Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015464.1 Corchorus capsularis cultivar CVL-1 contig15485, 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: 113343
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7167 original size:10 final size:9
Alignment explanation
Indices: 7133--7168 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
7123 TCTGGTCGAA
7133 ATTTTTTTT
1 ATTTTTTTT
7142 ATTTTATTTT
1 ATTTT-TTTT
7152 ATTTTTTTT
1 ATTTTTTTT
7161 ATATTTTT
1 AT-TTTTT
7169 CGATATAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 11 0.44
10 14 0.56
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:8250 original size:33 final size:33
Alignment explanation
Indices: 8174--8286 Score: 149
Period size: 33 Copynumber: 3.4 Consensus size: 33
8164 TAGACAAAGG
* *
8174 GTCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA-
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCC-AT
** *
8207 GTCGTTTGGCCGGTTGTAGCCGGACATGTCCAT
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
8240 GTCGCGTGGCCGG-TGATGGCCGGACATGTCCAT
1 GTCGCGTGGCCGGTTG-TGGCCGGACATGTCCAT
8273 GTCGCGTGGCCGGT
1 GTCGCGTGGCCGGT
8287 CTTGTGGCGG
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
32 3 0.04
33 66 0.96
ACGTcount: A:0.09, C:0.27, G:0.42, T:0.23
Consensus pattern (33 bp):
GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
Found at i:9702 original size:23 final size:22
Alignment explanation
Indices: 9664--9795 Score: 94
Period size: 23 Copynumber: 6.0 Consensus size: 22
9654 GAAATTAGGC
* *
9664 AAAAGAAGACGGAAAAAAGACT
1 AAAAAAAGACTGAAAAAAGACT
*
9686 AAAAAAAGACTG-CAAAAG---
1 AAAAAAAGACTGAAAAAAGACT
9704 -AAAAAAGACTGAAAAAAAGACT
1 AAAAAAAGACTG-AAAAAAGACT
* *
9726 GAAAGAAGACTGAAAAGAAGACT
1 AAAAAAAGACTGAAAA-AAGACT
* * * *
9749 GAAACAAGACTGAAACAAGAAT
1 AAAAAAAGACTGAAAAAAGACT
*
9771 GAAAGAGAAGACTGAAAGAAAGACT
1 -AAA-AAAAGACTGAAA-AAAGACT
9796 GACTTAATTT
Statistics
Matches: 88, Mismatches: 12, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
17 11 0.12
19 5 0.06
21 5 0.06
22 19 0.22
23 32 0.36
24 11 0.12
25 5 0.06
ACGTcount: A:0.61, C:0.10, G:0.21, T:0.08
Consensus pattern (22 bp):
AAAAAAAGACTGAAAAAAGACT
Found at i:9719 original size:17 final size:17
Alignment explanation
Indices: 9687--9719 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9677 AAAAAGACTA
*
9687 AAAAAAGACTGCAAAAG
1 AAAAAAGACTGAAAAAG
9704 AAAAAAGACTGAAAAA
1 AAAAAAGACTGAAAAA
9720 AAGACTGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.09, G:0.15, T:0.06
Consensus pattern (17 bp):
AAAAAAGACTGAAAAAG
Found at i:9759 original size:74 final size:70
Alignment explanation
Indices: 9664--9797 Score: 169
Period size: 74 Copynumber: 1.9 Consensus size: 70
9654 GAAATTAGGC
*
9664 AAAAGAAGACGGAAAAAAGACTAAAAAAAGACTGCAAAAGAAAAAAGACTGAAAAAAAGACTGAA
1 AAAAGAAGACGGAAAAAAGACTAAAAAAAGAATG--AAAG--AAAAGACTGAAAAAAAGACTGAA
9729 AGAAGACTG
62 AGAAGACTG
* * * * * *
9738 AAAAGAAGACTGAAACAAGACTGAAACAAGAATGAAAGAGAAGACTGAAAGAAAGACTGA
1 AAAAGAAGACGGAAAAAAGACTAAAAAAAGAATGAAAGAAAAGACTGAAAAAAAGACTGA
9798 CTTAATTTCA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
70 20 0.38
72 4 0.08
74 29 0.55
ACGTcount: A:0.61, C:0.10, G:0.22, T:0.07
Consensus pattern (70 bp):
AAAAGAAGACGGAAAAAAGACTAAAAAAAGAATGAAAGAAAAGACTGAAAAAAAGACTGAAAGAA
GACTG
Found at i:9795 original size:12 final size:11
Alignment explanation
Indices: 9664--9797 Score: 116
Period size: 11 Copynumber: 12.1 Consensus size: 11
9654 GAAATTAGGC
*
9664 AAAAGAAGACGG
1 AAAA-AAGACTG
*
9676 AAAAAAGACTA
1 AAAAAAGACTG
9687 AAAAAAGACTG
1 AAAAAAGACTG
*
9698 --CAAA-A--G
1 AAAAAAGACTG
9704 AAAAAAGACTG
1 AAAAAAGACTG
9715 AAAAAAAGACTG
1 -AAAAAAGACTG
*
9727 AAAGAAGACTG
1 AAAAAAGACTG
9738 AAAAGAAGACTG
1 AAAA-AAGACTG
*
9750 AAACAAGACTG
1 AAAAAAGACTG
* *
9761 AAACAAGAATG
1 AAAAAAGACTG
9772 AAAGAGAAGACTG
1 AAA-A-AAGACTG
9785 AAAGAAAGACTG
1 AAA-AAAGACTG
9797 A
1 A
9798 CTTAATTTCA
Statistics
Matches: 102, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
6 1 0.01
8 4 0.04
9 4 0.04
11 49 0.48
12 33 0.32
13 11 0.11
ACGTcount: A:0.61, C:0.10, G:0.22, T:0.07
Consensus pattern (11 bp):
AAAAAAGACTG
Found at i:9825 original size:36 final size:36
Alignment explanation
Indices: 9785--10061 Score: 318
Period size: 36 Copynumber: 7.8 Consensus size: 36
9775 GAGAAGACTG
*
9785 AAAGAAAGACTGACTTAATTTCAAGGAAATTAGGTA
1 AAAGAAAGACTGGCTTAATTTCAAGGAAATTAGGTA
* * * *
9821 AAAG-AAGACTAGCTTAGTTTCAAGGATATTAAGT-
1 AAAGAAAGACTGGCTTAATTTCAAGGAAATTAGGTA
9855 AAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTA
1 AAAG-AAAGACTGGCTTAATTTCAAGGAAATTAGGTA
* * *
9892 AAAG-AAGACTGGCTTAGTTTCAAGGAAACTAAGT-
1 AAAGAAAGACTGGCTTAATTTCAAGGAAATTAGGTA
* *
9926 AAAGAAAAGATTGGCTTAGA-TTCAAGGAAACTAGGT-
1 AAAG-AAAGACTGGCTTA-ATTTCAAGGAAATTAGGTA
9962 AAAGAAATGACTGGCTTAATTTCAAGGAAATTAGGTA
1 AAAGAAA-GACTGGCTTAATTTCAAGGAAATTAGGTA
* * *
9999 AAGGAAAGACTGGCTTTATTTCAAGGAAATTAAGTA
1 AAAGAAAGACTGGCTTAATTTCAAGGAAATTAGGTA
* * *
10035 AAAG-GACACAGGCTTAATTTC-AGGAAA
1 AAAGAAAGACTGGCTTAATTTCAAGGAAA
10062 GGAAATTAAG
Statistics
Matches: 207, Mismatches: 25, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
34 14 0.07
35 69 0.33
36 114 0.55
37 10 0.05
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (36 bp):
AAAGAAAGACTGGCTTAATTTCAAGGAAATTAGGTA
Found at i:9873 original size:71 final size:71
Alignment explanation
Indices: 9785--10061 Score: 364
Period size: 71 Copynumber: 3.9 Consensus size: 71
9775 GAGAAGACTG
* * *
9785 AAAG-AAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTAGCTTAGTTTCAAGGATA
1 AAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAA
9849 TTAAGT
66 TTAAGT
9855 AAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAA
1 AAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAA
*
9920 CTAAGT
66 TTAAGT
* * *
9926 AAAGAAAAGATTGGCTTAGA-TTCAAGGAAACTAGGT-AAAGAAATGACTGGCTTAATTTCAAGG
1 AAAGAAAAGACTGGCTTA-ATTTCAAGGAAATTAGGTAAAAG-AA-GACTGGCTTAGTTTCAAGG
*
9989 AAATTAGGT
63 AAATTAAGT
* * * * * * *
9998 AAAGGAAAGACTGGCTTTATTTCAAGGAAATTAAGTAAAAGGACACAGGCTTAATTTC-AGGAAA
1 AAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAA
10062 GGAAATTAAG
Statistics
Matches: 184, Mismatches: 17, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
70 14 0.08
71 110 0.60
72 56 0.30
73 4 0.02
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (71 bp):
AAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAA
TTAAGT
Found at i:9950 original size:107 final size:106
Alignment explanation
Indices: 9785--10037 Score: 355
Period size: 107 Copynumber: 2.4 Consensus size: 106
9775 GAGAAGACTG
* * * * * *
9785 AAAGAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTAGCTTAGTTTCAAGGATAT
1 AAAGAAAGACTGGCTT-ATTTCAAGGAAATTAAGTAAAAAAAGACTAGCTTAGATTCAAGGAAAC
9850 TAAGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTA
65 TAAGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTA
* * *
9892 AAAG-AAGACTGGCTTAGTTTCAAGGAAACTAAGTAAAGAAAAGATTGGCTTAGATTCAAGGAAA
1 AAAGAAAGACTGGCTTA-TTTCAAGGAAATTAAGTAAA-AAAAGACTAGCTTAGATTCAAGGAAA
* *
9956 CTAGGTAAAGAAATGACTGGCTTAATTTCAAGGAAATTAGGTA
64 CTAAGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTA
*
9999 AAGGAAAGACTGGCTTTATTTCAAGGAAATTAAGTAAAA
1 AAAGAAAGACTGGC-TTATTTCAAGGAAATTAAGTAAAA
10038 GGACACAGGC
Statistics
Matches: 129, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
105 1 0.01
106 28 0.22
107 69 0.53
108 28 0.22
109 3 0.02
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (106 bp):
AAAGAAAGACTGGCTTATTTCAAGGAAATTAAGTAAAAAAAGACTAGCTTAGATTCAAGGAAACT
AAGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTA
Found at i:10092 original size:143 final size:141
Alignment explanation
Indices: 9785--10092 Score: 361
Period size: 143 Copynumber: 2.2 Consensus size: 141
9775 GAGAAGACTG
* * * *
9785 AAAG-AAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTAGCTTAGTTTCAAGGATA
1 AAAGAAAAGAATGACTTAA-TTCAAGGAAACTAGGTAAAAGAAGACTAGCTTAATTTCAAGGAAA
* * * *
9849 TTAAGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCA
65 TTAAGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAAGTAAAAGAACACAGGCTTAATTTCA
* *
9914 AGGAAACTAAGT
130 AGGAAACGAAAT
* * *
9926 AAAGAAAAGATTGGCTTAGATTCAAGGAAACTAGGT-AAAGAAATGACTGGCTTAATTTCAAGGA
1 AAAGAAAAGAATGACTTA-ATTCAAGGAAACTAGGTAAAAG-AA-GACTAGCTTAATTTCAAGGA
* * * *
9990 AATTAGGTAAAGGAAAGACTGGCTTTATTTCAAGGAAATTAAGTAAAAGGACACAGGCTTAATTT
63 AATTAAGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAAGTAAAAGAACACAGGCTTAATTT
*
10055 C-AGGAAAGGAAAT
128 CAAGGAAACGAAAT
* *
10068 TAAGTAAAATAATGAACTTAATTCA
1 AAAG-AAAAGAATG-ACTTAATTCA
10093 GTGTAATTAA
Statistics
Matches: 140, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
141 8 0.06
142 40 0.29
143 88 0.63
144 4 0.03
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.25
Consensus pattern (141 bp):
AAAGAAAAGAATGACTTAATTCAAGGAAACTAGGTAAAAGAAGACTAGCTTAATTTCAAGGAAAT
TAAGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAAGTAAAAGAACACAGGCTTAATTTCAA
GGAAACGAAAT
Found at i:10101 original size:32 final size:31
Alignment explanation
Indices: 10065--10177 Score: 100
Period size: 32 Copynumber: 3.4 Consensus size: 31
10055 CAGGAAAGGA
10065 AATTAAGTAAAATAATGAACTTAATTCAGTGT
1 AATTAAGTAAAATAATGAACTTAATTCAG-GT
* ** *
10097 AATTAAGTGAGGTCAATAAAAGGCTTAATTCAGGGT
1 AATTAAGTAAAAT-AAT-GAA--CTTAATTCA-GGT
* *
10133 AATTAAGTAGAATAAAGAACTTAATTCAAGGT
1 AATTAAGTAAAATAATGAACTTAATTC-AGGT
*
10165 AATTAAGTGAAAT
1 AATTAAGTAAAAT
10178 CAATAAAGAA
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
32 32 0.51
33 4 0.06
34 4 0.06
35 2 0.03
36 20 0.32
37 1 0.02
ACGTcount: A:0.46, C:0.06, G:0.18, T:0.30
Consensus pattern (31 bp):
AATTAAGTAAAATAATGAACTTAATTCAGGT
Found at i:10115 original size:36 final size:34
Alignment explanation
Indices: 10075--10193 Score: 129
Period size: 36 Copynumber: 3.4 Consensus size: 34
10065 AATTAAGTAA
*
10075 AATAATGAACTTAATTCAGTGTAATTAAGTGAGGTC
1 AATAAAGAACTTAATTCAG-GTAATTAAGTGA-GTC
*
10111 AATAAA-AGGCTTAATTCAGGGTAATTAAGT-AG--
1 AATAAAGA-ACTTAATTCA-GGTAATTAAGTGAGTC
*
10143 AATAAAGAACTTAATTCAAGGTAATTAAGTGAAATC
1 AATAAAGAACTTAATTC-AGGTAATTAAGTG-AGTC
10179 AATAAAGAACTTAAT
1 AATAAAGAACTTAAT
10194 CTAAAAAAGA
Statistics
Matches: 71, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
32 25 0.35
33 2 0.03
34 2 0.03
35 2 0.03
36 39 0.55
37 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (34 bp):
AATAAAGAACTTAATTCAGGTAATTAAGTGAGTC
Found at i:10192 original size:68 final size:68
Alignment explanation
Indices: 10065--10193 Score: 181
Period size: 68 Copynumber: 1.9 Consensus size: 68
10055 CAGGAAAGGA
* ** *
10065 AATTAAGTAAAATAATGAACTTAATTCAGTGTAATTAAGTGAGGTCAATAAAAGGCTTAATTCAG
1 AATTAAGTAAAATAAAGAACTTAATTCAGTGTAATTAAGTGAAATCAATAAAAGACTTAATTCAG
10130 GGT
66 GGT
*
10133 AATTAAGTAGAATAAAGAACTTAATTCAAG-GTAATTAAGTGAAATCAAT-AAAGAACTTAAT
1 AATTAAGTAAAATAAAGAACTTAATTC-AGTGTAATTAAGTGAAATCAATAAAAG-ACTTAAT
10194 CTAAAAAAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
67 4 0.07
68 48 0.89
69 2 0.04
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.29
Consensus pattern (68 bp):
AATTAAGTAAAATAAAGAACTTAATTCAGTGTAATTAAGTGAAATCAATAAAAGACTTAATTCAG
GGT
Found at i:12316 original size:2 final size:2
Alignment explanation
Indices: 12311--12339 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12301 TCTCTCTCTC
12311 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 T
12340 TGGTGTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13965 original size:2 final size:2
Alignment explanation
Indices: 13958--13983 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13948 AGGTTGTTTA
13958 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
13984 GATGTACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19397 original size:53 final size:53
Alignment explanation
Indices: 19340--19461 Score: 183
Period size: 53 Copynumber: 2.3 Consensus size: 53
19330 GTTTGAATGT
* * *
19340 TTTGAAGACTTGATG-GGAACTTTCCCACTTTTGAAAAGACCTAAATTGAACAC
1 TTTGAAAACTTGATGAGAAACTTTCCCA-ATTTGAAAAGACCTAAATTGAACAC
* *
19393 TTTGAAAACTTAATGAGAAACTTTCCCAATTTGAAAAGACCTAAATTGAACGC
1 TTTGAAAACTTGATGAGAAACTTTCCCAATTTGAAAAGACCTAAATTGAACAC
19446 TTTGAAAACTTGATGA
1 TTTGAAAACTTGATGA
19462 AACATTTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
53 51 0.82
54 11 0.18
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (53 bp):
TTTGAAAACTTGATGAGAAACTTTCCCAATTTGAAAAGACCTAAATTGAACAC
Found at i:23133 original size:20 final size:21
Alignment explanation
Indices: 23110--23177 Score: 70
Period size: 20 Copynumber: 3.3 Consensus size: 21
23100 GGCTTTGAAG
23110 AATTGAAATT-GAA-ACATTGA
1 AATTGAAATTCGAAGA-ATTGA
23130 AATTG-AATTCGAAGAATTGA
1 AATTGAAATTCGAAGAATTGA
* * *
23150 AATTGAAGTATGGAAGAATCGA
1 AATTGAAAT-TCGAAGAATTGA
23172 AATTGA
1 AATTGA
23178 GGCATTGACG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
19 4 0.10
20 18 0.44
21 3 0.07
22 16 0.39
ACGTcount: A:0.47, C:0.04, G:0.21, T:0.28
Consensus pattern (21 bp):
AATTGAAATTCGAAGAATTGA
Found at i:23168 original size:22 final size:20
Alignment explanation
Indices: 23125--23177 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 20
23115 AAATTGAAAC
23125 ATTGAAATTGAATTCGAAGA
1 ATTGAAATTGAATTCGAAGA
*
23145 ATTGAAATTGAAGTATGGAAGA
1 ATTGAAATTGAA-T-TCGAAGA
*
23167 ATCGAAATTGA
1 ATTGAAATTGA
23178 GGCATTGACG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 12 0.41
21 1 0.03
22 16 0.55
ACGTcount: A:0.45, C:0.04, G:0.23, T:0.28
Consensus pattern (20 bp):
ATTGAAATTGAATTCGAAGA
Found at i:23235 original size:22 final size:22
Alignment explanation
Indices: 23210--23270 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
23200 AGAATTGAAA
23210 TTGATGTATTGAAATTAAAGC-G
1 TTGAT-TATTGAAATTAAAGCAG
* * *
23232 TTGAAATATTGAAATTTAAGCAT
1 TTG-ATTATTGAAATTAAAGCAG
23255 TTGAATTATTGAAATT
1 TTG-ATTATTGAAATT
23271 GGAACATCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 17 0.52
23 16 0.48
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.41
Consensus pattern (22 bp):
TTGATTATTGAAATTAAAGCAG
Found at i:23258 original size:23 final size:22
Alignment explanation
Indices: 23216--23270 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
23206 GAAATTGATG
23216 TATTGAAATTAAAGCGTTGAAA
1 TATTGAAATTAAAGCGTTGAAA
* * *
23238 TATTGAAATTTAAGCATTTGAAT
1 TATTGAAATTAAAGC-GTTGAAA
23261 TATTGAAATT
1 TATTGAAATT
23271 GGAACATCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.40
Consensus pattern (22 bp):
TATTGAAATTAAAGCGTTGAAA
Found at i:23339 original size:22 final size:22
Alignment explanation
Indices: 23291--23445 Score: 92
Period size: 22 Copynumber: 7.2 Consensus size: 22
23281 AGGATTGAAT
* * * *
23291 TTGAAGAATAGCAATAGAAGCA
1 TTGAAGAATTGAAATTGAAACA
* *
23313 CTGAAGAATTGAAATTGAAACT
1 TTGAAGAATTGAAATTGAAACA
* *
23335 TTGAAGGATTGAATTTGAAGA-A
1 TTGAAGAATTGAAATTGAA-ACA
*
23357 TTG-A-AATTTAAGCATTGAAA-A
1 TTGAAGAATTGAA--ATTGAAACA
*
23378 -TG-A-AATTGGAATTGAAACA
1 TTGAAGAATTGAAATTGAAACA
*
23397 TTGAAGAATTGCAATTGAAACA
1 TTGAAGAATTGAAATTGAAACA
* * *
23419 TCGAAGGATTGAATTTGAAGA-A
1 TTGAAGAATTGAAATTGAA-ACA
23441 TTGAA
1 TTGAA
23446 ATTGGAACAT
Statistics
Matches: 104, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
18 7 0.07
19 1 0.01
20 15 0.14
21 4 0.04
22 75 0.72
23 2 0.02
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.28
Consensus pattern (22 bp):
TTGAAGAATTGAAATTGAAACA
Found at i:23370 original size:58 final size:57
Alignment explanation
Indices: 23239--23385 Score: 170
Period size: 58 Copynumber: 2.5 Consensus size: 57
23229 GCGTTGAAAT
* * *
23239 ATTGAAATTTAAGCATTTGAATTATTGAAATTGGAACATCGCAGGATTGAATTTGAAGA
1 ATTGAAATTTAAGCA-TTGAA-AATTGAAATTGAAACATCGAAGGATTGAATTTGAAGA
* * ** * * *
23298 ATAGCAATAGAAGCACTGAAGAATTGAAATTGAAACTTTGAAGGATTGAATTTGAAGA
1 ATTGAAATTTAAGCATTGAA-AATTGAAATTGAAACATCGAAGGATTGAATTTGAAGA
23356 ATTGAAATTTAAGCATTGAAAA-TGAAATTG
1 ATTGAAATTTAAGCATTGAAAATTGAAATTG
23386 GAATTGAAAC
Statistics
Matches: 72, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
56 8 0.11
57 2 0.03
58 51 0.71
59 11 0.15
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (57 bp):
ATTGAAATTTAAGCATTGAAAATTGAAATTGAAACATCGAAGGATTGAATTTGAAGA
Found at i:23378 original size:15 final size:15
Alignment explanation
Indices: 23325--23376 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 15
23315 GAAGAATTGA
23325 AATTGAAACTTTGAAG
1 AATTGAAA-TTTGAAG
*
23341 GATTG-AATTTGAAG
1 AATTGAAATTTGAAG
23355 AATTGAAATTT-AAG
1 AATTGAAATTTGAAG
*
23369 CATTGAAA
1 AATTGAAA
23377 ATGAAATTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 21 0.66
15 7 0.22
16 4 0.12
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (15 bp):
AATTGAAATTTGAAG
Found at i:23441 original size:36 final size:36
Alignment explanation
Indices: 23397--23476 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
23387 AATTGAAACA
*
23397 TTGAAGAATTGCAATTGAAACATCGAAGGATTGAAT
1 TTGAAGAATTGAAATTGAAACATCGAAGGATTGAAT
* * *
23433 TTGAAGAATTGAAATTGGAACATTGTAGGATTGAAT
1 TTGAAGAATTGAAATTGAAACATCGAAGGATTGAAT
*
23469 TTGGAGAA
1 TTGAAGAA
23477 AAAACCACCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30
Consensus pattern (36 bp):
TTGAAGAATTGAAATTGAAACATCGAAGGATTGAAT
Found at i:23666 original size:22 final size:20
Alignment explanation
Indices: 23610--24373 Score: 195
Period size: 22 Copynumber: 35.7 Consensus size: 20
23600 GTATTGAAGT
23610 ATTGAAATATTGAAGCATTGACA
1 ATTGAAA-ATTGAAG-ATTGA-A
* * *
23633 TTTGGAATTTGAAGGATTGAA
1 ATTGAAAATTGAA-GATTGAA
* * *
23654 ATTGAAACATTGACATATTTAG
1 ATTGAAA-ATTGA-AGATTGAA
* *
23676 ATCGAAGCATTGAAGTATTGAA
1 ATTGAA-AATTGAAG-ATTGAA
23698 ATTGAAACATTGAAGAATT-AA
1 ATTGAAA-ATTGAAG-ATTGAA
*
23719 ATTTGAAGAATTGGA-ATTGAGA
1 A-TTGAA-AATTGAAGATTGA-A
23741 CATTGAAATATTGAA-ATTGAAA
1 -ATTGAAA-ATTGAAGATTG-AA
* *
23763 CATTGAAGGATTGAA-TTTGAAGA
1 -ATTGAA-AATTGAAGATTG-A-A
23786 ATTGAAATATTGAAGCATTGACA
1 ATTGAAA-ATTGAAG-ATTGA-A
* * *
23809 TTTGGAATTTGAAGGATTGAA
1 ATTGAAAATTGAA-GATTGAA
*
23830 ATTG-AAGTCTGGAA-ATTGAA
1 ATTGAAAAT-T-GAAGATTGAA
*
23850 GTATTGAAGAATCGAA-ATTGAA
1 --ATTGAA-AATTGAAGATTGAA
* * * * * *
23872 GCACTGACATTTGGA-ACTAAA
1 --ATTGAAAATTGAAGATTGAA
23893 ATTG-AAATTGAAGCATTGAA
1 ATTGAAAATTGAAG-ATTGAA
* *
23913 GAATGGAAATTGAAGCATTGAGGA
1 -ATTGAAAATTGAAG-ATTGA--A
* *
23937 A-TGGAAATTGAGGCATTGAAGA
1 ATTGAAAATTGAAG-ATTG-A-A
23959 ATTGAAGAATTGAA-ATACTGAA
1 ATTGAA-AATTGAAGAT--TGAA
* * *
23981 ATTGAATCATTCAAGAATTGCA
1 ATTGAA-AATTGAAG-ATTGAA
24003 ATTGAAACATTGAAGAATTGAA
1 ATTGAAA-ATTGAAG-ATTGAA
* *
24025 ATTGAAGCATTTGAATATTGAA
1 ATTGAA--AATTGAAGATTGAA
*
24047 ATTGAAACATTGAAGAATTGAG
1 ATTGAAA-ATTGAAG-ATTGAA
*
24069 TTTGAAGAATTG-AGATTGAA
1 ATTGAA-AATTGAAGATTGAA
24089 GCATTG-AAA-T----ATTGAA
1 --ATTGAAAATTGAAGATTGAA
*
24105 ATTGAAACAGTGAAGAATTGAA
1 ATTGAAA-ATTGAAG-ATTGAA
* * *
24127 TTTGAAGCATTGGAATATTGAA
1 ATTGAA-AATT-GAAGATTGAA
24149 ATTGAAACATTGAAGAATTGAA
1 ATTGAAA-ATTGAAG-ATTGAA
*
24171 TTTGAAGAATTG-AGATTGAA
1 ATTGAA-AATTGAAGATTGAA
24191 CCATTG-AAA-T----ATTGAA
1 --ATTGAAAATTGAAGATTGAA
*
24207 ATTGAAACAGTGAAGAATTGAA
1 ATTGAAA-ATTGAAG-ATTGAA
* * *
24229 ACTGAAGCATTGAAATATTGAA
1 ATTGAA-AATTG-AAGATTGAA
24251 ATTGAAACATTGAAGAATTGAA
1 ATTGAAA-ATTGAAG-ATTGAA
24273 ATTGAAACATTGAA-A-T---
1 ATTGAAA-ATTGAAGATTGAA
*
24289 ACTG-AAATTGAAGCATTGAGTA
1 ATTGAAAATTGAAG-ATTGA--A
24311 ATTGAAGAATTGAAGAATTGGATA
1 ATTGAA-AATTGAAG-ATT-GA-A
24335 ATTGAAGAATTGAAGCATTCGATA
1 ATTGAA-AATTGAAG-ATT-GA-A
24359 ATTGAAGAATTGAAG
1 ATTGAA-AATTGAAG
24374 CAACAAATTG
Statistics
Matches: 572, Mismatches: 85, Indels: 167
0.69 0.10 0.20
Matches are distributed among these distances:
14 14 0.02
15 6 0.01
16 18 0.03
17 3 0.01
18 5 0.01
19 6 0.01
20 33 0.06
21 44 0.08
22 335 0.59
23 39 0.07
24 67 0.12
25 2 0.00
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (20 bp):
ATTGAAAATTGAAGATTGAA
Found at i:23724 original size:14 final size:15
Alignment explanation
Indices: 23697--24348 Score: 170
Period size: 14 Copynumber: 43.5 Consensus size: 15
23687 GAAGTATTGA
*
23697 AATTGAAACATTGAAG
1 AATTGAAA-TTTGAAG
23713 AATT-AAATTTGAAG
1 AATTGAAATTTGAAG
*
23727 AATTGGAA-TTG-AG
1 AATTGAAATTTGAAG
23740 ACATTGAAATATTG-A-
1 A-ATTGAAAT-TTGAAG
*
23755 AATTGAAACATTGAAG
1 AATTGAAA-TTTGAAG
*
23771 GATTG-AATTTGAAG
1 AATTGAAATTTGAAG
23785 AATTGAAATATTGAAG
1 AATTGAAAT-TTGAAG
* *
23801 CATTGACATTTG--G
1 AATTGAAATTTGAAG
23814 AATTTGAAGGA-TTG-A-
1 AA-TTGAA--ATTTGAAG
* * *
23829 AATTGAAGTCTGGA-
1 AATTGAAATTTGAAG
*
23843 AATTGAAGTATTGAAG
1 AATTGAAAT-TTGAAG
*
23859 AATCGAAA-TTGAAG
1 AATTGAAATTTGAAG
* * * *
23873 CACTGACATTTGGAACTAA
1 AATTGAAATTT-G-A--AG
23892 AATTGAAA-TTGAAG
1 AATTGAAATTTGAAG
* * *
23906 CATTGAAGA-ATGGA-
1 AATTGAA-ATTTGAAG
*
23920 AATTGAAGCA-TTGAGG
1 AATTGAA--ATTTGAAG
* *
23936 AATGGAAA-TTGAGG
1 AATTGAAATTTGAAG
* *
23950 CATTGAAGAATTGAAG
1 AATTGAA-ATTTGAAG
*
23966 AATTGAAATACTG-A-
1 AATTGAAAT-TTGAAG
*
23980 AATTGAATCATTCAAGAATTG
1 AATTGAA--ATT--TGAA--G
*
24001 CAATTGAAACATTGAAG
1 -AATTGAAA-TTTGAAG
24018 AATTGAAA-TTGAAG
1 AATTGAAATTTGAAG
*
24032 CATTTG-AATATTG-A-
1 -AATTGAAAT-TTGAAG
*
24046 AATTGAAACATTGAAG
1 AATTGAAA-TTTGAAG
*
24062 AATTG-AGTTTGAAG
1 AATTGAAATTTGAAG
*
24076 AATTGAGA-TTGAAG
1 AATTGAAATTTGAAG
*
24090 CATTGAAATATTG-A-
1 AATTGAAAT-TTGAAG
**
24104 AATTGAAACAGTGAAG
1 AATTGAAA-TTTGAAG
24120 AATTG-AATTTGAAG
1 AATTGAAATTTGAAG
* *
24134 CATTGGAATATTG-A-
1 AATTGAAAT-TTGAAG
*
24148 AATTGAAACATTGAAG
1 AATTGAAA-TTTGAAG
24164 AATTG-AATTTGAAG
1 AATTGAAATTTGAAG
* *
24178 AATTGAGA-TTGAAC
1 AATTGAAATTTGAAG
*
24192 CATTGAAATATTG-A-
1 AATTGAAAT-TTGAAG
**
24206 AATTGAAACAGTGAAG
1 AATTGAAA-TTTGAAG
*
24222 AATTGAAA-CTGAAG
1 AATTGAAATTTGAAG
*
24236 CATTGAAATATTG-A-
1 AATTGAAAT-TTGAAG
*
24250 AATTGAAACATTGAAG
1 AATTGAAA-TTTGAAG
24266 AATTGAAA-TTGAA-
1 AATTGAAATTTGAAG
*
24279 ACATTGAAATACTG-A-
1 A-ATTGAAAT-TTGAAG
24294 AATTGAAGCA-TTG-AG
1 AATTGAA--ATTTGAAG
*
24309 TAATTGAAGAATTGAAG
1 -AATTGAA-ATTTGAAG
24326 AATTGGATAA-TTGAAG
1 AATT-GA-AATTTGAAG
24342 AATTGAA
1 AATTGAA
24349 GCATTCGATA
Statistics
Matches: 479, Mismatches: 79, Indels: 158
0.67 0.11 0.22
Matches are distributed among these distances:
13 12 0.03
14 238 0.50
15 63 0.13
16 135 0.28
17 9 0.02
18 4 0.01
19 9 0.02
20 1 0.00
21 1 0.00
22 7 0.01
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.29
Consensus pattern (15 bp):
AATTGAAATTTGAAG
Found at i:23769 original size:44 final size:43
Alignment explanation
Indices: 23692--24324 Score: 236
Period size: 44 Copynumber: 15.1 Consensus size: 43
23682 GCATTGAAGT
* *
23692 ATTGAA-ATTGAAACATTGAAGAATT-AAA-TTTGAAGAATTGGA
1 ATTGAACATTGAAATATTG-A-AATTGAAACATTGAAGAATTGGA
*
23734 ATTGAGACATTGAAATATTGAAATTGAAACATTGAAGGATT-GA
1 ATTGA-ACATTGAAATATTGAAATTGAAACATTGAAGAATTGGA
* *
23777 ATTTGAAGAATTGAAATATTGAAGCATTG--ACATTTG--GAATTTGAAGG
1 A-TTGAA-CATTGAAATATTGAA--ATTGAAACA-TTGAAGAA-TTG--GA
* * * ** * *
23824 ATTGAA-ATTGAAGTCTGGAAATTGAAGTATTGAAGAATCGAA
1 ATTGAACATTGAAATATTGAAATTGAAACATTGAAGAATTGGA
* * * *
23866 ATTGAAGCACTGACAT-TTGGAACT-AAA-ATTG-A-AATT-GA
1 ATTGAA-CATTGAAATATTGAAATTGAAACATTGAAGAATTGGA
* * *
23904 A--G--CATTGAAGA-ATGGAAATTGAAGCATTGAGGAA-TGGAA
1 ATTGAACATTGAA-ATATTGAAATTGAAACATTGAAGAATTGG-A
* * *
23943 ATTGAGGCATTG--A-A--G-AATTGAAGA-ATTGAA-ATACTGAA
1 ATTGA-ACATTGAAATATTGAAATTGAA-ACATTGAAGA-ATTGGA
* * *
23981 ATTGAATCATTCAAGA-ATTGCAATTGAAACATTGAAGAATTGAA
1 ATTGAA-CATTGAA-ATATTGAAATTGAAACATTGAAGAATTGGA
24025 ATTGAAGCATTTG-AATATTGAAATTGAAACATTGAAGAATT-G-
1 ATTGAA-CA-TTGAAATATTGAAATTGAAACATTGAAGAATTGGA
* * * *
24067 A--G---TTTGAAGA-ATTGAGATTGAAGCATTGAA-ATATTGAA
1 ATTGAACATTGAA-ATATTGAAATTGAAACATTGAAGA-ATTGGA
* * *
24105 ATTGAAACAGTGAAGA-ATTGAATTTGAAGCATTG--GAA-T---
1 ATTG-AACATTGAA-ATATTGAAATTGAAACATTGAAGAATTGGA
* *
24143 ATTGAA-ATTGAAACATTGAAGAATTG-AA-TTTGAAGAATT-GA
1 ATTGAACATTGAAATATTG-A-AATTGAAACATTGAAGAATTGGA
* *
24184 GATTGAACCATTGAAATATTGAAATTGAAACAGTGAAGAATTGAA
1 -ATTGAA-CATTGAAATATTGAAATTGAAACATTGAAGAATTGGA
* *
24229 ACTGAAGCATTGAAATATTGAAATTGAAACATTGAAGAATTGAA
1 ATTGAA-CATTGAAATATTGAAATTGAAACATTGAAGAATTGGA
* *
24273 ATTGAAACATTGAAATACTGAAATTGAAGCATTG-AGTAATTGAAGA
1 ATTG-AACATTGAAATATTGAAATTGAAACATTGAAG-AATTG--GA
24319 ATTGAA
1 ATTGAA
24325 GAATTGGATA
Statistics
Matches: 452, Mismatches: 63, Indels: 149
0.68 0.09 0.22
Matches are distributed among these distances:
33 5 0.01
34 6 0.01
35 7 0.02
36 39 0.09
37 7 0.02
38 40 0.09
39 9 0.02
40 3 0.01
41 10 0.02
42 34 0.08
43 28 0.06
44 234 0.52
45 14 0.03
46 14 0.03
47 2 0.00
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.29
Consensus pattern (43 bp):
ATTGAACATTGAAATATTGAAATTGAAACATTGAAGAATTGGA
Found at i:23790 original size:102 final size:102
Alignment explanation
Indices: 23674--24346 Score: 481
Period size: 102 Copynumber: 6.6 Consensus size: 102
23664 TGACATATTT
* *
23674 AGATCGAAGCATTGAAGTATTGAAATTGAAACATTGAAGAATT-AAATTTGAAGAATTGGAATTG
1 AGATTGAAGCATTGAAATATTGAAATTGAAACATTGAAGAATTGAAA-TTGAAGAATTGGAATTG
* *
23738 AGACATTGAAATATTG-A-AATTGAAACATTGAAGGATTG
65 AGA-ATTGAAACATTGAAGAATTGAAA-ATTGAAGAATTG
*
23776 A-ATTTGAAGAATTGAAATATTGAAGCATTG--ACATTTG--GAATTTGAAGGATTG-A-AATT-
1 AGA-TTGAAGCATTGAAATATTGAA--ATTGAAACA-TTGAAGAA-TTGAA--ATTGAAGAATTG
** * * *
23833 GAAGTCTG-GAAATTGAAGTATTGAAGAATCG-AAATTGAAGCACTG
59 GAA-T-TGAG-AATTGAAACATTGAAGAATTGAAAATTGAAGAATTG
* * * *
23878 ACATTTGGAA-C--T-AAA-ATTGAAATTGAAGCATTGAAGAATGGAAATTGAAGCATTGAGGAA
1 AGA-TT-GAAGCATTGAAATATTGAAATTGAAACATTGAAGAATTGAAATTGAAGAATT--GGAA
* ** *
23938 TGGA-AATTGAGGCATTGAAGAATTGAAGAATTGAA-ATACTG
62 TTGAGAATTGAAACATTGAAGAATTGAA-AATTGAAGA-ATTG
* * * * * *
23979 AAATTGAATCATTCAAGA-ATTGCAATTGAAACATTGAAGAATTGAAATTGAAGCATTTGAATAT
1 AGATTGAAGCATTGAA-ATATTGAAATTGAAACATTGAAGAATTGAAATTGAAG-AATTGGA-AT
**
24043 TGA-AATTGAAACATTGAAGAATTG-AGTTTGAAGAATTG
63 TGAGAATTGAAACATTGAAGAATTGAAAATTGAAGAATTG
* * *
24081 AGATTGAAGCATTGAAATATTGAAATTGAAACAGTGAAGAATTGAATTTGAAGCATTGGAATATT
1 AGATTGAAGCATTGAAATATTGAAATTGAAACATTGAAGAATTGAAATTGAAGAATTGG-A-ATT
*
24146 GA-AATTGAAACATTGAAGAATTG-AATTTGAAGAATTG
64 GAGAATTGAAACATTGAAGAATTGAAAATTGAAGAATTG
* * * * *
24183 AGATTGAACCATTGAAATATTGAAATTGAAACAGTGAAGAATTGAAACTGAAGCATTGAAATATT
1 AGATTGAAGCATTGAAATATTGAAATTGAAACATTGAAGAATTGAAATTGAAGAATTG-GA-ATT
24248 GA-AATTGAAACATTGAAGAATTG-AAATTGAA-ACATTG
64 GAGAATTGAAACATTGAAGAATTGAAAATTGAAGA-ATTG
* **
24285 AAATACTGAA--ATTGAAGCATTGAGTAATTGAAGA-ATTGAAGAATTGGATAATTGAAGAATTG
1 AGAT--TGAAGCATTGAAATATTGA--AATTGAA-ACATTGAAGAATT-GA-AATTGAAGAATTG
24347 AAGCATTCGA
Statistics
Matches: 474, Mismatches: 50, Indels: 90
0.77 0.08 0.15
Matches are distributed among these distances:
97 8 0.02
98 4 0.01
99 36 0.08
100 11 0.02
101 27 0.06
102 258 0.54
103 22 0.05
104 91 0.19
105 6 0.01
106 11 0.02
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (102 bp):
AGATTGAAGCATTGAAATATTGAAATTGAAACATTGAAGAATTGAAATTGAAGAATTGGAATTGA
GAATTGAAACATTGAAGAATTGAAAATTGAAGAATTG
Found at i:23798 original size:38 final size:38
Alignment explanation
Indices: 23756--23831 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 38
23746 AAATATTGAA
23756 ATTGAAACATTGA-AGGATT-GAATTTGAAGAATTGAAAT
1 ATTGAAACATTGACA--ATTGGAATTTGAAGAATTGAAAT
* * *
23794 ATTGAAGCATTGACATTTGGAATTTGAAGGATTGAAAT
1 ATTGAAACATTGACAATTGGAATTTGAAGAATTGAAAT
23832 TGAAGTCTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 2 0.06
38 30 0.91
39 1 0.03
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (38 bp):
ATTGAAACATTGACAATTGGAATTTGAAGAATTGAAAT
Found at i:24153 original size:58 final size:58
Alignment explanation
Indices: 24038--24306 Score: 201
Period size: 58 Copynumber: 4.7 Consensus size: 58
24028 GAAGCATTTG
* * *
24038 AATATTGAAATTGAAACATTGAAGAATTGAGTTTGAAGAATT-G-AGATTGAAGCATTGA
1 AATATTGAAATTGAAACATTGAAGAATTGAATTTGAAGCATTGGAATATTGAA--ATTGA
*
24096 AATATTGAAATTGAAACAGTGAAGAATTGAATTTGAAGCATTGGAATATTGAAATTGA
1 AATATTGAAATTGAAACATTGAAGAATTGAATTTGAAGCATTGGAATATTGAAATTGA
* * * *
24154 AACATTGAAGAATTG-AA-TTTGAAGAATTGAGA-TTGAACCATTGAAATATTGAAATTGA
1 AATATTG-A-AATTGAAACATTGAAGAATTGA-ATTTGAAGCATTGGAATATTGAAATTGA
* * * * *
24212 AACAGTGAAGAATTGAAAC--TGAAGCATTGAAATATTGAA--ATTGAAACATTG-AA--G-
1 AATATTG-A-AATTGAAACATTGAAGAATTG-AAT-TTGAAGCATTGGAATATTGAAATTGA
* *
24266 -A-ATTGAAATTGAAACATTGAA-ATACTGAAATTGAAGCATTG
1 AATATTGAAATTGAAACATTGAAGA-ATTGAATTTGAAGCATTG
24307 AGTAATTGAA
Statistics
Matches: 180, Mismatches: 16, Indels: 36
0.78 0.07 0.16
Matches are distributed among these distances:
50 14 0.08
51 3 0.02
52 14 0.08
53 1 0.01
55 1 0.01
57 2 0.01
58 120 0.67
59 8 0.04
60 17 0.09
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.29
Consensus pattern (58 bp):
AATATTGAAATTGAAACATTGAAGAATTGAATTTGAAGCATTGGAATATTGAAATTGA
Found at i:24411 original size:8 final size:8
Alignment explanation
Indices: 23898--24412 Score: 164
Period size: 8 Copynumber: 68.2 Consensus size: 8
23888 CTAAAATTGA
23898 AATTGAAG
1 AATTGAAG
*
23906 CATTGAAG
1 AATTGAAG
*
23914 AA-TGGA-
1 AATTGAAG
23920 AATTGAAG
1 AATTGAAG
* *
23928 CATTGAGG
1 AATTGAAG
*
23936 AA-TGGA-
1 AATTGAAG
*
23942 AATTGAGG
1 AATTGAAG
*
23950 CATTGAAG
1 AATTGAAG
23958 AATTGAAG
1 AATTGAAG
23966 AATTGAA-
1 AATTGAAG
*
23973 ATACTG-A-
1 A-ATTGAAG
*
23980 AATTGAAT
1 AATTGAAG
* *
23988 CATTCAAG
1 AATTGAAG
*
23996 AATTG--C
1 AATTGAAG
24002 AATTGAA-
1 AATTGAAG
24009 ACATTGAAG
1 A-ATTGAAG
24018 AATTG-A-
1 AATTGAAG
24024 AATTGAAG
1 AATTGAAG
*
24032 CATTTGAA-
1 -AATTGAAG
*
24040 TATTG-A-
1 AATTGAAG
24046 AATTGAA-
1 AATTGAAG
24053 ACATTGAAG
1 A-ATTGAAG
24062 AATTG-AG
1 AATTGAAG
*
24069 -TTTGAAG
1 AATTGAAG
24076 AATTG-AG
1 AATTGAAG
24083 -ATTGAAG
1 AATTGAAG
*
24090 CATTGAA-
1 AATTGAAG
24097 ATATTG-A-
1 A-ATTGAAG
24104 AATTGAA-
1 AATTGAAG
*
24111 ACAGTGAAG
1 A-ATTGAAG
24120 AATTG-A-
1 AATTGAAG
*
24126 ATTTGAAG
1 AATTGAAG
*
24134 CATTGGAA-
1 AATT-GAAG
*
24142 TATTG-A-
1 AATTGAAG
24148 AATTGAA-
1 AATTGAAG
24155 ACATTGAAG
1 A-ATTGAAG
24164 AATTG-A-
1 AATTGAAG
*
24170 ATTTGAAG
1 AATTGAAG
24178 AATTG-AG
1 AATTGAAG
*
24185 -ATTGAAC
1 AATTGAAG
*
24192 CATTGAA-
1 AATTGAAG
24199 ATATTG-A-
1 A-ATTGAAG
24206 AATTGAA-
1 AATTGAAG
*
24213 ACAGTGAAG
1 A-ATTGAAG
24222 AATTG-A-
1 AATTGAAG
*
24228 AACTGAAG
1 AATTGAAG
*
24236 CATTGAA-
1 AATTGAAG
24243 ATATTG-A-
1 A-ATTGAAG
24250 AATTGAA-
1 AATTGAAG
24257 ACATTGAAG
1 A-ATTGAAG
24266 AATTG-A-
1 AATTGAAG
24272 AATTGAA-
1 AATTGAAG
24279 ACATTGAA-
1 A-ATTGAAG
*
24287 ATACTG-A-
1 A-ATTGAAG
24294 AATTGAAG
1 AATTGAAG
*
24302 CATTG-AG
1 AATTGAAG
24309 TAATTGAAG
1 -AATTGAAG
24318 AATTGAAG
1 AATTGAAG
* *
24326 AATTGGAT
1 AATTGAAG
24334 AATTGAAG
1 AATTGAAG
24342 AATTGAAG
1 AATTGAAG
* *
24350 CATTCG-AT
1 AATT-GAAG
24358 AATTGAAG
1 AATTGAAG
24366 AATTGAAG
1 AATTGAAG
24374 CAACAAATTGAAG
1 -----AATTGAAG
*
24387 TATTGAATG
1 AATTGAA-G
24396 -ATTGAAG
1 AATTGAAG
24403 AATTGAAG
1 AATTGAAG
24411 AA
1 AA
24413 AGAGACCGTT
Statistics
Matches: 387, Mismatches: 60, Indels: 120
0.68 0.11 0.21
Matches are distributed among these distances:
6 70 0.18
7 64 0.17
8 226 0.58
9 19 0.05
13 8 0.02
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.28
Consensus pattern (8 bp):
AATTGAAG
Found at i:24453 original size:16 final size:16
Alignment explanation
Indices: 24432--24462 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24422 TTTGAAATAA
*
24432 ATTGAAGCATTGAAGG
1 ATTGAAGAATTGAAGG
24448 ATTGAAGAATTGAAG
1 ATTGAAGAATTGAAG
24463 CTAATTGAAC
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:0.42, C:0.03, G:0.29, T:0.26
Consensus pattern (16 bp):
ATTGAAGAATTGAAGG
Found at i:30912 original size:52 final size:53
Alignment explanation
Indices: 30810--30925 Score: 180
Period size: 52 Copynumber: 2.2 Consensus size: 53
30800 GTTTGAATGT
* * *
30810 TTTGAAGACTTGATGGGAACTTTCCCACTTTTGAAAAGACCTAAATTGAACAC
1 TTTGAAAACTTAATGGGAACTTTCCCACATTTGAAAAGACCTAAATTGAACAC
* *
30863 TTTGAAAACTTAATGGGAACTTTTCCA-ATTTGAAAAGACCTAAATTGAACGC
1 TTTGAAAACTTAATGGGAACTTTCCCACATTTGAAAAGACCTAAATTGAACAC
30915 TTTGAAAACTT
1 TTTGAAAACTT
30926 TATGAAACTT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
52 34 0.59
53 24 0.41
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (53 bp):
TTTGAAAACTTAATGGGAACTTTCCCACATTTGAAAAGACCTAAATTGAACAC
Found at i:35360 original size:6 final size:6
Alignment explanation
Indices: 35349--35380 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
35339 ATTAATCTGC
35349 TTAGAT TTAGAT TTAGAT TTAGAT TTAGAT TT
1 TTAGAT TTAGAT TTAGAT TTAGAT TTAGAT TT
35381 GCTTTGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (6 bp):
TTAGAT
Found at i:35818 original size:17 final size:19
Alignment explanation
Indices: 35796--35831 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
35786 CCAATGTCTT
35796 CTAAACTAA-ATA-AATAA
1 CTAAACTAAGATAGAATAA
35813 CTAAACTAAGATAGAATAA
1 CTAAACTAAGATAGAATAA
35832 AGGCCCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.61, C:0.11, G:0.06, T:0.22
Consensus pattern (19 bp):
CTAAACTAAGATAGAATAA
Found at i:49741 original size:21 final size:21
Alignment explanation
Indices: 49715--49766 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
49705 GAAGAAGAAA
* **
49715 AAGAAGAAAGTGAGAACTAGG
1 AAGAAGAAAGTGAAAAAGAGG
*
49736 AAGAAGGAAGTGAAAAAGAGG
1 AAGAAGAAAGTGAAAAAGAGG
49757 AAGAAGAAAG
1 AAGAAGAAAG
49767 ACCTGCTGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.58, C:0.02, G:0.35, T:0.06
Consensus pattern (21 bp):
AAGAAGAAAGTGAAAAAGAGG
Found at i:49777 original size:18 final size:18
Alignment explanation
Indices: 49756--49798 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
49746 TGAAAAAGAG
* *
49756 GAAGAAGAAAGACCTGCT
1 GAAGAAGAAAAACCTGAT
*
49774 GAAGAAGAAAAATCTGAT
1 GAAGAAGAAAAACCTGAT
49792 GAAGAAG
1 GAAGAAG
49799 TTGATGAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.51, C:0.09, G:0.28, T:0.12
Consensus pattern (18 bp):
GAAGAAGAAAAACCTGAT
Found at i:69367 original size:7 final size:7
Alignment explanation
Indices: 69352--69383 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
69342 ACTAACTTAT
*
69352 AATAAAA
1 AATACAA
69359 AATACAA
1 AATACAA
69366 AATACAA
1 AATACAA
69373 AATACAA
1 AATACAA
69380 AATA
1 AATA
69384 ACTTTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (7 bp):
AATACAA
Found at i:69461 original size:17 final size:18
Alignment explanation
Indices: 69426--69462 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
69416 AAAAAATTTA
*
69426 AAAAATAAAAATAAGATT
1 AAAAATAAAAATAACATT
69444 AAAAATAAAAAT-ACATT
1 AAAAATAAAAATAACATT
69461 AA
1 AA
69463 TTACGTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (18 bp):
AAAAATAAAAATAACATT
Found at i:70045 original size:17 final size:19
Alignment explanation
Indices: 70026--70061 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
70016 TATTTTAATT
*
70026 AAAAA-TTTAGATATATTA
1 AAAAATTTTAAATATATTA
70044 AAAAATTTTAAATATATT
1 AAAAATTTTAAATATATT
70062 TCCTAAAGAC
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:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
AAAAATTTTAAATATATTA
Found at i:71998 original size:42 final size:43
Alignment explanation
Indices: 71951--72040 Score: 146
Period size: 42 Copynumber: 2.1 Consensus size: 43
71941 AAAGTTTCTC
* *
71951 AAACACAAAAGCAGTGGCTTAGATAACAAAAAGAAA-CCTTTG
1 AAACACAAAAACAATGGCTTAGATAACAAAAAGAAACCCTTTG
71993 AAACACAAAAACAATGGCTTAGATAACAAAAAGAAACCCTTTG
1 AAACACAAAAACAATGGCTTAGATAACAAAAAGAAACCCTTTG
*
72036 CAACA
1 AAACA
72041 GAAATCTTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 34 0.77
43 10 0.23
ACGTcount: A:0.52, C:0.19, G:0.13, T:0.16
Consensus pattern (43 bp):
AAACACAAAAACAATGGCTTAGATAACAAAAAGAAACCCTTTG
Found at i:72021 original size:21 final size:21
Alignment explanation
Indices: 71955--72024 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
71945 TTTCTCAAAC
* *
71955 ACAAAAGCAGTGGCTTAGATA
1 ACAAAAACAATGGCTTAGATA
* ** * *
71976 ACAAAAAGAA-ACCTTTGAAA
1 ACAAAAACAATGGCTTAGATA
71996 CACAAAAACAATGGCTTAGATA
1 -ACAAAAACAATGGCTTAGATA
72018 ACAAAAA
1 ACAAAAA
72025 GAAACCCTTT
Statistics
Matches: 35, Mismatches: 12, Indels: 4
0.69 0.24 0.08
Matches are distributed among these distances:
20 6 0.17
21 23 0.66
22 6 0.17
ACGTcount: A:0.54, C:0.16, G:0.14, T:0.16
Consensus pattern (21 bp):
ACAAAAACAATGGCTTAGATA
Found at i:81765 original size:123 final size:123
Alignment explanation
Indices: 81507--81740 Score: 301
Period size: 123 Copynumber: 1.9 Consensus size: 123
81497 CATAAAGTCT
* * *
81507 AAGGATAGGATCATCAAGGAAAGAAGAAATTCTTATCAAATGGTCAGAGAAGGGCAAGACACTCC
1 AAGGATAGGATTATCAACGAAAGAAGAAATTCTTATCAAATGGGCAGAGAAGGGCAAGACACTCC
* * * * * * *
81572 AAGTGATGATCAGTCAACCCATCAATAAAATTTTACTCATCATAGAGAACATAAACAT
66 AAGTGATGATCAATCAACCCAACAATAAAATTTAAATCATCAAACAGAACATAAACAG
* * *
81630 TAGGATAGGATTATCAACGAAAGAAGAAATTTTTATCAAATGGGGAGAG-AGAGGCAAGACACTC
1 AAGGATAGGATTATCAACGAAAGAAGAAATTCTTATCAAATGGGCAGAGAAG-GGCAAGACACTC
* *
81694 CAAGTGATGATCAATTAACCCAACAATTAAACTTTAAAT-ATCAAACA
65 CAAGTGATGATCAATCAACCCAACAA-TAAAATTTAAATCATCAAACA
81741 TGTAATAGAA
Statistics
Matches: 95, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
122 2 0.02
123 84 0.88
124 9 0.09
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.22
Consensus pattern (123 bp):
AAGGATAGGATTATCAACGAAAGAAGAAATTCTTATCAAATGGGCAGAGAAGGGCAAGACACTCC
AAGTGATGATCAATCAACCCAACAATAAAATTTAAATCATCAAACAGAACATAAACAG
Found at i:84134 original size:26 final size:26
Alignment explanation
Indices: 84104--84155 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
84094 AATGAATAAA
84104 CAACAAAAAAGAAGATAACTCAGTTT
1 CAACAAAAAAGAAGATAACTCAGTTT
84130 CAACAAAAAAGAAGATAACTCAGTTT
1 CAACAAAAAAGAAGATAACTCAGTTT
84156 TGACGTACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.19
Consensus pattern (26 bp):
CAACAAAAAAGAAGATAACTCAGTTT
Found at i:88105 original size:13 final size:14
Alignment explanation
Indices: 88079--88107 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
88069 AATACTGGAA
88079 AAACAATGAAAAAG
1 AAACAATGAAAAAG
88093 AAACAAT-AAAAAG
1 AAACAATGAAAAAG
88106 AA
1 AA
88108 GAAAGATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.76, C:0.07, G:0.10, T:0.07
Consensus pattern (14 bp):
AAACAATGAAAAAG
Found at i:92768 original size:7 final size:6
Alignment explanation
Indices: 92741--92765 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
92731 GGGGAATGGG
92741 AGAAAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA A
92766 AGATTTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:105028 original size:3 final size:3
Alignment explanation
Indices: 105020--105068 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
105010 TTATTAACAT
105020 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
105068 T
1 T
105069 GTGTCAATGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:108431 original size:25 final size:25
Alignment explanation
Indices: 108402--108485 Score: 95
Period size: 25 Copynumber: 3.5 Consensus size: 25
108392 GCAGGAGATT
108402 GACCTGTTCCTTACATTTGCAGCTG
1 GACCTGTTCCTTACATTTGCAGCTG
*
108427 GACCTGTTCCTTACATCCTGCA---G
1 GACCTGTTCCTTACAT-TTGCAGCTG
* * *
108450 GA-GTGGTGCTTACATTTGCAGCTG
1 GACCTGTTCCTTACATTTGCAGCTG
108474 GACCTGTTCCTT
1 GACCTGTTCCTT
108486 TAGGCCTGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
21 4 0.09
22 10 0.22
23 3 0.07
24 3 0.07
25 22 0.48
26 4 0.09
ACGTcount: A:0.15, C:0.27, G:0.23, T:0.35
Consensus pattern (25 bp):
GACCTGTTCCTTACATTTGCAGCTG
Found at i:109699 original size:19 final size:19
Alignment explanation
Indices: 109659--109696 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
109649 GATTTATCCT
109659 ATCTATCTGTTGAATTTGA
1 ATCTATCTGTTGAATTTGA
*
109678 ATCT-TCTGTTGGATTTGA
1 ATCTATCTGTTGAATTTGA
109696 A
1 A
109697 ATCCTATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47
Consensus pattern (19 bp):
ATCTATCTGTTGAATTTGA
Done.