Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011090.1 Corchorus capsularis cultivar CVL-1 contig11111, 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: 138234
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2194 original size:11 final size:11
Alignment explanation
Indices: 2151--2188 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2141 TTCCTATATA
*
2151 AAATAAATTAT
1 AAATTAATTAT
2162 CAAA-TAATTAT
1 -AAATTAATTAT
2173 AAATTAATTAT
1 AAATTAATTAT
2184 AAATT
1 AAATT
2189 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:2834 original size:26 final size:25
Alignment explanation
Indices: 2782--2838 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
2772 ATGAAACATG
*
2782 AAATTTTTAAGAATGTAGTATTTCT
1 AAATTTTTAAGAATGTAGTATTACT
*
2807 AAATTTTCTAAGAATGTGAG-GTTACT
1 AAATTTT-TAAGAATGT-AGTATTACT
2833 AAATTT
1 AAATTT
2839 ATGTAAAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 7 0.25
26 19 0.68
27 2 0.07
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (25 bp):
AAATTTTTAAGAATGTAGTATTACT
Found at i:3117 original size:24 final size:23
Alignment explanation
Indices: 3090--3147 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
3080 CAAATTAGTT
3090 ATTAAATCAATAATCAATATCAAA
1 ATTAAATCAATAATCAA-ATCAAA
* **
3114 ATTAAATCACTTCTTCAAATCAAA
1 ATTAAATCA-ATAATCAAATCAAA
3138 ATTAAATCAA
1 ATTAAATCAA
3148 ATCTAATTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (23 bp):
ATTAAATCAATAATCAAATCAAA
Found at i:3814 original size:31 final size:30
Alignment explanation
Indices: 3779--3842 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
3769 ATTTAATCTT
3779 AACTGCTGCTCTTGTT-TTGAAAAAAAAAAAA
1 AACTGCTGCTCTT-TTATT-AAAAAAAAAAAA
3810 AACTGCTGCTCTTTTCATTAAAAAAAAAAAA
1 AACTGCTGCTCTTTT-ATTAAAAAAAAAAAA
3841 AA
1 AA
3843 GCTAGCATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 2 0.06
31 27 0.87
32 2 0.06
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.28
Consensus pattern (30 bp):
AACTGCTGCTCTTTTATTAAAAAAAAAAAA
Found at i:14305 original size:6 final size:6
Alignment explanation
Indices: 14294--14321 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
14284 ATCTGGTTTT
14294 TTATCA TTATCA TTATCA TTATCA TTAT
1 TTATCA TTATCA TTATCA TTATCA TTAT
14322 ATTCTTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.54
Consensus pattern (6 bp):
TTATCA
Found at i:26387 original size:3 final size:3
Alignment explanation
Indices: 26373--26410 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
26363 GTCGGAAATA
26373 AAT AAT ATAT AAT AAT AAT AAT AAT AAT -AT ATAT AAT A
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT A-AT AAT A
26411 CATCAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.06
3 24 0.75
4 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:27457 original size:15 final size:15
Alignment explanation
Indices: 27437--27466 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27427 ATAAAATTTT
27437 AAAAAAAGAAGAAAA
1 AAAAAAAGAAGAAAA
*
27452 AAAAAAGGAAGAAAA
1 AAAAAAAGAAGAAAA
27467 GTAGTAGTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAGAAAA
Found at i:29871 original size:13 final size:13
Alignment explanation
Indices: 29831--29882 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
29821 AATCATTATG
29831 TTTTTCTTTCTTCT
1 TTTTTCTTT-TTCT
* **
29845 TTTTAACTAGTTCT
1 TTTT-TCTTTTTCT
29859 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
29872 TTTTTCTTTTT
1 TTTTTCTTTTT
29883 TTACTATACT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 17 0.55
14 12 0.39
15 2 0.06
ACGTcount: A:0.06, C:0.15, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:29884 original size:8 final size:7
Alignment explanation
Indices: 29855--29883 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
29845 TTTTAACTAG
29855 TTCTTTT
1 TTCTTTT
29862 TTC-TTT
1 TTCTTTT
29868 TTCTTTT
1 TTCTTTT
29875 TTCTTTT
1 TTCTTTT
29882 TT
1 TT
29884 TACTATACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTCTTTT
Found at i:30542 original size:13 final size:13
Alignment explanation
Indices: 30524--30548 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30514 CAACAAGGGG
30524 ATTGCAATTGCAA
1 ATTGCAATTGCAA
30537 ATTGCAATTGCA
1 ATTGCAATTGCA
30549 TAGAAGAAAA
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATTGCAATTGCAA
Found at i:36703 original size:16 final size:16
Alignment explanation
Indices: 36679--36709 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36669 CCAGAAATTT
36679 AAAAAAAAAAAAAAGG
1 AAAAAAAAAAAAAAGG
*
36695 AAAAGAAAAAAAAAG
1 AAAAAAAAAAAAAAG
36710 CTTCAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAGG
Found at i:38583 original size:24 final size:23
Alignment explanation
Indices: 38539--38583 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
38529 CCTAAATACC
*
38539 AATGTTTATAATATATATTGTAA
1 AATGTTTATAATAAATATTGTAA
* *
38562 AATGTTTTTCAATAAATTTTGT
1 AATGTTTAT-AATAAATATTGT
38584 TTAATAATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (23 bp):
AATGTTTATAATAAATATTGTAA
Found at i:44160 original size:6 final size:6
Alignment explanation
Indices: 44149--44176 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
44139 TTCCAATTCT
44149 CCAAAA CCAAAA CCAAAA CCAAAA CCAA
1 CCAAAA CCAAAA CCAAAA CCAAAA CCAA
44177 CCAAAGTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.64, C:0.36, G:0.00, T:0.00
Consensus pattern (6 bp):
CCAAAA
Found at i:45386 original size:19 final size:18
Alignment explanation
Indices: 45357--45392 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
45347 CACTTATTAT
*
45357 ATATTATATTAATTAATA
1 ATATTATATTAACTAATA
45375 ATATTAATATTAACTAAT
1 ATATT-ATATTAACTAAT
45393 TGTGTTCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTATATTAACTAATA
Found at i:51061 original size:17 final size:17
Alignment explanation
Indices: 51034--51088 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
51024 CGGATTACTA
*
51034 ATCTTTGATCACTGGTG
1 ATCTTAGATCACTGGTG
*
51051 ATCTT-GCATCACTGGTA
1 ATCTTAG-ATCACTGGTG
*
51068 ATCTTAGATCACTAGTG
1 ATCTTAGATCACTGGTG
51085 ATCT
1 ATCT
51089 GGGGGGTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 1 0.03
17 31 0.94
18 1 0.03
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (17 bp):
ATCTTAGATCACTGGTG
Found at i:52313 original size:2 final size:2
Alignment explanation
Indices: 52302--52344 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
52292 AAGGTACTAC
* *
52302 AT AT AT -T AT AT AT AT AT AT AC AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52343 AT
1 AT
52345 GACCACACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52620 original size:28 final size:29
Alignment explanation
Indices: 52577--52631 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
52567 TGTCTAGGGT
*
52577 TTTAGGTGAGACTC-AAAGAAGCTCCAGG
1 TTTAGGTGAGACTCAAAAAAAGCTCCAGG
**
52605 TTTAGGTGAGGTTCAAAAAAAGCTCCA
1 TTTAGGTGAGACTCAAAAAAAGCTCCA
52632 TGTTGTGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (29 bp):
TTTAGGTGAGACTCAAAAAAAGCTCCAGG
Found at i:70014 original size:2 final size:2
Alignment explanation
Indices: 70007--70041 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
69997 AAGCTCTTGC
70007 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
70042 CAAACTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:72008 original size:28 final size:29
Alignment explanation
Indices: 71984--72059 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
71974 TGGCATGTTG
71984 CATTTTT-TACAAGTGGCGTGCCATGTGT
1 CATTTTTGTACAAGTGGCGTGCCATGTGT
* * * * *
72012 CCTTTTTGTACACGTGGCATGCCACGTGG
1 CATTTTTGTACAAGTGGCGTGCCATGTGT
* *
72041 AATTTTTGGTACACGTGGC
1 CATTTTT-GTACAAGTGGC
72060 ATGCAACGTC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 6 0.15
29 22 0.56
30 11 0.28
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (29 bp):
CATTTTTGTACAAGTGGCGTGCCATGTGT
Found at i:72861 original size:14 final size:15
Alignment explanation
Indices: 72834--72875 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
72824 TATGGCCTCT
*
72834 TAAAAAATTGAAAAAG
1 TAAAAAA-TGAAAAAA
72850 TAAAAAAT-AAAAAA
1 TAAAAAATGAAAAAA
72864 TAAAAAATGAAA
1 TAAAAAATGAAA
72876 CCCAAGCAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 13 0.54
15 4 0.17
16 7 0.29
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
TAAAAAATGAAAAAA
Found at i:73304 original size:19 final size:19
Alignment explanation
Indices: 73280--73317 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
73270 ACATCTGCAG
73280 AAAAGAAAAAAGTTATGAA
1 AAAAGAAAAAAGTTATGAA
73299 AAAAGAAAAAAGTTATGAA
1 AAAAGAAAAAAGTTATGAA
73318 GGAAAATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (19 bp):
AAAAGAAAAAAGTTATGAA
Found at i:75173 original size:13 final size:13
Alignment explanation
Indices: 75141--75165 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
75131 GAAATCAATG
75141 CAAAAAACAAAAA
1 CAAAAAACAAAAA
75154 CAAAAAACAAAA
1 CAAAAAACAAAA
75166 GAAAAAAAGA
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:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAAAACAAAAA
Found at i:76511 original size:41 final size:43
Alignment explanation
Indices: 76451--76535 Score: 138
Period size: 41 Copynumber: 2.0 Consensus size: 43
76441 CGTGCGGCTG
76451 TTTTATTTTATAAAGTCTTTTAA-AAAAATTCAATT-AAGAAA
1 TTTTATTTTATAAAGTCTTTTAAGAAAAATTCAATTAAAGAAA
* *
76492 TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAAGAAA
1 TTTTATTTTATAAAGTCTTTTAAGAAAAATTCAATTAAAGAAA
76535 T
1 T
76536 GAAATTTTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
41 22 0.55
42 11 0.28
43 7 0.17
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.45
Consensus pattern (43 bp):
TTTTATTTTATAAAGTCTTTTAAGAAAAATTCAATTAAAGAAA
Found at i:77803 original size:78 final size:77
Alignment explanation
Indices: 77715--77953 Score: 359
Period size: 78 Copynumber: 3.2 Consensus size: 77
77705 TTTTTTTAAC
*
77715 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAA-TGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
77780 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
77793 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
77858 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* * *
77871 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAATAAAAATAGAG
1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
77929 TTTTTAGTTGAG
66 TTTTTAGTTGAG
77941 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
77954 ATCTAAACAA
Statistics
Matches: 155, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
70 56 0.36
71 3 0.02
72 1 0.01
73 2 0.01
74 3 0.02
75 1 0.01
77 1 0.01
78 88 0.57
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (77 bp):
TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG
Found at i:77804 original size:70 final size:71
Alignment explanation
Indices: 77721--77953 Score: 310
Period size: 70 Copynumber: 3.2 Consensus size: 71
77711 TAACTAAAAT
* *
77721 AGTAAAA-TTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTT
1 AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
77785 TAGTTG
66 TAGTTG
*
77791 AGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
1 AGT-AAA-ACT---A--GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
77856 GAGTTTTTAGTTG
59 GAGTTTTTAGTTG
* * * * *
77869 AGTAAAA-TAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTT
1 AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
77933 TAGTTG
66 TAGTTG
77939 AGTAAAACTA-TAAAA
1 AGTAAAACTAGTAAAA
77954 ATCTAAACAA
Statistics
Matches: 147, Mismatches: 7, Indels: 18
0.85 0.04 0.10
Matches are distributed among these distances:
70 71 0.48
71 5 0.03
72 2 0.01
73 1 0.01
75 1 0.01
76 1 0.01
77 3 0.02
78 63 0.43
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.37
Consensus pattern (71 bp):
AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
TAGTTG
Found at i:78087 original size:6 final size:6
Alignment explanation
Indices: 78041--78086 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
78031 GTACTTTTTA
*
78041 ATATAG -TATAG ATATAG ATATAG ATATAG ATATAG ATATAT ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
78087 TTCATTCTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (6 bp):
ATATAG
Found at i:86920 original size:321 final size:319
Alignment explanation
Indices: 86271--89481 Score: 3009
Period size: 321 Copynumber: 10.0 Consensus size: 319
86261 CTCCGAAACG
* * *** * *
86271 CGATTTCGGCTAAAAACTTACCCGGATTTTTTTTTCTCAATTTTTTACCACAATACACAGAAAAA
1 CGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAA
*
86336 ATATATAATTCAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGTTTTTCAATTTT
66 ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTC-ATTTT
* *
86401 TTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTAT
130 TTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAT
* * * * * *
86466 ATCCAATATTGCTGA-AATTAGTTCGATAAATATAGATATTTCAAGGAGTCTTTGCACCAAAAAT
195 ATCCAATGTGGCTGACATTTGGTTC-ATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAAT
* * * * ** *
86530 -ATGCAAAATTGAGCCGAGGCTACGGAACGCGATTTTAGCAAAAAACCGTGATGGTTAGTACA
259 CATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGAT--AAACTACA
*
86592 CGATTTCGACTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAA
1 CGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAA
* * * * *
86657 ATATATAATTCAACGCCAAAAAAATTAAATGGCTTTTCATGCTACTAATATCGTTTTTTCATTTT
66 ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCG-TTTTTCATTTT
* * * *
86722 TTTTCCAAATTAATTTCTAATTTATTCGAAACAAGATTCAGATGCTCGTAAAAACAAGTCCTTAT
130 TTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAT
* *
86787 ATCCAATGTGGCTGACATTTGGTTCATTGAATATAAATATTTTAAGGAGTCTTTGCGCCAAAAAT
195 ATCCAATGTGGCTGACATTTGGTTCA-TGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAAT
* * *
86852 CATGCAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGCAAAAAATCGTGATAAACTACA
259 CATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATAAACTACA
* * * * *
86913 TGATTTCGGCTAAAAATTGACCCGAATTATTTTTTTCTCAATTTTTTGCCACAATACACAGAAAA
1 CGATTTCGGCTAAAAACTGACCCGAA-AAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAA
* * * * * * * *
86978 AGTATATAATCCAACGCCTAAAAGATTGACGGGGTTTTCATGTTTCTAATATCGTTTTCCA-TTT
65 AATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTT
*
87042 TTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-AAAACCTTAT
130 TTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAT
* * * *
87106 ATCCAATGTGGCTGACATTTGATTCGTTAAATATAGATATTTCAAGGAGTATTTGCGCCAAAAAT
195 ATCCAATGTGGCTGACATTTGGTTC-ATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAAT
* * * * * *
87171 CATGCAAAAATGTGCCGGGGCTCCGAAATGCGTTTTTAACCAAAAACCGTGATGGAACATACA
259 CATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGAT-AAAC-TACA
* * ** *
87234 CGATTTCGGCTAAAAACTTATCCGAAATTTTTTTTTTCTCAATTTTTTGCCACAATACACA-AAA
1 CGATTTCGGCTAAAAACTGACCCGAAA--AGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAA
** * * * *
87298 AAATATATAATTCAATACCAAAAATATTTACGGGCTTTTCATGCTTCTAATATCGTTTTTTCA--
64 AAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCG-TTTTTCATT
* *
87361 TTTTTTCCGAATTAATTTCTAATGAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCCT
128 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* *
87426 ATATCCAATGTGGCTGACATTTGGTTCGTTGAATATAGATATTTCAAGGAGTCTTTACGCCAAAA
193 ATATCCAATGTGGCTGACATTTGGTTC-ATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAA
* *
87491 ATCATGCAAAATTGAGCCGGGGCTTCGGAACGCGTTTTTAGCCAAAAACCATGAT-AACGTACA
257 ATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATAAAC-TACA
* *
87554 CGATTTCGGCTAAAAACTTATCCGAAAAG-TTTTTCTCAATTTTTTGCCACAATACTCAGAAAAA
1 CGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAA
* * *
87618 ATATATAATTCAACGCAAAAAAAATTGACGGGCTTTTCACGCTTCTAATATCG----------TT
66 ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTT
* * * *
87673 TTTCC--ATT--TTTC----TAAATCGAAATAAGATTGAGATTCTCAG-AAAAACAAATTCTTAT
131 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC-GTAAAAACAAATCCTTAT
* * * * * *
87729 ATCCAATATGACTAATATTTGGTTCGATGAATATAGATATTTCAATGAGTCTTTACGCCAAAAAT
195 ATCCAATGTGGCTGACATTTGGTTC-ATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAAT
* * * * * *
87794 CTTGCAAAACTT-AGCTGGGGC-CCCGAAGCGCGTGTTTAGCCATAAACCGTTATTGAGTAAACG
259 CATGCAAAA-TTGAGCCGGGGCTCCGGAA-CGCGTTTTTAGCCAAAAACCG----TGA-TAAACT
*
87857 ATCT
317 A-CA
** * * *
87861 CGGAAATTTTTTTGC-AAAAACTGATCCGAAAA-TTTTTTCAACAATTCTTTTCCCACAATACCC
1 C-G--A--TTTCGGCTAAAAACTGACCCGAAAAGTTTTTTC-TCAATT-TTTTGCCACAATA--C
* * * **
87924 AAATACACACACACACACAGATATATATATAATTCAACACTAAAAAGATTGAAGGG-TTTTCAAT
57 ---T-------CAGA-A-A-A-A-ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACG
* * *
87988 CTTCTAATATCG--GTT--TTTTTTTT-CGAATTAATTTCTAATTAAAT-AAAACAAAATTCAGA
107 CTTCTAATATCGTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGA
* * * * * ** *
88047 AGCTCGTAAAAA-AAATCGTTAAATCGAATGTGACTGGGATTTGGTTTGATGAATATAGATATTT
172 TGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGG-TTCATGAATATAGATATTT
* * * * * *
88111 CAAGGAGTATTTGCGCTAGAAATCATGCAAAATTGAGTCGGGGCTCAGGAACGCGTTTTTAACCA
236 CAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCA
*
88176 AAAACCGTG---CA-TACA
301 AAAACCGTGATAAACTACA
* * * *
88191 CGATTTCGGCTAAAAACTGACTCGAAAAGGTTTTTCTCAAATTTTTGCCACAATACTTAGAAAAA
1 CGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAA
* **
88256 A-ATATAATTTAACGCCAAAAAGATTGACA-AACTTTTCACGCTTCTAATATCG----T--TTTT
66 ATATATAATTCAACGCCAAAAAGATTGA-AGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTT
* *
88313 TTTT-CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAGCAAATGCTTAT
130 TTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAT
** * * * * * **
88377 ATCCAGCGTAGCTGACATTTGGTTTGATAAATAAAGATATTTCAAGGAG--TATGTACCAAAAAT
195 ATCCAATGTGGCTGACATTTGG-TTCATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAAT
* * * ** *
88440 CATGCAAAATTAAGCTGTGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
259 CATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGAT--AAACTACA
* * * * ** * * *
88503 CAATTTCAGCCAAAAACTTACTTGAAAATTTTTTTCTCAATTTTTTTCCACAATACACAGAAAAA
1 CGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAA
* * ** * *
88568 ATATATAATTCAACGCCAAAAAAATTGACGGGCCCTTCACGCTTCTAATATCATTTTCCA--TTT
66 ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTT
88631 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATA
131 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATA
* * * * * *
88696 TCCAATGTGGCAGA-ATTTTGGTTTGATGAATATAGATATTTGAAGGAGTCTTTGCGCTAATAGT
196 TCCAATGTGGCTGACA-TTTGG-TTCATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAAT
* ** * * * *
88760 CATGCAAAATTAAGCCGGGGCTTTGGAACGCGTTTTTAGCCAAAAACCTTGATAGTTAGTTCA
259 CATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATA--AACTACA
* * * *
88823 CGATTTCTGCTAAAAACTGACCCGAGAAG-GTTTT-TCAATTTTTTGCCAGAATACTCAGAAAAA
1 CGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAA
* ** ** *
88886 ATATATAATTTAACGCCAAAAAGATTGTTGGATTTTTCACGTTTCTAATATCGTTTTTCCATTTT
66 ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTT-CATTTT
* * **
88951 CTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCAAAAAAACAAATCCTTAT
130 TTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAT
* * * * * * *
89016 ATCCAATATGACTGAGATTTAGTTCGATGAACATAGATATTTCAAGGAGTCTTTACACCAAAAAT
195 ATCCAATGTGGCTGACATTTGGTTC-ATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAAT
* * * * * * *
89081 CTTACAAAACTGAGCCGGTG-TCCCGGAACACGTTTTTAGCCATATACCGGTATGAGTAAACCAT
259 CATGCAAAATTGAGCCGGGGCT-CCGGAACGCGTTTTTAGCCAAAAACC-G--TGA-TAAA-C--
*
89145 TTCA
316 TACA
** * * * *
89149 -GATAAAATTTTGC-AAAAACTGATCCGAAAA-ATTTTCCTCAATTCTTTGCCACAATA--CA-A
1 CGAT----TTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGA
* * ** * * * * * *
89208 AAAAAAAAATAA-TCAAAACCAAAAAGATTGAAGGGTTTTTCAAGCTTTTAATATCATTTTCCTT
62 AAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCAT
*
89272 TTTTTTTCCTCGAATTAATGTT-TAATTAAATCGAAACAAGATT-ATGATGCTCGTAAAGACAAA
127 TTTTTTT-C-CGAATTAAT-TTCTAATTAAATCGAAACAAGATTCA-GATGCTCGTAAAAACAAA
* * * * * ** *
89335 TCGTTAAATCGAATGTGGCTGAGATTTAGTTCGATGAATATAGATATTTCAAAAAGTCTTTACGC
188 TCCTTATATCCAATGTGGCTGACATTTGGTTC-ATGAATATAGATATTTCAAGGAGTCTTTGCGC
* * * * * * * * * *
89400 TAAAAATTATTCAAAACTGAGCAGGGGCCCCAGAACGCGTTTTTAGCCATAAACCGTGAT-GAGT
252 CAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATAAACT
*
89464 AAA
317 ACA
*
89467 CGATTTCGGTTAAAA
1 CGATTTCGGCTAAAA
89482 TTTTGCAAAA
Statistics
Matches: 2405, Mismatches: 367, Indels: 241
0.80 0.12 0.08
Matches are distributed among these distances:
300 4 0.00
301 129 0.05
302 3 0.00
305 7 0.00
306 86 0.04
307 54 0.02
308 68 0.03
309 8 0.00
310 2 0.00
311 24 0.01
312 70 0.03
313 56 0.02
315 4 0.00
316 4 0.00
317 35 0.01
318 226 0.09
319 120 0.05
320 178 0.07
321 494 0.21
322 280 0.12
323 52 0.02
324 11 0.00
325 66 0.03
326 180 0.07
327 12 0.00
328 19 0.01
329 42 0.02
330 30 0.01
331 1 0.00
332 1 0.00
334 1 0.00
335 5 0.00
336 5 0.00
338 4 0.00
339 2 0.00
340 92 0.04
341 25 0.01
342 5 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (319 bp):
CGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAA
ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTT
TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATA
TCCAATGTGGCTGACATTTGGTTCATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCA
TGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATAAACTACA
Found at i:87522 original size:641 final size:634
Alignment explanation
Indices: 86271--89481 Score: 3209
Period size: 641 Copynumber: 5.0 Consensus size: 634
86261 CTCCGAAACG
** * * *
86271 CGATTTCGGCTAAAAACTT-ACCCGGATTTTTTTTTCTCAATTTTTTACCACAATACACAGAAAA
1 CGATTTCGGCTAAAAA-TTGACCC-GAAATGTTTTTCTCAATTTTTTGCCACAATACTCAGAAAA
*
86335 AATATATAATTCAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGTTTTTCAATTT
64 AATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCG-TTTTC-A-TT
86400 TTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTA
126 TTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAA-AAA-CCTTA
* * *
86465 TATCCAATATTGCTGAAATTAG-TTCGATAAATATAGATATTTCAAGGAGTCTTTGCACCAAAAA
189 TATCCAATATGGCTGACATTTGATTCGATAAATATAGATATTTCAAGGAGTCTTTGCACCAAAAA
* * * * * * *
86529 T-ATGCAAAATTGAGCCGAGGCTACGGAACGCGATTTTAGCAAAAAACCGTGATGGTTA-GTACA
254 TCATGCAAAACTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTAACATACA
* * *
86592 CGATTTCGACTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAA
319 CGATTTCGGC-AAAAACTGATCCGAAAA-TTTTTTCTCAATTTTTTGCCACAATACACAGAAAAA
* * * *
86657 ATATATAATTCAACGCCAAAAAAATTAAATGGCTTTTCATGCTACTAATATCGTTTTTTCATTTT
382 ATATATAATTCAACACCAAAAAAATTGAAGGGCTTTTCATGCTTCTAATATCGTTTTTTCA--TT
* * * *
86722 TTTTCCAAATTAATTTCTAATTTATTCGAAACAAGATTCAGATGCTCGTAAAAACAAGTCCTTAT
445 TTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAT
* * *
86787 ATCCAATGTGGCTGACATTTGGTTC-ATTGAATATAAATATTTTAAGGAGTCTTTGCGCCAAAAA
510 ATCCAATGTGGCTGACATTTGGTTCGA-TGAATATAGATATTTCAAGGAGTCTTTGCGCTAAAAA
* * * *
86851 TCATGCAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGCAAAAAATCGTGATAAACTACA
574 TCATGCAAAATTGAGCCGGGGCTTCGGAACGCGTTTTTAGCCAAAAACCGTGAT-AACTACA
* * *
86913 TGATTTCGGCTAAAAATTGACCCGAATTATTTTTTTCTCAATTTTTTGCCACAATACACAGAAAA
1 CGATTTCGGCTAAAAATTGACCCGAA--ATGTTTTTCTCAATTTTTTGCCACAATACTCAGAAAA
* * * * * *
86978 AGTATATAATCCAACGCCTAAAAGATTGACGGGGTTTTCATGTTTCTAATATCGTTTTCCATTTT
64 AATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTT-CATTTT
*
87043 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAACCTTATAT
128 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCG-AAAAAAAAACCTTATAT
* * * *
87108 CCAATGTGGCTGACATTTGATTCGTTAAATATAGATATTTCAAGGAGTATTTGCGCCAAAAATCA
192 CCAATATGGCTGACATTTGATTCGATAAATATAGATATTTCAAGGAGTCTTTGCACCAAAAATCA
* * * * *
87173 TGCAAAAATGTGCCGGGGCTCCGAAATGCGTTTTTAACCAAAAACCGTGATGG-AACATACACGA
257 TGCAAAACTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTAACATACACGA
* *
87237 TTTCGGCTAAAAACTTATCCGAAATTTTTTTTTTCTCAATTTTTTGCCACAATACACA-AAAAAA
322 TTTCGGC-AAAAACTGATCCGAAA---ATTTTTTCTCAATTTTTTGCCACAATACACAGAAAAAA
* * * *
87301 TATATAATTCAATACCAAAAATATTTACGGGCTTTTCATGCTTCTAATATCGTTTTTTCATTTTT
383 TATATAATTCAACACCAAAAAAATTGAAGGGCTTTTCATGCTTCTAATATCGTTTTTTCATTTTT
* *
87366 TCCGAATTAATTTCTAATGAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCCTATATC
448 TCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATC
* * *
87431 CAATGTGGCTGACATTTGGTTCGTTGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCAT
513 CAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCTAAAAATCAT
*
87496 GCAAAATTGAGCCGGGGCTTCGGAACGCGTTTTTAGCCAAAAACCATGATAACGTACA
578 GCAAAATTGAGCCGGGGCTTCGGAACGCGTTTTTAGCCAAAAACCGTGATAAC-TACA
* *
87554 CGATTTCGGCTAAAAACTT-ATCCGAAAAGTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAA
1 CGATTTCGGCTAAAAA-TTGACCCGAAATGTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAA
* *
87618 ATATATAATTCAACGCAAAAAAAATTGACGGGCTTTTCACGCTTCTAATATCG--------TTTT
65 ATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTCATTTTTT
* * **
87675 TCC--ATT--TTTC----TAAATCGAAATAAGATTGAGATTCTCAGAAAAACAAATTCTTATATC
130 TCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTC-GAAAAA-AAAACCTTATATC
* * * * * * * * *
87732 CAATATGACTAATATTTGGTTCGATGAATATAGATATTTCAATGAGTCTTTACGCCAAAAATCTT
193 CAATATGGCTGACATTTGATTCGATAAATATAGATATTTCAAGGAGTCTTTGCACCAAAAATCAT
* * * * * *
87797 GCAAAACTTAGCTGGGGC-CCCGAAGCGCGTGTTTAGCCATAAACCGTTATTGAGTAAACGAT-C
258 GCAAAACTGAGCCGGGGCTCCGGAA-CGCGTTTTTAGCCAAAAACCGTGA-TG-GT-AAC-ATAC
* ** * *
87860 TCGGAAATTTTTTTGCAAAAACTGATCCGAAAATTTTTTCAACAATTCTTTTCCCACAATACCCA
318 AC-G--A--TTTCGGCAAAAACTGATCCGAAAATTTTTTC-TCAATT-TTTT-GC-C---A--C-
* * *
87925 AATACACACACACACACAGATATATATATAATTCAACACTAAAAAGATTGAAGGG-TTTTCAAT-
368 AAT----ACACAGA-A-A-A-A-ATATATAATTCAACACCAAAAAAATTGAAGGGCTTTTC-ATG
* * * *
87988 CTTCTAATATCG-GTTTT--TTTTTT-CGAATTAATTTCTAATTAAAT-AAAACAAAATTCAGAA
423 CTTCTAATATCGTTTTTTCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGAT
* * * * ** *
88048 GCTCGTAAAAA-AAATCGTTAAATCGAATGTGACTGGGATTTGGTTTGATGAATATAGATATTTC
488 GCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTC
* * * *
88112 AAGGAGTATTTGCGCTAGAAATCATGCAAAATTGAGTCGGGGC-TCAGGAACGCGTTTTTAACCA
553 AAGGAGTCTTTGCGCTAAAAATCATGCAAAATTGAGCCGGGGCTTC-GGAACGCGTTTTTAGCCA
*
88176 AAAACCGTG--CA-TACA
617 AAAACCGTGATAACTACA
* * * * *
88191 CGATTTCGGCTAAAAACTGACTCGAAAAGGTTTTTCTCAAATTTTTGCCACAATACTTAGAAAAA
1 CGATTTCGGCTAAAAATTGACCCG-AAATGTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAA
* ***
88256 A-ATATAATTTAACGCCAAAAAGATTGACAAACTTTTCACGCTTCTAATATCG--TT--TTTTTT
65 ATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTCATTTTTT
* * **
88316 T-CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAGCAAATGCTTATATC
130 TCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCG-AAAA-AAAAACCTTATATC
*** * * * * * *
88380 CAGCGTAGCTGACATTTGGTTTGATAAATAAAGATATTTCAAGGAG--TATGTACCAAAAATCAT
193 CAATATGGCTGACATTTGATTCGATAAATATAGATATTTCAAGGAGTCTTTGCACCAAAAATCAT
* * * * * * *
88443 GCAAAATTAAGCTGTGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA-GTACACAAT
258 GCAAAACTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTAACATACACGAT
* * * *
88507 TTCAGCCAAAAACTTA-CTTGAAAATTTTTTTCTCAATTTTTTTCCACAATACACAGAAAAAATA
323 TTC-GGCAAAAACTGATC-CGAAAA-TTTTTTCTCAATTTTTTGCCACAATACACAGAAAAAATA
* * ** * * *
88571 TATAATTCAACGCCAAAAAAATTGACGGGCCCTTCACGCTTCTAATATC-ATTTTCCATTTTTTC
385 TATAATTCAACACCAAAAAAATTGAAGGGCTTTTCATGCTTCTAATATCGTTTTTTCATTTTTTC
88635 CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCA
450 CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCA
* * * * *
88700 ATGTGGCAGA-ATTTTGGTTTGATGAATATAGATATTTGAAGGAGTCTTTGCGCTAATAGTCATG
515 ATGTGGCTGACA-TTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCTAAAAATCATG
* * * * *
88764 CAAAATTAAGCCGGGGCTTTGGAACGCGTTTTTAGCCAAAAACCTTGATAGTTAGTTCA
579 CAAAATTGAGCCGGGGCTTCGGAACGCGTTTTTAGCCAAAAACCGTGATA---ACTACA
* * * *
88823 CGATTTCTGCTAAAAACTGACCCGAGAA-GGTTTT-TCAATTTTTTGCCAGAATACTCAGAAAAA
1 CGATTTCGGCTAAAAATTGACCCGA-AATGTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAA
* ** ** *
88886 ATATATAATTTAACGCCAAAAAGATTGTTGGATTTTTCACGTTTCTAATATCGTTTTTCCATTTT
65 ATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCG-TTTT-CATTTT
*
88951 CTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCAAAAAAACAAATCCTTAT
128 -TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAA-AAA-CCTTAT
* * * * *
89016 ATCCAATATGACTGAGATTT-AGTTCGATGAACATAGATATTTCAAGGAGTCTTTACACCAAAAA
190 ATCCAATATGGCTGACATTTGA-TTCGATAAATATAGATATTTCAAGGAGTCTTTGCACCAAAAA
* * * * * *
89080 TCTTACAAAACTGAGCCGGTG-TCCCGGAACACGTTTTTAGCCATATACCG-GTATGAGTAAACC
254 TCATGCAAAACTGAGCCGGGGCT-CCGGAACGCGTTTTTAGCCAAAAACCGTG-ATG-GT-AA-C
* ** * * *
89143 ATTTCA-GATAAAATTTTGCAAAAACTGATCCGAAAAATTTTCCTCAATTCTTTGCCACAATACA
314 A-TACACGAT----TTCGGCAAAAACTGATCCGAAAATTTTTTCTCAATTTTTTGCCACAATACA
* * * * * * *
89207 -A-AAAAAA-AAATAA-TCAAAACCAAAAAGATTGAAGGGTTTTTCAAGCTTTTAATATCATTTT
374 CAGAAAAAATATATAATTCAACACCAAAAAAATTGAAGGGCTTTTCATGCTTCTAATATCGTTTT
* *
89268 CCTT-TTTTTTTCCTCGAATTAATGTT-TAATTAAATCGAAACAAGATT-ATGATGCTCGTAAAG
439 --TTCATTTTTT-C-CGAATTAAT-TTCTAATTAAATCGAAACAAGATTCA-GATGCTCGTAAAA
* * * * * **
89330 ACAAATCGTTAAATCGAATGTGGCTGAGATTTAGTTCGATGAATATAGATATTTCAAAAAGTCTT
498 ACAAATCCTTATATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTT
* * * * * ** * *
89395 TACGCTAAAAATTATTCAAAACTGAGCAGGGGCCCCAGAACGCGTTTTTAGCCATAAACCGTGAT
563 TGCGCTAAAAATCATGCAAAATTGAGCCGGGGCTTCGGAACGCGTTTTTAGCCAAAAACCGTGAT
* * *
89460 GAGTAAA
628 AACTACA
*
89467 CGATTTCGGTTAAAA
1 CGATTTCGGCTAAAA
89482 TTTTGCAAAA
Statistics
Matches: 2139, Mismatches: 309, Indels: 240
0.80 0.11 0.09
Matches are distributed among these distances:
620 29 0.01
621 18 0.01
622 33 0.02
623 106 0.05
624 24 0.01
625 32 0.01
626 110 0.05
627 6 0.00
628 13 0.01
629 8 0.00
630 40 0.02
631 68 0.03
632 34 0.02
634 2 0.00
635 2 0.00
636 2 0.00
637 82 0.04
638 69 0.03
639 172 0.08
640 31 0.01
641 456 0.21
642 141 0.07
643 199 0.09
644 67 0.03
645 17 0.01
646 60 0.03
647 195 0.09
648 120 0.06
649 3 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (634 bp):
CGATTTCGGCTAAAAATTGACCCGAAATGTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAA
TATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTCATTTTTTT
CCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAAAAACCTTATATCCAA
TATGGCTGACATTTGATTCGATAAATATAGATATTTCAAGGAGTCTTTGCACCAAAAATCATGCA
AAACTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTAACATACACGATTTC
GGCAAAAACTGATCCGAAAATTTTTTCTCAATTTTTTGCCACAATACACAGAAAAAATATATAAT
TCAACACCAAAAAAATTGAAGGGCTTTTCATGCTTCTAATATCGTTTTTTCATTTTTTCCGAATT
AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGG
CTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCTAAAAATCATGCAAAATT
GAGCCGGGGCTTCGGAACGCGTTTTTAGCCAAAAACCGTGATAACTACA
Found at i:90195 original size:15 final size:16
Alignment explanation
Indices: 90177--90206 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
90167 ATAAATAATA
90177 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
90192 ATATTATAATCTAAA
1 ATATTATAATCTAAA
90207 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:90468 original size:178 final size:180
Alignment explanation
Indices: 90254--90579 Score: 577
Period size: 180 Copynumber: 1.8 Consensus size: 180
90244 GTGGATTATT
90254 AATATCTTTCCATAATTAATAAAAAAGTTGAATTAATCATCT-AAAAAAAAGTTAAATGACTAAA
1 AATATCTTTCCATAATTAATAAAAAAGTTGAATTAATCATCTGAAAAAAAAGTTAAATGACTAAA
90318 AAAAATACCTA-TAAAAAATTATTATACTATAATACTAAG-GATATTTATGAAATTTCCCAAGTA
66 AAAAATACCTATTAAAAAATTATTATACTATAATACTAAGTG-TATTTATGAAATTTCCCAAGTA
90381 GAATTTTTGAGTTCGTGATATAATTTTAAAAAATTTAAATATTGGATTTAC
130 GAATTTTTGAGTTCGTGATATAATTTTAAAAAATTTAAATATTGGATTTAC
*
90432 AATATCTTTCCATAATTAATAAAAAAGTTTAATTAATCATCTGAAAAAAAAGTTAAATGACTAAA
1 AATATCTTTCCATAATTAATAAAAAAGTTGAATTAATCATCTGAAAAAAAAGTTAAATGACTAAA
* * * *
90497 AAGAATACTTATTAAAAAATTATTTTACTATAATACTAAGTGTATTTATGAAATTTCCCAATTAG
66 AAAAATACCTATTAAAAAATTATTATACTATAATACTAAGTGTATTTATGAAATTTCCCAAGTAG
90562 AATTTTTGAGTTCGTGAT
131 AATTTTTGAGTTCGTGAT
90580 TTTATATAGT
Statistics
Matches: 140, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
178 41 0.29
179 31 0.22
180 67 0.48
181 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (180 bp):
AATATCTTTCCATAATTAATAAAAAAGTTGAATTAATCATCTGAAAAAAAAGTTAAATGACTAAA
AAAAATACCTATTAAAAAATTATTATACTATAATACTAAGTGTATTTATGAAATTTCCCAAGTAG
AATTTTTGAGTTCGTGATATAATTTTAAAAAATTTAAATATTGGATTTAC
Found at i:94966 original size:152 final size:152
Alignment explanation
Indices: 94689--94976 Score: 497
Period size: 152 Copynumber: 1.9 Consensus size: 152
94679 CTCCCATGTA
*
94689 TTATACCTTGTTTGTTTTCAAGTTTTAGCAATAAAAATACCAATTAAACACCAGATTTGACCCCA
1 TTATACCTTGTTTGTTTTCAAGTTTTAGCAATAAAAATACCAATTAAACACCAGATTTAACCCCA
*
94754 AATTAACAACAAATAATTAAATATAAGGGTTAGTCCTAAATTTTATTACATTTCCCATAGGGTTT
66 AATTAACAACAAATAATTAAATATAAGGGTTAGTCCTAAATTTTAATACATTTCCCATAGGGTTT
94819 TAGAATTATACATTCACCAGGT
131 TAGAATTATACATTCACCAGGT
* *
94841 TTATACCTTGTTTGTTTTCAAGTTTTAGCAATAAAAATACCAATTAAACACTAGGTTTAACCCCA
1 TTATACCTTGTTTGTTTTCAAGTTTTAGCAATAAAAATACCAATTAAACACCAGATTTAACCCCA
* **
94906 AATTAACAACAAATAATTATATATAAGGGTTAGTCCTAAATTTTAATACA-TTCATTATAGGGTT
66 AATTAACAACAAATAATTAAATATAAGGGTTAGTCCTAAATTTTAATACATTTC-CCATAGGGTT
94970 TTAGAAT
130 TTAGAAT
94977 GAAAATATAA
Statistics
Matches: 128, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
151 3 0.02
152 125 0.98
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (152 bp):
TTATACCTTGTTTGTTTTCAAGTTTTAGCAATAAAAATACCAATTAAACACCAGATTTAACCCCA
AATTAACAACAAATAATTAAATATAAGGGTTAGTCCTAAATTTTAATACATTTCCCATAGGGTTT
TAGAATTATACATTCACCAGGT
Found at i:95552 original size:109 final size:109
Alignment explanation
Indices: 95267--95560 Score: 441
Period size: 107 Copynumber: 2.7 Consensus size: 109
95257 ACTATTATAG
* * *
95267 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAA-T---TCTAATATCTTTATAATTACTT
95332 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
62 TATTTTTACC-AAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
95381 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAA-TCTAATATCTTTATAATTACTTTATT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATAATTACTTTATT
*
95445 TTTACCAAAAATTTGGATATATTAAAA-TTTTTCTAATATACAA
66 TTTACCAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* **
95488 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTC-AATATTTTATATAATTTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTT-TATAA-TTACTTTA
95552 TTTTTACCA
64 TTTTTACCA
95561 TTTTAATTTA
Statistics
Matches: 170, Mismatches: 7, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
107 61 0.36
108 27 0.16
109 47 0.28
114 35 0.21
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATAATTACTTTATT
TTTACCAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:96757 original size:28 final size:31
Alignment explanation
Indices: 96715--96776 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 31
96705 ATATGTAGCA
96715 AAAAAATCATATAAGTAA-TTAATT-TTAATT
1 AAAAAATCA-ATAAGTAATTTAATTATTAATT
96745 AAAAAATC-ATAAGTAATTTAATTAATTAATT
1 AAAAAATCAATAAGTAATTTAATT-ATTAATT
96776 A
1 A
96777 TTACTACTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 8 0.28
29 6 0.21
30 8 0.28
31 7 0.24
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (31 bp):
AAAAAATCAATAAGTAATTTAATTATTAATT
Found at i:114961 original size:15 final size:15
Alignment explanation
Indices: 114941--114970 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
114931 ACATTTCAGA
114941 AGCAATTTTCAATTG
1 AGCAATTTTCAATTG
114956 AGCAATTTTCAATTG
1 AGCAATTTTCAATTG
114971 TTTTTTAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (15 bp):
AGCAATTTTCAATTG
Found at i:119191 original size:24 final size:24
Alignment explanation
Indices: 119159--119220 Score: 97
Period size: 26 Copynumber: 2.5 Consensus size: 24
119149 TGAGAAAAAA
*
119159 ATACCAATAAAACATAACCCATAT
1 ATACTAATAAAACATAACCCATAT
119183 ATACTAATAAAAAACATAACCCATAT
1 ATACTAAT--AAAACATAACCCATAT
119209 ATACTAATAAAA
1 ATACTAATAAAA
119221 TGCCTTACCC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
24 11 0.31
26 24 0.69
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (24 bp):
ATACTAATAAAACATAACCCATAT
Found at i:119230 original size:26 final size:26
Alignment explanation
Indices: 119167--119220 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
119157 AAATACCAAT
119167 AAAACATAACCCATATATACTAATAA
1 AAAACATAACCCATATATACTAATAA
119193 AAAACATAACCCATATATACTAATAA
1 AAAACATAACCCATATATACTAATAA
119219 AA
1 AA
119221 TGCCTTACCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.59, C:0.19, G:0.00, T:0.22
Consensus pattern (26 bp):
AAAACATAACCCATATATACTAATAA
Found at i:119317 original size:160 final size:160
Alignment explanation
Indices: 119062--119380 Score: 629
Period size: 160 Copynumber: 2.0 Consensus size: 160
119052 AAGCCATCGA
119062 GCCTTACCCTTCTCATCATCTTAATTATCATCATTAACGTACGTCTATCTCACAATATTGAAGAA
1 GCCTTACCCTTCTCATCATCTTAATTATCATCATTAACGTACGTCTATCTCACAATATTGAAGAA
119127 TATTCATTTTTTTCTTGAACTCTGAGAAAAAAATACCAATAAAACATAACCCATATATACTAATA
66 TATTCATTTTTTTCTTGAACTCTGAGAAAAAAATACCAATAAAACATAACCCATATATACTAATA
119192 AAAAACATAACCCATATATACTAATAAAAT
131 AAAAACATAACCCATATATACTAATAAAAT
119222 GCCTTACCCTTCTCATCATCTTAATTATCATCATTAACGTACGTCTATCTCACAATATTGAAGAA
1 GCCTTACCCTTCTCATCATCTTAATTATCATCATTAACGTACGTCTATCTCACAATATTGAAGAA
*
119287 TATTCATTTTTTTCTTGAACTCTGAGAAAAAAATACCAATAAAACATAACTCATATATACTAATA
66 TATTCATTTTTTTCTTGAACTCTGAGAAAAAAATACCAATAAAACATAACCCATATATACTAATA
119352 AAAAACATAACCCATATATACTAATAAAA
131 AAAAACATAACCCATATATACTAATAAAA
119381 AAAGTCATGC
Statistics
Matches: 158, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 158 1.00
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (160 bp):
GCCTTACCCTTCTCATCATCTTAATTATCATCATTAACGTACGTCTATCTCACAATATTGAAGAA
TATTCATTTTTTTCTTGAACTCTGAGAAAAAAATACCAATAAAACATAACCCATATATACTAATA
AAAAACATAACCCATATATACTAATAAAAT
Found at i:119351 original size:24 final size:24
Alignment explanation
Indices: 119319--119380 Score: 88
Period size: 26 Copynumber: 2.5 Consensus size: 24
119309 TGAGAAAAAA
* *
119319 ATACCAATAAAACATAACTCATAT
1 ATACTAATAAAACATAACCCATAT
119343 ATACTAATAAAAAACATAACCCATAT
1 ATACTAAT--AAAACATAACCCATAT
119369 ATACTAATAAAA
1 ATACTAATAAAA
119381 AAAGTCATGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 11 0.32
26 23 0.68
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (24 bp):
ATACTAATAAAACATAACCCATAT
Found at i:119397 original size:26 final size:26
Alignment explanation
Indices: 119327--119382 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
119317 AAATACCAAT
*
119327 AAAACATAACTCATATATACTAATAA
1 AAAACATAACCCATATATACTAATAA
119353 AAAACATAACCCATATATACTAATAA
1 AAAACATAACCCATATATACTAATAA
119379 AAAA
1 AAAA
119383 AGTCATGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.23
Consensus pattern (26 bp):
AAAACATAACCCATATATACTAATAA
Found at i:123715 original size:2 final size:2
Alignment explanation
Indices: 123708--123741 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
123698 TAATCACATA
123708 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
123742 GAGATTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:126029 original size:41 final size:42
Alignment explanation
Indices: 125951--126036 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 42
125941 TGATTCTTAC
125951 TTACTTTTTATATTCATGTATTATTATTGTTGTTGTTCTAAATT
1 TTACTTTTTATATTCATGTATTATTA-T-TTGTTGTTCTAAATT
125995 TTACTTTTTATATTCATGTATTATTA-TTGTTGTTCTAAATT
1 TTACTTTTTATATTCATGTATTATTATTTGTTGTTCTAAATT
126036 T
1 T
126037 AAGGAACTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
41 16 0.38
44 26 0.62
ACGTcount: A:0.23, C:0.07, G:0.08, T:0.62
Consensus pattern (42 bp):
TTACTTTTTATATTCATGTATTATTATTTGTTGTTCTAAATT
Found at i:126209 original size:31 final size:31
Alignment explanation
Indices: 126171--126231 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
126161 AAGAAGCTCT
*
126171 CAAGTTTGAGATCTTGCGTATGCAATTGCCC
1 CAAGTTTGAGACCTTGCGTATGCAATTGCCC
*
126202 CAAGTTTGAGACCTTGCGTATGTAATTGCC
1 CAAGTTTGAGACCTTGCGTATGCAATTGCC
126232 TCTGTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (31 bp):
CAAGTTTGAGACCTTGCGTATGCAATTGCCC
Found at i:126396 original size:14 final size:13
Alignment explanation
Indices: 126377--126406 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
126367 CCCATCAAAT
126377 AAAAAGAAAGAAAA
1 AAAAAGAAA-AAAA
126391 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
126404 AAA
1 AAA
126407 CCCTTTCCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAA
Found at i:134424 original size:54 final size:54
Alignment explanation
Indices: 134342--134448 Score: 196
Period size: 54 Copynumber: 2.0 Consensus size: 54
134332 TTAGATATGT
*
134342 GAAAGGGGAAAAACTCTAACCCTAGAAAAACAATTTGAACCAGATTAAACCTGA
1 GAAAGGGGAAAAACTCTAACCCTAGAAAAACAATTTGAACCAGACTAAACCTGA
*
134396 GAAAGGGGAAAAACTTTAACCCTAGAAAAACAATTTGAACCAGACTAAACCTG
1 GAAAGGGGAAAAACTCTAACCCTAGAAAAACAATTTGAACCAGACTAAACCTG
134449 CGAATAAAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.48, C:0.19, G:0.17, T:0.17
Consensus pattern (54 bp):
GAAAGGGGAAAAACTCTAACCCTAGAAAAACAATTTGAACCAGACTAAACCTGA
Done.