Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015404.1 Corchorus olitorius cultivar O-4 contig15437, 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: 112230
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1502 original size:325 final size:324
Alignment explanation
Indices: 857--1988 Score: 1401
Period size: 325 Copynumber: 3.5 Consensus size: 324
847 TTTTGCAAAA
* * * * *
857 TTTTAGCCGAAATCGTGTATTAACCAACACGGTTTTT-GGCTAAAAACGCGTTCTGGGGCCCCAG
1 TTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTTGGGCTAAAAACGCGTT-TCGGGCCCCGG
* **** * * * * * *
921 CTCAGTTTT-CAATGATTTTTCGCCCTGAGATTCCTCGACATATCTAT-ATTCATCTAACCATAT
65 CTCAGTTTTGC-ATGATTTTTAGCAGAAAGACTCCT-TAAATATCTATAATT-ATCGAATCAAAT
* * * * * ** * *
984 TTTAGCCAAATTGGATTTAAGGATTTGACTTTACGAGCATCAGAATCGTGATTT-GATTTAATCA
127 CTCAGCCACATAGGATATAAGGATTTGTTTTTACGAGCATCTGAATCGTG-TTTGGATTTAATTA
* * ** * * * *
1048 GAAATTAATTAAGAAATATATA-GGAAAATCGATATTAGAAGCGTGAAAAGCCATTTAATCTTTT
191 GGAATAAATTCGGAAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCATTTAATCTTTT
* * *
1112 TGGCATTGAATTATATAACATTTTCTACA-AACTGTGTTAAAAACAATTATGAAAAAACA--TTG
256 TGGCGTTGAATTATATAACTTTTTCTA-AGAATTGTGTTAAAAA-AATTATGAAAAAA-ATTTTG
1174 GGTCAGT
318 GGTCAGT
* * *
1181 TTTTACCCGAAATCGTGTACTAACCATCATGGTTTTGGGGCTAAAATCGCGTTTCAGGGCCCCGG
1 TTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTTGGGCTAAAAACGCGTTTC-GGGCCCCGG
* * *
1246 CTCCGTTTTACATGATTTTTAGCAGAAAGACTCCTTAAAATATCTATAATTATCGAATGAAATCT
65 CTCAGTTTTGCATGATTTTTAGCAGAAAGACTCCTT-AAATATCTATAATTATCGAATCAAATCT
*
1311 CAGCCACATAGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTGGATTTAATTAGGA
129 CAGCCACATAGGATATAAGGATTTGTTTTTACGAGCATCTGAATCGTGTTTGGATTTAATTAGGA
* *
1376 ATAAATTCGGAAAAAAAAATTGAAAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGG
194 ATAAATTCGGAAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCATTTAATCTTTTTGG
*
1441 CGTTGAATTATATAACTTTTTCTAAGAATTGTGTT-AAAAATTTATGAAAAAAATTTTGGGTCAG
259 CGTTGAATTATATAACTTTTTCTAAGAATTGTGTTAAAAAAATTATGAAAAAAATTTTGGGTCAG
1505 T
324 T
*
1506 TTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTTGGGCTAAAAACGCTTTTCGGGGCCCCGG
1 TTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTTGGGCTAAAAACGCGTTTC-GGGCCCCGG
* * *
1571 CTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTTATCGAACCAAATCT
65 CTCAGTTTTGCATGATTTTTAGCAGAAAGACTCCTT-AAATATCTATAATTATCGAATCAAATCT
*
1636 CAGCCACATAGGATATAAGGATTTGTTTTAACGAGCATCTGAATCGTGTTTGGATTTAATTAGGA
129 CAGCCACATAGGATATAAGGATTTGTTTTTACGAGCATCTGAATCGTGTTTGGATTTAATTAGGA
* * *
1701 ATAAATTCGGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCATTTAATCCTTTTGA
194 ATAAATTCGGAAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCATTTAATCTTTTTGG
* * *
1766 AGTTGAATTATATAATTTTTTCTAAGAATTGTGTTAAAAAAAATTATG-AAAAAATTTTCGGTTC
259 CGTTGAATTATATAACTTTTTCTAAGAATTGTGTT-AAAAAAATTATGAAAAAAATTTT-GGGTC
1830 AGT
322 AGT
* **
1833 TTTTAGCCGAAATCGTGTACGT---TATCATGGTTTTTGGTTTAAAAACGCGTTTCGGTGCCCCG
1 TTTTAGCCGAAATCGTGTAC-TAACCATCATGGTTTTTGGGCTAAAAACGCGTTTCGG-GCCCCG
* * * * *
1895 ACTCAGTTTTGCATGATTTCTAGCAGAAAGACTCCTCTAAATATCTAT-ATTGTTTGAATCATAT
64 GCTCAGTTTTGCATGATTTTTAGCAGAAAGACTCCT-TAAATATCTATAATT-ATCGAATCAAAT
* *
1959 CTCGGCCATATAGGATATAAGGATTTGTTT
127 CTCAGCCACATAGGATATAAGGATTTGTTT
1989 CTTTGGGGTA
Statistics
Matches: 709, Mismatches: 82, Indels: 33
0.86 0.10 0.04
Matches are distributed among these distances:
323 1 0.00
324 52 0.07
325 531 0.75
326 87 0.12
327 37 0.05
328 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (324 bp):
TTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTTGGGCTAAAAACGCGTTTCGGGCCCCGGC
TCAGTTTTGCATGATTTTTAGCAGAAAGACTCCTTAAATATCTATAATTATCGAATCAAATCTCA
GCCACATAGGATATAAGGATTTGTTTTTACGAGCATCTGAATCGTGTTTGGATTTAATTAGGAAT
AAATTCGGAAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCATTTAATCTTTTTGGCG
TTGAATTATATAACTTTTTCTAAGAATTGTGTTAAAAAAATTATGAAAAAAATTTTGGGTCAGT
Found at i:7599 original size:3 final size:3
Alignment explanation
Indices: 7591--7624 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
7581 AATAAAGTTG
* *
7591 AAT AAT AAT AAT GAT AAT AAA AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
7625 TTATTATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:11806 original size:19 final size:20
Alignment explanation
Indices: 11774--11811 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
11764 TATGCACATG
*
11774 CATGCATACTTGGA-ATATC
1 CATGCATACATGGATATATC
*
11793 CATGCATGCATGGATATAT
1 CATGCATACATGGATATAT
11812 TTTTTAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (20 bp):
CATGCATACATGGATATATC
Found at i:12179 original size:29 final size:29
Alignment explanation
Indices: 12146--12202 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
12136 ATTAACGGGG
12146 CTTCAA-ATTGAAACTTCAG-GGAACAAAAC
1 CTTCAATATT-AAACTTCAGAGG-ACAAAAC
*
12175 CTTCAATATTAAAGTTCAGAGGACAAAA
1 CTTCAATATTAAACTTCAGAGGACAAAA
12203 TGTCCAAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.23
Consensus pattern (29 bp):
CTTCAATATTAAACTTCAGAGGACAAAAC
Found at i:13368 original size:17 final size:16
Alignment explanation
Indices: 13337--13372 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
13327 CCGTATACTT
13337 CATTATTTGTCTGGGC
1 CATTATTTGTCTGGGC
*
13353 CATTAGTTTGTTTGGGC
1 CATTA-TTTGTCTGGGC
13370 CAT
1 CAT
13373 GAATTTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.14, C:0.17, G:0.25, T:0.44
Consensus pattern (16 bp):
CATTATTTGTCTGGGC
Found at i:17466 original size:31 final size:31
Alignment explanation
Indices: 17425--17593 Score: 108
Period size: 31 Copynumber: 5.6 Consensus size: 31
17415 TTTGGTTAAT
17425 TGCTCAAATAAGGGCCTAACGTTTATCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTATCAAAA
* * **
17456 TGTTCAAATAAGGG-TTCAATC-TTT-T-AATT
1 TGCTCAAATAAGGGCCT-AA-CGTTTATCAAAA
*
17485 TGAC-CAAATAAGGGCCTAATG-TTATCGAAAA
1 TG-CTCAAATAAGGGCCTAACGTTTATC-AAAA
*** **
17516 TGCTCAAATAAGGGTCCGGTC-TTT-T-AATT
1 TGCTCAAATAAGGG-CCTAACGTTTATCAAAA
17545 TGGC-CAAATAAGGGCCTAACG-TTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTATC-AAAA
17576 TGCTCAAATAAGGGCCTA
1 TGCTCAAATAAGGGCCTA
17594 GCGTCGAAAA
Statistics
Matches: 101, Mismatches: 20, Indels: 34
0.65 0.13 0.22
Matches are distributed among these distances:
28 7 0.07
29 31 0.31
30 8 0.08
31 50 0.50
32 5 0.05
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTATCAAAA
Found at i:17503 original size:60 final size:60
Alignment explanation
Indices: 17429--17589 Score: 252
Period size: 60 Copynumber: 2.7 Consensus size: 60
17419 GTTAATTGCT
* *
17429 CAAATAAGGGCCTAACGTTTATC-AAAATGTTCAAATAAGGGTTCAATCTTTTAATTTGAC
1 CAAATAAGGGCCTAACG-TTATCGAAAATGCTCAAATAAGGGTCCAATCTTTTAATTTGAC
* ** *
17489 CAAATAAGGGCCTAATGTTATCGAAAATGCTCAAATAAGGGTCCGGTCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCCAATCTTTTAATTTGAC
17549 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGG
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGG
17590 CCTAGCGTCG
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
59 5 0.05
60 88 0.95
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCCAATCTTTTAATTTGAC
Found at i:17609 original size:28 final size:29
Alignment explanation
Indices: 17549--17610 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
17539 TTAATTTGGC
17549 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACG-T-TCGAAAATGCT
* *
17580 CAAATAAGGGCCTAGCG-TCGAAAATTCT
1 CAAATAAGGGCCTAACGTTCGAAAATGCT
17608 CAA
1 CAA
17611 GCGTCATCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 13 0.45
31 16 0.55
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (29 bp):
CAAATAAGGGCCTAACGTTCGAAAATGCT
Found at i:17731 original size:60 final size:60
Alignment explanation
Indices: 17630--17794 Score: 233
Period size: 60 Copynumber: 2.8 Consensus size: 60
17620 AAACTGACGC
* *
17630 CAGACCCTTATTTGAGCATCTTCGA-TAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
1 CAGACCCTTATTTGAGCAT-TTTGACAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
* * * * *
17690 CAGACCTTTATTTGAGCATTTTGACAAATGTTAAGCTCTTATTTGGCCAAATTAAAATAT
1 CAGACCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
* *
17750 CAGACCCATATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
1 CAGACCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTG
17795 AGCAATTAGC
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
59 4 0.04
60 87 0.96
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (60 bp):
CAGACCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
Found at i:18073 original size:2 final size:2
Alignment explanation
Indices: 18066--18098 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18056 AATCTTTAGG
18066 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
18099 TAAAAACTCA
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:31124 original size:15 final size:15
Alignment explanation
Indices: 31095--31143 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
31085 TGGTACGAAG
*
31095 GAAATGGGAAGGAAA
1 GAAAGGGGAAGGAAA
31110 GAAGAGGGG-AGGAAA
1 GAA-AGGGGAAGGAAA
*
31125 GAAAGGGGAAGGAAT
1 GAAAGGGGAAGGAAA
31140 GAAA
1 GAAA
31144 AGGGTTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 5 0.17
15 21 0.70
16 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.45, T:0.04
Consensus pattern (15 bp):
GAAAGGGGAAGGAAA
Found at i:32196 original size:18 final size:18
Alignment explanation
Indices: 32173--32208 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
32163 TTTTTGGCAC
* *
32173 AAATAAACTAAGGTTATA
1 AAATAAACAAAGCTTATA
32191 AAATAAACAAAGCTTATA
1 AAATAAACAAAGCTTATA
32209 TACAACTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.25
Consensus pattern (18 bp):
AAATAAACAAAGCTTATA
Found at i:33621 original size:16 final size:17
Alignment explanation
Indices: 33592--33627 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
33582 AAGCTATTAA
33592 AAATAAAATCAATTCTT
1 AAATAAAATCAATTCTT
*
33609 AAAT-AAATTAATTCTT
1 AAATAAAATCAATTCTT
33625 AAA
1 AAA
33628 CCCATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATAAAATCAATTCTT
Found at i:33968 original size:26 final size:27
Alignment explanation
Indices: 33902--33962 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
33892 CCAAATCCAA
*
33902 AATAAGAA-AAAAAAAACTTTAATCTG
1 AATAATAATAAAAAAAACTTTAATCTG
* *
33928 AATTATAATAAAAAAATCTTTAATCTG
1 AATAATAATAAAAAAAACTTTAATCTG
33955 AATAATAA
1 AATAATAA
33963 CCAAAAGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 6 0.20
27 24 0.80
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.30
Consensus pattern (27 bp):
AATAATAATAAAAAAAACTTTAATCTG
Found at i:33968 original size:27 final size:27
Alignment explanation
Indices: 33902--33973 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 27
33892 CCAAATCCAA
*
33902 AATAAGAA-AAAAAAAACTTTAATCTG
1 AATAATAACAAAAAAAACTTTAATCTG
* * *
33928 AATTATAATAAAAAAATCTTTAATCTG
1 AATAATAACAAAAAAAACTTTAATCTG
33955 AATAATAACCAAAAGAAAA
1 AATAATAA-CAAAA-AAAA
33974 GAGGCTCATT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
26 6 0.16
27 24 0.65
28 4 0.11
29 3 0.08
ACGTcount: A:0.61, C:0.08, G:0.06, T:0.25
Consensus pattern (27 bp):
AATAATAACAAAAAAAACTTTAATCTG
Found at i:45955 original size:63 final size:63
Alignment explanation
Indices: 45877--46001 Score: 214
Period size: 63 Copynumber: 2.0 Consensus size: 63
45867 CACAGCTGCT
*
45877 CTCGTAACTTTCAACTTCGATCGAGTAGCCTCCGTCGCCAGAGAAGAAGACGCTTTCCGCTTA
1 CTCGTAACTTTCAACTTCGATCGACTAGCCTCCGTCGCCAGAGAAGAAGACGCTTTCCGCTTA
* * *
45940 CTCGTAACTTTCAACTTCGATGGCCTAGCCTCCGTCGCCGGAGAAGAAGACGCTTTCCGCTT
1 CTCGTAACTTTCAACTTCGATCGACTAGCCTCCGTCGCCAGAGAAGAAGACGCTTTCCGCTT
46002 CCTCTGCATT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.26
Consensus pattern (63 bp):
CTCGTAACTTTCAACTTCGATCGACTAGCCTCCGTCGCCAGAGAAGAAGACGCTTTCCGCTTA
Found at i:51769 original size:24 final size:23
Alignment explanation
Indices: 51740--51790 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
51730 AAAAAGTTTA
* *
51740 TTTTTTAAAAATAAATAAATAACT
1 TTTTTTAAAAACAAAAAAATAA-T
*
51764 TTTTTTCAAAACAAAAAAATAAT
1 TTTTTTAAAAACAAAAAAATAAT
51787 TTTT
1 TTTT
51791 ATAATCATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTTTTAAAAACAAAAAAATAAT
Found at i:51867 original size:28 final size:28
Alignment explanation
Indices: 51813--51868 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
51803 TATACAACCT
**** *
51813 AAACAATTTTCACAAAACTGGCCAAAAA
1 AAACAATTTTCACAAAAAACACAAAAAA
51841 AAACAATTTTCACAAAAAACACAAAAAA
1 AAACAATTTTCACAAAAAACACAAAAAA
51869 TTCATCAAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.61, C:0.20, G:0.04, T:0.16
Consensus pattern (28 bp):
AAACAATTTTCACAAAAAACACAAAAAA
Found at i:58822 original size:20 final size:20
Alignment explanation
Indices: 58797--58838 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
58787 ATAGTATAAG
58797 GTAGGAAATAACTTTAGCAT
1 GTAGGAAATAACTTTAGCAT
58817 GTAGGAAATAACTTTAGCAT
1 GTAGGAAATAACTTTAGCAT
58837 GT
1 GT
58839 TTGAATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (20 bp):
GTAGGAAATAACTTTAGCAT
Found at i:76340 original size:331 final size:330
Alignment explanation
Indices: 75532--78350 Score: 2251
Period size: 331 Copynumber: 8.5 Consensus size: 330
75522 CATTACAAAA
* * * * *
75532 ATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAATTAATTTAG-AAAAATAAG
1 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATG
* * * * * *
75596 AAATACAATATTAAAAGCGTAAAAAACCCTCCATTAATCTTTTTGACGTTGAATTATATAT-TTT
66 AAAAACGATATTAAAAGCGT-GAAAA--GTCC-TCAATCTTTTTGGCGTTGAATTATATATATTT
* * **
75660 TATGAGTATTTTAGCCAAAAATTGAGGAGAAATCA-TCCATGTCAATTTTTGCAAAATTTTAGCC
127 TATGAGTATTTTAGCCAAAAATTGAGGAAAAAT-ATTTCGGGTCAATTTTTGCAAAATTTTAGCC
* * ** * * *
75724 GAAATCTTGCACTAACAAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGAGACCC-GACTCA
191 GAAATCGTG---TAA-TAACCATCATAGTTTTTGGCTAAAAACGCGTTT-GG-GGCCCTGGCTCA
* ** * * *
75788 ATTTTGCATGATTTTTGGCTTCAAAACTACTTGAAATATCTATATTCATCCAATCAAATCTCAGC
250 GTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGC
* *
75853 CACAATGGATTTAAAG
315 CACATTGGATTTAAGG
* * ** *
75869 ATTTGTTTTCACGTGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGG
1 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATG
* * * * * * * *
75934 AAAAACGATATTAGAATCATCAAAAGCCCTTCAATTTTTTTGACGTTGAATTTTATATATTTTAT
66 AAAAACGATATTAAAAGCGTGAAAAGTCC-TCAATCTTTTTGGCGTTGAATTATATATATTTTAT
* * *
75999 GAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAA
130 GAGTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAA
* *
76064 TCGTGTAATAACCATCATAGTTTTTGGCTAGAAAA-GCGTTCTGGGGCCCTGCCTCAATTTTGCA
195 TCGTGTAATAACCATCATAGTTTTTGGCTA-AAAACGCGTT-TGGGGCCCTGGCTCAGTTTTGCA
* * * * * * *
76128 TGATTTTTGGCGCCAAGACTCCTAGAGATATCCATATTCATCAAATTAAATCTCAGTCACATTGC
258 TGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGG
76193 ATTTAAGG
323 ATTTAAGG
* * * *
76201 A-TTGTTTTTACGAGCATCTAAATCTTATTTCGATTTAAATAGAAATTAATACAGAAAAAATATG
1 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATG
* * * * *
76265 AAAAATGATATGAAAAGCGTGAAAAGTCCTCAAATCTTTTTGGCATTAAATTATATATATTTCAT
66 AAAAACGATATTAAAAGCGTGAAAAGTCCTC-AATCTTTTTGGCGTTGAATTATATATATTTTAT
* * * * * *
76330 GAGTATTTTAGTCAAAAATTGA-GAAAAAAATTTTCTGGTGATTTTTTGCAAAATTTTCGCCGAA
130 GAGTATTTTAGCCAAAAATTGAGGAAAAATA-TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAA
* * * * * * * *
76394 ATCGTGTACTAATCATCACGACTTTTT-GCTAAAAATGTCTTTTGAGGTCCC-GGCTCAGTATTG
194 ATCGTGTAATAACCATCA-TAGTTTTTGGCTAAAAACG-CGTTTG-GGGCCCTGGCTCAGTTTTG
* * * *
76457 CATGATTTTTGGCGTCGAGCCAT-CTTGAAATATCTATATTCATCTAATCAAATTTCAGCCACAT
256 CATGATTTTTGGCGCCAAGAC-TCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACAT
*
76521 TGCATTTAAGG
320 TGGATTTAAGG
* *
76532 ATTTGTTTTTACGAGCATCTGAATCTTGTTTTGGTTTAATTAGAAATTAATTCAG-AAAAATATG
1 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATG
* * *
76596 AAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTGTGGAGTTGAATTATATACATTTTAT
66 AAAAACGATATTAAAAGCGTGAAAAGTCCT-CAATCTTTTTGGCGTTGAATTATATATATTTTAT
* * * * ** * *
76661 AATTATTTTAGACAAAAAATTGAGAAAAAATATTTTTGGTCAATTTTTTTTGCAAAATATTAGCT
130 GAGTATTTTAG-CCAAAAATTGAGGAAAAATATTTCGGGTCAA---TTTTTGCAAAATTTTAGCC
* * * * ** *
76726 GAAATCGTATACTTTAGTCGAAATCACGGTTTTTTTTGGGCTAAAAACGCGTTTCAGGG--CT--
191 GAAATCGTGTA--ATA-AC--CATCA---TAGTTTTT-GGCTAAAAACGCGTTT-GGGGCCCTGG
* * * * *
76787 C-C-G-GTTGCATGA-TTTTGGTGCCGAGACTCCTTGAAATCTCTATATTCATCTAACCAAATC-
246 CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCT
* * *
76847 CTAACTACATTGGATTTAACG
311 C-AGCCACATTGGATTTAAGG
**** * * * * * * ** *
76868 ATTTG-AAAAACAAGCATTTGAATCATGTTTCAATTTAATTTGAAATTAATTCGGGAAATGATAG
1 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-AGAAAAAATAT
* * ** * *
76932 GAAAAACGATATTGAAAGCATGAAAAACCCCTTCAATCTTTTTGGTGTTCAATTATATA-ATTTT
65 GAAAAACGATATTAAAAGCGTG-AAAAGTCC-TCAATCTTTTTGGCGTTGAATTATATATA-TTT
* * * * * * ** * * * *
76996 TATAAGTATTGTGGCTAAAAATTGAGGAAATAGATTTCGATTTAATTTTTGCAAAATTCTAACCA
127 TATGAGTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCG
* * ** ** * * * *
77061 AAATCATGTAATAAACATCACGGTTTTTAGATAATAAAAACGCTTTTTGGGG-TCTCGACTTAGT
192 AAATCGTGTAATAACCATCATAGTTTTT-G--GCTAAAAACGC-GTTTGGGGCCCT-GGCTCAGT
* *
77125 TTTGCATGATTTTTGGTGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCA
252 TTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCA
*
77190 CATTGGATTTAAGA
317 CATTGGATTTAAGG
* * * ** * * *
77204 ATTTGTTTTTACGAGCATCTGAATCATGTTTCGTTTTATTTATTAATTAATTCGGAAAAAAAAAG
1 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAAATAT
* * * *
77269 GAAAAACGATATTAGAAGCGTTAAAAGCCCTTCAATATTTTTGGCGTTGAATTATATAT-TTTTA
65 GAAAAACGATATTAAAAGCGTGAAAAGTCC-TCAATCTTTTTGGCGTTGAATTATATATATTTTA
* * * * * *
77333 TGACG-ATTGTGGCTAAAAATAGAGGAAAAATATTTCGGGTCGATTTTTGCAAAATATTAGCCGA
129 TGA-GTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGA
* * ** ** * * * * *
77397 AATCGTGTAA-CATCATGGGTTTTTTTTTTTTTTGCTAAAACCCCGTTTCGGGGCCCCGGGTCAG
193 AATCGTGTAATAACCA------TCATAGTTTTTGGCTAAAAACGCGTTT-GGGGCCCTGGCTCAG
* * * * *
77461 TTTTCCATGATTTTTGGCTCTAAAACTCCTTGAAATATTTATATTCATCTAATCAAATCTCAGCC
251 TTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCC
* *
77526 ACAATGGATTTAAAG
316 ACATTGGATTTAAGG
** * * * * *
77541 ATTTG-TTTTATTAGCATCTAAATCATGTCTT-GATTTGATTAGAAATTAATTCGGAAAAAGTAT
1 ATTTGTTTTTACGAGCATCTGAATCTTGT-TTCGATTTAATTAGAAATTAATTCAGAAAAAATAT
** * * * * *
77604 GAAAAATAATATTAGAAGCGTAAAAAATCCTTCAATATTTTTCGCGTTGAATTATA-AT-TTTT-
65 GAAAAACGATATTAAAAGCGTGAAAAGTCC-TCAATCTTTTTGGCGTTGAATTATATATATTTTA
* * * * *
77666 T---TA---T-GCCAAAAATTAAGGAAATATCTTTCCGGTCAGTTTTTTTGCAAAATTTTAGCCG
129 TGAGTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGGTCA--ATTTTTGCAAAATTTTAGCCG
** ** *
77724 AAATCGTGTAATAATTATCACGGTTTTTGGCTAAAAACGCG-TT----CCATGG-TCCAAG----
192 AAATCGTGTAATAACCATCATAGTTTTTGGCTAAAAACGCGTTTGGGGCCCTGGCT-C-AGTTTT
* * * * * * *
77779 GCA-G-TTTTAT---GCTAAAACTCATGGAGATATCCATATTCATCTATTCAAATCTCAGCCACA
255 GCATGATTTT-TGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACA
*
77839 TTGTATTTAAGG
319 TTGGATTTAAGG
* * * *
77851 ATTTCTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAATATAAATTAATTCAAAAAAAATATG
1 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATG
* * * * *
77916 AAAAACGAAATGAAAAGCGTGAAAAGTCCACCCATCTTTTTGGCGTT-AACTTATATATATTTCA
66 AAAAACGATATTAAAAGCGTGAAAAGTCC-TCAATCTTTTTGGCGTTGAA-TTATATATATTTTA
** * * * *
77980 TGAGTATTTTAGCCAAAAATTGCTGAAAAATTTTTCAGAT-AATTTTTTGCAAAATTTTAGTCGA
129 TGAGTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGGTCAA-TTTTTGCAAAATTTTAGCCGA
* * * * * * *
78044 AATCGTGTACTAACTATCACTATTTTTTTTGCTAAAAACGCATTTCAGGGTCAC-GGCTCAGTTT
193 AATCGTGTAATAACCATCA-TA-GTTTTTGGCTAAAAACGCGTTT--GGGGCCCTGGCTCAGTTT
** *
78108 TGCATGATTTTTGGCATCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACA
254 TGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACA
* *
78173 TTGCATTTAATG
319 TTGGATTTAAGG
*
78185 ATTTGTTTTTACGAGCATCTGAATCTTGTTCCGATTTAATTAGAAATTAATTCAG-AAAAATATG
1 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATG
*** * **
78249 AAAAGTTATATTAAAAGTGTGAAAAGTCCTCCAATCTTTTTGGATTTGAATTATATATATATTTT
66 AAAAACGATATTAAAAGCGTGAAAAGTCCT-CAATCTTTTTGGCGTTGAA-T-TATATATATTTT
* * *
78314 AAGAGTATTTTAGACAAAATTTGAGGAAAAATATTTC
128 ATGAGTATTTTAGCCAAAAATTGAGGAAAAATATTTC
78351 CGATTTAGTC
Statistics
Matches: 1979, Mismatches: 397, Indels: 214
0.76 0.15 0.08
Matches are distributed among these distances:
310 60 0.03
311 86 0.04
312 6 0.00
313 5 0.00
314 3 0.00
316 1 0.00
317 7 0.00
318 2 0.00
319 37 0.02
320 2 0.00
321 38 0.02
322 4 0.00
323 16 0.01
326 32 0.02
327 4 0.00
328 44 0.02
329 12 0.01
330 15 0.01
331 327 0.17
332 186 0.09
333 60 0.03
334 136 0.07
335 261 0.13
336 270 0.14
337 263 0.13
338 68 0.03
339 2 0.00
340 11 0.01
341 1 0.00
342 5 0.00
343 6 0.00
344 9 0.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (330 bp):
ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATG
AAAAACGATATTAAAAGCGTGAAAAGTCCTCAATCTTTTTGGCGTTGAATTATATATATTTTATG
AGTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAAT
CGTGTAATAACCATCATAGTTTTTGGCTAAAAACGCGTTTGGGGCCCTGGCTCAGTTTTGCATGA
TTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATT
TAAGG
Found at i:79591 original size:332 final size:327
Alignment explanation
Indices: 78498--80858 Score: 1663
Period size: 332 Copynumber: 7.1 Consensus size: 327
78488 CTTAATCATA
* * * * * * *
78498 TTTCGATTTAATTAGAAATTAGTTCGGTACATAATAGGAAAAGACGATACTAGAAGCATGAAAAA
1 TTTCGATTTAATTAGAAATTAATTCAG-A-AAAATA-TAAAAAACGATATTAGAAGCGTG-AAAA
* * * *
78563 GCCCTTCAATCTTTTTGGCGTTAAATTACATAATTTTTATGAGTATTGTGTCCAAAAATTGA-GA
62 GCCCTTCAATCTTTTTGGCGTTGAATTATAT-ATTTTTATGAGTATTTTG-CTAAAAATTGAGGA
* ** * * *
78627 AAATAACTTTCAAGTCATTTTTTGCAAAATTCTAGCTGAAATCGTGTAATAATCATCACAGTTTT
125 AAA-ATCTTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACAGTTTT
* * ** * * *
78692 TGGCAAAAAAAAAAAAAGCGTTTCGGGGCCCTGACTTAGTTTTGCATGATTTTTTGCGCCT-AGA
189 TGGC------TAAAAACGCG-TTCCAGGCCCGGA-TCAGTTTTGCATGATTTTTTGTG-CTAAGA
* * *
78756 ATCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAA-GAATT-TTTTT
245 CTCCTTGAAATATCAATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
*
78819 ACGAGCATCTGAATCA-CG
310 ACGAGCATCTGAAT-ATTG
* * *
78837 TTTCGTTTTAATTAGAAATTAATTTAGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGC
1 TTTCGATTTAATTAGAAATTAATTCAGAAAAATATA--AAAAACGATATTAGAAGCGTGAAAAGC
* * * *
78902 CCTTAAATCTTTTTGGCGTTGAATTATATATTTGTTATGACTATTGTGGCTAAAAATTGAGAAAA
64 CCTTCAATCTTTTTGGCGTTGAATTATATATTT-TTATGAGTATT-TTGCTAAAAATTGAG-GAA
* * * * ***
78967 AAATATTT-TGGGTCAATTTTTGCAAAATATTAGGCGAAATCATGTAAATAA-C--C-TTTTTTT
126 AAATCTTTCT-GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT-AATAATCATCACAGTTTT
* * * * * *
79027 TTGCTAAAAACGCTTTCCGAGGCCCCGGGTTAGTTTTCCATGATTTTTTGTGCTAAAACTCCTTG
189 TGGCTAAAAACGCGTTCC-AGG-CCCGGATCAGTTTTGCATGATTTTTTGTGCTAAGACTCCTTG
* * * * * * *
79092 AAATATCTAATATTCATCTGATCAAATCTCAACCATAATGGATTTAAAGATTTGTTTCTATGAGC
252 AAATATC-AATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
* *
79157 ATCT-AAAACATG
316 ATCTGAATA-TTG
* * *** * * *
79169 TTTCGACTTAATTAGAAATTAATTCTGAAAAAGTA-GGGAAACGATATTACAAGCGTAAAAAACC
1 TTTCGATTTAATTAGAAATTAATTCAGAAAAA-TATAAAAAACGATATTAGAAGCGTGAAAAGCC
* * * *
79233 CTTCAATATTTTTGGCGTTGAATTATATATTTTGTATGAGTATTTTAGCCAAAAATTAAGGAAAT
65 CTTCAATCTTTTTGGCGTTGAATTATATATTTT-TATGAGTATTTT-GCTAAAAATTGAGGAAAA
*
79298 ATCTTTCTGGT-AATGTTTTTGCAAAATTTTAGCCGAAATCGTATAATAATCATCACAGTTTTTG
128 ATCTTTCTGGTCAA--TTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACAGTTTTTG
** * *
79362 GCTAAAAACGCGTTCCACTACCTCAGATCAGATTTGCATGA-TTTTTGACT-CTAAGACT-CTTG
191 GCTAAAAACGCGTTCCA-GGCC-CGGATCAGTTTTGCATGATTTTTTG--TGCTAAGACTCCTT-
* * * * *
79424 GAGATATCAATATTCATATAATCAAATCTCAGCCACATTGCATTTCAGGATTTCTTTTTACGAGC
251 GAAATATCAATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
79489 ATCTGAATATTG
316 ATCTGAATATTG
* * * * * *
79501 TTTCTATTTAAATATAAATTAATTCAGAAAAATATAAAAAACAATATTAAAAGCGTGAAAAGTCC
1 TTTCGATTTAATTAGAAATTAATTCAGAAAAATATAAAAAACGATATTAGAAGCGTGAAAAGCCC
* * * * * *
79566 TCCAATCTTTTTGGCGTTAAATTATATATATATATATATATTATGAGCATTGTGACTGAAAATTT
66 TTCAATCTTTTTGGCG-T---TGA-AT-TATATAT-T-T-TTATGAGTATTTTG-CTAAAAATTG
* * *
79631 AGGAAAAAAT-TTTCTGGTCCATTTTTGCAAAATTTTAGTCGAAATCGTG---TAA-CATCACGG
121 AGG-AAAAATCTTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACAG
* ** * * *
79691 TTTCTTTGTCTAAAAACGCGTTCTGGGGCCCCGATTCAGTTTTCCATGATTTTTTGTGCTAAAAC
185 -TT-TTTGGCTAAAAACGCGTTC-CAGGCCCGGA-TCAGTTTTGCATGATTTTTTGTGCTAAGAC
* * * * * *
79756 TCCTTGAAATATATATATATTCATTTAACCAAACCTTAAG-CACATTGGAGTTAAGGATTTGTTT
246 TCCTTGAAATAT-CA-ATATTCATCTAATCAAATC-TCAGCCACATTGGATTTAAGGATTTGTTT
*
79820 TTACGAGCATTTGAATCA-TG
308 TTACGAGCATCTGAAT-ATTG
* * *
79840 TTTCGATTTAATTAGAAATTAATT-TGAAAAAATAGAAAAAACGATGTTAGAAGCGTGAAAAGCC
1 TTTCGATTTAATTAGAAATTAATTCAG-AAAAATATAAAAAACGATATTAGAAGCGTGAAAAGCC
* *
79904 CGTCAATCTTTTTGGCGTTAAATTATATATTTTTATGAGTATTATTGTGGCTAAAAATTGAGG-A
65 CTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTA-T-TT-T-GCTAAAAATTGAGGAA
* * * * * ***
79968 AAATAATTT-GGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTACCATTATGAT--TTTTTT
126 AAAT-CTTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA--ATAATCATCACAGTTT
* * * * * * *
80030 TTTGCTAAAAACGCGTTCTGAGGCCTTGGGTTAGTTTTACATGATTTTTGGTG-TCAAGACTCCT
188 TTGGCTAAAAACGCGTTC-CAGGCC-CGGATCAGTTTTGCATGATTTTTTGTGCT-AAGACTCCT
* * * * * *
80094 TAAAATATTTCTACATTCATCTAA-CTAAATCTTAACCACATTGTATTTAAGGATTTGTTTTTAC
250 TGAAATA--TCAATATTCATCTAATC-AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTAC
** * * *
80158 GAGTTTCTAAATTTTA
312 GAGCATCTGAATATTG
* * * ** * *
80174 TTTCAATTTAATCAGAAATTATTTTGGAAATAAAAGAGGAAAAACGATATTAGAAGCGTGAAAAA
1 TTTCGATTTAATTAGAAATTAATTCAGAAA-AATATA--AAAAACGATATTAGAAGCGTG-AAAA
* * * * * * *
80239 GGCTTTCAATTTTTTTGGTGTTGAATTATATATTTTTTATGATTATTTTTGCTAGAAATCGAGGA
62 GCCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTA-TTTTGCTAAAAATTGAGGA
* * * * * *
80304 AAAATCTTTCAGGTCAATTTTTACAAAACTTTAGTCGAAATCGTGTATTAACCATCAC-GATTTT
125 AAAATCTTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACAG-TTTT
* * *** * * * *
80368 CGGCTAAAAACGTGTTATGGAGCCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCGTGA
189 TGGCTAAAAACGCGTTCCAG-GCCCGGATCAGTTTTGCATGATTTTTTGTGCTAAGACTCCTTGA
* * * * *
80433 AATATCTATATTCATCTAACCAAATCTCAGCTACATTAGATTTAAGGATTTGTTTTTACGAGTAT
253 AATATCAATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
*
80498 CTGAATGTTG
318 CTGAATATTG
* * * * * * *
80508 TTTCGATTTAATTATAAATTAATTCGGAAAAAAATATGAAAAACAATATTAGGAGCATAAAAAGC
1 TTTCGATTTAATTAGAAATTAATTC--AGAAAAATATAAAAAACGATATTAGAAGCGTGAAAAGC
** * *
80573 CCTTCAATCTTTTTGATGTCGAATTATATATATGTTT-TGAGAATTTTAG-TCAAAAATTGA-GA
64 CCTTCAATCTTTTTGGCGTTGAATTATATAT-T-TTTATGAGTATTTT-GCT-AAAAATTGAGGA
* * **
80635 AAATATCTTTC-GGATAAATTTTTGCAAAATTTT-------AT--T-TGA-AATCAT--GGGTTT
125 AAA-ATCTTTCTGG-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACAGTTT
* * ** * * * * ** *
80686 TTGGCTAAAAACGCATTTCGATTCCCCGGCTTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCA
188 TTGGCTAAAAACGC-GTTCCA-GGCCCGG-ATCAGTTTTGCATGATTTTTTGTGCTAAGACTCCT
* * * * **
80751 TAAAATATCTATATT-ATCTAATCAAATCTCAGGCATATTCTATTTAAGGATTT-TTTTTACGAG
250 TGAAATATCAATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
* * * *
80814 TATTTAAATCTTG
315 CATCTGAATATTG
* *
80827 TTTCTATTTAATTAGAAATTAATTCAAAAAAA
1 TTTCGATTTAATTAGAAATTAATTCAGAAAAA
80859 ATATGAAACA
Statistics
Matches: 1616, Mismatches: 304, Indels: 226
0.75 0.14 0.11
Matches are distributed among these distances:
317 7 0.00
319 58 0.04
320 40 0.02
321 49 0.03
322 1 0.00
323 1 0.00
325 2 0.00
328 7 0.00
329 63 0.04
330 147 0.09
331 28 0.02
332 270 0.17
333 98 0.06
334 213 0.13
335 33 0.02
336 74 0.05
337 185 0.11
338 106 0.07
339 194 0.12
340 33 0.02
341 7 0.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.37
Consensus pattern (327 bp):
TTTCGATTTAATTAGAAATTAATTCAGAAAAATATAAAAAACGATATTAGAAGCGTGAAAAGCCC
TTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTGCTAAAAATTGAGGAAAAATC
TTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACAGTTTTTGGCTAA
AAACGCGTTCCAGGCCCGGATCAGTTTTGCATGATTTTTTGTGCTAAGACTCCTTGAAATATCAA
TATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATAT
TG
Found at i:79946 original size:670 final size:660
Alignment explanation
Indices: 78483--80866 Score: 2025
Period size: 671 Copynumber: 3.6 Consensus size: 660
78473 TTGTAACACA
* * * * * * *
78483 AGCATCTTAATCATATTTCGATTTAATTAGAAATTAGTTCGGTACATAATAGGAAAAGACGATAC
1 AGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAA-ACGATAT
* *
78548 TAGAAGCATGAAAAAGCCCTTCAATCTTTTTGGCGTTAAATTACATAATTTTTATGAGTATTGT-
65 TAGAAGCAT-AAAAAGCCCTTCAATCTTTTTGGCGTTAAATTATAT-ATTTTTATGAGTATTTTA
* * * * *
78612 GTCCAAAAATTGAGAAAATAACTTTCAAGTCATTTTTTGCAAAATTCTAGCTGAAATCGTGTAAT
128 G-CCAAAAATTGAGAAAATATCTTTC-GGT-AATTTTTGCAAAATTTTAGCCGAAATCGTGTAAT
* * ** *
78677 AATCATCACAGTTTTTGGCAAAAAAAAAAAAAGCGTTTCGGGGCC-CTGACTTAGTTTTGCATGA
190 AATCATCACAGTTTTTGGC------TAAAAACGCG-TTCCAGGCCTCAGA-TTAGTTTTGCATGA
* * *
78741 TTTTTTGCGCCT-AGAATCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGAT
247 -TTTTTGC-TCTAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCAT
* * * *
78805 TTAAGAATTTTTTTACGAGCATCTGAATCA-CGTTTCGT-TTTAATTAGAAATTAATTTAGAAAA
310 TTAGGATTTTTTTTACGAGCATCTGAAT-ATTGTTTC-TATTTAAATAGAAATTAATTTAGAAAA
* *
78868 AAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTAAATCTTTTTGGCG-T--TGA-AT-TA
373 AAATA-GAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTAATTATATATA
* *
78928 TATATT-TGTTATGACTATTGTGGCTAAAAATTGAGAAAAAAATATTT-TGGGTCAATTTTTGCA
437 TATATTATATTATGAC-ATTGT-GCT-AAAATTGAGGAAAAAATATTTCT-GGTCAATTTTTGCA
* * * * * * * * *
78991 AAATATTAGGCGAAATCATGTAA-ATAACCTTTTTTTTTGCTAAAAACGCTTTCCGAGGCCCCGG
498 AAATTTTAGTCGAAATCGTGTAACATCA-CGTTTTTTGT-CTAAAAACGCGTTCTGGGGCCCC-G
* * *
79055 GTT-AGTTTTCCATGATTTTTTGTGCTAAAACTCCTTGAAATATCTA-ATATTCATCTGATCAAA
560 GTTCAGTTTTCCATGATTTTTTGTGCTAAAACTCCTTGAAATATATATATATTCATCTAACCAAA
* * * * * * *
79118 TCTCAACCATAATGGATTTAAAGATTTGTTTCTATG
625 TCTTAAGCACATTGGATTTAAGGATTTGTTTTTACG
* * * * * *
79154 AGCATCTAAAACATGTTTCGACTTAATTAGAAATTAATTCTG-AAAAAGTAGG-GAAACGATATT
1 AGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATT
* * * * *
79217 ACAAGCGTAAAAAACCCTTCAATATTTTTGGCGTTGAATTATATATTTTGTATGAGTATTTTAGC
66 AGAAGCATAAAAAGCCCTTCAATCTTTTTGGCGTTAAATTATATATTTT-TATGAGTATTTTAGC
* * *
79282 CAAAAATTAAGGAAATATCTTTCTGGTAATGTTTTTGCAAAATTTTAGCCGAAATCGTATAATAA
130 CAAAAATTGAGAAAATATCTTTC-GGTAA--TTTTTGCAAAATTTTAGCCGAAATCGTGTAATAA
** * *
79347 TCATCACAGTTTTTGGCTAAAAACGCGTTCCACTACCTCAGATCAGATTTGCATGATTTTTGACT
192 TCATCACAGTTTTTGGCTAAAAACGCGTTCCA-GGCCTCAGATTAGTTTTGCATGATTTTTG-CT
* * *
79412 CTAAGACT-CTTGGAGATATCAATATTCATATAATCAAATCTCAGCCACATTGCATTTCAGGATT
255 CTAAGACTCCTT-GAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTT-AGGATT
* * *
79476 TCTTTTTACGAGCATCTGAATATTGTTTCTATTTAAATATAAATTAATTCAGAAAAATATA-AAA
318 T-TTTTTACGAGCATCTGAATATTGTTTCTATTTAAATAGAAATTAATTTAGAAAAAAATAGAAA
* * * *
79540 AACAATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCGTTAAATTATATATATATATATAT
382 AACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTT-AATTATATATATATAT-TAT
* *
79605 ATTATGAGCATTGTGACTGAAAATTTAGGAAAAAAT-TTTCTGGTCCATTTTTGCAAAATTTTAG
445 ATTATGA-CATTGTG-CT-AAAATTGAGGAAAAAATATTTCTGGTCAATTTTTGCAAAATTTTAG
*
79669 TCGAAATCGTGTAACATCACGGTTTCTTTGTCTAAAAACGCGTTCTGGGGCCCCGATTCAGTTTT
507 TCGAAATCGTGTAACATCAC-GTTT-TTTGTCTAAAAACGCGTTCTGGGGCCCCGGTTCAGTTTT
* *
79734 CCATGATTTTTTGTGCTAAAACTCCTTGAAATATATATATATTCATTTAACCAAACCTTAAGCAC
570 CCATGATTTTTTGTGCTAAAACTCCTTGAAATATATATATATTCATCTAACCAAATCTTAAGCAC
*
79799 ATTGGAGTTAAGGATTTGTTTTTACG
635 ATTGGATTTAAGGATTTGTTTTTACG
* * * *
79825 AGCATTTGAATCATGTTTCGATTTAATTAGAAATTAATT-TG-AAAAAATAGAAAAAACGATGTT
1 AGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATT
* * * *
79888 AGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTAAATTATATATTTTTATGAGTATTATTGTG
66 AGAAGCATAAAAAGCCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTATGAGTA-T-TT-TA
* * * *
79953 GCTAAAAATTGAGGAAAATA-ATTTGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTACCA
128 GCCAAAAATTGA-GAAAATATCTTTCGGT-AATTTTTGCAAAATTTTAGCCGAAATCGTGTA--A
* * *** * * ** * *
80017 TTATGAT--TTTTTTTTTGCTAAAAACGCGTTCTGAGGCCTTGGGTTAGTTTTACATGATTTTTG
189 TAATCATCACAGTTTTTGGCTAAAAACGCGTTC-CAGGCCTCAGATTAGTTTTGCATGATTTTTG
* * * * * * *
80080 GTGTCAAGACTCCTTAAAATATTTCTACATTCATCTAA-CTAAATCTTAACCACATTGTATTTAA
253 CTCT-AAGACTCCTTGAAATA--TCTATATTCATCTAATC-AAATCTCAGCCACATTGCATTT-A
** * * * * * *
80144 GGATTTGTTTTTACGAGTTTCTAAATTTTATTTCAATTT-AATCAGAAATTATTTTGGAAATAAA
313 GGATTT-TTTTTACGAGCATCTGAATATTGTTTCTATTTAAAT-AGAAATTAATTTAGAAA-AAA
* * * * *
80208 AGAGGAAAAACGATATTAGAAGCGTGAAAAAGGCTTTCAATTTTTTTGGTGTTGAATTATATAT-
375 ATA-GAAAAACGATATTAGAAGCGTG-AAAAGCCCTTCAATCTTTTTGGCGTT-AATTATATATA
* * * * * *
80272 T-TTTTATGATTAT----TTTTGCTAGAAATCGAGG-AAAAATCTTTCAGGTCAATTTTTACAAA
437 TATATTAT-ATTATGACATTGTGCTA-AAATTGAGGAAAAAATATTTCTGGTCAATTTTTGCAAA
* * * * * * *
80331 ACTTTAGTCGAAATCGTGTATTAACCATCACGATTTTCGGCTAAAAACGTGTTATGGAG-CCCGG
500 ATTTTAGTCGAAATCGTG---TAA-CATCACGTTTTTTGTCTAAAAACGCGTTCTGGGGCCCCGG
* * * * * * *
80395 CTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCGTG-AA-ATATCTATATTCATCTAACCAAAT
561 TTCAGTTTTCCATGATTTTTTGTGCTAAAACTCCTTGAAATATATATATATTCATCTAACCAAAT
* *
80458 C-TCAGCTACATTAGATTTAAGGATTTGTTTTTACG
626 CTTAAGC-ACATTGGATTTAAGGATTTGTTTTTACG
* ** * * *
80493 AGTATCTGAATGTTGTTTCGATTTAATTATAAATTAATTCGGAAAAAAATATGAAAAACAATATT
1 AGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATT
* ** ** *
80558 AGGAGCATAAAAAGCCCTTCAATCTTTTTGATGTCGAATTATATATATGTTT-TGAGAATTTTAG
66 AGAAGCATAAAAAGCCCTTCAATCTTTTTGGCGTTAAATTATATAT-T-TTTATGAGTATTTTAG
* *
80622 TCAAAAATTGAGAAAATATCTTTCGGATAAATTTTTGCAAAATTTT-------AT--T-TGA-AA
129 CCAAAAATTGAGAAAATATCTTTCGG-T-AATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAA
** * * ** * * *
80676 TCAT--GGGTTTTTGGCTAAAAACGCATTTCGATTCCCCGGCTTTAGTTTTGCATGATTTTTGGC
192 TCATCACAGTTTTTGGCTAAAAACGC-GTTCCAGGCCTCAG-ATTAGTTTTGCATGATTTTT-GC
* ** * * * *
80739 GCCGAGACTCCATAAAATATCTATATT-ATCTAATCAAATCTCAGGCATATT-CTATTTAAGGAT
254 TCTAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGC-ATTT-AGGAT
* * * * * *
80802 TTTTTTTACGAGTATTTAAATCTTGTTTCTATTTAATTAGAAATTAATTCA-AAAAAAATATGAA
317 TTTTTTTACGAGCATCTGAATATTGTTTCTATTTAAATAGAAATTAATTTAGAAAAAAATA-GAA
80866 A
381 A
80867 CAAAATTTTG
Statistics
Matches: 1403, Mismatches: 242, Indels: 156
0.78 0.13 0.09
Matches are distributed among these distances:
651 9 0.01
652 3 0.00
653 37 0.03
654 32 0.02
655 8 0.01
656 26 0.02
657 36 0.03
658 1 0.00
659 1 0.00
660 1 0.00
661 14 0.01
662 110 0.08
663 11 0.01
664 50 0.04
666 8 0.01
667 79 0.06
668 174 0.12
669 110 0.08
670 221 0.16
671 274 0.20
672 22 0.02
673 105 0.07
674 13 0.01
675 7 0.00
676 20 0.01
677 31 0.02
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.37
Consensus pattern (660 bp):
AGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATT
AGAAGCATAAAAAGCCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTATGAGTATTTTAGCC
AAAAATTGAGAAAATATCTTTCGGTAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCAT
CACAGTTTTTGGCTAAAAACGCGTTCCAGGCCTCAGATTAGTTTTGCATGATTTTTGCTCTAAGA
CTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAGGATTTTTTTTAC
GAGCATCTGAATATTGTTTCTATTTAAATAGAAATTAATTTAGAAAAAAATAGAAAAACGATATT
AGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTAATTATATATATATATTATATTATGACATT
GTGCTAAAATTGAGGAAAAAATATTTCTGGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTAA
CATCACGTTTTTTGTCTAAAAACGCGTTCTGGGGCCCCGGTTCAGTTTTCCATGATTTTTTGTGC
TAAAACTCCTTGAAATATATATATATTCATCTAACCAAATCTTAAGCACATTGGATTTAAGGATT
TGTTTTTACG
Found at i:81147 original size:66 final size:66
Alignment explanation
Indices: 81035--81994 Score: 428
Period size: 66 Copynumber: 14.6 Consensus size: 66
81025 AATTTGGGAA
* * * * * *
81035 ACTAGAATTTCATAGATTGGTTACTAGAATTTCATAAG-AAGATTACCAGAATTTCATAGGTGGG
1 ACTAGAATTTCATAGGTAGGTTACCAAAATTTCAT-AGTGAGGTTACCAGAATTTCATAGGTGGG
81099 TT
65 TT
* *
81101 ACTAGTACTTCATAGGTAGGTTACCAAAATTTCATAGTGAGGTTACC-GAAATTTCATA-GT---
1 ACTAGAATTTCATAGGTAGGTTACCAAAATTTCATAGTGAGGTTACCAG-AATTTCATAGGTGGG
81161 TT
65 TT
* * * *
81163 -CATCA-ATATTTCATATATAGTGAGGTTA-CAAAATTTCATAAG-CAGGTTACCAAAATCTCAT
1 AC-T-AGA-ATTTC--ATA-GGT-AGGTTACCAAAATTTCAT-AGTGAGGTTACCAGAATTTCAT
*
81224 TGGTGGGTT
58 AGGTGGGTT
* * *
81233 TCTAGAATTTCATAGGTAGGCTACCAAAATTTCATACG-GAGGTTATCA-AACTTTCATAGGTGG
1 ACTAGAATTTCATAGGTAGGTTACCAAAATTTCATA-GTGAGGTTACCAGAA-TTTCATAGGTGG
81296 GTT
64 GTT
* * * *
81299 ACTGGAATTTAATATGG-AGGTTACCAAAATTTCATAG-GGGCGTTACTAG-ATTTCATAGGTGG
1 ACTAGAATTTCATA-GGTAGGTTACCAAAATTTCATAGTGAG-GTTACCAGAATTTCATAGGTGG
81361 GTT
64 GTT
* * * * * *
81364 ATTAGAATTTCATAGGTAAGTTACCAAAAATTAATAATGAGGTTACC-GAAATTTCAT-TGTGAG
1 ACTAGAATTTCATAGGTAGGTTACCAAAATTTCATAGTGAGGTTACCAG-AATTTCATAGGTG-G
81427 GTT
64 GTT
* * * * * * * * * *
81430 ACCAAAATTTTATA-GTAAGGGGTTACCGAAA-TTCTTAGTGAGGTTATCAAAATATCATAGTTT
1 ACTAGAATTTCATAGGT-A--GGTTACCAAAATTTCATAGTGAGGTTACCAGAATTTCATAGGTG
**
81493 CATCT
63 GGT-T
* * * *
81498 GC-A-ATATTTCATA-GTGAGGTTA-CAAGAATTTCATAG-AAGGTTACCAAAATTTCTTAGGTG
1 ACTAGA-ATTTCATAGGT-AGGTTACCAA-AATTTCATAGTGAGGTTACCAGAATTTCATAGGTG
* *
81558 AGTC
63 GGTT
* *
81562 ACTAGAATTTCATAAGG-AAGTTACAAAAATTTC--A-TGAGGTTACCAGAATTTCATAGAG-GG
1 ACTAGAATTTCAT-AGGTAGGTTACCAAAATTTCATAGTGAGGTTACCAGAATTTCATAG-GTGG
81622 GTT
64 GTT
* ** ** * * **
81625 ACGAGAATTTCATAGCAAGGTTTTCGAAATTTCATA-TGGAGGTTACCAGAATTTAATAAGGAAG
1 ACTAGAATTTCATAGGTAGGTTACCAAAATTTCATAGT-GAGGTTACCAGAATTTCAT-AGGTGG
*
81689 TTAT
64 GT-T
* * * * * ** * * *
81693 ACCATAATTTCATAAAG-AGGTTACCAGAATTGCATAGCAAGATTATCAAAATTTCATAGG-GAG
1 ACTAGAATTTCAT-AGGTAGGTTACCAAAATTTCATAGTGAGGTTACCAGAATTTCATAGGTG-G
81756 GTT
64 GTT
* * * ** * * * * **
81759 ACCAGAATTGCACAGCAAGGTACTTATCAAAATTTCATA--AAGTTTACTAGAATTTCATAGAAG
1 ACTAGAATTTCATAGGTAGG---TTACCAAAATTTCATAGTGAGGTTACCAGAATTTCATAGGTG
81822 GGTT
63 GGTT
* * * ** * * * * *
81826 GCTCGAATTTTATAGCAAGGTTACCAAAATTTCAAAGGGAGTTTACCAAAAATTCATAGG-GAGG
1 ACTAGAATTTCATAGGTAGGTTACCAAAATTTCATAGTGAGGTTACCAGAATTTCATAGGTG-GG
81890 TT
65 TT
* * * * * * * * * ** *
81892 ACCA-AATTTTCATAGGAAGGTTATCAGAATTTCATGGTAAGGTTACTAAAATTTCAGAGAAGGT
1 ACTAGAA-TTTCATAGGTAGGTTACCAAAATTTCATAGTGAGGTTACCAGAATTTCATAGGTGGG
81956 TT
65 TT
* *
81958 ACTAAAATTTCATATGG-AGGTTACCAGAATTTCATAG
1 ACTAGAATTTCATA-GGTAGGTTACCAAAATTTCATAG
81995 CATGGATTCC
Statistics
Matches: 678, Mismatches: 150, Indels: 132
0.71 0.16 0.14
Matches are distributed among these distances:
61 1 0.00
62 5 0.01
63 50 0.07
64 21 0.03
65 122 0.18
66 304 0.45
67 97 0.14
68 53 0.08
69 20 0.03
70 4 0.01
71 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (66 bp):
ACTAGAATTTCATAGGTAGGTTACCAAAATTTCATAGTGAGGTTACCAGAATTTCATAGGTGGGT
T
Found at i:81160 original size:22 final size:22
Alignment explanation
Indices: 81077--82099 Score: 344
Period size: 22 Copynumber: 46.5 Consensus size: 22
81067 CATAAGAAGA
*
81077 TTACCAGAATTTCATAGGTG-GG
1 TTACCAAAATTTCATA-GTGAGG
* ** *
81099 TTACTAGTACTTCATAG-GTAGG
1 TTACCAAAATTTCATAGTG-AGG
81121 TTACCAAAATTTCATAGTGAGG
1 TTACCAAAATTTCATAGTGAGG
*
81143 TTACCGAAATTTCATAGT----
1 TTACCAAAATTTCATAGTGAGG
* *
81161 TTCATCAATATTTCATATATAGTGAGG
1 TT-ACCAAAATTTC----ATAGTGAGG
*
81188 TTA-CAAAATTTCATAAG-CAGG
1 TTACCAAAATTTCAT-AGTGAGG
* *
81209 TTACCAAAATCTCATTGGTG-GG
1 TTACCAAAATTTCA-TAGTGAGG
* * *
81231 TTTCTAGAATTTCATAG-GTAGG
1 TTACCAAAATTTCATAGTG-AGG
*
81253 CTACCAAAATTTCATACG-GAGG
1 TTACCAAAATTTCATA-GTGAGG
* *
81275 TTATCAAACTTTCATAGGTG-GG
1 TTACCAAAATTTCATA-GTGAGG
*** *
81297 TTACTGGAATTTAATA-TGGAGG
1 TTACCAAAATTTCATAGT-GAGG
*
81319 TTACCAAAATTTCATAG-GGGCG
1 TTACCAAAATTTCATAGTGAG-G
* *
81341 TTA-CTAGATTTCATAGGTG-GG
1 TTACCAAAATTTCATA-GTGAGG
** * *
81362 TTATTAGAATTTCATAG-GTAAG
1 TTACCAAAATTTCATAGTG-AGG
* * *
81384 TTACCAAAAATTAATAATGAGG
1 TTACCAAAATTTCATAGTGAGG
* *
81406 TTACCGAAATTTCATTGTGAGG
1 TTACCAAAATTTCATAGTGAGG
* *
81428 TTACCAAAATTTTATAGTAAGGGG
1 TTACCAAAATTTCATAGT--GAGG
* *
81452 TTACCGAAA-TTCTTAGTGAGG
1 TTACCAAAATTTCATAGTGAGG
* * ****
81473 TTATCAAAATATCATAGTTTCA
1 TTACCAAAATTTCATAGTGAGG
* *
81495 TCT-GCAATATTTCATAGTGAGG
1 T-TACCAAAATTTCATAGTGAGG
*
81517 TTA-CAAGAATTTCATAG-AAGG
1 TTACCAA-AATTTCATAGTGAGG
*
81538 TTACCAAAATTTCTTAGGTGA-G
1 TTACCAAAATTTCATA-GTGAGG
* * * *
81560 TCACTAGAATTTCATAAG-GAAG
1 TTACCAAAATTTCAT-AGTGAGG
*
81582 TTACAAAAATTTC--A-TGAGG
1 TTACCAAAATTTCATAGTGAGG
* * *
81601 TTACCAGAATTTCATAGAGGGG
1 TTACCAAAATTTCATAGTGAGG
* * **
81623 TTACGAGAATTTCATAGCAAGG
1 TTACCAAAATTTCATAGTGAGG
** *
81645 TTTTCGAAATTTCATA-TGGAGG
1 TTACCAAAATTTCATAGT-GAGG
* * *
81667 TTACCAGAATTTAATAAG-GAAGT
1 TTACCAAAATTTCAT-AGTG-AGG
* **
81690 TATACCATAATTTCATAAAGAGG
1 T-TACCAAAATTTCATAGTGAGG
* * ** *
81713 TTACCAGAATTGCATAGCAAGA
1 TTACCAAAATTTCATAGTGAGG
* *
81735 TTATCAAAATTTCATAGGGAGG
1 TTACCAAAATTTCATAGTGAGG
* * * **
81757 TTACCAGAATTGCACAGCAAGG
1 TTACCAAAATTTCATAGTGAGG
* * *
81779 TACTTATCAAAATTTCATA--AAGT
1 ---TTACCAAAATTTCATAGTGAGG
* * *
81802 TTACTAGAATTTCATAG-AAGGG
1 TTACCAAAATTTCATAGTGA-GG
* * * **
81824 TTGCTC-GAATTTTATAGCAAGG
1 TTAC-CAAAATTTCATAGTGAGG
* * *
81846 TTACCAAAATTTCAAAGGGAGT
1 TTACCAAAATTTCATAGTGAGG
* *
81868 TTACCAAAAATTCATAGGGAGG
1 TTACCAAAATTTCATAGTGAGG
*
81890 TTACCAAATTTTCATAG-GAAGG
1 TTACCAAAATTTCATAGTG-AGG
* * * *
81912 TTATCAGAATTTCATGGTAAGG
1 TTACCAAAATTTCATAGTGAGG
* * *
81934 TTACTAAAATTTCAGAG-AAGG
1 TTACCAAAATTTCATAGTGAGG
*
81955 TTTACTAAAATTTCATA-TGGAGG
1 -TTACCAAAATTTCATAGT-GAGG
* *
81978 TTACCAGAATTTCATAGCATG-GA
1 TTACCAAAATTTCATAG--TGAGG
*
82001 TT-CCAAAATTTCATACG-AAGG
1 TTACCAAAATTTCATA-GTGAGG
* **
82022 TTACCATAATTGAATAGCT-AGG
1 TTACCAAAATTTCATAG-TGAGG
* * * *
82044 TTATCGAAATTACATAGAGAGG
1 TTACCAAAATTTCATAGTGAGG
* * *
82066 TTATCAAAATTCCATA-TAAAGG
1 TTACCAAAATTTCATAGT-GAGG
*
82088 TTACCAGAATTT
1 TTACCAAAATTT
82100 TATAAAGAGA
Statistics
Matches: 732, Mismatches: 195, Indels: 148
0.68 0.18 0.14
Matches are distributed among these distances:
18 2 0.00
19 23 0.03
20 17 0.02
21 72 0.10
22 528 0.72
23 41 0.06
24 25 0.03
25 21 0.03
26 1 0.00
27 2 0.00
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (22 bp):
TTACCAAAATTTCATAGTGAGG
Found at i:81353 original size:21 final size:22
Alignment explanation
Indices: 81035--81380 Score: 155
Period size: 22 Copynumber: 15.8 Consensus size: 22
81025 AATTTGGGAA
* *
81035 ACTAGAATTTCATAGATTGGTT
1 ACTAGAATTTCATAGGTGGGTT
* ** *
81057 ACTAGAATTTCATAAGAAGATT
1 ACTAGAATTTCATAGGTGGGTT
*
81079 ACCAGAATTTCATAGGTGGGTT
1 ACTAGAATTTCATAGGTGGGTT
* * *
81101 ACTAGTACTTCATAGGTAGGTT
1 ACTAGAATTTCATAGGTGGGTT
* *
81123 ACCAAAATTTCATA-GTGAGGTT
1 ACTAGAATTTCATAGGTG-GGTT
*
81145 AC-CGAAATTTCATA-GT---TT
1 ACTAG-AATTTCATAGGTGGGTT
*
81163 -CATCA-ATATTTCATATATAGTGAGGTT
1 AC-T-AGA-ATTTC--ATA-GGTG-GGTT
* * **
81190 AC-AAAATTTCATAAGCAGGTT
1 ACTAGAATTTCATAGGTGGGTT
* * * *
81211 ACCAAAATCTCATTGGTGGGTT
1 ACTAGAATTTCATAGGTGGGTT
* * *
81233 TCTAGAATTTCATAGGTAGGCT
1 ACTAGAATTTCATAGGTGGGTT
* * *
81255 ACCAAAATTTCATACGG-AGGTT
1 ACTAGAATTTCATA-GGTGGGTT
81277 A-TCA-AACTTTCATAGGTGGGTT
1 ACT-AGAA-TTTCATAGGTGGGTT
* * *
81299 ACTGGAATTTAATATGG-AGGTT
1 ACTAGAATTTCATA-GGTGGGTT
* *
81321 ACCAAAATTTCATAGG-GGCGTT
1 ACTAGAATTTCATAGGTGG-GTT
81343 ACTAG-ATTTCATAGGTGGGTT
1 ACTAGAATTTCATAGGTGGGTT
*
81364 ATTAGAATTTCATAGGT
1 ACTAGAATTTCATAGGT
81381 AAGTTACCAA
Statistics
Matches: 244, Mismatches: 53, Indels: 54
0.70 0.15 0.15
Matches are distributed among these distances:
17 1 0.00
18 3 0.01
19 5 0.02
21 35 0.14
22 178 0.73
23 12 0.05
25 6 0.02
26 1 0.00
27 2 0.01
28 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (22 bp):
ACTAGAATTTCATAGGTGGGTT
Found at i:81490 original size:45 final size:46
Alignment explanation
Indices: 81404--81490 Score: 124
Period size: 45 Copynumber: 1.9 Consensus size: 46
81394 TTAATAATGA
* *
81404 GGTTACCGAAATTTCATTGTGAGGTTACCAAAATTTTATAGTAAGG
1 GGTTACCGAAATTTCATTGTGAGGTTACCAAAATATCATAGTAAGG
*
81450 GGTTACCGAAA-TTC-TTAGTGAGGTTATCAAAATATCATAGT
1 GGTTACCGAAATTTCATT-GTGAGGTTACCAAAATATCATAGT
81491 TTCATCTGCA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
44 2 0.05
45 24 0.65
46 11 0.30
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.34
Consensus pattern (46 bp):
GGTTACCGAAATTTCATTGTGAGGTTACCAAAATATCATAGTAAGG
Found at i:81626 original size:41 final size:41
Alignment explanation
Indices: 81512--81637 Score: 114
Period size: 41 Copynumber: 3.0 Consensus size: 41
81502 TATTTCATAG
* *
81512 TGAGGTTACAAGAATTTCATAGA-AGGTTACCAAAATTTCTTA
1 TGAGGTTACAAGAATTTCATAGAGGGGTTACAAAAATTTC--A
* * *
81554 GGTGA-GTCACTAGAATTTCATA-AGGAAGTTACAAAAATTTCA
1 --TGAGGTTACAAGAATTTCATAGAGG-GGTTACAAAAATTTCA
* * *
81596 TGAGGTTACCAGAATTTCATAGAGGGGTTACGAGAATTTCA
1 TGAGGTTACAAGAATTTCATAGAGGGGTTACAAAAATTTCA
81637 T
1 T
81638 AGCAAGGTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
40 3 0.04
41 29 0.43
42 5 0.07
43 15 0.22
44 16 0.24
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (41 bp):
TGAGGTTACAAGAATTTCATAGAGGGGTTACAAAAATTTCA
Found at i:82187 original size:24 final size:24
Alignment explanation
Indices: 82142--82187 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
82132 TTTCCAAAAT
* *
82142 TTCATAGGGTTATATGTGTGTGCG
1 TTCATAGGGTTATATCTATGTGCG
82166 TTCATAGGGTTATATCTATGTG
1 TTCATAGGGTTATATCTATGTG
82188 TGGGCTAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.20, C:0.09, G:0.28, T:0.43
Consensus pattern (24 bp):
TTCATAGGGTTATATCTATGTGCG
Found at i:82238 original size:35 final size:35
Alignment explanation
Indices: 82192--82262 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
82182 TATGTGTGGG
*
82192 CTAATCTATGTTCCTACGCATCAAAGACTTGTACC
1 CTAATCTATGTTCCTACGCATCAAAGACTTGCACC
82227 CTAATCTATGTTCCTACGCATCAAAGACTTGCACC
1 CTAATCTATGTTCCTACGCATCAAAGACTTGCACC
82262 C
1 C
82263 ATGTATAGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.30
Consensus pattern (35 bp):
CTAATCTATGTTCCTACGCATCAAAGACTTGCACC
Found at i:82892 original size:20 final size:20
Alignment explanation
Indices: 82867--82904 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
82857 CATTCATATA
*
82867 TTTTTTTCTTATATTTACCT
1 TTTTTTTCTTACATTTACCT
*
82887 TTTTTTTTTTACATTTAC
1 TTTTTTTCTTACATTTAC
82905 AAGTTAGTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTTTCTTACATTTACCT
Found at i:86199 original size:11 final size:11
Alignment explanation
Indices: 86185--86210 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
86175 TTTAGCCTTG
86185 AAAAATAAAAT
1 AAAAATAAAAT
86196 AAAAATAAAAT
1 AAAAATAAAAT
86207 AAAA
1 AAAA
86211 TACAAGTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:87040 original size:10 final size:10
Alignment explanation
Indices: 87027--87052 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
87017 TAAAAATAAT
87027 AAAAAAAGAA
1 AAAAAAAGAA
87037 AAAAAAAGAA
1 AAAAAAAGAA
87047 AAAAAA
1 AAAAAA
87053 GACACGTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:100015 original size:321 final size:319
Alignment explanation
Indices: 99396--102817 Score: 2609
Period size: 321 Copynumber: 10.4 Consensus size: 319
99386 GATTTTTAAC
* * * * *
99396 CAATTTTTGGCAAAAATACTCA-TAAATATATATAATTCAACGCCAAAAAGATTGGA-GGACTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATT-GACGG-CTTT
* * * *
99459 TCACGCTTTTAATATCG--TTTCACATATTTTTTCTGAATTAATTTCTAATTAAATCGAAATAAA
64 TCACGCTTCTAATATCGTTTTTC-CAT-TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAG
* * * *
99522 ATTCAGATGCAT-GTAAAAGCAAATCCTTAAATCCAATGTGGCTGGGATTTGATTAGATGAATAA
127 ATTCAGATGC-TCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATAT
** * *
99586 AGATATTTCAAGGAGTCTCGACGCCAAAAATCATGCAAAA-TAGAG--GTGTGGCCCCGGAACGC
191 AGATATTTCAAGGAGTCT-TTCGCCAAAAATCATGCAAAACT-GAGCCG-GT-GCTCCGAAACGC
* * * * * * *
99648 TTTTTTAGTCAAAAACTGTGATGATTAGTACACAATTTCGGCTAAAAATTGACCTGAAACGTTTA
252 GTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCTGAAAAGTTT-
99713 TTCT
316 TTCT
* * * * *
99717 CAAATATTTGCCACAATATTCAG-AAAAATATATAATTCAACGCAAAAAATATTGACGGCCTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGG-CTTTT
*
99781 CACGCTTCTAATATCGTTTTTCCAGTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT
65 CACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT
* * * *
99846 CAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATGTGGTTCA-ATGAATATAAA
130 CAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTT-AGATGAATATAGA
* ** *
99910 TATTTCAAGGAGTCTTTACGGCAAAAATCATGCAAAGTTGAGCCGGTGCTCCGGAACGCGTTTTT
194 TATTTCAAGGAGTCTTT-CGCCAAAAATCATGCAAAACTGAGCCGGTGCTCCGAAACGCGTTTTT
* * **
99975 AGCCAAAACCCGTGATGGTTAGTACACGATTTTC-GCTAAAATTTTGCAAAAACTAACCCCAAAA
258 AGCCAAAAACCGTGATGGTTAGTACACGA-TTTCGGC--------T--AAAAACTGA-CCTGAAA
100039 AGTTTTTCCT
311 AGTTTTT-CT
* * **
100049 CAAGTTTTT-CCACAATACTCAGAAAAAATATATAATTTAACGCCAAAAA-ATTGAACGATTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTG-ACG-GCTTT
*
100112 TCACGCTTCTAATATCGTTTTTCCTTTTTTTTCCGAATTTAA-TTCTAATTAAATCGAAACAAAG
64 TCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAA-TTAATTTCTAATTAAATCGAAAC-AAG
* ** * *
100176 ATTGAGATGCTCGTAAAAACAAATTATTAAATCCATTGTGGCTGAGATTTTGTTAGATGAATATA
127 ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATA
** * * *
100241 GATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACTGAGCC-GAGATCCGAAATGCGTTT
192 GATATTTCAAGGAGTCTTTC-GCCAAAAATCATGCAAAACTGAGCCGGTGCTCCGAAACGCGTTT
* * * * * * * *
100305 TAAGCCAAAAATCGTAATGGTTTGTACACGATTTCCGCTAAAAACTAACCCGAAAAATTTTTCT
256 TTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCTGAAAAGTTTTTCT
* * *
100369 CAATTTTTTG-CAAAATATTCAGAAAAAAATATATAATTCAACGCCAAAAAGATTGACAGCCTTT
1 CAATTTTTTGCCACAATACTCAG-AAAAAATATATAATTCAACGCCAAAAAGATTGAC-GGCTTT
* * * * * *
100433 TCGCTCTTCTAATATCGTTTTTCCAGTTTTTTCCAAATTGATTTCTAATTAAATCGAAACAAAAT
64 TCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
* * * * * *
100498 TCGGATGCTTGTAAAAACAATTCCTTATATACAATGTGGCTGAGATTTGGTTCGATGAATATAGA
129 TCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGA
* * ** *
100563 TATTTCAAGGAGTCTTTACGCAAAAAATCATGCAAAATTGAATCGG-GACTCCGAAACGTGTTTT
194 TATTTCAAGGAGTCTTT-CGCCAAAAATCATGCAAAACTGAGCCGGTG-CTCCGAAACGCG---T
* * * **
100627 TTTTTGCCAAAAACCGTGATAGTTAGTACATGATTTCGTTGGCTACAAAAAAAGTACACGATTTC
254 TTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTC---GGCT--AAAAACTG-AC-C----T-
*
100692 GGCTAAAA-TTTTGCAAAAACTGACC
307 -G--AAAAGTTTT--------T--CT
* * * ** ** * **** * **
100717 CGAAAAGTTTTT-CCTCAATATTTTGCCACAATACTCAGTAA---AAAAATATAATTATTTAACG
1 C---AATTTTTTGCCACAATACTCAGAAAAAATA-T-A-TAATTCAACGCCAAAAAGA-TT---G
* * * * * *
100778 CCAAAAAATTGAAGGGTTTTTCACGTTTCTAATATCGTTCTTCCTTTTTTTTCCGAATTTATTTC
56 AC-----------GGCTTT-TCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTC
* * * * * * *
100843 TAATTAAATCGAAACAAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCTATTGTGACTAAA
109 TAATTAAATCGAAAC-AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
* * **
100908 ATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTTTTTGCC-AAAATCATTTAAAACTGAGCC
173 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTC-TTTCGCCAAAAATCATGCAAAACTGAGCC
* * * * *
100972 GG-GATCCGAAACGCGTTTTTAGCCAAAAATCGTGATGATTAGTACACGATTTCAGCTAAAAAGT
237 GGTGCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACT
* ***
101036 GACATGAATTTTTTTTTTCT
302 GACCTGAA--AAGTTTTTCT
** * ** * * * *
101056 C-ATTTTTTGTGA-AATATTTTGAAAAAATATATAATTCAATGCCGAAAATATTGACAGGTTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAC-GGCTTTT
* * * * * * * *
101119 CACCCATATAATATCTTTTTTCCATTTGTTTT-CGAAATAATTTCTAATTAAATCAAAATACGA-
65 CACGCTTCTAATATCGTTTTTCCATTT-TTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
** * * * * *
101182 TCGAGATGCTAATAAAAACAAATCCTTATATCCAATGTGGTTGACACTTGGTTCGATGAATATAG
129 TC-AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAG
* * * * *
101247 ATATTTCAAGGAGTCTTTGTGCCAAAAAAATCCTGCAAAATTGAACCGGCT-CTCCGGAACGCGT
193 ATATTTCAAGGAGTCTTT-CGCC--AAAAATCATGCAAAACTGAGCCGG-TGCTCCGAAACGCGT
* * * *
101311 CTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGA
254 TTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC--------T--AAAAACTGACCTGA
101376 AAAGTTTTTCCT
309 AAAGTTTTT-CT
* * * * * * *
101388 CAATTTTTTTCCAGAATACTAAGAAAAAATATATAATTCAACACCAAAAAAATTGAAGGGTTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTG-ACGGCTTTT
*
101453 CACGCTTCTAATATCGTTTTT--ATTTTTTTCCCGAATTTATTTCTAATTAAATCGAAACAAGAT
65 CACGCTTCTAATATCGTTTTTCCATTTTTTT-CCGAATTAATTTCTAATTAAATCGAAACAAGAT
* ** *
101516 TCAGATGCTCGTAAAAA-AAATTCTTAAATCCAATGTGGCTGAGATTTAATTAGATGTATATAGA
129 TCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGA
* * * *
101580 TATTTCATGGAGTCTTTCTGCCTAAAATCATGCAAAACTGAGCCGG-GAC-CCTAAAACACGTTT
194 TATTTCAAGGAGTCTTTC-GCCAAAAATCATGCAAAACTGAGCCGGTG-CTCC-GAAACGCGTTT
* * * * ** * ** *
101643 TTAGCAAAAAAAAACTGTGATGGTTATTACATGATTTTAGTTAAAATTTCGAAAAACTGACAAAA
256 TTAGC---CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACT-G---ACCTG----AA
**
101708 AAAATTTTCT
310 AAGTTTTTCT
* * * * * *
101718 CAATTTTTTGCCACAATACTCAGAAAAAATATATAACTGAACG-AAAAAAAATTGAAGGATTTTC
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGCTTTTC
* * * * *
101782 ACGCTTCTAATATCATTTTTCCATTTTTTTCCTAATTTATTTCTAATTAAATCTAAACAAGATTT
66 ACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTC
* * * * * * *
101847 AGACGCTCGTAAAAACAAATCCGTGAATCTAATGTAGTTGAGATTTTGTTAGATGAATATAGATA
131 AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATA
* * * *
101912 TTTCAAGGATTCTTTCTGCCAAAAATCATGCAAAACTAAACCGGGGC-CGCGAAACGCGTTTTTA
196 TTTCAAGGAGTCTTTC-GCCAAAAATCATGCAAAACTGAGCCGGTGCTC-CGAAACGCGTTTTTA
** ** * *
101976 GCCAAAAACCGT-AACGTT--TACACGATTTCGGCTAAAAACAAACCAGAAAATTTTTTTCT
259 GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCTGAAAA-GTTTTTCT
* * * ** *
102035 CAACTTTTTGCCACAATACTCATAAAAACTATATAATTCAATTCCAAAAAGATTGACGGGTTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAC-GGCTTTT
*** * *
102100 TGGGCTTCTAATATCGGTTTTCCATTTTTTGTCCAAATTAATTTCTAATTAAATCGAAACAA-AT
65 CACGCTTCTAATATCGTTTTTCCATTTTTT-TCCGAATTAATTTCTAATTAAATCGAAACAAGA-
** * * * *
102164 TTCAGAAACTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGATTTGGATCGATTAATATAG
128 TTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAG
* * * * * *
102229 ATATTTCAAGGAGTCTTTGTGCCAAAAATCAAGTAAAATTGAGCC-ATGACTCCGGAACGCGTTT
193 ATATTTCAAGGAGTCTTT-CGCCAAAAATCATGCAAAACTGAGCCGGTG-CTCCGAAACGCGTTT
*
102293 TTAGCCAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAGAACTGACCTGA
256 TTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC----------T-AAA-AACTGACCTGA
*
102358 AAAGCTTTTCCT
309 AAAG-TTTTTCT
* * * * *
102370 CAATTTTTTGCCACAATACTCAGAATAAATATACAATTCAACGCCAAAAAAATTGAAGGTGTTTT
1 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGG-CTTTT
* * * * * * *
102435 CACACTTTTAATATTGTTTTT-CTTTTTTTTCTGAATTTATTTCTAATAAAAT-GAAAACAAGAT
65 CACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCG-AAACAAGAT
* * * * * *
102498 TCAGATGCTCATAAAAAAAAATCTTTAAATCCAATGTGGCTGAGATTTGGTTACATGAGTTTAGA
129 TCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGA
* * * * * * *
102563 TATTTAAAGAATTCTGTAT-GCCAAAAACCATGCAAAACTGAG-TGGAAGC-CTCGGAACGCGTT
194 TATTTCAAGGAGTCT-T-TCGCCAAAAATCATGCAAAACTGAGCCGG-TGCTC-CGAAACGCGTT
** * *
102625 TTTAGCCAAAAACAATGATGGTTATTACACGATTTCGGCTAAAAACTGACAC-GAAAAATTTTTA
255 TTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGAC-CTGAAAAGTTTTT-
102689 CT
318 CT
* * * *
102691 CAATTTTTTGCCACAATACTCTGAAAAAAAAATATAATTCAACGCCAAAAAGATTGAAGGGTTTT
1 CAATTTTTTGCCACAATACTCAG-AAAAAATATATAATTCAACGCCAAAAAGATTGACGGCTTTT
*
102756 CACGCTTCTAATATCGTTTTTCCATTTATTTTCTGAATTAATTTCTAATTAAATCGAAACAA
65 CACGCTTCTAATATCGTTTTTCCATTT-TTTTCCGAATTAATTTCTAATTAAATCGAAACAA
102818 CACGATTTCG
Statistics
Matches: 2473, Mismatches: 447, Indels: 360
0.75 0.14 0.11
Matches are distributed among these distances:
316 4 0.00
317 42 0.02
318 14 0.01
319 104 0.04
320 318 0.13
321 409 0.17
322 82 0.03
323 102 0.04
324 49 0.02
325 1 0.00
326 4 0.00
327 14 0.01
328 27 0.01
329 64 0.03
330 177 0.07
331 52 0.02
332 214 0.09
333 345 0.14
334 78 0.03
335 111 0.04
337 1 0.00
338 4 0.00
339 6 0.00
341 1 0.00
346 3 0.00
348 3 0.00
349 4 0.00
350 12 0.00
351 18 0.01
352 1 0.00
353 3 0.00
354 2 0.00
355 2 0.00
356 6 0.00
358 3 0.00
361 33 0.01
364 15 0.01
365 71 0.03
366 71 0.03
367 3 0.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (319 bp):
CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGCTTTTC
ACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTC
AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATA
TTTCAAGGAGTCTTTCGCCAAAAATCATGCAAAACTGAGCCGGTGCTCCGAAACGCGTTTTTAGC
CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCTGAAAAGTTTTTCT
Found at i:103922 original size:25 final size:27
Alignment explanation
Indices: 103879--103930 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
103869 ATTAATTAAT
*
103879 AAAAAGTTGAATCATCTAAAAA-AATA
1 AAAAAGTTAAATCATCTAAAAAGAATA
*
103905 AAAAAGTTAAATGA-CTAAAAAGAATA
1 AAAAAGTTAAATCATCTAAAAAGAATA
103931 CTTATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.63, C:0.06, G:0.10, T:0.21
Consensus pattern (27 bp):
AAAAAGTTAAATCATCTAAAAAGAATA
Found at i:109623 original size:15 final size:15
Alignment explanation
Indices: 109603--109631 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
109593 TTGCTTTCGT
109603 TTTCCTTTTCTTTTC
1 TTTCCTTTTCTTTTC
109618 TTTCCTTTTCTTTT
1 TTTCCTTTTCTTTT
109632 TTCATTTATT
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTCCTTTTCTTTTC
Found at i:111276 original size:330 final size:322
Alignment explanation
Indices: 110628--112189 Score: 1312
Period size: 330 Copynumber: 4.8 Consensus size: 322
110618 CCATGATGGT
* *
110628 AAAAATGACCCAAAAGATTTTTCCTCAATTTTT-GTTAAAAATACCCATAAAAAACTATATAATT
1 AAAAATGACCC-AAAGA-TTTTCCTCAATTTTTAG-CAAAAATACTCAT-AAAAA-TATATAATT
* **** * * * * ** *
110692 CAATGCCAAAAATATTGGAGGACTTGTCACGCTTTTACGATCGTTTTT-CATATTTTTTCTGAAT
61 TAACATAAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCA-ATTTTTTCTAAAT
* * * *
110756 TAAATTTCTAATTAAATCGAAATAAGATTCAGATACACGTAAAAATAAATCTTTAAATCCAATGT
125 T-AATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * * *
110821 GGCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTCGGCACCAAAAATCATGCAAAA
189 GGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGACACCAAAAATCATGCAAAA
** * * *
110886 CAAAGCCATGACCCTGGAACGCGTTTTTAGCCAAAACCGTGATGGTTAGTACACGATTTCGGCTA
254 CTGAG-CAGGTCCC-GGAACGCGTTTTTAGCC-AAACCGTGAT-G-AAGTACACGATTTCGGCTA
110951 AAATTTTGC
314 AAATTTTGC
* *
110960 AAAAAATTGACCCGAAAGATATTTCCTCAATTTTTTGTAAAAATACTCATAAAAATATATAATTT
1 -AAAAA-TGACCC-AAAGAT-TTTCCTCAATTTTTAGCAAAAATACTCATAAAAATATATAATTT
* * * * *
111025 GACATAAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCAATTTTTTCTGAATTA
62 AACATAAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCAATTTTTTCTAAATTA
*
111090 ATTTCTAATTAAATCGAAATAAGATTCAGATGCTTGTAAAAACAAATCCTTAAATCCAATGTGGC
127 ATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
*
111155 T-AGATTTGGTTATATGAATATAGATATTTCAAGGAGTCTTGACACCAAAAATCATGCAAAACTG
192 TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGACACCAAAAATCATGCAAAACTG
* * * *
111219 AGCAGGGTCCCGGAACAG-GTTTTTAGTCGCAATCTGTGATGATTAGTATAAGATTTCGGCTAAA
257 AGCA-GGTCCCGGAAC-GCGTTTTTAG-C-CAAACCGTGATGA--AGTACACGATTTCGGCTAAA
111283 ATTTTGC
316 ATTTTGC
* * * *
111290 AAAAATGAGCCGAAAGATTTTTCCTCAAATTCTAG-AGAAAATACTCATAAAAAAAAATATAATT
1 AAAAATGA-CCCAAAGA-TTTTCCTCAATTTTTAGCA-AAAATACTCAT--AAAAATATATAATT
* ** * * * * *
111354 CAACGCCAAAAAA-ATTGAAAGTCTTTTTCACGCTTCCAATATCGTTTTTCCTATTTTATTTCCA
61 TAAC-ATAAAAAAGATTGAAGGAC-TTTTCACGCTTCTAATATCGTTTTTCC-AATTT-TTTCTA
* * * * * *
111418 AATTAATTGCTGATTAAATCGAAATAAGATT-AGATACTCGTAAAAATAAATCTTTAAATACAAT
122 AATTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * * * *
111482 GTGACCGAGATTTGGTTAGATGAATATAGATGTAATTT-ATGGAGTCTTGACGCAAAAAATCATG
187 GTGGCTGAGATTTGGTTAGATGAATATAGA--T-ATTTCAAGGAGTCTTGACACCAAAAATCATG
* * * * *
111546 CAAAACTGACCCGGGGCCTTGGAACGCGTTTTTAGCC-AA-----A--AA-T--GCG--TTCGGC
249 CAAAACTGA-GCAGGTCC-CGGAACGCGTTTTTAGCCAAACCGTGATGAAGTACACGATTTCGGC
111598 TAAAATTTTGC
312 TAAAATTTTGC
* * * * * * *
111609 AAAAATGTTCCCAATTG-TTTTTCT-AATTTTTAGCCACAATACTCACAAAAAATATATAATTCA
1 AAAAATG-ACCCAA-AGATTTTCCTCAATTTTTAGCAAAAATACTCA-TAAAAATATATAATTTA
**** * * * * *
111672 ATGCCAAAATGATTGAAGGGCTTCTT-ACGCTTCCAATATCGTTTTCCCTATTTTTTC-AAATTA
63 ACATAAAAAAGATTGAAGGACTT-TTCACGCTTCTAATATCGTTTTTCCAATTTTTTCTAAATTA
* * * *
111735 ATTTCTAATTAAATTGAAACATGATTCA-AGTGCTCGTAAAAAAAAAAAATCCTTAAATCCAATG
127 ATTTCTAATTAAATCGAAATAAGATTCAGA-TGCTCGT---AAAAACAAATCCTTAAATCCAATG
* * * *
111799 TGGCTAAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTTTTG-CAACCAAAAGTCATGCAA
188 TGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGAC-ACCAAAAATCATGCAA
* *
111863 AACTGA-C---TCGCCGGAATGCGATTTTTAGCCAAAAAAAACCGTGATG--GTACACGATTTCA
252 AACTGAGCAGGTC-CCGGAACGCG-TTTTTAGCC-----AAACCGTGATGAAGTACACGATTTCG
*
111922 GCTAAAATTTTAC
310 GCTAAAATTTTGC
* * * * *
111935 AAAAATTGACCC---GATTTTCCTCAATTTTTAGCCACAATACTCACAAATTATATATAATTCAA
1 AAAAA-TGACCCAAAGATTTTCCTCAATTTTTAGCAAAAATACTCATAAA-AATATATAATTTAA
* * * * * *
111997 C-TGAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCATTTTTCGTAA--TTTTCAAAATTAA
64 CATAAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTC-CAATTTTTTCTAAATTAA
* * * *
112059 TTTCTAATTAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCT
128 TTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT
* * * * * *
112124 GAGATTTGATTAGATAAATATAGATATTTCAAGAAGTCTCGACGCCAAAAATCATGAAAAACTGA
193 GAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGACACCAAAAATCATGCAAAACTGA
112189 G
258 G
112190 TCGGGGCCCC
Statistics
Matches: 1014, Mismatches: 146, Indels: 150
0.77 0.11 0.11
Matches are distributed among these distances:
309 8 0.01
310 10 0.01
312 29 0.03
313 16 0.02
314 32 0.03
315 28 0.03
316 74 0.07
317 16 0.02
318 6 0.01
319 28 0.03
320 81 0.08
321 3 0.00
322 9 0.01
323 81 0.08
324 39 0.04
326 24 0.02
327 3 0.00
328 33 0.03
329 24 0.02
330 120 0.12
331 93 0.09
332 92 0.09
333 69 0.07
334 38 0.04
335 40 0.04
336 18 0.02
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (322 bp):
AAAAATGACCCAAAGATTTTCCTCAATTTTTAGCAAAAATACTCATAAAAATATATAATTTAACA
TAAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCAATTTTTTCTAAATTAATTT
CTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGACACCAAAAATCATGCAAAACTGAGCA
GGTCCCGGAACGCGTTTTTAGCCAAACCGTGATGAAGTACACGATTTCGGCTAAAATTTTGC
Found at i:112223 original size:324 final size:321
Alignment explanation
Indices: 111633--112230 Score: 760
Period size: 320 Copynumber: 1.8 Consensus size: 321
111623 TTGTTTTTCT
* *
111633 AATTTTTAGCCACAATACTCACAAAAAATATATAATTCAATGCCAAAATGATTGAAGGGCTTCTT
1 AATTTTTAGCCACAATACTCACAAAAAATATATAATTCAATG-CAAAAAGATTGAAGGACTTCTT
* * *
111698 ACGCTTCCAATATCGTTTTCCCTATTTTTTCAAATTAATTTCTAATTAAATTGAAACATGATTCA
65 ACGCTTCCAATATCATTTTCCCTATATTTTCAAATTAATTTCTAATTAAATTGAAACAAGATTCA
* *
111763 AGTGCTCGTAAAAAAAAAAAATCCTTAAATCCAATGTGGCTAAGACTTGGTTAGATGAATATAGA
130 AGTGCTCGT--AAAAAAAAAATCCTTAAATCCAATGTGGCTAAGACTTGATTAGATAAATATAGA
* * * * * * * *
111828 TATTTCAAGGAGTTTTGCAACCAAAAGTCATGCAAAACTGACTCGCCGGAATGCGATTTTTAGCC
193 TATTTCAAGAAGTCTCGCAACCAAAAATCATGAAAAACTGACTCGCCGAAACGCGATTTTTAGCA
111893 AAAAAAAACCGTGATGGTACACGATTTCAGCTAAAATTTTACAAAAATTGACCCGATTTTCCTC
258 AAAAAAAACCGTGATGGTACACGATTTCAGCTAAAATTTTACAAAAATTGACCCGATTTTCCTC
** *
111957 AATTTTTAGCCACAATACTCACAAATTATATATAATTCAACTG-AAAAAGATTGGAGGACTT-TT
1 AATTTTTAGCCACAATACTCACAAAAAATATATAATTCAA-TGCAAAAAGATTGAAGGACTTCTT
** * *
112020 CACGCTTTTAATATCATTTTTCGTA-ATTTTCAAAATTAATTTCTAATTAAATTGAAACAAGATT
65 -ACGCTTCCAATATCATTTTCCCTATATTTTC-AAATTAATTTCTAATTAAATTGAAACAAGATT
* * * * *
112084 -TAGATGCTCGT-AAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATAAATATAG
128 CAAG-TGCTCGTAAAAAAAAAATCCTTAAATCCAATGTGGCTAAGACTTGATTAGATAAATATAG
* *
112147 ATATTTCAAGAAGTCTCG-ACGCCAAAAATCATGAAAAACTGAGTCGGGGCCCCGAAACGC-ATT
192 ATATTTCAAGAAGTCTCGCA-ACCAAAAATCATGAAAAACTGACTC---G--CCGAAACGCGATT
*
112210 TTTAGGAAAAAAAAACCGTGA
251 TTTAGCAAAAAAAAACCGTGA
Statistics
Matches: 234, Mismatches: 30, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
319 1 0.00
320 82 0.35
322 9 0.04
323 73 0.31
324 60 0.26
325 9 0.04
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (321 bp):
AATTTTTAGCCACAATACTCACAAAAAATATATAATTCAATGCAAAAAGATTGAAGGACTTCTTA
CGCTTCCAATATCATTTTCCCTATATTTTCAAATTAATTTCTAATTAAATTGAAACAAGATTCAA
GTGCTCGTAAAAAAAAAATCCTTAAATCCAATGTGGCTAAGACTTGATTAGATAAATATAGATAT
TTCAAGAAGTCTCGCAACCAAAAATCATGAAAAACTGACTCGCCGAAACGCGATTTTTAGCAAAA
AAAAACCGTGATGGTACACGATTTCAGCTAAAATTTTACAAAAATTGACCCGATTTTCCTC
Done.