Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019628.1 Corchorus olitorius cultivar O-4 contig19661, 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: 164684
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2598 original size:33 final size:35
Alignment explanation
Indices: 2541--2608 Score: 104
Period size: 33 Copynumber: 2.0 Consensus size: 35
2531 ATCCGGATAA
*
2541 GTCAGAGCAACAAACTCTAAATACCGGGTGGTGAG
1 GTCAGAGCAACAAACTCTAAATACCGGATGGTGAG
*
2576 GTCAGAGC-A-AAACTCTACATACCGGATGGTGAG
1 GTCAGAGCAACAAACTCTAAATACCGGATGGTGAG
2609 CATAACTCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 22 0.71
34 1 0.03
35 8 0.26
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.18
Consensus pattern (35 bp):
GTCAGAGCAACAAACTCTAAATACCGGATGGTGAG
Found at i:3638 original size:19 final size:19
Alignment explanation
Indices: 3616--3666 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
3606 GGGCTGAAAT
3616 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
3635 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
3654 TAATT-ATTATTAA
1 TAATTAATTATTAA
3667 AAATCCCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:4932 original size:23 final size:22
Alignment explanation
Indices: 4878--4934 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
4868 GCCCAGCGGT
*
4878 AAAAGAAAAAAAAACTGGAGGAA
1 AAAAGAAAAAAAAACTGAAGG-A
4901 AAAAGGAAAAAAAAACTGAAATGG-
1 AAAA-GAAAAAAAAACTG-AA-GGA
4925 AAAAGAAAAA
1 AAAAGAAAAA
4935 GGAAGAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 10 0.33
24 17 0.57
25 1 0.03
26 2 0.07
ACGTcount: A:0.72, C:0.04, G:0.19, T:0.05
Consensus pattern (22 bp):
AAAAGAAAAAAAAACTGAAGGA
Found at i:10086 original size:16 final size:16
Alignment explanation
Indices: 10065--10098 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
10055 TTTTTCCTAT
10065 TTTATTTCAAAATTAA
1 TTTATTTCAAAATTAA
10081 TTTATTTCAAAATTAA
1 TTTATTTCAAAATTAA
10097 TT
1 TT
10099 CTTGATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTATTTCAAAATTAA
Found at i:10987 original size:330 final size:328
Alignment explanation
Indices: 9307--12788 Score: 2281
Period size: 330 Copynumber: 10.4 Consensus size: 328
9297 CCTTAAAGAT
* * * *
9307 TTTTCCTCAATTCTTGGCAAAAATACTCAAAAAATATATATAATTCAACGCTAAAATGATTGGAG
1 TTTTCCTCAATTTTTGGC-AAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGGAG
* * *
9372 GACTTTTCACGCTTTTAATATTGTTTTTCATATTTTTTTTCTAAATTAATTTCTAATTGAATCGA
65 GA-TTTTCACGCTTTTAATATCGTTTTTCATA----TTTTCTGAATTAATTTCTAATTAAATCGA
* * * * * * * *
9437 AACAAAATTCAGACGCACATAAAACCAAATCCTTAAATCCAATGTGGTTAATATTTGATT--A-G
125 AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATG
* * * * * * * *
9499 -ATA-AGATATTTCAAGGAGTCTCGGCGCAAAAAATCATGCAAAACAGAGTTGTGACCCTGTAAT
190 AATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGCTGGGGCCC-GAAAC
* *
9562 GCGTTTTTAGC-CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA
254 GCGTTTTTAGCAAAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA
*
9626 CCCGAAAGATA
319 CCCGAAA-AAA
* * * **** *
9637 TTTT-CTCAATTTTTGGCTGAAATACTCATAAAAAATATATAATTCGATATAAAAAAGATTGAAG
1 TTTTCCTCAATTTTTGGC-AAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGGA-
* * * ** * * ** *
9701 GGCTTTTAACGCTTCTAATATTATTTTTCCTATTTTTTCCA--AATTATCTAATTAAATAGAAAC
64 GGATTTTCACGCTTTTAATATCGTTTTTCATATTTTCTGAATTAATT-TCTAATTAAATCGAAAC
* * *
9764 AAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCTAATGTGGCTGAGATTTGGTTAGATGAAT
128 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* * * * * * * * * * *
9829 ATAAATATTTCAAAGAGTCTTGGCACAAAAAATAATGCAAAACTGAGCCGGGCCCCGGAACACGT
193 ATAGATATTTCAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGCTGGGGCCCGAAACGCGT
** * *
9894 TTTTAGC-CGAAAACCGTGATGGGGTTAGTACACGCTTTCGGCT-AAATTTTGCAAAAATTGACC
258 TTTTAGCAAAAAAACCGTGAT--GATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC
* *
9957 CGAAAGAT
321 CGAAAAAA
* * *
9965 TTTTCCTCGATTTCTAGCGAAAATACTCATAAAAATATATATAATTCAACGCCAAAAA-AGTT-G
1 TTTTCCTCAATTTTTGGC-AAAATACTCAT-AAAATATATATAATTCAACGCCAAAAAGA-TTGG
** * * * * ** **
10028 AAAACTTTTTTCACGCTTCTGATATCGTTTTTCCTA-TTT-T-ATTTCAAAAT-TAATTTATTTC
63 AGGA---TTTTCACGCTTTTAATATCGTTTTTCATATTTTCTGAATT-AATTTCTAA-TTAAATC
* ** * ** * * * * * * * *
10089 AAAATTA-ATTCTTGATTAAATCGAAATAAGATTTAGAAACTCGTAAA--AATATATGGATGATA
123 GAAACAAGATTC-AGA-T-GCTCGTAA-AA-A--CA-AATC-CTTAAATCCA-ATGTGGCTGAGA
* * * *
10151 TTTGATTATAT-ATATATACACACACATATATT-AAGGAGTCTTGCCGCCAAAAATCATGCAAAA
178 TTTGATTAGATGA-ATAT------AGATAT-TTCAAGGAGTCTCGACGCCAAAAATCATGCAAAA
** * * * *
10214 CTGA-CATAAGACCAC-AGAACGCGTTTTTAGCCAAAAAACC---ATGA-TGGTACACGATTTTG
235 CTGAGC-TGGGGCC-CGA-AACGCGTTTTTAGCAAAAAAACCGTGATGATTAGTACACGATTTCG
* * *
10273 GCTAAAATTTTGTAAAAATTGACCCG-GAATA
297 GCTAAAATTTTGCAAAAATTGACCCGAAAAAA
* * * * * * *
10304 TTTTTCTCGATATTTAGCCACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAG
1 TTTTCCTCAAT-TTTTGGCAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGGA-
* * * * * *
10369 GGCTTCTCACGCTTCTAAAATCGTTTTT--T-TTTTC-AAATTAATTTCTAATTAAATTGAAACA
64 GGATTTTCACGCTTTTAATATCGTTTTTCATATTTTCTGAATTAATTTCTAATTAAATCGAAACA
* * * * * *
10430 TGATTCAAATGGTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGAATT-AGTTAAATGAAT
129 AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGA-TTAGATGAAT
* * * *** * * * * *
10494 ATACATATTTCAAGGAGTGTTTCCACAAAAAAAATCATGCAAAAATGACCCGAGGTCTC-AGAAC
193 ATAGATATTTCAAGGA--GTCTCGACGCCAAAAATCATGCAAAACTGAGCTG-GGGCCCGA-AAC
* * * * *
10558 ACGTTTTTAGCCAAAAAAA-C-TG-TGA-TGGTACACCATTTAGGTTAAAATTTTGCAAAAATTG
254 GCGTTTTTAG-CAAAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTG
* * *
10619 ACCCGATATAT
318 ACCCGAAAAAA
* * * * *
10630 TTTTCCTCAATTTTTAGCCACAATACTCATAGAATATATATAATTAAACGCCAAAAAGATTGGAT
1 TTTTCCTCAATTTTT-GGCAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGGAG
** *
10695 GATTCTTCACGCTTTTAGCATCGTTTTTCATATTTTCTGAATTAATTTCTAATTAAATTGAAACA
65 GATT-TTCACGCTTTTAATATCGTTTTTCATATTTTCTGAATTAATTTCTAATTAAATCGAAACA
* * *
10760 AGATTCAGATGCTCGTGAAAACAAATGCTTAAAAT-CAAAGTGGCTGAGATTTGATTAGATGAAT
129 AGATTCAGATGCTCGTAAAAACAAATCCTT-AAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* * *
10824 ATAGATATTTCAAGGAGTCTCGGCGTCAAAAATCATGCAAAACTAAGCTGGGGTCCCGAAACGCG
193 ATAGATATTTCAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGCTGGGG-CCCGAAACGCG
* ** * *
10889 TTTTTAGC-AAAAAACCGTGATG-TTAGTACATGATTTCTTCTAAAATTTTGCAAAAAATGACCT
257 TTTTTAGCAAAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC
10952 GAAAAAA
322 GAAAAAA
* * * *
10959 TTTTCAGTTAATTTTTGGCATAAATACTCATAAAATATATATAATTGAACGCCAAAAATATTGGA
1 TTTTC-CTCAATTTTTGGCA-AAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGGA
11024 GGACTTTTCACGCTTTTAATATCGTTTTTTCATATTTTCTGAATTAATTTCTAATTAAATCGAAA
64 GGA-TTTTCACGCTTTTAATATCG-TTTTTCATATTTTCTGAATTAATTTCTAATTAAATCGAAA
* * ** *
11089 CAAAATTCAGATGCTCGTAAAAA-AAATTCTTAAATCCAATGTAACTAAGATTTGATTAGATGAA
127 CAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAA
* * * * * * * * *
11153 TATGGATATCTCAAAGAGTCTTGATGGCAAAAATCATGCAAAACTTAGATGGGGCCCCGGAACGC
192 TATAGATATTTCAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGCTGGGG-CCCGAAACGC
* * * * * **
11218 GTTTTTAGC-CAAAAACCGTGACGATTATTACACGATTTCGGCTAAAATTTTACAAAACTTGATT
256 GTTTTTAGCAAAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC
* **
11282 TG-AAAGT
321 CGAAAAAA
* * * *
11289 TATTTCCTCAATTTTTAGCGACAATACTCATAACAAT-TATATAATTCAATGCCAAAAAGATTGA
1 T-TTTCCTCAATTTTTGGC-AAAATACTCATAA-AATATATATAATTCAACGCCAAAAAGATTGG
* * * *
11353 AGGGCTTTTCATGCTTCTAATATCGTTTTTCCTATTATTTT-TCGAATTGATTGT-TAATTAAAT
63 A-GGATTTTCACGCTTTTAATATCGTTTTT-C-A-TATTTTCT-GAATTAATT-TCTAATTAAAT
* * * * *** * * * *
11416 CGAAACATGATTCAAATACTTGT-TTTACAAATCCTTAAATCCATTGTGGATGACATTTGGTTAG
122 CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAG
* * * ** * *
11480 ATTAATTTAGATATATTTCAAGGAGTCTCGACGCAAAAAATCATGCAACGCTGAACCGGGGCCCT
187 ATGAATATAG--ATATTTCAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGCTGGGGCCC-
* * *** * * * *
11545 GGAACACGTTTTTAGCCAAAAAAAAATATGATTTCGACTAACGTACATGATTTCGACTAATATTT
249 GAAACGCGTTTTTAG-C-AAAAAAACCGTGA--T-GA-TTA-GTACACGATTTCGGCTAAAATTT
*
11610 TGCAAAAGTTGA-CC-AAAAATA
307 TGCAAAAATTGACCCGAAAAA-A
** ** *
11631 CTTTTCCTCAATTTTTTTTGTTTAAAATACTCATAAAATATATATAATTCAACTTCAAAAATATT
1 -TTTTCCTCAA---TTTTTG-GCAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATT
* * *
11696 GGAGGACTTTTCACGCTTTTAATATCCTTTTTCATATATTTCTAAAAATTAATTTTTAATT-AAT
61 GGAGGA-TTTTCACGCTTTTAATATCGTTTTTCATAT-TTTCT--GAATTAATTTCTAATTAAAT
* * **
11760 CGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTAAATGCAATGTGTATGAGATTTGATTAG
122 CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAG
* * * *
11825 ATGAATATATATATATTTTAAGGAGCCTCGATGCCAAAAATCATGCAAAACTGAG-TCGGGGCCT
187 ATG-A-ATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGCT-GGGGCC-
* * * *
11889 CGAAACGCGTTTTAAGCAAAAAAACTGTGATGGTTAGTACACGATTTCGCCTAAAATTTTGCAAA
248 CGAAACGCGTTTTTAGCAAAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAA
*
11954 ACA-TGACCAGAAAAAA
313 A-ATTGACCCGAAAAAA
* * ** * * * * *
11970 TTTTCCTCAA-TTTTGGACAAAAAATATTTTCCTCAATTTTTGGCTAAAATACTC-ATG-AAATA
1 TTTTCCTCAATTTTTGG-C--AAAATA--CTCAT-AAAATAT--ATATAAT--TCAACGCCAA-A
* * * ** * *
12032 TATATAATTTAACGCCAAAAAGA-TTGGACGACTTTT--CAT-GCTTTTCATATTTTTTCTGAAT
55 -A-A-GA-TT---G----GAGGATTTTCACG-CTTTTAATATCGTTTTTCATA--TTTTCTGAAT
* * *
12093 TAATTTCTAATTAAATCGAAATAAGATTCACATGCTCGTAAAAACAAATCCTTAAATGCAATGTG
106 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * * *
12158 GCTGAGATTTGATTAGATAAATATTGATATTTCAAGTAGTCT-TAGTGCCAAAAATCATGCAAAA
171 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGA-CGCCAAAAATCATGCAAAA
* * ** * * *
12222 CTGA-CTCGAGGCCCTGAAACGCATTTTTAGC-CCAATACCGTGATGATTATTACACGATTTTGG
235 CTGAGCT-GGGGCCC-GAAACGCGTTTTTAGCAAAAAAACCGTGATGATTAGTACACGATTTCGG
**
12285 CTAAAATTTTGCAAAAATTGACCCG-AAAGT
298 CTAAAATTTTGCAAAAATTGACCCGAAAAAA
** * * * *
12315 TATTTCCTCAATTTTTTACCAAATTA-TCATCAAAAAATATATAATTCAACGCCAAAAATATTGA
1 T-TTTCCTCAA-TTTTTGGCAAAATACTCAT-AAAATATATATAATTCAACGCCAAAAAGATTGG
* * * * * * *
12379 AGGGTTTTTTACGCTTCTAATATCG-TTTTCCTACCTTTTCCGAACTAATTTCTAACTAAATCGA
63 A-GGATTTTCACGCTTTTAATATCGTTTTTCATA--TTTTCTGAATTAATTTCTAATTAAATCGA
* * *
12443 AACAAGATTTAGATACTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGATTTGATTAGATG
125 AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATG
* * * * * * * * *
12508 AATATAGATAGTTCAAGGAGTTTTGGCACCAAAAATCATGCAATACTGACCCGGGGTCCCGTAAC
190 AATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGCTGGGG-CCCGAAAC
**** * * *
12573 GCGTTTATT-G-AAAAAAAAAAAGAGTGA-T-GTTACACGATTTCGGCTTATATTTTGCAAAAAA
254 GCGTTT-TTAGCAAAAAAACCGTGA-TGATTAG-TACACGATTTCGGCTAAAATTTTGCAAAAAT
* * *
12634 TGACCTGAAATAT
316 TGACCCGAAAAAA
12647 TTTTCCTCAATTTTTAGTTGC--AATACTCATAAACA-ATATATAATTCAACGCC-AAAAGATTG
1 TTTTCCTCAATTTTT-G--GCAAAATACTCATAAA-ATATATATAATTCAACGCCAAAAAGATTG
* * ** * * * *
12708 AAGGGCTTTTCACGCTTCCAATACCGTTTTTCCTATTTTTTTCCGAATTAATTTCTAATTAAAAC
62 GA-GGATTTTCACGCTTTTAATATCGTTTTT-C-A-TATTTTCTGAATTAATTTCTAATTAAATC
*
12773 GAAACATGATTCAGAT
123 GAAACAAGATTCAGAT
12789 CCTTATAAAA
Statistics
Matches: 2464, Mismatches: 505, Indels: 364
0.74 0.15 0.11
Matches are distributed among these distances:
321 2 0.00
322 11 0.00
323 4 0.00
324 99 0.04
325 62 0.03
326 80 0.03
327 11 0.00
328 97 0.04
329 239 0.10
330 432 0.18
331 362 0.15
332 142 0.06
333 12 0.00
334 59 0.02
335 18 0.01
336 20 0.01
337 56 0.02
338 78 0.03
339 49 0.02
340 40 0.02
341 13 0.01
342 53 0.02
343 57 0.02
344 48 0.02
345 179 0.07
346 61 0.02
347 66 0.03
348 19 0.01
349 74 0.03
350 7 0.00
351 6 0.00
352 5 0.00
353 3 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (328 bp):
TTTTCCTCAATTTTTGGCAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGGAGG
ATTTTCACGCTTTTAATATCGTTTTTCATATTTTCTGAATTAATTTCTAATTAAATCGAAACAAG
ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATA
GATATTTCAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGCTGGGGCCCGAAACGCGTTTT
TAGCAAAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA
AAA
Found at i:13619 original size:330 final size:329
Alignment explanation
Indices: 12944--14057 Score: 1255
Period size: 330 Copynumber: 3.3 Consensus size: 329
12934 GATATTTTGT
*
12944 ATACTCATAAAAAAATATATAATTCAACGCAAAAAAGA-TTGAAGGGCTTTTGACGCTTTTAATA
1 ATACTCAT-AAAAAATATATAATTCAACGC--CAAAGATTTGAAGGGCTTTTGACGCTTTTAATA
* * * * * *
13008 TCGTTTTTCATATTTTTTCTAAATTCATTTTTAATTAAATCGAAATATGATTCAGATGCTCATAA
63 TC-ATTTTCATATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* *
13073 AAAAGAAAATCTTAAATGCAATGTGGCTAAGATTTTATTAGATGAATATAGATATTTCAAGGAGT
127 AAAA-AAAATCTTAAATCCAATGTGGCTGAGATTTTATTAGATGAATATAGATATTTCAAGGAGT
* * * *
13138 GTCGGCGCCAAAAATCATGCAAAACTGAGCTGGTGCCGCAAAACGCATTATTAGT-CAAAAACCG
191 CTCGGCGCCAAAAATCATGCAAAACTGAGCTGGGGCCCCAAAACGCATTTTTA-TCCAAAAACCG
* * * * *
13202 TGATGGTTAGTATACGATTTTGACTAAAATTTTACAAAAAAATGACCCGAAAAATTTTTCCTCAA
255 TGATGGTTAGTACACGATTTCGGCTAAAATTTT-GAAAAAAATGACCCGAAAGA-TTTTCCTCAA
13267 TTTTTGGATAAA
318 TTTTTGGATAAA
* * *
13279 ATACTCATAAAATATATATAATTTAACGCCAAAGATTTG-AGGAG-TTTTCACGCTTTTAATATC
1 ATACTCATAAAAAATATATAATTCAACGCCAAAGATTTGAAGG-GCTTTTGACGCTTTTAATATC
* * * *
13342 ATTTTCATA-TTTTTCTGAATTAATTTTTAATTAAATCGAAACAAGATTTAGATGCTTGT-AAAA
65 ATTTTCATATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
* * * *
13405 ACAAATTTTCAAATCCAATGTGGCTGAGATTTTATTTGATGAATATATATATATTTCAAGGAGTC
130 AAAAATCTT-AAATCCAATGTGGCTGAGATTTTATTAGATG-A-ATATAGATATTTCAAGGAGTC
* * * *
13470 TTC-GCGCCAAAAATCATGCAAGACTGAGAC-GGGGCCCCAGAACGCTTTTTTATCCAAAAACTG
192 -TCGGCGCCAAAAATCATGCAAAACTGAG-CTGGGGCCCCAAAACGCATTTTTATCCAAAAACCG
* * *
13533 TGATGGTTATTACACGATTTCGGCTAAAATTTTGTACAAAATGACCCGAAAGATATTTCCTCAAT
255 TGATGGTTAGTACACGATTTCGGCTAAAATTTTGAAAAAAATGACCCGAAAGAT-TTTCCTCAAT
13598 TTTTGGATAAA
319 TTTTGGATAAA
* * *
13609 ATACTCATAAAAAATATATAACTCATCGCCAAAAATATTGAAGGGCTTTTGACG-TTTCTAATAT
1 ATACTCATAAAAAATATATAATTCAACGCCAAAGAT-TTGAAGGGCTTTTGACGCTTT-TAATAT
* * * *
13673 CATTTTTTCCTA-TTTTTCCAAATTAATTTCTAATTAAATTGATACAAGATTCAGATGCTCGTAA
64 CA--TTTTCATATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT--
** * * **
13737 AAAAAAAAAATCCTTAAATCTGATGTGGGTGAGATTTGATTAGATGAATATAGATATTTCAACTA
125 AAAAAAAAAAT-CTTAAATCCAATGTGGCTGAGATTTTATTAGATGAATATAGATATTTCAAGGA
* * * * * * * * *
13802 ATCTCGGAGCTAAAAATCATGCAAAATTTAGCTAGGTCCCCATAACGCATTTTTAGCCAAAAACC
189 GTCTCGGCGCCAAAAATCATGCAAAACTGAGCTGGGGCCCCAAAACGCATTTTTATCCAAAAACC
* *
13867 GTGATGGTTTGTTAGTACATGATTTCGG-TAAAAATTTTGCAAAAAATGACCCGAAAGATTTCTC
254 GTGAT-G---GTTAGTACACGATTTCGGCT-AAAATTTTGAAAAAAATGACCCGAAAGATTT-TC
* *
13931 CTCAATGTTTGGCTAAA
313 CTCAATTTTTGGATAAA
* * *
13948 ATACT-AGAAAAAATATATAATTCAACGCCAAAAAGA-TTGGAGGGCTTTTTACGCTTTTAATAT
1 ATACTCATAAAAAATATATAATTCAACGCC--AAAGATTTGAAGGGCTTTTGACGCTTTTAATAT
* *
14011 CGTATTTCTTATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAA
64 CAT-TTTCATATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAA
14058 ATTTTTAAAT
Statistics
Matches: 660, Mismatches: 87, Indels: 61
0.82 0.11 0.08
Matches are distributed among these distances:
328 6 0.01
329 34 0.05
330 113 0.17
331 112 0.17
332 47 0.07
333 4 0.01
334 72 0.11
335 76 0.12
336 3 0.00
337 41 0.06
338 80 0.12
339 68 0.10
340 4 0.01
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (329 bp):
ATACTCATAAAAAATATATAATTCAACGCCAAAGATTTGAAGGGCTTTTGACGCTTTTAATATCA
TTTTCATATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAA
AAAATCTTAAATCCAATGTGGCTGAGATTTTATTAGATGAATATAGATATTTCAAGGAGTCTCGG
CGCCAAAAATCATGCAAAACTGAGCTGGGGCCCCAAAACGCATTTTTATCCAAAAACCGTGATGG
TTAGTACACGATTTCGGCTAAAATTTTGAAAAAAATGACCCGAAAGATTTTCCTCAATTTTTGGA
TAAA
Found at i:14474 original size:15 final size:16
Alignment explanation
Indices: 14456--14485 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
14446 ATAAATAATA
14456 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
14471 ATATTATAATCTAAA
1 ATATTATAATCTAAA
14486 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:15092 original size:69 final size:69
Alignment explanation
Indices: 15017--15162 Score: 283
Period size: 69 Copynumber: 2.1 Consensus size: 69
15007 CGCCAGGAAT
15017 TGATTTGATTTGATAATATTGTAACATTAGGGACTTAATTAACTAAATTAAAAAGTTAGGACCAG
1 TGATTTGATTTGATAATATTGTAACATTAGGGACTTAATTAACTAAATTAAAAAGTTAGGACCAG
15082 GGAC
66 GGAC
*
15086 TGATTTGATTTGATAATATTGTAACATTAGGGACTTAATTAACTAAATTAAAAAGTTAGGACTAG
1 TGATTTGATTTGATAATATTGTAACATTAGGGACTTAATTAACTAAATTAAAAAGTTAGGACCAG
15151 GGAC
66 GGAC
15155 TGATTTGA
1 TGATTTGA
15163 GTCGATATTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 76 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (69 bp):
TGATTTGATTTGATAATATTGTAACATTAGGGACTTAATTAACTAAATTAAAAAGTTAGGACCAG
GGAC
Found at i:19270 original size:87 final size:87
Alignment explanation
Indices: 19039--19249 Score: 341
Period size: 87 Copynumber: 2.4 Consensus size: 87
19029 GGATACCCCA
*
19039 CATTTTTCCAAATAAATTTGCCCTGCAGCTTCAAAACGTCCGGCACGAGTAAAACATTTTGCAGC
1 CATTTTTCCAAATAAATTTGACCTGCAGCTTCAAAACGTCCGGCACGAGTAAAACATTTTGCAGC
**
19104 TTGTTCTGGCATTGCAGGATGG
66 TTGTTCTGGCAGCGCAGGATGG
* * * * *
19126 CATTCTTCCAGATAAATTTGAGCTGCAGCTTCAAAACGTCCAGCACGAGTAAAACATTTTGCTGC
1 CATTTTTCCAAATAAATTTGACCTGCAGCTTCAAAACGTCCGGCACGAGTAAAACATTTTGCAGC
19191 TTGTTCTGGCAGCGCAGGATGG
66 TTGTTCTGGCAGCGCAGGATGG
*
19213 CATTTTTCCAAATAAATTTGACCTGCAGTTTCAAAAC
1 CATTTTTCCAAATAAATTTGACCTGCAGCTTCAAAAC
19250 ATTTGGCAAG
Statistics
Matches: 112, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 112 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (87 bp):
CATTTTTCCAAATAAATTTGACCTGCAGCTTCAAAACGTCCGGCACGAGTAAAACATTTTGCAGC
TTGTTCTGGCAGCGCAGGATGG
Found at i:26705 original size:87 final size:87
Alignment explanation
Indices: 26582--26744 Score: 254
Period size: 87 Copynumber: 1.9 Consensus size: 87
26572 CAGCACGGAA
* *
26582 AAAACATTCTGCAGCTTTCTCCAGATGAGATCCCCCACATTTTTCCAAATAAATTTGACCTGCAG
1 AAAACATTCTGCAGCTTTCTCCAGATGAGATCCCCCACATCTTTCCAAATAAATTTCACCTGCAG
26647 CTTCAAAACATCCAGCTAGAAT
66 CTTCAAAACATCCAGCTAGAAT
* * * *
26669 AAAACATTCTGCTGCTTTCTCTAGATGAGTTTCCCCACATCTTTCCAAATAAATTTCACCTGCAG
1 AAAACATTCTGCAGCTTTCTCCAGATGAGATCCCCCACATCTTTCCAAATAAATTTCACCTGCAG
* *
26734 TTTCAGAACAT
66 CTTCAAAACAT
26745 TACTTTCTGA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 68 1.00
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (87 bp):
AAAACATTCTGCAGCTTTCTCCAGATGAGATCCCCCACATCTTTCCAAATAAATTTCACCTGCAG
CTTCAAAACATCCAGCTAGAAT
Found at i:49325 original size:8 final size:8
Alignment explanation
Indices: 49312--49351 Score: 80
Period size: 8 Copynumber: 5.0 Consensus size: 8
49302 CTAAAAACAA
49312 GTCTTCTC
1 GTCTTCTC
49320 GTCTTCTC
1 GTCTTCTC
49328 GTCTTCTC
1 GTCTTCTC
49336 GTCTTCTC
1 GTCTTCTC
49344 GTCTTCTC
1 GTCTTCTC
49352 CCATTCTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.00, C:0.38, G:0.12, T:0.50
Consensus pattern (8 bp):
GTCTTCTC
Found at i:70195 original size:23 final size:23
Alignment explanation
Indices: 70165--70212 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
70155 ACACTCAAGA
70165 GCCAACTCTTCGCAGGGGTTGCC
1 GCCAACTCTTCGCAGGGGTTGCC
70188 GCCAACTCTTCGCAGGGGTTGCC
1 GCCAACTCTTCGCAGGGGTTGCC
70211 GC
1 GC
70213 ATTTGAAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.12, C:0.35, G:0.31, T:0.21
Consensus pattern (23 bp):
GCCAACTCTTCGCAGGGGTTGCC
Found at i:76225 original size:42 final size:42
Alignment explanation
Indices: 76166--76245 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
76156 ACTAAGTCTT
76166 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
* * *
76208 GAAAATTTTTTGTAAATTAAGAACTACTCAACTCAAAT
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAAT
76246 ACTGATCCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.31
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:76416 original size:56 final size:57
Alignment explanation
Indices: 76312--76425 Score: 187
Period size: 56 Copynumber: 2.0 Consensus size: 57
76302 TTTATTCTGT
* *
76312 AGAATAATTAAGTAGAGATAGGGGGGATAGAATTTATTATAATATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGAGGATAGAATTTATTATAACATTTATTGTGTGAA
76369 AGAATAATTAAGTAGAGATA-GGAGGATATG-ATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGAGGATA-GAATTTATTATAACATTTATTGTGTGAA
76425 A
1 A
76426 TTTAACGGAT
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
56 33 0.61
57 21 0.39
ACGTcount: A:0.41, C:0.01, G:0.23, T:0.35
Consensus pattern (57 bp):
AGAATAATTAAGTAGAGATAGGGAGGATAGAATTTATTATAACATTTATTGTGTGAA
Found at i:78162 original size:16 final size:17
Alignment explanation
Indices: 78136--78168 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
78126 ATTTTCTGGC
78136 AAAAAGAAAAAAGAAAA
1 AAAAAGAAAAAAGAAAA
78153 AAAAAG-AAAAAGAAAA
1 AAAAAGAAAAAAGAAAA
78169 TTTGATTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAAGAAAA
Found at i:86827 original size:3 final size:3
Alignment explanation
Indices: 86804--86845 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
86794 CAGCTGAAGT
* *
86804 TTG TTG CTG TTG -TG TTTG TTG TTG TTG TTG TTC TTG TTG TTG
1 TTG TTG TTG TTG TTG -TTG TTG TTG TTG TTG TTG TTG TTG TTG
86846 GGTGTTGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.88
4 2 0.06
ACGTcount: A:0.00, C:0.05, G:0.31, T:0.64
Consensus pattern (3 bp):
TTG
Found at i:87330 original size:3 final size:3
Alignment explanation
Indices: 87322--87364 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
87312 GTAGTTGCTT
* *
87322 TGG TGG TGG TGA TGTG CGG TGG TTGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TG-G TGG TGG -TGG TGG TGG TGG TGG TGG TG
87365 ACTTGAAGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
3 30 0.88
4 4 0.12
ACGTcount: A:0.02, C:0.02, G:0.60, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:102166 original size:20 final size:20
Alignment explanation
Indices: 102141--102180 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
102131 ATATATAGCC
102141 TATCATCTGTTACAGTAGTT
1 TATCATCTGTTACAGTAGTT
102161 TATCATCTGTTACAGTAGTT
1 TATCATCTGTTACAGTAGTT
102181 GTATATTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (20 bp):
TATCATCTGTTACAGTAGTT
Found at i:102448 original size:7 final size:7
Alignment explanation
Indices: 102438--102465 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
102428 TTAGAGGCAT
102438 GTGGAGG
1 GTGGAGG
102445 GTGGAGG
1 GTGGAGG
102452 GTGGAGG
1 GTGGAGG
102459 GTGGAGG
1 GTGGAGG
102466 CGGAGGGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.71, T:0.14
Consensus pattern (7 bp):
GTGGAGG
Found at i:106260 original size:42 final size:44
Alignment explanation
Indices: 106209--106302 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
106199 AGTGCATTAC
*
106209 CTAA-ATTCTACT-C-CATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCGCATCTCTAGATAATTCATCAAAATAAAG
*
106250 CTAATATTCTACTCCTGCATCTCTAGATAATTCATCAACATAAAG
1 CTAATATTCTACTCC-GCATCTCTAGATAATTCATCAAAATAAAG
106295 CTAATATT
1 CTAATATT
106303 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
43 1 0.02
45 34 0.72
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.34
Consensus pattern (44 bp):
CTAATATTCTACTCCGCATCTCTAGATAATTCATCAAAATAAAG
Found at i:108092 original size:23 final size:24
Alignment explanation
Indices: 108053--108106 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
108043 ATTAATGGTA
*
108053 TTATTA-AAATAATAAATTGGGTT
1 TTATTAGAAATAAAAAATTGGGTT
108076 TTATTAGAAA-AAAAAATTGGGTT
1 TTATTAGAAATAAAAAATTGGGTT
*
108099 TCATTAGA
1 TTATTAGA
108107 TAATCATAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 25 0.89
24 3 0.11
ACGTcount: A:0.44, C:0.02, G:0.15, T:0.39
Consensus pattern (24 bp):
TTATTAGAAATAAAAAATTGGGTT
Found at i:109697 original size:3 final size:3
Alignment explanation
Indices: 109689--109767 Score: 149
Period size: 3 Copynumber: 26.3 Consensus size: 3
109679 ATATTATAGT
109689 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
109737 ATA ATA ATA ATA ATA ATA ATA AGA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
109768 CATAGGAGAA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:109943 original size:7 final size:7
Alignment explanation
Indices: 109931--109957 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
109921 TTGTTATGTC
109931 ATTTCTA
1 ATTTCTA
109938 ATTTCTA
1 ATTTCTA
109945 ATTTCTA
1 ATTTCTA
109952 ATTTCT
1 ATTTCT
109958 TTGGTTTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTTCTA
Found at i:110853 original size:2 final size:2
Alignment explanation
Indices: 110846--110873 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
110836 AAGGAAGTTG
110846 AT 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
110874 CTTTCCTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112426 original size:7 final size:7
Alignment explanation
Indices: 112414--112446 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
112404 ACACAAATTA
112414 TATGAAT
1 TATGAAT
112421 TATGAAT
1 TATGAAT
112428 TATGAAT
1 TATGAAT
112435 TATGAA-
1 TATGAAT
112441 TATGAA
1 TATGAA
112447 GCAAAATCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.39
Consensus pattern (7 bp):
TATGAAT
Found at i:114092 original size:2 final size:2
Alignment explanation
Indices: 114080--114110 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
114070 ATAATTACCC
114080 AT AT GAT 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
114111 GAGACTAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:116932 original size:2 final size:2
Alignment explanation
Indices: 116925--116981 Score: 73
Period size: 2 Copynumber: 29.5 Consensus size: 2
116915 AGGAGAAAGC
* * *
116925 AT AT AT AT AT AC AT AT AC AT AT AT AT AT GT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
116966 AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT A
116982 GCATAGCCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:116965 original size:17 final size:17
Alignment explanation
Indices: 116925--116981 Score: 78
Period size: 17 Copynumber: 3.3 Consensus size: 17
116915 AGGAGAAAGC
* *
116925 ATATATATATACATATAC
1 ATATATATATATATAT-T
*
116943 ATATATATATGTATATT
1 ATATATATATATATATT
116960 ATATATATATATATATT
1 ATATATATATATATATT
116977 ATATA
1 ATATA
116982 GCATAGCCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
17 21 0.60
18 14 0.40
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (17 bp):
ATATATATATATATATT
Found at i:123813 original size:41 final size:41
Alignment explanation
Indices: 123754--123835 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
123744 TAACTAGTTA
* *
123754 GGGGCTAAATCTGGATTTAATTTATTGCCTTAATTATTAGG
1 GGGGCTAAACCTGCATTTAATTTATTGCCTTAATTATTAGG
*
123795 GGGGCTAAACCTGCATTTAATTTATTTCCTTAATTATTAGG
1 GGGGCTAAACCTGCATTTAATTTATTGCCTTAATTATTAGG
123836 AGAGACAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (41 bp):
GGGGCTAAACCTGCATTTAATTTATTGCCTTAATTATTAGG
Found at i:123982 original size:2 final size:2
Alignment explanation
Indices: 123975--124003 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
123965 ACATACATAC
123975 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
124004 CCTCCTGCTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:125505 original size:2 final size:2
Alignment explanation
Indices: 125498--125530 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
125488 GAGTTTCATG
125498 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
125531 ACTAATTGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:127545 original size:2 final size:2
Alignment explanation
Indices: 127538--127570 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
127528 AAATACATAC
127538 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
127571 GAAATTGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:128608 original size:16 final size:17
Alignment explanation
Indices: 128578--128623 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
128568 TATTTTTCTT
128578 AAGAAAAATAAAAGA-A
1 AAGAAAAATAAAAGAGA
*
128594 GAAGAAAAA-ATAAGAGA
1 -AAGAAAAATAAAAGAGA
128611 AAGAAAAATAAAA
1 AAGAAAAATAAAA
128624 ACAAACAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (17 bp):
AAGAAAAATAAAAGAGA
Found at i:135074 original size:2 final size:2
Alignment explanation
Indices: 135067--135096 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
135057 CTTTATTTAT
135067 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
135097 CAAACCAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:158528 original size:32 final size:32
Alignment explanation
Indices: 158476--158772 Score: 254
Period size: 41 Copynumber: 8.2 Consensus size: 32
158466 CATTTGGGAA
*
158476 ATTTGGATGTG-ATTAAGGCAAGTTCAATGTT
1 ATTTGGATGTGAATTAAGGCAAGTTCAATGTC
158507 ATTTGGATGTGAATTAAGGCAAGTTCAATGTC
1 ATTTGGATGTGAATTAAGGCAAGTTCAATGTC
158539 ATTTGGATGTGAATTAAGGCAAGTTCAATGTC
1 ATTTGGATGTGAATTAAGGCAAGTTCAATGTC
158571 ATTTGGGAAATTTGGATGTGAATTAAGGCAAGTTCAATGTC
1 ---------ATTTGGATGTGAATTAAGGCAAGTTCAATGTC
158612 ATTTGGGAAAGTTGGATGTGAATTAAGGCAAGTTCAATGTC
1 A--T-------TTGGATGTGAATTAAGGCAAGTTCAATGTC
158653 ATTTGGGAAAGTTGGATGTGAATTAAGGCAAGTTCAATGTC
1 A--T-------TTGGATGTGAATTAAGGCAAGTTCAATGTC
158694 ATTTGGGAAAGTTGGATTTGAATTAAGGCAAGTTCAATGTC
1 ATTT-GG--A--T-G---TGAATTAAGGCAAGTTCAATGTC
158735 ATTTGGATGTGAATTAAGGCAAGTTCAATGTC
1 ATTTGGATGTGAATTAAGGCAAGTTCAATGTC
158767 ATTTGG
1 ATTTGG
158773 GAAAGTTAAA
Statistics
Matches: 237, Mismatches: 1, Indels: 55
0.81 0.00 0.19
Matches are distributed among these distances:
31 11 0.05
32 83 0.35
33 2 0.01
34 1 0.00
35 2 0.01
36 1 0.00
37 1 0.00
38 2 0.01
39 1 0.00
40 2 0.01
41 131 0.55
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.34
Consensus pattern (32 bp):
ATTTGGATGTGAATTAAGGCAAGTTCAATGTC
Found at i:158596 original size:41 final size:41
Alignment explanation
Indices: 158541--158789 Score: 399
Period size: 41 Copynumber: 6.3 Consensus size: 41
158531 TCAATGTCAT
*
158541 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAG
158582 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAG
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAG
158623 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAG
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAG
158664 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAG
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAG
*
158705 TTGGATTTGAATTAAGGCAAGTTCAATGTCA--T-------
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAG
158737 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAG
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAG
**
158778 TTAAATGTGAAT
1 TTGGATGTGAAT
158790 GTGCCGCGTG
Statistics
Matches: 194, Mismatches: 5, Indels: 18
0.89 0.02 0.08
Matches are distributed among these distances:
32 30 0.15
34 1 0.01
39 1 0.01
41 162 0.84
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.33
Consensus pattern (41 bp):
TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAG
Found at i:158611 original size:73 final size:73
Alignment explanation
Indices: 158507--158772 Score: 298
Period size: 82 Copynumber: 3.5 Consensus size: 73
158497 GTTCAATGTT
158507 ATTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATGTCA
1 ATTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATGTCA
158572 TTTGGGAA
66 TTTGGGAA
158580 ATTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGAATTAAGGCAAGT
1 ATTTGGATGTGAATTAAGGCAAGTTCAATGTCA--T-------TTGGATGTGAATTAAGGCAAGT
158645 TCAATGTCATTTGGGAA
57 TCAATGTCATTTGGGAA
*
158662 AGTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATTTGAATTAAGGCAAGT
1 ATTTGGATGTGAATTAAGGCAAGTTCAATGTCATTT-GG--A--T-G---TGAATTAAGGCAAGT
158727 TCAATGTC---------
57 TCAATGTCATTTGGGAA
158735 ATTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGG
1 ATTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGG
158773 GAAAGTTAAA
Statistics
Matches: 173, Mismatches: 2, Indels: 37
0.82 0.01 0.17
Matches are distributed among these distances:
72 2 0.01
73 70 0.40
74 2 0.01
75 1 0.01
76 1 0.01
78 1 0.01
79 1 0.01
80 1 0.01
82 94 0.54
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.34
Consensus pattern (73 bp):
ATTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATGTCA
TTTGGGAA
Found at i:158630 original size:20 final size:20
Alignment explanation
Indices: 158566--158710 Score: 92
Period size: 20 Copynumber: 7.1 Consensus size: 20
158556 GGCAAGTTCA
*
158566 ATGTCATTTGGGAAATTTGG
1 ATGTCATTTGGGAAAGTTGG
* ** * **
158586 ATGTGAATTAAGGCAAGTTCA
1 ATGT-CATTTGGGAAAGTTGG
158607 ATGTCATTTGGGAAAGTTGG
1 ATGTCATTTGGGAAAGTTGG
* ** * **
158627 ATGTGAATTAAGGCAAGTTCA
1 ATGT-CATTTGGGAAAGTTGG
158648 ATGTCATTTGGGAAAGTTGG
1 ATGTCATTTGGGAAAGTTGG
* ** * **
158668 ATGTGAATTAAGGCAAGTTCA
1 ATGT-CATTTGGGAAAGTTGG
158689 ATGTCATTTGGGAAAGTTGG
1 ATGTCATTTGGGAAAGTTGG
158709 AT
1 AT
158711 TTGAATTAAG
Statistics
Matches: 85, Mismatches: 37, Indels: 6
0.66 0.29 0.05
Matches are distributed among these distances:
20 44 0.52
21 41 0.48
ACGTcount: A:0.31, C:0.07, G:0.29, T:0.33
Consensus pattern (20 bp):
ATGTCATTTGGGAAAGTTGG
Found at i:160173 original size:238 final size:234
Alignment explanation
Indices: 159615--160328 Score: 776
Period size: 238 Copynumber: 3.0 Consensus size: 234
159605 TAATATTGAC
159615 CAATCATTAGTCTTTTCACCAACCCGATTTCAGATCTCTACTAATTGTAAATTGTTAGGGTAAAT
1 CAATCATTAGTCTTTTCACCAACCCGATTTCAGATCTCTACTAATTGT-AA-----A-GGTAAAT
* * ** * *
159680 GACCTCTCTTTCTCTAGTATTCTTATTTTACGTAGTCTGAAACATTTTGCAGGCTTCTGAGGTAT
59 GACCTCTCTTTCTCTAATATTCTCATTTTACGTAGTAAGAAACATTTTACAGGCTT-TGAGGCAT
* * * *
159745 TTTATATTTTAAACATTTTGAAAAAATTTGGACATATATCATAGATGATCTTTTTAAAATGAAAA
123 TTTATATTTCAGACATTTTGAAAAAATTTGGACATACATCATAGATGACCTTTTTAAAATGAAAA
* *
159810 ATAAAATGTCAGTTGTTTTTTAATATACCAACCTTCTTTTATTCTTCT
188 AT-AAATGTCAGTCGTTTTCTAATATACCAACCTTCTTTTATTCTTCT
* * ** *
159858 CAATCATTAGTCTTTTCACTAACCCGATTTCAGATCTCTAGTAATTGTATGGGTAAAAGA--TCT
1 CAATCATTAGTCTTTTCACCAACCCGATTTCAGATCTCTACTAATTGTAAAGGTAAATGACCTCT
* * * *
159921 CTGTTCATCTAATATTCTCATCTAACGTAGTAAGAAAAATTTAACAGGCTTTGGAGGCATTTTAT
66 CT-TTC-TCTAATATTCTCATTTTACGTAGTAAGAAACATTTTACAGGCTTT-GAGGCATTTTAT
* *
159986 ATTTCAGACATTTTGAAAAAATTTGGTCATACATCACAGGTGAGGTGACCTTTTTAAAATGAAAA
128 ATTTCAGACATTTTGAAAAAATTTGGACATACAT--CA--T-AGATGACCTTTTTAAAATGAAAA
* *
160051 AT-ATTGTCAGTCGTTTTCTAATTTACCAACCTTCTTTTATTC-TCT
188 ATAAATGTCAGTCGTTTTCTAATATACCAACCTTCTTTTATTCTTCT
* ** * *
160096 CAATCATTAGTGTTTTCACCAACAGGATTTCAGATCTCTATTAATTGTAAAGGTAAATGACCTCC
1 CAATCATTAGTCTTTTCACCAACCCGATTTCAGATCTCTACTAATTGTAAAGGTAAATGACCTCT
* ** * *
160161 CTTTCCCTAATATTCTCATTTTACGTAGTTCGAAACATTTTACAAGCTTTTTAGGCATTTTATAT
66 CTTTCTCTAATATTCTCATTTTACGTAGTAAGAAACATTTTACAGGC-TTTGAGGCATTTTATAT
* * * * * * *
160226 ATCAGACATTTT-AAAAAATTTGGACAT--ATCAAAGGTGATCTTTTTGAATTGAAATATAAAAT
130 TTCAGACATTTTGAAAAAATTTGGACATACATCATAGATGACCTTTTTAAAATGAAAAAT-AAAT
* * * * *
160288 GCCAGTCGTTTTTTTAATTTACCAACCTTATATTATTCTTC
194 GTCAGTCG-TTTTCTAATATACCAACCTTCTTTTATTCTTC
160329 CTTTTAAAAT
Statistics
Matches: 401, Mismatches: 55, Indels: 39
0.81 0.11 0.08
Matches are distributed among these distances:
230 21 0.05
232 9 0.02
233 28 0.07
234 7 0.02
235 6 0.01
236 84 0.21
237 14 0.03
238 115 0.29
239 42 0.10
240 5 0.01
241 23 0.06
242 1 0.00
243 46 0.11
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.40
Consensus pattern (234 bp):
CAATCATTAGTCTTTTCACCAACCCGATTTCAGATCTCTACTAATTGTAAAGGTAAATGACCTCT
CTTTCTCTAATATTCTCATTTTACGTAGTAAGAAACATTTTACAGGCTTTGAGGCATTTTATATT
TCAGACATTTTGAAAAAATTTGGACATACATCATAGATGACCTTTTTAAAATGAAAAATAAATGT
CAGTCGTTTTCTAATATACCAACCTTCTTTTATTCTTCT
Found at i:160601 original size:74 final size:74
Alignment explanation
Indices: 160480--160628 Score: 226
Period size: 74 Copynumber: 2.0 Consensus size: 74
160470 GGTCAAATAA
* *
160480 AGTTTAGGAGTAGGGATCGCTACTCCATGTCTAACACCAAGGCAAATCCGATCCAATTTGGAATT
1 AGTTTAGGAGTAGGGATCGCTACTCCATCTCCAACACCAAGGCAAATCCGATCCAATTTGGAATT
160545 TATGAATCC
66 TATGAATCC
** ** * *
160554 AGTTTAGGAGTAGGGATTTCTACTCCATCTCCAACATTAGGGCAAATCTGATCCAATTTGGAATT
1 AGTTTAGGAGTAGGGATCGCTACTCCATCTCCAACACCAAGGCAAATCCGATCCAATTTGGAATT
160619 TATGAATCC
66 TATGAATCC
160628 A
1 A
160629 TTGGATTTTC
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 67 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (74 bp):
AGTTTAGGAGTAGGGATCGCTACTCCATCTCCAACACCAAGGCAAATCCGATCCAATTTGGAATT
TATGAATCC
Found at i:162048 original size:17 final size:21
Alignment explanation
Indices: 162008--162048 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
161998 ATCCATATAA
162008 AATTACTATAGAACAACAATC
1 AATTACTATAGAACAACAATC
162029 AATTACTATA-AACAAACAAT
1 AATTACTATAGAAC-AACAAT
162049 ACACTCCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.56, C:0.17, G:0.02, T:0.24
Consensus pattern (21 bp):
AATTACTATAGAACAACAATC
Found at i:162538 original size:50 final size:50
Alignment explanation
Indices: 162461--162933 Score: 748
Period size: 50 Copynumber: 9.5 Consensus size: 50
162451 CAACACGCGA
*
162461 AGACACGAAGGTACACGAGAAGAGAGAGGCCTCCGCAGTGAGGCAAGGCC
1 AGACACGAAGGTACACGAGAAGAGAGAGGCCTCCGCAGTGAGGCGAGGCC
* *
162511 AGACACGAAGGTAGACGAGAAGCGAGAGGCCTCCGCAGTGAGGCGAGGCC
1 AGACACGAAGGTACACGAGAAGAGAGAGGCCTCCGCAGTGAGGCGAGGCC
* *
162561 AGACACGAAGGTACACGAGAAGAGAGAGGCCTTCGCAGTGAGGCAAGGCC
1 AGACACGAAGGTACACGAGAAGAGAGAGGCCTCCGCAGTGAGGCGAGGCC
* * *
162611 AGACACGAAGGTGCATGAGAAGCGAGAGGCCTCCGCAGTGAGGCGAGGCC
1 AGACACGAAGGTACACGAGAAGAGAGAGGCCTCCGCAGTGAGGCGAGGCC
* * *
162661 AGACACGAAGGTGCACGAGAAGCGAGAGGCCTCCGCAGTGAGGCGAGGCA
1 AGACACGAAGGTACACGAGAAGAGAGAGGCCTCCGCAGTGAGGCGAGGCC
*
162711 AGATACGAAGGTACACGAGAAGAGAGAGGCCTCCGCAGTGAGGCGAGGCC
1 AGACACGAAGGTACACGAGAAGAGAGAGGCCTCCGCAGTGAGGCGAGGCC
* * *
162761 AGACACGAAGGTATACGAGAAGATAGAGGCCTCTGCAGTGAGGCGAGGCC
1 AGACACGAAGGTACACGAGAAGAGAGAGGCCTCCGCAGTGAGGCGAGGCC
* *
162811 AGACACGAAGGTACACGAGAAGATAGAGGCCTCCGCAATGAGGCGAGGCC
1 AGACACGAAGGTACACGAGAAGAGAGAGGCCTCCGCAGTGAGGCGAGGCC
* * *
162861 AGACACGAAGCTACACGAGAAGACAGAGGCCTCCGTAGTGAGGCGAGGCC
1 AGACACGAAGGTACACGAGAAGAGAGAGGCCTCCGCAGTGAGGCGAGGCC
* *
162911 AGACACGAAGCTACATGAGAAGA
1 AGACACGAAGGTACACGAGAAGA
162934 CACGGCGGTG
Statistics
Matches: 393, Mismatches: 30, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 393 1.00
ACGTcount: A:0.33, C:0.23, G:0.37, T:0.08
Consensus pattern (50 bp):
AGACACGAAGGTACACGAGAAGAGAGAGGCCTCCGCAGTGAGGCGAGGCC
Found at i:164393 original size:645 final size:641
Alignment explanation
Indices: 163288--164676 Score: 2168
Period size: 645 Copynumber: 2.2 Consensus size: 641
163278 ATAATTGTGT
* * * * * *
163288 TTTCTGCCACAAATCAAGCAAAACTGAGCTGGGGCCCCGAAACTCG-ATTTTAG-C-CAAATCCG
1 TTTCTGCCATAAATCATGCAAAACTGAACAGGGACCCCGAAACTCGTA-TTTAGTCAAAAATCCG
* * * * *
163350 TGATGGTTAGTACACGACTTCGCCTAAAAACTAACCTGAAATATTTTTTTCTCAATTTTCTGCAA
65 TGATGGTT-GTACACGATTTCGGCTAAAAATTGACCCG-AA-ATTTTTTTCTCAATTTTCTGCAA
* * * * *
163415 AATATTCCGAAAAAATATACAATTCAACGCCGAAACAAGTTGAAGGGCTTTCCAAGCATCTAATA
127 AATACTCCGAAAAAATATACAATTCAACGCCAAAAAAAATCGAAGGGCTTTCCAAGCATCTAATA
* * * * *
163480 TCGTTTTCCCATTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
192 TCGTTTTCCAATTTTCTCCAAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCACGTAAA
163545 AACAAATCCTTAAATTCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATCGCAAGGAGTCT
257 AACAAATCCTTAAATTCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATCGCAAGGAGTCT
* *
163610 TTCTGCCAAAAATCATGCAAAACTGAGGCGGGGCCCCAAAACTCGATTTTAGACCAAATTCGTGA
322 TTCTGCCAAAAATCATGCAAAACTGAGACAGGGCCCCAAAACTCGATTTTAGACCAAATTCGTGA
*
163675 TAGTACACGATTTCGGCTAAAAACTGACCCGAAATGTTTATTTCTTAATTTTTTGCAAAATATTC
387 TAGTACACGATTTCGGCTAAAAACTGACCCGAAATGTTTATTTCTCAATTTTTTGCAAAATATTC
163740 CGAAAAAATAAACAATTCAACGCCGAAACAAATTGAAGGGTTTTCCAAGTTTCTAATATCGTTTT
452 CGAAAAAATAAACAATTCAACGCCGAAACAAATTGAAGGGTTTTCCAAGTTTCTAATATCGTTTT
*
163805 TCCATATTTTCCCCGAATTTATTTCTAATTAAATTGAAACAAGATTCCCATGCTCGTAAAAACAA
517 TCCATATTTTCCCCGAATTTATTTCTAATTAAATTGAAACAAGATTCACATGCTCGTAAAAACAA
**
163870 ATCC-TTAAATTCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAGGGAGTC
582 ATCCAAAAAATTCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAGGGAGTC
*
163929 TTTCTGCCATAAATCATGCAAAACTGAACCGGGACCCCGAAACTCGTATTTAGTCAAAAATCCGT
1 TTTCTGCCATAAATCATGCAAAACTGAACAGGGACCCCGAAACTCGTATTTAGTCAAAAATCCGT
* **
163994 GATGGTTTGTACACGATTTCGGCTAAAAATTGACCCGAAATTTTTTTCTCAATTTTTTGCCACGA
66 GATGG-TTGTACACGATTTCGGCTAAAAATTGACCCGAAATTTTTTTCTCAATTTTCTG-CAAAA
* * * * *
164059 TACTCTGAAAAAATATATAATTCAATGCCAAAAAAAATCGAAGGGTTTTTC-A-CATTTCTAATA
129 TACTCCGAAAAAATATACAATTCAACGCCAAAAAAAATCGAAGGGCTTTCCAAGCA--TCTAATA
164122 TCGTTTTTTCCAATTTTACTCCAAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCACGT
192 TCG--TTTTCCAATTTT-CTCCAAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCACGT
*
164187 GAAAACAAATCCTTAAATTCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATCGCAAGGAG
254 AAAAACAAATCCTTAAATTCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATCGCAAGGAG
*
164252 TCTTTCTGCCAAAAATCATGCAAAACTGAGACAGGGCCCCGAAACTCGATTTTAG-CCAAAATTC
319 TCTTTCTGCCAAAAATCATGCAAAACTGAGACAGGGCCCCAAAACTCGATTTTAGACC-AAATTC
** *
164316 GTGAT-GTACACGATTTCGGCTAAAAACTGATTCGAAATGTTTTTTTCTCAATTTTTTGCAAAAT
383 GTGATAGTACACGATTTCGGCTAAAAACTGACCCGAAATGTTTATTTCTCAATTTTTTGCAAAAT
164380 ATTCCGAAAAAAATAAACAATTCAACGCCGAAACAAATTGAAGGGTTTTCCAAGTTTCTAATATC
448 ATTCCG-AAAAAATAAACAATTCAACGCCGAAACAAATTGAAGGGTTTTCCAAGTTTCTAATATC
*
164445 GTTTTTCCATTTTTTCCCCGAATTTATTTCTAATTAAATTGAAACAAGATTCACATGCTCGTAAA
512 GTTTTTCCATATTTTCCCCGAATTTATTTCTAATTAAATTGAAACAAGATTCACATGCTCGTAAA
164510 AACAAATCCAAAAAATTCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAGGGAGTC
577 AACAAATCCAAAAAATTCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAGGGAGTC
* *
164575 TTTCTGCCATAAATCATGCAAAACTGAATAGGGACCCCGAAACTCGTATTTAGTCATAAATCCGT
1 TTTCTGCCATAAATCATGCAAAACTGAACAGGGACCCCGAAACTCGTATTTAGTCAAAAATCCGT
* * *
164640 GATGG--GTATACGATTTCGGCTGAATATTGACCCGAAA
66 GATGGTTGTACACGATTTCGGCTAAAAATTGACCCGAAA
164677 AGTTTTTT
Statistics
Matches: 688, Mismatches: 47, Indels: 24
0.91 0.06 0.03
Matches are distributed among these distances:
640 2 0.00
641 66 0.10
642 58 0.08
643 66 0.10
644 76 0.11
645 300 0.44
646 120 0.17
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (641 bp):
TTTCTGCCATAAATCATGCAAAACTGAACAGGGACCCCGAAACTCGTATTTAGTCAAAAATCCGT
GATGGTTGTACACGATTTCGGCTAAAAATTGACCCGAAATTTTTTTCTCAATTTTCTGCAAAATA
CTCCGAAAAAATATACAATTCAACGCCAAAAAAAATCGAAGGGCTTTCCAAGCATCTAATATCGT
TTTCCAATTTTCTCCAAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCACGTAAAAACA
AATCCTTAAATTCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATCGCAAGGAGTCTTTCT
GCCAAAAATCATGCAAAACTGAGACAGGGCCCCAAAACTCGATTTTAGACCAAATTCGTGATAGT
ACACGATTTCGGCTAAAAACTGACCCGAAATGTTTATTTCTCAATTTTTTGCAAAATATTCCGAA
AAAATAAACAATTCAACGCCGAAACAAATTGAAGGGTTTTCCAAGTTTCTAATATCGTTTTTCCA
TATTTTCCCCGAATTTATTTCTAATTAAATTGAAACAAGATTCACATGCTCGTAAAAACAAATCC
AAAAAATTCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAGGGAGTC
Found at i:164558 original size:321 final size:320
Alignment explanation
Indices: 163288--164684 Score: 1875
Period size: 320 Copynumber: 4.3 Consensus size: 320
163278 ATAATTGTGT
* * *
163288 TTTCTGCCACAAATCAAGCAAAACTGAG-CTGGGGCCCCGAAACTCGATTTTAGCC-AAATCCGT
1 TTTCTGCCAAAAATCATGCAAAACTGAGAC-AGGGCCCCGAAACTCGATTTTAGCCAAAATCCGT
* * * * * *
163351 GATGGTTAGTACACGACTTCGCCTAAAAACTAACCTGAAATATTTTTTTCTCAATTTTCTGCAAA
65 GA----TAGTACACGATTTCGGCTAAAAACTGACCCGAAATGTTTTTTTCTCAATTTTTTGCAAA
* * * **
163416 ATATTCCGAAAAAATATACAATTCAACGCCGAAACAAGTTGAAGGGCTTTCCAAGCATCTAATAT
126 ATATTCCGAAAAAATAAACAATTCAACGCCGAAACAAATTGAAGGGTTTTCCAAGTTTCTAATAT
* * *
163481 CGTTTTCCCATTTTTT--TCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
191 CGTTTTTCCATTTTTTCCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCACATGCTCGTAA
163544 AAACAAATCCTTAAATTCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATCGCAAGGAGTC
256 AAACAAATCCTTAAATTCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATCGCAAGGAGTC
* * * *
163609 TTTCTGCCAAAAATCATGCAAAACTGAGGCGGGGCCCCAAAACTCGATTTTAGACC-AAATTCGT
1 TTTCTGCCAAAAATCATGCAAAACTGAGACAGGGCCCCGAAACTCGATTTTAG-CCAAAATCCGT
* *
163673 GATAGTACACGATTTCGGCTAAAAACTGACCCGAAATGTTTATTTCTTAATTTTTTGCAAAATAT
65 GATAGTACACGATTTCGGCTAAAAACTGACCCGAAATGTTTTTTTCTCAATTTTTTGCAAAATAT
163738 TCCGAAAAAATAAACAATTCAACGCCGAAACAAATTGAAGGGTTTTCCAAGTTTCTAATATCGTT
130 TCCGAAAAAATAAACAATTCAACGCCGAAACAAATTGAAGGGTTTTCCAAGTTTCTAATATCGTT
* * *
163803 TTTCCATATTTTCCCCGAATTTATTTCTAATTAAATTGAAACAAGATTCCCATGCTCGTAAAAAC
195 TTTCCATTTTTTCCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCACATGCTCGTAAAAAC
** *
163868 AAATCCTTAAATTCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAGGGAGTC
260 AAATCCTTAAATTCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATCGCAAGGAGTC
* * *
163929 TTTCTGCCATAAATCATGCAAAACTGA-ACCGGGACCCCGAAACTCG-TATTTAGTCAAAAATCC
1 TTTCTGCCAAAAATCATGCAAAACTGAGACAGGG-CCCCGAAACTCGAT-TTTAG-CCAAAATCC
* *
163992 GTGATGGTTTGTACACGATTTCGGCTAAAAATTGACCCGAAA--TTTTTTTCTCAATTTTTTGCC
63 GTGA----TAGTACACGATTTCGGCTAAAAACTGACCCGAAATGTTTTTTTCTCAATTTTTTG-C
** * * * * * * * * *
164055 ACGATACTCTGAAAAAATATATAATTCAATGCCAAAAAAAATCGAAGGGTTTTTCACA-TTTCTA
123 AAAATATTCCGAAAAAATAAACAATTCAACGCCGAAACAAATTGAAGGGTTTTCCA-AGTTTCTA
* * * * * *
164119 ATATCGTTTTTTCCAATTTTACTCCAAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCA
187 ATATCG-TTTTTCCATTTTTTCCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCACATGCT
*
164184 CGTGAAAACAAATCCTTAAATTCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATCGCAAG
251 CGTAAAAACAAATCCTTAAATTCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATCGCAAG
164249 GAGTC
316 GAGTC
*
164254 TTTCTGCCAAAAATCATGCAAAACTGAGACAGGGCCCCGAAACTCGATTTTAGCCAAAATTCGTG
1 TTTCTGCCAAAAATCATGCAAAACTGAGACAGGGCCCCGAAACTCGATTTTAGCCAAAATCCGTG
**
164319 AT-GTACACGATTTCGGCTAAAAACTGATTCGAAATGTTTTTTTCTCAATTTTTTGCAAAATATT
66 ATAGTACACGATTTCGGCTAAAAACTGACCCGAAATGTTTTTTTCTCAATTTTTTGCAAAATATT
164383 CCGAAAAAAATAAACAATTCAACGCCGAAACAAATTGAAGGGTTTTCCAAGTTTCTAATATCGTT
131 CCG-AAAAAATAAACAATTCAACGCCGAAACAAATTGAAGGGTTTTCCAAGTTTCTAATATCGTT
*
164448 TTTCCATTTTTTCCCCGAATTTATTTCTAATTAAATTGAAACAAGATTCACATGCTCGTAAAAAC
195 TTTCCATTTTTTCCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCACATGCTCGTAAAAAC
** ** *
164513 AAATCCAAAAAATTCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAGGGAGTC
260 AAATCC-TTAAATTCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATCGCAAGGAGTC
* * *
164575 TTTCTGCCATAAATCATGCAAAACTGA-ATAGGGACCCCGAAACTCG-TATTTAGTCATAAATCC
1 TTTCTGCCAAAAATCATGCAAAACTGAGACAGGG-CCCCGAAACTCGAT-TTTAGCCA-AAATCC
* * * * * *
164638 GTGATGGGTATACGATTTCGGCTGAATATTGACCCGAAAAGTTTTTT
63 GTGAT-AGTACACGATTTCGGCTAAAAACTGACCCGAAATGTTTTTT
Statistics
Matches: 947, Mismatches: 103, Indels: 49
0.86 0.09 0.04
Matches are distributed among these distances:
318 125 0.13
319 34 0.04
320 229 0.24
321 221 0.23
322 22 0.02
323 17 0.02
324 102 0.11
325 191 0.20
326 6 0.01
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (320 bp):
TTTCTGCCAAAAATCATGCAAAACTGAGACAGGGCCCCGAAACTCGATTTTAGCCAAAATCCGTG
ATAGTACACGATTTCGGCTAAAAACTGACCCGAAATGTTTTTTTCTCAATTTTTTGCAAAATATT
CCGAAAAAATAAACAATTCAACGCCGAAACAAATTGAAGGGTTTTCCAAGTTTCTAATATCGTTT
TTCCATTTTTTCCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCACATGCTCGTAAAAACA
AATCCTTAAATTCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATCGCAAGGAGTC
Done.