Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011429.1 Corchorus olitorius cultivar O-4 contig11462, 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: 4598
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Found at i:493 original size:154 final size:153
Alignment explanation
Indices: 1--2410 Score: 3402
Period size: 154 Copynumber: 15.8 Consensus size: 153
* *
1 GCCC-AAAT-ACAAGTGTTCCAAATGAGCT-AAAAGTTCACAGTGGACTAATCT-AAC-AAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
61 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
* *
126 TACGTCACTAATGGGCCCCGATAG
131 AACG-AACTAATGGGCCCCGATAG
* * *
150 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGAGGACTAATCTAAACAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * * * * *
215 TTATAGGTAGGCCATAAACAATGGAAACAAACGACATTGAGGCTTGCCAATTCGAAGAAGATTCA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAG-CATTGAGGTTTGCCAAATCGAAGACGATTCA
* * * ** **
280 ATACGTCACCAATAAGTTCCGATAG
130 AAACG-AACTAATGGGCCCCGATAG
* * * *
305 GCCCAAAATAACAAGTGTTACACATGAGCTAAAAAGTTCACAGTGGACAAATCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* *
370 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCAAAGACTATTCAA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
* * *
435 TACGTAACTAATGGGCTCGGATAG
131 AACG-AACTAATGGGCCCCGATAG
* * ** * *
459 GCCCAAAATGACAAGTATTCTGAATGAGCTAAAAATTTCACAGTGGACTAATCTAACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
*
524 TTATAGTTAGGCCATAAACAATGTAAAGAAAAGCATTGAGGTTT-CCAAATCGAAGACGATTCAA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
*
588 AACGGAACTAATGAGCCCCGATAG
131 AAC-GAACTAATGGGCCCCGATAG
* *
612 GCCCAAATTAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACTAATCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * * *
677 TTATAGTTAGGCCATAAAAAATAGAAAGAAAAGCATTGAGGTTTCCCAAATCAAAGACGATTCAA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
*
742 AACAGAACTAATGGTCCCCGATAG
131 AAC-GAACTAATGGGCCCCGATAG
* *
766 GCCCAAAATAACAAGTGTTCCAAATGAGCT-AAAACTTCACACTGGACTAATCTCACCAAAATAA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * *
830 TTATAATTAGGCCATAAAC------AA-ATAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAG
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
888 AACGGAACTAATGGGCCCCGATAG
131 AAC-GAACTAATGGGCCCCGATAG
*
912 GCCCAAAATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * * *
977 TTATAGTTAGTCCATAAAAAATGGAAAGAAAACCTTTGAGGTTTGCCAAATCGAAGACGATTCAA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
1042 AACGGAACTAATGGGCCCCGATAG
131 AAC-GAACTAATGGGCCCCGATAG
*
1066 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * *
1131 TTAGAGTTAGGCCATAAACAACGGAAAGAAAAGCATTGAGG-TTACCAAATCGAAGACGATTCAA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
*
1195 AACGAACTAATGGGCCCAGATAG
131 AACGAACTAATGGGCCCCGATAG
* * *
1218 GCACAAAATAACAAGTGTCCCAAAT-AACTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * * *
1282 TTATAGGTAAGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTACCAAATAGAAGACGATTCAA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
*
1347 AACGACACTAATAGGCCCCGATAG
131 AACGA-ACTAATGGGCCCCGATAG
*
1371 GCCCAAAATAACAAGTGATCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * * *
1436 TTATAGGTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTACCAAATCGAAGATGATTCAT
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
*
1500 AACGACACTAATTGGCCCCGATAG
131 AACGA-ACTAATGGGCCCCGATAG
* * * * *
1524 GCACAAAATAACAAGTGTTCCAAATAACCTAAAAACTTCACAGTGGAGTAATCTTACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * * *
1589 TTATAGGTAGGCCATAAACAATGGAAAGAAAAGCATTTAGGTTT-CTAAATCGAAGACGATTCAG
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
1653 AACGACACTAATGGGCCCCGATAG
131 AACGA-ACTAATGGGCCCCGATAG
1677 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * *
1742 TTTTAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTACCAAATCGAAGACGATTCAT
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
1806 AACGACACTAATGGGCCCCGATAG
131 AACGA-ACTAATGGGCCCCGATAG
* * * *
1830 ACACAAAATAACAAGTGTTCCAAAAGACCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT-A
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * * *
1894 TTATAGGTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATAGAAGACGATTCAG
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
*
1959 AACGACACTAATGGGTCCCGATAG
131 AACGA-ACTAATGGGCCCCGATAG
** * * ** * *
1983 GCCCAAAATAACATCTGTTTCGAATGAGCTAAAAACTTCACAGTGTTCAAATCTCACCGAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * ** * ** *
2048 TTATTGTTAGGCCATCAACAATGGAAAGAAAAGCATCAAGGGTTGCCAAATCGATTACGATTCCA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
* **
2113 AACGTCACTAATGGGCCATGATAG
131 AACG-AACTAATGGGCCCCGATAG
* *
2137 GCCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * * * *
2202 TTATAGTTAGGCTATAATCATTGGAAAGAAAAGCATTGAGGGTTGCCAAATTGAAGACGATTCAA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
* * *
2267 AACGGAACTAATGGTCCTCGATAT
131 AAC-GAACTAATGGGCCCCGATAG
* *
2291 GCCCAAAATAACGAGTGTTCCAAATGAGCTAAAAACTTAACAGTGGACTAATCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* *
2356 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCGAATCGAA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAA
2411 AAACTTAACA
Statistics
Matches: 2027, Mismatches: 209, Indels: 45
0.89 0.09 0.02
Matches are distributed among these distances:
146 84 0.04
147 50 0.02
149 4 0.00
150 4 0.00
151 94 0.05
152 132 0.07
153 727 0.36
154 795 0.39
155 137 0.07
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21
Consensus pattern (153 bp):
GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
AACGAACTAATGGGCCCCGATAG
Found at i:1707 original size:306 final size:305
Alignment explanation
Indices: 5--4598 Score: 4290
Period size: 308 Copynumber: 14.7 Consensus size: 305
1 GCCC
* *
5 AAAT-ACAAGTGTTCCAAATGAGCT-AAAAGTTCACAGTGGACTAATCT-AAC-AAATGATTATA
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
*
66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGT
66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG-
* *
131 CACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGAGG
130 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
* * * * *
196 ACTAATCTAAACAAAATGATTATAGGTAGGCCATAAACAATGGAAACAAACGACATTGAGGCTTG
195 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG-CATTGAGG-TTG
* * * * ** ** *
261 CCAATTCGAAGAAGATTCAATACGTCACCAATAAGTTCCGATAGGCCCA
258 CCAAATCGAAGACGATTCAA-ACGACACTAATGGGCCCCGATAGGCACA
* * * *
310 AAATAACAAGTGTTACACATGAGCTAAAAAGTTCACAGTGGACAAATCTCACCAAAATGATTATA
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
* * *
375 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCAAAGACTATTCAATACGT
66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG-
* * * * ** *
440 AACTAATGGGCTCGGATAGGCCCAAAATGACAAGTATTCTGAATGAGCTAAAAATTTCACAGTGG
130 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
* * *
505 ACTAATCTAACCAAAATGATTATAGTTAGGCCATAAACAATGTAAAGAAAAGCATTGAGGTTTCC
195 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTGCC
* *
570 AAATCGAAGACGATTCAAAACGGA-ACTAATGAGCCCCGATAGGCCCA
260 AAATCGAAGACGATTC-AAAC-GACACTAATGGGCCCCGATAGGCACA
* *
617 AATTAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACTAATCTCACCAAAATGATTATA
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
* * * *
682 GTTAGGCCATAAAAAATAGAAAGAAAAGCATTGAGGTTTCCCAAATCAAAGACGATTCAAAACAG
66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-G
* *
747 AACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT-AAAACTTCACACTGG
130 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
* * *
811 ACTAATCTCACCAAAATAATTATAATTAGGCCATAAAC------AA-ATAAGCATTGAGGTTTGC
195 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTGC
*
869 CAAATCGAAGACGATTCAGAACGGA-ACTAATGGGCCCCGATAGGCCCA
259 CAAATCGAAGACGATTCA-AAC-GACACTAATGGGCCCCGATAGGCACA
*
917 AAATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
* * * *
982 GTTAGTCCATAAAAAATGGAAAGAAAACCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGG
66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-G
*
1047 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGG
130 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
* * *
1112 ACTAATCTCACCAAAATGATTAGAGTTAGGCCATAAACAACGGAAAGAAAAGCATTGAGGTTACC
195 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTGCC
*
1177 AAATCGAAGACGATTCAAAACGA-ACTAATGGGCCCAGATAGGCACA
260 AAATCGAAGACGATTC-AAACGACACTAATGGGCCCCGATAGGCACA
* *
1223 AAATAACAAGTGTCCCAAAT-AACTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
* * * *
1287 GGTAAGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTACCAAATAGAAGACGATTCAAAACGA
66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGA
* *
1352 CACTAATAGGCCCCGATAGGCCCAAAATAACAAGTGATCCAAATGAGCTAAAAACTTCACAGTGG
131 -ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
* *
1417 ACTAATCTCACCAAAATGATTATAGGTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTACC
195 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTGCC
* *
1482 AAATCGAAGATGATTCATAACGACACTAATTGGCCCCGATAGGCACA
260 AAATCGAAGACGATTCA-AACGACACTAATGGGCCCCGATAGGCACA
* * * *
1529 AAATAACAAGTGTTCCAAATAACCTAAAAACTTCACAGTGGAGTAATCTTACCAAAATGATTATA
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
* * * *
1594 GGTAGGCCATAAACAATGGAAAGAAAAGCATTTAGGTTT-CTAAATCGAAGACGATTCAGAACGA
66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGA
1658 CACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
131 -ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
* *
1723 ACTAATCTCACCAAAATGATTTTAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTACC
195 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTGCC
*
1788 AAATCGAAGACGATTCATAACGACACTAATGGGCCCCGATAGACACA
260 AAATCGAAGACGATTCA-AACGACACTAATGGGCCCCGATAGGCACA
* *
1835 AAATAACAAGTGTTCCAAAAGACCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT-ATTATA
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
* * * *
1899 GGTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATAGAAGACGATTCAGAACGA
66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGA
* ** * * *
1964 CACTAATGGGTCCCGATAGGCCCAAAATAACATCTGTTTCGAATGAGCTAAAAACTTCACAGTGT
131 -ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
* * * * * **
2029 TCAAATCTCACCGAAATGATTATTGTTAGGCCATCAACAATGGAAAGAAAAGCATCAAGGGTTGC
195 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTGC
** * **
2094 CAAATCGATTACGATTCCAAACGTCACTAATGGGCCATGATAGGC-CAA
259 CAAATCGAAGACGATT-CAAACGACACTAATGGGCCCCGATAGGCAC-A
*
2142 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATA
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
* * * * *
2207 GTTAGGCTATAATCATTGGAAAGAAAAGCATTGAGGGTTGCCAAATTGAAGACGATTCAAAACGG
66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-G
* * * * *
2272 AACTAATGGTCCTCGATATGCCCAAAATAACGAGTGTTCCAAATGAGCTAAAAACTTAACAGTGG
130 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
2337 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGC
195 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTGC
* * ** ** * * * * *
2402 CGAATCGAA-A-AACTT--AACAGTGGACTAAT-CTCACCAAAATG-ATTA
259 CAAATCGAAGACGA-TTCAAAC-G-ACACTAATGGGCCCCGATAGGCA-CA
** * * *** * * * * * * * * *
2447 TAGTTAGGCCA-T-AAACAATTGGAAG--AAAAGCATTGA-GGTTTTGCCAAATCGAAGACGATT
1 -AAATA-ACAAGTGTTCCAAAT-G-AGCTAAAAAC-TTCACAG--TGGACTAATC----TC-A-C
* * * * ** * * ** * ** ** *
2507 CAATATG-TCACTA-ATGGGCCCCGATAGGCCCA---AAATAACAAGTGTTCCAAATGAGCTAAA
53 CAAAATGATTA-TAGTTAGG--CC-ATA-AACAATGGAAAGAA-AAGCATT-GAGGTTTGC--CA
* * * * * ** **
2567 AACTTC-ATAGTGGACTAATCTAAACAAAATGATTATAGTTAGG--CC-ATAAACAATTGAAAGA
109 AA--TCGA-A---GACGATTCAAAACGAACT-A--AT-G---GGCCCCGATAGGC---CCAAA-A
* * *** * * ** **
2628 AAAGCATTGAG-GTTTGCCAAATCGAAGACGATTCAAAACGGAACAAATGAGCCCCGATAGGC-C
157 TAA-CA---AGTG-TT-CCAAAT-G-AG-C---TAAAAACTTCAC-AGTG-G-ACTAAT-CTCAC
* ** * * *
2691 CAAAATAACAAGT-GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG-AT
206 CAAAATGATTA-TAGTT----A-G-GCCATAAA---CA-A-TGG---AA----A-GAAAA-GCAT
* * *** * * * * *
2754 T-ATAGTTAGGCCATAAAC-AATG--GAAAGAAAAG-CATTGA-GGTTTGCCAAATCGA-AGACT
250 TGA-GGTT--GCCA-AATCGAA-GACGATTCAAACGACACTAATGG---GCC---CCGATAGGC-
2812 ATTCA
303 A--CA
** * * * ** * ** * * * *
2817 GTACGTAACTAATGGGCTCC-GAT-AGGCCCAAAA--TAACGAGTGTTCCAA-ATGAGCTAAAA-
1 --AAATAAC-AA-GTGTTCCAAATGA-GCTAAAAACTTCAC-AGTGGACTAATCTCA-CCAAAAT
* ** ** * **
2876 -ACTTCACAGTGGACTAATCTCACCAA-AATGATTATAGTTAGGCCATAAAAAATTGAAAGAAAA
59 GA-TT-ATAGT----TAGGC-CATAAACAATG--GA-A---A-G--A-AAAGCATTG--AG----
* ***** * * *
2939 GCATTGAGGTTTGCCAAACCGAAGACGATTCAAAACGGAACTAATGGGCGCCGATAGGCCTAAAA
101 G-TTTGCCAAAT--CGAA--G-A--CGATTCAAAAC-GAACTAATGGGCCCCGATAGGCCCAAAA
** * * * * * *
3004 TAACAAGTGTTCCACGTGATCTATAAAGTTCACAGTGAACTAGTCTCACCAAAATTATTATAGTT
157 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
3069 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA-A
222 AGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTGCCAAATCGAAGACGATTC-AAAC-GACA
* * *
3133 CTAATGAGCCCCCATAGGCCCA
284 CTAATGGGCCCCGATAGGCACA
* *
3155 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGAGGACTAATCTCTCCAAAATGATTATA
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
*
3220 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGT
66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG-
* *
3285 CACTAATGGGCCCGGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
130 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
* * *
3350 ACTAATCTCACCAAAATGATTATAGTTAGGACATAAATAATTGAAAGAAAAGCATTGAGGTTTGC
195 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTGC
* * *
3415 CAAATCGTAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCA
259 CAAATCGAAGACGATTCAA-ACGACACTAATGGGCCCCGATAGGCACA
3463 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
* * *
3528 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGGTTCAATATGT
66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG-
* * * *
3593 CACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGTGCTAAAAACATCAAAGTGG
130 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
* * *
3658 ACCAATCTAAACAAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG
195 ACTAATCT-CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTG
* * *
3723 CCAAATCGAAGACGATTACAATATGTCACTAAGTCGGGCCCCGAGTACGGACCCA
258 CCAAATCGAAGACGATT-CAA-ACGACACTAA-T-GGGCCCCGA-TA-GG-CACA
*
3778 AAATAAACAAGTTGTTACCAAATGAGACT-AAAACATCACAGTGGACTAATCTCACCAAAATGAT
1 AAAT-AACAAG-TGTT-CCAAATGAG-CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
* * * *
3842 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCAGTGAGGTTTGCCAAATCAAACACCATTCAAA
62 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
* * * * * *
3907 ACGGAACTAATGAGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAACTGAGATAAAAAGTTTACA
127 AC-GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
3972 GTGGACTAATCTCACCAAAATGATTATAAG-TAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
191 GTGGACTAATCTCACCAAAATGATTAT-AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
* * * * * *
4036 TTTGCCAAATCAAACACCATTCAAAACGGA-ACTAATGAGCCCCGAAAGGCCCA
255 -TTGCCAAATCGAAGACGATTC-AAAC-GACACTAATGGGCCCCGATAGGCACA
** * *
4089 AAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAGTAGACTAATCTCACCAAAATTATTATA
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
* ** *
4154 GTTAGGCCATAAACAATGGAATGAAAAGCATTGAGGTTTGATAAATCGAAGACGATTCAATACGT
66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG-
* * * * * *
4219 CACTAATGGACCCCAATAAGCCCAAAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCACAGTTG
130 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
* * * * *
4284 TCAAATCTCACCAAAGTTATTATAGTTAGGCCATAAACAATGGAAACAAAAGCATTGAGGTTTGC
195 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTGC
* * *
4349 TAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCA
259 CAAATCGAAGACGATTCAA-ACGACACTAATGGGCCCCGATAGGCACA
*
4397 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATAATTATA
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
* * * * * *
4462 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGATGCTTGCCAAATCGAAGTCGGTTCAATATGT
66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG-
* *
4527 CACTAATGGGCCCCGATAGGCCCAGAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
130 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
4592 ACTAATC
195 ACTAATC
Statistics
Matches: 3555, Mismatches: 514, Indels: 437
0.79 0.11 0.10
Matches are distributed among these distances:
299 13 0.00
300 218 0.06
301 48 0.01
304 6 0.00
305 305 0.09
306 541 0.15
307 447 0.13
308 992 0.28
309 250 0.07
310 20 0.01
311 11 0.00
312 17 0.00
313 19 0.01
314 16 0.00
315 19 0.01
316 15 0.00
317 75 0.02
318 168 0.05
319 5 0.00
320 2 0.00
321 3 0.00
322 18 0.01
323 1 0.00
324 2 0.00
325 6 0.00
326 2 0.00
328 4 0.00
329 4 0.00
330 2 0.00
331 4 0.00
332 8 0.00
333 4 0.00
334 11 0.00
335 11 0.00
336 23 0.01
337 7 0.00
338 3 0.00
340 11 0.00
341 10 0.00
342 8 0.00
343 28 0.01
344 9 0.00
345 4 0.00
346 1 0.00
347 1 0.00
348 3 0.00
349 6 0.00
351 3 0.00
352 3 0.00
353 3 0.00
354 3 0.00
356 6 0.00
357 3 0.00
358 1 0.00
361 7 0.00
362 24 0.01
363 6 0.00
364 14 0.00
365 11 0.00
367 3 0.00
368 4 0.00
369 3 0.00
370 12 0.00
371 11 0.00
372 5 0.00
373 5 0.00
374 2 0.00
375 2 0.00
376 3 0.00
377 10 0.00
378 2 0.00
379 3 0.00
380 6 0.00
381 5 0.00
382 1 0.00
383 10 0.00
384 3 0.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (305 bp):
AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGA
ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTGCCA
AATCGAAGACGATTCAAACGACACTAATGGGCCCCGATAGGCACA
Found at i:2323 original size:308 final size:307
Alignment explanation
Indices: 1--2410 Score: 3383
Period size: 306 Copynumber: 7.9 Consensus size: 307
* *
1 GCCC-AAAT-ACAAGTGTTCCAAATGAGCT-AAAAGTTCACAGTGGACTAATCT-AAC-AAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
61 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
* **
126 TACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
131 AACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
* * * * * *
191 AGAGGACTAATCTAAACAAAATGATTATAGGTAGGCCATAAACAATGGAAACAAACGACATTGAG
196 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG-CATTGAG
* * * * ** **
256 GCTTGCCAATTCGAAGAAGATTCAATACGTCACCAATAAGTTCCGATAG
260 GGTTGCCAAATCGAAGACGATTCAA-ACGTCACTAATGGGCCCCGATAG
* * * *
305 GCCCAAAATAACAAGTGTTACACATGAGCTAAAAAGTTCACAGTGGACAAATCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* *
370 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCAAAGACTATTCAA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
* * * * * * ** *
435 TACGTAACTAATGGGCTCGGATAGGCCCAAAATGACAAGTATTCTGAATGAGCTAAAAATTTCAC
131 AACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
* *
500 AGTGGACTAATCTAACCAAAATGATTATAGTTAGGCCATAAACAATGTAAAGAAAAGCATTGA-G
196 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
* ** *
564 GTTTCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCCCGATAG
261 GTTGCCAAATCGAAGACGATTC-AAACGTCACTAATGGGCCCCGATAG
* *
612 GCCCAAATTAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACTAATCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * * *
677 TTATAGTTAGGCCATAAAAAATAGAAAGAAAAGCATTGAGGTTTCCCAAATCAAAGACGATTCAA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
* *
742 AACAGAACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT-AAAACTTCAC
131 AACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
* * * *
806 ACTGGACTAATCTCACCAAAATAATTATAATTAGGCCATAAAC------AA-ATAAGCATTGAGG
196 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
* **
864 TTTGCCAAATCGAAGACGATTCAGAACGGAACTAATGGGCCCCGATAG
261 GTTGCCAAATCGAAGACGATTCA-AACGTCACTAATGGGCCCCGATAG
*
912 GCCCAAAATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * * *
977 TTATAGTTAGTCCATAAAAAATGGAAAGAAAACCTTTGAGGTTTGCCAAATCGAAGACGATTCAA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
*
1042 AACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCAC
131 AACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
* *
1107 AGTGGACTAATCTCACCAAAATGATTAGAGTTAGGCCATAAACAACGGAAAGAAAAGCATTGA-G
196 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
* * *
1171 GTTACCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCAGATAG
261 GTTGCCAAATCGAAGACGATTC-AAACGTCACTAATGGGCCCCGATAG
* * *
1218 GCACAAAATAACAAGTGTCCCAAAT-AACTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * * *
1282 TTATAGGTAAGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTACCAAATAGAAGACGATTCAA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
* *
1347 AAC-GACACTAATAGGCCCCGATAGGCCCAAAATAACAAGTGATCCAAATGAGCTAAAAACTTCA
131 AACGGA-ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
*
1411 CAGTGGACTAATCTCACCAAAATGATTATAGGTAGGCCATAAACAATGGAAAGAAAAGCATTGA-
195 CAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG
* * * *
1475 GGTTACCAAATCGAAGATGATTCATAACGACACTAATTGGCCCCGATAG
260 GGTTGCCAAATCGAAGACGATTCA-AACGTCACTAATGGGCCCCGATAG
* * * * *
1524 GCACAAAATAACAAGTGTTCCAAATAACCTAAAAACTTCACAGTGGAGTAATCTTACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * * *
1589 TTATAGGTAGGCCATAAACAATGGAAAGAAAAGCATTTAGGTTT-CTAAATCGAAGACGATTCAG
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
1653 AAC-GACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
131 AACGGA-ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
*
1717 CAGTGGACTAATCTCACCAAAATGATTTTAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-
195 CAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG
* *
1781 GGTTACCAAATCGAAGACGATTCATAACGACACTAATGGGCCCCGATAG
260 GGTTGCCAAATCGAAGACGATTCA-AACGTCACTAATGGGCCCCGATAG
* * * *
1830 ACACAAAATAACAAGTGTTCCAAAAGACCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT-A
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * * *
1894 TTATAGGTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATAGAAGACGATTCAG
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
* ** * *
1959 AAC-GACACTAATGGGTCCCGATAGGCCCAAAATAACATCTGTTTCGAATGAGCTAAAAACTTCA
131 AACGGA-ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
** * * * * **
2023 CAGTGTTCAAATCTCACCGAAATGATTATTGTTAGGCCATCAACAATGGAAAGAAAAGCATCAAG
195 CAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG
** **
2088 GGTTGCCAAATCGATTACGATTCCAAACGTCACTAATGGGCCATGATAG
260 GGTTGCCAAATCGAAGACGATT-CAAACGTCACTAATGGGCCCCGATAG
* *
2137 GCCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * * * *
2202 TTATAGTTAGGCTATAATCATTGGAAAGAAAAGCATTGAGGGTTGCCAAATTGAAGACGATTCAA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
* * * * *
2267 AACGGAACTAATGGTCCTCGATATGCCCAAAATAACGAGTGTTCCAAATGAGCTAAAAACTTAAC
131 AACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
2332 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
196 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
*
2397 GTTGCCGAATCGAA
261 GTTGCCAAATCGAA
2411 AAACTTAACA
Statistics
Matches: 1903, Mismatches: 177, Indels: 48
0.89 0.08 0.02
Matches are distributed among these distances:
299 11 0.01
300 219 0.12
301 48 0.03
304 7 0.00
305 288 0.15
306 524 0.28
307 425 0.22
308 202 0.11
309 179 0.09
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21
Consensus pattern (307 bp):
GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
AACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
GTTGCCAAATCGAAGACGATTCAAACGTCACTAATGGGCCCCGATAG
Found at i:2473 original size:88 final size:89
Alignment explanation
Indices: 2321--2499 Score: 317
Period size: 88 Copynumber: 2.0 Consensus size: 89
2311 CAAATGAGCT
2321 AAAAACTTAACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTAACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
*
2386 AAGCATTGAGG-GTTGCCGAATCG
66 AAGCATTGAGGTGTTGCCAAATCG
2409 AAAAACTTAACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATTGG-AAGA
1 AAAAACTTAACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAGA
*
2473 AAAGCATTGAGGTTTTGCCAAATCG
65 AAAGCATTGAGGTGTTGCCAAATCG
2498 AA
1 AA
2500 GACGATTCAA
Statistics
Matches: 87, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
88 72 0.83
89 15 0.17
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (89 bp):
AAAAACTTAACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
AAGCATTGAGGTGTTGCCAAATCG
Found at i:2597 original size:243 final size:242
Alignment explanation
Indices: 2167--2653 Score: 762
Period size: 243 Copynumber: 2.0 Consensus size: 242
2157 CAAATGAGCT
* *
2167 AAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCTATAATCATTGGAAAGAA
1 AAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACATTGGAAAGAA
* * * *
2232 AAGCATTGAGGGTTGCCAAATTGAAGACGATTCAAAACGGAACTAATGGTCCTCGATATGCCCAA
66 AAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
* * *
2297 AATAACGAGTGTTCCAAATGAGCTAAAAACTTAACAGTGGACTAATCTCACCAAAATGATTATAG
131 AATAACAAGTGTTCCAAATGAGCTAAAAACTTAACAGTGGACTAATCTAAACAAAATGATTATAG
*
2362 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCGAATCG
196 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCG
2409 AAAAACTT-AACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATTGG-AAG
1 AAAAACTTCAA-AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC-ATTGGAAAG
* * * **
2472 AAAAGCATTGAGGTTTTGCCAAATCGAAGACGATTCAATATGTCACTAATGGGCCCCGATAGGCC
64 AAAAGCATTGAGG-GTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
* *
2537 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCATAGTGGACTAATCTAAACAAAATGATTA
128 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTAACAGTGGACTAATCTAAACAAAATGATTA
* *
2602 TAGTTAGGCCATAAACAATTGAAAGAAAAGCATTGAGGTTTGCCAAATCG
193 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCG
2652 AA
1 AA
2654 GACGATTCAA
Statistics
Matches: 223, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
241 2 0.01
242 65 0.29
243 156 0.70
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (242 bp):
AAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACATTGGAAAGAA
AAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
AATAACAAGTGTTCCAAATGAGCTAAAAACTTAACAGTGGACTAATCTAAACAAAATGATTATAG
TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCG
Found at i:2725 original size:154 final size:154
Alignment explanation
Indices: 2409--4598 Score: 3333
Period size: 154 Copynumber: 14.1 Consensus size: 154
2399 TGCCGAATCG
*
2409 AAAAACTTAACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATTGG-AAGA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAGA
*
2473 AAAGCATTGAGGTTTTGCCAAATCGAAGACGATTCAATATGTCACTAATGGGCCCCGATAGGCCC
65 AAAGCATTGAGG-TTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCC
2538 AAAATAACAAGTGTTCCAAATGAGCT
129 AAAATAACAAGTGTTCCAAATGAGCT
* * * *
2564 AAAAACTTCATAGTGGACTAATCTAAACAAAATGATTATAGTTAGGCCATAAACAATTGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* ** * *
2629 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACAAATGAGCCCCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAA
2694 AATAACAAGTGTTCCAAATGAGCT
131 AATAACAAGTGTTCCAAATGAGCT
2718 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* * * *
2783 AAGCATTGAGGTTTGCCAAATCGAAGACTATTCAGTACGTAACTAATGGGCTCCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAA
*
2848 AATAACGAGTGTTCCAAATGAGCT
131 AATAACAAGTGTTCCAAATGAGCT
* *
2872 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAAAATTGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* * ** * *
2937 AAGCATTGAGGTTTGCCAAACCGAAGACGATTCAAAACGGAACTAATGGGCGCCGATAGGCCTAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAA
** *
3002 AATAACAAGTGTTCCACGTGATCT
131 AATAACAAGTGTTCCAAATGAGCT
* * * * *
3026 ATAAAGTTCACAGTGAACTAGTCTCACCAAAATTATTATAGTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* ** * *
3091 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCCCCATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAA
3156 AATAACAAGTGTTCCAAATGAGCT
131 AATAACAAGTGTTCCAAATGAGCT
* *
3180 AAAAACTTCACAGAGGACTAATCTCTCCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
*
3245 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCGGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAA
3310 AATAACAAGTGTTCCAAATGAGCT
131 AATAACAAGTGTTCCAAATGAGCT
* * *
3334 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGACATAAATAATTGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
*
3399 AAGCATTGAGGTTTGCCAAATCGTAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAA
3464 AATAACAAGTGTTCCAAATGAGCT
131 AATAACAAGTGTTCCAAATGAGCT
3488 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* *
3553 AAGCATTGAGGTTTGCCAAATCGAAGACGGTTCAATATGTCACTAATGGGCCCCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAA
*
3618 AATAACAAGTGTTCCAAATGTGCT
131 AATAACAAGTGTTCCAAATGAGCT
* * * * *
3642 AAAAACATCAAAGTGGACCAATCTAAACAAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
1 AAAAACTTCACAGTGGACTAATCT-CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
*
3707 AAAGCATTGAGGTTTGCCAAATCGAAGACGATTACAATATGTCACTAAGTCGGGCCCCGAGTACG
65 AAAGCATTGAGGTTTGCCAAATCGAAGACGATT-CAATACGTCACTAA-T-GGGCCCCGA-TA-G
3772 GACCCAAAATAAACAAGTTGTTACCAAATGAGACT
125 G-CCCAAAAT-AACAAG-TGTT-CCAAATGAG-CT
*
3807 -AAAACATCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* * * * * ** * *
3871 AAGCAGTGAGGTTTGCCAAATCAAACACCATTCAAAACGGAACTAATGAGCCCCGAAAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAA
* *
3936 AATAACAAGTGTTCCAACTGAGAT
131 AATAACAAGTGTTCCAAATGAGCT
* *
3960 AAAAAGTTTACAGTGGACTAATCTCACCAAAATGATTATAAG-TAGGCCATAAACAATGGAAAGA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT-AGTTAGGCCATAAACAATGGAAAGA
* * * * ** * *
4024 AAAGCATTGAGGTTTGCCAAATCAAACACCATTCAAAACGGAACTAATGAGCCCCGAAAGGCCCA
65 AAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCA
**
4089 AAATAACAAGTGTTCTGAATGAGCT
130 AAATAACAAGTGTTCCAAATGAGCT
* * *
4114 AAAAACTTCACAGTAGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAACAATGGAATGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
** * * *
4179 AAGCATTGAGGTTTGATAAATCGAAGACGATTCAATACGTCACTAATGGACCCCAATAAGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAA
*
4244 AATAAGAAGTGTTCCAAATGAGCT
131 AATAACAAGTGTTCCAAATGAGCT
* * * * * *
4268 AAAAACTTCACAGTTGTCAAATCTCACCAAAGTTATTATAGTTAGGCCATAAACAATGGAAACAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
*
4333 AAGCATTGAGGTTTGCTAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAA
4398 AATAACAAGTGTTCCAAATGAGCT
131 AATAACAAGTGTTCCAAATGAGCT
*
4422 AAAAACTTCACAGTGGACTAATCTCACCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* * * * * *
4487 AAGCATTGATGCTTGCCAAATCGAAGTCGGTTCAATATGTCACTAATGGGCCCCGATAGGCCCAG
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAA
4552 AATAACAAGTGTTCCAAATGAGCT
131 AATAACAAGTGTTCCAAATGAGCT
4576 AAAAACTTCACAGTGGACTAATC
1 AAAAACTTCACAGTGGACTAATC
Statistics
Matches: 1866, Mismatches: 154, Indels: 31
0.91 0.08 0.02
Matches are distributed among these distances:
153 3 0.00
154 1539 0.82
155 144 0.08
156 20 0.01
157 9 0.00
158 11 0.01
159 3 0.00
160 10 0.01
161 9 0.00
162 16 0.01
163 71 0.04
164 29 0.02
165 2 0.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAA
AATAACAAGTGTTCCAAATGAGCT
Done.