Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020832.1 Corchorus olitorius cultivar O-4 contig20865, 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: 54230
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Found at i:25084 original size:15 final size:15
Alignment explanation
Indices: 25064--25094 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
25054 TTTAAGTTCT
25064 AAATCTAAAAGCTTG
1 AAATCTAAAAGCTTG
25079 AAATCTAAAAGCTTG
1 AAATCTAAAAGCTTG
25094 A
1 A
25095 GCTCGTCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (15 bp):
AAATCTAAAAGCTTG
Found at i:25192 original size:63 final size:63
Alignment explanation
Indices: 25093--25319 Score: 373
Period size: 63 Copynumber: 3.6 Consensus size: 63
25083 CTAAAAGCTT
* * *
25093 GAGCTCGTCCAAGAATAAGTCGACAGCTGAATCAGTTTTGCATGTTCTTCGAGAATCAAGACC
1 GAGCTCGTCCAAGGATAAATCCACAGCTGAATCAGTTTTGCATGTTCTTCGAGAATCAAGACC
* *
25156 GAGCTCGTCCAAGGATAAGTCGACAGCTGAATCAGTTTTGCATGTTCTTCGAGAATCAAGACC
1 GAGCTCGTCCAAGGATAAATCCACAGCTGAATCAGTTTTGCATGTTCTTCGAGAATCAAGACC
* * * *
25219 GAGCTCGTCCAAGGTTAAATCCACAGCTGAATCACTTTTGGATGTTTTTCGAGAATCAAGACC
1 GAGCTCGTCCAAGGATAAATCCACAGCTGAATCAGTTTTGCATGTTCTTCGAGAATCAAGACC
25282 GAGCTCGTCCAAGGATAAATCCACAGCTGAATCAGTTT
1 GAGCTCGTCCAAGGATAAATCCACAGCTGAATCAGTTT
25320 CAAGACCGAG
Statistics
Matches: 155, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 155 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (63 bp):
GAGCTCGTCCAAGGATAAATCCACAGCTGAATCAGTTTTGCATGTTCTTCGAGAATCAAGACC
Found at i:25338 original size:45 final size:45
Alignment explanation
Indices: 25274--25364 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
25264 TTTTCGAGAA
25274 TCAAGACCGAGCTCGTCCAAGGATAAATCCACAGCTGAATCAGTT
1 TCAAGACCGAGCTCGTCCAAGGATAAATCCACAGCTGAATCAGTT
25319 TCAAGACCGAGCTCGTCCAAGGATAAATCCACAGCTGAATCAGTT
1 TCAAGACCGAGCTCGTCCAAGGATAAATCCACAGCTGAATCAGTT
25364 T
1 T
25365 TGGATGTTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (45 bp):
TCAAGACCGAGCTCGTCCAAGGATAAATCCACAGCTGAATCAGTT
Found at i:25406 original size:30 final size:30
Alignment explanation
Indices: 25370--25429 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
25360 AGTTTTGGAT
25370 GTTCTTCGAGACTCAAGAACGAGCTCGTCC
1 GTTCTTCGAGACTCAAGAACGAGCTCGTCC
25400 GTTCTTCGAGACTCAAGAACGAGCTCGTCC
1 GTTCTTCGAGACTCAAGAACGAGCTCGTCC
25430 AAGCATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.23
Consensus pattern (30 bp):
GTTCTTCGAGACTCAAGAACGAGCTCGTCC
Found at i:25506 original size:57 final size:57
Alignment explanation
Indices: 25418--25530 Score: 199
Period size: 57 Copynumber: 2.0 Consensus size: 57
25408 AGACTCAAGA
*
25418 ACGAGCTCGTCCAAGCATAAATCCACAGCTGAATCAGTTTTGGATGTTCTTCGAGAC
1 ACGAGCTCGTCCAAGCATAAATCCACAGCTGAATCAGTTTTGGATGTTCTCCGAGAC
* *
25475 ACGAGCTTGTCCAAGGATAAATCCACAGCTGAATCAGTTTTGGATGTTCTCCGAGA
1 ACGAGCTCGTCCAAGCATAAATCCACAGCTGAATCAGTTTTGGATGTTCTCCGAGA
25531 ATCAAGAACA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (57 bp):
ACGAGCTCGTCCAAGCATAAATCCACAGCTGAATCAGTTTTGGATGTTCTCCGAGAC
Found at i:29118 original size:32 final size:32
Alignment explanation
Indices: 29077--29139 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
29067 TTGCCCCTTC
29077 AACTTGGGGCCCAAAATACAATTTCCGGAAAA
1 AACTTGGGGCCCAAAATACAATTTCCGGAAAA
*
29109 AACTTGGGGCCCAAAATATAATTTCCGGAAA
1 AACTTGGGGCCCAAAATACAATTTCCGGAAA
29140 TCATCGAGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (32 bp):
AACTTGGGGCCCAAAATACAATTTCCGGAAAA
Found at i:39344 original size:5 final size:5
Alignment explanation
Indices: 39334--39367 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
39324 ATTAATTTAT
*
39334 AGAAA AAAAA AG-AA AGAAA AGAAA AGAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
39368 GAGGGGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:39428 original size:13 final size:13
Alignment explanation
Indices: 39412--39438 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39402 AAAACTAAAA
39412 AAGAAAAAGGAAG
1 AAGAAAAAGGAAG
39425 AAGAAAAAGGAAG
1 AAGAAAAAGGAAG
39438 A
1 A
39439 GGGAGGTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGGAAG
Found at i:49724 original size:26 final size:26
Alignment explanation
Indices: 49675--49724 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
49665 TGCCAAAAAA
*
49675 AAGTATGGTATATATTCAACATCTGT
1 AAGTATGGTATATATTCAAAATCTGT
*
49701 AAGTATGGTATATATTTAAAATCT
1 AAGTATGGTATATATTCAAAATCT
49725 AATAAATAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (26 bp):
AAGTATGGTATATATTCAAAATCTGT
Found at i:51139 original size:321 final size:320
Alignment explanation
Indices: 50288--52886 Score: 3445
Period size: 323 Copynumber: 8.0 Consensus size: 320
50278 AAGCCGCAAG
* * * * *
50288 AACGATATTAAAAGTGTGAAAAGCCCATCAATGTTTTTGGCGTTGAATTATATATTTTCTCTGAG
1 AACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAG
* * * * *
50353 TATTGTGGTAAAAAAATGAGAAAACATTTTTCGGGTCAGTTTTTAGCCGAAAATTGTGTACTAAT
66 TATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAG-CG-AAATCGTGTACTAA-
* * *
50418 CATATCACGGTTTTTAGCTAAAAACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGTC
128 C-CATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGC
* * *
50483 GCAAAGACTCCTTAAAATATCTATATTCATCGAACCAAATCTCAACCATATTGGATATAAGGATT
192 GCAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATCTCAGCCATATTGGATATAAGGATT
* * *
50548 TGGTTTTACGAGCATCTCAATCTTGTTTTGATTTAATTAGAAATTAATTCAGAAAATAAATGGAA
257 TGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTC-GGAAA-AAATGGAA
50613 A
320 A
* * *
50614 AACGATATTAGAAGCTTGAAAAACCCGCCAATCTTTTTGGCGTTGAATTATATA-TTTTTCTGAG
1 AACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAG
* * * * * *
50678 TATTGTGGCAACAAATTCAGAAAATACTTTTCGGGTCAGTTTTTTGCCGAAATTGTGTAGTAACC
66 TATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAG-CGAAATCGTGTACTAACC
* * ** *
50743 ATCACGGTTTTTGGCTAAAAACGAGTTCCGGAG-CCCAAGCTCAATTTTGCATGATTTTTTCCGA
130 ATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGA-CTCAATTTTGCATGATTTTTGGCGC
* *
50807 AAAGACTCCTTGAAATATCTATATTAATCGAAGCAAATCTCAGCAATATTGGATATAAGGATTTG
194 AAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATCTCAGCCATATTGGATATAAGGATTTG
* * * * * * *
50872 TTTTTTCAAGCATGTCAATCTTGTTTCGATTTAGTTATAAATTAGTTAGG-AAAAATGGAAA
259 TTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGGAAA
* * ***
50933 AATGATATTAGAAACGTGAAAAGTTTGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCT-AT
1 AACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGA-
* * ** * * *
50997 GTATTGTGGCAAAAAATTGATAAAAAAAATTACCGGGCCAGATTTTAGTCGAAATCGTGTTCTAA
65 GTATTGTGGCAAAAAATTGA-GAAAAAACTTTTCGGGTCAGTTTTTAG-CGAAATCGTGTACTAA
* * * * *
51062 CCATCACGGTTTTTTGCTAAAAACGTGTTCCGGAGGCCCGGCTCAATTTTGCACGATTTTTGGCG
128 CCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGCG
* * * * *
51127 AAAAAACTCCTTGAAATATCTATATTTATCGAA-CGAAATGTCAGCCACATTGGATATAAGGATT
193 CAAAGACTCCTTGAAATATCTATATTCATCGAAGC-AAATCTCAGCCATATTGGATATAAGGATT
*
51191 TGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAA
257 TGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGG--AAAAAATGGAA
51256 A
320 A
51257 AACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATAATTTTTTTC
1 AACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAA-T-TATAT-A-TTTTTTC
* * ** * *
51322 TGAGTATTGTGGCAAAAAATTGAGAAAATACTTTTCGGGTAAGTTTTCT-GAAAAATAGTGTAAT
62 TGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTT-TAGCGAAATCGTGTACT
* * *
51386 AACCATCACGGTTTTTGGCTAAAAATGCGTTCCGTAGCCCAC-ACTCAATTTTGCATTATTTTTG
126 AACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCC-CGACTCAATTTTGCATGATTTTTG
* * * * * *
51450 TCACAAAGACTGCTTGAAATATCTATATTCATCAAAACAAATCTCAGCAATATTGGATATAACTC
190 GCGCAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATCTCAGCCATATTGG-----A-T-
* *
51515 ATATAGGGATTTGTTTTTCCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGTAA
248 ATA-A-GGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAA
*
51580 AAAATGGGAA
311 AAAATGGAAA
* * * * * *
51590 AACGATATTAAAAGTGTGAAAAGCCCATCAATGTTTTAGGCGTTGAATTATATATTTTTTATGAG
1 AACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAG
* *
51655 TATTGTGGCAAAAAATTGAGAAAAAATTTTTCGGGTCAGTTTTTAGTCGAACTCGTGTACTAACC
66 TATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAG-CGAAATCGTGTACTAACC
*
51720 ATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCAACTCAATTTTGCATGATTTTTGGCGCA
130 ATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCA
* * * *
51785 AAGACTCCTTAAAATATCTAAATTTATTGAAGCAAATCTCAGCCATATTGGATATAAGGATTTGT
195 AAGACTCCTTGAAATATCTATATTCATCGAAGCAAATCTCAGCCATATTGGATATAAGGATTTGT
*
51850 TTTTACGAGTATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGGAAA
260 TTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGGAAA
* * * * *
51911 AACGATATTAGAAGTGTGAAAAGCCTGTTAATCTGTTTGGTGTTGAATTATATATTTTTTCTGAG
1 AACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAG
*
51976 TATTGTGGCAAAAAATTGAGAAAAAAGTTTTCGGGTCAGTTTTTAGCTGAAATCGTGTACTAACC
66 TATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGC-GAAATCGTGTACTAACC
* * * *
52041 ATCACGGTTTTTGGCTAAGAACGCGTTCCGGAGCCCCGGCCCAATTTTGCATGATTTTTGACGCA
130 ATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCA
*
52106 AAGACTCCTTGAAATATCTATATTCATCGAAGCAAATCTCAGCCATATTGGATATATGGATTTGT
195 AAGACTCCTTGAAATATCTATATTCATCGAAGCAAATCTCAGCCATATTGGATATAAGGATTTGT
* * * * * * **
52171 TTTTTCGAGCATCGCAATCTTATTTTGATTTAATTAGCAATTAATTCAGAAAAAAAATTAAAA
260 TTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTC-G-GAAAAAATGGAAA
* * *
52234 AACGATCTTAGAAGCGTGAAAAGCCCGCCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAG
1 AACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAG
* ** * * *
52299 TTTTGTGGCAAAAAATTGAGAAAAAAAATTTCGGGTCAATTTTTAGCTGAAATCGTGCACATTA-
66 TATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGC-GAAATCGTGTAC-TAAC
* * * *
52363 CATCACGGTTTTTGGATAAAAATGCGTTCCGGAGCCCCGACTCAATTTTACAAGATTTTTGGCGC
129 CATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGC
* *
52428 AAAGACACCTTGAAATATCTATATTCATCGAAGCAAATCTCTGCCATATTGGATATAAGGATTTG
194 AAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATCTCAGCCATATTGGATATAAGGATTTG
*
52493 TTTTTACGAGCATCTCAATCTTGTTTCGATTTTATTAGAAATTAATTCGGAAAAAAAATGGAAA
259 TTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGG--AAAAAATGGAAA
* ** *
52557 AACGATATTAGAAGTGTGAAAAGCTTGTCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAG
1 AACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAG
* * * **
52622 TATTATTGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTTGCTGAAATCGTGTACTAATA
66 TATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGC-GAAATCGTGTACTAACC
*
52687 ATCACGGTTTTTGGCTAAGAACGCGTTCCGGAGCCCC-AGCTCAATTTTGCATGATTTTTGGCGC
130 ATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGA-CTCAATTTTGCATGATTTTTGGCGC
52751 AAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATCTCAGCCATATTGGATATAAGGATTTG
194 AAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATCTCAGCCATATTGGATATAAGGATTTG
* * * * *
52816 TTTTTTCGAGCATCTAAATCTAGTTTCGGTTTAAGTA-AATATTAATTCGGAAAAAATGGAAA
259 TTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAA-ATTAATTCGGAAAAAATGGAAA
52878 AACGATATT
1 AACGATATT
52887 TAAGAAAAAA
Statistics
Matches: 1994, Mismatches: 241, Indels: 81
0.86 0.10 0.03
Matches are distributed among these distances:
319 56 0.03
320 29 0.01
321 556 0.28
322 163 0.08
323 572 0.29
324 69 0.03
325 53 0.03
326 159 0.08
327 20 0.01
328 30 0.02
329 53 0.03
330 115 0.06
331 6 0.00
332 2 0.00
333 56 0.03
334 1 0.00
335 54 0.03
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (320 bp):
AACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAG
TATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCGAAATCGTGTACTAACCA
TCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAA
AGACTCCTTGAAATATCTATATTCATCGAAGCAAATCTCAGCCATATTGGATATAAGGATTTGTT
TTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGGAAA
Found at i:52173 original size:977 final size:963
Alignment explanation
Indices: 50288--52886 Score: 3595
Period size: 977 Copynumber: 2.7 Consensus size: 963
50278 AAGCCGCAAG
* * * * *
50288 AACGATATTAAAAGTGTGAAAAGCCCATCAATGTTTTTGGCGTTGAATTATATATTTTCTCTGAG
1 AACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAG
* * * * * * * *
50353 TATTGTGGTAAAAAAATGAGAAAACATTTTTCGGGTCAGTTTTTAGCCGAAAATTGTGTACTAAT
66 TATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTAAG-TTTT--CTGAAAATAGTGTAATAA-
* * *
50418 CATATCACGGTTTTTAGCTAAAAACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGTC
127 C-CATCACGGTTTTTGGCTAAAAATGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGTC
* * *
50483 GCAAAGACTCCTTAAAATATCTATATTCATCGAACCAAATCTCAACCATATTGGATATAAGGATT
191 GCAAAGACTCCTTGAAATATCTATATTCATCGAAACAAATCTCAGCCATATTGGATATAAGGATT
* *
50548 TGGTTTTACGAGCATCTCAATCTTGTTTTGATTTAATTAGAAATTAATTCAGAAAATAAATGGAA
256 TGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAA-AAATGGAA
* *
50613 AAACGATATTAGAAGCT-TGAAAAACCCGCCAATCTTTTTGGCGTTGAATTATATA-TTTTTCTG
320 AAACGATATTAGAAG-TGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTG
* * * * *
50676 AGTATTGTGGCAACAAATTCAGAAAATACTTTTCGGGTCAGTTTTTTGCCGAAATTGTGTAGTAA
384 AGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTTG-CGAAATCGTGTACTAA
* **
50741 CCATCACGGTTTTTGGCTAAAAACGAGTTCCGGAG-CCCAAGCTCAATTTTGCATGATTTTTTCC
448 CCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCAA-CTCAATTTTGCATGATTTTTGGC
* *
50805 GAAAAGACTCCTTGAAATATCTATATTAATCGAAGCAAATCTCAGCAATATTGGATATAAGGATT
512 GCAAAGACTCCTTGAAATATCTATATTAATCGAAGCAAATCTCAGCCATATTGGATATAAGGATT
* * * * *
50870 TGTTTTTTCAAGCATGTCAATCTTGTTTCGATTTAGTTATAAATTAGTTAGG-AAAAATGGAAAA
577 TGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTA-AAATTAATTCGGAAAAAATGGAAAA
* ** *
50934 ATGATATTAGAAACGTGAAAAGTTTGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTATGT
641 ACGATATTAGAAACGTGAAAAGCCTGTCAATCTGTTTGGCGTTGAATTATATATTTTTTCTATGT
*
50999 ATTGTGGCAAAAAATTGATAAAAAAAATTACCGGGCCAGATTTTAGTCGAAATCGTGTTCTAACC
706 ATTGTGGCAAAAAATTGATAAAAAAAATTACCGGGCCAGATTTTAGTCGAAATCGTGTACTAACC
* * * * *
51064 ATCACGGTTTTTTGCTAAAAACGTGTTCCGGAGGCCCGGCTCAATTTTGCACGATTTTTGGCGAA
771 ATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCCCAATTTTGCACGATTTTTGACGAA
* *
51129 AAAACTCCTTGAAATATCTATATTTATCGAACGAAATGTCAGCCACATTGGATATAAGGATTTGT
836 AAAACTCCTTGAAATATCTATATTCATCGAACGAAATCTCAGCCACATTGGATATAAGGATTTGT
* * *
51194 TTTTACGAGCATCTG-AATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAA
901 TTTTACGAGCATC-GCAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAAAAATGAAAA
51257 AACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATAATTTTTTTC
1 AACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAA-T-TATAT-A-TTTTTTC
* *
51322 TGAGTATTGTGGCAAAAAATTGAGAAAATACTTTTCGGGTAAGTTTTCTGAAAAATAGTGTAATA
62 TGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTAAGTTTTCTG-AAAATAGTGTAATA
* *
51387 ACCATCACGGTTTTTGGCTAAAAATGCGTTCCGTAGCCCAC-ACTCAATTTTGCATTATTTTTGT
126 ACCATCACGGTTTTTGGCTAAAAATGCGTTCCGGAGCCC-CGACTCAATTTTGCATGATTTTTGT
* * * *
51451 CACAAAGACTGCTTGAAATATCTATATTCATCAAAACAAATCTCAGCAATATTGGATATAACTCA
190 CGCAAAGACTCCTTGAAATATCTATATTCATCGAAACAAATCTCAGCCATATTGG-----A-T-A
* *
51516 TATAGGGATTTGTTTTTCCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTC-GTAA
248 TA-A-GGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAA
* * * * *
51580 AAAATGGGAAAACGATATTAAAAGTGTGAAAAGCCCATCAATGTTTTAGGCGTTGAATTATATAT
311 AAAATGGAAAAACGATATTAGAAGTGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATAT
* * * *
51645 TTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAATTTTTCGGGTCAGTTTTTAGTCGAACTCG
376 TTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTTG-CGAAATCG
51710 TGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCAACTCAATTTTGCATGAT
440 TGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCAACTCAATTTTGCATGAT
* * * *
51775 TTTTGGCGCAAAGACTCCTTAAAATATCTAAATTTATTGAAGCAAATCTCAGCCATATTGGATAT
505 TTTTGGCGCAAAGACTCCTTGAAATATCTATATTAATCGAAGCAAATCTCAGCCATATTGGATAT
* *
51840 AAGGATTTGTTTTTACGAGTATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA
570 AAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTA-AAATTAATTCGGAAAAAA
** * *
51905 TGGAAAAACGATATTAGAAGTGTGAAAAGCCTGTTAATCTGTTTGGTGTTGAATTATATATTTTT
634 TGGAAAAACGATATTAGAAACGTGAAAAGCCTGTCAATCTGTTTGGCGTTGAATTATATATTTTT
* * ** * *
51970 TCTGA-GTATTGTGGCAAAAAATTGA-GAAAAAAGTTTTCGGGTCAGTTTTTAG-CTGAAATCGT
699 TCT-ATGTATTGTGGCAAAAAATTGATAAAAAAAATTACCGGGCCAGATTTTAGTC-GAAATCGT
* *
52032 GTACTAACCATCACGGTTTTTGGCTAAGAACGCGTTCCGGAGCCCCGGCCCAATTTTGCATGATT
762 GTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCCCAATTTTGCACGATT
* * *
52097 TTTGACGCAAAGACTCCTTGAAATATCTATATTCATCGAA-GCAAATCTCAGCCATATTGGATAT
827 TTTGACGAAAAAACTCCTTGAAATATCTATATTCATCGAACG-AAATCTCAGCCACATTGGATAT
* * * *
52161 ATGGATTTGTTTTTTCGAGCATCGCAATCTTATTTTGATTTAATTAGCAATTAATTCAGAAAAAA
891 AAGGATTTGTTTTTACGAGCATCGCAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAAA
*
52226 AATTAAAA
956 AATGAAAA
* * *
52234 AACGATCTTAGAAGCGTGAAAAGCCCGCCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAG
1 AACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAG
* * * * * *
52299 TTTTGTGGCAAAAAATTGAGAAAAAAAATTTCGGGTCAATTTTTAGCTG-AAATCGTGCACATTA
66 TATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGT-AAGTTTT--CTGAAAATAGTGTA-ATAA
* * * *
52363 -CATCACGGTTTTTGGATAAAAATGCGTTCCGGAGCCCCGACTCAATTTTACAAGATTTTTGGCG
127 CCATCACGGTTTTTGGCTAAAAATGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGTCG
* * *
52427 CAAAGACACCTTGAAATATCTATATTCATCGAAGCAAATCTCTGCCATATTGGATATAAGGATTT
192 CAAAGACTCCTTGAAATATCTATATTCATCGAAACAAATCTCAGCCATATTGGATATAAGGATTT
* *
52492 GTTTTTACGAGCATCTCAATCTTGTTTCGATTTTATTAGAAATTAATTCGGAAAAAAAATGGAAA
257 GTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAAAATGGAAA
** *
52557 AACGATATTAGAAGTGTGAAAAGCTTGTCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAG
321 AACGATATTAGAAGTGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAG
* * **
52622 TATTATTGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTTGCTGAAATCGTGTACTAATA
386 TATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTTGC-GAAATCGTGTACTAACC
* *
52687 ATCACGGTTTTTGGCTAAGAACGCGTTCCGGAGCCCCAGCTCAATTTTGCATGATTTTTGGCGCA
450 ATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCAACTCAATTTTGCATGATTTTTGGCGCA
*
52752 AAGACTCCTTGAAATATCTATATTCATCGAAGCAAATCTCAGCCATATTGGATATAAGGATTTGT
515 AAGACTCCTTGAAATATCTATATTAATCGAAGCAAATCTCAGCCATATTGGATATAAGGATTTGT
* * * *
52817 TTTTTCGAGCATCTAAATCTAGTTTCGGTTTAAGTAAATATTAATTCGGAAAAAATGGAAAAACG
580 TTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAAA-ATTAATTCGGAAAAAATGGAAAAACG
52882 ATATT
644 ATATT
52887 TAAGAAAAAA
Statistics
Matches: 1445, Mismatches: 153, Indels: 66
0.87 0.09 0.04
Matches are distributed among these distances:
965 53 0.04
966 5 0.00
967 312 0.22
968 1 0.00
969 147 0.10
970 5 0.00
971 18 0.01
972 5 0.00
973 88 0.06
974 118 0.08
975 10 0.01
976 64 0.04
977 476 0.33
978 142 0.10
979 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (963 bp):
AACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAG
TATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTAAGTTTTCTGAAAATAGTGTAATAACCAT
CACGGTTTTTGGCTAAAAATGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGTCGCAAA
GACTCCTTGAAATATCTATATTCATCGAAACAAATCTCAGCCATATTGGATATAAGGATTTGTTT
TTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATGGAAAAACGA
TATTAGAAGTGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTG
TGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTTGCGAAATCGTGTACTAACCATCACG
GTTTTTGGCTAAAAACGCGTTCCGGAGCCCCAACTCAATTTTGCATGATTTTTGGCGCAAAGACT
CCTTGAAATATCTATATTAATCGAAGCAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTTC
GAGCATCTCAATCTTGTTTCGATTTAATTAAAATTAATTCGGAAAAAATGGAAAAACGATATTAG
AAACGTGAAAAGCCTGTCAATCTGTTTGGCGTTGAATTATATATTTTTTCTATGTATTGTGGCAA
AAAATTGATAAAAAAAATTACCGGGCCAGATTTTAGTCGAAATCGTGTACTAACCATCACGGTTT
TTGGCTAAAAACGCGTTCCGGAGCCCCGGCCCAATTTTGCACGATTTTTGACGAAAAAACTCCTT
GAAATATCTATATTCATCGAACGAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGC
ATCGCAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAAAAATGAAAA
Found at i:53651 original size:321 final size:323
Alignment explanation
Indices: 52891--53767 Score: 1194
Period size: 321 Copynumber: 2.7 Consensus size: 323
52881 GATATTTAAG
*
52891 AAAAAACTTTTCGGGT-AGGTTTTTAGCAGAAACA-CGTGTACTAATCATCACGGTTTTTGGCTA
1 AAAAAACTTTTCGGGTCA-GTTTTTAGCAGAAA-ATCGTGTACTAATCATCACGGGTTTTGGCTA
* *
52954 AAAACGCGTTCCGGAGACTC-AGCTCAATTTTGTATGATTTTTGGCGCATAGACTCCTTAAAATA
64 AAAACGCGTTCCGGAGACCCGA-CTCAATTTTGTATGATTTTTGGCGCAAAGACTCCTTAAAATA
* * *
53018 TCTAAATTTATCGTATCAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTACGAGAATCTCA
128 TCTAAATTTATCGAACCAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTCA
* * * *
53083 ATCTTG-TTTGATTTAAGTAGAAATTATTTCATTAAAAAAAATGAAAAAATGATATTAGAAGCGT
193 ATCTTGTTTTGATTTAAGTAGAAATTAATTC---AGAAAAAATGAAAAAATGATATTAGAAGAGG
*
53147 GAAAAGCCCGCCAATGTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT
255 GAAAAGCCCGCCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT
53212 GAGA
320 GAGA
* * * *
53216 AAAAAA-TTTTCGGATCATTTTTTAACCG-AAATCGTGTACTAATCATCACGGGTTTTGGCTAAA
1 AAAAAACTTTTCGGGTCAGTTTTTAGCAGAAAATCGTGTACTAATCATCACGGGTTTTGGCTAAA
* * * * *
53279 AACGCGTTCCGAAGACCCGACTTAATTTTGTATGATTTTTGGAGAAAAGACTCCTTTAAATATCT
66 AACGCGTTCCGGAGACCCGACTCAATTTTGTATGATTTTTGGCGCAAAGACTCCTTAAAATATCT
* * *
53344 ATATTCATCGAACCAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTACAAGCATCTCAATC
131 AAATTTATCGAACCAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATC
* * * * ** * *
53409 TTGTTTTGATTTAATTAGCAATTAGTTCAGAAAAAATTAAAAGCT-ATCTTAGAAGAGGGAAAAT
196 TTGTTTTGATTTAAGTAGAAATTAATTCAGAAAAAATGAAAAAATGATATTAGAAGAGGGAAAAG
* *
53473 TCCGCCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAATTGAGA
261 CCCGCCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGA
* * * * *
53535 AAAAAACCTCTCGGGTCAGTTTTTAGCTGAAAATAGTGTACTAACCATCACGGGTTTTGGCTAAA
1 AAAAAACTTTTCGGGTCAGTTTTTAGCAGAAAATCGTGTACTAATCATCACGGGTTTTGGCTAAA
* * * *
53600 AACGCTTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTACTTAAAATATCT
66 AACGCGTTCCGGAGACCCGACTCAATTTTGTATGATTTTTGGCGCAAAGACTCCTTAAAATATCT
* * * * *
53665 AAATTTATTGAAGCAAATCTCAACCATATTGGATATAAGGATTTGTTTTTTCGAGCATCTTAATC
131 AAATTTATCGAACCAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATC
* * *
53730 TTGTTTCGATTTAAGTAAAAATTAATTCGGAAAAAATG
196 TTGTTTTGATTTAAGTAGAAATTAATTCAGAAAAAATG
53768 GAAACACGAT
Statistics
Matches: 482, Mismatches: 64, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
319 17 0.04
320 79 0.16
321 190 0.39
322 1 0.00
323 150 0.31
324 38 0.08
325 7 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (323 bp):
AAAAAACTTTTCGGGTCAGTTTTTAGCAGAAAATCGTGTACTAATCATCACGGGTTTTGGCTAAA
AACGCGTTCCGGAGACCCGACTCAATTTTGTATGATTTTTGGCGCAAAGACTCCTTAAAATATCT
AAATTTATCGAACCAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATC
TTGTTTTGATTTAAGTAGAAATTAATTCAGAAAAAATGAAAAAATGATATTAGAAGAGGGAAAAG
CCCGCCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGA
Found at i:53895 original size:894 final size:891
Alignment explanation
Indices: 51994--54230 Score: 3245
Period size: 896 Copynumber: 2.5 Consensus size: 891
51984 CAAAAAATTG
* * * *
51994 AGAAAAAAGTTTTCGGGTCA-GTTTTTAGCTGAAA-TCGTGTACTAACCATCACGGTTTTTGGCT
1 AGAAAAAACTTTTCGGGT-AGGTTTTTAGCAGAAACACGTGTACTAATCATCACGGTTTTTGGCT
* * * *
52057 AAGAACGCGTTCCGGAGCCCCGGCCCAATTTTGCATGATTTTTGACGCAAAGACTCCTTGAAATA
65 AAAAACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATA
* * *
52122 TCTATATTCATCGAAGCAAATCTCAGCCATATTGGATATATGGATTTGTTTTTTCGAGCATCGCA
130 TCTATATTCATCGAAGCAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTCA
* * * *
52187 ATCTTATTTTGATTTAATTAGCAATTAATTCAGAAAAAAAATTAAAAAACGATCTTAGAAGCGTG
195 ATCTT-GTTTGATTTAATTAGAAATTAATTCA-AAAAAAAATGAAAAAACGATATTAGAAGCGTG
*
52252 AAAAGCCCGCCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTTTTGTGGCAAAAAATTG
258 AAAAGCCCGCCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTG
* * * * *
52317 AGAAAAAAAATTTCGGGTCAATTTTTAGCTGAAATCGTGCAC-ATTACATCACGGTTTTTGGATA
323 AGAAAAAAATTTTCGGATCAATTTTTAGCCGAAATCGTGTACTAAT-CATCACGGTTTTTGGATA
* * ** * * * *
52381 AAAATGCGTTCCGGAGCCCCGACTCAATTTTACAAGATTTTTGGCGCAAAGACACCTTGAAATAT
387 AAAA-GCGTTCCGGAGACCCGACTTAATTTTGTATGATTTTTGGAGAAAAGACTCCTTGAAATAT
* * *
52446 CTATATTCATCGAAGCAAATCTCTGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTCAA
451 CTATATTCATCGAACCAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTACAAGCATCTCAA
* * *
52511 TCTTGTTTCGATTTTATTAGAAATTAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGTGTGA
516 TCTTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAAAATGGAAAAACGATATTAGAAGAGGGA
* *
52576 AAAGCTTGTCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTATTGCAAAAAATTGA
580 AAA-CTTGCCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTATGGCAAAAAATTGA
* * * * * * *
52641 GAAAAAACTTTTCGGGTCAGTTTTTTGCTGAAATCGTGTACTAATAATCACGGTTTTTGGCTAAG
644 GAAAAAACCTCTCGGGTCAGTTTTTAGCTGAAATAGTGTACTAACAATCACGGGTTTTGGCTAAA
* *
52706 AACGCGTTCCGGAGCCCCAGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCT
709 AACGCGTTCCGGAGCCCCAGCTCAATTTTGCATGATTTTTGGCGCAAAGACTACTTAAAATATCT
* *
52771 ATATTCATCGAAGCAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTTCGAGCATCTAAATC
774 AAATTCATCGAAGCAAATCTCAACCATATTGGATATAAGGATTTGTTTTTTCGAGCATCTAAATC
* *
52836 TAGTTTCGGTTTAAGTAAATATTAATTCGGAAAAAATGGAAAAACGATATTTA
839 TAGTTTCGATTTAAGTAAAAATTAATTCGGAAAAAATGGAAAAACGATATTTA
52889 AGAAAAAACTTTTCGGGTAGGTTTTTAGCAGAAACACGTGTACTAATCATCACGGTTTTTGGCTA
1 AGAAAAAACTTTTCGGGTAGGTTTTTAGCAGAAACACGTGTACTAATCATCACGGTTTTTGGCTA
* * * * *
52954 AAAACGCGTTCCGGAGACTC-AGCTCAATTTTGTATGATTTTTGGCGCATAGACTCCTTAAAATA
66 AAAACGCGTTCCGGAGCCCCGA-CTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATA
* * * * *
53018 TCTAAATTTATCGTATCAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTACGAGAATCTCA
130 TCTATATTCATCGAAGCAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTCA
* * *
53083 ATCTTGTTTGATTTAAGTAGAAATTATTTCATTAAAAAAAATGAAAAAATGATATTAGAAGCGTG
195 ATCTTGTTTGATTTAATTAGAAATTAATTCA--AAAAAAAATGAAAAAACGATATTAGAAGCGTG
* *
53148 AAAAGCCCGCCAATGTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTG
258 AAAAGCCCGCCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTG
* * * *
53213 AGAAAAAAATTTTCGGATCATTTTTTAACCGAAATCGTGTACTAATCATCACGGGTTTTGGCTAA
323 AGAAAAAAATTTTCGGATCAATTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTGGATAA
* *
53278 AAACGCGTTCCGAAGACCCGACTTAATTTTGTATGATTTTTGGAGAAAAGACTCCTTTAAATATC
388 AAA-GCGTTCCGGAGACCCGACTTAATTTTGTATGATTTTTGGAGAAAAGACTCCTTGAAATATC
53343 TATATTCATCGAACCAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTACAAGCATCTCAAT
452 TATATTCATCGAACCAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTACAAGCATCTCAAT
* * * * * * * *
53408 CTTGTTTTGATTTAATTAGCAATTAGTTC-AGAAAAAAT-TAAAAGCTATCTTAGAAGAGGGAAA
517 CTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAATGGAAAAACGATATTAGAAGAGGGAAA
*
53471 A-TTCCGCCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAATTGAG
582 ACTT--GCCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTATGGCAAAAAATTGAG
*
53534 AAAAAAACCTCTCGGGTCAGTTTTTAGCTGAAAATAGTGTACTAACCATCACGGGTTTTGGCTAA
645 -AAAAAACCTCTCGGGTCAGTTTTTAGCTG-AAATAGTGTACTAACAATCACGGGTTTTGGCTAA
*
53599 AAACGCTTTCCGGAGCCCC-GACTCAATTTTGCATGATTTTTGGCGCAAAGACTACTTAAAATAT
708 AAACGCGTTCCGGAGCCCCAG-CTCAATTTTGCATGATTTTTGGCGCAAAGACTACTTAAAATAT
* * *
53663 CTAAATTTATTGAAGCAAATCTCAACCATATTGGATATAAGGATTTGTTTTTTCGAGCATCTTAA
772 CTAAATTCATCGAAGCAAATCTCAACCATATTGGATATAAGGATTTGTTTTTTCGAGCATCTAAA
* *
53728 TCTTGTTTCGATTTAAGTAAAAATTAATTCGGAAAAAATGGAAACACGATATTTA
837 TCTAGTTTCGATTTAAGTAAAAATTAATTCGGAAAAAATGGAAAAACGATATTTA
* * *
53783 AGAAAAAACTTTTCGGGTTGGTTTTTAGCAGAAACACGTGTACTAATCATCACAGTTTTTGACTA
1 AGAAAAAACTTTTCGGGTAGGTTTTTAGCAGAAACACGTGTACTAATCATCACGGTTTTTGGCTA
* *
53848 AAAACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTATGGCGCAAAGACTCCATGAAATAT
66 AAAACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATAT
*
53913 CTATATTCATCGAAGCAAATCTCAGCCATATTGGATATAAGGATTTGCTTTTACGAGCATCTCAA
131 CTATATTCATCGAAGCAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTCAA
* * *
53978 TCTTGTTTCGATTTAATTAGAAATTAATTC-AGAAAAAATGGAAAAACGATATTAGAAGTGTGAA
196 TCTTGTTT-GATTTAATTAGAAATTAATTCAAAAAAAAATGAAAAAACGATATTAGAAGCGTGAA
* * *
54042 AAGCCTGTCAATCTTTTTGGTGTTGAATTATATATTTTTTTATGAGTATTGTGGCAAAAAATTGA
260 AAGCCCGCCAATCTTTTTGGTGTTGAATTATATA-TTTTTTCTGAGTATTGTGGCAAAAAATTGA
* * * *
54107 GAAAAAAATTTTC-GAGTCAGTCTTTAGCCGAAATCCTGTACTAATCATCACTGTTTTTGGATAA
324 GAAAAAAATTTTCGGA-TCAATTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTGGATAA
* * * *
54171 AGAATCTTTCTGGAGACCCGACTTAATTTTGTATGATTTTTTGGGGAAAAGACTCCTTGA
388 A-AAGCGTTCCGGAGACCCGACTTAATTTTGTATGA-TTTTTGGAGAAAAGACTCCTTGA
Statistics
Matches: 1197, Mismatches: 129, Indels: 33
0.88 0.09 0.02
Matches are distributed among these distances:
891 2 0.00
892 72 0.06
893 204 0.17
894 416 0.35
895 72 0.06
896 429 0.36
897 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (891 bp):
AGAAAAAACTTTTCGGGTAGGTTTTTAGCAGAAACACGTGTACTAATCATCACGGTTTTTGGCTA
AAAACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATAT
CTATATTCATCGAAGCAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTACGAGCATCTCAA
TCTTGTTTGATTTAATTAGAAATTAATTCAAAAAAAAATGAAAAAACGATATTAGAAGCGTGAAA
AGCCCGCCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGA
AAAAAATTTTCGGATCAATTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTGGATAAAAA
GCGTTCCGGAGACCCGACTTAATTTTGTATGATTTTTGGAGAAAAGACTCCTTGAAATATCTATA
TTCATCGAACCAAATCTCAGCCATATTGGATATAAGGATTTGTTTTTACAAGCATCTCAATCTTG
TTTCGATTTAATTAGAAATTAATTCGAAAAAAAATGGAAAAACGATATTAGAAGAGGGAAAACTT
GCCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTATGGCAAAAAATTGAGAAAAAA
CCTCTCGGGTCAGTTTTTAGCTGAAATAGTGTACTAACAATCACGGGTTTTGGCTAAAAACGCGT
TCCGGAGCCCCAGCTCAATTTTGCATGATTTTTGGCGCAAAGACTACTTAAAATATCTAAATTCA
TCGAAGCAAATCTCAACCATATTGGATATAAGGATTTGTTTTTTCGAGCATCTAAATCTAGTTTC
GATTTAAGTAAAAATTAATTCGGAAAAAATGGAAAAACGATATTTA
Found at i:53982 original size:250 final size:250
Alignment explanation
Indices: 53535--54030 Score: 742
Period size: 250 Copynumber: 2.0 Consensus size: 250
53525 AAAATTGAGA
* * *
53535 AAAAAACCTCTCGGGTCAGTTTTTAGCTGAAAATAGTGTACTAACCATCACGGGTTTTGGCTAAA
1 AAAAAACCTCTCGGGTCAGTTTTTAGCAGAAAATAGTGTACTAACCATCACAGGTTTTGACTAAA
* * *
53600 AACGCTTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTACTTAAAATATCT
66 AACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTATGGCGCAAAGACTACATAAAATATCT
* * * * *
53665 AAATTTATTGAAGCAAATCTCAACCATATTGGATATAAGGATTTGTTTTTTCGAGCATCTTAATC
131 AAATTCATCGAAGCAAATCTCAACCATATTGGATATAAGGATTTGCTTTTACGAGCATCTCAATC
* *
53730 TTGTTTCGATTTAAGTAAAAATTAATTCGGAAAAAATGGAAACACGATATTTAAG
196 TTGTTTCGATTTAAGTAAAAATTAATTCAGAAAAAATGGAAAAACGATATTTAAG
* * ** * * *
53785 AAAAAACTTTTCGGGTTGGTTTTTAGCAGAAACA-CGTGTACTAATCATCACAGTTTTTGACTAA
1 AAAAAACCTCTCGGGTCAGTTTTTAGCAGAAA-ATAGTGTACTAACCATCACAGGTTTTGACTAA
* *
53849 AAACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTATGGCGCAAAGACTCCATGAAATATC
65 AAACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTATGGCGCAAAGACTACATAAAATATC
* *
53914 TATATTCATCGAAGCAAATCTCAGCCATATTGGATATAAGGATTTGCTTTTACGAGCATCTCAAT
130 TAAATTCATCGAAGCAAATCTCAACCATATTGGATATAAGGATTTGCTTTTACGAGCATCTCAAT
* *
53979 CTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATGGAAAAACGATATT
195 CTTGTTTCGATTTAAGTAAAAATTAATTCAGAAAAAATGGAAAAACGATATT
54031 AGAAGTGTGA
Statistics
Matches: 219, Mismatches: 26, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
250 218 1.00
251 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (250 bp):
AAAAAACCTCTCGGGTCAGTTTTTAGCAGAAAATAGTGTACTAACCATCACAGGTTTTGACTAAA
AACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTATGGCGCAAAGACTACATAAAATATCT
AAATTCATCGAAGCAAATCTCAACCATATTGGATATAAGGATTTGCTTTTACGAGCATCTCAATC
TTGTTTCGATTTAAGTAAAAATTAATTCAGAAAAAATGGAAAAACGATATTTAAG
Done.