Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014285.1 Kokia drynarioides strain JFW-HI SEQ_129318, 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: 377859
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 116 characters in sequence are not A, C, G, or T
Found at i:3109 original size:96 final size:96
Alignment explanation
Indices: 2935--3120 Score: 234
Period size: 96 Copynumber: 1.9 Consensus size: 96
2925 TTTTTCGGGA
* * * *
2935 AAGGATATTCGATTATCCCAATTTGAAAAAAGGTTGCACCTAGTGAGTTAAGGCGCAATATTTCA
1 AAGGATATTCAATTATCCCAATTTGAAAAAAGATTACACCTAGTGAGTTAAGGCGAAATATTTCA
*
3000 GAATCGAAGATAAGAAAACATTGCCTCGGTT
66 AAATCGAAGATAAGAAAACATTGCCTCGGTT
* **
3031 AAGGGTATTCAATTATTTCAATTTGAAGAAAA-ATTACACCTAGTGAGTTAAGGCGTAAAT-TTT
1 AAGGATATTCAATTATCCCAATTTGAA-AAAAGATTACACCTAGTGAGTTAAGGCG-AAATATTT
* *
3094 CAAAATCCGAA-ATAAGAGAATATTGCC
64 CAAAAT-CGAAGATAAGAAAACATTGCC
3121 CTGATTTTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
96 66 0.86
97 11 0.14
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (96 bp):
AAGGATATTCAATTATCCCAATTTGAAAAAAGATTACACCTAGTGAGTTAAGGCGAAATATTTCA
AAATCGAAGATAAGAAAACATTGCCTCGGTT
Found at i:3381 original size:29 final size:28
Alignment explanation
Indices: 3348--3705 Score: 206
Period size: 30 Copynumber: 12.2 Consensus size: 28
3338 GCATGAGGGG
* * **
3348 CAAAATGGTAGTTTTGGAAGGTTCGAAAT
1 CAAAATGGGATTTTTGGAA-GTTCGAGGT
3377 CAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 C-AAAATGGGATTTTTGGAAGTTCGA-GGT
* * * *
3407 -AAAATGGTAATTTTAGAAAGGTTCGGGGT
1 CAAAATGG-GATTTTTGGAA-GTTCGAGGT
3436 CAAAATGGGATTTTTGGAAGTTCGAGGGT
1 CAAAATGGGATTTTTGGAAGTTCGA-GGT
* * *
3465 -AAATATGGTAATTTTTAGAAGGTTCGGGGTT
1 CAAA-ATGG-GATTTTTGGAA-GTTCGAGG-T
* * *
3496 AAAAATGGGATTTTTGGAAGTTTAGGGGT
1 CAAAATGGGATTTTTGGAAG-TTCGAGGT
* * **
3525 -AAAATGGTAATTTTGGAAAGTTTAAGGT
1 CAAAATGGGATTTTTGG-AAGTTCGAGGT
* * * *
3553 CGAAAATTGGATTTTTTGAAATTCAGGGGT
1 C-AAAATGGGATTTTTGGAAGTTC-GAGGT
* *
3583 -AAAATGGTAATTTTTGGAGAGTTCGACGT
1 CAAAATGG-GATTTTTGGA-AGTTCGAGGT
*
3612 CAAAAATGGGATTTTTGGAAGTTCAGGGGT
1 C-AAAATGGGATTTTTGGAAGTTC-GAGGT
** * *
3642 -AAAATTGTAATTTTTAGAGAGTTCGGGGT
1 CAAAA-TGGGATTTTTGGA-AGTTCGAGGT
* *
3671 CAAAAATGGGATTATTGGAAGTTCGGGGT
1 C-AAAATGGGATTTTTGGAAGTTCGAGGT
3700 -AAAATG
1 CAAAATG
3706 CTAATTTTTG
Statistics
Matches: 257, Mismatches: 47, Indels: 52
0.72 0.13 0.15
Matches are distributed among these distances:
27 6 0.02
28 44 0.17
29 83 0.32
30 100 0.39
31 21 0.08
32 3 0.01
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (28 bp):
CAAAATGGGATTTTTGGAAGTTCGAGGT
Found at i:3445 original size:58 final size:60
Alignment explanation
Indices: 3342--3713 Score: 401
Period size: 59 Copynumber: 6.3 Consensus size: 60
3332 TCGAATGCAT
* * * ***
3342 GAGGGGCAAAATGGTAGTTTT-GGAAGGTTCGAAATCAAAAATGGGATTTTTGGAAGTTC
1 GAGGGGTAAAATGGTAATTTTAGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC
3401 GA-GGGTAAAATGGTAATTTTAGAAAGGTTCGGGGTC-AAAATGGGATTTTTGGAAGTTC
1 GAGGGGTAAAATGGTAATTTTAGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC
*
3459 GA-GGGTAAATATGGTAATTTTTAG-AAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTT-
1 GAGGGGTAAA-ATGGTAA-TTTTAGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC
* * *** * * * *
3518 TAGGGGTAAAATGGTAATTTTGGAAA-GTTTAAGGTCGAAAATTGGATTTTTTGAAATTC
1 GAGGGGTAAAATGGTAATTTTAGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC
* * **
3577 -AGGGGTAAAATGGTAATTTTTG-GAGAGTTCGACGTCAAAAATGGGATTTTTGGAAGTTC
1 GAGGGGTAAAATGGTAATTTTAGAAAG-GTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC
* * *
3636 -AGGGGTAAAATTGTAATTTTTAGAGA-GTTCGGGGTCAAAAATGGGATTATTGGAAGTTC
1 GAGGGGTAAAATGGTAA-TTTTAGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC
*
3695 --GGGGTAAAATGCTAATTTT
1 GAGGGGTAAAATGGTAATTTT
3714 TGGAAAGTTT
Statistics
Matches: 269, Mismatches: 33, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
57 5 0.02
58 110 0.41
59 113 0.42
60 39 0.14
61 2 0.01
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (60 bp):
GAGGGGTAAAATGGTAATTTTAGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC
Found at i:3654 original size:176 final size:175
Alignment explanation
Indices: 3343--3727 Score: 494
Period size: 176 Copynumber: 2.2 Consensus size: 175
3333 CGAATGCATG
* * * * * *
3343 AGGGGCAAAATGGTAGTTTTGGAAGGTTCGAA-ATCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AGGGGTAAAATGGTAATTTTGGAAAGTT-TAAGGTCAAAAATGGGATTTTTGGAAATTCGAGGGT
**
3407 AAAATGGTAATTTTAGAAAGGTTCGGGGTCAAAATGGGATTTTTGGAAGTTCGAGGGTAAATATG
65 AAAATGGTAATTTTAGAAAGGTTCGACGTCAAAATGGGATTTTTGGAAGTTCGAGGGTAAATATG
* *
3472 GTAATTTTTAGA-AGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTT
130 GTAATTTTTAGAGA-GTTCGGGGTCAAAAATGGGATTATTGGAAG-TT
* * *
3519 AGGGGTAAAATGGTAATTTTGGAAAGTTTAAGGTCGAAAATTGGATTTTTTGAAATTC-AGGGGT
1 AGGGGTAAAATGGTAATTTTGGAAAGTTTAAGGTCAAAAATGGGATTTTTGGAAATTCGA-GGGT
* *
3583 AAAATGGTAATTTTTG-GAGAGTTCGACGTCAAAAATGGGATTTTTGGAAGTTC-AGGGGTAAA-
65 AAAATGGTAATTTTAGAAAG-GTTCGACGTC-AAAATGGGATTTTTGGAAGTTCGA-GGGTAAAT
*
3645 ATTGTAATTTTTAGAGAGTTCGGGGTCAAAAATGGGATTATTGGAAGTT
127 ATGGTAATTTTTAGAGAGTTCGGGGTCAAAAATGGGATTATTGGAAGTT
* *
3694 CGGGGTAAAATGCTAATTTTTGGAAAGTTTAAGG
1 AGGGGTAAAATGGTAA-TTTTGGAAAGTTTAAGG
3728 ACCTCCGGAG
Statistics
Matches: 184, Mismatches: 18, Indels: 14
0.85 0.08 0.06
Matches are distributed among these distances:
175 21 0.11
176 133 0.72
177 30 0.16
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (175 bp):
AGGGGTAAAATGGTAATTTTGGAAAGTTTAAGGTCAAAAATGGGATTTTTGGAAATTCGAGGGTA
AAATGGTAATTTTAGAAAGGTTCGACGTCAAAATGGGATTTTTGGAAGTTCGAGGGTAAATATGG
TAATTTTTAGAGAGTTCGGGGTCAAAAATGGGATTATTGGAAGTT
Found at i:4820 original size:33 final size:32
Alignment explanation
Indices: 4762--4832 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 32
4752 AATGCCTTTT
*
4762 TTATTATTAATGATTTTTTTTAAAAGATATTA
1 TTATTATTAATGATTTTTTTTAAAAGAAATTA
*
4794 TTATTATT-ATTATTATTGTTTTAAAAGAAATTA
1 TTATTATTAATGATT-TT-TTTTAAAAGAAATTA
4827 TTATTA
1 TTATTA
4833 ATAAATATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
31 5 0.14
32 10 0.29
33 20 0.57
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (32 bp):
TTATTATTAATGATTTTTTTTAAAAGAAATTA
Found at i:4890 original size:24 final size:23
Alignment explanation
Indices: 4857--4903 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
4847 AAACCGCCCA
4857 CTTGTCATTAATGCC-ATTATTATT
1 CTTGTCATTAA--CCAATTATTATT
*
4881 CTTGTTATTAACCAATTATTATT
1 CTTGTCATTAACCAATTATTATT
4904 AATGATCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 9 0.43
24 10 0.48
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (23 bp):
CTTGTCATTAACCAATTATTATT
Found at i:5514 original size:17 final size:16
Alignment explanation
Indices: 5492--5554 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 16
5482 TGGACTTTTC
5492 TAAATTTAATTTTATAA
1 TAAATTTAATTTTA-AA
*
5509 TAAATTTAAATTTCAAA
1 TAAATTT-AATTTTAAA
* * *
5526 TTAACTTAAATTTAAAA
1 -TAAATTTAATTTTAAA
*
5543 TAAATTCAATTT
1 TAAATTTAATTT
5555 CCAACGGGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
16 10 0.26
17 17 0.45
18 11 0.29
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATTTAATTTTAAA
Found at i:15177 original size:18 final size:18
Alignment explanation
Indices: 15150--15190 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
15140 TTGCAATATA
15150 TTTC-TCTTCTTTTCTCT
1 TTTCTTCTTCTTTTCTCT
* *
15167 TTTCTTCTTCTTTTTTTT
1 TTTCTTCTTCTTTTCTCT
15185 TTTCTT
1 TTTCTT
15191 TTTGTGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTCTTCTTCTTTTCTCT
Found at i:23139 original size:22 final size:22
Alignment explanation
Indices: 23108--23161 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
23098 CAAATGATGA
* *
23108 TGTCGTGACAACCACGTATCTG
1 TGTCGCGACAACCACGTATCCG
*
23130 TGTCGCGACAACCATGTATCCG
1 TGTCGCGACAACCACGTATCCG
23152 TGTCGCGACA
1 TGTCGCGACA
23162 TAGGAGGCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.22, C:0.30, G:0.24, T:0.24
Consensus pattern (22 bp):
TGTCGCGACAACCACGTATCCG
Found at i:23987 original size:43 final size:43
Alignment explanation
Indices: 23937--24220 Score: 275
Period size: 43 Copynumber: 6.6 Consensus size: 43
23927 CTGGCATAAT
* *
23937 TATACTGGCACACAAAGTGCATCATCGAATATACCGAAGCAAC
1 TATACTGGCACACACAGTGCATCATCGAATATACCGAAGTAAC
**
23980 TGCACTGGCACACACAGTGCATCATCGAATATACCGAAGTAAC
1 TATACTGGCACACACAGTGCATCATCGAATATACCGAAGTAAC
* * *
24023 TATACTAGCACATACAGTGCATCATCGAATAAACCGAAGTAAC
1 TATACTGGCACACACAGTGCATCATCGAATATACCGAAGTAAC
* * * * ** *
24066 TATACTGGTACACACAGTGCATCAT-TAGATAAATCGAAAAAAA
1 TATACTGGCACACACAGTGCATCATCGA-ATATACCGAAGTAAC
* * * *
24109 TATACTAGCACACACAGTGCATCATC-AGATAAATCGAAGCAAC
1 TATACTGGCACACACAGTGCATCATCGA-ATATACCGAAGTAAC
* * ** * * * **
24152 TATACTGGCATACACTGCACATCATCGGATAAACCGAAGCAGT
1 TATACTGGCACACACAGTGCATCATCGAATATACCGAAGTAAC
* *
24195 TATACTAGCACACATAGTGCATCATC
1 TATACTGGCACACACAGTGCATCATC
24221 ATATAACCAA
Statistics
Matches: 201, Mismatches: 37, Indels: 6
0.82 0.15 0.02
Matches are distributed among these distances:
42 1 0.00
43 200 1.00
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.21
Consensus pattern (43 bp):
TATACTGGCACACACAGTGCATCATCGAATATACCGAAGTAAC
Found at i:24147 original size:129 final size:128
Alignment explanation
Indices: 23987--24219 Score: 308
Period size: 129 Copynumber: 1.8 Consensus size: 128
23977 AACTGCACTG
* * *
23987 GCACACACAGTGCATCATCGAATATACCGAAGTAACTATACTAGCACATACAGTG-CATCATCGA
1 GCACACACAGTGCATCATCGAATAAACCGAAGCAACTATACT-G-ACATACACTGACATCATCGA
* * *
24051 ATAAACCGAAGTAACTATACTGGTACACACAGTGCATCATTAGATAAATCGAAAAAAATATACTA
64 ATAAACCGAAGCAACTATACTAGCACACACAGTGCATCATTAGATAAATCGAAAAAAATATACTA
* * *
24116 GCACACACAGTGCATCATC-AGATAAATCGAAGCAACTATACTGGCATACACTGCACATCATCGG
1 GCACACACAGTGCATCATCGA-ATAAACCGAAGCAACTATACTGACATACACTG-ACATCATCGA
** *
24180 ATAAACCGAAGCAGTTATACTAGCACACATAGTGCATCAT
64 ATAAACCGAAGCAACTATACTAGCACACACAGTGCATCAT
24220 CATATAACCA
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
127 8 0.09
128 2 0.02
129 79 0.89
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (128 bp):
GCACACACAGTGCATCATCGAATAAACCGAAGCAACTATACTGACATACACTGACATCATCGAAT
AAACCGAAGCAACTATACTAGCACACACAGTGCATCATTAGATAAATCGAAAAAAATATACTA
Found at i:24221 original size:86 final size:86
Alignment explanation
Indices: 23909--24220 Score: 333
Period size: 86 Copynumber: 3.6 Consensus size: 86
23899 CTGACATGTA
* * * * *
23909 AGTGCATCATCGGATGAACTG--GCATAATTATACTGGCACACAAAGTGCATCATCGAATATACC
1 AGTGCATCATCGGATAAACCGAAG-A-AATTATACTAGCACACACAGTGCATCATCGAATAAACC
**
23972 GAAGCAACTGCACTGGCACACAC
64 GAAGCAACTATACTGGCACACAC
* * * * *
23995 AGTGCATCATCGAATATACCGAAGTAACTATACTAGCACATACAGTGCATCATCGAATAAACCGA
1 AGTGCATCATCGGATAAACCGAAGAAATTATACTAGCACACACAGTGCATCATCGAATAAACCGA
* *
24060 AGTAACTATACTGGTACACAC
66 AGCAACTATACTGGCACACAC
** * * * *
24081 AGTGCATCATTAGATAAATCGAAAAAAATATACTAGCACACACAGTGCATCATC-AGATAAATCG
1 AGTGCATCATCGGATAAACCGAAGAAATTATACTAGCACACACAGTGCATCATCGA-ATAAACCG
*
24145 AAGCAACTATACTGGCATACAC
65 AAGCAACTATACTGGCACACAC
* ** * * *
24167 TGCACATCATCGGATAAACCGAAGCAGTTATACTAGCACACATAGTGCATCATC
1 AGTGCATCATCGGATAAACCGAAGAAATTATACTAGCACACACAGTGCATCATC
24221 ATATAACCAA
Statistics
Matches: 185, Mismatches: 38, Indels: 6
0.81 0.17 0.03
Matches are distributed among these distances:
85 1 0.01
86 183 0.99
88 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (86 bp):
AGTGCATCATCGGATAAACCGAAGAAATTATACTAGCACACACAGTGCATCATCGAATAAACCGA
AGCAACTATACTGGCACACAC
Found at i:27944 original size:6 final size:6
Alignment explanation
Indices: 27935--27966 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
27925 TCTTTTTCTT
27935 TTCATA TTCATA TTCATA TTCATA TTCATA TT
1 TTCATA TTCATA TTCATA TTCATA TTCATA TT
27967 ATTATTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.16, G:0.00, T:0.53
Consensus pattern (6 bp):
TTCATA
Found at i:27971 original size:3 final size:3
Alignment explanation
Indices: 27963--27999 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
27953 TTCATATTCA
*
27963 TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
28000 GCTTCAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:27972 original size:12 final size:12
Alignment explanation
Indices: 27935--27996 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
27925 TCTTTTTCTT
27935 TTCATATTCA-TA
1 TTCATATT-ATTA
27947 TTCATATTCA-TA
1 TTCATATT-ATTA
27959 TTCATATTATTA
1 TTCATATTATTA
27971 TT-ATTATTATTA
1 TTCA-TATTATTA
**
27983 TTGTTATTATTA
1 TTCATATTATTA
27995 TT
1 TT
27997 ATTGCTTCAA
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
11 2 0.04
12 44 0.96
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.60
Consensus pattern (12 bp):
TTCATATTATTA
Found at i:27978 original size:18 final size:18
Alignment explanation
Indices: 27939--27996 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
27929 TTTCTTTTCA
27939 TATTCATATTCA-TATTCA-
1 TATTCATATT-ATTATT-AT
27957 TATTCATATTATTATTAT
1 TATTCATATTATTATTAT
*
27975 TATT-ATTATTGTTATTAT
1 TATTCA-TATTATTATTAT
27993 TATT
1 TATT
27997 ATTGCTTCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
17 3 0.08
18 33 0.92
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (18 bp):
TATTCATATTATTATTAT
Found at i:30464 original size:183 final size:183
Alignment explanation
Indices: 30127--30518 Score: 476
Period size: 182 Copynumber: 2.1 Consensus size: 183
30117 ATTAAATGAT
* * *
30127 ACATCTATTACTATATTTAAGTGTTAGATTGATTTGGCGTCATCCACAACTCAATTATCAACTCA
1 ACATCTATTA-TATATTTAAGTATTAGATTGATTCGGCGTCATCCACAACTCAATTACCAACTCA
* * * * *
30192 GAAATAAATTTATTAAAAGTCGCTGACCTTAATAAGCAATAGATATTATTTTGATAGCACTTTTG
65 GAAAAAAATTTATCAAAAGTCGCTGACCTTAATAAGCAATAGATATTATTTTGACAGCAATTTTA
* **
30257 TCTTTTGAAATAAAATCTAGAAAAATACTTATGCATAAT-G-TTTGAATCCAAA
130 TCTTTTCAAATAAAATCTAGAAAAATACTTACCCATAATGGATTTGAATCCAAA
* * *
30309 ACATCTATTAGTATATTTAAGTATTAGATTGATTCGGTGTCA-CTCACAAC-CTAGTTACCAATT
1 ACATCTATTA-TATATTTAAGTATTAGATTGATTCGGCGTCATC-CACAACTC-AATTACCAACT
* *
30372 CA-AAAAAGAATTTATCAAAAG-C-CT-ACATTTAATAAGAAGCAATAGATATTATTTTGACAGT
63 CAGAAAAA-AATTTATCAAAAGTCGCTGAC-CTTAAT---AAGCAATAGATATTATTTTGACAGC
30433 AATTTTATCTTTTCAAATAAAATCTAGAAAAATACTTACCCATAATGGGATTTGAATCCAAA
123 AATTTTATCTTTTCAAATAAAATCTAGAAAAATACTTACCCATAAT-GGATTTGAATCCAAA
* *
30495 ACATATATTACATATTTAAGTATT
1 ACATCTATTATATATTTAAGTATT
30519 TTATTGAGTT
Statistics
Matches: 181, Mismatches: 19, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
179 2 0.01
180 7 0.04
181 7 0.04
182 66 0.36
183 64 0.35
185 14 0.08
186 21 0.12
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.36
Consensus pattern (183 bp):
ACATCTATTATATATTTAAGTATTAGATTGATTCGGCGTCATCCACAACTCAATTACCAACTCAG
AAAAAAATTTATCAAAAGTCGCTGACCTTAATAAGCAATAGATATTATTTTGACAGCAATTTTAT
CTTTTCAAATAAAATCTAGAAAAATACTTACCCATAATGGATTTGAATCCAAA
Found at i:33012 original size:20 final size:19
Alignment explanation
Indices: 32962--33017 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
32952 TAGTCAAAAA
*
32962 TTGTTATTTTCTTATTTTTG
1 TTGTTATTTTCTT-TTTTAG
* *
32982 TTTTTATTTTTATTTTTTAAG
1 TTGTTA-TTTTCTTTTTT-AG
33003 TTGTTATTTTCTTTT
1 TTGTTATTTTCTTTT
33018 GACTAAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.12, C:0.04, G:0.07, T:0.77
Consensus pattern (19 bp):
TTGTTATTTTCTTTTTTAG
Found at i:38322 original size:2 final size:2
Alignment explanation
Indices: 38315--38340 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38305 AAAATACACT
38315 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
38341 ACAATTTCCA
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:46129 original size:27 final size:27
Alignment explanation
Indices: 46091--46145 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
46081 ATCACTATCA
*
46091 CTATCTCCCTCTGGAACAGCTTCCTCC
1 CTATCTCCCTCTAGAACAGCTTCCTCC
*
46118 CTATTTCCCTCTAGAACAGCTTCCTCC
1 CTATCTCCCTCTAGAACAGCTTCCTCC
46145 C
1 C
46146 CTCCCTCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.16, C:0.44, G:0.09, T:0.31
Consensus pattern (27 bp):
CTATCTCCCTCTAGAACAGCTTCCTCC
Found at i:49767 original size:60 final size:60
Alignment explanation
Indices: 49670--49813 Score: 191
Period size: 60 Copynumber: 2.4 Consensus size: 60
49660 TCGTATTTGT
* * * * * *
49670 TACTCACGATGACACCA-AGTCATTGGACCGTTGTTTCGCATTGGAATTCATTTCATTTCA
1 TACTCACGATGTCA-TATAGTCATCGGACCCTTGTTTCGCATTGGAACTCATTTCATTTAA
* *
49730 TACTCATGATGTCATATAGTCATCGGACCCTTTTTTCGCATTGGAACTCATTTCATTTAA
1 TACTCACGATGTCATATAGTCATCGGACCCTTGTTTCGCATTGGAACTCATTTCATTTAA
*
49790 TACTCACGATGTTATATAGTCATC
1 TACTCACGATGTCATATAGTCATC
49814 AACCTCTTGT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
59 1 0.01
60 72 0.99
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (60 bp):
TACTCACGATGTCATATAGTCATCGGACCCTTGTTTCGCATTGGAACTCATTTCATTTAA
Found at i:49904 original size:51 final size:51
Alignment explanation
Indices: 49806--50026 Score: 241
Period size: 51 Copynumber: 4.3 Consensus size: 51
49796 CGATGTTATA
** * * * *
49806 TAGTCATC-AACCTCTTGTTCCATATAGGAATTCATATACTCATGATGACACA
1 TAGTCATCGAACCT-TTAATCCATAAAGG-ATTCATTTACTCACGATGACACT
* * * *
49858 AAGTCATCGAACCCTTAATCCATCATGGATTCATTTACTCACGATGACACT
1 TAGTCATCGAACCTTTAATCCATAAAGGATTCATTTACTCACGATGACACT
*
49909 TAGTCATCGTACCTTTAAT-CAGTAAAGGATTCATTTACTCACGATGACACT
1 TAGTCATCGAACCTTTAATCCA-TAAAGGATTCATTTACTCACGATGACACT
* * * *
49960 TAGTCATC-AGACCTTTAATCCGTAAAGGATTCATTTTCTCACAAAGACACT
1 TAGTCATCGA-ACCTTTAATCCATAAAGGATTCATTTACTCACGATGACACT
*
50011 TAGTCATCGGACCTTT
1 TAGTCATCGAACCTTT
50027 TCGTTTATAG
Statistics
Matches: 143, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
50 2 0.01
51 120 0.84
52 17 0.12
53 4 0.03
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (51 bp):
TAGTCATCGAACCTTTAATCCATAAAGGATTCATTTACTCACGATGACACT
Found at i:57168 original size:51 final size:51
Alignment explanation
Indices: 57099--57290 Score: 278
Period size: 51 Copynumber: 3.8 Consensus size: 51
57089 TCGTATAGGA
* * * * * *
57099 ATTCATATACTCACGATGACA-TAAAGTCATCGGACCCTTAATCCATCATGG
1 ATTCATTTACTCATGATGACACT-TAGTCATCGGACCTTTAATCCATAAAGG
*
57150 ATTCATTTACTCATGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
1 ATTCATTTACTCATGATGACACTTAGTCATCGGACCTTTAATCCATAAAGG
* *
57201 ATTCATTTACTCATGATGACACTTAGTCATCAGACCTTTAATTCATAAAGG
1 ATTCATTTACTCATGATGACACTTAGTCATCGGACCTTTAATCCATAAAGG
*
57252 ATTCATTTACTCATGATGACACTTAGTCATCGTACCTTT
1 ATTCATTTACTCATGATGACACTTAGTCATCGGACCTTT
57291 TCATTTATAG
Statistics
Matches: 128, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
51 127 0.99
52 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (51 bp):
ATTCATTTACTCATGATGACACTTAGTCATCGGACCTTTAATCCATAAAGG
Found at i:59408 original size:88 final size:88
Alignment explanation
Indices: 59295--59471 Score: 311
Period size: 88 Copynumber: 2.0 Consensus size: 88
59285 TATCGATAGA
*
59295 AGCATGACATGTTTCGATAGAAGTCATACTTGTATCGGTAGTATTGTTTCAAGTACCAGG-AGAA
1 AGCATGACATGTTCCGATAGAAGTCATACTTGTATCGGTAGTATTGTTTCAAGTACC-GGTAGAA
*
59359 GTCTGCACTATTCTTGAACTGTTT
65 GTCTACACTATTCTTGAACTGTTT
*
59383 AGCATGACATGTTCCGGTAGAAGTCATACTTGTATCGGTAGTATTGTTTCAAGTACCGGTAGAAG
1 AGCATGACATGTTCCGATAGAAGTCATACTTGTATCGGTAGTATTGTTTCAAGTACCGGTAGAAG
59448 TCTACACTATTCTTGAACTGTTT
66 TCTACACTATTCTTGAACTGTTT
59471 A
1 A
59472 TTGATTTGAA
Statistics
Matches: 85, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
87 2 0.02
88 83 0.98
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.35
Consensus pattern (88 bp):
AGCATGACATGTTCCGATAGAAGTCATACTTGTATCGGTAGTATTGTTTCAAGTACCGGTAGAAG
TCTACACTATTCTTGAACTGTTT
Found at i:61291 original size:138 final size:137
Alignment explanation
Indices: 61044--61309 Score: 399
Period size: 138 Copynumber: 1.9 Consensus size: 137
61034 TTAAACCTTC
*
61044 TCTTATTTCAAATTTTGTTAAACCATCTTTGATTTTTTTCTTTTTTCCAAAACCCTAAATAGCAT
1 TCTTATTTCAAATTTTGTTAAACCATCTTTGATTTTTTTCTTTTTTCCAAAACCCTAAATAGCAG
* * *
61109 CTACTTTATTACTAAATTTTATGGATTTCAAGTTCTTCCAGTCACGTGTTGTATATTGTTTTCAA
66 ATACTTTATTACTAAATTTTATGGATTTCAAGTTCTTCCAGTCACATGTTGTATAGTGTTTTCAA
61174 GTTCTTG
131 GTTCTTG
* * * * *
61181 TCTTATTTCAAATTTTTTTAAACCTTCTTTTATTTATTCTTTTTTTTTTCAAAACCCT-AATAGC
1 TCTTATTTCAAATTTTGTTAAACCATCTTTGATTT-TT-TTCTTTTTTCCAAAACCCTAAATAGC
* * *
61245 AGATACTTTCTTCCTAAATTTTATGGATTTTAAGTTCTTCCAGTCACATGTTGTATAGTGTTTTC
64 AGATACTTTATTACTAAATTTTATGGATTTCAAGTTCTTCCAGTCACATGTTGTATAGTGTTTTC
61310 TAGTACTAAA
Statistics
Matches: 115, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
137 32 0.28
138 66 0.57
139 17 0.15
ACGTcount: A:0.24, C:0.17, G:0.09, T:0.50
Consensus pattern (137 bp):
TCTTATTTCAAATTTTGTTAAACCATCTTTGATTTTTTTCTTTTTTCCAAAACCCTAAATAGCAG
ATACTTTATTACTAAATTTTATGGATTTCAAGTTCTTCCAGTCACATGTTGTATAGTGTTTTCAA
GTTCTTG
Found at i:62664 original size:25 final size:25
Alignment explanation
Indices: 62630--62681 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
62620 CTACTTCAAC
62630 TTAAAAACAAGCAAATTAATCCGTG
1 TTAAAAACAAGCAAATTAATCCGTG
62655 TTAAAAACAAGCAAATTAATCCGTG
1 TTAAAAACAAGCAAATTAATCCGTG
62680 TT
1 TT
62682 CTTTATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (25 bp):
TTAAAAACAAGCAAATTAATCCGTG
Found at i:85053 original size:16 final size:16
Alignment explanation
Indices: 85015--85045 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
85005 CATATATTAA
*
85015 AATAAATATATGATAG
1 AATAATTATATGATAG
85031 AATAATTATATGATA
1 AATAATTATATGATA
85046 AGTGAATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
AATAATTATATGATAG
Found at i:88139 original size:17 final size:17
Alignment explanation
Indices: 88119--88162 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
88109 AGGTTAACGA
*
88119 TTTATGGATTTAAACAT
1 TTTAGGGATTTAAACAT
* *
88136 TTTAGGGATTTCAATAT
1 TTTAGGGATTTAAACAT
88153 TTTAGGGATT
1 TTTAGGGATT
88163 CAAAGAAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.30, C:0.05, G:0.18, T:0.48
Consensus pattern (17 bp):
TTTAGGGATTTAAACAT
Found at i:88270 original size:16 final size:17
Alignment explanation
Indices: 88239--88272 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
88229 TGGATGTTAT
88239 GGATTTGAGAAATTTGG
1 GGATTTGAGAAATTTGG
*
88256 GGATTTTAG-AATTTGG
1 GGATTTGAGAAATTTGG
88272 G
1 G
88273 AAAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.38
Consensus pattern (17 bp):
GGATTTGAGAAATTTGG
Found at i:89523 original size:14 final size:15
Alignment explanation
Indices: 89504--89536 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
89494 TGTGAAAGCA
89504 TAAAAATAAAA-AAG
1 TAAAAATAAAATAAG
89518 TAAAAATAAAATAAG
1 TAAAAATAAAATAAG
89533 TAAA
1 TAAA
89537 TAAGAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (15 bp):
TAAAAATAAAATAAG
Found at i:120973 original size:17 final size:17
Alignment explanation
Indices: 120947--120985 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
120937 CCATTTTTAG
*
120947 ATTTATTTTAAG-TCTAA
1 ATTTAATTTAAGTTC-AA
120964 ATTTAATTTAAGTTCAA
1 ATTTAATTTAAGTTCAA
120981 ATTTA
1 ATTTA
120986 TTCTAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (17 bp):
ATTTAATTTAAGTTCAA
Found at i:122668 original size:29 final size:29
Alignment explanation
Indices: 122642--122967 Score: 256
Period size: 29 Copynumber: 11.2 Consensus size: 29
122632 CCATAATTGT
*
122642 ATTTTTATCC-TAAACTTCTCAAAAATTAC
1 ATTTTTACCCTTAAACTTCT-AAAAATTAC
* * * *
122671 AATTTTGCCCTTAAACTTCTTAGAAAGTAC
1 ATTTTTACCCTTAAACTTC-TAAAAATTAC
* * *
122701 ATTTTTACCCCTAAACTTTTCAAAATTAC
1 ATTTTTACCCTTAAACTTCTAAAAATTAC
* * *
122730 ATTTTTGCCCATAAACTTCTAAAAATTAT
1 ATTTTTACCCTTAAACTTCTAAAAATTAC
*
122759 ATTTTTACCCTTAAACTTCTTAAAATTAC
1 ATTTTTACCCTTAAACTTCTAAAAATTAC
* *
122788 A-TTTTGCCCCTAAACTTCTAAAAATTAC
1 ATTTTTACCCTTAAACTTCTAAAAATTAC
* *
122816 ATATTTT-CCCTCAAACTT-TCAAAAATCAC
1 AT-TTTTACCCTTAAACTTCT-AAAAATTAC
** * *
122845 ATTTTTACCCACGAAA-TTCGT-ACAATTAA
1 ATTTTTACCC-TTAAACTTC-TAAAAATTAC
* * *
122874 AATTTTACCCCTTAAACTTCCAAAAATCAC
1 ATTTTTA-CCCTTAAACTTCTAAAAATTAC
* *
122904 TTTTTTACCC-TAAACTTTCCT-AAAATGAC
1 ATTTTTACCCTTAAAC-TT-CTAAAAATTAC
*
122933 ATTTTTACCCCTAAAACTTTCT-AAAATTAC
1 ATTTTTA-CCCTTAAAC-TTCTAAAAATTAC
122963 ATTTT
1 ATTTT
122968 AACACTGAAC
Statistics
Matches: 235, Mismatches: 46, Indels: 31
0.75 0.15 0.10
Matches are distributed among these distances:
28 35 0.15
29 120 0.51
30 71 0.30
31 9 0.04
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (29 bp):
ATTTTTACCCTTAAACTTCTAAAAATTAC
Found at i:122959 original size:59 final size:58
Alignment explanation
Indices: 122652--122967 Score: 245
Period size: 59 Copynumber: 5.4 Consensus size: 58
122642 ATTTTTATCC
* * * * * *
122652 TAAACTTCTCAAAAATTACAATTTTGCCCTTAAACTTCTTAGAAAGTACATTTTTACCCC-
1 TAAACTT-TCTAAAATCACATTTTTACCC-TAAACTTC-TAAAAATTACATTTTTACCCCT
* * *
122712 TAAACTTT-TCAAAATTACATTTTTGCCCATAAACTTCTAAAAATTATATTTTTA-CCCT
1 TAAACTTTCT-AAAATCACATTTTTACCC-TAAACTTCTAAAAATTACATTTTTACCCCT
* **
122770 TAAAC-TTCTTAAAATTACATTTTGCCCCTAAACTTCTAAAAATTACATATTTT--CCCT
1 TAAACTTTC-TAAAATCACATTTTTACCCTAAACTTCTAAAAATTACAT-TTTTACCCCT
* * * * * *
122827 CAAACTTTCAAAAATCACATTTTTACCC-ACGAAATTCGT-ACAATTAAAATTTTACCCCT
1 TAAACTTTCTAAAATCACATTTTTACCCTA--AACTTC-TAAAAATTACATTTTTACCCCT
* * * *
122886 TAAACTTCCAAAAATCACTTTTTTACCCTAAACTTTCCT-AAAATGACATTTTTACCCCT
1 TAAACTTTCTAAAATCACATTTTTACCCTAAAC-TT-CTAAAAATTACATTTTTACCCCT
* *
122945 AAAACTTTCTAAAATTACATTTT
1 TAAACTTTCTAAAATCACATTTT
122968 AACACTGAAC
Statistics
Matches: 211, Mismatches: 31, Indels: 29
0.78 0.11 0.11
Matches are distributed among these distances:
56 1 0.00
57 51 0.24
58 56 0.27
59 94 0.45
60 9 0.04
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (58 bp):
TAAACTTTCTAAAATCACATTTTTACCCTAAACTTCTAAAAATTACATTTTTACCCCT
Found at i:134577 original size:39 final size:39
Alignment explanation
Indices: 134486--134812 Score: 241
Period size: 39 Copynumber: 8.4 Consensus size: 39
134476 TAAAGATTCC
* * * * * *
134486 AATCTTTTACCCCGACCATGGGGCAGATCACAATCATCT
1 AATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCA
** * * *
134525 GGTCTTTTTCCCCGAGCTTGGGGCAGATCATCATCAGCA
1 AATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCA
*
134564 AATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAGCA
1 AATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCA
* *
134603 AATCTCTTACCCCGAGCTTGGGGTAGATCATCATCAGCA
1 AATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCA
* * *
134642 AATCTCTTAGCTCGAGCCTGGGGCAGATTGCAACCATTC-G--
1 AATCTCTTACCCCGAGCTTGGGGCAGA-T-C-ACCA-TCAGCA
* * * * *
134682 -ATCTTTTACCTCGAGCTTCGGGTAGATCACCATTAGCA
1 AATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCA
* * * * * ***
134720 AATCTCTTACCCCGATCATGGGGCATATTA-CAGCTATTT
1 AATCTCTTACCCCGAGCTTGGGGCAGATCACCATC-AGCA
* * ** * * *
134759 GATCTTTTACCTTGAGCTTAGGGCAGATCATCATCAGTA
1 AATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCA
134798 AATCTCTTACCCCGA
1 AATCTCTTACCCCGA
134813 TCATAAGCTA
Statistics
Matches: 220, Mismatches: 58, Indels: 20
0.74 0.19 0.07
Matches are distributed among these distances:
35 1 0.00
36 5 0.02
37 1 0.00
38 3 0.01
39 199 0.90
40 4 0.02
41 1 0.00
42 4 0.02
43 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (39 bp):
AATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCA
Found at i:134658 original size:117 final size:116
Alignment explanation
Indices: 134537--134812 Score: 281
Period size: 117 Copynumber: 2.4 Consensus size: 116
134527 TCTTTTTCCC
*
134537 CGAGCTTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAGC
1 CGAGCTTGGGGCAGATCATCATCAG-AAATCTCTTACCCCGAGCTTCGGGCAGATCACCATTAGC
* * * *
134602 AAATCTCTTACCCCGAGCTTGGGGTAGATCATCATC-AGCAAATCTCTTAGCT
65 AAATCTCTTACCCCGAGCATGGGGCAGATCA-CAGCTAGCAAATCTCTTACCT
* * * * *
134654 CGAGCCTGGGGCAGATTGCAACCATTC-G--ATCTTTTACCTCGAGCTTCGGGTAGATCACCATT
1 CGAGCTTGGGGCAGA-T-C-ATCA-TCAGAAATCTCTTACCCCGAGCTTCGGGCAGATCACCATT
* * * **** *
134716 AGCAAATCTCTTACCCCGATCATGGGGCATATTACAGCTATTTGATCTTTTACCT
62 AGCAAATCTCTTACCCCGAGCATGGGGCAGATCACAGCTAGCAAATCTCTTACCT
* *
134771 TGAGCTTAGGGCAGATCATCATCAGTAAATCTCTTACCCCGA
1 CGAGCTTGGGGCAGATCATCATCAG-AAATCTCTTACCCCGA
134813 TCATAAGCTA
Statistics
Matches: 126, Mismatches: 24, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
113 2 0.02
114 4 0.03
115 1 0.01
116 4 0.03
117 107 0.85
118 1 0.01
119 1 0.01
120 4 0.03
121 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (116 bp):
CGAGCTTGGGGCAGATCATCATCAGAAATCTCTTACCCCGAGCTTCGGGCAGATCACCATTAGCA
AATCTCTTACCCCGAGCATGGGGCAGATCACAGCTAGCAAATCTCTTACCT
Found at i:134816 original size:78 final size:76
Alignment explanation
Indices: 134486--134812 Score: 318
Period size: 78 Copynumber: 4.2 Consensus size: 76
134476 TAAAGATTCC
* * * * *
134486 AATCTTTTACCCCGACCATGGGGCAGA-TCACAATCATCT-GGTCTTTTTCCCCGAGCTTGGGGC
1 AATCTCTTACCCCGAGCATGGGGCAGATTCAC---CAT-TAGATCTTTTACCTCGAGCTTGGGGC
134549 AGATCATCATCAGCA
62 AGATCATCATCAGCA
* * * *
134564 AATCTCTTACCCCGAGCTTGGGGCAGA-TCACCATTAGCAAATCTCTTACCCCGAGCTTGGGGTA
1 AATCTCTTACCCCGAGCATGGGGCAGATTCACCATTAG---ATCTTTTACCTCGAGCTTGGGGCA
134628 GATCATCATCAGCA
63 GATCATCATCAGCA
* * * * * *
134642 AATCTCTTAGCTCGAGCCTGGGGCAGATTGCAACCATTCGATCTTTTACCTCGAGCTTCGGGTAG
1 AATCTCTTACCCCGAGCATGGGGCAGATT-C-ACCATTAGATCTTTTACCTCGAGCTTGGGGCAG
* *
134707 ATCACCATTAGCA
64 ATCATCATCAGCA
* * * * * *
134720 AATCTCTTACCCCGATCATGGGGCATATTACAGCTATTTGATCTTTTACCTTGAGCTTAGGGCAG
1 AATCTCTTACCCCGAGCATGGGGCAGATT-CA-CCATTAGATCTTTTACCTCGAGCTTGGGGCAG
*
134785 ATCATCATCAGTA
64 ATCATCATCAGCA
134798 AATCTCTTACCCCGA
1 AATCTCTTACCCCGA
134813 TCATAAGCTA
Statistics
Matches: 211, Mismatches: 30, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
74 1 0.00
75 4 0.02
77 1 0.00
78 196 0.93
79 1 0.00
80 1 0.00
81 7 0.03
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (76 bp):
AATCTCTTACCCCGAGCATGGGGCAGATTCACCATTAGATCTTTTACCTCGAGCTTGGGGCAGAT
CATCATCAGCA
Found at i:134826 original size:156 final size:153
Alignment explanation
Indices: 134527--134902 Score: 350
Period size: 156 Copynumber: 2.4 Consensus size: 153
134517 AATCATCTGG
* * *
134527 TCTTTTTCCCCGAGCTTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCTTGGGGCAGAT
1 TCTTTTACCCCGAGCTT-GGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCATGGGGCAGAT
* * * *
134592 CACCATTAGCAAATCTCTTACCCCGAGCTTGGGGTAGATCATCATCAGCAAATCTCTTAGCTCGA
65 CACCATTAG--AATCTCTTACCCCGAGCTTAGGGCAGATCATCATCAGCAAATCTCTTACCCCGA
* **
134657 GCCTGGGGCAGATTGCAA-CCATTCGA
128 GCATGAAGCAGATT-CAAGCCATTCGA
* * * * *
134683 TCTTTTACCTCGAGCTTCGGGTAGATCACCATTAGCAAATCTCTTACCCCGATCATGGGGCATAT
1 TCTTTTACCCCGAGCTT-GGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCATGGGGCAGA-
* * * ** *
134748 TACAGCTATTTG-ATCTTTTACCTTGAGCTTAGGGCAGATCATCATCAGTAAATCTCTTACCCCG
64 T-CA-CCATTAGAATCTCTTACCCCGAGCTTAGGGCAGATCATCATCAGCAAATCTCTTACCCCG
* * *
134812 ATCAT-AAGCTAGATTTAAGCCATTCTA
127 AGCATGAAGC-AGATTCAAGCCATTCGA
* * * * * *
134839 TCTCTTACCCCGAGCCTGGGACAGATCACCATC--C-GATCTCTTACCTCAAGCCTGGGGCAGAT
1 TCTTTTACCCCGAGCTTGGG-CAGATCACCATCAGCAAATCTCTTACCCCGAGCATGGGGCAGAT
134901 CA
65 CA
134903 TCATCAGCCA
Statistics
Matches: 178, Mismatches: 36, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
151 2 0.01
152 1 0.01
153 21 0.12
154 1 0.01
155 7 0.04
156 138 0.78
157 1 0.01
158 2 0.01
159 5 0.03
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (153 bp):
TCTTTTACCCCGAGCTTGGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCATGGGGCAGATC
ACCATTAGAATCTCTTACCCCGAGCTTAGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCA
TGAAGCAGATTCAAGCCATTCGA
Found at i:134847 original size:78 final size:78
Alignment explanation
Indices: 134537--134853 Score: 279
Period size: 78 Copynumber: 4.1 Consensus size: 78
134527 TCTTTTTCCC
* * * * *
134537 CGAGCTTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCTTGGGGCAGA--TCA-CCATT
1 CGAGCTTAGGGTAGATCATCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTTAAGCCATT
* *
134599 AGCAAATCTCTTACCC
66 --C-TATCTCTTACCT
* * * * * *
134615 CGAGCTTGGGGTAGATCATCATCAGCAAATCTCTTAGCTCGAGCCTGGGGCAGATTGCAA-CCAT
1 CGAGCTTAGGGTAGATCATCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATT-TAAGCCAT
* *
134679 TCGATCTTTTACCT
65 TCTATCTCTTACCT
* * * * *
134693 CGAGCTTCGGGTAGATCACCATTAGCAAATCTCTTACCCCGATCATGGGGCATA-TTACAGCTAT
1 CGAGCTTAGGGTAGATCATCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTTA-AGCCAT
*
134757 T-TGATCTTTTACCT
65 TCT-ATCTCTTACCT
* * * **
134771 TGAGCTTAGGGCAGATCATCATCAGTAAATCTCTTACCCCGATCAT-AAGCTAGATTTAAGCCAT
1 CGAGCTTAGGGTAGATCATCATCAGCAAATCTCTTACCCCGATCATGGGGC-AGATTTAAGCCAT
*
134835 TCTATCTCTTACCC
65 TCTATCTCTTACCT
134849 CGAGC
1 CGAGC
134854 CTGGGACAGA
Statistics
Matches: 197, Mismatches: 33, Indels: 18
0.79 0.13 0.07
Matches are distributed among these distances:
76 1 0.01
77 4 0.02
78 181 0.92
79 5 0.03
81 6 0.03
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.28
Consensus pattern (78 bp):
CGAGCTTAGGGTAGATCATCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTTAAGCCATT
CTATCTCTTACCT
Found at i:134891 original size:36 final size:36
Alignment explanation
Indices: 134838--134907 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
134828 AAGCCATTCT
*
134838 ATCTCTTACCCCGAGCCTGGGACAGATCACCATCCG
1 ATCTCTTACCCCAAGCCTGGGACAGATCACCATCCG
* * *
134874 ATCTCTTACCTCAAGCCTGGGGCAGATCATCATC
1 ATCTCTTACCCCAAGCCTGGGACAGATCACCATC
134908 AGCCAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.23
Consensus pattern (36 bp):
ATCTCTTACCCCAAGCCTGGGACAGATCACCATCCG
Found at i:135379 original size:18 final size:18
Alignment explanation
Indices: 135358--135410 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
135348 ATTTTTAGAA
* *
135358 TTATTTTTAAGTTTAAAT
1 TTATTCTTAAATTTAAAT
*
135376 TTATTCTTAAATTTGAAT
1 TTATTCTTAAATTTAAAT
*
135394 TTATTC-TAAATTAAAAT
1 TTATTCTTAAATTTAAAT
135411 GTCCAAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 9 0.30
18 21 0.70
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (18 bp):
TTATTCTTAAATTTAAAT
Found at i:137260 original size:29 final size:30
Alignment explanation
Indices: 137135--137404 Score: 188
Period size: 30 Copynumber: 9.2 Consensus size: 30
137125 AGAAGGTCCC
*
137135 TAAACTATCT-AAAAA-T-CATATTTTAACCT
1 TAAACT-TCTCAAAAATTACAT-TTTTACCCT
* *
137164 CTAAACTTTTCCAAAATTACATTTTTA-CCT
1 -TAAACTTCTCAAAAATTACATTTTTACCCT
* * * *
137194 CTAAACTTCTAAAAAATTACATTATTGCCCA
1 -TAAACTTCTCAAAAATTACATTTTTACCCT
*
137225 TGAACTTCTCAAAAATTACA-TTTTACCCT
1 TAAACTTCTCAAAAATTACATTTTTACCCT
*
137254 TAAACTTC-CAAAAATTACATTTTTTCCCT
1 TAAACTTCTCAAAAATTACATTTTTACCCT
* * *
137283 CAAACTT-TCAAAAGTCACATTTTTACCCT
1 TAAACTTCTCAAAAATTACATTTTTACCCT
* *
137312 TGAAA-TT-TAAAAAAAATACATTTTTACCC-
1 T-AAACTTCT-CAAAAATTACATTTTTACCCT
* * * *
137341 CAAGCGTTC-CCAAAATGACATTTTTACCCCT
1 TAAAC-TTCTCAAAAATTACATTTTTA-CCCT
* * *
137372 AAAACTT-TCCAAAATTACATTTTAACCC-
1 TAAACTTCTCAAAAATTACATTTTTACCCT
137400 TAAAC
1 TAAAC
137405 CCTTCGAAAC
Statistics
Matches: 191, Mismatches: 35, Indels: 30
0.75 0.14 0.12
Matches are distributed among these distances:
28 17 0.09
29 66 0.35
30 94 0.49
31 11 0.06
32 3 0.02
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.36
Consensus pattern (30 bp):
TAAACTTCTCAAAAATTACATTTTTACCCT
Found at i:137391 original size:59 final size:58
Alignment explanation
Indices: 137172--137404 Score: 158
Period size: 59 Copynumber: 4.0 Consensus size: 58
137162 CTCTAAACTT
* * ** * * *
137172 TTCCAAAATTACATTTTTACCTCT-AAACTTCTAAAAAATTACATTATTGCCCAT-GAAC
1 TTCCAAAATCACATTTTTACCCCTAAAACTT-TCCAAAATTACATTTTTACCC-TCAAAC
* * *
137230 TTCTCAAAAATTACA-TTTTA-CCCTTAAAC-TTCCAAAAATTACATTTTTTCCCTCAAAC
1 TTC-C-AAAATCACATTTTTACCCCTAAAACTTTCC-AAAATTACATTTTTACCCTCAAAC
* * * ** * *
137288 TTTCAAAAGTCACATTTTTACCCTTGAAA-TTTAAAAAAAATACATTTTTACCC-CAAGC
1 TTCCAAAA-TCACATTTTTACCCCTAAAACTTT-CCAAAATTACATTTTTACCCTCAAAC
* *
137346 GTTCCCAAAATGACATTTTTACCCCTAAAACTTTCCAAAATTACATTTTAACCCT-AAAC
1 -TT-CCAAAATCACATTTTTACCCCTAAAACTTTCCAAAATTACATTTTTACCCTCAAAC
137405 CCTTCGAAAC
Statistics
Matches: 137, Mismatches: 24, Indels: 27
0.73 0.13 0.14
Matches are distributed among these distances:
56 4 0.03
57 7 0.05
58 37 0.27
59 72 0.53
60 17 0.12
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (58 bp):
TTCCAAAATCACATTTTTACCCCTAAAACTTTCCAAAATTACATTTTTACCCTCAAAC
Found at i:137423 original size:29 final size:30
Alignment explanation
Indices: 137236--137428 Score: 93
Period size: 29 Copynumber: 6.6 Consensus size: 30
137226 GAACTTCTCA
*
137236 AAAATTACA-TTTT-ACCCTTAAA-CTTCC
1 AAAATTACATTTTTAACCCTAAAACCTTCC
* * *
137263 AAAAATTACATTTTT-TCCCTCAAA-CTTTC
1 -AAAATTACATTTTTAACCCTAAAACCTTCC
* * * **
137292 AAAAGTCACATTTTT-ACCCTTGAAA-TTTAAA
1 AAAA-TTACATTTTTAACCC-TAAAACCTT-CC
* * * *
137323 AAAAATACATTTTT-ACCC-CAAGCGTTCCC
1 AAAATTACATTTTTAACCCTAAAACCTT-CC
* * *
137352 AAAATGACATTTTTACCCCTAAAACTTTCC
1 AAAATTACATTTTTAACCCTAAAACCTTCC
* *
137382 AAAATTACA-TTTTAACCCTAAACCCTTCG
1 AAAATTACATTTTTAACCCTAAAACCTTCC
*
137411 AAACTT-CATTTTTAACCC
1 AAAATTACATTTTTAACCC
137429 CATTTTTTTC
Statistics
Matches: 128, Mismatches: 29, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
28 17 0.13
29 71 0.55
30 31 0.24
31 9 0.07
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTTAACCCTAAAACCTTCC
Found at i:137513 original size:28 final size:29
Alignment explanation
Indices: 137482--137543 Score: 65
Period size: 30 Copynumber: 2.1 Consensus size: 29
137472 TTTTAAATTA
* *
137482 ATTTTGTATTTCTCAT-TTATTTTT-TCAT
1 ATTTTATATTTCTCAATTTATTTTTGT-AT
*
137510 ATTTTATTTTTCTCATATTTATTTTTGTAT
1 ATTTTATATTTCTCA-ATTTATTTTTGTAT
137540 ATTT
1 ATTT
137544 GTTCATTCTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
28 13 0.46
30 14 0.50
31 1 0.04
ACGTcount: A:0.19, C:0.08, G:0.03, T:0.69
Consensus pattern (29 bp):
ATTTTATATTTCTCAATTTATTTTTGTAT
Found at i:137517 original size:15 final size:15
Alignment explanation
Indices: 137496--137535 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
137486 TGTATTTCTC
137496 ATTTATTTTT-TCAT
1 ATTTATTTTTCTCAT
137510 ATTTTATTTTTCTCAT
1 A-TTTATTTTTCTCAT
137526 ATTTATTTTT
1 ATTTATTTTT
137536 GTATATTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 1 0.04
15 18 0.75
16 5 0.21
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.72
Consensus pattern (15 bp):
ATTTATTTTTCTCAT
Found at i:137778 original size:97 final size:97
Alignment explanation
Indices: 137667--137857 Score: 249
Period size: 97 Copynumber: 2.0 Consensus size: 97
137657 AAAATATTTA
* ** * *
137667 AAATTGAGGCAATATTTTTTTATTTCAGGTTTTG-AAAATTCGTGCCTCAACATACTAAGCGCGA
1 AAATCGAGGCAATATTCCTTTATTTCAGGTTTTGAAAAATT-ATGCCTCAACATACTAAGCGCAA
* *
137731 TTTTTCTTCAAATCGGGATAATCGAATACCCTT
65 CTTTTCTTCAAACCGGGATAATCGAATACCCTT
* * * * *
137764 AAATCGAGGCAATATTCCTTTATTTCGGGTTTTGAAAAATTATGTCTTAACTTACTAGGCGCAAC
1 AAATCGAGGCAATATTCCTTTATTTCAGGTTTTGAAAAATTATGCCTCAACATACTAAGCGCAAC
*
137829 TTTTCTTCAAACCGGGATAATTGAATACC
66 TTTTCTTCAAACCGGGATAATCGAATACC
137858 ATTTTTCAAG
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
97 74 0.93
98 6 0.08
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (97 bp):
AAATCGAGGCAATATTCCTTTATTTCAGGTTTTGAAAAATTATGCCTCAACATACTAAGCGCAAC
TTTTCTTCAAACCGGGATAATCGAATACCCTT
Found at i:143927 original size:26 final size:26
Alignment explanation
Indices: 143896--143954 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
143886 TTACCCCAAC
** * *
143896 AAAATTTTGATGATTTTAGTTCTTGT
1 AAAATTTTGACAATTTTAGCTCTAGT
*
143922 AAAATTTTGACAATTTTGGCTCTAGT
1 AAAATTTTGACAATTTTAGCTCTAGT
143948 AAAATTT
1 AAAATTT
143955 CGAGAAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (26 bp):
AAAATTTTGACAATTTTAGCTCTAGT
Found at i:148659 original size:14 final size:14
Alignment explanation
Indices: 148640--148669 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
148630 CTTCCTTTTC
*
148640 TTTATTTTTTTTAA
1 TTTATTTTCTTTAA
148654 TTTATTTTCTTTAA
1 TTTATTTTCTTTAA
148668 TT
1 TT
148670 CAAATCCCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTCTTTAA
Found at i:149297 original size:29 final size:29
Alignment explanation
Indices: 149265--149332 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
149255 TCATTTAACG
*
149265 GAGATCGCCACAAAAGTGA-TTCCTTT-ATA
1 GAGATCGCCAC--AAGGGATTTCCTTTAATA
*
149294 GAGATTGCCACAAGGGATTTCCTTTAATA
1 GAGATCGCCACAAGGGATTTCCTTTAATA
*
149323 GATATCGCCA
1 GAGATCGCCA
149333 TAAATGCGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 5 0.15
28 7 0.21
29 21 0.64
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (29 bp):
GAGATCGCCACAAGGGATTTCCTTTAATA
Found at i:149377 original size:29 final size:29
Alignment explanation
Indices: 149340--149426 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 29
149330 CCATAAATGC
* * *
149340 GTTTACTTTACAAAGATT-TCCACAATGGT
1 GTTTCCTTTACAAAGATTGT-CACAAAGGA
149369 GTTTCCTTTA-AAGAGATTGTCACAAAGGA
1 GTTTCCTTTACAA-AGATTGTCACAAAGGA
* * *
149398 GTTTCCTTTAACAAAAATCGCCACAAAGG
1 GTTTCCTTT-ACAAAGATTGTCACAAAGG
149427 CTTACCCTTC
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
28 2 0.04
29 30 0.62
30 14 0.29
31 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (29 bp):
GTTTCCTTTACAAAGATTGTCACAAAGGA
Found at i:153530 original size:29 final size:29
Alignment explanation
Indices: 153494--153552 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
153484 TTGAGAATTG
153494 AAAGCGAGCTTCAATCCGGTGATGAATCA
1 AAAGCGAGCTTCAATCCGGTGATGAATCA
153523 AAAGCGAGCTTCAATCCGGTGATGAATCA
1 AAAGCGAGCTTCAATCCGGTGATGAATCA
153552 A
1 A
153553 TTACTTGGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (29 bp):
AAAGCGAGCTTCAATCCGGTGATGAATCA
Found at i:157122 original size:18 final size:18
Alignment explanation
Indices: 157099--157134 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
157089 CACTAACACT
157099 AAAATGCAATGACAATGG
1 AAAATGCAATGACAATGG
*
157117 AAAATGTAATGACAATGG
1 AAAATGCAATGACAATGG
157135 GAACGCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.22, T:0.19
Consensus pattern (18 bp):
AAAATGCAATGACAATGG
Found at i:166345 original size:31 final size:31
Alignment explanation
Indices: 166307--166368 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
166297 CTATAGCAAT
*
166307 GTCGAGGCTCCACTCCTAGCTCTCACTGTTA
1 GTCGAGGCTCCACTCCTAGCTCTCACCGTTA
166338 GTCGAGGCTCCACTCCTAGCTCTCACCGTTA
1 GTCGAGGCTCCACTCCTAGCTCTCACCGTTA
166369 ACTTTGCCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.16, C:0.37, G:0.19, T:0.27
Consensus pattern (31 bp):
GTCGAGGCTCCACTCCTAGCTCTCACCGTTA
Found at i:169803 original size:132 final size:130
Alignment explanation
Indices: 169568--169832 Score: 469
Period size: 132 Copynumber: 2.0 Consensus size: 130
169558 TATAGGTAAA
*
169568 AAGATATTATTTGTACCATGAAGTGAATAATATGAGGAAACAAGTGTGCTAGTATATATGATAAA
1 AAGATATTATTTGTACCATGAAGTGAATAATATGAGGAAACAAGCGTGCTAGTATATATGATAAA
* *
169633 TTGTAATTTTGGGATTGTGTGATGAAATTGATGTTTATCCATATAAAGATGTTTAGGGATGACCT
66 TTGTAATTTTGGGATTGTGTGATGAAATTGAAGTTTATCCATATAAAGATGTTTAAGGATGACCT
169698 AAGATATTATTTGTACCAAATGACA-TGAATAATATGAGGAAACAAGCGTGCTAGTATATATGAT
1 AAGATATTATTTGTACC--ATGA-AGTGAATAATATGAGGAAACAAGCGTGCTAGTATATATGAT
169762 AAATTGTAATTTTGGGATTGTGTGATGAAATTGAAGTTTATCCATATAAAGATGTTTAAGGATGA
63 AAATTGTAATTTTGGGATTGTGTGATGAAATTGAAGTTTATCCATATAAAGATGTTTAAGGATGA
169827 CCT
128 CCT
169830 AAG
1 AAG
169833 GCATTGTTTG
Statistics
Matches: 129, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
130 17 0.13
132 111 0.86
133 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.35
Consensus pattern (130 bp):
AAGATATTATTTGTACCATGAAGTGAATAATATGAGGAAACAAGCGTGCTAGTATATATGATAAA
TTGTAATTTTGGGATTGTGTGATGAAATTGAAGTTTATCCATATAAAGATGTTTAAGGATGACCT
Found at i:180132 original size:21 final size:22
Alignment explanation
Indices: 180106--180157 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
180096 TAAAATCATG
180106 AAAACCCAAT-ACCCAAACCCT
1 AAAACCCAATCACCCAAACCCT
* *
180127 AAAACCAAATCACCTAAACCCT
1 AAAACCCAATCACCCAAACCCT
180149 -AAACCCAAT
1 AAAACCCAAT
180158 TCGATTTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.50, C:0.38, G:0.00, T:0.12
Consensus pattern (22 bp):
AAAACCCAATCACCCAAACCCT
Found at i:180147 original size:22 final size:21
Alignment explanation
Indices: 180106--180156 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
180096 TAAAATCATG
*
180106 AAAACCCAATACCCAAACCCT
1 AAAACCAAATACCCAAACCCT
*
180127 AAAACCAAATCACCTAAACCCT
1 AAAACCAAAT-ACCCAAACCCT
*
180149 AAACCCAA
1 AAAACCAA
180157 TTCGATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.51, C:0.39, G:0.00, T:0.10
Consensus pattern (21 bp):
AAAACCAAATACCCAAACCCT
Found at i:189358 original size:8 final size:8
Alignment explanation
Indices: 189347--189373 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
189337 TTTTGAGTTT
189347 TTTAATTA
1 TTTAATTA
189355 TTTAATTA
1 TTTAATTA
189363 TTTAATTA
1 TTTAATTA
189371 TTT
1 TTT
189374 TTATTGTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTAATTA
Found at i:192580 original size:29 final size:28
Alignment explanation
Indices: 192547--192604 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
192537 TTCTAAAAAG
* * *
192547 AAAATATGAGGATTGAATTTTGAAATTTT
1 AAAATATAAGGATTAAATCTT-AAATTTT
192576 AAAATATAAGGATTAAATCTTAAATTTT
1 AAAATATAAGGATTAAATCTTAAATTTT
192604 A
1 A
192605 TCAAAGTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.47, C:0.02, G:0.12, T:0.40
Consensus pattern (28 bp):
AAAATATAAGGATTAAATCTTAAATTTT
Found at i:221089 original size:15 final size:16
Alignment explanation
Indices: 221069--221101 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
221059 AAGGACGAGG
221069 AAGAAGATGCTGA-AA
1 AAGAAGATGCTGAGAA
*
221084 AAGAAGGTGCTGAGAA
1 AAGAAGATGCTGAGAA
221100 AA
1 AA
221102 AATTAACTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.52, C:0.06, G:0.30, T:0.12
Consensus pattern (16 bp):
AAGAAGATGCTGAGAA
Found at i:223078 original size:22 final size:19
Alignment explanation
Indices: 223053--223105 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 19
223043 ACAAGAAAAT
223053 TTCTTATTTAGATTAGTTAGAG
1 TTCTTATTTAGATTA---AGAG
*
223075 TTCTAATTTA-ATTAAGAG
1 TTCTTATTTAGATTAAGAG
223093 TT-TTATTTAGATT
1 TTCTTATTTAGATT
223106 TATTTAGCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 6 0.21
18 9 0.32
21 4 0.14
22 9 0.32
ACGTcount: A:0.30, C:0.04, G:0.13, T:0.53
Consensus pattern (19 bp):
TTCTTATTTAGATTAAGAG
Found at i:226813 original size:16 final size:17
Alignment explanation
Indices: 226780--226813 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
226770 ATGAGTTAGA
*
226780 ATAATGTTTAGATATTT
1 ATAATGGTTAGATATTT
226797 ATAATGGTTAG-TATTT
1 ATAATGGTTAGATATTT
226813 A
1 A
226814 GGGTTTCAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (17 bp):
ATAATGGTTAGATATTT
Found at i:232021 original size:13 final size:13
Alignment explanation
Indices: 232003--232033 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
231993 GTTTAGGTAC
*
232003 TACAAGTCATTGG
1 TACAAGCCATTGG
232016 TACAAGCCATTGG
1 TACAAGCCATTGG
232029 TACAA
1 TACAA
232034 ATTGATGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (13 bp):
TACAAGCCATTGG
Found at i:234309 original size:13 final size:13
Alignment explanation
Indices: 234291--234326 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
234281 TTACTTAGGC
*
234291 TTTAGTTTTTAGT
1 TTTAGTTTTTACT
234304 TTTAGTTTTTACT
1 TTTAGTTTTTACT
234317 TTTCAGTTTT
1 TTT-AGTTTT
234327 GAAATGAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.14, C:0.06, G:0.11, T:0.69
Consensus pattern (13 bp):
TTTAGTTTTTACT
Found at i:239666 original size:38 final size:38
Alignment explanation
Indices: 239618--239694 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
239608 AGGGGACTAC
239618 ACATTAGGGACAATGTGTTTTCTAAAGTGTAAGGGGTA
1 ACATTAGGGACAATGTGTTTTCTAAAGTGTAAGGGGTA
* **
239656 ACATTGGGGACAATGTGTTTTCTAAAGTGTGCGGGGTA
1 ACATTAGGGACAATGTGTTTTCTAAAGTGTAAGGGGTA
239694 A
1 A
239695 TATAGTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.09, G:0.31, T:0.31
Consensus pattern (38 bp):
ACATTAGGGACAATGTGTTTTCTAAAGTGTAAGGGGTA
Found at i:242359 original size:18 final size:18
Alignment explanation
Indices: 242336--242402 Score: 80
Period size: 18 Copynumber: 3.7 Consensus size: 18
242326 AATCTCATAA
*
242336 GGTGATGGGAATTGGGGT
1 GGTGATGGGAATTGAGGT
* **
242354 GGTGATGAGAATTGAGAC
1 GGTGATGGGAATTGAGGT
242372 GGTGATGGGAATTGAGGT
1 GGTGATGGGAATTGAGGT
**
242390 GGCAATGGGAATT
1 GGTGATGGGAATT
242403 ATGTTGGGGA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.25, C:0.03, G:0.46, T:0.25
Consensus pattern (18 bp):
GGTGATGGGAATTGAGGT
Found at i:242593 original size:18 final size:18
Alignment explanation
Indices: 242558--242598 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
242548 ACTTGAAAAT
**
242558 GGATACATATAAGGGTTA
1 GGATACATATAACAGTTA
242576 GGATACATATAACAGTTA
1 GGATACATATAACAGTTA
*
242594 TGATA
1 GGATA
242599 TGCACTTGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.29
Consensus pattern (18 bp):
GGATACATATAACAGTTA
Found at i:245182 original size:24 final size:24
Alignment explanation
Indices: 245154--245212 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
245144 TAGAGTAATA
* *
245154 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAC
* *
245178 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
245202 AGAGTTTAACT
1 AGAGTTTAACT
245213 AAAAGATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:247199 original size:24 final size:24
Alignment explanation
Indices: 247138--247200 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
247128 TAGAGTAATA
* * *
247138 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
*
247162 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
247186 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
247201 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:247500 original size:22 final size:22
Alignment explanation
Indices: 247448--247500 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
247438 ATTGTCATGG
247448 ATGTATTATGCCAATATAATAGA
1 ATGT-TTATGCCAATATAATAGA
* ** *
247471 TTAATTATGCCAATATAATTGA
1 ATGTTTATGCCAATATAATAGA
247493 ATGTTTAT
1 ATGTTTAT
247501 ATGTTAAAAG
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.42
Consensus pattern (22 bp):
ATGTTTATGCCAATATAATAGA
Found at i:254691 original size:11 final size:11
Alignment explanation
Indices: 254675--254707 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
254665 ATTGAGCGAA
254675 TCAAAGAAAGT
1 TCAAAGAAAGT
254686 TCAAAGAAAGT
1 TCAAAGAAAGT
254697 TCAAAGAAAGT
1 TCAAAGAAAGT
254708 ACAACTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.55, C:0.09, G:0.18, T:0.18
Consensus pattern (11 bp):
TCAAAGAAAGT
Found at i:260126 original size:6 final size:6
Alignment explanation
Indices: 260115--260147 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
260105 GTGGGTTTCA
260115 TTTCTT TTTCTT TTTCTT TTT-TT TTGTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TT-TCTT TTT
260148 GAGGTTTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 4 0.16
6 17 0.68
7 4 0.16
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:263547 original size:110 final size:110
Alignment explanation
Indices: 263354--263569 Score: 405
Period size: 110 Copynumber: 2.0 Consensus size: 110
263344 TACCCCACTT
*
263354 CTTTTTTTATCATTGTCTATTGTTGATCTTTCTTAATAACAGTAAGGAGAAGTGTGTACATATGT
1 CTTTTTTTATCATTGTCTACTGTTGATCTTTCTTAATAACAGTAAGGAGAAGTGTGTACATATGT
263419 CTTTTAGATTCGAAGCTTGGTAGGCAATGGAGGATTCTTTTACTC
66 CTTTTAGATTCGAAGCTTGGTAGGCAATGGAGGATTCTTTTACTC
*
263464 CTTTTTTTATCATTGTCTACTGTTTATCTTTCTTAATAACAGTAAGGAGAAGTGTGTACATATGT
1 CTTTTTTTATCATTGTCTACTGTTGATCTTTCTTAATAACAGTAAGGAGAAGTGTGTACATATGT
*
263529 CTTTTAGATTCGAAGCTTGGTGGGCAATGGAGGATTCTTTT
66 CTTTTAGATTCGAAGCTTGGTAGGCAATGGAGGATTCTTTT
263570 GAAAATGAGG
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 103 1.00
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.43
Consensus pattern (110 bp):
CTTTTTTTATCATTGTCTACTGTTGATCTTTCTTAATAACAGTAAGGAGAAGTGTGTACATATGT
CTTTTAGATTCGAAGCTTGGTAGGCAATGGAGGATTCTTTTACTC
Found at i:267302 original size:18 final size:19
Alignment explanation
Indices: 267281--267321 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
267271 ATTTTGGGAT
267281 TTTTATAAA-TATCTTG-AA
1 TTTTA-AAATTATCTTGTAA
*
267299 TTTTAAAATTATTTTGTAA
1 TTTTAAAATTATCTTGTAA
267318 TTTT
1 TTTT
267322 TGTTCAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 3 0.15
18 11 0.55
19 6 0.30
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTAAAATTATCTTGTAA
Found at i:270298 original size:22 final size:21
Alignment explanation
Indices: 270273--270347 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 21
270263 GGTGACGTCA
*
270273 CGATGACTCGAAGACACGACGG
1 CGATGTCTCGAA-ACACGACGG
*
270295 CGATGTCTCAACAACACGACGG
1 CGATGTCTCGA-AACACGACGG
* *
270317 CAATGTCTCGACAACACGACGA
1 CGATGTCTCGA-AACACGACGG
*
270339 CAATGTCTC
1 CGATGTCTC
270348 TACAAGGAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 46 0.98
23 1 0.02
ACGTcount: A:0.32, C:0.31, G:0.23, T:0.15
Consensus pattern (21 bp):
CGATGTCTCGAAACACGACGG
Found at i:270352 original size:22 final size:22
Alignment explanation
Indices: 270286--270352 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
270276 TGACTCGAAG
*
270286 ACACGACGGCGATGTCTCAACA
1 ACACGACGGCAATGTCTCAACA
*
270308 ACACGACGGCAATGTCTCGACA
1 ACACGACGGCAATGTCTCAACA
* *
270330 ACACGACGACAATGTCTCTACA
1 ACACGACGGCAATGTCTCAACA
270352 A
1 A
270353 GGAAGCATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.34, C:0.31, G:0.19, T:0.15
Consensus pattern (22 bp):
ACACGACGGCAATGTCTCAACA
Found at i:272164 original size:5 final size:5
Alignment explanation
Indices: 272154--272192 Score: 60
Period size: 5 Copynumber: 7.4 Consensus size: 5
272144 ATGAAACCCA
272154 AAAAT AAAAT AAAAT AAAAT AAAAGAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT -AAA-AT AAAAT AAAAT AA
272193 TCTATAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 24 0.75
6 6 0.19
7 2 0.06
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:272199 original size:17 final size:17
Alignment explanation
Indices: 272154--272192 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
272144 ATGAAACCCA
272154 AAAAT-AAA-ATAAAAT
1 AAAATAAAAGATAAAAT
272169 AAAATAAAAGATAAAAT
1 AAAATAAAAGATAAAAT
272186 AAAATAA
1 AAAATAA
272193 TCTATAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 5 0.23
16 3 0.14
17 14 0.64
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAATAAAAGATAAAAT
Found at i:278553 original size:6 final size:6
Alignment explanation
Indices: 278542--278573 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
278532 TCTATAGTTG
278542 AAATAA AAATAA AAATAA AAATAAA AAATAA A
1 AAATAA AAATAA AAATAA AAAT-AA AAATAA A
278574 TTTCCAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:278688 original size:17 final size:16
Alignment explanation
Indices: 278659--278693 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
278649 TATGAAACCC
278659 AAAAATAAAATAAAAT
1 AAAAATAAAATAAAAT
*
278675 AAAAGATAAGATAAAAT
1 AAAA-ATAAAATAAAAT
278692 AA
1 AA
278694 TCTATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (16 bp):
AAAAATAAAATAAAAT
Found at i:281033 original size:25 final size:27
Alignment explanation
Indices: 280993--281043 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
280983 GGTCCCAAAA
* *
280993 TTATTCTTTTAGAAAATTTTAATTTTT
1 TTATTCTTTTAGAAAATATAAATTTTT
281020 TTATT-TTTTA-AAAATATAAATTTT
1 TTATTCTTTTAGAAAATATAAATTTT
281044 GAAAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 12 0.55
26 5 0.23
27 5 0.23
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (27 bp):
TTATTCTTTTAGAAAATATAAATTTTT
Found at i:281043 original size:24 final size:27
Alignment explanation
Indices: 280993--281043 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 27
280983 GGTCCCAAAA
* *
280993 TTATTCTTTTAGAAAATTTTAATTTTT
1 TTATTCTTTTAGAAAATTATAAATTTT
281020 TTATT-TTTTA-AAAA-TATAAATTTT
1 TTATTCTTTTAGAAAATTATAAATTTT
281044 GAAAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 8 0.36
25 4 0.18
26 5 0.23
27 5 0.23
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (27 bp):
TTATTCTTTTAGAAAATTATAAATTTT
Found at i:281270 original size:14 final size:14
Alignment explanation
Indices: 281251--281280 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
281241 TGACTCGAAT
281251 AATTCGAATAACTC
1 AATTCGAATAACTC
*
281265 AATTCGATTAACTC
1 AATTCGAATAACTC
281279 AA
1 AA
281281 AATTTGATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (14 bp):
AATTCGAATAACTC
Found at i:286030 original size:36 final size:36
Alignment explanation
Indices: 285979--286066 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 36
285969 TAGCTCAAAA
* *
285979 GGCATGTCTCGTCATTTGTCTTTGAGGAGATGAAAT
1 GGCATGTCTCTTCATTTGTCTTTGAGGAGATGAAAG
* * *
286015 GGCATGTCTCTTCATTTGTCTTTTAGTATATGAAAG
1 GGCATGTCTCTTCATTTGTCTTTGAGGAGATGAAAG
* *
286051 GGCATGTATTTTCATT
1 GGCATGTCTCTTCATT
286067 AGTCCTTGGA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.22, C:0.14, G:0.23, T:0.42
Consensus pattern (36 bp):
GGCATGTCTCTTCATTTGTCTTTGAGGAGATGAAAG
Found at i:286642 original size:50 final size:49
Alignment explanation
Indices: 286574--286766 Score: 208
Period size: 50 Copynumber: 3.8 Consensus size: 49
286564 TTATTTTTTA
* *
286574 ATGATGCAAACTTTAACTAACATGAGAATTACATAATGCATGAT-ATAATTT
1 ATGATGCATAC-TTAACTAACATGA-AATTACATAATGCATG-TCATTATTT
* * * * *
286625 ATGATACATATTTAACTAACATGTAAGTTACTTAATGCATGTCTTTATTT
1 ATGATGCATACTTAACTAACATG-AAATTACATAATGCATGTCATTATTT
* * * *
286675 ATAATGCAAACTTAACTAATCATGACAGTTTCATAATGCATGTCATTATTT
1 ATGATGCATACTTAACTAA-CATGA-AATTACATAATGCATGTCATTATTT
*
286726 ATGATGCATACTTAACTAATATGAAAGTTACATAATGCATG
1 ATGATGCATACTTAACTAACATGAAA-TTACATAATGCATG
286767 ACTTTATTAA
Statistics
Matches: 118, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
49 2 0.02
50 64 0.54
51 52 0.44
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (49 bp):
ATGATGCATACTTAACTAACATGAAATTACATAATGCATGTCATTATTT
Found at i:286710 original size:101 final size:99
Alignment explanation
Indices: 286577--286783 Score: 274
Period size: 101 Copynumber: 2.1 Consensus size: 99
286567 TTTTTTAATG
* *
286577 ATGCAAACTTTAACTAACATGAGAATTACATAATGCATGAT-ATAATTTATGATACATATTTAAC
1 ATGCAAACTTTAACTAACATGACAATTACATAATGCATG-TCATAATTTATGATACATACTTAAC
* * *
286641 TAACATGTAAGTTACTTAATGCATGTCTTTATTTATA
65 TAACATGAAAGTTACATAATGCATGACTTTA-TTA-A
* * * *
286678 ATGCAAAC-TTAACTAATCATGACAGTTTCATAATGCATGTCATTATTTATGATGCATACTTAAC
1 ATGCAAACTTTAACTAA-CATGACAATTACATAATGCATGTCATAATTTATGATACATACTTAAC
*
286742 TAATATGAAAGTTACATAATGCATGACTTTATTAA
65 TAACATGAAAGTTACATAATGCATGACTTTATTAA
286777 ATGCAAA
1 ATGCAAA
286784 ACACATAATG
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
99 8 0.09
100 12 0.13
101 74 0.79
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.37
Consensus pattern (99 bp):
ATGCAAACTTTAACTAACATGACAATTACATAATGCATGTCATAATTTATGATACATACTTAACT
AACATGAAAGTTACATAATGCATGACTTTATTAA
Found at i:290704 original size:12 final size:12
Alignment explanation
Indices: 290687--290730 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
290677 ATAAGAAATT
*
290687 AAAGAATAAAAG
1 AAAGAAAAAAAG
290699 AAAGAAAAAAAG
1 AAAGAAAAAAAG
* *
290711 AAACAAAAGAAG
1 AAAGAAAAAAAG
*
290723 GAAGAAAA
1 AAAGAAAA
290731 GAGGCTCGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.02
Consensus pattern (12 bp):
AAAGAAAAAAAG
Found at i:306282 original size:47 final size:48
Alignment explanation
Indices: 306228--306359 Score: 158
Period size: 47 Copynumber: 2.7 Consensus size: 48
306218 AATTATGTGA
* * **
306228 CAGTTTATTTGCAAAAGGGGTGGCTTGTCCACAAAATGTT-TCGGTGG
1 CAGTTTATTTGCAAAAGTGGTGGCATGTCCACAAAATGTTATCAATGG
* * *
306275 CAGTTTATTAGCATAAGTGGTGACATGTCCACAAAATGTTATCAATGG
1 CAGTTTATTTGCAAAAGTGGTGGCATGTCCACAAAATGTTATCAATGG
* *
306323 CAGTTTATCTGAAAATCAGTGGTGGCATGTCCACAAA
1 CAGTTTATTTGCAAA--AGTGGTGGCATGTCCACAAA
306360 TGGTGCTTTA
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
47 35 0.50
48 16 0.23
50 19 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (48 bp):
CAGTTTATTTGCAAAAGTGGTGGCATGTCCACAAAATGTTATCAATGG
Found at i:306355 original size:50 final size:47
Alignment explanation
Indices: 306246--306359 Score: 138
Period size: 50 Copynumber: 2.4 Consensus size: 47
306236 TTGCAAAAGG
* ** **
306246 GGTGGCTTGTCCACAAAATGTTTCGGTGGCAGTTTATTAGCATAAGT
1 GGTGGCATGTCCACAAAATGTTTCAATGGCAGTTTATTAAAATAAGT
* *
306293 GGTGACATGTCCACAAAATGTTATCAATGGCAGTTTATCTGAAAATCAGT
1 GGTGGCATGTCCACAAAATGTT-TCAATGGCAGTTTAT-T-AAAATAAGT
306343 GGTGGCATGTCCACAAA
1 GGTGGCATGTCCACAAA
306360 TGGTGCTTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
47 20 0.36
48 13 0.23
49 1 0.02
50 22 0.39
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (47 bp):
GGTGGCATGTCCACAAAATGTTTCAATGGCAGTTTATTAAAATAAGT
Found at i:309959 original size:11 final size:11
Alignment explanation
Indices: 309943--309971 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
309933 TTATATAGTC
309943 ATCTTAACATT
1 ATCTTAACATT
309954 ATCTTAACATT
1 ATCTTAACATT
309965 ATCTTAA
1 ATCTTAA
309972 TGTTTGCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (11 bp):
ATCTTAACATT
Found at i:312530 original size:20 final size:19
Alignment explanation
Indices: 312496--312536 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
312486 TGATAATTTT
*
312496 TTAAAAAATGTAAAAAAAA
1 TTAAAAAATGGAAAAAAAA
312515 TTAAATAAATGGAAAAAAAA
1 TTAAA-AAATGGAAAAAAAA
312535 TT
1 TT
312537 CTTAGACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.24
Consensus pattern (19 bp):
TTAAAAAATGGAAAAAAAA
Found at i:315459 original size:28 final size:25
Alignment explanation
Indices: 315428--315483 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 25
315418 ATGAAGGCAA
315428 AAATATAAATAGCATAAAAATAACAAAT
1 AAATA-AAATA-CATAAAAA-AACAAAT
*
315456 AAATAAAATACATAAAAAAATAAAT
1 AAATAAAATACATAAAAAAACAAAT
315481 AAA
1 AAA
315484 ATTAATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 9 0.33
26 8 0.30
27 5 0.19
28 5 0.19
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (25 bp):
AAATAAAATACATAAAAAAACAAAT
Found at i:315485 original size:26 final size:29
Alignment explanation
Indices: 315427--315485 Score: 81
Period size: 26 Copynumber: 2.2 Consensus size: 29
315417 AATGAAGGCA
315427 AAAATATAAATAGCATAAAAATAACAAAT
1 AAAATATAAATAGCATAAAAATAACAAAT
*
315456 -AAATA-AAATA-CATAAAAA-AATAAAT
1 AAAATATAAATAGCATAAAAATAACAAAT
315481 AAAAT
1 AAAAT
315486 TAATTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 6 0.21
26 12 0.43
27 5 0.18
28 5 0.18
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (29 bp):
AAAATATAAATAGCATAAAAATAACAAAT
Found at i:315545 original size:15 final size:15
Alignment explanation
Indices: 315527--315560 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
315517 ATGAATAACC
*
315527 AATAAATAAATAATA
1 AATAAATAAACAATA
315542 AATAAATAAACAATA
1 AATAAATAAACAATA
315557 AATA
1 AATA
315561 TATGAAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAAATAAACAATA
Found at i:315548 original size:11 final size:11
Alignment explanation
Indices: 315527--315560 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
315517 ATGAATAACC
315527 AATAAATAAAT
1 AATAAATAAAT
315538 AATAAATAAAT
1 AATAAATAAAT
315549 AA-ACAATAAAT
1 AATA-AATAAAT
315560 A
1 A
315561 TATGAAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 1 0.05
11 21 0.95
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:315715 original size:15 final size:15
Alignment explanation
Indices: 315661--315718 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
315651 TAAATAAACA
315661 AGATAAACAATAAATAG
1 AGAT-AACAATAAA-AG
* *
315678 AAATTA-AATAAAA-
1 AGATAACAATAAAAG
*
315691 A-ATAATAATAAAAG
1 AGATAACAATAAAAG
315705 AGATAACAATAAAA
1 AGATAACAATAAAA
315719 TGACATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
12 3 0.09
13 8 0.24
14 2 0.06
15 17 0.50
16 1 0.03
17 3 0.09
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.19
Consensus pattern (15 bp):
AGATAACAATAAAAG
Found at i:316707 original size:50 final size:50
Alignment explanation
Indices: 316635--317285 Score: 582
Period size: 50 Copynumber: 13.0 Consensus size: 50
316625 GTTTTAATTC
* * * * ** * *
316635 GCCCCTCTAAAACTTTAAGGGTATAGGATTTTCTTTTGTAGCTTTAATCT
1 GCCCCTCTACAGCTTTAGGGGTATAAGATTCGCTTTTGCAGCTTCAATCT
* ** **
316685 GCCCCTCTACAGTTTTAGGGGTATAAGATTTACTTTTATAGCTTCAATCT
1 GCCCCTCTACAGCTTTAGGGGTATAAGATTCGCTTTTGCAGCTTCAATCT
* * * * * * * *
316735 GCCCCTCTACAGCTTTAAGGGTGTAATATTTGCTTTTCCATCTTTAATTT
1 GCCCCTCTACAGCTTTAGGGGTATAAGATTCGCTTTTGCAGCTTCAATCT
* * * * *
316785 GCCTCTCTATAACTTTAGGGGTATAAGATTCGCCTTCGCAGCTTCAATCT
1 GCCCCTCTACAGCTTTAGGGGTATAAGATTCGCTTTTGCAGCTTCAATCT
* ** * * *
316835 ACCCCTCTACAGCTTTAGGTATATAAGATTCACTTTTGCAACTTTAATCT
1 GCCCCTCTACAGCTTTAGGGGTATAAGATTCGCTTTTGCAGCTTCAATCT
* * * * * *
316885 GCCTCTTTACAGCTTTAAGGGTACAAGATTCGCTTTTGCAGCTTTAATTT
1 GCCCCTCTACAGCTTTAGGGGTATAAGATTCGCTTTTGCAGCTTCAATCT
* ** * * *
316935 GCCCCTTTACAATTTTAGGGGGTATAAGATTTGTTTTTGTAGCTTCAATCT
1 GCCCCTCTACAGCTTTA-GGGGTATAAGATTCGCTTTTGCAGCTTCAATCT
* * * * * * * * *
316986 ACCTCTTTACAGCTTTAAGGATATAAGATTTGCCTTTGCGGCTTCAATTT
1 GCCCCTCTACAGCTTTAGGGGTATAAGATTCGCTTTTGCAGCTTCAATCT
* * * * *
317036 GCCCCTCTACAGCTTTAGGGGTATAAGATTTGTTTTTGTAGCTTTAATTT
1 GCCCCTCTACAGCTTTAGGGGTATAAGATTCGCTTTTGCAGCTTCAATCT
* *
317086 TCCTCTCTACAGCTTTAGGGGTATAAGATTCGCTTTTGCAGCTTCAATCT
1 GCCCCTCTACAGCTTTAGGGGTATAAGATTCGCTTTTGCAGCTTCAATCT
* * * * ** * *
317136 GCACCTCTACAGCTTTAAGGGTATAAGATTCTCCTTCACGGCTTCTATCT
1 GCCCCTCTACAGCTTTAGGGGTATAAGATTCGCTTTTGCAGCTTCAATCT
* * * * *
317186 GCCCCTCTAAAGCTTTAAGGGTATAAGATTCGCCTTCGTAGCTTCAATCT
1 GCCCCTCTACAGCTTTAGGGGTATAAGATTCGCTTTTGCAGCTTCAATCT
* * * * * *
317236 GCCTCTCTACAGTTTTAGGGGTATAAGATTCACCTTCGCGGCTTCAATCT
1 GCCCCTCTACAGCTTTAGGGGTATAAGATTCGCTTTTGCAGCTTCAATCT
317286 ACTCTTTTAC
Statistics
Matches: 486, Mismatches: 114, Indels: 2
0.81 0.19 0.00
Matches are distributed among these distances:
50 447 0.92
51 39 0.08
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (50 bp):
GCCCCTCTACAGCTTTAGGGGTATAAGATTCGCTTTTGCAGCTTCAATCT
Found at i:316898 original size:150 final size:150
Alignment explanation
Indices: 316627--317287 Score: 660
Period size: 150 Copynumber: 4.4 Consensus size: 150
316617 TACTGTGAGT
* * * * * ** * * *
316627 TTTAATTCGCCCCTCTAAAACTTTAAGGGTATAGGATTTTCTTTTGTAGCTTTAATCTGCCCCTC
1 TTTAATTTGCCTCTCTACAACTTTAGGGGTATAAGATTCGCTTTTGCAGCTTCAATCTACCCCTC
* * * * * *
316692 TACAGTTTTAGGGGTATAAGATTTACTTTTATAGCTTCAATCTGCCCCTCTACAGCTTTAAGGGT
66 TACAGCTTTAAGGATATAAGATTCACCTTTACAGCTTCAATCTGCCCCTCTACAGCTTTAAGGGT
* * * *
316757 GTAATATTTGCTTTTCCATC
131 ATAAGATTCGCTTTTCCAGC
* * *
316777 TTTAATTTGCCTCTCTATAACTTTAGGGGTATAAGATTCGCCTTCGCAGCTTCAATCTACCCCTC
1 TTTAATTTGCCTCTCTACAACTTTAGGGGTATAAGATTCGCTTTTGCAGCTTCAATCTACCCCTC
* * * * * *
316842 TACAGCTTT-AGGTATATAAGATTCACTTTTGCAACTTTAATCTGCCTCTTTACAGCTTTAAGGG
66 TACAGCTTTAAGG-ATATAAGATTCACCTTTACAGCTTCAATCTGCCCCTCTACAGCTTTAAGGG
* *
316906 TACAAGATTCGCTTTTGCAGC
130 TATAAGATTCGCTTTTCCAGC
* * * * * * *
316927 TTTAATTTGCCCCTTTACAATTTTAGGGGGTATAAGATTTGTTTTTGTAGCTTCAATCTACCTCT
1 TTTAATTTGCCTCTCTACAACTTTA-GGGGTATAAGATTCGCTTTTGCAGCTTCAATCTACCCCT
* ** * * * *
316992 TTACAGCTTTAAGGATATAAGATTTGCCTTTGCGGCTTCAATTTGCCCCTCTACAGCTTTAGGGG
65 CTACAGCTTTAAGGATATAAGATTCACCTTTACAGCTTCAATCTGCCCCTCTACAGCTTTAAGGG
* * **
317057 TATAAGATTTGTTTTTGTAGC
130 TATAAGATTCGCTTTTCCAGC
* * * *
317078 TTTAATTTTCCTCTCTACAGCTTTAGGGGTATAAGATTCGCTTTTGCAGCTTCAATCTGCACCTC
1 TTTAATTTGCCTCTCTACAACTTTAGGGGTATAAGATTCGCTTTTGCAGCTTCAATCTACCCCTC
* * * * * *
317143 TACAGCTTTAAGGGTATAAGATTCTCCTTCACGGCTTCTATCTGCCCCTCTAAAGCTTTAAGGGT
66 TACAGCTTTAAGGATATAAGATTCACCTTTACAGCTTCAATCTGCCCCTCTACAGCTTTAAGGGT
* *
317208 ATAAGATTCGC-CTTCGTAGC
131 ATAAGATTCGCTTTTC-CAGC
* * ** * * * *
317228 TTCAATCTGCCTCTCTACAGTTTTAGGGGTATAAGATTCACCTTCGCGGCTTCAATCTAC
1 TTTAATTTGCCTCTCTACAACTTTAGGGGTATAAGATTCGCTTTTGCAGCTTCAATCTAC
317288 TCTTTTACAG
Statistics
Matches: 420, Mismatches: 87, Indels: 8
0.82 0.17 0.02
Matches are distributed among these distances:
149 4 0.01
150 293 0.70
151 120 0.29
152 3 0.01
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.39
Consensus pattern (150 bp):
TTTAATTTGCCTCTCTACAACTTTAGGGGTATAAGATTCGCTTTTGCAGCTTCAATCTACCCCTC
TACAGCTTTAAGGATATAAGATTCACCTTTACAGCTTCAATCTGCCCCTCTACAGCTTTAAGGGT
ATAAGATTCGCTTTTCCAGC
Found at i:322390 original size:21 final size:20
Alignment explanation
Indices: 322362--322411 Score: 82
Period size: 21 Copynumber: 2.5 Consensus size: 20
322352 GAGAATTTTT
322362 ATTTTTTATTTGATTTTATA
1 ATTTTTTATTTGATTTTATA
*
322382 ATATTTTTATTTGATTTTATT
1 AT-TTTTTATTTGATTTTATA
322403 ATTTTTTAT
1 ATTTTTTAT
322412 GAAATTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (20 bp):
ATTTTTTATTTGATTTTATA
Found at i:326040 original size:29 final size:29
Alignment explanation
Indices: 325977--326042 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
325967 AATTAATAAC
* *
325977 ACAATAAAAATATAATTATAGTAGTAAAT
1 ACAATAAAAATATAATCATAGTAATAAAT
*
326006 AAAATAAAAATATAATCATAGTAAT-AAT
1 ACAATAAAAATATAATCATAGTAATAAAT
326034 GACAATAAA
1 -ACAATAAA
326043 TATTAATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 3 0.09
29 29 0.91
ACGTcount: A:0.62, C:0.05, G:0.06, T:0.27
Consensus pattern (29 bp):
ACAATAAAAATATAATCATAGTAATAAAT
Found at i:326554 original size:6 final size:6
Alignment explanation
Indices: 326515--326551 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
326505 ATTAAATGTC
* *
326515 AAAATA AAAATA AAAATA AAAATA ATAATA ATAATA A
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA A
326552 TAAGTGAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (6 bp):
AAAATA
Found at i:340202 original size:21 final size:22
Alignment explanation
Indices: 340177--340219 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
340167 TTTAGTATGT
* *
340177 TTTAAAT-CTTTTACTTTAACC
1 TTTAAATAATTTTAATTTAACC
340198 TTTAAATAATTTTAATTTAACC
1 TTTAAATAATTTTAATTTAACC
340220 CGTGTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.35, C:0.14, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTAAATAATTTTAATTTAACC
Found at i:344526 original size:13 final size:14
Alignment explanation
Indices: 344510--344541 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
344500 GGAGATAAAA
344510 AAAAGAAAAG-AAG
1 AAAAGAAAAGAAAG
344523 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
344537 AAAAG
1 AAAAG
344542 GTCAAGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:344611 original size:58 final size:62
Alignment explanation
Indices: 344510--344636 Score: 162
Period size: 58 Copynumber: 2.1 Consensus size: 62
344500 GGAGATAAAA
344510 AAAAGAAAAGAAGAAAAGAAAAGAAAGAAAAGGTCAAGATGAAAACCCTT-AAAGGGCATCTTT
1 AAAAGAAAAGAAGAAAAGAAAAGAAAGAAAAGGTCAAGATGAAAA--CTTCAAAGGGCATCTTT
*
344573 AAAA-AAAA-AAGAAAA-CAAA-AAAGAAAA-GTCAAGATGAAAACTTGCAAAGGGCATC-TT
1 AAAAGAAAAGAAGAAAAGAAAAGAAAGAAAAGGTCAAGATGAAAACTT-CAAAGGGCATCTTT
344630 -AAAGAAA
1 AAAAGAAA
344637 TCTCCTTCAC
Statistics
Matches: 60, Mismatches: 1, Indels: 12
0.82 0.01 0.16
Matches are distributed among these distances:
56 6 0.10
57 5 0.08
58 23 0.38
59 8 0.13
60 3 0.05
61 7 0.12
62 4 0.07
63 4 0.07
ACGTcount: A:0.61, C:0.09, G:0.18, T:0.12
Consensus pattern (62 bp):
AAAAGAAAAGAAGAAAAGAAAAGAAAGAAAAGGTCAAGATGAAAACTTCAAAGGGCATCTTT
Found at i:346077 original size:112 final size:112
Alignment explanation
Indices: 345898--346114 Score: 254
Period size: 112 Copynumber: 1.9 Consensus size: 112
345888 AACCAATGAC
* * * * * *
345898 CTTTTCATTCATGCAAGCTTTACCTTCAATCAAATTCAATTTCATCCATCTCACAGCCATGTTCA
1 CTTTTCATTCACGCAAGCTTTACCTTCAATAAAATTCAATTTCATCCACCTCACAACCATATGCA
345963 AGCACGTTTGCATTAAAATAACAGCTAGTGGACTAATGATTCTTAAT
66 AGCACGTTTGCATTAAAATAACAGCTAGTGGACTAATGATTCTTAAT
* * * * * * *
346010 CTTTTCATTCACGCAAGCTTTGCCTTTAATAAAATTCATTTTTATCGACCTTACAACCCTATGCA
1 CTTTTCATTCACGCAAGCTTTACCTTCAATAAAATTCAATTTCATCCACCTCACAACCATATGCA
** * * * * *
346075 AGCATTTTTGTATTGAAATGACAGTTAGTGGTCTAATGAT
66 AGCACGTTTGCATTAAAATAACAGCTAGTGGACTAATGAT
346115 ATAAGGAATA
Statistics
Matches: 85, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
112 85 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (112 bp):
CTTTTCATTCACGCAAGCTTTACCTTCAATAAAATTCAATTTCATCCACCTCACAACCATATGCA
AGCACGTTTGCATTAAAATAACAGCTAGTGGACTAATGATTCTTAAT
Found at i:346589 original size:49 final size:50
Alignment explanation
Indices: 346498--347209 Score: 347
Period size: 49 Copynumber: 14.6 Consensus size: 50
346488 TCACCACAAG
* * * * * * * *
346498 GATATGGA-GGAAAGGTTTAAGTCGCAATGGTGAACCTTGTACCTTAAAA
1 GATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAAAA
* * * *
346547 G-CATGAATGGAAAGATTTAAGCCGTAACGGCGAATCTAGTA-C-CATGAA
1 GATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCA-AAA
* * * * * * *
346595 GATATGGAGGGAAAGGTTTAAGTCGTAATGGCGAACCTTGTACCTCAAAA
1 GATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAAAA
* * ** * *
346645 G-CATGAAGAGAAAGATTTAAGCCGC-A--GTAAATCTAATA--TCACGAA
1 GATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCA-AAA
* * * * * ** * *
346690 GATATGAAGGGAAAGATTTAAGCCGTAATGACAAATCCAGTACAAC-GAG
1 GATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAAAA
* * ** ** * * *
346739 GATATGGAGGGAAAGGTTTAAGTTGCAACGATGAACCTTGTACCTCAGAA
1 GATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAAAA
* * *** *
346789 G-CATGAAGAGAAAGATTTAAGCTATAACGGCGAATCCAGTA-C-CAAGAA
1 GATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAA-AA
* * * * ** * *
346837 GATATGAAAGGAAAGGTTTAAGTCGTAACTACGAACCTTGTACCTCAAAA
1 GATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAAAA
* * *
346887 G-CATGAAGGAAAAGATTTAAGCCGCAACGGCGAATCTAGTA-C-CATGAA
1 GATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCA-AAA
* * * * * *
346935 GATATGAAGGGAAATATTTAAGCTGCAACGACGAATCCAATA-C-CATGAA
1 GATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCA-AAA
* * ** * * *
346984 GATATGGAGGGAAAGGTTTAAATCGCAACGGTGAACCTTGTACCTCAAAA
1 GATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAAAA
* * * * *
347034 G-CATGAAGGAAAAGATTTAAGCCGCAATGGCAAATCTAGTACCAC-AAA
1 GATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAAAA
* * * * * * * *
347082 GATATGGAGGGAAAGGTTTAAGTCGAAACGGTGAA-CATTGTAGCTCAGAA
1 GATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC-TAGTACCTCAAAA
* * * * *
347132 -ACATGAAGGGAAATATTTAAGCCGCAACGGTGAATCTAGTACCAC-GAA
1 GATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAAAA
* ** *
347180 GATTTGAAGGGAAAGGCTTAAGTCGCAACG
1 GATATGAAGGGAAAGATTTAAGCCGCAACG
347210 ACAAACCTTG
Statistics
Matches: 486, Mismatches: 151, Indels: 52
0.71 0.22 0.08
Matches are distributed among these distances:
44 3 0.01
45 3 0.01
46 28 0.06
47 6 0.01
48 25 0.05
49 395 0.81
50 18 0.04
51 8 0.02
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (50 bp):
GATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAAAA
Found at i:346809 original size:144 final size:144
Alignment explanation
Indices: 346549--346810 Score: 398
Period size: 144 Copynumber: 1.8 Consensus size: 144
346539 CCTTAAAAGC
* * * * * *
346549 ATGAATGGAAAGATTTAAGCCGTAACGGCGAATCTAGTACCATGAAGATATGGAGGGAAAGGTTT
1 ATGAAGGGAAAGATTTAAGCCGTAACGACAAATCCAGTACAACGAAGATATGGAGGGAAAGGTTT
* * *
346614 AAGTCGTAATGGCGAACCTTGTACCTCAAAAGCATGAAGAGAAAGATTTAAGCCGCAGTAAATCT
66 AAGTCGCAACGACGAACCTTGTACCTCAAAAGCATGAAGAGAAAGATTTAAGCCGCAGTAAATCT
346679 AATATCACGAAGAT
131 AATATCACGAAGAT
* *
346693 ATGAAGGGAAAGATTTAAGCCGTAATGACAAATCCAGTACAACGAGGATATGGAGGGAAAGGTTT
1 ATGAAGGGAAAGATTTAAGCCGTAACGACAAATCCAGTACAACGAAGATATGGAGGGAAAGGTTT
* * *
346758 AAGTTGCAACGATGAACCTTGTACCTCAGAAGCATGAAGAGAAAGATTTAAGC
66 AAGTCGCAACGACGAACCTTGTACCTCAAAAGCATGAAGAGAAAGATTTAAGC
346811 TATAACGGCG
Statistics
Matches: 104, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
144 104 1.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.21
Consensus pattern (144 bp):
ATGAAGGGAAAGATTTAAGCCGTAACGACAAATCCAGTACAACGAAGATATGGAGGGAAAGGTTT
AAGTCGCAACGACGAACCTTGTACCTCAAAAGCATGAAGAGAAAGATTTAAGCCGCAGTAAATCT
AATATCACGAAGAT
Found at i:347004 original size:98 final size:98
Alignment explanation
Indices: 346498--347241 Score: 460
Period size: 98 Copynumber: 7.6 Consensus size: 98
346488 TCACCACAAG
* * * * *
346498 GATATGGA-GGAAAGGTTTAAGTCGCAATGGTGAACCTTGTACC-TTAAAAGCATGAATGGAAAG
1 GATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCATGAAAA-CATGAAGGGAAAG
* *
346561 ATTTAAGCCGTAACGGCGAATCTAGTACCATGAA
65 ATTTAAGCCGCAACGACGAATCTAGTACCATGAA
* * * * *
346595 GATATGGAGGGAAAGGTTTAAGTCGTAATGGCGAACCTTGTACC-TCAAAAGCATGAAGAGAAAG
1 GATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCATGAAAA-CATGAAGGGAAAG
* * *
346659 ATTTAAGCCGC-A-GTA--AATCTAATATCACGAA
65 ATTTAAGCCGCAACG-ACGAATCTAGTACCATGAA
* * * * * * * * * ** * *
346690 GATATGAAGGGAAAGATTTAAGCCGTAATGACAAATCC-AGTACAACGAGGATATGGAGGGAAAG
1 GATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAA-CCTTGTACCATGAAAACATGAAGGGAAAG
* ** * * *
346754 GTTTAAGTTGCAACGATGAACCTTGTACC-TCAGAA
65 ATTTAAGCCGCAACGACGAATCTAGTACCAT--GAA
* * * ** * * * * *
346789 G-CATGAAGAGAAAGATTTAAG-CTATAACGGCGAATCC-AGTACCAAGAAGATATGAAAGGAAA
1 GATATGAAGGGAAAGGTTTAAGTC-GCAACGGCGAA-CCTTGTACCATGAAAACATGAAGGGAAA
* * * * * * *
346851 GGTTTAAGTCGTAACTACGAACCTTGTACC-TCAA
64 GATTTAAGCCGCAACGACGAATCTAGTACCATGAA
* * * * * * * * * *
346885 AAGCATGAAGGAAAAGATTTAAGCCGCAACGGCGAATCTAGTACCATGAAGATATGAAGGGAAAT
1 GA-TATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCATGAAAACATGAAGGGAAAG
* * *
346950 ATTTAAGCTGCAACGACGAATCCAATACCATGAA
65 ATTTAAGCCGCAACGACGAATCTAGTACCATGAA
* * * * *
346984 GATATGGAGGGAAAGGTTTAAATCGCAACGGTGAACCTTGTACC-TCAAAAGCATGAAGGAAAAG
1 GATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCATGAAAA-CATGAAGGGAAAG
* * * **
347048 ATTTAAGCCGCAATGGCAAATCTAGTACCACAAA
65 ATTTAAGCCGCAACGACGAATCTAGTACCATGAA
* * * *
347082 GATATGGAGGGAAAGGTTTAAGTCGAAACGGTGAACATTGTAGCTCA-G-AAACATGAAGGGAAA
1 GATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTA-C-CATGAAAACATGAAGGGAAA
* ** *
347145 TATTTAAGCCGCAACGGTGAATCTAGTACCACGAA
64 GATTTAAGCCGCAACGACGAATCTAGTACCATGAA
* * * * * *
347180 GATTTGAAGGGAAAGGCTTAAGTCGCAACGACAAACCTTGTACC-TCAGAAACATAAAGGGAA
1 GATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCATGA-AAACATGAAGGGAA
347242 GGTTGAGGTC
Statistics
Matches: 514, Mismatches: 110, Indels: 45
0.77 0.16 0.07
Matches are distributed among these distances:
95 65 0.13
96 10 0.02
97 17 0.03
98 408 0.79
99 13 0.03
100 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (98 bp):
GATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCATGAAAACATGAAGGGAAAGA
TTTAAGCCGCAACGACGAATCTAGTACCATGAA
Found at i:347070 original size:147 final size:147
Alignment explanation
Indices: 346791--347103 Score: 446
Period size: 147 Copynumber: 2.1 Consensus size: 147
346781 CCTCAGAAGC
* * * *
346791 ATGAAGAGAAAGATTTAAGCTATAACGGCGAATCCAGTACCAAGAAGATATGAAAGGAAAGGTTT
1 ATGAAGGGAAAGATTTAAGCTACAACGACGAATCCAATACCAAGAAGATATGAAAGGAAAGGTTT
* * * *
346856 AAGTCGTAACTACGAACCTTGTACCTCAAAAGCATGAAGGAAAAGATTTAAGCCGCAACGGCGAA
66 AAATCGCAACGACGAACCTTGTACCTCAAAAGCATGAAGGAAAAGATTTAAGCCGCAACGGCAAA
**
346921 TCTAGTACCATGAAGAT
131 TCTAGTACCACAAAGAT
* * * * *
346938 ATGAAGGGAAATATTTAAGCTGCAACGACGAATCCAATACCATGAAGATATGGAGGGAAAGGTTT
1 ATGAAGGGAAAGATTTAAGCTACAACGACGAATCCAATACCAAGAAGATATGAAAGGAAAGGTTT
** *
347003 AAATCGCAACGGTGAACCTTGTACCTCAAAAGCATGAAGGAAAAGATTTAAGCCGCAATGGCAAA
66 AAATCGCAACGACGAACCTTGTACCTCAAAAGCATGAAGGAAAAGATTTAAGCCGCAACGGCAAA
347068 TCTAGTACCACAAAGAT
131 TCTAGTACCACAAAGAT
* *
347085 ATGGAGGGAAAGGTTTAAG
1 ATGAAGGGAAAGATTTAAG
347104 TCGAAACGGT
Statistics
Matches: 145, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
147 145 1.00
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.20
Consensus pattern (147 bp):
ATGAAGGGAAAGATTTAAGCTACAACGACGAATCCAATACCAAGAAGATATGAAAGGAAAGGTTT
AAATCGCAACGACGAACCTTGTACCTCAAAAGCATGAAGGAAAAGATTTAAGCCGCAACGGCAAA
TCTAGTACCACAAAGAT
Found at i:347625 original size:42 final size:42
Alignment explanation
Indices: 347560--347703 Score: 209
Period size: 42 Copynumber: 3.4 Consensus size: 42
347550 GTTACGTCAC
* *
347560 CATCCAATCTCTTACCCCAATCATGGGGCAGATTGAAAACAT
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
* *
347602 TATCCAATCTCTTACCCCGATCATGGGGCAGATT-ACAGCCAT
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGA-AGACAT
* *
347644 CATCTAATCTCTTACCCCGATCATGGGGCAGATTGAAGACCT
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
*
347686 CATCCAATCTTTTACCCC
1 CATCCAATCTCTTACCCC
347704 TAAGTCAAGA
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
41 1 0.01
42 88 0.98
43 1 0.01
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (42 bp):
CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
Found at i:348736 original size:2 final size:2
Alignment explanation
Indices: 348719--348781 Score: 74
Period size: 2 Copynumber: 32.0 Consensus size: 2
348709 CTTCGAAGAG
* * * *
348719 AT AT -T AT AT AT GT AT AT AT GT AT AT AT GT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
348760 AT GT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
348782 GTGTGTATAT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (2 bp):
AT
Found at i:348736 original size:8 final size:8
Alignment explanation
Indices: 348719--348795 Score: 106
Period size: 8 Copynumber: 10.0 Consensus size: 8
348709 CTTCGAAGAG
348719 ATAT-TAT
1 ATATGTAT
348726 ATATGTAT
1 ATATGTAT
348734 ATATGTAT
1 ATATGTAT
348742 ATATGTAT
1 ATATGTAT
348750 ATATGTAT
1 ATATGTAT
348758 ATATGTAT
1 ATATGTAT
348766 ATA--TAT
1 ATATGTAT
*
348772 ATATATAT
1 ATATGTAT
* *
348780 ATGTGTGT
1 ATATGTAT
348788 ATATGTAT
1 ATATGTAT
348796 TTTTGCCCAT
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.10
7 4 0.06
8 52 0.84
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.51
Consensus pattern (8 bp):
ATATGTAT
Found at i:365543 original size:29 final size:29
Alignment explanation
Indices: 365498--365557 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
365488 AACATAAGGT
**
365498 TCACTAGGAAATAGTGACGGAGTATACAA
1 TCACTAGGAAATAGTGACAAAGTATACAA
*
365527 TCACTAGGAAATGGTGACAAAGTATACAA
1 TCACTAGGAAATAGTGACAAAGTATACAA
365556 TC
1 TC
365558 CATGGGGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.22
Consensus pattern (29 bp):
TCACTAGGAAATAGTGACAAAGTATACAA
Found at i:367978 original size:23 final size:21
Alignment explanation
Indices: 367952--368003 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
367942 ACTTATTTTT
*
367952 ATGATGTTTAGAAACATATTTAC
1 ATGATGTTTAG-AA-ATAATTAC
* *
367975 ATGAT-TTGAGTAATAATTAC
1 ATGATGTTTAGAAATAATTAC
367995 ATGATGTTT
1 ATGATGTTT
368004 TATAAATGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 12 0.50
21 3 0.12
22 4 0.17
23 5 0.21
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (21 bp):
ATGATGTTTAGAAATAATTAC
Done.