Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022435.1 Corchorus olitorius cultivar O-4 contig22468, 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: 39842
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:744 original size:332 final size:328
Alignment explanation
Indices: 125--2076 Score: 1814
Period size: 332 Copynumber: 5.9 Consensus size: 328
115 GCCGAAATCG
* * * * * * *
125 CGGTTTTTGGCTAAAAATGCGTTTCGGGGCACCGGCTTAATTTTGCAAGATTTTTGGCGCCGAGA
1 CGGTTTTTGGCTAAAAACGCGTTCCGGGAC-CCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGA
* * *
190 CTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCTACATTGGATTTAAGCATTTATTTTT
65 CTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
* * * *
255 ATGAGCATCTGAATCTTTTTTCGATTTAATTAGAAATTAATTCAGAAAAATATAAAAAACGATAT
130 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATGAAAAACGATAT
* * * * * * *
320 TGAAAGCGTGAAGAGTCCTCCAATAC-TTTTGACGTTAAATTATATATATTTTATGAGTATTTTA
195 TAAAAGCGTGAAAAGT-CTTCAAT-CTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTGA
* * *
384 GCCAAAAATTGATGGAAAAATTTTTCAGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACT
258 GCCAAAAATTGA-GGAAAAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT
449 ATCCATCA
322 A-CCATCA
* * * * ** * * *
457 CGATTTCTAGCTAAAAACACGTTTTGGGACCCTGGCTTAGTTTTGCATGATTTTTGGCACCGAGA
1 CGGTTTTTGGCTAAAAACGCGTTCCGGGACCC-GGCTCAGTTTTGCATGATTTTTGGCGCCAAGA
* *
522 CTCCTTGAAATATCTATATTCATCAAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTT
65 CTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
* * *
587 ACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATT-ATGAAAAACATGAAAAGCGATA
130 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCA-GAAAAAAATGAAAAACGATA
* ** * * *
651 TTAAAAGCGTGAAAAGTCATCCTTCTTTTTGGCCTTTAATTATATATATATTCTATGAGTATTGT
194 TTAAAAGCGTGAAAAGTCTTCAATCTTTTTGGCGTTGAATTATATAT-T-TTTTATGAGTATT-T
* * * * * * *
716 GA-CTAAAAATTGAGGAGAAATATTTCAGGTTAATTTTTGCAAAATTTTACCCGAGAT--TGT-T
256 GAGCCAAAAATTGAGGAAAAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC
777 TACCATCA
321 TACCATCA
* * * * * ** *
785 CTGTTTTTTGGCT---AAC-CG----AGGTCCCGGGTCAGTTTTGCATGATTTTTGGTGGAAAAA
1 C-GGTTTTTGGCTAAAAACGCGTTCCGGGACCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGA
* * * * *
842 CTCCTT-AAATATATATATACATCTAACCAAATCTTAACCACATTGGATTTAAGGATTTGTTTTT
65 CTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
* * * *
906 ACGAGCATTTGAAT-TATGTTTCGATTTAATTAAAAATTAATT-TGAAAAAAAAGGAAAAACGAT
130 ACGAGCATCTGAATCT-TGTTTCGATTTAATTAGAAATTAATTCAG-AAAAAAATGAAAAACGAT
* * * * * * *
969 ATTAGAAGCGTGAGAAGCCCTTCAATCTTTTTGACTTTCAATTATATAATTTTTATGAGTAGTAT
193 ATTAAAAGCGTGAAAAG-TCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTA-T-T
* * * * * *
1034 TGTGGCTAAAAATTGA-GAAAAATATTT-TGGTTCAATTTTTGCAAAATTTTAGCCAAAATCGTT
255 TG-AGCCAAAAATTGAGGAAAAATCTTTCAGG-TCAATTTTTGCAAAATTTTAGCCGAAATCGTG
* *
1097 TACCATCAT-A
318 TACTACCATCA
* * * * * * *
1107 TGGTTTTTTTTTTTTTGCTAAAAACGCATTACGGAACCCTAGG-TCAGTTTTGCATGATTATTGC
1 CGG-------TTTTTGGCTAAAAACGCGTTCCGGGACCC--GGCTCAGTTTTGCATGATTTTTGG
* * * * ** *
1171 CGTCAAGACTCCTTAAAATATATCTTTATTCATCTAATCAAATCTCATCCGTATTGTATTTAAGG
57 CGCCAAGACTCCTT-GAA-ATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGG
** * * **
1236 ATTTGTTTTTACGAGTTTCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAATAAAATA
120 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAA-AAAAT-
* *
1301 GAAAAAAAAACGATATTAGAAA-CGTGAAAAAGGTTTTCAATTTTTTTTGG-GTTGAATTATATA
183 G----AAAAACGATATTA-AAAGCGTG-AAAA-GTCTTCAA-TCTTTTTGGCGTTGAATTATATA
* * * * *
1364 TTTTTTATGAGTATTTTAGCTAGAAA-TGAAGGAAAAATCTTTCAGGGCCATTTTTGCAAAA-TT
240 TTTTTTATGAGTATTTGAGCCAAAAATTG-AGGAAAAATCTTTCAGGTCAATTTTTGCAAAATTT
*
1427 TAGCCGAAATCGTGTACGGACCATCA
304 TAGCCGAAATCGTGTAC-TACCATCA
* * * * *
1453 CGGTTTTCGGCAAAAAACGCGTTCCGGGGCCCAGCTCAGTTTTGCATGATTTTTGGTGCCAAGAC
1 CGGTTTTTGGCTAAAAACGCGTTCCGGGACCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGAC
* *
1518 TCCTTGAAATATCTATATTCATTTAA-CGAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTT
66 TCCTTGAAATATCTATATTCATCTAATC-AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
* *
1582 ACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATTAATTCA-AAAAAAATAGAAAAAACAAT
130 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAAT-G-AAAAACGAT
* * * * * ** *
1646 ATTAGAAGCATTAAAAGCCCTTCAATATTTTTGATGTCGAATTATATATTTTTTATGAGTACTTT
193 ATTAAAAGCGTGAAAAG-TCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTA-TTT
* * * **
1711 -AGCCAAAATTTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAATCGAAATCGTGTAC
256 GAGCCAAAAATTGAGGAAAAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC
*
1775 TAACCATTA
321 T-ACCATCA
** * **
1784 CGGTTTTTGGCTAAAAACGCGTTACAAGG-CCACGACTCTA-TTTTGCATGATTTTTTACGCCAA
1 CGGTTTTTGGCTAAAAACGCGTT-CCGGGACC-CGGCTC-AGTTTTGCATGATTTTTGGCGCCAA
* *
1847 GACT-C--GAAATATCT-TCATTCATCTAATTAAATCTCAACCACATTGGATTTAAGGATTTGTT
63 GACTCCTTGAAATATCTAT-ATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTT
* * *
1908 TTTATGTGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACG
127 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAA-ATGAAAAACG
* * * * **
1973 ATATTAAAAGTGTGTAAAGTCCTGCAATCTTTTTTGCGTTGAATTATATATGATTTATGAGTATT
191 ATATTAAAAGCGTGAAAAGT-CTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATT
**
2038 TTTGCCAAAAATTGAGGAAAAATCTTTCAGGTC-ATTTTT
255 TGAGCCAAAAATTGAGGAAAAATCTTTCAGGTCAATTTTT
2077 ACCATCATGG
Statistics
Matches: 1322, Mismatches: 225, Indels: 150
0.78 0.13 0.09
Matches are distributed among these distances:
318 11 0.01
319 125 0.09
320 88 0.07
321 17 0.01
322 3 0.00
323 4 0.00
325 2 0.00
326 3 0.00
328 25 0.02
329 191 0.14
330 81 0.06
331 96 0.07
332 252 0.19
333 23 0.02
334 9 0.01
335 4 0.00
336 88 0.07
337 32 0.02
338 33 0.02
339 24 0.02
340 84 0.06
341 6 0.00
342 1 0.00
343 2 0.00
344 25 0.02
345 29 0.02
346 23 0.02
347 33 0.02
348 8 0.01
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Consensus pattern (328 bp):
CGGTTTTTGGCTAAAAACGCGTTCCGGGACCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGAC
TCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTA
CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATGAAAAACGATATT
AAAAGCGTGAAAAGTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTGAGCC
AAAAATTGAGGAAAAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTACCA
TCA
Found at i:9261 original size:363 final size:363
Alignment explanation
Indices: 8596--9328 Score: 1448
Period size: 363 Copynumber: 2.0 Consensus size: 363
8586 CAGTGTTTTT
8596 AAGTCTTCGGAGTATTGACTACGTGTTTAGAATTTCAACCCACAAAATGGGTTTAGAAACTTTCC
1 AAGTCTTCGGAGTATTGACTACGTGTTTAGAATTTCAACCCACAAAATGGGTTTAGAAACTTTCC
8661 ATACATTGACGATAACGACTTAACGACATGGTGGAGTAGTGGGGCATGAAACTAGAAAAAAGGTG
66 ATACATTGACGATAACGACTTAACGACATGGTGGAGTAGTGGGGCATGAAACTAGAAAAAAGGTG
8726 AAAGGAAATTAATAAGGCTTTGATTTTAAGTTTGATTTCGATTGCAGTAATATAAATCTTGTTTG
131 AAAGGAAATTAATAAGGCTTTGATTTTAAGTTTGATTTCGATTGCAGTAATATAAATCTTGTTTG
8791 GGGAGGAAAGAATTAAATATATTTTCCAGAGTAATTTAGGAAATTCAACATATCTTTTGATTGTG
196 GGGAGGAAAGAATTAAATATATTTTCCAGAGTAATTTAGGAAATTCAACATATCTTTTGATTGTG
8856 GAATATTGTTCGAAGGATGGGTTAAGTTTCAGATTTCCAGGACTTGTGGAAAAGATTGCACCGCA
261 GAATATTGTTCGAAGGATGGGTTAAGTTTCAGATTTCCAGGACTTGTGGAAAAGATTGCACCGCA
8921 GGGACACTTCCATTCCATGTCCCACATTGTGTGGAATG
326 GGGACACTTCCATTCCATGTCCCACATTGTGTGGAATG
8959 AAGTCTTCGGAGTATTGACTACGTGTTTAGAATTTCAACCCACAAAATGGGTTTAGAAACTTTCC
1 AAGTCTTCGGAGTATTGACTACGTGTTTAGAATTTCAACCCACAAAATGGGTTTAGAAACTTTCC
*
9024 ATACATTGACGATAACGACTTAACGACATGGTGGAGTAGTGGGGCATGAAACTAGAGAAAAGGTG
66 ATACATTGACGATAACGACTTAACGACATGGTGGAGTAGTGGGGCATGAAACTAGAAAAAAGGTG
9089 AAAGGAAATTAATAAGGCTTTGATTTTAAGTTTGATTTCGATTGCAGTAATATAAATCTTGTTTG
131 AAAGGAAATTAATAAGGCTTTGATTTTAAGTTTGATTTCGATTGCAGTAATATAAATCTTGTTTG
9154 GGGAGGAAAGAATTAAATATATTTTCCAGAGTAATTTAGGAAATTCAACATATCTTTTGATTGTG
196 GGGAGGAAAGAATTAAATATATTTTCCAGAGTAATTTAGGAAATTCAACATATCTTTTGATTGTG
9219 GAATATTGTTCGAAGGATGGGTTAAGTTTCAGATTTCCAGGACTTGTGGAAAAGATTGCACCGCA
261 GAATATTGTTCGAAGGATGGGTTAAGTTTCAGATTTCCAGGACTTGTGGAAAAGATTGCACCGCA
9284 GGGACACTTCCATTCCATGTCCCACATTGTGTGGAATG
326 GGGACACTTCCATTCCATGTCCCACATTGTGTGGAATG
*
9322 AATTCTT
1 AAGTCTT
9329 GTGCAATTCC
Statistics
Matches: 368, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
363 368 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (363 bp):
AAGTCTTCGGAGTATTGACTACGTGTTTAGAATTTCAACCCACAAAATGGGTTTAGAAACTTTCC
ATACATTGACGATAACGACTTAACGACATGGTGGAGTAGTGGGGCATGAAACTAGAAAAAAGGTG
AAAGGAAATTAATAAGGCTTTGATTTTAAGTTTGATTTCGATTGCAGTAATATAAATCTTGTTTG
GGGAGGAAAGAATTAAATATATTTTCCAGAGTAATTTAGGAAATTCAACATATCTTTTGATTGTG
GAATATTGTTCGAAGGATGGGTTAAGTTTCAGATTTCCAGGACTTGTGGAAAAGATTGCACCGCA
GGGACACTTCCATTCCATGTCCCACATTGTGTGGAATG
Found at i:11706 original size:333 final size:328
Alignment explanation
Indices: 10094--12044 Score: 1621
Period size: 333 Copynumber: 5.9 Consensus size: 328
10084 TCCTTTTGGC
** * * ** *
10094 ACTAACCATCATTGTTTTAGGCTAAAAACGCGTTTCGGGGCCCCGACTCTGTTTTGCATGGTTTT
1 ACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTAAGTTTTGCATGATTTT
* * * * * *
10159 TGGTGCCGACACTCCTTGAAATATCCATACTCATCTAA-TAAAATCTTAGCCACATTGCATTTAA
66 TGGCGCCAAGACTCCTTGAAATAT-CATAATCATCTAACT--AATCTCAGCCACATTGGATTTAA
* * **
10223 AGATTTGTTTTTACGAGTATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATA
128 GGATTTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG--AAAATA
* *
10288 TGAAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAA-T-TATATATTT
191 TG-AAAAACGATATTAAAAGCATGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATATTT
* * * * *
10351 TATGAGTATTAT-GACTAAAAATTGA-GAAGATATCTTTCGGGTCAACTTTTGCAAAATTTTAGC
255 TATGAGTATTTTAG-CTAAAAATCGAGGAA-AAATATTTCGGGTCAATTTTTGCAAAATTTTAGC
*
10414 CGAAATCATGT
318 CGAAATCGTGT
* * * * * * * *
10425 AATAATCATCACGATTAATTTGGCT-AAAACGCGTTCCAGGG-CCCGGTTCAA-CTTTGAATGAT
1 ACTAACCATCACGGTT--TTTGGCTAAAAACGCGTTTCGGGGCCCCGGCT-AAGTTTTGCATGAT
* * * * * *
10487 TTTTGGCACTAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCCCA-AC-CATT-G--TT
63 TTTTGGCGCCAAGACTCCTTGAAATATC-ATAATCATCTAA-CTAATCTCAGCCACATTGGATTT
* ** ** * *
10547 ----A-------TTACAAATATTTGAATCATGTTTCGTTTTAATTAGAAATTAATTCAGAAAAAA
126 AAGGATTTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG--AAAA
* * * * * * ** *
10601 CAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTTGGTATTGAATTATATATTTT
189 TATGAAAAACGATATTAAAAGCATGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATATT
* * * * * * * *
10666 TTATGAGTATTGTGGCTAAAAATTGA-GAGAATATTTTTCTGGTCATTTTTTGTAAAATTTTAGC
254 TTATGAGTATTTTAGCTAAAAATCGAGGA-AAAATATTTCGGGTCAATTTTTGCAAAATTTTAGC
10730 CGAAATCGTGT
318 CGAAATCGTGT
* * * * *
10741 ACTAACCATCATTGTTTTTTTTTGCTAAAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCATGAT
1 ACTAACCATCA-CG--GTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTAAGTTTTGCATGAT
* * * *
10806 TTTTGGCATCGAA-ACTCCTCGAAATATC-T-AT-AT-T-A--AATCTCAGCCACATTGCATTTA
63 TTTTGGC-GCCAAGACTCCTTGAAATATCATAATCATCTAACTAATCTCAGCCACATTGGATTTA
** * *
10863 AGGATTTGTTTTTACGAGCATCTAAATCTTATTTTGATTTAATTAGAAATTAATTCAGAATAAT-
127 AGGATTTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAA-AATA
* * *
10927 TAGAAAAACGATATTAAAAGTGA-GAAAAGTCCTCCAATCTTTTTGGAGTTGAATTATATATATT
191 T-GAAAAACGATATTAAAAG-CATGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATATT
* ** ** * *
10991 TTATGAGTATTTTAGAC-AAATATTTAGGAAAAATATTTTTGGTCAATTATTGCAAAATATTAGC
254 TTATGAGTATTTTAG-CTAAAAATCGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGC
*
11055 CGAAATCATACGTT
318 CGAAATCGT--G-T
* * **
11069 AGTCGAA--ATCACGGTTTTTGGCTAAAAACGCGTTTCGAGGCCCCGG-TACAGCGTTGCATGAT
1 A--CTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTA-AGTTTTGCATGAT
* * *
11131 TTTTTGCGTCGAGACTCCTTGAAATAT-ATACATTCATCTAACTAAATCTCAGCCACATTGGATT
63 TTTTGGCGCCAAGACTCCTTGAAATATCATA-A-TCATCTAACT-AATCTCAGCCACATTGGATT
*** * * * * *
11195 TAAGGATTTG-TAAAACAAGTATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAT
125 TAAGGATTTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAT
** *
11259 AATAGGAAAAACGATATTGGAAGCATGAAAA-ACCTTCAATCTTTTTGGCGTTGAATTATATA-A
190 -AT--GAAAAACGATATTAAAAGCATGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATA
* * * * * *
11322 TTTTTATGAGTATTGTGGATAAAAA-CTGAGGAAATAA-CTTTCGAGTCAATTTTTGCAAAATTC
252 -TTTTATGAGTATTTTAGCTAAAAATC-GAGGAAA-AATATTTCGGGTCAATTTTTGCAAAATTT
11385 TAGCCGAAATCGTGT
314 TAGCCGAAATCGTGT
* * * * * *
11400 AATAATCATCACAGTTTTTTTGGCTAAAAATGCGTTCCGGGGCCCCGGCTAAGTTTTGCTTGATT
1 ACTAACCATCAC-G-GTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTAAGTTTTGCATGATT
* * * ** **
11465 TTTGGCGCCAAGACTCTTTGAGATATCCATAATCATTTAATCTAATCTCAGTTACATTGGATTGC
64 TTTGGCGCCAAGACTCCTTGAAATAT-CATAATCATCTAA-CTAATCTCAGCCACATTGGATTTA
* *
11530 AGAATTTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAACTAGAAATTAATTCAGAAAATAT
127 AGGATTTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAATAT
* * * *
11595 GAAAAACAATATTAAAAGCATGAAAAGTCCTCCAATCTTTTTGACGTTAAATTATATATATTTTA
192 GAAAAACGATATTAAAAGCATGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATATTTTA
*
11660 TGAGTATTTTAGCCAAAAATCGATGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGA
257 TGAGTATTTTAGCTAAAAATCGA-GGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGA
11725 AATCGTGT
321 AATCGTGT
* * * * * *
11733 ACTAACCATCACGGTTTTCGGTTAAAAACGCATTTCGGGG-CCTGACTCAGTTTTGCATGATTTT
1 ACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTAAGTTTTGCATGATTTT
** * * * *
11797 TGGTTCCGAGACTCCTTGAATAAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGAATT
66 TGGCGCCAAGACTCCTTG----AAATATC-ATAATCATCTAA-CTAATCTCAGCCACATTGGATT
* * *
11862 TAAGGA-TT-TTTTTACGAGTATCCAAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAA
125 TAAGGATTTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAATTAGAAATTAATTC-AGAAAA
* ** * * * *
11925 TATG-AAAA-GTTTATTAAAAGTGTGAAAAAGGCTTTCAGT-TTTTTGGGCGTTTAATTATATAT
189 TATGAAAAACG-ATATTAAAAGCATG-AAAAGTCCTTCAATCTTTTT-GGCGTTGAATTATATAT
* * * * *
11987 TTTTTATGAGTATTTTCA-CTAGAATTCGAGGAAAAATCTTTCGAGTCAATTTTTGCAA
251 ATTTTATGAGTATTTT-AGCTAAAAATCGAGGAAAAATATTTCGGGTCAATTTTTGCAA
12045 CCATCACGGT
Statistics
Matches: 1301, Mismatches: 232, Indels: 173
0.76 0.14 0.10
Matches are distributed among these distances:
310 6 0.00
311 1 0.00
312 4 0.00
313 1 0.00
314 47 0.04
315 54 0.04
316 81 0.06
317 10 0.01
318 15 0.01
319 39 0.03
320 3 0.00
322 1 0.00
324 4 0.00
325 170 0.13
326 43 0.03
327 3 0.00
328 7 0.01
329 8 0.01
330 40 0.03
331 114 0.09
332 163 0.13
333 258 0.20
334 203 0.16
335 26 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (328 bp):
ACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTAAGTTTTGCATGATTTT
TGGCGCCAAGACTCCTTGAAATATCATAATCATCTAACTAATCTCAGCCACATTGGATTTAAGGA
TTTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAATATGAAA
AACGATATTAAAAGCATGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAG
TATTTTAGCTAAAAATCGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCG
TGT
Found at i:12168 original size:971 final size:971
Alignment explanation
Indices: 11146--12904 Score: 2380
Period size: 971 Copynumber: 1.8 Consensus size: 971
11136 GCGTCGAGAC
* * *
11146 TCCTTGAAATATATACATTCATCTAACTAAATCTCAGCCACATTGGATTTAAGGATTTG-TAAAA
1 TCCTTGAAATATATACATTCATCTAACCAAATCTCAACCACATTAGATTTAAGGATTTGTTAAAA
* *
11210 CAAGTATCTGAATCATGTTTCGATTTAATTAGAA-ATTAATTCGGAAAATAATAGGAAAAACGAT
66 CAAGCATCTGAATCATGTTTCGATTTAATTAGAATA-TAATT-GGAAAA-AATAGGAAAAACAAT
* *
11274 ATTGGAAGCATGAAAA-ACCTTCAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTGT
128 ATTGGAAGCATGAAAAGACCTTCAATCTTTTTGACGTCGAATTATATAATTTTTATGAGTATTGT
* ** *
11338 GGATAAAAACTGAGGAAATAA-CTTTC-GAGTCAATTTTTGCAAAATTCTAGCCGAAATCGTGTA
193 CGATAAAAACCAAGGAAA-AATCTTTCGGA-TCAATTTTTGCAAAATTCTAGCCGAAATCATGTA
** * ** * **
11401 ATAA-TCATCACAGTTTTTTTGGCTAAAAATGCGTTCCGGGGCCCCGGCTAAGTTTTGCTTGATT
256 ATAACT-ATCACAG--TTTTCAGCTAAAAACGCGTTCCGGGG-CCCAACTAAGTTTTCCAAGATT
* * * * ** **
11465 TTTGGCGCCAAGACTCTTTGAGATATCCATAA-TCATTTAATC-TAATCTCAGTTACATTGGATT
317 TTTGGCGCCAAGACTCCTTGAAATATCCA-AATTCATCTAA-CAAAATCTCAGCGACATTAAATT
* *
11528 GCAGAATTTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAACTAGAAATTAA-TTCAGAAAA
380 GAAGAATTTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAACTAGAAATTAATTTCAAAAAA
* * *
11592 TATGAAAAACAATATTAAAAGCATGAAAAGTCCTCCAATCTTTTTGACGTTAAATTATATA-TAT
445 TAGGAAAAACAATATTAAAAGCATGAAAAGCCCTCCAATCTTTTTGACGTCAAATTATATATTAT
11656 TTTATGAGTATTTTAGCCAAAAATCGATGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAG
510 TTTATGAGTATTTTAGCCAAAAATCGA-GGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAG
* * * * **
11721 CCGAAATCGTGTACTAACCATCAC-G-GTTTTCGGTTAAAAACGCATTTCGGGGCCTGA-CTCAG
574 CCGAAATCGTCTACTAACCATCACAGTGTTTTCGGCTAAAAACGCATTACAGGGCCACAGCTCAG
* *
11783 TTTTGCATGATTTTTGGTTCCGAGACTCCTTGAATAAAATATCTATATTCATCTAATCAAATCTC
639 TTTTGCATAATTTTTGGTACCGAGACTCCTTG----AAATATCTATATTCATCTAATCAAATCTC
* * *
11848 AGCCACATTGAATTTAAGGA-TT-TTTTTACGAGTATCCAAATCTTGTTTCGATTTAATTAGAAA
700 AGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCCAAATCTTGTTTCAATTTAATTAAAAA
11911 TTAATTCAAAAAA-ATATGAAAAGTTTATTAAAAGTGTGAAAAAGGCTTTCAGTTTTTTGGGCGT
765 TTAATTCAAAAAATATATGAAAAGTTTATTAAAAGTGTGAAAAAGGCTTTCAGTTTTTTGGGCGT
11975 TTAATTATATATTTTTTATGAGTATTTTCACTAGAATTCGAGGAAAAATCTTTCGAGTCAATTTT
830 TTAATTATATATTTTTTATGAGTATTTTCACTAGAATTCGAGGAAAAATCTTTCGAGTCAATTTT
12040 TGCAACCATCACGGTTTTCGGCTAAAACCGCGTTCCGGGGGCCCGGCTCAGTTTTGCACGATTTT
895 TGCAACCATCACGGTTTTCGGCTAAAACCGCGTTCCGGGGGCCCGGCTCAGTTTTGCACGATTTT
12105 TGGTGCCAAGGT
960 TGGTGCCAAGGT
* * ***
12117 TCCTTGAAATATCTATATTCATCTAACCAAATCTCAACCACATTAGATTTAAGGATTTGTTTTTA
1 TCCTTGAAATATATACATTCATCTAACCAAATCTCAACCACATTAGATTTAAGGATTTGTTAAAA
* * * *
12182 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAATATAATTTGAAAAAATAGGAAAAATAATATT
66 CAAGCATCTGAATCATGTTTCGATTTAATTAGAATATAATTGGAAAAAATAGGAAAAACAATATT
* * * * * *
12247 GGAAGCGTTAAAAGCCCTTCAATCTTTTTGACGTCGAATTATATATTTTTTATGAGTATTTTCGC
131 GGAAGCATGAAAAGACCTTCAATCTTTTTGACGTCGAATTATATAATTTTTATGAGTATTGTCGA
* * * * * *
12312 TAGAAACCAAGGAAAAATCTTTTGGATCAATTTTTGCAAAGTTTTAGTCGAAATCATGTATTAAC
196 TAAAAACCAAGGAAAAATCTTTCGGATCAATTTTTGCAAAATTCTAGCCGAAATCATGTAATAAC
* * *
12377 TATCACAGTTTTCAGCTAAAACCGCGTTCCGGGGCCCAACTCAGTTTTCCAAGATTTTTGGTGCC
261 TATCACAGTTTTCAGCTAAAAACGCGTTCCGGGGCCCAACTAAGTTTTCCAAGATTTTTGGCGCC
* * *
12442 AAGACTCCTTGAAATATCTAAATTCATCTAACAAAATCTCAGCGACATTAAATTTAAGGATTTGT
326 AAGACTCCTTGAAATATCCAAATTCATCTAACAAAATCTCAGCGACATTAAATTGAAGAATTTGT
** * *
12507 TTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGAAAAAATAGGAAAAACA
391 TTTTACGAGCATCCGAATCTTGTTTCGATTTAACTAGAAATTAATTTCAAAAAATAGGAAAAACA
* ** * * * * *
12572 ATATTAGAAGTGTTAAAAGCCCTTCAATCTTTTTGATGTCAAATTATATATTTTTTTATGATTAT
456 ATATTAAAAGCATGAAAAGCCCTCCAATCTTTTTGACGTCAAATTATATATTATTTTATGAGTAT
* * *
12637 TTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTCT
521 TTTAGCCAAAAATCGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTCT
* * * * * *
12702 ACTAACCATGACAGTTTTTTTTGGCTAAAAACGCGTTACAGGGCCACAGCTCTGTTTTGTATAAT
586 ACTAACCATCACAG-TGTTTTCGGCTAAAAACGCATTACAGGGCCACAGCTCAGTTTTGCATAAT
* *
12767 TTTTGGTACCGAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCTCAGGCACATTGAATTT
650 TTTTGGTACCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTT
** **
12832 AAGGATTTGTTTTTATTAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAATTCAAAAAATA
715 AAGGATTTGTTTTTACGAGCATCCAAATCTTGTTTCAATTTAATTAAAAATTAATTCAAAAAATA
12897 TATGAAAA
780 TATGAAAA
12905 ACGATATTGA
Statistics
Matches: 674, Mismatches: 97, Indels: 33
0.84 0.12 0.04
Matches are distributed among these distances:
967 3 0.00
968 113 0.17
969 185 0.27
970 59 0.09
971 206 0.31
972 74 0.11
973 34 0.05
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (971 bp):
TCCTTGAAATATATACATTCATCTAACCAAATCTCAACCACATTAGATTTAAGGATTTGTTAAAA
CAAGCATCTGAATCATGTTTCGATTTAATTAGAATATAATTGGAAAAAATAGGAAAAACAATATT
GGAAGCATGAAAAGACCTTCAATCTTTTTGACGTCGAATTATATAATTTTTATGAGTATTGTCGA
TAAAAACCAAGGAAAAATCTTTCGGATCAATTTTTGCAAAATTCTAGCCGAAATCATGTAATAAC
TATCACAGTTTTCAGCTAAAAACGCGTTCCGGGGCCCAACTAAGTTTTCCAAGATTTTTGGCGCC
AAGACTCCTTGAAATATCCAAATTCATCTAACAAAATCTCAGCGACATTAAATTGAAGAATTTGT
TTTTACGAGCATCCGAATCTTGTTTCGATTTAACTAGAAATTAATTTCAAAAAATAGGAAAAACA
ATATTAAAAGCATGAAAAGCCCTCCAATCTTTTTGACGTCAAATTATATATTATTTTATGAGTAT
TTTAGCCAAAAATCGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTCT
ACTAACCATCACAGTGTTTTCGGCTAAAAACGCATTACAGGGCCACAGCTCAGTTTTGCATAATT
TTTGGTACCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTA
AGGATTTGTTTTTACGAGCATCCAAATCTTGTTTCAATTTAATTAAAAATTAATTCAAAAAATAT
ATGAAAAGTTTATTAAAAGTGTGAAAAAGGCTTTCAGTTTTTTGGGCGTTTAATTATATATTTTT
TATGAGTATTTTCACTAGAATTCGAGGAAAAATCTTTCGAGTCAATTTTTGCAACCATCACGGTT
TTCGGCTAAAACCGCGTTCCGGGGGCCCGGCTCAGTTTTGCACGATTTTTGGTGCCAAGGT
Found at i:14390 original size:26 final size:26
Alignment explanation
Indices: 14361--14411 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
14351 TTGCGCCAAA
14361 TTTTCA-ATAATAATTACAGTGTTTTT
1 TTTTCAGAT-ATAATTACAGTGTTTTT
* *
14387 TTTTGAGGTATAATTACAGTGTTTT
1 TTTTCAGATATAATTACAGTGTTTT
14412 AGTTGTTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.27, C:0.06, G:0.14, T:0.53
Consensus pattern (26 bp):
TTTTCAGATATAATTACAGTGTTTTT
Found at i:15209 original size:2 final size:2
Alignment explanation
Indices: 15202--15231 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15192 TATTATAGAT
15202 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15232 GTTATTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16494 original size:12 final size:12
Alignment explanation
Indices: 16477--16501 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16467 AGAACCACAG
16477 AAAACTTTGAAT
1 AAAACTTTGAAT
16489 AAAACTTTGAAT
1 AAAACTTTGAAT
16501 A
1 A
16502 GATTAATTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (12 bp):
AAAACTTTGAAT
Found at i:17184 original size:15 final size:16
Alignment explanation
Indices: 17164--17196 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
17154 CTCAATGCCC
17164 TTTC-TTCTCCTGAGT
1 TTTCTTTCTCCTGAGT
17179 TTTCTTTCTCCTGAGT
1 TTTCTTTCTCCTGAGT
17195 TT
1 TT
17197 ATATGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.06, C:0.24, G:0.12, T:0.58
Consensus pattern (16 bp):
TTTCTTTCTCCTGAGT
Found at i:22236 original size:30 final size:31
Alignment explanation
Indices: 22200--22276 Score: 97
Period size: 29 Copynumber: 2.6 Consensus size: 31
22190 CATCAGAAAA
22200 GGGCTTATTTGGCCATTTAA-AAGAATTCAG
1 GGGCTTATTTGGCCATTTAATAAGAATTCAG
* * *
22230 GGGCTTATTTGG-C-TGTAATTAGAGTTCAG
1 GGGCTTATTTGGCCATTTAATAAGAATTCAG
*
22259 GGGCTTATTTGACCATTT
1 GGGCTTATTTGGCCATTT
22277 TGTGTAAGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 4 0.10
29 20 0.51
30 13 0.33
31 2 0.05
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (31 bp):
GGGCTTATTTGGCCATTTAATAAGAATTCAG
Found at i:31849 original size:2 final size:2
Alignment explanation
Indices: 31842--31879 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
31832 TCACTGTTCC
31842 AT AT 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 AT AT
31880 TTATCATTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.