Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005395.1 Hibiscus syriacus cultivar Beakdansim tig00012362_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: 235915
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:6563 original size:17 final size:17
Alignment explanation
Indices: 6538--6573 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6528 GTGTATTGAC
* *
6538 TTGTTCTCTGCTTGTGT
1 TTGTACTCTGCTTCTGT
6555 TTGTACTCTGCTTCTGT
1 TTGTACTCTGCTTCTGT
6572 TT
1 TT
6574 CGTTGTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.03, C:0.19, G:0.19, T:0.58
Consensus pattern (17 bp):
TTGTACTCTGCTTCTGT
Found at i:9224 original size:18 final size:17
Alignment explanation
Indices: 9201--9234 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9191 CTAAATTTAA
9201 TAATAATATATTTTATTT
1 TAATAAT-TATTTTATTT
*
9219 TAATAATTTTTTTATT
1 TAATAATTATTTTATT
9235 AATTATCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TAATAATTATTTTATTT
Found at i:9635 original size:54 final size:54
Alignment explanation
Indices: 9572--9680 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
9562 TGTTGCTTTT
9572 CTTGTCTTCTATTAATATTAATTATTTTATTATTTTTAAAAAATATTAAAAATA
1 CTTGTCTTCTATTAATATTAATTATTTTATTATTTTTAAAAAATATTAAAAATA
9626 CTTGTCTTCTATTAATATTAATTATTTTATTATTTTTAAAAAATATTAAAAATA
1 CTTGTCTTCTATTAATATTAATTATTTTATTATTTTTAAAAAATATTAAAAATA
9680 C
1 C
9681 AAGTACAATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.51
Consensus pattern (54 bp):
CTTGTCTTCTATTAATATTAATTATTTTATTATTTTTAAAAAATATTAAAAATA
Found at i:11581 original size:2 final size:2
Alignment explanation
Indices: 11576--11607 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11566 AGTAAAAAAA
11576 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
11608 GTGTCTTTTT
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:18445 original size:16 final size:17
Alignment explanation
Indices: 18415--18449 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
18405 TCTGAACCGG
18415 CCCGACCCGACCGTTGA
1 CCCGACCCGACCGTTGA
*
18432 CCCGA-CCGATCGTTGA
1 CCCGACCCGACCGTTGA
18448 CC
1 CC
18450 GTTGATTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.17, C:0.46, G:0.23, T:0.14
Consensus pattern (17 bp):
CCCGACCCGACCGTTGA
Found at i:20938 original size:24 final size:26
Alignment explanation
Indices: 20906--20974 Score: 83
Period size: 24 Copynumber: 2.8 Consensus size: 26
20896 ACATGACCTA
* *
20906 AATTTTGTTTTGATTTATGATTTC-G
1 AATTCTGTTTTGATTTCTGATTTCTG
*
20931 -ATTCTGTTTTGATATCT-A-TTCTG
1 AATTCTGTTTTGATTTCTGATTTCTG
20954 AATTCTGTTTTGATTTCTGAT
1 AATTCTGTTTTGATTTCTGAT
20975 ATCTTCGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
22 3 0.08
23 2 0.06
24 30 0.83
25 1 0.03
ACGTcount: A:0.19, C:0.09, G:0.14, T:0.58
Consensus pattern (26 bp):
AATTCTGTTTTGATTTCTGATTTCTG
Found at i:23012 original size:22 final size:22
Alignment explanation
Indices: 22995--23061 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
22985 CTCGTATAAA
22995 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
23017 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
23039 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
23061 T
1 T
23062 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:23320 original size:30 final size:30
Alignment explanation
Indices: 23275--23333 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
23265 ATCGCGTAGT
*
23275 CATATTATTTCCATACCTTTATCACATAGA
1 CATATCATTTCCATACCTTTATCACATAGA
*
23305 CATATCATTTTCATACCTTTATCACATAG
1 CATATCATTTCCATACCTTTATCACATAG
23334 CTCATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
CATATCATTTCCATACCTTTATCACATAGA
Found at i:23818 original size:68 final size:67
Alignment explanation
Indices: 23700--23851 Score: 205
Period size: 68 Copynumber: 2.3 Consensus size: 67
23690 TTTTTCTCAT
* * * *
23700 GGGGGAATAGGTTCCCCCCCTGGGGGTATCGATTCCCCTCACGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTTCCCCCCCTAGGGGTATCGATTCCCCTCACGCAATCTGGAAATTCAT-TACGA
23765 TGA
65 TGA
** * * *
23768 GGGGGTATCGGTTCCCCCCCTAGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCATTTCGTT
1 GGGGGTATCGGTTCCCCCCCTAGGGGTATCGATTCCCCTCACGCAATCTGGAAATTCATTACGAT
23833 GA
66 GA
*
23835 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
23852 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
67 22 0.30
68 52 0.70
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCCTAGGGGTATCGATTCCCCTCACGCAATCTGGAAATTCATTACGAT
GA
Found at i:23861 original size:21 final size:21
Alignment explanation
Indices: 23831--23873 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
23821 ATTCATTTCG
* *
23831 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
23852 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
23873 T
1 T
23874 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:29920 original size:22 final size:22
Alignment explanation
Indices: 29903--29969 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
29893 CTCGTATAAA
*
29903 TGCACCGAAGTACCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
29925 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
29947 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
29969 T
1 T
29970 ATGTCCATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:30233 original size:30 final size:30
Alignment explanation
Indices: 30183--30241 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
30173 ATCGCGTAGT
*
30183 CATATTATTTCCATAACTTTATCACATAGA
1 CATATCATTTCCATAACTTTATCACATAGA
* *
30213 CATATCATTTTCATACCTTTATCACATAG
1 CATATCATTTCCATAACTTTATCACATAG
30242 CTCATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.41
Consensus pattern (30 bp):
CATATCATTTCCATAACTTTATCACATAGA
Found at i:30726 original size:68 final size:67
Alignment explanation
Indices: 30608--30759 Score: 214
Period size: 68 Copynumber: 2.3 Consensus size: 67
30598 TTTTTCTCAT
* * *
30608 GGGGGAATAGGTTCCCCCCCTGGGGGTATCGATTCCCCTCACGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCACGCAATCTGGAAATTCAT-TACGA
30673 TGA
65 TGA
** * * *
30676 GGGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCATTTCGTT
1 GGGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCACGCAATCTGGAAATTCATTACGAT
30741 GA
66 GA
*
30743 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
30760 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 22 0.29
68 53 0.71
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCACGCAATCTGGAAATTCATTACGAT
GA
Found at i:30769 original size:21 final size:21
Alignment explanation
Indices: 30739--30781 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
30729 ATTCATTTCG
* *
30739 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
30760 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
30781 T
1 T
30782 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:31891 original size:17 final size:17
Alignment explanation
Indices: 31869--31926 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
31859 AACGGTCAAC
31869 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
31886 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
* *
31903 GGTCAACAGTCAGGTCG
1 GGTCAACGGTCGGGTCG
31920 GGTCAAC
1 GGTCAAC
31927 CCGGTTCAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:31940 original size:10 final size:10
Alignment explanation
Indices: 31922--31990 Score: 63
Period size: 9 Copynumber: 7.1 Consensus size: 10
31912 TCAGGTCGGG
*
31922 TCAACCCGGT
1 TCAAACCGGT
*
31932 TCAGACCGG-
1 TCAAACCGGT
31941 TCAAACCGGT
1 TCAAACCGGT
*
31951 TCGAACCGG-
1 TCAAACCGGT
*
31960 TCAAACCGAT
1 TCAAACCGGT
*
31970 TCAAAACTGG-
1 TC-AAACCGGT
31980 TCAAACCGGT
1 TCAAACCGGT
31990 T
1 T
31991 TTCCAGCAGC
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 21 0.46
10 20 0.43
11 5 0.11
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:31944 original size:19 final size:19
Alignment explanation
Indices: 31920--31990 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
31910 AGTCAGGTCG
*
31920 GGTCAACCCGGTTC-AGACC
1 GGTCAAACCGGTTCGA-ACC
31939 GGTCAAACCGGTTCGAACC
1 GGTCAAACCGGTTCGAACC
* * *
31958 GGTCAAACCGATTCAAAACT
1 GGTCAAACCGGTTC-GAACC
31978 GGTCAAACCGGTT
1 GGTCAAACCGGTT
31991 TTCCAGCAGC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 29 0.64
20 16 0.36
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCGAACC
Found at i:36009 original size:20 final size:20
Alignment explanation
Indices: 35973--36033 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
35963 AAATATTCAC
35973 GTTTCAATAGTCA-TTTTATCT
1 GTTT-AATA-TCATTTTTATCT
*
35994 GTTTAATATCATTTTTATTGT
1 GTTTAATATCATTTTTA-TCT
36015 GTTTAAT-T-ATTTTTA-CT
1 GTTTAATATCATTTTTATCT
36032 GT
1 GT
36034 GATGACAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
17 3 0.08
19 10 0.28
20 10 0.28
21 13 0.36
ACGTcount: A:0.23, C:0.08, G:0.10, T:0.59
Consensus pattern (20 bp):
GTTTAATATCATTTTTATCT
Found at i:36026 original size:19 final size:21
Alignment explanation
Indices: 35993--36034 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
35983 TCATTTTATC
*
35993 TGTTTAATATCATTTTTATTG
1 TGTTTAATATCATTTTTACTG
36014 TGTTTAAT-T-ATTTTTACTG
1 TGTTTAATATCATTTTTACTG
36033 TG
1 TG
36035 ATGACAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
20 1 0.05
21 8 0.40
ACGTcount: A:0.21, C:0.05, G:0.12, T:0.62
Consensus pattern (21 bp):
TGTTTAATATCATTTTTACTG
Found at i:36983 original size:2 final size:2
Alignment explanation
Indices: 36976--37006 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
36966 TAGGTCATTA
36976 AT 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 AT A
37007 AAAGAATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40984 original size:15 final size:15
Alignment explanation
Indices: 40964--40994 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40954 CAACAAATAG
40964 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
40979 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
40994 A
1 A
40995 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:48684 original size:23 final size:23
Alignment explanation
Indices: 48658--48726 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
48648 CACCACAGCT
* **
48658 CGTATAAATGCACTAAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
48681 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
48704 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
48727 TATAAGGTTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:49202 original size:2 final size:2
Alignment explanation
Indices: 49195--49220 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
49185 ATTCATCTTC
49195 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
49221 CATTTTTCCT
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):
AT
Found at i:50442 original size:21 final size:21
Alignment explanation
Indices: 50416--50491 Score: 152
Period size: 21 Copynumber: 3.6 Consensus size: 21
50406 TTACCCTTGA
50416 TGCATCGATGCACCTTGAATG
1 TGCATCGATGCACCTTGAATG
50437 TGCATCGATGCACCTTGAATG
1 TGCATCGATGCACCTTGAATG
50458 TGCATCGATGCACCTTGAATG
1 TGCATCGATGCACCTTGAATG
50479 TGCATCGATGCAC
1 TGCATCGATGCAC
50492 ATAGCCCATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.28
Consensus pattern (21 bp):
TGCATCGATGCACCTTGAATG
Found at i:66398 original size:29 final size:29
Alignment explanation
Indices: 66356--66415 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
66346 ACTCATCATC
66356 TGCTCTAAGTTAGTATTAGTAATTATTTT
1 TGCTCTAAGTTAGTATTAGTAATTATTTT
*
66385 TGCTCTAAGTTAGTATTAGTAATTGTTTT
1 TGCTCTAAGTTAGTATTAGTAATTATTTT
66414 TG
1 TG
66416 AAATCATGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.07, G:0.17, T:0.52
Consensus pattern (29 bp):
TGCTCTAAGTTAGTATTAGTAATTATTTT
Found at i:70490 original size:23 final size:23
Alignment explanation
Indices: 70460--70503 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
70450 TGTTTGGCAT
70460 GTCATTTAGTGATATTAAGCCTA
1 GTCATTTAGTGATATTAAGCCTA
70483 GTCATTTAGTGATATTAAGCC
1 GTCATTTAGTGATATTAAGCC
70504 ATGTTAGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (23 bp):
GTCATTTAGTGATATTAAGCCTA
Found at i:82241 original size:200 final size:202
Alignment explanation
Indices: 81897--82301 Score: 742
Period size: 200 Copynumber: 2.0 Consensus size: 202
81887 AGGTTTGATA
*
81897 TTTCTTCTGTAATTGACCTTGAAGCATCAGTCAGTGATCGATTTGTCTCCACTATCCTAGATCGA
1 TTTCTTCTGTAACTGACCTTGAAGCATCAGTCAGTGATCGATTTGTCTCCACTATCCTAGATCGA
81962 TCTTTATGATATTTTGCGACTCCTATTGATACTTTCCTCCCATCTATCCACGACCCGTTTATATT
66 TCTTTATGATATTTTGCGACTCCTATTGATACTTTCCTCCCATCTATCCACGACCCGTTTATATT
82027 CTCGATTGCCTTTCTCAGACCTACCTCATTACCAAACCGCACAAA-GCGAATGTGGAGGATTTGT
131 CTCGATTGCCTTTCTCAGACCTACCTCATTACCAAACCGCACAAAGGCGAATGTGGAGGATTTGT
82091 ACTTTGG
196 ACTTTGG
82098 TTTCTTCTGTAACTGACCTTGAAGCA-CAGTCAGTGATCGATTTGTCTCCACTATCCTAGATCGA
1 TTTCTTCTGTAACTGACCTTGAAGCATCAGTCAGTGATCGATTTGTCTCCACTATCCTAGATCGA
* *
82162 TCTTTCTGATATTTTGCGACTCCTATTGATACTTTCCTCCCATCTATCCACGATCCGTTTATATT
66 TCTTTATGATATTTTGCGACTCCTATTGATACTTTCCTCCCATCTATCCACGACCCGTTTATATT
**
82227 CTCGATTGCCTTTCTCAGACCTGTCTCATTACCAAACCGCACAAAGGCGAATGTGGAGGATTTGT
131 CTCGATTGCCTTTCTCAGACCTACCTCATTACCAAACCGCACAAAGGCGAATGTGGAGGATTTGT
*
82292 TCTTTGG
196 ACTTTGG
82299 TTT
1 TTT
82302 ATTCGTTTCA
Statistics
Matches: 197, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
200 144 0.73
201 53 0.27
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.37
Consensus pattern (202 bp):
TTTCTTCTGTAACTGACCTTGAAGCATCAGTCAGTGATCGATTTGTCTCCACTATCCTAGATCGA
TCTTTATGATATTTTGCGACTCCTATTGATACTTTCCTCCCATCTATCCACGACCCGTTTATATT
CTCGATTGCCTTTCTCAGACCTACCTCATTACCAAACCGCACAAAGGCGAATGTGGAGGATTTGT
ACTTTGG
Found at i:89888 original size:23 final size:23
Alignment explanation
Indices: 89844--89888 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
89834 ATTATTATTA
*** *
89844 TTTTTGGATAATTTTTTTAATTT
1 TTTTTGGATAATTAAGTAAATTT
89867 TTTTTGGATAATTAAGTAAATT
1 TTTTTGGATAATTAAGTAAATT
89889 ATTATTACTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.60
Consensus pattern (23 bp):
TTTTTGGATAATTAAGTAAATTT
Found at i:90600 original size:2 final size:2
Alignment explanation
Indices: 90595--90640 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
90585 GGGAAATTAG
90595 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
90637 AT AT
1 AT AT
90641 TGTAACAACC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92706 original size:12 final size:12
Alignment explanation
Indices: 92689--92719 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
92679 ATTATCTCTA
*
92689 ATGTTTTATAAT
1 ATGTTTTATAAG
92701 ATGTTTTATAAG
1 ATGTTTTATAAG
92713 ATGTTTT
1 ATGTTTT
92720 TAAATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (12 bp):
ATGTTTTATAAG
Found at i:99587 original size:42 final size:42
Alignment explanation
Indices: 99540--99640 Score: 184
Period size: 42 Copynumber: 2.4 Consensus size: 42
99530 GTATTTCTTA
*
99540 AGGGTAGTATCGATACCCGTTGAGGAGGGTATCGATACTGAG
1 AGGGTAGTATCGATACCCGTTGAGGAGAGTATCGATACTGAG
*
99582 AGGGTAGTATCGATACTCGTTGAGGAGAGTATCGATACTGAG
1 AGGGTAGTATCGATACCCGTTGAGGAGAGTATCGATACTGAG
99624 AGGGTAGTATCGATACC
1 AGGGTAGTATCGATACC
99641 AGGGGATGGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.25
Consensus pattern (42 bp):
AGGGTAGTATCGATACCCGTTGAGGAGAGTATCGATACTGAG
Found at i:99591 original size:20 final size:20
Alignment explanation
Indices: 99568--99639 Score: 101
Period size: 20 Copynumber: 3.5 Consensus size: 20
99558 GTTGAGGAGG
99568 GTATCGATACTGAGAGGGTA
1 GTATCGATACTGAGAGGGTA
*
99588 GTATCGATACTCGTTGAGGAG-A
1 GTATCGATACT-G-AGAGG-GTA
99610 GTATCGATACTGAGAGGGTA
1 GTATCGATACTGAGAGGGTA
99630 GTATCGATAC
1 GTATCGATAC
99640 CAGGGGATGG
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
19 1 0.02
20 26 0.57
21 2 0.04
22 16 0.35
23 1 0.02
ACGTcount: A:0.29, C:0.12, G:0.32, T:0.26
Consensus pattern (20 bp):
GTATCGATACTGAGAGGGTA
Found at i:99620 original size:22 final size:22
Alignment explanation
Indices: 99545--99620 Score: 95
Period size: 22 Copynumber: 3.5 Consensus size: 22
99535 TCTTAAGGGT
*
99545 AGTATCGATACCCGTTGAGGAG
1 AGTATCGATACTCGTTGAGGAG
* *
99567 GGTATCGATACT-G-AGAGG-G
1 AGTATCGATACTCGTTGAGGAG
99586 TAGTATCGATACTCGTTGAGGAG
1 -AGTATCGATACTCGTTGAGGAG
99609 AGTATCGATACT
1 AGTATCGATACT
99621 GAGAGGGTAG
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
19 1 0.02
20 15 0.33
21 2 0.04
22 26 0.58
23 1 0.02
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.26
Consensus pattern (22 bp):
AGTATCGATACTCGTTGAGGAG
Found at i:99764 original size:20 final size:20
Alignment explanation
Indices: 99726--99764 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
99716 CAATACCCTT
* *
99726 GAAGGGAAGTATCGGTACTG
1 GAAGGGAAGTACCGATACTG
*
99746 GAAGGGTAGTACCGATACT
1 GAAGGGAAGTACCGATACT
99765 TCTAGGCATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.13, G:0.36, T:0.21
Consensus pattern (20 bp):
GAAGGGAAGTACCGATACTG
Found at i:101452 original size:17 final size:17
Alignment explanation
Indices: 101430--101483 Score: 99
Period size: 17 Copynumber: 3.2 Consensus size: 17
101420 CACGGTCAAC
101430 GGTCAACGATCGGGTCG
1 GGTCAACGATCGGGTCG
101447 GGTCAACGATCGGGTCG
1 GGTCAACGATCGGGTCG
*
101464 GGTCAACGGTCGGGTCG
1 GGTCAACGATCGGGTCG
101481 GGT
1 GGT
101484 TGGTCAGACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.15, C:0.22, G:0.44, T:0.19
Consensus pattern (17 bp):
GGTCAACGATCGGGTCG
Found at i:102432 original size:18 final size:18
Alignment explanation
Indices: 102409--102446 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
102399 GATCGAAAAC
*
102409 TTTATAATTTCTTTTATG
1 TTTATAAATTCTTTTATG
102427 TTTATAAATTCTTTTATG
1 TTTATAAATTCTTTTATG
102445 TT
1 TT
102447 ATATTTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTATAAATTCTTTTATG
Found at i:102537 original size:21 final size:21
Alignment explanation
Indices: 102511--102582 Score: 126
Period size: 21 Copynumber: 3.4 Consensus size: 21
102501 TGATTATGGA
102511 AATGTGAACTTTGAACAAGTG
1 AATGTGAACTTTGAACAAGTG
102532 AATGTGAACTTTGAACAAGTG
1 AATGTGAACTTTGAACAAGTG
* *
102553 AATGTGAATTTTGAACCAGTG
1 AATGTGAACTTTGAACAAGTG
102574 AATGTGAAC
1 AATGTGAAC
102583 AGACTCTATG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.29
Consensus pattern (21 bp):
AATGTGAACTTTGAACAAGTG
Found at i:102834 original size:21 final size:21
Alignment explanation
Indices: 102716--102878 Score: 143
Period size: 21 Copynumber: 7.7 Consensus size: 21
102706 TCGAGGGTTT
*
102716 TATGTGGTC-CTTCGGGACAAA
1 TATGTGG-CACTTCGAGACAAA
*
102737 TATGTGGCACTTCG-GTGCAAAA
1 TATGTGGCACTTCGAG-AC-AAA
*
102759 TTATATGGTCA-TTCGAGACAAA
1 -TATGTGG-CACTTCGAGACAAA
*
102781 TATGTGGTACTTCGAGACAAA
1 TATGTGGCACTTCGAGACAAA
*
102802 TATGTGGTACTTCGAGACAAA
1 TATGTGGCACTTCGAGACAAA
* * * **
102823 TATGTGACACTTCGGGATAGT
1 TATGTGGCACTTCGAGACAAA
* * *
102844 TATGTGACACTTCGAGATAAT
1 TATGTGGCACTTCGAGACAAA
102865 TATGTGGCACTTCG
1 TATGTGGCACTTCG
102879 GTGCAAATTA
Statistics
Matches: 121, Mismatches: 14, Indels: 14
0.81 0.09 0.09
Matches are distributed among these distances:
20 3 0.02
21 98 0.81
22 6 0.05
23 11 0.09
24 3 0.02
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (21 bp):
TATGTGGCACTTCGAGACAAA
Found at i:102999 original size:2 final size:2
Alignment explanation
Indices: 102992--103046 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
102982 ATAAAGTGAA
102992 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
103034 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
103047 GTGTACTTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:104185 original size:32 final size:31
Alignment explanation
Indices: 104147--104223 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
104137 CGGGGCCGTG
* *
104147 GGGCCTACCTAAGAACACATCTTAGTGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
104179 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
104210 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
104224 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.31, G:0.26, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:104206 original size:63 final size:63
Alignment explanation
Indices: 104100--104223 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
104090 CACTAAGGGA
* * ** *
104100 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* * *
104163 ACATCTTAGTGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
104224 GTCACATTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.26, C:0.29, G:0.27, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:105105 original size:7 final size:7
Alignment explanation
Indices: 105093--105130 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
105083 ATAAAAGAAA
105093 GTCAACG
1 GTCAACG
105100 GTCAACG
1 GTCAACG
105107 GTCAACG
1 GTCAACG
105114 GTCAACG
1 GTCAACG
105121 GTCAACG
1 GTCAACG
105128 GTC
1 GTC
105131 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:105148 original size:22 final size:22
Alignment explanation
Indices: 105120--105184 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
105110 AACGGTCAAC
105120 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
105142 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
105164 GGTCAACCGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
105185 AGACCAGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.09, C:0.25, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:105184 original size:5 final size:5
Alignment explanation
Indices: 105127--105167 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
105117 AACGGTCAAC
*
105127 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC
105168 AACCGTCGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:105207 original size:19 final size:18
Alignment explanation
Indices: 105181--105278 Score: 108
Period size: 19 Copynumber: 5.2 Consensus size: 18
105171 CGTCGGGTCG
*
105181 GGTCAGACCAGTCAAACC
1 GGTCAGACCGGTCAAACC
105199 GGCTCAGACCGGTCAAACC
1 GG-TCAGACCGGTCAAACC
105218 GAGTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
*
105237 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
*
105257 GGTCAAACCGGTCAGAACC
1 GGTCAGACCGGTCA-AACC
105276 GGT
1 GGT
105279 TGAAAACCGG
Statistics
Matches: 69, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
18 6 0.09
19 54 0.78
20 9 0.13
ACGTcount: A:0.29, C:0.31, G:0.28, T:0.13
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:105223 original size:29 final size:28
Alignment explanation
Indices: 105181--105298 Score: 98
Period size: 29 Copynumber: 4.1 Consensus size: 28
105171 CGTCGGGTCG
* *
105181 GGTCAGACC-AGTCAAACCGGCTCAGACC
1 GGTCAAACCGAGTCAAACCGG-TCAAACC
*
105209 GGTCAAACCGAGTCAGACCGGTCAAACC
1 GGTCAAACCGAGTCAAACCGGTCAAACC
* *
105237 GGTTCGAACCG-GTTGAAACCGGTCAAACC
1 GG-TCAAACCGAG-TCAAACCGGTCAAACC
* *
105266 GGTCAGAACCG-GTTGAAAACCGGTTAAACC
1 GGTCA-AACCGAG-T-CAAACCGGTCAAACC
105296 GGT
1 GGT
105299 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
28 19 0.25
29 41 0.54
30 16 0.21
ACGTcount: A:0.30, C:0.29, G:0.27, T:0.14
Consensus pattern (28 bp):
GGTCAAACCGAGTCAAACCGGTCAAACC
Found at i:105233 original size:38 final size:38
Alignment explanation
Indices: 105181--105298 Score: 118
Period size: 38 Copynumber: 3.1 Consensus size: 38
105171 CGTCGGGTCG
*
105181 GGTCAGACCAGTCAAACCGGCTC-AGACCGG-TCAAACC
1 GGTCAGACCGGTCAAACCGGCTCGA-ACCGGTTCAAACC
* *
105218 GAGTCAGACCGGTCAAACCGGTTCGAACCGGTTGAAACC
1 G-GTCAGACCGGTCAAACCGGCTCGAACCGGTTCAAACC
* *
105257 GGTCAAACCGGTCAGAACCGG-TTGAAAACCGGTT-AAACC
1 GGTCAGACCGGTCA-AACCGGCTCG--AACCGGTTCAAACC
105296 GGT
1 GGT
105299 TTCCAGCAGC
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
37 1 0.01
38 39 0.56
39 22 0.31
40 8 0.11
ACGTcount: A:0.30, C:0.29, G:0.27, T:0.14
Consensus pattern (38 bp):
GGTCAGACCGGTCAAACCGGCTCGAACCGGTTCAAACC
Found at i:105299 original size:9 final size:9
Alignment explanation
Indices: 105181--105298 Score: 101
Period size: 9 Copynumber: 12.3 Consensus size: 9
105171 CGTCGGGTCG
*
105181 GGTCAGACC
1 GGTCAAACC
*
105190 AGTCAAACC
1 GGTCAAACC
*
105199 GGCTCAGACC
1 GG-TCAAACC
105209 GGTCAAACC
1 GGTCAAACC
*
105218 GAGTCAGACC
1 G-GTCAAACC
105228 GGTCAAACC
1 GGTCAAACC
*
105237 GGTTCGAACC
1 GG-TCAAACC
*
105247 GGTTGAAACC
1 GG-TCAAACC
105257 GGTCAAACC
1 GGTCAAACC
105266 GGTCAGAACC
1 GGTCA-AACC
*
105276 GGTTGAAAACC
1 GG-T-CAAACC
*
105287 GGTTAAACC
1 GGTCAAACC
105296 GGT
1 GGT
105299 TTCCAGCAGC
Statistics
Matches: 90, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
9 43 0.48
10 39 0.43
11 7 0.08
12 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.27, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:111574 original size:32 final size:31
Alignment explanation
Indices: 111536--111612 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
111526 CGGGGCCGTG
* *
111536 GGGCCTACCTAAGAACACATCTTAGTGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
111568 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
111599 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
111613 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.31, G:0.26, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:111595 original size:63 final size:63
Alignment explanation
Indices: 111489--111612 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
111479 CACTAAGGGA
* * ** *
111489 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* * *
111552 ACATCTTAGTGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
111613 GTCACATTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.26, C:0.29, G:0.27, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:112495 original size:7 final size:7
Alignment explanation
Indices: 112483--112520 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
112473 ATAAAAGAAA
112483 GTCAACG
1 GTCAACG
112490 GTCAACG
1 GTCAACG
112497 GTCAACG
1 GTCAACG
112504 GTCAACG
1 GTCAACG
112511 GTCAACG
1 GTCAACG
112518 GTC
1 GTC
112521 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:112538 original size:22 final size:22
Alignment explanation
Indices: 112510--112552 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
112500 AACGGTCAAC
*
112510 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACCGTCGGGTCGGGTCG
112532 GGTCAACCGTCGGGTCGGGTC
1 GGTCAACCGTCGGGTCGGGTC
112553 AGACCGGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.26, G:0.47, T:0.19
Consensus pattern (22 bp):
GGTCAACCGTCGGGTCGGGTCG
Found at i:112543 original size:17 final size:18
Alignment explanation
Indices: 112523--112558 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
112513 CAACGGTCGG
112523 GTCGGGTCGGGTCA-ACC
1 GTCGGGTCGGGTCAGACC
112540 GTCGGGTCGGGTCAGACC
1 GTCGGGTCGGGTCAGACC
112558 G
1 G
112559 GTCAAACCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.11, C:0.28, G:0.44, T:0.17
Consensus pattern (18 bp):
GTCGGGTCGGGTCAGACC
Found at i:112575 original size:19 final size:18
Alignment explanation
Indices: 112549--112646 Score: 117
Period size: 19 Copynumber: 5.2 Consensus size: 18
112539 CGTCGGGTCG
112549 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
112567 GGCTCAGACCGGTCAAACC
1 GG-TCAGACCGGTCAAACC
112586 GAGTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
*
112605 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
*
112625 GGTCAAACCGGTCAGAACC
1 GGTCAGACCGGTCA-AACC
112644 GGT
1 GGT
112647 TGAAAACCGG
Statistics
Matches: 70, Mismatches: 3, Indels: 13
0.81 0.03 0.15
Matches are distributed among these distances:
18 6 0.09
19 55 0.79
20 9 0.13
ACGTcount: A:0.28, C:0.31, G:0.29, T:0.13
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:112592 original size:38 final size:38
Alignment explanation
Indices: 112549--112666 Score: 127
Period size: 38 Copynumber: 3.1 Consensus size: 38
112539 CGTCGGGTCG
112549 GGTCAGACCGGTCAAACCGGCTC-AGACCGG-TCAAACC
1 GGTCAGACCGGTCAAACCGGCTCGA-ACCGGTTCAAACC
* *
112586 GAGTCAGACCGGTCAAACCGGTTCGAACCGGTTGAAACC
1 G-GTCAGACCGGTCAAACCGGCTCGAACCGGTTCAAACC
* *
112625 GGTCAAACCGGTCAGAACCGG-TTGAAAACCGGTT-AAACC
1 GGTCAGACCGGTCA-AACCGGCTCG--AACCGGTTCAAACC
112664 GGT
1 GGT
112667 TTCCAGCAGC
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
37 1 0.01
38 40 0.56
39 22 0.31
40 8 0.11
ACGTcount: A:0.29, C:0.29, G:0.28, T:0.14
Consensus pattern (38 bp):
GGTCAGACCGGTCAAACCGGCTCGAACCGGTTCAAACC
Found at i:112647 original size:29 final size:28
Alignment explanation
Indices: 112549--112666 Score: 116
Period size: 29 Copynumber: 4.1 Consensus size: 28
112539 CGTCGGGTCG
*
112549 GGTCAG-ACCGGTCAAACCGGCTCAGACC
1 GGTCAGAACCGGTCAAACCGG-TCAAACC
*
112577 GGTCA-AACCGAGTCAGACCGGTCAAACC
1 GGTCAGAACCG-GTCAAACCGGTCAAACC
*
112605 GGTTC-GAACCGGTTGAAACCGGTCAAACC
1 GG-TCAGAACCGG-TCAAACCGGTCAAACC
* *
112634 GGTCAGAACCGGTTGAAAACCGGTTAAACC
1 GGTCAGAACCGG-T-CAAACCGGTCAAACC
112664 GGT
1 GGT
112667 TTCCAGCAGC
Statistics
Matches: 77, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
28 20 0.26
29 41 0.53
30 16 0.21
ACGTcount: A:0.29, C:0.29, G:0.28, T:0.14
Consensus pattern (28 bp):
GGTCAGAACCGGTCAAACCGGTCAAACC
Found at i:112667 original size:9 final size:9
Alignment explanation
Indices: 112549--112666 Score: 110
Period size: 9 Copynumber: 12.3 Consensus size: 9
112539 CGTCGGGTCG
*
112549 GGTCAGACC
1 GGTCAAACC
112558 GGTCAAACC
1 GGTCAAACC
*
112567 GGCTCAGACC
1 GG-TCAAACC
112577 GGTCAAACC
1 GGTCAAACC
*
112586 GAGTCAGACC
1 G-GTCAAACC
112596 GGTCAAACC
1 GGTCAAACC
*
112605 GGTTCGAACC
1 GG-TCAAACC
*
112615 GGTTGAAACC
1 GG-TCAAACC
112625 GGTCAAACC
1 GGTCAAACC
112634 GGTCAGAACC
1 GGTCA-AACC
*
112644 GGTTGAAAACC
1 GG-T-CAAACC
*
112655 GGTTAAACC
1 GGTCAAACC
112664 GGT
1 GGT
112667 TTCCAGCAGC
Statistics
Matches: 92, Mismatches: 11, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
9 45 0.49
10 39 0.42
11 7 0.08
12 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.28, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:129863 original size:21 final size:21
Alignment explanation
Indices: 129837--129879 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
129827 TTTCTGGGTT
* *
129837 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
129858 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
129879 A
1 A
129880 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:129940 original size:66 final size:66
Alignment explanation
Indices: 129859--130007 Score: 219
Period size: 66 Copynumber: 2.3 Consensus size: 66
129849 ACCCATTCAA
* * *
129859 GGGGAACCGATACCCCTTCAACGAATATGATTTCCAGAATGC-TAGAGGGGAATCGGTACCCCAG
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTTA-AGGGGAATCGATACCCCAG
129923 GG
65 GG
* * *
129925 GGGGAACCGATACCCCCTCATCGTATATGAATTCCAGATTGCTTAAGGGGAATCGATACCCCAGG
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTTAAGGGGAATCGATACCCCAGG
129990 G
66 G
*
129991 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
130008 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
66 73 0.97
67 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (66 bp):
GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTTAAGGGGAATCGATACCCCAGG
G
Found at i:130346 original size:29 final size:29
Alignment explanation
Indices: 130312--130383 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
130302 CATATTATGA
**
130312 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
* *
130341 TACATGACATGAATTCATCTTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
130370 TACATGACATGAAT
1 TACATGACATGAAT
130384 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:130748 original size:22 final size:22
Alignment explanation
Indices: 130674--130740 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
130664 TTATGGACAA
130674 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
130696 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
130718 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
130740 A
1 A
130741 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:132579 original size:12 final size:12
Alignment explanation
Indices: 132562--132588 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
132552 CTTTTTCACA
132562 AAGAGGCAGAGG
1 AAGAGGCAGAGG
132574 AAGAGGCAGAGG
1 AAGAGGCAGAGG
132586 AAG
1 AAG
132589 GAACCCGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.07, G:0.48, T:0.00
Consensus pattern (12 bp):
AAGAGGCAGAGG
Found at i:136792 original size:21 final size:21
Alignment explanation
Indices: 136766--136808 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
136756 TTTCTGGGTT
* *
136766 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
136787 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
136808 A
1 A
136809 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:136883 original size:67 final size:66
Alignment explanation
Indices: 136788--136937 Score: 212
Period size: 67 Copynumber: 2.3 Consensus size: 66
136778 ACCCATTCAA
* * *
136788 GGGGAACCGATACCCCTTCAACGAATATGATTTCCAGAATGC-TAGAGGGGAATCGGTACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTTA-AGGGGAATCGATA-CCCCA
136852 GGG
64 GGG
* * *
136855 GGGGAACCGATACCCCCTCATCGTATATGAATTCCAGATTGCTTAAGGGGAATCGATACCCCAGG
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTTAAGGGGAATCGATACCCCAGG
136920 G
66 G
*
136921 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
136938 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
66 24 0.32
67 49 0.65
68 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (66 bp):
GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTTAAGGGGAATCGATACCCCAGG
G
Found at i:137276 original size:29 final size:29
Alignment explanation
Indices: 137242--137313 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
137232 CATATTATGA
**
137242 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
* *
137271 TACATGACATGAATTCATCTTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
137300 TACATGACATGAAT
1 TACATGACATGAAT
137314 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:137368 original size:30 final size:31
Alignment explanation
Indices: 137328--137386 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
137318 AGAAAAGTTC
*
137328 TATGCACTATGTGATAAAAGTATGTAAATGA
1 TATGCACTATGTGATAAAAGTATGGAAATGA
* *
137359 TATGC-CTATGTGTTAAAGGTATGGAAAT
1 TATGCACTATGTGATAAAAGTATGGAAAT
137387 ACTATGTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (31 bp):
TATGCACTATGTGATAAAAGTATGGAAATGA
Found at i:137680 original size:22 final size:22
Alignment explanation
Indices: 137606--137672 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
137596 TTATGGACAA
137606 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
137628 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
137650 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
137672 A
1 A
137673 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:144235 original size:18 final size:17
Alignment explanation
Indices: 144212--144258 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
144202 TGTTTCTGAG
144212 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
* *
144230 GGAATTAGAATCTGTCA
1 GGAATTGGAATCTGTAA
144247 GGAATTGGAATC
1 GGAATTGGAATC
144259 CAATTCCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:145080 original size:248 final size:251
Alignment explanation
Indices: 144611--145219 Score: 935
Period size: 249 Copynumber: 2.4 Consensus size: 251
144601 CTCCATCCGA
144611 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAC
1 GACCCGACCCGACCAAAATAAAGTTT----C-ACCCGACCCGAATATATGAATTAGAAACCCGAC
* *
144676 CCGACTCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTAACTTAATTAGAAAAAATA
61 CCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTAACTTAATTAGAAAAAAAA
* *
144741 TATAGAGAGAGGGGAATTATTGTAATTATTCATAAATATATAAGATAAAATTATTTTATTTTTTG
126 TATAGAGAGAGGGGAATTATTGTAATTATTCATAAATATATAAGATAAAATTATTATATTTTTCG
144806 GGTCGGGTATTTTTCACCCTAAACCCG-A-ACCCGACCCGAATATCACACTTAAAAAAACC
191 GGTCGGGTATTTTTCACCCTAAACCCGAAGACCCGACCCGAATATCACACTTAAAAAAACC
* *
144865 GACCTGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAATCCGACCCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAACCCGACCCGAC
*
144930 CCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATT-GAAAAAAAATATAG
66 CCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTAACTTAATTAGAAAAAAAATATAG
*
144994 AGAGAGGGGTATTATTGTAATTATTTC-TAAATATATAA-AGTAAAATTA-TATATATTTTCGGG
131 AGAGAGGGGAATTATTGTAATTA-TTCATAAATATATAAGA-TAAAATTATTATAT-TTTTCGGG
*
145056 TCGGGTATTTTTCACCCTAAACCCGAACTAGACCCGACTCGAATATCACACTTAAAAAAACC
193 TCGGGTATTTTTCACCCTAAACCCG-A--AGACCCGACCCGAATATCACACTTAAAAAAACC
*
145118 GACCCGACCCGACTAAAATAAAGTTTCACCCGACTCGACCCGAATATATGAATTAGAAACCCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCA--C--C-CGACCCGAATATATGAATTAGAAACCCGAC
145183 CCGACCCGAAATAATAAAAAAA-TATTTTTATTCAATA
61 CCGACCCGAAATAATAAAAAAATTATTTTTATTCAATA
145220 TATGAATAAG
Statistics
Matches: 330, Mismatches: 12, Indels: 23
0.90 0.03 0.06
Matches are distributed among these distances:
247 5 0.02
248 86 0.26
249 88 0.27
250 1 0.00
252 1 0.00
253 56 0.17
254 25 0.08
255 1 0.00
257 16 0.05
258 51 0.15
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (251 bp):
GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAACCCGACCCGAC
CCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTAACTTAATTAGAAAAAAAATATAG
AGAGAGGGGAATTATTGTAATTATTCATAAATATATAAGATAAAATTATTATATTTTTCGGGTCG
GGTATTTTTCACCCTAAACCCGAAGACCCGACCCGAATATCACACTTAAAAAAACC
Found at i:151717 original size:42 final size:42
Alignment explanation
Indices: 151663--151898 Score: 445
Period size: 42 Copynumber: 5.6 Consensus size: 42
151653 CAAACCTTAC
151663 TGGTGCATACCAAGGAGATCCTAAGGAGGCGGTGACCACTGG
1 TGGTGCATACCAAGGAGATCCTAAGGAGGCGGTGACCACTGG
151705 TGGTGCATACCAAGGAGATCCTAAGGAGGCGGTGACCACTGG
1 TGGTGCATACCAAGGAGATCCTAAGGAGGCGGTGACCACTGG
151747 TGGTGCATACCAAGGAGATCCTAAGGAGGCGGTGACCACTGG
1 TGGTGCATACCAAGGAGATCCTAAGGAGGCGGTGACCACTGG
* *
151789 TGGTGCATACCAAGGAGATCCTAAGGAGGTGTTGACCACTGG
1 TGGTGCATACCAAGGAGATCCTAAGGAGGCGGTGACCACTGG
*
151831 TGGTGCATACCAAGGAGATCCTAAGGAGGTGGTGACCACTGG
1 TGGTGCATACCAAGGAGATCCTAAGGAGGCGGTGACCACTGG
151873 TGGTGCATACCAAGGAGATCCTAAGG
1 TGGTGCATACCAAGGAGATCCTAAGG
151899 GTGAAATCCA
Statistics
Matches: 191, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 191 1.00
ACGTcount: A:0.27, C:0.20, G:0.35, T:0.18
Consensus pattern (42 bp):
TGGTGCATACCAAGGAGATCCTAAGGAGGCGGTGACCACTGG
Found at i:157155 original size:60 final size:62
Alignment explanation
Indices: 157048--157179 Score: 150
Period size: 60 Copynumber: 2.2 Consensus size: 62
157038 AATTGATCCA
* **
157048 TAAACTTTT--AAATGTTCAAATTTCATCCCTAAATTATGATTATCATTCTAAATTAG-CCC
1 TAAACTTTTGAAAATGTTCAAATTTCATCCCTAAAATATGAGCATCATTCTAAATTAGTCCC
* *
157107 TTAAACTTTTGAAAAT-TTCAACTTT-ATCCCTAAAATATG-GCATGCATTCTAAATTGGTCCC
1 -TAAACTTTTGAAAATGTTCAAATTTCATCCCTAAAATATGAGCAT-CATTCTAAATTAGTCCC
*
157168 CAAACTTTTGAA
1 TAAACTTTTGAA
157180 CAGTCCAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
59 2 0.03
60 45 0.73
61 11 0.18
62 4 0.06
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.39
Consensus pattern (62 bp):
TAAACTTTTGAAAATGTTCAAATTTCATCCCTAAAATATGAGCATCATTCTAAATTAGTCCC
Found at i:158818 original size:19 final size:19
Alignment explanation
Indices: 158794--158853 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
158784 AAACATAGTG
158794 AAAAAAAGTACAAATAAAC
1 AAAAAAAGTACAAATAAAC
***
158813 AAAAAAA--AC--ATAGTG
1 AAAAAAAGTACAAATAAAC
158828 AAAAAAAGTACAAATAAAC
1 AAAAAAAGTACAAATAAAC
158847 AAAAAAA
1 AAAAAAA
158854 ACGTAGTGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
15 10 0.32
17 4 0.13
19 17 0.55
ACGTcount: A:0.75, C:0.08, G:0.07, T:0.10
Consensus pattern (19 bp):
AAAAAAAGTACAAATAAAC
Found at i:158850 original size:17 final size:17
Alignment explanation
Indices: 158796--158851 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
158786 ACATAGTGAA
158796 AAAAAGTACAAATAAAC
1 AAAAAGTACAAATAAAC
** * *
158813 AAAAAAAACATAGTGAA-
1 AAAAAGTACA-AATAAAC
158830 AAAAAGTACAAATAAAC
1 AAAAAGTACAAATAAAC
158847 AAAAA
1 AAAAA
158852 AAACGTAGTG
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
16 4 0.14
17 21 0.72
18 4 0.14
ACGTcount: A:0.73, C:0.09, G:0.07, T:0.11
Consensus pattern (17 bp):
AAAAAGTACAAATAAAC
Found at i:158851 original size:33 final size:34
Alignment explanation
Indices: 158784--158879 Score: 149
Period size: 34 Copynumber: 2.8 Consensus size: 34
158774 AAACACTCAT
158784 AAACATAGTGAAAAAAAGTACAAATAAACAAAAA
1 AAACATAGTGAAAAAAAGTACAAATAAACAAAAA
158818 AAACATAGTGAAAAAAAGTACAAATAAACAAAAA
1 AAACATAGTGAAAAAAAGTACAAATAAACAAAAA
* * *
158852 AAACGTAGTG-ATAAGAGTACAAACTAAA
1 AAACATAGTGAAAAAAAGTACAAA-TAAA
158880 AACAGAAGAA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 11 0.19
34 47 0.81
ACGTcount: A:0.66, C:0.09, G:0.11, T:0.14
Consensus pattern (34 bp):
AAACATAGTGAAAAAAAGTACAAATAAACAAAAA
Found at i:159724 original size:31 final size:30
Alignment explanation
Indices: 159653--159730 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
159643 ATTTTTTATT
*
159653 TAAGTACCTAAAG-TGTTTTTTGATCAAAA
1 TAAGTACCTAAAGTTATTTTTTGATCAAAA
* * *
159682 TAATTATCTAAAGTTATATTTTTGGTCAAAA
1 TAAGTACCTAAAGTTAT-TTTTTGATCAAAA
*
159713 TAGGTACCTAAAG-TATTT
1 TAAGTACCTAAAGTTATTT
159731 GATTTTTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 13 0.32
30 5 0.12
31 22 0.55
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (30 bp):
TAAGTACCTAAAGTTATTTTTTGATCAAAA
Found at i:159888 original size:30 final size:30
Alignment explanation
Indices: 159821--159889 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
159811 TCAAATAGAA
* * *
159821 AGGTACCTATTTTGACAAAAAAAAAACTTT
1 AGGTACTTATTTTGACAAAAAAAAAACCTC
* *
159851 AGATACTTATTTTGACAAAAAAAATACCTC
1 AGGTACTTATTTTGACAAAAAAAAAACCTC
159881 AGGTACTTA
1 AGGTACTTA
159890 AACTAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.30
Consensus pattern (30 bp):
AGGTACTTATTTTGACAAAAAAAAAACCTC
Found at i:164742 original size:35 final size:35
Alignment explanation
Indices: 164703--164814 Score: 170
Period size: 35 Copynumber: 3.2 Consensus size: 35
164693 AAAACAGTCC
*
164703 TCAATTTCATTCTAAACCCCAATTTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
164738 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
** * *
164773 TCAATTAAATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
164808 TCAATTT
1 TCAATTT
164815 AAGGTTTAGA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 69 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:166617 original size:35 final size:35
Alignment explanation
Indices: 166577--166685 Score: 155
Period size: 35 Copynumber: 3.1 Consensus size: 35
166567 TCTAAACCTT
** *
166577 AAATTGAAGAATTTTAGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* *
166612 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* *
166647 AAATTGAATTAGTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
166682 AAAT
1 AAAT
166686 CGAGGACTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.36, C:0.00, G:0.25, T:0.39
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
Found at i:174972 original size:6 final size:7
Alignment explanation
Indices: 174956--174980 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
174946 TTCATATTAA
174956 TTTTGAT
1 TTTTGAT
174963 TTTTGAT
1 TTTTGAT
174970 TTTTGAT
1 TTTTGAT
174977 TTTT
1 TTTT
174981 AAATTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (7 bp):
TTTTGAT
Found at i:180979 original size:11 final size:11
Alignment explanation
Indices: 180965--181022 Score: 82
Period size: 11 Copynumber: 5.4 Consensus size: 11
180955 TGTTAGAGTA
180965 TTATTAGTTTG
1 TTATTAGTTTG
180976 TTATTAGTTTG
1 TTATTAGTTTG
* *
180987 TTA-TGGGTTG
1 TTATTAGTTTG
*
180997 TTATTAGTTGG
1 TTATTAGTTTG
181008 TTATTAGTTTG
1 TTATTAGTTTG
181019 TTAT
1 TTAT
181023 GTTGGTTGCT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
10 8 0.20
11 32 0.80
ACGTcount: A:0.17, C:0.00, G:0.22, T:0.60
Consensus pattern (11 bp):
TTATTAGTTTG
Found at i:182762 original size:11 final size:11
Alignment explanation
Indices: 182748--182805 Score: 73
Period size: 11 Copynumber: 5.4 Consensus size: 11
182738 TGTTAGAGTA
182748 TTATTAGTTTG
1 TTATTAGTTTG
182759 TTATTAGTTTG
1 TTATTAGTTTG
* *
182770 TTA-TGGGTTG
1 TTATTAGTTTG
* *
182780 TTATTAGCTGG
1 TTATTAGTTTG
182791 TTATTAGTTTG
1 TTATTAGTTTG
182802 TTAT
1 TTAT
182806 GTTGGTTACT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
10 8 0.21
11 31 0.79
ACGTcount: A:0.17, C:0.02, G:0.22, T:0.59
Consensus pattern (11 bp):
TTATTAGTTTG
Found at i:191573 original size:16 final size:16
Alignment explanation
Indices: 191549--191581 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
191539 CACCCGACAC
191549 AGAGAAAGAGGGAAAG
1 AGAGAAAGAGGGAAAG
*
191565 AGAGGAAGAGGGAAAG
1 AGAGAAAGAGGGAAAG
191581 A
1 A
191582 CTGCCCACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (16 bp):
AGAGAAAGAGGGAAAG
Found at i:198449 original size:174 final size:183
Alignment explanation
Indices: 198220--198596 Score: 496
Period size: 184 Copynumber: 2.1 Consensus size: 183
198210 TTTTCTAATT
*
198220 TATATAA-AAATTAA-ATATTTTTAAATTCAAAAAAAGTTTATAATTAATTTAAAT-A-ATA-AA
1 TATATAATATATTAATAT-TTTTTAAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAA
** *
198280 -T-CAAAAT-AAAATTTTAGATAAATTTTTTAATTAATT-A-A-TGCTTTAAGTTTAAAAGTTAT
65 TTACAAAATAAAAAAATTAGAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
* *
198339 TGGATCTTAAATTATT-ATTGGG-TTTTAATGGTTTGAGCTT-AGCCCATATGTTA
129 TGGATCTTAAAGTATTAATTGGGTTTTTAATGATTTG-GCTTAAGCCCATATGTTA
* *
198392 TATATAATATATTAATATTTTTTTAATT-AAAAAACATTTTAATAATTAATTTAAATAATATATA
1 TATATAATATATTAATATTTTTTAAATTCAAAAAA-AGTTT-ATAATTAATTTAAATAATATATA
* *
198456 ATTATAAAATAAAAAAATTATATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
64 ATTACAAAATAAAAAAATTAGATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
*
198521 TGGATCTTAAAGTATTAATTGGGTTTTTAATGATTTGGGTTAAGCCCATATGTTA
129 TGGATCTTAAAGTATTAATTGGGTTTTTAATGATTTGGCTTAAGCCCATATGTTA
198576 TATATAATATATTTAATATTT
1 TATATAATATA-TTAATATTT
198597 AAAATTTAAT
Statistics
Matches: 177, Mismatches: 11, Indels: 21
0.85 0.05 0.10
Matches are distributed among these distances:
172 13 0.07
173 19 0.11
174 17 0.10
175 1 0.01
176 3 0.02
177 2 0.01
178 1 0.01
179 21 0.12
180 10 0.06
181 1 0.01
182 35 0.20
183 9 0.05
184 36 0.20
185 9 0.05
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (183 bp):
TATATAATATATTAATATTTTTTAAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
TACAAAATAAAAAAATTAGATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTG
GATCTTAAAGTATTAATTGGGTTTTTAATGATTTGGCTTAAGCCCATATGTTA
Found at i:201174 original size:25 final size:25
Alignment explanation
Indices: 201140--201189 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
201130 CAAAACCAAC
201140 GAAGAAATGGCGACGCTATCAGTGG
1 GAAGAAATGGCGACGCTATCAGTGG
201165 GAAGAAATGGCGACGCTATCAGTGG
1 GAAGAAATGGCGACGCTATCAGTGG
201190 ACATCGCCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (25 bp):
GAAGAAATGGCGACGCTATCAGTGG
Found at i:204288 original size:18 final size:18
Alignment explanation
Indices: 204265--204305 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
204255 AAAGATCATG
204265 ATCATGATCATGACCACA
1 ATCATGATCATGACCACA
* *
204283 ATCATGATCATGGCCACG
1 ATCATGATCATGACCACA
204301 ATCAT
1 ATCAT
204306 CACCATCATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (18 bp):
ATCATGATCATGACCACA
Found at i:206380 original size:2 final size:2
Alignment explanation
Indices: 206337--206364 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
206327 AGCTTTACGA
206337 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
206365 TGATTAAACC
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:206693 original size:17 final size:15
Alignment explanation
Indices: 206653--206699 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
206643 AAATAATATA
206653 TTAAAATTAAATTTT
1 TTAAAATTAAATTTT
*
206668 TTAAAATTAATTTTT
1 TTAAAATTAAATTTT
206683 TTATAATATTAACATTT
1 TTA-AA-ATTAA-ATTT
206700 ATATGTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 17 0.63
16 2 0.07
17 5 0.19
18 3 0.11
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAAAATTAAATTTT
Found at i:210097 original size:31 final size:31
Alignment explanation
Indices: 210059--210181 Score: 212
Period size: 31 Copynumber: 4.0 Consensus size: 31
210049 GGGTCGAGGG
210059 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
210090 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
210121 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
210152 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
210182 GTCCTTCGGG
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:212628 original size:12 final size:12
Alignment explanation
Indices: 212613--212639 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
212603 ACCAGCAATG
212613 TCACCAACATTA
1 TCACCAACATTA
212625 TCACCAACATTA
1 TCACCAACATTA
212637 TCA
1 TCA
212640 GCAATGACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.26
Consensus pattern (12 bp):
TCACCAACATTA
Found at i:216614 original size:19 final size:19
Alignment explanation
Indices: 216590--216628 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
216580 TAATATTAAA
216590 AATTATAAAATAATATTTT
1 AATTATAAAATAATATTTT
* *
216609 AATTATAAATTACTATTTT
1 AATTATAAAATAATATTTT
216628 A
1 A
216629 TTGAGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTATAAAATAATATTTT
Found at i:220306 original size:17 final size:17
Alignment explanation
Indices: 220275--220307 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
220265 AAATATTATT
220275 TTATTATTTATTTTAAA
1 TTATTATTTATTTTAAA
220292 TTATT-TTTATATTTAA
1 TTATTATTTAT-TTTAA
220308 TAATATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTATTTATTTTAAA
Found at i:220363 original size:21 final size:19
Alignment explanation
Indices: 220333--220372 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 19
220323 TTTATGTCAT
220333 ATAAAAATAATAATAAAATA
1 ATAAAAATAATAA-AAAATA
220353 ATAAAGAATAATAAAAAATA
1 ATAAA-AATAATAAAAAATA
220373 TTTAATGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (19 bp):
ATAAAAATAATAAAAAATA
Found at i:224303 original size:24 final size:24
Alignment explanation
Indices: 224276--224325 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
224266 ACAAATGTTT
224276 TAGGTGGATGAACTTCTTGTGCGG
1 TAGGTGGATGAACTTCTTGTGCGG
224300 TAGGTGGATGAACTTCTTGTGCGG
1 TAGGTGGATGAACTTCTTGTGCGG
224324 TA
1 TA
224326 AATTCAAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.18, C:0.12, G:0.36, T:0.34
Consensus pattern (24 bp):
TAGGTGGATGAACTTCTTGTGCGG
Found at i:226035 original size:14 final size:14
Alignment explanation
Indices: 226016--226050 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
226006 AATTATTGAA
226016 TAAAGACGGTTCCC
1 TAAAGACGGTTCCC
*
226030 TAAAGAAGGTTCCC
1 TAAAGACGGTTCCC
*
226044 TAGAGAC
1 TAAAGAC
226051 TATTCATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (14 bp):
TAAAGACGGTTCCC
Found at i:235753 original size:26 final size:26
Alignment explanation
Indices: 235724--235789 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
235714 TTAACAAAAT
235724 ATATTTTTACATAAAAATAA-AATAAA
1 ATATTTTTA-ATAAAAATAATAATAAA
* **
235750 ATATTTTTAAATTAAGTTAATAATAAA
1 ATATTTTT-AATAAAAATAATAATAAA
*
235777 ATATATTTAATAA
1 ATATTTTTAATAA
235790 GTTAATATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
26 19 0.58
27 14 0.42
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (26 bp):
ATATTTTTAATAAAAATAATAATAAA
Found at i:235796 original size:25 final size:27
Alignment explanation
Indices: 235744--235809 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 27
235734 ATAAAAATAA
*
235744 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATATTTAAATTAAGTTAAT
235771 AATAAAATATATTT-AA-TAAGTTAAT
1 AATAAAATATATTTAAATTAAGTTAAT
235796 ATATATAAATATAT
1 A-ATA-AAATATAT
235810 GAATTTAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
25 10 0.28
26 5 0.14
27 21 0.58
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (27 bp):
AATAAAATATATTTAAATTAAGTTAAT
Done.