Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1296
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: 83545
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:271 original size:38 final size:38
Alignment explanation
Indices: 202--281 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 38
192 AGGACAAAAG
* *
202 AAAAAAAGGAAAATGAAATACGTCCTGCTCTTTGAGGAA
1 AAAAAAAGGAAAATAAAACACGTCCTGCTCTTTG-GGAA
* * *
241 AAAAAAAGGAAAATAAAACGCGTTCT-CTCTTTGGGAC
1 AAAAAAAGGAAAATAAAACACGTCCTGCTCTTTGGGAA
278 AAAA
1 AAAA
282 GGAAAAGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
37 7 0.19
38 7 0.19
39 22 0.61
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (38 bp):
AAAAAAAGGAAAATAAAACACGTCCTGCTCTTTGGGAA
Found at i:355 original size:45 final size:44
Alignment explanation
Indices: 275--361 Score: 113
Period size: 45 Copynumber: 2.0 Consensus size: 44
265 CTCTCTTTGG
275 GACAAAAGGAAAAGAAAGAATGAAGTGTGTATTGCTCGTTGAAA
1 GACAAAAGGAAAAGAAAGAATGAAGTGTGTATTGCTCGTTGAAA
* * * *
319 GACAAAAGGGGAAAAGAAGGATTGAA-TGTGTCTTGCTCTTTGA
1 GACAAAA--GGAAAAGAAAGAATGAAGTGTGTATTGCTCGTTGA
362 GGACAGAGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 7 0.19
45 15 0.41
46 15 0.41
ACGTcount: A:0.40, C:0.08, G:0.29, T:0.23
Consensus pattern (44 bp):
GACAAAAGGAAAAGAAAGAATGAAGTGTGTATTGCTCGTTGAAA
Found at i:677 original size:122 final size:127
Alignment explanation
Indices: 453--983 Score: 645
Period size: 122 Copynumber: 4.3 Consensus size: 127
443 GGATAAAGAA
* * *
453 AAAAAGAATAAAGGTGTCCTACTCTTT-AGGACTAGAAA---TGCCACCAACTTGTGTGGGCTTT
1 AAAAAGAA-AAAGGCGTCCTGCTCTTTGAGGACTA-AAAGGGTGCCACCAACTCGTGTGGGCTTT
* ** *
514 GAAAAGAAAAAA-A-GTGTCCCTCTTTGAGGACTAAAA-GGTGCCACCAACTCGTTTGGGCTTT
64 GAAAAGAAAAAAGACGTCTTGCTCTTTGAGGACTAAAATGGTGCCACCAACTCGTGTGGGCTTT
* *
575 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAGAAGGGTGCCACCAAC-CGTGTGGGCTTTG-
1 AAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGGTGCCACCAACTCGTGTGGGCTTTGA
*
638 AAAGAAAAAAG-TGTCTTGCTCTTTGAGGACT-AAA-GGTGCCACCAACTCGTGTGGGCTTT
66 AAAGAAAAAAGACGTCTTGCTCTTTGAGGACTAAAATGGTGCCACCAACTCGTGTGGGCTTT
* * * * *
697 GAAAAGAAAAAGGCATCTTGCTCTTTGATGACTAAAAGGGTGCCACCAACTCGTGTGGGCGTTGA
1 AAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGGTGCCACCAACTCGTGTGGGCTTTGA
*
762 AAAGAAAAAAGACGTCTTGCTCTTTGAGGACTAAAATGGTGCCACCAACTCATGTGGGGCTTT
66 AAAGAAAAAAGACGTCTTGCTCTTTGAGGACTAAAATGGTGCCACCAACTCGTGT-GGGCTTT
** *
825 AAAAAG-AAAAGTTTGTCCTACTCTTTGAGGACTAAAAGGGTG-CACCAACTCGT-T-GGCTTTG
1 AAAAAGAAAAAG-GCGTCCTGCTCTTTGAGGACTAAAAGGGTGCCACCAACTCGTGTGGGCTTTG
* * *
886 -AAAGAACAAAGACGTCCTACAT-TTT-AGGACT-AAATGGTGCCACCAACTCGTGTGGGCTTT
65 AAAAGAAAAAAGACGTCTTGC-TCTTTGAGGACTAAAATGGTGCCACCAACTCGTGTGGGCTTT
* * *
946 AAAAAGAAAAAGAC-TCATGCTTTTTGAGGACTAAAAGG
1 AAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGG
984 CTAAAGAAGT
Statistics
Matches: 361, Mismatches: 33, Indels: 32
0.85 0.08 0.08
Matches are distributed among these distances:
120 21 0.06
121 31 0.09
122 123 0.34
123 46 0.13
124 41 0.11
125 26 0.07
126 4 0.01
127 33 0.09
128 36 0.10
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (127 bp):
AAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGGTGCCACCAACTCGTGTGGGCTTTGA
AAAGAAAAAAGACGTCTTGCTCTTTGAGGACTAAAATGGTGCCACCAACTCGTGTGGGCTTT
Found at i:938 original size:249 final size:245
Alignment explanation
Indices: 491--983 Score: 665
Period size: 249 Copynumber: 2.0 Consensus size: 245
481 GGACTAGAAA
* * *
491 TGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAAAGTGTCCCTCTTTGAGGACTAAAAGGTGCC
1 TGCCACCAACTCGTGTGGGCGTTGAAAAGAAAAAAAGTCTCCCTCTTTGAGGACTAAAAGGTGCC
* * * * *
556 ACCAACTCGTTTGGGCTTTGAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAGAAGGGTGCCAC
66 ACCAACTCATTGGGGCTTTAAAAAGAAAAAGGCGTCCTACTCTTTGAGGACTAAAAGGGTGCCAC
* * *
621 CAACCGTGTGGGCTTTGAAAGAAAAAAGTGTCTTGCTCTTTGAGGACTAAAGGTGCCACCAACTC
131 CAACCGTGTGGGCTTTGAAAGAAAAAAGCGTCCTACTCTTTGAGGACTAAAGGTGCCACCAACTC
* * * *
686 GTGTGGGCTTTGAAAAGAAAAAGGCATCTTGCTCTTTGATGACTAAAAGGG
196 GTGTGGGCTTTAAAAAGAAAAAGAC-TCATGCTCTTTGAGGACTAAAAGGG
**
737 TGCCACCAACTCGTGTGGGCGTTGAAAAGAAAAAAGACGTCTTGCTCTTTGAGGACTAAAATGGT
1 TGCCACCAACTCGTGTGGGCGTTGAAAAGAAAAAA-A-GTCTCCCTCTTTGAGGACTAAAA-GGT
**
802 GCCACCAACTCATGTGGGGCTTTAAAAAG-AAAAGTTTGTCCTACTCTTTGAGGACTAAAAGGGT
63 GCCACCAACTCAT-TGGGGCTTTAAAAAGAAAAAG-GCGTCCTACTCTTTGAGGACTAAAAGGGT
*
866 G-CACCAACTCGT-T-GGCTTTGAAAGAACAAAGACGTCCTACAT-TTT-AGGACTAAATGGTGC
126 GCCACCAAC-CGTGTGGGCTTTGAAAGAAAAAAG-CGTCCTAC-TCTTTGAGGACTAAA-GGTGC
*
926 CACCAACTCGTGTGGGCTTTAAAAAGAAAAAGACTCATGCTTTTTGAGGACTAAAAGG
187 CACCAACTCGTGTGGGCTTTAAAAAGAAAAAGACTCATGCTCTTTGAGGACTAAAAGG
984 CTAAAGAAGT
Statistics
Matches: 217, Mismatches: 21, Indels: 16
0.85 0.08 0.06
Matches are distributed among these distances:
246 33 0.15
247 1 0.00
248 67 0.31
249 73 0.34
250 43 0.20
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (245 bp):
TGCCACCAACTCGTGTGGGCGTTGAAAAGAAAAAAAGTCTCCCTCTTTGAGGACTAAAAGGTGCC
ACCAACTCATTGGGGCTTTAAAAAGAAAAAGGCGTCCTACTCTTTGAGGACTAAAAGGGTGCCAC
CAACCGTGTGGGCTTTGAAAGAAAAAAGCGTCCTACTCTTTGAGGACTAAAGGTGCCACCAACTC
GTGTGGGCTTTAAAAAGAAAAAGACTCATGCTCTTTGAGGACTAAAAGGG
Found at i:978 original size:61 final size:62
Alignment explanation
Indices: 491--980 Score: 558
Period size: 61 Copynumber: 8.0 Consensus size: 62
481 GGACTAGAAA
* * * *
491 TGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAAAGTGTCC--CTCTTTGAGGACTAAAAGG
1 TGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGA-CGTCCTGCTCTTTGAGGACTAAAGGG
* *
552 TGCCACCAACTCGTTTGGGCTTTGAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAGAAGGG
1 TGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGCTCTTTGAGGACTA-AAGGG
* *
615 TGCCACCAAC-CGTGTGGGCTTTG-AAAGAAAAA-AGTGTCTTGCTCTTTGAGGACTAAA-GG
1 TGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGA-CGTCCTGCTCTTTGAGGACTAAAGGG
* * * *
674 TGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCTTGCTCTTTGATGACTAAAAGGG
1 TGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGCTCTTTGAGGACT-AAAGGG
* * *
737 TGCCACCAACTCGTGTGGGCGTTGAAAAGAAAAAAGACGTCTTGCTCTTTGAGGACTAAAATGG
1 TGCCACCAACTCGTGTGGGCTTTGAAAAG-AAAAAGACGTCCTGCTCTTTGAGGACT-AAAGGG
* * ** *
801 TGCCACCAACTCATGTGGGGCTTTAAAAAG-AAAAGTTTGTCCTACTCTTTGAGGACTAAAAGGG
1 TGCCACCAACTCGTGT-GGGCTTTGAAAAGAAAAAG-ACGTCCTGCTCTTTGAGGACT-AAAGGG
* *
865 TG-CACCAACTCGT-T-GGCTTTG-AAAGAACAAAGACGTCCTACAT-TTT-AGGACTAAATGG
1 TGCCACCAACTCGTGTGGGCTTTGAAAAGAA-AAAGACGTCCTGC-TCTTTGAGGACTAAAGGG
* * *
923 TGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGAC-TCATGCTTTTTGAGGACTAAA
1 TGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGCTCTTTGAGGACTAAA
981 AGGCTAAAGA
Statistics
Matches: 373, Mismatches: 35, Indels: 42
0.83 0.08 0.09
Matches are distributed among these distances:
58 7 0.02
59 34 0.09
60 44 0.12
61 112 0.30
62 36 0.10
63 59 0.16
64 70 0.19
65 11 0.03
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (62 bp):
TGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGCTCTTTGAGGACTAAAGGG
Found at i:2376 original size:29 final size:29
Alignment explanation
Indices: 2329--2386 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
2319 ATTCTTGGAC
*
2329 AGTTTTCTTGTTTGGCCCCCCAAATGTGGG
1 AGTTTTCTTGTTTGCCCCCCCAAA-GTGGG
* *
2359 AGTTTT-TTGTTTTCCCCCCCCAAGTGGG
1 AGTTTTCTTGTTTGCCCCCCCAAAGTGGG
2387 GGTGATCCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.20
29 14 0.56
30 6 0.24
ACGTcount: A:0.12, C:0.26, G:0.24, T:0.38
Consensus pattern (29 bp):
AGTTTTCTTGTTTGCCCCCCCAAAGTGGG
Found at i:4122 original size:37 final size:37
Alignment explanation
Indices: 4045--4122 Score: 90
Period size: 37 Copynumber: 2.1 Consensus size: 37
4035 AGATATTAAA
**
4045 AAATAAATATAATTAATTTGGTCAAAACATTTTTTGT
1 AAATAAATATAATTAATTTACTCAAAACATTTTTTGT
4082 AAATAAAT-TAATTTAATTTACTCACAAA-ATTATTTT-T
1 AAATAAATATAA-TTAATTTACTCA-AAACATT-TTTTGT
4119 AAAT
1 AAAT
4123 TGAGTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
36 3 0.08
37 26 0.72
38 7 0.19
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (37 bp):
AAATAAATATAATTAATTTACTCAAAACATTTTTTGT
Found at i:7396 original size:52 final size:52
Alignment explanation
Indices: 7318--7468 Score: 212
Period size: 52 Copynumber: 2.9 Consensus size: 52
7308 CCCGAAATAT
*
7318 GAAAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCGGG
1 GAAAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATAGGG
** * *
7370 GAAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATATGG
1 GAAAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATAGGG
* * ** *
7422 GTAAATTTGCCTACATGTATCGATACAAAGATTAGTGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACA
7469 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 86 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATAGGG
Found at i:7475 original size:13 final size:13
Alignment explanation
Indices: 7457--7481 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7447 CAAAGATTAG
7457 TGTATCGATACAA
1 TGTATCGATACAA
7470 TGTATCGATACA
1 TGTATCGATACA
7482 TTGAAGTGAT
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:7563 original size:13 final size:13
Alignment explanation
Indices: 7545--7569 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7535 AAAAAAAATA
7545 TGTATCGATACAT
1 TGTATCGATACAT
7558 TGTATCGATACA
1 TGTATCGATACA
7570 ACACTTTATG
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:8551 original size:95 final size:93
Alignment explanation
Indices: 8424--8655 Score: 313
Period size: 95 Copynumber: 2.4 Consensus size: 93
8414 AAGATGAGAA
* *
8424 AAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAA
1 AAAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT-G--AAGATGCCAA
* *
8489 TATGCTGATTCAAGGCTAACTATATTGGACTT
62 TATGCTGATTCAAGGCCAACGATATTGGACTT
*
8521 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGATGCCAATATG
*
8585 CTGATTCAAGGCCAGCGATATTGGACTT
66 CTGATTCAAGGCCAACGATATTGGACTT
* *
8613 AAAGGCGAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTG
1 AAA----AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
8656 GGCTTAAAAG
Statistics
Matches: 122, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
92 38 0.31
93 2 0.02
94 1 0.01
95 42 0.34
96 5 0.04
97 34 0.28
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (93 bp):
AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGATGCCAATATG
CTGATTCAAGGCCAACGATATTGGACTT
Found at i:8598 original size:49 final size:48
Alignment explanation
Indices: 8429--8663 Score: 264
Period size: 48 Copynumber: 4.9 Consensus size: 48
8419 GAGAAAAAAG
* * * *
8429 GATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAA
1 GATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G---A
* * *
8481 GGTGCCAATATGCTGATTCAAGGCTAACTATATTGGACTT-AA-A-G-
1 GATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGA
* *
8525 G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA
1 GATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG-A
* **
8573 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGCGA
1 GATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGA
* *
8621 GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAA
1 GATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
8664 AGGAGACGCC
Statistics
Matches: 158, Mismatches: 19, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
43 34 0.22
44 3 0.02
45 1 0.01
46 1 0.01
48 43 0.27
49 40 0.25
50 1 0.01
51 2 0.01
52 33 0.21
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (48 bp):
GATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGA
Found at i:8740 original size:28 final size:28
Alignment explanation
Indices: 8683--8806 Score: 135
Period size: 28 Copynumber: 4.3 Consensus size: 28
8673 CACCAACTTG
*
8683 TGTGGGCTTTTGAGAGGTTTG-CA-TCAACT
1 TGTGGGCTTTTGA-AGG-TTGCCACT-GACT
* *
8712 TGTGTGCTTTTGAAGGTTGCTACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
*
8740 TGTGGGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* *
8768 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
8798 TGTGGGCTT
1 TGTGGGCTT
8807 AAAAAGAAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
27 3 0.04
28 43 0.52
29 13 0.16
30 23 0.28
ACGTcount: A:0.17, C:0.15, G:0.31, T:0.37
Consensus pattern (28 bp):
TGTGGGCTTTTGAAGGTTGCCACTGACT
Found at i:8889 original size:29 final size:29
Alignment explanation
Indices: 8849--9022 Score: 181
Period size: 29 Copynumber: 6.0 Consensus size: 29
8839 TTACAAAAGA
* * *
8849 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGA-TGCCACTGACTTGTGGGCTTTGG
**
8879 AAAAGATGCCACCCACTTGTGGGCTTTGG
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
8908 AAAAGGGTGCCACTGATTTGTGGGCTTT-G
1 AAAA-GATGCCACTGACTTGTGGGCTTTGG
* * *
8937 -AAGGTTGCCACTGACTTGTGGGCTTTTGA
1 AAAAGATGCCACTGACTTGTGGGC-TTTGG
* *
8966 AAAAAATGCCACTGACTTGTGGGCTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
8995 AAAATATGCCACTGACTTGTGGACTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
9023 AAGGGTGAGG
Statistics
Matches: 123, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
27 18 0.15
28 5 0.04
29 55 0.45
30 45 0.37
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (29 bp):
AAAAGATGCCACTGACTTGTGGGCTTTGG
Found at i:8968 original size:57 final size:59
Alignment explanation
Indices: 8847--9022 Score: 185
Period size: 57 Copynumber: 3.0 Consensus size: 59
8837 GTTTACAAAA
* * * * * * **
8847 GAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCCACTTGTGGGCTTTG
1 GAAAAA-AATGCCACTGACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGGCTTTG
*** * ** *
8907 GAAAAGGGTGCCACTGATTTGTGGGCTTTG-AAGGT-TGCCACTGACTTGTGGGCTTTT
1 GAAAAAAATGCCACTGACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGGCTTTG
*
8964 GAAAAAAATGCCACTGACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGACTTTG
1 GAAAAAAATGCCACTGACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGGCTTTG
9023 AAGGGTGAGG
Statistics
Matches: 95, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
57 45 0.47
58 5 0.05
59 40 0.42
60 5 0.05
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (59 bp):
GAAAAAAATGCCACTGACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGGCTTTG
Found at i:9005 original size:86 final size:86
Alignment explanation
Indices: 8856--9026 Score: 218
Period size: 86 Copynumber: 2.0 Consensus size: 86
8846 AGAAAAAGAG
* * * * *
8856 TGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCCACTTGTGGGCTTTGGAAAAGGGTGCCAC
1 TGCCACGGACTTGTGGACTTTGAAAAAAATGCCACCCACTTGTGGGCTTTGGAAAAAGATGCCAC
* *
8921 TGATTTGTGGGCTTTGAAGGT
66 TGACTTGTGGACTTTGAAGGT
* * ** *
8942 TGCCACTGACTTGTGGGCTTTTGAAAAAAATGCCACTGACTTGTGGGCTTT-GAAAAATATGCCA
1 TGCCACGGACTTGTGGAC-TTTGAAAAAAATGCCACCCACTTGTGGGCTTTGGAAAAAGATGCCA
9006 CTGACTTGTGGACTTTGAAGG
65 CTGACTTGTGGACTTTGAAGG
9027 GTGAGGAATG
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
86 44 0.61
87 28 0.39
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (86 bp):
TGCCACGGACTTGTGGACTTTGAAAAAAATGCCACCCACTTGTGGGCTTTGGAAAAAGATGCCAC
TGACTTGTGGACTTTGAAGGT
Found at i:9023 original size:29 final size:29
Alignment explanation
Indices: 8733--9024 Score: 189
Period size: 30 Copynumber: 9.7 Consensus size: 29
8723 GAAGGTTGCT
* * *
8733 ACTGACTTGTGGGCTTT-TAAAGGTTGCC
1 ACTGACTTGTGGGCTTTGAAAAAGATGCC
* *
8761 ACTGACTTGTGGGCTTTTGAAAAGGGTGCC
1 ACTGACTTGTGGGC-TTTGAAAAAGATGCC
* * *
8791 ACTAACTTGTGGGCTTAAAAAGAAAAAGAGTGCT
1 ACTGACTTGTGGGCTT----TGAAAAAGA-TGCC
* *
8825 A-TAGAGTTGTGAG-TTTACAAAAGAAAAAGAGTGCC
1 ACT-GACTTGTGGGCTTT------GAAAAAGA-TGCC
* * * *
8860 ACGGAGTTGTGGACTTTGGAAAAGATGCC
1 ACTGACTTGTGGGCTTTGAAAAAGATGCC
** * *
8889 ACCCACTTGTGGGCTTTGGAAAAGGGTGCC
1 ACTGACTTGTGGGCTTT-GAAAAAGATGCC
* * *
8919 ACTGATTTGTGGGCTTTG--AAGGTTGCC
1 ACTGACTTGTGGGCTTTGAAAAAGATGCC
*
8946 ACTGACTTGTGGGCTTTTGAAAAAAATGCC
1 ACTGACTTGTGGGC-TTTGAAAAAGATGCC
*
8976 ACTGACTTGTGGGCTTTGAAAAATATGCC
1 ACTGACTTGTGGGCTTTGAAAAAGATGCC
*
9005 ACTGACTTGTGGACTTTGAA
1 ACTGACTTGTGGGCTTTGAA
9025 GGGTGAGGAA
Statistics
Matches: 211, Mismatches: 33, Indels: 39
0.75 0.12 0.14
Matches are distributed among these distances:
27 21 0.10
28 18 0.09
29 56 0.27
30 72 0.34
33 9 0.04
34 11 0.05
35 21 0.10
36 3 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (29 bp):
ACTGACTTGTGGGCTTTGAAAAAGATGCC
Found at i:12430 original size:52 final size:52
Alignment explanation
Indices: 12345--12469 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
12335 ATATGAAAAG
* *
12345 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
12397 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
12449 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
12470 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:12482 original size:52 final size:51
Alignment explanation
Indices: 12345--12489 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
12335 ATATGAAAAG
*
12345 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
12397 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
12449 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
12490 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:12496 original size:13 final size:13
Alignment explanation
Indices: 12478--12502 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12468 CAAAGATCAG
12478 TGTATCGATACAA
1 TGTATCGATACAA
12491 TGTATCGATACA
1 TGTATCGATACA
12503 TGTGAGTAAT
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:12585 original size:13 final size:13
Alignment explanation
Indices: 12567--12591 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12557 CAAAAAAATA
12567 TGTATCGATACAT
1 TGTATCGATACAT
12580 TGTATCGATACA
1 TGTATCGATACA
12592 ACATTTTATG
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:12587 original size:33 final size:33
Alignment explanation
Indices: 12545--12611 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
12535 AGTAGCTTAA
12545 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
12578 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
12611 A
1 A
12612 AATCGTTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:14022 original size:1 final size:1
Alignment explanation
Indices: 14016--14116 Score: 94
Period size: 1 Copynumber: 101.0 Consensus size: 1
14006 ATCCGGACCC
* * * * * * * *
14016 TTTTTTTTGTTTTTTTTGTTTGTTTTTTGTTTGTTTTTTTTTGTTTTTGTTTTTTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
14081 TTTTTGTTTTGTTTTGTTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
14117 GTGGAGGACG
Statistics
Matches: 76, Mismatches: 24, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (1 bp):
T
Found at i:14031 original size:10 final size:10
Alignment explanation
Indices: 14016--14115 Score: 132
Period size: 11 Copynumber: 9.8 Consensus size: 10
14006 ATCCGGACCC
14016 TTTTTTTTG-
1 TTTTTTTTGT
14025 TTTTTTTTGT
1 TTTTTTTTGT
14035 TTGTTTTTTGT
1 TT-TTTTTTGT
14046 TTGTTTTTT-T
1 TT-TTTTTTGT
*
14056 TTGTTTTTGTT
1 TTTTTTTTG-T
14067 TTTTTTTTGTT
1 TTTTTTTTG-T
14078 TTTTTTTTGT
1 TTTTTTTTGT
*
14088 TTTGTTTTGT
1 TTTTTTTTGT
14098 TTTTTTTTGT
1 TTTTTTTTGT
14108 TTTTTTTT
1 TTTTTTTT
14116 TGTGGAGGAC
Statistics
Matches: 83, Mismatches: 4, Indels: 7
0.88 0.04 0.07
Matches are distributed among these distances:
9 14 0.17
10 32 0.39
11 37 0.45
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:14053 original size:31 final size:30
Alignment explanation
Indices: 14016--14118 Score: 154
Period size: 31 Copynumber: 3.3 Consensus size: 30
14006 ATCCGGACCC
14016 TTTTTTTTGTTTTTTTTGTTTGTTTTTTGTT
1 TTTTTTTTGTTTTTTTTGTTT-TTTTTTGTT
*
14047 TGTTTTTTT-TTGTTTTTGTTTTTTTTTTGTT
1 T-TTTTTTTGTTTTTTTTG-TTTTTTTTTGTT
14078 TTTTTTTTGTTTTGTTTTGTTTTTTTTTGTT
1 TTTTTTTTGTTTT-TTTTGTTTTTTTTTGTT
14109 TTTTTTTTGT
1 TTTTTTTTGT
14119 GGAGGACGCC
Statistics
Matches: 66, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
30 7 0.11
31 44 0.67
32 15 0.23
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (30 bp):
TTTTTTTTGTTTTTTTTGTTTTTTTTTGTT
Found at i:14076 original size:42 final size:42
Alignment explanation
Indices: 14016--14118 Score: 158
Period size: 42 Copynumber: 2.5 Consensus size: 42
14006 ATCCGGACCC
*
14016 TTTTTTTTG--TTTTTTTTGTTTGTTTTTTG-TTTGTTTTTT
1 TTTTTTTTGTTTTTTTTTTGTTTGTTTTTTGTTTTGTTTTGT
*
14055 TTTGTTTTTGTTTTTTTTTTGTTTTTTTTTTGTTTTGTTTTGT
1 TTT-TTTTTGTTTTTTTTTTGTTTGTTTTTTGTTTTGTTTTGT
14098 TTTTTTTTGTTTTTTTTTTGT
1 TTTTTTTTGTTTTTTTTTTGT
14119 GGAGGACGCC
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
39 3 0.05
40 6 0.10
42 37 0.64
43 12 0.21
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (42 bp):
TTTTTTTTGTTTTTTTTTTGTTTGTTTTTTGTTTTGTTTTGT
Found at i:27996 original size:52 final size:51
Alignment explanation
Indices: 27918--28066 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 51
27908 CGAAATATGA
27918 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCGGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCGGGGC
* * * *
27970 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCGGGGC
**
28022 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
28067 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCGGGGC
Found at i:28073 original size:13 final size:13
Alignment explanation
Indices: 28055--28079 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28045 CAAAGATCAG
28055 TGTATCGATACAA
1 TGTATCGATACAA
28068 TGTATCGATACA
1 TGTATCGATACA
28080 TTGAAGTGAT
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:28159 original size:13 final size:13
Alignment explanation
Indices: 28141--28165 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28131 ACAAAAAAAA
28141 TGTATCGATACAT
1 TGTATCGATACAT
28154 TGTATCGATACA
1 TGTATCGATACA
28166 ACACTTTATG
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:30588 original size:28 final size:28
Alignment explanation
Indices: 30556--30617 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
30546 CTTCTTTATG
* *
30556 GATTTCTTTTCCTTTGAAATTTCTTGCTT
1 GATTTCGTTTCCTTTCAAATTTCTTG-TT
*
30585 -ATTTCGTTTCCTTTCATATTTCTTGTT
1 GATTTCGTTTCCTTTCAAATTTCTTGTT
30612 GATTTC
1 GATTTC
30618 ACTTCTTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 2 0.07
28 27 0.93
ACGTcount: A:0.13, C:0.18, G:0.10, T:0.60
Consensus pattern (28 bp):
GATTTCGTTTCCTTTCAAATTTCTTGTT
Found at i:33073 original size:28 final size:28
Alignment explanation
Indices: 33017--33088 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
33007 GGAATAAAGC
** *
33017 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
33045 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
**
33073 CAAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
33089 TCGACTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:33227 original size:104 final size:104
Alignment explanation
Indices: 33076--33296 Score: 243
Period size: 104 Copynumber: 2.1 Consensus size: 104
33066 GAAATAACAA
* * * * *
33076 GGTTGGAGTAT-CCTCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATC-GGAGTTGGAGTAT
1 GGTTGGAGTATCCCTCGACTGTGAAAAATTAGTAGTTTTAGAAATAAAACCGGGA-TTGGAATAT
*** *
33139 CCCCGATTAAAGAAAAATTGGTGTTTTGAAAATAAAACCGG
65 CCCCGATT-AAGAAAAATCAATATTTTGAAAATAAAACCGG
* *
33180 GGTTGGAGTATCCCT-GATTGTGGAAAAATTAGT-GTTTTAGCAATAAAACCGGGATTGGAATAT
1 GGTTGGAGTATCCCTCGACTGT-GAAAAATTAGTAGTTTTAGAAATAAAACCGGGATTGGAATAT
* * * **
33243 CTCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
65 CCCCGATTAAGAAAAATCAATATTTTGAAAATAAAACCGG
33283 GGTTGGAGTATCCC
1 GGTTGGAGTATCCC
33297 CTCGGAAATA
Statistics
Matches: 98, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
103 38 0.39
104 44 0.45
105 16 0.16
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.30
Consensus pattern (104 bp):
GGTTGGAGTATCCCTCGACTGTGAAAAATTAGTAGTTTTAGAAATAAAACCGGGATTGGAATATC
CCCGATTAAGAAAAATCAATATTTTGAAAATAAAACCGG
Found at i:33344 original size:27 final size:26
Alignment explanation
Indices: 33280--33355 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 26
33270 GAAATAAAGT
33280 CGGGGTTGGAGTATCCCCTCGGA-AATAA
1 CGGGGTTGGAGTAT-CCC-C-GATAATAA
*
33308 CGGGGTTGGAGTATCCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCGATAAT-AA
33335 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
33356 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.04
26 3 0.07
27 26 0.58
28 14 0.31
ACGTcount: A:0.21, C:0.22, G:0.34, T:0.22
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCCCGATAATAA
Found at i:33447 original size:51 final size:52
Alignment explanation
Indices: 33077--33461 Score: 214
Period size: 52 Copynumber: 7.3 Consensus size: 52
33067 AAATAACAAG
* * * * * *
33077 GTTGGAGTATCCTCGACTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAGAAAAATTAGT-GTTTTGAAAATAAAATCGGA
* * * *
33129 GTTGGAGTATCCCCGATTAAAGAAAAATTGGTGTTTTGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGGA
* * * * *
33181 GTTGGAGTATCCCTGATTGTGGAAAAATTAGTGTTTT-AGCAATAAAACCGG-
1 GTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGA-AAATAAAATCGGA
* * * * * * * *
33232 GATTGGAATATCTCCGATTAT-GAAAAATCAATATTTTGGAAATAAAGTCGGG
1 G-TTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGGA
* **** * *** ** * *
33284 GTTGGAGTATCCCCTCGGA-AATA-ACGGGGTTGGAGTATCCCCGATGAT-CAA-CGGG
1 GTTGGAGTAT-CCC-C-GATTATAGA-AAAATT--AGTGT-TTTGAAAATAAAATCGGA
* * * *
33339 GTTGGAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTGGAAATAAAATCGAA
1 GTTGGAGTATCCCCGATTATAGAA-AAATTAGTG--TTTTGAAAATAAAATCGGA
33393 GTTGGAGTATCCCCGATTATAG-AAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGGA
*
33444 GTTGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
33462 GTGGAGAATT
Statistics
Matches: 248, Mismatches: 64, Indels: 43
0.70 0.18 0.12
Matches are distributed among these distances:
51 68 0.27
52 98 0.40
53 31 0.12
54 28 0.11
55 15 0.06
56 5 0.02
57 3 0.01
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:33464 original size:263 final size:262
Alignment explanation
Indices: 32966--33466 Score: 772
Period size: 263 Copynumber: 1.9 Consensus size: 262
32956 TCGAAAATAA
* * * *
32966 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
* *
33031 CCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACAAGGTTGGAGTATCCTCGACTG
66 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-AATAACAAGGTTGGAGTATCCCCGACTG
* *
33096 TGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAAATTGGT
130 TGAAAAATTGGTATTTTTGGAAATAAAATCGAAGTTGGAGTATCCCCGATTAAAGAAAAATTAGT
* * *
33161 GTTTTGAAAATAAAACCGGGGTTGGAGTATCCCTGATTGTGGAAAAATTAGTGTTTTAGCAATAA
195 GTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
33226 AAC
260 AAC
* * *
33229 CGGGATTGGAATATCTCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTAT
1 CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
** *
33294 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATCAACGGGGTTGGAGTATCCCCGATTG
66 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAT-AACAAGGTTGGAGTATCCCCGACTG
* *
33358 TGAAGAAATTGGTGTTTTTTGGAAATAAAATCGAAGTTGGAGTATCCCCGATTATAG-AAAATTA
130 TGAA-AAATTGGT-ATTTTTGGAAATAAAATCGAAGTTGGAGTATCCCCGATTAAAGAAAAATTA
*
33422 GTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
193 GTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
33467 GAATTGAGAA
Statistics
Matches: 215, Mismatches: 20, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
261 2 0.01
262 25 0.12
263 148 0.69
264 40 0.19
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (262 bp):
CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAATAACAAGGTTGGAGTATCCCCGACTGT
GAAAAATTGGTATTTTTGGAAATAAAATCGAAGTTGGAGTATCCCCGATTAAAGAAAAATTAGTG
TTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAA
AC
Found at i:35843 original size:33 final size:33
Alignment explanation
Indices: 35805--35871 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
35795 AAAATTTCCA
***
35805 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
* *
35838 AATGTATTGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
35871 A
1 A
35872 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:36006 original size:21 final size:21
Alignment explanation
Indices: 35982--36038 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
35972 CATTTGTAGG
35982 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
36003 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
36024 ATGTATCGATACATT
1 ATGTATCGATACATT
36039 TGGATAATTT
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:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:36061 original size:13 final size:13
Alignment explanation
Indices: 36043--36071 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
36033 TACATTTGGA
36043 TAATTTTTTTTTT
1 TAATTTTTTTTTT
36056 TAATTTTTTTTTT
1 TAATTTTTTTTTT
36069 TAA
1 TAA
36072 ACACTCTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TAATTTTTTTTTT
Found at i:43859 original size:58 final size:58
Alignment explanation
Indices: 43762--43878 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 58
43752 GAAGAATAAA
* ** * *
43762 GCTTTGAGCCCAATTCGTATGTCCAAGAAGAGTTAAGCCCAATTTGCATGTATTCATG
1 GCTTGGAGCCCAATTCACATGTCCAAGAAGAGTGAAGCCCAATTTGCATATATTCATG
* *
43820 GCTTGGAGCCCAATTCACATGTCCAAGAAGAGTGGAGCCCAATTTGCATATATTTATG
1 GCTTGGAGCCCAATTCACATGTCCAAGAAGAGTGAAGCCCAATTTGCATATATTCATG
43878 G
1 G
43879 GCCTATTGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (58 bp):
GCTTGGAGCCCAATTCACATGTCCAAGAAGAGTGAAGCCCAATTTGCATATATTCATG
Found at i:44541 original size:15 final size:16
Alignment explanation
Indices: 44512--44545 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
44502 ATTATTTTAC
*
44512 AATTTAAATTAAATTA
1 AATTAAAATTAAATTA
44528 AATTAAAATT-AATTA
1 AATTAAAATTAAATTA
44543 AAT
1 AAT
44546 ATATGATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTAAAATTAAATTA
Found at i:44551 original size:59 final size:59
Alignment explanation
Indices: 44481--44605 Score: 171
Period size: 59 Copynumber: 2.1 Consensus size: 59
44471 AGTACAAATG
* * * * * **
44481 TTAAATGTATGATTCATGATAATTATTTTACAATTTAAATTAAATTAAAT-TAAAATTAA
1 TTAAATATATGATTAATGAAAATTATTTTAAAATTTAAATCAAAACAAATCTAAAA-TAA
44540 TTAAATATATGATTAATGAAAATTATTTTAAAATTTAAATCAAAACAAATCTAAAATAA
1 TTAAATATATGATTAATGAAAATTATTTTAAAATTTAAATCAAAACAAATCTAAAATAA
44599 TTAAATA
1 TTAAATA
44606 CATAATTTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 53 0.91
60 5 0.09
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (59 bp):
TTAAATATATGATTAATGAAAATTATTTTAAAATTTAAATCAAAACAAATCTAAAATAA
Found at i:44623 original size:59 final size:59
Alignment explanation
Indices: 44496--44626 Score: 158
Period size: 59 Copynumber: 2.2 Consensus size: 59
44486 TGTATGATTC
* * ** * *
44496 ATGATAATTATTTTACAATTTAAATTAAATTAAATTAAAATTAATTAAATATATGATTA
1 ATGATAATTATTTTAAAATTTAAATCAAAACAAATTAAAATTAATTAAATACATAATTA
*
44555 ATGAAAATTATTTTAAAATTTAAATCAAAACAAATCTAAAA-TAATTAAATACATAATTTA
1 ATGATAATTATTTTAAAATTTAAATCAAAACAAAT-TAAAATTAATTAAATACATAA-TTA
*
44615 A-GGTAATTATTT
1 ATGATAATTATTT
44627 AAAGTAATCC
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
59 52 0.85
60 9 0.15
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (59 bp):
ATGATAATTATTTTAAAATTTAAATCAAAACAAATTAAAATTAATTAAATACATAATTA
Found at i:46197 original size:17 final size:17
Alignment explanation
Indices: 46171--46210 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
46161 AACAATTAAA
46171 AAATAAAATTAAA-GAT
1 AAATAAAATTAAATGAT
*
46187 ATAATATAATTAAATGAT
1 A-AATAAAATTAAATGAT
46205 AAATAA
1 AAATAA
46211 TTATAATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 15 0.75
18 4 0.20
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (17 bp):
AAATAAAATTAAATGAT
Found at i:46321 original size:2 final size:2
Alignment explanation
Indices: 46314--46350 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
46304 AATGAAAAGC
46314 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 T
46351 CTAATCTCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:47731 original size:12 final size:12
Alignment explanation
Indices: 47714--47750 Score: 56
Period size: 12 Copynumber: 2.9 Consensus size: 12
47704 ATTTATTAAG
47714 ATAAAATAAAAA
1 ATAAAATAAAAA
47726 ATAAAATAAATAA
1 ATAAAATAAA-AA
47739 ATAAAATGAAAA
1 ATAAAAT-AAAA
47751 TGTTTTTCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.43
13 10 0.43
14 3 0.13
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (12 bp):
ATAAAATAAAAA
Found at i:48147 original size:15 final size:17
Alignment explanation
Indices: 48116--48151 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
48106 CTCAACAGTT
48116 AAGAAACGAATAATAAA
1 AAGAAACGAATAATAAA
48133 AAGAAACGAAATAA-AAA
1 AAGAAACG-AATAATAAA
48150 AA
1 AA
48152 ATCAATAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.75, C:0.06, G:0.11, T:0.08
Consensus pattern (17 bp):
AAGAAACGAATAATAAA
Found at i:48151 original size:18 final size:17
Alignment explanation
Indices: 48116--48152 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
48106 CTCAACAGTT
*
48116 AAGAAACGAATAATAAA
1 AAGAAACGAATAAAAAA
48133 AAGAAACGAAATAAAAAA
1 AAGAAACG-AATAAAAAA
48151 AA
1 AA
48153 TCAATAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.76, C:0.05, G:0.11, T:0.08
Consensus pattern (17 bp):
AAGAAACGAATAAAAAA
Found at i:54248 original size:2 final size:2
Alignment explanation
Indices: 54241--54283 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
54231 TTTGCATCGC
54241 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54283 T
1 T
54284 TTCATTCCCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:64268 original size:7 final size:7
Alignment explanation
Indices: 64256--64287 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
64246 TATAAAAAAA
64256 TTTTAAT
1 TTTTAAT
64263 TTTTAAT
1 TTTTAAT
64270 TTTTAAT
1 TTTTAAT
64277 TTTTAAT
1 TTTTAAT
64284 TTTT
1 TTTT
64288 TCATAATGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTAAT
Found at i:65292 original size:16 final size:16
Alignment explanation
Indices: 65273--65310 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
65263 ATTAGAGTTT
65273 AATAAAAAAATTAAAA
1 AATAAAAAAATTAAAA
65289 AATAAAAAAATTAAAA
1 AATAAAAAAATTAAAA
*
65305 ATTAAA
1 AATAAA
65311 GAGCTCTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AATAAAAAAATTAAAA
Found at i:65294 original size:7 final size:8
Alignment explanation
Indices: 65277--65310 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
65267 GAGTTTAATA
65277 AAAAAATT
1 AAAAAATT
*
65285 AAAAAATA
1 AAAAAATT
65293 AAAAAATT
1 AAAAAATT
65301 -AAAAATT
1 AAAAAATT
65308 AAA
1 AAA
65311 GAGCTCTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAAATT
Found at i:76521 original size:36 final size:36
Alignment explanation
Indices: 76444--76522 Score: 88
Period size: 37 Copynumber: 2.2 Consensus size: 36
76434 ATATTTTTAT
* *
76444 AATTTTGTATACAATTATATTTAATAAAAATAATTA
1 AATTTTGTATACAATCATATTTAATAAAAATAATAA
* * * *
76480 GATTTTGTAATATAATCATATTTATTATAAATAA-AA
1 AATTTTGT-ATACAATCATATTTAATAAAAATAATAA
76516 AATTTTG
1 AATTTTG
76523 AATTGATCTA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
36 14 0.40
37 21 0.60
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.46
Consensus pattern (36 bp):
AATTTTGTATACAATCATATTTAATAAAAATAATAA
Found at i:76790 original size:15 final size:14
Alignment explanation
Indices: 76768--76802 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
76758 TATATTGAAG
76768 TTAATTTTTTACAA
1 TTAATTTTTTACAA
*
76782 TTCAATTTTTTTCAA
1 TT-AATTTTTTACAA
76797 TTAATT
1 TTAATT
76803 AATTAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (14 bp):
TTAATTTTTTACAA
Found at i:77556 original size:2 final size:2
Alignment explanation
Indices: 77549--77580 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
77539 TATCTTCCTT
77549 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
77581 ATAAAGTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:78033 original size:2 final size:2
Alignment explanation
Indices: 78028--78063 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
78018 AAAACTTTTA
78028 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
78064 GCTTTTTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82781 original size:3 final size:3
Alignment explanation
Indices: 82773--82813 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
82763 GTTATTAACA
82773 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
82814 AAGGTAACAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Done.