Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021140.1 Corchorus olitorius cultivar O-4 contig21173, 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: 26562
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1758 original size:18 final size:18
Alignment explanation
Indices: 1735--1779 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
1725 AGTAATAATT
1735 AATACTATAGCAAGTAGC
1 AATACTATAGCAAGTAGC
1753 AATACTATAGCAAGTAGC
1 AATACTATAGCAAGTAGC
1771 AATACTATA
1 AATACTATA
1780 AGGTTGCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (18 bp):
AATACTATAGCAAGTAGC
Found at i:2043 original size:30 final size:30
Alignment explanation
Indices: 2007--2068 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
1997 GTTAATAAGC
*
2007 CATTAAAATTTGAGAGTATAAGAGAAAAGT
1 CATTAAAATTTGAGAGCATAAGAGAAAAGT
* *
2037 CATTAAAATTTGAGTGCATAAGAGGAAAGT
1 CATTAAAATTTGAGAGCATAAGAGAAAAGT
2067 CA
1 CA
2069 AGATAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.47, C:0.06, G:0.21, T:0.26
Consensus pattern (30 bp):
CATTAAAATTTGAGAGCATAAGAGAAAAGT
Found at i:9235 original size:321 final size:321
Alignment explanation
Indices: 8259--9374 Score: 1225
Period size: 321 Copynumber: 3.4 Consensus size: 321
8249 AATATAATTT
* *
8259 TTTAATTAGAAATTAATTCGGAAAAAGGTAGGAAAAACGATATTAGAAGTGTGAGAATCCCTTCA
1 TTTAATTAGAAATTAATTCGGAAAAA--TA-GAAAAACGATATTAGAAGCGTGAGAAGCCCTTCA
* * * *
8324 GTCTTTTTGGCGTTGAGTTATATATTTTTTATTAGTATTGTGGGCCAAAATTGAGGAGAAATTTC
63 ATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATCGT-GGCCAAAATTGAGGAGAAATTT-
* *
8389 TCGAGTCAATTTTTCAAAATTTTAGCTGAAATCATGTACTAACCATCACGGTTTTTTACTAAAAA
126 TC-AGTCAATTTTTCAAAATTTTAGCCG-AA--ATGTACTAA-CATCACGGTTTTTGACTAAAAA
* * * * *
8454 CGCG-TTCTGGAGCCCCGGCTCTGTTTTACACGATTTTTGGCGCCAAGTCTCATTGAAATATCTA
186 CGCGTTTC-GGGGTCCCGGCTCTGTTTTGCATGATTTTTTGCGCCAAGTCTCATTGAAATATCTA
* * * *
8518 TATCCATCTAACCAAATCTTAACCACATTGGATTTAAAGATTTGTTTTTACGA-CTATATGAATC
250 TATCCATCTAACCAAATCTCAA-CACATTGGATTTAAGGATTTGTTTTTACGAGC-ATCTCAATC
8582 ATGTTTCGA
313 ATGTTTCGA
* * *
8591 TTCAATTAGGAATTAATTCGGGAAAAATAGGAAAAACGATATTAGAAGCGTGA-ATAGCCTTTCA
1 TTTAATTAGAAATTAATTC-GGAAAAATA-GAAAAACGATATTAGAAGCGTGAGA-AGCCCTTCA
* *
8655 ATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGA-GAAAAATTCT
63 ATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATCGTGGCC-AAAATTGAGGAGAAA---T
** * *
8719 TTTGGGTCAATTTTTACAAAATTTTATCCGAAATCGTGAACTAACTATCACGGTTTTTGGCTAAA
124 TTTCAGTCAATTTTT-CAAAATTTTAGCCGAAAT-GT--ACTAAC-ATCACGGTTTTTGACTAAA
* * *
8784 AAAGCGTTGT-GGGCTTGTGGCCCCGGCTCAGTTTTGCATGA-TTTTTGACGCCAAGACTCATTG
184 AACGCGTT-TCGGG---GT---CCCGGCTCTGTTTTGCATGATTTTTTG-CGCCAAGTCTCATTG
** * * *
8847 AAATATCTATATTTATCTAACAAAATTTCAGGCACATTGGATTTAAGGATTTGTTTTTACGAGCA
241 AAATATCTATATCCATCTAACCAAATCTCA-ACACATTGGATTTAAGGATTTGTTTTTACGAGCA
**
8912 TCTCAATCCGGTTTCGA
305 TCTCAATCATGTTTCGA
*
8929 TTTAATTAGAAATTAATTCGGAAAAA-A-AAAAACAATATT-GAAAGCGTGAGAAGCCCTTCAAT
1 TTTAATTAGAAATTAATTCGGAAAAATAGAAAAACGATATTAG-AAGCGTGAGAAGCCCTTCAAT
* * * * * * *
8991 CATTTTGGCGTTGAGTTACATATTTTTTATGAATATGGTGTCCGGAAATTGAGGAGAAATGTTTC
65 CTTTTTGGCGTTGAATTATATATTTTTTATGAGTATCGTGGCC-AAAATTGAGGAGAAAT-TTTC
* *
9056 ATGTCAATTTTTGCAAAATTTTAGCCGAAAT-TA-T-GCATCACAGTTTTTGACTAAAAACGCGT
128 A-GTCAATTTTT-CAAAATTTTAGCCGAAATGTACTAACATCACGGTTTTTGACTAAAAACGCGT
*
9118 TTCGGGGTCCTGGCTCTGTTTTGCATGATTTTTTGCGCCAAGTCTCATTGAAATATCTATATCCA
191 TTCGGGGTCCCGGCTCTGTTTTGCATGATTTTTTGCGCCAAGTCTCATTGAAATATCTATATCCA
* *
9183 TCTAACCAAATCTCAACTACATTGGATTTAAGGATTTGTTTTTACAAGCATCTCTATCATGTTTC
256 TCTAACCAAATCTCAAC-ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCATGTTTC
9248 GA
320 GA
* * *
9250 TTTAATTAGAAATTAATTCGGAAAAAATAAGAAAACCGATATTAGAAGCGTGAAAAGCCTTTC-A
1 TTTAATTAGAAATTAATTCGG-AAAAAT-AGAAAAACGATATTAGAAGCGTGAGAAGCCCTTCAA
* ** * * *
9314 TTTTTTTTACGTTGAATTATATATTTTTTATGAGTATCATGGCAAAAAATTTAGGA-AAATT
64 TCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATCGTGGC-CAAAATTGAGGAGAAATT
9375 CTTTCGGGTA
Statistics
Matches: 661, Mismatches: 87, Indels: 82
0.80 0.10 0.10
Matches are distributed among these distances:
320 1 0.00
321 124 0.19
322 12 0.02
323 4 0.01
324 46 0.07
325 26 0.04
326 2 0.00
327 27 0.04
328 1 0.00
329 3 0.00
330 13 0.02
331 89 0.13
332 61 0.09
333 15 0.02
334 100 0.15
335 7 0.01
336 1 0.00
337 12 0.02
338 116 0.18
339 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.36
Consensus pattern (321 bp):
TTTAATTAGAAATTAATTCGGAAAAATAGAAAAACGATATTAGAAGCGTGAGAAGCCCTTCAATC
TTTTTGGCGTTGAATTATATATTTTTTATGAGTATCGTGGCCAAAATTGAGGAGAAATTTTCAGT
CAATTTTTCAAAATTTTAGCCGAAATGTACTAACATCACGGTTTTTGACTAAAAACGCGTTTCGG
GGTCCCGGCTCTGTTTTGCATGATTTTTTGCGCCAAGTCTCATTGAAATATCTATATCCATCTAA
CCAAATCTCAACACATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCATGTTTCGA
Found at i:9900 original size:19 final size:20
Alignment explanation
Indices: 9871--9908 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
9861 CTAAAAATAT
9871 AATTTATAATTAATAATAAC
1 AATTTATAATTAATAATAAC
9891 AATTTA-AATTAATAATAA
1 AATTTATAATTAATAATAA
9909 TTAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTTATAATTAATAATAAC
Found at i:18394 original size:14 final size:14
Alignment explanation
Indices: 18375--18405 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
18365 TCTTTGCTAA
18375 TCCATAATATAGTT
1 TCCATAATATAGTT
18389 TCCATAATATAGTT
1 TCCATAATATAGTT
18403 TCC
1 TCC
18406 CAACCTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (14 bp):
TCCATAATATAGTT
Found at i:21137 original size:309 final size:318
Alignment explanation
Indices: 20356--21195 Score: 881
Period size: 330 Copynumber: 2.6 Consensus size: 318
20346 AATATTCGGT
* * * * * *
20356 AAAATATATAATTAAATGTCAAAATG-TTAGAC-GGACTTTTCACGTTTCTAACATCGTTTTTCC
1 AAAATATATAATTCAACGCCAAAAAGATT-GACAGG-CTTTTCACGCTTCTAATATCGTTTTTCC
* *
20419 ATTTTTTTTCAAATTAATTTCTAATTAAATCAAAATAAGATTTAGATGCTCGTAAAAACAAATCC
64 ATTTTTTTTCAAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCC
** * * * * * **
20484 TTATGTCCAATGTGCCTGAGATTTTGTTTGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAA
129 TTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATACAGATATTTCAAGGAATCTTTATGCC-A
* * *
20549 AAATCATGCAAAATTGAACCAAGGCTCTAGAACGCGTTTTTAGCCAAAAACCGTGAAAGTTAGTA
193 AAATCATG--AAATCGAACC-A--CTCGAGAACGCGTTATTAGCCAAAAACCGTGAAAGTTAGTA
* *
20614 CACGAATTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTTGCCACA
253 CACGAATTCGGCTAAAA--TT------ACTGACCCGAAAAGTTTTTCATCAATTTTTTTCCCACA
*
20679 ATACTCAGA
310 ATACTCAAA
* * * * *
20688 AAAATTTATAATTCAACGCAAAAAAATATTGA-AGGGTTTTCACGCTTTTAATATCGTTTTTCCA
1 AAAATATATAATTCAACGC-CAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCA
* * * *
20752 --TTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTTAGACGCTCGTAAAAACAAATCCT
65 TTTTTTTTCAAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCT
20815 TAAATCCAATGTGGCTGAGATTTGGTTAGATGAATACAGATATTTCAAGGAATCTTTATG-CAAA
130 TAAATCCAATGTGGCTGAGATTTGGTTAGATGAATACAGATATTTCAAGGAATCTTTATGCCAAA
* * * * *
20879 A-C-TG-AGTCGATGCC-C-CGA-AATGCGTTATTAGCCAAAAACCGT-AATGGTTAGTACCCGA
195 ATCATGAAATCGA-ACCACTCGAGAACGCGTTATTAGCCAAAAACCGTGAA-AGTTAGTACACGA
* * * *
20937 TTTCGGCTAAAA-T-CTGACTCGAAGA-TTTTCTTATCAA-TTTTTTCCCACAATACTCATAA
258 ATTCGGCTAAAATTACTGACCCGAAAAGTTTT-TCATCAATTTTTTTCCCACAATACTCA-AA
20996 AAAATATATAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCG-TTTTCCAT
1 AAAATATATAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCAT
* * * **
21060 TTTTTTTCAAATTAACTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAACTACAAATCCTT
66 TTTTTTTCAAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTT
* * * * *
21125 AAATCGAATGTGGCTGGGATTTGATTCGATGAATATC-GATATTTCAAGGAATCTTAATGCCAAA
131 AAATCCAATGTGGCTGAGATTTGGTTAGATGAATA-CAGATATTTCAAGGAATCTTTATGCC-AA
21189 AATCATG
194 AATCATG
21196 CAAAACTGAG
Statistics
Matches: 433, Mismatches: 60, Indels: 49
0.80 0.11 0.09
Matches are distributed among these distances:
307 39 0.09
308 56 0.13
309 107 0.25
310 2 0.00
311 4 0.01
312 1 0.00
313 2 0.00
315 1 0.00
317 2 0.00
318 44 0.10
319 2 0.00
320 1 0.00
323 4 0.01
324 2 0.00
326 2 0.00
327 1 0.00
328 4 0.01
329 1 0.00
330 108 0.25
332 40 0.09
333 8 0.02
334 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (318 bp):
AAAATATATAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCAT
TTTTTTTCAAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTT
AAATCCAATGTGGCTGAGATTTGGTTAGATGAATACAGATATTTCAAGGAATCTTTATGCCAAAA
TCATGAAATCGAACCACTCGAGAACGCGTTATTAGCCAAAAACCGTGAAAGTTAGTACACGAATT
CGGCTAAAATTACTGACCCGAAAAGTTTTTCATCAATTTTTTTCCCACAATACTCAAA
Found at i:22669 original size:319 final size:321
Alignment explanation
Indices: 21260--22736 Score: 1160
Period size: 319 Copynumber: 4.6 Consensus size: 321
21250 CCACTATTAA
* * ** * * * *
21260 AAGGTTTTTCCCGCTTTTAATATCATTTTTACAGTTTTCCCG-ATTTAATTTCTAATTAAATCGA
1 AAGGGTTTTCACGCTTTTAATATTGTTTTTCCATTTTTTCTGAATTT-ATTTCTAATTAAATCGA
* * * * * *
21324 AACAAAATTAAGATACTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGGGATTTGGTTTGATG
65 AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATG
* ** * * * * * *
21389 AATATAGATATTGCAAGAAGTCTTTACGCCCAAAATCTTGCAAAACTGAGCTG-G-GCCCCAGAA
130 AATATAGATATTTCAAGGTGTCTTTATGCCAAAAATCATGC-AAACTGAGCCGAGATCCCGA-AA
* * * *
21452 CGCGTTTTTAG-CAAAAACCTGCGAT-GC----ACGA--TTTTGGCGAAAATTTTACAAAAACTG
193 CGCGTTTTTAGCCAAAAACC-GTGATGGCTAGTAC-ACCCTTT--CG-GAA--TT-CAAAAACAG
* ** * * * *
21509 ACCCAA-AATTTTTTTCCTCAATTCATTGCGA-GA-A--C-----AATGTATAATTAAACGCAAA
250 ACCCAAGAA-GTTTTTCCTCAATTTTTTGCCACAATACTCAAAAAAATATATAATTCAACGC---
* *
21564 AAAAAAAACTG
311 CAAAAAAATTG
* * * * * * *
21575 AAGAGTTTTTTACTCTTCTAATATCGCTTTTTCCATTTTTTTCCCG-ATTTTTTTCTAATTAAAT
1 AAG-GGTTTTCACGCTTTTAATATTG-TTTTTCCA-TTTTTT-CTGAATTTATTTCTAATTAAAT
* * * * *
21639 CGAAACAAGATTCATATGCTCGTAATAACAAATCCTTAAAACCAATGCGGCTGAGATTTGGTTTG
62 CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAG
** * * * * * * *
21704 AAAAAATATAGATATATCAAAGAGTCTTTACGCCAAAAATCATTG-AAATTGAGCCGAG-GCTAC
127 -ATGAATATAGATATTTCAAGGTGTCTTTATGCCAAAAATCA-TGCAAACTGAGCCGAGATC-CC
* * * * * * *
21767 -ATATGTGTTTTTAGCAAAAAACCGTGATGGTTGGTACACGCTTTCGGCTAAAATTTTGCAAAAA
189 GAAACGCGTTTTTAGCCAAAAACCGTGATGGCTAGTACACCCTTTCGG----AA--TT-CAAAAA
** **
21831 TTGATCTGAA-AAGTTTTTCCTCAATTTTTTGCCACAATA--CAAAAATATATATATAATTCAAC
247 CAGA-CCCAAGAAGTTTTTCCTCAATTTTTTGCCACAATACTCAAAAA-A-ATATATAATTC-A-
*
21893 ACGCCAAAAATATTG
307 ACGCCAAAAAAATTG
* *
21908 ACGGGCTTTTCACG-TTTCTAATATTGTTTTTCCATTTTTTTTCTGAATTAATTTCTAATTAAAT
1 AAGGG-TTTTCACGCTTT-TAATATTGTTTTTCCA--TTTTTTCTGAATTTATTTCTAATTAAAT
* * * *
21972 CAAAACAAGATTCAGATGCTCATAAAAACAGATCCTTAAATCCAAT-TGGACTGAGATTTGGTTT
62 CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG-CTGAGATTTGGTTA
* * * * * * *
22036 GATGAATATAGATATTTCAAGGAGTCTTTATACTAAAAATCATGCAAATTGAGCCGGGATTCCGG
126 GATGAATATAGATATTTCAAGGTGTCTTTATGCCAAAAATCATGCAAACTGAGCCGAGATCCCGA
* * * *
22101 AACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGCTTTCGGTTAAAATTTTGCAAAAACT
191 AACGCGTTTTTAGCCAAAAACCGTGATGGCTAGTACACCCTTTCGG----AA--TT-CAAAAACA
* *
22166 GACCCTAGAAGTTTTTCCTCAATTTTTTTGCCGCAATACTCAGAAAAAATATATAATTCAACG-C
249 GACCCAAGAAGTTTTTCCTCAA-TTTTTTGCCACAATACTCA-AAAAAATATATAATTCAACGCC
22230 AAAAAAATTG
312 AAAAAAATTG
** * *
22240 AAGGG-TTTCACGCTTTTAATATCCTTTTTCTATTTTTTCTAAATTTATTTCTAATTAAATCGAA
1 AAGGGTTTTCACGCTTTTAATATTGTTTTTCCATTTTTTCTGAATTTATTTCTAATTAAATCGAA
* * *
22304 ATAAGATTCAGATTCTTGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGA
66 ACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGA
* * *
22369 ATATAGATATTTCAAGGTGTCTTTATGCCAAAAATCATGCAAACCTGTGTCGAG-TCCCCGAAAT
131 ATATAGATATTTCAAGGTGTCTTTATGCCAAAAATCATGCAAA-CTGAGCCGAGAT-CCCGAAAC
* * *
22433 GCGTTTTTAGCTAAAAACCGTGATGGCTAGTACCCCCTTTCGG-A-T-AAAAACAGACCCAATAA
194 GCGTTTTTAGCCAAAAACCGTGATGGCTAGTACACCCTTTCGGAATTCAAAAACAGACCCAAGAA
*
22495 -TTTTTTCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTG
259 GTTTTTCCTCAATTTTTTGCCACAATACTCA-AAAAAATATATAATTCAACGCCAAAAAAATTG
* * * *
22558 AAGGGTTTTCTCGCTCTTAATATTGTTTTTCCATTTTTTCCGAATTTATTTCT-TTTCAAATCGA
1 AAGGGTTTTCACGCTTTTAATATTGTTTTTCCATTTTTTCTGAATTTATTTCTAATT-AAATCGA
* ** *
22622 AACAAGATTCAGATGCCCGTAAAAACAAATCCTTAAATCTGATGTGGCTGAGAATTT-GTGAGAT
65 AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG-ATTTGGTTAGAT
* * * * *
22686 GAATACAGATATTTCAAGGTGACTTAATGCCAAAAACCAAGCATAACTGAG
129 GAATATAGATATTTCAAGGTGTCTTTATGCCAAAAATCATGCA-AACTGAG
22737 TCGTTTGCAA
Statistics
Matches: 961, Mismatches: 147, Indels: 104
0.79 0.12 0.09
Matches are distributed among these distances:
315 3 0.00
316 17 0.02
317 45 0.05
318 124 0.13
319 207 0.22
320 9 0.01
321 1 0.00
322 3 0.00
323 2 0.00
324 4 0.00
325 33 0.03
326 6 0.01
327 2 0.00
328 125 0.13
329 52 0.05
330 20 0.02
331 5 0.01
332 78 0.08
333 178 0.19
334 24 0.02
335 12 0.01
336 7 0.01
337 4 0.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (321 bp):
AAGGGTTTTCACGCTTTTAATATTGTTTTTCCATTTTTTCTGAATTTATTTCTAATTAAATCGAA
ACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGA
ATATAGATATTTCAAGGTGTCTTTATGCCAAAAATCATGCAAACTGAGCCGAGATCCCGAAACGC
GTTTTTAGCCAAAAACCGTGATGGCTAGTACACCCTTTCGGAATTCAAAAACAGACCCAAGAAGT
TTTTCCTCAATTTTTTGCCACAATACTCAAAAAAATATATAATTCAACGCCAAAAAAATTG
Found at i:22966 original size:267 final size:265
Alignment explanation
Indices: 22493--22971 Score: 639
Period size: 267 Copynumber: 1.8 Consensus size: 265
22483 CAGACCCAAT
* ** **
22493 AATTTTTTCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTG
1 AATTTTTTCTCAAATCCTTGCCACAATACTCATAAAAAATATATAATTCAACAACAAAAAAATTG
* * * * *
22558 AAGGGTTTTCTCGCTCTTAATATTGTTTTTCCATTTTTTCCGAATTTATTTCTTTTCAAATCGAA
66 AAGGGTTTTCACGCTCTCAATATCGTTTTCCCATTTTTTCCGAATTTATTTCTATTCAAATCGAA
* ** *
22623 ACAAGATTCAGATGCCCGTAAAAACAAATCCTTAAATCTGATGTGGCTGAGAATTTGTGAGATGA
131 ACAAGATTCAGATGCCCGTAAAAACAAATCCATAAATCCAAAGTGGCTGAGAATTTGTGAGATGA
* *
22688 ATACAGATATTTCAAGGTGACTTAATGCCAAAAACCAAGCATAACTGAGTCGTTTGCAAAAATTG
196 ATAAAGATATTTAAAGGTGACTTAATGCCAAAAACCAAGCATAACTGAGTCGTTTGCAAAAATTG
22753 ATCCG
261 ATCCG
*
22758 AATTTTTTCCTCAAATCCTTGCCACAGTACT-A-AAAAATATATATAATTCAACAACAAAAAAAT
1 AATTTTTT-CTCAAATCCTTGCCACAATACTCATAAAAA-ATATATAATTCAACAACAAAAAAAT
*
22821 TGAAGTGTTTTCCACGCT-TCCAATATCGTTTTCCCATTTTTTTCC-AACTTTATTTCTAATT-A
64 TGAAGGGTTTT-CACGCTCT-CAATATCGTTTTCCCA-TTTTTTCCGAA-TTTATTTCT-ATTCA
* *
22883 AATCGAAACAAGATTCAGATGCTCGTAAAAATAAATCCATAAATCCAAAGTGGCTGAG-ATTTGA
124 AATCGAAACAAGATTCAGATGCCCGTAAAAACAAATCCATAAATCCAAAGTGGCTGAGAATTTG-
*
22947 TTAGATGACA-AAAGATATTTAAAGG
188 TGAGATGA-ATAAAGATATTTAAAGG
22972 AGTCTCAGCG
Statistics
Matches: 184, Mismatches: 21, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
264 5 0.03
265 43 0.23
266 43 0.23
267 90 0.49
268 3 0.02
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (265 bp):
AATTTTTTCTCAAATCCTTGCCACAATACTCATAAAAAATATATAATTCAACAACAAAAAAATTG
AAGGGTTTTCACGCTCTCAATATCGTTTTCCCATTTTTTCCGAATTTATTTCTATTCAAATCGAA
ACAAGATTCAGATGCCCGTAAAAACAAATCCATAAATCCAAAGTGGCTGAGAATTTGTGAGATGA
ATAAAGATATTTAAAGGTGACTTAATGCCAAAAACCAAGCATAACTGAGTCGTTTGCAAAAATTG
ATCCG
Found at i:26302 original size:322 final size:318
Alignment explanation
Indices: 22758--26562 Score: 3484
Period size: 322 Copynumber: 11.8 Consensus size: 318
22748 AATTGATCCG
* ** * **
22758 AATTTTTTCCTCAAATCCTTGCCACAGTACT-A-AAAAATATATATAATTCAACAACAAAAAAAT
1 AATTTTTT-CTCAATTTTTTGCCACAATACTCAGAAAAA-ATATATAATTCAACGCCAAAAAAAT
* * * *
22821 TGAAGTGTTTTCCACGCTTCCAATATCGTTTTCCCATTTTTTTCC-AACTTTATTTCTAATTAAA
64 TGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCA--TTTTTCCGAA-TTTATTTCTAATTAAA
* * * *
22885 TCGAAACAAGATTCAGATGCTCGTAAAAATAAATCCATAAATCCAAAGTGGCTGAGATTTGATTA
126 TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTA
* * * *
22950 GATGACA-AAAGATATTTAAAGGAGTC-TCA-GCGCAAAAAATCATGCAAAA-TAGAGCCGTGGC
191 GATGA-ATATAGATATTTCAAGGAGTCTTTATGC-C-AAAAATCATGCAAAACT-GAGCCGGGGC
* * * *
23011 CTCAAAACGCGTTCTTAG-TACAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAACCTTACC
252 C-CGAAACGCGTTTTTAGCCA-AAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTTACC
23075 CGAA
315 CGAA
* * * *
23079 AAGTTTTTTCTAAAGTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACGCCAAAAAAGTT
1 AA-TTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATT
* ** * * * *
23144 GACGGACTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTTTTAATTAGATC
65 GAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCA--TTTTTCCGAATTTATTTCTAATTAAATC
* * * *
23209 GAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAATATGGCTGGGATTTGGCTAGA
128 GAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGA
* * *
23274 TGAATATAGATATTTCAAGGACTCTTTCTGCAAAAATATCATGCAAAACTGAGCCGGGGCCCCGA
193 TGAATATAGATATTTCAAGGAGTCTTTATGCCAAAA-ATCATGCAAAACTGAGCCGGGG-CCCGA
* * * **
23339 AACGTGTTTTTAGCCCAAGAACCGTGATTGTTAGTACACGATTTCGG-TAAAAA-TTGA-CTTAA
256 AACGCGTTTTTAG-CCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTT-ACCCGAA
* * * * *
23401 ATTTTTTTTTTTGGAATTTTTTGCCACAATACTCATAAAAAATATATAATTCAAAG-CAAAAAAG
1 A--ATTTTTTCT-CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAA-
* *
23465 ATTGAAGGGTCTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTTAATTCTAATTAAA
62 ATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTCCGAATTTATTTCTAATTAAA
* *
23530 TCGAAACAAGTTTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT-ACTTGAGATTTGGTT
126 TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC-TGAGATTTGGTT
* * * * * *
23594 AGATGAATATAGACATTTCAAGGAATCTTTATGCC-AAAACCATG-AAAAGTTGAGTCGAGGCCC
190 AGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAA-CTGAGCCGGGGCCC
* ** * * *
23657 GAAACACG-TTTTAGCCAAAAACAATGATAGTTAGTACCCGATTTCGGCTAAAAACTGACCCCGA
254 GAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTTA-CCCGA
23721 A
318 A
* * * *
23722 AATTCTTTTCACAGTTTTTTGCCACAATACTCATAAAAAATATATTATTCAACGCCAAAAAAATT
1 AATT-TTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATT
*
23787 GAAGGGTTTTTTCACGCTTCTAATATCGTTTTTCTATTTTTCCGAATTTATTTCTAATTAAATCG
65 GAAGGG-TTTTTCACGCTTCTAATATCGTTTTTCCATTTTTCCGAATTTATTTCTAATTAAATCG
* * * * * *
23852 AAACAAGATTCAGATGCTCATGAAAACAAATCCTTAGATCCAATGTAGTTGAGATTTGGTAAGAT
129 AAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGAT
* * * *
23917 GAATATAGATATTTAAAGGAGTCTTTCTGCCAAAAATCTTGCAAAACTGAGCTGGGGCCCCGAAA
194 GAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGCCGGGG-CCCGAAA
* * * *
23982 CACGTTTTTAGCCAAAAACTGTGATGGTTAGTGCACGATTTCGGC-AAAAAATTGACCCGAA
258 CGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTT-ACCCGAA
* * * * * * *
24043 AAGTTTTATCTCAATTTTTTACCACAATA-TTAGGAAAAAATATATAATTAAATGCTAAAAATAT
1 AA-TTTTTTCTCAATTTTTTGCCACAATACTCA-GAAAAAATATATAATTCAACGCCAAAAAAAT
** ** * * * *
24107 TGGCGGGCGTTTCACGTTTCTAATATCGTTTTTCTATTTTTTTTCCGAAATAATTTCTAATTAAA
64 TGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCA---TTTTTCCGAATTTATTTCTAATTAAA
* * * * ** * ** *
24172 TCGAAACACGATTTAGATCCTCCTAAAGGCAAATCCTTATATCCTAA-GTAACTGAGATTTAGTT
126 TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC-AATGTGGCTGAGATTTGGTT
* * * * * *
24236 CGATTAATATAGCTATTTCAAGGTGT-TTT-TGCGTAAAAAAATCATGCAAAATTGAGCCGGGGC
190 AGATGAATATAGATATTTCAAGGAGTCTTTATGC---CAAAAATCATGCAAAACTGAGCCGGGGC
* ** * * ** * *
24299 TCCGGAACGCGTTTTTAGCCAAAAACCGTGATAATCATGCTTTCGGCTAAAATTT-TGCAAAAAA
252 -CCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTA-G---T--AC-ACGATTTCGGCTAAAAA
24363 CTTACCC-AA
309 CTTACCCGAA
* * * *
24372 GAAGTTTGTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATAGAAGTCAAACGCCAAAAAAA
1 -AA-TTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTC-AACGCCAAAAAAA
* * ** *
24437 TTGAAGGTTTTTTCACGCTTCCAATATCGTTTTTCCATTTTT-TTAATTTAGTTCTAATTAAATC
63 TTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTCCGAATTTATTTCTAATTAAATC
* * *
24501 G-TACCAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAAATTTGGTTAGA
128 GAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGA
* * * *
24565 TGAATATAGATATTTCAAGGAATCTTTATGCCAAAAACCATGCAAAACTGAGTCGAGGCCCCGAA
193 TGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGCCG-GGGCCCGAA
* * * **
24630 ACGCGTTATTAGCTAAAAACAC-TGATGGTTAGTAC-CTGATTTTGGCTAAAAACCGACCC-AA
257 ACGCGTTTTTAGCCAAAAAC-CGTGATGGTTAGTACAC-GATTTCGGCTAAAAACTTACCCGAA
* *
24691 AA----TT-T---TTTTTTGCCACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTG
1 AATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTG
* * *
24748 AAGGGTTTTTCACGCTTCTAATATTGTTTTTCCATTTTTTCTGAATTTATTTTTAATTAAATCGA
66 AAGGGTTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTCCGAATTTATTTCTAATTAAATCGA
* * *
24813 AACAAGATTCAGATGCTCGTAAAACCAAATCCTTAAATCCAATGTGGTTGAGACTTGGTTAGATG
130 AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATG
* ** * * * *
24878 AATATAGATATTTCAAGGAGACTTTCGGCC-AAAATAAGGAAAAACTGAGCCGAGGCCCCGAAAC
195 AATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGCCG-GGGCCCGAAAC
* * *** * * * * * *
24942 ACGTTTTTAGCCACAATTTG-GTTAGAT-GTACACGATTTCGGTTAAAAACTGACCAGGAA
259 GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTTACC-CGAA
* * * * *
25001 AGTTTTTTCTCAATTTTTTGCCACAATACTC-GGAAAAATATATAATTAAATGCCAAAAAGATTG
1 AATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTG
* * * * * *
25065 ACGGGCTTTTCATGCCTCTAATATCGTTTTCCCATTGTTTTCCGAATTAATTTCTAATTAAATCG
66 AAGGGTTTTTCACGCTTCTAATATCGTTTTTCCA-T-TTTTCCGAATTTATTTCTAATTAAATCG
* * * *** * ** *
25130 AAATAAGATTCAGATGCTTGAAAAAACAAATCCTTTTGTCCAATGTGCCTGAGATTTATTTCGAT
129 AAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGAT
** * * * *
25195 GAATATAGATATTTCAAGGAGTCTTTGCGCCAAAATTCATGCAAAATTGAGCCGGGGCTCTAGAA
194 GAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGCCGGGGCCCGA-AA
** *
25260 CGCGTTTTTAGCCAAAAACCGTGAAAGTTAGTACACGATTTCGGCTAAAATTTTTCATAAACTGA
258 CGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCT---A------A-AAACTTA
25325 CCCGAA
313 CCCGAA
* * * * *
25331 AAGTTTTTCCTCAATTTTTGGCCATAATACTTAGAAAAAATATATAATTCAAAGCCAAAAAAAAA
1 AA-TTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCC---AAAAAA
25396 ATTGAAGGG-TTTTCACGC-TCTTAATATCGTTTTTCCAATTTTTCCCGAATTTATTTCTAATTA
62 ATTGAAGGGTTTTTCACGCTTC-TAATATCGTTTTTCC-ATTTTT-CCGAATTTATTTCTAATTA
* * ** * * * *
25459 AATCAAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTCTATCCAATATGACTAAGATTTGAT
124 AATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGT
* * * * * *
25524 TTGATAAATATAGATATTTGAAGGAGTCTTAACGCCAAAAATCATGC-AAATTGAGCCGGGGCTC
189 TAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGCCGGGGC-C
* * * * * * * *
25588 CGTAACGCGTTTTTAGCAAAAAAAGCCCGTGACGGTAAGTAAATGCTTTTGGCTAAAAGTTTCCA
253 CGAAACGCGTTTTTAGC-CAAAAA--CCGTGATGGTTAGTACACGATTTCGGC--------T--A
25653 AAAACTTACCCGAA
305 AAAACTTACCCGAA
* * *
25667 AACTTTTTCCTCAATTTTTTGCCATAATACTCTA-AAAAAATATATAATTCAAAGCCAAAAAAAT
1 AA-TTTTTTCTCAATTTTTTGCCACAATACTC-AGAAAAAATATATAATTCAACGCCAAAAAAAT
* *
25731 TGAAGGG-TTTTCACGC-TCTTAATTTCGTTTTTCCAATTTTTTTCCCAAATTTATTTCTAATTA
64 TGAAGGGTTTTTCACGCTTC-TAATATCGTTTTTCC-A--TTTTT-CCGAATTTATTTCTAATTA
** * * *
25794 AATAAAAACAAGATTCAGATG--C-T-------AATCCTTATATCCAATGCGGTTGAGATTTGGT
124 AATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGT
* * * * * * *
25849 TTGATAAATATAGATATTTGAAGGAGTGTTTACGCCAAAAATCATGC-AAATTGAGCCGGAGCTC
189 TAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGCCGGGGC-C
* * * *
25913 CGGAATGCGTTTTTAGCCAAAAACCGTGATGCTTAGTAAAC-ACTTTCGGCTAAAAGTTTCCAAA
253 CGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGA-TTTCGGC--------T--AAA
25977 AACTTACCCGAA
307 AACTTACCCGAA
* * * * *
25989 AATTTTTTACTCAATTTCTTGCCATAATACTCA-AAAAATTTATATAACATCAACGCCAAAAAGA
1 AATTTTTT-CTCAATTTTTTGCCACAATACTCAGAAAAA-ATATATAA-TTCAACGCCAAAAAAA
* *
26053 TTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTTCCATTTTTCTGCATTTATTTCTAATTAAAT
63 TTGAAGGGTTTTTCACGCTTCTAATATCG-TTTTTCCATTTTTCCGAATTTATTTCTAATTAAAT
* ** *
26118 CGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATAAAATGTGGCTGAGATTTGGTTGG
127 CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAG
* * ** *
26183 ATGAATATAGATATTCCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTTGAGGCCCTGA
192 ATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGCCGGGGCCC-GA
* * * *
26248 AACGCGTTTTTAGCCAAAAACTGTGATGGTTAG-ATCTCGATTTCGGCTAAAAACTGACCCGGGA
256 AACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTA-CACGATTTCGGCTAAAAACTTACCC-GAA
* * * * * * * * *
26312 ATTTTTTTCTCAGTTTTTTACCATAAAACTCA-TAAAAATATATAATTCAATGCCCAAAAGATTG
1 AATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTG
* *
26376 AAGGGTTTTTCACGCTTCTAATATCGTTTTTTCCATTTTTCCGAATTTATTTTTTAGTTAAATCG
66 AAGGGTTTTTCACGCTTCTAATATCG-TTTTTCCATTTTTCCGAATTTA-TTTCTAATTAAATCG
* * * * * * * *
26441 AAACAAAATTTAGATGCTCGTAAAAATAAATCTTTAAATCCATTGTGGTTGAGATTTGATTGGAT
129 AAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGAT
* * * *
26506 GAATGTAGATATTTCAAGGAGTCTTTCTGCCAAAAATAATGCAAAACTAAGCCGGGG
194 GAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGCCGGGG
Statistics
Matches: 2891, Mismatches: 457, Indels: 272
0.80 0.13 0.08
Matches are distributed among these distances:
308 68 0.02
309 43 0.01
310 64 0.02
311 85 0.03
312 1 0.00
313 1 0.00
314 2 0.00
315 1 0.00
317 59 0.02
318 162 0.06
319 225 0.08
320 161 0.06
321 304 0.11
322 328 0.11
323 296 0.10
324 184 0.06
325 162 0.06
326 69 0.02
327 21 0.01
328 9 0.00
329 2 0.00
330 52 0.02
331 157 0.05
332 70 0.02
333 80 0.03
334 141 0.05
335 57 0.02
336 83 0.03
337 2 0.00
343 1 0.00
344 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (318 bp):
AATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTG
AAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTCCGAATTTATTTCTAATTAAATCGAA
ACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGA
ATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGCCGGGGCCCGAAACGC
GTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTTACCCGAA
Done.