Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000963.1 Hibiscus syriacus cultivar Beakdansim tig00001925_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: 69215
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:3085 original size:34 final size:38
Alignment explanation
Indices: 3039--3122 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 38
3029 CATATATATA
*
3039 TATATATATATACGTTTCAAAAC-CATTTTTTA-AAAA-
1 TATATAT-TATACATTTCAAAACACATTTTTTAGAAAAC
* *
3075 T-TATATTATACATTTCCAAACATATTTTTTAGAAAAC
1 TATATATTATACATTTCAAAACACATTTTTTAGAAAAC
3112 TATATATTATA
1 TATATATTATA
3123 TATGTTTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 13 0.32
35 13 0.32
36 5 0.12
37 1 0.02
38 9 0.22
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.44
Consensus pattern (38 bp):
TATATATTATACATTTCAAAACACATTTTTTAGAAAAC
Found at i:3135 original size:75 final size:70
Alignment explanation
Indices: 3037--3206 Score: 164
Period size: 75 Copynumber: 2.4 Consensus size: 70
3027 ATCATATATA
* * *
3037 TATATATATATATACG-TTTCAAAACCATTTTTTAAAA-ATTATATTATACATTTCCAAACATAT
1 TATATAT-TATATATGTTTTCAAAACCATTTTCTAAAATA-TATATTATACATTTCC-AA-A-AC
*
3100 TTTTTAGAAAAC
61 GTTTT--AAAAC
** * * *
3112 TATATATTATATATGTTTTCAAAAATATTTTCTAAACTATATATTATATATTTTCAAAACGTTTT
1 TATATATTATATATGTTTTCAAAACCATTTTCTAAAATATATATTATACATTTCCAAAACGTTTT
*
3177 AAAGC
66 AAAAC
*
3182 TATATATTATATATATTTTCAAAAC
1 TATATATTATATATGTTTTCAAAAC
3207 TATATATATT
Statistics
Matches: 81, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
70 27 0.33
72 5 0.06
73 1 0.01
74 9 0.11
75 38 0.47
76 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (70 bp):
TATATATTATATATGTTTTCAAAACCATTTTCTAAAATATATATTATACATTTCCAAAACGTTTT
AAAAC
Found at i:3213 original size:25 final size:25
Alignment explanation
Indices: 3173--3227 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 25
3163 TTTCAAAACG
*
3173 TTTTAAAGC-TATATATTATATATA
1 TTTTAAAACATATATATTATATATA
3197 TTTTCAAAACTATATATATTATATATA
1 TTTT-AAAAC-ATATATATTATATATA
3224 TTTT
1 TTTT
3228 TTCAAAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 4 0.15
25 4 0.15
27 19 0.70
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (25 bp):
TTTTAAAACATATATATTATATATA
Found at i:3255 original size:2 final size:2
Alignment explanation
Indices: 3248--3282 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3238 TTTCCAAAAC
3248 TA TA TA 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 TA TA TA T
3283 TTCAAAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3267 original size:55 final size:53
Alignment explanation
Indices: 3207--3317 Score: 161
Period size: 55 Copynumber: 2.1 Consensus size: 53
3197 TTTTCAAAAC
* *
3207 TATATATAT-TATATATATTTTTTCAAAAATGTTTCCAAAACTATATATATATATA
1 TATATATATATATATATA-TATTTCAAAAATGTTT-CAAAACTATATA-ATATACA
*
3262 TATATATATATATATATATATTTCAAAAATGTTTTAAAACTATATAATATACA
1 TATATATATATATATATATATTTCAAAAATGTTTCAAAACTATATAATATACA
3315 TAT
1 TAT
3318 TTTCGGGAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
53 9 0.17
54 11 0.21
55 24 0.46
56 8 0.15
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (53 bp):
TATATATATATATATATATATTTCAAAAATGTTTCAAAACTATATAATATACA
Found at i:3376 original size:38 final size:38
Alignment explanation
Indices: 3264--3622 Score: 473
Period size: 38 Copynumber: 9.4 Consensus size: 38
3254 TATATATATA
3264 TATATATATATATATATATTTC-AAAAATGTTTT-AAAAC
1 TATATAT-TATATATAT-TTTCGAAAAATGTTTTCAAAAC
* * ***
3302 TATATAATATACATATTTTCGGGAAAAA-AAATTCAAAAC
1 TATATATTATATATATTTTC--GAAAAATGTTTTCAAAAC
*
3341 TATATA-T-TATATATTTTCAAAAAAAAATG-TTTCAAAAC
1 TATATATTATATATATTTTC---GAAAAATGTTTTCAAAAC
3379 TATATATTATATATATTTTCGAAAAATGTTTTCAAAAC
1 TATATATTATATATATTTTCGAAAAATGTTTTCAAAAC
* *
3417 TACATATTATATATATTTTTGAAAAATGTTTTCAAAAC
1 TATATATTATATATATTTTCGAAAAATGTTTTCAAAAC
*
3455 TACATATTATATATATTTTCGAAAAATGTTTTCAAAAC
1 TATATATTATATATATTTTCGAAAAATGTTTTCAAAAC
*
3493 TACATATTATATATATTTTCGAAAAATGTTTTCAAAAC
1 TATATATTATATATATTTTCGAAAAATGTTTTCAAAAC
3531 TATATATTATATATATTTTC-AAAAATGTTTTCAAAAC
1 TATATATTATATATATTTTCGAAAAATGTTTTCAAAAC
* *
3568 TATATATTATATATATTTTC-AAAAATATTCTCAAAAC
1 TATATATTATATATATTTTCGAAAAATGTTTTCAAAAC
3605 TATAATATATATATATAT
1 TAT-ATAT-TATATATAT
3623 ATATATTAAA
Statistics
Matches: 292, Mismatches: 18, Indels: 21
0.88 0.05 0.06
Matches are distributed among these distances:
36 4 0.01
37 80 0.27
38 171 0.59
39 26 0.09
40 11 0.04
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.42
Consensus pattern (38 bp):
TATATATTATATATATTTTCGAAAAATGTTTTCAAAAC
Found at i:9530 original size:42 final size:41
Alignment explanation
Indices: 9475--9565 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 41
9465 GATAAACAAG
* *
9475 TAAATAAATAACACCATAACACCATTAAGTCTCAATAAGTC
1 TAAATAAACAACACCATAACACCAATAAGTCTCAATAAGTC
*
9516 TAAAATAAACAACACCATAACACTAATAAGTCTCAATAAGTC
1 T-AAATAAACAACACCATAACACCAATAAGTCTCAATAAGTC
9558 TAAATAAA
1 TAAATAAA
9566 ATCAACATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 8 0.17
42 38 0.83
ACGTcount: A:0.53, C:0.20, G:0.04, T:0.23
Consensus pattern (41 bp):
TAAATAAACAACACCATAACACCAATAAGTCTCAATAAGTC
Found at i:10981 original size:42 final size:42
Alignment explanation
Indices: 10856--10983 Score: 184
Period size: 42 Copynumber: 3.0 Consensus size: 42
10846 AGATTTTGCC
* * *
10856 TCATTACATTCTTGCAAAGACGCCTCAAGTTTCTGTTTTTCC
1 TCATTACATTCTTGCAAAGATGCTTCAAGTTTCTGTTTTTCT
* * *
10898 CCGTTGCATTCTTGCAAAGATGCTTCAAGTTTCTGTTTTTCT
1 TCATTACATTCTTGCAAAGATGCTTCAAGTTTCTGTTTTTCT
* *
10940 TCATTACATTCTTGCAAACATGCTTCAACTTTCTGTTTTTCT
1 TCATTACATTCTTGCAAAGATGCTTCAAGTTTCTGTTTTTCT
10982 TC
1 TC
10984 CTTGCAGTAT
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.45
Consensus pattern (42 bp):
TCATTACATTCTTGCAAAGATGCTTCAAGTTTCTGTTTTTCT
Found at i:11962 original size:252 final size:252
Alignment explanation
Indices: 11517--12012 Score: 857
Period size: 252 Copynumber: 2.0 Consensus size: 252
11507 ATTTGAGTGG
** *
11517 TCTGTTCATCCAATTTAGCTTTGAGTACTAAGACATTGAATTCCAGTTCTTCCTTCAATACCATC
1 TCTGTTCATCCAATTTAGCTTTGAGTACTAAGACACAGAATTCCAGTTCTTCCTTCAATACAATC
*
11582 AGATTATCAATCTCTTCTCGGGAGCAGCCAAGTAAGTGCTTCAGCCTTTCAACTTCAAGAGCATG
66 AGACTATCAATCTCTTCTCGGGAGCAGCCAAGTAAGTGCTTCAGCCTTTCAACTTCAAGAGCATG
*
11647 CTGATGGTTATCCTCAGAGTAAACAAACTCAATCTTTTCGATCCTACTTTTGTAGTCCTGAAGCT
131 CTGATGATTATCCTCAGAGTAAACAAACTCAATCTTTTCGATCCTACTTTTGTAGTCCTGAAGCT
* *
11712 CAGCTATTACAGAGCTATTTTTATTGATAAGTATCTGGTTTTCATCCATCTGAATGC
196 CAGCTATTACAGAGCTATTTTTATTGAGAAGTATCTGGTTTTCAACCATCTGAATGC
*
11769 TCTGTTCATCCAATTTAGCTTTGAGTACTAAGACGCAGAATTCCAGTTCTTCCTTCAATACAATC
1 TCTGTTCATCCAATTTAGCTTTGAGTACTAAGACACAGAATTCCAGTTCTTCCTTCAATACAATC
* * *
11834 AGACTGTCAATCTCTTCTCGTGAGCAGCCAAGTAAGTGCTTCAGCCTTTCAACTTCAAGTGCATG
66 AGACTATCAATCTCTTCTCGGGAGCAGCCAAGTAAGTGCTTCAGCCTTTCAACTTCAAGAGCATG
* * *
11899 CTGATGATTATCCTCAGAGTAAGCAAACTCAATCTTTTCGCTCTTACTTTTGTAGTCCTGAAGCT
131 CTGATGATTATCCTCAGAGTAAACAAACTCAATCTTTTCGATCCTACTTTTGTAGTCCTGAAGCT
*
11964 CAGCTATTACAGAGCTATTTTTATTGAGAAGTGTCTGGTTTTCAACCAT
196 CAGCTATTACAGAGCTATTTTTATTGAGAAGTATCTGGTTTTCAACCAT
12013 GGAAGCTTCT
Statistics
Matches: 229, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
252 229 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (252 bp):
TCTGTTCATCCAATTTAGCTTTGAGTACTAAGACACAGAATTCCAGTTCTTCCTTCAATACAATC
AGACTATCAATCTCTTCTCGGGAGCAGCCAAGTAAGTGCTTCAGCCTTTCAACTTCAAGAGCATG
CTGATGATTATCCTCAGAGTAAACAAACTCAATCTTTTCGATCCTACTTTTGTAGTCCTGAAGCT
CAGCTATTACAGAGCTATTTTTATTGAGAAGTATCTGGTTTTCAACCATCTGAATGC
Found at i:19266 original size:48 final size:47
Alignment explanation
Indices: 19174--19266 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 47
19164 TAAGCAGGAG
*
19174 AAAAACAATGTAAAAGCAAACAAAGAGGAATTTTATTTAAAAGAAGA
1 AAAAACAATGTAAAAGCAAACAAAGAGGAATTTTATTAAAAAGAAGA
* *
19221 AAAAACAATGTAAAAGCAATCAAAAGAAGG-TTTTTATTAAAAAGAA
1 AAAAACAATGTAAAAGCAAAC-AAAG-AGGAATTTTATTAAAAAGAA
19267 CCCAATTACA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
47 20 0.49
48 18 0.44
49 3 0.07
ACGTcount: A:0.59, C:0.06, G:0.14, T:0.20
Consensus pattern (47 bp):
AAAAACAATGTAAAAGCAAACAAAGAGGAATTTTATTAAAAAGAAGA
Found at i:22707 original size:24 final size:25
Alignment explanation
Indices: 22677--22727 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
22667 ATTATAAATA
22677 TAATAATAATATATAA-AAAGTTTGATT
1 TAATAA-AATAT-TAATAAA-TTTGATT
22704 TAATAAAATATTAATAAATTTGAT
1 TAATAAAATATTAATAAATTTGAT
22728 CAGTTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 9 0.39
26 8 0.35
27 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (25 bp):
TAATAAAATATTAATAAATTTGATT
Found at i:22761 original size:16 final size:17
Alignment explanation
Indices: 22734--22765 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
22724 TGATCAGTTA
22734 AAATTATTTTATATTTT
1 AAATTATTTTATATTTT
22751 AAATT-TTTTATATTT
1 AAATTATTTTATATTT
22766 AATATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
AAATTATTTTATATTTT
Found at i:22764 original size:23 final size:22
Alignment explanation
Indices: 22737--22792 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
22727 TCAGTTAAAA
*
22737 TTATTTTATATTTTAAATT-TTT
1 TTATTTTATATATT-AATTATTT
*
22759 TATATTTAATATATTAATTATTT
1 T-TATTTTATATATTAATTATTT
22782 TTACTTTTATA
1 TTA-TTTTATA
22793 AGGTAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 7 0.25
23 21 0.75
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
TTATTTTATATATTAATTATTT
Found at i:28770 original size:36 final size:36
Alignment explanation
Indices: 28684--28759 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 36
28674 GGTCAGCGTG
*
28684 ATTGGCTCCCT-CTAATGATGAAGAGAAGTCCACGTA
1 ATTGGCTCCTTGC-AATGATGAAGAGAAGTCCACGTA
28720 ATTGGCTCCTTGCAATGATGAAGAGAAGTCCACGTA
1 ATTGGCTCCTTGCAATGATGAAGAGAAGTCCACGTA
28756 ATTG
1 ATTG
28760 CGTGGTTGCA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
36 37 0.97
37 1 0.03
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (36 bp):
ATTGGCTCCTTGCAATGATGAAGAGAAGTCCACGTA
Found at i:30970 original size:2 final size:2
Alignment explanation
Indices: 30963--31009 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
30953 TAGAATCTGG
30963 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
31005 TA TA T
1 TA TA T
31010 TAAACATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31064 original size:12 final size:12
Alignment explanation
Indices: 31043--31078 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
31033 TATATTTTTT
*
31043 TATAAAATTAAC
1 TATAAAATTAAA
*
31055 TATTAAATTAAA
1 TATAAAATTAAA
31067 TATAAAATTAAA
1 TATAAAATTAAA
31079 GGAATAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (12 bp):
TATAAAATTAAA
Found at i:31945 original size:30 final size:29
Alignment explanation
Indices: 31883--32195 Score: 207
Period size: 30 Copynumber: 10.6 Consensus size: 29
31873 CAGAACAATA
* **
31883 AAAAATTTAAAGGACCAAAATATGATTAA-
1 AAAAACTTAAAGGACCAAAATA-GAAAAAC
*
31912 AAAAACTT-GAGGACCAAAATAGCAAAAAC
1 AAAAACTTAAAGGACCAAAATAG-AAAAAC
* *
31941 AAAAACTTAAAGGACTAAAATAGAAAAAT
1 AAAAACTTAAAGGACCAAAATAGAAAAAC
* * * * *
31970 AGAAATTTAAAGGACTAAAATAGCACAAAT
1 AAAAACTTAAAGGACCAAAATAG-AAAAAC
* ** * * *
32000 AGAAACTTAAACTACTAAAATAACAAAAAT
1 AAAAACTTAAAGGACCAAAAT-AGAAAAAC
* * *
32030 AAAAACTTAAAGGACTAAAATAGCACAAAG
1 AAAAACTTAAAGGACCAAAATAG-AAAAAC
* * * *
32060 AGAAACTTAAAGGACTAAAATAGCATAAAT
1 AAAAACTTAAAGGACCAAAATAG-AAAAAC
* * *
32090 AGAAACTTAAAGGACTAAAATAGCACAAAC
1 AAAAACTTAAAGGACCAAAATAG-AAAAAC
* * *
32120 AAAAATTTAAAGGACTAAAATAGCACAAAC
1 AAAAACTTAAAGGACCAAAATAG-AAAAAC
* * * * *
32150 AGAAACTTAAAGAACTAAAATATCACAAAC
1 AAAAACTTAAAGGACCAAAATA-GAAAAAC
*
32180 AAAAATTTAAAGGACC
1 AAAAACTTAAAGGACC
32196 GAATCATAAA
Statistics
Matches: 241, Mismatches: 36, Indels: 13
0.83 0.12 0.04
Matches are distributed among these distances:
27 1 0.00
28 15 0.06
29 42 0.17
30 182 0.76
31 1 0.00
ACGTcount: A:0.59, C:0.12, G:0.11, T:0.17
Consensus pattern (29 bp):
AAAAACTTAAAGGACCAAAATAGAAAAAC
Found at i:32053 original size:60 final size:60
Alignment explanation
Indices: 31921--32194 Score: 361
Period size: 60 Copynumber: 4.6 Consensus size: 60
31911 AAAAAACTTG
* * * *
31921 AGGACCAAAATAGCAAAAACAAAAACTTAAAGGACTAAAAT-AGAAAAATAGAAATTTAA
1 AGGACTAAAATAGCACAAACAAAAACTTAAAGGACTAAAATAACAAAAATAGAAACTTAA
* * ** *
31980 AGGACTAAAATAGCACAAATAGAAACTTAAACTACTAAAATAACAAAAATAAAAACTTAA
1 AGGACTAAAATAGCACAAACAAAAACTTAAAGGACTAAAATAACAAAAATAGAAACTTAA
* * * *
32040 AGGACTAAAATAGCACAAAGAGAAACTTAAAGGACTAAAATAGCATAAATAGAAACTTAA
1 AGGACTAAAATAGCACAAACAAAAACTTAAAGGACTAAAATAACAAAAATAGAAACTTAA
* * * *
32100 AGGACTAAAATAGCACAAACAAAAATTTAAAGGACTAAAATAGCACAAACAGAAACTTAA
1 AGGACTAAAATAGCACAAACAAAAACTTAAAGGACTAAAATAACAAAAATAGAAACTTAA
* * *
32160 AGAACTAAAATATCACAAACAAAAATTTAAAGGAC
1 AGGACTAAAATAGCACAAACAAAAACTTAAAGGAC
32195 CGAATCATAA
Statistics
Matches: 192, Mismatches: 22, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
59 35 0.18
60 157 0.82
ACGTcount: A:0.60, C:0.13, G:0.11, T:0.16
Consensus pattern (60 bp):
AGGACTAAAATAGCACAAACAAAAACTTAAAGGACTAAAATAACAAAAATAGAAACTTAA
Found at i:32190 original size:90 final size:90
Alignment explanation
Indices: 31921--32194 Score: 388
Period size: 90 Copynumber: 3.1 Consensus size: 90
31911 AAAAAACTTG
* * * *
31921 AGGACCAAAATAGCAAAAACAAAAACTTAAAGGACTAAAATAG-AAAAATAGAAATTTAAAGGAC
1 AGGACTAAAATAGCAAAAACAAAAACTTAAAGGACTAAAATAGCACAAACAGAAACTTAAAGGAC
31985 TAAAATAGCACAAATAGAAACTTAA
66 TAAAATAGCACAAATAGAAACTTAA
** * * *
32010 ACTACTAAAATAACAAAAATAAAAACTTAAAGGACTAAAATAGCACAAAGAGAAACTTAAAGGAC
1 AGGACTAAAATAGCAAAAACAAAAACTTAAAGGACTAAAATAGCACAAACAGAAACTTAAAGGAC
*
32075 TAAAATAGCATAAATAGAAACTTAA
66 TAAAATAGCACAAATAGAAACTTAA
* * *
32100 AGGACTAAAATAGCACAAACAAAAATTTAAAGGACTAAAATAGCACAAACAGAAACTTAAAGAAC
1 AGGACTAAAATAGCAAAAACAAAAACTTAAAGGACTAAAATAGCACAAACAGAAACTTAAAGGAC
* * * *
32165 TAAAATATCACAAACAAAAATTTAA
66 TAAAATAGCACAAATAGAAACTTAA
32190 AGGAC
1 AGGAC
32195 CGAATCATAA
Statistics
Matches: 162, Mismatches: 22, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
89 38 0.23
90 124 0.77
ACGTcount: A:0.60, C:0.13, G:0.11, T:0.16
Consensus pattern (90 bp):
AGGACTAAAATAGCAAAAACAAAAACTTAAAGGACTAAAATAGCACAAACAGAAACTTAAAGGAC
TAAAATAGCACAAATAGAAACTTAA
Found at i:33548 original size:3 final size:3
Alignment explanation
Indices: 33540--33595 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
33530 ATATATATAT
* * *
33540 TAA TAA TAA TAA TAA AAA TAA TAA TAC TAA TAC TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
33588 TAA TAA TA
1 TAA TAA TA
33596 GTATTTTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:33982 original size:134 final size:131
Alignment explanation
Indices: 33794--34144 Score: 452
Period size: 131 Copynumber: 2.7 Consensus size: 131
33784 GGTCATCTAA
* * * * * ** **
33794 GGGTGAGACGTCTCCTACGTGATGAGGAGATCTGGTCGGGGTATGATACGGTTCCTACACGATGA
1 GGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACATAGTTCCTACGTGATGA
* * * *
33859 GGATGATA-GACCATGTTTAGGGAGGGTGATAACACGGTTCCTACGTGATAAGGATGACTGGTTA
66 GGACGACATG-CCATCTTTA--G-GGGTGATAACACGGTTCCTACGTGATAAGGACGACTGGTTA
33923 TCAAG
127 TCAAG
* **
33928 GGGTGACATGACTCCTACACGATGAGGAGGTCTGGTCGGGGGATGACATAGTTCCTACGTGATGA
1 GGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACATAGTTCCTACGTGATGA
* * * * *
33993 GGACGACATGCCATCTTTAGGGGTGATAACATGGTTCCTACGTTATGAGGGCGACTGGTTATCTA
66 GGACGACATGCCATCTTTAGGGGTGATAACACGGTTCCTACGTGATAAGGACGACTGGTTATCAA
34058 G
131 G
*
34059 GGGTGGCACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACATAGTTCCTACGTGATGA
1 GGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACATAGTTCCTACGTGATGA
*
34124 GGACGGCATGCCATCTTTAGG
66 GGACGACATGCCATCTTTAGG
34145 AATAATGGTT
Statistics
Matches: 190, Mismatches: 26, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
131 121 0.64
132 1 0.01
134 67 0.35
135 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.25
Consensus pattern (131 bp):
GGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACATAGTTCCTACGTGATGA
GGACGACATGCCATCTTTAGGGGTGATAACACGGTTCCTACGTGATAAGGACGACTGGTTATCAA
G
Found at i:34275 original size:66 final size:65
Alignment explanation
Indices: 34153--34296 Score: 175
Period size: 66 Copynumber: 2.2 Consensus size: 65
34143 GGAATAATGG
* *
34153 TTTCAAGGGAAACTGACTCAAAGATGATGCTTCAAGAGAAGCTGTCTCAAGAGAGACAAAA-TTC
1 TTTCAAGGGAAACTGACCCAAAGATGATGCTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT-
34217 A
65 A
* * * *
34218 TTTCAAGGGAAAC-GATCCCAAAGATGGGTGTTTTAAGAGAAACTGTCTCAAGGGAGACAAAACT
1 TTTCAAGGGAAACTGA-CCCAAAGAT-GATGCTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
*
34282 TG
64 TA
*
34284 TTTAAAGGGAAAC
1 TTTCAAGGGAAAC
34297 AAACTCAAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
64 2 0.03
65 21 0.31
66 43 0.63
67 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (65 bp):
TTTCAAGGGAAACTGACCCAAAGATGATGCTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
Found at i:34493 original size:36 final size:34
Alignment explanation
Indices: 34446--34540 Score: 118
Period size: 36 Copynumber: 2.7 Consensus size: 34
34436 TTTCTCAAAG
* * *
34446 GAAAAATGTCTCAAGCAAGACAAAATTTGTTTTAGT
1 GAAAACTGTCTCAAGCGAGACAAAA-TTGTTTTA-A
*
34482 GAAAACTGTCTCGAGCGAGAACAAAATTGTTTTAA
1 GAAAACTGTCTCAAGCGAG-ACAAAATTGTTTTAA
34517 GAAAACTTGTCTCAAGCGAGACAA
1 GAAAAC-TGTCTCAAGCGAGACAA
34541 CCCATTGTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
35 10 0.19
36 36 0.69
37 6 0.12
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (34 bp):
GAAAACTGTCTCAAGCGAGACAAAATTGTTTTAA
Found at i:35753 original size:27 final size:27
Alignment explanation
Indices: 35723--35796 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
35713 TTTTTCTTTG
*
35723 TTTTTTTTTCTTT-CATTTTCCTTTTCT
1 TTTTTTTTTCTTTGC-TTTTCCTTTGCT
*
35750 TTTTTTTTTCTTTGCTTTTTCTTTGCT
1 TTTTTTTTTCTTTGCTTTTCCTTTGCT
*
35777 ATTTTTTTTCTTTGCCTTTT
1 TTTTTTTTTCTTTG-CTTTT
35797 ATCCTAGCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 36 0.86
28 6 0.14
ACGTcount: A:0.03, C:0.16, G:0.04, T:0.77
Consensus pattern (27 bp):
TTTTTTTTTCTTTGCTTTTCCTTTGCT
Found at i:35757 original size:16 final size:16
Alignment explanation
Indices: 35714--35796 Score: 55
Period size: 16 Copynumber: 5.2 Consensus size: 16
35704 TCTTGTCCAT
*
35714 TTTTCTTTGTTTTT--
1 TTTTCTTTTTTTTTCC
**
35728 TTTTCTTTCATTTTCC
1 TTTTCTTTTTTTTTCC
*
35744 TTTTCTTTTTTTTTTC
1 TTTTCTTTTTTTTTCC
* * *
35760 TTTGCTTTTTCTTTGC
1 TTTTCTTTTTTTTTCC
*
35776 TATTT-TTTTTCTTTGCC
1 T-TTTCTTTTT-TTTTCC
35793 TTTT
1 TTTT
35797 ATCCTAGCCT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
14 12 0.23
16 35 0.66
17 6 0.11
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (16 bp):
TTTTCTTTTTTTTTCC
Found at i:48880 original size:27 final size:27
Alignment explanation
Indices: 48850--48932 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 27
48840 AATATTTAAG
48850 GAAATATAATAGAAACAAATGTGATGA
1 GAAATATAATAGAAACAAATGTGATGA
* * * * * *
48877 GAAATGTAAAATAAA-ATAT-TTAAG-
1 GAAATATAATAGAAACAAATGTGATGA
* *
48901 GAAATCTAATAGAAACAAATGTGATTA
1 GAAATATAATAGAAACAAATGTGATGA
48928 GAAAT
1 GAAAT
48933 GTAAAATAAA
Statistics
Matches: 40, Mismatches: 13, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
24 12 0.30
25 6 0.15
26 5 0.12
27 17 0.43
ACGTcount: A:0.55, C:0.04, G:0.16, T:0.25
Consensus pattern (27 bp):
GAAATATAATAGAAACAAATGTGATGA
Found at i:48916 original size:51 final size:51
Alignment explanation
Indices: 48840--48949 Score: 202
Period size: 51 Copynumber: 2.2 Consensus size: 51
48830 GAATATTATT
48840 AATATTTAAGGAAATATAATAGAAACAAATGTGATGAGAAATGTAAAATAA
1 AATATTTAAGGAAATATAATAGAAACAAATGTGATGAGAAATGTAAAATAA
* *
48891 AATATTTAAGGAAATCTAATAGAAACAAATGTGATTAGAAATGTAAAATAA
1 AATATTTAAGGAAATATAATAGAAACAAATGTGATGAGAAATGTAAAATAA
48942 AATATTTA
1 AATATTTA
48950 CAACATAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.55, C:0.03, G:0.14, T:0.28
Consensus pattern (51 bp):
AATATTTAAGGAAATATAATAGAAACAAATGTGATGAGAAATGTAAAATAA
Found at i:49102 original size:29 final size:29
Alignment explanation
Indices: 49053--49109 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
49043 AAAAATTTAA
* *
49053 AGGACCAAAATATGACTAACATAAACTTG
1 AGGACCAAAATATGACAAACAGAAACTTG
*
49082 AGGACCAAAATA-GCAGAAACAGAAACTT
1 AGGACCAAAATATG-ACAAACAGAAACTT
49110 AAAAGATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.51, C:0.18, G:0.16, T:0.16
Consensus pattern (29 bp):
AGGACCAAAATATGACAAACAGAAACTTG
Found at i:49124 original size:30 final size:30
Alignment explanation
Indices: 49049--49351 Score: 319
Period size: 30 Copynumber: 10.2 Consensus size: 30
49039 AATAAAAAAT
* * *
49049 TTAAAGGACCAAAATATG-ACTAACATAAAC
1 TTAAAGGACTAAAATA-GCACAAACAGAAAC
* * *
49079 TT-GAGGACCAAAATAGCAGAAACAGAAAC
1 TTAAAGGACTAAAATAGCACAAACAGAAAC
* * * * * *
49108 TTAAAAGATTAAAATAGAAAAAAATAGAAAT
1 TTAAAGGACTAAAATAG-CACAAACAGAAAC
* *
49139 TTAAAGGACTAAAATAGTACAAATAGAAAC
1 TTAAAGGACTAAAATAGCACAAACAGAAAC
* * *
49169 TTAAAAGACTAAAATA--A-AAAAAAAAAC
1 TTAAAGGACTAAAATAGCACAAACAGAAAC
49196 TTAAAGGACTAAAATAGCACAAACAGAAAC
1 TTAAAGGACTAAAATAGCACAAACAGAAAC
*
49226 TTAAAGGACTAAAATAGCACAAACATAAAC
1 TTAAAGGACTAAAATAGCACAAACAGAAAC
* * * *
49256 TTAAAGGACTAAAATAGCATAAATATAAAT
1 TTAAAGGACTAAAATAGCACAAACAGAAAC
* *
49286 TTAAAGGACTAAAATAGCATAAACAAAAAC
1 TTAAAGGACTAAAATAGCACAAACAGAAAC
* *
49316 TTAAAGGACTAAAATAGCACAAACATAAAT
1 TTAAAGGACTAAAATAGCACAAACAGAAAC
49346 TTAAAG
1 TTAAAG
49352 AATCGAATCA
Statistics
Matches: 234, Mismatches: 33, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
27 23 0.10
28 2 0.01
29 24 0.10
30 161 0.69
31 24 0.10
ACGTcount: A:0.59, C:0.12, G:0.11, T:0.18
Consensus pattern (30 bp):
TTAAAGGACTAAAATAGCACAAACAGAAAC
Found at i:49204 original size:147 final size:150
Alignment explanation
Indices: 49028--49337 Score: 396
Period size: 147 Copynumber: 2.1 Consensus size: 150
49018 CATAAGGGAT
* * * *
49028 TAAAATAGAACAATAAAAAATTTAAAGGACCAAAATATG-ACTAACATAAACTT-GAGGACCAAA
1 TAAAATAGAACAATAAAAAACTTAAAGGACCAAAATA-GCACAAACAGAAACTTAAAGGACCAAA
* *
49091 ATAGCAGAAACAGAAACTTAAAAGATTAAAATAGAAAAAAATAGAAATTTAAAGGACTAAAATAG
65 ATAGCACAAACAGAAACTTAAAAGACTAAAATAG-AAAAAATAGAAATTTAAAGGACTAAAATAG
* * *
49156 TACAAATAGAAACTTAAAAGAC
129 CACAAACAAAAACTTAAAAGAC
* *
49178 TAAAATA-AA-AA-AAAAAACTTAAAGGACTAAAATAGCACAAACAGAAACTTAAAGGACTAAAA
1 TAAAATAGAACAATAAAAAACTTAAAGGACCAAAATAGCACAAACAGAAACTTAAAGGACCAAAA
* * * * *
49240 TAGCACAAACATAAACTTAAAGGACTAAAATAGCATAAATATAAATTTAAAGGACTAAAATAGCA
66 TAGCACAAACAGAAACTTAAAAGACTAAAATAGAAAAAATAGAAATTTAAAGGACTAAAATAGCA
* *
49305 TAAACAAAAACTTAAAGGAC
131 CAAACAAAAACTTAAAAGAC
*
49325 TAAAATAGCACAA
1 TAAAATAGAACAA
49338 ACATAAATTT
Statistics
Matches: 137, Mismatches: 19, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
146 1 0.01
147 84 0.61
148 41 0.30
149 4 0.03
150 7 0.05
ACGTcount: A:0.60, C:0.11, G:0.11, T:0.18
Consensus pattern (150 bp):
TAAAATAGAACAATAAAAAACTTAAAGGACCAAAATAGCACAAACAGAAACTTAAAGGACCAAAA
TAGCACAAACAGAAACTTAAAAGACTAAAATAGAAAAAATAGAAATTTAAAGGACTAAAATAGCA
CAAACAAAAACTTAAAAGAC
Found at i:60031 original size:45 final size:44
Alignment explanation
Indices: 59981--60169 Score: 218
Period size: 45 Copynumber: 4.5 Consensus size: 44
59971 TTTTATGTTG
**
59981 ATAATGCACCCATATGCATTTCAACTTTGACATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTTCAACTAAG-CATCCTTTCATGCCA
*
60026 ATAATGCACCCATATGCATTTCAGCTAAGGCATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTTCAACTAA-GCATCCTTTCATGCCA
* *
60071 ATAATGCACCCATATGCA-TT--A-T-----T-CTTTTATGCCG
1 ATAATGCACCCATATGCATTTCAACTAAGCATCCTTTCATGCCA
* *
60105 ATAATGCACCCATATGCATTTCAGCTAAGTCATCCTTTTATGCCA
1 ATAATGCACCCATATGCATTTCAACTAAG-CATCCTTTCATGCCA
60150 ATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATT
60170 ATTCTTTTGA
Statistics
Matches: 124, Mismatches: 8, Indels: 24
0.79 0.05 0.15
Matches are distributed among these distances:
34 27 0.22
35 3 0.02
38 1 0.01
41 1 0.01
44 3 0.02
45 88 0.71
46 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (44 bp):
ATAATGCACCCATATGCATTTCAACTAAGCATCCTTTCATGCCA
Found at i:60103 original size:34 final size:34
Alignment explanation
Indices: 60060--60177 Score: 119
Period size: 34 Copynumber: 3.1 Consensus size: 34
60050 CTAAGGCATC
*
60060 CTTTCATGCCAATAATGCACCCATATGCATTATT
1 CTTTTATGCCAATAATGCACCCATATGCATTATT
*
60094 CTTTTATGCCGATAATGCACCCATATGCATTTCAGCTAAGTCAT
1 CTTTTATGCCAATAATGCACCCATATGCA--T----T-A-T--T
60138 CCTTTTATGCCAATAATGCACCCATATGCATTATT
1 -CTTTTATGCCAATAATGCACCCATATGCATTATT
60173 CTTTT
1 CTTTT
60178 GATCATTCGT
Statistics
Matches: 70, Mismatches: 3, Indels: 22
0.74 0.03 0.23
Matches are distributed among these distances:
34 32 0.46
35 1 0.01
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 1 0.01
41 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
45 28 0.40
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.37
Consensus pattern (34 bp):
CTTTTATGCCAATAATGCACCCATATGCATTATT
Found at i:60151 original size:79 final size:79
Alignment explanation
Indices: 60015--60177 Score: 290
Period size: 79 Copynumber: 2.1 Consensus size: 79
60005 CTTTGACATC
*
60015 CTTTCATGCCAATAATGCACCCATATGCATTTCAGCTAAGGCATCCTTTCATGCCAATAATGCAC
1 CTTTTATGCCAATAATGCACCCATATGCATTTCAGCTAAGGCATCCTTTCATGCCAATAATGCAC
60080 CCATATGCATTATT
66 CCATATGCATTATT
* * *
60094 CTTTTATGCCGATAATGCACCCATATGCATTTCAGCTAAGTCATCCTTTTATGCCAATAATGCAC
1 CTTTTATGCCAATAATGCACCCATATGCATTTCAGCTAAGGCATCCTTTCATGCCAATAATGCAC
60159 CCATATGCATTATT
66 CCATATGCATTATT
60173 CTTTT
1 CTTTT
60178 GATCATTCGT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (79 bp):
CTTTTATGCCAATAATGCACCCATATGCATTTCAGCTAAGGCATCCTTTCATGCCAATAATGCAC
CCATATGCATTATT
Found at i:62700 original size:3 final size:3
Alignment explanation
Indices: 62688--62737 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
62678 TACAAAAATG
*
62688 TAA T-A TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
62733 TAA TA
1 TAA TA
62738 GTATTTTTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:63586 original size:12 final size:12
Alignment explanation
Indices: 63569--63607 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
63559 GACTCAAAAA
*
63569 TCAAATCGTTTT
1 TCAAATCATTTT
63581 TCAAATCATTTT
1 TCAAATCATTTT
*
63593 TCAAATCATATT
1 TCAAATCATTTT
63605 TCA
1 TCA
63608 TCGTTCCCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.33, C:0.18, G:0.03, T:0.46
Consensus pattern (12 bp):
TCAAATCATTTT
Found at i:64591 original size:31 final size:31
Alignment explanation
Indices: 64556--64617 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
64546 ATCTTGTTGG
*
64556 TACTAA-TTCATTTTTTTTCTTTTGTTTGTGT
1 TACTAACTT-ATTTCTTTTCTTTTGTTTGTGT
64587 TACTAACTTATTTCTTTTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTTTCTTTTGTTTGTGT
64618 CACTTTTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.13, C:0.11, G:0.10, T:0.66
Consensus pattern (31 bp):
TACTAACTTATTTCTTTTCTTTTGTTTGTGT
Found at i:66578 original size:33 final size:33
Alignment explanation
Indices: 66517--66584 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
66507 GAATCAGTGC
* * *
66517 TGAAGCAATCAACATCGAGTATTGGGGCATCTT
1 TGAAGCAATCAACATCAAATATTGGGGCAACTT
* *
66550 TGAAGCAATCAACATCAAATGTTTGGGCAACTT
1 TGAAGCAATCAACATCAAATATTGGGGCAACTT
66583 TG
1 TG
66585 GGGATTCAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (33 bp):
TGAAGCAATCAACATCAAATATTGGGGCAACTT
Found at i:66755 original size:36 final size:36
Alignment explanation
Indices: 66700--66786 Score: 95
Period size: 36 Copynumber: 2.4 Consensus size: 36
66690 CAAAGTGTCA
* **
66700 TCTCGCTAGAGACAATTTTCTTAAAAACA-AATTTTG
1 TCTCGCTTGAGACAATTTTCGCAAAAA-AGAATTTTG
* *
66736 TCTCGCTTGAGATAGTTTTCGCAAAAAATGAATTTTG
1 TCTCGCTTGAGACAATTTTCGCAAAAAA-GAATTTTG
*
66773 TCTCACTTGAGACA
1 TCTCGCTTGAGACA
66787 TTTCTTTCGA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
35 1 0.02
36 22 0.52
37 19 0.45
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (36 bp):
TCTCGCTTGAGACAATTTTCGCAAAAAAGAATTTTG
Found at i:66970 original size:62 final size:61
Alignment explanation
Indices: 66848--66990 Score: 171
Period size: 62 Copynumber: 2.3 Consensus size: 61
66838 ACTTTGAAAT
*
66848 TGTTTCTCTTGAAACAAAATTTTGTCTCTTTGAGACATTTTCTTTTAAAAAAAATCTGAGTA
1 TGTTTCACTTGAAACAAAATTTTGTCTCTTTGAGACATTTTC-TTTAAAAAAAATCTGAGTA
* * * * ** * *
66910 TGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTTC-TTGAGAAATCTTTGAGTC
1 TGTTTCACTTGAAACAAAATTTTGTCTCT-TTGAGACA-TTTTCTTTAAAAAAAATCTGAGTA
66972 TGTTTCACTTGAAACAAAA
1 TGTTTCACTTGAAACAAAA
66991 CAAAAAAAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
62 56 0.81
63 8 0.12
64 5 0.07
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.41
Consensus pattern (61 bp):
TGTTTCACTTGAAACAAAATTTTGTCTCTTTGAGACATTTTCTTTAAAAAAAATCTGAGTA
Found at i:67006 original size:38 final size:38
Alignment explanation
Indices: 66959--67065 Score: 169
Period size: 38 Copynumber: 2.8 Consensus size: 38
66949 TTTTCTTGAG
66959 AAATCTTTGAGTCTGTTTCACTTGAAACAAAACAAAAA
1 AAATCTTTGAGTCTGTTTCACTTGAAACAAAACAAAAA
* **
66997 AAATATTTGAGTCTGTTTCACTTGAAACAAAATGAAAA
1 AAATCTTTGAGTCTGTTTCACTTGAAACAAAACAAAAA
* *
67035 AAATCTTTGAGTCTATTTCCCTTGAAACAAA
1 AAATCTTTGAGTCTGTTTCACTTGAAACAAA
67066 GTTTTTTCTC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 63 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (38 bp):
AAATCTTTGAGTCTGTTTCACTTGAAACAAAACAAAAA
Found at i:67140 original size:34 final size:33
Alignment explanation
Indices: 67097--67162 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 33
67087 TTTTTGAGAA
*
67097 ATCTTTGAGTCTATTTTACTTGAAACAAAAAAAG
1 ATCTTTGAGTCTATTTCACTTGAAA-AAAAAAAG
*
67131 ATCTTTGAGTCTGTTTCACTTGAAAAAAAAAA
1 ATCTTTGAGTCTATTTCACTTGAAAAAAAAAA
67163 TCATTGAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 7 0.23
34 23 0.77
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (33 bp):
ATCTTTGAGTCTATTTCACTTGAAAAAAAAAAG
Found at i:67170 original size:31 final size:31
Alignment explanation
Indices: 67095--67186 Score: 112
Period size: 31 Copynumber: 2.9 Consensus size: 31
67085 TTTTTTTGAG
* *
67095 AAATCTTTGAGTCTATTTTACTTGAAACAAAAA
1 AAATCTTTGAGTCTGTTTCACTTG-AA-AAAAA
67128 AAGATCTTTGAGTCTGTTTCACTTGAAAAAAA
1 AA-ATCTTTGAGTCTGTTTCACTTGAAAAAAA
* * *
67160 AAATCATTGAGTTTGTTTCCCTTGAAA
1 AAATCTTTGAGTCTGTTTCACTTGAAA
67187 CAAAGTTTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
31 22 0.42
32 7 0.13
33 4 0.08
34 20 0.38
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (31 bp):
AAATCTTTGAGTCTGTTTCACTTGAAAAAAA
Found at i:67557 original size:127 final size:127
Alignment explanation
Indices: 67292--67765 Score: 501
Period size: 129 Copynumber: 3.7 Consensus size: 127
67282 TGAAACCATT
* * * *
67292 ATCCCTAAAGATGACATGTCATCCTCATCACGTAGGAACCATGTCATCCACTGACCATACCCTCA
1 ATCCCTAAAGATGGCATATCATCCTCATCACGTAGGAACCATGTCATCCACCGACCAGACCCTCA
* * * *
67357 TCATGTAGGAGTCGTGTCAACCTCAGATAACCAGCCGTCTTCATCACGTAGGAA-TCGTGTTATC
66 TCACGTAGGAGCCGTGTC-ACCCCAGATAACCAG-CGTCCTCATCACGTAGGAACT-GTGTTATC
* * * ** * *
67421 ATCCCTAAAGATGGTATACCATCCTCATCACGTATGAACTGTTTCATCC-CCTAACCAGA-CCTC
1 ATCCCTAAAGATGGCATATCATCCTCATCACGTAGGAACCATGTCATCCACC-GACCAGACCCTC
* * * *
67484 ATCACGTAGGAGCCGTGTCACCCCTGATAACCAGTCATCCTAATCATGTAGGAACTGTGTTATC
65 ATCACGTAGGAGCCGTGTCACCCCAGATAACCAG-CGTCCTCATCACGTAGGAACTGTGTTATC
* *
67548 ATCCCTAAAGATGGTATGTCATCCTCATCACGTAGGAACCATGTCATCCACCGACCAGACCTCCT
1 ATCCCTAAAGATGGCATATCATCCTCATCACGTAGGAACCATGTCATCCACCGACCAGA-C-CCT
** * *
67613 CATCACGTAGGAGCCGTGTCA-CCCAGATAATAAGCGTCCTCATCGCGTAGGAACCGTGTTATC
64 CATCACGTAGGAGCCGTGTCACCCCAGATAACCAGCGTCCTCATCACGTAGGAACTGTGTTATC
* * * * ** *
67676 ACTCTCCTAAAG-TGGCCAAAAC-TCTTCATCACGTATGAGTCGTGTCATCCACCGACCAGATCT
1 A-TC-CCTAAAGATGG-CATATCATCCTCATCACGTAGGAACCATGTCATCCACCGACCAGA-C-
*
67739 CCTTATCACGTAGGAGCCGTGTCACCC
61 CCTCATCACGTAGGAGCCGTGTCACCC
67766 TTAAACGACC
Statistics
Matches: 289, Mismatches: 46, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
127 85 0.29
128 50 0.17
129 119 0.41
130 35 0.12
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.25
Consensus pattern (127 bp):
ATCCCTAAAGATGGCATATCATCCTCATCACGTAGGAACCATGTCATCCACCGACCAGACCCTCA
TCACGTAGGAGCCGTGTCACCCCAGATAACCAGCGTCCTCATCACGTAGGAACTGTGTTATC
Done.