Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016327.1 Corchorus olitorius cultivar O-4 contig16360, 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: 25823
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1160 original size:329 final size:331
Alignment explanation
Indices: 1--2646 Score: 3447
Period size: 330 Copynumber: 8.1 Consensus size: 331
*
1 CTGATATTTGGTTAGATGAATATAGATATTTCAAGGA-TCTTGGCGCAAAAAATCATGCAAAACT
1 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACT
65 GAGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGA----T-G--CACGATTTCTGCTAA
66 GAGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTTAGTACACGATTTCTGCTAA
* *
123 AATTTTGCAAAACTGACCCGAAAAATTTTTCTTTTATTATTGGCCACAACACTTGTAAAAAATAT
131 AATTTTGCAAAACTGACCCGAAAAATTTTTCTTTTATTTTTGGCCACAATACTTGTAAAAAATAT
*
188 ATAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTGTCCTATTTTTTT
196 ATAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTT
*
253 CGAATTAATTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACATATCCTTAAATCGG
261 CGAATTAATTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCGG
318 TTGTGG
326 TTGTGG
* * *
324 CTGATATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGC-AAAAATCATGCCAAACT
1 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACT
** *
388 GAGCCATGGTCCCGGAATGCGTTTTTCACCAAAAACTGTGATGGTTAGTACACGATTTCTGCTAA
66 GAGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTTAGTACACGATTTCTGCTAA
* * * *
453 AATTTTGCAAAACTGACCCGAAAATTTTTTCTTTTATTATTGGTCACAACACTTGTAAAAAATAT
131 AATTTTGCAAAACTGACCCGAAAAATTTTTCTTTTATTTTTGGCCACAATACTTGTAAAAAATAT
*
518 ATAATTCAATGCCAAAAATATTAAAGGGCGTTTCACGCTTCGAATATCGTTTTTCCTATTTTTTT
196 ATAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTT
* * *
583 CGAATTAATTTATAATAAAATCGAAACAAGATTCCGATGTTCGT-AAAACATATCCTTAAATAGG
261 CGAATTAATTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCGG
647 TTGTGG
326 TTGTGG
* * * *
653 CTGATATTTGGTTAGATGGATATAGATATTTCAAGGAGTTTTGGCGCGAAAAATCATGCAAAACT
1 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACT
* *
718 GAGCCGGGGTCCCGGAATGTGTTTTTCGCCAAAAACTGTGATGGTTAGTACAAGATTTCTGCTAA
66 GAGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTTAGTACACGATTTCTGCTAA
* *
783 AATTTTGCAAAACTGACCCGAAAAATTTTTCTTTTATTATTGGCCACAACACTTGTAAAAAATAT
131 AATTTTGCAAAACTGACCCGAAAAATTTTTCTTTTATTTTTGGCCACAATACTTGTAAAAAATAT
848 ATAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTT
196 ATAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTT
* * *
913 AGAATTAATTTATAAT-AAATCGAAAGAAGATTCCGATGCTCGAAAAAACAAATCCTTAAATCGG
261 CGAATTAATTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCGG
977 TTGTGG
326 TTGTGG
* * * *
983 CTGAGATTTGGTTAGATGAATATTGA-ATTTCAAGGAGCCTTGGTGCAAAAAATCATGCAAAATT
1 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACT
* *
1047 GAGCCGGGGTCCCAGAATGTGTTTTTCGCCAAAAACTGTGATGGTTAGTACACGATTTCTGCTAA
66 GAGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTTAGTACACGATTTCTGCTAA
* * * *
1112 AATTTTGCAAAACTGACCCGAAAAAGTTTTATATTATTTTTTGCCACAATACTTGTAAAAAATAT
131 AATTTTGCAAAACTGACCCGAAAAATTTTTCTTTTATTTTTGGCCACAATACTTGTAAAAAATAT
* * ** * *
1177 ATAATTCAATGCCATAAATATTAAAGGGCATTTTATTCTTCGAATATCGTTTTTGCTATATTTTT
196 ATAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTT
* * * * *
1242 CTGAATTAATTTATAATAAAATCGAAACACGATTCTGATGCTCGTAAAAATAAATCCTTAATTCC
261 C-GAATTAATTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCG
**
1307 AATGTGG
325 GTTGTGG
* * * *
1314 ATGAGATTTGGTTAGATGAATATAGATATTTCAAAGAGTCTTGACGCAAAAAATAATGCAAAACT
1 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACT
*** * *
1379 GA-AATGGGTCCCGGAATGCGTTTTTCGCCAAAAAACTGTGATAG--AGTACACGATTTCCGCTA
66 GAGCCGGGGTCCCGGAATGCGTTTTTCGCC-AAAAACTGTGATGGTTAGTACACGATTTCTGCTA
* * *
1441 AAATTTTGCAAAACTGACCCGAAAAAATTTTCTATTATTTTTGGCCACAATACTTGTAAAAATTA
130 AAATTTTGCAAAACTGACCCGAAAAATTTTTCTTTTATTTTTGGCCACAATACTTGTAAAAAATA
* *
1506 TATAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATTGTTTTTCGTATTTTTT
195 TATAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTT
* *
1571 TCGAATTAATTTATAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACATATCCTTAAATCG
260 TCGAATTAATTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCG
1636 GTTGTGG
325 GTTGTGG
1643 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACT
1 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACT
*
1708 GAGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTTTGTACACGATTTCTGCTAA
66 GAGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTTAGTACACGATTTCTGCTAA
* *
1773 AATTTTGCAAAACTGACCCGAAAAATTTTTCTTTTATTTTTGGGCACAATACTTGTAAAAATTAT
131 AATTTTGCAAAACTGACCCGAAAAATTTTTCTTTTATTTTTGGCCACAATACTTGTAAAAAATAT
* * * *
1838 ATATTTTAATGCTAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCATATTTTTTT
196 ATAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTT
* * * *
1903 CTAAATTAATTTATAATAAAATCGAAACAAGATTCTGATACTCGTAAAAACAAGTCCTTAAATCG
261 C-GAATTAATTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCG
1968 GTTGTGG
325 GTTGTGG
* *
1975 CTCAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTGTTGGCGCAAAAAATCATGCAAAACT
1 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACT
* * * * * *
2040 GAGCTGGAGTCCTGGAATGCGATTTTCGCCAAAAACTGTGATGGTTAGTTCACGATTTTCGGCT-
66 GAGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTTAGTACACGA-TTTCTGCTA
* ** * ** * *
2104 --A------AAAACTGACTCG--ATTTTTTTCCTGAATTTTTTGCCACAATACTCAG-AAAAAAT
130 AAATTTTGCAAAACTGACCCGAAAAATTTTTCTTTTATTTTTGGCCACAATACT-TGTAAAAAAT
* ** * * * * ** * *
2158 ATATAAATCAACACCAAAAAGATTGATGGTC-TCTTCACGCTTTTAATATC-ATTTTCCAAATTT
194 ATATAATTCAATGCCAAAAATATTAAAGGGCAT-TTCACGCTTCGAATATCGTTTTTCC-TATTT
* * * *
2221 TTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAT
257 TTTT-CGAATTAATTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAA
***
2286 ATCCAATGTGG
321 ATCGGTTGTGG
* * * * * *
2297 CTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATTCAAAATT
1 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACT
* ** * * * * * *
2362 GAGTCGGGG-CTTGGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATCCACGATTTCGGC--
66 GAGCCGGGGTC-CCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTTAGTACACGATTTCTGCTA
* * * *** * * *
2424 ------T--AAAACTGATCGGAAAAGTTTTTTCTCAAATTTTT-GACACAATACTCAG-AAAAAG
130 AAATTTTGCAAAACTGACCCGAAAA-ATTTTTCTTTTATTTTTGGCCACAATACT-TGTAAAAAA
* * * * * * * *
2479 TATATAATTCAACGCCAAAAAGATTGACGAGCTTTTCACGCTTCTAATATCGTTTTTCC-A--TA
193 TATATAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTT
* * * * *
2541 TTTCAGAATTAATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAA
258 TTTC-GAATTAATTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAA
***
2606 TCGAACGTGG
322 TCGGTTGTGG
* * * *
2616 CTGGGATTTTGTTCGATGAATATAAATATTT
1 CTGAGATTTGGTTAGATGAATATAGATATTT
2647 GAAAGAGTAT
Statistics
Matches: 2084, Mismatches: 208, Indels: 66
0.88 0.09 0.03
Matches are distributed among these distances:
318 1 0.00
319 94 0.05
320 9 0.00
321 15 0.01
322 295 0.14
323 114 0.05
324 19 0.01
327 1 0.00
328 1 0.00
329 446 0.21
330 626 0.30
331 231 0.11
332 225 0.11
333 7 0.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (331 bp):
CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACT
GAGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTTAGTACACGATTTCTGCTAA
AATTTTGCAAAACTGACCCGAAAAATTTTTCTTTTATTTTTGGCCACAATACTTGTAAAAAATAT
ATAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTT
CGAATTAATTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCGG
TTGTGG
Found at i:1824 original size:661 final size:661
Alignment explanation
Indices: 1--2646 Score: 3424
Period size: 661 Copynumber: 4.0 Consensus size: 661
*
1 CTGATATTTGGTTAGATGAATATAGATATTTCAAGGA-TCTTGGCGCAAAAAATCATGCAAAACT
1 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACT
65 GAGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGA---T-G--CACGATTTCTGCTAAA
66 GAGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTAGTACACGATTTCTGCTAAA
*
124 ATTTTGCAAAACTGACCCGAAAAATTTTTCTTTTATTATTGGCCACAACACTTGTAAAAAATATA
131 ATTTTGCAAAACTGACCCGAAAAATTTTTCTATTATTATTGGCCACAACACTTGTAAAAAATATA
*
189 TAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTGTCCTATTTTTTTC
196 TAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTTC
*
254 GAATTAATTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACATATCCTTAAATCGGT
261 GAATTAATTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCGGT
* * *
319 TGTGGCTGATATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGC-AAAAATCATGCC
326 TGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCA
** *
383 AAACTGAGCCATGGTCCCGGAATGCGTTTTTCACCAAAAACTGTGATGGTTAGTACACGATTTCT
391 AAACTGAGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTTAGTACACGATTTCT
* * * *
448 GCTAAAATTTTGCAAAACTGACCCGAAAATTTTTTCTTTTATTATTGGTCACAACACTTGTAAAA
456 GCTAAAATTTTGCAAAACTGACCCGAAAAATTTTTCTTTTATTTTTGGCCACAATACTTGTAAAA
*
513 AATATATAATTCAATGCCAAAAATATTAAAGGGCGTTTCACGCTTCGAATATCGTTTTTCCTATT
521 AATATATAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTT-CTATT
* *
578 TTTTTC-GAATTAATTTATAATAAAATCGAAACAAGATTCCGATGTTCGTAAAACAT--ATCCTT
585 TTTTTCTGAATTAATTTATAATAAAATCGAAACAAGATTCTGATGCTCGTAAAA-ATAAATCCTT
*
640 AAATAGGTTGTGG
649 AAATCGGTTGTGG
* * * *
653 CTGATATTTGGTTAGATGGATATAGATATTTCAAGGAGTTTTGGCGCGAAAAATCATGCAAAACT
1 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACT
* *
718 GAGCCGGGGTCCCGGAATGTGTTTTTCGCCAAAAACTGTGATGGTTAGTACAAGATTTCTGCTAA
66 GAGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGG-TAGTACACGATTTCTGCTAA
*
783 AATTTTGCAAAACTGACCCGAAAAATTTTTCTTTTATTATTGGCCACAACACTTGTAAAAAATAT
130 AATTTTGCAAAACTGACCCGAAAAATTTTTCTATTATTATTGGCCACAACACTTGTAAAAAATAT
848 ATAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTT
195 ATAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTT
* * *
913 AGAATTAATTTATAAT-AAATCGAAAGAAGATTCCGATGCTCGAAAAAACAAATCCTTAAATCGG
260 CGAATTAATTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCGG
* * *
977 TTGTGGCTGAGATTTGGTTAGATGAATATTGA-ATTTCAAGGAGCCTTGGTGCAAAAAATCATGC
325 TTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGC
* * *
1041 AAAATTGAGCCGGGGTCCCAGAATGTGTTTTTCGCCAAAAACTGTGATGGTTAGTACACGATTTC
390 AAAACTGAGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTTAGTACACGATTTC
* * * *
1106 TGCTAAAATTTTGCAAAACTGACCCGAAAAAGTTTTATATTATTTTTTGCCACAATACTTGTAAA
455 TGCTAAAATTTTGCAAAACTGACCCGAAAAATTTTTCTTTTATTTTTGGCCACAATACTTGTAAA
* * **
1171 AAATATATAATTCAATGCCATAAATATTAAAGGGCATTTTATTCTTCGAATATCGTTTTTGCTAT
520 AAATATATAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTT-CTAT
* *
1236 ATTTTTCTGAATTAATTTATAATAAAATCGAAACACGATTCTGATGCTCGTAAAAATAAATCCTT
584 TTTTTTCTGAATTAATTTATAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAATAAATCCTT
* ***
1301 AATTCCAATGTGG
649 AAATCGGTTGTGG
* * * *
1314 ATGAGATTTGGTTAGATGAATATAGATATTTCAAAGAGTCTTGACGCAAAAAATAATGCAAAACT
1 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACT
*** * *
1379 GA-AATGGGTCCCGGAATGCGTTTTTCGCCAAAAAACTGTGATAG-AGTACACGATTTCCGCTAA
66 GAGCCGGGGTCCCGGAATGCGTTTTTCGCC-AAAAACTGTGATGGTAGTACACGATTTCTGCTAA
* * * *
1442 AATTTTGCAAAACTGACCCGAAAAAATTTTCTATTATTTTTGGCCACAATACTTGTAAAAATTAT
130 AATTTTGCAAAACTGACCCGAAAAATTTTTCTATTATTATTGGCCACAACACTTGTAAAAAATAT
* *
1507 ATAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATTGTTTTTCGTATTTTTTT
195 ATAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTT
* *
1572 CGAATTAATTTATAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACATATCCTTAAATCGG
260 CGAATTAATTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCGG
1637 TTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGC
325 TTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGC
*
1702 AAAACTGAGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTTTGTACACGATTTC
390 AAAACTGAGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTTAGTACACGATTTC
*
1767 TGCTAAAATTTTGCAAAACTGACCCGAAAAATTTTTCTTTTATTTTTGGGCACAATACTTGTAAA
455 TGCTAAAATTTTGCAAAACTGACCCGAAAAATTTTTCTTTTATTTTTGGCCACAATACTTGTAAA
* * * *
1832 AATTATATATTTTAATGCTAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCATAT
520 AAATATATAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTC-TAT
* * * *
1897 TTTTTTCTAAATTAATTTATAATAAAATCGAAACAAGATTCTGATACTCGTAAAAACAAGTCCTT
584 TTTTTTCTGAATTAATTTATAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAATAAATCCTT
1962 AAATCGGTTGTGG
649 AAATCGGTTGTGG
* *
1975 CTCAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTGTTGGCGCAAAAAATCATGCAAAACT
1 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACT
* * * * * *
2040 GAGCTGGAGTCCTGGAATGCGATTTTCGCCAAAAACTGTGATGGTTAGTTCACGATTTTCGGCT-
66 GAGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGG-TAGTACACGA-TTTCTGCTA
* ** * *
2104 --A------AAAACTGACTCG--ATTTTTTTCCTGAATT-TT-TT-GCCACAATACTCAG-AAAA
129 AAATTTTGCAAAACTGACCCGAAAAATTTTT-CT--ATTATTATTGGCCACAACACT-TGTAAAA
* ** * * * * ** * *
2155 AATATATAAATCAACACCAAAAAGATTGATGGTC-TCTTCACGCTTTTAATATC-ATTTTCCAAA
190 AATATATAATTCAATGCCAAAAATATTAAAGGGCAT-TTCACGCTTCGAATATCGTTTTTCC-TA
* * *
2218 TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT
253 TTTTTTT-CGAATTAATTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCT
* *** * * * *
2283 TATATCCAATGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAA
317 TAAATCGGTTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAA
* * * ** * * * * *
2348 AATCATTCAAAATTGAGTCGGGG-CTTGGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATC
382 AATCATGCAAAACTGAGCCGGGGTC-CCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTTAGTA
* * * * *** *
2412 CACGATTTCGGC--------T--AAAACTGATCGGAAAAGTTTTTTCTCAAATTTTT-GACACAA
446 CACGATTTCTGCTAAAATTTTGCAAAACTGACCCGAAAA-ATTTTTCTTTTATTTTTGGCCACAA
* * * * * * * * *
2466 TACTCAG-AAAAAGTATATAATTCAACGCCAAAAAGATTGACGAGCTTTTCACGCTTCTAATATC
510 TACT-TGTAAAAAATATATAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATC
* * * * * * *
2530 GTTTTTCCA--TATTTCAGAATTAATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAA
574 GTTTTTCTATTTTTTTCTGAATTAATTTATAATAAAATCGAAACAAGATTCTGATGCTCGTAAAA
* * ***
2593 ACAAATACTTAAATCGAACGTGG
639 ATAAATCCTTAAATCGGTTGTGG
* * * *
2616 CTGGGATTTTGTTCGATGAATATAAATATTT
1 CTGAGATTTGGTTAGATGAATATAGATATTT
2647 GAAAGAGTAT
Statistics
Matches: 1766, Mismatches: 198, Indels: 71
0.87 0.10 0.03
Matches are distributed among these distances:
641 90 0.05
643 1 0.00
644 77 0.04
645 14 0.01
646 1 0.00
652 42 0.02
653 134 0.08
654 177 0.10
655 13 0.01
656 3 0.00
657 1 0.00
658 18 0.01
659 423 0.24
660 301 0.17
661 435 0.25
662 21 0.01
663 8 0.00
664 7 0.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (661 bp):
CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACT
GAGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTAGTACACGATTTCTGCTAAA
ATTTTGCAAAACTGACCCGAAAAATTTTTCTATTATTATTGGCCACAACACTTGTAAAAAATATA
TAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTTC
GAATTAATTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCGGT
TGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCA
AAACTGAGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTTAGTACACGATTTCT
GCTAAAATTTTGCAAAACTGACCCGAAAAATTTTTCTTTTATTTTTGGCCACAATACTTGTAAAA
AATATATAATTCAATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCTATTT
TTTTCTGAATTAATTTATAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAATAAATCCTTAA
ATCGGTTGTGG
Found at i:3213 original size:885 final size:880
Alignment explanation
Indices: 1984--4442 Score: 3321
Period size: 885 Copynumber: 2.8 Consensus size: 880
1974 GCTCAGATTT
* * * * * *
1984 GGTTAGATGAATATAGATATTTCAAGGAGTGTTGGC-GCAAAAAATCATGCAAAACTGAGCTGGA
1 GGTTAGATG-ATATAGATATTTCAAGGAGTCTT-TCTGCCAAAAATCATGCAAAATTGAGCCGGG
* * * * * ** * *
2048 GTCCT-GGAATGCGATTTTCG-CCAAAAACTGTGATGGTTAGTTCACGATTTTCGGCTAAAAACT
64 GCCCTCGAAACGCGTTTTTAGCCCAAAAACCATGATTGTTAGTACACGATTTTCGGCTAAAAACT
* * *
2111 GACTCG--ATTTTTTTCCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAAATCAACACCA
129 GACCCGAAATTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCA
*
2174 AAAAGATTGATGGTCTCTTCACGCTTTTAATATCA-TTTTCCAAATTTTTTTCCGAATTAATTTC
194 AAAAGATTGATGGTCTTTTCACGCTTTTAATATCATTTTTCC-AATTTTTTTCCGAATTAATTTC
*
2238 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACA
258 TAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACA
* *
2303 TTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATTCAAAATTGAGTCG
323 TTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCA
* *
2368 GGGCTTGGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATCCACGATTTCGGCTAAAACTGA
388 GGGCTCGGGAACGCGTTTTTAGCCAAAAACC-TGATGGTTAATACACGATTTCGGCTAAAACTGA
*
2433 TCGGAAAAGTTTTTTCTCAAATTTTTGACACAATACTCAGAAAAAGTATATAATTCAACGCCAAA
452 TCGGAAAAGTTTTTTCTCAAATTTTTGACACAATACTCAGAAAAAATATATAATTCAACGCCAAA
2498 AAGATTGACGAGCTTTTCACGCTTCTAATATCGTTTTTCCATATTTCAGAATTAATTTTTAATTA
517 AAGATTGACGAGCTTTTCACGCTTCTAATATCGTTTTTCCATATTTCAGAATTAATTTTTAATTA
2563 AATTGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCGAACGTGGCTGGGATTTTGT
582 AATTGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCGAACGTGGCTGGGATTTTGT
* *
2628 TCGATGAATATAAATATTTGAAAGAGTATTTATGTCAAAAATCATACAAAAACAAAAAGAAATAT
647 TCGATGAATATAAATATTTCAAAGAGTATTTACGTCAAAAATCATACAAAAACAAAAA-AAA-AT
* * * * *
2693 TTTTGGCAAAAAATACACAATTCAACGC-AAGAAAAA-AATTGTAATATTTTTCTCGCTTTAAAT
710 ATTAGGCAAAAAATACACAATTCAACGCAAAAAAAAAGAATTGAAATAATTTTCTCGCTTTAAAT
2756 ATCATTTTTCTA-TTTTTTTCCGAATCTATTTCTAATTAAATCGAAACAATACTCAGATGCTCGT
775 ATCATTTTTCTATTTTTTTTCCGAATCTATTTCTAATTAAATCGAAACAATACTCAGATGCTCGT
*
2820 AAA-AGTAAATCCTTAAATCAAATGTGGCTGAGAGCCTGAGA
840 AAATA-TAAATCCTTAAATCAAATGTGGCTCAGAGCCTGAGA
*
2861 TCGGTTAGATGATTATAGATATTTCAAGGAGTCTTTCTACCAAAAATCATGCAAAATTGAGCCGG
1 --GGTTAGATGA-TATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAATTGAGCCGG
2926 GGCCCTCGAAACGCGTTTTTAGCCCAAAAACCATGATTGTTAGTACACGATTTTCGGCTAAAAAC
63 GGCCCTCGAAACGCGTTTTTAGCCCAAAAACCATGATTGTTAGTACACGATTTTCGGCTAAAAAC
*
2991 TGACCCGAAACTTTTTTTTCTGAATTTTTTGCTACAATACTCAGAAAAAATATATAATTCAACAC
128 TGACCCGAAA-TTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACAC
* * * * * *
3056 CAAAAAGATTGATGGTTTTTTAACGGTTTTAAAATAATTTTTCCAATTTTTTTTCCGAATTATTT
192 CAAAAAGATTGATGGTCTTTTCACGCTTTTAATATCATTTTTCCAA-TTTTTTTCCGAATTAATT
* *
3121 TCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAATCAAATCCTTATATCCAATGTGCCTGA
256 TCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTATATCCAATGTGGCTGA
*
3186 CATTTGGTTTGATGAATATAGATATTTCAAGAAGTCTTTGCGCCAAAAATCATGCAAAATTGAGT
321 CATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGT
*
3251 CAGGGCTCGGGAACGCGTTTTTAGCCAAAAACCATGATGGTTAGTACACGATTTCGGCTTAAAAC
386 CAGGGCTCGGGAACGCGTTTTTAGCCAAAAACC-TGATGGTTAATACACGATTTCGGC-TAAAAC
*
3316 TGATCGGAAAAGTTTTTTCTCAAATTTTTGCCACAATACTCAGAAAAAAATATATAATTCAACGC
449 TGATCGGAAAAGTTTTTTCTCAAATTTTTGACACAATACTCAG-AAAAAATATATAATTCAACGC
* *
3381 CAAAAATATTGACGAGCTTTTCACGCTTCTAATATCGTTTTCCCATATTTTTCAGAATTAATTTT
513 CAAAAAGATTGACGAGCTTTTCACGCTTCTAATATCGTTTTTCCATA--TTTCAGAATTAATTTT
* * *
3446 TAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAATAATTACTTATATCGAACGTGGCTGGGA
576 TAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCGAACGTGGCTGGGA
* * *
3511 TTTTGTTCGATGAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCAAAAACAAAAAA
641 TTTTGTTCGATGAATATAAATATTTCAAAGAGTATTTACGTCAAAAATCATACAAAAACAAAAAA
*
3576 AAATATTAGGCAAAAAATACACAATTCGACGCAAAAAAAAAAAGAATTGAAATAATTTTCTCGCT
706 AAATATTAGGCAAAAAATACACAATTCAACGC--AAAAAAAAAGAATTGAAATAATTTTCTCGCT
* *
3641 TTAAATATCATTTTTCTATTTTTTTTCCGAATCTATTTCTAATTAAATCGAAATAATATTCAGAT
769 TTAAATATCATTTTTCTATTTTTTTTCCGAATCTATTTCTAATTAAATCGAAACAATACTCAGAT
*
3706 GCTCGTAAATATAAATCCTTAAATCTAATGTGGCTCAGAGCCTGAGA
834 GCTCGTAAATATAAATCCTTAAATCAAATGTGGCTCAGAGCCTGAGA
* *
3753 --TT-G--G-T-T--AT-TTTCAAGGAGTCTTTCTGTCAAAAATTATGCAAAATTGAGCCGGGGC
1 GGTTAGATGATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAATTGAGCCGGGGC
* *
3808 CCTCGAAACGCGTTTTTAGCCCAAAAACCATGA-TGCTTAGTACACAATTTTCAGCTAAAAACTG
66 CCTCGAAACGCGTTTTTAGCCCAAAAACCATGATTG-TTAGTACACGATTTTCGGCTAAAAACTG
* *
3872 ACCTGAAATTTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACAACA
130 ACCCGAAA-TTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCA
* * *
3937 AAAATATTGATGGTCTTTTCGCGCTTTTAATATCATTTTTCCAATTTTTTTCTGAATTAATTTCT
194 AAAAGATTGATGGTCTTTTCACGCTTTTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCT
* * * * * * *
4002 AATTAAATCGAAACCAGATTCAGATACTCGTAAAAGCAAATCTTTAAATCTAATGTGGCAGAGAG
259 AATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACA-
*
4067 TTTGAGATTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CTGCCAAAAATCATGCAAAAC
323 TTTG-G--T--TT-GATGAATATAGATATTTCAAGGAGTCTTTGC-GCCAAAAATCATGCAAAAT
* * * * * *
4131 TGAGCCCAGGCCCCCGAAACGCGTTTTTAGCCCAAAAACC--AT-GATAACGTACACGATTTTCG
381 TGAG-TCAGGGCTCGGGAACGCGTTTTTAG-CCAAAAACCTGATGGTTAA--TACACGA-TTTCG
** * *
4193 GCTAAAACCTGACTC-G--ATTTTTTTTC-CTGAATTTTTTACCACAATACTCAGAAAAAATATA
441 GCTAAAA-CTGA-TCGGAAAAGTTTTTTCTC-AAATTTTTGA-CACAATACTCAGAAAAAATATA
* * * * * *
4254 TAAATTCAACACCAAAAAGATTGATG-GTCTCTTCACGCTTTTAATATC-ATTTTCCAAATTTTT
502 T-AATTCAACGCCAAAAAGATTGACGAG-CTTTTCACGCTTCTAATATCGTTTTTCC--A--TAT
* * * *
4317 TTCCGAATTAATTTTCAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT-CATTATA
561 TTCAGAATTAATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATAC-TTAAA
* * * * * * * * * *
4381 TCCAATGTGGCTGACG-TATGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGCG-CAAAAA
625 TCGAACGTGGCTG-GGATTTTGTTCGATGAATATAAATATTTCAAAGAGTATTTACGTCAAAAA
4443 AATCATTCAA
Statistics
Matches: 1415, Mismatches: 120, Indels: 84
0.87 0.07 0.05
Matches are distributed among these distances:
878 79 0.06
879 262 0.19
880 14 0.01
881 44 0.03
882 2 0.00
883 6 0.00
884 121 0.09
885 322 0.23
886 185 0.13
887 105 0.07
888 6 0.00
889 137 0.10
890 7 0.00
891 37 0.03
892 87 0.06
893 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (880 bp):
GGTTAGATGATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAATTGAGCCGGGGC
CCTCGAAACGCGTTTTTAGCCCAAAAACCATGATTGTTAGTACACGATTTTCGGCTAAAAACTGA
CCCGAAATTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAA
AAGATTGATGGTCTTTTCACGCTTTTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAA
TTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTT
GGTTTGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCAGGG
CTCGGGAACGCGTTTTTAGCCAAAAACCTGATGGTTAATACACGATTTCGGCTAAAACTGATCGG
AAAAGTTTTTTCTCAAATTTTTGACACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGA
TTGACGAGCTTTTCACGCTTCTAATATCGTTTTTCCATATTTCAGAATTAATTTTTAATTAAATT
GAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCGAACGTGGCTGGGATTTTGTTCGA
TGAATATAAATATTTCAAAGAGTATTTACGTCAAAAATCATACAAAAACAAAAAAAAATATTAGG
CAAAAAATACACAATTCAACGCAAAAAAAAAGAATTGAAATAATTTTCTCGCTTTAAATATCATT
TTTCTATTTTTTTTCCGAATCTATTTCTAATTAAATCGAAACAATACTCAGATGCTCGTAAATAT
AAATCCTTAAATCAAATGTGGCTCAGAGCCTGAGA
Found at i:4390 original size:331 final size:322
Alignment explanation
Indices: 3631--4767 Score: 1079
Period size: 331 Copynumber: 3.5 Consensus size: 322
3621 ATTGAAATAA
* * * *
3631 TTTTCTCGCTTTAAATATCATTTTTCTATTTTTTTTCCGAATCT-A-TTTCTAATTAAATCGAAA
1 TTTTCACGCTTTTAATATCA-TTTTCCAATTTTTTTCCGAAT-TAATTTTC-AATTAAATCGAAA
* * * * * * * **
3694 TAATATTCAGATGCTCGTAAATATAAATCCTTAAATCTAATGTGGCTCA-G--A--GCCT-GA-G
63 CAAGATTCAGATGCTCGTAAAAACAAATCATTAAATCCAATGTGGCTGAGGTTATTGGTTAGATG
* * * * * *
3752 -AT-TGGTTATTTTCAAGGAGTCTTTCTGTCAAAAATTATGCAAAATTGAGCCGGGGCCCTCGAA
128 AATATAGATA-TTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAATTGAGCCCGGGCCCCCGAA
*
3815 ACGCGTTTTTAGCCCAAAAACCATGAT-GCTTAGTACACAATTTTCAGCTAAAAACTGAC-CTGA
192 ACGCGTTTTTAGCCCAAAAACCATGATAAC---GTACAC-ATTTTCAGCTAAAAACTGACTC-G-
*
3878 AATTTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACAACAAAAATA
251 AA-TTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAC-ACAAAAAGA
3943 TTGATGGTC
314 TTGATGGTC
* *
3952 TTTTCGCGCTTTTAATATCATTTTTCCAATTTTTTTCTGAATTAA-TTTCTAATTAAATCGAAAC
1 TTTTCACGCTTTTAATATCA-TTTTCCAATTTTTTTCCGAATTAATTTTC-AATTAAATCGAAAC
* * * * * *
4016 CAGATTCAGATACTCGTAAAAGCAAATCTTTAAATCTAATGTGGCAGAGAGTTTGAGATTGGTTA
64 AAGATTCAGATGCTCGTAAAAACAAATCATTAAATCCAATGTGGCTGAG-G-TT---ATTGGTTA
* *
4081 GATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCCAGGCCCCC
124 GATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAATTGAGCCCGGGCCCCC
* *
4146 GAAACGCGTTTTTAGCCCAAAAACCATGATAACGTACACGATTTTCGGCTAAAACCTGACTCG-A
189 GAAACGCGTTTTTAGCCCAAAAACCATGATAACGTACAC-ATTTTCAGCTAAAAACTGACTCGAA
*
4210 TTTTTTTTCCTGAATTTTTTACCACAATACTCAGAAAAAATATATAAATTCAACACCAAAAAGAT
253 TTTTTTTT-CTGAATTTTTTGCCACAATACTCAGAAAAAATATAT-AATTCAACA-CAAAAAGAT
4275 TGATGGTC
315 TGATGGTC
*
4283 TCTTCACGCTTTTAATATCATTTTCCAAATTTTTTTCCGAATTAATTTTCAATTAAATCGAAACA
1 TTTTCACGCTTTTAATATCATTTTCC-AATTTTTTTCCGAATTAATTTTCAATTAAATCGAAACA
* * *
4348 AGATTCAGATGCTCGTAAAAACAAATCATTATATCCAATGTGGCTGACG-TA-TGGTTTGATGAA
65 AGATTCAGATGCTCGTAAAAACAAATCATTAAATCCAATGTGGCTGAGGTTATTGGTTAGATGAA
* * * * * * *
4411 TATAGATATTTCAAGGAGTCTTTGC-GCAAAAAAATCATTCAAAATTGAG-TCGGGGCTCGGGAA
130 TATAGATATTTCAAGGAGTCTTT-CTGC-CAAAAATCATGCAAAATTGAGCCCGGGCCCCCGAAA
* * * * * *
4474 CGCATTTTTAG-CCAAAAACCGTGATGGTTAA--TACACAATATCAGCTAAAAACTGATTGGAAA
193 CGCGTTTTTAGCCCAAAAACC---AT-GATAACGTACACATTTTCAGCTAAAAACTGACTCG-AA
** * *
4536 AGTTTTTTCTCAATTTTTTTGCCACAATACTCAGAAAAAGTATATAATTCAACGACAAAAAGATT
253 TTTTTTTTCTGAA-TTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAC-ACAAAAAGATT
*
4601 GACGGGT-
316 GA-TGGTC
* * * * *
4608 TTTTCACGCTTCT-A-AT-A---T-C---GTTTTTCCGAATTAATTTTTAATTAAATTGGAACAA
1 TTTTCACGCTTTTAATATCATTTTCCAATTTTTTTCCGAATTAATTTTCAATTAAATCGAAACAA
* * *
4663 GATTCAGATGCTCGTAAAAACAAAT-ACTTAAATCGAACGTGGCTG-GGATT-TT-GTTCGATGA
66 GATTCAGATGCTCGTAAAAACAAATCA-TTAAATCCAATGTGGCTGAGG-TTATTGGTTAGATGA
* * * *
4724 ATATAAATATTTCAAGGAGTATTTATGTCAAAAATCATGCAAAA
129 ATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAA
4768 ACAAAAAGAA
Statistics
Matches: 695, Mismatches: 83, Indels: 84
0.81 0.10 0.10
Matches are distributed among these distances:
313 16 0.02
314 103 0.15
315 2 0.00
318 1 0.00
319 1 0.00
320 1 0.00
321 95 0.14
322 1 0.00
323 12 0.02
324 72 0.10
325 60 0.09
326 42 0.06
327 4 0.01
328 1 0.00
329 9 0.01
330 44 0.06
331 116 0.17
332 31 0.04
333 2 0.00
334 77 0.11
335 5 0.01
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (322 bp):
TTTTCACGCTTTTAATATCATTTTCCAATTTTTTTCCGAATTAATTTTCAATTAAATCGAAACAA
GATTCAGATGCTCGTAAAAACAAATCATTAAATCCAATGTGGCTGAGGTTATTGGTTAGATGAAT
ATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAATTGAGCCCGGGCCCCCGAAACGC
GTTTTTAGCCCAAAAACCATGATAACGTACACATTTTCAGCTAAAAACTGACTCGAATTTTTTTT
CTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACAAAAAGATTGATGGTC
Found at i:5763 original size:883 final size:874
Alignment explanation
Indices: 3965--6002 Score: 3080
Period size: 883 Copynumber: 2.3 Consensus size: 874
3955 TCGCGCTTTT
* * * * *
3965 AATATCATTTTTCCAATTTTTTTCTGAAT-TAATTTCTAATTAAATCGAAACCAGATTCAGATAC
1 AATATCATTTTT-CTATTTTTTTCCGAATCT-ATTTCTAATTAAATCGAAACAATATTCAGATGC
* * **
4029 TCGTAAAAGCAAATCTTTAAATCTAATGTGGCAGAGAGTTTGAGATTGGTTAGATGAATATAGAT
64 TCGTAAAAGCAAATCCTTAAATCTAATGTGGCTGAGAGCCTGAGATTGGTTAGATGAATATAGAT
*
4094 ATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCCAGGCCCCCGAAACGCGTTTTT
129 ATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGAGG-CCCCGAAACGCGTTTTT
* * * *
4159 AGCCCAAAAACCATGA--TAACGTACACGATTTTCGGCTAAAACCTGACTCGATTTTTTTTCCTG
193 AGCCCAAAAACCATGATGTTA-GTAAACGATTTTCGGCTAAAAACTGACTCGATTTTTTTTTCTG
*
4222 AATTTTTTACCACAATACTCAGAAAAAATATATAAATTCAACACCAAAAAGATTGATGGTCTCTT
257 AATTTTTTGCCACAATACTCAGAAAAAATATATAAATTCAACACCAAAAAGATTGATGGTCTCTT
*
4287 CACGCTTTTAATATCATTTTCCAAATTTTTTTCCGAATTAATTTTCAATTAAATCGAAACAAGAT
322 CACGCTTTTAAAATCATTTTCCAAATTTTTTTCCGAATTAATTTTCAATTAAATCGAAACAAGAT
*
4352 TCAGATGCTCGTAAAAACAAATCATTATATCCAATGTGGCTGACGTATGGTTTGATGAATATAGA
387 TCAGATGCTCGTAAAAACAAATCATTATATCCAATGTGGCTGACATATGGTTTGATGAATATAGA
* * *
4417 TATTTCAAGGAGTCTTTGCGCAAAAAAATCATTCAAAATTGAGTCGGGGCTCGGGAACGCATTTT
452 TATTTCAAGGAGTCTTTGCGCAAAAAAATCATGCAAAATTGAATCGGGGCTCGGGAACGCAGTTT
*
4482 TAGCCAAAAACCGTGATGGTTAATACACAATATCAGCTAAAAACTGATTGGAAAAGTTTTTTCTC
517 TAGCCAAAAACCGTGATGGTTAATACACAATATCAGCTAAAAACTGATCGGAAAAGTTTTTTCTC
* * ** *
4547 AATTTTTTTGCCACAATACTCAGAAAAAGTATATAATTCAACGACAAAAAGATTGACGGGTTTTT
582 AATATTTTTGCCACAATACTCAGAAAAAGAATATAATTCAACGACAAAAAGATTGACAAGCTTTT
* *
4612 CACGCTTCTAATATCGTTTTTCCGAATTAATTTTTAATTAAATTGGAACAAGATTCAGATGCTCG
647 CACGCTTATAATATCGTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAGATGCTCG
*
4677 TAAAAACAAATACTTAAATCGAACGTGGCTGGGATTTTGTTCGATGAATATAAATATTTCAAGGA
712 TAAAAACAAATACCTAAATCGAACGTGGCTGGGATTTTGTTCGATGAATATAAATATTTCAAGGA
* *
4742 GTATTTATGTCAAAAATCATGCAAAAACAAAAAGAAATATTTTCAGCAAAAAATACACAATTCAA
777 GTATTTACGTCAAAAATCATGCAAAAACAAAAAAAAATATTTTCAGCAAAAAATACACAATTCAA
* *
4807 CGCAAAAAAAATTGTAATATTTTTCTCGCTTTA
842 CGCAAAAAAAATTGAAATATTTTTCTCGCCTTA
*
4840 AATATCTTTTTTCTATTTTTTTCCGAATCTATTTCTAATTAAATCGAAACAATATTCAGATGCTC
1 AATATCATTTTTCTATTTTTTTCCGAATCTATTTCTAATTAAATCGAAACAATATTCAGATGCTC
*
4905 GTAAAAGCAAATCCTTAAATCTAATGTGGCTGAGAGCCTGAGATTGGTTAGATGATTATAGATAT
66 GTAAAAGCAAATCCTTAAATCTAATGTGGCTGAGAGCCTGAGATTGGTTAGATGAATATAGATAT
* * *
4970 TTCAAGGAGTCTTTCTGGCAAAAATCATGCAAAACTGAGTCGGGGCCCTCGAAACGCGTTTTTAG
131 TTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGAGGCCC-CGAAACGCGTTTTTAG
* *
5035 CCCAAAAACCATGATTGTTAGTAAACGATTTTCGGCTAAAAACTTACCCGAATTTTTTTTTCTGA
195 CCCAAAAACCATGA-TGTTAGTAAACGATTTTCGGCTAAAAACTGACTCG-ATTTTTTTTTCTGA
* * *
5100 ATTTTTTGCTACAATACTCAGAAAAATTATAT-AATTCAACACCAAAAAGATTGATGGTCTTTTC
258 ATTTTTTGCCACAATACTCAGAAAAAATATATAAATTCAACACCAAAAAGATTGATGGTCTCTTC
* *
5164 ACGGTTTTAAAATCATTTTTCCAATTTTTTTTCCGAATTAA-TTTCTAATTAAATCGAAACAAGA
323 ACGCTTTTAAAATCA-TTTTCCAAATTTTTTTCCGAATTAATTTTC-AATTAAATCGAAACAAGA
* * *
5228 TTCAGATGCTCGTAAAATCAAATTC-TTATATCCAATGTGGCTGCCATTTGGTTTGATGAATATA
386 TTCAGATGCTCGTAAAAACAAA-TCATTATATCCAATGTGGCTGACATATGGTTTGATGAATATA
* *
5292 GATATTTCATGGAGTCTTTGCGC-CAAAAATCATGCAAAATTGAATCGGGGCTCGGGAACGC-GT
450 GATATTTCAAGGAGTCTTTGCGCAAAAAAATCATGCAAAATTGAATCGGGGCTCGGGAACGCAGT
* * * * *
5355 TTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCGGAAAAGTTTTTTC
515 TTTAGCCAAAAACCGTGATGGTTAATACACAATATCAGCTAAAAACTGATCGGAAAAGTTTTTTC
* *
5420 TCAA-ATTTTTGCCACAATACTCAGAAAAA-AATATAATTCAACGCCAAAAATATTGACAAGCTT
580 TCAATATTTTTGCCACAATACTCAGAAAAAGAATATAATTCAACGACAAAAAGATTGACAAGCTT
5483 TTCACGCTTATAATATCGTTTTTCCATTCTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGA
645 TTCACGCTTATAATATCG---------T-TTTTCCGAATTAATTTTTAATTAAATTGAAACAAGA
* * * *
5548 TTCAGATGCTCGTAAAAACAAATACCTATATCGAACGTGGCTGGGCTTTTGTTTGATGAATATAG
700 TTCAGATGCTCGTAAAAACAAATACCTAAATCGAACGTGGCTGGGATTTTGTTCGATGAATATAA
* *
5613 ATATTTCAAGGAGTATTTACGTCAAAAATCATGCAAAAATAAAAAAATATATATTTTCGGCAAAA
765 ATATTTCAAGGAGTATTTACGTCAAAAATCATGCAAAAACAAAAAAA-A-ATATTTTCAGCAAAA
5678 AATACACAATTCAACGC-AAAAAAATT-AAATATTTTTCTCGCCTTA
828 AATACACAATTCAACGCAAAAAAAATTGAAATATTTTTCTCGCCTTA
* * *
5723 AATAACATTTTTCTATCTTTTTCGGAATCTATTTCTAATTAAATCGAAACAATATTCAGATGCTC
1 AATATCATTTTTCTATTTTTTTCCGAATCTATTTCTAATTAAATCGAAACAATATTCAGATGCTC
** * * *
5788 GTAAAAATAAATCCTTAAATCTAATGTTGCTCAGAGCCTGAGATTGGTTAGATTAATATAGATAT
66 GTAAAAGCAAATCCTTAAATCTAATGTGGCTGAGAGCCTGAGATTGGTTAGATGAATATAGATAT
* * *
5853 TTCAAGGAGTCTTTCTGTCAAAAATCATGCAAAACAGAGCCGAGACCCCGAAACGCGTTTTTAGC
131 TTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGAGGCCCCGAAACGCGTTTTTAGC
*
5918 CCAAAAACCATGATGGTTAGTAGAA-GATTTTCGGCTAAAAACTGACTCG--GTTTTTTTCTGAA
196 CCAAAAACCATGAT-GTTAGTA-AACGATTTTCGGCTAAAAACTGACTCGATTTTTTTTTCTGAA
5980 TTTTTTGCCACAATACTCAGAAA
259 TTTTTTGCCACAATACTCAGAAA
6003 TCATGCAAAA
Statistics
Matches: 1058, Mismatches: 82, Indels: 42
0.90 0.07 0.04
Matches are distributed among these distances:
873 48 0.05
874 201 0.19
875 76 0.07
876 109 0.10
877 165 0.16
878 2 0.00
879 34 0.03
881 1 0.00
882 60 0.06
883 321 0.30
884 10 0.01
885 31 0.03
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (874 bp):
AATATCATTTTTCTATTTTTTTCCGAATCTATTTCTAATTAAATCGAAACAATATTCAGATGCTC
GTAAAAGCAAATCCTTAAATCTAATGTGGCTGAGAGCCTGAGATTGGTTAGATGAATATAGATAT
TTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGAGGCCCCGAAACGCGTTTTTAGC
CCAAAAACCATGATGTTAGTAAACGATTTTCGGCTAAAAACTGACTCGATTTTTTTTTCTGAATT
TTTTGCCACAATACTCAGAAAAAATATATAAATTCAACACCAAAAAGATTGATGGTCTCTTCACG
CTTTTAAAATCATTTTCCAAATTTTTTTCCGAATTAATTTTCAATTAAATCGAAACAAGATTCAG
ATGCTCGTAAAAACAAATCATTATATCCAATGTGGCTGACATATGGTTTGATGAATATAGATATT
TCAAGGAGTCTTTGCGCAAAAAAATCATGCAAAATTGAATCGGGGCTCGGGAACGCAGTTTTAGC
CAAAAACCGTGATGGTTAATACACAATATCAGCTAAAAACTGATCGGAAAAGTTTTTTCTCAATA
TTTTTGCCACAATACTCAGAAAAAGAATATAATTCAACGACAAAAAGATTGACAAGCTTTTCACG
CTTATAATATCGTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAA
AACAAATACCTAAATCGAACGTGGCTGGGATTTTGTTCGATGAATATAAATATTTCAAGGAGTAT
TTACGTCAAAAATCATGCAAAAACAAAAAAAAATATTTTCAGCAAAAAATACACAATTCAACGCA
AAAAAAATTGAAATATTTTTCTCGCCTTA
Found at i:6614 original size:322 final size:313
Alignment explanation
Indices: 6016--6707 Score: 917
Period size: 322 Copynumber: 2.2 Consensus size: 313
6006 TGCAAAATTT
* * *
6016 TTTGATGAATATAGATATTTTAAGGAGTTTTTGCACCAAAAATCATGCAAAATTGAGTCGGGGCT
1 TTTGATGAATATAGATATTTTAAGGAGTATTTGCGCCAAAAATCATGCAAAATTGAGTCGAGGCT
* * *
6081 TGGAAACGGCGTTTTCAGCAAAAAACCGTGACGTACACGATTTTCGGCTAAAAACTGACTTGAAA
66 CGGAAACGGCGTTTTCAGCAAAAAACCGTGAAGTACACGATTTTCGGCTAAAAACTGACTGGAAA
*** *
6146 TTTTTTTATTTTTGCCACAATACTCAGAAAAAATATAAAATTCAACACCAAAAAGATTGGTGGTC
131 TTTTTTTATTTTTGCCACAATACTCAGAAAAAATATAAAATTCAACACCAAAAAGATTAACGGGC
* * * *
6211 TTTTCGCGCTTTTAATATCATTTTTCCAATTTTTTCCGAGTTAATTTCTAATTAAATCGAAACAA
196 TTTTCACGCTTCTAATATCATGTTTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAA
* *
6276 GATTCAGATGCTCGTAAAAACAAATCCTTATATCCAA-GATGGCTGACATTTGG
261 GATTCAGATGCTCGTAAAAACAAATACTTAAATCCAACG-TGGCTGACATTTGG
* *
6329 TTTGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGAGGCT
1 TTTGATGAATATAGATATTTTAAGGAGTATTTGCGCCAAAAATCATGCAAAATTGAGTCGAGGCT
* * *
6394 CGGGAAC-GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGA-TTTCGGCTAAAAACTGA-T
66 CGGAAACGGCGTTTTCAGCAAAAAACCGTGA-----AGTACACGATTTTCGGCTAAAAACTGACT
* *
6456 CGGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATTCAACACCAAAA
126 -GG-AAA-TTTTTT-T--A-TTTTTGCCACAATACTCAGAAAAAATATAAAATTCAACACCAAAA
* *
6521 AGATTAACGGGCTTTTCACGCTTCTAATATCGTGTTTCC-ATTTTTTCCGAATTAATTTTTAATT
184 AGATTAACGGGCTTTTCACGCTTCTAATATCATGTTTCCAATTTTTTCCGAATTAATTTCTAATT
* * ** *
6585 AAATTGAAACAAGATTCAGATGCCTCGTAAAAACAAATACTTAAATCGAACGTGGCTGGGATTTT
249 AAATCGAAACAAGATTCAGATG-CTCGTAAAAACAAATACTTAAATCCAACGTGGCTGACATTTG
6650 G
313 G
* * * *
6651 TTCGATGAATATAGATATTTTAAGGAGTATTTACGTCAAAAATCATGCAAAACTGAG
1 TTTGATGAATATAGATATTTTAAGGAGTATTTGCGCCAAAAATCATGCAAAATTGAG
6708 CCAATTCTAA
Statistics
Matches: 330, Mismatches: 35, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
312 21 0.06
313 66 0.20
315 1 0.00
316 18 0.05
317 11 0.03
318 6 0.02
319 1 0.00
321 45 0.14
322 160 0.48
323 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (313 bp):
TTTGATGAATATAGATATTTTAAGGAGTATTTGCGCCAAAAATCATGCAAAATTGAGTCGAGGCT
CGGAAACGGCGTTTTCAGCAAAAAACCGTGAAGTACACGATTTTCGGCTAAAAACTGACTGGAAA
TTTTTTTATTTTTGCCACAATACTCAGAAAAAATATAAAATTCAACACCAAAAAGATTAACGGGC
TTTTCACGCTTCTAATATCATGTTTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAA
GATTCAGATGCTCGTAAAAACAAATACTTAAATCCAACGTGGCTGACATTTGG
Found at i:7208 original size:29 final size:29
Alignment explanation
Indices: 7166--7225 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
7156 ATAATAATAT
7166 TAATAAAAAAGTTAAATCATCTAAAAA-AA
1 TAATAAAAAAGTTAAATCA-CTAAAAAGAA
* *
7195 TAATAAAAAGGTTAAATGACTAAAAAGAA
1 TAATAAAAAAGTTAAATCACTAAAAAGAA
7224 TA
1 TA
7226 CTTCTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.63, C:0.05, G:0.08, T:0.23
Consensus pattern (29 bp):
TAATAAAAAAGTTAAATCACTAAAAAGAA
Found at i:22301 original size:22 final size:22
Alignment explanation
Indices: 22275--22316 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
22265 CGTTTGCCCC
*
22275 TTTCTGTTC-AAATCCAAAATCT
1 TTTCTGCTCTAAA-CCAAAATCT
22297 TTTCTGCTCTAAACCAAAAT
1 TTTCTGCTCTAAACCAAAAT
22317 ATTTAACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (22 bp):
TTTCTGCTCTAAACCAAAATCT
Done.