Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold35
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: 4812169
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 17994 characters in sequence are not A, C, G, or T
File 16 of 30
Found at i:2597988 original size:31 final size:31
Alignment explanation
Indices: 2597953--2598019 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
2597943 TTAAATGACA
2597953 ACATGCTCATAACAAAAGAAATGACACAAGG
1 ACATGCTCATAACAAAAGAAATGACACAAGG
*
2597984 ACATGCTCATAATAAAAGAAATGACACAAGG
1 ACATGCTCATAACAAAAGAAATGACACAAGG
2598015 ACATG
1 ACATG
2598020 ATTCACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.51, C:0.18, G:0.16, T:0.15
Consensus pattern (31 bp):
ACATGCTCATAACAAAAGAAATGACACAAGG
Found at i:2600197 original size:1 final size:1
Alignment explanation
Indices: 2600193--2600269 Score: 64
Period size: 1 Copynumber: 77.0 Consensus size: 1
2600183 ATTCTTTTTC
* * * * * * * *
2600193 AAAAAAAAACAAAAAAACAAAAAACAAAAAAAACAAAAAAAAACAAACAAAATAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
**
2600258 GGAAAAAAAAAA
1 AAAAAAAAAAAA
2600270 GAACCTGCTT
Statistics
Matches: 58, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.87, C:0.08, G:0.04, T:0.01
Consensus pattern (1 bp):
A
Found at i:2600216 original size:15 final size:15
Alignment explanation
Indices: 2600196--2600244 Score: 73
Period size: 16 Copynumber: 3.3 Consensus size: 15
2600186 CTTTTTCAAA
2600196 AAAAAACAAAAAAAC
1 AAAAAACAAAAAAAC
2600211 AAAAAACAAAAAAAAC
1 AAAAAAC-AAAAAAAC
*
2600227 AAAAAA-AAACAAAC
1 AAAAAACAAAAAAAC
2600241 AAAA
1 AAAA
2600245 TAAAGAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
14 11 0.34
15 7 0.22
16 14 0.44
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAACAAAAAAAC
Found at i:2600230 original size:23 final size:23
Alignment explanation
Indices: 2600194--2600257 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
2600184 TTCTTTTTCA
*
2600194 AAAAAAAACAAAAAAACAAAAAAC
1 AAAAAAAACAAAAAAA-AACAAAC
2600218 AAAAAAAACAAAAAAAAACAAAC
1 AAAAAAAACAAAAAAAAACAAAC
* *
2600241 AAAATAAAGAAAAAAAA
1 AAAAAAAACAAAAAAAA
2600258 GGAAAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
23 21 0.57
24 16 0.43
ACGTcount: A:0.88, C:0.09, G:0.02, T:0.02
Consensus pattern (23 bp):
AAAAAAAACAAAAAAAAACAAAC
Found at i:2600269 original size:34 final size:34
Alignment explanation
Indices: 2600192--2600257 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
2600182 CATTCTTTTT
2600192 CAAAAAAAAACAAAAAAACAAAAAACAAAAAAAA
1 CAAAAAAAAACAAAAAAACAAAAAACAAAAAAAA
* *
2600226 CAAAAAAAAACAAACAAAATAAAGAA-AAAAAA
1 CAAAAAAAAACAAA-AAAACAAAAAACAAAAAA
2600258 GGAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 20 0.69
35 9 0.31
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.02
Consensus pattern (34 bp):
CAAAAAAAAACAAAAAAACAAAAAACAAAAAAAA
Found at i:2601534 original size:60 final size:61
Alignment explanation
Indices: 2601361--2601577 Score: 229
Period size: 60 Copynumber: 3.7 Consensus size: 61
2601351 GCCTTTCAGG
* * *
2601361 GCCCACACAAGTTGGTGGCACCTT-TCAGTCCTCAAAGAGC-AG-GA---T-GCCTTTTAAA
1 GCCCACACAAGCTGGTGGCACCTTCT-AGTCCTCAAAGAGCAAGACACCTTCTCCTTTTAAA
* * * * * * *
2601416 GCCCACAC-GGGTCAGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAA
1 GCCCACACAAGCT-GGTGGCACCTTCTAGTCCTCAAAGAGCAAGACACCTTCTCCTTTTAAA
*
2601477 GCCCACATAAGCTGGTGGCACCTT-TAGTCCTCAAAGAGCAAGACACCTTCTCCTTTTAAA
1 GCCCACACAAGCTGGTGGCACCTTCTAGTCCTCAAAGAGCAAGACACCTTCTCCTTTTAAA
*
2601537 GCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCA
1 GCCCACACAAGCTGGTGGCACCTT-CTAGTCCTCAAAGAGCA
2601578 GGACGCTCTC
Statistics
Matches: 133, Mismatches: 18, Indels: 16
0.80 0.11 0.10
Matches are distributed among these distances:
54 2 0.02
55 32 0.24
56 2 0.02
59 3 0.02
60 51 0.38
61 41 0.31
62 2 0.02
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.24
Consensus pattern (61 bp):
GCCCACACAAGCTGGTGGCACCTTCTAGTCCTCAAAGAGCAAGACACCTTCTCCTTTTAAA
Found at i:2601570 original size:121 final size:110
Alignment explanation
Indices: 2601327--2601583 Score: 286
Period size: 121 Copynumber: 2.2 Consensus size: 110
2601317 CTCCTTTCAC
** *
2601327 CCTT-TAGTCCTCAAAGAGCAGGACGCCTTTCAGGGCCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTCAGTC
* **
2601391 CTCAAAGAGCAGGATGCCTTTTAAAGCCCACACGGGTCAGTGGCA
66 CTCAAAGAGCAGCATGCCTTTTAAAGCCCACACAAGTCAGTGGCA
*
2601436 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACATAAGCTGGTGGCACCTT
1 CCTTCTAGTCCTCAAAGAGCAGGACGCC--TTTC----AAAGCCCACACAAGCTGGTGGCACCTT
* **
2601501 T-AGTCCTCAAAGAGCAAGACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
60 TCAGTCCTCAAAGAGC-AG-CA---T-GCCTTTTAAAGCCCACACAAGTCAGTGGCA
2601557 -CTTCCTAGTCCTCAAAGAGCAGGACGC
1 CCTT-CTAGTCCTCAAAGAGCAGGACGC
2601584 TCTCTCCTTT
Statistics
Matches: 124, Mismatches: 10, Indels: 16
0.83 0.07 0.11
Matches are distributed among these distances:
109 4 0.03
110 23 0.19
112 4 0.03
115 14 0.11
116 26 0.21
117 1 0.01
120 4 0.03
121 48 0.39
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (110 bp):
CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTCAGTC
CTCAAAGAGCAGCATGCCTTTTAAAGCCCACACAAGTCAGTGGCA
Found at i:2601593 original size:61 final size:61
Alignment explanation
Indices: 2601327--2601593 Score: 271
Period size: 55 Copynumber: 4.6 Consensus size: 61
2601317 CTCCTTTCAC
**
2601327 CCTT-TAGTCCTCAAAGAGCAGGACGCCTT-T-C----AGGGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* ** **
2601381 CCTT-TCAGTCCTCAAAGAGCAGGA-----T-GCCTTTTAAAGCCCACACGGGTCAGTGGCA
1 CCTTCT-AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
2601436 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACATAAGCTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
2601497 CCTT-TAGTCCTCAAAGAGCAAGACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
2601557 -CTTCCTAGTCCTCAAAGAGCAGGACG-CTCTCTCCTTT
1 CCTT-CTAGTCCTCAAAGAGCAGGACGCCT-TCTCCTTT
2601594 CTCCTTTTTG
Statistics
Matches: 174, Mismatches: 23, Indels: 25
0.78 0.10 0.11
Matches are distributed among these distances:
50 1 0.01
51 1 0.01
54 5 0.03
55 57 0.33
56 1 0.01
59 3 0.02
60 53 0.30
61 53 0.30
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.25
Consensus pattern (61 bp):
CCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:2601759 original size:215 final size:216
Alignment explanation
Indices: 2601388--2601799 Score: 589
Period size: 215 Copynumber: 1.9 Consensus size: 216
2601378 GCACCTTTCA
* * *
2601388 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACGGGTCAGTGGCACCTTCTAGTCCTCAAAG
1 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACGGCTCAGTGGAACCTTCTAATCCTCAAAG
* * *
2601453 AGCAGGACGCCTTTTTCTTTTAAAGCCCACATAAGCTGGTGGCACCTTTAGTCCTCAAAGAGCAA
66 AGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTAGTCCTCAAAGAGCAA
2601518 GACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTCCTAGTCCTCAAAGAGCAGGAC
131 GACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCTAGTCCTCAAAGAGCAGGAC
2601582 GCTCTCTCCTTTCTCCTTTTT
196 GCTCTCTCCTTTCTCCTTTTT
* *
2601603 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACATGCT-GGTGGAACCTTC-AATCCTCAAA
1 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACAC-GGCTCAGTGGAACCTTCTAATCCTCAAA
* * * * *
2601666 GAGTAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCTTCAAAGAGT
65 GAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTT-AGTCCTCAAAGAGC
** * * * * *
2601731 AAGATGCTTTCT-TTTTGTAAAGCCCACACATGTTGGTGGCACTTTTCTAGTCCTCAAAGAGTAG
129 AAGACACCTTCTCCTTT-TAAAGCCCACACAAGTTGGTGGCACTTTCCTAGTCCTCAAAGAGCAG
2601795 GACGC
193 GACGC
2601800 CTTTTCCTTT
Statistics
Matches: 173, Mismatches: 20, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
214 56 0.32
215 91 0.53
216 26 0.15
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (216 bp):
GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACGGCTCAGTGGAACCTTCTAATCCTCAAAG
AGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTAGTCCTCAAAGAGCAA
GACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCTAGTCCTCAAAGAGCAGGAC
GCTCTCTCCTTTCTCCTTTTT
Found at i:2602036 original size:56 final size:55
Alignment explanation
Indices: 2601603--2602137 Score: 595
Period size: 55 Copynumber: 9.4 Consensus size: 55
2601593 TCTCCTTTTT
* * * *
2601603 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACATGCTGGTGGAAC-CTTCA
1 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCA
* * *
2601657 ATCCTCAAAGAGTAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCA
1 GTCCTCAAAGAGCAGGA-----T-GCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCA
* * * *
2601718 GTCTTCAAAGAGTAAGATGCTTTCTTTTTGTAAAGCCCACACATGTTGGTGGCACTTTTCTA
1 GTCCTCAAAGAGCAGGATGC---C--TTT-TAAAGCCCACACAAGTTGGTGGCACTTTTC-A
* * *
2601780 GTCCTCAAAGAGTAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCA
1 GTCCTCAAAGAGCAGGATGCC---T--TTT-AAAGCCCACACAAGTTGGTGGCACTTTTCA
* * * *
2601841 ATCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCA
1 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCA
* *
2601896 GTCCTCAAAGAGCAGGATGTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCA
1 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCA
* * * *
2601951 GTCCTCAAAGAGCACGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTTTA
1 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTTCA
* *
2602007 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTTTA
1 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTTCA
* * **
2602063 GTCCTCAAAGAGTAAGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCA
1 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCA
*
2602118 GTCCTTAAAGAGCAGGATGC
1 GTCCTCAAAGAGCAGGATGC
2602138 TCGCTTTTTT
Statistics
Matches: 419, Mismatches: 43, Indels: 37
0.84 0.09 0.07
Matches are distributed among these distances:
54 15 0.04
55 145 0.35
56 107 0.26
58 2 0.00
59 2 0.00
60 33 0.08
61 68 0.16
62 47 0.11
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (55 bp):
GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCA
Found at i:2602059 original size:28 final size:28
Alignment explanation
Indices: 2601972--2602059 Score: 72
Period size: 28 Copynumber: 3.1 Consensus size: 28
2601962 GCACGACGCC
2601972 TTTTAAAGCCCACACAAGTTGGTGGCAT
1 TTTTAAAGCCCACACAAGTTGGTGGCAT
** * * * ** *
2602000 TTTTTTAGTCCTCAAAGAGCAGGAT-GC-C
1 TTTTAAAGCCCACACA-AGTTGG-TGGCAT
2602028 TTTTAAAGCCCACACAAGTTGGTGGCAT
1 TTTTAAAGCCCACACAAGTTGGTGGCAT
2602056 TTTT
1 TTTT
2602060 TTAGTCCTCA
Statistics
Matches: 40, Mismatches: 16, Indels: 8
0.62 0.25 0.12
Matches are distributed among these distances:
26 1 0.03
27 6 0.15
28 26 0.65
29 6 0.15
30 1 0.03
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (28 bp):
TTTTAAAGCCCACACAAGTTGGTGGCAT
Found at i:2602483 original size:13 final size:13
Alignment explanation
Indices: 2602465--2602489 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2602455 TTCAACGATT
2602465 TGTATCGATACAA
1 TGTATCGATACAA
2602478 TGTATCGATACA
1 TGTATCGATACA
2602490 TAAGTTTTGT
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):
TGTATCGATACAA
Found at i:2602579 original size:13 final size:13
Alignment explanation
Indices: 2602561--2602585 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2602551 ATTACTCAAA
2602561 TGTATCGATACAT
1 TGTATCGATACAT
2602574 TGTATCGATACA
1 TGTATCGATACA
2602586 CTGATCTTTG
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:2602638 original size:52 final size:52
Alignment explanation
Indices: 2602594--2602722 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
2602584 CACTGATCTT
* *
2602594 TGTATCGATACATGCAGGCAAATTTGCTCAGATGTATTGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
2602646 TGTATCGATACGTACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
2602698 TGTATCGATACATGTAGACAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2602723 TCACATTTTG
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:2605944 original size:42 final size:42
Alignment explanation
Indices: 2605885--2606078 Score: 203
Period size: 42 Copynumber: 4.5 Consensus size: 42
2605875 GTGGTACTTT
2605885 TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTCTCC
1 TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTCTCC
* * ** * *
2605927 TTTGTCCTCAAAGAGCAGGACACACTTCATTCCCTTATTTTCTCT
1 TTTGTCCTCAAAGAGCAGGACGCACTTTATT---TTCCTCTCTCC
* * *
2605972 TTTGTTCTCAAAGAGCAGGACGCACTTTATTTTCCTCTTTCT
1 TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTCTCC
* * *
2606014 TTTGTCCTCAAAGAGCAGGACGCA-TTTCGTTTTCCTTTTTTCC
1 TTTGTCCTCAAAGAGCAGGACGCACTTT-ATTTTCC-TCTCTCC
*
2606057 TTTATCCTCGAAA-AGCAGGACG
1 TTTGTCCTC-AAAGAGCAGGACG
2606079 TACTCTTTTT
Statistics
Matches: 128, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
41 3 0.02
42 65 0.51
43 22 0.17
44 3 0.02
45 35 0.27
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.38
Consensus pattern (42 bp):
TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTCTCC
Found at i:2606055 original size:87 final size:86
Alignment explanation
Indices: 2605884--2606078 Score: 270
Period size: 87 Copynumber: 2.3 Consensus size: 86
2605874 GGTGGTACTT
2605884 TTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTCTCCTTTGTCCTCAAAGAGCAGGACA
1 TTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTCTCCTTTGTCCTCAAAGAGCAGGACA
2605949 CACTTCATTCCCTTATTTTCTC
66 CACTTCATTCCCTTATTTTC-C
* * * *
2605971 TTTTGTTCTCAAAGAGCAGGACGCACTTTATTTTCCTCTTTCTTTTGTCCTCAAAGAGCAGGACG
1 TTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTCTCCTTTGTCCTCAAAGAGCAGGACA
* * *
2606036 CATTTCGTTTTCCTT-TTTTCC
66 CACTTC-ATTCCCTTATTTTCC
*
2606057 -TTTATCCTCGAAA-AGCAGGACG
1 TTTTGTCCTC-AAAGAGCAGGACG
2606079 TACTCTTTTT
Statistics
Matches: 97, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
85 16 0.16
86 4 0.04
87 71 0.73
88 6 0.06
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.38
Consensus pattern (86 bp):
TTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTCTCCTTTGTCCTCAAAGAGCAGGACA
CACTTCATTCCCTTATTTTCC
Found at i:2606824 original size:21 final size:21
Alignment explanation
Indices: 2606800--2606875 Score: 152
Period size: 21 Copynumber: 3.6 Consensus size: 21
2606790 TTCAATAATT
2606800 TGTATCGATACATTCAGTAAA
1 TGTATCGATACATTCAGTAAA
2606821 TGTATCGATACATTCAGTAAA
1 TGTATCGATACATTCAGTAAA
2606842 TGTATCGATACATTCAGTAAA
1 TGTATCGATACATTCAGTAAA
2606863 TGTATCGATACAT
1 TGTATCGATACAT
2606876 AAGTTTTGTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (21 bp):
TGTATCGATACATTCAGTAAA
Found at i:2606900 original size:13 final size:13
Alignment explanation
Indices: 2606882--2606961 Score: 79
Period size: 13 Copynumber: 5.5 Consensus size: 13
2606872 ACATAAGTTT
2606882 TGTATCGATACAA
1 TGTATCGATACAA
2606895 TGTATCGATACATAA
1 TGTATCGATAC--AA
2606910 GTTGTATCGATACAA
1 --TGTATCGATACAA
2606925 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
2606940 GTTGCATCGATACAA
1 --TGTATCGATACAA
2606955 TGTATCG
1 TGTATCG
2606962 TCACGAAGCT
Statistics
Matches: 57, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
13 28 0.49
15 8 0.14
17 21 0.37
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2606917 original size:17 final size:17
Alignment explanation
Indices: 2606863--2606953 Score: 99
Period size: 17 Copynumber: 5.7 Consensus size: 17
2606853 ATTCAGTAAA
2606863 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG--T
2606882 TGTATCGATAC--AA--
1 TGTATCGATACATAAGT
2606895 TGTATCGATACATAAGT
1 TGTATCGATACATAAGT
2606912 TGTATCGATAC--AA--
1 TGTATCGATACATAAGT
2606925 TGTATCGATACATAAGT
1 TGTATCGATACATAAGT
*
2606942 TGCATCGATACA
1 TGTATCGATACA
2606954 ATGTATCGTC
Statistics
Matches: 63, Mismatches: 1, Indels: 18
0.77 0.01 0.22
Matches are distributed among these distances:
13 22 0.35
15 6 0.10
17 24 0.38
19 11 0.17
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.34
Consensus pattern (17 bp):
TGTATCGATACATAAGT
Found at i:2606917 original size:30 final size:30
Alignment explanation
Indices: 2606861--2606961 Score: 175
Period size: 30 Copynumber: 3.3 Consensus size: 30
2606851 ACATTCAGTA
2606861 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAG--TTGTATCGATAC
2606893 AATGTATCGATACATAAGTTGTATCGATAC
1 AATGTATCGATACATAAGTTGTATCGATAC
*
2606923 AATGTATCGATACATAAGTTGCATCGATAC
1 AATGTATCGATACATAAGTTGTATCGATAC
2606953 AATGTATCG
1 AATGTATCG
2606962 TCACGAAGCT
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
30 50 0.74
32 18 0.26
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Consensus pattern (30 bp):
AATGTATCGATACATAAGTTGTATCGATAC
Found at i:2607004 original size:21 final size:21
Alignment explanation
Indices: 2606978--2607019 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2606968 AGCTACTGCC
2606978 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
*
2606999 AAGGAAATGTATCGATGCATT
1 AAGGAAATGTATCGATACATT
2607020 GTATCGATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:2609463 original size:52 final size:51
Alignment explanation
Indices: 2609396--2609793 Score: 218
Period size: 52 Copynumber: 7.6 Consensus size: 51
2609386 TTAAGTTTCT
*
2609396 CAATTGTT-CATAATCGGGGATACTCCAACCTCGGTTTTATTTTCAAAACAC
1 CAATT-TTCCATAATCGGGGATACTCCAACCTCGGTTTTATTTCCAAAACAC
* *
2609447 CAATTTTCCTTTAATCGGGGATACTCCAA-CTCCGATTTTATTTCCAAAAACAC
1 CAATTTTCC-ATAATCGGGGATACTCCAACCT-CGGTTTTATTTCC-AAAACAC
* * ** * ** ***** * *
2609500 CAATTTTTCACAATCGATGATACTCCAATCTCATTATTTCATCGGGGATACTC
1 CAATTTTCCATAATCGGGGATACTCCAACCTCGGT-TTT-ATTTCCAAAACAC
* * * * * * * * *
2609553 CAACCCCGTTACC-T-CTGAGGGGATACTCCAACCCCAGCTTTATTTCCAAAATAT
1 CAA----TTTTCCATAAT-CGGGGATACTCCAACCTCGGTTTTATTTCCAAAACAC
** * *
2609607 TGA-TTTCTCATAATC-GGGATACTCCAACCCCGGTTTTATTTCTAAAACAC
1 CAATTTTC-CATAATCGGGGATACTCCAACCTCGGTTTTATTTCCAAAACAC
* * * *
2609657 TAATTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATCTT-TAAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACCTCGGTTTTAT-TTCCAAAACAC
** * *
2609708 CAATTTTCTTTTAATCGAGGATACTCCAA-CTCCGATTTTATTTCCAAAAACAC
1 CAATTTTC-CATAATCGGGGATACTCCAACCT-CGGTTTTATTTCC-AAAACAC
* * * *
2609761 CAATTTTTCACAATCGAGGATACTCTAACCTCG
1 CAATTTTCCATAATCGGGGATACTCCAACCTCG
2609794 TTATTTCATC
Statistics
Matches: 261, Mismatches: 63, Indels: 45
0.71 0.17 0.12
Matches are distributed among these distances:
49 3 0.01
50 41 0.16
51 55 0.21
52 91 0.35
53 43 0.16
54 7 0.03
55 4 0.02
56 14 0.05
57 3 0.01
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (51 bp):
CAATTTTCCATAATCGGGGATACTCCAACCTCGGTTTTATTTCCAAAACAC
Found at i:2609631 original size:50 final size:51
Alignment explanation
Indices: 2609571--2609790 Score: 178
Period size: 51 Copynumber: 4.3 Consensus size: 51
2609561 TTACCTCTGA
* * * *
2609571 GGGGATACTCCAACCCCAGCTTTATTTCCAAAATATTGA-TTTCTCATAATC
1 GGGGATACTCCAACCCCAGCTTTATTTCCAAAACACTAATTTTC-CACAATC
* * *
2609622 -GGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTCCACAATC
1 GGGGATACTCCAACCCCAGCTTTATTTCCAAAACACTAATTTTCCACAATC
* * * * ***
2609672 GGGGATACTCCAACCCCGGTTTTATCTT-TAAAACACCAATTTTCTTTTAATC
1 GGGGATACTCCAACCCCAGCTTTAT-TTCCAAAACACTAATTTTC-CACAATC
* * * * *
2609724 GAGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCAG-CTTTATTTCC-AAAACACTAATTTTCCACAATC
* *
2609776 GAGGATACTCTAACC
1 GGGGATACTCCAACC
2609791 TCGTTATTTC
Statistics
Matches: 142, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
50 38 0.27
51 46 0.32
52 44 0.31
53 14 0.10
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCAGCTTTATTTCCAAAACACTAATTTTCCACAATC
Found at i:2609687 original size:51 final size:52
Alignment explanation
Indices: 2609571--2609790 Score: 225
Period size: 52 Copynumber: 4.3 Consensus size: 52
2609561 TTACCTCTGA
* * * * *** *
2609571 GGGGATACTCCAACCCCAGCTTTATTTCCAAAATATTGA-TTTCTCATAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTCTCACAATC
*
2609622 -GGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTC-CACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTCTCACAATC
***
2609672 GGGGATACTCCAACCCCGGTTTTATCTT-TAAAACACCAATTTTCTTTTAATC
1 GGGGATACTCCAACCCCGGTTTTAT-TTCTAAAACACCAATTTTCTCACAATC
* * * *
2609724 GAGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTT-TCACAATC
1 GGGGATACTCCAACCCCGGTTTTATTT-CTAAAACACCAATTTTCTCACAATC
* *
2609776 GAGGATACTCTAACC
1 GGGGATACTCCAACC
2609791 TCGTTATTTC
Statistics
Matches: 143, Mismatches: 20, Indels: 11
0.82 0.11 0.06
Matches are distributed among these distances:
50 38 0.27
51 45 0.31
52 46 0.32
53 14 0.10
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.32
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTCTCACAATC
Found at i:2609871 original size:261 final size:262
Alignment explanation
Indices: 2609407--2609900 Score: 859
Period size: 261 Copynumber: 1.9 Consensus size: 262
2609397 AATTGTTCAT
* *
2609407 AATCGGGGATACTCCAACCTCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
1 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGAGGATACT
* *
2609472 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGATGATACTCCAATCTCATTAT
66 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCATTAT
*
2609537 TTCATCGGGGATACTCCAACCCCGTTACCTCTGAGGGGATACTCCAACCCCAGCTTTATTTCCAA
131 TTCATCGGGGATACTCCAACCCCGTTACCTCTGAGGGGATACTCCAACCCCAGCTTTATTCCCAA
2609602 AATATTGATTTCTCATAA-TCGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTCC
196 AATATTGATTTCTCATAATTCGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTCC
2609666 AC
261 AC
*
2609668 AATCGGGGATACTCCAACCCCGGTTTTATCTTT-AAAACACCAATTTTCTTTTAATCGAGGATAC
1 AATCGGGGATACTCCAACCCCGGTTTTAT-TTTCAAAACACCAATTTTCCTTTAATCGAGGATAC
* *
2609732 TCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCTAACCTCGTTA
65 TCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCATTA
*
2609797 TTTCATCGGGGATACTCCAACCCCGTTACCT-TCGAGGGGATACTCCAACCCCGGCTTTATTCCC
130 TTTCATCGGGGATACTCCAACCCCGTTACCTCT-GAGGGGATACTCCAACCCCAGCTTTATTCCC
*
2609861 AAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
194 AAAATATTGATTTCTCATAATTCGGGATACTCCAACCCCG
2609901 TTATTTTCGA
Statistics
Matches: 220, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
260 1 0.00
261 198 0.90
262 21 0.10
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.32
Consensus pattern (262 bp):
AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGAGGATACT
CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCATTAT
TTCATCGGGGATACTCCAACCCCGTTACCTCTGAGGGGATACTCCAACCCCAGCTTTATTCCCAA
AATATTGATTTCTCATAATTCGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTCC
AC
Found at i:2609894 original size:79 final size:79
Alignment explanation
Indices: 2609803--2610037 Score: 287
Period size: 79 Copynumber: 3.0 Consensus size: 79
2609793 GTTATTTCAT
** *
2609803 CGGGGATACTCCAACCCCGTTACCTTCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTCCCAAAATAT
*
2609868 TGATTTCTCATAAT
66 TGATTTCTCATAAC
* * * * *
2609882 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTATTTCC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTCCCAAAAT-A
* * *
2609946 TCGATTTTTCACAAC
65 TTGATTTCTCATAAC
*
2609961 CGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCC-GTTATTA-TCTCCAAAAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT-TTATTC-CCAAAAT
*
2610024 ATTAAATTTCTCAT
64 ATT-GATTTCTCAT
2610038 CGAGAAATAT
Statistics
Matches: 129, Mismatches: 22, Indels: 9
0.81 0.14 0.06
Matches are distributed among these distances:
78 6 0.05
79 113 0.88
80 10 0.08
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTCCCAAAATAT
TGATTTCTCATAAC
Found at i:2612086 original size:4 final size:4
Alignment explanation
Indices: 2612077--2612109 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
2612067 TATTTTGAGG
*
2612077 TATT TATT TATT TATT TATT TATT GATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT T
2612110 GTTTTGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:2612838 original size:13 final size:13
Alignment explanation
Indices: 2612820--2612845 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2612810 TACACCAAGT
2612820 ATGTATCGATACA
1 ATGTATCGATACA
2612833 ATGTATCGATACA
1 ATGTATCGATACA
2612846 CCAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2612864 original size:34 final size:32
Alignment explanation
Indices: 2612802--2612866 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
2612792 TAGCCAAACT
**
2612802 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
2612834 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
2612867 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:2615104 original size:22 final size:21
Alignment explanation
Indices: 2615077--2615128 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
2615067 TTGTAAGTTG
2615077 AAATAAAAAATTTAGCTAATG-A
1 AAATAAAAAA-TTAGCTAA-GAA
**
2615099 AAATAATGAATTAGCTAAGAA
1 AAATAAAAAATTAGCTAAGAA
2615120 AAATAAAAA
1 AAATAAAAA
2615129 CTTGCATGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 16 0.64
22 8 0.32
ACGTcount: A:0.63, C:0.04, G:0.10, T:0.23
Consensus pattern (21 bp):
AAATAAAAAATTAGCTAAGAA
Found at i:2619030 original size:13 final size:13
Alignment explanation
Indices: 2619012--2619050 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2619002 ACATCTTTCT
2619012 TTGTATCGATACA
1 TTGTATCGATACA
2619025 TTGTATCGATACA
1 TTGTATCGATACA
*
2619038 CTGTATCGATACA
1 TTGTATCGATACA
2619051 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2621493 original size:20 final size:20
Alignment explanation
Indices: 2621470--2621523 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
2621460 ACAATTCAAA
2621470 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2621490 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2621510 GTATCGATACATGT
1 GTATCGATACATGT
2621524 CATTGGGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2621589 original size:13 final size:13
Alignment explanation
Indices: 2621571--2621596 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2621561 TACACCAAGT
2621571 ATGTATCGATACA
1 ATGTATCGATACA
2621584 ATGTATCGATACA
1 ATGTATCGATACA
2621597 CCAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2621615 original size:34 final size:32
Alignment explanation
Indices: 2621553--2621617 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
2621543 TAGCCAAACT
**
2621553 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
2621585 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
2621618 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:2632366 original size:1 final size:1
Alignment explanation
Indices: 2632360--2632441 Score: 74
Period size: 1 Copynumber: 82.0 Consensus size: 1
2632350 CTTCTCTTCT
* * * ** * * *
2632360 AAAAAAAAAACAAAAACAAAAACAAAAGCAAAAAAAAAAAAACAAAAAAAAACAAAAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
**
2632425 AAAAAGGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAA
2632442 CTTGCTTAAC
Statistics
Matches: 64, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.88, C:0.09, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:2632393 original size:19 final size:19
Alignment explanation
Indices: 2632362--2632442 Score: 99
Period size: 19 Copynumber: 4.0 Consensus size: 19
2632352 TCTCTTCTAA
2632362 AAAAAAAACAAAAACAAAAAC
1 AAAAAAAA-AAAAA-AAAAAC
*
2632383 AAAAGCAAAAAAAAAAAAAC
1 AAAA-AAAAAAAAAAAAAAC
*
2632403 AAAAAAAAACAAAAAAAAC
1 AAAAAAAAAAAAAAAAAAC
2632422 AAAAAAAAGGAAAAAAAAAAC
1 AAAAAAAA--AAAAAAAAAAC
2632443 TTGCTTAACC
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
19 21 0.40
20 10 0.19
21 19 0.36
22 3 0.06
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAAAAC
Found at i:2632394 original size:20 final size:18
Alignment explanation
Indices: 2632363--2632440 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 18
2632353 CTCTTCTAAA
2632363 AAAAAAACAAAAACAAAAAC
1 AAAAAAA-AAAAA-AAAAAC
2632383 AAAAGCAAAAAAAAAAAAAC
1 AAAA--AAAAAAAAAAAAAC
2632403 AAAAAAAAACAAAAAAAAC
1 AAAAAAAAA-AAAAAAAAC
2632422 AAAAAAAAGGAAAAAAAAA
1 AAAAAAAA--AAAAAAAAA
2632441 ACTTGCTTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.09
19 17 0.32
20 22 0.42
21 6 0.11
22 3 0.06
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAAAC
Found at i:2632394 original size:30 final size:27
Alignment explanation
Indices: 2632360--2632442 Score: 94
Period size: 30 Copynumber: 2.9 Consensus size: 27
2632350 CTTCTCTTCT
* *
2632360 AAAAAAAAAACAAAAACAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAACAAAA
2632387 GCAAAAAAAAAAAAACAAAAAAAAACAAAA
1 --AAAAAAAAAAAAA-AAAAAAAAACAAAA
2632417 AAAACAAAAAAAAGGAAAAAAAAAAC
1 AAAA-AAAAAAAA--AAAAAAAAAAC
2632443 TTGCTTAACC
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
28 4 0.08
29 20 0.42
30 23 0.48
31 1 0.02
ACGTcount: A:0.87, C:0.10, G:0.04, T:0.00
Consensus pattern (27 bp):
AAAAAAAAAAAAAAAAAAAAAACAAAA
Found at i:2632400 original size:26 final size:25
Alignment explanation
Indices: 2632362--2632426 Score: 105
Period size: 26 Copynumber: 2.6 Consensus size: 25
2632352 TCTCTTCTAA
2632362 AAAAAAAACAAAAACAAAAACAAAAGC
1 AAAAAAAACAAAAACAAAAA-AAAA-C
2632389 AAAAAAAA-AAAAACAAAAAAAAAC
1 AAAAAAAACAAAAACAAAAAAAAAC
2632413 AAAAAAAACAAAAA
1 AAAAAAAACAAAAA
2632427 AAAGGAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
24 9 0.24
25 9 0.24
26 11 0.30
27 8 0.22
ACGTcount: A:0.88, C:0.11, G:0.02, T:0.00
Consensus pattern (25 bp):
AAAAAAAACAAAAACAAAAAAAAAC
Found at i:2633579 original size:55 final size:54
Alignment explanation
Indices: 2633496--2633752 Score: 255
Period size: 55 Copynumber: 4.5 Consensus size: 54
2633486 CTCCTTTCAC
**
2633496 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAGGGCCCACACAAGTTGGTGGCA
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * **
2633550 CCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAGGTCAGTGGCA
1 CCTTT-AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
2633605 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACATAAGCTGGTGGCA
1 CCTT-TAGTCCTCAAAGAGCAGGACGCC--TTTC----AAAGCCCACACAAGTTGGTGGCA
* *
2633666 CCTTTAGTCCTCAAAGAGCAAGACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTT-T-C----AAAGCCCACACAAGTTGGTGGCA
*
2633726 -CTTCCTAGTCCTCATAGAGCAGGACGC
1 CCTT--TAGTCCTCAAAGAGCAGGACGC
2633753 TCTCTCCTTT
Statistics
Matches: 170, Mismatches: 21, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
54 5 0.03
55 67 0.39
56 1 0.01
57 3 0.02
58 2 0.01
59 4 0.02
60 47 0.28
61 41 0.24
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.24
Consensus pattern (54 bp):
CCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:2633703 original size:60 final size:60
Alignment explanation
Indices: 2633530--2633746 Score: 243
Period size: 60 Copynumber: 3.7 Consensus size: 60
2633520 GCCTTTCAGG
* *
2633530 GCCCACACAAGTTGGTGGCACCTT-TCAGTCCTCAAAGAGC-AG-GA---TGCCTTTTAAA
1 GCCCACACAAGTTGGTGGCACCTTCT-AGTCCTCAAAGAGCAAGACACCTTTCCTTTTAAA
* ** * * *
2633585 GCCCACACAGGTCAGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAA
1 GCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAAGACACC-TTTCCTTTTAAA
* *
2633646 GCCCACATAAGCTGGTGGCACCTT-TAGTCCTCAAAGAGCAAGACACCTTCTCCTTTTAAA
1 GCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAAGACACCTT-TCCTTTTAAA
*
2633706 GCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCATAGAGCA
1 GCCCACACAAGTTGGTGGCACCTT-CTAGTCCTCAAAGAGCA
2633747 GGACGCTCTC
Statistics
Matches: 133, Mismatches: 19, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
55 35 0.26
56 2 0.02
59 5 0.04
60 48 0.36
61 43 0.32
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.24
Consensus pattern (60 bp):
GCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAAGACACCTTTCCTTTTAAA
Found at i:2633739 original size:121 final size:110
Alignment explanation
Indices: 2633496--2633752 Score: 286
Period size: 121 Copynumber: 2.2 Consensus size: 110
2633486 CTCCTTTCAC
** *
2633496 CCTT-TAGTCCTCAAAGAGCAGGACGCCTTTCAGGGCCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTCAGTC
* *
2633560 CTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAGGTCAGTGGCA
66 CTCAAAGAGCAGCATGCCTTTTAAAGCCCACACAAGTCAGTGGCA
*
2633605 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACATAAGCTGGTGGCACCTT
1 CCTTCTAGTCCTCAAAGAGCAGGACGCC--TTTC----AAAGCCCACACAAGCTGGTGGCACCTT
* **
2633670 T-AGTCCTCAAAGAGCAAGACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
60 TCAGTCCTCAAAGAGC-AG-CA---T-GCCTTTTAAAGCCCACACAAGTCAGTGGCA
*
2633726 -CTTCCTAGTCCTCATAGAGCAGGACGC
1 CCTT-CTAGTCCTCAAAGAGCAGGACGC
2633753 TCTCTCCTTT
Statistics
Matches: 124, Mismatches: 10, Indels: 16
0.83 0.07 0.11
Matches are distributed among these distances:
109 4 0.03
110 23 0.19
112 4 0.03
115 14 0.11
116 26 0.21
117 1 0.01
120 4 0.03
121 48 0.39
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.24
Consensus pattern (110 bp):
CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTCAGTC
CTCAAAGAGCAGCATGCCTTTTAAAGCCCACACAAGTCAGTGGCA
Found at i:2633928 original size:215 final size:216
Alignment explanation
Indices: 2633557--2633968 Score: 589
Period size: 215 Copynumber: 1.9 Consensus size: 216
2633547 GCACCTTTCA
* * * *
2633557 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAGGTCAGTGGCACCTTCTAGTCCTCAAAG
1 GTCCTCAAAGAACAGGATGCCTTTTAAAGCCCACACAGCTCAGTGGAACCTTCTAATCCTCAAAG
* * *
2633622 AGCAGGACGCCTTTTTCTTTTAAAGCCCACATAAGCTGGTGGCACCTTTAGTCCTCAAAGAGCAA
66 AGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTAGTCCTCAAAGAGCAA
*
2633687 GACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTCCTAGTCCTCATAGAGCAGGAC
131 GACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCTAGTCCTCAAAGAGCAGGAC
2633751 GCTCTCTCCTTTCGCCTTTTT
196 GCTCTCTCCTTTCGCCTTTTT
*
2633772 GTCCTCAAAGAACAGGATGCCTTTTAAAGCCCACACATGCT-GGTGGAACCTTC-AATCCTCAAA
1 GTCCTCAAAGAACAGGATGCCTTTTAAAGCCCACACA-GCTCAGTGGAACCTTCTAATCCTCAAA
* * * *
2633835 GAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCTTCAAAGAGT
65 GAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTT-AGTCCTCAAAGAGC
** * * * * *
2633900 AAGATGCTTTCT-TTTTGTAAAGCCCACACATGTTGGTGGCACTTTTCTAGTCCTCAAAGAGTAG
129 AAGACACCTTCTCCTTT-TAAAGCCCACACAAGTTGGTGGCACTTTCCTAGTCCTCAAAGAGCAG
2633964 GACGC
193 GACGC
2633969 CTTTTCCTTT
Statistics
Matches: 173, Mismatches: 20, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
214 57 0.33
215 91 0.53
216 25 0.14
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (216 bp):
GTCCTCAAAGAACAGGATGCCTTTTAAAGCCCACACAGCTCAGTGGAACCTTCTAATCCTCAAAG
AGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTAGTCCTCAAAGAGCAA
GACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCTAGTCCTCAAAGAGCAGGAC
GCTCTCTCCTTTCGCCTTTTT
Found at i:2634270 original size:60 final size:59
Alignment explanation
Indices: 2633792--2634270 Score: 512
Period size: 61 Copynumber: 8.1 Consensus size: 59
2633782 AACAGGATGC
* * * *
2633792 CTTTTAAAGCCCACACATGCTGGTGGAACC-TTCAATCCTCAAAGAGCAGGACGCCTTCT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC-TCT
* * * * * *
2633851 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCTTCAAAGAGTAAGATGCTTTCT
1 -CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGC-CTCT
* * * * *
2633912 TTTTGTAAAGCCCACACATGTTGGTGGCACTTTTCTAGTCCTCAAAGAGTAGGACGCCTTTT
1 CTTT-TAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCC-TCT
** *
2633974 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAATCCTCAAAGAGCAGGACG---C-
1 -CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTCT
* * *
2634030 CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCA--A-G-ATGT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTCT
* * *
2634085 CTTTCAAAGCCCATACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC--TCT
* * *
2634146 CTTTTAAAGCCCACATAAGCTGGTGGCACC-TTCAGTCCTCAAAAAGCAGGACGCCTTCT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC-TCT
*
2634205 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACGCTCTCT
1 -CTTTTAAAGCCCACACAAGTTGGTGGCACCTT-TCAGTCCTCAAAGAGCAGGACGC-CTCT
2634266 CTTTT
1 CTTTT
2634271 TGCCCTTTAG
Statistics
Matches: 359, Mismatches: 41, Indels: 38
0.82 0.09 0.09
Matches are distributed among these distances:
52 1 0.00
53 1 0.00
55 93 0.26
57 1 0.00
58 1 0.00
59 4 0.01
60 85 0.24
61 121 0.34
62 49 0.14
63 3 0.01
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (59 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTCT
Found at i:2634294 original size:39 final size:39
Alignment explanation
Indices: 2634240--2634338 Score: 180
Period size: 39 Copynumber: 2.5 Consensus size: 39
2634230 GGCACTTCCC
2634240 AGTCCTCAAAGAGCAGGACGCTCTCTCTTTTTGCCCTTT
1 AGTCCTCAAAGAGCAGGACGCTCTCTCTTTTTGCCCTTT
*
2634279 AGTCCGCAAAGAGCAGGACGCTCTCTCTTTTTGCCCTTT
1 AGTCCTCAAAGAGCAGGACGCTCTCTCTTTTTGCCCTTT
*
2634318 AGTCCTCAAAGAACAGGACGC
1 AGTCCTCAAAGAGCAGGACGC
2634339 CTTTTAAAGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.27
Consensus pattern (39 bp):
AGTCCTCAAAGAGCAGGACGCTCTCTCTTTTTGCCCTTT
Found at i:2634640 original size:13 final size:13
Alignment explanation
Indices: 2634622--2634678 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
2634612 TTCAACAATT
2634622 TGTATCGATACAA
1 TGTATCGATACAA
*
2634635 TGTATCGATGCATAA
1 TGTATCGAT--ACAA
2634650 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
2634667 TGTATCGATACA
1 TGTATCGATACA
2634679 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 21 0.58
15 3 0.08
17 3 0.08
19 9 0.25
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2634662 original size:32 final size:32
Alignment explanation
Indices: 2634621--2634705 Score: 152
Period size: 32 Copynumber: 2.7 Consensus size: 32
2634611 TTTCAACAAT
*
2634621 TTGTATCGATACAATGTATCGATGCATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
2634653 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
2634685 TTGTATCGATACAATGTATCG
1 TTGTATCGATACAATGTATCG
2634706 CTGCGAAGCT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:2634691 original size:19 final size:18
Alignment explanation
Indices: 2634635--2634697 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
2634625 ATCGATACAA
*
2634635 TGTATCGATGCATAAGTGT
1 TGTATCGATACATAAGT-T
2634654 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
2634667 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
2634686 TGTATCGATACA
1 TGTATCGATACA
2634698 ATGTATCGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 11 0.30
15 2 0.05
17 2 0.05
19 22 0.59
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:2640577 original size:79 final size:78
Alignment explanation
Indices: 2640374--2640633 Score: 364
Period size: 79 Copynumber: 3.3 Consensus size: 78
2640364 AAATTTCTAG
* * *
2640374 ATTTTT-AATATCGGGGATACTCCAACCCCGTTATTCTCGAGGGCATACTCCAATCCCGGTTTTA
1 ATTTTTCAA-ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTA
2640438 TTTCTAAAACATCA
65 TTTCTAAAACATCA
**
2640452 ATTTTTC--ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAATTTTAT
1 ATTTTTCAAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTAT
*
2640515 TTTTAAAACATCA
66 TTCTAAAACATCA
* *
2640528 ATTTTTCATAATTGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTA
1 ATTTTTCA-AATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTA
*
2640593 TTTCTAAAACACCA
65 TTTCTAAAACATCA
* * *
2640607 ATTCTCCACAATCGAGGATACTCCAAC
1 ATTTTTCA-AATCGGGGATACTCCAAC
2640634 TCCGATTTTA
Statistics
Matches: 161, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
76 70 0.43
78 6 0.04
79 85 0.53
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (78 bp):
ATTTTTCAAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTAT
TTCTAAAACATCA
Found at i:2640643 original size:51 final size:51
Alignment explanation
Indices: 2640571--2640687 Score: 148
Period size: 51 Copynumber: 2.3 Consensus size: 51
2640561 ATTTTCGAGG
*
2640571 GGATACTCCAACCCCGGTTTTA-TTTCTAAAACACCAATTCTCCACAATCGA
1 GGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTCTCCACAATCGA
* ** * * *
2640622 GGATACTCCAACTCCGATTTTATTTTCAAAACATTAATTTTTCACAATCGG
1 GGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTCTCCACAATCGA
2640673 GGATA-TCCAACCCCG
1 GGATACTCCAACCCCG
2640688 TTATTTCATT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
50 9 0.16
51 44 0.77
52 4 0.07
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.30
Consensus pattern (51 bp):
GGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTCTCCACAATCGA
Found at i:2640711 original size:28 final size:28
Alignment explanation
Indices: 2640672--2640743 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
2640662 TTCACAATCG
2640672 GGGATA-TCCAACCCCGTTA-TTTC-ATTA
1 GGGATACTCCAACCCCGTTATTTTCGA--A
* *
2640699 GGGATACTCCAACCCCATTATTTTCGAG
1 GGGATACTCCAACCCCGTTATTTTCGAA
2640727 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
2640744 ACTTTATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
27 6 0.15
28 28 0.72
29 4 0.10
30 1 0.03
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATTTTCGAA
Found at i:2640828 original size:157 final size:158
Alignment explanation
Indices: 2640542--2640844 Score: 366
Period size: 157 Copynumber: 1.9 Consensus size: 158
2640532 TTCATAATTG
** **
2640542 GGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCA
1 GGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGACTTTATTTCTAAAACACCA
* ** * *
2640607 ATTCTCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACATTAATTTTTCACAATCG
66 ATTCTCCACAATCGAGGATACTCCAACCCCGACCTTATTTTCAAAACATCAATTTTCCACAATCG
2640672 -GGGATA-TCCAACCCCGTTATTTCATTA
131 AGGG-TACTCCAACCCCGTTATTTCATTA
* **
2640699 GGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGACTTTATTT-TCAAAATATT
1 GGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGACTTTATTTCT-AAAACACC
* * * * *
2640763 GATT-TCTCACAATC-AGGGATACTTCAACCCCGGCCTTA-TTTCTAAAGCATCAATTTTCCATA
65 AATTCTC-CACAATCGA-GGATACTCCAACCCCGACCTTATTTTC-AAAACATCAATTTTCCACA
2640825 ATCGAGGGTACTCCAACCCC
127 ATCGAGGGTACTCCAACCCC
2640845 ATTGTTATCT
Statistics
Matches: 123, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
156 8 0.07
157 103 0.84
158 12 0.10
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.31
Consensus pattern (158 bp):
GGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGACTTTATTTCTAAAACACCA
ATTCTCCACAATCGAGGATACTCCAACCCCGACCTTATTTTCAAAACATCAATTTTCCACAATCG
AGGGTACTCCAACCCCGTTATTTCATTA
Found at i:2645257 original size:20 final size:21
Alignment explanation
Indices: 2645201--2645259 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
2645191 AATTCAAAGA
2645201 TGTACCAATACAA-TGCATAT
1 TGTACCAATACAATTGCATAT
*** **
2645221 TGTATTGATACGTTTGCA-AT
1 TGTACCAATACAATTGCATAT
2645241 TGTACCAATACAATTGCAT
1 TGTACCAATACAATTGCAT
2645260 TCCCAAGTTT
Statistics
Matches: 27, Mismatches: 10, Indels: 3
0.68 0.25 0.08
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTACCAATACAATTGCATAT
Found at i:2646396 original size:7 final size:7
Alignment explanation
Indices: 2646386--2646412 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2646376 ATAATTTTAG
2646386 TTTTTTC
1 TTTTTTC
2646393 TTTTTTC
1 TTTTTTC
2646400 TTTTTTC
1 TTTTTTC
2646407 TTTTTT
1 TTTTTT
2646413 TAATTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:2648359 original size:24 final size:24
Alignment explanation
Indices: 2648334--2648378 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2648324 AAAGTATGAT
2648334 TTTTA-TTTATAAAATTAATTTAA
1 TTTTATTTTATAAAATTAATTTAA
* *
2648357 TTTTATTTTATTAAATTTATTT
1 TTTTATTTTATAAAATTAATTT
2648379 TTACATGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTTATTTTATAAAATTAATTTAA
Found at i:2649203 original size:130 final size:134
Alignment explanation
Indices: 2648933--2649179 Score: 396
Period size: 130 Copynumber: 1.9 Consensus size: 134
2648923 ATTAAAAAGG
* * *
2648933 GTTTATTATTATTATTTTTTAATAAAATTAAAAATAATATTTAATTAAGTTTAAAAAAATTATAT
1 GTTTTTTATTATTAATTTTTAATAAAATTAAAAATAATATTTAATTAAGTTTAAAAAAATTACAT
2648998 TAACAAATTAAAATATTAATTATTATGTTTTTATAAAAATAAAAATTTAAAATAAAAAATAAAAA
66 TAACAAATTAAAATATTAATTATTATGTTTTTATAAAAATAAAAATTTAAAATAAAAAATAAAAA
2649063 AAAA
131 AAAA
* *
2649067 GTTTTTTATTA-TAATTTTTAATAAAA-T-AAAA-AATATTTAATTAAGTTTATAAAATTTACAT
1 GTTTTTTATTATTAATTTTTAATAAAATTAAAAATAATATTTAATTAAGTTTAAAAAAATTACAT
* *
2649128 TAACAAATTAAAATATTAATTATTATGTTTTT-TAAAATTAAAAATTTTAAAT
66 TAACAAATTAAAATATTAATTATTATGTTTTTATAAAAATAAAAATTTAAAAT
2649180 TAACATTTTA
Statistics
Matches: 106, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
129 18 0.17
130 59 0.56
131 4 0.04
132 1 0.01
133 14 0.13
134 10 0.09
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (134 bp):
GTTTTTTATTATTAATTTTTAATAAAATTAAAAATAATATTTAATTAAGTTTAAAAAAATTACAT
TAACAAATTAAAATATTAATTATTATGTTTTTATAAAAATAAAAATTTAAAATAAAAAATAAAAA
AAAA
Found at i:2649486 original size:28 final size:28
Alignment explanation
Indices: 2649455--2649511 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
2649445 TAAGTCGTTA
2649455 CTAAAAAAAATATATACGTCTGTAAATT
1 CTAAAAAAAATATATACGTCTGTAAATT
2649483 CTAAAAAAAATATATACGTCTGTAAATT
1 CTAAAAAAAATATATACGTCTGTAAATT
2649511 C
1 C
2649512 GAAATAAGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (28 bp):
CTAAAAAAAATATATACGTCTGTAAATT
Found at i:2651563 original size:34 final size:35
Alignment explanation
Indices: 2651525--2651591 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2651515 CCTTACAATA
2651525 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
2651559 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
2651592 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:2652221 original size:21 final size:21
Alignment explanation
Indices: 2652181--2652221 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2652171 GTCAACCTTG
*
2652181 TGTATTGATACCAATAGTATA
1 TGTATTGATACCAACAGTATA
2652202 TGTATTGATA-CAACACGTAT
1 TGTATTGATACCAACA-GTAT
2652222 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (21 bp):
TGTATTGATACCAACAGTATA
Found at i:2653333 original size:17 final size:17
Alignment explanation
Indices: 2653307--2653345 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2653297 AGTCTATTGG
*
2653307 ATAAAATTAATTAATAA
1 ATAAAATTAATTAAAAA
*
2653324 ATAAATTTAATTAAAAA
1 ATAAAATTAATTAAAAA
2653341 ATAAA
1 ATAAA
2653346 GAAATAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAAATTAATTAAAAA
Found at i:2656626 original size:21 final size:21
Alignment explanation
Indices: 2656593--2656633 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2656583 CTAAGTAAAA
2656593 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
2656614 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
2656634 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:2656813 original size:13 final size:13
Alignment explanation
Indices: 2656795--2656820 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2656785 TACACCAAGT
2656795 ATGTATCGATACA
1 ATGTATCGATACA
2656808 ATGTATCGATACA
1 ATGTATCGATACA
2656821 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2656818 original size:32 final size:33
Alignment explanation
Indices: 2656777--2656840 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2656767 TAGCCAAACT
* **
2656777 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2656809 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2656841 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2659045 original size:84 final size:84
Alignment explanation
Indices: 2658868--2659046 Score: 195
Period size: 84 Copynumber: 2.1 Consensus size: 84
2658858 TCTAAACTCA
* * * *
2658868 AAGAAGAAAATAAATCAATAAGTGTAGAGAATCATATTCTTGAAAAGAAATTAAGTGAATTAGAG
1 AAGAAGAAAATAAATCAATAAGTGTAGAAAATCATATTCTTAAAAAGAAAATAAATGAATTAGAG
* *
2658933 AAGAGTATGAAAGAGTTAC
66 AAGAGAAAGAAAGAGTTAC
* *
2658952 AA-AATGAAAATAAATCAATGAGTTTAGAAAAT-A-ATTCTTTTAAAAAGAAAATAAATGAATTA
1 AAGAA-GAAAATAAATCAATAAGTGTAGAAAATCATATTC--TTAAAAAGAAAATAAATGAATTA
* *
2659014 GAGGAGA-AAAGAAATGAGTTGC
63 GAGAAGAGAAAGAAA-GAGTTAC
*
2659036 AAGAGGAAAAT
1 AAGAAGAAAAT
2659047 GATGAATTGA
Statistics
Matches: 79, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
82 4 0.05
83 8 0.10
84 66 0.84
85 1 0.01
ACGTcount: A:0.54, C:0.04, G:0.19, T:0.23
Consensus pattern (84 bp):
AAGAAGAAAATAAATCAATAAGTGTAGAAAATCATATTCTTAAAAAGAAAATAAATGAATTAGAG
AAGAGAAAGAAAGAGTTAC
Found at i:2660469 original size:13 final size:13
Alignment explanation
Indices: 2660451--2660475 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2660441 TTTTCCAGAT
2660451 TGTATCGATACAA
1 TGTATCGATACAA
2660464 TGTATCGATACA
1 TGTATCGATACA
2660476 TTACTTCAGT
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):
TGTATCGATACAA
Found at i:2662081 original size:21 final size:21
Alignment explanation
Indices: 2662048--2662088 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2662038 CTAAGTAAAA
2662048 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
2662069 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
2662089 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:2662268 original size:13 final size:13
Alignment explanation
Indices: 2662250--2662275 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2662240 TACACCAAGT
2662250 ATGTATCGATACA
1 ATGTATCGATACA
2662263 ATGTATCGATACA
1 ATGTATCGATACA
2662276 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2662273 original size:32 final size:33
Alignment explanation
Indices: 2662232--2662295 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2662222 TAGCCAAACT
* **
2662232 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2662264 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2662296 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2666474 original size:13 final size:13
Alignment explanation
Indices: 2666456--2666515 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 13
2666446 ACAAAGATCA
2666456 AATGTATCGATAC
1 AATGTATCGATAC
2666469 AATGTATCGATAC
1 AATGTATCGATAC
*
2666482 ATTG-A--G-T--
1 AATGTATCGATAC
2666489 AATGTATCGATAC
1 AATGTATCGATAC
2666502 AATGTATCGATAC
1 AATGTATCGATAC
2666515 A
1 A
2666516 TTGAGTAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
7 3 0.08
8 1 0.03
9 1 0.03
10 2 0.05
11 1 0.03
12 1 0.03
13 30 0.77
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:2666494 original size:20 final size:20
Alignment explanation
Indices: 2666469--2666537 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
2666459 GTATCGATAC
2666469 AATGTATCGATACATTGAGT
1 AATGTATCGATACATTGAGT
2666489 AATGTATCGATAC-------
1 AATGTATCGATACATTGAGT
2666502 AATGTATCGATACATTGAGT
1 AATGTATCGATACATTGAGT
2666522 AATGTATCGATACATT
1 AATGTATCGATACATT
2666538 TCCTTGGCAG
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 13 0.31
20 29 0.69
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTGAGT
Found at i:2666498 original size:33 final size:33
Alignment explanation
Indices: 2666456--2666535 Score: 160
Period size: 33 Copynumber: 2.4 Consensus size: 33
2666446 ACAAAGATCA
2666456 AATGTATCGATACAATGTATCGATACATTGAGT
1 AATGTATCGATACAATGTATCGATACATTGAGT
2666489 AATGTATCGATACAATGTATCGATACATTGAGT
1 AATGTATCGATACAATGTATCGATACATTGAGT
2666522 AATGTATCGATACA
1 AATGTATCGATACA
2666536 TTTCCTTGGC
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:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (33 bp):
AATGTATCGATACAATGTATCGATACATTGAGT
Found at i:2667173 original size:23 final size:23
Alignment explanation
Indices: 2667116--2667185 Score: 83
Period size: 22 Copynumber: 3.1 Consensus size: 23
2667106 AATATATAAT
*
2667116 AAAATAAAAAATAAATT--TCTTA
1 AAAAT-AAAAATAAATTAATTTTA
*
2667138 AAAAT-AAATTAAATTAATTTTA
1 AAAATAAAAATAAATTAATTTTA
2667160 AAAATAAAAATAAATTAGATTTTA
1 AAAATAAAAATAAATTA-ATTTTA
2667184 AA
1 AA
2667186 TTTTTTAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
20 9 0.22
22 14 0.34
23 10 0.24
24 8 0.20
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (23 bp):
AAAATAAAAATAAATTAATTTTA
Found at i:2667503 original size:31 final size:34
Alignment explanation
Indices: 2667465--2667557 Score: 93
Period size: 34 Copynumber: 2.7 Consensus size: 34
2667455 AAATCATACC
2667465 TTAAATTTTTTAAATTTAATTAA-ATATTA-TT-
1 TTAAATTTTTTAAATTTAATTAATATATTATTTA
* **
2667496 TTAAATTTTATAAAAAATAAAAATTAATATATTATTTA
1 TTAAATTTT-T--TAAAT-TTAATTAATATATTATTTA
*
2667534 TTAATTTTTTTAAATTTAATTAAT
1 TTAAATTTTTTAAATTTAATTAAT
2667558 TTACGTTGAG
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
31 9 0.19
32 1 0.02
34 11 0.23
35 10 0.21
36 6 0.12
37 3 0.06
38 8 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
TTAAATTTTTTAAATTTAATTAATATATTATTTA
Found at i:2668190 original size:21 final size:20
Alignment explanation
Indices: 2668166--2668213 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
2668156 CCTTTAAACT
* *
2668166 ATTATTTTTTATATAATTTTA
1 ATTATTATTTATA-AATATTA
2668187 ATTATTATTTATAAATATTA
1 ATTATTATTTATAAATATTA
2668207 ATT-TTAT
1 ATTATTAT
2668214 AAATATAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 4 0.16
20 9 0.36
21 12 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTATTATTTATAAATATTA
Found at i:2668410 original size:2 final size:2
Alignment explanation
Indices: 2668403--2668441 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2668393 AAACCAATTT
2668403 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2668442 GTTGACAACC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2674872 original size:2 final size:2
Alignment explanation
Indices: 2674865--2674891 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2674855 CAAATACCCA
2674865 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
2674892 GAGATATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2675849 original size:6 final size:6
Alignment explanation
Indices: 2675838--2675879 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
2675828 CTTAAAAAGG
2675838 AAGGCA AAGGCA AAGGCA AAGGCA AAGGCA AAGGCA AAGGCA
1 AAGGCA AAGGCA AAGGCA AAGGCA AAGGCA AAGGCA AAGGCA
2675880 GCAGTGGCAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.50, C:0.17, G:0.33, T:0.00
Consensus pattern (6 bp):
AAGGCA
Found at i:2677743 original size:14 final size:14
Alignment explanation
Indices: 2677724--2677753 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2677714 TTATAAATCA
*
2677724 ATAAATTTTATTAT
1 ATAAATTTTAATAT
2677738 ATAAATTTTAATAT
1 ATAAATTTTAATAT
2677752 AT
1 AT
2677754 CTATATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATAAATTTTAATAT
Found at i:2678310 original size:26 final size:27
Alignment explanation
Indices: 2678281--2678336 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
2678271 TTTTTACTTG
*
2678281 ATAA-ATATGTCAA-AATTTAATATTAT
1 ATAAGATATATCAATAATTT-ATATTAT
*
2678307 ATAATGATATATTAATAATTTATATTAT
1 ATAA-GATATATCAATAATTTATATTAT
2678335 AT
1 AT
2678337 TATATTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 4 0.16
28 16 0.64
29 5 0.20
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (27 bp):
ATAAGATATATCAATAATTTATATTAT
Found at i:2678321 original size:21 final size:21
Alignment explanation
Indices: 2678297--2678351 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 21
2678287 ATGTCAAAAT
2678297 TTAATATTATATAATGA-TATA
1 TTAATATTATATAAT-ATTATA
*
2678318 TTAATAATTTATATTATATTATA
1 TTAAT-A-TTATATAATATTATA
*
2678341 TTTATATTATA
1 TTAATATTATA
2678352 AAAATTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 10 0.34
22 3 0.10
23 16 0.55
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTAATATTATATAATATTATA
Found at i:2678336 original size:5 final size:5
Alignment explanation
Indices: 2678300--2678430 Score: 50
Period size: 5 Copynumber: 27.4 Consensus size: 5
2678290 TCAAAATTTA
* *
2678300 ATATT ATATA ATGA-T ATATT A-ATA AT-TT ATATT ATATT ATATTT ATATT
1 ATATT ATATT AT-ATT ATATT ATATT ATATT ATATT ATATT ATA-TT ATATT
** * * *
2678349 ATAAAA ATTTT AATATT TTA-T ATATT -TATT TTATT -T-TT AATATT
1 AT-ATT ATATT -ATATT ATATT ATATT ATATT ATATT ATATT -ATATT
* * *
2678393 A-ATT -T-TT ATATC ATATT ATATT TTATT A-AGT ATATT AT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT AT
2678431 CAAAGACGTT
Statistics
Matches: 92, Mismatches: 18, Indels: 32
0.65 0.13 0.23
Matches are distributed among these distances:
3 4 0.04
4 22 0.24
5 51 0.55
6 15 0.16
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:2678345 original size:16 final size:18
Alignment explanation
Indices: 2678314--2678351 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
2678304 TATATAATGA
2678314 TATATTAATAATTTATAT
1 TATATTAATAATTTATAT
2678332 TATATT-AT-ATTTATAT
1 TATATTAATAATTTATAT
2678348 TATA
1 TATA
2678352 AAAATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 12 0.60
17 2 0.10
18 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATATTAATAATTTATAT
Found at i:2678375 original size:17 final size:17
Alignment explanation
Indices: 2678313--2678418 Score: 53
Period size: 17 Copynumber: 6.0 Consensus size: 17
2678303 TTATATAATG
*
2678313 ATATATTAATAATTTAT
1 ATATATTAATATTTTAT
2678330 ATTATATT-ATATTTATATT
1 A-TATATTAATATTT-TA-T
*
2678349 ATAAAAATTTTAATATTTTAT
1 AT----ATATTAATATTTTAT
*
2678370 ATAT-TTATTTTATTTT-T
1 ATATATTA--ATATTTTAT
2678387 A-ATATTAAT-TTTTAT
1 ATATATTAATATTTTAT
2678402 ATCATATT-ATATTTTAT
1 AT-ATATTAATATTTTAT
2678419 TAAGTATATT
Statistics
Matches: 70, Mismatches: 4, Indels: 30
0.67 0.04 0.29
Matches are distributed among these distances:
14 4 0.06
15 3 0.04
16 7 0.10
17 24 0.34
18 15 0.21
19 2 0.03
21 3 0.04
22 6 0.09
23 6 0.09
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATATTAATATTTTAT
Found at i:2682968 original size:32 final size:32
Alignment explanation
Indices: 2682911--2682988 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 32
2682901 TACATTGAAA
2682911 AATGTATCGATACATTTAGGAAAAAAACCTAG
1 AATGTATCGATACATTTAGGAAAAAAACCTAG
* * * *
2682943 AATGTATTGATATATTTGGGTAAAAAACCTAG
1 AATGTATCGATACATTTAGGAAAAAAACCTAG
2682975 AATGTATCGATACA
1 AATGTATCGATACA
2682989 ATGAGAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (32 bp):
AATGTATCGATACATTTAGGAAAAAAACCTAG
Found at i:2685059 original size:20 final size:20
Alignment explanation
Indices: 2685036--2685084 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
2685026 ACATGCTCCT
2685036 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
2685056 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
2685076 ATGTATCGA
1 ATGTATCGA
2685085 AACATGCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATTCATA
Found at i:2685137 original size:10 final size:10
Alignment explanation
Indices: 2685122--2685187 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
2685112 GGCTCAATGT
2685122 ATAGTGATGA
1 ATAGTGATGA
*
2685132 ATAGTGATGT
1 ATAGTGATGA
* *
2685142 ATCGATACATGA
1 ATAG-T-GATGA
*
2685154 ACAGTGATGA
1 ATAGTGATGA
*
2685164 ACAGTGATGA
1 ATAGTGATGA
*
2685174 ATAAATGATGA
1 AT-AGTGATGA
2685185 ATA
1 ATA
2685188 ATGAAAAATA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
10 28 0.64
11 11 0.25
12 5 0.11
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.27
Consensus pattern (10 bp):
ATAGTGATGA
Found at i:2685413 original size:13 final size:13
Alignment explanation
Indices: 2685395--2685432 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
2685385 GATAAAGTGT
2685395 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
2685408 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
2685421 ---AAAAAAAAAA
1 TTGAAAAAAAAAA
2685431 TT
1 TT
2685433 TATCCAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.43
13 13 0.57
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (13 bp):
TTGAAAAAAAAAA
Found at i:2685463 original size:21 final size:21
Alignment explanation
Indices: 2685439--2685495 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2685429 AATTTATCCA
2685439 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
2685460 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
2685481 AATGTATCGATACAT
1 AATGTATCGATACAT
2685496 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:2685575 original size:19 final size:19
Alignment explanation
Indices: 2685551--2685618 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2685541 AATTCAACAA
2685551 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2685570 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2685585 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2685602 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2685619 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2685590 original size:13 final size:13
Alignment explanation
Indices: 2685572--2685596 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2685562 ACATAAGTTT
2685572 TGTATCGATACAA
1 TGTATCGATACAA
2685585 TGTATCGATACA
1 TGTATCGATACA
2685597 TAAGTATTGT
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):
TGTATCGATACAA
Found at i:2685594 original size:32 final size:32
Alignment explanation
Indices: 2685553--2685615 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2685543 TTCAACAATT
*
2685553 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
2685585 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2685616 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:2685676 original size:13 final size:13
Alignment explanation
Indices: 2685658--2685683 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2685648 CATTTTTCTG
2685658 TGTATCGATACAT
1 TGTATCGATACAT
2685671 TGTATCGATACAT
1 TGTATCGATACAT
2685684 AGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2685680 original size:33 final size:33
Alignment explanation
Indices: 2685638--2685704 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2685628 GCCAAGGAAA
***
2685638 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATAGATCTGTGTATCGATACAT
*
2685671 TGTATCGATACATAGATCTTTGTATCGATACAT
1 TGTATCGATACATAGATCTGTGTATCGATACAT
2685704 T
1 T
2685705 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATAGATCTGTGTATCGATACAT
Found at i:2688226 original size:28 final size:27
Alignment explanation
Indices: 2688159--2688231 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
2688149 CTTCACAATC
* *
2688159 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
2688186 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
2688214 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
2688232 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:2688276 original size:51 final size:51
Alignment explanation
Indices: 2688214--2688384 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
2688204 TTATTTCTGA
* * *
2688214 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
2688265 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
2688318 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
2688370 GAGGATACTCCAACC
1 GGGGATACTCCAACC
2688385 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:2688403 original size:28 final size:28
Alignment explanation
Indices: 2688367--2688448 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
2688357 ATTTTTCACA
*
2688367 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
2688395 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
2688423 --CGAAGGAACACTCCAACCTCGTTATT
1 ATCG--GGGATACTCCAACCTCGTTATT
2688449 ATCTCCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 2 0.04
28 43 0.96
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:2688492 original size:213 final size:211
Alignment explanation
Indices: 2688050--2688477 Score: 524
Period size: 211 Copynumber: 2.0 Consensus size: 211
2688040 AATTCTCCAC
* * **
2688050 AATCGAGGATATTCCAACTCCGATTTTACTTTCAAAACATTAATTTTCTATAATCGGGGATACTC
1 AATCGGGGATATTCCAACCCCGATTTTACTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
*
2688115 CAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGACACTCCAACCCCGTTA
66 CAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTTA
* * * * * * *
2688180 ATCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGACTTTATTTTCAA
131 ATCATCGGGGATACTCCAACCCCGTTACTTCCGAAGGAACACTCCAACCCCGACTTTATCTCCAA
* **
2688245 AATATCGATTTTTCAT
196 AACATCGAAATTTCAT
* * * * *
2688261 AATCGGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATCGGGGATAC
1 AATCGGGGATATTCCAACCCCGATTTTACTTTCAAAACACCAATTT-T-CTATAATCGGGGATAC
* * * *
2688326 TCCAATTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAACCTCGT
64 TCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGT
* * *
2688389 TATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAAGGAACACTCCAACCTCG-TTATTATCT
129 TA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAAGGAACACTCCAACCCCGACT-TTATCT
*
2688453 CCAAAACAT-TAAATTTC-T
192 CCAAAACATCGAAATTTCAT
*
2688471 CATCGGG
1 AATCGGG
2688478 AAATATATTC
Statistics
Matches: 184, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
210 7 0.04
211 71 0.39
212 71 0.39
213 35 0.19
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (211 bp):
AATCGGGGATATTCCAACCCCGATTTTACTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
CAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTTA
ATCATCGGGGATACTCCAACCCCGTTACTTCCGAAGGAACACTCCAACCCCGACTTTATCTCCAA
AACATCGAAATTTCAT
Found at i:2696896 original size:51 final size:50
Alignment explanation
Indices: 2696740--2696909 Score: 180
Period size: 51 Copynumber: 3.3 Consensus size: 50
2696730 ATGAAATAAC
* * *
2696740 GGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCG
1 GGGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAAT-AAATCG
** * * * * *
2696792 GAATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAA-AAACCG
1 GGGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAATCG
* *
2696843 GGGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCG
1 GGGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAA-TCG
2696894 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
2696910 TCAGAAATAA
Statistics
Matches: 95, Mismatches: 19, Indels: 9
0.77 0.15 0.07
Matches are distributed among these distances:
49 17 0.18
50 3 0.03
51 41 0.43
52 17 0.18
53 7 0.07
54 10 0.11
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (50 bp):
GGGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAATCG
Found at i:2699413 original size:13 final size:13
Alignment explanation
Indices: 2699395--2699420 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2699385 ACAAAGATCC
2699395 ATGTATCGATACA
1 ATGTATCGATACA
2699408 ATGTATCGATACA
1 ATGTATCGATACA
2699421 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2699416 original size:33 final size:33
Alignment explanation
Indices: 2699374--2699440 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2699364 AAAATTTCCA
***
2699374 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2699407 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2699440 A
1 A
2699441 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2699484 original size:19 final size:18
Alignment explanation
Indices: 2699460--2699527 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
2699450 CAGTAGCTAA
2699460 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2699479 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2699494 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2699511 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2699528 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2699500 original size:13 final size:13
Alignment explanation
Indices: 2699482--2699506 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2699472 ACAATACTTA
2699482 TGTATCGATACAT
1 TGTATCGATACAT
2699495 TGTATCGATACA
1 TGTATCGATACA
2699507 AAACTTATGT
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:2699504 original size:32 final size:32
Alignment explanation
Indices: 2699463--2699525 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2699453 TAGCTAATTA
*
2699463 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2699495 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2699526 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2699588 original size:21 final size:21
Alignment explanation
Indices: 2699562--2699640 Score: 88
Period size: 21 Copynumber: 3.7 Consensus size: 21
2699552 GTTGGGACCC
* **
2699562 TGTATCGATACATTTGTAGGA
1 TGTATCGATACATTTCTAAAA
*
2699583 TGTATCGATACA-TTCCACAAA
1 TGTATCGATACATTTCTA-AAA
*
2699604 TGTATCGATACATATTCTACAA
1 TGTATCGATACAT-TTCTAAAA
2699626 TGTATCGATACATTT
1 TGTATCGATACATTT
2699641 GATAAATTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.06
21 27 0.55
22 15 0.31
23 4 0.08
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (21 bp):
TGTATCGATACATTTCTAAAA
Found at i:2699672 original size:13 final size:13
Alignment explanation
Indices: 2699656--2699681 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2699646 ATTTTTTTTT
2699656 TTTTTTTTTTCAA
1 TTTTTTTTTTCAA
2699669 TTTTTTTTTTCAA
1 TTTTTTTTTTCAA
2699682 ACACTTTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTTCAA
Found at i:2700371 original size:54 final size:53
Alignment explanation
Indices: 2700209--2701038 Score: 1060
Period size: 54 Copynumber: 15.3 Consensus size: 53
2700199 ATAAATTGTA
* * * * *
2700209 TCCTGCTCATTGAGGAGTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
* *
2700263 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
2700318 TCCTGCTCTTTGA-GACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
* *
2700372 TCCTGTTCTTTGAGGACTGGAAAATGCCACC-ACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
2700426 TTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 -TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
2700482 TCCTGCTC-TTGGGGACTGAAAGGTG-CACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
* *
2700535 TCCTGCTCTTTGGGGACTGAAAGGTG-CACCAACTTGTGTGGGCTTTAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAGGTG
*
2700588 TCC-GCCCTTTGAGGACTGGACAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GA-AAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
2700642 TCCTGCTCTTTGAGGACTGAAAGGTTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-G-TGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
2700698 TCCTGCTCTTTGGGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
* *
2700752 TCCTGCTCTTTTAGGACTGGACAA-TGCCACCAACTTGTGTTGGGCTTTGAAGGTG
1 TCCTGCTCTTTGAGGACT-GA-AAGTGCCACCAACTTGTG-TGGGCTTTAAAGGTG
*
2700807 T-CTGCTCTTTGAGGACTGAAAGGTGCCACCAACGT-TGTGGGCTTT-AAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAGGTG
* *
2700858 TCCTGCTCTTTTGGGGACTGAAAGGTGCCACCAAACTTTTGTGTGGCTTTAAGAGGTG
1 TCCTGCTC-TTTGAGGACTGAAA-GTGCCACC-AACTTGTGTG-GGCTTTAA-AGGTG
*
2700916 TCCTGCTCGTTGAGGACTGGAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
*
2700970 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTG-GT-GGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
2701022 TCCT-CTCTTTGGGGACT
1 TCCTGCTCTTTGAGGACT
2701039 AAAAAGCGGA
Statistics
Matches: 709, Mismatches: 32, Indels: 73
0.87 0.04 0.09
Matches are distributed among these distances:
51 21 0.03
52 45 0.06
53 99 0.14
54 275 0.39
55 150 0.21
56 93 0.13
57 9 0.01
58 17 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (53 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAGGTG
Found at i:2700536 original size:163 final size:161
Alignment explanation
Indices: 2700209--2701038 Score: 1129
Period size: 163 Copynumber: 5.1 Consensus size: 161
2700199 ATAAATTGTA
* * * * * *
2700209 TCCTGCTCATTGAGGAGTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGTGTCCTGCTCTTT
1 TCCTGCTCTTTGGGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTT
* *
2700274 GGGGAAT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGA-GACTGG
65 GAGGACTGGAAA--TGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACT-G
*
2700337 AAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
126 AAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * *
2700372 TCCTGTTCTTTGAGGACTGGAAAATGCCACC-ACTTGTGTGGGCTTTGAAAGGTGTTCCTGCTCT
1 TCCTGCTCTTTGGGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG-TCCTGCTCT
*
2700436 TTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTC-TTGGGGACT
63 TTGAGGACTGGAAA--TGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACT
2700499 GAAAGGTG-CACCAACTTGTGTGGGCTTTAAGAGGTG
125 GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
2700535 TCCTGCTCTTTGGGGACTGAAAGGTG-CACCAACTTGTGTGGGCTTTAGAGGTGTCC-GCCCTTT
1 TCCTGCTCTTTGGGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTT
2700598 GAGGACTGGACAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAA
65 GAGGACTGGA-AATGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGAGGACTGAA
2700663 AGGTTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
128 AGG-TGCCACCAACTTGTGTGGGCTTTAAGAGGTG
2700698 TCCTGCTCTTTGGGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTT
1 TCCTGCTCTTTGGGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTT
* *
2700763 TAGGACTGGACAATGCCACCAACTTGTGTTGGGCTTTGAAGGTGT-CTGCTCTTTGAGGACTGAA
65 GAGGACTGGA-AATGCCACCAACTTGTG-TGGGCTTTAAAGGTGTCCTGCTCTTTGAGGACTGAA
*
2700827 AGGTGCCACCAACGT-TGTGGGCTTT-A-AGGTG
128 AGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2700858 TCCTGCTCTTTTGGGGACTGAAAGGTGCCACCAAACTTTTGTGTGGCTTTAAGAGGTGTCCTGCT
1 TCCTGCTC-TTTGGGGACTGAAA-GTGCCACC-AACTTGTGTG-GGCTTTAA-AGGTGTCCTGCT
*
2700923 CGTTGAGGACTGGAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT
61 CTTTGAGGACTGGAAATGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGAGGACT
2700988 G-AAGGTGCCACCAACTTG-GT-GGCTTTAAGAGGTG
125 GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
2701022 TCCT-CTCTTTGGGGACT
1 TCCTGCTCTTTGGGGACT
2701039 AAAAAGCGGA
Statistics
Matches: 614, Mismatches: 27, Indels: 53
0.88 0.04 0.08
Matches are distributed among these distances:
160 62 0.10
161 36 0.06
162 65 0.11
163 237 0.39
164 166 0.27
165 40 0.07
166 8 0.01
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (161 bp):
TCCTGCTCTTTGGGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTTG
AGGACTGGAAATGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTTGAGGACTGAAAGG
TGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:2700586 original size:27 final size:27
Alignment explanation
Indices: 2700502--2700587 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
2700492 GGGGACTGAA
2700502 AGGTGCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCACCAACTTGTGTGGGCTTT-AG
* ** * * *
2700530 AGGTG-TCCTGCTCTTTG-GGGAC-TGAA
1 AGGTGCACCAACT-TGTGTGGG-CTTTAG
2700556 AGGTGCACCAACTTGTGTGGGCTTTAG
1 AGGTGCACCAACTTGTGTGGGCTTTAG
2700583 AGGTG
1 AGGTG
2700588 TCCGCCCTTT
Statistics
Matches: 41, Mismatches: 12, Indels: 11
0.64 0.19 0.17
Matches are distributed among these distances:
26 10 0.24
27 22 0.54
28 9 0.22
ACGTcount: A:0.19, C:0.17, G:0.35, T:0.29
Consensus pattern (27 bp):
AGGTGCACCAACTTGTGTGGGCTTTAG
Found at i:2700945 original size:272 final size:269
Alignment explanation
Indices: 2700209--2701038 Score: 1163
Period size: 272 Copynumber: 3.1 Consensus size: 269
2700199 ATAAATTGTA
* * * * *
2700209 TCCTGCTCATTGAGGAGTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGTGTCCTGCTCTTT
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTG-AAGGTGTCCTGCTCTTT
* *
2700274 GGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTT-GAGACTGGA
65 GGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AGAGGTGTCCTGCTCTTTGGGGACTGG-
*
2700338 AAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGTTCTTTGAGGACTGGAAAATGCCACC
128 AAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGG-AAATGCCACC
2700403 -ACTTGTGTGGGCTTTGAAAGGTGTTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGT
192 AACTTGTGTGGGCTTTGAAAGGTG-TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGT
2700467 GGGCTTTAAGAGGTG
255 GGGCTTTAAGAGGTG
* *
2700482 TCCTGCTC-TTGGGGACTGAAAGGTG-CACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGA-AGGTGTCCTGCTCTT
* *
2700545 TGGGGACTGAAAGGTG-CACCAACTTGTGTGGGCTTTAGAGGTGTCC-GCCCTTTGAGGACTGGA
64 TGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAGAGGTGTCCTGCTCTTTGGGGACTGGA
2700608 CAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT-GAAAGGTTGCCA
129 -AATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAA---TGCCA
*
2700672 CCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGGGGACTGAAAGTGCCACCAACTTGTG
190 CCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTG
2700736 TGGGCTTTAAGAGGTG
254 TGGGCTTTAAGAGGTG
*
2700752 TCCTGCTCTTTTAGGACTGGACAA-TGCCACCAACTTGTGTTGGGCTTTGAAGGTGT-CTGCTCT
1 TCCTGCTCTTTGAGGACT-GA-AAGTGCCACCAACTTGTG-TGGGCTTTGAAGGTGTCCTGCTCT
* *
2700815 TTGAGGACTGAAAGGTGCCACCAACGT-TGTGGGCTTTA-AGGTGTCCTGCTCTTTTGGGGACT-
63 TTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAGAGGTGTCCTGCTC-TTTGGGGACTG
* *
2700877 GAAAGGTGCCACCAAACTTTTGTGTGGCTTT-AAGAGGTGTCCTGCTCGTTGAGGACTGGAAATG
127 GAAA--TGCCACC-AACTTGTGTG-GGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGGAAATG
*
2700941 CCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTG
187 CCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTG
2701006 -GT-GGCTTTAAGAGGTG
252 TGTGGGCTTTAAGAGGTG
*
2701022 TCCT-CTCTTTGGGGACT
1 TCCTGCTCTTTGAGGACT
2701039 AAAAAGCGGA
Statistics
Matches: 508, Mismatches: 25, Indels: 52
0.87 0.04 0.09
Matches are distributed among these distances:
268 3 0.01
269 19 0.04
270 134 0.26
271 101 0.20
272 184 0.36
273 35 0.07
274 28 0.06
275 4 0.01
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (269 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAGGTGTCCTGCTCTTTG
GGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAGAGGTGTCCTGCTCTTTGGGGACTGGAAA
TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAATGCCACCAACT
TGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTT
TAAGAGGTG
Found at i:2702737 original size:55 final size:55
Alignment explanation
Indices: 2702652--2703493 Score: 1307
Period size: 55 Copynumber: 15.3 Consensus size: 55
2702642 TCCGCTTTTT
*
2702652 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
2702707 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
*
2702762 AGTCCTCAACGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
2702817 AGTCCCCAAAGAGCAGGACACCTCTTAAAG-CCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
2702871 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA--TTGTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTT-T-C
2702926 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
2702981 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
2703036 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA--TTGTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTT-T-C
2703091 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
2703146 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
2703201 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
2703256 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
2703311 AGTCCTCAAAGAACAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
2703366 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * * * *
2703421 ATTCCCCAAAGAGCAGGACA-CTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* *
2703476 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
2703494 TACAATTTAT
Statistics
Matches: 741, Mismatches: 24, Indels: 44
0.92 0.03 0.05
Matches are distributed among these distances:
53 6 0.01
54 68 0.09
55 647 0.87
56 16 0.02
57 4 0.01
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:2703153 original size:29 final size:29
Alignment explanation
Indices: 2703121--2703208 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
2703111 CCTCTTAAAG
2703121 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
** * *
2703150 CCCA-A-AGAG-CAG-GACACCTCTTAAAG--
1 CCCACACA-AGTTGGTGGCACCT-TT-CAGTC
2703176 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
2703205 CCCA
1 CCCA
2703209 AAGAGCAGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 18
0.62 0.12 0.26
Matches are distributed among these distances:
26 10 0.24
27 9 0.21
28 9 0.21
29 14 0.33
ACGTcount: A:0.26, C:0.35, G:0.19, T:0.19
Consensus pattern (29 bp):
CCCACACAAGTTGGTGGCACCTTTCAGTC
Found at i:2704052 original size:13 final size:13
Alignment explanation
Indices: 2704034--2704059 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2704024 GATAAAGTGT
2704034 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
2704047 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
2704060 AAAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
TTGAAAAAAAAAA
Found at i:2704101 original size:21 final size:21
Alignment explanation
Indices: 2704077--2704133 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2704067 AATTTATCCA
2704077 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
2704098 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
2704119 AATGTATCGATACAT
1 AATGTATCGATACAT
2704134 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:2704213 original size:19 final size:19
Alignment explanation
Indices: 2704189--2704256 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2704179 AATTCAACAA
2704189 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2704208 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2704223 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2704240 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2704257 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2704228 original size:13 final size:13
Alignment explanation
Indices: 2704210--2704234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2704200 ACATAAGTTT
2704210 TGTATCGATACAA
1 TGTATCGATACAA
2704223 TGTATCGATACA
1 TGTATCGATACA
2704235 TAAGTATTGT
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):
TGTATCGATACAA
Found at i:2704232 original size:32 final size:32
Alignment explanation
Indices: 2704191--2704253 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2704181 TTCAACAATT
*
2704191 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
2704223 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2704254 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:2704314 original size:13 final size:13
Alignment explanation
Indices: 2704296--2704321 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2704286 CATTTTTCTG
2704296 TGTATCGATACAT
1 TGTATCGATACAT
2704309 TGTATCGATACAT
1 TGTATCGATACAT
2704322 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2704318 original size:33 final size:33
Alignment explanation
Indices: 2704276--2704342 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2704266 GCCAAGGAAA
***
2704276 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2704309 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2704342 T
1 T
2704343 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2706864 original size:28 final size:27
Alignment explanation
Indices: 2706797--2706869 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
2706787 CTTCACAATC
* *
2706797 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
2706824 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
2706852 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
2706870 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:2706914 original size:51 final size:51
Alignment explanation
Indices: 2706852--2707022 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
2706842 TTATTTCTGA
* * *
2706852 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
2706903 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
2706956 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
2707008 GAGGATACTCCAACC
1 GGGGATACTCCAACC
2707023 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Done.