Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009458.1 Hibiscus syriacus cultivar Beakdansim tig00113719_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: 1407308
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:373778 original size:21 final size:21
Alignment explanation
Indices: 373724--373964 Score: 236
Period size: 21 Copynumber: 11.6 Consensus size: 21
373714 CGGAGTGTGG
*
373724 CGGCGGACGGCAGACGG-GG-
1 CGGCGGACGGCGGACGGCGGA
* *
373743 CGGCGG-CGACGGACGGCGGT
1 CGGCGGACGGCGGACGGCGGA
* *
373763 CGACGGACGGCGGACGGCGGT
1 CGGCGGACGGCGGACGGCGGA
* *
373784 CGACGGACGGCAGACGGCGGA
1 CGGCGGACGGCGGACGGCGGA
* * *
373805 CGGCGGTCGACGGACGGCAGA
1 CGGCGGACGGCGGACGGCGGA
* *
373826 CGGCGGACGGCGGTCGACGGA
1 CGGCGGACGGCGGACGGCGGA
* *
373847 CGGCAGACGGCGGACGGCGGT
1 CGGCGGACGGCGGACGGCGGA
* *
373868 CGACGGACGGCAGACGGCGGA
1 CGGCGGACGGCGGACGGCGGA
* *
373889 CGGCGGACGGCGGTCGACGGA
1 CGGCGGACGGCGGACGGCGGA
* * *
373910 CGGCGGTCGACGGACGGCGGT
1 CGGCGGACGGCGGACGGCGGA
* * *
373931 CGACGGACGGCGGTCGACGGA
1 CGGCGGACGGCGGACGGCGGA
*
373952 CGACGGACGGCGG
1 CGGCGGACGGCGG
373965 TCGGTGATGA
Statistics
Matches: 180, Mismatches: 39, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
18 8 0.04
19 8 0.04
20 5 0.03
21 159 0.88
ACGTcount: A:0.16, C:0.29, G:0.51, T:0.04
Consensus pattern (21 bp):
CGGCGGACGGCGGACGGCGGA
Found at i:373805 original size:28 final size:28
Alignment explanation
Indices: 373768--373964 Score: 284
Period size: 28 Copynumber: 7.3 Consensus size: 28
373758 GCGGTCGACG
373768 GACGGCGGACGGCGGTCGACGGACGGCA
1 GACGGCGGACGGCGGTCGACGGACGGCA
373796 GACGGCGGACGGCGGTCGACGGACGGCA
1 GACGGCGGACGGCGGTCGACGGACGGCA
373824 GACGGCGGACGGCGGTCGACGGACGGCA
1 GACGGCGGACGGCGGTCGACGGACGGCA
373852 GACGGCGGACGGCGGTCGACGGACGGCA
1 GACGGCGGACGGCGGTCGACGGACGGCA
373880 GACGGCGGACGGC-G--GACGG-CGGTC-
1 GACGGCGGACGGCGGTCGACGGACGG-CA
*
373904 GA---CGGACGGCGGTCGACGGACGGCG
1 GACGGCGGACGGCGGTCGACGGACGGCA
* * * *
373929 GTCGACGGACGGCGGTCGACGGACGACG
1 GACGGCGGACGGCGGTCGACGGACGGCA
373957 GACGGCGG
1 GACGGCGG
373965 TCGGTGATGA
Statistics
Matches: 156, Mismatches: 4, Indels: 18
0.88 0.02 0.10
Matches are distributed among these distances:
21 8 0.05
22 1 0.01
24 11 0.07
25 10 0.06
27 1 0.01
28 125 0.80
ACGTcount: A:0.17, C:0.28, G:0.51, T:0.04
Consensus pattern (28 bp):
GACGGCGGACGGCGGTCGACGGACGGCA
Found at i:373963 original size:35 final size:35
Alignment explanation
Indices: 373796--373967 Score: 146
Period size: 35 Copynumber: 4.9 Consensus size: 35
373786 ACGGACGGCA
* * *
373796 GACGGCGGACGGCGGTCGACGGACGGCAGACGGCG
1 GACGGCGGACGGCGGTCGACGGACGGCGGTCGACG
* * * * * * *
373831 GACGGCGGTCGACGGACGGCAGACGGCGGACGGCG
1 GACGGCGGACGGCGGTCGACGGACGGCGGTCGACG
* * * * * * *
373866 GTCGACGGACGGCAGACGGCGGACGGCGGACGGCG
1 GACGGCGGACGGCGGTCGACGGACGGCGGTCGACG
* *
373901 GTCGACGGACGGCGGTCGACGGACGGCGGTCGACG
1 GACGGCGGACGGCGGTCGACGGACGGCGGTCGACG
* * *
373936 GACGGCGGTCGACGGACGACGGACGGCGGTCG
1 GACGGCGGACGGCGGTCGACGGACGGCGGTCG
373968 GTGATGATTA
Statistics
Matches: 115, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 115 1.00
ACGTcount: A:0.16, C:0.28, G:0.51, T:0.05
Consensus pattern (35 bp):
GACGGCGGACGGCGGTCGACGGACGGCGGTCGACG
Found at i:376822 original size:289 final size:290
Alignment explanation
Indices: 376326--376908 Score: 1066
Period size: 288 Copynumber: 2.0 Consensus size: 290
376316 CGGTATTAAA
376326 GCTAGCACTTCTCTGCAAGTGGGGACCTCCTGACAATGCTGAATTGCATCTGTGACCAAAGAACT
1 GCTAGCACTTCTCTGCAAGTGGGGACCTCCTGACAATGCTGAATTGCATCTGTGACCAAAGAACT
376391 TTGCCCAAACACTATGTCCTGAGTTTGTCACACCGTTCAACAGCGCACTGTTCATATCTCCCGAA
66 TTGCCCAAACACTATGTCCTGAGTTTGTCACACCGTTCAACAGCGCACTGTTCATATCTCCCGAA
376456 ACCGGACCCAGATTAGAACGCCAGTTCCGGGAACTGAATTAGATGAGTTCTCATAAGGTGAGCTC
131 ACCGGACCCAGATTAGAACGCCAGTTCCGGGAACTGAATTAGATGAGTTCTCATAAGGTGAGCTC
376521 AAGCGAGAGTTAACTAAAGCCTGGGACTGCCCATCTCCTTGGAAGAAAATTCCAG-CGAGGAAGA
196 AAGCGAGAGTTAACTAAAGCCTGGGACTGCCCATCTCCTTGGAAGAAAATTCCAGACGAGGAAGA
376585 -TGGGTTAACCCCCCAGCCA-CCGAGAAGGT
261 TTGGGTT-ACCCCCCAGCCACCCGAGAAGGT
376614 GCTAGCACTTCTCTGCAAGTGGGGACCTCCTGACAATGCTGAATTTGCATCTGTGACCAAAGAAC
1 GCTAGCACTTCTCTGCAAGTGGGGACCTCCTGACAATGCTGAA-TTGCATCTGTGACCAAAGAAC
*
376679 -TTGCCCCAACACTATGTCCTGAGTTTGTCACACCGTTCAACAGCGCACTGTTCATATCTCCCGA
65 TTTGCCCAAACACTATGTCCTGAGTTTGTCACACCGTTCAACAGCGCACTGTTCATATCTCCCGA
376743 AACCGGACCCAGATTAGAACGCCCAGTTCCGGGAACTGAATTAGATGAGTTCTCATAAGGTGAGC
130 AACCGGACCCAGATTAGAACG-CCAGTTCCGGGAACTGAATTAGATGAGTTCTCATAAGGTGAGC
376808 TCAAGCGAGAGTTAACTAAAGCCTGGGACTGCCCATCTCCTTGGAAGAAAATTCCAGAACTCGAG
194 TCAAGCGAGAGTTAACTAAAGCCTGGGACTGCCCATCTCCTTGGAAGAAAATTCCAG-A--CGAG
*
376873 GAAGATTGGGTTCCCCCCCAGCCACCCGAGAAGGT
256 GAAGATTGGGTTACCCCCCAGCCACCCGAGAAGGT
376908 G
1 G
376909 TCATTGGAGG
Statistics
Matches: 285, Mismatches: 2, Indels: 10
0.96 0.01 0.03
Matches are distributed among these distances:
288 127 0.45
289 121 0.42
293 20 0.07
294 17 0.06
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.22
Consensus pattern (290 bp):
GCTAGCACTTCTCTGCAAGTGGGGACCTCCTGACAATGCTGAATTGCATCTGTGACCAAAGAACT
TTGCCCAAACACTATGTCCTGAGTTTGTCACACCGTTCAACAGCGCACTGTTCATATCTCCCGAA
ACCGGACCCAGATTAGAACGCCAGTTCCGGGAACTGAATTAGATGAGTTCTCATAAGGTGAGCTC
AAGCGAGAGTTAACTAAAGCCTGGGACTGCCCATCTCCTTGGAAGAAAATTCCAGACGAGGAAGA
TTGGGTTACCCCCCAGCCACCCGAGAAGGT
Found at i:378662 original size:20 final size:20
Alignment explanation
Indices: 378630--378757 Score: 105
Period size: 20 Copynumber: 6.3 Consensus size: 20
378620 AATTGGGAAA
378630 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
378650 ATCTCAATACGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
378670 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* * *
378691 ATCGTAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
378711 TTCGCAACGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
378731 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
*
378751 TTCGCAA
1 ATCGCAA
378758 CGTAATAATA
Statistics
Matches: 89, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
19 2 0.02
20 73 0.82
21 12 0.13
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:378694 original size:61 final size:61
Alignment explanation
Indices: 378627--378743 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 61
378617 GCGAATTGGG
* * * * * *
378627 AAAATCGCAATGCGATACTGACTATCTCAATACGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATACTGACTATCGCAACGCGATAATAC
* * * *
378688 AAAATCGTAACGAGATACTGACTTTCGCAACGCGATACTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATACTGACTATCGCAACGCGAT
378744 TCTGACTTTC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 46 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATACTGACTATCGCAACGCGATAATAC
Found at i:378758 original size:20 final size:20
Alignment explanation
Indices: 378696--378759 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
378686 ACAAAATCGT
*
378696 AACGAGATACTGACTTTCGC
1 AACGCGATACTGACTTTCGC
378716 AACGCGATACTGACTTTCGC
1 AACGCGATACTGACTTTCGC
*
378736 AACGCGATTCTGACTTTCGC
1 AACGCGATACTGACTTTCGC
378756 AACG
1 AACG
378760 TAATAATACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (20 bp):
AACGCGATACTGACTTTCGC
Found at i:378979 original size:22 final size:22
Alignment explanation
Indices: 378951--378994 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
378941 TCACTCTCTC
*
378951 ACCCATCTCCGACGAAATCCGT
1 ACCCATCTCAGACGAAATCCGT
*
378973 ACCCATCTCAGGCGAAATCCGT
1 ACCCATCTCAGACGAAATCCGT
378995 CTATCTCCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.39, G:0.16, T:0.18
Consensus pattern (22 bp):
ACCCATCTCAGACGAAATCCGT
Found at i:379263 original size:20 final size:19
Alignment explanation
Indices: 379222--379282 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
379212 GAAACTAAAA
**
379222 TCGCTTGCGATAGTCAAAT
1 TCGCTTGCGATAGTCATTT
379241 TCGCGTTGCGATAGTCATTT
1 TCGC-TTGCGATAGTCATTT
* **
379261 TCGTATTGCGATTTTCATTT
1 TCG-CTTGCGATAGTCATTT
379281 TC
1 TC
379283 AGAAACTATC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 4 0.11
20 31 0.89
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCTTGCGATAGTCATTT
Found at i:379471 original size:25 final size:24
Alignment explanation
Indices: 379417--379471 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
379407 TGTTTATTAT
* *
379417 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
379441 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
379467 TGTTT
1 TGTTT
379472 ATTATTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:381116 original size:20 final size:20
Alignment explanation
Indices: 381091--381132 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
381081 TAGTTTACTT
381091 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
381111 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
381131 TC
1 TC
381133 ACAATGCGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:381145 original size:19 final size:20
Alignment explanation
Indices: 381102--381146 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
381092 CGCAACACGA
*
381102 AAATGACTATCGCAACGCGG
1 AAATGACTATCACAACGCGG
* *
381122 AAATGGCTATCACAATGC-G
1 AAATGACTATCACAACGCGG
381141 AAATGA
1 AAATGA
381147 AATCGCAACG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AAATGACTATCACAACGCGG
Found at i:381175 original size:32 final size:32
Alignment explanation
Indices: 381134--381219 Score: 147
Period size: 32 Copynumber: 2.7 Consensus size: 32
381124 ATGGCTATCA
381134 CAATGCGAAATG-AAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGAC-AAATCG
381166 CAATGCGAAATGAAAATCGCAACGACAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAATCG
*
381198 CAACGCGAAATGAAAATCGCAA
1 CAATGCGAAATGAAAATCGCAA
381220 TGCGATTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
32 39 0.75
33 13 0.25
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.12
Consensus pattern (32 bp):
CAATGCGAAATGAAAATCGCAACGACAAATCG
Found at i:381181 original size:19 final size:19
Alignment explanation
Indices: 381159--381224 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
381149 TCGCAACGAC
381159 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
381178 AAAATCGCAA--CG--A--
1 AAAATCGCAATGCGAAATG
* *
381191 CAAATCGCAACGCGAAATG
1 AAAATCGCAATGCGAAATG
381210 AAAATCGCAATGCGA
1 AAAATCGCAATGCGA
381225 TTTGTGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
13 9 0.24
15 3 0.08
17 3 0.08
19 23 0.61
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:381296 original size:19 final size:19
Alignment explanation
Indices: 381262--381316 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
381252 TTGCGATTTT
*
381262 TCATTTCGCATTGCGATAG
1 TCATTTCGCGTTGCGATAG
*
381281 -CTTTTCCGCGTTGCGATAG
1 TCATTT-CGCGTTGCGATAG
381300 TCATTTCGCGTTGCGAT
1 TCATTTCGCGTTGCGAT
381317 TTTAAGTTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 4 0.13
19 23 0.74
20 4 0.13
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.38
Consensus pattern (19 bp):
TCATTTCGCGTTGCGATAG
Found at i:383369 original size:18 final size:19
Alignment explanation
Indices: 383341--383404 Score: 86
Period size: 18 Copynumber: 3.7 Consensus size: 19
383331 GCAACGAGAG
383341 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
383360 AATC-CAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
383378 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
383392 AATCGCAATGCGA
1 AATCGCAATGCGA
383405 TAGCCATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
14 11 0.27
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.44
19 7 0.17
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:383849 original size:20 final size:20
Alignment explanation
Indices: 383770--383857 Score: 88
Period size: 20 Copynumber: 4.3 Consensus size: 20
383760 TATTATCTCG
* * *
383770 TTGCGAAAGTCAGAATCGCG
1 TTGCGATAGTCAGTATCGCA
* *
383790 TTGCGAAAGTCAGTATCGCG
1 TTGCGATAGTCAGTATCGCA
* *
383810 TTGCGATTTTGT-ATTATCGCA
1 TTGCGA--TAGTCAGTATCGCA
383831 TTGCGATAGTCAGTATCGCA
1 TTGCGATAGTCAGTATCGCA
383851 TTGCGAT
1 TTGCGAT
383858 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.05
20 40 0.69
21 13 0.22
22 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGTATCGCA
Found at i:383876 original size:41 final size:41
Alignment explanation
Indices: 383784--383878 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
383774 GAAAGTCAGA
* * ** *
383784 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
*
383825 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CCAAT
383867 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
383879 TTACTTATTC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
41 44 0.96
42 2 0.04
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:385978 original size:21 final size:20
Alignment explanation
Indices: 385952--386045 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 20
385942 TATGCCATCT
385952 CCGCAGGGTTACATTCTGAGC
1 CCGCAGGGTTACATTCT-AGC
* *
385973 CCGCAGGGTTATATTCCGAGC
1 CCGCAGGGTTACATT-CTAGC
385994 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATT-CTAGC
* *
386015 CTGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACAT-TCTAGC
386036 CCGCAGGGTT
1 CCGCAGGGTT
386046 TTATACCATA
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
20 2 0.03
21 57 0.92
22 3 0.05
ACGTcount: A:0.18, C:0.31, G:0.28, T:0.23
Consensus pattern (20 bp):
CCGCAGGGTTACATTCTAGC
Found at i:386025 original size:42 final size:42
Alignment explanation
Indices: 385952--386045 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 42
385942 TATGCCATCT
* *
385952 CCGCAGGGTTACATTCTGAGCCCGCAGGGTTATATTCCGAGC
1 CCGCAGGGTTACATTCTGAGCCCGCAGGGTTACATGCCGAGC
* *
385994 CCGCAGGGTTACATTCCT-AGCCTGCCA-GGTTACATGCCTAGC
1 CCGCAGGGTTACATT-CTGAGCCCG-CAGGGTTACATGCCGAGC
386036 CCGCAGGGTT
1 CCGCAGGGTT
386046 TTATACCATA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 42 0.91
43 4 0.09
ACGTcount: A:0.18, C:0.31, G:0.28, T:0.23
Consensus pattern (42 bp):
CCGCAGGGTTACATTCTGAGCCCGCAGGGTTACATGCCGAGC
Found at i:386671 original size:34 final size:34
Alignment explanation
Indices: 386566--386672 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
386556 ATAAATGTTT
* *
386566 TTAAAATACAAATTACATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* *
386600 TAAAAATAAAAATAATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* * *
386634 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
386668 TTAAA
1 TTAAA
386673 TTTCAACTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.36
Consensus pattern (34 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAAA
Found at i:387265 original size:128 final size:128
Alignment explanation
Indices: 387034--387515 Score: 840
Period size: 128 Copynumber: 3.8 Consensus size: 128
387024 TTCACAATCC
387034 ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATCTGACAAAAT
1 ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATCTGACAAAAT
* * *
387099 AATGGAAGGCGCGCCCCTGGGAACGCGCTTTCATGTCCCCTGAGAAATAATAGGTACTGATAT
66 AATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATAT
* *
387162 ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATAATAACATATTCTCTGACAAAAT
1 ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATCTGACAAAAT
387227 AATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATAT
66 AATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATAT
*
387290 ATCTAGTGTCCCTGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATCTGACAAAAT
1 ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATCTGACAAAAT
* *
387355 AATGGAAGGCGCGCACCCGAGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATAT
66 AATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATAT
* * *
387418 GA-ATAGTATCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAA
1 -ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATCTGACAAAA
*
387482 TAATGGAAGGCGCGTCCCCGGGAACGCGCCTTCA
65 TAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCA
387516 TGTGAATAGT
Statistics
Matches: 336, Mismatches: 17, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
128 335 1.00
129 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (128 bp):
ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATCTGACAAAAT
AATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATAT
Found at i:399004 original size:21 final size:19
Alignment explanation
Indices: 398969--399007 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
398959 GACCCGACCC
398969 AAAATAATATATTTTATTT
1 AAAATAATATATTTTATTT
398988 AAAATAAATATTATTTTATT
1 AAAAT-AATA-TATTTTATT
399008 CAATAAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAAATAATATATTTTATTT
Found at i:402835 original size:50 final size:50
Alignment explanation
Indices: 402774--402875 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
402764 AAAATTATTG
402774 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
1 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
402824 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
1 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
402874 AA
1 AA
402876 ATAGGATAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.25
Consensus pattern (50 bp):
AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
Found at i:403055 original size:30 final size:30
Alignment explanation
Indices: 403019--403090 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
403009 CAAACTGCAT
403019 GGCGACCTTCATTAGTCGCCCAGACCACCC
1 GGCGACCTTCATTAGTCGCCCAGACCACCC
*
403049 GGCGACCTTCATTGGTCGCCCAGACCACCC
1 GGCGACCTTCATTAGTCGCCCAGACCACCC
403079 -GCGACCTTCATT
1 GGCGACCTTCATT
403091 CGACCTGTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 12 0.29
30 29 0.71
ACGTcount: A:0.18, C:0.42, G:0.21, T:0.19
Consensus pattern (30 bp):
GGCGACCTTCATTAGTCGCCCAGACCACCC
Found at i:411043 original size:18 final size:18
Alignment explanation
Indices: 410993--411043 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
410983 ATTCTTCATA
*
410993 ATTTTGATAATATTAATT
1 ATTTTTATAATATTAATT
411011 ATTTTATATAA-ATTAATT
1 ATTTT-TATAATATTAATT
411029 -TCTTTTATAATATTA
1 AT-TTTTATAATATTA
411044 TTTTATTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 6 0.21
18 19 0.66
19 4 0.14
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
ATTTTTATAATATTAATT
Found at i:414668 original size:34 final size:33
Alignment explanation
Indices: 414625--414706 Score: 148
Period size: 32 Copynumber: 2.5 Consensus size: 33
414615 CCATAATTGT
414625 GACCACTTGATGTGATTTTTTTTTTTTGATAAAA
1 GACCACTTGATGTGA-TTTTTTTTTTTGATAAAA
414659 GACCACTTGATGTGA-TTTTTTTTTTGATAAAA
1 GACCACTTGATGTGATTTTTTTTTTTGATAAAA
414691 GACCACTTGATGTGAT
1 GACCACTTGATGTGAT
414707 GAACAAAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
32 32 0.68
34 15 0.32
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (33 bp):
GACCACTTGATGTGATTTTTTTTTTTGATAAAA
Found at i:415782 original size:16 final size:17
Alignment explanation
Indices: 415753--415792 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
415743 CCCCCTCATT
415753 AAAAAAATGAGGAAAAAG
1 AAAAAAAT-AGGAAAAAG
*
415771 AAAAAAAT-GGAAACAG
1 AAAAAAATAGGAAAAAG
415787 AAAAAA
1 AAAAAA
415793 CACTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.62
18 8 0.38
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.05
Consensus pattern (17 bp):
AAAAAAATAGGAAAAAG
Found at i:419266 original size:12 final size:12
Alignment explanation
Indices: 419249--419284 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
419239 CACTAAATAC
419249 GCAAAACAAAGT
1 GCAAAACAAAGT
419261 GCAAAACAAAGT
1 GCAAAACAAAGT
* *
419273 ACAAATCAAAGT
1 GCAAAACAAAGT
419285 TCGCCCCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.58, C:0.17, G:0.14, T:0.11
Consensus pattern (12 bp):
GCAAAACAAAGT
Found at i:420745 original size:18 final size:18
Alignment explanation
Indices: 420722--420757 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
420712 ACTGAATATT
*
420722 TGTCCCAAATGACCACTA
1 TGTCCCAAAGGACCACTA
*
420740 TGTCCCGAAGGACCACTA
1 TGTCCCAAAGGACCACTA
420758 ATAATTCCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.33, G:0.17, T:0.19
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:423306 original size:22 final size:22
Alignment explanation
Indices: 423253--423306 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
423243 TCGGGTTGAG
*
423253 TCTCGGGTGAAAGATTTATTGT
1 TCTCGGGTGGAAGATTTATTGT
*
423275 TCTCTGGTGGAAGATTCT-TTGT
1 TCTCGGGTGGAAGATT-TATTGT
423297 TCTCGGGTGG
1 TCTCGGGTGG
423307 GGTCGGGTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.15, C:0.13, G:0.31, T:0.41
Consensus pattern (22 bp):
TCTCGGGTGGAAGATTTATTGT
Found at i:434726 original size:21 final size:21
Alignment explanation
Indices: 434701--434752 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
434691 TATTTTAGGA
434701 TTTAAGTTTATAATTCAAAGG
1 TTTAAGTTTATAATTCAAAGG
* * *
434722 TTTAAGTTTATAATTTAGAGT
1 TTTAAGTTTATAATTCAAAGG
434743 TTTAAGTTTA
1 TTTAAGTTTA
434753 GAGTAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (21 bp):
TTTAAGTTTATAATTCAAAGG
Found at i:434752 original size:14 final size:15
Alignment explanation
Indices: 434721--434756 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
434711 TAATTCAAAG
434721 GTTTA-AGTTTATAA
1 GTTTAGAGTTTATAA
434735 -TTTAGAGTTT-TAA
1 GTTTAGAGTTTATAA
434748 GTTTAGAGT
1 GTTTAGAGT
434757 AAATATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (15 bp):
GTTTAGAGTTTATAA
Found at i:440627 original size:36 final size:35
Alignment explanation
Indices: 440572--440640 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 35
440562 CCCATTCCTA
440572 TTTTCAAGAAACATCTACCAAACTTTGAAAATATT
1 TTTTCAAGAAACATCTACCAAACTTTGAAAATATT
* *
440607 TTTTCAAATAAACATTTACCAAACTTTGAAAATA
1 TTTTC-AAGAAACATCTACCAAACTTTGAAAATA
440641 AAATTTAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 5 0.16
36 26 0.84
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (35 bp):
TTTTCAAGAAACATCTACCAAACTTTGAAAATATT
Found at i:442779 original size:34 final size:32
Alignment explanation
Indices: 442726--442795 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
442716 ACCTTACAAC
*
442726 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
442758 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
442792 TCCC
1 TCCC
442796 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:443101 original size:21 final size:21
Alignment explanation
Indices: 443077--443119 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
443067 CCCAGAATAG
*
443077 AGGGAATC-AGTACCTCTTCAT
1 AGGGAATCGA-TACCCCTTCAT
443098 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
443119 A
1 A
443120 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:443195 original size:20 final size:19
Alignment explanation
Indices: 443155--443191 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
443145 CTGTTGAACA
443155 GGGGGGAATCGGTACCCCT
1 GGGGGGAATCGGTACCCCT
443174 GGGGGGAATCGGTACCCC
1 GGGGGGAATCGGTACCCC
443192 CTGGACATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.27, G:0.43, T:0.14
Consensus pattern (19 bp):
GGGGGGAATCGGTACCCCT
Found at i:443247 original size:21 final size:21
Alignment explanation
Indices: 443221--443300 Score: 91
Period size: 21 Copynumber: 4.1 Consensus size: 21
443211 GCTTTAGACA
*
443221 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
*
443242 GGGGGGTATCTGTA--CCC--
1 GGGGGGAATCTGTACCCCCTG
*
443259 --GGGGTATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
443278 GGGGGGAATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
443299 GG
1 GG
443301 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
21 32 0.64
ACGTcount: A:0.12, C:0.28, G:0.40, T:0.20
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCCTG
Found at i:443262 original size:15 final size:15
Alignment explanation
Indices: 443244--443273 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
443234 ACCCCCTGGG
443244 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
443259 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
443274 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:443279 original size:36 final size:36
Alignment explanation
Indices: 443223--443294 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
443213 TTTAGACAGG
*
443223 GGGGAATCGGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCC
* *
443259 GGGGTATCTGTACCCCCTGGGGGGGAATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCC
443295 CCTGGGCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.14, C:0.28, G:0.38, T:0.21
Consensus pattern (36 bp):
GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCC
Found at i:444745 original size:19 final size:20
Alignment explanation
Indices: 444702--444749 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
444692 TCTAAATCCT
*
444702 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
444722 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
444741 TTTTCAAAA
1 TTTTCAAAA
444750 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:445645 original size:32 final size:34
Alignment explanation
Indices: 445609--445678 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
445599 ACCTTACAAC
*
445609 TCCCTAG-TTTTTC-CGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
*
445641 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
445675 TCCC
1 TCCC
445679 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
Found at i:445984 original size:21 final size:21
Alignment explanation
Indices: 445960--446002 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
445950 CCCAGAATAG
*
445960 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
445981 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
446002 A
1 A
446003 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:446064 original size:21 final size:21
Alignment explanation
Indices: 446038--446081 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
446028 CTGTTGAACA
446038 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
446059 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
446080 GG
1 GG
446082 ACATTCTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.27, G:0.45, T:0.14
Consensus pattern (21 bp):
GGGGGGGAATCGGTACCCCCT
Found at i:446148 original size:15 final size:15
Alignment explanation
Indices: 446130--446159 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
446120 ACCCCCTGGG
446130 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
446145 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
446160 CTTGGGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:449155 original size:2 final size:2
Alignment explanation
Indices: 449148--449207 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
449138 CATGGAGTTC
449148 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
449190 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
449208 CAACTGGTGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:451933 original size:2 final size:2
Alignment explanation
Indices: 451926--451957 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
451916 TAATTATCGA
451926 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
451958 GAAGCTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:453383 original size:30 final size:30
Alignment explanation
Indices: 453334--453407 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
453324 GAAAATCGAA
*
453334 TTAAACAGGGACGGAGAAAAATCGTTTATG
1 TTAAACGGGGACGGAGAAAAATCGTTTATG
* *
453364 TTAAACGGGGATGGGGAAAAATCGTTTATG
1 TTAAACGGGGACGGAGAAAAATCGTTTATG
453394 TTAAACGGGGACGG
1 TTAAACGGGGACGG
453408 GTTTAGTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.35, C:0.09, G:0.32, T:0.23
Consensus pattern (30 bp):
TTAAACGGGGACGGAGAAAAATCGTTTATG
Found at i:453679 original size:25 final size:24
Alignment explanation
Indices: 453642--453695 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
453632 TTTAAATCCC
*
453642 TACGGTTTTTTAAGCGGGGACGGG
1 TACGGTTTTTTAAACGGGGACGGG
*
453666 TACGCGTTTTTTAAATGGGGACGGG
1 TACG-GTTTTTTAAACGGGGACGGG
*
453691 GACGG
1 TACGG
453696 GGGACCAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.19, C:0.13, G:0.41, T:0.28
Consensus pattern (24 bp):
TACGGTTTTTTAAACGGGGACGGG
Found at i:458179 original size:71 final size:71
Alignment explanation
Indices: 458011--458334 Score: 320
Period size: 71 Copynumber: 4.6 Consensus size: 71
458001 TTTTATTAAG
* * * * * *
458011 GTCGTAACGCTCGTGTGCTTTTATGATCTTATAAGAAGTGAATTTGGATAATATGATGTTCTTTC
1 GTCGTAACACTCCTGTGCTTTTATGATCTTTTAAGAAGTGAATTAGGATCATATGATGATCTTTC
458076 TATGTT
66 TATGTT
* ** ** * * * * * *
458082 GTGGTAATGCTTATGCGATTTGATGATCTTTTAAGAAGTAAATTAGGATCATACGATGATCCTTC
1 GTCGTAACACTCCTGTGCTTTTATGATCTTTTAAGAAGTGAATTAGGATCATATGATGATCTTTC
458147 TATGTT
66 TATGTT
* * * *
458153 GTCGTAACCCTCCTGTTCTTTTATGATCTTTTAAGAAGTGAATTATGAT-ATTAT-ATTAATCTT
1 GTCGTAACACTCCTGTGCTTTTATGATCTTTTAAGAAGTGAATTAGGATCA-TATGA-TGATCTT
458216 TCTATGTT
64 TCTATGTT
* *
458224 GTCGTAACACT-C-GTGCTTTTATGATCTTTT-A-AA-TGAATTAGGATCATATAATGATCTTTT
1 GTCGTAACACTCCTGTGCTTTTATGATCTTTTAAGAAGTGAATTAGGATCATATGATGATCTTTC
*
458284 TAAGTT
66 TATGTT
* * *
458290 GTCGTAACGAACGCCTGTGTTTTTATGATCTTTTAATAAGTGAAT
1 GTCGTAAC--ACTCCTGTGCTTTTATGATCTTTTAAGAAGTGAAT
458335 CTAGCACCCT
Statistics
Matches: 206, Mismatches: 36, Indels: 20
0.79 0.14 0.08
Matches are distributed among these distances:
66 33 0.16
67 4 0.02
68 3 0.01
69 18 0.09
70 20 0.10
71 121 0.59
72 2 0.01
73 5 0.02
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (71 bp):
GTCGTAACACTCCTGTGCTTTTATGATCTTTTAAGAAGTGAATTAGGATCATATGATGATCTTTC
TATGTT
Found at i:461993 original size:15 final size:15
Alignment explanation
Indices: 461962--461995 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
461952 GTTTTGGTTG
*
461962 TTTTGGTTCTAGTTA
1 TTTTGGTTCTAGATA
*
461977 TTTTGGTTCTGGATA
1 TTTTGGTTCTAGATA
461992 TTTT
1 TTTT
461996 TCGGTTTGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.06, G:0.21, T:0.62
Consensus pattern (15 bp):
TTTTGGTTCTAGATA
Found at i:464451 original size:12 final size:12
Alignment explanation
Indices: 464434--464458 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
464424 TTGAGACTTT
464434 AAACCGAACCGA
1 AAACCGAACCGA
464446 AAACCGAACCGA
1 AAACCGAACCGA
464458 A
1 A
464459 TAATGTCAAA
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:0.52, C:0.32, G:0.16, T:0.00
Consensus pattern (12 bp):
AAACCGAACCGA
Found at i:464471 original size:20 final size:20
Alignment explanation
Indices: 464446--464498 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
464436 ACCGAACCGA
464446 AAACCGAACCGAATAATGTC
1 AAACCGAACCGAATAATGTC
*
464466 AAACCGAACTGAATAATGTC
1 AAACCGAACCGAATAATGTC
464486 AAACCGAACCGAA
1 AAACCGAACCGAA
464499 CCGTTTTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.47, C:0.25, G:0.15, T:0.13
Consensus pattern (20 bp):
AAACCGAACCGAATAATGTC
Found at i:465023 original size:14 final size:14
Alignment explanation
Indices: 465004--465032 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
464994 ATTAACCAAA
465004 AATATAAATTATTT
1 AATATAAATTATTT
465018 AATATAAATTATTT
1 AATATAAATTATTT
465032 A
1 A
465033 TAAATTTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATAAATTATTT
Found at i:472801 original size:140 final size:140
Alignment explanation
Indices: 472549--472801 Score: 497
Period size: 140 Copynumber: 1.8 Consensus size: 140
472539 AAAAAGGATT
472549 TGGTTAAACCAATGAATCACAGAATAACCCGAACCCTCAGAGCTACCCAAATACATGTAAAGCAA
1 TGGTTAAACCAATGAATCACAGAATAACCCGAACCCTCAGAGCTACCCAAATACATGTAAAGCAA
472614 CAAACAGGAAATACCCACAAAGGAGAAAAGAAAGGAATTGTGGTAATCGTTGAAGAAGAGCCTGG
66 CAAACAGGAAATACCCACAAAGGAGAAAAGAAAGGAATTGTGGTAATCGTTGAAGAAGAGCCTGG
472679 TTTGAAGATC
131 TTTGAAGATC
*
472689 TGGTTAAACCAATGAATCCCAGAATAACCCGAACCCTCAGAGCTACCCAAATACATGTAAAGCAA
1 TGGTTAAACCAATGAATCACAGAATAACCCGAACCCTCAGAGCTACCCAAATACATGTAAAGCAA
472754 CAAACAGGAAATACCCACAAAGGAGAAAAGAAAGGAATTGTGGTAATC
66 CAAACAGGAAATACCCACAAAGGAGAAAAGAAAGGAATTGTGGTAATC
472802 ATTGTGGTAA
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 112 1.00
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.16
Consensus pattern (140 bp):
TGGTTAAACCAATGAATCACAGAATAACCCGAACCCTCAGAGCTACCCAAATACATGTAAAGCAA
CAAACAGGAAATACCCACAAAGGAGAAAAGAAAGGAATTGTGGTAATCGTTGAAGAAGAGCCTGG
TTTGAAGATC
Found at i:475436 original size:12 final size:12
Alignment explanation
Indices: 475419--475444 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
475409 ACTTCAGCTT
475419 TTATAAAATTTG
1 TTATAAAATTTG
475431 TTATAAAATTTG
1 TTATAAAATTTG
475443 TT
1 TT
475445 TAATCAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (12 bp):
TTATAAAATTTG
Found at i:486350 original size:23 final size:24
Alignment explanation
Indices: 486319--486363 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
486309 GATAACGTAT
* *
486319 ATTTTATCATATATA-TATTTTTA
1 ATTTAATCATACATATTATTTTTA
486342 ATTTAATCATACATATTATTTT
1 ATTTAATCATACATATTATTTT
486364 GAGGAATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTTAATCATACATATTATTTTTA
Found at i:486637 original size:37 final size:35
Alignment explanation
Indices: 486580--486660 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 35
486570 AATTGAACGT
486580 TAAATTTTGAACAGAATACTAAAATCAAACAAAAC
1 TAAATTTTGAACAGAATACTAAAATCAAACAAAAC
* * * *
486615 TAAAGTTTTTAACAAGAGTACTAAAATGAAACAAAAAT
1 TAAA-TTTTGAAC-AGAATACTAAAATCAAAC-AAAAC
486653 TAAATTTT
1 TAAATTTT
486661 AAGTATGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 4 0.10
36 7 0.18
37 20 0.51
38 8 0.21
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.28
Consensus pattern (35 bp):
TAAATTTTGAACAGAATACTAAAATCAAACAAAAC
Found at i:500602 original size:3 final size:3
Alignment explanation
Indices: 500594--500625 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
500584 AATTGAGAAC
500594 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
500626 TTGTTGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:501116 original size:30 final size:30
Alignment explanation
Indices: 501082--501178 Score: 169
Period size: 30 Copynumber: 3.2 Consensus size: 30
501072 TTCAAAAACT
501082 ATAAAATAATTATTAAAGTTT-TAAATTATA
1 ATAAAATAATTATTAAA-TTTATAAATTATA
*
501112 ATAAAATGATTATTAAATTTATAAATTATA
1 ATAAAATAATTATTAAATTTATAAATTATA
501142 ATAAAATAATTATTAAATTTATAAATTATA
1 ATAAAATAATTATTAAATTTATAAATTATA
501172 ATAAAAT
1 ATAAAAT
501179 TTATCAAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
29 3 0.05
30 61 0.95
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (30 bp):
ATAAAATAATTATTAAATTTATAAATTATA
Found at i:501148 original size:19 final size:18
Alignment explanation
Indices: 501125--501182 Score: 65
Period size: 19 Copynumber: 3.5 Consensus size: 18
501115 AAATGATTAT
501125 TAAATTTATAAATTATAA
1 TAAATTTATAAATTATAA
501143 TAAA---AT-AATTAT--
1 TAAATTTATAAATTATAA
501155 TAAATTTATAAATTATAA
1 TAAATTTATAAATTATAA
501173 TAAAATTTAT
1 T-AAATTTAT
501183 CAAAATATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
12 4 0.12
14 6 0.18
15 4 0.12
16 6 0.18
18 5 0.15
19 8 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTTATAAATTATAA
Found at i:501178 original size:11 final size:11
Alignment explanation
Indices: 501104--501179 Score: 56
Period size: 11 Copynumber: 7.5 Consensus size: 11
501094 TTAAAGTTTT
501104 AAATTATAATA
1 AAATTATAATA
* * *
501115 AAATGATTATT
1 AAATTATAATA
501126 AAATT-T-AT-
1 AAATTATAATA
501134 AAATTATAATA
1 AAATTATAATA
* * *
501145 AAATAATTATT
1 AAATTATAATA
501156 AAATT-T-AT-
1 AAATTATAATA
501164 AAATTATAATA
1 AAATTATAATA
501175 AAATT
1 AAATT
501180 TATCAAAATA
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
8 10 0.20
9 6 0.12
10 6 0.12
11 29 0.57
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (11 bp):
AAATTATAATA
Found at i:501369 original size:2 final size:2
Alignment explanation
Indices: 501364--501405 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
501354 CAAAAATTGG
501364 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
501405 T
1 T
501406 TTTTAATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:504899 original size:31 final size:31
Alignment explanation
Indices: 504864--504931 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
504854 TTAAAACTTA
504864 CAATATAATCTCCT-AACATTTAATCCGTTTG
1 CAATATAATC-CCTCAACATTTAATCCGTTTG
** *
504895 CAATATGGTCCCTCAACATTTAGTCCGTTTG
1 CAATATAATCCCTCAACATTTAATCCGTTTG
504926 CAATAT
1 CAATAT
504932 GGTCCCCGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 3 0.09
31 30 0.91
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (31 bp):
CAATATAATCCCTCAACATTTAATCCGTTTG
Found at i:504932 original size:31 final size:31
Alignment explanation
Indices: 504878--504937 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
504868 ATAATCTCCT
504878 AACATTTAATCCGTTTGCAATATGGTCCCTC
1 AACATTTAATCCGTTTGCAATATGGTCCCTC
*
504909 AACATTTAGTCCGTTTGCAATATGGTCCC
1 AACATTTAATCCGTTTGCAATATGGTCCC
504938 CGACGTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (31 bp):
AACATTTAATCCGTTTGCAATATGGTCCCTC
Found at i:509871 original size:19 final size:19
Alignment explanation
Indices: 509847--509885 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
509837 TCGAATGCAT
509847 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
509866 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
509885 T
1 T
509886 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:509902 original size:65 final size:63
Alignment explanation
Indices: 509784--509992 Score: 217
Period size: 65 Copynumber: 3.2 Consensus size: 63
509774 TATTCAAAGG
* *
509784 CATGCACCGATGCA-TCAGTCCATGCATCGATGCATCGATGAAT-TAATT-GAACATCGAATGCA
1 CATGCACCGATGCACTC--TCCATGCATCGATGCATC--TGAATAT-TTTCAAACATCGAATGCA
*
509846 TTC
61 TTT
509849 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCA-TCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * **
509914 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATA-TTTTCAAACATCGAATGCATTT
*
509978 CATGCATCGATGCAC
1 CATGCACCGATGCAC
509993 ACTTGGTGCA
Statistics
Matches: 126, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
63 7 0.06
64 53 0.42
65 64 0.51
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (63 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATATTTTCAAACATCGAATGCATTT
Found at i:509986 original size:64 final size:65
Alignment explanation
Indices: 509833--509993 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
509823 GAATTAATTG
* * *** *
509833 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
509898 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
509961 A
65 A
509962 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
509994 CTTGGTGCAC
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 48 0.56
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:510008 original size:64 final size:64
Alignment explanation
Indices: 509784--510013 Score: 225
Period size: 64 Copynumber: 3.6 Consensus size: 64
509774 TATTCAAAGG
* * * *
509784 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT--GAACATCGAATGCA
1 CATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCA
*
509846 TTC
62 TTT
* * *
509849 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTT
* ** **
509914 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAAAACATCGAATGCATTT
*** *
509978 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTCCATGCATCGATGCATCA
510014 AGTGTTCCAA
Statistics
Matches: 139, Mismatches: 21, Indels: 11
0.81 0.12 0.06
Matches are distributed among these distances:
63 6 0.04
64 69 0.50
65 64 0.46
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:518511 original size:65 final size:64
Alignment explanation
Indices: 518419--518575 Score: 172
Period size: 65 Copynumber: 2.4 Consensus size: 64
518409 GAATTAATTG
* * * *** * *
518419 AACATCGAATGCATTCCATTCACCGATGAACTCTATATGCATCGATGCACTCTGAATA-TTTTCA
1 AACATCGAATGCATTTCATGCATCGATGAACAAGACATGCATCGATGCA-TCAGAATATTTTTC-
518483 A
64 A
* * * **
518484 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTCA
1 AACATCGAATGCATTTCATGCATCGATGAACAAGACATGCATCGATGCATCAGAATATTTTTCA
518548 AACATCGAATGCATTTCATGCATCGATG
1 AACATCGAATGCATTTCATGCATCGATG
518576 CACACTTGGT
Statistics
Matches: 77, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
64 33 0.43
65 44 0.57
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGAACAAGACATGCATCGATGCATCAGAATATTTTTCA
Found at i:518569 original size:64 final size:65
Alignment explanation
Indices: 518455--518579 Score: 191
Period size: 64 Copynumber: 1.9 Consensus size: 65
518445 TGAACTCTAT
* *
518455 ATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTGATGCATCGATGCACAAGCC
1 ATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTTCATGCATCGATGCACAAGCC
**
518520 ATGCATCGATGCA-TCAGGCTATTTTTC-AAACATCGAATGCATTTCATGCATCGATGCACA
1 ATGCATCGATGCACTCAGAATA-TTTTCAAAACATCGAATGCATTTCATGCATCGATGCACA
518580 CTTGGTGCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
64 37 0.67
65 18 0.33
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (65 bp):
ATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTTCATGCATCGATGCACAAGCC
Found at i:524928 original size:23 final size:23
Alignment explanation
Indices: 524882--524952 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
524872 GTCGTGGTCG
*
524882 TGGAATAAATCGCAA--CGAATT
1 TGGAATAAATCGCAACGCGAACT
* *
524903 TGGAATAAATCGTAGCGCGAACT
1 TGGAATAAATCGCAACGCGAACT
524926 TGGAATAAATCGCAACGCGAACT
1 TGGAATAAATCGCAACGCGAACT
524949 TGGA
1 TGGA
524953 CTATCGCAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 13 0.30
23 30 0.70
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (23 bp):
TGGAATAAATCGCAACGCGAACT
Found at i:524960 original size:21 final size:22
Alignment explanation
Indices: 524882--524961 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
524872 GTCGTGGTCG
*
524882 TGGAATAAATCGCAA--CGAATT
1 TGGAAT-AATCGCAACGCGAACT
* *
524903 TGGAATAAATCGTAGCGCGAACT
1 TGGAAT-AATCGCAACGCGAACT
524926 TGGAATAAATCGCAACGCGAACT
1 TGGAAT-AATCGCAACGCGAACT
*
524949 TGGACT-ATCGCAA
1 TGGAATAATCGCAA
524962 TGCACATATT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
21 20 0.39
23 31 0.61
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.21
Consensus pattern (22 bp):
TGGAATAATCGCAACGCGAACT
Found at i:525419 original size:2 final size:2
Alignment explanation
Indices: 525412--525440 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
525402 GTGTATGTGA
525412 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
525441 AATAAGTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:525791 original size:12 final size:12
Alignment explanation
Indices: 525774--525880 Score: 130
Period size: 12 Copynumber: 9.2 Consensus size: 12
525764 GTTTAGCTAT
525774 TTCTTCTCTTCC
1 TTCTTCTCTTCC
* *
525786 TTCTTCTCCTCT
1 TTCTTCTCTTCC
525798 TTCTTCTCTTCC
1 TTCTTCTCTTCC
* *
525810 TTCTTCTCCTCT
1 TTCTTCTCTTCC
*
525822 TTCTTCTCTTCT
1 TTCTTCTCTTCC
*
525834 TTCTTCTCCT-C
1 TTCTTCTCTTCC
*
525845 -T-TTCTTTTCC
1 TTCTTCTCTTCC
525855 TTCTTCTCTTCC
1 TTCTTCTCTTCC
525867 TTCTTCTCTTCC
1 TTCTTCTCTTCC
525879 TT
1 TT
525881 AGCAGGTCCG
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
9 5 0.06
10 2 0.03
11 1 0.01
12 72 0.90
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (12 bp):
TTCTTCTCTTCC
Found at i:525800 original size:24 final size:24
Alignment explanation
Indices: 525773--525880 Score: 168
Period size: 24 Copynumber: 4.6 Consensus size: 24
525763 CGTTTAGCTA
525773 TTTCTTCTCTTCCTTCTTCTCCTC
1 TTTCTTCTCTTCCTTCTTCTCCTC
525797 TTTCTTCTCTTCCTTCTTCTCCTC
1 TTTCTTCTCTTCCTTCTTCTCCTC
*
525821 TTTCTTCTCTTCTTTCTTCTCCTC
1 TTTCTTCTCTTCCTTCTTCTCCTC
*
525845 TTTC-T-T-TTCCTTCTTCTCTTC
1 TTTCTTCTCTTCCTTCTTCTCCTC
*
525866 CTTCTTCTCTTCCTT
1 TTTCTTCTCTTCCTT
525881 AGCAGGTCCG
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
21 16 0.21
22 2 0.03
23 2 0.03
24 57 0.74
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTCTTCTCTTCCTTCTTCTCCTC
Found at i:525802 original size:4 final size:5
Alignment explanation
Indices: 525775--525877 Score: 67
Period size: 5 Copynumber: 21.0 Consensus size: 5
525765 TTTAGCTATT
* *
525775 TCTTC TCTTC -CTTC TTCTCC TCTT- TCTTC TCTTC -CTTC TTCTCC TCTT-
1 TCTTC TCTTC TCTTC -TCTTC TCTTC TCTTC TCTTC TCTTC -TCTTC TCTTC
* * *
525823 TCTTC TCTTC T-TTC TTCTCC TCTT- TCTTT TCCT- TCTTC TCTTCC TTCTTC
1 TCTTC TCTTC TCTTC -TCTTC TCTTC TCTTC TCTTC TCTTC TCTT-C -TCTTC
525873 TCTTC
1 TCTTC
525878 CTTAGCAGGT
Statistics
Matches: 78, Mismatches: 8, Indels: 24
0.71 0.07 0.22
Matches are distributed among these distances:
4 26 0.33
5 38 0.49
6 10 0.13
7 4 0.05
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
TCTTC
Found at i:525813 original size:33 final size:33
Alignment explanation
Indices: 525776--525880 Score: 129
Period size: 33 Copynumber: 3.1 Consensus size: 33
525766 TTAGCTATTT
*
525776 CTTCTCTTCCTTCTTCTCCTCTTTCTTCTCTTC
1 CTTCTCTTCCTTCTTCTCTTCTTTCTTCTCTTC
* *
525809 CTTCTTCTCCTCTTTCTTCTCTTCTTTCTTCTCCTC
1 CTTC-TCT--TCCTTCTTCTCTTCTTTCTTCTCTTC
* * *
525845 TTTCTTTTCCTTCTTCTCTTCCTTCTTCTCTTC
1 CTTCTCTTCCTTCTTCTCTTCTTTCTTCTCTTC
525878 CTT
1 CTT
525881 AGCAGGTCCG
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
33 29 0.48
34 3 0.05
35 2 0.03
36 26 0.43
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (33 bp):
CTTCTCTTCCTTCTTCTCTTCTTTCTTCTCTTC
Found at i:525869 original size:9 final size:8
Alignment explanation
Indices: 525774--525870 Score: 74
Period size: 9 Copynumber: 11.9 Consensus size: 8
525764 GTTTAGCTAT
525774 TTCTTCTC
1 TTCTTCTC
*
525782 TTCCT-TC
1 TTCTTCTC
*
525789 TTCTCCTC
1 TTCTTCTC
525797 TTTCTTCTC
1 -TTCTTCTC
*
525806 TTCCT-TC
1 TTCTTCTC
*
525813 TTCTCCTC
1 TTCTTCTC
525821 TTTCTTCTC
1 -TTCTTCTC
525830 TTCTT-TC
1 TTCTTCTC
*
525837 TTCTCCTC
1 TTCTTCTC
*
525845 TTTCTTTTCC
1 -TTCTTCT-C
525855 TTCTTCTC
1 TTCTTCTC
525863 TTCCTTCT
1 TT-CTTCT
525871 TCTCTTCCTT
Statistics
Matches: 69, Mismatches: 12, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
7 16 0.23
8 22 0.32
9 30 0.43
10 1 0.01
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (8 bp):
TTCTTCTC
Found at i:527097 original size:7 final size:8
Alignment explanation
Indices: 527082--527111 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
527072 TTTTAAAGCA
527082 TAAATTTT
1 TAAATTTT
527090 TAAATTTT
1 TAAATTTT
527098 TAAATTTT
1 TAAATTTT
*
527106 AAAATT
1 TAAATT
527112 ACCTTATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TAAATTTT
Found at i:540583 original size:351 final size:351
Alignment explanation
Indices: 540019--540723 Score: 1383
Period size: 351 Copynumber: 2.0 Consensus size: 351
540009 TCAAAACCAT
540019 ATATAACATTTAGTTATTGTTTCATTTTAGTATCTCACTATTAAAAACTTACAAGAACTTTTAGA
1 ATATAACATTTAGTTATTGTTTCATTTTAGTATCTCACTATTAAAAACTTACAAGAACTTTTAGA
540084 ACTTGGCATTCTTTATCAGTAAATTACATCATGCATCACTCAACTATCTTCTCACTCATATTTTG
66 ACTTGGCATTCTTTATCAGTAAATTACATCATGCATCACTCAACTATCTTCTCACTCATATTTTG
540149 GTCATTGAAGTTTAGTTTTTAAATTTAATTACTTAACTTTCAAATTACTCCTAATTTAATCACTC
131 GTCATTGAAGTTTAGTTTTTAAATTTAATTACTTAACTTTCAAATTACTCCTAATTTAATCACTC
540214 TACTTTCAATTTTTTTTATTTTAATTGTATATTAATAAAATAATAAAAATATCATGTCACAAAAT
196 TACTTTCAATTTTTTTTATTTTAATTGTATATTAATAAAATAATAAAAATATCATGTCACAAAAT
540279 ATTATTAATAAAATAAATTAAAGTGATTAAAACATGAGTAATTTGAAAGTTAAGTAGTTAAATTA
261 ATTATTAATAAAATAAATTAAAGTGATTAAAACATGAGTAATTTGAAAGTTAAGTAGTTAAATTA
*
540344 AAAAATTTTAAACTTTAATAACGAAA
326 AAAAATTTTAAACTTTAATAACAAAA
540370 ATATAACATTTAGTTATTGTTTCATTTTAGTATCTCACTATTAAAAACTTACAAGAACTTTTAGA
1 ATATAACATTTAGTTATTGTTTCATTTTAGTATCTCACTATTAAAAACTTACAAGAACTTTTAGA
540435 ACTTGGCATTCTTTATCAGTAAATTACATCATGCATCACTCAACTATCTTCTCACTCATATTTTG
66 ACTTGGCATTCTTTATCAGTAAATTACATCATGCATCACTCAACTATCTTCTCACTCATATTTTG
*
540500 GTCATTGAAGTTTAGTTTTTTAATTTAATTACTTAACTTTCAAATTACTCCTAATTTAATCACTC
131 GTCATTGAAGTTTAGTTTTTAAATTTAATTACTTAACTTTCAAATTACTCCTAATTTAATCACTC
*
540565 TACTTTCAATTTTTTTTATTTTAATTGTATATTAATAACATAATAAAAATATCATGTCACAAAAT
196 TACTTTCAATTTTTTTTATTTTAATTGTATATTAATAAAATAATAAAAATATCATGTCACAAAAT
540630 ATTATTAATAAAATAAATTAAAGTGATTAAAACATGAGTAATTTGAAAGTTAAGTAGTTAAATTA
261 ATTATTAATAAAATAAATTAAAGTGATTAAAACATGAGTAATTTGAAAGTTAAGTAGTTAAATTA
540695 AAAAATTTTAAACTTTAATAACAAAA
326 AAAAATTTTAAACTTTAATAACAAAA
540721 ATA
1 ATA
540724 GGAGTGACAA
Statistics
Matches: 351, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
351 351 1.00
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (351 bp):
ATATAACATTTAGTTATTGTTTCATTTTAGTATCTCACTATTAAAAACTTACAAGAACTTTTAGA
ACTTGGCATTCTTTATCAGTAAATTACATCATGCATCACTCAACTATCTTCTCACTCATATTTTG
GTCATTGAAGTTTAGTTTTTAAATTTAATTACTTAACTTTCAAATTACTCCTAATTTAATCACTC
TACTTTCAATTTTTTTTATTTTAATTGTATATTAATAAAATAATAAAAATATCATGTCACAAAAT
ATTATTAATAAAATAAATTAAAGTGATTAAAACATGAGTAATTTGAAAGTTAAGTAGTTAAATTA
AAAAATTTTAAACTTTAATAACAAAA
Found at i:559712 original size:184 final size:185
Alignment explanation
Indices: 559336--559693 Score: 505
Period size: 184 Copynumber: 2.0 Consensus size: 185
559326 TTTAAAATTC
559336 AATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTAT
1 AATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTAT
*
559401 ATAAAATTTTTATTTTATAATTATATATTATTTAAATTAATTGTAAACTATTTTTTTGAATTAAA
66 ATAAAATTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTTGAATTAAA
** * ** ** **
559466 AAATATTAAATATATTATATATAACATATGAGCTTAGCCCAAACCATTTAAAACCC
131 AAATATTAAATATATTATATATAACATAAAAACTTA-CAAAAAAAATTTAAAACAA
*
559522 AATTAATAATTTAAGATTCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAA-TT-T
1 AATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTAT
* *
559585 ATAAAATTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTATA
66 ATAAAATTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTTGAATTAAA
* *
559650 AAATATTTAAT-T-TT-TATATAA-ATTAAAAAATTTA-AAAAAAAATT
131 AAATATTAAATATATTATATATAACA-T-AAAAACTTACAAAAAAAATT
559694 GGTTAATTCG
Statistics
Matches: 157, Mismatches: 13, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
180 7 0.04
181 8 0.05
182 7 0.04
183 1 0.01
184 73 0.46
185 2 0.01
186 59 0.38
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (185 bp):
AATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTAT
ATAAAATTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTTGAATTAAA
AAATATTAAATATATTATATATAACATAAAAACTTACAAAAAAAATTTAAAACAA
Found at i:559961 original size:18 final size:18
Alignment explanation
Indices: 559938--559983 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
559928 ACTTGAAATT
559938 TTTTCGA-TTCGAGTCAAA
1 TTTTCGAGTT-GAGTCAAA
559956 TTTTCGAGTTGAGTCAAA
1 TTTTCGAGTTGAGTCAAA
559974 TTTTCGAGTT
1 TTTTCGAGTT
559984 TGTGTTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 25 0.93
19 2 0.07
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (18 bp):
TTTTCGAGTTGAGTCAAA
Found at i:560383 original size:2 final size:2
Alignment explanation
Indices: 560378--560427 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
560368 CCTATATACA
560378 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
560420 AT AT AT AT
1 AT AT AT AT
560428 TTCTTCATAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:561058 original size:31 final size:31
Alignment explanation
Indices: 561022--561081 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
561012 AACTTAAAAG
* *
561022 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAAAACTGAAATTTAAATAATTTT
*
561053 AGTTTTATAAAACTGAAATTTAAATAATT
1 AGTTTTACAAAACTGAAATTTAAATAATT
561082 CATACAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (31 bp):
AGTTTTACAAAACTGAAATTTAAATAATTTT
Found at i:561154 original size:22 final size:22
Alignment explanation
Indices: 561104--561445 Score: 460
Period size: 22 Copynumber: 15.6 Consensus size: 22
561094 ATAATAAATT
561104 TTTTAAAATAAATCAAT-TCATA
1 TTTTAAAATAAATCAATCT-ATA
561126 -TTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCTATA
*
561147 TTTTAAAATAAATCGATCTATA
1 TTTTAAAATAAATCAATCTATA
*
561169 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCTATA
** *
561191 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCTATA
561213 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCTATA
*
561235 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCTATA
*
561257 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCTATA
* *
561279 TTTTAAAATAAATCAATTTACA
1 TTTTAAAATAAATCAATCTATA
561301 TTTTAAAATAAATCAAT-TCATA
1 TTTTAAAATAAATCAATCT-ATA
*
561323 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCTATA
*
561345 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCTATA
* ** *
561367 TTTTAAAATAACT-TTTTTCATA
1 TTTTAAAATAAATCAATCT-ATA
* *
561389 TTTTAAAAGAAATCAATCCATA
1 TTTTAAAATAAATCAATCTATA
561411 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCTATA
561433 TTTTAAAATAAAT
1 TTTTAAAATAAAT
561446 TTTAAAATAT
Statistics
Matches: 285, Mismatches: 27, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
21 25 0.09
22 255 0.89
23 5 0.02
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.40
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCTATA
Found at i:561222 original size:66 final size:66
Alignment explanation
Indices: 561104--561445 Score: 535
Period size: 66 Copynumber: 5.2 Consensus size: 66
561094 ATAATAAATT
* *
561104 TTTTAAAATAAATCAATTCATA-TTTAAAATAAATCAATCTATATTTTAAAATAAATCGATCTAT
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTAT
561168 A
66 A
* **
561169 TTTTAAAATAAATCAATCCATATTTTAAAATAAAAT-TTTCCATATTTTAAAATAAATCAATCTA
1 TTTTAAAATAAATCAATTCATATTTTAAAAT-AAATCAATCCATATTTTAAAATAAATCAATCTA
561233 TA
65 TA
* * *
561235 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTTAC
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTAT
561300 A
66 A
*
561301 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTAT
561366 A
66 A
* *** *
561367 TTTTAAAATAACTTTTTTCATATTTTAAAAGAAATCAATCCATATTTTAAAATAAATCAATCTAT
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTAT
561432 A
66 A
561433 TTTTAAAATAAAT
1 TTTTAAAATAAAT
561446 TTTAAAATAT
Statistics
Matches: 254, Mismatches: 20, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
65 25 0.10
66 225 0.89
67 4 0.02
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.40
Consensus pattern (66 bp):
TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTAT
A
Found at i:561462 original size:11 final size:12
Alignment explanation
Indices: 561429--561459 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
561419 TAAATCAATC
561429 TATATTTTAAAA
1 TATATTTTAAAA
*
561441 TAAATTTTAAAA
1 TATATTTTAAAA
561453 TATATTT
1 TATATTT
561460 AAATGATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TATATTTTAAAA
Found at i:561463 original size:22 final size:23
Alignment explanation
Indices: 561429--561471 Score: 54
Period size: 21 Copynumber: 1.9 Consensus size: 23
561419 TAAATCAATC
561429 TATATTTTAAAATAAATTTTAAAA
1 TATATTTTAAAAT-AATTTTAAAA
*
561453 TATA-TTT-AAATGATTTTAA
1 TATATTTTAAAATAATTTTAA
561472 TTTTTCCGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 3 0.17
24 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TATATTTTAAAATAATTTTAAAA
Found at i:562902 original size:20 final size:21
Alignment explanation
Indices: 562877--562969 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
562867 TTTTCCCAAT
*
562877 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
562897 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
562918 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
562938 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
562959 TCGCAATGCGA
1 TCGCAATGCGA
562970 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:562922 original size:41 final size:41
Alignment explanation
Indices: 562877--562969 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
562867 TTTTCCCAAT
562877 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
562918 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
562959 TCGCAATGCGA
1 TCGCAATGCGA
562970 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:562982 original size:41 final size:41
Alignment explanation
Indices: 562896--563030 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
562886 GAATAAGTAA
* *
562896 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
562937 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
562978 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
563019 TTCGCAACGCGA
1 ATCGCAACGCGA
563031 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:562983 original size:20 final size:20
Alignment explanation
Indices: 562958--563052 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
562948 AATTGGGAAA
*
562958 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
562978 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
562999 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
563019 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
563039 TTCGCAACGCGATA
1 ATCGCAACGCGATA
563053 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:563268 original size:22 final size:22
Alignment explanation
Indices: 563240--563283 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
563230 CACTCTCTCA
563240 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
563262 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
563284 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:564908 original size:18 final size:18
Alignment explanation
Indices: 564887--564931 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
564877 CTCCACTTCG
*
564887 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
564905 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
564923 GAGCCATCA
1 GAGCCATCA
564932 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:565467 original size:19 final size:20
Alignment explanation
Indices: 565413--565479 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
565403 TAGTTTACTT
* *
565413 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
565433 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
565453 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
565472 TCGCAACG
1 TCGCAACG
565480 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:565487 original size:14 final size:14
Alignment explanation
Indices: 565468--565507 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
565458 ATGCGAAATG
565468 AAAATCGCAACGAC
1 AAAATCGCAACGAC
565482 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
565496 AAAAGCGCAACG
1 AAAATCGCAACG
565508 CGAAACACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.50, C:0.28, G:0.17, T:0.05
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:565551 original size:14 final size:14
Alignment explanation
Indices: 565532--565589 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
565522 CAATGTTTCG
565532 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
565546 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
565562 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
565578 CGTTGCGATTTT
1 CGTTGCGATTTT
565590 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:565563 original size:32 final size:33
Alignment explanation
Indices: 565527--565605 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
565517 AATCGCAATG
565527 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
565559 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
565592 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
565606 AGTCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:565604 original size:19 final size:19
Alignment explanation
Indices: 565546--565663 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
565536 GCGATTTTGT
565546 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
565564 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
565578 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* **
565597 CATTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
565617 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
* *
565636 CGTTGCGAATTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
565656 TGTTGCGA
1 CGTTGCGA
565664 AAGTAAACTA
Statistics
Matches: 82, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.13
19 26 0.32
20 30 0.37
ACGTcount: A:0.14, C:0.19, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:565624 original size:20 final size:19
Alignment explanation
Indices: 565578--565643 Score: 96
Period size: 19 Copynumber: 3.4 Consensus size: 19
565568 GCGATTTTGT
**
565578 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
565597 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
565617 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
565636 CGTTGCGA
1 CGTTGCGA
565644 ATTTAAGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 24 0.57
20 18 0.43
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:567660 original size:14 final size:15
Alignment explanation
Indices: 567641--567708 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 15
567631 CGAAATGGCT
567641 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
567655 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
567673 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
567692 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
567706 ATC
1 ATC
567709 ACAATGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
14 14 0.31
15 1 0.02
16 4 0.09
17 2 0.04
18 13 0.29
19 9 0.20
20 1 0.02
21 1 0.02
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:567705 original size:19 final size:19
Alignment explanation
Indices: 567651--567698 Score: 89
Period size: 18 Copynumber: 2.6 Consensus size: 19
567641 ATCGCAACGA
567651 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
567670 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
567688 GAAAATCGCAA
1 GAAAATCGCAA
567699 CGAGAAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 18 0.64
19 10 0.36
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:567793 original size:20 final size:20
Alignment explanation
Indices: 567736--567793 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
567726 TCGCATTGCG
* *
567736 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
567756 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
567776 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
567794 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:571412 original size:39 final size:36
Alignment explanation
Indices: 571369--571521 Score: 155
Period size: 33 Copynumber: 4.4 Consensus size: 36
571359 TCTTAATGTC
571369 AATCGCAACGCGAAAATTACTATCGCAATGCGAAATGAA
1 AATCGCAACGCG-AAA-TA-TATCGCAATGCGAAATGAA
* *
571408 AATCGCAA--CGAGAGA-ATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATATATCGCAATGCGAAATGAA
*
571441 AATCGCAACGC-TAAT-T-TCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATATATCGCAATGCGAAATGAA
***
571474 AATCGCAA--CGAGGGA-ATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATATATCGCAATGCGAAATGAA
571507 AATCGCAACGC-AAAT
1 AATCGCAACGCGAAAT
571522 TTAATTTCGC
Statistics
Matches: 94, Mismatches: 12, Indels: 21
0.74 0.09 0.17
Matches are distributed among these distances:
31 1 0.01
33 76 0.81
34 2 0.02
35 3 0.03
36 2 0.02
37 2 0.02
39 8 0.09
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (36 bp):
AATCGCAACGCGAAATATATCGCAATGCGAAATGAA
Found at i:571432 original size:33 final size:33
Alignment explanation
Indices: 571390--571516 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
571380 GAAAATTACT
571390 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
571423 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
571455 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
571489 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
571517 CAAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:571497 original size:66 final size:66
Alignment explanation
Indices: 571391--571523 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
571381 AAAATTACTA
*
571391 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCAAAT
571456 T
66 T
*
571457 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCAAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCAAAT
571522 T
66 T
571523 T
1 T
571524 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCAAAT
T
Found at i:571547 original size:19 final size:19
Alignment explanation
Indices: 571525--571591 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
571515 CGCAAATTTA
*
571525 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
571544 ATTTTGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTC
*
571561 -CTTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
571577 ATTTCGCATTGCGAT
1 ATTTCGCATTGCGAT
571592 AGTACTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
14 6 0.16
16 6 0.16
17 7 0.18
19 19 0.50
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.46
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:571713 original size:13 final size:14
Alignment explanation
Indices: 571697--571731 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
571687 CATCAATTAA
571697 ACAAATCA-CTTTT
1 ACAAATCACCTTTT
571710 ACAAATCACCTTTT
1 ACAAATCACCTTTT
571724 ACAAATCA
1 ACAAATCA
571732 ATTAAACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCACCTTTT
Found at i:573152 original size:21 final size:21
Alignment explanation
Indices: 573086--573152 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
573076 GTGAATCGGG
*
573086 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
573106 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
573128 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
573149 CTCT
1 CTCT
573153 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:575268 original size:18 final size:20
Alignment explanation
Indices: 575234--575276 Score: 72
Period size: 18 Copynumber: 2.2 Consensus size: 20
575224 GATAATGGGA
575234 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
575254 ATCGC-ACGC-GAAATGACT
1 ATCGCAACGCGGAAATGACT
575272 ATCGC
1 ATCGC
575277 GACCAGACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 14 0.61
19 4 0.17
20 5 0.22
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:575319 original size:20 final size:19
Alignment explanation
Indices: 575205--575355 Score: 134
Period size: 20 Copynumber: 8.1 Consensus size: 19
575195 ATCTTTGGTT
*
575205 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
575224 GATAATGGGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
575244 GGAAATGACTATCGC-ACGC
1 -GAAATGAAAATCGCAACGC
** *
575263 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
575281 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
575296 GAAATGAAAATCGCAACTGC
1 GAAATGAAAATCGCAAC-GC
*
575316 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
575335 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
575354 GA
1 GA
575356 TTTTGGTTCG
Statistics
Matches: 111, Mismatches: 12, Indels: 18
0.79 0.09 0.13
Matches are distributed among these distances:
14 10 0.09
15 2 0.02
18 16 0.14
19 40 0.36
20 41 0.37
21 2 0.02
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:575372 original size:18 final size:18
Alignment explanation
Indices: 575351--575395 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
575341 AAAATCGCAA
*
575351 TGCGATTTTGGTTCGCGT
1 TGCGATTTTAGTTCGCGT
*
575369 TGCGAATTTTTATTTCGCGT
1 TGCG-A-TTTTAGTTCGCGT
575389 TGCGATT
1 TGCGATT
575396 ATCTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 6 0.26
19 2 0.09
20 15 0.65
ACGTcount: A:0.11, C:0.16, G:0.27, T:0.47
Consensus pattern (18 bp):
TGCGATTTTAGTTCGCGT
Found at i:575972 original size:20 final size:20
Alignment explanation
Indices: 575947--575999 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
575937 GCGCTATGTA
575947 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
575967 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
575987 TATCTCGTTGCGA
1 AATCGCGTTGCGA
576000 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:576036 original size:20 final size:20
Alignment explanation
Indices: 576008--576061 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
575998 GATTTTGTAT
*
576008 TATCACATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
576028 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
576048 TATCGCATTGCGAT
1 TATCGCATTGCGAT
576062 TTTCCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:582996 original size:16 final size:16
Alignment explanation
Indices: 582975--583008 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
582965 TCATGGTTGT
582975 CCAAGACTCCGAGTTC
1 CCAAGACTCCGAGTTC
582991 CCAAGACTCCGAGTTC
1 CCAAGACTCCGAGTTC
583007 CC
1 CC
583009 TTTTTTTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.41, G:0.18, T:0.18
Consensus pattern (16 bp):
CCAAGACTCCGAGTTC
Found at i:591847 original size:11 final size:11
Alignment explanation
Indices: 591831--591893 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
591821 AAAATTATAT
591831 TATTAAAAATA
1 TATTAAAAATA
591842 TATTAAAAATA
1 TATTAAAAATA
* ***
591853 CATTATTGATA
1 TATTAAAAATA
591864 -ATTATAAAAT-
1 TATTA-AAAATA
591874 T-TTAAAAATA
1 TATTAAAAATA
591884 TATTAAAAAT
1 TATTAAAAAT
591894 TCTATAATAC
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:592012 original size:7 final size:7
Alignment explanation
Indices: 592000--592064 Score: 58
Period size: 7 Copynumber: 9.3 Consensus size: 7
591990 ATTTGTAATG
592000 AACCCTA
1 AACCCTA
592007 AACCCTA
1 AACCCTA
**
592014 AACTATA
1 AACCCTA
*
592021 AACCCTT
1 AACCCTA
**
592028 AATACTA
1 AACCCTA
* *
592035 AATCATA
1 AACCCTA
*
592042 AATCCTA
1 AACCCTA
592049 AACCCTA
1 AACCCTA
592056 AACCCTA
1 AACCCTA
592063 AA
1 AA
592065 TTCGATTATG
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.22
Consensus pattern (7 bp):
AACCCTA
Found at i:592026 original size:21 final size:22
Alignment explanation
Indices: 592000--592058 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 22
591990 ATTTGTAATG
592000 AACCCTAAACCCTAAACT-ATA
1 AACCCTAAACCCTAAACTCATA
* **
592021 AACCCTTAATACTAAA-TCATA
1 AACCCTAAACCCTAAACTCATA
*
592042 AATCCTAAACCCTAAAC
1 AACCCTAAACCCTAAAC
592059 CCTAAATTCG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (22 bp):
AACCCTAAACCCTAAACTCATA
Found at i:601873 original size:27 final size:27
Alignment explanation
Indices: 601841--601892 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
601831 AAACTATATT
* * *
601841 TTTCGAGTCAGAATTCACATAAACATC
1 TTTCGAGCCAAAATTCACACAAACATC
601868 TTTCGAGCCAAAATTCACACAAACA
1 TTTCGAGCCAAAATTCACACAAACA
601893 ATCTGAGAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (27 bp):
TTTCGAGCCAAAATTCACACAAACATC
Done.