Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019211.1 Corchorus olitorius cultivar O-4 contig19244, 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: 4989
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.34
Found at i:1619 original size:652 final size:646
Alignment explanation
Indices: 98--1525 Score: 1947
Period size: 652 Copynumber: 2.2 Consensus size: 646
88 GTCTATTTCT
* * * * * * * * *
98 AATTAAATCGAATCAATATTCAGATGCTCGTAAAAGCAAATCCTTAAATCTAATGTGGCTCAGAG
1 AATTAAATTGAAACAAGATTCAGATACTAGTAAAAACAAATACTTAAATCGAACGTGGCT-A-AG
*
163 CCTGAGATTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACT
64 -C-GAGATTGGTTAGATGAATATAGATATTTCAAGGAGTATTTCTGCCAAAAATCATGCAAAACT
* **** * ** ** * *
228 GAGCCGGGGCCCCCGAAACGCGTTTTTAGCCCAAAAAGCATGATAGTTA-GTACATGATTTTCGG
127 GAGTCGGGGCCAAAAAAACACAATTCAAG-CCAAAAA-CA--A-A---ACGTAAATGATTTTCCG
* **
292 CTAAAAACTGACCATAA-TTTTTTTTTCTGAAATTTTTGCCACAATACTCAGAAAAAATATATAA
184 CTAAAAACTCACCGGAATTTTTTTTTTCTGAAATTTTTGCCACAATACTCAGAAAAAATATATAA
356 CTCAAGACCAAAAAGATTGATGGTCTGTTCACGCTTTTAATATCATTTTTCCAATTTTTTTTCCG
249 CTCAAGACCAAAAAGATTGATGGTCTGTTCACGCTTTTAATATCATTTTTCCAATTTTTTTTCCG
* *
421 AATTAATTTCTAATTAAATCGAAACAAGACTCAGATGCTCGTAAAATCAAATCCTTATATCCAAT
314 AAGTAATTTCTAATTAAAGCGAAACAAGACTCAGATGCTCGTAAAATCAAATCCTTATATCCAAT
* *
486 GTGGCTGACATTTGGTTTGATGTATATGGATATTTCAAGGAGTCTTTGCGCCAAAAACCATGCAA
379 GTGGCTCACATTTGGTTTGATGTATATAGATATTTCAAGGAGTCTTTGCGCCAAAAACCATGCAA
* *
551 AATTGAGTCGGGGCTCGGGAACGCGTTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCGG
444 AATTGAGTCGGGACTCGGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGG
* *
616 CTAAAAACTGATCGGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTTAGAAAAAATATATAAT
509 CTAAAAACTAATCAGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTTAGAAAAAATATATAAT
* * * *
681 TCAACGCCAAAAAGATTGTCTGGCTTTTCACGCTTCTAATATCGCTTTTCCATTTTTTTCCGAAT
574 TCAAAGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCACTTTTCCATTTTTTTCCGAAT
*
746 TAATTTTT
639 TAATTTTA
* * * * *
754 AATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTCAGAG
1 AATTAAATTGAAACAAGATTCAGATACTAGTAAAAACAAATACTTAAATCGAACGTGGCT-A-AG
819 CCTGAGATTGGTTAGATGAATATAGATATTTCAAGGAGTATTTCTGCCAAAAATCATGCAAAACT
64 -C-GAGATTGGTTAGATGAATATAGATATTTCAAGGAGTATTTCTGCCAAAAATCATGCAAAACT
**** * ** ** * * *
884 GAGTCGGGGCCCCCGAAACGCGTTTTTAGCCCAAAAAGCATAACGTACATGATTTTCGGCTAAAA
127 GAGTCGGGGCCAAAAAAACACAATTCAAG-CCAAAAA-CAAAACGTAAATGATTTTCCGCTAAAA
* * *
949 ACTGACCGGAATTTTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAG
190 ACTCACCGGAATTTTTTTTTTCTGAAATTTTTGCCACAATACTCAGAAAAAATATATAACTCAAG
*
1014 ACCAAAAAGATTGATGGTCTTTTCACGCTTTTAATATCATTTTTCCAATTTTTTTTCCGAAGTAA
255 ACCAAAAAGATTGATGGTCTGTTCACGCTTTTAATATCATTTTTCCAATTTTTTTTCCGAAGTAA
* *
1079 TTTCTAATTAAAGCGAAACAAGATTCAGATGCTCGTAAAATCAAATCTTTATATCCAATGTGGCT
320 TTTCTAATTAAAGCGAAACAAGACTCAGATGCTCGTAAAATCAAATCCTTATATCCAATGTGGCT
*
1144 CACATTTGGTTTGAT-TAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTG
385 CACATTTGGTTTGATGT-ATATAGATATTTCAAGGAGTCTTTGCGCCAAAAACCATGCAAAATTG
*
1208 AGTCGGGACTCGGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTATACGATTTCGGC-AAA
449 AGTCGGGACTCGGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
1272 AATCTAATCAGAAAAG-TTTTTCTCAATTTTTTGCCACAATACTTAGAAAAAATATATAATTCAA
514 AA-CTAATCAGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTTAGAAAAAATATATAATTCAA
* *
1336 AGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCTATTTTTTTCCGAATTAAT
578 AGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCACTTTTCCATTTTTTTCCGAATTAAT
1401 TTTA
643 TTTA
* * *
1405 AATTAAATTGGAACAAGATTCAGATACTAGTTAAAACAAATACTTATATCGAACGTGGCT-AG-G
1 AATTAAATTGAAACAAGATTCAGATACTAGTAAAAACAAATACTTAAATCGAACGTGGCTAAGCG
* * * * *
1468 A-TTTTGTTCGATGAATATAGATATTTCAAGGAGTATTTAC-GTCAAAAATTATGCAAAA
66 AGATTGGTTAGATGAATATAGATATTTCAAGGAGTATTT-CTGCCAAAAATCATGCAAAA
1526 ACAAAAAAAA
Statistics
Matches: 723, Mismatches: 44, Indels: 22
0.92 0.06 0.03
Matches are distributed among these distances:
644 50 0.07
645 3 0.00
648 2 0.00
650 1 0.00
651 198 0.27
652 304 0.42
653 1 0.00
656 164 0.23
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (646 bp):
AATTAAATTGAAACAAGATTCAGATACTAGTAAAAACAAATACTTAAATCGAACGTGGCTAAGCG
AGATTGGTTAGATGAATATAGATATTTCAAGGAGTATTTCTGCCAAAAATCATGCAAAACTGAGT
CGGGGCCAAAAAAACACAATTCAAGCCAAAAACAAAACGTAAATGATTTTCCGCTAAAAACTCAC
CGGAATTTTTTTTTTCTGAAATTTTTGCCACAATACTCAGAAAAAATATATAACTCAAGACCAAA
AAGATTGATGGTCTGTTCACGCTTTTAATATCATTTTTCCAATTTTTTTTCCGAAGTAATTTCTA
ATTAAAGCGAAACAAGACTCAGATGCTCGTAAAATCAAATCCTTATATCCAATGTGGCTCACATT
TGGTTTGATGTATATAGATATTTCAAGGAGTCTTTGCGCCAAAAACCATGCAAAATTGAGTCGGG
ACTCGGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTAAT
CAGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTTAGAAAAAATATATAATTCAAAGCCAAAA
AGATTGACGGGCTTTTCACGCTTCTAATATCACTTTTCCATTTTTTTCCGAATTAATTTTA
Found at i:2139 original size:565 final size:550
Alignment explanation
Indices: 1039--2612 Score: 1733
Period size: 565 Copynumber: 2.9 Consensus size: 550
1029 GGTCTTTTCA
* * * *
1039 CGCTTTTAATATCATTTTTCCAATTTTTTTTCCGAAGTA-ATTTCTAATTAAAGCGAAACAAGAT
1 CGCTTTAAATATCATTTTT-C-TTTTTTTTTCC-AAATATATTTCTAATTAAATCGAAACAAGAT
* * * * * * *
1103 TCAGATGCTCGTAAAATCAAATCTTTATATCCAATGTGGCTCACATTTGGTTTGATTAATATAGA
63 TCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTCACAATTGGTTAGATGAATATAGA
* * * * *
1168 TATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGACTCGGGAACGCGTTTTT
128 TATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGAAACGCGTTTTT
* * *
1233 AGCCAAAAACCGTGATGGTTAGTATACGATTTCGGCAAAAATCTAATCAGAAAAGTTTTTCTCAA
193 AGCCAAAAACCATGATGATTAGTACACGATTTCGGCAAAAATCTAATCAGAAAAGTTTTTCTCAA
* * * *
1298 TTTTTTGCCACAATACTTAGAAAAAATATATAATTCAAAGCCAAAAAGATTGACGGGCTTTTCAC
258 TTTTTGGCCAAAATACTCAGAAAAAATATATAATTCAAAGCCAAAAAGATTGACGAGCTTTTCAC
* * *
1363 GCTTCTAATATCATTTTTCTATTTTTTTCCGAATTAATTTTAAATTAAATTGGAACAAGATTCAG
323 GCTTCAAATATCATTTTTCTATTTTTTTCCGAATTAATTTTAAACTAAATTGAAACAAGATTCAG
*
1428 ATACTAGTTAAAACAAATACTTATATCGAACGTGGCTAGGATTTTGTTCGATGAATATAGATATT
388 ATACTAGTAAAAACAAATACTTATATCGAACGTGGCTAGGATTTTGTTCGATGAATATAGATATT
* * * *
1493 TCAAGGAGTATTTACGTCAAAAATTATGCAAAAACAAAAAAAATATTTTTGGCAAAAAATACACA
453 TCAAGGAGTATTTACGTCAAAAATCATGCAAAAACAAAAAAAATACTTTCGGAAAAAAATACACA
* *
1558 ATTCAATGCAAAAAAAAATTGAAATATTTTCCC
518 ATTCAACGCAAAAAAAAAATGAAATATTTTCCC
*
1591 CGCTTTAAATATCATTTTTCTTTTTTTTTCCAAAAATATATTTCTAATTAAATCGAAACAATATT
1 CGCTTTAAATATCATTTTTCTTTTTTTTTCC--AAATATATTTCTAATTAAATCGAAACAAGATT
*
1656 TAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTCAGAGCTTGAGATTGGTTAGATGAA
64 CAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTC--A-C---A-ATTGGTTAGATGAA
* *
1721 TATAGATATTTCAAGGAGT-TTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCCGAAAC
122 TATAGATATTTCAAGGAGTCTTTGC-GCCAAAAATCATGCAAAACTGAGCC-GGGACCCCGAAAC
* *
1785 GCGTTTTTAGACCAAAAACCATGATGATTAGTACACGATTTCGGCTAAAAA-CTTATCGGAAAAG
185 GCGTTTTTAG-CCAAAAACCATGATGATTAGTACACGATTTCGGC-AAAAATCTAATCAGAAAAG
* * *
1849 TTTTTTCTCAATTTTTGGCCAAAATACTCATAAAAAATTATGTAATTCAACGCCAAAAAGATTGA
248 -TTTTTCTCAATTTTTGGCCAAAATACTCAGAAAAAA-TATATAATTCAAAGCCAAAAAGATTGA
* *
1914 CGAGCTTTTCACGCTTCAAATATCATTTTTCCATTTTTTTTTCCGAATTAATTTTTAACTAAATT
311 CGAGCTTTTCACGCTTCAAATATCATTTTT-C-TATTTTTTTCCGAATTAATTTTAAACTAAATT
* * * *
1979 GAAACAAGATTCAGATGCTCGTAAAAACAAATACTTATTTCGAACGTGGCTGGGATTTTGTTCGA
374 GAAACAAGATTCAGATACTAGTAAAAACAAATACTTATATCGAACGTGGCTAGGATTTTGTTCGA
2044 TGAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCAAAAACAAAAAAAAATACTTTC
439 TGAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCAAAAAC-AAAAAAAATACTTTC
* * *
2109 GGAAAAAAATACACAATTCAACGC-AAAAAAAAATGAGATATTTTTCT
503 GGAAAAAAATACACAATTCAACGCAAAAAAAAAATGAAATATTTTCCC
* * * * *
2156 CGCTTTAAATATCATTTTTCTATTTTTTACCGAATCTATTTCTAATTAAATCGAAACCAGATTCA
1 CGCTTTAAATATCATTTTTCTTTTTTTTTCCAAATATATTTCTAATTAAATCGAAACAAGATTCA
*
2221 GTTGCTCGTAAAAACAAATCCTTAAATCTAA--T-G-T-AC---T--TT--A-G-----AG----
66 GATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTCACAATTGGTTAGATGAATATAGATAT
* * * *
2264 --C----A-T-TTT-TGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCCGAAACGCATTTTTAG
131 TTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAG-CCGGGACCCCGAAACGCGTTTTTAG
* * * * *** *
2320 CCCAAAAACCATGAT-AGTTAGTACACGATTTTCAGCTAAAAA-CTGACCTG-ATTTTTTTTCTG
195 -CCAAAAACCATGATGA-TTAGTACACGA-TTTCGGC-AAAAATCTAATCAGAAAAGTTTTTCTC
* * * * *
2382 AATTTTTTGCCACAATACTCAGAAAATATATATAATTCAACA-CCAAAACGATTGATG-GTCTTT
256 AATTTTTGGCCAAAATACTCAGAAAAAATATATAATTCAA-AGCCAAAAAGATTGACGAG-CTTT
** * * *
2445 TCACGCTTTTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCT-AATTAAATCGAAACAAG
319 TCACGCTTCAAATATCATTTTT-CTATTTTTTTCCGAATTAATTT-TAAACTAAATTGAAACAAG
* * * * * * * * * *
2509 ATTTAGATGCTTGTAAAATCAAATCCTTATATCCAATGTGGCTTA-CATTTGGTTTGATGAATAT
382 ATTCAGATACTAGTAAAAACAAATACTTATATCGAACGTGGC-TAGGATTTTGTTCGATGAATAT
*
2573 AGATATTTCAAGGAGT-CTT-CGTGCCAAAAATCATGCAAAA
446 AGATATTTCAAGGAGTATTTACGT--CAAAAATCATGCAAAA
2613 TTGAGTTGGG
Statistics
Matches: 897, Mismatches: 98, Indels: 84
0.83 0.09 0.08
Matches are distributed among these distances:
520 3 0.00
521 2 0.00
522 118 0.13
523 52 0.06
524 32 0.04
525 71 0.08
526 18 0.02
527 4 0.00
528 1 0.00
532 1 0.00
538 2 0.00
543 1 0.00
544 1 0.00
546 2 0.00
548 1 0.00
550 10 0.01
551 5 0.01
552 78 0.09
554 1 0.00
555 2 0.00
556 1 0.00
558 5 0.01
559 54 0.06
560 20 0.02
561 43 0.05
562 37 0.04
563 112 0.12
564 1 0.00
565 184 0.21
566 35 0.04
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (550 bp):
CGCTTTAAATATCATTTTTCTTTTTTTTTCCAAATATATTTCTAATTAAATCGAAACAAGATTCA
GATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTCACAATTGGTTAGATGAATATAGATAT
TTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGAAACGCGTTTTTAGC
CAAAAACCATGATGATTAGTACACGATTTCGGCAAAAATCTAATCAGAAAAGTTTTTCTCAATTT
TTGGCCAAAATACTCAGAAAAAATATATAATTCAAAGCCAAAAAGATTGACGAGCTTTTCACGCT
TCAAATATCATTTTTCTATTTTTTTCCGAATTAATTTTAAACTAAATTGAAACAAGATTCAGATA
CTAGTAAAAACAAATACTTATATCGAACGTGGCTAGGATTTTGTTCGATGAATATAGATATTTCA
AGGAGTATTTACGTCAAAAATCATGCAAAAACAAAAAAAATACTTTCGGAAAAAAATACACAATT
CAACGCAAAAAAAAAATGAAATATTTTCCC
Found at i:3041 original size:329 final size:323
Alignment explanation
Indices: 2270--3264 Score: 1297
Period size: 329 Copynumber: 3.1 Consensus size: 323
2260 AGAGCATTTT
*
2270 TGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCCGAAACGCATTTTTAGCCCAAAAACCATGAT
1 TGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCCGAAACGCGTTTTTAG-CCAAAAACCATGAT
* * * *
2335 AGTTAGTACACGATTTTCAGCTAAAAACTGACC-TGATTTTTTTTCTGAATTTTTTGCCACAATA
65 GGTTAGTACACGATTTTCGGCTAAAAACTGACCATAAATTTTTTTCTGAATTTTTTGCCACAATA
* *
2399 CTCAGAAAATATATATAATTCAACACCAAAACGATTGATGGTCTTTTCACGCTTTTAATATCATT
130 CTCAGAAAAAATATATAATTCAACACCAAAACGATTGATGGCCTTTTCACGCTTTTAATATCATT
* *
2464 TTTCCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGTAAAATC
195 TTTCCAA-TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAATC
* * *
2529 AAATCCTTATATCCAATGTGGCTTACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTCG
259 AAATCCTTATATCCAATGTGGCTTACAATTGGTTTAATGAATATAAATATTTCAAGGAGTCTTCG
* * * * * **
2594 TGCCAAAAATCATGCAAAATTGAGTTGGGG-CTCGGGAACGCGTTTTTAGCCAAAAACTGTGATG
1 TGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCCGAAACGCGTTTTTAGCCAAAAACCATGATG
* * ** *
2658 GTTAGTACACGA-TTTCGGCTAAAAACTGATCGGA-AAAGTTTTTTCACAATTTTTTGCCACAGT
66 GTTAGTACACGATTTTCGGCTAAAAACTGA-C-CATAAATTTTTTTCTGAATTTTTTGCCACAAT
* * * * * *
2721 ACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGT
129 ACTCAGAAAAAATATATAATTCAACACCAAAACGATTGATGGCCTTTTCACGCTTTTAATATCAT
* *
2786 TTTTCC-ATTTTTTCCCGAATTAATTTTTAATTAAATTC-AAATAAGATTCAGATGCTCGTAAAA
194 TTTTCCAATTTTTT-CCGAATTAATTTCTAATTAAA-TCGAAACAAGATTCAGATGCTCGTAAAA
* * * *
2849 ACAAATCATTAAATCTAATGTGGCTCATAGCCTGAGATTGG-TTAATGAATATAAATATTTCAAG
257 TCAAATCCTTATATCCAATGTGGCT--TA--C--A-ATTGGTTTAATGAATATAAATATTTCAAG
2913 GAGTCTTTC-
315 GAGTC-TTCG
* * * *
2922 TTCGAAAAATCATGCAAAGCTGAATCGGGGCCCCCGAAACGCGTTTTTAGCCAAAAACCATGATG
1 TGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCCGAAACGCGTTTTTAGCCAAAAACCATGATG
*
2987 GTTAGTACACGATTTTCGGCTAAAAACTGACCATAACTTTTTTTCTGAATTTTTTGCCACAATAC
66 GTTAGTACACGATTTTCGGCTAAAAACTGACCATAAATTTTTTTCTGAATTTTTTGCCACAATAC
* *
3052 TCCGAAAAAATATATAATTGAACACCAAAACGATTGATGGCCTTTTCACAG-TTTTAATATCATT
131 TCAGAAAAAATATATAATTCAACACCAAAACGATTGATGGCCTTTTCAC-GCTTTTAATATCATT
* * * *
3116 TTTCCAATTTTTTTCGAATTAATTTCTAATTAAAACGAAACAAGACTCAGATGCTCGCAAAATCA
195 TTTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAATCA
* * * * *
3181 AATCCTTATATCCAATGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTG
260 AATCCTTATATCCAATGTGGCTTACAATTGGTTTAATGAATATAAATATTTCAAGGAGTCTTCG
* *
3245 CGCCAAAAAAACATGCAAAA
1 TGCC-AAAAATCATGCAAAA
3265 TTGTGCAATA
Statistics
Matches: 569, Mismatches: 80, Indels: 44
0.82 0.12 0.06
Matches are distributed among these distances:
321 22 0.04
322 95 0.17
323 132 0.23
324 43 0.08
325 1 0.00
326 1 0.00
327 1 0.00
328 53 0.09
329 196 0.34
330 25 0.04
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (323 bp):
TGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCCGAAACGCGTTTTTAGCCAAAAACCATGATG
GTTAGTACACGATTTTCGGCTAAAAACTGACCATAAATTTTTTTCTGAATTTTTTGCCACAATAC
TCAGAAAAAATATATAATTCAACACCAAAACGATTGATGGCCTTTTCACGCTTTTAATATCATTT
TTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAATCAA
ATCCTTATATCCAATGTGGCTTACAATTGGTTTAATGAATATAAATATTTCAAGGAGTCTTCG
Found at i:4284 original size:324 final size:326
Alignment explanation
Indices: 3630--4468 Score: 816
Period size: 324 Copynumber: 2.5 Consensus size: 326
3620 GATTAGAGGA
* ** * * * * * *
3630 CTTTTCACGTTTTTAATATCGTTTTTCATATTTTTTCTGAACTAATTTCAAATTAAATCAAAACA
1 CTTTTCACGCTTCCAATATTGTTTTTCCTATTTTTTCCGAAATAATTTCTAATTAAATCGAAACA
* * * * *
3695 AGATTCAGATGCACATAAAAACAAATCCTTAAATCCAATTTGGTTGAAATTTGATTAGATGAATA
66 AGATTCAAATGCTCGTAAAAACAAATCCTTAAAT-CAATGTGGCTGAAATTTG----GATGAATA
* * ** ** * *
3760 AAGATATTTCAAGGAGCCCTGGCACCAAAAATCATGCAAAATAAAACCGTGGCCCTGTAATGCGT
126 AAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAAT-TGATTGTGG-CCTATAACGCGT
* *
3825 TTTAAGTCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTATAAAAATTGACCCGA
189 TTTAAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGA
* * * * * * * *
3890 AAGATATTTCCCCAATTTTTGACTAAAATACTCATAAAAAAATATATAATTCGACATCAAAAAGA
254 AAGATATTTCCCCAATTTCTAACGAAAATACTAATAAAAAAATAAATAATTCAACATAAAAAAAA
*
3955 TTGAAAGG
319 TTGAAAGC
* ** * *
3963 C-TTTCAACGCTTCTAATATTGTTTTTTTTTATTCTTTTCCGAATTAATTTCTAATTAGATCGAA
1 CTTTTC-ACGCTTCCAATATTG-TTTTTCCTATT-TTTTCCGAAATAATTTCTAATTAAATCGAA
* *
4027 ACAAGATTCAAATGCTCGTAAAAACAAATCC-T-AATCTAATGTGGCTGAGATTTGGATGAATAT
63 ACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATC-AATGTGGCTGAAATTTGGATGAATAA
* * *
4090 AGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAATTGATTTTTG-C-ATAACGTGTTTT
127 AGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAATTGATTGTGGCCTATAACGCGTTTT
** * * * *
4153 TTGCCGAAAACCGTGATGGTTAGTTCACGTTTTCGGCT-AAATTTTGCAAAAATT-ATCCCGAAA
192 AAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGA-CCCGAAA
* * *
4216 GATTTTTCCTCGATTTCTAACGAAAATACTAAT-AAAAAATAAATAATTCAACGCA-AAAAAAAA
256 GATATTTCCCCAATTTCTAACGAAAATACTAATAAAAAAATAAATAATTCAA--CATAAAAAAAA
4279 TTGAAAGC
319 TTGAAAGC
* *
4287 CTTTTCACGCTTCCAATATTGTTTTTCCTATTTTATTTCCAAAATAATTTCTGATTAAATCGAAA
1 CTTTTCACGCTTCCAATATTGTTTTTCCTA-TTT-TTTCCGAAATAATTTCTAATTAAATCGAAA
* * * * * *
4352 CGAGATTTAGAA-ACTCGTAAAAACAAATCCTTAAATACAATGTGACTGATATTCGGTTAGATGA
64 CAAGATTCA-AATGCTCGTAAAAACAAATCCTTAAAT-CAATGTGGCTGA-AAT---TTGGATGA
* * *
4416 ATAAAGATATACTTTAAGGAGTCTTGACGCCAAAAATCATGCAAAACTTGATT
123 ATAAAGATAT--TTCAAGGAGTCTTGGCACCAAAAATCATGCAAAA-TTGATT
4469 AGATGAATAT
Statistics
Matches: 419, Mismatches: 66, Indels: 42
0.80 0.13 0.08
Matches are distributed among these distances:
323 25 0.06
324 127 0.30
325 50 0.12
326 14 0.03
327 2 0.00
328 3 0.01
329 47 0.11
330 16 0.04
332 36 0.09
333 36 0.09
334 10 0.02
335 53 0.13
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (326 bp):
CTTTTCACGCTTCCAATATTGTTTTTCCTATTTTTTCCGAAATAATTTCTAATTAAATCGAAACA
AGATTCAAATGCTCGTAAAAACAAATCCTTAAATCAATGTGGCTGAAATTTGGATGAATAAAGAT
ATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAATTGATTGTGGCCTATAACGCGTTTTAAGC
CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAGATAT
TTCCCCAATTTCTAACGAAAATACTAATAAAAAAATAAATAATTCAACATAAAAAAAATTGAAAG
C
Found at i:4638 original size:21 final size:22
Alignment explanation
Indices: 4614--4681 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
4604 ACGAGCATCT
*
4614 AAATCTTGATAAT-TTATAATA
1 AAATCTTGATAATATTAAAATA
* *
4635 AAAT-TTTATTATATTAAAATA
1 AAATCTTGATAATATTAAAATA
*
4656 AAATCTTTACT-ATATTAAAATA
1 AAATCTTGA-TAATATTAAAATA
4678 AAAT
1 AAAT
4682 TTTAATATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.15
21 15 0.37
22 19 0.46
23 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (22 bp):
AAATCTTGATAATATTAAAATA
Found at i:4690 original size:21 final size:21
Alignment explanation
Indices: 4631--4690 Score: 93
Period size: 22 Copynumber: 2.8 Consensus size: 21
4621 GATAATTTAT
*
4631 AATAAAATTTTATTATATTAA
1 AATAAAATTTTAATATATTAA
*
4652 AATAAAATCTTTACTATATTAA
1 AATAAAAT-TTTAATATATTAA
4674 AATAAAATTTTAATATA
1 AATAAAATTTTAATATA
4691 AATCTTTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 16 0.44
22 20 0.56
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (21 bp):
AATAAAATTTTAATATATTAA
Found at i:4695 original size:34 final size:33
Alignment explanation
Indices: 4652--4718 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 33
4642 ATTATATTAA
4652 AATAAAATCTTTAC-TATATTAAAATAAAATTTT
1 AATAAAATCTTTACATA-ATTAAAATAAAATTTT
*
4685 AATATAAATCTTTTCATAATTAAAATAAAATTTT
1 AATA-AAATCTTTACATAATTAAAATAAAATTTT
4719 CATGACTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
33 4 0.13
34 25 0.81
35 2 0.06
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (33 bp):
AATAAAATCTTTACATAATTAAAATAAAATTTT
Found at i:4707 original size:21 final size:20
Alignment explanation
Indices: 4695--4749 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
4685 AATATAAATC
4695 TTTTCATAATTAAAATAAAA
1 TTTTCATAATTAAAATAAAA
* *
4715 TTTTCATGACTATAAATAATAA
1 TTTTCATAATTA-AAATAA-AA
*
4737 TATT-ATAATTAAA
1 TTTTCATAATTAAA
4750 TATATTATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 12 0.43
21 11 0.39
22 5 0.18
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (20 bp):
TTTTCATAATTAAAATAAAA
Found at i:4754 original size:15 final size:16
Alignment explanation
Indices: 4736--4765 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4726 ATAAATAATA
4736 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
4751 ATATTATAATCTAAA
1 ATATTATAATCTAAA
4766 AATAATCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:4760 original size:56 final size:56
Alignment explanation
Indices: 4622--4766 Score: 140
Period size: 56 Copynumber: 2.6 Consensus size: 56
4612 CTAAATCTTG
* * *
4622 ATAATTTATAATAAAATTTTATTAT-ATTAAAATAAAATCTTTACTATATTAAAATA
1 ATAATTTATAATTAAA-TATATTATAATTAAAATAAAATCTTTACTATACTAAAATA
* *
4678 A-AATTT-TAATATAAATCTTTTCATAATTAAAATAAAAT-TTT-C-ATGACTATAAATA
1 ATAATTTATAAT-TAAATATATT-ATAATTAAAATAAAATCTTTACTAT-ACTA-AAATA
4733 ATAATATTATAATTAAATATATTATAATCTAAAA
1 ATAAT-TTATAATTAAATATATTATAAT-TAAAA
4767 ATAATCATTA
Statistics
Matches: 74, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
53 2 0.03
54 12 0.16
55 19 0.26
56 22 0.30
57 15 0.20
58 4 0.05
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.43
Consensus pattern (56 bp):
ATAATTTATAATTAAATATATTATAATTAAAATAAAATCTTTACTATACTAAAATA
Done.