Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015340.1 Corchorus olitorius cultivar O-4 contig15373, 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: 116910
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1012 original size:330 final size:331
Alignment explanation
Indices: 1--2228 Score: 2930
Period size: 330 Copynumber: 6.7 Consensus size: 331
*
1 TTGGAAAAACGATATTAGAAGCC-GTAAAAACCCTTCAATC-TTTTGTCTTTGAA-TA-ATTTTT
1 TTGGAAAAACGATATTAGAAGCCTG-AAAAACCCTTCAATCTTTTTGTCTTTGAATTATATATTT
* * * * *
62 TTTATGAGAATTGTGGCCAAAAATTGAGGAAAAGTCTTT-CGAATCAATTTAGCAAAATTTCAGC
65 TCTATGAGAATTGTGGCCAAAAATTGAGGAAAAAT-TTTCCGGATCAATTTTGCAAAATTTTAGC
* * * * * *
126 CGAAATCGTGTACTTTCCATCAAGATTTTAAGCTCAAAATGCGTTTTG-GGACACCGACTCAGTT
129 CGAAATCGTGTACTTTCCATCACGGTTTTAAGCTAAAAACGCGTTTCGAGG-CCCCGACTCAGTT
* *
190 TTGCATGATTTTTTGCACGAAGAATCCTTGAAATATTTATATTCATCTGACCAAATCTCAGCCAC
193 TTGCATGATTTTTGGCACGAAGACTCCTTGAAATATTTATATTCATCTGACCAAATCTCAGCCAC
* * * *
255 TTTGGATTTAAGGATTTGCTTTTACGAGCATTTGTATCATGTTTCGATTTAATTTGAAATTAATT
258 TTTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTCGAAATTAATT
320 CAGAAAAAA
323 CAGAAAAAA
* * * *
329 TTGGAAAAACGATATTAGTAGCCTGAAAAACCCTTCAATCTTTTTGCCTTTGAACTATATATTGT
1 TTGGAAAAACGATATTAGAAGCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATATTTT
* *
394 CTATGAGAGTTGTGGCC-AAAATTGAGGAAAAATTTTCCGGATCAATTTTTGCAAAATTTTAGCA
66 CTATGAGAATTGTGGCCAAAAATTGAGGAAAAATTTTCCGGATCAA-TTTTGCAAAATTTTAGCC
* * * **
458 GAAATCGTGTACTTT-CATCACGGTTTTAAGCTAAAAACACGTTTCGAGACACCGACTTTGTTTT
130 GAAATCGTGTACTTTCCATCACGGTTTTAAGCTAAAAACGCGTTTCGAGGCCCCGACTCAGTTTT
*
522 GCATGATTTATT-GCAC-AA-AGT--TTGAAATATTTATATTCATCTGACCAAATCTCAGCCACT
195 GCATGATTT-TTGGCACGAAGACTCCTTGAAATATTTATATTCATCTGACCAAATCTCAGCCACT
* * * * * * *
582 TTGGATTTAAGGATTTGTTTCTACGAGCGTTTGTATCATGTTTCTATTTAATTCAAAATTAATTA
259 TTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTCGAAATTAATTC
647 AGAAAAAA
324 AGAAAAAA
* *
655 TTGGAAAAACGATATTAAAAGCCTGAAAAACCTTTCAATCTTTTTGTCTTTGAATTATATATTTT
1 TTGGAAAAACGATATTAGAAGCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATATTTT
*
720 CTATGAGAATTGTGGCC-AAAATTGAGGAAAAAGTTTTCCGGATCAATTTTGCAAAATTTCAGCC
66 CTATGAGAATTGTGGCCAAAAATTGAGGAAAAA-TTTTCCGGATCAATTTTGCAAAATTTTAGCC
*
784 GAAATCGTGTACTATCCATCACGGTTTTAAGCT-AAAACGCGTTTCGAGGCCCCGACTCAGTTTT
130 GAAATCGTGTACTTTCCATCACGGTTTTAAGCTAAAAACGCGTTTCGAGGCCCCGACTCAGTTTT
* *
848 GCATGATTTTTGGCACGAAGACTCCTTGAAATATCTATATTCATCTGACTAAATCTCAGCCACTT
195 GCATGATTTTTGGCACGAAGACTCCTTGAAATATTTATATTCATCTGACCAAATCTCAGCCACTT
*
913 TGGATTTAAGGATTTGCTTTTACGAGCATCTGAATCATGTTTCGATTTAATTCGAAATTAATTCA
260 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTCGAAATTAATTCA
978 GAAAAAA
325 GAAAAAA
* *
985 TTTGAAAAACGATATTAGTAGCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATATATA
1 TTGGAAAAACGATATTAGAAGCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATAT-T-
* *
1050 TTTTATGAGAATTGTGGCCAAAAATTGAGGAAAAATTTTCCGGATCAATTTTGCAAAGTTTTAGC
64 TTCTATGAGAATTGTGGCCAAAAATTGAGGAAAAATTTTCCGGATCAATTTTGCAAAATTTTAGC
* * * *
1115 CGAAATAGTGTACACTTTCTATCACAGTTTTAAGCTAAAAACGCGTTTC-A-TCGCCCGACTCAG
129 CGAAATCGTGT--ACTTTCCATCACGGTTTTAAGCTAAAAACGCGTTTCGAGGC-CCCGACTCAG
* * * * ** *
1178 TTTTGCATGACTTTTGGCAAGAAGACTTCTTGAAATATTTATAATT-ATCTAAGAAAATCTAAGC
191 TTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATATTTAT-ATTCATCTGACCAAATCTCAGC
* * * * * *
1242 CACATTGGATTTAAGTATTTGTTTTTACAACCATCTGAATCATGTTTCGATTTTATTTGAAATTA
255 CACTTTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTCGAAATTA
1307 ATTCA-AAAAGAA
320 ATTCAGAAAA-AA
* * * *
1319 TTGGGAAAACGATATTAGAAGCGTG-AAAACCCTTCAATCTTTTTGGCTTTGAATTGTATATATT
1 TTGGAAAAACGATATTAGAAGCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATAT-TT
* * * *
1383 T-TATGAGAGTTGTGGCCAAAAATTGAGGAAAATTTTTCCGGATCTATTTTTGCAAAATCTTA-C
65 TCTATGAGAATTGTGGCCAAAAATTGAGGAAAAATTTTCCGGATC-AATTTTGCAAAATTTTAGC
* * * ** *
1446 CAGAAATCGTATACTTTCCATCACGGCTTTAAGCTAAAAACACGTTTCG-GGACAGCGACTTAGT
129 C-GAAATCGTGTACTTTCCATCACGGTTTTAAGCTAAAAACGCGTTTCGAGG-CCCCGACTCAGT
* * *
1510 TTTGCATGATTTTTTGCACAAAGACTCCATGAAATATTTATATTCATCTGACCAAATCTCAGCCA
192 TTTGCATGATTTTTGGCACGAAGACTCCTTGAAATATTTATATTCATCTGACCAAATCTCAGCCA
* * * * ** *
1575 CTTTGGATTTAAGAATTTGTTTTTACGAGCGTTTGTATCATGTTTTTATTTAATTCCAAATTAAT
257 CTTTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTCGAAATTAAT
*
1640 TAAGAAAAAAA
322 TCAG-AAAAAA
* * * * * *
1651 TTGGAAAAACAATATTAAAATCCTAAAAAACCTTTCAAGT-TTTTTGTCTTGGAATTATATATTT
1 TTGGAAAAACGATATTAGAAGCCTGAAAAACCCTTCAA-TCTTTTTGTCTTTGAATTATATATTT
* *
1715 TCTATGAGAATTGTGGCCAAAAATTGAGGAAAATTTTTCCTGATCAAATTTTGCAAAATTTTAGC
65 TCTATGAGAATTGTGGCCAAAAATTGAGGAAAAATTTTCCGGATC-AATTTTGCAAAATTTTAGC
* **
1780 CGAAATCGTGTACTATCCATCACGGTTTTAAGCTAAAAACGTATTTCGAGGCCCCGACTCAGTTT
129 CGAAATCGTGTACTTTCCATCACGGTTTTAAGCTAAAAACGCGTTTCGAGGCCCCGACTCAGTTT
* * * *
1845 TGCATGATTTTTGGCACGAAGAGTCCTTGAAATATCTATATTCATCTGACCAAATTTAAGCCACT
194 TGCATGATTTTTGGCACGAAGACTCCTTGAAATATTTATATTCATCTGACCAAATCTCAGCCACT
* * * *
1910 TTTGTTTTAAGGATTTATTTTTATGAGCATCTGAATCATGTTTCTG-TTTAATTCGAAATTAATT
259 TTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTC-GATTTAATTCGAAATTAATT
1974 CAGAAAAAA
323 CAGAAAAAA
* * * *
1983 TTTGAAAAACGATATTAGAAGCCTTAAAAGCCCTTCAATCTTTTTGTATTTGAATTATATA-TTT
1 TTGGAAAAACGATATTAGAAGCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATATTTT
* * * *
2047 -TATGAGAACTT-TGGCCAAAAAGTGAGGAAAAATTTTCCGAAACAATTTTTGCAAAATTTTAGT
66 CTATGAGAA-TTGTGGCCAAAAATTGAGGAAAAATTTTCCGGATCAA-TTTTGCAAAATTTTAGC
* * * *
2110 CGAAATCGTGTACTTTTCATCACGATTTTAAGCTAAAAACACGTTTCGAGGCCCAG-CTCAGTTT
129 CGAAATCGTGTACTTTCCATCACGGTTTTAAGCTAAAAACGCGTTTCGAGGCCCCGACTCAGTTT
* * *
2174 TGCATGATTTTTGGCCCGAAAACTCCTTGAAATATCTATATTCATCTGACCAAAT
194 TGCATGATTTTTGGCACGAAGACTCCTTGAAATATTTATATTCATCTGACCAAAT
2229 TTTTTTTGGC
Statistics
Matches: 1666, Mismatches: 193, Indels: 81
0.86 0.10 0.04
Matches are distributed among these distances:
325 2 0.00
326 264 0.16
327 32 0.02
328 41 0.02
329 80 0.05
330 370 0.22
331 217 0.13
332 161 0.10
333 310 0.19
334 174 0.10
335 15 0.01
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (331 bp):
TTGGAAAAACGATATTAGAAGCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATATTTT
CTATGAGAATTGTGGCCAAAAATTGAGGAAAAATTTTCCGGATCAATTTTGCAAAATTTTAGCCG
AAATCGTGTACTTTCCATCACGGTTTTAAGCTAAAAACGCGTTTCGAGGCCCCGACTCAGTTTTG
CATGATTTTTGGCACGAAGACTCCTTGAAATATTTATATTCATCTGACCAAATCTCAGCCACTTT
GGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTCGAAATTAATTCAG
AAAAAA
Found at i:1838 original size:664 final size:656
Alignment explanation
Indices: 1--2228 Score: 2918
Period size: 664 Copynumber: 3.4 Consensus size: 656
* * * *
1 TTGGAAAAACGATATTAGAAGCCGTAAAAACCCTTCAATC-TTTTGTCTTTGAATAATTTTTTTT
1 TTGGAAAAACGATATTAGAAGCC-TGAAAACCCTTCAATCTTTTTGTCTTTGAATTATATATTTT
* *
65 ATGAGAATTGTGGCCAAAAATTGAGGAAAAGTCTTT-CGAATCAATTTAGCAAAATTTCAGCCGA
65 ATGAGAATTGTGGCCAAAAATTGAGGAAAA-TTTTTCCGAATCAATTTTGCAAAATTTCAGCCGA
* * ** *
129 AATCGTGTACTTTCCATCAAGATTTTAAGCTCAAAATGCGTTTTG-GGACACCGACTCAGTTTTG
129 AATCGTGTACTTTCCATCACGATTTTAAGCTAAAAACACGTTTCGAGG-CACCGACTCAGTTTTG
* * * *
193 CATGATTTTTTGCACGAAGAATCCTTGAAATATTTATATTCATCTGACCAAATCTCAGCCACTTT
193 CATGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTCATCTGACCAAATCTCAGCCACTTT
*
258 GGATTTAAGGATTTGCTTTTACGAGCATTTGTATCATGTTTCGATTTAATTTGAAATTAATTCAG
258 GGATTTAAGGATTTGCTTTTACGAGCATTTGTATCATGTTTCGATTTAATTCGAAATTAATTCAG
* *
323 AAAAAATTGGAAAAACGATATTAGTAGCCTGAAAAACCCTTCAATCTTTTTGCCTTTGAACTATA
323 AAAAAATTGGAAAAACGATATTAGTAGCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATA
* * *
388 TATTGTCTATGAGAGTTGTGGCC-AAAATTGAGGAAAAATTTTCCGGATCAATTTTTGCAAAATT
388 TATTTTCTATGAGAATTGTGGCCAAAAATTGAGGAAAAATTTTCCGGATCAAATTTTGCAAAATT
* * * * **
452 TTAGCAGAAATCGTGTACTTTCATCACGGTTTTAAGCTAAAAACACGTTTCGAGACACCGACTTT
453 TTAGCCGAAATCGTGTACTTCCATCACGGTTTTAAGCTAAAAACGCGTTTCGAGACCCCGACTCA
* *
517 GTTTTGCATGATTTATTGCACA-AAG--T-TTGAAATATTTATATTCATCTGACCAAATCTCAGC
518 GTTTTGCATGATTT-TGGCA-AGAAGATTCTTGAAATATTTATATTCATCTGACCAAATCTAAGC
* * * * * *
578 CACTTTGGATTTAAGGATTTGTTTCTACGAGCGTTTGTATCATGTTTCTATTTAATTCAAAATTA
581 CACTTTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTCGAAATTA
*
643 ATTAAGAAAAAA
646 ATTCA-AAAAAA
* *
655 TTGGAAAAACGATATTAAAAGCCTGAAAAACCTTTCAATCTTTTTGTCTTTGAATTATATATTTT
1 TTGGAAAAACGATATTAGAAGCCTG-AAAACCCTTCAATCTTTTTGTCTTTGAATTATATA-TTT
* *
720 CTATGAGAATTGTGGCC-AAAATTGAGGAAAAAGTTTTCCGGATCAATTTTGCAAAATTTCAGCC
64 -TATGAGAATTGTGGCCAAAAATTGAGG-AAAATTTTTCCGAATCAATTTTGCAAAATTTCAGCC
* * * *
784 GAAATCGTGTACTATCCATCACGGTTTTAAGCT-AAAACGCGTTTCGAGGCCCCGACTCAGTTTT
127 GAAATCGTGTACTTTCCATCACGATTTTAAGCTAAAAACACGTTTCGAGGCACCGACTCAGTTTT
* *
848 GCATGATTTTTGGCACGAAGACTCCTTGAAATATCTATATTCATCTGACTAAATCTCAGCCACTT
192 GCATGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTCATCTGACCAAATCTCAGCCACTT
* *
913 TGGATTTAAGGATTTGCTTTTACGAGCATCTGAATCATGTTTCGATTTAATTCGAAATTAATTCA
257 TGGATTTAAGGATTTGCTTTTACGAGCATTTGTATCATGTTTCGATTTAATTCGAAATTAATTCA
*
978 GAAAAAATTTGAAAAACGATATTAGTAGCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTAT
322 GAAAAAATTGGAAAAACGATATTAGTAGCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTAT
*
1043 ATATATATTTTATGAGAATTGTGGCCAAAAATTGAGGAAAAATTTTCCGGATC-AATTTTGCAAA
387 ATAT-T-TTCTATGAGAATTGTGGCCAAAAATTGAGGAAAAATTTTCCGGATCAAATTTTGCAAA
* * * * *
1107 GTTTTAGCCGAAATAGTGTACACTTTCTATCACAGTTTTAAGCTAAAAACGCGTTTC-A-TCGCC
450 ATTTTAGCCGAAATCGTGT--AC-TTCCATCACGGTTTTAAGCTAAAAACGCGTTTCGAGAC-CC
* **
1170 CGACTCAGTTTTGCATGACTTTTGGCAAGAAGACTTCTTGAAATATTTATAATT-ATCTAAGAAA
511 CGACTCAGTTTTGCATGA-TTTTGGCAAGAAGA-TTCTTGAAATATTTAT-ATTCATCTGACCAA
* * * * *
1234 ATCTAAGCCACATTGGATTTAAGTATTTGTTTTTACAACCATCTGAATCATGTTTCGATTTTATT
573 ATCTAAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATT
*
1299 TGAAATTAATTCAAAAAGAA
638 CGAAATTAATTCAAAAA-AA
* * *
1319 TTGGGAAAACGATATTAGAAGCGTGAAAACCCTTCAATCTTTTTGGCTTTGAATTGTATATATTT
1 TTGGAAAAACGATATTAGAAGCCTGAAAACCCTTCAATCTTTTTGTCTTTGAA-T-TATATATTT
* * *
1384 TATGAGAGTTGTGGCCAAAAATTGAGGAAAATTTTTCCGGATCTATTTTTGCAAAATCTT-A-CC
64 TATGAGAATTGTGGCCAAAAATTGAGGAAAATTTTTCCGAATC-AATTTTGCAAAAT-TTCAGCC
* ** * *
1447 AGAAATCGTATACTTTCCATCACGGCTTTAAGCTAAAAACACGTTTCG-GGACAGCGACTTAGTT
127 -GAAATCGTGTACTTTCCATCACGATTTTAAGCTAAAAACACGTTTCGAGG-CACCGACTCAGTT
* * *
1511 TTGCATGATTTTTTGCACAAAGACTCCATGAAATATTTATATTCATCTGACCAAATCTCAGCCAC
190 TTGCATGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTCATCTGACCAAATCTCAGCCAC
* * * ** *
1576 TTTGGATTTAAGAATTTGTTTTTACGAGCGTTTGTATCATGTTTTTATTTAATTCCAAATTAATT
255 TTTGGATTTAAGGATTTGCTTTTACGAGCATTTGTATCATGTTTCGATTTAATTCGAAATTAATT
* * ** * * * *
1641 AAGAAAAAAATTGGAAAAACAATATTAAAATCCTAAAAAACCTTTCAAGT-TTTTTGTCTTGGAA
320 CAG-AAAAAATTGGAAAAACGATATTAGTAGCCTGAAAAACCCTTCAA-TCTTTTTGTCTTTGAA
* *
1705 TTATATATTTTCTATGAGAATTGTGGCCAAAAATTGAGGAAAATTTTTCCTGATCAAATTTTGCA
383 TTATATATTTTCTATGAGAATTGTGGCCAAAAATTGAGGAAAAATTTTCCGGATCAAATTTTGCA
** *
1770 AAATTTTAGCCGAAATCGTGTACTATCCATCACGGTTTTAAGCTAAAAACGTATTTCGAGGCCCC
448 AAATTTTAGCCGAAATCGTGTACT-TCCATCACGGTTTTAAGCTAAAAACGCGTTTCGAGACCCC
* * *
1835 GACTCAGTTTTGCATGATTTTTGGCACGAAGAGTCCTTGAAATATCTATATTCATCTGACCAAAT
512 GACTCAGTTTTGCATGA-TTTTGGCAAGAAGA-TTCTTGAAATATTTATATTCATCTGACCAAAT
* * * * *
1900 TTAAGCCACTTTTGTTTTAAGGATTTATTTTTATGAGCATCTGAATCATGTTTCTG-TTTAATTC
575 CTAAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTC-GATTTAATTC
1964 GAAATTAATTCAGAAAAAA
639 GAAATTAATTCA-AAAAAA
* * *
1983 TTTGAAAAACGATATTAGAAGCCTTAAAAGCCCTTCAATCTTTTTGTATTTGAATTATATATTTT
1 TTGGAAAAACGATATTAGAAGCCTGAAAA-CCCTTCAATCTTTTTGTCTTTGAATTATATATTTT
* * * * *
2048 ATGAGAACTT-TGGCCAAAAAGTGAGGAAAAATTTTCCGAAACAATTTTTGCAAAATTTTAGTCG
65 ATGAGAA-TTGTGGCCAAAAATTGAGGAAAATTTTTCCGAATCAA-TTTTGCAAAATTTCAGCCG
*
2112 AAATCGTGTACTTTTCATCACGATTTTAAGCTAAAAACACGTTTCGAGGC-CC-AGCTCAGTTTT
128 AAATCGTGTACTTTCCATCACGATTTTAAGCTAAAAACACGTTTCGAGGCACCGA-CTCAGTTTT
*
2175 GCATGATTTTTGGCCCGAAA-ACTCCTTGAAATATCTATATTCATCTGACCAAAT
192 GCATGATTTTTGGCAC-AAAGACTCCTTGAAATATCTATATTCATCTGACCAAAT
2229 TTTTTTTGGC
Statistics
Matches: 1379, Mismatches: 148, Indels: 86
0.85 0.09 0.05
Matches are distributed among these distances:
653 1 0.00
654 35 0.03
655 17 0.01
656 230 0.17
657 77 0.06
658 42 0.03
659 28 0.02
660 27 0.02
661 33 0.02
662 59 0.04
663 199 0.14
664 363 0.26
665 209 0.15
666 58 0.04
667 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (656 bp):
TTGGAAAAACGATATTAGAAGCCTGAAAACCCTTCAATCTTTTTGTCTTTGAATTATATATTTTA
TGAGAATTGTGGCCAAAAATTGAGGAAAATTTTTCCGAATCAATTTTGCAAAATTTCAGCCGAAA
TCGTGTACTTTCCATCACGATTTTAAGCTAAAAACACGTTTCGAGGCACCGACTCAGTTTTGCAT
GATTTTTGGCACAAAGACTCCTTGAAATATCTATATTCATCTGACCAAATCTCAGCCACTTTGGA
TTTAAGGATTTGCTTTTACGAGCATTTGTATCATGTTTCGATTTAATTCGAAATTAATTCAGAAA
AAATTGGAAAAACGATATTAGTAGCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATAT
TTTCTATGAGAATTGTGGCCAAAAATTGAGGAAAAATTTTCCGGATCAAATTTTGCAAAATTTTA
GCCGAAATCGTGTACTTCCATCACGGTTTTAAGCTAAAAACGCGTTTCGAGACCCCGACTCAGTT
TTGCATGATTTTGGCAAGAAGATTCTTGAAATATTTATATTCATCTGACCAAATCTAAGCCACTT
TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTCGAAATTAATTCA
AAAAAA
Found at i:2900 original size:334 final size:331
Alignment explanation
Indices: 2273--4231 Score: 1857
Period size: 334 Copynumber: 5.9 Consensus size: 331
2263 GAGTTGTGCT
* * * * * * * *
2273 AAAAAATTTTCTGATCAATTTTTGTAAAATGTTAGCCGAAATCGTATACTTTCCATCAAGACTTT
1 AAAAAATTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCACGATTTT
* * * * * * *
2338 AAACTAAAAACGCGTTTTGGGACACCGACTTAGTTTTGCATGACGTTTT-GCACGAACAATCCTT
66 AAGCTAAAAACGCGTTTCGGGACATCGACTCAGTTTTGCATGA-TTTTTGGCACGAAGACTCCTT
* * *
2402 GAAATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAA-GATTT-TGTTTTAACGA
130 GAAATATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTAT-TTTT-ACGA
* *
2465 GCATTTGTATCATGTTTCTATTTAATTCAAAATTAATTCAGAAAAAATTGGAAAAATGATATTAA
193 GCATTTGAATCATGTTTCTATTTAATTCAAAATTAATTCAGAAAAAATTGGAAAAACGATATTAA
* * *
2530 AAGCCTGAAAAACCCTTCAAGCTTTTTTTTTCTTTGAATTATATATTGTCTATGAGAATTGTGGC
258 AAGCCTGAAAAACCCTTCAA--TCTTTTTGTCTTTGAATTATATATT-TTTATGAGAATTGTGGC
*
2595 CTAAAATTGAGG
320 CAAAAATTGAGG
* * *
2607 AAAAAATTTCCGGATCAATTTTTGCAAAATTTTAGACAAAATCGTGCACTATCCATCACGATTTT
1 AAAAAATTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCACGATTTT
2672 AAGCTAAAAACGCGTTTCGAGG-CATCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTT
66 AAGCTAAAAACGCGTTTCG-GGACATCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTT
* * * * * *
2736 -AAACTATATATATCCATTTGACCAAATCTCAGCCACTTTAGATTTAAGGATTTTTTTTTACGAG
130 GAAA-TATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTATTTTTACGAG
* *
2800 CATCTGAATCATGTTTCTATTTAATTCACAATTAATTCAGAAAAAATATTGGAAAAACGATATTA
194 CATTTGAATCATGTTTCTATTTAATTCAAAATTAATTCAG-AAAAA-ATTGGAAAAACGATATTA
* * *
2865 GAATCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATTTTTTTTATGAGAATTGTGGCC
257 AAAGCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATA-TATTTTTATGAGAATTGTGGCC
2930 AAAAATTGAGG
321 AAAAATTGAGG
* ** * *
2941 -AAAAATCTTTCGGATCAA-TTCAGCAAAATTTTAGCCGAAATCATGTACTTTCCATCAC-AGTT
1 AAAAAAT-TTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCACGA-TT
* * ** * *
3003 TTAAGCTAAAAAAGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAAGAAGACTTCT
64 TTAAGCTAAAAACGCGTTTCGGGACATCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCT
* * *
3068 TGAAATATATATATTTTAATATTTATCTAACCAAGTCTCAGCCACATTGGATTTAAGGATTTGTT
129 TG--A-A-ATATA---T-ATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTATT
* * * * **
3133 TTTACGACCATTCGAATCATGTTTCGATTTTATTTGAAATTAATTCAGAAAAAATTGGAAAAACG
186 TTTACGAGCATTTGAATCATGTTTCTATTTAATTCAAAATTAATTCAGAAAAAATTGGAAAAACG
* ** * * * *
3198 ATATTAGAAGTGTGAAAAACCCTTCAATCATTTTGGCTTTGAATTATTTATATTTTATGAGAGTT
251 ATATTAAAAGCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATAT-TTTTATGAGAATT
3263 GTGGCCAAAAATTGAGG
315 GTGGCCAAAAATTGAGG
* * * * *
3280 AAAAATTTTCCGGATCAGTTTTTACAAAATTTTAGCAGAAATC--G-----T--ATCACGACTTT
1 AAAAAATTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCACGATTTT
* * * * * *
3336 AAGCTAAAAACACTTTTCGGGACATCGACTTAGTTTTGCATGATTTTTTGCACAAAAACTCCTTG
66 AAGCTAAAAACGCGTTTCGGGACATCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTG
* * * *
3401 AAATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATATAAGGATTTATTTTTACGAGCA
131 AAATATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTATTTTTACGAGCA
* * *
3466 TTTGTATCATGTTTCTATTTAATTCAAAATTAATTAAGAAAAAATTGGAAAAACAATATTAAAAG
196 TTTGAATCATGTTTCTATTTAATTCAAAATTAATTCAGAAAAAATTGGAAAAACGATATTAAAAG
* *
3531 CCTGAAAAACCTTTCAAGCTTTTTGTCTTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAA
261 CCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATA-TTTTTATGAGAATTGTGGCC-AAA
*
3596 AAATGAGG
324 AATTGAGG
* * * * **
3604 AAAAATTTTCCGAATCAAATTTTGCAAAATTTTAGCCGAAATCCATGATGGTTAGT--AT-ACGA
1 AAAAAATTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAAT-CGTG-T-ACTA-TCCATCACGA
** * * * * * *
3666 -TTTCGGTTAAAAACCCGTTCCGGGGCCTTG-CTCAGTTTTGCATGATTTTTTGTGC-C-AAGAC
62 TTTTAAGCTAAAAACGCGTTTCGGGACATCGACTCAGTTTTGCATGA-TTTTTG-GCACGAAGAC
* * * * ** * *
3727 TCCTTGGAATATCTATATTCATTTAACCAAATCTCAGTCACATTAAATTTAAGAATTTGTTTTTA
125 TCCTTGAAATATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTATTTTTA
* * * * * *
3792 TGAGCATCTGAATCTTATTTCGATTTAATT-AGAAATTAATTC-GGAAAAA-T------A--ATA
190 CGAGCATTTGAATCATGTTTCTATTTAATTCA-AAATTAATTCAGAAAAAATTGGAAAAACGATA
* * * * * ** * * *
3846 TTAGAAGCGTTAAAAGCCCTTCAATCTTTTTGAT-GTCAAATTATATATTTTTATGAGTATTTTA
254 TTAAAAGCCTGAAAAACCCTTCAATCTTTTTG-TCTTTGAATTATATATTTTTATGAGAATTGTG
* *
3910 GCAAAAAATTCAGG
318 GCCAAAAATTGAGG
** * * * * *
3924 -AATTATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATTGTGTACTAAACCATCACGGTT
1 AAAAAAT-TTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT-ATCCATCACGATT
** * * ** * *
3988 TTTGGCTAAAAACGCGTTCCAGGGCCAT-GACTTTGTTTTACTTGATTTTTGGTGC-CG-AGACT
64 TTAAGCTAAAAACGCGTTTC-GGGACATCGACTCAGTTTTGCATGATTTTT-G-GCACGAAGACT
* * * *
4050 CCTTGAAATATCTTTATTCATCTAATCAAATTTCAGCCACATTGGATTTAAGGATTTATTTTTAC
126 CCTTGAAATATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTATTTTTAC
*
4115 GTA-CATTTGAATCTTGTTTC-ATTTAATT-AGAAATTAATTCTA-AAAAAATAT-GAAAAACGA
191 G-AGCATTTGAATCATGTTTCTATTTAATTCA-AAATTAATTC-AGAAAAAAT-TGGAAAAACGA
* * ** * * *
4175 TATTAAAAGCGTGACAAGTCCTCCAATCTTTTTGGCATTGAATTATATATTTTTATG
252 TATTAAAAGCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATATTTTTATG
4232 GGTATTTTTG
Statistics
Matches: 1349, Mismatches: 212, Indels: 131
0.80 0.13 0.08
Matches are distributed among these distances:
317 1 0.00
318 2 0.00
319 7 0.01
320 43 0.03
321 60 0.04
322 140 0.10
323 159 0.12
324 51 0.04
325 1 0.00
327 5 0.00
328 1 0.00
329 2 0.00
330 1 0.00
331 116 0.09
332 109 0.08
333 134 0.10
334 246 0.18
335 22 0.02
336 38 0.03
337 5 0.00
338 4 0.00
339 92 0.07
340 31 0.02
341 79 0.06
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (331 bp):
AAAAAATTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCACGATTTT
AAGCTAAAAACGCGTTTCGGGACATCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTG
AAATATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTATTTTTACGAGCA
TTTGAATCATGTTTCTATTTAATTCAAAATTAATTCAGAAAAAATTGGAAAAACGATATTAAAAG
CCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATATTTTTATGAGAATTGTGGCCAAAAA
TTGAGG
Found at i:3575 original size:664 final size:660
Alignment explanation
Indices: 2298--3646 Score: 1733
Period size: 664 Copynumber: 2.0 Consensus size: 660
2288 CAATTTTTGT
* * * *
2298 AAAATGTTAGCCGAAATCGTATACTTTCCATCAAGACTTTAAACTAAAAACGCGTTTTGGGACAC
1 AAAATTTTAGCCGAAATCATATACTTTCCATCAAGACTTTAAACTAAAAAAGCGTTTCGGGACAC
* * *
2363 CGACTTAGTTTTGCATGACGTTTTGCACGAACAATCCTTGAAATATTTATATTCATCTGACCAAA
66 CGACTCAGTTTTGCATGACGTTTTGCAAGAACAATCCTTGAAATATTTATATTCATCTAACCAAA
* * * * *
2428 TCTCAGCCACTTTGGATTTAAGATTTTGTTTTAACGAGCATTTGTATCATGTTTCTATTTAATTC
131 TCTCAGCCACATTGGATTTAAGATTTTGTTTTAACGACCATTCGAATCATGTTTCGATTTAATTC
* **
2493 AAAATTAATTCAGAAAAAATTGGAAAAATGATATTAAAAGCCTGAAAAACCCTTCAAGCTTTTTT
196 AAAATTAATTCAGAAAAAATTGGAAAAACGATATTAAAAGCCTGAAAAACCCTTCAA-CTCATTT
** *
2558 TTTCTTTGAATTATATATTGTCTATGAGAATTGTGGCCTAAAATTGAGGAAAAAATTTCCGGATC
260 TGGCTTTGAATTATATATTGTCTATGAGAATTGTGGCCAAAAATTGAGGAAAAAATTTCCGGATC
* * *
2623 AATTTTTGCAAAATTTTAGACAAAATCGTGCACTATCCATCACGATTTTAAGCTAAAAACGCGTT
325 AATTTTTACAAAATTTTAGACAAAATCG-G----AT-CATCACGACTTTAAGCTAAAAACACGTT
* *
2688 TCGAGGCATCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTAAACTATATATATCCAT
384 TCGAGGCATCGACTCAGTTTTGCATGATTTTTGGCACAAAAACTCCTTAAACTATATATATCCAT
* * *
2753 TTGACCAAATCTCAGCCACTTTAGATTTAAGGATTTTTTTTTACGAGCATCTGAATCATGTTTCT
449 CTGACCAAATCTCAGCCACTTTAGATATAAGGATTTATTTTTACGAGCATCTGAATCATGTTTCT
* * * * *
2818 ATTTAATTCACAATTAATTCAGAAAAAATATTGGAAAAACGATATTAGAATCCTGAAAAACCCTT
514 ATTTAATTCAAAATTAATTAAGAAAAAATATTGGAAAAACAATATTAAAAGCCTGAAAAACCCTT
* *
2883 CAATCTTTTTGTCTTTGAATTATATTTTTTTTATGAGAATTGTGGCC-AAAAATTGAGGAAAAAT
579 CAAGCTTTTTGTCTTTGAATTATA--TTTTTTATGAGAATTGTGGCCAAAAAAATGAGGAAAAAT
*
2947 CTTT-CGGATC-AATTCAGC
642 -TTTCCGAATCAAATTCAGC
* * * * *
2965 AAAATTTTAGCCGAAATCATGTACTTTCCATCACAG-TTTTAAGCTAAAAAAGCGTTTCGGGGCC
1 AAAATTTTAGCCGAAATCATATACTTTCCATCA-AGACTTTAAACTAAAAAAGCGTTTCGGGACA
* * * * *
3029 CCGACTCAGTTTTGCATGA-TTTTTGGCAAGAAGACTTCTTGAAATATATATATTTTAATATTTA
65 CCGACTCAGTTTTGCATGACGTTTT-GCAAGAACAATCCTTG----A-A-ATA-TTT-ATATTCA
* *
3093 TCTAACCAAGTCTCAGCCACATTGGATTTAAGGA-TTTGTTTTTACGACCATTCGAATCATGTTT
121 TCTAACCAAATCTCAGCCACATTGGATTTAA-GATTTTGTTTTAACGACCATTCGAATCATGTTT
* ** * **
3157 CGATTTTATTTGAAATTAATTCAGAAAAAATTGGAAAAACGATATTAGAAGTGTGAAAAACCCTT
185 CGATTTAATTCAAAATTAATTCAGAAAAAATTGGAAAAACGATATTAAAAGCCTGAAAAACCCTT
*
3222 CAA-TCATTTTGGCTTTGAATTATTTATATT-T-TATGAGAGTTGTGGCCAAAAATTGAGGAAAA
250 CAACTCATTTTGGCTTTGAATTA--TATATTGTCTATGAGAATTGTGGCCAAAAATTGAGGAAAA
* *
3284 ATTTTCCGGATCAGTTTTTACAAAATTTTAG-CAGAAATC-G-T-ATCACGACTTTAAGCTAAAA
313 AATTTCCGGATCAATTTTTACAAAATTTTAGACA-AAATCGGATCATCACGACTTTAAGCTAAAA
* * * *
3345 ACACTTTTCG-GGACATCGACTTAGTTTTGCATGATTTTTTGCACAAAAACTCCTTGAAA-TATT
377 ACACGTTTCGAGG-CATCGACTCAGTTTTGCATGATTTTTGGCACAAAAACTCCTT-AAACTATA
* * * *
3408 TATATTCATCTGACCAAATCTCAGCCACTTTGGATATAAGGATTTATTTTTACGAGCATTTGTAT
440 TATATCCATCTGACCAAATCTCAGCCACTTTAGATATAAGGATTTATTTTTACGAGCATCTGAAT
3473 CATGTTTCTATTTAATTCAAAATTAATTAAG-AAAAA-ATTGGAAAAACAATATTAAAAGCCTGA
505 CATGTTTCTATTTAATTCAAAATTAATTAAGAAAAAATATTGGAAAAACAATATTAAAAGCCTGA
*
3536 AAAACCTTTCAAGCTTTTTGTCTTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAAAAATG
570 AAAACCCTTCAAGCTTTTTGTCTTTGAA-T-TATATTTTTTATGAGAATTGTGGCCAAAAAAATG
**
3601 AGGAAAAATTTTCCGAATCAAATTTTGC
633 AGGAAAAATTTTCCGAATCAAATTCAGC
3629 AAAATTTTAGCCGAAATC
1 AAAATTTTAGCCGAAATC
3647 CATGATGGTT
Statistics
Matches: 595, Mismatches: 66, Indels: 45
0.84 0.09 0.06
Matches are distributed among these distances:
662 74 0.12
663 29 0.05
664 183 0.31
665 3 0.01
666 5 0.01
667 82 0.14
668 2 0.00
671 2 0.00
672 3 0.01
673 80 0.13
674 4 0.01
675 126 0.21
676 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (660 bp):
AAAATTTTAGCCGAAATCATATACTTTCCATCAAGACTTTAAACTAAAAAAGCGTTTCGGGACAC
CGACTCAGTTTTGCATGACGTTTTGCAAGAACAATCCTTGAAATATTTATATTCATCTAACCAAA
TCTCAGCCACATTGGATTTAAGATTTTGTTTTAACGACCATTCGAATCATGTTTCGATTTAATTC
AAAATTAATTCAGAAAAAATTGGAAAAACGATATTAAAAGCCTGAAAAACCCTTCAACTCATTTT
GGCTTTGAATTATATATTGTCTATGAGAATTGTGGCCAAAAATTGAGGAAAAAATTTCCGGATCA
ATTTTTACAAAATTTTAGACAAAATCGGATCATCACGACTTTAAGCTAAAAACACGTTTCGAGGC
ATCGACTCAGTTTTGCATGATTTTTGGCACAAAAACTCCTTAAACTATATATATCCATCTGACCA
AATCTCAGCCACTTTAGATATAAGGATTTATTTTTACGAGCATCTGAATCATGTTTCTATTTAAT
TCAAAATTAATTAAGAAAAAATATTGGAAAAACAATATTAAAAGCCTGAAAAACCCTTCAAGCTT
TTTGTCTTTGAATTATATTTTTTATGAGAATTGTGGCCAAAAAAATGAGGAAAAATTTTCCGAAT
CAAATTCAGC
Found at i:8282 original size:14 final size:16
Alignment explanation
Indices: 8263--8299 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
8253 AGAAAACCCT
8263 TTGAAATT-CATT-AC
1 TTGAAATTCCATTGAC
8277 TTGAAATTCCATTGAC
1 TTGAAATTCCATTGAC
8293 -TGAAATT
1 TTGAAATT
8300 AAATTTAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 11 0.52
16 2 0.10
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (16 bp):
TTGAAATTCCATTGAC
Found at i:12353 original size:15 final size:16
Alignment explanation
Indices: 12333--12365 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12323 AGTAACCAGC
*
12333 AGAAGGTGGAGG-AGG
1 AGAAGGCGGAGGAAGG
12348 AGAAGGCGGAGGAAGG
1 AGAAGGCGGAGGAAGG
12364 AG
1 AG
12366 CAGCTGAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.36, C:0.03, G:0.58, T:0.03
Consensus pattern (16 bp):
AGAAGGCGGAGGAAGG
Found at i:19484 original size:21 final size:21
Alignment explanation
Indices: 19446--19485 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19436 TCCGCCAGGC
*
19446 CCACCAGGACCTCCCGGTGGT
1 CCACCAGGACCTCACGGTGGT
19467 CCACCAGGACC-CTACGGTG
1 CCACCAGGACCTC-ACGGTG
19486 ACCCGCCAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.17, C:0.42, G:0.28, T:0.12
Consensus pattern (21 bp):
CCACCAGGACCTCACGGTGGT
Found at i:31725 original size:22 final size:20
Alignment explanation
Indices: 31711--31751 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
31701 ATAATATTGG
31711 CAAATTCCTTGTATAAT-CT
1 CAAATTCCTTGTATAATACT
*
31730 CAATTTCCTTGTATAATACT
1 CAAATTCCTTGTATAATACT
31750 CA
1 CA
31752 TCGAAAATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
CAAATTCCTTGTATAATACT
Found at i:40009 original size:14 final size:14
Alignment explanation
Indices: 39990--40023 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
39980 TTTTATAATT
39990 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
40004 ATTTTATTTTTACT
1 ATTTTATTTTTACC
40018 ATTTTA
1 ATTTTA
40024 ATTTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:41243 original size:54 final size:54
Alignment explanation
Indices: 41178--41282 Score: 149
Period size: 54 Copynumber: 1.9 Consensus size: 54
41168 GCTTGTCAAA
* * *
41178 TGGATGATGATTTTAAGCTA-TTGCCTGAGCTACTTGATGACATGAAGAATTTAC
1 TGGATAATGATTTTAAGCTACTT-CCTGAGCCACCTGATGACATGAAGAATTTAC
* *
41232 TGGATAATGATTTTGAGCTACTTCCTGAGCCACCTGATGATATGAAGAATT
1 TGGATAATGATTTTAAGCTACTTCCTGAGCCACCTGATGACATGAAGAATT
41283 AATTGGATGC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
54 43 0.96
55 2 0.04
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (54 bp):
TGGATAATGATTTTAAGCTACTTCCTGAGCCACCTGATGACATGAAGAATTTAC
Found at i:50196 original size:21 final size:24
Alignment explanation
Indices: 50138--50217 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 24
50128 TTAGTAATTA
50138 AATATATATTATTTATTTATTT--T
1 AATATATATTA-TTATTTATTTAAT
*
50161 GAA-CTA-ATTATT-TATTATTTAA-
1 -AATATATATTATTAT-TTATTTAAT
50183 AATATAT-TTATTATTTATTTAAT
1 AATATATATTATTATTTATTTAAT
50206 AATATATATTAT
1 AATATATATTAT
50218 ATCTAAGATA
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
20 1 0.02
21 10 0.22
22 19 0.41
23 10 0.22
24 6 0.13
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (24 bp):
AATATATATTATTATTTATTTAAT
Found at i:50212 original size:25 final size:25
Alignment explanation
Indices: 50167--50215 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
50157 TTTTGAACTA
*
50167 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
50192 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
50216 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:56381 original size:21 final size:19
Alignment explanation
Indices: 56356--56412 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
56346 CGCTGCTCTA
* *
56356 ATAATTTCATATGTACAAT
1 ATAATCTCATCTGTACAAT
*
56375 ACCTAATCTAATCTGTACAAT
1 A--TAATCTCATCTGTACAAT
56396 ATAATCTCATCTGTACA
1 ATAATCTCATCTGTACA
56413 GTTTCTAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (19 bp):
ATAATCTCATCTGTACAAT
Found at i:70640 original size:17 final size:18
Alignment explanation
Indices: 70618--70652 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
70608 TTTGTCAAAT
70618 GAAGAGACAGAA-AGAAA
1 GAAGAGACAGAAGAGAAA
*
70635 GAAGAGAGAGAAGAGAAA
1 GAAGAGACAGAAGAGAAA
70653 CTGTGGATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.63, C:0.03, G:0.34, T:0.00
Consensus pattern (18 bp):
GAAGAGACAGAAGAGAAA
Found at i:81732 original size:7 final size:7
Alignment explanation
Indices: 81720--81750 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
81710 TTGCAAACCT
81720 CCACTTC
1 CCACTTC
81727 CCACTTC
1 CCACTTC
81734 CCACTTC
1 CCACTTC
81741 CCACTTC
1 CCACTTC
81748 CCA
1 CCA
81751 GGCATTAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.58, G:0.00, T:0.26
Consensus pattern (7 bp):
CCACTTC
Found at i:85468 original size:221 final size:222
Alignment explanation
Indices: 85074--85510 Score: 569
Period size: 221 Copynumber: 2.0 Consensus size: 222
85064 GATTTGACGT
* *
85074 GACTCAACTTTGGACTAGTCGGAATTCAATATGATTACTGAATACCAGAGGATTAACTTTCACAT
1 GACTCAACTTTGGACTAGTCGGAATTCAATATGATTACCGAATACCAGAGGATTAACTTTCACAG
* * *
85139 AATTGAGTTTAGAATGTCATCTCTCATGTTTAAGCCTAACTCGACTTATGAACAACTATTGTTTT
66 AATTGAGTTTAGAATGTCATCTCTCATGTTGAAGCCTAACTCGACCTATGAACAACTATTGCTTT
* * *
85204 AAAATAAATGGGCCTGAATTGTGCTCAAGCCCAACCTATGAACATTTCTATACTTGTAAATTGAT
131 AAAATAAATGGGCCTGAATTATGCTCAAACCCAACCTATGAACATTTCTATACATGTAAATTGAT
*
85269 GAAAATGTGAGGGCATTTTTTTTACGA
196 GAAAATATGAGGGCATTTTTTTTACGA
* * * * * * * *
85296 GACTCAATTTTGGAGTAGTTGGGATTCAATATGATTACCGAATATCGGAGGATTAAATTTTTCAT
1 GACTCAACTTTGGACTAGTCGGAATTCAATATGATTACCGAATACCAGAGGATT-AA-CTTTCAC
* * * *
85361 AGAATTGCGTTTAGAA-G-GA-CTCTTATGTTGAAGCCTAACTTGACCTATGAACAACTA-TGCT
64 AGAATTGAGTTTAGAATGTCATCTCTCATGTTGAAGCCTAACTCGACCTATGAACAACTATTGCT
* * * * *
85422 TTGAAATAAAATGGGCCTGAATTATGCTCAAATCCGACAC-ATGAACATTTTTATGCATGTAAAT
129 TTAAAAT-AAATGGGCCTGAATTATGCTCAAACCCAAC-CTATGAACATTTCTATACATGTAAAT
85486 TGATGAAAATATGAGGGCATTTTTT
192 TGATGAAAATATGAGGGCATTTTTT
85511 GGAAGTCAAC
Statistics
Matches: 185, Mismatches: 26, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
220 9 0.05
221 105 0.57
222 49 0.26
223 3 0.02
224 19 0.10
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (222 bp):
GACTCAACTTTGGACTAGTCGGAATTCAATATGATTACCGAATACCAGAGGATTAACTTTCACAG
AATTGAGTTTAGAATGTCATCTCTCATGTTGAAGCCTAACTCGACCTATGAACAACTATTGCTTT
AAAATAAATGGGCCTGAATTATGCTCAAACCCAACCTATGAACATTTCTATACATGTAAATTGAT
GAAAATATGAGGGCATTTTTTTTACGA
Found at i:86241 original size:226 final size:226
Alignment explanation
Indices: 85836--86299 Score: 687
Period size: 226 Copynumber: 2.1 Consensus size: 226
85826 AAACTCATGG
* * * *
85836 ACAACTATACTTTGAAGTAAATGGGTTTGAATTGGACTCGACCCCGACCCATGAACATTTTTGTG
1 ACAACTCTACTTTGAAGTAAATGGGCTTGAATTGGACTCGACCCCGACCCATGAACATTTCTATG
85901 CTTGTAAATTGATAAAAATATAAGGGCATTTTTAAAAAAGTTATAACTAAATTGCATACAATATC
66 CTTGTAAATTGATAAAAATATAAGGGCATTTTTAAAAAAGTTATAACTAAATTGCATACAATATC
*
85966 TTGATTCCATGATCAAGTTTGTAAGATCATCAATCTCTCCCGAAACCGAATCCATAAGATCATTC
131 TTGATTCCATGATCAAGTTTGTAAGATCATCAATCTCTCCCGAAACCGAATCCATAAGATCATCC
*
86031 TCACCTTTAACAGGTCTAACTCGACTCATAA
196 TCACCTTTAACAGGCCTAACTCGACTCATAA
* * * *
86062 ACAAACTCTACTTTGAAGTAAATGGGCTTGAATTGGGCTCGAGCCTGGCCCATGAACATTTCTAT
1 AC-AACTCTACTTTGAAGTAAATGGGCTTGAATTGGACTCGACCCCGACCCATGAACATTTCTAT
* * ** * * * *
86127 GCTTGTAAATTTATGAAGGTATGAGGGCATTTTT-TAAAAGTTGTAACTAAATTGTATACAATAT
65 GCTTGTAAATTGATAAAAATATAAGGGCATTTTTAAAAAAGTTATAACTAAATTGCATACAATAT
* * * *
86191 CTTGATTGCATGATCGAGTTTGTAAGATCATCAATCTCTCCCGGAACCGAATCCGTAAGATCATC
130 CTTGATTCCATGATCAAGTTTGTAAGATCATCAATCTCTCCCGAAACCGAATCCATAAGATCATC
* **
86256 CTCACGTTTAACAGGCCTAACTCGACTCATGG
195 CTCACCTTTAACAGGCCTAACTCGACTCATAA
86288 ACAACTCTACTT
1 ACAACTCTACTT
86300 CAATCCTCAC
Statistics
Matches: 212, Mismatches: 25, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
225 10 0.05
226 119 0.56
227 83 0.39
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (226 bp):
ACAACTCTACTTTGAAGTAAATGGGCTTGAATTGGACTCGACCCCGACCCATGAACATTTCTATG
CTTGTAAATTGATAAAAATATAAGGGCATTTTTAAAAAAGTTATAACTAAATTGCATACAATATC
TTGATTCCATGATCAAGTTTGTAAGATCATCAATCTCTCCCGAAACCGAATCCATAAGATCATCC
TCACCTTTAACAGGCCTAACTCGACTCATAA
Found at i:86325 original size:49 final size:49
Alignment explanation
Indices: 86253--86348 Score: 192
Period size: 49 Copynumber: 2.0 Consensus size: 49
86243 CCGTAAGATC
86253 ATCCTCACGTTTAACAGGCCTAACTCGACTCATGGACAACTCTACTTCA
1 ATCCTCACGTTTAACAGGCCTAACTCGACTCATGGACAACTCTACTTCA
86302 ATCCTCACGTTTAACAGGCCTAACTCGACTCATGGACAACTCTACTT
1 ATCCTCACGTTTAACAGGCCTAACTCGACTCATGGACAACTCTACTT
86349 TGAAGTAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.28, C:0.32, G:0.12, T:0.27
Consensus pattern (49 bp):
ATCCTCACGTTTAACAGGCCTAACTCGACTCATGGACAACTCTACTTCA
Found at i:104092 original size:16 final size:16
Alignment explanation
Indices: 104071--104102 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
104061 CATGAATCTT
*
104071 TGAAAAAGTAAATAAA
1 TGAAAAAATAAATAAA
104087 TGAAAAAATAAATAAA
1 TGAAAAAATAAATAAA
104103 AGAGGATCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (16 bp):
TGAAAAAATAAATAAA
Found at i:104346 original size:15 final size:15
Alignment explanation
Indices: 104328--104358 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
104318 AGATCGATCA
104328 TACCAGGTTCGAATT
1 TACCAGGTTCGAATT
*
104343 TACCGGGTTCGAATT
1 TACCAGGTTCGAATT
104358 T
1 T
104359 TGGGGAACCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (15 bp):
TACCAGGTTCGAATT
Found at i:109880 original size:14 final size:14
Alignment explanation
Indices: 109861--109892 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
109851 GTGAAGGAGT
109861 ATATATATAAAAGA
1 ATATATATAAAAGA
109875 ATATATATAAAAGA
1 ATATATATAAAAGA
109889 ATAT
1 ATAT
109893 TTCATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (14 bp):
ATATATATAAAAGA
Found at i:110411 original size:22 final size:20
Alignment explanation
Indices: 110380--110427 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
110370 ATTTTTCAAA
110380 AAAAAATTAAAAACTACAAACT
1 AAAAAATTAAAAACTA-AAA-T
* *
110402 AAAAATTTAAAATCTAAAAT
1 AAAAAATTAAAAACTAAAAT
110422 AAAAAA
1 AAAAAA
110428 GGATATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.26
21 3 0.13
22 14 0.61
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAAAATTAAAAACTAAAAT
Done.