Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021124.1 Corchorus olitorius cultivar O-4 contig21157, 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: 131118
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:13937 original size:90 final size:90
Alignment explanation
Indices: 13805--13984 Score: 315
Period size: 90 Copynumber: 2.0 Consensus size: 90
13795 AGTATTATGG
*
13805 AGAGATTGAAGCAGAAGAGGCAGTAGATGAAGATGATCATGAACAAGAGGACCAAGAGGACGATG
1 AGAGATTGAAGCAGAAGAGGCAGTAGATGAAGATGATCATGAAAAAGAGGACCAAGAGGACGATG
13870 CTTATGAAAATGTTGAACAGGTTCC
66 CTTATGAAAATGTTGAACAGGTTCC
* * * *
13895 AGAGATTGAAGCAGAAGATGCCGTAGATGAAGATGATGATGAAAAAGAGGACCAAGAGGATGATG
1 AGAGATTGAAGCAGAAGAGGCAGTAGATGAAGATGATCATGAAAAAGAGGACCAAGAGGACGATG
13960 CTTATGAAAATGTTGAACAGGTTCC
66 CTTATGAAAATGTTGAACAGGTTCC
13985 CGAAGAACAT
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 85 1.00
ACGTcount: A:0.40, C:0.11, G:0.30, T:0.19
Consensus pattern (90 bp):
AGAGATTGAAGCAGAAGAGGCAGTAGATGAAGATGATCATGAAAAAGAGGACCAAGAGGACGATG
CTTATGAAAATGTTGAACAGGTTCC
Found at i:14109 original size:60 final size:60
Alignment explanation
Indices: 14036--14150 Score: 221
Period size: 60 Copynumber: 1.9 Consensus size: 60
14026 TTGAGGAACC
*
14036 TGAGGCTATGATTGAGCTGGATCATTTAGAGGCAGAGGAGAACAAAGGAGTTGAAGGTAT
1 TGAGGCTATGATTGAGCTGGATCATTTAGAGGCAGAAGAGAACAAAGGAGTTGAAGGTAT
14096 TGAGGCTATGATTGAGCTGGATCATTTAGAGGCAGAAGAGAACAAAGGAGTTGAA
1 TGAGGCTATGATTGAGCTGGATCATTTAGAGGCAGAAGAGAACAAAGGAGTTGAA
14151 CTTATTGCTG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.35, C:0.09, G:0.34, T:0.23
Consensus pattern (60 bp):
TGAGGCTATGATTGAGCTGGATCATTTAGAGGCAGAAGAGAACAAAGGAGTTGAAGGTAT
Found at i:14217 original size:45 final size:46
Alignment explanation
Indices: 14140--14229 Score: 146
Period size: 45 Copynumber: 1.9 Consensus size: 46
14130 GAAGAGAACA
*
14140 AAGGAGTTGAACTTATTGCTGCTCAGTTTGATGCTGAACATCAAACCG
1 AAGGAGTTGAAC-T-TTGCTGCTCAGTCTGATGCTGAACATCAAACCG
14188 AAGGAGTTGAAC-TTGCTGCTCAGTCTGATGCTGAACATCAAA
1 AAGGAGTTGAACTTTGCTGCTCAGTCTGATGCTGAACATCAAA
14230 GCAATGTCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
45 29 0.71
48 12 0.29
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (46 bp):
AAGGAGTTGAACTTTGCTGCTCAGTCTGATGCTGAACATCAAACCG
Found at i:21603 original size:2 final size:2
Alignment explanation
Indices: 21592--21638 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
21582 TTCCACTTTG
21592 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
21633 CT CT CT
1 CT CT CT
21639 TGTTTTTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:22559 original size:221 final size:221
Alignment explanation
Indices: 22176--22832 Score: 1206
Period size: 221 Copynumber: 3.0 Consensus size: 221
22166 ATGATTGTTC
* *
22176 TTTATCTGGTTTGAGTGTAAGATGAAATCTATTATTTTCTTAATACACACGAGTATAACCTTTCA
1 TTTATCTGGTTTGAGTGTAAGATGAAATCTATTATTTCCTTAATACACACGATTATAACCTTTCA
* * *
22241 AACCAGTGGCTACCCCTTGTGGAACATGCATCAAAAGACTCAGGCATTTTATGTCAAATGTCTTC
66 ACCCAGTGGCTACCCCTTTTGGAACATGCATCAAAAGACTTAGGCATTTTATGTCAAATGTCTTC
* *
22306 TCTATGAGGTGGCATGGTCTTACCATAAGTTCTCTGTTATTTGTGAGTGCTCAACATGGCAGCTT
131 TCTATGAGGTGGCATGGTCTTACCATAAGTTCTCTGTTATTTGTAAGAGCTCAACATGGCAGCTT
22371 AAGATAGAAGCATGGAGGTGTACGCA
196 AAGATAGAAGCATGGAGGTGTACGCA
*
22397 TTTATCTGGTTTGAGTGTAAGATGAAATCTATTATTTCCTTAATACACACGATTATAACCTCTCA
1 TTTATCTGGTTTGAGTGTAAGATGAAATCTATTATTTCCTTAATACACACGATTATAACCTTTCA
22462 ACCCAGTGGCTACCCCTTTTGGAACATGCATCAAAAGACTTAGGCATTTTATGTCAAATGTCTTC
66 ACCCAGTGGCTACCCCTTTTGGAACATGCATCAAAAGACTTAGGCATTTTATGTCAAATGTCTTC
22527 TCTATGAGGTGGCATGGTCTTACCATAAGTTCTCTGTTATTTGTAAGAGCTCAACATGGCAGCTT
131 TCTATGAGGTGGCATGGTCTTACCATAAGTTCTCTGTTATTTGTAAGAGCTCAACATGGCAGCTT
22592 AAGATAGAAGCATGGAGGTGTACGCA
196 AAGATAGAAGCATGGAGGTGTACGCA
22618 TTTATCTGGTTTGAGTGTAAGATGAAATCTATTATTTCCTTAATACACACGATTATAACCTTTCA
1 TTTATCTGGTTTGAGTGTAAGATGAAATCTATTATTTCCTTAATACACACGATTATAACCTTTCA
22683 ACCCAGTGGCTACCCCTTTTGGAACATGCATCAAAAGACTTAGGCATTTTATGTCAAATGTCTTC
66 ACCCAGTGGCTACCCCTTTTGGAACATGCATCAAAAGACTTAGGCATTTTATGTCAAATGTCTTC
* *
22748 TCTATGAGTGTGGCATGGTCTTACCATAAGTTTTCTGTTATTTTTAAGAGCTCAACATGGCAGCT
131 TCTATGAG-GTGGCATGGTCTTACCATAAGTTCTCTGTTATTTGTAAGAGCTCAACATGGCAGCT
*
22813 TAAGATAGAAGCATGCAGGT
195 TAAGATAGAAGCATGGAGGT
22833 TTATGCCTTT
Statistics
Matches: 423, Mismatches: 12, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
221 350 0.83
222 73 0.17
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (221 bp):
TTTATCTGGTTTGAGTGTAAGATGAAATCTATTATTTCCTTAATACACACGATTATAACCTTTCA
ACCCAGTGGCTACCCCTTTTGGAACATGCATCAAAAGACTTAGGCATTTTATGTCAAATGTCTTC
TCTATGAGGTGGCATGGTCTTACCATAAGTTCTCTGTTATTTGTAAGAGCTCAACATGGCAGCTT
AAGATAGAAGCATGGAGGTGTACGCA
Found at i:41673 original size:26 final size:27
Alignment explanation
Indices: 41637--41693 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
41627 TTTTAATAAG
*
41637 TATTCTTTTTAG-TCATTTAACTTTTT
1 TATTCTTTTTAGATCATTCAACTTTTT
* *
41663 TATTTTTTTTAGATGATTCAACTTTTT
1 TATTCTTTTTAGATCATTCAACTTTTT
41690 TATT
1 TATT
41694 AATTGTGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.21, C:0.09, G:0.05, T:0.65
Consensus pattern (27 bp):
TATTCTTTTTAGATCATTCAACTTTTT
Found at i:42905 original size:331 final size:332
Alignment explanation
Indices: 42194--44334 Score: 1783
Period size: 331 Copynumber: 6.5 Consensus size: 332
42184 ATATTTTAAA
* ** * * * *
42194 TCATCTAACCAAATCTTTGCAACATTGGATTTAAAAATTTGTTTTTACGAGCATTTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
42259 TTCAATTTAATTAGAAATTAAATTTGAAAAAAAATAAGG-AATACGATATTA-AAAGGGTGAAAA
66 TTCGATTTAATTAGAAATT-AATTCG-AAAAAAAT-AGGAAAAACGATATTAGAAA-CGTGAAAA
* * * * * ***
42322 TCCCTCCAATCTTTTTGGCATTGAATTATATA-CTTTTATGAGTATTTTAGCCAAAAAAAAAAAG
127 GCCCTTCAATCTTTTTGGCGTTGAAATATATATTTTTTATGAGTATTTTAGCC--AAAAATTGAG
* * * * * *
42386 AGAA-ATCTTTCGTGTCAATTTTTGCAAAATTTTAG-CTGAAATCGTGTACTAACTAACCATCAC
190 AGAATATCTTTCGGGTCAATTTTTACAAAATTTTAGTC-AAAATCGTGTAATAA-TCATCAT-A-
* * * * * * *
42449 GATTTTTGGCTTAAAACGCGTTCCGGGGACCC-GCCTCATTTTTGCATGATCTTTGGCTCCGAGA
251 G-TTTTTGGCTAAAAACGCGTTTCGGGG-CCCTGGCTCAGTTTTGCATGATTTTTGGCGCCAAGA
* * *
42513 CTACTTGAAATAACCACAT
314 CTCCTTGAAATATCCATAT
* * * *
42532 TCATCTAATCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTAT
1 TCATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
42597 TTCGATTTAATTAGAAATTAATTCGAAAAAAATAGGGAAAACAATATTAGAAACGTCAAAAGCTC
66 TTCGATTTAATTAGAAATTAATTCGAAAAAAATAGGAAAAACGATATTAGAAACGTGAAAAGCCC
* *
42662 TTCAATTTTTTTGGCGTTGAAATATATATTTTTTACGAGTATTTTAGCCAAAAATTGAGAGAATA
131 TTCAATCTTTTTGGCGTTGAAATATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGAGAATA
* *
42727 TCTTTCGGGTCAATTTTTATAAATTTTTAGTC-AAATCGTGTAATAATCATCATAGTTTTTGGCT
196 TCTTTCGGGTCAATTTTTACAAAATTTTAGTCAAAATCGTGTAATAATCATCATAGTTTTTGGCT
* * * **
42791 AAAAATGCGTTTCGGGGCCCTGGCTCAATTTTGCATGATTTTTGGTGCCAAGACTCCTTGAGCTA
261 AAAAACGCGTTTCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATA
42856 TCCATAT
326 TCCATAT
* *
42863 TCATCTAATCAAATTTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATATTGT
1 TCATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
* * *
42928 TTCGATTTAATTAGAAATTAATTC-AAAAAAATATGAAAAACAATATTA-AAAGCGTGAAAAGTC
66 TTCGATTTAATTAGAAATTAATTCGAAAAAAATAGGAAAAACGATATTAGAAA-CGTGAAAAGCC
* * * *
42991 CTCCAATCTTTTTGGAGTT-AAATTATATATATTTTATGAGTATTTTATCCAAAAATTGAG-GAA
130 CTTCAATCTTTTTGGCGTTGAAA-TATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGAG-A
* * * * * * * * * *
43054 AAAT-TTTCGGGTCATTTTTTTACCAAGTTTTAGCCAAAATTGTGTACTAACCTTCATGGTTTTT
193 ATATCTTTCGGGTCA-ATTTTTACAAAATTTTAGTCAAAATCGTGTAATAATCATCATAGTTTTT
* * * * *
43118 GGCTAAAAACGCGTTCCGGGGCCCCGGTTCAGTTTTGCATGATTTTTGGCGCCGAGAATCCTTGA
257 GGCTAAAAACGCGTTTCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGA
*
43183 AATATCTATAT
322 AATATCCATAT
** * * * * *
43194 TTGTCAAATAAAATCTTAGCCACATTGCATTTAAGAATTTGTTTTTACAAGCTTCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
* *
43259 TTCGATTTAATTAGAAATTAATTCAGAAAAAAAATATG-AAAACGATATTAAAAACGTGAAAAGC
66 TTCGATTTAATTAGAAATTAATTC-G-AAAAAAATAGGAAAAACGATATTAGAAACGTGAAAAGC
** * * * **
43323 CCTTCAATCTTTTTGAAGTT-AAAT-TATATATGTTTATGAGTATTGTGGATAAAAATTGAG-GA
129 CCTTCAATCTTTTTGGCGTTGAAATATATAT-TTTTTATGAGTATTTTAGCCAAAAATTGAGAG-
* * * *
43385 AATATCTTT-GGGTCATTTTTTGCAAAATTTTA-CCAAAAATCGTGTAATAATCATCACAGTTTT
192 AATATCTTTCGGGTCAATTTTTACAAAATTTTAGTC-AAAATCGTGTAATAATCATCATAGTTTT
* * * ** *
43448 TGACTAAAAACGCG-TTCTAGGG-CC-GGTTCAGTTTTGCATGA-TTTTGGCATCAAGAATCCTT
256 TGGCTAAAAACGCGTTTC-GGGGCCCTGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT
**
43509 GAAATATATATAT
320 GAAATATCCATAT
* * * *** * * * * *
43522 AT-ATATATAT-ATATAT-ATATATATT-CATCTAACCAACTCCCAGCCATTATTTTTACAAGCA
1 -TCATCTA-ATCAAATCTCAGCCACATTGCATTTAA-GAA-T--------TTGTTTTTACGAGCA
* * * * *
43583 TCTG-ATCATATTTTGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAG
54 TCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAATAGGAAAAACGATATTAGAAA
* * * * ** * * * **
43647 CGTGAAAAGTCCTTCAATATTTTTGGCGTTCAATTATATATACTTTACGAGTATTGTGGTTAAAA
119 CGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAAATATATATTTTTTATGAGTATTTTAGCCAAAA
* * * * * * *
43712 ATTGAG-GAAAAATATTTCGGGTCAATTTTTGCAAAATATTAG-CTGAAATCGTCTACT-ATCA-
184 ATTGAGAG-AATATCTTTCGGGTCAATTTTTACAAAATTTTAGTC-AAAATCGTGTAATAATCAT
* ** * * * *
43773 CA-A-TTTTTGGCTAAAAACGCGTTT-TGGGCCCCAGATCAGTTTTTCATCATTTTTGGCGCAAA
247 CATAGTTTTTGGCTAAAAACGCGTTTCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGCGCCAA
* * * *
43835 AACTACTTGAATTATCTATAT
312 GACTCCTTGAAATATCCATAT
* *
43856 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGAATTT-TTTTTACGAGCATCTAAAATCTT
1 TCATCTAATCAAATCTCAGCCACATTGCATTTAA-GAATTTGTTTTTACGAGCATCT-GAATCTT
* *
43920 GTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAGAAACGATATTAGAAACCTCAAAAC
64 GTTTCGATTTAATTAGAAATTAATTCGAAAAAAATAGGAA-AAACGATATTAGAAA---C----G
* * * * * * *
43985 TCAAAAGCCCATCAAT-TGTTTTGGTGTTGAAATATATATATTTCATGAGTATTCTAG---ACAA
121 TGAAAAGCCCTTCAATCT-TTTTGGCGTTGAAATATATATTTTTTATGAGTATTTTAGCCAAAAA
* *
44046 -T-------TATCTTTCAGGTCAATTTTTACAAAA-TTT--T----A-CGTGTAATAATCATCAC
185 TTGAGAGAATATCTTTCGGGTCAATTTTTACAAAATTTTAGTCAAAATCGTGTAATAATCATCAT
* * * * ** *
44095 AGTTTTTGGCTAAAAAAGCGTTCCGGGGCCCTGACTTAGTTTTGCATGATTTTTGG-TACAAAAC
250 AGTTTTTGGCTAAAAACGCGTTTCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGCGCCAAGAC
*
44159 TCCTTGAGATATCCATAT
315 TCCTTGAAATATCCATAT
* * *
44177 TCATCTAATCAAATATCAGCCACATTGCATTAAAGAATTTGTTTTTACGAGTATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * *
44242 TTTGATTTATTTAGAAATTAATTC-AGAAAAAATATGAAAAACAATATTAAAAACGTGAAAGGTC
66 TTCGATTTAATTAGAAATTAATTCGA-AAAAAATAGGAAAAACGATATTAGAAACGTGAAAAG-C
*
44306 CAC-T-AATCTTTTTGGAGTT-AAATATATAT
129 C-CTTCAATCTTTTTGGCGTTGAAATATATAT
44335 ATATATATAT
Statistics
Matches: 1496, Mismatches: 241, Indels: 159
0.79 0.13 0.08
Matches are distributed among these distances:
311 10 0.01
312 17 0.01
313 4 0.00
314 1 0.00
316 1 0.00
317 6 0.00
318 5 0.00
319 15 0.01
320 48 0.03
321 83 0.06
322 24 0.02
324 2 0.00
325 22 0.01
326 20 0.01
327 9 0.01
328 78 0.05
329 51 0.03
330 108 0.07
331 374 0.25
332 58 0.04
333 76 0.05
334 95 0.06
335 104 0.07
336 182 0.12
337 27 0.02
338 76 0.05
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (332 bp):
TCATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
TTCGATTTAATTAGAAATTAATTCGAAAAAAATAGGAAAAACGATATTAGAAACGTGAAAAGCCC
TTCAATCTTTTTGGCGTTGAAATATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGAGAATA
TCTTTCGGGTCAATTTTTACAAAATTTTAGTCAAAATCGTGTAATAATCATCATAGTTTTTGGCT
AAAAACGCGTTTCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATA
TCCATAT
Found at i:43519 original size:2 final size:2
Alignment explanation
Indices: 43512--43545 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
43502 AATCCTTGAA
43512 AT AT AT 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 AT AT AT
43546 TCATCTAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46143 original size:329 final size:325
Alignment explanation
Indices: 44406--46490 Score: 1684
Period size: 330 Copynumber: 6.3 Consensus size: 325
44396 TTAGCCAAAA
* * * * * *
44406 TTTTGGCTAAAAACGCCTTTCGGGGCCCGGGCTAAGTTTTGCAAGATTTTTGGCGCCAAGACTCC
1 TTTTGGCTAAAAACGCGTTT-GAGGCCCAGACTCAGTTTTGCATGATTTTT-GCGCCAAGACTCC
** * * *
44471 TTGAAATATCTATATTTGTCTGATAAAATCTTAGCCACATTGCATTTAAGGATTTGTTTTTACGA
64 TTGAAATATC-ATATTCATCTAATAAAATCTCAGCCACATTACATTTAAGGATTTGTTTTTACGA
* * * * * * *
44536 GCATCTGAATCTTGTTTCGATCTAATGAGAAATTAATTCAGAAAAAAAATTAAAAATGATATTAA
128 GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GGAAAAATATGAAAAACGATATAAA
* * * *
44601 AAGCGTAAAAAGCCCTTCAATCTTTTTGGCGTTGAATT-T-TTTTTTGTATTAGTATTGT-G-GA
192 AAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTT-TATGAGTATTGTAGCCA
* * * * * * * * **
44662 TAAAATTGAGGAAATATCTTTCGGATCAA-TTTTGCAAAATTTTAGCCAAAATCGTGTAATAATC
256 -AAAATCGAGGAAAAATATTTTGGGTCAATTTTTACAAAATATTAGCCGAAATCGTGT-ACCATC
44726 ATCACGGTT
319 A-CA-GGTT
* ** * ** * * ****
44735 TTTTTGCTAAAAACGCGTTCCAGGACTC-GGTTCAGTTTTGCATCATTTTGGCATTGAGACTCCT
1 TTTTGGCTAAAAACGCGTTTGAGG-CCCAGACTCAGTTTTGCATGATTTTTGCGCCAAGACTCCT
** * * *
44799 TGAAATATACATATTCATCTAACCAAATCCCAG---C----C--------A-TTGTTCTTACAAG
65 TGAAATAT-CATATTCATCTAATAAAATCTCAGCCACATTACATTTAAGGATTTGTTTTTACGAG
** * *
44848 CATCTG-ATGATGTTTCGATTTAATTAAAAATTAATTCGGGAAAAAAATATGAAAAACGATATTA
129 CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GG--AAAAATATGAAAAACGATATAA
* * * * *
44912 GAAGCGTGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATATATATTTTATGAGTATTGTGGCT
191 AAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTATTGTAGCC
* * * * * *
44977 AAAAATTGAGGAAAAATATTTTGGGTCCATCTTTGCAAAATATTAGTCGAAATCGTATACCATCA
255 AAAAATCGAGGAAAAATATTTTGGGTCAATTTTTACAAAATATTAGCCGAAATCGTGTACCATCA
* *
45042 CTGTTTTT
320 CAG--GTT
* * *
45050 TTTTGTTGCTAAAAACGCGTTCTGTGGTCCAG-GTCAGTTTTGCATGATTTTTG-GCGCAGAGAC
1 TTTTG--GCTAAAAACGCGTT-TGAGGCCCAGACTCAGTTTTGCATGATTTTTGCGC-CA-AGAC
* * *
45113 TCCTTGAAATATCCATATTCATCTAATCAAATCTCAGCCACATTAGATTTAATGATTTGTTTTTA
61 TCCTTGAAATAT-CATATTCATCTAATAAAATCTCAGCCACATTACATTTAAGGATTTGTTTTTA
* * * *
45178 CGAGAATCTGAATCTTGTTTCGATTTAATTAGAAATTAAATCGGAAAAAATAGGAAAAATGATAT
125 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AAAAATATGAAAAACGATA-
* * * * * *
45243 TAGAAAA--GTAAAAAACCCATCAATCTTTTTGGCGTTGAAATAT-TTTTTTTATGAGTATTTTA
188 TA-AAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTGTA
* * ** *
45305 GCCAAAAATCGAGGAAATATCTTTCAGGTCAATTTTTACAAAACT-TTAGCCGAAATTGTGTAAT
252 GCCAAAAATCGAGGAAAAATATTTTGGGTCAATTTTTACAAAA-TATTAGCCGAAATCGTG---T
**
45369 AACCATCACA--AC
313 -ACCATCACAGGTT
* * ** *
45381 TTATGGCTAAAAAAGCGTTTCGAGGCCTTGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCC
1 TTTTGGCTAAAAACGCGTTT-GAGGCCCAGACTCAGTTTTGCATGATTTTT-GCGCCAAGACTCC
* * * *
45446 TTGAGATATTCATATTCATCTAATTAAATCTCAGACACATTGCATTT-AGGAATTTGTTTTTACG
64 TTGAAATA-TCATATTCATCTAATAAAATCTCAGCCACATTACATTTAAGG-ATTTGTTTTTACG
* * * * * *
45510 AGCATCTAAATCTTGTTTCGATATAATTAGAAATTAATTCAGAAAAAATATGAAAACCAATATTA
127 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GGAAAAATATGAAAAACGATATAA
* * * * * * * *
45575 AAAGCGTGAAAAGTCCTCCAATATTTTTGGAGTTAAATTATATATTTTTAT-AATGATTTTATCC
191 AAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGT-ATTGTAGCC
* * * * * **
45639 AAAAATTGAGAAAAAAAATTTCT-GGTCATTTTTTTACAAAATTTTAGCTAAAATCGTGTACCAT
255 AAAAATCGAGGAAAAATATTT-TGGGTCA-ATTTTTACAAAATATTAGCCGAAATCGTGTACCAT
45703 CAC-GGTTT
318 CACAGG-TT
* * * * * * *
45711 TTTTGGCTAAGACCGCGTTTTG-GTGCCCCGACTCAGTTTTGAATGATTCTTGGCACCGAGACTC
1 TTTTGGCTAAAAACGCG-TTTGAG-GCCCAGACTCAGTTTTGCATGATT-TTTGCGCCAAGACTC
* * * *
45775 CTTGAAATATCTATATTCGTCTAATAAAATCTAAGCCACACTACATTTAATGATTTGTTTTTACG
63 CTTGAAATATC-ATATTCATCTAATAAAATCTCAGCCACATTACATTTAAGGATTTGTTTTTACG
* * *
45840 AGCATTTGAATCTTGTATCGATTTAATTAGAAATTAATTCGGAAAAATATGAAAAATGATATAAA
127 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAATATGAAAAACGATATAAA
* * * *
45905 AAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATATATTATGAGTATTGTGGCTA
192 AAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTATTGTAGCCA
* *
45970 AAAATCAAGGAAAAATATTTTGGGAT-AATTTTTGCAAAATATTAGCCGAAATCGTGTACCATCA
256 AAAATCGAGGAAAAATATTTTGGG-TCAATTTTTACAAAATATTAGCCGAAATCGTGTACCATCA
46034 CAGGTT
320 CAGGTT
* * * * * *
46040 TTTTGGCTAAAAATGCGTTATG-GGCCACAG-GTTAGTTTTGCATTATCTTTTGCGCCAAGAATT
1 TTTTGGCTAAAAACGCGTT-TGAGGCC-CAGACTCAGTTTTGCATGAT-TTTTGCGCCAAGACTC
* ** *
46103 CTTGAAATATCGATATTCATCTAATCAAAATTTCAGCCACATTGGATTTAAGGATTTGATTTTAC
63 CTTGAAATATC-ATATTCATCTAAT-AAAATCTCAGCCACATTACATTTAAGGATTTGTTTTTAC
* * *
46168 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAATACGAAAAACAATGTTA
126 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAATATGAAAAACGAT-ATA
* * *
46233 GAAA-CGTCAAAAGCCCTTCAATCTTTTTTGGCGTTGAATTATATATTTTTCATGAGTATTTTAG
190 AAAAGCGTGAAAAGCCCTTCAATC-TTTTTGGCGTTGAATTATATATTTTT-ATGAGTATTGTAG
* * ** * * * *
46297 CAAAAAATTGAAAAAAAAAAATCTTTCGAGTCAATTTTTACAAAATTTTTAGCCGGAATCGTTAA
253 CCAAAAATCG-AGGAAAAATAT-TTT-GGGTCAATTTTTACAAAA-TATTAGCCGAAATCG-T--
*
46362 ATAACCATCACA-G-T
311 GT-ACCATCACAGGTT
* ** ** * * * *
46376 TTTTGGATAAAAAAACGTTCCAGGACCCTGGCACAGTTTTGCATCG-TTTTTGGTGCCAAGACTC
1 TTTTGGCTAAAAACGCGTTTGAGG-CCCAGACTCAGTTTTGCAT-GATTTTT-GCGCCAAGACTC
* *
46440 CTTGAAATATCTATATAT-ATCTAATCAAATCTCAGCCACATTGCATTTAAG
63 CTTGAAATATC-ATAT-TCATCTAATAAAATCTCAGCCACATTACATTTAAG
46491 AAAAAATAAT
Statistics
Matches: 1400, Mismatches: 265, Indels: 175
0.76 0.14 0.10
Matches are distributed among these distances:
310 27 0.02
311 17 0.01
312 55 0.04
313 2 0.00
314 14 0.01
315 38 0.03
316 24 0.02
317 33 0.02
318 41 0.03
320 1 0.00
321 1 0.00
324 1 0.00
327 34 0.02
328 83 0.06
329 266 0.19
330 367 0.26
331 125 0.09
332 32 0.02
333 63 0.05
334 33 0.02
335 39 0.03
336 48 0.03
337 46 0.03
338 10 0.01
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (325 bp):
TTTTGGCTAAAAACGCGTTTGAGGCCCAGACTCAGTTTTGCATGATTTTTGCGCCAAGACTCCTT
GAAATATCATATTCATCTAATAAAATCTCAGCCACATTACATTTAAGGATTTGTTTTTACGAGCA
TCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAATATGAAAAACGATATAAAAAGC
GTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTGTAGCCAAAAAT
CGAGGAAAAATATTTTGGGTCAATTTTTACAAAATATTAGCCGAAATCGTGTACCATCACAGGTT
Found at i:46198 original size:659 final size:649
Alignment explanation
Indices: 44440--46316 Score: 1899
Period size: 659 Copynumber: 2.9 Consensus size: 649
44430 GCCCGGGCTA
* * * *
44440 AGTTTTGCAA-GATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTTGTCTGATAAAATCTTA
1 AGTTTTG-AATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCGTCTAATAAAATCTAA
* * * *
44504 GCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATCTAATGAGAAAT
65 GCCACATTACATTTAATGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
* * * *
44569 TAATTCAGAAAAAAAATTAAAAATGATATTAAAAGCGTAAAAAGCCCTTCAATCTTTTTGGCGTT
130 TAATTC-GGAAAAATATGAAAAATGATATAAAAAGCGTAAAAA-CCCTTCAATCTTTTTGGCGTT
* * * *
44634 GAATT-T-TTTTTTGTATTAGTATTGTGGAT-AAAATTGAGG--AAATATCTTTCGGATCAA-TT
193 GAATTATATTTTTT-TATGAGTATTGTGGCTAAAAATCGAGGAAAAATAT-TTTAGGATCAATTT
* ** * * *
44693 TTGCAAAATTTTAGCCAAAATCGTGTAATAATCATCACGGTTTTTTTGCTAAAAACGCGTTCCAG
256 TTGCAAAA-TTTAGCCGAAATCGTGTAACCATCA-CA-GGTTTTTTGGCTAAAAAAGCGTT--TG
* * * ****
44758 GACTCGGTTCAGTTTTGCATCATTTTGGCATTGAGACTCCTTGAAATATACATATTCATCTAA-C
316 GGCCCGGTT-AGTTTTGCATCATTTTTGCGCCAAGACTCCTTGAAATAT-CATATTCATCTAATC
* * * * **
44822 CAAATCCCAGC-C----A-TT--G---T-TCTTACAAGCATCTG-ATGATGTTTCGATTTAATTA
379 AAAATCTCAGCACATTGATTTAGGATTTGTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
* * * * *
44874 AAAATTAATTCGGGAAAAAAATATGAAAAACGATATTAGAAGCGTGAAAAGCCCTTAAATCTTTT
444 GAAATTAATTC--G-AAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGCCCTTCAATATTTT
* * * * * *
44939 TGGTGTTGAATTATATATATTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAATATTTTGGGTC
506 TGGAGTTGAATTATATAT-TTTTATGAGTATTTTAGCAAAAAATTGAGAAAAAAAATTTTGGGTC
* * *
45004 CATCTTTGCAAAATATTAGTCGAAATCGTATACCATCACTGTTTTTTTTTGTTGCTAAAAACGCG
570 CATCTTTACAAAATATTAGTCAAAATCGTATACCATCACTGTGTTTTTTTG-TGCTAAAAACGCG
*
45069 TTCTGTGGTCCAGGTC
634 TTCTGTGGTCCAGCTC
* * * * * *
45085 AGTTTTGCATGATTTTTGGCGCAGAGACTCCTTGAAATATCCATATTCATCTAATCAAATCTCAG
1 AGTTTTGAATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCGTCTAATAAAATCTAAG
* *
45150 CCACATTAGATTTAATGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAGAAATT
66 CCACATTACATTTAATGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* * *
45215 AAATCGGAAAAAATAGGAAAAATGATATTAGAAAA--GTAAAAAACCCATCAATCTTTTTGGCGT
131 AATTCGG-AAAAATATGAAAAATGATA-TA-AAAAGCGT-AAAAACCCTTCAATCTTTTTGGCGT
* * * * * * *
45278 TGAAATAT-TTTTTTTATGAGTATTTTAGCCAAAAATCGAGGAAATATCTTTCAGG-TCAATTTT
192 TGAATTATATTTTTTTATGAGTATTGTGGCTAAAAATCGAGGAAAAATATTTTAGGATCAATTTT
* * ** *
45341 TACAAAACTTTAGCCGAAATTGTGTAATAACCATCACA--ACTTATGGCTAAAAAAGCGTTTCGA
257 TGCAAAA-TTTAGCCGAAATCGTG---TAACCATCACAGGTTTTTTGGCTAAAAAAGCGTTT-G-
* * * * * *
45404 GGCCTTGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAGATATTCATATTCATCTAA
316 GGCC-CG-GTTAGTTTTGCATCATTTTT-GCGCCAAGACTCCTTGAAATA-TCATATTCATCTAA
* * *
45469 T-TAAATCTCAGACACATTGCATTTAGGAATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATA
377 TCAAAATCTCAG-CACATTG-ATTTAGG-ATTTG-TTTTACGAGCATCTGAATCTTGTTTCGATT
* * *
45533 TAATTAGAAATTAATTCAGAAAAAATATGAAAACCAATATTAAAAGCGTGAAAAGTCCTCCAATA
438 TAATTAGAAATTAATTC-GAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGCCCTTCAATA
* * * *
45598 TTTTTGGAGTTAAATTATATATTTTTAT-AATGATTTTATCCAAAAATTGAGAAAAAAAATTTCT
502 TTTTTGGAGTTGAATTATATATTTTTATGAGT-ATTTTAGCAAAAAATTGAGAAAAAAAATTT-T
* * *
45662 -GGT-CATTTTTTTACAAAATTTTAG-CTAAAATCGTGTACCATCAC-G-GTTTTTTTG-GCTAA
565 GGGTCCA--TCTTTACAAAATATTAGTC-AAAATCGTATACCATCACTGTGTTTTTTTGTGCTAA
* * *
45721 GACCGCGTT-T-TGGTGCCCCGACTC
627 AAACGCGTTCTGTGGT--CCAG-CTC
* *
45745 AGTTTTGAATGATTCTTGGCACCGAGACTCCTTGAAATATCTATATTCGTCTAATAAAATCTAAG
1 AGTTTTGAATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCGTCTAATAAAATCTAAG
* * *
45810 CCACACTACATTTAATGATTTGTTTTTACGAGCATTTGAATCTTGTATCGATTTAATTAGAAATT
66 CCACATTACATTTAATGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
45875 AATTCGGAAAAATATGAAAAATGATATAAAAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGA
131 AATTCGGAAAAATATGAAAAATGATATAAAAAGCGT-AAAAACCCTTCAATCTTTTTGGCGTTGA
* * * *
45940 ATTATATATATATTATGAGTATTGTGGCTAAAAATCAAGGAAAAATATTTTGGGAT-AATTTTTG
195 ATTATAT-TTTTTTATGAGTATTGTGGCTAAAAATCGAGGAAAAATATTTTAGGATCAATTTTTG
*
46004 CAAAATATTAGCCGAAATCGTGT-ACCATCACAGGTTTTTTGGCTAAAAATGCGTTATGGGCCAC
259 CAAAAT-TTAGCCGAAATCGTGTAACCATCACAGGTTTTTTGGCTAAAAAAGCGTT-TGGGCC-C
* * *
46068 AGGTTAGTTTTGCATTATCTTTTGCGCCAAGAATTCTTGAAATATCGATATTCATCTAATCAAAA
321 -GGTTAGTTTTGCATCAT-TTTTGCGCCAAGACTCCTTGAAATATC-ATATTCATCTAATCAAAA
*
46133 TTTCAGCCACATTGGATTTAAGGATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
383 TCTCAG-CACATT-GATTT-AGGATTTG-TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
* * * * *
46198 GAAATTAATTCGGAAAAATACGAAAAACAATGTTAGAAA-CGTCAAAAGCCCTTCAATCTTTTTT
444 GAAATTAATTCGAAAAAATATGAAAAACAATATTA-AAAGCGTGAAAAGCCCTTCAAT-ATTTTT
* *
46262 GGCGTTGAATTATATATTTTTCATGAGTATTTTAGCAAAAAATTGAAAAAAAAAA
507 GGAGTTGAATTATATATTTTT-ATGAGTATTTTAGCAAAAAATTGAGAAAAAAAA
46317 ATCTTTCGAG
Statistics
Matches: 1011, Mismatches: 157, Indels: 113
0.79 0.12 0.09
Matches are distributed among these distances:
644 2 0.00
645 171 0.17
646 44 0.04
647 47 0.05
648 41 0.04
649 4 0.00
650 8 0.01
655 1 0.00
656 2 0.00
657 19 0.02
658 87 0.09
659 184 0.18
660 158 0.16
661 76 0.08
662 37 0.04
663 90 0.09
664 13 0.01
665 27 0.03
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (649 bp):
AGTTTTGAATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCGTCTAATAAAATCTAAG
CCACATTACATTTAATGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
AATTCGGAAAAATATGAAAAATGATATAAAAAGCGTAAAAACCCTTCAATCTTTTTGGCGTTGAA
TTATATTTTTTTATGAGTATTGTGGCTAAAAATCGAGGAAAAATATTTTAGGATCAATTTTTGCA
AAATTTAGCCGAAATCGTGTAACCATCACAGGTTTTTTGGCTAAAAAAGCGTTTGGGCCCGGTTA
GTTTTGCATCATTTTTGCGCCAAGACTCCTTGAAATATCATATTCATCTAATCAAAATCTCAGCA
CATTGATTTAGGATTTGTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCG
AAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGCCCTTCAATATTTTTGGAGTTGAATTATA
TATTTTTATGAGTATTTTAGCAAAAAATTGAGAAAAAAAATTTTGGGTCCATCTTTACAAAATAT
TAGTCAAAATCGTATACCATCACTGTGTTTTTTTGTGCTAAAAACGCGTTCTGTGGTCCAGCTC
Found at i:46525 original size:12 final size:12
Alignment explanation
Indices: 46492--46531 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
46482 GCATTTAAGA
46492 AAAAATAATATT
1 AAAAATAATATT
*
46504 AAGAAA-AATATG
1 AA-AAATAATATT
46516 AAAAATAATATT
1 AAAAATAATATT
46528 AAAA
1 AAAA
46532 GCGTGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 3 0.12
12 18 0.75
13 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (12 bp):
AAAAATAATATT
Found at i:46909 original size:333 final size:330
Alignment explanation
Indices: 46501--47162 Score: 945
Period size: 333 Copynumber: 2.0 Consensus size: 330
46491 AAAAAATAAT
* * * * *
46501 ATTAAGAAAAATATGAAAAATAATATTAAAAGCGTGAAAAATTCTTCACTCTTTTTGGAGTTAAA
1 ATTAAGAAAAACATGAAAAATAATATTAAAAGCGTCAAAAATCCTCCAATCTTTTTGGAGTTAAA
* *
46566 TTATATATATTTCATGAGTATTTTATCCAAAAATCAAGGAAAAATTTTTCGGGTCAT-TTTTTAC
66 TTATATATATTTCATGAGTATTTTATCCAAAAATCAAGGAAAAATTTCTCGAGTCATCTTTTTAC
* *
46630 AGAATTTTAGCCAAAATCGTGTGTACAAACCATCACGGTTTTTTGATAAAAAC-TCATTTCGGGG
131 AAAATTTTAGCCAAAATC--GTGTACAAACCATCA-GGTTTTTGGATAAAAACGT-ATTTCGGGG
* ** * * *
46694 CCCCGGCTCAGTTTTGCATGATT-TTTGGTGCCAAGACTCCTTGAGATATCCATATTTGTCTAAT
192 CCCCGACTCAGTTTTGCATGATTCTTT--CACCAAGACACCTTGAAATATCCATATTCGTCTAAT
* * * *
46758 CAAATCTCAGCCACATTGCATTTAAGAATTT-TTTTTACGAGCATCTGAATCTTGTTTCGATTTA
255 AAAATCTAAGCCACACTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTGTCGATTTA
46822 ATTAGAAATGA
320 ATTAGAAATGA
**
46833 ATTAAGAAAAAACATGAAAAATAATATTAAAAGCGTCAAAGGTCCTCCAATCTTTTTGGAGTTAA
1 ATTAAG-AAAAACATGAAAAATAATATTAAAAGCGTCAAAAATCCTCCAATCTTTTTGGAGTTAA
46898 ATTATATATATTTCATGAGTATTTTATCCAAAAATCAAGGAAAAATTTCTCGAGTCATCTTTTTA
65 ATTATATATATTTCATGAGTATTTTATCCAAAAATCAAGGAAAAATTTCTCGAGTCATCTTTTTA
* * * * * *
46963 CAAAATTTTAGCCAAAATCGTGTACTAACCATCATGTTTTTGGCTAAAACCGTGTTTCGGTGCCC
130 CAAAATTTTAGCCAAAATCGTGTACAAACCATCAGGTTTTTGGATAAAAACGTATTTCGGGGCCC
* **
47028 CGACTCAGTTTTGCATGATTCTTTCACCGAGACACCTTGAAATATCTGTATTCGTCTAATAAAAT
195 CGACTCAGTTTTGCATGATTCTTTCACCAAGACACCTTGAAATATCCATATTCGTCTAATAAAAT
* *
47093 CTAAGCCACACTGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTGTCGATTTAATTAG
260 CTAAGCCACACTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTGTCGATTTAATTAG
47158 AAATG
325 AAATG
47163 TCAAAAGCCC
Statistics
Matches: 293, Mismatches: 32, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
330 55 0.19
331 83 0.28
332 24 0.08
333 107 0.37
334 24 0.08
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (330 bp):
ATTAAGAAAAACATGAAAAATAATATTAAAAGCGTCAAAAATCCTCCAATCTTTTTGGAGTTAAA
TTATATATATTTCATGAGTATTTTATCCAAAAATCAAGGAAAAATTTCTCGAGTCATCTTTTTAC
AAAATTTTAGCCAAAATCGTGTACAAACCATCAGGTTTTTGGATAAAAACGTATTTCGGGGCCCC
GACTCAGTTTTGCATGATTCTTTCACCAAGACACCTTGAAATATCCATATTCGTCTAATAAAATC
TAAGCCACACTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTGTCGATTTAATTAGA
AATGA
Found at i:47682 original size:12 final size:12
Alignment explanation
Indices: 47652--47682 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
47642 CCTGGCAATC
*
47652 CGTGTTCCGTGT
1 CGTGTTTCGTGT
47664 CGTGTTTCGTGT
1 CGTGTTTCGTGT
47676 CGTGTTT
1 CGTGTTT
47683 ACATAGGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.19, G:0.32, T:0.48
Consensus pattern (12 bp):
CGTGTTTCGTGT
Found at i:49097 original size:296 final size:297
Alignment explanation
Indices: 48538--50704 Score: 1361
Period size: 332 Copynumber: 7.0 Consensus size: 297
48528 AAAGGTCCTC
* **
48538 CAAT-CTTTTTGGAGTT-AAATTATATAAATTTCATGAGTATTTTATCCAAAAATTAAGGAAAAA
1 CAATCCTTTTTGGCGTTGAAATTATATATTTTTCATGAGTATTTTATCCAAAAATTAAGGAAAAA
*
48601 TTTTTCGGGTCATTTTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTTGG
66 TTTTTCGGGTCA-TTTTTTACAAAATTTTAGCCAAAATCGTGTAATAACCATCACGG-TTTTTGG
* * * ** * ** * * * *
48666 CTAAAACCGTGTTTCGGTGCCCCAACTCAGTTTTGCATGATTCTTGGCACCGAGACACCTTAAAA
129 CTAAAAACGCGTTCCGG-GCCCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAGA
** * * * * * *
48731 TATCTGTATTCGTCTAATAAAATCTAAGGCACACTGCATTTAAGGATTTGTTTTTACGAGCATTT
193 TATCCATATTCATCTAATAAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCT
* * *
48796 GAATCTTGTATCGATTTATTTAGAAATGTCAAAAGCCCTT
258 GAATCTTGTTTCGATTTAATTAGAAATGTCAAAAGCCATT
* *
48836 CAAT-CTTTTTGGCGTTGAAA-TATATATTTTTCATGAGTATTTTAGCCAAAAATTGAGGAAAAA
1 CAATCCTTTTTGGCGTTGAAATTATATATTTTTCATGAGTATTTTATCCAAAAATTAAGGAAAAA
* * * * * * *
48899 TTTTTCGAGTCAATTTTTACAAAATTTTAGCCGAGATCATGTAATAACCATCACAGTTTTTGGAT
66 TTTTTCGGGTCATTTTTTACAAAATTTTAGCCAAAATCGTGTAATAACCATCACGGTTTTTGGCT
* *
48964 AAAAAAGCGTTCCGGGACCCTGGCTCAGTTTTGCATTG-TTTTTGGTGCCAAGACTCCTTGAGAT
131 AAAAACGCGTTCCGGG-CCCCGGCTCAGTTTTGCA-TGATTTTTGGTGCCAAGACTCCTTGAGAT
* *
49028 ATCCATATTTATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTG
194 ATCCATATTCATCTAATAAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTG
* ** *
49093 AATCTTGTTTCGATTTAATTAGAAATGAATTAAGAAAAAACATAGAA
259 AATCTTGTTTCGATTTAATTAGAAATG---T--CAAAAGCCAT---T
* ** ** * *
49140 AAATAATATTAAAAGCGTCAAAGGTCCTCCAATCTTTTTGGAGTTAAATTATATATATTTCATGA
1 CAATCCT-TT--TTG-G-C----GT--T-GAA----AT------T--A-TATAT-T-TTTCATGA
* *
49205 GTATTTTATCCAAAAATCAAGGAAAAATTTTTCGGGTCATTTTTTACAAAATTTTAGCAAAAATC
39 GTATTTTATCCAAAAATTAAGGAAAAATTTTTCGGGTCATTTTTTACAAAATTTTAGCCAAAATC
* * * *
49270 GTGTGTACA-AACCATCACGGTTTTTTGCTAAAAACTCGTTTCGGGGACCCGGCTCAGTTTTGCA
104 --GTGTA-ATAACCATCACGGTTTTTGGCTAAAAACGCG-TTCCGGGCCCCGGCTCAGTTTTGCA
* * *
49334 TGATTTTTGGTGCCAAGACTCCTTGAGATATCCATATTTATTTAATCAAATCTCAGCCACATTGC
165 TGATTTTTGGTGCCAAGACTCCTTGAGATATCCATATTCATCTAATAAAATCTCAGCCACATTGC
*
49399 ACTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATGAATTAAGAA
230 ATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATG---T-----
* **
49464 AAAATATGAAAAATAATATT
287 CAAA-A-G-------CCATT
** * *
49484 ACAAGTGTGAACAGTCCTTCAATCTTTTTGGAGTT-AAATTATATATATTTCATGAGTATTTTAT
1 -CAA---T-------CCTT---T-TTGG---CGTTGAAATTATATATTTTTCATGAGTATTTTAT
* *
49548 CCAAAAATCAAGGAAAATTTTTTCGGGTCATTTTTTACAAAATTTTAGCCAAAATCGTGTACA-A
48 CCAAAAATTAAGGAAAAATTTTTCGGGTCATTTTTTACAAAATTTTAGCCAAAATCGTGTA-ATA
** * * * *
49612 ACCATCACGGTTTTTACCTAAAAACTCGTTTCGAGGCCCCAGCTCAATTTTGCATGATTTTTGGT
112 ACCATCACGGTTTTTGGCTAAAAACGCGTTCCG-GGCCCCGGCTCAGTTTTGCATGATTTTTGGT
* * *
49677 GCCAAGACTCCTTGAGATATCCATATTCATCTAATTAAATCTCAGGCACATTGCATTTAGGAATT
176 GCCAAGACTCCTTGAGATATCCATATTCATCTAATAAAATCTCAGCCACATTGCATTTAAGAATT
* * *
49742 TGTTTTTACGAGGATCTGAATCTTTTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAA
241 TGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA-T--GTC-----AAA-A-G---
49807 ACCAATATT
293 -CC---ATT
* * *
49816 GAAAGCGTGCAAATTCCGCCAATATTTTTGGAGTT-AAATTATATATTCTTTACA--ATTATTTT
1 -----C-----AA-T---CC--TTT--TTGGCGTTGAAATTATATATT-TTT-CATGAGTATTTT
* * * * * * * * *
49878 ATCCAAAAGTTGATGAAAAAATTTTCGGATCATTTTTTTCAAACTTTTAGCCAAAATTGTGTACT
46 ATCCAAAAATTAAGGAAAAATTTTTCGGGTCATTTTTTACAAAATTTTAGCCAAAATCGTGTAAT
* * * * *
49943 --CCATCACGGTTTTTGGCTAAAACCGCGTTTCGGTGCCCCGACTCAGTTTTGAATGATTCTTGG
111 AACCATCACGGTTTTTGGCTAAAAACGCGTTCCGG-GCCCCGGCTCAGTTTTGCATGATTTTTGG
** * * * * * * *
50006 CACCGAGACAT-CTTGAAATATCTATATTCGTCTAATAAAATCTAAGCCACACTGCATTTAAGGA
175 TGCCAAGAC-TCCTTGAGATATCCATATTCATCTAATAAAATCTCAGCCACATTGCATTTAAGAA
* * * * *
50070 TTTGTTTTTACCAGCATTTGAATATTGTATCGATTTAATTAGAAATGTCAAAAGCCCTT
239 TTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATGTCAAAAGCCATT
* * *
50129 CAAT-CTTTTTGACGTTGAAA-TATATATTTTTCATGAGTATTTTAGCCAAAAATTGAGGAAAAA
1 CAATCCTTTTTGGCGTTGAAATTATATATTTTTCATGAGTATTTTATCCAAAAATTAAGGAAAAA
* * * *** * **
50192 TCTTTCGAGTCAATTTTTACAAAATTTTAGCCGGGATCGTGTAATAACCATCACAGTTTTTGTAT
66 TTTTTCGGGTCATTTTTTACAAAATTTTAGCCAAAATCGTGTAATAACCATCACGGTTTTTGGCT
* * * *
50257 AAAAAAGCGTTCCAAGACCCTGGCTCAGTTTTGCATTG-TTTTTGGTGCCAAGACTCCTTGAGAT
131 AAAAACGCGTTCC-GGGCCCCGGCTCAGTTTTGCA-TGATTTTTGGTGCCAAGACTCCTTGAGAT
* * * * ** ** * * **
50321 ATTCATATTTATTTAATTAAATCTCAGCCACATTGCATTTAAGGAAAAATAATATTAAGAAAAAA
194 ATCCATATTCATCTAATAAAATCTCAGCCACATTGCATTTAA-G-AATTTGTTTTTACG--AGCA
* *** ** * * *
50386 TATGAAAAAT-AAT---TTTAA-AAG-CATG--AAAAGTCC-TC
255 TCTGAATCTTGTTTCGATTTAATTAGAAATGTCAAAAG-CCATT
* * * * *
50421 CACT-CTTTTTGGAGTT-ATATTATATATATTTCATGAGTATTTTATCCAAAAATCAAGGAAAAA
1 CAATCCTTTTTGGCGTTGAAATTATATATTTTTCATGAGTATTTTATCCAAAAATTAAGGAAAAA
* *
50484 TTTTTCGGGTCATTTTTTACAAAATATTAGCCAAAATCGTGTGTACA-AACCATCACGGTTTTTT
66 TTTTTCGGGTCATTTTTTACAAAATTTTAGCCAAAATC--GTGTA-ATAACCATCACGGTTTTTG
** * * * *
50548 GCT-AAAACTTGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAA
128 GCTAAAAACGCG-TTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAG
* * * * * * * * * *
50612 ATATCTATATTCTTTTGATAAAATCTTAGCCACGTTACATTTAAGGATTTGTTTTTATGAGTATC
192 ATATCCATATTCATCTAATAAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATC
* * *
50677 TAAATCTTGTTTCGATTAAATTATAAAT
257 TGAATCTTGTTTCGATTTAATTAGAAAT
50705 TAATTTAGAA
Statistics
Matches: 1466, Mismatches: 276, Indels: 257
0.73 0.14 0.13
Matches are distributed among these distances:
289 7 0.00
290 1 0.00
291 9 0.01
292 94 0.06
293 88 0.06
294 99 0.07
295 10 0.01
296 233 0.16
297 44 0.03
298 72 0.05
299 6 0.00
300 9 0.01
301 6 0.00
302 1 0.00
303 2 0.00
304 3 0.00
305 1 0.00
306 2 0.00
308 2 0.00
309 1 0.00
310 1 0.00
313 2 0.00
314 2 0.00
316 3 0.00
317 2 0.00
320 1 0.00
321 1 0.00
322 3 0.00
327 2 0.00
328 1 0.00
329 5 0.00
330 142 0.10
331 9 0.01
332 249 0.17
333 69 0.05
334 76 0.05
335 168 0.11
336 13 0.01
337 2 0.00
338 5 0.00
339 3 0.00
341 2 0.00
345 3 0.00
347 3 0.00
348 1 0.00
349 2 0.00
351 1 0.00
353 2 0.00
354 1 0.00
355 1 0.00
357 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.37
Consensus pattern (297 bp):
CAATCCTTTTTGGCGTTGAAATTATATATTTTTCATGAGTATTTTATCCAAAAATTAAGGAAAAA
TTTTTCGGGTCATTTTTTACAAAATTTTAGCCAAAATCGTGTAATAACCATCACGGTTTTTGGCT
AAAAACGCGTTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAGATAT
CCATATTCATCTAATAAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAA
TCTTGTTTCGATTTAATTAGAAATGTCAAAAGCCATT
Found at i:49444 original size:335 final size:331
Alignment explanation
Indices: 48827--50116 Score: 1671
Period size: 332 Copynumber: 3.9 Consensus size: 331
48817 AGAAATGTCA
* * * * * **
48827 AAAGCCCTTCAATCTTTTTGGCGTTGAAA-TATATATTTTTCATGAGTATTTTAGCCAAAAATTG
1 AAAGTCCTCCAATCTTTTTGGAGTT-AAATTATATATATTTCATGAGTATTTTATCCAAAAATCA
* * * * * *
48891 AGGAAAAATTTTTCGAGTCAATTTTTACAAAATTTTAGCCGAGATCATGTA-ATAACCATCACAG
65 AGGAAAAATTTTTCGGGTCATTTTTTACAAAATTTTAGCCAAAATCGTGTACA-AACCATCACGG
* * *
48955 TTTTTGGATAAAAAAGCG-TTCCGGGACCCTGGCTCAGTTTTGCATTG-TTTTTGGTGCCAAGAC
129 TTTTTGGCTAAAAACGCGTTTCGGGGACCC-GGCTCAGTTTTGCA-TGATTTTTGGTGCCAAGAC
*
49018 TCCTTGAGATATCCATATTTATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTA
192 TCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTA
*
49083 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATGAATTAAGAAAAAACATAGAAAAATAATA
257 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATGAATTAAGAAAAAATAT-GAAAAATAATA
49148 TTAAAAGCGTC
321 TTAAAAGCGTC
49159 AAAGGTCCTCCAATCTTTTTGGAGTTAAATTATATATATTTCATGAGTATTTTATCCAAAAATCA
1 AAA-GTCCTCCAATCTTTTTGGAGTTAAATTATATATATTTCATGAGTATTTTATCCAAAAATCA
*
49224 AGGAAAAATTTTTCGGGTCATTTTTTACAAAATTTTAGCAAAAATCGTGTGTACAAACCATCACG
65 AGGAAAAATTTTTCGGGTCATTTTTTACAAAATTTTAGCCAAAATC--GTGTACAAACCATCACG
* *
49289 GTTTTTTGCTAAAAACTCGTTTCGGGGACCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACT
128 GTTTTTGGCTAAAAACGCGTTTCGGGGACCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACT
* * *
49354 CCTTGAGATATCCATATTTATTTAATCAAATCTCAGCCACATTGCACTTAAGAATTTGTTTTTAC
193 CCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTAC
49419 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATGAATTAAGAAAAAATATGAAAAATAATATT
258 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATGAATTAAGAAAAAATATGAAAAATAATATT
* * *
49484 ACAAGTGTG
323 AAAAGCGTC
*
49493 AACAGTCCTTCAATCTTTTTGGAGTTAAATTATATATATTTCATGAGTATTTTATCCAAAAATCA
1 AA-AGTCCTCCAATCTTTTTGGAGTTAAATTATATATATTTCATGAGTATTTTATCCAAAAATCA
*
49558 AGGAAAATTTTTTCGGGTCATTTTTTACAAAATTTTAGCCAAAATCGTGTACAAACCATCACGGT
65 AGGAAAAATTTTTCGGGTCATTTTTTACAAAATTTTAGCCAAAATCGTGTACAAACCATCACGGT
** * * * * *
49623 TTTTACCTAAAAACTCGTTTCGAGGCCCCAGCTCAATTTTGCATGATTTTTGGTGCCAAGACTCC
130 TTTTGGCTAAAAACGCGTTTCGGGGACCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCC
* * *
49688 TTGAGATATCCATATTCATCTAATTAAATCTCAGGCACATTGCATTTAGGAATTTGTTTTTACGA
195 TTGAGATATCCATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGA
* * * * ** *
49753 GGATCTGAATCTTTTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAACCAATATTGA
260 GCATCTGAATCTTGTTTCGATTTAATTAGAAATGAATTAAGAAAAAATATGAAAAATAATATTAA
49818 AAGCGTGC
325 AAGCGT-C
* * * * * * *
49826 AAATTCCGCCAATATTTTTGGAGTTAAATTATATATTCTTTACA--ATTATTTTATCCAAAAGTT
1 AAAGTCCTCCAATCTTTTTGGAGTTAAATTATATA-TATTT-CATGAGTATTTTATCCAAAAATC
* * * * * * * *
49889 GATGAAAAAATTTTCGGATCATTTTTTTCAAACTTTTAGCCAAAATTGTGTAC--TCCATCACGG
64 AAGGAAAAATTTTTCGGGTCATTTTTTACAAAATTTTAGCCAAAATCGTGTACAAACCATCACGG
* * * * * * ** *
49952 TTTTTGGCTAAAACCGCGTTTCGGTGCCCCGACTCAGTTTTGAATGATTCTTGGCACCGAGACAT
129 TTTTTGGCTAAAAACGCGTTTCGGGGACCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGAC-T
* * * * * * *
50017 -CTTGAAATATCTATATTCGTCTAATAAAATCTAAGCCACACTGCATTTAAGGATTTGTTTTTAC
193 CCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTAC
* * * *
50081 CAGCATTTGAATATTGTATCGATTTAATTAGAAATG
258 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATG
50117 TCAAAAGCCC
Statistics
Matches: 849, Mismatches: 97, Indels: 26
0.87 0.10 0.03
Matches are distributed among these distances:
330 142 0.17
331 1 0.00
332 295 0.35
333 97 0.11
334 129 0.15
335 174 0.20
336 11 0.01
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (331 bp):
AAAGTCCTCCAATCTTTTTGGAGTTAAATTATATATATTTCATGAGTATTTTATCCAAAAATCAA
GGAAAAATTTTTCGGGTCATTTTTTACAAAATTTTAGCCAAAATCGTGTACAAACCATCACGGTT
TTTGGCTAAAAACGCGTTTCGGGGACCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCT
TGAGATATCCATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAG
CATCTGAATCTTGTTTCGATTTAATTAGAAATGAATTAAGAAAAAATATGAAAAATAATATTAAA
AGCGTC
Found at i:53196 original size:329 final size:328
Alignment explanation
Indices: 51392--53722 Score: 1976
Period size: 329 Copynumber: 7.1 Consensus size: 328
51382 AAAGCCCTTC
* * ** * ** *
51392 AGTATTTAAGCCAAAAATTGAGGAATTATCTTTCAAATCAATTTTTACAAAGA-TTTAGCCGAAA
1 AGTATTTTAGCTAAAAATTGA-GAAAAATATTTCAGGTCAATTTTTGCAAA-ATTTTAGCCGAAA
* * * * * *
51456 TCGTATAATAACCATCACAGTTTTTGGCTAAGAAA-GCATTCCTGGGCCCTTG-CTCAGTTTTGC
64 TCGTGTACT-A-CATCACGGTTTTTGGCTAA-AAACGCGTTCCGGGGCCC--GACTAAGTTTTGC
* * * * *
51519 TTTATTTTTGGTC-CCAAGACTCCTTGAGATATCCATATTTATCTAATCAAATCTCAGCCACATT
124 ATGATTTTTGG-CGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATT
* * * * * * * *
51583 GCATTTATGAATTTGTTTCTAGGAGGATCTGAATCTTGTTTCGATTTAATTAAAAATTAA--TGC
188 GGATTTAAGGATTTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAATTAGAAATTAATTTG-
* * * * * * * *
51646 AGAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGTCC-TCAAATATTTTTGGAGTTAAATTA
252 AAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTC-AATCTTTTTGGCGTTGAATTA
* *
51710 TATA--TATTGTG
316 TATATTTTTTATG
* * * * * * *
51721 ATTATTTTATCCAAAAATTGAGGAAAAATTTTTCAGGTCATTTTTTACAAAATTTTA-CCTAAAA
1 AGTATTTTAGCTAAAAATTGA-GAAAAATATTTCAGGTCAATTTTTGCAAAATTTTAGCC-GAAA
* * *
51785 TCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGCTT-CGGGGCTCCGGCTCAGTTTTACA
64 TCGTGTACT-A-CATCACGGTTTTTGGCTAAAAACGCG-TTCCGGGGC-CCGACTAAGTTTTGCA
* * * * * * *
51849 TGATTTTTGGCGCCGAGACTACTTGAAATATCTATATTCATCTAATAAAATTTTAGTCACATTGC
125 TGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGG
* * * * *
51914 ATTTAAGGATTTGTTTTTACGAGCATCTGCATCTTGTTTCAATTTAACTAGAAATTAATTT-AGA
190 ATTTAAGGATTTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAATTAGAAATTAATTTGAAA
* * * * * ***
51978 AAAATA--TAAAA-GATATTAAAAGCGTGAATAGTCCTCCAATCTTTTTTTAGTTGAATTATATA
255 AAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATA
*
52040 TATTTTATG
320 TTTTTTATG
* * * *
52049 AGAATTTTAGAC-AAGAATTGAGGAAAAATATTTCTGGTCAATTTTTGCAAAATATTAGCCGAAA
1 AGTATTTTAG-CTAAAAATTGA-GAAAAATATTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAA
* * * * * ** * *
52113 TCCTGTACGTTAGTCGAAATCCCGATTTTTTGCCTAAAAACTCGTTCCGGGGTCCCGGTTCAGTG
64 TCGTGTAC--TA--C---ATCACG-GTTTTTGGCTAAAAACGCGTTCCGGGG-CCCGACTAAGTT
* * * * *
52178 TTGCATGATTTTCGGCGCCGAA-ACTCCTTGAAATATCTATATTGATCTTACCAAATCTCAGCTA
120 TTGCATGATTTTTGGCGCC-AAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCA
52242 CATTGGATTTAAGGATTTG----T------A----AA-C--GTTTCGATTTAATTAGAAATTAAT
184 CATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAATTAGAAATTAAT
* * * *
52290 TCGGAAAATAATAGGAAAAACGATATTAGAAACATGAAAAGCCCTTCAATCTTTTTGGCGTTGAA
249 T-TGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAA
*
52355 TTATATAATTTTTATG
313 TTATATATTTTTTATG
* * * * *
52371 AGTATTGTGGCTAAAAATTGAG-AAAATAACTTTCAGGTCAATTTTTGTAAAATTTTAGCTGCAA
1 AGTATTTTAGCTAAAAATTGAGAAAAAT-A-TTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAA
* * * * * *
52435 TCGTGTAATAATCATCACGATTTTTGGCTACAAACGCATTCCGTGGCCCCTACTAAGTTTTGCAT
64 TCGTGTACT-A-CATCACGGTTTTTGGCTAAAAACGCGTTCCG-GGGCCCGACTAAGTTTTGCAT
* * * * * * *
52500 GATTTTCGGCGCCAAGACTCTTTGAGATATCCATATTTATCTAATCAAATTTCAGCTACATTGGA
126 GATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGA
** * *
52565 TTTAATAATTTGTTTTTACGAGCATCCAAATCTTGTTTCGACTTTCGATATAATTATAAATTAA-
191 TTTAAGGATTTGTTTTTACGAGCATCCGAATCTTGTTTCGA---T---T-TAATTAGAAATTAAT
* * * ** * * *
52629 TTCAGAAAAATATGAATGACGATATTAAAAGCGTGAAAAGTCC-TCTAATCTTTTTGGCGTTAAA
249 TTGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTC-AATCTTTTTGGCGTTGAA
* *
52693 TTATAT-TATATTATG
313 TTATATATTTTTTATG
** * * *
52708 AGTATTTTAGC-AAAAATTTGAGGAAAAAT-TTTTTGTTTCATTTTTTTGCAAAA-TTTAGCTGA
1 AGTATTTTAGCTAAAAA-TTGA-GAAAAATATTTCAG-GTCA-ATTTTTGCAAAATTTTAGCCGA
* * * * * *
52770 AATCATGTACTAACCATTACGGTTTTTGACTAAAAGCGCGTTTC-GGGCCCGACTTAGTTTTGCA
62 AATCGTGTACT-A-CATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCGACTAAGTTTTGCA
* * **
52834 TGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCATATTAA
125 TGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGG
* * * *
52899 ATTTAAGGGTTTGTTTATACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTTAAA
190 ATTTAAGGATTTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAATTAGAAATTAATTTGAAA
* *
52964 AAAATAGGAAAAACGATATTAGAAGCGT-AAGAAGCCCTTCAATGTTTTTGGCATTGAATTATAT
255 AAAATAGGAAAAACGATATTAGAAGCGTGAA-AAGCCCTTCAATCTTTTTGGCGTTGAATTATAT
53028 ATTTTTTATG
319 ATTTTTTATG
* * * * *
53038 AGTATTGTGGCTAAAAATTGAGAAAAATATTTCAGGTCATTTTTTACAAAATTTTAGCCAAAATC
1 AGTATTTTAGCTAAAAATTGAGAAAAATATTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATC
* * *** **
53103 GTGTA-T-CATCACGGGTTTTTAGCTAAAAAC-CGTTCTGGGGTTTTGGGTAAGTTTTGCATGAT
66 GTGTACTACATCAC-GGTTTTTGGCTAAAAACGCGTTCCGGGG-CCCGACTAAGTTTTGCATGAT
* * * * *
53165 TTTTTGCACCAAGACTCCTTAAAATATATCTATATCCATCTAATCAAATCTCAAG-CACATTGTA
129 TTTTGGCGCCAAGACTCCTT-GAA-ATATCTATATTCATCTAATCAAATCTC-AGCCACATTGGA
* * * * * * * *
53229 TTTAGGGATTTTTTTTTATGAGTAT-CTAATTCTTGTTTTGATTTAATCAAAAATTAATTTGGAA
191 TTTAAGGATTTGTTTTTACGAGCATCCGAA-TCTTGTTTCGATTTAATTAGAAATTAATTT-GAA
* * * * * * *
53293 ATAAAATAGGAAAAAAGATATTAGAAGTGTGAAAAAGACTTTCAATTTTTTTGACGTTGAACTAT
254 A-AAAATAGGAAAAACGATATTAGAAGCGTG-AAAAGCCCTTCAATCTTTTTGGCGTTGAATTAT
53358 ATATTTTTTATG
317 ATATTTTTTATG
* * *
53370 AGTATTTTCGCTAGAAATTGAGGAAAAATCTTT-AGGGTCAATTTTTGCAAAATTTTAGCCGAAA
1 AGTATTTTAGCTAAAAATTGA-GAAAAATATTTCA-GGTCAATTTTTGCAAAATTTTAGCCGAAA
* * *
53434 TCGTGTACTAACCATCATGGTTTTTGGCTAAAAACGCGTTCCGGGGCCC-AGCTTAGTTTTGTAT
64 TCGTGTACT-A-CATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCGA-CTAAGTTTTGCAT
* * * *
53498 GATTTTTGGTGCCAAGACTCCATGAAATATCTATATTTATGTAA-CAAAATCTCAGCCACATTGG
126 GATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATC-AAATCTCAGCCACATTGG
* *
53562 ATTTAAGGATTTGTTTTTACTAGCATCCGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAA
190 ATTTAAGGATTTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAATTAGAAATTAATT-TGAA
* * * *
53627 AAAAATAGGAAAAACTATATTAGAAGCGTTAAAAGCCTTTCAATCTTTTTGGTGTTGAATTATAT
254 AAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATAT
53692 A-TTTTTATG
319 ATTTTTTATG
*
53701 AGTATTTTAGCCAAAAATTGAG
1 AGTATTTTAGCTAAAAATTGAG
53723 GAAATATCTT
Statistics
Matches: 1616, Mismatches: 291, Indels: 189
0.77 0.14 0.09
Matches are distributed among these distances:
315 2 0.00
316 97 0.06
317 30 0.02
319 8 0.00
320 10 0.01
321 8 0.00
322 99 0.06
324 1 0.00
325 9 0.01
326 60 0.04
327 37 0.02
328 100 0.06
329 367 0.23
330 41 0.03
331 59 0.04
332 88 0.05
333 87 0.05
334 179 0.11
335 114 0.07
336 55 0.03
337 80 0.05
338 65 0.04
339 7 0.00
340 13 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (328 bp):
AGTATTTTAGCTAAAAATTGAGAAAAATATTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATC
GTGTACTACATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCGACTAAGTTTTGCATGATTT
TTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAA
GGATTTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAATTAGAAATTAATTTGAAAAAAATA
GGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTT
ATG
Found at i:53607 original size:663 final size:646
Alignment explanation
Indices: 51429--53722 Score: 2173
Period size: 663 Copynumber: 3.5 Consensus size: 646
51419 ATCTTTCAAA
* * * *
51429 TCAATTTTTACAAAGATTTAGCCGAAATCGTATAATAACCATCACAGTTTTTGGCTAAGAAA-GC
1 TCAATTTTTGCAAA-ATTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAA-AAACGC
* * * * * * *
51493 ATTCCTGGGCCCTTGCTCAGTTTTGCTTTATTTTTGGTC-CCAAGACTCCTTGAGATATCCATAT
64 GTTCCGGGGCCC--GCTTAGTTTTGCATGATTTTTGG-CGCCAAGACTCCTTGAAATATCTATAT
* * * * *
51557 TTATCTAATCAAATCTCAGCCACATTGCATTTATGAATTTGTTTCTAGGAGGATCTGAATCTTGT
126 TTATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTT-TACGAGCATCTGAATCTTGT
* * * * * * *
51622 TTCGATTTAATTAAAAATTAA-T-GCAGAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGTC
190 TTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCC
* * * * * * *
51685 C-TCAAATATTTTTGG-AGTTAAATTATATA-TATTGTGATTATTTTATCCAAAAATTGAGGAAA
255 CTTC-AATCTTTTTGGCA-TTGAATTATATATTTTTATGAGTATTGTAGCCAAAAATTGA-GAAA
*
51747 AATTTTTCAGGTCATTTTTTACAAAATTTTA-CCTAAAATCGTGTACTAACCATCACGGTTTTTG
317 AATATTTCAGGTCATTTTTTACAAAATTTTAGCC-AAAATCGTGTA-T---CATCACGGTTTTTG
* * * * *
51811 GCTAAAAACGCGCTTCGGGGCTCCGGCTCAGTTTTACATGATTTTTGGCGCCGAGACTACTTGAA
377 GCTAAAAACGCG-TTCGGGGCTCTGGCTAAGTTTTGCATGATTTTTGGCGCCAAGACT-CTTAAA
* *
51876 ATATCTATATTCATCTAATAAAATTTTAGTCACATTGCATTTAAGGATTTGTTTTTACGAGCATC
440 ATATCTATATTCATCTAATCAAA-TTCAG-CACATTGCATTTAAGGATTTGTTTTTACGAGCATC
* * * *
51941 TGCATCTTGTTTCAATTTAA-CTAGAAATTAATTTAGAAAAAT--ATAAAAGATATTAAAAGCGT
503 T-AATCTTGTTTCGATTTAATC-AAAAATTAATTTAGAAAAATAGAAAAAAGATATTAAAAGCGT
* * * * * *
52003 GAATAGTCCTCCAATCTTTTTTTA-GTTGAATTATATATATTTTATGAGAATTTTAGACA-AGAA
566 GAAAAGT-CTTCAAT-TTTTTTGACGTTGAAATATATATTTTTTATGAGTATTTTAG-CAGA-AA
**
52066 TTGAGGAAAAATATTTCTGG
627 TTGAGGAAAAATATTTAGGG
* * * * * *
52086 TCAATTTTTGCAAAATATTAGCCGAAATCCTGTACGTTAGTCGAAATCCCGATTTTTTGCCTAAA
1 TCAATTTTTGCAAAAT-TTAGCCGAAATCGTGTAC--TA-AC--CATCACG-GTTTTTGGCTAAA
* * * *
52151 AACTCGTTCCGGGGTCCCGGTTCAGTGTTGCATGATTTTCGGCGCCGAA-ACTCCTTGAAATATC
59 AACGCGTTCCGGGG-CCCGCTT-AGTTTTGCATGATTTTTGGCGCC-AAGACTCCTTGAAATATC
* * * *
52215 TATATTGATCTTACCAAATCTCAGCTACATTGGATTTAAGGATTTG---T------A----AA-C
121 TATATTTATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTACGAGCATCTGAATC
* * *
52266 --GTTTCGATTTAATTAGAAATTAATTCGGAAAATAATAGGAAAAACGATATTAGAAACATGAAA
186 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAA
* * *
52329 AGCCCTTCAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTGTGGCTAAAAATTGAG-
251 AGCCCTTCAATCTTTTTGGCATTGAATTATAT-ATTTTTATGAGTATTGTAGCCAAAAATTGAGA
* ** *** *
52393 AAAATAACTTTCAGGTCAATTTTTGTAAAATTTTAGCTGCAATCGTGTAATAATCATCACGATTT
315 AAAAT-A-TTTCAGGTCATTTTTTACAAAATTTTAGCCAAAATCGTG---T-ATCATCACGGTTT
* * * * * *
52458 TTGGCTACAAACGCATTCCGTGGCCCCT-ACTAAGTTTTGCATGATTTTCGGCGCCAAGACTCTT
374 TTGGCTAAAAACGCGTT-CG-GGGCTCTGGCTAAGTTTTGCATGATTTTTGGCGCCAAGACTC-T
* * * * * **
52522 TGAGATATCCATATTTATCTAATCAAATTTCAGCTACATTGGATTTAATAATTTGTTTTTACGAG
436 TAAAATATCTATATTCATCTAATCAAA-TTCAGC-ACATTGCATTTAAGGATTTGTTTTTACGAG
* * * ** *
52587 CATCCAAATCTTGTTTCGACTTTCGATATAATTATAAATTAATTCAGAAAAATATGAATGACGAT
499 CAT-CTAATCTTGTTTCGA-TTT--A-ATCA--A-AAATTAATTTAGAAAAATA-GAAAAAAGAT
* * * *
52652 ATTAAAAGCGTGAAAAGTCCTCTAATCTTTTTGGCGTT-AAAT-TATATTATATTATGAGTATTT
555 ATTAAAAGCGTGAAAAGTCTTC-AATTTTTTTGACGTTGAAATATATATT-TTTTATGAGTATTT
* * * **
52715 TAGCAAAAATTTGAGGAAAAATTTTTTGTT
618 TAGCAGAAA-TTGAGGAAAAATATTTAGGG
* * * * * *
52745 TCATTTTTTTGCAAAATTTAGCTGAAATCATGTACTAACCATTACGGTTTTTGACTAAAAGCGCG
1 TCA-ATTTTTGCAAAATTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCG
* * *
52810 TTTC-GGGCCCGACTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCA
65 TTCCGGGGCCCG-CTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTTA
* ** *
52874 TCTAATCAAATCTCAGCCATATTAAATTTAAGGGTTTGTTTATACGAGCATCTGAATCTTGTTTC
129 TCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTT-TACGAGCATCTGAATCTTGTTTC
**
52939 GATTTAATTAGAAATTAATT-TTAAAAAAATAGGAAAAACGATATTAGAAGCGT-AAGAAGCCCT
193 GATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAA-AAGCCCT
* * *
53002 TCAATGTTTTTGGCATTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTGAGAAAAATA
257 TCAATCTTTTTGGCATTGAATTATATA-TTTTTATGAGTATTGTAGCCAAAAATTGAGAAAAATA
*
53067 TTTCAGGTCATTTTTTACAAAATTTTAGCCAAAATCGTGTATCATCACGGGTTTTTAGCTAAAAA
321 TTTCAGGTCATTTTTTACAAAATTTTAGCCAAAATCGTGTATCATCAC-GGTTTTTGGCTAAAAA
* * * * *
53132 C-CGTTCTGGGGTTTTGGGTAAGTTTTGCATGATTTTTTGCACCAAGACTCCTTAAAATATATCT
385 CGCGTTC-GGGGCTCTGGCTAAGTTTTGCATGATTTTTGGCGCCAAGACT-CTT-AAA-ATATCT
* * * * * *
53196 ATATCCATCTAATCAAATCTCAAGCACATTGTATTTAGGGATTTTTTTTTATGAGTATCTAATTC
446 ATATTCATCTAATCAAAT-TC-AGCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAA-TC
* * * *
53261 TTGTTTTGATTTAATCAAAAATTAATTTGGAAATAAAATAGGAAAAAAGATATTAGAAGTGTGAA
508 TTGTTTCGATTTAATCAAAAATTAATTT--AGA-AAAATA-GAAAAAAGATATTAAAAGCGTG-A
* * *
53326 AAAGACTTTCAATTTTTTTGACGTTGAACTATATATTTTTTATGAGTATTTTCGCTAGAAATTGA
568 AAAGTC-TTCAATTTTTTTGACGTTGAAATATATATTTTTTATGAGTATTTTAGC-AGAAATTGA
*
53391 GGAAAAATCTTTAGGG
631 GGAAAAATATTTAGGG
*
53407 TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTTGGCTAAAAACGCG
1 TCAATTTTTGCAAAA-TTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCG
* * *
53472 TTCCGGGGCCCAGCTTAGTTTTGTATGATTTTTGGTGCCAAGACTCCATGAAATATCTATATTTA
65 TTCCGGGGCCC-GCTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTTA
* * *
53537 TGTAA-CAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACTAGCATCCGAATCTTGTTT
129 TCTAATC-AAATCTCAGCCACATTGGATTTAAGGATTTG-TTTTACGAGCATCTGAATCTTGTTT
* * *
53601 CGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACTATATTAGAAGCGTTAAAAGCCTT
192 CGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCT
** *
53666 TCAATCTTTTTGGTGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAG
257 TCAATCTTTTTGGCATTGAATTATATATTTTTATGAGTATTGTAGCCAAAAATTGAG
53723 GAAATATCTT
Statistics
Matches: 1330, Mismatches: 214, Indels: 180
0.77 0.12 0.10
Matches are distributed among these distances:
646 22 0.02
647 1 0.00
648 59 0.04
649 10 0.01
650 176 0.13
651 87 0.07
652 5 0.00
653 22 0.02
654 7 0.01
655 1 0.00
656 3 0.00
657 56 0.04
658 10 0.01
659 65 0.05
660 67 0.05
661 36 0.03
662 139 0.10
663 273 0.21
664 127 0.10
665 7 0.01
666 37 0.03
667 90 0.07
668 30 0.02
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (646 bp):
TCAATTTTTGCAAAATTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGT
TCCGGGGCCCGCTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTTATC
TAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTACGAGCATCTGAATCTTGTTTCGAT
TTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAA
TCTTTTTGGCATTGAATTATATATTTTTATGAGTATTGTAGCCAAAAATTGAGAAAAATATTTCA
GGTCATTTTTTACAAAATTTTAGCCAAAATCGTGTATCATCACGGTTTTTGGCTAAAAACGCGTT
CGGGGCTCTGGCTAAGTTTTGCATGATTTTTGGCGCCAAGACTCTTAAAATATCTATATTCATCT
AATCAAATTCAGCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAATCTTGTTTCGATTTA
ATCAAAAATTAATTTAGAAAAATAGAAAAAAGATATTAAAAGCGTGAAAAGTCTTCAATTTTTTT
GACGTTGAAATATATATTTTTTATGAGTATTTTAGCAGAAATTGAGGAAAAATATTTAGGG
Found at i:67143 original size:30 final size:29
Alignment explanation
Indices: 67077--67143 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
67067 AAAGGAAAAT
67077 TTTGACTCTTGAACTTTCATTTTAGACAA
1 TTTGACTCTTGAACTTTCATTTTAGACAA
* * * * *
67106 GTTGACTCTTGAATTTTGATTTTTGGATAA
1 TTTGACTCTTGAACTTTCA-TTTTAGACAA
67136 TTTGACTC
1 TTTGACTC
67144 AAATTGAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 16 0.52
30 15 0.48
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (29 bp):
TTTGACTCTTGAACTTTCATTTTAGACAA
Found at i:67453 original size:41 final size:44
Alignment explanation
Indices: 67408--67504 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 44
67398 AAAGTGTATT
*
67408 ACCTAA-ATTATACT-T-CATCTCTAGGTAATTCATCAAAATAA
1 ACCTAATATTATACTATCCATCTCTAGATAATTCATCAAAATAA
*
67449 ACCTAATATTCTACTCATCCATCTCTAGATAATTCATCAAAATAA
1 ACCTAATATTATACT-ATCCATCTCTAGATAATTCATCAAAATAA
*
67494 AGCTAATATTA
1 ACCTAATATTA
67505 ATTGTTGCTT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
41 6 0.12
42 7 0.15
44 1 0.02
45 34 0.71
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.34
Consensus pattern (44 bp):
ACCTAATATTATACTATCCATCTCTAGATAATTCATCAAAATAA
Found at i:69437 original size:19 final size:19
Alignment explanation
Indices: 69417--69453 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
69407 AATTAATTAT
69417 TTTA-ATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
*
69435 TTTATATATTATATTTTTA
1 TTTATATATTAAATTTTTA
69454 CTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTAAATTTTTA
Found at i:87004 original size:28 final size:29
Alignment explanation
Indices: 86972--87027 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
86962 TTCTTCAAAC
86972 TTTCTAAT-TTCAAGAACGCTAAAGAACA
1 TTTCTAATCTTCAAGAACGCTAAAGAACA
87000 TTTCTAATCTTCAAGAACGCTAAAGAAC
1 TTTCTAATCTTCAAGAACGCTAAAGAAC
87028 GTGGAATAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.29
Consensus pattern (29 bp):
TTTCTAATCTTCAAGAACGCTAAAGAACA
Found at i:92174 original size:15 final size:15
Alignment explanation
Indices: 92154--92184 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
92144 TACCTAAAAC
92154 AGCATTTCTACCATG
1 AGCATTTCTACCATG
92169 AGCATTTCTACCATG
1 AGCATTTCTACCATG
92184 A
1 A
92185 TCAATTTCAG
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:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (15 bp):
AGCATTTCTACCATG
Found at i:100450 original size:32 final size:33
Alignment explanation
Indices: 100394--100459 Score: 125
Period size: 32 Copynumber: 2.0 Consensus size: 33
100384 GTTCTTGCAA
100394 TTGAGACATGAACCGGGGTCTCTTGATTGGTGC
1 TTGAGACATGAACCGGGGTCTCTTGATTGGTGC
100427 TTGAGACATGAACC-GGGTCTCTTGATTGGTGC
1 TTGAGACATGAACCGGGGTCTCTTGATTGGTGC
100459 T
1 T
100460 GGATTCTGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 19 0.58
33 14 0.42
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.32
Consensus pattern (33 bp):
TTGAGACATGAACCGGGGTCTCTTGATTGGTGC
Found at i:108637 original size:19 final size:19
Alignment explanation
Indices: 108613--108651 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
108603 GCCAATGATC
108613 TCCTAACAAAACTGTTTCA
1 TCCTAACAAAACTGTTTCA
108632 TCCTAACAAAACTGTTTCA
1 TCCTAACAAAACTGTTTCA
108651 T
1 T
108652 TCATAACTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (19 bp):
TCCTAACAAAACTGTTTCA
Found at i:121378 original size:2 final size:2
Alignment explanation
Indices: 121365--121396 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
121355 TCATTGCACA
*
121365 AT AT AC 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 AT AT
121397 TTGGTACTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:122015 original size:27 final size:27
Alignment explanation
Indices: 121983--122039 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
121973 ACAGATGAGA
*
121983 TTATTAGAGCAGCGATTTAAACGGAGT
1 TTATTAGAGCAGCGATTGAAACGGAGT
122010 TTATTAGAGCAGCGATTGAAACGGAGT
1 TTATTAGAGCAGCGATTGAAACGGAGT
122037 TTA
1 TTA
122040 CACTTAACCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (27 bp):
TTATTAGAGCAGCGATTGAAACGGAGT
Found at i:125323 original size:2 final size:2
Alignment explanation
Indices: 125316--125344 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
125306 GTTTAATTTC
125316 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 T
125345 CAAAATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:127303 original size:40 final size:40
Alignment explanation
Indices: 127251--127331 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
127241 TTTATAACTA
* * *
127251 GGGGCTAAACCTGGATTTAATTTCTTACCTTGATTATTAG
1 GGGGCTAAACCTGAATTTAATTTATTACCTTAATTATTAG
*
127291 GGGGCTAAACCTGAATTTAATTTATTTCCTTAATTATTAG
1 GGGGCTAAACCTGAATTTAATTTATTACCTTAATTATTAG
127331 G
1 G
127332 AGGGTCAAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.41
Consensus pattern (40 bp):
GGGGCTAAACCTGAATTTAATTTATTACCTTAATTATTAG
Found at i:127348 original size:13 final size:13
Alignment explanation
Indices: 127330--127366 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
127320 TTAATTATTA
*
127330 GGAGGGTCAAGTT
1 GGAGGGTCAAATT
*
127343 GGAGGGACAAATT
1 GGAGGGTCAAATT
127356 GGAGGGTCAAA
1 GGAGGGTCAAA
127367 AAGAATTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.08, G:0.43, T:0.16
Consensus pattern (13 bp):
GGAGGGTCAAATT
Found at i:127975 original size:2 final size:2
Alignment explanation
Indices: 127968--127994 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
127958 CACCTATTAC
127968 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
127995 TGTATTAAAT
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
Done.