Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017617.1 Corchorus olitorius cultivar O-4 contig17650, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 73489
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1864 original size:9 final size:9
Alignment explanation
Indices: 1831--1893 Score: 60
Period size: 9 Copynumber: 7.1 Consensus size: 9
1821 ATTGAGAAAC
1831 TATTATATA
1 TATTATATA
1840 TAATT-TA-A
1 T-ATTATATA
*
1848 TA-TATGTA
1 TATTATATA
*
1856 TATTATGTA
1 TATTATATA
*
1865 TATATACATA
1 TAT-TATATA
1875 TATTATATA
1 TATTATATA
1884 TATTATATA
1 TATTATATA
1893 T
1 T
1894 GCGTCATATA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
6 1 0.02
7 2 0.04
8 5 0.11
9 27 0.60
10 10 0.22
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (9 bp):
TATTATATA
Found at i:1875 original size:17 final size:15
Alignment explanation
Indices: 1831--1885 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
1821 ATTGAGAAAC
*
1831 TATTATATATA-ATT
1 TATTATATATACATA
* * *
1845 TAATATATGTATAT-
1 TATTATATATACATA
1859 TATGTATATATACATA
1 TAT-TATATATACATA
1875 TATTATATATA
1 TATTATATATA
1886 TTATATATGC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
14 11 0.33
15 19 0.58
16 3 0.09
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (15 bp):
TATTATATATACATA
Found at i:2832 original size:2 final size:2
Alignment explanation
Indices: 2825--2854 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2815 AATAGGTAGG
2825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2855 TATGGAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9927 original size:15 final size:16
Alignment explanation
Indices: 9909--9938 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9899 AGAAGAAGAT
9909 AAAAGAGA-AAAAAAC
1 AAAAGAGATAAAAAAC
9924 AAAAGAGATAAAAAA
1 AAAAGAGATAAAAAA
9939 AGGAAAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.80, C:0.03, G:0.13, T:0.03
Consensus pattern (16 bp):
AAAAGAGATAAAAAAC
Found at i:11008 original size:20 final size:20
Alignment explanation
Indices: 10983--11047 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
10973 AAAGAAGAAG
10983 GTAAATGGTAATCGGTAAAA
1 GTAAATGGTAATCGGTAAAA
11003 GTAAATGGTAATCGGTAAAA
1 GTAAATGGTAATCGGTAAAA
* * *
11023 GCAAATGGTAATCAGTAAGA
1 GTAAATGGTAATCGGTAAAA
11043 GTAAA
1 GTAAA
11048 ATAGTAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.46, C:0.06, G:0.25, T:0.23
Consensus pattern (20 bp):
GTAAATGGTAATCGGTAAAA
Found at i:11111 original size:25 final size:25
Alignment explanation
Indices: 11057--11112 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
11047 AATAGTAATA
* *
11057 AGTAATTAAGGTCAAAGAGTAAAAT
1 AGTAATTAAGGTCAAAAAGTAAAAC
* *
11082 AGTAATTAAGTTCAAAAAGTGAAAC
1 AGTAATTAAGGTCAAAAAGTAAAAC
*
11107 GGTAAT
1 AGTAAT
11113 CCAAAAAGTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.25
Consensus pattern (25 bp):
AGTAATTAAGGTCAAAAAGTAAAAC
Found at i:11172 original size:21 final size:20
Alignment explanation
Indices: 11148--11199 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
11138 ATTCATTTCA
11148 AAAAGTAAACTGCTAATCAGT
1 AAAAGTAAA-TGCTAATCAGT
*
11169 AAAATGGT-AATGGTAATCAGT
1 AAAA--GTAAATGCTAATCAGT
11190 AAATAGTAAA
1 AAA-AGTAAA
11200 ACGGTAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
20 2 0.08
21 19 0.73
22 3 0.12
23 2 0.08
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.25
Consensus pattern (20 bp):
AAAAGTAAATGCTAATCAGT
Found at i:11274 original size:21 final size:21
Alignment explanation
Indices: 11250--11538 Score: 247
Period size: 21 Copynumber: 13.6 Consensus size: 21
11240 AGAGTAAAAG
11250 AGTAATCAGTAAAATG-GTAAT
1 AGTAATCAGTAAAA-GAGTAAT
11271 AGTAATCAGTAAAAGAGTAAT
1 AGTAATCAGTAAAAGAGTAAT
*
11292 AGTAATCAGT-AAAGAGTAAAG
1 AGTAATCAGTAAAAGAGT-AAT
* *
11313 AGTAATCAAG-AAATG-GTAAG
1 AGTAATC-AGTAAAAGAGTAAT
11333 AGTAATCAGTAAAAGAGT-AT
1 AGTAATCAGTAAAAGAGTAAT
*
11353 AGCAATCAGT-AAAGAGTAAT
1 AGTAATCAGTAAAAGAGTAAT
11373 AGTAATCAGTAAAAGAGTAAT
1 AGTAATCAGTAAAAGAGTAAT
* * * *
11394 AGTAGTAAAT-AAAGAGTAAAG
1 AGTAATCAGTAAAAGAGT-AAT
**
11415 AGTAATCAACAAAA-AGTAAT
1 AGTAATCAGTAAAAGAGTAAT
*
11435 AGTAATCAGTAAAAGAGTAAAC
1 AGTAATCAGTAAAAGAGT-AAT
*
11457 AGTAAACAGTAAACAGTAAAATGGTAAT
1 AGTAATCAGTAAA-AG----A--GTAAT
* *
11485 AGTAATCGGT-AAAGAGTAAAG
1 AGTAATCAGTAAAAGAGT-AAT
11506 AGTAATCAGTAAAATG-GTAAT
1 AGTAATCAGTAAAA-GAGTAAT
*
11527 GGTAATCAGTAA
1 AGTAATCAGTAA
11539 TTAAAATTCA
Statistics
Matches: 221, Mismatches: 25, Indels: 44
0.76 0.09 0.15
Matches are distributed among these distances:
19 9 0.04
20 66 0.30
21 98 0.44
22 28 0.13
23 3 0.01
26 2 0.01
27 3 0.01
28 10 0.05
29 2 0.01
ACGTcount: A:0.52, C:0.06, G:0.20, T:0.22
Consensus pattern (21 bp):
AGTAATCAGTAAAAGAGTAAT
Found at i:11300 original size:42 final size:42
Alignment explanation
Indices: 11161--11538 Score: 303
Period size: 42 Copynumber: 8.7 Consensus size: 42
11151 AGTAAACTGC
* *
11161 TAATCAGTAAAATGGTAATGGTAATCAGTAAATAGTAAA-ACGG
1 TAATCAGTAAAATGGTAATAGTAATCAGTAAAGAGTAAAGA--G
** *
11204 TAAAGAGTAAAATGGTAATCAGTAATTAGAATTCAAAGAGTAAAAGAG
1 TAATCAGTAAAATGGTAAT-AGTAATCAG---T-AAAGAGT-AAAGAG
*
11252 TAATCAGTAAAATGGTAATAGTAATCAGTAAAAGAGT-AATAG
1 TAATCAGTAAAATGGTAATAGTAATCAGT-AAAGAGTAAAGAG
*
11294 TAATCAGT-AAA-GAGTAAAGAGTAATCAAG-AAATG-GT-AAGAG
1 TAATCAGTAAAATG-GT-AATAGTAATC-AGTAAA-GAGTAAAGAG
* *
11335 TAATCAGTAAAA-GAGT-ATAGCAATCAGTAAAGAGT-AATAG
1 TAATCAGTAAAATG-GTAATAGTAATCAGTAAAGAGTAAAGAG
* * *
11375 TAATCAGTAAAA-GAGTAATAGTAGTAAATAAAGAGTAAAGAG
1 TAATCAGTAAAATG-GTAATAGTAATCAGTAAAGAGTAAAGAG
** *
11417 TAATCAACAAAA-AGTAATAGTAATCAGTAAAAGAGTAAACAGTAAACAG
1 TAATCAGTAAAATGGTAATAGTAATCAGT-AAAGAGT-AA-AG-----AG
* *
11466 TAAACAGTAAAATGGTAATAGTAATCGGTAAAGAGTAAAGAG
1 TAATCAGTAAAATGGTAATAGTAATCAGTAAAGAGTAAAGAG
*
11508 TAATCAGTAAAATGGTAATGGTAATCAGTAA
1 TAATCAGTAAAATGGTAATAGTAATCAGTAA
11539 TTAAAATTCA
Statistics
Matches: 276, Mismatches: 34, Indels: 51
0.76 0.09 0.14
Matches are distributed among these distances:
39 3 0.01
40 33 0.12
41 49 0.18
42 80 0.29
43 21 0.08
44 17 0.06
47 11 0.04
48 26 0.09
49 21 0.08
50 15 0.05
ACGTcount: A:0.51, C:0.06, G:0.20, T:0.23
Consensus pattern (42 bp):
TAATCAGTAAAATGGTAATAGTAATCAGTAAAGAGTAAAGAG
Found at i:11387 original size:102 final size:102
Alignment explanation
Indices: 11253--11453 Score: 314
Period size: 102 Copynumber: 2.0 Consensus size: 102
11243 GTAAAAGAGT
* *
11253 AATCAGTAAAATGGTAATAGTAATCAGTAAAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGTAA
1 AATCAGTAAAA-GGTAATAGTAATCAGTAAAAGAGTAATAGTAATAAATAAAGAGTAAAGAGTAA
* **
11318 TCAAGAAATGGTAAGAGTAATCAGTAAAAGAGTATAGC
65 TCAACAAAAAGTAAGAGTAATCAGTAAAAGAGTATAGC
*
11356 AATCAGT-AAAGAGTAATAGTAATCAGTAAAAGAGTAATAGTAGTAAATAAAGAGTAAAGAGTAA
1 AATCAGTAAAAG-GTAATAGTAATCAGTAAAAGAGTAATAGTAATAAATAAAGAGTAAAGAGTAA
*
11420 TCAACAAAAAGTAATAGTAATCAGTAAAAGAGTA
65 TCAACAAAAAGTAAGAGTAATCAGTAAAAGAGTA
11454 AACAGTAAAC
Statistics
Matches: 90, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
101 1 0.01
102 82 0.91
103 7 0.08
ACGTcount: A:0.53, C:0.05, G:0.20, T:0.22
Consensus pattern (102 bp):
AATCAGTAAAAGGTAATAGTAATCAGTAAAAGAGTAATAGTAATAAATAAAGAGTAAAGAGTAAT
CAACAAAAAGTAAGAGTAATCAGTAAAAGAGTATAGC
Found at i:11469 original size:14 final size:14
Alignment explanation
Indices: 11435--11476 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
11425 AAAAAGTAAT
* *
11435 AGTAATCAGTAAAAG
1 AGTAAACAGT-AAAC
11450 AGTAAACAGTAAAC
1 AGTAAACAGTAAAC
11464 AGTAAACAGTAAA
1 AGTAAACAGTAAA
11477 ATGGTAATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.57, C:0.10, G:0.17, T:0.17
Consensus pattern (14 bp):
AGTAAACAGTAAAC
Found at i:11504 original size:102 final size:102
Alignment explanation
Indices: 11266--11475 Score: 303
Period size: 102 Copynumber: 2.0 Consensus size: 102
11256 CAGTAAAATG
* * * * **
11266 GTAATAGTAATCAGTAAAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGTAATCAAGAAATGGTA
1 GTAATAGTAATCAGTAAAAGAGTAATAGTAGTAAATAAAGAGTAAAGAGTAATCAACAAAAAGTA
* * *
11331 AGAGTAATCAGTAAAAGAGTATAGCAATCAGTAAAGA
66 AGAGTAATCAGTAAAAGAGTACAGCAAACAGTAAACA
11368 GTAATAGTAATCAGTAAAAGAGTAATAGTAGTAAATAAAGAGTAAAGAGTAATCAACAAAAAGTA
1 GTAATAGTAATCAGTAAAAGAGTAATAGTAGTAAATAAAGAGTAAAGAGTAATCAACAAAAAGTA
* *
11433 ATAGTAATCAGTAAAAGAGTAAACAGTAAACAGTAAACA
66 AGAGTAATCAGTAAAAGAGT--ACAGCAAACAGTAAACA
11472 GTAA
1 GTAA
11476 AATGGTAATA
Statistics
Matches: 95, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
102 78 0.82
104 17 0.18
ACGTcount: A:0.53, C:0.06, G:0.20, T:0.21
Consensus pattern (102 bp):
GTAATAGTAATCAGTAAAAGAGTAATAGTAGTAAATAAAGAGTAAAGAGTAATCAACAAAAAGTA
AGAGTAATCAGTAAAAGAGTACAGCAAACAGTAAACA
Found at i:11623 original size:36 final size:36
Alignment explanation
Indices: 11573--11683 Score: 179
Period size: 36 Copynumber: 3.1 Consensus size: 36
11563 TAAAAAGATT
* *
11573 AAAAAGAATGAAAATGGTATTCAGTAATTAAAGTAA
1 AAAAAGAGTAAAAATGGTATTCAGTAATTAAAGTAA
* *
11609 AAAAAGGGTAAAAATGGTATTCAGTAATCAAAGT-A
1 AAAAAGAGTAAAAATGGTATTCAGTAATTAAAGTAA
11644 AAAAAGAGTAAAAATGGTATTCAGTAATTAAAGTAA
1 AAAAAGAGTAAAAATGGTATTCAGTAATTAAAGTAA
11680 AAAA
1 AAAA
11684 GGCAAAAAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 33 0.49
36 35 0.51
ACGTcount: A:0.56, C:0.04, G:0.17, T:0.23
Consensus pattern (36 bp):
AAAAAGAGTAAAAATGGTATTCAGTAATTAAAGTAA
Found at i:11655 original size:35 final size:35
Alignment explanation
Indices: 11573--11684 Score: 179
Period size: 35 Copynumber: 3.2 Consensus size: 35
11563 TAAAAAGATT
* *
11573 AAAAAGAATGAAAATGGTATTCAGTAATTAAAGTAA
1 AAAAAGAGTAAAAATGGTATTCAGTAATTAAAGT-A
* *
11609 AAAAAGGGTAAAAATGGTATTCAGTAATCAAAGTA
1 AAAAAGAGTAAAAATGGTATTCAGTAATTAAAGTA
11644 AAAAAGAGTAAAAATGGTATTCAGTAATTAAAGTA
1 AAAAAGAGTAAAAATGGTATTCAGTAATTAAAGTA
11679 AAAAAG
1 AAAAAG
11685 GCAAAAAATG
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 40 0.57
36 30 0.43
ACGTcount: A:0.55, C:0.04, G:0.18, T:0.23
Consensus pattern (35 bp):
AAAAAGAGTAAAAATGGTATTCAGTAATTAAAGTA
Found at i:11719 original size:71 final size:71
Alignment explanation
Indices: 11564--11719 Score: 190
Period size: 71 Copynumber: 2.2 Consensus size: 71
11554 TAAAAATGGT
* * ** * *
11564 AAAAAGATTAAAAAGAATGAAAATGGTATTCAGTAATTAAAGTAAAAAAAGGGTAAAAATGGTAT
1 AAAAAGAGTAAAAAGAATAAAAATGGTATTCAGTAATTAAAGTAAAAAAAGGCAAAAAATGGAAA
*
11629 TCAGTA
66 CCAGTA
** *
11635 ATCAA-AGTAAAAAAGAGTAAAAATGGTATTCAGTAATTAAAGT-AAAAAAGGCAAAAAATGGAA
1 AAAAAGAGT-AAAAAGAATAAAAATGGTATTCAGTAATTAAAGTAAAAAAAGGCAAAAAATGGAA
11698 ACCAGTAA
65 ACCAGT-A
11706 AAAAAGAGTAAAAA
1 AAAAAGAGTAAAAA
11720 AATGGTAATA
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
70 23 0.33
71 44 0.63
72 3 0.04
ACGTcount: A:0.58, C:0.04, G:0.17, T:0.20
Consensus pattern (71 bp):
AAAAAGAGTAAAAAGAATAAAAATGGTATTCAGTAATTAAAGTAAAAAAAGGCAAAAAATGGAAA
CCAGTA
Found at i:11733 original size:29 final size:28
Alignment explanation
Indices: 11674--11765 Score: 86
Period size: 27 Copynumber: 3.4 Consensus size: 28
11664 TCAGTAATTA
* * *
11674 AAGT-AAAAAAG-GCAAAAAATGGAAAC
1 AAGTAAAAAAAGAGTAAAAAATGGTAAT
*
11700 CAGTAAAAAAAGAGTAAAAAAATGGTAAT
1 AAGTAAAAAAAGAGT-AAAAAATGGTAAT
*
11729 AAGT--AAGAAGAGT-AAAAATGGTAAT
1 AAGTAAAAAAAGAGTAAAAAATGGTAAT
*
11754 TAGTAAAAAAAG
1 AAGTAAAAAAAG
11766 TGAGGGTAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
25 15 0.28
26 3 0.06
27 20 0.38
28 1 0.02
29 14 0.26
ACGTcount: A:0.62, C:0.03, G:0.20, T:0.15
Consensus pattern (28 bp):
AAGTAAAAAAAGAGTAAAAAATGGTAAT
Found at i:12513 original size:41 final size:42
Alignment explanation
Indices: 12454--12547 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 42
12444 GCATCATAAT
* **
12454 ATATCCTTCAAAAATAAATCCTTT-TAAAAATACATTCTTAA
1 ATATCCTTCAAAAATAAATCCTTTAAAAAAATACATAATTAA
* * *
12495 ATATCCTTTAAAATTAAATCCTTTAAAAAAATATATAATTAA
1 ATATCCTTCAAAAATAAATCCTTTAAAAAAATACATAATTAA
12537 ATATCCTTCAA
1 ATATCCTTCAA
12548 CATGGAGGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.49
42 23 0.51
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (42 bp):
ATATCCTTCAAAAATAAATCCTTTAAAAAAATACATAATTAA
Found at i:15064 original size:32 final size:32
Alignment explanation
Indices: 14982--15044 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
14972 AAACCCAGCC
* *
14982 CGAACCCGAATTAACCTGACCCAAAATTGACA
1 CGAACCCGAATCAACCTGACCCAAAATTAACA
*
15014 CGAACCCGAATCAACCTGACCCAAATTTAAC
1 CGAACCCGAATCAACCTGACCCAAAATTAAC
15045 CCGACCTGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.40, C:0.33, G:0.11, T:0.16
Consensus pattern (32 bp):
CGAACCCGAATCAACCTGACCCAAAATTAACA
Found at i:17662 original size:2 final size:2
Alignment explanation
Indices: 17655--17681 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17645 AATCAAAGTG
17655 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 T
17682 GTTTATACTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27181 original size:21 final size:22
Alignment explanation
Indices: 27157--27208 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
27147 GGCATGGAAT
*
27157 GGTGATGGCACGG-GCATGGCC
1 GGTGATGGCACGGTGAATGGCC
* *
27178 GGTGGTGGCACGGTGAATGGGC
1 GGTGATGGCACGGTGAATGGCC
*
27200 GGTAATGGC
1 GGTGATGGC
27209 TTAGTAGTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.15, C:0.17, G:0.50, T:0.17
Consensus pattern (22 bp):
GGTGATGGCACGGTGAATGGCC
Found at i:27488 original size:21 final size:23
Alignment explanation
Indices: 27464--27506 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
27454 CGGGCAGGCG
*
27464 GCGCGGA-TGG-CCGGTTGTGGT
1 GCGCGGACTGGTCCGGGTGTGGT
27485 GCGCGGACTGGTCCGGGTGTGG
1 GCGCGGACTGGTCCGGGTGTGG
27507 CCAGGTAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 3 0.16
23 9 0.47
ACGTcount: A:0.05, C:0.21, G:0.53, T:0.21
Consensus pattern (23 bp):
GCGCGGACTGGTCCGGGTGTGGT
Found at i:27553 original size:54 final size:54
Alignment explanation
Indices: 27467--27585 Score: 159
Period size: 54 Copynumber: 2.2 Consensus size: 54
27457 GCAGGCGGCG
* * * * * *
27467 CGGATGGCCGGTTGTGGTGCGCGGACTGGTCCGGGTGTGGCCAGGTAGATGGCT
1 CGGATGGCCGATTGTGGTACGCGGACGGGTCCGGGCGTGGCCAGGCAGATGGAT
*
27521 CGGGTGGCCGATTGTGGTACGCGGA-GGAGTCCGGGCGTGGCCAGGCAGATGGAT
1 CGGATGGCCGATTGTGGTACGCGGACGG-GTCCGGGCGTGGCCAGGCAGATGGAT
27575 CGGATGGCCGA
1 CGGATGGCCGA
27586 GCTATGGCCG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
53 1 0.02
54 55 0.98
ACGTcount: A:0.13, C:0.21, G:0.48, T:0.18
Consensus pattern (54 bp):
CGGATGGCCGATTGTGGTACGCGGACGGGTCCGGGCGTGGCCAGGCAGATGGAT
Found at i:30566 original size:48 final size:46
Alignment explanation
Indices: 30514--30605 Score: 123
Period size: 48 Copynumber: 2.0 Consensus size: 46
30504 TTCAAAAAAA
*
30514 ACGCAGACACAAAAAT-AGAAAACGCAAAAATAACAAATTTTTTTTATG
1 ACGCAAACACAAAAATCA-AAAACG-AAAAA-AACAAATTTTTTTTATG
* *
30562 ACGCAAACACAAAAATCAAAAACGGAAAAAACAATTTTTTTTTA
1 ACGCAAACACAAAAATCAAAAACGAAAAAAACAAATTTTTTTTA
30606 GATTAAAAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
46 14 0.35
47 4 0.10
48 21 0.52
49 1 0.03
ACGTcount: A:0.53, C:0.15, G:0.09, T:0.23
Consensus pattern (46 bp):
ACGCAAACACAAAAATCAAAAACGAAAAAAACAAATTTTTTTTATG
Found at i:33469 original size:73 final size:73
Alignment explanation
Indices: 33378--33522 Score: 281
Period size: 73 Copynumber: 2.0 Consensus size: 73
33368 TATGTTTTTT
*
33378 ACTGTGAAGTTGGAGTTAATATAGGATCCATATTAATATAGGATTAAGATGAATTTTAGGAACAT
1 ACTGTGAAGTTGGAGTTAATATAGGATCCATATTAATATAGGATTAAGATGAATATTAGGAACAT
33443 TGCTGCTC
66 TGCTGCTC
33451 ACTGTGAAGTTGGAGTTAATATAGGATCCATATTAATATAGGATTAAGATGAATATTAGGAACAT
1 ACTGTGAAGTTGGAGTTAATATAGGATCCATATTAATATAGGATTAAGATGAATATTAGGAACAT
33516 TGCTGCT
66 TGCTGCT
33523 GATGACTGAT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.34
Consensus pattern (73 bp):
ACTGTGAAGTTGGAGTTAATATAGGATCCATATTAATATAGGATTAAGATGAATATTAGGAACAT
TGCTGCTC
Found at i:35944 original size:17 final size:17
Alignment explanation
Indices: 35922--35957 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
35912 ATGCAAGTGC
35922 AATTGTAGTACAAAGCT
1 AATTGTAGTACAAAGCT
35939 AATTGTAGTACAAAGCT
1 AATTGTAGTACAAAGCT
35956 AA
1 AA
35958 GAAAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (17 bp):
AATTGTAGTACAAAGCT
Found at i:36086 original size:28 final size:27
Alignment explanation
Indices: 36034--36107 Score: 112
Period size: 28 Copynumber: 2.7 Consensus size: 27
36024 AGTGAACCTA
* * *
36034 AAATGACCAAAATGCCCTTGGACGTGC
1 AAATGACTAAAATGCCCCTGCACGTGC
36061 AAATGACTAAAAATGCCCCTGCACGTGC
1 AAATGACT-AAAATGCCCCTGCACGTGC
36089 AAATGACTAAAATGCCCCT
1 AAATGACTAAAATGCCCCT
36108 AGGTGACCCT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 18 0.42
28 25 0.58
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTGCACGTGC
Found at i:36613 original size:27 final size:27
Alignment explanation
Indices: 36582--36652 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
36572 AGTTAACCTA
* *
36582 AAATGACCAAAATGCCCATGGACGTGC
1 AAATGACTAAAATGCCCATGGACCTGC
* *
36609 GAATGACTAAAATGCCCTTGGACCTGC
1 AAATGACTAAAATGCCCATGGACCTGC
36636 AAATGACTAAAATGCCC
1 AAATGACTAAAATGCCC
36653 CTAGGTGACC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (27 bp):
AAATGACTAAAATGCCCATGGACCTGC
Found at i:37361 original size:69 final size:68
Alignment explanation
Indices: 37172--37378 Score: 272
Period size: 69 Copynumber: 3.0 Consensus size: 68
37162 GGAAATGAAC
* * * *
37172 TTGGCTTATGGAAAATCCCTTGTTGCTTGGGTGGAACCAAGGCTTAAACTGGCTTGTATGGAAAC
1 TTGGCTTATGGAAAA-GCCTTGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
*
37237 GGGT
65 GAGT
* * *
37241 TTGGCTTAATGGAAGAG-CTTCCGTGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAA
1 TTGGCTT-ATGGAAAAGCCTT--GTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAA
37305 ACGAGT
63 ACGAGT
* *
37311 TTGGCTTGTGGAAAAGCCTATGTTGCTTGGATGGAACCAAGGCTTAAACTGAATCGTATGGAAAC
1 TTGGCTTATGGAAAAGCCT-TGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
37376 GAG
65 GAG
37379 CTTAGTCTTG
Statistics
Matches: 120, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
68 3 0.03
69 58 0.48
70 58 0.48
71 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (68 bp):
TTGGCTTATGGAAAAGCCTTGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACG
AGT
Found at i:37489 original size:69 final size:69
Alignment explanation
Indices: 37416--37622 Score: 362
Period size: 69 Copynumber: 3.0 Consensus size: 69
37406 GGAAATGAAC
* * * *
37416 TTGGCTTATGGAAAAGCCCCTG-TCGCTTGGGTGGAACCAAGGATTCAACTGACTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCCCCTGCT-GCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAA
37480 CGAGT
65 CGAGT
37485 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
37550 GAGT
66 GAGT
37554 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
37619 GAGT
66 GAGT
37623 GATTGAGCCA
Statistics
Matches: 133, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
69 132 0.99
70 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (69 bp):
TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
GAGT
Found at i:44764 original size:33 final size:32
Alignment explanation
Indices: 44722--44783 Score: 115
Period size: 33 Copynumber: 1.9 Consensus size: 32
44712 TCCTACTCGA
44722 CCATATCCGCCGATTGCCGCGCCATCTACCCGG
1 CCATATCCGCCGATTGCCGCGCCA-CTACCCGG
44755 CCATATCCGCCGATTGCCGCGCCACTACC
1 CCATATCCGCCGATTGCCGCGCCACTACC
44784 AAGCCATTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 5 0.17
33 24 0.83
ACGTcount: A:0.16, C:0.47, G:0.19, T:0.18
Consensus pattern (32 bp):
CCATATCCGCCGATTGCCGCGCCACTACCCGG
Found at i:44833 original size:21 final size:21
Alignment explanation
Indices: 44804--44858 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
44794 CGGCCATTCA
* **
44804 CCGTACCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCCAAGC
*
44825 CCGTGCCACCACCGGCCATGC
1 CCGTGCCACCACCGGCCAAGC
*
44846 CCGTGCCATCACC
1 CCGTGCCACCACC
44859 ATTCCATGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.49, G:0.20, T:0.13
Consensus pattern (21 bp):
CCGTGCCACCACCGGCCAAGC
Found at i:48536 original size:91 final size:91
Alignment explanation
Indices: 48427--48605 Score: 304
Period size: 91 Copynumber: 2.0 Consensus size: 91
48417 ATACCTTTGG
* *
48427 AAAATAACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAATGACCAATG
1 AAAATAACTCTGAATCTGATGTTATAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAATG
**
48492 TGCGGTCAACTTGAAAAACAACTTGA
66 TGCAATCAACTTGAAAAACAACTTGA
*
48518 AAAATAACTCTGAGTCTGATGTTATAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAATG
1 AAAATAACTCTGAATCTGATGTTATAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAATG
*
48583 TGCAATCAACTTGAAAAATAACT
66 TGCAATCAACTTGAAAAACAACT
48606 CTGGTCTGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 82 1.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (91 bp):
AAAATAACTCTGAATCTGATGTTATAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAATG
TGCAATCAACTTGAAAAACAACTTGA
Found at i:49102 original size:29 final size:29
Alignment explanation
Indices: 49052--49112 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
49042 TAGACTCACA
*
49052 AATGGAATGCAATCTTACTTTGAAAAGCG
1 AATGGAAAGCAATCTTACTTTGAAAAGCG
* **
49081 AATGGAAAGCAATTTTGTTTTGAAAAGCG
1 AATGGAAAGCAATCTTACTTTGAAAAGCG
49110 AAT
1 AAT
49113 TTTGATCTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (29 bp):
AATGGAAAGCAATCTTACTTTGAAAAGCG
Found at i:49143 original size:50 final size:50
Alignment explanation
Indices: 49103--49198 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 50
49093 TTTTGTTTTG
*
49103 AAAAGCGAATTTTGATCTT-GAACTCACAAACGGAATGCAATCTTATTATA
1 AAAAGCGAATTTTGACCTTAG-ACTCACAAACGGAATGCAATCTTATTATA
* * *
49153 AAAAGCGAATTTTGACCTTAGACTCACAAATGGAATACGATCTTAT
1 AAAAGCGAATTTTGACCTTAGACTCACAAACGGAATGCAATCTTAT
49199 CGTAAAACTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 40 0.98
51 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.29
Consensus pattern (50 bp):
AAAAGCGAATTTTGACCTTAGACTCACAAACGGAATGCAATCTTATTATA
Found at i:50293 original size:17 final size:17
Alignment explanation
Indices: 50244--50294 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
50234 TTCCAAGTGC
* *
50244 TTTTTCCATTTTCTTTT
1 TTTTTTCATTCTCTTTT
50261 TTTTTTCATTCAT-TTTT
1 TTTTTTCATTC-TCTTTT
*
50278 TTCTTTC-TTCTCTTTT
1 TTTTTTCATTCTCTTTT
50294 T
1 T
50295 ATTATTGGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 1 0.03
16 8 0.28
17 19 0.66
18 1 0.03
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTCATTCTCTTTT
Found at i:52547 original size:19 final size:18
Alignment explanation
Indices: 52523--52558 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
52513 TGAAGACATA
52523 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
52542 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
52559 ATTATTCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:62765 original size:17 final size:17
Alignment explanation
Indices: 62743--62778 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
62733 ATGCAAGTGC
62743 AATTGTAGTACAAAGCT
1 AATTGTAGTACAAAGCT
62760 AATTGTAGTACAAAGCT
1 AATTGTAGTACAAAGCT
62777 AA
1 AA
62779 GAAGAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (17 bp):
AATTGTAGTACAAAGCT
Found at i:64917 original size:106 final size:105
Alignment explanation
Indices: 64719--64919 Score: 357
Period size: 106 Copynumber: 1.9 Consensus size: 105
64709 TACCCCTTAG
64719 CTTCGGTGCTCTACCAGGAGAGGGCAACCCAGATAAATACCCAGAGAAAAGGTTTTCCTGAACTG
1 CTTCGGTGCTCTACCAGGAGAGGGCAACCCAGATAAATACCCAGAGAAAAGGTTTTCCTGAACTG
* *
64784 AAGAAGGCCAGCAAGATAAGAAGATTTATCAATCTTGTTT
66 AAGAAGGACAGCAAGATAAAAAGATTTATCAATCTTGTTT
* *
64824 CTTCGGTGCTCTATCCAGGAGAGGGCAACCCAGATAAATACCCAGAGAAGAGGTTTTCTTGAACT
1 CTTCGGTGCTCTA-CCAGGAGAGGGCAACCCAGATAAATACCCAGAGAAAAGGTTTTCCTGAACT
64889 GAAGAAGGACAGCAAGATAAAAAGATTTATC
65 GAAGAAGGACAGCAAGATAAAAAGATTTATC
64920 CTCCACAACT
Statistics
Matches: 91, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
105 13 0.14
106 78 0.86
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.22
Consensus pattern (105 bp):
CTTCGGTGCTCTACCAGGAGAGGGCAACCCAGATAAATACCCAGAGAAAAGGTTTTCCTGAACTG
AAGAAGGACAGCAAGATAAAAAGATTTATCAATCTTGTTT
Found at i:68860 original size:87 final size:87
Alignment explanation
Indices: 68769--68943 Score: 341
Period size: 87 Copynumber: 2.0 Consensus size: 87
68759 CTACAGTAGT
*
68769 TAAGCTTTGTTTGATTTTTTCATTTAAATGTTTTTGCCAAGCAAAAGGGCCACTCTAAATATCAT
1 TAAGCTTTGTTTGATTTTTTCATTTAAATGTTTTTGCCAAACAAAAGGGCCACTCTAAATATCAT
68834 AAATTATACTACAACTTAAGTA
66 AAATTATACTACAACTTAAGTA
68856 TAAGCTTTGTTTGATTTTTTCATTTAAATGTTTTTGCCAAACAAAAGGGCCACTCTAAATATCAT
1 TAAGCTTTGTTTGATTTTTTCATTTAAATGTTTTTGCCAAACAAAAGGGCCACTCTAAATATCAT
68921 AAATTATACTACAACTTAAGTA
66 AAATTATACTACAACTTAAGTA
68943 T
1 T
68944 TATAAATATT
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (87 bp):
TAAGCTTTGTTTGATTTTTTCATTTAAATGTTTTTGCCAAACAAAAGGGCCACTCTAAATATCAT
AAATTATACTACAACTTAAGTA
Found at i:70155 original size:24 final size:24
Alignment explanation
Indices: 70112--70159 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
70102 GATGTGCATA
*
70112 TTTAGTTACTGTATAGTTGAGATG
1 TTTAGTTACTGCATAGTTGAGATG
* *
70136 TTTAGTTGCTGCATATTTGAGATG
1 TTTAGTTACTGCATAGTTGAGATG
70160 ATGTGAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.06, G:0.25, T:0.46
Consensus pattern (24 bp):
TTTAGTTACTGCATAGTTGAGATG
Found at i:72167 original size:22 final size:21
Alignment explanation
Indices: 72111--73485 Score: 464
Period size: 22 Copynumber: 62.9 Consensus size: 21
72101 GTCTCTGTGT
* * *
72111 GGTTATTAAAATATCATAAGA
1 GGTTATCAAAATTTCATAGGA
* *
72132 TGGTTATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
* *
72155 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
72177 GGTTATCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATA-GGA
* * *
72199 AGTTATC-AAATTTTATTGGGAA
1 GGTTATCAAAATTTCA-TAGG-A
* *
72221 GGTTATCAAAATTTCATTGTGT
1 GGTTATCAAAATTTCATAG-GA
* *
72243 GGTTACCAAAATTTAATAGGATCA
1 GGTTATCAAAATTTCATAGG---A
* *
72267 GGTTATTAAAATTTCTTAGGAA
1 GGTTATCAAAATTTCATAGG-A
** *
72289 GGTTATTGAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
72311 GGTTATCACAAACTTT-ATAGAAA
1 GGTTATCA-AAA-TTTCATAG-GA
*
72334 GGTTATCAAAATGTCATAGCGA
1 GGTTATCAAAATTTCATAG-GA
*
72356 GGTTAT-AAGAATTTCATAGTGT
1 GGTTATCAA-AATTTCATAG-GA
*
72378 GGTTAACAAAATTTCATAAGGA
1 GGTTATCAAAATTTCAT-AGGA
* *
72400 GGTTA-CTAATATTTCATGGGGA
1 GGTTATC-AAAATTTCAT-AGGA
* *
72422 GGTTTTCAAAATTTCATAAGAA
1 GGTTATCAAAATTTCAT-AGGA
*
72444 GGTTATAAAAGTCTCAATTTCATA--A
1 GGTTAT-CAA-----AATTTCATAGGA
* * * * *
72469 GGAGTACCAACATTTGATAGAA
1 GG-TTATCAAAATTTCATAGGA
*
72491 GGTTATC-AAATCTCATA-GA
1 GGTTATCAAAATTTCATAGGA
* *
72510 GTGATTATCGAAATTTCACAGAGA
1 G-G-TTATCAAAATTTCATAG-GA
72534 TCGGATTATCAAAATTT-ATAGGAA
1 --GG-TTATCAAAATTTCATAGG-A
* *
72558 GATTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
* * *
72580 TGTTATGAAAATTTCAAAGCGA
1 GGTTATCAAAATTTCATAG-GA
* * *
72602 GGTTATCAAAATTACATAATGT
1 GGTTATCAAAATTTCAT-AGGA
* * *
72624 GATTATCAAAATTTTAATAGAGG
1 GGTTATCAAAA-TTTCATAG-GA
* * *
72647 GGTCAACAAAATTTTATAGAGA
1 GGTTATCAAAATTTCATAG-GA
*
72669 GGTTATCAAAATTTCATAAAGA
1 GGTTATCAAAATTTCAT-AGGA
* * * *
72691 GGTTATCAAATTTTCAAAATGT
1 GGTTATCAAAATTTC-ATAGGA
** * * *
72713 CATTACCAACATTTCATA-GT
1 GGTTATCAAAATTTCATAGGA
* * **
72733 GGTATTTCTGGGGAGGTTATCA-A--A
1 GGT-TATC----AAAATT-TCATAGGA
* * * * *
72757 -ATT-TCATAGTAT-ATA-TA
1 GGTTATCAAAATTTCATAGGA
*
72774 TGGTTA-CCAAA--T--TAGGAA
1 -GGTTATCAAAATTTCATAGG-A
* * *
72792 GGTTATTAAACTTTTATTATGGA
1 GGTTATCAAAATTTCA-TA-GGA
* *
72815 -GTAATCAAAATTTCA-GGGA
1 GGTTATCAAAATTTCATAGGA
* *
72834 GGATATCAAAATTTCATATGAA
1 GGTTATCAAAATTTCATA-GGA
*
72856 GGTTATCAAAATTTCATAGTTTA
1 GGTTATCAAAATTTCATAG--GA
* *
72879 -GTTTTCAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
* *
72899 GGGTTATCAAAATTTTATAGTA
1 -GGTTATCAAAATTTCATAGGA
* * *
72921 TGTAGATCAAAATTTCATATGAA
1 GGT-TATCAAAATTTCATA-GGA
*
72944 GGTTATCAAAATTTCATAGCTTA
1 GGTTATCAAAATTTCATAG--GA
*
72967 -GTTTTCAAAATTTCATAGGA
1 GGTTATCAAAATTTCATAGGA
*
72987 GGATTATCAAAATTTCATAGTA
1 GG-TTATCAAAATTTCATAGGA
* *
73009 TGTAGATCAAAATTTCATAGGGA
1 GGT-TATCAAAATTTCATA-GGA
* * *
73032 GATTAACAAAATTTCATAATGA
1 GGTTATCAAAATTTCAT-AGGA
**
73054 GGTTAT-AAAAAATCATAGGGA
1 GGTTATCAAAATTTCATA-GGA
* *
73075 GGTTAT-AAAAATT--T-GTA
1 GGTTATCAAAATTTCATAGGA
*
73092 -GTTATCAAGATTTCATAAGGA
1 GGTTATCAAAATTTCAT-AGGA
*
73113 GGTTATCAAAATTTTATAGGGA
1 GGTTATCAAAATTTCATA-GGA
*
73135 GGTTTATCAAAATTTTATAGGAA
1 GG-TTATCAAAATTTCATAGG-A
73158 GGTTTATCAAAATTTCATAGAGA
1 GG-TTATCAAAATTTCATAG-GA
* * *
73181 GGTTATGACAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
* * * *
73203 GATTATCAATATTTCAAAGTGT
1 GGTTATCAAAATTTCATAG-GA
* *
73225 GATTA-CTAACAA-TCCATACGGA
1 GGTTATC-AA-AATTTCATA-GGA
* * * * *
73247 GGTTCTTAAATTTTCATAACGT
1 GGTTATCAAAATTTCAT-AGGA
* *
73269 GGTTATCAATATATCATATGGA
1 GGTTATCAAAATTTCATA-GGA
* * *
73291 GGTTATCAACATCTCATAGTGTT
1 GGTTATCAAAATTTCATAG-G-A
*
73314 GGTTATCAAAATTTCATTGGGA
1 GGTTATCAAAATTTCA-TAGGA
* *
73336 AGTTATCAAAATTTCATAATGA
1 GGTTATCAAAATTTCAT-AGGA
*
73358 GGTCT-TCAAAATTTCTTAGAGA
1 GGT-TATCAAAATTTCATAG-GA
* *
73380 GGTTAACAAAATTTCATAAGAA
1 GGTTATCAAAATTTCAT-AGGA
** **
73402 GGTTAAAAAAAATTT-ATAAAAA
1 GGTT-ATCAAAATTTCAT-AGGA
* * * *
73424 GGTTCTCGAAATTCCATAGTA
1 GGTTATCAAAATTTCATAGGA
* *
73445 TCGTTATTAAAATTTCATAGGAA
1 -GGTTATCAAAATTTCATAGG-A
73468 GGTTATCAAAATTTCATA
1 GGTTATCAAAATTTCATA
73486 AGGA
Statistics
Matches: 1009, Mismatches: 235, Indels: 218
0.69 0.16 0.15
Matches are distributed among these distances:
15 1 0.00
16 9 0.01
17 16 0.02
18 3 0.00
19 11 0.01
20 35 0.03
21 88 0.09
22 642 0.64
23 137 0.14
24 30 0.03
25 22 0.02
26 6 0.01
27 1 0.00
28 8 0.01
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:72369 original size:67 final size:68
Alignment explanation
Indices: 72133--72706 Score: 272
Period size: 67 Copynumber: 8.6 Consensus size: 68
72123 ATCATAAGAT
* * * *
72133 GGTTATTATAATTTCATGAGG-AGGTTATCAAAATTCCATAGTGTGGTTATCA-AAATTTCATAT
1 GGTTATCAAAATTTCAT-AGGAAGGTTATCAAAATTTCATAGTGTGGTTATCACAAATTTAATA-
72196 GG-AA
64 GGAAA
* * * *
72200 -GTTATC-AAATTTTATTGGGAAGGTTATCAAAATTTCATTGTGTGGTTACCA-AAATTTAATAG
1 GGTTATCAAAATTTCA-TAGGAAGGTTATCAAAATTTCATAGTGTGGTTATCACAAATTTAATAG
*
72262 GATCA
65 GA-AA
* * **
72267 GGTTATTAAAATTTCTTAGGAAGGTTATTGAAATTTCATAGTGTGGTTATCACAAACTTT-ATA-
1 GGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGGTTATCACAAA-TTTAATAG
72330 GAAA
65 GAAA
* * *
72334 GGTTATCAAAATGTCATAGCG-AGGTTAT-AAGAATTTCATAGTGTGGTTAACA-AAATTTCATA
1 GGTTATCAAAATTTCATAG-GAAGGTTATCAA-AATTTCATAGTGTGGTTATCACAAATTTAAT-
72396 AGG--A
63 AGGAAA
* * * * ** *
72400 GGTTA-CTAATATTTCATGGGGAGGTTTTCAAAATTTCATAAG-AAGGTTAT-A-AAAGTCTCAA
1 GGTTATC-AAAATTTCATAGGAAGGTTATCAAAATTTCAT-AGTGTGGTTATCACAAA-T-TTAA
***
72461 TTTCATAA
62 TAGGA-AA
* * * * * * * * * *
72469 GGAGTACCAACATTTGATA-GAAGGTTATC-AAATCTCATAGAGTGATTATC-GAAATTTCACAG
1 GG-TTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGGTTATCACAAATTTAATAG
**
72531 AGATC
65 -GAAA
* * *
72536 GGATTATCAAAATTT-ATAGGAAGATTATCAAAATTTCATAGTGTTGTTATGA-AAATTTCAA-A
1 GG-TTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGGTTATCACAAATTT-AATA
72598 GCG--A
64 G-GAAA
* * * * * * * *
72602 GGTTATCAAAATTACATA--ATGTGATTATCAAAATTTTAATAGAGGGGTCAACA-AAATTTTAT
1 GGTTATCAAAATTTCATAGGAAG-G-TTATCAAAA-TTTCATAGTGTGGTTATCACAAATTTAAT
*
72664 A-GAGA
63 AGGAAA
* *
72669 GGTTATCAAAATTTCATA-AAGAGGTTATCAAATTTTCA
1 GGTTATCAAAATTTCATAGGA-AGGTTATCAAAATTTCA
72707 AAATGTCATT
Statistics
Matches: 386, Mismatches: 80, Indels: 83
0.70 0.15 0.15
Matches are distributed among these distances:
64 2 0.01
65 31 0.08
66 106 0.27
67 123 0.32
68 82 0.21
69 28 0.07
70 13 0.03
71 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (68 bp):
GGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGGTTATCACAAATTTAATAGG
AAA
Found at i:73069 original size:21 final size:21
Alignment explanation
Indices: 73045--73085 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
73035 TAACAAAATT
*
73045 TCATAATGAGGTTATAAAAAA
1 TCATAAGGAGGTTATAAAAAA
*
73066 TCATAGGGAGGTTATAAAAA
1 TCATAAGGAGGTTATAAAAA
73086 TTTGTAGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.05, G:0.20, T:0.27
Consensus pattern (21 bp):
TCATAAGGAGGTTATAAAAAA
Found at i:73341 original size:45 final size:45
Alignment explanation
Indices: 73268--73353 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
73258 TTTCATAACG
* * *
73268 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
73313 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATA
73354 ATGAGGTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Done.