTACGAAT
40580947 TGGCATG-ATTTGGTATAGATTATA
1 TGGCATGAATTTGGTATAGATTATA
*
40580971 -AGCATGAATTTGGTTGATA-ATTATA
1 TGGCATGAATTTGG-T-ATAGATTATA
40580996 TGGCATGAAT
1 TGGCATGAAT
40581006 GGTGTATGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 5 0.17
24 6 0.21
25 7 0.24
26 11 0.38
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (25 bp):
TGGCATGAATTTGGTATAGATTATA
Found at i:40585160 original size:33 final size:33
Alignment explanation
Indices: 40585117--40585179 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
40585107 TACAGTAATG
* * *
40585117 GTCTGGGCCTAAGCCCTATTCATTAACAGTACA
1 GTCTAGGCCTAAGCCCTATGCAGTAACAGTACA
40585150 GTCTAGGCCTAAGCCCTATGCAGTAACAGT
1 GTCTAGGCCTAAGCCCTATGCAGTAACAGT
40585180 GTGGGCCTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (33 bp):
GTCTAGGCCTAAGCCCTATGCAGTAACAGTACA
Found at i:40590189 original size:48 final size:47
Alignment explanation
Indices: 40590111--40590535 Score: 317
Period size: 48 Copynumber: 8.9 Consensus size: 47
40590101 GGTAAGATGC
* * * * *
40590111 CGATGACATGTCCCAGACAAGGTCTTACACTGGCTTTCATATATCGGTG
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGC--TCACATATCGGTG
* *
40590160 CGATGCCATGTTCCAAACAT-GTCTTACACTAGC-C-CATAAGTCAAGG-C
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACAT-A-TC--GGTG
* * * **
40590207 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAATG
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCGGTG
*
40590254 CCGATGCCATAGT-CAAAACATGGTCTTACACTAGCTCACATATCAAGGT-
1 -CGATGCCAT-GTCCCAAACATGGTCTTACACTAGCTCACATATC--GGTG
* * * ***
40590303 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTTAATG
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCGGTG
* * * * * *
40590350 TCGATTCCATGTTCTAAACATGGCCTTACATTGGCTCACATATCGAG-G
1 -CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCG-GTG
* * * **
40590398 CCGATGCCATGTCCCATACATGGTCTTACACTAGCTCTCATCTCAATG
1 -CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCGGTG
* * * *
40590446 CCAATGTCATGACCCAAACATGGTCTTACACTGGCTCACATATCGAG-G
1 -CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCG-GTG
* * *
40590494 CTGATGCCATGTCCCAGACATGGTCTTACACTACCTCCCATA
1 C-GATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATA
40590536 ACCCTAGTAT
Statistics
Matches: 291, Mismatches: 66, Indels: 39
0.73 0.17 0.10
Matches are distributed among these distances:
44 2 0.01
45 2 0.01
46 3 0.01
47 21 0.07
48 240 0.82
49 19 0.07
50 4 0.01
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.27
Consensus pattern (47 bp):
CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCGGTG
Found at i:40590280 original size:96 final size:96
Alignment explanation
Indices: 40590109--40590526 Score: 531
Period size: 96 Copynumber: 4.4 Consensus size: 96
40590099 AGGGTAAGAT
* * * * * **
40590109 GCCGATGACATGTCCCAGACAAGGTCTTACACTGGCTTTCATATATCGGTG-CGATGCCATGTTC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTC--ATCTCAATGCCGATGCCATGTTC
40590173 CAAACAT-GTCTTACACTAGC-C-CATAAGTCAAG
64 CAAACATGGTCTTACACTAGCTCACAT-A-TCAAG
*
40590205 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAATGCCGATGCCATAG-TCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAATGCCGATGCCAT-GTTCC
40590269 AAACATGGTCTTACACTAGCTCACATATCAAG
65 AAACATGGTCTTACACTAGCTCACATATCAAG
* * * * *
40590301 GTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTTAATGTCGATTCCATGTTCTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAATGCCGATGCCATGTTCCA
* * * *
40590366 AACATGGCCTTACATTGGCTCACATATCGAG
66 AACATGGTCTTACACTAGCTCACATATCAAG
* * * **
40590397 GCCGATGCCATGTCCCATACATGGTCTTACACTAGCTCTCATCTCAATGCCAATGTCATGACCCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAATGCCGATGCCATGTTCCA
* *
40590462 AACATGGTCTTACACTGGCTCACATATCGAG
66 AACATGGTCTTACACTAGCTCACATATCAAG
*
40590493 GCTGATGCCATGTCCCAGACATGGTCTTACACTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTA
40590527 CCTCCCATAA
Statistics
Matches: 285, Mismatches: 31, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
94 6 0.02
95 18 0.06
96 256 0.90
97 2 0.01
98 3 0.01
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (96 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAATGCCGATGCCATGTTCCA
AACATGGTCTTACACTAGCTCACATATCAAG
Found at i:40607858 original size:55 final size:55
Alignment explanation
Indices: 40607797--40607973 Score: 237
Period size: 55 Copynumber: 3.2 Consensus size: 55
40607787 ATATTAAGTC
* * *
40607797 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* * *
40607852 CGCACACTTAGTGCTACATAGTCAACTCGCACACTCAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * * *
40607907 CGCACACTTAGTGCTACATATTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAA-TCAAACT
40607963 CGCACACTTAG
1 CGCACACTTAG
40607974 CGCCAATCTC
Statistics
Matches: 107, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
55 91 0.85
56 16 0.15
ACGTcount: A:0.31, C:0.30, G:0.13, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:40607861 original size:28 final size:27
Alignment explanation
Indices: 40607797--40607948 Score: 223
Period size: 27 Copynumber: 5.6 Consensus size: 27
40607787 ATATTAAGTC
* *
40607797 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
40607824 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
40607852 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
40607879 CGCACACTCAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
40607907 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
40607934 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40607949 GCACAATTTA
Statistics
Matches: 116, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
27 65 0.56
28 51 0.44
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:40611062 original size:48 final size:48
Alignment explanation
Indices: 40610946--40611373 Score: 320
Period size: 48 Copynumber: 8.9 Consensus size: 48
40610936 AGGGTAAGAT
* * * * *
40610946 GTCGATGCCATGTCCTAGACATGGTCTTACACTGGCTTTTATATATC--G
1 GTCGATGCCATGTCCCAAACATGGTCTTACACTAGC-CTCATA-ATCAAG
* * *
40610994 GTGCCAATGCCATGTTCCAAACATGGTCTTA-ACCTAGCCT-ATAAGTCGAG
1 GT--CGATGCCATGTCCCAAACATGGTCTTACA-CTAGCCTCATAA-TCAAG
* *
40611044 GTCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCAT-CTCAAT
1 GTCGATGCCATGTCCCAAACATGGTCTTACACTAGC-CTCATAATCAAG
* * *
40611092 GTCGATGCCATGTTCCAAACATGGTCTTACACTAG-CTCACATATCCAG
1 GTCGATGCCATGTCCCAAACATGGTCTTACACTAGCCTCATA-ATCAAG
* * * *
40611140 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-CTCAAT
1 GTCGATGCCATGTCCCAAACATGGTCTTACACTAGC-CTCATAATCAAG
* * * *
40611188 GCCGATGTCATGTTCCAAACATGGTCTTACACTAG-CTCACATATCAAG
1 GTCGATGCCATGTCCCAAACATGGTCTTACACTAGCCTCATA-ATCAAG
* * * * * * *
40611236 GCCGATGCAATGTCCCAGACATGGTCTTATATTAGCTCTCAT-CTCAAT
1 GTCGATGCCATGTCCCAAACATGGTCTTACACTAGC-CTCATAATCAAG
* * * * *
40611284 GTTGATGCCATGTTCCAAACATGGTCTTACACT-GGCTCACATATCGAG
1 GTCGATGCCATGTCCCAAACATGGTCTTACACTAGCCTCATA-ATCAAG
* ** *
40611332 G-CTGATACCATGTTTCAGACATGGTCTTACACTAGCTCTCAT
1 GTC-GATGCCATGTCCCAAACATGGTCTTACACTAGC-CTCAT
40611374 TGTAACACCC
Statistics
Matches: 302, Mismatches: 56, Indels: 42
0.75 0.14 0.10
Matches are distributed among these distances:
46 12 0.04
47 2 0.01
48 238 0.79
49 6 0.02
50 44 0.15
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (48 bp):
GTCGATGCCATGTCCCAAACATGGTCTTACACTAGCCTCATAATCAAG
Done.