Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016286.1 Corchorus olitorius cultivar O-4 contig16319, 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: 59813
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:6979 original size:20 final size:21
Alignment explanation
Indices: 6935--6979 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
6925 GTAACCCATT
* * *
6935 TAATTTTCTTTAAAAATTACT
1 TAATTTCCTTTAAAAATAACA
6956 TAATTTCCTTTAAAAA-AACA
1 TAATTTCCTTTAAAAATAACA
6976 TAAT
1 TAAT
6980 ATTACTAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATTTCCTTTAAAAATAACA
Found at i:7777 original size:42 final size:44
Alignment explanation
Indices: 7726--7819 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
7716 AATGCATTAC
*
7726 CTAA-ATTCTACT-T-CATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
7767 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACT-CTCCATCTCTAGATAATTCATCAAAATAAAG
*
7812 CTAGTATT
1 CTAATATT
7820 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
44 1 0.02
45 34 0.72
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.35
Consensus pattern (44 bp):
CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:29522 original size:31 final size:30
Alignment explanation
Indices: 29484--29542 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 30
29474 TAAATAGTTT
*
29484 AATATGGGAACTATTGTTCTCTAAAAAAAAA
1 AATATGGGAACTATTGTTCAC-AAAAAAAAA
29515 AATATGGGAACTATTGTTCACAAAAAAA
1 AATATGGGAACTATTGTTCACAAAAAAA
29543 TAAGGGAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (30 bp):
AATATGGGAACTATTGTTCACAAAAAAAAA
Found at i:31989 original size:16 final size:16
Alignment explanation
Indices: 31958--32006 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
31948 GATTAATCAC
*
31958 AATAATTAAA-TTTTA
1 AATAAATAAATTTTTA
31973 AATAAATAAATTTTTA
1 AATAAATAAATTTTTA
* * *
31989 ACTAAATTAGTTTTTA
1 AATAAATAAATTTTTA
32005 AA
1 AA
32007 AATATGAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 9 0.32
16 19 0.68
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (16 bp):
AATAAATAAATTTTTA
Found at i:32473 original size:125 final size:127
Alignment explanation
Indices: 32255--32504 Score: 380
Period size: 125 Copynumber: 1.9 Consensus size: 127
32245 AAATATATTT
*
32255 AAAAAATTCTAATCTATATAAGTTTTTTAATTAAAATAGTAAAATGGTACAAATAAAATAGGTAT
1 AAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGT---AATAAAAT--GTAT
* * *
32320 AAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAGTATATT
61 AAAGATATTAGATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTATAAAAGTATATT
32385 CA
126 CA
*
32387 AAAAAATTTTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGT-A-AAAAT-TATAAAG
1 AAAAAATTCTAATATATATAAG-TTTTTTAATTAAAATAGTAAAATGGTAATAAAATGTATAAAG
32449 ATATTAGATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTATAAAAGT
65 ATATTAGATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTATAAAAGT
32505 TTAAACAATG
Statistics
Matches: 112, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
125 60 0.54
128 5 0.04
129 1 0.01
132 20 0.18
133 26 0.23
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (127 bp):
AAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAATAAAATGTATAAAGA
TATTAGATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTATAAAAGTATATTCA
Found at i:42247 original size:32 final size:32
Alignment explanation
Indices: 42211--42274 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
42201 CTAAAGGAGG
42211 CTGATTTTTCAACATTGGTCTTCTTTATCGTT
1 CTGATTTTTCAACATTGGTCTTCTTTATCGTT
42243 CTGATTTTTCAACATTGGTCTTCTTTATCGTT
1 CTGATTTTTCAACATTGGTCTTCTTTATCGTT
42275 TTCAACATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.16, C:0.19, G:0.12, T:0.53
Consensus pattern (32 bp):
CTGATTTTTCAACATTGGTCTTCTTTATCGTT
Found at i:42276 original size:25 final size:25
Alignment explanation
Indices: 42248--42297 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
42238 TCGTTCTGAT
*
42248 TTTTCAACATTGGTCTTCTTTATCG
1 TTTTCAACATTGGTATTCTTTATCG
42273 TTTTCAACATTGGTATTCTTTATCG
1 TTTTCAACATTGGTATTCTTTATCG
42298 ATATGGGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.52
Consensus pattern (25 bp):
TTTTCAACATTGGTATTCTTTATCG
Found at i:48029 original size:31 final size:33
Alignment explanation
Indices: 47983--48044 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
47973 GAGGGAAAGG
*
47983 AGGGTCCACATTTGA-TGCCAGATGGGAATTTC
1 AGGGTCCACATTTGATTGCCAGATCGGAATTTC
*
48015 AGGGTCCACA-TTGATTGCCAGCTCGGAATT
1 AGGGTCCACATTTGATTGCCAGATCGGAATT
48045 AGTGGGGTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 4 0.15
32 23 0.85
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (33 bp):
AGGGTCCACATTTGATTGCCAGATCGGAATTTC
Found at i:50304 original size:318 final size:320
Alignment explanation
Indices: 48718--55928 Score: 6208
Period size: 318 Copynumber: 22.8 Consensus size: 320
48708 CGCATGATTT
* * * ** * * * **
48718 AACTCACCTTTATTGAAAAGAACTCATTTTCGCACTCATTTTTATTATTCTCACCAAACTCTGCT
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTAAT
* **** * *
48783 ACAAAACGACACA-CTGAGTTTGTCGATTTGTGAGAATTTGTTGGTCTGTAAAGAAGTTTTTCAT
66 ACAAAACGACACATC-GAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTGTCAT
* * * * **
48847 GTTTAAAATTAATGTATGAACCGTTTCAAATATTTAAAGTTTTGATTCTTTCTGACTTTCATTGA
130 ATTTAAAATGAATGTATGAACCGTTTCAAATGTTAAAAAATTTGATTCTTTCTGACTTTCATTGA
* * * * * *
48912 ATTT--C------ACTATGAAACCGGTGCAAAAAAGCAACTCATGTTTTTTCATTAGTAATTTTC
195 ATTTCACTGTGAAACTATGAAACTGGTGTAAGAAA-TAACTCATGCTTTTTAATTAGTAATTTTC
* * * * *** *
48969 TTTCCTTTTTTTTTACTCTCCCTCTTTAATTTAC-TTC-ATTTTAAAATGCTTTCAACA-TTTTC
259 TTT-CTTTTTTTGT--TCTCCCTCTTCAATCTACTTTCTTTTTTTTTATGCTTTCAACATTTTTA
* * * * * *
49031 AACTCAACTTTATAAAATAAAAGACATTTTTGCACTCCTTTTAATTTTTCTCAACAAACTCTACT
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTAAT
* * * * * * *
49096 ATAAAACAACACATTGAGTTTGTCAATTTGTGGGAATCTGCCGATCTGTAAAGCAGTTTGTCGTA
66 ACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTGTCATA
* * * * *
49161 TTTAAAAATGAATGCAAGAACCGTTTCAAACGTT-ACAAATCTTGATTCTTTCTGACTTTCAATG
131 TTT-AAAATGAATGTATGAACCGTTTCAAATGTTAAAAAAT-TTGATTCTTTCTGACTTTCATTG
* *
49225 AATTTCATTGTGAAACTATGAAACTGGTGTAAGAAATAACTCATGCTTTTGAATTAGTAATTTTC
194 AATTTCACTGTGAAACTATGAAACTGGTGTAAGAAATAACTCATGCTTTTTAATTAGTAATTTTC
* * * *
49290 TTCCTTTTTTTTATTGTTCTCCCTCTTCAATCTAGC-TACTTTCCTTTTTATATGTTTTCAATAT
259 -T--TTCTTTTT-TTGTTCTCCCTCTTCAATCTA-CTTTCTTT--TTTTT-TATGCTTTCAACA-
*
49354 TTTTTT
315 TTTTTA
* *
49360 AACTCACCTTTATAGAATATAAGACATTTTTGCACTTCTTTTTATTTTTCTCACCAAACTCTGAT
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTAAT
* * * * * * **
49425 ACAAAACGACATATCGAGTTTGTCGATTTGTGACAATTTACCAATCTGTAAAGCACTCTGTCACG
66 ACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTGTCATA
* **
49490 TTTAAAATGAATGTATGGACCGTTTCAAATGTTAAAAAAAAATGATTCTTTCTTG-CTTTCATTG
131 TTTAAAATGAATGTATGAACCGTTTCAAATGTT-AAAAAATTTGATTCTTTC-TGACTTTCATTG
* * * * *
49554 AATTTCATTGTGAAACTATGAAATTGGTGTAATAAATAACTCATGCTTTTGAATTAATAATTTTC
194 AATTTCACTGTGAAACTATGAAACTGGTGTAAGAAATAACTCATGCTTTTTAATTAGTAATTTTC
* * * *
49619 TTGCCCTTTTTTTTTGTTCTCCCTATTCAATCTACTTTCTTTTTCTTCTTTTTTTAATGTTTTCG
259 TT----TCTTTTTTTGTTCTCCCTCTTCAATCTA----C--TTTCTT-TTTTTTT-ATGCTTTCA
49684 ACATTTTT-
312 ACATTTTTA
* * * * * *
49692 AACTCAGCTTTATAGAGTATAAGACATTTTTGCACTCTTTTTTATTTTTCTCACCAAAATTTGAT
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTAAT
* * * * * *
49757 ACAAAACAACACATCAAGTTTGTCTATTTGTGAGAATCTGCCTATCTGTAAAGCAGTTTTTAATA
66 ACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTGTCATA
* *
49822 TTTAAAATTAATGCT-TGAACCGTTTCAAACGTTAAAAAATTTTGATTCTTTCTGACTTTCATTA
131 TTTAAAATGAATG-TATGAACCGTTTCAAATGTTAAAAAA-TTTGATTCTTTCTGACTTTCATT-
* * *
49886 GAA-GTCAC--TG------TGAAACTGGTGTAA-AACATAACTCATG-TTTTTGAATTAGCAGTT
193 GAATTTCACTGTGAAACTATGAAACTGGTGTAAGAA-ATAACTCATGCTTTTT-AATTAGTAATT
* * * *
49940 TTCGTCCTTTTTTTTGTTCTCCCTATTCAATCTACTTTCTTTTCTTTTTTTTTGTGCTTTCAA-A
256 TTCTTTC-TTTTTTTGTTCTCCCTCTTCAATCTA----C-TTTCTTTTTTTTTATGCTTTCAACA
* *
50004 ATTTCA
315 TTTTTA
* * * * * * *
50010 AATTCACCTTTATAGAATACAACACATCTTTGCACTCCTTTTTATTGTTCTCCCCAAATTCTAAT
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTAAT
* * * * * * *
50075 ACAAAACGACACATCAAGTTTGTCGATTTGTGACAATTTACCAATCTGTAAAGCACTCTGTCATG
66 ACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTGTCATA
* ** *
50140 TTTAAAATGAATGTATGGACCGTTTCAAATG-TAAAAAAAATGATTCTTTCTTACTTTCATTGAA
131 TTTAAAATGAATGTATGAACCGTTTCAAATGTTAAAAAATTTGATTCTTTCTGACTTTCATTGAA
* * * * *
50204 TTTCATTGTGAAACTATGAAATTGGTGTAATAAATAACCCATGCTTTTTAATTTGTAATTTTCTT
196 TTTCACTGTGAAACTATGAAACTGGTGTAAGAAATAACTCATGCTTTTTAATTAGTAATTTTCTT
*
50269 GTCTTTTTTT-TTCTCCCTCATCAATCTACTTTC---TTTTTT-T-C---CAACATTTTT-
261 -TCTTTTTTTGTTCTCCCTCTTCAATCTACTTTCTTTTTTTTTATGCTTTCAACATTTTTA
** * * * *
50320 AACTTTCCATTATATATTATAAGATATTTTTGCACT-CTTTTT-TTTTTCTCTGACCAAACTCTG
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTC--ACCAAACTCT-
* * *
50383 AA-ACAAAACGACATATCGAGTTTGTCGATTTGTGAGAATCTGCCGATCTGTAAAGTAGTTTGTC
63 AATACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTGTC
* * * *
50447 GTA-TTCAAATGAATGCATGAACCGTTTCAAATGTTAAAAATTTTGATTCTTTCTGACTTTCATT
128 ATATTTAAAATGAATGTATGAACCGTTTCAAATGTTAAAAAATTTGATTCTTTCTGACTTTCATT
* * *
50511 GAA-TTC-C------ACTGTGAAACTGGTCTAA-AACATAACTCATG-TTTTTGAATTAGAAATT
193 GAATTTCACTGTGAAACTATGAAACTGGTGTAAGAA-ATAACTCATGCTTTTT-AATTAGTAATT
* * **** * * *
50566 TTCCTTC-CTTTTTGCATTAAATCTATTCAATCTACTTTTTTTTCTTCTTGTTTTTTTCTTTTAC
256 TTCTTTCTTTTTTTG--TTCTCCCTCTTCAATCTAC-------T-TTC---TTTTTTT-TTATGC
* *
50630 TTTCAAGATTTTCA
307 TTTCAACATTTTTA
* * * *
50644 AACTCACCTTTATAGAATAAAACACATGTTTGCACTCC-TTTT-TTTTTCTCACCAAACTCTAGT
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTAAT
* *
50707 ACAAAACGACACATCGAGTTTGTCGATTTGTG-GAAATCTGCCGATCTGTAAAGCAGTTTGTCGT
66 ACAAAACGACACATCGAGTTTGTCGATTTGTGAG-AATCTGCCAATCTGTAAAGCAGTTTGTCAT
* * * ** * *
50771 AATTATAAATTGAATGCAAGAACCGTTTCAAGCGTTAAAAATTTTGATTCTTTCTGATTTTCATT
130 -ATT-TAAAATGAATGTATGAACCGTTTCAAATGTTAAAAAATTTGATTCTTTCTGACTTTCATT
* * *
50836 GAATTTCACTGTGAAACTATGAAACTAGCGTAAGAAATAACTCATGCTTTTAAATTTA-TAATTT
193 GAATTTCACTGTGAAACTATGAAACTGGTGTAAGAAATAACTCATGCTTTTTAA-TTAGTAATTT
* * * *
50900 TC-TTCTTTTTTTGTTCTCCCTCTTTAATCTAGTTTC--CTTTTTTATGTTTTCAACATTTTT-
257 TCTTTCTTTTTTTGTTCTCCCTCTTCAATCTACTTTCTTTTTTTTTATGCTTTCAACATTTTTA
* * * *
50960 TACTCACCTTTATAGAACATAAGACATATTTGCACTCCTTTTTATTTTTCTCACCAAACTCTACT
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTAAT
* * *
51025 ACAAAACGACACATCGAGTTTGTCGATTTATGAGAATCTG-TAAGTCTGTAAAGAAGTTTGTCAT
66 ACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAA-TCTGTAAAGCAGTTTGTCAT
* * * **
51089 GTTTAAAATTAATGTATGAACCGTTTCAAATGTTTAAAGTTTTGATTCTTTCTGACTTTCATTGA
130 ATTTAAAATGAATGTATGAACCGTTTCAAATGTTAAAAAATTTGATTCTTTCTGACTTTCATTGA
* * * * * * *
51154 ATTT--C------ACTATGAAGCCGGTGCAAAAAACAACTCATGTTTTTTCATTAGTAATTTTCT
195 ATTTCACTGTGAAACTATGAAACTGGTGTAAGAAATAACTCATGCTTTTTAATTAGTAATTTTCT
** * * ** * *
51211 TTCCTTTTCTTTACTCTCCCTCTTCAATTTAC-TTCATTTTTTAAATGCTTTCAATA-TTTTC
260 TT-CTTTT-TTTGTTCTCCCTCTTCAATCTACTTTCTTTTTTTTTATGCTTTCAACATTTTTA
* * * * *
51272 AACTCAACTTTATAAAATAAAAGACATTTTTGCACTCTTTTTTATTTTTTCTCAACAAACTCTAA
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTA-TTTTTCTCACCAAACTCTAA
* * * * *
51337 TACAAAACAACACATCGAGTTTGTCAATTTGTGGGAATCTGCCAATCTGTAAAGTAGTTTGTTAT
65 TACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTGTCAT
* * * * * * *
51402 ATTTAAAATGAATGCAAGAACTGTTTCAAACGTTACAAATTTTGATT-TTTCTGACTTTCAATGA
130 ATTTAAAATGAATGTATGAACCGTTTCAAATGTTAAAAAATTTGATTCTTTCTGACTTTCATTGA
*
51466 ATTTCACTGTGAAACTATGAAACTGGTGTAAGAAATAACTCATGCTTTTGAATTAGTAATTTTCT
195 ATTTCACTGTGAAACTATGAAACTGGTGTAAGAAATAACTCATGCTTTTTAATTAGTAATTTTCT
* * * * *
51531 TCCTTTTTTTGTTCTCCCTCTTTAATCTACTTTC--CTTTTTTATGTTTTCAATATTTTTTTA
260 TTCTTTTTTTGTTCTCCCTCTTCAATCTACTTTCTTTTTTTTTATGCTTTCAACA--TTTTTA
* *
51592 ACTCACCTTTACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTCATTTTTCTCACCAAACT
1 A---A-C-TCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACT
* * * * ** * *
51657 TTGAT---AAACG--ACATAGAGTTTGTCGATTTGTGACAATCAACCAATCTGTAAAGTACTTTG
61 CTAATACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTG
* * * * *
51717 TCATGTTTAAAATGAATGTATCG-GCTGTTTCAAATG-TAAAAAA-TTGATTCTTTCTTATTTTC
126 TCATATTTAAAATGAATGTAT-GAACCGTTTCAAATGTTAAAAAATTTGATTCTTTCTGACTTTC
* * * *
51779 ATTGAATTTCATTGTGAAACTATGAAATTGGTGTAATAAATAACTCATGCTTTTGAATTAGTAAT
190 ATTGAATTTCACTGTGAAACTATGAAACTGGTGTAAGAAATAACTCATGCTTTTTAATTAGTAAT
* * * *
51844 TTTCTTGCCTTTTTTTTCAATGTTTTCCCTCTTGAATCTACTTTC--TTCTTTT-T--TTTCAAC
255 TTTCTT---TCTTTTTT---TGTTCTCCCTCTTCAATCTACTTTCTTTTTTTTTATGCTTTCAAC
51904 A-TTTTA
314 ATTTTTA
** * * * * *
51910 AACTTTCCATTATATATTATAAGATATTTTTACACT-C--TTT-TTTTTCTCACCAAACTCTGAA
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTCT-AA
* * * * * * * *
51971 -ACAAAATGACATATCGAGTTTGTTGAGTTGTGAGAATCTTCCGATCTGTAAAGCAATTTGTCTT
65 TACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTGTCAT
* * * * * *
52035 ATTCAAGATGAATGCATAAATCGTTTCAAATGTTAAAAATTTTGATTCTTTCTGACTTTCATTGA
130 ATTTAAAATGAATGTATGAACCGTTTCAAATGTTAAAAAATTTGATTCTTTCTGACTTTCATTGA
* *
52100 ATTTCACTGTGAAAC------A--GGTGTAA-AACATAACTCAT-ATTTTTGAATTAGAAATTTT
195 ATTTCACTGTGAAACTATGAAACTGGTGTAAGAA-ATAACTCATGCTTTTT-AATTAGTAATTTT
* ** * * * * *
52155 CCTTCCTTTTTTCATTAC-ACCTATTCAATCTAATTT-TTTTTTTTT-TGCTTTCAAGATTTTCA
258 -CTTTCTTTTTTTGTT-CTCCCTCTTCAATCTACTTTCTTTTTTTTTATGCTTTCAACATTTTTA
* * * * * * *
52217 AACTCGCCTTTATAGAATAGAACACATCTCTGCACTCC-TTTT-TTTTCCTCACCAAACTCTAGT
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTAAT
* * * * *
52280 ACAAAATGACACATCGAGTTTATCGATTTGTGGGAATCTGCCGATCTGTAAAGCAGTTTGTCGTA
66 ACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTGTCATA
* * ** * *
52345 TTTATAAATTGAATGCAAGAACCGTTTCAAACATT-AAAAATTTGGATTCCTTCTGACTTGCATT
131 TTTA-AAA-TGAATGTATGAACCGTTTCAAATGTTAAAAAATTT-GATTCTTTCTGACTTTCATT
* * *
52409 GAATGTCACTGTGAAACTATGAAACTAGTGTAAGAAATAACTCATGCTTTTGAATTAGTAATTTT
193 GAATTTCACTGTGAAACTATGAAACTGGTGTAAGAAATAACTCATGCTTTTTAATTAGTAATTTT
* * * * *
52474 CTTCCTTTTTTTGGTCTCCCTCTAT-AATCTAGTTTC-CTTTTTTTATGTTTTCAACATTTTT-
258 CTTTCTTTTTTTGTTCTCCCTCT-TCAATCTACTTTCTTTTTTTTTATGCTTTCAACATTTTTA
** * * *
52535 TGCTCACCTTTATAGAATATAAGGCATATTTGCACTCCTTTTTATTTTTCTCACCAAACTCTGAT
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTAAT
* * * * * * *
52600 ACAAAACGACATATCAAGTTT-ACAAATTTGTGAGAATCTACTAATCTGTAAAGCATTTTGTCAT
66 ACAAAACGACACATCGAGTTTGTC-GATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTGTCAT
* * * * * *
52664 GTTTAAAATTAATGTATGAACCGTTTCAAATGTT-TAAAGTTTTATTCTTTCTAACTTTCATTGA
130 ATTTAAAATGAATGTATGAACCGTTTCAAATGTTAAAAAATTTGATTCTTTCTGACTTTCATTGA
* * * * *
52728 ATTTCAC--T---AC---GAAACCGGTGCAA-AAAGCAACTCATGTTTTTTCATTAGTAATTATT
195 ATTTCACTGTGAAACTATGAAACTGGTGTAAGAAA-TAACTCATGCTTTTTAATTAGTAATT-TT
* * * * * **
52784 ATTCCTTTTTATTTTTACTCTCCCTCTTCAATTTAC-TTCACTTTTTTAAATGCTTTCAACA-TT
258 CTTTC-TTTT-TTTGT--TCTCCCTCTTCAATCTACTTTC-TTTTTTTTTATGCTTTCAACATTT
*
52847 TTC
318 TTA
* * * *
52850 AACTCAACTTTATAAAATAAAAGACATTTTTGCACTCCTTTTTTATTTTTCTCAACAAACTCTAA
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCC-TTTTTATTTTTCTCACCAAACTCTAA
* * * * * *
52915 TACAAAACAACACATCGAGTTTGTCAATTTGTGGGAATCTGCCGATCTGTAAAGCAATTTGTCGT
65 TACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTGTCAT
* * * * * *
52980 ATTTAAAATGAATGCAAGAACCGTTTCAAACGTTACAAATTTTGATTCTTTCTGACTTTCAATGA
130 ATTTAAAATGAATGTATGAACCGTTTCAAATGTTAAAAAATTTGATTCTTTCTGACTTTCATTGA
* * * *
53045 ATTTCACTTTGAAACTATGAAACTGATGTAAGAAATAACTTATGCTTTTGAATTAGTAATTTTCT
195 ATTTCACTGTGAAACTATGAAACTGGTGTAAGAAATAACTCATGCTTTTTAATTAGTAA--TT-T
* * * * *
53110 TCCTTTTTTTTTTTGTTCTCCCTCTTCAATCTAGCTACTCTCCTTTTTTTATGTTTTCAATATTT
257 T-CTTTCTTTTTTTGTTCTCCCTCTTCAATCTA-CT-TTCT-TTTTTTTTATGCTTTCAACA-TT
*
53175 TTTT
317 TTTA
* *
53179 AACTCACCTTTATAGAATATAAGACATTTTTGCACTTCTTTTTATTTTTCTCACCAAACTCTGAT
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTAAT
* * * * * *
53244 ACAAAACGACATATCGAGTTTGTCGATTTGTGACAATTTACCAATCTGTAAAGCACTCTTGTCAC
66 ACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGT-TTGTCAT
* * ** *
53309 GTTTAAAATGAATGTATGGACCGTTTCAAATG-TAAAAAAAATGATTCTTTCTTACTTTCATTGA
130 ATTTAAAATGAATGTATGAACCGTTTCAAATGTTAAAAAATTTGATTCTTTCTGACTTTCATTGA
* * * * *
53373 ATTTCATTGTGAAACTATAAAAATTGGTGTAATAAATAACTCATGCTTTTGAATTAGTAATTTTC
195 ATTTCACTGTGAAACTAT-GAAACTGGTGTAAGAAATAACTCATGCTTTTTAATTAGTAATTTTC
*
53438 TTGCCTTTTTTTTTTGTTCTCCCTCTTCAATCTA----CTTTTTTTTT-T-C---CAACATTTTT
259 -T---TTCTTTTTTTGTTCTCCCTCTTCAATCTACTTTCTTTTTTTTTATGCTTTCAACATTTTT
53494 -
320 A
** * * *
53494 AACTTTCCATTATA-AATTATAAGATATTTTTGCACTCC---TT-TTTTTCTTACCAAACTCTAA
1 AACTCACCTTTATAGAA-TATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTAA
* * * * *
53554 TACAAAACTACATATCGAGTTTGTCGATTTGTGGGAATCTGCCGATCTGTAAAGCAGTTTGTCGT
65 TACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTGTCAT
* * ** * * *
53619 ATTCAAAATGAATGCATGAACTATTTCAAATG-TAAAAATTTTGATTCTTTTTGACTCTCATTGA
130 ATTTAAAATGAATGTATGAACCGTTTCAAATGTTAAAAAATTTGATTCTTTCTGACTTTCATTGA
* *
53683 ATTT--C------ACTATGAAACTGGTGTAA-AACATAACTCAT-TTTTTTGAATTAGAAATTTT
195 ATTTCACTGTGAAACTATGAAACTGGTGTAAGAA-ATAACTCATGCTTTTT-AATTAGTAATTTT
* * * * * * * *
53738 CCTTCCATTTTTCGTTAC-ACCTATTCAATCAAC-TT-TTTTTTTTT-TGCTTTCAAGATTTTCA
258 -CTTTCTTTTTTTGTT-CTCCCTCTTCAATCTACTTTCTTTTTTTTTATGCTTTCAACATTTTTA
* * * * * * *
53799 AAGTCACCTTTATAGAATAGAACACATCTCTGCACTCC-TTTT-TTTTTCTCACAAAACTCTATT
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTAAT
* *
53862 ACAAAACGACACATCGAGTTTGTCGATTTGTGGGAATCTGCCGATCTGTAAAGCAGTTTGTCATA
66 ACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTGTCATA
* * * * *
53927 TTTATAAATTGAACGCAAGAACCGTTTCAAACGTTAAAAATTTTGATTCTTTCTGACTTTCATTG
131 TTTA-AAA-TGAATGTATGAACCGTTTCAAATGTTAAAAAATTTGATTCTTTCTGACTTTCATTG
* * *
53992 AATTTCACTGTGAAACTATGAAACTAGTGTAAGAAATAACTCATGCTTTTAAATTAGTATTTTTC
194 AATTTCACTGTGAAACTATGAAACTGGTGTAAGAAATAACTCATGCTTTTTAATTAGTAATTTTC
* * * * * *
54057 TTCCTTTTTTTGTTCTCCCTCTTTAATTTAGTTTCCTTTTTTTTAATGTTTTCAACATTTTCT-
259 TTTCTTTTTTTGTTCTCCCTCTTCAATCTACTTT-CTTTTTTTTTATGCTTTCAACATTTT-TA
* *
54120 -ACTCACCTTTATAGAATATAAGACATGTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTGAT
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTAAT
* * * * * * *
54184 ACAAAACGACATATCGAGTTTATCAATTTGTGAGAATCTACTAATCTGTAAAGCAGTCTATCATA
66 ACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTGTCATA
* * *
54249 TTTAAAATGAATGTATGGACCGTTTCAAATGTAAAAAAATTT-ATTCTTTCTTACTTTCATTGAA
131 TTTAAAATGAATGTATGAACCGTTTCAAATGTTAAAAAATTTGATTCTTTCTGACTTTCATTGAA
** * * * *
54313 TTTCACTGTGAAACTATGAAACTTATATAATAAATAACTCATGCTTTTGAATTAGTAATTTTGTT
196 TTTCACTGTGAAACTATGAAACTGGTGTAAGAAATAACTCATGCTTTTTAATTAGTAATTTTCTT
* * * *
54378 CCCTTTTTTTGTTCTCCCTATTCAATCTACTTTCTTTTTCTTCTTTTTTTAATGTTTTCGACATT
261 -TCTTTTTTTGTTCTCCCTCTTCAATCTA----C--TTTCTT-TTTTTTT-ATGCTTTCAACATT
54443 TTT-
317 TTTA
* * * * *
54446 AACTCAGCTTTATAGAGTATAAGACATTTTTGCACTCTTTTTTATTTTTCTCACCAAACTTTGAT
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTAAT
* * * * * *
54511 ACAAAACAACACATCAAGTTTGTCTATTTGTGAGAATCTGCCTATCTGTAAAGCAGTTTTTAATA
66 ACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTGTCATA
* * * *
54576 TTTAAAATTAATGCT-TGAACCGTTTCAAACGTTAAAAAATTTTGATTCTTTCGGGCTTTCATTA
131 TTTAAAATGAATG-TATGAACCGTTTCAAATGTTAAAAAA-TTTGATTCTTTCTGACTTTCATT-
* * *
54640 GAA-GTCAC--TG------TGAAACTGGTGTAA-AACATAACTCATG-TTTTTGAATTAGCAGTT
193 GAATTTCACTGTGAAACTATGAAACTGGTGTAAGAA-ATAACTCATGCTTTTT-AATTAGTAATT
* * * * *
54694 TTCGTCCTTTTTTTTGTTCTCCCTATTCAATCTACTTTCTTTCTTTTTTTTTGTGCTTTCAAAAT
256 TTCTTTC-TTTTTTTGTTCTCCCTCTTCAATCTA----CTTTCTTTTTTTTTATGCTTTCAACAT
*
54759 TTTCA
316 TTTTA
* * * * * *
54764 AATTCACCTTTATAGAATACAACACCTCTTTGCACTCCTTTTTATTTTTCTCCCCAAACTCTAAT
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTAAT
* * *
54829 ACAAAACGACACATCAAGTTTGTCGATTTGTGAGAATCTGCCTATCTGTAAAGCAGTTTGTCGTA
66 ACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTGTCATA
* * *
54894 TTAAAAATGAAT-TCATGAACCGTTTCAAACGTTAAAAATTTTGATTCTTTCTGA----C-----
131 TTTAAAATGAATGT-ATGAACCGTTTCAAATGTTAAAAAATTTGATTCTTTCTGACTTTCATTGA
* * *
54949 -TTTCACTGTGAAACTATGGAACTGGTGTAAGAAATAACTCATGCTTTTGAATTGGTAATTTTCT
195 ATTTCACTGTGAAACTATGAAACTGGTGTAAGAAATAACTCATGCTTTTTAATTAGTAATTTTCT
* * ** * **
55013 TCCCCTTTTTTGTTCTCCAACCTCAATCTACTTTCCGTTTTTTTCATTTTATATTTTCAACATTT
260 T-TCTTTTTTTGTTCTCCCTCTTCAATCTACTTT-C---TTTTT--TTTTATGCTTTCAACATTT
*
55078 TTT
318 TTA
* * * *
55081 AACTCGCCTTTATAGAATAAAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTTTGAT
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTAAT
* * * * * * * * *
55146 AGAAAATGACATATCGAGTTTGTCGATTTGTGAGAATCTGCTAATCTATAAAGCAATTTATCGTG
66 ACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTGTCATA
** *** * *
55211 TTTAAAATGAATGTATGAACCGTTT-AAATGCAAAAAAAAAAAGTTTCTTTCTTACTTTCATTGA
131 TTTAAAATGAATGTATGAACCGTTTCAAATG-TTAAAAAATTTGATTCTTTCTGACTTTCATTGA
* * *
55275 ATTTCACTGTGAAA-T-T---AC----G--A-AACTTA-TCATGCTTTTGAATTAGTAATTTTCT
195 ATTTCACTGTGAAACTATGAAACTGGTGTAAGAAATAACTCATGCTTTTTAATTAGTAATTTTCT
* * * * *
55327 TCCATTTTTTCTTCTCCCTCTTCAATCTA-TATTC-TTTTTTTAATGTTTTCAACA-TTTTA
260 TTCTTTTTTTGTTCTCCCTCTTCAATCTACT-TTCTTTTTTTTTATGCTTTCAACATTTTTA
* *
55386 AACTCACCTTTATAGAATATAAGTCATTTTTGCACTCCTTTTCATTTTTCTCACCAAACTCTGAA
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTCT-AA
* * * * **
55451 -ACAAAACGACATATCGAGTTTCTCGATTTGTGAGAATCTGTCGATCTGTAAAGCAGTTTGTTGT
65 TACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTGTCAT
* * *
55515 ATTCAAAATGAATGCATGAACAGTTTC-AATCG-TAAAAAATTGTGATTCTTTCTGACTTTCATT
130 ATTTAAAATGAATGTATGAACCGTTTCAAAT-GTTAAAAAATT-TGATTCTTTCTGACTTTCATT
* * *
55578 GAATTTCAC--TG------TGAAACTGGTGTAAGACATAACTCATG-TTTTTCAAAGTAGTAGTT
193 GAATTTCACTGTGAAACTATGAAACTGGTGTAAGAAATAACTCATGCTTTTT--AATTAGTAATT
* * * * *
55634 TACTTCCTTTTTTTGTTCTCCCTATTCAA---A------TTTTTTTTGTGC--TCAACATTTTCA
256 TTCTTTCTTTTTTTGTTCTCCCTCTTCAATCTACTTTCTTTTTTTTTATGCTTTCAACATTTTTA
* * * * * * ** **
55688 AACTCACCGTTATAGAGTAGAACACATCTCTGCACTCCTTTTTATTTTTCTCAATAAACTCCGAT
1 AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTAAT
* * * * *
55753 ACAAAACTACACATCGAGTTTGTTGATTTGTGAGAATCT---AATCTGTAAAGGAATTTGTCATG
66 ACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTGTCATA
* * * * *
55815 TTTAAAATGAATGTATGAACCGTTTCAAATGGTAAAAAAATTGATTCTTTTTTACTTTCACTGAA
131 TTTAAAATGAATGTATGAACCGTTTCAAATGTTAAAAAATTTGATTCTTTCTGACTTTCATTGAA
* * * * *
55880 TTTCACTGTGAAACAATGAAATTGGTGTAATAATTAACTCGTGCTTTTT
196 TTTCACTGTGAAACTATGAAACTGGTGTAAGAAATAACTCATGCTTTTT
55929 GATTTTTTGA
Statistics
Matches: 5627, Mismatches: 930, Indels: 687
0.78 0.13 0.09
Matches are distributed among these distances:
298 20 0.00
299 70 0.01
300 32 0.01
301 52 0.01
302 135 0.02
303 40 0.01
304 21 0.00
305 193 0.03
306 32 0.01
307 149 0.03
308 91 0.02
309 198 0.04
310 248 0.04
311 197 0.04
312 87 0.02
313 278 0.05
314 170 0.03
315 159 0.03
316 275 0.05
317 332 0.06
318 618 0.11
319 230 0.04
320 239 0.04
321 161 0.03
322 194 0.03
323 46 0.01
324 186 0.03
325 136 0.02
326 28 0.00
327 214 0.04
328 148 0.03
329 369 0.07
330 18 0.00
331 20 0.00
332 163 0.03
333 49 0.01
334 24 0.00
335 4 0.00
336 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.42
Consensus pattern (320 bp):
AACTCACCTTTATAGAATATAAGACATTTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTAAT
ACAAAACGACACATCGAGTTTGTCGATTTGTGAGAATCTGCCAATCTGTAAAGCAGTTTGTCATA
TTTAAAATGAATGTATGAACCGTTTCAAATGTTAAAAAATTTGATTCTTTCTGACTTTCATTGAA
TTTCACTGTGAAACTATGAAACTGGTGTAAGAAATAACTCATGCTTTTTAATTAGTAATTTTCTT
TCTTTTTTTGTTCTCCCTCTTCAATCTACTTTCTTTTTTTTTATGCTTTCAACATTTTTA
Found at i:56841 original size:311 final size:303
Alignment explanation
Indices: 56038--56846 Score: 838
Period size: 305 Copynumber: 2.6 Consensus size: 303
56028 GTTTAATGTC
* * * * * * *
56038 TTCAAAATTTTTAACTCAGCTTTATAGAATAAAACACATTTTTGCACTCATTTTTATTTTTCTCA
1 TTCAACATTTTCAACTCACCTTTATAGAATAGAACACA-TTTTGCACCCCTTTTTAATTTTCTCA
* * * * ** * *
56103 ACAAACTCTGATATAAAATGGCACATCGAGTTTGTCGATTTGTGATAATTTGTCGATATGTAAAG
65 ACAAACTTTGATACAAAATGACACATCGAGTTTGTCGATTTGTGAGAAACTATCGATATGTAAAA
* * *
56168 CAGTTTGTCGTGTTTAAAATGAATGTATGAACCGTTTCGAATGTTATAAATTTTTATTCTTTCTG
130 CAGTTTGTCGTGTTTAAAATGAATGTATGAACCGTTTCAAATGTTAAAAATTTTGATTCTTT-TG
* *
56233 ACTTTCATTGAATTTCACTATGAAACTAATGTAAAAAATAACTCATGATTTTGAATTAGTAATTT
194 ACTTTCATGGAATTTCACTATGAAACCAATGTAAAAAATAACTCATGATTTTGAATTAGTAATTT
* *
56298 TTTCCCTTTTTTGTTCTCCCTCTTTTCTTTTATTTCTTTTTAAGCT
259 TTTCCCTTTTTTGTTCT-CCTCTTTTCATCTATTTCTTTTTAAGCT
* * *
56344 TTCAACATTTTCAACTCACCTTTATAGAATAGAACATAATTTTGCA-CTCTTTTTTATTCTT-TC
1 TTCAACATTTTCAACTCACCTTTATAGAATAGAACA-CATTTTGCACCCCTTTTTAATT-TTCTC
* ** * * * *
56407 AACATACTTTGATACAATTTGACACATCGATTTTGTCAATTTGTGAGAAACTATCAATCTGTAAA
64 AACAAACTTTGATACAAAATGACACATCGAGTTTGTCGATTTGTGAGAAACTATCGATATGTAAA
* * * * *
56472 GA-TGTTTGTTGT-TTTCAAAATGAATGTATGAACCGTTTCTAATGTTAAGAACTTTGATTCTTT
129 -ACAGTTTGTCGTGTTT-AAAATGAATGTATGAACCGTTTCAAATGTTAAAAATTTTGATTCTTT
* ** * * *
56535 TAGACTTTCATGGAATTTCACTGTGAAACCGGTGTAAGAAATAACTCATGCTTTTGAATTTGTAA
192 T-GACTTTCATGGAATTTCACTATGAAACCAATGTAAAAAATAACTCATGATTTTGAATTAGTAA
* *
56600 TTTTCTTCTCTTTTTTTGTTCT-CTGTTTTCAATCTATTTTCGTTTATTAATG-T
256 TTTT-TTC-CCTTTTTTGTTCTCCTCTTTTC-ATCTA-TTTC-TTT-TTAA-GCT
* * *** * *
56653 TTACAGCATTTTTAACTCTTTTTTTATAGAATAGAACACATTTCGAACCCCTTTTTAATTTTCTC
1 TT-CAACATTTTCAACTC-ACCTTTATAGAATAGAACACATTTTGCACCCCTTTTTAATTTTCTC
** * ** * ** * *
56718 AACAAACTTTGATACAAAACAACATATTTAGTTTGTTGATTTGTGAGAGGCTATTGATATGCAAA
64 AACAAACTTTGATACAAAATGACACATCGAGTTTGTCGATTTGTGAGAAACTATCGATATGTAAA
* * *
56783 ACAATTTGTCGTGTTTAAAATGAATGTGTGAACCGTTTCAAATATTAAAAATTTTGATTCTTTT
129 ACAGTTTGTCGTGTTTAAAATGAATGTATGAACCGTTTCAAATGTTAAAAATTTTGATTCTTTT
56847 TTAGTTTGAC
Statistics
Matches: 406, Mismatches: 79, Indels: 31
0.79 0.15 0.06
Matches are distributed among these distances:
304 4 0.01
305 176 0.43
306 47 0.12
307 17 0.04
308 3 0.01
309 7 0.02
310 23 0.06
311 126 0.31
312 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (303 bp):
TTCAACATTTTCAACTCACCTTTATAGAATAGAACACATTTTGCACCCCTTTTTAATTTTCTCAA
CAAACTTTGATACAAAATGACACATCGAGTTTGTCGATTTGTGAGAAACTATCGATATGTAAAAC
AGTTTGTCGTGTTTAAAATGAATGTATGAACCGTTTCAAATGTTAAAAATTTTGATTCTTTTGAC
TTTCATGGAATTTCACTATGAAACCAATGTAAAAAATAACTCATGATTTTGAATTAGTAATTTTT
TCCCTTTTTTGTTCTCCTCTTTTCATCTATTTCTTTTTAAGCT
Found at i:56959 original size:60 final size:60
Alignment explanation
Indices: 56865--57030 Score: 221
Period size: 60 Copynumber: 2.8 Consensus size: 60
56855 ACTAATTGCT
* * * *
56865 CAAATAAGGGCCTAACTTTTTGCCAAAATGCTCAAATAAGGGCCTGGTCT-TTTATTCTGGC
1 CAAATAAGAGCCTAA-TATTTGCCAAAATGCTCAAATAAGGGCCTGATCTATTAATT-TGGC
* *
56926 CAAATAAGAGCCTAATGTTTGCCAAAATGCTCAAATAAGAG-CTCGATCTATTAATTTGGC
1 CAAATAAGAGCCTAATATTTGCCAAAATGCTCAAATAAGGGCCT-GATCTATTAATTTGGC
*
56986 CAAATAAGA-CCTAACATTTGCCAAAATGCTCAAATAAGGGCCTGA
1 CAAATAAGAGCCTAATATTTGCCAAAATGCTCAAATAAGGGCCTGA
57031 CATCGAAAAT
Statistics
Matches: 94, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
59 32 0.34
60 43 0.46
61 19 0.20
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.27
Consensus pattern (60 bp):
CAAATAAGAGCCTAATATTTGCCAAAATGCTCAAATAAGGGCCTGATCTATTAATTTGGC
Found at i:59710 original size:2 final size:2
Alignment explanation
Indices: 59703--59739 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
59693 TTGTGAACCA
59703 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59740 AGATCAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.