Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015830.1 Corchorus olitorius cultivar O-4 contig15863, 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: 67950
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:14220 original size:22 final size:21
Alignment explanation
Indices: 14184--14227 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
14174 TTACTGCAGA
14184 AATTGTTTCTTGAAGTGTTAG
1 AATTGTTTCTTGAAGTGTTAG
*
14205 AATTGTTTGTTAGAAGTGTTAG
1 AATTGTTTCTT-GAAGTGTTAG
14227 A
1 A
14228 GGGGAAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.45
Consensus pattern (21 bp):
AATTGTTTCTTGAAGTGTTAG
Found at i:17973 original size:22 final size:22
Alignment explanation
Indices: 17948--17994 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
17938 ATTACACTAT
*
17948 TTTTGATGAC-CTCCTTATGAAA
1 TTTTGATAACTCTCC-TATGAAA
*
17970 TTTTGATAACTTTCCTATGAAA
1 TTTTGATAACTCTCCTATGAAA
17992 TTT
1 TTT
17995 CAATAACGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.47
Consensus pattern (22 bp):
TTTTGATAACTCTCCTATGAAA
Found at i:18121 original size:23 final size:24
Alignment explanation
Indices: 18091--18135 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
18081 TTTGAAGACT
18091 CACTATGAAAT-TTTGATAACCAA
1 CACTATGAAATATTTGATAACCAA
*
18114 CACTATGAGATATTTGATAACC
1 CACTATGAAATATTTGATAACC
18136 TCCATATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (24 bp):
CACTATGAAATATTTGATAACCAA
Found at i:19641 original size:26 final size:25
Alignment explanation
Indices: 19592--19643 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
19582 ATTTCCATTA
19592 TTTTAATAATGAAATAATTAAAATAT
1 TTTTAATAATGAAAT-ATTAAAATAT
19618 TTTTAATAATGACAAT-TTAGAAATAT
1 TTTTAATAATGA-AATATTA-AAATAT
19644 ATTTGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 3 0.12
26 18 0.75
27 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (25 bp):
TTTTAATAATGAAATATTAAAATAT
Found at i:21633 original size:255 final size:253
Alignment explanation
Indices: 20877--21604 Score: 999
Period size: 254 Copynumber: 2.9 Consensus size: 253
20867 CTTTAAATCT
* *
20877 AATGTGGCTGAGATTTGGTTAGATGAATATAGAT-ATTTTAAGGAGTCTTAGC-ACCAAAATCAT
1 AATGTGGCTGAGATTTGGTTAGATGAATATAGATAATTTTAAGGAGTCTTGGCAACAAAAATCAT
* * * * * ** * * * *
20940 GCAAAACTGAG-TC-GGGACGCGGATTGCGTTTTTAGCC--GAAAACCGTGATGGTTAGTATGCG
66 GCAACACTG-GCACAGGGCCCCGTAACGCGTTTTTAGCCAAAAAAACCATGATGG-TA-CA--AG
* *
21001 ATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCGATTTCTAGCGAAAATAGT
126 ATTTCTGCTAAAA-TTTGCAAAAATTGACCCGAAATATTTTTCCTCGATTTCTAGCGAAAATAGT
21066 CATAAAAAATATATAATTCAACGCCAAAAAAATTGAAAGCCTTTTTCACGCTTCTAATAAATAC
190 CATAAAAAATATATAATTCAACGCCAAAAAAATTGAAAGCCTTTTTCACGCTTCTAATAAATAC
* * * *
21130 AATGTGACTGAAATTT-GTTAGATGAATATAGATATATTTTAATGAGTCTTGACAACAAAAATCA
1 AATGTGGCTGAGATTTGGTTAGATGAATATAGATA-ATTTTAAGGAGTCTTGGCAACAAAAATCA
* *
21194 TGCAACACTAGCACAGGGCCCCGTAACGCGTTTTTAGCCAAATAAACCATGATGGTACAAGATTT
65 TGCAACACTGGCACAGGGCCCCGTAACGCGTTTTTAGCCAAAAAAACCATGATGGTACAAGATTT
* *
21259 CTGCTAAAACTTTGCAAAAATTGATCCGAAATATTTTTCCTTGATTTCTAGCGAAAATAGTCATA
130 CTGCTAAAA-TTTGCAAAAATTGACCCGAAATATTTTTCCTCGATTTCTAGCGAAAATAGTCATA
*
21324 AAAAATATATAATTCAACGTCAAAAAAATTGAAAGCCTTTTTCACGCTTCTAATAAATAC
194 AAAAATATATAATTCAACGCCAAAAAAATTGAAAGCCTTTTTCACGCTTCTAATAAATAC
21384 AATGTGGCTGAGATTTGGTTAGATGAATATAGATAAATTTTAAGGAGTCTTGGCAACAAAAATCA
1 AATGTGGCTGAGATTTGGTTAGATGAATATAGAT-AATTTTAAGGAGTCTTGGCAACAAAAATCA
*
21449 TGCAACACTGGCACAGGGCCCCATAACGCGTTTTTAGCCAAAAAAACCATGATGGTACAAGATTT
65 TGCAACACTGGCACAGGGCCCCGTAACGCGTTTTTAGCCAAAAAAACCATGATGGTACAAGATTT
* * * * * *
21514 CTGCTAAAATTTGGCAAAAATTGACCCAAAATATTTTT-CTCAATTTTTAGCCACAATACT-A-A
130 CTGCTAAAATTT-GCAAAAATTGACCCGAAATATTTTTCCTCGATTTCTAGCGAAAATAGTCATA
*
21576 AAAAATTATATAATTCAATGCCAAAAAAA
194 AAAAA-TATATAATTCAACGCCAAAAAAA
21605 AGATTGAAGG
Statistics
Matches: 422, Mismatches: 42, Indels: 22
0.87 0.09 0.05
Matches are distributed among these distances:
252 23 0.05
253 36 0.09
254 173 0.41
255 156 0.37
256 21 0.05
257 2 0.00
258 11 0.03
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (253 bp):
AATGTGGCTGAGATTTGGTTAGATGAATATAGATAATTTTAAGGAGTCTTGGCAACAAAAATCAT
GCAACACTGGCACAGGGCCCCGTAACGCGTTTTTAGCCAAAAAAACCATGATGGTACAAGATTTC
TGCTAAAATTTGCAAAAATTGACCCGAAATATTTTTCCTCGATTTCTAGCGAAAATAGTCATAAA
AAATATATAATTCAACGCCAAAAAAATTGAAAGCCTTTTTCACGCTTCTAATAAATAC
Found at i:22149 original size:334 final size:335
Alignment explanation
Indices: 21377--24382 Score: 1555
Period size: 334 Copynumber: 9.1 Consensus size: 335
21367 ACGCTTCTAA
* * * *
21377 TAAATACAATGTGGCTGAGATTTGGTTAGATGAATATAGATAAATTTTAAGGAGTCTTG-GCAAC
1 TAAATTCAATGTGGCTGAGATTTGGTTAGATAAATATAGAT--ATTTCAAAGAGTCTTGCGC--C
* * * * * * *
21441 AAAAATCATGCAACAC-TGGCACAGGGCCC-CATAACGCGTTTTTAGC----CAAAAAAACCATG
62 AAAAATCATGCAAAACTTAG-TCGGGGCCCTGA-AACGCGTTTTTAGCTAAAAAAAAAAACCGTG
** * * * * * * *
21500 --A-TGGTACAAGATTTCTG-CTAAAATTTGGCAAAAATTGACCCAAAATAT-TTTTCTCAATTT
125 ATATTATTACACGATTTC-GCCTAGAATTTTGCAAAAAATGACTCAAAAAATATTTCCTCAATTT
* * * *
21560 TTAGCCACAATACT-AA-AAAAATTATATAATTCAATGCCAAAAAAAAGATTGAAGGGCTTCTCA
189 TTAGCTAAAATACTCAATAAAAATTATATAATTCAACGCC---AAAAAGATTGAA-GGCTTTTCA
* * * * * *
21623 CGCATCTAATATCGTTTTCCTTATTTTTTTCAAATTAATTTTTAATTAAATCGAAACATGATTCA
250 CGCTTCTAATATCGTTTTTCATATTTTTCT-GAATTAATTTCTAATTAAATCGAAACATGATTCA
21688 AATGCTCGTAAAAACAAATCCT
314 AATGCTCGTAAAAACAAATCCT
* * * * * * *
21710 TAAATCCAATGTGGCTAAGATTTGGTTAGATAAATATAGAAATTTCAAGGAGTTTTGCAACAAAA
1 TAAATTCAATGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCTTGC-GCCAAA
** * *
21775 AAT-ATGCAAAAAC-TAACCTGGGGTCCTGAAACGTGTTTTTAGCTAAAAAAAAAAAGCCGT-AT
65 AATCATGC-AAAACTTAGTC-GGGGCCCTGAAACGCGTTTTTAGCTAAAAAAAAAAA-CCGTGAT
* *
21837 -TTA-TACACGATTTCGCCT-GAAATTTTGCAAAAAAATGACTTAAAAAATATTTTCGTCAATTT
127 ATTATTACACGATTTCGCCTAG-AATTTTGC-AAAAAATGACTCAAAAAATA-TTTCCTCAATTT
* * * * * *
21899 TTTGCTAAAATACTC-AT-AATA-TATATAGTTTAACGCTAAAAAGATTGGAGGACTTTTCACGC
189 TTAGCTAAAATACTCAATAAAAATTATATAATTCAACGCCAAAAAGATTGAAGG-CTTTTCACGC
* * * * *
21961 TTTTAATTTTGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG
253 TTCTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACATGATTCAAATG
*
22026 CTCGTAAAAACAAATTCT
318 CTCGTAAAAACAAATCCT
* * * * *
22044 TAAATTCAATGTAGCTGAGATTTGATTAGATGAATATGGATATCTCAAAGAGTCTTGACGCCAAA
1 TAAATTCAATGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCTTG-CGCCAAA
* * * *
22109 AATCATGCAAAACTTAGTCGGGGCCCTGGAACACGTTTTTAG-T----CAAATAACCGTGATGAT
65 AATCATGCAAAACTTAGTCGGGGCCCTGAAACGCGTTTTTAGCTAAAAAAAAAAACCGTGAT-AT
* * * * **
22169 TATTACACGATTTCGGCTAGAATTTTGCAAAAATTGAGTCGAAAGTTATTTCCTCAATTTTTAGC
129 TATTACACGATTTCGCCTAGAATTTTGCAAAAAATGACTCAAAAAATATTTCCTCAATTTTTAGC
* * * *
22234 TACAATACTCAATAAAAATTATATAATTCAACGCCAAAAAGATTGAATTGCTTTTCATGCTTCTG
194 TAAAATACTCAATAAAAATTATATAATTCAACGCCAAAAAGATTGAA-GGCTTTTCACGCTTCTA
* * * * *
22299 ATATCGTTTTTCCTATTATTTTCCGAATTAATTTCTAATTAAATCGAAACATTATTCAAAAGCTT
258 ATATCGTTTTTCATA-T-TTTTCTGAATTAATTTCTAATTAAATCGAAACATGATTCAAATGCTC
***
22364 GT-TTTACAAATCCT
321 GTAAAAACAAATCCT
* * * *
22378 TAAA-T--ACG-GGCTGAGATTTGGTTAGATTAATATAGTTATTTC-AAGAAGTCTCGGCGCCAA
1 TAAATTCAATGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAG-AGTCT-TGCGCCAA
* * * ** ** * *
22438 AAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCATTTTTAGC-AAAAAACCGTATTCGGCTAA
64 AAATCATGCAAAACTTAGTCGGGGCCCTGAAACGCGTTTTTAGCTAAAAAA--AAAAACCG-TGA
* * * * * * * *
22502 AATT-TTGGTCACGATTTCGTCTA-AATTTTGCAAAAATTAAC-CGGAAAGATATTTCCTTAATT
126 TATTATT--ACACGATTTCGCCTAGAATTTTGCAAAAAATGACTC-AAAAAATATTTCCTCAATT
* * *
22564 TTTGGCTAAAATACTC-AT---AA--A-AT-ATT----G------A-A--G--GGTTTTTTACGC
188 TTTAGCTAAAATACTCAATAAAAATTATATAATTCAACGCCAAAAAGATTGAAGGCTTTTCACGC
* * * * * *
22606 TTCTAATATCGTTTTTCCTACTTTTCCTGAATTAACTTCTAATTAAATCGAAACAAGATTTAGAT
253 TTCTAATATCGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACATGATTCAAAT
*
22671 GCTCGTAAAAATAAATCCT
317 GCTCGTAAAAACAAATCCT
* * ** * * * *
22690 TAAATCCAATGTGCCTGAGATTTCATTAGATGAATATAGATATTTCAAGGAGTGTTGCCGTCAAA
1 TAAATTCAATGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCTTG-CGCCAAA
* * * * *
22755 GATCATGCAAAA-TTGGCCCGGGGCTCC-GGAACGCGTTTTTAGCTAAAGAAAAAAAAACG-G-T
65 AATCATGCAAAACTTAG-TCGGGGC-CCTGAAACGCGTTTTTAGCTAAA-AAAAAAAACCGTGAT
* * * * ** * * *
22816 GA-TGTTACACGATTTCGGCTA-ATATTTTGCAAAAATTGACCCGGAATATTTTTTCTCAATTTT
127 -ATTATTACACGATTTCGCCTAGA-ATTTTGCAAAAAATGACTCAAAAAATATTTCCTCAATTTT
* * * * *
22879 TAGCCACAATACTC-ATAAAAAATATATAATTCAACACCAAAAAGATTGAAGGTTTTTTCACGCT
190 TAGCTAAAATACTCAATAAAAATTATATAATTCAACGCCAAAAAGATTGAAGG-CTTTTCACGCT
* * * * * *
22943 TTTAATGTCGTTTTTCTTTTTTCTTTTTCTTTTCCCAAATTAATTTCTAATTAAATTGAAACATG
254 TCTAATATCGTTTTTC----ATATTTTTC---T---GAATTAATTTCTAATTAAATCGAAACATG
* *
23008 ATTCAGATGCTTGT-------AA----
309 ATTCAAATGCTCGTAAAAACAAATCCT
* ** * * * *
23024 -AAA--CAA--TGGCTGGGATTCAGTTAAATGAATATAGATATTTCAAGGAGTCTTGACACCAAA
1 TAAATTCAATGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCTTG-CGCCAAA
* * * * * * * *
23084 AGTTATTCAAAA-TT-GAACCGGGCCCTGGAACACGTTTTTAGC------CAAAAACCGTGATGA
65 AATCATGCAAAACTTAG-TCGGGGCCCTGAAACGCGTTTTTAGCTAAAAAAAAAAACCGTGAT-A
* * * * * * *
23141 TTATTGCATGATTTCGGCTAAAATTTTTGCAAAAATTGA-TCCGAAAGATATTTCCTCAA-TTTT
128 TTATTACACGATTTCGCCTAGAA-TTTTGCAAAAAATGACT-CAAAAAATATTTCCTCAATTTTT
* * * * * *
23204 AGCCATAATACTC-ATAAAAAATATATGATTCAACGCCAAAACGATTGAAGGGCTTTTCATGCTT
191 AGCTAAAATACTCAATAAAAATTATATAATTCAACGCCAAAAAGATTGAA-GGCTTTTCACGCTT
* * * *
23268 TTAATATCGTTTTTCAT-TTTTTTTGAATTAATTTCTAATTAAATCAAAACAAGATTCAAATGCT
255 CTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACATGATTCAAATGCT
23332 CGTAAAAACAAATCCT
320 CGTAAAAACAAATCCT
* * * ** * ** * *
23348 TAAATGCAATGTAGCTAAGATTTTATTAGATGAATATAGATATTTCATGGAGTGTCGGCGCCAAA
1 TAAATTCAATGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCT-TGCGCCAAA
* * * * ** *
23413 AATCATGCAAAACTAAATCGGGGCCCCGAAACGCGTTTTTAGC------CAAAAATTGTGATGGT
65 AATCATGCAAAACTTAGTCGGGGCCCTGAAACGCGTTTTTAGCTAAAAAAAAAAACCGTGAT-AT
* * * * * * *
23472 TAGTACACGATTTTGGCTA-AACTTTTGCAAAAAAATGACTCGAAAATTTTTTCCTCAATTTTTG
129 TATTACACGATTTCGCCTAGAA-TTTTGC-AAAAAATGACTCAAAAAATATTTCCTCAATTTTTA
* * * *
23536 GAC-AAAATACTCATAATATACATATATATATATATTTAACACCAAAAAGATTGGAGGACTTTTC
192 G-CTAAAATACTC--AATA-A-AAAT-TATATA-ATTCAACGCCAAAAAGATTGAAGG-CTTTTC
* * * * *
23600 TCGCTTTTAATATCGTATTTCATATTTTTCTGAATTAATTTCCAATTAAATCGAAACAAGATTCA
249 ACGCTTCTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACATGATTCA
* ** *
23665 GATGCTTTTAAAAACAAATTCT
314 AATGCTCGTAAAAACAAATCCT
* * * * * * ** **
23687 TTAATCCAATGTGGCCGAGATTTGATTAGATGAATATGGATAACTCACGGAGTCTTGGCGCCAAA
1 TAAATTCAATGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCTT-GCGCCAAA
* * * * * ** * * *
23752 AATAATGCGAAACTGAGCCGGGTCCCCAAAATG-GTTTTTTAGCT------ATAAACTGTGATGA
65 AATCATGCAAAACTTAGTCGGGGCCCTGAAACGCG-TTTTTAGCTAAAAAAAAAAACCGTGAT-A
* * * * * * * *
23810 TTATTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAGATATTTCCGT-AATTTTTG
128 TTATTACACGATTTCGCCTAGAATTTTGCAAAAAATGACTCAAAAAATATTTCC-TCAATTTTTA
* * * * * *
23874 GCTAAAATACTC-ATAAACAA-TATATAATTCAATGCCTAAAAGATTGAATGACTTTTGATGTTT
192 GCTAAAATACTCAATAAA-AATTATATAATTCAACGCCAAAAAGATTGAA-GGCTTTTCACGCTT
* ** * ** * * *
23937 TTAATATCAATTTTCTTATTTTTTCCAAAATAATTTCTAATTAAATCGAAACAAGATTCAGATGC
255 CTAATATCGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACATGATTCAAATGC
* * *
24002 TTGCAAGAA-AAATCCT
319 TCGTAAAAACAAATCCT
* * * * * * * * * *
24018 TAAATCCAATATGGTTGAGACTAGATTAGATGAATATAGATATTTCAAATAGTCTTGGAGTCAAA
1 TAAATTCAATGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCTT-GCGCCAAA
* * ** * * * ***** ** * *
24083 AATCATGCAAAA-TTGAGTCAGGTCTTTGGAACTCGTTTTTAGCCAAAAACCGTGATGGT-TTGT
65 AATCATGCAAAACTT-AGTCGGGGCCCTGAAACGCGTTTTTAGCTAAAAAAAAAAACCGTGATAT
* * * * * * *
24146 TAGTACAGGATTTCTG-CTAAAATGTTGCAAAAATTGA-T-ATGAAAGAT-TTCTCCT-ATTTTT
129 TATTACACGATTTC-GCCTAGAATTTTGCAAAAAATGACTCA--AAAAATATT-TCCTCAATTTT
* * * * * *
24206 TGGTTTAAATACTC-ATAAAAA-TATATAATTCAACGCCAAAAAGATTGGAGGGTTTTTTACGCT
190 TAGCTAAAATACTCAATAAAAATTATATAATTCAACGCCAAAAAGATT-GAAGGCTTTTCACGCT
* * * * * * *
24269 TTTAATATCGTATTTCTTATTTTTTCTTAATTAATTTCTAATTAAATCGAAACAAGATTCAGATA
254 TCTAATATCGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACATGATTCAAATG
* *
24334 CTCATAAAAACAAATTCT
318 CTCGTAAAAACAAATCCT
* *
24352 TAAATCCAATG-GTACTGAGATTTGGTTAGAT
1 TAAATTCAATGTG-GCTGAGATTTGGTTAGAT
24383 GATGTAAAGT
Statistics
Matches: 2094, Mismatches: 419, Indels: 319
0.74 0.15 0.11
Matches are distributed among these distances:
311 40 0.02
312 54 0.03
313 83 0.04
314 4 0.00
315 6 0.00
316 75 0.04
317 8 0.00
318 5 0.00
319 7 0.00
320 6 0.00
321 7 0.00
322 1 0.00
323 3 0.00
324 91 0.04
325 35 0.02
327 5 0.00
328 28 0.01
329 124 0.06
330 183 0.09
331 206 0.10
332 85 0.04
333 192 0.09
334 207 0.10
335 151 0.07
336 102 0.05
337 42 0.02
338 97 0.05
339 206 0.10
340 3 0.00
342 1 0.00
345 37 0.02
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (335 bp):
TAAATTCAATGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCTTGCGCCAAAA
ATCATGCAAAACTTAGTCGGGGCCCTGAAACGCGTTTTTAGCTAAAAAAAAAAACCGTGATATTA
TTACACGATTTCGCCTAGAATTTTGCAAAAAATGACTCAAAAAATATTTCCTCAATTTTTAGCTA
AAATACTCAATAAAAATTATATAATTCAACGCCAAAAAGATTGAAGGCTTTTCACGCTTCTAATA
TCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACATGATTCAAATGCTCGTAAA
AACAAATCCT
Found at i:24074 original size:331 final size:330
Alignment explanation
Indices: 22598--24384 Score: 1435
Period size: 339 Copynumber: 5.4 Consensus size: 330
22588 TTGAAGGGTT
* * * * * * *
22598 TTTTACGCTTCTAATATCGTTTTTCCTACTTTTCCTGAATTAACTTCTAATTAAATCGAAACAAG
1 TTTTATGCTTTTAATATCGTATTTCTTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAG
* * * * *
22663 ATTTAGATGCTCGTAAAAATAAATCCTTAAATCCAATGTGCCTGAGATTTCATTAGATGAATATA
66 ATTCAGATGCTTGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATA
* * * * * * * * * *
22728 GATATTTCAAGGAGTGTTGCCGTCAAAGATCATGCAAAATTG-GCCCGGGGCTCCGGAACGCGTT
131 GATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAG-TCGGGTCCCCGAAATG-GTT
* ***** * * * *
22792 TTTAGCTAAAGAAAAAAAAACGGTGATGTTACACGATTTCGGCTAATATTTTGCAAAAATTGACC
194 TTTAGC-CAA-AAACCGTGATGATTA-G-TACACGATTTCGGCTAAAATTTTGCAAAAATTGACC
* * * * * * * * *
22857 CGGAATATTTTTTCTCAATTTTTAGCCACAATACTCATAAAAAATATATAATTCAACACCAAAAA
255 CGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAACAATATATAATTCAACGCCAAAAA
**
22922 GATTGAAGGTT
320 GATTGAAGGAC
* * * * *
22933 TTTTCACGCTTTTAATGTCGTTTTTCTTTTTTCTTTTTCTTTTCCCAAATTAATTTCTAATTAAA
1 TTTT-ATGCTTTTAATATCGTATTTC--TTAT-TTTTTC---T---GAATTAATTTCTAATTAAA
* * * *
22998 TTGAAACATGATTCAGATGCTTGT-------AA-----AAA--CAA--TGGCTGGGA-TTCAGTT
56 TCGAAACAAGATTCAGATGCTTGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGA-TT
* * * * * * * **
23046 AAATGAATATAGATATTTCAAGGAGTCTTGACACCAAAAGTTATTCAAAATTGAACCGGG-CCCT
120 AGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGTCGGGTCCC-
* * * * *
23110 GGAACA-CGTTTTTAGCCAAAAACCGTGATGATTATTGCATGATTTCGGCTAAAATTTTTGCAAA
184 CGAA-ATGGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAA-TTTTGCAAA
* * * * * *
23174 AATTGATCCGAAAGATATTTCCTCAA-TTTTAGCCATAATACTCATAAAAAATATATGATTCAAC
247 AATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAACAATATATAATTCAAC
* *
23238 GCCAAAACGATTGAAGGGC
312 GCCAAAAAGATTGAAGGAC
* * *
23257 TTTTCATGCTTTTAATATCGT-TTT-TCATTTTTTTTGAATTAATTTCTAATTAAATCAAAACAA
1 TTTT-ATGCTTTTAATATCGTATTTCTTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAA
* * * * * *
23320 GATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATGTAGCTAAGATTTTATTAGATGAATAT
65 GATTCAGATGCTTGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATAT
* * * * * * *
23385 AGATATTTCATGGAGTGTCGGCGCCAAAAATCATGCAAAACTAAATCGGGGCCCCGAAACGCGTT
130 AGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGTCGGGTCCCCGAAATG-GTT
** * * * * *
23450 TTTAGCCAAAAATTGTGATGGTTAGTACACGATTTTGGCTAAACTTTTGCAAAAAAATGACTCGA
194 TTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGC-AAAAATTGACCCGA
* * *
23515 AA-ATTTTTTCCTCAATTTTTGGAC-AAAATACTCATAATATACATATATATATATATTTAACAC
258 AAGA-TATTTCCTCAATTTTTGG-CTAAAATACTCAT-A-A-AC--A-ATATATA-ATTCAACGC
*
23578 CAAAAAGATTGGAGGAC
314 CAAAAAGATTGAAGGAC
* * *
23595 TTTTCTCGCTTTTAATATCGTATTTCATA-TTTTTCTGAATTAATTTCCAATTAAATCGAAACAA
1 TTTTAT-GCTTTTAATATCGTATTTCTTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAA
* * * *
23659 GATTCAGATGCTTTTAAAAACAAATTCTTTAATCCAATGTGGCCGAGATTTGATTAGATGAATAT
65 GATTCAGATGCTTGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATAT
* ** * * * * *
23724 GGATAACTCACGGAGTCTTGGCGCCAAAAATAATGCGAAACTGAGCCGGGTCCCCAAAATGGTTT
130 AGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGTCGGGTCCCCGAAATGG-TT
* * * * *
23789 TTTAGCTATAAACTGTGATGATTATTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAA
194 TTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAA
* *
23854 AGATATTTCCGT-AATTTTTGGCTAAAATACTCATAAACAATATATAATTCAATGCCTAAAAGAT
259 AGATATTTCC-TCAATTTTTGGCTAAAATACTCATAAACAATATATAATTCAACGCCAAAAAGAT
*
23918 TGAATGAC
323 TGAAGGAC
* * ** *
23926 TTTTGATGTTTTTAATATC-AATTTTCTTATTTTTTCCAAAATAATTTCTAATTAAATCGAAACA
1 TTTT-ATGCTTTTAATATCGTA-TTTCTTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACA
* * * * * *
23990 AGATTCAGATGCTTGCAAGAA-AAATCCTTAAATCCAATATGGTTGAGACTAGATTAGATGAATA
64 AGATTCAGATGCTTGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATA
** * * * * *** * *
24054 TAGATATTTCAAATAGTCTTGGAGTCAAAAATCATGCAAAATTGAGTCAGGTCTTTGGAACTCGT
129 TAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGTCGGGTC-CCCGAAATGGT
* * * * *
24119 TTTTAGCCAAAAACCGTGATGGTTTGTTAGTACAGGATTTCTGCTAAAATGTTGCAAAAATTGAT
193 TTTTAGCCAAAAACCGTGAT-G---ATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
** * * *
24184 ATGAAAGAT-TTCTCCT-ATTTTTTGGTTTAAATACTCATAAA-AATATATAATTCAACGCCAAA
254 CCGAAAGATATT-TCCTCAATTTTTGGCTAAAATACTCATAAACAATATATAATTCAACGCCAAA
* **
24246 AAGATTGGAGGGTT
318 AAGATT-GAAGGAC
* *
24260 TTTTACGCTTTTAATATCGTATTTCTTATTTTTTCTTAATTAATTTCTAATTAAATCGAAACAAG
1 TTTTATGCTTTTAATATCGTATTTCTTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAG
* ** * * *
24325 ATTCAGATACTCATAAAAACAAATTCTTAAATCCAATG-GTACTGAGATTTGGTTAGATGA
66 ATTCAGATGCTTGTAAAAACAAATCCTTAAATCCAATGTG-GCTGAGATTTGATTAGATGA
24385 TGTAAAGTAT
Statistics
Matches: 1161, Mismatches: 225, Indels: 133
0.76 0.15 0.09
Matches are distributed among these distances:
313 37 0.03
316 1 0.00
319 5 0.00
320 4 0.00
323 3 0.00
324 86 0.07
325 33 0.03
326 7 0.01
327 5 0.00
328 16 0.01
329 126 0.11
330 70 0.06
331 153 0.13
332 63 0.05
333 98 0.08
334 65 0.06
335 49 0.04
336 21 0.02
337 9 0.01
338 83 0.07
339 188 0.16
340 1 0.00
342 1 0.00
345 37 0.03
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (330 bp):
TTTTATGCTTTTAATATCGTATTTCTTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAG
ATTCAGATGCTTGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATA
GATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGTCGGGTCCCCGAAATGGTTTT
TAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAG
ATATTTCCTCAATTTTTGGCTAAAATACTCATAAACAATATATAATTCAACGCCAAAAAGATTGA
AGGAC
Found at i:24845 original size:43 final size:43
Alignment explanation
Indices: 24798--24883 Score: 104
Period size: 42 Copynumber: 2.0 Consensus size: 43
24788 AAGTAAATTA
*
24798 TTAAATAAGTGCA-TTATTAATATCTTTCCATAATT-TAAAAAAT
1 TTAAAT-AGTGCATTTA-CAATATCTTTCCATAATTATAAAAAAT
* *
24841 TTAAATATTGGATTTACAATATCTTTCCATAATTAATAAAAAA
1 TTAAATAGTGCATTTACAATATCTTTCCATAATT-ATAAAAAA
24884 AGTTGATTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
42 21 0.57
43 9 0.24
44 7 0.19
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (43 bp):
TTAAATAGTGCATTTACAATATCTTTCCATAATTATAAAAAAT
Found at i:25039 original size:13 final size:13
Alignment explanation
Indices: 25021--25075 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
25011 ATATATAATA
*
25021 ATAAGACAGTAAG
1 ATAAGATAGTAAG
25034 ATAAGATACG-ATAG
1 ATAAGATA-GTA-AG
*
25048 -TAAGATAGTATG
1 ATAAGATAGTAAG
25060 ATAAGATAGTAAG
1 ATAAGATAGTAAG
25073 ATA
1 ATA
25076 GGTGGGAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
12 2 0.06
13 30 0.86
14 3 0.09
ACGTcount: A:0.51, C:0.04, G:0.22, T:0.24
Consensus pattern (13 bp):
ATAAGATAGTAAG
Found at i:31304 original size:31 final size:30
Alignment explanation
Indices: 31266--31349 Score: 100
Period size: 29 Copynumber: 2.8 Consensus size: 30
31256 TTAATGCCCT
* *
31266 TTTTGCCCCCTGAACTTGTATGATTTTGG-CG
1 TTTTGCCCCCTAAACTTGTA--ATTTTGGACA
31297 TTTTGCCCCCTAAACTT-TAATTTTGGACA
1 TTTTGCCCCCTAAACTTGTAATTTTGGACA
* *
31326 TTTTGCCCCTTAAACTTGCAATTT
1 TTTTGCCCCCTAAACTTGTAATTT
31350 GAAGCCATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 7 0.15
29 17 0.36
30 7 0.15
31 16 0.34
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (30 bp):
TTTTGCCCCCTAAACTTGTAATTTTGGACA
Found at i:31334 original size:28 final size:29
Alignment explanation
Indices: 31266--31342 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 29
31256 TTAATGCCCT
* *
31266 TTTTGCCCCC-TGAACTTGTATGATTTTGGCG
1 TTTTGCCCCCTTAAACTT-TA--ATTTTGGCA
31297 TTTTGCCCCC-TAAACTTTAATTTTGGACA
1 TTTTGCCCCCTTAAACTTTAATTTTGG-CA
31326 TTTTG-CCCCTTAAACTT
1 TTTTGCCCCCTTAAACTT
31343 GCAATTTGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
28 11 0.26
29 13 0.31
30 2 0.05
31 16 0.38
ACGTcount: A:0.18, C:0.25, G:0.14, T:0.43
Consensus pattern (29 bp):
TTTTGCCCCCTTAAACTTTAATTTTGGCA
Found at i:45461 original size:12 final size:14
Alignment explanation
Indices: 45435--45471 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
45425 TTAATTATTA
45435 GGAGGGACAAATTT
1 GGAGGGACAAATTT
45449 -GAGGGAC-AATTT
1 GGAGGGACAAATTT
*
45461 GGAGGGTCAAA
1 GGAGGGACAAA
45472 AAGAAATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
12 5 0.25
13 13 0.65
14 2 0.10
ACGTcount: A:0.35, C:0.08, G:0.38, T:0.19
Consensus pattern (14 bp):
GGAGGGACAAATTT
Found at i:51817 original size:11 final size:11
Alignment explanation
Indices: 51791--51826 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
51781 TAGGCAAAGT
*
51791 ATATATA-TAT
1 ATATATACTAC
51801 ATATATACTAC
1 ATATATACTAC
51812 ATATATACTAC
1 ATATATACTAC
51823 ATAT
1 ATAT
51827 TATTTGAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 7 0.29
11 17 0.71
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (11 bp):
ATATATACTAC
Found at i:60219 original size:36 final size:36
Alignment explanation
Indices: 60172--60243 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
60162 TAGAAATTAG
*
60172 TAGGTTGCTTAAGATTTTAATTTTCATTTAATTTAA
1 TAGGTTGCTTAAGATTTTAATTTTAATTTAATTTAA
60208 TAGGTTGCTTAAGATTTTAATTTTAATTTAATTTAA
1 TAGGTTGCTTAAGATTTTAATTTTAATTTAATTTAA
60244 ACATATTAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.53
Consensus pattern (36 bp):
TAGGTTGCTTAAGATTTTAATTTTAATTTAATTTAA
Found at i:65416 original size:328 final size:321
Alignment explanation
Indices: 64595--65842 Score: 1269
Period size: 325 Copynumber: 3.8 Consensus size: 321
64585 AAATACTGAT
* * * * * *
64595 AAAATATATATAATTCAACGCCAAAAAGATTGGAGGACTTTTCACGTTTTTAATATCGTTTCACA
1 AAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTT--C-
* * *
64660 TATTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCACGTAAAAGA-AAAT
63 TATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA-ACAAAT
* * * **
64724 CCTTAGATCCAATATGGCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTC--GGCG
127 CCTTATATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCTTTACG
* * * * * * * *
64787 CCAAAAATTATGCAAAACAGAGCCCTGGTTCAGGAACGC-TTTCTAAGTCAAAAACCATGATGGT
192 CCAAAAATCATGCAAAACTGAG-CCGGGGTCCGGAACGCGTTT-TTAGCCAAAAACCGTGATGGT
* * * *
64851 TAGTACACAATTTCGGCTAAAAACTG-ACCCGAAACGCTTATTCTCAATTTCTTGCCACAATACT
255 TAGTACACGATTTCGGCTAAAAATTGAACCCGAAAAG-TTTTTCTCAATTT-TTGCCACAATACT
*
64915 AAGAAA
318 CAG--A
* * * *
64921 AAAAAATATATAATTGAATG-CAAAAAATATTGACGGCCTTTTCACGCTTCTAATATCGTTTTTC
1 AAAAAATATATAATTCAACGCCAAAAAA-ATTGAAGGGCTTTTCACGCTTCTAATATCG--TTTC
* *
64985 CATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATC
63 TATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATC
* * *
65050 CTTATATCCAATGTGGCTCACATTTGATTCGATGAATAT-GAATATTTCAAGGAGTCTTACTTTA
128 CTTATATCCAATGTGGCTGAGATTTGATTAGATGAATATAG-ATATTTCAAGGAGTC-T-CTTTA
* *
65114 CGCCAAAAATCAAGCAAAATTGAGCCGGGGCTCCGGAACGC-TTTTTAGCCAAAAACCGTGATGG
190 CGCCAAAAATCATGCAAAACTGAGCCGGGG-TCCGGAACGCGTTTTTAGCCAAAAACCGTGATGG
* *
65178 TTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTCCGAAAAGTTTTTCCTCAAGTTTTGCCAC
254 TTAGTACACGATTTCGGCTAAAA-ATTG----AAC-CCGAAAAGTTTTT-CTCAATTTTTGCCAC
65243 AATACTCAG-
312 AATACTCAGA
* * * *
65252 AAAAAATATATCATTTAACGCCAAAAAAATTTGAAGGGTTTTTCACGCTTTTAATATCG-TT-T-
1 AAAAAATATATAATTCAACGCCAAAAAAA-TTGAAGGGCTTTTCACGCTTCTAATATCGTTTCTA
* * * * * *
65314 TTTTTTTCCGAATTTATTTCTTATTAAATAGAAACAAAGATTGAGATGCTTGTAAAAACAAATTC
65 TTTTTTTCCGAATTAATTTCTAATTAAATCGAAAC-AAGATTCAGATGCTCGTAAAAACAAATCC
* * * *
65379 TTAAATGCATTGTGGATGAGATTTTG-TTA-AGTGAATATAGATATTTCAAGGAG--TCTTT-CT
129 TTATATCCAATGTGGCTGAGA-TTTGATTAGA-TGAATATAGATATTTCAAGGAGTCTCTTTAC-
** * * * * *
65439 GCCAAAAAAATCATTTAAAACTGAGCCGGGATCCGAAATGCGTTTTTAGCCAAAAATCGTGATGC
191 GCC--AAAAATCATGCAAAACTGAGCCGGGGTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGG
* * *
65504 TTAGTACACGATTTCGGCTAAAAATT-AACCCGAAGAGTTTTTCTCAATTGTTTG-CAAAATATT
254 TTAGTACACGATTTCGGCTAAAAATTGAACCCGAAAAGTTTTTCTCAATT-TTTGCCACAATACT
65567 CAGA
318 CAGA
* * * * *
65571 AAAAAATATATAATTCAACGCCAAAAAGACTGACGGGCTTTTCGCGCTTCTAATATCGTTTTTCC
1 AAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCG--TTTCT
** * *
65636 ATTTTTTTTCAAAATTAATTTCTAATTAAATCGAAACAAGATTCGGATGCTCGAAAAAACAAATC
64 A-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATC
* * * * *
65701 CTTATATACAATGTGGCTGAGATTTGGTTCGATTAATATAGATATTTCAAGGAG--TCTTTATGC
128 CTTATATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCTTTACGC
* * * * *
65764 CAAAAATCATGCGAAATTGAGCCGGGAGTCCGGAACGCGTTTTTTTGCAAAAAACCGTGATAGTT
193 CAAAAATCATGCAAAACTGAGCCGGG-GTCCGGAACGCG-TTTTTAGCCAAAAACCGTGATGGTT
65829 AGTACACGATTTCG
256 AGTACACGATTTCG
65843 TTGGCAAAAA
Statistics
Matches: 768, Mismatches: 113, Indels: 85
0.80 0.12 0.09
Matches are distributed among these distances:
318 40 0.05
319 42 0.05
320 3 0.00
321 23 0.03
322 13 0.02
323 107 0.14
324 40 0.05
325 123 0.16
326 109 0.14
327 34 0.04
328 108 0.14
329 41 0.05
331 18 0.02
332 32 0.04
334 21 0.03
335 14 0.02
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (321 bp):
AAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTCTAT
TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
ATATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCTTTACGCCAA
AAATCATGCAAAACTGAGCCGGGGTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTAC
ACGATTTCGGCTAAAAATTGAACCCGAAAAGTTTTTCTCAATTTTTGCCACAATACTCAGA
Found at i:66019 original size:270 final size:269
Alignment explanation
Indices: 65618--66111 Score: 672
Period size: 270 Copynumber: 1.8 Consensus size: 269
65608 CTTTTCGCGC
65618 TTCTAATATCGTTTTTCCATTTTTTTTCAAAATTAATTTCTAATTAAATCGAAACAAGATTCGGA
1 TTCTAATATCGTTTTTCCA-TTTTTTTCAAAATTAATTTCTAATTAAATCGAAACAAGATTCGGA
*
65683 TGCTCGAAAAAACAAATCCTTATATACAATGTGGCTGAGATTTGGTTCGATTAATATAGATATTT
65 TGCTCGAAAAAACAAATCCTTATATACAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTT
* * * ** *
65748 CAAGGAGTCTTTATGCCAAAAATCATGCGAAATTGAGCCGGGAGTCCG-GAACGCGTTTTTTTGC
130 CAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGCCGGGA-TCCGAAAACATG-TTTTTAGC
* *
65812 AAAAAACCGTGATAGTTAGTACACGATTTCGTTGGCAAAAAAAAAAAACACACGATTTTGGCTAA
193 AAAAAACCGTGATAATTAGTACACGAATTCGTTGGCAAAAAAAAAAAACACACGATTTTGGCTAA
65877 AAAAACATACGT
258 AAAAACATACGT
** *
65889 TTCTAATATCGTTTTTCC-TTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAGATT-GAG
1 TTCTAATATCGTTTTTCCATTTTTTTCAAAATTAATTTCTAATTAAATCGAAAC-AAGATTCG-G
* * * * * * * * *
65952 ATGTTCGTAAAAATAAATTCTT-TAATCCATTGTGGCTGAGATTTTGTTTGATGAATATTGATAT
64 ATGCTCGAAAAAACAAATCCTTAT-ATACAATGTGGCTGAGATTTGGTTCGATGAATATAGATAT
* **
66016 TTCAAGGAGTCTTTTTGCCAAAAATCATTTAAAACTGAGCCGGGATCCGAAAACATGTTTTTAGC
128 TTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGCCGGGATCCGAAAACATGTTTTTAGC
* *
66081 CAAAAATCGTGATAATTAGTACACGAATTCG
193 AAAAAACCGTGATAATTAGTACACGAATTCG
66112 GCTAAAAACT
Statistics
Matches: 193, Mismatches: 26, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
269 72 0.37
270 103 0.53
271 18 0.09
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (269 bp):
TTCTAATATCGTTTTTCCATTTTTTTCAAAATTAATTTCTAATTAAATCGAAACAAGATTCGGAT
GCTCGAAAAAACAAATCCTTATATACAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTC
AAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGCCGGGATCCGAAAACATGTTTTTAGCAAA
AAACCGTGATAATTAGTACACGAATTCGTTGGCAAAAAAAAAAAACACACGATTTTGGCTAAAAA
AACATACGT
Found at i:66861 original size:330 final size:329
Alignment explanation
Indices: 65889--67743 Score: 1973
Period size: 330 Copynumber: 5.6 Consensus size: 329
65879 AAACATACGT
* * * *
65889 TTCTAATATCGTTTTTCCTTTT-TTTCCGAATTTATTTCTAATTAAATCGAAACAAAGATTGAGA
1 TTCTAATATCGTTTTTCCTTTTGTTTCAGAATTAATTTCTAATTAAATCAAAAC-AAGATCGAGA
* * * * * * * *
65953 TGTTCGTAA-AAATAAATTCTT-TAATCCATTGTGGCTGAGATTTTGTTTGATGAATATTGATAT
65 TG--C-TAATAAAAAAATCCTTAT-ATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATAT
* ** * * **
66016 TTCAAGGAGTCTTTT-TGCCAAAAATCATTTAAAACTGAGCCGGGA-TCCGAAAACATGTTTTTA
126 TTCAAGGAGT-TTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGCACTCCG-AAACGCGTTTTTA
* ** *
66079 GCCAAAAATCGTGATAATTAGTACACGAATTCGGCTAAAA---AC------TGACACGAAAA-TT
189 GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTACAAAAATTGACACGAAAAGTT
* * * *
66134 TTTTTTCTCAATTTTTTTACCA-AATATTTAG-AAAAATATATAATTCAATGCCAAAAAGATTGA
254 TTTTTT-TCAA-TTTTTTGCCAGAATACTCAGAAAAAATATATAATTCAAAGCCAAAAA-ATTGA
* * *
66197 CGGGCTTTTCACCC
316 AGGGTTTTTCACGC
* *
66211 TTCTAATATCGTCTTTCCATTTGTTTCAGAATTAATTTCTAATTAAATCAAAACAAGATCGAGAT
1 TTCTAATATCGTTTTTCCTTTTGTTTCAGAATTAATTTCTAATTAAATCAAAACAAGATCGAGAT
*
66276 GCTAATAAAAACAAATCCTTATATCGAATGTGGTTGACAATTGACATTTGGTTCGATGAATATAG
66 GCTAAT-AAAA-AAATCCTTATATCCAATGT-G--G----TTGACATTTGGTTCGATGAATATAG
* * * * * *
66341 ATATTTCATGGAGTATTTGTGCC-AAAATCCTGCAAATTTGAGCCGGCACGCCGGAACAC-TATT
122 ATATTTCAAGGAGTTTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGCACTCCGAAACGCGT-TT
* * *
66404 TTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTGGCAAAAATTGACCCG-AA
186 TTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTT-ACAAAAATTGACACGAAA
* ** *
66468 AGGTTTTTCCTCAATTTTTTGCAAGAATACTCAGAAAAAATATATAATTCAAAGCCAAAAAAATT
250 AGTTTTTTTTTCAATTTTTTGCCAGAATACTCAGAAAAAATATATAATTCAAAGCC-AAAAAATT
*
66533 GAAGGGTTTTTCATGC
314 GAAGGGTTTTTCACGC
* *
66549 TTCTAATATTGTTTTTCCTTTTGTTTCAGAATTAATTTCTAATAAAATCAAAACAAGATCGAGAT
1 TTCTAATATCGTTTTTCCTTTTGTTTCAGAATTAATTTCTAATTAAATCAAAACAAGATCGAGAT
* *
66614 GCTAATAAAAAAATCCTTATATCCAATGTGGTTGACATTTGGTCCGATGATTATAGATATTTCAA
66 GCTAATAAAAAAATCCTTATATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATTTCAA
* *
66679 GGAGTTTTTGTGCCAAAAATCCTGCAAATTTGAGCCGGCACTCCGAAACGCGTTTTTAGCTAAAA
131 GGAGTTTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGCACTCCGAAACGCGTTTTTAGCCAAAA
*
66744 ACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACACGAAAAGTTTTTTTT
196 ACCGTGATGGTTAGTACACGATTTCGGCTAAAA-TTTACAAAAATTGACACGAAAAGTTTTTTTT
66809 TCAATTTTTTGCCAGAATACTCAGAAAAAATATATAATTCAAAGCCAAAAAATTGAAGGGTTTTT
260 TCAATTTTTTGCCAGAATACTCAGAAAAAATATATAATTCAAAGCCAAAAAATTGAAGGGTTTTT
*
66874 CAAGC
325 CACGC
* *
66879 TTCTAATATTGTTTTTCCTTTTGTTTCAGAATTAATTTCTAATAAAATCAAAACAAGATCGAGAT
1 TTCTAATATCGTTTTTCCTTTTGTTTCAGAATTAATTTCTAATTAAATCAAAACAAGATCGAGAT
* * * *
66944 GCTAATAAAAAAAACCTTATATCCAATGTGGTTGACATTTGGTTCGATGATTATAGATATGTGAA
66 GCTAATAAAAAAATCCTTATATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATTTCAA
* ** * *
67009 GGAGTTTTTGTGCCAAAACTCCTGCAAAATTGAGCCAACACTCCGGAACGCATTTTTAGCCAAAA
131 GGAGTTTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGCACTCCGAAACGCGTTTTTAGCCAAAA
* * * * *
67074 ACCGTGATGGTTAGTACACGATTTCGACTAAAATTTTGCAAAAATTGACCCAAAAAGTTTTTTTC
196 ACCGTGATGGTTAGTACACGATTTCGGCTAAAA-TTTACAAAAATTGACACGAAAAGTTTTTTTT
*
67139 TCAATTTTTTGCCAGAATACTCATAAAAAATATATAATTCAAAGCCAAAAAAATTGAAGGGTTTT
260 TCAATTTTTTGCCAGAATACTCAGAAAAAATATATAATTCAAAGCC-AAAAAATTGAAGGGTTTT
67204 TCACGC
324 TCACGC
* * * * * *
67210 TTCTAATATCG-TTTTCCTTTTTTTTCTCGAATTTATTTCTAATTAATTCGAAACAATATTC-AG
1 TTCTAATATCGTTTTTCCTTTTGTTTC-AGAATTAATTTCTAATTAAATCAAAACAAGA-TCGAG
* * * * * * ** *
67273 ATGCTCATAAAAACAAATTCTTAAATCCATTGTGGCTGAGATTTAATTAGATGAATATAGATATT
64 ATGCTAAT-AAAA-AAATCCTTATATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATT
* * * * * ** * * *
67338 TTAAGGAGTGTTTCTTCCAAAAATCATTTAAAACTGAGCCGGGA-TCCGAAACCCGTTTTTAGCC
127 TCAAGGAGTTTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGCACTCCGAAACGCGTTTTTAGCC
* * * * *
67402 AAAAATCGTGATGGGTAGTAGACGATTTCGGCTAAAA---AC------TGAAACGAAAATATTTT
192 AAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTACAAAAATTGACACGAAAA-GTTTT
** * * * * * *
67458 TTTTCTCAATTTTTT-ATAAAATATTTAG-AAAAATATATAACTGAATGCCAAAAAGATTGACA-
256 TTTT-TCAATTTTTTGCCAGAATACTCAGAAAAAATATATAATTCAAAGCCAAAAA-ATTGA-AG
* *
67520 GGCTTTTCGCGC
318 GGTTTTTCACGC
*** *
67532 TTCTAATATCGTTTTTCCAAGTGTTTCAGAATTAATTTCTAATTAAATCAAAACAAGATCAAGAT
1 TTCTAATATCGTTTTTCCTTTTGTTTCAGAATTAATTTCTAATTAAATCAAAACAAGATCGAGAT
* *
67597 GCTCATAAAAAAAAATCCTTATATCGAATGTGGTTGACAATTGACATTTGGTTCGATGAATATAG
66 GCT-A-ATAAAAAAATCCTTATATCCAATGT-G--G----TTGACATTTGGTTCGATGAATATAG
* * *
67662 ATATTTCAAGGAGTATTTGTGCC-AAAATCCTGCAAATTTGAGCCGGCACTCCGGAACGCGTTTT
122 ATATTTCAAGGAGTTTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGCACTCCGAAACGCGTTTT
**
67726 TAGGTAAAAACCGTGATG
187 TAGCCAAAAACCGTGATG
67744 CAAAAATTGA
Statistics
Matches: 1304, Mismatches: 175, Indels: 101
0.83 0.11 0.06
Matches are distributed among these distances:
319 3 0.00
320 1 0.00
321 10 0.01
322 145 0.11
323 61 0.05
324 11 0.01
325 2 0.00
327 1 0.00
328 86 0.07
329 151 0.12
330 415 0.32
331 125 0.10
332 57 0.04
333 73 0.06
335 1 0.00
336 26 0.02
337 18 0.01
338 113 0.09
339 5 0.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (329 bp):
TTCTAATATCGTTTTTCCTTTTGTTTCAGAATTAATTTCTAATTAAATCAAAACAAGATCGAGAT
GCTAATAAAAAAATCCTTATATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATTTCAA
GGAGTTTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGCACTCCGAAACGCGTTTTTAGCCAAAA
ACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTACAAAAATTGACACGAAAAGTTTTTTTTT
CAATTTTTTGCCAGAATACTCAGAAAAAATATATAATTCAAAGCCAAAAAATTGAAGGGTTTTTC
ACGC
Found at i:67285 original size:661 final size:650
Alignment explanation
Indices: 65889--67743 Score: 2435
Period size: 661 Copynumber: 2.8 Consensus size: 650
65879 AAACATACGT
*
65889 TTCTAATATCGTTTTTCC-TTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAGATTGAGA
1 TTCTAATATCGTTTTTCCTTTTTTTTCCGAATTTATTTCTAATTAAATCGAAAC-AAGATTCAGA
* * * * * *
65953 TGTTCGTAAAAATAAATTCTT-TAATCCATTGTGGCTGAGATTTTGTTTGATGAATATTGATATT
65 TGCTCATAAAAACAAATTCTTAT-ATCCATTGTGGCTGAGATTTAGTTAGATGAATATAGATATT
*
66017 TCAAGGAGTCTTTTTGCCAAAAATCATTTAAAACTGAGCCGGGATCCGAAAACATGTTTTTAGCC
129 TCAAGGAGT-TTTTTGCCAAAAATCATTTAAAACTGAGCCGGGATCCG-AAACACGTTTTTAGCC
** *
66082 AAAAATCGTGATAATTAGTACACGAATTCGGCTAAAAACTGACACGAAAATTTTTTTTCTCAATT
192 AAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACACGAAAATTTTTTTTCTCAA-T
* *
66147 TTTTTACCAAATATTTAGAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCACCCT
256 TTTTT-CCAAATATTTAGAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCT
*
66212 TCTAATATCGTCTTTCCATTTGTTTCAGAATTAATTTCTAATTAAATCAAAACAAGATCGAGATG
320 TCTAATATCGTTTTTCCATTTGTTTCAGAATTAATTTCTAATTAAATCAAAACAAGATCGAGATG
66277 CTAATAAAAACAAATCCTTATATCGAATGTGGTTGACAATTGACATTTGGTTCGATGAATATAGA
385 CTAATAAAAA-AAATCCTTATATCGAATGTGG-TG---ATTGACATTTGGTTCGATGAATATAGA
* * *
66342 TATTTCATGGAGTATTTGTGCCAAAATCCTGCAAATTTGAGCCGGCACGCCGGAACACTATTTTA
445 TATTTCAAGGAGTATTTGTGCCAAAATCCTGCAAATTTGAGCCGGCACTCCGGAACGCT-TTTTA
* *
66407 GCTAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTGGCAAAAATTGACCCGAAAGGT
509 GCTAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAATTTGGCAAAAATTGACCCAAAAGGT
66472 TTTTCCTCAATTTTTTGCAAGAATACTCAGAAAAAATATATAATTCAAAGCCAAAAAAATTGAAG
574 TTTTCCTCAATTTTTTGCAAGAATACTCAGAAAAAATATATAATTCAAAGCCAAAAAAATTGAAG
*
66537 GGTTTTTCATGC
639 GGTTTTTCACGC
* * * * * *
66549 TTCTAATATTGTTTTTCCTTTTGTTTCAGAATTAATTTCTAATAAAATCAAAACAAGA-TCGAGA
1 TTCTAATATCGTTTTTCCTTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTC-AGA
* * * * * * ** *
66613 TGCTAAT-AAAA-AAATCCTTATATCCAATGTGGTTGACATTTGGTCCGATGATTATAGATATTT
65 TGCTCATAAAAACAAATTCTTATATCCATTGTGGCTGAGATTTAGTTAGATGAATATAGATATTT
* ** ** * * *
66676 CAAGGAGTTTTTGTGCCAAAAATCCTGCAAATTTGAGCCGGCACTCCGAAACGCGTTTTTAGCTA
130 CAAGGAGTTTTT-TGCCAAAAATCATTTAAAACTGAGCCGGGA-TCCGAAACACGTTTTTAGCCA
66741 AAAA-CTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACACGAAAAGTTTT
193 AAAATC-GTGATGGTTAGTACACGATTTCGGCTAAAA----AC------TGACACGAAAA-TTTT
* * *
66805 TTTT-TCAATTTTTTGCCAGAATACTCAGAAAAAATATATAATTCAAAGCCAAAAA-ATTGAAGG
246 TTTTCTCAATTTTTT-CCA-AATATTTAG-AAAAATATATAATTCAATGCCAAAAAGATTGAAGG
* * * * *
66868 GTTTTTCAAGCTTCTAATATTGTTTTTCCTTTTGTTTCAGAATTAATTTCTAATAAAATCAAAAC
308 GCTTTTCACGCTTCTAATATCGTTTTTCCATTTGTTTCAGAATTAATTTCTAATTAAATCAAAAC
*
66933 AAGATCGAGATGCTAATAAAAAAAA-CCTTATATCCAATGT-G-G-TTGACATTTGGTTCGATGA
373 AAGATCGAGATGCTAATAAAAAAAATCCTTATATCGAATGTGGTGATTGACATTTGGTTCGATGA
* * * * * **
66994 TTATAGATATGTGAAGGAGTTTTTGTGCCAAAACTCCTGCAAAATTGAGCCAACACTCCGGAACG
438 ATATAGATATTTCAAGGAGTATTTGTGCCAAAA-TCCTGCAAATTTGAGCCGGCACTCCGGAACG
* *
67059 CATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAATTTTGCAAAAATTGACC
502 C-TTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAATTTGGCAAAAATTGACC
* * * *
67124 CAAAAAGTTTTTTTCTCAATTTTTTGCCAGAATACTCATAAAAAATATATAATTCAAAGCCAAAA
566 C-AAAAGGTTTTTCCTCAATTTTTTGCAAGAATACTCAGAAAAAATATATAATTCAAAGCCAAAA
67189 AAATTGAAGGGTTTTTCACGC
630 AAATTGAAGGGTTTTTCACGC
* *
67210 TTCTAATATCG-TTTTCCTTTTTTTTCTCGAATTTATTTCTAATTAATTCGAAACAATATTCAGA
1 TTCTAATATCGTTTTTCCTTTTTTTTC-CGAATTTATTTCTAATTAAATCGAAACAAGATTCAGA
* *
67274 TGCTCATAAAAACAAATTCTTAAATCCATTGTGGCTGAGATTTAATTAGATGAATATAGATATTT
65 TGCTCATAAAAACAAATTCTTATATCCATTGTGGCTGAGATTTAGTTAGATGAATATAGATATTT
* *
67339 TAAGGAGTGTTTCTT-CCAAAAATCATTTAAAACTGAGCCGGGATCCGAAACCCGTTTTTAGCCA
130 CAAGGAGT-TTT-TTGCCAAAAATCATTTAAAACTGAGCCGGGATCCGAAACACGTTTTTAGCCA
* * *
67403 AAAATCGTGATGGGTAGTAGACGATTTCGGCTAAAAACTGAAACGAAAATATTTTTTTTCTCAAT
193 AAAATCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACACG-AAA-ATTTTTTTTCTCAAT
** * * *
67468 TTTTTATAAAATATTTAGAAAAATATATAACTGAATGCCAAAAAGATTGACA-GGCTTTTCGCGC
256 TTTTT-CCAAATATTTAGAAAAATATATAATTCAATGCCAAAAAGATTGA-AGGGCTTTTCACGC
** *
67532 TTCTAATATCGTTTTTCCAAGTGTTTCAGAATTAATTTCTAATTAAATCAAAACAAGATCAAGAT
319 TTCTAATATCGTTTTTCCATTTGTTTCAGAATTAATTTCTAATTAAATCAAAACAAGATCGAGAT
*
67597 GCTCATAAAAAAAAATCCTTATATCGAATGTGGTTGACAATTGACATTTGGTTCGATGAATATAG
384 GCTAAT-AAAAAAAATCCTTATATCGAATGTGG-TG---ATTGACATTTGGTTCGATGAATATAG
67662 ATATTTCAAGGAGTATTTGTGCCAAAATCCTGCAAATTTGAGCCGGCACTCCGGAACGCGTTTTT
444 ATATTTCAAGGAGTATTTGTGCCAAAATCCTGCAAATTTGAGCCGGCACTCCGGAACGC-TTTTT
*
67727 AGGTAAAAACCGTGATG
508 AGCTAAAAACCGTGATG
67744 CAAAAATTGA
Statistics
Matches: 1029, Mismatches: 123, Indels: 85
0.83 0.10 0.07
Matches are distributed among these distances:
652 29 0.03
653 96 0.09
654 21 0.02
655 14 0.01
656 1 0.00
657 5 0.00
658 121 0.12
659 57 0.06
660 129 0.13
661 202 0.20
662 107 0.10
663 73 0.07
664 4 0.00
665 2 0.00
666 14 0.01
667 12 0.01
668 109 0.11
669 33 0.03
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (650 bp):
TTCTAATATCGTTTTTCCTTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAT
GCTCATAAAAACAAATTCTTATATCCATTGTGGCTGAGATTTAGTTAGATGAATATAGATATTTC
AAGGAGTTTTTTGCCAAAAATCATTTAAAACTGAGCCGGGATCCGAAACACGTTTTTAGCCAAAA
ATCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACACGAAAATTTTTTTTCTCAATTTTTT
CCAAATATTTAGAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAAT
ATCGTTTTTCCATTTGTTTCAGAATTAATTTCTAATTAAATCAAAACAAGATCGAGATGCTAATA
AAAAAAATCCTTATATCGAATGTGGTGATTGACATTTGGTTCGATGAATATAGATATTTCAAGGA
GTATTTGTGCCAAAATCCTGCAAATTTGAGCCGGCACTCCGGAACGCTTTTTAGCTAAAAACCGT
GATGGTTAGTACACGATTTCGACTAAAATTTGGCAAAAATTGACCCAAAAGGTTTTTCCTCAATT
TTTTGCAAGAATACTCAGAAAAAATATATAATTCAAAGCCAAAAAAATTGAAGGGTTTTTCACGC
Done.