Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023573.1 Corchorus olitorius cultivar O-4 contig23606, 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: 13229
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Found at i:493 original size:22 final size:22
Alignment explanation
Indices: 451--549 Score: 85
Period size: 22 Copynumber: 4.5 Consensus size: 22
441 TAATAACTAC
*
451 ACTATGAAATTCTGATAACCAT
1 ACTATGAAATTTTGATAACCAT
* * *
473 CCTATGAAATTTTGGTCACCAT
1 ACTATGAAATTTTGATAACCAT
* *
495 ACTCTGAAATTTTGATAACCAC
1 ACTATGAAATTTTGATAACCAT
* * *
517 AGTAT-AATTTTGTGATAACCTCT
1 ACTATGAAATTT-TGATAACC-AT
540 A-TATGAAATT
1 ACTATGAAATT
550 AATTTTGATG
Statistics
Matches: 59, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
21 5 0.08
22 49 0.83
23 5 0.08
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.36
Consensus pattern (22 bp):
ACTATGAAATTTTGATAACCAT
Found at i:666 original size:22 final size:22
Alignment explanation
Indices: 641--725 Score: 89
Period size: 22 Copynumber: 3.8 Consensus size: 22
631 GATAATCAAA
641 CTATGGAATTTTGATAACCTCC
1 CTATGGAATTTTGATAACCTCC
* *
663 CTATGGAATGTTGATAACTTCC
1 CTATGGAATTTTGATAACCTCC
* * * *
685 CTATAGAATTTAGTGTTAATCTCA
1 CTATGGAATTT--TGATAACCTCC
*
709 CTATGAAATTTTGATAA
1 CTATGGAATTTTGATAA
726 ACACAATTTG
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
22 34 0.68
24 16 0.32
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (22 bp):
CTATGGAATTTTGATAACCTCC
Found at i:779 original size:22 final size:23
Alignment explanation
Indices: 707--807 Score: 86
Period size: 22 Copynumber: 4.6 Consensus size: 23
697 GTGTTAATCT
*
707 CACTATGAAATTT-TGATAAACA
1 CACTATGAAATTTCTGATAACCA
* * * *
729 CAATTTGAAACTT-TGATTACC-
1 CACTATGAAATTTCTGATAACCA
**
750 TTCTATGAAATTTCTG-TAACCA
1 CACTATGAAATTTCTGATAACCA
* *
772 CATTATGAAATTT-TGATAGCCA
1 CACTATGAAATTTCTGATAACCA
794 CACTATGAAATTTC
1 CACTATGAAATTTC
808 AATAATCTAC
Statistics
Matches: 59, Mismatches: 16, Indels: 7
0.72 0.20 0.09
Matches are distributed among these distances:
21 14 0.24
22 45 0.76
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (23 bp):
CACTATGAAATTTCTGATAACCA
Found at i:4420 original size:321 final size:324
Alignment explanation
Indices: 3567--4645 Score: 1044
Period size: 333 Copynumber: 3.3 Consensus size: 324
3557 GGTAAAAATG
* * *
3567 ACCCGAAAGATTTTTCCTCAATTTTTGATAAAAATACTCAT-AAATATATATAATTCAACGCCAA
1 ACCCGAAAGATTTTTCCTCAATTTTAGAT-AAAATACTCATAAAAAATATATAATTCAACGTCAA
*
3631 AAAGATTTG-AGGACTTTTCACGCTTTTAATATTGTTTT--TCATTTT-TTTCTGAATTAATTTC
65 AAAGA-TTGAAGGACTTTTCACGCTTTTAATATTGTTTTCCTTATTTTCTTTC-GAATTAATTTC
* * * *
3692 TAATTAAATCGATACAAGATTCAGATGCACATAAAAACAAATCGTTAAATCCAATGTGGCTAAGA
128 TAATTAAATCGAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAAT-CAATGTGGCTAAGA
** * * ** *
3757 TTTTATTAGATGAATAAAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCAAAACAGAGCTG
192 TTTGGTTAGATGAATATAGATATTTCAAGGAGTATCGGCACCAAAAATCATGCAAAACAGAGCCG
* **
3822 TGGCCTTGGAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTTGGCTAAAATTTT
257 TGACCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTA-T--ACGA---T-GCTAAAATTTT
*
3887 ACAAAAATTG
315 ACAAAAATTA
* * * * * * * * **
3897 ACCCGAAAGATATTTCTTCAATTTTTGGCTAAAATACTTAGAAAAAATATATGATTCGATATCAA
1 ACCCGAAAGATTTTTCCTCAA-TTTTAGATAAAATACTCATAAAAAATATATAATTCAACGTCAA
* * *
3962 AAAGATTGAAGGGCTTTTAACGCTTCTAATATTGTTTTTCC-TA-TTTCTTTCCGAATTAATTTC
65 AAAGATTGAAGGACTTTTCACGCTTTTAATATTG-TTTTCCTTATTTTCTTT-CGAATTAATTTC
* *
4025 CAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTAAGA
128 TAATTAAATCGAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATC-AATGTGGCTAAGA
* * *
4090 TTCGGTTAGATGAATATAGATATTTCAAGGAGTATTGGCACCAAAAATCATGCAAAACTGAGCCG
192 TTTGGTTAGATGAATATAGATATTTCAAGGAGTATCGGCACCAAAAATCATGCAAAACAGAGCCG
* * *
4155 -GACCCCGGAACGTGTTTTT-GACCGAAAACCGTGATG-TT-T-C-A-GCTAAAATTTTTCAAAA
257 TGACCCCGGAACGCGTTTTTAG-CCAAAAACCGTGATGATTATACGATGCTAAAATTTTACAAAA
4213 ATTA
321 ATTA
* *
4217 ACCCGAAAAATTTTTCCTCGATTTCTAG-TGAAAATACTCATAAAAAATATATAATTCAACGTCA
1 ACCCGAAAGATTTTTCCTCAATTT-TAGAT-AAAATACTCATAAAAAATATATAATTCAACGTCA
* * * *
4281 AAAA-AATGAAAGCCTTTTTCACGCTTTTAATATCGTTTTCCTTATTTTCTTTCGAAATTAATTT
64 AAAAGATTGAAGGAC-TTTTCACGCTTTTAATATTGTTTTCCTTATTTTCTTTCG-AATTAATTT
* *** * *
4345 CTAATTAAATCAAAACAAGATTTAGAAATTCATAAAAACAAATCCTTTAATACAATGTGGCTGAG
127 CTAATTAAATCGAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAAT-CAATGTGGCTAAG
* * *** *
4410 ATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTCGGCGGAAAAAATTATGCAAAACTA-AGC
191 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTATCGGCACCAAAAATCATGCAAAAC-AGAGC
* * * * * * *
4474 C-TGGTCCTCGAAACGCGTTGTTAACCAAAAACCATGATGATTAGTACACTATTTTGGCTAAAAT
255 CGT-GACCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTA-T--ACGA---T-GCTAAAAT
* *
4538 TTTGCAAAAATTG
312 TTTACAAAAATTA
* * * * * * * *
4551 ACCCGAAAAATTTTTCCGACAATTTTTGGCTAAAATACTCATAAAATATATATAATTTAATGCCA
1 ACCCGAAAGATTTTTCC-TCAA-TTTTAGATAAAATACTCATAAAAAATATATAATTCAACGTCA
* *
4616 AAAA-ATTGGAGAACTTTTCACGCTTTTAAT
64 AAAAGATTGAAGGACTTTTCACGCTTTTAAT
4646 GCTAAAAATC
Statistics
Matches: 618, Mismatches: 95, Indels: 68
0.79 0.12 0.09
Matches are distributed among these distances:
319 17 0.03
320 91 0.15
321 126 0.20
322 28 0.05
323 2 0.00
325 2 0.00
326 1 0.00
328 1 0.00
329 2 0.00
330 31 0.05
331 53 0.09
332 37 0.06
333 127 0.21
334 53 0.09
335 43 0.07
336 4 0.01
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (324 bp):
ACCCGAAAGATTTTTCCTCAATTTTAGATAAAATACTCATAAAAAATATATAATTCAACGTCAAA
AAGATTGAAGGACTTTTCACGCTTTTAATATTGTTTTCCTTATTTTCTTTCGAATTAATTTCTAA
TTAAATCGAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATCAATGTGGCTAAGATTTG
GTTAGATGAATATAGATATTTCAAGGAGTATCGGCACCAAAAATCATGCAAAACAGAGCCGTGAC
CCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTATACGATGCTAAAATTTTACAAAAATTA
Found at i:4829 original size:22 final size:20
Alignment explanation
Indices: 4777--4817 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
4767 TTAGCCACAA
4777 TACTCATAAAAATATATAAT
1 TACTCATAAAAATATATAAT
4797 TACTCATAAAAATATATAAT
1 TACTCATAAAAATATATAAT
4817 T
1 T
4818 CAACGTCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (20 bp):
TACTCATAAAAATATATAAT
Found at i:5731 original size:330 final size:328
Alignment explanation
Indices: 4797--6724 Score: 1792
Period size: 330 Copynumber: 5.8 Consensus size: 328
4787 AATATATAAT
* * * * * * *
4797 TACTCATAAAA-ATATATAATTCAACGTCTAAAAGATTGAAGGGCTTCTCACGCTTCTAATATCG
1 TACTCATAAAATATATATAATTCAATGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCG
* ** * * **
4861 TTTTTCCTATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAAATGCTCACAGAA
66 TTTTT-C-ATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA-AA
* * *
4926 ACAAATCCTTAAAT-CAAGCGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTTT
128 ACAAATCCTTAAATCCAA-TGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCT
* * * * * * * *
4990 TGCCACCAAAAATCATGCAAAACTAA-CCTGGGGTCCTGGAACGCGTTTTTTGCCAAAAAAC-TG
192 CGGCGCCAAAAATCATGCAAAACTAAGTC-GGGG-CCCGAAACGCGTTTTTAGCCAAAAACCATG
**
5053 -TGATGGTACACGATTTCGGCTAAAATTTTGCAAAAA-TGACCC-AAAATATTTTGT-CTCAATT
255 ATGATTATACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAA-ATTTT-TCCTCAATT
* * * *
5114 TGTAGCCACAA
318 TTTGGCTAAAA
* ** * *
5125 CACTCATAAAATATATATAATTCAACACCAAAAAGACTGGAGGACTTTTCACGCTTTTAATATCC
1 TACTCATAAAATATATATAATTCAATGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCG
*
5190 TTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAAATTCAGA-GACTCGTAAAAA
66 TTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG-CTCGT-AAAA
* * *
5254 CAAATCCTTAAATTCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCTCG
129 CAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCG
** * * *
5319 GCGGAAAAAATCATGCAAAACTAAGCCTGGGCCTCGAAACGCGTTTTTAACCAAAAACCATGATG
194 GCGCCAAAAATCATGCAAAACTAAGTCGGGGCC-CGAAACGCGTTTTTAGCCAAAAACCATGATG
* *
5384 ATTAGTACACAATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCGACAATTTTT
258 ATTA-TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCC-TCAATTTTT
5449 GGCTAAAA
321 GGCTAAAA
* * * *
5457 TACTCATAAAATATATATAATTTAATGCCAAAAAAATTGGAGAACTTTTCACGCTTTTAATATCA
1 TACTCATAAAATATATATAATTCAATGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCG
* * * * *
5522 TTTTT-AT-TATTTTCTAAATTGATTTTTAATTAAATCGAAATAAGATTCAGATGCTCATAAAAT
66 TTTTTCATAT-TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA-
* ** * * * * *
5585 CAAATTCTTAAATCCAATGTTTCTGATATTTGATTAGATGAATATGGATATCTCAAAGAGTCTTG
129 CAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCG
* * * *
5650 GCGCCAAAAATCACGCAAAACTGAGTCGGGTCCCGAAACGCGATTTTAGCCAAAAACCATGATGA
194 GCGCCAAAAATCATGCAAAACTAAGTCGGGGCCCGAAACGCGTTTTTAGCCAAAAACCATGATGA
* * * * * *
5715 TTATCAAACGATTTCGGCTAGAATTTTACAAAAATTGACTCG-AAAGTTATTTCCTCAATTTTTA
259 TTAT-ACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATT-TTTCCTCAATTTTTG
* *
5779 GCCACAA
322 GCTAAAA
* * * * ** *
5786 CACTCATTAAAAT-TATATAATTCAACAG-CAATAAGATT-GAAGAGCTTTTCATTCTTCTAATA
1 TACTCA-TAAAATATATATAATTCAA-TGCCAAAAAGATTGGAGGA-CTTTTCACGCTTTTAATA
* * * *
5848 TCGTTTTTCCAATTATTTTTC-GAATCAA-TTCTGATTAAATCGAAACATGATTCAGATGCTTGT
63 TCGTTTTT-C-A-TATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
*** * * *
5911 TTTAGAATTCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT
125 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGT
* * * * *
5976 CTCAGCGCCAAAATTCATGCAACACT--GTACGGGGAGCCCGAAACACGTTTTTAGCAAAAAAAA
190 CTCGGCGCCAAAAATCATGCAAAACTAAGT-C-GGG-GCCCGAAACGCGTTTTTAGC-----CAA
* * * * * * **
6039 AAACCTCAAT-TTCGACTAACTTACACGATTTCTGCTAATATTTTGTAAAAATTGACCAGAAGTA
247 AAA-C-C-ATGAT-GA-TTA--TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAA
*
6103 TTTTTCCTCAATTTTTGTCTAAAA
305 TTTTTCCTCAATTTTTGGCTAAAA
* * * *
6127 TAGTCATAAAATATATATATTTCAATGCCAAAAAGATTGCAGGACTTTTCACTCTTTTAATATCG
1 TACTCATAAAATATATATAATTCAATGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCG
* * * * *
6192 TTTTTCATATTTTTCTGATTTAGTTTCAAATTAAATCAAAACAAGATTCAGATGCTTGTAAAAAC
66 TTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-AAAAC
* * * * * *
6257 ACATCCTTAAATGCAATGTGGCTGAGATTTGATTAAATAAATATAGATTTTTCAAGGAGTCTCGA
130 AAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGG
* * *
6322 CGCCAAAAATCATGCAATACTAAGTCGGGGCCCAAAACGCGTTTTTCGCAAAAAAAAAAAAAAAA
195 CGCCAAAAATCATGCAAAACTAAGTCGGGGCCCGAAACGCGTTTTTAGC----------------
* * * * * * *
6387 AAAATAACCGTAATGGTTATTACACGATTTCGACTAAAATTTTGCAAAAAATGACCAGAAAAATT
244 CAAA-AACCATGATGATTA-TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATT
*
6452 TTTCCTCAATTTTTGACTAAAA
307 TTTCCTCAATTTTTGGCTAAAA
* *
6474 TACTCATGAAAATATATATAATTTAATGCCAAAAAGATTGGAGGACTTTTCACGCTTTTCATATC
1 TACTCAT-AAAATATATATAATTCAATGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATC
* *
6539 GTTTTTCATATTTTTTTGAATTAATTTGTAATTAAATCGAAACAAGATAT-AGATGCTCGTAAAA
65 GTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGAT-TCAGATGCTCGTAAAA
* * * * * * * **
6603 CAAATCATTAAATGCAATGTGGATGAGATTTGATTAGATTAATATGGATATCTCAAGGATTCTTA
129 CAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCG
* * * * * * *
6668 ACGCAAAAAATCATGCAAAACTGACTTGGGGCCCTGGAACGTGTTTTTAGCCAAAAA
194 GCGCCAAAAATCATGCAAAACTAAGTCGGGGCCC-GAAACGCGTTTTTAGCCAAAAA
6725 TCGTGATGTT
Statistics
Matches: 1311, Mismatches: 223, Indels: 129
0.79 0.13 0.08
Matches are distributed among these distances:
326 3 0.00
327 146 0.11
328 24 0.02
329 119 0.09
330 187 0.14
331 184 0.14
332 87 0.07
333 6 0.00
334 1 0.00
336 5 0.00
337 1 0.00
338 10 0.01
339 9 0.01
340 58 0.04
341 174 0.13
342 8 0.01
343 2 0.00
347 153 0.12
348 117 0.09
349 3 0.00
350 2 0.00
351 10 0.01
352 2 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (328 bp):
TACTCATAAAATATATATAATTCAATGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCG
TTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAACA
AATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGC
GCCAAAAATCATGCAAAACTAAGTCGGGGCCCGAAACGCGTTTTTAGCCAAAAACCATGATGATT
ATACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTA
AAA
Found at i:5925 original size:661 final size:660
Alignment explanation
Indices: 4797--6691 Score: 1734
Period size: 661 Copynumber: 2.8 Consensus size: 660
4787 AATATATAAT
* * * * * * *
4797 TACTCATAAAA-ATATATAATTCAACGTCTAAAAGATTGAAGGGCTTCTCACGCTTCTAATATCG
1 TACTCATAAAATATATATAATTTAATGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATC-
* * * * * *
4861 TTTTTCCTATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAAATGCTCACAGAA
65 ATTTT--TATTATTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATA-AA
* * *
4926 ACAAATCCTTAAATCAAGCGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTTTT
127 ACAAATCCTTAAATCAA-TGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTT
* * * * * * *
4991 GCCACCAAAAATCATGCAAAACTAACCTGGGGTCCTGGAACGCGTTTTTTGCCAAAAAACTGTGA
191 GACGCCAAAAATCATGCAAAACTAA-GTCGGGTCCCGAAACGCGTTTTTAGCCAAAAAACTGTGA
* * * *
5056 TGGTACACGATTTCGGCTAAAATTTTGCAAAAATGACCCAAAATATTTTGTCTCAATTTGTAGCC
255 TGATAAACGATTTCGGCTAAAATTTTACAAAAATGACCCAAAATATTTTGCCTCAATTTGTAGCC
* *
5121 ACAACACTCATAAAATATATATAATTCAACACCAAAAAGACTGGAGGACTTTTCACGCTTTTAAT
320 ACAACACTCATAAAATATATATAATTCAACACCAAAAAGACTGAAGGACTTTTCACGCTTCTAAT
*
5186 ATCCTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAAATTCAGAGACTCGTAA
385 ATCCTTTTTCATATTTTTCTGAATCAATTTCTAATTAAATCGAAACAAAATTCAGAGACTCGTAA
*
5251 AAACAAATCCTTAAATTCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGAAGTC
450 AAACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGAAGTC
* * * * **
5316 TCGGCGGAAAAAATCATGCAAAACT-AAGCCTGG-GCCTCGAAACGCGTTTTT-AACCAAAAA-C
515 TCAGCGCAAAAAATCATGCAAAACTGAA-CCGGGAGCC-CGAAACACGTTTTTAAAAAAAAAACC
* *
5377 -C-ATGAT-GA-TTA-GTACACAATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTT
578 TCAAT-ATCGACTAACGTACACAATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAAAATTTTT
5437 CCGACAATTTTTGGCTAAAA
642 CC-ACAATTTTTGGCTAAAA
* * *
5457 TACTCATAAAATATATATAATTTAATGCCAAAAAAATTGGAGAACTTTTCACGCTTTTAATATCA
1 TACTCATAAAATATATATAATTTAATGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCA
* * *
5522 TTTTTATTATTTTCTAAATTGATTTTTAATTAAATCGAAATAAGATTCAGATGCTCATAAAATCA
66 TTTTTATTATTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAA-CA
* ** * * * * *
5587 AATTCTTAAATCCAATGTTTCTGATATTTGATTAGATGAATATGGATATCTCAAAGAGTCTTGGC
130 AATCCTTAAAT-CAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGAC
* * * * *
5652 GCCAAAAATCACGCAAAACTGAGTCGGGTCCCGAAACGCGATTTTAGCCAAAAACCATGATGATT
194 GCCAAAAATCATGCAAAACTAAGTCGGGTCCCGAAACGCGTTTTTAGCCAAAAAAC-TG-TGATG
* * * *
5717 ATCAAACGATTTCGGCTAGAATTTTACAAAAATTGACTCGAAAGT-TATTT-CCTCAATTTTTAG
257 AT-AAACGATTTCGGCTAAAATTTTACAAAAA-TGAC-CCAAAATAT-TTTGCCTCAATTTGTAG
* * * **
5780 CCACAACACTCATTAAAAT-TATATAATTCAACAGCAATAAGATTGAA-GAGCTTTTCATTCTTC
318 CCACAACACTCA-TAAAATATATATAATTCAACACCAAAAAGACTGAAGGA-CTTTTCACGCTTC
* * **
5843 TAATATCGTTTTTCCAATTATTTTTC-GAATCAA-TTCTGATTAAATCGAAACATGATTCAGATG
381 TAATATCCTTTTT-C-A-TATTTTTCTGAATCAATTTCTAATTAAATCGAAACAAAATTCAGA-G
* *** * * * *
5906 -CTTGT-TTTAGAATTCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTC
442 ACTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTC
* * * * * *
5969 AAGGAGTCTCAGCGCCAAAATTCATGCAACACTGTACGGGGAGCCCGAAACACGTTTTTAGCAAA
507 AAGAAGTCTCAGCGCAAAAAATCATGCAAAACTGAACCGGGAGCCCGAAACACGTTTTT----AA
* * * * * *
6034 AAAAAAAACCTCAATTTCGACTAACTTACACGATTTCTGCTAATATTTTGTAAAAATTGACCAGA
568 AAAAAAAACCTCAATATCGACTAACGTACACAATTTCGGCTAAAATTTTGCAAAAATTGACCAGA
** * *
6099 AGTATTTTTCCTCAATTTTTGTCTAAAA
633 AAAATTTTTCCACAATTTTTGGCTAAAA
* * *
6127 TAGTCATAAAATATATAT-ATTTCAATGCCAAAAAGATTGCAGGACTTTTCACTCTTTTAATATC
1 TACTCATAAAATATATATAATTT-AATGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATC
* * * * * * **
6191 GTTTTTCA-TATTTTTCTGATTTAGTTTCAAATTAAATCAAAACAAGATTCAGATGCTTGTAAAA
65 ATTTTT-ATTA-TTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCAT-AAA
* * * * *
6255 ACACATCCTTAAATGCAATGTGGCTGAGATTTGATTAAATAAATATAGATTTTTCAAGGAGTCTC
127 ACAAATCCTTAAAT-CAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTT
* * * *
6320 GACGCCAAAAATCATGCAATACTAAGTCGGGGCCCAAAACGCGTTTTTCGCAAAAAAAAAAAAAA
191 GACGCCAAAAATCATGCAAAACTAAGTCGGGTCCCGAAACGCGTTTTTAGC--------------
* * * * * * *
6385 AAAAAATAACCGTAATGGTTATTACACGATTTCGACTAAAATTTTGCAAAAAATGA-CCAGAAAA
242 -CAAAA-AACTGTGAT-G--A-TAAACGATTTCGGCTAAAATTTTAC-AAAAATGACCCA-AAAT
* * * * * * ** *
6449 ATTTTTCCTCAATTT-TTGACTAAAATACTCATGAAAATATATATAATTTAATGCCAAAAAGATT
299 ATTTTGCCTCAATTTGTAG-CCACAACACTCAT-AAAATATATATAATTCAACACCAAAAAGACT
* * * * * * *
6513 GGAGGACTTTTCACGCTTTTCATATCGTTTTTCATATTTTTTTGAATTAATTTGTAATTAAATCG
362 GAAGGACTTTTCACGCTTCTAATATCCTTTTTCATATTTTTCTGAATCAATTTCTAATTAAATCG
* * * * *
6578 AAACAAGATAT-AGATG-CTCGT-AAAACAAATCATTAAATGCAATGTGGATGAGATTTGATTAG
427 AAACAAAAT-TCAGA-GACTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAG
* * * * * * *
6640 ATTAATATGGATATCTCAAGGATTCTTAACGCAAAAAATCATGCAAAACTGA
490 ATGAATATAGATATTTCAAGAAGTCTCAGCGCAAAAAATCATGCAAAACTGA
6692 CTTGGGGCCC
Statistics
Matches: 990, Mismatches: 182, Indels: 98
0.78 0.14 0.08
Matches are distributed among these distances:
657 30 0.03
658 120 0.12
659 8 0.01
660 43 0.04
661 209 0.21
662 48 0.05
663 8 0.01
664 8 0.01
666 7 0.01
667 1 0.00
668 2 0.00
669 8 0.01
670 78 0.08
671 177 0.18
672 4 0.00
685 3 0.00
686 14 0.01
687 17 0.02
688 152 0.15
689 51 0.05
690 2 0.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (660 bp):
TACTCATAAAATATATATAATTTAATGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCA
TTTTTATTATTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAACAA
ATCCTTAAATCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGACGC
CAAAAATCATGCAAAACTAAGTCGGGTCCCGAAACGCGTTTTTAGCCAAAAAACTGTGATGATAA
ACGATTTCGGCTAAAATTTTACAAAAATGACCCAAAATATTTTGCCTCAATTTGTAGCCACAACA
CTCATAAAATATATATAATTCAACACCAAAAAGACTGAAGGACTTTTCACGCTTCTAATATCCTT
TTTCATATTTTTCTGAATCAATTTCTAATTAAATCGAAACAAAATTCAGAGACTCGTAAAAACAA
ATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCTCAGCG
CAAAAAATCATGCAAAACTGAACCGGGAGCCCGAAACACGTTTTTAAAAAAAAAACCTCAATATC
GACTAACGTACACAATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAAAATTTTTCCACAATTT
TTGGCTAAAA
Found at i:6165 original size:341 final size:340
Alignment explanation
Indices: 5722--6690 Score: 945
Period size: 341 Copynumber: 2.8 Consensus size: 340
5712 TGATTATCAA
* * * * * * *
5722 ACGATTTCGGCTAGAATTTTACAAAAATTGACTC-G-AAAGTTATTTCCTCAATTTTT-AGCCAC
1 ACGATTTCGACTAAAATTTTGCAAAAAATGAC-CAGAAAAATT-TTTCCTCAATTTTTGA-CTAA
* * * * * *
5784 AACACTCATTAAAAT-TATATAATTCAACAG-CAATAAGATTGAA-GAGCTTTTCATTCTTCTAA
63 AATACTCA-TAAAATATATATATTTCAA-TGCCAAAAAGATTGAAGGA-CTTTTCACTCTTTTAA
* *
5846 TATCGTTTTTCCAATTATTTTTCGAATCAATTCTGATTAAATCGAAACATGATTCAGATGCTTGT
125 TATCGTTTTT-CAATTATTTTTCGAATTAATTCTGATTAAATCGAAACAAGATTCAGATGCTTGT
** * * * * *
5911 TTTAGAATTCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT
189 TAAAAAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATAAATATAGATATTTCAAGGAGT
* * *
5976 CTCAGCGCCAAAATTCATGCAACACTGTACGGGGAGCCCGAAACACGTTTTTAGC-AAAAAAAAA
254 CTCAGCGCCAAAAATCATGCAAAACTGT-C-GGG-GCCCAAAACACGTTTTTAGCAAAAAAAAAA
**** ** * *
6040 AACCTCAATTTCGA-C-TAA-CTTAC
316 AAAAAAAAAAT-AACCGTAATATTAC
* * * ** *
6063 ACGATTTCTG-CTAATATTTTGTAAAAATTGACCAGAAGTATTTTTCCTCAATTTTTGTCTAAAA
1 ACGATTTC-GACTAAAATTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTGACTAAAA
* *
6127 TAGTCATAAAATATATATATTTCAATGCCAAAAAGATTGCAGGACTTTTCACTCTTTTAATATCG
65 TACTCATAAAATATATATATTTCAATGCCAAAAAGATTGAAGGACTTTTCACTCTTTTAATATCG
* * ** *
6192 TTTTTC-A-TATTTTTCTGATTTAGTTTCAAATTAAATCAAAACAAGATTCAGATGCTTG-TAAA
130 TTTTTCAATTATTTTTC-GAATTA-ATTCTGATTAAATCGAAACAAGATTCAGATGCTTGTTAAA
* *
6254 AACACATCCTTAAATGCAATGTGGCTGAGATTTGATTAAATAAATATAGATTTTTCAAGGAGTCT
193 AA-A-ATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATAAATATAGATATTTCAAGGAGTCT
* * *
6319 C-GACGCCAAAAATCATGCAATACTAAGTCGGGGCCCAAAACGCGTTTTTCGCAAAAAAAAAAAA
256 CAG-CGCCAAAAATCATGCAAAACT--GTCGGGGCCCAAAACACGTTTTTAGCAAAAAAAAAAAA
6383 AAAAAAAATAACCGTAATGGTTATTAC
318 AAAAAAAATAACCGTAA----TATTAC
6410 ACGATTTCGACTAAAATTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTGACTAAAAT
1 ACGATTTCGACTAAAATTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTGACTAAAAT
* * *
6475 ACTCATGAAAATATATATAATTT-AATGCCAAAAAGATTGGAGGACTTTTCACGCTTTTCATATC
66 ACTCAT-AAAATATATAT-ATTTCAATGCCAAAAAGATTGAAGGACTTTTCACTCTTTTAATATC
*
6539 GTTTTTCATATT-TTTTT-GAATTAATT-TGTAATTAAATCGAAACAAGATAT-AGATGCTCG-T
129 GTTTTTCA-ATTATTTTTCGAATTAATTCTG--ATTAAATCGAAACAAGAT-TCAGATGCTTGTT
* * * * * *
6599 AAAACAAATCATTAAATGCAATGTGGATGAGATTTGATTAGATTAATATGGATATCTCAAGGATT
190 AAAA-AAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATAAATATAGATATTTCAAGGAGT
* * *
6664 CTTAACGCAAAAAATCATGCAAAACTG
254 CTCAGCGCCAAAAATCATGCAAAACTG
6691 ACTTGGGGCC
Statistics
Matches: 520, Mismatches: 75, Indels: 62
0.79 0.11 0.09
Matches are distributed among these distances:
338 8 0.02
339 8 0.02
340 59 0.11
341 187 0.36
342 10 0.02
343 2 0.00
345 1 0.00
346 1 0.00
347 139 0.27
348 92 0.18
349 6 0.01
350 6 0.01
351 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.34
Consensus pattern (340 bp):
ACGATTTCGACTAAAATTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTGACTAAAAT
ACTCATAAAATATATATATTTCAATGCCAAAAAGATTGAAGGACTTTTCACTCTTTTAATATCGT
TTTTCAATTATTTTTCGAATTAATTCTGATTAAATCGAAACAAGATTCAGATGCTTGTTAAAAAA
ATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATAAATATAGATATTTCAAGGAGTCTCAGCG
CCAAAAATCATGCAAAACTGTCGGGGCCCAAAACACGTTTTTAGCAAAAAAAAAAAAAAAAAAAA
TAACCGTAATATTAC
Found at i:6679 original size:347 final size:347
Alignment explanation
Indices: 6059--6685 Score: 929
Period size: 347 Copynumber: 1.8 Consensus size: 347
6049 TTCGACTAAC
* * * ** *
6059 TTACACGATTTCTGCTAATATTTTGTAAAAATTGACCAGAAGTATTTTTCCTCAATTTTTGTCTA
1 TTACACGATTTCTGCTAAAATTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTGACTA
* *
6124 AAATAGTCATAAAATATATATATTTCAATGCCAAAAAGATTGCAGGACTTTTCACTCTTTTAATA
66 AAATACTCATAAAATATATATATTTCAATGCCAAAAAGATTGCAGGACTTTTCACGCTTTTAATA
* * *
6189 TCGTTTTTCATATTTTTCTGATTTAGTTTCAAATTAAATCAAAACAAGATTCAGATGCTTGTAAA
131 TCGTTTTTCATATTTTTCTGAATTAATTTCAAATTAAATCAAAACAAGATTCAGATGCTCGTAAA
* * * * *
6254 AACACATCCTTAAATGCAATGTGGCTGAGATTTGATTAAATAAATATAGATTTTTCAAGGAGTCT
196 AACAAATCATTAAATGCAATGTGGATGAGATTTGATTAAATAAATATAGATATCTCAAGGAGTCT
* *
6319 CGACGCCAAAAATCATGCAATACTAAGTCGGGGCCCAAAACGCGTTTTTCGCAAAAAAAAAAAAA
261 CAACGCAAAAAATCATGCAATACTAAGTCGGGGCCCAAAACGCGTTTTTCGCAAAAAAAAAAAAA
6384 AAAAAAATAACCGTAATGGTTA
326 AAAAAAATAACCGTAATGGTTA
6406 TTACACGATTTC-GACTAAAATTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTGACT
1 TTACACGATTTCTG-CTAAAATTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTGACT
* *
6470 AAAATACTCATGAAAATATATATAATTT-AATGCCAAAAAGATTGGAGGACTTTTCACGCTTTTC
65 AAAATACTCAT-AAAATATATAT-ATTTCAATGCCAAAAAGATTGCAGGACTTTTCACGCTTTTA
* ** *
6534 ATATCGTTTTTCATATTTTTTTGAATTAATTTGTAATTAAATCGAAACAAGATAT-AGATGCTCG
128 ATATCGTTTTTCATATTTTTCTGAATTAATTTCAAATTAAATCAAAACAAGAT-TCAGATGCTCG
* * *
6598 T-AAAACAAATCATTAAATGCAATGTGGATGAGATTTGATTAGATTAATATGGATATCTCAAGGA
192 TAAAAACAAATCATTAAATGCAATGTGGATGAGATTTGATTAAATAAATATAGATATCTCAAGGA
* *
6662 TTCTTAACGCAAAAAATCATGCAA
257 GTCTCAACGCAAAAAATCATGCAA
6686 AACTGACTTG
Statistics
Matches: 247, Mismatches: 29, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
346 1 0.00
347 141 0.57
348 100 0.40
349 5 0.02
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (347 bp):
TTACACGATTTCTGCTAAAATTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTGACTA
AAATACTCATAAAATATATATATTTCAATGCCAAAAAGATTGCAGGACTTTTCACGCTTTTAATA
TCGTTTTTCATATTTTTCTGAATTAATTTCAAATTAAATCAAAACAAGATTCAGATGCTCGTAAA
AACAAATCATTAAATGCAATGTGGATGAGATTTGATTAAATAAATATAGATATCTCAAGGAGTCT
CAACGCAAAAAATCATGCAATACTAAGTCGGGGCCCAAAACGCGTTTTTCGCAAAAAAAAAAAAA
AAAAAAATAACCGTAATGGTTA
Found at i:7925 original size:332 final size:331
Alignment explanation
Indices: 6733--8226 Score: 1264
Period size: 331 Copynumber: 4.6 Consensus size: 331
6723 AATCGTGATG
* * * * * *
6733 TTCCTCAAGTTTT-GACTAAAATACTCATAAAAAATATAAAATTCATCGCCAAAAATATTGAAGG
1 TTCCTCAATTTTTGGA-TAAAATACTCATAAAATATATATAATTCAACACCAAAAAGATTGAAGG
* * * * * * *
6797 GTTTTTTATGCTTCTAATATCATTTTTCCTACTTTTTTCGAATTAATTTCTAATTAAATCGAAAC
65 GCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTC-AATTAATTTCTAATTAAATCGAAAC
* * * * * *
6862 AAGATTTAGATGCTCGTAAAAA-AAATCCTTAATTCGAATGTGGCTGAGATTTGATTAGATAAAT
129 AAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGATT
* * * * * * * * * *
6926 ATAGATATTTGC-ATGA-TTTTTG-GCCAAAAATCATGCAAAACTGACCCGAGGCCTCAGAACGC
194 ATAAATATCT-CAAGGAGTGTCTGCGCCAAAAATCAGGCAAAACTGAGCCGGGGCCCCAAAACGC
* * * * * * *
6988 AG-TTTTGGCAAAAAAAAAAAACCGTGAT-GTTA-T--ACGATTTCGGCTAATATTTTGCAAAAA
258 -GTTTTTAGC------CAAAAACTGTGATGGTTATTACACGGTTTTGACTAAAATTTTGCAAAAA
** * *
7048 TTGACCCAAAATATTT
316 TTGACCTGAAAGATAT
* * * ** * * ** *
7064 TTCATCAACTTTTAGCCACAATACTCATAAAAAATATATAATTCAACGGCAAACAGATTGAAGGG
1 TTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTCAACACCAAAAAGATTGAAGGG
* * * *
7129 CTTTTCATGCTTCTAATA-CTGCTTTTTCTTATTTTTTTCCTAATTAATTTCTAATTAAAACGAA
66 CTTTTCACGCTTTTAATATC-G-TTTTTCATATTTTTTT-C-AATTAATTTCTAATTAAATCGAA
* * * *
7193 ACATGATTCAGATGCTTGT-------AA-----AAA--CAA--TGGCTGGGATTTGGTT---TGA
127 ACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGA
* * * * * ** * *
7239 ATATAAATATTTCAAGGAGTTTCGGCACC--AAATCATTCAAAACTGA-ACTGGGCCCCAAAACG
192 TTATAAATATCTCAAGGAGTGTCTGCGCCAAAAATCAGGCAAAACTGAGCCGGGGCCCCAAAACG
* * * *
7301 CGTTTTTAGCCAAAAACCGTGATGATTATTACAC-GATTTGACTAAAATTTTGCAAAAATTAACC
257 CGTTTTTAGCCAAAAACTGTGATGGTTATTACACGGTTTTGACTAAAATTTTGCAAAAATTGACC
7365 TGAAAGATAT
322 TGAAAGATAT
* ** * * *
7375 TTCCTCAAGTTTATCCAT--AATACTCAATAAAAT-T-TATAATTCGACGCCAAAAAGATAGAAG
1 TTCCTCAA-TTTTTGGATAAAATACTC-ATAAAATATATATAATTCAACACCAAAAAGATTGAAG
* * *
7436 GGCTTTTCGA-GCTATTAATATCGTTTTTCATATTTTTTTTGAATTAATTTCTAATT-AATCAAA
64 GGCTTTTC-ACGCTTTTAATATCGTTTTTCATA-TTTTTTTCAATTAATTTCTAATTAAATCGAA
* ** * *
7499 ACAAGATTCAGATGCTCGT-AAAACAAATCCTTAAATGGAATGTGGCTAAGATTTTATTAGATGA
127 ACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGA
* * * * * *
7563 ATATAAATATTTCAAGGAGTGTCTGCGCCAAAAATCATGCAAAACTGGGCCGGGGCCCCGAAACA
192 TTATAAATATCTCAAGGAGTGTCTGCGCCAAAAATCAGGCAAAACTGAGCCGGGGCCCCAAAACG
* * * * *
7628 CGTTTTTAGCCAAAAACTGTGATGGTTAGTGCACGGTTTTGGCTAAAATTCTGCAAAAAAATGAC
257 CGTTTTTAGCCAAAAACTGTGATGGTTATTACACGGTTTTGACTAAAATTTTGC-AAAAATTGAC
*
7693 CTGAAAAAT-T
321 CTGAAAGATAT
*
7703 CTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAACACCAAAACA-ATTGGAA
1 -TTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTCAACACCAAAA-AGATT-GAA
* **
7767 -GACTTTTCACGCTTTTAATATTATTTTTCATATTTTTTTCAATTAATTTCTAATTAAATCGAAA
63 GGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCAATTAATTTCTAATTAAATCGAAA
*
7831 CAAGATTCAGATGCTTGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAT
128 CAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAT
** * * * *
7896 TATGGATATCTCAAGGAGTCT-TCGCGCCAAAAATTAGGCAAAACTGAGCCGGGGTCCTAAAACG
193 TATAAATATCTCAAGGAGTGTCT-GCGCCAAAAATCAGGCAAAACTGAGCCGGGGCCCCAAAACG
* * * * *
7960 CATTTTTAGCCAAAAACTGTGATGGTTATTACATGATTTCGACTAAAATTTTGTAAAAATTGA-C
257 CGTTTTTAGCCAAAAACTGTGATGGTTATTACACGGTTTTGACTAAAATTTTGCAAAAATTGACC
*
8024 TCGAAAGATGT
322 T-GAAAGATAT
* * * * *
8035 TTCCTCAATTTTTGGTTAAAATACTTATAAAAAATATATAATTCAACATCAAAAAGATTGAATGG
1 TTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTCAACACCAAAAAGATTGAAGGG
* * * * *
8100 CTTTTGACG-TTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCTAATTAAATCGAAAAA
66 CTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTC-AATTAATTTCTAATTAAATCGAAACA
* * * * * *
8164 AGATTTAGATACTCGTAAAAACAAATTCATAAATCCAATGTTGCTGAGGTTTGGTTAGATGAT
130 AGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAT
8227 GTAAAGTATT
Statistics
Matches: 952, Mismatches: 155, Indels: 112
0.78 0.13 0.09
Matches are distributed among these distances:
306 22 0.02
307 15 0.02
308 20 0.02
309 50 0.05
310 11 0.01
311 43 0.05
312 7 0.01
313 1 0.00
314 19 0.02
315 32 0.03
316 4 0.00
317 5 0.01
318 14 0.01
319 2 0.00
320 2 0.00
321 12 0.01
322 2 0.00
324 29 0.03
326 15 0.02
327 44 0.05
328 23 0.02
329 31 0.03
330 61 0.06
331 293 0.31
332 156 0.16
333 39 0.04
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (331 bp):
TTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTCAACACCAAAAAGATTGAAGGG
CTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCAATTAATTTCTAATTAAATCGAAACAA
GATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGATTAT
AAATATCTCAAGGAGTGTCTGCGCCAAAAATCAGGCAAAACTGAGCCGGGGCCCCAAAACGCGTT
TTTAGCCAAAAACTGTGATGGTTATTACACGGTTTTGACTAAAATTTTGCAAAAATTGACCTGAA
AGATAT
Found at i:8901 original size:2 final size:2
Alignment explanation
Indices: 8894--8926 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
8884 ATAAGATAAG
8894 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
8927 AAAGTTCAAT
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:9110 original size:23 final size:23
Alignment explanation
Indices: 9084--9127 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
9074 CACTGGAAAT
*
9084 ATTA-GATATTTATCCAGATTTGC
1 ATTACGATATTT-TCCAAATTTGC
*
9107 ATTACTATATTTTCCAAATTT
1 ATTACGATATTTTCCAAATTT
9128 CCAGATGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.48
Consensus pattern (23 bp):
ATTACGATATTTTCCAAATTTGC
Found at i:10273 original size:30 final size:27
Alignment explanation
Indices: 10188--10270 Score: 121
Period size: 30 Copynumber: 3.0 Consensus size: 27
10178 GTTAATTTAG
10188 ACTTATTATTATTATAATAATTATTAA
1 ACTTATTATTATTATAATAATTATTAA
*
10215 ACTTATTATTAGTGGTATTATAATTATTAA
1 ACTTATTATTA-T--TATAATAATTATTAA
*
10245 ACTTATTATTATAATAATAATTATTA
1 ACTTATTATTATTATAATAATTATTA
10271 TTAGTGGTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
27 23 0.46
28 1 0.02
29 1 0.02
30 25 0.50
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (27 bp):
ACTTATTATTATTATAATAATTATTAA
Done.