Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010698.1 Corchorus capsularis cultivar CVL-1 contig10719, 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: 56313
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1956 original size:319 final size:316
Alignment explanation
Indices: 42--4697 Score: 2859
Period size: 321 Copynumber: 14.4 Consensus size: 316
32 GTAGCCCCAG
* * * * * *
42 CTCAATTTTGAATGATTTTT-G-ATGCAAAGACTCCTTGAAATATCTATCTTCATCGAATCAATT
1 CTCAGTTTTGCATGATTTTTGGCAT--AAAGACTCCTTGAAATATCTATATTCATCTAACCAAAT
* * ** * * *
105 CTCAGCCTCATTGGATAAAAGCG-TTTGTTTTTACGGGCATCTAAATCTTGTTT-G----CATTA
64 ATCAGCCACATT-GATTTAAG-GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
* *
164 GAAATTAATTC-GAGAAAAAA-ATGAAAAACGATATTAGAAGCGTGAAAACCCCGTCAATCTTTT
127 GAAATTAATTCGGA-AAAAAATATGAAAAACGATATTAGAAGCGTGAAAA-CCCTTCAATTTTTT
* * * * * * * *
227 TGGTGTTGAATTATATATTTCTT-TAAATATTGTGGCAAGAATTTGAGAAAAAAAATTTCATGTC
190 TGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG-AAAAAATTTTCAGGTC
* * * * * * *
291 AG-TTTTACCCAAAATCGTGTA-CGTTAC-AGTTTTTGGCTAAAAACGTGTTTCGGGGGCTCGA
254 AGTTTTTAGCCGAAATCGTATACCATCACGA-TTTTTGGCTAAAAACGCGTTTCGGGGCCTCGA
* * ** *
352 CTCCGTTTTGCATGGTTTTTTACATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCT
1 CTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATAT
* *
417 CAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGTATCTTGTTTCGATTTAATTAGAA
66 CAGCCACATT-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
* * * *
482 ATAAATTCGG--AAAAATATGAAAAACGATATTAGAAGAGTGAAAAACCCTTCAATTATTCTGGC
130 ATTAATTCGGAAAAAAATATGAAAAACGATATTAGAAGCGTG-AAAACCCTTCAATTTTTTTGGC
* * * * * *
545 ATTGAATTATATATATATATATTTTTAGTATTGCGGCAAAAAATTGAGGAAAAACTTTTTTCGGG
194 GTTGAATTATATAT-T-T-T-TTCTGAGTATTGTGGCAAAAAATTGA-GAAAAA--ATTTTCAGG
* * *
610 TTAGTTTTTGCAAAATTTTAGCCGAAATCGTATACTAACCATCACGGTTTGTGGCTAAAAACGCG
252 TCAG----T------TTTTAGCCGAAATCG--TA-T-ACCATCACGATTTTTGGCTAAAAACGCG
* *** *
675 TTCCATAGCCCCTG-
303 TTTCGGGGCCTC-GA
* * * ** * * * * * *
689 CTCAATTTTGAATGATTTTTGACGCAAAGACTCTTTGAAATATCCATATTCATCGAATCAATTCT
1 CTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATAT
* * ** * * *
754 CAACCTCATTGGATAAAAGCATTTGTTTTTACGGGCATCTGAATCTTGTTT-GCATTTAATTATA
66 CAGCCACATT-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCG-ATTTAATTAGA
** * *
818 AATTAATTC-GAGAAAAAA-ATGAAAAACGATATTAGAAGCGTGAAAACCCCCGACAATCTTTAT
129 AATTAATTCGGA-AAAAAATATGAAAAACGATATTAGAAGCGTGAAAA--CCCTTCAATTTTTTT
* * * * *
881 GGGGTTGAATTTTATATTTTTTTTAAGTATTGTAGCAAAAAATTGAGAAAAAAACTTTTC-GTGT
191 GGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG-AAAAAA-TTTTCAG-GT
* * * * *
945 CAGTTTTTAGCCAAAAT-ATACTAACCATCGCGATTTTTGGCTAAAAACGCGTTTCAGGGTCTCG
253 CAGTTTTTAGCCGAAATCGTA-T-ACCATCACGATTTTTGGCTAAAAACGCGTTTCGGGGCCTCG
1009 A
316 A
* * * ** * * *
1010 CTCCGTTTTGTATGGTTTTTTACATAAAGACTCATTGAAATATCTATATTTATCTAACCAAATCT
1 CTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATAT
* * *
1075 CAGTCACATTGGATTTAA-GA--------TACGAGCATCTGTATCTTGTTTCGATTTAATTATAA
66 CAGCCACATT-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
* * * * * * *
1131 ATAAATTCGG--AAAGATATGAAAGACGTTATTAGAAGAGTGAAAAACCTTTCAATTATTTTGGC
130 ATTAATTCGGAAAAAAATATGAAAAACGATATTAGAAGCGTG-AAAACCCTTCAATTTTTTTGGC
* * *
1194 ATTG-A-T-T-T-TTTTTT-TGAGTATTGTGGCAAAATAAATTGAGAAAAAACTTTTCGGGTTAG
194 GTTGAATTATATATTTTTTCTGAGTATTGTGGC-AAA-AAATTGAGAAAAAA-TTTTCAGGTCAG
* * * * *
1253 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACTATCGCGGTTTTTGGCTAAAAATGCGTTGC
256 ----T------TTTTAGCCGAAATC--GTA-T-ACCATCACGATTTTTGGCTAAAAACGCGTTTC
** *
1318 GTAGCC-CCA
307 GGGGCCTCGA
* * ** * * * *
1327 GCTCAATTTTGCATGATTTTTGACGCAAAGACTCCTTGAAATATCTATATTCATCGAATCAATTC
1 -CTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATA
* ** * * *
1392 TCAGCCTCATTGGATAAAAGCG-TTTGTTTTTACGGGTATCTAAATCTTGTTT-GCATTTAATTA
65 TCAGCCACATT-GATTTAAG-GATTTGTTTTTACGAGCATCTGAATCTTGTTTCG-ATTTAATTA
* * * *
1455 TAAATTAATTC-GAGAAAAA-ATGAAAAACGATATTAGAAGCGTGAAAACCCCATCAATATTTTT
127 GAAATTAATTCGGAAAAAAATATGAAAAACGATATTAGAAGCGTGAAAA-CCCTTCAATTTTTTT
* * *
1518 GGCGTTGAATTATATATTTTTT-TAAATATTGTGGCAAAAGATTGAGAAAAAAATTTTC-GTGTC
191 GGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG-AAAAAATTTTCAG-GTC
* ** * * * *
1581 AATTTTTTTCCCAAAATCGTGTA-CATCAC-AGTTTTTTGCTAAAAACGCGTTTCGGGGCCTTGA
254 -AGTTTTTAGCCGAAATCGTATACCATCACGA-TTTTTGGCTAAAAACGCGTTTCGGGGCCTCGA
* * * * * *
1644 CTTAGTTTTGTATGATTTTTGTCAAAAAGACTCCTTGAAATATCGATATTCATCTAACCAAATGT
1 CTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATAT
* * * *
1709 TAGCCACAAATT-TTTTAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAAA
66 CAGCCAC--ATTGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* * *
1773 AATAAATTCGGAAAAAAAATATGAAAAACGATATTAGAAGCATGAAAAGTCCTTCAATTTTTTTG
129 AATTAATTCGG-AAAAAAATATGAAAAACGATATTAGAAGCGTGAAAA-CCCTTCAATTTTTTTG
* * * * *
1838 GCGTTAAATTATGTATTTTTTATGAGTACTATGGCAAAAAATTGAGAAAAAATTTTCAGGTCAGT
192 GCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTTTCAGGTCAGT
***
1903 TTTTAGCCGAAATCGTATACCATCACGATTTTTTAATAAAAACGCGTTTCGGGGCCTCGA
257 TTTTAGCCGAAATCGTATACCATCACGATTTTTGGCTAAAAACGCGTTTCGGGGCCTCGA
* * * * * *
1963 CTCAGTTTCGTATGGTTTCTGACATAAAGACT-CTATGAAATATCTATATTCATCTAACCAAATC
1 CTCAGTTTTGCATGATTTTTGGCATAAAGACTCCT-TGAAATATCTATATTCATCTAACCAAATA
* * *
2027 TCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTTAATCTTGTTTTGATTTAATTAGA
65 TCAGCCACATT-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* * * *
2092 AATAAATTCGGAAAAAAATATTAAAAACGATATTAGAAGCGTGAAAACCCCTTTAATTTTTCTGG
129 AATTAATTCGGAAAAAAATATGAAAAACGATATTAGAAGCGTGAAAA-CCCTTCAATTTTTTTGG
* * * *
2157 CATTGAATTATATATTTTTTCTTAGTATTGTGGCAAAAAATTGAGAAAATACTTTTTAGGTCAGT
193 CGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAA-AATTTTCAGGTCAG-
* * * * **
2222 TTTTGCAAAATTTTAGCCGAAATCGTGTACCACCACGGTTTTTGGCTAAGAAACGCGTTCCAGAT
256 ---T------TTTTAGCCGAAATCGTATACCATCACGATTTTTGGCTAA-AAACGCGTTTC-GGG
* *
2287 ACC-CGG
310 GCCTCGA
* ** * * *
2293 CTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATATATATGT-ATATATA-TATAT
1 CTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATAT-TCATCTA-ACCA-A-
* *** * * ** ** * * **** * * ** *
2356 ATATATATATATATTCATCGAACCAATTCTCAGCCACATTGGGTATAAGGAT-TTGTTTTTACGA
62 ATAT-CAGCCACATTGATTTAAGGATTTGT-TTTTAC---GAGCATCTGAATCTTG--TTT-CGA
* * * ** ** * *
2420 TCATCTGAATCTTGTTTGCATTTAATT-TTAAATTAATTTGGGAAAACGATATTAGAAGCGTG-A
119 T--T-T-AA-----TTAGAAATTAATTCGGAAAAAAATAT-GAAAAACGATATTAGAAGCGTGAA
* * * *
2483 AACCCTTCGATTTTTTTCGCGTTGAATTATAT-TATTTTTCTGGGTATTGTGGTAAAAAATTGAG
174 AACCCTTCAATTTTTTTGGCGTTGAATTATATAT-TTTTTCTGAGTATTGTGGCAAAAAATTGA-
* *
2547 GAAAAAACTTTTCAGGTCAGATTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATGGTT
237 GAAAAAA-TTTTCAGGTCAG----T------TTTTAGCCGAAATC--GTA-T-ACCATCACGATT
* * * * * * *
2612 TTTGACTAAAAATGCATTACGGAGCCCCGT
287 TTTGGCTAAAAACGCGTTTCGGGGCCTCGA
* * * * *
2642 CTCAATTGTGCATGATTTTTGGCACAAAGACTCCTTGAAATATCCTA-ATTCATCGAACCAAATC
1 CTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATAT-CTATATTCATCTAACCAAATA
* ** * * * *
2706 TCAGCTACATTGGATACAAGGATTTGTTTTTACGAGGAACTGAATTTTATTTCGATTTAATTAGA
65 TCAGCCACATT-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* * * *
2771 AATTATTTCAGAAAAAAAT-GGGAAAACGATATTAGAAGCGTGAAAA-CCTGTCAAGTTTTTTT-
129 AATTAATTCGGAAAAAAATATGAAAAACGATATTAGAAGCGTGAAAACCCT-TCAA-TTTTTTTG
* * *
2833 GCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAAAAATGAAAAAAAAAACTTTTCAGG
192 GCGTTGAATTATATATTTTTTCTGAGTATTGTGGC--AAAAAATTG--AGAAAAAA-TTTTCAGG
* * * *
2898 TCAGTTTTTAAACCGAAATCGTGT---ATCACGGTTTTTTTGGCTAAAAACGCGATTT-GGAGTC
252 TCAGTTTTT-AGCCGAAATCGTATACCATCAC-G-ATTTTTGGCTAAAAACGCG-TTTCGG-GGC
*
2959 C-CGG
312 CTCGA
* * * **
2963 CTCAGTTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATCAATATTCATCTAATAAAATAT
1 CTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATAT
* * *
3028 CAGCCACAATTTATTTAAGGATTTATTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAA
66 CAGCCAC-ATTGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
* * * * *
3093 ATAAATTCGG--CAAAA-A--AAAACCGATATTAGAAGCGTGAAAAATCCTTCAA-TTTTTTGGT
130 ATTAATTCGGAAAAAAATATGAAAAACGATATTAGAAGCGTG-AAAACCCTTCAATTTTTTTGGC
* * *
3152 GTTGAATCATATATATCTTT-TGAGTATTGTGGCAAAGAATTGAAGAAAAAAATTTT--GCGTCA
194 GTTGAATTATATAT-TTTTTCTGAGTATTGTGGCAAAAAATTG-AG-AAAAAATTTTCAG-GTC-
* * * * * *
3214 ATTTTTGTAAAATTTTAGCCGAAATCGTATACTCATCATGGTTTTTTTTGTTAAAAACGCATTCC
254 A-----GT----TTTTAGCCGAAATCGTATAC-CATCA-CG-ATTTTTGGCTAAAAACGCGTTTC
*
3279 GCGGTCCAT-G-
307 G-GGGCC-TCGA
* * * * ** * * *
3289 CTCAGTTTTGCAT-ATTTTTGGCGTAAATACTCCTTAAAATGTAAAAAATTTATCTAACCAAATC
1 CTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATAT-CTATATTCATCTAACCAAATA
* *
3353 GCAGCCACATTCGATTTAACGATTTGTTTTTACGAGCATGATCTGAATCTTGTTTCGATTTAATT
65 TCAGCCACATT-GATTTAAGGATTTGTTTTTACGAGC---ATCTGAATCTTGTTTCGATTTAATT
* * * * * *
3418 AGAAATTAATTC--AAAAAAA-AGGAAAAATGATATTAGAAGCTTGAAAAACTCTGCAATCTTTT
126 AGAAATTAATTCGGAAAAAAATATGAAAAACGATATTAGAAGCGTG-AAAACCCTTCAATTTTTT
* * * * * * *
3480 TGGTGTTTAATTATATA-TTTTTATGAGTATTGTGGAAAAAAATTGAGAACAAATTTTCCGGGAC
190 TGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTTT-CAGGTC
*
3544 AGTTTTTAGCCGAAATCGTGTACTAACCATCAC-AGTTTTGGCTAAAAACGCGTTTCGGGGCCTC
254 AGTTTTTAGCCGAAATC--GTA-T-ACCATCACGATTTTTGGCTAAAAACGCGTTTCGGGGCCTC
3608 GA
315 GA
* * * * * * * *
3610 TTCAATTGTGCATGGTTTTTGACATAAAGATTCCTTGAAATATTTATATTCATCTAATCAAATAT
1 CTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATAT
* * * * *
3675 CAGCCACGTTAGATTGAAGGATTTG-TTTTACAAGCATTTGAATCTTGTTTCGATTTAATTATAA
66 CAGCCACATT-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
* *
3739 ATAAATTCGGAAAAAAAATGTATGAAAAACGATATTAGAAGCGTGAAATACCCTTCAATTTTTCT
130 ATTAATTCGG-AAAAAAA--TATGAAAAACGATATTAGAAGCGTGAAA-ACCCTTCAATTTTTTT
* * * * * * *
3804 GGCATTGATTTATATATTATTTCTGAGTATTGTGGGAAAAAATTGAGGAAAAACTTTTCGGGCCA
191 GGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA-GAAAAAATTTTCAGGTCA
** * * * * *
3869 GTTTTTGCAAAATTTTAGTTGTAATCGTGTACTAACCATCATG-GTTTTGGCTAAAAACGCATCT
255 G----T------TTTTAGCCGAAATC--GTA-T-ACCATCACGATTTTTGGCTAAAAACGCGTTT
* *
3933 -GGAGCCCCGA
306 CGGGGCCTCGA
* * * * *
3943 CTCAATTTTGCATGA--TTTGGCACAAAGACT-CTGTGAAATATCTATATTCATCAAACCAATTC
1 CTCAGTTTTGCATGATTTTTGGCATAAAGACTCCT-TGAAATATCTATATTCATCTAACCAAATA
* * * * *
4005 CCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTAAACCTTGTTT-GCATTTAATTAT
65 TCAGCCACATT-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCG-ATTTAATTAG
* * * * * *
4069 AAATTAATTCGGGAATAAAAT-GGAAAATCGGTATTAGAAGCGTGAAAAACCCGTCAATCTTTTT
128 AAATTAATTC-GGAAAAAAATATGAAAAACGATATTAGAAGCGTG-AAAACCCTTCAATTTTTTT
* *
4133 GGCATTGAATTATATATATTTTTCTGAGTATTGTGGTAAAAAATTGAGAAAAAACTTTTTC-GAG
191 GGCGTTGAATTATATAT-TTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAA--TTTTCAG-G
* * * * * *
4197 TCAGTGTTTAGTCG--A--G-AT--CATCACGGTTTTTGACTAAAAACGTGTTTCGGTGCCTCGA
252 TCAGTTTTTAGCCGAAATCGTATACCATCACGATTTTTGGCTAAAAACGCGTTTCGGGGCCTCGA
** * ** * * * *
4255 CTTTGTTTTGCATGATTTTTGGCGTCGAGTCTCCTTGAAATATCTTTATTCCTCTAATCAAATAT
1 CTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATAT
** * *
4320 CAGCCACATTAGATTTAAAAATTTGTTTTTACGTGCATCCGAATCTTGTTTCGATTTAATTAGAA
66 CAGCCACATT-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
* * ** * * **
4385 ATTAATTCAG-AAAAAATATGAAAAACGATATTTA-ATGTTTTAAAAGTCCTTCAATCCTTTTGG
130 ATTAATTCGGAAAAAAATATGAAAAACGATA-TTAGAAGCGTGAAAA-CCCTTCAATTTTTTTGG
* * * * * * * *
4448 CGTTGAATTATATATATATTATGAGTATTTTTGCCAAAAATTGAGGAAAAATCTTTTCGGGTCA-
193 CGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA-GAAAAA-ATTTTCAGGTCAG
* * * * * * **
4512 -----A----TAAT--TTTACCATCATGGTTTTTGCCTAAAAACGTG-TTCCAGGCCTC-A
256 TTTTTAGCCGAAATCGTATACCATCACGATTTTTGGCTAAAAACGCGTTTCGGGGCCTCGA
* * ** *
4560 GCTCAGTTTTGCATAATTTATGGCACCAAGACTCCTTGAAATATCTATATT-ATCTAATCAAA-A
1 -CTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATA
* * * * * *
4623 TTCAGGCATATTGGATTTAAGGATTTGTTTTTACGAGTATTTAAATCTTGTTTCGATTTAATTAA
65 -TCAGCCACATT-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
4688 AAATTAATTC
128 AAATTAATTC
4698 ATAATATGAA
Statistics
Matches: 3439, Mismatches: 640, Indels: 539
0.74 0.14 0.12
Matches are distributed among these distances:
304 13 0.00
305 100 0.03
306 60 0.02
307 25 0.01
308 1 0.00
309 2 0.00
310 119 0.03
311 38 0.01
312 107 0.03
313 59 0.02
314 155 0.05
315 49 0.01
316 143 0.04
317 88 0.03
318 235 0.07
319 278 0.08
320 49 0.01
321 338 0.10
322 44 0.01
323 54 0.02
324 53 0.02
325 45 0.01
326 99 0.03
327 79 0.02
328 6 0.00
329 139 0.04
330 111 0.03
331 162 0.05
332 152 0.04
333 44 0.01
334 64 0.02
335 51 0.01
336 11 0.00
337 151 0.04
338 29 0.01
339 30 0.01
340 1 0.00
341 5 0.00
342 5 0.00
343 6 0.00
344 3 0.00
345 52 0.02
346 58 0.02
347 40 0.01
348 8 0.00
349 58 0.02
350 20 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (316 bp):
CTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATAT
CAGCCACATTGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
TTAATTCGGAAAAAAATATGAAAAACGATATTAGAAGCGTGAAAACCCTTCAATTTTTTTGGCGT
TGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTTTCAGGTCAGTTTTT
AGCCGAAATCGTATACCATCACGATTTTTGGCTAAAAACGCGTTTCGGGGCCTCGA
Found at i:2339 original size:2 final size:2
Alignment explanation
Indices: 2332--2369 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2322 ACTCCTTGAA
*
2332 AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2370 TCATCGAACC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9608 original size:6 final size:6
Alignment explanation
Indices: 9597--9625 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
9587 CTACTCCATT
9597 TTCATC TTCATC TTCATC TTCATC TTCAT
1 TTCATC TTCATC TTCATC TTCATC TTCAT
9626 AATAAACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.31, G:0.00, T:0.52
Consensus pattern (6 bp):
TTCATC
Found at i:10120 original size:12 final size:12
Alignment explanation
Indices: 10103--10131 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
10093 GTAGACTCTT
10103 TGGCGTTGGCGG
1 TGGCGTTGGCGG
10115 TGGCGTTGGCGG
1 TGGCGTTGGCGG
10127 TGGCG
1 TGGCG
10132 GTGGTGAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.59, T:0.24
Consensus pattern (12 bp):
TGGCGTTGGCGG
Found at i:10764 original size:17 final size:18
Alignment explanation
Indices: 10731--10764 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
10721 AACAAAGGCA
*
10731 ATGAAATGAAGAGTGAAC
1 ATGAAATGAAAAGTGAAC
10749 ATGAAA-GAAAAGTGAA
1 ATGAAATGAAAAGTGAA
10765 AGGGGAGAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.56, C:0.03, G:0.26, T:0.15
Consensus pattern (18 bp):
ATGAAATGAAAAGTGAAC
Found at i:11843 original size:5 final size:6
Alignment explanation
Indices: 11812--11842 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
11802 CACCATGCTT
11812 CCCA-C CCCACC CCCACC CCCACC CCCACC CC
1 CCCACC CCCACC CCCACC CCCACC CCCACC CC
11843 AATCTCTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.16, C:0.84, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCACC
Found at i:13560 original size:2 final size:2
Alignment explanation
Indices: 13553--13581 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13543 AGACAAGTAC
13553 TA TA 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 TA TA T
13582 TTCTAAATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17993 original size:3 final size:3
Alignment explanation
Indices: 17987--18027 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
17977 ATGTGAAAAA
17987 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG ATA- AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG AAG AAG AA
18028 AGATTGGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 1 0.03
3 34 0.94
4 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:24142 original size:34 final size:34
Alignment explanation
Indices: 24099--24200 Score: 204
Period size: 34 Copynumber: 3.0 Consensus size: 34
24089 CAATTACTAG
24099 ATAACTGTAGTTGGTTTGTAAGCACTTTGAGTAA
1 ATAACTGTAGTTGGTTTGTAAGCACTTTGAGTAA
24133 ATAACTGTAGTTGGTTTGTAAGCACTTTGAGTAA
1 ATAACTGTAGTTGGTTTGTAAGCACTTTGAGTAA
24167 ATAACTGTAGTTGGTTTGTAAGCACTTTGAGTAA
1 ATAACTGTAGTTGGTTTGTAAGCACTTTGAGTAA
24201 TACTGGCACA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 68 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (34 bp):
ATAACTGTAGTTGGTTTGTAAGCACTTTGAGTAA
Found at i:27350 original size:14 final size:14
Alignment explanation
Indices: 27331--27358 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
27321 TAATTCATAC
27331 TGCTTAGATTAATA
1 TGCTTAGATTAATA
27345 TGCTTAGATTAATA
1 TGCTTAGATTAATA
27359 CTAAATGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
TGCTTAGATTAATA
Done.