Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008733.1 Hibiscus syriacus cultivar Beakdansim tig00111806_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: 774200
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:587093 original size:2 final size:2
Alignment explanation
Indices: 587086--587111 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
587076 TATGAAGAAG
587086 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
587112 ATTAGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:590049 original size:21 final size:20
Alignment explanation
Indices: 589963--590120 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
589953 AAATGACCAA
**
589963 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
589982 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
590002 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
590022 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
590043 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
590064 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
590084 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
590105 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
590121 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:590111 original size:20 final size:20
Alignment explanation
Indices: 590086--590201 Score: 108
Period size: 20 Copynumber: 5.8 Consensus size: 20
590076 GCGATTTTCC
*
590086 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGAATACG
*
590106 AAAATCGCAACGCGAACAC-
1 AAAATCGCAACGCGAATACG
* *
590125 ATAAATCGCAACGCGTATCCG
1 A-AAATCGCAACGCGAATACG
* ** *
590146 TAAATCGCAACGATAATACAT
1 AAAATCGCAACGCGAATAC-G
* *
590167 AAAATCGCAACGCGTATCCG
1 AAAATCGCAACGCGAATACG
*
590187 TAAATCGCAACGCGA
1 AAAATCGCAACGCGA
590202 TATTTAAAGC
Statistics
Matches: 74, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
19 1 0.01
20 59 0.80
21 14 0.19
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGAATACG
Found at i:590136 original size:40 final size:41
Alignment explanation
Indices: 590086--590201 Score: 162
Period size: 40 Copynumber: 2.9 Consensus size: 41
590076 GCGATTTTCC
* ** *
590086 AAAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
** *
590127 -AAATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
590167 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
590202 TATTTAAAGC
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
40 33 0.51
41 32 0.49
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (41 bp):
AAAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:590621 original size:33 final size:33
Alignment explanation
Indices: 590582--590652 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
590572 TTCACTTAGA
* *
590582 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
590615 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
590648 TTTCA
1 TTTCA
590653 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:590776 original size:20 final size:20
Alignment explanation
Indices: 590732--590841 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
590722 TGCAGAAGAG
*
590732 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
590753 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
590773 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
590794 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
590808 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
590827 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
590842 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:590789 original size:41 final size:38
Alignment explanation
Indices: 590725--590841 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
590715 TTCAATTTGC
* *
590725 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
590763 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
590804 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
590837 AGAAT
1 AGAAT
590842 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:590811 original size:14 final size:14
Alignment explanation
Indices: 590792--590848 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
590782 GAGAAATGAA
590792 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
590806 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
590825 AATCGCAACGAGAG
1 AATCGCAACGAGAG
590839 AATCGCAACG
1 AATCGCAACG
590849 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:590824 original size:33 final size:33
Alignment explanation
Indices: 590784--590864 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
590774 CGCAACGAGA
590784 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
590817 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
590850 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
590865 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:590882 original size:19 final size:19
Alignment explanation
Indices: 590860--590957 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
590850 GAAACCAAAA
*
590860 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
590879 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
590893 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
590912 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
590926 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
590945 TCGCGTTGCGATT
1 TCGCGTTGCGATT
590958 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:590901 original size:14 final size:14
Alignment explanation
Indices: 590882--590971 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
590872 TTTCATTTCG
590882 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
590896 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
590915 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
590929 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
590946 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
590962 CGTTGCGATT
1 CGTTGCGATT
590972 TTCATTTCTA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:590907 original size:33 final size:33
Alignment explanation
Indices: 590865--590979 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
590855 CAAAATCGCA
590865 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
590898 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
590931 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
590964 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
590980 TACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:592834 original size:93 final size:93
Alignment explanation
Indices: 592675--592871 Score: 385
Period size: 93 Copynumber: 2.1 Consensus size: 93
592665 TAGATTGCTT
592675 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
592740 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
592768 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
592833 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
592861 AGTAAATTTAT
1 AGTAAATTTAT
592872 CCATTCAAGT
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 102 1.00
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:592953 original size:19 final size:19
Alignment explanation
Indices: 592913--593041 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
592903 TAGTTTACTT
* *
592913 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
592933 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
592952 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
592971 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
592985 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
593004 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
593018 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
593037 TCGCA
1 TCGCA
593042 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:592992 original size:33 final size:32
Alignment explanation
Indices: 592949--593041 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
592939 CGCGAAACCA
**
592949 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
592981 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
593014 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
593042 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:593039 original size:52 final size:52
Alignment explanation
Indices: 592913--593041 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
592903 TAGTTTACTT
**
592913 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
592965 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
593018 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
593042 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:593059 original size:19 final size:19
Alignment explanation
Indices: 593037--593171 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
593027 GAAACCAAAA
*
593037 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
593056 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
593072 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
593089 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
593105 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
593122 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
593141 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
593161 TCGTGTTGCGA
1 TCGCGTTGCGA
593172 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:593078 original size:14 final size:14
Alignment explanation
Indices: 593059--593115 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
593049 TTTCATTTCG
593059 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
593073 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
593090 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
593106 CGTTGCGATT
1 CGTTGCGATT
593116 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:593084 original size:33 final size:33
Alignment explanation
Indices: 593042--593134 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
593032 CAAAATCGCA
*
593042 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
593075 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
593108 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
593135 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:595113 original size:14 final size:14
Alignment explanation
Indices: 595094--595129 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
595084 ATTGTTTAAT
595094 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
595108 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
595122 TGATTTGT
1 TGATTTGT
595130 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:595260 original size:19 final size:19
Alignment explanation
Indices: 595236--595333 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
595226 AAAATTGACT
595236 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
595255 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
595274 ATCGCAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
595288 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
595307 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
595327 ATCGCAA
1 ATCGCAA
595334 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 11 0.15
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 40 0.56
20 16 0.23
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:595365 original size:53 final size:53
Alignment explanation
Indices: 595236--595352 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
595226 AAAATTGACT
*
595236 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
595288 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
595341 ATCGTAATGCGA
1 ATCGCAATGCGA
595353 TTTTCATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:597847 original size:24 final size:24
Alignment explanation
Indices: 597813--597859 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
597803 CTGAAACATC
597813 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
597837 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
597860 GACCAAATTC
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:598565 original size:20 final size:20
Alignment explanation
Indices: 598537--598786 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
598527 AAATTTCAGT
* *
598537 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
598557 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
598577 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
598597 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
598617 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
598637 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
598657 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
598677 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
598697 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
598717 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
598737 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
598757 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
598777 GTTGCGATTT
1 GTTGCGATTT
598787 TGGAAAATCG
Statistics
Matches: 200, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 199 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:600787 original size:20 final size:20
Alignment explanation
Indices: 600759--600847 Score: 88
Period size: 20 Copynumber: 4.3 Consensus size: 20
600749 ACCCAGTTTC
*
600759 TAAATTCGCAACGCGAATATG
1 TAAA-TCGCAACGCGAATTTG
** * *
600780 TAAATCGCATTGCGATTTTC
1 TAAATCGCAACGCGAATTTG
* * *
600800 CAAATTCGCAACGCGAATCTA
1 TAAA-TCGCAACGCGAATTTG
600821 TAAATCGCAACGCGAATTTG
1 TAAATCGCAACGCGAATTTG
600841 TAAATCG
1 TAAATCG
600848 TAACATAGAA
Statistics
Matches: 53, Mismatches: 14, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 35 0.66
21 18 0.34
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (20 bp):
TAAATCGCAACGCGAATTTG
Found at i:600880 original size:20 final size:20
Alignment explanation
Indices: 600856--600904 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
600846 CGTAACATAG
*
600856 AAGTCAAATTCGTAACGCGA
1 AAGTCAAATTCGCAACGCGA
* *
600876 TAGTCAAATTTGCAACGCGA
1 AAGTCAAATTCGCAACGCGA
600896 AAGTCAAAT
1 AAGTCAAAT
600905 GTTTTTACGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.22
Consensus pattern (20 bp):
AAGTCAAATTCGCAACGCGA
Found at i:601446 original size:20 final size:19
Alignment explanation
Indices: 601411--601464 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
601401 AAATCGCAAC
601411 GCGATTTTAGTTTCGCATT
1 GCGATTTTAGTTTCGCATT
* *
601430 GCGATTTTCATTTTCGCGTT
1 GCGATTTT-AGTTTCGCATT
*
601450 GCGAATTTAAGTTTC
1 GCG-ATTTTAGTTTC
601465 AGAAACTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 8 0.28
20 17 0.59
21 4 0.14
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.46
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCATT
Found at i:603853 original size:66 final size:60
Alignment explanation
Indices: 603718--603857 Score: 181
Period size: 66 Copynumber: 2.2 Consensus size: 60
603708 TTTTACATTG
*
603718 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTATTTTTTGATTAATTTATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTATTTTTTGATTAATTGATTTGTA
* * * *
603778 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAG-A-T-TTATTTT--TTGATTAATTGATTTGT
603843 A
60 A
603844 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
603858 ATTTCTAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
60 17 0.25
61 14 0.20
62 1 0.01
63 1 0.01
64 6 0.09
66 30 0.43
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.51
Consensus pattern (60 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTATTTTTTGATTAATTGATTTGTA
Found at i:603942 original size:20 final size:20
Alignment explanation
Indices: 603916--603971 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
603906 GTTGAAGGTA
603916 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* * * *
603936 TAAATTCGAAATGTGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
603956 CAAATTTGCAACGCGA
1 CAAATTCGCAACGCGA
603972 TTTTTGGTTT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:604285 original size:39 final size:39
Alignment explanation
Indices: 604230--604316 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
604220 TCAAGTTGTA
*
604230 GATTTTGATTTTCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
604269 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
604308 GATTTTGAT
1 GATTTTGAT
604317 GAGTATGGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:604651 original size:18 final size:18
Alignment explanation
Indices: 604628--604664 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
604618 CGAAATTGAT
604628 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
604646 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
604664 A
1 A
604665 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:604683 original size:24 final size:24
Alignment explanation
Indices: 604620--604672 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
604610 AGTGGAGCCG
*
604620 AAATTGATATTGAAATTCAAACTC
1 AAATTGAAATTGAAATTCAAACTC
*
604644 AAATTGAAATTTAAATTCAAACTC
1 AAATTGAAATTGAAATTCAAACTC
*
604668 CAATT
1 AAATT
604673 ACATATGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (24 bp):
AAATTGAAATTGAAATTCAAACTC
Found at i:607583 original size:12 final size:12
Alignment explanation
Indices: 607566--607590 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
607556 TCTTCGGGGA
607566 CTTTTTCTTCTT
1 CTTTTTCTTCTT
607578 CTTTTTCTTCTT
1 CTTTTTCTTCTT
607590 C
1 C
607591 AGGGTTATAT
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:607832 original size:24 final size:24
Alignment explanation
Indices: 607781--607832 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
607771 ATCTGAGTAT
** *
607781 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
607805 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
607829 TGAC
1 TGAC
607833 TAGTACTCAT
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:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:607966 original size:12 final size:12
Alignment explanation
Indices: 607945--607979 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
607935 GGTTGTGGGT
*
607945 TTTGAGATTGTG
1 TTTGATATTGTG
607957 TTTGATATTGTG
1 TTTGATATTGTG
*
607969 TTTGGTATTGT
1 TTTGATATTGT
607980 AAATGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:608747 original size:19 final size:20
Alignment explanation
Indices: 608723--608795 Score: 71
Period size: 19 Copynumber: 3.7 Consensus size: 20
608713 AACTAAAACC
608723 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAAATTGAAATTCG
608742 TGTTGC-AAATTTGAAATTC-
1 TGTTGCGAAA-TTGAAATTCG
* *
608761 AGTTGCGAATTTGAAATTCCG
1 TGTTGCGAAATTGAAATT-CG
* *
608782 CGTTGCGAATTTGA
1 TGTTGCGAAATTGA
608796 CTTTTGTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
18 3 0.07
19 21 0.46
20 9 0.20
21 13 0.28
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (20 bp):
TGTTGCGAAATTGAAATTCG
Found at i:608827 original size:40 final size:40
Alignment explanation
Indices: 608762--608930 Score: 139
Period size: 40 Copynumber: 4.2 Consensus size: 40
608752 TTGAAATTCA
* * * * *
608762 GTTGCGAATTTGAAATTCCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTG-ACTTCTGTGTTGCGAATTTGACTTTCGC
* *
608803 GTTACGAATTTGACTTCTGTGTTGCG-ATTT-ACAAATTCGC
1 GTTGCGAATTTGACTTCTGTGTTGCGAATTTGAC--TTTCGC
* * * *
608843 GTTGCGAATTTGTCTTTTGTGTTGCAAATTTGACTATCGC
1 GTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTTTCGC
* * *
608883 GTTGCAAATTTGACTTCCGTGTTGCG-ATTT-ACAAATTCGC
1 GTTGCGAATTTGACTTCTGTGTTGCGAATTTGAC--TTTCGC
608923 GTTGCGAA
1 GTTGCGAA
608931 AATAGAAACT
Statistics
Matches: 101, Mismatches: 21, Indels: 13
0.75 0.16 0.10
Matches are distributed among these distances:
38 4 0.04
39 8 0.08
40 72 0.71
41 15 0.15
42 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (40 bp):
GTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTTTCGC
Found at i:608874 original size:80 final size:80
Alignment explanation
Indices: 608783--608930 Score: 233
Period size: 80 Copynumber: 1.9 Consensus size: 80
608773 GAAATTCCGC
* * * * * *
608783 GTTGCGAATTTGACTTTTGTGTTACGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGC
1 GTTGCAAATTTGACTATCGCGTTACAAATTTGACTTCCGTGTTGCGATTTACAAATTCGCGTTGC
608848 GAATTTGTCTTTTGT
66 GAATTTGTCTTTTGT
*
608863 GTTGCAAATTTGACTATCGCGTTGCAAATTTGACTTCCGTGTTGCGATTTACAAATTCGCGTTGC
1 GTTGCAAATTTGACTATCGCGTTACAAATTTGACTTCCGTGTTGCGATTTACAAATTCGCGTTGC
608928 GAA
66 GAA
608931 AATAGAAACT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 61 1.00
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.41
Consensus pattern (80 bp):
GTTGCAAATTTGACTATCGCGTTACAAATTTGACTTCCGTGTTGCGATTTACAAATTCGCGTTGC
GAATTTGTCTTTTGT
Found at i:608887 original size:60 final size:61
Alignment explanation
Indices: 608741--608893 Score: 172
Period size: 60 Copynumber: 2.5 Consensus size: 61
608731 AATTAAATTC
* *
608741 GTGTTGCAAATTTGA-AATTC-AGTTGCGAATTTGAAATTCCGCGTTGCGAATTTGACTTTT
1 GTGTTGCAAATTTGACTA-TCGAGTTGCGAATTTCAAATTCCGCGTTGCGAATTTGACTTTT
* * * *
608801 GTGTTACGAATTTGACT-TCTGTGTTGCG-ATTTACAAATT-CGCGTTGCGAATTTGTCTTTT
1 GTGTTGCAAATTTGACTATC-GAGTTGCGAATTT-CAAATTCCGCGTTGCGAATTTGACTTTT
* *
608861 GTGTTGCAAATTTGACTATCGCGTTGCAAATTT
1 GTGTTGCAAATTTGACTATCGAGTTGCGAATTT
608894 GACTTCCGTG
Statistics
Matches: 77, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
59 2 0.03
60 58 0.75
61 17 0.22
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.42
Consensus pattern (61 bp):
GTGTTGCAAATTTGACTATCGAGTTGCGAATTTCAAATTCCGCGTTGCGAATTTGACTTTT
Found at i:608906 original size:20 final size:19
Alignment explanation
Indices: 608723--608909 Score: 110
Period size: 20 Copynumber: 9.4 Consensus size: 19
608713 AACTAAAACC
* * *
608723 TGTTGCGAAATTAAATTCG
1 TGTTGCGAATTTGACTTCG
* *
608742 TGTTGCAAATTTGAAATTC-
1 TGTTGCGAATTTG-ACTTCG
* *
608761 AGTTGCGAATTTGAAATTCCG
1 TGTTGCGAATTTG-ACTT-CG
* *
608782 CGTTGCGAATTTGACTTTTG
1 TGTTGCGAATTTGAC-TTCG
*
608802 TGTTACGAATTTGACTTCTG
1 TGTTGCGAATTTGACTTC-G
608822 TGTTGCG-ATTT-ACAAATTCG
1 TGTTGCGAATTTGAC---TTCG
* * *
608842 CGTTGCGAATTTGTCTTTTG
1 TGTTGCGAATTTGAC-TTCG
*
608862 TGTTGCAAATTTGACTATCG
1 TGTTGCGAATTTGACT-TCG
* *
608882 CGTTGCAAATTTGACTTCCG
1 TGTTGCGAATTTGACTT-CG
608902 TGTTGCGA
1 TGTTGCGA
608910 TTTACAAATT
Statistics
Matches: 133, Mismatches: 23, Indels: 23
0.74 0.13 0.13
Matches are distributed among these distances:
18 2 0.02
19 34 0.26
20 75 0.56
21 21 0.16
22 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (19 bp):
TGTTGCGAATTTGACTTCG
Found at i:608947 original size:80 final size:80
Alignment explanation
Indices: 608809--608974 Score: 210
Period size: 80 Copynumber: 2.1 Consensus size: 80
608799 TTGTGTTACG
* * * **** *
608809 AATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGAATTTGTCTTTTGTGTTGC-AAATT
1 AATTTGACTTCCGTGTTGCGATTTACAAATTCGCGTTGCGAAATAGTAAACTGGGTTGCAAAATT
* *
608873 TGACTATCGCGTTGCA
66 GGA-GATCGCGTTGCA
608889 AATTTGACTTCCGTGTTGCGATTTACAAATTCGCGTTGCGAAAATAG-AAACTGGGTTGCAAAAT
1 AATTTGACTTCCGTGTTGCGATTTACAAATTCGCGTTGCG-AAATAGTAAACTGGGTTGCAAAAT
608953 TGGAGATCGCGTTGCA
65 TGGAGATCGCGTTGCA
608969 AATTTG
1 AATTTG
608975 TTGGTCATTT
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
80 63 0.85
81 11 0.15
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.37
Consensus pattern (80 bp):
AATTTGACTTCCGTGTTGCGATTTACAAATTCGCGTTGCGAAATAGTAAACTGGGTTGCAAAATT
GGAGATCGCGTTGCA
Found at i:612480 original size:21 final size:21
Alignment explanation
Indices: 612437--612476 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
612427 AAAGAAGGAT
612437 AAATAACAAAGTATGATGATA
1 AAATAACAAAGTATGATGATA
612458 AAATAAC-AAGTATGATGAT
1 AAATAACAAAGTATGATGAT
612477 TAAACCCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.25
Consensus pattern (21 bp):
AAATAACAAAGTATGATGATA
Found at i:615080 original size:25 final size:25
Alignment explanation
Indices: 615015--615083 Score: 129
Period size: 25 Copynumber: 2.8 Consensus size: 25
615005 GTACGGATGC
*
615015 TTAATGAGTTGAACAACTCATGTGT
1 TTAATGAGTTGAACAGCTCATGTGT
615040 TTAATGAGTTGAACAGCTCATGTGT
1 TTAATGAGTTGAACAGCTCATGTGT
615065 TTAATGAGTTGAACAGCTC
1 TTAATGAGTTGAACAGCTC
615084 GTGAGTAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (25 bp):
TTAATGAGTTGAACAGCTCATGTGT
Found at i:615582 original size:16 final size:16
Alignment explanation
Indices: 615561--615594 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
615551 GATAAAATTT
*
615561 CAATGAGTTTAACGAG
1 CAATGAGCTTAACGAG
615577 CAATGAGCTTAACGAG
1 CAATGAGCTTAACGAG
615593 CA
1 CA
615595 GCGAGTCGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.21
Consensus pattern (16 bp):
CAATGAGCTTAACGAG
Found at i:618615 original size:16 final size:16
Alignment explanation
Indices: 618596--618626 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
618586 TATATGTAAC
*
618596 GTAAATAATATATAAA
1 GTAAATAATAAATAAA
618612 GTAAATAATAAATAA
1 GTAAATAATAAATAA
618627 TAAAATTGAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
GTAAATAATAAATAAA
Found at i:622452 original size:21 final size:21
Alignment explanation
Indices: 622422--622462 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
622412 ATATGTGTTA
*
622422 TATGTGGTCATTCGAGACATC
1 TATGTAGTCATTCGAGACATC
*
622443 TATGTAGTCATTCGGGACAT
1 TATGTAGTCATTCGAGACAT
622463 TTCTACGCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TATGTAGTCATTCGAGACATC
Found at i:623510 original size:19 final size:19
Alignment explanation
Indices: 623486--623552 Score: 107
Period size: 19 Copynumber: 3.5 Consensus size: 19
623476 TTCAAGGTGT
* *
623486 ATCGATGCACATGAAGTGC
1 ATCGATGCACAAGTAGTGC
*
623505 ATCGATGCACAAGTAGGGC
1 ATCGATGCACAAGTAGTGC
623524 ATCGATGCACAAGTAGTGC
1 ATCGATGCACAAGTAGTGC
623543 ATCGATGCAC
1 ATCGATGCAC
623553 CCCCTTAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.19
Consensus pattern (19 bp):
ATCGATGCACAAGTAGTGC
Found at i:624268 original size:23 final size:23
Alignment explanation
Indices: 624242--624298 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
624232 AATCTTATAT
*
624242 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* *
624265 GGCACTTCGGTGTAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
624288 GGCACTTCGGT
1 GGCACTTCGGT
624299 ACGTTTATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:627600 original size:16 final size:16
Alignment explanation
Indices: 627579--627612 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
627569 ATATGTTTGA
* *
627579 AAAGAATAGAGCAAGT
1 AAAGAATAAAGAAAGT
627595 AAAGAATAAAGAAAGT
1 AAAGAATAAAGAAAGT
627611 AA
1 AA
627613 GGATTTTGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.21, T:0.12
Consensus pattern (16 bp):
AAAGAATAAAGAAAGT
Found at i:629868 original size:19 final size:19
Alignment explanation
Indices: 629844--629896 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
629834 GAATGCCATC
629844 AGTGTATCGATGCACAAGT
1 AGTGTATCGATGCACAAGT
629863 AGTGTATCGATGCACAAGT
1 AGTGTATCGATGCACAAGT
*
629882 AGTGCATCGATGCAC
1 AGTGTATCGATGCAC
629897 CCCCTTAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (19 bp):
AGTGTATCGATGCACAAGT
Found at i:629954 original size:82 final size:83
Alignment explanation
Indices: 629785--629959 Score: 205
Period size: 82 Copynumber: 2.1 Consensus size: 83
629775 TTCAAGGTGT
* * **
629785 ATCGATGCACATGAAGTGCATCGATGCACTCTTTTAAAATACAAACATCGAATGCCATCAGTGTA
1 ATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAATGCCATCAGTGTA
*
629850 TCGATGCACAAGTAGTGT
66 TCGATGCACAAGTAGTGC
* * * *
629868 ATCGATGCACAAGTAGTGCATCGATGCACCCCCTT-AAATACTAACATCGAATAG-GATTTA-TG
1 ATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAAT-GCCA-TCAGTG
*
629930 TATCGATGCA-TAGATAGTGC
64 TATCGATGCACAAG-TAGTGC
629950 ATCGATGCAC
1 ATCGATGCAC
629960 CCATCAAGGG
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
81 2 0.03
82 44 0.56
83 33 0.42
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (83 bp):
ATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAATGCCATCAGTGTA
TCGATGCACAAGTAGTGC
Found at i:630650 original size:23 final size:23
Alignment explanation
Indices: 630605--630650 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
630595 CAATCTTATA
*
630605 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
* *
630628 TGGCACTTCGGTGCATTTATACG
1 TGGCACTACGGTGCAATTATACG
630651 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:631818 original size:14 final size:14
Alignment explanation
Indices: 631799--631834 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
631789 TTATGTGATC
631799 ATAAGAAATAAGAT
1 ATAAGAAATAAGAT
631813 ATAAGAAATAAGAT
1 ATAAGAAATAAGAT
*
631827 ATATGAAA
1 ATAAGAAA
631835 AAAGGTATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.22
Consensus pattern (14 bp):
ATAAGAAATAAGAT
Found at i:631858 original size:15 final size:14
Alignment explanation
Indices: 631803--631861 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
631793 GTGATCATAA
* **
631803 GAAATAAGATATAA
1 GAAAAAAGATATGT
* *
631817 GAAATAAGATATAT
1 GAAAAAAGATATGT
*
631831 GAAAAAAGGTATGT
1 GAAAAAAGATATGT
631845 GAAAAAGAGATATGT
1 GAAAAA-AGATATGT
631860 GA
1 GA
631862 TTACATGTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
14 30 0.77
15 9 0.23
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (14 bp):
GAAAAAAGATATGT
Found at i:631998 original size:39 final size:39
Alignment explanation
Indices: 631922--632172 Score: 308
Period size: 39 Copynumber: 6.4 Consensus size: 39
631912 TGGGATATGA
* * *
631922 TTGCTGTAAGGACTTATCCTGTGCACAAAGTA-GAGGAGC
1 TTGCGGTAAGGACTTACCCTGAGCACAAAG-ACGAGGAGC
* * * *
631961 ATGTGGTAAAGAATTACCCTGAGCACAAAGACGAGGAGC
1 TTGCGGTAAGGACTTACCCTGAGCACAAAGACGAGGAGC
*
632000 TTGCGGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGC
1 TTGCGGTAAGGACTTACCCTGAGCACAAAGACGAGGAGC
* *
632039 TTACGGTAAGGACTTACCCTGAGCACAAAGTCGAGGAGC
1 TTGCGGTAAGGACTTACCCTGAGCACAAAGACGAGGAGC
* * *
632078 TTACGGTAAGGACTTACCCTTAGCACAAAGCCGAGGAGC
1 TTGCGGTAAGGACTTACCCTGAGCACAAAGACGAGGAGC
* * *
632117 TTGCGGTAAGGACTTACCTTGAGAACAAAG-CTGAGAAGC
1 TTGCGGTAAGGACTTACCCTGAGCACAAAGAC-GAGGAGC
* *
632156 CTGCGGTAAGGGCTTAC
1 TTGCGGTAAGGACTTAC
632173 AAGTCATAAA
Statistics
Matches: 187, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
38 2 0.01
39 185 0.99
ACGTcount: A:0.31, C:0.22, G:0.29, T:0.19
Consensus pattern (39 bp):
TTGCGGTAAGGACTTACCCTGAGCACAAAGACGAGGAGC
Found at i:632133 original size:117 final size:117
Alignment explanation
Indices: 631927--632172 Score: 339
Period size: 117 Copynumber: 2.1 Consensus size: 117
631917 TATGATTGCT
* * **
631927 GTAAGGACTTATCCTGTGCACAAAGTAGAGGAGCATGTGGTAAAGAATTACCCTGAGCACAAAGA
1 GTAAGGACTTACCCTGAGCACAAAGTAGAGGAGCATACGGTAAAGAATTACCCTGAGCACAAAGA
* * *
631992 CGAGGAGCTTGCGGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCTTACG
66 CGAGGAGCTTGCGGTAAGGACTTACCCTGAGAACAAAGCCGAGAAGCCTACG
* * * * * *
632044 GTAAGGACTTACCCTGAGCACAAAGTCGAGGAGCTTACGGTAAGGACTTACCCTTAGCACAAAGC
1 GTAAGGACTTACCCTGAGCACAAAGTAGAGGAGCATACGGTAAAGAATTACCCTGAGCACAAAGA
* * *
632109 CGAGGAGCTTGCGGTAAGGACTTACCTTGAGAACAAAGCTGAGAAGCCTGCG
66 CGAGGAGCTTGCGGTAAGGACTTACCCTGAGAACAAAGCCGAGAAGCCTACG
*
632161 GTAAGGGCTTAC
1 GTAAGGACTTAC
632173 AAGTCATAAA
Statistics
Matches: 112, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
117 112 1.00
ACGTcount: A:0.31, C:0.22, G:0.29, T:0.18
Consensus pattern (117 bp):
GTAAGGACTTACCCTGAGCACAAAGTAGAGGAGCATACGGTAAAGAATTACCCTGAGCACAAAGA
CGAGGAGCTTGCGGTAAGGACTTACCCTGAGAACAAAGCCGAGAAGCCTACG
Found at i:638704 original size:78 final size:78
Alignment explanation
Indices: 638477--638714 Score: 251
Period size: 78 Copynumber: 3.1 Consensus size: 78
638467 TGTGTAGGTT
* *** * * * * *
638477 CTTACCCTGTGCACAAAGTAGAGGAGCCTACGGTAATGACTTACCCTAAGCACAAAGTCGAGGAG
1 CTTACCCTGAGCACAAAGCCCAGGAGCATACAGTAAGGACTTACCCTGAGCACAAAGTCGATGAG
* **
638542 CTTGCCGTAAGGA
66 CATGTGGTAAGGA
* * * * * *
638555 CTTACTCTGAGCATAAAGCCCAGGAGCCTACAGTAAGGACTTACCCTGAGCACAGAGCCGATAAG
1 CTTACCCTGAGCACAAAGCCCAGGAGCATACAGTAAGGACTTACCCTGAGCACAAAGTCGATGAG
638620 CATGTGGTAAGGA
66 CATGTGGTAAGGA
* * * * *
638633 CTTACCCTTAGCACAAAGCCGAGGATCATATAGTAAGGACTTACCCTGAGCACAAAGTTGATGAG
1 CTTACCCTGAGCACAAAGCCCAGGAGCATACAGTAAGGACTTACCCTGAGCACAAAGTCGATGAG
* *
638698 CCTGTGGTAAGTA
66 CATGTGGTAAGGA
638711 CTTA
1 CTTA
638715 TAAGTCATAA
Statistics
Matches: 131, Mismatches: 29, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
78 131 1.00
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.21
Consensus pattern (78 bp):
CTTACCCTGAGCACAAAGCCCAGGAGCATACAGTAAGGACTTACCCTGAGCACAAAGTCGATGAG
CATGTGGTAAGGA
Found at i:638714 original size:39 final size:39
Alignment explanation
Indices: 638477--638689 Score: 210
Period size: 39 Copynumber: 5.5 Consensus size: 39
638467 TGTGTAGGTT
* ** *
638477 CTTACCCTGTGCACAAAGTAGAGGAGCCTACGGTAATGA
1 CTTACCCTGAGCACAAAGCCGAGGAGCCTACGGTAAGGA
* * * * *
638516 CTTACCCTAAGCACAAAGTCGAGGAGCTTGCCGTAAGGA
1 CTTACCCTGAGCACAAAGCCGAGGAGCCTACGGTAAGGA
* * * *
638555 CTTACTCTGAGCATAAAGCCCAGGAGCCTACAGTAAGGA
1 CTTACCCTGAGCACAAAGCCGAGGAGCCTACGGTAAGGA
* ** * **
638594 CTTACCCTGAGCACAGAGCCGATAAGCATGTGGTAAGGA
1 CTTACCCTGAGCACAAAGCCGAGGAGCCTACGGTAAGGA
* * * **
638633 CTTACCCTTAGCACAAAGCCGAGGATCATATAGTAAGGA
1 CTTACCCTGAGCACAAAGCCGAGGAGCCTACGGTAAGGA
638672 CTTACCCTGAGCACAAAG
1 CTTACCCTGAGCACAAAG
638690 TTGATGAGCC
Statistics
Matches: 141, Mismatches: 33, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 141 1.00
ACGTcount: A:0.32, C:0.25, G:0.24, T:0.19
Consensus pattern (39 bp):
CTTACCCTGAGCACAAAGCCGAGGAGCCTACGGTAAGGA
Found at i:640731 original size:21 final size:21
Alignment explanation
Indices: 640707--640747 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
640697 ATGTTTAATG
**
640707 AAAAAGATGTCAATTGTTAAC
1 AAAAAGACATCAATTGTTAAC
*
640728 AAAAGGACATCAATTGTTAA
1 AAAAAGACATCAATTGTTAA
640748 AAAGTTACCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.27
Consensus pattern (21 bp):
AAAAAGACATCAATTGTTAAC
Found at i:649579 original size:34 final size:34
Alignment explanation
Indices: 649498--649572 Score: 141
Period size: 34 Copynumber: 2.2 Consensus size: 34
649488 TCATTCACTC
649498 ATATGCCATGGCATAGCGGAGTGTCCCTCTATAG
1 ATATGCCATGGCATAGCGGAGTGTCCCTCTATAG
*
649532 ATATTCCATGGCATAGCGGAGTGTCCCTCTATAG
1 ATATGCCATGGCATAGCGGAGTGTCCCTCTATAG
649566 ATATGCC
1 ATATGCC
649573 TAGGCATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (34 bp):
ATATGCCATGGCATAGCGGAGTGTCCCTCTATAG
Found at i:655714 original size:13 final size:13
Alignment explanation
Indices: 655696--655731 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
655686 AACCGGTCCG
655696 ACCCGACCCGTTA
1 ACCCGACCCGTTA
* *
655709 ACCCGACCAGTTG
1 ACCCGACCCGTTA
655722 ACCCGACCCG
1 ACCCGACCCG
655732 ACCCGTTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.22, C:0.47, G:0.19, T:0.11
Consensus pattern (13 bp):
ACCCGACCCGTTA
Found at i:655716 original size:18 final size:18
Alignment explanation
Indices: 655693--655749 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
655683 CCGAACCGGT
655693 CCGACCCGACCCGTTAAC
1 CCGACCCGACCCGTTAAC
*
655711 CCGA-CC-A---GTTGAC
1 CCGACCCGACCCGTTAAC
*
655724 CCGACCCGACCCGTTATC
1 CCGACCCGACCCGTTAAC
655742 CCGACCCG
1 CCGACCCG
655750 TTGACCGTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
13 9 0.29
14 2 0.06
15 1 0.03
16 1 0.03
17 2 0.06
18 16 0.52
ACGTcount: A:0.19, C:0.49, G:0.19, T:0.12
Consensus pattern (18 bp):
CCGACCCGACCCGTTAAC
Found at i:655728 original size:31 final size:31
Alignment explanation
Indices: 655693--655755 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
655683 CCGAACCGGT
655693 CCGACCCGACCCGTTAACCCGACCAGTTGAC
1 CCGACCCGACCCGTTAACCCGACCAGTTGAC
* *
655724 CCGACCCGACCCGTTATCCCGACCCGTTGAC
1 CCGACCCGACCCGTTAACCCGACCAGTTGAC
655755 C
1 C
655756 GTTGACTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.19, C:0.48, G:0.19, T:0.14
Consensus pattern (31 bp):
CCGACCCGACCCGTTAACCCGACCAGTTGAC
Found at i:656884 original size:117 final size:117
Alignment explanation
Indices: 656699--656973 Score: 532
Period size: 117 Copynumber: 2.4 Consensus size: 117
656689 TTGTGTTCTT
656699 AGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTACACATTTTGGTGAT
1 AGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTACACATTTTGGTGAT
*
656764 TGGAGTGATTGGATGGGAAAGTTATTACCGTAGGCTCCTCGGCTTTGTGCTC
66 TGGAGTGATTGGATGGGAAAGTTATTACCGCAGGCTCCTCGGCTTTGTGCTC
*
656816 AGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTACACATTTTGGTTAT
1 AGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTACACATTTTGGTGAT
656881 TGGAGTGATTGGATGGGAAAGTTATTACCGCAGGCTCCTCGGCTTTGTGCTC
66 TGGAGTGATTGGATGGGAAAGTTATTACCGCAGGCTCCTCGGCTTTGTGCTC
656933 AGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCT
1 AGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCT
656974 AGAAAATATA
Statistics
Matches: 156, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
117 156 1.00
ACGTcount: A:0.17, C:0.15, G:0.35, T:0.33
Consensus pattern (117 bp):
AGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTACACATTTTGGTGAT
TGGAGTGATTGGATGGGAAAGTTATTACCGCAGGCTCCTCGGCTTTGTGCTC
Found at i:657704 original size:14 final size:14
Alignment explanation
Indices: 657685--657714 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
657675 AAGTGATCCT
657685 CCTGTTAGATCTGA
1 CCTGTTAGATCTGA
657699 CCTGTTAGATCTGA
1 CCTGTTAGATCTGA
657713 CC
1 CC
657715 CTTTGTCATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (14 bp):
CCTGTTAGATCTGA
Found at i:670168 original size:25 final size:26
Alignment explanation
Indices: 670117--670193 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 26
670107 TTTTTCTTAT
**
670117 TTTTTTATTTCTTTTACTTTTACTTTTA
1 TTTTTTA-TT-TTTTAAATTTACTTTTA
670145 TTTTTTATTTTTTAAATTTA-TTTTA
1 TTTTTTATTTTTTAAATTTACTTTTA
* *
670170 TTTTTT-TATTTTAAATTTAGTTTT
1 TTTTTTATTTTTTAAATTTACTTTT
670194 TTAGTAATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
24 12 0.27
25 15 0.33
26 9 0.20
27 2 0.04
28 7 0.16
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.75
Consensus pattern (26 bp):
TTTTTTATTTTTTAAATTTACTTTTA
Found at i:670169 original size:37 final size:36
Alignment explanation
Indices: 670104--670174 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
670094 TTTAATTCAG
* *
670104 TTTTTTTTCTTATTTTTTTATTTCTTTTACTTTTAC
1 TTTTTTTTCTTATTTTTTAATTTATTTTACTTTTAC
*
670140 TTTTATTTT-TTATTTTTTAAATTTATTTTATTTTT
1 TTTT-TTTTCTTATTTTTT-AATTTATTTTACTTTT
670175 TTATTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 13 0.43
37 17 0.57
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (36 bp):
TTTTTTTTCTTATTTTTTAATTTATTTTACTTTTAC
Found at i:670181 original size:24 final size:27
Alignment explanation
Indices: 670113--670193 Score: 89
Period size: 26 Copynumber: 3.1 Consensus size: 27
670103 GTTTTTTTTC
** *
670113 TTATTTTTTTATTTCTTTTACTTTTACTT
1 TTATTTTTTTA-TT-TTTTAAATTTAGTT
670142 TTA-TTTTTTATTTTTTAAATTTA-TT
1 TTATTTTTTTATTTTTTAAATTTAGTT
670167 TTATTTTTTTA--TTTTAAATTTAGTT
1 TTATTTTTTTATTTTTTAAATTTAGTT
670192 TT
1 TT
670194 TTAGTAATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
24 11 0.23
25 9 0.19
26 16 0.33
27 2 0.04
28 7 0.15
29 3 0.06
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.75
Consensus pattern (27 bp):
TTATTTTTTTATTTTTTAAATTTAGTT
Found at i:670182 original size:13 final size:13
Alignment explanation
Indices: 670104--670182 Score: 58
Period size: 13 Copynumber: 6.0 Consensus size: 13
670094 TTTAATTCAG
*
670104 TTTTTTT-TCTTA
1 TTTTTTTATTTTA
670116 TTTTTTTATTTCT-
1 TTTTTTTATTT-TA
670129 TTTACTTTTACTTTTA
1 TTT--TTTTA-TTTTA
670145 -TTTTTTATTTT-
1 TTTTTTTATTTTA
**
670156 TTAAATTTATTTTA
1 TT-TTTTTATTTTA
670170 TTTTTTTATTTTA
1 TTTTTTTATTTTA
670183 AATTTAGTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 17
0.71 0.07 0.23
Matches are distributed among these distances:
12 12 0.23
13 27 0.51
14 3 0.06
15 8 0.15
16 3 0.06
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTTTATTTTA
Found at i:670187 original size:20 final size:20
Alignment explanation
Indices: 670119--670196 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 20
670109 TTTCTTATTT
*
670119 TTTTATTTCTTTTACTTTT-AC
1 TTTTATTT-TTTTA-TTTTAAA
*
670140 TTTTATTTTTTATTTTTTAAATTTA
1 TTTTATTTTTT-TATTTT-AA---A
670165 TTTTATTTTTTTATTTTAAA
1 TTTTATTTTTTTATTTTAAA
*
670185 -TTTAGTTTTTTA
1 TTTTATTTTTTTA
670197 GTAATTATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
19 11 0.23
20 8 0.17
21 9 0.19
22 1 0.02
23 2 0.04
24 5 0.11
25 11 0.23
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (20 bp):
TTTTATTTTTTTATTTTAAA
Found at i:670188 original size:19 final size:18
Alignment explanation
Indices: 670148--670196 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
670138 ACTTTTATTT
* *
670148 TTTATTTTTTAAATTTAT
1 TTTATTTTTTTAATTTAA
*
670166 TTTATTTTTTTATTTTAAA
1 TTTATTTTTTTAATTT-AA
*
670185 TTTAGTTTTTTA
1 TTTATTTTTTTA
670197 GTAATTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTATTTTTTTAATTTAA
Found at i:673652 original size:60 final size:60
Alignment explanation
Indices: 673546--673837 Score: 184
Period size: 61 Copynumber: 4.9 Consensus size: 60
673536 AAGTTAAGAT
* * * * * **
673546 AATAAAATATATTATTTGAAGCTAAGATAATAACAACATATATTTTTTAAGTTATTAAAAG
1 AATAAAATACATT-TTTTAAGTTAAGATAAGAACAACATATATTTTTGAAGTTAAGAAAAG
* * * *
673607 AATAAAATACATTTTTTAAGTTAAGATAAGAATAA-ATATTTTTTTTGAAGTTAAGATAAT
1 AATAAAATACATTTTTTAAGTTAAGATAAGAACAACATA-TATTTTTGAAGTTAAGAAAAG
* * * * **
673667 AACAAAATACA-TTTTTAAGTT-A-A-AAGAACAAAACATATTTTTTAAGTTAAGGTAAG
1 AATAAAATACATTTTTTAAGTTAAGATAAGAACAACATATATTTTTGAAGTTAAGAAAAG
* ** * * * * * * *
673723 ATTAAAATTTATTATTTGAAGTTAAGATAATAATAAAATATATTTTTAAAATT-AGACTAAG
1 AATAAAATACATT-TTTTAAGTTAAGATAAGAACAACATATATTTTTGAAGTTAAGA-AAAG
*** * * *
673784 AATAAAATACATTGAATAAGTTGA-ATAAAAACAAAATATATATTTTTGAAGTTA
1 AATAAAATACATTTTTTAAGTTAAGATAAGAAC--AACATATATTTTTGAAGTTA
673838 GGATATGAGT
Statistics
Matches: 178, Mismatches: 42, Indels: 21
0.74 0.17 0.09
Matches are distributed among these distances:
56 31 0.17
57 4 0.02
58 9 0.05
59 20 0.11
60 52 0.29
61 62 0.35
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (60 bp):
AATAAAATACATTTTTTAAGTTAAGATAAGAACAACATATATTTTTGAAGTTAAGAAAAG
Found at i:673761 original size:87 final size:88
Alignment explanation
Indices: 673546--673771 Score: 305
Period size: 86 Copynumber: 2.6 Consensus size: 88
673536 AAGTTAAGAT
* * * *
673546 AATAAAATATATTATTTGAAGCTAAGATAATAACAACATATATTTTTTAAGTTATTAAAAGAATA
1 AATAAAATTTATTATTTGAAGTTAAGATAATAACAAAATATA-TTTTTAAG-T-TTAAAAGAACA
*
673611 AAATACATTTTTTAAGTTAAGATAAG
63 AAACACATTTTTTAAGTTAAGATAAG
*
673637 AATAAATATTT-TT-TTTGAAGTTAAGATAATAACAAAATACATTTTTAAG-TTAAAAGAACAAA
1 AATAAA-ATTTATTATTTGAAGTTAAGATAATAACAAAATATATTTTTAAGTTTAAAAGAACAAA
* *
673699 ACATATTTTTTAAGTTAAGGTAAG
65 ACACATTTTTTAAGTTAAGATAAG
* *
673723 ATTAAAATTTATTATTTGAAGTTAAGATAATAATAAAATATATTTTTAA
1 AATAAAATTTATTATTTGAAGTTAAGATAATAACAAAATATATTTTTAA
673772 AATTAGACTA
Statistics
Matches: 121, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
85 4 0.03
86 40 0.33
87 33 0.27
89 8 0.07
90 25 0.21
91 8 0.07
92 3 0.02
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.39
Consensus pattern (88 bp):
AATAAAATTTATTATTTGAAGTTAAGATAATAACAAAATATATTTTTAAGTTTAAAAGAACAAAA
CACATTTTTTAAGTTAAGATAAG
Found at i:673790 original size:30 final size:30
Alignment explanation
Indices: 673519--673792 Score: 224
Period size: 30 Copynumber: 9.3 Consensus size: 30
673509 TTTAATAAAA
* *
673519 AATAAAATATATATTTAAAGTTAAGAT---
1 AATAAAATATATTTTTGAAGTTAAGATAAG
* *
673546 AATAAAATATATTATTTGAAGCTAAGATAAT
1 AATAAAATATATT-TTTGAAGTTAAGATAAG
* * * ** *
673577 AACAACATATATTTTTTAAGTTATTAAAAG
1 AATAAAATATATTTTTGAAGTTAAGATAAG
* *
673607 AATAAAATACATTTTTTAAGTTAAGATAAG
1 AATAAAATATATTTTTGAAGTTAAGATAAG
* *
673637 AAT-AAATATTTTTTTTGAAGTTAAGATAAT
1 AATAAAATA-TATTTTTGAAGTTAAGATAAG
* *
673667 AACAAAATACATTTTT-AAGTT-A-A-AAG
1 AATAAAATATATTTTTGAAGTTAAGATAAG
* * * *
673693 AACAAAACATATTTTTTAAGTTAAGGTAAG
1 AATAAAATATATTTTTGAAGTTAAGATAAG
* * *
673723 ATTAAAATTTATTATTTGAAGTTAAGATAAT
1 AATAAAATATATT-TTTGAAGTTAAGATAAG
* *
673754 AATAAAATATATTTTTAAAATT-AGACTAAG
1 AATAAAATATATTTTTGAAGTTAAGA-TAAG
673784 AATAAAATA
1 AATAAAATA
673793 CATTGAATAA
Statistics
Matches: 195, Mismatches: 40, Indels: 21
0.76 0.16 0.08
Matches are distributed among these distances:
26 16 0.08
27 18 0.09
28 14 0.07
29 13 0.07
30 93 0.48
31 41 0.21
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (30 bp):
AATAAAATATATTTTTGAAGTTAAGATAAG
Found at i:674821 original size:31 final size:32
Alignment explanation
Indices: 674785--674846 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
674775 TATCATTTTG
674785 AAAAATTAAAAGTTTA-GATACTAAA-ACATAT
1 AAAAATTAAAAGTTTATG-TACTAAATACATAT
*
674816 AAAAATTAATAGTTTATGTACTAAATACATA
1 AAAAATTAAAAGTTTATGTACTAAATACATA
674847 ATTTTCCCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 22 0.79
32 6 0.21
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (32 bp):
AAAAATTAAAAGTTTATGTACTAAATACATAT
Found at i:676074 original size:23 final size:23
Alignment explanation
Indices: 675987--676066 Score: 142
Period size: 23 Copynumber: 3.5 Consensus size: 23
675977 TTGAAAAAGA
675987 GATATACTTCAAACTTTTGTTTT
1 GATATACTTCAAACTTTTGTTTT
*
676010 GATGTACTTCAAACTTTTGTTTT
1 GATATACTTCAAACTTTTGTTTT
676033 GATATACTTCAAACTTTTGTTTT
1 GATATACTTCAAACTTTTGTTTT
*
676056 GATATATTTCA
1 GATATACTTCA
676067 TTGTTTTGAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.51
Consensus pattern (23 bp):
GATATACTTCAAACTTTTGTTTT
Found at i:680003 original size:2 final size:2
Alignment explanation
Indices: 679998--680052 Score: 51
Period size: 2 Copynumber: 28.5 Consensus size: 2
679988 TCATACCTTC
* * *
679998 AT AT AT AT AT AT AT AT AT AT AT AT A- AT GT -T AT AT AT GT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
680038 AT AT AC AT AA AT AT A
1 AT AT AT AT AT AT AT A
680053 AGTAATGATA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:680746 original size:130 final size:129
Alignment explanation
Indices: 680429--680748 Score: 312
Period size: 129 Copynumber: 2.5 Consensus size: 129
680419 TGTTTTTCTA
* * * * *
680429 GGTAATCAGATCTGAAAATTTTTTATTCACTTC-GTTGCTCTTCAGGGAAGGTTGAATCGAAGTC
1 GGTAATTAGATCTGAAAATTTTTGATTCACTTCACTT-CTCTTCAGGGAAGGTTGAATCAAAGTA
* * * * * *
680493 GATTTGCTTCATTGCTCTTTAGGAAGACCAAATCTGAAAGAAGAATCTGGTCCACTACTCTTTAG
65 GATTTACTTCACTGCTATTCAGGAAGACCAAATCTAAAAGAAGAATATGGTCCACTACTCTTTAG
* ** * * *
680558 GGGAGA-TAGA-CATGAAAAAATTTGATCCACTTCACTGT-TCTTCAGAGAATGTTGAATCAAAG
1 GGTA-ATTAGATC-TGAAAATTTTTGATTCACTTCACT-TCTCTTCAGGGAAGGTTGAATCAAAG
* * * * *
680620 TAGATTTATTTCGCTGCTATTCAGGAAGATCAAATCTAAAAGAAGAAGAATAT-GTTC-CT-CTT
63 TAGATTTACTTCACTGCTATTCAGGAAGACCAAATCT--AA-AAGAAGAATATGGTCCACTACTC
680682 TTTAG
125 TTTAG
*
680687 GGTAATTAGATCTTGAAAATTTTTGATTCACTTCACTTCTCTTCGGGGAAGGTTGAATCAAA
1 GGTAATTAGATC-TGAAAATTTTTGATTCACTTCACTTCTCTTCAGGGAAGGTTGAATCAAA
680749 CTTAATTTGA
Statistics
Matches: 151, Mismatches: 30, Indels: 19
0.75 0.15 0.09
Matches are distributed among these distances:
128 2 0.01
129 88 0.58
130 46 0.30
131 5 0.03
132 10 0.07
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (129 bp):
GGTAATTAGATCTGAAAATTTTTGATTCACTTCACTTCTCTTCAGGGAAGGTTGAATCAAAGTAG
ATTTACTTCACTGCTATTCAGGAAGACCAAATCTAAAAGAAGAATATGGTCCACTACTCTTTAG
Found at i:705156 original size:36 final size:36
Alignment explanation
Indices: 705106--705213 Score: 155
Period size: 36 Copynumber: 3.0 Consensus size: 36
705096 ATATTGATGT
* *
705106 TAATAAATCATGTCACTTGATTAATAGACTTATTAA
1 TAATAAGTCATGTCACTTGATGAATAGACTTATTAA
* *
705142 TAATAAGTCTTGTCACTTGGTGAATAGACTTATTAA
1 TAATAAGTCATGTCACTTGATGAATAGACTTATTAA
**
705178 TAATAAGTCACATCA-TTGATGAATAGACTTATTAA
1 TAATAAGTCATGTCACTTGATGAATAGACTTATTAA
705213 T
1 T
705214 TTTTAGTTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
35 20 0.31
36 44 0.69
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (36 bp):
TAATAAGTCATGTCACTTGATGAATAGACTTATTAA
Found at i:711795 original size:3 final size:3
Alignment explanation
Indices: 711787--711838 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
711777 TCCCGACATT
711787 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
711834 TTA TT
1 TTA TT
711839 TTCATGCAGG
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:715537 original size:22 final size:21
Alignment explanation
Indices: 715504--715546 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
715494 TATAGTTGGA
*
715504 AATTGAGAATTCATTTTTATTT
1 AATTGAGAATTC-TTTTGATTT
715526 AATTGATG-ATTCTTTTGATTT
1 AATTGA-GAATTCTTTTGATTT
715547 CTTTCAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 10 0.53
23 1 0.05
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.56
Consensus pattern (21 bp):
AATTGAGAATTCTTTTGATTT
Found at i:719113 original size:27 final size:27
Alignment explanation
Indices: 719051--719149 Score: 162
Period size: 27 Copynumber: 3.6 Consensus size: 27
719041 GCAAGAAGCC
* * *
719051 AACCTGGAACACATTGCTTCCCCAAATT
1 AACCTGAAACACATTACTT-CCCTAATT
719079 AACCTGAAACACATTACTTCCCTAATT
1 AACCTGAAACACATTACTTCCCTAATT
719106 AACCTGAAACACATTACTTCCCTAATT
1 AACCTGAAACACATTACTTCCCTAATT
719133 AACCTGAAACACATTAC
1 AACCTGAAACACATTAC
719150 CTTCTCAAGT
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
27 51 0.75
28 17 0.25
ACGTcount: A:0.37, C:0.30, G:0.06, T:0.26
Consensus pattern (27 bp):
AACCTGAAACACATTACTTCCCTAATT
Found at i:722067 original size:45 final size:44
Alignment explanation
Indices: 722009--722098 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 44
721999 ACCCTCTTTG
* *
722009 ATATTAGTATGTACAGATGGTTGTCATATTATGATATCTTTGAT
1 ATATTAGTATGTACAGATGGTTGTCAGATTATGATAGCTTTGAT
* *
722053 ATATATAGTATGTACATATGGTTGTTAGATTATGATAGCTTTGAT
1 ATAT-TAGTATGTACAGATGGTTGTCAGATTATGATAGCTTTGAT
722098 A
1 A
722099 CTTTGGGATA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 4 0.10
45 37 0.90
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (44 bp):
ATATTAGTATGTACAGATGGTTGTCAGATTATGATAGCTTTGAT
Found at i:726963 original size:21 final size:22
Alignment explanation
Indices: 726939--726981 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
726929 GATATAAAAT
*
726939 TTTTATATTTGT-AGTTATGTA
1 TTTTATATTTCTAAGTTATGTA
* *
726960 TTTTTTCTTTCTAAGTTATGTA
1 TTTTATATTTCTAAGTTATGTA
726982 AAATGAACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.21, C:0.05, G:0.12, T:0.63
Consensus pattern (22 bp):
TTTTATATTTCTAAGTTATGTA
Found at i:727191 original size:14 final size:13
Alignment explanation
Indices: 727163--727198 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
727153 CGAAAATAAA
727163 ATATTAAAATAGT
1 ATATTAAAATAGT
*
727176 ATATTAATATTAGT
1 ATATTAA-AATAGT
727190 ATATTAAAA
1 ATATTAAAA
727199 GATGATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (13 bp):
ATATTAAAATAGT
Found at i:728215 original size:13 final size:13
Alignment explanation
Indices: 728197--728221 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
728187 ATTTCTTAGA
728197 GACAACTTTGAGT
1 GACAACTTTGAGT
728210 GACAACTTTGAG
1 GACAACTTTGAG
728222 AAACAATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (13 bp):
GACAACTTTGAGT
Found at i:728313 original size:35 final size:35
Alignment explanation
Indices: 728273--728343 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
728263 TTGATGTTAT
* *
728273 TTATAATAAGTCATGTCACTTTGTGAATAGACTTA
1 TTATAATAAATCATGTCACTTGGTGAATAGACTTA
*
728308 TTATAATAAATCATGTCACTTGGTGAATGGACTTA
1 TTATAATAAATCATGTCACTTGGTGAATAGACTTA
728343 T
1 T
728344 ATTTTAGTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.39
Consensus pattern (35 bp):
TTATAATAAATCATGTCACTTGGTGAATAGACTTA
Found at i:728401 original size:21 final size:21
Alignment explanation
Indices: 728377--728449 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
728367 AACAATTCTC
*
728377 TTCATGAAAAGATTAAATCCT
1 TTCATGAAAAGATTAAGTCCT
* * *
728398 TTCAAGAAAAGGTTAAGCCCT
1 TTCATGAAAAGATTAAGTCCT
*
728419 TTCATCAAAATGA-TAAGTCCT
1 TTCATGAAAA-GATTAAGTCCT
728440 TTCATCGAAA
1 TTCAT-GAAA
728450 GGACTTAACC
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
21 37 0.90
22 4 0.10
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (21 bp):
TTCATGAAAAGATTAAGTCCT
Found at i:728891 original size:3 final size:3
Alignment explanation
Indices: 728883--728910 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
728873 ATAATACTAT
728883 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
728911 CATCATCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:731789 original size:35 final size:35
Alignment explanation
Indices: 731718--731789 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
731708 TTGATGTTAT
* *
731718 TTATAATAAGTCATGTCACTTGGTGAATATATTTA
1 TTATAATAAGTCATGTCACATGGTGAATATACTTA
731753 TTATAATAAGTCATGTCACATGGTGAATGA-ACTTA
1 TTATAATAAGTCATGTCACATGGTGAAT-ATACTTA
731788 TT
1 TT
731790 TTTTAGTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 33 0.97
36 1 0.03
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (35 bp):
TTATAATAAGTCATGTCACATGGTGAATATACTTA
Found at i:731863 original size:21 final size:21
Alignment explanation
Indices: 731839--731897 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
731829 AACAATTCTC
*
731839 TTCATAAAAAGATTGAA-TCCT
1 TTCATAAAAAGATT-AAGCCCT
** *
731860 TTCACGAAAAGGTTAAGCCCT
1 TTCATAAAAAGATTAAGCCCT
*
731881 TTCATAAAAAGAATAAG
1 TTCATAAAAAGATTAAG
731898 TCTTTTTATC
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (21 bp):
TTCATAAAAAGATTAAGCCCT
Found at i:732009 original size:24 final size:24
Alignment explanation
Indices: 731974--732028 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
731964 ACAATTCTAT
*
731974 GACACAACACAACATAAGTTATAA
1 GACACAACACAACATAAGTTACAA
*
731998 GATACAACACAACATAAGTTACAA
1 GACACAACACAACATAAGTTACAA
732022 GACACAA
1 GACACAA
732029 TTCACAATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.55, C:0.22, G:0.09, T:0.15
Consensus pattern (24 bp):
GACACAACACAACATAAGTTACAA
Found at i:734630 original size:22 final size:21
Alignment explanation
Indices: 734600--734643 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
734590 AAATAAAAGT
734600 TAGTAGCTAAATCAGAAATAAA
1 TAGTAGCTAAATCA-AAATAAA
* *
734622 TAGTGGCTAAATTAAAATAAA
1 TAGTAGCTAAATCAAAATAAA
734643 T
1 T
734644 TAAAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.27
Consensus pattern (21 bp):
TAGTAGCTAAATCAAAATAAA
Found at i:736193 original size:92 final size:90
Alignment explanation
Indices: 736004--736272 Score: 319
Period size: 92 Copynumber: 3.0 Consensus size: 90
735994 GAGGTGTCGT
* * * * * * *
736004 TGATTCGAAATGTCATGAATCGAGCAAAGG--AAACAAGCTATTCTTTATGAATTCTCTACTGGA
1 TGATTCGAAATGCCATAAATCGAGCCAAGGTTGAATAAGTTATTC-TCATGAATTCTCTACTGG-
* * *
736067 AATGTTGT-TCTCAAGTGAGGCGTCGC
64 AATGTTGTCCCTCAAGTAAGGCGTCAC
** *
736093 TGATTCGAAATGCTTTGAATCGAGCCAAGGTTGAATAAGTTATTCTCATGAATTCTCTACTAGGA
1 TGATTCGAAATGCCATAAATCGAGCCAAGGTTGAATAAGTTATTCTCATGAATTCTCTACT-GGA
*
736158 ATGTTGATCCCTCAATTAAGGCGTCAC
65 ATGTTG-TCCCTCAAGTAAGGCGTCAC
*
736185 TGATTCGAAATGCCATAAATCGAGCCAAGGTTGAATAAGTTCTTCTCATGAATTCTCTACTGGAA
1 TGATTCGAAATGCCATAAATCGAGCCAAGGTTGAATAAGTTATTCTCATGAATTCTCTACTGGAA
* *
736250 TGTTGGTCCCTCATGTTAGGCGT
66 TGTT-GTCCCTCAAGTAAGGCGT
736273 GGTTGATTCA
Statistics
Matches: 155, Mismatches: 19, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
89 26 0.17
90 22 0.14
91 35 0.23
92 72 0.46
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (90 bp):
TGATTCGAAATGCCATAAATCGAGCCAAGGTTGAATAAGTTATTCTCATGAATTCTCTACTGGAA
TGTTGTCCCTCAAGTAAGGCGTCAC
Found at i:736523 original size:39 final size:39
Alignment explanation
Indices: 736405--736620 Score: 324
Period size: 39 Copynumber: 5.5 Consensus size: 39
736395 ATTTTAAGAA
* * *
736405 AAACAATCTCAAGTGAGATAAAAATCTACTGTTTCGAGTG
1 AAACTATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTG
* * *
736445 AAAATATCTCAAGTGAGATAAAAATCTTCTATTTCGAGTG
1 AAACTATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTG
* *
736485 AAACTATTTCAAGCGAGATAAAGTCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
*
736524 AAACTATCTCAAGCAAGATAAAATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
*
736563 AAACTATCTCAAGCGAGATAAAATATTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
736602 AAACTATCTCAAGCGAGAT
1 AAACTATCTCAAGCGAGAT
736621 GTAGATCCCT
Statistics
Matches: 162, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
39 110 0.68
40 52 0.32
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (39 bp):
AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
Found at i:736817 original size:42 final size:41
Alignment explanation
Indices: 736704--736817 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 41
736694 ACCCGAAGGT
* * *
736704 CTTATAAATGGCCCGAAGGACTTATCATCTTGCTCTAAAGA
1 CTTATAGATGGCCCGAAGGACTTATCATCATGCTCAAAAGA
** * *
736745 CTTATAGATTACCCGAAGGATTTAAGCATCATGCTCAAAAGA
1 CTTATAGATGGCCCGAAGGACTT-ATCATCATGCTCAAAAGA
*
736787 CTTACT-GATGGCCCGATGGACTTACTCATCA
1 CTTA-TAGATGGCCCGAAGGACTTA-TCATCA
736818 AGAAACCCTT
Statistics
Matches: 58, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
41 20 0.34
42 37 0.64
43 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTATCATCATGCTCAAAAGA
Found at i:736910 original size:38 final size:38
Alignment explanation
Indices: 736850--736925 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
736840 TAGTTTCTTA
* * * *
736850 AAATCTTTTGTTTCGAGCGAAACTATCTCAAGTGAGAT
1 AAATCTTCTATTTCAAGCGAAACTATCTCAAGCGAGAT
*
736888 AAATCTTCTATTTCAAGTGAAACTATCTCAAGCGAGAT
1 AAATCTTCTATTTCAAGCGAAACTATCTCAAGCGAGAT
736926 GTTGATCCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (38 bp):
AAATCTTCTATTTCAAGCGAAACTATCTCAAGCGAGAT
Found at i:741448 original size:22 final size:22
Alignment explanation
Indices: 741393--741449 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
741383 AAAATGCATG
741393 AAAATAAAAGTTAGTAGCTAAATC
1 AAAATAAAA--TAGTAGCTAAATC
* *
741417 AGAAAT-AAATAGTGGCTAAATT
1 A-AAATAAAATAGTAGCTAAATC
741439 AAAATAAAATA
1 AAAATAAAATA
741450 AAATTTAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 4 0.14
22 17 0.59
24 4 0.14
25 4 0.14
ACGTcount: A:0.58, C:0.05, G:0.12, T:0.25
Consensus pattern (22 bp):
AAAATAAAATAGTAGCTAAATC
Found at i:742528 original size:58 final size:60
Alignment explanation
Indices: 742437--742549 Score: 167
Period size: 58 Copynumber: 1.9 Consensus size: 60
742427 TACACCATTC
*
742437 TTCATCTAACTTACATTAGTGGCACCTTTCTGCC-AAATACAATGTTAGGCATTTGACTT
1 TTCATCTAACTTACATTAGTGGCACCTTTCTGCCAAAATACAACGTTAGGCATTTGACTT
* * *
742496 TTCATCTAAC-TGCATTAGTGGTACCTTTCTGCCAAAAATACACCGTTAGGCATT
1 TTCATCTAACTTACATTAGTGGCACCTTTCTGCC-AAAATACAACGTTAGGCATT
742550 GAAAAGGGGT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
58 21 0.44
59 10 0.21
60 17 0.35
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (60 bp):
TTCATCTAACTTACATTAGTGGCACCTTTCTGCCAAAATACAACGTTAGGCATTTGACTT
Found at i:742621 original size:54 final size:54
Alignment explanation
Indices: 742563--742866 Score: 371
Period size: 54 Copynumber: 5.7 Consensus size: 54
742553 AAGGGGTTAT
* * * * * *
742563 ACACTTAGTGCTTATACGGTCGTTCATAAACAAATTATGAATTACATGGGTTGC
1 ACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTACGTGGGTTGC
* * *
742617 ACACTTAGTGCCTATACGATCGTTCATCAACATATGATGAATTTCGTGGGTTGC
1 ACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTACGTGGGTTGC
* * * * *
742671 ACACTTAGAGCATGTATGGTCGTTCATCAACATATGATGAATT-CTGTGGGTTGC
1 ACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTAC-GTGGGTTGC
* * *
742725 ACACATAGTGCCTATATGGTTGTTCATC-A-ATATGAAGAATTACGTGGGTTGC
1 ACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTACGTGGGTTGC
* * * *
742777 ACACATAGTGCCTATATGGTTGTTCATCAACATATGATGAATTTCGTAGGTTGC
1 ACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTACGTGGGTTGC
* *
742831 ACACATAGTGCATATACGGTCGTTCATTAACATATG
1 ACACATAGTGCCTATACGGTCGTTCATCAACATATG
742867 CATTTAATCA
Statistics
Matches: 221, Mismatches: 25, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
52 48 0.22
53 4 0.02
54 169 0.76
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (54 bp):
ACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTACGTGGGTTGC
Found at i:742805 original size:106 final size:108
Alignment explanation
Indices: 742563--742866 Score: 382
Period size: 106 Copynumber: 2.8 Consensus size: 108
742553 AAGGGGTTAT
* * * * * * *
742563 ACACTTAGTGCTTATACGGTCGTTCATAAACAAATTATGAATTAC-ATGGGTTGCACACTTAGTG
1 ACACTTAGTGCATATATGGTCGTTCATCAACATATGATGAATT-CTGTGGGTTGCACACATAGTG
* * *
742627 CCTATACGATCGTTCATCAACATATGATGAATTTCGTGGGTTGC
65 CCTATACGGTCGTTCATCAACATATGAAGAATTACGTGGGTTGC
* *
742671 ACACTTAGAGCATGTATGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACATAGTGC
1 ACACTTAGTGCATATATGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACATAGTGC
* *
742736 CTATATGGTTGTTCATC-A-ATATGAAGAATTACGTGGGTTGC
66 CTATACGGTCGTTCATCAACATATGAAGAATTACGTGGGTTGC
* * * *
742777 ACACATAGTGCCTATATGGTTGTTCATCAACATATGATGAATT-TCGTAGGTTGCACACATAGTG
1 ACACTTAGTGCATATATGGTCGTTCATCAACATATGATGAATTCT-GTGGGTTGCACACATAGTG
* *
742841 CATATACGGTCGTTCATTAACATATG
65 CCTATACGGTCGTTCATCAACATATG
742867 CATTTAATCA
Statistics
Matches: 168, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
105 1 0.01
106 91 0.54
107 3 0.02
108 73 0.43
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (108 bp):
ACACTTAGTGCATATATGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACATAGTGC
CTATACGGTCGTTCATCAACATATGAAGAATTACGTGGGTTGC
Found at i:745275 original size:44 final size:43
Alignment explanation
Indices: 745149--745277 Score: 123
Period size: 44 Copynumber: 2.9 Consensus size: 43
745139 CGAATATCTG
* * * *
745149 GTATATAGCGGCTTTTTTTTTATACAAACACCGCAAAAGGTCTT
1 GTATATAGCGGC-ATTTTTATATATAAACACCGCTAAAGGTCTT
** ***
745193 GTATATAGCGGCATTTTTCGGATATAAACACTTTTAAAGGTCTT
1 GTATATAGCGGCATTTTT-ATATATAAACACCGCTAAAGGTCTT
* * *
745237 GTATATAGCGCCGTTTATTATATATAAACGCCGCTAAAGGT
1 GTATATAGCGGCATTT-TTATATATAAACACCGCTAAAGGT
745278 ATGGGATATA
Statistics
Matches: 67, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
43 5 0.07
44 60 0.90
45 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (43 bp):
GTATATAGCGGCATTTTTATATATAAACACCGCTAAAGGTCTT
Found at i:750901 original size:16 final size:16
Alignment explanation
Indices: 750882--750915 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
750872 TAATAACTCC
750882 TAAATT-ATAAAACTTT
1 TAAATTGATAAAA-TTT
750898 TAAATTGATAAAATTT
1 TAAATTGATAAAATTT
750914 TA
1 TA
750916 TGGGAGCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (16 bp):
TAAATTGATAAAATTT
Found at i:759845 original size:30 final size:31
Alignment explanation
Indices: 759798--759862 Score: 114
Period size: 30 Copynumber: 2.1 Consensus size: 31
759788 ACCTCTGTTG
759798 AAATCACAAATTTTATGTAAAAATTTGTATT
1 AAATCACAAATTTTATGTAAAAATTTGTATT
*
759829 AAATCACAAA-TTTATGTAACAATTTGTATT
1 AAATCACAAATTTTATGTAAAAATTTGTATT
759859 AAAT
1 AAAT
759863 TATTAATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 23 0.70
31 10 0.30
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (31 bp):
AAATCACAAATTTTATGTAAAAATTTGTATT
Found at i:763723 original size:49 final size:49
Alignment explanation
Indices: 763661--763761 Score: 168
Period size: 49 Copynumber: 2.1 Consensus size: 49
763651 TTTATGTCCG
* *
763661 TAATTAGAATTCATTATTCTTTGAATTCTTTGAATTAATTTAGTTTTTC
1 TAATTAGAATTCATTATTCTTTGAATTCTTTGAATTAATTTAGCTTTAC
763710 TAATTA-ACATTCATTATTCTTTGAATTCTTTGAATTAATTTAGCTTTAC
1 TAATTAGA-ATTCATTATTCTTTGAATTCTTTGAATTAATTTAGCTTTAC
763759 TAA
1 TAA
763762 CTTATCTCTT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
48 1 0.02
49 48 0.98
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (49 bp):
TAATTAGAATTCATTATTCTTTGAATTCTTTGAATTAATTTAGCTTTAC
Found at i:766988 original size:2 final size:2
Alignment explanation
Indices: 766981--767013 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
766971 GCTAAAGTCC
766981 TA TA TA TA 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 TA TA TA TA T
767014 TAAATCCAGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.