Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007687.1 Corchorus capsularis cultivar CVL-1 contig07708, 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: 29980
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1599 original size:330 final size:331
Alignment explanation
Indices: 24--7627 Score: 6000
Period size: 330 Copynumber: 22.9 Consensus size: 331
14 CTGGGCCCCA
* * * *
24 ACTCAGTTTTGCAT-ACTTTTTGGCGCCAAGACTCATTGAATTATCTATATTCATCTAACGAAAT
1 ACTCTGTTTTGCATGA-TTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAAT
* * * * * * *
88 CTCAGCCACATTGGATTTAATGATTTGTTTTAACGAGCATCTCAATC-TGGTTTCAATTGAATTG
65 CTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT-AATCATGTTTTCGATTTAATTA
* * * *
152 GAAATTAATTCGGAAAAAAAAATAGTAAAA-CAATATAAGAAGCGTGAGAAGCCCTTCAATCTTT
129 GAAATTAATTCGG---AAAAAATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTT
** * * * *
216 TTAACGTTGAATTATATATTTTTTATGAGTGTTGTGGCAAAAAATTGAGGATAAATTTTTTGGGT
191 TTGGCGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGAGGAGAAATTTTTTGGGT
* * * *
281 CAATTTTCGCAAAATTTTAGCCAAAATCGTGTACTAACCATCAC-GATTTTTGTCT-AAAACGTG
256 CAATTTTTGCAAAA-TTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTG-CTAAAAACGCG
* *
344 TTCCGAAACCCCG
319 TTCCGAAGCCCGG
* * * *
357 ACTCTATTTTGCATGATTTTTGGTGTCAAGACTCCTTGAAATATCTATATTCATCTAACGAAATC
1 ACTCTGTTTTGCATGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATC
** * * *
422 TCAGTCACATTGGATTTAACGATTTTTTTTTACGAGCATCTGAATCATG-TTTCGATTTAATAAG
66 TCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT-AATCATGTTTTCGATTTAATTAG
* * * * * *
486 AAATTTATTC-G-TAAAATAGGAAAATCGACATTAGAAGCGTGAATAGTCTTTCAATCTTTTTGG
130 AAATTAATTCGGAAAAAATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGG
* * * * * *
549 CATTGAATTATACAGTTTTTATGAGTATTATAGCAAAAAATTGAGCAGAAATTTTTTGGGTCAAT
195 CGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGAGGAGAAATTTTTTGGGTCAAT
* * * **
614 TTTTGGCAAAATTAAGCTGAAATCGTGTACTAACTATCACGGTTTTTTGCTAAAATTGCGTTCC-
260 TTTT-GCAAAATTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTCCG
* *
678 AGTGCCC-C
324 A-AGCCCGG
* * * * *
686 AGCTCTATTTTGCATGATTTTT-GTCGTCAAGTCTCATTGAAATATCTAT-TTCCATATAATCAA
1 A-CTCTGTTTTGCATGATTTTTGGT-GCCAAGACTCATTGAAATATCTATATT-CATCTAACCAA
** ** * * * *
749 ATCTTTCCCACATTAAATTTAAGGATTTGTTTTTATGAGTATCTAATCTTG-TCTCGATTTAATT
63 ATCTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAATCATGTTTTCGATTTAATT
** * * * * *
813 AGAAATTAATTCATAAAAAATAGGAAAAACGATATTAAAATCTTGAAAAACCCTTCAATCTTTTT
128 AGAAATTAATTCGGAAAAAATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTT
* * * * ***
878 GTCTTTGAATTATATATATATATATATTTTATGAGTATTATGGCTAAAAATGGAGGA-AAAAAAT
193 GGCGTTG----A-AT-TATATAT-T-TTTTATGAGTATTATGGCCAAAAATTGAGGAGAAATTTT
* * * * * ** *
942 TTCGGTTATTTTTTTTTGTAAAATTTAGCCGAAATCGTGTACTAACAATCACATTATTTTTTGTT
250 TTGGGTCA---ATTTTTGCAAAATTTAGCCGAAATCGTGTACTAACCATCAC--GGTTTTTTGCT
* **
1007 AAAAACGAGTTTTGGGAA-CCC-G
310 AAAAACGCG--TTCCGAAGCCCGG
** * * * * *
1029 TTTCAGTTTTGCATGCTTTTTGGCAG-TAAGACTCATTGAAATATCTATATATTCATCTAACAAA
1 ACTCTGTTTTGCATGATTTTTGG-TGCCAAGACTCATTGAAATATC--TATATTCATCTAACCAA
* * * * * **
1093 ATCTCAACCATATTGGTTTTAATGATTTGTTTTAACGAGCATCTCAATCCGGTTTT-GATTTAAT
63 ATCTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT-AATCATGTTTTCGATTTAAT
* * * * *
1157 TAGAATTTAATTCGGAAAAAAATAGGAAAAT-GATATAAGAAGCGTGAGAAGCGCTTCAATATTT
127 TAGAAATTAATTCGG-AAAAAATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTT
* ** * * * *
1221 TTAGTTTTGAATTACATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAGAATTTTTTTGGTT
191 TTGGCGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGAGGAGAAATTTTTTGGGT
*
1286 CAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGT
256 CAATTTTTGCAAAA-TTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGT
*
1351 TCTGAAGCCCGG
320 TCCGAAGCCCGG
* * * *
1363 ACTCTGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAATTATCTATAATCATCTAACGAAATC
1 ACTCTGTTTTGCATGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATC
* * *
1428 TCAGCCACATTGGATCTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTTC-AATTAATTAG
66 TCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT-AATCATGTTTTCGATTTAATTAG
* * ** **
1492 AAATTTATTC-G-TAAAATAGGAAAATCGATATTAGAAGCGTGAGTAGCGTTTCAATCTTTTTGG
130 AAATTAATTCGGAAAAAATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGG
* * * **
1555 CGTTGAATTATATATTTTTTATGAGTATTATAGCAAAAAATTGAGAAGAAATTTCCTGGGTCAAT
195 CGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGAGGAGAAATTTTTTGGGTCAAT
* ** * * * *
1620 TTTTGGCTAAATGAAGCTGAAATCGTGTA-T-----GCACGATTTTTTGCT-AAAACGCGTT-CT
260 TTTT-GCAAAATTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTCCG
*
1677 AGAGCCCCG
324 A-AGCCCGG
* * * * * *
1686 TCTCTATTTTGCATGATTTTT-GTCGCCAAGTCTCATTGAAATATTTATGTCCATCTAACCAAAT
1 ACTCTGTTTTGCATGATTTTTGGT-GCCAAGACTCATTGAAATATCTATATTCATCTAACCAAAT
* * * * * *
1750 CTTACCCACATTAGATTTAAGGATTTGTTTTTATGAGTATCTAATCTTG-TTTCAATTTAATTAG
65 CTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAATCATGTTTTCGATTTAATTAG
* * * * * * *
1814 AAATTAATTCAGAAAAAATAGAAAAAACAATATTAAAAGCGTGAAAAACCCTTCAATCTTTTT-T
130 AAATTAATTCGGAAAAAATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGG
* * *
1878 CTTTGAATTATATATATTTTATGAGTATTATCTATTATGGCTAAAAATGGAGGGAAAAAATTTGG
195 CGTTGAATTATATATTTTTTATGAG-------TATTATGGC-------------CAAAAA-TT-G
* * * *
1943 TTAATGTTTTGAGAAGAAATTTTTTGGGTAAATATTTTGCAAAATTAAGCCGAAATCGTATACTA
238 ---A-G----GAG-A-AATTTT-TTGGGTCAAT-TTTTGCAAAATTTAGCCGAAATCGTGTACTA
* * * ** *
2008 ACAATCACAGTTTTTTGCTAAAAACTCGTTCCGGGGCCC-T
291 ACCATCACGGTTTTTTGCTAAAAACGCGTTCCGAAGCCCGG
* * ** * * *
2048 AGCTCAGTTTTGCATAATTTTTGACGCGAAGAATCATTGAAATATCTATATTCATCTAACAAAAT
1 A-CTCTGTTTTGCATGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAAT
* * ** * *
2113 CTCAGCCACATTGGATTTAATGATTTGTTTGAACGAGCATCTCAATC-CGGTTTCGATTTAATTA
65 CTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT-AATCATGTTTTCGATTTAATTA
* * ***
2177 GAAATTATTTCGGGAAAAAAATAGGAAAA-CGATATAAGAAGCAG-GGGTAGCCC-TCAATCTTT
129 GAAATTAATTC-GG-AAAAAATAGGAAAATCGATATTAGAAGC-GTGAAAAGCCCTTCAATCTTT
* **
2239 TTAGCGTTGAATTATATGGAATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAGAAATTTTT
191 TTGGCGTTGAA-T-TAT---ATATTTTTTATGAGTATTATGGCCAAAAATTGAGGAGAAATTTTT
*
2304 TGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA-TAAACCATCACGGTTTTTGGCTAAAA
251 TGGGTCAATTTTTGCAAAA-TTTAGCCGAAATCGTGTACT-AACCATCACGGTTTTTTGCTAAAA
*
2368 ACGCGCTCCGAAGCCCCGG
314 ACGCGTTCCGAAG-CCCGG
* * * * * * *
2387 -CTCTGTTTTACATGATTTTTGGTGTCAAGACTCCTAGAAATCTTTATATTCATCTAACTAAATC
1 ACTCTGTTTTGCATGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATC
* * *
2451 TAACCGACATTGGATTTAAGGATTTGTTTTTACGAGTATCTAAATCATG-TTTCGATTTAATTAG
66 TCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT-AATCATGTTTTCGATTTAATTAG
* * * ** *
2515 AAATTAATTCTTG---AAATAGAAAAATCGATATTAGAAACGTGAGTAGCCTTTCAATCTTTTTG
130 AAATTAATTC-GGAAAAAATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTG
* * * * *
2577 GTGTTAAATTATATATTTTTTATGAGTATTATAGCAAAAAATTGAGGATAAATTTTTTGGGTCAA
194 GCGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGAGGAGAAATTTTTTGGGTCAA
* ** * *** *
2642 TTTTTGGCAAAATTAAGCTAAAATCGTGTATTAACCATGACAATTTTTTTTTTTTTGCTAAAATC
259 TTTTT-GCAAAATTTAGCCGAAATCGTGTACTAACCAT--C-A----CGGTTTTTTGCTAAAAAC
*
2707 GCGTT-CTAGAGCCACGG
316 GCGTTCCGA-AGCC-CGG
* * * *
2724 -CTCTATTTTGCATGATTTTT-GTCGCCAAGTCTCATTGAAATATCTATGTCCATCTAACCAAAT
1 ACTCTGTTTTGCATGATTTTTGGT-GCCAAGACTCATTGAAATATCTATATTCATCTAACCAAAT
* * * * *
2787 CTTACCCACATTAGATTTAAGGATTTGTTTTTATGAGAATCTAAT-AT-TGTCTCGATTTAATTA
65 CTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAATCATGT-TTTCGATTTAATTA
* * * * * ** *
2850 AAAATTATTTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAATCCTTTAATCTTTTTG
129 GAAATTAATTCGGAAAAAATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTG
*** * * * *** * *
2915 TATTTGAATTATATATATTTTATGAGTATTATGGCTAAAAATGGAGG-GAAAAAATTTCGGTTAA
194 GCGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGAGGAGAAATTTTTTGGGTCAA
* * * *
2979 TTTTTTGCAAAAATTTAGTCGAAATCGTGTACAAAGCATCATAGGTTTTTTTGCTAAAAACGCGT
259 -TTTTTGC-AAAATTTAGCCGAAATCGTGTACTAACCATCA-CGG-TTTTTTGCTAAAAACGCGT
** * *
3044 TCCGGGGTCCTG
320 TCCGAAGCCCGG
* * * * *
3056 ACTCAGTTTTGCATGATTTTT-GTCGCCAAGACCCATTGAAACATCTATATTCATATAACAAAAT
1 ACTCTGTTTTGCATGATTTTTGGT-GCCAAGACTCATTGAAATATCTATATTCATCTAACCAAAT
* * * * *
3120 ATCAGCCACATTGGATTTAATGATTTGTTTTTATGAGCATCTCAATC-TGCTTTCGATTTAATTA
65 CTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT-AATCATGTTTTCGATTTAATTA
*
3184 GAAATTAATTCGGAGAAAAATAGGAAAA-CGATATAAGAAGCGTGAGAAA-CCCTTCAATCTGTT
129 GAAATTAATTCGGA-AAAAATAGGAAAATCGATATTAGAAGCGTGA-AAAGCCCTTCAATCT-TT
* * * *
3247 TTAGCGTTGAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAGGAGAAAATTTTTGGGT
191 TTGGCGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGAGGAGAAATTTTTTGGGT
* * * **
3312 CAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACATGT
256 CAATTTTTGCAAAA-TTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGT
* **
3377 TCCGACGCCCCA
320 TCCGAAGCCCGG
* * * *
3389 ACTCTGTTTTGCATGATTTTTGGTGCCAAGACTCCTTAAAATATCTGTATTCATCTAACGAAATC
1 ACTCTGTTTTGCATGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATC
* *
3454 TCACCCACATTGGATTTAAGGATTTGTTTTTACAAGTATCTGAATCATG-TTTCGATTTAATTAG
66 TCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT-AATCATGTTTTCGATTTAATTAG
* * * * * ** ** *
3518 AAATTTATTC-G-TAAAATAGGAAAATCAATATTAGAAACATGAGTAGCTTTTCAATCTTTTTAG
130 AAATTAATTCGGAAAAAATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGG
*
3581 CGTTGAATTATATATTTTTCATGAGTATTATGGCCAAAAATTGAGGAGAAATTTTTTGGGTCAAT
195 CGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGAGGAGAAATTTTTTGGGTCAAT
* * * * * *
3646 TTTTGGCAAAATTAAGCTGAAATCGTGTACTAACCATCACAGTTTTTTGCTAAAAGCGCGTCCCA
260 TTTT-GCAAAATTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTCCG
3711 AAGCCCCGG
324 AAG-CCCGG
* ** * * * * * *
3720 -CTCTATTTTGCATGATTTTTCTTGCCAAGTCTCATTGGAATATGTATGTCCATCTATCCAAATC
1 ACTCTGTTTTGCATGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATC
* * * * * *
3784 TTACCCACATTAGATTTAAGGACTTT-CTTTTATGAGTATCTAATC-T-TCTATCGATTTAATTA
66 TCACCCACATTGGATTTAAGGA-TTTGTTTTTACGAGCATCTAATCATGT-TTTCGATTTAATTA
* * * * * * * *
3846 GAAATTAATTCAGAAAAAATAGAAAAAAT-AATATTAAAAGCATGAAAAACCCTTCAATCATTAT
129 GAAATTAATTCGGAAAAAATAG-GAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTT
* * * * ** ** * * ** *
3910 GTCTTTAAATTATATATATTTTATGAGTATTACAGCTGAAAATGGAGGGGAAAAATTTT-GGTTA
193 GGCGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGAGGAGAAATTTTTTGGGTCA
* **** *
3974 ATTTTTTGCAAAAATTTAGCCGAAATC----ACCTCA-CAT-TTTTTTTTTTGGCTAAAAACGCA
258 A-TTTTTGC-AAAATTTAGCCGAAATCGTGTA-CTAACCATCACGGTTTTTT-GCTAAAAACGCG
**
4033 TTCCGGGGCCTCGG
319 TTCCGAAGCC-CGG
* * * * * * * **
4047 -TTCAGTTTTGCATTATTTTTTGAGCAAAGACTCATTGAAATATCTATATTCATCAAAATAAATC
1 ACTCTGTTTTGCATGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATC
* * * *
4111 TCATCCACATTGGATTTAATGATATT-TTTTTACGAGCATCTCAATC-CGGTTTCGATTTAATTA
66 TCACCCACATTGGATTTAAGGAT-TTGTTTTTACGAGCATCT-AATCATGTTTTCGATTTAATTA
* *
4174 GAAATTAATTCGGAAAAAATAGGAAAA-AGATA-TATGAAGCGTGAGAAGCCCTTCAATCTTTTT
129 GAAATTAATTCGGAAAAAATAGGAAAATCGATATTA-GAAGCGTGAAAAGCCCTTCAATCTTTTT
* * *
4237 AGTGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAGAAATTTTTTGGGTCA
193 GGCGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGAGGAGAAATTTTTTGGGTCA
* * *
4302 ATTTTTGTAAAATTTTAG-C-----C--G----AA--ATCAC-GATTTTTGACTAAAAACACGTT
258 ATTTTTGCAAAA-TTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTG-CTAAAAACGCGTT
*
4352 CCGAAGCCC-C
321 CCGAAGCCCGG
* * * * * *
4362 AGCTCTGTTTTGCATGATTTTTGGTGACAAGACTCCTAGAAATCTTTATATTCATCTAACTAAAT
1 A-CTCTGTTTTGCATGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAAT
* * ** *
4427 CTAAGCCACATTGGATTTATTGATTTCTTTTTACGAGCATCTGAATCATG-TTTCGATTTAATTA
65 CTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT-AATCATGTTTTCGATTTAATTA
** * * * * * *
4491 GAAATTAATTC--TTAAAATAGAAAAATCGATATTAGAAACGTGAATAGTCTTTCAATATTTTTG
129 GAAATTAATTCGGAAAAAATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTG
*** * * *
4554 TTATTCAATTATATATTTTTTATGAGTATTATAGCAAAAAATTGAGGAGAAATTTTTTGGGTCAA
194 GCGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGAGGAGAAATTTTTTGGGTCAA
* * * * *
4619 TTTTTGGCAAAATTAAGCTGAAATAGTGTATTAACCATGACAGTTTTTTTTTGTTTTTTTGTTTT
259 TTTTT-GCAAAATTTAGCCGAAATCGTGTACTAACCATCAC-G---------G-TTTTTTG----
* * *
4684 TTTTTTTCTAAAATCACGTT-CTAGAGCCAC-G
308 -------CTAAAAACGCGTTCCGA-AGCC-CGG
* * * *
4715 ACTCTATTTTGCATGATTTTT-GTCGCCAAGTCTCATTGAAATATCTATGTCCATCTAACCAAAT
1 ACTCTGTTTTGCATGATTTTTGGT-GCCAAGACTCATTGAAATATCTATATTCATCTAACCAAAT
* * * * * * *
4779 CTTACCCACATTAGATTTAAGGATTTGTTTTTATGAGAATCTAATCTTG-TCTCGATTTAATTAA
65 CTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAATCATGTTTTCGATTTAATTAG
* * * ** * *
4843 AAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAATCCTTTAATCTTTTTGT
130 AAATTAATTCGGAAAAAATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGG
* * * ** *
4908 CTTTGAATTATATATATTTTATGAGTATTATGGCTAAAAA-TGAAGG-GAAAAAATTTT-GGTTA
195 CGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTG-AGGAG-AAATTTTTTGGGTCA
* * * *
4970 ATTTTTTTGCAAAAATTTAGCCGAAATCGTGTACGAAGCATCATAGTTTTTTTTGCTAAAAACGC
258 A--TTTTTGC-AAAATTTAGCCGAAATCGTGTACTAACCATCA-CG-GTTTTTTGCTAAAAACGC
* * * *
5035 GTTTCG-GGATCCTG
318 GTTCCGAAG-CCCGG
* * * * **
5049 ACTCAGTTTTGCATGATTTTTGGCGCCAAAACTCATTGAAACATCTATATTCATCTAATGAAATC
1 ACTCTGTTTTGCATGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATC
* * * *
5114 TCAACCACATTGGATTTAATGATTTATTTTTATGAGCATCTCAATC-T-TATTTCGATTTAATTA
66 TCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT-AATCATGT-TTTCGATTTAATTA
* *
5177 GAAATTAATTCGGAAAAAATAGGAAAA-CGATATAAGAAGCGTGACAAA-CCCTTCAATATTTTC
129 GAAATTAATTCGGAAAAAATAGGAAAATCGATATTAGAAGCGTGA-AAAGCCCTTCAATCTTTT-
* * * * * * *
5240 TAGCATTGAATTATATATATTTTATGAGTATTGTAGCCAAAAATCGAGGAGAAAATTTTTGGGTC
192 TGGCGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGAGGAGAAATTTTTTGGGTC
* * ** * *
5305 AATTTCTGCAAAACTTTAACCGAAATCACGTACTAACCATCAC-GTTTTTGGCTAAAAACGTGTT
257 AATTTTTGCAAAA-TTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTT
* **
5369 TCGAAGCCCCA
321 CCGAAGCCCGG
* * * * *
5380 ACTCTGTTTTGCATGATTTTTGGTGTCAAGACTCCTTAAAATATCTGTATTCATCTAACGAAATC
1 ACTCTGTTTTGCATGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATC
* *
5445 TCGCCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCATG-TTTCGATTTAATTAG
66 TCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT-AATCATGTTTTCGATTTAATTAG
* * * ** * * *
5509 AAATTTATTC-G-TAAAATAGGAAAATCGATATTAGAAACGTGAGTAGCCTTTCAATATTTTTAG
130 AAATTAATTCGGAAAAAATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGG
* * *
5572 CATTGAATTATATATTTTTCATGAGTATTATGGCCAAAAATTGAGGAGAAATTTTTTGAGTCAAT
195 CGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGAGGAGAAATTTTTTGGGTCAAT
* * ** * * *
5637 TTTTGGGAAAATTAAGTTGAAATCGTGTACGT---TATCA-GAGTTTTTTGCTAAAAGCGCGTCC
260 TTTT-GCAAAATTTAGCCGAAATCGTGTAC-TAACCATCACG-GTTTTTTGCTAAAAACGCGTTC
* *
5698 CAAAGCCCCG
322 CGAAGCCCGG
* * * * * * * * *
5708 TCTCTATTTTGCATGATTTTTGTTGCCAAGTCTCATTAAAATATGTATGTCCATCTATCCAAATC
1 ACTCTGTTTTGCATGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATC
* * * ** * *
5773 TTACCCACATTAGATTTAAGGATTT-TCTTTTATGAATATTTAATC-T-TCTATCGATTTAATTA
66 TCACCCACATTGGATTTAAGGATTTGT-TTTTACGAGCATCTAATCATGT-TTTCGATTTAATTA
* * * * * * *
5835 GAAATTAATTCAGAAAAAATAGAAAAAAT-AATATTAAAAGCATGAAAAACCCTTCAATCATTTT
129 GAAATTAATTCGGAAAAAATAG-GAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTT
* * * * * ** * * ** *
5899 GTCTTTGAATTATATATATGTTATGAGTATTACGGCTGAAAATGGAGGGAAAAAAATTTT--GTT
193 GGCGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGA-GGAGAAATTTTTTGGGTC
* *
5962 AATTTTTTGCAAAAAATTTAGCCGAAATC--G--C--ATCA-CA-GTTTTTTTTGCTAAAAACGC
257 AA-TTTTTGC--AAAATTTAGCCGAAATCGTGTACTAACCATCACG-GTTTTTTGCTAAAAACGC
**
6019 GTTCCGGGGCCCCGG
318 GTTCCGAAG-CCCGG
* * ** * * * ** *
6034 -CTCAGTTTTGCATTATTTTTGAAGCC-AGAATCATCGAAATATCTATATTCATCAAAATAGATC
1 ACTCTGTTTTGCATGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATC
* * * * * *
6097 TCATCCACATTGGATTTAATGATTTTTTTTTACGAGTATCTCAATC-CGGTTTCGATTTAATTAG
66 TCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT-AATCATGTTTTCGATTTAATTAG
* * *
6161 AAATTAATTCGGAAAAAATAGGAAAA-CGATATAAGAAGCGTGAGAAGCCCTTCAATCTTTTTAG
130 AAATTAATTCGGAAAAAATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGG
* * * * *
6225 TGTTGAATTATATATTTTTTTATTAGTATTGTGGCTAAAAATTGAGGAGAATTTTTTTGGGTCAA
195 CGTTGAATTATATA-TTTTTTATGAGTATTATGGCCAAAAATTGAGGAGAAATTTTTTGGGTCAA
* * *
6290 TTTTTGCAAAATTTTAGTCGAAATCATGTACTAACCATCACGG-TGTTTGACTAAAAACGCGTTC
259 TTTTTGCAAAA-TTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTG-CTAAAAACGCGTTC
*
6354 CGAAGCCC-C
322 CGAAGCCCGG
* * * **
6363 AGCTCTGTTTTACATGATTTTTGGTGCCAAGACGCCTTGAAATATCTATATTCATCTAAGGAAAT
1 A-CTCTGTTTTGCATGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAAT
* * * * * *
6428 CTCAGCCACATTGAATTTAGGGATTTGTTTTTACAAGCATCTGAATCAT-ATTTGGATTTAATTA
65 CTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT-AATCATGTTTTCGATTTAATTA
* * ** * *
6492 GAAATTTATTCGTAAAAAA-AGGAAAATCGATATTAGAAGCGTGACTAGCCTTTCAATATTTTTG
129 GAAATTAATTCGGAAAAAATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTG
* * *
6556 GCATTGAATTATATATTTTTTTATGAGTATTATGGCAAAAAATTGAAGAGAAATTTTTTGGGTCA
194 GCGTTGAATTATATA-TTTTTTATGAGTATTATGGCCAAAAATTGAGGAGAAATTTTTTGGGTCA
* * * * ** *
6621 TTTTTTGGCAAAATTAAGCTGAAGTCGTGTACTAACCATCACGACTTTTTGCTAAAAACTCGTT-
258 ATTTTT-GCAAAATTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTC
6685 ---A--CCGG
322 CGAAGCCCGG
* * * * * * * *
6690 GCTGTATTTTGCATGATTTTTGTTGCCAAGTCTCATTGAAATATGTAT-GTCAATCTAACTAAAT
1 ACTCTGTTTTGCATGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTC-ATCTAACCAAAT
* * * * * * * *
6754 TTTACCCACATTAGATTTATGGATATGTTTTTATGAGTATCTAATC-T-TCTATCGATTTAATTA
65 CTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAATCATGT-TTTCGATTTAATTA
* * * * * * *
6817 GAAATTAATTC--AGAAAATAGGAAAAACGATATTAGTTA-CATGAAAAGACCATAAATCTTTTT
129 GAAATTAATTCGGAAAAAATAGGAAAATCGATATTAG-AAGCGTGAAAAGCCCTTCAATCTTTTT
* * * * * *
6879 GGTGTTGAGTTATATATATTTTTATTATTATTGTGGCCAAAAATTGAGGAGAAATTTTTTGGGTT
193 GGCGTTGAATTATATAT-TTTTTATGAGTATTATGGCCAAAAATTGAGGAGAAATTTTTTGGGTC
* * ** *
6944 AATTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTTATTAAAAACGTGTT
257 AATTTTTGCAAAA-TTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTT
** *
7009 CCGCGGCCCCG
321 CCGAAGCCCGG
* * * ** * * * *
7020 CCTATGTGTTGCATGATTTTAAGCGCCAAGTCTCATTTAAATATCTATATCCATCTAACCAAATC
1 ACTCTGTTTTGCATGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATC
* * * *
7085 TCACCCACATTGGATTTAACGATTTATTTTTACGAGCATTTGAATCAT-CTTTCGATTTAATTAG
66 TCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT-AATCATGTTTTCGATTTAATTAG
* * * *
7149 AAATTAATTCGGAAAAAATAGGAAAA-CAGATATTTGAAGTGTGAAAAGCCTTTCAATATTTTTG
130 AAATTAATTCGGAAAAAATAGGAAAATC-GATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTG
* * * * * * * *
7213 GTGTTGAATTATATA-TTTTT-T---TATTGTGGCCAAAGATTAAGTAAAAATTCTTTCGGGTAA
194 GCGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGAGGAGAAATT-TTTTGGGTCA
* * * * * *
7273 ATTTTTGTAAAATTTAACCGAAATCGTG---TAA-CATCAC-GATTCTTGACTAAAAACACGTTA
258 ATTTTTGCAAAATTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTG-CTAAAAACGCGTTC
**
7333 CGGGGCCCAGG
322 CGAAGCCC-GG
* * * * **
7344 -CTCAGTTATACATGATTTTT-GTCGCAAAGAAGCATTGAAATATCTATATTCATCTAACCAAAT
1 ACTCTGTTTTGCATGATTTTTGGT-GCCAAGACTCATTGAAATATCTATATTCATCTAACCAAAT
** * * * *
7407 CTCATACATATTGGATTTAAGGATTTGTTTTTATGAGTATCTAAT-AT-TGTCTCGATTTAATTA
65 CTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAATCATGT-TTTCGATTTAATTA
* * * * * * **
7470 GAAATTAATTCAGAAAAAATAGGAAAAACTATATTAAAAACGTGAAAAACCCTTTGATCTTTTTG
129 GAAATTAATTCGGAAAAAATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTG
* * * * * * * *
7535 TCTTTGAATTATATATATTTTATGAATATTATGGCTAAAAATTGA-GAGGAAA--ATTTCGGTTA
194 GCGTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGAGGA-GAAATTTTTTGGGTCA
7597 ATTTTTTGCAAAAATTTAGCCGAAATCGTGT
258 A-TTTTTGC-AAAATTTAGCCGAAATCGTGT
7628 TTATTCCTCG
Statistics
Matches: 5789, Mismatches: 1165, Indels: 640
0.76 0.15 0.08
Matches are distributed among these distances:
315 11 0.00
316 98 0.02
317 146 0.03
318 2 0.00
321 7 0.00
322 112 0.02
323 252 0.04
324 323 0.06
325 149 0.03
326 131 0.02
327 273 0.05
328 196 0.03
329 354 0.06
330 680 0.12
331 413 0.07
332 329 0.06
333 456 0.08
334 293 0.05
335 217 0.04
336 93 0.02
337 323 0.06
338 135 0.02
339 34 0.01
340 36 0.01
341 7 0.00
342 53 0.01
343 11 0.00
344 49 0.01
345 68 0.01
346 17 0.00
348 2 0.00
349 3 0.00
350 5 0.00
351 33 0.01
352 108 0.02
353 92 0.02
354 32 0.01
355 4 0.00
356 28 0.00
357 5 0.00
362 12 0.00
363 105 0.02
364 39 0.01
365 22 0.00
366 15 0.00
367 3 0.00
370 13 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (331 bp):
ACTCTGTTTTGCATGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATC
TCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAATCATGTTTTCGATTTAATTAGA
AATTAATTCGGAAAAAATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGC
GTTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGAGGAGAAATTTTTTGGGTCAATT
TTTGCAAAATTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGAA
GCCCGG
Found at i:8909 original size:9 final size:9
Alignment explanation
Indices: 8895--8930 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
8885 CACTTCCTCC
*
8895 ATGTTATTA
1 ATGTTAGTA
8904 ATGTTAGTA
1 ATGTTAGTA
8913 ATGTTAGTA
1 ATGTTAGTA
8922 ATGTTAGTA
1 ATGTTAGTA
8931 TTTTTCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.47
Consensus pattern (9 bp):
ATGTTAGTA
Found at i:10543 original size:29 final size:29
Alignment explanation
Indices: 10526--10607 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
10516 TTTTGCTCTA
10526 TGAACTTCAATTTTGGACATTTTATCCCC
1 TGAACTTCAATTTTGGACATTTTATCCCC
10555 TGAACTTCAATTTTGGACATTTTATCCCC
1 TGAACTTCAATTTTGGACATTTTATCCCC
*
10584 TGAACTTCAATTTTGTGACGTTTT
1 TGAACTTCAATTTTG-GACATTTT
10608 GCCCCCTCAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 44 0.86
30 7 0.14
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.44
Consensus pattern (29 bp):
TGAACTTCAATTTTGGACATTTTATCCCC
Found at i:10812 original size:29 final size:29
Alignment explanation
Indices: 10758--10818 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
10748 CGCAAACGTC
* *
10758 CCAAAATTGAAGTTCAGGAGGTAAAATAT
1 CCAAAATTGAAGTTCAGGAGGCAAAACAT
10787 CCAAAATTGAAGTTCA-GAGGGCAAAACAT
1 CCAAAATTGAAGTTCAGGA-GGCAAAACAT
10816 CCA
1 CCA
10819 TACGCTACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (29 bp):
CCAAAATTGAAGTTCAGGAGGCAAAACAT
Found at i:20979 original size:329 final size:324
Alignment explanation
Indices: 19131--20980 Score: 1644
Period size: 329 Copynumber: 5.7 Consensus size: 324
19121 CCAACTAAAT
** * * *
19131 TTTTGCATGATTTTT-GTATAAATACTCCTTGAAATATCTATATTCACCGAACAAAATCTCAGCC
1 TTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCC
* * * * *
19195 ACGTTCGATTTAAGTATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAAAAATTAA
66 ACATTAGATATAAG-ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * *
19260 TTCGAAAAAAATGGAAAAA--ATATTAAAAGCGTGAAAAGCCCATCAATCTTTTTGGAGTTGAAT
130 TTTGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAAT
*
19323 TATATATTTTTTGTGAGTATTGTGGCAAAAAATTGAGAAAAAAAAAACCTTTTCGGGTCAGTTTT
195 TATATATTTTTTATGAGTATTGTGGCAAAAAATTGAG---AAAAAAA--TTTTCGGGTCAGTTTT
* * * *
19388 T----A-GCCGAAATCGTGTACTAACCATCACAGTTTCTGACTAAAAACGCGTTCCGAAGCCCCG
255 TCAAAATGCTGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCCGGA-CCCCG
*
19448 ACTCAA
319 GCTCAA
* * * * *
19454 TTTTGCATGATTTTTAGTGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATGTCAACC
1 TTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCC
*
19519 ACATTAGATATAAGAATTTGTTTTTACGTAGCTTCTGAATCTTGTTTCGATTTAATTAGAAATTA
66 ACATTAGATATAAG-ATTTGTTTTTACG-AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
** * * *
19584 ATTCAAACAAAAATTCGAAAAACGATATTAGAAGCTTGAAAAACCCTTCAAT-TTTTTCGGCGTT
129 ATTTGAA-AAAAA-TGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTT-GGCGTT
* * * * * * *
19648 GAATTATATATTTTTTCTGGGTATTGTGGCAAAGAATTAAGGAAAAAAATTTTCTGATCGGTTTT
191 GAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGA-GAAAAAAATTTTCGGGTCAGTTTT
** * * * *
19713 TACAAAATTTTATTCGAAATCGT-T--T----ATCACGGTTTATGGCTAAAAACGCGTTCTGGGG
255 T-CAAAA---TGCT-GAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTC-CGGA
* * * *
19771 TCCTGTCTCAG
314 CCCCGGCTCAA
* * * *
19782 TTTTGCCTGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATTTCAGTC
1 TTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCC
* * *
19847 ATATTGGATATAACGATTTATCTTTT-CGAGCATCTGAATCTTGTTTCGATTTAATT-GAAAATT
66 ACATTAGATATAA-GATTTGT-TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG-AAATT
* * *
19910 AATTCAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAAGCCCGTCAATATTTTTGGCGTT
128 AATT-TGAAAAAAATGGAAAAACGATATTAGAAGCGTG-AAAAGCCCTTCAATCTTTTTGGCGTT
* * * * * * * * *
19975 GAATTATATATTTTTTTTGAGTATTATAGTAAAAAATTAAGAAAGAACTTTTCTGGTAAGTTTTT
191 GAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTTTTT
* * ** * *
20040 ---AGT-C-AAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACGCGTTCCCGAGCCCCGG
256 CAAAATGCTGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCCGGA-CCCCGG
20100 CTCAA
320 CTCAA
* * * * * * *
20105 TTTTACATGATTTTTGGCGCAAAAACTCCTTCAAGTATCTATATTCATCAAACCAAATGTCAGCC
1 TTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCC
* * *
20170 ACATTGGATATAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAATAA
66 ACATTAGATATAA-GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * *
20235 -TT--------TGGAAAAATGATATTAGAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAAT
130 TTTGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAAT
* * * ** *
20291 TATATATTTTTTTCTGATTATTGTGGCAAAAAATTCAGAAAAAAA-AATCGGGTTAGTTTTT---
195 TATATA-TTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTTTTTCAA
* * * * *
20352 -A-GCCGAAATCGTGTA-T---CATCACGGTTTTTGGGCTAAAAACGCATTTCGGAGCCCGGCTC
259 AATGCTGAAATCGTGTACTAACCATCACGGTTTTT-GACTAAAAACGCGTTCCGGACCCCGGCTC
20411 AA
323 AA
* * * *
20413 TTTTCCATGATTTTTGGCAG-AAAGACTCATTGAAATATGTATATTCATCTAACCAAATCTCAGC
1 TTTTGCATGATTTTTGGC-GTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGC
* * * *
20477 CACATTAGATTTAACGATTTGTTTTTACGTGTATCTGAATATTGTTTCGATTTAATTAGAAA-TA
65 CACATTAGATATAA-GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * * * ** *
20541 AATTGAAAAAAATGGGAAAACGATATTTA-AAGCGAGAGAAA-CCTTTC-ATTTTTTTTTCATTG
129 ATTTGAAAAAAATGGAAAAACGATA-TTAGAAGCGTGA-AAAGCCCTTCAATCTTTTTGGCGTTG
* * * *
20603 AATTGTGTATTTTTCTA--ACTATTGTGGAAAAAGAAATTGAGGAAAAAAATTTT-GGGTCAGTT
192 AATTATATATTTTT-TATGAGTATTGTGG-CAAA-AAATTGA-GAAAAAAATTTTCGGGTCAGTT
* * * * * * **
20665 TTTGCAAAATTTTCGCTGAAATCCTTTACTAACCATCATGGTTTTTTATTAAAATCATGTTCCGG
253 TTT-CAAAA---T-GCTGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCC-G
*
20730 GACCCCGGCTCAG
312 GACCCCGGCTCAA
* * * **
20743 TTTTGCATGA-TTTTGGCGTAAATACTCCTTGAAATATCTATATTCATCGAACAAAATCCCAATC
1 TTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCC
* * * * * * *
20807 AAATTCGATTTAATGATTTATTTTTACGAGCATCTAAATCTTGTTTTGTTTTAATTAGAAATTAA
66 ACATTAGATATAA-GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* *
20872 TTTGGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAAT-TTTTTGGCGTTAAA
130 TTT-GAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAA
* * *
20936 TTATATATTTTTTATGACTATTTTTGCAAAAAATTGAGAAAAAAA
194 TTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAAA
20981 AAATTCTGTT
Statistics
Matches: 1244, Mismatches: 204, Indels: 152
0.78 0.13 0.09
Matches are distributed among these distances:
307 3 0.00
308 132 0.11
309 18 0.01
311 2 0.00
312 54 0.04
313 62 0.05
314 8 0.01
315 24 0.02
316 47 0.04
317 8 0.01
319 2 0.00
321 1 0.00
322 7 0.01
323 157 0.13
324 67 0.05
325 53 0.04
326 59 0.05
327 108 0.09
328 120 0.10
329 183 0.15
330 55 0.04
331 54 0.04
332 11 0.01
334 1 0.00
335 8 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (324 bp):
TTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCC
ACATTAGATATAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAAT
TTGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATT
ATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTTTTTCAAAA
TGCTGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCCGGACCCCGGCTCAA
Found at i:21403 original size:2 final size:2
Alignment explanation
Indices: 21396--21422 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21386 GGTGTTGAAT
21396 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
21423 TAGGTATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21677 original size:326 final size:318
Alignment explanation
Indices: 21076--22427 Score: 990
Period size: 323 Copynumber: 4.2 Consensus size: 318
21066 TTTCAAAGTA
* ** * * *
21076 TTGGCGTTGAATTATATATTTTTTTTGAGTATTGTGGGAAAGAATTGAGGAAAAA--TTT----T
1 TTGGCGTTGAATTATATATTTTTTATGAGTATTGTGACAAAAAATTTAGAAAAAACTTTTCCGAT
* * *
21135 -AGTTTTTGCAAAATTTTAGT-CGAAATCGTTTACTCATCACGGTTTATGGCTTAAAACACGTTA
66 CAGTTTTTGCAAAATTTTA-TCCGAAATCGTTTACTCATCACGGTTTATGGCTAAAAACGCGTTC
* * * * *
21198 TGAGGCCCTAACTCAGTTTTG-AATAATTTTTTAGCGTAAAGACTCTTTTGAAATATCTATATTC
130 CGGGGCCC-CACTCAGTTTTGCAA-GA-TTTTTAGCGTAAAGACTC-CTTGAAATATCTATATTC
* * * * * * * * *
21262 ATCGAACCAAATCCCAGCCACATTCGATTTAACGATTTGTTTTTACGAGCATCTTAATGTTGTTT
191 ATCAAACCAAATCTCAGCCATATTGGATATAAGGATTT-TTTTTTCGAGCATCTCAATCTTGTTT
21327 CGATTTAAATAGAAATTAATTCGGAAAAAAAAAAAAAA-GA-A-A-AA-C-CCT-TCAATCTTT
255 CGATTTAAATAGAAATTAATTCGGAAAAAAAAAAAAAACGATATAGAAGCACCTATCAATCTTT
* * * * *
21384 TTGGTGTTGAATTATATATATATATATATATATATATATTAGGTATTGTGGC-AAAGATTTGAGG
1 TTGGCGTTG------A-AT-TATATAT-T-T-T-T-TATGA-GTATTGTGACAAAAAATTT-AGA
* *
21448 AAAAATTTTTCCGATCAGTTTTTGCAAAATTTTATCCGAAATCGTTTACTCATCACGGTTTATGA
51 AAAAACTTTTCCGATCAGTTTTTGCAAAATTTTATCCGAAATCGTTTACTCATCACGGTTTATGG
21513 CTAAAAACGCGTTCCGGGGCCCCAGCTCAGTTTTGCAAGATTTTT-GCGTAAAGACTCCTTGAAA
116 CTAAAAACGCGTTCCGGGGCCCCA-CTCAGTTTTGCAAGATTTTTAGCGTAAAGACTCCTTGAAA
*
21577 TATCTATATTCATCAAAGCAAATCTCAGCCATATTGGATATAAGGATTTCTTTTTTCGAGCATCT
180 TATCTATATTCATCAAACCAAATCTCAGCCATATTGGATATAAGGATTT-TTTTTTCGAGCATCT
* *
21642 CAATCTTGTTTCGACTTAAATAGAAACTAATTCGGAAAAAAAAATGGAAAAACGATATTAGAAGC
244 CAATCTTGTTTCGATTTAAATAGAAATTAATTCGGAAAAAAAAA---AAAAACGATA-TAGAAGC
21707 GTTAAAATCCTATCAATCTTT
305 ------A-CCTATCAATCTTT
* * * * *
21728 TTGGCGTTGAATTGTATATTTTTTCTGAGTATTTTGACAAAAAATTTAGAAAAAACTTTTCGGGT
1 TTGGCGTTGAATTATATATTTTTTATGAGTATTGTGACAAAAAATTTAGAAAAAACTTTTCCGAT
* * *
21793 CAG----T------TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGT
66 CAGTTTTTGCAAAATTTTATCCGAAATCGTTTACT---CATCACGGTTTATGGCTAAAAACGCGT
* * * * * *
21848 TCCGGAGGCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATTTTCA
128 TCCGG-GGCCCCACTCAGTTTTGCAAGATTTTTAGCGTAAAGACTCCTTGAAATATCTATATTCA
21913 TCAAACCAAATCTCAGCCATATTGGATATAAGGA-TTTTTTTTCGAGCATCTCAATCTTGTTTCG
192 TCAAACCAAATCTCAGCCATATTGGATATAAGGATTTTTTTTTCGAGCATCTCAATCTTGTTTCG
* * * * *
21977 ATTTAATTAGGAATTAATTCGGAAAAGAAAAATGGAAAAACGATATTAGAAACGTGAAAAGCTCG
257 ATTTAAATAGAAATTAATTCGGAAAA-AAAAA---AAAAACGATA-TAG-AA---G--CACCT-A
22042 TCAATCTTT
310 TCAATCTTT
* * * * * * * *
22051 TTGGCGTTAAATTGTATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGATAAAACTTTTCGGGT
1 TTGGCGTTGAATTATATATTTTTTATGAGTATTGTGACAAAAAATTTAGAAAAAACTTTTCCGAT
* * * **
22116 CAGTTTTTAGCCAAA----AT-CG---T-GTACTAAC-CATCACGGTTTTTTACTAAAAACGCGT
66 CAGTTTTT-GCAAAATTTTATCCGAAATCGT--TTACTCATCACGGTTTATGGCTAAAAACGCGT
* * * * * * **
22171 T-TGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGATTTATCTATATTCA
128 TCCGGGGCCCC-ACTCAGTTTTGCAAGATTTTTAGCGTAAAGACTCCTTGAAATATCTATATTCA
** * * * * *
22235 TCGCACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTACGTAGCATCTGAATTTTGTTT
192 TCAAACCAAATCTCAGCCATATTGGATATAAGGATTT-TTTTTTCG-AGCATCTCAATCTTGTTT
* * * ** * * ** *
22300 CGATTTAATTAGAAATTAGTTCGGAAAATATGAAAAAACAATATTAGAAACGTGAAAAGCCCGTT
255 CGATTTAAATAGAAATTAATTCGGAAAAAAAAAAAAAACGATA-TAG-AA---G--CA-CCTATC
22365 AATCTTT
312 AATCTTT
* * *
22372 TTGGCGTTGAATTATATA--TTTTCTGAGTATTGTGGCAAAAAATTGAG-AAAAACTTT
1 TTGGCGTTGAATTATATATTTTTTATGAGTATTGTGACAAAAAATTTAGAAAAAACTTT
22428 CGGGTCATTT
Statistics
Matches: 875, Mismatches: 94, Indels: 140
0.79 0.08 0.13
Matches are distributed among these distances:
308 8 0.01
314 1 0.00
315 2 0.00
316 7 0.01
317 1 0.00
318 9 0.01
319 30 0.03
320 20 0.02
321 61 0.07
322 150 0.17
323 173 0.20
324 82 0.09
325 44 0.05
326 104 0.12
327 16 0.02
328 8 0.01
329 81 0.09
330 30 0.03
331 11 0.01
332 1 0.00
333 2 0.00
334 3 0.00
335 2 0.00
336 6 0.01
337 2 0.00
338 1 0.00
343 3 0.00
344 17 0.02
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (318 bp):
TTGGCGTTGAATTATATATTTTTTATGAGTATTGTGACAAAAAATTTAGAAAAAACTTTTCCGAT
CAGTTTTTGCAAAATTTTATCCGAAATCGTTTACTCATCACGGTTTATGGCTAAAAACGCGTTCC
GGGGCCCCACTCAGTTTTGCAAGATTTTTAGCGTAAAGACTCCTTGAAATATCTATATTCATCAA
ACCAAATCTCAGCCATATTGGATATAAGGATTTTTTTTTCGAGCATCTCAATCTTGTTTCGATTT
AAATAGAAATTAATTCGGAAAAAAAAAAAAAACGATATAGAAGCACCTATCAATCTTT
Found at i:22261 original size:322 final size:323
Alignment explanation
Indices: 21477--22765 Score: 1537
Period size: 323 Copynumber: 4.0 Consensus size: 323
21467 TTTTGCAAAA
* * * * *
21477 TTTTATCCGAAATCGTTTACT---CATCACGGTTTATGACTAAAAACGCGTTCCGGGGCCCCAGC
1 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCCGGAGCCCCGGC
* * *
21539 TCAGTTTTGCAAGATTTTT-GCGTAAAGACTCCTTGAAATATCTATATTCATCAAAGCAAATCTC
66 TCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTC
* * * *
21603 AGCCATATTGGATATAAGGATTTCTTTTTTCGAGCATCTCAATCTTGTTTCGACTTAAATAGAAA
131 AGCCACATTGGATATAAGGACTTCTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAA
* * * * *
21668 CTAATTCGGAAAAAAAAATGGAAAAACGATATTAGAAGCGTTAAAATC-CTATCAATCTTTTTGG
196 TTAATTCGGAAAAAAAAATGGAAAAACGATATTAGAAACGTGAAAAGCTC-GTCAATCTTTTTGG
* * *
21732 CGTTGAATTGTATATTTTTTCTGAGTATTTTGACAAAAAATTTAGAAAAAACTTTTCGGGTCAGT
260 CGTTGAATTGTATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG-AAAAACTTTTCGGGTCAGT
* * *
21797 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGGCCCGAC
1 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCCGGAGCCCCGGC
* *
21862 TCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATTTTCATCAAACCAAATCTC
66 TCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTC
* *
21927 AGCCATATTGGATATAAGGA-TT-TTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGGAA
131 AGCCACATTGGATATAAGGACTTCTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAA
21990 TTAATTCGGAAAAGAAAAATGGAAAAACGATATTAGAAACGTGAAAAGCTCGTCAATCTTTTTGG
196 TTAATTCGGAAAA-AAAAATGGAAAAACGATATTAGAAACGTGAAAAGCTCGTCAATCTTTTTGG
*
22055 CGTTAAATTGTATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGATAAAACTTTTCGGGTCAGT
260 CGTTGAATTGTATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGA-AAAACTTTTCGGGTCAGT
* * *
22120 TTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTTACTAAAAACGCGTT-TGGAGCCCCGGC
1 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCCGGAGCCCCGGC
** ** *
22184 TCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGATTTATCTATATTCATCGCACCAAATGTC
66 TCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTC
* * * * *
22249 AGCCACATTGGATATAAGGATTTGTTTTTACGTAGCATCTGAATTTTGTTTCGATTTAATTAGAA
131 AGCCACATTGGATATAAGGACTTCTTTTTTCG-AGCATCTCAATCTTGTTTCGATTTAATTAGAA
* * * * * *
22314 ATTAGTTCGG---AAAATATGAAAAAACAATATTAGAAACGTGAAAAGCCCGTTAATCTTTTTGG
195 ATTAATTCGGAAAAAAAAATGGAAAAACGATATTAGAAACGTGAAAAGCTCGTCAATCTTTTTGG
* *
22376 CGTTGAA-T-TATATATTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAC-TTTCGGGTCATT
260 CGTTGAATTGTATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAACTTTTCGGGTCAGT
* * * * * *
22437 TTTTAGCCGAAATCGTGTACTAACCATCACGGATTTTGACTAAAGACGCATTCCGGGGTCACGGC
1 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCCGGAGCCCCGGC
* * * * ** * *
22502 TCTATTTTACATGGTTTTTGGTGTTGAGACTCCTTGAAATATCTTTATT-AGTCAAATCAAATCT
66 TCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCA-TCAAACCAAATCT
* * * * ** *
22566 -AGGTCACATTGGAATATTTAAGGACTTGTTTTTACGTGCATCGGAATATTGTTTCGATTTAATT
130 CA-GCCACATTGG-ATA--TAAGGACTTCTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATT
* ** * * *
22630 AGAAATTAATTC--AAAAAAATAT-TTAAAATGATATTA-AAAGCATGAAAAG-TCCTCCAATCT
191 AGAAATTAATTCGGAAAAAAAAATGGAAAAACGATATTAGAAA-CGTGAAAAGCTCGT-CAATCT
* * * * *
22690 TTTTGGCGTTGAATTATATATATTTTTATTGAGTGTT-TTGCCAAAAATTGAGGAAAAATCTTTT
254 TTTTGGCGTTGAATTGTATAT-TTTTT-CTGAGTATTGTGGCAAAAAATTGA-GAAAAA-CTTTT
22754 -GGGTCA-T
315 CGGGTCAGT
22761 TTTTA
1 TTTTA
22766 CCATCATGGT
Statistics
Matches: 848, Mismatches: 93, Indels: 52
0.85 0.09 0.05
Matches are distributed among these distances:
317 60 0.07
318 71 0.08
319 43 0.05
320 92 0.11
321 77 0.09
322 143 0.17
323 225 0.27
324 89 0.10
325 45 0.05
326 3 0.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (323 bp):
TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCCGGAGCCCCGGC
TCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTC
AGCCACATTGGATATAAGGACTTCTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAA
TTAATTCGGAAAAAAAAATGGAAAAACGATATTAGAAACGTGAAAAGCTCGTCAATCTTTTTGGC
GTTGAATTGTATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAACTTTTCGGGTCAGT
Found at i:26257 original size:27 final size:27
Alignment explanation
Indices: 26219--26274 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
26209 CTTCTTATTC
26219 ATAGGTTCATCTCCCTATTTAGATTGG
1 ATAGGTTCATCTCCCTATTTAGATTGG
26246 ATAGGTTCATCTCCCTATTTAGATTGG
1 ATAGGTTCATCTCCCTATTTAGATTGG
26273 AT
1 AT
26275 GCATGAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (27 bp):
ATAGGTTCATCTCCCTATTTAGATTGG
Found at i:29879 original size:23 final size:24
Alignment explanation
Indices: 29849--29898 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
29839 TCTTTTAAAT
29849 AATAATTAG-CTATTTTAAAAAAA
1 AATAATTAGCCTATTTTAAAAAAA
*
29872 AATAATTAGCTCTTTTTTAAAAAAA
1 AATAATTAGC-CTATTTTAAAAAAA
29897 AA
1 AA
29899 AAAAGGGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 9 0.38
25 15 0.62
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (24 bp):
AATAATTAGCCTATTTTAAAAAAA
Done.