Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020762.1 Corchorus olitorius cultivar O-4 contig20795, 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: 8579
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:1433 original size:649 final size:661
Alignment explanation
Indices: 40--1894 Score: 1766
Period size: 649 Copynumber: 2.8 Consensus size: 661
30 ACTTCTTGGA
* * * * * * *
40 ATATCTATATTCA-ACTAATAAAATCTTAGCCACATTGCTTTTAAGTAT-TTTTTTTACGAGCAT
1 ATATCCATATTCATA-TAATCAAATCTCAGCCACATTGCATTTAAGAATATGTTTGTACGAGCAT
* * * * * * * *
103 CTGAATCTTGTTTTGATTTAATTATAAATTAATTCA-AAAAAAAATGAAAAACGATATTAAAAGA
65 CTGAATCTTATTTCGATTTAATTAGAAATTAATTTATAAAAAAAATGAAAAACAAAATGAAAAGC
** * * * * * * *
167 GTGAAAAGCCCTTCAATCA-TTTTGGCGTTGAATTATATATTTTTTATGAGTATTATGGCTAAAA
130 GTGAAAAATCCTCCAAT-ATTTTTGGCGTTAAATTATATATATTTCATGAGTATTTTAGCCAAAA
* * * * * * *
231 ATTGA-GGAAATATCTTTCAAATAAATTTTTTGCAAAAATTTTAGCCGAAATCGTGCAATAATCA
194 ATTGATGGAAAAATTTTTCAAGTCATTTTTTTGC-AAAATTTTA---TAAATC--GCGA-AATCA
* * * * * *
295 TCACTGT-TTG-TGGCTAAAAACGTGTTCCAGGG--CCCGATTTA-ATTTTGAATGA-TTTTTG-
252 -CA--GTATTGTTTGCTAAAAACGCGTT-CAGGGACCCCGACTCAGTTTTTGCATGATTTTTTGT
* * * *
353 CTGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCCCAG---C--T---ATT---G-
313 C-G-CAAAACTCCTTGAAATAACTATATTAATCTAACCAAATCTCAGCCACATTGGAATTAAAGA
* * *
406 CTT-TT---ACAAGTA-TCTGAATCATGTTTCGTTTTAATTAGAAATTAATTCGAAAAAAAA-A-
376 TTTGTTAAAACAAGCATTCTGAATCATGTTTCGATTTAATTAGAAATTAATT-GAAAAAAAATAG
** * *
464 GAAAAACGATATT------A-GAAAA-CCCTTCAAAATTTTTGGCATTGAATTATATACTTTTTA
440 GAAAAACGATATTAGAAGCATGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATAATTTTTA
* * * * * * *
521 TGATTATTTTAGCCAAAAATTGAGGAAATATCTTTCCGGTCAATTTTTGCAAAATTTTAGCCGAA
505 TGAGTATTGTGGCTAAAAATTGAGGAAATAACTTTCAGGTCAATTTTTGCAAAATTCTAGCCGAA
* * * * *
586 ATCGTGTAATAATTATCACGGTTTTTGGCTAAAAACGCGTTCAAGGGCCCCAGGTTAGTTGTGTA
570 ACCGTGTAATAATCATCACGGTTTTTGACTAAAAACGCGTTCAAGGGCCCCAGGTAAGTTGTGCA
** *
651 TTATTTTTAGCGCTAAGACTCCTTTAG
635 AGATTTTTAGCGCCAAGACTCCTTTAG
*
678 ATATCCATATTCATATAATCAAATCTCAGCCACATTGCATTTAAGGATATGTTTGTACGAGCATC
1 ATATCCATATTCATATAATCAAATCTCAGCCACATTGCATTTAAGAATATGTTTGTACGAGCATC
* * ** * *
743 TGAATCTTATTTCGATTTAATTAGAATTTAATTTATAAAAAATATGAAAAATGATATGAAGAGCG
66 TGAATCTTATTTCGATTTAATTAGAAATTAATTTATAAAAAAAATGAAAAACAAAATGAAAAGCG
*
808 TGAAAAGTCCTCCAATATTTTTGGCGTTAAATTATATATATTTCATGAGTATTTTAGCCAAAAAT
131 TGAAAAATCCTCCAATATTTTTGGCGTTAAATTATATATATTTCATGAGTATTTTAGCCAAAAAT
**
873 TGA-GGAACAAATTTTT-TGGTCA-TTTTTTGCAAAA-TTT-T-AA-C-CG-AAT-AC-G-ATTG
196 TGATGGAA-AAATTTTTCAAGTCATTTTTTTGCAAAATTTTATAAATCGCGAAATCACAGTATTG
* * * * * *
926 TTTGCTAAAAATGCATTTTAGGG-CCCCGACTCAG-TTTTGCATGATTTTTTG-CGCCGAGACTT
260 TTTGCTAAAAACGC-GTTCAGGGACCCCGACTCAGTTTTTGCATGATTTTTTGTCG-CAAAACTC
*
988 CTTGAAATAACTATATTAATCTAACCAAATCTCAGCCGCATTGGAATTAAAGATTTG-TAAAACA
323 CTTGAAATAACTATATTAATCTAACCAAATCTCAGCCACATTGGAATTAAAGATTTGTTAAAACA
1052 AGC-TTCTGAATCATGTTTCGATTTAATTAGAAATTAATTGAAAAAATAATAGGAAAAACGATAT
388 AGCATTCTGAATCATGTTTCGATTTAATTAGAAATTAATTGAAAAAA-AATAGGAAAAACGATAT
*
1116 TAGAAGCATGAAAAGCCATTCAATCTTTTTGGCCGTTGAATTATATAATTTTTATGAGTATTGTG
452 TAGAAGCATGAAAAGCCCTTCAATCTTTTTGG-CGTTGAATTATATAATTTTTATGAGTATTGTG
* *
1181 GATAAAAATTGAGGAAATAACTTTCAAGTCAATTTTTGCAAAATTCTAGCCGAAACCGTGTAATA
516 GCTAAAAATTGAGGAAATAACTTTCAGGTCAATTTTTGCAAAATTCTAGCCGAAACCGTGTAATA
* ** * *
1246 ATCATCACGGTTATTTGACTAAAAACGTGTTCCGGGGCCCC-GGCTAAGTTTTGCAAGATTTTTG
581 ATCATCACGGTT-TTTGACTAAAAACGCGTTCAAGGGCCCCAGG-TAAGTTGTGCAAGATTTTTA
1310 GCGCCAAGACT-CTTTGAG
644 GCGCCAAGACTCCTTT-AG
* * * * * *
1328 ATATCCATATTCATCTAATCAGATCTCAGCTACATTAG-ATTTAAGAATTTGTTTTTACGAGTAT
1 ATATCCATATTCATATAATCAAATCTCAGCCACATT-GCATTTAAGAATATGTTTGTACGAGCAT
* * * *
1392 CTGAATCTTGTTTCGATTTAATTCGAAATTAA-TTCTAAAAAAAATGAAAAACAAAATTAAAAGC
65 CTGAATCTTATTTCGATTTAATTAGAAATTAATTTATAAAAAAAATGAAAAACAAAATGAAAAGC
* ** *
1456 GTGAAAAATCCTCCAATCTTTTTGGCGTTAAATTATATATATTTTGTGAGTATTTTATCCAAAAA
130 GTGAAAAATCCTCCAATATTTTTGGCGTTAAATTATATATATTTCATGAGTATTTTAGCCAAAAA
* *
1521 TTTATGGAAAAATTTTTCAAGTCATTTTTTTGCAAAATTTTAGTCGAAATCGTGTATAAATCACA
195 TTGATGGAAAAATTTTTCAAGTCATTTTTTTGCAAAATTTTA-T--AAATCGCG---AAATCACA
* * * ** * *
1586 GCTTTTTTTTTGCTAAAAACGCGTTCCGGGACCCCGGGTTAGTTTTTGCATGATTTTTTGTTGCA
254 G--TATTGTTTGCTAAAAACGCGTTCAGGGACCCCGACTCAGTTTTTGCATGATTTTTTGTCGCA
* * * * * * * *
1651 AAACTCCTTGAGATATCTATATTCATTTAACCAAATCTTAGCCATATTGGATTTAAGGATTTGTT
317 AAACTCCTTGAAATAACTATATTAATCTAACCAAATCTCAGCCACATTGGAATTAAAGATTTGTT
*** * * *
1716 TTTACGAGCATT-TGAATCATGTTTCGATTTAATTAAAAATTAATTTGAAAAAAAATAGGGAAAA
382 AAAACAAGCATTCTGAATCATGTTTCGATTTAATTAGAAATTAA-TTGAAAAAAAATAGGAAAAA
* *
1780 CGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTTTGGCGTTGAATTCTAT-ATTTTTATGAG
446 CGATATTAGAAGCATGAAAAGCCCTTCAATC--TTTTTGGCGTTGAATTATATAATTTTTATGAG
* * * *
1844 TATTGTGGCTAAAAATTGAGAAAATTA-TTTCGGGTCAATTTTTGCCAAATT
509 TATTGTGGCTAAAAATTGAGGAAATAACTTTCAGGTCAATTTTTGCAAAATT
1895 TTAGTAGAAA
Statistics
Matches: 1006, Mismatches: 139, Indels: 113
0.80 0.11 0.09
Matches are distributed among these distances:
621 4 0.00
622 14 0.01
623 58 0.06
624 8 0.01
625 1 0.00
626 4 0.00
628 2 0.00
631 4 0.00
632 2 0.00
634 1 0.00
635 3 0.00
637 10 0.01
638 86 0.09
639 55 0.05
640 101 0.10
641 6 0.01
646 1 0.00
647 5 0.00
648 14 0.01
649 198 0.20
650 142 0.14
651 13 0.01
652 3 0.00
654 1 0.00
657 2 0.00
658 1 0.00
659 1 0.00
663 3 0.00
664 2 0.00
665 1 0.00
667 5 0.00
668 23 0.02
669 91 0.09
670 111 0.11
671 23 0.02
672 7 0.01
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (661 bp):
ATATCCATATTCATATAATCAAATCTCAGCCACATTGCATTTAAGAATATGTTTGTACGAGCATC
TGAATCTTATTTCGATTTAATTAGAAATTAATTTATAAAAAAAATGAAAAACAAAATGAAAAGCG
TGAAAAATCCTCCAATATTTTTGGCGTTAAATTATATATATTTCATGAGTATTTTAGCCAAAAAT
TGATGGAAAAATTTTTCAAGTCATTTTTTTGCAAAATTTTATAAATCGCGAAATCACAGTATTGT
TTGCTAAAAACGCGTTCAGGGACCCCGACTCAGTTTTTGCATGATTTTTTGTCGCAAAACTCCTT
GAAATAACTATATTAATCTAACCAAATCTCAGCCACATTGGAATTAAAGATTTGTTAAAACAAGC
ATTCTGAATCATGTTTCGATTTAATTAGAAATTAATTGAAAAAAAATAGGAAAAACGATATTAGA
AGCATGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTGTGGCTAA
AAATTGAGGAAATAACTTTCAGGTCAATTTTTGCAAAATTCTAGCCGAAACCGTGTAATAATCAT
CACGGTTTTTGACTAAAAACGCGTTCAAGGGCCCCAGGTAAGTTGTGCAAGATTTTTAGCGCCAA
GACTCCTTTAG
Found at i:1888 original size:335 final size:332
Alignment explanation
Indices: 4--2037 Score: 1522
Period size: 335 Copynumber: 6.2 Consensus size: 332
1 CTC
* * * * * ** *
4 AGTTTTTCATGATTTTTTGCGCCGACACTTCTTG-GAATATCTATATTCAACTAATAAAATCTTA
1 AGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAG-ATATCTATATTCATCTAACCAAATCTCA
** * * * * *
68 GCCACATTGCTTTTAAGTATTT-TTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTATAAAT
65 GCCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCATGTTTCGATTTAATTAGAAAT
* * * * *
132 TAA-TTCAAAAAAAA-ATGAAAAACGATATTAAAAGAGTGAAAAGCCCTTCAATCATTTTGGCGT
130 TAATTTGAAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGT
* * * * *
195 TGAATTATATATTTTTTATGAGTATTATGGCTAAAAATTGAGGAAATATCTTTCAAATAAATTTT
195 TGAATTATATA-TTTTTATGAGTATTGTGGCTAAAAATTGAGAAAAT-TATTTCAAGTCAA-TTT
* * * * * *
260 TTGCAAAAATTTTAGCCGAAATCGTGCAATAATCATCACTGTT-TGTGGCTAAAAACGTGTTCCA
257 TTGC-AAAATTTTAGTCGAAATCGTGTAATAATCATCACGGTTATTTGACTAAAAACGCGTTCC-
**
324 GGG--CCCGATTTA
320 GGGACCCCG-GCTA
* *
336 A-TTTTGAATGA-TTTTTGCTGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAA--T--
1 AGTTTTGCATGATTTTTTGC-GCCAAGACTCCTTGAGATATCTATATTCATCTAACCAAATCTCA
* * * * * *
395 -CC-CA---G--CT----A-TTGCTTTTACAAGTATCTGAATCATGTTTCGTTTTAATTAGAAAT
65 GCCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCATGTTTCGATTTAATTAGAAAT
* ** *
448 TAATTCGAAAAAAAA-A-GAAAAACGATATT---A----GAAAA-CCCTTCAAAATTTTTGGCAT
130 TAATTTGAAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGT
* * * * * * **
503 TGAATTATATACTTTTTATGATTATTTTAGCCAAAAATTGAGGAAATATCTTTCCGGTCAATTTT
195 TGAATTATATA-TTTTTATGAGTATTGTGGCTAAAAATTGAGAAAAT-TATTTCAAGTCAATTTT
* * * *
568 TGCAAAATTTTAGCCGAAATCGTGTAATAATTATCACGGTT-TTTGGCTAAAAACGCGTTCAAGG
258 TGCAAAATTTTAGTCGAAATCGTGTAATAATCATCACGGTTATTTGACTAAAAACGCGTTC-CGG
*
632 G-CCCCAGG-TT
322 GACCCC-GGCTA
* * * * * * * * *
642 AGTTGTGTATTATTTTTAGCGCTAAGACTCCTTTAGATATCCATATTCATATAATCAAATCTCAG
1 AGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAGATATCTATATTCATCTAACCAAATCTCAG
* * * * * * *
707 CCACATTGCATTTAAGGATATGTTTGTACGAGCATCTGAATCTTATTTCGATTTAATTAGAATTT
66 CCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCATGTTTCGATTTAATTAGAAATT
* * * * * * *
772 AATTT-ATAAAAAATATGAAAAATGATATGA-AGAGCGTGAAAAGTCCTCCAATATTTTTGGCGT
131 AATTTGAAAAAAAATAGGAAAAACGATATTAGA-AGCGTGAAAAGCCCTTCAATCTTTTTGGCGT
* * * * * ** *
835 TAAATTATATATATTTCATGAGTATTTTAGCCAAAAATTGAGGAACAAATT-TTT-TGGTCATTT
195 TGAATTATATAT-TTTTATGAGTATTGTGGCTAAAAATTGA-G-A-AAATTATTTCAAGTCAATT
* * * * * **
898 TTTGCAAAA-TTT--T---AA-C-CG-----A--AT-ACGATTGTTTG-CTAAAAATGCATTTTA
256 TTTGCAAAATTTTAGTCGAAATCGTGTAATAATCATCACGGTTATTTGACTAAAAACGC-GTTCC
* *
946 GGG-CCCCGACTC
320 GGGACCCCGGCTA
* * * * *
958 AGTTTTGCATGATTTTTTGCGCCGAGACTTCTTGAAATAACTATATTAATCTAACCAAATCTCAG
1 AGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAGATATCTATATTCATCTAACCAAATCTCAG
* * * *** *
1023 CCGCATTGGAATTAAAGATTTG-TAAAACAAGC-TTCTGAATCATGTTTCGATTTAATTAGAAAT
66 CCACATTGGATTTAAGGATTTGTTTTTACGAGCATT-TGAATCATGTTTCGATTTAATTAGAAAT
* *
1086 TAA-TTGAAAAAATAATAGGAAAAACGATATTAGAAGCATGAAAAGCCATTCAATCTTTTTGGCC
130 TAATTTGAAAAAA-AATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGG-C
* * *
1150 GTTGAATTATATAATTTTTATGAGTATTGTGGATAAAAATTGAGGAAATAACTTTCAAGTCAATT
193 GTTGAATTATAT-ATTTTTATGAGTATTGTGGCTAAAAATTGAGAAAATTA-TTTCAAGTCAATT
* * * *
1215 TTTGCAAAATTCTAGCCGAAACCGTGTAATAATCATCACGGTTATTTGACTAAAAACGTGTTCCG
256 TTTGCAAAATTTTAGTCGAAATCGTGTAATAATCATCACGGTTATTTGACTAAAAACGCGTTCCG
*
1280 GGGCCCCGGCTA
321 GGACCCCGGCTA
* * * * * *
1292 AGTTTTGCAAGATTTTTGGCGCCAAGACTCTTTGAGATATCCATATTCATCTAATCAGATCTCAG
1 AGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAGATATCTATATTCATCTAACCAAATCTCAG
* * * * * * *
1357 CTACATTAGATTTAAGAATTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTCGAAATT
66 CCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCATGTTTCGATTTAATTAGAAATT
* * * ** *
1422 AATTCT-AAAAAAAAT--GAAAAACAAAATTAAAAGCGTGAAAAATCCTCCAATCTTTTTGGCGT
131 AATT-TGAAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGT
* * * ** * * *
1484 TAAATTATATATATTTTGTGAGTATTTTATCCAAAAATTTATGGAAAAATT-TTTCAAGTCATTT
195 TGAATTATATAT-TTTTATGAGTATTGTGGCTAAAAATTGA--G-AAAATTATTTCAAGTCA-AT
** *
1548 TTTTGCAAAATTTTAGTCGAAATCGTGT-ATAAATCA-CAGCTTTTTTTTTG-CTAAAAACGCGT
255 TTTTGCAAAATTTTAGTCGAAATCGTGTAAT-AATCATCA-C-GGTTATTTGACTAAAAACGCGT
* *
1610 TCCGGGACCCCGGGTT
317 TCCGGGACCCCGGCTA
* * * *
1626 AGTTTTTGCATGATTTTTTGTTG-CAAAACTCCTTGAGATATCTATATTCATTTAACCAAATCTT
1 AG-TTTTGCATGATTTTTTG-CGCCAAGACTCCTTGAGATATCTATATTCATCTAACCAAATCTC
* *
1690 AGCCATATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCATGTTTCGATTTAATTAAAAA
64 AGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCATGTTTCGATTTAATTAGAAA
*
1755 TTAATTTGAAAAAAAATAGGGAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTTTGG
129 TTAATTTGAAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATC--TTTTTGG
* **
1820 CGTTGAATTCTATATTTTTATGAGTATTGTGGCTAAAAATTGAGAAAATTATTTCGGGTCAATTT
192 CGTTGAATTATATATTTTTATGAGTATTGTGGCTAAAAATTGAGAAAATTATTTCAAGTCAATTT
* * * * * * * *
1885 TTGCCAAATTTTAGTAGAAATC-T-T-GT-ACCATCATGGTTTTTTGGCTAAAAACGCGTTACGG
257 TTGCAAAATTTTAGTCGAAATCGTGTAATAATCATCACGGTTATTTGACTAAAAACGCGTTCCGG
** *
1946 GACCTTGTGC-C
322 GACCCCG-GCTA
* * * ** * **
1957 AGTGTTGCATGA-TTTTTGTTGCCAAGAGTCCATAAAATATATCTATATTCATCTAACTGAATCT
1 AGTTTTGCATGATTTTTTG-CGCCAAGACTCC-T-TGAGATATCTATATTCATCTAACCAAATCT
* *
2021 CAGCCACACTGTATTTA
63 CAGCCACATTGGATTTA
2038 TTAGATTCAT
Statistics
Matches: 1348, Mismatches: 259, Indels: 190
0.75 0.14 0.11
Matches are distributed among these distances:
306 57 0.04
307 50 0.04
308 75 0.06
309 6 0.00
312 2 0.00
313 3 0.00
314 7 0.01
315 42 0.03
316 186 0.14
317 69 0.05
318 5 0.00
319 1 0.00
320 1 0.00
322 8 0.01
323 44 0.03
324 13 0.01
325 4 0.00
326 4 0.00
327 1 0.00
329 10 0.01
330 31 0.02
331 77 0.06
332 144 0.11
333 70 0.05
334 147 0.11
335 200 0.15
336 18 0.01
337 31 0.02
338 22 0.02
339 20 0.01
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (332 bp):
AGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAGATATCTATATTCATCTAACCAAATCTCAG
CCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCATGTTTCGATTTAATTAGAAATT
AATTTGAAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTT
GAATTATATATTTTTATGAGTATTGTGGCTAAAAATTGAGAAAATTATTTCAAGTCAATTTTTGC
AAAATTTTAGTCGAAATCGTGTAATAATCATCACGGTTATTTGACTAAAAACGCGTTCCGGGACC
CCGGCTA
Found at i:3157 original size:31 final size:30
Alignment explanation
Indices: 3119--3286 Score: 137
Period size: 31 Copynumber: 5.6 Consensus size: 30
3109 CAAGGCTAAT
3119 TGCTCAAATAAGGGCCTAATGTTTATCAAAA
1 TGCTCAAATAAGGGCCTAATGTTT-TCAAAA
* * **
3150 TGCTCAAATAAGGGCCCAATCTTTT-AATT
1 TGCTCAAATAAGGGCCTAATGTTTTCAAAA
* *
3179 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAATGTTT-TCAAAA
** * **
3210 TGCTCAAATAAGGGCCCGATCTTTT-AATT
1 TGCTCAAATAAGGGCCTAATGTTTTCAAAA
* * *
3239 TGGC-CAAATAAAGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAATGTTT-TCAAAA
3270 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
3287 GACATAATAA
Statistics
Matches: 103, Mismatches: 26, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
29 38 0.37
30 9 0.09
31 56 0.54
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAATGTTTTCAAAA
Found at i:3191 original size:60 final size:60
Alignment explanation
Indices: 3123--3285 Score: 281
Period size: 60 Copynumber: 2.7 Consensus size: 60
3113 GCTAATTGCT
* **
3123 CAAATAAGGGCCTAATGTTTATCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGC
*
3183 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGC
*
3243 CAAATAAAGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
3286 TGACATAATA
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 98 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGC
Found at i:3366 original size:31 final size:31
Alignment explanation
Indices: 3328--3428 Score: 102
Period size: 31 Copynumber: 3.3 Consensus size: 31
3318 TGATGCCAGA
3328 CCCTTATTTGAGCATTTTCAATAACGTTAGG
1 CCCTTATTTGAGCATTTTCAATAACGTTAGG
** **
3359 CCCTTATTTG-GCCAAATT-AA-AA-GATCGGG
1 CCCTTATTTGAG-CATTTTCAATAACG-TTAGG
* *
3388 CCTTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCAATAACGTTAGG
3419 CCCTTATTTG
1 CCCTTATTTG
3429 GTCAAATTAA
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
28 1 0.02
29 18 0.34
30 5 0.09
31 28 0.53
32 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.38
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTCAATAACGTTAGG
Found at i:3483 original size:59 final size:60
Alignment explanation
Indices: 3328--3487 Score: 227
Period size: 60 Copynumber: 2.7 Consensus size: 60
3318 TGATGCCAGA
*
3328 CCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGAG
* * *
3388 CCTTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGTCAAATTAAAAGATC-AG
1 CCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGAG
* *
3447 CCCTTATTTGAGTATTTTGTC-A-AACGTTAGACCCTTATTTG
1 CCCTTATTTGAGCA-TTT-TCAATAACGTTAGGCCCTTATTTG
3488 AGCAATTAGC
Statistics
Matches: 91, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
59 31 0.34
60 58 0.64
61 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGAG
Done.