Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020034.1 Corchorus olitorius cultivar O-4 contig20067, 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: 75901
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4817 original size:15 final size:15
Alignment explanation
Indices: 4797--4827 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4787 ACAATACATT
4797 AACTATCAAATAGAA
1 AACTATCAAATAGAA
4812 AACTATCAAATAGAA
1 AACTATCAAATAGAA
4827 A
1 A
4828 CATGTTAATC
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:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (15 bp):
AACTATCAAATAGAA
Found at i:4874 original size:14 final size:14
Alignment explanation
Indices: 4855--4889 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
4845 CCTTTTAAAT
4855 TAAAATAGTAAAAA
1 TAAAATAGTAAAAA
*
4869 TAAAATGGTAAAAA
1 TAAAATAGTAAAAA
4883 TAAAATA
1 TAAAATA
4890 ATTATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (14 bp):
TAAAATAGTAAAAA
Found at i:7775 original size:4 final size:4
Alignment explanation
Indices: 7768--7795 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
7758 TTAAGCGGAA
7768 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
7796 CCCAACAGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:10430 original size:26 final size:26
Alignment explanation
Indices: 10394--10446 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
10384 CAATATCAAT
10394 GGTGCTAGGACCCTTGTGCAGTCCAC
1 GGTGCTAGGACCCTTGTGCAGTCCAC
10420 GGTGCTAGGACCCTTGTGCAGTCCAC
1 GGTGCTAGGACCCTTGTGCAGTCCAC
10446 G
1 G
10447 TGAACATGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.15, C:0.30, G:0.32, T:0.23
Consensus pattern (26 bp):
GGTGCTAGGACCCTTGTGCAGTCCAC
Found at i:11284 original size:14 final size:14
Alignment explanation
Indices: 11265--11294 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
11255 TATATGGGTT
11265 AAAAGAAATACTAG
1 AAAAGAAATACTAG
11279 AAAAGAAATACTAG
1 AAAAGAAATACTAG
11293 AA
1 AA
11295 TTAGAATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (14 bp):
AAAAGAAATACTAG
Found at i:20704 original size:56 final size:56
Alignment explanation
Indices: 20618--20726 Score: 218
Period size: 56 Copynumber: 1.9 Consensus size: 56
20608 GTTTGTTATG
20618 TCTTTTGCTCATAAAGTCATATCCTTTCTTAGATCAGCTAACCATAGATTAAATGT
1 TCTTTTGCTCATAAAGTCATATCCTTTCTTAGATCAGCTAACCATAGATTAAATGT
20674 TCTTTTGCTCATAAAGTCATATCCTTTCTTAGATCAGCTAACCATAGATTAAA
1 TCTTTTGCTCATAAAGTCATATCCTTTCTTAGATCAGCTAACCATAGATTAAA
20727 CAGCTGTTCC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (56 bp):
TCTTTTGCTCATAAAGTCATATCCTTTCTTAGATCAGCTAACCATAGATTAAATGT
Found at i:28403 original size:2 final size:2
Alignment explanation
Indices: 28396--28425 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28386 TTAGCTCCTT
28396 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28426 ATTCAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38273 original size:331 final size:330
Alignment explanation
Indices: 37498--42630 Score: 3730
Period size: 331 Copynumber: 15.4 Consensus size: 330
37488 ATACTTTACA
* * * *
37498 TCATCTAACCAAATCTCAGCAACATTGGATTTAAGAATTTATTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * *
37563 TTCGATTTAATTAGAAATTAATTTC-GAAAAAAAAAGAAATACAATATTA-AAAGCGTAAAAAGC
66 TTCGATTTAATTAGAAATTAA-TTCAG-AAAAATATGAAAAACGATATTAGAAA-CGTGAAAAGC
* * * * *
37626 CCTCCAATTTTTTTTGGCGTTGAATTATATA-TTTTAATGAGTATTTTAGCCAAAAATTGA-GAA
128 CCTTCAA-TCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTGAGGAA
* * * * * *
37689 GAAATCTTTCGTGTCAATTTTTACAAAATTTTAGCCGACATCGAGTACTAACAAACCATCACGGT
192 -ATATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATC--GT-GTAA-TAATCATCACGGT
* * * * * * * *
37754 TTTTGGCTAAAAACACGTTCCGGGGACCCGGCTCAATTTCGCATGATTTCTGGCTA-CGAGACTA
252 TTTTGGCTAAAAACGCGTTCC-GGGCCCCGACTCAGTTTTGCATGATTTTTGGC-ACCAAGACTC
*
37818 CTTGAAATATCCATAT
315 CTTGAAATATCTATAT
* * * * *
37834 TCATCTAATCAAATCTCACCCACATTAGATTTAACGATTTGTCTTTACGAGCATCTGAATTTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * *
37899 TTCGATTTAATTAAAAATTAATTC-GAAAAAAAAAGACAAACGATATTAGAAATGTCAAAAGCCC
66 TTCGATTTAATTAGAAATTAATTCAG-AAAAATATGAAAAACGATATTAGAAACGTGAAAAGCCC
* * * * *
37963 TTCAATCTTTTTGGCACTGAGTTATGTATTTTTTATGAGTATTTTATCAAAAAATTGAGGAAATA
130 TTCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTGAGGAAATA
* *
38028 TCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATCACAGTTTTTGGAT
195 TCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTTTTTGGCT
* ** * * *
38093 AAAAAAGCGTTTTGTGGCCCCGACTTAGTTTTACATGATTTTTGGCACCAAGACTCCTTGAGATA
260 AAAAACGCGTTCCG-GGCCCCGACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATA
*
38158 TCTATAC
324 TCTATAT
* ** * *
38165 TCATCTAATCAAATCACAGCCACATTGGATTTAAAAATTTGTTTTTACAAGCATCTAAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
38230 TTCGATTTAATTAGAAATTAATACAGAAAAATATGAAAAACGATATTA-AAAGCATGAAAAGTCA
66 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAGAAA-CGTGAAAAGCCC
* * * * * * *
38294 TCCAATCTTTTTGCCGTT-AAGTTATATATATTTTA-GAAGTATTATATCCAAAAATTGAGGAAA
130 TTCAATCTTTTTGGCATTGAA-TTATATATTTTTTATG-AGTATTTTAGCTAAAAATTGAGG--A
* * * * * * * *
38357 AACAATTTTTTGGGT-TATATTTTGCAAAATTTTAACCAAAATCGTG---T-ACCATCACGG-TT
191 AA-TATCTTTCGGGTCAAT-TTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTTT
* * * * * * * *
38416 TTCGCTAAACACGCATTTCGGGGCACC-AGCTCAGTTTTGCATGATTTTTGACACCGACACTCCT
254 TTGGCTAAAAACGC-GTTCCGGGCCCCGA-CTCAGTTTTGCATGATTTTTGGCACCAAGACTCCT
**
38480 TGAAATAAATATAT
317 TGAAATATCTATAT
* * * * ** * *
38494 TCATCTAATAAAATCTTAGCCACATTGCACTTAATATATATTTTTTTTAACGATCATCTGAAT-T
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAA-GGAT-TTGTTTTT-ACGAGCATCTGAATCT
* * * * * * *
38558 ATATTTCGACTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATCACAAGCGTCAAAA
63 -TGTTTCGATTTAATTAGAAATTAATTCAG-AAAAATATGAAAAACGATATTAGAAACGTGAAAA
* * *
38623 GCCCTTCAATCTTTTTGG-AGTTGAATTATATATTTTTTATGAATATTATGGCTAAAAATTGAGG
126 GCCCTTCAATCTTTTTGGCA-TTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTGAGG
* *
38687 AAATATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTTTT
190 AAATATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTTTT
* * * * * ** *
38752 TGGCTAAAAACGCGTTCCGAGACCC-ATTTCAGTTTTGAATAATTTTTGGCGTCGAGACTCCTTG
255 TGGCTAAAAACGCGTTCCGGGCCCCGA-CTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTG
38816 AAATATCTATAT
319 AAATATCTATAT
* * * * *
38828 TCATCTAA-CTAAATCCCAG-C-C-----A-TT---G---TCTTTATA--AGCATTTGAATCATG
1 TCATCTAATC-AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
** * * * * * **
38876 TTTCTTTTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGGTATTTGAAGCGTGGGAAGCC
65 TTTCGATTTAATTAGAAATTAATTCAG-AAAAATATGAAAAACGATATTAGAAACGTGAAAAGCC
* * * * * *
38941 CTTCAATCTTTTTAGCGTTGAATTATATATATTTTTATGACTATTGT-GACTACAAGTTGAGGAA
129 CTTCAATCTTTTTGGCATTGAATTATATAT-TTTTTATGAGTATTTTAG-CTAAAAATTGAGGAA
* * * * * * * * **
39005 AAATATTTCGGGTCATTTTTTGCAAAATATTAGCTGAAATCGTGCAA-CATCA-CGATCTCTTTT
192 ATATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATC-A-C-GGTTT
* * * ** * **
39068 TTGGATAAAAACGCGTTCCACGACCCCGGGTCAG-ATTGCAAAATTTTTGGCACCAAGACTCCTT
254 TTGGCTAAAAACGCGTTCC-GGGCCCCGACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTT
*
39132 GAATTATCTATAT
318 GAAATATCTATAT
* * * ** * * *
39145 TAAACTAATCAATTCTCAGCTGCATTGGATTTTAGGATTTGTTTTTGCGAGCATCTAAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * ***
39210 TTCGATTTAATTAGAAATTAATTC-GAAAATAGTAGGAAAAACGATATTTGAAGCGTAAAAAATG
66 TTCGATTTAATTAGAAATTAATTCAGAAAA-A-TATGAAAAACGATATTAGAAACGTGAAAAGCC
* * *
39274 CTTCAATATTTTTGGCATAGAATTATATTATTTTTTATGA-TAATTTAGC-AGGAAAATTGAGGA
129 CTTCAATCTTTTTGGCATTGAATTATA-TATTTTTTATGAGTATTTTAGCTA--AAAATTGAGGA
* * **
39337 AATATTTTTCCGGTCAATTTTTACAAAATTTTAGGTGAAATCGTGTAATAATCATCACGGTTTTT
191 AATATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTTTTT
* * *** * * * * *
39402 GACTAAAAATGCGTTCCAGGGCCTTTAGTTAGTTTTGCATTATTTTTGGCACTAAGACTACTTGA
256 GGCTAAAAACGCGTTCC-GGGCCCCGACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGA
* *
39467 GATATCCATAT
320 AATATCTATAT
* * * * * *
39478 TCATCTAATTAAATCTTAGACACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTAT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
39543 TTCGATTAAATTAGAAATTAATTTAGAAAAATTATGAAAAACGATATGA-AAATCGTGAAACA-T
66 TTCGATTTAATTAGAAATTAATTCAGAAAAA-TATGAAAAACGATATTAGAAA-CGTGAAA-AGC
* *
39606 CCTCCAATCTTTTTGGCGTTAATTATATATATATATATATATATATATATTTCATGAGTATTTTA
128 CCTTCAATCTTTTTGGC---------AT-T-GA-AT-TATATAT-T-T-TTT-ATGAGTATTTTA
* * * * * ** *
39671 GCCAAAAATTGATGAAA-ATTTTTCTGGTC-TTTTTTACAAAATTTTAGGTGAAATCGTGTACTA
176 GCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATA
* * * * * *
39734 A-CAATCACAGTTTTTTTTTTTTTGCTAAAAACGCGTTTCAGGTCCCGGCTCAGTTTTGCATGAT
241 ATC-ATCAC-G------GTTTTTGGCTAAAAACGCGTTCCGGGCCCCGACTCAGTTTTGCATGAT
* * * *
39798 TTTTGGCATCGAGGCTCCTTGAAATATATATAT
298 TTTTGGCACCAAGACTCCTTGAAATATCTATAT
* * * * * * *
39831 TCATCTAATTAAATCTCAGTCACATTGCATTTTAA-GATTTATTTTTACGAGTATCTGAATTTTA
1 TCATCTAATCAAATCTCAGCCACATTGGA-TTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
** * * *
39895 TTTCGATTTAATTAGATTTTAATTCAGAAAAATATGAGAAACGATATTA-AAAGTGTGAAAAGTC
65 TTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAGAAA-CGTGAAAAGCC
* *
39959 C-TCTAATATTTTTGG-AGTTGAATTATATATATATATATATATTATGAATATTTTAG--ACAAA
129 CTTC-AATCTTTTTGGCA-TTG-A--AT-TATATAT-T-T-T-TTATGAGTATTTTAGCTA-AAA
* * * * * * * *
40020 ATTGAGGAAA-A-CTAACTCTGTTAAATTTTTACAAAATATTAGTCGAAATCGTGTACGTTAGTC
183 ATTGAGGAAATATCT--TTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTA--ATAATC
* * ** * ** ** * *
40083 GAAATCGCCGTTTTTTACTAAAAACGCCTTCCAAAGCCCCGGTTCAGTGTTGCATGATTTTTTGC
244 ---ATCACGGTTTTTGGCTAAAAACGCGTTCC-GGGCCCCGACTCAGTTTTGCATGATTTTTGGC
* * * *
40148 GCCATGATTCCTTGAAATATCCATAT
305 ACCAAGACTCCTTGAAATATCTATAT
* * * * *** * * *
40174 TAATCTAACCAAATCTCATCCACAATGGATTTAAGGATTTG-TAAAACAAGCATCTGAATCATAT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * * * *
40238 TTCGATTTAATTAGAATTTAATTCTGAAAATAATAGGAAAAACGCTACTAGAAGCATGAAAATCC
66 TTCGATTTAATTAGAAATTAATTCAG-AAA-AATATGAAAAACGATATTAGAAACGTGAAAAGCC
* *** *
40303 CTTCAATATTTTTGGCATTGAATTATATGA--TTTTACTGAGTATTGCGGCTAAAATTTGAGGAA
129 CTTCAATCTTTTTGGCATTGAATTATAT-ATTTTTTA-TGAGTATTTTAGCTAAAAATTGAGGAA
* * * * **
40366 ATAACTTTCGAGTCAATTATTACAAAATTATAGCCGAAATCGTGTAATAATCATCATTGTTTTTG
192 ATATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTTTTTG
* * * * * * * * * *
40431 GCTAAAAACACATTCCGGGTCCCGTCTAAGTTTTGCATGATTTTTGACGCCAAAACTCTTTGAGA
257 GCTAAAAACGCGTTCCGGGCCCCGACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAA
40496 TATCTATAT
322 TATCTATAT
* * * * * *
40505 TGATCTAATCAAATCTCAGCTACATCGGATTTAAGAATTTGTTTTTATGAGCAGCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* *
40570 TTCGGTTTAATTAGAAATTAATTCA-AAAAATATGAAAAACGATATTA-AAAGCGTGAAAAGTCC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAGAAA-CGTGAAAAGCCC
* * * *
40633 TCCAATCCTTTTGGCGTTAAATTATATATATATATATATATATATATTATGAGTA-TTTATGCTG
130 TTCAATCTTTTTGGC-----A-T-T-GA-AT-TATATAT-T-T-T-TTATGAGTATTTTA-GCTA
* * * * * * * *
40697 AAATTTGACAGAAAAATTTTTCGGGTCATTTTTTACAAAATTTTAGCCGAAATCGTATACTAATT
180 AAAATTGA-GGAAATATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAATC
* * * * * *
40762 ATCACGGTTTTTGGCTAAAAACGCGTTTCGGGACCTCAACTTAGTTTTGCATGATTTTTTGCGCC
244 ATCACGGTTTTTGGCTAAAAACGCGTTCCGGG-CCCCGACTCAGTTTTGCATGATTTTTGGCACC
*
40827 AAGACTCTTTGAAATATCTATAT
308 AAGACTCCTTGAAATATCTATAT
* * * * * * *
40850 TTATCTAGTCAAATCTCAACCACATTGAATGTATGAATTTGTTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * *
40915 TTGGATATAATTAGAAACTAATTCAG-AAAATATG-AAAACGATATTA-AAAGCGTGAAGAGTCC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAGAAA-CGTGAAAAGCCC
* * * * * * * * * *
40977 TCCAAACTTTTTGGCTTTTAATTATATATATTCTATGAGTATTGTGGCTAAAAATGGAGGAAAAA
130 TTCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTGAGG-AAAT
* ** * *
41042 AT-TTT-GGGTGAATTTTTGGAAAATTTTAGCCGAAATCATG---T-ACCATCACGGTTTTTTGG
194 ATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATCACGG-TTTTTGG
* * * *** * * * *
41101 CTAAAAACGCGTTCTGGGGCCCCGAGTCAGTTTTGCATGATTTTTAGTGGCAACATTGCTTGAAG
258 CTAAAAACGCGTTC-CGGGCCCCGACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAA
41166 TATCTATAT
322 TATCTATAT
* * * * *
41175 TCATCTAGTCAAATC-CTACCCACTTTGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCATG
1 TCATCTAATCAAATCTC-AGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * * * * * *
41239 TTTCAATTTAATTAGAAATTAATTTGAAAACAAATAGGAAAAATGATATTAGAAGCGTGAGAAGC
65 TTTCGATTTAATTAGAAATTAA-TTCAGAA-AAATATGAAAAACGATATTAGAAACGTGAAAAGC
* * * * * *
41304 CTTTCAATCTTTTTGGCGTTGAATTATATATTTTTCATGAGTATTGTGGCTAAAAATTGAGAAAA
128 CCTTCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTGAG-GAA
* ** * * * *
41369 ATATC--TGGGGTCAATTTTTTGTAAAATTGTAACCGAAAT--TGT-AT-ACCATCATGGGTTTT
192 ATATCTTTCGGGTCAA-TTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATCA-CGG----
* * * * *
41428 TTTTTTTTTTGCTAAAAACGCGTTCTGAGG-CTCTAGGTCAGTTTTGCATGATTTTTGG-----A
251 ----TTTTTGGCTAAAAACGCGTTCCG-GGCCCCGA-CTCAGTTTTGCATGATTTTTGGCACCAA
41487 G--T-C---AAGAT-TCCT-TAT
310 GACTCCTTGAA-ATAT-CTATAT
* * * * * ** * *
41502 GCATCTAACCAAATCTCAACCACATTGTATTTAAGGATTTGTTTGTACGAGTTTCTAAATCCTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* ** * * * *
41567 TTCGATTTAATCAGAAATTAATTTTGAAATAAAATAGGAAAACGATATTAGAAGCGTGAAAAAGG
66 TTCGATTTAATTAGAAATTAATTCAGAAA-AATAT-GAAAAACGATATTAGAAACGTG-AAAAGC
* * * * * * * **
41632 CTTTCAGT-TTTTTTGAAGTTGAATTATTTGTTTTTTATGAGTATTTTCGCTAGAAAA-CAAGGA
128 CCTTCAATCTTTTTGGCA-TTGAATTATATATTTTTTATGAGTATTTTAGCTA-AAAATTGAGGA
* ** * * * *
41695 AAAAAATTTTGGGTCAATTTTTGCAAAA-TTTAGCCGAAATC--GT-AT-A-GATCACGGTTTTC
191 AATATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTTTTT
* * * **
41754 GGCAAAAAACGCGTTCCGGGGTCCGGA-TCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGA
256 GGCTAAAAACGCGTTCC-GGGCCCCGACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGA
* *
41818 AATTTTTATAT
320 AATATCTATAT
* *
41829 TCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * *
41894 TTCTATTTAATTAGAAATTAATTCTGAAAAATTAGGAAAAAC-AAATTAGAAGCGTTAAAAGCCC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAA-TATGAAAAACGATATTAGAAACGTGAAAAGCCC
* * ** * * *
41958 TTTAATTTTTTTGATATCGAAATATATATTTTTTATGAGTATTTTAG-TCAAAAATTGAGAAAAT
130 TTCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCT-AAAAATTGAGGAAAT
* *
42022 ATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTACTAATCATCACAGTTTTTGGC
194 ATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTTTTTGGC
* * ** * * * * *
42087 TAAAAACGCGTTACAGGACAACGGCTCTGTTTTGCATAATTTTTTGCACCGAGACTCCTTGAAAT
259 TAAAAACGCGTT-CCGGGCCCCGACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAAT
*
42152 ATCTTTAT
323 ATCTATAT
* * *
42160 TCATCTAACCAAATCTCAGTCACATCGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * *
42225 TTCTATTTAATTAGAAAATAATTCAGAAAAAAATAGGAAAAACAATATTAGAAGCGTTAAAAGCC
66 TTCGATTTAATTAGAAATTAATTCAG--AAAAATATGAAAAACGATATTAGAAACGTGAAAAGCC
* ** * * *
42290 CTTCAATTTTTTTGATATCGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGAAAAT
129 CTTCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTGAGGAAAT
* ** *
42355 ATCTTTCGAGTCAATTTTTACAAAATTTTAATCGAAATCGTGT-A-CATCATCACGGTTTTTGGC
194 ATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTTTTTGGC
* *** * * * * *
42418 TAAAAACGCGTTACAGGGGAACAACTCTGTTTTGCATAATTTTTTGCACCGAGACTCCTTGAAAT
259 TAAAAACGCGTT-CCGGGCCCCGACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAAT
*
42483 ATCTTTAT
323 ATCTATAT
* * * * * **
42491 TCATCTAACCAAATTTCAGCCACATTGGATTTAAGGATTTGTTTTTATGTGCATCCGAATCTAAT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* *
42556 TTCGATTTAATTAGAAATAAATT-AGAAAAATATGAAAAACGATATTA-AAATCGTGAAAAGTCC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAGAAA-CGTGAAAAGCCC
*
42619 TCCAATCTTTTT
130 TTCAATCTTTTT
42631 TAGCATTTTT
Statistics
Matches: 3857, Mismatches: 724, Indels: 440
0.77 0.14 0.09
Matches are distributed among these distances:
314 1 0.00
315 95 0.02
316 89 0.02
317 91 0.02
318 16 0.00
319 1 0.00
321 2 0.00
323 6 0.00
324 74 0.02
325 171 0.04
326 30 0.01
327 216 0.06
328 139 0.04
329 221 0.06
330 143 0.04
331 616 0.16
332 147 0.04
333 500 0.13
334 150 0.04
335 127 0.03
336 94 0.02
337 50 0.01
338 50 0.01
339 7 0.00
340 5 0.00
341 5 0.00
342 84 0.02
343 129 0.03
344 182 0.05
345 140 0.04
346 8 0.00
347 40 0.01
348 15 0.00
349 21 0.01
350 8 0.00
351 3 0.00
352 37 0.01
353 121 0.03
354 23 0.01
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (330 bp):
TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAGAAACGTGAAAAGCCCT
TCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTGAGGAAATAT
CTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTTTTTGGCTA
AAAACGCGTTCCGGGCCCCGACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATC
TATAT
Found at i:39517 original size:333 final size:330
Alignment explanation
Indices: 38861--42630 Score: 2511
Period size: 333 Copynumber: 11.3 Consensus size: 330
38851 TGTCTTTATA
* * ** * *
38861 AGCATTTGAATCATGTTTCTTTTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGGTATTT
1 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAATAGGAAAAACGATATTA
** ** * * * *
38926 GAAGCGTGGGAAGCCCTTCAATCTTTTTAGCGTTGAATTATA-TATATTTTTATGACT-ATTGT-
65 GAAGCGTGAAAAATCCTTCAATATTTTTGGCATTGAATTATATTAT-TTTTTATGAGTAATT-TA
* * * * * * * *
38988 GACTACAAGTTGAGGAAAAATATTTCGGGTCATTTTTTGCAAAATATTAGCTGAAATCGTGCAA-
128 G-C-AAAAATTGAGGAAAAATTTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAAT
* ** * * * * * * **
39052 CATCA-CGATCTCTTTTTTGGATAAAAACGCGTTCCACGACCCCGGGTCAG-ATTGCAAAATTTT
191 AATCATC-A-C-GGTTTTTGGCTAAAAACGCGTTCCAGGGCCCC-AGTTAGTTTTGCATGATTTT
* * * * ** *
39115 TGGCACCAAGACTCCTTGAATTATCTATATTAAACTAATCAATTCTCAGCTGCATTGGATTTTAG
252 TGGCACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAG
*
39180 GATTTGTTTTTGCG
317 GATTTGTTTTTACG
* * *
39194 AGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAATAGTAGGAAAAACGATATTT
1 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAA-AATAGGAAAAACGATATTA
* * *
39259 GAAGCGTAAAAAATGCTTCAATATTTTTGGCATAGAATTATATTATTTTTTATGA-TAATTTAGC
65 GAAGCGTGAAAAATCCTTCAATATTTTTGGCATTGAATTATATTATTTTTTATGAGTAATTTAGC
* * **
39323 AGGAAAATTGAGGAAATATTTTTCCGGTCAATTTTTACAAAATTTTAGGTGAAATCGTGTAATAA
130 A--AAAATTGAGGAAAAATTTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAA
* * ** *
39388 TCATCACGGTTTTTGACTAAAAATGCGTTCCAGGGCCTTTAGTTAGTTTTGCATTATTTTTGGCA
193 TCATCACGGTTTTTGGCTAAAAACGCGTTCCAGGGCC-CCAGTTAGTTTTGCATGATTTTTGGCA
* * * * * * * *
39453 CTAAGACTACTTGAGATATCCATATTCATCTAATTAAATCTTAGACACATTGCATTTAAGGATTT
257 CCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTT
39518 GTTTTTACG
322 GTTTTTACG
* * * * * * *
39527 AGCATCTAAATCTTATTTCGATTAAATTAGAAATTAATTTAGAAAAATTATGAAAAACGATATGA
1 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TTCGAAAAAATAGGAAAAACGATATTA
* * * * * *
39592 AAATCGTGAAACATCCTCCAATCTTTTTGGCGTTAATTATATATATATATATATATATATATATT
65 GAAGCGTGAAAAATCCTTCAATATTTTTGGC-------AT-T-GA-AT-TATAT-TAT-T-T-TT
* * * * **
39657 TCATGAGTATTTTAGCCAAAAATTGATG-AAAATTTTTCTGGTC-TTTTTTACAAAATTTTAGGT
115 T-ATGAGTAATTTAG-CAAAAATTGAGGAAAAATTTTTCGGGTCAATTTTTACAAAATTTTAGCC
* * * * * *
39720 GAAATCGTGTACTAA-CAATCACAGTTTTTTTTTTTTTGCTAAAAACGCGTTTCA-GGTCCCGGC
178 GAAATCGTGTAATAATC-ATCAC-G------GTTTTTGGCTAAAAACGCGTTCCAGGGCCCCAG-
* * * * * *
39783 TCAGTTTTGCATGATTTTTGGCATCGAGGCTCCTTGAAATATATATATTCATCTAATTAAATCTC
234 TTAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTC
* * *
39848 AGTCACATTGCATTTTAA-GATTTATTTTTACG
299 AGCCACATTGGA-TTTAAGGATTTGTTTTTACG
* * * ** * *
39880 AGTATCTGAATTTTATTTCGATTTAATTAGATTTTAATTC-AGAAAAATATGAGAAACGATATTA
1 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGA-AAAAATAGGAAAAACGATATTA
* * * *
39944 AAAGTGTGAAAAGTCC-TCTAATATTTTTGG-AGTTGAATTATATATATATATATATATTATGAA
65 GAAGCGTGAAAAATCCTTC-AATATTTTTGGCA-TTGAA-T-TATAT-TAT-T-T-T-TTATGAG
* * *** * * * * *
40007 TATTTTAG-ACAAAATTGAGGAAAACTAACTCTGTTAAATTTTTACAAAATATTAGTCGAAATCG
121 TAATTTAGCA-AAAATTGAGGAAAAATTTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCG
* * * * ** * ** * *
40071 TGTACGTTAGTCGAAATCGCCGTTTTTTACTAAAAACGCCTTCCAAAGCCCCGGTTCAGTGTTGC
185 TGTA--ATAATC---ATCACGGTTTTTGGCTAAAAACGCGTTCCAGGGCCCCAGTT-AGTTTTGC
* * * * * * * * *
40136 ATGATTTTTTGCGCCATGATTCCTTGAAATATCCATATTAATCTAACCAAATCTCATCCACAATG
244 ATGATTTTTGGCACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTG
*** *
40201 GATTTAAGGATTTG-TAAAACA
309 GATTTAAGGATTTGTTTTTACG
* * * * *
40222 AGCATCTGAATCATATTTCGATTTAATTAGAATTTAATTCTGAAAATAATAGGAAAAACGCTACT
1 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GAAAA-AATAGGAAAAACGATATT
* *
40287 AGAAGCATG-AAAATCCCTTCAATATTTTTGGCATTGAATTATATGA--TTTTACTGAGT-ATTG
64 AGAAGCGTGAAAAAT-CCTTCAATATTTTTGGCATTGAATTATATTATTTTTTA-TGAGTAATT-
** * * * * *
40348 CGGCTAAAATTTGAGGAAATAA-CTTTCGAGTCAATTATTACAAAATTATAGCCGAAATCGTGTA
126 TAGC-AAAAATTGAGGAAA-AATTTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTA
** * * *
40412 ATAATCATCATTGTTTTTGGCTAAAAACACATTCC-GGGTCCC-GTCTAAGTTTTGCATGATTTT
189 ATAATCATCACGGTTTTTGGCTAAAAACGCGTTCCAGGGCCCCAGT-T-AGTTTTGCATGATTTT
* * * * * * * *
40475 TGACGCCAAAACTCTTTGAGATATCTATATTGATCTAATCAAATCTCAGCTACATCGGATTTAAG
252 TGGCACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAG
* *
40540 AATTTGTTTTTATG
317 GATTTGTTTTTACG
* * * *
40554 AGCAGCTGAATCTTGTTTCGGTTTAATTAGAAATTAATTC-AAAAAATATGAAAAACGATATTAA
1 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATAGGAAAAACGATATTAG
* * ** *
40618 AAGCGTGAAAAGTCCTCCAATCCTTTTGGCGTTAAATTATATATATATATATATATATATATTAT
66 AAGCGTGAAAAATCCTTCAATATTTTTGGC-----ATT-GA-AT-TATAT-TAT-T-T-T-TTAT
* * * *
40683 GAGT-ATTTATGCTGAAATTTGACAGAAAAATTTTTCGGGTCATTTTTTACAAAATTTTAGCCGA
118 GAGTAATTTA-GC-AAAAATTGA-GGAAAAATTTTTCGGGTCAATTTTTACAAAATTTTAGCCGA
* * * * * *
40747 AATCGTATACTAATTATCACGGTTTTTGGCTAAAAACGCGTTTC-GGGACCTCAACTTAGTTTTG
180 AATCGTGTAATAATCATCACGGTTTTTGGCTAAAAACGCGTTCCAGGG-CC-CCAGTTAGTTTTG
* * * * * *
40811 CATGATTTTTTGCGCCAAGACTCTTTGAAATATCTATATTTATCTAGTCAAATCTCAACCACATT
243 CATGATTTTTGGCACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATT
* * * *
40876 GAATGTATGAATTTGTTTTTACG
308 GGATTTAAGGATTTGTTTTTACG
* * * * * *
40899 AGCATCTGAATCTTGTTTGGATATAATTAGAAACTAATTC-AGAAAATATG-AAAACGATATTAA
1 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATAGGAAAAACGATATTAG
* * * * * * * *
40962 AAGCGTGAAGAGTCCTCCAA-ACTTTTTGGCTTTTAATTATA-TATATTCTATGAGT-ATTGTGG
66 AAGCGTGAAAAATCCTTCAATA-TTTTTGGCATTGAATTATATTATTTTTTATGAGTAATT-TAG
* * * ** *
41024 CTAAAAATGGAGGAAAAAATTTT-GGGTGAATTTTTGGAAAATTTTAGCCGAAATCATG---T-A
129 C-AAAAATTGAGGAAAAATTTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAA
* ** * * *
41084 CCATCACGGTTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGAGTCAGTTTTGCATGATTTTTAGT
193 TCATCACGG-TTTTTGGCTAAAAACGCGTTCCAGGGCCCC-AGTTAGTTTTGCATGATTTTTGGC
** * * * * * * *
41149 GGCAACATTGCTTGAAGTATCTATATTCATCTAGTCAAATC-CTACCCACTTTGGATTTAAGGAT
256 ACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTC-AGCCACATTGGATTTAAGGAT
41213 TTGTTTTTACG
320 TTGTTTTTACG
* * * * *
41224 AGCATTTGAATCATGTTTCAATTTAATTAGAAATTAATTTGAAAACAAATAGGAAAAATGATATT
1 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCG-AAA-AAATAGGAAAAACGATATT
* * * * *
41289 AGAAGCGTG-AGAAGCCTTTCAATCTTTTTGGCGTTGAATTATA-TATTTTTCATGAGT-ATTGT
64 AGAAGCGTGAAAAATCC-TTCAATATTTTTGGCATTGAATTATATTATTTTTTATGAGTAATT-T
* * * * ** * *
41351 GGCTAAAAATTGA-GAAAAATATCTGGGGTCAATTTTTTGTAAAATTGTAACCGAAAT--TGT-A
127 AGC-AAAAATTGAGGAAAAATTTTTCGGGTCAA-TTTTTACAAAATTTTAGCCGAAATCGTGTAA
* * * * * * *
41412 T-ACCATCATGGGTTTTTTTTTTTTTTGCTAAAAACGCGTT-CTGAGGCTCTAGGTCAGTTTTGC
190 TAATCATCA-CGG--------TTTTTGGCTAAAAACGCGTTCCAG-GGCCCCA-GTTAGTTTTGC
* * *
41475 ATGATTTTTGG-----AG--T-C---AAGAT-TCCT-TATGCATCTAACCAAATCTCAACCACAT
244 ATGATTTTTGGCACCAAGACTCCTTGAA-ATAT-CTATATTCATCTAATCAAATCTCAGCCACAT
* *
41527 TGTATTTAAGGATTTGTTTGTACG
307 TGGATTTAAGGATTTGTTTTTACG
** * * * *
41551 AGTTTCTAAATCCTGTTTCGATTTAATCAGAAATTAATTTTGAAATAAAATAGG-AAAACGATAT
1 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TTCG-AA-AAAATAGGAAAAACGATAT
* * * * * * *
41615 TAGAAGCGTGAAAAAGGCTTTCAGT-TTTTTTGAAGTTGAATTAT-TTGTTTTTTATGAGTATTT
63 TAGAAGCGTGAAAAA-TCCTTCAATATTTTTGGCA-TTGAATTATATTATTTTTTATGAGTAATT
* ** * *
41678 TCGCTAGAAAA-CAAGGAAAAAAATTTT-GGGTCAATTTTTGCAAAA-TTTAGCCGAAATC--GT
126 TAGC-A-AAAATTGAGG-AAAAATTTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGT
* * * ** * *
41738 -AT-A-GATCACGGTTTTCGGCAAAAAACGCGTTCC-GGGGTCCGGATCAGTTTTGCATGATTTT
188 AATAATCATCACGGTTTTTGGCTAAAAACGCGTTCCAGGGCCCCAG-TTAGTTTTGCATGATTTT
** * * * *
41799 TGGTGCCAAGACTCCTTGAAATTTTTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAG
252 TGGCACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAG
41864 GATTTGTTTTTACG
317 GATTTGTTTTTACG
* * *
41878 AGCATCTGAATCTTGTTTCTATTTAATTAGAAATTAATTCTGAAAAATTAGGAAAAAC-AAATTA
1 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAATAGGAAAAACGATATTA
* ** * * ** * * *
41942 GAAGCGTTAAAAGCCCTTTAATTTTTTTGATATCGAAATATA-TATTTTTTATGAGTATTTTAGT
65 GAAGCGTGAAAAATCCTTCAATATTTTTGGCATTGAATTATATTATTTTTTATGAGTAATTTAG-
* *
42006 CAAAAATTGA-GAAAATATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTACTAA
129 CAAAAATTGAGGAAAA-ATTTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAA
* * * ** * * *
42070 TCATCACAGTTTTTGGCTAAAAACGCGTTACAGGACAACGGCTCT-GTTTTGCATAATTTTTTGC
193 TCATCACGGTTTTTGGCTAAAAACGCGTTCCAGGGCCCCAG-T-TAGTTTTGCATGATTTTTGGC
* * * * *
42134 ACCGAGACTCCTTGAAATATCTTTATTCATCTAACCAAATCTCAGTCACATCGGATTTAAGGATT
256 ACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATT
42199 TGTTTTTACG
321 TGTTTTTACG
* * *
42209 AGCATCTGAATCTTGTTTCTATTTAATTAGAAAATAATTCAGAAAAAAATAGGAAAAACAATATT
1 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-G-AAAAAATAGGAAAAACGATATT
* ** * ** * *
42274 AGAAGCGTTAAAAGCCCTTCAATTTTTTTGATATCGAATTATA-TATTTTTTATGAGTATTTTAG
64 AGAAGCGTGAAAAATCCTTCAATATTTTTGGCATTGAATTATATTATTTTTTATGAGTAATTTAG
* * ** *
42338 CCAAAAATTGA-GAAAATATCTTTCGAGTCAATTTTTACAAAATTTTAATCGAAATCGTGT-A-C
129 -CAAAAATTGAGGAAAA-ATTTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATA
* ** * * * *
42400 ATCATCACGGTTTTTGGCTAAAAACGCGTTACAGGGGAACAACTCT-GTTTTGCATAATTTTTTG
192 ATCATCACGGTTTTTGGCTAAAAACGCGTTCCA-GGGCCCCAGT-TAGTTTTGCATGATTTTTGG
* * * *
42464 CACCGAGACTCCTTGAAATATCTTTATTCATCTAACCAAATTTCAGCCACATTGGATTTAAGGAT
255 CACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGAT
*
42529 TTGTTTTTATG
320 TTGTTTTTACG
* * ** * * * *
42540 TGCATCCGAATCTAATTTCGATTTAATTAGAAATAAATTAG-AAAAATATGAAAAACGATATTAA
1 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATAGGAAAAACGATATTAG
* * * *
42604 AATCGTGAAAAGTCCTCCAATCTTTTT
66 AAGCGTGAAAAATCCTTCAATATTTTT
42631 TAGCATTTTT
Statistics
Matches: 2777, Mismatches: 496, Indels: 333
0.77 0.14 0.09
Matches are distributed among these distances:
315 1 0.00
316 25 0.01
317 18 0.01
318 1 0.00
321 2 0.00
322 4 0.00
323 10 0.00
324 61 0.02
325 181 0.07
326 19 0.01
327 202 0.07
328 156 0.06
329 137 0.05
330 92 0.03
331 368 0.13
332 113 0.04
333 417 0.15
334 21 0.01
335 11 0.00
336 12 0.00
337 53 0.02
338 50 0.02
339 2 0.00
340 2 0.00
341 2 0.00
342 82 0.03
343 140 0.05
344 188 0.07
345 134 0.05
346 6 0.00
347 41 0.01
348 17 0.01
349 18 0.01
350 7 0.00
351 4 0.00
352 44 0.02
353 112 0.04
354 24 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (330 bp):
AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATAGGAAAAACGATATTAG
AAGCGTGAAAAATCCTTCAATATTTTTGGCATTGAATTATATTATTTTTTATGAGTAATTTAGCA
AAAATTGAGGAAAAATTTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCA
TCACGGTTTTTGGCTAAAAACGCGTTCCAGGGCCCCAGTTAGTTTTGCATGATTTTTGGCACCAA
GACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTT
TTACG
Found at i:39636 original size:2 final size:2
Alignment explanation
Indices: 39629--39655 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39619 TGGCGTTAAT
39629 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
39656 TTCATGAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40662 original size:2 final size:2
Alignment explanation
Indices: 40655--40679 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40645 GGCGTTAAAT
40655 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
40680 TATGAGTATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44664 original size:21 final size:21
Alignment explanation
Indices: 44627--44670 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
44617 TGATCATTGT
* *
44627 AATTTCATTTTTATAAATGAA
1 AATTACATTTTTATAAAAGAA
44648 AATTACATTTTCT-TAAAAGAA
1 AATTACATTTT-TATAAAAGAA
44669 AA
1 AA
44671 AATAAGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (21 bp):
AATTACATTTTTATAAAAGAA
Found at i:45173 original size:22 final size:21
Alignment explanation
Indices: 45128--45181 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
45118 CCATATTTTT
*
45128 TATAA-ATATATTTTATGTAG
1 TATAATATATATTTGATGTAG
45148 TATAATATATATTGTGATGTTA-
1 TATAATATATATT-TGATG-TAG
*
45170 TATATTATATAT
1 TATAATATATAT
45182 AAATAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 5 0.17
21 7 0.24
22 15 0.52
23 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (21 bp):
TATAATATATATTTGATGTAG
Found at i:45226 original size:21 final size:21
Alignment explanation
Indices: 45200--45246 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
45190 AAGATATATG
* * *
45200 TATTATATGTAATATATATAC
1 TATTATATATAATATAAATAA
45221 TATTATATATAATATAAATAA
1 TATTATATATAATATAAATAA
45242 TATTA
1 TATTA
45247 ATACAGGCCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
TATTATATATAATATAAATAA
Found at i:47275 original size:30 final size:30
Alignment explanation
Indices: 47240--47296 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
47230 TTTTCTCCTC
*
47240 TCTTCTATCTTCTTCCTCCTTTGTTTACTT
1 TCTTCTATCTTCTTCCTCCTCTGTTTACTT
47270 TCTTCTATCTTCTTCCTCCTCTGTTTA
1 TCTTCTATCTTCTTCCTCCTCTGTTTA
47297 GGGCTTCTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.07, C:0.32, G:0.04, T:0.58
Consensus pattern (30 bp):
TCTTCTATCTTCTTCCTCCTCTGTTTACTT
Found at i:47720 original size:95 final size:95
Alignment explanation
Indices: 47619--47805 Score: 329
Period size: 95 Copynumber: 2.0 Consensus size: 95
47609 AGGGTTTAGG
* * * *
47619 GTTGATTTGATTTCTATTTAATTTGAGTTTTTCGGGTTTATTTTGGATGTTCATTTGGATTTCTT
1 GTTGATTTGATTTCAATTTAATTTGAGCTTTTAGGATTTATTTTGGATGTTCATTTGGATTTCTT
47684 ACAGGTTGGAGGAGGGAGTGATTTTTTCGT
66 ACAGGTTGGAGGAGGGAGTGATTTTTTCGT
47714 GTTGATTTGATTTCAATTTAATTTGAGCTTTTAGGATTTATTTTGGATGTTCATTTGGATTTCTT
1 GTTGATTTGATTTCAATTTAATTTGAGCTTTTAGGATTTATTTTGGATGTTCATTTGGATTTCTT
*
47779 ACAGGTTGGAGGAGGGTGTGATTTTTT
66 ACAGGTTGGAGGAGGGAGTGATTTTTT
47806 TGTATGGATT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 87 1.00
ACGTcount: A:0.18, C:0.06, G:0.26, T:0.50
Consensus pattern (95 bp):
GTTGATTTGATTTCAATTTAATTTGAGCTTTTAGGATTTATTTTGGATGTTCATTTGGATTTCTT
ACAGGTTGGAGGAGGGAGTGATTTTTTCGT
Found at i:47807 original size:49 final size:49
Alignment explanation
Indices: 47659--47807 Score: 125
Period size: 49 Copynumber: 3.1 Consensus size: 49
47649 TTCGGGTTTA
*
47659 TTTTGGATGTTCATTTGGATTTCTTACAGGTTGGAGGAGGGAGTGA-TT
1 TTTTGGATGTTCATTTGGATTTCTTACAGGTTGGAGGAGGGTGTGATTT
* * * ****
47707 TTTTCG-TGTTGATTT-GATTTCAATTTA-A--TTTGA-GCTTTTAG-GATTT
1 TTTTGGATGTTCATTTGGATTTC---TTACAGGTTGGAGGAGGGT-GTGATTT
47753 ATTTTGGATGTTCATTTGGATTTCTTACAGGTTGGAGGAGGGTGTGATTT
1 -TTTTGGATGTTCATTTGGATTTCTTACAGGTTGGAGGAGGGTGTGATTT
47803 TTTTG
1 TTTTG
47808 TATGGATTGA
Statistics
Matches: 73, Mismatches: 15, Indels: 25
0.65 0.13 0.22
Matches are distributed among these distances:
45 3 0.04
46 16 0.22
47 14 0.19
48 14 0.19
49 19 0.26
50 7 0.10
ACGTcount: A:0.18, C:0.06, G:0.28, T:0.48
Consensus pattern (49 bp):
TTTTGGATGTTCATTTGGATTTCTTACAGGTTGGAGGAGGGTGTGATTT
Found at i:50986 original size:15 final size:15
Alignment explanation
Indices: 50966--51003 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
50956 CTCTCCTTGT
50966 TGGGCCTGCAGTTGC
1 TGGGCCTGCAGTTGC
*
50981 TGGGCCTGCAGTTTC
1 TGGGCCTGCAGTTGC
50996 TGGGCCTG
1 TGGGCCTG
51004 GATTATCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.05, C:0.26, G:0.39, T:0.29
Consensus pattern (15 bp):
TGGGCCTGCAGTTGC
Found at i:51861 original size:2 final size:2
Alignment explanation
Indices: 51854--51886 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
51844 TCTAACTTAG
51854 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51887 GTTTATTGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58278 original size:18 final size:17
Alignment explanation
Indices: 58255--58325 Score: 69
Period size: 18 Copynumber: 4.2 Consensus size: 17
58245 CATAAATAAA
58255 AAATAAAAACATAAAATT
1 AAATAAAAA-ATAAAATT
*
58273 AAAT--AAAATTAAA--
1 AAATAAAAAATAAAATT
58286 AAATAAAAACATAAAATT
1 AAATAAAAA-ATAAAATT
*
58304 AAATAAAAAAAAAAACTT
1 AAATAAAAAATAAAA-TT
58322 AAAT
1 AAAT
58326 GTGGGGAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
13 4 0.09
15 8 0.18
16 8 0.18
17 5 0.11
18 19 0.43
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (17 bp):
AAATAAAAAATAAAATT
Found at i:58280 original size:10 final size:10
Alignment explanation
Indices: 58265--58311 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
58255 AAATAAAAAC
58265 ATAAAATTAA
1 ATAAAATTAA
58275 ATAAAATTAA
1 ATAAAATTAA
**
58285 A-AAATAAAAA
1 ATAAA-ATTAA
58295 CATAAAATTAA
1 -ATAAAATTAA
58306 ATAAAA
1 ATAAAA
58312 AAAAAAACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
9 3 0.10
10 20 0.67
11 4 0.13
12 3 0.10
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (10 bp):
ATAAAATTAA
Found at i:58289 original size:31 final size:31
Alignment explanation
Indices: 58251--58311 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
58241 AAGACATAAA
58251 TAAAAAATAAAAACATAAAATTAAATAAAAT
1 TAAAAAATAAAAACATAAAATTAAATAAAAT
58282 TAAAAAATAAAAACATAAAATTAAATAAAA
1 TAAAAAATAAAAACATAAAATTAAATAAAA
58312 AAAAAAACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.21
Consensus pattern (31 bp):
TAAAAAATAAAAACATAAAATTAAATAAAAT
Found at i:58301 original size:21 final size:22
Alignment explanation
Indices: 58275--58316 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
58265 ATAAAATTAA
*
58275 ATAAAATTAAA-AAATAAAAAC
1 ATAAAATTAAATAAAAAAAAAC
58296 ATAAAATTAAATAAAAAAAAA
1 ATAAAATTAAATAAAAAAAAA
58317 AACTTAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (22 bp):
ATAAAATTAAATAAAAAAAAAC
Found at i:58318 original size:31 final size:31
Alignment explanation
Indices: 58252--58318 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
58242 AGACATAAAT
**
58252 AAAAAATAAAAACATAAAATTAAATAAAATT
1 AAAAAATAAAAACATAAAATTAAATAAAAAA
58283 AAAAAATAAAAACATAAAATTAAATAAAAAA
1 AAAAAATAAAAACATAAAATTAAATAAAAAA
58314 AAAAA
1 AAAAA
58319 CTTAAATGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (31 bp):
AAAAAATAAAAACATAAAATTAAATAAAAAA
Found at i:66940 original size:21 final size:21
Alignment explanation
Indices: 66914--66964 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
66904 TAATGTGGAT
66914 TGTTTGTGGATTTATCTTGAA
1 TGTTTGTGGATTTATCTTGAA
* * *
66935 TGTTTGTGCATTTTTTTTGAA
1 TGTTTGTGGATTTATCTTGAA
*
66956 TGTATGTGG
1 TGTTTGTGG
66965 GTTTTGTATG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.04, G:0.25, T:0.55
Consensus pattern (21 bp):
TGTTTGTGGATTTATCTTGAA
Found at i:69013 original size:25 final size:25
Alignment explanation
Indices: 68956--69015 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
68946 CCCAGTATAT
***
68956 AAAAAAAAATTATATATCTTAACTC
1 AAAAAAAAATTATATATCTTAAAAA
*
68981 AAAAAAAAATTATATATCTAAAAAA
1 AAAAAAAAATTATATATCTTAAAAA
69006 AAACAAAAAA
1 AAA-AAAAAA
69016 AAGGGGTCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 24 0.80
26 6 0.20
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.23
Consensus pattern (25 bp):
AAAAAAAAATTATATATCTTAAAAA
Found at i:69439 original size:13 final size:13
Alignment explanation
Indices: 69421--69446 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
69411 CTTAGCAAAG
69421 CTCTCTCTCTCCA
1 CTCTCTCTCTCCA
69434 CTCTCTCTCTCCA
1 CTCTCTCTCTCCA
69447 TTTTTCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.54, G:0.00, T:0.38
Consensus pattern (13 bp):
CTCTCTCTCTCCA
Found at i:75812 original size:12 final size:12
Alignment explanation
Indices: 75797--75835 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
75787 TATTAAAAGA
75797 TAAAAGAAAATC
1 TAAAAGAAAATC
*
75809 TAAAAG-GAAT-
1 TAAAAGAAAATC
75819 TAAAAGAAAATC
1 TAAAAGAAAATC
75831 TAAAA
1 TAAAA
75836 AGATAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 6 0.26
11 6 0.26
12 11 0.48
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.18
Consensus pattern (12 bp):
TAAAAGAAAATC
Found at i:75845 original size:22 final size:21
Alignment explanation
Indices: 75791--75849 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 21
75781 AATACTTATT
75791 AAAAGAT-AAAAGAAAATCTA
1 AAAAGATAAAAAGAAAATCTA
* *
75811 AAAGGAATTAAAAGAAAATCTA
1 AAAAG-ATAAAAAGAAAATCTA
*
75833 AAAAGATAAAAAAAAAA
1 AAAAGATAAAAAGAAAA
75850 CGCAGCGACC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 4 0.12
21 12 0.36
22 17 0.52
ACGTcount: A:0.73, C:0.03, G:0.10, T:0.14
Consensus pattern (21 bp):
AAAAGATAAAAAGAAAATCTA
Done.