Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168127.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_370, 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: 30524
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Found at i:6521 original size:41 final size:41
Alignment explanation
Indices: 6464--6636 Score: 184
Period size: 41 Copynumber: 4.2 Consensus size: 41
6454 ATGGTTGTTA
*
6464 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGAGCCTCTGTTTAG
* * * *
6505 AGGAGTAATTTACTTTTGAAAGTCGTGGTGCCTCTATTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGAGCCTCTGTTTAG
* * *** * *
6546 AGGAGCATTTTATTTTTTTGAGTCGTTGAGCCTCTGATTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGAGCCTCTGTTTAG
* * * *
6587 AGGAGCCATTTATGTTTCTCAAAGTCGTTGAGCCTCTGCTTAG
1 AGGAGCAATTTA-CTTT-TCAAAGTCGTGGAGCCTCTGTTTAG
6630 AGGAGCA
1 AGGAGCA
6637 TTGATCAAAA
Statistics
Matches: 109, Mismatches: 21, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
41 79 0.72
42 3 0.03
43 27 0.25
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.37
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGAGCCTCTGTTTAG
Found at i:6656 original size:8 final size:8
Alignment explanation
Indices: 6643--6681 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
6633 AGCATTGATC
6643 AAAAAATAA
1 AAAAAAT-A
*
6652 AAAAAAAA
1 AAAAAATA
6660 CAAAAAATA
1 -AAAAAATA
6669 AAAAAATA
1 AAAAAATA
6677 AAAAA
1 AAAAA
6682 TATCGAGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 14 0.52
9 13 0.48
ACGTcount: A:0.90, C:0.03, G:0.00, T:0.08
Consensus pattern (8 bp):
AAAAAATA
Found at i:6673 original size:15 final size:15
Alignment explanation
Indices: 6653--6683 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6643 AAAAAATAAA
6653 AAAAAAACAAAAAAT
1 AAAAAAACAAAAAAT
*
6668 AAAAAAATAAAAAAT
1 AAAAAAACAAAAAAT
6683 A
1 A
6684 TCGAGTTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAAACAAAAAAT
Found at i:6938 original size:3 final size:3
Alignment explanation
Indices: 6899--7061 Score: 84
Period size: 3 Copynumber: 50.3 Consensus size: 3
6889 TCTTATGTAT
*
6899 TTA TTA TTTA TTTA TTTA TTA ATA TATA TCT- TTA TTA TTA TTA TTA
1 TTA TTA -TTA -TTA -TTA TTA TTA T-TA T-TA TTA TTA TTA TTA TTA
*
6945 TTA TTA TTA TTA TT- TTA TT- TTA TT- TTA -TA TGTA TTT TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA -TTA
* *
6988 TCTA GTTG TATA TTTA TTA TTA TTTA TTCA TTTA TATA TTA TAA TTTA
1 T-TA -TTA T-TA -TTA TTA TTA -TTA TT-A -TTA T-TA TTA TTA -TTA
* *
7036 TCTG TTA TTA TTA TTA TTT TTA TTA T
1 T-TA TTA TTA TTA TTA TTA TTA TTA T
7062 CTTGTAATAT
Statistics
Matches: 128, Mismatches: 13, Indels: 38
0.72 0.07 0.21
Matches are distributed among these distances:
2 9 0.07
3 76 0.59
4 39 0.30
5 4 0.03
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:7089 original size:44 final size:44
Alignment explanation
Indices: 7031--7141 Score: 124
Period size: 44 Copynumber: 2.5 Consensus size: 44
7021 ATATATTATA
7031 ATTTATCTGTTATTATTATTATTTT-T-ATTATCT-TGTAATATTTTTT
1 ATTTATC--TTATTATT-TT-TTTTCTAATTATCTAT-TAATATTTTTT
7077 ATTTATCTTATTATTTTTTTTCTAATTATCTATTAATATTTTTT
1 ATTTATCTTATTATTTTTTTTCTAATTATCTATTAATATTTTTT
7121 -TTTAT-TTATCTGATTTTTTTT
1 ATTTATCTTAT-T-ATTTTTTTT
7142 ATGGGGGGGG
Statistics
Matches: 60, Mismatches: 0, Indels: 12
0.83 0.00 0.17
Matches are distributed among these distances:
42 8 0.13
43 9 0.15
44 35 0.58
45 1 0.02
46 7 0.12
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (44 bp):
ATTTATCTTATTATTTTTTTTCTAATTATCTATTAATATTTTTT
Found at i:7093 original size:19 final size:19
Alignment explanation
Indices: 7046--7095 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
7036 TCTGTTATTA
7046 TTATTA-TTTTTATTATCT
1 TTATTATTTTTTATTATCT
*
7064 TGTAATATTTTTTATTTATC-
1 T-TATTATTTTTTA-TTATCT
7084 TTATTATTTTTT
1 TTATTATTTTTT
7096 TTCTAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 1 0.04
19 14 0.52
20 7 0.26
21 5 0.19
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (19 bp):
TTATTATTTTTTATTATCT
Found at i:7105 original size:23 final size:22
Alignment explanation
Indices: 7031--7141 Score: 84
Period size: 25 Copynumber: 4.9 Consensus size: 22
7021 ATATATTATA
7031 ATTTATCTGTTATTATTATTATTTTT
1 ATTTATC--TTATTATT-TT-TTTTT
* * *
7057 A-TTATCTT-GTAATATTTTTT
1 ATTTATCTTATTATTTTTTTTT
7077 ATTTATCTTATTATTTTTTTTCT
1 ATTTATCTTATTATTTTTTTT-T
* *
7100 AATTATCTATTAATATTTTTTTTT
1 ATTTATC--TTATTATTTTTTTTT
*
7124 ATTTATCTGATT-TTTTTT
1 ATTTATCTTATTATTTTTT
7142 ATGGGGGGGG
Statistics
Matches: 69, Mismatches: 11, Indels: 15
0.73 0.12 0.16
Matches are distributed among these distances:
20 6 0.09
21 14 0.20
22 14 0.20
23 9 0.13
24 7 0.10
25 18 0.26
26 1 0.01
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (22 bp):
ATTTATCTTATTATTTTTTTTT
Found at i:8027 original size:5 final size:5
Alignment explanation
Indices: 8017--8103 Score: 51
Period size: 5 Copynumber: 17.6 Consensus size: 5
8007 TTCTTTAATC
* *
8017 TTTAT TTTATT TTTATT TTTGT TTTACT TTT-C TTTAT TTT-T TTTA-
1 TTTAT TTTA-T TTTA-T TTTAT TTTA-T TTTAT TTTAT TTTAT TTTAT
* *
8062 TTT-T TTTAT TTTCGCT TTTAT TTTGT TTTA- -TTAT TTTAT TTT
1 TTTAT TTTAT TTT--AT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
8104 CTTTAAATAA
Statistics
Matches: 64, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
3 3 0.05
4 13 0.20
5 30 0.47
6 14 0.22
7 4 0.06
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:8067 original size:7 final size:8
Alignment explanation
Indices: 8021--8073 Score: 54
Period size: 8 Copynumber: 6.1 Consensus size: 8
8011 TTAATCTTTA
8021 TTTTATTT
1 TTTTATTT
8029 TTATT-TTT
1 TT-TTATTT
8037 GTTTTACTTT
1 -TTTTA-TTT
8047 TCTTTATTTT
1 T-TTTA-TTT
8057 TTTTATTT
1 TTTTATTT
8065 TTTTATTT
1 TTTTATTT
8073 T
1 T
8074 CGCTTTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
8 19 0.49
9 9 0.23
10 11 0.28
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.83
Consensus pattern (8 bp):
TTTTATTT
Found at i:8069 original size:17 final size:17
Alignment explanation
Indices: 8021--8073 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 17
8011 TTAATCTTTA
*
8021 TTTTATTTTTATT-TTTG
1 TTTTATTTTT-TTATTTT
8038 TTTTACTTTTCTTTATTTT
1 TTTTA-TTTT-TTTATTTT
8057 TTTTATTTTTTTATTTT
1 TTTTATTTTTTTATTTT
8074 CGCTTTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 13 0.41
18 10 0.31
19 9 0.28
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.83
Consensus pattern (17 bp):
TTTTATTTTTTTATTTT
Found at i:8073 original size:38 final size:38
Alignment explanation
Indices: 8018--8108 Score: 100
Period size: 38 Copynumber: 2.4 Consensus size: 38
8008 TCTTTAATCT
*
8018 TTATTTTA--TTTTTATTTTTG-TTTTACTTTTC-TTTA
1 TTATTTTATTTTTTTATTTTCGCTTTTA-TTTTCTTTTA
* *
8053 TTTTTTTTATTTTTTTATTTTCGCTTTTATTTTGTTTTA
1 -TTATTTTATTTTTTTATTTTCGCTTTTATTTTCTTTTA
8092 TTATTTTATTTTCTTTA
1 TTATTTTATTTT-TTTA
8109 AATAAAATCC
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
36 7 0.15
38 26 0.57
39 13 0.28
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.78
Consensus pattern (38 bp):
TTATTTTATTTTTTTATTTTCGCTTTTATTTTCTTTTA
Found at i:8091 original size:30 final size:29
Alignment explanation
Indices: 8021--8104 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 29
8011 TTAATCTTTA
*
8021 TTTTATTTTTATTT-TTGTTTTACTTTT--C
1 TTTTATTTTT-TTTATTATTTTA-TTTTCGC
*
8049 -TTTATTTTTTTTATTTTTTTATTTTCGC
1 TTTTATTTTTTTTATTATTTTATTTTCGC
8077 TTTTATTTTGTTTTATTATTTTATTTTC
1 TTTTATTTT-TTTTATTATTTTATTTTC
8105 TTTAAATAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
26 7 0.14
27 16 0.33
28 1 0.02
29 8 0.16
30 17 0.35
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.79
Consensus pattern (29 bp):
TTTTATTTTTTTTATTATTTTATTTTCGC
Found at i:8108 original size:17 final size:17
Alignment explanation
Indices: 8017--8108 Score: 62
Period size: 18 Copynumber: 5.0 Consensus size: 17
8007 TTCTTTAATC
8017 TTTATTTTATTTTTATT-
1 TTTATTTTATTTTT-TTA
*
8034 TTTGTTTTACTTTTCTTTA
1 TTTATTTTA-TTTT-TTTA
*
8053 TTTTTTTTATTTTTTTA
1 TTTATTTTATTTTTTTA
*
8070 TTTTCGCTTTTATTTTGTTT-
1 -TTT--ATTTTATTTT-TTTA
8090 TATTATTTTATTTTCTTTA
1 T-TTATTTTATTTT-TTTA
8109 AATAAAATCC
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
17 12 0.20
18 25 0.41
19 10 0.16
20 11 0.18
21 3 0.05
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTATTTTATTTTTTTA
Found at i:8191 original size:58 final size:58
Alignment explanation
Indices: 8120--8249 Score: 208
Period size: 59 Copynumber: 2.2 Consensus size: 58
8110 ATAAAATCCA
** * *
8120 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAACTTTC
8178 AAAAAAAGGTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAACTTTC
1 AAAAAAAGG-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAACTTTC
8237 -AAAAAAGGTTTTT
1 AAAAAAAGGTTTTT
8250 CCTATTTTCC
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
57 5 0.07
58 15 0.22
59 47 0.70
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (58 bp):
AAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAACTTTC
Found at i:8261 original size:39 final size:39
Alignment explanation
Indices: 8214--8288 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
8204 GAAAGTATCA
8214 ATTTTCCTTAAAAATAAACTTTCAAAAAAGGTTTTTCCT
1 ATTTTCCTTAAAAATAAACTTTCAAAAAAGGTTTTTCCT
8253 ATTTTCCTTAAAAATAAACTTTCAAAAAAGGTTTTT
1 ATTTTCCTTAAAAATAAACTTTCAAAAAAGGTTTTT
8289 GAGGAAAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.41
Consensus pattern (39 bp):
ATTTTCCTTAAAAATAAACTTTCAAAAAAGGTTTTTCCT
Found at i:8306 original size:96 final size:97
Alignment explanation
Indices: 8155--8344 Score: 312
Period size: 96 Copynumber: 2.0 Consensus size: 97
8145 GAAAGTATCA
*
8155 ATTTTCCTTAAAAATAAATTTTCAAAAAAAGGTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTC
1 ATTTTCCTTAAAAATAAACTTTCAAAAAAAGGTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTC
8220 CTTAAAAATAAACTTTCAAAAAAGGTTTTTCCT
66 CTTAAAAATAAA-TTTCAAAAAAGGTTTTTCCT
*
8253 ATTTTCCTTAAAAATAAACTTTC-AAAAAAGG-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTT
1 ATTTTCCTTAAAAATAAACTTTCAAAAAAAGGTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTC
** *
8316 CTTAAAAATAAATTTTTAAAACGGTTTTT
66 CTTAAAAATAAATTTCAAAAAAGGTTTTT
8345 GAGGAAAAGT
Statistics
Matches: 87, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
95 14 0.16
96 43 0.49
97 8 0.09
98 22 0.25
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.39
Consensus pattern (97 bp):
ATTTTCCTTAAAAATAAACTTTCAAAAAAAGGTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTC
CTTAAAAATAAATTTCAAAAAAGGTTTTTCCT
Found at i:8354 original size:56 final size:55
Alignment explanation
Indices: 8253--8712 Score: 476
Period size: 56 Copynumber: 8.1 Consensus size: 55
8243 GGTTTTTCCT
* ** *
8253 ATTTTCCTTAAAAATAAACTTTCAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCA
1 ATTTTTCTTAAAAATAAA-TTT-TTAAAAGATTTTTGAGGAAAAGTTGAAAGTATCA
* *
8310 ATTTTTCTTAAAAATAAATTTTTAAAACGGTTTTTGAGGAAAAGTTAAAAGTATCA
1 ATTTTTCTTAAAAATAAATTTTTAAAA-GATTTTTGAGGAAAAGTTGAAAGTATCA
** * ** * *
8366 ATTTTTCTCGAAATTAAAGTTTCCAAAAAATATTTTTG-GAAAAAAGTTGAAAGTATCA
1 ATTTTTCTTAAAAATAAA-TTT--TTAAAAGATTTTTGAG-GAAAAGTTGAAAGTATCA
* *
8424 ATTTTTCTTAAAAATAAATTTTTAAAATGGTTTTTGAGGAAAAGTTGAAAATATCA
1 ATTTTTCTTAAAAATAAATTTTTAAAA-GATTTTTGAGGAAAAGTTGAAAGTATCA
8480 ATTTTTCTTAAAAATAAATTTTTAAAACGATTTTTGAGGAAAAGTTGAAAGTATCA
1 ATTTTTCTTAAAAATAAATTTTTAAAA-GATTTTTGAGGAAAAGTTGAAAGTATCA
* * * * *
8536 ATTTTCCCTAAAAATAAATTTTCAAAAAAGGGTTTTTGAGAAAAAGTTGAAAGTATCA
1 ATTTTTCTTAAAAATAAATTTT--TAAAA-GATTTTTGAGGAAAAGTTGAAAGTATCA
* * * *
8594 ATTTTTCTCAAAATTAAAGTTTCAAAAGATATTTTG-GAGAAAAGTTGAAAGTATCA
1 ATTTTTCTTAAAAATAAATTTTTAAAAGAT-TTTTGAG-GAAAAGTTGAAAGTATCA
* * * * * * *
8650 ATTTTCCTTGAGATTAAAATTTCTAAAAAATATTTTG-GGGAAAGTTGAAAGTATCA
1 ATTTTTCTTAAAAAT-AAATTTTTAAAAGAT-TTTTGAGGAAAAGTTGAAAGTATCA
8706 ATTTTTC
1 ATTTTTC
8713 CTGCACAAAA
Statistics
Matches: 342, Mismatches: 49, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
55 11 0.03
56 200 0.58
57 43 0.13
58 84 0.25
59 4 0.01
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.37
Consensus pattern (55 bp):
ATTTTTCTTAAAAATAAATTTTTAAAAGATTTTTGAGGAAAAGTTGAAAGTATCA
Found at i:8402 original size:114 final size:112
Alignment explanation
Indices: 8253--8712 Score: 525
Period size: 114 Copynumber: 4.1 Consensus size: 112
8243 GGTTTTTCCT
* * * * * *
8253 ATTTTCCTTAAAAATAAACTTTCAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCT
1 ATTTTTCTCAAAATTAAAGTTTCAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
8318 TAAAAATAAATTTTTAAAACGGTTTTTGAGGAAAAGTTAAAAGTATCA
66 TAAAAATAAATTTTTAAAA-GGTTTTTGAGGAAAAGTTAAAAGTATCA
* * * *
8366 ATTTTTCTCGAAATTAAAGTTTCCAAAAAATATTTTTG-GAAAAAAGTTGAAAGTATCAATTTTT
1 ATTTTTCTCAAAATTAAAGTTT-CAAAAAAGATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTC
8430 CTTAAAAATAAATTTTTAAAATGGTTTTTGAGGAAAAGTTGAAAA-TATCA
64 CTTAAAAATAAATTTTTAAAA-GGTTTTTGAGGAAAAGTT-AAAAGTATCA
* * ** * *
8480 ATTTTTCTTAAAAATAAA-TTTTTAAAACGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCC
1 ATTTTTCTCAAAATTAAAGTTTCAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* * *
8544 TAAAAATAAATTTTCAAAAAAGGGTTTTTGAGAAAAAGTTGAAAGTATCA
66 TAAAAATAAATTTT--TAAAA-GGTTTTTGAGGAAAAGTTAAAAGTATCA
* * *
8594 ATTTTTCTCAAAATTAAAGTTTCAAAAGATATTTTGGA-GAAAAGTTGAAAGTATCAATTTTCCT
1 ATTTTTCTCAAAATTAAAGTTTCAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* * * * ** * *
8658 TGAGATTAAAATTTCTAAAAAATATTTTG-GGGAAAGTTGAAAGTATCA
66 TAAAAAT-AAATTTTTAAAAGGT-TTTTGAGGAAAAGTTAAAAGTATCA
8706 ATTTTTC
1 ATTTTTC
8713 CTGCACAAAA
Statistics
Matches: 296, Mismatches: 41, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
112 73 0.25
113 34 0.11
114 166 0.56
115 23 0.08
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.37
Consensus pattern (112 bp):
ATTTTTCTCAAAATTAAAGTTTCAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
TAAAAATAAATTTTTAAAAGGTTTTTGAGGAAAAGTTAAAAGTATCA
Found at i:8582 original size:170 final size:169
Alignment explanation
Indices: 8253--8710 Score: 568
Period size: 170 Copynumber: 2.7 Consensus size: 169
8243 GGTTTTTCCT
* *
8253 ATTTTCCTTAAAAATAAACTTTCAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCT
1 ATTTTTCTTAAAAATAAA-TTT-TAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCT
* * * * *
8318 TAAAAATAAATTTTTAAAACGGTTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTCGAAATTAA
64 TAAAAATAAATTTTTAAAACGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAA
*
8383 AGTTTCCAAAAAATATTTTTGGAAAAAAGTTGAAAGTATCA
129 AGTTTCCAAAAAAGATTTTTGGAAAAAAGTTGAAAGTATCA
* *
8424 ATTTTTCTTAAAAATAAATTTTTAAAATGGTTTTTGAGGAAAAGTTGAAAATATCAATTTTTCTT
1 ATTTTTCTTAAAAATAAA-TTTTAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT
8489 AAAAATAAATTTTTAAAACGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC-CTAAAAATAA
65 AAAAATAAATTTTTAAAACGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTC-AAAAATAA
* *
8553 A-TTTTCAAAAAAGGGTTTTT-GAGAAAAAGTTGAAAGTATCA
129 AGTTTCCAAAAAA-GATTTTTGGA-AAAAAGTTGAAAGTATCA
* * * * * *
8594 ATTTTTCTCAAAATTAAAGTTTCAAAAGATATTTTG-GAGAAAAGTTGAAAGTATCAATTTTCCT
1 ATTTTTCTTAAAAATAAATTTTAAAAAGGT-TTTTGAG-GAAAAGTTGAAAGTATCAATTTTTCT
* * * * * *
8658 TGAGATTAAAATTTCTAAAA-AATATTTTG-GGGAAAGTTGAAAGTATCAATTTT
64 TAAAAAT-AAATTTTTAAAACGAT-TTTTGAGGAAAAGTTGAAAGTATCAATTTT
8711 TCCTGCACAA
Statistics
Matches: 253, Mismatches: 27, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
169 22 0.09
170 195 0.77
171 36 0.14
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (169 bp):
ATTTTTCTTAAAAATAAATTTTAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTA
AAAATAAATTTTTAAAACGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAAG
TTTCCAAAAAAGATTTTTGGAAAAAAGTTGAAAGTATCA
Found at i:9865 original size:13 final size:12
Alignment explanation
Indices: 9849--9882 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
9839 GCTGGCATAA
9849 AAAAAAAAGAAAG
1 AAAAAAAA-AAAG
9862 AAAAAGAAAAAAG
1 AAAAA-AAAAAAG
9875 AAAAAAAA
1 AAAAAAAA
9883 TAATAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 14 0.70
14 3 0.15
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:9871 original size:17 final size:15
Alignment explanation
Indices: 9847--9882 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
9837 AAGCTGGCAT
9847 AAAAAAAAAAGAAAGA
1 AAAAAAAAAAGAAA-A
9863 AAAAGAAAAAAGAAAA
1 AAAA-AAAAAAGAAAA
9879 AAAA
1 AAAA
9883 TAATAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGAAAA
Found at i:11478 original size:35 final size:36
Alignment explanation
Indices: 11439--11513 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
11429 AAAATATTAA
11439 AAAAAAATTTAT-ATA-AAAAATTAAATTGATGCAT-T
1 AAAAAAA-TTATGATACAAAAATTAAATTGA-GCATCT
* *
11474 AAAAAAATTATGTTACATAAATTAAATTGAGCATCT
1 AAAAAAATTATGATACAAAAATTAAATTGAGCATCT
11510 AAAA
1 AAAA
11514 TAAAAGCATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
34 4 0.11
35 13 0.37
36 18 0.51
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (36 bp):
AAAAAAATTATGATACAAAAATTAAATTGAGCATCT
Found at i:17443 original size:89 final size:89
Alignment explanation
Indices: 17292--17474 Score: 321
Period size: 89 Copynumber: 2.1 Consensus size: 89
17282 ATATTGAAAA
*
17292 ATTAAGTGTTAAACTTCAAAGATTAATTACACATTTGATACTTGAATTAGAGTAAAATTCTTTGA
1 ATTAAGTGTTAAACTTCAAAAATTAATTACACATTTGATACTTGAATTAGAGTAAAATTCTTTGA
17357 AACTTAAATTTGAAAAGTTACAAT
66 AACTTAAATTTGAAAAGTTACAAT
*
17381 ATTAAGTGTTAAACTTCAAAAATTAATTACGCATTTGATACTTGAATTAGAGTAAAATTCTTTGA
1 ATTAAGTGTTAAACTTCAAAAATTAATTACACATTTGATACTTGAATTAGAGTAAAATTCTTTGA
* *
17446 TACTTAAATTTGAAAAGTTATAAT
66 AACTTAAATTTGAAAAGTTACAAT
*
17470 CTTAA
1 ATTAA
17475 TACTACTTGT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (89 bp):
ATTAAGTGTTAAACTTCAAAAATTAATTACACATTTGATACTTGAATTAGAGTAAAATTCTTTGA
AACTTAAATTTGAAAAGTTACAAT
Found at i:17726 original size:16 final size:16
Alignment explanation
Indices: 17705--17736 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
17695 AAGAACATTG
17705 TTGCTGGAAATGTCTC
1 TTGCTGGAAATGTCTC
17721 TTGCTGGAAATGTCTC
1 TTGCTGGAAATGTCTC
17737 GATGAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (16 bp):
TTGCTGGAAATGTCTC
Found at i:19632 original size:144 final size:144
Alignment explanation
Indices: 19367--20258 Score: 1179
Period size: 144 Copynumber: 6.2 Consensus size: 144
19357 GCTTCGACAT
* * * *
19367 GTTTCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACACAAAGTAAGTGAGAG
1 GTTTCCTATTGAAGCAGGGATTGAACCAGAGAAATTATTATGACTCAACTCAAAGTCAGTGAGAG
* * *
19432 ATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATTG-AGGTTGAGAGT
66 ATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTATGA-TGAAGGTAGAGAAT
*
19496 GGATAAGCTAGTCAA
130 GGATAAACTAGTCAA
* * * *
19511 GTTTCCTGTTGAAGCAGGGATTGAACCAGAGAAATTATTTTCA-TCCAACTTAAAGTCAGTGAGA
1 GTTTCCTATTGAAGCAGGGATTGAACCAGAGAAATTATTATGACT-CAACTCAAAGTCAGTGAGA
* * * *
19575 GATTTAAGCATCCCTATCTCTTTAGGTATCAACCCAGAAAACATATTTTGATCG-AGGTGGAGAA
65 GATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTATGAT-GAAGGTAGAGAA
*
19639 TGGATAAGCTAGTCAA
129 TGGATAAACTAGTCAA
* * *
19655 GTTTCCTATTGAAGCAGGGATTGAACCAGAGAAATTATTTTCACACAACTCAAAGTCAGTGAGAG
1 GTTTCCTATTGAAGCAGGGATTGAACCAGAGAAATTATTATGACTCAACTCAAAGTCAGTGAGAG
* *
19720 ATTTAAGCATCCCTATCTCTTTAGGTATCGACCCAGAAAACATATTATGATGAAGGTAGAGAGTG
66 ATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTATGATGAAGGTAGAGAATG
*
19785 GATAAACTGGTCAA
131 GATAAACTAGTCAA
** * * *
19799 GTTTTTTA-TGAAAGCAGGGATTGAACCAGAGAAATTATTATGACTCAACTGAAGGTTAGTGAGA
1 GTTTCCTATTG-AAGCAGGGATTGAACCAGAGAAATTATTATGACTCAACTCAAAGTCAGTGAGA
* *
19863 GATTTAAGCATCCCTATCTCTTGAGGTATTGACCCAGAAAACATATTATGATGAAGGTAAAGAAT
65 GATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTATGATGAAGGTAGAGAAT
**
19928 GGATAAACGGGTCAA
130 GGATAAACTAGTCAA
** * * *
19943 GTTTTTTA-TGAAAGCAGGGATTGAACCAGAGAAATTATTATGACTCAACTGAAGGTTAGTGAGA
1 GTTTCCTATTG-AAGCAGGGATTGAACCAGAGAAATTATTATGACTCAACTCAAAGTCAGTGAGA
* * *
20007 GATTTAAGCATCCCTATCCCTTGAGGTATTGACCCAGAAAACATATTATGATGAAGGTAAAGAAT
65 GATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTATGATGAAGGTAGAGAAT
*
20072 GGATAAACTGGTCAA
130 GGATAAACTAGTCAA
**
20087 GTTTTTTA-TGAAAGCAGGGATTGAACCAGAGAAATTATTATGACTCAACTCAAAGTCAGTGAGA
1 GTTTCCTATTG-AAGCAGGGATTGAACCAGAGAAATTATTATGACTCAACTCAAAGTCAGTGAGA
* * * * *
20151 GATTTAAGCATCCCTATTTCTTGAGGTATCGATCCACAAAACATATTTTGAT-AGAGGTGGAGAA
65 GATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTATGATGA-AGGTAGAGAA
** *
20215 CAGAT-AAGTAGGTCAA
129 TGGATAAACTA-GTCAA
* *
20231 GTTTCCTATGGAAGCAGGGATAGAACCA
1 GTTTCCTATTGAAGCAGGGATTGAACCA
20259 CGTAGATAGT
Statistics
Matches: 687, Mismatches: 53, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
143 9 0.01
144 677 0.99
145 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (144 bp):
GTTTCCTATTGAAGCAGGGATTGAACCAGAGAAATTATTATGACTCAACTCAAAGTCAGTGAGAG
ATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTATGATGAAGGTAGAGAATG
GATAAACTAGTCAA
Found at i:19838 original size:72 final size:72
Alignment explanation
Indices: 19762--20129 Score: 161
Period size: 72 Copynumber: 5.1 Consensus size: 72
19752 CCAGAAAACA
19762 TATTATGATGAAGGTAGAGAGTGGATAAACTGGTCAAGTTTTTTATGAAAGCAGGGATTGAACCA
1 TATTATGATGAAGGTAGAGAGTGGATAAACTGGTCAAGTTTTTTATGAAAGCAGGGATTGAACCA
19827 GAGAAAT
66 GAGAAAT
* * * * * * * *** **** *
19834 TATTATGACTCAACTGAAG-GTTAGT-GAGAGA-T--TTAAGCATCCCTATCTCTTG-AGGTATT
1 TATTATGA-TGAA-GGTAGAG--AGTGGATAAACTGGTCAAG-TTTTTTAT-GAAAGCAGGGATT
* *
19893 GACCCAGA-AAACA
60 GAACCAGAGAAA-T
* * *
19906 TATTATGATGAAGGTAAAGAATGGATAAACGGGTCAAGTTTTTTATGAAAGCAGGGATTGAACCA
1 TATTATGATGAAGGTAGAGAGTGGATAAACTGGTCAAGTTTTTTATGAAAGCAGGGATTGAACCA
19971 GAGAAAT
66 GAGAAAT
* * * * * * * *** **** *
19978 TATTATGACTCAACTGAAG-GTTAGT-GAGAGA-T--TTAAGCATCCCTATCCCTTG-AGGTATT
1 TATTATGA-TGAA-GGTAGAG--AGTGGATAAACTGGTCAAG-TTTTTTAT-GAAAGCAGGGATT
* *
20037 GACCCAGA-AAACA
60 GAACCAGAGAAA-T
* *
20050 TATTATGATGAAGGTAAAGAATGGATAAACTGGTCAAGTTTTTTATGAAAGCAGGGATTGAACCA
1 TATTATGATGAAGGTAGAGAGTGGATAAACTGGTCAAGTTTTTTATGAAAGCAGGGATTGAACCA
20115 GAGAAAT
66 GAGAAAT
20122 TATTATGA
1 TATTATGA
20130 CTCAACTCAA
Statistics
Matches: 192, Mismatches: 76, Indels: 56
0.59 0.23 0.17
Matches are distributed among these distances:
69 4 0.02
70 12 0.06
71 25 0.13
72 108 0.56
73 25 0.13
74 13 0.07
75 5 0.03
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.28
Consensus pattern (72 bp):
TATTATGATGAAGGTAGAGAGTGGATAAACTGGTCAAGTTTTTTATGAAAGCAGGGATTGAACCA
GAGAAAT
Found at i:21977 original size:15 final size:15
Alignment explanation
Indices: 21957--22021 Score: 51
Period size: 15 Copynumber: 4.0 Consensus size: 15
21947 ATAATTTATA
21957 AAATAAAATTATATT
1 AAATAAAATTATATT
*
21972 AAATAAATATATTTATT
1 AAATAAA-AT-TATATT
*
21989 AAATATTTAAATTATTAAT
1 AAATA---AAATTA-TATT
22008 AAAT-AAATTATATT
1 AAATAAAATTATATT
22022 TAACTAGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
14 3 0.08
15 13 0.32
16 2 0.05
17 10 0.25
18 1 0.03
19 9 0.22
20 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATAAAATTATATT
Found at i:21993 original size:32 final size:35
Alignment explanation
Indices: 21950--22023 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 35
21940 TTTTTTGATA
*
21950 ATTTATAAAATA-AAATTA-TATTAAATAAA-TAT
1 ATTTATAAAATATAAATTATTAATAAATAAATTAT
*
21982 ATTTATTAAATATTTAAATTATTAATAAATAAATTAT
1 ATTTA-TAAA-ATATAAATTATTAATAAATAAATTAT
22019 ATTTA
1 ATTTA
22024 ACTAGTGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 5 0.14
33 4 0.11
34 2 0.06
35 6 0.17
36 10 0.29
37 8 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (35 bp):
ATTTATAAAATATAAATTATTAATAAATAAATTAT
Found at i:22743 original size:17 final size:17
Alignment explanation
Indices: 22701--22743 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
22691 ATTTAGTTAT
*
22701 TAATTTTTATAGAATAA
1 TAATTTTTATAAAATAA
**
22718 TAAAATTTATAAAATAA
1 TAATTTTTATAAAATAA
22735 TAATTTTTA
1 TAATTTTTA
22744 ATTCATAAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
TAATTTTTATAAAATAA
Found at i:23836 original size:18 final size:17
Alignment explanation
Indices: 23809--23861 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 17
23799 CATTCATATC
23809 TTTTTATTTAATAATTT
1 TTTTTATTTAATAATTT
* *
23826 TTTTATATTTAATAAATA
1 TTTT-TATTTAATAATTT
23844 TTTTTATTTAAT-ATTT
1 TTTTTATTTAATAATTT
23860 TT
1 TT
23862 ACGTGCGGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 4 0.13
17 12 0.39
18 15 0.48
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTATTTAATAATTT
Found at i:23849 original size:19 final size:18
Alignment explanation
Indices: 23804--23850 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
23794 TGTGGCATTC
23804 ATATCTTTT-TATTTAATA
1 ATAT-TTTTATATTTAATA
*
23822 ATTTTTTTATATTTAATAA
1 ATATTTTTATATTTAAT-A
23841 ATATTTTTAT
1 ATATTTTTAT
23851 TTAATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.16
18 11 0.44
19 10 0.40
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
ATATTTTTATATTTAATA
Found at i:23856 original size:13 final size:13
Alignment explanation
Indices: 23809--23862 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
23799 CATTCATATC
23809 TTTTTATTTAATA
1 TTTTTATTTAATA
*
23822 ATTTT-TTT-ATA
1 TTTTTATTTAATA
* *
23833 --TTTAATAAATA
1 TTTTTATTTAATA
23844 TTTTTATTTAATA
1 TTTTTATTTAATA
23857 TTTTTA
1 TTTTTA
23863 CGTGCGGACC
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
9 3 0.09
10 1 0.03
11 6 0.19
12 3 0.09
13 19 0.59
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTTATTTAATA
Found at i:24507 original size:21 final size:18
Alignment explanation
Indices: 24476--24519 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
24466 AATTGACATG
* *
24476 TTTTAATAA-TAATATAT
1 TTTTAAAAATTAATAAAT
*
24493 TTATAAAAATTAATAAAT
1 TTTTAAAAATTAATAAAT
24511 TTTTAAAAA
1 TTTTAAAAA
24520 CTCTATCATC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTTAAAAATTAATAAAT
Found at i:24541 original size:3 final size:3
Alignment explanation
Indices: 24533--24581 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
24523 TATCATCTAT
24533 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
24580 AT
1 AT
24582 TATTAAATGA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:24925 original size:12 final size:13
Alignment explanation
Indices: 24908--24936 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
24898 TATCTCTAAA
24908 ATTTAA-TTTTTT
1 ATTTAATTTTTTT
24920 ATTTAATTTTTTT
1 ATTTAATTTTTTT
24933 ATTT
1 ATTT
24937 TTATTCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTAATTTTTTT
Found at i:25239 original size:19 final size:20
Alignment explanation
Indices: 25211--25253 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
25201 ATTATTTAAC
*
25211 ATTTATAAAATTAATAAATT
1 ATTTATAAAATCAATAAATT
25231 ATTTA-AAAATCAATAAATT
1 ATTTATAAAATCAATAAATT
25250 ATTT
1 ATTT
25254 TTATGTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTATAAAATCAATAAATT
Found at i:25827 original size:14 final size:14
Alignment explanation
Indices: 25806--25839 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
25796 TTAAAAATAT
25806 TAAATTTAAATTAA
1 TAAATTTAAATTAA
*
25820 TTAATTTAAATTAA
1 TAAATTTAAATTAA
25834 TAAATT
1 TAAATT
25840 AAAAAAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAATTTAAATTAA
Found at i:26544 original size:6 final size:6
Alignment explanation
Indices: 26527--26573 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
26517 TTTTTATTAA
26527 AAAATT -AAATT AAAATT AAAATT AAAATCT -AAATT CATAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAAT-T AAAATT -A-AAATT AAAA
26574 AAATCTTGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
5 6 0.17
6 23 0.64
7 2 0.06
8 5 0.14
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:27219 original size:49 final size:49
Alignment explanation
Indices: 27162--27258 Score: 176
Period size: 49 Copynumber: 2.0 Consensus size: 49
27152 TTATGCATCA
27162 GCTATAATTTTATATATTGATAATGAAAATTTAAAAATTTAAAAATGAT
1 GCTATAATTTTATATATTGATAATGAAAATTTAAAAATTTAAAAATGAT
* *
27211 GCTATAATTTTATATATTGATAATGAAATTTTTAAAATTTAAAAATGA
1 GCTATAATTTTATATATTGATAATGAAAATTTAAAAATTTAAAAATGA
27259 GATAACGGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.42
Consensus pattern (49 bp):
GCTATAATTTTATATATTGATAATGAAAATTTAAAAATTTAAAAATGAT
Found at i:27314 original size:20 final size:22
Alignment explanation
Indices: 27277--27316 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
27267 AATTGGCACA
27277 AATTTATTTAATTTTAATAATT
1 AATTTATTTAATTTTAATAATT
27299 AATTT-TTTAA-TTTAATAA
1 AATTTATTTAATTTTAATAA
27317 ATATATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AATTTATTTAATTTTAATAATT
Found at i:27325 original size:20 final size:21
Alignment explanation
Indices: 27277--27325 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
27267 AATTGGCACA
*
27277 AATTTATTTAATTTTAATAATT
1 AATTT-TTTAATTTTAATAAAT
27299 AATTTTTTAA-TTTAATAAAT
1 AATTTTTTAATTTTAATAAAT
27319 ATATTTT
1 A-ATTTT
27326 AGTGGAATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 10 0.40
21 10 0.40
22 5 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AATTTTTTAATTTTAATAAAT
Found at i:28223 original size:20 final size:22
Alignment explanation
Indices: 28184--28229 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
28174 GGTGTTAATT
28184 TTAATATAAATGGTTATATTTA
1 TTAATATAAATGGTTATATTTA
28206 TTAATATAAATGG-T-TATTTA
1 TTAATATAAATGGTTATATTTA
28226 TTAA
1 TTAA
28230 AAACTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 10 0.42
21 1 0.04
22 13 0.54
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (22 bp):
TTAATATAAATGGTTATATTTA
Done.