Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018370.1 Corchorus olitorius cultivar O-4 contig18403, 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: 6871
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:825 original size:333 final size:328
Alignment explanation
Indices: 3--923 Score: 1377
Period size: 333 Copynumber: 2.8 Consensus size: 328
1 AT
* * ** * * *
3 CTTTCGGGTAAATTTTTGTAAAATTTTAGCCGAAATCGTTTACTAACCATCACCTGTTTTAGATA
1 CTTTCGGGT-AATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAGTTTTTTTGGCTA
* *
68 AAAACGCGTTCCGAG-CCCGACTCAATTTTTAATGATTTTTGGCCCCGAGACTCCTTGACATATC
65 AAAACGCGTTCCGGGCCCCGACTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGACATATC
* * *
132 TATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGATCATCAGAAT
130 TATATTCATCTAACCAAATCTCAGTCAAATTGGATTTAAGGATTTGATTTTACGAGCATCAAAAT
*
197 CATGTTTCGATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAA
195 CATGTTTCGATTTAATCAGAAATTAATTCGGAAACATATAGGAAAATCGATATTAGAAGCGTGAA
* * *
262 AAACCCTTCAAACTTTTGGCGTTGAATTATATATATTCTATAAGTGTTTGGACGAAGATTGTGGA
260 AAACCCTTCAAACTTTTGGCGTTGAATTATACATATTCTATAAGTGTTTGGACAAAGATTGTGAA
327 AAAA
325 AAAA
331 CTTTCGGGTAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTTGGCT
1 CTTTCGGGTAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA--GTTTTTTTGGCT
** * *
396 -AAAACGCGTTATGGGCCCC-ATCTCAGTTTTTAATGATTTTTTGCCCCGAGACTCCTTTACATA
64 AAAAACGCGTTCCGGGCCCCGA-CTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGACATA
459 TCTATATTCATCTAACCAAATCTCA-TCCAAATTGGATTTAAGGATTTGATTTTACGAGCATCAA
128 TCTATATTCATCTAACCAAATCTCAGT-CAAATTGGATTTAAGGATTTGATTTTACGAGCATCAA
* *
523 AATCATGTTTCGATTTAATTAGAAATGAATTCGGAAACATATAGGAAAATCGATATTAGAAGCGT
192 AATCATGTTTCGATTTAATCAGAAATTAATTCGGAAACATATAGGAAAATCGATATTAGAAGCGT
* * * *
588 GAAAAACCCTTCAATCTTTTAGGCTTTGAATTATACATATTCTATAAGTTTTTTGGCCAAAGATT
257 GAAAAACCCTTCAAACTTTT-GGCGTTGAATTATACATATTCTATAAG-TGTTTGGACAAAGATT
653 GTGTAAAAAA
320 GTG-AAAAAA
663 CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA-CATCATGTTTTTTTGGCT
1 CTTTCGGGT-AATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA-GTTTTTTTGGCT
* * * *
727 AAAAACGCGTTCCGGGGCCCCGGCTTAGTTTCTAATGATTTTTGGACCCGAGACTCCTTGACATA
64 AAAAACGCGTTCC-GGGCCCCGACTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGACATA
*
792 TCTATATTCATCTAACCAAATCTCAGTCAAATTGGATTCAAGGATTTGATTTTACGAGCATCAAA
128 TCTATATTCATCTAACCAAATCTCAGTCAAATTGGATTTAAGGATTTGATTTTACGAGCATCAAA
* * * *
857 ATCATGTTTCGAGTTAATCAAAAATTAATTC-AAGAACATATAGGTAAATCGATATTAGAAGCGT
193 ATCATGTTTCGATTTAATCAGAAATTAATTCGGA-AACATATAGGAAAATCGATATTAGAAGCGT
921 GAA
257 GAA
924 TTATACGGGT
Statistics
Matches: 537, Mismatches: 42, Indels: 23
0.89 0.07 0.04
Matches are distributed among these distances:
327 40 0.07
328 22 0.04
329 190 0.35
330 25 0.05
331 28 0.05
332 30 0.06
333 201 0.37
334 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Consensus pattern (328 bp):
CTTTCGGGTAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAGTTTTTTTGGCTAA
AAACGCGTTCCGGGCCCCGACTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGACATATCT
ATATTCATCTAACCAAATCTCAGTCAAATTGGATTTAAGGATTTGATTTTACGAGCATCAAAATC
ATGTTTCGATTTAATCAGAAATTAATTCGGAAACATATAGGAAAATCGATATTAGAAGCGTGAAA
AACCCTTCAAACTTTTGGCGTTGAATTATACATATTCTATAAGTGTTTGGACAAAGATTGTGAAA
AAA
Found at i:1612 original size:40 final size:40
Alignment explanation
Indices: 1555--1631 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
1545 CGAATTATAT
*
1555 ATATTCTATAAGGGTTTTGGCCAAAAATTGTGGAAAATAC
1 ATATTCTATAAGGGTTTTGGCCAAAAATTATGGAAAATAC
* * *
1595 ATATTCTATTAGTGTTTTGGCTAAAAATTATGGAAAA
1 ATATTCTATAAGGGTTTTGGCCAAAAATTATGGAAAA
1632 AAATCTTTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (40 bp):
ATATTCTATAAGGGTTTTGGCCAAAAATTATGGAAAATAC
Found at i:1816 original size:375 final size:363
Alignment explanation
Indices: 1228--1966 Score: 1075
Period size: 375 Copynumber: 2.0 Consensus size: 363
1218 GCAATGAATT
* * * * *
1228 ATACATATTTTATAAGTGTTTTGGCCAAAGATTGTTGAAAAAATCTTTCGGGTAAATTTTTGCAA
1 ATACATATTCTATAAGTGTTTTGGCCAAAAATTATGGAAAAAATCTTTCGGGTAAAGTTTTGCAA
* * *
1293 AATTTTTAGCCGAAATCGTTTACGGGTTTTAGATAAACACGCGTTTCGGAGCCCCGGCTCAGTTT
66 AATTTTTAGCCGAAATCGTTTACGGGTTTTAGATAAAAACGCGTTCCGGAGCCCCGACTCAGTTT
* * * *
1358 TTAATGATTTTTAGCCCGAGCCTCCTTGACATATCTATATTCATATAGCAAATCTCAGCCAAATT
131 TTAATGATTTATAGCCCGAGACTCCTAGACATATCTATATTCATATACCAAATCTCAGCCAAATT
* * * *
1423 GCATTTAAGGATTTGATTTTACGATCATCAGAATCATGTTTCGATTTAATCAGGAATTAATTCGG
196 GCATTTAAGGATTTGATTTTACGAGCATCAAAATCATGTTTCGATTTAATCAGAAATTAATTCAG
* *
1488 AAAGATATAAGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTCGAATTAT
261 AAACATATAAGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCATCGAATTAT
1553 ATATATTCTATAAGGGTTTTGGCCAAAAATTGTGGAAA
326 ATATATTCTATAAGGGTTTTGGCCAAAAATTGTGGAAA
* * *
1591 ATACATATTCTATTAGTGTTTTGGCTAAAAATTATGGAAAAAAATCTTTCGGGTCAAGTTTTGCA
1 ATACATATTCTATAAGTGTTTTGGCCAAAAATTATGG-AAAAAATCTTTCGGGTAAAGTTTTGCA
* * *
1656 AAA-TTTTAGCCGAAATCGTGTATAAGCCATCACGGGTTTTGGCTAAAAACGCGTTCCGGGGCCC
65 AAATTTTTAGCCGAAATC--GT-T------T-ACGGGTTTTAGATAAAAACGCGTTCCGGAGCCC
* * *
1720 TGACTCAGTTTTTAATGATTTATGGCCCGAGACTCCTAGACCATATCTATATTCATCTAACCAAA
120 CGACTCAGTTTTTAATGATTTATAGCCCGAGACTCCTAGA-CATATCTATATTCATAT-ACCAAA
1785 TCTCAGCCAAATTGCATTTAAGGATTTGATTTTACGAGCATCAAAATCATGTTTCGATTTAATCA
183 TCTCAGCCAAATTGCATTTAAGGATTTGATTTTACGAGCATCAAAATCATGTTTCGATTTAATCA
*
1850 GAAATTAATTCAGAAACATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTT
248 GAAATTAATTCAGAAACATATAAGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTT
* * *
1915 GGCATTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAA
313 GGCATCGAATTATATATATTCTATAAGGGTTTTGGCCAAAAATTGTGGAAA
1966 A
1 A
1967 ATTTTTCGGG
Statistics
Matches: 332, Mismatches: 31, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
363 45 0.14
364 28 0.08
365 2 0.01
366 1 0.00
372 1 0.00
373 62 0.19
374 16 0.05
375 177 0.53
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (363 bp):
ATACATATTCTATAAGTGTTTTGGCCAAAAATTATGGAAAAAATCTTTCGGGTAAAGTTTTGCAA
AATTTTTAGCCGAAATCGTTTACGGGTTTTAGATAAAAACGCGTTCCGGAGCCCCGACTCAGTTT
TTAATGATTTATAGCCCGAGACTCCTAGACATATCTATATTCATATACCAAATCTCAGCCAAATT
GCATTTAAGGATTTGATTTTACGAGCATCAAAATCATGTTTCGATTTAATCAGAAATTAATTCAG
AAACATATAAGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCATCGAATTAT
ATATATTCTATAAGGGTTTTGGCCAAAAATTGTGGAAA
Found at i:2516 original size:665 final size:668
Alignment explanation
Indices: 989--5132 Score: 3351
Period size: 711 Copynumber: 6.0 Consensus size: 668
979 TTTGAATTAT
* * * * *
989 ACGGGTTTTTGGCTAAAAACGC-TTCTGGGGCCCCGGCTCAGTTTTTAATAATTTTTGGCCTCGA
1 ACGGG-TTTTGGCTAAAAACGCGTTCCGGGGCCCTGACTCAGTTTTTAATGATTTTTGGCCCCGA
* * *
1053 GACTCCTTGACATATTTATATTCATCTAACCAAATCTCAGCCAAGTTGGATTTAAGGGTTTGATT
65 GACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATT
* * * * * *
1118 TTTCGAGCATTAGAATTATGTTTCGATTTAACCAGAAATTAATTCGGAAATATATAGGAAAATCG
130 TTACGAGCATCAAAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAACATATAGGAAAATCG
* ** * *
1183 ATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCAATGAATTATACATATTTTATAAGTGTT
195 ATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATATTCTATAAGTGTT
* * ** *
1248 TTGGCCAAAGATTGTTGAAAAAATCTTTCGGGTAAATTTTTGCAAAATTTTTAGCCGA-A----A
260 TTGGCCAAAGATTGTGGAAAAAATTTTTCGGGCCAATTTTTGCAAAA-TTTTAGCCGATATCGTT
* * * *
1308 T-CGT-T----T-ACGGGTTTTAGATAAACACGCGTTTCGGAGCCC-CGGCTCAGTTTTTAATGA
324 TACGTATACCATCACGGGTTTTGGCTAAAAACGCGTTCCGG-GCCCTCGGCTCAGTTTTTAATGA
* * * * * *
1365 TTTTTAG-CCCGAGCCTCCTTGACATATCTATATTCATAT-AGCAAATCTCAGCCAAATTGCATT
388 TTTATGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCCAAATTGAATT
* * *
1428 TAAGGATTTGATTTTACGATCATCAGAATCATGTTTCGATTTAATCAGGAATTAATTCGGAAAGA
453 TAAGGATTTGATTTTACGAGCATCAGAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAA-C
* *
1493 TATAAGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTCGAATTATATATA
517 TAT-AGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCATTGAATTATATATA
* * * * *
1558 TTCTATAAGGGTTTTGGCCAAAAATTGTGGAAAATACAT-ATTCTA-TTAGTGTTTTGGCTAAAA
581 TTCTATAAGTGTTTTGGCCAAAAATTGTGGAAAA-A-ATCTTTCGAGTCAAT-TTTT-GC--AAA
* * *** * ***
1621 ATTATGGAAAAAAATC-T-TTCGGGTCAAGTTTTGC
640 ATTTTAG-CCGAAATCGTGTAC---T-AA-CCAT-C
*** * ** *
1655 A-AAATTTTAGCCGAAATCGTGTATAAGCCATCACGGGTTTTGGCTAAAAACGCGTTCCGGGGCC
1 ACGGGTTTT-G--G----C---TA-AA---A--ACGCG--TT--C------CG-G----GGCCCT
* * *
1719 CTGACTCAGTTTTTAATGATTTATGG-CCCGAGACTCCTAGACCATATCTATATTCATCTAACCA
35 G--ACTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGA-CATATCTATATTCATCTAACCA
*
1783 AATCTCAGCCAAATTGCATTTAAGGATTTGATTTTACGAGCATCAAAATCATGTTTCGATTTAAT
97 AATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGAGCATCAAAATCATGTTTCGATTTAAT
*
1848 CAGAAATTAATTCAGAAACATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTT
162 CAGAAATTAATTCGGAAACATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTT
*
1913 TTGGCATTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATTGTGG-AAAAATTTTTCGGG
227 TTGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAAAATTTTTCGGG
* * *
1977 CCAATTTTTGCAAAATGTTAGCCGATATCGTTTACGT-TACCATTACGGTTTTTGGCTAAAAACG
292 CCAATTTTTGCAAAATTTTAGCCGATATCGTTTACGTATACCATCACGGGTTTTGGCTAAAAACG
* * * * *
2041 CGTTTCCGGGCCCTCGGCTCAGTTTTCAATGATTTTTGACCCCGTGACTCCTTTACATATCTATA
357 CG-TTCCGGGCCCTCGGCTCAGTTTTTAATGATTTATGGCCCCGAGACTCCTTGACATATCTATA
* * *
2106 TTCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTAATTTTACAAGCATCAGAATCATG
421 TTCATCTAACCAAATCTCAGCCAAATTGAATTTAAGGATTTGATTTTACGAGCATCAGAATCATG
2171 TTTCGATTTAATCAGAAATTAATTCGGAAAC-AT-GAAAATCGATATTAGAAGCGTGAAAAACCC
486 TTTCGATTTAATCAGAAATTAATTCGGAAACTATAGAAAATCGATATTAGAAGCGTGAAAAACCC
* * * * *
2234 TTCGATCTTTTTGACATTGAATTATACATATTCTATAAGTTTTTTGGCCAAAGATTGTGGAAAAA
551 TTCAATCTTTTTGGCATTGAATTATATATATTCTATAAGTGTTTTGGCCAAAAATTGTGGAAAAA
* *
2299 ATCTTTCGAGTAAATTTTTGCAAAATTTTAGCGGAAATCGTGTACTAACCATC
616 ATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATC
* * * *
2352 ACGGGTTTTAGATAAAAACGCGTTCCGGGGCCCTGCCTCAGTTTCTAATGATTTTTGGCCCCGAG
1 ACGGGTTTTGGCTAAAAACGCGTTCCGGGGCCCTGACTCAGTTTTTAATGATTTTTGGCCCCGAG
*
2417 ATTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTT
66 ACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTT
* *
2482 TACGAGCATCAAAATCATGTTTCGCTTTAATCAGAAATTAATTCAGAAACATATAGGAAAATCGA
131 TACGAGCATCAAAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAACATATAGGAAAATCGA
*
2547 TATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTCGAATTATATATATTCTATAAGTGTTT
196 TATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATATTCTATAAGTGTTT
* ** * * * *
2612 TGGCCAAAAATCATGGAAAATACATATTCTATTAGTGTTTTGGCCAAAGATTGTGGAAAAAATCT
261 TGGCCAAAGATTGTGG-AAA-A-A-ATT-T-TT--CG----GGCC--A-ATTTTTG-CAAAAT-T
* * * * *
2677 TTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATAAACCATCACGGGTTTTTGGCTAA
309 TT--AGCCGA--TAT-C----GTTT-------A-C--GTAT--ACCATCACGGG-TTTTGGCTAA
* * *
2742 AAACGCGTTCCGGGGCCCT-GGCTCAGTTTTTAATAATATATGGCCCTGAGACTCCTTGACATAT
352 AAACGCGTTCC-GGGCCCTCGGCTCAGTTTTTAATGATTTATGGCCCCGAGACTCCTTGACATAT
2806 CTATATTCATCTAACCAAATCTCAGCCAAATTGAATTTAAGGATTTGATTTTACGAGCATCAGAA
416 CTATATTCATCTAACCAAATCTCAGCCAAATTGAATTTAAGGATTTGATTTTACGAGCATCAGAA
* * * *
2871 TCATGTTTCGCTTTAATCATAAATTAATTCAGAAACATATAGGAAAATCGATATTAGAAGCATGA
481 TCATGTTTCGATTTAATCAGAAATTAATTCGGAAAC-TATA-GAAAATCGATATTAGAAGCGTGA
* * * *
2936 AAAACCCTTCTATCTTTTTGGTATTGAATTATATATATTCTATAAGTGTTTTGGCCAAATATTTT
544 AAAACCCTTCAATCTTTTTGGCATTGAATTATATATATTCTATAAGTGTTTTGGCCAAAAATTGT
* *
3001 GGAAAAAA-CTTTC-AGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTACAAACCATC
609 GGAAAAAATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATC
* * ** *
3059 ACGGGTTTTTGGCT-AAAACGCGTTCCGGGG-CCTGACTCAGTTTTCAATG---TTCGGCCGAGT
1 ACGGG-TTTTGGCTAAAAACGCGTTCCGGGGCCCTGACTCAGTTTTTAATGATTTTTGGCCCCGA
* * * * *
3119 GACTCCTTTATATATCTATATTCATCTAACCAAATCTCAGCCACAGTAGATTTAAGGATTTGATT
65 GACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATT
* * *
3184 TTACGAGCATCAAAATCTTGTTTCGATTTAATCAAAAATTAATTCGGAAACTTATAGGAAAATCG
130 TTACGAGCATCAAAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAACATATAGGAAAATCG
* *
3249 ATATTAGAAGCGTG-AAAACCCTTCAATCTTTTTGGCTTTGAATTATATATATTCTATTAGTGTT
195 ATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATATTCTATAAGTGTT
* * * * *
3313 TTGGCCAAAAATTGTGGAAAAAACTTTTTCGTGTCTATTTTTGCAAAATTTTAGCCGAAATCG--
260 TTGGCCAAAGATTGTGGAAAAAA-TTTTTCGGGCCAATTTTTGCAAAATTTTAGCCGATATCGTT
* * *
3376 TGCATAAACCCATCACGGGTTTTGGCTAAAAACGCGTTCCGGGGCCCT-GGCTCAGTTTTTAATG
324 TACGTATA-CCATCACGGGTTTTGGCTAAAAACGCGTTCC-GGGCCCTCGGCTCAGTTTTTAATG
* *
3440 ATTTATGGCCCCGAGACTCCTTGACATATCTATATTCATCAAACCAAATCTCAGCCAAATTGCAT
387 ATTTATGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCCAAATTGAAT
* * *
3505 TGAAGGATTTGATTTAACGAGCATCAAAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAAC
452 TTAAGGATTTGATTTTACGAGCATCAGAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAAC
3570 ATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCATTGAATTATATAT
517 -TATA-GAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCATTGAATTATATAT
* * * *
3635 ATTCTATAAGTGTTTTGGCCAAAAATTGTGGAAAATACAT-ATTCTA-TTAGTGTTTTGGCCAAA
580 ATTCTATAAGTGTTTTGGCCAAAAATTGTGGAAAA-A-ATCTTTCGAGTCAAT-TTTT-G-CAAA
* * *** * * ***
3698 GATTGTGGAAAAAATC-TTTCCGGTCAATTTTTGC
640 -ATTTTAGCCGAAATCGTGTAC--T-AA-CCAT-C
*** * ** * * *** * * * * *
3732 A-AAATTTTAGCCGAAATCGTGTAT---AAACCAT--CACAGGTTTTTGGCTAAAAACGCGTTCC
1 ACGGGTTTTGGCTAAAAACGCGT-TCCGGGGCCCTGACTCA-G-TTTT---T---AATG-ATT-T
** * * * * * * * * *
3791 GGGGCCCTG-G-CTCAGTTTTTA-ATGATTTATGGCCCCGAGACTCCTTGACATATCTATATTCA
55 TTGGCCCCGAGACTC---CTTGACAT-ATCTAT---------A-TTCAT--C-TAACCA-AATC-
* * * *** ** **
3853 TCTAACCAAATCTCAGCCAAATT--GGATTTAAGGA-TTT--GATTTTACGAGCATCA-GAATC-
101 TC-AGCCAAAT-T--G--GATTTAAGGATTT---GATTTTACGAGCAT-C-AAAATCATGTTTCG
** * *
3911 ATGTT--TC-GATTTAATCTGAAATTAATTTGGAAAGATATAGGAAAATCGATATTAGAAGCGTG
155 AT-TTAATCAGA---AAT-T--AA-T--TCGGAAAC-ATATAGGAAAATCGATATTAGAAGCGTG
* *
3973 AAAAACCCTTCAATCGTTTTGGCGTTGAATTATACATATTCTATAAGTGTTTTGGCCAAAGATTG
209 AAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATTG
* ** * * * * * * *
4038 TGAAAAAAAACTTTCGGGTCTATTTTTCCAAAATTTTAGCCGAAATCGTGTA-TTA-ACGATCAC
274 TGGAAAAAATTTTTCGGGCCAATTTTTGCAAAATTTTAGCCGATATCGTTTACGTATACCATCAC
*** * *
4101 TTTTTTTTTGGCTAAAAACGCGTTCCGGAGCCC-CAGCTCAGTTTTTAATGATTTATGGCCCCAA
339 --GGGTTTTGGCTAAAAACGCGTTCCGG-GCCCTCGGCTCAGTTTTTAATGATTTATGGCCCCGA
* *
4165 GACTCCTTGACATATCTATATTCATCTAACGAAATCTCAGCCAAGTTGAATTTAAGGATTTGATT
401 GACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCCAAATTGAATTTAAGGATTTGATT
*
4230 TTACGAGCATCA-ACATCATGTTTCGATTTAATCAGAAATTAATTTGGAAACTTATAGGAAAATC
466 TTACGAGCATCAGA-ATCATGTTTCGATTTAATCAGAAATTAATTCGGAAAC-TATA-GAAAATC
* * * *
4294 GATATTAGAAACGTGAAAAGCCCTTCAATATTTTTGGCGTTGAATTATATATATATATTTCTATA
528 GATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCATTG-A--AT-TATATATA-TTCTATA
* * * *
4359 AGTGTTTTGGCCAAACATTGTGGAAAAAAACTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAA
588 AGTGTTTTGGCCAAAAATTGTGGAAAAAATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAA
* **
4424 TCATGTACTAAGAATC
653 TCGTGTACTAACCATC
* ** * *
4440 ACGGTTTTTGTTTGTCTAAAAACGCGTTATGGGGCCCCGACTAAGTTTTTAATGATTTTTGGCCC
1 ACGGGTTTTG---G-CTAAAAACGCGTTCCGGGGCCCTGACTCAGTTTTTAATGATTTTTGGCCC
* * * *
4505 CGAGACTCCTTGATATGTCTACATTCATCTAACCAAATCTCAGTCAAATTGGATTTAAGGATTTG
62 CGAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTG
* * *
4570 ATTTTACGGGCATCAGAATCATGTTTCGATTTAAAT-AGAAATTAATTCGGAAAGATATAGGAAA
127 ATTTTACGAGCATCAAAATCATGTTTCGATTT-AATCAGAAATTAATTCGGAAACATATAGGAAA
* *
4634 ATCGATACTAGAAGCGTG----A---TTCAATCTTTTTGGCGTCGAATTATATATATTCTATAAG
191 ATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATATTCTATAAG
* * * *
4692 TGTTTTGGCCAAAGATTGTGGAAAATACATATTCTATTAGTGTTTTGGCCAAAGATTGTGGAAAA
256 TGTTTTGGCCAAAGATTGTGG-AAA-A-A-ATT-T-TT--CG----GGCC--A-ATTTTTG--CA
* * * * * ***
4757 AAATCTTTCGGGTCAATATTTGCAAAATCTTATCCGAAATCGTGTACCATCTTTGGTTTTGGCTA
304 AAAT-TTT--AGCCGATA--T-C-----GTT-T-----A-CGTATACCATCACGGGTTTTGGCTA
* * *
4822 AAAACGCGTTCTAGGGCCC-CGACTCAGTTTTCAATGATTTATGGCCCCGAGACTCCTTGACATA
351 AAAACGCGTTC-CGGGCCCTCGGCTCAGTTTTTAATGATTTATGGCCCCGAGACTCCTTGACATA
* * *
4886 TCTATAATTCATTTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAG
415 TCTAT-ATTCATCTAACCAAATCTCAGCCAAATTGAATTTAAGGATTTGATTTTACGAGCATCAG
* * *
4951 ATTCATGTTTCGATTTCATCAGAAATTAATTCGGAAACTTATAGGAAAATCGATATTAGAAACGT
479 AATCATGTTTCGATTTAATCAGAAATTAATTCGGAAAC-TATA-GAAAATCGATATTAGAAGCGT
** * *
5016 GAAAAACCCTTCAATCTTTTTGGTGTTGAATTATATATATTCTATATGTGTTTTGGCCAAAGATT
542 GAAAAACCCTTCAATCTTTTTGGCATTGAATTATATATATTCTATAAGTGTTTTGGCCAAAAATT
* *
5081 ATGGAAAAAA-CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA
607 GTGGAAAAAATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA
5133 TATATATATA
Statistics
Matches: 2831, Mismatches: 392, Indels: 474
0.77 0.11 0.13
Matches are distributed among these distances:
663 260 0.09
664 15 0.01
665 225 0.08
666 19 0.01
667 8 0.00
668 8 0.00
669 15 0.01
670 4 0.00
671 17 0.01
672 68 0.02
673 6 0.00
674 4 0.00
675 5 0.00
676 1 0.00
677 4 0.00
678 8 0.00
679 27 0.01
680 14 0.00
681 7 0.00
682 18 0.01
683 15 0.01
684 9 0.00
685 17 0.01
686 12 0.00
687 24 0.01
688 8 0.00
689 9 0.00
690 9 0.00
691 5 0.00
692 12 0.00
693 7 0.00
694 2 0.00
695 4 0.00
696 20 0.01
697 48 0.02
698 215 0.08
699 11 0.00
700 6 0.00
701 12 0.00
702 128 0.05
703 185 0.07
704 23 0.01
705 158 0.06
706 139 0.05
707 167 0.06
708 187 0.07
709 143 0.05
710 149 0.05
711 280 0.10
712 15 0.01
713 15 0.01
714 4 0.00
715 21 0.01
716 37 0.01
717 2 0.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (668 bp):
ACGGGTTTTGGCTAAAAACGCGTTCCGGGGCCCTGACTCAGTTTTTAATGATTTTTGGCCCCGAG
ACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTT
TACGAGCATCAAAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAACATATAGGAAAATCGA
TATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATATTCTATAAGTGTTT
TGGCCAAAGATTGTGGAAAAAATTTTTCGGGCCAATTTTTGCAAAATTTTAGCCGATATCGTTTA
CGTATACCATCACGGGTTTTGGCTAAAAACGCGTTCCGGGCCCTCGGCTCAGTTTTTAATGATTT
ATGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCCAAATTGAATTTAA
GGATTTGATTTTACGAGCATCAGAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAACTATA
GAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCATTGAATTATATATATTCTA
TAAGTGTTTTGGCCAAAAATTGTGGAAAAAATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGA
AATCGTGTACTAACCATC
Found at i:3006 original size:375 final size:374
Alignment explanation
Indices: 2257--2994 Score: 1253
Period size: 375 Copynumber: 2.0 Consensus size: 374
2247 ACATTGAATT
*
2257 ATACATATTCTATAAGTTTTTTGGCCAAAGATTGTGGAAAAAATCTTTCGAGTAAATTTTTGCAA
1 ATACATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAAAATCTTTCGAGTAAATTTTTGCAA
*
2322 AATTTTAGCGGAAATCGTGTACTAACCATCACGGGTTTTAGATAAAAACGCGTTCCGGGGCCCTG
66 AATTTTAGCCGAAATCGTGTACTAACCATCACGGGTTTTAGATAAAAACGCGTTCCGGGGCCCTG
* * * *
2387 CCTCAGTTTCTAATGATTTTTGGCCCCGAGATTCCTTGACATATCTATATTCATCTAACCAAATC
131 CCTCAGTTTCTAATAATATATGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATC
*
2452 TCAGCCAAATTGGATTTAAGGATTTGATTTTACGAGCATCAAAATCATGTTTCGCTTTAATCAGA
196 TCAGCCAAATTGAATTTAAGGATTTGATTTTACGAGCATCAAAATCATGTTTCGCTTTAATCAGA
*
2517 AATTAATTCAGAAACATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGG
261 AATTAATTCAGAAACATATAGGAAAATCGATATTAGAAGCATGAAAAACCCTTCAATCTTTTTGG
*
2582 CGTCGAATTATATATATTCTATAAGTGTTTTGGCCAAAAATCATGGAAA
326 CATCGAATTATATATATTCTATAAGTGTTTTGGCCAAAAATCATGGAAA
* * *
2631 ATACATATTCTATTAGTGTTTTGGCCAAAGATTGTGGAAAAAATCTTTCGGGTCAATTTTTGCAA
1 ATACATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAAAATCTTTCGAGTAAATTTTTGCAA
* *
2696 AATTTTAGCCGAAATCGTGTA-TAAACCATCACGGGTTTTTGGCTAAAAACGCGTTCCGGGGCCC
66 AATTTTAGCCGAAATCGTGTACT-AACCATCACGGG-TTTTAGATAAAAACGCGTTCCGGGGCCC
* * *
2760 TGGCTCAGTTTTTAATAATATATGGCCCTGAGACTCCTTGACATATCTATATTCATCTAACCAAA
129 TGCCTCAGTTTCTAATAATATATGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAA
*
2825 TCTCAGCCAAATTGAATTTAAGGATTTGATTTTACGAGCATCAGAATCATGTTTCGCTTTAATCA
194 TCTCAGCCAAATTGAATTTAAGGATTTGATTTTACGAGCATCAAAATCATGTTTCGCTTTAATCA
* *
2890 TAAATTAATTCAGAAACATATAGGAAAATCGATATTAGAAGCATGAAAAACCCTTCTATCTTTTT
259 GAAATTAATTCAGAAACATATAGGAAAATCGATATTAGAAGCATGAAAAACCCTTCAATCTTTTT
* *
2955 GGTATTGAATTATATATATTCTATAAGTGTTTTGGCCAAA
324 GGCATCGAATTATATATATTCTATAAGTGTTTTGGCCAAA
2995 TATTTTGGAA
Statistics
Matches: 340, Mismatches: 22, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
373 1 0.00
374 93 0.27
375 246 0.72
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (374 bp):
ATACATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAAAATCTTTCGAGTAAATTTTTGCAA
AATTTTAGCCGAAATCGTGTACTAACCATCACGGGTTTTAGATAAAAACGCGTTCCGGGGCCCTG
CCTCAGTTTCTAATAATATATGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATC
TCAGCCAAATTGAATTTAAGGATTTGATTTTACGAGCATCAAAATCATGTTTCGCTTTAATCAGA
AATTAATTCAGAAACATATAGGAAAATCGATATTAGAAGCATGAAAAACCCTTCAATCTTTTTGG
CATCGAATTATATATATTCTATAAGTGTTTTGGCCAAAAATCATGGAAA
Found at i:3543 original size:335 final size:334
Alignment explanation
Indices: 1595--4716 Score: 2017
Period size: 335 Copynumber: 9.1 Consensus size: 334
1585 TGGAAAATAC
* * * * * * *
1595 ATATTCTATTAGTGTTTTGGCTAAAAATTATGGAAAAAAATCTTTCGGGTCAAGTTTTGCAAAAT
1 ATATTCTATAAGTGTTTTGGCCAAAAATTGTGGAAAAAACTTTTTCGAGTCAATTTTTGCAAAAT
*
1660 TTTAGCCGAAATCGTGTATAAGCCATCACGGGTTTTGGCTAAAAACGCGTTCCGGGGCCCTGACT
66 TTTAGCCGAAATCGTGTATAA-CCATCACGGGTTTTGGCTAAAAACGCGTTCCGGGGCCCTGGCT
*
1725 CAGTTTTTAATGATTTATGG-CCCGAGACTCCTAGACCATATCTATATTCATCTAACCAAATCTC
130 CAGTTTTTAATGATTTATGGCCCCGAGACTCCTTGA-CATATCTATATTCATCTAACCAAATCTC
1789 AGCCAAATTGCATTTAAGGATTTGATTTTACGAGCATCAAAATCATGTTTCGATTTAATCAGAAA
194 AGCCAAATTGCATTTAAGGATTTGATTTTACGAGCATCAAAATCATGTTTCGATTTAATCAGAAA
1854 TTAATTCAGAAACATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCA
259 TTAATTCAGAAACATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCA
1919 TTGAATTATAT
324 TTGAATTATAT
* * *
1930 ATATTCTATAAGTGTTTTGGCCAAAGATTGTGG-AAAAA-TTTTTCGGGCCAATTTTTGCAAAAT
1 ATATTCTATAAGTGTTTTGGCCAAAAATTGTGGAAAAAACTTTTTCGAGTCAATTTTTGCAAAAT
* * * * * *
1993 GTTAGCCGATATCGTTTACGTTACCATTACGGTTTTTGGCTAAAAACGCGTTTCC-GGGCCCTCG
66 TTTAGCCGAAATCGTGTA--TAACCATCACGGGTTTTGGCTAAAAACGCG-TTCCGGGGCCCT-G
* * * * *
2057 GCTCAGTTTTCAATGATTTTTGACCCCGTGACTCCTTTACATATCTATATTCATCTAACCAAATC
127 GCTCAGTTTTTAATGATTTATGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATC
* * * *
2122 TCAGCCAAATTGGATTTAAGGATTTAATTTTACAAGCATCAGAATCATGTTTCGATTTAATCAGA
192 TCAGCCAAATTGCATTTAAGGATTTGATTTTACGAGCATCAAAATCATGTTTCGATTTAATCAGA
* * *
2187 AATTAATTCGGAAAC--AT--GAAAATCGATATTAGAAGCGTGAAAAACCCTTCGATCTTTTTGA
257 AATTAATTCAGAAACATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGG
*
2248 CATTGAATTATAC
322 CATTGAATTATAT
* * * *
2261 ATATTCTATAAGTTTTTTGGCCAAAGATTGTGGAAAAAA-TCTTTCGAGTAAATTTTTGCAAAAT
1 ATATTCTATAAGTGTTTTGGCCAAAAATTGTGGAAAAAACTTTTTCGAGTCAATTTTTGCAAAAT
* * * *
2325 TTTAGCGGAAATCGTGTACTAACCATCACGGGTTTTAGATAAAAACGCGTTCCGGGGCCCTGCCT
66 TTTAGCCGAAATCGTGTA-TAACCATCACGGGTTTTGGCTAAAAACGCGTTCCGGGGCCCTGGCT
* * *
2390 CAGTTTCTAATGATTTTTGGCCCCGAGATTCCTTGACATATCTATATTCATCTAACCAAATCTCA
130 CAGTTTTTAATGATTTATGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCA
* *
2455 GCCAAATTGGATTTAAGGATTTGATTTTACGAGCATCAAAATCATGTTTCGCTTTAATCAGAAAT
195 GCCAAATTGCATTTAAGGATTTGATTTTACGAGCATCAAAATCATGTTTCGATTTAATCAGAAAT
*
2520 TAATTCAGAAACATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGT
260 TAATTCAGAAACATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCAT
*
2585 CGAATTATAT
325 TGAATTATAT
** * * * * * *
2595 ATATTCTATAAGTGTTTTGGCCAAAAATCATGGAAAATACATATTCTA-TTAGTGTTTTGGCCAA
1 ATATTCTATAAGTGTTTTGGCCAAAAATTGTGGAAAAAACTTTTTCGAGTCAAT-TTTT-G-CAA
* * *** * ** *** *** * ** * * **
2659 AGATTGTGGAAAAAATCTTTCGGGTCAATTTTTGCA-AAATTTTAGCCGAAATCGTGTAT---AA
63 A-ATTTTAGCCGAAATC-GT-GTAT-AA-CCAT-CACGGGTTTTGGCTAAAAACGCGT-TCCGGG
* * * * ** *** * ** * * * * * * *
2720 ACCAT--CACGGGTTTTTGGCT-AAAAACGCGTTCCGGGGC-CCTGGCTCAGTTTTTAATAAT-A
121 GCCCTGGCTC-AGTTTTT-AATGATTTATG-GCCCCGAGACTCCTTG-ACA-TATCT-ATATTCA
* ** * * * * * ** * * * * * *
2780 TATGGCCCTGAGA-CTCCTTGACATATCTATATTCATCTAACCA---AATCTCAGCCA-AATTGA
180 TCT-AACC--AAATCT-C-AGCCA-A---AT-TGCATTTAAGGATTTGATTTTA-CGAGCA-TCA
** * * * **
2840 ATTTAAGGATTT-GATTTTACGAGCATCAGAATCATGT--TTC-GCTTTAATCATAAATTAATTC
233 AAATCATG-TTTCGA-TTT---A--ATCAGAA--AT-TAATTCAG----AAACAT--A-T-A-GG
* * * *
2901 AGAAACATATAGGAAAATCGATATTAGAAGCATGAAAAACCCTTCTATCTTTTTGGTATTGAATT
279 AAAA-------------TCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCATTGAATT
2966 ATAT
331 ATAT
* *
2970 ATATTCTATAAGTGTTTTGGCCAAATATTTTGGAAAAAAC--TTTC-AGTCAATTTTTGCAAAAT
1 ATATTCTATAAGTGTTTTGGCCAAAAATTGTGGAAAAAACTTTTTCGAGTCAATTTTTGCAAAAT
* * *
3032 TTTAGCCAAAATCGTGTACAAACCATCACGGGTTTTTGGCT-AAAACGCGTTCCGGGG-CCTGAC
66 TTTAGCCGAAATCGTGTA-TAACCATCACGGG-TTTTGGCTAAAAACGCGTTCCGGGGCCCTGGC
* * ** * * *
3095 TCAGTTTTCAATG--TT-CGGCCGAGTGACTCCTTTATATATCTATATTCATCTAACCAAATCTC
129 TCAGTTTTTAATGATTTATGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCTC
* * * *
3157 AGCCACAGTAG-ATTTAAGGATTTGATTTTACGAGCATCAAAATCTTGTTTCGATTTAATCAAAA
194 AGCCA-AATTGCATTTAAGGATTTGATTTTACGAGCATCAAAATCATGTTTCGATTTAATCAGAA
* *
3221 ATTAATTCGGAAACTTATAGGAAAATCGATATTAGAAGCGTG-AAAACCCTTCAATCTTTTTGGC
258 ATTAATTCAGAAACATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGC
*
3285 TTTGAATTATAT
323 ATTGAATTATAT
* * *
3297 ATATTCTATTAGTGTTTTGGCCAAAAATTGTGGAAAAAACTTTTTCGTGTCTATTTTTGCAAAAT
1 ATATTCTATAAGTGTTTTGGCCAAAAATTGTGGAAAAAACTTTTTCGAGTCAATTTTTGCAAAAT
*
3362 TTTAGCCGAAATCGTGCATAAACCCATCACGGGTTTTGGCTAAAAACGCGTTCCGGGGCCCTGGC
66 TTTAGCCGAAATCGTGTAT-AA-CCATCACGGGTTTTGGCTAAAAACGCGTTCCGGGGCCCTGGC
*
3427 TCAGTTTTTAATGATTTATGGCCCCGAGACTCCTTGACATATCTATATTCATCAAACCAAATCTC
129 TCAGTTTTTAATGATTTATGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCTC
* *
3492 AGCCAAATTGCATTGAAGGATTTGATTTAACGAGCATCAAAATCATGTTTCGATTTAATCAGAAA
194 AGCCAAATTGCATTTAAGGATTTGATTTTACGAGCATCAAAATCATGTTTCGATTTAATCAGAAA
*
3557 TTAATTCGGAAACATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCA
259 TTAATTCAGAAACATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCA
3622 TTGAATTATAT
324 TTGAATTATAT
* * * * * *
3633 ATATTCTATAAGTGTTTTGGCCAAAAATTGTGGAAAATACATATTCTA-TTAGTGTTTTGGCCAA
1 ATATTCTATAAGTGTTTTGGCCAAAAATTGTGGAAAAAACTTTTTCGAGTCAAT-TTTT-G-CAA
* * *** * **** *** * ** * * *
3697 AGATTGTGGAAAAAATCTTTCCGGTCA-ATTTTTGCA-AAATTTTAGCCGAAATCGTGTAT---A
63 A-ATTTTAGCCGAAATC-GT---GT-ATAACCAT-CACGGGTTTTGGCTAAAAACGCGT-TCCGG
** * * ** *** * ** * * * * * *
3757 AACCAT--CACAGGTTTTTGGCT-AAAAACGCGTTCCGGGGC-CCTGGCTCAGTTTTTAATGATT
120 GGCCCTGGCTCA-GTTTTT-AATGATTTATG-GCCCCGAGACTCCTTG-ACA-TATCT-AT-ATT
* **** * * * * * ** * * * * * **
3818 TATGGCCCCGAGA-CTCCTTGACATATCTATATTCATCTAACCA---AATCTCAGCCA-AATTGG
178 CATCTAACC-AAATCT-C-AGCCA-A---AT-TGCATTTAAGGATTTGATTTTA-CGAGCA-TCA
** * * *
3878 ATTTAAGGATTT-GATTTTACGAGCATCAGAATCATGT--TTC-GATTTAATCTGAAATTAATTT
233 AAATCATG-TTTCGA-TTT---A--ATCAGAA--AT-TAATTCAGA---AA-C--ATA-TA----
* * *
3939 GGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCGTTTTGGCGTTGAATT
277 GG-AA-A-AT-CG---A----TATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCATTGAATT
*
4004 ATAC
331 ATAT
* * * * *
4008 ATATTCTATAAGTGTTTTGGCCAAAGATTGTGAAAAAAAAC--TTTCGGGTCTATTTTTCCAAAA
1 ATATTCTATAAGTGTTTTGGCCAAAAATTGTG-GAAAAAACTTTTTCGAGTCAATTTTTGCAAAA
* *** * **
4071 TTTTAGCCGAAATCGTGTATTAACGATCACTTTTTTTTTGGCTAAAAACGCGTTCCGGAGCCCCA
65 TTTTAGCCGAAATCGTGTA-TAACCATCAC--GGGTTTTGGCTAAAAACGCGTTCCGGGGCCCTG
* *
4136 GCTCAGTTTTTAATGATTTATGGCCCCAAGACTCCTTGACATATCTATATTCATCTAACGAAATC
127 GCTCAGTTTTTAATGATTTATGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATC
* * *
4201 TCAGCCAAGTTGAATTTAAGGATTTGATTTTACGAGCATCAACATCATGTTTCGATTTAATCAGA
192 TCAGCCAAATTGCATTTAAGGATTTGATTTTACGAGCATCAAAATCATGTTTCGATTTAATCAGA
** * * * *
4266 AATTAATTTGGAAACTTATAGGAAAATCGATATTAGAAACGTGAAAAGCCCTTCAATATTTTTGG
257 AATTAATTCAGAAACATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGG
*
4331 CGTTGAATTATATATAT
322 CATTG-A--AT-TATAT
* *
4348 ATATTTCTATAAGTGTTTTGGCCAAACATTGTGGAAAAAAAC-TTTT-GGGTCAATTTTTGCAAA
1 ATA-TTCTATAAGTGTTTTGGCCAAAAATTGTGG-AAAAAACTTTTTCGAGTCAATTTTTGCAAA
* ** * **
4411 ATTTTAGCCGAAATCATGTACTAAGAATCACGGTTTTTGTTTGTCTAAAAACGCGTTATGGGGCC
64 ATTTTAGCCGAAATCGTGTA-TAACCATCACGGGTTTTG---G-CTAAAAACGCGTTCCGGGGCC
* * * * * * *
4476 CCGACTAAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGATATGTCTACATTCATCTAACCAA
124 CTGGCTCAGTTTTTAATGATTTATGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAA
* * * *
4541 ATCTCAGTCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGTTTCGATTTAAAT
189 ATCTCAGCCAAATTGCATTTAAGGATTTGATTTTACGAGCATCAAAATCATGTTTCGATTT-AAT
* * *
4606 -AGAAATTAATTCGGAAAGATATAGGAAAATCGATACTAGAAGCGTG----A---TTCAATCTTT
253 CAGAAATTAATTCAGAAACATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTT
* *
4663 TTGGCGTCGAATTATAT
318 TTGGCATTGAATTATAT
*
4680 ATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAA
1 ATATTCTATAAGTGTTTTGGCCAAAAATTGTGGAAAA
4717 TACATATTCT
Statistics
Matches: 2138, Mismatches: 449, Indels: 405
0.71 0.15 0.14
Matches are distributed among these distances:
327 68 0.03
328 16 0.01
329 4 0.00
330 184 0.09
331 173 0.08
332 67 0.03
333 41 0.02
334 131 0.06
335 302 0.14
336 145 0.07
337 11 0.01
338 38 0.02
339 43 0.02
340 21 0.01
341 116 0.05
342 23 0.01
343 179 0.08
344 13 0.01
345 3 0.00
346 16 0.01
347 21 0.01
348 18 0.01
349 17 0.01
350 7 0.00
351 4 0.00
352 2 0.00
353 17 0.01
354 13 0.01
355 13 0.01
356 16 0.01
357 13 0.01
358 9 0.00
359 7 0.00
360 7 0.00
361 3 0.00
362 16 0.01
363 13 0.01
364 16 0.01
365 15 0.01
366 11 0.01
367 21 0.01
368 12 0.01
369 22 0.01
370 20 0.01
371 15 0.01
372 20 0.01
373 19 0.01
374 10 0.00
375 161 0.08
376 6 0.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (334 bp):
ATATTCTATAAGTGTTTTGGCCAAAAATTGTGGAAAAAACTTTTTCGAGTCAATTTTTGCAAAAT
TTTAGCCGAAATCGTGTATAACCATCACGGGTTTTGGCTAAAAACGCGTTCCGGGGCCCTGGCTC
AGTTTTTAATGATTTATGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAG
CCAAATTGCATTTAAGGATTTGATTTTACGAGCATCAAAATCATGTTTCGATTTAATCAGAAATT
AATTCAGAAACATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCATT
GAATTATAT
Found at i:3688 original size:40 final size:40
Alignment explanation
Indices: 3633--3709 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
3623 TGAATTATAT
3633 ATATTCTATAAGTGTTTTGGCCAAAAATTGTGGAAAATAC
1 ATATTCTATAAGTGTTTTGGCCAAAAATTGTGGAAAATAC
* *
3673 ATATTCTATTAGTGTTTTGGCCAAAGATTGTGGAAAA
1 ATATTCTATAAGTGTTTTGGCCAAAAATTGTGGAAAA
3710 AATCTTTCCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.36
Consensus pattern (40 bp):
ATATTCTATAAGTGTTTTGGCCAAAAATTGTGGAAAATAC
Found at i:3862 original size:375 final size:376
Alignment explanation
Indices: 3297--4044 Score: 1295
Period size: 375 Copynumber: 2.0 Consensus size: 376
3287 TGAATTATAT
* *
3297 ATATTCTATTAGTGTTTTGGCCAAAAATTGTGGAAAAAACTTTTTCGTGTCTATTTTTGCAAAAT
1 ATATTCTATTAGTGTTTTGGCCAAAAATTGTGGAAAAAACTTTTCCGTGTCAATTTTTGCAAAAT
3362 TTTAGCCGAAATCGTGCATAAACCCATCACGGGTTTTGGCTAAAAACGCGTTCCGGGGCCCTGGC
66 TTTAGCCGAAATCGTGCATAAACCCATCACGGGTTTTGGCTAAAAACGCGTTCCGGGGCCCTGGC
3427 TCAGTTTTTAATGATTTATGGCCCCGAGACTCCTTGACATATCTATATTCATCAAACCAAATCTC
131 TCAGTTTTTAATGATTTATGGCCCCGAGACTCCTTGACATATCTATATTCATCAAACCAAATCTC
3492 AGCCAAATTGCATTGAAGGATTTGATTTAACGAGCATCAAAATCATGTTTCGATTTAATCAGAAA
196 AGCCAAATTGCATTGAAGGATTTGATTTAACGAGCATCAAAATCATGTTTCGATTTAATCAGAAA
*
3557 TTAATTCGGAAACATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCA
261 TTAATTCGGAAACATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCGTTTTGGCA
* *
3622 TTGAATTATATATATTCTATAAGTGTTTTGGCCAAAAATTGTGGAAAATAC
326 TTGAATTATACATATTCTATAAGTGTTTTGGCCAAAAATTGTGAAAAATAC
*
3673 ATATTCTATTAGTGTTTTGGCCAAAGATTGTGGAAAAAA-TCTTTCCG-GTCAATTTTTGCAAAA
1 ATATTCTATTAGTGTTTTGGCCAAAAATTGTGGAAAAAACT-TTTCCGTGTCAATTTTTGCAAAA
* *
3736 TTTTAGCCGAAATCGTGTATAAA-CCATCACAGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCTG
65 TTTTAGCCGAAATCGTGCATAAACCCATCAC-GGGTTTTGGCTAAAAACGCGTTCCGGGGCCCTG
*
3800 GCTCAGTTTTTAATGATTTATGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATC
129 GCTCAGTTTTTAATGATTTATGGCCCCGAGACTCCTTGACATATCTATATTCATCAAACCAAATC
* * * * *
3865 TCAGCCAAATTGGATTTAAGGATTTGATTTTACGAGCATCAGAATCATGTTTCGATTTAATCTGA
194 TCAGCCAAATTGCATTGAAGGATTTGATTTAACGAGCATCAAAATCATGTTTCGATTTAATCAGA
* *
3930 AATTAATTTGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCGTTTTGG
259 AATTAATTCGGAAACATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCGTTTTGG
* *
3995 CGTTGAATTATACATATTCTATAAGTGTTTTGGCCAAAGATTGTGAAAAA
324 CATTGAATTATACATATTCTATAAGTGTTTTGGCCAAAAATTGTGAAAAA
4045 AAACTTTCGG
Statistics
Matches: 352, Mismatches: 18, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
374 7 0.02
375 302 0.86
376 43 0.12
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (376 bp):
ATATTCTATTAGTGTTTTGGCCAAAAATTGTGGAAAAAACTTTTCCGTGTCAATTTTTGCAAAAT
TTTAGCCGAAATCGTGCATAAACCCATCACGGGTTTTGGCTAAAAACGCGTTCCGGGGCCCTGGC
TCAGTTTTTAATGATTTATGGCCCCGAGACTCCTTGACATATCTATATTCATCAAACCAAATCTC
AGCCAAATTGCATTGAAGGATTTGATTTAACGAGCATCAAAATCATGTTTCGATTTAATCAGAAA
TTAATTCGGAAACATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCGTTTTGGCA
TTGAATTATACATATTCTATAAGTGTTTTGGCCAAAAATTGTGAAAAATAC
Found at i:4735 original size:40 final size:40
Alignment explanation
Indices: 4680--4756 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
4670 CGAATTATAT
4680 ATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAATAC
1 ATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAATAC
*
4720 ATATTCTATTAGTGTTTTGGCCAAAGATTGTGGAAAA
1 ATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAA
4757 AAATCTTTCG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (40 bp):
ATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAATAC
Found at i:5304 original size:23 final size:23
Alignment explanation
Indices: 5260--5304 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
5250 ACTCAATTAC
* * * *
5260 TGTTCATGAACACGTTCGTTTAT
1 TGTTCACGAACAAGTCCATTTAT
5283 TGTTCACGAACAAGTCCATTTA
1 TGTTCACGAACAAGTCCATTTA
5305 AACGAGCCGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (23 bp):
TGTTCACGAACAAGTCCATTTAT
Found at i:6610 original size:67 final size:67
Alignment explanation
Indices: 6497--6627 Score: 244
Period size: 67 Copynumber: 2.0 Consensus size: 67
6487 TTTCATATGA
*
6497 TGCTAAGTAACGCAAAAACATATAGATTTATATACATACCACACACACTGAAGAAGACGAGAGAA
1 TGCTAAGTAACGCAAAAACATATAGATTTATATACATACCACACACACTAAAGAAGACGAGAGAA
6562 AG
66 AG
*
6564 TGCTAAGTAACGCAAAAACATATAGATTTATATACATACCATACACACTAAAGAAGACGAGAGA
1 TGCTAAGTAACGCAAAAACATATAGATTTATATACATACCACACACACTAAAGAAGACGAGAGA
6628 GAGAGAGAGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.19
Consensus pattern (67 bp):
TGCTAAGTAACGCAAAAACATATAGATTTATATACATACCACACACACTAAAGAAGACGAGAGAA
AG
Found at i:6627 original size:2 final size:2
Alignment explanation
Indices: 6622--6871 Score: 475
Period size: 2 Copynumber: 124.5 Consensus size: 2
6612 TAAAGAAGAC
6622 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
6664 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GTA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G-A
6707 GA GA GA GTA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA G-A GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
6750 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
6792 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
6834 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
Statistics
Matches: 245, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.00
2 240 0.98
3 4 0.02
ACGTcount: A:0.49, C:0.00, G:0.50, T:0.01
Consensus pattern (2 bp):
GA
Done.