Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017543.1 Corchorus olitorius cultivar O-4 contig17576, 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: 48421
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:176 original size:21 final size:22
Alignment explanation
Indices: 149--199 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
139 AGGTGTAAGC
*
149 TTTCAAACTTG-TTACCTAACCA
1 TTTCAAA-TTGATTACATAACCA
*
171 -TTCAAATTGATTTCATAACCA
1 TTTCAAATTGATTACATAACCA
192 TTTCAAAT
1 TTTCAAAT
200 GTTTACTCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 3 0.12
21 15 0.60
22 7 0.28
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (22 bp):
TTTCAAATTGATTACATAACCA
Found at i:9819 original size:22 final size:22
Alignment explanation
Indices: 9750--9819 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
9740 AGAAACTTGG
9750 CAAATATCCAGATAGAGGAATC
1 CAAATATCCAGATAGAGGAATC
* * * * * *
9772 TAAAT-T-GAAATTGAGAAACTGG
1 CAAATATCCAGATAGAGGAA-T-C
9794 CAAATATCCAGATAGAGGAATC
1 CAAATATCCAGATAGAGGAATC
9816 CAAA
1 CAAA
9820 AGAAGAAAGT
Statistics
Matches: 32, Mismatches: 12, Indels: 8
0.62 0.23 0.15
Matches are distributed among these distances:
20 8 0.25
21 2 0.06
22 12 0.38
23 2 0.06
24 8 0.25
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (22 bp):
CAAATATCCAGATAGAGGAATC
Found at i:12237 original size:28 final size:27
Alignment explanation
Indices: 12196--12252 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
12186 CAAGCTTTTT
*
12196 TTTTTTTCTTCAAAAGTAATTAGGTCTA
1 TTTTTTTCTGC-AAAGTAATTAGGTCTA
*
12224 TTTTTTTGTGCAAAGTAATTAGGTCTA
1 TTTTTTTCTGCAAAGTAATTAGGTCTA
12251 TT
1 TT
12253 CAAGATTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 18 0.67
28 9 0.33
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.51
Consensus pattern (27 bp):
TTTTTTTCTGCAAAGTAATTAGGTCTA
Found at i:14253 original size:2 final size:2
Alignment explanation
Indices: 14246--14270 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14236 CGATGTTGTC
14246 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 A
14271 CTCCATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29858 original size:14 final size:17
Alignment explanation
Indices: 29839--29875 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
29829 ATCCAGATAT
29839 ATATTTTT-TT-TATA-
1 ATATTTTTCTTGTATAC
29853 ATATTTTTCTTGTATAC
1 ATATTTTTCTTGTATAC
29870 ATATTT
1 ATATTT
29876 CTTATATGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 2 0.10
16 4 0.20
17 6 0.30
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (17 bp):
ATATTTTTCTTGTATAC
Found at i:30714 original size:2 final size:2
Alignment explanation
Indices: 30707--30736 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
30697 CAGGTGGAAG
*
30707 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30737 CATCTTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:43294 original size:332 final size:332
Alignment explanation
Indices: 42694--47560 Score: 6442
Period size: 333 Copynumber: 14.8 Consensus size: 332
42684 AATGGCTAGT
* * * * ** **
42694 CCTTCAATCTTTTTGGCTTTGAGTTAAATATTTTTTATGAGTATTGTAGCCAAAAATTGAGG-AA
1 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAATTGAGGAAA
* * * * *
42758 GATGTTTTGGGTCAATTTTTGCAAAATTTTTACCGAAATCATG---TA-CATCACGGTTTTTGGC
66 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTACCATCACGGTTTTTGGC
* * *
42819 TAAAAACGCGTTCCGG-GGCCCGGCTCGGTTTTGCATGATTTTTGGTGCCAAGACTCATTGAAAT
131 TAAAAACGCGTTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAAT
* * *
42883 ATCTATATTAATC-TAACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCA
196 ATCTATATTAATCAT-CCCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCT
* * *
42947 GAATCTTGTTTCGATTTAATTAGAAATTAATTTGGGAAAAAATTGAAAAAATGATATCAGAAGCG
260 GAATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAAAATTGAAAAAATGATATTAGAAGCG
43012 TGAAAAGC
325 TGAAAAGC
*
43020 CCTTCAATATTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAATTGAGGAAA
1 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAATTGAGGAAA
43085 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTACCATCACGGTTTTTGGC
66 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTACCATCACGGTTTTTGGC
* * * *
43150 TAAAAATGCGTTCCGGTGCACCGGCTTAGTTTTGCATGATTTTTGGAGCCAAGACTCATTGAAAT
131 TAAAAACGCGTTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAAT
* * * * * *
43215 ATCTATATTCATCATCCCAAATCTTAGCCACATTGGAATTAAGGATTTGATTTTACGAGCATCTG
196 ATCTATATTAATCATCCCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCTG
* * * *
43280 AATCATGTTTCGATTT-AATCGGAAATTAATAC-GGAAAAAATTGAAAAAAATGATATTAGACGC
261 AATCTTGTTTCGATTTAAAT-AGAAATTAATTCGGGAAAAAATTG-AAAAAATGATATTAGAAGC
*
43343 CTGAAAAGC
324 GTGAAAAGC
* * * * *
43352 CCTTCAATCTTTCTGCCGTTAAATTATATATTTTTTAC-ATGTATTGCGGTTCAAAATTAAGGAA
1 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGA-GTATTGCGGTTAAAAATTGAGGAA
* * *
43416 AAATCTTTCAGGTCAATTTTTGCAAAGTTTTTGCCGAAATCGTGTACCAACCATCACGGTTTTTG
65 AAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTA-CTACCATCACGGTTTTTG
* *
43481 GCTAAAAACGCGTTCCGGTGCCCCGACTCAGTTTTGAATGATTTTTGGCGCCAAGACTCATTGAA
129 GCTAAAAACGCGTTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAA
*
43546 ATATCTATATTAATCATCCCAAATCTCAGCCACAATGGATTTAAGAATTTGTTTTTACGATCATC
194 ATATCTATATTAATCATCCCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATC
* * *
43611 TGATTTTTGTTTCGATTTAAATAGAAATTAATTTGGG-AAAAATTGAAAAAATGATATTAGAAGC
259 TGAATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAAAATTGAAAAAATGATATTAGAAGC
43675 GTGAAAAGC
324 GTGAAAAGC
* * *
43684 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTACTGCAGTTAAAAATTGAGAAAA
1 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAATTGAGGAAA
* *
43749 AATCTTTCGGGTCAATTTTTGCAAATTTTTTGCCAAAATCGTGTACT-CCATCACGGTTTTTGGC
66 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTACCATCACGGTTTTTGGC
* *
43813 TAAAAACGCGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAAT
131 TAAAAACGCGTTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAAT
* *
43878 ATCTATATTAATC-TAACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCT
196 ATCTATATTAATCAT-CCCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCT
43942 GAATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAGAAATTGAAAAAATGATATTAGAAGC
260 GAATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAA-AAATTGAAAAAATGATATTAGAAGC
44007 GTGAAAAGC
324 GTGAAAAGC
* *
44016 CCTTCAATCTTTTTGGCGTT-AACTTATATATTTTTTACGAGTATTGTGGTTAAAAATTTAGGAA
1 CCTTCAATCTTTTTGGCGTTGAA-TTATATATTTTTTACGAGTATTGCGGTTAAAAATTGAGGAA
* *
44080 AAATCTTTCGGGACAGTTTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTT
65 AAATCTTTCGGGTCA-ATTTTTGCAAAATTTTTGCCGAAATCGTGTACT-ACCATCACGG-TTTT
* * *
44145 TGGCTAAAAACGCGTTCCAGG-GCCCCAGCTTAGTTTTGCATGATTTTTGGTGCCAAGACTCATT
127 TGGCTAAAAACGCGTTCC-GGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATT
* * * * * **
44209 GAAATATGTATATTCATCATCCCAAATCTCAGTCACATTGGATTTAAGGATTTGATTTTACGAGA
191 GAAATATCTATATTAATCATCCCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGATC
* *
44274 ATCTAAATCTTGTTTCGATTTAAATAGAAATTAATTTGGG-AAAAATTGAAAAAATGATATTAGA
256 ATCTGAATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAAAATTGAAAAAATGATATTAGA
44338 AGCGTGAAAAGC
321 AGCGTGAAAAGC
* *
44350 CCTTCAATCTTTTTGGCATTGAATTATATATTTTTCACGAGTATTGCGGTTAAAAATTGAGGAAA
1 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAATTGAGGAAA
* *
44415 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAAATCGTGTATGTTA-TATCACGGTTTTT
66 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCG-AAATCGTGTA--CTACCATCACGGTTTTT
* * * *
44479 GGCTATAAACGCGTTACGGTGCCCCGGCTCAGTTTTCCATGATTTTTGGAGCCAAGACTCATTGA
128 GGCTAAAAACGCGTTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGA
* * ** * * *
44544 AATATCTATATTCATTATCCCAAATCTCA-ATACCATTGGATTTAAGGATTTGATTTTACGAGCA
193 AATATCTATATTAATCATCCCAAATCTCAGCCA-CAATGGATTTAAGGATTTGTTTTTACGATCA
* * *
44608 TCTGAATCATGTTTCGATTT-AATCGGAAATTAATAC-GGAAAAAATTGAAAAAAATGATATTAG
257 TCTGAATCTTGTTTCGATTTAAAT-AGAAATTAATTCGGGAAAAAATTG-AAAAAATGATATTAG
* * *
44671 ACGCCTGAAAAAC
320 AAGCGTGAAAAGC
* * * * ** * * * *
44684 CCTTCAATCTTTCTGTCATTGAATTATATATTTTTTATGAGTATTATGGTTCAAATTTAAGGGAA
1 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAATTGAGGAAA
*
44749 AATCTTTCGGGTCAATTTTTGCAAAGTTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGG
66 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACT-ACCATCACGGTTTTTGG
* * *
44814 CTAAAAACGCGTTCCGGTGCCCCGACTCAGTTTTGCATGATTATTGGCGCCAAGACTCATTGTAA
130 CTAAAAACGCGTTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAA
* * *
44879 TATCTATATTAATCATCCCAAATCTTAGCCACAATGGATTTAAGGCTTTGTTTCTACGATCATCT
195 TATCTATATTAATCATCCCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCT
* * * * *
44944 GATTCTTGTTTCGATTTAAATGGAAATTAATTTGGG-AACAATTGATAAAATGATATTAGAAGCG
260 GAATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAAAATTGAAAAAATGATATTAGAAGCG
*
45008 TGAATAGC
325 TGAAAAGC
* * * * *
45016 CCTTCAATCATTTTGGCGTTTAATTATATATTTTTTACGAGTACTGCTGTCAAAAATTGAGGAAA
1 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAATTGAGGAAA
* * *
45081 AATCTTTCGGGTTAATTTTTGTAAAATTTTTGTCGAAATC--G---------CA--GTTTTTGGC
66 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTACCATCACGGTTTTTGGC
* * ** * *
45133 TAAAAACGGGTTTCGG-GACCCCAACTCAATTTTGCATGATTTTTGGCGCCAAGACTCATTGAAT
131 TAAAAACGCGTTCCGGTG-CCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAA
* * *
45197 TATCAATACTAATCATCCCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGATCATCT
195 TATCTATATTAATCATCCCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCT
* * *
45262 GAATTTTGTTTCGATTTAATTAGAAATTAATTC-GGAAAAGAATTGGAAAAATGATATTAGAAGC
260 GAATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAA-AATTGAAAAAATGATATTAGAAGC
45326 GTGAAAAGC
324 GTGAAAAGC
* * * * *
45335 CCTTCAATCTTTTTGGAGTTGAATTATATA-ATTTTACAAGTATTGCGGTTAAAAATTTATGAAA
1 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAATTGAGGAAA
*
45399 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCACAGTTTTTGG
66 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACT-ACCATCACGGTTTTTGG
* * * * *
45464 CTAAAGACGCGATCCGATGCCCCGGCTCAGTTTTACATGATTTTTGGCGCCAAGACTCATTGAAT
130 CTAAAAACGCGTTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAA
* * *
45529 TATCTATATTAATC-TAACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATG
195 TATCTATATTAATCAT-CCCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATC
*
45593 TGAATCTTCTTTCGATTTAAATAGAAATTAATTCGGGAAAAAATTGAAAAAATGATATTAGAAGC
259 TGAATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAAAATTGAAAAAATGATATTAGAAGC
*
45658 GTGAAAAAC
324 GTGAAAAGC
* * *
45667 ACTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGTGGTTAAAAATTGAGCAAA
1 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAATTGAGGAAA
* * *
45732 AATCTTTCGGGTCAGTTTGTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCACAGTTTTTGG
66 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACT-ACCATCACGGTTTTTGG
*
45797 CTAAAGACGCGTTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAA
130 CTAAAAACGCGTTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAA
* *
45862 TATCTATATTAATC-TAACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATC
195 TATCTATATTAATCAT-CCCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATC
* * * *
45926 TGAATCTTGTTTTGATTTAAATATAAATTAATTCGAG-AAAAA-TGAAAAAATGATATTAGTAGC
259 TGAATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAAAATTGAAAAAATGATATTAGAAGC
*
45989 GTAAAAAGC
324 GTGAAAAGC
* ** *
45998 CCTTCAATCATTTTGGCGTTGAATTATATATTTTTTACGAACATTGCGGTAAAAAATTGAGGAAA
1 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAATTGAGGAAA
46063 AATCTTTCGGGTCAATGTTTTGCAAAATTTTTGCCGAAATCGTG---T---AT---GG-TTTTGG
66 AATCTTTCGGGTCAAT-TTTTGCAAAATTTTTGCCGAAATCGTGTACTACCATCACGGTTTTTGG
** * * *
46118 CTAAAAACGCGTTTTGGGGCCCCGGCTCAATTTTGCATGA-TTTTGGACACCAAGACTCATTGAA
130 CTAAAAACGCGTTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGG-CGCCAAGACTCATTGAA
* * * * *
46182 ATATCTATATTAATTATCCCAAATTTAAGCCACAATGGATTTAAGGATTTGGTTTTACGATCATT
194 ATATCTATATTAATCATCCCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATC
* * * * *
46247 TGAATCTTGTTTCGATTTAATTAAGAAATTAATTAGGGAAAGAATTGAAAAGATGATATCAGAAG
259 TGAATCTTGTTTCGATTTAAAT-AGAAATTAATTCGGGAAAAAATTGAAAAAATGATATTAGAAG
46312 CGTGAAAAGC
323 CGTGAAAAGC
* * *
46322 CCTTCAATCTTTTTGACGTTGAATTATATATTTTTAACGAGTACTGCGGTTAAAAATTGAGGAAA
1 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAATTGAGGAAA
* ** * *
46387 AATTTTTAAGGTCAATTTTTGCAAAATTGTTGGCGAAATCGTGTACTAACCATCACGGTTTTTGG
66 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACT-ACCATCACGGTTTTTGG
* * * ** * *
46452 TTAAAGACGCGTTCCGGTGCCCCGGCTTAGTTTTGTTTTATTTTTGGTGCCAAGACTCATTGAAA
130 CTAAAAACGCGTTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAA
* ** * * * * ** *
46517 TATGTATATTCGTTATCCCAAATCTCAGCTACATTTGATTTAAGGATTTAATTTTACGAGCATCT
195 TATCTATATTAATCATCCCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCT
* *
46582 GAATCTTGTTTTGATTTAAATAGAAATTAATTCGGG-AAAAA-TGAAAATATGATATTAGAAGCG
260 GAATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAAAATTGAAAAAATGATATTAGAAGCG
46645 TGAAAAGC
325 TGAAAAGC
* * * * *
46653 CCTTCAATCATTTTGGAGGTGAATTATA-A-ATTTTACGAGTATTGAGGTTAAAAATTGAGGAAA
1 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAATTGAGGAAA
* *
46716 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTATTACCATCACAGTTTTTGGC
66 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTACCATCACGGTTTTTGGC
* * * **
46781 TAAAAACGCGTTCCGGGGCCACGGCTCAATTTTGCATGATTTTTTACGCCAAGACTCATTGAAAT
131 TAAAAACGCGTTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAAT
* * *
46846 ATATATATTAATCATCCCAAATTTCAGTCACAATGGATTTAAGGATTTGTTTTTACGATCATCTG
196 ATCTATATTAATCATCCCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCTG
* * * *
46911 AA-CTTTCTTTCAATTTAATTAAGAAATTAATTCGGGAAAGAATTGAAAAAATGATATTAGAAGC
261 AATC-TTGTTTCGATTTAAAT-AGAAATTAATTCGGGAAAAAATTGAAAAAATGATATTAGAAGC
*
46975 GTGAAAATC
324 GTGAAAAGC
* * * *
46984 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTAACGAGTACTACGGTTAAAAATTCAGGAAA
1 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAATTGAGGAAA
* * * *
47049 AATCTTTTGGTTCAGTTTTTACAAAATTTTTGCCG-AA------A-T--CAT----G-TTTTGGC
66 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTACCATCACGGTTTTTGGC
* *
47099 TAAAAACGCGGTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCAATGAAAT
131 TAAAAACGCGTTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAAT
* * * *
47164 ATCTATATTAAT-ATAACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCGTTT
196 ATCTATATTAATCAT-CCCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCT
*
47228 GAATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAAAATTGAAGAAATGATATTAGAAGCG
260 GAATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAAAATTGAAAAAATGATATTAGAAGCG
47293 TGAAAAGC
325 TGAAAAGC
* * *
47301 CCTTTAATGTTTTTGGCGTTGAATTATATA-TTTTTACGAGTATTGAC-GTTAAAAATTGAGAAA
1 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTG-CGGTTAAAAATTGAGGAA
* * *
47364 AAATTTTTCGGGTCAGTTTTTGGC--AATTTTTGCCGAAATC--GTA-TA-CATCACAGTTTTTG
65 AAATCTTTCGGGTCAATTTTT-GCAAAATTTTTGCCGAAATCGTGTACTACCATCACGGTTTTTG
* * * * *
47423 GCTAAAGACGCGTTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCAAGTCTCACTAAA
129 GCTAAAAACGCGTTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAA
* * * *
47488 ATATCTATATTAATC-TAACCATATATCAGCCACAATGGATTTAGGGATTTGTTTTTACGATCAT
194 ATATCTATATTAATCAT-CCCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCAT
47552 CTGAATCTT
258 CTGAATCTT
47561 TTAGAAGGTT
Statistics
Matches: 3995, Mismatches: 447, Indels: 198
0.86 0.10 0.04
Matches are distributed among these distances:
315 11 0.00
316 46 0.01
317 84 0.02
318 353 0.09
319 59 0.01
320 11 0.00
321 137 0.03
322 14 0.00
323 32 0.01
324 97 0.02
325 4 0.00
326 187 0.05
327 41 0.01
328 137 0.03
329 88 0.02
330 184 0.05
331 257 0.06
332 837 0.21
333 868 0.22
334 371 0.09
335 20 0.01
336 154 0.04
337 3 0.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.36
Consensus pattern (332 bp):
CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAATTGAGGAAA
AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTACCATCACGGTTTTTGGC
TAAAAACGCGTTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAAT
ATCTATATTAATCATCCCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCTG
AATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAAAATTGAAAAAATGATATTAGAAGCGT
GAAAAGC
Found at i:45740 original size:983 final size:983
Alignment explanation
Indices: 42694--47560 Score: 6475
Period size: 983 Copynumber: 4.9 Consensus size: 983
42684 AATGGCTAGT
* * * * * **
42694 CCTTCAATCTTTTTGGCTTTGAGTTAAATATTTTTTATGAGTATTGTAGCCAAAAATTGAGG-AA
1 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGTGGTTAAAAATTGAGGAAA
* * * * *
42758 GATGTTTTGGGTCAATTTTTGCAAAATTTTTACCGAAATCATG---TA-CATCACGGTTTTTGGC
66 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTACCATCACGGTTTTTGGC
* *
42819 TAAAAACGCGTTCCGGGG-CCCGGCTCGGTTTTGCATGATTTTTGGTGCCAAGACTCATTGAAAT
131 TAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAAT
*
42883 ATCTATATTAATCTAACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCAG
196 ATCTATATTAATCTAACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCTG
* * *
42948 AATCTTGTTTCGATTTAATTAGAAATTAATTTGGGAAAAAATTGAAAAAATGATATCAGAAGCGT
261 AATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAAAATTGAAAAAATGATATTAGAAGCGT
43013 GAAAAGCCCTTCAAT-ATTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAAT
326 GAAAAGCCCTTCAATCA-TTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAAT
43077 TGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTACCATCACGG
390 TGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCG-G---------CAC-G
* * * *
43142 TTTTTGGCTAAAAATGCGTTCCGGTGCACCGGCTTAGTTTTGCATGATTTTTGGAGCCAAGACTC
444 TTTTTGGCTAAAAACGCGTTCCGG-GCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTC
* * * *
43207 ATTGAAATATCTATATTCATCATCCCAAATCTTAGCCACATTGGAATTAAGGATTTGATTTTACG
508 ATTGAAATATCTATATTAATCATCCCAAATCTCAGCCACAATGGATTTAAGGATTTGATTTTACG
* * ** * *
43272 AGCATCTGAATCATGTTTCGATTTAATCGGAAATTAATACGGAAAAAATTGAAAAAAATGATATT
573 ATCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATTG-GAAAAATGATATT
* * * ** *
43337 AGACGCCTGAAAAGCCCTTCAATCTTTCTGCCGTTAAATTATATATTTTTTAC-ATGTATTGCGG
637 AGAAGCGTGAAAAGCCCTTCAATCTTTTTGGAGTTGAATTATATA-TTTTTACGA-GTATTGCGG
* * * * *
43401 TTCAAAATTAAGGAAAAATCTTTCAGGTCAATTTTTGCAAAGTTTTTGCCGAAATCGTGTACCAA
700 TTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAA
* *
43466 CCATCACGGTTTTTGGCTAAAAACGCGTTCCGGTGCCCCGACTCAGTTTTGA-ATGATTTTTGGC
765 CCATCACGGTTTTTGGCTAAAGACGCGTTCCGGTGCCCCGGCTCAGTTTT-ACATGATTTTTGGC
*
43530 GCCAAGACTCATTGAAATATCTATATTAATC-ATCCCAAATCTCAGCCACAATGGATTTAAGAAT
829 GCCAAGACTCATTGAAATATCTATATTAATCTATCCCAAATCTCAGCCACAATGGATTTAAGGAT
* * *
43594 TTGTTTTTACGATCATCTGATTTTTGTTTCGATTTAAATAGAAATTAATTTGGGAAAAATTGAAA
894 TTGTTTTTACGATCATCTGAATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAAATTGAAA
*
43659 AAATGATATTAGAAGCGTGAAAAGC
959 AAATGATATTAGAAGCGTGAAAAAC
* ** *
43684 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTACTGCAGTTAAAAATTGAGAAAA
1 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGTGGTTAAAAATTGAGGAAA
* *
43749 AATCTTTCGGGTCAATTTTTGCAAATTTTTTGCCAAAATCGTGTACT-CCATCACGGTTTTTGGC
66 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTACCATCACGGTTTTTGGC
*
43813 TAAAAACGCGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAAT
131 TAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAAT
43878 ATCTATATTAATCTAACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCTG
196 ATCTATATTAATCTAACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCTG
43943 AATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAGAAATTGAAAAAATGATATTAGAAGCG
261 AATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAA-AAATTGAAAAAATGATATTAGAAGCG
* *
44008 TGAAAAGCCCTTCAATCTTTTTGGCGTT-AACTTATATATTTTTTACGAGTATTGTGGTTAAAAA
325 TGAAAAGCCCTTCAATCATTTTGGCGTTGAA-TTATATATTTTTTACGAGTATTGCGGTTAAAAA
* * *
44072 TTTAGGAAAAATCTTTCGGGACAGTTTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCA
389 TTGAGGAAAAATCTTTCGGGTCA-ATTTTTGCAAAATTTTTGCCGAAATCG-G----------CA
* * *
44137 CGGTTTTTTGGCTAAAAACGCGTTCCAGGGCCCCAGCTTAGTTTTGCATGATTTTTGGTGCCAAG
442 C-G-TTTTTGGCTAAAAACGCGTTCC-GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAG
* * * *
44202 ACTCATTGAAATATGTATATTCATCATCCCAAATCTCAGTCACATTGGATTTAAGGATTTGATTT
504 ACTCATTGAAATATCTATATTAATCATCCCAAATCTCAGCCACAATGGATTTAAGGATTTGATTT
** * * * * *
44267 TACGAGAATCTAAATCTTGTTTCGATTTAAATAGAAATTAATTTGGGAAAAATTGAAAAAATGAT
569 TACGATCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATTGGAAAAATGAT
44332 ATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCA-TTGAATTATATATTTTTCACGAGTATTG
634 ATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGG-AGTTGAATTATATATTTTT-ACGAGTATTG
44396 CGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAAATCGTGTA
697 CGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCG-AAATCGTGTA
* * * * *
44461 TGTTA-TATCACGGTTTTTGGCTATAA-ACGCGTTACGGTGCCCCGGCTCAGTTTTCCATGATTT
761 -CTAACCATCACGGTTTTTGGCTA-AAGACGCGTTCCGGTGCCCCGGCTCAGTTTTACATGATTT
* * ** *
44524 TTGGAGCCAAGACTCATTGAAATATCTATATTCAT-TATCCCAAATCTCA-ATACCATTGGATTT
824 TTGGCGCCAAGACTCATTGAAATATCTATATTAATCTATCCCAAATCTCAGCCA-CAATGGATTT
* * * * * *
44587 AAGGATTTGATTTTACGAGCATCTGAATCATGTTTCGATTT-AATCGGAAATTAATACGGAAAAA
888 AAGGATTTGTTTTTACGATCATCTGAATCTTGTTTCGATTTAAAT-AGAAATTAATTCGGGAAAA
* *
44651 ATTGAAAAAAATGATATTAGACGCCTGAAAAAC
952 ATTG-AAAAAATGATATTAGAAGCGTGAAAAAC
* * * * * * * * *
44684 CCTTCAATCTTTCTGTCATTGAATTATATATTTTTTATGAGTATTATGGTTCAAATTTAAGGGAA
1 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGTGGTTAAAAATTGAGGAAA
*
44749 AATCTTTCGGGTCAATTTTTGCAAAGTTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGG
66 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACT-ACCATCACGGTTTTTGG
* * * *
44814 CTAAAAACGCGTTCCGGTGCCCCGACTCAGTTTTGCATGATTATTGGCGCCAAGACTCATTGTAA
130 CTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAA
* * * * *
44879 TATCTATATTAATC-ATCCCAAATCTTAGCCACAATGGATTTAAGGCTTTGTTTCTACGATCATC
195 TATCTATATTAATCTA-ACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATC
* * * * *
44943 TGATTCTTGTTTCGATTTAAATGGAAATTAATTTGGG-AACAATTGATAAAATGATATTAGAAGC
259 TGAATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAAAATTGAAAAAATGATATTAGAAGC
* * * * *
45007 GTGAATAGCCCTTCAATCATTTTGGCGTTTAATTATATATTTTTTACGAGTACTGCTGTCAAAAA
324 GTGAAAAGCCCTTCAATCATTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAA
* * *
45072 TTGAGGAAAAATCTTTCGGGTTAATTTTTGTAAAATTTTTGTCGAAATC-GCA-GTTTTTGGCTA
389 TTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGGCACGTTTTTGGCTA
* * ** * *
45135 AAAACGGGTTTCGGGACCCCAACTCAATTTTGCATGATTTTTGGCGCCAAGACTCATTGAATTAT
454 AAAACGCGTTCCGGG-CCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATAT
* * * *
45200 CAATACTAATCATCCCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGATCATCTGAA
518 CTATATTAATCATCCCAAATCTCAGCCACAATGGATTTAAGGATTTGATTTTACGATCATCTGAA
*
45265 TTTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAGAATTGGAAAAATGATATTAGAAGCGTGA
583 TCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAA-AATTGGAAAAATGATATTAGAAGCGTGA
* * * *
45330 AAAGCCCTTCAATCTTTTTGGAGTTGAATTATATAATTTTACAAGTATTGCGGTTAAAAATTTAT
647 AAAGCCCTTCAATCTTTTTGGAGTTGAATTATATATTTTTACGAGTATTGCGGTTAAAAATTGAG
*
45395 GAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCACAGTTT
712 GAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCACGGTTT
* *
45460 TTGGCTAAAGACGCGATCCGATGCCCCGGCTCAGTTTTACATGATTTTTGGCGCCAAGACTCATT
777 TTGGCTAAAGACGCGTTCCGGTGCCCCGGCTCAGTTTTACATGATTTTTGGCGCCAAGACTCATT
* * *
45525 GAATTATCTATATTAATCTA-ACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGAT
842 GAAATATCTATATTAATCTATCCCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGAT
* *
45589 CATGTGAATCTTCTTTCGATTTAAATAGAAATTAATTCGGGAAAAAATTGAAAAAATGATATTAG
907 CATCTGAATCTTGTTTCGATTTAAATAGAAATTAATTCGGG-AAAAATTGAAAAAATGATATTAG
45654 AAGCGTGAAAAAC
971 AAGCGTGAAAAAC
* *
45667 ACTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGTGGTTAAAAATTGAGCAAA
1 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGTGGTTAAAAATTGAGGAAA
* * *
45732 AATCTTTCGGGTCAGTTTGTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCACAGTTTTTGG
66 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACT-ACCATCACGGTTTTTGG
* *
45797 CTAAAGACGCGTTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAA
130 CTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAA
45862 TATCTATATTAATCTAACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCT
195 TATCTATATTAATCTAACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCT
* * * *
45927 GAATCTTGTTTTGATTTAAATATAAATTAATTCGAG-AAAAA-TGAAAAAATGATATTAGTAGCG
260 GAATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAAAATTGAAAAAATGATATTAGAAGCG
* ** *
45990 TAAAAAGCCCTTCAATCATTTTGGCGTTGAATTATATATTTTTTACGAACATTGCGGTAAAAAAT
325 TGAAAAGCCCTTCAATCATTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAAT
* * *
46055 TGAGGAAAAATCTTTCGGGTCAATGTTTTGCAAAATTTTTGCCGAAATCGTGTATGGTTTTGGCT
390 TGAGGAAAAATCTTTCGGGTCAAT-TTTTGCAAAATTTTTGCCGAAATCG-GCACGTTTTTGGCT
** * *
46120 AAAAACGCGTTTTGGGGCCCCGGCTCAATTTTGCATGA-TTTTGGACACCAAGACTCATTGAAAT
453 AAAAACGCG-TTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGG-CGCCAAGACTCATTGAAAT
* * * * *
46184 ATCTATATTAATTATCCCAAATTTAAGCCACAATGGATTTAAGGATTTGGTTTTACGATCATTTG
516 ATCTATATTAATCATCCCAAATCTCAGCCACAATGGATTTAAGGATTTGATTTTACGATCATCTG
* * *
46249 AATCTTGTTTCGATTTAATTAAGAAATTAATTAGGGAAAGAATT-GAAAAGATGATATCAGAAGC
581 AATCTTGTTTCGATTTAATT-AGAAATTAATT-CGGAAAAAATTGGAAAA-ATGATATTAGAAGC
*
46313 GTGAAAAGCCCTTCAATCTTTTT-GACGTTGAATTATATATTTTTAACGAGTACTGCGGTTAAAA
643 GTGAAAAGCCCTTCAATCTTTTTGGA-GTTGAATTATATATTTTT-ACGAGTATTGCGGTTAAAA
* ** * *
46377 ATTGAGGAAAAATTTTTAAGGTCAATTTTTGCAAAATTGTTGGCGAAATCGTGTACTAACCATCA
706 ATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCA
* * *** * *
46442 CGGTTTTTGGTTAAAGACGCGTTCCGGTGCCCCGGCTTAGTTTTGTTTTATTTTTGGTGCCAAGA
771 CGGTTTTTGGCTAAAGACGCGTTCCGGTGCCCCGGCTCAGTTTTACATGATTTTTGGCGCCAAGA
* ** * * * **
46507 CTCATTGAAATATGTATATTCGT-TATCCCAAATCTCAGCTACATTTGATTTAAGGATTTAATTT
836 CTCATTGAAATATCTATATTAATCTATCCCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTT
* * *
46571 TACGAGCATCTGAATCTTGTTTTGATTTAAATAGAAATTAATTCGGGAAAAA-TGAAAATATGAT
901 TACGATCATCTGAATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAAATTGAAAAAATGAT
*
46635 ATTAGAAGCGTGAAAAGC
966 ATTAGAAGCGTGAAAAAC
* * * * *
46653 CCTTCAATCATTTTGGAGGTGAATTATA-A-ATTTTACGAGTATTGAGGTTAAAAATTGAGGAAA
1 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGTGGTTAAAAATTGAGGAAA
* *
46716 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTATTACCATCACAGTTTTTGGC
66 AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTACCATCACGGTTTTTGGC
* * **
46781 TAAAAACGCGTTCCGGGGCCACGGCTCAATTTTGCATGATTTTTTACGCCAAGACTCATTGAAAT
131 TAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAAT
* * * *
46846 ATATATATTAATC-ATCCCAAATTTCAGTCACAATGGATTTAAGGATTTGTTTTTACGATCATCT
196 ATCTATATTAATCTA-ACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCT
* * * *
46910 GAA-CTTTCTTTCAATTTAATTAAGAAATTAATTCGGGAAAGAATTGAAAAAATGATATTAGAAG
260 GAATC-TTGTTTCGATTTAAAT-AGAAATTAATTCGGGAAAAAATTGAAAAAATGATATTAGAAG
* * * * *
46974 CGTGAAAATCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTAACGAGTACTACGGTTAAAA
323 CGTGAAAAGCCCTTCAATCATTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAA
* * * * * *
47039 ATTCAGGAAAAATCTTTTGGTTCAGTTTTTACAAAATTTTTGCCGAAAT---CATG-TTTTGGCT
388 ATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGGCACGTTTTTGGCT
* *
47100 AAAAACGCGGTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCAATGAAATA
453 AAAAACGCGTTCCGG-GCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATA
* * * * *
47165 TCTATATTAAT-ATAACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCGTTTG
517 TCTATATTAATCAT-CCCAAATCTCAGCCACAATGGATTTAAGGATTTGATTTTACGATCATCTG
*
47229 AATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAAAATT-GAAGAAATGATATTAGAAGCG
581 AATCTTGTTTCGATTTAATTAGAAATTAATTC-GGAAAAAATTGGAA-AAATGATATTAGAAGCG
* * *
47293 TGAAAAGCCCTTTAATGTTTTTGGCGTTGAATTATATATTTTTACGAGTATTGAC-GTTAAAAAT
644 TGAAAAGCCCTTCAATCTTTTTGGAGTTGAATTATATATTTTTACGAGTATTG-CGGTTAAAAAT
* * *
47357 TGAGAAAAAATTTTTCGGGTCAGTTTTTGGC--AATTTTTGCCGAAATC--GTA-T-A-CATCAC
708 TGAGGAAAAATCTTTCGGGTCAATTTTT-GCAAAATTTTTGCCGAAATCGTGTACTAACCATCAC
* * * *
47415 AGTTTTTGGCTAAAGACGCGTTCCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCAAGTC
772 GGTTTTTGGCTAAAGACGCGTTCCGGTGCCCCGGCTCAGTTTTACATGATTTTTGGCGCCAAGAC
* * * * * *
47480 TCACTAAAATATCTATATTAATCTA-ACCATATATCAGCCACAATGGATTTAGGGATTTGTTTTT
837 TCATTGAAATATCTATATTAATCTATCCCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTT
47544 ACGATCATCTGAATCTT
902 ACGATCATCTGAATCTT
47561 TTAGAAGGTT
Statistics
Matches: 3443, Mismatches: 370, Indels: 146
0.87 0.09 0.04
Matches are distributed among these distances:
972 125 0.04
973 3 0.00
974 1 0.00
975 3 0.00
977 14 0.00
978 42 0.01
979 83 0.02
980 134 0.04
981 9 0.00
982 106 0.03
983 626 0.18
984 315 0.09
985 100 0.03
986 285 0.08
987 83 0.02
988 228 0.07
990 53 0.02
991 38 0.01
994 35 0.01
995 145 0.04
996 104 0.03
997 34 0.01
998 123 0.04
999 354 0.10
1000 226 0.07
1001 5 0.00
1002 169 0.05
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.36
Consensus pattern (983 bp):
CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGTGGTTAAAAATTGAGGAAA
AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTACCATCACGGTTTTTGGC
TAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAAT
ATCTATATTAATCTAACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCTG
AATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAAAATTGAAAAAATGATATTAGAAGCGT
GAAAAGCCCTTCAATCATTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAATT
GAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGGCACGTTTTTGGCTAAA
AACGCGTTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTA
TATTAATCATCCCAAATCTCAGCCACAATGGATTTAAGGATTTGATTTTACGATCATCTGAATCT
TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATTGGAAAAATGATATTAGAAGCGTGAAAAG
CCCTTCAATCTTTTTGGAGTTGAATTATATATTTTTACGAGTATTGCGGTTAAAAATTGAGGAAA
AATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGG
CTAAAGACGCGTTCCGGTGCCCCGGCTCAGTTTTACATGATTTTTGGCGCCAAGACTCATTGAAA
TATCTATATTAATCTATCCCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATC
TGAATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAAATTGAAAAAATGATATTAGAAGCG
TGAAAAAC
Found at i:48340 original size:333 final size:332
Alignment explanation
Indices: 47699--48421 Score: 1173
Period size: 333 Copynumber: 2.2 Consensus size: 332
47689 TTTTTGACGC
* * *
47699 TCTATATTAATCATCCCAAATTTCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCTTG
1 TCTATATTAATCTTACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCTTG
47764 ATCTTATTTCGATTTAAATAAAAATTAATTCGGGAAAAATTGAAAAAATGATATTAGAAGCGTGA
66 ATCTTATTTCGATTTAAATAAAAATTAATTCGGGAAAAATTGAAAAAATGATATTAGAAGCGTGA
* *
47829 AAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTACTGCGGTTAAAAATTGA
131 AAAGCCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTACGAGTACTACGGTTAAAAATTGA
*
47894 GGAAAAATCTTTTGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCACGGTT
196 GGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCACGGTT
* * * *
47959 TTTGGCTAAAGACGCGTTCCGGTGCCCCGGCTCAGTTTTGCTTGATTTTTGGCACCAAGACTCAT
261 TTTGGCTAAAAACGCGATCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCAT
48024 TGAAATA
326 TGAAATA
48031 TCTATATTAATCTTACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATC-TG
1 TCTATATTAATCTTACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCTTG
* *
48095 AATCTTGTTTCGATTTAAATAGAAATTAATTCGGGAAAAAAATT-AAAAAATGATATTAGAAGCG
66 -ATCTTATTTCGATTTAAATAAAAATTAATTCGGG--AAAAATTGAAAAAATGATATTAGAAGCG
* * *
48159 TGAAAAGCCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTACGAGTATTATGGTTAATAAT
128 TGAAAAGCCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTACGAGTACTACGGTTAAAAAT
*
48224 TGAGGAAAAATCTTTCGGGTCAGTTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCACG
193 TGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCACG
* * * **
48289 GTTTTTTGGCTAAAAACGCGATCCGGGGCCCTGGCTTAG-TTTGCATGATTTTTTGCGGCAAGAC
258 G-TTTTTGGCTAAAAACGCGATCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGAC
48353 TCATTGAAATA
322 TCATTGAAATA
* * *
48364 TCTATATTAATCTAAACAAATATCAGCTACAATGGATTTAAGGATTTGTTTTTACGAT
1 TCTATATTAATCTTACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGAT
Statistics
Matches: 363, Mismatches: 24, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
331 2 0.01
332 91 0.25
333 231 0.64
334 39 0.11
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (332 bp):
TCTATATTAATCTTACCAAATATCAGCCACAATGGATTTAAGGATTTGTTTTTACGATCATCTTG
ATCTTATTTCGATTTAAATAAAAATTAATTCGGGAAAAATTGAAAAAATGATATTAGAAGCGTGA
AAAGCCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTACGAGTACTACGGTTAAAAATTGA
GGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCACGGTT
TTTGGCTAAAAACGCGATCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCAT
TGAAATA
Done.