Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014368.1 Kokia drynarioides strain JFW-HI SEQ_129405, 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: 133989
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:6733 original size:13 final size:14
Alignment explanation
Indices: 6704--6738 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
6694 TTGAATTATT
6704 AAAAATTAAAATAA
1 AAAAATTAAAATAA
*
6718 AAAAATTAAACTAA
1 AAAAATTAAAATAA
6732 AATAAAT
1 AA-AAAT
6739 GAATTGAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAATTAAAATAA
Found at i:9881 original size:15 final size:15
Alignment explanation
Indices: 9863--9902 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
9853 AACTTAATGT
*
9863 ATAACAATAACAATA
1 ATAACAATAACAACA
9878 ATAACAATAACAACA
1 ATAACAATAACAACA
*
9893 ATAATAATAA
1 ATAACAATAA
9903 TAGCCCTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (15 bp):
ATAACAATAACAACA
Found at i:9882 original size:9 final size:9
Alignment explanation
Indices: 9868--9904 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
9858 AATGTATAAC
9868 AATAACAAT
1 AATAACAAT
9877 AATAACAAT
1 AATAACAAT
*
9886 AACAACAAT
1 AATAACAAT
*
9895 AATAATAAT
1 AATAACAAT
9904 A
1 A
9905 GCCCTAGTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.22
Consensus pattern (9 bp):
AATAACAAT
Found at i:10148 original size:15 final size:16
Alignment explanation
Indices: 10121--10162 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
10111 AAAATTATTA
10121 TATATTT-TTTAATAT
1 TATATTTATTTAATAT
10136 T-TATTTATTTAATAT
1 TATATTTATTTAATAT
10151 TATATTATATTT
1 TATATT-TATTT
10163 TCATTTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.21
15 10 0.42
16 4 0.17
17 5 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATATTTATTTAATAT
Found at i:16274 original size:16 final size:16
Alignment explanation
Indices: 16249--16286 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
16239 ATCCTTAGTT
*
16249 GTGGAAAGCTAACG-TA
1 GTGGAGAGCTAA-GATA
16265 GTGGAGAGCTAAGATA
1 GTGGAGAGCTAAGATA
16281 GTGGAG
1 GTGGAG
16287 TAGGCATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 1 0.05
16 19 0.95
ACGTcount: A:0.34, C:0.08, G:0.39, T:0.18
Consensus pattern (16 bp):
GTGGAGAGCTAAGATA
Found at i:17739 original size:18 final size:18
Alignment explanation
Indices: 17716--17752 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17706 ACAATTCATA
17716 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
17734 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
17752 T
1 T
17753 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:22331 original size:28 final size:25
Alignment explanation
Indices: 22289--22389 Score: 94
Period size: 28 Copynumber: 3.7 Consensus size: 25
22279 TTTTTAAATA
22289 TAATTTTTTACAATTTTTATATTTGCT
1 TAATTTTTTACAATTTTTATATTT--T
*
22316 TAATATTTTTATAATTTTTAATTATATTT
1 TAAT-TTTTTACAATTTTT-A-TAT-TTT
*
22345 TAATTTTTTTACAATTTATAATAATTTT
1 TAA-TTTTTTACAATTT-TTAT-ATTTT
*
22373 TAATTTTTTATAATTTT
1 TAATTTTTTACAATTTT
22390 ATTACAATTT
Statistics
Matches: 63, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
26 1 0.02
27 16 0.25
28 20 0.32
29 19 0.30
30 5 0.08
31 2 0.03
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (25 bp):
TAATTTTTTACAATTTTTATATTTT
Found at i:22350 original size:27 final size:27
Alignment explanation
Indices: 22289--22389 Score: 107
Period size: 29 Copynumber: 3.6 Consensus size: 27
22279 TTTTTAAATA
*
22289 TAATTTTTTACAATTTTT-AT-ATTTGCT
1 TAATTTTTTATAATTTTTAATAATTT--T
*
22316 TAATATTTTTATAATTTTTAATTATATTT
1 TAAT-TTTTTATAATTTTTAATAAT-TTT
* *
22345 TAATTTTTTTACAATTTATAATAATTTT
1 TAA-TTTTTTATAATTTTTAATAATTTT
22373 TAATTTTTTATAATTTT
1 TAATTTTTTATAATTTT
22390 ATTACAATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
27 16 0.25
28 19 0.30
29 23 0.37
30 3 0.05
31 2 0.03
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (27 bp):
TAATTTTTTATAATTTTTAATAATTTT
Found at i:22396 original size:38 final size:39
Alignment explanation
Indices: 22326--22399 Score: 116
Period size: 38 Copynumber: 1.9 Consensus size: 39
22316 TAATATTTTT
*
22326 ATAATTTTTAATTATATTTTAATTTTTTTACAATTTATA
1 ATAATTTTTAATTATATTTTAATTTTATTACAATTTATA
22365 ATAATTTTTAATT-T-TTTATAATTTTATTACAATTT
1 ATAATTTTTAATTATATTT-TAATTTTATTACAATTT
22400 CAATAATCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 3 0.09
38 17 0.52
39 13 0.39
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (39 bp):
ATAATTTTTAATTATATTTTAATTTTATTACAATTTATA
Found at i:22398 original size:28 final size:27
Alignment explanation
Indices: 22271--22399 Score: 81
Period size: 28 Copynumber: 4.7 Consensus size: 27
22261 GTGGTACTTC
* *
22271 TTATAATTTTTTTAAA--TATAATTTT
1 TTATAATTTTATTAAATTTTTAATTTT
* *
22296 TTACAA-TTT-TTATATTTGCTTAATATTT
1 TTATAATTTTATTAAATTT--TTAAT-TTT
*
22324 TTATAATTTTTAATTATA-TTTTAATTTT
1 TTATAA-TTTT-ATTAAATTTTTAATTTT
* *
22352 TT-TACAATTTATAATAATTTTTAATTTT
1 TTATA-ATTTTATTA-AATTTTTAATTTT
22380 TTATAATTTTATTACAATTT
1 TTATAATTTTATTA-AATTT
22400 CAATAATCTA
Statistics
Matches: 81, Mismatches: 10, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
23 4 0.05
24 3 0.04
25 6 0.07
26 3 0.04
27 10 0.12
28 38 0.47
29 7 0.09
30 3 0.04
31 2 0.02
32 5 0.06
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (27 bp):
TTATAATTTTATTAAATTTTTAATTTT
Found at i:32173 original size:19 final size:20
Alignment explanation
Indices: 32142--32195 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
32132 GAAAATATAA
32142 ATTTTGAAATTTTTATAAAT
1 ATTTTGAAATTTTTATAAAT
*
32162 ATTTTG-AA-TTTT-TGAAT
1 ATTTTGAAATTTTTATAAAT
*
32179 ATTTTTGTAATTTTTAT
1 A-TTTTGAAATTTTTAT
32196 TGAGAGAGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 5 0.17
18 9 0.31
19 4 0.14
20 10 0.34
21 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.61
Consensus pattern (20 bp):
ATTTTGAAATTTTTATAAAT
Found at i:32191 original size:9 final size:9
Alignment explanation
Indices: 32143--32193 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
32133 AAAATATAAA
32143 TTTTGAAAT
1 TTTTGAAAT
*
32152 TTTTATAAAT
1 TTTT-GAAAT
32162 ATTTTG-AAT
1 -TTTTGAAAT
32171 TTTTGAATAT
1 TTTTGAA-AT
*
32181 TTTTGTAAT
1 TTTTGAAAT
32190 TTTT
1 TTTT
32194 ATTGAGAGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
8 5 0.14
9 14 0.40
10 12 0.34
11 4 0.11
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (9 bp):
TTTTGAAAT
Found at i:32469 original size:13 final size:13
Alignment explanation
Indices: 32453--32478 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32443 TTCTCTGGAG
32453 AAGTTGAAACGGT
1 AAGTTGAAACGGT
32466 AAGTTGAAACGGT
1 AAGTTGAAACGGT
32479 GAGCCATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (13 bp):
AAGTTGAAACGGT
Found at i:38576 original size:9 final size:9
Alignment explanation
Indices: 38560--38611 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
38550 ATTTACATAC
38560 TTATTTTAT
1 TTATTTTAT
*
38569 TCATTTTATT
1 TTATTTTA-T
38579 TTATTTTAT
1 TTATTTTAT
38588 TTA-TTTAT
1 TTATTTTAT
*
38596 TT-TGATTAT
1 TTAT-TTTAT
38605 TTATTTT
1 TTATTTT
38612 TGCTACTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
8 7 0.20
9 19 0.54
10 9 0.26
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (9 bp):
TTATTTTAT
Found at i:38584 original size:19 final size:18
Alignment explanation
Indices: 38560--38598 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
38550 ATTTACATAC
38560 TTATTTTATTCATTTTATT
1 TTATTTTATTCA-TTTATT
*
38579 TTATTTTATTTATTTATT
1 TTATTTTATTCATTTATT
38597 TT
1 TT
38599 GATTATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (18 bp):
TTATTTTATTCATTTATT
Found at i:38596 original size:13 final size:14
Alignment explanation
Indices: 38573--38611 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
38563 TTTTATTCAT
38573 TTTATTTTATTTT-A
1 TTTA-TTTATTTTGA
38587 TTTATTTATTTTGA
1 TTTATTTATTTTGA
38601 -TTATTTATTTT
1 TTTATTTATTTT
38612 TGCTACTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 19 0.79
14 5 0.21
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTATTTATTTTGA
Found at i:38637 original size:14 final size:14
Alignment explanation
Indices: 38585--38644 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 14
38575 TATTTTATTT
38585 TATTTATTTATTTTGA
1 TATTTA-TT-TTTTGA
*
38601 TTATTTA-TTTTTGC
1 -TATTTATTTTTTGA
38615 TACTCTTATTTTTTGA
1 TA-T-TTATTTTTTGA
38631 TATTTATATTTTTG
1 TATTTAT-TTTTTG
38645 TCCCATTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 2 0.05
14 10 0.27
15 11 0.30
16 8 0.22
17 6 0.16
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (14 bp):
TATTTATTTTTTGA
Found at i:38815 original size:23 final size:23
Alignment explanation
Indices: 38780--38826 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
38770 TTCTTATTTA
38780 TTTATTATTTTTATATATTTATT
1 TTTATTATTTTTATATATTTATT
*
38803 TTTATT-TTGTTTATTTATTTATT
1 TTTATTATT-TTTATATATTTATT
38826 T
1 T
38827 CTAGCTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTATTATTTTTATATATTTATT
Found at i:39842 original size:26 final size:25
Alignment explanation
Indices: 39803--39857 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
39793 TATATTATTG
*
39803 TTTTGGTGCTTTTTTTTTTTTTACTA
1 TTTTGGTGC-TTTTTTTTTTATACTA
39829 TTTTGGTTGC-TTTTTTTTTATACTA
1 TTTTGG-TGCTTTTTTTTTTATACTA
39854 TTTT
1 TTTT
39858 TGTGTTGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 18 0.67
26 6 0.22
27 3 0.11
ACGTcount: A:0.09, C:0.07, G:0.11, T:0.73
Consensus pattern (25 bp):
TTTTGGTGCTTTTTTTTTTATACTA
Found at i:39926 original size:21 final size:22
Alignment explanation
Indices: 39914--39954 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39904 GTTGTTTTCG
39914 TGCTATTTTTTGTTAATTTTGT
1 TGCTATTTTTTGTTAATTTTGT
*
39936 TGCTATTTTTT-TTATTTTT
1 TGCTATTTTTTGTTAATTTT
39955 AATGTTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.12, C:0.05, G:0.10, T:0.73
Consensus pattern (22 bp):
TGCTATTTTTTGTTAATTTTGT
Found at i:39988 original size:12 final size:12
Alignment explanation
Indices: 39919--40007 Score: 62
Period size: 12 Copynumber: 7.8 Consensus size: 12
39909 TTTCGTGCTA
*
39919 TTTT-TTGTTAA
1 TTTTGTTGTTAT
*
39930 TTTTGTTGCTA-
1 TTTTGTTGTTAT
39941 TTTT-TT-TTAT
1 TTTTGTTGTTAT
** *
39951 TTTTAATGTT-G
1 TTTTGTTGTTAT
* *
39962 TTTTGCTATTAT
1 TTTTGTTGTTAT
*
39974 TTTTGTTGTTGT
1 TTTTGTTGTTAT
*
39986 TTTGGTTGTTAT
1 TTTTGTTGTTAT
39998 TTTTGTTGTT
1 TTTTGTTGTT
40008 TGGATGTTAT
Statistics
Matches: 59, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
9 2 0.03
10 6 0.10
11 16 0.27
12 35 0.59
ACGTcount: A:0.10, C:0.02, G:0.16, T:0.72
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:40015 original size:20 final size:21
Alignment explanation
Indices: 39979--40021 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
39969 ATTATTTTTG
*
39979 TTGTTGTTTTGGTTGTTATTT
1 TTGTTGTTTTGGATGTTATTT
40000 TTGTTG-TTTGGATGTTATTT
1 TTGTTGTTTTGGATGTTATTT
40020 TT
1 TT
40022 ATGCGTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.07, C:0.00, G:0.23, T:0.70
Consensus pattern (21 bp):
TTGTTGTTTTGGATGTTATTT
Found at i:40961 original size:25 final size:25
Alignment explanation
Indices: 40933--40980 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40923 CTAAACTTTA
40933 ATAAAATTGAAGAAAAATAATTTTT
1 ATAAAATTGAAGAAAAATAATTTTT
** *
40958 ATAAAATTTTATAAAAATAATTT
1 ATAAAATTGAAGAAAAATAATTT
40981 AGTTTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (25 bp):
ATAAAATTGAAGAAAAATAATTTTT
Found at i:41114 original size:98 final size:99
Alignment explanation
Indices: 40987--41165 Score: 243
Period size: 99 Copynumber: 1.8 Consensus size: 99
40977 ATTTAGTTTT
* * * * *
40987 TTTTATAAATTTTTATTGTTTTTAATTAATTTCTAA-CAATTTTTAAAATTAATTATTTTTAAAC
1 TTTTATAAAATTTTATGGTTCTCAATTAATTTCTAACCAATTTTTAAAATTAATTATTTCTAAAC
41051 TTTTATGGTTTTTAATAAATTGTATTTTTATAAG
66 TTTTATGGTTTTTAATAAATTGTATTTTTATAAG
* * ** * *
41085 TTTTATAAAATTTTATGGTTCTCATTTAATTTCTAACCATTTTTTAAAATTGTTTGTTTCTAAAT
1 TTTTATAAAATTTTATGGTTCTCAATTAATTTCTAACCAATTTTTAAAATTAATTATTTCTAAAC
*
41150 TTTTATTGTTTTTAAT
66 TTTTATGGTTTTTAAT
41166 TTTTAATTAA
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
98 31 0.46
99 37 0.54
ACGTcount: A:0.31, C:0.05, G:0.06, T:0.59
Consensus pattern (99 bp):
TTTTATAAAATTTTATGGTTCTCAATTAATTTCTAACCAATTTTTAAAATTAATTATTTCTAAAC
TTTTATGGTTTTTAATAAATTGTATTTTTATAAG
Found at i:41186 original size:19 final size:20
Alignment explanation
Indices: 41162--41199 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41152 TTATTGTTTT
*
41162 TAATTTT-TAATTAAAATAA
1 TAATTTTATAAATAAAATAA
41181 TAATTTTATAAATAAAATA
1 TAATTTTATAAATAAAATA
41200 TTTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATTTTATAAATAAAATAA
Found at i:41195 original size:15 final size:15
Alignment explanation
Indices: 41174--41214 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
41164 ATTTTTAATT
41174 AAAATAATAATTTTA
1 AAAATAATAATTTTA
*
41189 TAAATAA-AATATTTA
1 AAAATAATAAT-TTTA
41204 AAAAT-ATAATT
1 AAAATAATAATT
41215 GATATTGACC
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATAATAATTTTA
Found at i:45819 original size:20 final size:20
Alignment explanation
Indices: 45794--45832 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
45784 ACACTGCACA
*
45794 ACATAAATGGGAATAGCTTT
1 ACATAAATGAGAATAGCTTT
45814 ACATAAATGAGAATAGCTT
1 ACATAAATGAGAATAGCTT
45833 GTAACACTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (20 bp):
ACATAAATGAGAATAGCTTT
Found at i:49777 original size:16 final size:16
Alignment explanation
Indices: 49758--49811 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
49748 AGAATAGGAC
49758 TGTAATGAAATAGAAT
1 TGTAATGAAATAGAAT
*
49774 TGTAATGAAATAAAAT
1 TGTAATGAAATAGAAT
* *
49790 TGTAATAAAATAGAAC
1 TGTAATGAAATAGAAT
49806 TGTAAT
1 TGTAAT
49812 TAGAAATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.52, C:0.02, G:0.15, T:0.31
Consensus pattern (16 bp):
TGTAATGAAATAGAAT
Found at i:50853 original size:21 final size:21
Alignment explanation
Indices: 50827--50877 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
50817 ATTATAGCAT
50827 AATCCAAATATAAAGTTTAAA
1 AATCCAAATATAAAGTTTAAA
* *
50848 AATCCAAACATAAAGTTTATA
1 AATCCAAATATAAAGTTTAAA
*
50869 AATCAAAAT
1 AATCCAAAT
50878 TACATAATCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.57, C:0.12, G:0.04, T:0.27
Consensus pattern (21 bp):
AATCCAAATATAAAGTTTAAA
Found at i:57695 original size:18 final size:18
Alignment explanation
Indices: 57672--57706 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
57662 CTTTGAAGTT
57672 TTTTAAGTATATCTCGAG
1 TTTTAAGTATATCTCGAG
* *
57690 TTTTAATTATATGTCGA
1 TTTTAAGTATATCTCGA
57707 AAATATTCAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.49
Consensus pattern (18 bp):
TTTTAAGTATATCTCGAG
Found at i:61604 original size:3 final size:3
Alignment explanation
Indices: 61596--61674 Score: 50
Period size: 3 Copynumber: 26.0 Consensus size: 3
61586 AATACAACAT
* * * * * * * * *
61596 TTA TTA TTA TTA TTA TTA TTG TTG TTG TTG TTG TTG TTG TTG TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
61644 TTG TTA TTA TTA TTA TTA TTG TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
61675 ATGACTGAGA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
3 66 0.96
4 3 0.04
ACGTcount: A:0.19, C:0.00, G:0.14, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:61610 original size:9 final size:9
Alignment explanation
Indices: 61596--61669 Score: 67
Period size: 9 Copynumber: 8.2 Consensus size: 9
61586 AATACAACAT
*
61596 TTATTATTA
1 TTATTGTTA
*
61605 TTATTATTA
1 TTATTGTTA
* *
61614 TTGTTGTTG
1 TTATTGTTA
* *
61623 TTGTTGTTG
1 TTATTGTTA
*
61632 TTGTTGTTA
1 TTATTGTTA
*
61641 TTGTTGTTA
1 TTATTGTTA
*
61650 TTATTATTA
1 TTATTGTTA
61659 TTATTGTTA
1 TTATTGTTA
61668 TT
1 TT
61670 TATTAATGAC
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 58 1.00
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.68
Consensus pattern (9 bp):
TTATTGTTA
Found at i:85156 original size:16 final size:16
Alignment explanation
Indices: 85131--85161 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
85121 ATAATGTGAA
85131 AATAAAAATGAAATGC
1 AATAAAAATGAAATGC
*
85147 AATAATAATGAAATG
1 AATAAAAATGAAATG
85162 GGGTCCCCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.13, T:0.23
Consensus pattern (16 bp):
AATAAAAATGAAATGC
Found at i:85953 original size:55 final size:54
Alignment explanation
Indices: 85882--86040 Score: 147
Period size: 55 Copynumber: 2.9 Consensus size: 54
85872 GGCAGCTGTT
* * * * *
85882 AGATGCAGCGACAATTCTATGCGTAATTCTAGATATGCTCAAGCAGCGAGCTGTC
1 AGATGCAACGATAATTCT-GGCGTAATTCTAGATATGCTCATGCAGCGAGCTATC
** * * * * ***
85937 AGATGTGACGATAATTCTGGGCATAATTCTTGATATGATTATGCAATAAGCTATC
1 AGATGCAACGATAATTCT-GGCGTAATTCTAGATATGCTCATGCAGCGAGCTATC
* *
85992 AGATGCAACGATAATTCTGGACGCAATTCTGGATATGCTCATGCAGCGA
1 AGATGCAACGATAATTCTGG-CGTAATTCTAGATATGCTCATGCAGCGA
86041 CATTAGTAGT
Statistics
Matches: 78, Mismatches: 25, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
54 2 0.03
55 76 0.97
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (54 bp):
AGATGCAACGATAATTCTGGCGTAATTCTAGATATGCTCATGCAGCGAGCTATC
Found at i:94645 original size:28 final size:28
Alignment explanation
Indices: 94614--94675 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
94604 AAAATGTGAT
94614 TTTTGGAT-ACTCGGGGGCAAAATGGTAA
1 TTTTGG-TCACTCGGGGGCAAAATGGTAA
* *
94642 TTTTAGTCACTTGGGGGCAAAATGGTAA
1 TTTTGGTCACTCGGGGGCAAAATGGTAA
94670 TTTTGG
1 TTTTGG
94676 GAAAGTTGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 1 0.03
28 29 0.97
ACGTcount: A:0.26, C:0.10, G:0.31, T:0.34
Consensus pattern (28 bp):
TTTTGGTCACTCGGGGGCAAAATGGTAA
Found at i:94686 original size:28 final size:28
Alignment explanation
Indices: 94626--94701 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
94616 TTGGATACTC
**
94626 GGGGGCAAAATGGTAATTTTAGTCACTT
1 GGGGGCAAAATGGTAATTTTAGAAACTT
* *
94654 GGGGGCAAAATGGTAATTTTGGGAAAGTT
1 GGGGGCAAAATGGTAATTTT-AGAAACTT
94683 GGGGGTC-AAATGG-AATTTT
1 GGGGG-CAAAATGGTAATTTT
94702 TAAACATCCG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 26 0.62
29 15 0.36
30 1 0.02
ACGTcount: A:0.29, C:0.07, G:0.34, T:0.30
Consensus pattern (28 bp):
GGGGGCAAAATGGTAATTTTAGAAACTT
Found at i:94803 original size:29 final size:28
Alignment explanation
Indices: 94771--94856 Score: 68
Period size: 29 Copynumber: 3.0 Consensus size: 28
94761 TGTGTGTTCG
94771 GGGGTAAAATGATCATTTTTGGAAAAATT
1 GGGGTAAAATGAT-ATTTTTGGAAAAATT
* **
94800 GGGGTTAAAAATTGA-ATTTTTAG-AAGTTT
1 GGGG-T-AAAA-TGATATTTTTGGAAAAATT
* *
94829 GGGGTAAAATGGTAATTTTAGGAAAAAT
1 GGGGTAAAATGAT-ATTTTTGGAAAAAT
94857 CGAGGTTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
26 2 0.05
27 4 0.09
28 7 0.16
29 15 0.35
30 8 0.19
31 4 0.09
32 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.26, T:0.35
Consensus pattern (28 bp):
GGGGTAAAATGATATTTTTGGAAAAATT
Found at i:94819 original size:30 final size:29
Alignment explanation
Indices: 94785--95058 Score: 150
Period size: 29 Copynumber: 9.4 Consensus size: 29
94775 TAAAATGATC
*
94785 ATTTTTGGAAAAATTGGGGTTAAAAATTGA
1 ATTTTTGG-AAAATTGGGGTTAAAAATGGA
* **
94815 ATTTTTAGAAGTTTGGGG-T-AAAATGGTA
1 ATTTTTGGAAAATTGGGGTTAAAAATGG-A
* * *
94843 ATTTTAGGAAAAATCGAGGTTAAAAATGGA
1 ATTTTTGG-AAAATTGGGGTTAAAAATGGA
* ** *
94873 ATTTTTAGAAGTTTGGGGGT-AAAATGGTA
1 ATTTTTGGAAAATTGGGGTTAAAAATGG-A
* ***
94902 ATTTTTGAAAAAAATCATGGTTAAAAATGGA
1 ATTTTTG--GAAAATTGGGGTTAAAAATGGA
** * **
94933 A-TTTTGGAAAGCTCGGGTGTAAAAATATA
1 ATTTTTGGAAAATTGGGGT-TAAAAATGGA
* *
94962 AATTTTGGAAAATTGGGGTCAAAAATGGA
1 ATTTTTGGAAAATTGGGGTTAAAAATGGA
* *
94991 ATTTTT-G-AAGTTCGAGGG-TAAAAATGTA
1 ATTTTTGGAAAATT-G-GGGTTAAAAATGGA
*** *
95019 ATTTTTGGAAAAATCAAGGTCAAAAATGGA
1 ATTTTTGG-AAAATTGGGGTTAAAAATGGA
95049 A-TTTTGGAAA
1 ATTTTTGGAAA
95059 GTGACACATT
Statistics
Matches: 179, Mismatches: 49, Indels: 34
0.68 0.19 0.13
Matches are distributed among these distances:
27 10 0.06
28 40 0.22
29 61 0.34
30 43 0.24
31 18 0.10
32 7 0.04
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (29 bp):
ATTTTTGGAAAATTGGGGTTAAAAATGGA
Found at i:94853 original size:58 final size:58
Alignment explanation
Indices: 94655--95053 Score: 312
Period size: 58 Copynumber: 6.8 Consensus size: 58
94645 TAGTCACTTG
* * * * * * * *
94655 GGGGCAAAATGGTAA-TTTTGGGAAAGTTGGGGGT-CAAATGGAATTTTTA-AACATCC
1 GGGGTAAAATGGTAATTTTTGGAAAAATCGGGGTTAAAAATGGAATTTTTAGAA-GTTC
* ** * * * **
94711 GGGACTAAAATGGTACCTTTTGGAATAATCAGGGTCAAAAATGGAATTTTT-GTGTGTTC
1 GGG-GTAAAATGGTAATTTTTGGAAAAATCGGGGTTAAAAATGGAATTTTTAG-AAGTTC
* * * * *
94770 GGGGGTAAAATGATCATTTTTGGAAAAATTGGGGTTAAAAATTGAATTTTTAGAAGTTT
1 -GGGGTAAAATGGTAATTTTTGGAAAAATCGGGGTTAAAAATGGAATTTTTAGAAGTTC
* * *
94829 GGGGTAAAATGGTAATTTTAGGAAAAATCGAGGTTAAAAATGGAATTTTTAGAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGAAAAATCGGGGTTAAAAATGGAATTTTTAGAAG-TTC
* ** * *
94888 GGGGTAAAATGGTAATTTTTGAAAAAAATCATGGTTAAAAATGGAA-TTTTGGAAAGCTC
1 GGGGTAAAATGGTAATTTTTG-GAAAAATCGGGGTTAAAAATGGAATTTTTAG-AAGTTC
* * * *
94947 GGGTGTAAAAAT-ATAAATTTTGG-AAAATTGGGGTCAAAAATGGAATTTTT-GAAGTTC
1 GGG-GT-AAAATGGTAATTTTTGGAAAAATCGGGGTTAAAAATGGAATTTTTAGAAGTTC
** *
95004 GAGGGTAAAAAT-GTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTT
1 G-GGGT-AAAATGGTAATTTTTGGAAAAATCGGGGTTAAAAATGGAATTTT
95054 GGAAAGTGAC
Statistics
Matches: 273, Mismatches: 55, Indels: 28
0.77 0.15 0.08
Matches are distributed among these distances:
56 3 0.01
57 32 0.12
58 105 0.38
59 90 0.33
60 38 0.14
61 5 0.02
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGAAAAATCGGGGTTAAAAATGGAATTTTTAGAAGTTC
Found at i:94870 original size:117 final size:115
Alignment explanation
Indices: 94716--95059 Score: 329
Period size: 117 Copynumber: 2.9 Consensus size: 115
94706 CATCCGGGAC
* *
94716 TAAAATGGTACCTTTTGGAATAATC-AGGGTCAAAAATGGAATTTTTGTGTGTTCGGGGGTAAAA
1 TAAAATGGTA-ATTTTGGAAAAATCGA-GGTCAAAAATGGAATTTTTG-GTGTTCGGGGGTAAAA
* ** * * *
94780 TGATCATTTTTGGAAAAATTGGGGTTAAAAATTGAATTTTTAG-AAGTTTGGG-G
63 TG-TAATTTTTGGAAAAATCAGGGTTAAAAATGGAA-TTTTAGAAAGCTCGGGTG
* ** *
94833 TAAAATGGTAATTTTAGGAAAAATCGAGGTTAAAAATGGAATTTTTAGAAGTTTGGGGGTAAAAT
1 TAAAATGGTAATTTT-GGAAAAATCGAGGTCAAAAATGGAATTTTT-GGTGTTCGGGGGTAAAAT
* * *
94898 GGTAATTTTTGAAAAAAATCATGGTTAAAAATGGAATTTTGGAAAGCTCGGGTG
64 -GTAATTTTTG-GAAAAATCAGGGTTAAAAATGGAATTTTAGAAAGCTCGGGTG
* * * ** *
94952 TAAAAAT-ATAAATTTTGG-AAAATTGGGGTCAAAAATGGAATTTTTGAAGTTCGAGGGTAAAAA
1 T-AAAATGGT-AATTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGTGTTCGGGGGT-AAAA
* * *
95015 TGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTGGAAAG
63 TGTAATTTTTGGAAAAATCAGGGTTAAAAATGGAATTTTAGAAAG
95060 TGACACATTC
Statistics
Matches: 193, Mismatches: 24, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
116 35 0.18
117 84 0.44
118 58 0.30
119 5 0.03
120 11 0.06
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (115 bp):
TAAAATGGTAATTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGTGTTCGGGGGTAAAATGT
AATTTTTGGAAAAATCAGGGTTAAAAATGGAATTTTAGAAAGCTCGGGTG
Found at i:96530 original size:6 final size:6
Alignment explanation
Indices: 96519--96547 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
96509 AAACAAGGGG
96519 AAAATT AAAATT AAAATT AAAATT AAAAT
1 AAAATT AAAATT AAAATT AAAATT AAAAT
96548 AATCAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:98689 original size:15 final size:16
Alignment explanation
Indices: 98671--98704 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
98661 ATCAAAGAGG
98671 AGAAAGAAGAAGA-AA
1 AGAAAGAAGAAGAGAA
*
98686 AGAAAGAAGGAGAGAA
1 AGAAAGAAGAAGAGAA
98702 AGA
1 AGA
98705 GGAAGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (16 bp):
AGAAAGAAGAAGAGAA
Found at i:99441 original size:17 final size:17
Alignment explanation
Indices: 99419--99453 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
99409 TGAATGTGAT
*
99419 TGAATGTTGTATCGTTC
1 TGAATGTTGTATCCTTC
99436 TGAATGTTGTATCCTTC
1 TGAATGTTGTATCCTTC
99453 T
1 T
99454 ATTTTTGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.14, G:0.20, T:0.49
Consensus pattern (17 bp):
TGAATGTTGTATCCTTC
Found at i:99803 original size:19 final size:20
Alignment explanation
Indices: 99769--99807 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
99759 CGCATAAAAG
*
99769 AAAAGAAAGAACAATATATA
1 AAAAGAAAGAAAAATATATA
99789 AAAAGAAA-AAAAATATATA
1 AAAAGAAAGAAAAATATATA
99808 TATATATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (20 bp):
AAAAGAAAGAAAAATATATA
Found at i:99808 original size:21 final size:20
Alignment explanation
Indices: 99769--99809 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
99759 CGCATAAAAG
* *
99769 AAAAGAAAGAACAATATATA
1 AAAAGAAAAAAAAATATATA
99789 AAAAGAAAAAAAATATATATA
1 AAAAGAAAAAAAA-ATATATA
99810 TATATAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.17
Consensus pattern (20 bp):
AAAAGAAAAAAAAATATATA
Found at i:104442 original size:17 final size:17
Alignment explanation
Indices: 104420--104460 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
104410 ATGTAGATGC
*
104420 AGTGACAATAAAAGTGT
1 AGTGACAATAAAAATGT
*
104437 AGTGACAGTAAAAATGT
1 AGTGACAATAAAAATGT
*
104454 AGGGACA
1 AGTGACA
104461 GTTATACTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.46, C:0.07, G:0.27, T:0.20
Consensus pattern (17 bp):
AGTGACAATAAAAATGT
Found at i:112044 original size:29 final size:27
Alignment explanation
Indices: 111986--112366 Score: 103
Period size: 29 Copynumber: 13.0 Consensus size: 27
111976 CTCGAGGGTA
*
111986 AAAATGTAATTTTGAAAGTTTAGGGGT
1 AAAATGTAATTTTGAAAGTTTAGGGAT
*
112013 AAAATGGTATTTTTGAAAAGTTT-GAGGAT
1 AAAAT-GTAATTTTG-AAAGTTTAG-GGAT
* * * *
112042 AAAATATGATTTTTTGGAAGTTCGAGGG-T
1 AAAATGT-A-ATTTTGAAAGTT-TAGGGAT
* * * *
112071 AAAATCATAATTTTGGAAGTTCAGGGGT
1 AAAAT-GTAATTTTGAAAGTTTAGGGAT
* *
112099 AAAATTGTAATTTTTGGAAGTTCGAGGG-T
1 AAAA-TGTAA-TTTTGAAAGTT-TAGGGAT
* ** *
112128 AAAAAT-TATAATTTGTAGAAGTTCGGGGGT
1 -AAAATGTA-ATTTTG-A-AAGTTTAGGGAT
112158 AAAATGGTAAATTTTTG-AAGTTCTAGGG-T
1 AAAAT-GT-AA-TTTTGAAAGTT-TAGGGAT
* * *
112187 GAAAATATGATTTTTGGAAAGTTTAGGGGT
1 -AAAATGT-AATTTT-GAAAGTTTAGGGAT
* *
112217 AAAATGTGATTTTTGGAAAGTTCGAGTGG-T
1 AAAATGT-AATTTT-GAAAGTT-TAG-GGAT
* *
112247 AAAAATGTGACTTTTGGAAAG-TTCGAGGAGT
1 -AAAATGT-AATTTT-GAAAGTTTAG-GGA-T
* * *
112278 GAAATGGTAATTTTTAGAAATTTTGAGGGTT
1 AAAAT-GTAA-TTTT-GAAAGTTT-AGGGAT
*
112309 AAAATGTAATTTTTAGAAAGTTTAGGGGT
1 AAAATGTAA-TTTT-GAAAGTTTAGGGAT
*
112338 CAAAATATAATTTTTGGAAAGTTTAGGGA
1 -AAAATGTAA-TTTT-GAAAGTTTAGGGA
112367 CCTCTTGGAT
Statistics
Matches: 281, Mismatches: 37, Indels: 69
0.73 0.10 0.18
Matches are distributed among these distances:
27 9 0.03
28 39 0.14
29 94 0.33
30 89 0.32
31 40 0.14
32 9 0.03
33 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (27 bp):
AAAATGTAATTTTGAAAGTTTAGGGAT
Found at i:112178 original size:59 final size:57
Alignment explanation
Indices: 112052--112356 Score: 251
Period size: 59 Copynumber: 5.2 Consensus size: 57
112042 AAAATATGAT
*
112052 TTTTTGGAAGTTCGAGGGT-AAAATCATAATTTTGGAAGTTCAGGGGTAAAATTGTAA
1 TTTTTGGAAGTTCGAGGGTAAAAATTATAATTTTGGAAGTTCAGGGGTAAAA-TGTAA
* *
112109 TTTTTGGAAGTTCGAGGGTAAAAATTATAATTTGTAGAAGTTCGGGGGTAAAATGGTAAA
1 TTTTTGGAAGTTCGAGGGTAAAAATTATAATTT-TGGAAGTTCAGGGGTAAAAT-GT-AA
* * * * *
112169 TTTTT-GAAGTTCTAGGGTGAAAA-TATGATTTTTGGAAAGTTTAGGGGTAAAATGTGA
1 TTTTTGGAAGTTCGAGGGTAAAAATTAT-AATTTTGG-AAGTTCAGGGGTAAAATGTAA
* * * *
112226 TTTTTGGAAAGTTCGAGTGGTAAAAATGT-GACTTTTGGAAAGTTCGAGGAGTGAAATGGTAA
1 TTTTTGG-AAGTTCGAG-GGTAAAAAT-TATAATTTTGG-AAGTTC-AGGGGTAAAAT-GTAA
* * * * * * * *
112288 TTTTTAGAAATTTTGAGGGTTAAAATGTA-ATTTTTAGAAAGTTTAGGGGTCAAAATATAA
1 TTTTT-GGAAGTTCGAGGGTAAAAAT-TATAATTTT-GGAAGTTCAGGGGT-AAAATGTAA
112348 TTTTTGGAA
1 TTTTTGGAA
112357 AGTTTAGGGA
Statistics
Matches: 202, Mismatches: 29, Indels: 32
0.77 0.11 0.12
Matches are distributed among these distances:
57 25 0.12
58 21 0.10
59 65 0.32
60 40 0.20
61 33 0.16
62 17 0.08
63 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (57 bp):
TTTTTGGAAGTTCGAGGGTAAAAATTATAATTTTGGAAGTTCAGGGGTAAAATGTAA
Found at i:112358 original size:30 final size:29
Alignment explanation
Indices: 111981--112365 Score: 240
Period size: 30 Copynumber: 13.1 Consensus size: 29
111971 TGTCACTCGA
111981 GGGTAAAAATGTAA-TTTT-GAAAGTTTAG
1 GGGT-AAAATGTAATTTTTGGAAAGTTTAG
*
112009 GGGTAAAATGGT-ATTTTTGAAAAGTTT-G
1 GGGTAAAAT-GTAATTTTTGGAAAGTTTAG
* * * *
112037 AGGATAAAATATGATTTTTTGG-AAG-TTCG
1 -GGGTAAAATGT-AATTTTTGGAAAGTTTAG
* *
112066 AGGGTAAAATCATAA-TTTTGG-AAGTTCAG
1 -GGGTAAAAT-GTAATTTTTGGAAAGTTTAG
*
112095 GGGTAAAATTGTAATTTTTGG-AAG-TTCG
1 GGGTAAAA-TGTAATTTTTGGAAAGTTTAG
* * * **
112123 AGGGTAAAAATTATAATTTGTAG-AAGTTCGG
1 -GGGT-AAAA-TGTAATTTTTGGAAAGTTTAG
112154 GGGTAAAATGGTAAATTTTT-G-AAGTTCTA-
1 GGGTAAAAT-GT-AATTTTTGGAAAGTT-TAG
* *
112183 GGGTGAAAATATGATTTTTGGAAAGTTTAG
1 GGGT-AAAATGTAATTTTTGGAAAGTTTAG
* *
112213 GGGTAAAATGTGATTTTTGGAAAGTTCGAG
1 GGGTAAAATGTAATTTTTGGAAAGTT-TAG
* * * *
112243 TGGTAAAAATGTGACTTTTGGAAAGTTCGAG
1 GGGT-AAAATGTAATTTTTGGAAAGTT-TAG
* * * *
112274 GAGTGAAATGGTAATTTTTAGAAATTTTGAG
1 GGGTAAAAT-GTAATTTTTGGAAAGTTT-AG
* *
112305 GGTTAAAATGTAATTTTTAGAAAGTTTAG
1 GGGTAAAATGTAATTTTTGGAAAGTTTAG
*
112334 GGGTCAAAATATAATTTTTGGAAAGTTTAG
1 GGGT-AAAATGTAATTTTTGGAAAGTTTAG
112364 GG
1 GG
112366 ACCTCTTGGA
Statistics
Matches: 289, Mismatches: 42, Indels: 50
0.76 0.11 0.13
Matches are distributed among these distances:
27 6 0.02
28 43 0.15
29 90 0.31
30 100 0.35
31 50 0.17
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.36
Consensus pattern (29 bp):
GGGTAAAATGTAATTTTTGGAAAGTTTAG
Found at i:117428 original size:56 final size:56
Alignment explanation
Indices: 117357--117497 Score: 194
Period size: 56 Copynumber: 2.5 Consensus size: 56
117347 TGTGGATCCA
* * * *
117357 CATCCTAACTGATTATATTAAAAATTTTCACAAGTATAAAATAGCTCCC-GAATTCG
1 CATCCTAACTGATTATCTTAGAAATTTTCACAAGTATAAAACAACTCCCAG-ATTCG
* * *
117413 CATCCCAACTTATTATCTTAGAAATTTTCACAAGTATAAAACAACTCGCAGATTCG
1 CATCCTAACTGATTATCTTAGAAATTTTCACAAGTATAAAACAACTCCCAGATTCG
*
117469 CATCCTAACTGATAATCTTAGAAATTTTC
1 CATCCTAACTGATTATCTTAGAAATTTTC
117498 TCATCGCTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
56 73 0.99
57 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.33
Consensus pattern (56 bp):
CATCCTAACTGATTATCTTAGAAATTTTCACAAGTATAAAACAACTCCCAGATTCG
Found at i:120885 original size:12 final size:12
Alignment explanation
Indices: 120868--120897 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
120858 CCGAGTTAGG
120868 TTGTAATATAGT
1 TTGTAATATAGT
*
120880 TTGTAATGTAGT
1 TTGTAATATAGT
120892 TTGTAA
1 TTGTAA
120898 ATTATACACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (12 bp):
TTGTAATATAGT
Found at i:128210 original size:137 final size:137
Alignment explanation
Indices: 127964--128239 Score: 516
Period size: 137 Copynumber: 2.0 Consensus size: 137
127954 GAAGGGAGAA
127964 TTAGAGTCGTTAGCTGGTGGTTGTGGATCTCATTGTGGATTCAAGGCTACCGAGGACATCTTTCA
1 TTAGAGTCGTTAGCTGGTGGTTGTGGATCTCATTGTGGATTCAAGGCTACCGAGGACATCTTTCA
*
128029 ATCACTATCGTCACCTTTCCATCTTTTATTCTCCTTAAGAATTATGTTTCGTTAGTTCTTTATTA
66 ATCACCATCGTCACCTTTCCATCTTTTATTCTCCTTAAGAATTATGTTTCGTTAGTTCTTTATTA
128094 TTTGTTT
131 TTTGTTT
* *
128101 TTAGAGTCGTTAGCTGGTGGTTGTGGATCTCATTGTGGATTCAAGGCTGCCGAGGGCATCTTTCA
1 TTAGAGTCGTTAGCTGGTGGTTGTGGATCTCATTGTGGATTCAAGGCTACCGAGGACATCTTTCA
*
128166 ATCACCATTGTCACCTTTCCATCTTTTATTCTCCTTAAGAATTATGTTTCGTTAGTTCTTTATTA
66 ATCACCATCGTCACCTTTCCATCTTTTATTCTCCTTAAGAATTATGTTTCGTTAGTTCTTTATTA
128231 TTTGTTT
131 TTTGTTT
128238 TT
1 TT
128240 TATTTCATTT
Statistics
Matches: 135, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 135 1.00
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (137 bp):
TTAGAGTCGTTAGCTGGTGGTTGTGGATCTCATTGTGGATTCAAGGCTACCGAGGACATCTTTCA
ATCACCATCGTCACCTTTCCATCTTTTATTCTCCTTAAGAATTATGTTTCGTTAGTTCTTTATTA
TTTGTTT
Found at i:131172 original size:29 final size:30
Alignment explanation
Indices: 131129--131198 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
131119 TAATTAGAGT
* * *
131129 TTCATGTGTATAATT-ACACCAAATTAAAA
1 TTCATGTATACAATTCACACCAAATCAAAA
**
131158 TTCATGTATACAATTGCACATTAAATCAAAA
1 TTCATGTATACAATT-CACACCAAATCAAAA
131189 TTCATGTATA
1 TTCATGTATA
131199 ATTTTGAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 13 0.38
31 21 0.62
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (30 bp):
TTCATGTATACAATTCACACCAAATCAAAA
Found at i:132865 original size:21 final size:23
Alignment explanation
Indices: 132814--132874 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
132804 AAGAAATCGA
132814 AATTAAATTATAATTTTTATAAT
1 AATTAAATTATAATTTTTATAAT
*
132837 AA-TAAAATATAATTTTTA-AA-
1 AATTAAATTATAATTTTTATAAT
*
132857 AGATTAAATTAAAATTTT
1 A-ATTAAATTATAATTTT
132875 ATCATTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 1 0.03
21 3 0.09
22 27 0.82
23 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
AATTAAATTATAATTTTTATAAT
Found at i:132907 original size:31 final size:29
Alignment explanation
Indices: 132848--132911 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
132838 ATAAAATATA
* *
132848 ATTTTTAAAAGATTAAATTAAAATTTTAT
1 ATTTTTAAAAGATTAAAATAAAACTTTAT
*
132877 CATTTTTAATAAGATTAAAATATAACTTTAT
1 -ATTTTTAA-AAGATTAAAATAAAACTTTAT
132908 ATTT
1 ATTT
132912 GCTAATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 12 0.40
31 18 0.60
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (29 bp):
ATTTTTAAAAGATTAAAATAAAACTTTAT
Found at i:133897 original size:6 final size:6
Alignment explanation
Indices: 133886--133937 Score: 58
Period size: 6 Copynumber: 9.0 Consensus size: 6
133876 TTTATTTTAT
133886 TTTAAA TTTAAA TTT--A TTTAAAA TTTAAA TTT--A TTATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TT-TAAA TTTAAA
133932 TTTAAA
1 TTTAAA
133938 ATGTCCAAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
4 7 0.17
5 1 0.03
6 25 0.62
7 7 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:133903 original size:17 final size:17
Alignment explanation
Indices: 133868--133935 Score: 93
Period size: 17 Copynumber: 4.1 Consensus size: 17
133858 GGCCTATTGG
* *
133868 ATTTTGAATTT-ATTTT
1 ATTTTAAATTTAAATTT
133884 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
133901 ATTTAAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
133918 ATTATAAATTTAAATTT
1 ATTTTAAATTTAAATTT
133935 A
1 A
133936 AAATGTCCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
16 10 0.22
17 36 0.78
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Done.