Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018376.1 Corchorus olitorius cultivar O-4 contig18409, 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: 43852
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1270 original size:325 final size:322
Alignment explanation
Indices: 1--2145 Score: 2427
Period size: 325 Copynumber: 6.5 Consensus size: 322
** * *
1 TTTTTTTTTCCTCAGAATTAA-TTTTTATTAAATGGAACCATGATTCAGATGCTCGTAAAAACAA
1 TTTTTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGCTCGTAAAAACAA
** *
65 ATCCTTAAATTCAAAATGAATGTGATTTGGTTAGATTAAAATAGATATTTCAAGGAGTCATGGCA
66 ATCCTTAAATTCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGTCATGG-A
* *
130 -CCAAAAATCATGCAAAATTGAGCCGAGTACTCGGAACGCG-TTTTAGCAAAAAACCGTGATGGT
130 GCCAAAAATCATGCAAAATTGAGCCG-GT-CCCGGAACGCGTTTTTAGC-AAAAACCGTGAAGGT
*
193 TAGTACACGATTTTGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTC-ATTTTTGGC
192 TAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTGGC
* * *
257 CACAATACTCATAAAGAATAACTAATTCAAAGCCAAAAAGACTGAAGGTCTTTTCACGCTTCTTT
257 CACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGTGTTTTCACGCTTCTTA
322 G
322 G
* *
323 TTGTTTTTTTTTT-CGAATTAATTTTTTATTATAT-GTAACCATGATTCAGATGCTTGTAAAAAC
1 TT-TTTTTTTTTTCCGAATTAATTTTTTATTAAATCG-AACCATGATTCAGATGCTCGTAAAAAC
* *
386 AAATCCTTAAATTCAAAATGGTTGAGATTTGGTTAGATTAACAA-AGATATTTCAATGAGTCATG
64 AAATCCTTAAATTCAAAATGGCTGAGATTTGGTTAGATTAA-AATAGATATTTCAAGGAGTCATG
* * * * *
450 ACAG-CAAAAATCATGCAAAATTGAACAGGGTCCCCTGAACGCGTTTTTAGGCAAAAACCGTGAT
128 -GAGCCAAAAATCATGCAAAATTGAGC-CGGT-CCCGGAACGCGTTTTTA-GCAAAAACCGTGAA
* *
514 GCTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGAATTTTCCTCAATTTTT
189 GGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTT
* * *
579 GGCCATAATACTCATAAAGAATATCTAATTCAAAGCCAAAACGACTGAAGGTCTTTTCACGCTTC
254 GGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGTGTTTTCACGCTTC
644 TTAGTTG
319 TTA---G
*
651 TTTTTCTTTTTTTAAAAAAAAAATTTTCTGAATTAATTTTTTATTAAATCGAACCATGATTCAGA
1 ----T-TTTTTTT----------TTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTCAGA
* *
716 TGCTCGTAAAAACAAATCCGTAAATTCAAAATGGCTGTGATTTGGTTAGATTAAAATAGATATTT
51 TGCTCGTAAAAACAAATCCTTAAATTCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTT
*
781 CAAGGAGTCATGGAGCCAAAAATCATGCAAAATTGAGCCGGGTACCCGGAACGCGTTTGTAGCAG
116 CAAGGAGTCATGGAGCCAAAAATCATGCAAAATTGAGCC-GGT-CCCGGAACGCGTTTTTAGCA-
** *
846 AAAACCGTGGTGGTTAGTACACGATTTCGGCTACAATTTTGCTAAAATTGACCCGAAAGATTTTT
178 AAAACCGTGAAGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTT
*
911 CCTCAATTTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACAGAAGGTGT
243 CCTCAATTTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGTGT
976 TTTCACGCTTCTTAG
308 TTTCACGCTTCTTAG
* *
991 TTTTTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGC-CTTTTAAAA-A
1 TTTTTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGCTC-GTAAAAACA
*
1054 AATACCTTAAATTCAAAATGGCTGTGATTTGGTTAGATTAAAATAGATATTTCAAGGAGTCATGG
65 AAT-CCTTAAATTCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGTCATGG
1119 AGCCAAAAATCATGCAAAATTGAGCCAGGTCCCGGGAACGCGTTTTTAGCTAAAAACCGTGAAGG
129 AGCCAAAAATCATGCAAAATTGAGCC-GGTCCC-GGAACGCGTTTTTAGC-AAAAACCGTGAAGG
** * * * *
1184 TTAGTACACGATTTTTGCTAAAATTTAGCAAAAATTGACTCGAAA-AGTTTTTCCTCAGTTTTTG
191 TTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGA-TTTTTCCTCAATTTTTG
* *
1248 GCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGACG-CTTCACGCTTC
255 GCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGG-TGTTTTCACGCTTC
*
1312 TAATATTAAT
319 -----TT-AG
* * * * *
1322 TTTCTTTTTTTTTCCGAAATAATTTTTTATTATATCGAATCATGATTCTA-TTGCACGTAAAAAC
1 TTT-TTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTC-AGATGCTCGTAAAAAC
* ** * * *
1386 AAATCCTTAAATCCAATGTGACTGAGATTT-GTTAGATTAAAGTTGATATTTCAAGGAGTCATGG
64 AAATCCTTAAATTCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGTCATGG
* ** ** * *
1450 CGCCTCAAATCATGCAAAATTGAGTTGCGTCCCCGGAACTCGTTTTTTGCCAAAAACCGTG-A--
129 AGCCAAAAATCATGCAAAATTGAGCCG-GT-CCCGGAACGCGTTTTTAG-CAAAAACCGTGAAGG
* * * * * *
1512 -TGGTACACGATTTCGGGTACAATTTTGCCAAAATTGACTCGAAAGATTTTTCCTCATTTTTTAG
191 TTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTGG
* * * * * * * *
1576 CCACAATACTCATAAAAAATATATAATTCAACGCCATAAATA-TTAAAGTGCTTTTCACGATTCT
256 CCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGTG-TTTTCACGCTTCT
1640 AATATCG
320 --TA--G
* * * **
1647 TTTTTCCTACTTTTTT-CGAATTAATTTCTAATTAAATCGAAAC-TCGATTCTTATGCTCGTAAA
1 TTTTT--T--TTTTTTCCGAATTAATTTTTTATTAAATCGAACCAT-GATTCAGATGCTCGTAAA
** * *
1710 AACAAATCCTTAAA-T-AAAATGTGGCTGAGATTTGAATAGATTAAAATGGATATTTCAAGGAAT
61 AACAAATCCTTAAATTCAAAA--TGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
* * * * * *
1773 CATGGCGCAAAAAATCTTACAAAATTGAGCCGGTCCCAGGAAGGCGTTTTTAGTTAAAAACCGTG
124 CATGGAGCCAAAAATCATGCAAAATTGAGCCGGTCCC-GGAACGCGTTTTTAG-CAAAAACCGTG
* * * *
1838 AATGTTAATACACGATTTCGTCTAAAATTTTGCAAAAATTGACCCGAAAG-TTTTTCCTCAATTT
187 AAGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTT
* *
1902 TTGGCCACAAATACTCATAAAAAATACCTAATTCAAAGCCAAAAAGACTGAAGG-GCTTTTCACG
252 TTGGCCAC-AATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGTG-TTTTCACG
1966 CTTCTAATA-
315 CTTCT--TAG
** * ** *
1975 TGGTTTTTTTTTCCGAATTAATTTTTTATTAAATCAAATTATGATTTTA-ATGCTCGTAAAAACA
1 TTTTTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGA-TTCAGATGCTCGTAAAAACA
* * * * * * *
2039 AATCCTTAAATCCAATATGGTTGAGATTTGGTTAGATTAAAACAGATATTTTAAGGAGTCTTGGC
65 AATCCTTAAATTCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGTCATGGA
* *
2104 GCCAAAAGTCATGCAAAATTTAGCCGGGTCCTCGGAACGCGT
130 GCCAAAAATCATGCAAAATTGAGCC-GGTCC-CGGAACGCGT
2146 AAGAAAATGA
Statistics
Matches: 1567, Mismatches: 173, Indels: 162
0.82 0.09 0.09
Matches are distributed among these distances:
322 11 0.01
323 136 0.09
324 93 0.06
325 465 0.30
326 28 0.02
327 188 0.12
328 61 0.04
330 24 0.02
331 171 0.11
332 85 0.05
333 7 0.00
335 7 0.00
336 1 0.00
340 1 0.00
342 11 0.01
343 277 0.18
344 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (322 bp):
TTTTTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGCTCGTAAAAACAA
ATCCTTAAATTCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGTCATGGAG
CCAAAAATCATGCAAAATTGAGCCGGTCCCGGAACGCGTTTTTAGCAAAAACCGTGAAGGTTAGT
ACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTGGCCACA
ATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGTGTTTTCACGCTTCTTAG
Found at i:1295 original size:668 final size:649
Alignment explanation
Indices: 1--2145 Score: 2591
Period size: 668 Copynumber: 3.3 Consensus size: 649
*
1 TTTTTTTTTCCTCAGAATTAA-TTTTTATTAAATGGAACCATGATTCAGATGCTCGTAAAAACAA
1 TTTTTTTTT-C-C-GAATTAATTTTTTATTAAATCGAACCATGATTCA-ATGCTCGTAAAAACAA
* * *
65 ATCCTTAAATTCAAAATGAATGTGATTTGGTTAGATTAAAATAGATATTTCAAGGAGTCATGGCA
62 ATCCTTAAATCCAAAATGACTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGTCATGG-A
* *
130 -CCAAAAATCATGCAAAATTGAGCCGAGTACTCGGAACGCGTTTTAGCAAAAAACCGTGATGGTT
126 GCCAAAAATCATGCAAAATTGAGCCGGGTACCCGGAACGCGTTTTAGC-AAAAACCGTGATGGTT
*
194 AGTACACGATTTTGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTC-ATTTTTGGCC
190 AGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTGGCC
* * * *
258 ACAATACTCATAAAGAATAACTAATTCAAAGCCAAAAAGACTGAAGGTCTTTTCACGCTTCTTTG
255 ACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACAGAAGGTGTTTTCACGCTTCTTAG
*
323 TTGTTTTTTTTTTCGAATTAATTTTTTATTATAT-GTAACCATGATTCAGATGCTTGTAAAAACA
320 TT-TTTTTTTTTTCGAATTAATTTTTTATTAAATCG-AACCATGATTCAGATGCTTGTAAAAACA
* *
387 AATCCTTAAATTCAAAATGGTTGAGATTTGGTTAGATTAACAA-AGATATTTCAATGAGTCATGA
383 AATCCTTAAATTCAAAATGGCTGAGATTTGGTTAGATTAA-AATAGATATTTCAAGGAGTCATG-
* * **
451 CAG-CAAAAATCATGCAAAATTGA-ACAGGGTCCCCTGAACGCGTTTTTAGGC-AAAAACCGTGA
446 GAGCCAAAAATCATGCAAAATTGAGCCA-GGTCCCAGGAACGCGTTTTTA-GCTAAAAACCGTGA
* * * *
513 TGCTTAGTACACGA-TTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGAATTTTCCTCAATTT
509 AGGTTAGTACACGATTTTC-GCTAAAATTTTGCAAAAATTGACCCGAAAG-TTTTTCCTCAATTT
* * *
577 TTGGCCATAATACTCATAAAGAATATCTAATTCAAAGCCAAAACGACTGAAGGTCTTTTCACGCT
572 TTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGACTTTTCACGCT
642 TCTTAGTTGTTTTTC
637 TCTTA-TTG-TTTTC
*
657 TTTTTTTAAAAAAAAAATTTTCTGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGCTCG
1 --TTTTT----------TTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTCA-ATGCTCG
* * * *
722 TAAAAACAAATCCGTAAATTCAAAATGGCTGTGATTTGGTTAGATTAAAATAGATATTTCAAGGA
53 TAAAAACAAATCCTTAAATCCAAAATGACTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGA
787 GTCATGGAGCCAAAAATCATGCAAAATTGAGCCGGGTACCCGGAACGCGTTTGTAGCAGAAAACC
118 GTCATGGAGCCAAAAATCATGCAAAATTGAGCCGGGTACCCGGAACGCGTTT-TAGCA-AAAACC
* *
852 GTGGTGGTTAGTACACGATTTCGGCTACAATTTTGCTAAAATTGACCCGAAAGATTTTTCCTCAA
181 GTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAA
917 TTTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACAGAAGGTGTTTTCAC
246 TTTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACAGAAGGTGTTTTCAC
982 GCTTCTTAGTTTTTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGCCTT
311 GCTTCTTAGTTTTTTTTTTTT-CGAATTAATTTTTTATTAAATCGAACCATGATTCAGATG-CTT
* *
1047 -TTAAAA-AAATACCTTAAATTCAAAATGGCTGTGATTTGGTTAGATTAAAATAGATATTTCAAG
374 GTAAAAACAAAT-CCTTAAATTCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAG
*
1110 GAGTCATGGAGCCAAAAATCATGCAAAATTGAGCCAGGTCCCGGGAACGCGTTTTTAGCTAAAAA
438 GAGTCATGGAGCCAAAAATCATGCAAAATTGAGCCAGGTCCCAGGAACGCGTTTTTAGCTAAAAA
* * *
1175 CCGTGAAGGTTAGTACACGATTTTTGCTAAAATTTAGCAAAAATTGACTCGAAAAGTTTTTCCTC
503 CCGTGAAGGTTAGTACACGATTTTCGCTAAAATTTTGCAAAAATTGACCCG-AAAGTTTTTCCTC
* **
1240 AGTTTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGACGCTTC
567 AATTTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGACTTTTC
*
1305 ACGCTTCTAATATTAATTTTC
632 ACGCTTCT--TATT-GTTTTC
* * * * *
1326 TTTTTTTTTCCGAAATAATTTTTTATTATATCGAATCATGATTCTATTGCACGTAAAAACAAATC
1 TTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTC-AATGCTCGTAAAAACAAATC
** * * * *
1391 CTTAAATCCAATGTGACTGAGATTT-GTTAGATTAAAGTTGATATTTCAAGGAGTCATGGCGCCT
65 CTTAAATCCAAAATGACTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGTCATGGAGCCA
* ** * * * *
1455 CAAATCATGCAAAATTGAGTTGCGTCCCCGGAACTCGTTTTTTGCCAAAAACCGTGAT-G---GT
130 AAAATCATGCAAAATTGAGCCGGGTACCCGGAACGCG-TTTTAG-CAAAAACCGTGATGGTTAGT
* * * * *
1516 ACACGATTTCGGGTACAATTTTGCCAAAATTGACTCGAAAGATTTTTCCTCATTTTTTAGCCACA
193 ACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTGGCCACA
* * * * * * *
1581 ATACTCATAAAAAATATATAATTCAACGCCATAAATATTA-AA-GTGCTTTTCACGATTCTAATA
258 ATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGA-CAGAAGGTG-TTTTCACGCTTCT--TA
* * * ** *
1644 TCGTTTTTCCTACTTTTTTCGAATTAATTTCTAATTAAATCGAAAC-TCGATTCTTATGCTCGTA
319 --GTTTTT--T--TTTTTTCGAATTAATTTTTTATTAAATCGAACCAT-GATTCAGATGCTTGTA
** *
1708 AAAACAAATCCTTAAA-T-AAAATGTGGCTGAGATTTGAATAGATTAAAATGGATATTTCAAGGA
377 AAAACAAATCCTTAAATTCAAAA--TGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGA
* * * * * * *
1771 ATCATGGCGCAAAAAATCTTACAAAATTGAGCC-GGTCCCAGGAAGGCGTTTTTAGTTAAAAACC
440 GTCATGGAGCCAAAAATCATGCAAAATTGAGCCAGGTCCCAGGAACGCGTTTTTAGCTAAAAACC
* *
1835 GTGAATGTTAATACACGA-TTTCGTCTAAAATTTTGCAAAAATTGACCCGAAAGTTTTTCCTCAA
505 GTGAAGGTTAGTACACGATTTTCG-CTAAAATTTTGCAAAAATTGACCCGAAAGTTTTTCCTCAA
* * *
1899 TTTTTGGCCACAAATACTCATAAAAAATACCTAATTCAAAGCCAAAAAGACTGAAGGGCTTTTCA
569 TTTTTGGCCAC-AATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGACTTTTCA
* *
1964 CGCTTCTAATATG----G
633 CGCTTCTTAT-TGTTTTC
* ** *
1978 TTTTTTTTTCCGAATTAATTTTTTATTAAATCAAATTATGATTTTAATGCTCGTAAAAACAAATC
1 TTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGA-TTCAATGCTCGTAAAAACAAATC
* ** * * * *
2043 CTTAAATCCAATATGGTTGAGATTTGGTTAGATTAAAACAGATATTTTAAGGAGTCTTGGCGCCA
65 CTTAAATCCAAAATGACTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGTCATGGAGCCA
* *
2108 AAAGTCATGCAAAATTTAGCCGGGT-CCTCGGAACGCGT
130 AAAATCATGCAAAATTGAGCCGGGTACC-CGGAACGCGT
2146 AAGAAAATGA
Statistics
Matches: 1306, Mismatches: 129, Indels: 110
0.85 0.08 0.07
Matches are distributed among these distances:
651 3 0.00
652 188 0.14
653 63 0.05
654 2 0.00
655 1 0.00
656 86 0.07
657 110 0.08
658 133 0.10
659 108 0.08
660 10 0.01
665 8 0.01
666 144 0.11
667 96 0.07
668 332 0.25
669 20 0.02
670 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (649 bp):
TTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTCAATGCTCGTAAAAACAAATCC
TTAAATCCAAAATGACTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGTCATGGAGCCAA
AAATCATGCAAAATTGAGCCGGGTACCCGGAACGCGTTTTAGCAAAAACCGTGATGGTTAGTACA
CGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTGGCCACAATA
CTCATAAAGAATATCTAATTCAAAGCCAAAAAGACAGAAGGTGTTTTCACGCTTCTTAGTTTTTT
TTTTTTCGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGCTTGTAAAAACAAATCCTTA
AATTCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGTCATGGAGCCAAAAA
TCATGCAAAATTGAGCCAGGTCCCAGGAACGCGTTTTTAGCTAAAAACCGTGAAGGTTAGTACAC
GATTTTCGCTAAAATTTTGCAAAAATTGACCCGAAAGTTTTTCCTCAATTTTTGGCCACAATACT
CATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGACTTTTCACGCTTCTTATTGTTTTC
Found at i:2048 original size:984 final size:978
Alignment explanation
Indices: 1--2145 Score: 2701
Period size: 984 Copynumber: 2.2 Consensus size: 978
*
1 TTTTTTTTTCCTCAGAATTAA-TTTTTATTAAATGGAACCATGATTCAGATGCTCGTAAAAACAA
1 TTTTTTTTT-C-C-GAATTAATTTTTTATTAAATCGAACCATGATTCAGATGCTCGTAAAAACAA
*
65 ATCCTTAAATTCAAAATGAATGTGATTTGGTTAGATTAAAATAGATATTTCAAGGAGTCATGGCA
63 ATCCTTAAATTCAAAATGGATGTGATTTGGTTAGATTAAAATAGATATTTCAAGGAGTCATGG-A
* *
130 -CCAAAAATCATGCAAAATTGAGCCGAGTACTCGGAACGCG-TTTTAGCAAAAAACCGTGATGGT
127 GCCAAAAATCATGCAAAATTGAGCCG-GT-CCCGGAACGCGTTTTTAGCAAAAAACCGTGAAGGT
* *
193 TAGTACACGATTTTGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCATTTTTGGCC
190 TAGTACACGATTTTGGCTAAAATTTAGCAAAAATTGACCCGAAAGATTTTTCCTCATTTTTGGCC
* ** *
258 ACAATACTCATAAAGAATAACTAATTCAAAGCCAAAAAGACTGAAGGTCTTTTCACGCTTCTTTG
255 ACAATACTCATAAAGAATAACTAATTCAAAGCCAAAAAGACTGAAGGACGCTTCACGCTTCTTTA
* **
323 TTGTTTTTTTTTTCGAATTAATTTTTTATTATATGTAACCATGATTCAGATGCTTGTAAAAACAA
320 TTGTTTTTTTTTTCGAAATAATTTTTTATTATATGTAACCATGATTCAGATGCACGTAAAAACAA
* ** *
388 ATCCTTAAATTCAAAATGGTTGAGATTTGGTTAGATTAACAAAGATATTTCAATGAGTCATGACA
385 ATCCTTAAATCCAAAATGACTGAGATTTGGTTAGATTAACAAAGATATTTCAAGGAGTCATGACA
* * *
453 GCAAAAATCATGCAAAATTGAACAGGGTCCCCTGAACGCGTTTTTAGGCAAAAACCGTGATGCTT
450 GCAAAAATCATGCAAAATTGAACAGCGTCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATG--T
*
518 AGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGAATTTTCCTCAATTTTTGGCC
513 -GTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGAATTTTCCTCAATTTTTAGCC
* * * * *
583 ATAATACTCATAAAGAATATCTAATTCAAAGCCAAAACGACTGAAGGTCTTTTCACGCTTCTTAG
577 ACAATACTCATAAAAAATATATAATTCAAAGCCAAAACGACTAAAGGTCTTTTCACGATTCTTAG
* * ** * * *
648 TTGTTTTTCTTTTTTTAAAAAAAAAATTTTCTGAATTAATTTTTTATTAAATCGAACCATGATTC
642 TCGTTTTTCTCTACTT---------ATTTTCTGAATTAATTTCTAATTAAATCGAAACATGATTC
* **
713 AGATGCTCGTAAAAACAAATCCGTAAATTCAAAATGGCTGTGATTTGGTTAGATTAAAATAGATA
698 AGATGCTCGTAAAAACAAATCCGTAAATTCAAAATGGCTGAGATTTGAATAGATTAAAATAGATA
* * *
778 TTTCAAGGAGTCATGGAGCCAAAAATCATGCAAAATTGAGCCGGGTACCCGGAACGCGTTTGTAG
763 TTTCAAGGAATCATGGAGCAAAAAATCATACAAAATTGAGCCGGGTACCCGGAACGCGTTTGTAG
* * * *
843 CAGAAAACCGTGGTGGTTAGTACACGATTTCGGCTACAATTTTGCTAAAATTGACCCGAAAGATT
828 CAGAAAACCGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATT
* *
908 TTTCCTCAATTTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACAGAAGG
893 TTTCCTCAATTTTTGGCCACAATACTCATAAAAAATACCTAATTCAAAGCCAAAAAGACAGAAGG
**
973 TGTTTTCACGCTTCTTAGTTT
958 TGTTTTCACGCTTCTTAGTGG
* *
994 TTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGC-CTTTTAAAA-AAAT
1 TTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGCTC-GTAAAAACAAAT
*
1057 ACCTTAAATTCAAAATGGCTGTGATTTGGTTAGATTAAAATAGATATTTCAAGGAGTCATGGAGC
65 -CCTTAAATTCAAAATGGATGTGATTTGGTTAGATTAAAATAGATATTTCAAGGAGTCATGGAGC
*
1122 CAAAAATCATGCAAAATTGAGCCAGGTCCCGGGAACGCGTTTTTAGCTAAAAACCGTGAAGGTTA
129 CAAAAATCATGCAAAATTGAGCC-GGTCCC-GGAACGCGTTTTTAGCAAAAAACCGTGAAGGTTA
* *
1187 GTACACGATTTTTGCTAAAATTTAGCAAAAATTGACTCGAAA-AGTTTTTCCTCAGTTTTTGGCC
192 GTACACGATTTTGGCTAAAATTTAGCAAAAATTGACCCGAAAGA-TTTTTCCTCA-TTTTTGGCC
*
1251 ACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGACGCTTCACGCTTCTAAT
255 ACAATACTCATAAAGAATAACTAATTCAAAGCCAAAAAGACTGAAGGACGCTTCACGCTTC---T
* * *
1316 ATTAATTTTCTTTTTTTTTCCGAAATAATTTTTTATTATATCG-AATCATGATTCTA-TTGCACG
317 -TT-ATTGT-TTTTTTTTT-CGAAATAATTTTTTATTATAT-GTAACCATGATTC-AGATGCACG
** **
1379 TAAAAACAAATCCTTAAATCCAATGTGACTGAGATTT-GTTAGATTAA-AGTTGATATTTCAAGG
376 TAAAAACAAATCCTTAAATCCAAAATGACTGAGATTTGGTTAGATTAACA-AAGATATTTCAAGG
* ** *** * *
1442 AGTCATGGC-GCCTCAAATCATGCAAAATTGAGTTGCGTCCCCGGAACTCGTTTTTTGCCAAAAA
440 AGTCATGACAG-CAAAAATCATGCAAAATTGAACAGCGTCCCCGGAACGCGTTTTTAGCCAAAAA
* * * * *
1506 CCGTGATG-GTACACGATTTCGGGTACAATTTTGCCAAAATTGACTCGAAAGATTTTTCCTCATT
504 CCGTGATGTGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGAATTTTCCTCAAT
* * *
1570 TTTTAGCCACAATACTCATAAAAAATATATAATTCAACGCCATAAA-TATTAAA-GTGCTTTTCA
569 TTTTAGCCACAATACTCATAAAAAATATATAATTCAAAGCCA-AAACGACTAAAGGT-CTTTTCA
1633 CGATTCTAATA-TCGTTTTTC-CTACTT-TTTTC-GAATTAATTTCTAATTAAATCGAAAC-TCG
632 CGATTCT--TAGTCGTTTTTCTCTACTTATTTTCTGAATTAATTTCTAATTAAATCGAAACAT-G
** *
1693 ATTCTTATGCTCGTAAAAACAAATCCTTAAA-T-AAAATGTGGCTGAGATTTGAATAGATTAAAA
694 ATTCAGATGCTCGTAAAAACAAATCCGTAAATTCAAAA--TGGCTGAGATTTGAATAGATTAAAA
* * * *
1756 TGGATATTTCAAGGAATCATGGCGCAAAAAATCTTACAAAATTGAGCC-GGT-CCCAGGAAGGCG
757 TAGATATTTCAAGGAATCATGGAGCAAAAAATCATACAAAATTGAGCCGGGTACCC-GGAACGCG
* * *
1819 TTTTTAGTTA-AAAACCGTGAAT-GTTAATACACGATTTCGTCTAAAATTTTGCAAAAATTGACC
821 TTTGTAG-CAGAAAACCGTG-ATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAATTGACC
1882 CGAAAG-TTTTTCCTCAATTTTTGGCCACAAATACTCATAAAAAATACCTAATTCAAAGCCAAAA
884 CGAAAGATTTTTCCTCAATTTTTGGCCAC-AATACTCATAAAAAATACCTAATTCAAAGCCAAAA
*
1946 AGACTGAAGG-GCTTTTCACGCTTCTAATA-TGG
948 AGACAGAAGGTG-TTTTCACGCTTCT--TAGTGG
* ** *
1978 TTTTTTTTTCCGAATTAATTTTTTATTAAATCAAATTATGATTTTA-ATGCTCGTAAAAACAAAT
1 TTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGA-TTCAGATGCTCGTAAAAACAAAT
* * * * * * * *
2042 CCTTAAATCCAATATGGTTGAGATTTGGTTAGATTAAAACAGATATTTTAAGGAGTCTTGGCGCC
65 CCTTAAATTCAAAATGGATGTGATTTGGTTAGATTAAAATAGATATTTCAAGGAGTCATGGAGCC
* *
2107 AAAAGTCATGCAAAATTTAGCCGGGTCCTCGGAACGCGT
130 AAAAATCATGCAAAATTGAGCC-GGTCC-CGGAACGCGT
2146 AAGAAAATGA
Statistics
Matches: 1009, Mismatches: 105, Indels: 85
0.84 0.09 0.07
Matches are distributed among these distances:
982 30 0.03
983 125 0.12
984 257 0.25
985 16 0.02
990 15 0.01
991 130 0.13
992 73 0.07
993 75 0.07
994 2 0.00
995 108 0.11
996 12 0.01
997 4 0.00
998 5 0.00
999 89 0.09
1000 66 0.07
1001 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (978 bp):
TTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGCTCGTAAAAACAAATC
CTTAAATTCAAAATGGATGTGATTTGGTTAGATTAAAATAGATATTTCAAGGAGTCATGGAGCCA
AAAATCATGCAAAATTGAGCCGGTCCCGGAACGCGTTTTTAGCAAAAAACCGTGAAGGTTAGTAC
ACGATTTTGGCTAAAATTTAGCAAAAATTGACCCGAAAGATTTTTCCTCATTTTTGGCCACAATA
CTCATAAAGAATAACTAATTCAAAGCCAAAAAGACTGAAGGACGCTTCACGCTTCTTTATTGTTT
TTTTTTTCGAAATAATTTTTTATTATATGTAACCATGATTCAGATGCACGTAAAAACAAATCCTT
AAATCCAAAATGACTGAGATTTGGTTAGATTAACAAAGATATTTCAAGGAGTCATGACAGCAAAA
ATCATGCAAAATTGAACAGCGTCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGTGTACACGA
TTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGAATTTTCCTCAATTTTTAGCCACAATACTC
ATAAAAAATATATAATTCAAAGCCAAAACGACTAAAGGTCTTTTCACGATTCTTAGTCGTTTTTC
TCTACTTATTTTCTGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAA
ATCCGTAAATTCAAAATGGCTGAGATTTGAATAGATTAAAATAGATATTTCAAGGAATCATGGAG
CAAAAAATCATACAAAATTGAGCCGGGTACCCGGAACGCGTTTGTAGCAGAAAACCGTGATGGTT
AATACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTGGCC
ACAATACTCATAAAAAATACCTAATTCAAAGCCAAAAAGACAGAAGGTGTTTTCACGCTTCTTAG
TGG
Found at i:2204 original size:21 final size:21
Alignment explanation
Indices: 2175--2215 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2165 CAAAAAAGTC
2175 AAAAATGGGGCGGTAGTTAGT
1 AAAAATGGGGCGGTAGTTAGT
* *
2196 AAAACTGGGGCGGTATTTAG
1 AAAAATGGGGCGGTAGTTAG
2216 CAATTCCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.07, G:0.37, T:0.24
Consensus pattern (21 bp):
AAAAATGGGGCGGTAGTTAGT
Found at i:2986 original size:73 final size:73
Alignment explanation
Indices: 2867--3015 Score: 298
Period size: 73 Copynumber: 2.0 Consensus size: 73
2857 AAATTAAGCA
2867 TTTAGCCGAAAAGACCATGAACAGAAGGATATAAAACAAAGGAAAACCTATTATTTTGCAATATG
1 TTTAGCCGAAAAGACCATGAACAGAAGGATATAAAACAAAGGAAAACCTATTATTTTGCAATATG
2932 CATCAAGT
66 CATCAAGT
2940 TTTAGCCGAAAAGACCATGAACAGAAGGATATAAAACAAAGGAAAACCTATTATTTTGCAATATG
1 TTTAGCCGAAAAGACCATGAACAGAAGGATATAAAACAAAGGAAAACCTATTATTTTGCAATATG
3005 CATCAAGT
66 CATCAAGT
3013 TTT
1 TTT
3016 CTTCCGGATA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (73 bp):
TTTAGCCGAAAAGACCATGAACAGAAGGATATAAAACAAAGGAAAACCTATTATTTTGCAATATG
CATCAAGT
Found at i:6941 original size:2 final size:2
Alignment explanation
Indices: 6936--6974 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
6926 CTCCTGTGTG
6936 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
6975 CATTCATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15807 original size:139 final size:139
Alignment explanation
Indices: 15591--15868 Score: 529
Period size: 139 Copynumber: 2.0 Consensus size: 139
15581 AATGTTTTGG
* *
15591 AATGGTGATGAAGTTGAGATAGTTTATGCTGACACGAGACCATTCAAAGTGGAATCTAATGTTGT
1 AATGGTGATGAAGTTGAGATAGTTTATGCTGACACGAGACCATTCAAAGTGGAATCAAATGCTGT
*
15656 GGAGGCAAGATACTATGATGAATCTATTGGCACCACCCGTTTCCTAGGGCAAGACAAGTTTGGGC
66 GGAGGCAAGATACTATGATGAATCTATTGGCACCACCCGTTTCCTAGGGCAAGACAAGTTTGGGA
15721 GACCCATGC
131 GACCCATGC
15730 AATGGTGATGAAGTTGAGATAGTTTATGCTGACACGAGACCATTCAAAGTGGAATCAAATGCTGT
1 AATGGTGATGAAGTTGAGATAGTTTATGCTGACACGAGACCATTCAAAGTGGAATCAAATGCTGT
15795 GGAGGCAAGATACTATGATGAATCTATTGGCACCACCCGTTTCCTAGGGCAAGACAAGTTTGGGA
66 GGAGGCAAGATACTATGATGAATCTATTGGCACCACCCGTTTCCTAGGGCAAGACAAGTTTGGGA
15860 GACCCATGC
131 GACCCATGC
15869 CCATAGTGCC
Statistics
Matches: 136, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
139 136 1.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (139 bp):
AATGGTGATGAAGTTGAGATAGTTTATGCTGACACGAGACCATTCAAAGTGGAATCAAATGCTGT
GGAGGCAAGATACTATGATGAATCTATTGGCACCACCCGTTTCCTAGGGCAAGACAAGTTTGGGA
GACCCATGC
Found at i:30621 original size:6 final size:6
Alignment explanation
Indices: 30612--30636 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
30602 AGCAAAAGCA
30612 AAACCC AAACCC AAACCC AAACCC A
1 AAACCC AAACCC AAACCC AAACCC A
30637 GTTTCCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACCC
Found at i:37654 original size:29 final size:29
Alignment explanation
Indices: 37574--37642 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
37564 ACGTGTCACC
*
37574 TGCCACGTCAGCAAAAAAGATGGTGTTAG
1 TGCCACGTCAGCAAAAAAGACGGTGTTAG
37603 TGCCACGTCAGCAAAAAAGACGGTGTTAG
1 TGCCACGTCAGCAAAAAAGACGGTGTTAG
37632 TGCCACGTCAG
1 TGCCACGTCAG
37643 TATATTTGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.32, C:0.22, G:0.28, T:0.19
Consensus pattern (29 bp):
TGCCACGTCAGCAAAAAAGACGGTGTTAG
Found at i:42027 original size:28 final size:28
Alignment explanation
Indices: 41975--42032 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
41965 CAAGGAACCC
*
41975 AAAAACCCTAATTTTATGTAGAAAAAAA
1 AAAAACCCTAATTTTATGCAGAAAAAAA
*
42003 AAAAACCCTAATTTTCTGGCA-AAAAAAA
1 AAAAACCCTAATTTTAT-GCAGAAAAAAA
42031 AA
1 AA
42033 GGAAGGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.22
Consensus pattern (28 bp):
AAAAACCCTAATTTTATGCAGAAAAAAA
Found at i:42512 original size:6 final size:6
Alignment explanation
Indices: 42502--42535 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
42492 GGATTTGAAG
* *
42502 AACCCG AACCCG AACCCA AACCCA AACCCA AACC
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACC
42536 GTAGTTCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.44, C:0.50, G:0.06, T:0.00
Consensus pattern (6 bp):
AACCCA
Done.