Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009701.1 Corchorus olitorius cultivar O-4 contig09733, 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: 11478
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.33
Found at i:2880 original size:334 final size:327
Alignment explanation
Indices: 2100--4010 Score: 1130
Period size: 332 Copynumber: 5.7 Consensus size: 327
2090 ACTAAACTTA
* **
2100 AAAAACATATCCTTAAATCCAATGTGGCAAAAATTTTATTAGATGAATATA-GATATTTCAAGGA
1 AAAAACATATCATTAAATCCAATGTGGCTGAAA-TTTATTAGATGAATA-AGGATATTTCAAGGA
* * * * * * *
2164 GTCGCGGTGCTAAAAATTATTCAAAACTGAGCCGGGGC-CTCGGAACGCGTTTTTAGCCAAATAT
64 GTCTCAGTGCCAAAAATCATGCAAAACTGAGCC-GGGCTC-CGGAACGCGTTTTTAG-CAAAAAA
* * * * * *
2228 CGTGATGGTTAATACGCGATTTCCGCTAAAATTTTGCAAAAACTGACCCGAAAAAGTTTTCCACA
126 CGTGATGGTTAATACACGATTTCCGCTAAAATTTTGCAAAAA-TTAACTGAAAAAATTTTCCTCA
* * * * *
2293 ATTTTTCGCCAAAATAATCATGAAAAATA-ATAATTCAATGCCAAAAAGATTGAAGGCGTTTCAT
190 ATTTTTCGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGCTTTTCAT
* * * * *
2357 GTTTCTAATATCATTTTTCATTTTTGTTTTCCAAATTAATTTCTAATTAAAACGAAACAAGATAC
255 GCTTCTAATATCATTTTTCA-TATTGTTTTCCAAATTAATTTCTAATTAAATCGAAAC-CGATTC
*
2422 AATTGCTCAT
318 AATTGCTCGT
* * * *
2432 AAAAATATATCATTAAATCCAATGTGGCTGAGA-TT-TGAGATGAA-AAGGATATTTTAAGGAGT
1 AAAAACATATCATTAAATCCAATGTGGCTGAAATTTATTAGATGAATAAGGATATTTCAAGGAGT
* * * **
2494 CTCAGCT-CCACAAATCATGCAAAACTGAGCCGGACTCCAAGAACATGTTTTTAGCAAAAAAAAC
66 CTCAG-TGCCAAAAATCATGCAAAACTGAGCCGGGCTCC-GGAACGCGTTTTTAGC--AAAAAAC
** * * * * * *
2558 AAAGATAGTTAATACACGATTTCTGCTAAAATATTACAAAAATTAACTAGAAATATTTTATCCTC
127 -GTGATGGTTAATACACGATTTCCGCTAAAATTTTGCAAAAATTAACT-GAAAAAATTT-TCCTC
* * * * * **
2623 AATTTTTCGTTAAAATTCTTATAAAAAATATATACTTCAGCGCCAAAAAGATTTTAGGACTTTTC
189 AATTTTTCGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGG-CTTTTC
* * * * * *
2688 AAGCTTCTAATATCATTTTTTCCTATT-TTTTCTAAATTTATTTCTACTTAAATCGAAACCGGTT
253 ATGCTTCTAATATCA-TTTTTCATATTGTTTTCCAAATTAATTTCTAATTAAATCGAAACC-GAT
2752 TCAGA-TGCTCGT
316 TCA-ATTGCTCGT
* * * * *
2764 AAAAGCATATCCTTAAATCCAATTTGGCTGAAATTT-CTAGATGAATATA-AATATTTCAAGGAG
1 AAAAACATATCATTAAATCCAATGTGGCTGAAATTTATTAGATGAATA-AGGATATTTCAAGGAG
*
2827 TCTCAGTGCCAAAAATCATGCAAAACTGAGCCAGGGTTCCGGAACGCGTTTTTAGCAAAAAACCG
65 TCTCAGTGCCAAAAATCATGCAAAACTGAGCC-GGGCTCCGGAACGCGTTTTTAGCAAAAAA-CG
* * * * * * *
2892 TGATGGTTAGTAAATGATTTCGGCTAATATTTTCGCAAAAACTGACCTGAAAAAATTTTCCTCAA
128 TGATGGTTAATACACGATTTCCGCTAAAATTTT-GCAAAAA-TTAACTGAAAAAATTTTCCTCAA
* *
2957 TTTTTTGCTAAAATACTCATAAAAAATATATAAATT-AACGCCAAAAAGATTGGAGGGCTTTTCA
191 TTTTTCGCTAAAATACTCATAAAAAATATAT-AATTCAACGCCAAAAAGATT-GAAGGCTTTTCA
* * *
3021 TGCTTCTAATATCA-TTTTCATATTTGTTTTCCAAATGAATTTCTAATTAACTCGAAAGACGATT
254 TGCTTCTAATATCATTTTTCATA-TTGTTTTCCAAATTAATTTCTAATTAAATCGAAA-CCGATT
3085 CAATTGCTCGT
317 CAATTGCTCGT
* * *
3096 AAAAACATATCAGTAAATCCAATGTGGCTGAGATTTGATTAGACGAATAAGGATATTTCAAGGAG
1 AAAAACATATCATTAAATCCAATGTGGCTGAAATTT-ATTAGATGAATAAGGATATTTCAAGGAG
* * * * * * * * * *
3161 TCTCGGCGGCACAAATCATGCAAAACTGATCCGGGCTCCAAGAACGTGTTATTAACCAAAAACAG
65 TCTCAGTGCCAAAAATCATGCAAAACTGAGCCGGGCTCC-GGAACGCGTTTTTAGCAAAAAAC-G
* ** *** * *
3226 TGATAGTTTTTTTTAGA-ACAAAAAATAGTGATGATTAATACATGATTTCGGCTAAAATTTCACA
128 TGAT-G-----GTTA-ATAC--ACGAT--TTCCG-CTAA-A-AT--TTT--GC-AAAAATT----
* * *
3290 AAAATTAACCCGAAATATTTTTTCCTCAAATTTTCGCCT-AAATACTCATAAATAAATATATAAT
170 -AACTGAA----AAA-A--TTTTCCTCAATTTTTCG-CTAAAATACTCATAAA-AAATATATAAT
* * *
3354 TCAACGCTAAAAAGATT--TGTCATTTTC---C--C-----T-A-TTTTC-T-TTG-------AA
225 TCAACGCCAAAAAGATTGAAGGC-TTTTCATGCTTCTAATATCATTTTTCATATTGTTTTCCAAA
* * * * *
3396 TTTATTTCTACTTAAATCGAAACCGGTTTAAGATGCTCGT
289 TTAATTTCTAATTAAATCGAAACCGATTCAA-TTGCTCGT
** * * * * * *
3436 AAAAACATATCCCTCAATCCAATATGACTGAAATTTGATTGGATAAATATA-GATA-TTCTAAAG
1 AAAAACATATCATTAAATCCAATGTGGCTGAAATTT-ATTAGATGAATA-AGGATATTTC-AAGG
** *
3499 AGTCTC-GATGCCAAAAAAAAAATAGCAAAACTGA-CTCGGGGCCCCGGAACGCGTTTTTTAGCC
63 AGTCTCAG-TGCC--AAAAATCAT-GCAAAACTGAGC-C-GGGCTCCGGAACGCG-TTTTTAG-C
* * * * * *
3562 AAAAACCGTGATGG-TAGTAAACGATTT-CGACTGAAATTTTGC-AAAATTGAACCGAAAAATTT
120 AAAAAACGTGATGGTTAATACACGATTTCCG-CTAAAATTTTGCAAAAATT-AACTGAAAAA-AT
* * * *
3624 TTTCCTCAATTTTTTTC-CCAAAATACTCAT-AAAAATATATGATTCAACGCCAAAAATATTGGT
182 TTTCCTCAA--TTTTTCGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATT-GA
* * * ** ** * * *
3687 GGGCTATTCACGCTTCTAATATTGTTTTTTC-TATT-TTTTCTGAGTTTATTTTTACA-TAAATC
244 AGGCTTTTCATGCTTCTAATA-TCATTTTTCATATTGTTTTCCAAATTAATTTCTA-ATTAAATC
* * *
3749 GAAACTGGTTTCAAATGCTCGT
307 GAAAC-CGATTCAATTGCTCGT
* * * * * *
3771 AAAAACAGATCCTTAAGTCCAATTTGGCTGAAATTTGATTAGATGAATATA-GATATTTTAAGTA
1 AAAAACATATCATTAAATCCAATGTGGCTGAAATTT-ATTAGATGAATA-AGGATATTTCAAGGA
* * * * *
3835 GTCTCAATGCCAAAAATCATGCAAAACTGAGCCGGGGTCCCCAGAACACGTTTTTAGCCAAAAAC
64 GTCTCAGTGCCAAAAATCATGCAAAACTGAGCC-GGG-CTCCGGAACGCGTTTTTAG-CAAAAAA
* * * *
3900 CGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTAACCCGAATAAAA-TTTCCTC
126 CGTGATGGTTAATACACGATTTCCGCTAAAATTTTGCAAAAATTAA-CTGAA-AAAATTTTCCTC
* * *
3964 -----TTCACCAAAATA-TCATAAGAGCAATATATAATTCAACGCCAAAAAGA
189 AATTTTTCGCTAAAATACTCATAA-A-AAATATATAATTCAACGCCAAAAAGA
4011 AACTGGTTTG
Statistics
Matches: 1231, Mismatches: 227, Indels: 245
0.72 0.13 0.14
Matches are distributed among these distances:
313 25 0.02
314 13 0.01
315 14 0.01
316 11 0.01
318 1 0.00
320 5 0.00
324 5 0.00
326 10 0.01
327 15 0.01
328 61 0.05
329 42 0.03
330 53 0.04
331 32 0.03
332 326 0.26
333 112 0.09
334 147 0.12
335 101 0.08
336 7 0.01
337 3 0.00
339 10 0.01
340 86 0.07
341 1 0.00
342 10 0.01
343 18 0.01
344 18 0.01
345 9 0.01
347 5 0.00
349 4 0.00
350 9 0.01
351 5 0.00
355 4 0.00
356 1 0.00
358 1 0.00
359 3 0.00
360 3 0.00
361 5 0.00
362 32 0.03
363 24 0.02
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (327 bp):
AAAAACATATCATTAAATCCAATGTGGCTGAAATTTATTAGATGAATAAGGATATTTCAAGGAGT
CTCAGTGCCAAAAATCATGCAAAACTGAGCCGGGCTCCGGAACGCGTTTTTAGCAAAAAACGTGA
TGGTTAATACACGATTTCCGCTAAAATTTTGCAAAAATTAACTGAAAAAATTTTCCTCAATTTTT
CGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGCTTTTCATGCTTCT
AATATCATTTTTCATATTGTTTTCCAAATTAATTTCTAATTAAATCGAAACCGATTCAATTGCTC
GT
Found at i:4845 original size:325 final size:320
Alignment explanation
Indices: 4072--5729 Score: 1154
Period size: 325 Copynumber: 5.1 Consensus size: 320
4062 ATTTTTCCAC
* * * * * * * *
4072 GCTTCTAATATCATTTTTCCTTTTCTTTTTTGAATTTATTTCTAGTCAAATCGAAACTGGTTTAA
1 GCTTCTTATATTATTTTT-CTATT-TTTTCTGAATTTATTTCTACTTAAATCGAAACCGGTTTCA
* * * * * *
4137 GAT-ACTCGTAAAAACATATCCTTTAATCC-AATATGGCTGAAATTTAATTTCGATAAATATAGA
64 -ATGGCTCGTAAAAACATATCCTTAAATCCAAAT-TGGCTGAAATTTGAGTTAGATGAATATAGA
* * * *** *
4200 TATTTCAAGGAGTCTCGGTACCAAAAATCATGCAAAACTGAGCTGGTGCCTGGGAACGCGTTTTT
127 TATTTCAAGGAGTCTCGGT-GCAAAAATCATGCAAAACTGAGCCGGGGCCCCAGAACACGTTTTT
*
4265 AG-GCAAAAACCGTGAT-GTACACGATTTCGGCTAAAATTTAGCAAAAACTGACCCGAAA-----
191 AGCG-AAAAACCGTGATAGT--ACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAATTTTC
* *
4323 -T-ATTTTTC-CCAAAATACTCATAAAAAATATATAATTCAATGCCAAAAACATTGGTGGGCTTT
253 CTCATTTTTCACCAAAATACTCAT-AAAAATATATAATTCAACGCCAAAAACATTGGAGGGCTTT
*
4385 TCAC
317 TCAT
* *
4389 GCTTC-TAGTATTGTTATTT-TATTTTTTCTGAGTTTATTTCTACTTAAATCGAAACCGGTTTCA
1 GCTTCTTA-TATTATT-TTTCTATTTTTTCTGAATTTATTTCTACTTAAATCGAAACCGGTTTCA
* * * * * *
4452 GAT-GCTTGTAAAAACAGATCCTTAACTCCAATTTGGCTTG-ATTTTGA-TTAGAAGAATATAGA
64 -ATGGCTCGTAAAAACATATCCTTAAATCCAAATTGGC-TGAAATTTGAGTTAGATGAATATAGA
* * * * *
4514 TATTTCAAGGAGTCTTGGTGCAAAAATCATGCAAAACTGAGCCAGAGCCCCGGAACACATTTTTA
127 TATTTCAAGGAGTCTCGGTGCAAAAATCATGCAAAACTGAGCCGGGGCCCCAGAACACGTTTTTA
* **
4579 GCGAAAAACCGTGAT-G-ACGATTTCGGCTAAAATTTTGCAAAAATTGACCAAAAAATTTTTTCC
192 GCGAAAAACCGTGATAGTACGATTTCGGCTAAAATTTTGCAAAAACTGACC-CGAAA--TTTTCC
*
4642 TCGATTTTTCACCAAAATACTCATAAAAAGTATATAATTCAACGCCAAAAAGATTGGAGGGCTTT
254 TC-ATTTTTCACCAAAATACTCATAAAAA-TATATAATTCAACGCCAAAAACATTGGAGGGCTTT
4707 TCAT
317 TCAT
** * * *
4711 GCTTCTTATATTATTTTTCATATTTGTTTTCCAAATTAATTTCTAATTAAATCGAAACAC-GATT
1 GCTTCTTATATTATTTTTC-TA-TT-TTTTCTGAATTTATTTCTACTTAAATCGAAAC-CGGTTT
* * * *
4775 CAATGGCTCGTAAAAACATATCATTAAATCCAAAGTGGCT-AAGATTTGA-TTAGACGAATAAAG
62 CAATGGCTCGTAAAAACATATCCTTAAATCCAAATTGGCTGAA-ATTTGAGTTAGATGAATATAG
* * * * * * *
4838 ATATTTCAAGAAGCCTCGGTGCCACAAACCATGCAAAACTGAG-CTGGGCTCCAAGAACATGTTT
126 ATATTTCAAGGAGTCTCGGTG-CAAAAATCATGCAAAACTGAGCCGGGGC-CCCAGAACACGTTT
** * * * *
4902 TTAGCGAAAAATAGTGATAGTTAATACACGAGTTT-TGCTAAAACTTTGCAAAAATTAACCCGAA
189 TTAGCGAAAAACCGTGATAG----T--ACGA-TTTCGGCTAAAATTTTGCAAAAACTGACCCG-A
* * * ** * **
4966 ATATTTTTCCTCAATTTTCGCAAAAATACTCAT---AA-ATATAATTCAACATCAAAAAGATTTT
246 A-A-TTTTCCTCATTTTTCACCAAAATACTCATAAAAATATATAATTCAACGCCAAAAACATTGG
5027 AGGGC-TTTCACT
309 AGGGCTTTTCA-T
* * * * *
5039 -CTTCTAATATCATTTTTCCGATTTTTTCTGAATTTATTTCTACTTAAACCAAAACCGGTTTC-A
1 GCTTCTTATATTATTTTT-CTATTTTTTCTGAATTTATTTCTACTTAAATCGAAACCGGTTTCAA
* * * *
5102 GGTGCTCGTAAATACATATCCTTAACTCCAATTTGGCTGAAATTT-AGTTAGATGAATATAGATA
65 TG-GCTCGTAAAAACATATCCTTAAATCCAAATTGGCTGAAATTTGAGTTAGATGAATATAGATA
* * * * *
5166 TTTCAAGGAGTCTCGGTACGAAGAATAAGGCAAAACTGAGCCGGGGCCCCAGAACGCGTTTTTAG
129 TTTCAAGGAGTCTCGGTGC-AAAAATCATGCAAAACTGAGCCGGGGCCCCAGAACACGTTTTTAG
* * * * * *
5231 CCAAAAACCGTGATGGTTTATAAAGGATTTCGACAAAAATTTTGCAAAAACTGATCCG-AATTTT
193 CGAAAAACCGTGATAG----T--ACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAATTTT
* *
5295 CCTCAATTTTTGACCAAAATACTCATAAAAATATATAATTCAACGCCAAAAACATTGTAGGGCTT
252 CCTC-ATTTTTCACCAAAATACTCATAAAAATATATAATTCAACGCCAAAAACATTGGAGGGCTT
*
5360 TTCACA
316 TTCA-T
* * * * *
5366 G-TTC-TA-A-TA----TC--GTTTTTCT-TA-TT-TTTCTGAATTAAATCGAAATCGGTTTC-T
1 GCTTCTTATATTATTTTTCTATTTTTTCTGAATTTATTTCT-ACTTAAATCGAAACCGGTTTCAA
* * * * *
5417 TGATGCTTGTAAAAGCATATCCTTAATTCC-AATGTCGCTGAAATTTGA-TTAGATGGATATAGA
65 TG--GCTCGTAAAAACATATCCTTAAATCCAAAT-TGGCTGAAATTTGAGTTAGATGAATATAGA
* * * * * *
5480 TATTTAAAGGTGTCTCGGTGCCAAAAATCATGCAAAACTGAGCTGGTGCCCCAGAA-AGCATATT
127 TATTTCAAGGAGTCTCGGTG-CAAAAATCATGCAAAACTGAGCCGGGGCCCCAGAACA-CGTTTT
* * ** * * * *
5544 TAGCCAATAACCGTTATGGTTAATACACACGATTTTGGCTAAAATTTTGCAAAAACTAAACTGAA
190 TAGCGAAAAACCG---T-G---ATA-GTACGATTTCGGCTAAAATTTTGCAAAAACTGACCCG-A
* * * *
5609 AATTTTTTCCTCAATATTTGC-CTAAAATACTCAGTAGAAATATATAATTCAAGGCCAAAAACAT
246 AA--TTTTCCTC-AT-TTTTCACCAAAATACTCA-TAAAAATATATAATTCAACGCCAAAAACAT
* * * *
5673 TGCA-AGATTTGTCAC
306 TGGAGGGCTTT-TCAT
* *
5688 GCTTCTAATA-TAGTTTTTCCTATTTTTTCTGACTTTATTTCT
1 GCTTCTTATATTA-TTTTT-CTATTTTTTCTGAATTTATTTCT
5730 TTCTTTTTTT
Statistics
Matches: 1066, Mismatches: 184, Indels: 163
0.75 0.13 0.12
Matches are distributed among these distances:
310 31 0.03
311 3 0.00
313 52 0.05
314 36 0.03
315 89 0.08
316 119 0.11
317 19 0.02
318 31 0.03
319 3 0.00
320 4 0.00
321 23 0.02
322 104 0.10
323 47 0.04
324 16 0.02
325 269 0.25
326 83 0.08
327 31 0.03
328 29 0.03
330 3 0.00
331 1 0.00
333 25 0.02
334 37 0.03
335 6 0.01
336 5 0.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (320 bp):
GCTTCTTATATTATTTTTCTATTTTTTCTGAATTTATTTCTACTTAAATCGAAACCGGTTTCAAT
GGCTCGTAAAAACATATCCTTAAATCCAAATTGGCTGAAATTTGAGTTAGATGAATATAGATATT
TCAAGGAGTCTCGGTGCAAAAATCATGCAAAACTGAGCCGGGGCCCCAGAACACGTTTTTAGCGA
AAAACCGTGATAGTACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAATTTTCCTCATTTT
TCACCAAAATACTCATAAAAATATATAATTCAACGCCAAAAACATTGGAGGGCTTTTCAT
Found at i:5695 original size:650 final size:641
Alignment explanation
Indices: 4333--5729 Score: 1453
Period size: 650 Copynumber: 2.1 Consensus size: 641
4323 TATTTTTCCC
* * * *
4333 AAAATACTCATAAAAAATATATAATTCAATGCCAAAAACATTGGTGGGCTTTTCACGCTTCTAGT
1 AAAATACTCAT--AAAATATATAATTCAACGCCAAAAACATT-GTAGGATTTTCACGCTTCTAAT
* * * * *
4398 AT-TGTTATT-TTATTTTTTCTGAGTTTATTTCTACTTAAATCGAAACCGGTTTCAGATGCTTGT
63 ATAT-TT-TTCCTATTTTTTCTGAATTTATTTCTACTTAAACCAAAACCGGTTTCAGATGCTCGT
*
4461 AAAAACAGATCCTTAACTCCAATTTGGCTTGATTTTGATTAGAAGAATATAGATATTTCAAGGAG
126 AAAAACAGATCCTTAACTCCAATTTGGCTTGATTTAGATTAGAAGAATATAGATATTTCAAGGAG
* * * * * *
4526 TCTTGGTGCAAAAATCATGCAAAACTGAGCCAGAGCCCCGGAACACATTTTTAGCGAAAAACCGT
191 TCTCGGTACAAAAATAAGGCAAAACTGAGCCAGAGCCCCAGAACACATTTTTAGCCAAAAACCGT
* * * *
4591 GATGACGATTTCGGCTAAAATTTTGCAAAAATTGACCAAAAAATTTTTTCCTCGATTTTTCACCA
256 GATGACGATTTCGACAAAAATTTTGCAAAAACTGACC--AAAA-TTTTTCCTCAATTTTTCACCA
* *
4656 AAATACTCATAAAAAGTATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCATGCTTCTTATA
318 AAATACTCATAAAAAGTATATAATTCAACGCCAAAAACATTGGAGGGCTTTTCAAGCTTCTTATA
*
4721 TTATTTTTCATATTTGTTTTCCAAATTAATTTCTAATTAAATCGAAACACGATTCAATGGCTCGT
383 TTA---TTCATATTTGTCTT---AATT-ATTTCTAATTAAATCGAAACACGATTCAATGGCTCGT
* *
4786 AAAAACATATCATTAAATCCAAAGTGGCTAAGATTTGATTAGACGAATAAAGATATTTCAAGAAG
441 AAAAACATATCATTAAATCCAAAGTCGCTAAGATTTGATTAGACGAATAAAGATATTTAAAGAAG
* * * * *
4851 CCTCGGTGCCACAAACCATGCAAAACTGAGCTGGGCTCCAAGAACATGTTTTTAGCGAAAAATAG
506 CCTCGGTGCCAAAAACCATGCAAAACTGAGCTGGGCCCCAAGAACA-GTATTTAGCCAAAAACAG
* *
4916 TGATAGTTAATACACGAGTTTTGCTAAAACTTTGCAAAAATTAACCCGAAATATTTTTCCTCAAT
570 TGATAGTTAATACACGAGTTTTGCTAAAACTTTGCAAAAACTAAACCGAAATATTTTTCCTCAAT
4981 TTTCGCA
635 TTTCGCA
** * * ** *
4988 AAAATACTCAT--AA-ATATAATTCAACATCAAAAAGATTTTAGGGCTTTCACTCTTCTAATATC
1 AAAATACTCATAAAATATATAATTCAACGCCAAAAACATTGTAGGATTTTCACGCTTCTAATAT-
* * *
5050 ATTTTTCCGATTTTTTCTGAATTTATTTCTACTTAAACCAAAACCGGTTTCAGGTGCTCGTAAAT
65 ATTTTTCCTATTTTTTCTGAATTTATTTCTACTTAAACCAAAACCGGTTTCAGATGCTCGTAAAA
* *
5115 ACATATCCTTAACTCCAATTTGGC-TGAAATTTAG-TTAGATGAATATAGATATTTCAAGGAGTC
130 ACAGATCCTTAACTCCAATTTGGCTTG--ATTTAGATTAGAAGAATATAGATATTTCAAGGAGTC
* * * * *
5178 TCGGTACGAAGAATAAGGCAAAACTGAGCCGGGGCCCCAGAACGCGTTTTTAGCCAAAAACCGTG
193 TCGGTAC-AAAAATAAGGCAAAACTGAGCCAGAGCCCCAGAACACATTTTTAGCCAAAAACCGTG
* *
5243 ATGGTTTATAAAGGATTTCGACAAAAATTTTGCAAAAACTGATCC-GAA-TTTTCCTCAATTTTT
257 AT-G-------ACGATTTCGACAAAAATTTTGCAAAAACTGA-CCAAAATTTTTCCTCAATTTTT
* *
5306 GACCAAAATACTCATAAAAA-TATATAATTCAACGCCAAAAACATTGTAGGGCTTTTCACAG-TT
313 CACCAAAATACTCATAAAAAGTATATAATTCAACGCCAAAAACATTGGAGGGCTTTTCA-AGCTT
* * * *
5369 C-TA-A-TA-TCGT-TTT-TCTT-ATT-TTTCTGAATTAAATCGAAATC-GGTTTC-TTGATGCT
377 CTTATATTATTCATATTTGTCTTAATTATTTCT-AATTAAATCGAAA-CACGATTCAATG--GCT
* * * * * * * *
5424 TGTAAAAGCATATCCTTAATTCCAATGTCGCTGAA-ATTTGATTAGATGGATATAGATATTTAAA
438 CGTAAAAACATATCATTAAATCCAAAGTCGCT-AAGATTTGATTAGACGAATAAAGATATTTAAA
** * *
5488 GGTGTCTCGGTGCCAAAAATCATGCAAAACTGAGCTGGTGCCCC-AGAA-AGCATATTTAGCCAA
502 GAAGCCTCGGTGCCAAAAACCATGCAAAACTGAGCTGG-GCCCCAAGAACAG--TATTTAGCCAA
* * * * * *
5551 TAACCGTTATGGTTAATACAC-ACGATTTTGGCTAAAATTTTGCAAAAACTAAACTGAAA-ATTT
564 AAACAGTGATAGTTAATACACGA-G-TTTT-GCTAAAACTTTGCAAAAACTAAACCGAAATA-TT
*
5614 TTTCCTCAATATTT-GCCT
625 TTTCCTCAAT-TTTCG-CA
* * *
5632 AAAATACTCAGTAGAAATATATAATTCAAGGCCAAAAACATTGCAAGATTTGTCACGCTTCTAAT
1 AAAATACTCA-TA-AAATATATAATTCAACGCCAAAAACATTGTAGGATTT-TCACGCTTCTAAT
*
5697 ATAGTTTTTCCTATTTTTTCTGACTTTATTTCT
63 ATA-TTTTTCCTATTTTTTCTGAATTTATTTCT
5730 TTCTTTTTTT
Statistics
Matches: 618, Mismatches: 87, Indels: 79
0.79 0.11 0.10
Matches are distributed among these distances:
639 8 0.01
640 19 0.03
641 121 0.20
642 11 0.02
643 38 0.06
644 14 0.02
645 4 0.01
646 3 0.00
647 3 0.00
648 2 0.00
649 47 0.08
650 169 0.27
651 60 0.10
652 2 0.00
653 2 0.00
654 39 0.06
655 45 0.07
657 2 0.00
659 27 0.04
660 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (641 bp):
AAAATACTCATAAAATATATAATTCAACGCCAAAAACATTGTAGGATTTTCACGCTTCTAATATA
TTTTTCCTATTTTTTCTGAATTTATTTCTACTTAAACCAAAACCGGTTTCAGATGCTCGTAAAAA
CAGATCCTTAACTCCAATTTGGCTTGATTTAGATTAGAAGAATATAGATATTTCAAGGAGTCTCG
GTACAAAAATAAGGCAAAACTGAGCCAGAGCCCCAGAACACATTTTTAGCCAAAAACCGTGATGA
CGATTTCGACAAAAATTTTGCAAAAACTGACCAAAATTTTTCCTCAATTTTTCACCAAAATACTC
ATAAAAAGTATATAATTCAACGCCAAAAACATTGGAGGGCTTTTCAAGCTTCTTATATTATTCAT
ATTTGTCTTAATTATTTCTAATTAAATCGAAACACGATTCAATGGCTCGTAAAAACATATCATTA
AATCCAAAGTCGCTAAGATTTGATTAGACGAATAAAGATATTTAAAGAAGCCTCGGTGCCAAAAA
CCATGCAAAACTGAGCTGGGCCCCAAGAACAGTATTTAGCCAAAAACAGTGATAGTTAATACACG
AGTTTTGCTAAAACTTTGCAAAAACTAAACCGAAATATTTTTCCTCAATTTTCGCA
Found at i:7168 original size:670 final size:657
Alignment explanation
Indices: 6375--9995 Score: 2808
Period size: 670 Copynumber: 5.5 Consensus size: 657
6365 AATACACAAT
* * * * * ** * * **
6375 TTCAACGCCGAAAACATTGGTGGGCTTTTCACGCATCTAATATCGTTCCTCATATTTTTTTTTGT
1 TTCAACGCCAAAAAGATTGGAGGGCTTTT-ACACTTCTAATATCGTTTTTCCTATTTTTTTCTAA
* *
6440 GTTAATTTCTACTTAAATCAATATCGGTTTCAGATACTCGTAAAAACATATCCTTAAATCCAATG
65 GTTAATTTCTACTTAAATCAAAATCGGTTTCAGATGCTCGTAAAAACATATCCTTAAATCCAATG
* * * * * *
6505 TGCTTGAAATTTGGTTGGATGAATAAAGATATTTCAAGGAGACTCGGCACCGAAAATCATGCAAA
130 TGCCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCC-AAAATCATGCAAA
* * * *
6570 ACTGAGCCGGGCTCCAAGAACGTGTTTTTTTTTGCCAAAAACTATGATAGTTAATACACAATTTC
194 ACTGAGCCGGGC-CCCAGAACGTG---TTTTTAGCCAAAAACTATGATAGTTAGTACACGATTTC
* * *
6635 GGCTAAAATTTTGTAAAAATTAACCCGAAATATTTTCCACAATTTTTCGCCAAAACACTCATAAA
255 GGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTCCACAATTTTTCGCCAAAATACTCAT-AA
* *** * *
6700 AAATATATATAATTCAACGCCAAAAAGATTTGACTCCTTTTCATGCTTCTAATATTATTTTTCCT
319 AAA-ATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATCATTTTTCCT
* * * *
6765 AATTTTTATGAATTTATTTCCACTTAAATCGAAACTGGTTTTAGATGCTCGTAAAAGCATATCCT
383 AATTTTTATGAATTTATTTCTACTTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACATATCCT
* * *
6830 TAAATCCAATTTGTCTTAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGTGTCAAA
448 TAAATCCAATGTGGCTTAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGTGTCAAA
* * *
6895 AATCATGCAAAACTGACCCAGGGCCCCGAAATGCGTTTTTAACCAAAAACCGTGATGGTTAGGAC
513 AATCATGCAAAACTGAGCCAGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTT---AC
* *
6960 ACGATTTCGGATAAAATATTGCAAAAAATT-ACCCAAAATATTTTTTCCTCAATTTTTGCCCAAA
575 ACGATTTCGGATAAAATTTTGC-AAAAATTGACCCGAAATA-TTTTTCCTCAATTTTTG-CCAAA
7024 ATACTCATAAAAAATATATAA
637 ATACTCATAAAAAATATATAA
* * * *
7045 TTCAACGCCAAAAACATTGGTGGTCTTTTACACTTCTTATATCGTTTTTCCTATTTTTTTTCTAA
1 TTCAACGCCAAAAAGATTGGAGGGCTTTTACACTTCTAATATCGTTTTTCCTA-TTTTTTTCTAA
* * *
7110 GTTTATTTCTACTTAAATCAAAATCGGTTTCAGATGCCCGTAAAAACATATCCTTAAATCCAATT
65 GTTAATTTCTACTTAAATCAAAATCGGTTTCAGATGCTCGTAAAAACATATCCTTAAATCCAATG
** * * *
7175 TGAATAAAATTTAATTAGATGAATATAGATATTTCAAGGAGTGTCGGCGCCAAAAATCATGCAAA
130 TGCCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCC-AAAATCATGCAAA
* * * *** * * * *
7240 ACTAAGTCGGGGCCCGAGAATACGTTTTTAACCAAAAAC-AGTGAT-GATTAATAAACGATTTCA
194 ACTGAG-CCGGGCCCCAGAACGTGTTTTTAGCCAAAAACTA-TGATAG-TTAGTACACGATTTCG
* * * * * *
7303 GCT-AAA--TTGCAAAAACTT-ACCTGAAAAATTTTTCCACAATTGTTGGCCATAATACTCATAT
256 GCTAAAATTTTGCAAAAA-TTGACCCGAAATA-TTTTCCACAATTTTTCGCCAAAATACTCATAA
* *
7364 AAAATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAAAATCATTTTCCCTA
319 AAAATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATCATTTTTCCTA
* * *
7429 TTTTTTA-GAATTTATTTCTACTTAAATCGAAATCGGTTTCAGATACTCGTAAAAACATATCCTT
384 ATTTTTATGAATTTATTTCTACTTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACATATCCTT
*
7493 AAATCCAATGTGGC-TAACATTTGATTAGAAGAATATAGATATTTCAAGGAG--TC----TC---
449 AAATCCAATGTGGCTTAA-ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGTGTCAAA
* * * * * ** *
7548 -A-CAT------TTGA---A--GCCCAG-AACGCCTTTTTTGCCAAAACCGTTGATTAAACGATT
513 AATCATGCAAAACTGAGCCAGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGA-T----GGTT
* * ** * * *
7599 --TCG---GCTAAAAT---TTTGCAAAAATTAACCCGAGAA-ATTTTTTCCTCAATTTTTCGCCA
573 ACACGATTTCGGATAAAATTTTGCAAAAATTGACCCGA-AATA-TTTTTCCTCAATTTTT-GCCA
*
7655 AAATAGTCATAAAAAATATATAA
635 AAATACTCATAAAAAATATATAA
* * *
7678 TTCAACTCCCAAAAGATTAGAGGGC-TTTACACGCTTCTAATA-------T-CTA-TTTTTTCTG
1 TTCAACGCCAAAAAGATTGGAGGGCTTTTACA--CTTCTAATATCGTTTTTCCTATTTTTTTCT-
* * * * * * *
7733 AA-TTTATTTCTACTTAAATCGAAACCGGTTTCAGATGGTCATAAAAACATATCCTTAGATTCAA
63 AAGTTAATTTCTACTTAAATCAAAATCGGTTTCAGATGCTCGTAAAAACATATCCTTAAATCCAA
** * * *
7797 TGTGGTTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTAGGTGCCAGAAATCATTCA
128 TGTGCCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCA-AAATCATGCA
* * * * * * * **
7862 AAATTGAACTAGAGCCCCGGAGCGCGTTTTTAG-CAAAGAACCGTGA-AGGTTAGTACACGATTT
192 AAACTGAGC-CGGGCCCCAGAACGTGTTTTTAGCCAAA-AACTATGATA-GTTAGTACACGATTT
* * * * * * * * *
7925 CGGTTAAAATTTTGCAGAAACTGTCCCGAAAAATTTTTTCCTCCATTTTTCACCAAAATAGTCAT
254 CGGCTAAAATTTTGCAAAAATTGACCCG--AAATATTTTCCACAATTTTTCGCCAAAATACTCAT
* * * * *
7990 AAAAAATAAATAATTCAACTCCAAAAAGATTGGAGGGCTTTTCACGCTTCCAACATCATTTTTCA
317 AAAAAATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATCATTTTTCC
* * * *
8055 T-ATTTTTGTTGAATTTATTTCTACATAAATCGAAACCGATTGCAGATGCTCGTAAAAACATATC
382 TAATTTTT-ATGAATTTATTTCTACTTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACATATC
* * * * * * * * *
8119 TTTAAATCTAATGTGCCTGAAATTTGGTTAGATTAATATAGATATTTCAAGGAGACTTGGCT-TT
446 CTTAAATCCAATGTGGCTTAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGG-TGTC
* * * * * * **
8183 AAAAATCATGCCAAATTGAACC-GGGGCCCTAGAACGCGTTTTTAGCCTAAAACCGTGA--CCTA
510 AAAAATCATGCAAAACTGAGCCAGGGCCCCGA-AACGCGTTTTTAGCCAAAAACCGTGATGGTTA
* * * * ** * *
8245 CACGATTTCAGCTAAAATTTTGGAATAATTGACCCGAAATAAAATTTCCTCAATTTTTTTGTCAC
574 CACGATTTCGGATAAAATTTTGCAAAAATTGACCCGAAAT-ATTTTTCCTCAA--TTTTTGCCAA
8310 AATACTCA-AGAAAAATATATAA
636 AATACTCATA-AAAAATATATAA
* * * * * * * ** * **
8332 TTTAATGTCAAAATGATTGAAGGTCTTTTCACGCAACTAATATCATTTTTTATATTTGTTTTGC-
1 TTCAACGCCAAAAAGATTGGAGGGCTTTT-ACACTTCTAATATCGTTTTTCCTATTT-TTTT-CT
* * ** * *
8396 AAATTAATTTCTAATTAAATCGAAAA-AAGATTCA-ACTGCTGGTAAAAACATATATCCTTAAAT
63 AAGTTAATTTCTACTTAAATC-AAAATCGGTTTCAGA-TGCTCGTAAAAAC--ATATCCTTAAAT
* * * * * *
8459 CCAATGTGCCTGAAATTTGTTTTGTTGAATATAGATTTTTCAAGGATTCTCGGTGTCCAAAATCA
124 CCAATGTGCCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCG-CCAAAATCA
* * * * * * *
8524 TGCTAAACTGACCCGGGGCCCCGGAAC-TCGTTTTTAGCAAAAAAAACTGTTATGGTTAGTACAC
188 TGCAAAACTGAGCC-GGGCCCCAGAACGT-GTTTTTAGC--CAAAAACTATGATAGTTAGTACAC
* * * * * *
8588 GATTTCGGTTAAAATTTTGCAGAAACTGACCCGAAAAAGTTTTCCTCAATTTTTTTTGCCAAAAT
249 GATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATA-TTTTCCACAA--TTTTTCGCCAAAAT
* * * * * * * *
8653 ACACATAAAAAATATATAATCCAATGCCTAAAAGATTGGAAGGC-TTTGAGCGCTTCTTATATTA
311 ACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCA-CGCTTCTAATATCA
* * * * * * * * *
8717 -TTTTCCTATTTTTTCTAAAATTATATCTATTTAAATGGAAACCGGTTGCAGATGCTTGTAAAAA
375 TTTTTCCTAATTTTTATGAATTTATTTCTACTTAAATCGAAACCGGTTTCAGATGCTCGTAAAAA
* * * *
8781 TATATCCTTAAATCCAATATGGTCGT-AATTTGATTAGATGAATATAGATATTTCAAGAAGTCTC
440 CATATCCTTAAATCCAATGTGG-CTTAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC
* * *
8845 GGTGCCAAAAATCATGCAAAACTGAGTCA-GG----G---C-CGTTTTTAGCCAAAAACCGT-AA
504 GGTGTCAAAAATCATGCAAAACTGAGCCAGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGAT
* * * *
8900 CG-TACACGATTTCGGTTATAATTTTACAAAAATTGACCCGAAATATTTTTCC-CAATTTTTGCC
569 GGTTACACGATTTCGGATAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTTG-C
*
8963 CAGAATACTCATAAAGAAA-ATATAA
633 CAAAATACTCATAAA-AAATATATAA
* * * * * *
8988 TTCAACGCCAATAATATTGGTGGGCTTTTTACGCTTCTAATATCGTTCTTCCTATTTTTTT-TGA
1 TTCAACGCCAAAAAGATTGGAGGGC-TTTTACACTTCTAATATCGTTTTTCCTATTTTTTTCTAA
** **
9052 GTTAATTTCTACTTAAATTGAAATCGAATTCAGATGCTCGTAAAAA-ATATCCTTAAATCCAATG
65 GTTAATTTCTACTTAAATCAAAATCGGTTTCAGATGCTCGTAAAAACATATCCTTAAATCCAATG
* *
9116 TGCCTGAAATTTGGTTAGATGAATATAGATATTTCAAGGAGACTCGGCGCCAAAATCATGCAAAA
130 TGCCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAATCATGCAAAA
* * * * *
9181 CTGAGTCGTGGCCCTAGAACGCGTTTTTAGCCAAAAACCGTGATGTTTGATGGTTAGTGCACGAT
195 CTGAGCCG-GGCCCCAGAACGTGTTTTTAGCCAAAAA-C-T-A----TGATAGTTAGTACACGAT
* * * * * *
9246 TTCGACTAAAATTTTGGAAAAATTGACCCGAAATATTTTCCCCCAATTTTTGGTCACAATACTCA
252 TTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTT-CCACAATTTTTCGCCAAAATACTCA
** * * * * *
9311 T-GGAAATATATAATTCAATGCCAAAACGATTGAAGGGTTTTTCAAGCTTCTAATATCATTTTTC
316 TAAAAAATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATCATTTTTC
* * * * * ** * ** *
9375 AT-ATTTGTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCA-ATTATTGGTAAAAACA
381 CTAATTT-TTAT--GAATTTATTTCTACTTAAATCGAAACCGGTTTCAGA-TGCTCGTAAAAACA
* * * * * * * * *
9438 TATCATGAAATCCAGTGTGGCTGAAATTTGATTAGATGAATAAACATGTTTCAGGGAGTCTCGGC
442 TATCCTTAAATCCAATGTGGCTTAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGT
* * * ** * ** *
9503 GCCAAAAATCATGCAAAACTAAGAC-GCTCTCAAAGAACGCGTTTTTAGCC-AAAACAGTGATAG
507 GTCAAAAATCATGCAAAACTGAGCCAGGGCCCCGA-AACGCGTTTTTAGCCAAAAACCGTGAT-G
* * * *
9566 TTAAATACACGATTTTGGCTAAAATTTTG-AAAAATTAACCCGAAATATTTTTTCCTCAATTTTT
570 GT---TACACGATTTCGGATAAAATTTTGCAAAAATTGACCCGAAATA-TTTTTCCTCAATTTTT
* *
9630 GCCAAAATACTCATTGAAAAATATATGA
631 GCCAAAATACTCA-TAAAAAATATATAA
** *
9658 TTCAACGCCAAAAAGATTTCAGGGCTTTT-CATCCTTCTAATATCATTTTTCCTA-TTTTTTCTG
1 TTCAACGCCAAAAAGATTGGAGGGCTTTTACA--CTTCTAATATCGTTTTTCCTATTTTTTTCT-
* * * * *
9721 AA-TTTATTTATACTTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACATATCCTCAAATCCAA
63 AAGTTAATTTCTACTTAAATCAAAATCGGTTTCAGATGCTCGTAAAAACATATCCTTAAATCCAA
* * * * * * *
9785 TGTGGCTGAAATTTGATTAAATGAATGTAGATATTTTAAGGATTCTTGGAGCCAAAGATCATGCA
128 TGTGCCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAA-ATCATGCA
* * ** *
9850 AAACTGAGGCGGGGCCCC-GTAACGCGTTTTTAGGCCAAAAAAACCGTGAT-GGT-G-ACACGAT
192 AAACTGA-GCCGGGCCCCAG-AACGTGTTTTTA-GCC--AAAAACTATGATAGTTAGTACACGAT
* * * ** * * *
9911 ATCAGCT-AAATTTTGCAAAAACTGACAAGAAAAAATTTTCCTCAATTTTTCGCCAAAATACTTA
252 TTCGGCTAAAATTTTGCAAAAATTGACCCG-AAATATTTTCCACAATTTTTCGCCAAAATACTCA
* *
9975 CATAAAATATATAATTCAACG
316 TAAAAAATATATAATTCAACG
9996 TTGATCGGTC
Statistics
Matches: 2341, Mismatches: 448, Indels: 329
0.75 0.14 0.11
Matches are distributed among these distances:
623 6 0.00
624 158 0.07
625 6 0.00
626 4 0.00
627 17 0.01
628 82 0.04
629 96 0.04
630 2 0.00
631 1 0.00
632 13 0.01
633 71 0.03
634 11 0.00
635 1 0.00
636 3 0.00
639 22 0.01
640 9 0.00
642 1 0.00
644 3 0.00
645 4 0.00
646 4 0.00
647 2 0.00
648 5 0.00
649 2 0.00
650 44 0.02
651 63 0.03
652 66 0.03
653 58 0.02
654 85 0.04
655 178 0.08
656 59 0.03
657 11 0.00
658 7 0.00
659 55 0.02
660 2 0.00
661 4 0.00
662 97 0.04
663 73 0.03
664 105 0.04
665 66 0.03
666 99 0.04
667 48 0.02
668 193 0.08
669 136 0.06
670 257 0.11
671 69 0.03
672 32 0.01
673 5 0.00
674 1 0.00
675 5 0.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (657 bp):
TTCAACGCCAAAAAGATTGGAGGGCTTTTACACTTCTAATATCGTTTTTCCTATTTTTTTCTAAG
TTAATTTCTACTTAAATCAAAATCGGTTTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGT
GCCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAATCATGCAAAAC
TGAGCCGGGCCCCAGAACGTGTTTTTAGCCAAAAACTATGATAGTTAGTACACGATTTCGGCTAA
AATTTTGCAAAAATTGACCCGAAATATTTTCCACAATTTTTCGCCAAAATACTCATAAAAAATAT
ATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATCATTTTTCCTAATTTTTA
TGAATTTATTTCTACTTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACATATCCTTAAATCCA
ATGTGGCTTAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGTGTCAAAAATCATGC
AAAACTGAGCCAGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTACACGATTTCGGA
TAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTTGCCAAAATACTCATAAAAAA
TATATAA
Found at i:7175 original size:334 final size:330
Alignment explanation
Indices: 6375--7547 Score: 1281
Period size: 334 Copynumber: 3.5 Consensus size: 330
6365 AATACACAAT
* * * * ** * *
6375 TTCAACGCCGAAAACATTGGTGGGCTTTTCACGCATCTAATATCGTTCCTCATATTTTTTTTTGT
1 TTCAACGCCAAAAACATTGGTGGGCTTTTCACACTTCTAATATCATTTTTCCTA-TTTTTTTTGA
* * *
6440 GTTAATTTCTACTTAAATCAATATCGGTTTCAGATACTCGTAAAAACATATCCTTAAATCCAATG
65 ATTTATTTCTACTTAAATCAAAATCGGTTTCAGATACTCGTAAAAACATATCCTTAAATCCAATG
* * * * * *
6505 TGCTTGAAATTTGGTTGGATGAATAAAGATATTTCAAGGAGACTCGGCACCGAAAATCATGCAAA
130 TGCTT-AAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAA
* * ** ** * *
6570 ACTGAGCCGGGCTCCAAGAACGTGTTTTTTTTTGCCAAAAACTA-TGATAGTTAATACACAATTT
194 ACTGAGCCGGGC-CC-CGAA-ATG-CGTTTTTAACCAAAAAC-AGTGATGGTTAATACACGATTT
* * * *
6634 CGGCTAAAATTTTG-TAAAAATTAACCCGAAATA-TTTTCCACAATTTTT-CGCCAAAACACTCA
254 CGGCTAAAATATTGCAAAAAATT-ACCCAAAATATTTTTCCACAATTTTTGC-CCAAAATACTCA
6696 TAAAAAATATATATAA
317 T-AAAAA-ATATATAA
* * **** ** * * *
6712 TTCAACGCCAAAAAGATTTGACTCCTTTTCATGCTTCTAATATTATTTTTCCTAATTTTTATGAA
1 TTCAACGCCAAAAACATTGGTGGGCTTTTCACACTTCTAATATCATTTTTCCTATTTTTTTTGAA
* * * * * *
6777 TTTATTTCCACTTAAATCGAAA-CTGGTTTTAGATGCTCGTAAAAGCATATCCTTAAATCCAATT
66 TTTATTTCTACTTAAATCAAAATC-GGTTTCAGATACTCGTAAAAACATATCCTTAAATCCAATG
* * *
6841 TGTCTTAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGTGTCAAAAATCATGCAAA
130 TG-CTTAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAA
* * ** *
6906 ACTGACCCAGGGCCCCGAAATGCGTTTTTAACCAAAAACCGTGATGGTTAGGACACGATTTCGGA
194 ACTGAGCC-GGGCCCCGAAATGCGTTTTTAACCAAAAACAGTGATGGTTAATACACGATTTCGGC
*
6971 TAAAATATTGCAAAAAATTACCCAAAATATTTTTTCCTCAATTTTTGCCCAAAATACTCATAAAA
258 TAAAATATTGCAAAAAATTACCCAAAATA-TTTTTCCACAATTTTTGCCCAAAATACTCATAAAA
7036 AATATATAA
322 AATATATAA
* * * *
7045 TTCAACGCCAAAAACATTGGTGGTCTTTT-ACACTTCTTATATCGTTTTTCCTATTTTTTTTCTA
1 TTCAACGCCAAAAACATTGGTGGGCTTTTCACACTTCTAATATCATTTTTCCTATTTTTTTT-GA
* *
7109 AGTTTATTTCTACTTAAATCAAAATCGGTTTCAGATGCCCGTAAAAACATATCCTTAAATCCAAT
65 A-TTTATTTCTACTTAAATCAAAATCGGTTTCAGATACTCGTAAAAACATATCCTTAAATCCAAT
* * * * *
7174 TTGAATAAAATTTAATTAGATGAATATAGATATTTCAAGGAGTGTCGGCGCCAAAAATCATGCAA
129 GTG-CTTAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAA
* * * * * * *
7239 AACTAAGTCGGGGCCCGAGAATACGTTTTTAACCAAAAACAGTGATGATTAATAAACGATTTCAG
193 AACTGAGCCGGGCCCCGA-AATGCGTTTTTAACCAAAAACAGTGATGGTTAATACACGATTTCGG
* * * * * *
7304 CT--AA-ATTGCAAAAACTTACCTGAAAA-ATTTTTCCACAATTGTTGGCCATAATACTCATATA
257 CTAAAATATTGCAAAAAATTACC-CAAAATATTTTTCCACAATTTTTGCCCAAAATACTCATAAA
7365 AAATATATAA
321 AAATATATAA
* * * * * *
7375 TTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAAAATCATTTTCCCTA-TTTTTTAGAA
1 TTCAACGCCAAAAACATTGGTGGGCTTTTCACACTTCTAATATCATTTTTCCTATTTTTTTTGAA
*
7439 TTTATTTCTACTTAAATCGAAATCGGTTTCAGATACTCGTAAAAACATATCCTTAAATCCAATGT
66 TTTATTTCTACTTAAATCAAAATCGGTTTCAGATACTCGTAAAAACATATCCTTAAATCCAATGT
*
7504 GGC-TAACATTTGATTAGAAGAATATAGATATTTCAAGGAGTCTC
131 -GCTTAA-ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC
7548 ACATTTGAAG
Statistics
Matches: 702, Mismatches: 118, Indels: 41
0.82 0.14 0.05
Matches are distributed among these distances:
327 2 0.00
328 95 0.14
329 3 0.00
330 71 0.10
331 35 0.05
332 31 0.04
333 91 0.13
334 173 0.25
335 31 0.04
336 123 0.18
337 47 0.07
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.34
Consensus pattern (330 bp):
TTCAACGCCAAAAACATTGGTGGGCTTTTCACACTTCTAATATCATTTTTCCTATTTTTTTTGAA
TTTATTTCTACTTAAATCAAAATCGGTTTCAGATACTCGTAAAAACATATCCTTAAATCCAATGT
GCTTAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAAC
TGAGCCGGGCCCCGAAATGCGTTTTTAACCAAAAACAGTGATGGTTAATACACGATTTCGGCTAA
AATATTGCAAAAAATTACCCAAAATATTTTTCCACAATTTTTGCCCAAAATACTCATAAAAAATA
TATAA
Found at i:9910 original size:332 final size:329
Alignment explanation
Indices: 7557--9995 Score: 2056
Period size: 333 Copynumber: 7.4 Consensus size: 329
7547 CACATTTGAA
* *
7557 GCCCAGAACGCCTTTTTTGCC-AAAACCGTTGAT--TA-A-ACGATTTCGGCTAAAATTTTGCAA
1 GCCCAGAACGCGTTTTTAGCCAAAAACCG-TGATGGTAGACACGATTTCGGCTAAAATTTTGCAA
* * *
7617 AAATTAACCCGAGAA-ATTTTTTCCTCAATTTTTCGCCAAAATAGTCATAAAAAATATATAATTC
65 AAATTGACCCGA-AATAATTTTTCCTCAATTTTTCGCCAAAATACTCATAAAAAATATATAATTC
* * * *
7681 AACTCCCAAAAGATTAGAGGGCTTTACACGCTTCT-A-AT-A----T-CTATTTTTTCTGAATTT
129 AACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATCATTTTTCCTATTTTTTCTGAATTT
* * * * *
7738 ATTTCTACTTAAATCGAAACCGGTTTCAGATGGTCATAAAAACATATCCTTAGATTCAATGTGGT
194 ATTTCTACTTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGC
* * * *
7803 TGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTAGGTGCCAGAAATCATTCAAAATTG
259 TGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCA-AAATCATGCAAAACTG
*
7868 A-ACTAGAG
323 AGAC--GGG
* * * * *
7876 CCCCGGAGCGCGTTTTTAG-CAAAGAACCGTGAAGGTTAGTACACGATTTCGGTTAAAATTTTGC
1 GCCCAGAACGCGTTTTTAGCCAAA-AACCGTGATGG-TAG-ACACGATTTCGGCTAAAATTTTGC
* * * * * * *
7940 AGAAACTGTCCCGAAA-AATTTTTTCCTCCATTTTTCACCAAAATAGTCATAAAAAATAAATAAT
63 AAAAATTGACCCGAAATAA-TTTTTCCTCAATTTTTCGCCAAAATACTCATAAAAAATATATAAT
* * * *
8004 TCAACTCCAAAAAGATTGGAGGGCTTTTCACGCTTCCAACATCATTTTTCATATTTTTGT-TGAA
127 TCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATCATTTTTCCTATTTTT-TCTGAA
* * * * *
8068 TTTATTTCTACATAAATCGAAACCGATTGCAGATGCTCGTAAAAACATATCTTTAAATCTAATGT
191 TTTATTTCTACTTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGT
* * * * * *** *
8133 GCCTGAAATTTGGTTAGATTAATATAGATATTTCAAGGAGACTTGGCTTTAAAAATCATGCCAAA
256 GGCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGC-GCCAAAATCATGCAAAA
*
8198 TTGA-ACCGGG
320 CTGAGA-CGGG
* ** * *
8208 GCCCTAGAACGCGTTTTTAGCCTAAAACCGTGA-CCT--ACACGATTTCAGCTAAAATTTTGGAA
1 GCCC-AGAACGCGTTTTTAGCCAAAAACCGTGATGGTAGACACGATTTCGGCTAAAATTTTGCAA
* ** * * *
8270 TAATTGACCCGAAATAAAATTTCCTCAATTTTTTTGTCACAATACTCA-AGAAAAATATATAATT
65 AAATTGACCCGAAATAATTTTTCCTCAA-TTTTTCGCCAAAATACTCATA-AAAAATATATAATT
* * * * * * ** **
8334 TAATGTCAAAATGATTGAAGGTCTTTTCACGCAACTAATATCATTTTTTATATTTGTTT-TGCAA
128 CAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATCATTTTTCCTATTT-TTTCTG--A
* * *** * *
8398 ATTAATTTCTAATTAAATCGAAAAAAGATTCA-ACTGCTGGTAAAAACATATATCCTTAAATCCA
190 ATTTATTTCTACTTAAATCGAAACCGGTTTCAGA-TGCTCGTAAAAAC--ATATCCTTAAATCCA
* * * * * * *
8462 ATGTGCCTGAAATTTGTTTTGTTGAATATAGATTTTTCAAGGATTCTCGGTGTCCAAAATCATGC
252 ATGTGGCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCG-CCAAAATCATGC
* **
8527 TAAACTGACCCGGG
316 AAAACTGAGACGGG
* * * * * *
8541 GCCCCGGAACTCGTTTTTAGCAAAAAAAACTGTTATGGTTAGTACACGATTTCGGTTAAAATTTT
1 G-CCCAGAACGCGTTTTTAGC--CAAAAACCGTGATGG-TAG-ACACGATTTCGGCTAAAATTTT
* * * * *
8606 GCAGAAACTGACCCGAAA-AAGTTTTCCTCAATTTTTTTTGCCAAAATACACATAAAAAATATAT
61 GCAAAAATTGACCCGAAATAATTTTTCCTCAA--TTTTTCGCCAAAATACTCATAAAAAATATAT
* * * * * * *
8670 AATCCAATGCCTAAAAGATTGGAAGGC-TTTGAGCGCTTCTTATATTA-TTTTCCTATTTTTTCT
124 AATTCAACGCCAAAAAGATTGGAGGGCTTTTCA-CGCTTCTAATATCATTTTTCCTATTTTTTCT
* * * * * * * *
8733 AAAATTATATCTATTTAAATGGAAACCGGTTGCAGATGCTTGTAAAAATATATCCTTAAATCCAA
188 GAATTTATTTCTACTTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACATATCCTTAAATCCAA
* * * *
8798 TATGG-TCGTAATTTGATTAGATGAATATAGATATTTCAAGAAGTCTCGGTGCCAAAAATCATGC
253 TGTGGCT-GAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCC-AAAATCATGC
* *
8862 AAAACTGAGTC-AG
316 AAAACTGAGACGGG
** * * *
8875 G----G--C-CGTTTTTAGCCAAAAACCGT-AACGT--ACACGATTTCGGTTATAATTTTACAAA
1 GCCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTAGACACGATTTCGGCTAAAATTTTGCAAA
*
8930 AATTGACCCGAAAT-ATTTTTCC-CAATTTTT-GCCCAGAATACTCATAAAGAAA-ATATAATTC
66 AATTGACCCGAAATAATTTTTCCTCAATTTTTCG-CCAAAATACTCATAAA-AAATATATAATTC
* * * * * * * * *
8991 AACGCCAATAATATTGGTGGGCTTTTTACGCTTCTAATATCGTTCTTCCTATTTTTTTTGAGTTA
129 AACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATCATTTTTCCTATTTTTTCTGAATTT
* * ** *
9056 ATTTCTACTTAAATTGAAATCGAATTCAGATGCTCGTAAAAA-ATATCCTTAAATCCAATGTGCC
194 ATTTCTACTTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGC
* *
9120 TGAAATTTGGTTAGATGAATATAGATATTTCAAGGAGACTCGGCGCCAAAATCATGCAAAACTGA
259 TGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAATCATGCAAAACTGA
* *
9185 GTCGTG
324 GACGGG
* *
9191 GCCCTAGAACGCGTTTTTAGCCAAAAACCGTGATGTTTGATGGTTAGTGCACGATTTCGACTAAA
1 GCCC-AGAACGCGTTTTTAGCCAAAAACC-----G--TGATGG-TAG-ACACGATTTCGGCTAAA
* * * * * * **
9256 ATTTTGGAAAAATTGACCCGAAAT-ATTTTCCCCCAATTTTTGGTCACAATACTCAT-GGAAATA
56 ATTTTGCAAAAATTGACCCGAAATAATTTTTCCTCAATTTTTCGCCAAAATACTCATAAAAAATA
* * * * * *
9319 TATAATTCAATGCCAAAACGATTGAAGGGTTTTTCAAGCTTCTAATATCATTTTTCATATTTGTT
121 TATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATCATTTTTCCTA-TT-TT
** * * ** * ** * * *
9384 TTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCA-ATTATTGGTAAAAACATATCATGAAA
184 TTCTGAATTTATTTCTACTTAAATCGAAACCGGTTTCAGA-TGCTCGTAAAAACATATCCTTAAA
* * * * *
9448 TCCAGTGTGGCTGAAATTTGATTAGATGAATAAACATGTTTCAGGGAGTCTCGGCGCCAAAAATC
248 TCCAATGTGGCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCC-AAAATC
* *
9513 ATGCAAAACTAAGAC-GC
312 ATGCAAAACTGAGACGGG
* * * * * *
9530 TCTCAAAGAACGCGTTTTTAGCC-AAAACAGTGATAGTTAAATACACGATTTTGGCTAAAATTTT
1 GC-C-CAGAACGCGTTTTTAGCCAAAAACCGTGAT-GGT--AGACACGATTTCGGCTAAAATTTT
* * * *
9594 G-AAAAATTAACCCGAAATATTTTTTCCTCAATTTTT-GCCAAAATACTCATTGAAAAATATATG
61 GCAAAAATTGACCCGAAATAATTTTTCCTCAATTTTTCGCCAAAATACTCA-TAAAAAATATATA
**
9657 ATTCAACGCCAAAAAGATTTCAGGGCTTTTCATC-CTTCTAATATCATTTTTCCTATTTTTTCTG
125 ATTCAACGCCAAAAAGATTGGAGGGCTTTTCA-CGCTTCTAATATCATTTTTCCTATTTTTTCTG
* *
9721 AATTTATTTATACTTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACATATCCTCAAATCCAAT
189 AATTTATTTCTACTTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACATATCCTTAAATCCAAT
* * * * * *
9786 GTGGCTGAAATTTGATTAAATGAATGTAGATATTTTAAGGATTCTTGGAGCCAAAGATCATGCAA
254 GTGGCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAA-ATCATGCAA
*
9851 AACTGAGGCGGG
318 AACTGAGACGGG
* * *
9863 GCCCCGTAACGCGTTTTTAGGCCAAAAAAACCGTGATGGT-GACACGATATCAGCT-AAATTTTG
1 GCCCAG-AACGCGTTTTTA-GCC--AAAAACCGTGATGGTAGACACGATTTCGGCTAAAATTTTG
* ** * * * *
9926 CAAAAACTGACAAGAAA-AAATTTTCCTCAATTTTTCGCCAAAATACTTACATAAAATATATAAT
62 CAAAAATTGACCCGAAATAATTTTTCCTCAATTTTTCGCCAAAATACTCATAAAAAATATATAAT
9990 TCAACG
127 TCAACG
9996 TTGATCGGTC
Statistics
Matches: 1688, Mismatches: 330, Indels: 192
0.76 0.15 0.09
Matches are distributed among these distances:
315 22 0.01
316 116 0.07
317 58 0.03
318 4 0.00
319 62 0.04
320 5 0.00
321 1 0.00
322 3 0.00
323 3 0.00
324 30 0.02
325 106 0.06
326 11 0.01
327 3 0.00
328 43 0.03
329 77 0.05
330 3 0.00
331 83 0.05
332 202 0.12
333 279 0.17
334 71 0.04
335 87 0.05
336 100 0.06
337 57 0.03
338 44 0.03
339 90 0.05
340 127 0.08
341 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (329 bp):
GCCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTAGACACGATTTCGGCTAAAATTTTGCAAA
AATTGACCCGAAATAATTTTTCCTCAATTTTTCGCCAAAATACTCATAAAAAATATATAATTCAA
CGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATCATTTTTCCTATTTTTTCTGAATTTAT
TTCTACTTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTG
AAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAATCATGCAAAACTGAGA
CGGG
Done.