Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013279.1 Kokia drynarioides strain JFW-HI SEQ_128300, 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: 104545
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Warning! 41 characters in sequence are not A, C, G, or T
Found at i:2698 original size:33 final size:33
Alignment explanation
Indices: 2640--2703 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
2630 GTTATATCAT
*
2640 TTTTATTTTTTAAAATATTAAAATATTAATATA
1 TTTTATTTTTTAAAATATTAAAATATAAATATA
*
2673 TTTTATTTATTT-ATAT-TTAATAATATAAATA
1 TTTTATTT-TTTAAAATATTAA-AATATAAATA
2704 ATTATTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 4 0.15
33 20 0.74
34 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
TTTTATTTTTTAAAATATTAAAATATAAATATA
Found at i:2841 original size:32 final size:32
Alignment explanation
Indices: 2755--2828 Score: 141
Period size: 32 Copynumber: 2.3 Consensus size: 32
2745 ATAATAATTT
2755 AAAATTTAAATGATATTATAATATATTATTAA
1 AAAATTTAAATGATATTATAATATATTATTAA
2787 AAAATTTAAATGATATTATAATATATTATT-A
1 AAAATTTAAATGATATTATAATATATTATTAA
2818 AAAATTTAAAT
1 AAAATTTAAAT
2829 TAACATTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 12 0.29
32 30 0.71
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (32 bp):
AAAATTTAAATGATATTATAATATATTATTAA
Found at i:3432 original size:13 final size:13
Alignment explanation
Indices: 3414--3445 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3404 CACCTCAAAC
3414 TCTAAAAGATAAA
1 TCTAAAAGATAAA
3427 TCTAAAAGATAAA
1 TCTAAAAGATAAA
*
3440 TATAAA
1 TCTAAA
3446 TTAAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.25
Consensus pattern (13 bp):
TCTAAAAGATAAA
Found at i:3951 original size:43 final size:42
Alignment explanation
Indices: 3902--3986 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 42
3892 GAGATCGATG
* *
3902 GTGAGGAGTGAGAGGGAAGG-GAGCTGTGGTGGGTGTTCGGACA
1 GTGAGGAGTGAGAGGGAAGGCGAG-GGTGGTGGGGGTT-GGACA
3945 GTGAGGAGTGAGAGGGAAGGCGAGGGTGGTGGGGGTTGGACA
1 GTGAGGAGTGAGAGGGAAGGCGAGGGTGGTGGGGGTTGGACA
3987 CAATGGTGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
42 5 0.13
43 31 0.79
44 3 0.08
ACGTcount: A:0.21, C:0.06, G:0.56, T:0.16
Consensus pattern (42 bp):
GTGAGGAGTGAGAGGGAAGGCGAGGGTGGTGGGGGTTGGACA
Found at i:7435 original size:95 final size:96
Alignment explanation
Indices: 7249--7439 Score: 241
Period size: 95 Copynumber: 2.0 Consensus size: 96
7239 TTTTTGGGAA
* *
7249 AAGGATATTCAATTATCTTGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCAATTATCTTGATTTGAAGAAAGATTGCACCTAGTAAGTTAAGGCACAATATTTCA
*
7314 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAGAAACATTGCCTCGATT
* *
7345 AAGGGTATTCAATTAT-TTCGATTTGAAGAAA-ATTGCACCTAGTAAGTTAAGGTACAA-ATTTT
1 AAGGATATTCAATTATCTT-GATTTGAAGAAAGATTGCACCTAGTAAGTTAAGGCACAATA-TTT
*
7407 C-GAAACTCGAA-ATAAA-AGAATATTGCCTCGATT
64 CAG-AA-TCGAAGATAAAGA-AACATTGCCTCGATT
7440 TTACAGTTTT
Statistics
Matches: 84, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
94 3 0.04
95 49 0.58
96 32 0.38
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (96 bp):
AAGGATATTCAATTATCTTGATTTGAAGAAAGATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:7746 original size:59 final size:56
Alignment explanation
Indices: 7669--7977 Score: 242
Period size: 59 Copynumber: 5.3 Consensus size: 56
7659 GGATACTTGA
* * ** *
7669 GGGGGAAAAATGGTAATTTTGGGAAAATTCGAGGTTTAAAATGGAATTTTTAGATATTT
1 GGGGGTAAAATGG-AATTTTGGG-AATTTCGAGGTCAAAAATGGAATTTTTGGA-ATTT
* * * * * * * *
7728 AGGGGTAAAAGGGTAATTTTGAGAGTTTTGAGGTCGAAAATGGATTTTTTGGACATTC
1 GGGGGTAAAATGG-AATTTTGGGAATTTCGAGGTCAAAAATGGAATTTTTGGA-ATTT
*
7786 GGGGGTAAAATTGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTT
1 GGGGGTAAAA-TGGAATTTTGGGAA-TTTCGAGGTCAAAAATGGAATTTTTGGAA-TTT
* * * *
7845 GGGGGTAAAAATGGAATTTTTGGAAGTTCAAGGGT-AAAAATGGAATTTTTGGAAGTTC
1 GGGGGT-AAAATGGAATTTTGGGAATTTCGA-GGTCAAAAATGGAATTTTTGGAA-TTT
** * * * * * *
7903 AAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTTGAAAGTTC
1 GGGGGT-AAAATGGAATTTTGGGAA-TTTCGAGGTCAAAAATGGAATTTTTGGAA-TTT
7962 GGGGGTAAATATGGAA
1 GGGGGTAAA-ATGGAA
7978 AATTTTGAAG
Statistics
Matches: 208, Mismatches: 34, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
58 99 0.48
59 105 0.50
60 4 0.02
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (56 bp):
GGGGGTAAAATGGAATTTTGGGAATTTCGAGGTCAAAAATGGAATTTTTGGAATTT
Found at i:7808 original size:29 final size:29
Alignment explanation
Indices: 7764--8054 Score: 318
Period size: 29 Copynumber: 9.9 Consensus size: 29
7754 TTTGAGGTCG
*
7764 AAAATGGATTTTTTGGACA-TTCGGGGGTA
1 AAAATGGAATTTTTGGA-AGTTCGGGGGTA
* *
7793 AAATTGGAATTTTTGGAAGTTTC-GAGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGGGGGT-A
*
7823 AAAATGGAATTTTTGGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTCGGGGGTA
**
7852 AAAATGGAATTTTTGGAAGTTCAAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGGGGGTA
**
7881 AAAATGGAATTTTTGGAAGTTCAAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGGGGGTA
* *
7910 AAAATGGAATTTTTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAG-TTCGGGGGTA
*
7940 AAAATGGAATTTTTGAAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTCGGGGGTA
* * * *
7969 AATATGGAAAATTTT-GAAGTTAGGGGATA
1 AAAATGG-AATTTTTGGAAGTTCGGGGGTA
* ***
7998 AAAATGGAGTTTTTGGAAGTTTTAGGGTAA
1 AAAATGGAATTTTTGGAAGTTCGGGGGT-A
*
8028 AAAATGGATTTTTTGGAAGTTTCGGGG
1 AAAATGGAATTTTTGGAAG-TTCGGGG
8055 TCGAAATATA
Statistics
Matches: 221, Mismatches: 32, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
28 6 0.03
29 136 0.62
30 75 0.34
31 4 0.02
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGGGGGTA
Found at i:7820 original size:117 final size:117
Alignment explanation
Indices: 7669--8051 Score: 345
Period size: 117 Copynumber: 3.3 Consensus size: 117
7659 GGATACTTGA
* ** *
7669 GGGGG-AAAAATGGTAATTTTGGGAAAATTCGAGGTTTAAAATGGAATTTTTAGATA-TTTAGGG
1 GGGGGTAAAAATGG-AATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTAGA-AGTTTAGGG
** * *
7732 GT-AAAAGGGTAA-TTTT-GAGAGTT-TTGAGGTCGAAAATGGATTTTTTGGACA-TTC
64 GTAAAAAGGG-AATTTTTGGA-AGTTCAAG-GGT-AAAAATGGAATTTTTGGA-AGTTC
* * * *
7786 GGGGGTAAAATTGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGT
1 GGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTAGAAGTTTAGGGGT
*
7851 AAAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGGAAGTTC
66 AAAAAGGGAATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGGAAGTTC
** * * **
7903 AAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTT-GAAAGTTCGGGGG
1 GGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTAG-AAGTTTAGGGG
* * * * * *
7967 TAAATATGGAAAATTTT-GAAGTT-AGGGGATAAAAATGGAGTTTTTGGAAGTTT
65 TAAA-AAGGGAATTTTTGGAAGTTCAAGGG-TAAAAATGGAATTTTTGGAAGTTC
** *
8020 TAGGGTAAAAAATGGATTTTTTGGAAGTTTCG
1 GGGGGT-AAAAATGGAATTTTTGGAAGTTTCG
8052 GGGTCGAAAT
Statistics
Matches: 225, Mismatches: 30, Indels: 21
0.82 0.11 0.08
Matches are distributed among these distances:
116 7 0.03
117 160 0.71
118 55 0.24
119 3 0.01
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (117 bp):
GGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTAGAAGTTTAGGGGT
AAAAAGGGAATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGGAAGTTC
Found at i:7988 original size:59 final size:59
Alignment explanation
Indices: 7764--8055 Score: 340
Period size: 59 Copynumber: 5.0 Consensus size: 59
7754 TTTGAGGTCG
* * * * *
7764 AAAATGGATTTTTTGGACA-TTCGGGGGTAAAATTGGAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGA-AGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTAGGGGTTA
* * *
7823 AAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTCAAGGG-TA
1 AAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTAGGGGTTA
** *
7881 AAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTAGGGGTTA
* * * *
7940 AAAATGGAATTTTTGAAAGTTCGGGGGTAAATATGGAAAATTTT-GAAG-TTAGGGGATA
1 AAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGG-AATTTTTGGAAGTTTAGGGGTTA
* *** * *
7998 AAAATGGAGTTTTTGGAAGTTTTAGGGTAAAAAATGGATTTTTTGGAAGTTTCGGGGT
1 AAAATGGAATTTTTGGAAGTTCGGGGGT-AAAAATGGAATTTTTGGAAGTTTAGGGGT
8056 CGAAATATAA
Statistics
Matches: 196, Mismatches: 31, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
58 88 0.45
59 96 0.49
60 12 0.06
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.35
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTAGGGGTTA
Found at i:8055 original size:88 final size:85
Alignment explanation
Indices: 7669--8054 Score: 368
Period size: 88 Copynumber: 4.4 Consensus size: 85
7659 GGATACTTGA
* * * ** * *
7669 GGGGGAAAAATGGTAATTTTGGGAAAATTCGAGGTTTAAAATGGAATTTTTAGATATTTAGGGGT
1 GGGGTAAAAATGG-AATTTTTGG-AAGTTCG-GGGGTAAAATGGAATTTTTGGA-AGTTAGGGGT
*
7734 -AAAAGGGTAA-TTTT-GAGAGTTTT
62 AAAAATGG-AATTTTTGGA-AGTTTT
* * * * *
7757 GAGGTCGAAAATGGATTTTTTGGACA-TTCGGGGGTAAAATTGGAATTTTTGGAAGTTTCGAGGT
1 GGGGT-AAAAATGGAATTTTTGGA-AGTTCGGGGGTAAAA-TGGAATTTTTGGAAG-TTAGGGGT
*
7821 CAAAAATGGAATTTTTGGAAGTTTG
62 -AAAAATGGAATTTTTGGAAGTTTT
** *
7846 GGGGTAAAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGGAAGTTCAAGGGTAA
1 GGGGTAAAAATGGAATTTTTGGAAGTTCGGGGGT-AAAATGGAATTTTTGGAAGTT-AGGGGTAA
7911 AAATGGAATTTTTGGAAGTTTT
64 AAATGGAATTTTTGGAAGTTTT
* *
7933 GGGGTTAAAAATGGAATTTTTGAAAGTTCGGGGGTAAATATGGAAAATTTT-GAAGTTAGGGGAT
1 GGGG-TAAAAATGGAATTTTTGGAAGTTCGGGGGTAAA-ATGG-AATTTTTGGAAGTTAGGGG-T
*
7997 AAAAATGGAGTTTTTGGAAGTTTT
62 AAAAATGGAATTTTTGGAAGTTTT
* *
8021 AGGGTAAAAAATGGATTTTTTGGAAGTTTCGGGG
1 GGGGT-AAAAATGGAATTTTTGGAAG-TTCGGGG
8055 TCGAAATATA
Statistics
Matches: 250, Mismatches: 31, Indels: 33
0.80 0.10 0.11
Matches are distributed among these distances:
86 8 0.03
87 61 0.24
88 136 0.54
89 43 0.17
90 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (85 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGGAATTTTTGGAAGTTAGGGGTAAAA
ATGGAATTTTTGGAAGTTTT
Found at i:8068 original size:117 final size:116
Alignment explanation
Indices: 7764--8070 Score: 370
Period size: 117 Copynumber: 2.6 Consensus size: 116
7754 TTTGAGGTCG
* ** * *
7764 AAAATGGATTTTTTGGACA-TTCGGGGGTAAAATTGGAATTTTTGGAAGTTTCGAGGTCAAAAAT
1 AAAATGGAATTTTTGGA-AGTTCAAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAAT
* * *
7828 GGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTCAAGGGTA
65 -GAATTTTTGAAAGTTCGGGGGTAAAAATGGAAATTTTGGAAGTTCAAGGGTA
* *
7881 AAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATG
1 AAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAAT-
* *
7946 GAATTTTTGAAAGTTCGGGGGTAAATATGGAAAATTTT-GAAGTT-AGGGGATA
65 GAATTTTTGAAAGTTCGGGGGTAAAAATGG-AAATTTTGGAAGTTCAAGGG-TA
* ** * *
7998 AAAATGGAGTTTTTGGAAGTTTTAGGGTAAAAAATGGATTTTTTGGAAGTTTCGGGGTCGAAATA
1 AAAATGGAATTTTTGGAAGTTCAAGGGT-AAAAATGGAATTTTTGGAAGTTTCGGGGTC-AAAAA
8063 T-AATTTTT
64 TGAATTTTT
8071 TGACAGTTTA
Statistics
Matches: 166, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
116 5 0.03
117 123 0.74
118 33 0.20
119 5 0.03
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (116 bp):
AAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATG
AATTTTTGAAAGTTCGGGGGTAAAAATGGAAATTTTGGAAGTTCAAGGGTA
Found at i:10193 original size:28 final size:31
Alignment explanation
Indices: 10130--10198 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 31
10120 ACTTAATGTA
* *
10130 CACTTCAAT-CTTAAAGTTTATTATTTTTCT
1 CACTTTAATCCTTAAAGTTTATTATTTGTCT
*
10160 CACTTTGATCCTTAAAGTTT-TT-TTTGTC-
1 CACTTTAATCCTTAAAGTTTATTATTTGTCT
10188 CACTTTAATCC
1 CACTTTAATCC
10199 CTTTGACATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 10 0.29
29 5 0.15
30 9 0.26
31 10 0.29
ACGTcount: A:0.23, C:0.20, G:0.06, T:0.51
Consensus pattern (31 bp):
CACTTTAATCCTTAAAGTTTATTATTTGTCT
Found at i:10450 original size:19 final size:19
Alignment explanation
Indices: 10426--10476 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
10416 TATATAATTG
10426 TTTAAAAATTA-AAAAAACA
1 TTTAAAAATTATAAAAAA-A
* *
10445 TTTAAAAACTATGAAAAAA
1 TTTAAAAATTATAAAAAAA
10464 TTATAAAAATTAT
1 TT-TAAAAATTAT
10477 TAGAAATTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (19 bp):
TTTAAAAATTATAAAAAAA
Found at i:12462 original size:27 final size:28
Alignment explanation
Indices: 12419--12485 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 28
12409 AAACCCCATT
*
12419 AAAA-ATAATAGAAAATACAAATT-T-TA
1 AAAATATAATATAAAATA-AAATTATATA
*
12445 AAAATATAATATATAATAAAATTATATA
1 AAAATATAATATAAAATAAAATTATATA
*
12473 AATAATTTAATAT
1 AA-AATATAATAT
12486 TTGTAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 9 0.26
27 12 0.35
28 4 0.12
29 9 0.26
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (28 bp):
AAAATATAATATAAAATAAAATTATATA
Found at i:14940 original size:90 final size:90
Alignment explanation
Indices: 14815--15012 Score: 306
Period size: 90 Copynumber: 2.2 Consensus size: 90
14805 GTATATTCTC
** *
14815 GACAGCTCGTGTGAGCAATATCGTTAGGGAACAGTTATATGCACAGATACCGTATCAATGGCTGA
1 GACAGCTCGTGTGAGCAGCATCATTAGGGAACAGTTATATGCACAGATACCGTATCAATGGCTGA
* **
14880 GGTAACTCATATGTTGTGAGTCCAT
66 GGTAACGCATATGTTGCAAGTCCAT
* *
14905 GACAGCTCGTGTGAGCAGCATCATTAGGGACCAGTTATATGCACAGATACCGTATCGATGGCTGA
1 GACAGCTCGTGTGAGCAGCATCATTAGGGAACAGTTATATGCACAGATACCGTATCAATGGCTGA
*
14970 GGTAACGCATATGTTGCAAGTCCTT
66 GGTAACGCATATGTTGCAAGTCCAT
*
14995 GATAGCTCGTGTGAGCAG
1 GACAGCTCGTGTGAGCAG
15013 TATCGTGACT
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 98 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (90 bp):
GACAGCTCGTGTGAGCAGCATCATTAGGGAACAGTTATATGCACAGATACCGTATCAATGGCTGA
GGTAACGCATATGTTGCAAGTCCAT
Found at i:15976 original size:21 final size:21
Alignment explanation
Indices: 15944--15995 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
15934 AGAGTTTTTA
*
15944 GTATCAGTAGAA-TCATGACAT
1 GTATCGGTAGAAGTCAT-ACAT
* *
15965 GTTTCGGTAGAAGTCATACTT
1 GTATCGGTAGAAGTCATACAT
15986 GTATCGGTAG
1 GTATCGGTAG
15996 TATTGTCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAAGTCATACAT
Found at i:24307 original size:15 final size:16
Alignment explanation
Indices: 24287--24316 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24277 ATCATAATTT
24287 TTTTTC-TTCTTTTTA
1 TTTTTCTTTCTTTTTA
24302 TTTTTCTTTCTTTTT
1 TTTTTCTTTCTTTTT
24317 CTCATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTCTTTCTTTTTA
Found at i:24323 original size:19 final size:18
Alignment explanation
Indices: 24283--24327 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
24273 ATTTATCATA
*
24283 ATTTTTTTTCTTCTTTTT
1 ATTTTTTTTCTTCTTTTC
24301 ATTTTTCTTTCTT-TTTCTC
1 ATTTTT-TTTCTTCTTT-TC
24320 ATTTTTTT
1 ATTTTTTT
24328 AAGTGATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (18 bp):
ATTTTTTTTCTTCTTTTC
Found at i:36509 original size:24 final size:24
Alignment explanation
Indices: 36442--36500 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
36432 TTAAAATCTG
*
36442 TCTGGCCTCGTAAGAGCTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
36466 TCTGGGCTCGTAAGAGCTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
*
36490 TTTGGGCTCGT
1 TCTGGGCTCGT
36501 GTAGGCTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.29
Consensus pattern (24 bp):
TCTGGGCTCGTAAGAGCTAACCAT
Found at i:40585 original size:22 final size:23
Alignment explanation
Indices: 40560--40617 Score: 82
Period size: 22 Copynumber: 2.5 Consensus size: 23
40550 GACACCTCTA
40560 TTTTTTATTTTTTTTAATTCTGT
1 TTTTTTATTTTTTTTAATTCTGT
* *
40583 TTTCTT-TTATTTTTAATTCTGT
1 TTTTTTATTTTTTTTAATTCTGT
40605 TTCTTTTATTTTT
1 TT-TTTTATTTTT
40618 CCTCAGATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 17 0.59
23 8 0.28
24 4 0.14
ACGTcount: A:0.12, C:0.07, G:0.03, T:0.78
Consensus pattern (23 bp):
TTTTTTATTTTTTTTAATTCTGT
Found at i:40607 original size:21 final size:22
Alignment explanation
Indices: 40570--40617 Score: 89
Period size: 21 Copynumber: 2.2 Consensus size: 22
40560 TTTTTTATTT
40570 TTTTTAATTCTGTTTTCTTTTA
1 TTTTTAATTCTGTTTTCTTTTA
40592 TTTTTAATTCTG-TTTCTTTTA
1 TTTTTAATTCTGTTTTCTTTTA
40613 TTTTT
1 TTTTT
40618 CCTCAGATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.12, C:0.08, G:0.04, T:0.75
Consensus pattern (22 bp):
TTTTTAATTCTGTTTTCTTTTA
Found at i:41983 original size:35 final size:35
Alignment explanation
Indices: 41937--42011 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
41927 CAAGTTTCAA
41937 GTTTCAAGATTGACATTAGAACCTTTTAGTGGCAT
1 GTTTCAAGATTGACATTAGAACCTTTTAGTGGCAT
** *
41972 GTTTCAAGATTGACATTAGAATTTTTTAGTGGCGT
1 GTTTCAAGATTGACATTAGAACCTTTTAGTGGCAT
42007 GTTTC
1 GTTTC
42012 GGTCCTGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.41
Consensus pattern (35 bp):
GTTTCAAGATTGACATTAGAACCTTTTAGTGGCAT
Found at i:46723 original size:18 final size:18
Alignment explanation
Indices: 46696--46730 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
46686 TAAATCGATT
46696 AATTGATCGA-TTAATCA
1 AATTGATCGATTTAATCA
46713 AATTAGATCGATTTAATC
1 AATT-GATCGATTTAATC
46731 GAATAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 6 0.38
19 6 0.38
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (18 bp):
AATTGATCGATTTAATCA
Found at i:50466 original size:3 final size:3
Alignment explanation
Indices: 50458--50492 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
50448 TCAAAAAAGG
50458 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
50493 GAGGTATGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:52037 original size:96 final size:96
Alignment explanation
Indices: 51863--52054 Score: 237
Period size: 96 Copynumber: 2.0 Consensus size: 96
51853 ATTTTGGGAA
* *** *
51863 AAGGATATTCGATTATATCGATTTGAAGAAGGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATATCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
*
51928 AAATCAAAGAT-AAAGAAACATTGCCTCGATT
66 AAATCAAAGATAAAAG-AACATTACCTCGATT
* *
51959 AAGGGTATTCGATTATTTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCGATTATATCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTTC
* * *
52023 GAAACTCGAA-ATAAAAGAATATTACCTCGATT
65 -AAAATCAAAGATAAAAGAACATTACCTCGATT
52055 TTAAAGTCTT
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
95 1 0.01
96 70 0.85
97 11 0.13
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATATCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
AAATCAAAGATAAAAGAACATTACCTCGATT
Found at i:52403 original size:29 final size:29
Alignment explanation
Indices: 52371--52721 Score: 233
Period size: 29 Copynumber: 11.9 Consensus size: 29
52361 TTTTTAAACA
52371 TTCGGGAGTAAAAATGGAATTTTTGG-AGT
1 TTCGGG-GTAAAAATGGAATTTTTGGAAGT
* * * *
52400 TTCGAGGTCGAAAATAGAGTTTTTGG-A-T
1 TTCGGGGT-AAAAATGGAATTTTTGGAAGT
*
52428 ATTCGGGGGT-AAAAT-GATATTTTTTTTGAAAGT
1 -TTC-GGGGTAAAAATGGA-A---TTTTTGGAAGT
* * *
52461 TTCGAGGTCAAAAATGGAAATTTTGG-AGG
1 TTCGGGGT-AAAAATGGAATTTTTGGAAGT
*
52490 TTCGAGGGTAAAAATGTAATTTTTGGAAGT
1 TTCG-GGGTAAAAATGGAATTTTTGGAAGT
* * * *
52520 TTTGGGGTCGAAAATGGAATTTTTAGAAGA
1 TTCGGGGT-AAAAATGGAATTTTTGGAAGT
*
52550 TT-GAGGGTAAAAATAGAA-TTTTGGAAGT
1 TTCG-GGGTAAAAATGGAATTTTTGGAAGT
* * *
52578 TTCGAGGTCAAAGATGGAATATTTGGAAG-
1 TTCGGGGT-AAAAATGGAATTTTTGGAAGT
*
52607 TTCAGGGGTCAAAATGGAATTTTTGGAAG-
1 TTC-GGGGTAAAAATGGAATTTTTGGAAGT
*
52636 TTCGGGGGTCAAAAT-GAGATTTTTGGAAGT
1 TTC-GGGGTAAAAATGGA-ATTTTTGGAAGT
* * *
52666 TTCGAGGTCGAAAATAGAATTTTTGGAAG-
1 TTCGGGGT-AAAAATGGAATTTTTGGAAGT
* *
52695 TTCGGGGGT-AAACTGGAAATTTTGGAA
1 TTC-GGGGTAAAAATGGAATTTTTGGAA
52722 ATTTTGGAAA
Statistics
Matches: 258, Mismatches: 39, Indels: 51
0.74 0.11 0.15
Matches are distributed among these distances:
27 2 0.01
28 38 0.15
29 118 0.46
30 75 0.29
31 12 0.05
32 4 0.02
33 7 0.03
34 2 0.01
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (29 bp):
TTCGGGGTAAAAATGGAATTTTTGGAAGT
Found at i:52432 original size:58 final size:57
Alignment explanation
Indices: 52370--52696 Score: 265
Period size: 59 Copynumber: 5.5 Consensus size: 57
52360 ATTTTTAAAC
* * *
52370 ATTCGGGAGTAAAAATGGAATTTTTGG-AGTTTCGAGGTCGAAAATAGAGTTTTTGGAT
1 ATTCGGG-GTAAAAATGGAATTTTTGGAAGTTTCGAGGTC-AAAATGGAATTTTTGGAG
* *
52428 ATTCGGGGGT-AAAAT-GATATTTTTTTTGAAAGTTTCGAGGTCAAAAATGGAAATTTTGGAG
1 ATTC-GGGGTAAAAATGGA-A---TTTTTGGAAGTTTCGAGGTC-AAAATGGAATTTTTGGAG
* * * * *
52489 GTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCGAAAATGGAATTTTTAGAAG
1 ATTCG-GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTC-AAAATGGAATTTTT-GGAG
* *
52549 ATT-GAGGGTAAAAATAGAA-TTTTGGAAGTTTCGAGGTCAAAGATGGAATATTTGGA-
1 ATTCG-GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAA-ATGGAATTTTTGGAG
* *
52605 AGTTCAGGGGTCAAAATGGAATTTTTGGAAG-TTCGGGGGTCAAAAT-GAGATTTTTGGAAG
1 A-TTC-GGGGTAAAAATGGAATTTTTGGAAGTTTC-GAGGTCAAAATGGA-ATTTTTGG-AG
* * * *
52665 TTTCGAGGTCGAAAATAGAATTTTTGGAAGTT
1 ATTCGGGGT-AAAAATGGAATTTTTGGAAGTT
52697 CGGGGGTAAA
Statistics
Matches: 219, Mismatches: 29, Indels: 40
0.76 0.10 0.14
Matches are distributed among these distances:
56 3 0.01
57 15 0.07
58 61 0.28
59 87 0.40
60 13 0.06
61 33 0.15
62 6 0.03
63 1 0.00
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (57 bp):
ATTCGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAATGGAATTTTTGGAG
Found at i:52603 original size:88 final size:86
Alignment explanation
Indices: 52378--52717 Score: 300
Period size: 88 Copynumber: 3.9 Consensus size: 86
52368 ACATTCGGGA
* * * *
52378 GTAAAAATGGAATTTTTGG-AGTTTCGAGGTCGAAAATAGAGTTTTTGGATA-TTCGGGGGT-AA
1 GTAAAAATAGAA-TTTTGGAAGTTTCGAGGTC-AAAATGGAATTTTTGGA-AGTTCAGGGGTCAA
*
52440 AAT-GATATTTTTTTTGAAAGTTTCGA-G
63 AATGGA-A--TTTTTAG-AAG-TTCGAGG
* * * * **
52467 GTCAAAAATGGAAATTTTGG-AGGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCGA
1 GT-AAAAATAG-AATTTTGGAAGTTTCGA-GGTCAAAATGGAATTTTTGGAAGTTCAGGGGTC-A
52531 AAATGGAATTTTTAGAAGATT-GAGG
62 AAATGGAATTTTTAGAAG-TTCGAGG
*
52556 GTAAAAATAGAATTTTGGAAGTTTCGAGGTCAAAGATGGAATATTTGGAAGTTCAGGGGTCAAAA
1 GTAAAAATAGAATTTTGGAAGTTTCGAGGTCAAA-ATGGAATTTTTGGAAGTTCAGGGGTCAAAA
* *
52621 TGGAATTTTTGGAAGTTCGGGG
65 TGGAATTTTTAGAAGTTCGAGG
* * * *
52643 GTCAAAATGAGATTTTTGGAAGTTTCGAGGTCGAAAATAGAATTTTTGGAAGTTCGGGGGT-AAA
1 GTAAAAAT-AGAATTTTGGAAGTTTCGAGGTC-AAAATGGAATTTTTGGAAGTTCAGGGGTCAAA
* *
52707 CTGGAAATTTT
64 ATGGAATTTTT
52718 GGAAATTTTG
Statistics
Matches: 213, Mismatches: 25, Indels: 28
0.80 0.09 0.11
Matches are distributed among these distances:
86 2 0.01
87 54 0.25
88 82 0.38
89 14 0.07
90 48 0.23
91 5 0.02
92 6 0.03
93 2 0.01
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (86 bp):
GTAAAAATAGAATTTTGGAAGTTTCGAGGTCAAAATGGAATTTTTGGAAGTTCAGGGGTCAAAAT
GGAATTTTTAGAAGTTCGAGG
Found at i:52722 original size:9 final size:9
Alignment explanation
Indices: 52708--52737 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
52698 GGGGGTAAAC
52708 TGGAAATTT
1 TGGAAATTT
52717 TGGAAATTT
1 TGGAAATTT
52726 TGGAAATTT
1 TGGAAATTT
52735 TGG
1 TGG
52738 GGTCGAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (9 bp):
TGGAAATTT
Found at i:53837 original size:3 final size:3
Alignment explanation
Indices: 53829--53861 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
53819 TAAAAAATAC
53829 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
53862 ATTAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:54627 original size:24 final size:25
Alignment explanation
Indices: 54600--54646 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
54590 TTATATTTGT
54600 TTTGAACTTTTAA-TTTAATTTTTA
1 TTTGAACTTTTAATTTTAATTTTTA
**
54624 TTTGTGCTTTTAATTTTAATTTT
1 TTTGAACTTTTAATTTTAATTTT
54647 AATATTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.66
Consensus pattern (25 bp):
TTTGAACTTTTAATTTTAATTTTTA
Found at i:54690 original size:6 final size:6
Alignment explanation
Indices: 54679--54814 Score: 68
Period size: 6 Copynumber: 22.8 Consensus size: 6
54669 TCAAATTTGA
** * *
54679 TTAAAT TTAAAT TTAAA- GCAAAT TTAAAT TTAAAAAG ATAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT--AAAT TTAAAT TTAAAT
** * *
54727 GCAAAT TTAAAT TTAAAAAG ATAAAT TTAAAT TTAAGA- -TAAAT TTAAAT
1 TTAAAT TTAAAT TT--AAAT TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT
* * * * *
54776 TTAAAA ATAAAT TTAAA- -TCAAT TTAAAC TTAATT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
54815 ATCAAAGGTT
Statistics
Matches: 93, Mismatches: 26, Indels: 22
0.66 0.18 0.16
Matches are distributed among these distances:
4 4 0.04
5 9 0.10
6 71 0.76
7 1 0.01
8 8 0.09
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.38
Consensus pattern (6 bp):
TTAAAT
Found at i:54726 original size:37 final size:37
Alignment explanation
Indices: 54680--54793 Score: 147
Period size: 31 Copynumber: 3.3 Consensus size: 37
54670 CAAATTTGAT
54680 TAAATTTAAATTTAAAGCAAATTTAAATTTAAAAAG-
1 TAAATTTAAATTTAAAGCAAATTTAAATTTAAAAAGA
54716 ---A--TAAATTTAAAGCAAATTTAAATTTAAAAAGA
1 TAAATTTAAATTTAAAGCAAATTTAAATTTAAAAAGA
*
54748 TAAATTTAAATTT-AAGATAAATTTAAATTT-AAAA-A
1 TAAATTTAAATTTAAAG-CAAATTTAAATTTAAAAAGA
54783 TAAATTTAAAT
1 TAAATTTAAAT
54794 CAATTTAAAC
Statistics
Matches: 70, Mismatches: 1, Indels: 15
0.81 0.01 0.17
Matches are distributed among these distances:
31 30 0.43
33 1 0.01
35 13 0.19
36 7 0.10
37 19 0.27
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (37 bp):
TAAATTTAAATTTAAAGCAAATTTAAATTTAAAAAGA
Found at i:54812 original size:22 final size:23
Alignment explanation
Indices: 54773--54819 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
54763 GATAAATTTA
54773 AATTTAAAAATAAATTT-AAATC
1 AATTTAAAAATAAATTTAAAATC
** *
54795 AATTTAAACTTAATTTTAAAATC
1 AATTTAAAAATAAATTTAAAATC
54818 AA
1 AA
54820 AGGTTATCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.38
Consensus pattern (23 bp):
AATTTAAAAATAAATTTAAAATC
Found at i:58007 original size:33 final size:33
Alignment explanation
Indices: 57942--58022 Score: 99
Period size: 33 Copynumber: 2.5 Consensus size: 33
57932 TTTTTTTAAC
* * * *
57942 TTATCAATTTTTAAGGGACTCGATTTTTTTTTT
1 TTATCAATTTTTAAGGGACCCAAATTTATTTTT
* * *
57975 TTTTTAATTTTTAAGGGTCCCAAATTTATTTTT
1 TTATCAATTTTTAAGGGACCCAAATTTATTTTT
58008 TTATCAATTTTTAAG
1 TTATCAATTTTTAAG
58023 AGACAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.25, C:0.09, G:0.10, T:0.57
Consensus pattern (33 bp):
TTATCAATTTTTAAGGGACCCAAATTTATTTTT
Found at i:60029 original size:3 final size:3
Alignment explanation
Indices: 60021--60047 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
60011 GATAAATAAA
60021 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
60048 TAGGTTTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:72626 original size:7 final size:7
Alignment explanation
Indices: 72590--72632 Score: 50
Period size: 8 Copynumber: 5.7 Consensus size: 7
72580 GTTTATTAGT
72590 ATTAAAA
1 ATTAAAA
72597 TATTAAAA
1 -ATTAAAA
*
72605 TTCTAAAA
1 AT-TAAAA
72613 ATATAAAA
1 AT-TAAAA
72621 ATTAAAA
1 ATTAAAA
72628 ATTAA
1 ATTAA
72633 TCAAATGAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
7 11 0.35
8 20 0.65
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (7 bp):
ATTAAAA
Found at i:97071 original size:14 final size:13
Alignment explanation
Indices: 97040--97074 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
97030 GAGAGCTTTG
97040 TTTATTTT-TAAT
1 TTTATTTTATAAT
97052 TTTATTTTATAAT
1 TTTATTTTATAAT
97065 ATTTATTTTA
1 -TTTATTTTA
97075 GGACATCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.38
13 4 0.19
14 9 0.43
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATTTTATAAT
Found at i:103634 original size:40 final size:38
Alignment explanation
Indices: 103566--103700 Score: 96
Period size: 40 Copynumber: 3.4 Consensus size: 38
103556 ACCAGAATGG
* *
103566 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAAAGTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAG-AATAAAGTGA
* *
103606 CACCCAGTGTCTCATCGGCCTAGCCGAAG--TAAAGTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAATAAAGTGA
* * * * *
103643 TACCCAGTACCTCATCGAATCTATCCGAAGTAA-AATAATGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAG-AATAA-AGTGA
*
103684 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
103701 ACTCAAGGTC
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
37 21 0.28
38 9 0.12
40 24 0.32
41 20 0.27
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAATAAAGTGA
Found at i:103698 original size:41 final size:38
Alignment explanation
Indices: 103598--103701 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
103588 TTCGAAGCAA
* *
103598 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
103635 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
103673 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
103702 CTCAAGGTCA
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Done.