Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009550.1 Corchorus olitorius cultivar O-4 contig09582, 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: 6849
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:2436 original size:323 final size:320
Alignment explanation
Indices: 1--5319 Score: 3333
Period size: 322 Copynumber: 16.2 Consensus size: 320
*
1 CCAAATCTC-GCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
1 CCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
* * * *
65 AATTAGAAA-TAGATTCTGAAAAAAAATTGAAAAATGATATTAGAAGCGTGAAAAACACTTCAAT
66 AATTAGAAATTA-ATTC-GGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAT
* * * * *
129 TTTTGTAGGCATTAAATTATATATTTTTTCTGATTATTGTGGCAAAAAATTGAGAAAAAACTTTT
129 TTTT-TTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTT
* * *
194 CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATTTTATCAC-GATTTTTGGCTAAAAAC
193 CGGGTCAGTTTTTGCAAAATTTTAGCTGAAATC---------ATCACGGTTTTTTGGCTAAAAAC
* * *
258 GC-ATTCTGGATCCCCGACTCAATTTTGCATG-TTTTCTG-GCGTAAAGACTCCTTGAAATATCT
249 GCGTTTC-GG-GCCCCGACTCAGTTTTGCATGATTTT-TGAGC--AAAGACTCCTTGAAATATCT
*
320 ATATTCATCGAA
309 ATATTCATCTAA
* * * * * * * * * *
332 TCAAATATCAGTCACATTGGATATAAGGATTTGTTTGTACGGGCATCAGAATCCTGCTTGGATTT
1 CCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
* * * * * * * *
397 AATTAAAAAATGATTCGGAAAAAAATAG-AAAACGATATTAGAAGCTTGAAAAGCCC-GCCATTC
66 AATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATT-
* * * * * * * * *
460 TTTTTGGCGTTAAATCAAATATTTTTTCTTAGCATTGTGGCAAAAAATTTAGAAAAAAATTTTCA
130 TTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCG
* * * * * * *
525 AGTCATTTTTTAGCCAAAA---TCG-TGTACTCCATCACGGGTTTTGGGCTAAAAACGCGTTTCG
195 GGTCAGTTTTT-G-CAAAATTTTAGCTGAAAT-CATCACGGTTTTTTGGCTAAAAACGCGTTTC-
* ** * * * *
586 GGGTCTTGGCTTAGTTTTGCATGATTTTTG-GCAAAAAGACTTCTTGAAATAAT-TATATTCAAC
256 GGGCCCCGACTCAGTTTTGCATGATTTTTGAGC--AAAGACTCCTTGAAAT-ATCTATATTCATC
*
649 GAA
318 TAA
* * * *
652 CCAAATCCCAACCACATTGGATAT-AGGTATTTGTTTCTATGAGCATTTAAATCGTTTCGATGAA
1 CCAAATCTCAGCCACATTGGATTTAAGG-ATTTG----T-T-----TTT--A------CGA-GCA
* *
716 TGTTTGATGAATCTTGTTTCGATTTAATTAGAAACTAATTCGGAAAAGAAAATGGAAAAACGATA
46 ----T-CTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAA--AAAATGGAAAAACGATA
* * * * * * * *
781 TTAGAAGCATGAAAAGCCCGTCAATCTTTATGGTGTTGAATTATATATTTTTT-TTAGTATTGTA
104 TTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTG
* * * * * *
845 CCAAAAAAATTCA-GAAAAACATTTCGAGTCAGTTTTTAGCCGAAATTGTCTA-CT--AACCATC
169 GC-AAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTT-G-CAAAATT-T-TAGCTGAAATCATC
* * * * * *
906 ACGATTTCTGGGCTAAAAACGCATTTCGGGACTCC-AGTTCAGTTTTGCATGATTTTTG-GCAGA
229 ACGGTTTTTTGGCTAAAAACGCGTTTCGGG-CCCCGA-CTCAGTTTTGCATGATTTTTGAGC--A
*
969 AAGACTTCTTGAAATATCTATATTCATCTAA
290 AAGACTCCTTGAAATATCTATATTCATCTAA
* * * *
1000 CCAAATCTTAGCGACATTGGATTTAAGGATTCGTTTTTACGAGCATCTGAATCTTATTTCGATTT
1 CCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
** * * *
1065 AATTAGAAAAAAATTCGGGAAAAAATGGAAAAACGATACTAGAAGCGTGAAAAATCCTTCAATTT
66 AATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTT
* * * * *
1130 TTTTTGCGTTGAATTATATA-TTTTTCTAAGTATTGTGGCGAAAAGTTAAGGACAAATA-TTTT-
131 TTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGA-AAA-ACTTTTC
*
1192 GGGTCAGTTTTTGCAAAATTTTTGCTGAAATCGTGTACTAACCATCACGG-TTTTTGGCTAAAAA
194 GGGTCAGTTTTTGCAAAATTTTAGCTG-AA------A-T---CATCACGGTTTTTTGGCTAAAAA
* *** * ** *
1256 CGCGTTCCGGGGTGTC-AGCTCGGCATTGCATGGTTTTT-AGCATAAAGACTCCTTGAAATATCT
248 CGCGTTTC-GGGCCCCGA-CTCAGTTTTGCATGATTTTTGAGC--AAAGACTCCTTGAAATATCT
1319 ATATTCATCTAA
309 ATATTCATCTAA
* * *
1331 CCAAATCTCAGCCACATTGGATTTAAGGATTTAATTTTT-CGAGCATCTAAATCATGTTTCGATT
1 CCAAATCTCAGCCACATTGGATTTAAGGATTT-GTTTTTACGAGCATCTGAATCTTGTTTCGATT
* * *
1395 TAATTAGAAATAAATTCGGAAAAAAAATGGAAAAAACGATATTAGAAGCGTGAAAAACCATTAAA
65 TAATTAGAAATTAATTCGG-AAAAAAATGG-AAAAACGATATTAGAAGCGTGAAAAACCCTTCAA
* * * *
1460 TTTTTTTCGGTGTTGAATTATAT-GTTTTTCTGAGTTTTGTGGAAAAAAATTGAGGAAAAAC-TT
128 TTTTTTT-GGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTT
* * *
1523 TCAGGGGTCAGTTTTTGCTAAATTTTAGCCGAAATCGTGTACATCACTG-TTTTTGGCTAAAAAC
192 TC--GGGTCAGTTTTTGCAAAATTTTAGCTGAAA-----T-CATCACGGTTTTTTGGCTAAAAAC
* * * * * *
1587 GCGTTCCGGAGCCCCGGCTAAGTTTTGCTTGATTTTTGGTGCAAA-ACTCCTTAAAATATCTATA
249 GCGTTTCGG-GCCCCGACTCAGTTTTGCATGATTTTT-GAGCAAAGACTCCTTGAAATATCTATA
*
1651 TTCATCGAA
312 TTCATCTAA
* * *
1660 CCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCCGAATCTTGTTTTGATTT
1 CCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
* * * * *
1725 AGTTA-ATAA-TAAATCGGAAAAAGAAAGAAGACGAGAAAAACGATATTAGAAGCTTGAAAAGCC
66 AATTAGA-AATTAATTCGG----A-AAA-AA-ATG-GAAAAACGATATTAGAAGCGTGAAAAACC
* * * * * * ** *
1788 CGTCAATCTTTTTTTGCATTGGATTATATATTTTTTCTTAGTATTGTTGCAGCAAATTCCGAAGA
122 CTTCAAT-TTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT--GAGGA
** * * ** * * * * * *
1853 AAAAAATTTCGGGTCAGCTTTTAGCCCAAATCAT-G-TAATAACCATTATGGTTTTTAGGATAAA
184 AAAACTTTTCGGGTCAG-TTTTTG-CAAAATTTTAGCTGA-AATCATCACGGTTTTTTGGCTAAA
* ** * *
1916 AACGCGTTCCGTGGCCTGGGCACAGTTTTGCATGATTTTTG-GCATAAAGA---C-T---ATATC
246 AACGCGTTTCG-GGCCCCGACTCAGTTTTGCATGATTTTTGAGC--AAAGACTCCTTGAAATATC
1973 ----TTCATCTAA
308 TATATTCATCTAA
* * * *
1982 CTATATCTCAGCCACATTGGATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCAATTT
1 CCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
** * * * **
2047 AATTAG-AATTAAATTC-GAATCAAATAGAAAAACGATATTAGAAACTTGAAAAACTTTTCAAAT
66 AATTAGAAATT-AATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTC-AAT
* *
2110 TTTTTTGGCGTTGAATTATATATTTTTTCAGAGTATTGTGGTAAAAAATTGAGGAAAAACTTTTC
129 TTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTC
* * * * * *
2175 GTGACAGTTTTTGCAAAATTTTAGCTGAAATCGTGCAGGGTTTTTTTGTTAAAAACGCGTTTCGG
194 GGGTCAGTTTTTGCAAAATTTTAGCTGAAATCAT-CACGGTTTTTTGGCTAAAAACGCGTTTCGG
* * * *
2240 GCCCCGACTCAATTTTGCATGATTTTTGATGCAAAGACTTCTTGAAACATCTATACTCAT-TGAA
258 GCCCCGACTCAGTTTTGCATGATTTTTGA-GCAAAGACTCCTTGAAATATCTATATTCATCT-AA
* * * * * *
2304 CCAAATCCCAACAACATTGGATATAAAGATTTTTTTTCTACGAGCATTCT-AATCTTGTTTCGAT
1 CCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTT-TACGAGCA-TCTGAATCTTGTTTCGAT
* * * * * *
2368 TTAATTAGAAATTAATTTGGACAAAAATGGAAAAATGATATTAGAAGCATGAAAAGCCCGTCAAT
64 TTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAT
* * * * * *
2433 TTTTTTGGTGTTGGATTATATATTTTTTCTGAATATTGTGGCGAAAAATTTA-GAAAAACATTTC
129 TTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTC
* * * * * * *
2497 GGGTCAATTTTCAGCCGAAATTGTATA-CT--AACCATCACAG-TTTTCGAGCTAAAAAGGCGTT
194 GGGTCAGTTTT-TG-CAAAATT-T-TAGCTGAAATCATCACGGTTTTTTG-GCTAAAAACGCGTT
* * *
2558 TCAGGGCCCCGGCTCAGTTTTGCATGTTTTTTGA-CAGAAAGACTCTTTGAAATATCTATATTCA
254 TC-GGGCCCCGACTCAGTTTTGCATGATTTTTGAGC--AAAGACTCCTTGAAATATCTATATTCA
2622 TCTAA
316 TCTAA
* *
2627 TCATATCTCAGCCACATTGGATTTAAGGATTT-TTTTTAACGAGCATCTGAATCTTGTTTCGATT
1 CCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT-ACGAGCATCTGAATCTTGTTTCGATT
* * * * * *
2691 TAAATAAAAATAAATTCCGAAAAAAAAGGAAATACGATATTAGAAGCGTGAAAAACCCTTCAATT
65 TAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATT
* * ** * * *
2756 TTTTTTGCGATGAATTATATATTTTTAT-TGA-TATTGTGGCAAGGAATCGAGGAAAAATTTTTT
130 TTTTTGGCGTTGAATTATATATTTTT-TCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTC
* *
2819 GGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTACCTCTACCATTACAGTTTTTATTTT
194 GGGTCAGTTTTTGCAAAATTTTAGCTGAAA-----T-C-A----T--C---AC-G-----GTTTT
** * * * * *
2884 TTTTCTTAAAACACGTTCTGGGGCCCCGACTCAGTTTTGCAAT-ATTTTTG-GCGTAAAGATTTC
237 TTGGCTAAAAACGCGTT-TCGGGCCCCGACTCAGTTTTGC-ATGATTTTTGAGC--AAAGACTCC
*
2947 TTGAAATATCTATTATTCATCGAA
298 TTGAAATATCTA-TATTCATCTAA
* * * * * ** *
2971 CCAAATCCCATCCACATTGGATTTCAGGAATTGTTTTCAAAAGCATCTTAATCTTGTTTCGATTT
1 CCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
* * *
3036 AATTAGAAATTAATTCGGAAAAAAATGGCAAAACGATAGTAGAAGCGTGAAAAACCCTTCAATCT
66 AATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTT
* **
3101 TTTTAGCGTTGAATTATATATTTTTTCTGAGTATTGTGG-AAAAAA-AAAGGAAAAACTTTTCGG
131 TTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGG
* *
3164 GTCAGTTTTTGCAAAAGTTTAGCCGAAATCGTGTACTAACCATCACGG-TTTTTGGCTAAAAACG
196 GTCAGTTTTTGCAAAATTTTA---G----C-TG-A--AATCATCACGGTTTTTTGGCTAAAAACG
* * * * * * * *
3228 CGTTCCGGAGCCTCGGCTTAATTTTACATGATTTTTGGTGCAAAAACTCCTTGAAATATCTATAT
250 CGTTTCGG-GCCCCGACTCAGTTTTGCATGATTTTT-GAGCAAAGACTCCTTGAAATATCTATAT
* *
3293 TCGTCGAA
313 TCATCTAA
* * * * *
3301 CCAAATCTCAGCCACATTGGATATAAGGATTTATTTTTACGAGCATGTGAGTCTTGTTTTGATTT
1 CCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
* * * * * *
3366 AAATAAAAATTAATTC-GAAAAATATAGAAAAACGATATTAGAAGCTTG-AAAACCCAGTCAATC
66 AATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCC-TTCAAT-
* * * * ** **
3429 TTTTTTTGCGTTGAATTATATATTTTTTTCTTAGTATTGTTGTAAAAAATTCTGAAAAAAAAAGT
129 TTTTTTGGCGTTGAATTATATA-TTTTTTCTGAGTATTGTGGCAAAAAA-T-TGAGGAAAAACTT
* ** ** * *
3494 TTCGGGTCAGTTTTTAGCCGAAATCGT-G-T-ACGTTATCACGGTTTTTGGGCT----A--CG--
191 TTCGGGTCAGTTTTT-G-CAAAATTTTAGCTGAAATCATCACGGTTTTTTGGCTAAAAACGCGTT
* * *
3548 --GGGCCACGGCTCAATTTTGCATGATTTTTTGAAG-AAAGACTCCTTGAAATATCTATATTCAT
254 TCGGGCCCCGACTCAGTTTTGCATGA-TTTTTG-AGCAAAGACTCCTTGAAATATCTATATTCAT
3610 CTAA
317 CTAA
*
3614 CC-AATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
1 CCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
* * * * * * * **
3678 AGTTAAAAATTAATTCAGAAAAAAATAGAGAAACGATATTAGAAGCTTGAAAAGCCAGTCAATCT
66 AATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAT-T
* * * * * * ** ** *
3743 TTTTT-TCATTGAATTATATATTTTTTCTTATTATTGTTGCAAAAAATTTCAAAAAAATAAATAT
130 TTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAA-TTGAGGAAAA-ACTTTT
* * * * * * * * *
3807 AGGGTCAGCTTTTAGCCGAAATCGTGTA-CT--AACCATCACAGTTTTTGGGATAAAAACGAGTT
193 CGGGTCAG-TTTTTG-CAAAAT--TTTAGCTGAAATCATCACGGTTTTTTGGCTAAAAACGCGTT
* * * * *
3869 TCGTGCCCCCAGCTCAGTTTTGCATTATTTTTG-GCAGAAAAACTCCTTGAAATATCTATCTTCA
254 TCGGGCCCCGA-CTCAGTTTTGCATGATTTTTGAGC--AAAGACTCCTTGAAATATCTATATTCA
3933 TCTAA
316 TCTAA
* * * * *
3938 CCATATTTCAGCCACATTGGATTTAAGGATTTCTTTTTATGAGCATCTAAATCTTGTTTCGATTT
1 CCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
* * ** *
4003 AATTAAAAATAAATTCTTAAAAAAAAATGGAAAAACGATACT-GAAAGCGTGAAAAACCCTTCAA
66 AATTAGAAATTAATTC--GGAAAAAAATGGAAAAACGATATTAG-AAGCGTGAAAAACCCTTCAA
* * * * *
4067 GTTTTGTTGGCATTGAATTATATATTTTTTCTGAGTATTATGGCAAAAGATTGAGGAAACACTTT
128 -TTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTT
* * *
4132 TCGGATCAGTTTTTGCAAAATTTTAGTCGAGATTGTGTACTAATCATCACAGTTTTTTTTTTGCT
192 TCGGGTCAGTTTTTGCAAAATTTTAG-C-------TG-A--AATCATCAC-G--GTTTTTTGGCT
* *
4197 AAAAACGCG-TT-----CCGGA-T---TTTTG-ACG-----T----AAAGACTCCTTGAAATATC
243 AAAAACGCGTTTCGGGCCCCGACTCAGTTTTGCATGATTTTTGAGCAAAGACTCCTTGAAATATC
*
4242 TATATTCATCAAA
308 TATATTCATCTAA
** * * * * * *
4255 CCAAATAACAGTCACATTGGATATAAGGATTTGTTTTTACGGGCATCAGAATTTTGTTTGGATTT
1 CCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
* *** * * * * * *
4320 AATTAGAAATTAATTCGAAAAAAAATTTTAAAACTCATAGTGGAAGCTTGAAAAGCCCGTC-ATT
66 AATTAGAAATTAATTCGGAAAAAAATGGAAAAAC-GATATTAGAAGCGTGAAAAACCCTTCAATT
* * *
4384 CTTTTTGGCGTTGAATCATATATTTTTTCTTAGTATTTTGGCAAAAAAATT-AGGAAAAACATTT
130 -TTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAAATTGAGGAAAAAC-TTT
** ** * * * * * * * *
4448 TTAGGTCAGTTTTTAGC-CGA-TATCG-TGTACTCTATCACGGATTTTGGGCTAAAAACACGATT
192 TCGGGTCAGTTTTT-GCAAAATTTTAGCTGAAATC-ATCACGGTTTTTTGGCTAAAAACGCGTTT
* * * * *
4510 CAGGGCCCCGATTCAGTTTTGCATGACTTTTG-GTAAAAAGACTTCTTGAAATAACTATATTCAT
255 C-GGGCCCCGACTCAGTTTTGCATGATTTTTGAG--CAAAGACTCCTTGAAATATCTATATTCAT
*
4574 CGAA
317 CTAA
* * * *
4578 CCAAATCCCAACCATATTGGATATAAGGATTTGTTTGTACGAGTATTTAAATCTTGTTTGGATAA
1 CCAAATCTCAGCCACATTGGATTTAAGGA----TTTGT-----T-TTT--A-C-------G---A
* *
4643 GCATTTGAATCTTGTTTCGATTTAATAAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAG
43 GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAG
** * * * * * *
4708 -AGACGTG-AAAAGTCTGTCAATCTTTTTGGTGTTGAATTATATATTATTTCTGAGAATTTTGCC
108 AAG-CGTGAAAAACCCT-TCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGC
* * * *
4771 AAAAAATTCA-GAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGT-GCT--AACCATCACG
171 AAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTT-G-CAAAAT--TTTAGCTGAAATCATCACG
* * * *
4832 G-TTTCTGAGCTAAAAATGCATTTCGGGGCTCC-AGCTCAGTTTTGCATGATTTTTG-GCAGAAA
232 GTTTTTTG-GCTAAAAACGCGTTTC-GGGCCCCGA-CTCAGTTTTGCATGATTTTTGAGC--AAA
* *
4894 AACTTCTTGAAATATCTATATTCATCTAA
292 GACTCCTTGAAATATCTATATTCATCTAA
* * *
4923 CCAAATCTCAGCTACATTGGATTTGAGGATTTGTTTTTTATGAGCATCTGAATCTTGTTTCGATT
1 CCAAATCTCAGCCACATTGGATTTAAGGATTTG-TTTTTACGAGCATCTGAATCTTGTTTCGATT
* * * *
4988 TAATTAGAAATAAATTCGGAAGAGAAATGGAAAAACGATATTAGAAGCGTTAAAAATCCTTC-AT
65 TAATTAGAAATTAATTCGGAA-AAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAT
*
5052 TTTTTT-GCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAGATTGAGGACAAATA-TTT
129 TTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGA-AAA-ACTTT
* *
5115 T-GGGTCAGTTTTTGCAAACTTTTAGCCGAAAATTGTGTACTCAGAAACACATCACGG-TTTTTG
192 TCGGGTCAGTTTTTGCAAAATTTT--------A----G--CT--GAAA-TCATCACGGTTTTTTG
* * * * * * * * *
5178 GCTAAAAACACATTCCAGGGCCTCGGCTCAGTATTGCATGGTTTTT-AGCATAAAGAATTCTTGA
240 GCTAAAAACGCGTTTC-GGGCCCCGACTCAGTTTTGCATGATTTTTGAGC--AAAGACTCCTTGA
*
5242 AATAACTATATTCATCTAA
302 AATATCTATATTCATCTAA
* * ***
5261 CCAAATCTCAGTCACATT-GTTTTAAGGATTAAATTTTACGAGCATCTGAATCTTGTTTC
1 CCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTC
5320 TAAATTCAAA
Statistics
Matches: 3921, Mismatches: 720, Indels: 689
0.74 0.14 0.13
Matches are distributed among these distances:
301 15 0.00
302 2 0.00
303 4 0.00
304 5 0.00
306 2 0.00
308 4 0.00
309 1 0.00
310 14 0.00
311 84 0.02
312 134 0.03
313 115 0.03
314 86 0.02
315 67 0.02
316 43 0.01
317 101 0.03
318 11 0.00
319 16 0.00
320 99 0.03
321 58 0.01
322 388 0.10
323 308 0.08
324 175 0.04
325 90 0.02
326 18 0.00
327 58 0.01
328 66 0.02
329 187 0.05
330 184 0.05
331 241 0.06
332 149 0.04
333 54 0.01
334 88 0.02
335 75 0.02
336 47 0.01
337 35 0.01
338 105 0.03
339 30 0.01
341 5 0.00
342 1 0.00
343 110 0.03
344 213 0.05
345 156 0.04
346 95 0.02
347 65 0.02
348 106 0.03
349 4 0.00
350 1 0.00
351 3 0.00
352 1 0.00
354 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (320 bp):
CCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
AATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTT
TTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGG
GTCAGTTTTTGCAAAATTTTAGCTGAAATCATCACGGTTTTTTGGCTAAAAACGCGTTTCGGGCC
CCGACTCAGTTTTGCATGATTTTTGAGCAAAGACTCCTTGAAATATCTATATTCATCTAA
Found at i:6284 original size:334 final size:319
Alignment explanation
Indices: 5364--6847 Score: 1521
Period size: 334 Copynumber: 4.6 Consensus size: 319
5354 GCGTGAAGAC
** *
5364 TTTTTGGCGCAAAGACTTTTTGAAACATCTATATTCATTGAACCAAATC-CGAACCACATTGGAT
1 TTTTTGGCGC-AAGACTCCTTGAAATATCTATATTCATTGAACCAAATCTC-AACCACATTGGAT
* * * *
5428 ATAAGGATTTTTTTTCTCCAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAA
64 TTAAGGATTTATTTTC-ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AA
* *
5493 AAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCT-TTGAATTATAT
127 AAAAATAGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTTG-TGTTGAATTATAT
* * * *
5557 ATTTTTTTCTGAATTTTGTGGCAATAAATTCG-GAAAAACATTTCGGGTCAGTTTTTAGCCGAAA
191 A-TTTTTTCTGAGTATTGTGGCAAAAAATT-GTGAAAAAAATTTCGGGTCAGTTTTTAGCCGAAA
* * * *
5621 TCGTGT--A-CGTCACGGTTTTTGAGCTAAAAACGCGTTTCGAGGCCCCGACTCAATTTTGCATG
254 TCGTGTACACCATCACGGTTTTTAAGCTAAAAACGCGTTTCGGGGCCTCGACTCAATTTTGCATG
5683 A
319 A
** *
5684 TTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCT-AACCATATCTCAACCACATTGGAT
1 TTTTTGGC-GCAAGACTCCTTGAAATATCTATATTCAT-TGAACCAAATCTCAACCACATTGGAT
* * * * *
5748 TTAAGGATTTATTTTTATGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATGCCGAAAA
64 TTAAGGATTTATTTTCACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAA
* * * * * * *
5813 AAAAAGGAAAGACGATATTAGAAGCGTGAAAAACCCTTCAAT-TATTTTTGCGATGAATCATATA
129 AAATA-GAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCT-TTTTTGTGTTGAATTATATA
* * * *
5877 TTTTTCCTGAGTATTGTGGCAAAGAATCGAGGAAAAAAATTTCGGGTCAGTTTTTGCAAAATTTT
192 TTTTTTCTGAGTATTGTGGCAAAAAATTG-TGAAAAAAATTTCGGGTCAG----T------TTTT
* * ** * ** ** *
5942 AGCCGAAATTGTGTACCAACCATCACAGTTTTTTTGCTTAAAACTTG-TTCTGGGAAAC-CGGCT
246 AGCCGAAATCGTGTA-C-ACCATCACGGTTTTTAAGCTAAAAACGCGTTTC-GGG-GCCTCGACT
*
6005 CAGTTTTGCATGA
307 CAATTTTGCATGA
* * * *
6018 TTTTTGGCGTCAAGACTTCTTGAAGTATCTATTATTCATTGAACCAAATCCCAACCATATTGGAT
1 TTTTTGGCG-CAAGACTCCTTGAAATATCTA-TATTCATTGAACCAAATCTCAACCACATTGGAT
* * *
6083 TTAAGGAATTGTTTTCACGAGCATCTTAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAA
64 TTAAGGATTTATTTTCACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAA
* * * * * **
6148 AAATAGCAAAAGGATAGTAGAAGCGTGAAAAACCCTTCAATCTTTTTAATGTTGAATTATATATT
129 AAATAGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTTGTGTTGAATTATATATT
* * *
6213 TTTTCTGAGTATTATGGCAAAAAATTGTGAAAAAACTTTTTGGGTCAGTTTTTGCAAAAGTTTAA
194 TTTTCTGAGTATTGTGGCAAAAAATTGTGAAAAAA-ATTTCGGGTCAGTTTTT-----AG-----
* * * *
6278 CCGAAATCGTGTACTAACCATCACGG-TTTTATGCTAAAAACGCATTTCGGAGCCTCGACTTAAT
248 CCGAAATCGTGTAC--ACCATCACGGTTTTTAAGCTAAAAACGCGTTTCGGGGCCTCGACTCAAT
6342 TTTGCATGA
311 TTTGCATGA
* * * *** *
6351 TTTTTGGCGCAAAGACTCCTTGAAATATTTATATTCATCGAACCAAATATCAGTTACATTGGATA
1 TTTTTGGCGC-AAGACTCCTTGAAATATCTATATTCATTGAACCAAATCTCAACCACATTGGATT
* * * * *
6416 TAAGGATTTATTTT-ATGAACATCTGAGTCTTATTTCGACTTAATTAGAAATTAATTCGGAAAAA
65 TAAGGATTTATTTTCACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAA
* *
6480 AATAGAAAAACGATATTAGAAGCTTGAAAAGCCAGTCAATCTTTTTTTGTGTTGAATTATATATT
130 AATAGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATC-TTTTTTGTGTTGAATTATATATT
* * * *
6545 TTTTCTTAGTATTGTTGCAAAAAATTCTG-AAAAAA--T--GGTCAATTTTTAGCCGAAATCGTG
194 TTTTCTGAGTATTGTGGCAAAAAATTGTGAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTG
** *
6605 TACATTATCACGGTTTTTAAGCTAAAAACGCGTTTCGGGGCCTCGACTCAGTTTTGCATGA
259 TACACCATCACGGTTTTTAAGCTAAAAACGCGTTTCGGGGCCTCGACTCAATTTTGCATGA
* * * *
6666 TTTTTGGCAGAAATACTCCTTGAAATATCTATATTCATCT-AACCATATCTCAGCCACATTGGAT
1 TTTTTGGC-GCAAGACTCCTTGAAATATCTATATTCAT-TGAACCAAATCTCAACCACATTGGAT
* * * *
6730 TTAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTCGATGTAATTAGAAATTAATTCGG-AAA
64 TTAAGGATTTATTTTCACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAA
* * *
6794 AAATGGAAAAAATGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGTGTT
129 AAATAG-AAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTTGTGTT
6848 AA
Statistics
Matches: 964, Mismatches: 150, Indels: 105
0.79 0.12 0.09
Matches are distributed among these distances:
314 8 0.01
315 126 0.13
316 88 0.09
317 1 0.00
318 30 0.03
319 105 0.11
320 66 0.07
321 4 0.00
323 1 0.00
324 4 0.00
326 10 0.01
328 1 0.00
329 19 0.02
330 1 0.00
331 83 0.09
332 86 0.09
333 68 0.07
334 172 0.18
335 91 0.09
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (319 bp):
TTTTTGGCGCAAGACTCCTTGAAATATCTATATTCATTGAACCAAATCTCAACCACATTGGATTT
AAGGATTTATTTTCACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA
ATAGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTTGTGTTGAATTATATATTTT
TTCTGAGTATTGTGGCAAAAAATTGTGAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTA
CACCATCACGGTTTTTAAGCTAAAAACGCGTTTCGGGGCCTCGACTCAATTTTGCATGA
Done.