Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1424
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: 50187
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:4114 original size:78 final size:79
Alignment explanation
Indices: 3930--4107 Score: 227
Period size: 78 Copynumber: 2.3 Consensus size: 79
3920 AGATAACAAC
* * * *
3930 GGGGCTGGAGTATCCCCGATTATGGAAAATCGGTGTTCCAGAAATAAAATCGGGGTTGAGTATCC
1 GGGGTTGGAGTATCCCCGATTATAGAAAATCAGTGTTCCAGAAATAAAATCAGGGTTGAGTATCC
*
3995 CTTCAAAAATAACA
66 CCTCAAAAATAACA
* * **
4009 -GGGTTGGAGTATCCCTGATTATAGAAAATCAGTATT-TTGAAAATAAAATCAGGGTTGGAGTAT
1 GGGGTTGGAGTATCCCCGATTATAGAAAATCAGTGTTCCAG-AAATAAAATCAGGGTT-GAGTAT
*
4072 CCCCTCGAAAATAA-A
64 CCCCTCAAAAATAACA
4087 GGGGTTGGAGTATCCCCGATT
1 GGGGTTGGAGTATCCCCGATT
4108 GTGAAAAATT
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
77 1 0.01
78 47 0.55
79 37 0.44
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (79 bp):
GGGGTTGGAGTATCCCCGATTATAGAAAATCAGTGTTCCAGAAATAAAATCAGGGTTGAGTATCC
CCTCAAAAATAACA
Found at i:4133 original size:79 final size:79
Alignment explanation
Indices: 3930--4133 Score: 204
Period size: 79 Copynumber: 2.6 Consensus size: 79
3920 AGATAACAAC
* * * * * *
3930 GGGGCTGGAGTATCCCCGATTATGGAAAATCGGTG-TTCCAGAAATAAAATCGGGGTTGAGTATC
1 GGGGTTGGAGTATCCCCGATTATGAAAAATTGATGATT-TAGAAATAAAATCAGGGTTGAGTATC
*
3994 CCTTCAAAAATAACA
65 CCCTCAAAAATAACA
* * *
4009 -GGGTTGGAGTATCCCTGATTAT-AGAAAA-TCA-GTATTTTGAAAATAAAATCAGGGTTGGAGT
1 GGGGTTGGAGTATCCCCGATTATGA-AAAATTGATG-ATTTAG-AAATAAAATCAGGGTT-GAGT
*
4070 ATCCCCTCGAAAATAA-A
62 ATCCCCTCAAAAATAACA
* *
4087 GGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGATTTAGGAATAA
1 GGGGTTGGAGTATCCCCGATTATGAAAAATTGATGATTTAGAAATAA
4134 GGCCGGGGTT
Statistics
Matches: 100, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
76 1 0.01
77 1 0.01
78 42 0.42
79 47 0.47
80 8 0.08
81 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (79 bp):
GGGGTTGGAGTATCCCCGATTATGAAAAATTGATGATTTAGAAATAAAATCAGGGTTGAGTATCC
CCTCAAAAATAACA
Found at i:4271 original size:28 final size:28
Alignment explanation
Indices: 4240--4315 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
4230 GAAATAAAAT
* *
4240 CGGGGTTGGAGTATTCCCTAAAAAATAA
1 CGGGGTTGGAGTATCCCCGAAAAAATAA
* * **
4268 CGGGATTAGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAAAAAATAA
* *
4296 CGGAGTTGGAGTACCCCCGA
1 CGGGGTTGGAGTATCCCCGA
4316 TTATGAAAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.21
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAAAAAATAA
Found at i:4460 original size:51 final size:51
Alignment explanation
Indices: 4405--4501 Score: 158
Period size: 51 Copynumber: 1.9 Consensus size: 51
4395 CAATTGTGAA
* * *
4405 AAATTGGTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTGCTGT
1 AAATTGCTGCTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTGCTGT
*
4456 AAATTGCTGCTTTAGAAATAAAATCGGAGTTGGGGTATCCCCGATT
1 AAATTGCTGCTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATT
4502 AAGAAAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (51 bp):
AAATTGCTGCTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTGCTGT
Found at i:4511 original size:51 final size:52
Alignment explanation
Indices: 4402--4512 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 52
4392 CCTCAATTGT
* * * **
4402 GAAAAATTGGTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTGCT
1 GAAAAATTGCTGCTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTGAA
* *
4454 G-TAAATTGCTGCTTTAGAAATAAAATCGGAGTTGGGGTATCCCCGATT-AA
1 GAAAAATTGCTGCTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTGAA
4504 GAAAAATTG
1 GAAAAATTG
4513 ATGTTTTGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
50 1 0.02
51 48 0.96
52 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (52 bp):
GAAAAATTGCTGCTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTGAA
Found at i:6889 original size:20 final size:19
Alignment explanation
Indices: 6846--7018 Score: 94
Period size: 20 Copynumber: 9.7 Consensus size: 19
6836 AAAATGCCTG
* *
6846 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATG-AC
6866 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
*
6886 AATGTAT---T--GAT-AC
1 AATGTATCGATACAATGAC
*
6899 AATGTATCGATATAATGAGC
1 AATGTATCGATACAATGA-C
*
6919 AATGTAT---T--GAT-AC
1 AATGTATCGATACAATGAC
6932 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
6952 AATG--T--AT-CAAT-AC
1 AATGTATCGATACAATGAC
*
6965 AATTTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
*
6985 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AC
*
7005 AATGTATCAATACA
1 AATGTATCGATACA
7019 TCTGGGTAAA
Statistics
Matches: 120, Mismatches: 10, Indels: 46
0.68 0.06 0.26
Matches are distributed among these distances:
13 20 0.17
14 3 0.03
15 9 0.08
16 4 0.03
17 4 0.03
18 9 0.08
19 4 0.03
20 66 0.55
21 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.30
Consensus pattern (19 bp):
AATGTATCGATACAATGAC
Found at i:6901 original size:13 final size:13
Alignment explanation
Indices: 6885--6981 Score: 65
Period size: 13 Copynumber: 8.4 Consensus size: 13
6875 ATACAATGAG
*
6885 CAATGTATTGATA
1 CAATGTATCGATA
6898 CAATGTATCGATA
1 CAATGTATCGATA
*
6911 TAATG-A--G---
1 CAATGTATCGATA
*
6918 CAATGTATTGATA
1 CAATGTATCGATA
6931 CAATGTATCGATA
1 CAATGTATCGATA
6944 CAATG-A--G---
1 CAATGTATCGATA
*
6951 CAATGTATCAATA
1 CAATGTATCGATA
*
6964 CAATTTATCGATA
1 CAATGTATCGATA
6977 CAATG
1 CAATG
6982 AGCAATGTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 24
0.67 0.08 0.25
Matches are distributed among these distances:
7 9 0.14
8 2 0.03
10 3 0.05
12 2 0.03
13 48 0.75
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:6908 original size:33 final size:33
Alignment explanation
Indices: 6866--7001 Score: 227
Period size: 33 Copynumber: 4.1 Consensus size: 33
6856 TACATTGTAA
*
6866 AATGTATCGATACAATGAGCAATGTATTGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
* *
6899 AATGTATCGATATAATGAGCAATGTATTGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
*
6932 AATGTATCGATACAATGAGCAATGTATCAATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
*
6965 AATTTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
6998 AATG
1 AATG
7002 CAAAATGTAT
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 96 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (33 bp):
AATGTATCGATACAATGAGCAATGTATCGATAC
Found at i:7800 original size:42 final size:42
Alignment explanation
Indices: 7753--7943 Score: 199
Period size: 42 Copynumber: 4.5 Consensus size: 42
7743 AAAAATAGTA
* *
7753 CGTCCTGCT-TTTCGAGGATAAAGGAAAAAGGAAAACGAAA-TG
1 CGTCCTGCTCTTT-GAGGACAAAAGAAAAAGGAAAA-GAAAGTG
* *
7795 CGTCCTGCTCTTTGAGGACAAAAGAAAGAGGAAAAATAAAGTG
1 CGTCCTGCTCTTTGAGGACAAAAGAAAAAGG-AAAAGAAAGTG
*
7838 CGTCCTGCTCTTTGAGGACAAAAGAGAAAAGAAAGGAATGAAA-TG
1 CGTCCTGCTCTTTGAGGACAAAAGA-AAAAGGAA--AA-GAAAGTG
* * * * * *
7883 TGTTCTGTTCTTTGAGGACAAAGGAAAGAGGAAAATAAAGTG
1 CGTCCTGCTCTTTGAGGACAAAAGAAAAAGGAAAAGAAAGTG
7925 CGTCCTGCTCTTTGAGGAC
1 CGTCCTGCTCTTTGAGGAC
7944 TAGAAAGTGC
Statistics
Matches: 124, Mismatches: 17, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
41 3 0.02
42 47 0.38
43 36 0.29
44 10 0.08
45 25 0.20
46 3 0.02
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.21
Consensus pattern (42 bp):
CGTCCTGCTCTTTGAGGACAAAAGAAAAAGGAAAAGAAAGTG
Found at i:8020 original size:61 final size:60
Alignment explanation
Indices: 7919--8183 Score: 335
Period size: 61 Copynumber: 4.4 Consensus size: 60
7909 AGAGGAAAAT
* * *
7919 AAAGTGCGTCCTGCTCTTTGAGGACTAGAAAGTGCTACCAACTCGTGTGGGCTTTGAAAAGG
1 AAAG-GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTG-AAAGG
* *
7981 AAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGTCACCAACTTGTGTGGGCTTTGCAAAGAG
1 AAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTG-AAAG-G
* * *
8043 AAA-GCATCCTGCTCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGG
1 AAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGG
* * *
8102 AAAAGGCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTATGGGCTTT---A--
1 -AAAGGCGTCCTGCTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGG
8159 AAAGGCGTCCTGCTCTTTGAGGACT
1 AAAGGCGTCCTGCTCTTTGAGGACT
8184 AAAGGGCGAA
Statistics
Matches: 183, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
56 24 0.13
59 2 0.01
60 7 0.04
61 116 0.63
62 34 0.19
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (60 bp):
AAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGG
Found at i:8258 original size:94 final size:95
Alignment explanation
Indices: 8096--8280 Score: 291
Period size: 94 Copynumber: 2.0 Consensus size: 95
8086 TGTGGGCTTT
8096 GAAAGGAAAAGGCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTATGGGCTTTAAA
1 GAAAGGAAAAGGCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTATGGGCTTTAAA
* *
8161 AGGCGTCCTGCTCTTTGAGGACTAAAGGGC
66 AGGCATCCTACTCTTTGAGGACTAAAGGGC
* * * ** *
8191 GAAAGGAGAGGGCGTCCTGCTCTTTGAGGACT-GGTAAGTGCCACCAACTTGTGTGGGCTTTAAA
1 GAAAGGAAAAGGCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTATGGGCTTTAAA
8255 AGGCATCCTACTCTTTGAGGACTAAA
66 AGGCATCCTACTCTTTGAGGACTAAA
8281 AAAAAATGCC
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
94 53 0.65
95 29 0.35
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (95 bp):
GAAAGGAAAAGGCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTATGGGCTTTAAA
AGGCATCCTACTCTTTGAGGACTAAAGGGC
Found at i:8367 original size:55 final size:56
Alignment explanation
Indices: 8201--8505 Score: 418
Period size: 55 Copynumber: 5.4 Consensus size: 56
8191 GAAAGGAGAG
*** *
8201 GGCGTCCTGCTCTTTGAGGACTGGTAA-GTGCCACCAACTTGTGTGGGCTTTAAAA
1 GGCGTCCTGCTCTTTGAGGACTAAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA
* * ** *
8256 GGCATCCTACTCTTTGAGGACTAAAAAAAAATGCCACCAACTTCTGTGGGCTTTGAAA
1 GGCGTCCTGCTCTTTGAGGACT--AAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA
* * * *
8314 GGCATCCTGCTCTTTCAGGACT-GAAAGGTGCCACCAACTTATGTGGGCTTTGAAA
1 GGCGTCCTGCTCTTTGAGGACTAAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA
**
8369 GGCGTCCTGCTCTTTGAGGACTAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAA
1 GGCGTCCTGCTCTTTGAGGACT-AAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA
8426 GGCGTCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA
1 GGCGTCCTGCTCTTTGAGGACTAAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA
*
8481 GGCGTCTTGCTCTTTGAGGACTAAA
1 GGCGTCCTGCTCTTTGAGGACTAAA
8506 GGGTGAAAGG
Statistics
Matches: 221, Mismatches: 23, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
55 121 0.55
56 2 0.01
57 53 0.24
58 45 0.20
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.28
Consensus pattern (56 bp):
GGCGTCCTGCTCTTTGAGGACTAAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA
Found at i:8453 original size:112 final size:112
Alignment explanation
Indices: 8201--8505 Score: 495
Period size: 112 Copynumber: 2.7 Consensus size: 112
8191 GAAAGGAGAG
* * * *
8201 GGCGTCCTGCTCTTTGAGGACTGGTAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTA
1 GGCGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTG
8265 CTCTTTGAGGACTAAAAAAAAATGCCACCAACTTCTGTGGGCTTTGAAA
65 CTCTTTGAGGACT-AAAAAAAATGCCACCAACTTCTGTGGGCTTTGAAA
* * *
8314 GGCATCCTGCTCTTTCAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAGGCGTCCTGC
1 GGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGC
*
8379 TCTTTGAGGACTAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAA
66 TCTTTGAGGACTAAAAAAAATGCCACCAACTTCTGTGGGCTTTGAAA
* *
8426 GGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCTTGC
1 GGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGC
8491 TCTTTGAGGACTAAA
66 TCTTTGAGGACTAAA
8506 GGGTGAAAGG
Statistics
Matches: 178, Mismatches: 13, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
112 112 0.63
113 66 0.37
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.28
Consensus pattern (112 bp):
GGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGC
TCTTTGAGGACTAAAAAAAATGCCACCAACTTCTGTGGGCTTTGAAA
Found at i:8508 original size:319 final size:323
Alignment explanation
Indices: 7980--8576 Score: 893
Period size: 319 Copynumber: 1.8 Consensus size: 323
7970 CTTTGAAAAG
* * * * *
7980 GAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGTCACCAACTTGTGTGGGCTTTGCAAAGAGAA
1 GAAAGGCATCCTGCTCTTTCAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTG-AAAGAG--
***
8045 AGCATCCTGCTCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCA
63 AGCATCCTGCTCTTTGAGGATAAAAAAATGCCACCAACTTGTGTGGGCTTT---A-GAAAAGGCA
8110 TCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTATGGGCTTTAAAAGGCGTCCTGCTCT
124 TCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTATGGGCTTTAAAAGGCGTCCTGCTCT
* * *
8175 TTGAGGACTAAAGGGCGAAAGGAGAGGGCGTCCTGCTCTTTGAGGACTGGTAA-GTGCCACCAAC
189 TTGAGGACTAAAGGGCGAAAGGAGAGAGCGTCCTACTCTTTGAGGACTAG-AAGGTGCCACCAAC
8239 TTGTGTGGGCTTTAAAAGGCATCCTACTCTTTGAGGACTAAAAAAAAATGCCACCAACTTCTGTG
253 TTGTGTGGGCTTTAAAAGGCATCCTACTCTTTGAGGACTAAAAAAAAATGCCACCAACTTCTGTG
8304 GGCTTT
318 GGCTTT
8310 GAAAGGCATCCTGCTCTTTCAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTG-AA-AG-GC
1 GAAAGGCATCCTGCTCTTTCAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAGAGAGC
* *
8372 GTCCTGCTCTTTGAGGACTAAAAAAAATGCCACCAACTTGTGTGGGCTTT-G-AAAGGCGTCCTG
66 ATCCTGCTCTTTGAGGA-T-AAAAAAATGCCACCAACTTGTGTGGGCTTTAGAAAAGGCATCCTG
* * * *
8435 CTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCTTGCTCTTTGAG
129 CTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTATGGGCTTTAAAAGGCGTCCTGCTCTTTGAG
*
8499 GACTAAAGGGTGAAAGGAGAGAGCGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGT
194 GACTAAAGGGCGAAAGGAGAGAGCGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGT
8564 GGGCTTTAAAAGG
259 GGGCTTTAAAAGG
8577 AAAAGGCATC
Statistics
Matches: 246, Mismatches: 18, Indels: 17
0.88 0.06 0.06
Matches are distributed among these distances:
318 2 0.01
319 117 0.48
320 25 0.10
321 1 0.00
324 18 0.07
325 1 0.00
326 27 0.11
327 2 0.01
328 2 0.01
330 51 0.21
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (323 bp):
GAAAGGCATCCTGCTCTTTCAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAGAGAGC
ATCCTGCTCTTTGAGGATAAAAAAATGCCACCAACTTGTGTGGGCTTTAGAAAAGGCATCCTGCT
CTTTGAGGACTAGAAAAGTGCCACCAACTTGTATGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGA
CTAAAGGGCGAAAGGAGAGAGCGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGG
GCTTTAAAAGGCATCCTACTCTTTGAGGACTAAAAAAAAATGCCACCAACTTCTGTGGGCTTT
Found at i:16857 original size:52 final size:50
Alignment explanation
Indices: 16796--17192 Score: 239
Period size: 52 Copynumber: 7.6 Consensus size: 50
16786 GGAAATAACG
* *
16796 GGGTTGGAGTATCCCAGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCA
1 GGGTTGGAGTATCCCCGATTATGAAAAATTGGTG-TTTTGGAAATAAAA-CA
* * * *
16848 GAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACTA
1 GGGTTGGAGTATCCCCGATT-ATGAAAAATTGGTGTTTTGGAAATAAAAC-A
* * * *
16900 GGGTTGGAGTATCCCCGATTGT-AGAAAATTAGTGTTTTAGAAATAAAACCG
1 GGGTTGGAGTATCCCCGATTATGA-AAAATTGGTGTTTTGGAAATAAAA-CA
* *** * * *
16951 GGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCTG
1 GGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAAC-A
* **** * ** * *
17002 GGGTTTGAGTATCCCCTCGGAGGTAACAGGGTTGGAGTATCCGTGATGAAAT--AAC-
1 GGGTTGGAGTATCCCCGATTATG-AA-A-AATTGGTGT-T--TTG--GAAATAAAACA
* * *
17057 GAGGTTGGAGTATCCTCGCTTGTGAAAAATTGGTGTTTTTGGAAATAAAATC-
1 G-GGTTGGAGTATCCCCGATTATGAAAAATTGGTG-TTTTGGAAATAAAA-CA
* * * *
17109 GGAGTTGGAGTATCCTCGATTAATGGAAAATTGGTGTTTTGAAAATAAAACCG
1 GG-GTTGGAGTATCCCCGATT-ATGAAAAATTGGTGTTTTGGAAATAAAA-CA
*
17162 GGGTTGGAGTATCCTCGATTAT-AAACAATTG
1 GGGTTGGAGTATCCCCGATTATGAAA-AATTG
17193 AGAAACTTAA
Statistics
Matches: 268, Mismatches: 54, Indels: 47
0.73 0.15 0.13
Matches are distributed among these distances:
49 5 0.02
50 3 0.01
51 91 0.34
52 105 0.39
53 32 0.12
54 4 0.01
55 4 0.01
56 15 0.06
57 4 0.01
59 5 0.02
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (50 bp):
GGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAACA
Found at i:16948 original size:51 final size:50
Alignment explanation
Indices: 16796--17017 Score: 221
Period size: 51 Copynumber: 4.3 Consensus size: 50
16786 GGAAATAACG
* * *
16796 GGGTTGGAGTATCCCAGATTGTGAAAAATTGGTGTTTTTGGAAATAAAA-TCA
1 GGGTTGGAGTATCCCCGATTATG-AAAATTAGTG-TTTTGGAAATAAAACT-A
* * * *
16848 GAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACTA
1 GGGTTGGAGTATCCCCGATT--ATGAAAATTAGTGTTTTGGAAATAAAACTA
* * **
16900 GGGTTGGAGTATCCCCGATTGTAGAAAATTAGTGTTTTAGAAATAAAACCG
1 GGGTTGGAGTATCCCCGATTAT-GAAAATTAGTGTTTTGGAAATAAAACTA
* * * * *
16951 GGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCTG
1 GGGTTGGAGTATCCCCGATTATGA-AAATTAGTGTTTTGGAAATAAAACTA
*
17002 GGGTTTGAGTATCCCC
1 GGGTTGGAGTATCCCC
17018 TCGGAGGTAA
Statistics
Matches: 144, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
50 2 0.01
51 79 0.55
52 51 0.35
53 11 0.08
54 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (50 bp):
GGGTTGGAGTATCCCCGATTATGAAAATTAGTGTTTTGGAAATAAAACTA
Found at i:19561 original size:13 final size:13
Alignment explanation
Indices: 19543--19568 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19533 ACAAAGATCG
19543 ATGTATCGATACA
1 ATGTATCGATACA
19556 ATGTATCGATACA
1 ATGTATCGATACA
19569 CTTCCTTAAT
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:19579 original size:21 final size:21
Alignment explanation
Indices: 19555--19596 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
19545 GTATCGATAC
19555 AATGTATCGATACACTTCCTT
1 AATGTATCGATACACTTCCTT
*
19576 AATGTATCGATACATTTCCTT
1 AATGTATCGATACACTTCCTT
19597 GGCAGTAGCT
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:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (21 bp):
AATGTATCGATACACTTCCTT
Found at i:20841 original size:171 final size:171
Alignment explanation
Indices: 20530--21341 Score: 874
Period size: 171 Copynumber: 4.7 Consensus size: 171
20520 TGCATCCGGA
*
20530 TCTTTGAGGACTA-AAAAGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCT
1 TCTTTGAGGACTAGAAAA-TGCCACCAACTCGTGTGGGCTTT----A--AAAGGCGTCCTGCTCT
* * *
20594 TTAAGGACT-AGAAGGTGCCACCAACTTGTGCGGGCTTT----GAAAAGCGTCCTGCTCTTTAAG
59 TTGAGGACTGAGAA-GTGCCACCAACTTGTGTGGGCTTTAAAGGAAAAGCGTCCTGCTCTTTGAG
* * *
20654 GACTGGAAAATGCCACCAAATTGCGTGGGCTTT-AAG-AGGCGTCCTGC
123 GAATGGAAAATGCCACCAACTTGTGTGGGCTTTGAAGAAGGCGTCCTGC
* * *
20701 TTTTTGAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGA
1 TCTTTGAGGACTAGAAAATGCCACCAACTCGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGA
* * *
20766 CTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAGGCGTCCTACTCTTTGAGGAATGG
66 CTGAGAAGTGCCACCAACTTGTGTGGGCTTT--AAAGGAAAAGCGTCCTGCTCTTTGAGGAATGG
** * *
20831 AAGGTGCCACCAACTTGTGCGGGCTTTGAA-AA-ACGTCCTGC
129 AAAATGCCACCAACTTGTGTGGGCTTTGAAGAAGGCGTCCTGC
* * * * * *
20872 TCTTTGAGGGCTGGGAAGTGCCACCAAC-CTGTGTGGGCTTTAAAAGGCATCATGCTCTTTGAGG
1 TCTTTGAGGACTAGAAAATGCCACCAACTC-GTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGG
* * *
20936 ACTGAAAAGTGCCCCCAACTTGTGTGGGCTTT----GAAAAGCGTCCTGCTCTTTGAGGACTGGA
65 ACTGAGAAGTGCCACCAACTTGTGTGGGCTTTAAAGGAAAAGCGTCCTGCTCTTTGAGGAATGGA
* * *
20997 AAATGCCACCAACTTGTGTGGGCTCTGAAAAGAAAAGGCATCCCGC
130 AAATGCCACCAACTTGTGTGGGCTTTG--AAG--AAGGCGTCCTGC
* * *
21043 TCTTTGAGGACTACAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGACGTCCTGCTCTTTGAGG
1 TCTTTGAGGACTAGAAAA-TGCCACCAACTCGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGG
* *
21108 ACTG-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTCTTGCTCTTTGA-GAAC
65 ACTGAG-AAGTGCCACCAACTTGTGTGGGCTTT-AAAGGAAAA-GCGTCCTGCTCTTTGAGGAA-
**
21171 TAAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTCCTGC
126 TGGAAAA-TGCCACCAACTTGTGTGGGCTTTG-AA-G--AAGGCGTCCTGC
* * *
21222 TCTTTGAGGGCTAGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGCGTCCTGCTCTTTGAGGA
1 TCTTTGAGGACTAGAAAATGCCACCAACTCGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGA
* * *
21287 CTGA-AGGTGCCACCAACTCGTGTGGGCTTT-AA--AAAGGCGTCCTGCTCTTTGAGGA
66 CTGAGAAGTGCCACCAACTTGTGTGGGCTTTAAAGGAAAAGCGTCCTGCTCTTTGAGGA
21342 CTGAAAGGTG
Statistics
Matches: 545, Mismatches: 65, Indels: 60
0.81 0.10 0.09
Matches are distributed among these distances:
165 96 0.18
166 3 0.01
167 2 0.00
170 3 0.01
171 190 0.35
172 91 0.17
173 5 0.01
175 2 0.00
177 30 0.06
178 71 0.13
179 52 0.10
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (171 bp):
TCTTTGAGGACTAGAAAATGCCACCAACTCGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGA
CTGAGAAGTGCCACCAACTTGTGTGGGCTTTAAAGGAAAAGCGTCCTGCTCTTTGAGGAATGGAA
AATGCCACCAACTTGTGTGGGCTTTGAAGAAGGCGTCCTGC
Found at i:20935 original size:226 final size:224
Alignment explanation
Indices: 20530--21344 Score: 1016
Period size: 226 Copynumber: 3.6 Consensus size: 224
20520 TGCATCCGGA
**
20530 TCTTTGAGGACTA-AAAAGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCT
1 TCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCT
* * *
20594 TTAAGGACTAGAAGGTGCCACCAACTTGTGCGGGCTTTGAAAAGCGTCCTGCTCTTTAAGGACTG
65 TTGAGGACT-GAAGGTGCCACCAACTTGTGCGGGCTTT-AAAAACGTCCTGCTCTTTGAGGACTG
* * * * *
20659 GAAAATGCCACCAAATTGCGTGGGCTTTAAGAGGCGTCCTGCTTTTTGAGGACTGGAAAA-TGCC
128 GAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCATGCTCTTTGAGGACT-GAAAAGTGCC
*
20723 ACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGC
192 ACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGC
* * * * *
20756 TCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAGGCGTCCTACTCTT
1 TCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCTT
* *
20821 TGAGGAATGGAAGGTGCCACCAACTTGTGCGGGCTTTGAAAAACGTCCTGCTCTTTGAGGGCTGG
66 TGAGGACT-GAAGGTGCCACCAACTTGTGCGGGCTTT-AAAAACGTCCTGCTCTTTGAGGACTGG
* * * * *
20886 GAAGTGCCACCAACCTGTGTGGGCTTTAAAAGGCATCATGCTCTTTGAGGACTGAAAAGTGCCCC
129 AAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCATGCTCTTTGAGGACTGAAAAGTGCCAC
*
20951 CAACTTGTGTGGGCTTTGAAAAGCGTCCTGC
194 CAACTTGTGTGGGCTTTGAAAGGCGTCCTGC
* * * * *
20982 TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTCTGAAAAGAAAAGGCATCCCGCTCTT
1 TCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCTT
* * *
21047 TGAGGACTACAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGACGTCCTGCTCTTTGAGGACTG
66 TGAGGACT--GAAGGTGCCACCAACTTGTGCGGGCTTTAAAA-ACGTCCTGCTCTTTGAGGACTG
* * *
21112 GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTCTTGCTCTTTGAGAACTAAAAA
128 GAAAATGCCACCAACTTGTGTGGGCTTT------AAAAGGCGTCATGCTCTTTGAGGACT-GAAA
21177 AGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTCCTGC
186 AGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCGTCCTGC
*
21222 TCTTTGAGGGCTAGAAAATGCCACCAACTTGTGTGGGCTTT---AA-G--AGGCGTCCTGCTCTT
1 TCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCTT
* *
21281 TGAGGACTGAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGGCGTCCTGCTCTTTGAGGACTG
66 TGAGGACTGAAGGTGCCACCAACTTGTGCGGGCTTTAAAAA--CGTCCTGCTCTTTGAGGACTG
21345 AAAGGTGAAA
Statistics
Matches: 513, Mismatches: 57, Indels: 31
0.85 0.09 0.05
Matches are distributed among these distances:
225 5 0.01
226 260 0.51
227 73 0.14
231 1 0.00
232 29 0.06
233 44 0.09
234 48 0.09
237 2 0.00
239 1 0.00
240 50 0.10
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (224 bp):
TCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCTT
TGAGGACTGAAGGTGCCACCAACTTGTGCGGGCTTTAAAAACGTCCTGCTCTTTGAGGACTGGAA
AATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCATGCTCTTTGAGGACTGAAAAGTGCCACCA
ACTTGTGTGGGCTTTGAAAGGCGTCCTGC
Found at i:21345 original size:55 final size:56
Alignment explanation
Indices: 20530--21348 Score: 868
Period size: 55 Copynumber: 14.3 Consensus size: 56
20520 TGCATCCGGA
** **
20530 TCTTTGAGGACTAAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAGGCGTCCTGC
1 TCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT---AA--AAAGGCGTCCTGC
* * * * *
20591 TCTTTAAGGACTAGAAGGTGCCACCAACTTGTGCGGGCTTTGAAAA-GCGTCCTGC
1 TCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGGCGTCCTGC
* * * * *
20646 TCTTTAAGGACTGGAAAATGCCACCAAATTGCGTGGGCTTT-AAGAGGCGTCCTGC
1 TCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGGCGTCCTGC
* * * *
20701 TTTTTGAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTT-GAAAGGCGTCCTGC
1 TCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGGCGTCCTGC
* *
20756 TCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAGGCGTCCTAC
1 TCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT---AA--AAAGGCGTCCTGC
* * *
20817 TCTTTGAGGAATGGAAGGTGCCACCAACTTGTGCGGGCTTTGAAAAA--CGTCCTGC
1 TCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAAGGCGTCCTGC
* * * * *
20872 TCTTTGAGGGCTGGGAAGTGCCACCAACCTGTGTGGGCTTT-AAAAGGCATCATGC
1 TCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGGCGTCCTGC
* * *
20927 TCTTTGAGGACTGAAAAGTGCCCCCAACTTGTGTGGGCTTTGAAAA-GCGTCCTGC
1 TCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGGCGTCCTGC
* * * *
20982 TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTCTGAAAAGAAAAGGCATCCCGC
1 TCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCT-T---TA-AAAAGGCGTCCTGC
** *
21043 TCTTTGAGGACTACAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGACGTCCTGC
1 TCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGGCGTCCTGC
* *
21099 TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTCTTGC
1 TCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT---A--AAAAGGCGTCCTGC
* **
21160 TCTTTGAGAACTAAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTCCTGC
1 TCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTT---A--AAAAGGCGTCCTGC
* * * *
21222 TCTTTGAGGGCTAGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGCGTCCTGC
1 TCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGGCGTCCTGC
* *
21277 TCTTTGAGGACT-GAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGGCGTCCTGC
1 TCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGGCGTCCTGC
21332 TCTTTGAGGACT-GAAAG
1 TCTTTGAGGACTGGAAAG
21349 GTGAAAGGAG
Statistics
Matches: 650, Mismatches: 83, Indels: 56
0.82 0.11 0.07
Matches are distributed among these distances:
53 4 0.01
54 28 0.04
55 344 0.53
56 31 0.05
57 3 0.00
58 1 0.00
59 2 0.00
60 4 0.01
61 154 0.24
62 79 0.12
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (56 bp):
TCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGGCGTCCTGC
Found at i:21457 original size:100 final size:93
Alignment explanation
Indices: 21264--21459 Score: 241
Period size: 100 Copynumber: 2.0 Consensus size: 93
21254 GTGGGCTTTA
* * *
21264 AGAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGGCGTCC
1 AGAGGCGTCCTACTCTTTGAGGACTGAAGATGCCACCAACTCGTGTGGGCTTTAAAAAGGCATCC
* **
21329 TGCTCTTTGAGGACTGAAAGGTGAAAGG
66 TGCTCTTTGAGGACTAAAAAATGAAAGG
*
21357 AGAGAGCGTCCTACTCTTTGAGGACTAGGAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
1 AGAG-GCGTCCTACTCTTTGAGGACT--GAAGATGCCACCAACTCGTGTGGGCTTT---A--AAA
*
21421 AGGCATCCTGCTCTTTGAGGACTAAAAAATGGAAGG
58 AGGCATCCTGCTCTTTGAGGACTAAAAAATGAAAGG
21457 AGA
1 AGA
21460 AGGTTTAGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
93 4 0.05
94 20 0.23
95 22 0.25
96 3 0.03
98 1 0.01
100 37 0.43
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.23
Consensus pattern (93 bp):
AGAGGCGTCCTACTCTTTGAGGACTGAAGATGCCACCAACTCGTGTGGGCTTTAAAAAGGCATCC
TGCTCTTTGAGGACTAAAAAATGAAAGG
Found at i:28289 original size:79 final size:79
Alignment explanation
Indices: 28157--28329 Score: 231
Period size: 79 Copynumber: 2.2 Consensus size: 79
28147 CAACGGGGCC
* *
28157 GGAGTATCCCCGATTATGGAAAATCGGTGTTCCAGAAATAAAACCGAGATTGGAGTATCCCCTCG
1 GGAGTATCCCCGATTATAGAAAATCAGTGTTCCAGAAATAAAACCGAGATTGGAGTATCCCCTCG
* *
28222 GAAATAATAGGGTT
66 AAAATAACAGGGTT
* * ** * *
28236 GGAGTATCCCTGATTATAGAAAATCAGTATT-TTGAAAATAAAATCGAGGTTGGAGTATCCCCTC
1 GGAGTATCCCCGATTATAGAAAATCAGTGTTCCAG-AAATAAAACCGAGATTGGAGTATCCCCTC
*
28300 GAAAATAACGGGGTT
65 GAAAATAACAGGGTT
28315 GGAGTATCCCCGATT
1 GGAGTATCCCCGATT
28330 GTGAAAAATC
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
78 1 0.01
79 80 0.99
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (79 bp):
GGAGTATCCCCGATTATAGAAAATCAGTGTTCCAGAAATAAAACCGAGATTGGAGTATCCCCTCG
AAAATAACAGGGTT
Found at i:28355 original size:79 final size:78
Alignment explanation
Indices: 28148--28376 Score: 230
Period size: 79 Copynumber: 2.9 Consensus size: 78
28138 TTGAGATAAC
** * * * * *
28148 AACGGGGCCGGAGTATCCCCGATTATGGAAAATCGGTG-TTCCAGAAATAAAACCGAGATTGGAG
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATC-ATGATT-TAGAAATAAAATCGAGGTTGGAG
*
28212 TATCCCCTCGGAAAT
64 TATCCCCTCGAAAAT
** * *
28227 AATAGGGTTGGAGTATCCCTGATTAT-AGAAAATCA-GTATTTTGAAAATAAAATCGAGGTTGGA
1 AACGGGGTTGGAGTATCCCCGATTATGA-AAAATCATG-ATTTAG-AAATAAAATCGAGGTTGGA
28290 GTATCCCCTCGAAAAT
63 GTATCCCCTCGAAAAT
* * ** *
28306 AACGGGGTTGGAGTATCCCCGATTGTGAAAAATCTATGATTTAGGAATAAGGTCGAGGTTGAAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATC-ATGATTTAGAAATAAAATCGAGGTTGGAGT
28371 ATCCCC
65 ATCCCC
28377 CGATTATGAG
Statistics
Matches: 122, Mismatches: 21, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
77 1 0.01
78 1 0.01
79 112 0.92
80 7 0.06
81 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (78 bp):
AACGGGGTTGGAGTATCCCCGATTATGAAAAATCATGATTTAGAAATAAAATCGAGGTTGGAGTA
TCCCCTCGAAAAT
Found at i:28372 original size:51 final size:50
Alignment explanation
Indices: 28310--28479 Score: 164
Period size: 51 Copynumber: 3.3 Consensus size: 50
28300 GAAAATAACG
* * **
28310 GGGTTGGAGTATCCCCGATTGTGAAAAATCTATGATTTAGG-AATAAGGTC
1 GGGTTGGAGTATCCCCGATTATGAAAAATCAAT-ATTTAGGAAATAAAATC
* * *
28360 GAGGTTGAAGTATCCCCCGATTATGAGAAATCAATATTTTGGAAATAAAATC
1 G-GGTTGGAGTAT-CCCCGATTATGAAAAATCAATATTTAGGAAATAAAATC
* * ***
28412 GGAGTTGGAGTATCCCCGATTATGGAAATTTGGTATTTTA-GAAATAAAATC
1 GG-GTTGGAGTATCCCCGATTATGAAAAATCAATA-TTTAGGAAATAAAATC
28463 GGGATTGGAGTATCCCC
1 GGG-TTGGAGTATCCCC
28480 TCGAAAATAA
Statistics
Matches: 99, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
50 2 0.02
51 59 0.60
52 38 0.38
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (50 bp):
GGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTAGGAAATAAAATC
Found at i:28666 original size:51 final size:51
Alignment explanation
Indices: 28608--28772 Score: 172
Period size: 51 Copynumber: 3.2 Consensus size: 51
28598 AACGGGATTA
* * * *
28608 GAGTATCCACAATTATGAAAAATTGGTGTTTTGGAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAATCGGAGTTG
** ** * *
28659 GAGTATCCCCGATTGCGGTAAATCGCTGCTTTT-GAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTAAGAAAAATTGATG-TTTTGGAAATAAAATCGGAGTTG
* ** *
28710 GGGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATGGAA-CTGGGGTTG
1 GAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAATC-GGAGTTG
28761 GAGTATCCCCGA
1 GAGTATCCCCGA
28773 GATGAAAAAT
Statistics
Matches: 92, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
50 5 0.05
51 83 0.90
52 4 0.04
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (51 bp):
GAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAATCGGAGTTG
Found at i:28764 original size:291 final size:289
Alignment explanation
Indices: 28204--28770 Score: 646
Period size: 291 Copynumber: 2.0 Consensus size: 289
28194 ATAAAACCGA
** * * *
28204 GATTGGAGTATCCCCTCGGAAATAATAGGGTTGGAGTATCCCTGATTATAGAAAATCAGTATTTT
1 GATTGGAGTATCCCCGAGGAAATAATAGGGTTGGAGTACCCCTGATTATAAAAAATCAATATTTT
* * * * * *
28269 GAAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGA
66 GAAAATAAAACCGAGGTTGGAGTATCCCCTCGAAAATAACGGGATTAGAGTATCCACAATTATGA
** *
28334 AAAATCTATGATTTAGGAATAAGGTCGAGGTTGAAGTATCCCCCGATTATGAGAAATCAATATTT
131 AAAATCTATGATTTAGGAATAAAATCGAGGTTGAAGTATCCCCCGATTACGAGAAATCAATATTT
* * * *
28399 TGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATGGAAATTTGGTATTTTAGAAATAAAATCG
196 TGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGAAAAATTGATATTTTAGAAATAAAATCG
28464 GGATTGGAGTATCCCCTCGAAAATAACGG
261 GGATTGGAGTATCCCCTCGAAAATAACGG
* * *
28493 GATTGGAGTATTCCCGATGAAATAGTAGGGTTGGAGTACCCCTGATTATGAAAAAAATCAATATT
1 GATTGGAGTATCCCCGAGGAAATAATAGGGTTGGAGTACCCCTGATTAT--AAAAAATCAATATT
* * * *
28558 TTTAGATATAAAGCC-AGGGTTGGAGTATCCCCTCGGAAATAACGGGATTAGAGTATCCACAATT
64 TTGA-AAATAAAACCGA-GGTTGGAGTATCCCCTCGAAAATAACGGGATTAGAGTATCCACAATT
* * * *
28622 ATGAAAAAT-TGGTG-TTTTGGAAATAAAATCG-GAGTTGGAGTAT-CCCCGATTGCG-GTAAAT
127 ATGAAAAATCT-ATGATTTAGG-AATAAAATCGAG-GTTGAAGTATCCCCCGATTACGAG-AAAT
** * * * *
28682 CGCTGCTTTT-GAAATAAAATCGGAGTTGGGGTATCCCCGATTAAGAAAAATTGATGTTTTGGAA
188 CAAT-ATTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGAAAAATTGATATTTTAGAA
** *
28746 ATGGAA-CTGGGGTTGGAGTATCCCC
252 ATAAAATC-GGGATTGGAGTATCCCC
28771 GAGATGAAAA
Statistics
Matches: 230, Mismatches: 38, Indels: 18
0.80 0.13 0.06
Matches are distributed among these distances:
289 43 0.19
290 2 0.01
291 105 0.46
292 80 0.35
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.29
Consensus pattern (289 bp):
GATTGGAGTATCCCCGAGGAAATAATAGGGTTGGAGTACCCCTGATTATAAAAAATCAATATTTT
GAAAATAAAACCGAGGTTGGAGTATCCCCTCGAAAATAACGGGATTAGAGTATCCACAATTATGA
AAAATCTATGATTTAGGAATAAAATCGAGGTTGAAGTATCCCCCGATTACGAGAAATCAATATTT
TGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGAAAAATTGATATTTTAGAAATAAAATCG
GGATTGGAGTATCCCCTCGAAAATAACGG
Found at i:31053 original size:20 final size:20
Alignment explanation
Indices: 31028--31102 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
31018 AAAATGCTTG
31028 AATGTATCGATACATTGTAA
1 AATGTATCGATACATTGTAA
*
31048 AATGTATCGATACA--ATAA
1 AATGTATCGATACATTGTAA
* * *
31066 GCAATGTATTGATACAATGCAA
1 --AATGTATCGATACATTGTAA
31088 AATGTATCGATACAT
1 AATGTATCGATACAT
31103 CTAGGTAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 3 0.07
20 40 0.89
22 2 0.04
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATTGTAA
Found at i:31142 original size:20 final size:20
Alignment explanation
Indices: 31117--31171 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
31107 GTAAACCCAG
31117 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAC
*
31137 AATGTATTGATACAATGAAC
1 AATGTATCGATACAATGAAC
31157 AATGTATCGATACAA
1 AATGTATCGATACAA
31172 ATTGTGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:38538 original size:20 final size:20
Alignment explanation
Indices: 38513--38680 Score: 106
Period size: 20 Copynumber: 7.8 Consensus size: 20
38503 AAAAAAACAC
38513 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
* *
38533 AGAATGTATCGATACAGTCA
1 AGAATGTATCGATACATTGA
*
38553 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
38573 AAAATGTATCGATACATCTGGGTA
1 AGAATGTATCGATACAT-T--G-A
*
38597 AGAAGATAGAATGCATCAATACATTGA
1 AG-A-AT-G--T--ATCGATACATTGA
* *
38624 AGAATGTATCGATACAGTCA
1 AGAATGTATCGATACATTGA
* *
38644 TA-CATGTATCGATACATTAA
1 -AGAATGTATCGATACATTGA
* *
38664 AAAATGTATTGATACAT
1 AGAATGTATCGATACAT
38681 CTAGGTAAAA
Statistics
Matches: 117, Mismatches: 16, Indels: 30
0.72 0.10 0.18
Matches are distributed among these distances:
19 2 0.02
20 85 0.73
21 3 0.03
22 1 0.01
23 1 0.01
24 3 0.03
25 3 0.03
26 3 0.03
27 4 0.03
28 1 0.01
29 1 0.01
30 1 0.01
31 9 0.08
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:38620 original size:91 final size:91
Alignment explanation
Indices: 38465--38747 Score: 435
Period size: 91 Copynumber: 3.1 Consensus size: 91
38455 TTTTAACTAG
* * * * * *
38465 ATGTATCGATACATTG-AAAATATATCGATACATCAGGGAAAAAAACACAGAATGTATCGATACA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGG-TAAAAAGATAGAATGTATCAATACA
38529 TTGAAGAATGTATCGATACAGTCATAC
65 TTGAAGAATGTATCGATACAGTCATAC
* *
38556 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAGAAGATAGAATGCATCAATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAGAATGTATCAATACAT
38621 TGAAGAATGTATCGATACAGTCATAC
66 TGAAGAATGTATCGATACAGTCATAC
* * *
38647 ATGTATCGATACATTAAAAAATGTATTGATACATCTAGGTAAAAAGATAGAATGTATCAATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAGAATGTATCAATACAT
38712 TGAAGAATGTATCGATACA-TCCATAC
66 TGAAGAATGTATCGATACAGT-CATAC
38738 ATGTATCGAT
1 ATGTATCGAT
38748 CGATACATTA
Statistics
Matches: 177, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
90 1 0.01
91 156 0.88
92 20 0.11
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (91 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAGAATGTATCAATACAT
TGAAGAATGTATCGATACAGTCATAC
Found at i:39066 original size:20 final size:20
Alignment explanation
Indices: 39037--39108 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
39027 TTTTTACCCT
39037 AATGTATCGATATATTTTTC
1 AATGTATCGATATATTTTTC
* * * * *
39057 AATATATCGATACATGTATG
1 AATGTATCGATATATTTTTC
* *
39077 AATGTATCGATATATTCTGC
1 AATGTATCGATATATTTTTC
39097 AATGTATCGATA
1 AATGTATCGATA
39109 CATTATGTCT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (20 bp):
AATGTATCGATATATTTTTC
Found at i:39092 original size:40 final size:39
Alignment explanation
Indices: 39037--39115 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 39
39027 TTTTTACCCT
* *
39037 AATGTATCGATATATTTTTCAATATATCGATACATGTATG
1 AATGTATCGATATATTCTGCAATATATCGATACAT-TATG
*
39077 AATGTATCGATATATTCTGCAATGTATCGATACATTATG
1 AATGTATCGATATATTCTGCAATATATCGATACATTATG
39116 TCTTTTTACC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (39 bp):
AATGTATCGATATATTCTGCAATATATCGATACATTATG
Done.