Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015663.1 Corchorus olitorius cultivar O-4 contig15696, 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: 22753
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:806 original size:31 final size:31
Alignment explanation
Indices: 764--827 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
754 AACAGCCAAT
764 AAAGCCCAATACTAA-CTAAAATAAGAAAATA
1 AAAGCCCAATACTAATCT-AAATAAGAAAATA
*
795 AAAGCCTAATACTAATCTAAATAAGAAAATA
1 AAAGCCCAATACTAATCTAAATAAGAAAATA
826 AA
1 AA
828 GACAAACTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.61, C:0.14, G:0.06, T:0.19
Consensus pattern (31 bp):
AAAGCCCAATACTAATCTAAATAAGAAAATA
Found at i:1002 original size:21 final size:20
Alignment explanation
Indices: 956--1002 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
946 TCCTCTTGCC
*
956 TTTCCATCGAGTCCTTGTCT
1 TTTCCATCGAGTCCTTGTAT
976 TCTTCCATCGAGTCCTTGTAT
1 T-TTCCATCGAGTCCTTGTAT
997 ATTTCC
1 -TTTCC
1003 TGTAAATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.13, C:0.30, G:0.13, T:0.45
Consensus pattern (20 bp):
TTTCCATCGAGTCCTTGTAT
Found at i:1959 original size:22 final size:23
Alignment explanation
Indices: 1920--1962 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
1910 AATCCTAATC
1920 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
1943 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
1963 ACTCCTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:6094 original size:11 final size:11
Alignment explanation
Indices: 6074--6108 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
6064 TTGACAGCGC
6074 AACAAAAACAA
1 AACAAAAACAA
*
6085 AACGAAAACAA
1 AACAAAAACAA
6096 AACAAAAACAA
1 AACAAAAACAA
6107 AA
1 AA
6109 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:10994 original size:334 final size:332
Alignment explanation
Indices: 10286--13254 Score: 2278
Period size: 334 Copynumber: 9.1 Consensus size: 332
10276 GCGGCCTCGC
* * * * * *
10286 CTCAGTTTTGCATGATTTTTGACGCC-AAGACTCGTT-ATGATATCCATATTTATTTAATCAAAG
1 CTCAGTTTTGCATGATTTTTGGCGCCGAAGACTCGTTGA-AATATCTATATTCATCTAATCAAAT
**
10349 CTCAGCCACATTGGATTT-AAGAATTTGTTTTTAAAAGCATCTGAATCTTGTTTCGATTTAATT-
65 CTCAGCCACATTGGATTTAAAG-ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
* *
10412 GAAATTAATTC---AAAAATATGAAAAACGATATTAAAAGCGCGAAAAGTCCTCCAAT-ATTTTT
129 GAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAG-CCTCCAATCTTTTTT
* * * * ** * *
10473 GGC-GTGAAATTATTTATATATTATGAGTATTTTATCCAAAAATTGAGGAAAAAAATTT-TGGGT
193 GGCATTG-AATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAAAATATTTCT-GGT
* * * * * *
10536 CATTTTTTGCAAAATTTTTAGCCAAAATCGTTTACTAACCATCACGGTTTTTTGGCTAAAAACGC
256 CAATTTTTGCAAAA-TTTTAGCCGAAATCGTGTAATAATCATCATGG-TTTTTGGCTAAAAACGC
* * **
10601 GTTTCGGGGCTTCGA
319 -ATTCCGGGCCCCGA
* * * * *
10616 CTCAGTTTTGGATGATTTTTGGCGCCG-ACATTCTTTGTAATATCTATATTCATCTAAT-ATAAT
1 CTCAGTTTTGCATGATTTTTGGCGCCGAAGACTCGTTGAAATATCTATATTCATCTAATCA-AAT
* * *
10679 CTTAGCCAAATTGCATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
65 CTCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
* *
10744 AAATTAATTCAGAAATAATATGAAAAACGATATTAAAAGCGTGAAAAGCCATTCAATCTTTTTTT
130 AAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCC-TCCAATC--TTTTT
* * * *
10809 TTGCATTGAATTATATATTTTTTATGAGTATTATGGCTAAAAATTGAGGAAATATCTTTCTGGTC
192 TGGCATTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAAAATATTTCTGGTC
* *
10874 AATTTGTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCATGGTTTTTGGCTAAAAACGCAAT
257 AATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCATGGTTTTTGGCTAAAAACGCATT
*
10939 CCGGGACCCGA
322 CCGGGCCCCGA
* * * * *
10950 TTCAATTTTGAATGATTTTTGGTGCCGAAG-CTCGTTGAAATATCTATATTCATCTAACCAAATC
1 CTCAGTTTTGCATGATTTTTGGCGCCGAAGACTCGTTGAAATATCTATATTCATCTAATCAAATC
* * * *
11014 CCAG-C-C-----A-TT---G--TT-TTTATA--AGCATCTGAATCATGTTTCGTTTTAATTAGA
66 TCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* * * * * *
11063 AATTTAATTCGGAAAAAATAGGAAAAACGATATTGAAAGCTTGATAAGCCCTTCAATC-TTTTTG
131 AA-TTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAG-CCTCCAATCTTTTTTG
* * * *
11127 GCGTTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTAAGAAAAAAATATTTC-GGATC
194 GCATTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAG-GAAAAATATTTCTGG-TC
* * * ** ** * *
11191 AATTTTTGCAAAATATTAGCCGAAATCGTGTAA-CAT-AACGATTTTTTTTTACTAAAAACACGT
257 AATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATC-ATGGTTTTTGGCTAAAAACGCAT
** *
11254 TATGGGGCCCCGG
321 T-CCGGGCCCCGA
* * * ** * *
11267 GTTAGTTTTGCATGAGTTTTGGTACC-AAGACTCCTTGAAATATCTATATTTATCTAATCAAATC
1 CTCAGTTTTGCATGATTTTTGGCGCCGAAGACTCGTTGAAATATCTATATTCATCTAATCAAATC
* * * *
11331 -CGAGCCACATTGGATTTAAGGATTAGTTTTTACGAGTATCTAAATCTTGTTTCGATTTAATTAG
66 TC-AGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
** * * * * * *
11395 AAATTAATTTGGAAAAAAGTAGGAAAAACGATATTAGAAGCGTAAAATACCCTTCAAT-ATTTTT
130 AAATTAATTCAGAAAAAA-TATGAAAAACGATATTAAAAGCGTGAAA-AGCCTCCAATCTTTTTT
* * * * * * * *
11459 GGCGTTGAATTATATATTTTTTTATGAGTATATTTTAGC-CAAAATGGAGGAAATATCTTTTTAG
193 GGCATTGAATTATATA-TTTTTTATGAG--TATTTTGGCTAAAAATTGAGGAAAAATATTTCTGG
* * * * *
11523 TCAA-CTTTGCAAAATTTTAGCCGAAATCGTGTAATAATTATCGTGGTTTTTGACT--ACACGCA
255 TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCATGGTTTTTGGCTAAAAACGCA
* *
11585 TTTCAGGG-CCCGG
320 -TTCCGGGCCCCGA
* * * ** * * *
11598 GT-ATGTTTTGCATTATTTTTGGTG-TTAAGACT-GCTTGAGATATCCATATTCATCTAATGAAA
1 CTCA-GTTTTGCATGATTTTTGGCGCCGAAGACTCG-TTGAAATATCTATATTCATCTAATCAAA
* * * * *
11660 TCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGGTCTAATTA
64 TCTCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
* **
11725 GAAATTAATTCATAAAAAATATGAAAAACGATAGAAAAAGCGTGAAAAGTCCTCCAATC-TTTTT
129 GAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAG-CCTCCAATCTTTTTT
* * * * * * *
11789 CGCATTAAATTATATATATATTTCAAGAGTATTTTAGCTAAAAATTGAGGAAAAACTTTTTTTGG
193 GGCATTGAATTATATAT-T-TTTTATGAGTATTTTGGCTAAAAATTGAGGAAAAA-TATTTCTGG
* * * * *
11854 T-AATTTTTTACAAAATTTTAGTCGAAATCGTG------T-A-C-TGTTTTTTTGCTAAAAATGC
255 TCAA-TTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCATGGTTTTTGGCTAAAAACGC
* *
11909 ATTTCGGGGCTCCGA
319 A-TTCCGGGCCCCGA
* * * * * *
11924 CTCGGTTTTGCATGATTTTTGACGTCG-AGTCTCTTTAAAATATCTATATTCATCTAATCAAATC
1 CTCAGTTTTGCATGATTTTTGGCGCCGAAGACTCGTTGAAATATCTATATTCATCTAATCAAATC
* * * *
11988 TTAGCCACATTGAATTT-AAGTATTT-TTTTTACGAGCATCTCAATCTTGTTTCAATTTAATTAG
66 TCAGCCACATTGGATTTAAAG-ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
* * *
12051 AAATTAATTTAG-AAAGATATGAAAAACGATATTAAAAGCGTGAAAATTCCTCCAATC-TTTTTG
130 AAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAA-GCCTCCAATCTTTTTTG
* * *
12114 G-AGTTGAATTATATATATTTTATGAGTATTTAAGAC-AAAAATTGAGGAAAAATATTTCTGGTC
194 GCA-TTGAATTATATATTTTTTATGAGTATTT-TGGCTAAAAATTGAGGAAAAATATTTCTGGTC
* * * * * *
12177 AATTTTTGTAAAATATTAGGCGAAATCGTGTATGTTAGTCAAAATCATAGTTTTTGGCTAAAAAC
257 AATTTTTGCAAAATTTTAGCCGAAATCGTGTA--ATAATC---ATCATGGTTTTTGGCTAAAAAC
** * *
12242 GTGTTCCAGGGCCACGG
317 GCATTCC-GGGCCCCGA
* * * * * *
12259 TTCAGTGTTGCAT-AATTTTGGCACCG-AGAATCGTTG-AATATCTATATTCATCTAATCAAATA
1 CTCAGTTTTGCATGATTTTTGGCGCCGAAGACTCGTTGAAATATCTATATTCATCTAATCAAATC
* * * * *** * * * *
12321 TCAGTCTCATTGGAATTAAGGATTTGTAAAT-CAAGCATCTGAATCATGTTTCAATTTAATTATA
66 TCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* * * * * *
12385 AATTAATTCAGAAAATAATAGGAAAAACGATATTAGAAGCATGAAATGCCCTTCAAT-ATTTTTG
131 AATTAATTCAGAAAA-AATATGAAAAACGATATTAAAAGCGTGAAAAG-CCTCCAATCTTTTTTG
** * * * *
12449 GTGTTAAATTATATAATTTTTATGATTATTGTGGCTAAAAATTGAGG--AAATGACTTTC-GAGT
194 GCATTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAAAAT-A-TTTCTG-GT
** * *
12511 CAATTTTTAAAAAATTCTAGCCGAAATCGTGTAATAATCATCATGGTTTTTTTGGCTAAAAATG-
256 CAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCATGG--TTTTTGGCTAAAAACGC
* *
12575 AGTTCTGGGGCCCCGG
319 A-TTC-CGGGCCCCGA
* * * *
12591 CTAAATTTTGCATGATTTTTCGCGCC-AAGACTC-TTCGAGATATCTATATTCATCTAATCAAAT
1 CTCAGTTTTGCATGATTTTTGGCGCCGAAGACTCGTT-GAAATATCTATATTCATCTAATCAAAT
* * * * * *
12654 CTCAGCTATATTGGATTT-AAGAATTTTTTTTTGCGAACATCTGAATCTTGTTTCAATTTAATTA
65 CTCAGCCACATTGGATTTAAAG-ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
* *
12718 GAAATTAATTCAGAAAAAATATGAAAAACGATACTAAAAGCGTGAAAAGTCCTCCAAT-ATTTTT
129 GAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAG-CCTCCAATCTTTTTT
* * * * *
12782 GGCATTAAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACGGAAAAATTTTTC-GAGT
193 GGCATTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGA-GGAAAAATATTTCTG-GT
* * * * * * *
12846 CATTTTTTGCAAAATTTCAGCCGAAATCTTGT-AT--T--TTACGGTTTTTGTCTAAAAACGCGT
256 CAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCATGGTTTTTGGCTAAAAACGCAT
*
12906 TTCGTGGCCCCGA
321 TCCG-GGCCCCGA
* * * *
12919 --C----TT--A-G--TTTTGGAGTCG-AGACTC---GAAATATATGTATTTC-TCTAATCAAAT
1 CTCAGTTTTGCATGATTTTTGGCGCCGAAGACTCGTTGAAATATCTATA-TTCATCTAATCAAAT
* ** * * * *
12968 CTCAGCCAGATTAAATTTAATGATTTGTTTTAACGAGCATTTGAAT-TTGGTTTCGATTTAATTT
65 CTCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTGAATCTT-GTTTCGATTTAATTA
* * **
13032 GAAATTAATTTAG-AAAAATATGAAAAATGATATTAAAAGCGTGCAAACTCCTCCAATC-TTTTT
129 GAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTG-AAAAGCCTCCAATCTTTTTT
** * * * * * *
13095 GGTGTTTAATTATATATATTTTATGAGT-TTTGTGGCTAAAAATTTAGAAAAAATATTTCGGGTT
193 GGCATTGAATTATATATTTTTTATGAGTATTT-TGGCTAAAAATTGAGGAAAAATATTTCTGGTC
* * * ** * * *
13159 AATTTTTACAAAATTTTAACCAAAATCGTGTACCAATCA-CGAT--TTTTTGTCTAAAAATGCGT
257 AATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATC-ATGGTTTTTGGCTAAAAACGCAT
* * *
13221 TTCGGAGTTCCGGA
321 TCCGG-G-CCCCGA
13235 -TCAGTTTTGCATGATTTTTG
1 CTCAGTTTTGCATGATTTTTG
13255 ACGAAAAATA
Statistics
Matches: 2117, Mismatches: 382, Indels: 284
0.76 0.14 0.10
Matches are distributed among these distances:
312 41 0.02
313 80 0.04
314 82 0.04
315 31 0.01
316 77 0.04
317 117 0.06
318 32 0.02
319 48 0.02
320 8 0.00
321 36 0.02
322 32 0.02
323 13 0.01
324 61 0.03
325 60 0.03
326 78 0.04
327 2 0.00
328 24 0.01
329 13 0.01
330 178 0.08
331 162 0.08
332 84 0.04
333 220 0.10
334 286 0.14
335 248 0.12
336 34 0.02
337 67 0.03
338 3 0.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (332 bp):
CTCAGTTTTGCATGATTTTTGGCGCCGAAGACTCGTTGAAATATCTATATTCATCTAATCAAATC
TCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
AATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCTCCAATCTTTTTTGGC
ATTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAAAATATTTCTGGTCAATT
TTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCATGGTTTTTGGCTAAAAACGCATTCCGG
GCCCCGA
Found at i:12390 original size:333 final size:327
Alignment explanation
Indices: 10325--12879 Score: 1383
Period size: 335 Copynumber: 7.7 Consensus size: 327
10315 ACTCGTTATG
* * * * * * *
10325 ATATCCATATTTATTTAATCAAAGCTCAGCCACATTGGATTTAAGAATTTGTTTTTAAAAGCATC
1 ATATCTATATTCATCTAATCAAATCTCAG-CTCATTGGAATTAAGAATTT-TTTTTACAAGCATC
* *
10390 TGAATCTTGTTTCGATTTAATT-GAAATTAATTCA-AAAATATGAAAAACGATATTAAAAGCGCG
64 TGAATCTTGTTTCAATTTAATTAGAAATTAATTCAGAAAATATGAAAAACGATATTAAAAGCGTG
* * * * * **
10453 AAAAGTCCTCCAATATTTTTGGCGTGAAATTATTTATATATTATGAGTATTTTATCCAAAAATTG
129 AAAATTCCTCCAATATTTTTGGAGTTAAATTATATATATTTTATGAGTA-TTTAGACAAAAATTG
* * * * * * * *
10518 AGGAAAAAAATTTTGGGTCATTTTTTGCAAAATTTTTAGCCAAAATCGT-T-TACTAACCATCAC
193 AGGAAAAATATTTCGAGTCAATTTTTG-AAAA-ATTTAGCCGAAATCGTGTATA-TAATCATCAT
* * * * ** * * * * * * * * * *
10581 GGTTTTTTGGCTAAAAACGCGTTTCGGGGCTTCGACTCAGTTTTGGATGATTTTTGGCGCCGACA
255 AGTTTTTTGGCTAAAAACGAGTTCCAGGGCCACGGCTAAATGTTGCATGAATTTTCGCACCAAGA
* *
10646 TTCTTTGTA
320 ATCTTCG-A
* * * *
10655 ATATCTATATTCATCTAAT-ATAATCTTAGC-CAAATTGCATTTAA-AGATTTGTTTTTACGAGC
1 ATATCTATATTCATCTAATCA-AATCTCAGCTC--ATTGGAATTAAGA-ATTT-TTTTTACAAGC
*
10717 ATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAATAATATGAAAAACGATATTAAAA
61 ATCTGAATCTTGTTTCAATTTAATTAGAAATTAATTCAG-AA-AATATGAAAAACGATATTAAAA
* * * * * *
10782 GCGTGAAAA-GCCATTCAATCTTTTTTTTTGCA-TTGAATTATATATTTTTTATGAGTA-TTATG
124 GCGTGAAAATTCC-TCCAA----TATTTTTGGAGTTAAATTATATATATTTTATGAGTATTTA-G
* * * * *
10844 GCTAAAAATTGAGGAAATATCTTTCTG-GTCAATTTGTGCAAAATTTTAGCCGAAATCGTGTA-A
183 AC-AAAAATTGAGGAAAAATATTTC-GAGTCAATTTTTG-AAAAATTTAGCCGAAATCGTGTATA
* * ** * * * *
10907 TAATCATCAT-GGTTTTTGGCTAAAAACGCA-ATCC-GGGACC-CGATTCAATTTTGAATGATTT
245 TAATCATCATAGTTTTTTGGCTAAAAACG-AGTTCCAGGG-CCACGGCTAAATGTTGCATGAATT
* ** *
10968 TTGGTGCCGAAG-CTCGTT-GAA
308 TTCGCACC-AAGAATC-TTCG-A
* * *
10989 ATATCTATATTCATCTAACCAAATCCCAGC-C------ATT--G-----TTTTTATAAGCATCTG
1 ATATCTATATTCATCTAATCAAATCTCAGCTCATTGGAATTAAGAATTTTTTTTACAAGCATCTG
* ** * * * *
11040 AATCATGTTTCGTTTTAATTAGAAATTTAATTCGGAAAAAATAGGAAAAACGATATTGAAAGCTT
66 AATCTTGTTTCAATTTAATTAGAAA-TTAATTC--AGAAAATATGAAAAACGATATTAAAAGCGT
* ** * * * * * *
11105 GATAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGT-GGCTAAAAAT
128 GAAAATTCCTCCAATATTTTTGGAGTTAAATTATATATATTTTATGAGTATT-TAGAC-AAAAAT
* * * *
11169 TAAGAAAAAAATATTTCG-GATCAATTTTTGCAAAATATTAGCCGAAATCGTGTAACATAA-CGA
191 TGAG-GAAAAATATTTCGAG-TCAATTTTTGAAAAAT-TTAGCCGAAATCGTGT-ATATAATC-A
** *** * * * * * * * *
11232 T--T--TTTTTTTACTAAAAAC-ACGTTATGGGGCCCCGGGTTAGTTTTGCATGAGTTTTGGTAC
251 TCATAGTTTTTTGGCTAAAAACGA-GTTCCAGGGCCACGGCTAAATGTTGCATGAATTTTCGCAC
*
11292 CAAGACTCCTT-GAA
315 CAAGAAT-CTTCG-A
* * * * * * *
11306 ATATCTATATTTATCTAATCAAATC-CGAGCCACATTGGATTTAAGGATTAGTTTTTACGAGTAT
1 ATATCTATATTCATCTAATCAAATCTC-AG-CTCATTGGAATTAAGAATT-TTTTTTACAAGCAT
* * * * * *
11370 CTAAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAGTAGGAAAAACGATATTAGAAG
63 CTGAATCTTGTTTCAATTTAATTAGAAATTAA-TT-CAGAAAA-TATGAAAAACGATATTAAAAG
* * * * *
11435 CGT-AAAATACCCTTCAATATTTTTGGCGTTGAATTATATATTTTTTTATGAGTATATTTTAG-C
125 CGTGAAAAT-TCCTCCAATATTTTTGGAGTTAAATTATATA-TATTTTATGAG--TA-TTTAGAC
* * * * ** * *
11498 CAAAATGGAGGAAATATCTTTTTAGTCAA-CTTTGCAAAATTTTAGCCGAAATCGTGTA-ATAAT
185 AAAAATTGAGGAAAAATATTTCGAGTCAATTTTTG-AAAAATTTAGCCGAAATCGTGTATATAAT
* * * * * * * ** * * * * *
11561 TATCGT-GGTTTTTGACT--ACACGCA-TTTCAGGGCC-CGGGTATGTTTTGCATTATTTTTGGT
249 CATCATAGTTTTTTGGCTAAAAACG-AGTTCCAGGGCCACGGCTAAATGTTGCATGAATTTTCGC
*** *
11621 GTTAAGACTGCTT-GA
313 ACCAAGAAT-CTTCGA
* * * * * * * *
11636 GATATCCATATTCATCTAATGAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGTAT
1 -ATATCTATATTCATCTAATCAAATCTCAG-CTCATTGGAATTAAGAATTT-TTTTTACAAGCAT
** * * **
11701 CTGAATCTTGTTTCGGTCTAATTAGAAATTAATTCATAAAAAATATGAAAAACGATAGAAAAAGC
63 CTGAATCTTGTTTCAATTTAATTAGAAATTAATTC--AGAAAATATGAAAAACGATATTAAAAGC
* * * *
11766 GTGAAAAGTCCTCCAATCTTTTTCGCA-TTAAATTATATATATATTTCAAGAGTATTTTAG-CTA
126 GTGAAAATTCCTCCAATATTTTT-GGAGTTAAATTATATATAT-TTT-ATGAGTA-TTTAGAC-A
* * * *
11829 AAAATTGAGGAAAAACTTTTTTTG-GT-AATTTTTTACAAAATTTTAGTCGAAATCGTG------
186 AAAATTGAGGAAAAA--TATTTCGAGTCAATTTTTGA-AAAA-TTTAGCCGAAATCGTGTATATA
* * * * * *** *
11886 -T-A-C-T-GTTTTTTTGCTAAAAATGCA-TTTCGGGGCTC-CGACTCGGTTTTGCATG-ATTTT
247 ATCATCATAGTTTTTTGGCTAAAAACG-AGTTCCAGGGC-CACGGCTAAATGTTGCATGAATTTT
* * ** **
11943 TG-ACGTCGAGTCTCTTTAAA
310 CGCAC--CAAGAATC-TTCGA
* * * *
11963 ATATCTATATTCATCTAATCAAATCTTAGCCACATT-GAATTTAAGTATTTTTTTTACGAGCATC
1 ATATCTATATTCATCTAATCAAATCTCAG-CTCATTGGAA-TTAAGAATTTTTTTTACAAGCATC
* *
12027 TCAATCTTGTTTCAATTTAATTAGAAATTAATTTAGAAAGATATGAAAAACGATATTAAAAGCGT
64 TGAATCTTGTTTCAATTTAATTAGAAATTAATTCAGAAA-ATATGAAAAACGATATTAAAAGCGT
* *
12092 GAAAATTCCTCCAATCTTTTTGGAGTTGAATTATATATATTTTATGAGTATTTAAGACAAAAATT
128 GAAAATTCCTCCAATATTTTTGGAGTTAAATTATATATATTTTATGAGTATTT-AGACAAAAATT
* * * *
12157 GAGGAAAAATATTTCTG-GTCAATTTTTGTAAAATATTAGGCGAAATCGTGTATGTTAGTCAAAA
192 GAGGAAAAATATTTC-GAGTCAATTTTTGAAAAAT-TTAGCCGAAATCGTGTAT-ATAATC---A
* * * * *
12221 TCATAG-TTTTTGGCTAAAAACGTGTTCCAGGGCCACGGTTCAGTGTTGCAT-AATTTTGGCACC
251 TCATAGTTTTTTGGCTAAAAACGAGTTCCAGGGCCACGGCTAAATGTTGCATGAATTTTCGCACC
*
12284 GAGAATCGTT-GA
316 AAGAATC-TTCGA
* * * **
12296 ATATCTATATTCATCTAATCAAATATCAGTCTCATTGGAATTAAGGA-TTTGTAAATCAAGCATC
1 ATATCTATATTCATCTAATCAAATCTCAG-CTCATTGGAATTAAGAATTTTTTTTA-CAAGCATC
* * *
12360 TGAATCATGTTTCAATTTAATTATAAATTAATTCAGAAAATAATAGGAAAAACGATATTAGAAGC
64 TGAATCTTGTTTCAATTTAATTAGAAATTAATTCAGAAAAT-AT--GAAAAACGATATTAAAAGC
* * * * * *
12425 ATG-AAATGCCCTTCAATATTTTTGGTGTTAAATTATATA-ATTTTTATGATTATTGT-GGCTAA
126 GTGAAAAT-TCCTCCAATATTTTTGGAGTTAAATTATATATA-TTTTATGAGTATT-TAGAC-AA
*
12487 AAATTGAGG--AAATGACTTTCGAGTCAATTTTTAAAAAATTCTAGCCGAAATCGTGTA-ATAAT
187 AAATTGAGGAAAAAT-A-TTTCGAGTCAATTTTTGAAAAATT-TAGCCGAAATCGTGTATATAAT
* * ** * * *
12549 CATCATGGTTTTTTTGGCTAAAAATGAGTTCTGGGGCCCCGGCTAAATTTTGCATGATTTTTCGC
249 CATCATAG-TTTTTTGGCTAAAAACGAGTTCCAGGGCCACGGCTAAATGTTGCATGAATTTTCGC
* *
12614 GCCAAGACTCTTCGA
313 ACCAAGAATCTTCGA
* * *
12629 GATATCTATATTCATCTAATCAAATCTCAGCTATATTGGATTTAAGAATTTTTTTTTGCGAA-CA
1 -ATATCTATATTCATCTAATCAAATCTCAGCT-CATTGGAATTAAGAA-TTTTTTTTAC-AAGCA
*
12693 TCTGAATCTTGTTTCAATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATACTAAAAG
62 TCTGAATCTTGTTTCAATTTAATTAGAAATTAATTCAG--AAAATATGAAAAACGATATTAAAAG
* *
12758 CGTGAAAAGTCCTCCAATATTTTTGGCA-TTAAATTATATATATTTTATGAGTATTTTAGCCAAA
125 CGTGAAAATTCCTCCAATATTTTTGG-AGTTAAATTATATATATTTTATGAGTA-TTTAGACAAA
* * * *
12822 AATTGACGGAAAAATTTTTCGAGTCATTTTTTGCAAAATTTCAGCCGAAATCTTGTAT
188 AATTGA-GGAAAAATATTTCGAGTCAATTTTTGAAAAATTT-AGCCGAAATCGTGTAT
12880 TTTACGGTTT
Statistics
Matches: 1789, Mismatches: 276, Indels: 314
0.75 0.12 0.13
Matches are distributed among these distances:
314 1 0.00
315 7 0.00
316 64 0.04
317 93 0.05
318 42 0.02
319 46 0.03
320 9 0.01
321 25 0.01
322 31 0.02
323 19 0.01
324 58 0.03
325 65 0.04
326 64 0.04
327 2 0.00
328 1 0.00
329 15 0.01
330 142 0.08
331 158 0.09
332 90 0.05
333 223 0.12
334 258 0.14
335 262 0.15
336 40 0.02
337 66 0.04
338 8 0.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.38
Consensus pattern (327 bp):
ATATCTATATTCATCTAATCAAATCTCAGCTCATTGGAATTAAGAATTTTTTTTACAAGCATCTG
AATCTTGTTTCAATTTAATTAGAAATTAATTCAGAAAATATGAAAAACGATATTAAAAGCGTGAA
AATTCCTCCAATATTTTTGGAGTTAAATTATATATATTTTATGAGTATTTAGACAAAAATTGAGG
AAAAATATTTCGAGTCAATTTTTGAAAAATTTAGCCGAAATCGTGTATATAATCATCATAGTTTT
TTGGCTAAAAACGAGTTCCAGGGCCACGGCTAAATGTTGCATGAATTTTCGCACCAAGAATCTTC
GA
Found at i:14939 original size:20 final size:20
Alignment explanation
Indices: 14914--14951 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
14904 GCAACATCAT
* *
14914 GCCACATTAGCACTTTTTGA
1 GCCACATCAGCAATTTTTGA
14934 GCCACATCAGCAATTTTT
1 GCCACATCAGCAATTTTT
14952 TACGATCGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.34
Consensus pattern (20 bp):
GCCACATCAGCAATTTTTGA
Done.