Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018060.1 Corchorus olitorius cultivar O-4 contig18093, 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: 151365
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1487 original size:2 final size:2
Alignment explanation
Indices: 1475--1510 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1465 GGAAACCCAA
*
1475 AT AT GT 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
1511 TAAAAAGGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1931 original size:108 final size:108
Alignment explanation
Indices: 1742--1942 Score: 375
Period size: 108 Copynumber: 1.9 Consensus size: 108
1732 ATTCGGTTAC
1742 TATAATATCTTTAAACAGTTAAATAAGAGAAGTAATACTGTATAGTAAACATGTCTCCTTGTCCT
1 TATAATATCTTTAAACAGTTAAATAAGAGAAGTAATACTGTATAGTAAACATGTCTCCTTGTCCT
*
1807 ACTGAAATTTCGAATTGCCAAGACGGATTTTACATGTCTATAA
66 ACTAAAATTTCGAATTGCCAAGACGGATTTTACATGTCTATAA
**
1850 TATAATATCTTTACGCAGTTAAATAAGAGAAGTAATACTGTATAGTAAACATGTCTCCTTGTCCT
1 TATAATATCTTTAAACAGTTAAATAAGAGAAGTAATACTGTATAGTAAACATGTCTCCTTGTCCT
1915 ACTAAAATTTCGAATTGCCAAGACGGAT
66 ACTAAAATTTCGAATTGCCAAGACGGAT
1943 AGCTTACAAG
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 90 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (108 bp):
TATAATATCTTTAAACAGTTAAATAAGAGAAGTAATACTGTATAGTAAACATGTCTCCTTGTCCT
ACTAAAATTTCGAATTGCCAAGACGGATTTTACATGTCTATAA
Found at i:4418 original size:33 final size:33
Alignment explanation
Indices: 4371--4434 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
4361 AGGCAACCCC
*
4371 CCATGGGGCGTGCCGCCCTACTAGGACGGCATG
1 CCATGGGGCATGCCGCCCTACTAGGACGGCATG
* *
4404 CCATGGGGCATGCCGCCCTGCTAGGATGGCA
1 CCATGGGGCATGCCGCCCTACTAGGACGGCA
4435 CCACCATGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.16, C:0.33, G:0.36, T:0.16
Consensus pattern (33 bp):
CCATGGGGCATGCCGCCCTACTAGGACGGCATG
Found at i:4663 original size:22 final size:21
Alignment explanation
Indices: 4637--4680 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
4627 CAAAACTGTC
*
4637 AAAAGGGGGACGGTAAGTAGCA
1 AAAAGGGGG-CGGTAAATAGCA
4659 AAAAGGGGGCGGTAAATAGCA
1 AAAAGGGGGCGGTAAATAGCA
4680 A
1 A
4681 CTCTCTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.43, C:0.09, G:0.39, T:0.09
Consensus pattern (21 bp):
AAAAGGGGGCGGTAAATAGCA
Found at i:14253 original size:16 final size:16
Alignment explanation
Indices: 14200--14253 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 16
14190 AATATTTAAT
14200 ATATATATATATATATA
1 ATATATAT-TATATATA
*
14217 ACA-A-ATTATATA-A
1 ATATATATTATATATA
*
14230 TTAT-TATTATATATA
1 ATATATATTATATATA
14245 ATATATATT
1 ATATATATT
14254 TAATTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 9
0.69 0.10 0.21
Matches are distributed among these distances:
13 2 0.07
14 14 0.48
15 6 0.21
16 5 0.17
17 2 0.07
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATATATTATATATA
Found at i:15934 original size:20 final size:20
Alignment explanation
Indices: 15909--15947 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
15899 GACTATCCGG
*
15909 TATTTTCTTTCTATTTACAA
1 TATTTTCTTTCCATTTACAA
15929 TATTTTCTTTCCATTTACA
1 TATTTTCTTTCCATTTACA
15948 TATAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.18, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTTTCTTTCCATTTACAA
Found at i:19780 original size:21 final size:21
Alignment explanation
Indices: 19756--19796 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19746 AGCAATTTAA
*
19756 GGAGGAAAATTTGCTATCAAG
1 GGAGGAAAATCTGCTATCAAG
* *
19777 GGAGGTAAATCTGCTGTCAA
1 GGAGGAAAATCTGCTATCAA
19797 ATTTGACAGA
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:0.34, C:0.12, G:0.29, T:0.24
Consensus pattern (21 bp):
GGAGGAAAATCTGCTATCAAG
Found at i:20229 original size:17 final size:15
Alignment explanation
Indices: 20197--20241 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 15
20187 TGGAAGGATA
20197 TTTATCTTATATTGCTT
1 TTTAT-TTA-ATTGCTT
20214 TCTTATTTCAATTGCTT
1 T-TTATTT-AATTGCTT
20231 TTTATTTAATT
1 TTTATTTAATT
20242 TGTTTTTGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.15
16 6 0.23
17 11 0.42
18 5 0.19
ACGTcount: A:0.20, C:0.11, G:0.04, T:0.64
Consensus pattern (15 bp):
TTTATTTAATTGCTT
Found at i:21877 original size:22 final size:22
Alignment explanation
Indices: 21852--21895 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
21842 AAATTAAGTC
21852 ACTTTTCTTATTGAATTTGGAA
1 ACTTTTCTTATTGAATTTGGAA
21874 ACTTTTCTTATTGAATTTGGAA
1 ACTTTTCTTATTGAATTTGGAA
21896 CATAAGACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (22 bp):
ACTTTTCTTATTGAATTTGGAA
Found at i:22139 original size:2 final size:2
Alignment explanation
Indices: 22132--22161 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
22122 ATTTTCCTAG
*
22132 TA TA TA TA TG 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
22162 GTGCTAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23797 original size:2 final size:2
Alignment explanation
Indices: 23790--23817 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
23780 CATTTGAAAA
23790 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
23818 GGTATTAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29891 original size:162 final size:162
Alignment explanation
Indices: 29617--31074 Score: 2403
Period size: 162 Copynumber: 9.0 Consensus size: 162
29607 TTTTGGTTTG
* *
29617 TACAAAAGCCCACTATGTGGCAAGGCATTGGTGATTAAGAAACCCACTATAACTCACACCTAGTC
1 TACAAAAGCCCACTATGTGGCAAGGCATTGGTGATTGAGAAACCCACTATAGCTCACACCTAGTC
* *
29682 TTCCTTGTAAGATGTATTGTTCACCATCATCAAGGCATGGGAAGGCATCACGCCGCCGGTGATTG
66 TTCCTTGTATGATGTATTGTTCACCATCATCAAGGCATGGCAAGGCATCACGCCGCCGGTGATTG
29747 AGACAACCTATAGTTCTCACCGTGTCTCTATT
131 AGACAACCTATAGTTCTCACCGTGTCTCTATT
* * *
29779 TACAAAAGCCTACTATGTGGCAAGACAATGGTGATTGAGAAACCCACTATAGCTCACACCTAGTC
1 TACAAAAGCCCACTATGTGGCAAGGCATTGGTGATTGAGAAACCCACTATAGCTCACACCTAGTC
* *
29844 TTCTTTGTATGATGTATTGTTCACCATCATCAAGGAATGGCAAGGCATCACGCCGCCGGTGATTG
66 TTCCTTGTATGATGTATTGTTCACCATCATCAAGGCATGGCAAGGCATCACGCCGCCGGTGATTG
29909 AGACAACCTATAGTTCTCACCGTGTCTCTATT
131 AGACAACCTATAGTTCTCACCGTGTCTCTATT
* *
29941 TACAAAAGCCCACTATGTGGCAAGGCAGTGGTGATTGAGAAACCCACTATAGCTCACACCTAGTT
1 TACAAAAGCCCACTATGTGGCAAGGCATTGGTGATTGAGAAACCCACTATAGCTCACACCTAGTC
* * * *
30006 TTCCTTATATGATGTATTGTTCACCATCATCAAGGCATGGAAAGGCATCACACCACCGGTGATTG
66 TTCCTTGTATGATGTATTGTTCACCATCATCAAGGCATGGCAAGGCATCACGCCGCCGGTGATTG
* *
30071 AGACAACCTATAGTTATCACCGCGTCTCTATT
131 AGACAACCTATAGTTCTCACCGTGTCTCTATT
* *
30103 TACAAAAGCCCACTATGTGGCAAGGCATTGGTGATTGAGAAACACACTATAGCTCACACCTAGTT
1 TACAAAAGCCCACTATGTGGCAAGGCATTGGTGATTGAGAAACCCACTATAGCTCACACCTAGTC
* * *
30168 TTCCTTGTATGATGTATTGTTCACCATCGTCAAGTCATGGCAAGGCATCATGCCGCCGGTGATTG
66 TTCCTTGTATGATGTATTGTTCACCATCATCAAGGCATGGCAAGGCATCACGCCGCCGGTGATTG
* * *
30233 AGACAACTTATAGTTCTCATCGTGTATCTATT
131 AGACAACCTATAGTTCTCACCGTGTCTCTATT
* * * *
30265 TACAAAAGCCCATTATGTGGCAAGGCATTGGTGATTGAGAAACCCACTATAACACATACCTAGTC
1 TACAAAAGCCCACTATGTGGCAAGGCATTGGTGATTGAGAAACCCACTATAGCTCACACCTAGTC
* *
30330 TTCCTTGTTTGATGTATTGTTCACCATCATCAAGGCATGTCAAGGCATCACGCCGCCGGTGATTG
66 TTCCTTGTATGATGTATTGTTCACCATCATCAAGGCATGGCAAGGCATCACGCCGCCGGTGATTG
30395 AGACAACCTATAGTTCTCACCGTGTCTCTATT
131 AGACAACCTATAGTTCTCACCGTGTCTCTATT
* *
30427 TACAAAAGCCCACTATGTGGCAAGGCATTGGTGATTGAGAAACCCACTATAGCTCACATCTAGTT
1 TACAAAAGCCCACTATGTGGCAAGGCATTGGTGATTGAGAAACCCACTATAGCTCACACCTAGTC
* * * * *
30492 TTCCTTATATGATGTATTGTTCACCATCATCAAGGAATGGAAAGACATCACGCCACCGGTGATTG
66 TTCCTTGTATGATGTATTGTTCACCATCATCAAGGCATGGCAAGGCATCACGCCGCCGGTGATTG
*
30557 AGACAACCTATATTTCTCACCGTGTCTCTATT
131 AGACAACCTATAGTTCTCACCGTGTCTCTATT
* * * **
30589 TACAAAAGCCTACTGTGTGGTAAGGCATTGGTGATTGAGAAATACACTATAGCTCACACCTAGTC
1 TACAAAAGCCCACTATGTGGCAAGGCATTGGTGATTGAGAAACCCACTATAGCTCACACCTAGTC
*
30654 TTCCTTGTATGATGTATTGTTCACCATCATCAAGACATGGCAAGGCATCACGCCGCCGGTGATTG
66 TTCCTTGTATGATGTATTGTTCACCATCATCAAGGCATGGCAAGGCATCACGCCGCCGGTGATTG
30719 AGACAACCTATAGTTCTCACCGTGTCTCTATT
131 AGACAACCTATAGTTCTCACCGTGTCTCTATT
*
30751 TACAAAAGCCCATTATGTGGCAAGGCATTGGTGATTGAGAAACCCACTATAGCTCACACCTAGTC
1 TACAAAAGCCCACTATGTGGCAAGGCATTGGTGATTGAGAAACCCACTATAGCTCACACCTAGTC
* * *
30816 TTCCTTGTATGATGTATTGTTCACCATCATCAAGGAATGGCAAGGCATCACGCCGTCAGTGATTG
66 TTCCTTGTATGATGTATTGTTCACCATCATCAAGGCATGGCAAGGCATCACGCCGCCGGTGATTG
*
30881 AGACAACCTATAGTTCTCACTGTGTCTCTATT
131 AGACAACCTATAGTTCTCACCGTGTCTCTATT
* *
30913 TACAAAAGCCCACTATGTGGTAAGGCATTGGTGATTGAGAAACCCACTATAGCCCACACCTAGTC
1 TACAAAAGCCCACTATGTGGCAAGGCATTGGTGATTGAGAAACCCACTATAGCTCACACCTAGTC
* **
30978 TTCCTTGTATGATGTATTGTTCACCATCATTAAGGCATGGCAAGGCATCATACCGCCGGTGATTG
66 TTCCTTGTATGATGTATTGTTCACCATCATCAAGGCATGGCAAGGCATCACGCCGCCGGTGATTG
* *
31043 AGACAACCTATAGTTCTCACCTTGTCTTTATT
131 AGACAACCTATAGTTCTCACCGTGTCTCTATT
31075 ATTATGATAC
Statistics
Matches: 1196, Mismatches: 100, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
162 1196 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (162 bp):
TACAAAAGCCCACTATGTGGCAAGGCATTGGTGATTGAGAAACCCACTATAGCTCACACCTAGTC
TTCCTTGTATGATGTATTGTTCACCATCATCAAGGCATGGCAAGGCATCACGCCGCCGGTGATTG
AGACAACCTATAGTTCTCACCGTGTCTCTATT
Found at i:31814 original size:20 final size:21
Alignment explanation
Indices: 31789--31831 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
31779 TGAAGGGAAT
31789 CTTGT-CATAAGCATTAAATG
1 CTTGTCCATAAGCATTAAATG
* *
31809 CTTGTCCTTGAGCATTAAATG
1 CTTGTCCATAAGCATTAAATG
31830 CT
1 CT
31832 GATGGAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (21 bp):
CTTGTCCATAAGCATTAAATG
Found at i:33282 original size:9 final size:9
Alignment explanation
Indices: 33270--33294 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
33260 GGGGGGGGGG
33270 GGCATCAGC
1 GGCATCAGC
33279 GGCATCAGC
1 GGCATCAGC
33288 GGCATCA
1 GGCATCA
33295 CCTTTGCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.32, G:0.32, T:0.12
Consensus pattern (9 bp):
GGCATCAGC
Found at i:34977 original size:124 final size:123
Alignment explanation
Indices: 34801--35143 Score: 512
Period size: 124 Copynumber: 2.8 Consensus size: 123
34791 GGACTGCCTT
* * * *
34801 GCTGACGTGTCACTCTGGCGAGGAGGAGGTTCCGCCGCTGGAAAGTTTTGCTGGGCACTTTCACC
1 GCTGACGTGTCACTCTGCCGAGGAAGAGGTTCCGCCGCTGAAAAGTGTTGCTGGGCACTTTCACC
34866 AAAGTGTTATCCTTCATCAACAAAGGAGGTCAGCAGCATGGCTAACCTGGTGCAACCTC
66 AAAGT-TTATCCTTCATCAACAAAGGAGGTCAGCAGCATGGCTAACCTGGTGCAACCTC
* * * *
34925 GCTGACGTGTCACTCTGCCGAGGAAGAGGTTACGCCGTTGAAAAGGGCTGCTGGGCACTTTCACC
1 GCTGACGTGTCACTCTGCCGAGGAAGAGGTTCCGCCGCTGAAAAGTGTTGCTGGGCACTTTCACC
* * *
34990 AAAGTCTTATCCTTCATCAACAAAGGAGGTCAACAGCATGGCTAACCTGGTGCCATCTC
66 AAAGT-TTATCCTTCATCAACAAAGGAGGTCAGCAGCATGGCTAACCTGGTGCAACCTC
*
35049 GCTGACGTGTCACTCTGCCGAGGAAGAGGTTCCGCCGCTGAAAAGTGTTGCTAGGCACTTTC-CC
1 GCTGACGTGTCACTCTGCCGAGGAAGAGGTTCCGCCGCTGAAAAGTGTTGCTGGGCACTTTCACC
* *
35113 AAAAGTCT-T-CTTCATCAACAAAGGCGGTCAG
66 -AAAGTTTATCCTTCATCAACAAAGGAGGTCAG
35144 TAGCTATGTT
Statistics
Matches: 198, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
121 20 0.10
122 1 0.01
123 3 0.02
124 174 0.88
ACGTcount: A:0.24, C:0.26, G:0.27, T:0.23
Consensus pattern (123 bp):
GCTGACGTGTCACTCTGCCGAGGAAGAGGTTCCGCCGCTGAAAAGTGTTGCTGGGCACTTTCACC
AAAGTTTATCCTTCATCAACAAAGGAGGTCAGCAGCATGGCTAACCTGGTGCAACCTC
Found at i:38306 original size:36 final size:36
Alignment explanation
Indices: 38264--38344 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 36
38254 ACAAGACATG
* * * *
38264 TTCTCAACATAGGCATGACTGCTAGCAGAAGATGTT
1 TTCTCAACACAGGCATGACTGCCAACAGAAGAAGTT
* *
38300 TTCTCAACGCATGCATGACTGCCAACAGAAGAAGTT
1 TTCTCAACACAGGCATGACTGCCAACAGAAGAAGTT
38336 TTCTCAACA
1 TTCTCAACA
38345 GAAGGCGTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (36 bp):
TTCTCAACACAGGCATGACTGCCAACAGAAGAAGTT
Found at i:39965 original size:29 final size:29
Alignment explanation
Indices: 39930--40002 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
39920 ATGTTGTCTT
39930 TCTCAGCAGCAACAACTACAACATGTTGC
1 TCTCAGCAGCAACAACTACAACATGTTGC
*
39959 TCTCAGCA-AAATCAACTACAACATGTTGC
1 TCTCAGCAGCAA-CAACTACAACATGTTGC
* *
39988 ACTCGGCAGCAACAA
1 TCTCAGCAGCAACAA
40003 TGTCCTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 2 0.05
29 34 0.89
30 2 0.05
ACGTcount: A:0.37, C:0.30, G:0.14, T:0.19
Consensus pattern (29 bp):
TCTCAGCAGCAACAACTACAACATGTTGC
Found at i:40119 original size:42 final size:42
Alignment explanation
Indices: 40060--40213 Score: 155
Period size: 42 Copynumber: 3.7 Consensus size: 42
40050 AACAATATGG
* *
40060 TCAACAACGATCTTTCTACAAACGTTGGTTGTTGTTGCATCC
1 TCAACAACGATCTTTCTACAAACATTGGTTGATGTTGCATCC
* * ** * * * *
40102 TCAACAACGATTTTTCTACAAGCATCAGCTGCTGTTTCATTC
1 TCAACAACGATCTTTCTACAAACATTGGTTGATGTTGCATCC
* * * *
40144 TCAGCAATGATCTTTCTACAAGCATTGGTTGATGTTGTATCC
1 TCAACAACGATCTTTCTACAAACATTGGTTGATGTTGCATCC
* * *
40186 TCAGCAACGATCTTTCTATAAACGTTGG
1 TCAACAACGATCTTTCTACAAACATTGG
40214 CTGGTGCTAC
Statistics
Matches: 89, Mismatches: 23, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 89 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (42 bp):
TCAACAACGATCTTTCTACAAACATTGGTTGATGTTGCATCC
Found at i:44648 original size:15 final size:15
Alignment explanation
Indices: 44630--44658 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
44620 GTTTCTAGTA
44630 TAATTGTTTTCTTTT
1 TAATTGTTTTCTTTT
44645 TAATTGTTTTCTTT
1 TAATTGTTTTCTTT
44659 CAACCTCTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
TAATTGTTTTCTTTT
Found at i:51397 original size:16 final size:15
Alignment explanation
Indices: 51363--51412 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
51353 AGCCAGATCG
51363 CAAAAAA-AA-AAAA
1 CAAAAAACAACAAAA
51376 -AAAAAACAACAACAA
1 CAAAAAACAACAA-AA
*
51391 CAAAAAACGACAAAA
1 CAAAAAACAACAAAA
51406 CAAAAAA
1 CAAAAAA
51413 GAGTGGAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 6 0.19
13 2 0.06
14 2 0.06
15 11 0.34
16 11 0.34
ACGTcount: A:0.82, C:0.16, G:0.02, T:0.00
Consensus pattern (15 bp):
CAAAAAACAACAAAA
Found at i:51891 original size:12 final size:12
Alignment explanation
Indices: 51874--51915 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
51864 ACTACACTTA
51874 AAAAAACCAAAC
1 AAAAAACCAAAC
*
51886 AAAAAAACAAAC
1 AAAAAACCAAAC
51898 AAAAAA-CAAAC
1 AAAAAACCAAAC
51909 AAAAAAC
1 AAAAAAC
51916 ACTTGGCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 11 0.39
12 17 0.61
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAACCAAAC
Found at i:51901 original size:11 final size:11
Alignment explanation
Indices: 51874--51916 Score: 68
Period size: 11 Copynumber: 3.7 Consensus size: 11
51864 ACTACACTTA
51874 AAAAAACCAAAC
1 AAAAAA-CAAAC
51886 AAAAAAACAAAC
1 -AAAAAACAAAC
51898 AAAAAACAAAC
1 AAAAAACAAAC
51909 AAAAAACA
1 AAAAAACA
51917 CTTGGCTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 19 0.63
12 5 0.17
13 6 0.20
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAC
Found at i:54032 original size:67 final size:67
Alignment explanation
Indices: 53928--54068 Score: 264
Period size: 67 Copynumber: 2.1 Consensus size: 67
53918 AAATACACTA
* *
53928 GAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGAATACAT
1 GAAGACGGTTTGCTAGAAAGAATTTTCAAAAGCTGATTGGAAGACAATCTCATTAAGGAATACAT
53993 CG
66 CG
53995 GAAGACGGTTTGCTAGAAAGAATTTTCAAAAGCTGATTGGAAGACAATCTCATTAAGGAATACAT
1 GAAGACGGTTTGCTAGAAAGAATTTTCAAAAGCTGATTGGAAGACAATCTCATTAAGGAATACAT
54060 CG
66 CG
54062 GAAGACG
1 GAAGACG
54069 ATCTTGTCAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 72 1.00
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (67 bp):
GAAGACGGTTTGCTAGAAAGAATTTTCAAAAGCTGATTGGAAGACAATCTCATTAAGGAATACAT
CG
Found at i:54165 original size:64 final size:64
Alignment explanation
Indices: 54060--54201 Score: 266
Period size: 64 Copynumber: 2.2 Consensus size: 64
54050 AGGAATACAT
54060 CGGAAGACGATCTTGTCAAGCAGTACACCAGAAGATAGTTTCTCAACAATTTTCAGAAGATGAG
1 CGGAAGACGATCTTGTCAAGCAGTACACCAGAAGATAGTTTCTCAACAATTTTCAGAAGATGAG
* *
54124 CGGAAGACGATCTTGTCAAGCAGTACAGCAGAAGATGGTTTCTCAACAATTTTCAGAAGATGAG
1 CGGAAGACGATCTTGTCAAGCAGTACACCAGAAGATAGTTTCTCAACAATTTTCAGAAGATGAG
54188 CGGAAGACGATCTT
1 CGGAAGACGATCTT
54202 TTCTCAAGAG
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 76 1.00
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (64 bp):
CGGAAGACGATCTTGTCAAGCAGTACACCAGAAGATAGTTTCTCAACAATTTTCAGAAGATGAG
Found at i:54205 original size:39 final size:39
Alignment explanation
Indices: 54162--54240 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
54152 CAGAAGATGG
54162 TTTCTCAACAATTTTCAGAAGATGAGCGGAAGACGATCT
1 TTTCTCAACAATTTTCAGAAGATGAGCGGAAGACGATCT
* * * * *
54201 TTTCTCAAGAGTTTTCCGAAGTTGATCGGAAGACGATCT
1 TTTCTCAACAATTTTCAGAAGATGAGCGGAAGACGATCT
54240 T
1 T
54241 GTCAAGAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.32
Consensus pattern (39 bp):
TTTCTCAACAATTTTCAGAAGATGAGCGGAAGACGATCT
Found at i:54345 original size:168 final size:167
Alignment explanation
Indices: 54058--54369 Score: 441
Period size: 168 Copynumber: 1.9 Consensus size: 167
54048 TAAGGAATAC
* * * *
54058 ATCGGAAGACGATCTTGTCAAGCAGTACACCAGAAGATAGTTTCTCAACAATTTTCAGAAGATGA
1 ATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATAGTTTCTAAAAAATTTTCAGAAGATCA
* *
54123 GCGGAAGACGATCTTGTCAAGCAGTACAGCAGAAGATGGTTTCTCAACAATTTTCAGAAGATGAG
66 GCGGAAGACGATCTTGTCAAGAAGTACAGCAGAAGATGGTTTCTCAAAAATTTTCAGAAGATGAG
54188 CGGAAGACGATCTTTTCTCAAGAGTTTTCCGAAGTTG
131 CGGAAGACGATCTTTTCTCAAGAGTTTTCCGAAGTTG
* * *
54225 ATCGGAAGACGATCTTGTCAAGAAGTACGCTAGAAGATGGTTTCTAAAAAAAATTTT-AGAA-AT
1 ATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATAGTTTCT--AAAAAATTTTCAGAAGAT
* * * *
54288 ACATCGGAAGACGATCTTGTCAAGAAGTAC-GCCATAAGATGGTTTTTCAAAAATTTTCAGAAGT
64 -CAGCGGAAGACGATCTTGTCAAGAAGTACAG-CAGAAGATGGTTTCTCAAAAATTTTCAGAAGA
*
54352 TGATCGGAAGACGATCTT
127 TGAGCGGAAGACGATCTT
54370 GTTAAAAAGT
Statistics
Matches: 127, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
167 44 0.35
168 75 0.59
169 8 0.06
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (167 bp):
ATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATAGTTTCTAAAAAATTTTCAGAAGATCA
GCGGAAGACGATCTTGTCAAGAAGTACAGCAGAAGATGGTTTCTCAAAAATTTTCAGAAGATGAG
CGGAAGACGATCTTTTCTCAAGAGTTTTCCGAAGTTG
Found at i:54380 original size:64 final size:64
Alignment explanation
Indices: 54212--54441 Score: 282
Period size: 65 Copynumber: 3.6 Consensus size: 64
54202 TTCTCAAGAG
* * *
54212 TTTTCCGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACGCTAGAAGATGGTTTCTAAAAAAA
1 TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACGCCAGAAGATGGTTT-T-TAAAAA
54277 A
64 A
* ** * *
54278 TTTT-AGAAATACATCGGAAGACGATCTTGTCAAGAAGTACGCCATAAGATGGTTTTTCAAAAA
1 TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACGCCAGAAGATGGTTTTTAAAAAA
* * * * *
54341 TTTTCAGAAGTTGATCGGAAGACGATCTTGTTAAAAAGTACACCAGAAGATAGTTTTTTGAAAAA
1 TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACGCCAGAAGAT-GGTTTTTAAAAAA
* * *
54406 GTTTCAGAAGTTGATCAGAAGACGATCTTGTTAAGA
1 TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGA
54442 GATGCACCGG
Statistics
Matches: 142, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
63 9 0.06
64 40 0.28
65 89 0.63
66 4 0.03
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (64 bp):
TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACGCCAGAAGATGGTTTTTAAAAAA
Found at i:54740 original size:50 final size:50
Alignment explanation
Indices: 54686--54884 Score: 229
Period size: 50 Copynumber: 3.9 Consensus size: 50
54676 TTGAAACACG
*
54686 AGCGGAAGACGATCCTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATA
1 AGCGGAAGACGATCCTTTTAAGATTGAATTGGAAGACAATTCAAAGGATA
* *
54736 AGCGGAAGACAATCCTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATA
1 AGCGGAAGACGATCCTTTTAAGATTGAATTGGAAGACAATTCAAAGGATA
* * * * * *
54786 AGCAGAATACGGTCCTTTTAATATTGGATTGGAAGACAATTCAAAGAAGTTGA
1 AGCGGAAGACGATCCTTTTAAGATTGAATTGGAAGACAATTCAAAG--GAT-A
** ***
54839 TTCGGAAGACGATTCC-CCGAAGATTGAATTGGAAGACAATTCAAAG
1 AGCGGAAGACGA-TCCTTTTAAGATTGAATTGGAAGACAATTCAAAG
54885 AAGATTGATC
Statistics
Matches: 126, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
50 88 0.70
52 2 0.02
53 33 0.26
54 3 0.02
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (50 bp):
AGCGGAAGACGATCCTTTTAAGATTGAATTGGAAGACAATTCAAAGGATA
Found at i:54873 original size:27 final size:26
Alignment explanation
Indices: 54812--54893 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 26
54802 TTTAATATTG
54812 GATTGGAAGACAATTCAAAGAAG-TT
1 GATTGGAAGACAATTCAAAGAAGATT
* ***
54837 GATTCGGAAGACGATTCCCCGAAGATT
1 GATT-GGAAGACAATTCAAAGAAGATT
54864 GAATTGGAAGACAATTCAAAGAAGATT
1 G-ATTGGAAGACAATTCAAAGAAGATT
54891 GAT
1 GAT
54894 CGGGAGACGA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
25 4 0.09
26 17 0.37
27 22 0.48
28 3 0.07
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.23
Consensus pattern (26 bp):
GATTGGAAGACAATTCAAAGAAGATT
Found at i:57035 original size:124 final size:124
Alignment explanation
Indices: 56855--57198 Score: 508
Period size: 124 Copynumber: 2.8 Consensus size: 124
56845 TTGTGGGACT
* * * * * * *
56855 ACCTTGCTGACGTGTCACTCTGGCGAGGAGGAGGTTCCGCCGCTGGAAAGTTCTGCTGGGCACTT
1 ACCTCGCTGACGTGTCACTCTGCCGAGGAAGAGGTTCCGCCACTGAAAAGTGCTGCTAGGCACTT
* * *
56920 TCACCAAAGTCTTATCCTTCATCAACAAAGGAGGTCAGCATCTTGGCAAACCTGGTGCA
66 TCACCAAAGTCTTATCCTTCATCAACAAAGGAGGTCAACAGCATGGCAAACCTGGTGCA
* * *
56979 ACCTCGCTGACGTGTCACTCTGCCGAGGAAGACGTTCCGCCACTAAAAAGGGCTGCTAGGCACTT
1 ACCTCGCTGACGTGTCACTCTGCCGAGGAAGAGGTTCCGCCACTGAAAAGTGCTGCTAGGCACTT
* * *
57044 TCACCAAAGTCTTATCCTTTATCAACAAAGGAGGTCAACAGCATGGCTAACCTGGTTCA
66 TCACCAAAGTCTTATCCTTCATCAACAAAGGAGGTCAACAGCATGGCAAACCTGGTGCA
* *
57103 ACCTCGCTGACGTGTCACTCTGCCGAGGAAGAGGTTCCACCACTGAAAAGTGTTGCTAGGCACTT
1 ACCTCGCTGACGTGTCACTCTGCCGAGGAAGAGGTTCCGCCACTGAAAAGTGCTGCTAGGCACTT
* *
57168 GCACCAAAGTTTTATCCTTCATCAACAAAGG
66 TCACCAAAGTCTTATCCTTCATCAACAAAGG
57199 CGATCAGTAG
Statistics
Matches: 196, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
124 196 1.00
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.24
Consensus pattern (124 bp):
ACCTCGCTGACGTGTCACTCTGCCGAGGAAGAGGTTCCGCCACTGAAAAGTGCTGCTAGGCACTT
TCACCAAAGTCTTATCCTTCATCAACAAAGGAGGTCAACAGCATGGCAAACCTGGTGCA
Found at i:57501 original size:18 final size:18
Alignment explanation
Indices: 57480--57514 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
57470 AAGGTGATTT
57480 GGTGCCACAACATCATTA
1 GGTGCCACAACATCATTA
* *
57498 GGTGCCATATCATCATT
1 GGTGCCACAACATCATT
57515 GCTGACTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (18 bp):
GGTGCCACAACATCATTA
Found at i:61407 original size:94 final size:95
Alignment explanation
Indices: 61238--61426 Score: 362
Period size: 94 Copynumber: 2.0 Consensus size: 95
61228 GTGTGGTCAT
61238 CATAAGTGTGATAGATAGCATAAAATGCATGATAAAAAAAAAACAAAAACAAACAACTAATTCAT
1 CATAAGTGTGATAGATAGCATAAAATGCATGAT-AAAAAAAAACAAAAACAAACAACTAATTCAT
61303 ATCAAGGAAGCAATAGAAGCAATATTCAATG
65 ATCAAGGAAGCAATAGAAGCAATATTCAATG
61334 CATAAGTGTGATAGATAGCATAAAATGCATGAT-AAAAAAAACAAAAACAAACAACTAATTCATA
1 CATAAGTGTGATAGATAGCATAAAATGCATGATAAAAAAAAACAAAAACAAACAACTAATTCATA
61398 TCAAGGAAGCAATAGAAGCAATATTCAAT
66 TCAAGGAAGCAATAGAAGCAATATTCAAT
61427 CAAAGCAAAG
Statistics
Matches: 93, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
94 60 0.65
96 33 0.35
ACGTcount: A:0.54, C:0.13, G:0.13, T:0.20
Consensus pattern (95 bp):
CATAAGTGTGATAGATAGCATAAAATGCATGATAAAAAAAAACAAAAACAAACAACTAATTCATA
TCAAGGAAGCAATAGAAGCAATATTCAATG
Found at i:62146 original size:18 final size:19
Alignment explanation
Indices: 62109--62147 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
62099 CTCAACTTCT
62109 CTTAGCCCAAATCACAAACA
1 CTTAGCCCAAAT-ACAAACA
*
62129 CTTAGCCTAAAT-CAAACA
1 CTTAGCCCAAATACAAACA
62147 C
1 C
62148 AAAATACCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.44, C:0.33, G:0.05, T:0.18
Consensus pattern (19 bp):
CTTAGCCCAAATACAAACA
Found at i:62262 original size:17 final size:19
Alignment explanation
Indices: 62236--62276 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
62226 TCCTAAAGGG
*
62236 CATTATTTCA-TCAAAGCC
1 CATTATTTCATTAAAAGCC
62254 CATTA-TTCATTAAAAGCC
1 CATTATTTCATTAAAAGCC
62272 CATTA
1 CATTA
62277 CTCACAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (19 bp):
CATTATTTCATTAAAAGCC
Found at i:62779 original size:25 final size:27
Alignment explanation
Indices: 62745--62803 Score: 95
Period size: 25 Copynumber: 2.3 Consensus size: 27
62735 CCCCATGGTT
*
62745 CAATACAAAGCCCAC-A-CCTACGTGG
1 CAATACAAAGCCCACTATCATACGTGG
62770 CAATACAAAGCCCACTATCATACGTGG
1 CAATACAAAGCCCACTATCATACGTGG
62797 CAATACA
1 CAATACA
62804 TTGGTGATCG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 15 0.48
26 1 0.03
27 15 0.48
ACGTcount: A:0.39, C:0.32, G:0.14, T:0.15
Consensus pattern (27 bp):
CAATACAAAGCCCACTATCATACGTGG
Found at i:63243 original size:20 final size:21
Alignment explanation
Indices: 63204--63246 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
63194 TTTCCCTTAA
*
63204 TTCCATTATCTATTCATCTAT
1 TTCCATTATCTATCCATCTAT
*
63225 TTCCATTATTTA-CCATCTAT
1 TTCCATTATCTATCCATCTAT
63245 TT
1 TT
63247 ATTGAAGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.53
Consensus pattern (21 bp):
TTCCATTATCTATCCATCTAT
Found at i:73690 original size:41 final size:41
Alignment explanation
Indices: 73633--73718 Score: 118
Period size: 41 Copynumber: 2.1 Consensus size: 41
73623 TCTTTTTGTT
* * * *
73633 GATATATCCAAGCTGTAAAGTGTAATTATGGCTAAGCATTG
1 GATATATCCAAACTGTAAAGTATAATTATGGCTAAACAATG
* *
73674 GATATTTCCAAACTGTAAATTATAATTATGGCTAAACAATG
1 GATATATCCAAACTGTAAAGTATAATTATGGCTAAACAATG
73715 GATA
1 GATA
73719 ATTCTTAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (41 bp):
GATATATCCAAACTGTAAAGTATAATTATGGCTAAACAATG
Found at i:74437 original size:94 final size:96
Alignment explanation
Indices: 74312--74582 Score: 386
Period size: 94 Copynumber: 2.8 Consensus size: 96
74302 AATTAACTAG
** * *
74312 TAAAGAAATAATTA-AAGTTTTTTATTAGATTATATTTGAAATAATAGAAAAGAATTGTGCGGTG
1 TAAAGAAATAAAAAGAACTTTTTTATTCGATTATATTTGAAATAATAGAAAAGAATTGTGCGGTG
* *
74376 CGGGTTTTAGAGTTC-AATGTCAGTTTTTAA
66 CGGGTTTTAGAGTTCAAACGTCAGTTTTCAA
74406 TAAAGAAATAAAAAGAAC-TTTTTATTCGATTATATTTGAAATAATAGAAAAGAATTGTGCGGTG
1 TAAAGAAATAAAAAGAACTTTTTTATTCGATTATATTTGAAATAATAGAAAAGAATTGTGCGGTG
74470 CGGGTTTTAGAGTTCAAACGTCAGTTTTCAA
66 CGGGTTTTAGAGTTCAAACGTCAGTTTTCAA
* *
74501 TAAAGAAATAATATGAACTTTTTTATTCGATTATATTTGAAATAAAATATGATTAATAGAATTGT
1 TAAAGAAATAAAAAGAACTTTTTTATTCGATTATATTTGAAAT--AATA-GA--AA-AGAATTGT
*
74566 GCGGTGCGAGTTTTAGA
60 GCGGTGCGGGTTTTAGA
74583 AATCATCGTT
Statistics
Matches: 159, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
94 72 0.45
95 31 0.19
96 24 0.15
98 4 0.03
99 2 0.01
101 2 0.01
102 24 0.15
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.37
Consensus pattern (96 bp):
TAAAGAAATAAAAAGAACTTTTTTATTCGATTATATTTGAAATAATAGAAAAGAATTGTGCGGTG
CGGGTTTTAGAGTTCAAACGTCAGTTTTCAA
Found at i:76469 original size:2 final size:2
Alignment explanation
Indices: 76462--76493 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
76452 TATAAAGTAA
76462 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
76494 TACCAAAAGA
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:79281 original size:443 final size:437
Alignment explanation
Indices: 78479--79428 Score: 1494
Period size: 443 Copynumber: 2.2 Consensus size: 437
78469 ATTTTTTTGT
78479 TTATTTATCAAATGAT-TCATATACTTTTATACTTTATGCTATTTAGTCCCTCACAATTTATGGG
1 TTATTTATCAAATGATCTCA-A-ACTTTTATACTTTATGCTATTTAGTCCCTCACAATTTATGGG
* *
78543 TTGGACGACTGAAGTTTCGGCTTTAATTTTTTTATTTTTTGTTTTGCTTGTCCGGTCAAGGTGAT
64 TTGGACGACTGAAGTTTCGGCTTTAATTTTTTTATTTTTTCTTTTGCTTGTCCGATCAAGGTGAT
* *
78608 TCAAGTGTCTATTAAAACGTAATTTCGTGATCTACAACTTCCATAAAGGACTCAAAACCAATTTT
129 TCAAGTGTCTATTAAAACGTAATTTCATGATCTACAACTTCCATAAAGGACTCAAAACCAAATTT
* * *
78673 AATGTTTTGATTTTGAAAAATGCTTTTGAAATTTTGTGGTCTTGATTGTCGGTCTATTTGATATC
194 AATGTTTTGATTTTAAAAAATGCTTTTGAAATTTTGTGGTCTTGATTGCCAGTCTATTTGATATC
*
78738 GTATAATTTTTGTTCCACTTGTTCGATTGAGGTTATTCAAGTGTCGGTTAAAAGGTTATTGTGTG
259 GTATAATTTTTGTTCCACTTGTCCGATTGAGGTTATTCAAGTGTCGGTTAAAAGGTTATTGTGTG
* * * * *
78803 ATCTATGGCTTTCGTTAAGGGCTTCAAAGCTGAATTTGATTAATGAGTTTCGTGGAGGGTTCAAG
324 ATCTACGGATTTCGTTAAGGGCCTCAAAACTGAATTTGATTAATGAGTTTCGTAGAGGGTTCAAG
* * * *
78868 AGGGAATTTTTATATTTGGTCTCCATAAATAAATATTTTTTTTGCTGGA
389 AGAGAATTTCTATATTTGGTCTCCATAAACAAACATTTTTTTTGCTGGA
* * * *
78917 TTATTTATCAAATAATCCTCAAACTTTTATGCTTTATGCTATTTAGTCCCTAACAATTTCTGGGT
1 TTATTTATCAAATGAT-CTCAAACTTTTATACTTTATGCTATTTAGTCCCTCACAATTTATGGGT
*
78982 TGGACGACTGAACGTTTCGGCTTTAATTCTTTTATTTTTTTTTCTTTTGCTTGTCCGATCAAGGT
65 TGGACGACTGAA-GTTTCGGCTTTAA-T-TTTT-TTATTTTTTCTTTTGCTTGTCCGATCAAGGT
* * *
79047 GATTTAAGTGTCTATTAAAAGGTAACTTT-ATGATCTACAACTTCCATGAAGGACTCAAAAGCCA
126 GATTCAAGTGTCTATTAAAACGTAA-TTTCATGATCTACAACTTCCATAAAGGACTCAAAA-CCA
79111 AATTTAATGTTTTGATTTTAAAAAATGCTTTTGAAATTTTGTGGTCTTGATTGCCAGTCTATTTG
189 AATTTAATGTTTTGATTTTAAAAAATGCTTTTGAAATTTTGTGGTCTTGATTGCCAGTCTATTTG
79176 ATATCGTATAATTTTT-TGTCCACTTGTCCGATTGAGGTTATTCAAGTGTCGGTTAAAAGGTTAT
254 ATATCGTATAATTTTTGT-TCCACTTGTCCGATTGAGGTTATTCAAGTGTCGGTTAAAAGGTTAT
79240 TGTGTGATCTACGGATTTCGTTAAGGGCCTCAAAACTGAATTTGATTAATGAGTTTCGTAGAGGG
318 TGTGTGATCTACGGATTTCGTTAAGGGCCTCAAAACTGAATTTGATTAATGAGTTTCGTAGAGGG
*
79305 TTCAAGAGAGAATTTCTATGTTTGGTCTCCATAAACAAACATTTTTTTTGCTGGA
383 TTCAAGAGAGAATTTCTATATTTGGTCTCCATAAACAAACATTTTTTTTGCTGGA
* * * * *
79360 TTATTTATCAAATGATTCTCAGATTTTTATATTTTATGCTATTTAATCCCTCATAA-TTATGGGT
1 TTATTTATCAAATGA-TCTCAAACTTTTATACTTTATGCTATTTAGTCCCTCACAATTTATGGGT
79424 TGGAC
65 TGGAC
79429 CATTTAATTC
Statistics
Matches: 467, Mismatches: 35, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
438 67 0.14
439 14 0.03
440 4 0.01
441 4 0.01
442 93 0.20
443 284 0.61
444 1 0.00
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (437 bp):
TTATTTATCAAATGATCTCAAACTTTTATACTTTATGCTATTTAGTCCCTCACAATTTATGGGTT
GGACGACTGAAGTTTCGGCTTTAATTTTTTTATTTTTTCTTTTGCTTGTCCGATCAAGGTGATTC
AAGTGTCTATTAAAACGTAATTTCATGATCTACAACTTCCATAAAGGACTCAAAACCAAATTTAA
TGTTTTGATTTTAAAAAATGCTTTTGAAATTTTGTGGTCTTGATTGCCAGTCTATTTGATATCGT
ATAATTTTTGTTCCACTTGTCCGATTGAGGTTATTCAAGTGTCGGTTAAAAGGTTATTGTGTGAT
CTACGGATTTCGTTAAGGGCCTCAAAACTGAATTTGATTAATGAGTTTCGTAGAGGGTTCAAGAG
AGAATTTCTATATTTGGTCTCCATAAACAAACATTTTTTTTGCTGGA
Found at i:80551 original size:31 final size:31
Alignment explanation
Indices: 80511--80571 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
80501 GCGTACACGG
80511 TACACGCCATTCCACCAATATCAACTTCATT
1 TACACGCCATTCCACCAATATCAACTTCATT
* ** *
80542 TACATGCCATTCCGTCAATGTCAACTTCAT
1 TACACGCCATTCCACCAATATCAACTTCAT
80572 GTTTTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.30, C:0.33, G:0.07, T:0.31
Consensus pattern (31 bp):
TACACGCCATTCCACCAATATCAACTTCATT
Found at i:82202 original size:2 final size:2
Alignment explanation
Indices: 82195--82239 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
82185 CTTGATTTTC
* *
82195 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TT TA -A T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
82235 TA TA T
1 TA TA T
82240 TCTGGCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:88488 original size:33 final size:33
Alignment explanation
Indices: 88446--88510 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
88436 TACCTGCGCA
88446 CACCAAATTTTCTCACCACTAAACAACAATTAC
1 CACCAAATTTTCTCACCACTAAACAACAATTAC
* *
88479 CACCAAATTTTCTCTCTACTAAACAACAATTA
1 CACCAAATTTTCTCACCACTAAACAACAATTA
88511 AAATAAAACC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.28
Consensus pattern (33 bp):
CACCAAATTTTCTCACCACTAAACAACAATTAC
Found at i:90319 original size:22 final size:21
Alignment explanation
Indices: 90251--90398 Score: 86
Period size: 22 Copynumber: 6.8 Consensus size: 21
90241 TGAATATTTT
* *
90251 TATGAAATCTTGATAAGTACCC
1 TATGAAATTTTGATAACTA-CC
* * *
90273 TATTAAATTTTGACAACCACGC
1 TATGAAATTTTGATAACTAC-C
*
90295 TATGAAATTTTGATAATTTACC
1 TATGAAATTTTGATAA-CTACC
* *
90317 TATAAAATTATGATAAACT-CC
1 TATGAAATTTTGAT-AACTACC
* * *
90338 ATATTAAACTTTGATAACCT-TC
1 -TATGAAATTTTGATAA-CTACC
* *
90360 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTGAT-AA-CTACC
90383 TATGAAATTTTG-TAAC
1 TATGAAATTTTGATAAC
90399 CTTCATATGA
Statistics
Matches: 98, Mismatches: 21, Indels: 16
0.73 0.16 0.12
Matches are distributed among these distances:
20 1 0.01
21 18 0.18
22 63 0.64
23 16 0.16
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGATAACTACC
Found at i:90376 original size:43 final size:42
Alignment explanation
Indices: 90329--90425 Score: 99
Period size: 43 Copynumber: 2.3 Consensus size: 42
90319 TAAAATTATG
*
90329 ATAAACTCCATATTAAACTTTGATAACCTTC-TATGAAATTTTA
1 ATAAACTCCATATGAAACTTTG-TAACCTTCATATG-AATTTTA
* * *
90372 ATAAACCTTCC-TATGAAATTTTGTAACCTTCATATGATTTTTG
1 ATAAA-C-TCCATATGAAACTTTGTAACCTTCATATGAATTTTA
*
90415 ATAACCTCCAT
1 ATAAACTCCAT
90426 TAAGATTTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
41 3 0.07
42 2 0.04
43 22 0.49
44 15 0.33
45 3 0.07
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.40
Consensus pattern (42 bp):
ATAAACTCCATATGAAACTTTGTAACCTTCATATGAATTTTA
Found at i:90401 original size:21 final size:22
Alignment explanation
Indices: 90271--90421 Score: 116
Period size: 22 Copynumber: 7.0 Consensus size: 22
90261 TGATAAGTAC
* * *
90271 CCTATTAAATTTTGACAACC-A
1 CCTATGAAATTTTGATAACCTT
*
90292 CGCTATGAAATTTTGATAA-TTT
1 C-CTATGAAATTTTGATAACCTT
* * *
90314 ACCTATAAAATTATGATAAAC-T
1 -CCTATGAAATTTTGATAACCTT
* *
90336 CCATATTAAACTTTGATAACCTT
1 CC-TATGAAATTTTGATAACCTT
*
90359 -CTATGAAATTTTAATAAACCTT
1 CCTATGAAATTTTGAT-AACCTT
90381 CCTATGAAATTTTG-TAACCTT
1 CCTATGAAATTTTGATAACCTT
* *
90402 CATATG-ATTTTTGATAACCT
1 CCTATGAAATTTTGATAACCT
90422 CCATTAAGAT
Statistics
Matches: 104, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
20 6 0.06
21 31 0.30
22 53 0.51
23 14 0.13
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40
Consensus pattern (22 bp):
CCTATGAAATTTTGATAACCTT
Found at i:90434 original size:21 final size:19
Alignment explanation
Indices: 90389--90436 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
90379 TTCCTATGAA
* *
90389 ATTTTGTAACCTTCATATG
1 ATTTTGTAACCTCCATAAG
90408 ATTTTTGATAACCTCCATTAAG
1 A-TTTTG-TAACCTCCA-TAAG
90430 ATTTTGT
1 ATTTTGT
90437 TAATCTCCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 6 0.25
21 13 0.54
22 4 0.17
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (19 bp):
ATTTTGTAACCTCCATAAG
Found at i:93432 original size:2 final size:2
Alignment explanation
Indices: 93427--93457 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
93417 ATATATATAT
*
93427 AG AG AG AG AG AG AG AG AG AT AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
93458 TAATGGGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.45, T:0.03
Consensus pattern (2 bp):
AG
Found at i:95545 original size:20 final size:21
Alignment explanation
Indices: 95513--95553 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
95503 AGACAAAATC
95513 AAGAAAACAAAATAAAAATAA
1 AAGAAAACAAAATAAAAATAA
95534 AAGAAAAC-AAATAAAAATAA
1 AAGAAAACAAAATAAAAATAA
95554 GAGTTGTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.80, C:0.05, G:0.05, T:0.10
Consensus pattern (21 bp):
AAGAAAACAAAATAAAAATAA
Found at i:101037 original size:2 final size:2
Alignment explanation
Indices: 101025--101166 Score: 58
Period size: 2 Copynumber: 76.5 Consensus size: 2
101015 CTGATTACTA
* * * *
101025 AT AT AT A- AT AT AT AT AT CT -T AA AT AT AT TT A- AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
101064 A- AT A- AA AT AT AT AT TT AT TT AT AT AT AT AT A- AT AA AA ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* *
101104 -T AT -T ACT A- AT AT AT A- AT AT AT AT AT TT A- AT AT TT AT A-
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
101141 AT A- AA AT AT AT AT TT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
101167 AGAAAAACTG
Statistics
Matches: 104, Mismatches: 21, Indels: 30
0.67 0.14 0.19
Matches are distributed among these distances:
1 13 0.12
2 89 0.86
3 2 0.02
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:101040 original size:33 final size:31
Alignment explanation
Indices: 100999--101127 Score: 87
Period size: 33 Copynumber: 4.3 Consensus size: 31
100989 ATTATCTTAT
100999 ATATATATAATAAAAACTGATTACTAATATATA
1 ATATATATAAT-AAAACT-ATTACTAATATATA
* * *
101032 ATATATAT-AT----CT-TAAAT-ATATTTA
1 ATATATATAATAAAACTATTACTAATATATA
* * * *
101056 ATATTTATAATAAAA-TATATATTTATTTAT-
1 ATATATATAATAAAACTAT-TACTAATATATA
101086 ATATATATAATAAAAACTTATTACTAATATATA
1 ATATATATAAT-AAAAC-TATTACTAATATATA
101119 ATATATATA
1 ATATATATA
101128 TTTAATATTT
Statistics
Matches: 72, Mismatches: 12, Indels: 24
0.67 0.11 0.22
Matches are distributed among these distances:
24 13 0.18
25 5 0.07
27 2 0.03
28 1 0.01
29 1 0.01
30 12 0.17
31 8 0.11
32 10 0.14
33 20 0.28
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (31 bp):
ATATATATAATAAAACTATTACTAATATATA
Found at i:101115 original size:26 final size:23
Alignment explanation
Indices: 101078--101173 Score: 79
Period size: 24 Copynumber: 4.0 Consensus size: 23
101068 AAATATATAT
101078 TTATTTATATATATATAATAAAAA
1 TTATTTA-ATATATATAATAAAAA
* * *
101102 CTTA-TTACTAATATATAATATATA
1 -TTATTTAAT-ATATATAATAAAAA
*
101126 -TATTTAATATTTATAATAAAATA
1 TTATTTAATATATATAATAAAA-A
*
101149 TATATTTATATATATATAAGAAAAA
1 T-TATTTA-ATATATATAATAAAAA
101174 CTGATTACTA
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
22 12 0.21
23 6 0.11
24 15 0.27
25 10 0.18
26 13 0.23
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (23 bp):
TTATTTAATATATATAATAAAAA
Found at i:101173 original size:72 final size:75
Alignment explanation
Indices: 101047--101199 Score: 258
Period size: 72 Copynumber: 2.1 Consensus size: 75
101037 TATATCTTAA
* *
101047 ATATATTTAATATTTATAATAAAATATATATTTATTTATATATATATAATAAAAACTTATTACTA
1 ATATATTTAATATTTATAATAAAATATATA-TTATTTATATATATATAAGAAAAACTGATTACTA
101112 ATATATAATAT
65 ATATATAATAT
101123 ATATATTTAATATTTATAAT-AAA-ATATA-TATTTATATATATATAAGAAAAACTGATTACTAA
1 ATATATTTAATATTTATAATAAAATATATATTATTTATATATATATAAGAAAAACTGATTACTAA
101185 TATATAATAT
66 TATATAATAT
101195 ATATA
1 ATATA
101200 ATATATATCT
Statistics
Matches: 75, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
72 47 0.63
74 5 0.07
75 3 0.04
76 20 0.27
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (75 bp):
ATATATTTAATATTTATAATAAAATATATATTATTTATATATATATAAGAAAAACTGATTACTAA
TATATAATAT
Found at i:101215 original size:22 final size:23
Alignment explanation
Indices: 101086--101243 Score: 84
Period size: 22 Copynumber: 7.0 Consensus size: 23
101076 ATTTATTTAT
101086 ATATATATAATAAAA-ACT-TATTA
1 ATATATATAATAAAATA-TATA-TA
* * *
101109 CTAATATATAAT-ATATATATTTA
1 AT-ATATATAATAAAATATATATA
*
101132 ATATTTATAATAAAATATATATTTA
1 ATATATATAATAAAATATATA--TA
*
101157 TATATATATAAGAAAA-ACTGAT-TA
1 -ATATATATAATAAAATA-T-ATATA
*
101181 CTA-ATAT-AT--AATATATATA
1 ATATATATAATAAAATATATATA
* * *
101200 ATATATAT-CTTAAATATATTTA
1 ATATATATAATAAAATATATATA
*
101222 ATATTTATAATAAAATATATAT
1 ATATATATAATAAAATATATAT
101244 TCGGGTTCTC
Statistics
Matches: 102, Mismatches: 18, Indels: 30
0.68 0.12 0.20
Matches are distributed among these distances:
18 2 0.02
19 7 0.07
20 6 0.06
21 1 0.01
22 28 0.27
23 26 0.25
24 13 0.13
25 3 0.03
26 14 0.14
27 2 0.02
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (23 bp):
ATATATATAATAAAATATATATA
Found at i:111077 original size:20 final size:20
Alignment explanation
Indices: 111054--111093 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
111044 GTTTATCATG
* *
111054 AATAAATTATATTTATATAT
1 AATAAATAATATATATATAT
*
111074 AATATATAATATATATATAT
1 AATAAATAATATATATATAT
111094 GAGTCCTACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATAAATAATATATATATAT
Found at i:113603 original size:13 final size:13
Alignment explanation
Indices: 113566--113610 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
113556 AAGCCAACAA
* *
113566 CAAACAACAAGGAC
1 CAAACAACAA-AAT
113580 CAAAGCAACAAAAT
1 CAAA-CAACAAAAT
113594 CAAACAACAAAAT
1 CAAACAACAAAAT
113607 CAAA
1 CAAA
113611 AAGAAATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 13 0.46
14 9 0.32
15 6 0.21
ACGTcount: A:0.64, C:0.24, G:0.07, T:0.04
Consensus pattern (13 bp):
CAAACAACAAAAT
Found at i:114213 original size:43 final size:43
Alignment explanation
Indices: 114152--114346 Score: 295
Period size: 43 Copynumber: 4.6 Consensus size: 43
114142 CCAATAACTA
* *
114152 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTCC
114195 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTCC
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTCC
*
114238 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATA-T-C
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTCC
* * *
114279 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCCATTCC
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTCC
* * *
114322 AAATTCCTTAAACACATATACAACA
1 AAAGTCCTCAAACACATATATAACA
114347 TAGAAACATT
Statistics
Matches: 139, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
41 36 0.26
42 2 0.01
43 101 0.73
ACGTcount: A:0.41, C:0.28, G:0.09, T:0.22
Consensus pattern (43 bp):
AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTCC
Found at i:114312 original size:84 final size:86
Alignment explanation
Indices: 114152--114346 Score: 295
Period size: 84 Copynumber: 2.3 Consensus size: 86
114142 CCAATAACTA
* * * *
114152 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATATTCCAAAGTCCCCAAACACATATATA
*
114217 ACACAGAGGCATCTCTATTCC
66 ACACAGAGGCATCTCCATTCC
114238 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATA-T-CAAAGTCCCCAAACACATATATA
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATATTCCAAAGTCCCCAAACACATATATA
*
114301 ACACAGGGGCATCTCCATTCC
66 ACACAGAGGCATCTCCATTCC
* * *
114322 AAATTCCTTAAACACATATACAACA
1 AAAGTCCTCAAACACATATATAACA
114347 TAGAAACATT
Statistics
Matches: 100, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
84 63 0.63
85 1 0.01
86 36 0.36
ACGTcount: A:0.41, C:0.28, G:0.09, T:0.22
Consensus pattern (86 bp):
AAAGTCCTCAAACACATATATAACACAGAGGCATCTATATTCCAAAGTCCCCAAACACATATATA
ACACAGAGGCATCTCCATTCC
Found at i:114440 original size:2 final size:2
Alignment explanation
Indices: 114435--114462 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
114425 TATATATCTC
114435 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
114463 ACAAGGGCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:118933 original size:47 final size:47
Alignment explanation
Indices: 118867--118972 Score: 178
Period size: 47 Copynumber: 2.3 Consensus size: 47
118857 TTGACTACTC
*
118867 TTTACT-TCTTAGTTTAATTACCTAGAATTAAAGTAATTTCTTCTTCT
1 TTTACTAT-TTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
118914 TTTACTATTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
1 TTTACTATTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
*
118961 TTTACCATTTAG
1 TTTACTATTTAG
118973 GTTATGTTTG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
47 55 0.98
48 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (47 bp):
TTTACTATTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
Found at i:119371 original size:47 final size:47
Alignment explanation
Indices: 119302--119953 Score: 903
Period size: 47 Copynumber: 13.6 Consensus size: 47
119292 AAACGCAACC
119302 TTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTAT
1 TTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTAT
*
119349 TTAGTTCAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTAT
1 TTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTAT
* *
119396 TTAGTTCAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTAT
*
119443 TTAGTTTAATTACATAGAATTAAACTAATTTCTTCTTCTTTTACTAT
1 TTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTAT
* * * * *
119490 TTAGTTTAATTACCCAGAATTAAACTAATCTCCTCCTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTAT
* * *
119537 TTAGCTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTAT
*
119584 TTAGTTTAATTACCTAGAATTAAATTAATTTCTTCTTCTTTTACTAT
1 TTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTAT
119631 TTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTAT
1 TTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTAT
*
119678 TTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACCAT
1 TTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTAT
* * **
119725 TTAGTTTAATTACCCATAATTAAACTAACATCTTCTTCTTTTACTAT
1 TTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTAT
119772 TTAGTTTAATTATCC-AGAATTAAACTAATCTCCGTTCACTTCTTCTTTTACTAT
1 TTAGTTTAATTA-CCTAGAATTAAACTAA--T---TT--CTTCTTCTTTTACTAT
* * * **
119826 TTAGTTCAATTACCCAAAATTAAACTAACCTCTTCTTCTTTTACTAT
1 TTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTAT
* * * *
119873 TCAGTTTAATTACCAAGAATTAAACTAATTACTGCTCACTTTTCTTTTACTCT
1 TTAGTTTAATTACCTAGAATTAAACTAATT--T-CT---TCTTCTTTTACTAT
*
119926 TTAGTTTAATTGCTCT-GAATTAAACTAA
1 TTAGTTTAATTAC-CTAGAATTAAACTAA
119954 CTATTACTCT
Statistics
Matches: 545, Mismatches: 44, Indels: 26
0.89 0.07 0.04
Matches are distributed among these distances:
47 461 0.85
48 2 0.00
49 2 0.00
50 2 0.00
52 1 0.00
53 37 0.07
54 40 0.07
ACGTcount: A:0.30, C:0.18, G:0.04, T:0.47
Consensus pattern (47 bp):
TTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTAT
Found at i:119961 original size:38 final size:38
Alignment explanation
Indices: 119919--119994 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
119909 CACTTTTCTT
119919 TTACTCTTTAGTTTAATTGCTCTGAATTAAACTAACTA
1 TTACTCTTTAGTTTAATTGCTCTGAATTAAACTAACTA
*
119957 TTACTCTTTAGTTTAATTGCTTTGAATTAAACTAACTA
1 TTACTCTTTAGTTTAATTGCTCTGAATTAAACTAACTA
119995 CTGACTTTAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (38 bp):
TTACTCTTTAGTTTAATTGCTCTGAATTAAACTAACTA
Found at i:125103 original size:30 final size:31
Alignment explanation
Indices: 125051--125108 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 31
125041 TCCTGCCGCA
* *
125051 AGTCAAGTACCATTATGCCGCAG-GAAAAGC
1 AGTCAAGCACCATCATGCCGCAGAGAAAAGC
* *
125081 AGTCAAGCACCATCCTGTCGCAGAGAAA
1 AGTCAAGCACCATCATGCCGCAGAGAAA
125109 GCATCCTGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (31 bp):
AGTCAAGCACCATCATGCCGCAGAGAAAAGC
Found at i:125745 original size:72 final size:71
Alignment explanation
Indices: 125662--125827 Score: 287
Period size: 72 Copynumber: 2.3 Consensus size: 71
125652 CCCCTTCTTC
*
125662 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTTGCACAATCCTTACATGATAAT
1 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA-ATGATAAT
125727 CTCCCAT
65 CTCCCAT
*
125734 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAATGATAATC
1 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAATGATAATC
*
125799 TTCCAT
66 TCCCAT
*
125805 ATTACGATTGTAGCCGAGGCAGT
1 ATTGCGATTGTAGCCGAGGCAGT
125828 CCTTCGTACA
Statistics
Matches: 89, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
71 35 0.39
72 54 0.61
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.30
Consensus pattern (71 bp):
ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAATGATAATC
TCCCAT
Found at i:125833 original size:55 final size:56
Alignment explanation
Indices: 125767--125883 Score: 173
Period size: 56 Copynumber: 2.1 Consensus size: 56
125757 TCCCACATTT
125767 GGCAGTCCTTCGCACAATCCTTA-ATGATAATCTTCCATATTACGATTGTAGCCGA
1 GGCAGTCCTTCGCACAATCCTTATATGATAATCTTCCATATTACGATTGTAGCCGA
* * * * * *
125822 GGCAGTCCTTCGTACAATCCTTATGTGATTATCTTCCTTATTGCGGTTGTAGCCGA
1 GGCAGTCCTTCGCACAATCCTTATATGATAATCTTCCATATTACGATTGTAGCCGA
125878 GGCAGT
1 GGCAGT
125884 TCCCACATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
55 22 0.40
56 33 0.60
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (56 bp):
GGCAGTCCTTCGCACAATCCTTATATGATAATCTTCCATATTACGATTGTAGCCGA
Found at i:125913 original size:72 final size:71
Alignment explanation
Indices: 125822--125986 Score: 285
Period size: 72 Copynumber: 2.3 Consensus size: 71
125812 TTGTAGCCGA
* * *
125822 GGCAGTCCTTCGTACAATCCTTATGTGATTATCTTCCTTATTGCGGTTGTAGCCGAGGCAGTTCC
1 GGCAGTCCTTCGCACAATCCTTATGTGATTATCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCC
125887 CACATTT
66 CACA-TT
*
125894 GGCAGTCCTTCGCACAATCCTTATGTGATTATTTTCCTCATTGCGATTGTAGCCGAGGCAGTTCC
1 GGCAGTCCTTCGCACAATCCTTATGTGATTATCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCC
125959 CACATT
66 CACATT
125965 GGCAGTCCTTCGCACAATCCTT
1 GGCAGTCCTTCGCACAATCCTT
125987 GCTACTAATC
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
71 24 0.27
72 65 0.73
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.34
Consensus pattern (71 bp):
GGCAGTCCTTCGCACAATCCTTATGTGATTATCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCC
CACATT
Found at i:129403 original size:43 final size:42
Alignment explanation
Indices: 129342--129670 Score: 493
Period size: 43 Copynumber: 7.8 Consensus size: 42
129332 CCAATAACCA
*
129342 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATCC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATCC
** * *
129384 TAAAGTCCTAAAACACATATATAACATAGAGGCATCTATAT-C
1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATCC
*
129426 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTA-TCC
* *
129469 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATAT-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATCC
129510 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATCCC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTAT-CC
* *
129553 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATAT-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATCC
*
129594 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTA-TCC
*
129637 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGAGGCAT
129671 TTCTCTTTAT
Statistics
Matches: 258, Mismatches: 22, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
41 110 0.43
42 4 0.02
43 144 0.56
ACGTcount: A:0.41, C:0.27, G:0.11, T:0.21
Consensus pattern (42 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATCC
Found at i:129699 original size:84 final size:84
Alignment explanation
Indices: 129342--129670 Score: 606
Period size: 84 Copynumber: 3.9 Consensus size: 84
129332 CCAATAACCA
*
129342 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTA-TCCTAAAGTCCTAAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC-AAAGTCCTCAAACACATATAT
*
129406 AACATAGAGGCATCTATATC
65 AACACAGAGGCATCTATATC
129426 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
129491 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
* *
129510 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATCCCAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
129575 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
129594 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
129659 ACACAGAGGCAT
66 ACACAGAGGCAT
129671 TTCTCTTTAT
Statistics
Matches: 238, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
84 235 0.99
85 3 0.01
ACGTcount: A:0.41, C:0.27, G:0.11, T:0.21
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Found at i:129743 original size:2 final size:2
Alignment explanation
Indices: 129736--129762 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
129726 ATTCCTATCT
129736 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 T
129763 GTAACAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:133374 original size:2 final size:2
Alignment explanation
Indices: 133367--133392 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
133357 TCTTTCTTCC
133367 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
133393 CTAGTTTAAG
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:134323 original size:35 final size:35
Alignment explanation
Indices: 134278--134716 Score: 544
Period size: 35 Copynumber: 12.4 Consensus size: 35
134268 ATCAATGTGA
* * *
134278 AGATCAACTCTGATCATCGAAAACTTCTTAAAATA
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
134313 AGATCAACTCTGATCATAAAAAAAACTTCTTGAAATA
1 AGATCAACTCTGATCAT--CAAAAACTTCTTGAAATG
*
134350 AGATCAACTCTGATCATC-AAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
*
134384 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
*
134419 AGATCAACTCTGATCATAAAAAAAAACCTTCTTGAAATG
1 AGATCAACTCTGATCAT---CAAAAA-CTTCTTGAAATG
* * *
134458 AGATCAACTCTGATCAACGAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* ** *
134493 AGATCAACTCTGATAATTGAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
134528 AGATCAACTCTGATCAT-AAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
*
134562 AGATCAACTCTGATCAT-AAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* ** *
134596 AGATCAACTCTGATAAAAAAAAGAACTTTTTGAAATG
1 AGATCAACTCTGAT-CATCAAA-AACTTCTTGAAATG
* * *
134633 AGATCAACTCTGATCAACCAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
134668 AGATCAACTCTGATAATCGAAAACTTCTTGAAAAT-
1 AGATCAACTCTGATCATCAAAAACTTCTTG-AAATG
134703 AGATCAACTCTGAT
1 AGATCAACTCTGAT
134717 TTCTATAAAT
Statistics
Matches: 360, Mismatches: 33, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
34 94 0.26
35 162 0.45
36 14 0.04
37 58 0.16
38 4 0.01
39 28 0.08
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (35 bp):
AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
Found at i:134358 original size:19 final size:19
Alignment explanation
Indices: 134299--134358 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
134289 GATCATCGAA
*
134299 AACTTCTTAAAATAAGATC
1 AACTTCTTGAAATAAGATC
* * **
134318 AAC-TC-TGATCATAAAAAA
1 AACTTCTTGA-AATAAGATC
134336 AACTTCTTGAAATAAGATC
1 AACTTCTTGAAATAAGATC
134355 AACT
1 AACT
134359 CTGATCATCA
Statistics
Matches: 29, Mismatches: 9, Indels: 6
0.66 0.20 0.14
Matches are distributed among these distances:
17 2 0.07
18 10 0.34
19 14 0.48
20 3 0.10
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.28
Consensus pattern (19 bp):
AACTTCTTGAAATAAGATC
Found at i:134682 original size:175 final size:178
Alignment explanation
Indices: 134278--134716 Score: 652
Period size: 175 Copynumber: 2.5 Consensus size: 178
134268 ATCAATGTGA
* * ** * *
134278 AGATCAACTCTGATCATCGAAAACTTCTTAAAATAAGATCAACTCTGATCATAAAAAAAACTTCT
1 AGATCAACTCTGATCAACGAAAACTTCTTGAAACGAGATCAACTCTGAT-A-ATAGAAAACTTCT
* * *
134343 TGAAATAAGATCAACTCTGATCATCAAAACTTCTTGAAACGAGATCAACTCTGATCATCGAAAAC
64 TGAAAAAAGATCAACTCTGATCATAAAAACTTCTTGAAACGAGATCAACTCTGATCATCAAAAAC
*
134408 TTCTTGAAATGAGATCAACTCTGATCATAAAAAAAAACCTTCTTGAAATG
129 TTCTTGAAACGAGATCAACTCTGATCATAAAAAAAAACCTTCTTGAAATG
* *
134458 AGATCAACTCTGATCAACGAAAACTTCTTGAAAGGAGATCAACTCTGATAATTGAAAACTTCTTG
1 AGATCAACTCTGATCAACGAAAACTTCTTGAAACGAGATCAACTCTGATAATAGAAAACTTCTTG
** *
134523 AAAGGAGATCAACTCTGATCATAAAAACTTCTTGAAATGAGATCAACTCTGATCAT-AAAAACTT
66 AAAAAAGATCAACTCTGATCATAAAAACTTCTTGAAACGAGATCAACTCTGATCATCAAAAACTT
*
134587 CTTGAAACGAGATCAACTCTGAT-A-AAAAAAAGAA-CTTTTTGAAATG
131 CTTGAAACGAGATCAACTCTGATCATAAAAAAA-AACCTTCTTGAAATG
* *
134633 AGATCAACTCTGATCAACCAAAACTTCTTGAAACGAGATCAACTCTGATAATCGAAAACTTCTTG
1 AGATCAACTCTGATCAACGAAAACTTCTTGAAACGAGATCAACTCTGATAATAGAAAACTTCTTG
*
134698 AAAATAGATCAACTCTGAT
66 AAAAAAGATCAACTCTGAT
134717 TTCTATAAAT
Statistics
Matches: 239, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
175 97 0.41
176 3 0.01
177 29 0.12
178 64 0.27
179 1 0.00
180 45 0.19
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (178 bp):
AGATCAACTCTGATCAACGAAAACTTCTTGAAACGAGATCAACTCTGATAATAGAAAACTTCTTG
AAAAAAGATCAACTCTGATCATAAAAACTTCTTGAAACGAGATCAACTCTGATCATCAAAAACTT
CTTGAAACGAGATCAACTCTGATCATAAAAAAAAACCTTCTTGAAATG
Found at i:134805 original size:55 final size:56
Alignment explanation
Indices: 134703--134962 Score: 263
Period size: 54 Copynumber: 4.8 Consensus size: 56
134693 TCTTGAAAAT
* * * * * *
134703 AGATCAACTCT-GAT-TTCT-ATAAATTTCTTTGAAAGGCCGCACGGGGTCAACTTA
1 AGATCAACTTTAGATCTTCTGA-AAACTTCTATGAAAGACCGCACTGGGTCATCTTA
* * * *
134757 AGATCAACTCT-GATCAT-TGAAAACTTCCTATGAAAGACCGCACAGGGTCATCTGA
1 AGATCAACTTTAGATCTTCTGAAAACTT-CTATGAAAGACCGCACTGGGTCATCTTA
*
134812 AGATCAAC-TTAGAT-TTCTGAAAACTTCTATGAAAGACCGCACTTGGTCATCTTA
1 AGATCAACTTTAGATCTTCTGAAAACTTCTATGAAAGACCGCACTGGGTCATCTTA
*** *
134866 AGAT-TTGTTTAGATCTT-TGAAAACTTCTATGAAAGACCACACTGGGTCATCTTA
1 AGATCAACTTTAGATCTTCTGAAAACTTCTATGAAAGACCGCACTGGGTCATCTTA
** *
134920 AGATC-TGTTTAGATC-TCTGAAAACTTCTATGAAAGACCACACT
1 AGATCAACTTTAGATCTTCTGAAAACTTCTATGAAAGACCGCACT
134963 AGTCATTTTA
Statistics
Matches: 180, Mismatches: 17, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
53 1 0.01
54 132 0.73
55 47 0.26
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (56 bp):
AGATCAACTTTAGATCTTCTGAAAACTTCTATGAAAGACCGCACTGGGTCATCTTA
Found at i:134845 original size:109 final size:108
Alignment explanation
Indices: 134703--134957 Score: 291
Period size: 108 Copynumber: 2.4 Consensus size: 108
134693 TCTTGAAAAT
* * *
134703 AGATCAACTCT-GATTTCT-ATAAATTTCTTTGAAAGGCCGCACGGGGTCAACTTAAGATCAACT
1 AGATCAACT-TAGATTTCTGA-AAACTTCTATGAAAGACCGCACGGGGTCAACTTAAGAT-AACT
*
134766 CT-GATCATTGAAAACTTCCTATGAAAGACCGCACAGGGTCATCTGA
63 CTAGATCATTGAAAACTT-CTATGAAAGACCACACAGGGTCATCTGA
** * *** *
134812 AGATCAACTTAGATTTCTGAAAACTTCTATGAAAGACCGCACTTGGTCATCTTAAGATTTGTTTA
1 AGATCAACTTAGATTTCTGAAAACTTCTATGAAAGACCGCACGGGGTCAACTTAAGATAACTCTA
* * *
134877 GATCTTTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTA
66 GATCATTGAAAACTTCTATGAAAGACCACACAGGGTCATCTGA
*** *
134920 AGATCTGTTTAGATCTCTGAAAACTTCTATGAAAGACC
1 AGATCAACTTAGATTTCTGAAAACTTCTATGAAAGACC
134958 ACACTAGTCA
Statistics
Matches: 125, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
108 62 0.50
109 62 0.50
110 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (108 bp):
AGATCAACTTAGATTTCTGAAAACTTCTATGAAAGACCGCACGGGGTCAACTTAAGATAACTCTA
GATCATTGAAAACTTCTATGAAAGACCACACAGGGTCATCTGA
Found at i:139638 original size:2 final size:2
Alignment explanation
Indices: 139631--139656 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
139621 TCTTTCTTCC
139631 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
139657 CTAGTTTAAG
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:140772 original size:126 final size:126
Alignment explanation
Indices: 140546--140785 Score: 437
Period size: 126 Copynumber: 1.9 Consensus size: 126
140536 CCCTGGTGTG
* *
140546 GGTGGCTTGTTGGTTTTGCTGCACACTTGGGTGTTACGTCGTATATGGTGGCAGAACTTCATGCT
1 GGTGGCTTGTTGGTTTTGCTGCACACCTAGGTGTTACGTCGTATATGGTGGCAGAACTTCATGCT
140611 TTGAGCTTAGGTCTAGGTCGTGATTCTTCAAGTAGGGGGTT-GATTCGTGATTCTTCAGGTA
66 TTGAGCTTAGGTCTAGGTCGTGATTCTTCAAGTA-GGGGTTCGATTCGTGATTCTTCAGGTA
140672 GGTGGCTTGTTGGTTTTGCTGCACACCTAGGTGTTACGTCGTATATGGTGGCAGAACTTCATGCT
1 GGTGGCTTGTTGGTTTTGCTGCACACCTAGGTGTTACGTCGTATATGGTGGCAGAACTTCATGCT
*
140737 TTGAGCTTAGGTCTAGGTCGTGATTCTTCAGGTAGGGGTTCGATTCGTG
66 TTGAGCTTAGGTCTAGGTCGTGATTCTTCAAGTAGGGGTTCGATTCGTG
140786 CCCTGGTNTG
Statistics
Matches: 110, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
125 6 0.05
126 104 0.95
ACGTcount: A:0.15, C:0.16, G:0.32, T:0.37
Consensus pattern (126 bp):
GGTGGCTTGTTGGTTTTGCTGCACACCTAGGTGTTACGTCGTATATGGTGGCAGAACTTCATGCT
TTGAGCTTAGGTCTAGGTCGTGATTCTTCAAGTAGGGGTTCGATTCGTGATTCTTCAGGTA
Found at i:140784 original size:27 final size:26
Alignment explanation
Indices: 140754--140849 Score: 110
Period size: 27 Copynumber: 3.7 Consensus size: 26
140744 TAGGTCTAGG
140754 TCGTGATTCTTCAGGTAGGGGTTCGAT
1 TCGTGATTCTTCAGGTAGGGGTT-GAT
* * *
140781 TCGTG---C-CCTGGTNTGGGGTTGAT
1 TCGTGATTCTTCAGGT-AGGGGTTGAT
140804 TCGTGATTCTTCAGGTAGGGGGTTGAT
1 TCGTGATTCTTCAGGTA-GGGGTTGAT
140831 TCGTGATTCTTCAGGTAGG
1 TCGTGATTCTTCAGGTAGG
140850 TGGCTTGTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
23 12 0.21
24 7 0.12
26 3 0.05
27 35 0.61
ACGTcount: A:0.12, C:0.15, G:0.35, T:0.36
Consensus pattern (26 bp):
TCGTGATTCTTCAGGTAGGGGTTGAT
Found at i:140922 original size:176 final size:163
Alignment explanation
Indices: 140628--141048 Score: 598
Period size: 176 Copynumber: 2.5 Consensus size: 163
140618 TAGGTCTAGG
*
140628 TCGTGATTCTTCAAGTAGGGGGTTGATTCGTGATTCTTCAGGTAGGTGGCTTGTTGGTTTTGCTG
1 TCGTGATTCTTCAGGTAGGGGGTTGATTCGTGATTCTTCAGGTAGGTGGCTTGTTGGTTTTGCTG
* * *
140693 CACACCTAGGTGTTACGTCGTATATGGTGGCAGAACTTCATGCTTTGAGCTTAGGTCTAGGTCGT
66 CACACTTGGGTGTTACGTCGAATATGGTGGCAGAACTTCATGCTTTGAGCTTAGG--T---T-GT
* *
140758 GATTCTTCAGGTAG-GGGTTCGATTCGTGCCCTGGTNTGGGGTT-GAT
125 GATTCTTCAGGTAGAGGGTT-GA-T--TG--CT--T-TGAGCTTAGAT
140804 TCGTGATTCTTCAGGTAGGGGGTTGATTCGTGATTCTTCAGGTAGGTGGCTTGTTGGTTTTGCTG
1 TCGTGATTCTTCAGGTAGGGGGTTGATTCGTGATTCTTCAGGTAGGTGGCTTGTTGGTTTTGCTG
140869 CACACTTGGGTGTTACGTCGAATATGGTGGCAGAACTTCATGCTTTGAGCTTAGGTTGTGATTCT
66 CACACTTGGGTGTTACGTCGAATATGGTGGCAGAACTTCATGCTTTGAGCTTAGGTTGTGATTCT
*
140934 TCAGGTAGAGGGTTGATTGCTTTGAGCTTAGGT
131 TCAGGTAGAGGGTTGATTGCTTTGAGCTTAGAT
*
140967 T-GTGATTCTTCAGGTAGAGGGTTGATTCGTGATTCTTCAGGTAGGTGGCTTGTTGG-TTTGCTG
1 TCGTGATTCTTCAGGTAGGGGGTTGATTCGTGATTCTTCAGGTAGGTGGCTTGTTGGTTTTGCTG
*
141030 CATACTTGGGTGTTACGTC
66 CACACTTGGGTGTTACGTC
141049 TGCTTTGAGC
Statistics
Matches: 234, Mismatches: 9, Indels: 19
0.89 0.03 0.07
Matches are distributed among these distances:
161 25 0.11
162 59 0.25
163 4 0.02
165 2 0.01
167 2 0.01
169 1 0.00
170 18 0.08
171 6 0.03
174 1 0.00
176 116 0.50
ACGTcount: A:0.15, C:0.14, G:0.33, T:0.38
Consensus pattern (163 bp):
TCGTGATTCTTCAGGTAGGGGGTTGATTCGTGATTCTTCAGGTAGGTGGCTTGTTGGTTTTGCTG
CACACTTGGGTGTTACGTCGAATATGGTGGCAGAACTTCATGCTTTGAGCTTAGGTTGTGATTCT
TCAGGTAGAGGGTTGATTGCTTTGAGCTTAGAT
Found at i:140968 original size:42 final size:42
Alignment explanation
Indices: 140909--140993 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
140899 CAGAACTTCA
140909 TGCTTTGAGCTTAGGTTGTGATTCTTCAGGTAGAGGGTTGAT
1 TGCTTTGAGCTTAGGTTGTGATTCTTCAGGTAGAGGGTTGAT
140951 TGCTTTGAGCTTAGGTTGTGATTCTTCAGGTAGAGGGTTGAT
1 TGCTTTGAGCTTAGGTTGTGATTCTTCAGGTAGAGGGTTGAT
140993 T
1 T
140994 CGTGATTCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.16, C:0.09, G:0.33, T:0.41
Consensus pattern (42 bp):
TGCTTTGAGCTTAGGTTGTGATTCTTCAGGTAGAGGGTTGAT
Found at i:140973 original size:22 final size:22
Alignment explanation
Indices: 140909--140973 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
140899 CAGAACTTCA
140909 TGCTTTGAGCTTAGGTTGTGAT
1 TGCTTTGAGCTTAGGTTGTGAT
* * * *
140931 T-C-TTCAGGTAGAGGGT-TGAT
1 TGCTTTGAGCT-TAGGTTGTGAT
140951 TGCTTTGAGCTTAGGTTGTGAT
1 TGCTTTGAGCTTAGGTTGTGAT
140973 T
1 T
140974 CTTCAGGTAG
Statistics
Matches: 31, Mismatches: 8, Indels: 8
0.66 0.17 0.17
Matches are distributed among these distances:
20 10 0.32
21 10 0.32
22 11 0.35
ACGTcount: A:0.15, C:0.09, G:0.32, T:0.43
Consensus pattern (22 bp):
TGCTTTGAGCTTAGGTTGTGAT
Found at i:140989 original size:22 final size:22
Alignment explanation
Indices: 140922--140990 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
140912 TTTGAGCTTA
140922 GGTTGTGATTCTTCAGGTAGAG
1 GGTTGTGATTCTTCAGGTAGAG
* * *
140944 GG-T-TGATTGCTTTGAGCT-TA-
1 GGTTGTGATT-C-TTCAGGTAGAG
140964 GGTTGTGATTCTTCAGGTAGAG
1 GGTTGTGATTCTTCAGGTAGAG
140986 GGTTG
1 GGTTG
140991 ATTCGTGATT
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
20 12 0.34
21 6 0.17
22 17 0.49
ACGTcount: A:0.16, C:0.09, G:0.36, T:0.39
Consensus pattern (22 bp):
GGTTGTGATTCTTCAGGTAGAG
Found at i:140994 original size:20 final size:20
Alignment explanation
Indices: 140927--140994 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
140917 GCTTAGGTTG
140927 TGATTCTTCAGGTAGAGGGT
1 TGATTCTTCAGGTAGAGGGT
* * * *
140947 TGATTGCTTTGAGCT-TAGGTT
1 TGATT-C-TTCAGGTAGAGGGT
140968 GTGATTCTTCAGGTAGAGGGT
1 -TGATTCTTCAGGTAGAGGGT
140989 TGATTC
1 TGATTC
140995 GTGATTCTTC
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
20 16 0.44
21 10 0.28
22 10 0.28
ACGTcount: A:0.18, C:0.10, G:0.32, T:0.40
Consensus pattern (20 bp):
TGATTCTTCAGGTAGAGGGT
Found at i:141072 original size:18 final size:18
Alignment explanation
Indices: 141049--141083 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
141039 GTGTTACGTC
141049 TGCTTTGAGCTTAGGTCA
1 TGCTTTGAGCTTAGGTCA
141067 TGCTTTGAGCTTAGGTC
1 TGCTTTGAGCTTAGGTC
141084 TTTTACTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.17, G:0.29, T:0.40
Consensus pattern (18 bp):
TGCTTTGAGCTTAGGTCA
Found at i:146602 original size:16 final size:16
Alignment explanation
Indices: 146581--146625 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
146571 CAGTGTGTTT
146581 GGATAATTTTTTTGAA
1 GGATAATTTTTTTGAA
146597 GGATAATTTTTTTGAA
1 GGATAATTTTTTTGAA
146613 GGATAATTTTTTT
1 GGATAATTTTTTT
146626 TTTTTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (16 bp):
GGATAATTTTTTTGAA
Found at i:148694 original size:24 final size:24
Alignment explanation
Indices: 148662--148712 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
148652 AAAAGTCAAC
148662 AGTGCCATTCATTCTAACGGAGGG
1 AGTGCCATTCATTCTAACGGAGGG
148686 AGTGCCATTCATTCTAACGGAGGG
1 AGTGCCATTCATTCTAACGGAGGG
148710 AGT
1 AGT
148713 ATGTATAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.25
Consensus pattern (24 bp):
AGTGCCATTCATTCTAACGGAGGG
Found at i:148782 original size:12 final size:12
Alignment explanation
Indices: 148765--148790 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
148755 TTGTCTTAAC
148765 GAGAATTTATTA
1 GAGAATTTATTA
148777 GAGAATTTATTA
1 GAGAATTTATTA
148789 GA
1 GA
148791 AAAGATTTTT
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:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (12 bp):
GAGAATTTATTA
Found at i:149438 original size:1 final size:1
Alignment explanation
Indices: 149432--149504 Score: 65
Period size: 1 Copynumber: 73.0 Consensus size: 1
149422 AAATCGCCTG
* * * * * * * *
149432 AAAAAAAAAAAAAACAAAAAAAAAACAAAACAAACAAAAAAAAAACAAAACAAAACAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
149497 CAAAAAAA
1 AAAAAAAA
149505 CCCAAAGAAA
Statistics
Matches: 54, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:149450 original size:15 final size:15
Alignment explanation
Indices: 149432--149504 Score: 101
Period size: 15 Copynumber: 4.7 Consensus size: 15
149422 AAATCGCCTG
149432 AAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAC
149447 AAAAAAAAAACAAAAC
1 AAAAAAAAAA-AAAAC
*
149463 AAACAAAAAAAAAAC
1 AAAAAAAAAAAAAAC
* *
149478 AAAACAAAACAAAAC
1 AAAAAAAAAAAAAAC
149493 AAAACAAAAAAA
1 AAAA-AAAAAAA
149505 CCCAAAGAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
15 31 0.62
16 19 0.38
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAC
Found at i:149510 original size:20 final size:20
Alignment explanation
Indices: 149432--149505 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
149422 AAATCGCCTG
149432 AAAAAAA-AAAA-AAACAAA
1 AAAAAAACAAAACAAACAAA
149450 AAAAAAACAAAACAAACAAA
1 AAAAAAACAAAACAAACAAA
149470 AAAAAAACAAAACAAA-ACAA
1 AAAAAAACAAAACAAACA-AA
*
149490 AACAAAACAAAA-AAAC
1 AAAAAAACAAAACAAAC
149506 CCAAAGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
18 7 0.14
19 8 0.16
20 36 0.71
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (20 bp):
AAAAAAACAAAACAAACAAA
Found at i:149948 original size:33 final size:33
Alignment explanation
Indices: 149892--149965 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
149882 AAATGGTCGG
* * * *
149892 TGCCGCCCTTGGTGGGCGGCGTGGCCATGGGGA
1 TGCCGCCCCTGGTCGGCGACGTGGCCATGGGCA
*
149925 TGCCGCCCCTGGTCGGCGACGTGGCCATGGTCA
1 TGCCGCCCCTGGTCGGCGACGTGGCCATGGGCA
149958 TGCCGCCC
1 TGCCGCCC
149966 AAGGAGGGCG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.07, C:0.35, G:0.41, T:0.18
Consensus pattern (33 bp):
TGCCGCCCCTGGTCGGCGACGTGGCCATGGGCA
Done.