Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1213
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: 56421
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:4735 original size:26 final size:26
Alignment explanation
Indices: 4690--4739 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
4680 AATTTTTATA
4690 TATACATTTAATAAATAAAATTAATT
1 TATACATTTAATAAATAAAATTAATT
4716 TATACA-TTACATGAAA-AAAATTAA
1 TATACATTTA-AT-AAATAAAATTAA
4740 CTTTTATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 3 0.14
26 16 0.73
27 3 0.14
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (26 bp):
TATACATTTAATAAATAAAATTAATT
Found at i:5521 original size:21 final size:23
Alignment explanation
Indices: 5483--5528 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 23
5473 TTGTAGAATC
*
5483 TAATAATTTTAATATTAATAAATA
1 TAATAATTTT-ATATTAAAAAATA
5507 TAATAATTTT-T-TTAAAAAATA
1 TAATAATTTTATATTAAAAAATA
5528 T
1 T
5529 TTTTTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 1 0.05
24 10 0.48
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATAATTTTATATTAAAAAATA
Found at i:6603 original size:3 final size:3
Alignment explanation
Indices: 6595--6638 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
6585 CACACTAATA
6595 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
6639 ATTAATTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:9180 original size:20 final size:20
Alignment explanation
Indices: 9157--9194 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9147 TTACTTAACA
9157 TTAAAATTATT-TTTAAATAC
1 TTAAAATT-TTGTTTAAATAC
9177 TTAAAATTTTGTTTAAAT
1 TTAAAATTTTGTTTAAAT
9195 GAATGTTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
TTAAAATTTTGTTTAAATAC
Found at i:9368 original size:16 final size:16
Alignment explanation
Indices: 9347--9381 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9337 ATTAATGTAG
*
9347 TAAAATCTTATAAATA
1 TAAAATATTATAAATA
*
9363 TAAAATATTTTAAATA
1 TAAAATATTATAAATA
9379 TAA
1 TAA
9382 TTATGACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAAATATTATAAATA
Found at i:11146 original size:19 final size:19
Alignment explanation
Indices: 11118--11167 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
11108 CCAAAAAAAT
11118 AAAATAAAATATGATATAAA
1 AAAAT-AAATATGATATAAA
11138 AAAATAAATATGATATAAA
1 AAAATAAATATGATATAAA
* *
11157 TATATAAATAT
1 AAAATAAATAT
11168 TTTAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 23 0.82
20 5 0.18
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (19 bp):
AAAATAAATATGATATAAA
Found at i:11613 original size:16 final size:15
Alignment explanation
Indices: 11580--11625 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
11570 AACATAATGA
11580 TAAAAATAAAAAAAT
1 TAAAAATAAAAAAAT
* *
11595 TAAAAATCAAGAAATT
1 TAAAAAT-AAAAAAAT
11611 TAAAAATAAAAAAAT
1 TAAAAATAAAAAAAT
11626 CAATAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (15 bp):
TAAAAATAAAAAAAT
Found at i:11648 original size:16 final size:16
Alignment explanation
Indices: 11580--11650 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
11570 AACATAATGA
*
11580 TAAAAAT-AAAAAAAT
1 TAAAAATCAAAAATAT
11595 TAAAAATCAAGAAAT-T
1 TAAAAATCAA-AAATAT
* *
11611 TAAAAATAAAAAAATCAA
1 TAAAAAT-CAAAAAT-AT
*
11629 TAAAAATCAAAATTAT
1 TAAAAATCAAAAATAT
11645 TAAAAA
1 TAAAAA
11651 AATGATGAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
15 7 0.16
16 21 0.47
17 10 0.22
18 7 0.16
ACGTcount: A:0.72, C:0.04, G:0.01, T:0.23
Consensus pattern (16 bp):
TAAAAATCAAAAATAT
Found at i:11724 original size:39 final size:39
Alignment explanation
Indices: 11680--11791 Score: 197
Period size: 39 Copynumber: 2.9 Consensus size: 39
11670 TTGTTAAAGC
11680 ATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGT
1 ATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGT
*
11719 ATGAAATGATGATGCAAAGCATGTAACGTTGATGCAAGT
1 ATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGT
* *
11758 ATGAAATGATGATGCAAAGCATGAAATGTGGATG
1 ATGAAATGATGATGCAAAGCATGTAACGTGGATG
11792 TGGATGTAAG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 69 1.00
ACGTcount: A:0.39, C:0.09, G:0.28, T:0.24
Consensus pattern (39 bp):
ATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGT
Found at i:11791 original size:20 final size:20
Alignment explanation
Indices: 11675--11785 Score: 129
Period size: 20 Copynumber: 5.7 Consensus size: 20
11665 AAAAGTTGTT
11675 AAAGCATGAAATGATGATGC
1 AAAGCATGAAATGATGATGC
* *
11695 AAAGCATGTAACG-TGGATGC
1 AAAGCATGAAATGAT-GATGC
*
11715 -AAGTATGAAATGATGATGC
1 AAAGCATGAAATGATGATGC
* * *
11734 AAAGCATGTAACGTTGATGC
1 AAAGCATGAAATGATGATGC
*
11754 -AAGTATGAAATGATGATGC
1 AAAGCATGAAATGATGATGC
11773 AAAGCATGAAATG
1 AAAGCATGAAATG
11786 TGGATGTGGA
Statistics
Matches: 73, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
19 30 0.41
20 43 0.59
ACGTcount: A:0.41, C:0.10, G:0.26, T:0.23
Consensus pattern (20 bp):
AAAGCATGAAATGATGATGC
Found at i:12694 original size:20 final size:20
Alignment explanation
Indices: 12644--12694 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
12634 CTTTTGTTAG
*
12644 TTGATTTTTTATATATATAT
1 TTGATTTTTTGTATATATAT
*
12664 TTG-TTTGTTTGTGTATAT-T
1 TTGATTT-TTTGTATATATAT
12683 TTGATTTATTTG
1 TTGATTT-TTTG
12695 AAAATATTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.20, C:0.00, G:0.14, T:0.67
Consensus pattern (20 bp):
TTGATTTTTTGTATATATAT
Found at i:14601 original size:10 final size:9
Alignment explanation
Indices: 14589--14632 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
14579 TCGAAAATTT
14589 AAAAAAATA
1 AAAAAAATA
*
14598 TAAAAAATA
1 AAAAAAATA
14607 AAAAATAATA
1 AAAAA-AATA
14617 AAAATCAAATA
1 AAAA--AAATA
14628 AAAAA
1 AAAAA
14633 CATCATGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 13 0.43
10 8 0.27
11 8 0.27
12 1 0.03
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAAAATA
Found at i:15319 original size:73 final size:73
Alignment explanation
Indices: 15203--15422 Score: 255
Period size: 82 Copynumber: 2.9 Consensus size: 73
15193 CTCCAGGAAA
* * *
15203 CAGCAGCATCTATCAATACCAGCAGCAGCTCGAGCCTCTTCCAGCCCACGAACATGGCAGCAGCT
1 CAGCAGCATCCATCAATACCGGCAGCAGCTCGAGCTTCTTCCAGCCCACGAACATGGCAGCAGCT
15268 TCAGGCAG
66 TCAGGCAG
* *
15276 CAGCAGCATCCATCAATACCGGTAGCAGCTCGAGCTTCTTCCAGCCCACGAACACAGCAGCAGCT
1 CAGCAGCATCCATCAATACCGGCAGCAGCTCGAGCTTCTTCCAGCCCACG-A-ACA--TG--G--
15341 CCAGCAGCTTCAGGCAG
58 -CAGCAGCTTCAGGCAG
* * *
15358 CAGTAGCATCCATCAATACCGGCAGCAG-TACGAGCCTT-TTTCAGACCACGAACATGGCAGCAG
1 CAGCAGCATCCATCAATACCGGCAGCAGCT-CGAG-CTTCTTCCAGCCCACGAACATGGCAGCAG
15421 CT
64 CT
15423 CCAGCAGTTT
Statistics
Matches: 126, Mismatches: 10, Indels: 22
0.80 0.06 0.14
Matches are distributed among these distances:
73 54 0.43
74 1 0.01
75 3 0.02
76 1 0.01
77 1 0.01
78 1 0.01
79 1 0.01
80 3 0.02
81 2 0.02
82 56 0.44
83 3 0.02
ACGTcount: A:0.28, C:0.35, G:0.22, T:0.16
Consensus pattern (73 bp):
CAGCAGCATCCATCAATACCGGCAGCAGCTCGAGCTTCTTCCAGCCCACGAACATGGCAGCAGCT
TCAGGCAG
Found at i:15357 original size:82 final size:82
Alignment explanation
Indices: 15260--15451 Score: 257
Period size: 82 Copynumber: 2.3 Consensus size: 82
15250 ACGAACATGG
* *
15260 CAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACCGGTAGCAGCT-CGAG-CTTCTTCCAGCCC
1 CAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACCGGCAGCAG-TACGAGCCTT-TTCCAGACC
15323 ACGAACACAGCAGCAGCTC
64 ACGAACACAGCAGCAGCTC
* *
15342 CAGCAGCTTCAGGCAGCAGTAGCATCCATCAATACCGGCAGCAGTACGAGCCTTTTTCAGACCAC
1 CAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACCGGCAGCAGTACGAGCCTTTTCCAGACCAC
**
15407 GAACATGGCAGCAGCTC
66 GAACACAGCAGCAGCTC
*
15424 CAGCAGTTTCCA-GCAGCA-CTAGCATCCA
1 CAGCAGCTT-CAGGCAGCAGC-AGCATCCA
15452 CCAACACCAA
Statistics
Matches: 98, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
81 1 0.01
82 92 0.94
83 5 0.05
ACGTcount: A:0.28, C:0.34, G:0.22, T:0.16
Consensus pattern (82 bp):
CAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACCGGCAGCAGTACGAGCCTTTTCCAGACCAC
GAACACAGCAGCAGCTC
Found at i:15383 original size:155 final size:155
Alignment explanation
Indices: 15105--15422 Score: 431
Period size: 155 Copynumber: 2.1 Consensus size: 155
15095 CATCCGAAAC
* * *
15105 CAGCAGCTTCAGGCAGCATCAACATCCATCAATACCGACAGTAGCTCGAGCCTCTTCCAGCCCAT
1 CAGCAGCTTCAGGCAGCAGCAACATCCATCAATACCGACAGCAGCTCGAGCCTCTTCCAGCCCAC
** * *
15170 GAACATGGCAACAGCTCCAGTAACTCCAGGAAACAGCAGCATCTATCAATACCAGCAGCAGCT-C
66 GAACACAGCAACAGCTCCAGCAACTCCAGGAAACAGCAGCATCCATCAATACCAGCAGCAG-TAC
*
15234 GAGCCTCTTCCAGCCCACGAACATGG
130 GAGCCTCTTCCAGACCACGAACATGG
* ** *
15260 CAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACCGGTAGCAGCTCGAGCTTCTTCCAGCCCAC
1 CAGCAGCTTCAGGCAGCAGCAACATCCATCAATACCGACAGCAGCTCGAGCCTCTTCCAGCCCAC
* * * * * * *
15325 GAACACAGCAGCAGCTCCAGCAGCTTCAGGCAGCAGTAGCATCCATCAATACCGGCAGCAGTACG
66 GAACACAGCAACAGCTCCAGCAACTCCAGGAAACAGCAGCATCCATCAATACCAGCAGCAGTACG
* *
15390 AGCCTTTTTCAGACCACGAACATGG
131 AGCCTCTTCCAGACCACGAACATGG
15415 CAGCAGCT
1 CAGCAGCT
15423 CCAGCAGTTT
Statistics
Matches: 141, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
154 1 0.01
155 140 0.99
ACGTcount: A:0.29, C:0.34, G:0.21, T:0.16
Consensus pattern (155 bp):
CAGCAGCTTCAGGCAGCAGCAACATCCATCAATACCGACAGCAGCTCGAGCCTCTTCCAGCCCAC
GAACACAGCAACAGCTCCAGCAACTCCAGGAAACAGCAGCATCCATCAATACCAGCAGCAGTACG
AGCCTCTTCCAGACCACGAACATGG
Found at i:17252 original size:82 final size:82
Alignment explanation
Indices: 17107--17437 Score: 450
Period size: 82 Copynumber: 4.0 Consensus size: 82
17097 GGATGCTGGT
* * ** * * *
17107 GCTGTTGGAGCTGCTGTCGTGTTCGTGATCTGGAAGAGGCTC-ACGTTGCTGTCGGTATTGATGG
1 GCTGCTGGAGCTGCTGTAGTGTTCGTGGGCTGGAAGAGGCTCGA-GCTGCTGCCGATATTGATGG
*
17171 ATGCTGCTGCTGCCTAAA
65 ATGCTGCTGCTGCCTGAA
* * *
17189 GCTGCTGAAGCTGCTGTAGTGTTCGTGGGCTGGAAGAGGCTCGAGTTGCTGCCTATATTGATGGA
1 GCTGCTGGAGCTGCTGTAGTGTTCGTGGGCTGGAAGAGGCTCGAGCTGCTGCCGATATTGATGGA
* *
17254 TGCTGCTGTTGCTTGAA
66 TGCTGCTGCTGCCTGAA
*
17271 GCTGCTGGAGCTGCTGTCA-TGTTCGTGGGCTGGAAGAGGCTCGAGCTGCTGCCGGTATTGATGG
1 GCTGCTGGAGCTGCTGT-AGTGTTCGTGGGCTGGAAGAGGCTCGAGCTGCTGCCGATATTGATGG
17335 ATGCTGCTGCTGCCTGAA
65 ATGCTGCTGCTGCCTGAA
*** * *
17353 GCTGCTGGAGCTGCTACCGTGTTCGTGGGCTGGAAGAGGCTCGAGCTGCTACTGATATTGATGGA
1 GCTGCTGGAGCTGCTGTAGTGTTCGTGGGCTGGAAGAGGCTCGAGCTGCTGCCGATATTGATGGA
*
17418 TGCTGTTGCTGCCTGAA
66 TGCTGCTGCTGCCTGAA
17435 GCT
1 GCT
17438 ACTAGAGTTT
Statistics
Matches: 222, Mismatches: 24, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
82 220 0.99
83 2 0.01
ACGTcount: A:0.15, C:0.20, G:0.36, T:0.30
Consensus pattern (82 bp):
GCTGCTGGAGCTGCTGTAGTGTTCGTGGGCTGGAAGAGGCTCGAGCTGCTGCCGATATTGATGGA
TGCTGCTGCTGCCTGAA
Found at i:18029 original size:9 final size:9
Alignment explanation
Indices: 18011--18046 Score: 51
Period size: 8 Copynumber: 4.3 Consensus size: 9
18001 TTTCTATTAA
18011 TTTT-TATT
1 TTTTATATT
18019 TTTTATATT
1 TTTTATATT
18028 TTTTAT-TT
1 TTTTATATT
18036 TTTTA-ATT
1 TTTTATATT
18044 TTT
1 TTT
18047 GATTTCTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 16 0.62
9 10 0.38
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTATATT
Found at i:18030 original size:16 final size:16
Alignment explanation
Indices: 18007--18051 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
17997 TTGATTTCTA
18007 TTAA-TTTTTA-TTTT
1 TTAATTTTTTATTTTT
18021 TTATATTTTTTATTTTT
1 TTA-ATTTTTTATTTTT
*
18038 TTAATTTTTGATTT
1 TTAATTTTTTATTT
18052 CTATTTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 3 0.11
15 1 0.04
16 16 0.59
17 7 0.26
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (16 bp):
TTAATTTTTTATTTTT
Found at i:19409 original size:43 final size:43
Alignment explanation
Indices: 18529--20026 Score: 703
Period size: 42 Copynumber: 35.5 Consensus size: 43
18519 GATTCTCCCA
* * *
18529 GGTCAAAGCCGACAGGCAAACTTTA--GATAAGACAGTCT-TCAG
1 GGTCAAAGCCGACAGGCAGAC-TTAGGGATAGGAAAGTCTCT-AG
* * * *
18571 GGTCAAAGTCGACAGGCAGACTGAGGG-TAGAAAAGTCTCCAG
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGGAAAGTCTCTAG
* *
18613 GGTCAAAGCTGACAGGCAGAC-TACGGG-TAGAAAAGTCTCTAG
1 GGTCAAAGCCGACAGGCAGACTTA-GGGATAGGAAAGTCTCTAG
* * * * * * *
18655 GGTCAAAGTCGATAGACAAAATTTA--GAT--GAAGCAGTCTTTAA
1 GGTCAAAGCCGACAGGC-AGACTTAGGGATAGGAA--AGTCTCTAG
* * *
18697 GGTCAAAGCTGACAGGCAGACTGAGAG-TAGGAAAGTCTCCTA-
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGGAAAGTCT-CTAG
* * * * *
18739 GGTCAAAGCTGACACGCAGACTAAGGG-TAGAAAAGTCTCAAG
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGGAAAGTCTCTAG
* * * * *
18781 GGTCAAAGCCGCCAGGTAAACTTTA--GATGAGG-CAGTCTTTAG
1 GGTCAAAGCCGACAGGCAGAC-TTAGGGAT-AGGAAAGTCTCTAG
* * * *
18823 GGTTAAAGCCGACAGGCAGACTGAGGGA-AGAAAAGTCTCTCG
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGGAAAGTCTCTAG
* * * * * *
18865 GGTCAAAGCTGACCGGCAGACTGAGGG--A-GATAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGGAAAGTCTCTAG
* * * * *
18905 GGTCAAAGCCGACAAGCAGACTAAAGGG-TAAGAAAATCTCCAG
1 GGTCAAAGCCGACAGGCAGACT-TAGGGATAGGAAAGTCTCTAG
* * * ** * *
18948 GGTCAAAGCCGACAGCCAAACTTAGGAAGGGGAAAGTTTCCAG
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGGAAAGTCTCTAG
** * * *
18991 GGTCAAAGCCGACAGATAGACTTTA--GATGAGG-CAGT-TTTCAA
1 GGTCAAAGCCGACAGGCAGAC-TTAGGGAT-AGGAAAGTCTCT-AG
* * * * * *
19033 GGTCAAAGCCGATAGGCAAACTGAGGGA-AGAAAACTCTCTCG
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGGAAAGTCTCTAG
* * * *
19075 GGTCAAAGCCGACAGACAGACTAAGGG--AGG-CAGTCTCCAG
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGGAAAGTCTCTAG
* * * * *
19115 GGTCAAAGCTGATAGGTAGACTAAGGGTATA--AAAGTCT-TCAA
1 GGTCAAAGCCGACAGGCAGACTTAGGG-ATAGGAAAGTCTCT-AG
* * * * * *
19157 GATCAAAGTCGATAGGCAAACTTTA--GATGAGG-CAGTCT-TCAA
1 GGTCAAAGCCGACAGGCAGAC-TTAGGGAT-AGGAAAGTCTCT-AG
* * ** * *
19199 GGTTAAAGCCAACAGGCAGA-TTGAGGGA-AAAAAAATCTCTCG
1 GGTCAAAGCCGACAGGCAGACTT-AGGGATAGGAAAGTCTCTAG
* * ** *
19241 GGTCAAAGCCGACAAGCAGACTGAGGG--AGGCGA-TCT-TCAA
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGGAAAGTCTCT-AG
** * ** *
19281 GGTCAAAGCCGACAGGTGGAC--ATGGA-AAAAAAGTCT-TCAA
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGGAAAGTCTCT-AG
* * *
19321 GGTCAAAGCTGATAGGCAGA-TTGAGGGA-AAGAAAGTCTC-ACG
1 GGTCAAAGCCGACAGGCAGACTT-AGGGATAGGAAAGTCTCTA-G
* * **
19363 GGTCAAAGCCGATAGGTAGACTTAGGGAGGGGAAAGTCTCTAG
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGGAAAGTCTCTAG
** * * * *
19406 GGTCAAAGCTAATAGGCAGACTTTA--GATGAGGCAA-TCTCCAA
1 GGTCAAAGCCGACAGGCAGAC-TTAGGGAT-AGGAAAGTCTCTAG
* * * * * *
19448 GGTCAAAGCTGACATGTAGACTAAGGGATAGGAAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGGAAAGTCTCTAG
* ** * *
19491 GGTCAAAGCCGATAGGCAGACTTA-AAATAAGG-TAGTCTCCAG
1 GGTCAAAGCCGACAGGCAGACTTAGGGAT-AGGAAAGTCTCTAG
* * * *
19533 GGTCAAAGCCGACAGGTAGCCTAAGGGACAGGAAAGTCTCTAG
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGGAAAGTCTCTAG
* ** * *
19576 GGTCAAAGCCAACAGGCAGACTTA-AAATGAGG-CAGTCTCTAA
1 GGTCAAAGCCGACAGGCAGACTTAGGGAT-AGGAAAGTCTCTAG
* * * * ** * *
19618 GGTCAAAACTGACAGACAGACTAAGGGATATTAAAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTTAGGGATA-GGAAAGTCTCTAG
* *
19662 GGTCAAAGCCGACAGGCGGACTTAGGGATAGGAAAGTCTTTAG
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGGAAAGTCTCTAG
* * ** * *
19705 GGTCAAAGCCGACAAGTAGACTTTA--GAT-GAGTTAGTCTCCAC
1 GGTCAAAGCCGACAGGCAGAC-TTAGGGATAG-GAAAGTCTCTAG
* *
19747 GGTCAAAGCTGACAGGCAGACTAAGGGATAGGAAAGTCTCTAG
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGGAAAGTCTCTAG
* * * *
19790 GGTTAAAGCCGATAAGCAGACTTAGGGCTAGGAAAGTCTCTAG
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGGAAAGTCTCTAG
* * ** * * *
19833 GGTTAAAGCCGACATGCAGACTTTA--GATGAGG-CGGCCTCCAA
1 GGTCAAAGCCGACAGGCAGAC-TTAGGGAT-AGGAAAGTCTCTAG
* * *
19875 GGTCAAAGCCGACAAGCAGA-TTAAGGGATAGAAAAGTTTCTAG
1 GGTCAAAGCCGACAGGCAGACTT-AGGGATAGGAAAGTCTCTAG
* * * *
19918 GGTCAAAGCTGATAGGTAGACTTAGGGATAGAAAAGTCT-TCAG
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGGAAAGTCTCT-AG
* * * * *
19961 GGTCAAAGTCAATAGGCAAACTTAGGGATAGAAAAGTCTCTAG
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGGAAAGTCTCTAG
* * *
20004 GGTCAAAGTCGATAGGTAGACTT
1 GGTCAAAGCCGACAGGCAGACTT
20027 TAGATGAGGC
Statistics
Matches: 1096, Mismatches: 276, Indels: 167
0.71 0.18 0.11
Matches are distributed among these distances:
38 3 0.00
39 3 0.00
40 107 0.10
41 40 0.04
42 515 0.47
43 373 0.34
44 55 0.05
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (43 bp):
GGTCAAAGCCGACAGGCAGACTTAGGGATAGGAAAGTCTCTAG
Found at i:19453 original size:85 final size:85
Alignment explanation
Indices: 18529--20067 Score: 688
Period size: 85 Copynumber: 18.3 Consensus size: 85
18519 GATTCTCCCA
* * *
18529 GGTCAAAGCCGACAGGCAAACTTTA--GATA-AGACAGTCT-TCAGGGTCAAAGTCGACAGGCAG
1 GGTCAAAGCCGACAGGCAGAC-TTAGGGATAGA-AAAGTCTCT-AGGGTCAAAGCCGACAGGCAG
* * **
18590 AC-TGAG-GGTAGAAAAGTCTCCAG
63 ACTTTAGATG-AGGCAA-TCTCCAG
* * * * * *
18613 GGTCAAAGCTGACAGGCAGAC-TACGGG-TAGAAAAGTCTCTAGGGTCAAAGTCGATAGACAAAA
1 GGTCAAAGCCGACAGGCAGACTTA-GGGATAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGAC
* * ** *
18676 TTTAGATGAAGCAGTCTTTAA
65 TTTAGATGAGGCAATCTCCAG
* * * * * *
18697 GGTCAAAGCTGACAGGCAGACTGAGAG-TAGGAAAGTCTCCTA-GGTCAAAGCTGACACGCAGAC
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGAAAAGTCT-CTAGGGTCAAAGCCGACAGGCAGAC
* * ** *
18760 -TAAG-GGTAGAAAAGTCTCAAG
65 TTTAGATG-AGGCAA-TCTCCAG
* * * ** * *
18781 GGTCAAAGCCGCCAGGTAAACTTTA--GAT-GAGGCAGTCTTTAGGGTTAAAGCCGACAGGCAGA
1 GGTCAAAGCCGACAGGCAGAC-TTAGGGATAGA-AAAGTCTCTAGGGTCAAAGCCGACAGGCAGA
* * **
18843 C-TGAG-GGAAGAAAAGTCTCTC-G
64 CTTTAGATG-AGGCAA-TCTC-CAG
* * * * * * *
18865 GGTCAAAGCTGACCGGCAGACTGAGGG--AG-ATAGTCTCCAAGGTCAAAGCCGACAAGCAGACT
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACT
** * * **
18927 AAAGGGTAAGAAAATCTCCAG
66 TTA-GATGAGGCAATCTCCAG
* * * ** * * * **
18948 GGTCAAAGCCGACAGCCAAACTTAGGAAGGGGAAAGTTTCCAGGGTCAAAGCCGACAGATAGACT
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACT
* * * *
19013 TTAGATGAGGCAGTTTTCAA
66 TTAGATGAGGCAATCTCCAG
* * * * * *
19033 GGTCAAAGCCGATAGGCAAACTGAGGGA-AGAAAACTCTCTCGGGTCAAAGCCGACAGACAGAC-
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACT
* * *
19096 TAAG-GGAGGCAGTCTCCAG
66 TTAGATGAGGCAATCTCCAG
* * * * * * * * * *
19115 GGTCAAAGCTGATAGGTAGACTAAGGG-TATAAAAGTCT-TCAAGATCAAAGTCGATAGGCAAAC
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGAAAAGTCTCT-AGGGTCAAAGCCGACAGGCAGAC
* * *
19178 TTTAGATGAGGCAGTCTTCAA
65 TTTAGATGAGGCAATCTCCAG
* * * * * *
19199 GGTTAAAGCCAACAGGCAGA-TTGAGGGA-AAAAAAATCTCTCGGGTCAAAGCCGACAAGCAGAC
1 GGTCAAAGCCGACAGGCAGACTT-AGGGATAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGAC
* * * * *
19262 -TGAG-GGAGGCGATCTTCAA
65 TTTAGATGAGGCAATCTCCAG
** * * * * *
19281 GGTCAAAGCCGACAGGTGGAC--ATGGA-AAAAAAGTCT-TCAAGGTCAAAGCTGATAGGCAGA-
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGAAAAGTCTCT-AGGGTCAAAGCCGACAGGCAGAC
* * * *
19341 TTGAG-GGAAAGAAAGTCT-CACG
65 TTTAGATG-AGGCAA-TCTCCA-G
* * ** * ** *
19363 GGTCAAAGCCGATAGGTAGACTTAGGGAGGGGAAAGTCTCTAGGGTCAAAGCTAATAGGCAGACT
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACT
*
19428 TTAGATGAGGCAATCTCCAA
66 TTAGATGAGGCAATCTCCAG
* * * * * * * *
19448 GGTCAAAGCTGACATGTAGACTAAGGGATAGGAAAGTCTCCAAGGTCAAAGCCGATAGGCAGACT
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACT
* * * * *
19513 TAAAATAAGGTAGTCTCCAG
66 TTAGATGAGGCAATCTCCAG
* * * * * *
19533 GGTCAAAGCCGACAGGTAGCCTAAGGGACAGGAAAGTCTCTAGGGTCAAAGCCAACAGGCAGACT
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACT
* * * * *
19598 TAAAATGAGGCAGTCTCTAA
66 TTAGATGAGGCAATCTCCAG
* * * * * * * *
19618 GGTCAAAACTGACAGACAGACTAAGGGATATTAAAAGTCTCCAAGGTCAAAGCCGACAGGCGGAC
1 GGTCAAAGCCGACAGGCAGACTTAGGGATA-GAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGAC
* **
19683 -TTAGGGAT-AGGAAAGTCTTTAG
65 TTTA--GATGAGGCAA-TCTCCAG
* * ** * * *
19705 GGTCAAAGCCGACAAGTAGACTTTA--GAT-GAGTTAGTCTCCACGGTCAAAGCTGACAGGCAGA
1 GGTCAAAGCCGACAGGCAGAC-TTAGGGATAGA-AAAGTCTCTAGGGTCAAAGCCGACAGGCAGA
* * *
19767 C-TAAGGGAT-AGGAAAGTCTCTAG
64 CTTTA--GATGAGGCAA-TCTCCAG
* * * * * * *
19790 GGTTAAAGCCGATAAGCAGACTTAGGGCTAGGAAAGTCTCTAGGGTTAAAGCCGACATGCAGACT
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACT
*** *
19855 TTAGATGAGGCGGCCTCCAA
66 TTAGATGAGGCAATCTCCAG
* * * * *
19875 GGTCAAAGCCGACAAGCAGA-TTAAGGGATAGAAAAGTTTCTAGGGTCAAAGCTGATAGGTAGAC
1 GGTCAAAGCCGACAGGCAGACTT-AGGGATAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGAC
** *
19939 -TTAGGGAT-AGAAAAGTCTTCAG
65 TTTA--GATGAGGCAA-TCTCCAG
* * * * * * *
19961 GGTCAAAGTCAATAGGCAAACTTAGGGATAGAAAAGTCTCTAGGGTCAAAGTCGATAGGTAGACT
1 GGTCAAAGCCGACAGGCAGACTTAGGGATAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACT
*
20026 TTAGATGAGGCAGTCTCCAG
66 TTAGATGAGGCAATCTCCAG
* * *
20046 GGTTAAAGCCGATAGACAGACT
1 GGTCAAAGCCGACAGGCAGACT
20068 GAAGGCATAA
Statistics
Matches: 1108, Mismatches: 283, Indels: 127
0.73 0.19 0.08
Matches are distributed among these distances:
79 1 0.00
80 36 0.03
81 6 0.01
82 137 0.12
83 48 0.04
84 279 0.25
85 399 0.36
86 168 0.15
87 32 0.03
88 2 0.00
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (85 bp):
GGTCAAAGCCGACAGGCAGACTTAGGGATAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACT
TTAGATGAGGCAATCTCCAG
Found at i:19924 original size:171 final size:171
Alignment explanation
Indices: 18569--20057 Score: 454
Period size: 171 Copynumber: 8.8 Consensus size: 171
18559 GACAGTCTTC
* * ** * * *
18569 AGGGTCAAAG-TCGACAGGCAGACTGAGGG-TAGAAAAGTCTCCAGGGTCAAAGCTGACAGGCAG
1 AGGGTCAAAGCT-GACAGGCAGACTAAGGGATAGAAAAGTCTTCAGGGTCAAAGCCAATAAGCAA
* * * * * * * **
18632 AC-TACGGG-TAGAAAAGTCTCTAGGGTCAAAGTCGATAGACAAAATTTAGATGAAGCAGTCTTT
65 ACTTA-GGGATAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGCCTCC
* * * * * * *
18695 AAGGTCAAAGCTGACAGGCAGACTGAGAG-TAGGAAAGTCTCCT
129 AAGGTCAAAGCCGACAAGCAGATTAAGGGATAGAAAAGT-TTCT
* *** * *
18738 A-GGTCAAAGCTGACACGCAGACTAAGGG-TAGAAAAGTC-TCAAGGGTCAAAGCCGCCAGGTAA
1 AGGGTCAAAGCTGACAGGCAGACTAAGGGATAGAAAAGTCTTC-AGGGTCAAAGCCAATAAGCAA
** * * * * ** *
18800 ACTTTA--GAT-GAGGCAGTCTTTAGGGTTAAAGCCGACAGGCAGAC-TGAG-GGAAGAAAAGTC
65 AC-TTAGGGATAGA-AAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTTTAGATG-AG-GCAGCC
* * ** * * * * *
18860 TCTC-GGGTCAAAGCTGACCGGCAGACTGAGGG--AG-ATAGTCTCC
126 TC-CAAGGTCAAAGCCGACAAGCAGATTAAGGGATAGAAAAGTTTCT
* * * * * *
18903 AAGGTCAAAGCCGACAAGCAGACTAAAGGG-TAAGAAAA-TCTCCAGGGTCAAAGCCGA-CAGCC
1 AGGGTCAAAGCTGACAGGCAGACT-AAGGGAT-AGAAAAGTCTTCAGGGTCAAAGCCAATAAG-C
* ** * * * ** ** *
18965 AAACTTAGGAAGGGGAAAGTTTCCAGGGTCAAAGCCGACAGATAGACTTTAGATGAGGCAGTTTT
63 AAACTTAGGGATAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGCCTC
* * * * * * *
19030 CAAGGTCAAAGCCGATAGGCAAACTGAGGGA-AGAAAACTCTCT
128 CAAGGTCAAAGCCGACAAGCAGATTAAGGGATAGAAAAGTTTCT
* * * ** * ** * * *
19073 CGGGTCAAAGCCGACAGACAGACTAAGGG--AG-GCAGTCTCCAGGGTCAAAGCTGATAGGTAGA
1 AGGGTCAAAGCTGACAGGCAGACTAAGGGATAGAAAAGTCTTCAGGGTCAAAGCCAATAAGCAAA
* * * * * * * * *
19135 CTAAGGG-TATAAAAGTCT-TCAAGATCAAAGTCGATAGGCAAACTTTAGATGAGGCAGTCTTCA
66 CTTAGGGATAGAAAAGTCTCT-AGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGCCTCCA
* * * * * * *
19198 AGGTTAAAGCCAACAGGCAGATTGAGGGA-AAAAAAATCTCT
130 AGGTCAAAGCCGACAAGCAGATTAAGGGATAGAAAAGTTTCT
* * * * *** * * * * ***
19239 CGGGTCAAAGCCGACAAGCAGACTGAGGG--AGGCGA-TCTTCAAGGTCAAAGCCGACAGGTGGA
1 AGGGTCAAAGCTGACAGGCAGACTAAGGGATAGAAAAGTCTTCAGGGTCAAAGCCAATAAGCAAA
* * * * * * * ** *
19301 C--ATGGA-AAAAAAGTCT-TCAAGGTCAAAGCTGATAGGCAGA-TTGAGGGA-AAGAAAGTCT-
66 CTTAGGGATAGAAAAGTCTCT-AGGGTCAAAGCCGACAGGCAGACTTTA--GATGAGGCAGCCTC
* * * * ** * *
19359 CACGGGTCAAAGCCGATAGGTAGACTT-AGGGAGGGGAAAGTCTCT
128 CA-AGGTCAAAGCCGACAAGCAGA-TTAAGGGATAGAAAAGTTTCT
* * * ** * * ** * * *
19404 AGGGTCAAAGCTAATAGGCAGACTTTA--GATGAGGCAA-TCTCCAAGGTCAAAGCTGACATGTA
1 AGGGTCAAAGCTGACAGGCAGAC-TAAGGGAT-AGAAAAGTCTTCAGGGTCAAAGCCAATAAGCA
* * * * * * * * * * *
19466 GACTAAGGGATAGGAAAGTCTCCAAGGTCAAAGCCGATAGGCAGACTTAAAATAAGGTAGTCTCC
64 AACTTAGGGATAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGCCTCC
* * * ** * * *
19531 AGGGTCAAAGCCGACAGGTAGCCTAAGGGACAGGAAAGTCTCT
129 AAGGTCAAAGCCGACAAGCAGATTAAGGGATAGAAAAGTTTCT
** * ** * * ** *
19574 AGGGTCAAAGCCAACAGGCAGACTTAA--AAT-GAGGCAGTC-TCTAAGGTCAAAACTGA-CAGA
1 AGGGTCAAAGCTGACAGGCAGAC-TAAGGGATAGA-AAAGTCTTC-AGGGTCAAAGCCAATAAG-
* * * * * * *
19634 CAGACTAAGGGATATTAAAAGTCTCCAAGGTCAAAGCCGACAGGCGGAC-TTAGGGAT-AGGAAA
62 CAAACTTAGGGATA-GAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTTTA--GATGAGG-CA
* ** * * * ** * *
19697 GTCTTTAGGGTCAAAGCCGACAAGTAGACTTTA--GAT-GAGTTAGTCTCC
123 GCCTCCAAGGTCAAAGCCGACAAGCAGA-TTAAGGGATAGA-AAAGTTTCT
* * * * *
19745 ACGGTCAAAGCTGACAGGCAGACTAAGGGATAGGAAAGTC-TCTAGGGTTAAAGCCGATAAGCAG
1 AGGGTCAAAGCTGACAGGCAGACTAAGGGATAGAAAAGTCTTC-AGGGTCAAAGCCAATAAGCAA
* * * * *
19809 ACTTAGGGCTAGGAAAGTCTCTAGGGTTAAAGCCGACATGCAGACTTTAGATGAGGCGGCCTCCA
65 ACTTAGGGATAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGCCTCCA
19874 AGGTCAAAGCCGACAAGCAGATTAAGGGATAGAAAAGTTTCT
130 AGGTCAAAGCCGACAAGCAGATTAAGGGATAGAAAAGTTTCT
* * * * *
19916 AGGGTCAAAGCTGATAGGTAGACTTAGGGATAGAAAAGTCTTCAGGGTCAAAGTCAATAGGCAAA
1 AGGGTCAAAGCTGACAGGCAGACTAAGGGATAGAAAAGTCTTCAGGGTCAAAGCCAATAAGCAAA
* * * * *
19981 CTTAGGGATAGAAAAGTCTCTAGGGTCAAAGTCGATAGGTAGACTTTAGATGAGGCAGTCTCCAG
66 CTTAGGGATAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGCCTCCAA
*
20046 GGTTAAAGCCGA
131 GGTCAAAGCCGA
20058 TAGACAGACT
Statistics
Matches: 1022, Mismatches: 234, Indels: 126
0.74 0.17 0.09
Matches are distributed among these distances:
163 5 0.00
164 61 0.06
165 32 0.03
166 158 0.15
167 93 0.09
168 167 0.16
169 27 0.03
170 187 0.18
171 222 0.22
172 65 0.06
173 5 0.00
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (171 bp):
AGGGTCAAAGCTGACAGGCAGACTAAGGGATAGAAAAGTCTTCAGGGTCAAAGCCAATAAGCAAA
CTTAGGGATAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGCCTCCAA
GGTCAAAGCCGACAAGCAGATTAAGGGATAGAAAAGTTTCT
Found at i:19955 original size:299 final size:296
Alignment explanation
Indices: 19310--20072 Score: 777
Period size: 299 Copynumber: 2.6 Consensus size: 296
19300 ACATGGAAAA
*
19310 AAAGTCT-TCAAGGTCAAAGCTGATAGGCAGA-TTGAGGGAAAG-AAAGTCTCACGGGTCAAAGC
1 AAAGTCTCT-AAGGTCAAAGCTGATAGGCAGACTT-AGGGATAGAAAAGTCTCA-GGGTCAAAGC
* ** ** *
19372 CGATAGGTAGACTTAGGGAGGGGAAAGTCTCTAGGGTCAAAGCTAATAGGCAGACTTTAGATGAG
63 CGATAGGCAGACTTAGGGATAGGAAAGTCTCTAGGGTCAAAGCCGATAGGTAGACTTTAGATGAG
* * *
19437 GCAATCTCCAAGGTCAAAGCTGACATGTAGACTAAGGGATAGGAAAGTCTCCAAGGTCAAAGCCG
128 GCAGTCTCCAAGGTCAAAGCTGACAGGCAGACTAAGGGATAGGAAAGTCTCCAAGGTCAAAGCCG
* * *
19502 ATAGGCAGACTTAAAATAAGGTAGTCTCCAGGGTCAAAGCCGACAGGTAGCCTAAGGGACAGGAA
193 ATAAGCAGACTTAAAATAAGGAAGTCTCCAGGGTCAAAGCCGACAGGCAGCCTAA-GGACAGGAA
* * * *
19567 AGTCTCTAGGGTCAAAGCCAACAGGCAGACTTAAAATGAG
257 AGCCTCCAAGGTCAAAGCCAACAAGCAGACTTAAAATGAG
** * * * * * *
19607 GCAGTCTCTAAGGTCAAAACTGACAGACAGACTAAGGGATATTAAAAGTCTCCAAGGTCAAAGCC
1 AAAGTCTCTAAGGTCAAAGCTGATAGGCAGACTTAGGGATA-GAAAAGTCT-CAGGGTCAAAGCC
* * * * * *
19672 GACAGGCGGACTTAGGGATAGGAAAGTCTTTAGGGTCAAAGCCGACAAGTAGACTTTAGATGAGT
64 GATAGGCAGACTTAGGGATAGGAAAGTCTCTAGGGTCAAAGCCGATAGGTAGACTTTAGATGAGG
* * * * *
19737 TAGTCTCCACGGTCAAAGCTGACAGGCAGACTAAGGGATAGGAAAGTCTCTAGGGTTAAAGCCGA
129 CAGTCTCCAAGGTCAAAGCTGACAGGCAGACTAAGGGATAGGAAAGTCTCCAAGGTCAAAGCCGA
*** * * * * * *
19802 TAAGCAGACTTAGGGCT-AGGAAAGTCTCTAGGGTTAAAGCCGACATGCAGACTTTA-GATGAGG
194 TAAGCAGACTTA-AAATAAGG-AAGTCTCCAGGGTCAAAGCCGACAGGCAG-CCTAAGGA-CAGG
** * *
19865 -CGGCCTCCAAGGTCAAAGCCGACAAGCAGA-TTAAGGGAT-AG
255 AAAGCCTCCAAGGTCAAAGCCAACAAGCAGACTTAA--AATGAG
* * * *
19906 AAAAGTTTCTAGGGTCAAAGCTGATAGGTAGACTTAGGGATAGAAAAGTCTTCAGGGTCAAAGTC
1 -AAAGTCTCTAAGGTCAAAGCTGATAGGCAGACTTAGGGATAGAAAAGTC-TCAGGGTCAAAGCC
* * * *
19971 AATAGGCAAACTTAGGGATAGAAAAGTCTCTAGGGTCAAAGTCGATAGGTAGACTTTAGATGAGG
64 GATAGGCAGACTTAGGGATAGGAAAGTCTCTAGGGTCAAAGCCGATAGGTAGACTTTAGATGAGG
* * * * *
20036 CAGTCTCCAGGGTTAAAGCCGATAGACAGACTGAAGG
129 CAGTCTCCAAGGTCAAAGCTGACAGGCAGACT-AAGG
20073 CATAAAAAGA
Statistics
Matches: 375, Mismatches: 77, Indels: 25
0.79 0.16 0.05
Matches are distributed among these distances:
297 30 0.08
298 6 0.02
299 267 0.71
300 69 0.18
301 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Consensus pattern (296 bp):
AAAGTCTCTAAGGTCAAAGCTGATAGGCAGACTTAGGGATAGAAAAGTCTCAGGGTCAAAGCCGA
TAGGCAGACTTAGGGATAGGAAAGTCTCTAGGGTCAAAGCCGATAGGTAGACTTTAGATGAGGCA
GTCTCCAAGGTCAAAGCTGACAGGCAGACTAAGGGATAGGAAAGTCTCCAAGGTCAAAGCCGATA
AGCAGACTTAAAATAAGGAAGTCTCCAGGGTCAAAGCCGACAGGCAGCCTAAGGACAGGAAAGCC
TCCAAGGTCAAAGCCAACAAGCAGACTTAAAATGAG
Found at i:32423 original size:279 final size:276
Alignment explanation
Indices: 31924--32471 Score: 909
Period size: 279 Copynumber: 2.0 Consensus size: 276
31914 GAAGCCTGGG
* * *
31924 GGAATATAAAAGGCTTTCAAGGCTAAAATGTCTTTCATACCCTTTTGGAGCACTGGGAGAATACG
1 GGAATATAAAAGGCTTTCAAGGCCAAAATGTCTTTCATACCCTCTTGGAGCACCGGGAGAATACG
* *
31989 AAAGGTTTTTTAAATCATAAAATACCCGATTTTTATTTTGAAAATGATATTTCATCGTTAAAATA
66 AAAGGTTTTTTAAATAATAAAATACCCGATTTTTATTTTGAAAAGGATATTTCATCGTTAAAATA
*
32054 ATCCATGAAACCTCTCTCATATATATGGATGGGAGAAATTTCACATAACATTTTAACTTCAAGAC
131 ATCCATGAAACCTCTCCCATATATATGGATGGGAGAAATTTCACATAACATTTTAACTTCAAGAC
*
32119 ATTACCTTTATTTTTTTTCAAAATTCAAATTTTCAATAATAATTTAGATATTTAAGCGAAAA-AA
196 ATTACCTTTATTTTTTTTAAAAATTCAAATTTTCAATAATAATTTAGATATTTAAGC-AAAAGAA
*
32183 ACCAAACCTAGCCCAGA
260 AACAAACCTAGCCCAGA
* *
32200 GGAATATAGAAGGCTTTCAAGGCCAAAATGTCTTTCATACCCTCTTGGAGCACCGGGAGGATACG
1 GGAATATAAAAGGCTTTCAAGGCCAAAATGTCTTTCATACCCTCTTGGAGCACCGGGAGAATACG
*
32265 AAAGGTTTTTTTTAAAATAATAAAATACCCGATTTTTATTTTGAAAAGGGTATTTCATCGTTAAA
66 AAAGG--TTTTTT-AAATAATAAAATACCCGATTTTTATTTTGAAAAGGATATTTCATCGTTAAA
* *
32330 ATAATCCATGAAATCTTTCCCATATATATGGATGGGAGAAATTTCACATAACATTTTAACTTCAA
128 ATAATCCATGAAACCTCTCCCATATATATGGATGGGAGAAATTTCACATAACATTTTAACTTCAA
* * *
32395 GACCTTACCTTTGTTTTTTTTAAAAATTCAAATTTTCATTAATAATTTAGATATTTAAGCAAAAG
193 GACATTACCTTTATTTTTTTTAAAAATTCAAATTTTCAATAATAATTTAGATATTTAAGCAAAAG
32460 AAAACAAACCTA
258 AAAACAAACCTA
32472 TCTTTAGATA
Statistics
Matches: 252, Mismatches: 16, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
276 65 0.26
278 10 0.04
279 177 0.70
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (276 bp):
GGAATATAAAAGGCTTTCAAGGCCAAAATGTCTTTCATACCCTCTTGGAGCACCGGGAGAATACG
AAAGGTTTTTTAAATAATAAAATACCCGATTTTTATTTTGAAAAGGATATTTCATCGTTAAAATA
ATCCATGAAACCTCTCCCATATATATGGATGGGAGAAATTTCACATAACATTTTAACTTCAAGAC
ATTACCTTTATTTTTTTTAAAAATTCAAATTTTCAATAATAATTTAGATATTTAAGCAAAAGAAA
ACAAACCTAGCCCAGA
Found at i:38432 original size:20 final size:20
Alignment explanation
Indices: 38409--38473 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
38399 ACATTCAAAT
38409 GTATCGATACATGTTGCATA
1 GTATCGATACATGTTGCATA
38429 GTATCGATACA---T---T-
1 GTATCGATACATGTTGCATA
38442 GTATCGATACATGTTGCATA
1 GTATCGATACATGTTGCATA
38462 GTATCGATACAT
1 GTATCGATACAT
38474 TGTATCGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 1 0.03
17 1 0.03
19 1 0.03
20 23 0.61
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.35
Consensus pattern (20 bp):
GTATCGATACATGTTGCATA
Found at i:38447 original size:13 final size:13
Alignment explanation
Indices: 38429--38486 Score: 65
Period size: 13 Copynumber: 4.9 Consensus size: 13
38419 ATGTTGCATA
38429 GTATCGATACATT
1 GTATCGATACATT
38442 GTATCGATACA-T
1 GTATCGATACATT
*
38454 GT-T-G---CATA
1 GTATCGATACATT
38462 GTATCGATACATT
1 GTATCGATACATT
38475 GTATCGATACAT
1 GTATCGATACAT
38487 GACCAAATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
7 2 0.05
8 2 0.05
9 1 0.03
10 2 0.05
11 1 0.03
12 3 0.08
13 26 0.70
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:38450 original size:33 final size:33
Alignment explanation
Indices: 38408--38487 Score: 160
Period size: 33 Copynumber: 2.4 Consensus size: 33
38398 CACATTCAAA
38408 TGTATCGATACATGTTGCATAGTATCGATACAT
1 TGTATCGATACATGTTGCATAGTATCGATACAT
38441 TGTATCGATACATGTTGCATAGTATCGATACAT
1 TGTATCGATACATGTTGCATAGTATCGATACAT
38474 TGTATCGATACATG
1 TGTATCGATACATG
38488 ACCAAATGTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATGTTGCATAGTATCGATACAT
Found at i:38499 original size:20 final size:21
Alignment explanation
Indices: 38474--38526 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
38464 ATCGATACAT
**
38474 TGTATCGATACATGACCAA-A
1 TGTATCGATACATGAAAAAGA
*
38494 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAAGA
38515 TGTATCGATACA
1 TGTATCGATACA
38527 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAAGA
Found at i:38499 original size:33 final size:33
Alignment explanation
Indices: 38408--38504 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 33
38398 CACATTCAAA
** *
38408 TGTATCGATACATGTTGCATAGTATCGATACAT
1 TGTATCGATACATGTACCAAAGTATCGATACAT
** *
38441 TGTATCGATACATGTTGCATAGTATCGATACAT
1 TGTATCGATACATGTACCAAAGTATCGATACAT
38474 TGTATCGATACATG-ACCAAATGTATCGATAC
1 TGTATCGATACATGTACCAAA-GTATCGATAC
38505 TTGAAAAAGA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 3 0.05
33 57 0.95
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATGTACCAAAGTATCGATACAT
Found at i:38596 original size:13 final size:13
Alignment explanation
Indices: 38578--38602 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38568 ACACACAGTA
38578 TGTATCGATACAT
1 TGTATCGATACAT
38591 TGTATCGATACA
1 TGTATCGATACA
38603 CCGTAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:38599 original size:32 final size:31
Alignment explanation
Indices: 38558--38625 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 31
38548 GTAGCCAAAC
38558 TTGTATCGATACACACAGT-ATGTATCGATACA
1 TTGTATCGATACAC-C-GTAATGTATCGATACA
38590 TTGTATCGATACACCGTAAAATGTATCGATACA
1 TTGTATCGATACACCGT--AATGTATCGATACA
38623 TTG
1 TTG
38626 GCTTATAACG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
30 2 0.06
31 1 0.03
32 14 0.42
33 16 0.48
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (31 bp):
TTGTATCGATACACCGTAATGTATCGATACA
Found at i:44431 original size:13 final size:13
Alignment explanation
Indices: 44413--44448 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
44403 GCATTCTCTA
*
44413 TATCGATACATTG
1 TATCGATACACTG
44426 TATCGATACACTG
1 TATCGATACACTG
44439 TATCGATACA
1 TATCGATACA
44449 AGGGGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (13 bp):
TATCGATACACTG
Found at i:44622 original size:22 final size:21
Alignment explanation
Indices: 44570--44616 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
44560 AAATCTTTTG
44570 CAAAATTC-TTGTTTTTCACTT
1 CAAAATTCATTGTTTTTCAC-T
44591 CAAAATTCATTGTTTTTCA-T
1 CAAAATTCATTGTTTTTCACT
44611 CAAAAT
1 CAAAAT
44617 CATCATCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 7 0.28
21 8 0.32
22 10 0.40
ACGTcount: A:0.32, C:0.17, G:0.04, T:0.47
Consensus pattern (21 bp):
CAAAATTCATTGTTTTTCACT
Found at i:47027 original size:19 final size:20
Alignment explanation
Indices: 47003--47053 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
46993 TAGCCAAACT
**
47003 TGTATCGATACA-CACAGTA
1 TGTATCGATACACCACAAAA
*
47022 TGTATCGATACACCATAAAA
1 TGTATCGATACACCACAAAA
47042 TGTATCGATACA
1 TGTATCGATACA
47054 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (20 bp):
TGTATCGATACACCACAAAA
Found at i:53657 original size:18 final size:19
Alignment explanation
Indices: 53624--53662 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
53614 TCATTCATCA
*
53624 TTTTTTTGATAATTTTGAT
1 TTTTTTTGATAATTTTAAT
*
53643 TTTTTTTGAT-TTTTTAAT
1 TTTTTTTGATAATTTTAAT
53661 TT
1 TT
53663 CTTGATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (19 bp):
TTTTTTTGATAATTTTAAT
Found at i:53667 original size:16 final size:15
Alignment explanation
Indices: 53645--53693 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
53635 ATTTTGATTT
53645 TTTTTGATTTTTTAA
1 TTTTTGATTTTTTAA
*
53660 TTTCTTGATTTTTAAA
1 TTT-TTGATTTTTTAA
*
53676 TTTTTAATTTTTATAA
1 TTTTTGATTTTT-TAA
53692 TT
1 TT
53694 ATGTTATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.69
Consensus pattern (15 bp):
TTTTTGATTTTTTAA
Found at i:53673 original size:15 final size:14
Alignment explanation
Indices: 53645--53688 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
53635 ATTTTGATTT
53645 TTTTTGATTTTTTAA
1 TTTTTGA-TTTTTAA
53660 TTTCTTGATTTTTAAA
1 TTT-TTGATTTTT-AA
*
53676 TTTTTAATTTTTA
1 TTTTTGATTTTTA
53689 TAATTATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 1 0.04
15 16 0.62
16 9 0.35
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (14 bp):
TTTTTGATTTTTAA
Found at i:54766 original size:84 final size:84
Alignment explanation
Indices: 54678--55085 Score: 507
Period size: 84 Copynumber: 4.9 Consensus size: 84
54668 TTAAGGGTGA
* * * **
54678 AAAAGTATCCAAGGTCAAAGTCGACAGGTATACTTTAGATGAGGCAGTCTCTAAGGTCAAAGTTG
1 AAAAGTCTCCAAGGTCAAAGTCGACAGGTAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCG
* * *
54743 ATAGGCAGACTGAGAGTAG
66 ACAGGCAAACTGAGGGTAG
* * * *
54762 AAAAGTCTCCAGGGTCAAAG-CTGACAGGCAGACTTTAGATGAGGCAATCTCTAGGGTCAAAGTC
1 AAAAGTCTCCAAGGTCAAAGTC-GACAGGTAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCC
*
54826 GACAGGCAGACTGAGGGTAG
65 GACAGGCAAACTGAGGGTAG
* * * *
54846 AAAAGTCTCTAGGGTCAAAGTTGACAGGTAGACTTTAGATGAGGTAGTCTCTAAGGGTCAAAGCC
1 AAAAGTCTCCAAGGTCAAAGTCGACAGGTAGACTTTAGATGAGGCAGTCTCT-AGGGTCAAAGCC
54911 GACAGGCAAACTGAGGGTAG
65 GACAGGCAAACTGAGGGTAG
* * * *
54931 AAAAGTCTCCAAGGTCAAAGTC--CCGGACAGACTTTAGATGAGACAGTCTCTAGGGTCAAAGCT
1 AAAAGTCTCCAAGGTCAAAGTCGACAGG-TAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCC
*
54994 GACAGACAAACTGAGGGTAG
65 GACAGGCAAACTGAGGGTAG
* * * * * * *
55014 AAAAGTCTCTAAGGTCAAAGCCGACAGATAGATTTTAGATGAGGCAATCTCCAGGGTCAAAACCG
1 AAAAGTCTCCAAGGTCAAAGTCGACAGGTAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCG
55079 ACAGGCA
66 ACAGGCA
55086 GACTTTAGAT
Statistics
Matches: 281, Mismatches: 37, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
83 54 0.19
84 176 0.63
85 51 0.18
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.20
Consensus pattern (84 bp):
AAAAGTCTCCAAGGTCAAAGTCGACAGGTAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCG
ACAGGCAAACTGAGGGTAG
Found at i:55157 original size:252 final size:252
Alignment explanation
Indices: 54678--55166 Score: 594
Period size: 252 Copynumber: 1.9 Consensus size: 252
54668 TTAAGGGTGA
* * * *
54678 AAAAGTATCCAAGGTCAAAGTCGACAGGTATACTTTAGATGAGGCAGTCTCTAAGGTCAAAGTTG
1 AAAAGTATCCAAGGTCAAAGTC-ACAGGCAGACTTTAGATGAGACAGTCTCTAAGGTCAAAGCTG
* * * * * *
54743 ATAGGCAGACTGAGAGTAGAAAAGTCTCCAGGGTCAAAGCTGACAGGCAGACTTTAGATGAGGCA
65 ACAGACAAACTGAGAGTAGAAAAGTCTCCAAGGTCAAAGCCGACAGACAGACTTTAGATGAGGCA
* ** *
54808 ATCTCTAGGGTCAAAGTCGACAGGCAGACTGAGGGTAGAAAAGTCTCTAGGGTCAAAGTTGACAG
130 ATCTCCAGGGTCAAAACCGACAGGCAGACTGAGGGTAGAAAAGTCTCTAGGGTCAAAGTCGACAG
* * *
54873 GTAGACTTTAGATGAGGTAGTCTCTAAGGGTCAAAGCCGACAGGCAAACTGAGGGTAG
195 GCAGACTTGAGATGAGGAAGTCTCTAAGGGTCAAAGCCGACAGGCAAACTGAGGGTAG
* * *
54931 AAAAGTCTCCAAGGTCAAAGTC-CCGGACAGACTTTAGATGAGACAGTCTCTAGGGTCAAAGCTG
1 AAAAGTATCCAAGGTCAAAGTCACAGG-CAGACTTTAGATGAGACAGTCTCTAAGGTCAAAGCTG
* * * *
54995 ACAGACAAACTGAGGGTAGAAAAGTCTCTAAGGTCAAAGCCGACAGATAGATTTTAGATGAGGCA
65 ACAGACAAACTGAGAGTAGAAAAGTCTCCAAGGTCAAAGCCGACAGACAGACTTTAGATGAGGCA
* * ** * *
55060 ATCTCCAGGGTCAAAACCGACAGGCAGACTTTA-GATGAGGCAA-TTTCTAGGGTCAAAGTCGAT
130 ATCTCCAGGGTCAAAACCGACAGGCAGAC-TGAGGGT-AGAAAAGTCTCTAGGGTCAAAGTCGAC
*
55123 AGGCAGAC-TGAGGGAT-AGGAAAGTCTC-CAGGGTCAAAGCCGACA
193 AGGCAGACTTGA--GATGAGG-AAGTCTCTAAGGGTCAAAGCCGACA
55167 AACAGACTTT
Statistics
Matches: 199, Mismatches: 31, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
251 5 0.03
252 158 0.79
253 36 0.18
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (252 bp):
AAAAGTATCCAAGGTCAAAGTCACAGGCAGACTTTAGATGAGACAGTCTCTAAGGTCAAAGCTGA
CAGACAAACTGAGAGTAGAAAAGTCTCCAAGGTCAAAGCCGACAGACAGACTTTAGATGAGGCAA
TCTCCAGGGTCAAAACCGACAGGCAGACTGAGGGTAGAAAAGTCTCTAGGGTCAAAGTCGACAGG
CAGACTTGAGATGAGGAAGTCTCTAAGGGTCAAAGCCGACAGGCAAACTGAGGGTAG
Found at i:55158 original size:85 final size:84
Alignment explanation
Indices: 55061--55343 Score: 302
Period size: 85 Copynumber: 3.3 Consensus size: 84
55051 GATGAGGCAA
* * *
55061 TCTCCAGGGTCAAAACCGACAGGCAGACTTTAGATGAGGCAATTTCTAGGGTCAAAGTCGATAGG
1 TCTCCAGGGTCAAAGCCGACAAGCAGACTTTAGATGAGGCAGTTTCTAGGGTCAAAG-CGATAGG
55126 CAGACTGAGGGATAGGAAAG
65 CAGACTGAGGGATAGGAAAG
* * * * * *
55146 TCTCCAGGGTCAAAGCCGACAAACAGACTTTAAATGAAGTAGTCTCCTA-GGTCAAAGCCAATAG
1 TCTCCAGGGTCAAAGCCGACAAGCAGACTTTAGATGAGGCAGT-TTCTAGGGTCAAAG-CGATAG
* *
55210 GCAGACTAAAGGATAGGAAAG
64 GCAGACTGAGGGATAGGAAAG
** * * * * * *
55231 TCTCCAATGTCAAAGTCGACAAGCAGACTTTAGATAAGGCAGTCTCTAGGTTCAAAGCTGACAAG
1 TCTCCAGGGTCAAAGCCGACAAGCAGACTTTAGATGAGGCAGTTTCTAGGGTCAAAGC-GATAGG
*
55296 CA-ATTGAAGGG-TAGGAAAG
65 CAGACTG-AGGGATAGGAAAG
* *
55315 TCTCTAGGGTCAAAGCCGACAGGCAGACT
1 TCTCCAGGGTCAAAGCCGACAAGCAGACT
55344 GAGGGTAGAA
Statistics
Matches: 160, Mismatches: 34, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
84 38 0.24
85 118 0.74
86 4 0.03
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (84 bp):
TCTCCAGGGTCAAAGCCGACAAGCAGACTTTAGATGAGGCAGTTTCTAGGGTCAAAGCGATAGGC
AGACTGAGGGATAGGAAAG
Found at i:55349 original size:42 final size:42
Alignment explanation
Indices: 54723--55371 Score: 352
Period size: 42 Copynumber: 15.4 Consensus size: 42
54713 TAGATGAGGC
* ** * *
54723 AGTCTCTAAGGTCAAAGTTGATAGGCAGACTGA-GAGTAGAAA
1 AGTCTCTAGGGTCAAAGCCGACAGGCAGACTGAGGA-TAGGAA
* * * *
54765 AGTCTCCAGGGTCAAAGCTGACAGGCAGACTTTA-GATGAGGCA
1 AGTCTCTAGGGTCAAAGCCGACAGGCAGAC-TGAGGAT-AGGAA
* * *
54808 A-TCTCTAGGGTCAAAGTCGACAGGCAGACTGAGGGTAGAAA
1 AGTCTCTAGGGTCAAAGCCGACAGGCAGACTGAGGATAGGAA
** * * *
54849 AGTCTCTAGGGTCAAAGTTGACAGGTAGACTTTA-GATGAGG-T
1 AGTCTCTAGGGTCAAAGCCGACAGGCAGAC-TGAGGAT-AGGAA
* * *
54891 AGTCTCTAAGGGTCAAAGCCGACAGGCAAACTGAGGGTAGAAA
1 AGTCTCT-AGGGTCAAAGCCGACAGGCAGACTGAGGATAGGAA
* * * *
54934 AGTCTCCAAGGTCAAAGTCC--C-GGACAGACTTTA-GAT-GAGAC
1 AGTCTCTAGGGTCAAAG-CCGACAGG-CAGAC-TGAGGATAG-GAA
* * * * *
54975 AGTCTCTAGGGTCAAAGCTGACAGACAAACTGAGGGTAGAAA
1 AGTCTCTAGGGTCAAAGCCGACAGGCAGACTGAGGATAGGAA
* ** * * *
55017 AGTCTCTAAGGTCAAAGCCGACAGATAGATTTTA-GATGAGGCA
1 AGTCTCTAGGGTCAAAGCCGACAGGCAGA-CTGAGGAT-AGGAA
* * * *
55060 A-TCTCCAGGGTCAAAACCGACAGGCAGACTTTA-GATGAGGCA
1 AGTCTCTAGGGTCAAAGCCGACAGGCAGAC-TGAGGAT-AGGAA
* * *
55102 A-TTTCTAGGGTCAAAGTCGATAGGCAGACTGAGGGATAGGAA
1 AGTCTCTAGGGTCAAAGCCGACAGGCAGACTGA-GGATAGGAA
* ** * *
55144 AGTCTCCAGGGTCAAAGCCGACAAACAGACTTTA--A-ATGAA
1 AGTCTCTAGGGTCAAAGCCGACAGGCAGAC-TGAGGATAGGAA
* * *
55184 GTAGTCTCCTA-GGTCAAAGCCAATAGGCAGACTAAAGGATAGGAA
1 --AGTCT-CTAGGGTCAAAGCCGACAGGCAGACT-GAGGATAGGAA
* ** * * * *
55229 AGTCTCCAATGTCAAAGTCGACAAGCAGACTTTA-GATAAGG-C
1 AGTCTCTAGGGTCAAAGCCGACAGGCAGAC-TGAGGAT-AGGAA
* * * * *
55271 AGTCTCTAGGTTCAAAGCTGACAAGCA-ATTGAAGGGTAGGAA
1 AGTCTCTAGGGTCAAAGCCGACAGGCAGACTG-AGGATAGGAA
* *
55313 AGTCTCTAGGGTCAAAGCCGACAGGCAGACTGAGGGTAGAAA
1 AGTCTCTAGGGTCAAAGCCGACAGGCAGACTGAGGATAGGAA
*
55355 AGTCTCTA-TGTCAAAGC
1 AGTCTCTAGGGTCAAAGC
55372 TAACATGCAG
Statistics
Matches: 463, Mismatches: 105, Indels: 79
0.72 0.16 0.12
Matches are distributed among these distances:
40 9 0.02
41 48 0.10
42 294 0.63
43 104 0.22
44 4 0.01
45 4 0.01
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.20
Consensus pattern (42 bp):
AGTCTCTAGGGTCAAAGCCGACAGGCAGACTGAGGATAGGAA
Found at i:55359 original size:84 final size:82
Alignment explanation
Indices: 54689--55387 Score: 413
Period size: 84 Copynumber: 8.3 Consensus size: 82
54679 AAAGTATCCA
* * * * ** *
54689 AGGTCAAAG-TCGACAGGTATACTTTAGATGAGG-CAGTCTCTAAGGTCAAAGTTGATAGGCAGA
1 AGGTCAAAGCT-GACAGGCAGA-TTTAGAT-AGGAAAGTCTCTAGGGTCAAAGCCGACAGGCAGA
* *
54752 CTGAGAGTAGAAAAGTCTCC
63 CTGAGGGTAGAAAAGTCTCT
* *
54772 AGGGTCAAAGCTGACAGGCAGACTTTAGATGAGGCAA-TCTCTAGGGTCAAAGTCGACAGGCAGA
1 A-GGTCAAAGCTGACAGGCAGA-TTTAGAT-AGGAAAGTCTCTAGGGTCAAAGCCGACAGGCAGA
54836 CTGAGGGTAGAAAAGTCTCT
63 CTGAGGGTAGAAAAGTCTCT
* * * *
54856 AGGGTCAAAGTTGACAGGTAGACTTTAGATGAGG-TAGTCTCTAAGGGTCAAAGCCGACAGGCAA
1 A-GGTCAAAGCTGACAGGCAGA-TTTAGAT-AGGAAAGTCTCT-AGGGTCAAAGCCGACAGGCAG
*
54920 ACTGAGGGTAGAAAAGTCTCCA
62 ACTGAGGGTAGAAAAGTCT-CT
* * * * * *
54942 AGGTCAAAG-T-CCCGGACAGACTTTAGAT-GAGACAGTCTCTAGGGTCAAAGCTGACAGACAAA
1 AGGTCAAAGCTGACAGG-CAGA-TTTAGATAG-GAAAGTCTCTAGGGTCAAAGCCGACAGGCAGA
55004 CTGAGGGTAGAAAAGTCTCT
63 CTGAGGGTAGAAAAGTCTCT
* ** * * *
55024 AAGGTCAAAGCCGACAGATAGATTTTAGATGAGGCAA-TCTCCAGGGTCAAAACCGACAGGCAGA
1 -AGGTCAAAGCTGACAGGCAGA-TTTAGAT-AGGAAAGTCTCTAGGGTCAAAGCCGACAGGCAGA
* * ** *
55088 CTTTA-GATGAGGCAA-TTTCT
63 C-TGAGGGT-AGAAAAGTCTCT
* * * * **
55108 AGGGTCAAAG-TCGATAGGCAGACTGAGGGATAGGAAAGTCTCCAGGGTCAAAGCCGACAAACAG
1 A-GGTCAAAGCT-GACAGGCAGATTTA--GATAGGAAAGTCTCTAGGGTCAAAGCCGACAGGCAG
* ** *
55172 ACTTTA-AAT-GAAGTAGTCTCCT
62 AC-TGAGGGTAGAA-AAGTCT-CT
** * ** * ** * *
55194 AGGTCAAAGCCAATAGGCAGACTAAAGGATAGGAAAGTCTCCAATGTCAAAGTCGACAAGCAGAC
1 AGGTCAAAGCTGACAGGCAGA-TTTA-GATAGGAAAGTCTCTAGGGTCAAAGCCGACAGGCAGAC
* * **
55259 TTTA-GATA-AGGCAGTCTCT
64 -TGAGGGTAGA-AAAGTCTCT
* * *
55278 AGGTTCAAAGCTGACAAGCA-ATTGAAGGGTAGGAAAGTCTCTAGGGTCAAAGCCGACAGGCAGA
1 AGG-TCAAAGCTGACAGGCAGATT-TA-GATAGGAAAGTCTCTAGGGTCAAAGCCGACAGGCAGA
55342 CTGAGGGTAGAAAAGTCTCT
63 CTGAGGGTAGAAAAGTCTCT
* * *
55362 ATGTCAAAGCTAACATGCAGACTTTA
1 AGGTCAAAGCTGACAGGCAGA-TTTA
55388 AATGAGGCAG
Statistics
Matches: 497, Mismatches: 85, Indels: 67
0.77 0.13 0.10
Matches are distributed among these distances:
82 2 0.00
83 74 0.15
84 241 0.48
85 173 0.35
86 7 0.01
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (82 bp):
AGGTCAAAGCTGACAGGCAGATTTAGATAGGAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTG
AGGGTAGAAAAGTCTCT
Found at i:55382 original size:41 final size:42
Alignment explanation
Indices: 55271--55384 Score: 133
Period size: 42 Copynumber: 2.7 Consensus size: 42
55261 TAGATAAGGC
* *
55271 AGTCTCTAGGTTCAAAGCTGACAAGCA-ATTGAAGGGTAGGAA
1 AGTCTCTAGG-TCAAAGCTGACAAGCAGACTGAAGGGTAGAAA
* *
55313 AGTCTCTAGGGTCAAAGCCGACAGGCAGACTG-AGGGTAGAAA
1 AGTCTCTA-GGTCAAAGCTGACAAGCAGACTGAAGGGTAGAAA
* * *
55355 AGTCTCTATGTCAAAGCTAACATGCAGACT
1 AGTCTCTAGGTCAAAGCTGACAAGCAGACT
55385 TTAAATGAGG
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
41 18 0.29
42 39 0.63
43 5 0.08
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.20
Consensus pattern (42 bp):
AGTCTCTAGGTCAAAGCTGACAAGCAGACTGAAGGGTAGAAA
Done.