Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022414.1 Corchorus olitorius cultivar O-4 contig22447, 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: 161879
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1086 original size:322 final size:322
Alignment explanation
Indices: 11--2796 Score: 2592
Period size: 322 Copynumber: 8.6 Consensus size: 322
1 AATTTATTTT
* * * *
11 ATTAAATCCAAATAAGATTAAGATGCTCGTAAAAACAAATCCTTA-ATTCCACTGTGGCTGAGAT
1 ATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTATA-TCCAATGTGGCTGAGAT
* * * * *
75 TTGGTTAGATGAAAATAGATATTTCAA-G-C-C----T----AAAATCATGTATAATTGAGCTAG
65 TTGGTTAGATGAATATAGATATTTCAAGGACTCTTTGTGCCAAAAATCATGCAAAACTGAG-TCG
* * *
129 GGCCCCAAAACGCGTTTTTAACCCAAAAACCGTGATCA-TTAGTACACGATTTCTGCTAAAAACT
129 GGCCCCGAAACGCGTTTTTAGCCCAAAAACCGTGAT-AGTTAGTACACGATTTCGGCTAAAAACT
*
193 GA-CCTAAGAAGTTTTTTCTGAA-TTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACGC
193 GACCCGAA-AA-TTTTTTCTGAATTTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACGC
*** *
256 CAAAAAGATTGACGGGCTTTTCACTAGTCTAATATCGTTTTTCAATTTTTTTCTGAATTAATTTC
256 CAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTCCGAATTAATTTC
321 TA
321 TA
* * * * * *
323 ATTAAATCGAAAAAAGATTTAGATTCTTGTAAAAAAAAATCCTTATATCCAATGTGGTTGACATT
1 ATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATT
* * *
388 TAGTTCA-ATGAATATAGATATTTCAAGGACTCTTTGTGCCAAAAATCATGCAAAATTGAGTTGG
66 TGGTT-AGATGAATATAGATATTTCAAGGACTCTTTGTGCCAAAAATCATGCAAAACTGAGTCGG
* * * * * * *
452 GCTCCGGAATGCGTTTTTAGTCAAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTG
130 GCCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATAGTTAGTACACGATTTCGGC--------T-
* ** * *
517 ACAAAACTGACCCGAAAAGTTTTTTCGTCAATTTTTTCACCACAATACTCGGAAAAAATATATAA
186 A-AAAACTGACCCGAAAA-TTTTTTC-TGAATTTTTTTGCCAAAATACTCAGAAAAAATATATAA
* *** * * * * *
582 TTTAACGCCAAAAA-ATTTTGGGGTTTTTCATGCTTCTAATA-AGATTTTCCATTTTTTT-CGAA
248 TTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTCCGAA
*
644 TTTA-TT-TA
313 TTAATTTCTA
* * * * *
652 ATTAAATCGAAACAATATTAAGATGCTCGTAAAAACAAATCCTTAAATCCACTGTGGCTGTGATT
1 ATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATT
* * * * * * *
717 TGGTTAGATGAATATAGTTATTTCAAGAAGTCTTTCTGCCTAAAATCATGTATAACTGAGTCGGG
66 TGGTTAGATGAATATAGATATTTCAAGGACTCTTTGTGCCAAAAATCATGCAAAACTGAGTCGGG
* * * *
782 CCCCAAAACGCGTTTTTAGCCCAAAAACCGTGATAGTTAGTACATGATTTCGGTTGAAAACTGAC
131 CCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAAACTGAC
* *
847 CTGAGAAATTTTTTCTGAATTTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACGCCATA
196 CCGA-AAATTTTTTCTGAATTTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACGCCAAA
** * *
912 AAGATTGACGGGCTTTTCACAATTCTAATATCGTTTTTCAATTTTTTTCCGAATTATTTTCGA
260 AAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTCCGAATTAATTTCTA
* *
975 ATTAAATCGAAA-AAGATTTAGATGCTTGTAAAAACAAATCCTTATATCCAATGTGGTTGAGATT
1 ATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATT
* * * * * *
1039 TAGTTTGATGAATATAGATATTTCAGGGCCTCTTTGTGCCAAAAATCATGCAAAATTGAGACGGG
66 TGGTTAGATGAATATAGATATTTCAAGGACTCTTTGTGCCAAAAATCATGCAAAACTGAGTCGGG
** * * ** *
1104 CTGCGGAATGCGTTTTTAGCAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGC
131 CCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATAGTTAGTACACGATTTCGGC--------T--
* * * * ** *
1169 AAAAACTGGCCCGAAAAGTTTTTCCTCAATTTTTTTACCGCAATACTCGGAAAAAATATATAATT
186 AAAAACTGACCCGAAAA-TTTTTTCTGAATTTTTTTGCCAAAATACTCAGAAAAAATATATAATT
* * * * * *
1234 CAATGCCAAAAA-ATT-AAGGGTTTTTCACGCTTCTAATACCGATTTTCCA-TTTTTT-CGAATT
250 CAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTCCGAATT
*
1295 TA-TT-TA
315 AATTTCTA
* * * * *
1301 ATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCACTATGACTGAGATT
1 ATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATT
* * * * * * *
1366 TGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCTAAAATCATGTATAACTGAGCCGGG
66 TGGTTAGATGAATATAGATATTTCAAGGACTCTTTGTGCCAAAAATCATGCAAAACTGAGTC-GG
1431 GCCCC-AAACGCGTTTTTAGCCCAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAAACTGA
130 GCCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAAACTGA
* * *
1495 CCTGATAAGTTTTTTCTGAA-TTTTTTGCCAAAATACTCAGAGAAAATATATAATTCAACGCCAA
195 CCCGA-AAATTTTTTCTGAATTTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACGCCAA
** *
1559 AAAGATTGACGGGCTTTTCACTATTCTAATATCGTTTTTCAACTTTTTTCCGAATTAATTTCTA
259 AAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTCCGAATTAATTTCTA
* * *
1623 ATTAAATCGAAAAAAGATTTAGATGCTTGTAAAAACAAATCCTTATATCCAATGTGGTTGAGATT
1 ATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATT
** * * ** * *
1688 TAATTCGATCAATATAGATATTTCTGGGACTCTTTGTGCCAAAATTCATGCAAAATTGAGTCGGG
66 TGGTTAGATGAATATAGATATTTCAAGGACTCTTTGTGCCAAAAATCATGCAAAACTGAGTCGGG
* * * * * * *
1753 CTCCGGAACGCGTTTTTAG-TCAAAAACTGTGATGGTTTGTATACGATTTCGGCTAAGATTTTGC
131 CCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATAGTTAGTACACGATTTCGGC--------T--
* * *
1817 AAAAACTGACCCGAAAATTTTTTCCT-AAATTTTATGCCATAATACTCAGAAAAAATTATATAAT
186 AAAAACTGACCCGAAAATTTTTT-CTGAATTTTTTTGCCAAAATACTCAGAAAAAA-TATATAAT
* * ** *
1881 TCAACACCAAAAAAAATT-AAAGG-TTTCTCACGCTTCTATTATCGTTTTTTC-ATTTTTTTCCG
249 TCAACGCC-AAAAAGATTGACGGGCTTT-TCACGCTTCTAATATCG-TTTTTCAATTTTTTTCCG
*
1943 AATTTATTTCTA
311 AATTAATTTCTA
* * * *
1955 ATTAAATCGAAAAAGGATCGAAACAAGATTAATATGCTCGTAAAAAAAAATCCTTAAATCCAATG
1 A-T---T-----AA--ATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATG
* * * * *
2020 TGGCTGACATCTGGTTAGATAAATATAGATATTTCAATGAGC-CTTTCTGCCAAAAATCATGCAA
55 TGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGA-CTCTTTGTGCCAAAAATCATGCAA
* * * *
2084 AACTGA-ACTGGGATCCCGAAAAGCGTTTTTAGCCCAAAAACCGTGATGGTTA-TACACGATTTC
119 AACTGAGTC-GGG-CCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATAGTTAGTACACGATTTC
* * * * *
2147 AGCTAAAAACTGACCCGAGAATTTTGTTCTTG-ATTTTTTTGCGACAAATACTTAGAAAAATTAT
182 GGCTAAAAACTGACCCGAAAATTTT-TTC-TGAATTTTTTTGCCA-AAATACTCAGAAAAAATAT
* * * * *
2211 ATATTTCAACGCCAAAAAGTTTGACGGGATTTTCACGCTTCTAAGATCGTTTTTCCA-TTTTTT-
244 ATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTC
*
2274 CGAATTAATTTATA
309 CGAATTAATTTCTA
* * * * * * * *
2288 AATAAATCGAAACTAGATTCAGATTCTCGTAAAAACAAATCCTTACATCAAATGTCGATGAGATT
1 ATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATT
* * * * * *
2353 TGGTTCGAAGAATATAGATATTTCAAGGAGTCTTTGTGCTAAAAACCATGCAAAACTGAGTCAAG
66 TGGTTAGATGAATATAGATATTTCAAGGACTCTTTGTGCCAAAAATCATGCAAAACTGAGTC-GG
* * * * * *
2418 GCCACGAAACACGTTTTTAG-CAAAAAACCGTGATAATTAATACCCGATTTCGGCTAAAAACTGA
130 GCCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAAACTGA
* * * * * * ** * *
2482 CCCGAAGATTTTTTTCTCAA-TTTTGTGCCTAAATACTAATAATTAATATATAGTTCAAAGCCAA
195 CCCGAA-AATTTTTTCTGAATTTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACGCCAA
* * * * * *
2546 AAATATTGAAGGGTTTTTCACGCTT-TCAATATCGTTTTTTAATTTTTTTTCTGAATTAATCTCT
259 AAAGATTGACGGGCTTTTCACGCTTCT-AATATCGTTTTTCAA-TTTTTTTCCGAATTAATTTCT
2610 A
322 A
* *
2611 ATTAAATCGAAACAAGATTTAGATGCTCG-AAAAA-AAA-CATTATATCCAATGTGACTGAGATT
1 ATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATT
* * * * * * * *
2673 TGGTTCGATTAATATAGATATTTAAAGGATTTTTTATGCCAAAAATCATACAAAACTAAG-CTGA
66 TGGTTAGATGAATATAGATATTTCAAGGACTCTTTGTGCCAAAAATCATGCAAAACTGAGTC-G-
* *** * * * * *
2737 GACAAAGGAACGCATTTTTA-CCCAAAAACCATGATGGTTAGTACACGATTTCAGCTAAAA
129 GGCCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAA
2797 TTTTTGCAAA
Statistics
Matches: 1997, Mismatches: 373, Indels: 200
0.78 0.15 0.08
Matches are distributed among these distances:
312 76 0.04
313 3 0.00
314 1 0.00
315 1 0.00
316 41 0.02
317 24 0.01
318 74 0.04
319 49 0.02
320 199 0.10
321 71 0.04
322 465 0.23
323 74 0.04
324 2 0.00
326 13 0.01
327 141 0.07
328 12 0.01
329 161 0.08
330 41 0.02
331 54 0.03
332 148 0.07
333 54 0.03
334 82 0.04
335 45 0.02
336 18 0.01
341 2 0.00
342 1 0.00
343 101 0.05
344 28 0.01
345 16 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (322 bp):
ATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATT
TGGTTAGATGAATATAGATATTTCAAGGACTCTTTGTGCCAAAAATCATGCAAAACTGAGTCGGG
CCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAAACTGAC
CCGAAAATTTTTTCTGAATTTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACGCCAAAA
AGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTCCGAATTAATTTCTA
Found at i:1499 original size:649 final size:650
Alignment explanation
Indices: 1--2796 Score: 3371
Period size: 649 Copynumber: 4.3 Consensus size: 650
* * * *
1 AATTTATTTTATTAAATCCAAATAAGATTAAGATGCTCGTAAAAACAAATCCTTAATTCCACTGT
1 AATTTATTTAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCACTGT
*
66 GGCTGAGATTTGGTTAGATGAAAATAGATATTTC---AA--------GCCTAAAATCATGTATAA
66 GGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCTAAAATCATGTATAA
* ** * *
120 TTGAGCTAGGGCCCCAAAACGCGTTTTTAACCCAAAAACCGTGATCA-TTAGTACACGATTTCTG
131 CTGAGCCGGGGCCCCAAAACGCGTTTTTAGCCCAAAAACCGTGAT-AGTTAGTACACGATTTCGG
* *
184 CTAAAAACTGACCTAAGAAGTTTTTTCTGAATTTTTTGCCAAAATACTCAGAAAAAATATATAAT
195 CTAAAAACTGACCTGAGAAATTTTTTCTGAATTTTTTGCCAAAATACTCAGAAAAAATATATAAT
* *
249 TCAACGCCAAAAAGATTGACGGGCTTTTCACTAGTCTAATATCGTTTTTCAATTTTTTTCTGAAT
260 TCAACGCCAAAAAGATTGACGGGCTTTTCACTATTCTAATATCGTTTTTCAATTTTTTTCCGAAT
* *
314 TAATTTCTAATTAAATCGAAAAAAGATTTAGATTCTTGTAAAAAAAAATCCTTATATCCAATGTG
325 TAATTTCTAATTAAATCGAAAAAAGATTTAGATGCTTGTAAAAACAAATCCTTATATCCAATGTG
* *
379 GTTGACATTTAGTTCAATGAATATAGATATTTCAAGGACTCTTTGTGCCAAAAATCATGCAAAAT
390 GTTGAGATTTAGTTCGATGAATATAGATATTTCAAGGACTCTTTGTGCCAAAAATCATGCAAAAT
* * *
444 TGAGTTGGGCTCCGGAATGCGTTTTTAGTCAAAAAACTGTGATGGTTAGTACACGATTTCGGCTA
455 TGAGTCGGGCTCCGGAACGCGTTTTTAGTCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
* * *
509 AAATTTTGACAAAACTGACCCGAAAAGTTTTTTCGTCAATTTTTTCACCACAATACTCGGAAAAA
520 AAATTTTGA-AAAACTGACCCGAAAAG-TTTTTCCTCAATTTTTTTACCACAATACTCAGAAAAA
* ** * *
574 ATATATAATTTAACGCCAAAAAATTTTGGGGTTTTTCATGCTTCTAATA-AGATTTTCCATTTTT
583 ATATATAATTCAACGCCAAAAAA-TTAAGGGTTTTTCACGCTTCTAATATCGATTTTCCATTTTT
638 TTCG
647 TTCG
*
642 AATTTATTTAATTAAATCGAAACAATATTAAGATGCTCGTAAAAACAAATCCTTAAATCCACTGT
1 AATTTATTTAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCACTGT
* *
707 GGCTGTGATTTGGTTAGATGAATATAGTTATTTCAAGAAGTCTTTCTGCCTAAAATCATGTATAA
66 GGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCTAAAATCATGTATAA
* * *
772 CTGAGTC-GGGCCCCAAAACGCGTTTTTAGCCCAAAAACCGTGATAGTTAGTACATGATTTCGGT
131 CTGAGCCGGGGCCCCAAAACGCGTTTTTAGCCCAAAAACCGTGATAGTTAGTACACGATTTCGGC
*
836 TGAAAACTGACCTGAGAAATTTTTTCTGAATTTTTTTGCCAAAATACTCAGAAAAAATATATAAT
196 TAAAAACTGACCTGAGAAATTTTTTCTGAA-TTTTTTGCCAAAATACTCAGAAAAAATATATAAT
* *
901 TCAACGCCATAAAGATTGACGGGCTTTTCACAATTCTAATATCGTTTTTCAATTTTTTTCCGAAT
260 TCAACGCCAAAAAGATTGACGGGCTTTTCACTATTCTAATATCGTTTTTCAATTTTTTTCCGAAT
* *
966 TATTTTCGAATTAAATCG-AAAAAGATTTAGATGCTTGTAAAAACAAATCCTTATATCCAATGTG
325 TAATTTCTAATTAAATCGAAAAAAGATTTAGATGCTTGTAAAAACAAATCCTTATATCCAATGTG
* * *
1030 GTTGAGATTTAGTTTGATGAATATAGATATTTCAGGGCCTCTTTGTGCCAAAAATCATGCAAAAT
390 GTTGAGATTTAGTTCGATGAATATAGATATTTCAAGGACTCTTTGTGCCAAAAATCATGCAAAAT
* * *
1095 TGAGACGGGCTGCGGAATGCGTTTTTAG-CAAAAAAACCGTGATGGTTAGTACACGATTTCGGCT
455 TGAGTCGGGCTCCGGAACGCGTTTTTAGTC-AAAAAACCGTGATGGTTAGTACACGATTTCGGCT
* * *
1159 AAAATTTTGCAAAAACTGGCCCGAAAAGTTTTTCCTCAATTTTTTTACCGCAATACTCGGAAAAA
519 AAAATTTTG-AAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTTACCACAATACTCAGAAAAA
* *
1224 ATATATAATTCAATGCCAAAAAATTAAGGGTTTTTCACGCTTCTAATACCGATTTTCCA-TTTTT
583 ATATATAATTCAACGCCAAAAAATTAAGGGTTTTTCACGCTTCTAATATCGATTTTCCATTTTTT
1288 TCG
648 TCG
*
1291 AATTTATTTAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCACTAT
1 AATTTATTTAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCACTGT
*
1356 GACTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCTAAAATCATGTATAA
66 GGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCTAAAATCATGTATAA
1421 CTGAGCCGGGGCCCC-AAACGCGTTTTTAGCCCAAAAACCGTGATAGTTAGTACACGATTTCGGC
131 CTGAGCCGGGGCCCCAAAACGCGTTTTTAGCCCAAAAACCGTGATAGTTAGTACACGATTTCGGC
* * *
1485 TAAAAACTGACCTGATAAGTTTTTTCTGAATTTTTTGCCAAAATACTCAGAGAAAATATATAATT
196 TAAAAACTGACCTGAGAAATTTTTTCTGAATTTTTTGCCAAAATACTCAGAAAAAATATATAATT
*
1550 CAACGCCAAAAAGATTGACGGGCTTTTCACTATTCTAATATCGTTTTTCAACTTTTTTCCGAATT
261 CAACGCCAAAAAGATTGACGGGCTTTTCACTATTCTAATATCGTTTTTCAATTTTTTTCCGAATT
1615 AATTTCTAATTAAATCGAAAAAAGATTTAGATGCTTGTAAAAACAAATCCTTATATCCAATGTGG
326 AATTTCTAATTAAATCGAAAAAAGATTTAGATGCTTGTAAAAACAAATCCTTATATCCAATGTGG
* * ** *
1680 TTGAGATTTAATTCGATCAATATAGATATTTCTGGGACTCTTTGTGCCAAAATTCATGCAAAATT
391 TTGAGATTTAGTTCGATGAATATAGATATTTCAAGGACTCTTTGTGCCAAAAATCATGCAAAATT
* * *
1745 GAGTCGGGCTCCGGAACGCGTTTTTAGTC-AAAAACTGTGATGGTTTGTATACGATTTCGGCTAA
456 GAGTCGGGCTCCGGAACGCGTTTTTAGTCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
* * * * * *
1809 GATTTTGCAAAAACTGACCCGAAAATTTTTTCCT-AAATTTTATGCCATAATACTCAGAAAAAAT
521 AATTTTG-AAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTTACCACAATACTCAGAAAAAA-
* * * * * *
1873 TATATAATTCAACACCAAAAAAAATTAAAGGTTTCTCACGCTTCTATTATCGTTTTTTCATTTTT
584 TATATAATTCAACGCC--AAAAAATTAAGGGTTTTTCACGCTTCTAATATCGATTTTCCATTTTT
1938 TTCCG
647 TT-CG
* *
1943 AATTTATTTCTAATTAAATCGAAAAAGGATCGAAACAAGATTAATATGCTCGTAAAAAAAAATCC
1 AATTTA-TT-TAA-T---T-----AA--ATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCC
* * * * * *
2008 TTAAATCCAATGTGGCTGACATCTGGTTAGATAAATATAGATATTTCAATG-AGCCTTTCTGCCA
53 TTAAATCCACTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAA-GAAGTCTTTCTGCCT
* * * * * * *
2072 AAAATCATGCAAAACTGAACTGGGATCCCGAAAA-GCGTTTTTAGCCCAAAAACCGTGATGGTTA
117 AAAATCATGTATAACTGAGCCGGG-GCCCCAAAACGCGTTTTTAGCCCAAAAACCGTGATAGTTA
* * * *
2136 -TACACGATTTCAGCTAAAAACTGACCCGAG-AATTTTGTTCTTGATTTTTTTGCGACAAATACT
181 GTACACGATTTCGGCTAAAAACTGACCTGAGAAATTTT-TTC-TGAATTTTTTGCCA-AAATACT
* * * * * ** *
2199 TAGAAAAATTATATATTTCAACGCCAAAAAGTTTGACGGGATTTTCACGCTTCTAAGATCGTTTT
243 CAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACTATTCTAATATCGTTTT
* * * ** * * *
2264 TCCA-TTTTTT-CGAATTAATTTATAAATAAATCGAAACTAGATTCAGATTCTCGTAAAAACAAA
308 TCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAAAAAAGATTTAGATGCTTGTAAAAACAAA
* * * * * * *
2327 TCCTTACATCAAATGTCGATGAGATTTGGTTCGAAGAATATAGATATTTCAAGGAGTCTTTGTGC
373 TCCTTATATCCAATGTGGTTGAGATTTAGTTCGATGAATATAGATATTTCAAGGACTCTTTGTGC
* * * * * * **
2392 TAAAAACCATGCAAAACTGAGTCAAGGC-CACGAAACACGTTTTTAG-CAAAAAACCGTGATAAT
438 CAAAAATCATGCAAAATTGAGTC-GGGCTC-CGGAACGCGTTTTTAGTCAAAAAACCGTGATGGT
* * * * * * *
2455 TAATACCCGATTTCGGC--------T-AAAAACTGACCCGAAGATTTTTTTCTCAA-TTTTGTGC
501 TAGTACACGATTTCGGCTAAAATTTTGAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTTAC
* * ** * *
2510 CTA-AATACTAATAATTAATATATAGTTCAAAGCCAAAAATATTGAAGGGTTTTTCACGCTT-TC
566 C-ACAATACTCAGAAAAAATATATAATTCAACGCCAAAAA-ATT-AAGGGTTTTTCACGCTTCT-
* **
2573 AATATCGTTTTTTAATTTTTTTTCTG
627 AATATCGATTTTCCA-TTTTTTTC-G
* * * * *
2599 AATTAATCTCTAATTAAATCGAAACAAGATTTAGATGCTCG-AAAAA-AAA-CATTATATCCAAT
1 AATTTAT-T-TAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCACT
* * * * * * * * * ** *
2661 GTGACTGAGATTTGGTTCGATTAATATAGATATTTAAAGGATTTTTTATGCCAAAAATCATACAA
64 GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCTAAAATCATGTAT
* * * * * * * *
2726 AACTAAG-CTGAG-ACAAAGGAACGCATTTTTA-CCCAAAAACCATGATGGTTAGTACACGATTT
129 AACTGAGCCGGGGCCCCAA--AACGCGTTTTTAGCCCAAAAACCGTGATAGTTAGTACACGATTT
*
2788 CAGCTAAAA
192 CGGCTAAAA
2797 TTTTTGCAAA
Statistics
Matches: 1900, Mismatches: 196, Indels: 117
0.86 0.09 0.05
Matches are distributed among these distances:
639 3 0.00
641 114 0.06
642 95 0.05
643 3 0.00
644 7 0.00
645 22 0.01
647 25 0.01
648 188 0.10
649 365 0.19
650 110 0.06
651 271 0.14
652 143 0.08
653 7 0.00
654 7 0.00
655 45 0.02
656 61 0.03
657 3 0.00
658 2 0.00
663 2 0.00
664 5 0.00
665 260 0.14
666 93 0.05
667 69 0.04
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (650 bp):
AATTTATTTAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCACTGT
GGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCTAAAATCATGTATAA
CTGAGCCGGGGCCCCAAAACGCGTTTTTAGCCCAAAAACCGTGATAGTTAGTACACGATTTCGGC
TAAAAACTGACCTGAGAAATTTTTTCTGAATTTTTTGCCAAAATACTCAGAAAAAATATATAATT
CAACGCCAAAAAGATTGACGGGCTTTTCACTATTCTAATATCGTTTTTCAATTTTTTTCCGAATT
AATTTCTAATTAAATCGAAAAAAGATTTAGATGCTTGTAAAAACAAATCCTTATATCCAATGTGG
TTGAGATTTAGTTCGATGAATATAGATATTTCAAGGACTCTTTGTGCCAAAAATCATGCAAAATT
GAGTCGGGCTCCGGAACGCGTTTTTAGTCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
AATTTTGAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTTACCACAATACTCAGAAAAAATA
TATAATTCAACGCCAAAAAATTAAGGGTTTTTCACGCTTCTAATATCGATTTTCCATTTTTTTCG
Found at i:7233 original size:42 final size:42
Alignment explanation
Indices: 7187--7266 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
7177 TCCAGAATCT
*
7187 GGTCGGCTGGAAATGCTAGCAGATGGATTCCCAGAGAACTGA
1 GGTCGACTGGAAATGCTAGCAGATGGATTCCCAGAGAACTGA
* * * *
7229 GGTCGATTGGAAATGCTGGCAGATGGATTTCCGGAGAA
1 GGTCGACTGGAAATGCTAGCAGATGGATTCCCAGAGAA
7267 TTGAACCGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.28, C:0.16, G:0.35, T:0.21
Consensus pattern (42 bp):
GGTCGACTGGAAATGCTAGCAGATGGATTCCCAGAGAACTGA
Found at i:16919 original size:15 final size:15
Alignment explanation
Indices: 16901--16930 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16891 ATATATAATA
16901 AAATAATAAATAAAT
1 AAATAATAAATAAAT
*
16916 AAATAGTAAATAAAT
1 AAATAATAAATAAAT
16931 TATATTTGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AAATAATAAATAAAT
Found at i:19006 original size:23 final size:23
Alignment explanation
Indices: 18976--19022 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
18966 TTGTAATCCC
18976 AATCTCTTCAAGAAATGAAAATG
1 AATCTCTTCAAGAAATGAAAATG
18999 AATCTCTTCAAGAAATGAAAATG
1 AATCTCTTCAAGAAATGAAAATG
19022 A
1 A
19023 TTGTTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.26
Consensus pattern (23 bp):
AATCTCTTCAAGAAATGAAAATG
Found at i:42547 original size:2 final size:2
Alignment explanation
Indices: 42540--42576 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
42530 CTTTTCTAAT
* *
42540 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42577 GTATGTATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42577 original size:12 final size:12
Alignment explanation
Indices: 42546--42584 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
42536 TAATTATATA
* *
42546 TATATATATATA
1 TATATATGTATG
42558 TATATATGTATG
1 TATATATGTATG
42570 TATATATGTATG
1 TATATATGTATG
42582 TAT
1 TAT
42585 GTACCACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (12 bp):
TATATATGTATG
Found at i:51013 original size:2 final size:2
Alignment explanation
Indices: 51008--51032 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50998 AAAAAAAAGT
51008 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
51033 TTTGGTTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55508 original size:19 final size:20
Alignment explanation
Indices: 55471--55512 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
55461 ATTTTTAAAT
*
55471 TTAATTATAATAATTATTAA
1 TTAATTATAATAATGATTAA
*
55491 TTAATT-TATTAATGATTAA
1 TTAATTATAATAATGATTAA
55510 TTA
1 TTA
55513 GTTTTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TTAATTATAATAATGATTAA
Found at i:59034 original size:2 final size:2
Alignment explanation
Indices: 59029--59054 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
59019 CCCTTTTTTG
59029 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
59055 CTATCATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:71405 original size:2 final size:2
Alignment explanation
Indices: 71388--71422 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
71378 ACTAATCAAT
*
71388 TA TA TCA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
71423 GTTTTGGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:73066 original size:30 final size:31
Alignment explanation
Indices: 73021--73107 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 31
73011 GCACATGGTG
* * *
73021 TTTTTAACACGTGGCGTGCCACGTGTCCCT-
1 TTTTTTACACATGGCGTGTCACGTGTCCCTA
*
73051 TTTTTTACACATGGCGCGTCACGTGT-CCTA
1 TTTTTTACACATGGCGTGTCACGTGTCCCTA
* * *
73081 TTTTATACACATGACGTGTCACTTGTC
1 TTTTTTACACATGGCGTGTCACGTGTC
73108 ATTTTTTGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 3 0.06
30 44 0.94
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.37
Consensus pattern (31 bp):
TTTTTTACACATGGCGTGTCACGTGTCCCTA
Found at i:74620 original size:12 final size:12
Alignment explanation
Indices: 74600--74633 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
74590 GTAAGCCAAG
74600 TATATATATGCA
1 TATATATATGCA
*
74612 TATACATATGCA
1 TATATATATGCA
74624 TATATATATG
1 TATATATATG
74634 GCACATGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (12 bp):
TATATATATGCA
Found at i:80109 original size:27 final size:27
Alignment explanation
Indices: 80079--80145 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 27
80069 ATTACTTCAT
80079 TATTACATCAT-TTTTCTTTGAGAAATA
1 TATTACATCATATTTTCTTTGAGAAA-A
* *
80106 TATTACATCATAATTTTTTTTGAGATAA
1 TATTACATCAT-ATTTTCTTTGAGAAAA
80134 TATTACATCATA
1 TATTACATCATA
80146 ATTAGTGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 12 0.33
28 12 0.33
29 12 0.33
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (27 bp):
TATTACATCATATTTTCTTTGAGAAAA
Found at i:80143 original size:28 final size:29
Alignment explanation
Indices: 80079--80148 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 29
80069 ATTACTTCAT
80079 TATTACATCAT--TTTTCTTTGAGAAATA
1 TATTACATCATAATTTTCTTTGAGAAATA
* *
80106 TATTACATCATAATTTTTTTTGAGATA-A
1 TATTACATCATAATTTTCTTTGAGAAATA
80134 TATTACATCATAATT
1 TATTACATCATAATT
80149 AGTGCATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
27 11 0.28
28 16 0.41
29 12 0.31
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.49
Consensus pattern (29 bp):
TATTACATCATAATTTTCTTTGAGAAATA
Found at i:86360 original size:29 final size:30
Alignment explanation
Indices: 86301--86380 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
86291 GCTAAATATC
* *
86301 CAAAAAAATCCCTTATGTTTTGTTTTTGGGA
1 CAAAATAATCCCTTATG-TTTGTTTTCGGGA
*
86332 CAAAATAATTCCTTATGTTT-TTTTCGGGA
1 CAAAATAATCCCTTATGTTTGTTTTCGGGA
* *
86361 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
86381 CAAAAATGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 25 0.58
30 3 0.07
31 15 0.35
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.42
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTGTTTTCGGGA
Found at i:86578 original size:31 final size:31
Alignment explanation
Indices: 86505--86603 Score: 130
Period size: 31 Copynumber: 3.1 Consensus size: 31
86495 AAGGGACTGA
86505 TTTGTCCCAAAAGAAAAA-CATAAGGGCAATTTT
1 TTTGTCCCAAAAGAAAAATCATAAGGG--A-TTT
86538 TTTGATCCCAAAAGAAAAATCATAAGGGATTT
1 TTTG-TCCCAAAAGAAAAATCATAAGGGATTT
*
86570 TTTGTCCCAAAAGAAAAAT-ATAAGAGAATTT
1 TTTGTCCCAAAAGAAAAATCATAAG-GGATTT
86601 TTT
1 TTT
86604 TAGTATTTAG
Statistics
Matches: 62, Mismatches: 1, Indels: 8
0.87 0.01 0.11
Matches are distributed among these distances:
30 5 0.08
31 23 0.37
32 7 0.11
33 5 0.08
34 14 0.23
35 8 0.13
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAATCATAAGGGATTT
Found at i:87386 original size:127 final size:125
Alignment explanation
Indices: 87217--87456 Score: 340
Period size: 127 Copynumber: 1.9 Consensus size: 125
87207 CTTAATTTTC
* **
87217 AAATATATTTTTTAAATACCATTTTTAAACTTTTACAATTTTACTCAATTAAAAACTCTATTTTT
1 AAATATATTTATTAAATACCATTTTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTTT
*
87282 ATTTAATCAAA-TCTAATATATTTTATAACTATTTTATTTTTACCATTTTACTATTTTAATT
66 ATTTAATCAAATTC-AATAT-TTTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
* * ** *
87343 AAATATATTTATTAAATGA-CATTATTTAAACTTTTACAGTTTTATTTTACCAAAAATTCTATTT
1 AAATATATTTATTAAAT-ACCATT-TTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTT
*
87407 TTATTTAATTAAATTCAATATTTTTATAACTATTTTATCTTTACCATTTT
64 TTATTTAATCAAATTCAATATTTTTATAACTATTTTATCTTTACCATTTT
87457 TTTAGGGAAT
Statistics
Matches: 101, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
126 48 0.48
127 51 0.50
128 2 0.02
ACGTcount: A:0.36, C:0.10, G:0.01, T:0.53
Consensus pattern (125 bp):
AAATATATTTATTAAATACCATTTTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTTT
ATTTAATCAAATTCAATATTTTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
Found at i:87562 original size:15 final size:15
Alignment explanation
Indices: 87542--87573 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
87532 AAAGGAGAAG
87542 AAGGAAAAAAGAAAA
1 AAGGAAAAAAGAAAA
*
87557 AAGGAAAAAGGAAAA
1 AAGGAAAAAAGAAAA
87572 AA
1 AA
87574 ATCAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAGGAAAAAAGAAAA
Found at i:87683 original size:31 final size:32
Alignment explanation
Indices: 87616--87706 Score: 148
Period size: 32 Copynumber: 2.9 Consensus size: 32
87606 ACTGAATACT
*
87616 AAAAAAATCCCTAATGTTTTTCTTTTGGGACA
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGACA
*
87648 AAAAAAAACCCTTATGTTTTTCTTTTGGGAC-
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGACA
*
87679 AAAAAAATCCCTTATGTTTTTTTTTTGG
1 AAAAAAATCCCTTATGTTTTTCTTTTGG
87707 ATAAATTAGT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (32 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGGACA
Found at i:87906 original size:30 final size:31
Alignment explanation
Indices: 87856--87926 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
87846 CTCATTTTTG
* * **
87856 AAACGTAAGGGATTAATTTGTCCTGAAAA-A
1 AAACATAAGGAATTAATTTGTCCCAAAAATA
*
87886 AAACATAAGGAATTATTTTGTCCCAAAAATA
1 AAACATAAGGAATTAATTTGTCCCAAAAATA
87917 AAACATAAGG
1 AAACATAAGG
87927 GATTTTTCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 24 0.69
31 11 0.31
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.25
Consensus pattern (31 bp):
AAACATAAGGAATTAATTTGTCCCAAAAATA
Found at i:92391 original size:22 final size:22
Alignment explanation
Indices: 92363--92407 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
92353 TCGAGCTCGA
92363 CTGAAAAATTCAAGCTCGAGCT
1 CTGAAAAATTCAAGCTCGAGCT
*
92385 CTGAAAAATTCGAGCTCGAGCT
1 CTGAAAAATTCAAGCTCGAGCT
92407 C
1 C
92408 GGCCCCGACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (22 bp):
CTGAAAAATTCAAGCTCGAGCT
Found at i:92810 original size:18 final size:19
Alignment explanation
Indices: 92770--92810 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
92760 CTCTTATCTT
92770 ATTTTTTATTATCCCATAG
1 ATTTTTTATTATCCCATAG
* *
92789 -TTTTTTTTTTTCCCA-AG
1 ATTTTTTATTATCCCATAG
92806 ATTTT
1 ATTTT
92811 CTCTAAGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.20, C:0.15, G:0.05, T:0.61
Consensus pattern (19 bp):
ATTTTTTATTATCCCATAG
Found at i:94359 original size:23 final size:23
Alignment explanation
Indices: 94333--94380 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
94323 AAACTATCCG
94333 AATGATTCATTAGTTAGTCAATA
1 AATGATTCATTAGTTAGTCAATA
* *
94356 AATGATTCATTAGTTCGTCGATA
1 AATGATTCATTAGTTAGTCAATA
94379 AA
1 AA
94381 GCAGCCTGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (23 bp):
AATGATTCATTAGTTAGTCAATA
Found at i:100188 original size:32 final size:33
Alignment explanation
Indices: 100151--100229 Score: 88
Period size: 38 Copynumber: 2.3 Consensus size: 33
100141 TATTCACATC
100151 ATAAGACTC-CATCTATTTTCTTTTCTCTATTT
1 ATAAGACTCTCATCTATTTTCTTTTCTCTATTT
*
100183 ATAAGACTCGAACTTCATCTGTTTTCTTTTCTCTATTT
1 ATAAGACT----C-TCATCTATTTTCTTTTCTCTATTT
*
100221 ACAAGACTC
1 ATAAGACTC
100230 GAACAAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
32 8 0.21
34 1 0.03
36 1 0.03
38 29 0.74
ACGTcount: A:0.24, C:0.23, G:0.06, T:0.47
Consensus pattern (33 bp):
ATAAGACTCTCATCTATTTTCTTTTCTCTATTT
Found at i:100211 original size:38 final size:38
Alignment explanation
Indices: 100160--100233 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
100150 CATAAGACTC
*
100160 CATCTATTTTCTTTTCTCTATTTATAAGACTCGAACTT
1 CATCTATTTTCTTTTCTCTATTTACAAGACTCGAACTT
*
100198 CATCTGTTTTCTTTTCTCTATTTACAAGACTCGAAC
1 CATCTATTTTCTTTTCTCTATTTACAAGACTCGAAC
100234 AAAAATCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.47
Consensus pattern (38 bp):
CATCTATTTTCTTTTCTCTATTTACAAGACTCGAACTT
Found at i:105348 original size:21 final size:19
Alignment explanation
Indices: 105322--105380 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 19
105312 CGCTGCTCTA
105322 ATAATCTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
*
105341 ACATAATCTAATCTGTACAGT
1 --ATAATCTCATCTGTACAGT
* *
105362 GTAATTTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
105381 TGCAAAACAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.47
21 18 0.53
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (19 bp):
ATAATCTCATCTGTACAGT
Found at i:107039 original size:24 final size:24
Alignment explanation
Indices: 107007--107054 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
106997 GACACCTCTC
*
107007 CCCCTAGTTTCGTCTATGCTGTCA
1 CCCCTAGTTCCGTCTATGCTGTCA
107031 CCCCTAGTTCCGTCTATGCTGTCA
1 CCCCTAGTTCCGTCTATGCTGTCA
107055 GTGGAGTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.35, G:0.17, T:0.35
Consensus pattern (24 bp):
CCCCTAGTTCCGTCTATGCTGTCA
Found at i:110944 original size:31 final size:31
Alignment explanation
Indices: 110906--111009 Score: 169
Period size: 31 Copynumber: 3.5 Consensus size: 31
110896 GTTTATATAC
110906 GGGTTTCTAAGGGTTTTTTTTTTGGCAGTAA
1 GGGTTTCTAAGGGTTTTTTTTTTGGCAGTAA
110937 GGGTTTCTAAGGGTTTTTTTTTTGGCAGTAA
1 GGGTTTCTAAGGGTTTTTTTTTTGGCAGTAA
**
110968 GGGTTTCTAA-GG--TTTTTTTTGGCACAAA
1 GGGTTTCTAAGGGTTTTTTTTTTGGCAGTAA
110996 GGGTTTCTAAGGGT
1 GGGTTTCTAAGGGT
111010 ACCCTTTTTT
Statistics
Matches: 69, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
28 24 0.35
29 2 0.03
30 2 0.03
31 41 0.59
ACGTcount: A:0.17, C:0.08, G:0.30, T:0.45
Consensus pattern (31 bp):
GGGTTTCTAAGGGTTTTTTTTTTGGCAGTAA
Found at i:120372 original size:30 final size:29
Alignment explanation
Indices: 120299--120372 Score: 121
Period size: 29 Copynumber: 2.5 Consensus size: 29
120289 ACTTGTAGCG
120299 TTTGGACGTTTTGCCCCATGAACTTCAAT
1 TTTGGACGTTTTGCCCCATGAACTTCAAT
* *
120328 TTTGGACATTTTGCCCCCTGAACTTCAAT
1 TTTGGACGTTTTGCCCCATGAACTTCAAT
120357 TTTGGAACGTTTTGCC
1 TTTGG-ACGTTTTGCC
120373 TCCTCAGGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 32 0.78
30 9 0.22
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.39
Consensus pattern (29 bp):
TTTGGACGTTTTGCCCCATGAACTTCAAT
Found at i:126122 original size:30 final size:30
Alignment explanation
Indices: 126083--126195 Score: 118
Period size: 30 Copynumber: 3.8 Consensus size: 30
126073 CCACCACCAG
* * *
126083 CACCTGCACCTGCACCTCCTCCAAATCCTC
1 CACCAGCACCAGCACCACCTCCAAATCCTC
* * *
126113 CGCCAGCACCAGCACCACCTCCTAGTCCTC
1 CACCAGCACCAGCACCACCTCCAAATCCTC
* * * *
126143 CCCCACCACCGGCACCACCACCAAATCCTC
1 CACCAGCACCAGCACCACCTCCAAATCCTC
* *
126173 CACCAGCACCACCACCAGCTCCA
1 CACCAGCACCAGCACCACCTCCA
126196 CCTCCAACTC
Statistics
Matches: 65, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.24, C:0.56, G:0.09, T:0.12
Consensus pattern (30 bp):
CACCAGCACCAGCACCACCTCCAAATCCTC
Found at i:126187 original size:12 final size:12
Alignment explanation
Indices: 126145--126197 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
126135 TAGTCCTCCC
*
126145 CCACCACCGGCA
1 CCACCACCAGCA
*
126157 CCACCACCA-AA
1 CCACCACCAGCA
*
126168 TCCTCCACCAGCA
1 -CCACCACCAGCA
*
126181 CCACCACCAGCT
1 CCACCACCAGCA
126193 CCACC
1 CCACC
126198 TCCAACTCCT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
11 1 0.03
12 31 0.94
13 1 0.03
ACGTcount: A:0.28, C:0.58, G:0.08, T:0.06
Consensus pattern (12 bp):
CCACCACCAGCA
Found at i:126191 original size:72 final size:72
Alignment explanation
Indices: 126019--126215 Score: 193
Period size: 72 Copynumber: 2.7 Consensus size: 72
126009 ATGTCCCCCT
* * *
126019 CCAAATCCTCCACCAGCACCACCTCCA-AATCCACCACCTCCTCCTAGTCCTCCCCCACCACCAG
1 CCAAATCCTCCACCAGCACCACCACCAGCA-CCACCACCACCTCCTAGTCCTCCCCCACCACCAG
**
126083 CACCTGCA
65 CACCACCA
** * * * * * *
126091 CCTGCA-CCTCCTCCA-AATCCTCCGCCAGCACCAGCACCACCTCCTAGTCCTCCCCCACCACCG
1 CC-AAATCCTCCACCAGCA-CCACCACCAGCACCACCACCACCTCCTAGTCCTCCCCCACCACCA
126154 GCACCACCA
64 GCACCACCA
* * * *
126163 CCAAATCCTCCACCAGCACCACCACCAGCTCCACCTCCAACTCCTAGACCTCC
1 CCAAATCCTCCACCAGCACCACCACCAGCACCACCACCACCTCCTAGTCCTCC
126216 ACCTTTTCCA
Statistics
Matches: 97, Mismatches: 23, Indels: 10
0.75 0.18 0.08
Matches are distributed among these distances:
71 2 0.02
72 92 0.95
73 3 0.03
ACGTcount: A:0.24, C:0.56, G:0.07, T:0.13
Consensus pattern (72 bp):
CCAAATCCTCCACCAGCACCACCACCAGCACCACCACCACCTCCTAGTCCTCCCCCACCACCAGC
ACCACCA
Found at i:126241 original size:24 final size:24
Alignment explanation
Indices: 126214--126561 Score: 116
Period size: 24 Copynumber: 14.0 Consensus size: 24
126204 TCCTAGACCT
* *
126214 CCACCTTTTCCACCTCCAAAACCA
1 CCACCTTCTCCACCTCCAACACCA
**
126238 CCACCGGCTCCACCTCCAGCACCACCA
1 CCACCTTCTCCACCTCCA--A-CACCA
* * * *
126265 CCAGCTCCTCCTCCGATGCCTACACCA
1 CCACCTTCTCCACC--T-CCAACACCA
* *
126292 CCACCTTTTCCACCTCCAAAACCA
1 CCACCTTCTCCACCTCCAACACCA
** *
126316 CCACCCGCTCCACCTCCAGCACCTCCA
1 CCACCTTCTCCACCTCCA--A-CACCA
* * * *
126343 CCAGCTCCTCCTCCGATGCCTACACCA
1 CCACCTTCTCCACC--T-CCAACACCA
* *
126370 CCACCTTTTCCACCTCCAAAACCA
1 CCACCTTCTCCACCTCCAACACCA
** *
126394 CCACCCGCTCCACCTCCAGCACCTCCA
1 CCACCTTCTCCACCTCCA--A-CACCA
* * * *
126421 CCAGCTCCTCCTCCGATGCCTACACCA
1 CCACCTTCTCCACC--T-CCAACACCA
* * *
126448 CCACCTTTTCCACCTCCAAAACTA
1 CCACCTTCTCCACCTCCAACACCA
**
126472 CCACCCGCTCCACCT------CCA
1 CCACCTTCTCCACCTCCAACACCA
* * * *
126490 GCACCTCCTCCA-ATGCCTACACCA
1 CCACCTTCTCCACCT-CCAACACCA
* *
126514 CCACCTTTTCCACCTCCAAAACCA
1 CCACCTTCTCCACCTCCAACACCA
** *
126538 CCACCGGCTCCACCTCCACCACCA
1 CCACCTTCTCCACCTCCAACACCA
126562 AGTCCTCCTC
Statistics
Matches: 229, Mismatches: 69, Indels: 52
0.65 0.20 0.15
Matches are distributed among these distances:
17 1 0.00
18 11 0.05
24 115 0.50
25 4 0.02
26 3 0.01
27 83 0.36
28 3 0.01
29 3 0.01
30 6 0.03
ACGTcount: A:0.23, C:0.55, G:0.06, T:0.16
Consensus pattern (24 bp):
CCACCTTCTCCACCTCCAACACCA
Found at i:126257 original size:78 final size:78
Alignment explanation
Indices: 126175--126639 Score: 578
Period size: 78 Copynumber: 6.0 Consensus size: 78
126165 AAATCCTCCA
* * * *
126175 CCAGCACCACCACCAGCTCCACCTCCAACT-CCTAGACCTCCACCTTTTCCACCTCCAAAACCAC
1 CCAGCACCACCACCAGCTCCTCCTCCGA-TGCCTACACCACCACCTTTTCCACCTCCAAAACCAC
*
126239 CACCGGCTCCACCT
65 CACCCGCTCCACCT
126253 CCAGCACCACCACCAGCTCCTCCTCCGATGCCTACACCACCACCTTTTCCACCTCCAAAACCACC
1 CCAGCACCACCACCAGCTCCTCCTCCGATGCCTACACCACCACCTTTTCCACCTCCAAAACCACC
126318 ACCCGCTCCACCT
66 ACCCGCTCCACCT
*
126331 CCAGCACCTCCACCAGCTCCTCCTCCGATGCCTACACCACCACCTTTTCCACCTCCAAAACCACC
1 CCAGCACCACCACCAGCTCCTCCTCCGATGCCTACACCACCACCTTTTCCACCTCCAAAACCACC
126396 ACCCGCTCCACCT
66 ACCCGCTCCACCT
* *
126409 CCAGCACCTCCACCAGCTCCTCCTCCGATGCCTACACCACCACCTTTTCCACCTCCAAAACTACC
1 CCAGCACCACCACCAGCTCCTCCTCCGATGCCTACACCACCACCTTTTCCACCTCCAAAACCACC
126474 ACCCGCTCCACCT
66 ACCCGCTCCACCT
*
126487 CCAG---------CA---CCTCCTCCAATGCCTACACCACCACCTTTTCCACCTCCAAAACCACC
1 CCAGCACCACCACCAGCTCCTCCTCCGATGCCTACACCACCACCTTTTCCACCTCCAAAACCACC
*
126540 ACCGGCTCCACCT
66 ACCCGCTCCACCT
* * * * * ** ** * *
126553 CCACCACCAAGTCCTCCTCCAGCGCCACCTCCAACTCCTATGCCTCCACCTTTTCCACCTCCGAA
1 CCAGCACC-A-----CCACCAGCTCCTCCTCCGATGCCTACACCACCACCTTTTCCACCTCCAAA
*
126618 ACCACCACCGGCTCCACCT
60 ACCACCACCCGCTCCACCT
126637 CCA
1 CCA
126640 CCGCCAAGTC
Statistics
Matches: 350, Mismatches: 18, Indels: 32
0.88 0.05 0.08
Matches are distributed among these distances:
66 60 0.17
69 2 0.01
77 1 0.00
78 229 0.65
81 2 0.01
84 56 0.16
ACGTcount: A:0.23, C:0.54, G:0.07, T:0.17
Consensus pattern (78 bp):
CCAGCACCACCACCAGCTCCTCCTCCGATGCCTACACCACCACCTTTTCCACCTCCAAAACCACC
ACCCGCTCCACCT
Found at i:126292 original size:54 final size:53
Alignment explanation
Indices: 126234--126489 Score: 177
Period size: 54 Copynumber: 4.9 Consensus size: 53
126224 CACCTCCAAA
*
126234 ACCACCACCGGCTCCACCTCCAGCACCACCACCAGCTCCTCCTCCGATGCCTAC
1 ACCACCACCTGCTCCACCTCCAGCACCACCACCAGCTCCTCCTCC-ATGCCTAC
** ** * *
126288 ACCACCACCTTTTCCACCTCCAAAACCACCACCCGCTCCACCTCCA-G----C
1 ACCACCACCTGCTCCACCTCCAGCACCACCACCAGCTCCTCCTCCATGCCTAC
* * * * ** * * *
126336 ACCTCCACCAGCTCCTCCTCCGATGC-CTACACCACCACCTTTTCCACC-T-CCAAA
1 ACCACCACCTGCTCCACCTCC-A-GCAC--CACCACCAGCTCCTCCTCCATGCCTAC
* *
126390 ACCACCACCCGCTCCACCTCCAGCACCTCCACCAGCTCCTCCTCCGATGCCTAC
1 ACCACCACCTGCTCCACCTCCAGCACCACCACCAGCTCCTCCTCC-ATGCCTAC
** ** * * *
126444 ACCACCACCTTTTCCACCTCCAAAACTACCACCCGCTCCACCTCCA
1 ACCACCACCTGCTCCACCTCCAGCACCACCACCAGCTCCTCCTCCA
126490 GCACCTCCTC
Statistics
Matches: 149, Mismatches: 40, Indels: 27
0.69 0.19 0.12
Matches are distributed among these distances:
48 17 0.11
49 2 0.01
51 27 0.18
52 3 0.02
53 5 0.03
54 95 0.64
ACGTcount: A:0.22, C:0.55, G:0.07, T:0.16
Consensus pattern (53 bp):
ACCACCACCTGCTCCACCTCCAGCACCACCACCAGCTCCTCCTCCATGCCTAC
Found at i:126461 original size:66 final size:66
Alignment explanation
Indices: 126403--126560 Score: 190
Period size: 66 Copynumber: 2.4 Consensus size: 66
126393 ACCACCCGCT
* * * * *
126403 CCACCTCCAGCACCTCCACCAGCTCCTCCTCCGATGCCTACACCACCACCTTTTCCACCTCCAAA
1 CCACCACCAGCACCACCACCAGCACCTCCTCCAATGCCTACACCACCACCTTTTCCACCACCAAA
126468 A
66 A
* * * * *
126469 CTACCACCCGCTCCACCTCCAGCACCTCCTCCAATGCCTACACCACCACCTTTTCCACCTCCAAA
1 CCACCACCAGCACCACCACCAGCACCTCCTCCAATGCCTACACCACCACCTTTTCCACCACCAAA
126534 A
66 A
* * * *
126535 CCACCACCGGCTCCACCTCCACCACC
1 CCACCACCAGCACCACCACCAGCACC
126561 AAGTCCTCCT
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 81 1.00
ACGTcount: A:0.23, C:0.55, G:0.06, T:0.16
Consensus pattern (66 bp):
CCACCACCAGCACCACCACCAGCACCTCCTCCAATGCCTACACCACCACCTTTTCCACCACCAAA
A
Found at i:126557 original size:42 final size:42
Alignment explanation
Indices: 126522--126681 Score: 135
Period size: 42 Copynumber: 3.8 Consensus size: 42
126512 CACCACCTTT
*
126522 TCCACCTCCAAAACCACCACCGGCTCCACCTCCACCACCAAG
1 TCCACCTCCAAAACCACCACCAGCTCCACCTCCACCACCAAG
* *** * * * ***
126564 TCCTCCTCCAGCGCCACCTCCAACTCCTA--TGCCTCCACCTTT
1 TCCACCTCCAAAACCACCACCAGCTCC-ACCT-CCACCACCAAG
* * *
126606 TCCACCTCCGAAACCACCACCGGCTCCACCTCCACCGCCAAG
1 TCCACCTCCAAAACCACCACCAGCTCCACCTCCACCACCAAG
* **
126648 TCCCCCTCCAGCACCACCACCAGCTCCACCTCCA
1 TCCACCTCCAAAACCACCACCAGCTCCACCTCCA
126682 AAACCACCAC
Statistics
Matches: 85, Mismatches: 29, Indels: 8
0.70 0.24 0.07
Matches are distributed among these distances:
41 2 0.02
42 81 0.95
43 2 0.02
ACGTcount: A:0.22, C:0.56, G:0.08, T:0.14
Consensus pattern (42 bp):
TCCACCTCCAAAACCACCACCAGCTCCACCTCCACCACCAAG
Found at i:126572 original size:24 final size:24
Alignment explanation
Indices: 126545--126591 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
126535 CCACCACCGG
* *
126545 CTCCACCTCCACCACCAAGTCCTC
1 CTCCACCGCCACCACCAACTCCTC
* *
126569 CTCCAGCGCCACCTCCAACTCCT
1 CTCCACCGCCACCACCAACTCCT
126592 ATGCCTCCAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.19, C:0.57, G:0.06, T:0.17
Consensus pattern (24 bp):
CTCCACCGCCACCACCAACTCCTC
Found at i:126602 original size:84 final size:84
Alignment explanation
Indices: 126514--126674 Score: 268
Period size: 84 Copynumber: 1.9 Consensus size: 84
126504 GCCTACACCA
* *
126514 CCACCTTTTCCACCTCCAAAACCACCACCGGCTCCACCTCCACCACCAAGTCCTCCTCCAGCGCC
1 CCACCTTTTCCACCTCCAAAACCACCACCGGCTCCACCTCCACCACCAAGTCCCCCTCCAGCACC
*
126579 ACCTCCAACTCCTATGCCT
66 ACCACCAACTCCTATGCCT
* *
126598 CCACCTTTTCCACCTCCGAAACCACCACCGGCTCCACCTCCACCGCCAAGTCCCCCTCCAGCACC
1 CCACCTTTTCCACCTCCAAAACCACCACCGGCTCCACCTCCACCACCAAGTCCCCCTCCAGCACC
*
126663 ACCACCAGCTCC
66 ACCACCAACTCC
126675 ACCTCCAAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 71 1.00
ACGTcount: A:0.21, C:0.55, G:0.08, T:0.16
Consensus pattern (84 bp):
CCACCTTTTCCACCTCCAAAACCACCACCGGCTCCACCTCCACCACCAAGTCCCCCTCCAGCACC
ACCACCAACTCCTATGCCT
Found at i:126633 original size:24 final size:23
Alignment explanation
Indices: 126606--126705 Score: 84
Period size: 24 Copynumber: 4.4 Consensus size: 23
126596 CTCCACCTTT
*
126606 TCCACCTCCGAAACCACCACCGGC
1 TCCACCTCC-AAACCACCACCAGC
*
126630 TCCACCTCC--ACCGCCA--AG-
1 TCCACCTCCAAACCACCACCAGC
* *
126648 TCCCCCTCCAGCACCACCACCAGC
1 TCCACCTCCA-AACCACCACCAGC
*
126672 TCCACCTCCAAAACCACCACCTGC
1 TCCACCTCC-AAACCACCACCAGC
*
126696 ACCACCTCCA
1 TCCACCTCCA
126706 CCACCAAGTC
Statistics
Matches: 61, Mismatches: 8, Indels: 15
0.73 0.10 0.18
Matches are distributed among these distances:
18 8 0.13
19 1 0.02
21 12 0.20
23 3 0.05
24 36 0.59
25 1 0.02
ACGTcount: A:0.25, C:0.57, G:0.08, T:0.10
Consensus pattern (23 bp):
TCCACCTCCAAACCACCACCAGC
Found at i:126663 original size:150 final size:150
Alignment explanation
Indices: 126350--126740 Score: 444
Period size: 150 Copynumber: 2.6 Consensus size: 150
126340 CCACCAGCTC
*
126350 CTCCTCCGATGCCTACACCACCACCTTTTCCACCTCCAAAACCACCACCCGCTCCACCT---CCA
1 CTCCTCCAATGCCTACACCACCACCTTTTCCACCTCCAAAACCACCACCCGCTCCACCTCCACCA
* * * * * *
126412 GC-A--CCTCCACCAGCTCCTCCTCCGATGCCTACACCACCACCTTTTCCACCTCCAAAACTACC
66 CCAAGTCCTCCTCCAGCACCACCTCCAATGCCTACACCACCACCTTTTCCACCTCCAAAACCACC
*
126474 ACCCGCTCCACCTCCAGCAC
131 ACCCGCTCCACCTCCAGCAA
*
126494 CTCCTCCAATGCCTACACCACCACCTTTTCCACCTCCAAAACCACCACCGGCTCCACCTCCACCA
1 CTCCTCCAATGCCTACACCACCACCTTTTCCACCTCCAAAACCACCACCCGCTCCACCTCCACCA
* ** * *
126559 CCAAGTCCTCCTCCAGCGCCACCTCCAACT-CCTATGCCTCCACCTTTTCCACCTCCGAAACCAC
66 CCAAGTCCTCCTCCAGCACCACCTCCAA-TGCCTACACCACCACCTTTTCCACCTCCAAAACCAC
*
126623 CACCGGCTCCACCTCCACCGCCAA
130 CACCCGCTCCACCTCCA--G-CAA
* * *** * *
126647 GTCC-CC-CT-CC-AGCACCACCACCAGCTCCACCTCCAAAACCACCACCTGCACCACCTCCACC
1 CTCCTCCAATGCCTA-CACCACCACCTTTTCCACCTCCAAAACCACCACCCGCTCCACCTCCACC
* *
126708 ACCAAGTCCTCCTCCTGCACCACCGCCAATGCC
65 ACCAAGTCCTCCTCCAGCACCACCTCCAATGCC
126741 ACCCCCTTTA
Statistics
Matches: 211, Mismatches: 24, Indels: 18
0.83 0.09 0.07
Matches are distributed among these distances:
144 57 0.27
147 4 0.02
148 1 0.00
149 2 0.01
150 137 0.65
151 2 0.01
152 3 0.01
153 5 0.02
ACGTcount: A:0.23, C:0.54, G:0.07, T:0.16
Consensus pattern (150 bp):
CTCCTCCAATGCCTACACCACCACCTTTTCCACCTCCAAAACCACCACCCGCTCCACCTCCACCA
CCAAGTCCTCCTCCAGCACCACCTCCAATGCCTACACCACCACCTTTTCCACCTCCAAAACCACC
ACCCGCTCCACCTCCAGCAA
Found at i:126668 original size:66 final size:66
Alignment explanation
Indices: 126606--126731 Score: 198
Period size: 66 Copynumber: 1.9 Consensus size: 66
126596 CTCCACCTTT
* * *
126606 TCCACCTCCGAAACCACCACCGGCTCCACCTCCACCGCCAAGTCCCCCTCCAGCACCACCACCAG
1 TCCACCTCCAAAACCACCACCGGCACCACCTCCACCACCAAGTCCCCCTCCAGCACCACCACCAG
126671 C
66 C
* * *
126672 TCCACCTCCAAAACCACCACCTGCACCACCTCCACCACCAAGTCCTCCTCCTGCACCACC
1 TCCACCTCCAAAACCACCACCGGCACCACCTCCACCACCAAGTCCCCCTCCAGCACCACC
126732 GCCAATGCCA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.24, C:0.57, G:0.08, T:0.11
Consensus pattern (66 bp):
TCCACCTCCAAAACCACCACCGGCACCACCTCCACCACCAAGTCCCCCTCCAGCACCACCACCAG
C
Found at i:126676 original size:12 final size:12
Alignment explanation
Indices: 126655--126711 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
126645 AAGTCCCCCT
126655 CCAGCACCACCA
1 CCAGCACCACCA
* *
126667 CCAGCTCCACCT
1 CCAGCACCACCA
**
126679 CCAAAACCACCA
1 CCAGCACCACCA
* *
126691 CCTGCACCACCT
1 CCAGCACCACCA
*
126703 CCACCACCA
1 CCAGCACCA
126712 AGTCCTCCTC
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.30, C:0.58, G:0.05, T:0.07
Consensus pattern (12 bp):
CCAGCACCACCA
Found at i:126705 original size:30 final size:30
Alignment explanation
Indices: 126665--126731 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
126655 CCAGCACCAC
* *
126665 CACCAGCTCCACCTCCAAAACCACCACCTG
1 CACCACCTCCACCACCAAAACCACCACCTG
** * *
126695 CACCACCTCCACCACCAAGTCCTCCTCCTG
1 CACCACCTCCACCACCAAAACCACCACCTG
126725 CACCACC
1 CACCACC
126732 GCCAATGCCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.57, G:0.06, T:0.12
Consensus pattern (30 bp):
CACCACCTCCACCACCAAAACCACCACCTG
Found at i:127978 original size:7 final size:7
Alignment explanation
Indices: 127966--127998 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
127956 TCGGAAATCT
127966 TTTCTTC
1 TTTCTTC
127973 TTTCTTC
1 TTTCTTC
127980 TTTCTTC
1 TTTCTTC
*
127987 TTTCATC
1 TTTCTTC
127994 TTTCT
1 TTTCT
127999 GTCGCCCTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTCTTC
Found at i:157854 original size:30 final size:26
Alignment explanation
Indices: 157797--157848 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
157787 CTACCCAGAC
157797 CAACTCTCACGAAATGTGAGTTTGTT
1 CAACTCTCACGAAATGTGAGTTTGTT
*
157823 CAACTCTCACGGAATGTGAGTTTGTT
1 CAACTCTCACGAAATGTGAGTTTGTT
157849 TGTTCATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (26 bp):
CAACTCTCACGAAATGTGAGTTTGTT
Found at i:160204 original size:16 final size:15
Alignment explanation
Indices: 160175--160218 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 15
160165 TTTTGGGCTT
160175 TTTTTTTTTGGTTTTG
1 TTTTTTTTT-GTTTTG
160191 TTTCTTTTTTGTTTTG
1 TTT-TTTTTTGTTTTG
160207 TTTTTTATTTGT
1 TTTTTT-TTTGT
160219 CAACCCAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 3 0.12
16 17 0.65
17 6 0.23
ACGTcount: A:0.02, C:0.02, G:0.14, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTGTTTTG
Found at i:160700 original size:30 final size:32
Alignment explanation
Indices: 160664--160734 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 32
160654 TCTCTAAGAA
*
160664 TCAGAGATAGAA-CAC-ATCTGTTTCTGACAG
1 TCAGAGACAGAAGCACAATCTGTTTCTGACAG
*
160694 TCAGAGACGGAAGCACAAATCTGTTTCTGACAG
1 TCAGAGACAGAAGCAC-AATCTGTTTCTGACAG
160727 TCAGAGAC
1 TCAGAGAC
160735 GGAATCAGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 10 0.28
31 3 0.08
33 23 0.64
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.23
Consensus pattern (32 bp):
TCAGAGACAGAAGCACAATCTGTTTCTGACAG
Done.