Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011794.1 Corchorus capsularis cultivar CVL-1 contig11815, 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: 153445
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5421 original size:23 final size:24
Alignment explanation
Indices: 5395--5442 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
5385 ACAATGACGA
*
5395 CAAAATCATCAAAGC-A-ATGAAAT
1 CAAAATCA-AAAAGCGATATGAAAT
5418 CAAAATCAAAAAGCGATATGAAAT
1 CAAAATCAAAAAGCGATATGAAAT
5442 C
1 C
5443 GATGAAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 9 0.41
24 8 0.36
ACGTcount: A:0.56, C:0.17, G:0.10, T:0.17
Consensus pattern (24 bp):
CAAAATCAAAAAGCGATATGAAAT
Found at i:6646 original size:24 final size:24
Alignment explanation
Indices: 6619--6666 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
6609 TTTATTAAAG
6619 AAAAAA-AAAGTTTAATCGAAAAAT
1 AAAAAAGAAA-TTTAATCGAAAAAT
6643 AAAAAAGAAATTTAATCGAAAAAT
1 AAAAAAGAAATTTAATCGAAAAAT
6667 TGCTTTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.67, C:0.04, G:0.08, T:0.21
Consensus pattern (24 bp):
AAAAAAGAAATTTAATCGAAAAAT
Found at i:7277 original size:18 final size:16
Alignment explanation
Indices: 7255--7286 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
7245 ATTAAAACCA
7255 TATATATGTCAAGATC
1 TATATATGTCAAGATC
7271 TATATATGTCAAGATC
1 TATATATGTCAAGATC
7287 GCTCTTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (16 bp):
TATATATGTCAAGATC
Found at i:12460 original size:2 final size:2
Alignment explanation
Indices: 12453--12489 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12443 ATGTATGAAT
12453 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12490 TTCATTTGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14023 original size:29 final size:29
Alignment explanation
Indices: 13972--14063 Score: 89
Period size: 28 Copynumber: 3.1 Consensus size: 29
13962 TTGATGGGGT
*
13972 AAAACGTCCTAAAATTGAA-TTCAATGAGC
1 AAAACGTCC-AAAATTAAAGTTCAATGAGC
* **
14001 AAAATGTCCAAAATTAAAGTTCAGGGA-C
1 AAAACGTCCAAAATTAAAGTTCAATGAGC
* *
14029 AAAACGTCCAAACACTACAAGTTCAATGAGG
1 AAAACGTCCAAA-ATTA-AAGTTCAATGAGC
14060 AAAA
1 AAAA
14064 TGGTAAATAC
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
28 20 0.40
29 17 0.34
30 9 0.18
31 4 0.08
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.20
Consensus pattern (29 bp):
AAAACGTCCAAAATTAAAGTTCAATGAGC
Found at i:40705 original size:2 final size:2
Alignment explanation
Indices: 40700--40726 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40690 ATATATTGAA
40700 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 A
40727 ATCATCATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43808 original size:13 final size:13
Alignment explanation
Indices: 43790--43815 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43780 GAGACAGCAC
43790 TGCAAGCAAAGGA
1 TGCAAGCAAAGGA
43803 TGCAAGCAAAGGA
1 TGCAAGCAAAGGA
43816 AGTCATAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.31, T:0.08
Consensus pattern (13 bp):
TGCAAGCAAAGGA
Found at i:48183 original size:51 final size:51
Alignment explanation
Indices: 48107--48208 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
48097 GCCATATCAA
48107 TACGAGATTGACAACCTGAAGATGGAGTCTCTTGATGTTTCCATCAGCAGG
1 TACGAGATTGACAACCTGAAGATGGAGTCTCTTGATGTTTCCATCAGCAGG
48158 TACGAGATTGACAACCTGAAGATGGAGTCTCTTGATGTTTCCATCAGCAGG
1 TACGAGATTGACAACCTGAAGATGGAGTCTCTTGATGTTTCCATCAGCAGG
48209 AGTAATTTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (51 bp):
TACGAGATTGACAACCTGAAGATGGAGTCTCTTGATGTTTCCATCAGCAGG
Found at i:49611 original size:2 final size:2
Alignment explanation
Indices: 49599--49654 Score: 60
Period size: 2 Copynumber: 28.0 Consensus size: 2
49589 GTGTGATAAT
* * * *
49599 TA TA TA AA TA TA TA CA TA TA TA CA TA TA TA TA TA TA CA TA TGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
49642 -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
49655 CACACACTAC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
1 1 0.02
2 42 0.95
3 1 0.02
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (2 bp):
TA
Found at i:51826 original size:2 final size:2
Alignment explanation
Indices: 51819--51848 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
51809 AGGCAAGGCC
51819 AT 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 AT
51849 TTTTTTTTTT
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):
AT
Found at i:52809 original size:89 final size:86
Alignment explanation
Indices: 52612--52823 Score: 230
Period size: 89 Copynumber: 2.4 Consensus size: 86
52602 CAGGCACAAA
* * * * *
52612 ATCCTCCACCAAATCAGTTTCCAAAGATTTTGCATCATTACTAACTAAAACTCCATTAGGAAGAT
1 ATCCTCCACCATATCAGTTTCCAAAGATTTTGCACCATAACCAACCAAAACTCCATTAGGAAGAT
*
52677 CACTGAAATTTGAATTCAAATT
66 CAC-GAAAATTGAATTCAAATT
* * * *
52699 ATCCTCTACCATAAT-ATTTTCCAAAGATTTTGCACCATAACCACCCCATAATCTCCATTAGGAA
1 ATCCTCCACCAT-ATCAGTTTCCAAAGATTTTGCACCATAACCA-ACCA-AAACTCCATTAGGAA
52763 GATCAC-AATCAATTGAATTCAAATT
63 GATCACGAA--AATTGAATTCAAATT
* * * *
52788 ATTCTCCACCCTATCAGTTTCCATAGAATTTGCACC
1 ATCCTCCACCATATCAGTTTCCAAAGATTTTGCACC
52824 TAAAAATCCT
Statistics
Matches: 103, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
87 36 0.35
88 6 0.06
89 61 0.59
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.31
Consensus pattern (86 bp):
ATCCTCCACCATATCAGTTTCCAAAGATTTTGCACCATAACCAACCAAAACTCCATTAGGAAGAT
CACGAAAATTGAATTCAAATT
Found at i:55476 original size:6 final size:6
Alignment explanation
Indices: 55465--55490 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
55455 GAAAGGAGGA
55465 GAGAAT GAGAAT GAGAAT GAGAAT GA
1 GAGAAT GAGAAT GAGAAT GAGAAT GA
55491 ATGGGTATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (6 bp):
GAGAAT
Found at i:56764 original size:30 final size:29
Alignment explanation
Indices: 56730--56788 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
56720 TCTAATAGAT
56730 TTAAGTTTGGGGCGGTTTTCTTTTCAAATG
1 TTAAGTTTGGGGCGGTTTT-TTTTCAAATG
*
56760 TTAAGTTTGGGGTGGTTTTTTTTCAAATG
1 TTAAGTTTGGGGCGGTTTTTTTTCAAATG
56789 GATTATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 10 0.36
30 18 0.64
ACGTcount: A:0.17, C:0.07, G:0.27, T:0.49
Consensus pattern (29 bp):
TTAAGTTTGGGGCGGTTTTTTTTCAAATG
Found at i:57790 original size:22 final size:22
Alignment explanation
Indices: 57764--57806 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
57754 CGCGTGCGAC
57764 CCGTGATTGCGT-GCGATCCGGA
1 CCGTGA-TGCGTCGCGATCCGGA
*
57786 CCGTGATGGGTCGCGATCCGG
1 CCGTGATGCGTCGCGATCCGG
57807 GCGCGACCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.12, C:0.28, G:0.40, T:0.21
Consensus pattern (22 bp):
CCGTGATGCGTCGCGATCCGGA
Found at i:59889 original size:18 final size:18
Alignment explanation
Indices: 59866--59900 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
59856 TGATTCCCTA
59866 TCCCTAAAAAAAATTAAT
1 TCCCTAAAAAAAATTAAT
* *
59884 TCCCTATAAACAATTAA
1 TCCCTAAAAAAAATTAA
59901 ATTATTACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (18 bp):
TCCCTAAAAAAAATTAAT
Found at i:70710 original size:18 final size:17
Alignment explanation
Indices: 70678--70725 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
70668 ATACTACTAC
70678 TATTATTAT-TAATATTA
1 TATTATTATAT-ATATTA
70695 TTATTATTATATATA-TA
1 -TATTATTATATATATTA
70712 TA-TA-TATATATATT
1 TATTATTATATATATT
70726 CCCACGTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
14 8 0.29
15 3 0.11
16 2 0.07
17 2 0.07
18 12 0.43
19 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTATTATATATATTA
Found at i:92859 original size:16 final size:16
Alignment explanation
Indices: 92840--92895 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
92830 GAATCCACGT
92840 TTCCACTTATACTTAC
1 TTCCACTTATACTTAC
** * *
92856 TTCCACCAAGACTTATTT
1 TTCCACTTATACTTA--C
92874 TTCCACTTATACTTAC
1 TTCCACTTATACTTAC
92890 TTCCAC
1 TTCCAC
92896 CAAGACTTAT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
16 18 0.60
18 12 0.40
ACGTcount: A:0.25, C:0.32, G:0.02, T:0.41
Consensus pattern (16 bp):
TTCCACTTATACTTAC
Found at i:92878 original size:34 final size:34
Alignment explanation
Indices: 92839--92906 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
92829 AGAATCCACG
92839 TTTCCACTTATACTTACTTCCACCAAGACTTATT
1 TTTCCACTTATACTTACTTCCACCAAGACTTATT
92873 TTTCCACTTATACTTACTTCCACCAAGACTTATT
1 TTTCCACTTATACTTACTTCCACCAAGACTTATT
92907 CCTCAAACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.29, G:0.03, T:0.41
Consensus pattern (34 bp):
TTTCCACTTATACTTACTTCCACCAAGACTTATT
Found at i:92879 original size:18 final size:18
Alignment explanation
Indices: 92855--92907 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
92845 CTTATACTTA
92855 CTTCCACCAAGACTTATT
1 CTTCCACCAAGACTTATT
* ** *
92873 TTTCCACTTATACTTA--
1 CTTCCACCAAGACTTATT
92889 CTTCCACCAAGACTTATT
1 CTTCCACCAAGACTTATT
92907 C
1 C
92908 CTCAAACATG
Statistics
Matches: 25, Mismatches: 8, Indels: 4
0.68 0.22 0.11
Matches are distributed among these distances:
16 12 0.48
18 13 0.52
ACGTcount: A:0.26, C:0.32, G:0.04, T:0.38
Consensus pattern (18 bp):
CTTCCACCAAGACTTATT
Found at i:92903 original size:16 final size:16
Alignment explanation
Indices: 92850--92908 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
92840 TTCCACTTAT
92850 ACTTACTTCCACCAAG
1 ACTTACTTCCACCAAG
* ** *
92866 ACTTATTTTTCCACTTAT
1 ACTTA--CTTCCACCAAG
92884 ACTTACTTCCACCAAG
1 ACTTACTTCCACCAAG
92900 ACTTA-TTCC
1 ACTTACTTCC
92909 TCAAACATGG
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
15 4 0.12
16 17 0.52
18 12 0.36
ACGTcount: A:0.27, C:0.32, G:0.03, T:0.37
Consensus pattern (16 bp):
ACTTACTTCCACCAAG
Found at i:95779 original size:322 final size:307
Alignment explanation
Indices: 95366--95986 Score: 739
Period size: 322 Copynumber: 2.0 Consensus size: 307
95356 AAATATTCAT
* * *
95366 AAAATATATATAATTCAACGCCAAAAAAATTGACGGGCTATTCTCACTTCTAATATCGTTTTTCC
1 AAAAAATATATAATTCAACCCCAAAAAAATTGACGGGCTATTCACACTTCTAATATCGTTTTTCC
** * *
95431 ATTTTTTCTCAATTAATTTCTAATTAAATTGAAACAAGATTAAGATGCTTGTAAAAACAAATCGT
66 ATTTTTTCTCAATTAATTTCTAATTAAATCAAAACAAGATTAAGATGCTCGTAAAAACAAATCCT
* * * *
95496 TAAATCGAATGTGACTGGGATTTGCTTCGATGAATATAGATATTTCAAGGAGTTTTTAC-GCCTA
131 TAAATCCAATGTGACTGAGATTTGATTCGATG-A-AT--ATA--TCAAGGAGTCTTT-CTGCC-A
* * * * **
95560 AAAGT-ATTCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGTTAAAAACCGT-GATGGCTAG
188 AAAATCATGCAAAACTAAGTCGGGGCCCCGAAACGCG-TTTTAG-CAAAAA-AATAG-T-G--A-
* * *
95623 TACACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCATCAATTTTTTGCCAAAACACTCAG
245 TA-ACGATTTCGGCTAAAAACTAACACGAAAATATTTTT-ATCAATTTTTTGCCAAAACACTCAG
* * * * * *
95688 AAAAAATATATAATTCAACCCCGAAAAGATTGATGGGTTTTTCACGCTTCTAATATCGTTTTTCC
1 AAAAAATATATAATTCAACCCCAAAAAAATTGACGGGCTATTCACACTTCTAATATCGTTTTTCC
*
95753 ATTTTTT-TCCGAATTAATTT-TAATTAAATCAAAATAAGATTAAGATGCTCGTAAAAACAAATC
66 ATTTTTTCT-C-AATTAATTTCTAATTAAATCAAAACAAGATTAAGATGCTCGTAAAAACAAATC
* **
95816 CTTATATCCAATGTGGTTGAGATTTGATTCGATGAATATATCAAGGAGTCTTTCTGCCAAAAATC
129 CTTAAATCCAATGTGACTGAGATTTGATTCGATGAATATATCAAGGAGTCTTTCTGCCAAAAATC
* *
95881 ATGCAAAACTAAGTCGGGGTCTCGAAACGCGTTTTAGCAAAAAAATAGTGATAACGATTTCGGCT
194 ATGCAAAACTAAGTCGGGGCCCCGAAACGCGTTTTAGCAAAAAAATAGTGATAACGATTTCGGCT
95946 AAAAACTAACACGAAAATATTTTTATCAATTTTTTGCCAAA
259 AAAAACTAACACGAAAATATTTTTATCAATTTTTTGCCAAA
95987 CCCGGGTTCA
Statistics
Matches: 262, Mismatches: 32, Indels: 25
0.82 0.10 0.08
Matches are distributed among these distances:
307 17 0.06
308 33 0.13
309 2 0.01
310 1 0.00
312 1 0.00
313 2 0.01
314 6 0.02
315 12 0.05
316 42 0.16
318 3 0.01
320 2 0.01
321 2 0.01
322 130 0.50
323 9 0.03
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (307 bp):
AAAAAATATATAATTCAACCCCAAAAAAATTGACGGGCTATTCACACTTCTAATATCGTTTTTCC
ATTTTTTCTCAATTAATTTCTAATTAAATCAAAACAAGATTAAGATGCTCGTAAAAACAAATCCT
TAAATCCAATGTGACTGAGATTTGATTCGATGAATATATCAAGGAGTCTTTCTGCCAAAAATCAT
GCAAAACTAAGTCGGGGCCCCGAAACGCGTTTTAGCAAAAAAATAGTGATAACGATTTCGGCTAA
AAACTAACACGAAAATATTTTTATCAATTTTTTGCCAAAACACTCAG
Found at i:96265 original size:31 final size:31
Alignment explanation
Indices: 96230--96298 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
96220 AAACAAACCC
* * *
96230 ATTTTCTTAATTAATCCTCGTGGGTAGATTT
1 ATTTTATTAATTAATCCCCGTGAGTAGATTT
96261 ATTTTATTAATTAATCCCCGTGAGTAGATTT
1 ATTTTATTAATTAATCCCCGTGAGTAGATTT
96292 ATTTTAT
1 ATTTTAT
96299 ATTGATTCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.26, C:0.12, G:0.13, T:0.49
Consensus pattern (31 bp):
ATTTTATTAATTAATCCCCGTGAGTAGATTT
Found at i:97817 original size:2 final size:2
Alignment explanation
Indices: 97810--97835 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
97800 ATCTAGTTCG
97810 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
97836 TTAAAGGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98344 original size:324 final size:320
Alignment explanation
Indices: 96349--98672 Score: 2856
Period size: 324 Copynumber: 7.2 Consensus size: 320
96339 CAATCAATTT
* *
96349 AATACTCAGAAAAAATATATAATTCAACGCCGAAAAGATTGATGGGCTTTTCACGCTTTTAATAT
1 AATACTCAGAAAAAATATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATAT
* *
96414 TGTATTTACATTTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAA
66 CGT-TTTCCA-TTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAA
* * *
96479 ACAAATCCTTATATCCAATGTGGCCGAGATTTGGTTCGATGAATATATATATATATATATTTCAA
129 ACAAATCCTTATATCCAATTTGGCTGAGATTTGGTTC----AAT-GA-A-A-ATATATATTTCAA
* * *
96544 GAAGTCTTTCTGCCAAAAATCATACAAAACTGAGCCGGAGTCTCGAAACGCGTTTTTAGCAAAAA
186 GGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGTCTCGAAACGCGTTTTTAGCAAAAA
*
96609 ACCGTGAT-G--A-T----GATTTCGGCTAAAAACTGACCC-AAAATTTTTTTTCCTTAATTTTT
251 ACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTT-CTCAATTTTT
*
96665 TGCTAA
315 TGCCAA
* * *
96671 AATACTCAG-AATAATATATAATTCAACGCCGAAAAGA-T--T-GGCTTTTCACACTTCTAATAT
1 AATACTCAGAAAAAATATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATAT
* * *
96731 CGTTTTTACATTTTTTCCAAATTAATTTTAATTAAATCAATATAAGATTCAGATGCTCGTAAAAA
66 CG-TTTTCCATTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAA
* * * * *
96796 CAAATCCTTATATCCAATGTGGCTGAGATTTAGTTCGATGAATATATATATTTCAAGGAGTATTT
130 CAAATCCTTATATCCAATTTGGCTGAGATTTGGTTCAATGAAAATATATATTTCAAGGAGTCTTT
* *
96861 CTACCAAAAATCATGCAAAACTGAGCCGGGGTCTCGAAACGCGTTTTTAGCAAAAAACCGTGAAG
195 CTGCCAAAAATCATGCAAAACTGAGCCGGGGTCTCGAAACGCGTTTTTAGCAAAAAACCGTGATG
96926 GTTAGTACACGATTTCGGCTAAAAACTGACCCG-AAATTTTTTTTCTCAATTTTTTGCCAA
260 GTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTTCTCAATTTTTTGCCAA
* * * *
96986 AATACTCAGAAAAAAAAATATAATTCAACGCCGAAAACATCGATGGGCTTTTATCGCTTCTAATA
1 AATACTCAG-AAAAAATATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATA
* *
97051 TTTC-TTTTCCATTTTTTTCAGAATTAATTTTAATTAAATCAAAATAAGATTCAGATGCTCATAA
65 --TCGTTTTCCA-TTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCAGATGCTCGTAA
* * * * *
97115 AAACAAATCCTTATATCCAATTTGGCTGAAATTTGGTT-AGAAGAACATATAAATTTTAAGGAGT
127 AAACAAATCCTTATATCCAATTTGGCTGAGATTTGGTTCA-ATGAAAATATATATTTCAAGGAGT
* * * * * * * *
97179 CTTTCTTCCAAATATCATGCAAAACTGAGTCAGGGTCTCGAAATGCATTTTTAGTAAAAAACTGT
191 CTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGTCTCGAAACGCGTTTTTAGCAAAAAACCGT
* * *
97244 GATGATTAGTACACGATTTCGGCTAAAAACTAACCCG--AATTTTTTTTCTCAATTTTTTGGCAA
256 GATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTTCTCAATTTTTTGCCAA
* * * * *
97307 AATACTCAGAAAGAATATAT-ATTCAACGCAGAAGAGATTGATGGACTTTTCACGCTTCTAATAT
1 AATACTCAGAAAAAATATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATAT
* * *
97371 CCTTGTTACATTTTTTTCCGAATTAATTTTATTTAAATCAAAATAAGATTCAGATGCTCGTAAAA
66 CGTT-TTCCA-TTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAA
* * * * * *
97436 ACAAATCCTTATATACAATTTGACTGAGATTTAGTTCGATGAATATATATATTTAAAGGAGTCTT
129 ACAAATCCTTATATCCAATTTGGCTGAGATTTGGTTCAATGAAAATATATATTTCAAGGAGTCTT
* * * * *
97501 TCTGCCTAAAATCATGCAAAACTGATCCAGGGACTCGAAACGCGTTTTTTGCAAAAAACCGTGAT
194 TCTGCCAAAAATCATGCAAAACTGAGCCGGGGTCTCGAAACGCGTTTTTAGCAAAAAACCGTGAT
* * * * *
97566 GGTTAGTACACGATTTTCGACTAAAAACTAACCCGGATACTTTTTTTC-CAATTTTTTGCCAA
259 GGTTAGTACACGA-TTTCGGCTAAAAACTGACCCGAAAATTTTTTTTCTCAATTTTTTGCCAA
* * * * *
97628 AATACTCA-AAAAAACTATACCTAATTGACCGCCGTAAAGGAGTGATGGG-TTCTAACTATCGGG
1 AATACTCAGAAAAAA-TATA--TAATTCAACGCCG-AAAAGATTGATGGGCTT-T---TAAC--G
* *
97691 CTTCTAAAATATTTCGTTTTTCCAAAATTTTTT-CGAATTAAGTTTTAATTTAATGAAAATAAGA
56 CTTCT--AATA--TCG-TTTTCC---ATTTTTTCCGAATTAA-TTTTAATTAAATCAAAATAAGA
* * * *
97755 TTCACATGCTCGTAAAAACAAATCCTTATATCCAATTTGGCTAAGATCTAGTTCGATATATATAT
112 TTCAGATGCTCGTAAAAACAAATCCTTATATCCAATTTGGCTGAGA--T--TT-GGT-T-CA-AT
* * * *
97820 ATATATATATATATATTTAAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGCCGGGGTTTC
169 -GA-A-A-ATATATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGTCTC
* * * *
97885 GAAACACGTTTTTAGC-AAAAA-----ATCGTTATTACACGATTTTCGACTAAAAACTGACCCGA
230 GAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGA-TTTCGGCTAAAAACTGACCCGA
* *
97944 AAATTTGTTTTCTCAATATTTTGCCAA
294 AAATTTTTTTTCTCAATTTTTTGCCAA
*
97971 AATACTTAGAAAAAATATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATAT
1 AATACTCAGAAAAAATATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATAT
* *
98036 CATTTTGCCATTTTTTCCGAATTAATTTTAATTAAATAAAAATAAGATTCAGATGCTCGTAAAAA
66 CGTTTT-CCATTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAA
98101 CAAATCCTTATATCCAATTTGGCTGAGATTTGGTTCAATGAAAATATATATTTCAAGGAGTCTTT
130 CAAATCCTTATATCCAATTTGGCTGAGATTTGGTTCAATGAAAATATATATTTCAAGGAGTCTTT
* *
98166 CTGCCAAAAATCATGCAAAACTGAGCCGGGGTCTCAAAATGCGTTTTTAGCAAAAAAACCCGTGA
195 CTGCCAAAAATCATGCAAAACTGAGCCGGGGTCTCGAAACGCGTTTTTAGC-AAAAAA-CCGTGA
* * *
98231 TGGTTAGTACACGATTTCGACTAAAAACTGACTCGAAAATTATTTTTCTCAATTTTTTTGCCAA
258 TGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTTCTCAA-TTTTTTGCCAA
* *
98295 AATACTCAGAAAAAATATATAATTTAACGCCGAAAATATTGATGGGCTTTTAACGCTTCTAATAT
1 AATACTCAGAAAAAATATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATAT
*
98360 CGTTTTTCCATTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATGCTCGTAAAAA
66 CG-TTTTCCATTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAA
*
98425 CAAATCCTTATATCCAATTTGGCTGAGATTTGGTTCGATGAATATATATATATTTCAAGGAGTCT
130 CAAATCCTTATATCCAATTTGGCTGAGATTTGGTTCAATGAA-A-ATATATATTTCAAGGAGTCT
* *
98490 TTCTGCCAAAAACCATGCAAAACTGAGCCGGGGTCTCAAAACGCGTTTTTAGCAAAAAAACCGTG
193 TTCTGCCAAAAATCATGCAAAACTGAGCCGGGGTCTCGAAACGCGTTTTTAGC-AAAAAACCGTG
* * * * * *
98555 ATGGTTTGTACACGATTTCGGCTAAAAACTGACCAGAAAATTATTTTTCTCAGTTTTTTGCGAC
257 ATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTTCTCAATTTTTTGCCAA
* *
98619 AATACTCA-AAACATATATATAATTCAACGACGAAAAGATTGATGGGCTTTTAAC
1 AATACTCAGAAA-AAATATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAAC
98673 CCTTTGTTAA
Statistics
Matches: 1749, Mismatches: 177, Indels: 150
0.84 0.09 0.07
Matches are distributed among these distances:
308 80 0.05
309 1 0.00
310 1 0.00
311 2 0.00
312 3 0.00
315 23 0.01
316 187 0.11
317 54 0.03
318 10 0.01
319 214 0.12
320 38 0.02
321 110 0.06
322 212 0.12
323 43 0.02
324 250 0.14
325 69 0.04
326 79 0.05
328 73 0.04
329 8 0.00
330 10 0.01
331 4 0.00
332 4 0.00
333 4 0.00
334 5 0.00
335 16 0.01
336 67 0.04
337 4 0.00
338 1 0.00
340 15 0.01
341 14 0.01
342 44 0.03
343 24 0.01
344 8 0.00
345 1 0.00
346 1 0.00
347 5 0.00
348 65 0.04
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (320 bp):
AATACTCAGAAAAAATATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATAT
CGTTTTCCATTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAAC
AAATCCTTATATCCAATTTGGCTGAGATTTGGTTCAATGAAAATATATATTTCAAGGAGTCTTTC
TGCCAAAAATCATGCAAAACTGAGCCGGGGTCTCGAAACGCGTTTTTAGCAAAAAACCGTGATGG
TTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTTCTCAATTTTTTGCCAA
Found at i:101112 original size:320 final size:319
Alignment explanation
Indices: 100217--102185 Score: 2641
Period size: 321 Copynumber: 6.2 Consensus size: 319
100207 CTGAGCCGGG
** * *
100217 ACACGATTTTCGACCGAAAACTAACCCGAAATTTTTTTTTCAATTTTTTGCCAAAATACTCATAA
1 ACACGATTTTCGACTAAAAACTAACCCGAAATTTTTTTCTCAATTTTTTGCCAAAATACTCAGAA
*
100282 AAAAAATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATATCATTTTTACAT
66 AAAAAATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATATCATTTTTCCA-
100347 TTTTTTTCTGAATTAATTTTAATTAAAGTCAAAATAAGATTCAGATGCTCGTAAAAACAAATCCT
130 TTTTTTTC-GAATTAATTTTAATTAAA-TCAAAATAAGATTCAGATGCTCGTAAAAACAAATCCT
* * * * * *
100412 TATATCCAATTTGGCTGAGATTTGGTTTGATTAAAAAAATATATGTTTCAAGGAGTCTTTCTGCC
193 TATATCCAATTTGGCTGAGATTTAGTTCGA-T--GAATATATATATTTAAAGGAGTCTTTCTGCC
* *
100477 AAAAATCATG-AAAACTGAGCCGGGGTCTCAAAACGTGTTTTTAGCAAAAAAACCGTGATGGTTA
255 AAAAATCATGCAAAACTGAGCCGGGGTCTCGAAACGCGTTTTTAGC-AAAAAACCGTGAT-GTTA
100541 GT
318 GT
*
100543 ACACGATTTTCGACTGAAAACTAACCCGAAATTTTTTTTCTCAA-TTTTTGCCAAAATACTCAGA
1 ACACGATTTTCGACTAAAAACTAACCCGAAA-TTTTTTTCTCAATTTTTTGCCAAAATACTCAGA
* * *
100607 AAAAATATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATATCCTTTTTACA
65 AAAAAAATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATATCATTTTTCCA
* *
100672 TTTTTTTTGGAATTAATTTTAACTAAATCAAAATAAGATTCAGATGCTCGTAAAAACAAATCCTT
130 -TTTTTTTCGAATTAATTTTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAACAAATCCTT
* * *
100737 ATATCCAATTTGGCTGAGATATAGTTCGATGAATATATATATTTAAAGGAGTCTTTCTGCCTAAT
194 ATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTAAAGGAGTCTTTCTGCCAAAA
* * * * * *
100802 ATCATGCAATACTGATCCAGGGTCTCGGAACGCGTTTTTTGCAAAAAACCGTGATGGTTAAT
259 ATCATGCAAAACTGAGCCGGGGTCTCGAAACGCGTTTTTAGCAAAAAACCGTGAT-GTTAGT
* * *
100864 ACACGATTTTCGACTAAAAACTAACCAGGATATTTTTTTC-CAATTTTTTTCCAAAATACTCAGA
1 ACACGATTTTCGACTAAAAACTAACC-CGAAATTTTTTTCTCAATTTTTTGCCAAAATACTCAGA
* * * *
100928 AATAAAAATATAATTCACCGCCGAAAAGATTGATGGG-TTTTCATGCTTCTAATATCGTTTTTCC
65 AA-AAAAATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATATCATTTTTCC
** * **
100992 ATTTTTTTCGTCTTAATTTTAATTTAATTGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTT
129 ATTTTTTTCGAATTAATTTTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAACAAATCCTT
* *
101057 ATATCCAATTTGGCTGAGATTT-GAATCGATTAATATATATATTTAAAGGAGTCTTTCTGCCAAA
194 ATATCCAATTTGGCTGAGATTTAG-TTCGATGAATATATATATTTAAAGGAGTCTTTCTGCCAAA
* **
101121 AATCATGCAAAACTGAGCCGGGGTCTCGAAACGTGTTTTTAGCAAAAAATTGTGATGATTAGT
258 AATCATGCAAAACTGAGCCGGGGTCTCGAAACGCGTTTTTAGCAAAAAACCGTGATG-TTAGT
* *
101184 ACACGATTTTCAACTAAAAACTAACCCGAAAATTTTTTTCTCAATTTTTTGCCAAAATACTAAGA
1 ACACGATTTTCGACTAAAAACTAACCCG-AAATTTTTTTCTCAATTTTTTGCCAAAATACTCAGA
* **
101249 AAAAATATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATATCGCTTTTCC-
65 AAAAAAATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATATCATTTTTCCA
* *
101313 TTTTTTTCCGAATTAATTGTAATTAAATCAAAATAAGATTCATATGCTCGTAAAAACAAATCCTT
130 TTTTTTT-CGAATTAATTTTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAACAAATCCTT
*
101378 ATATCTAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTAAAGGAGTCTTTCTGCCAAAA
194 ATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTAAAGGAGTCTTTCTGCCAAAA
* **
101443 ATCATGCAAAACTGAGTCAAGGTCTCGAAA--C-------G--------CGT--T-TT--T
259 ATCATGCAAAACTGAGCCGGGGTCTCGAAACGCGTTTTTAGCAAAAAACCGTGATGTTAGT
* *
101482 ACACGATTTTCGACTAAAAACTAACCCGAAATTTTTTTCTCAATTTGTTGCCAAAATACTCCGAA
1 ACACGATTTTCGACTAAAAACTAACCCGAAATTTTTTTCTCAATTTTTTGCCAAAATACTCAGAA
* * *
101547 AAAAAATATAATTCAACGCAGAAAAGATTGATGGTCTTTTAACACTTCTAATATCATTTTGT-CA
66 AAAAAATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATATCATTTT-TCCA
* *
101611 TTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATGCTCGTAAAAACAAATCCTTA
130 TTTTTTTCGAATTAATTTTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * * *
101676 TATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATAATTCAAGGAGTTTTTCTGCCAAAAC
195 TATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTAAAGGAGTCTTTCTGCCAAAAA
** *
101741 TCATATAAAACTGAGCCGGGGTCTCGAAACGCATTTTTAGCAAAAAACCGTGAATGTTAGT
260 TCATGCAAAACTGAGCCGGGGTCTCGAAACGCGTTTTTAGCAAAAAACCGTG-ATGTTAGT
* * * * * *
101802 AAAC-AATTCCGGCTAAAAACTGATCCGAAAATTTTTTTCTCAATTTTTTGCCAAAATACTCAGA
1 ACACGATTTTCGACTAAAAACTAACCCG-AAATTTTTTTCTCAATTTTTTGCCAAAATACTCAGA
* * * * * *
101866 AAAAATATATAATTCAACGCCGAAAAGAATAATTGGTTTTTAACGCTTCTAATATCATTTTGCCA
65 AAAAAAATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATATCATTTTTCCA
* *
101931 TTTTTTTCAGAATTAATTTTACTTAAATCAAAATAAGATTTAGATGCTCGTAAAAACAAATCCTT
130 TTTTTTTC-GAATTAATTTTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAACAAATCCTT
* * * *
101996 ATATTCAATTTGGCTGAGATTTGGTTCGATGAATATATATATTTCAAGGAGCCTTTCTGCCAAAA
194 ATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTAAAGGAGTCTTTCTGCCAAAA
* *
102061 ATCATACAAAACTGAGCCGGGGTCTCGAAACGCGTTTTTAGCAAAAAAACCATGAATGTTAGT
259 ATCATGCAAAACTGAGCCGGGGTCTCGAAACGCGTTTTTAGC-AAAAAACCGTG-ATGTTAGT
* * *
102124 ACACGA-TTCCGGCTAAAAACTGACCCGAAAATTTTTTTTTCTCAATTTTTTTGCCAAAATAC
1 ACACGATTTTCGACTAAAAACTAACCCG-AAA--TTTTTTTCTCAA-TTTTTTGCCAAAATAC
102186 CATTGTTTTA
Statistics
Matches: 1464, Mismatches: 134, Indels: 91
0.87 0.08 0.05
Matches are distributed among these distances:
297 230 0.16
298 35 0.02
299 1 0.00
300 2 0.00
302 1 0.00
304 2 0.00
306 1 0.00
312 1 0.00
314 3 0.00
317 1 0.00
318 2 0.00
319 21 0.01
320 343 0.23
321 469 0.32
322 110 0.08
323 2 0.00
324 76 0.05
325 33 0.02
326 120 0.08
327 11 0.01
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (319 bp):
ACACGATTTTCGACTAAAAACTAACCCGAAATTTTTTTCTCAATTTTTTGCCAAAATACTCAGAA
AAAAAATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATATCATTTTTCCAT
TTTTTTCGAATTAATTTTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAT
ATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTAAAGGAGTCTTTCTGCCAAAAAT
CATGCAAAACTGAGCCGGGGTCTCGAAACGCGTTTTTAGCAAAAAACCGTGATGTTAGT
Found at i:102039 original size:618 final size:618
Alignment explanation
Indices: 100217--102100 Score: 2379
Period size: 618 Copynumber: 3.0 Consensus size: 618
100207 CTGAGCCGGG
** * * *
100217 ACACGATTTTCGACCGAAAACTAACC-CGAAATTTTTTTTTCAATTTTTTGCCAAAATACTCATA
1 ACACGATTTTCGACTAAAAACTAACCACGAAA-TTTTTTTCCAATTTGTTGCCAAAATACTCAGA
* * *
100281 AA-AAAAATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATATCATTTTTAC
65 AATAAAAATATAATTCAACGCAGAAAAGATTGAT-GGCTTTTAACACTTCTAATATCATTTTTCC
*
100345 ATTTTTTTTCTGAATTAATTTTAATTAAAGTCAAAATAAGATTCAGATGCTCGTAAAAACAAATC
129 A--TTTTTTCCGAATTAATTTTAATTAAA-TCAAAATAAGATTCAGATGCTCGTAAAAACAAATC
** * * * ** *
100410 CTTATATCCAATTTGGCTGAGATTTGGTTTGATTAAAAAAATATATGTTTCAAGGAGTCTTTCTG
191 CTTATATCCAATTTGGCTGAGATTTGAATCGA-T--GAATATATATAATTAAAGGAGTCTTTCTG
* * ** *
100475 CCAAAAATCAT-GAAAACTGAGCCGGGGTCTCAAAACGTGTTTTTAGCAAAAAAACCGTGATGGT
253 CCAAAAATCATACAAAACTGAGCCGGGGTCTCGAAACGCATTTTTAGC-AAAAAACCGTGATGAT
* * * * * *
100539 TAGTACACGATTTTCGACTGAAAACTAACCCGAAATTTTTTTTCTCAA-TTTTTGCCAAAATACT
317 TAGTAAACGAATTCCAACTAAAAACTAACCCGAAAATTTTTTTCTCAATTTTTTGCCAAAATACT
* * * **
100603 CAGAAAAAATATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATATCCTTTT
382 AAGAAAAAATATATAATTCAACGCCGAAAAGAATAATGGGCTTTTAACGCTTCTAATATCGATTT
* ** * *
100668 TACATTTTTTTTGGAATTAATTTTAACTAAATCAAAATAAGATTCAGATGCTCGTAAAAACAAAT
447 T-CCTTTTTTTCAGAATTAATTGTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAACAAAT
* * *
100733 CCTTATATCCAATTTGGCTGAGATATAGTTCGATGAATATATATATTTAAAGGAGTCTTTCTGCC
511 CCTTATATCTAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTAAAGGAGCCTTTCTGCC
* * * * * * *
100798 TAATATCATGCAATACTGATCCAGGGTCTCGGAACGCGTTTTTTGCAAAAAACCGTGATGGTTAA
576 AAAAATCATACAAAACTGAGCCAAGGTCTC-GAA-AC-------G--------CGT--T--TT--
100863 T
618 T
* * * *
100864 ACACGATTTTCGACTAAAAACTAACCAGGATATTTTTTTCCAATTTTTTTCCAAAATACTCAGAA
1 ACACGATTTTCGACTAAAAACTAACCACGAAATTTTTTTCCAATTTGTTGCCAAAATACTCAGAA
* * * * ** *
100929 ATAAAAATATAATTCACCGCCGAAAAGATTGATGGGTTTTCATGCTTCTAATATCGTTTTTCCAT
66 ATAAAAATATAATTCAACGCAGAAAAGATTGATGGCTTTTAACACTTCTAATATCATTTTTCCAT
* ** * **
100994 TTTTTTCGTCTTAATTTTAATTTAATTGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAT
131 TTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAT
* *
101059 ATCCAATTTGGCTGAGATTTGAATCGATTAATATATATATTTAAAGGAGTCTTTCTGCCAAAAAT
196 ATCCAATTTGGCTGAGATTTGAATCGATGAATATATATAATTAAAGGAGTCTTTCTGCCAAAAAT
* ** ** *
101124 CATGCAAAACTGAGCCGGGGTCTCGAAACGTGTTTTTAGCAAAAAATTGTGATGATTAGTACACG
261 CATACAAAACTGAGCCGGGGTCTCGAAACGCATTTTTAGCAAAAAACCGTGATGATTAGTAAACG
* *
101189 ATTTTCAACTAAAAACTAACCCGAAAATTTTTTTCTCAATTTTTTGCCAAAATACTAAGAAAAAA
326 AATTCCAACTAAAAACTAACCCGAAAATTTTTTTCTCAATTTTTTGCCAAAATACTAAGAAAAAA
* * *
101254 TATATAATTCAACGCCGAAAAGATTGATGGGCTTTTAACGCTTCTAATATCGCTTTTCCTTTTTT
391 TATATAATTCAACGCCGAAAAGAATAATGGGCTTTTAACGCTTCTAATATCGATTTTCCTTTTTT
* *
101319 TCCGAATTAATTGTAATTAAATCAAAATAAGATTCATATGCTCGTAAAAACAAATCCTTATATCT
456 TCAGAATTAATTGTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCT
* *
101384 AATTTGGCTGAGATTTAGTTCGATGAATATATATATTTAAAGGAGTCTTTCTGCCAAAAATCATG
521 AATTTGGCTGAGATTTAGTTCGATGAATATATATATTTAAAGGAGCCTTTCTGCCAAAAATCATA
*
101449 CAAAACTGAGTCAAGGTCTCGAAACGCGTTTTT
586 CAAAACTGAGCCAAGGTCTCGAAACGCGTTTTT
*
101482 ACACGATTTTCGACTAAAAACTAACC-CGAAATTTTTTTCTCAATTTGTTGCCAAAATACTCCGA
1 ACACGATTTTCGACTAAAAACTAACCACGAAATTTTTTTC-CAATTTGTTGCCAAAATACTCAGA
101546 AA-AAAAATATAATTCAACGCAGAAAAGATTGATGGTCTTTTAACACTTCTAATATCATTTTGT-
65 AATAAAAATATAATTCAACGCAGAAAAGATTGATGG-CTTTTAACACTTCTAATATCATTTT-TC
*
101609 CATTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATGCTCGTAAAAACAAATCCT
128 CATTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAACAAATCCT
* * *
101674 TATATCCAATTTGGCTGAGATTT-AGTTCGATGAATATATATAATTCAAGGAGTTTTTCTGCCAA
193 TATATCCAATTTGGCTGAGATTTGA-ATCGATGAATATATATAATTAAAGGAGTCTTTCTGCCAA
* *
101738 AACTCATATAAAACTGAGCCGGGGTCTCGAAACGCATTTTTAGCAAAAAACCGTGAATG-TTAGT
257 AAATCATACAAAACTGAGCCGGGGTCTCGAAACGCATTTTTAGCAAAAAACCGTG-ATGATTAGT
** * * *
101802 AAAC-AATTCCGGCTAAAAACTGATCCGAAAATTTTTTTCTCAATTTTTTGCCAAAATACTCAGA
321 AAACGAATTCCAACTAAAAACTAACCCGAAAATTTTTTTCTCAATTTTTTGCCAAAATACTAAGA
* *
101866 AAAAATATATAATTCAACGCCGAAAAGAATAATTGGTTTTTAACGCTTCTAATATC-ATTTTGCC
386 AAAAATATATAATTCAACGCCGAAAAGAATAATGGGCTTTTAACGCTTCTAATATCGATTTT-CC
* * *
101930 ATTTTTTTCAGAATTAATTTTACTTAAATCAAAATAAGATTTAGATGCTCGTAAAAACAAATCCT
450 -TTTTTTTCAGAATTAATTGTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAACAAATCCT
* *
101995 TATAT-TCAATTTGGCTGAGATTTGGTTCGATGAATATATATATTTCAAGGAGCCTTTCTGCCAA
514 TATATCT-AATTTGGCTGAGATTTAGTTCGATGAATATATATATTTAAAGGAGCCTTTCTGCCAA
**
102059 AAATCATACAAAACTGAGCCGGGGTCTCGAAACGCGTTTTT
578 AAATCATACAAAACTGAGCCAAGGTCTCGAAACGCGTTTTT
102100 A
1 A
102101 GCAAAAAAAC
Statistics
Matches: 1116, Mismatches: 109, Indels: 53
0.87 0.09 0.04
Matches are distributed among these distances:
616 4 0.00
617 151 0.14
618 397 0.36
619 4 0.00
620 2 0.00
622 1 0.00
624 3 0.00
632 1 0.00
639 1 0.00
640 3 0.00
641 238 0.21
642 113 0.10
643 1 0.00
644 62 0.06
645 21 0.02
647 81 0.07
648 33 0.03
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (618 bp):
ACACGATTTTCGACTAAAAACTAACCACGAAATTTTTTTCCAATTTGTTGCCAAAATACTCAGAA
ATAAAAATATAATTCAACGCAGAAAAGATTGATGGCTTTTAACACTTCTAATATCATTTTTCCAT
TTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAT
ATCCAATTTGGCTGAGATTTGAATCGATGAATATATATAATTAAAGGAGTCTTTCTGCCAAAAAT
CATACAAAACTGAGCCGGGGTCTCGAAACGCATTTTTAGCAAAAAACCGTGATGATTAGTAAACG
AATTCCAACTAAAAACTAACCCGAAAATTTTTTTCTCAATTTTTTGCCAAAATACTAAGAAAAAA
TATATAATTCAACGCCGAAAAGAATAATGGGCTTTTAACGCTTCTAATATCGATTTTCCTTTTTT
TCAGAATTAATTGTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCT
AATTTGGCTGAGATTTAGTTCGATGAATATATATATTTAAAGGAGCCTTTCTGCCAAAAATCATA
CAAAACTGAGCCAAGGTCTCGAAACGCGTTTTT
Found at i:103734 original size:642 final size:637
Alignment explanation
Indices: 102629--105046 Score: 3390
Period size: 642 Copynumber: 3.8 Consensus size: 637
102619 AACATTGCAA
* * *
102629 AATACTAAGAAAA-ATATATAATTCAACGCCGAAAGGATTGATGGGCTTTTAACGCTTCTAATAT
1 AATACTAAAAAAATATATATAATTCAACGACGAAAAGATTGATGGGCTTTTAACGCTTCTAATAT
* * * * *
102693 CGTTTTTCC-TTTTTTTCGGAATCAATTTTAATTAAATCAAAATTAGATTCTTATGCTCGTAAAA
66 CATTTTTCCATTTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATGCTCGTAAAA
* * *
102757 ACAAATCATTATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTCAAGGACTCTT
131 ACAAATCCTTATATCCAATTTGGCTGAGATTTAATTCGATGAATATATATATTTCAAGGAGTCTT
*
102822 TCTGCCAAAAATGATGCAAAACTGAGCCA-GGATCTCGAAACGCATTTTTACCAAAAAATCGTCG
196 TCTGCCAAAAATCATGCAAAACTGAGCCATGG-TCTCGAAACGCATTTTTACCAAAAAATC-T--
* * * * *
102886 TGATTATTACACGATTTTCGACTAAAAACTAACCCGAAAATTTTTTTCTTAAACTTTTGCCAAAA
257 TGATGAGTACAAGATTTTCGACTAAAAACTAACCCGAAAATTTTTTTCTCAAATTTTTGCCAAAA
* * *
102951 TACTCAG-AAAAATATATAATTCAACGCAGAAAAGATTGATGCTCTGTTAACACTTCTAATATCA
322 TACTAAGAAAAAATATATAATTCAACGCAGAAAAGATTGATGGTCTTTTAACACTTCTAATATCA
* * *
103015 TTTTGT-AATTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATCCTCGTAAAAACA
387 TTTTGTCATTTTTTCCCAATTAATTTTAATTAAATCAAAATAAGATTCATATACTCGTAAAAACA
* * *
103079 AATCCTAATATCCAATTTGGCTGAAATTTAGTTCGATAAATATATATATTT-AATGGAGTCTTTC
452 AATCCTTATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTCAA-GGAGT-TTTC
** * *
103143 CGCCAAAAATCATGCAAAACTTAGCCGGGGTCTCAAAACGCGTTTTTAGCAAAAAACTGTTATGT
515 AACCAAAAATCATGCAAAACTTAGCCGGGGTCTCAAAACGCGTTTTTTGCAAAAAACTGTGA-GT
* *
103208 TAGTACACGATTTCGGCTAAAAACTGACCCGAAAATTGTTTTTCTCAATTTTTTGCCAC
579 TAGTACACGATTTCGGCTAAAAACTGACCCGAAAATTATTTTTCTCAGTTTTTTGCCAC
* * **
103267 AATACTCAAAAAAATATATATAATTCAACAACGAAAAGATTGATTGTTTTTTAACGCTTCTAATA
1 AATACT-AAAAAAATATATATAATTCAACGACGAAAAGATTGATGGGCTTTTAACGCTTCTAATA
*
103332 TCATTTTGCCATTTATTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATGCTCGTAA
65 TCATTTTTCCATTT-TTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATGCTCGTAA
* * * *
103397 AAACAAATCCTTATATCTAATTTGGCTGAGATTTAATTCTATGAATTTATATATTTAAAGGAGTC
129 AAACAAATCCTTATATCCAATTTGGCTGAGATTTAATTCGATGAATATATATATTTCAAGGAGTC
* * * * * *
103462 TTTCTGCCAAAAACCATGGAAAACTGAGTCATTGTCTCGAAACGCGTTTTTAGCAAAAAATCTTG
194 TTTCTGCCAAAAATCATGCAAAACTGAGCCATGGTCTCGAAACGCATTTTTACCAAAAAATCTTG
* * *
103527 ATGAGTACAAGATTTTCGACTAAAAACTAACCTGAAAATTTTTTTCTCAATTTTTTGTCAAAATA
259 ATGAGTACAAGATTTTCGACTAAAAACTAACCCGAAAATTTTTTTCTCAAATTTTTGCCAAAATA
*
103592 CTAAGAAAAAATATATAATTCAACGCAGAAAAGATTTATGGTCTTTTAACACTTCTAATATCATT
324 CTAAGAAAAAATATATAATTCAACGCAGAAAAGATTGATGGTCTTTTAACACTTCTAATATCATT
* *
103657 TTGTCATTTTTTCCCAATTAATTTTAATTAAATCAAAATAAGATTCTTATACTCGTAATAAAGAA
389 TTGTCATTTTTTCCCAATTAATTTTAATTAAATCAAAATAAGATTCATATACTCGTAA-AAACAA
*
103722 ATCTTTATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTCAAGGAGTTTTTCTA
453 ATCCTTATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTCAAGGAG-TTTTC-A
* * * *
103787 ACCAAAAATCATGCAAAA-TTGAGTCGGGGTCTCAAAACGCGTTTTTTGTAAAAAACCGTGA-TA
516 ACCAAAAATCATGCAAAACTT-AGCCGGGGTCTCAAAACGCGTTTTTTGCAAAAAACTGTGAGTT
103850 ACGTACACGATTTCGGCTAAAAACTGACCCGAAAATTATTTTTCTCAGTTTTTTGCCAC
580 A-GTACACGATTTCGGCTAAAAACTGACCCGAAAATTATTTTTCTCAGTTTTTTGCCAC
**
103909 AATACT-AAAAAATATATATAATTCAACGACGAAAAGATTGATGGGCGATTAACGCTTCTAATAT
1 AATACTAAAAAAATATATATAATTCAACGACGAAAAGATTGATGGGCTTTTAACGCTTCTAATAT
* * *
103973 CGTTTTTCCA-TTTTTTCCAAATTAATTTTAATTGAAT-AAAATAAGATTCATATGCTCGTAAAA
66 CATTTTTCCATTTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATGCTCGTAAAA
* **
104036 AC-AATCCTTATATCCAATTTGGCTGAGATTTGATTCGGGGAATATATATATTTCAAGGAGTCTT
131 ACAAATCCTTATATCCAATTTGGCTGAGATTTAATTCGATGAATATATATATTTCAAGGAGTCTT
* * * *
104100 TCTGCCAAAAATCATGGAAAACTGAGCCATTGTCTCGAAACACGTTTTTACCAAAAAAAATCTTG
196 TCTGCCAAAAATCATGCAAAACTGAGCCATGGTCTCGAAACGCATTTTTACC--AAAAAATCTTG
* * *
104165 ATGATTAGTACATGATTTTCAACTAAAAACTAACCCG-AAATTTTTTTTTCAAATTTTTGCCAAA
259 ATG---AGTACAAGATTTTCGACTAAAAACTAACCCGAAAATTTTTTTCTCAAATTTTTGCCAAA
* *
104229 ATACTAAGAAAAAATATATAATTCAACACAGAAAAGACTGATGGTCTTTTAACACTTCTAATATC
321 ATACTAAGAAAAAATATATAATTCAACGCAGAAAAGATTGATGGTCTTTTAACACTTCTAATATC
* *
104294 ATTTTGTCATTTTTTCCCAATTAATTTTAA-TAAATCAAAATAAGATTCTTATACTCGTAAAAAG
386 ATTTTGTCATTTTTTCCCAATTAATTTTAATTAAATCAAAATAAGATTCATATACTCGTAAAAAC
* *
104358 AAATCTTTATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTCAAGGAGTTTTCT
451 AAATCCTTATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTCAAGGAGTTTTCA
*
104423 ACC-AAAAT-ATGCAAAACTGAGCCGGGGTCTCAAAACGCGTTTTTTGCAAAAAAAACTGTGACG
516 ACCAAAAATCATGCAAAACTTAGCCGGGGTCTCAAAACGCGTTTTTTGC--AAAAAACTGTGA--
104486 GTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATTATTTTTCTCAGTTTTTTGCCAC
577 GTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATTATTTTTCTCAGTTTTTTGCCAC
104547 AATACTAAAAAAATATATATAATTCAACGACGAAAAGATTGATGGGCTTTTAACGCTTCTAATAT
1 AATACTAAAAAAATATATATAATTCAACGACGAAAAGATTGATGGGCTTTTAACGCTTCTAATAT
* * *
104612 CATTTTTCCATTTTTTTTTCCGAAATAATTTTAATTGAATAAAAATAAGATTCATATGCTCGTAA
66 CATTTTTCCA--TTTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATGCTCGTAA
* *
104677 AAACAAATCCTTATATCCAATTTGGCTGAGATTTGATTCGATGAATATATATATTTCAATGAGTC
129 AAACAAATCCTTATATCCAATTTGGCTGAGATTTAATTCGATGAATATATATATTTCAAGGAGTC
* * * * * *
104742 TTTCTGCCAAAAATCATTTCAAAACTGAGTCAGGGTCTCGAAACGCATTTTTAGC--AAGA--TA
194 TTTCTGCCAAAAATCA-TGCAAAACTGAGCCATGGTCTCGAAACGCATTTTTACCAAAAAATCTT
* * * **
104803 G-TTAGTACACA-ATTTTCGATTAAAAACTAACCCGAAAATTATTTTCTC-AATTTTCCCCAAAA
258 GATGAGTACA-AGATTTTCGACTAAAAACTAACCCGAAAATTTTTTTCTCAAATTTTTGCCAAAA
* * * * * * *
104865 TACTCAGAAAAAATATATAATTCAATGCCGAAAAGATTGTTGGGCCTTTTCACGCTTCTAATATC
322 TACTAAGAAAAAATATATAATTCAACGCAGAAAAGATTGAT-GGTCTTTTAACACTTCTAATATC
* * * *
104930 ATTTT-TCCATTTTTTTTCCGAATTAATTTTAATTAAATCAATATAAGATTCAGATGCTCGTAAA
386 ATTTTGT-CA--TTTTTTCCCAATTAATTTTAATTAAATCAAAATAAGATTCATATACTCGTAAA
* * * *
104994 AACAAATCCTTCTATCCAATGTGGCTGAGGTTTGGTTCGATGAATATATATAT
448 AACAAATCCTTATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATAT
105047 ATATATGATA
Statistics
Matches: 1602, Mismatches: 140, Indels: 75
0.88 0.08 0.04
Matches are distributed among these distances:
634 34 0.02
635 81 0.05
636 155 0.10
637 33 0.02
638 190 0.12
639 244 0.15
640 288 0.18
641 86 0.05
642 304 0.19
643 84 0.05
644 73 0.05
645 30 0.02
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (637 bp):
AATACTAAAAAAATATATATAATTCAACGACGAAAAGATTGATGGGCTTTTAACGCTTCTAATAT
CATTTTTCCATTTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATGCTCGTAAAA
ACAAATCCTTATATCCAATTTGGCTGAGATTTAATTCGATGAATATATATATTTCAAGGAGTCTT
TCTGCCAAAAATCATGCAAAACTGAGCCATGGTCTCGAAACGCATTTTTACCAAAAAATCTTGAT
GAGTACAAGATTTTCGACTAAAAACTAACCCGAAAATTTTTTTCTCAAATTTTTGCCAAAATACT
AAGAAAAAATATATAATTCAACGCAGAAAAGATTGATGGTCTTTTAACACTTCTAATATCATTTT
GTCATTTTTTCCCAATTAATTTTAATTAAATCAAAATAAGATTCATATACTCGTAAAAACAAATC
CTTATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTCAAGGAGTTTTCAACCAA
AAATCATGCAAAACTTAGCCGGGGTCTCAAAACGCGTTTTTTGCAAAAAACTGTGAGTTAGTACA
CGATTTCGGCTAAAAACTGACCCGAAAATTATTTTTCTCAGTTTTTTGCCAC
Found at i:103794 original size:320 final size:318
Alignment explanation
Indices: 102626--105421 Score: 3003
Period size: 320 Copynumber: 8.7 Consensus size: 318
102616 AAAAACATTG
* * *
102626 CAAAATACTAAG-AAAAATATATAATTCAACGCCGAAAGGATTGATGGGCTTTTAACGCTTCTAA
1 CAAAATACTAAGAAAAAATATATAATTCAACGCAGAAAAGATTGATGGTCTTTTAACGCTTCTAA
* * * * * *
102690 TATCGTTTTTCCTTTTTTTCGGAATCAATTTTAATTAAATCAAAATTAGATTCTTATGCTCGTAA
66 TATCATTTTTCCATTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATGCTCGTAA
* *
102755 AAACAAATCATTATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTCAAGGACTC
131 AAACAAATCCTTATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTCAAGGAGTC
* * * *
102820 TTTCTGCCAAAAATGATGCAAAACTGAGCCAGGATCTCGAAACGCATTTTTACCAAAAAATCGTC
196 TTTCTGCCAAAAATCATGCAAAACTGAGCCAGGGTCTCGAAACGCGTTTTTAGCAAAAAATC-T-
* * * **
102885 GTGATTATTACACGATTTTCGACTAAAAACTAACCCGAAAATTTTTTTCTTAAACTTTTGC
259 -TGATGAGTACACGATTTTCGACTAAAAACTAACCCGAAAATTTTTTTCTCAATTTTTTGC
* * * *
102946 CAAAATACTCAG-AAAAATATATAATTCAACGCAGAAAAGATTGATGCTCTGTTAACACTTCTAA
1 CAAAATACTAAGAAAAAATATATAATTCAACGCAGAAAAGATTGATGGTCTTTTAACGCTTCTAA
* *
103010 TATCATTTTGT--AATTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATCCTCGTA
66 TATCATTTT-TCCATTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATGCTCGTA
* * *
103073 AAAACAAATCCTAATATCCAATTTGGCTGAAATTTAGTTCGATAAATATATATATTT-AATGGAG
130 AAAACAAATCCTTATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTCAA-GGAG
* * * *
103137 TCTTTCCGCCAAAAATCATGCAAAACTTAGCCGGGGTCTCAAAACGCGTTTTTAGCAAAAAA-CT
194 TCTTTCTGCCAAAAATCATGCAAAACTGAGCCAGGGTCTCGAAACGCGTTTTTAGCAAAAAATCT
* * *
103201 GTTATGTTAGTACACGA-TTTCGGCTAAAAACTGACCCGAAAATTGTTTTTCTCAATTTTTTGC
259 -TGATG--AGTACACGATTTTCGACTAAAAACTAACCCGAAAATT-TTTTTCTCAATTTTTTGC
* * * *
103264 CACAATACTCAA-AAAAATATATATAATTCAAC-AACGAAAAGATTGATTGTTTTTTAACGCTTC
1 CAAAATACT-AAGAAAAA-ATATATAATTCAACGCA-GAAAAGATTGATGGTCTTTTAACGCTTC
*
103327 TAATATCATTTTGCCATTTATTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATGCT
63 TAATATCATTTTTCCA-TT-TTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATGCT
* * * * *
103392 CGTAAAAACAAATCCTTATATCTAATTTGGCTGAGATTTAATTCTATGAATTTATATATTTAAAG
126 CGTAAAAACAAATCCTTATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTCAAG
* * * **
103457 GAGTCTTTCTGCCAAAAACCATGGAAAACTGAGTCATTGTCTCGAAACGCGTTTTTAGCAAAAAA
191 GAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCAGGGTCTCGAAACGCGTTTTTAGCAAAAAA
* * *
103522 TCTTGATGAGTACAAGATTTTCGACTAAAAACTAACCTGAAAATTTTTTTCTCAATTTTTTGT
256 TCTTGATGAGTACACGATTTTCGACTAAAAACTAACCCGAAAATTTTTTTCTCAATTTTTTGC
* *
103585 CAAAATACTAAGAAAAAATATATAATTCAACGCAGAAAAGATTTATGGTCTTTTAACACTTCTAA
1 CAAAATACTAAGAAAAAATATATAATTCAACGCAGAAAAGATTGATGGTCTTTTAACGCTTCTAA
* * *
103650 TATCATTTTGT-CATTTTTTCCCAATTAATTTTAATTAAATCAAAATAAGATTCTTATACTCGTA
66 TATCATTTT-TCCATTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATGCTCGTA
* *
103714 ATAAAGAAATCTTTATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTCAAGGAG
130 A-AAACAAATCCTTATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTCAAGGAG
* * * * * * * * *
103779 TTTTTCTAACCAAAAATCATGCAAAATTGAGTCGGGGTCTCAAAACGCGTTTTTTGTAAAAAACC
194 TCTTTCT-GCCAAAAATCATGCAAAACTGAGCCAGGGTCTCGAAACGCGTTTTTAGCAAAAAATC
* * * * *
103844 GTGATAACGTACACGA-TTTCGGCTAAAAACTGACCCGAAAATTATTTTTCTCAGTTTTTTGC
258 TTGATGA-GTACACGATTTTCGACTAAAAACTAACCCGAAAATT-TTTTTCTCAATTTTTTGC
* * * **
103906 CACAATACTAA-AAAATATATATAATTCAACG-ACGAAAAGATTGATGGGCGATTAACGCTTCTA
1 CAAAATACTAAGAAAAAATATATAATTCAACGCA-GAAAAGATTGATGGTCTTTTAACGCTTCTA
* * *
103969 ATATCGTTTTTCCATTTTTTCCAAATTAATTTTAATTGAAT-AAAATAAGATTCATATGCTCGTA
65 ATATCATTTTTCCATTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATGCTCGTA
**
104033 AAAAC-AATCCTTATATCCAATTTGGCTGAGATTT-GATTCGGGGAATATATATATTTCAAGGAG
130 AAAACAAATCCTTATATCCAATTTGGCTGAGATTTAG-TTCGATGAATATATATATTTCAAGGAG
* ** * *
104096 TCTTTCTGCCAAAAATCATGGAAAACTGAGCCATTGTCTCGAAACACGTTTTTACCAAAAAAAAT
194 TCTTTCTGCCAAAAATCATGCAAAACTGAGCCAGGGTCTCGAAACGCGTTTTTAGC--AAAAAAT
* * * *
104161 CTTGATGATTAGTACATGATTTTCAACTAAAAACTAACCCG-AAATTTTTTTTTCAAATTTTTGC
257 CTTGATG---AGTACACGATTTTCGACTAAAAACTAACCCGAAAATTTTTTTCTCAATTTTTTGC
* * *
104225 CAAAATACTAAGAAAAAATATATAATTCAACACAGAAAAGACTGATGGTCTTTTAACACTTCTAA
1 CAAAATACTAAGAAAAAATATATAATTCAACGCAGAAAAGATTGATGGTCTTTTAACGCTTCTAA
* * *
104290 TATCATTTTGT-CATTTTTTCCCAATTAATTTTAA-TAAATCAAAATAAGATTCTTATACTCGTA
66 TATCATTTT-TCCATTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATGCTCGTA
* *
104353 AAAAGAAATCTTTATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTCAAGGAGT
130 AAAACAAATCCTTATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTCAAGGAGT
* * * * *
104418 -TTTCTACC-AAAAT-ATGCAAAACTGAGCCGGGGTCTCAAAACGCGTTTTTTGCAAAAAAAACT
195 CTTTCTGCCAAAAATCATGCAAAACTGAGCCAGGGTCTCGAAACGCGTTTTTAGC-AAAAAATCT
* * * *
104480 GTGACGGTTAGTACACGA-TTTCGGCTAAAAACTGACCCGAAAATTATTTTTCTCAGTTTTTTGC
259 -TGA---TGAGTACACGATTTTCGACTAAAAACTAACCCGAAAATT-TTTTTCTCAATTTTTTGC
* *
104544 CACAATACTAA-AAAAATATATATAATTCAACG-ACGAAAAGATTGATGGGCTTTTAACGCTTCT
1 CAAAATACTAAGAAAAA-ATATATAATTCAACGCA-GAAAAGATTGATGGTCTTTTAACGCTTCT
* * *
104607 AATATCATTTTTCCATTTTTTTTTCCGAAATAATTTTAATTGAATAAAAATAAGATTCATATGCT
64 AATATCATTTTTCCA---TTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATGCT
104672 CGTAAAAACAAATCCTTATATCCAATTTGGCTGAGATTT-GATTCGATGAATATATATATTTCAA
126 CGTAAAAACAAATCCTTATATCCAATTTGGCTGAGATTTAG-TTCGATGAATATATATATTTCAA
* * * *
104736 TGAGTCTTTCTGCCAAAAATCATTTCAAAACTGAGTCAGGGTCTCGAAACGCATTTTTAGC--AA
190 GGAGTCTTTCTGCCAAAAATCA-TGCAAAACTGAGCCAGGGTCTCGAAACGCGTTTTTAGCAAAA
* * * * * * **
104799 GA--TAG-TTAGTACACAATTTTCGATTAAAAACTAACCCGAAAATTATTTTCTCAA-TTTTCCC
254 AATCTTGATGAGTACACGATTTTCGACTAAAAACTAACCCGAAAATTTTTTTCTCAATTTTTTGC
* * * * * *
104860 CAAAATACTCAGAAAAAATATATAATTCAATGCCGAAAAGATTGTTGGGCCTTTTCACGCTTCTA
1 CAAAATACTAAGAAAAAATATATAATTCAACGCAGAAAAGATTGAT-GGTCTTTTAACGCTTCTA
* *
104925 ATATCATTTTTCCATTTTTTTTCCGAATTAATTTTAATTAAATCAATATAAGATTCAGATGCTCG
65 ATATCATTTTTCCA--TTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATGCTCG
* * * *
104990 TAAAAACAAATCCTTCTATCCAATGTGGCTGAGGTTTGGTTCGATGAATATATATATATATATGA
128 TAAAAACAAATCCTTATATCCAATTTGGCTGAGATTTAGTTC---G---------------ATGA
* * * *
105055 TATATATATATATATCAAGGAATTTTTTTGCCAAAAATCATGCAAAACT-AGGCAGGGTCCTCGA
175 -ATATATATAT-T-TCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCAGGGT-CTCGA
* * * * **
105119 AACACGTTTTTAGTAAAAAATCGTGATGGTTAGTACAC-AATTTCAGCAAAAAAAACGT-ACCCG
236 AACGCGTTTTTAGCAAAAAATCTTGAT-G--AGTACACGATTTTC-G-ACTAAAAAC-TAACCCG
*
105182 AAAACTTTTTTCTCAAATTTTTT--
295 AAAATTTTTTTCTC-AATTTTTTGC
* * * * * *
105205 TAACAATACTCAGAAAAAATATATAATTCAATGTCA-ACAAGATTGACCGGT-TTTTCACGCTTC
1 CAA-AATACTAAGAAAAAATATATAATTCAACG-CAGAAAAGATTGA-TGGTCTTTTAACGCTTC
* ** * * ** * *
105268 TAATATCGTTTTT--ATTTTTT-TTAATTAAATTCTAATTAAATCGAAGCAAGATACAGATGCTC
63 TAATATCATTTTTCCATTTTTTCCGAATT-AATTTTAATTAAATCAAAATAAGATTCATATGCTC
* ** * * * * * * **
105330 ATAAAAACAAATCCTTATATCCAACATGGCTGATATTTGGTTCAATTAGTATAGATATTTCAAAA
127 GTAAAAACAAATCCTTATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTCAAGG
* *
105395 AGTCTTTGTGCCAAGAATCATGCAAAA
192 AGTCTTTCTGCCAAAAATCATGCAAAA
105422 TCCTTTCAAA
Statistics
Matches: 2100, Mismatches: 276, Indels: 200
0.82 0.11 0.08
Matches are distributed among these distances:
316 164 0.08
317 166 0.08
318 173 0.08
319 362 0.17
320 468 0.22
321 152 0.07
322 55 0.03
323 247 0.12
324 14 0.01
325 5 0.00
326 1 0.00
327 32 0.02
334 4 0.00
335 18 0.01
336 25 0.01
337 22 0.01
338 3 0.00
340 5 0.00
341 73 0.03
343 6 0.00
344 8 0.00
345 50 0.02
346 42 0.02
347 5 0.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (318 bp):
CAAAATACTAAGAAAAAATATATAATTCAACGCAGAAAAGATTGATGGTCTTTTAACGCTTCTAA
TATCATTTTTCCATTTTTTCCGAATTAATTTTAATTAAATCAAAATAAGATTCATATGCTCGTAA
AAACAAATCCTTATATCCAATTTGGCTGAGATTTAGTTCGATGAATATATATATTTCAAGGAGTC
TTTCTGCCAAAAATCATGCAAAACTGAGCCAGGGTCTCGAAACGCGTTTTTAGCAAAAAATCTTG
ATGAGTACACGATTTTCGACTAAAAACTAACCCGAAAATTTTTTTCTCAATTTTTTGC
Found at i:105044 original size:2 final size:2
Alignment explanation
Indices: 105037--105069 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
105027 GGTTCGATGA
105037 AT AT AT AT AT AT AT AT GAT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
105070 CAAGGAATTT
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:105059 original size:15 final size:15
Alignment explanation
Indices: 105039--105067 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
105029 TTCGATGAAT
105039 ATATATATATATATG
1 ATATATATATATATG
105054 ATATATATATATAT
1 ATATATATATATAT
105068 ATCAAGGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATATATATATATATG
Found at i:105059 original size:17 final size:17
Alignment explanation
Indices: 105037--105069 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
105027 GGTTCGATGA
105037 ATATATATATATATATG
1 ATATATATATATATATG
105054 ATATATATATATATAT
1 ATATATATATATATAT
105070 CAAGGAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
ATATATATATATATATG
Found at i:105674 original size:23 final size:22
Alignment explanation
Indices: 105648--105705 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
105638 TTTATATATA
105648 ATAAATAAAAATAGTAACATAAG
1 ATAAAT-AAAATAGTAACATAAG
* *
105671 ATAAGATAAGATAGTAAGATAAG
1 ATAA-ATAAAATAGTAACATAAG
105694 ATTAAATTAAAA
1 A-TAAA-TAAAA
105706 GTTCAGTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 20 0.69
24 9 0.31
ACGTcount: A:0.62, C:0.02, G:0.12, T:0.24
Consensus pattern (22 bp):
ATAAATAAAATAGTAACATAAG
Found at i:107745 original size:37 final size:37
Alignment explanation
Indices: 107671--107745 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
107661 GGTTACTGAA
* * **
107671 TGATTTACGACTTTCATGAAGATTCCGAAAGTTAATT
1 TGATCTACGACTTTCATGAAGATTCCAAAAGAGAATT
*
107708 TGATCTACGAGTTTCATGAAGGATT-CAAAAGAGAATT
1 TGATCTACGACTTTCATGAA-GATTCCAAAAGAGAATT
107745 T
1 T
107746 TTATGTTTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 28 0.88
38 4 0.12
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (37 bp):
TGATCTACGACTTTCATGAAGATTCCAAAAGAGAATT
Found at i:108006 original size:443 final size:440
Alignment explanation
Indices: 106990--108004 Score: 1219
Period size: 444 Copynumber: 2.3 Consensus size: 440
106980 CGCGTTGCCT
* *
106990 TTTATTTTTGTATTT-TTTTTTCTATTTGTCTGATTAAGGTGATTTAAGTGTCTATTAAAAGGTA
1 TTTATTTTT-T-TTTCTTTGTTCTATTTGTCAGATTAAGGTGATTTAAGTGTCTATTAAAAGGTA
* * *
107054 ATTTCATAATCTACAATTTTCATGCAGAACTCAAAAG-TCAATTTTAATGTTTTGATTCT-AAAA
64 ATTTCATGATCTACAATTTTCATGAAGAACTCAAAAGCT-AATTTTAATGTTTTAATTCTAAAAA
* * **
107117 AATACTTCCGAAATTCTGTGGTTTTGATTGCCGGTCAATTTAATATCATATAATTTTTTATCCAC
128 AATACTTCCGAAATTCTGTGGTTTCGATTGCCGGTCAATTTAATACCATATAATTTTCGATCCAC
* * * * * * *
107182 ATATCCGATTGAATTTATTGAAGTGTCGGTTAAAAGGTTATTGTATGATTTAGGACTTTCATGAA
193 ATATCCGATTAAAGTTATTCAAGAGTCGGTTAAAAGGTTACTGAATGATTTACGACTTTCATGAA
* * *
107247 GGACCCGAAAGCTAAATTTGATCTATGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGCTTC
258 GGACCCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGATTCAAAAGAGAATTTTTATGCTTC
* * *
107312 AAGATCTCCATTAACAAACATTTTCTTATTTGGATTATTTATCAAATGACCCTCATATTTTTCTA
323 AAGATATCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGACCCTCATATTTTTCTA
107377 ATTTATACTACTTAGTCCTTACAAATTCTATCTTAATCTAACATCTAACATTTAAGA
388 ATTTATACTACTTAGTCCTTACAAATTCTATCTTAATC--ACATCTAACA-TT-AGA
* ** * * *
107434 TTTATTTTTTTATTCTTTGTTCTATTTGTCCGATTAAATTGATTCATGTATCTATTAAAAGGTAA
1 TTTATTTTTTT-TTCTTTGTTCTATTTGTCAGATTAAGGTGATTTAAGTGTCTATTAAAAGGTAA
* * * *
107499 TTTCATGATCTACAATTTTCATGAAGGACTCAAAAACAAATTTTTATGTTTTAATTC-AAAAAAA
65 TTTCATGATCTACAATTTTCATGAAGAACTCAAAAGCTAATTTTAATGTTTTAATTCTAAAAAAA
* * * ** *
107563 TGCTTCCTAAATT-TGGTTGTTTCGATTGTTGGTCTATTTAATACCATATAATTTTCGATCCACA
130 TACTTCCGAAATTCT-GTGGTTTCGATTGCCGGTCAATTTAATACCATATAATTTTCGATCCACA
*
107627 TATCCGATTAAAGTTATTCAAGAGTTGGTTAAAAGGTTACTGAATGATTTACGACTTTCATGAA-
194 TATCCGATTAAAGTTATTCAAGAGTCGGTTAAAAGGTTACTGAATGATTTACGACTTTCATGAAG
* * *
107691 GATTCCGAAAG-TTAATTTGATCTACGAGTTTCATGAAGGATTCAAAAGAGAATTTTTATGTTTC
259 GA-CCCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGATTCAAAAGAGAATTTTTATGCTTC
* * *
107755 AAGATATCTATTAAGAAATATTTTCTTATTTGAATTAGTTATCAAATGACCCTCATACTTTTCTA
323 AAGATATCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGACCCTCATA---TT-T-
* * * * *
107820 TTTTATATTTTATGCTACTTAGTCATTTACAAATTCTATCTTAATC-GAT-TTA-A-T-G-
383 TTCTA-A-TTTATACTACTTAGTC-CTTACAAATTCTATCTTAATCACATCTAACATTAGA
* * *
107875 TTTCATTTTTTTTTCTTTGTTCTATTTGTCAAATTAAGGTAATTTAGGTGTCTATTAAAAGGTAA
1 TTT-ATTTTTTTTTCTTTGTTCTATTTGTCAGATTAAGGTGATTTAAGTGTCTATTAAAAGGTAA
* * * * * * **
107940 TTTTATGATCTATAACTTTCATGAAAAACTCGAAAGCTAATTTTCATGTTCCAATTCTAAAAAAA
65 TTTCATGATCTACAATTTTCATGAAGAACTCAAAAGCTAATTTTAATGTTTTAATTCTAAAAAAA
108005 ATTACTTTTG
Statistics
Matches: 487, Mismatches: 68, Indels: 34
0.83 0.12 0.06
Matches are distributed among these distances:
441 94 0.19
442 17 0.03
443 105 0.22
444 223 0.46
446 3 0.01
447 3 0.01
448 6 0.01
449 1 0.00
450 15 0.03
451 20 0.04
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (440 bp):
TTTATTTTTTTTTCTTTGTTCTATTTGTCAGATTAAGGTGATTTAAGTGTCTATTAAAAGGTAAT
TTCATGATCTACAATTTTCATGAAGAACTCAAAAGCTAATTTTAATGTTTTAATTCTAAAAAAAT
ACTTCCGAAATTCTGTGGTTTCGATTGCCGGTCAATTTAATACCATATAATTTTCGATCCACATA
TCCGATTAAAGTTATTCAAGAGTCGGTTAAAAGGTTACTGAATGATTTACGACTTTCATGAAGGA
CCCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGATTCAAAAGAGAATTTTTATGCTTCAAG
ATATCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGACCCTCATATTTTTCTAATT
TATACTACTTAGTCCTTACAAATTCTATCTTAATCACATCTAACATTAGA
Found at i:108594 original size:17 final size:18
Alignment explanation
Indices: 108572--108606 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
108562 TTTCTTCTAT
*
108572 TTATCTCATGC-AATATA
1 TTATCTCACGCTAATATA
108589 TTATCTCACGCTAATATA
1 TTATCTCACGCTAATATA
108607 GTGGATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (18 bp):
TTATCTCACGCTAATATA
Found at i:110431 original size:15 final size:15
Alignment explanation
Indices: 110407--110443 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
110397 AGTGATTAGT
* *
110407 CTTTGGGAAGATTTG
1 CTTTGTGAAGAATTG
110422 CTTTGTGAAGAATTG
1 CTTTGTGAAGAATTG
110437 CTTTGTG
1 CTTTGTG
110444 CAACGGGTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.08, G:0.30, T:0.43
Consensus pattern (15 bp):
CTTTGTGAAGAATTG
Found at i:117948 original size:2 final size:2
Alignment explanation
Indices: 117941--117965 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
117931 GAATATAAGA
117941 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 A
117966 AAATAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:119224 original size:24 final size:25
Alignment explanation
Indices: 119197--119246 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
119187 TATTTTTTGA
119197 TACTATTAATTTAACAAAG-TAAAT
1 TACTATTAATTTAACAAAGATAAAT
* **
119221 TACTTTTAATTTGCCAAAGATAAAT
1 TACTATTAATTTAACAAAGATAAAT
119246 T
1 T
119247 TAAACTCGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (25 bp):
TACTATTAATTTAACAAAGATAAAT
Found at i:120431 original size:2 final size:2
Alignment explanation
Indices: 120424--120456 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
120414 ATTATAATCT
120424 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
120457 TTCCTCTCTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:134699 original size:15 final size:15
Alignment explanation
Indices: 134679--134709 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
134669 GCAATGTATC
134679 ATAATACCAACATCT
1 ATAATACCAACATCT
134694 ATAATACCAACATCT
1 ATAATACCAACATCT
134709 A
1 A
134710 GAAGAGATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (15 bp):
ATAATACCAACATCT
Found at i:140306 original size:24 final size:24
Alignment explanation
Indices: 140279--140349 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
140269 AGCAGGAACT
*
140279 GGTGGAGGGCTA-GATGACGTGGCA
1 GGTGGAGAGCTAGGA-GACGTGGCA
* *
140303 GGTGGTGAGCTAGGAGCCGTGGCA
1 GGTGGAGAGCTAGGAGACGTGGCA
*
140327 GGTGGAGTGCT-GG-GA-GTGGCA
1 GGTGGAGAGCTAGGAGACGTGGCA
140348 GG
1 GG
140350 AGTGGCCGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 8 0.20
22 1 0.03
23 2 0.05
24 27 0.68
25 2 0.05
ACGTcount: A:0.17, C:0.13, G:0.54, T:0.17
Consensus pattern (24 bp):
GGTGGAGAGCTAGGAGACGTGGCA
Found at i:140384 original size:24 final size:24
Alignment explanation
Indices: 140352--140420 Score: 111
Period size: 24 Copynumber: 2.9 Consensus size: 24
140342 GTGGCAGGAG
*
140352 TGGCCGGTGGAGAGCTGGGAGACT
1 TGGCGGGTGGAGAGCTGGGAGACT
140376 TGGCGGGTGGAGAGCTGGGAGACT
1 TGGCGGGTGGAGAGCTGGGAGACT
* *
140400 TAGCGGGTGGAGAGCTAGGAG
1 TGGCGGGTGGAGAGCTGGGAG
140421 GAGTGGCCGG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.19, C:0.13, G:0.52, T:0.16
Consensus pattern (24 bp):
TGGCGGGTGGAGAGCTGGGAGACT
Found at i:140439 original size:12 final size:12
Alignment explanation
Indices: 140424--140453 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
140414 CTAGGAGGAG
140424 TGGCCGGAGACT
1 TGGCCGGAGACT
*
140436 TGGCGGGAGACT
1 TGGCCGGAGACT
140448 TGGCCG
1 TGGCCG
140454 CAGGTGGTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (12 bp):
TGGCCGGAGACT
Found at i:145173 original size:26 final size:26
Alignment explanation
Indices: 145136--145190 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
145126 ATTCAGCATT
*
145136 TACCAGAAAACTATTAAAAGGAATGC
1 TACCAGAAAACTATTAAAAGGAAAGC
*
145162 TACCAGAGAACTATTAAAAGGAAAGC
1 TACCAGAAAACTATTAAAAGGAAAGC
145188 TAC
1 TAC
145191 AATCGGTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.18
Consensus pattern (26 bp):
TACCAGAAAACTATTAAAAGGAAAGC
Found at i:147933 original size:5 final size:5
Alignment explanation
Indices: 147896--147936 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
147886 AAGACAGAAT
*
147896 GAAAA -AAAA AAAAA G-AAA -AAAA GAAAA GAAAA GAAAA GAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAA
147937 GGCTTACTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
4 10 0.31
5 22 0.69
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:151060 original size:2 final size:2
Alignment explanation
Indices: 151053--151156 Score: 208
Period size: 2 Copynumber: 52.0 Consensus size: 2
151043 TAAATCACAT
151053 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
151095 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
151137 GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA
151157 AGAAGTAAAA
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 102 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:152703 original size:11 final size:11
Alignment explanation
Indices: 152689--152726 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
152679 ATTCATAACA
152689 AATTTATAATT
1 AATTTATAATT
152700 AATTTATAATT
1 AATTTATAATT
152711 -ATTTGATAATT
1 AATTT-ATAATT
*
152722 TATTT
1 AATTT
152727 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Done.