Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold618
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: 64484
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:6443 original size:22 final size:24
Alignment explanation
Indices: 6392--6448 Score: 73
Period size: 22 Copynumber: 2.4 Consensus size: 24
6382 CTTGATCAGT
*
6392 GTGGTTAGCTTCGCGCTACATTTCA
1 GTGG-TAGCTTCGCGCTACATTCCA
*
6417 GTGGTAGCTTTG-GCTACA-TCCA
1 GTGGTAGCTTCGCGCTACATTCCA
6439 GTGGTAGCTT
1 GTGGTAGCTT
6449 GGTTGCTACT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 13 0.43
23 6 0.20
24 7 0.23
25 4 0.13
ACGTcount: A:0.16, C:0.21, G:0.28, T:0.35
Consensus pattern (24 bp):
GTGGTAGCTTCGCGCTACATTCCA
Found at i:13833 original size:24 final size:23
Alignment explanation
Indices: 13802--13898 Score: 146
Period size: 23 Copynumber: 4.3 Consensus size: 23
13792 ATAAGTGCCA
13802 CACTGATATGTAGCCGAAAGCTAC
1 CACTGATATGTAGCCG-AAGCTAC
13826 CACTGATATGTAGCCGAAGCTA-
1 CACTGATATGTAGCCGAAGCTAC
*
13848 CACTG--ATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
13869 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
13892 CACTGAT
1 CACTGAT
13899 CAATAACACT
Statistics
Matches: 67, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
20 14 0.21
21 5 0.07
22 5 0.07
23 27 0.40
24 16 0.24
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:13868 original size:43 final size:45
Alignment explanation
Indices: 13809--13898 Score: 157
Period size: 43 Copynumber: 2.0 Consensus size: 45
13799 CCACACTGAT
*
13809 ATGTAGCCGAAAGCTACCACTGATATGTAGCCGAAGCTA-CACTG
1 ATGTAGCCGAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
13853 ATGTAGCC-AAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCGAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
13897 AT
1 AT
13899 CAATAACACT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
43 29 0.66
44 15 0.34
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (45 bp):
ATGTAGCCGAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
Found at i:21182 original size:23 final size:23
Alignment explanation
Indices: 21156--21253 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
21146 ATAAGTGCCA
21156 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
21179 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
21202 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
21224 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
21247 CACTGAT
1 CACTGAT
21254 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:21221 original size:45 final size:45
Alignment explanation
Indices: 21163--21251 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
21153 CCACACTGAT
* *
21163 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
21208 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
21252 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:23151 original size:47 final size:47
Alignment explanation
Indices: 23042--23152 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
23032 CCGGGATAAG
* *
23042 CACATAGTGCTTCATCGGAATAAATCCGAAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
* * *
23089 CACAAAGTACTTCATCGGAACAAATCCGAAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTA-TAGTA
23136 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
23153 ACTCAATGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
Found at i:24008 original size:42 final size:43
Alignment explanation
Indices: 23912--24008 Score: 139
Period size: 42 Copynumber: 2.3 Consensus size: 43
23902 TTTATTTCTT
* *
23912 TCTTTCT-TTCCTTCTTTCTTTCTCACGTTTGCTCTCTGTTAG
1 TCTTTCTATTCTTTCTTTCTTTCTCACGTTTGCTCTCTGTTAC
23954 TCTTTCTA-TCTTTCTTTCTTTCTCACGTTTGCTCTCT-TTAAC
1 TCTTTCTATTCTTTCTTTCTTTCTCACGTTTGCTCTCTGTT-AC
23996 T-TTTCTATTCTTT
1 TCTTTCTATTCTTT
24009 ACTTATTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
41 8 0.16
42 42 0.84
ACGTcount: A:0.07, C:0.27, G:0.06, T:0.60
Consensus pattern (43 bp):
TCTTTCTATTCTTTCTTTCTTTCTCACGTTTGCTCTCTGTTAC
Found at i:26229 original size:13 final size:13
Alignment explanation
Indices: 26209--26242 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
26199 AATTTATTTT
26209 TATA-TTTTAAAA
1 TATATTTTTAAAA
26221 TATATTTTTAAAA
1 TATATTTTTAAAA
*
26234 AATATTTTT
1 TATATTTTT
26243 TTTAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATATTTTTAAAA
Found at i:31406 original size:12 final size:12
Alignment explanation
Indices: 31389--31413 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31379 ATTTTAAGCA
31389 ACTTGATTGATG
1 ACTTGATTGATG
31401 ACTTGATTGATG
1 ACTTGATTGATG
31413 A
1 A
31414 AATGAAATGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (12 bp):
ACTTGATTGATG
Found at i:32728 original size:16 final size:16
Alignment explanation
Indices: 32707--32776 Score: 79
Period size: 16 Copynumber: 4.2 Consensus size: 16
32697 TATGTGAGTG
32707 AAAAATAATAATTTTT
1 AAAAATAATAATTTTT
32723 AAAAATAAT-ATTTATT
1 AAAAATAATAATTT-TT
*
32739 AAAAATAATCAATTTTA
1 AAAAATAAT-AATTTTT
*
32756 AAATAAAAATAACTTTTT
1 AAA-AATAATAA-TTTTT
32774 AAA
1 AAA
32777 GTGAATTATT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
15 4 0.09
16 20 0.43
17 6 0.13
18 16 0.35
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAAATAATAATTTTT
Found at i:34427 original size:11 final size:11
Alignment explanation
Indices: 34394--34436 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
34384 AAATCATTTT
34394 GAAGAGAGAAA
1 GAAGAGAGAAA
* * *
34405 GAAAAAAAAAA
1 GAAGAGAGAAA
*
34416 GAAGGGAGAAA
1 GAAGAGAGAAA
34427 GAAGAGAGAA
1 GAAGAGAGAA
34437 GGGAGGGGGG
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (11 bp):
GAAGAGAGAAA
Found at i:34914 original size:19 final size:19
Alignment explanation
Indices: 34890--34936 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
34880 TTTCTTGGTT
34890 TTTTTTTTTGGGGGTTAGG
1 TTTTTTTTTGGGGGTTAGG
**
34909 TTTTTTTTTTTGGGTTAGG
1 TTTTTTTTTGGGGGTTAGG
34928 TTTTTTTTT
1 TTTTTTTTT
34937 TGGGTGCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.04, C:0.00, G:0.26, T:0.70
Consensus pattern (19 bp):
TTTTTTTTTGGGGGTTAGG
Found at i:34937 original size:19 final size:19
Alignment explanation
Indices: 34886--34941 Score: 87
Period size: 18 Copynumber: 2.9 Consensus size: 19
34876 AGGGTTTCTT
34886 GGTTTTTTTTTTTGGGGGTTA
1 GGTTTTTTTTTTT--GGGTTA
34907 GGTTTTTTTTTTTGGGTTA
1 GGTTTTTTTTTTTGGGTTA
34926 GG-TTTTTTTTTTGGGT
1 GGTTTTTTTTTTTGGGT
34942 GCTTAATGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 14 0.40
19 8 0.23
21 13 0.37
ACGTcount: A:0.04, C:0.00, G:0.30, T:0.66
Consensus pattern (19 bp):
GGTTTTTTTTTTTGGGTTA
Found at i:35851 original size:78 final size:77
Alignment explanation
Indices: 35688--35925 Score: 261
Period size: 78 Copynumber: 3.1 Consensus size: 77
35678 AAATCAAATT
*
35688 TTGAAAATACCT-CGATATGTGACTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTT
1 TTGAAAATACCTCCG-TGTGTGACTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
* * *
35750 TGAAAAATATAAA
65 TGAAAGACAGAAA
* *
35763 TTGAAAAAAATACCTCCGTGTGTGATCTGAA-GCTCAACTCACCTCTTGCAATATGAGTTGATTT
1 TTG---AAAATACCTCCGTGTGTGA-CTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TT
*
35827 TTTTTTAAAGACAGAAA
61 TTTTTGAAAGACAGAAA
* * * * *
35844 TTGAAAATAGCTCAGCGCGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTT
1 TTGAAAATACCTCCGTGTGTGA-CTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
*
35908 TGAAAGGCAGAAA
65 TGAAAGACAGAAA
35921 TTGAA
1 TTGAA
35926 TAACGGAAAT
Statistics
Matches: 137, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
75 3 0.02
77 24 0.18
78 88 0.64
79 6 0.04
81 16 0.12
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (77 bp):
TTGAAAATACCTCCGTGTGTGACTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
GAAAGACAGAAA
Found at i:46178 original size:90 final size:87
Alignment explanation
Indices: 46070--46238 Score: 230
Period size: 90 Copynumber: 1.9 Consensus size: 87
46060 CAAAATAATC
* * *
46070 AACTCATATTGCGAGAGGTGAGTTGGGCCTCAGGTCACACGCTGAGGTATTTTCAATTTCCGTTT
1 AACTCATATTGCGAGAGGTGAGCTGAGCCTC-GG-CACACGCCGAGGTATTTTCAATTTCCG-TT
46135 TTTCAATTTATGCTTTTCAAAAATT
63 TTTCAATTTATGCTTTTCAAAAATT
** * **
46160 AACTCATATTGCGAGAGGTGAGCTGAGCCTCGGGGCACGCCGAGGTATTTTTAATTTTTGTTTTT
1 AACTCATATTGCGAGAGGTGAGCTGAGCCTCGGCACACGCCGAGGTATTTTCAATTTCCGTTTTT
*
46225 CAATTTCTGCTTTT
66 CAATTTATGCTTTT
46239 AATTTCTGTT
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
87 18 0.26
88 21 0.30
89 2 0.03
90 29 0.41
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (87 bp):
AACTCATATTGCGAGAGGTGAGCTGAGCCTCGGCACACGCCGAGGTATTTTCAATTTCCGTTTTT
CAATTTATGCTTTTCAAAAATT
Found at i:46251 original size:13 final size:13
Alignment explanation
Indices: 46207--46251 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
46197 CGCCGAGGTA
*
46207 TTTTTAATTTTTG
1 TTTTTAATTTCTG
46220 TTTTTCAATTTCTG
1 TTTTT-AATTTCTG
*
46234 CTTTTAATTTCTG
1 TTTTTAATTTCTG
46247 TTTTT
1 TTTTT
46252 TCAAAAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.13, C:0.09, G:0.07, T:0.71
Consensus pattern (13 bp):
TTTTTAATTTCTG
Found at i:46252 original size:14 final size:14
Alignment explanation
Indices: 46207--46252 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
46197 CGCCGAGGTA
*
46207 TTTTTAATTTTTGT
1 TTTTTAATTTCTGT
*
46221 TTTTCAATTTCTG-
1 TTTTTAATTTCTGT
*
46234 CTTTTAATTTCTGT
1 TTTTTAATTTCTGT
46248 TTTTT
1 TTTTT
46253 CAAAAATCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.13, C:0.09, G:0.07, T:0.72
Consensus pattern (14 bp):
TTTTTAATTTCTGT
Found at i:46323 original size:101 final size:100
Alignment explanation
Indices: 46145--46424 Score: 386
Period size: 101 Copynumber: 2.8 Consensus size: 100
46135 TTTCAATTTA
* * * *
46145 TGCTTTTCAAAAATTAACTCATATTGCGAGAGGTGAGCTGAGCCTCGGGGCACGCCGAGGTATTT
1 TGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTT
* ** *
46210 TTAATTTTTGTTTTTCAATTTCTG-CTTTTAATTTC
66 TCAA-TTTTGTTTTTCAATTTCTGCCTTACAAATTC
* *
46245 TGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAATTGAGCCTCAGGGCACGCTGAGGTATT
1 TG-CTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATT
*
46310 TTCAATTTCTGTTTTTCAATTTTTGCCTTACAAATTC
65 TTCAATTT-TGTTTTTCAATTTCTGCCTTACAAATTC
* *
46347 TGCTTTTC--AAATCAACTCATATTGCGAGAGCTGAGTTGAGCCTCAGGACACGCTGAGGTATTT
1 TGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTT
46410 TCAATTTTCGTTTTT
66 TCAATTTT-GTTTTT
46425 TTAATTTATG
Statistics
Matches: 161, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
98 1 0.01
99 65 0.40
100 5 0.03
101 80 0.50
102 10 0.06
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (100 bp):
TGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTT
TCAATTTTGTTTTTCAATTTCTGCCTTACAAATTC
Found at i:46618 original size:148 final size:147
Alignment explanation
Indices: 46422--47965 Score: 840
Period size: 148 Copynumber: 9.7 Consensus size: 147
46412 AATTTTCGTT
* * * * * *
46422 TTTTTAATTTATGTTTCT-AAAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACA
* * * *
46486 CGCTAAGGTAATTTCAATTTTTGTTTGTCAAAACTCAACTCATATTGCAAGAGGTGAGTTGAGCT
66 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
46551 TCAAGACAAGTTGAGGTA
131 TCAAGAC-AGTTGAGGTA
* *
46569 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACA
* *
46634 TGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCC
66 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
46699 TCAAGACACGTTGAGGTA
131 TCAAGACA-GTTGAGGTA
* * * * *
46717 TTTTCAATTTCAGTCTTTAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACA
* * * * * *
46782 CGTTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAA
66 CGCTGAGGTAATTTCAATTTTTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
*
46847 CCTCAAGAC-GCTGAGGTA
129 CCTCAAGACAGTTGAGGTA
* * * *
46865 ATTTCAATTTTTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCA--AGA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACA
* * * *
46926 CGCTGAGGTGTTTTCCATTTCTGTTCTTCAATTTCTGTGTT-TCAAAAAAATCAGCTCATATTGT
66 CGCTGA-G-G---T--A------AT-TTCAATTTTTGT-TTGTC--AAAAATCAACTCATATTGC
* * * ** *
46990 GAGTGATGAGTTGAGCCTTGACTCACACGCTGAGGTA
114 GAGAGGTGAGTTGAGCC-TCA-AGACA-GTTGAGGTA
47027 TTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCCAAAAAAA-CAACTCATATTGCGAGAGGTGAG
1 TTTTC-AA-------TTTC------TGTTTTT-CAAAAAAATCAACTCATATTGCGAGAGGTGAG
* * * * **
47091 TTGAGCCTC-GGCTCACGTGCTGAGATATTTTCAATTTCTACTTT-TCAAAAGAATCAACTCATA
51 TTGAACCTCAGG-ACAC--GCTGAGGTAATTTCAATTT-TTGTTTGTC-AAA-AATCAACTCATA
* * *
47154 TTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTAAGGTA
110 TTGCGAGAGGTGAGTTGAGCCTCAAGACA-GTTGAGGTA
* * *
47193 CTTTT-AATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAC
1 -TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGAC
* * * * *
47257 ACGTTGAGGTATTTTCAATTTCTATCTTTCAAAAAAAAATCAAAAAAATCAAATCATATTGCGAG
65 ACGCTGAGGTAATTTCAATTT-T-TGTTT---------GTC--AAAAATCAACTCATATTGCGAG
*
47322 AGGTGAGTTGAGCCTCAAGAC-GCTGAGGTA
117 AGGTGAGTTGAGCCTCAAGACAGTTGAGGTA
* *
47352 TTTTCAATTTCCGTTTGTCAAATTATTTTTCAAAAATCCAACTCATATTGCGAGAGGTGAGTTGA
1 TTTTCAATTTCTGTTTTTC--A--A------AAAAAT-CAACTCATATTGCGAGAGGTGAGTTGA
* * * * * *
47417 GCCTC-GGCTCACGTGCTAAGGTATTTTCAATTTCTGCTTTTTAATTTCTACTTTTCAAAAGAAT
55 ACCTCAGG-ACAC--GCTGAGGTAATTTCAA----------TT--TTTGT--TTGTC-AAA-AAT
* * *
47481 CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGCAA
101 CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA-GTTGAGG-TA
* * * *
47530 TTTT-AATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTAAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACA
* * *
47594 CGTTGAGGTATTTTCAATTTCTGTCTT-TCAAAAAAAAATAAAAAAAAAATCAACTCATATTGCG
66 CGCTGAGGTAATTTCAATTTTTGT-TTGTC---------------AAAAATCAACTCATATTGCG
*
47658 AGAGGTGAGTTGAGCCTCAAGAC-GCTGAGGTA
115 AGAGGTGAGTTGAGCCTCAAGACAGTTGAGGTA
* * *
47690 TTTTCAATTTCCGTTTGTCAATTTATTTTTCAAAAATCCAACTCATATTGCGAGAGGTAAGTTGA
1 TTTTCAATTTCTGTTTTTC-A---A------AAAAAT-CAACTCATATTGCGAGAGGTGAGTTGA
* * * * * *
47755 GCCTC-GGCTCACCTGCTAAGGTATTTTCAATTTCTGCTTTTCAATTTCTACTTTTCAAAAGAAT
55 ACCTCAGG-ACA-C-GCTGAGGTAATTTCAA---------TT---TTTGT--TTGTC-AAA-AAT
* *
47819 CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAA
101 CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA-GTTGAGGT-A
* * *
47868 TTTT-AATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACA
* * *
47932 CGTTGAGGTATTTTCAATTTCTGTCTT-TCAAAAA
66 CGCTGAGGTAATTTCAATTTTTGT-TTGTCAAAAA
47966 AAAATAAAAA
Statistics
Matches: 1137, Mismatches: 116, Indels: 287
0.74 0.08 0.19
Matches are distributed among these distances:
144 7 0.01
145 1 0.00
146 39 0.03
147 16 0.01
148 223 0.20
149 4 0.00
150 63 0.06
151 19 0.02
152 47 0.04
153 1 0.00
154 2 0.00
155 2 0.00
157 2 0.00
158 54 0.05
159 23 0.02
160 7 0.01
161 60 0.05
162 18 0.02
163 42 0.04
164 32 0.03
165 4 0.00
166 77 0.07
167 24 0.02
168 41 0.04
169 10 0.01
170 38 0.03
171 7 0.01
172 47 0.04
173 3 0.00
174 22 0.02
175 81 0.07
176 7 0.01
177 41 0.04
178 41 0.04
179 5 0.00
180 2 0.00
181 1 0.00
182 10 0.01
183 3 0.00
184 3 0.00
186 3 0.00
187 3 0.00
188 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (147 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACA
CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
TCAAGACAGTTGAGGTA
Found at i:46622 original size:75 final size:75
Alignment explanation
Indices: 46422--46956 Score: 651
Period size: 75 Copynumber: 7.3 Consensus size: 75
46412 AATTTTCGTT
* * * * * *
46422 TTTTTAATTTATGTTTCT-AAAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
46486 CGCTAAGGTA
66 CGCTGAGGTA
* * * * * *
46496 ATTTCAATTTTTGTTTGTC--AAAACTCAACTCATATTGCAAGAGGTGAGTTGAGCTTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* *
46559 AGTTGAGGTA
66 CGCTGAGGTA
* *
46569 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
46634 TGCTGAGGTA
66 CGCTGAGGTA
* * * *
46644 ATTTCAATTTTTGTTTGTC--AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
46707 CGTTGAGGTA
66 CGCTGAGGTA
* * * * *
46717 TTTTCAATTTCAGTCTTTAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
46782 CGTTGAGGTA
66 CGCTGAGGTA
* *
46792 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAACCTCAAG--A
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
46855 CGCTGAGGTA
66 CGCTGAGGTA
* * * *
46865 ATTTCAATTTTTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAG--A
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
46926 CGCTGAGGTG
66 CGCTGAGGTA
* *
46936 TTTTCCATTTCTGTTCTTCAA
1 TTTTCAATTTCTGTTTTTCAA
46957 TTTCTGTGTT
Statistics
Matches: 400, Mismatches: 54, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
71 64 0.16
73 151 0.38
74 14 0.04
75 171 0.43
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (75 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
CGCTGAGGTA
Found at i:47047 original size:91 final size:90
Alignment explanation
Indices: 46866--47138 Score: 272
Period size: 91 Copynumber: 3.1 Consensus size: 90
46856 GCTGAGGTAA
* * * * *
46866 TTTCAATTTT-TGTTTGTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC-A---AG
1 TTTCAATTTTGTGTTT-CCAAAAAAACAACTCATATTGCGAGAGATGAGTTGAGCCTCGACTCAC
* *
46925 ACGCTGAGGTGTTTTCCATTTCTGTT
65 ACGCTGAGGTATTTTCAATTTCTGTT
* * * * *
46951 CTTCAATTTCTGTGTTT-CAAAAAAATCAGCTCATATTGTGAGTGATGAGTTGAGCCTTGACTCA
1 TTTCAATTT-TGTGTTTCCAAAAAAA-CAACTCATATTGCGAGAGATGAGTTGAGCCTCGACTCA
*
47015 CACGCTGAGGTATTTTCAAATTCTGTT
64 CACGCTGAGGTATTTTCAATTTCTGTT
* * *
47042 TTTCAAATTTTGTTTTTCCAAAAAAACAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCAC
1 TTTC-AATTTTGTGTTTCCAAAAAAACAACTCATATTGCGAGAGATGAGTTGAGCCTCGACTCAC
** * **
47107 GTGCTGAGATATTTTCAATTTCTACT
65 ACGCTGAGGTATTTTCAATTTCTGTT
47133 TTTCAA
1 TTTCAA
47139 AAGAATCAAC
Statistics
Matches: 152, Mismatches: 26, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
85 9 0.06
86 6 0.04
87 31 0.20
88 1 0.01
90 2 0.01
91 90 0.59
92 13 0.09
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (90 bp):
TTTCAATTTTGTGTTTCCAAAAAAACAACTCATATTGCGAGAGATGAGTTGAGCCTCGACTCACA
CGCTGAGGTATTTTCAATTTCTGTT
Found at i:47063 original size:15 final size:14
Alignment explanation
Indices: 47027--47059 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
47017 CGCTGAGGTA
47027 TTTTCAAATTCTGT
1 TTTTCAAATTCTGT
*
47041 TTTTCAAATTTTGT
1 TTTTCAAATTCTGT
47055 TTTTC
1 TTTTC
47060 CAAAAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (14 bp):
TTTTCAAATTCTGT
Found at i:47231 original size:75 final size:75
Alignment explanation
Indices: 47041--47451 Score: 359
Period size: 75 Copynumber: 5.2 Consensus size: 75
47031 CAAATTCTGT
*
47041 TTTTCAAATTT-TGTTTTTCCAAAAAAA-CAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGC
1 TTTTC-AATTTCTATTTTT-CAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-
* *
47103 TCACGTGCTGAGATA
63 ACAC--GCTGAGGTA
* *
47118 TTTTCAATTTCTACTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
*
47183 CGCTAAGGTA
66 CGCTGAGGTA
*
47193 CTTTT-AATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAC
1 -TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
*
47257 ACGTTGAGGTA
65 ACGCTGAGGTA
*
47268 TTTTCAATTTCTATCTTTCAAAAAAAAATCAAAAAAATCAAATCATATTGCGAGAGGTGAGTTGA
1 TTTTCAATTTCTAT-TTT----------TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
*
47333 GCCTCA--AGACGCTGAGGTA
55 GCCTCAGGACACGCTGAGGTA
***
47352 TTTTCAATTTCCGTTTGTCAAATTATTTTTCAAAAATCCAACTCATATTGCGAGAGGTGAGTTGA
1 TTTTCAATTT-C-----T---ATT-TTTCAAAAAAAT-CAACTCATATTGCGAGAGGTGAGTTGA
* *
47417 GCCTC-GGCTCACGTGCTAAGGTA
55 GCCTCAGG-ACAC--GCTGAGGTA
47440 TTTTCAATTTCT
1 TTTTCAATTTCT
47452 GCTTTTTAAT
Statistics
Matches: 281, Mismatches: 21, Indels: 59
0.78 0.06 0.16
Matches are distributed among these distances:
74 4 0.01
75 81 0.29
76 19 0.07
77 45 0.16
78 2 0.01
82 1 0.00
83 7 0.02
84 52 0.19
85 1 0.00
86 44 0.16
87 1 0.00
88 18 0.06
90 1 0.00
92 1 0.00
93 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (75 bp):
TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
CGCTGAGGTA
Found at i:47462 original size:14 final size:14
Alignment explanation
Indices: 47440--47474 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
47430 TGCTAAGGTA
*
47440 TTTTCAATTTCTGC
1 TTTTCAATTTCTAC
*
47454 TTTTTAATTTCTAC
1 TTTTCAATTTCTAC
47468 TTTTCAA
1 TTTTCAA
47475 AAGAATCAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.03, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTAC
Found at i:47581 original size:75 final size:74
Alignment explanation
Indices: 47455--47629 Score: 251
Period size: 75 Copynumber: 2.3 Consensus size: 74
47445 AATTTCTGCT
** * * * *
47455 TTTTAATTTCTACTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
1 TTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTAAGTTGAGCCTCAAGACAC
47520 GCTGAGGCAA
66 GCTGAGG-AA
47530 TTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTAAGTTGAGCCTCAAGACAC
1 TTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTAAGTTGAGCCTCAAGACAC
* *
47595 GTTGAGGTA
66 GCTGAGGAA
*
47604 TTTTCAATTTCTGTCTTTCAAAAAAA
1 TTTT-AATTTCTGTTTTTCAAAAAAA
47630 AATAAAAAAA
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
74 5 0.06
75 85 0.94
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (74 bp):
TTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTAAGTTGAGCCTCAAGACAC
GCTGAGGAA
Found at i:47797 original size:14 final size:14
Alignment explanation
Indices: 47778--47812 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
47768 TGCTAAGGTA
*
47778 TTTTCAATTTCTGC
1 TTTTCAATTTCTAC
47792 TTTTCAATTTCTAC
1 TTTTCAATTTCTAC
47806 TTTTCAA
1 TTTTCAA
47813 AAGAATCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.57
Consensus pattern (14 bp):
TTTTCAATTTCTAC
Found at i:47844 original size:91 final size:84
Alignment explanation
Indices: 47543--48345 Score: 652
Period size: 88 Copynumber: 9.5 Consensus size: 84
47533 TAATTTCTGT
* * * *
47543 TTTTCAAAAAAATCAACTCATATTACGAGAGGTAAGTTGAGCCTCAAGACACGTTGAGGTATTTT
1 TTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGCACGCTGAGGTATTTT
*** *
47608 CAATTTCTGTCTTTCAAAAAAAAA
64 CAATTTCTGT-TTTC--AATTTAC
**** *
47632 TAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-ACGCTGAGGTATTTTCA
1 TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACGCTGAGGTATTTTCA
* *
47696 ATTTCCGTTTGTCAATTTAT
66 ATTTCTGTTT-TCAATTTAC
* *
47716 TTTTC-AAAAATCCAACTCATATTGCGAGAGGTAAGTTGAGCCTC-GGCTCACCTGCTAAGGTAT
1 TTTTCAAAAAAT-CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--CA-C-GCTGAGGTAT
47779 TTTCAATTTCTGCTTTTCAATTTCTAC
61 TTTCAATTTCTG-TTTTCAA-TT-TAC
47806 TTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTT
1 TTTTCAAAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-CACGCTGAGGT-ATTT
47871 T-AATTTCTG--TT---TTT-C
63 TCAATTTCTGTTTTCAATTTAC
* * * *
47886 ----AAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTC
1 TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGCACGCTGAGGTATTTTC
*** *
47947 AATTTCTGTCTTTCAAAAAAAA
65 AATTTCTGT-TTTC-AATTTAC
* *** * * *
47969 ATAAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTAAGCCTCAAG-ACGCTGAGGTATTTTCA
1 TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACGCTGAGGTATTTTCA
* *
48033 ATTTCCGTTTGTCAATTTAT
66 ATTTCTGTTT-TCAATTTAC
* * * *
48053 TTTTCAAAAATTCAACTCATATTGCGAGAGGTGAATTAAGCCTCAGCTCACGTGCTGAGGTATTT
1 TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG-GCAC--GCTGAGGTATTT
48118 TCAATTTCTGCTTTTCAATTTCTAC
63 TCAATTTCTG-TTTTCAA-TT-TAC
* *
48143 TTTTCAAAAGAATCAACTAATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTT
1 TTTTCAAAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-CACGCTGAGGTATTTT
*
48208 CAATTTCTGTTGTC-----A-
64 CAATTTCTGTTTTCAATTTAC
* * * ** * * *
48223 -----AAAAAATCAACTCGTATTACGAGAGGTGAGTTGAGTCTTGGGCCATATGCCGAGGTCTTT
1 TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-C--ACGCTGAGGTATTT
*
48283 TCAAATTCTGTTTTCAATTTA-
63 TCAATTTCTGTTTTCAATTTAC
*
48304 TGCTTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
1 T--TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
48346 TCACGGGCAA
Statistics
Matches: 583, Mismatches: 79, Indels: 105
0.76 0.10 0.14
Matches are distributed among these distances:
74 38 0.07
75 56 0.10
76 29 0.05
78 2 0.00
80 1 0.00
81 3 0.01
82 2 0.00
83 7 0.01
84 78 0.13
85 27 0.05
86 31 0.05
87 39 0.07
88 122 0.21
89 47 0.08
90 24 0.04
91 72 0.12
92 5 0.01
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (84 bp):
TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACGCTGAGGTATTTTCA
ATTTCTGTTTTCAATTTAC
Found at i:47920 original size:75 final size:75
Alignment explanation
Indices: 47792--47967 Score: 273
Period size: 75 Copynumber: 2.3 Consensus size: 75
47782 CAATTTCTGC
** * * *
47792 TTTTCAATTTCTACTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAAGACA
47857 CGCTGAGGTAA
66 CGCTGAGGT-A
47868 TTTT-AATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAAGACA
*
47932 CGTTGAGGTA
66 CGCTGAGGTA
*
47942 TTTTCAATTTCTGTCTTTCAAAAAAA
1 TTTTCAATTTCTGTTTTTCAAAAAAA
47968 AATAAAAAAA
Statistics
Matches: 92, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
74 5 0.05
75 83 0.90
76 4 0.04
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (75 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAAGACA
CGCTGAGGTA
Found at i:48134 original size:14 final size:14
Alignment explanation
Indices: 48115--48149 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
48105 TGCTGAGGTA
*
48115 TTTTCAATTTCTGC
1 TTTTCAATTTCTAC
48129 TTTTCAATTTCTAC
1 TTTTCAATTTCTAC
48143 TTTTCAA
1 TTTTCAA
48150 AAGAATCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.57
Consensus pattern (14 bp):
TTTTCAATTTCTAC
Found at i:48342 original size:337 final size:337
Alignment explanation
Indices: 47118--48257 Score: 2034
Period size: 338 Copynumber: 3.4 Consensus size: 337
47108 TGCTGAGATA
47118 TTTTCAATTTCTACTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTACTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
* * * *
47183 CGCTAAGGTACTTTTAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
66 CGCTGAGGTAATTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAG
* * *
47248 CCTCAAGACACGTTGAGGTATTTTCAATTTCTATCTTTCAAAAAAAAAT-CAAAAAAATCAAATC
131 CCTCAAGACACGTTGAGGTATTTTCAATTTCTGTCTTTCAAAAAAAAATAAAAAAAAATCAACTC
*
47312 ATATTGCGAGAGGTGAGTTGAGCCTCAAGACGCTGAGGTATTTTCAATTTCCGTTTGTCAAATTA
196 ATATTGCGAGAGGTGAGTTGAGCCTCAAGACGCTGAGGTATTTTCAATTTCCGTTTGTCAATTTA
*
47377 TTTTTCAAAAATCCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACGTGCTAAGGTATT
261 TTTTTCAAAAATCCAACTCATATTGCGAGAGGTGAATTGAGCCTCGGCTCACGTGCTAAGGTATT
47442 TTCAATTTCTGC
326 TTCAATTTCTGC
*
47454 TTTTTAATTTCTACTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTACTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
* *
47519 CGCTGAGGCAATTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTAAGTTGAG
66 CGCTGAGGTAATTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAG
47584 CCTCAAGACACGTTGAGGTATTTTCAATTTCTGTCTTTCAAAAAAAAATAAAAAAAAAATCAACT
131 CCTCAAGACACGTTGAGGTATTTTCAATTTCTGTCTTTCAAAAAAAAAT-AAAAAAAAATCAACT
47649 CATATTGCGAGAGGTGAGTTGAGCCTCAAGACGCTGAGGTATTTTCAATTTCCGTTTGTCAATTT
195 CATATTGCGAGAGGTGAGTTGAGCCTCAAGACGCTGAGGTATTTTCAATTTCCGTTTGTCAATTT
*
47714 ATTTTTCAAAAATCCAACTCATATTGCGAGAGGT-AAGTTGAGCCTCGGCTCACCTGCTAAGGTA
260 ATTTTTCAAAAATCCAACTCATATTGCGAGAGGTGAA-TTGAGCCTCGGCTCACGTGCTAAGGTA
47778 TTTTCAATTTCTGC
324 TTTTCAATTTCTGC
47792 TTTTCAATTTCTACTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTACTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
47857 CGCTGAGGTAATTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAG
66 CGCTGAGGTAATTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAG
*
47922 CCTCAAGACACGTTGAGGTATTTTCAATTTCTGTCTTTCAAAAAAAAATAAAAAAAAATCAACTT
131 CCTCAAGACACGTTGAGGTATTTTCAATTTCTGTCTTTCAAAAAAAAATAAAAAAAAATCAACTC
*
47987 ATATTGCGAGAGGTGAGTTAAGCCTCAAGACGCTGAGGTATTTTCAATTTCCGTTTGTCAATTTA
196 ATATTGCGAGAGGTGAGTTGAGCCTCAAGACGCTGAGGTATTTTCAATTTCCGTTTGTCAATTTA
* * * *
48052 TTTTTCAAAAATTCAACTCATATTGCGAGAGGTGAATTAAGCCTCAGCTCACGTGCTGAGGTATT
261 TTTTTCAAAAATCCAACTCATATTGCGAGAGGTGAATTGAGCCTCGGCTCACGTGCTAAGGTATT
48117 TTCAATTTCTGC
326 TTCAATTTCTGC
*
48129 TTTTCAATTTCTACTTTTCAAAAGAATCAACTAATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTACTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
* * *
48194 CGCTGAGGTAATTTCAATTTCTG-TTGTCAAAAAAATCAACTCGTATTACGAGAGGTGAGTTGAG
66 CGCTGAGGTAATTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAG
48258 TCTTGGGCCA
Statistics
Matches: 773, Mismatches: 27, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
336 210 0.27
337 235 0.30
338 328 0.42
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (337 bp):
TTTTCAATTTCTACTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
CGCTGAGGTAATTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAG
CCTCAAGACACGTTGAGGTATTTTCAATTTCTGTCTTTCAAAAAAAAATAAAAAAAAATCAACTC
ATATTGCGAGAGGTGAGTTGAGCCTCAAGACGCTGAGGTATTTTCAATTTCCGTTTGTCAATTTA
TTTTTCAAAAATCCAACTCATATTGCGAGAGGTGAATTGAGCCTCGGCTCACGTGCTAAGGTATT
TTCAATTTCTGC
Found at i:49584 original size:15 final size:17
Alignment explanation
Indices: 49556--49587 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
49546 TTGTATATAT
49556 TATATTTATATTATGTA
1 TATATTTATATTATGTA
49573 TATATTT-T-TTATGTA
1 TATATTTATATTATGTA
49588 CGTTTCCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TATATTTATATTATGTA
Found at i:50209 original size:18 final size:18
Alignment explanation
Indices: 50188--50232 Score: 76
Period size: 17 Copynumber: 2.6 Consensus size: 18
50178 ACAATTCAGG
50188 TTTCAAAAATTTTCGTGT
1 TTTCAAAAATTTTCGTGT
50206 TTTC-AAAATTTTCGTGT
1 TTTCAAAAATTTTCGTGT
50223 TTT-AAAAATT
1 TTTCAAAAATT
50233 CTCATTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (18 bp):
TTTCAAAAATTTTCGTGT
Found at i:51613 original size:12 final size:12
Alignment explanation
Indices: 51596--51631 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
51586 ATTCATTTGA
51596 CATTCATGCATT
1 CATTCATGCATT
*
51608 CATTCATGCATC
1 CATTCATGCATT
*
51620 CATTCATTCATT
1 CATTCATGCATT
51632 GCATATCCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.25, C:0.28, G:0.06, T:0.42
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:51625 original size:16 final size:17
Alignment explanation
Indices: 51604--51635 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
51594 GACATTCATG
51604 CATTCATTCA-TGCATC
1 CATTCATTCATTGCATC
51620 CATTCATTCATTGCAT
1 CATTCATTCATTGCAT
51636 ATCCCATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.28, G:0.06, T:0.41
Consensus pattern (17 bp):
CATTCATTCATTGCATC
Found at i:58179 original size:18 final size:19
Alignment explanation
Indices: 58138--58183 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
58128 GAAAATGAGA
58138 ATTTTGAAAACACGGAAAG
1 ATTTTGAAAACACGGAAAG
*
58157 ATTTTGAAAACAC-GAAAT
1 ATTTTGAAAACACGGAAAG
*
58175 TTTTTGAAA
1 ATTTTGAAA
58184 CCTAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (19 bp):
ATTTTGAAAACACGGAAAG
Found at i:59489 original size:1 final size:1
Alignment explanation
Indices: 59483--59525 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
59473 ATTAAGAAAG
* * * *
59483 AAAAAAAAAAAAAAAAAAAATAAACACAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
59526 GATTCGAAAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.91, C:0.05, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:61777 original size:77 final size:76
Alignment explanation
Indices: 61692--62015 Score: 279
Period size: 78 Copynumber: 4.3 Consensus size: 76
61682 GTGCCGCCGA
61692 GCTCAACTCACCCTCTCGCAATATTGAGTTGATTTTTTGAAAACAGAAAATTGAAATTACCTCAG
1 GCTCAACTCA-CCTCTCGCAATATTGAGTTGATTTTTTGAAAACAGAAAATTGAAATTACCTCAG
*
61757 CGCTGTCTCCGA-
65 CG-TGTCTCTGAG
61769 GCTCAACTCAACCCTCTCGCAAT-TAT-AG-TGATTTTTTTGAAAAACA-ACAAATTTGACAA--
1 GCTCAACTC-A-CCTCTCGCAATAT-TGAGTTGA-TTTTTTG-AAAACAGA-AAA-TTGA-AATT
* *
61828 AACTCAGCATGTCT-TGAG
58 ACCTCAGCGTGTCTCTGAG
* *
61846 GCTCAACTCA-TTCTCG-AA-A-TG-GTTGCA-TTTTTGAAAACAGAAATTTGAAATTACCTCAG
1 GCTCAACTCACCTCTCGCAATATTGAGTTG-ATTTTTTGAAAACAGAAAATTGAAATTACCTCAG
*
61905 -GTCGTCGCTGAG
65 CGT-GTCTCTGAG
** * *
61917 GCTCAACTCATTTCTCGCCAATTGAATGAGTTGATTTTTCTTAACAACAG-AAA-TGAAATTACC
1 GCTCAACTCACCTCTCG-CAA-T-ATTGAGTTGATTTTT-TGAA-AACAGAAAATTGAAATTACC
61980 TCAGCGTGTC-CTGAG
61 TCAGCGTGTCTCTGAG
61995 GCTCAACTCACCTCTCGCAAT
1 GCTCAACTCACCTCTCGCAAT
62016 GTGAGCAGAA
Statistics
Matches: 206, Mismatches: 12, Indels: 59
0.74 0.04 0.21
Matches are distributed among these distances:
68 2 0.01
69 5 0.02
70 17 0.08
71 23 0.11
72 8 0.04
73 3 0.01
74 7 0.03
76 7 0.03
77 38 0.18
78 53 0.26
79 29 0.14
80 9 0.04
81 5 0.02
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (76 bp):
GCTCAACTCACCTCTCGCAATATTGAGTTGATTTTTTGAAAACAGAAAATTGAAATTACCTCAGC
GTGTCTCTGAG
Done.