Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023829.1 Corchorus olitorius cultivar O-4 contig23862, 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: 31508
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:612 original size:333 final size:326
Alignment explanation
Indices: 3--2274 Score: 1989
Period size: 333 Copynumber: 6.8 Consensus size: 326
1 AG
* * * * * *
3 ATCATGCAAAACTGAG-CCGGAACCTCGAAACGCGTTTTGAGCTTAAAAACGTGAT-AAAAGTAC
1 ATCATGCAAAACTGAGTCAGG-GCC-CGAAACGCGTTTTTAGCTTAAAACCGTGATGGATAGTAC
* * * * *
66 CCGATTTCGACTAAAATTTTGCAAAAATTGGTTCGGAAAATTTTTCCTCACTTTTTGGCTAAAAT
64 ACGATTTCGGCTAAAATTTTGCAAAAATT-G-ACCGAAAATTTTTCCTCAATTTTTGGCTAAAAT
* * ** * * * *
131 TCTCATAAAAATATATAATTCAAAGACAAAAAGATTGAAGGGCTTTAAGGCTTCTAATATCATTT
127 ACTCATAAAAATATATAATTCAAAGCCAAAAAGATTGAAGGTTTTTCACGCTTTTAATATCGTTT
* * * * *
196 TTCCAATTTGTTT-TGAATTAATTTCGAATTAAATAGAAACATGATTCAGATGCTCGTAAAAGCA
192 TTCCAATTTTTTTCTGAATTAATTT-TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
* * ** *
260 AATCCTTAAAACAAAAGTGGCTTAA-ATTTGGTCAGATGAATATAGATATTTCAAGGAGTCTTCG
256 AATCCTTAAATC-AATGTGGC-TAACATTTAATTAGATGAATATAGATATTTCAAGGAGTCTTCG
*
324 TGCCGAAA
319 TGCCAAAA
*
332 ATCATGCAAAACTGAGTTAGGGCCTCGAAACGCGTTTTTAGCTTAAAACCGTGATGGATAGTACA
1 ATCATGCAAAACTGAGTCAGGGCC-CGAAACGCGTTTTTAGCTTAAAACCGTGATGGATAGTACA
* * * *
397 CGATTTCGGCTAAAATTTTGCAAAAATTGATCCGGAAAATTTTTCCTCAATTTTTGCCCACAATT
65 CGATTTCGGCTAAAATTTTGCAAAAATTGA-CC-GAAAATTTTTCCTCAATTTTTGGCTAAAATA
* * * *
462 CTCATAGAAAATATATAATTCAAAGACAAAAAGCTTGAAAGGTTTTTTAGGCTTTTAATATCGTT
128 CTCATA-AAAATATATAATTCAAAGCCAAAAAGATTG-AAGGTTTTTCACGCTTTTAATATCGTT
* * * * *
527 TTTCCAATTTTTTTCTTAATTAATTTTGAATTAAATAGAAACATGATACAAATGCTCGTAAAAAC
191 TTTCCAATTTTTTTCTGAATTAATTTT-AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
* * * ** * * *
592 AAATCCTTAAATCTAAAGTGGCTGAGATTTGGTCAGATGAATATAAATATTTCAAGGAGTCTTTG
255 AAATCCTTAAATC-AATGTGGCTAACATTTAATTAGATGAATATAGATATTTCAAGGAGTCTTCG
***
657 TTTAAAAA
319 TGCCAAAA
* * * * * *
665 ATCATGCAAAACTAAGTC-GGTGTCCCGAAATGTGTTTTTAGCTTAAAGCCGTGATGGAAAGTAT
1 ATCATGCAAAACTGAGTCAGG-G-CCCGAAACGCGTTTTTAGCTTAAAACCGTGATGGATAGTAC
* * * *
729 ACGATTTCTGTTAAAATTTTGCAAAAATTGATCCGGAAAATTTTTCCTCAATTTTTGGCCACAAC
64 ACGATTTCGGCTAAAATTTTGCAAAAATTGA-CC-GAAAATTTTTCCTCAATTTTTGGCTA-AAA
794 T-CTCATAAAATATATATAATTCAAAGCCAAAAAGATTGAAGGGTTTTTCACG-TTTCTAATATC
126 TACTCATAAAA-ATATATAATTCAAAGCCAAAAAGATTGAA-GGTTTTTCACGCTTT-TAATATC
* * * * *
857 ATTTTTCCAA-TTTTTTCTGAATTAATTTCAAATAAAATCGAAACATGATTCAGATG-TCATAAA
188 GTTTTTCCAATTTTTTTCTGAATTAATTT-TAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* * * * * * *
920 AACAAATCCTTAAATCCAATGTGGCTGAGATTTAGTTTGATAAATATAAATATTTCAAGAAGTCT
252 AACAAATCCTTAAAT-CAATGTGGCTAACATTTAATTAGATGAATATAGATATTTCAAGGAGTCT
*
985 TCTTGCCAAAA
316 TCGTGCCAAAA
* * * * *
996 ATCATGTAAAATTGAGTCGGGGCCCCGAAACGTGTTTTTAGCTTAAAACTGTGATGGAAAATGAT
1 ATCATGCAAAACTGAGTCAGGG-CCCGAAACGCGTTTTTAGCTTAAAACCGTGAT-G-----GA-
* * * * * *
1061 TATTACACAATTTCGGCTAAACTTTTGCAAAAATTGACCCGAAAGATATTTCCTCAAATTTTAG-
58 TAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA-CCGAAA-ATTTTTCCTCAATTTTTGGC
* * * * ** *
1125 TCACAATACTCATAAAAAATATATAATTCAACGCCAAGAAGATTGAAGGGCTTTTCGTGATTTTA
121 T-AAAATACTCAT-AAAAATATATAATTCAAAGCCAAAAAGATTGAA-GGTTTTTCACGCTTTTA
* * * *
1190 ATATCGTTTTT-C-ATATTTTTTCAGAATTAATATCTAATTAAATCGAAACAACATTCAGTTGCT
183 ATATCGTTTTTCCAAT-TTTTTTCTGAATTAAT-TTTAATTAAATCGAAACAAGATTCAGATGCT
* * *
1253 CGTAAAAATAAATCCTTAAATGCAATGCGGCTAACATTTTATTAGATGAATATAGATATTTCAAG
246 CGTAAAAACAAATCCTTAAAT-CAATGTGGCTAACATTTAATTAGATGAATATAGATATTTCAAG
*
1318 GAGTC-TCGGCGCCAAAA
310 GAGTCTTC-GTGCCAAAA
* * ** *
1335 ATCATGCAAAACTGAGTCGGGGCCACGAAACGCGTTTTTATCCAAAAACCATGAT-GATTAGTAC
1 ATCATGCAAAACTGAGTCAGGGCC-CGAAACGCGTTTTTAGCTTAAAACCGTGATGGA-TAGTAC
* ** * *
1399 ACGATTTTGTTTAAAATTTTGCAAAAGA-TGACACGAAGAATTTTTTCCTCAGTTTTTGGATAAA
64 ACGATTTCGGCTAAAATTTTGCAAAA-ATTGAC-CGAA-AA-TTTTTCCTCAATTTTTGGCTAAA
* * * * * *
1463 ATACTCATTAAATATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATTTC
125 ATACTCA-TAAAAATATATAATTCAAAGCCAAAAAGATTGAAGG-TTTTTCACGCTTTTAATATC
* * * * * * * *
1528 TTTTTTCTTAGTTTTTTTTCTAAATTAATTTTTAATTATATCGAAACAAGATTCATATACTCATA
188 GTTTTTC-CA-ATTTTTTTCTGAATTAA-TTTTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* ** * * * * * *
1593 AAAATAAATTTTTAAATCCAATCTAGCTAAGATTTAATTAGATGAATATGGATATCTCAAGGAGA
250 AAAACAAATCCTTAAAT-CAATGTGGCTAACATTTAATTAGATGAATATAGATATTTCAAGGAGT
*
1658 CTT-GGGTCC----
314 CTTCGTG-CCAAAA
* * * * ** * *
1667 A--A-GCAAAATTGAGACAGGGCCCTGCAACGC-TTTGTTAGC-CAAAAGTTGTGATGGTTATTA
1 ATCATGCAAAACTGAGTCAGGGCCC-GAAACGCGTTT-TTAGCTTAAAA-CCGTGATGGATAGTA
* * * * *
1727 CACGATTTTGACTAAAATTTTGTAAAAATTGACTCGAAAGATATTTCCTCAATTTTTAGCTAAAA
63 CACGATTTCGGCTAAAATTTTGCAAAAATTGAC-CGAAA-ATTTTTCCTCAATTTTTGGCTAAAA
*
1792 TAATCATAAAAATAATATAATTCAACA-CCAAAAAGATTGAAGTGTTTTTCACGCTTTTAATATC
126 TACTCATAAAAAT-ATATAATTCAA-AGCCAAAAAGATTGAAG-GTTTTTCACGCTTTTAATATC
* *
1856 GTTTTT-C-A-TTTTTTCTGATTTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAA
188 GTTTTTCCAATTTTTTTCTGAATTAATTT-TAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* *
1918 AACAAATCCTTAAATGCAATGCGGCTAACATTTTATTAGATGAATATAGATATTTCAAGGAGTC-
252 AACAAATCCTTAAAT-CAATGTGGCTAACATTTAATTAGATGAATATAGATATTTCAAGGAGTCT
1982 TCAGTGCCAAAA
316 TC-GTGCCAAAA
* * * * * * * ** *
1994 ATTATGCTAAATTGAGCCAGGGCCCCGGAATGCGTTTTCAGCCAAAAACTGTGATGGTTAGTTAG
1 ATCATGCAAAACTGAGTCAGGG-CCCGAAACGCGTTTTTAGCTTAAAACCGTGATGG--A--TAG
* * * *
2059 TACACGATTTCGGCTAAAATTGTGCAAAAATTGACACGAAAGATTTCTGCTCAGTTTTTGGCTAA
61 TACACGATTTCGGCTAAAATTTTGCAAAAATTGAC-CGAAA-ATTTTTCCTCAATTTTTGGCTAA
* * * * *
2124 AATACTAATAAAAATATATAATTCAACGCTAAAAAGATTGGAGGGCTTTTCACGCTTTTAATATC
124 AATACTCATAAAAATATATAATTCAAAGCCAAAAAGATT-GAAGGTTTTTCACGCTTTTAATATC
* ** * *
2189 GTATTTCTTA-TTTTTTGTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCCTC-TAA
188 GTTTTTCCAATTTTTTTCTGAATTAATTT-TAATTAAATCGAAACAAGATTCAGATG-CTCGTAA
* **
2252 AAGCAAATTTTTAAATCCAATGT
251 AAACAAATCCTTAAAT-CAATGT
2275 TATTGAGATT
Statistics
Matches: 1607, Mismatches: 255, Indels: 156
0.80 0.13 0.08
Matches are distributed among these distances:
322 4 0.00
323 97 0.06
324 2 0.00
327 7 0.00
328 82 0.05
329 118 0.07
330 102 0.06
331 154 0.10
332 130 0.08
333 391 0.24
334 79 0.05
335 66 0.04
336 102 0.06
337 12 0.01
338 143 0.09
339 118 0.07
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (326 bp):
ATCATGCAAAACTGAGTCAGGGCCCGAAACGCGTTTTTAGCTTAAAACCGTGATGGATAGTACAC
GATTTCGGCTAAAATTTTGCAAAAATTGACCGAAAATTTTTCCTCAATTTTTGGCTAAAATACTC
ATAAAAATATATAATTCAAAGCCAAAAAGATTGAAGGTTTTTCACGCTTTTAATATCGTTTTTCC
AATTTTTTTCTGAATTAATTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
TTAAATCAATGTGGCTAACATTTAATTAGATGAATATAGATATTTCAAGGAGTCTTCGTGCCAAA
A
Found at i:1969 original size:659 final size:657
Alignment explanation
Indices: 3--2272 Score: 2115
Period size: 670 Copynumber: 3.4 Consensus size: 657
1 AG
* ** * * * **
3 ATCATGCAAAACTGAGCCGGAACCTCGAAACGCGTTTTGAGCTTAAAAA-CGTGAT--AAAAGTA
1 ATCATGCAAAACTGAGTCGGGGCC-CGAAATGCGTTTTTAGC-CAAAAACCGTGATGGATTAGTA
* * * *** *
65 CCCGATTTCGACTAAAATTTTGCAAAAATTGGTTCGGAAAATTTTTCCTCACTTTTTGGCTAAAA
64 CACGATTTTG-TTAAAATTTTGCAAAAATTGACAC-GAAAATTTTTCCTCAGTTTTTGGCTAAAA
* * * * * * * *
130 TTCTCA-TAAAAATATATAATTCAAAGACAAAAAGATTGAAGGGC-TTTAAGGCTTCTAATATCA
127 TACTCATTAAATATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTTTAATATCA
** * * * * *
193 TTTTTCCAATTTGTTT-TGAATTAATTTCGAATTAAATAGAAACATGATTCAGATGCTCGTAAAA
192 TTTTTCTTATTT-TTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGAT-CTCATAAAA
* ** * * ** * ** * * * * * *
257 GCAAATCCTTAAAACAAAAGTGGCTTAA-ATTTGGTCAGATGAATATAGATATTTCAAGGAGTCT
255 ACAAATTTTTAAATCCAATCTAGC-TAAGATTTAATTAGATAAATATAAATATCTCAAGAAGACT
* ** * * * * *
321 TCGTGCCGAAAATCATGCAAAACTGAGTTAGGGCCTCGAAACGCGTTTTTAGCTTAAAAC--CGT
319 TCGTGCC---AA-CATGCAAAATTGAGACAGGGCCCCGAAACGTGTTGTTAGCTCAAAACTGTGT
* * *
384 GATGGATAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA-TCCGGAAA-ATTTTTCCTCAA
380 GATGGTTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACT-C-GAAAGATATTTCCTCAA
* * * *
447 TTTTT-GCCCACAATTCTCATAGAAAAT-ATATAATTCAA-AGACAAAAAGCTTGAAAGGTTTTT
443 TTTTTAG-CTACAATACTCATA-AAAATAATATAATTCAACA-CCAAAAAGATTG-AAGGTTTTT
* * * * *
509 TAGGCTTTTAATATCGTTTTTCCAATTTTTTTCTTAATTAATTT-TGAATTAAATAGAAACATGA
504 CACGCTTTTAATATCGTTTTT-CAA-TTTTTTCTGAATTAATTTCT-AATTAAATCGAAACAAGA
* * * * * * ** *
573 TACAAATGCTCGTAAAAACAAATCCTTAAAT-CTAAAGTGGCTGAGATTTGGTCAGATGAATATA
566 TTCAGATGCTCGTAAAAACAAATCCTTAAATGC-AATGCGGCTAACATTTTATTAGATGAATATA
* ** ***
637 AATATTTCAAGGAGTCTTTGTTTAAAAA
630 GATATTTCAAGGAGTCTCAGTGCCAAAA
* * * ** * * *
665 ATCATGCAAAACTAAGTCGGTGTCCCGAAATGTGTTTTTAGCTTAAAGCCGTGATGGA-AAGTAT
1 ATCATGCAAAACTGAGTCGG-GGCCCGAAATGCGTTTTTAGCCAAAAACCGTGATGGATTAGTAC
* *
729 ACGATTTCTGTTAAAATTTTGCAAAAATTGATC-CGGAAAATTTTTCCTCAATTTTTGGCCACAA
65 ACGATTT-TGTTAAAATTTTGCAAAAATTGA-CAC-GAAAATTTTTCCTCAGTTTTTGGCTA-AA
* * * * *
793 CT-CTCATAAAATATATATAATTCAAAGCCAAAAAGATTGAAGGGTTTTTCACG-TTTCTAATAT
126 ATACTCATTAAATATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTT-TAATAT
** * * * * *
856 CATTTTTCCAATTTTTTCTGAATTAATTTCAAATAAAATCGAAACATGATTCAGATGTCATAAAA
190 CATTTTTCTTATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATCTCATAAAA
** * * * * * * *
921 ACAAATCCTTAAATCCAATGTGGCTGAGATTTAGTTTGATAAATATAAATATTTCAAGAAGTCTT
255 ACAAATTTTTAAATCCAATCTAGCTAAGATTTAATTAGATAAATATAAATATCTCAAGAAGACTT
* * * * * *
986 CTTGCCAAAAATCATGTAAAATTGAGTCGGGGCCCCGAAACGTGTTTTTAGCTTAAAACTGTGAT
320 CGTGCC---AA-CATGCAAAATTGAGACAGGGCCCCGAAACGTGTTGTTAGCTCAAAACTGTG-T
* * * *
1051 GGAAAATGATTATTACACAATTTCGGCTAAACTTTTGCAAAAATTGACCCGAAAGATATTTCCTC
380 -G---ATGGTTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAAGATATTTCCTC
* * * *
1116 AAATTTTAG-TCACAATACTCATAAAAA-ATATATAATTCAACGCCAAGAAGATTGAAGGGCTTT
441 AATTTTTAGCT-ACAATACTCATAAAAATA-ATATAATTCAACACCAAAAAGATTGAA-GGTTTT
** * * * *
1179 TCGTGATTTTAATATCGTTTTTCATATTTTTTCAGAATTAATATCTAATTAAATCGAAACAACAT
503 TCACGCTTTTAATATCGTTTTTCA-ATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGAT
* *
1244 TCAGTTGCTCGTAAAAATAAATCCTTAAATGCAATGCGGCTAACATTTTATTAGATGAATATAGA
567 TCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGCGGCTAACATTTTATTAGATGAATATAGA
* *
1309 TATTTCAAGGAGTCTCGGCGCCAAAA
632 TATTTCAAGGAGTCTCAGTGCCAAAA
* * *
1335 ATCATGCAAAACTGAGTCGGGGCCACGAAACGCGTTTTTATCCAAAAACCATGAT-GATTAGTAC
1 ATCATGCAAAACTGAGTCGGGGCC-CGAAATGCGTTTTTAGCCAAAAACCGTGATGGATTAGTAC
*
1399 ACGATTTTGTTTAAAATTTTGCAAAAGA-TGACACGAAGAATTTTTTCCTCAGTTTTTGGATAAA
65 ACGATTTTG-TTAAAATTTTGCAAAA-ATTGACACGAA-AA-TTTTTCCTCAGTTTTTGGCTAAA
* * *
1463 ATACTCATTAAATATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATTTC
126 ATACTCATTAAATATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTTTAATATC
* * * *
1528 TTTTTTCTTAGTTTTTTTTCTAAATTAATTTTTAATTATATCGAAACAAGATTCATATACTCATA
191 ATTTTTCTTA---TTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGAT-CTCATA
* * ** *
1593 AAAATAAATTTTTAAATCCAATCTAGCTAAGATTTAATTAGATGAATATGGATATCTCAAGGAGA
252 AAAACAAATTTTTAAATCCAATCTAGCTAAGATTTAATTAGATAAATATAAATATCTCAAGAAGA
* * * *
1658 CTT-GGGTCC-A-A-GCAAAATTGAGACAGGGCCCTGCAACGCT-TTGTTAGC-CAAAAGT-TGT
317 CTTCGTG-CCAACATGCAAAATTGAGACAGGGCCCCGAAACG-TGTTGTTAGCTCAAAACTGTGT
* * *
1716 GATGGTTATTACACGATTTTGACTAAAATTTTGTAAAAATTGACTCGAAAGATATTTCCTCAATT
380 GATGGTTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAAGATATTTCCTCAATT
* *
1781 TTTAGCTAAAATAATCATAAAAATAATATAATTCAACACCAAAAAGATTGAAGTGTTTTTCACGC
445 TTTAGCTACAATACTCATAAAAATAATATAATTCAACACCAAAAAGATTGAAG-GTTTTTCACGC
* *
1846 TTTTAATATCGTTTTTC-ATTTTTTCTGATTTAATTTCTAATTAAATCGAAACAAGATTTAGATG
509 TTTTAATATCGTTTTTCAATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG
1910 CTCGTAAAAACAAATCCTTAAATGCAATGCGGCTAACATTTTATTAGATGAATATAGATATTTCA
574 CTCGTAAAAACAAATCCTTAAATGCAATGCGGCTAACATTTTATTAGATGAATATAGATATTTCA
1975 AGGAGTCTCAGTGCCAAAA
639 AGGAGTCTCAGTGCCAAAA
* * * * * * * *
1994 ATTATGCTAAATTGAGCCAGGGCCCCGGAATGCGTTTTCAGCCAAAAACTGTGATGGTTAGTTAG
1 ATCATGCAAAACTGAGTC-GGGGCCCGAAATGCGTTTTTAGCCAAAAACCGTGATGG--A-TTAG
* * * * *
2059 TACACGATTTCGGCTAAAATTGTGCAAAAATTGACACGAAAGATTTCTGCTCAGTTTTTGGCTAA
62 TACACGATTT-TGTTAAAATTTTGCAAAAATTGACACGAAA-ATTTTTCCTCAGTTTTTGGCTAA
* * *
2124 AATACT-AATAAAAATATATAATTCAACGCTAAAAAGATTGGAGGGCTTTTCACGCTTTTAATAT
125 AATACTCATTAAATATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTTTAATAT
* * *
2188 CGTATTTCTTATTTTTTGTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCCTC-TAA
190 CATTTTTCTTATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGAT--CTCATAA
*
2252 AAGCAAATTTTTAAATCCAAT
253 AAACAAATTTTTAAATCCAAT
2273 GTTATTGAGA
Statistics
Matches: 1344, Mismatches: 207, Indels: 118
0.81 0.12 0.07
Matches are distributed among these distances:
658 63 0.05
659 163 0.12
660 7 0.01
661 189 0.14
662 68 0.05
663 102 0.08
664 155 0.12
665 61 0.05
666 3 0.00
667 6 0.00
668 30 0.02
669 13 0.01
670 192 0.14
671 188 0.14
672 4 0.00
674 39 0.03
675 61 0.05
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (657 bp):
ATCATGCAAAACTGAGTCGGGGCCCGAAATGCGTTTTTAGCCAAAAACCGTGATGGATTAGTACA
CGATTTTGTTAAAATTTTGCAAAAATTGACACGAAAATTTTTCCTCAGTTTTTGGCTAAAATACT
CATTAAATATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTTTAATATCATTTT
TCTTATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATCTCATAAAAACAAAT
TTTTAAATCCAATCTAGCTAAGATTTAATTAGATAAATATAAATATCTCAAGAAGACTTCGTGCC
AACATGCAAAATTGAGACAGGGCCCCGAAACGTGTTGTTAGCTCAAAACTGTGTGATGGTTATTA
CACGATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAAGATATTTCCTCAATTTTTAGCTACAA
TACTCATAAAAATAATATAATTCAACACCAAAAAGATTGAAGGTTTTTCACGCTTTTAATATCGT
TTTTCAATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
AATCCTTAAATGCAATGCGGCTAACATTTTATTAGATGAATATAGATATTTCAAGGAGTCTCAGT
GCCAAAA
Found at i:2655 original size:15 final size:16
Alignment explanation
Indices: 2637--2666 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2627 ATAAATAATA
2637 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
2652 ATATTATAATCTAAA
1 ATATTATAATCTAAA
2667 AGTAATTATT
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:2925 original size:8 final size:8
Alignment explanation
Indices: 2912--2960 Score: 62
Period size: 8 Copynumber: 5.9 Consensus size: 8
2902 TATAGTATAA
*
2912 TAAGATGG
1 TAAGATAG
*
2920 TAAGATAA
1 TAAGATAG
2928 TAAGATAG
1 TAAGATAG
2936 TAAGATAAG
1 TAAGAT-AG
2945 ATAAGATAG
1 -TAAGATAG
2954 TAAGATA
1 TAAGATA
2961 AGATTATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
8 26 0.72
9 4 0.11
10 6 0.17
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.24
Consensus pattern (8 bp):
TAAGATAG
Found at i:2929 original size:16 final size:16
Alignment explanation
Indices: 2908--2961 Score: 81
Period size: 16 Copynumber: 3.2 Consensus size: 16
2898 ATTTTATAGT
*
2908 ATAATAAGATGGTAAG
1 ATAATAAGATAGTAAG
2924 ATAATAAGATAGTAAG
1 ATAATAAGATAGTAAG
2940 ATAAGATAAGATAGTAAG
1 AT-A-ATAAGATAGTAAG
2958 ATAA
1 ATAA
2962 GATTATTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
16 18 0.51
17 2 0.06
18 15 0.43
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (16 bp):
ATAATAAGATAGTAAG
Found at i:12760 original size:30 final size:31
Alignment explanation
Indices: 12724--12785 Score: 117
Period size: 30 Copynumber: 2.0 Consensus size: 31
12714 TTTGACTAAC
12724 ACTTTCTCTCTATCTTT-AAAGAGGAATAAT
1 ACTTTCTCTCTATCTTTAAAAGAGGAATAAT
12754 ACTTTCTCTCTATCTTTAAAAGAGGAATAAT
1 ACTTTCTCTCTATCTTTAAAAGAGGAATAAT
12785 A
1 A
12786 GTAGTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (31 bp):
ACTTTCTCTCTATCTTTAAAAGAGGAATAAT
Found at i:13947 original size:44 final size:44
Alignment explanation
Indices: 13829--13952 Score: 142
Period size: 44 Copynumber: 2.8 Consensus size: 44
13819 TTGCTTACGT
*
13829 TTTTAAGCAAATATATTATTCATTTTACTCTTTTGATTAGTACTCC
1 TTTTAAGC--ATATATTATACATTTTACTCTTTTGATTAGTACTCC
** * * * *
13875 -TTTACCCCTATATATAAAAATTTCACTCTTTTGATTAGTACTCC
1 TTTTAAGCATATAT-TATACATTTTACTCTTTTGATTAGTACTCC
*
13919 TTTTAAGCATATATTATGCATTTTACTCTTTTGA
1 TTTTAAGCATATATTATACATTTTACTCTTTTGA
13953 GTATATGTTT
Statistics
Matches: 62, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
43 5 0.08
44 42 0.68
45 15 0.24
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.48
Consensus pattern (44 bp):
TTTTAAGCATATATTATACATTTTACTCTTTTGATTAGTACTCC
Found at i:14651 original size:27 final size:27
Alignment explanation
Indices: 14594--14651 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
14584 GGTTCGTGGT
*** *
14594 TTTGACTTATATTTTTTTTTTGAAAGT
1 TTTGACTTATATTTTGAATTTGAAAGC
14621 TTTGACTTATATTTTGAATTTGCAAA-C
1 TTTGACTTATATTTTGAATTTG-AAAGC
14648 TTTG
1 TTTG
14652 CATGTGAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.24, C:0.07, G:0.12, T:0.57
Consensus pattern (27 bp):
TTTGACTTATATTTTGAATTTGAAAGC
Found at i:30642 original size:20 final size:21
Alignment explanation
Indices: 30606--30648 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
30596 GAAATATTTC
*
30606 ATTAGAAATTAATTTCTAATA
1 ATTACAAATTAATTTCTAATA
30627 ATTACAAATT-ATTTCTAATA
1 ATTACAAATTAATTTCTAATA
30647 AT
1 AT
30649 ATTTATTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (21 bp):
ATTACAAATTAATTTCTAATA
Found at i:30680 original size:34 final size:34
Alignment explanation
Indices: 30632--30711 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 34
30622 TAATAATTAC
* *
30632 AAATTATTTCTAATAATATTTATTGCATATTAAAT
1 AAATTATTTCTAATAATATTTATTACAAATT-AAT
30667 AAATTA-TTC---TAATATTTATTACAAATTAAT
1 AAATTATTTCTAATAATATTTATTACAAATTAAT
30697 AAA-TATTTCTAATAA
1 AAATTATTTCTAATAA
30712 AATCAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
29 2 0.05
30 9 0.23
31 16 0.41
33 3 0.08
34 3 0.08
35 6 0.15
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46
Consensus pattern (34 bp):
AAATTATTTCTAATAATATTTATTACAAATTAAT
Done.