Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000132.1 Hibiscus syriacus cultivar Beakdansim tig00000238_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: 187689
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2571 original size:2 final size:2
Alignment explanation
Indices: 2566--2594 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2556 ATTTTTTTTT
2566 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2595 TCTTTAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2674 original size:25 final size:22
Alignment explanation
Indices: 2642--2687 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
2632 TATATTGTAA
*
2642 TTATCTTTATCTAGTTATATTTTT
1 TTATCTTTA-ATAGTT-TATTTTT
2666 TTATACTTTAATAGTTTATTTT
1 TTAT-CTTTAATAGTTTATTTT
2688 ATACCTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 9 0.45
25 5 0.25
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65
Consensus pattern (22 bp):
TTATCTTTAATAGTTTATTTTT
Found at i:2787 original size:7 final size:7
Alignment explanation
Indices: 2767--2798 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
2757 TATAACTTTA
2767 TATATAT
1 TATATAT
2774 ATATATAT
1 -TATATAT
2782 TATATAT
1 TATATAT
2789 TATATAT
1 TATATAT
2796 TAT
1 TAT
2799 TTTTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATATAT
Found at i:3041 original size:38 final size:40
Alignment explanation
Indices: 2990--3066 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
2980 AGTGAGAGAG
*
2990 TAGCTTTTCTATTTT-TAAATA-TTTGTTGTATATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
3028 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATAT
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATAT
3067 TTCCTTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 12 0.35
39 7 0.21
40 15 0.44
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:3119 original size:9 final size:9
Alignment explanation
Indices: 3107--3131 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3097 CCTTATCTTA
3107 TTTATTTAT
1 TTTATTTAT
3116 TTTATTTAT
1 TTTATTTAT
3125 TTTATTT
1 TTTATTT
3132 TTTCCCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTATTTAT
Found at i:3161 original size:18 final size:18
Alignment explanation
Indices: 3140--3183 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3130 TTTTTCCCTT
*
3140 TTATTTATTCTCTTTATC
1 TTATTTATTCTCTTTACC
* *
3158 TTATTTGTTTTCTTTACC
1 TTATTTATTCTCTTTACC
*
3176 TTTTTTAT
1 TTATTTAT
3184 CTAACACATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.70
Consensus pattern (18 bp):
TTATTTATTCTCTTTACC
Found at i:5279 original size:85 final size:83
Alignment explanation
Indices: 5115--5283 Score: 220
Period size: 84 Copynumber: 2.0 Consensus size: 83
5105 TGGAAACCAC
* * * *
5115 CATATAGAAAGATAAGTATTTTTTTCTTTATCTGTTTTTTATTTTTGTTATTTTTGTTTTATTTG
1 CATATAGAAAGATAAGTATTTTTTTCCTTATCTATTTTTTATTTTTGTTATTTTTGTTATATCT-
5180 CTTCCCCTTTTTTTTTTTT
65 CTTCCCCTTTTTTTTTTTT
*
5199 CATATTAGAAAGATAAGTA-TTTTTTCCTTATCTATTTTTTGTTTTT-TT-TTTTTGTTATATC-
1 CATA-TAGAAAGATAAGTATTTTTTTCCTTATCTATTTTTTATTTTTGTTATTTTTGTTATATCT
*
5260 CTTTCCCTTTTTTACTTTTTT
65 CTTCCCCTTTTTT--TTTTTT
5281 CAT
1 CAT
5284 GTTTAATGTT
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
80 12 0.16
82 20 0.26
83 2 0.03
84 28 0.37
85 14 0.18
ACGTcount: A:0.18, C:0.11, G:0.07, T:0.64
Consensus pattern (83 bp):
CATATAGAAAGATAAGTATTTTTTTCCTTATCTATTTTTTATTTTTGTTATTTTTGTTATATCTC
TTCCCCTTTTTTTTTTTT
Found at i:6313 original size:18 final size:18
Alignment explanation
Indices: 6292--6332 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
6282 TTCGTCCTCG
*
6292 TCCTCATCGTCACCGTCA
1 TCCTCATCGTCACCGGCA
* *
6310 TCCTCATCTTCATCGGCA
1 TCCTCATCGTCACCGGCA
6328 TCCTC
1 TCCTC
6333 TCTCACTGTC
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:0.15, C:0.44, G:0.10, T:0.32
Consensus pattern (18 bp):
TCCTCATCGTCACCGGCA
Found at i:10470 original size:35 final size:33
Alignment explanation
Indices: 10397--10504 Score: 182
Period size: 35 Copynumber: 3.2 Consensus size: 33
10387 GCCCTGATTA
10397 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTT-TATTAAT
10431 TATATATATAATATTTTATATTTGTTTGTATTAAT
1 TATATATATAATATTTTATATTT-TTT-TATTAAT
10466 TATATATATAATATTTTATATTTTTTTA-TAAT
1 TATATATATAATATTTTATATTTTTTTATTAAT
10498 TATATAT
1 TATATAT
10505 TTTTCAGGTT
Statistics
Matches: 72, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
32 11 0.15
33 2 0.03
34 26 0.36
35 33 0.46
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (33 bp):
TATATATATAATATTTTATATTTTTTTATTAAT
Found at i:16035 original size:17 final size:17
Alignment explanation
Indices: 16010--16049 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
16000 GTATGTTGTT
*
16010 CATTAAAGCATGGATTG
1 CATTTAAGCATGGATTG
* *
16027 CATTTAAGCATGTATTT
1 CATTTAAGCATGGATTG
16044 CATTTA
1 CATTTA
16050 GGGAAGTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGGATTG
Found at i:21283 original size:42 final size:42
Alignment explanation
Indices: 21176--21292 Score: 153
Period size: 42 Copynumber: 2.8 Consensus size: 42
21166 TCGAAGGTTC
* *
21176 TATGTGGCCCTTCGGGACATATATATGATTCTTTGGAACATA
1 TATGTGGTCCTTCGGGACATATATATGATCCTTTGGAACATA
** * * * *
21218 TATAAGGTCCTTCGAGACGTATATTTGGTCCTTTGGAACATA
1 TATGTGGTCCTTCGGGACATATATATGATCCTTTGGAACATA
*
21260 TATGTGGTCCTTGGGGACATATATATGATCCTT
1 TATGTGGTCCTTCGGGACATATATATGATCCTT
21293 GCTAATTCAG
Statistics
Matches: 60, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (42 bp):
TATGTGGTCCTTCGGGACATATATATGATCCTTTGGAACATA
Found at i:21293 original size:21 final size:21
Alignment explanation
Indices: 21184--21292 Score: 101
Period size: 21 Copynumber: 5.2 Consensus size: 21
21174 TCTATGTGGC
*
21184 CCTTCGGGACATATATATGAT
1 CCTTCGGGACATATATATGGT
* * * *
21205 TCTTTGGAACATATATAAGGT
1 CCTTCGGGACATATATATGGT
* * *
21226 CCTTCGAGACGTATATTTGGT
1 CCTTCGGGACATATATATGGT
* * *
21247 CCTTTGGAACATATATGTGGT
1 CCTTCGGGACATATATATGGT
* *
21268 CCTTGGGGACATATATATGAT
1 CCTTCGGGACATATATATGGT
21289 CCTT
1 CCTT
21293 GCTAATTCAG
Statistics
Matches: 67, Mismatches: 21, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 67 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37
Consensus pattern (21 bp):
CCTTCGGGACATATATATGGT
Found at i:22490 original size:31 final size:31
Alignment explanation
Indices: 22452--22513 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
22442 AGTTTAAAAA
* *
22452 GTAACAAAATGATCACTAATGTTATCGATTT
1 GTAACAAAATAATCACTAATATTATCGATTT
*
22483 GTAACAAATTAATCACTAATATTATCGATTT
1 GTAACAAAATAATCACTAATATTATCGATTT
22514 ATAATAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (31 bp):
GTAACAAAATAATCACTAATATTATCGATTT
Found at i:25453 original size:95 final size:95
Alignment explanation
Indices: 25263--25449 Score: 358
Period size: 94 Copynumber: 2.0 Consensus size: 95
25253 TCAAATAGGG
*
25263 TGGAGAAAATATAACAAAATAGAGAAAAGGTCTGAAGGTATCATTTTTCATGAAGTGATTTGTTT
1 TGGAGAAAATATAACAAAATAGAGAAAAAGTCTGAAGGTATCATTTTTCATGAAGTGATTTGTTT
25328 CAATGACCCCAAAATTTTCCAATTTTTTAT
66 CAATGACCCCAAAATTTTCCAATTTTTTAT
25358 TGGAGAAAATATAACAAAATAGAGAAAAAGTCTGAAGGTATCA-TTTTCATGAAGTGATTTGTTT
1 TGGAGAAAATATAACAAAATAGAGAAAAAGTCTGAAGGTATCATTTTTCATGAAGTGATTTGTTT
25422 CAATGACCCCAAAATTTTCCAATTTTTT
66 CAATGACCCCAAAATTTTCCAATTTTTT
25450 TATTTGTTGT
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
94 49 0.54
95 42 0.46
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.34
Consensus pattern (95 bp):
TGGAGAAAATATAACAAAATAGAGAAAAAGTCTGAAGGTATCATTTTTCATGAAGTGATTTGTTT
CAATGACCCCAAAATTTTCCAATTTTTTAT
Found at i:30775 original size:16 final size:16
Alignment explanation
Indices: 30756--30789 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
30746 ATTGACATTT
*
30756 ACTTTATATTGGATTG
1 ACTTTATATGGGATTG
30772 ACTTTATATGGGATTG
1 ACTTTATATGGGATTG
30788 AC
1 AC
30790 ATACTTGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (16 bp):
ACTTTATATGGGATTG
Found at i:34371 original size:21 final size:21
Alignment explanation
Indices: 34320--34373 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
34310 ATTCTGACTA
34320 TCGTATTGCGATTTTTTAAAT
1 TCGTATTGCGATTTTTTAAAT
** *
34341 TCGCGTTGCGATTTTTTGAAT
1 TCGTATTGCGATTTTTTAAAT
*
34362 TCGTAATGCGAT
1 TCGTATTGCGAT
34374 AGCCCAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.46
Consensus pattern (21 bp):
TCGTATTGCGATTTTTTAAAT
Found at i:34415 original size:21 final size:21
Alignment explanation
Indices: 34391--34448 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
34381 AATCGCATTG
34391 CGATAGCACTGTTCACCGTTA
1 CGATAGCACTGTTCACCGTTA
* * *
34412 CGATAGCACTGTTAACTGTTG
1 CGATAGCACTGTTCACCGTTA
34433 CGATAGCACTGTTCAC
1 CGATAGCACTGTTCAC
34449 ATTGCGAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (21 bp):
CGATAGCACTGTTCACCGTTA
Found at i:35192 original size:21 final size:21
Alignment explanation
Indices: 35126--35197 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
35116 ATTTTGATCA
* *
35126 CTATCGTAATGGTGAACAGTG
1 CTATCGCAACGGTGAACAGTG
* * *
35147 CTACCGTAACGGTGAACAGTA
1 CTATCGCAACGGTGAACAGTG
35168 CTATCGCAACGGTGAACAGTG
1 CTATCGCAACGGTGAACAGTG
35189 CTATCGCAA
1 CTATCGCAA
35198 TGCGATTTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (21 bp):
CTATCGCAACGGTGAACAGTG
Found at i:35213 original size:21 final size:21
Alignment explanation
Indices: 35189--35242 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
35179 GTGAACAGTG
*
35189 CTATCGCAATGCGATTTTGGA
1 CTATCGCAATGCGAATTTGGA
*
35210 CTATCGCATTGCGAATTTGGA
1 CTATCGCAATGCGAATTTGGA
**
35231 AAATCGCAATGC
1 CTATCGCAATGC
35243 AATAGTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (21 bp):
CTATCGCAATGCGAATTTGGA
Found at i:36078 original size:21 final size:20
Alignment explanation
Indices: 36052--36248 Score: 175
Period size: 21 Copynumber: 9.6 Consensus size: 20
36042 GTTTCCAGAT
*
36052 TCGCAACGCGAACTTGGACTA
1 TCGCAATGCGAA-TTGGACTA
36073 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAA-TTGGACTA
* *
36094 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAAT-TGGACTA
*
36114 TCGCAATGCGATAGTGGACTA
1 TCGCAATGCGA-ATTGGACTA
*
36135 TCGCAATGCGAACTTAGACTA
1 TCGCAATGCGAA-TTGGACTA
* *
36156 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAAT-TGGACTA
* * *
36176 TCGCAATGCGGTAGTCGACTA
1 TCGCAATGC-GAATTGGACTA
*
36197 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAA-TTGGACTA
* *
36218 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAAT-TGGACTA
36238 TCGCAATGCGA
1 TCGCAATGCGA
36249 TAGTCCAAGT
Statistics
Matches: 146, Mismatches: 21, Indels: 19
0.78 0.11 0.10
Matches are distributed among these distances:
20 45 0.31
21 101 0.69
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATTGGACTA
Found at i:36117 original size:41 final size:41
Alignment explanation
Indices: 36072--36248 Score: 170
Period size: 41 Copynumber: 4.3 Consensus size: 41
36062 AACTTGGACT
36072 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTA-A
1 ATCGCAATGCGAA-TTGGACTATCGCAATGCGAATATGTACA
* *
36113 ATCGCAATGCGATAGTGGACTATCGCAATGCGAACT-TAG-ACT
1 ATCGCAATGCGA-ATTGGACTATCGCAATGCGAA-TAT-GTACA
* * * *
36155 ATCGCAATGCGAATATGTA-AATCGCAATGCG-GTA-GTCGACT
1 ATCGCAATGCGAAT-TGGACTATCGCAATGCGAATATGT--ACA
*
36196 ATCGCAATGCGAACTTCGACTATCGCAATGCGAATATGTA-A
1 ATCGCAATGCGAA-TTGGACTATCGCAATGCGAATATGTACA
36237 ATCGCAATGCGA
1 ATCGCAATGCGA
36249 TAGTCCAAGT
Statistics
Matches: 112, Mismatches: 11, Indels: 26
0.75 0.07 0.17
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
41 75 0.67
42 31 0.28
43 2 0.02
44 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (41 bp):
ATCGCAATGCGAATTGGACTATCGCAATGCGAATATGTACA
Found at i:36200 original size:83 final size:83
Alignment explanation
Indices: 36052--36229 Score: 204
Period size: 83 Copynumber: 2.1 Consensus size: 83
36042 GTTTCCAGAT
* * *
36052 TCGCAACGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
1 TCGCAATGCGAACTTAGACTATCGCAATGCGAACTTGGACAATCGCAATGCGAATATGTAAATCG
*
36117 CAATGCGATA-GTGGACTA
66 CAATGCGA-ACGTCGACTA
* * *
36135 TCGCAATGCGAACTTAGACTATCGCAATGCGAA-TATGTA-AATCGCAATGCG-GTA-GTCGACT
1 TCGCAATGCGAACTTAGACTATCGCAATGCGAACT-TGGACAATCGCAATGCGAATATGT--A-A
*
36196 ATCGCAATGCGAACTTCGACTA
62 ATCGCAATGCGAACGTCGACTA
36218 TCGCAATGCGAA
1 TCGCAATGCGAA
36230 TATGTAAATC
Statistics
Matches: 82, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
80 2 0.02
81 2 0.02
82 14 0.17
83 64 0.78
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.23
Consensus pattern (83 bp):
TCGCAATGCGAACTTAGACTATCGCAATGCGAACTTGGACAATCGCAATGCGAATATGTAAATCG
CAATGCGAACGTCGACTA
Found at i:36253 original size:62 final size:62
Alignment explanation
Indices: 36068--36253 Score: 336
Period size: 62 Copynumber: 3.0 Consensus size: 62
36058 CGCGAACTTG
* *
36068 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTG
1 GACTATCGCAATGCGAACTTAGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
*
36130 GACTATCGCAATGCGAACTTAGACTATCGCAATGCGAATATGTAAATCGCAATGCGGTAGTC
1 GACTATCGCAATGCGAACTTAGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
*
36192 GACTATCGCAATGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAACTTAGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
36254 CAAGTTCGTT
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 119 1.00
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (62 bp):
GACTATCGCAATGCGAACTTAGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
Found at i:36873 original size:5 final size:5
Alignment explanation
Indices: 36859--36889 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
36849 CGTGCGCCGC
36859 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
36890 GGTCGTGTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.00, C:0.42, G:0.23, T:0.35
Consensus pattern (5 bp):
CGTCT
Found at i:36895 original size:15 final size:15
Alignment explanation
Indices: 36863--36910 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
36853 CGCCGCCGTC
*
36863 CGTCTCGTCTCGTCT
1 CGTCTCGTCTCGTGT
*
36878 CGTCTCGTCTCGGGT
1 CGTCTCGTCTCGTGT
* *
36893 CGTGTCGTGTCGTGT
1 CGTCTCGTCTCGTGT
36908 CGT
1 CGT
36911 GGTCGCGGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.00, C:0.31, G:0.31, T:0.38
Consensus pattern (15 bp):
CGTCTCGTCTCGTGT
Found at i:36920 original size:6 final size:6
Alignment explanation
Indices: 36890--36931 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
36880 TCTCGTCTCG
*
36890 GGTCGT -GTCGT -GTCGT -GTCGT GGTCGC GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
36932 AATACGTGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 15 0.45
6 18 0.55
ACGTcount: A:0.00, C:0.19, G:0.48, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:37083 original size:42 final size:42
Alignment explanation
Indices: 37020--37156 Score: 229
Period size: 42 Copynumber: 3.3 Consensus size: 42
37010 TGCGATTTTG
* *
37020 GACTATCGCAACGAATCTGGAATAGATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
37062 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
37104 GACTATCGCAACGAACTTGGAATAAATCGCAATGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
37146 GACTATCGCAA
1 GACTATCGCAA
37157 TGCAAATATG
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 90 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:37159 original size:21 final size:20
Alignment explanation
Indices: 37017--37156 Score: 108
Period size: 21 Copynumber: 6.7 Consensus size: 20
37007 CGTTGCGATT
37017 TTGGACTATCGCAA-CGAA-
1 TTGGACTATCGCAAGCGAAC
*
37035 TCTGGAATAGATCGCAACGCGAAC
1 T-TGGACT--ATCGCAA-GCGAAC
* *
37059 TTCGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
*
37078 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
37101 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
*
37120 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
37143 TTGGACTATCGCAA
1 TTGGACTATCGCAA
37157 TGCAAATATG
Statistics
Matches: 96, Mismatches: 12, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
18 1 0.01
19 24 0.25
21 42 0.44
23 28 0.29
24 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:37836 original size:23 final size:23
Alignment explanation
Indices: 37792--37837 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
37782 ATAAAAATAA
*
37792 TTATATCTTTGTAACACGTTTTT
1 TTATATCTTTGTAACACATTTTT
* * *
37815 TTATATTTTTGTGATACATTTTT
1 TTATATCTTTGTAACACATTTTT
37838 ATCTTATTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.61
Consensus pattern (23 bp):
TTATATCTTTGTAACACATTTTT
Found at i:38589 original size:21 final size:21
Alignment explanation
Indices: 38563--38602 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
38553 CCACAACGGC
*
38563 CGCAATAGCGTCCGCGACGAT
1 CGCAATAGCGCCCGCGACGAT
38584 CGCAATAGCGCCCGCGACG
1 CGCAATAGCGCCCGCGACG
38603 GCCGTAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.38, G:0.30, T:0.10
Consensus pattern (21 bp):
CGCAATAGCGCCCGCGACGAT
Found at i:41613 original size:60 final size:60
Alignment explanation
Indices: 41497--41614 Score: 146
Period size: 60 Copynumber: 2.0 Consensus size: 60
41487 TTGAGTGATC
** * * *
41497 ATTTTATAACTTTTAATAGTCGGGGGACTCAACAAAGCAACACCCTATAATTGAAGGACT
1 ATTTTATAACTTTTAATAGTCAAGAGACTCAACAAAACAACACCCTATAATCGAAGGACT
* * * * *
41557 ATTTTATAACTTTTAATATTCAAGAGATTCAACAAAACATCACCTTATAGTCGAAGGA
1 ATTTTATAACTTTTAATAGTCAAGAGACTCAACAAAACAACACCCTATAATCGAAGGA
41615 TCATTTGTAT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.31
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTCAAGAGACTCAACAAAACAACACCCTATAATCGAAGGACT
Found at i:42922 original size:8 final size:8
Alignment explanation
Indices: 42905--42934 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
42895 TCCTCCAAGG
42905 CTTT-GAA
1 CTTTGGAA
42912 CTTTGGAA
1 CTTTGGAA
42920 CTTTGGAA
1 CTTTGGAA
42928 CTTTGGA
1 CTTTGGA
42935 TACCTTGCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.18
8 18 0.82
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (8 bp):
CTTTGGAA
Found at i:43158 original size:31 final size:31
Alignment explanation
Indices: 43123--43190 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
43113 AATAATCATT
43123 GACTATAAGATATTACTTTGTTGAGTCCCTC
1 GACTATAAGATATTACTTTGTTGAGTCCCTC
43154 GACTATAAGATATTACTTTGTTGAGTCCCTC
1 GACTATAAGATATTACTTTGTTGAGTCCCTC
43185 GACTAT
1 GACTAT
43191 TAAAAGTTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.38
Consensus pattern (31 bp):
GACTATAAGATATTACTTTGTTGAGTCCCTC
Found at i:43787 original size:16 final size:16
Alignment explanation
Indices: 43766--43816 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
43756 AAATATTATT
43766 ATTTTTTTAATTTTTA
1 ATTTTTTTAATTTTTA
*
43782 ATTTTTATTAA-GTTTA
1 ATTTTT-TTAATTTTTA
*
43798 ATATTTTT-ATATTTTA
1 ATTTTTTTAAT-TTTTA
43814 ATT
1 ATT
43817 AAATTTCCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 1 0.04
15 2 0.07
16 21 0.75
17 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
ATTTTTTTAATTTTTA
Found at i:43805 original size:18 final size:18
Alignment explanation
Indices: 43765--43807 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
43755 AAAATATTAT
* *
43765 TATTTTT-TTAATTTTTA
1 TATTTTTATTAAGTTTAA
43782 -ATTTTTATTAAGTTTAA
1 TATTTTTATTAAGTTTAA
43799 TATTTTTAT
1 TATTTTTAT
43808 ATTTTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 8 0.36
18 8 0.36
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
TATTTTTATTAAGTTTAA
Found at i:48320 original size:21 final size:21
Alignment explanation
Indices: 48234--48377 Score: 135
Period size: 21 Copynumber: 6.7 Consensus size: 21
48224 CTAGTAGAAT
* *
48234 TGTCCCGAAGGACCACATAGAAA
1 TGTCCCAAAGGACCACAT--ATA
* *
48257 TGTCCCGAAGGACCACATAGAA
1 TGTCCCAAAGGACCACATA-TA
* *
48279 TTGTCCCTAAGGGCCACATATA
1 -TGTCCCAAAGGACCACATATA
* *
48301 TGTTCCAAAGGACCAAATATA
1 TGTCCCAAAGGACCACATATA
* *
48322 TATCCCGAAGGACCACATATA
1 TGTCCCAAAGGACCACATATA
* *
48343 TGTTCCAAAGGATCACATATA
1 TGTCCCAAAGGACCACATATA
*
48364 TGTCCCGAAGGACC
1 TGTCCCAAAGGACC
48378 GCGTAGAACC
Statistics
Matches: 101, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
21 63 0.62
22 3 0.03
23 35 0.35
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (21 bp):
TGTCCCAAAGGACCACATATA
Found at i:48341 original size:42 final size:42
Alignment explanation
Indices: 48234--48377 Score: 171
Period size: 42 Copynumber: 3.3 Consensus size: 42
48224 CTAGTAGAAT
* * * *
48234 TGTCCCGAAGGACCACATAGAAATGTCCCGAAGGACCACATAGAA
1 TGTCCCGAAGGACCACAT--ATATGTTCCAAAGGACCACATA-TA
* * *
48279 TTGTCCCTAAGGGCCACATATATGTTCCAAAGGACCAAATATA
1 -TGTCCCGAAGGACCACATATATGTTCCAAAGGACCACATATA
* *
48322 TATCCCGAAGGACCACATATATGTTCCAAAGGATCACATATA
1 TGTCCCGAAGGACCACATATATGTTCCAAAGGACCACATATA
48364 TGTCCCGAAGGACC
1 TGTCCCGAAGGACC
48378 GCGTAGAACC
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
42 50 0.59
43 1 0.01
44 18 0.21
46 16 0.19
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (42 bp):
TGTCCCGAAGGACCACATATATGTTCCAAAGGACCACATATA
Found at i:54262 original size:22 final size:22
Alignment explanation
Indices: 54236--54292 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
54226 CGGTCATCGA
*
54236 CCGGTCACTATTCCGGCCACTG
1 CCGGTCACTATTCCGACCACTG
*
54258 CCGGTCACTATTCTGACCACTG
1 CCGGTCACTATTCCGACCACTG
*
54280 TCGGTCACTATTC
1 CCGGTCACTATTC
54293 ACTGTCACTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.16, C:0.37, G:0.19, T:0.28
Consensus pattern (22 bp):
CCGGTCACTATTCCGACCACTG
Found at i:54961 original size:3 final size:3
Alignment explanation
Indices: 54955--55034 Score: 76
Period size: 3 Copynumber: 26.7 Consensus size: 3
54945 GTATTATTTG
* *
54955 TAA TAA TAA -ATA TAT TAA TATA TAA TAA TAA TAG TAA TAA TAA TAAA
1 TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA T-AA
* *
55002 TAA TAA TAC T-A TAA TAA T-A TAG TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
55035 TATGCAAACT
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
2 4 0.06
3 52 0.83
4 7 0.11
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:54998 original size:25 final size:23
Alignment explanation
Indices: 54955--55037 Score: 100
Period size: 22 Copynumber: 3.6 Consensus size: 23
54945 GTATTATTTG
*
54955 TAATAATAA-ATATATTAATATA
1 TAATAATAATATATAATAATATA
*
54977 TAATAATAATA-GTAATAATA-A
1 TAATAATAATATATAATAATATA
54998 TAAATAATAATACTATAATAATATA
1 T-AATAATAATA-TATAATAATATA
55023 GTAATAATAATATAT
1 -TAATAATAATATAT
55038 GCAAACTCGA
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
21 2 0.04
22 26 0.50
23 1 0.02
24 11 0.21
25 11 0.21
26 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.37
Consensus pattern (23 bp):
TAATAATAATATATAATAATATA
Found at i:55273 original size:75 final size:75
Alignment explanation
Indices: 55167--55328 Score: 243
Period size: 75 Copynumber: 2.2 Consensus size: 75
55157 CGACCTGAAA
* *
55167 GATTTAATTTTCATGAGAAAACATCATACCCTGAGGTTTTACAGATGACCCGTAAGACTTACAAA
1 GATTTAATTTTCATGAGAAAACATCATACCCTAAGGTTTTACAGATGACCCGGAAGACTTACAAA
*
55232 TTACCCGGAG
66 TTACCCAGAG
* * * * *
55242 GATTTAATTTTCATGAGAAAACATCCTACCCTAAGGTTTTATAGATGACCTGGAGGATTTACAAA
1 GATTTAATTTTCATGAGAAAACATCATACCCTAAGGTTTTACAGATGACCCGGAAGACTTACAAA
55307 TTACCCAGAG
66 TTACCCAGAG
*
55317 GTTTTAATTTTC
1 GATTTAATTTTC
55329 TAGAGCATTA
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (75 bp):
GATTTAATTTTCATGAGAAAACATCATACCCTAAGGTTTTACAGATGACCCGGAAGACTTACAAA
TTACCCAGAG
Found at i:55494 original size:99 final size:98
Alignment explanation
Indices: 55294--55519 Score: 326
Period size: 99 Copynumber: 2.3 Consensus size: 98
55284 AGATGACCTG
* * * *
55294 GAGGATTTACAAATTACCCAGAGGTTTTAATTTTCTAGAGCATTAAATGAGAAACTTTAAAAATT
1 GAGG-TTTATAAATGACCCAGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTAAAAATC
*
55359 GCTTTCTCATTTTCATGCGAAAACATCCTACACT
65 GCTTTCTCATTTTCATGCGAAAACATCATACACT
* * ***
55393 GAGGTTTTATAGATGACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGGTAATC
1 GAGG-TTTATAAATGACCCAGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTAAAAATC
*
55458 GCTTTCTCATTTTCATGCGAAAACATCATACCCT
65 GCTTTCTCATTTTCATGCGAAAACATCATACACT
*
55492 GAGGTTTATAAATGACCCAGAGGATTTA
1 GAGGTTTATAAATGACCCAGAGGTTTTA
55520 CAAATTACCC
Statistics
Matches: 112, Mismatches: 15, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
98 21 0.19
99 91 0.81
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (98 bp):
GAGGTTTATAAATGACCCAGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTAAAAATCG
CTTTCTCATTTTCATGCGAAAACATCATACACT
Found at i:55539 original size:20 final size:19
Alignment explanation
Indices: 55486--55537 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
55476 GAAAACATCA
* *
55486 TACCCTGAGGTTTATAAAT
1 TACCCAGAGGTTTACAAAT
*
55505 GACCCAGAGGATTTACAAAT
1 TACCCAGAGG-TTTACAAAT
55525 TACCCAGAGGTTT
1 TACCCAGAGGTTT
55538 TAATTTTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (19 bp):
TACCCAGAGGTTTACAAAT
Found at i:55948 original size:42 final size:42
Alignment explanation
Indices: 55868--55949 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
55858 AAGGACTTAT
* * *
55868 CATCTTGCTCGAAAGACTAACATATAACCCGAAAGATTTAAG
1 CATCATGCTCGAAAGACTAAAAGATAACCCGAAAGATTTAAG
*
55910 CATCATGCTCGAAAGACTAAAAGATGACCC-AAAGGATTTA
1 CATCATGCTCGAAAGACTAAAAGATAACCCGAAA-GATTTA
55950 CAAATTTGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 3 0.09
42 32 0.91
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (42 bp):
CATCATGCTCGAAAGACTAAAAGATAACCCGAAAGATTTAAG
Found at i:57515 original size:51 final size:51
Alignment explanation
Indices: 57439--57780 Score: 371
Period size: 51 Copynumber: 6.5 Consensus size: 51
57429 TATGCTGGAA
* * *
57439 TGAGCCTTCAAGATGCCTCACATGGATTACTTCTATCTTTTTCATGTTGATG
1 TGAGCCTTCAAGATACC-CACATGGATAACTTCTATCTTTTTCATGCTGATG
* * *
57491 TGAGCCTTTAAGATACCCACATGGATAACTTATATCTTTTTTATGCTGATG
1 TGAGCCTTCAAGATACCCACATGGATAACTTCTATCTTTTTCATGCTGATG
* * * *
57542 TGAGCCTTCAAGATGCCTCACATGGATTACTTCTGTCTTTTCCATGCTGATG
1 TGAGCCTTCAAGATACC-CACATGGATAACTTCTATCTTTTTCATGCTGATG
* * * * *
57594 TGAGCCTTTAATATACCCACATGGATAACTTATTTCTTTTTTATGCTGATG
1 TGAGCCTTCAAGATACCCACATGGATAACTTCTATCTTTTTCATGCTGATG
* * * * *
57645 CGAGCCTTCAAGATGCCCCAGATTGATTACTTCTATC-TTTTCATGCTGATG
1 TGAGCCTTCAAGAT-ACCCACATGGATAACTTCTATCTTTTTCATGCTGATG
* * *
57696 TGAGCCTTCAAGATACCCACATTGATAACTTCTGACTCTTTTTTTTAATGCTGACG
1 TGAGCCTTCAAGATACCCACATGGATAACTTCT-A-TC---TTTTTCATGCTGATG
* *
57752 TGAGACTTCAAGATGACCCAGATGGATAA
1 TGAGCCTTCAAGAT-ACCCACATGGATAA
57781 TATAAACCTT
Statistics
Matches: 241, Mismatches: 40, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
50 16 0.07
51 112 0.46
52 76 0.32
56 25 0.10
57 12 0.05
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (51 bp):
TGAGCCTTCAAGATACCCACATGGATAACTTCTATCTTTTTCATGCTGATG
Found at i:57604 original size:103 final size:102
Alignment explanation
Indices: 57425--57766 Score: 479
Period size: 103 Copynumber: 3.3 Consensus size: 102
57415 TATCCCAACA
* *
57425 TTTTTATGCTGGA-ATGAGCCTTCAAGATGCCTCACATGGATTACTTCTATCTTTTTCATGTTGA
1 TTTTTATGCT-GATGTGAGCCTTCAAGATGCCTCACATGGATTACTTCTATC-TTTTCATGCTGA
57489 TGTGAGCCTTTAAGATACCCACATGGATAACTTATATCT
64 TGTGAGCCTTTAAGATACCCACATGGATAACTTATATCT
*
57528 TTTTTATGCTGATGTGAGCCTTCAAGATGCCTCACATGGATTACTTCTGTCTTTTCCATGCTGAT
1 TTTTTATGCTGATGTGAGCCTTCAAGATGCCTCACATGGATTACTTCTATCTTTT-CATGCTGAT
* *
57593 GTGAGCCTTTAATATACCCACATGGATAACTTATTTCT
65 GTGAGCCTTTAAGATACCCACATGGATAACTTATATCT
* * * *
57631 TTTTTATGCTGATGCGAGCCTTCAAGATGCCCCAGATTGATTACTTCTATCTTTTCATGCTGATG
1 TTTTTATGCTGATGTGAGCCTTCAAGATGCCTCACATGGATTACTTCTATCTTTTCATGCTGATG
* * *
57696 TGAGCCTTCAAGATACCCACATTGATAACTTCTGACTCTTT
66 TGAGCCTTTAAGATACCCACATGGATAACTTAT-A-TC--T
* *
57737 TTTTTAATGCTGACGTGAGACTTCAAGATG
1 TTTTT-ATGCTGATGTGAGCCTTCAAGATG
57767 ACCCAGATGG
Statistics
Matches: 214, Mismatches: 18, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
102 45 0.21
103 140 0.65
104 2 0.01
106 6 0.03
107 21 0.10
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.39
Consensus pattern (102 bp):
TTTTTATGCTGATGTGAGCCTTCAAGATGCCTCACATGGATTACTTCTATCTTTTCATGCTGATG
TGAGCCTTTAAGATACCCACATGGATAACTTATATCT
Found at i:65026 original size:3 final size:3
Alignment explanation
Indices: 65020--65102 Score: 73
Period size: 3 Copynumber: 27.7 Consensus size: 3
65010 GTATTATTTG
* *
65020 TAA TAA TAA -ATA TAT TAA TATA TAA TAA TAA TAG TAA TAA TAAA TAA
1 TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA T-AA TAA
* * *
65067 TAG TAA TAG T-A TAA TAC T-A TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
65103 TATGCAAACT
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
2 3 0.05
3 54 0.84
4 7 0.11
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:65048 original size:22 final size:21
Alignment explanation
Indices: 65020--65105 Score: 97
Period size: 22 Copynumber: 4.0 Consensus size: 21
65010 GTATTATTTG
65020 TAATAATAAATA-TATTAATATA
1 TAATAAT-AATAGTA-TAATATA
*
65042 TAATAATAATAGTAATAATAAA
1 TAATAATAATAGT-ATAATATA
*
65064 TAATAGTAATAGTATAATACTA
1 TAATAATAATAGTATAATA-TA
65086 TAATAATAATA--ATAATATA
1 TAATAATAATAGTATAATATA
65105 T
1 T
65106 GCAAACTTGG
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
19 3 0.05
20 6 0.11
21 10 0.18
22 37 0.65
23 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.37
Consensus pattern (21 bp):
TAATAATAATAGTATAATATA
Found at i:67296 original size:19 final size:19
Alignment explanation
Indices: 67272--67323 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
67262 TATACATGAG
67272 CTATGTGTTACATGTCATC
1 CTATGTGTTACATGTCATC
67291 CTATGTGTTACATGTCATC
1 CTATGTGTTACATGTCATC
67310 CTATGTGTTACATG
1 CTATGTGTTACATG
67324 ATTTATGTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.42
Consensus pattern (19 bp):
CTATGTGTTACATGTCATC
Found at i:70544 original size:54 final size:54
Alignment explanation
Indices: 70485--70713 Score: 280
Period size: 54 Copynumber: 4.2 Consensus size: 54
70475 TACCAAATAA
* *
70485 GCACTAAGTGTGCATTTCACGGAATTCATCGTATGTGGATGAATAACCGTTTCG
1 GCACTAAGTGTGCATTTCACAGAATTCATCATATGTGGATGAATAACCGTTTCG
* * *
70539 GCACTAAGTGTGCATTTCACAAAATTCATCTTATGTGGGTGAATAACCGCTTT-G
1 GCACTAAGTGTGCATTTCACAGAATTCATCATATGTGGATGAATAACCG-TTTCG
* * * *
70593 ACACTAATTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACTGTTTCG
1 GCACTAAGTGTGCATTTCACAGAATTCATCATATGTGGATGAATAACCGTTTCG
** * * * ** *
70647 ATACTAAGTATGTATTTCACGGAATTCATCATATGTGGATGAATAATTGTTTGG
1 GCACTAAGTGTGCATTTCACAGAATTCATCATATGTGGATGAATAACCGTTTCG
*
70701 GCACTATGTGTGC
1 GCACTAAGTGTGC
70714 TAAAATGTTA
Statistics
Matches: 150, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
53 3 0.02
54 144 0.96
55 3 0.02
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (54 bp):
GCACTAAGTGTGCATTTCACAGAATTCATCATATGTGGATGAATAACCGTTTCG
Found at i:70807 original size:58 final size:59
Alignment explanation
Indices: 70697--70808 Score: 163
Period size: 58 Copynumber: 1.9 Consensus size: 59
70687 GAATAATTGT
* * * *
70697 TTGGGCACTATGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGCATGAATTTCTGTA
1 TTGGGCACTATATGTGCTAAAAAGATAAGAAACTCATACTAAGTGCATGAATTTCTGTA
* *
70756 TTGGGCACTTTATGTGC-AAAAAGATAAGAAACTCATACTAAGTGTATGAATTT
1 TTGGGCACTATATGTGCTAAAAAGATAAGAAACTCATACTAAGTGCATGAATTT
70809 TCACATGGGA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
58 32 0.68
59 15 0.32
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.34
Consensus pattern (59 bp):
TTGGGCACTATATGTGCTAAAAAGATAAGAAACTCATACTAAGTGCATGAATTTCTGTA
Found at i:71349 original size:2 final size:2
Alignment explanation
Indices: 71342--71420 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
71332 AGAATGGATG
71342 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
71384 AT AT AT 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 AT AT AT A
71421 ATGTACAATA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:72613 original size:30 final size:30
Alignment explanation
Indices: 72577--72660 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
72567 CCCGAAGGAC
* *
72577 CTATCCAGAGGTCACAAGGAACCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
* *
72607 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
* * * *
72637 CTGTCCATAGGTCCCGAAGAACCT
1 CTATCCAGAGGTCACAAAGAACCT
72661 AGGTATATTG
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGGCAA
Found at i:72723 original size:31 final size:31
Alignment explanation
Indices: 72640--72759 Score: 107
Period size: 31 Copynumber: 3.8 Consensus size: 31
72630 TCGGCAACTG
* * * *
72640 TCCATAGGTCCCGAAGAACCTAGGTATATTG
1 TCCATATGTCCCGAAGAACATAGGTATACTA
* * **
72671 TCCATATATTCCTTAGAACATAGGTATACTA
1 TCCATATGTCCCGAAGAACATAGGTATACTA
* *
72702 TCCATATGTCCCGAA-AGACATAGGTAATTCTG
1 TCCATATGTCCCGAAGA-ACATAGGT-ATACTA
* *
72734 TCCATATGTTCCGTAGAACATAGGTA
1 TCCATATGTCCCGAAGAACATAGGTA
72760 AACCCTCGAC
Statistics
Matches: 70, Mismatches: 16, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
30 1 0.01
31 43 0.61
32 25 0.36
33 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (31 bp):
TCCATATGTCCCGAAGAACATAGGTATACTA
Found at i:72757 original size:63 final size:62
Alignment explanation
Indices: 72640--72759 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 62
72630 TCGGCAACTG
* *
72640 TCCATAGGTCCCGAAGAACCTAGGTATATTGTCCATATATTCCTTAGAACATAGGTATACTA
1 TCCATAGGTCCCGAAGAACATAGGTATATTGTCCATATATTCCGTAGAACATAGGTATACTA
* *
72702 TCCATATGTCCCGAA-AGACATAGGTA-ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 TCCATAGGTCCCGAAGA-ACATAGGTATA-T-TGTCCATATATTCCGTAGAACATAGGTA
72760 AACCCTCGAC
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
61 2 0.04
62 23 0.45
63 26 0.51
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (62 bp):
TCCATAGGTCCCGAAGAACATAGGTATATTGTCCATATATTCCGTAGAACATAGGTATACTA
Found at i:92493 original size:132 final size:132
Alignment explanation
Indices: 92346--92709 Score: 503
Period size: 132 Copynumber: 2.8 Consensus size: 132
92336 GCTTCCTTGC
* *
92346 CTTTCTCCGCTGCATAGTCCTTATATTCAGTCGCTTTCTCTATTGTAGCATCCTTTGCATCCTTA
1 CTTTCTCCGCTGCATAGTCCTTATATTCAGCCGCTTTCTCCATTGTAGCATCCTTTGCATCCTTA
* * * *
92411 GCTTTCTGTGCTGCATAATCTGTATATTCGGAAGCCTTTTGCGCGGTTGTATCTTTTGCATCCTT
66 GCTTTCTGTGCTGCATAATCTGTATATTCGGAAGCCTTTTGCCCGGTGGCATCTCTTGCATCCTT
92476 AG
131 AG
* * *
92478 CTTTCTCCGCAGCATAGTCCTTATATTCAGCCGCTTTCTCCATTGTAGTATCCTTTGTATCCTTA
1 CTTTCTCCGCTGCATAGTCCTTATATTCAGCCGCTTTCTCCATTGTAGCATCCTTTGCATCCTTA
* * * * * *
92543 GCTTTCTGTGCTGCATAATCTGCATAATAGGAAGCCTTTTGCCCTGTGGCATCTCTTGCCTGCTT
66 GCTTTCTGTGCTGCATAATCTGTATATTCGGAAGCCTTTTGCCCGGTGGCATCTCTTGCATCCTT
*
92608 GG
131 AG
* ** * * *
92610 CTTTCTCAGCTGTGTAATCCTTATATTCAGCCGCTTTCCCCATTGTAGCATCCTTCGCATCCTTA
1 CTTTCTCCGCTGCATAGTCCTTATATTCAGCCGCTTTCTCCATTGTAGCATCCTTTGCATCCTTA
* * *
92675 GATTTCTGTGCTGTATAATCTGTATATTCAGAAGC
66 GCTTTCTGTGCTGCATAATCTGTATATTCGGAAGC
92710 TTTACCGGTG
Statistics
Matches: 201, Mismatches: 31, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
132 201 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (132 bp):
CTTTCTCCGCTGCATAGTCCTTATATTCAGCCGCTTTCTCCATTGTAGCATCCTTTGCATCCTTA
GCTTTCTGTGCTGCATAATCTGTATATTCGGAAGCCTTTTGCCCGGTGGCATCTCTTGCATCCTT
AG
Found at i:92688 original size:66 final size:66
Alignment explanation
Indices: 92354--92705 Score: 247
Period size: 66 Copynumber: 5.3 Consensus size: 66
92344 GCCTTTCTCC
* * * *
92354 GCTGCATAGTCCTTATATTCAGTCGCTTTCTCTATTGTAGCATCCTTTGCATCCTTAGCTTTCTG
1 GCTGCATAATCCTTATATTCAGCCGCTTTCCCCATTGTAGCATCCTTTGCATCCTTAGCTTTCTG
92419 T
66 T
* * ** *
92420 GCTGCATAAT-CTGTATATTCGGAAGCC-TTTTGCGCGGTTGT---ATCTTTTGCATCCTTAGCT
1 GCTGCATAATCCT-TATATTC---AGCCGCTTT-CCCCATTGTAGCATCCTTTGCATCCTTAGCT
**
92480 TTCTCC
61 TTCTGT
* * * * *
92486 GCAGCATAGTCCTTATATTCAGCCGCTTTCTCCATTGTAGTATCCTTTGTATCCTTAGCTTTCTG
1 GCTGCATAATCCTTATATTCAGCCGCTTTCCCCATTGTAGCATCCTTTGCATCCTTAGCTTTCTG
92551 T
66 T
* *** * * * * * *
92552 GCTGCATAATCTGCATAATAGGAAGCC-TTTTGCCC--TGTGGCAT-CTCTTGCCTGCTTGGCTT
1 GCTGCATAATC--C-TTATATTCAGCCGCTTTCCCCATTGTAGCATCCT-TTGCATCCTTAGCTT
**
92613 TCTCA
62 TCTGT
** * *
92618 GCTGTGTAATCCTTATATTCAGCCGCTTTCCCCATTGTAGCATCCTTCGCATCCTTAGATTTCTG
1 GCTGCATAATCCTTATATTCAGCCGCTTTCCCCATTGTAGCATCCTTTGCATCCTTAGCTTTCTG
92683 T
66 T
*
92684 GCTGTATAAT-CTGTATATTCAG
1 GCTGCATAATCCT-TATATTCAG
92706 AAGCTTTACC
Statistics
Matches: 214, Mismatches: 53, Indels: 38
0.70 0.17 0.12
Matches are distributed among these distances:
63 18 0.08
64 10 0.05
65 6 0.03
66 150 0.70
67 4 0.02
68 9 0.04
69 17 0.08
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (66 bp):
GCTGCATAATCCTTATATTCAGCCGCTTTCCCCATTGTAGCATCCTTTGCATCCTTAGCTTTCTG
T
Found at i:92754 original size:132 final size:131
Alignment explanation
Indices: 92333--92738 Score: 435
Period size: 132 Copynumber: 3.1 Consensus size: 131
92323 CGTCGCGTCC
* * * * * *
92333 TTGGCTTCCTTGCCTTTCTCCGCTGCATAGTCCTTATATTCAGTCGCTTTCTCTATTGTAGCATC
1 TTGGCTT-CTTGGCTTTCTCAGCTGTATAATCCTTATATTCAGCCGCTTTCTCCATTGTAGCATC
* *
92398 CTTTGCATCCTTAGCTTTCTGTGCTGCATAATCTGTATATTCGGAAGCCTTTTGCGCGGT-TGTA
65 CTTTGCATCCTTAGCTTTCTGTGCTGCATAATCTGTATATTCAGAAGCCTTTTGC-CGGTGTGAA
92462 TCT
129 TCT
* * * * * * * *
92465 TTTGCATCCTTAGCTTTCTCCGCAGCATAGTCCTTATATTCAGCCGCTTTCTCCATTGTAGTATC
1 TTGGC-TTCTTGGCTTTCTCAGCTGTATAATCCTTATATTCAGCCGCTTTCTCCATTGTAGCATC
* * * * *
92530 CTTTGTATCCTTAGCTTTCTGTGCTGCATAATCTGCATAAT-AGGAAGCCTTTTGCC-CTGTGGC
65 CTTTGCATCCTTAGCTTTCTGTGCTGCATAATCTGTATATTCA-GAAGCCTTTTGCCGGTGT-GA
92593 ATCT
128 ATCT
* * * *
92597 CTTGCCTGCTTGGCTTTCTCAGCTGTGTAATCCTTATATTCAGCCGCTTTCCCCATTGTAGCATC
1 -TTGGCTTCTTGGCTTTCTCAGCTGTATAATCCTTATATTCAGCCGCTTTCTCCATTGTAGCATC
* * * *
92662 CTTCGCATCCTTAGATTTCTGTGCTGTATAATCTGTATATTCAGAAG-C-TTTACCGGTGACTGA
65 CTTTGCATCCTTAGCTTTCTGTGCTGCATAATCTGTATATTCAGAAGCCTTTTGCCGGTG--TGA
92725 ATCT
128 ATCT
*
92729 TTGGTTTCTT
1 TTGGCTTCTT
92739 TGGTCTTTTG
Statistics
Matches: 228, Mismatches: 37, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
130 6 0.03
131 12 0.05
132 204 0.89
133 6 0.03
ACGTcount: A:0.16, C:0.26, G:0.17, T:0.41
Consensus pattern (131 bp):
TTGGCTTCTTGGCTTTCTCAGCTGTATAATCCTTATATTCAGCCGCTTTCTCCATTGTAGCATCC
TTTGCATCCTTAGCTTTCTGTGCTGCATAATCTGTATATTCAGAAGCCTTTTGCCGGTGTGAATC
T
Found at i:93796 original size:17 final size:18
Alignment explanation
Indices: 93763--93796 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
93753 CCGCTACTAG
93763 TGAACCGGTCAGAACCGT
1 TGAACCGGTCAGAACCGT
*
93781 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
93797 GATCGGTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGT
Found at i:93976 original size:29 final size:29
Alignment explanation
Indices: 93911--93977 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
93901 GCTGAGCTCG
**
93911 ACTCAAACTTTAAAAGTAAGCTCAAATTG
1 ACTCAAACTTTAAAAGTAAGCTCAAATCA
* *
93940 ACTTAAACTTTAAAAGTAAGCTCAACTCA
1 ACTCAAACTTTAAAAGTAAGCTCAAATCA
93969 ACTCAAACT
1 ACTCAAACT
93978 CACGAACTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.27
Consensus pattern (29 bp):
ACTCAAACTTTAAAAGTAAGCTCAAATCA
Found at i:95139 original size:106 final size:106
Alignment explanation
Indices: 95000--95222 Score: 428
Period size: 106 Copynumber: 2.1 Consensus size: 106
94990 TTTGAATATT
*
95000 ATAATTTAATCCCTAAACTATGTCTCTTTTTCAAAATTGATCCCCAAACTTTTGAATATTCCAAT
1 ATAATTTAACCCCTAAACTATGTCTCTTTTTCAAAATTGATCCCCAAACTTTTGAATATTCCAAT
95065 TTCATCCCCAAATTCATCCAAATATGTAATTAGTTTCAACC
66 TTCATCCCCAAATTCATCCAAATATGTAATTAGTTTCAACC
*
95106 ATAATTCAACCCCTAAACTATGTCTCTTTTTCAAAATTGATCCCCAAACTTTTGAATATTCCAAT
1 ATAATTTAACCCCTAAACTATGTCTCTTTTTCAAAATTGATCCCCAAACTTTTGAATATTCCAAT
95171 TTCATCCCCAAATTCATCCAAATATGTAATTAGTTTCAACC
66 TTCATCCCCAAATTCATCCAAATATGTAATTAGTTTCAACC
95212 ATAATTTAACC
1 ATAATTTAACC
95223 TAAATTTTGT
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 114 1.00
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (106 bp):
ATAATTTAACCCCTAAACTATGTCTCTTTTTCAAAATTGATCCCCAAACTTTTGAATATTCCAAT
TTCATCCCCAAATTCATCCAAATATGTAATTAGTTTCAACC
Found at i:95454 original size:60 final size:60
Alignment explanation
Indices: 95305--95473 Score: 177
Period size: 60 Copynumber: 2.8 Consensus size: 60
95295 GTGTATACAT
* * *
95305 ATAGTTTGGGATGAAATTGGAATATTCAAAA-ACTTTGGGGACCAATTTAGAATGAAGGTC
1 ATAGTTTGGGATGAAATTGGAATATTTAAAAGAC-TTGAGGACCAATTTAGAATCAAGGTC
** * *
95365 ATAGTTTGGAGATGAAATTGCCATGTTTAAAAGA-TTGAGGACTAATTTAGAATCATA-GTC
1 ATAGTTTGG-GATGAAATTGGAATATTTAAAAGACTTGAGGACCAATTTAGAATCA-AGGTC
* *
95425 ATAGTTTAGGGATGAAATTGGAACATTTAAAAG--TTTATGGACCAATTTA
1 ATAGTTT-GGGATGAAATTGGAATATTTAAAAGACTTGA-GGACCAATTTA
95474 AAATGAGGAT
Statistics
Matches: 91, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
59 3 0.03
60 66 0.73
61 21 0.23
62 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (60 bp):
ATAGTTTGGGATGAAATTGGAATATTTAAAAGACTTGAGGACCAATTTAGAATCAAGGTC
Found at i:99728 original size:51 final size:51
Alignment explanation
Indices: 99652--99751 Score: 182
Period size: 51 Copynumber: 2.0 Consensus size: 51
99642 CCTCTGCTTC
* *
99652 GTTTCAAGGGGAGAGCTATGGTTTCATTTACGCATAATATCGTACCATTTT
1 GTTTCAAGGGCAGAGCTATGGTTTCATGTACGCATAATATCGTACCATTTT
99703 GTTTCAAGGGCAGAGCTATGGTTTCATGTACGCATAATATCGTACCATT
1 GTTTCAAGGGCAGAGCTATGGTTTCATGTACGCATAATATCGTACCATT
99752 CGCTGCCGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (51 bp):
GTTTCAAGGGCAGAGCTATGGTTTCATGTACGCATAATATCGTACCATTTT
Found at i:105954 original size:2 final size:2
Alignment explanation
Indices: 105942--105993 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
105932 AACTCGAATA
*
105942 AT AT AT GT 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
105984 AT AT AT AT AT
1 AT AT AT AT AT
105994 CTTTTAACAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:111069 original size:26 final size:26
Alignment explanation
Indices: 111040--111109 Score: 131
Period size: 26 Copynumber: 2.7 Consensus size: 26
111030 TAATGCACCG
*
111040 AAAGTGCATTGGTTGACAACAATGAT
1 AAAGTGCATTAGTTGACAACAATGAT
111066 AAAGTGCATTAGTTGACAACAATGAT
1 AAAGTGCATTAGTTGACAACAATGAT
111092 AAAGTGCATTAGTTGACA
1 AAAGTGCATTAGTTGACA
111110 TAATGATTCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.27
Consensus pattern (26 bp):
AAAGTGCATTAGTTGACAACAATGAT
Found at i:122810 original size:17 final size:17
Alignment explanation
Indices: 122784--122827 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
122774 GGTCTTGGCC
122784 TGCTGGACTTGGACCAT
1 TGCTGGACTTGGACCAT
* *
122801 TGCTGAACTTGGACCCT
1 TGCTGGACTTGGACCAT
122818 TGCTGGACTT
1 TGCTGGACTT
122828 TTACTGGACC
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:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (17 bp):
TGCTGGACTTGGACCAT
Found at i:122902 original size:20 final size:19
Alignment explanation
Indices: 122874--122914 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
122864 ATAAGCAATA
* *
122874 ATAAAAATAAATAAATGAT
1 ATAAAAATAAAAAAATAAT
122893 ATAAATAATAAAAAAATAAT
1 ATAAA-AATAAAAAAATAAT
122913 AT
1 AT
122915 TATATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
ATAAAAATAAAAAAATAAT
Found at i:123027 original size:39 final size:37
Alignment explanation
Indices: 122933--123287 Score: 372
Period size: 37 Copynumber: 9.6 Consensus size: 37
122923 TATATATATT
* * * * *
122933 TATTATATTTATTTTCCAAAATGTTTTTAAAACCACA
1 TATTATATATATTTTTCAAAATGTTTTCAAAACTATA
122970 TATTATAT-TCA-TTTTCAAAATGTTTTCAAAAACTATA
1 TATTATATAT-ATTTTTCAAAATGTTTTC-AAAACTATA
*
123007 TATTATATATATGTTTTCAAAAATATTTTCAAAAACTATA
1 TATTATATATAT-TTTTC-AAAATGTTTTC-AAAACTATA
123047 TATTATATATATGTTTTCAAAATGTTTTCAAAAACTATA
1 TATTATATATAT-TTTTCAAAATGTTTTC-AAAACTATA
* * * *
123086 TATTATACATATTTTTAAAAATATTTTCAAAATTATA
1 TATTATATATATTTTTCAAAATGTTTTCAAAACTATA
*
123123 TATTATATATA-TTTTCAGAAAGGTTTTCAAAACTATA
1 TATTATATATATTTTTCA-AAATGTTTTCAAAACTATA
*
123160 TA--ATATATA-TTTTCAAAAAGGTTTTCAAAACTATA
1 TATTATATATATTTTTC-AAAATGTTTTCAAAACTATA
* *
123195 TAATATATATA-TTTTCAAAAATCATTTTCAAAACTATA
1 TATTATATATATTTTTC-AAAAT-GTTTTCAAAACTATA
* * *
123233 TATTATACATA-TTTTCAAAAAGGCTTTCAAAACTATA
1 TATTATATATATTTTTC-AAAATGTTTTCAAAACTATA
123270 TA--ATATATA-TTTTCAAAA
1 TATTATATATATTTTTCAAAA
123288 CCTATATTAT
Statistics
Matches: 284, Mismatches: 23, Indels: 25
0.86 0.07 0.08
Matches are distributed among these distances:
34 4 0.01
35 44 0.15
36 21 0.07
37 93 0.33
38 48 0.17
39 36 0.13
40 38 0.13
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.44
Consensus pattern (37 bp):
TATTATATATATTTTTCAAAATGTTTTCAAAACTATA
Found at i:123298 original size:22 final size:22
Alignment explanation
Indices: 123257--123299 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
123247 TCAAAAAGGC
123257 TTTCAAAACTATATAATATATAT
1 TTTCAAAACTATAT-ATATATAT
123280 TTTCAAAACCTATAT-TATAT
1 TTTCAAAA-CTATATATATAT
123300 CATTATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 8 0.42
24 6 0.32
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTCAAAACTATATATATATAT
Found at i:123577 original size:22 final size:22
Alignment explanation
Indices: 123549--123592 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
123539 ACTATATGGT
* *
123549 ATGAACAGTATCGTGAACAATA
1 ATGAACAGTACCATGAACAATA
*
123571 ATGAACATTACCATGAACAATA
1 ATGAACAGTACCATGAACAATA
123593 CTACTATAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.23
Consensus pattern (22 bp):
ATGAACAGTACCATGAACAATA
Found at i:126454 original size:22 final size:22
Alignment explanation
Indices: 126429--126489 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
126419 TGCATATGAA
*
126429 ATTTGTCTCGAATGACCTATGT
1 ATTTGTCCCGAATGACCTATGT
* * *
126451 ATTTGTCCCAAAGGACCTCTGT
1 ATTTGTCCCGAATGACCTATGT
*
126473 ATATGTCCCGAATGACC
1 ATTTGTCCCGAATGACC
126490 GCGTAGACCC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (22 bp):
ATTTGTCCCGAATGACCTATGT
Found at i:129479 original size:2 final size:2
Alignment explanation
Indices: 129472--129525 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
129462 AGATAACCCT
129472 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
129514 TA TA TA TA TA TA
1 TA TA TA TA TA TA
129526 GGGTTATGAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:130929 original size:3 final size:3
Alignment explanation
Indices: 130921--130975 Score: 92
Period size: 3 Copynumber: 18.0 Consensus size: 3
130911 AAATTTAAAT
*
130921 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
130969 TTTA TTA
1 -TTA TTA
130976 AATATTACAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:131133 original size:30 final size:30
Alignment explanation
Indices: 131097--131170 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
131087 TTTCAAACCT
* *
131097 AGCTCCAGCCGCTGCCTCAAGCTTCTAGTG
1 AGCTCCAGCCGCCGCCTCAAGCTTCCAGTG
131127 AGCTCCAGCCGCCGCCTCAAGCTTCCAGTG
1 AGCTCCAGCCGCCGCCTCAAGCTTCCAGTG
* *
131157 AGTTCCAGCTGCCG
1 AGCTCCAGCCGCCG
131171 TTGGGAAGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.16, C:0.39, G:0.24, T:0.20
Consensus pattern (30 bp):
AGCTCCAGCCGCCGCCTCAAGCTTCCAGTG
Found at i:132563 original size:120 final size:120
Alignment explanation
Indices: 132446--132683 Score: 279
Period size: 120 Copynumber: 2.0 Consensus size: 120
132436 ATTTTAATCC
* * * * *
132446 TATTTTAA-TATTTATTTATTTTCCAATAT-TAAG-AAAGGGCAGTCTTAAAATAAC-TGGATGT
1 TATTTTAATTATTTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTT-AAAGAACTTAGAAGT
*
132507 CCATTTTCTGATATTTTTAAATAAATAAATATCTTATTTTATAAATTATATATTAAT
65 CC-TTTTCTGATATTTCTAAATAAATAAATATCTTATTTTATAAATTATATATTAAT
* ** * * * *
132564 TGTTTTAATTATTTATTTATTTTTTATTATCAAAGAAAAGAGCTGTCTTAAGGCACTTAGAAGTC
1 TATTTTAATTATTTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAGAACTTAGAAGTC
* *
132629 CTTTTCTGATATTTCTAAATAAATAAATATTTTA-TTTATAAATATATAAATTAAT
66 CTTTTCTGATATTTCTAAATAAATAAATATCTTATTTTATAAAT-TATATATTAAT
132684 ATATATTTTT
Statistics
Matches: 100, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
118 7 0.07
119 27 0.27
120 48 0.48
121 18 0.18
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.47
Consensus pattern (120 bp):
TATTTTAATTATTTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAGAACTTAGAAGTC
CTTTTCTGATATTTCTAAATAAATAAATATCTTATTTTATAAATTATATATTAAT
Found at i:132575 original size:20 final size:19
Alignment explanation
Indices: 132550--132593 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
132540 TTATTTTATA
132550 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
132570 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
132589 -ATTAT
1 AATTAT
132594 CAAAGAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 5 0.23
19 4 0.18
20 13 0.59
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:133234 original size:26 final size:28
Alignment explanation
Indices: 133185--133237 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
133175 TCAAATTTTT
**
133185 TATATACTTATTATTTTTATAGTATTTA
1 TATATACTTATTATTTGCATAGTATTTA
133213 TATATA-TTATTATTTGCA-AGTATTT
1 TATATACTTATTATTTGCATAGTATTT
133238 TCATTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 7 0.30
27 10 0.43
28 6 0.26
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (28 bp):
TATATACTTATTATTTGCATAGTATTTA
Found at i:135321 original size:7 final size:7
Alignment explanation
Indices: 135286--135326 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
135276 TTTTCATATA
135286 TGCATTT
1 TGCATTT
135293 T-CATTT
1 TGCATTT
135299 TGCATCTT
1 TGCAT-TT
135307 TGCATTT
1 TGCATTT
*
135314 TTCATTT
1 TGCATTT
135321 TGCATT
1 TGCATT
135327 CATACTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.20
7 17 0.57
8 7 0.23
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:139722 original size:114 final size:114
Alignment explanation
Indices: 139516--139741 Score: 398
Period size: 114 Copynumber: 2.0 Consensus size: 114
139506 AAGTGCCACG
139516 TTCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TTCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * *
139581 TGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATT
66 TGGTTCGGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATT
139630 TTCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TTCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * *
139695 TGGTTCGGTAGGAACCCCAGAATCAATCATTGGAATTGAAAGATGAA
66 TGGTTCGGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAA
139742 CTGCATGATC
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 106 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (114 bp):
TTCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTCGGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATT
Found at i:142215 original size:22 final size:22
Alignment explanation
Indices: 142186--142240 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
142176 ATCTACACTC
142186 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
142208 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
142230 TTCAAAGATGA
1 TTCAAAGATGA
142241 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:143030 original size:164 final size:164
Alignment explanation
Indices: 142755--143075 Score: 543
Period size: 164 Copynumber: 2.0 Consensus size: 164
142745 AAAATGAGCA
* * *
142755 TTATCTTGAGATTGGGGCATGTTACCTAATCGACGTGTTATTTCGAAAAATAATGAGAAAACGAT
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCGAAAAATAATGAGAAAACGAT
** * * *
142820 TTCCACAGTTTCTCATTTTATCTTTTCTAAAATGAAGTTGTTGAAAAGTAAGAAAACGATTTTCT
66 TTCCACAGTTTCTCATTCAATCTTTTCTAAAATGAAATTATTGAAAAGTAAGAAAACGATTTTCA
*
142885 TAGTTTTTTACTTAGTAAACTATTTCCAACAACT
131 TAGTTTCTTACTTAGTAAACTATTTCCAACAACT
*
142919 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTTGAAAAATAATGAGAAAACGAT
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCGAAAAATAATGAGAAAACGAT
*
142984 TTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTATTGAAAAGTAAGAAAACGATTTTCA
66 TTCCACAGTTTCTCATTCAATCTTTTCTAAAATGAAATTATTGAAAAGTAAGAAAACGATTTTCA
143049 TAGTTTCTTACTTAGTAAACTATTTCC
131 TAGTTTCTTACTTAGTAAACTATTTCC
143076 TATATCTGTA
Statistics
Matches: 146, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
164 146 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (164 bp):
TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCGAAAAATAATGAGAAAACGAT
TTCCACAGTTTCTCATTCAATCTTTTCTAAAATGAAATTATTGAAAAGTAAGAAAACGATTTTCA
TAGTTTCTTACTTAGTAAACTATTTCCAACAACT
Found at i:143205 original size:76 final size:76
Alignment explanation
Indices: 143079--143332 Score: 454
Period size: 76 Copynumber: 3.3 Consensus size: 76
143069 TATTTCCTAT
*
143079 ATCTGTAAGTCTTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
143144 GCCTTAGGGTC
66 GCCTTAGGGTC
143155 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
143220 GCCTTAGGGTC
66 GCCTTAGGGTC
*
143231 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAACCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
*
143296 ACCTTAGGGTC
66 GCCTTAGGGTC
* * *
143307 ATCTGTATGTCATGCAGTACATGATG
1 ATCTGTAAGTCCTGCAGTGCATGATG
143333 ATTTTAAGAC
Statistics
Matches: 172, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 172 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (76 bp):
ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
GCCTTAGGGTC
Found at i:143508 original size:21 final size:21
Alignment explanation
Indices: 143483--143548 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
143473 ATTTTTCATT
143483 TTAAATTTAAATTTATTATTA
1 TTAAATTTAAATTTATTATTA
* * **
143504 TTAAAATTAAAATTAAAATTA
1 TTAAATTTAAATTTATTATTA
*
143525 TT--ATTTATTATTTATTATTTA
1 TTAAATTTA-AATTTATTA-TTA
143546 TTA
1 TTA
143549 TTTATTAAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 5
0.70 0.19 0.11
Matches are distributed among these distances:
19 4 0.12
20 5 0.15
21 24 0.73
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAATTTAAATTTATTATTA
Found at i:143534 original size:7 final size:7
Alignment explanation
Indices: 143522--143555 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
143512 AAAATTAAAA
143522 TTATTAT
1 TTATTAT
143529 TTATTAT
1 TTATTAT
143536 TTATTAT
1 TTATTAT
143543 TTATTAT
1 TTATTAT
143550 TTATTA
1 TTATTA
143556 AATATTACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTATTAT
Found at i:143561 original size:21 final size:21
Alignment explanation
Indices: 143522--143562 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
143512 AAAATTAAAA
**
143522 TTATTATTTATTATTTATTAT
1 TTATTATTTATTAAATATTAT
143543 TTATTATTTATTAAATATTA
1 TTATTATTTATTAAATATTA
143563 CAAAGCCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTATTATTTATTAAATATTAT
Found at i:143714 original size:30 final size:30
Alignment explanation
Indices: 143678--143751 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
143668 TTCAAACCCT
143678 AGCTCCAGCCGCCGCCTCAAGCTTCCAGTG
1 AGCTCCAGCCGCCGCCTCAAGCTTCCAGTG
*
143708 AGCTCCACCCGCCGCCTCAAGCTTCCAGTG
1 AGCTCCAGCCGCCGCCTCAAGCTTCCAGTG
*
143738 AGTTCCAGCCGCCG
1 AGCTCCAGCCGCCG
143752 TTGGGAAGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.16, C:0.45, G:0.23, T:0.16
Consensus pattern (30 bp):
AGCTCCAGCCGCCGCCTCAAGCTTCCAGTG
Found at i:145157 original size:20 final size:19
Alignment explanation
Indices: 145132--145173 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
145122 TTATTTTATA
145132 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
145152 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
145171 AAT
1 AAT
145174 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:145175 original size:119 final size:119
Alignment explanation
Indices: 145030--145265 Score: 291
Period size: 120 Copynumber: 2.0 Consensus size: 119
145020 TTTAATCCTA
* * * *
145030 TTTTAATATTTATTTATTTTCCAATAT-TAAG-AAAGGGCAGTCTTAAAATAAC-TGGATGTCCA
1 TTTTAATATTTATTTATTTTCCAATATCAAAGAAAAGGGCAGTCTT-AAAGAACTTAGAAGTCC-
* *
145092 TTTTCTGATATTTTTAAATAAATAAATATCTTATTTTATAAAT-TATATATTAATTG
64 TTTTCTGATATTTCTAAATAAATAAATATCTTA-TTTATAAATATATAAATTAATTG
** * * * *
145148 TTTTAATTATTTATTTATTTTTTAATATCAAAGAAAATGGCTGTCTTAAGGCACTTAGAAGTCCT
1 TTTTAA-TATTTATTTATTTTCCAATATCAAAGAAAAGGGCAGTCTTAAAGAACTTAGAAGTCCT
*
145213 TTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATAAATTAAT
65 TTTCTGATATTTCTAAATAAATAAATATCTTATTTATAAATATATAAATTAAT
145266 ATATATTTTT
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
118 6 0.06
119 28 0.28
120 48 0.48
121 18 0.18
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.47
Consensus pattern (119 bp):
TTTTAATATTTATTTATTTTCCAATATCAAAGAAAAGGGCAGTCTTAAAGAACTTAGAAGTCCTT
TTCTGATATTTCTAAATAAATAAATATCTTATTTATAAATATATAAATTAATTG
Found at i:145328 original size:7 final size:7
Alignment explanation
Indices: 145318--145347 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
145308 AATTAAATAT
145318 ATTTTTA
1 ATTTTTA
145325 ATTTTTA
1 ATTTTTA
145332 ATTTTTA
1 ATTTTTA
*
145339 ATTTCTA
1 ATTTTTA
145346 AT
1 AT
145348 AATAGAGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (7 bp):
ATTTTTA
Found at i:150039 original size:3 final size:3
Alignment explanation
Indices: 150031--150112 Score: 164
Period size: 3 Copynumber: 27.3 Consensus size: 3
150021 ATGGAGTAAT
150031 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
150079 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
150113 ATAAAAGAAA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:152602 original size:2 final size:2
Alignment explanation
Indices: 152595--152621 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
152585 AGTTATAATA
152595 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 A
152622 GATAGATAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:152867 original size:2 final size:2
Alignment explanation
Indices: 152860--152884 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
152850 TCTTTTGTAT
152860 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
152885 GTGTGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:153502 original size:24 final size:24
Alignment explanation
Indices: 153441--153502 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
153431 TTACAATTTA
* *
153441 AAATTATTTAAAACTTAATTTTTT
1 AAATTATATAAAAATTAATTTTTT
* * *
153465 TAATCAAATAAAAAATTAATTTTTT
1 AAATTATAT-AAAAATTAATTTTTT
*
153490 AAATTATGTAAAA
1 AAATTATATAAAA
153503 TTTCACGCAT
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
24 9 0.32
25 19 0.68
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (24 bp):
AAATTATATAAAAATTAATTTTTT
Found at i:160514 original size:18 final size:18
Alignment explanation
Indices: 160488--160530 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
160478 AACGGCGGTG
*
160488 GCGGCATCACATATGGTC
1 GCGGTATCACATATGGTC
160506 GCGGTATCACATATGGTC
1 GCGGTATCACATATGGTC
160524 GCGGTAT
1 GCGGTAT
160531 ATAAGTCACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (18 bp):
GCGGTATCACATATGGTC
Found at i:172741 original size:32 final size:32
Alignment explanation
Indices: 172686--172750 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
172676 CTCATCAATC
* *
172686 TTTTGGTATTCGGGTTGGATTTTTTAAAAAAA
1 TTTTGGGATTCGGGTCGGATTTTTTAAAAAAA
**
172718 TTTTGGGA-TCGGGTCGGATTTTTTTTAAAAA
1 TTTTGGGATTCGGGTCGGATTTTTTAAAAAAA
172749 TT
1 TT
172751 CCAAGTTCGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 22 0.76
32 7 0.24
ACGTcount: A:0.25, C:0.05, G:0.23, T:0.48
Consensus pattern (32 bp):
TTTTGGGATTCGGGTCGGATTTTTTAAAAAAA
Found at i:173719 original size:16 final size:16
Alignment explanation
Indices: 173698--173753 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
173688 AAGTTTCAGA
173698 TTCAGATTCCAATTCC
1 TTCAGATTCCAATTCC
173714 TTCAGATTCCAATTCC
1 TTCAGATTCCAATTCC
*
173730 TTCACAGATTCTAATTCC
1 TT--CAGATTCCAATTCC
*
173748 CTCAGA
1 TTCAGA
173754 AATATTTCAG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
16 22 0.61
18 14 0.39
ACGTcount: A:0.27, C:0.30, G:0.07, T:0.36
Consensus pattern (16 bp):
TTCAGATTCCAATTCC
Found at i:179302 original size:30 final size:29
Alignment explanation
Indices: 179262--179319 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
179252 ATTTTAGATT
*
179262 TAAGATTTTTAGTTTGATCATTTTATTAA
1 TAAGATTTTTAGTTTGATCACTTTATTAA
*
179291 TAAGTATTTTTAGTTTGATTACTTTATTA
1 TAAG-ATTTTTAGTTTGATCACTTTATTA
179320 TTATTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.57
Consensus pattern (29 bp):
TAAGATTTTTAGTTTGATCACTTTATTAA
Found at i:184824 original size:19 final size:19
Alignment explanation
Indices: 184802--184838 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
184792 TTGTTATTTT
* *
184802 TCAAAAAATTCCTAAAATA
1 TCAAAAAAGTCCCAAAATA
184821 TCAAAAAAGTCCCAAAAT
1 TCAAAAAAGTCCCAAAAT
184839 CCTTTATTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.19, G:0.03, T:0.22
Consensus pattern (19 bp):
TCAAAAAAGTCCCAAAATA
Found at i:185317 original size:29 final size:30
Alignment explanation
Indices: 185261--185317 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
185251 ATAACATTAG
* *
185261 AAATATTAGGCACCTAAATTGAACAAGAAA
1 AAATATTAGCCACCTAAATTGAAAAAGAAA
185291 AAAT-TTAGCCACCTAAA-TGAGAAAAGA
1 AAATATTAGCCACCTAAATTGA-AAAAGA
185318 TGTATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 17 0.71
30 4 0.17
ACGTcount: A:0.53, C:0.14, G:0.14, T:0.19
Consensus pattern (30 bp):
AAATATTAGCCACCTAAATTGAAAAAGAAA
Found at i:186311 original size:4 final size:4
Alignment explanation
Indices: 186302--186326 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
186292 CCTAGTAAGA
186302 ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC A
186327 CATAAATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:186564 original size:23 final size:23
Alignment explanation
Indices: 186538--186606 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
186528 CACCACATCT
*
186538 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
186561 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
* *
186584 CGTAGAAATACAACGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
186607 TATAAGATGT
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:0.33, C:0.25, G:0.26, T:0.16
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Done.