Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014160.1 Corchorus capsularis cultivar CVL-1 contig14181, 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: 11341
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Found at i:643 original size:321 final size:320
Alignment explanation
Indices: 1--4080 Score: 3561
Period size: 311 Copynumber: 12.6 Consensus size: 320
* * * * * *
1 TTAAGTCCATTGTGGTTGAGATTCGGTTAAATGAATATAGATATTTCAAGGAGTCTTTCTGCAAA
1 TTAAATCCATTGTGGCTGAGATTTGATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAA
* * * *
66 AAAATCCTGC-AAATTGAGTCGGGTCTCCGGAACTCGTTTTTAGGCAAAAACGGTGATGGTTAGT
66 AAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAAAC-GTGATGGTTAGT
* *
130 ACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCTTCAATTTTTTGCCACAACACTCAGAA
130 ACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAA
* *** *
195 AAAAGATATAAATTTTCGCCAAAAAAATGATGGGTTTTTCACGGTTCTAATATCGTTTTTCCATT
195 AAAATATATAAATCAACGCCAAAAAAATGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCATT
*
260 TTTTTCCGAATTTATTTCAAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAAGAAATCC
260 TTTTTCCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-AAATCC
* * * * * *
322 TTAAGTCCATTGTGGTTGAGATTCGGTTAAATGAATATAGATATTTCAAGGAGTCTTTCTGCAAA
1 TTAAATCCATTGTGGCTGAGATTTGATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAA
* * * * *
387 AAAATCCTGC-AAATTGAGTCGAGTCTCCGGAACTCGTTTTTAGGCAAAAACGATGATGGTTAGT
66 AAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAAACG-TGATGGTTAGT
* *
451 ACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCTTCAATTTTTTTGCCACAACACTCAGA
130 ACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCTCAA-TTTTTTGCCACAATACTCAGA
* * * *
516 AAAAAGATATAAATTATCGCCAAAAAAATGATGGGTTTTTCACGGTTCTAATATCGTTTTTCCAT
194 AAAAATATATAAATCAACGCCAAAAAAATGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCAT
581 TTTTTTCCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAATCC
259 TTTTTTCCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAATCC
* * *
643 TTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCAAA
1 TTAAATCCATTGTGGCTGAGATTTGATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAA
* * *
708 AAAATCCTGCAAAATTGAGTCGGGTCTCCGGAACTCGTTTTTAGCCAAAAAC------G---GT-
66 AAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAAACGTGATGGTTAGTA
* *
763 CACAATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAACACTCAGAAA
131 CACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAA
* * * *
828 AGAGATATAAATTATCGCCAAAAAAATGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTT
196 AAATATATAAATCAACGCCAAAAAAATGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCA-TT
893 TTTTTCCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAATCC
260 TTTTTCCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAATCC
* * *
954 TTAAATCCATTGTGGCTAAGATTTGGTTTGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAA
1 TTAAATCCATTGTGGCTGAGATTTGATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAA
* * * * *
1019 AAAATCCTGCAAAATTGAGTCGGGTCTCCGGAACTCATTTTTAGCCAAAAACCGTGATGGTTAAT
66 AAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAAA-CGTGATGGTTAGT
* ** * * * *
1084 CCA-GAAAATATAAAT-TTCTAAAATGAATT-ATCATCTAATAA-TTAATTATCATATAATAATC
130 ACACG---AT-T---TCGGCT-AAA--AATTGA-C-CCGAA-AAGTT--TT-TCCT-CAAT--T-
** ** **** * * * **** * *
1145 AATAATGATGA-AATTACAAATTTCTAAAATTATTAGAAATTAAAAAAAAAAGTAAAAG-CGAGG
175 --TTTTG-CCACAA-TAC---TCAGAAAAAATA-TATAAATCAACGCCAAAA--AAATGATG-GG
* ** * ** *** ** * *
1208 TTAGTAAACGATTTCGGCTAA-A-AATTGACCCGAAAAGTTCTTCCTCAATTT-TTTGCCACAA-
229 TT-TTTCACG-CTT---CTAATATCGTTTTTCC---ATTTTTTTCC-GAATTTATTT--CA-AAT
* * * * * * * **
1269 T-ACTCAGAAAAAATATAT-ATAT-AT-ATATATATCAA-CGC
282 TAAATC-GAAACAAGAT-TCAGATGCTCGTA-AAAAAAATC-C
** * * *** ** * * ** * * *
1307 CAAAAT-AAGTGCAACACAAAGA-AT-ATTACACAAACCAAGACAATGA-TT-AA-TAGGT-TTT
1 TTAAATCCATTG--TGGCTGAGATTTGATTAGATGAA--TATA-AAT-ATTTCAAGGA-GTCTTT
* ** * ** ** ****
1365 AAATTTATTAAAAAATCACT-TAAAA-TG-G-C-ATTCTTACCCTTCAAAAAATTTTATA-CACA
59 --CTGCA--AAAAAATCA-TGCAAAATTGAGCCGGGTC-T--CC-GGAACGCGTTTT-TAGC-CA
** * ** * * ** * * ** * **
1424 ATTA-GATAAAATTCTT-CT-CTCCCTTCCCAGCTTTCCAAGATAATTAAAGATTC-AACTA-CC
113 AAAACG-T--GATGGTTAGTACACGATT-TCGGC--T--AA-A-AATT---GACCCGAA-AAGTT
** * ** * ** * * * ** **** *
1484 TAACCAACACA--AGTAGGGATATATA-T-GGAAAAAAT-TACAAATTACATTGGTTTTATAAAT
164 TTTCC-TCA-ATTTTTTGCCACA-ATACTCAGAAAAAATATATAAA-T-CA-ACGCCAAAAAAAT
* ** * * * * * * * * * * ** **
1544 GTTGCACTTAATATTAATGACTGCAAATCTTGAAATGTTGCACTTATTTT--GAATGGGA---GG
223 GATG-GGTT--T-TTCACG-CTTCTAATATCG--TTTTTCCA-TTTTTTTCCGAAT-TTATTTCA
* * * * * *
1604 GAGTAAATCGAAAAAAAAATTCAAATGCTAGTAAAAAGAAATCC
279 AATTAAATCG-AAACAAGATTCAGATGCTCGTAAAAA-AAATCC
* *
1648 TTAAATCCATTGTGGCTGAGATTTCG-TTAGATGAATATAGATATTTCAAGGAGTCATTCTGCCA
1 TTAAATCCATTGTGGCTGAGATTT-GATTAGATGAATATAAATATTTCAAGGAGTCTTTCTG-C-
1712 AAAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAAAACGGTGATGGT
63 AAAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCC-AAAAAC-GTGATGGT
* * * **
1777 TAGTACACGATTTCGGCTAAAAATTAACCCGAAAATTTTTTCCTCAATTTTTTACCATGATACTC
126 TAGTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTC
*
1842 AGAAAAAATATATAAATCAAAGCCAAAAAAATGATGGGTTTTTCACGCTTCTAATATCGTTTTTC
191 AGAAAAAATATATAAATCAACGCCAAAAAAATGATGGGTTTTTCACGCTTCTAATATCGTTTTTC
* *
1907 GAAATTTTTTCCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAAAT
256 -CATTTTTTTCCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-AAAT
1972 CC
319 CC
* * ** * * * **
1974 ATAAATCCAATGTAACTGAGATTTGATTAAATGAATATAAATATTTCAAAGAGTTTTTC-GGTAA
1 TTAAATCCATTGTGGCTGAGATTTGATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAA
* * *
2038 AAAATCATGCAAAATTGAGTCGGGTCTCCGGAAAGCGTTTTTAGTCAAAAAAAACGTGATGGTTA
66 AAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAG-C--CAAAAACGTGATGGTTA
* * *
2103 GTACACGATTTCGGCTAAAAATTTACCCGAAAAGTTTTTCCTCAATTTCTTGCCACAATACTAAG
128 GTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAG
* *
2168 GAAAAATATATAAATCAACGCC-AAAAAATGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCA
193 AAAAAATATATAAATCAACGCCAAAAAAATGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCA
*
2232 TTATTTTTCCGAACTTTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAATAGAAAT
258 TT-TTTTTCCGAA--TTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAA-AAAAAT
*
2297 CA
319 CC
*
2299 TTAAATCCATTGTAGCTGAGATTTGATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGC-AA
1 TTAAATCCATTGTGGCTGAGATTTGATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAA
* * **
2363 AAACTCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAAACCGCGATGGTTAAC
66 AAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAAA-CGTGATGGTTAGT
* ** * * * *
2428 ACGCGATTTCGGCTACTAATTGACTCGAAAAGATTTTCCTCAATTTATTGCCACAATACTCGGAA
130 ACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAA
* * *
2493 AAAATATATAAATCAACGCCAAAAAAATGAAGGGTGTTTCACGCTTCTAATATCGTTTTTCCTTT
195 AAAATATATAAATCAACGCCAAAAAAATGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCATT
** * * *
2558 TTTTTCCGAATTTATTTTTAATTAAATCGAAACAAAATTCAGATACTCGTAATAAGAAATCC
260 TTTTTCCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAA-AAAAAATCC
* * *
2620 TTAAATCCATTGTGGCTGAGATCTGGTTAGATGAATATAAATATTTCAAGGAGTCATTCTGC-AA
1 TTAAATCCATTGTGGCTGAGATTTGATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAA
* *
2684 AAAATCATGCAAAATTGAGCCGGTTCTCCGGAACGCGTTTATAGCCAAAAACGGTGAT-G---GT
66 AAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAAAC-GTGATGGTTAGT
* *
2745 ACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCTCTATTTTTTGCCACAATACTCAAAA
130 ACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTC-AGA
* *
2810 AAAATATATATAAATCAACGCCAAAAAAATGATGGGTTTTTCACGCTTCTAATATTGTATTTCCA
194 AAAA-ATATATAAATCAACGCCAAAAAAATGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCA
* * *
2875 ATTTTTTCCGAATTTATTTCAAATTGAATCGAAACAAGATTCAGATGCTAGTAAAAAGAAATCC
258 TTTTTTTCCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-AAATCC
* * * * *
2939 TTAAATCCATTCTAGATGAGATTTGATTAGATGAATATAAATATTTCAAGGAGT-TGTTTTG-TA
1 TTAAATCCATTGTGGCTGAGATTTGATTAGATGAATATAAATATTTCAAGGAGTCT-TTCTGCAA
* * **
3002 AAAAATCATGCAAAATTAAGCCGGGTCTCCGGAACGCGTTTTTAG-CAAAAA---AACCG-T-G-
65 AAAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAAACGTGATGGTTAGT
*
3060 --ACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCTCTATTTTTTGCCACAATACTCAGAA
130 ACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAA
* *
3123 AAAATATATAAATCAACGCCAAAAAAATGATGGATTTTTCACGCTTCTAATATCGTTTTTCCAAT
195 AAAATATATAAATCAACGCCAAAAAAATGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCATT
* *
3188 TTTTTCCGAATTTATTTCAAATTGAATCGAAACAAGATTCAGATGCTAGTAAAAAGAAATCC
260 TTTTTCCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-AAATCC
* * * *
3250 TTAAATCCATTGTAGCTGAGATTTGATTAGATCAATATAAATATTTCAAGGAGTTTTTCTG-TAA
1 TTAAATCCATTGTGGCTGAGATTTGATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAA
* *
3314 AAAATAATACAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGT
66 AAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAAA-CGTGATGGTTAGT
* * ** *
3379 ACACGATTTCAGCT-AAAATTGACCTGAAAAAATTTTCCTCAATTTTTTGCCACAATACTAAGAA
130 ACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAA
* *
3443 AAAAAATATAAATCAACGCC-AAAAAATGATGGGTTTTTCACACTTCTAATATCGTTTTTCC-TT
195 AAAATATATAAATCAACGCCAAAAAAATGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCATT
* *
3506 TTTTTCCGAACTTTTATTTCAAATTAAATCGAAA-AAGGATTCAGATGCTCGTAAATAGAAATAC
260 TTTTTCCGAA--TTTATTTCAAATTAAATCGAAACAA-GATTCAGATGCTCGTAAA-AAAAATCC
* * ** * * *
3570 TTCAATCCATTCTTACTGAGATTTGATTAGATGAATATAAATATTTCAATGAGTTTTTCTG-TAA
1 TTAAATCCATTGTGGCTGAGATTTGATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAA
* *
3634 AAAATCATGCAAAATTGAGTCGGGTCTTCGGAACGCGTTTTTAGCCAAAAACGGTGATGGTTAGT
66 AAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAAAC-GTGAT-G---GT
*
3699 TAGTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTA
126 TAGTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTC
* * * * *
3764 AGGAAAAATATATAAATCAACGCAAAAAAAAAGGATGGGTTTTTTACACTTCTAATATCGTTTTT
191 AGAAAAAATATATAAATCAACGC-CAAAAAAATGATGGGTTTTTCACGCTTCTAATATCGTTTTT
* *
3829 CCATTTTTTTTTTCCGAACTTTTTTTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAG
255 CCA---TTTTTTTCCGAA--TTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
3894 AAATCC
315 AAATCC
* *
3900 TTAAATCCATTGTGGCCGAGATTTGATTAGATGAAAATAAATATTTCAAGGAGTCTTTCTGC-AA
1 TTAAATCCATTGTGGCTGAGATTTGATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAA
*
3964 AAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAAAC-----CG-T--TA
66 AAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAAACGTGATGGTTAGTA
* * * * *
4021 CACAATTTCGCCTAAAAATTGACCCGAAAAGTTTATACTCGATTTTTTGCCACAATACTC
131 CACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTC
4081 GGATCGTAAA
Statistics
Matches: 3122, Mismatches: 436, Indels: 406
0.79 0.11 0.10
Matches are distributed among these distances:
310 83 0.03
311 436 0.14
312 16 0.01
313 59 0.02
314 1 0.00
315 2 0.00
316 3 0.00
317 111 0.04
318 26 0.01
319 247 0.08
320 221 0.07
321 416 0.13
322 189 0.06
323 196 0.06
324 155 0.05
325 229 0.07
326 83 0.03
327 50 0.02
328 4 0.00
329 4 0.00
330 134 0.04
331 69 0.02
332 13 0.00
333 11 0.00
334 4 0.00
335 5 0.00
337 3 0.00
338 12 0.00
339 46 0.01
340 27 0.01
341 27 0.01
342 20 0.01
343 12 0.00
344 11 0.00
345 18 0.01
346 4 0.00
347 10 0.00
348 8 0.00
349 3 0.00
350 4 0.00
351 1 0.00
352 24 0.01
353 27 0.01
354 30 0.01
355 15 0.00
356 12 0.00
357 26 0.01
358 10 0.00
359 4 0.00
360 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (320 bp):
TTAAATCCATTGTGGCTGAGATTTGATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAA
AAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAAACGTGATGGTTAGTA
CACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAA
AAATATATAAATCAACGCCAAAAAAATGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTT
TTTTCCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAATCC
Found at i:1132 original size:18 final size:18
Alignment explanation
Indices: 1100--1143 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1090 AATATAAATT
1100 TCTAA-AATGAATTATCA
1 TCTAATAATGAATTATCA
*
1117 TCTAATAATTAATTATCA
1 TCTAATAATGAATTATCA
*
1135 TATAATAAT
1 TCTAATAAT
1144 CAATAATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (18 bp):
TCTAATAATGAATTATCA
Found at i:3329 original size:630 final size:633
Alignment explanation
Indices: 1607--4079 Score: 3273
Period size: 630 Copynumber: 3.9 Consensus size: 633
1597 TGGGAGGGAG
* * * * *
1607 TAAATCGAAAAAAAAATTCAAATGCTAGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGATTT
1 TAAATCG-AAACAAGATTCAGATGCTAGTAAAAAGAAATCCTTAAATCCATTCTAGCTGAGATTT
* * *
1672 CG-TTAGATGAATATAGATATTTCAAGGAGTCATTCTGCCAAAAAAAATCATGCAAAATTGAGCC
65 -GATTAGATGAATATAAATATTTCAAGGAGT-TTTCTG---TAAAAAATCATGCAAAATTGAGCC
** *
1736 GGGTCTCCGGAACGCGTTTTTAGCCAAAAAACGGTGATGGTTAGTACACGATTTCGGCTAAAAAT
125 GGGTCTCCGGAACGCGTTTTTAGCCAAAAAA----GACCGATAG-A-ACGATTTCGGCTAAAAAT
* * * ** *
1801 TAACCCGAAAATTTTTTCCTCAATTTTTTACCATGATACTCAGAAAAAATATATAAATCAAAGCC
184 TGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAATCAACGCC
*
1866 AAAAAAATGATGGGTTTTTCACGCTTCTAATATCGTTTTTCGAAATTTTTTCCGAATTTATTTCA
249 AAAAAAATGATGGGTTTTTCACGCTTCTAATATCGTTTTTC-CAATTTTTTCCGAATTTATTTCA
* * *
1931 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAAATCCATAAATCCAATGTAACTGAGAT
313 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCATTGTAGCTGAGAT
* * * * * *
1996 TTGATTAAATGAATATAAATATTTCAAAGAGTTTTTCGGTAAAAAATCATGCAAAATTGAGTCGG
378 TTGATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAAAAATCATGCAAAATTGAGCCGG
* *
2061 GTCTCCGGAAAGCGTTTTTAGTCAAAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAAATT
443 GTCTCCGGAACGCGTTTTTAG-C--CAAAAACGTGATGG-T-GTACACGATTTCGGCTAAAAATT
* * **
2126 TACCCGAAAAGTTTTTCCTCAATTTCTTGCCACAATACTAAGGAAAAATATATAAATCAACGCCA
503 GACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTAAAAAAAAATATATAAATCAACGCCA
*
2191 AAAAATGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTATTTTTCCGAACTTTTATTTCA
568 AAAAATGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCATT-TTTTTCCGAAC-TTTATTTCA
2256 AAT
631 AAT
* * * *
2259 TAAATCGAAACAAGATTCAGATGCTCGTAAATAGAAATCATTAAATCCATTGTAGCTGAGATTTG
1 TAAATCGAAACAAGATTCAGATGCTAGTAAAAAGAAATCCTTAAATCCATTCTAGCTGAGATTTG
* *
2324 ATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAAAACTCATGCAAAATTGAGCCGGGTC
66 ATTAGATGAATATAAATATTTCAAGGAGT-TTTCTGTAAAAAATCATGCAAAATTGAGCCGGGTC
* * **
2389 TCCGGAACGCGTTTTTAGCC-AAAAA-CCGCGATGGTTAACACGCGATTTCGGCTACTAATTGAC
130 TCCGGAACGCGTTTTTAGCCAAAAAAGAC-CGATAG---A-A--CGATTTCGGCTAAAAATTGAC
* * * *
2452 TCGAAAAGATTTTCCTCAATTTATTGCCACAATACTCGGAAAAAATATATAAATCAACGCCAAAA
188 CCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAATCAACGCCAAAA
* * ** **
2517 AAATGAAGGGTGTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTTCCGAATTTATTTTTAATTA
253 AAATGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCAATTTTTTCCGAATTTATTTCAAATTA
* * * * * *
2582 AATCGAAACAAAATTCAGATACTCGTAATAAGAAATCCTTAAATCCATTGTGGCTGAGATCTGGT
318 AATCGAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCATTGTAGCTGAGATTTGAT
* *
2647 TAGATGAATATAAATATTTCAAGGAGTCATTCTGCAAAAAATCATGCAAAATTGAGCCGGTTCTC
383 TAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTCTC
*
2712 CGGAACGCGTTTATAGCCAAAAACGGTGAT-G-GTACACGATTTCGGCTAAAAATTGACCCGAAA
448 CGGAACGCGTTTTTAGCCAAAAAC-GTGATGGTGTACACGATTTCGGCTAAAAATTGACCCGAAA
*
2775 AGTTTTTCCTCTATTTTTTGCCACAATACTCAAAAAAAATATATATAAATCAACGCCAAAAAAAT
512 AGTTTTTCCTCAATTTTTTGCCACAATACT-AAAAAAAA-ATATATAAATCAACGCC-AAAAAAT
* * *
2840 GATGGGTTTTTCACGCTTCTAATATTGTATTTCCAATTTTTTCCGAA-TTTATTTCAAAT
574 GATGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAACTTTATTTCAAAT
* *
2899 TGAATCGAAACAAGATTCAGATGCTAGTAAAAAGAAATCCTTAAATCCATTCTAGATGAGATTTG
1 TAAATCGAAACAAGATTCAGATGCTAGTAAAAAGAAATCCTTAAATCCATTCTAGCTGAGATTTG
* *
2964 ATTAGATGAATATAAATATTTCAAGGAGTTGTTTTGTAAAAAATCATGCAAAATTAAGCCGGGTC
66 ATTAGATGAATATAAATATTTCAAGGAGTT-TTCTGTAAAAAATCATGCAAAATTGAGCCGGGTC
3029 TCCGGAACGCGTTTTTAG-CAAAAAA-ACCG-T-G-ACGATTTCGGCTAAAAATTGACCCGAAAA
130 TCCGGAACGCGTTTTTAGCCAAAAAAGACCGATAGAACGATTTCGGCTAAAAATTGACCCGAAAA
*
3089 GTTTTTCCTCTATTTTTTGCCACAATACTCAGAAAAAATATATAAATCAACGCCAAAAAAATGAT
195 GTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAATCAACGCCAAAAAAATGAT
* *
3154 GGATTTTTCACGCTTCTAATATCGTTTTTCCAATTTTTTCCGAATTTATTTCAAATTGAATCGAA
260 GGGTTTTTCACGCTTCTAATATCGTTTTTCCAATTTTTTCCGAATTTATTTCAAATTAAATCGAA
* *
3219 ACAAGATTCAGATGCTAGTAAAAAGAAATCCTTAAATCCATTGTAGCTGAGATTTGATTAGATCA
325 ACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCATTGTAGCTGAGATTTGATTAGATGA
* * * *
3284 ATATAAATATTTCAAGGAGTTTTTCTGTAAAAAATAATACAAAATTGAGCCGGGTCTCCGGAACG
390 ATATAAATATTTCAAGGAGTCTTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAACG
* * **
3349 CGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGCT-AAAATTGACCTGAAAAAATT
455 CGTTTTTAGCCAAAAA-CGTGATGG-T-GTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTT
3413 TTCCTCAATTTTTTGCCACAATACTAAGAAAAAAA-ATATAAATCAACGCCAAAAAATGATGGGT
517 TTCCTCAATTTTTTGCCACAATACTAA-AAAAAAATATATAAATCAACGCCAAAAAATGATGGGT
*
3477 TTTTCACACTTCTAATATCGTTTTTCC-TTTTTTTCCGAACTTTTATTTCAAAT
581 TTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAAC-TTTATTTCAAAT
* * * *
3530 TAAATCGAAA-AAGGATTCAGATGCTCGTAAATAGAAATACTTCAATCCATTCTTA-CTGAGATT
1 TAAATCGAAACAA-GATTCAGATGCTAGTAAAAAGAAATCCTTAAATCCATTC-TAGCTGAGATT
* *
3593 TGATTAGATGAATATAAATATTTCAATGAGTTTTTCTGTAAAAAATCATGCAAAATTGAGTCGGG
64 TGATTAGATGAATATAAATATTTCAAGGAG-TTTTCTGTAAAAAATCATGCAAAATTGAGCCGGG
* * **
3658 TCTTCGGAACGCGTTTTTAGCCAAAAACGGTGATGGTTAGTTAGTACACGATTTCGGCTAAAAAT
128 TCTCCGGAACGCGTTTTTAGCCAAAAA---AGACCG--A--TAG-A-ACGATTTCGGCTAAAAAT
* *
3723 TGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTAAGGAAAAATATATAAATCAACGCA
184 TGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAATCAACGC-
* * * * * *
3788 AAAAAAAAGGATGGGTTTTTTACACTTCTAATATCGTTTTTCCATTTTTTTTTTCCGAACTTTTT
248 CAAAAAAATGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCA---ATTTTTTCCGAA--TTTA
* *
3853 TTTCAAATTAAATCGAAACAAGATTCAGATGCTCGT-AAAAGAAATCCTTAAATCCATTGTGGCC
308 TTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCATTGTAGCT
*
3917 GAGATTTGATTAGATGAAAATAAATATTTCAAGGAGTCTTTCTGCAAAAAATCATGCAAAATTGA
373 GAGATTTGATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAAAAATCATGCAAAATTGA
* * *
3982 GCCGGGTCTCCGGAACGCGTTTTTAGCCAAAAAC-----CGT-TACACAATTTCGCCTAAAAATT
438 GCCGGGTCTCCGGAACGCGTTTTTAGCCAAAAACGTGATGGTGTACACGATTTCGGCTAAAAATT
* * *
4041 GACCCGAAAAGTTTATACTCGATTTTTTGCCACAATACT
503 GACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACT
4080 CGGATCGTAA
Statistics
Matches: 1618, Mismatches: 159, Indels: 98
0.86 0.08 0.05
Matches are distributed among these distances:
629 11 0.01
630 319 0.20
631 157 0.10
632 14 0.01
633 47 0.03
634 15 0.01
636 2 0.00
637 1 0.00
638 1 0.00
639 4 0.00
640 213 0.13
641 19 0.01
642 67 0.04
643 51 0.03
644 6 0.00
645 83 0.05
646 189 0.12
647 114 0.07
648 47 0.03
649 12 0.01
650 119 0.07
651 120 0.07
652 7 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32
Consensus pattern (633 bp):
TAAATCGAAACAAGATTCAGATGCTAGTAAAAAGAAATCCTTAAATCCATTCTAGCTGAGATTTG
ATTAGATGAATATAAATATTTCAAGGAGTTTTCTGTAAAAAATCATGCAAAATTGAGCCGGGTCT
CCGGAACGCGTTTTTAGCCAAAAAAGACCGATAGAACGATTTCGGCTAAAAATTGACCCGAAAAG
TTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAATCAACGCCAAAAAAATGATG
GGTTTTTCACGCTTCTAATATCGTTTTTCCAATTTTTTCCGAATTTATTTCAAATTAAATCGAAA
CAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCATTGTAGCTGAGATTTGATTAGATGAA
TATAAATATTTCAAGGAGTCTTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGC
GTTTTTAGCCAAAAACGTGATGGTGTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCC
TCAATTTTTTGCCACAATACTAAAAAAAAATATATAAATCAACGCCAAAAAATGATGGGTTTTTC
ACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAACTTTATTTCAAAT
Found at i:5194 original size:324 final size:324
Alignment explanation
Indices: 4223--6261 Score: 2238
Period size: 320 Copynumber: 6.4 Consensus size: 324
4213 CCCATGATGG
* *
4223 TTCCGAATTTATTTCTAATTAAATCGAAACAA-ATTTCAGATGCTCATTAAAA-AAATCCTTAAA
1 TTCCGAATTTATTTCTAATTAAATCGAAACAAGA-TTCAGATGCTCGTAAAAAGAAATCCTTAAA
* *
4286 TCCATTGTGGCTGAGATTTGGTTAGATGAATATAGAAATTTCAAGGAGTCTTTCT--ACAAAAAA
65 TCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCAAAAAAAA
* * * *
4349 TCATGCAAAATTTAGCCGAGTCTCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACAC
130 TCATGCAAAATTGAGACGGGTCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACAC
* *
4414 GATTTCGGCTAAAAATTAACCCGAAAAGTTTTTCCTCAAGTTTTTTGCCACTATACTCAGAAAGA
195 GATTTCGGCTAAAAATTAACCCGAAAAGTTTTTCCTCAA-TTTTTTGCCACAATACTCAGAAAAA
*
4479 ATATAT-ATATCAACGCCAAAAAAATGAAGGATTTTTCACGCTTCTAATATCGTTTTTCCATTTT
259 ATATATAAT-TCAACGCCAAAAAAATGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTT
4543 TT
323 TT
* * * *
4545 TTCCGAATTTATTTTTAATTAAATCGAAACAAAATTCAGATGCTCATAAAAAGAAATGCTTAAAT
1 TTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAAT
**
4610 CCATTGTCACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGC--AAAAAAT
66 CCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCAAAAAAAAT
* * *
4673 CATGCAAAATTGATATGGGTCTCTGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACG
131 CATGCAAAATTGAGACGGGTCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACG
* * * * * * * *
4738 ATTACAGTTAAAAATTGAGCTGAAAAGTTTTTCCTTAATTTTTTGCCACAATACTCTGAAAAAAT
196 ATTTCGGCTAAAAATTAACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAAT
*
4803 ATATAATTCAACGCCAAAAAAATGAAGGGTTTTTCATGCTTCTAATATCGTTTTTCCAATTTTTT
261 ATATAATTCAACGCCAAAAAAATGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCC-A-TTTTT
4868 T
324 T
4869 TTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAAT
1 TTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAAT
* * * * * *
4934 CTATTGTGGCTGAGATTTTGTTAGATAAACATAGATATCTCAGGGAGTCTTTCTGCAAAAAAAAA
66 CCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGC-AAAAAAAA
*
4999 TCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACAC
130 TCATGCAAAATTGAGACGGGTCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACAC
*
5064 GATTTCGGCTAATAATTAACCC-AAATAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAA
195 GATTTCGGCTAAAAATTAACCCGAAA-AGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAA
* * *
5128 ATATATAATTCAATGCCAAAAAAATGGAGGGTTTTTCATGCTTCTAATATCGTTTTTCCATTTTT
259 ATATATAATTCAACGCCAAAAAAATGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTT
5193 T
324 T
* * * * *
5194 TAT--GAATTAATTTCTAATTAAATCGAAATAAGATTCAGATACTCGTAAAAACAAATCCTTATA
1 T-TCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAA
* * * * ** * *
5257 TCCAATCTAGCTGAGATTTGGTTCGAAAAATATAGATATTTCAAGGA-T-TTTTTGCACAAAAAA
65 TCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCAAAAAAAA
*
5320 TCATGCAAAATTGAGACGGGTCT-CGGAACGCGTTTTTAGCCAAAAACCGTGATTGTTAGTACAC
130 TCATGCAAAATTGAGACGGGTCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACAC
* *
5384 GATTTCGGTTAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAA
195 GATTTCGGCTAAAAATTAACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAA
* * *
5449 TATATAATTTAACGCCAAAAAAATGAAGGGTTTTTCACACTTCTATTATCGTTTTTCCATTTTTT
260 TATATAATTCAACGCCAAAAAAATGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTT
5514 TT-CGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAAT
1 TTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAAT
*
5578 CCATTGTGGCTGAGATTTGGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGC----AAAA
66 CCATTGTGGCTGAGATTT-GGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCAAAAAAAA
* * * * * *
5639 T--TG---AGTCTG-GAC----C-CCGGCACGCGTTTTTAACCAAAAATCATGATGATTAGTACA
130 TCATGCAAAAT-TGAGACGGGTCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
* * * * * ** **
5693 CGATTTAGGCTAAAAACTT-ACCCGAAAAGTTTTTACGCAATTTTTTTTTG-TAAAATGTTCCTA
194 CGATTTCGGCTAAAAA-TTAACCCGAAAAGTTTTTCCTCAA---TTTTTTGCCACAATACTCAGA
* * * ** *
5756 AAAATATATATAATTCATCGCCAAAAAGATTGACGGGCATTTCACGCTTATAATA-CTGTTTTTC
255 AAAA-ATATATAATTCAACGCCAAAAA-AATGAAGGGTTTTTCACGCTTCTAATATC-GTTTTTC
5820 CA--TTTT
317 CATTTTTT
* * * * * * *
5826 TTCAGAATTAATTTTTAATTAAATCGAAAAAAGATTCAGATACTCGTAAAAACAAATCCTTGAAT
1 TTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAAT
* * * * * * ** *
5891 CCAATGTAGG-TGAGATTTGATTATATGAATATGGATATATCAATGAGTCATGGC-GC--CAAAA
66 CCATTGT-GGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC-TTTCTGCAAAAAAA
* * * * ** *
5952 A-C-TG---AGTT--G--GGG-CCCCGAAACGCTTTTTTAGCCAAAAATTGTGATGGTTATTACA
129 ATCATGCAAAATTGAGACGGGTCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
* * * * * * *
6007 CGATTTCGACTAAAATTTTGTAAAAAGTGATCCGAAATA-TATTTCCTCAATTTTTGGCTAAAAT
194 CGATTTCGGCTAAAA--AT-T----A---ACCCGAAA-AGTTTTTCCTCAATTTTTTGCCACAAT
* * * * * ** * * * *
6071 ACTCATAAATAATATATATTTCAACGCTAAAAAGATTGAAATGCTTTTGACGTTTCTAATATCAT
248 ACTCAGAAAAAATATATAATTCAACGCCAAAAA-AATGAAGGGTTTTTCACGCTTCTAATATCGT
*
6136 TTTTCC-TATTTT
312 TTTTCCATTTTTT
* * * *
6148 TT-CGAA-TTAGTTTCCAATTAAATCGAAACAAGATTCGGATGCTCGTAAAAATAAATTCTTAAA
1 TTCCGAATTTA-TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAA
* * * * *
6211 TCCAATGTGACTGAGATTTGATTAGATAAATATAGATATTTCAAGTAGTCT
65 TCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCT
6262 CGGAGTCAAA
Statistics
Matches: 1480, Mismatches: 183, Indels: 110
0.83 0.10 0.06
Matches are distributed among these distances:
310 68 0.05
311 2 0.00
312 45 0.03
313 101 0.07
314 91 0.06
315 3 0.00
316 1 0.00
317 2 0.00
319 6 0.00
320 233 0.16
321 198 0.13
322 151 0.10
323 169 0.11
324 222 0.15
325 8 0.01
326 5 0.00
327 175 0.12
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (324 bp):
TTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAAT
CCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCAAAAAAAAT
CATGCAAAATTGAGACGGGTCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACG
ATTTCGGCTAAAAATTAACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAAT
ATATAATTCAACGCCAAAAAAATGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTT
Done.