Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020407.1 Corchorus olitorius cultivar O-4 contig20440, 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: 27374
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--25 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1 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 T
26 TCATCTAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7754 original size:23 final size:22
Alignment explanation
Indices: 7713--7761 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
7703 TAGGGCAACC
* *
7713 ATTTAGTATGTTGATCTCTGAA
1 ATTTAGGATGTTAATCTCTGAA
7735 ATTTAGGATAGTTAATCTCTGAA
1 ATTTAGGAT-GTTAATCTCTGAA
7758 ATTT
1 ATTT
7762 TGACACGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTTAGGATGTTAATCTCTGAA
Found at i:9219 original size:331 final size:331
Alignment explanation
Indices: 8463--9239 Score: 919
Period size: 331 Copynumber: 2.3 Consensus size: 331
8453 ATATATATAT
* * * * *
8463 ATATATAATTCAACACCAAAAAGACTGGAGTACTTTTCACGCTTTTAATATCG-TTTTTC-ATAT
1 ATATATAATTCAACACCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTTCTATTT
* * * * *
8526 TTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATACAGATGCACGTAAAAACAAATCCTTA
66 TTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTA
** * * *
8591 AATCCAATGTGGCTGAGATTTGATTAGATGAATAAAGATATTTCAAGAAGTCTTGGCGCAAAATA
131 AAAACAATGTGGCTGAGATTTGATTACATGAATAAAGATATTTCAAGAAGGCTTGGAGCAAAATA
* ** *
8656 TCATGCAAAACAAAGCCGTGGCCCCGGAACGCGTTTTTAGCCAAAAGCCGTGATGGTTAGTACAC
196 TCATGCAAAACAAACCCGTGGCCCCAAAACGCGTTTTTAGCCAAAAACCGTGATGG-TAGTACAC
* * * * *
8721 GATTTCGGCTAAAATTTTACAAAAATTGACCCAAAATTTTTTTCCTCAATTTCTAGCGAAAATAC
260 GATTTCGACTAAAATTTTACAAAAAATGACCCAAAATATTTATCCGCAATTTCTAGCGAAAATAC
8786 TCATAAA
325 TCATAAA
* * * *
8793 ATATATAATTCAACACCAAAAAAATTGAAAGCCTTTTTCACGCTTCCAATATCGTTTTTTCTATT
1 ATATATAATTCAACACCAAAAAGATTGAAGGAC-TTTTCACGCTTCTAATATCGTTTTTTCTATT
* * *
8858 TTATTTCTAAATTAATTTCTGATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATTCTT
65 TTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTT
* * * *
8923 AAAAACAATGTGGCTTAGATTTGGTTACATGAATAAAGATATATTTTAAGGAGGCTTGGAGTCAA
130 AAAAACAATGTGGCTGAGATTTGATTACATGAATAAAG--ATATTTCAAGAAGGCTTGGAG-CAA
* ** *
8988 AA-ATCATGTAAAACTGACCCG-GGACCCCAAAACGCGTTTTTAGCCAACAAACTGTGAT-G-A-
192 AATATCATGCAAAACAAACCCGTGG-CCCCAAAACGCGTTTTTAGCCAA-AAACCGTGATGGTAG
* * * * *
9048 TACACGATTTCGACTAAAGTTTTGCAAAAAATGACCCTAAATATTTAT-CGCATTTTTTAGTC-A
255 TACACGATTTCGACTAAAATTTTACAAAAAATGACCCAAAATATTTATCCGCAATTTCTAG-CGA
*
9111 CAATACTCATAAAA
319 AAATACTCAT-AAA
* * * * *
9125 ATATATAATTCAACGCTAAAAAGATTGAAGGGCTTCTCACGCTTCTAACATCGTTTTTTCTATTT
1 ATATATAATTCAACACCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTTCTATTT
*
9190 TTTTT-TCAAATTAAATTT-TAATTAAATCGAAACATGATTCAAATGCTCGT
66 TTTTTCT-AAATT-AATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGT
9240 GTAACACACA
Statistics
Matches: 379, Mismatches: 56, Indels: 23
0.83 0.12 0.05
Matches are distributed among these distances:
330 28 0.07
331 105 0.28
332 84 0.22
333 93 0.25
334 2 0.01
335 54 0.14
336 13 0.03
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (331 bp):
ATATATAATTCAACACCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTTCTATTT
TTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTA
AAAACAATGTGGCTGAGATTTGATTACATGAATAAAGATATTTCAAGAAGGCTTGGAGCAAAATA
TCATGCAAAACAAACCCGTGGCCCCAAAACGCGTTTTTAGCCAAAAACCGTGATGGTAGTACACG
ATTTCGACTAAAATTTTACAAAAAATGACCCAAAATATTTATCCGCAATTTCTAGCGAAAATACT
CATAAA
Found at i:9691 original size:44 final size:41
Alignment explanation
Indices: 9642--9758 Score: 152
Period size: 37 Copynumber: 2.9 Consensus size: 41
9632 TTCAAGAATA
*
9642 ATAATAATTCTCCACATACGTGGATCTTCTTTCAATCTTGTTTG
1 ATAATAATCCTCCACATACGTGGATCTTCTTTCAATC---TTTG
9686 ATAATAATCCTCCACATACGTGGA---TC-TTCAATCTTTG
1 ATAATAATCCTCCACATACGTGGATCTTCTTTCAATCTTTG
* *
9723 AAAATAATCCTCCACATACATGGATCTTCTTTCAAT
1 ATAATAATCCTCCACATACGTGGATCTTCTTTCAAT
9759 AATCCTCCTT
Statistics
Matches: 66, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
37 26 0.39
40 9 0.14
41 8 0.12
44 23 0.35
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (41 bp):
ATAATAATCCTCCACATACGTGGATCTTCTTTCAATCTTTG
Found at i:10953 original size:27 final size:27
Alignment explanation
Indices: 10912--10983 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
10902 AAAATATTTG
* * *
10912 AATTACCAAAATACCCGTGA-TGGATAA
1 AATTACCATATTACCCCTGATTGG-TAA
*
10939 ATTTACCATATTACCCCTGATTGGTAA
1 AATTACCATATTACCCCTGATTGGTAA
* *
10966 AATTACGATTTTACCCCT
1 AATTACCATATTACCCCT
10984 ATAATGAGGA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
27 34 0.92
28 3 0.08
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (27 bp):
AATTACCATATTACCCCTGATTGGTAA
Found at i:12728 original size:42 final size:43
Alignment explanation
Indices: 12677--12770 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
12667 AGTGCATTAT
*
12677 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
*
12718 CTGATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
12763 CTAATATT
1 CTAATATT
12771 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 3 0.07
42 6 0.13
45 37 0.80
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:14742 original size:334 final size:331
Alignment explanation
Indices: 13787--14852 Score: 1360
Period size: 343 Copynumber: 3.2 Consensus size: 331
13777 TTTTTCCACA
* * * * *
13787 AAAAATCATGCAAAAGTAACCCGGGACCCCGG-AACGCGTTTTTAGCCAAAAAATCGTGAT-G--
1 AAAAATCATGCAAAACTAAGCC-GGAGCCCGGAAACGCGTTTTTAGCAAAAAAACCGTGATGGTT
* * * *
13848 -GTACACGATTTCGGCTATAATTTTACAAAAATAGACCCGAAATATTTTTCCTCAATTTTTAGCC
65 AGTACACGATTTCGGCTATAATTTTGCAAAAAT-GACCCGAAAAATTTTTCTTCAATTTTTAGCT
* * *
13912 ACAATACTCATAAAATATATATAATTCAACTCCAAAAAGATT-AGAGGACTTTTCACGCTTTTAA
129 AAAATACTCATAAAATATATATAATTTAACGCCAAAAAGATTGA-AGGACTTTTCACGCTTTTAA
* * *
13976 TATCGTTTTCCATATTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTA
193 TATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTA
* * * *
14041 AAAACAAATCATTAAATTCAGATGTGGCTAAGATTTGATTAGATGAGTATAAATATTTCAAGGAG
258 TAAACAAATCATTAAATTCA-ATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAG
*
14106 TCTATG-TGCC
322 TCT-CGATGCC
* * * * *
14116 AAAAATCATGCAAAACTAAGTCGG-GGCCGCAAAACGCGTTTTTAGC-CAAAAACCGTGAAGGTT
1 AAAAATCATGCAAAACTAAGCCGGAGCCCG-GAAACGCGTTTTTAGCAAAAAAACCGTGATGGTT
* * * * * *
14179 AGTACACGATTCCAGCTTTAATTTTGTAGAAAATGACCCGACAAATTTTTTTCTCAATTTTTAGC
65 AGTACACGATTTCGGCTATAATTTTGCA-AAAATGACCCGAAAAATTTTTCT-TCAATTTTTAGC
* *
14244 TAAAATACTCATAATATATATATATATATATATAATTTAACGCCTAAAAGATTGGAGGACTTTTC
128 TAAAATACTC-------ATA-A-A-ATATATATAATTTAACGCCAAAAAGATTGAAGGACTTTTC
*
14309 ATGCTTTTAATATCGTTTTTCATA-TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCA
183 ACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCA
* * * *
14373 AATGCTCGCATAAAAAAATTATTTAAATTCAATGTGGCTGAGATTTGATTAGATGATTTATAGAT
248 AATGCTCGTATAAACAAATCA-TTAAATTCAATGTGGCTGAGATTTGATTAGATGA-ATATAGAT
* *
14438 ATTTCAAAGAGTCTCGACGCC
311 ATTTCAAGGAGTCTCGATGCC
* *
14459 AAAAATCATGCAAAACTGAGTCGGAGCCCGGAAACGCGTTTTTAGCAAAAAAACCGTGATGGTTA
1 AAAAATCATGCAAAACTAAGCCGGAGCCCGGAAACGCGTTTTTAGCAAAAAAACCGTGATGGTTA
* *
14524 GTTACACGATTTCGGCTAAAATTTTGCCAAAAATGACCCGAAAAATTTTTCTTCAATTTTTGGCT
66 G-TACACGATTTCGGCTATAATTTTG-CAAAAATGACCCGAAAAATTTTTCTTCAATTTTTAGCT
* * *
14589 AAAATACTCATGAAATATATATAATTTAACGCCAAAAAGGTTGAAGGACTTTTCGCGCTTTTAAT
129 AAAATACTCATAAAATATATATAATTTAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAAT
*
14654 ATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCATAT
194 ATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAT
* * *
14719 AAACAAATCCTTAAATGCAATGTGGCTGAGATTTAATTAGATGAATATAGATATTTCAAGGAGTC
259 AAACAAATCATTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTC
* *
14784 TCAATGTC
324 TCGATGCC
* *
14792 GAAAATCATGCAAAACTAAGCCGGAGCCCCGAAACGCGTTTTTAGCAAAAAAAACCGTGAT
1 AAAAATCATGCAAAACTAAGCCGGAGCCCGGAAACGCGTTTTTAGC-AAAAAAACCGTGAT
14853 AATTGTTCAC
Statistics
Matches: 636, Mismatches: 73, Indels: 51
0.84 0.10 0.07
Matches are distributed among these distances:
327 3 0.00
328 12 0.02
329 34 0.05
332 36 0.06
333 91 0.14
334 105 0.17
335 57 0.09
336 1 0.00
337 2 0.00
340 3 0.00
341 1 0.00
342 81 0.13
343 126 0.20
344 42 0.07
345 41 0.06
346 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (331 bp):
AAAAATCATGCAAAACTAAGCCGGAGCCCGGAAACGCGTTTTTAGCAAAAAAACCGTGATGGTTA
GTACACGATTTCGGCTATAATTTTGCAAAAATGACCCGAAAAATTTTTCTTCAATTTTTAGCTAA
AATACTCATAAAATATATATAATTTAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATAT
CGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTATAA
ACAAATCATTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC
GATGCC
Found at i:20787 original size:332 final size:332
Alignment explanation
Indices: 19753--21401 Score: 1149
Period size: 331 Copynumber: 4.9 Consensus size: 332
19743 TGTTTTCATA
* * * * *
19753 AGCATCTGAATCATGTTTCG-TTTGAAATAGAAATTAATTCGGAAAAAATAGGAAAAACGATATT
1 AGCATCTAAATCTTGTTTCGATTT-AATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATT
* * * ** * * * *
19817 AGAAGCGTGAAAAGCCCTTCAACCTTTTTGGCGTTGAATTTTATAT-TTTTATGAGTATTGTGAC
65 A-AAACGTGAAAAGTCCTCCAATATTTTTGGAGTTAAATTATATATATTTTATGAGTATT-TTAC
* * * * * * * *
19881 TAAAAATTGAGGAAGAATATTTC-GAGTCATTTTTTGCAAAATATTAGCTGAAATATGTGCAATA
128 AAAAAATTGAGGAA-AATTTTTCTG-GTCATATTTTGCAAAATTTTAGCCGAAAT-CGTGTACTA
* * * * *
19945 TCACGATTTTTCTTTTTCTTTTTTTTTTTTGCTAAAAACGCATTTCAGGACCCCAGGTCAGTATT
190 --ACCA----TC----ACTTTTTTTTTTTTGCTAAAAACGCGTTTC-GGGCCCCAGGTCAGTTTT
* * * * *
20010 GCTTGATTTTTGGCACCAAGACTCCTGGAACTATCTAAATTCATCTAATCAAATCTCAGCCACAT
244 GCATGATTTTTGGCATCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACAT
*
20075 TGGATTTAAGGATTTGTTTTTACG
309 TGCATTTAAGGATTTGTTTTTACG
* *
20099 AGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAACTAGGAAAAACGATATTA
1 AGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTA
* * * * * * *
20164 GAAACGT-ACAAAATCCTTCAATATTTTTGGCG-TAGAATTATATTTTTTTTATTA-TAATTTAG
66 -AAACGTGA-AAAGTCCTCCAATATTTTTGGAGTTA-AATTATATATATTTTATGAGTATTTTA-
*
20226 CAAAAAATTGAGGAAATATCTTTTC-GGTC-TATTTTTGCAAAATTTTAGCCGAAATCGTGTAAT
127 CAAAAAATTGAGGAAA-AT-TTTTCTGGTCATA-TTTTGCAAAATTTTAGCCGAAATCGTGTACT
* ** * * * * * * * *
20289 AATCATCAC----GGTGTTTGGTTAAAAATGTGATCCAGGGCCCCGGGTCAGTTTTGCATGATTT
189 AACCATCACTTTTTTTTTTTTGCTAAAAACGCGTTTC-GGGCCCCAGGTCAGTTTTGCATGATTT
* * * ** *
20350 TTGACGC-T-AAGACTACTTGAGATATCCATATTCATCTAATCAAATCTTTGACACATTGCATTT
253 TTG--GCATCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTT
20413 AAGGATTTGTTTTTACG
316 AAGGATTTGTTTTTACG
* *
20430 AGCATCTAAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATGA
1 AGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTA
* * * * * *
20495 AAATTGTGAAACGTCCTCCAATCTTTTTGGTGTTAAATTATATATATTTCATGAGTATTTTATCC
66 AAA-CGTGAAAAGTCCTCCAATATTTTTGGAGTTAAATTATATATATTTTATGAGTATTTTA-CA
* *
20560 AAAAATTGAGGAAAATTTTTCTTGTCATATTTTGC-AAATTTTAGGCGAAATCGTGTACTAACCA
129 AAAAATTGAGGAAAATTTTTCTGGTCATATTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCA
* * *
20624 TCACCTTTTTTTTTTTTGCTAAAAACGCGTTTCGGGTTCCC-GCTCAGTTTTGCCT-ATTTTTGG
194 TCA-CTTTTTTTTTTTTGCTAAAAACGCGTTTCGGG-CCCCAGGTCAGTTTTGCATGATTTTTGG
* *
20687 CATCGAGGCTCCTTGAAATAT-TATATTCATCTAATCAAATCTCAGCCACATTGCATTTCAA-GA
257 CATCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTT-AAGGA
20750 TTTGTTTTTACG
321 TTTGTTTTTACG
* * * *
20762 AGCATCTGAATCTTGTTTAGATTTAACTA-AATTTTAATTCAG-AAAAATATGAAAAACGATATT
1 AGCATCTAAATCTTGTTTCGATTTAATTAGAA-ATTAATTCAGAAAAAATATGAAAAACGATATT
* ** ** *
20825 AAAAGCGTGAAAAGTCGTGTAATATTTTTGGAGTCGAATTATATATATTTTATGAGTATTTTAGA
65 AAAA-CGTGAAAAGTCCTCCAATATTTTTGGAGTTAAATTATATATATTTTATGAGTATTTTACA
* * *
20890 AAAAATTGAGGAAAATTATTTATGGTTAGT-TTTTGCAAAATATTAGCCGAAATCGTGTACGTTA
129 AAAAATTGAGGAAAATT-TTTCTGGTCA-TATTTTGCAAAATTTTAGCCGAAATCGTGTAC--TA
* * *** * * * * *
20954 GTCGAAATCA---GGGTTTTTTTCCTAAAAACGTGTTCCAAGGCCCC-GGTTCAGTGTTGCATGA
190 -AC--CATCACTTTTTTTTTTTTGCTAAAAACGCGTTTC-GGGCCCCAGG-TCAGTTTTGCATGA
** ** * ** * * * *
21015 TTTTTTACGCCGAGACTCCTTGAAATATCTATA-AAATCTAACCAAATCTCATCCACAATGAATT
250 TTTTTGGCATCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATT
*** *
21079 TAAGGATTTG-TAAAACA
315 TAAGGATTTGTTTTTACG
* * * * * * *
21096 AGTATCCAAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAATAATAGGTAAAACGATACT
1 AGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAA-AATATGAAAAACGATATT
* * * * * * ** * * **
21161 AGAAGCATGAAAAGCCCTTCAATCTTTTTCGCA-TCGAGTTGTATA-ATTTTTATGAGTATTGCG
65 A-AAACGTGAAAAGTCCTCCAATATTTTT-GGAGTTAAATTATATATA-TTTTATGAGTATT-TT
* * * * * *
21224 GCTAAAACTTGATGAAAATAACTTTC-GAGTCA-ATTTTTGCAAAATTCTAGCCGAAATCGTGTA
126 ACAAAAAATTGAGGAAAAT--TTTTCTG-GTCATA-TTTTGCAAAATTTTAGCCGAAATCGTGTA
* * ** * * * * * *
21287 ATAATCAT-A-TTACTGTTATTGGCTAAAAACGCGTTCCGGAGACCC-GGCTAAGTTTTGCATGA
187 CTAACCATCACTTTTTTTTTTTTGCTAAAAACGCGTTTCGG-GCCCCAGG-TCAGTTTTGCATGA
* * * * * *
21349 TTTTAGCGC--CAAAAATCTTTTGAGATATCCATATTCATCTAATCAAATCTCAG
250 TTTTTG-GCATCAAGACTC-CTTGAAATATCTATATTCATCTAATCAAATCTCAG
21402 TGATAAGTGT
Statistics
Matches: 1039, Mismatches: 207, Indels: 125
0.76 0.15 0.09
Matches are distributed among these distances:
330 54 0.05
331 300 0.29
332 131 0.13
333 56 0.05
334 117 0.11
335 98 0.09
336 63 0.06
337 23 0.02
338 33 0.03
339 2 0.00
343 2 0.00
345 13 0.01
346 132 0.13
347 15 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (332 bp):
AGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTA
AAACGTGAAAAGTCCTCCAATATTTTTGGAGTTAAATTATATATATTTTATGAGTATTTTACAAA
AAATTGAGGAAAATTTTTCTGGTCATATTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATC
ACTTTTTTTTTTTTGCTAAAAACGCGTTTCGGGCCCCAGGTCAGTTTTGCATGATTTTTGGCATC
AAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGT
TTTTACG
Found at i:21809 original size:69 final size:69
Alignment explanation
Indices: 21667--21896 Score: 379
Period size: 69 Copynumber: 3.3 Consensus size: 69
21657 CAGATCTTGG
* *
21667 CCAAGTCCTGTCCGGGACTTGTGCTGTTGAGGAATGCAAAATTACAGGACAAGACCTGGGCAGGA
1 CCAAGTCCTGTCCCGGACTTGTGCTGTTGAGGAACGC-AAATTACAGGACAAGACCTGGGCAGGA
21732 GTTAC
65 GTTAC
* * *
21737 CCAAGTCCTGTCCCGGACTTGTGCTGTTGAAGAACGCAAATTACAAGACAAGACCTGGGCGGGAG
1 CCAAGTCCTGTCCCGGACTTGTGCTGTTGAGGAACGCAAATTACAGGACAAGACCTGGGCAGGAG
21802 TTAC
66 TTAC
*
21806 CCAAGTCCTGTCCCGGACTTGTGCTGTTGAGGAGCGCAAATTACAGGACAAGACCTGGGCAGGAG
1 CCAAGTCCTGTCCCGGACTTGTGCTGTTGAGGAACGCAAATTACAGGACAAGACCTGGGCAGGAG
21871 TTAC
66 TTAC
* *
21875 CCAAGTCCTGTCCAGGAGTTGT
1 CCAAGTCCTGTCCCGGACTTGT
21897 TGCGGGAAAT
Statistics
Matches: 149, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
69 115 0.77
70 34 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (69 bp):
CCAAGTCCTGTCCCGGACTTGTGCTGTTGAGGAACGCAAATTACAGGACAAGACCTGGGCAGGAG
TTAC
Found at i:23554 original size:328 final size:322
Alignment explanation
Indices: 22824--23718 Score: 897
Period size: 331 Copynumber: 2.7 Consensus size: 322
22814 ATTGTGATCA
* ** * ** *
22824 CTCAGCTACATTGGATTTAATAATTTGCTTTTACGAGCATCTGTGTCTTATTTCGATTTAATTAG
1 CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTC-ATTTAATTAG
* * *** *
22889 AAATTAATTCAGAAAAAAATGAAAAATGGTATTAAAAGCGTGAAAAGTCCTTCAATCCTTTTGG-
65 AAATTAATTAAGAAAAATATGAAAAACAATATTAAAAGCGTG-AGAGTCCTTCAAT--TTTTGGC
* * * * *
22953 TGTTAAATTATATATATTAAATTAGTATT-TATGC-CAAAATTGATGAAAAAAATTTTCGGGTCA
127 T-TTAAATTATATATATTATATAAGTATTGT-GGCTAAAAATTGA-GAAAAATA-TTTCGGGTCA
* ** * * * *
23016 TTTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATCACGG-TTTTTGGCTGAAAACATGTT
188 ATTTTTGTAAAA-TTTAGCCGAAATC--G-AGT-ACCATCACGGTTTTTTGACTAAAAACACGTT
* * * **
23080 TCGGGACCCCGGCTTAGTTTTGCATGATTTTTGGTGCCGAGACTCCTTGAAATATCTATATTCAT
248 TCGGGACCCAGGCTCAGTTTTGCATGATTTTTAGTGCAAAGACTCCTTGAAATATCTATATTCAT
* *
23145 CTTATCAAAT
313 CTAACCAAAT
* * *
23155 CTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAA
1 CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG-TTTCATTTAATTAG
*
23220 AAATTAATTTAGAAAAATATGAAAAACAATATTAAAAGCGTGACGAGTCCTTCAATTTTTTTGGC
65 AAATTAATTAAGAAAAATATGAAAAACAATATTAAAAGCGTGA-GAGTCCTTCAA--TTTTTGGC
* * * *
23285 TTTTAATTATATATATTCTATGAGTATTGTGGCTAAAAATAGAGGAAAAATATTTCGGGTCAATT
127 TTTAAATTATATATATTATATAAGTATTGTGGCTAAAAATTGA-GAAAAATATTTCGGGTCAATT
* *
23350 TTTGTAAAACTTTAGCCGAAATCGAGTACCATCACGGTTTTTTGACTAAAAACGCG-TTCTGGGG
191 TTTGTAAAA-TTTAGCCGAAATCGAGTACCATCACGGTTTTTTGACTAAAAACACGTTTC-GGGA
* * *
23414 CCTCAGG-TCAGTTTTGCATGATTTTTAGTGGAAATATTCCTTGAAATATCTATATTCATCTAAC
254 CC-CAGGCTCAGTTTTGCATGATTTTTAGTGCAAAGACTCCTTGAAATATCTATATTCATCTAAC
23478 CAAAT
318 CAAAT
* * *
23483 CTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCATGTTTCATTTTAATTAG
1 CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCA-TTTAATTAG
* * * * * *
23548 AAATTAATTAAAAAACAAATAGGAAAAACAATATTAGAAGCGTGAGAAGCCCTTCAA--TCTGAC
65 AAATTAATT-AAGAA-AAATATGAAAAACAATATTAAAAGCGTGAG-AGTCCTTCAATTTTTGGC
* * * * * * *
23611 GTTGAATTATATATTTTTTTATAAGTACTGTGGCTAAAAATTGAGAAAGATATTTCGGATCAATT
127 TTTAAATTATATA-TATTATATAAGTATTGTGGCTAAAAATTGAGAAAAATATTTCGGGTCAATT
* * * * *
23676 TTTGTAAAATTTGAACCCAAATTGTGTACCATCAAGGTTTTTT
191 TTTGTAAAATTT-AGCCGAAATCGAGTACCATCACGGTTTTTT
23719 TTTTCTTTTG
Statistics
Matches: 476, Mismatches: 72, Indels: 37
0.81 0.12 0.06
Matches are distributed among these distances:
325 3 0.01
326 68 0.14
327 42 0.09
328 137 0.29
329 8 0.02
330 37 0.08
331 161 0.34
332 19 0.04
333 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (322 bp):
CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCATTTAATTAGA
AATTAATTAAGAAAAATATGAAAAACAATATTAAAAGCGTGAGAGTCCTTCAATTTTTGGCTTTA
AATTATATATATTATATAAGTATTGTGGCTAAAAATTGAGAAAAATATTTCGGGTCAATTTTTGT
AAAATTTAGCCGAAATCGAGTACCATCACGGTTTTTTGACTAAAAACACGTTTCGGGACCCAGGC
TCAGTTTTGCATGATTTTTAGTGCAAAGACTCCTTGAAATATCTATATTCATCTAACCAAAT
Found at i:23963 original size:278 final size:272
Alignment explanation
Indices: 23468--23965 Score: 610
Period size: 272 Copynumber: 1.8 Consensus size: 272
23458 AATATCTATA
* * * *
23468 TTCATCTAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCATG
1 TTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTATTTGTACGAGCATTTAAATCATG
* *
23533 TTTCATTTTAATTAGAAATTAATTAAAAAACAAATAGGAAAAACAATATTAGAAGCGTGAGAAGC
66 TTTCATTTTAATCAGAAATTAATTAAAAAACAAATAGGAAAAACAATATTAGAAGCGTGAAAAGC
** * *
23598 CCTTCAATCTGACGTTGAATTATATATTTTTTTATAAGTACTGTGGCTAAAAATTGAGAAAGATA
131 CCTTCAATCTGACGTTGAATTATATATTTTTTTATAAGTACTGTCACTAAAAATCGAGAAAAATA
23663 TTTCGGATCAATTTTTGTAAAATTTGAACCCAAATTGTGTACCATCAAGGTTTTTTTTTTCTTTT
196 TTTCGGATCAATTTTTGTAAAATTTGAACCCAAATTGTGTACCATCAAGGTTTTTTTTTTCTTTT
23728 GCTAAAAACGCG
261 GCTAAAAACGCG
* * * * *
23740 TTCATCTAACCAGATCTCAGCCATATTGTATTTAAGGATTTATTTGTACGA-CTTTCTAAATCCT
1 TTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTATTTGTACGAGCATT-TAAATCAT
* * *
23804 GTTTCGA-TTTAATCAGAAATTAATTTTGAAATA-AAATAGGAAAAACGATATTAGAAGCGTGAA
65 GTTTC-ATTTTAATCAGAAATTAA--TTAAAAAACAAATAGGAAAAACAATATTAGAAGCGTG-A
* * * * * * * *
23867 AAAGGCTTTCAATTTTTTTGGCGTTGAATTATTTA-TTTTTTATGAGTATTTTCACTAGAAAA-C
126 AAAGCCCTTCAA----TCTGACGTTGAATTATATATTTTTTTATAAGTACTGTCACTA-AAAATC
* *
23930 GAGGAAAAATTTTTCGGGTCAATTTTTGTAAAATTT
186 GA-GAAAAATATTTCGGATCAATTTTTGTAAAATTT
23966 AGCCGAAATC
Statistics
Matches: 187, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
271 3 0.02
272 71 0.38
273 28 0.15
274 16 0.09
277 19 0.10
278 50 0.27
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (272 bp):
TTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTATTTGTACGAGCATTTAAATCATG
TTTCATTTTAATCAGAAATTAATTAAAAAACAAATAGGAAAAACAATATTAGAAGCGTGAAAAGC
CCTTCAATCTGACGTTGAATTATATATTTTTTTATAAGTACTGTCACTAAAAATCGAGAAAAATA
TTTCGGATCAATTTTTGTAAAATTTGAACCCAAATTGTGTACCATCAAGGTTTTTTTTTTCTTTT
GCTAAAAACGCG
Found at i:24311 original size:25 final size:25
Alignment explanation
Indices: 24283--24331 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
24273 TCGGGTCAAT
24283 TTTTGCAAAATGTTAGCCGAAATCG
1 TTTTGCAAAATGTTAGCCGAAATCG
24308 TTTTGCAAAATGTTAGCCGAAATC
1 TTTTGCAAAATGTTAGCCGAAATC
24332 ATGTACTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (25 bp):
TTTTGCAAAATGTTAGCCGAAATCG
Found at i:25494 original size:199 final size:193
Alignment explanation
Indices: 25162--25539 Score: 516
Period size: 199 Copynumber: 1.9 Consensus size: 193
25152 GTCAATAATT
*
25162 TTTCCAGGCAATAATTTCTAAGCAAAAAGTTTATTGCATATATATAATTTCTCCACAATTTTCTT
1 TTTCCAGGCAATAATTTCTAAGCAAAAAGTTTATTGCACATATATAATTTCTCCACAATTTTCTT
* *
25227 AAAAGCATATTTAAGCTTTCCAGCCAATAAAGTTTAATAATTTCTCATGAGCAGATTTAGACCCT
66 AAAAGCAGATTTAAGCTTTCCAGCCAATAAAGTTTAATAATTTCTCATAAGCAGATTTAGACCCT
*
25292 TCTTCCCCCAACACTTCATTTGGTAAAGCTTTTC-AC-A-ATTTTCTCAAGAGCAGATTTATGC
131 TCTTCCCCCAACACTTCAATTGGTAAAGC-TTTCGACAATATTTTCTCAAGAGCAGATTTATGC
* * *
25353 TTTCCAGGCAATAATTGTCCT-AGCAATAATTTTATT-C-CATATATAATTTCTCCACAGTTTTC
1 TTTCCAGGCAATAATT-T-CTAAGCAAAAAGTTTATTGCACATATATAATTTCTCCACAATTTTC
* *
25415 TTTCTCAAAGCAGATTTAAGCTTTCGACTTCGAGGCAATAAAGTTTAATAATTTCTCATAAGCAG
64 --T-TAAAAGCAGATTTAAGCTTT---C--C-AGCCAATAAAGTTTAATAATTTCTCATAAGCAG
*
25480 ATTTAGACCCTTCTTTCCCCAACACTTCAATTGGTAAAGCTTTCGACAATATTTTCTCAA
120 ATTTAGACCCTTCTTCCCCCAACACTTCAATTGGTAAAGCTTTCGACAATATTTTCTCAA
25540 AGGCAATAAT
Statistics
Matches: 163, Mismatches: 10, Indels: 18
0.85 0.05 0.09
Matches are distributed among these distances:
190 23 0.14
191 17 0.10
192 15 0.09
193 20 0.12
196 1 0.01
198 5 0.03
199 71 0.44
200 1 0.01
201 10 0.06
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (193 bp):
TTTCCAGGCAATAATTTCTAAGCAAAAAGTTTATTGCACATATATAATTTCTCCACAATTTTCTT
AAAAGCAGATTTAAGCTTTCCAGCCAATAAAGTTTAATAATTTCTCATAAGCAGATTTAGACCCT
TCTTCCCCCAACACTTCAATTGGTAAAGCTTTCGACAATATTTTCTCAAGAGCAGATTTATGC
Done.