Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019268.1 Corchorus olitorius cultivar O-4 contig19301, 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: 12948
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Found at i:815 original size:287 final size:288
Alignment explanation
Indices: 308--829 Score: 748
Period size: 287 Copynumber: 1.8 Consensus size: 288
298 TAAAAAGATC
*** *
308 TAATTCAACGCCAACAAAATTGAAGGGGTTTCACGCTTTTAACATCGTTTTTCCATTTTTTTCCG
1 TAATTCAACGCCAACAAAATTGAAACAGTTTCACGCTTTTAACAACGTTTTTCCA-TTTTTTCCG
* *
373 AATTTATTTCTAATTAACTCGAAACAAGGTTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
65 AATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* *
438 GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGTGAAAAACCATACAA
130 GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTACGTCAAAAACCATACAA
* *
503 AAATGAGTCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACTGACCTAAAAATTTTTTTCTCAATT
195 AAATGAGTCCAGGCCCCGAAACGCGTTTTTAGCAAAAAACTGACCTAAAAATTTTTTTCTCAATT
568 TTATACAACAAAACTCATAAAACATTATA
260 TTATACAACAAAACTCATAAAACATTATA
* * * *
597 TAATTCAACGCCAA-AAAGATTGAAACATTTTCACGCTTTTAATAACTTTTTTCCA-TTTTTCGG
1 TAATTCAACGCCAACAAA-ATTGAAACAGTTTCACGCTTTTAACAACGTTTTTCCATTTTTTCCG
* *
660 AATTTATTTCTAATTAAATCGAAACAAGATTTAGATGCTCG-AAACAACAAATCCTTAAATCCAT
65 AATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA-AACAAATCCTTAAATCCAA
* * *
724 TGTGGCTGGGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGTCAAAAATCATGA-
129 TGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTACGTCAAAAACCAT-AC
*** * *
788 AATTCTGAG-CCAGGACCCTGGAACGCGTTTTTAGCAAAAAAC
193 AAAAATGAGTCCAGG-CCCCGAAACGCGTTTTTAGCAAAAAAC
830 CATGATGGTT
Statistics
Matches: 205, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
286 7 0.03
287 150 0.73
288 4 0.02
289 44 0.21
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (288 bp):
TAATTCAACGCCAACAAAATTGAAACAGTTTCACGCTTTTAACAACGTTTTTCCATTTTTTCCGA
ATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
TGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTACGTCAAAAACCATACAAA
AATGAGTCCAGGCCCCGAAACGCGTTTTTAGCAAAAAACTGACCTAAAAATTTTTTTCTCAATTT
TATACAACAAAACTCATAAAACATTATA
Found at i:1685 original size:331 final size:328
Alignment explanation
Indices: 536--7711 Score: 3439
Period size: 330 Copynumber: 21.9 Consensus size: 328
526 CGTTTTTAGC
** * * * * * *
536 CAAAAACTGACCTAAAAATTTTTTTCTCAATT-TTATACAACAAAACTCATAAAACATTATATAA
1 CAAAAACTGACCCGAAAATTTTTTCCTCAATTCTT-TGCCACAATACTCAGAAAA-AATATATAA
*** * * *
600 TTCAACGCCAAAAAGATTGAAACATTTTCACGCTTTTAATAACTTTTTTCCA--TTTTTCGGAAT
64 TTCAACGCCAAAAA-ATTGAAGGGTTTTCACGCTTTTAATATCGTTTTTCCATTTTTTTCCGAAT
* *
663 TTATTTCTAATTAAATCGAAACAAGATTTAGATGCTCG-AAACAACAAATCCTTAAATCCATTGT
128 TTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA-AACAAATCCTTAAATCCAATGT
* * *
727 GGCTGGGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGTCAAAAATCATGAAATT
192 GGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGAAAAT
* * * * * *
792 CTGAGCCAGGACCCTGGAACGCGTTTTTAGCAAAAAACCATGATGGTTAATACACGATTTCAGAT
257 -TGAGCCGGGGCCC-GGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCT
857 AAAATTTTG
320 AAAATTTTG
* * * *
866 CAAAAACTTA-CTGAAAATTTTTTACCTCAATTCTTTGGCATAATACTCAGAAAAAATATATAAT
1 CAAAAACTGACCCGAAAATTTTTT-CCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAAT
* * *
930 ACAACGCCAAAAAAATTGAAGGGTTTTCACGCTTTTAATATCATTTTTCTATTTTTTTCCG-ATT
65 TCAACGCC-AAAAAATTGAAGGGTTTTCACGCTTTTAATATCGTTTTTCCATTTTTTTCCGAATT
* * * * * *
994 TATTTCTAACTAAATCAAAATAAGATTCAGATGCTCGTAAAAACAAATTCTTAAAACCAATGTAG
129 TATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * *
1059 CTGAGATTTGGTTAGATGAATATAGATATTTCAATGAGTATTTATGCCAAAAAATCATGCAAAAC
194 CTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCC-AAAAATCATG-AAAAT
* * * * * *
1124 TGAGTC-GAGCCCTGAATCACATTTTTAGCCAGAAAACCCTGATGG--AAGTACACGATTTCGGC
257 TGAGCCGGGGCCCGGAA-CGCGTTTTTAGCCA-AAAACCGTGATGGTTAA-TACACGATTTCGGC
1186 --------T-
319 TAAAATTTTG
* * * ** *
1187 -AAAAACTGACCTGAAAATTTTTTTCACAATAT-TTTAACACAATACTCATAAAAAA-ATATTAA
1 CAAAAACTGACCCGAAAATTTTTTCCTCAAT-TCTTTGCCACAATACTCAGAAAAAATATA-TAA
* * ** ** **
1249 TTTAACGCCAAAAAGATGGAAGGGTTTTTCTTGCTTAAAATATCGTTTTTCTTTTTTTTTCCGAA
64 TTCAACGCCAAAAA-ATTGAAGGG-TTTTCACGCTTTTAATATCGTTTTTCCATTTTTTTCCGAA
** * * *
1314 TAAATTTTTAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCATTGT
127 TTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * * *
1379 GGTTGTGATTTGGTTCGATGAATATATATATTTCAAGGAGTCTTTACACCAAAAATCATGAAAAA
192 GGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATG-AAAA
* * *
1444 TTGAGCCGGGGCTCCGGAACGCGTTTTTAG-CAGAGACCCGTGATGGTTAATAAACGATTTCGGC
256 TTGAGCCGGGGC-CCGGAACGCGTTTTTAGCCA-AAAACCGTGATGGTTAATACACGATTTCGGC
1508 TAAAATTTTG
319 TAAAATTTTG
* * * * *
1518 CAAAAACTGACCCGAAAATATTTTCCGCAATTCTTTGCCACAGTACTC-TAAAAAATATATAACT
1 CAAAAACTGACCCGAAAATTTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATT
* *
1582 CAACGCCAAACAAATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCGGAATT
66 CAACGCCAAA-AAATTGAAGGG-TTTTCACGCTTTTAATATCGTTTTTCCATTTTTTTCCGAATT
* * *
1647 TATTTCTAATCAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAACCCTTAAATCCAATATGG
129 TATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * * * *
1712 TTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTATGCGAAAAACCATGTAAAAAT
194 CTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATG-AAAATT
* * * *
1777 GTGTCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGAT-G--AAGTACACGATTTCGG---
258 GAGCCG-GGGCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAA-TACACGATTTCGGCTA
1836 -------G
321 AAATTTTG
* * * * * * *
1837 TAAAAACTTACCTGAAAA-TTTTT-CTAAATT-TTTGGCACAATACTCATAAAAAATATGTAATT
1 CAAAAACTGACCCGAAAATTTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATT
* * ** * *
1899 CAATGCCAAAAAGATTGAAGGGTTTTTCTCGCTTAAAATATCATTTTT-CTTTTTTTTCCGAATT
66 CAACGCCAAAAA-ATTGAAGGG-TTTTCACGCTTTTAATATCGTTTTTCCATTTTTTTCCGAATT
* *
1963 AATTTCTAATTAAATCGAAACAAGATT-AGGATGCTCGTAAAAACAAATCCTTAAATCCATTGTG
129 TATTTCTAATTAAATCGAAACAAGATTCA-GATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * *
2027 GCTG-GCATTTGGTTC-ATTGAATATTGATATTTCAAGGAGTCTTTACGCCAATAATCATGCTAA
193 GCTGAG-ATTTGGTTCGA-TGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATG-AAA
* * * * * * * * * *
2090 ACTAAGTCGGGACCCCGAGACGCGTTTTTAGCAAAAAACCGTGATTGATAATACACAATTTCAGC
255 ATTGAGCCGGGGCCCGGA-ACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGC
2155 TAAAATTTTG
319 TAAAATTTTG
* * * ** * *
2165 CAAAAACTGA-ACTAAAATTTTTTTTCCTCCATTCTTCACCATAATATTCAGAAAAAATATATAA
1 CAAAAACTGACCCGAAAA--TTTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAA
* *
2229 TGCAACGCCAAAAAAATTGTAGGGTTTTCACGCTTTTAATA-------T-C--TTTTTTCC-AA-
64 TTCAACGCC-AAAAAATTGAAGGGTTTTCACGCTTTTAATATCGTTTTTCCATTTTTTTCCGAAT
* * *
2282 --A----T-A--AAATCGGAAA-AAGATTCAGAGGCTCGTAAAAACAAACCCCTAAATCCAATGT
128 TTATTTCTAATTAAATC-GAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * * *** **
2337 GGCTGAGATTTGGTTTGATGAATATAGGTATTTCAAGGAGTCTATACATTAAAAATCATGCTAAT
192 GGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGAAAAT
* * * * * * * **
2402 TCAGTCGGGGTTCCGGAACGTGTTTTTAGTCAAAAACCGTAATGGTTAGTACACGATTTCAACTA
257 TGAGCCGGGG-CCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCTA
2467 AAATTTTG
321 AAATTTTG
* * *
2475 CAAAAACTGACCCGAAACGTTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAT
1 CAAAAACTGACCCGAAA-ATTTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAAT
* *
2540 TCAATGCCAACAAAATTGAAGGGTTTTCACGC-TTT-A-ATCGTTTTTCCA-TTTTTTCGGAATT
65 TCAACGCCAA-AAAATTGAAGGGTTTTCACGCTTTTAATATCGTTTTTCCATTTTTTTCCGAATT
*
2601 TATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG-AATAAACAAATCCTTAAATCCATTGTG
129 TATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA-AAACAAATCCTTAAATCCAATGTG
* * *
2665 GCTGGGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACACCAAAAATCATGAAATTC
193 GCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGAAAAT-
* * * * * *
2730 TAAGCCAGGGCCCCGGAATGCGTTTTTAG-CAAAAACCGTTATGGTTAGTACACGATTTCGGATA
257 TGAGCC-GGGGCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCTA
*
2794 AAATTTTT
321 AAATTTTG
* * * *
2802 CAAAAACTGATCC-AAATGTTTTTTTCTCAAATT-TTTGCCATAATACTCAGAAAAAATATATAA
1 CAAAAACTGACCCGAAA-ATTTTTTCCTC-AATTCTTTGCCACAATACTCAGAAAAAATATATAA
* * * *
2865 TTCAACGCCAACAAATTTGAAGGGTTTCCACGCTTTTAATATGGTTTTTCCA-TTTTTTCGGAAT
64 TTCAACGCCAA-AAAATTGAAGGGTTTTCACGCTTTTAATATCGTTTTTCCATTTTTTTCCGAAT
* * *
2929 TTATTTCTAATTAAATCGAAACAAGATTCGGATGCTCGTAAAAACAAATACCTCAAATCCACTGT
128 TTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT-CCTTAAATCCAATGT
* * * *
2994 GGCTGGGATTTGGTTCGATGAATATAGATATTTCAAGGAGCCTTTACGCCTAAAATCATAAAAAA
192 GGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCAT-GAAAA
* * * * * ** * *
3059 CTGAGTCAGGTCCCTGGAAAGCGTTTTTAG-CAAAAATCTTTGATGGTTAGTATACGATTTCGGC
256 TTGAGCCGGGGCCC-GGAACGCGTTTTTAGCCAAAAA-CCGTGATGGTTAATACACGATTTCGGC
3123 TAAAATTTTG
319 TAAAATTTTG
* * * * * * * *
3133 CAAAACCTGACCCAAAAAATTTTTCCTCTATTCTTCGACAAAATACTCAGAAAAAATATATAACT
1 CAAAAACTGACCCGAAAATTTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATT
* *
3198 CAACATCCAAAAGAATTGAAGGGTTTTTCACGCTTCTAATATCG----------TTTTTCCGAAT
66 CAAC-GCCAAAA-AATTGAAGGG-TTTTCACGCTTTTAATATCGTTTTTCCATTTTTTTCCGAAT
* * * *
3253 TAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCCATATG
128 TTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
** * * * *
3318 GCTGAGATTTGGTTAAATGTATATAGATTTTTCATGGAGGCTTT-CTGCCAAAAATCATG-----
193 GCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTAC-GCCAAAAATCATGAAAAT
* * * * * *
3377 -CAGCTGGGGCCCCGAAAACGCGTTTTTAGCTCAAAAACCGTGATCGTTACAAAAAC-ATTTCGG
257 TGAGCCGGGG-CCCG-GAACGCGTTTTTAGC-CAAAAACCGTGATGGTTA-ATACACGATTTCGG
3440 C-------TT-
318 CTAAAATTTTG
** ** *
3443 --AAAACTGACCCGAATTTTTTTTTAT-GATTCTTTTGCCACAATACTCAGATATATATATATAT
1 CAAAAACTGACCCGAAAATTTTTTCCTCAATTC-TTTGCCACAATACTCAG------------A-
* ** * ***
3505 ATATATATATATATATATATCAACGCCAAAAAGATTGACTGACTTTTCACGCTTCTAA-AAAATT
52 A-A-A-A-ATATATA-AT-TCAACGCCAAAAA-ATTGA-AGGGTTTTCACGCTTTTAATATCGTT
* * * * *
3569 TTTCCCTTTTTTCCCGAATTCATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGCAAAAACA
109 TTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
* *
3634 AAT-CTCTAAATCCAATGTGGCTGAGATTTGGATT-GATGAGTATAGGTATTTCAAGGAGTCTTT
174 AATCCT-TAAATCCAATGTGGCTGAGATTTGG-TTCGATGAATATAGATATTTCAAGGAGTCTTT
* ** *
3697 ACGACAAAAATCATGCTAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAACCCGTGATGG
237 ACGCCAAAAATCATGAAAATTGAGCCGGGGC-CCGGAACGCGTTTTTAGCCAAAAACCGTGATGG
*
3762 TTAATATACGATTTCGGCTAAAATTTTG
301 TTAATACACGATTTCGGCTAAAATTTTG
* * * * *
3790 CAAAAACTGACCCGGAAAGTTTTTCCTCAATTTTTTGCCACAATACTCA-TAAAAATATATAACT
1 CAAAAACTGACCCGAAAATTTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATT
* * *
3854 CAACGCCAACAAAATTGAAGGGATTTCACGCTTTTAACATCGTTTTTCCAATTTTTTCCCGAATT
66 CAACGCCAA-AAAATTGAAGGGTTTTCACGCTTTTAATATCGTTTTTCC-ATTTTTTTCCGAATT
*
3919 TATTTCTAATTAAATCGAAACAAGGTTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
129 TATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * ** * * *
3984 CCGATATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGTGCAAAAAACCATGCAAA--G
194 CTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGAAAATTG
* * *
4047 -G-C----CCCGAAACGCGTTTTTAGCTAAAAACCGTGAT-G--AGCT-CACGATTTCGGC----
259 AGCCGGGGCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA-ATACACGATTTCGGCTAAA
4098 ----T-
323 ATTTTG
* * * * *
4099 -AAAAACTGACACTGAAAATTTTATT-CTCAATTTTTTACCACAAAACTCATAAAAAATATATAA
1 CAAAAACTGAC-CCGAAAATTTT-TTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAA
* * ** * * *
4162 TTCAAGGCCAAAAAGATTTAAATGTTTGCACGCTTTTAATAACTTTTTTCCATTTTTTTCCGAAT
64 TTCAACGCCAAAAA-ATTGAAGGGTTTTCACGCTTTTAATATCGTTTTTCCATTTTTTTCCGAAT
* * * * ** * *
4227 TTCTTTTTAAATAAATCGAAACATGATTCAGATGCTCGTTGAAAGAAATCCTTAAATCTAATGTG
128 TTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * * *
4292 GCTGAGATTTGGTTAGATTAATATAGATTTTTCATGGAGTCTTT-CTGTCAAAAATCATGCAAAA
193 GCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTAC-GCCAAAAATCATG-AAAA
** * * ** * * ** *
4356 CAG-GATCGAGGCCCCCAAACGCTTTTTTAGCCCAAAAACCGTGATAGTTACCACACGATTTCAG
256 TTGAG-CCG-GGGCCCGGAACGCGTTTTTAG-CCAAAAACCGTGATGGTTAATACACGATTTCGG
4420 C--------T-
318 CTAAAATTTTG
* ** * * * *
4422 -AAAAACTTG-CCCGAAATTTTTTTTATGATTTTTTTGCCACAATACTCAG-AAATATATATATA
1 CAAAAAC-TGACCCGAAAATTTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATA-A
* * * * ** ** * * * * * *
4484 TAT-ATA-G---ATATATAGATA---TATAT-A-TATATAGATATATAGATATAT--ATATATAT
64 T-TCA-ACGCCAAAAAATTGA-AGGGT-TTTCACGCT-TTTA-ATATCG-TTTTTCCATTTTTTT
* * * * ** * **
4537 -AG-A--TATATAT-ATCAACGCCAAA-AAGATT--GACTGGCTTTTCACGCTTACTAA-AAAT-
122 CCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGA-T-GC---T--CG--TAAAAACAAATC
** ** * ** * * ** * * * * ** *
4592 -TT-TTTCCCTTTTTTTCCCGA-ATTCAT-TTTTTATTAA-ATCGA-A--ACAA-GATTCAGATG
178 CTTAAAT-CC-AATGTGGCTGAGATT--TGGTTCGATGAATATAGATATTTCAAGGAGTC-TTTA
* ** ** ** * * * * **
4648 CTCGCAAAAA-CAAATCCCTAAATCCA-ATGTGG--CTG-A-G-ATTTGCTTTG---ATGA--GT
238 CGC-CAAAAATC--AT--GAAAATTGAGCCGGGGCCCGGAACGCGTTT--TTAGCCAAAAACCGT
* * * * * * **
4701 -ATAGG-TATTTCAAGGAGTCTTTATGACAAAAATCATG
296 GAT-GGTTAATAC-ACGA---TTT-CGGCTAAAATTTTG
* * * **** ** * * * ****
4738 C--TAATTGAGCCG-----GGGCTCCGGAATGCGTTTTTAGCCA-AAAAC-C-GTGATGGTTATA
1 CAAAAACTGACCCGAAAATTTTTTCCTCAAT---TCTTT-GCCACAATACTCAG-AAAAAATATA
* * ** **** * ***
4793 TACGATTTC--GGCTAAAATTTTGCAA--AAACTGAC-C-CGGAA-A--GTTTTTCCTCAATTTT
61 TA--A-TTCAACGCCAAAAAATTG-AAGGGTTTTCACGCTTTTAATATCGTTTTT-C-C-ATTTT
* * * * * * * * * * *
4849 TTGCCACAATACTCATAAAAAATATATAATTCAA-CGCCAACAAAATTGAAGGGATTTCACGCTT
119 TTTCC-GAAT--T--T-----ATTTCTAATTAAATCG-AAACAAGATT-CA--GA-TGCTCG-TA
** * ** * * ** * ** * * * *
4913 GTAAC--ATCGTT-TTTCCATTTTTTCCCGA-ATTTATTTCTAATTAA-ATCGA-A--ACAAGGT
168 AAAACAAATCCTTAAATCCA-ATGTGGCTGAGATTTGGTTC-GATGAATATAGATATTTCAAGG-
** * * ** ** *
4970 TCAGATGC--T-CGTAAAACAAATCCT-TAAATCCA-ATGTGG-CC-GATA----TTTGGTTAG-
230 --AG-T-CTTTACG-CCAA-AAATCATGAAAATTGAGCCGGGGCCCGGA-ACGCGTTT--TTAGC
** * * * * * ** * ***
5023 -ATGAA---T-ATAGATATTTCAAGGAATCTCTATGCCAAAACCATG
286 CAAAAACCGTGATGGTTAATAC-ACG-AT-T-TCGGCTAAAATTTTG
* * *
5065 -AAAAACTGAGTTGTGGCCCGAAACGCATTTTTAGTCAAAAAACGAGGCACAATT-TTGGCTA-A
1 CAAAAACTGA-------CCCGAAA---ATTTTT--T-------C----CTCAATTCTTTGCCACA
* * * * * ** * ** ***
5127 AAACTGACCGGAAAAATTTTTTCTTAATTTTTTAC-CACAATACTTTGAAAAAATATATAATTCA
43 ATACT---CAGAAAAA--ATAT-ATAA--TTCAACGC-CAAAAAATTG---AAGGGT-T--TTC-
* **** ** * *
5191 ATGTCAAAAAGATTGAAGGGTCTCTCACGCTTCTAATATCATTTTTTC--ATTT-TTTCCGAATT
92 ACG-CTTTTA-A-T--ATCGT-T-T-----TTC-CAT-T--TTTTTCCGAATTTATTT-C----T
*
5253 AATTTCTAAATAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTGG
136 AA----T---TAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * * * *
5318 CTGGGATTTGCTTCGATGAATATAGATATTTCAAGGAATTTTTATGCTAAAAATCATGCAAAACT
194 CTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATG-AAAATT
* * * * * * * *
5383 GAGCAGGGGCCTCAGATCGCGTTTTTAACCAAAAACTGTGATGG-T-ACACAGGATTTCGACTAA
258 GAGCCGGGGCC-CGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCTAA
5446 AATTTTG
322 AATTTTG
* * * * * *
5453 CAAAAACAGAGCTGAAAAATTTTTCCTCAATTCTCTACCACAATACTCAGAAAAAATATATAATT
1 CAAAAACTGACCCGAAAATTTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATT
* * * * * * *
5518 CAACGACAAGACAATTGAAAGGCTGTTCACGCTTCTAATATTGTGTTTCCA-TTTTTTCCGAATT
66 CAACGCCAA-AAAATTG-AAGGGTTTTCACGCTTTTAATATCGTTTTTCCATTTTTTTCCGAATT
* ** * *
5582 TATTTCTAATTAAATCGAAACCAGATTCAGATGCTCGTAAAAACAAATTTTTAAAACCAATTTGG
129 TATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * * *
5647 CTGAGATTTAGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGTCAAAAACCATGCAAAACT
194 CTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATG-AAAATT
** * * * *
5712 GAGTTGTGGCCTGAAACGCGTTTTTAACCAAAAACC--G-T-G-----ACACGATTTCGGC----
258 GAGCCGGGGCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCTAAA
5764 ----T-
323 ATTTTG
* * ** ** *
5765 -AAAAACTTACCAGAAAATTTTTTTTATCAATT-TTTGCCACAATACTTTGAAAAAATATATAGT
1 CAAAAACTGACCCGAAAA-TTTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAAT
* * * **
5828 TCAATGCCTAAAAGATTGAAGGGTTTTTCACGCTTCTAATA-------T-CA-TTTTTTCTAAAT
65 TCAACGCC-AAAAAATTGAAGGG-TTTTCACGCTTTTAATATCGTTTTTCCATTTTTTTCCGAAT
** * * * ** *
5884 CAATTTGTAATTAAATCGAAACACGATTCAGATGCTAGTATTAACAGATCCTTAAATCCAATGTG
128 TTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * * * * * *
5949 GCAGGGATTTGATTCAATAAATATAGATATTTCAAGGAGTTTTTGCGCCAAAAATCATGTAAAAC
193 GCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATG-AAAAT
* * * * *** ** * * ** * *
6014 TGAGTCGGGGCCTCGGATCGCGTTTTTAACAAAAAAAAAATCTTTGATGGTACACGATTTCAGTT
257 TGAGCCGGGGCC-CGGAACGCGTTTTTAGC-CAAAAACCGTGATGGTTAATACACGATTTCGGCT
6079 AAAATTTTG
320 AAAATTTTG
* * * * *** * *
6088 TAAAAATTGACCCGAAAAATTTTTCCTCAATTCTCTAATACAATACTCCGAAAAGATATATAATT
1 CAAAAACTGACCCGAAAATTTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATT
* * * *
6153 CAACGCCAAGACAATTGAAGGTTTTTTCAAGCTTCTAATATCGTTTTTCCATTTTTTTTTCCGAA
66 CAACGCCAA-AAAATTGAAGG-GTTTTCACGCTTTTAATATCGTTTTTCCA--TTTTTTTCCGAA
* * *
6218 CTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCGTAAATCCAATGT
127 TTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * **
6283 GGCTGAGATTTAGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CTGCTTAAAATCATGCAAA
192 GGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTAC-GCCAAAAATCATG-AAA
* * * * **
6347 ACTAAGTCGGGTCCCCAAAACGCGTTTTTAGCCAAAAAGAAAAAAAAAAAAACCTGTGATGGTTA
255 ATTGAGCCGGG-GCCCGGAACGCGTTTTTAGCC--------------AAAAACC-GTGATGGTTA
* * *
6412 GTGCACGATTTCGGCTCAAATTTTG
304 ATACACGATTTCGGCTAAAATTTTG
* * * * *
6437 CAAAAACTGCCCCGAGAA-TTTTTCCTCAATTCTTTGCCACAGTACTCAGAAAATACATATAATT
1 CAAAAACTGACCCGAAAATTTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATT
* * *
6501 CAATGCCAAAAAAAGTTGAATGGTTTTCACGCTTTTAATATCATTTTTCCATTTTTTTCCGAATT
66 CAACGCC-AAAAAA-TTGAAGGGTTTTCACGCTTTTAATATCGTTTTTCCATTTTTTTCCGAATT
*
6566 TATTTCTAGTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT-CTCTAAATCC-ATGGT
129 TATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT-TAAATCCAAT-GT
* * * *
6629 GGCTGGGATTTTGTTCAATGAATATAGATAATTCAAGGAGTCTTTACGCCAAAAATCATGCAAAA
192 GGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATG-AAAA
* * * *
6694 CTGAGCCGGGGCCCTGGAACACGTTTTTAGCCAAAAACCATGATGAG-T-A-A-ACGATTTCGAC
256 TTGAGCCGGGGCCC-GGAACGCGTTTTTAGCCAAAAACCGTGATG-GTTAATACACGATTTCGGC
6755 TAAAATTTTG
319 TAAAATTTTG
*
6765 CAAAAACTGACTCCGAAAATTTATTT-CTCAATTCTTTACCACAATACT-A-AAAAAATACT-TA
1 CAAAAACTGAC-CCGAAAATTT-TTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATA-TATA
* * * *
6826 ATTCAACTCCCAAAAAACTTGAAGCGATTTTCACGCTTCTAATATGGTTTTTCCATTTTTTT-CG
63 ATTCAAC-GCCAAAAAA-TTGAAG-GGTTTTCACGCTTTTAATATCGTTTTTCCATTTTTTTCCG
* * * * *
6890 AATTTATTTTTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAAGAAATCATTAAATCCACT
125 AATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * * *
6955 GTGGCTGAGATTTGGTTAGATGAGTATAGATATTTCAAGGAGTCTTT-CTACTAAAAATCATGCA
190 GTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTAC-GCCAAAAATCATG-A
* * * * *** * * *
7019 AAACTAAGCCGAGGCCACGAAACGCGTTTTTATTTAAAAACCGTGATGATTAGTACATGATTTC-
253 AAATTGAGCCGGGGCC-CGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCG
*
7083 GC-------CT-
317 GCTAAAATTTTG
* * * *
7087 -AAAAACTGACCCGAAATTTTTTTTCTCAATT-TTGTG-CAAAATATTCAGAAAAAATATATAAT
1 CAAAAACTGACCCGAAAATTTTTTCCTCAATTCTT-TGCCACAATACTCAGAAAAAATATATAAT
* * * * * * * *
7149 TCAACACTAAAAAGATTGAAGGACTTTTTATGCTTCTAATATCATTTTTCCATTTTTTTTCGAAT
65 TCAACGCCAAAAA-ATTGAAGG-GTTTTCACGCTTTTAATATCGTTTTTCCATTTTTTTCCGAAT
* * * * * ** *
7214 TAATTTCTAATTAAATCGAAACAAAATTTAGATGCTTGTAAAAATAAAAACTTATATCCAATGTG
128 TTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* *
7279 GCTGAGATTTGGTTCGATGAACATAGATATTT-AAGGAGTCTTTGCGCCAAAAATCATGTAAAAT
193 GCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATG-AAAAT
** * * **
7343 TGAGTTGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGG-TAGTACACGATTTTCAACT
257 TGAGCCGGGG-CCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGA-TTTCGGCT
*
7407 AAAATATTG
320 AAAATTTTG
* * *
7416 CAAAAAACTGATCCGAAAAGTTTTTCCTC-ATTTTTTGCCAC-A-ACTCAGAAAAAATATATAAT
1 C-AAAAACTGACCCGAAAATTTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAAT
*
7478 TCAACGCCAAAAAATTTGAAGGG-TTTCACACTTTTAATATCGTTTTTCCATTTTTTTCCCGAAT
65 TCAACGCCAAAAAA-TTGAAGGGTTTTCACGCTTTTAATATCGTTTTTCCATTTTTTT-CCGAAT
* *
7542 TTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAGCAAATCCTTAAATCCAATGTG
128 TTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * *
7607 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCC-AAAACCATGCAAAAC
193 GCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATG-AAAAT
** * * *
7671 TGAGTTGTGGCCCGAAACACGTTTTTAGCCAAAAACCGTGA
257 TGAGCCGGGGCCCGGAACGCGTTTTTAGCCAAAAACCGTGA
7712 CACGATTTCG
Statistics
Matches: 5286, Mismatches: 1028, Indels: 1067
0.72 0.14 0.14
Matches are distributed among these distances:
302 5 0.00
303 132 0.02
304 15 0.00
305 7 0.00
306 3 0.00
307 9 0.00
308 47 0.01
309 161 0.03
310 210 0.04
311 178 0.03
312 35 0.01
313 25 0.00
314 37 0.01
315 39 0.01
316 199 0.04
317 85 0.02
318 52 0.01
319 77 0.01
320 190 0.04
321 254 0.05
322 168 0.03
323 104 0.02
324 133 0.03
325 11 0.00
326 109 0.02
327 234 0.04
328 429 0.08
329 431 0.08
330 433 0.08
331 412 0.08
332 121 0.02
333 25 0.00
334 5 0.00
335 255 0.05
336 11 0.00
338 10 0.00
339 24 0.00
340 21 0.00
341 13 0.00
342 1 0.00
343 3 0.00
345 7 0.00
346 149 0.03
347 1 0.00
348 78 0.01
349 82 0.02
350 6 0.00
351 8 0.00
352 4 0.00
353 2 0.00
354 2 0.00
355 4 0.00
356 9 0.00
357 6 0.00
358 3 0.00
359 11 0.00
360 7 0.00
361 5 0.00
362 3 0.00
363 3 0.00
365 7 0.00
366 7 0.00
367 4 0.00
368 5 0.00
369 1 0.00
370 2 0.00
371 1 0.00
372 2 0.00
375 1 0.00
377 6 0.00
378 2 0.00
379 10 0.00
380 5 0.00
381 23 0.00
382 28 0.01
383 10 0.00
384 16 0.00
385 13 0.00
386 1 0.00
387 2 0.00
388 11 0.00
389 9 0.00
390 8 0.00
391 3 0.00
392 1 0.00
393 2 0.00
394 3 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (328 bp):
CAAAAACTGACCCGAAAATTTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATT
CAACGCCAAAAAATTGAAGGGTTTTCACGCTTTTAATATCGTTTTTCCATTTTTTTCCGAATTTA
TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT
GAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGAAAATTGAG
CCGGGGCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCTAAAATT
TTG
Found at i:3498 original size:2 final size:2
Alignment explanation
Indices: 3491--3524 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3481 CAATACTCAG
3491 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3525 CAACGCCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4486 original size:8 final size:8
Alignment explanation
Indices: 4475--4545 Score: 115
Period size: 8 Copynumber: 8.9 Consensus size: 8
4465 ACTCAGAAAT
*
4475 ATATATAT
1 ATATATAG
4483 ATATATAG
1 ATATATAG
4491 ATATATAG
1 ATATATAG
*
4499 ATATATAT
1 ATATATAG
4507 ATATATAG
1 ATATATAG
4515 ATATATAG
1 ATATATAG
*
4523 ATATATAT
1 ATATATAG
4531 ATATATAG
1 ATATATAG
4539 ATATATA
1 ATATATA
4546 TATCAACGCC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 58 1.00
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (8 bp):
ATATATAG
Found at i:4507 original size:24 final size:24
Alignment explanation
Indices: 4475--4545 Score: 142
Period size: 24 Copynumber: 3.0 Consensus size: 24
4465 ACTCAGAAAT
4475 ATATATATATATATAGATATATAG
1 ATATATATATATATAGATATATAG
4499 ATATATATATATATAGATATATAG
1 ATATATATATATATAGATATATAG
4523 ATATATATATATATAGATATATA
1 ATATATATATATATAGATATATA
4546 TATCAACGCC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (24 bp):
ATATATATATATATAGATATATAG
Found at i:7013 original size:328 final size:326
Alignment explanation
Indices: 6416--7711 Score: 1385
Period size: 328 Copynumber: 4.0 Consensus size: 326
6406 TGGTTAGTGC
* * * * *
6416 ACGATTTCGGCTCAAATTTTGC-AAAAACTG-CCCCGAGAATTTTTCCTCAATTCTTTGCCACAG
1 ACGATTTCGACTAAAATTTTGCAAAAAACTGACTCCGAAAATTTTTCCTCAATTCTTTGCCACAA
* * * * *
6479 TACTCAGAAAATACATATAATTCAATGCCAAAAAAAGTTGAATGGTTTTCACGCTTTTAATATCA
66 TACTCAGAAAAAATATATAATTCAA-CCCCAAAAAA-TTGAA-GGTTTTCACGCTTCTAATATCA
*
6544 TTTTTCCATTTTTTTCCGAATTTATTTCTAGTTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
128 TTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
* * * *
6609 CAAATC-TCTAAATCC-ATGGTGGCTGGGATTTTGTTCA-ATGAATATAGATAATTCAAGGAGTC
193 GAAATCAT-TAAATCCAAT-GTGGCTGAGATTTGGTT-AGATGAATATAGATATTTCAAGGAGTC
* *
6671 TTTACGCCAAAAATCATGCAAAACTGAGCCGGGGCCCTGGAACACGTTTTTAGCCAAAAACCATG
255 TTTACGCCAAAAATCATGCAAAACTGAGCCGGGGCCC-GAAACACGTTTTTAGCCAAAAACCGTG
6736 ATGAGTAA
319 ATGAGTAA
* *
6744 ACGATTTCGACTAAAATTTTGC-AAAAACTGACTCCGAAAATTTATTTCTCAATTCTTTACCACA
1 ACGATTTCGACTAAAATTTTGCAAAAAACTGACTCCGAAAATTT-TTCCTCAATTCTTTGCCACA
6808 ATACT-A-AAAAAATACT-TAATTCAACTCCCAAAAAACTTGAAGCGATTTTCACGCTTCTAATA
65 ATACTCAGAAAAAATA-TATAATTCAAC-CCCAAAAAA-TTGAAG-G-TTTTCACGCTTCTAATA
** * *
6870 TGGTTTTTCCATTTTTTT-CGAATTTATTTTTAATTAAATCGAAACAAGATTTAGATGCTCGTAA
125 TCATTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* *
6934 AAAGAAATCATTAAATCCACTGTGGCTGAGATTTGGTTAGATGAGTATAGATATTTCAAGGAGTC
190 AAAGAAATCATTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC
* * * * * ***
6999 TTT-CTACTAAAAATCATGCAAAACTAAGCCGAGGCCACGAAACGCGTTTTTATTTAAAAACCGT
255 TTTAC-GCCAAAAATCATGCAAAACTGAGCCGGGGCC-CGAAACACGTTTTTAGCCAAAAACCGT
*
7063 GATGA-T-T
318 GATGAGTAA
** * * * *
7070 A-G---T--AC-ATGATTTCGCCTAAAAACTGAC-CCGAAATTTTTTTTCTCAATT-TTGTG-CA
1 ACGATTTCGACTAAAATTTTG-CAAAAAACTGACTCCGAAA-ATTTTTCCTCAATTCTT-TGCCA
* * * * * *
7125 AAATATTCAGAAAAAATATATAATTCAACACTAAAAAGATTGAAGGACTTTTTATGCTTCTAATA
63 CAATACTCAGAAAAAATATATAATTCAACCCCAAAAA-ATTGAAGG--TTTTCACGCTTCTAATA
* * * * *
7190 TCATTTTTCCATTTTTTTTCGAATTAATTTCTAATTAAATCGAAACAAAATTTAGATGCTTGTAA
125 TCATTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* * * * *
7255 AAATAAA-AACTTATATCCAATGTGGCTGAGATTTGGTTCGATGAACATAGATATTT-AAGGAGT
190 AAAGAAATCA-TTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT
* * * ** * * *
7318 CTTTGCGCCAAAAATCATGTAAAATTGAGTTGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGT
254 CTTTACGCCAAAAATCATGCAAAACTGAGCCGGGG-CCCGAAACACGTTTTTAGCCAAAAACCGT
*
7383 GATGGTAGTAC
318 GAT-G-AGTAA
* * *
7394 ACGATTTTCAACTAAAATATTGCAAAAAACTGA-TCCGAAAAGTTTTTCCTC-ATTTTTTGCCAC
1 ACGA-TTTCGACTAAAATTTTGCAAAAAACTGACTCCGAAAA-TTTTTCCTCAATTCTTTGCCAC
* * * * *
7457 -A-ACTCAGAAAAAATATATAATTCAACGCCAAAAAATTTGAAGGGTTTCACACTTTTAATATCG
64 AATACTCAGAAAAAATATATAATTCAACCCCAAAAAA-TTGAAGGTTTTCACGCTTCTAATATCA
*
7520 TTTTTCCATTTTTTTCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCAT-AAA
128 TTTTTCCATTTTTTT-CCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
*
7584 AGCAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCT
192 AG-AAATCATTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCT
* * ** *
7649 TTATGCC-AAAACCATGCAAAACTGAGTTGTGGCCCGAAACACGTTTTTAGCCAAAAACCGTGA
256 TTACGCCAAAAATCATGCAAAACTGAGCCGGGGCCCGAAACACGTTTTTAGCCAAAAACCGTGA
7712 CACGATTTCG
Statistics
Matches: 811, Mismatches: 112, Indels: 91
0.80 0.11 0.09
Matches are distributed among these distances:
319 16 0.02
320 123 0.15
321 124 0.15
322 2 0.00
323 1 0.00
324 1 0.00
325 2 0.00
326 1 0.00
327 65 0.08
328 314 0.39
329 99 0.12
330 28 0.03
331 30 0.04
332 5 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (326 bp):
ACGATTTCGACTAAAATTTTGCAAAAAACTGACTCCGAAAATTTTTCCTCAATTCTTTGCCACAA
TACTCAGAAAAAATATATAATTCAACCCCAAAAAATTGAAGGTTTTCACGCTTCTAATATCATTT
TTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAA
ATCATTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTACG
CCAAAAATCATGCAAAACTGAGCCGGGGCCCGAAACACGTTTTTAGCCAAAAACCGTGATGAGTA
A
Found at i:8772 original size:12 final size:12
Alignment explanation
Indices: 8741--8775 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
8731 TCTCAATTTC
8741 TTTTCTTCTA-T
1 TTTTCTTCTAGT
8752 TTTTC-TCTAGT
1 TTTTCTTCTAGT
8763 TTTTCTTCTAGT
1 TTTTCTTCTAGT
8775 T
1 T
8776 CTAGTCAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.18
11 11 0.50
12 7 0.32
ACGTcount: A:0.09, C:0.17, G:0.06, T:0.69
Consensus pattern (12 bp):
TTTTCTTCTAGT
Found at i:10422 original size:322 final size:324
Alignment explanation
Indices: 9403--10539 Score: 1328
Period size: 322 Copynumber: 3.5 Consensus size: 324
9393 ATTAATTTCA
** *
9403 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTTTTAAATCCAATATGGCTG
1 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTG
* **
9468 AGATTTAGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCTTAAAATCATGCAAAACTGAG
66 AGATTTAGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAG
* * * * *
9533 CCGGGGCCCCGAAACGCATTTTTAGCCAAACAAAAAAAAATCATGATGATTAGTGCACGATTTCG
131 -CGGGGCCCCGAAATGCGTTTTTAG-C---C-AAAAAAAACCGTGATG-GTAGTGCACGATTTCG
* * ** *
9598 GCTCAAATTTTGCATAAACTGGCCCGAGAATTTTTCCTCAATTATTTGCCACAATACTCAGAAAA
189 GCTAAAATTTTGCAAAAACTAACCCGA-AATTTTTCCTC-ATTCTTTGCCACAATACT-A-AAAA
9663 AATATATAATTCAACGCCAAAAAAATATTGAAGGGTTTTCACGCTTTTAATATCGTTTTTCCATT
250 AATATATAATTCAACGCC--AAAAA-ATTGAAGGGTTTTCACGCTTTTAATATCGTTTTTCCA--
*
9728 TTTTTCCGAATTTAT
310 TTTTTCTGAATTTAT
* * *
9743 TTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAACAAATCCTTTAATCCATTGTGGCT-
1 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTG
* ** * *
9807 AGATTTTGTTCCATGAATATAGATATTTCAAGGAGTCTTAACGCCAAAAATCATGCAAAACTGAG
66 AGATTTAGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAG
* * * *
9872 CTAGGGCCTCGTAATGCGTTTTTAGCC---AAAAACTGTGATGGTA---CACGATTTCGGCTAAA
131 C-GGGGCCCCGAAATGCGTTTTTAGCCAAAAAAAACCGTGATGGTAGTGCACGATTTCGGCTAAA
* * * *
9931 ATTTTGCAAAAACTAACCTGAAAATTTTTCCTCTATTCTCTACCAGAATACTAAAAAATATATAT
195 ATTTTGCAAAAACTAACCCG-AAATTTTTCCTC-ATTCTTTGCCACAATACTAAAAAA-ATATAT
* * *
9996 AATTCAACGCCAAGACAATTGAAGGGTTTTTACGCTTCTAATATCG-TTTTCCA----T-T-AAT
257 AATTCAACGCCAA-AAAATTGAAGGGTTTTCACGCTTTTAATATCGTTTTTCCATTTTTCTGAAT
10054 TTAT
321 TTAT
* * * * * *
10058 TTCTACTTAAATCGAAACAAGATTCATATGCTCGTCAAAACAAATTCTTAAATCCAATGTAGTTG
1 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTG
* * * * *
10123 AGTTTTAGTTAGATGAATATAGATATTTCAAGGAGTTTTTTTGCCTAAAATCATGCAAAATTGAG
66 AGATTTAGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAG
*
10188 TCGGGGCCCCGAAATGCGTCTTTA-CCAAAAAAAACCGTGATGGTCAGTGCACGATTTCGGCTAA
131 -CGGGGCCCCGAAATGCGTTTTTAGCCAAAAAAAACCGTGATGGT-AGTGCACGATTTCGGCTAA
* *
10252 AATTTTGCAAAAACTACCCCG-AATATTTT-CTCACTTCTTTGCCACAAAACT-AAAAAA-ATAT
194 AATTTTGCAAAAACTAACCCGAAAT-TTTTCCTCA-TTCTTTGCCACAATACTAAAAAAATATAT
*
10313 AATTCAACGCCAAAAAATTGAA-GGTTTTCACGCTTTTAATATTGTTTTTCCATTTTTCTGAATT
257 AATTCAACGCCAAAAAATTGAAGGGTTTTCACGCTTTTAATATCGTTTTTCCATTTTTCTGAATT
10377 TAT
322 TAT
* * *
10380 TTTTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTGGCTA
1 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTG
* * *
10445 AGATTTGGTTAGATGAATATAGATATTTCGAGGAGTCTTTATGCCAAAAACCATGC-AAACTGAG
66 AGATTTAGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAG
* * * * *
10509 TTGTGG-CTCGAAACGCGTTTTTATCCAAAAA
131 -CGGGGCCCCGAAATGCGTTTTTAGCCAAAAA
10540 CCGTGACACG
Statistics
Matches: 681, Mismatches: 93, Indels: 65
0.81 0.11 0.08
Matches are distributed among these distances:
315 83 0.12
316 88 0.13
317 19 0.03
318 15 0.02
319 7 0.01
320 34 0.05
321 23 0.03
322 146 0.21
323 7 0.01
324 29 0.04
325 7 0.01
326 18 0.03
327 56 0.08
328 1 0.00
330 2 0.00
331 10 0.01
335 1 0.00
338 2 0.00
339 75 0.11
340 58 0.09
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (324 bp):
TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTG
AGATTTAGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAG
CGGGGCCCCGAAATGCGTTTTTAGCCAAAAAAAACCGTGATGGTAGTGCACGATTTCGGCTAAAA
TTTTGCAAAAACTAACCCGAAATTTTTCCTCATTCTTTGCCACAATACTAAAAAAATATATAATT
CAACGCCAAAAAATTGAAGGGTTTTCACGCTTTTAATATCGTTTTTCCATTTTTCTGAATTTAT
Found at i:10624 original size:17 final size:17
Alignment explanation
Indices: 10602--10645 Score: 70
Period size: 18 Copynumber: 2.5 Consensus size: 17
10592 AATTTATAGT
10602 GAAATTTATTAAATTCC
1 GAAATTTATTAAATTCC
*
10619 GAAATTTTATTAAATTTC
1 GAAA-TTTATTAAATTCC
10637 GAAATTTAT
1 GAAATTTAT
10646 AGTTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (17 bp):
GAAATTTATTAAATTCC
Done.