Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008689.1 Hibiscus syriacus cultivar Beakdansim tig00111715_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: 959342
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 4
Found at i:314908 original size:19 final size:19
Alignment explanation
Indices: 314892--314969 Score: 112
Period size: 19 Copynumber: 4.4 Consensus size: 19
314882 AAAAATGACT
314892 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
314911 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
314930 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
314944 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
314963 ATCGCAA
1 ATCGCAA
314970 CGAGAGAATC
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 36 0.69
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:314948 original size:14 final size:14
Alignment explanation
Indices: 314929--314983 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
314919 GCGAAATGAA
314929 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
314943 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
314962 AATCGCAACGAGAG
1 AATCGCAACGAGAG
314976 AATCGCAA
1 AATCGCAA
314984 TGCGATTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:315001 original size:33 final size:33
Alignment explanation
Indices: 314910--314988 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
314900 GCGAAATGAA
314910 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
314943 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
314976 AATCGCAATGCGA
1 AATCGCAATGCGA
314989 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:315041 original size:14 final size:14
Alignment explanation
Indices: 315022--315076 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
315012 CATTTCCGCA
315022 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
315036 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
315053 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
315069 TTGCGATT
1 TTGCGATT
315077 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:315046 original size:53 final size:49
Alignment explanation
Indices: 314984--315272 Score: 223
Period size: 53 Copynumber: 5.5 Consensus size: 49
314974 AGAATCGCAA
314984 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTC-TTT-CG-ATTGCGATT-TCTCGT
* * * *
315037 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC-ATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGATT-T-TC-TTTCGA-TTGCGATTTCTCGT
*
315089 TGCGATTTTCATTTCGCATTGCGA--TTCTCTCG-TTGCGATTTTCATTTCGTAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCTTTCGATTGCGA-TTTC---TCG--T
* * *
315141 TGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGT-GATTTTC-ATTTCGCAT
1 TGCGATTTTCATTT-CGCATTGCGATT-T-TC-TT-TCGA-TTGCGATTTCTCGT
315194 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTT-TCATGT
1 TGCGATTTTCATTTCGCATTGCGATTTTC-TTT-CG-ATTGCGATTTCTC--GT
*
315247 TGGGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
315273 CTCTCGTTGC
Statistics
Matches: 192, Mismatches: 19, Indels: 50
0.74 0.07 0.19
Matches are distributed among these distances:
45 3 0.02
46 1 0.01
47 7 0.04
48 2 0.01
49 2 0.01
50 5 0.03
51 6 0.03
52 60 0.31
53 81 0.42
54 6 0.03
55 5 0.03
56 1 0.01
57 2 0.01
58 6 0.03
59 2 0.01
60 3 0.02
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (49 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCTTTCGATTGCGATTTCTCGT
Found at i:315294 original size:33 final size:33
Alignment explanation
Indices: 315002--315286 Score: 299
Period size: 33 Copynumber: 8.2 Consensus size: 33
314992 TCATTTCGCA
315002 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
315036 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
315069 TTGCGATTTTCATTTCGCATTGCGATT-T-TCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* * * * *
315100 TTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCG
1 TTGCG-ATTTTC-ATT-TCGCATTGCGA--TTC-TCTCG
315138 TATTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
* *
315174 TTGTGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
315210 CATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
315246 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
315279 TTGCGATT
1 TTGCGATT
315287 GTAATTTCCG
Statistics
Matches: 212, Mismatches: 19, Indels: 41
0.78 0.07 0.15
Matches are distributed among these distances:
31 9 0.04
32 6 0.03
33 86 0.41
34 43 0.20
35 5 0.02
36 10 0.05
37 7 0.03
38 17 0.08
39 22 0.10
40 7 0.03
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:315294 original size:105 final size:106
Alignment explanation
Indices: 314978--315286 Score: 472
Period size: 105 Copynumber: 2.9 Consensus size: 106
314968 AACGAGAGAA
* *
314978 TCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGTTGCGA
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATCGTTGCGA
315042 TTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
66 TTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
315083 TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATTTCGTATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCA--TCG--TT
*
315142 GCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGTGATTTTCATT
62 GCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
315188 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGA
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATCGTTGCGA
315252 TTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
66 TTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
315287 GTAATTTCCG
Statistics
Matches: 185, Mismatches: 7, Indels: 24
0.86 0.03 0.11
Matches are distributed among these distances:
99 10 0.05
101 2 0.01
102 5 0.03
103 3 0.02
104 15 0.08
105 115 0.62
106 14 0.08
107 3 0.02
108 3 0.02
109 3 0.02
111 12 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (106 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATCGTTGCGA
TTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:317587 original size:12 final size:12
Alignment explanation
Indices: 317570--317594 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
317560 TCTTCGGGGA
317570 CTTTTTCTTCTT
1 CTTTTTCTTCTT
317582 CTTTTTCTTCTT
1 CTTTTTCTTCTT
317594 C
1 C
317595 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:317803 original size:24 final size:24
Alignment explanation
Indices: 317769--317815 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
317759 CTGAAACATC
317769 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
317793 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
317816 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:318530 original size:20 final size:20
Alignment explanation
Indices: 318502--318692 Score: 224
Period size: 20 Copynumber: 9.6 Consensus size: 20
318492 AAATTTTAGT
* * * *
318502 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
318522 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
318542 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
318562 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
318582 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
318602 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
*
318622 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
318642 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
318662 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
318682 GTTGCGATTTA
1 GTTGCGATTTA
318693 TGTGTTCGCG
Statistics
Matches: 149, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.02
20 144 0.97
21 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:318702 original size:20 final size:20
Alignment explanation
Indices: 318679--318730 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
318669 TTTACGGATA
* *
318679 CGCGTTGCGATTTAT-GTGTT
1 CGCGTTGCGATTT-TCATATT
*
318699 CGCGTTACGATTTTCATATT
1 CGCGTTGCGATTTTCATATT
318719 CGCGTTGCGATT
1 CGCGTTGCGATT
318731 CTTGAAAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.42
Consensus pattern (20 bp):
CGCGTTGCGATTTTCATATT
Found at i:318725 original size:60 final size:60
Alignment explanation
Indices: 318563--318729 Score: 167
Period size: 60 Copynumber: 2.8 Consensus size: 60
318553 CAGATTCTCG
* * *
318563 TTGCGATTTACGGATTA-TCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGCA
1 TTGCGATTTACGGA-TACGCGTTACGATTTACAGATACGCGTTGCGATATACGGATACGCA
* * * * * * *
318623 TTGCGATTTACGGATACGCGTTGCTATTTACGGATACACGTTGCGGTTTACGGATACGCG
1 TTGCGATTTACGGATACGCGTTACGATTTACAGATACGCGTTGCGATATACGGATACGCA
* * * * *
318683 TTGCGATTTATGTG-TTCGCGTTACGATTTTCATATTCGCGTTGCGAT
1 TTGCGATTTACG-GATACGCGTTACGATTTACAGATACGCGTTGCGAT
318730 TCTTGAAAAT
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
59 2 0.02
60 86 0.97
61 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (60 bp):
TTGCGATTTACGGATACGCGTTACGATTTACAGATACGCGTTGCGATATACGGATACGCA
Found at i:318748 original size:21 final size:20
Alignment explanation
Indices: 318718--318800 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 20
318708 ATTTTCATAT
*
318718 TCGCGTTGCGATTCTTGAAAA
1 TCGCATTGCGATT-TTGAAAA
* * **
318739 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTG-AAAA
*
318760 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
318781 TCGCGTTGCGATTTTGAAAA
1 TCGCATTGCGATTTTGAAAA
318801 CTGATTTGCG
Statistics
Matches: 48, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
20 6 0.12
21 42 0.88
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:328179 original size:22 final size:21
Alignment explanation
Indices: 328137--328176 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
328127 TGAGTTTATT
*
328137 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
328158 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
328177 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:330640 original size:23 final size:23
Alignment explanation
Indices: 330614--330662 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
330604 CCTATTTTAA
* *
330614 TATATAAACGCTACCTATTACGT
1 TATATAAACACTACCTAATACGT
* *
330637 TATATAAGCACTACCTAATATGT
1 TATATAAACACTACCTAATACGT
330660 TAT
1 TAT
330663 TGTGATTGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (23 bp):
TATATAAACACTACCTAATACGT
Found at i:330772 original size:23 final size:23
Alignment explanation
Indices: 330690--330763 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
330680 CTAGTAATTA
** *
330690 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGAT
330713 ACCTATTACATTATATAAGCGAT
1 ACCTATTACATTATATAAGCGAT
*
330736 ACCTATTACATTATATAAGCGGT
1 ACCTATTACATTATATAAGCGAT
330759 ACCTA
1 ACCTA
330764 ATATGTTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.36
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGAT
Found at i:330796 original size:110 final size:110
Alignment explanation
Indices: 330614--330841 Score: 366
Period size: 110 Copynumber: 2.1 Consensus size: 110
330604 CCTATTTTAA
* * * *
330614 TATATAAACGCTACCTATTACGTTATATAAGCACTACCTAATATGTTATTGTGATTGATAATGTT
1 TATATAAGCGATACCTATTACATTATATAAGCACTACCTAATATGTTATTGTGATTAATAATGTT
* *
330679 TCTAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACAT
66 ACCAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACAT
** *
330724 TATATAAGCGATACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGCTTAATAATGTT
1 TATATAAGCGATACCTATTACATTATATAAGCACTACCTAATATGTTATTGTGATTAATAATGTT
*
330789 ACCAGTAATTAACCTATTTTATTATATAAGCGCTATCTATTACAT
66 ACCAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACAT
330834 TATATAAG
1 TATATAAG
330842 TGGTATCTAA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
110 108 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (110 bp):
TATATAAGCGATACCTATTACATTATATAAGCACTACCTAATATGTTATTGTGATTAATAATGTT
ACCAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACAT
Found at i:330804 original size:87 final size:87
Alignment explanation
Indices: 330713--330937 Score: 351
Period size: 87 Copynumber: 2.6 Consensus size: 87
330703 TATAAGCGCT
** * *
330713 ACCTATTACATTATATAAGCGATACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGC
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGA
330778 TTAATAATGTTACCAGTAATTA
66 TTAATAATGTTACCAGTAATTA
* * *
330800 ACCTATTTTATTATATAAGCGCTATCTATTACATTATATAAGTGGTATCTAATATGTTATTGTGA
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGA
* * *
330865 TTGATAATGTTTCTAGTAATTA
66 TTAATAATGTTACCAGTAATTA
*
330887 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTA
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGGTACCTA
330938 TTACATTATA
Statistics
Matches: 124, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 124 1.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (87 bp):
ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGA
TTAATAATGTTACCAGTAATTA
Found at i:330859 original size:23 final size:23
Alignment explanation
Indices: 330809--330853 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
330799 AACCTATTTT
*
330809 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTATCTAATAC
* *
330832 ATTATATAAGTGGTATCTAATA
1 ATTATATAAGCGCTATCTAATA
330854 TGTTATTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (23 bp):
ATTATATAAGCGCTATCTAATAC
Found at i:330930 original size:197 final size:197
Alignment explanation
Indices: 330595--330982 Score: 677
Period size: 197 Copynumber: 2.0 Consensus size: 197
330585 TAACAAATTA
*
330595 AGTAATTAACCTATTTTAATATATAAACGCTACCTATTACGTTATATAAGCACTACCTAATATGT
1 AGTAATTAACCTATTTTAATATATAAACGCTACCTATTACATTATATAAGCACTACCTAATATGT
330660 TATTGTGATTGATAATGTTTCTAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATT
66 TATTGTGATTGATAATGTTTCTAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATT
*
330725 ATATAAGCGATACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGCTTAATAATGTTA
131 ATATAAGCGATACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTACTTAATAATGTTA
330790 CC
196 CC
* * * *** *
330792 AGTAATTAACCTATTTTATTATATAAGCGCTATCTATTACATTATATAAGTGGTATCTAATATGT
1 AGTAATTAACCTATTTTAATATATAAACGCTACCTATTACATTATATAAGCACTACCTAATATGT
330857 TATTGTGATTGATAATGTTTCTAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATT
66 TATTGTGATTGATAATGTTTCTAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATT
* *
330922 ATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTACTTGATAAT
131 ATATAAGCGATACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTACTTAATAAT
330983 ATTTCCGGTT
Statistics
Matches: 180, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
197 180 1.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (197 bp):
AGTAATTAACCTATTTTAATATATAAACGCTACCTATTACATTATATAAGCACTACCTAATATGT
TATTGTGATTGATAATGTTTCTAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATT
ATATAAGCGATACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTACTTAATAATGTTA
CC
Found at i:330969 original size:23 final size:23
Alignment explanation
Indices: 330887--330960 Score: 121
Period size: 23 Copynumber: 3.2 Consensus size: 23
330877 CTAGTAATTA
**
330887 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
330910 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
330933 ACCTATTACATTATATAAGCGGT
1 ACCTATTACATTATATAAGCGCT
330956 ACCTA
1 ACCTA
330961 ATATGTTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.36
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:335102 original size:20 final size:20
Alignment explanation
Indices: 335073--335121 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
335063 ATTTCTAATT
*
335073 TCAT-TATGCGAGGCATTCG
1 TCATGTATGCGAGGCACTCG
335092 TCATGTATGCGAGGCACTCG
1 TCATGTATGCGAGGCACTCG
335112 TCATGTATGC
1 TCATGTATGC
335122 TTTTATGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (20 bp):
TCATGTATGCGAGGCACTCG
Found at i:341006 original size:19 final size:19
Alignment explanation
Indices: 340979--341018 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
340969 AAAAATAGTC
*
340979 AATATCACAATTTACTATA
1 AATACCACAATTTACTATA
* *
340998 AATACCACAGTTTATTATA
1 AATACCACAATTTACTATA
341017 AA
1 AA
341019 AATCAAGAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (19 bp):
AATACCACAATTTACTATA
Found at i:356902 original size:177 final size:180
Alignment explanation
Indices: 356603--356945 Score: 656
Period size: 177 Copynumber: 1.9 Consensus size: 180
356593 CCACACATCT
356603 AATAAAGAAATTATCAGTTTTACTTTCAAATACCCGCTATGAATAGAATCAGGGACGTTTGGATT
1 AATAAAGAAATTATCAGTTTTACTTTCAAATACCCGCTATGAATAGAATCAGGGA-GTTTGGATT
356668 GGTATTAAGTTACAAAATCACTTCGTTGATCACTTCTCATTTACAAATTGGCAATACAAACACTA
65 GGTATTAAGTTACAAAATCACTTCGTTGATCACTTCTCATTTACAAATTGGCAATACAAACACTA
356733 ATCCGTTAGTAATTAGCCTTGCACAGAT-GGAATAAGATTGATTTTTGGAC
130 ATCCGTTAGTAATTAGCCTTGCACAGATGGGAATAAGATTGATTTTTGGAC
356783 AATAAAGAAATTATCAGTTTTACTTTCAAATACCCGCTATGAATAGAATCA-GG-GTTTGGATTG
1 AATAAAGAAATTATCAGTTTTACTTTCAAATACCCGCTATGAATAGAATCAGGGAGTTTGGATTG
356846 GTATTAAGTTACAAAATCACTTCGTTGATCACTTCTCATTTACAAATTGGCAATACAAACACTAA
66 GTATTAAGTTACAAAATCACTTCGTTGATCACTTCTCATTTACAAATTGGCAATACAAACACTAA
356911 TCCGTTAGTAATTAGCCTTGCACAGATGGGAATAA
131 TCCGTTAGTAATTAGCCTTGCACAGATGGGAATAA
356946 TGTTGCGGAA
Statistics
Matches: 162, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
177 102 0.63
178 7 0.04
179 2 0.01
180 51 0.31
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (180 bp):
AATAAAGAAATTATCAGTTTTACTTTCAAATACCCGCTATGAATAGAATCAGGGAGTTTGGATTG
GTATTAAGTTACAAAATCACTTCGTTGATCACTTCTCATTTACAAATTGGCAATACAAACACTAA
TCCGTTAGTAATTAGCCTTGCACAGATGGGAATAAGATTGATTTTTGGAC
Found at i:360369 original size:22 final size:23
Alignment explanation
Indices: 360344--360389 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
360334 CATCATACAT
360344 CTTCAATTTGATGG-TTCCCACG
1 CTTCAATTTGATGGTTTCCCACG
360366 CTTCAATTTGATGGTTTCCCACG
1 CTTCAATTTGATGGTTTCCCACG
360389 C
1 C
360390 CAACGATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.37
Consensus pattern (23 bp):
CTTCAATTTGATGGTTTCCCACG
Found at i:376614 original size:19 final size:19
Alignment explanation
Indices: 376590--376636 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
376580 GCAGGTAAGG
376590 AATGTCTCTTCTTAATATA
1 AATGTCTCTTCTTAATATA
376609 AATGTCTCTTCTTAATATA
1 AATGTCTCTTCTTAATATA
376628 AATGTCTCT
1 AATGTCTCT
376637 GTCCTGCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.30, C:0.17, G:0.06, T:0.47
Consensus pattern (19 bp):
AATGTCTCTTCTTAATATA
Found at i:379162 original size:25 final size:24
Alignment explanation
Indices: 379131--379205 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 24
379121 AAACCCAGAC
379131 AATGAATGAAAATATCAAACTTTGA
1 AATGAATGAAAA-ATCAAACTTTGA
* *
379156 AATGAATGAAAAACCAAA--ATGCA
1 AATGAATGAAAAATCAAACTTTG-A
379179 AATGCAATGAAAAGATCAAACTTTGA
1 AATG-AATGAAAA-ATCAAACTTTGA
379205 A
1 A
379206 GATCTTCCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
22 2 0.05
23 5 0.12
24 13 0.32
25 17 0.41
26 2 0.05
27 2 0.05
ACGTcount: A:0.55, C:0.11, G:0.13, T:0.21
Consensus pattern (24 bp):
AATGAATGAAAAATCAAACTTTGA
Found at i:380169 original size:18 final size:17
Alignment explanation
Indices: 380146--380192 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 17
380136 AGGGTTAAGA
380146 TTTGGGGATTTTAGAGAT
1 TTTGGGG-TTTTAGAGAT
*
380164 TTTGGGGCTTTAGAGAT
1 TTTGGGGTTTTAGAGAT
380181 TTTGGGGCTTTT
1 TTTGGGG-TTTT
380193 TGTAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 16 0.62
18 10 0.38
ACGTcount: A:0.15, C:0.04, G:0.34, T:0.47
Consensus pattern (17 bp):
TTTGGGGTTTTAGAGAT
Found at i:380981 original size:17 final size:17
Alignment explanation
Indices: 380959--381055 Score: 185
Period size: 17 Copynumber: 5.7 Consensus size: 17
380949 TCCTAAAATT
380959 TTATAAATTCATTTATC
1 TTATAAATTCATTTATC
*
380976 TTATAAAATCATTTATC
1 TTATAAATTCATTTATC
380993 TTATAAATTCATTTATC
1 TTATAAATTCATTTATC
381010 TTATAAATTCATTTATC
1 TTATAAATTCATTTATC
381027 TTATAAATTCATTTATC
1 TTATAAATTCATTTATC
381044 TTATAAATTCAT
1 TTATAAATTCAT
381056 CCCTCTAACA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
17 78 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (17 bp):
TTATAAATTCATTTATC
Found at i:381493 original size:61 final size:59
Alignment explanation
Indices: 381428--381620 Score: 163
Period size: 61 Copynumber: 3.2 Consensus size: 59
381418 CAGTTAAAAT
* * * *
381428 ATTAATTTAATTAATTAAATACCTAATTGAAAGAAGAAAAACTTATTAGGCTCAATTATTA
1 ATTAATATAACTAATTAAA-ACCTAATT-AAAGAAGATAAACTTATTAGGATCAATTATTA
* * ** * * * *
381489 ATTAATTTAACTAATTAAGGATGTAGCTCAAAGAAGCTAAACTTATTAGGATCGATTATTA
1 ATTAATATAACTAATTAA-AACCTA-ATTAAAGAAGATAAACTTATTAGGATCAATTATTA
* * ** *
381550 ATCAATATAGCTAATTAAGAACCTAATTCTAGATA-ACTAAACTTATTAGGTTCAATTATTA
1 ATTAATATAACTAATTAA-AACCTAATTAAAGA-AGA-TAAACTTATTAGGATCAATTATTA
381611 ATTAATATAA
1 ATTAATATAA
381621 TTAAATAAGG
Statistics
Matches: 103, Mismatches: 25, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
60 4 0.04
61 98 0.95
62 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.36
Consensus pattern (59 bp):
ATTAATATAACTAATTAAAACCTAATTAAAGAAGATAAACTTATTAGGATCAATTATTA
Found at i:382250 original size:2 final size:2
Alignment explanation
Indices: 382243--382291 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
382233 TCAATTAAAG
382243 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
382285 AT AT AT A
1 AT AT AT A
382292 ATAATTTTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:382489 original size:39 final size:40
Alignment explanation
Indices: 382387--382776 Score: 345
Period size: 41 Copynumber: 9.6 Consensus size: 40
382377 CATTTTTGGC
* * *
382387 GGCGTTTTTTAAACAAACGCCGGTAAATACTTGTACTTTAGT
1 GGCG-TTTTTATATAAACGCCGCTAAATAC-TGTACTTTAGT
*
382429 GGCGTTTTTATATAAACGCCGCTAAATACTGTAATTTAGT
1 GGCGTTTTTATATAAACGCCGCTAAATACTGTACTTTAGT
* * *
382469 -GCATTTTTATATAAATGCCGCTAAATAATGTACTTTAGT
1 GGCGTTTTTATATAAACGCCGCTAAATACTGTACTTTAGT
* * * * * *
382508 GGCGTTTTAAGCACAAACGCCACTAAATGCCCGTACTTTAGT
1 GGCGTTTTTA-TATAAACGCCGCTAAAT-ACTGTACTTTAGT
* * *
382550 GGCGTTTCTATATAAATGCCGCTAAATACTGTTCTTTAGT
1 GGCGTTTTTATATAAACGCCGCTAAATACTGTACTTTAGT
* * * * *
382590 GGCGTTTTAAGCACAAGCGCCGCTAAATTCTTGTACTTTAGT
1 GGCGTTTTTA-TATAAACGCCGCTAAATAC-TGTACTTTAGT
* * ** * *
382632 GGCGTCTCTATATAAATACTGCTAAATACTGTTCTTTAGT
1 GGCGTTTTTATATAAACGCCGCTAAATACTGTACTTTAGT
* * * *
382672 GG-GATTTTA-AGAACAAGCGCCGCAAAATTCTTGTACTTTAGT
1 GGCGTTTTTATA-TA-AA-CGCCGCTAAATAC-TGTACTTTAGT
* *
382714 GGCGTTTTTGTATAAACGCCGCTAAATACTATACTTTAGT
1 GGCGTTTTTATATAAACGCCGCTAAATACTGTACTTTAGT
* *
382754 GGCGTTTTAAGTACAAACGCCGC
1 GGCGTTTTTA-TATAAACGCCGC
382777 AAAAGATCCG
Statistics
Matches: 272, Mismatches: 64, Indels: 25
0.75 0.18 0.07
Matches are distributed among these distances:
38 1 0.00
39 40 0.15
40 67 0.25
41 104 0.38
42 53 0.19
43 6 0.02
44 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (40 bp):
GGCGTTTTTATATAAACGCCGCTAAATACTGTACTTTAGT
Found at i:382576 original size:82 final size:82
Alignment explanation
Indices: 382405--382804 Score: 450
Period size: 82 Copynumber: 4.9 Consensus size: 82
382395 TTAAACAAAC
* * * * * *
382405 GCCGGTAAATACTTGTACTTTAGTGGCGTTTTTA-TATAAACGCCGCTAAA-TACTGTAATTTAG
1 GCCGCTAAATAC-TGTACTTTAGTGGCGTTTTAAGCACAAACGCCGCTAAATTCCTGTACTTTAG
* *
382468 T-GCATTTTTATATAAAT
65 TGGCGTTTCTATATAAAT
* * * *
382485 GCCGCTAAATAATGTACTTTAGTGGCGTTTTAAGCACAAACGCCACTAAATGCCCGTACTTTAGT
1 GCCGCTAAATACTGTACTTTAGTGGCGTTTTAAGCACAAACGCCGCTAAATTCCTGTACTTTAGT
382550 GGCGTTTCTATATAAAT
66 GGCGTTTCTATATAAAT
* * *
382567 GCCGCTAAATACTGTTCTTTAGTGGCGTTTTAAGCACAAGCGCCGCTAAATTCTTGTACTTTAGT
1 GCCGCTAAATACTGTACTTTAGTGGCGTTTTAAGCACAAACGCCGCTAAATTCCTGTACTTTAGT
*
382632 GGCGTCTCTATATAAAT
66 GGCGTTTCTATATAAAT
* * * * * * *
382649 ACTGCTAAATACTGTTCTTTAGTGG-GATTTTAAGAACAAGCGCCGCAAAATTCTTGTACTTTAG
1 GCCGCTAAATACTGTACTTTAGTGGCG-TTTTAAGCACAAACGCCGCTAAATTCCTGTACTTTAG
* * *
382713 TGGCGTTTTTGTATAAAC
65 TGGCGTTTCTATATAAAT
* * * * * *
382731 GCCGCTAAATACTATACTTTAGTGGCGTTTTAAGTACAAACGCCGCAAAAGATCC-GTAGTTTAA
1 GCCGCTAAATACTGTACTTTAGTGGCGTTTTAAGCACAAACGCCGCTAAA-TTCCTGTACTTTAG
382795 TGGCGTTTCT
65 TGGCGTTTCT
382805 GCCTCTAAAT
Statistics
Matches: 275, Mismatches: 39, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
79 20 0.07
80 23 0.08
81 11 0.04
82 218 0.79
83 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (82 bp):
GCCGCTAAATACTGTACTTTAGTGGCGTTTTAAGCACAAACGCCGCTAAATTCCTGTACTTTAGT
GGCGTTTCTATATAAAT
Found at i:384970 original size:19 final size:19
Alignment explanation
Indices: 384934--384970 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
384924 GTTGCTTGGT
*
384934 TGTAGTTCTGCGCACTGGC
1 TGTAGTTCTACGCACTGGC
*
384953 TGTAGTTCTACGCGCTGG
1 TGTAGTTCTACGCACTGG
384971 TTATGATCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.24, G:0.32, T:0.32
Consensus pattern (19 bp):
TGTAGTTCTACGCACTGGC
Found at i:387054 original size:41 final size:42
Alignment explanation
Indices: 386930--387146 Score: 183
Period size: 42 Copynumber: 5.1 Consensus size: 42
386920 ATGGTAATTA
* * *
386930 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCATTTGTAT-CAAAAACACCGCTATAGATCTAACCTTTT
* * ** *
386973 GCGGCGTATATGT-CCAAAAACGTCGCTATAGATCTGACCTTTT
1 GCGGC--ATTTGTATCAAAAACACCGCTATAGATCTAACCTTTT
387016 GCGGCATTTGTAT-AAAAACACCGCTATTA-ATCTAACCTTTT
1 GCGGCATTTGTATCAAAAACACCGCTA-TAGATCTAACCTTTT
* * *
387057 GCGGCGTTTGT-TCCAAAAACACCGCTAAATATCTAACCTTTT
1 GCGGCATTTGTAT-CAAAAACACCGCTATAGATCTAACCTTTT
* ** * * *
387099 GCAGTGTTTGT-TCCATAAACGCCGCTATAGATCTCGACCTTTT
1 GCGGCATTTGTAT-CAAAAACACCGCTATAGATCT-AACCTTTT
387142 GCGGC
1 GCGGC
387147 GTTTTTGGTT
Statistics
Matches: 146, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
40 1 0.01
41 38 0.26
42 55 0.38
43 48 0.33
45 4 0.03
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (42 bp):
GCGGCATTTGTATCAAAAACACCGCTATAGATCTAACCTTTT
Found at i:387091 original size:42 final size:42
Alignment explanation
Indices: 386930--387150 Score: 261
Period size: 43 Copynumber: 5.2 Consensus size: 42
386920 ATGGTAATTA
386930 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
*
386973 GCGGCGTATATG-TCCAAAAACGTCGCTATAGATCTGACCTTTT
1 GCGGCGT-T-TGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
* * *
387016 GCGGCATTTGTAT--AAAAACACCGCTATTA-ATCTAACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTA-TAGATCTGACCTTTT
* * * *
387057 GCGGCGTTTGTTCCAAAAACACCGCTAAATATCTAACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
* * *
387099 GCAGTGTTTGTTCCATAAACGCCGCTATAGATCTCGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-GACCTTTT
387142 GCGGCGTTT
1 GCGGCGTTT
387151 TTGGTTCTCA
Statistics
Matches: 153, Mismatches: 16, Indels: 18
0.82 0.09 0.10
Matches are distributed among these distances:
40 1 0.01
41 35 0.23
42 56 0.37
43 58 0.38
44 1 0.01
45 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:388236 original size:29 final size:28
Alignment explanation
Indices: 388126--388236 Score: 69
Period size: 29 Copynumber: 3.8 Consensus size: 28
388116 CCTAAAGCAA
* ** *
388126 AAAAAATGGTTTAGGGACTTGTTTTGATC
1 AAAAAATAGTTTA-GGACTTAATTTGATT
* ** *
388155 AAAATATAGTTTAGGCACTTAAAATGGTT
1 AAAAAATAGTTTAGG-ACTTAATTTGATT
* * *
388184 GCATATAATAGTTTAAGGAGTTAATTTGATT
1 --AAAAAATAGTTT-AGGACTTAATTTGATT
388215 AAAAAATAGTTTAGGTACTTAA
1 AAAAAATAGTTTAGG-ACTTAA
388237 ACAAAAAAAT
Statistics
Matches: 59, Mismatches: 18, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
28 5 0.08
29 33 0.56
31 18 0.31
32 3 0.05
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.37
Consensus pattern (28 bp):
AAAAAATAGTTTAGGACTTAATTTGATT
Found at i:393416 original size:23 final size:23
Alignment explanation
Indices: 393386--393430 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
393376 AATAAATAGG
* *
393386 TAAATGAATAT-AATTTAAAAAT
1 TAAATGAAAATAAAGTTAAAAAT
393408 TAAATTGAAAATAAAGTTAAAAA
1 TAAA-TGAAAATAAAGTTAAAAA
393431 CACTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 6 0.32
24 9 0.47
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (23 bp):
TAAATGAAAATAAAGTTAAAAAT
Found at i:394851 original size:8 final size:8
Alignment explanation
Indices: 394838--394863 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
394828 AATAAAAATT
394838 AATAATAA
1 AATAATAA
394846 AATAATAA
1 AATAATAA
394854 AATAATAA
1 AATAATAA
394862 AA
1 AA
394864 AATTTCGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AATAATAA
Found at i:408905 original size:20 final size:19
Alignment explanation
Indices: 408865--408905 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
408855 TTGTTTCAAT
*
408865 ATGAAGCATAATTTTTAGA
1 ATGAAGCATAATTTATAGA
408884 ATGAAGCATAATTTAATAGA
1 ATGAAGCATAATTT-ATAGA
408904 AT
1 AT
408906 ATTATTGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.34
Consensus pattern (19 bp):
ATGAAGCATAATTTATAGA
Found at i:410826 original size:15 final size:17
Alignment explanation
Indices: 410798--410834 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
410788 ATATACTCAC
*
410798 TTTTTTCATATTA-TAT
1 TTTTTTAATATTATTAT
410814 TTTTTTAAT-TTATTAT
1 TTTTTTAATATTATTAT
410830 TTTTT
1 TTTTT
410835 GTTACTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTAATATTATTAT
Found at i:422712 original size:13 final size:13
Alignment explanation
Indices: 422693--422742 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
422683 CTTAAATTGT
422693 ATATTTTATTAAA
1 ATATTTTATTAAA
* *
422706 TTATTTTTTTAAA
1 ATATTTTATTAAA
**
422719 ATATTTTATTTTTA
1 ATATTTTA-TTAAA
422733 ATATTTTATT
1 ATATTTTATT
422743 TTGTTATTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
13 19 0.63
14 11 0.37
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
ATATTTTATTAAA
Found at i:422735 original size:14 final size:14
Alignment explanation
Indices: 422718--422744 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
422708 ATTTTTTTAA
422718 AATATTTTATTTTT
1 AATATTTTATTTTT
422732 AATATTTTATTTT
1 AATATTTTATTTT
422745 GTTATTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
AATATTTTATTTTT
Found at i:423575 original size:80 final size:80
Alignment explanation
Indices: 423487--423663 Score: 311
Period size: 80 Copynumber: 2.2 Consensus size: 80
423477 ATTATCCTCG
* *
423487 TTAA-AAAATAATTTATTACTTAATAATTTATTTTAATTATTTAAAAGTAAATAAAATTCATGGT
1 TTAATAAAATATTTTATTACTTAATAATTTATTTTAATTATTTAAAAGTAAATAAAATTCATGAT
423551 TTATATATTGAAATA
66 TTATATATTGAAATA
* *
423566 TTAATAAAATATTTTATTATTTAATAATTTATTTTAATTATTTAAAATTAAATAAAATTCATGAT
1 TTAATAAAATATTTTATTACTTAATAATTTATTTTAATTATTTAAAAGTAAATAAAATTCATGAT
423631 TTATATATTGAAATA
66 TTATATATTGAAATA
423646 TTAATAAAATATTTTATT
1 TTAATAAAATATTTTATT
423664 TCAAAGTGTT
Statistics
Matches: 93, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
79 4 0.04
80 89 0.96
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (80 bp):
TTAATAAAATATTTTATTACTTAATAATTTATTTTAATTATTTAAAAGTAAATAAAATTCATGAT
TTATATATTGAAATA
Found at i:423591 original size:20 final size:21
Alignment explanation
Indices: 423566--423610 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
423556 TATTGAAATA
423566 TTAATAAAATATTTT-ATTAT
1 TTAATAAAATATTTTAATTAT
**
423586 TTAATAATTTATTTTAATTAT
1 TTAATAAAATATTTTAATTAT
423607 TTAA
1 TTAA
423611 AATTAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAATAAAATATTTTAATTAT
Found at i:434005 original size:25 final size:25
Alignment explanation
Indices: 433977--434025 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
433967 AATTTTTAAA
*
433977 AAAATAAAAAT-AAAAATATTTTCTG
1 AAAA-AAAAATAAAAAATAATTTCTG
*
434002 AAAACAAAATAAAAAATAATTTCT
1 AAAAAAAAATAAAAAATAATTTCT
434026 TAAATTGCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (25 bp):
AAAAAAAAATAAAAAATAATTTCTG
Found at i:441164 original size:16 final size:18
Alignment explanation
Indices: 441128--441167 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
441118 GTATTTTTTT
441128 ATATACTATATATAATGAA
1 ATATACTATATATAA-GAA
441147 ATATACT-TATATAA-AA
1 ATATACTATATATAAGAA
441163 ATATA
1 ATATA
441168 AATTTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
18 7 0.33
19 7 0.33
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (18 bp):
ATATACTATATATAAGAA
Found at i:444811 original size:32 final size:29
Alignment explanation
Indices: 444737--444847 Score: 125
Period size: 29 Copynumber: 3.7 Consensus size: 29
444727 CAGCTTCAAA
* *
444737 ACCAAGGAGGTCGCCATGCACTCCGAGCG
1 ACCAAGGAGGTCGTCATGCACTCCGGGCG
444766 ACCAAGGAGGTCGTCATGCACTCCGGGCG
1 ACCAAGGAGGTCGTCATGCACTCCGGGCG
* *
444795 ACCAAGGAGGAGGTCGTCATGCACTTCAGGCG
1 ACC-A--AGGAGGTCGTCATGCACTCCGGGCG
* *
444827 A-CATGGTAGGTCGCCATGCAC
1 ACCAAGG-AGGTCGTCATGCAC
444848 GCCCCGCGAC
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
28 2 0.03
29 43 0.60
30 2 0.03
31 1 0.01
32 24 0.33
ACGTcount: A:0.23, C:0.30, G:0.32, T:0.14
Consensus pattern (29 bp):
ACCAAGGAGGTCGTCATGCACTCCGGGCG
Found at i:444857 original size:61 final size:61
Alignment explanation
Indices: 444741--444858 Score: 141
Period size: 61 Copynumber: 1.9 Consensus size: 61
444731 TTCAAAACCA
* * * **
444741 AGGAGGTCGCCATGCACTCCGAGCGACCAAGGAGGTCGTCATGCACTCCGGGCGACCAAGG
1 AGGAGGTCGCCATGCACTCAGAGCGACCAAGGAGGTCGCCATGCACGCCCCGCGACCAAGG
* *
444802 AGGAGGTCGTCATGCACTTCAG-GCGA-CATGGTAGGTCGCCATGCACGCCCCGCGACC
1 AGGAGGTCGCCATGCAC-TCAGAGCGACCAAGG-AGGTCGCCATGCACGCCCCGCGACC
444859 TTGTTTTTGG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 4 0.08
61 41 0.85
62 3 0.06
ACGTcount: A:0.21, C:0.32, G:0.33, T:0.14
Consensus pattern (61 bp):
AGGAGGTCGCCATGCACTCAGAGCGACCAAGGAGGTCGCCATGCACGCCCCGCGACCAAGG
Found at i:445222 original size:6 final size:6
Alignment explanation
Indices: 445211--445246 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
445201 GTTTGTTAGT
*
445211 TTAGGG TTAGGG TTAGGG TTA-GT TTAGGG TTAGGG T
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG T
445247 AAAAAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.17, C:0.00, G:0.44, T:0.39
Consensus pattern (6 bp):
TTAGGG
Found at i:445237 original size:11 final size:11
Alignment explanation
Indices: 445205--445243 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
445195 TTATTAGTTT
445205 GTTAGTTTAGG
1 GTTAGTTTAGG
*
445216 GTTAGGGTTAGG
1 GTTA-GTTTAGG
445228 GTTAGTTTAGG
1 GTTAGTTTAGG
445239 GTTAG
1 GTTAG
445244 GGTAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.18, C:0.00, G:0.41, T:0.41
Consensus pattern (11 bp):
GTTAGTTTAGG
Found at i:445536 original size:15 final size:16
Alignment explanation
Indices: 445508--445541 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
445498 GTTTGTTACT
445508 TTATAAGTTTATTATA
1 TTATAAGTTTATTATA
445524 TTATAAG-TTATTATA
1 TTATAAGTTTATTATA
445539 TTA
1 TTA
445542 AATTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATAAGTTTATTATA
Found at i:447758 original size:49 final size:50
Alignment explanation
Indices: 447695--447867 Score: 206
Period size: 49 Copynumber: 3.3 Consensus size: 50
447685 ATTACTAATC
447695 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
* * *
447745 ATTACT-AATCATTACTATCAAATCACTAAATATTAATAATAATTTCGTT
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
*
447794 ATTACTAATCATTACTAAATTATTACTATCAAATCATTAAATATTAGTAATAATTTCATT
1 ATTACTAA--A-T-C---ATTA--A-TATCAAATCATTAAATATTAATAATAATTTCATT
447854 ATTACT-AATCATTA
1 ATTACTAAATCATTA
447868 CTAAATCATT
Statistics
Matches: 105, Mismatches: 7, Indels: 20
0.80 0.05 0.15
Matches are distributed among these distances:
49 46 0.44
50 7 0.07
52 5 0.05
53 1 0.01
54 1 0.01
55 1 0.01
56 1 0.01
57 5 0.05
59 1 0.01
60 37 0.35
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (50 bp):
ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
Found at i:447816 original size:21 final size:21
Alignment explanation
Indices: 447792--447878 Score: 67
Period size: 21 Copynumber: 4.3 Consensus size: 21
447782 AATAATTTCG
447792 TTATTACTAATCATTACTAAA
1 TTATTACTAATCATTACTAAA
* *
447813 TTATTACT-ATCAAATCATTAAA
1 TTATTACTAATC--ATTACTAAA
* * *
447835 -TATTAGTAATAATT--T-CA
1 TTATTACTAATCATTACTAAA
447852 TTATTACTAATCATTACTAAA
1 TTATTACTAATCATTACTAAA
*
447873 TCATTA
1 TTATTA
447879 TTATAATTTC
Statistics
Matches: 49, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
17 1 0.02
18 13 0.27
20 6 0.12
21 20 0.41
22 9 0.18
ACGTcount: A:0.43, C:0.13, G:0.01, T:0.44
Consensus pattern (21 bp):
TTATTACTAATCATTACTAAA
Found at i:447819 original size:60 final size:60
Alignment explanation
Indices: 447745--447878 Score: 225
Period size: 60 Copynumber: 2.2 Consensus size: 60
447735 TAATTTCATT
*
447745 ATTACT-AATCATTACTATCAAATCACTAAATATTAATAATAATTTCGTTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCACTAAATATTAATAATAATTTCATTATTACTAATC
* * *
447804 ATTACTAAATTATTACTATCAAATCATTAAATATTAGTAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCACTAAATATTAATAATAATTTCATTATTACTAATC
447864 ATTACTAAATCATTA
1 ATTACTAAATCATTA
447879 TTATAATTTC
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
59 6 0.09
60 63 0.91
ACGTcount: A:0.43, C:0.13, G:0.01, T:0.42
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCACTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:447971 original size:14 final size:14
Alignment explanation
Indices: 447952--447999 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
447942 TTCAAGTCGT
447952 AAATCATTACTATC
1 AAATCATTACTATC
447966 AAATCATTAC--T-
1 AAATCATTACTATC
*
447977 AAATCATTAATATC
1 AAATCATTACTATC
447991 AAATCATTA
1 AAATCATTA
448000 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:447979 original size:25 final size:25
Alignment explanation
Indices: 447951--448420 Score: 107
Period size: 25 Copynumber: 19.3 Consensus size: 25
447941 GTTCAAGTCG
*
447951 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATCAAATCATTAC
447976 TAAATCATTAATATCAAATCA-T--
1 TAAATCATTAATATCAAATCATTAC
* *
447998 TAAAT-ATTAATAAT-AAATTATTAT
1 TAAATCATTAAT-ATCAAATCATTAC
448022 TAATAATCATTAATATCAAATCA-T--
1 T-A-AATCATTAATATCAAATCATTAC
* *
448046 TAAAT-ATTAATAAT-AATTTCATTAT
1 TAAATCATTAAT-ATCAA-ATCATTAC
*
448071 TACTAATCATT-AT-T-AAATCATTAGTA
1 TA--AATCATTAATATCAAATCATTA--C
*
448097 TCAAATCATTAAATAT-TAAT-A--A-
1 T-AAATCATT-AATATCAAATCATTAC
* * *
448119 TAAATTATTATTA-CTAATCATTAC
1 TAAATCATTAATATCAAATCATTAC
*
448143 T-AATCATTACTATCAAATCA-T--
1 TAAATCATTAATATCAAATCATTAC
* *
448164 TAAAT-ATTAATAAT-AAATTATTAT
1 TAAATCATTAAT-ATCAAATCATTAC
*
448188 TACTAATCATTACTATCAAATCATTA-
1 TA--AATCATTAATATCAAATCATTAC
* * * *** *
448214 AAAATTAATAATAATTTTATTATTAC
1 TAAATCATTAAT-ATCAAATCATTAC
* *
448240 T-AATCATT--TCT-AAATCATTAATA
1 TAAATCATTAATATCAAATCATT-A-C
*
448263 TCAAATCATTAAATAT-TAAT-A--A-
1 T-AAATCATT-AATATCAAATCATTAC
* * *
448285 TAATTTCATTATTA-CTAATCATTAC
1 TAA-ATCATTAATATCAAATCATTAC
* *
448310 TAAATCATTACTATCAAATCATTATTAT
1 TAAATCATTAATATCAAATC---ATTAC
* * *
448338 TAAATCATTATTAT--AATGATTAT
1 TAAATCATTAATATCAAATCATTAC
* * * *
448361 TATAATGATTATTATTAAATCATTAT
1 TA-AATCATTAATATCAAATCATTAC
* *
448387 TATAATGATTATTATCAAATCATTAC
1 TA-AATCATTAATATCAAATCATTAC
448413 TAAATCAT
1 TAAATCAT
448421 CAAATCATTA
Statistics
Matches: 339, Mismatches: 47, Indels: 118
0.67 0.09 0.23
Matches are distributed among these distances:
20 7 0.02
21 52 0.15
22 32 0.09
23 22 0.06
24 46 0.14
25 67 0.20
26 50 0.15
27 34 0.10
28 29 0.09
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAC
Found at i:448000 original size:14 final size:14
Alignment explanation
Indices: 447952--448048 Score: 65
Period size: 14 Copynumber: 6.7 Consensus size: 14
447942 TTCAAGTCGT
*
447952 AAATCATTACTATC
1 AAATCATTAATATC
*
447966 AAATCATT-A-CT-
1 AAATCATTAATATC
447977 AAATCATTAATATC
1 AAATCATTAATATC
*
447991 AAATCATTAAATATTA
1 AAATCATT-AATA-TC
* * *
448007 ATAATAAATTATTATTA
1 A-AAT-CATTAATA-TC
448024 ATAATCATTAATATC
1 A-AATCATTAATATC
448039 AAATCATTAA
1 AAATCATTAA
448049 ATATTAATAA
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
11 8 0.12
12 2 0.03
13 1 0.01
14 25 0.37
15 6 0.09
16 8 0.12
17 14 0.21
18 3 0.04
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATCATTAATATC
Found at i:448034 original size:48 final size:49
Alignment explanation
Indices: 447978--448093 Score: 186
Period size: 48 Copynumber: 2.4 Consensus size: 49
447968 ATCATTACTA
447978 AATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATTATTAAT
1 AATCATTAATATCAAATCATTAAATATTAATAATAAATTCATTATTAAT
* *
448026 AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTAATATCAAATCATTAAATATTAATAATAAATTCATTATTAAT
448075 AATCATT-AT-T-AAATCATTA
1 AATCATTAATATCAAATCATTA
448094 GTATCAAATC
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
46 9 0.14
47 1 0.02
48 40 0.62
49 15 0.23
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (49 bp):
AATCATTAATATCAAATCATTAAATATTAATAATAAATTCATTATTAAT
Found at i:448143 original size:10 final size:10
Alignment explanation
Indices: 448128--448154 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
448118 ATAAATTATT
448128 ATTACTAATC
1 ATTACTAATC
448138 ATTACTAATC
1 ATTACTAATC
448148 ATTACTA
1 ATTACTA
448155 TCAAATCATT
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:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:448160 original size:166 final size:168
Alignment explanation
Indices: 447967--448333 Score: 641
Period size: 166 Copynumber: 2.2 Consensus size: 168
447957 ATTACTATCA
*
447967 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTAATAATCAT
1 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTAATAATCAT
* *
448032 TAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAT-TAAATCATTAGT
66 TAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATT-TCTAAATCATTAAT
448096 ATCAAATCATTAAATATTAATAATAAATT-ATTATTACT
130 ATCAAATCATTAAATATTAATAATAAATTCATTATTACT
*
448134 AATCATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCAT
1 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTAATAATCAT
* *
448198 TACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACTAATCATTTCTAAATCATTAATA
66 TAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTTCTAAATCATTAATA
*
448263 TCAAATCATTAAATATTAATAATAATTTCATTATTACT
131 TCAAATCATTAAATATTAATAATAAATTCATTATTACT
448301 AATCATTACTAAATCATTACTATCAAATCATTA
1 AATCATTACTAAATCATTACTATCAAATCATTA
448334 TTATTAAATC
Statistics
Matches: 190, Mismatches: 7, Indels: 5
0.94 0.03 0.02
Matches are distributed among these distances:
165 1 0.01
166 138 0.73
167 29 0.15
168 22 0.12
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (168 bp):
AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTAATAATCAT
TAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTTCTAAATCATTAATA
TCAAATCATTAAATATTAATAATAAATTCATTATTACT
Found at i:448195 original size:48 final size:49
Alignment explanation
Indices: 448138--448247 Score: 195
Period size: 48 Copynumber: 2.3 Consensus size: 49
448128 ATTACTAATC
*
448138 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAA-ATTATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATATTATT
*
448186 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATATTATT
448235 ATTACTAATCATT
1 ATTACTAATCATT
448248 TCTAAATCAT
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
48 41 0.69
49 18 0.31
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATATTATT
Found at i:448265 original size:60 final size:60
Alignment explanation
Indices: 448186--448333 Score: 253
Period size: 60 Copynumber: 2.5 Consensus size: 60
448176 ATAAATTATT
*
448186 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* * *
448245 ATTTCTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
448305 ATTACTAAATCATTACTATCAAATCATTA
1 ATTACTAAATCATTACTATCAAATCATTA
448334 TTATTAAATC
Statistics
Matches: 82, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
59 5 0.06
60 77 0.94
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:448332 original size:38 final size:40
Alignment explanation
Indices: 448290--448498 Score: 187
Period size: 38 Copynumber: 5.2 Consensus size: 40
448280 AATAATAATT
* * * *
448290 TCATTATTACT-AATCATTACTA-AATCATTACTATCAAA
1 TCATTATTATTAAATCATTATTATAATGATTATTATCAAA
448328 TCATTATTATTAAATCATTATTATAATGATTATTAT--AA
1 TCATTATTATTAAATCATTATTATAATGATTATTATCAAA
*
448366 TGATTATTATTAAATCATTATTATAATGATTATTATCAAA
1 TCATTATTATTAAATCATTATTATAATGATTATTATCAAA
* * *
448406 TCATTACTAAATCATCAAATCATTAAATATTTAA--ATTATTATTATAA
1 TCATTA-T---T-ATTAAATCATT--AT-TATAATGATTATTATCA-AA
* * * *
448453 TGATTATTATCAAATTATTATTATAATGATTATTATCATA
1 TCATTATTATTAAATCATTATTATAATGATTATTATCAAA
448493 TCATTA
1 TCATTA
448499 CTAAATCATC
Statistics
Matches: 141, Mismatches: 15, Indels: 28
0.77 0.08 0.15
Matches are distributed among these distances:
38 47 0.33
39 14 0.10
40 25 0.18
41 10 0.07
42 10 0.07
43 1 0.01
44 1 0.01
45 10 0.07
46 10 0.07
47 9 0.06
48 4 0.03
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (40 bp):
TCATTATTATTAAATCATTATTATAATGATTATTATCAAA
Found at i:448385 original size:26 final size:26
Alignment explanation
Indices: 448292--448411 Score: 122
Period size: 26 Copynumber: 4.7 Consensus size: 26
448282 TAATAATTTC
* * *
448292 ATTATTACT-AATCATTACTA-AATC
1 ATTATTATTAAATCATTATTATAATG
* *
448316 ATTACTATCAAATCATTATTATTAA--
1 ATTATTATTAAATCATTATTA-TAATG
* *
448341 ATCATTATTATAATGATTATTATAATG
1 ATTATTATTA-AATCATTATTATAATG
448368 ATTATTATTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATG
*
448394 ATTATTATCAAATCATTA
1 ATTATTATTAAATCATTA
448412 CTAAATCATC
Statistics
Matches: 79, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
24 6 0.08
25 20 0.25
26 42 0.53
27 11 0.14
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (26 bp):
ATTATTATTAAATCATTATTATAATG
Found at i:448456 original size:87 final size:87
Alignment explanation
Indices: 448356--448545 Score: 321
Period size: 87 Copynumber: 2.2 Consensus size: 87
448346 TATTATAATG
*
448356 ATTATTATAATGATTATTATTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCAT
1 ATTATTATAATGATTATTATCAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCAT
448421 CAAATCATTAAATATTTAAATT-
66 CAAATCATTAAATA-TTAAATTC
* *
448443 ATTATTATAATGATTATTATCAAATTATTATTATAATGATTATTATCATATCATTACTAAATCAT
1 ATTATTATAATGATTATTATCAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCAT
448508 CAAATCATTAAATATTAAATTC
66 CAAATCATTAAATATTAAATTC
*
448530 ATTATTA-AATCATTAT
1 ATTATTATAATGATTAT
448546 AATGATTATT
Statistics
Matches: 98, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
86 15 0.15
87 83 0.85
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.45
Consensus pattern (87 bp):
ATTATTATAATGATTATTATCAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCAT
CAAATCATTAAATATTAAATTC
Found at i:448467 original size:26 final size:26
Alignment explanation
Indices: 448438--448490 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
448428 TTAAATATTT
448438 AAATTATTATTATAATGATTATTATC
1 AAATTATTATTATAATGATTATTATC
448464 AAATTATTATTATAATGATTATTATC
1 AAATTATTATTATAATGATTATTATC
448490 A
1 A
448491 TATCATTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (26 bp):
AAATTATTATTATAATGATTATTATC
Found at i:448761 original size:17 final size:18
Alignment explanation
Indices: 448741--448775 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
448731 TATTAGTAAA
448741 TCATTATTATT-ATAATT
1 TCATTATTATTAATAATT
448758 TCATTATTATTAATAATT
1 TCATTATTATTAATAATT
448776 ACTAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TCATTATTATTAATAATT
Found at i:452082 original size:20 final size:21
Alignment explanation
Indices: 452067--452108 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
452057 TATAAATTAA
452067 ACAAAATATTTTTAAAACAAC
1 ACAAAATATTTTTAAAACAAC
*
452088 ACTAAATATTTTTAAACACAA
1 ACAAAATATTTTTAAA-ACAA
452109 TATTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (21 bp):
ACAAAATATTTTTAAAACAAC
Found at i:452436 original size:28 final size:30
Alignment explanation
Indices: 452395--452456 Score: 110
Period size: 28 Copynumber: 2.1 Consensus size: 30
452385 ATTTTTTATA
452395 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
452425 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
452453 TAAT
1 TAAT
452457 TAACCAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:452584 original size:14 final size:15
Alignment explanation
Indices: 452562--452594 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
452552 ATGTTTGAGC
452562 CTTTATCTT-CTTTT
1 CTTTATCTTCCTTTT
*
452576 CTTTTTCTTCCTTTT
1 CTTTATCTTCCTTTT
452591 CTTT
1 CTTT
452595 CTCTCGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (15 bp):
CTTTATCTTCCTTTT
Found at i:452912 original size:23 final size:23
Alignment explanation
Indices: 452882--452926 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
452872 GCTTGGCTAC
452882 AATCTCCCAGCTATGGATGCAAG
1 AATCTCCCAGCTATGGATGCAAG
452905 AATCTCCCAGCTATGGATGCAA
1 AATCTCCCAGCTATGGATGCAA
452927 CCCATGCACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (23 bp):
AATCTCCCAGCTATGGATGCAAG
Found at i:452969 original size:22 final size:22
Alignment explanation
Indices: 452941--452986 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
452931 TGCACGAGGG
*
452941 AGCAGGGTTAAGTTTGGTCGCC
1 AGCAGGGATAAGTTTGGTCGCC
452963 AGCAGGGATAAGTTTGGTCGCC
1 AGCAGGGATAAGTTTGGTCGCC
452985 AG
1 AG
452987 AGCTTGGTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.37, T:0.24
Consensus pattern (22 bp):
AGCAGGGATAAGTTTGGTCGCC
Found at i:453052 original size:29 final size:29
Alignment explanation
Indices: 453020--453078 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
453010 GCGACCTACA
*
453020 AGGTCGCTGGGAGTGCATGGCGACCTTGT
1 AGGTCGATGGGAGTGCATGGCGACCTTGT
453049 AGGTCGATGGGAGTGCATGGCGACCTTGT
1 AGGTCGATGGGAGTGCATGGCGACCTTGT
453078 A
1 A
453079 TTATAGGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.17, C:0.19, G:0.41, T:0.24
Consensus pattern (29 bp):
AGGTCGATGGGAGTGCATGGCGACCTTGT
Found at i:453145 original size:33 final size:33
Alignment explanation
Indices: 453098--453167 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
453088 ACTTGGAGTG
453098 CATGGCGACCTGTGTTGGGGTGCTGGGGACGTA
1 CATGGCGACCTGTGTTGGGGTGCTGGGGACGTA
* * *
453131 CATGGCGACTTGTGTTGGGGTGTTGGGGACGTG
1 CATGGCGACCTGTGTTGGGGTGCTGGGGACGTA
453164 CATG
1 CATG
453168 TGCCATGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.16, G:0.46, T:0.27
Consensus pattern (33 bp):
CATGGCGACCTGTGTTGGGGTGCTGGGGACGTA
Found at i:455399 original size:8 final size:8
Alignment explanation
Indices: 455386--455418 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
455376 GTGTAAGTGA
455386 ACTATGTG
1 ACTATGTG
455394 ACTATGTG
1 ACTATGTG
455402 ACTATGTG
1 ACTATGTG
455410 ACTATGTG
1 ACTATGTG
455418 A
1 A
455419 TAATATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.36
Consensus pattern (8 bp):
ACTATGTG
Found at i:455831 original size:149 final size:148
Alignment explanation
Indices: 455562--455864 Score: 498
Period size: 149 Copynumber: 2.0 Consensus size: 148
455552 GAGTCGAGGG
* * * * * * * *
455562 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTTTGAGGCATATA
1 TCTACGCGGTCCTTCGGGACATATATATATTATGTGGAACATGTATGAAGTCTTTAAGACACATA
*
455627 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
66 CTTGATCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
455692 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
* *
455710 TCTACGCGGTCCTTCGGGATATATATATATTATGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTATGTGGAACATGTATGAAGTCTT-TAAGACACAT
455775 ACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
455840 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
455859 TCTACG
1 TCTACG
455865 TGCACTTCGG
Statistics
Matches: 143, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
148 47 0.33
149 96 0.67
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGACATATATATATTATGTGGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
ATGGCACTACGGTGCAAT
Found at i:455886 original size:22 final size:22
Alignment explanation
Indices: 455844--455886 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
455834 TTATTATATG
**
455844 GCACTACGGTGCAATTCTACGT
1 GCACTACGGTGCAATGATACGT
*
455866 GCACTTCGGTGCAATGATACG
1 GCACTACGGTGCAATGATACG
455887 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (22 bp):
GCACTACGGTGCAATGATACGT
Found at i:461102 original size:149 final size:148
Alignment explanation
Indices: 460833--461135 Score: 516
Period size: 149 Copynumber: 2.0 Consensus size: 148
460823 GAGTCGAGGG
* * * * * *
460833 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
*
460898 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
66 CTTGATCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
460963 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
* *
460981 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACAT
461046 ACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
461111 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
461130 TCTACG
1 TCTACG
461136 TGCACTTCGG
Statistics
Matches: 145, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
148 48 0.33
149 97 0.67
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.37
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
ATGGCACTACGGTGCAAT
Found at i:461157 original size:22 final size:22
Alignment explanation
Indices: 461115--461157 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
461105 TTATTATATG
**
461115 GCACTACGGTGCAATTCTACGT
1 GCACTACGGTGCAATGATACGT
*
461137 GCACTTCGGTGCAATGATACG
1 GCACTACGGTGCAATGATACG
461158 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (22 bp):
GCACTACGGTGCAATGATACGT
Found at i:466994 original size:37 final size:36
Alignment explanation
Indices: 466874--466995 Score: 93
Period size: 37 Copynumber: 3.2 Consensus size: 36
466864 TGATAATTAG
* *
466874 TATGATTACTTTTTAAAAGTTAAAACAAATTGTTAGT
1 TATGATTACTTTTTAAAAGTT-AAATAAATTGTTAAT
* * * *
466911 TATGATAATTTTTTTGACAA-TTAAATAAACTATGATAACT
1 TATGATTA-CTTTTT-AAAAGTTAAATAAA-T-TGTTAA-T
*
466951 AATATGATTACTCTTTAAAAGTTAATATAAATTGTTAAT
1 --TATGATTACTTTTTAAAAGTTAA-ATAAATTGTTAAT
466990 TATGAT
1 TATGAT
466996 AATTAAATTA
Statistics
Matches: 65, Mismatches: 11, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
37 19 0.29
38 8 0.12
39 8 0.12
40 9 0.14
41 9 0.14
42 12 0.18
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (36 bp):
TATGATTACTTTTTAAAAGTTAAATAAATTGTTAAT
Found at i:467058 original size:13 final size:14
Alignment explanation
Indices: 467023--467060 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
467013 ATTTTCTATA
467023 TTAATTAT-AATCC
1 TTAATTATAAATCC
467036 TTATATTATAAAT-C
1 TTA-ATTATAAATCC
467050 TTAATTATAAA
1 TTAATTATAAA
467061 CAGTAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 11 0.48
14 9 0.39
15 3 0.13
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
TTAATTATAAATCC
Found at i:467489 original size:39 final size:40
Alignment explanation
Indices: 467415--467490 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 40
467405 TAAAAGAGGG
* * *
467415 AAAATTGATTTTTTTGAGAATTTAGAAGAGAGAAGAGGAA
1 AAAATTGATTTTGTTGAGAATTTAAAAAAGAGAAGAGGAA
* *
467455 AAAATTGA-TTTGTTGGGAATTTAAAAAAGGGAAGAG
1 AAAATTGATTTTGTTGAGAATTTAAAAAAGAGAAGAG
467491 ATTTTTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
39 23 0.74
40 8 0.26
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (40 bp):
AAAATTGATTTTGTTGAGAATTTAAAAAAGAGAAGAGGAA
Found at i:467753 original size:2 final size:2
Alignment explanation
Indices: 467746--467865 Score: 67
Period size: 2 Copynumber: 60.0 Consensus size: 2
467736 ATGTTTAATG
467746 AT AT AT AT AT AT AGT -T ACT -T AT AT ACT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT A-T AT AT AT A-T AT AT AT AT AT AT AT
* *
467786 AT AT AT ACT -T AT AT AT -T AT ACT TT AT ACT -T AT AT AT AT TT
1 AT AT AT A-T AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT
* * *
467826 AT AT AC AT AC CT AT AT AT AGT -T ACT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT A-T AT AT AT AT AT AT AT AT
467866 GTGTGTGTGT
Statistics
Matches: 92, Mismatches: 10, Indels: 32
0.69 0.07 0.24
Matches are distributed among these distances:
1 8 0.09
2 76 0.83
3 8 0.09
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:467759 original size:30 final size:30
Alignment explanation
Indices: 467725--467865 Score: 99
Period size: 32 Copynumber: 4.8 Consensus size: 30
467715 AATCTTTTAT
*
467725 TATAGTCACTTATGT-TTA-ATGATATATATA
1 TATAGT-ACTTATATATTATAT-ATATATATA
467755 TATAGTTACTTATATACTTATATATATATATA
1 TATAG-TACTTATATA-TTATATATATATATA
*
467787 TATA-TACTTATATATTATACT-T-TATA-C
1 TATAGTACTTATATATTATA-TATATATATA
*
467814 T-TA-TA--TATAT-TTATATACATACCTATA
1 TATAGTACTTATATATTATATATATA--TATA
467841 TATAGTTACTTATATA-TATATATAT
1 TATAG-TACTTATATATTATATATAT
467866 GTGTGTGTGT
Statistics
Matches: 90, Mismatches: 5, Indels: 30
0.72 0.04 0.24
Matches are distributed among these distances:
22 1 0.01
23 5 0.06
24 7 0.08
26 6 0.07
27 2 0.02
28 6 0.07
29 6 0.07
30 25 0.28
31 1 0.01
32 29 0.32
33 2 0.02
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.50
Consensus pattern (30 bp):
TATAGTACTTATATATTATATATATATATA
Found at i:467779 original size:22 final size:21
Alignment explanation
Indices: 467751--467865 Score: 107
Period size: 22 Copynumber: 5.4 Consensus size: 21
467741 TAATGATATA
467751 TATATATAGTTACTTATATACT
1 TATATATA-TTACTTATATACT
467773 TATATATATATA-TATATATACT
1 TATATATAT-TACT-TATATACT
467795 TATATAT-TATACTT-TATACT
1 TATATATAT-TACTTATATACT
* *
467815 TATATATATTTA-TATACATACC
1 TATATATA-TTACT-TATATACT
467837 TATATATAGTTACTTATATA--
1 TATATATA-TTACTTATATACT
467857 TATATATAT
1 TATATATAT
467866 GTGTGTGTGT
Statistics
Matches: 81, Mismatches: 4, Indels: 19
0.78 0.04 0.18
Matches are distributed among these distances:
19 1 0.01
20 22 0.27
21 10 0.12
22 47 0.58
23 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (21 bp):
TATATATATTACTTATATACT
Found at i:467854 original size:42 final size:42
Alignment explanation
Indices: 467751--467865 Score: 148
Period size: 42 Copynumber: 2.8 Consensus size: 42
467741 TAATGATATA
*
467751 TATATATAGTTACTTATATACTTATATATATATATATATATAC
1 TATATATAGTTACTT-TATACTTATATATATATATATACATAC
* *
467794 T-TATATATTATACTTTATACTTATATATATTTATATACATACC
1 TATATATAGT-TACTTTATACTTATATATATATATATACATA-C
467837 TATATATAGTTAC-TTATA--TATATATATAT
1 TATATATAGTTACTTTATACTTATATATATAT
467866 GTGTGTGTGT
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
40 10 0.16
42 36 0.56
43 11 0.17
44 7 0.11
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (42 bp):
TATATATAGTTACTTTATACTTATATATATATATATACATAC
Found at i:467907 original size:18 final size:17
Alignment explanation
Indices: 467884--467934 Score: 68
Period size: 16 Copynumber: 3.0 Consensus size: 17
467874 GTGTATGTGT
*
467884 GTATAATTATATATATA
1 GTATAAGTATATATATA
*
467901 GGTATAAGTATACATAT-
1 -GTATAAGTATATATATA
467918 GTATAAGTATATATATA
1 GTATAAGTATATATATA
467935 CTTTTATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 15 0.52
18 14 0.48
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.41
Consensus pattern (17 bp):
GTATAAGTATATATATA
Found at i:467999 original size:16 final size:17
Alignment explanation
Indices: 467968--468006 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
467958 TAATGTATTG
* *
467968 TTATATATATTATATAT
1 TTATATATAGTATATAC
467985 TTATATA-AGTATATAC
1 TTATATATAGTATATAC
468001 TTATAT
1 TTATAT
468007 TGTATGCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
TTATATATAGTATATAC
Found at i:468777 original size:2 final size:2
Alignment explanation
Indices: 468728--468761 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
468718 ATGCATGGAA
*
468728 AT AT -T AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
468762 ACTATACGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:469644 original size:187 final size:186
Alignment explanation
Indices: 469323--469709 Score: 720
Period size: 187 Copynumber: 2.1 Consensus size: 186
469313 ATATTTGTTT
*
469323 CATTACTTAATGGAGAACATGATCCATCAAAGATTTCATATTGGAAGAATCAAAGGATAAAACTT
1 CATTA-TTAATGGAGAACATGATCCATCAAAGATTTCATATTGGAAGAATCAAACGATAAAACTT
*
469388 TGATCAAAGTGGTCTGTTCATAGATGGAAACAGAAACATGTACGAGCTAAAGTGTGTGAATCATT
65 TGATCAAAGTGGTCTGTTCATAGATGGAAACAGAAACATGTACAAGCTAAAGTGTGTGAATCATT
469453 GGGCCGACTGGCTGATGTATATTTAACAAAGATAGAGAACTTGTGCAGAATCTGCAC
130 GGGCCGACTGGCTGATGTATATTTAACAAAGATAGAGAACTTGTGCAGAATCTGCAC
469510 CATTAGTTAATGGAGAACATGATCCATCAAAGATTTCATATTGGAAGAATCAAACGATAAAACTT
1 CATTA-TTAATGGAGAACATGATCCATCAAAGATTTCATATTGGAAGAATCAAACGATAAAACTT
*
469575 TGATCAAAGTGGTCTGTTCATAGATGGAAACAGACACATGTACAAGCTAAAGTGTGTGAATCATT
65 TGATCAAAGTGGTCTGTTCATAGATGGAAACAGAAACATGTACAAGCTAAAGTGTGTGAATCATT
469640 GGGCCGACTGGCTGATGTATATTTAACAAAGATAGAGAACTTGTGCAGAATCTGCAC
130 GGGCCGACTGGCTGATGTATATTTAACAAAGATAGAGAACTTGTGCAGAATCTGCAC
*
469697 CATTATTATTGGA
1 CATTATTAATGGA
469710 AAAGAAAGGG
Statistics
Matches: 195, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
186 7 0.04
187 188 0.96
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.27
Consensus pattern (186 bp):
CATTATTAATGGAGAACATGATCCATCAAAGATTTCATATTGGAAGAATCAAACGATAAAACTTT
GATCAAAGTGGTCTGTTCATAGATGGAAACAGAAACATGTACAAGCTAAAGTGTGTGAATCATTG
GGCCGACTGGCTGATGTATATTTAACAAAGATAGAGAACTTGTGCAGAATCTGCAC
Found at i:475874 original size:25 final size:23
Alignment explanation
Indices: 475813--475867 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
475803 CTTTGTCAGT
475813 TTTCCCTCTGGTGTCGTGTGTAG
1 TTTCCCTCTGGTGTCGTGTGTAG
475836 TTTCCCTCTGGTGTCGTGTGTAG
1 TTTCCCTCTGGTGTCGTGTGTAG
475859 TTTCCCTCT
1 TTTCCCTCT
475868 TAGGTGTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.04, C:0.25, G:0.25, T:0.45
Consensus pattern (23 bp):
TTTCCCTCTGGTGTCGTGTGTAG
Found at i:484045 original size:6 final size:6
Alignment explanation
Indices: 484034--484106 Score: 60
Period size: 6 Copynumber: 11.3 Consensus size: 6
484024 GTAATTTTTT
*
484034 TAATAA TAATAA TAAT-A TATATAA TAATATA TATTATA TATATATA TATATAA
1 TAATAA TAATAA TAATAA TA-ATAA TAATA-A TAATA-A TA-ATA-A TA-ATAA
484087 TAATAA TAAT-A TAAATAA TA
1 TAATAA TAATAA T-AATAA TA
484107 TTTAAATGAA
Statistics
Matches: 59, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
5 5 0.08
6 27 0.46
7 17 0.29
8 10 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (6 bp):
TAATAA
Found at i:484053 original size:2 final size:2
Alignment explanation
Indices: 484048--484085 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
484038 AATAATAATA
484048 AT AT AT AT A- AT A- AT AT AT AT -T AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
484086 ATAATAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:484675 original size:97 final size:96
Alignment explanation
Indices: 484488--484681 Score: 271
Period size: 97 Copynumber: 2.0 Consensus size: 96
484478 TTGTAAACTT
* *
484488 TTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCAAACTGGAAAAGCTGATCCATCAAGTGAT
1 TTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCAAACTGGAAAAGCTAATCCATCAAATGAT
* ** * *
484553 GGATTTGAGCAAAAGGTTGAACAAATTCTTC
66 GAATTCAAACAAAAGGTTAAACAAATTCTTC
* * ***
484584 TTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTACCATGGAAATTTTAATCCATCAAATGA
1 TTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCAAAC-TGGAAAAGCTAATCCATCAAATGA
484649 TGAATTCAAACAAAAGGTTAAACAAATTCTTC
65 TGAATTCAAACAAAAGGTTAAACAAATTCTTC
484681 T
1 T
484682 CATTATGAAC
Statistics
Matches: 85, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
96 38 0.45
97 47 0.55
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (96 bp):
TTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCAAACTGGAAAAGCTAATCCATCAAATGAT
GAATTCAAACAAAAGGTTAAACAAATTCTTC
Found at i:484977 original size:113 final size:113
Alignment explanation
Indices: 484595--484989 Score: 583
Period size: 113 Copynumber: 3.5 Consensus size: 113
484585 TTCTTCAGAT
* **
484595 GATGAGTTCTTCTCATTATGAACTCTACCATGGAAATTTTAATCCATCAAATGATGAATTCAAAC
1 GATGAGTTCTTCTCATTATGAACTCTATC-TGGAAATGCTAATCCATCAAATGATGAATTCAAAC
*
484660 AAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
65 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* * * * *
484709 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAGCA
1 GATGAGTTCTTCTCATTATGAACTCTATCTGGAAATGCTAATCCATCAAATGATGAATTCAAACA
* *
484774 AAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
66 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* * * * * *
484822 GATGAGTTCTTCTTATTATGAACTCTTTCTGGCAATGTTAATCCATCAAATAATGAATTTAAACA
1 GATGAGTTCTTCTCATTATGAACTCTATCTGGAAATGCTAATCCATCAAATGATGAATTCAAACA
484887 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
66 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* * * * *
484935 GATGAGTTCTTCTTATTATGAACTCGAACTGGTAATGCTAATCCATCAATTGATG
1 GATGAGTTCTTCTCATTATGAACTCTATCTGGAAATGCTAATCCATCAAATGATG
484990 GATTTGAATC
Statistics
Matches: 251, Mismatches: 30, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
113 225 0.90
114 26 0.10
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (113 bp):
GATGAGTTCTTCTCATTATGAACTCTATCTGGAAATGCTAATCCATCAAATGATGAATTCAAACA
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
Found at i:486116 original size:23 final size:23
Alignment explanation
Indices: 486086--486129 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
486076 GCTTGGCTAC
*
486086 AATCTCCCATCTATGGATGCAGG
1 AATCTCCCAGCTATGGATGCAGG
486109 AATCTCCCAGCTATGGATGCA
1 AATCTCCCAGCTATGGATGCA
486130 ACCCATGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (23 bp):
AATCTCCCAGCTATGGATGCAGG
Found at i:486173 original size:22 final size:22
Alignment explanation
Indices: 486145--486190 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
486135 TGCACGAGGG
*
486145 AGCAGGGTTAAGTTTGGTCGCC
1 AGCAGGGATAAGTTTGGTCGCC
486167 AGCAGGGATAAGTTTGGTCGCC
1 AGCAGGGATAAGTTTGGTCGCC
486189 AG
1 AG
486191 AGCGACCAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.37, T:0.24
Consensus pattern (22 bp):
AGCAGGGATAAGTTTGGTCGCC
Found at i:486263 original size:22 final size:22
Alignment explanation
Indices: 486232--486274 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
486222 CATGAGGGAG
*
486232 CAGGGTTAAGTTTGGTCGCCAA
1 CAGGGATAAGTTTGGTCGCCAA
486254 CAGGGATAAGTTTGGTCGCCA
1 CAGGGATAAGTTTGGTCGCCA
486275 GAGCTTGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.26
Consensus pattern (22 bp):
CAGGGATAAGTTTGGTCGCCAA
Found at i:486377 original size:34 final size:30
Alignment explanation
Indices: 486309--486397 Score: 117
Period size: 34 Copynumber: 2.9 Consensus size: 30
486299 GCGACCTACA
486309 AGGTCGCTGGGAGTGCATGGCGACC-TTGT
1 AGGTCGCTGGGAGTGCATGGCGACCTTTGT
*
486338 AGGTCGATGGGAGTGCATGGCGACCTTGTATTGT
1 AGGTCGCTGGGAGTGCATGGCGACC---T-TTGT
*
486372 AGGTCGCTTGGAGTGCATGGCGACCT
1 AGGTCGCTGGGAGTGCATGGCGACCT
486398 GTGTTGGGGT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
29 24 0.46
31 1 0.02
34 27 0.52
ACGTcount: A:0.16, C:0.19, G:0.39, T:0.26
Consensus pattern (30 bp):
AGGTCGCTGGGAGTGCATGGCGACCTTTGT
Found at i:486429 original size:33 final size:33
Alignment explanation
Indices: 486387--486456 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
486377 GCTTGGAGTG
486387 CATGGCGACCTGTGTTGGGGTGCTGGGGACGTA
1 CATGGCGACCTGTGTTGGGGTGCTGGGGACGTA
* *
486420 CATGGCGACCTGTGTTGGGGTGTTGGGGACGTG
1 CATGGCGACCTGTGTTGGGGTGCTGGGGACGTA
486453 CATG
1 CATG
486457 TGCCATGCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.17, G:0.46, T:0.26
Consensus pattern (33 bp):
CATGGCGACCTGTGTTGGGGTGCTGGGGACGTA
Found at i:491650 original size:37 final size:36
Alignment explanation
Indices: 491530--491651 Score: 93
Period size: 37 Copynumber: 3.2 Consensus size: 36
491520 TGATAATTAG
* *
491530 TATGATTACTTTTTAAAAGTTAAAACAAATTGTTAGT
1 TATGATTACTTTTTAAAAGTT-AAATAAATTGTTAAT
* * * *
491567 TATGATAATTTTTTTGACAA-TTAAATAAACTATGATAACT
1 TATGATTA-CTTTTT-AAAAGTTAAATAAA-T-TGTTAA-T
*
491607 AATATGATTACTCTTTAAAAGTTAATATAAATTGTTAAT
1 --TATGATTACTTTTTAAAAGTTAA-ATAAATTGTTAAT
491646 TATGAT
1 TATGAT
491652 AATTAAATTA
Statistics
Matches: 65, Mismatches: 11, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
37 19 0.29
38 8 0.12
39 8 0.12
40 9 0.14
41 9 0.14
42 12 0.18
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (36 bp):
TATGATTACTTTTTAAAAGTTAAATAAATTGTTAAT
Found at i:491714 original size:13 final size:14
Alignment explanation
Indices: 491679--491716 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
491669 ATTTTCTATA
491679 TTAATTAT-AATCC
1 TTAATTATAAATCC
491692 TTATATTATAAAT-C
1 TTA-ATTATAAATCC
491706 TTAATTATAAA
1 TTAATTATAAA
491717 CAGTAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 11 0.48
14 9 0.39
15 3 0.13
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
TTAATTATAAATCC
Found at i:492147 original size:39 final size:40
Alignment explanation
Indices: 492073--492148 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 40
492063 TAAAAGAGGG
* * *
492073 AAAATTGATTTTTTTGAGAATTTAGAAGAGAGAAGAGGAA
1 AAAATTGATTTTGTTGAGAATTTAAAAAAGAGAAGAGGAA
* *
492113 AAAATTGA-TTTGTTGGGAATTTAAAAAAGGGAAGAG
1 AAAATTGATTTTGTTGAGAATTTAAAAAAGAGAAGAG
492149 ATTTTTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
39 23 0.74
40 8 0.26
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (40 bp):
AAAATTGATTTTGTTGAGAATTTAAAAAAGAGAAGAGGAA
Found at i:492411 original size:2 final size:2
Alignment explanation
Indices: 492404--492523 Score: 67
Period size: 2 Copynumber: 60.0 Consensus size: 2
492394 ATGTTTAATG
492404 AT AT AT AT AT AT AGT -T ACT -T AT AT ACT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT A-T AT AT AT A-T AT AT AT AT AT AT AT
*
492444 AT AT AT AT ACT -T AT AT AT -T AT ACT TT AT ACT -T AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT
* * * *
492484 TT AT AT AC AT AC CT AT AT AT AGT -T ACT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT A-T AT AT AT AT AT AT AT
492524 GTGTGTGTGT
Statistics
Matches: 92, Mismatches: 10, Indels: 32
0.69 0.07 0.24
Matches are distributed among these distances:
1 8 0.09
2 76 0.83
3 8 0.09
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:492417 original size:30 final size:31
Alignment explanation
Indices: 492383--492465 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 31
492373 AATCTTTTAT
*
492383 TATAGTCACTTATGT-TTA-ATGATATATATA
1 TATAGTCACTTATATATTATAT-ATATATATA
*
492413 TATAGTTACTTATATACTTATATATATATATA
1 TATAGTCACTTATATA-TTATATATATATATA
*
492445 TATA-TATACTTATATATTATA
1 TATAGT-CACTTATATATTATA
492466 CTTTATACTT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
30 13 0.28
31 6 0.13
32 26 0.55
33 2 0.04
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (31 bp):
TATAGTCACTTATATATTATATATATATATA
Found at i:492437 original size:22 final size:21
Alignment explanation
Indices: 492409--492523 Score: 96
Period size: 22 Copynumber: 5.3 Consensus size: 21
492399 TAATGATATA
492409 TATATATAGTTACTTATATACT
1 TATATATA-TTACTTATATACT
*
492431 TATATATATATATATATATATACT
1 TATATATAT-TA-CT-TATATACT
492455 TATATAT-TATACTT-TATACT
1 TATATATAT-TACTTATATACT
* *
492475 TATATATATTTA-TATACATACC
1 TATATATA-TTACT-TATATACT
492497 TATATATAGTTACTTATATA--
1 TATATATA-TTACTTATATACT
492517 TATATAT
1 TATATAT
492524 GTGTGTGTGT
Statistics
Matches: 79, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
20 21 0.27
21 5 0.06
22 32 0.41
23 6 0.08
24 15 0.19
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (21 bp):
TATATATATTACTTATATACT
Found at i:492579 original size:16 final size:16
Alignment explanation
Indices: 492541--492586 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 16
492531 TGTGTATGTG
* *
492541 TGTATAATTATATATA
1 TGTATAAGTATACATA
492557 TAGGTATAAGTATACATA
1 T--GTATAAGTATACATA
492575 TGTATAAGTATA
1 TGTATAAGTATA
492587 TATACTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.41
Consensus pattern (16 bp):
TGTATAAGTATACATA
Found at i:493432 original size:2 final size:2
Alignment explanation
Indices: 493383--493416 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
493373 ATGCATGGAA
*
493383 AT AT -T AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
493417 ACTATACGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:494299 original size:187 final size:186
Alignment explanation
Indices: 493978--494364 Score: 720
Period size: 187 Copynumber: 2.1 Consensus size: 186
493968 ATATTTGTTT
*
493978 CATTACTTAATGGAGAACATGATCCATCAAAGATTTCATATTGGAAGAATCAAAGGATAAAACTT
1 CATTA-TTAATGGAGAACATGATCCATCAAAGATTTCATATTGGAAGAATCAAACGATAAAACTT
*
494043 TGATCAAAGTGGTCTGTTCATAGATGGAAACAGAAACATGTACGAGCTAAAGTGTGTGAATCATT
65 TGATCAAAGTGGTCTGTTCATAGATGGAAACAGAAACATGTACAAGCTAAAGTGTGTGAATCATT
494108 GGGCCGACTGGCTGATGTATATTTAACAAAGATAGAGAACTTGTGCAGAATCTGCAC
130 GGGCCGACTGGCTGATGTATATTTAACAAAGATAGAGAACTTGTGCAGAATCTGCAC
494165 CATTAGTTAATGGAGAACATGATCCATCAAAGATTTCATATTGGAAGAATCAAACGATAAAACTT
1 CATTA-TTAATGGAGAACATGATCCATCAAAGATTTCATATTGGAAGAATCAAACGATAAAACTT
*
494230 TGATCAAAGTGGTCTGTTCATAGATGGAAACAGACACATGTACAAGCTAAAGTGTGTGAATCATT
65 TGATCAAAGTGGTCTGTTCATAGATGGAAACAGAAACATGTACAAGCTAAAGTGTGTGAATCATT
494295 GGGCCGACTGGCTGATGTATATTTAACAAAGATAGAGAACTTGTGCAGAATCTGCAC
130 GGGCCGACTGGCTGATGTATATTTAACAAAGATAGAGAACTTGTGCAGAATCTGCAC
*
494352 CATTATTATTGGA
1 CATTATTAATGGA
494365 AAAGAAAGGG
Statistics
Matches: 195, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
186 7 0.04
187 188 0.96
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.27
Consensus pattern (186 bp):
CATTATTAATGGAGAACATGATCCATCAAAGATTTCATATTGGAAGAATCAAACGATAAAACTTT
GATCAAAGTGGTCTGTTCATAGATGGAAACAGAAACATGTACAAGCTAAAGTGTGTGAATCATTG
GGCCGACTGGCTGATGTATATTTAACAAAGATAGAGAACTTGTGCAGAATCTGCAC
Found at i:500526 original size:25 final size:23
Alignment explanation
Indices: 500465--500519 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
500455 CTTTGTCAGT
500465 TTTCCCTCTGGTGTCGTGTGTAG
1 TTTCCCTCTGGTGTCGTGTGTAG
500488 TTTCCCTCTGGTGTCGTGTGTAG
1 TTTCCCTCTGGTGTCGTGTGTAG
500511 TTTCCCTCT
1 TTTCCCTCT
500520 TAGGTGTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.04, C:0.25, G:0.25, T:0.45
Consensus pattern (23 bp):
TTTCCCTCTGGTGTCGTGTGTAG
Found at i:501724 original size:19 final size:19
Alignment explanation
Indices: 501675--501731 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 19
501665 TGTTGAAAAT
501675 CAATGCATGGGCGGCTGAAAA
1 CAATGCATGGGCGGCT--AAA
501696 CAA-G--TGGGGCGGCTAAA
1 CAATGCAT-GGGCGGCTAAA
501713 CAATGCATGGGCGGCTAAA
1 CAATGCATGGGCGGCTAAA
501732 TGGTCAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
17 6 0.19
18 2 0.06
19 19 0.59
20 2 0.06
21 3 0.09
ACGTcount: A:0.32, C:0.19, G:0.35, T:0.14
Consensus pattern (19 bp):
CAATGCATGGGCGGCTAAA
Found at i:502166 original size:16 final size:17
Alignment explanation
Indices: 502145--502177 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
502135 TTACTGTTCA
502145 CGTGAATAGT-AAATTT
1 CGTGAATAGTGAAATTT
502161 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
502178 TGTCGGCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.36
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:522904 original size:94 final size:98
Alignment explanation
Indices: 522733--522924 Score: 311
Period size: 94 Copynumber: 2.0 Consensus size: 98
522723 GACTGATCAA
522733 AATGATGTTTATCTGTTATCATGTTGATATTCTCTGCTTTGGGCCCTCATATTAGAATTAGATAC
1 AATGATGTTTATCTGTTATCATGTTGATATTCTCTGCTTTGGGCCCTCATATTAGAATTAGATAC
* *
522798 ACGGTTTGCGTTCGTGGGTAGTTTTCTCAAATC
66 ACGGTTTACGTTCGTAGGTAGTTTTCTCAAATC
* *
522831 AATGATGTTT-T-TG-TATCATGTTGATCTTGTCTGCTTTGGG-CCTCATATTAGAATTAGATAC
1 AATGATGTTTATCTGTTATCATGTTGATATTCTCTGCTTTGGGCCCTCATATTAGAATTAGATAC
*
522892 ACGGTTTACGTTCGTAGTTAGTTTTCTCAAATC
66 ACGGTTTACGTTCGTAGGTAGTTTTCTCAAATC
522925 GCTTGACTCT
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
94 51 0.57
95 25 0.28
96 2 0.02
97 1 0.01
98 10 0.11
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.43
Consensus pattern (98 bp):
AATGATGTTTATCTGTTATCATGTTGATATTCTCTGCTTTGGGCCCTCATATTAGAATTAGATAC
ACGGTTTACGTTCGTAGGTAGTTTTCTCAAATC
Found at i:526357 original size:64 final size:66
Alignment explanation
Indices: 526252--526414 Score: 206
Period size: 65 Copynumber: 2.5 Consensus size: 66
526242 CGGTGCACCA
* *
526252 AGTGTGCATCGATGCATTAAATGCATTCGATG-TTTGAAAAATAGCCTG-GTGCATCGATGCATG
1 AGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCGATGCATG
526315 G
66 G
** **
526316 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATG
1 AGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCGATGCATG
526380 G
66 G
* * * **
526381 AGAGTGTATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATCAAATGCATTCGATGTT
526415 CAATTAATTC
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 37 0.44
65 47 0.56
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.31
Consensus pattern (66 bp):
AGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCGATGCATG
G
Found at i:526386 original size:19 final size:19
Alignment explanation
Indices: 526362--526412 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
526352 GAAAATATTC
526362 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
* *
526381 AGAGTGTATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
526400 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
526413 TTCAATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 3 0.11
18 6 0.22
19 18 0.67
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.25
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:527100 original size:17 final size:17
Alignment explanation
Indices: 527078--527121 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
527068 AATAGTCAAG
*
527078 CATCCAAATATCATAAA
1 CATCCAAATAACATAAA
*
527095 CATCCAAACAAACATAAA
1 CATCCAAA-TAACATAAA
527113 CATCCAAAT
1 CATCCAAAT
527122 CAAAAAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (17 bp):
CATCCAAATAACATAAA
Found at i:527112 original size:18 final size:19
Alignment explanation
Indices: 527089--527125 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
527079 ATCCAAATAT
527089 CATAAACATCCAAA-CAAA
1 CATAAACATCCAAATCAAA
527107 CATAAACATCCAAATCAAA
1 CATAAACATCCAAATCAAA
527126 AAGTTTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (19 bp):
CATAAACATCCAAATCAAA
Found at i:532911 original size:22 final size:21
Alignment explanation
Indices: 532869--532908 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
532859 GAGTTTGTTT
532869 TCATTTTTCAATTTTAAAACA
1 TCATTTTTCAATTTTAAAACA
532890 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
532909 ACAATTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:534960 original size:64 final size:65
Alignment explanation
Indices: 534857--534983 Score: 195
Period size: 64 Copynumber: 2.0 Consensus size: 65
534847 GTGCACCAAG
* *
534857 TGTGCATCGATGCATTAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGGCT
1 TGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAATAGCCAGAGTGCATCGATGCATGGCT
**
534921 TGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGG
1 TGTGCATCGATGCATCAAATGCATTCGATG-TTTGAAAAATAGCCAGAGTGCATCGATGCATGG
534984 TGTAACACCC
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
64 37 0.65
65 20 0.35
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (65 bp):
TGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAATAGCCAGAGTGCATCGATGCATGGCT
Done.