Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019408.1 Corchorus olitorius cultivar O-4 contig19441, 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: 40441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1115 original size:320 final size:322
Alignment explanation
Indices: 5--2407 Score: 1486
Period size: 320 Copynumber: 7.4 Consensus size: 322
1 GATG
* * * * * * *
5 GTACATGAATTCGGCTAAAATTTTGCAAAAAATGACTC-GAAAGATTTTTCCTCGATTTCTAGT-
1 GTACACGATTTCGGCTAATATTTTGCAAAAATTGAC-CAGAAATATTTTTCCTCAATTT-TTGTC
* * * * * *** *
68 GAAAATACTAAAAAAATATATATAATTCAACGTC-AAAAAAATTGAAAGCCTTTTTCACGCTTTT
64 AAAAATACT-CATAAATATATATAATTCAAC-TCTAAAAAGATTG-GAGGAATTTTCTCGCTTTT
*
132 AATATCGTGTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
126 AATATCGTTTTTC--A----T-T-AATTAA-TTCT-ATTAAATCGAAACAAGATTCAGATGCTCG
* * * * *
197 TAAAAACAAATCCTTAAATTCAATGTGCCT-AAGATTTGATAAGATGAATATAAATATTTCAAGG
181 TAAAAACAAATTCTTAAATCCAATGTGGCTGAA-ATTTGATTAGATGAATATAGATATTTCAAGG
* ** * * * *
261 AGTCTCGACATAAAAAATCATGCAAAACTAAGTC-AGCCCTCGGAATGCGTTTTTAGCCGAAAAC
245 AGTCTCGGC-GCAAAAATCATGCAAAACTGAGTCGGGCCC-CGGAACGCGTTTTTAGCCAAAAAC
* *
325 CGTGA--TG-GTTA-
308 CGTGATTTGACTAAC
* * * * * *
336 GTACACGATTTCGGCTAAAATTTTGCAAAAACTCACCCGAAAGATTTTTTCGTCTAA-TTTTG-C
1 GTACACGATTTCGGCTAATATTTTGCAAAAATTGACCAGAAATA-TTTTTCCTC-AATTTTTGTC
* * * *
399 ATAAAATA--CATACA-AT-T-TAA--C-GC-C-AAAAAGATTGGAGGACTTTTCACGCTTTTAA
64 A-AAAATACTCATAAATATATATAATTCAACTCTAAAAAGATTGGAGGAATTTTCTCGCTTTTAA
454 TATCGTTTTTCATGTTTTTCTAAATTAATTTCTAGTTAAATCGAAACAAGATTCAGATGCTCGTA
128 TATCGTTTTTCA------T-T-AATTAA-TTCTA-TTAAATCGAAACAAGATTCAGATGCTCGTA
* * * * * * * * *
519 AAAACAAATTCTTCAATCTAATGTAGCTGACATTAGATTAAATGAATATGGATATCTCAAAGAGT
183 AAAACAAATTCTTAAATCCAATGTGGCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGT
* * * * * * *
584 CTTGGCGGAAAAAATCATGCAAAACTTAGTC-GGCCCCTCGAACACGTTTTTAGCCAAAATCGGT
248 CTCGGC-GCAAAAATCATGCAAAACTGAGTCGGGCCCC-GGAACGCGTTTTTAGCCAAAAACCGT
*
648 GA--TGA-TTA-
311 GATTTGACTAAC
* * * *
656 TTACACGATTTCGGCTAGA-ATTTTGTAAAAATTGACTC-GAAAGT-TATTTCCTCAATTTTTAT
1 GTACACGATTTCGGCTA-ATATTTTGCAAAAATTGAC-CAGAAA-TATTTTTCCTCAATTTTTGT
* * * * * * * * *
718 CCACAATACTCATAAAAATTATATAATTCAACACCAAAAAAATTGAAAGG-TTTTTCAT-GCTTC
63 CAAAAATACTCATAAATA-TATATAATTCAACTCTAAAAAGATTG-GAGGAATTTTC-TCGCTTT
* * * ***
781 TAATATCATTTTTCA-T-ATT-A-T-T-TTAAATCGAAACATGATTCAGATGCTTGT-TTTACAA
125 TAATATCGTTTTTCATTAATTAATTCTATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * * *
839 ATCCTTAAATCCAATGTGGCTTAAATTTGGTTAGATGAATGTAGATATTTCAAGGAGTCTCGGCG
190 ATTCTTAAATCCAATGTGGCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCG
* ** * * *
904 CAAATAATCATGCAACACTGAACCGGGACCCTGGAACGCATTTTTAGCAAAAAACCGTGATTTCG
255 CAAA-AATCATGCAAAACTGAGTCGGG-CCCCGGAACGCGTTTTTAGCCAAAAACCGTGATTT-G
969 ACTAAC
317 ACTAAC
* *
975 GTACACGATTTTGGCTAATATTTTGCAAAAATTTACCAGAAATATTTTTCCTCAATTTTTGTCTA
1 GTACACGATTTCGGCTAATATTTTGCAAAAATTGACCAGAAATATTTTTCCTCAATTTTTGTC-A
1040 AAAATACTCATAATATATATATAATTCAACTCTAAAAAGATTGGAGGAATTTTCTCGCTTTTAAT
65 AAAATACTCATAA-ATATATATAATTCAACTCTAAAAAGATTGGAGGAATTTTCTCGCTTTTAAT
*
1105 ATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCGCGTAA
129 ATCGTTTTTC--A----T-T-AATTAA-TTCT-ATTAAATCGAAACAAGATTCAGATGCTCGTAA
** * * *
1170 AAACAAATTCTTAAATTAAATGTGGCTGAGATTTGATAAGATGAATATAAATATTTCAAGGAGTC
184 AAACAAATTCTTAAATCCAATGTGGCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTC
* * * *
1235 TCGACACAAAAAATCATGCAAAACTGAGTCGGGCCCCGGAATGCGTTTTTAGCCGAAAACCGTGA
249 TCGGCGC-AAAAATCATGCAAAACTGAGTCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGA
* *
1300 --TG-GTTA-
313 TTTGACTAAC
* * * * * *
1306 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCTGAAAGA-TTTTCAGTCAAATTTTG-CA
1 GTACACGATTTCGGCTAATATTTTGCAAAAATTGACCAGAAATATTTTTC-CTCAATTTTTGTCA
* * * *
1369 TAAAATA--CATACA-AT-T-TAA--C-GC-C-AAAAAGATTGGAGGACTTTTCACGCTTTTAAT
65 -AAAATACTCATAAATATATATAATTCAACTCTAAAAAGATTGGAGGAATTTTCTCGCTTTTAAT
*
1424 ATCGTTTTTCATGTTTTTCTGAATTAATTTCTAGTTAAATCGAAATAAGATTCAGATGCTCGTAA
129 ATCGTTTTTCA------T-T-AATTAA-TTCTA-TTAAATCGAAACAAGATTCAGATGCTCGTAA
* * * * * * * * *
1489 AAAAAAATTCTTCAATCCAATGTAGCTGACATTAGATTAAATGAATATGGATATCTCAAAGAGTC
184 AAACAAATTCTTAAATCCAATGTGGCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTC
* *
1554 TTGGCGCCAAAAATCATGCAAAACTTAGTCGTGGCCCCGGAACGCGTTTTTAGCCAAAAA-CGAT
249 TCGGCG-CAAAAATCATGCAAAACTGAGTCG-GGCCCCGGAACGCGTTTTTAGCCAAAAACCG-T
1618 GATTTTGACTAAC
311 GA-TTTGACTAAC
* * * * *
1631 GTATACGATTTTGCCTAATATTTTGCAAAAATTTACCAGAAATATTTTTCCTCAATTTTTGTCTA
1 GTACACGATTTCGGCTAATATTTTGCAAAAATTGACCAGAAATATTTTTCCTCAATTTTTGTCAA
1696 AAATACTCATAAAATATATATAATTCAACTCTAAAAAGATTGGAGGAATTTTCTCGCTTTTAATA
66 AAATACTCAT-AAATATATATAATTCAACTCTAAAAAGATTGGAGGAATTTTCTCGCTTTTAATA
* *
1761 TCGCTTTTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAAGAAGATTCAGATGCTCGTAAA
130 TCGTTTTTC--A-----TT-AATTAA-TTCT-ATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* * * **
1826 AATAAATCCTTAAATGCAATGTGGCTG--A---GATT---T-AATATAGATATTTTGAGGAGTCT
185 AACAAATTCTTAAATCCAATGTGGCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCT
*** ***
1882 CGATGC-CAAAAATCATGCAAAACTGAGTCGGGGCCCAAAAACGCGTTTTTAATAAAAAACCGTG
250 CG--GCGCAAAAATCATGCAAAACTGAGTC-GGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTG
* *
1946 A--TG-GTTA-
312 ATTTGACTAAC
* * * *
1953 GTACACGATTTCGGCTAAAATTTTACAAGAAA-TGACCAGAAA-AATATTCTCTCAATTTTTAG-
1 GTACACGATTTCGGCTAATATTTTGCAA-AAATTGACCAGAAATATTTTTC-CTCAATTTTT-GT
* * * * * * * ** *
2015 CCACAATACTCATAAAAAATATATAATTCAACACCAAAAAAATTGAAGGGCTTTT-TACGCTTCT
63 CAAAAATACTCAT-AAATATATATAATTCAACTCTAAAAAGATTGGAGGAATTTTCT-CGCTTTT
* * * *
2079 AATATCGTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAAACGAAACATGATTCAGATGTTT
126 AATATCGTTTTT-C-A----TT---AATTAA-TTCT-ATTAAATCGAAACAAGATTCAGATGCTC
** * *
2144 GT---AA-AAA--C---AAT--GGT-TGG--G--ATTTGGTTAGATTAATATAGATATTTCAAGG
180 GTAAAAACAAATTCTTAAATCCAATGTGGCTGAAATTTGATTAGATGAATATAGATATTTCAAGG
* * * * *
2193 AGTCTCGACGCCAAAAATCATTCAAAATTGA-ACTGGGCCTCGGAACGCGTTTTTAGCCAAAAAC
245 AGTCTCGGCG-CAAAAATCATGCAAAACTGAGTC-GGGCCCCGGAACGCGTTTTTAGCCAAAAAC
* *
2257 AGTGA--TGAGT-A-
308 CGTGATTTGACTAAC
* * * * * * ** *
2268 TTACACAATTTCGGATAACATATTGCAAAAATTGACCCGAAAGGTATTTCCTCAATTTTTAGTC-
1 GTACACGATTTCGGCTAATATTTTGCAAAAATTGACCAGAAATATTTTTCCTCAATTTTT-GTCA
* * * * * * * ** *
2332 ATAATACTCGTAAAAATATATAATTCAACGCCAAAAAGGTTGAAGGGCTTTTCACGCTTTTAATA
65 AAAATACTCATAAATATATATAATTCAACTCTAAAAAGATTGGAGGAATTTTCTCGCTTTTAATA
2397 TCGTTTTTCAT
130 TCGTTTTTCAT
2408 ATTTTTTTCA
Statistics
Matches: 1685, Mismatches: 271, Indels: 255
0.76 0.12 0.12
Matches are distributed among these distances:
308 1 0.00
309 2 0.00
311 3 0.00
312 9 0.01
313 70 0.04
314 114 0.07
315 87 0.05
316 49 0.03
317 5 0.00
318 9 0.01
319 244 0.14
320 309 0.18
321 33 0.02
322 111 0.07
323 49 0.03
324 9 0.01
325 55 0.03
326 11 0.01
327 72 0.04
328 14 0.01
329 9 0.01
330 49 0.03
331 98 0.06
332 18 0.01
333 4 0.00
334 4 0.00
335 1 0.00
336 158 0.09
337 84 0.05
338 4 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (322 bp):
GTACACGATTTCGGCTAATATTTTGCAAAAATTGACCAGAAATATTTTTCCTCAATTTTTGTCAA
AAATACTCATAAATATATATAATTCAACTCTAAAAAGATTGGAGGAATTTTCTCGCTTTTAATAT
CGTTTTTCATTAATTAATTCTATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTT
AAATCCAATGTGGCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCAAAAA
TCATGCAAAACTGAGTCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATTTGACTAAC
Found at i:1256 original size:650 final size:648
Alignment explanation
Indices: 5--2100 Score: 1949
Period size: 650 Copynumber: 3.2 Consensus size: 648
1 GATG
* * * * * *
5 GTACATGAATTCGGCTAAAATTTTGCAAAAAATGACTC-GAAAGATTTTTCCTCGATTTCTAGT-
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCAGAAAG-TATTTCCTCAATTTTTA-TC
* * * ** ** *
68 GAAAATACT-AAAAAAATATATATAATTCAACGTCAAAAAAATTGAAAGCCTTTTTCACGCTTTT
64 CACAATACTCATAAAAAT-TATATAATTCAACACCAAAAAAATTGAAAGGATTTTTCACGCTTCT
*
132 AATATCGTGTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
128 AATATCGTTTTTC--A------T--ATT-A--T-T--TTAAATCGAAACAAGATTCAGATGCTCG
* * * * *
197 TAAAAACAAATCCTTAAATTCAATGT-GCCT-AAGATTTGA-TAAGATGAATATAAATATTTCAA
177 TAAAAAAAAATCCTTAAATCCAATGTAG-CTGAA-ATTAGATTAA-ATGAATATAGATATCTCAA
* * *** * * * *
259 GGAGTCTCGACATAAAAAATCATGCAAAACT-AA--GTCAGCCCTCGGAATGCGTTTTTAGCCGA
239 AGAGTCTCGGCGCCAAAAATCATGCAAAACTGAACCGT-GGCCC-CGGAACGCATTTTTAG-CAA
* * * * * * * * * *
321 AAACCG-TGA--T-G-GTTA-GTACACGATTTCGGCTAAAATTTTGCAAAAACTCACCCGAAAGA
301 AAAACGATGATTTCGACTAACGTACACGATTTTGCCTAATATTTTGCAAAAATTTACCAGAAATA
* * *
380 TTTTTTCGTCTAA-TTTTG-CATAAAATA--CAT-ACA-AT-T-TAA--C-GC-C-AAAAAGATT
366 -TTTTTCCTC-AATTTTTGTC-TAAAATACTCATAAAATATATATAATTCAACTCTAAAAAGATT
* * * * *
432 GGAGGACTTTTCACGCTTTTAATATCGTTTTTCATGTTTTTCTAAATTAATTTCTAGTTAAATCG
428 GGAGGAATTTTCTCGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCG
* * * *
497 AAACAAGATTCAGATGCTCGTAAAAACAAATTCTTCAATCTAATGTAGCTGACATTAGATTAAAT
493 AAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAAT-TAATGTGGCTGAGATTTGA-TAAAT
* * * * * * * *
562 GAATATGGATATCTCAAAGAGTCTTGGCGGAAAAAATCATGCAAAACTTAGTC-GGCCCCTCGAA
556 GAATATAGATATTTCAAGGAGTCTCGACGCAAAAAATCATGCAAAACTGAGTCGGGCCCC-AGAA
* * *
626 CACGTTTTTAGCCAAAATCGGTGATGATTA
620 CGCGTTTTTAGCCAAAA-CCGTGATGGTTA
* * *
656 TTACACGATTTCGGCTAGAATTTTGTAAAAATTGACTC-GAAAGTTATTTCCTCAATTTTTATCC
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCAGAAAG-TATTTCCTCAATTTTTATCC
*
720 ACAATACTCATAAAAATTATATAATTCAACACCAAAAAAATTGAAAGG-TTTTTCATGCTTCTAA
65 ACAATACTCATAAAAATTATATAATTCAACACCAAAAAAATTGAAAGGATTTTTCACGCTTCTAA
* * * *** *
784 TATCATTTTTCATATTATTTTAAATCGAAACATGATTCAGATGCTTGT-TTTACAAATCCTTAAA
130 TATCGTTTTTCATATTATTTTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAA
* * * * * * * *
848 TCCAATGTGGCTTAAATTTGGTTAGATGAATGTAGATATTTCAAGGAGTCTCGGCG-CAAATAAT
195 TCCAATGTAGCTGAAATTAGATTAAATGAATATAGATATCTCAAAGAGTCTCGGCGCCAAA-AAT
* *
912 CATGCAACACTGAACCG-GGACCCTGGAACGCATTTTTAGCAAAAAACCG-TGATTTCGACTAAC
259 CATGCAAAACTGAACCGTGG-CCCCGGAACGCATTTTTAGCAAAAAA-CGATGATTTCGACTAAC
*
975 GTACACGATTTTGGCTAATATTTTGCAAAAATTTACCAGAAATATTTTTCCTCAATTTTTGTCTA
322 GTACACGATTTTGCCTAATATTTTGCAAAAATTTACCAGAAATATTTTTCCTCAATTTTTGTCT-
*
1040 AAAATACTCATAATATATATATAATTCAACTCTAAAAAGATTGGAGGAATTTTCTCGCTTTTAAT
386 AAAATACTCATAAAATATATATAATTCAACTCTAAAAAGATTGGAGGAATTTTCTCGCTTTTAAT
*
1105 ATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCGCGTAA
451 ATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
*
1170 AAACAAATTCTTAAATTAAATGTGGCTGAGATTTGATAAGATGAATATAAATATTTCAAGGAGTC
516 AAACAAATTCTTAAATT-AATGTGGCTGAGATTTGATAA-ATGAATATAGATATTTCAAGGAGTC
* * *
1235 TCGACACAAAAAATCATGCAAAACTGAGTCGGGCCCCGGAATGCGTTTTTAGCCGAAAACCGTGA
579 TCGACGCAAAAAATCATGCAAAACTGAGTCGGGCCCCAGAACGCGTTTTTAGCC-AAAACCGTGA
1300 TGGTTA
643 TGGTTA
* *
1306 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGA-TCTGAAAG-ATTT--TC-A-----GT-CA
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCAGAAAGTATTTCCTCAATTTTTATCCA
** * * * * * * * *
1360 -AATTTTGCAT-AAAATACATACAATTTAACGCCAAAAAGATTG-GAGGACTTTTCACGCTTTTA
66 CAATACT-CATAAAAAT-TATATAATTCAACACCAAAAAAATTGAAAGGATTTTTCACGCTTCTA
*
1422 ATATCGTTTTTCATGTTTTTCTGAATTAATTTCTAGTTAAATCGAAATAAGATTCAGATGCTCGT
129 ATATCGTTTTTCA--------T--ATT-A--T-T--TTAAATCGAAACAAGATTCAGATGCTCGT
* * * *
1487 AAAAAAAAATTCTTCAATCCAATGTAGCTGACATTAGATTAAATGAATATGGATATCTCAAAGAG
178 AAAAAAAAATCCTTAAATCCAATGTAGCTGAAATTAGATTAAATGAATATAGATATCTCAAAGAG
* * ** * *
1552 TCTTGGCGCCAAAAATCATGCAAAACTTAGTCGTGGCCCCGGAACGCGTTTTTAGCCAAAAACGA
243 TCTCGGCGCCAAAAATCATGCAAAACTGAACCGTGGCCCCGGAACGCATTTTTAGCAAAAAACGA
* *
1617 TGATTTTGACTAACGTATACGATTTTGCCTAATATTTTGCAAAAATTTACCAGAAATATTTTTCC
308 TGATTTCGACTAACGTACACGATTTTGCCTAATATTTTGCAAAAATTTACCAGAAATATTTTTCC
1682 TCAATTTTTGTCTAAAATACTCATAAAATATATATAATTCAACTCTAAAAAGATTGGAGGAATTT
373 TCAATTTTTGTCTAAAATACTCATAAAATATATATAATTCAACTCTAAAAAGATTGGAGGAATTT
* * *
1747 TCTCGCTTTTAATATCGCTTTTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAAGAAGATT
438 TCTCGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATT
* * *
1812 CAGATGCTCGTAAAAATAAATCCTTAAATGCAATGTGGCTGAGA--T--T---T-AATATAGATA
503 CAGATGCTCGTAAAAACAAATTCTTAAAT-TAATGTGGCTGAGATTTGATAAATGAATATAGATA
** * * * *
1869 TTTTGAGGAGTCTCGATGCCAAAAATCATGCAAAACTGAGTCGGGGCCCAAAAACGCGTTTTTAA
567 TTTCAAGGAGTCTCGACGCAAAAAATCATGCAAAACTGAGTC-GGGCCCCAGAACGCGTTTTT-A
***
1934 TAAAAAACCGTGATGGTTA
630 GCCAAAACCGTGATGGTTA
* * *
1953 GTACACGATTTCGGCTAAAATTTTACAAGAAA-TGAC-CAGAAA-AATATTCTCTCAATTTTTAG
1 GTACACGATTTCGGCTAAAATTTTGCAA-AAATTGACTCAGAAAGTAT-TTC-CTCAATTTTTAT
* * *
2015 CCACAATACTCATAAAAAATATATAATTCAACACCAAAAAAATTGAAGGGCTTTTT-ACGCTTCT
63 CCACAATACTCATAAAAATTATATAATTCAACACCAAAAAAATTGAAAGGATTTTTCACGCTTCT
*
2079 AATATCGTTTTTCCTATT-TTTT
128 AATATCGTTTTTCATATTATTTT
2101 CCGAATTAAT
Statistics
Matches: 1207, Mismatches: 160, Indels: 166
0.79 0.10 0.11
Matches are distributed among these distances:
632 3 0.00
633 72 0.06
634 53 0.04
635 3 0.00
636 3 0.00
637 4 0.00
638 28 0.02
639 96 0.08
640 4 0.00
641 5 0.00
642 3 0.00
643 3 0.00
644 2 0.00
645 4 0.00
646 48 0.04
647 72 0.06
648 15 0.01
649 10 0.01
650 254 0.21
651 99 0.08
652 9 0.01
653 2 0.00
655 180 0.15
656 169 0.14
657 6 0.00
658 46 0.04
659 14 0.01
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (648 bp):
GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCAGAAAGTATTTCCTCAATTTTTATCCA
CAATACTCATAAAAATTATATAATTCAACACCAAAAAAATTGAAAGGATTTTTCACGCTTCTAAT
ATCGTTTTTCATATTATTTTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAAT
CCAATGTAGCTGAAATTAGATTAAATGAATATAGATATCTCAAAGAGTCTCGGCGCCAAAAATCA
TGCAAAACTGAACCGTGGCCCCGGAACGCATTTTTAGCAAAAAACGATGATTTCGACTAACGTAC
ACGATTTTGCCTAATATTTTGCAAAAATTTACCAGAAATATTTTTCCTCAATTTTTGTCTAAAAT
ACTCATAAAATATATATAATTCAACTCTAAAAAGATTGGAGGAATTTTCTCGCTTTTAATATCGT
TTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
AATTCTTAAATTAATGTGGCTGAGATTTGATAAATGAATATAGATATTTCAAGGAGTCTCGACGC
AAAAAATCATGCAAAACTGAGTCGGGCCCCAGAACGCGTTTTTAGCCAAAACCGTGATGGTTA
Found at i:3236 original size:31 final size:31
Alignment explanation
Indices: 3195--3268 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
3185 GAAAAGAAAA
3195 AAGGGA-TTTTTTGTCCCAAAAGAAAAACAT
1 AAGGGATTTTTTTGTCCCAAAAGAAAAACAT
*
3225 AAGGGATTTTTTTGTCCCAAAAGAAAAATAT
1 AAGGGATTTTTTTGTCCCAAAAGAAAAACAT
3256 AAGGGATTTTTTT
1 AAGGGATTTTTTT
3269 AGTATTTAGT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 6 0.14
31 36 0.86
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (31 bp):
AAGGGATTTTTTTGTCCCAAAAGAAAAACAT
Found at i:4289 original size:30 final size:31
Alignment explanation
Indices: 4228--4301 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
4218 ACTAAATATA
* *
4228 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAATAATCCCTTATGTTTTTCTTATGGGAC
4259 AAAATAATCCCTTATGTTTTT-TTATGGGAC
1 AAAATAATCCCTTATGTTTTTCTTATGGGAC
* *
4289 AAATTAGTCCCTT
1 AAAATAATCCCTT
4302 GCTGACATGG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 19 0.49
31 20 0.51
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (31 bp):
AAAATAATCCCTTATGTTTTTCTTATGGGAC
Found at i:4510 original size:29 final size:29
Alignment explanation
Indices: 4434--4513 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
4424 CTCATTTTTG
* * * *
4434 AAACGTAACGGATTAATTTGTCCCGAAAA
1 AAACATAAGGGATTATTTTGTCCCAAAAA
*
4463 AAACTTAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTATTTTGTCCCAAAA--A
*
4494 AAACATAAGGGATTTTTTTG
1 AAACATAAGGGATTATTTTG
4514 GGTATTTAGC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 24 0.56
31 19 0.44
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (29 bp):
AAACATAAGGGATTATTTTGTCCCAAAAA
Found at i:6285 original size:1 final size:1
Alignment explanation
Indices: 6279--6305 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
6269 AACAGCTCTG
6279 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
6306 CAGCAAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:8284 original size:331 final size:329
Alignment explanation
Indices: 7594--9529 Score: 1842
Period size: 331 Copynumber: 5.9 Consensus size: 329
7584 CAAAATTTTG
* *
7594 TTTCATATTTTTTTGGATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
1 TTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
** * *
7659 ATCCTTAAATTTAACGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTT-G-G
66 ATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATA-ATATTTCAAGGAGTCTTGGCG
* * *
7722 -AAAAAATCCTGCAAAACTGAGCCGGGCCCCGGAATGCGGTTTTAGCCAAAAACCGTGATGGTTA
130 CCAAAAATCATGCAAAACTGAGCCGGG-CCCGGAATGCGTTTTTAGCCAAAAACCGTGATGGTTA
* * * * * *
7786 GTACATGATTTCGGCTAAAATTTT-TGCAAAAATTGACCCGAAAGACTTTTCCTCGATTTCTGGC
194 GTACACGATTTCGGCTAAAATTTTGT-CAAAAATTGACTCGAAAGATTTTTCCTCAATTTTTAGC
* * * * *
7850 AAAAATACTCAT-AAAAATATATAATTCAACGTCAAAAGGATTCG-AGTACTTTTCACGGTTTTA
258 TAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATT-GAAGGACTTTTCACGATTTTA
7913 ATATCGTT
322 ATATCGTT
* * * * *
7921 TTTCATATTTTTTCTGAATTAATTTGTAATTAAATCGAAACAAAATTCAGATACACATAAAAA-A
1 TTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
* *
7985 AGTTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATGAATATTTCAAGGAGTCTTGGC
65 AATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATAT-AATATTTCAAGGAGTCTTGGC
* * * ** *** *
8050 GCCAAAAATCATGCAAAACTGAGCCAGGGTCCCAGAACGCTTTTTTAGTAAAAAACTAAGATGAT
129 GCCAAAAATCATGCAAAACTGAGCC-GGG-CCCGGAATGCGTTTTTAGCCAAAAACCGTGATGGT
* * * * * * *
8115 TATTACACAATTTCGGCTAAAATTTTGTAAAAAATTGATTAGAAA-ATTAATTCCTCAATTTTTG
192 TAGTACACGATTTCGGCTAAAATTTTGTCAAAAATTGACTCGAAAGATT-TTTCCTCAATTTTTA
* * * *
8179 GCTAAAATACTTATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTGAC-ATTTC
256 GCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGATTT-
8243 TAATATCGTT
320 TAATATCGTT
* ** * * *
8253 TTTCCTATTTTTCAAAATTAATTTTTAATTAAATTGAAACAAGATTCAGATGCTAGTAAAAACAA
1 TTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * **
8318 ATCCTTAAATCTAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGAA
66 ATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATA-ATATTTCAAGGAGTCTTGGCG
* * * * *
8383 CCAAAAATCTTGCAAAACTAAGCCGGGCCCCGGAACGCGGTTTTAGCCGAAAACCGTGATGGTTA
130 CCAAAAATCATGCAAAACTGAGCCGGG-CCCGGAATGCGTTTTTAGCCAAAAACCGTGATGGTTA
* * *
8448 GTACATGATTTCGGCTAAAATTTTGT-AAAAATTGACTCGAAAGATTTTTCCTCGATTTCTAG-T
194 GTACACGATTTCGGCTAAAATTTTGTCAAAAATTGACTCGAAAGATTTTTCCTCAATTTTTAGCT
* * * * * * *
8511 GAAAATACTCATAAAAAGTGTTTAATTCAACGCCAAAAAAATTGAAAGCCTTTTTCACGCTTTTA
259 -AAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGAC-TTTTCACGATTTTA
*
8576 ATATCGTG
322 ATATCGTT
8584 TTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
1 TTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * * * * *
8649 ATCCTTAAATTCAATGTGGCTGAGATTTGATAAGATGAATATAAATATTTCAAGGAGTGTCGACA
66 ATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATAT-AATATTTCAAGGAGTCTTGGCG
* * * * *
8714 CAAAAAATCATGCAAAACTGAGTCGGGCCTCGAAATGCGTTTTTAGCCGAAAACTGTGATGGTTA
130 CCAAAAATCATGCAAAACTGAGCCGGGCC-CGGAATGCGTTTTTAGCCAAAAACCGTGATGGTTA
* * * *
8779 GTACACGATTTCGGCTAAAATTTTG-CAAAAATTGACCCGAAATATTTTTCTGTCAAATTTT-GC
194 GTACACGATTTCGGCTAAAATTTTGTCAAAAATTGACTCGAAAGATTTTTC-CTCAATTTTTAGC
* * *
8842 ATAAAATA--CAT--ACAAT-T-TAA--C-A--CCAAAAAGATTGGAGGACTTTTCACGCTTTTA
258 -TAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGATTTTA
8896 ATATCGTT
322 ATATCGTT
* *
8904 TTTCATGTTTTTCTGAATTAATTTCTAGTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
1 TTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * * * * * * * *
8969 ATTCTTCAATCCAATGTAGCTGACATTAGATTAAATGAATATGGATATCTCAAAGAGTCTTGGCG
66 ATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATAT-AATATTTCAAGGAGTCTTGGCG
* * * * * * * *
9034 GCAAAAATCATGCAGAACTTAGTCGAGGCCCTTGAATGCGTTTTTAACCAAAAACAGTGATGATT
130 CCAAAAATCATGCAAAACTGAGCCG-GGCCC-GGAATGCGTTTTTAGCCAAAAACCGTGATGGTT
* * *
9099 ATTACACGATTTCGGCTAGAATTTTG-CAAAAATTGACTCGAAAG-TTATTTCCTCAATTTTTAT
193 AGTACACGATTTCGGCTAAAATTTTGTCAAAAATTGACTCGAAAGATT-TTTCCTCAATTTTTAG
* * * * * * * * *
9162 CCATAATACTCATAAAAATTATATAATTCAACACCAAAGAGATTGAAAGG-TTTTTCAAGCTTCT
257 CTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTG-AAGGACTTTTCACGATTTT
9226 AATA-----
321 AATATCGTT
* * * ***
9230 --TCAT-TTTTCCT--ATT-A--T-T--TTAAATCGAAACATGATTCAGATGCTTGT-TTTACAA
1 TTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * * * * *
9283 ATCTTTAAATCCAATGTGGCTGAAATTTGGTTAGATAAATGTAGATATTTCAAGGAGTCTTGTCG
66 ATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATA-ATATTTCAAGGAGTCTTGGCG
* * * * *
9348 -CAAATAATCTTGCAACACTGAACCGGGACCTTGGAACGCGTTTTTAGCCAAAAAACCGTGATTT
130 CCAAA-AATCATGCAAAACTGAGCCGGG-CC-CGGAATGCGTTTTTAGCC-AAAAACCGTGA--T
* * * * * * *
9412 CGACTAACGTACACGATTTTGCCTAATATTTTG-CAAAAATTTAC-CAGAAATATTTTTCCTCAA
189 -G-GTTA-GTACACGATTTCGGCTAAAATTTTGTCAAAAATTGACTC-GAAAGATTTTTCCTCAA
** * * * *
9475 TTTTTTTCTAAAAAAACTCATAATATATATATATAATTCAACTCTAAAAAGATTG
250 TTTTTAGCT-AAAATACTCATAA-A-AAATATATAATTCAACGCCAAAAAGATTG
9530 GAGATTTTTC
Statistics
Matches: 1331, Mismatches: 224, Indels: 112
0.80 0.13 0.07
Matches are distributed among these distances:
313 6 0.00
314 84 0.06
315 37 0.03
317 2 0.00
318 2 0.00
319 3 0.00
320 221 0.17
321 106 0.08
322 4 0.00
323 31 0.02
324 8 0.01
325 1 0.00
326 6 0.00
327 63 0.05
328 54 0.04
329 3 0.00
330 95 0.07
331 451 0.34
332 153 0.11
333 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (329 bp):
TTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
ATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAATATTTCAAGGAGTCTTGGCGC
CAAAAATCATGCAAAACTGAGCCGGGCCCGGAATGCGTTTTTAGCCAAAAACCGTGATGGTTAGT
ACACGATTTCGGCTAAAATTTTGTCAAAAATTGACTCGAAAGATTTTTCCTCAATTTTTAGCTAA
AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGATTTTAATAT
CGTT
Found at i:11747 original size:34 final size:34
Alignment explanation
Indices: 11704--11772 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
11694 TGTCTGAAAT
11704 CAAGCATGGCATCTCTAACGACACCATATAAAAA
1 CAAGCATGGCATCTCTAACGACACCATATAAAAA
11738 CAAGCATGGCATCTCTAACGACACCATATAAAAA
1 CAAGCATGGCATCTCTAACGACACCATATAAAAA
11772 C
1 C
11773 TTAAAAGGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.43, C:0.28, G:0.12, T:0.17
Consensus pattern (34 bp):
CAAGCATGGCATCTCTAACGACACCATATAAAAA
Found at i:12742 original size:11 final size:11
Alignment explanation
Indices: 12722--12751 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
12712 TAATCGATCT
12722 CAAG-AAATTA
1 CAAGTAAATTA
12732 CAAGTAAATTA
1 CAAGTAAATTA
12743 CAAGTAAAT
1 CAAGTAAAT
12752 CAGTACTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (11 bp):
CAAGTAAATTA
Found at i:18852 original size:60 final size:59
Alignment explanation
Indices: 18781--18944 Score: 249
Period size: 60 Copynumber: 2.7 Consensus size: 59
18771 CCAAAATGCT
*
18781 CAAATAAGGGCCTAATGTTTGTCAAAATGCTCAAATAAGGGCCTAATCTTTTAATTTGGC
1 CAAATAAGGGCCTAA-ATTTGTCAAAATGCTCAAATAAGGGCCTAATCTTTTAATTTGGC
* *
18841 CAAATAAGGGCCTAACA-TTATCAAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGC
1 CAAATAAGGGCCTAA-ATTTGTC-AAAATGCTCAAATAAGGGCCTAATCTTTTAATTTGGC
*
18901 CAAATAAGGGCCTAACATTTGCCAAAATGCTCAAATAAGGGCCT
1 CAAATAAGGGCCTAA-ATTTGTCAAAATGCTCAAATAAGGGCCT
18945 GGCGTCGAAC
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
59 4 0.04
60 88 0.93
61 3 0.03
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (59 bp):
CAAATAAGGGCCTAAATTTGTCAAAATGCTCAAATAAGGGCCTAATCTTTTAATTTGGC
Found at i:18854 original size:29 final size:30
Alignment explanation
Indices: 18773--18944 Score: 158
Period size: 31 Copynumber: 5.7 Consensus size: 30
18763 AACGTTTGCC
* *
18773 AAAATGCTCAAATAAGGGCCTAATGTTTGT
1 AAAATGCTCAAATAAGGGCCTAATCTTTCT
18803 CAAAATGCTCAAATAAGGGCCTAATCTTT-T
1 -AAAATGCTCAAATAAGGGCCTAATCTTTCT
** *
18833 AATTTGGC-CAAATAAGGGCCTAA-CATTATCA
1 AAAAT-GCTCAAATAAGGGCCTAATC-TT-TCT
*
18864 AAAATGCTCAAATAAGGGCCCAATCTTT-T
1 AAAATGCTCAAATAAGGGCCTAATCTTTCT
** *
18893 AATTTGGC-CAAATAAGGGCCTAA-CATTTGCC
1 AAAAT-GCTCAAATAAGGGCCTAATC-TTT-CT
18924 AAAATGCTCAAATAAGGGCCT
1 AAAATGCTCAAATAAGGGCCT
18945 GGCGTCGAAC
Statistics
Matches: 116, Mismatches: 14, Indels: 22
0.76 0.09 0.14
Matches are distributed among these distances:
28 2 0.02
29 40 0.34
30 11 0.09
31 62 0.53
32 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (30 bp):
AAAATGCTCAAATAAGGGCCTAATCTTTCT
Found at i:22843 original size:31 final size:30
Alignment explanation
Indices: 22803--22881 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
22793 ATTTTTAGCC
22803 ACCAATTTGAGACTAAACCTTCCAAAAGTT-
1 ACCAATTTGAGACTAAACCTTCCAAAA-TTA
*
22833 ACTCAATTTGA-ACCTAAACTTTCCAAAATTA
1 AC-CAATTTGAGA-CTAAACCTTCCAAAATTA
*
22864 GACCAATTTGAGCCTAAA
1 -ACCAATTTGAGACTAAA
22882 ATCATAAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
30 5 0.12
31 35 0.83
32 2 0.05
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.28
Consensus pattern (30 bp):
ACCAATTTGAGACTAAACCTTCCAAAATTA
Found at i:37781 original size:39 final size:39
Alignment explanation
Indices: 37737--37828 Score: 175
Period size: 39 Copynumber: 2.4 Consensus size: 39
37727 ACCATGTGAC
37737 ATGCTGATGTGGCAAAAATTATTATGTTATTCACTTTTT
1 ATGCTGATGTGGCAAAAATTATTATGTTATTCACTTTTT
*
37776 ATGCTGATGTGGCAAAAATTATTATTTTATTCACTTTTT
1 ATGCTGATGTGGCAAAAATTATTATGTTATTCACTTTTT
37815 ATGCTGATGTGGCA
1 ATGCTGATGTGGCA
37829 TGCCACGTGA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (39 bp):
ATGCTGATGTGGCAAAAATTATTATGTTATTCACTTTTT
Found at i:37882 original size:31 final size:33
Alignment explanation
Indices: 37820--37882 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
37810 TTTTTATGCT
*
37820 GATGTGGCATGCCACGTGAGTAATTTTTCGTCC
1 GATGTGGCATGCCACGTGAGCAATTTTTCGTCC
**
37853 GATGTGGCATGTTACGTG-GCAA-TTTTCGTC
1 GATGTGGCATGCCACGTGAGCAATTTTTCGTC
37883 TGACATGGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 8 0.30
32 3 0.11
33 16 0.59
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.35
Consensus pattern (33 bp):
GATGTGGCATGCCACGTGAGCAATTTTTCGTCC
Done.