Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009317.1 Hibiscus syriacus cultivar Beakdansim tig00113073_pilon, whole genome shotgun sequence
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: 334282
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
File 1 of 2
Found at i:1122 original size:50 final size:51
Alignment explanation
Indices: 1005--1443 Score: 576
Period size: 50 Copynumber: 8.6 Consensus size: 51
995 GCAATTATTT
1005 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* *
1056 GTTGAAGATTGAGTCCTATGCTCTCTGAATGAATAGGGAGC-GACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* *
1106 GTTGAAGATTGAGTCCTATACTCTCTGAAAGAATA-GG-GCGGACAAGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1155 GTTGAAGATTG-GTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
1205 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATA-GGAGCGGACCAAG-TC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGA-CAAGTTC
1255 GTTGAAGATTGAGTCCTATACTCTCTG-AGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * **
1305 GTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTT-
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * * * *
1359 TTATGAAGATTGCTCGAGTTCTATACTCTCT---GGAATAGGGAGCGAACATGTTT
1 GT-TGAAGA-T--T-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
1412 GTTAAAGATTGAGTCCTATACTCTCTGAAGGA
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGA
1444 GTAGAAAGCG
Statistics
Matches: 347, Mismatches: 22, Indels: 38
0.85 0.05 0.09
Matches are distributed among these distances:
48 39 0.11
49 34 0.10
50 119 0.34
51 69 0.20
52 22 0.06
53 4 0.01
54 17 0.05
55 43 0.12
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.28
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:1210 original size:99 final size:100
Alignment explanation
Indices: 1005--1443 Score: 577
Period size: 99 Copynumber: 4.3 Consensus size: 100
995 GCAATTATTT
1005 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATA-GGAGCGGACAAGTTCGTTGAAGATTGAGT
* *
1070 CCTATGCTCTCTGAATGAATAGGGAGC-GACAAGTTC
65 CCTATACTCTCTG-AGGAATAGGGAGCGGACAAGTTC
* *
1106 GTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGG-GCGGACAAGTTTGTTGAAGATTG-GTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGAGCGGACAAGTTCGTTGAAGATTGAGTC
1169 CTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
66 CTATACTCTCTG-AGGAATAGGGAGCGGACAAGTTC
*
1205 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGAGCGGACCAAG-TCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGAGCGGA-CAAGTTCGTTGAAGATTGAGT
1269 CCTATACTCTCTGAGGAATAGGGAGCGGACAAGTTC
65 CCTATACTCTCTGAGGAATAGGGAGCGGACAAGTTC
* ** *
1305 GTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTT-TTATGAAGAT
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAG-GAGCGGACAAGTTCGT-TGAAGA-
* * * *
1369 TGCTCGAGTTCTATACTCTCT--GGAATAGGGAGCGAACATGTTT
59 T--T-GAGTCCTATACTCTCTGAGGAATAGGGAGCGGACAAGTTC
*
1412 GTTAAAGATTGAGTCCTATACTCTCTGAAGGA
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGA
1444 GTAGAAAGCG
Statistics
Matches: 306, Mismatches: 17, Indels: 28
0.87 0.05 0.08
Matches are distributed among these distances:
98 27 0.09
99 67 0.22
100 50 0.16
101 53 0.17
103 23 0.08
104 29 0.09
105 14 0.05
106 1 0.00
107 26 0.08
108 1 0.00
109 15 0.05
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.28
Consensus pattern (100 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGAGCGGACAAGTTCGTTGAAGATTGAGTC
CTATACTCTCTGAGGAATAGGGAGCGGACAAGTTC
Found at i:1490 original size:56 final size:55
Alignment explanation
Indices: 1307--1557 Score: 179
Period size: 55 Copynumber: 4.7 Consensus size: 55
1297 ACAAGTTCGT
* * * * *
1307 TGAAGATTGTTCGAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTA
1 TGAAGATTGTTCAAGTCT-TATACTCTCTGAAGGAATAGAAAGCAGACACATTTTA
* * ** *
1362 TGAAGATTGCTCGAGT-TCTATACTCTCT---GGAATAGGGAGC-GA-ACATGTTTGT
1 TGAAGATTGTTCAAGTCT-TATACTCTCTGAAGGAATAGAAAGCAGACACAT-TTT-A
* * * * *
1414 TAAAGATTG----AGTCCTATACTCTCTGAAGGAGTAGAAAGCGGAC-CTGTTTTA
1 TGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATAGAAAGCAGACAC-ATTTTA
* *
1465 TTGAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTTA
1 -TGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATAGAAAGCAGACACATTTTA
*
1521 TGAAGATTGTTCGAGTCTTATACT-TCCTGAA-GAATAG
1 TGAAGATTGTTCAAGTCTTATACTCT-CTGAAGGAATAG
1558 GGAACAGACT
Statistics
Matches: 160, Mismatches: 20, Indels: 33
0.75 0.09 0.15
Matches are distributed among these distances:
48 13 0.08
50 2 0.01
51 14 0.09
52 33 0.21
53 1 0.01
54 7 0.04
55 55 0.34
56 34 0.21
57 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.32
Consensus pattern (55 bp):
TGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATAGAAAGCAGACACATTTTA
Found at i:1496 original size:159 final size:152
Alignment explanation
Indices: 1002--1513 Score: 582
Period size: 149 Copynumber: 3.3 Consensus size: 152
992 GAAGCAATTA
*
1002 TTTGTTGAAGATTG---AGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA
1 TTTGTTGAAGATTGTTCAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACAAGTTCGTTGAAGA
*
1064 TTGAGTCCTATGCTCTCTGAATGAATAGGGAGCG-ACAAGTTCGTTGAAGATTGAGTCCTATACT
66 TTGAGTCCTATACTCTCTG-A-GAATAGGGAGCGAACAAGTTCGTTGAAGATTGAGTCCTATACT
* *
1128 CTCTGAAAGAATAGGGCGGACAAG
129 CTCTGAAGGAATAGAGCGGACAAG
*
1152 TTTGTTGAAGATTG----GTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA
1 TTTGTTGAAGATTGTTCAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACAAGTTCGTTGAAGA
*
1213 TTGAGTCCTATACTCTCTGAATGAATA-GGAGCGGACCAAG-TCGTTGAAGATTGAGTCCTATAC
66 TTGAGTCCTATACTCTCTG-A-GAATAGGGAGC-GAACAAGTTCGTTGAAGATTGAGTCCTATAC
1276 TCTCTG-AGGAATAGGGAGCGGACAAG
128 TCTCTGAAGGAATA--GAGCGGACAAG
* * ** *
1302 TTCGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTT-TTATGAA
1 TTTGTTGAAGATTGTTC-AGTCCTATACTCTCTGAAGGAATAGAGAGCGGACAAGTTCGT-TGAA
* * * *
1366 GATTGCTCGAGTTCTATACTCTCTG-GAATAGGGAGCGAACATGTTTGTTAAAGATTGAGTCCTA
64 GA-T--T-GAGTCCTATACTCTCTGAGAATAGGGAGCGAACAAGTTCGTTGAAGATTGAGTCCTA
* **
1430 TACTCTCTGAAGGAGTAGAAAGCGGACCTG
125 TACTCTCTGAAGGAATAG--AGCGGACAAG
* * * *
1460 TTTTATTGAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACA
1 -TTTGTTGAAGATTGTTC-AGTCCTATACTCTCTGAAGGAATAGAGAGCGGACA
1514 CATTTTATGA
Statistics
Matches: 316, Mismatches: 26, Indels: 31
0.85 0.07 0.08
Matches are distributed among these distances:
148 11 0.03
149 103 0.33
150 41 0.13
154 1 0.00
155 40 0.13
156 12 0.04
157 32 0.10
158 15 0.05
159 61 0.19
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (152 bp):
TTTGTTGAAGATTGTTCAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACAAGTTCGTTGAAGA
TTGAGTCCTATACTCTCTGAGAATAGGGAGCGAACAAGTTCGTTGAAGATTGAGTCCTATACTCT
CTGAAGGAATAGAGCGGACAAG
Found at i:6813 original size:3 final size:3
Alignment explanation
Indices: 6805--6830 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6795 ACAGTTAACA
6805 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
6831 ACCAACAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:15636 original size:31 final size:31
Alignment explanation
Indices: 15598--15720 Score: 212
Period size: 31 Copynumber: 4.0 Consensus size: 31
15588 CCCGAAGGAC
* *
15598 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
15629 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
15660 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
15691 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
15721 CCCTCGACCC
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:16425 original size:21 final size:21
Alignment explanation
Indices: 16395--16439 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
16385 ATTCTGTCGT
* *
16395 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
16416 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
16437 TTG
1 TTG
16440 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:20265 original size:31 final size:31
Alignment explanation
Indices: 20227--20380 Score: 274
Period size: 31 Copynumber: 5.0 Consensus size: 31
20217 CCCGAAGGAC
* *
20227 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
20258 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
20289 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
20320 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
20351 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
20381 CCCTCGACCC
Statistics
Matches: 120, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
31 119 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:21094 original size:21 final size:20
Alignment explanation
Indices: 21051--21090 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
21041 ATTCTGTCGT
* *
21051 TTGAAGGGGTATCGGTTCCC
1 TTGAAGGGGTACCGATTCCC
*
21071 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
21091 CTTGCCCAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (20 bp):
TTGAAGGGGTACCGATTCCC
Found at i:26837 original size:63 final size:62
Alignment explanation
Indices: 26729--26863 Score: 198
Period size: 63 Copynumber: 2.1 Consensus size: 62
26719 ATATTGAACC
* *
26729 TAAATATTATATAATTTGTTTGAATTCACATTTATTTTGGGGTAAATTACGTATTTAATATA
1 TAAATATCATATAATTTGTTTGAATTCACATTTATTTTGGAGTAAATTACGTATTTAATATA
* ** *
26791 TAAACTATCATATAATTTGTTTGAATTCACATTTATTTTTGAGTAAATTATTTATTTAATATT
1 TAAA-TATCATATAATTTGTTTGAATTCACATTTATTTTGGAGTAAATTACGTATTTAATATA
26854 TAAATTATCA
1 TAAA-TATCA
26864 GTTTTACTAA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
62 4 0.06
63 61 0.94
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.50
Consensus pattern (62 bp):
TAAATATCATATAATTTGTTTGAATTCACATTTATTTTGGAGTAAATTACGTATTTAATATA
Found at i:27256 original size:29 final size:28
Alignment explanation
Indices: 27188--27267 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
27178 TTTAAACAAG
* *
27188 TATTAAAATAAAAAAATTAAATTTTAAA
1 TATTAAAATAAACAAATTAAACTTTAAA
**
27216 TA-TAATTTTAAACAAATTATAACTTTAAA
1 TATTAA-AATAAACAAATTA-AACTTTAAA
27245 TATTAAAATAAATCAAAATTAAA
1 TATTAAAATAAA-C-AAATTAAA
27268 TAATTTTCGT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
27 3 0.07
28 12 0.29
29 14 0.34
30 6 0.15
31 6 0.15
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (28 bp):
TATTAAAATAAACAAATTAAACTTTAAA
Found at i:28106 original size:24 final size:23
Alignment explanation
Indices: 28064--28111 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
28054 ATATATTTTA
28064 TTTTTATCTCAACTATAAAAATAT
1 TTTTTATCTCAACTAT-AAAATAT
* * *
28088 TTTTTATCTTAATTTTAAAATAT
1 TTTTTATCTCAACTATAAAATAT
28111 T
1 T
28112 ATAAGAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTTATCTCAACTATAAAATAT
Found at i:30120 original size:17 final size:17
Alignment explanation
Indices: 30078--30122 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
30068 AAAAAAATCT
*
30078 TAAAACTT-AACTCAAT
1 TAAAACTTAAACTCAAC
*
30094 TGAAACCTTAAACTCAAC
1 T-AAAACTTAAACTCAAC
30112 TAAAACTTAAA
1 TAAAACTTAAA
30123 TACATAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 1 0.04
17 15 0.62
18 8 0.33
ACGTcount: A:0.51, C:0.20, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAAACTTAAACTCAAC
Found at i:30193 original size:65 final size:66
Alignment explanation
Indices: 30089--30224 Score: 190
Period size: 66 Copynumber: 2.1 Consensus size: 66
30079 AAAACTTAAC
*
30089 TCAATTGAAACCTTAAACTCAACTAAAACTTAAATACAT-AAAACTTTATACTATATTTT-AAAA
1 TCAAATGAAACCTTAAACTCAACTAAAACTT-AATACATAAAAACTTTATACTATATTTTAAAAA
30152 AA
65 AA
*
30154 TCAAATGAAACCTTAAAACTCAAACCTAAAACTT-A-ACATAAAAACTTTATATTATATTTTAAA
1 TCAAATGAAACCTT-AAACTC-AA-CTAAAACTTAATACATAAAAACTTTATACTATATTTTAAA
30217 AAAA
63 AAAA
30221 TCAA
1 TCAA
30225 CACATAAATT
Statistics
Matches: 64, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
65 17 0.27
66 26 0.41
67 12 0.19
68 9 0.14
ACGTcount: A:0.52, C:0.15, G:0.01, T:0.31
Consensus pattern (66 bp):
TCAAATGAAACCTTAAACTCAACTAAAACTTAATACATAAAAACTTTATACTATATTTTAAAAAA
A
Found at i:31752 original size:12 final size:12
Alignment explanation
Indices: 31732--31763 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
31722 ATTAGATAAA
*
31732 TAAAGACTTATT
1 TAAAAACTTATT
31744 TAAAAACTTATT
1 TAAAAACTTATT
31756 TAAAAACT
1 TAAAAACT
31764 ATATATTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (12 bp):
TAAAAACTTATT
Found at i:31976 original size:2 final size:2
Alignment explanation
Indices: 31969--32020 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
31959 ACAATAGGCA
31969 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32011 AT AT AT AT AT
1 AT AT AT AT AT
32021 TGGTAAAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39702 original size:20 final size:20
Alignment explanation
Indices: 39677--39736 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
39667 AGCAACAGAA
*
39677 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
39697 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
39717 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
39737 AACTAATAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:39769 original size:52 final size:51
Alignment explanation
Indices: 39698--39841 Score: 243
Period size: 52 Copynumber: 2.8 Consensus size: 51
39688 CTATCTAATT
*
39698 AAAAATGATCCTATCTAATTAAAAATGATCCTATCTAATAACTAATAGAAA
1 AAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAGAAA
39749 AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAGAATA
1 AAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAGAA-A
* *
39802 AAAATTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATA
39842 TTTAATTTAG
Statistics
Matches: 88, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 5 0.06
52 78 0.89
53 5 0.06
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.33
Consensus pattern (51 bp):
AAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAGAAA
Found at i:39778 original size:20 final size:21
Alignment explanation
Indices: 39749--39788 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
39739 CTAATAGAAA
*
39749 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
39770 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
39789 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:39830 original size:20 final size:20
Alignment explanation
Indices: 39802--39840 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39792 TAATAGAATA
* *
39802 AAAATTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
39822 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
39841 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:44360 original size:20 final size:20
Alignment explanation
Indices: 44335--44374 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
44325 AGCAACAAAA
*
44335 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
44355 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
44375 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:44466 original size:20 final size:20
Alignment explanation
Indices: 44441--44479 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
44431 TAATAGAATA
*
44441 AAAACTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
44461 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
44480 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:44472 original size:52 final size:52
Alignment explanation
Indices: 44333--44480 Score: 262
Period size: 53 Copynumber: 2.8 Consensus size: 52
44323 TTAGCAACAA
44333 AATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
*
44384 AATAAAAAACTGATTCTATCTAATTAAAAATTATCCTATCTAATAACTAATAG
1 AAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
*
44437 AATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
44481 TTTAATTTAG
Statistics
Matches: 92, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 3 0.03
52 44 0.48
53 45 0.49
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.34
Consensus pattern (52 bp):
AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
Found at i:51534 original size:114 final size:113
Alignment explanation
Indices: 51330--51550 Score: 329
Period size: 114 Copynumber: 1.9 Consensus size: 113
51320 TCCGTAAGCT
* * * *
51330 GCCTTACCTTCCATCCGTACCAAGTCTTACTAGCTGCTGGTGCTGCGGATGCTGTGTTTCTATCT
1 GCCTAACCTTCCATCCCTACCAAGTCTTACTAGCTGCAGGTGCTGCCGATGCTGTGTTTCTATCT
*
51395 ATGCTGATGACAACTCTCATACAAGATGAATGTTTGAATTCTTTCATG
66 ATGCCGATGACAACTCTCATACAAGATGAATGTTTGAATTCTTTCATG
* *
51443 GCCTAACCTTCCATCCCTACCAAGTCTTTCTAGCTGTCA-GTGGC-GCCGATGCCTGTGTTTCTG
1 GCCTAACCTTCCATCCCTACCAAGTCTTACTAGCTG-CAGGT-GCTGCCGATG-CTGTGTTTCTA
*
51506 TCTATGCCGATGACAACTCTCATGCAAGATGAATGTTTGAATTCT
63 TCTATGCCGATGACAACTCTCATACAAGATGAATGTTTGAATTCT
51551 GTCACGATTT
Statistics
Matches: 97, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
113 41 0.42
114 56 0.58
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (113 bp):
GCCTAACCTTCCATCCCTACCAAGTCTTACTAGCTGCAGGTGCTGCCGATGCTGTGTTTCTATCT
ATGCCGATGACAACTCTCATACAAGATGAATGTTTGAATTCTTTCATG
Found at i:56456 original size:18 final size:20
Alignment explanation
Indices: 56433--56469 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
56423 ATTTTTATCA
56433 AAAAATT-A-TTTAAATATT
1 AAAAATTAATTTTAAATATT
56451 AAAAATTAATTTTAAATAT
1 AAAAATTAATTTTAAATAT
56470 AGTTTAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 1 0.06
20 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAAAATTAATTTTAAATATT
Found at i:58504 original size:23 final size:23
Alignment explanation
Indices: 58468--58551 Score: 59
Period size: 23 Copynumber: 3.7 Consensus size: 23
58458 AAATAATAAT
* *
58468 ATATAACATAATAATTATAATAC
1 ATATAATATTATAATTATAATAC
58491 ATATAATATTATAA-TATATATA-
1 ATATAATATTATAATTATA-ATAC
* * *
58513 GTAT-ATAGTATACTATATAAATAC
1 ATATAATATTATAAT-TAT-AATAC
58537 TATATAATA-TATAAT
1 -ATATAATATTATAAT
58552 ATTAAATAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
21 7 0.15
22 7 0.15
23 21 0.45
24 1 0.02
25 8 0.17
26 3 0.06
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (23 bp):
ATATAATATTATAATTATAATAC
Found at i:58511 original size:2 final size:2
Alignment explanation
Indices: 58491--58596 Score: 68
Period size: 2 Copynumber: 54.5 Consensus size: 2
58481 ATTATAATAC
58491 AT AT A- AT AT -T AT A- AT AT AT AT AGT AT AT AGT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT A-T AT AT
* *
58531 AA AT ACT AT AT A- AT AT AT A- AT AT -T AA AT A- AT AT AT AT A-
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
58569 AT AT AT AC ACT AT AT A- AT AT ACT AT AT A
1 AT AT AT AT A-T AT AT AT AT AT A-T AT AT A
58597 AAATAATAGA
Statistics
Matches: 83, Mismatches: 6, Indels: 30
0.70 0.05 0.25
Matches are distributed among these distances:
1 9 0.11
2 63 0.76
3 11 0.13
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:58524 original size:12 final size:11
Alignment explanation
Indices: 58504--58596 Score: 70
Period size: 11 Copynumber: 8.5 Consensus size: 11
58494 TAATATTATA
*
58504 ATATATATAGT
1 ATATATATACT
58515 ATATAGTATACT
1 ATATA-TATACT
*
58527 ATATAAATACT
1 ATATATATACT
58538 ATATA-ATA-T
1 ATATATATACT
*
58547 ATA-ATATTA-A
1 ATATATA-TACT
58557 ATAATATATA-T
1 AT-ATATATACT
*
58568 AATATATACACT
1 -ATATATATACT
58580 ATATAATATACT
1 ATAT-ATATACT
58592 ATATA
1 ATATA
58597 AAATAATAGA
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
8 1 0.01
9 5 0.07
10 7 0.10
11 29 0.43
12 26 0.38
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (11 bp):
ATATATATACT
Found at i:58531 original size:7 final size:6
Alignment explanation
Indices: 58491--58596 Score: 68
Period size: 5 Copynumber: 18.2 Consensus size: 6
58481 ATTATAATAC
*
58491 ATATA- ATAT-T ATA-AT ATATAT AGTATAT AGTATACT ATATAA ATACTAT
1 ATATAT ATATAT ATATAT ATATAT A-TATAT A-TATA-T ATATAT ATA-TAT
* *
58540 ATA-AT ATATA- ATAT-T AAATA- ATATAT ATA-AT ATATAC ACTATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT A-TATAT
58584 A-ATAT ACTATAT A
1 ATATAT A-TATAT A
58597 AAATAATAGA
Statistics
Matches: 81, Mismatches: 6, Indels: 26
0.72 0.05 0.23
Matches are distributed among these distances:
5 37 0.46
6 12 0.15
7 30 0.37
8 2 0.02
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (6 bp):
ATATAT
Found at i:58553 original size:54 final size:53
Alignment explanation
Indices: 58463--58614 Score: 160
Period size: 54 Copynumber: 2.9 Consensus size: 53
58453 AATAAAAATA
*
58463 ATAATATATA-AC-ATAATAAT-TA-TA-ATACATATAATATTATAATATATAT
1 ATAATATATACACTAT-ATAATATACTATATAAATATAATATTATAATATATAT
*
58512 AGT-ATATAGTATACTATATAA-ATACTATATAATATATAATATTA-AATAATATAT
1 A-TAATATA-TACACTATATAATATACTATATAA-ATATAATATTATAAT-ATATAT
*
58566 ATAATATATACACTATATAATATACTATATAAA-ATAATAGATATAATAT
1 ATAATATATACACTATATAATATACTATATAAATATAATA-TTATAATAT
58615 GGTATAATAA
Statistics
Matches: 87, Mismatches: 3, Indels: 22
0.78 0.03 0.20
Matches are distributed among these distances:
49 6 0.07
50 3 0.03
51 8 0.09
52 10 0.11
53 23 0.26
54 37 0.43
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (53 bp):
ATAATATATACACTATATAATATACTATATAAATATAATATTATAATATATAT
Found at i:58582 original size:42 final size:42
Alignment explanation
Indices: 58460--58614 Score: 137
Period size: 42 Copynumber: 3.8 Consensus size: 42
58450 GTAAATAAAA
* * *
58460 ATAATA-ATATA-TAACATAATA-ATTATAATACATATAATATT
1 ATAATATATATATTAA-ATAATATACTATAATATATATACTA-T
* * *
58501 ATAATATATATAGTATATAGTATACTAT-ATA-A-ATACTAT
1 ATAATATATATATTAAATAATATACTATAATATATATACTAT
*
58540 ATAATATATAATATTAAATAATATA-TATAATATATACACTAT
1 ATAATATAT-ATATTAAATAATATACTATAATATATATACTAT
* *
58582 ATAATATACTATATAAAATAATAGA-TATAATAT
1 ATAATATA-TATATTAAATAATATACTATAATAT
58615 GGTATAATAA
Statistics
Matches: 96, Mismatches: 10, Indels: 15
0.79 0.08 0.12
Matches are distributed among these distances:
39 13 0.14
40 20 0.21
41 8 0.08
42 48 0.50
43 7 0.07
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (42 bp):
ATAATATATATATTAAATAATATACTATAATATATATACTAT
Found at i:58595 original size:28 final size:26
Alignment explanation
Indices: 58463--58597 Score: 108
Period size: 28 Copynumber: 5.2 Consensus size: 26
58453 AATAAAAATA
58463 ATAATATATAAC-ATAATAAT-TATA-
1 ATAATATATAACTAT-ATAATATATAT
*
58487 AT-ACATATAA-TATTATAATATATAT
1 ATAATATATAACTA-TATAATATATAT
58512 AGT-ATATAGTATACTATATAA-ATACTAT
1 A-TAATATA-TA-ACTATATAATATA-TAT
58540 ATAATATATAA-TAT-TAAATAATATAT
1 ATAATATATAACTATAT-AAT-ATATAT
58566 ATAATATATACACTATATAATATACTAT
1 ATAATATATA-ACTATATAATATA-TAT
58594 ATAA
1 ATAA
58598 AATAATAGAT
Statistics
Matches: 92, Mismatches: 2, Indels: 30
0.74 0.02 0.24
Matches are distributed among these distances:
23 13 0.14
24 8 0.09
25 6 0.07
26 19 0.21
27 15 0.16
28 28 0.30
29 3 0.03
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.40
Consensus pattern (26 bp):
ATAATATATAACTATATAATATATAT
Found at i:59687 original size:32 final size:32
Alignment explanation
Indices: 59646--59723 Score: 156
Period size: 32 Copynumber: 2.4 Consensus size: 32
59636 TTTTTTTTCC
59646 TGTTTTAATTATGAATATATATTTATAAGACA
1 TGTTTTAATTATGAATATATATTTATAAGACA
59678 TGTTTTAATTATGAATATATATTTATAAGACA
1 TGTTTTAATTATGAATATATATTTATAAGACA
59710 TGTTTTAATTATGA
1 TGTTTTAATTATGA
59724 TAATTTCACG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (32 bp):
TGTTTTAATTATGAATATATATTTATAAGACA
Found at i:59689 original size:18 final size:18
Alignment explanation
Indices: 59668--59721 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
59658 GAATATATAT
59668 TTATAAGACATGTTTTAA
1 TTATAAGACATGTTTTAA
* * *
59686 TTAT--GA-AT-ATATAT
1 TTATAAGACATGTTTTAA
59700 TTATAAGACATGTTTTAA
1 TTATAAGACATGTTTTAA
59718 TTAT
1 TTAT
59722 GATAATTTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 8
0.65 0.15 0.20
Matches are distributed among these distances:
14 7 0.27
15 2 0.08
16 4 0.15
17 2 0.08
18 11 0.42
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (18 bp):
TTATAAGACATGTTTTAA
Found at i:63505 original size:12 final size:12
Alignment explanation
Indices: 63488--63513 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
63478 TAGCTAAAGC
63488 ATACAAAAGTTG
1 ATACAAAAGTTG
63500 ATACAAAAGTTG
1 ATACAAAAGTTG
63512 AT
1 AT
63514 GTTCAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (12 bp):
ATACAAAAGTTG
Found at i:63745 original size:26 final size:25
Alignment explanation
Indices: 63695--63746 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
63685 ATTTAAGATG
63695 ATTTTTTTTATTGAAGATACTATTAT
1 ATTTTTTTTATTGAAGATAC-ATTAT
*
63721 ATTTTTTTATATTTAAGAATA-ATTAT
1 ATTTTTTT-TATTGAAG-ATACATTAT
63747 TATAATGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 13 0.57
27 7 0.30
28 3 0.13
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (25 bp):
ATTTTTTTTATTGAAGATACATTAT
Found at i:69132 original size:23 final size:23
Alignment explanation
Indices: 69101--69145 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
69091 CTGAATGATT
*
69101 CAGTACTGACTGATTCAGCAAAA
1 CAGTACTGAATGATTCAGCAAAA
*
69124 CAGTGCTGAATGATTCAGCAAA
1 CAGTACTGAATGATTCAGCAAA
69146 GAAGTACGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (23 bp):
CAGTACTGAATGATTCAGCAAAA
Found at i:69508 original size:19 final size:18
Alignment explanation
Indices: 69466--69508 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
69456 CGACCGTTAA
*
69466 TATTTTTTATTGTATTTT
1 TATTTTTTATTGTATCTT
*
69484 TCTTTTTATATTGTATCTT
1 TATTTTT-TATTGTATCTT
69503 TATTTT
1 TATTTT
69509 CTTTTATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (18 bp):
TATTTTTTATTGTATCTT
Found at i:73152 original size:17 final size:18
Alignment explanation
Indices: 73130--73170 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
73120 TGTTATAATT
* *
73130 ATAAAAGTTCAAA-AAGC
1 ATAAAAGTTAAAATAAAC
73147 ATAAAAGTTAAAATAAAC
1 ATAAAAGTTAAAATAAAC
73165 ATAAAA
1 ATAAAA
73171 TTACTACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.20
Consensus pattern (18 bp):
ATAAAAGTTAAAATAAAC
Found at i:73821 original size:20 final size:21
Alignment explanation
Indices: 73796--73835 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
73786 ATTTTATTGA
73796 TTGTGTCCA-CTTGAAATTTT
1 TTGTGTCCATCTTGAAATTTT
73816 TTGTGTCCATCTTGAAATTT
1 TTGTGTCCATCTTGAAATTT
73836 GGATTGTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.50
Consensus pattern (21 bp):
TTGTGTCCATCTTGAAATTTT
Found at i:77822 original size:237 final size:237
Alignment explanation
Indices: 77394--77872 Score: 645
Period size: 237 Copynumber: 2.0 Consensus size: 237
77384 AATAGAGATC
* **
77394 ACCATCGCAAGAGGTCAGATAAAGAGGGCTGCTATCGCAGAACTGAGTCAGACTCAGAAGATGAA
1 ACCATCGCAAGACGTCAGATAAAGAGGGCAACTATCGCAGAACTGAGTCAGACTCAGAAGATGAA
* * ** * * *
77459 TTGAAGGAAGCAGAAAGCCGAGAGAGGAGTTTCCACGGGAAGAAATATAGATATGAGGATCAAGA
66 TTGAAGGAAGCAGAAAGCCGAGAGAAGAATCGCCACAGGAAGAAATACAAATATGAGGATCAAGA
* * ** **
77524 TGATGTTAAGAGGAACCATGACAAATCTAAGCGTGATAAATATTCTTCTCAAGCTCCACGAAGTC
131 TGATATTAAAAGGAACCATGACAAATCTAAGCCAGATAAATATTCTTCTCAAGCTCCACGAAGGA
* * * *
77589 TTGATGCTGATAAAAATCATGAAAAAGGTGGACCAGCTTCTG
196 TTGAAGCAGATAAAAATCAAGAAAAAGATGGACCAGCTTCTG
* *
77631 ACCATCTCAAGACGTCAGATAAAGAGGGCAACTATCGCAGAATTGAGTCAGACTCAGAAGATGAA
1 ACCATCGCAAGACGTCAGATAAAGAGGGCAACTATCGCAGAACTGAGTCAGACTCAGAAGATGAA
* * * * * **
77696 TTGAAGGAAGCAGAGAGTCGAGAGAAGAATCGCCGCAGGCAGAAATACAAATATGATGATCGTGA
66 TTGAAGGAAGCAGAAAGCCGAGAGAAGAATCGCCACAGGAAGAAATACAAATATGAGGATCAAGA
* *
77761 TGATATTAAAAGGAACCATGATAAGTCTAAGCACAG-TAAATATTCTTCTCAAGCTCCACGAAGG
131 TGATATTAAAAGGAACCATGACAAATCTAAGC-CAGATAAATATTCTTCTCAAGCTCCACGAAGG
* *
77825 ATTGAAGCAGATAAAAATCAAGAGAAAGATGGACCATCTTCTG
195 ATTGAAGCAGATAAAAATCAAGAAAAAGATGGACCAGCTTCTG
77868 ACCAT
1 ACCAT
77873 AGAGACATTG
Statistics
Matches: 208, Mismatches: 33, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
237 207 1.00
238 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (237 bp):
ACCATCGCAAGACGTCAGATAAAGAGGGCAACTATCGCAGAACTGAGTCAGACTCAGAAGATGAA
TTGAAGGAAGCAGAAAGCCGAGAGAAGAATCGCCACAGGAAGAAATACAAATATGAGGATCAAGA
TGATATTAAAAGGAACCATGACAAATCTAAGCCAGATAAATATTCTTCTCAAGCTCCACGAAGGA
TTGAAGCAGATAAAAATCAAGAAAAAGATGGACCAGCTTCTG
Found at i:80187 original size:31 final size:33
Alignment explanation
Indices: 80120--80205 Score: 133
Period size: 32 Copynumber: 2.7 Consensus size: 33
80110 GTTCAGGTAT
80120 TAAAATGAAACAAAAAGTTAAC-ATCGTGATAC
1 TAAAATGAAACAAAAAGTTAACGATCGTGATAC
80152 TAAAATGAAACAAAAAGTTAACGA-CGTG-TAC
1 TAAAATGAAACAAAAAGTTAACGATCGTGATAC
* *
80183 TAAAATGAGACAAAAAGTAAACG
1 TAAAATGAAACAAAAAGTTAACG
80206 TTAGGTACCG
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
31 24 0.47
32 26 0.51
33 1 0.02
ACGTcount: A:0.55, C:0.12, G:0.15, T:0.19
Consensus pattern (33 bp):
TAAAATGAAACAAAAAGTTAACGATCGTGATAC
Found at i:85416 original size:15 final size:15
Alignment explanation
Indices: 85375--85416 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
85365 TTTGCTAGGC
*
85375 AGAAG-GAATGGAGA
1 AGAAGAGAATAGAGA
**
85389 AGAAGAGTCTAGAGA
1 AGAAGAGAATAGAGA
85404 AGAAGAGAATAGA
1 AGAAGAGAATAGA
85417 AAAATATTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.52, C:0.02, G:0.36, T:0.10
Consensus pattern (15 bp):
AGAAGAGAATAGAGA
Found at i:86728 original size:2 final size:2
Alignment explanation
Indices: 86721--86745 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
86711 ATAACACTAT
86721 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
86746 TATGTTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:91594 original size:18 final size:18
Alignment explanation
Indices: 91571--91609 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
91561 TTTAACAGTT
91571 CACGACTCCTATCAACAC
1 CACGACTCCTATCAACAC
91589 CACGACTCCTATCAACAC
1 CACGACTCCTATCAACAC
91607 CAC
1 CAC
91610 ACGCGAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.46, G:0.05, T:0.15
Consensus pattern (18 bp):
CACGACTCCTATCAACAC
Found at i:92029 original size:68 final size:67
Alignment explanation
Indices: 91938--92064 Score: 218
Period size: 68 Copynumber: 1.9 Consensus size: 67
91928 TTTTTTAGGA
*
91938 TAAACTACCATTTAATCACTTATATATTATCTAATTTATGTTTTGGTTACTCGATTATTATTTAA
1 TAAACTACCATTTAATCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTATTATTTAA
92003 GG
66 GG
**
92005 TAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTATT
1 TAAACTACC-ATTTAATCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTATT
92065 TTTTTTAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
67 9 0.16
68 47 0.84
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.48
Consensus pattern (67 bp):
TAAACTACCATTTAATCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTATTATTTAA
GG
Found at i:92054 original size:31 final size:31
Alignment explanation
Indices: 91953--92056 Score: 84
Period size: 31 Copynumber: 3.2 Consensus size: 31
91943 TACCATTTAA
91953 TCACTTATATATTATCTAATTTATGTTTTGG
1 TCACTTATATATTATCTAATTTATGTTTTGG
* * * * **
91984 TTACTCGAT-TATTATTTAAGGTAAACTACCTATTTGG
1 TCACT-TATATATTATCTAA--T---TTATGT-TTTGG
92021 TCACTTATATATTATCTAATTTATGTTTTGG
1 TCACTTATATATTATCTAATTTATGTTTTGG
92052 TCACT
1 TCACT
92057 CGATTATTTT
Statistics
Matches: 53, Mismatches: 12, Indels: 16
0.65 0.15 0.20
Matches are distributed among these distances:
31 23 0.43
32 5 0.09
33 1 0.02
35 1 0.02
36 5 0.09
37 18 0.34
ACGTcount: A:0.27, C:0.12, G:0.11, T:0.50
Consensus pattern (31 bp):
TCACTTATATATTATCTAATTTATGTTTTGG
Found at i:92192 original size:34 final size:34
Alignment explanation
Indices: 92149--92213 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
92139 TAACATGACA
* *
92149 TTTTTTTTAATTATGTTTGGATGTTGGACTAACT
1 TTTTTTTTAATTATGTTTGGATATTGAACTAACT
92183 TTTTTTTTAATTATGTTTGGATATTGAACTA
1 TTTTTTTTAATTATGTTTGGATATTGAACTA
92214 TGTAATTCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.57
Consensus pattern (34 bp):
TTTTTTTTAATTATGTTTGGATATTGAACTAACT
Found at i:97854 original size:21 final size:20
Alignment explanation
Indices: 97808--97854 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
97798 TGATATTAAA
*
97808 AAATAAATAATTAAAACAAT
1 AAATATATAATTAAAACAAT
*
97828 TAATATATAATTTAAAA-AAT
1 AAATATATAA-TTAAAACAAT
97848 AAGATAT
1 AA-ATAT
97855 TTATTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
AAATATATAATTAAAACAAT
Found at i:98030 original size:18 final size:18
Alignment explanation
Indices: 97991--98033 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
97981 AATAAATAAA
*
97991 ATAAATATTATTTATTAT
1 ATAAATATTATTTATTAG
*
98009 ATAAATATATATTTA-TGG
1 ATAAATAT-TATTTATTAG
98027 ATAAATA
1 ATAAATA
98034 ATAATAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (18 bp):
ATAAATATTATTTATTAG
Found at i:98034 original size:22 final size:18
Alignment explanation
Indices: 97989--98024 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
97979 TTAATAAATA
97989 AAATAAATATTATTTATT
1 AAATAAATATTATTTATT
*
98007 ATATAAATATATATTTAT
1 AAATAAATAT-TATTTAT
98025 GGATAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATAAATATTATTTATT
Found at i:98074 original size:14 final size:16
Alignment explanation
Indices: 98037--98090 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
98027 ATAAATAATA
* *
98037 ATAATAATAGTAATA-
1 ATAATAAAAGTAACAT
98052 ATAATTAAAAGTAA-AT
1 ATAA-TAAAAGTAACAT
*
98068 AT-ATAAAATTAACAT
1 ATAATAAAAGTAACAT
98083 ATAATAAA
1 ATAATAAA
98091 CAAGGACAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
14 8 0.24
15 10 0.30
16 15 0.45
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (16 bp):
ATAATAAAAGTAACAT
Found at i:98136 original size:27 final size:27
Alignment explanation
Indices: 98098--98161 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
98088 AAACAAGGAC
*
98098 AAAAATCAATAAAATTAAAA-TGATAGGT
1 AAAAAT-AATAAAATAAAAACTGATA-GT
* *
98126 ACAAATAATAAAATAAAAACTTATAGT
1 AAAAATAATAAAATAAAAACTGATAGT
98153 AAAAATAAT
1 AAAAATAAT
98162 TAGTAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 22 0.71
28 9 0.29
ACGTcount: A:0.64, C:0.05, G:0.06, T:0.25
Consensus pattern (27 bp):
AAAAATAATAAAATAAAAACTGATAGT
Found at i:99900 original size:18 final size:18
Alignment explanation
Indices: 99861--99903 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
99851 AATAAATAAA
*
99861 ATAAATATTATTTATTAT
1 ATAAATATTATTTATTAG
*
99879 ATAAATATATATTTA-TGG
1 ATAAATAT-TATTTATTAG
99897 ATAAATA
1 ATAAATA
99904 ATAATAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (18 bp):
ATAAATATTATTTATTAG
Found at i:99904 original size:22 final size:18
Alignment explanation
Indices: 99859--99894 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
99849 TTAATAAATA
99859 AAATAAATATTATTTATT
1 AAATAAATATTATTTATT
*
99877 ATATAAATATATATTTAT
1 AAATAAATAT-TATTTAT
99895 GGATAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATAAATATTATTTATT
Found at i:100007 original size:27 final size:27
Alignment explanation
Indices: 99969--100032 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
99959 AAACAAGGAC
*
99969 AAAAATCAATAAAATTAAAA-TGATAGCT
1 AAAAAT-AATAAAATAAAAACTGATAG-T
* *
99997 ACAAATAATAAAATAAAAACTTATAGT
1 AAAAATAATAAAATAAAAACTGATAGT
100024 AAAAATAAT
1 AAAAATAAT
100033 TAGTAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 21 0.68
28 10 0.32
ACGTcount: A:0.64, C:0.06, G:0.05, T:0.25
Consensus pattern (27 bp):
AAAAATAATAAAATAAAAACTGATAGT
Found at i:101205 original size:3 final size:3
Alignment explanation
Indices: 101197--101275 Score: 97
Period size: 3 Copynumber: 25.7 Consensus size: 3
101187 GGCCTGTTTG
**
101197 TAA TAA TAA TAA TTT TAA TAA TAA TATA TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
*
101242 TATA TAA AAA TAA TAA TAA TAA TAAA TAA TAA TA
1 TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TA
101276 GAAAATGGAG
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
2 2 0.03
3 55 0.83
4 9 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:101244 original size:19 final size:20
Alignment explanation
Indices: 101212--101275 Score: 105
Period size: 19 Copynumber: 3.2 Consensus size: 20
101202 ATAATAATTT
101212 TAATAATAATATATAAAATAA
1 TAATAATAATATAT-AAATAA
101233 TAATAATAATATATAAA-AA
1 TAATAATAATATATAAATAA
101252 TAATAATAATA-ATAAATAA
1 TAATAATAATATATAAATAA
101271 TAATA
1 TAATA
101276 GAAAATGGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.12
19 20 0.48
20 3 0.07
21 14 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAATAATAATATATAAATAA
Found at i:101559 original size:117 final size:120
Alignment explanation
Indices: 101417--101687 Score: 306
Period size: 124 Copynumber: 2.3 Consensus size: 120
101407 GTTGAATAAA
* * *
101417 TTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGG-G-GATGAT-A-ATA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGAGTGATGATGATATA
* * * *
101477 TCTCCTTCTGTGAT-GTAAT-TTGGAAAAGGGTTGAACAAG-TTCTTCTCATTATGAAC
65 TCTACTTCTCTGATAG-AATCATGCAAAA-GGTTGAACAAGCTT-TTCTCATTATGAAC
* *
101533 TTCTTTTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATGATGAT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGG--A-G-TGATGATGAT
* * *
101598 CTATCTATTTCTCTGATAGAGTCATGCAAAAGGTTGAACAAGCTTTTCTCATTATGAAC
62 ATATCTACTTCTCTGATAGAATCATGCAAAAGGTTGAACAAGCTTTTCTCATTATGAAC
101657 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
101688 TATCTGGCAA
Statistics
Matches: 129, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
116 9 0.07
117 34 0.26
120 1 0.01
122 6 0.05
123 1 0.01
124 69 0.53
125 9 0.07
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (120 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAGTGATGATGATATAT
CTACTTCTCTGATAGAATCATGCAAAAGGTTGAACAAGCTTTTCTCATTATGAAC
Found at i:101886 original size:113 final size:106
Alignment explanation
Indices: 101727--102267 Score: 756
Period size: 113 Copynumber: 5.0 Consensus size: 106
101717 GAATTCAAGT
101727 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
101792 TATGAACTCTACCTGGAAATGTTGATCCATC-A-A-G-T-G
66 TATGAACTCTACCTGGAAATGTTGATCCATCAAGATGATAG
101828 -AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
101892 TATGAACTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAG
66 TATGAACTCTACCTGGAAATGTTGATCCATC-AA-GATG-A-T--AG
101939 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 -AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
102004 TTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGAATTCAAG
65 TTATGAACTCTACCTGGAAATGTTGATCCATCAA--GATG-A-T--AG
102052 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 -AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
102117 TTATGAACTCTACCTGGAAATGCTGATCCATCAAGTGATGGATTTG
65 TTATGAACTCTACCTGGAAATGTTGATCCATCAA--GAT-GA-TAG
* *
102163 AACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCT
1 -A-AAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
** * *
102228 CATTATGAACTCTTTC-AGAAATGTTGATCCATTAA-ATGAT
63 CATTATGAACTCTACCTGGAAATGTTGATCCATCAAGATGAT
102268 GGATTTGAAC
Statistics
Matches: 411, Mismatches: 12, Indels: 28
0.91 0.03 0.06
Matches are distributed among these distances:
100 94 0.23
102 1 0.00
104 1 0.00
105 1 0.00
107 1 0.00
108 3 0.01
109 2 0.00
111 3 0.01
112 22 0.05
113 282 0.69
114 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (106 bp):
AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTACCTGGAAATGTTGATCCATCAAGATGATAG
Found at i:102099 original size:326 final size:324
Alignment explanation
Indices: 101499--102240 Score: 995
Period size: 326 Copynumber: 2.2 Consensus size: 324
101489 ATGTAATTTG
* * *
101499 GAAAAGGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATAAGTTCTTCTC
1 GAAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
101564 ATTATGAACTCTACCTGGAAATGTTGATGATGATCTATCTATTTCTCTGATAGAGTCATGCAAAA
66 ATTATGAACTCTACCTGGAAA---T-ATGATGATCCATCGA----TATGATAGAGTCAAGCAAAA
*
101629 GGTTGAACAAGCTTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCTATCTG
123 AGTTGAACAAGCTTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCTATCTG
* *
101694 GCAATGCTGATCCATCGAATGATGAATTCAAGTAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
188 GAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
*
101759 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCATC-
253 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGCTGATCCATCA
101823 A-A-G-T
318 AGAGGTT
101827 G-AAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GAAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
101890 ATTATGAACTCTACCTGG-AA-ATGCTGATCCATCGA-ATGAT-GAATTCAAGCAAAAAGTTGAA
66 ATTATGAACTCTACCTGGAAATATGATGATCCATCGATATGATAG-AGTCAAGCAAAAAGTTGAA
101951 CAAG-TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT
130 CAAGCTT-TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC----T--A---T
*
102015 ACCTGGAAATGTTGATCCATC-AAGTGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATT
185 --CTGGAAATGCTGATCCATCGAA-TGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATT
102079 ATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGCTGAT
247 ATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGCTGAT
102144 CCATCAAGTGATGGATTT
312 CCATCAA--GA-GG--TT
* *
102162 GAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTC
1 G-A-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
102227 TCATTATGAACTCT
64 TCATTATGAACTCT
102241 TTCAGAAATG
Statistics
Matches: 371, Mismatches: 16, Indels: 43
0.86 0.04 0.10
Matches are distributed among these distances:
314 3 0.01
315 69 0.19
319 1 0.00
320 12 0.03
321 1 0.00
324 1 0.00
325 4 0.01
326 199 0.54
327 4 0.01
328 1 0.00
330 1 0.00
332 1 0.00
335 2 0.01
338 4 0.01
339 68 0.18
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (324 bp):
GAAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTACCTGGAAATATGATGATCCATCGATATGATAGAGTCAAGCAAAAAGTTGAAC
AAGCTTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCTATCTGGAAATGCT
GATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
CCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGCTGATCCATCAAGAGGTT
Found at i:102700 original size:22 final size:22
Alignment explanation
Indices: 102675--102729 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
102665 GATAAAGCTT
*
102675 TCATCTTTGAAAA-GAGAATCTG
1 TCATCTTTGAAAATG-GAATCTA
*
102697 TCATCTTTAAAAATGGAATCTA
1 TCATCTTTGAAAATGGAATCTA
*
102719 TCCTCTTTGAA
1 TCATCTTTGAA
102730 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAATGGAATCTA
Found at i:103144 original size:50 final size:54
Alignment explanation
Indices: 103083--103237 Score: 176
Period size: 54 Copynumber: 2.9 Consensus size: 54
103073 AATCACTGGT
* *
103083 TCGTAAAACATTTGACAATACATTCATCTTTTCCTGTGGTTTCTG-TC-G-CGA
1 TCGTAAAACATTTGACAACACATTCATCTTTTCCTGTGGCTTCTGCTCAGACGA
* * * * * * *
103134 T-GTAAAACATTTGAAAACACATTCTTCCTTTCTTGTAGCTTCTGCTCAGATGT
1 TCGTAAAACATTTGACAACACATTCATCTTTTCCTGTGGCTTCTGCTCAGACGA
*
103187 TCGTAAAGCATTTGACAACACATTCATCCTTTT-CTGTGGCTTCTGCTCAGA
1 TCGTAAAACATTTGACAACACATTCAT-CTTTTCCTGTGGCTTCTGCTCAGA
103238 TTTCTCAATT
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
50 36 0.43
51 3 0.04
52 1 0.01
53 2 0.02
54 38 0.45
55 4 0.05
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (54 bp):
TCGTAAAACATTTGACAACACATTCATCTTTTCCTGTGGCTTCTGCTCAGACGA
Found at i:103425 original size:74 final size:74
Alignment explanation
Indices: 103299--103446 Score: 287
Period size: 74 Copynumber: 2.0 Consensus size: 74
103289 TCACAAGATC
103299 ACTTAAGAACAAAACTCAGTGGGGATACAAGTGAGATGTTGGTATGACCAAAAAGTTGGTCAAAT
1 ACTTAAGAACAAAACTCAGTGGGGATACAAGTGAGATGTTGGTATGACCAAAAAGTTGGTCAAAT
103364 TCGCGATAT
66 TCGCGATAT
*
103373 ACTTGAGAACAAAACTCAGTGGGGATACAAGTGAGATGTTGGTATGACCAAAAAGTTGGTCAAAT
1 ACTTAAGAACAAAACTCAGTGGGGATACAAGTGAGATGTTGGTATGACCAAAAAGTTGGTCAAAT
103438 TCGCGATAT
66 TCGCGATAT
103447 GTGCTAGTGT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (74 bp):
ACTTAAGAACAAAACTCAGTGGGGATACAAGTGAGATGTTGGTATGACCAAAAAGTTGGTCAAAT
TCGCGATAT
Found at i:105621 original size:114 final size:114
Alignment explanation
Indices: 105421--105638 Score: 357
Period size: 114 Copynumber: 1.9 Consensus size: 114
105411 TCATGCAGTC
* * * *
105421 CATCTTTTAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACTAGATCAGATAACTCAAAGAAC
1 CATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACTAGATCAGATAACTCAAAGAAC
*
105486 ACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATT
66 ACTTCCAGAAGATGCTATTGGGTCTCATTATTTCTACTATGAGCAAATT
* *
105535 CATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAA-TCAGATCAGATAACTCAAAGAA
1 CATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACT-AGATCAGATAACTCAAAGAA
105599 CACTTCCAGAAGATGCTATTGGGTCTCATTATTTCTACTA
65 CACTTCCAGAAGATGCTATTGGGTCTCATTATTTCTACTA
105639 CGAGAACGTG
Statistics
Matches: 96, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
113 1 0.01
114 95 0.99
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Consensus pattern (114 bp):
CATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACTAGATCAGATAACTCAAAGAAC
ACTTCCAGAAGATGCTATTGGGTCTCATTATTTCTACTATGAGCAAATT
Found at i:107892 original size:17 final size:16
Alignment explanation
Indices: 107870--107933 Score: 67
Period size: 17 Copynumber: 3.9 Consensus size: 16
107860 ATTTTCCTTC
*
107870 TTTTTTTTCCTTTTTA
1 TTTTTTTTTCTTTTTA
*
107886 TTTTTTTTTATTTTTTA
1 TTTTTTTTT-CTTTTTA
*
107903 TTTTTTTCTTCTTCTT-
1 TTTTTTT-TTCTTTTTA
*
107919 CTTTTTTTTCTTTTT
1 TTTTTTTTTCTTTTT
107934 CTTTCTTTGC
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
15 7 0.17
16 14 0.35
17 17 0.43
18 2 0.05
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTTTCTTTTTA
Found at i:107928 original size:18 final size:19
Alignment explanation
Indices: 107903--107941 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
107893 TTATTTTTTA
107903 TTTTTTTCTTCTTC-TTCT
1 TTTTTTTCTTCTTCTTTCT
*
107921 TTTTTTTCTTTTTCTTTCT
1 TTTTTTTCTTCTTCTTTCT
107940 TT
1 TT
107942 GCTGGATGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTTCTTCTTCTTTCT
Found at i:111099 original size:14 final size:14
Alignment explanation
Indices: 111066--111118 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
111056 ATGACATAAA
* *
111066 AAATGCAAAGATGCC
1 AAATGTAAATATG-C
111081 AAATGTAAATATGC
1 AAATGTAAATATGC
* *
111095 AAATGTAAAAATGT
1 AAATGTAAATATGC
111109 AAATGTAAAT
1 AAATGTAAAT
111119 TATTTAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
14 22 0.67
15 11 0.33
ACGTcount: A:0.53, C:0.08, G:0.15, T:0.25
Consensus pattern (14 bp):
AAATGTAAATATGC
Found at i:113400 original size:21 final size:20
Alignment explanation
Indices: 113360--113400 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
113350 TAAAAAATAA
*
113360 ATAATTAAAAAAATATATAT
1 ATAATTAAAAAAATAGATAT
*
113380 ATAATTTAAAAAATAAGATAT
1 ATAATTAAAAAAAT-AGATAT
113401 TTATTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
ATAATTAAAAAAATAGATAT
Found at i:113400 original size:23 final size:23
Alignment explanation
Indices: 113366--113415 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
113356 ATAAATAATT
*
113366 AAAAAAATATATATA-TAATTTA
1 AAAAAAAGATATATATTAATTTA
* *
113388 AAAAATAAGATATTTATTTATTTA
1 AAAAA-AAGATATATATTAATTTA
113412 AAAA
1 AAAA
113416 TATCAGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 5 0.22
23 8 0.35
24 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
AAAAAAAGATATATATTAATTTA
Found at i:113458 original size:116 final size:113
Alignment explanation
Indices: 113261--113478 Score: 260
Period size: 116 Copynumber: 1.9 Consensus size: 113
113251 TATATTAATT
* * * * *
113261 TATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGCCT
1 TATATATATTTAAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTACCT
* *
113326 TAAGACAGCTCTTTTCTTTGATATTAAAAAATAAATAATTAAAAAAATA
66 TAAGACAGCTCCTTTC-TTAATATTAAAAAATAAATAATTAAAAAAATA
* *
113375 TATATATAATTTAAAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTA
1 TATATAT-ATTT-AAAAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCAGGTA
** **
113440 TTTTAAGA-ATGC-CCTTTCTTAATATTGGAAAATAAATAA
63 CCTTAAGACA-GCTCCTTTCTTAATATTAAAAAATAAATAA
113479 ATATTAAAAT
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
114 7 0.08
115 22 0.25
116 41 0.47
117 17 0.20
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.38
Consensus pattern (113 bp):
TATATATATTTAAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTACCT
TAAGACAGCTCCTTTCTTAATATTAAAAAATAAATAATTAAAAAAATA
Found at i:113576 original size:18 final size:18
Alignment explanation
Indices: 113537--113579 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
113527 AATAAATAAA
*
113537 ATAAATATTATTTATTAT
1 ATAAATATTATTTATTAG
*
113555 ATAAATATATATTTA-TGG
1 ATAAATAT-TATTTATTAG
113573 ATAAATA
1 ATAAATA
113580 ATAATAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (18 bp):
ATAAATATTATTTATTAG
Found at i:113580 original size:22 final size:18
Alignment explanation
Indices: 113535--113570 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
113525 TTAATAAATA
113535 AAATAAATATTATTTATT
1 AAATAAATATTATTTATT
*
113553 ATATAAATATATATTTAT
1 AAATAAATAT-TATTTAT
113571 GGATAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATAAATATTATTTATT
Found at i:113683 original size:27 final size:27
Alignment explanation
Indices: 113645--113708 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
113635 AAACAAGGAC
*
113645 AAAAATCAATAAAATTAAAA-TGATAGGT
1 AAAAAT-AATAAAATAAAAACTGATA-GT
* *
113673 ACAAATAATAAAATAAAAACTTATAGT
1 AAAAATAATAAAATAAAAACTGATAGT
113700 AAAAATAAT
1 AAAAATAAT
113709 TAGTAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 22 0.71
28 9 0.29
ACGTcount: A:0.64, C:0.05, G:0.06, T:0.25
Consensus pattern (27 bp):
AAAAATAATAAAATAAAAACTGATAGT
Found at i:114942 original size:3 final size:3
Alignment explanation
Indices: 114934--115026 Score: 127
Period size: 3 Copynumber: 30.7 Consensus size: 3
114924 GGCCTGTTTG
**
114934 TAA TAA TAA TAA TTT TAA TAA TAA TAA -ATA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
114979 TAA TAA TAA TATA TAA -AA TAA TAA TAA TAAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
115025 TA
1 TA
115027 GAAAATGGAG
Statistics
Matches: 81, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
2 3 0.04
3 71 0.88
4 7 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:115045 original size:34 final size:34
Alignment explanation
Indices: 114953--115026 Score: 57
Period size: 34 Copynumber: 2.2 Consensus size: 34
114943 TAATTTTAAT
* *
114953 AATAATAAAT-ATAATAATAATAATA-ATAATAAT
1 AATAATAAATAATAATAATAAT-ATAGAAAATAAG
* *
114986 AATATATAAAATAATAATAATAA-ATA-ATAATAAT
1 AATA-AT-AAATAATAATAATAATATAGAAAATAAG
115020 AATAATA
1 AATAATA
115027 GAAAATGGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
32 1 0.03
33 6 0.16
34 17 0.45
35 4 0.11
36 10 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (34 bp):
AATAATAAATAATAATAATAATATAGAAAATAAG
Found at i:116304 original size:13 final size:13
Alignment explanation
Indices: 116286--116315 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
116276 TTTTTTATTT
*
116286 TTAAAATAAAATA
1 TTAAAAGAAAATA
116299 TTAAAAGAAAATA
1 TTAAAAGAAAATA
116312 TTAA
1 TTAA
116316 TATTAGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
TTAAAAGAAAATA
Found at i:117410 original size:20 final size:20
Alignment explanation
Indices: 117385--117456 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
117375 GGAGAATTCG
*
117385 CGTTGCGATTTATATATTAT
1 CGTTGCGATTTACATATTAT
* **
117405 CGTTGCGATTTACCTATTCG
1 CGTTGCGATTTACATATTAT
* *
117425 CGTTGAGAATTACATATTAT
1 CGTTGCGATTTACATATTAT
117445 CGTTGCGATTTA
1 CGTTGCGATTTA
117457 ACTATTCGCG
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTACATATTAT
Found at i:117442 original size:40 final size:40
Alignment explanation
Indices: 117380--117475 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
117370 AATTTGGAGA
* * *
117380 ATTCGCGTTGCGATTTATATATTATCGTTGCGATTTACCT
1 ATTCGCGTTGCGAATTACATATTATCGTTGCGATTTAACT
*
117420 ATTCGCGTTGAGAATTACATATTATCGTTGCGATTTAACT
1 ATTCGCGTTGCGAATTACATATTATCGTTGCGATTTAACT
117460 ATTCGCGTTGCGAATT
1 ATTCGCGTTGCGAATT
117476 TGGAAAATCG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.42
Consensus pattern (40 bp):
ATTCGCGTTGCGAATTACATATTATCGTTGCGATTTAACT
Found at i:117462 original size:20 final size:20
Alignment explanation
Indices: 117384--117472 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
117374 TGGAGAATTC
117384 GCGTTGCGATTTATA-TATTA
1 GCGTTGCGATTTA-ACTATTA
* * *
117404 TCGTTGCGATTTACCTATTC
1 GCGTTGCGATTTAACTATTA
* *
117424 GCGTTGAGAATT-ACATATTA
1 GCGTTGCGATTTAAC-TATTA
* *
117444 TCGTTGCGATTTAACTATTC
1 GCGTTGCGATTTAACTATTA
117464 GCGTTGCGA
1 GCGTTGCGA
117473 ATTTGGAAAA
Statistics
Matches: 53, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
19 1 0.02
20 50 0.94
21 2 0.04
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.40
Consensus pattern (20 bp):
GCGTTGCGATTTAACTATTA
Found at i:131091 original size:8 final size:8
Alignment explanation
Indices: 131078--131171 Score: 147
Period size: 8 Copynumber: 12.0 Consensus size: 8
131068 GAATCAAGCT
*
131078 TACATACA
1 TACATATA
131086 TACATATA
1 TACATATA
* *
131094 TACACAGA
1 TACATATA
131102 T--ATATA
1 TACATATA
131108 TACATATA
1 TACATATA
131116 TACATATA
1 TACATATA
131124 TACATATA
1 TACATATA
131132 TACATATA
1 TACATATA
131140 TACATATA
1 TACATATA
131148 TACATATA
1 TACATATA
131156 TACATATA
1 TACATATA
131164 TACATATA
1 TACATATA
131172 GATAGATAGA
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
6 4 0.05
8 75 0.95
ACGTcount: A:0.50, C:0.14, G:0.01, T:0.35
Consensus pattern (8 bp):
TACATATA
Found at i:132052 original size:2 final size:2
Alignment explanation
Indices: 132045--132074 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
132035 GTATTGAGGC
132045 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
132075 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:132079 original size:2 final size:2
Alignment explanation
Indices: 132074--132130 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
132064 ATATATATAT
132074 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
132116 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
132131 AGGCAACGGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:132498 original size:41 final size:40
Alignment explanation
Indices: 132444--132539 Score: 104
Period size: 41 Copynumber: 2.4 Consensus size: 40
132434 TTTATTTTTT
*
132444 TTAACAAAT-TAAAAAATATTTATATATTTTCTTTAAAAAA
1 TTAA-AAATATAAAAAATATATATATATTTTCTTTAAAAAA
* * ** * *
132484 TTTAAATTCATAAAATTTATATATATATTTTTTTTACAAAA
1 TTAAAAAT-ATAAAAAATATATATATATTTTCTTTAAAAAA
132525 TTAAAAATATAAAAA
1 TTAAAAATATAAAAA
132540 TGTTTAATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
39 3 0.07
40 9 0.20
41 32 0.73
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (40 bp):
TTAAAAATATAAAAAATATATATATATTTTCTTTAAAAAA
Found at i:135096 original size:32 final size:32
Alignment explanation
Indices: 135034--135136 Score: 109
Period size: 32 Copynumber: 3.2 Consensus size: 32
135024 AAAGTTTAGG
* * ** *
135034 TACTAATAACGGACTAAAACTGATGGTTTATT
1 TACTAAAAACAGACTAAAACTGATATTTTATA
*
135066 TCCTAAAAACAGACTAAAACTGATATTTTATA
1 TACTAAAAACAGACTAAAACTGATATTTTATA
* * *
135098 TACT-AAAACCGACCAAAACTAATATTATTATA
1 TACTAAAAACAGACTAAAACTGATATT-TTATA
135130 TACTAAA
1 TACTAAA
135137 TGTGTAGTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
31 19 0.32
32 38 0.64
33 2 0.03
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.31
Consensus pattern (32 bp):
TACTAAAAACAGACTAAAACTGATATTTTATA
Found at i:142260 original size:2 final size:2
Alignment explanation
Indices: 142253--142277 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
142243 AGCAAAAATG
142253 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
142278 GTTTAACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:142756 original size:14 final size:15
Alignment explanation
Indices: 142739--142769 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
142729 ATAATAAATG
142739 ATTAT-AAATATATT
1 ATTATAAAATATATT
142753 ATTATAAAATATATT
1 ATTATAAAATATATT
142768 AT
1 AT
142770 CTTAATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAAAATATATT
Found at i:143338 original size:2 final size:2
Alignment explanation
Indices: 143331--143360 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
143321 TTCTTTTTAT
*
143331 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
143361 ATTCATATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:145174 original size:10 final size:10
Alignment explanation
Indices: 145159--145185 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
145149 CATGCTCGAC
145159 GAGCACCGAT
1 GAGCACCGAT
145169 GAGCACCGAT
1 GAGCACCGAT
145179 GAGCACC
1 GAGCACC
145186 ATTAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.30, T:0.07
Consensus pattern (10 bp):
GAGCACCGAT
Found at i:145932 original size:20 final size:21
Alignment explanation
Indices: 145907--145960 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
145897 TACCAACAAA
145907 TTCGCAACGCGAA-CTCCAAT
1 TTCGCAACGCGAATCTCCAAT
* *
145927 TTCGCAAC-CCAATTTCCAAT
1 TTCGCAACGCGAATCTCCAAT
145947 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
145961 ATGTAAATCG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.10
20 22 0.76
21 4 0.14
ACGTcount: A:0.30, C:0.33, G:0.13, T:0.24
Consensus pattern (21 bp):
TTCGCAACGCGAATCTCCAAT
Found at i:146055 original size:20 final size:20
Alignment explanation
Indices: 146042--146100 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
146032 GCAACACATA
146042 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
*
146062 AGCCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
146082 AGTCAAATTCGCAACGCGA
1 AGTCAAATTCGCAACGCGA
146101 AACACAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAT
Found at i:146060 original size:40 final size:41
Alignment explanation
Indices: 146005--146101 Score: 112
Period size: 40 Copynumber: 2.4 Consensus size: 41
145995 TGTGATTTTC
* * *
146005 CAAATTCGTAACGCGAATCTG-TAAA-TCGCAACAC-ATAAGT
1 CAAATTCGCAACGCGAAT-AGCCAAATTCGCAACACGAT-AGT
*
146045 CAAATTCGCAACGCG-ATAGCCAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAATAGCCAAATTCGCAACACGATAGT
146085 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
146102 ACACAATATT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
38 1 0.02
39 5 0.10
40 40 0.82
41 3 0.06
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.19
Consensus pattern (41 bp):
CAAATTCGCAACGCGAATAGCCAAATTCGCAACACGATAGT
Found at i:146237 original size:22 final size:22
Alignment explanation
Indices: 146212--146258 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
146202 CTACGGCGAC
146212 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
146234 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
146256 ATC
1 ATC
146259 TGTCTATCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.45, G:0.15, T:0.19
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:157305 original size:94 final size:96
Alignment explanation
Indices: 157138--157330 Score: 354
Period size: 94 Copynumber: 2.0 Consensus size: 96
157128 TAGGGTTTGT
157138 AGATTGCATTAGTTTCAAAGGACATCATTTAGATCAATATCATATATATACATTCTGGACAATCA
1 AGATTGCATTAGTTTCAAAGGACATCATTTAGATC-A-ATCATATATATACATTCTGGACAATCA
157203 TAAGTAAAATATATTAGTGAGTGATAC-AATAC
64 TAAGTAAAATATATTAGTGAGTGATACAAATAC
157235 AGATTGCATTAGTTTCAAAGGACATCATTTAGATC-ATCATATATATACATTCTGGACAATCATA
1 AGATTGCATTAGTTTCAAAGGACATCATTTAGATCAATCATATATATACATTCTGGACAATCATA
157299 AGTAAAATATATTAGTGAGTGATACAAATAC
66 AGTAAAATATATTAGTGAGTGATACAAATAC
157330 A
1 A
157331 AATTTGAATA
Statistics
Matches: 95, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
94 54 0.57
95 6 0.06
97 35 0.37
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (96 bp):
AGATTGCATTAGTTTCAAAGGACATCATTTAGATCAATCATATATATACATTCTGGACAATCATA
AGTAAAATATATTAGTGAGTGATACAAATAC
Found at i:157741 original size:25 final size:24
Alignment explanation
Indices: 157713--157759 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
157703 TCAACGTGAC
157713 TTTAAATTAAATAATGAAAAAATTA
1 TTTAAATTAAATAAT-AAAAAATTA
* *
157738 TTTAAATTGAATTATAAAAAAT
1 TTTAAATTAAATAATAAAAAAT
157760 AATTGGATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (24 bp):
TTTAAATTAAATAATAAAAAATTA
Found at i:158129 original size:21 final size:21
Alignment explanation
Indices: 158095--158167 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
158085 GTACTGACTA
* *
158095 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
158116 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
158136 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
158157 TCGCAATGCGA
1 TCGCAATGCGA
158168 ATACGTAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:158182 original size:20 final size:20
Alignment explanation
Indices: 158157--158250 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
158147 TTTTCATAAT
158157 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
158177 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
158197 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
158218 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
158238 TCGCAATGTGAAT
1 TCGCAATGCGAAT
158251 TCTTATATAT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 45 0.71
21 18 0.29
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:158188 original size:41 final size:41
Alignment explanation
Indices: 158019--158228 Score: 144
Period size: 41 Copynumber: 5.1 Consensus size: 41
158009 AATTTCGCGT
* * *
158019 TGCGTTTTTCATAATTCGTAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
** * * *
158060 TGCGAATTTGGA-AAATCGCAATGCG-GTAC-TGACTATCGCAA
1 TGCG-ATTTTCATAATTCGCAATGCGAATACGT-A-AATCGCAA
* * * * * **
158101 TGCAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCATAATTCGCAATGCGA-ATACGTAAATCGCAA
158142 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
* * * * *
158183 CGCGA--TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCA-TAATTCGCAATGCGAA-TACGTAAATCGCAA
158224 TGCGA
1 TGCGA
158229 ATACGTAAAT
Statistics
Matches: 127, Mismatches: 32, Indels: 20
0.71 0.18 0.11
Matches are distributed among these distances:
39 4 0.03
40 27 0.21
41 88 0.69
42 4 0.03
43 3 0.02
44 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (41 bp):
TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
Found at i:158237 original size:41 final size:41
Alignment explanation
Indices: 158157--158251 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
158147 TTTTCATAAT
* *
158157 TCGCAATGCGAA-TACGTAAATCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
* * *
158197 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
*
158238 TCGCAATGTGAATT
1 TCGCAATGCGAATT
158252 CTTATATATC
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 12 0.25
41 36 0.75
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (41 bp):
TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
Found at i:158754 original size:14 final size:14
Alignment explanation
Indices: 158735--158795 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 14
158725 GGAAATGACT
*
158735 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
158749 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
*
158768 ATCGCAACGAGATA
1 ATCGCAACGAGAAA
*
158782 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
158796 CCAAAATCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:158772 original size:33 final size:33
Alignment explanation
Indices: 158714--158806 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
158704 CGAGAATGAA
**
158714 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAACGAGAG
* *
158748 AATCGCAATGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
**
158781 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
158807 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
33 42 0.81
34 10 0.19
ACGTcount: A:0.43, C:0.24, G:0.22, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:158872 original size:20 final size:20
Alignment explanation
Indices: 158838--158894 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
158828 GCGATCCTCT
**
158838 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCCG
*
158858 CGTTGCGATTTTCATTAT-CT
1 CGTTGCGATTTTCATT-TCCG
*
158878 CGTTGCTA-TTTCATTTC
1 CGTTGCGATTTTCATTTC
158895 AACCAAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 1 0.03
19 7 0.23
20 22 0.71
21 1 0.03
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTCCG
Found at i:160465 original size:174 final size:171
Alignment explanation
Indices: 160104--160465 Score: 629
Period size: 174 Copynumber: 2.1 Consensus size: 171
160094 GATGAGCAGC
160104 CTCCACTCCTCCACTTCGAGAGCCATCACCTCACCCAGAGCCATCACCTGATCGACCCGACTATA
1 CTCCAC-CCTCCACTTCGAGAGCCATCACCTCACCCAGAGCCATCACCTGATCGACCCGACTATA
160169 CACCTCTACAAGAGAGCCATCACCTATCTTGTCACATCATCGAGCCTCTTCTACCATCACCTCAT
65 CACCTCTACAAGAGAGCCATCACCTATCTTGTCACATCATCGAGCCTCTTCTACCATCACCTCAT
160234 GATAGGCGACCGACAAAGATGCATGACTTCTATCTCCTGTTA
130 GATAGGCGACCGACAAAGATGCATGACTTCTATCTCCTGTTA
160276 GCCTCCACTCCTCCACTTCGAGAGCCATCACCTCACCCAGAGCCATCACCTGATCGACCCGACTA
1 --CTCCAC-CCTCCACTTCGAGAGCCATCACCTCACCCAGAGCCATCACCTGATCGACCCGACTA
160341 TACACCTCTACAATGAGAGCCATCACCTATCTTGTCACATCATCGAGCCTCTTCTCCACCATCAC
63 TACACCTCTACAA-GAGAGCCATCACCTATCTTGTCACATCATCGAGCCTCTTCT--ACCATCAC
160406 CTCATGATAGGCGACCGACAAAGATGCCATGACTTCTATCTCCCTGTT-
125 CTCATGATAGGCGACCGACAAAGATG-CATGACTTCTATCT-CCTGTTA
160454 CTCCA-CCTCCAC
1 CTCCACCCTCCAC
160466 CTCCACGGGA
Statistics
Matches: 183, Mismatches: 0, Indels: 10
0.95 0.00 0.05
Matches are distributed among these distances:
174 83 0.45
175 41 0.22
176 5 0.03
177 34 0.19
178 14 0.08
179 6 0.03
ACGTcount: A:0.25, C:0.39, G:0.13, T:0.23
Consensus pattern (171 bp):
CTCCACCCTCCACTTCGAGAGCCATCACCTCACCCAGAGCCATCACCTGATCGACCCGACTATAC
ACCTCTACAAGAGAGCCATCACCTATCTTGTCACATCATCGAGCCTCTTCTACCATCACCTCATG
ATAGGCGACCGACAAAGATGCATGACTTCTATCTCCTGTTA
Found at i:160922 original size:94 final size:94
Alignment explanation
Indices: 160732--161071 Score: 564
Period size: 94 Copynumber: 3.7 Consensus size: 94
160722 TAGATTGCTT
* *
160732 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
160793 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
160822 AGTAAATTTATTCGGTTACTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
160887 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
160916 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
160981 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
161010 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTT
161072 TTTGGTTGAA
Statistics
Matches: 237, Mismatches: 8, Indels: 6
0.94 0.03 0.02
Matches are distributed among these distances:
90 34 0.14
92 3 0.01
93 22 0.09
94 178 0.75
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:161172 original size:12 final size:12
Alignment explanation
Indices: 161157--161182 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
161147 TTAGAAAAAC
161157 TGTTTTGTCTTT
1 TGTTTTGTCTTT
161169 TGTTTTGTCTTT
1 TGTTTTGTCTTT
161181 TG
1 TG
161183 GTTTCGCGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.19, T:0.73
Consensus pattern (12 bp):
TGTTTTGTCTTT
Found at i:161200 original size:19 final size:19
Alignment explanation
Indices: 161184--161240 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
161174 TGTCTTTTGG
161184 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
**
161203 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCA
*
161222 TTTTTCACGTTGCGATTTT
1 --TTTCGCGTTGCGATTTT
161241 AAGTTCCAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 17 0.55
21 14 0.45
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:162980 original size:14 final size:14
Alignment explanation
Indices: 162963--162996 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
162953 TGTTTATTTT
162963 ATTTGTAAAAGATG
1 ATTTGTAAAAGATG
*
162977 ATTTGTAAAAGTTG
1 ATTTGTAAAAGATG
162991 ATTTGT
1 ATTTGT
162997 TTAATTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (14 bp):
ATTTGTAAAAGATG
Found at i:163171 original size:19 final size:18
Alignment explanation
Indices: 163147--163258 Score: 78
Period size: 19 Copynumber: 6.4 Consensus size: 18
163137 TAAATTCACG
163147 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
**
163165 TTTGCGA--TTC-CCTCG-
1 -TTGCGATTTTCATTTCGC
163180 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
*
163198 ATTGCGA--TTC-TCTCG-
1 -TTGCGATTTTCATTTCGC
163213 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
**
163231 ATTGCGATAGTCATTTCCGC
1 -TTGCGATTTTCATTT-CGC
163251 GTTGCGAT
1 -TTGCGAT
163259 AGACATTAAG
Statistics
Matches: 73, Mismatches: 9, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
14 12 0.16
16 13 0.18
17 13 0.18
19 25 0.34
20 10 0.14
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGC
Found at i:163187 original size:33 final size:33
Alignment explanation
Indices: 163145--163238 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
163135 ACTAAATTCA
*
163145 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
163178 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
163211 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
163239 AGTCATTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:163257 original size:20 final size:19
Alignment explanation
Indices: 163211--163265 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
163201 GCGATTCTCT
**
163211 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
163230 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
163250 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
163266 AAGATGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:165577 original size:12 final size:12
Alignment explanation
Indices: 165560--165584 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
165550 TGTTCGGGGA
165560 CTTTTTCTTCTT
1 CTTTTTCTTCTT
165572 CTTTTTCTTCTT
1 CTTTTTCTTCTT
165584 C
1 C
165585 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:165797 original size:24 final size:24
Alignment explanation
Indices: 165770--165816 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
165760 CAAAATCCGA
*
165770 GTATTGACCAATATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
165794 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
165817 AATACTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:165825 original size:24 final size:24
Alignment explanation
Indices: 165774--165825 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
165764 ATCCGAGTAT
* ** *
165774 TGACCAATATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
165798 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
165822 TGAC
1 TGAC
165826 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:166668 original size:20 final size:20
Alignment explanation
Indices: 166542--166668 Score: 139
Period size: 20 Copynumber: 6.3 Consensus size: 20
166532 GATTCTGTAT
* *
166542 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
166562 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
166582 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
166602 TATCGCATTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
166622 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
166643 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
166663 TATCGC
1 TATCGC
166669 AAATTCGCAT
Statistics
Matches: 93, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.03
20 74 0.80
21 14 0.15
22 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:166745 original size:21 final size:22
Alignment explanation
Indices: 166694--166745 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
166684 TTTACTTATT
* *
166694 CGCATTGCG-AATTGGGAAAAT
1 CGCATTGCGAAATTGAGAAAAC
**
166715 CGCAACGCGAAATT-AGAAAAC
1 CGCATTGCGAAATTGAGAAAAC
166736 CGCATTGCGA
1 CGCATTGCGA
166746 TAGTCATAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (22 bp):
CGCATTGCGAAATTGAGAAAAC
Found at i:174439 original size:5 final size:5
Alignment explanation
Indices: 174425--174455 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
174415 ACAGATATTT
*
174425 AAATC CAATC AAATC AAATC AAATC AAATC A
1 AAATC AAATC AAATC AAATC AAATC AAATC A
174456 TCGTCCTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATC
Found at i:176280 original size:36 final size:36
Alignment explanation
Indices: 176209--176281 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
176199 GTTGAAAAAT
* *
176209 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTAAAAATCATAAA
176245 ATTTATATAATTTT-TTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATTAAAAATCATAAA
176281 A
1 A
176282 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 18 0.55
37 15 0.45
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTAAAAATCATAAA
Found at i:176880 original size:36 final size:36
Alignment explanation
Indices: 176847--176914 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
176837 TACAAATTGT
176847 AAAATATTTATAT-ATTTTCTTTA-AAAATTAAATTC
1 AAAATATTTATATAATTTT-TTTACAAAATTAAATTC
*
176882 ATAATATTTATATAATTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTTTTACAAAATTAAA
176915 AATATAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
35 16 0.53
36 14 0.47
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (36 bp):
AAAATATTTATATAATTTTTTTACAAAATTAAATTC
Found at i:192785 original size:2 final size:2
Alignment explanation
Indices: 192778--192810 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
192768 GTTTAGTAGT
192778 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
192811 TTTCGCTAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:194176 original size:63 final size:59
Alignment explanation
Indices: 194009--194238 Score: 289
Period size: 59 Copynumber: 3.8 Consensus size: 59
193999 TACCTCCCCA
* *** * * * *
194009 CCACATGATGTTAGTTTTTTCCCCTCAAACCCTAGAGCATTAAGCCTTCGCAACGCCCC
1 CCACGTGATGTTAGTTTTTTTAGCTCAAACCCCAAAGCATTAAGCCTTCGCAACGCTCT
* *
194068 CCACGTGATGTTAGTTTTTTTAGCTCAAACCCCAGAGCATTAAGCCTTCGAAACGCTCT
1 CCACGTGATGTTAGTTTTTTTAGCTCAAACCCCAAAGCATTAAGCCTTCGCAACGCTCT
**
194127 CCACGTGATGTTAGTTTTTTTTTTCAGCTCAAACCCCAAAGCATTAAGCCTTCGCAACTTTCT
1 CCACGTGATGTTAG---TTTTTTT-AGCTCAAACCCCAAAGCATTAAGCCTTCGCAACGCTCT
* * *
194190 CCATGTGATGTTAGTTCTTTTAGCTCAAACCCCAAAGCATTAAGTCTTC
1 CCACGTGATGTTAGTTTTTTTAGCTCAAACCCCAAAGCATTAAGCCTTC
194239 ATAACGTGCC
Statistics
Matches: 152, Mismatches: 15, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
59 92 0.61
60 6 0.04
62 7 0.05
63 47 0.31
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (59 bp):
CCACGTGATGTTAGTTTTTTTAGCTCAAACCCCAAAGCATTAAGCCTTCGCAACGCTCT
Done.