Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009947.1 Corchorus capsularis cultivar CVL-1 contig09968, 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: 124147
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:669 original size:337 final size:336
Alignment explanation
Indices: 1--6898 Score: 5985
Period size: 334 Copynumber: 20.7 Consensus size: 336
*
1 AAATCCATTGTGGGTGATATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCGAAA
1 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCGAAA
* * *
66 AATCGTGCAAAACTGAGTCGGGGCCCCGAAAAGCATTTTTGGCTAAAAACCGTGAT-G---G-AC
66 AATCATGCAAAACTGAGTCGGGGCCCCGAAATGCGTTTTTGGCTAAAAACCGTGATGGTTAGTAC
* *
126 ACAATTTCGGCTAAAATATTGGAAAAACTGACCCGAAATTTTTTTCATCAATTTTTTGCCACAAT
131 ACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTTTCATCAATTTTTTGCCACAAT
*
191 ACTTAGGAAAACATATATAATTCAACA-CAAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCA
196 ACTCA-GAAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCA
* *
255 TTTTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCAAAAAAAGATTCAGGTGCTCGTAA
260 TTTTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTAA
320 AAACAAATCCTT
325 AAACAAATCCTT
*
332 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGTTATTTCAAGGAGTCTTTCTGCCGAAA
1 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCGAAA
*
397 AATCATGCAAAACTGAGTCGGGGCCCCGAAATGTGTTTTTGGCTAAAAACCGTGATGGTTAGTAC
66 AATCATGCAAAACTGAGTCGGGGCCCCGAAATGCGTTTTTGGCTAAAAACCGTGATGGTTAGTAC
462 ACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTTTCATCAATTTTTTGCCACAAT
131 ACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTTTCATCAATTTTTTGCCACAAT
* *
527 ACTCAGGAAAACATATATAATTCAACACCAAAAAAATTGATGGGTTTTTCGTGCTTCTAATATCA
196 ACTCA-GAAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCA
*
592 TTTTTCAATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTAA
260 TTTTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTAA
657 AAACAAATCCTT
325 AAACAAATCCTT
*
669 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAA
1 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCGAAA
* *
734 AATCATGCAAAACTGATTCGGGGCCCCGAAATACGTTTTTGGCTAAAAACCGTGATGGTTAGTAC
66 AATCATGCAAAACTGAGTCGGGGCCCCGAAATGCGTTTTTGGCTAAAAACCGTGATGGTTAGTAC
*
799 ACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTTTTCCTCAACTTTTTTGCCACA
131 ACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAA-TTTTTTCATCAA-TTTTTTGCCACA
*
864 ATA-TACAGAAAACATATATAATTAAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATAT
194 ATACT-CAGAAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATAT
*
928 CATTTTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTTCTCGT
258 CATTTTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGT
993 AAAAACAAATCCTT
323 AAAAACAAATCCTT
* * * * *
1007 AAATCCATTGTGGCTGAGAATTGGTTAGATGAAAATAGATATTTCAAGGAGTATTTTTG-C-AAA
1 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCGAAA
* ** * * *
1070 AATCATGCGAAACTGAG-CAGTTGCCCCG-AATCGCGTTTTTAGCCAAAAACCATGATGGTTAGT
66 AATCATGCAAAACTGAGTC-GGGGCCCCGAAAT-GCGTTTTTGGCTAAAAACCGTGATGGTTAGT
* ** ** * *
1133 ACACAATTTCGGCTAAAATATTGGAAAAACAAACCCGAATTTTTTTTCCTCAAATTTTTGCCACA
129 ACACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTTTCATCAATTTTTTGCCACA
* * * * * *
1198 ATACTCAGAAAACA-AT-TACTCCCTC-ACATTCAAAATAAGTGCAACACTGGGAATATTACA--
194 ATACTCAGAAAACATATATAAT---TCAACA-CCAAAAAAATTG--A-A--GGG--TTTTTCATG
** * * * * * * * *
1258 CAAACCAAGA-CA---AT-GATTAATTGGTTTT-AAATTTA---GTAAA-AAATC-ACTTAA-AA
248 C-TTCTAATATCATTTTTCCATT-TTTTGTTTTCGAATTTATCTCTAAATAAATCGA---AACAA
* * * ** *
1311 TGACATTC--TTAC-CCTTCAAA-AAAT-TTT
308 -G--ATTCAGGTGCTCGTAAAAACAAATCCTT
* * * * * * *** *** ** * * ***
1338 ATAA-ACAAT-TAGATAAAATTT--TTCTCTCCCT-TCCCAAATTTCCAA-GA-TAATTAAAGAT
1 A-AATCCATTGTGGGTGAGATTTGGTTAGATGAATAT-AGATATTT-CAAGGAGT-CTTTCTG--
* ** * ** * * * **** * ******** * ***
1396 TC-AACTACCTAACCAACAC-AAGT-AGGG-ATATATATG-GAAACAAATTACAAATTAT-ATTG
60 CCGAAAAATC-ATGCAAAACTGAGTCGGGGCCCCGAAATGCGTTTTTGGCTAAAAACCGTGA-TG
* * * * ** ** * * *
1455 GTT-TTATA-AATGTT-GCACT-TAATA-TG-AATGACTGCGAATCTTG-AAA-TATTGCA-CTT
123 GTTAGTACACAAT-TTCG-GCTAAAATATTGCAAAAACT--G-A-CCCGAAAATTTTTTCATC-A
* ** * * * *** ** *
1511 ATTTTGAATGGGAGGGAGTA-TAATCCAACA-CCAGAA---AA-A---------TTGAAGGGTTT
181 ATTTT--TTGCCA--CAATACTCAGAAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTT
* * * *
1561 TTCATGCTTCTAATATCATTTTTCC--TTTTT-TTTCCGAATTTATCACTAATTAAATCTAAACA
242 TTCATGCTTCTAATATCATTTTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACA
* * *
1623 AGATTCAGGTGCTCGTAAATACAAATTCAT
307 AGATTCAGGTGCTCGTAAAAACAAATCCTT
** * * *
1653 AAATCCATTGTGACTGAAATTTGGTTAGATGAATATAGATATTTCAAGGCGTCTTTCTGCCAAAA
1 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCGAAA
* ** * *
1718 AATCATGCAAAACTAAGT-AAGG-ACCAAAACT-CGTTTTTGGCTAAAAACCGTGATGGTTAGTA
66 AATCATGCAAAACTGAGTCGGGGCCCCGAAA-TGCGTTTTTGGCTAAAAACCGTGATGGTTAGTA
** * * * *
1780 CACAATTTAAGCTAAAATAATGTAAAAACTGACCCGAAAATTTTTTCCTCAACTTTTTGCCACAA
130 CACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTTTCATCAATTTTTTGCCACAA
** * * * ** *
1845 TAAACAGAAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGATTTTTCACACTTCTAAAATC
195 TACTCAG-AAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATATC
* * * *
1910 GTTTTTCCA---TTT-TTTACGAATTTATCTCTGATTAAATCGAAACAAGATTCAGGTGCTCGTA
259 ATTTTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTA
1971 AAAACAAATCCTT
324 AAAACAAATCCTT
* * *
1984 AAATCCCTTGTGGGTGAAATTTGGTTAGATCAATATAGATATTTCAAGGAGTCTTTCTGCCGAAA
1 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCGAAA
* *
2049 AATCATGCAAAACTGAGTCGGGGCTCCGAAATGCGTTTTTGGCAAAAAACCGTGATGGTTAGTAC
66 AATCATGCAAAACTGAGTCGGGGCCCCGAAATGCGTTTTTGGCTAAAAACCGTGATGGTTAGTAC
* *
2114 ACAATTTAGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTTTCATCCATTTTTTGCCACAAT
131 ACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTTTCATCAATTTTTTGCCACAAT
*
2179 ACTCAGGAAAACATATATAATTCAACACCAAAAAAAATGAAGGGTTTTTCATGCTTCTAATATCA
196 ACTCA-GAAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCA
* * * *
2244 -TTTTCC-CTTTTT-TTTTCGAATTTATCACTAATTAAATCGAAACAAGATACAGGTGCTCGTAA
260 TTTTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTAA
*
2306 ATACAAATCCTT
325 AAACAAATCCTT
** * * * *
2318 AAATCCATTGTGAATGAAATTTGGTTAGATAAATATAGATATTTCAAGGTGTCTTTCTGCCAAAA
1 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCGAAA
* *
2383 AATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCTAAAAACCGTGATGGTTAGTAC
66 AATCATGCAAAACTGAGTCGGGGCCCCGAAATGCGTTTTTGGCTAAAAACCGTGATGGTTAGTAC
* * * * *
2448 ACAATTTCGGCTTAAATATTGTAAAAACTGTCTCGAAAATTTTTTCCTCAATTTTTTGCCACAAT
131 ACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTTTCATCAATTTTTTGCCACAAT
** * * * * * *
2513 AAACA-AAAA-AAATATAATTTAACGCCAAAAAAATTGACGGATTTTTCATGCTTCTAATATCGT
196 ACTCAGAAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCAT
* *
2576 TTTTCCA---TTT-TTTTCGAATTTATCTCTAATTAAATCGAAACAAGATTTAGGTGCTCGTAAA
261 TTTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTAAA
*
2637 AACAAATTCTT
326 AACAAATCCTT
* ** * * *
2648 AAATCCATTGTCGCCGAGATTTGGTTAGATGAAAATAGATATTTCAAGGAGACTTTTTG-C-AAA
1 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCGAAA
* * * * *
2711 AATCATGCGAAAA-TGAG-CAGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCATGATGATTAGT
66 AATCATGC-AAAACTGAGTC-GGGGCCCCGAAATGCGTTTTTGGCTAAAAACCGTGATGGTTAGT
* ** *
2774 AAACAATTTCGGCTAAAATATTGCAAAAACAAACCCGAAAATTTTTTCTTCAATTTTTTGCCACA
129 ACACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTTTCATCAATTTTTTGCCACA
**
2839 ATACTCAGAAAAACATATATAATTCAACACCAAAAAAATTGAAGACTTTTTCATGCTTCTAATAT
194 ATACTCAG-AAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATAT
* * * * *
2904 CATTTTT-CA-ATTTT-TTTTCGAATTTATCTCCAATTAAATCGAAACAAGATGCATGTGCTCGT
258 CATTTTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGT
*
2966 AAATACAAATCCTT
323 AAAAACAAATCCTT
** * * * * *
2980 AAATCCATTGTGACTGAAATTTTGTTAGATGAATATAGATATTTCAAGGTGTCTTTCGGCCAAAA
1 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCC-GAA
* * * *
3045 AAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCTAAAAAATCGTGTTGGTTAGT
65 AAATCATGCAAAACTGAGTCGGGGCCCCGAAATGCGTTTTTGGCT-AAAAACCGTGATGGTTAGT
* * * * * *
3110 ACACAATATCGGCTAAAATATCGTAAAATCTGACCCGAAGATTTTTTCCTCAATTTTTTGCCACA
129 ACACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTTTCATCAATTTTTTGCCACA
** * * * * * *
3175 ATAAACAGAAAAAAATATATAATTCAACGCCAAAGAAATTGAAGGATTTTTCACGCTTTTAATAT
194 ATACTCAG-AAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATAT
* * **
3240 CGTTTTTCCATTTTTT-TTTTCGAATTTATCTCT-AATGAAATCGAAACAAGATTCAGGTTCTAT
258 CATTTTTCCATTTTTTGTTTTCGAATTTATCTCTAAAT-AAATCGAAACAAGATTCAGGTGCTCG
3303 TAAAAACAAATCCTT
322 TAAAAACAAATCCTT
* * * * * * * *
3318 AAATCCATTGAGGCTGAGAATTGGTAAGATGAAAATAGATATTTCAATGAGTATTTTTG-C-AAA
1 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCGAAA
* * * * * * * *
3381 AATCATGCGAAACTAAGTCGGGGCCCCGAAACGTGTTTTTAGCCAAAAACCATGATGGTCAGTAC
66 AATCATGCAAAACTGAGTCGGGGCCCCGAAATGCGTTTTTGGCTAAAAACCGTGATGGTTAGTAC
* *
3446 ACAATTTCGGCTAAAATATTGCAAAAAC-AATCTCGAAAATTTTTTCCA-CAATTTTTTGCCACA
131 ACAATTTCGGCTAAAATATTGCAAAAACTGA-CCCGAAAATTTTTT-CATCAATTTTTTGCCACA
*
3509 ATACTCAGAAAAACATATATAATTCAACACCAAAAAAA-TGAAGGGTTTATCATGCTTCTAATAT
194 ATACTCAG-AAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATAT
* * *
3573 CATCTTTCC---TTTT-TTTTCGAATTTATCACTAATTAAATCGAAACAAGATAT-AGGTGCTCG
258 CATTTTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGAT-TCAGGTGCTCG
*
3633 TAAATACAAATCCTT
322 TAAAAACAAATCCTT
** * * * *
3648 AAATCCATTGTGACTGAAATTTGGTTAAATGAATATAGATATTTCAAGGTGTCTTTCTGCCAAAA
1 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCC-GAA
* * ** *
3713 AAAT-ATGCAAAACTAAGTAAGGACCCCCAAAACT-CGTTTTTGGCTAAAAACCGTGATGGTTAG
65 AAATCATGCAAAACTGAGT-CGGGGCCCCGAAA-TGCGTTTTTGGCTAAAAACCGTGATGGTTAG
* * * * * *
3776 TACACAATTTCAGCTAAAATATTGTAAAAACTGACCCGAAAATTTCTTCCTGAACTTTTTGCCAC
128 TACACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTTTCATCAATTTTTTGCCAC
** * * * * * ** *
3841 AATAAACAGAAAAAAAAATATAATTCAACGCCAAGAAAATTGAAGGATTTTTCACACTTCTAAAA
193 AATACTCAG-AAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATA
* * * *
3906 TCGTTTTTCCA--TTTT-TTTACGAATTTGTCTCTAATTAAATCGAAACAAGATTCAGGTGCTCG
257 TCATTTTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCG
3968 TAAAAACAAATCCTT
322 TAAAAACAAATCCTT
* *
3983 AAATCCATTGTCGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAA
1 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCGAAA
* * *
4048 AATCATGCAAAACTGAGTCGGGGCCCCGAAATGCGTTTTTCGTTAAAAACCGTGTTGGTTAAGTA
66 AATCATGCAAAACTGAGTCGGGGCCCCGAAATGCGTTTTTGGCTAAAAACCGTGATGGTT-AGTA
* *
4113 CACAATTTAGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTTTTCATCAATCTTTTGCCACA
130 CACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAA-TTTTTTCATCAATTTTTTGCCACA
* *
4178 ATACTCAGGAAAACATATATAATTCAACACCAAAAAAAATGAAGGGTTTTTCATGCTTTTAATAT
194 ATACTCA-GAAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATAT
*
4243 CATTTTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACACGATTCAGGTGCTCGT
258 CATTTTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGT
4308 AAAAACAAATCCTT
323 AAAAACAAATCCTT
* *
4322 AAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAA
1 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCGAAA
* * * *
4387 AATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTGGCGAAAACCCGTGATGGTTTGTAC
66 AATCATGCAAAACTGAGTCGGGGCCCCGAAATGCGTTTTTGGCTAAAAACCGTGATGGTTAGTAC
** * * * *
4452 ACAATTTCGGCTAAAATATTGCAAAAACAAACCCGAGAATTTTTTCCTCCATTTTTTGCCGCAAT
131 ACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTTTCATCAATTTTTTGCCACAAT
* ** * * *
4517 A-TACATAGAAAA-ATATGTAATTCAATGCCAAAAAAATTGAAGGATTTTTCACGCTTTTAATAT
196 ACT-C--AGAAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATAT
* * * * *
4580 CGTTTTTCCATTTTTT-TTCTTCGAATTTATCTCTAAATAAATAGCAACAAGATTCAGGTTCTCT
258 CATTTTTCCATTTTTTGTT-TTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCG
4644 TAAAAACAAATCCTT
322 TAAAAACAAATCCTT
* ** * * * *
4659 AAATCCATTGAGCCTGAGAATTGGTTAGATGAAAATAGATATTTCAAGGAGTATTTTTG-C-AAA
1 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCGAAA
* * *** * * *
4722 AATCATGCGAAACTGAGCCGGGGCCCCGAAACATGTTTTTAGCCAAAAACCATGATGGTTAGTAC
66 AATCATGCAAAACTGAGTCGGGGCCCCGAAATGCGTTTTTGGCTAAAAACCGTGATGGTTAGTAC
* * * *
4787 ACAATTTCGGCTAAAATATTGCAAAAAC-AATCCCGAAAATTTTTTTCCTCAAATTTTTGCCATA
131 ACAATTTCGGCTAAAATATTGCAAAAACTGA-CCCGAAAA-TTTTTTCATCAATTTTTTGCCACA
* * * * ** *
4851 GTACGCATAATACATATATTTTTCAACACCAAAAAAATTGAAGGGTTTTTCATGGTTCTAATATC
194 ATACTCAGAAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATATC
* * * * * *
4916 ATTTTT-C---TTTT-TTTTCCATTTTATCACTAATTAAATCGAAATAAGATTCAGATGCTCGTA
259 ATTTTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTA
*
4976 AATACAAATCCTT
324 AAAACAAATCCTT
* ** * * *
4989 AAGTCCATTGTGATTGAAATTTGGTTAGATGGATAAATATAGATATTTTAAGGTGTCTTTCTGCC
1 AAATCCATTGTGGGTGAGATTTGGTTAGAT-G---AATATAGATATTTCAAGGAGTCTTTCTGCC
* * * ** *
5054 AAAAAATCATGCAAAACTAAGTAAGGACCCCCAAAACT-CGTTTTTGGCTAAAAACCGTGATGGT
62 GAAAAATCATGCAAAACTGAGT-CGGGGCCCCGAAA-TGCGTTTTTGGCTAAAAACCGTGATGGT
* * * *
5118 TAGTACACAATTTCAGCTAAAATATTGTAAAAACTGACCCGAAAATTATTTTCCTCAACTTTTTG
125 TAGTACACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAATT-TTTTCATCAATTTTTTG
** * * * * **
5183 CCACAATAAACAGAAAA-AAATAATAATTTAACGCCAAAAAAATTGAAGGATTTTTCACACTTCT
189 CCACAATACTCAGAAAACATAT-ATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCT
* * * *
5247 AAAATCGTTTTTCCATTTTTTAG-----GAATTTATCTCTAATTAAATCGAAACAAGAATCAGGT
253 AATATCATTTTTCCATTTTTT-GTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGT
*
5307 TCTCGTAAAAACAAATCCTT
317 GCTCGTAAAAACAAATCCTT
5327 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCGAAA
1 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCGAAA
*
5392 AATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTGGCTAAAAACC------G-TAGTAC
66 AATCATGCAAAACTGAGTCGGGGCCCCGAAATGCGTTTTTGGCTAAAAACCGTGATGGTTAGTAC
* * *
5450 ACAATTTCGGCTAAAATATTGCAAAAATTGACCCGAAAATTTTTTCCTCAATTTTTTGTCACAAT
131 ACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTTTCATCAATTTTTTGCCACAAT
* * ** * * *
5515 AAAT-AGAAAAAATATATATAATTCAACGTCAAAAAAATT-AAGGATTTTTTACGCTTCTAATAT
196 -ACTCAG--AAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATAT
* * * **
5578 CGTTTTTCCA----TTATTTTCGAATTTATCTCTAATTAAATCGAAACAAGATTCTTGTGCTCGT
258 CATTTTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGT
* *
5639 GAAAAAAAAAATCATT
323 --AAAAACAAATCCTT
* ** ** ** * ** * * * *
5655 AATTGAAGGGT-TTTCATTTTTTCGAATTTGAAGGAT-AATTCTTAAATCCAATGTGGCTAA-GA
1 AAATCCATTGTGGGTGA-GATTT-G--GTT--A-GATGAA-T-ATAGAT---AT-T-TC-AAGGA
** * * *** ** **
5717 GT-TGATTC-GATGAATATAGAT-ATTTC--AA-GGAGTCTTTATG-CCAAAAACCTTGCGAAGC
51 GTCT--TTCTGCCGAA-A-A-ATCA-TGCAAAACTGAGTC--GGGGCCCCGAAA---TGCG--TT
* * * * ** ** * * ** * * * *
5775 TGTGTCGAGACCCCGAAACCCGTTTTTTGCCAAAAATCGTGAT-GGTTTACACGAT-TTCGACTA
103 TTTGGCTAAAAACCGTGA--TGGTTAGT-AC-ACAAT--T--TCGG-CTA-A-AATATT-G-C-A
* ** * * * *
5838 AAAACCT-ACCCGAAAAATTTTTCCCCAATTTCTTGCCACAATACTAAAAAAAAATATATAATTC
154 AAAA-CTGACCCGAAAATTTTTTCATCAATTTTTTGCCACAATACTCAGAAAACATATATAATTC
** *
5902 AATGCC-AAAAAATTGAAGGGTTTATCATGCTTCTAATATCATTTTTCCA--TTTT-TTTTCGAA
218 AACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCATTTTTCCATTTTTTGTTTTCGAA
* * *
5963 TTTATTTTTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCCTT
283 TTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCCTT
* * * * *
6017 AAATCCATTGTGGCTGAGATTTGATTAGATGAATATACATATTTCAAGGAGTTTTTCTACC-AAA
1 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCGAAA
* * * * * * * * *
6081 AATAATGCAAAACTAAGTCGGGACCTCGAAACGCGTTTTAAGCCAAAAAAATCGTGATGGTTAGT
66 AATCATGCAAAACTGAGTCGGGGCCCCGAAATGCGTTTT-TGGC-TAAAAACCGTGATGGTTAGT
* * *
6146 GCACAATTTCGGCTAAAATATTTCAAAAACTGATCC-AAAATTTTTTTTC-TCAATTTTTTGCCA
129 ACACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAA--TTTTTTCATCAATTTTTTGCCA
* * * * * *
6209 CAATACTTAGAAAAGATATATATTTCAACGCCAAAAAAATTGAAAGGG-TTTTCACGGTTCTAAT
192 CAATACTCAGAAAACATATATAATTCAACACCAAAAAAATTG-AAGGGTTTTTCATGCTTCTAAT
* ** * * * * *
6273 ATCTTTTTTCCA--TTTT-TTCACAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
256 ATCATTTTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTC
* * **
6335 GAAAAAATAAATAATT
321 GTAAAAACAAATCCTT
* * * * *
6351 AAATCCATTGTGGCTGAGATTTAGTTACATGAATATAGATATTTTAAAGAGTCTTTCTGCC-AAA
1 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCGAAA
* * * * * **
6415 AATCATGCAAAACTGTGTAGGGGCCCCGAAACGCATTTTTTGAC-AAAATTCGTGA----T-GT-
66 AATCATGCAAAACTGAGTCGGGGCCCCGAAATGC-GTTTTTGGCTAAAAACCGTGATGGTTAGTA
* * * *
6473 -ACGATTTCGGC--------T--AAAAACTGACCCGAAAA--TTTTCTTC---TTTTTGCAAAAA
130 CACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTTTCATCAATTTTTTGCCACAA
* * * * * **
6522 TATTCAGAAAA-ATCATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACCCTTCTAATAT-
195 TACTCAGAAAACAT-ATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATATC
* * * * * * * *
6585 AGTTTTTCCA--TTTT-TTTCCAAATTAATTTCTAATTAAATCGAAAAAAGATTTAGATGCTCGT
259 A-TTTTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGT
*
6647 AAAAACAAATTCTT
323 AAAAACAAATCCTT
* * * * * * *
6661 ATATGCAATGTGGCTGAGATTTGGTTCGATCAATCTAGATATTTCAAGGAGT-TTT-TG-CGAGA
1 AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCGA-A
* * ** * *
6723 TAAATCATGCAAAATTGAGTTGGGGTTCCGAAATGCGTTTTTAAGC-CAAAACCGTGATGGTTAG
65 -AAATCATGCAAAACTGAGTCGGGGCCCCGAAATGCGTTTTT-GGCTAAAAACCGTGATGGTTAG
* * *
6787 TTACTAAACGATTTCGGCTAAAATTTTACAAAAACTGACCCGAAATATTTTTTTC-TCAATTTTT
128 -TAC---ACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAA-A-TTTTTTCATCAATTTTT
* * * * * * **
6851 TGTCAGAATACTGAGAAAAAATTTATAATTTAAC-GTAAAAAAATTGAA
187 TGCCACAATACTCAGAAAACATATATAATTCAACACCAAAAAAATTGAA
6899 AATGTTTTCA
Statistics
Matches: 5372, Mismatches: 887, Indels: 611
0.78 0.13 0.09
Matches are distributed among these distances:
307 6 0.00
308 7 0.00
309 24 0.00
310 216 0.04
311 2 0.00
312 12 0.00
313 11 0.00
314 14 0.00
315 18 0.00
316 23 0.00
317 19 0.00
318 34 0.01
319 17 0.00
320 16 0.00
321 14 0.00
322 9 0.00
324 5 0.00
325 38 0.01
326 132 0.02
327 42 0.01
328 175 0.03
329 17 0.00
330 305 0.06
331 389 0.07
332 209 0.04
333 395 0.07
334 714 0.13
335 443 0.08
336 468 0.09
337 655 0.12
338 431 0.08
339 196 0.04
340 20 0.00
341 25 0.00
342 9 0.00
343 9 0.00
344 5 0.00
345 8 0.00
346 12 0.00
347 2 0.00
348 7 0.00
349 11 0.00
350 5 0.00
351 2 0.00
352 2 0.00
355 6 0.00
356 5 0.00
357 7 0.00
359 3 0.00
360 2 0.00
361 4 0.00
362 32 0.01
363 53 0.01
364 47 0.01
365 39 0.01
366 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (336 bp):
AAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCGAAA
AATCATGCAAAACTGAGTCGGGGCCCCGAAATGCGTTTTTGGCTAAAAACCGTGATGGTTAGTAC
ACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTTTCATCAATTTTTTGCCACAAT
ACTCAGAAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCAT
TTTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTAAA
AACAAATCCTT
Found at i:8594 original size:13 final size:14
Alignment explanation
Indices: 8568--8602 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
8558 TTACAAGGCA
8568 AAAACAAAATTTATT
1 AAAA-AAAATTTATT
8583 AAAAAAAA-TTATT
1 AAAAAAAATTTATT
8596 AAAAAAA
1 AAAAAAA
8603 GTCACGTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.60
14 4 0.20
15 4 0.20
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAAAAATTTATT
Found at i:11794 original size:16 final size:16
Alignment explanation
Indices: 11770--11802 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
11760 TATAATTCAA
*
11770 TATTCTAAATATTATT
1 TATTATAAATATTATT
11786 TATTATAAATATTATT
1 TATTATAAATATTATT
11802 T
1 T
11803 GAAATTCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTATAAATATTATT
Found at i:11948 original size:21 final size:21
Alignment explanation
Indices: 11923--11965 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
11913 AATAGTAAGA
11923 TATAGATAAATTAGTATAATC
1 TATAGATAAATTAGTATAATC
*
11944 TATAGATAGATTAGTATAATC
1 TATAGATAAATTAGTATAATC
11965 T
1 T
11966 GATGATCTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.40
Consensus pattern (21 bp):
TATAGATAAATTAGTATAATC
Found at i:19258 original size:2 final size:2
Alignment explanation
Indices: 19253--19287 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
19243 CAATGTTAAA
19253 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
19288 GAGTATGACT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21980 original size:14 final size:14
Alignment explanation
Indices: 21961--21989 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
21951 AGGGTGGGGA
21961 AGAAAGAGAGAGAG
1 AGAAAGAGAGAGAG
21975 AGAAAGAGAGAGAG
1 AGAAAGAGAGAGAG
21989 A
1 A
21990 CTTTGCTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (14 bp):
AGAAAGAGAGAGAG
Found at i:22868 original size:13 final size:14
Alignment explanation
Indices: 22850--22878 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
22840 GAGATTAATT
22850 AATTAATTAAA-AA
1 AATTAATTAAATAA
22863 AATTAATTAAATAA
1 AATTAATTAAATAA
22877 AA
1 AA
22879 GGGTTTTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AATTAATTAAATAA
Found at i:22868 original size:17 final size:17
Alignment explanation
Indices: 22846--22878 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
22836 TGGGGAGATT
*
22846 AATTAATTAATTAAAAA
1 AATTAATTAAATAAAAA
22863 AATTAATTAAATAAAA
1 AATTAATTAAATAAAA
22879 GGGTTTTAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTAATTAAATAAAAA
Found at i:32002 original size:37 final size:38
Alignment explanation
Indices: 31947--32023 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 38
31937 ACTACTCGAC
*
31947 CCGGCTCGACTTGATTACACTGCCTTAAAGCATTTATG
1 CCGGCTCGACTTGATTACACCGCCTTAAAGCATTTATG
31985 CCGG-TCGACTTGATTACACCGCCTTAAAGCATTTATG
1 CCGGCTCGACTTGATTACACCGCCTTAAAGCATTTATG
32022 CC
1 CC
32024 TCGTCAACAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 34 0.89
38 4 0.11
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.30
Consensus pattern (38 bp):
CCGGCTCGACTTGATTACACCGCCTTAAAGCATTTATG
Found at i:33481 original size:17 final size:14
Alignment explanation
Indices: 33450--33479 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
33440 AAGCCTAAGG
33450 ATTATTAAAGTATA
1 ATTATTAAAGTATA
33464 ATTATTAAAGTATA
1 ATTATTAAAGTATA
33478 AT
1 AT
33480 AACCCCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
ATTATTAAAGTATA
Found at i:38516 original size:21 final size:21
Alignment explanation
Indices: 38490--38531 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
38480 GTTCTTCTTT
38490 AAGGTTACTAAAAAA-GTTATA
1 AAGGTTA-TAAAAAATGTTATA
38511 AAGGTTATAAAAAATGTTATA
1 AAGGTTATAAAAAATGTTATA
38532 GTATTATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.31
Consensus pattern (21 bp):
AAGGTTATAAAAAATGTTATA
Found at i:38844 original size:21 final size:20
Alignment explanation
Indices: 38802--38845 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
38792 TCTTGTAATC
*
38802 TAAAATTACTAAAAAAGTTA
1 TAAAATTACTAAAAAAGCTA
* *
38822 TAAAAGTTATTAAAATAGCTA
1 TAAAA-TTACTAAAAAAGCTA
38843 TAA
1 TAA
38846 TGCTTTCCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
TAAAATTACTAAAAAAGCTA
Found at i:40166 original size:343 final size:331
Alignment explanation
Indices: 39525--40168 Score: 812
Period size: 343 Copynumber: 1.9 Consensus size: 331
39515 TGGTTATTGA
* * *
39525 TTTTCTTATCTAAGATTACTTAAAGTTATAAAGGTTATGGAAAACATTATAGTTCTATCTACATT
1 TTTTCTTACCTAAGATTACTTAAAGTTATAAAGGTTATGAAAAACATTATAGTACTATCTACATT
* * * * **
39590 TAAGTAATCTTACATCCTTATTAATTTTAGTAACTTTTAATCAATAATGGAAGTTACCAATTTTA
66 GAAATAACCTTACATCCTTATTAAGTTTAGTAACTTTTAATCAATAATAAAAGTTACCAATTTTA
* * *
39655 TTACTTAAGTGATCTACTGAAACACCTATAAAAGTTATTAAAATTGTATTACCAATCCTTAATAA
131 TTACTTAAGT-ATCTACTAAAAAACCTATAAAAGTAATTAAAATTGTATTACCAATCCTTAATAA
* * * *
39720 CATTAGTAAACTTTCATCAATGGTAATAATTTACCTTTTTTCTCTCAAAAGTTACTGAAAAACCT
195 CATGAGTAAACTTTCATCAATGGTAATAATTTACCGTGTTTCTCTCAAAAGTTACTAAAAAACCT
** * *
39785 ATAATTTTTATAAAAAAGGTATGATACTATCAACTAATTCAATGACCTTATATTATAAAGCTAAA
260 ATAATGATCATAAAAAAGGTATGATACTAACAACTAATTCAATGACCTTATATTATAAAGCTAAA
39850 GTACTGC
325 GTACTGC
* *
39857 TTTTCTTACCTAAGATTACTTAAAAGGTTATAAAGGTTATGAAAAACTTTATAGTACTATCTAGA
1 TTTTCTTACCTAAGATTACTT-AAA-GTTATAAAGGTTATGAAAAACATTATAGTACTATCTACA
* * *
39922 TTGAAATAACCTTACACGTTCTTATTAAGTTTAGTAACTTTTCATCATTAATAAAAGTTACCAAT
64 TTGAAATAACCTTACA--TCCTTATTAAGTTTAGTAACTTTTAATCAATAATAAAAGTTACCAAT
* *
39987 TTTATTACTTAAGT-T-TACTAAAAAAGCTATAAATGTAAATTAAAATTGTATTTACTAATCCTT
127 TTTATTACTTAAGTATCTACTAAAAAACCTATAAAAGT-AATTAAAATTGTA--T--T-A-CC--
*
40050 ACATTCTTAATAACATGAGTAAACTTTCATCAATGGTGAAT-ATTTACCCGTGTTT-TCTCAAAA
183 A-ATCCTTAATAACATGAGTAAACTTTCATCAATGGT-AATAATTTA-CCGTGTTTCTCTCAAAA
* * *
40113 GTTATTAAAAAACCTATAATGATCATAAAAGATGTAT-AGTACTAACAACTAATTCA
245 GTTACTAAAAAACCTATAATGATCATAAAAAAGGTATGA-TACTAACAACTAATTCA
40169 GTAACCTTGC
Statistics
Matches: 264, Mismatches: 31, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
332 20 0.08
333 20 0.08
334 61 0.23
336 56 0.21
338 1 0.00
339 1 0.00
340 2 0.01
342 2 0.01
343 92 0.35
344 9 0.03
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (331 bp):
TTTTCTTACCTAAGATTACTTAAAGTTATAAAGGTTATGAAAAACATTATAGTACTATCTACATT
GAAATAACCTTACATCCTTATTAAGTTTAGTAACTTTTAATCAATAATAAAAGTTACCAATTTTA
TTACTTAAGTATCTACTAAAAAACCTATAAAAGTAATTAAAATTGTATTACCAATCCTTAATAAC
ATGAGTAAACTTTCATCAATGGTAATAATTTACCGTGTTTCTCTCAAAAGTTACTAAAAAACCTA
TAATGATCATAAAAAAGGTATGATACTAACAACTAATTCAATGACCTTATATTATAAAGCTAAAG
TACTGC
Found at i:40701 original size:3 final size:3
Alignment explanation
Indices: 40687--40735 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
40677 TCAACAAATT
*
40687 TTA TTC TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40735 T
1 T
40736 ATTTTGATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:41038 original size:21 final size:21
Alignment explanation
Indices: 41014--41059 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
41004 CTCTACCAAA
*
41014 CTAATGAATGATCTATGTGAT
1 CTAATGAATGATCAATGTGAT
41035 CTAATGAATGATCAATGTGAT
1 CTAATGAATGATCAATGTGAT
41056 CTAA
1 CTAA
41060 AATAACATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (21 bp):
CTAATGAATGATCAATGTGAT
Found at i:44563 original size:11 final size:11
Alignment explanation
Indices: 44547--44574 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
44537 TTTTGAGCTT
44547 TATAGACTAGG
1 TATAGACTAGG
44558 TATAGACTAGG
1 TATAGACTAGG
44569 TATAGA
1 TATAGA
44575 TATATACGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.29
Consensus pattern (11 bp):
TATAGACTAGG
Found at i:65339 original size:151 final size:152
Alignment explanation
Indices: 65065--65573 Score: 625
Period size: 160 Copynumber: 3.3 Consensus size: 152
65055 TTATAGTTAG
*
65065 TCGTTAAGACCGTTATTTTTATCTTTATTAGAAAA-TAGATATTTTGGTCGGTCGTTAAAACCGT
1 TCGTTAAAACCGTTATTTTTATCTTTATTA-AAAATTAGATATTTTGGTCGGTCGTTAAAACCGT
65129 TAAATTTATACCTATAAACAAACAAGAAAAAGATATTCTGATCGATCGTTGAAAAAGTTATCATA
65 TAAA-TT-TACCTATAAACAAACAAGAAAAAGATATTCTGATCGATCGTTGAAAAAGTTATCATA
*
65194 TGTATAATCATTTGAA-A-TAC-T-
128 TGTACAATCATTTGAATACTACATA
*
65215 TCGTTAAAACCGTTATTTTTATGATCTTTATTAAAAATTAGATATTTTGATCGGTCGTTAAAACC
1 TCGTTAAAACCGTTA-TTTT-T-ATCTTTATTAAAAATTAGATATTTTGGTCGGTCGTTAAAACC
* * *
65280 GTTAAATTTACCTATAAACAAACAAGAAAAAGATATT-TCAATCTATCATTGAAAAAGTTATCAT
63 GTTAAATTTACCTATAAACAAACAAGAAAAAGATATTCT-GATCGATCGTTGAAAAAGTTATCAT
65344 ATGTACAATCATTTGAAATACTACAGTTAGTCGA
127 ATGTACAATCATTTG-AATACTAC----A-T--A
* * * *
65378 TCGTTAAAACCGTTATTTTTATCTCTATTAGAAATTAGATATTTTGGTCGATCGTTAAAATCGTT
1 TCGTTAAAACCGTTATTTTTATCTTTATTAAAAATTAGATATTTTGGTCGGTCGTTAAAACCGTT
* * *
65443 AAATTTATCTATAAACAAACAAGAAAAAGATATTCTGATCGATCGTTGAAAAAATTATCATACGT
66 AAATTTACCTATAAACAAACAAGAAAAAGATATTCTGATCGATCGTTGAAAAAGTTATCATATGT
* *
65508 ACAATCATTTGAAGTGCTATAATTA
131 ACAATCATTTGAA-TACTA-CA-TA
* * * * *
65533 GTCGCTAAGATCGTTATTTTTATCTCTATTAGAAATTAGAT
1 -TCGTTAAAACCGTTATTTTTATCTTTATTAAAAATTAGAT
65574 GTTTCTATTA
Statistics
Matches: 315, Mismatches: 23, Indels: 36
0.84 0.06 0.10
Matches are distributed among these distances:
150 15 0.05
151 69 0.22
152 9 0.03
153 43 0.14
154 3 0.01
155 1 0.00
156 37 0.12
157 2 0.01
159 2 0.01
160 113 0.36
161 2 0.01
162 4 0.01
163 15 0.05
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.37
Consensus pattern (152 bp):
TCGTTAAAACCGTTATTTTTATCTTTATTAAAAATTAGATATTTTGGTCGGTCGTTAAAACCGTT
AAATTTACCTATAAACAAACAAGAAAAAGATATTCTGATCGATCGTTGAAAAAGTTATCATATGT
ACAATCATTTGAATACTACATA
Found at i:71337 original size:2 final size:2
Alignment explanation
Indices: 71330--71361 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
71320 CTTATCGCTC
71330 TA 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 TA
71362 GTACTTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:78408 original size:26 final size:26
Alignment explanation
Indices: 78372--78424 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
78362 ACTTTAGGCC
78372 TAGATTCAATTCAAGACCCAATTGCT
1 TAGATTCAATTCAAGACCCAATTGCT
78398 TAGATTCAATTCAAGACCCAATTGCT
1 TAGATTCAATTCAAGACCCAATTGCT
78424 T
1 T
78425 TTTGGATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (26 bp):
TAGATTCAATTCAAGACCCAATTGCT
Found at i:90013 original size:18 final size:19
Alignment explanation
Indices: 89990--90026 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
89980 TGGAGGGGGA
*
89990 TGGTGATGGAGAT-GAGAT
1 TGGTGATAGAGATGGAGAT
90008 TGGTGATAGAGATGGAGAT
1 TGGTGATAGAGATGGAGAT
90027 AATGGTGACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.30, C:0.00, G:0.43, T:0.27
Consensus pattern (19 bp):
TGGTGATAGAGATGGAGAT
Found at i:90051 original size:21 final size:21
Alignment explanation
Indices: 90027--90067 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
90017 AGATGGAGAT
*
90027 AATGGTGACGGTGAAGGTGAA
1 AATGGCGACGGTGAAGGTGAA
* *
90048 AATGGCGATGGTGATGGTGA
1 AATGGCGACGGTGAAGGTGA
90068 TGGTGAAGAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.05, G:0.44, T:0.22
Consensus pattern (21 bp):
AATGGCGACGGTGAAGGTGAA
Found at i:92732 original size:33 final size:33
Alignment explanation
Indices: 92653--92759 Score: 87
Period size: 33 Copynumber: 3.3 Consensus size: 33
92643 CGTCCCAAGA
* *
92653 GGGCGGCTT-ACCGTGGCGAAGCCGCCACACTT
1 GGGCGGCTTCACCATGGCGAAGCCGCCACACTG
* * *
92685 GGGAGGC-TCAACCATGGTGAAGCCGCC-CTAGTG
1 GGGCGGCTTC-ACCATGGCGAAGCCGCCAC-ACTG
* * *
92718 GGGCGGCTTCACCATGG-GCAGGCCGCCCCACTA
1 GGGCGGCTTCACCATGGCG-AAGCCGCCACACTG
92751 GGGCGGCTT
1 GGGCGGCTT
92760 AGCCACGGCA
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
31 1 0.02
32 8 0.13
33 48 0.80
34 3 0.05
ACGTcount: A:0.16, C:0.33, G:0.36, T:0.15
Consensus pattern (33 bp):
GGGCGGCTTCACCATGGCGAAGCCGCCACACTG
Found at i:92893 original size:33 final size:33
Alignment explanation
Indices: 92856--92920 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
92846 GGGGTGCCCT
92856 GCCGTGGC-GAAGCCGCCCCAGTAGGGAGGCTCC
1 GCCGTGGCTGAA-CCGCCCCAGTAGGGAGGCTCC
* * *
92889 GCCGTGGCTGAACCGTCCTAGTGGGGAGGCTC
1 GCCGTGGCTGAACCGCCCCAGTAGGGAGGCTC
92921 AGTGTAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 25 0.89
34 3 0.11
ACGTcount: A:0.14, C:0.32, G:0.40, T:0.14
Consensus pattern (33 bp):
GCCGTGGCTGAACCGCCCCAGTAGGGAGGCTCC
Found at i:99068 original size:2 final size:2
Alignment explanation
Indices: 99061--99093 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
99051 TTAAAGTATC
99061 TA TA TA 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 TA TA TA T
99094 GTTCTCAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:101509 original size:29 final size:30
Alignment explanation
Indices: 101470--101551 Score: 112
Period size: 29 Copynumber: 2.7 Consensus size: 30
101460 GTCTCGTTTT
*
101470 TAAAAGTTAAGGGGTCAATTTGTCTCAAAA
1 TAAAAGTTAAGGGGTCAATTTGTCCCAAAA
*
101500 -AAAAGTTAAGGGGCCAATTTGTCCCAAAA
1 TAAAAGTTAAGGGGTCAATTTGTCCCAAAA
* *
101529 TAGATAGTTAAGGGGTTAATTTG
1 TA-AAAGTTAAGGGGTCAATTTG
101552 GGTATTAAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 27 0.60
30 1 0.02
31 17 0.38
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (30 bp):
TAAAAGTTAAGGGGTCAATTTGTCCCAAAA
Found at i:102365 original size:22 final size:22
Alignment explanation
Indices: 102340--102383 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
102330 AGTTGACATG
102340 TTTTTACTATTGAGTTTTTTCA
1 TTTTTACTATTGAGTTTTTTCA
102362 TTTTTACTATTGAGTTTTTTCA
1 TTTTTACTATTGAGTTTTTTCA
102384 AAACTACCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.64
Consensus pattern (22 bp):
TTTTTACTATTGAGTTTTTTCA
Found at i:105141 original size:17 final size:18
Alignment explanation
Indices: 105109--105144 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
105099 TTCTATTATA
*
105109 AAGAAATGATTAAACATT
1 AAGAAACGATTAAACATT
105127 AAGAAACGA-TAAACATT
1 AAGAAACGATTAAACATT
105144 A
1 A
105145 TCTACCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.58, C:0.08, G:0.11, T:0.22
Consensus pattern (18 bp):
AAGAAACGATTAAACATT
Found at i:106196 original size:21 final size:21
Alignment explanation
Indices: 106172--106214 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
106162 GATTAGTCGA
*
106172 CCCAATGTAGTTACTATATAC
1 CCCAATGTAGTTACTAGATAC
106193 CCCAATGTAGTTACTAGATAC
1 CCCAATGTAGTTACTAGATAC
106214 C
1 C
106215 GGAGGGTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.30
Consensus pattern (21 bp):
CCCAATGTAGTTACTAGATAC
Found at i:116183 original size:3 final size:3
Alignment explanation
Indices: 116170--116216 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
116160 TTCACCCTTT
116170 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
116217 CAGAAAAATC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.