Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011412.1 Corchorus capsularis cultivar CVL-1 contig11433, 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: 108363
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--28 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29 CTTTTGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3833 original size:8 final size:8
Alignment explanation
Indices: 3820--3855 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
3810 TTTCCTAGTA
3820 ATAATAAT
1 ATAATAAT
3828 ATAATAAT
1 ATAATAAT
3836 ATAATAAT
1 ATAATAAT
3844 A-ATATAAT
1 ATA-ATAAT
3852 ATAA
1 ATAA
3856 GTGTATCGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 1 0.04
8 24 0.92
9 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATAATAAT
Found at i:3834 original size:11 final size:11
Alignment explanation
Indices: 3818--3852 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
3808 TTTTTCCTAG
3818 TAATAATA-ATA
1 TAATAATATA-A
3829 TAATAATATAA
1 TAATAATATAA
3840 TAATAATATAA
1 TAATAATATAA
3851 TA
1 TA
3853 TAAGTGTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 22 0.96
12 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TAATAATATAA
Found at i:4671 original size:38 final size:38
Alignment explanation
Indices: 4618--4692 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
4608 AGGTCTTTGG
* *
4618 TAAATTCTCTGGGTCTTTCTAATAATATTTAGTATATA
1 TAAATTCCCTAGGTCTTTCTAATAATATTTAGTATATA
4656 TAAATTCCCTAGGTCTTTCTAATAATATTTAGTATAT
1 TAAATTCCCTAGGTCTTTCTAATAATATTTAGTATAT
4693 GTTTTTTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (38 bp):
TAAATTCCCTAGGTCTTTCTAATAATATTTAGTATATA
Found at i:14021 original size:19 final size:19
Alignment explanation
Indices: 13999--14036 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
13989 TTTGAGAAAA
13999 ATATTTTATTACTAATCCT
1 ATATTTTATTACTAATCCT
14018 ATATTTTATTACTAATCCT
1 ATATTTTATTACTAATCCT
14037 CGTAAGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATTTTATTACTAATCCT
Found at i:19569 original size:51 final size:51
Alignment explanation
Indices: 19514--19617 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
19504 CAAGTTAATT
*
19514 TCTTCATCCCCTGCTAAAAAATTAAAGGAGGATGACTCTGTGCAGAATGAC
1 TCTTCATCCCCTGCTAAAAAATTAAAGGAGGATGACTCTGTGCAGAAGGAC
*
19565 TCTTCATCCCCTGCTAAAAAATTAAAGGCGGATGACTCTGTGCAGAAGGAC
1 TCTTCATCCCCTGCTAAAAAATTAAAGGAGGATGACTCTGTGCAGAAGGAC
19616 TC
1 TC
19618 AGCAGTGAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (51 bp):
TCTTCATCCCCTGCTAAAAAATTAAAGGAGGATGACTCTGTGCAGAAGGAC
Found at i:26854 original size:37 final size:37
Alignment explanation
Indices: 26794--26864 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
26784 CTTTTTGAAT
*
26794 AATTTTGACCACCATCGGACGTGATCGTTAGTCTCGG
1 AATTTTGACCACCATCGAACGTGATCGTTAGTCTCGG
* * *
26831 AATTTTGGCCACCATC-AATCGTGATGGTTCGTCT
1 AATTTTGACCACCATCGAA-CGTGATCGTTAGTCT
26865 TGAAATTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 1 0.03
37 28 0.97
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (37 bp):
AATTTTGACCACCATCGAACGTGATCGTTAGTCTCGG
Found at i:37090 original size:40 final size:40
Alignment explanation
Indices: 37033--37360 Score: 539
Period size: 40 Copynumber: 8.2 Consensus size: 40
37023 TGAGGGCCAT
* * *
37033 TGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAA
1 TGTGAA-TAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGA
* * * * *
37074 TGTGAATAAGGAAAGTTCAATGTGAATTGGGAAAGCTGAA
1 TGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGA
*
37114 TGTGAATAAGGCAAGTTCAATGTCATTTGGGAAATTTGGA
1 TGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGA
* *
37154 TGTGAATAAGGCAAGTTCAATGTTATTTGGGAAATTTGGA
1 TGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGA
*
37194 TGTGAATAAGGCAAGTTCAATGTCATTTGGGAAATTTGGA
1 TGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGA
37234 TGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGA
1 TGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGA
37274 TGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGA
1 TGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGA
37314 TGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGA
1 TGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGA
37354 TGTGAAT
1 TGTGAAT
37361 TTGCCGCGTA
Statistics
Matches: 276, Mismatches: 11, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
40 270 0.98
41 6 0.02
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.31
Consensus pattern (40 bp):
TGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGA
Found at i:41446 original size:329 final size:326
Alignment explanation
Indices: 39712--43270 Score: 2330
Period size: 329 Copynumber: 10.8 Consensus size: 326
39702 TTTTTAGTTG
* * * * * *
39712 AAAATCGTGATGGTTAGTGCACGATTTCGACTAAAATTTTGCAAAAATCGACCCGAAATATTTTT
1 AAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA-ATTATT
* ******
39777 CCTCAATTTTTGCCTAAAATACTCATAAAAAATATATAATTTGTTATCAAAAATG-TTGAAGGGA
65 CCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAA-GATTGAA-GGA
* * * * * *
39841 -TTATAACGCTTCTAATATTGTTTTTCCTAT-TTTTCCAAATTAATTTCTAATTAAATCGAAACA
128 CTTTTCACGCTTTTAATATCGTTTTT-CTATATTTTTCGAATTAATTTCTAATTAAATC-AAA-A
* * ** * * * *
39904 -AGATTCAGATGCTCGTAAAAACATATTTTTAAATTTAACGTGGCTGAGATTTGGTTAGATGAAT
190 TAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGT-TCTGAGATTAGATTAGATGAAT
* * * * *
39968 ATAGATATTTCAAGGGGTCTT-G-GCACAAAAAATTATGCAAAACTAAGCCGGG-CCTCGGAACA
254 ATAGATATTT-AAGGAGTCTTCGTGC-C-AAAAATCATGCAAAACTGAGCCGGGTCC-CGAAACG
* *
40030 C-TGTTTTAGTCG
315 CGT-TTTTAGCCA
* * * * * *** *
40042 AAAACCGTGATGGTTAGAACATGATTTTGGCTACAATTTTGCAAAAATTGACCCGGCGGATTTTT
1 AAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC-GAAAATTATT
* * * * * * * * *
40107 CCTCGATTTTTTAGCAAAAATACTCATAAAAAATATATAATTCAACGTCACAAGGATCGGAGTAC
65 CCTC-AATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGAC
* *
40172 TTTTCACGCTTTTAATATTGCTTTTC-ATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACA
129 TTTTCACGCTTTTAATATCGTTTTTCTATA-TTTTTC-GAATTAATTTCTAATTAAATC-AAA-A
* * * * *
40236 -AAATTCAGATGCAT-ATAAAAA-AAATTTCTTAAATACAATGTGGCTGAGATTTGATTAGATGA
190 TAGATTCAGATGC-TCGTAAAAACAAA-TTCTTAAATCCAATGT-TCTGAGATTAGATTAGATGA
* * * ** * * *
40298 ATATGGATATCTCAAGGAGTCTTGGTGTAAAAAATCATGCAAAACTGAGTCAGGGCTGCAG-AAC
252 ATATAGATAT-TTAAGGAGTCTTCGTGCCAAAAATCATGCAAAACTGAG-CCGGG-TCCCGAAAC
** *
40362 GATTTTTTAGCAAA
314 GCGTTTTTAGC-CA
** * * * **** *
40376 AAAACTATGATGGTTATTACACGATTTCGGCTAAAATTTTGTAAAAATTGGTTAGAAAAATATTT
1 AAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAATTA-TT
* * * * * ***
40441 CCTCAATTTTAGGCTAAAGTACTTATAGAACATATATAATTCAACTTTAAAAAGA-TGAAGGACT
65 CCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACT
* * * * * *
40505 TTTGACGCTTCTAATATCATTTTTCCTAT-TTTTTCCAAATTAATTTTTAATTAAATCGAAATAA
130 TTTCACGCTTTTAATATCGTTTTT-CTATATTTTT-CGAATTAATTTCTAATTAAATCAAAAT-A
* * * * *
40569 GATTCAGATGCTCGTAAAAACAAA-TCTTTAAATCTAATG-T-GGAAATTTGGTTAGATGAATAT
192 GATTCAGATGCTCGTAAAAACAAATTC-TTAAATCCAATGTTCTGAGATTAGATTAGATGAATAT
* ** * * * * * *
40631 ATATATTTCAAGGAGTCTT-GCCACCAAAAATCATGCAAAATTAAGCCAGGCCCCGGAACGCGGT
256 AGATATTT-AAGGAGTCTTCG-TGCCAAAAATCATGCAAAACTGAGCCGGGTCCCGAAACGCGTT
*
40695 TTTAGCCG
319 TTTAGCCA
* * * * * *
40703 AAAACCGTGACGGTTAGTATATGATTTCGGCTAAAATTTTACAAAAATTGACTCGAAAGATT-TT
1 AAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA-ATTATT
* ** * * * * * * * ** *
40767 TCTTGATTTCTAGCGAAAATACTCCAAAAAAAAAAATATAATTCAACACCAAAAAAAATCAAAAG
65 CCTCAATTTTTGGCTAAAATACT-C-ATAAAAAATATATAATTCAACGCC-AAAAAGATTGAAGG
* * * *
40832 CCTTTTTCACGCTTTTAATATCGTTTTTTTTTTTTCATTTTTTTCTGAATTAATTTCTTATTAAA
127 AC-TTTTCACGCTTTTAATATCG-----TTTTTCT-ATATTTTTC-GAATTAATTTCTAATTAAA
* ** * * *
40897 TCGAAACA-AGATTCAGATGCTCGTAAAAACAAATCCTTAAATTTAACACG-GCTGAGATTTGAT
184 TC-AAA-ATAGATTCAGATGCTCGTAAAAACAAATTCTTAAA-TCCA-ATGTTCTGAGATTAGAT
*
40960 TAGATGAATATAGATATTTCAAGGAGTC-TCGACT-CCAAAAATCATGCAAAACTGAGTCGGG-C
245 TAGATGAATATAGATATTT-AAGGAGTCTTCG--TGCCAAAAATCATGCAAAACTGAGCCGGGTC
* * * **
41022 CCGGGAATGTG-TTTTAGCTG
307 CC-GAAACGCGTTTTTAGCCA
* * * *
41042 AAAACCATGATGGTTAGTACACGATTTCGGCTAAAATTTTGCACAAATTGACCCGAAATATTTTT
1 AAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA-ATTATT
* * * *
41107 CCATTCAATTTTTGGCTAAAATACTCATAAAATATATACAATTTAACGCCAAAAAGATTGGAGGA
65 CC--TCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGA
**
41172 CTTTTCACGCTTTTAATATCGTTTTT-TATATTTTTC-AATTAATTTCTTGTTAAATCAAAATAG
128 CTTTTCACGCTTTTAATATCGTTTTTCTATATTTTTCGAATTAATTTCTAATTAAATCAAAATAG
* * * *
41235 TATTCAGATGCTCCTAAAAACAAATTCTTCAATCCAATGTATTCCGAGATTAGATTAAATGAATA
193 -ATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATG--TTCTGAGATTAGATTAGATGAATA
* * * * * * * *
41300 TGGATATCTAGAAGAGTCTTTGTGTCAAAAATCATGCAAAACTTAGTCGGGGTCTCGAAACGCG-
255 TAGATATTTA-AGGAGTCTTCGTGCCAAAAATCATGCAAAACTGAG-CCGGGTCCCGAAACGCGT
*
41364 TTTTACCCA
318 TTTTAGCCA
* * * * ** *
41373 AAAATCGTGATGACTATTACACGATTTCGGCTAGAATTTTGCAAAAATTGACTTGAAATTTATGT
1 AAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAATTAT-T
* * * * ** *
41438 CCTCAATTTTT--ATACACAATACTCATAAAAATTATATGATTCAACGCCAAAAATATTTTAGGG
65 CCTCAATTTTTGGCTA-A-AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGA
* * * * * * *
41501 TTTTTCATGCTTCTAATATCATTTTTCCTATTATTTTCCGAATTAATTTCTAAGTAAATCGAAAT
128 CTTTTCACGCTTTTAATATCGTTTTT-CTA-TATTTTTCGAATTAATTTCTAATTAAATCAAAAT
* *** * *
41566 ATGATTCAGATGCTTGT-TTTACAAATTCTTAAATCCAATGTGACTGAGATTTGATTAGATGAAT
191 A-GATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGT-TCTGAGATTAGATTAGATGAAT
* * * * * *
41630 GTAGATATTTCAGGGAGT-GTCGATG-CAAAAATCATGCAACACTGAACCGGGTCCCCGAAACAC
254 ATAGATATTT-AAGGAGTCTTCG-TGCCAAAAATCATGCAAAACTGAGCCGGGT-CCCGAAACGC
*
41693 GTTTTTAGCAA
316 GTTTTTAGCCA
* * * * * * *
41704 AAAACCGTGATTTCAACTAACGTGCACGATTTTGGCTAATATTTTGCAAAAATTAACCAGAAATA
1 AAAACCGTGA--T-GA-TTA-GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA-A
* * * * * * *
41769 TT-TTCCCTCAATTTTTGTCTTAAATGCTCATAATATATATATAATTCAACTCCAAAAAGATTGG
60 TTATT-CCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGA
* *
41833 AGGACTTTTCTCGCTTTTAATATCGATTTTC-ATATTTTTTCTGAATTAATTTCTAATTAAATCG
124 AGGACTTTTCACGCTTTTAATATCGTTTTTCTATA-TTTTTC-GAATTAATTTCTAATTAAATC-
* * * * * *
41897 AAACA-AGATTCGGATGCTCGTAAAAATAAATCCTTAAATGCAATG---TG-GCTGAGATT---T
186 AAA-ATAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTTCTGAGATTAGATTAGAT
* * * * * **
41954 -AATATAGATATTTCGAGGAGTC-TCGATGTCAAAAATCATACAAAACTGAGTCGGGGCTTGAAA
250 GAATATAGATATTT-AAGGAGTCTTCG-TGCCAAAAATCATGCAAAACTGAGCCGGGTCCCGAAA
* *
42017 CGCGTTTTTAACAAA
313 CGCGTTTTTAGC-CA
* * * * ** *
42032 AAAACCGTGATGGTTAGTACACGATTTCGACTAAAATTTTACAAAAAATGA-CTAAAAAATATTC
1 AAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAATTATTC
* * * * * *
42096 TCTGAATTTTTTGCCATAATACTCATCAAAAAATATATAATTCAACACCAAAAAAATTGAAGGGA
66 -CTCAATTTTTGGCTAAAATACTCAT-AAAAAATATATAATTCAACGCCAAAAAGATTGAA-GGA
* *
42161 -TTTTCACGATTCTAATATCGTTTTTCCTAT-TTTTTCTGAATTAATTTCTAATTAAGA-CAAAA
128 CTTTTCACGCTTTTAATATCGTTTTT-CTATATTTTTC-GAATTAATTTCTAATTAA-ATCAAAA
* * * * ** *
42223 CAGGATTAAGATGTTTGTAAAAAC-AATGGTT--A--GAA--TT-TG-G-TTAGA-T---T-AAT
190 TA-GATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTTCTGAGATTAGATTAGATGAAT
* ** * * * * * * * * *
42273 ATAGATATTTTAAAGAGTCTAGGCGCCGAAAATCATTCAAAATTGAACCAGGCCCCGGAACGCAT
254 ATAGATA-TTTAAGGAGTCTTCGTGCCAAAAATCATGCAAAACTGAGCCGGGTCCCGAAACGCGT
*
42338 TTTTAGCTA
318 TTTTAGCCA
* * * *
42347 AAAACCGTGATGATTA-TAAAACGATTTCGGCTAATATTTTGCAAAAATTGACTC-AAAAGATAT
1 AAAACCGTGATGATTAGT-ACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAA-TTA-
* * *** * ** * *
42410 TTTCTAAATTTGCAG-TCACAATACAAATAAAAAATATATAATTCAATGCCAAAAAAATTGAAGG
63 TTCCTCAATTTTTGGCT-AAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGG
* *
42474 GCTTTTCACGCTTTTAATATCGTTTTTC-ATATTTTTTTGAATTAATTTCTAATTAAATCAAAAT
127 ACTTTTCACGCTTTTAATATCGTTTTTCTATA-TTTTTCGAATTAATTTCTAATTAAATCAAAAT
* * * * * ** *
42538 GAGATTTAGATGCTCGTAAAAACAAATAT-TGAAATGCAATGTGGCTAAGATTTTATTAGACGAA
191 -AGATTCAGATGCTCGTAAAAACAAAT-TCTTAAATCCAATGT-TCTGAGATTAGATTAGATGAA
* * * **
42602 TACAAATATTTCAAGGAGT-TTCG-GCGCAAAAAATTATGCAAAACTGAGCCGGACCCCGAAACG
253 TATAGATATTT-AAGGAGTCTTCGTGC-C-AAAAATCATGCAAAACTGAGCCGGGTCCCGAAACG
42665 CGTTTTTAGCCA
315 CGTTTTTAGCCA
* * * *
42677 AAACCCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCCGAAAAATT-TT
1 AAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCG-AAAATTATT
* * * * * * * * * *
42741 CCCCTATTTCTT-GATAAAATACTCATAATATATATATAATTTAACGCCAAAAATATAGGAGAAC
65 CCTCAATTT-TTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGAC
** * *
42805 TTTTCACATTTTTAATATCATTTTTC-ATA-TTTTCTGAATTAATTTCTAATTAAAT-AGAAACA
129 TTTTCACGCTTTTAATATCGTTTTTCTATATTTTTC-GAATTAATTTCTAATTAAATCA-AAA-T
* *
42867 AGATTAAGATGCTTGTAAAAACAAATTCTTAAAT-C------C--A-ATT-GATTAGATGAATAT
191 AGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTTCTGAGATTAGATTAGATGAATAT
* ** * * ** * *
42921 GGATATCCCAATGAGTCTTGGCACCAAAGATCATGCAAAACTGAGCCGGGTCCC-AGAACGCTTT
256 AGATAT-TTAAGGAGTCTTCGTGCCAAAAATCATGCAAAACTGAGCCGGGTCCCGA-AACGCGTT
42985 TTTAGCCA
319 TTTAGCCA
* * * *** *
42993 AAAACTGTGATGATTATTACACGATTTCGGCTAAAATTTTGTAAAAATTGATTAGAAAAATATTT
1 AAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAATTA-TT
* * * *
43058 CCTTAATTTTGGGCTAAAATACTCATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCT
65 CCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACT
* * * * * *
43123 TTTGACG-TATCTAATATCATTTTTCCTATATTTTCCAAATTAATTTCTAATTAAATCGAAAAAA
130 TTTCACGCT-TTTAATATCGTTTTT-CTATATTTTTCGAATTAATTTCTAATTAAATC-AAAATA
* * *
43187 GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATAT
192 GATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGT-TCTGAGATTAGATTAGATGAATAT
*
43252 AGATATTTCAAGTAGTCTT
256 AGATATTT-AAGGAGTCTT
43271 GGAATAAGGA
Statistics
Matches: 2518, Mismatches: 538, Indels: 345
0.74 0.16 0.10
Matches are distributed among these distances:
313 3 0.00
314 45 0.02
315 119 0.05
316 180 0.07
317 88 0.03
318 8 0.00
319 56 0.02
320 10 0.00
321 6 0.00
322 33 0.01
323 121 0.05
324 8 0.00
325 5 0.00
326 19 0.01
327 101 0.04
328 132 0.05
329 259 0.10
330 250 0.10
331 252 0.10
332 223 0.09
333 105 0.04
334 61 0.02
335 38 0.02
336 130 0.05
337 57 0.02
338 26 0.01
339 79 0.03
340 86 0.03
341 2 0.00
342 16 0.01
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (326 bp):
AAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAATTATTC
CTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTT
TTCACGCTTTTAATATCGTTTTTCTATATTTTTCGAATTAATTTCTAATTAAATCAAAATAGATT
CAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTTCTGAGATTAGATTAGATGAATATAGATA
TTTAAGGAGTCTTCGTGCCAAAAATCATGCAAAACTGAGCCGGGTCCCGAAACGCGTTTTTAGCC
A
Found at i:43041 original size:646 final size:641
Alignment explanation
Indices: 39712--43272 Score: 2666
Period size: 646 Copynumber: 5.4 Consensus size: 641
39702 TTTTTAGTTG
* * * * * * * * *
39712 AAAATCGTGATGGTTAGTGCACGATTTCGACTAAAATTTTGCAAAAATCGACCCGAAATAT-TTT
1 AAAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCAAAAAATATTT
* * *** **
39776 TCCTCAATTTTTGCCTAAAATACTCATAAAAAATATATAATTTGTTATCAAAAATG-TTGAAGGG
66 T-CTCAATTTTAGGCT-AAATACTCATAAAAAATATATAATTCAATGCCAAAAA-GATTGAA-GG
* * * * * *
39840 A-TTATAACGCTTCTAATATTGTTTTTCCTATTTTTCCAAATTAATTTCTAATTAAATCGAAACA
127 ACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCAAATTAATTTCTAATTAAATCAAAATA
* * ** * *
39904 AGATTCAGATGCTCGTAAAAACATATTTTTAAATTTAACGTGGCTGAGATTTGGTTAGATGAATA
192 AGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATA
* * * *
39969 TAGATATTTCAAGGGGTCTTGGCACAAAAAATTATGCAAAACTAAGCCGGGCCTCGGAACAC-TG
257 TAGATATTTCAAGGAGTCTTGGCAC-AAAAATCATGCAAAACTAAGCCGGGCCTCGAAACGCGT-
* * * * *
40033 TTTTAGTCGAAAACCGTGATGGTTAGAACATGATTTTGGCTACAATTTTGCAAAAATTGACCCGG
320 TTTTAG-CCAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC-G
*** * * * * * **
40098 CGGATTTTTCCTCGATTTTTTAGCA-AAAATACTCATAAAAAATATATAATTCAACGTCACAAGG
383 AAAAATTTTCCTCTATTTCTT-G-ATAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAA
* * * ***
40162 ATCGGAGTACTTTTCACGCTTTTAATATTGCTTTTCATATTTTTTCTGAATTAATTTCTAATTAA
446 ATAGAAGGACTTTTCACGCTTTTAATATCATTTTTCATA--TTTTCTGAATTAATTTCTAATTAA
* * *
40227 ATCGAAACAAAATTCAGATGCATATAAAAA-AAATTTCTTAAATACAATGTGGCTGAGATTTGAT
509 ATCGAAACAAGATTCAGATGCTTGTAAAAACAAA-TTCTTAAAT-C-------C--A-A-TTGAT
* * * * *
40291 TAGATGAATATGGATATCTCAAGGAGTCTTGGTGTA-AAAAATCATGCAAAACTGAGTCAGGGCT
561 TAGATGAATATGGATATTTCAAGGAGTC-TCG-GCACCAAAATCATGCAAAACTGAG-CCGGGC-
* *
40355 GCAGAACGATTTTTTAGCAAA
622 CCAGAACGCTTTTTTAGC-AA
** * * * *
40376 AAAACTATGATGGTTATTACACGATTTCGGCTAAAATTTTGTAAAAATTG-GTTAGAAAAATATT
1 AAAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCA-AAAAATATT
* * * * **
40440 TCCTCAATTTTAGGCTAAAGTACTTATAGAACATATATAATTCAACT-TTAAAAAGA-TGAAGGA
65 TTCTCAATTTTAGGCTAAA-TACTCATAAAAAATATATAATTCAA-TGCCAAAAAGATTGAAGGA
* * * *
40503 CTTTTGACGCTTCTAATATCATTTTTCCTATTTTTTCCAAATTAATTTTTAATTAAATCGAAATA
128 CTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTT-CAAATTAATTTCTAATTAAATCAAAATA
* * *
40568 AGATTCAGATGCTCGTAAAAACAAATCTTTAAATCTAATGT-G--GAAATTTGGTTAGATGAATA
192 AGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATA
* * * * * * *
40630 TATATATTTCAAGGAGTCTTGCCACCAAAAATCATGCAAAATTAAGCCAGGCCCCGGAACGCGGT
257 TAGATATTTCAAGGAGTCTTGGCA-CAAAAATCATGCAAAACTAAGCCGGGCCTCGAAACGCGTT
* * * * *
40695 TTTAGCCGAAAACCGTGACGGTTAGTATATGATTTCGGCTAAAATTTTACAAAAATTGACTCGAA
321 TTTAGCC-AAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAA
* * * ** * * *
40760 AGATTTTTCT-TGATTTCTAGCGAAAATACTCCAAAAAAAAAAATATAATTCAACACCAAAAAAA
385 AAATTTTCCTCT-ATTTCTTGATAAAATACT-C-ATAAAAAATATATAATTCAACGCC-AAAAAA
* * * *
40824 ATCA-AAAGCCTTTTTCACGCTTTTAATATCGTTTTTTTTTTTTCATTTTTTTCTGAATTAATTT
446 AT-AGAAGGAC-TTTTCACGCTTTTAATATC-------ATTTTTCA-TATTTTCTGAATTAATTT
* * *
40888 CTTATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTTAACACGGCTGAG
501 CTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAACAAATTCTTAAA--T----C--C--A-
* * * *
40953 ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGACTCCAAAAATCATGCAAAACTGAGTC
555 A-TTGATTAGATGAATATGGATATTTCAAGGAGTCTCGGCACC-AAAATCATGCAAAACTGAGCC
* * * **
41018 GGGCCCGGGAATG-TGTTTTAGCTG
618 GGGCCC-AGAACGCTTTTTTAGCAA
* * * * * * *
41042 AAAACCATGATGGTTAGTACACGATTTCGGCTAAAATTTTGCACAAATTGACCCGAAATAT-TTT
1 AAAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCAAAAAATATTT
* * * * * *
41106 TCCATTCAATTTTTGGCTAAAATACTCATAAAATATATACAATTTAACGCCAAAAAGATTGGAGG
66 T-C--TCAATTTTAGGCT-AAATACTCATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGG
* **
41171 ACTTTTCACGCTTTTAATATCGTTTTT--TATATTTTTC-AATTAATTTCTTGTTAAATCAAAAT
127 ACTTTTCACGCTTCTAATATCGTTTTTCCTAT-TTTTTCAAATTAATTTCTAATTAAATCAAAAT
* * ** * * *
41233 -AGTATTCAGATGCTCCTAAAAACAAAT-TCTTCAATCCAATGTATTCCGAGATTAGATTAAATG
191 AAG-ATTCAGATGCTCGTAAAAACAAATCT-TTAAATCCAATGT-GGCTGAGATTTGATTAGATG
* * * * * * *
41296 AATATGGATATCT-AGAAGAGTCTTTGTG-TCAAAAATCATGCAAAACTTAGTCGGGGTCTCGAA
253 AATATAGATATTTCA-AGGAGTC-TTG-GCACAAAAATCATGCAAAACTAAG-CCGGGCCTCGAA
* * ** * *
41359 ACGCG-TTTTACCCAAAAATCGTGATGACTATTACACGATTTCGGCTAGAATTTTGCAAAAATTG
314 ACGCGTTTTTAGCC-AAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTG
** * * * *
41423 ACTTG-AAATTTATGTCCTCAATTT-TT-ATACACAATACTCATAAAAATTATATGATTCAACGC
378 ACCCGAAAAATT-T-TCCTCTATTTCTTGATA-A-AATACTCATAAAAAATATATAATTCAACGC
* *** ** * * *
41485 CAAAAATATTTTAGGGTTTTTCATGCTTCTAATATCATTTTTCCTATTATTTTCCGAATTAATTT
439 CAAAAAAATAGAAGGACTTTTCACGCTTTTAATATCATTTTT-C-A-TATTTTCTGAATTAATTT
* * * *** *
41550 CTAAGTAAATCGAAATATGATTCAGATGCTTGT-TTTACAAATTCTTAAATCCAATGTGACTGAG
501 CTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAACAAATTCTTAAATCCAAT-TGA-TTAG
* * * *
41614 ATTTGATTAGATGAATGTAGATATTTCAGGGAGTGTCGATGCA--AAAATCATGCAACACTGAAC
564 A--TG---A-AT--ATG--GATATTTCAAGGAGTCTCG--GCACCAAAATCATGCAAAACTGAGC
* * *
41677 CGGGTCCCCGAAACACGTTTTTAGCAA
617 CGGG-CCCAG-AACGCTTTTTTAGCAA
* * * * * * * *
41704 AAAACCGTGATTTCAACTAACGTGCACGATTTTGGCTAATATTTTGCAAAAATTAAC-C-AGAAA
1 AAAACCGTGA--T-GA-TTA-TTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCAAAAAA
* * * * *
41767 TATTTTCCCTCAATTTTTGTCTTAAATGCTCATAATATATATATAATTCAACT-CCAAAAAGATT
61 TATTTT--CTCAATTTTAGGC-TAAATACTCATAAAAAATATATAATTCAA-TGCCAAAAAGATT
* * * * * *
41831 GGAGGACTTTTCTCGCTTTTAATATCGATTTTCATATTTTTTCTGAATTAATTTCTAATTAAATC
122 GAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTC-AAATTAATTTCTAATTAAATC
* * * * * *
41896 GAAACAAGATTCGGATGCTCGTAAAAATAAATCCTTAAATGCAATGTGGCT--GA---GATT---
186 AAAATAAGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGATTAGA
* * * * * * * *
41953 T-AATATAGATATTTCGAGGAGTCTCGATG-TCAAAAATCATACAAAACTGAGTCGGGGCTTGAA
251 TGAATATAGATATTTCAAGGAGTCTTG--GCACAAAAATCATGCAAAACTAAGCCGGGCCTCGAA
* * * * *
42016 ACGCGTTTTTAACAAAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAATTTTACAAAAAAT
314 ACGCGTTTTTAGC--CAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATT
** * * ** * *
42081 GA-CTAAAAAATATT-CTCTGAATTTTTTGCCATAATACTCATCAAAAAATATATAATTCAACAC
377 GACCCGAAAAATTTTCCTCT--ATTTCTTGATAAAATACTCAT-AAAAAATATATAATTCAACGC
* * * * *
42144 CAAAAAAATTGAAGGGA-TTTTCACGATTCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTT
439 CAAAAAAATAGAA-GGACTTTTCACGCTTTTAATATCATTTTT-C-ATATTTTCTGAATTAATTT
* * * * ** *
42208 CTAATTAAGA-CAAAACAGGATTAAGATGTTTGTAAAAAC-AATGGTTAGAAT----TTGGTTAG
501 CTAATTAA-ATCGAAACAAGATTCAGATGCTTGTAAAAACAAATTCTTA-AATCCAATTGATTAG
* * * * * * * * * * *
42267 ATTAATATAGATATTTTAAAGAGTCTAGGCGCCGAAAATCATTCAAAATTGAACCAGGCCCCGGA
564 ATGAATATGGATATTTCAAGGAGTCTCGGCACC-AAAATCATGCAAAACTGAGCC-GGGCCCAGA
* *
42332 ACGCATTTTTAGCTA
627 ACGCTTTTTTAGCAA
* * * *
42347 AAAACCGTGATGATTATAAAACGATTTCGGCTAATATTTTGCAAAAATTGACTCAAAAGATATTT
1 AAAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCAAAAAATATTT
* * * ** * *
42412 TCTAAATTTGCAGTC-ACAATACAAATAAAAAATATATAATTCAATGCCAAAAAAATTGAAGGGC
66 TCTCAATTT-TAGGCTA-AATACTCATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGAC
* * ** *
42476 TTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTGAATTAATTTCTAATTAAATCAAAATGAG
129 TTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCAAATTAATTTCTAATTAAATCAAAATAAG
* * * * * * * *
42541 ATTTAGATGCTCGTAAAAACAAATATTGAAATGCAATGTGGCTAAGATTTTATTAGACGAATACA
194 ATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATA
* * * * * *
42606 AATATTTCAAGGAGT-TTCGGCGCAAAAAATTATGCAAAACTGAGCCGGACCCCGAAACGCGTTT
259 GATATTTCAAGGAGTCTT-GGCAC-AAAAATCATGCAAAACTAAGCCGGGCCTCGAAACGCGTTT
* *
42670 TTAGCCAAAACCCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCCGAAA
322 TTAGCCAAAA-CCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA
* * * * * *
42735 AATTTTCCCCTATTTCTTGATAAAATACTCATAATATATATATAATTTAACGCCAAAAATATAGG
386 AATTTTCCTCTATTTCTTGATAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATAGA
* ** *
42800 AGAACTTTTCACATTTTTAATATCATTTTTCATATTTTCTGAATTAATTTCTAATTAAATAGAAA
451 AGGACTTTTCACGCTTTTAATATCATTTTTCATATTTTCTGAATTAATTTCTAATTAAATCGAAA
* **
42865 CAAGATTAAGATGCTTGTAAAAACAAATTCTTAAATCCAATTGATTAGATGAATATGGATATCCC
516 CAAGATTCAGATGCTTGTAAAAACAAATTCTTAAATCCAATTGATTAGATGAATATGGATATTTC
* * *
42930 AATGAGTCTTGGCACCAAAGATCATGCAAAACTGAGCCGGGTCCCAGAACGCTTTTTTAGCCA
581 AAGGAGTCTCGGCACCAAA-ATCATGCAAAACTGAGCCGGG-CCCAGAACGCTTTTTTAGCAA
* * *
42993 AAAACTGTGATGATTATTACACGATTTCGGCTAAAATTTTGTAAAAATTGA-TTAGAAAAATATT
1 AAAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCA-AAAAATATT
* * * *
43057 TCCTTAATTTTGGGCTAAAATACTCATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGC
65 TTCTCAATTTTAGGCT-AAATACTCATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGAC
* * *
43122 TTTTGACG-TATCTAATATCATTTTTCCTATATTTTCCAAATTAATTTCTAATTAAATCGAAAA-
129 TTTTCACGCT-TCTAATATCGTTTTTCCTAT-TTTTTCAAATTAATTTCTAATTAAATC-AAAAT
*
43185 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
191 AAGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
*
43250 ATAGATATTTCAAGTAGTCTTGG
256 ATAGATATTTCAAGGAGTCTTGG
43273 AATAAGGACA
Statistics
Matches: 2312, Mismatches: 438, Indels: 311
0.76 0.14 0.10
Matches are distributed among these distances:
637 65 0.03
638 107 0.05
639 8 0.00
640 10 0.00
641 4 0.00
642 57 0.02
643 46 0.02
644 75 0.03
645 77 0.03
646 260 0.11
647 103 0.04
648 7 0.00
649 1 0.00
650 4 0.00
651 6 0.00
653 7 0.00
654 2 0.00
655 2 0.00
656 4 0.00
657 18 0.01
658 107 0.05
659 122 0.05
660 44 0.02
661 179 0.08
662 77 0.03
663 58 0.03
664 148 0.06
665 92 0.04
666 121 0.05
667 67 0.03
668 116 0.05
669 174 0.08
670 112 0.05
671 30 0.01
674 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (641 bp):
AAAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCAAAAAATATTT
TCTCAATTTTAGGCTAAATACTCATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGACTT
TTCACGCTTCTAATATCGTTTTTCCTATTTTTTCAAATTAATTTCTAATTAAATCAAAATAAGAT
TCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGA
TATTTCAAGGAGTCTTGGCACAAAAATCATGCAAAACTAAGCCGGGCCTCGAAACGCGTTTTTAG
CCAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTT
TCCTCTATTTCTTGATAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATAGAAGGAC
TTTTCACGCTTTTAATATCATTTTTCATATTTTCTGAATTAATTTCTAATTAAATCGAAACAAGA
TTCAGATGCTTGTAAAAACAAATTCTTAAATCCAATTGATTAGATGAATATGGATATTTCAAGGA
GTCTCGGCACCAAAATCATGCAAAACTGAGCCGGGCCCAGAACGCTTTTTTAGCAA
Found at i:43836 original size:15 final size:16
Alignment explanation
Indices: 43818--43847 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
43808 ATAAATAATA
43818 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
43833 ATATTATAATCTAAA
1 ATATTATAATCTAAA
43848 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:45641 original size:82 final size:83
Alignment explanation
Indices: 45536--45703 Score: 239
Period size: 82 Copynumber: 2.0 Consensus size: 83
45526 ATGGAAATGG
* * * *
45536 AGGTACACGAGAAGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTGCGAGACT
1 AGGTACACGAG-AGACAGCGGCTCTCAACAGCGAGGCACTCAAAACGGCCGCCAACTGCGAGACT
* *
45601 CGCGACATGACACACACGA
65 CACGACACGACACACACGA
* *
45620 AGGTACACGAG-GACAGCGGCTCTCAACAGCGAGGCACTCAAAATGGCCGCCAACTGCGAGGCTC
1 AGGTACACGAGAGACAGCGGCTCTCAACAGCGAGGCACTCAAAACGGCCGCCAACTGCGAGACTC
*
45684 ACGACGCGACACACACGA
66 ACGACACGACACACACGA
45702 AG
1 AG
45704 ACACAGGTGC
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
82 64 0.85
84 11 0.15
ACGTcount: A:0.30, C:0.32, G:0.29, T:0.10
Consensus pattern (83 bp):
AGGTACACGAGAGACAGCGGCTCTCAACAGCGAGGCACTCAAAACGGCCGCCAACTGCGAGACTC
ACGACACGACACACACGA
Found at i:45810 original size:2 final size:2
Alignment explanation
Indices: 45803--45832 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
45793 AAACAGAAAT
45803 AG AG AG AG AG -G AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
45833 AGCTCGGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:53648 original size:46 final size:46
Alignment explanation
Indices: 53595--53687 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
53585 CCCTAAAGGG
53595 ACACATGTCACCCTTCAGGACCCGCTTGTGTAGTCTGTCACCCTTC
1 ACACATGTCACCCTTCAGGACCCGCTTGTGTAGTCTGTCACCCTTC
53641 ACACATGTCACCCTTCAGGACCCGCTTGTGTAGTCTGTCACCCTTC
1 ACACATGTCACCCTTCAGGACCCGCTTGTGTAGTCTGTCACCCTTC
53687 A
1 A
53688 GGACCGATTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.18, C:0.37, G:0.17, T:0.28
Consensus pattern (46 bp):
ACACATGTCACCCTTCAGGACCCGCTTGTGTAGTCTGTCACCCTTC
Found at i:53682 original size:30 final size:29
Alignment explanation
Indices: 53646--53703 Score: 98
Period size: 30 Copynumber: 2.0 Consensus size: 29
53636 CCTTCACACA
*
53646 TGTCACCCTTCAGGACCCGCTTGTGTAGTC
1 TGTCACCCTTCAGGA-CCGATTGTGTAGTC
53676 TGTCACCCTTCAGGACCGATTGTGTAGT
1 TGTCACCCTTCAGGACCGATTGTGTAGT
53704 GGTCTGCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.16, C:0.29, G:0.24, T:0.31
Consensus pattern (29 bp):
TGTCACCCTTCAGGACCGATTGTGTAGTC
Found at i:55718 original size:2 final size:2
Alignment explanation
Indices: 55713--55739 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55703 TGTGTGTGTG
55713 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
55740 TCTTGGACCA
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:70638 original size:30 final size:31
Alignment explanation
Indices: 70578--70652 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
70568 AAAATTGGTG
70578 AGGGACCCAATTGCTCAATTAACTCAACTTC
1 AGGGACCCAATTGCTCAATTAACTCAACTTC
* *
70609 AGGGACTCAATTGCTC-ATTAAGTTC-ACTTC
1 AGGGACCCAATTGCTCAATTAA-CTCAACTTC
* *
70639 AAGGACCCATTTGC
1 AGGGACCCAATTGC
70653 ATATTTGCCC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 21 0.55
31 17 0.45
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (31 bp):
AGGGACCCAATTGCTCAATTAACTCAACTTC
Found at i:71477 original size:30 final size:31
Alignment explanation
Indices: 71441--71507 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
71431 GTGCAAATGG
71441 GTCCCTGAAG-TGAACTT-AGTGAGCAATTGA
1 GTCCCTGAAGTTG-ACTTAAGTGAGCAATTGA
* * *
71471 GTCCCTGAAGTTGAGTTAATTGAGCAATTGG
1 GTCCCTGAAGTTGACTTAAGTGAGCAATTGA
71502 GTCCCT
1 GTCCCT
71508 CACCATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 13 0.41
31 19 0.59
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (31 bp):
GTCCCTGAAGTTGACTTAAGTGAGCAATTGA
Found at i:72503 original size:35 final size:35
Alignment explanation
Indices: 72464--72533 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
72454 ACACAAAGAC
**
72464 AGAAACATGACTTTATCTCCCCCATACTCTTACCT
1 AGAAACATGACCCTATCTCCCCCATACTCTTACCT
72499 AGAAACATGACCCTATCTCCCCCATACTCTTACCT
1 AGAAACATGACCCTATCTCCCCCATACTCTTACCT
72534 CTATCTTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.29, C:0.37, G:0.06, T:0.29
Consensus pattern (35 bp):
AGAAACATGACCCTATCTCCCCCATACTCTTACCT
Found at i:79377 original size:2 final size:2
Alignment explanation
Indices: 79334--79364 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
79324 TTTGGATTAG
*
79334 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
79365 TAAGATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:96907 original size:2 final size:2
Alignment explanation
Indices: 96900--96939 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
96890 TATCTTTAAG
*
96900 TA TA TA TA TA -A TG TA -A 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 TA TA TA TA TA TA
96940 CTTAATTGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:97772 original size:4 final size:4
Alignment explanation
Indices: 97756--97815 Score: 111
Period size: 4 Copynumber: 15.0 Consensus size: 4
97746 CTATACATCA
*
97756 TATG TATG CATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
97804 TATG TATG TATG
1 TATG TATG TATG
97816 CCTAGAGAGG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (4 bp):
TATG
Done.