Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold370
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: 857924
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:635398 original size:33 final size:33
Alignment explanation
Indices: 635356--635422 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
635346 GCCAAGGAAA
***
635356 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
635389 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
635422 T
1 T
635423 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:641095 original size:13 final size:13
Alignment explanation
Indices: 641077--641107 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
641067 ACATTTCTTC
641077 ATGTATCGATACA
1 ATGTATCGATACA
641090 ATGTATCGATACA
1 ATGTATCGATACA
*
641103 TTGTA
1 ATGTA
641108 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:641095 original size:33 final size:33
Alignment explanation
Indices: 641057--641120 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 33
641047 GTTACAAGCT
641057 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
641090 ATGTATCGATACATTGTACCATGTATCGATA
1 ATGTATCGATACATTGTACCATGTATCGATA
641121 TAAATAGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:641181 original size:21 final size:21
Alignment explanation
Indices: 641155--641207 Score: 74
Period size: 19 Copynumber: 2.6 Consensus size: 21
641145 CCAGTTTCAA
**
641155 GTATCGATACAATTTGTCCAT
1 GTATCGATACAATTTGAACAT
641176 GTATCGATAC-A-TTGAACAT
1 GTATCGATACAATTTGAACAT
641195 GTATCGATACAAT
1 GTATCGATACAAT
641208 GTATCGATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 16 0.57
20 2 0.07
21 10 0.36
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (21 bp):
GTATCGATACAATTTGAACAT
Found at i:641211 original size:13 final size:13
Alignment explanation
Indices: 641193--641219 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
641183 TACATTGAAC
641193 ATGTATCGATACA
1 ATGTATCGATACA
641206 ATGTATCGATACA
1 ATGTATCGATACA
641219 A
1 A
641220 GGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:641495 original size:21 final size:20
Alignment explanation
Indices: 641453--641489 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
641443 TGAGTGAATA
*
641453 AAACTTTTTTACGATTTTTC
1 AAACATTTTTACGATTTTTC
641473 AAACATTTTT-CGATTTT
1 AAACATTTTTACGATTTT
641490 ATTCAATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.27, C:0.14, G:0.05, T:0.54
Consensus pattern (20 bp):
AAACATTTTTACGATTTTTC
Found at i:643712 original size:13 final size:13
Alignment explanation
Indices: 643692--643732 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
643682 AATAGTACTT
643692 AATGTATCGATAC
1 AATGTATCGATAC
*
643705 ATTGTATCGATAC
1 AATGTATCGATAC
643718 AATGTATCGATAC
1 AATGTATCGATAC
643731 AA
1 AA
643733 GGAATGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:649930 original size:13 final size:13
Alignment explanation
Indices: 649912--649942 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
649902 ACATTTCTTC
649912 ATGTATCGATACA
1 ATGTATCGATACA
649925 ATGTATCGATACA
1 ATGTATCGATACA
*
649938 TTGTA
1 ATGTA
649943 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:649930 original size:33 final size:33
Alignment explanation
Indices: 649892--649958 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 33
649882 GTTACAAGCT
649892 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
649925 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
649958 A
1 A
649959 ATAGTGATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:650011 original size:19 final size:20
Alignment explanation
Indices: 649987--650037 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
649977 TTGCCAGTTT
*
649987 CATGTATCGATACATTG-AA
1 CATGTATCGATACAATGTAA
*
650006 CATGTATCGATACAATGTAG
1 CATGTATCGATACAATGTAA
650026 CATGTATCGATA
1 CATGTATCGATA
650038 TATCTGGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATGTAA
Found at i:651331 original size:21 final size:21
Alignment explanation
Indices: 651285--651331 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
651275 TATTAAAAGT
651285 TGCATTTTTTCATCCAAAAAA
1 TGCATTTTTTCATCCAAAAAA
* **
651306 GGCATTTTTTCATCCAACCAA
1 TGCATTTTTTCATCCAAAAAA
651327 TGCAT
1 TGCAT
651332 CATTTCATTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (21 bp):
TGCATTTTTTCATCCAAAAAA
Found at i:653139 original size:20 final size:21
Alignment explanation
Indices: 653100--653143 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
653090 TTAAGTATAG
*
653100 ATGTTTTTCATGCATAAAAATA
1 ATGTTTTTCAAG-ATAAAAATA
653122 ATGTTTTTCAAG-TAAAAATA
1 ATGTTTTTCAAGATAAAAATA
653142 AT
1 AT
653144 TCAAAGTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
22 11 0.52
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (21 bp):
ATGTTTTTCAAGATAAAAATA
Found at i:653279 original size:32 final size:33
Alignment explanation
Indices: 653219--653283 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
653209 CACACCCAGA
*
653219 TGTATCGATACATATTGCTTAGTGTCGATACAT
1 TGTATCGATACATATTGCTTAGTATCGATACAT
* *
653252 TGTATTGATACATGTT-CTTAGTATCGATACAT
1 TGTATCGATACATATTGCTTAGTATCGATACAT
653284 ATTGAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATATTGCTTAGTATCGATACAT
Found at i:653348 original size:13 final size:13
Alignment explanation
Indices: 653330--653356 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
653320 AAAACTCATT
653330 TTGTATCGATACA
1 TTGTATCGATACA
653343 TTGTATCGATACA
1 TTGTATCGATACA
653356 T
1 T
653357 GAAGAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:653367 original size:20 final size:20
Alignment explanation
Indices: 653342--653396 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
653332 GTATCGATAC
653342 ATTGTATCGATACATGAAGA
1 ATTGTATCGATACATGAAGA
**
653362 ATTGTATCGATACATGGTGA
1 ATTGTATCGATACATGAAGA
653382 ATTGTATCGATACAT
1 ATTGTATCGATACAT
653397 TGAGCCCAAT
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:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (20 bp):
ATTGTATCGATACATGAAGA
Found at i:654775 original size:10 final size:10
Alignment explanation
Indices: 654760--654785 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
654750 TTTGGATTTC
654760 AAAAAAAGAA
1 AAAAAAAGAA
654770 AAAAAAAGAA
1 AAAAAAAGAA
654780 AAAAAA
1 AAAAAA
654786 GAAGGGTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:673348 original size:16 final size:16
Alignment explanation
Indices: 673328--673368 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
673318 GCGTCCTCCG
*
673328 AAAAAAAAAAACAAAAC
1 AAAAAAACAAA-AAAAC
673345 AAAAAAACAAAAAAAC
1 AAAAAAACAAAAAAAC
673361 AACAAAAA
1 AA-AAAAA
673369 GGGTCCGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAACAAAAAAAC
Found at i:673350 original size:13 final size:12
Alignment explanation
Indices: 673328--673368 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
673318 GCGTCCTCCG
673328 AAAAAAAAAAAC
1 AAAAAAAAAAAC
673340 AAAACAAAAAAAC
1 AAAA-AAAAAAAC
*
673353 -AAAAAAACAAC
1 AAAAAAAAAAAC
673364 AAAAA
1 AAAAA
673369 GGGTCCGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 7 0.27
12 11 0.42
13 8 0.31
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:673350 original size:19 final size:19
Alignment explanation
Indices: 673328--673368 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
673318 GCGTCCTCCG
*
673328 AAAAAA-AAAAACAAAACA
1 AAAAAACAAAAAAAAAACA
*
673346 AAAAAACAAAAAAACAACA
1 AAAAAACAAAAAAAAAACA
673365 AAAA
1 AAAA
673369 GGGTCCGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (19 bp):
AAAAAACAAAAAAAAAACA
Found at i:673351 original size:8 final size:8
Alignment explanation
Indices: 673328--673368 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
673318 GCGTCCTCCG
*
673328 AAAAAAAA
1 AAAAAAAC
673336 AAACAAAAC
1 AAA-AAAAC
673345 AAAAAAAC
1 AAAAAAAC
673353 AAAAAAAC
1 AAAAAAAC
673361 AACAAAAA
1 AA-AAAAA
673369 GGGTCCGGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 18 0.60
9 12 0.40
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:674835 original size:29 final size:29
Alignment explanation
Indices: 674796--675115 Score: 209
Period size: 29 Copynumber: 10.7 Consensus size: 29
674786 TCACCCTTCA
674796 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
674825 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
674854 AAAGTCCACAAGTCAGTGGCAAC--CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * * *
674881 AAAGCCAACAAATCAGTTGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * *
674911 GAAGCCCACAAGTTAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * *
674940 AAAGTCCACAAACTCCGTGGCACTCATTTTCTTTTG
1 AAAGCCCAC-AAGTCAGTGGCA-TC----T-TTTTC
* * * *
674976 TAAGCCCACAACTCCGTAGCATTCTTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTT-C
* * * *
675007 TTTTAAGCCCACAAGTTAGTGGCACCCTTTTC
1 ---AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
675039 AAAAGCCCACAAGTCAGTGGCAAC--CTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * *
675067 AAAAGCCGACAAGTCAGTGGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
675096 AAAGCCCACAAGTCAGTGGC
1 AAAGCCCACAAGTCAGTGGC
675116 CACCTTCAAA
Statistics
Matches: 233, Mismatches: 43, Indels: 31
0.76 0.14 0.10
Matches are distributed among these distances:
27 20 0.09
28 46 0.20
29 66 0.28
30 51 0.22
31 3 0.01
32 1 0.00
33 5 0.02
34 17 0.07
35 14 0.06
36 10 0.04
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:674916 original size:86 final size:86
Alignment explanation
Indices: 674790--675115 Score: 246
Period size: 86 Copynumber: 3.6 Consensus size: 86
674780 CATTCCTCAC
* * * * *
674790 CCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTTCA
1 CCTTCAAAAGCCAACAAATCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCA
674855 AAGTCCACAAGTCAGTGGCAA
66 AAGTCCACAAGTCAGTGGCAA
* * *
674876 CCTTC-AAAGCCAACAAATCAGTTGCACCCTTTTCCGAAGCCCACAAGTTAGTGGCATCTTTTCC
1 CCTTCAAAAGCCAACAAATCAGTGGCA-CCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
* *
674940 AAAGTCCACAAACTCCGTGGC-A
65 AAAGTCCAC-AAGTCAGTGGCAA
** * * * * * * *
674962 CTCATTTTCTTTTGTAAGCCCACAACTCCGTAGCATTCTTTTTCCTTTTAAGCCCACAAGTTAGT
1 C-C---TTC----AAAAGCCAACAAATCAGTGGCA--CCTTTTCC---AAAGCCCACAAGTCAGT
* * *
675027 GGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAA
53 GGCA-TCTTTTCCAAAGTCCACAAGTCAGTGGCAA
* * *
675062 CCTTCAAAAGCCGACAAGTCAGTGGCAACC-TTT-AAAAGCCCACAAGTCAGTGGC
1 CCTTCAAAAGCCAACAAATCAGTGGC-ACCTTTTCCAAAGCCCACAAGTCAGTGGC
675116 CACCTTCAAA
Statistics
Matches: 189, Mismatches: 33, Indels: 36
0.73 0.13 0.14
Matches are distributed among these distances:
85 18 0.10
86 66 0.35
87 10 0.05
90 6 0.03
91 1 0.01
92 15 0.08
93 1 0.01
95 16 0.08
96 10 0.05
99 30 0.16
100 16 0.08
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (86 bp):
CCTTCAAAAGCCAACAAATCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCA
AAGTCCACAAGTCAGTGGCAA
Found at i:674930 original size:57 final size:57
Alignment explanation
Indices: 674796--675125 Score: 177
Period size: 56 Copynumber: 5.5 Consensus size: 57
674786 TCACCCTTCA
* * * * * *
674796 AAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCAAC-TCTTCAAAGCCAACAAATCAGTGGCACCTTTTCC
* *
674854 AAAGTCCACAAGTCAGTGGCAAC-CTTCAAAGCCAACAAATCAGTTGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAACTCTTCAAAGCCAACAAATCAGTGGCA-CCTTTTCC
* * * * *
674911 GAAGCCCACAAGTTAGTGGCATCTTTTCCAAAGTCC-ACAAACTCCGTGGCACTCATTTTCTTTT
1 AAAGCCCACAAGTCAGTGGCAACTCTT-CAAAG-CCAACAAA-TCAGTGGCAC-C-TTTTC----
*
674975 G
57 C
* * * * * ** * * * *
674976 TAAGCCCACAACTCCGTAGCATTCTTTTTCCTTTTAAGCCCACAAGTTAGTGGCACCCTTTTCA
1 AAAGCCCACAAGTCAGTGGCA-AC----T-CTTCAAAGCCAACAAATCAGTGGCA-CCTTTTCC
* * *
675040 AAAGCCCACAAGTCAGTGGCAAC-CTTCAAAAGCCGACAAGTCAGTGGCAACC-TTT-A
1 AAAGCCCACAAGTCAGTGGCAACTCTTC-AAAGCCAACAAATCAGTGGC-ACCTTTTCC
*
675096 AAAGCCCACAAGTCAGTGGCCAC-CTTCAAA
1 AAAGCCCACAAGTCAGTGGCAACTCTTCAAA
675126 AGCACACAAG
Statistics
Matches: 213, Mismatches: 38, Indels: 45
0.72 0.13 0.15
Matches are distributed among these distances:
55 3 0.01
56 48 0.23
57 31 0.15
58 42 0.20
59 12 0.06
60 10 0.05
61 5 0.02
63 1 0.00
64 17 0.08
65 16 0.08
66 2 0.01
68 5 0.02
69 10 0.05
70 9 0.04
71 2 0.01
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (57 bp):
AAAGCCCACAAGTCAGTGGCAACTCTTCAAAGCCAACAAATCAGTGGCACCTTTTCC
Found at i:675019 original size:34 final size:35
Alignment explanation
Indices: 674945--675020 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
674935 TTTCCAAAGT
* *
674945 CCACAAACTCCGTGGCACTCATTTTCTTTTGTAAGC
1 CCAC-AACTCCGTAGCACTCATTTTCCTTTGTAAGC
* *
674981 CCACAACTCCGTAGCATTCTTTTTCCTTT-TAAGC
1 CCACAACTCCGTAGCACTCATTTTCCTTTGTAAGC
675015 CCACAA
1 CCACAA
675021 GTTAGTGGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
34 11 0.31
35 21 0.58
36 4 0.11
ACGTcount: A:0.24, C:0.33, G:0.11, T:0.33
Consensus pattern (35 bp):
CCACAACTCCGTAGCACTCATTTTCCTTTGTAAGC
Found at i:675078 original size:28 final size:28
Alignment explanation
Indices: 675011--675162 Score: 182
Period size: 28 Copynumber: 5.3 Consensus size: 28
675001 TTTTCCTTTT
* *
675011 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC--TTCAA
675041 AAGCCCACAAGTCAGTGGCAACCTTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTCAA
* *
675069 AAGCCGACAAGTCAGTGGCAACCTTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTCAA
*
675097 AAGCCCACAAGTCAGTGGCCACCTTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTCAA
* *
675125 AAGCACACAAGT-TGAT-GCAACCCTTTCAA
1 AAGCCCACAAGTCAG-TGGCAA-CC-TTCAA
675154 AAGCCCACA
1 AAGCCCACA
675163 CAAGTTGATG
Statistics
Matches: 108, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
27 4 0.04
28 70 0.65
29 13 0.12
30 21 0.19
ACGTcount: A:0.35, C:0.31, G:0.17, T:0.17
Consensus pattern (28 bp):
AAGCCCACAAGTCAGTGGCAACCTTCAA
Found at i:675356 original size:52 final size:49
Alignment explanation
Indices: 675179--675417 Score: 238
Period size: 49 Copynumber: 4.9 Consensus size: 49
675169 GATGGCGTCT
* * * * * * *
675179 TCTTCTAAGTCCAATATCACTGGCCTTGAACCAGCATATTGGCACCTTTA
1 TCTT-TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCCTCA
* * *
675229 TCTTTAAAACTCAATATCGCTGGCCTTGAATCAGCATATT-G-A----CA
1 TCTTTAAGAC-CAATGTCGCTGGCCTTGAATCAGCACATTGGCACCCTCA
* * *
675273 CCTTGAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTAACCA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCCT---CA
*
675325 TCTTTAAGACCAATGTCGCTGGCCTCGAATCAGCACATTGGCACCCTCA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCCTCA
* * *
675374 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTAGCAC
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
675418 AAGTCCAATA
Statistics
Matches: 161, Mismatches: 18, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
43 27 0.17
44 9 0.06
45 1 0.01
48 1 0.01
49 47 0.29
50 31 0.19
52 45 0.28
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (49 bp):
TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCCTCA
Found at i:675402 original size:101 final size:93
Alignment explanation
Indices: 675179--675417 Score: 248
Period size: 101 Copynumber: 2.5 Consensus size: 93
675169 GATGGCGTCT
* * * *
675179 TCTTCTAAGTCCAATATCA-CTGGCCTTGAACCAGCATATTGGCACCTTTATCTTTAAAACTCAA
1 TCTT-TAAGTCCAATGT-AGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAAACTCAA
* *
675243 TATCGCTGGCCTTGAATCAGCATATTGACA
64 TATCGCTGGCCTCGAATCAGCACATTGACA
* * * * *
675273 CCTTGAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGAC-CA
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT---CATCTTTAAAACTCA
*
675337 ATGTCGCTGGCCTCGAATCAGCACATTGGCACCCTCA
63 ATATCGCTGGCCTCGAATCAGCACATT-G-A----CA
*
675374 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTAGCAC
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
675418 AAGTCCAATA
Statistics
Matches: 118, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
93 36 0.31
94 3 0.03
95 26 0.22
96 11 0.09
97 1 0.01
101 41 0.35
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (93 bp):
TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAAACTCAATA
TCGCTGGCCTCGAATCAGCACATTGACA
Found at i:679128 original size:52 final size:52
Alignment explanation
Indices: 679058--679178 Score: 233
Period size: 52 Copynumber: 2.3 Consensus size: 52
679048 GAAAATTTAT
679058 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
679110 CTGCATGTATCGATACATTTAATAGTGTATTGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
679162 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
679179 AAGATCAGTG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:679189 original size:52 final size:51
Alignment explanation
Indices: 679058--679198 Score: 221
Period size: 52 Copynumber: 2.7 Consensus size: 51
679048 GAAAATTTAT
679058 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
679110 CTGCATGTATCGATACATTTAATAGTGTATTGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
679162 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
679199 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
50 1 0.01
51 2 0.02
52 81 0.96
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:679205 original size:13 final size:13
Alignment explanation
Indices: 679187--679211 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
679177 CAAAGATCAG
679187 TGTATCGATACAA
1 TGTATCGATACAA
679200 TGTATCGATACA
1 TGTATCGATACA
679212 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:679295 original size:13 final size:13
Alignment explanation
Indices: 679277--679301 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
679267 AAAAAAAATA
679277 TGTATCGATACAT
1 TGTATCGATACAT
679290 TGTATCGATACA
1 TGTATCGATACA
679302 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:682727 original size:98 final size:97
Alignment explanation
Indices: 682540--682789 Score: 275
Period size: 98 Copynumber: 2.6 Consensus size: 97
682530 TTTAATTTTT
* * ** * * * * *
682540 AGTTGAAAGACGGGGTTAGAGTATCTTCTTAGAGGAAAGGGGTTAGAGTATCCCCGACGATGACA
1 AGTTTAAAAACGGGGTTAGAGTATCCCCTTGGAAGAATGGGGTTGGAGTATCCCCAACGATGACA
** * *
682605 ATTTAAGAAAAAATAAGGTTTAAATCTTGACAA
66 ATTTAAGAAAAAATAAAATCTAAATATTGAC-A
* * * * *
682638 ATTTTTAAAATGGGGTTAGAGTATCCCCTTGGAAGAATGGGGTTGGAGTGTCCCCAATGATGACA
1 AGTTTAAAAACGGGGTTAGAGTATCCCCTTGGAAGAATGGGGTTGGAGTATCCCCAACGATGACA
* ** *
682703 ATTTAGGTGAGAATAAAATCTAAATATTGACA
66 ATTTAAGAAAAAATAAAATCTAAATATTGACA
* *
682735 AGTTTAAAAACGGGATTAGAGTATCCCCTTGGAAGAATAGGGTTGGAGTATCCCC
1 AGTTTAAAAACGGGGTTAGAGTATCCCCTTGGAAGAATGGGGTTGGAGTATCCCC
682790 GATAAAGAAA
Statistics
Matches: 124, Mismatches: 28, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
97 50 0.40
98 74 0.60
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (97 bp):
AGTTTAAAAACGGGGTTAGAGTATCCCCTTGGAAGAATGGGGTTGGAGTATCCCCAACGATGACA
ATTTAAGAAAAAATAAAATCTAAATATTGACA
Found at i:682789 original size:97 final size:98
Alignment explanation
Indices: 682579--682789 Score: 262
Period size: 97 Copynumber: 2.2 Consensus size: 98
682569 TAGAGGAAAG
* * ** * * * *
682579 GGGTTAGAGTATCCCCGACGATGACAATTTAAGAAAAAATAAGGTTTAAATCTTGACAAATTTTT
1 GGGTTGGAGTATCCCCAACGATGACAATTTAAGAAAAAATAAAATCTAAATATTGACAAAGTTTA
* * *
682644 AAAATGGGGTTAGAGTATCCCCTTGGAAGAATG
66 AAAACGGGATTAGAGTATCCCCTTGGAAGAATA
* * * ** *
682677 GGGTTGGAGTGTCCCCAATGATGACAATTTAGGTGAGAATAAAATCTAAATATTGAC-AAGTTTA
1 GGGTTGGAGTATCCCCAACGATGACAATTTAAGAAAAAATAAAATCTAAATATTGACAAAGTTTA
682741 AAAACGGGATTAGAGTATCCCCTTGGAAGAATA
66 AAAACGGGATTAGAGTATCCCCTTGGAAGAATA
682774 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
682790 GATAAAGAAA
Statistics
Matches: 95, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
97 50 0.53
98 45 0.47
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.27
Consensus pattern (98 bp):
GGGTTGGAGTATCCCCAACGATGACAATTTAAGAAAAAATAAAATCTAAATATTGACAAAGTTTA
AAAACGGGATTAGAGTATCCCCTTGGAAGAATA
Found at i:685231 original size:51 final size:51
Alignment explanation
Indices: 685144--685333 Score: 220
Period size: 51 Copynumber: 3.7 Consensus size: 51
685134 ATTTAGTTGG
* * * * *
685144 ATGTATCGATACATTGCAGAATGTATTGATATATTTGGGTCAAAACCCAAA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTGGGTCAAAACCCAAA
* * *
685195 ATATATCGATACAATGAATAATGTATCGATACATTTGGGTAAAAAACCCAAA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTGGGT-CAAAACCCAAA
* * * * *
685247 ATGTATTGATACAATGAAAAATGTATGGATATATTTGGATC-AAACCCAGA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTGGGTCAAAACCCAAA
* *
685297 ATGTATCGATACAATAAAAAAATGTATCGATGCATTT
1 ATGTATCGATACAAT-GAAAAATGTATCGATACATTT
685334 TCTTTTCAGG
Statistics
Matches: 117, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
50 22 0.19
51 51 0.44
52 44 0.38
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (51 bp):
ATGTATCGATACAATGAAAAATGTATCGATACATTTGGGTCAAAACCCAAA
Found at i:685323 original size:103 final size:103
Alignment explanation
Indices: 685144--685333 Score: 265
Period size: 103 Copynumber: 1.8 Consensus size: 103
685134 ATTTAGTTGG
* * * * *
685144 ATGTATCGATACATTGCAGAATGTATTGATATATTTGGGTCAAAACCCAAAATATATCGATACAA
1 ATGTATCGATACAATGAAAAATGTATGGATATATTTGGATCAAAACCCAAAATATATCGATACAA
* *
685209 TGAATAATGTATCGATACATTTGGGTAAAAAACCCAAA
66 TAAAAAATGTATCGATACATTTGGGTAAAAAACCCAAA
* * *
685247 ATGTATTGATACAATGAAAAATGTATGGATATATTTGGATC-AAACCCAGAATGTATCGATACAA
1 ATGTATCGATACAATGAAAAATGTATGGATATATTTGGATCAAAACCCAAAATATATCGATACAA
*
685311 TAAAAAAATGTATCGATGCATTT
66 T-AAAAAATGTATCGATACATTT
685334 TCTTTTCAGG
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
102 22 0.29
103 53 0.71
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (103 bp):
ATGTATCGATACAATGAAAAATGTATGGATATATTTGGATCAAAACCCAAAATATATCGATACAA
TAAAAAATGTATCGATACATTTGGGTAAAAAACCCAAA
Found at i:686405 original size:52 final size:52
Alignment explanation
Indices: 685985--686426 Score: 329
Period size: 52 Copynumber: 8.4 Consensus size: 52
685975 TTGACAAATG
* * * ** * * *
685985 TGCCAATGTGCAGATTCAAGGCCTGTGATGTTAGACTTAAAGATGATAAGGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGA
* * *
686037 TGCCAATGTACTGATTCAAGGCCAGCGACATTGGGCTTTGGAAAGACGGTTTTGACAA-G-
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC-TT--AAAGA------TGAGAAGGA
* * * * * * * * *
686096 TACCGATATGCTAATTTAAGGCTAGCAACATTGGACTTAAAGATGATAAGGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGA
* * * * * * ***
686148 TGCTAATATGCTAATTCAAGACCAGTGATACCAGACTTAAAGATGAGAAGGA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGA
* * ** *
686200 TGCCAATATGCTAATTCAAGGCCAGTAACATTAGACTTAAAGATGAGAAGGA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGA
* * *
686252 TGCCAATGTACTGATTCAAGGCCATCGACATTGGACTTAAAGATAAGAAGGA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGA
* *
686304 TGCCAATGTGCTGATTCAA-G-TAGTGACATTGGACTTAAAGATGAGAA-GA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGA
** * *
686353 GTGATAATGTGTTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAA-GA
1 -TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGA
* * *
686405 GTGTCAATGTGTTGATTTAAGG
1 -TGCCAATGTGCTGATTCAAGG
686427 TCAACATTAG
Statistics
Matches: 315, Mismatches: 61, Indels: 28
0.78 0.15 0.07
Matches are distributed among these distances:
49 2 0.01
50 44 0.14
51 3 0.01
52 219 0.70
53 2 0.01
55 5 0.02
56 5 0.02
58 2 0.01
59 27 0.09
60 1 0.00
61 5 0.02
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.26
Consensus pattern (52 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGA
Found at i:686709 original size:33 final size:33
Alignment explanation
Indices: 686671--686854 Score: 136
Period size: 33 Copynumber: 5.3 Consensus size: 33
686661 TTTAATTATG
686671 ATGAATATTCAAATTCATGAATATACATAATTC
1 ATGAATATTCAAATTCATGAATATACATAATTC
* * * * *
686704 ATGAATATACATAATATTATTCATGTATATTCATAGTTT
1 ATGAATAT---TCA-A--ATTCATGAATATACATAATTC
* * *
686743 ATGAACATTTAAATTCATAAATATACATAATTC
1 ATGAATATTCAAATTCATGAATATACATAATTC
* * * * *
686776 ATGAAT-TTAATAACATTCATGTATATTCATAGTTT
1 ATGAATATT--CAA-ATTCATGAATATACATAATTC
* * *
686811 ATGAATATTCAAATTCATGAATTTACATGATTA
1 ATGAATATTCAAATTCATGAATATACATAATTC
686844 ATGAATATTCA
1 ATGAATATTCA
686855 TGCTTATCAA
Statistics
Matches: 116, Mismatches: 25, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
32 2 0.02
33 55 0.47
34 5 0.04
35 23 0.20
36 6 0.05
37 1 0.01
39 24 0.21
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (33 bp):
ATGAATATTCAAATTCATGAATATACATAATTC
Found at i:686825 original size:68 final size:70
Alignment explanation
Indices: 686671--686851 Score: 258
Period size: 68 Copynumber: 2.6 Consensus size: 70
686661 TTTAATTATG
**
686671 ATGAATATTCAAATTCATGAATATACATAATTCATGAATATACATAATATTATTCATGTATATTC
1 ATGAATATTCAAATTCATGAATATACATAATTCATGAATAT--ATAATAACATTCATGTATATTC
686736 ATAGTTT
64 ATAGTTT
* * *
686743 ATGAACATTTAAATTCATAAATATACATAATTCATGAAT-T-TAATAACATTCATGTATATTCAT
1 ATGAATATTCAAATTCATGAATATACATAATTCATGAATATATAATAACATTCATGTATATTCAT
686806 AGTTT
66 AGTTT
* * *
686811 ATGAATATTCAAATTCATGAATTTACATGATTAATGAATAT
1 ATGAATATTCAAATTCATGAATATACATAATTCATGAATAT
686852 TCATGCTTAT
Statistics
Matches: 97, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
68 59 0.61
69 1 0.01
71 1 0.01
72 36 0.37
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (70 bp):
ATGAATATTCAAATTCATGAATATACATAATTCATGAATATATAATAACATTCATGTATATTCAT
AGTTT
Found at i:686856 original size:17 final size:17
Alignment explanation
Indices: 686798--686856 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
686788 ACATTCATGT
*
686798 ATATTCAT-AGTTTATGA
1 ATATTCATGA-TTAATGA
* *
686815 ATATTCA-AATTCATGA
1 ATATTCATGATTAATGA
686831 AT-TTACATGATTAATGA
1 ATATT-CATGATTAATGA
686848 ATATTCATG
1 ATATTCATG
686857 CTTATCAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
15 2 0.06
16 10 0.29
17 21 0.60
18 2 0.06
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.42
Consensus pattern (17 bp):
ATATTCATGATTAATGA
Found at i:692772 original size:71 final size:71
Alignment explanation
Indices: 692654--692792 Score: 206
Period size: 71 Copynumber: 2.0 Consensus size: 71
692644 AAAAGTTACA
* * *
692654 TTTTTACCCAGATGTATCAATACATTTTTTAATATATCGATATATGTATGAACGTATCGATACAT
1 TTTTTACCCAGATATATCAATACATTTTTCAATATATCGATACATGTATGAACGTATCGATACAT
692719 TCTATT
66 TCTATT
* * * * *
692725 TTTTTACCTAGATATATCGATACATTTTTCAGTGTATCGATACATGTATGAATGTATCGATACAT
1 TTTTTACCCAGATATATCAATACATTTTTCAATATATCGATACATGTATGAACGTATCGATACAT
692790 TCT
66 TCT
692793 TTAATGTATC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (71 bp):
TTTTTACCCAGATATATCAATACATTTTTCAATATATCGATACATGTATGAACGTATCGATACAT
TCTATT
Found at i:692812 original size:20 final size:19
Alignment explanation
Indices: 692739--692810 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 19
692729 TACCTAGATA
*
692739 TATCGATACATTTTTCAGTG
1 TATCGATACATTTTT-AATG
* *
692759 TATCGATACATGTATGAATG
1 TATCGATACAT-TTTTAATG
692779 TATCGATACATTCTTTAATG
1 TATCGATACATT-TTTAATG
692799 TATCGATACATT
1 TATCGATACATT
692811 CTATCTTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
19 1 0.02
20 42 0.93
21 2 0.04
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (19 bp):
TATCGATACATTTTTAATG
Found at i:696996 original size:12 final size:12
Alignment explanation
Indices: 696981--697005 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
696971 ACCTTATAAA
696981 TATTTTTATATG
1 TATTTTTATATG
696993 TATTTTTATATG
1 TATTTTTATATG
697005 T
1 T
697006 CTTTATAAGG
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TATTTTTATATG
Found at i:698939 original size:28 final size:28
Alignment explanation
Indices: 698900--698959 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
698890 AACTAAAGTA
* *
698900 AAAGGAAAACCTTGATCAAGAAGAGGTT
1 AAAGGAAAACCTTGATCAAGAAAAGGCT
698928 AAAGGAAAACCTTGATCAAGAAAAGGCT
1 AAAGGAAAACCTTGATCAAGAAAAGGCT
698956 AAAG
1 AAAG
698960 ATTAAGGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.50, C:0.12, G:0.23, T:0.15
Consensus pattern (28 bp):
AAAGGAAAACCTTGATCAAGAAAAGGCT
Found at i:702042 original size:34 final size:35
Alignment explanation
Indices: 702004--702069 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
701994 CCTTACAACA
* *
702004 CTATCTTTTCG-A-AGGCTAAGATAGAACCTCTTCC
1 CTATCTTTT-GTAGAGGCCAAGATAAAACCTCTTCC
702038 CTATCTTTTGTAGAGGCCAAGATAAAACCTCT
1 CTATCTTTTGTAGAGGCCAAGATAAAACCTCT
702070 CAATCACTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 1 0.04
34 10 0.36
35 17 0.61
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (35 bp):
CTATCTTTTGTAGAGGCCAAGATAAAACCTCTTCC
Found at i:702663 original size:13 final size:13
Alignment explanation
Indices: 702645--702702 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
702635 TACAAAGAAC
702645 ATGTATCGATACA
1 ATGTATCGATACA
*
702658 ATGTATCAATACAAAGA
1 ATGTATCGATAC----A
702675 TTATGTATCGATACA
1 --ATGTATCGATACA
702690 ATGTATCGATACA
1 ATGTATCGATACA
702703 TCTGGGTGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
13 24 0.65
15 1 0.03
17 1 0.03
19 11 0.30
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:702681 original size:32 final size:32
Alignment explanation
Indices: 702634--702702 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
702624 TGGTGCATCG
702634 ATACAAAGAACATGTATCGATACAATGTATCA
1 ATACAAAGAACATGTATCGATACAATGTATCA
** *
702666 ATACAAAGATTATGTATCGATACAATGTATCG
1 ATACAAAGAACATGTATCGATACAATGTATCA
702698 ATACA
1 ATACA
702703 TCTGGGTGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (32 bp):
ATACAAAGAACATGTATCGATACAATGTATCA
Found at i:702852 original size:24 final size:23
Alignment explanation
Indices: 702808--702852 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
702798 ATTATTTTTA
* *
702808 CTTGAAAAACATTTGATTTATTG
1 CTTGAAAAACATTTAACTTATTG
702831 CTTGAAAAACATTTAAACTTAT
1 CTTGAAAAACATTT-AACTTAT
702853 CTCTAAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (23 bp):
CTTGAAAAACATTTAACTTATTG
Found at i:711290 original size:52 final size:52
Alignment explanation
Indices: 711223--711331 Score: 155
Period size: 52 Copynumber: 2.1 Consensus size: 52
711213 ATGCATTTGA
* * *
711223 AATTCTAGTCGTTGGACTCAATGTATCGATATAATTCATAATGTATCGATAT
1 AATTATAGTCGTTGGACTCAATGTATCGATACAATTCACAATGTATCGATAT
* * * *
711275 AATTATAGTTGTTGGACTTAATGTATCGATACAATTTACCATGTATCGATAT
1 AATTATAGTCGTTGGACTCAATGTATCGATACAATTCACAATGTATCGATAT
711327 AATTA
1 AATTA
711332 ACTTAGGGTA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (52 bp):
AATTATAGTCGTTGGACTCAATGTATCGATACAATTCACAATGTATCGATAT
Found at i:711414 original size:13 final size:13
Alignment explanation
Indices: 711396--711420 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
711386 TACAAAGAAC
711396 ATGTATCGATACA
1 ATGTATCGATACA
711409 ATGTATCGATAC
1 ATGTATCGATAC
711421 TAAGCAATAT
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):
ATGTATCGATACA
Found at i:711434 original size:33 final size:32
Alignment explanation
Indices: 711378--711441 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
711368 CATTTTATGG
711378 TGTATCAATACAAAGAACATGTATCGATACAA
1 TGTATCAATACAAAGAACATGTATCGATACAA
* * *
711410 TGTATCGATACTAAGCAATATGTATCGATACA
1 TGTATCAATACAAAG-AACATGTATCGATACA
711442 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCAATACAAAGAACATGTATCGATACAA
Found at i:711591 original size:24 final size:23
Alignment explanation
Indices: 711547--711591 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
711537 ATTATTTTTA
* *
711547 CTTGAAAAACATTTGATTTATTG
1 CTTGAAAAACATTTAACTTATTG
*
711570 CTTGAAAAATATTTAAACTTAT
1 CTTGAAAAACATTT-AACTTAT
711592 CTCTAAAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (23 bp):
CTTGAAAAACATTTAACTTATTG
Found at i:713820 original size:30 final size:31
Alignment explanation
Indices: 713784--713845 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
713774 ATAGGTTTTG
*
713784 ATTTAATGATAGA-TTGTACAAAAAAGACCT
1 ATTTAATGATAGAGTTGTACAAAAAAAACCT
713814 ATTTAATGATAGAGTTGTACAAAAAAAACCT
1 ATTTAATGATAGAGTTGTACAAAAAAAACCT
713845 A
1 A
713846 CACTTTGCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (31 bp):
ATTTAATGATAGAGTTGTACAAAAAAAACCT
Found at i:721830 original size:33 final size:33
Alignment explanation
Indices: 721783--721850 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
721773 TCTTCTCTCT
* * * *
721783 TCCTCCTGTTATCCCTCCTCTCTCTATTATATC
1 TCCTCCTATCATCCCTCCTATCTCTACTATATC
*
721816 TCCTCCTATCATCCCTCCTATCTCTACTATCTC
1 TCCTCCTATCATCCCTCCTATCTCTACTATATC
721849 TC
1 TC
721851 ATATTTCTCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.13, C:0.43, G:0.01, T:0.43
Consensus pattern (33 bp):
TCCTCCTATCATCCCTCCTATCTCTACTATATC
Found at i:722659 original size:17 final size:18
Alignment explanation
Indices: 722633--722669 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
722623 GCTGGTTTTT
722633 TTTC-TCTTTTTGTATTC
1 TTTCTTCTTTTTGTATTC
*
722650 TTTCTTTTTTTTGTATTC
1 TTTCTTCTTTTTGTATTC
722668 TT
1 TT
722670 GAAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.05, C:0.14, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTCTTCTTTTTGTATTC
Found at i:725272 original size:87 final size:87
Alignment explanation
Indices: 725126--725292 Score: 264
Period size: 87 Copynumber: 1.9 Consensus size: 87
725116 CTTTTTTCGT
* * * *
725126 TCACCCGCTGACTCAACCTTAGGCTTCAACCAGGCGAGATATGGTGGCTCGATTAACTCAAATTT
1 TCACCCACTGACTCAAACTTAGGATTCAACCAGGCGAGAGATGGTGGCTCGATTAACTCAAATTT
725191 AGGTCTTGGCCATCAACTTCTG
66 AGGTCTTGGCCATCAACTTCTG
* *
725213 TCACCCACTGACTCAAACTTAGGATTGAACCAGGCGAGGGATGGTGGC-CTGATTAACTCAAATT
1 TCACCCACTGACTCAAACTTAGGATTCAACCAGGCGAGAGATGGTGGCTC-GATTAACTCAAATT
725277 TAGGTCTTGGCCATCA
65 TAGGTCTTGGCCATCA
725293 GCTTGGTCTG
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
86 1 0.01
87 72 0.99
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (87 bp):
TCACCCACTGACTCAAACTTAGGATTCAACCAGGCGAGAGATGGTGGCTCGATTAACTCAAATTT
AGGTCTTGGCCATCAACTTCTG
Found at i:728144 original size:20 final size:20
Alignment explanation
Indices: 728119--728159 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
728109 ATTCACAAGT
*
728119 AAGACTTTTAAAATTTATGG
1 AAGACTTCTAAAATTTATGG
*
728139 AAGACTTCTATAATTTATGG
1 AAGACTTCTAAAATTTATGG
728159 A
1 A
728160 TGAGTCTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (20 bp):
AAGACTTCTAAAATTTATGG
Found at i:728371 original size:2 final size:2
Alignment explanation
Indices: 728358--728396 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
728348 ATTAGCCACC
*
728358 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
728397 TTGTTAAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:732429 original size:20 final size:20
Alignment explanation
Indices: 732394--732432 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
732384 GGCCACTCAT
**
732394 TTTCCTTTTTTTTATTTTTG
1 TTTCCTTTTTGATATTTTTG
732414 TTTCCTTTTTGATATTTTT
1 TTTCCTTTTTGATATTTTT
732433 TTTGTTAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.10, G:0.05, T:0.77
Consensus pattern (20 bp):
TTTCCTTTTTGATATTTTTG
Found at i:735856 original size:52 final size:52
Alignment explanation
Indices: 735776--735895 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
735766 AAAAGTTGCT
*
735776 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTACC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTACC
* *
735828 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTACC
735880 TGCATGTATCGATACA
1 TGCATGTATCGATACA
735896 AAGATCAGTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTACC
Found at i:735908 original size:52 final size:51
Alignment explanation
Indices: 735771--735915 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
735761 ATATGAAAAG
*
735771 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* * *
735823 TTACCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
735875 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
735916 ATGTATCGAT
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 81 0.98
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:735922 original size:13 final size:13
Alignment explanation
Indices: 735904--735928 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
735894 CAAAGATCAG
735904 TGTATCGATACAA
1 TGTATCGATACAA
735917 TGTATCGATACA
1 TGTATCGATACA
735929 TTTGAGTAAT
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:735996 original size:20 final size:20
Alignment explanation
Indices: 735967--736024 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
735957 GCAGTAGCTT
735967 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
735986 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
736006 TTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
736025 TCGTTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:736101 original size:21 final size:21
Alignment explanation
Indices: 736060--736101 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
736050 GTTGGGACCT
*
736060 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
736081 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
736102 ACATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:736650 original size:33 final size:32
Alignment explanation
Indices: 736607--736685 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
736597 TTGCTACTGT
* *
736607 CTTGCGTGGGCTTTAAAAAAAAGGTGCCACTAA
1 CTTGTGTGGGCTTT-AAAAAAAGGTGCCACCAA
* * * *
736640 CTTGTGTGGGCTTTGAAAAGAGTTGCCACCGA
1 CTTGTGTGGGCTTTAAAAAAAGGTGCCACCAA
*
736672 CTCGTGTGGGCTTT
1 CTTGTGTGGGCTTT
736686 GAAAGGGTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
32 26 0.67
33 13 0.33
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (32 bp):
CTTGTGTGGGCTTTAAAAAAAGGTGCCACCAA
Found at i:736744 original size:28 final size:28
Alignment explanation
Indices: 736629--737764 Score: 784
Period size: 28 Copynumber: 40.3 Consensus size: 28
736619 TTAAAAAAAA
* *
736629 GGTGCCACTAACTTGTGTGGGCTTTGAAAA
1 GGTGCCACTGAC-T-TGTGGGCTTTGAAAT
* *
736659 GAGTTGCCACCGACTCGTGTGGGCTTTGAAAG
1 G-G-TGCCACTGACT--TGTGGGCTTTGAAAT
* * *
736691 GGTATGCTATTGACTTGTGGGTTTTGAAAT
1 GG--TGCCACTGACTTGTGGGCTTTGAAAT
* * *
736721 GGTGGCACTAACTTATGGGCTTTGAAAT
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
** * * *
736749 AATGCCACTAACTTGTGAGCTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
* * *
736777 GATGTCACTGACTTGTGGGCTTT-AAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
* * ** *
736804 GGATGCCATTGACTTGTGAGCTTCAAAAA
1 GG-TGCCACTGACTTGTGGGCTTTGAAAT
* * *
736833 GATGCCACTGACTTGTGGGTTTTAAAAT
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
*
736861 GGTGCGACTGACTTGTGGGCTTTGAAA-
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
*
736888 GGATGCCACTGACTTGTGGGCTTGGAAAAT
1 GG-TGCCACTGACTTGTGGGCTTTG-AAAT
* * *
736918 -GTGTCACTGACTTGTGGGCTTGGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
*
736945 GGTGCCATTGACTTGTGGGCTTTGAAAT
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
* *
736973 GATGCCACTAACTTGTGGGCTTTGAAAT
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
* * *
737001 GATGCCACTGACTTGTAGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
*
737029 GGTGCCACTCACTTGTGGGCTTTGAAAT
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
*
737057 GGTGCCACTAACTTGTGGGCTTTGAAA-
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
* * *
737084 GGATGCCATTGACTTGTGGGC-TTAAAAA
1 GG-TGCCACTGACTTGTGGGCTTTGAAAT
*
737112 GATGCCACTGACTTGTGGGCTTTGAAAT
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
* * *
737140 GATGCCACTAACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
*
737168 GGTGCCACTGTCTTGTGGGCTTTGAAA-
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
* *
737195 GGATGCCACTGACTTATGGGC-TT-AAAA
1 GG-TGCCACTGACTTGTGGGCTTTGAAAT
* *
737222 GGATGCCAC-GAAGTTGTGGGCTTTCAAAT
1 GG-TGCCACTG-ACTTGTGGGCTTTGAAAT
* *
737251 GGGTTGCCACCGACTTGTGTGGGCTTTCAAAT
1 -GG-TGCCACTGAC-T-TGTGGGCTTTGAAAT
* *
737283 GAGTTGCCACCGACTTATGTGGGCTTTAAAAT
1 G-G-TGCCACTGAC-T-TGTGGGCTTTGAAAT
**
737315 GAGTTGCCACCAACTTGTGGGCTTTGAAAT
1 G-G-TGCCACTGACTTGTGGGCTTTGAAAT
* *
737345 GATGCCACTGACTTGTGGGCTTTAAAAT
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
737373 GGTGCCACTGACTTGTGGGCTTTGAAA-
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
* *
737400 GGATGCCACGGACTTGTGGGCTTTGAAAA
1 GG-TGCCACTGACTTGTGGGCTTTGAAAT
* * *
737429 GATGCCA-TGGACTTGTGGACTTT-AAAG
1 GGTGCCACT-GACTTGTGGGCTTTGAAAT
* * * * *
737456 GGTGCCACGGAGTTGTGGAC-TTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
* * * * *
737483 GGTGCCACGGAGTTGTGGAC-TTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
* * * * * *
737510 GGTGCCACGGAGTTGTGGAC-CTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
* * * * *
737537 GGTGCCACAGAGTTGTGGGC-CTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
* * *
737564 GGTGCCACGGAGTTGTGGACTTT-AAA-
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
* * *
737590 GGATGCCA-TAGAGTTGTGGGC-TTAAAAA
1 GG-TGCCACT-GACTTGTGGGCTTTGAAAT
* ** * * *
737618 GGTGCCACGGAGATGTGGAC-TTAAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
* * * * * *
737645 GATGCCACGGAGTTGTGGACTTTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
* * * * * *
737673 GGTGCCACTAAGTTGTGGACATTAAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
* * * * * *
737701 GGTGACACGGAGTTGTGGACTTTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
* * * * *
737729 GGTGCCACGGAGTTGTGGACTTTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAT
737757 GGTGCCAC
1 GGTGCCAC
737765 AGAGTTGTTG
Statistics
Matches: 950, Mismatches: 121, Indels: 72
0.83 0.11 0.06
Matches are distributed among these distances:
26 10 0.01
27 236 0.25
28 556 0.59
29 13 0.01
30 40 0.04
31 7 0.01
32 88 0.09
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.28
Consensus pattern (28 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAT
Found at i:736838 original size:84 final size:84
Alignment explanation
Indices: 736625--737764 Score: 880
Period size: 84 Copynumber: 13.5 Consensus size: 84
736615 GGCTTTAAAA
* *
736625 AAAAGG-TGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGAA
1 AAAAGGATGCCACTAAC-T-TGTGGGCTTTG-AAAG-GATGCCACTGACT--TGTGGGCTTTGAA
* * * *
736689 AGGGTATGCTATTGACTTGTGGGTTTT
60 AAGG--TGCCACTGACTTGTGGGCTTT
* * * ** * * *
736716 GAAATGG-TGGCACTAACTTATGGGCTTTGAAATAATGCCACTAACTTGTGAGCTTTGAAAAGAT
1 -AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGT
*
736780 GTCACTGACTTGTGGGCTTT
65 GCCACTGACTTGTGGGCTTT
* * * ** * *
736800 AAAAGGATGCCATTGACTTGTGAGCTTCAAAAAGATGCCACTGACTTGTGGG-TTTTAAAATGGT
1 AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAA-GGT
*
736864 GCGACTGACTTGTGGGCTTT
65 GCCACTGACTTGTGGGCTTT
* * * * * *
736884 GAAAGGATGCCACTGACTTGTGGGCTTGGAAAATG-TGTCACTGACTTGTGGGCTTGGAAAAGGT
1 AAAAGGATGCCACTAACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGT
*
736948 GCCATTGACTTGTGGGCTTT
65 GCCACTGACTTGTGGGCTTT
* * * * *
736968 GAAATGATGCCACTAACTTGTGGGCTTTGAAATGATGCCACTGACTTGTAGGCTTTGAAAGGGTG
1 AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGTG
*
737033 CCACTCACTTGTGGGCTTT
66 CCACTGACTTGTGGGCTTT
* * * *
737052 GAAATGG-TGCCACTAACTTGTGGGCTTTGAAAGGATGCCATTGACTTGTGGGC-TTAAAAAGAT
1 -AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGT
737115 GCCACTGACTTGTGGGCTTT
65 GCCACTGACTTGTGGGCTTT
* * * *
737135 GAAATGATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGTCTTGTGGGCTTTG-AAAGGAT
1 AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGG-T
*
737199 GCCACTGACTTATGGGC-TT
65 GCCACTGACTTGTGGGCTTT
* * * * * *
737218 AAAAGGATGCCACGAAGTTGTGGGCTTTCAAATGGGTTGCCACCGACTTGTGTGGGCTTTCAAAT
1 AAAAGGATGCCACTAACTTGTGGGCTTTGAAA--GGATGCCACTGAC-T-TGTGGGCTTTGAAA-
* *
737283 GAGTTGCCACCGACTTATGTGGGCTTT
61 -AGGTGCCACTGAC-T-TGTGGGCTTT
* * *
737310 AAAATGAGTTGCCACCAACTTGTGGGCTTTGAAATGATGCCACTGACTTGTGGGCTTT-AAAATG
1 AAAA-G-GATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAA-G
737374 GTGCCACTGACTTGTGGGCTTT
63 GTGCCACTGACTTGTGGGCTTT
* ** * * *
737396 GAAAGGATGCCACGGACTTGTGGGCTTTGAAAAGATGCCA-TGGACTTGTGGACTTT-AAAGGGT
1 AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACT-GACTTGTGGGCTTTGAAAAGGT
* * *
737459 GCCACGGAGTTGTGGAC-TT
65 GCCACTGACTTGTGGGCTTT
* ** * * * * * * * *
737478 AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-CT-AAAAGGGT
1 AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAA-GGT
* * *
737540 GCCACAGAGTTGTGGGC-CT
65 GCCACTGACTTGTGGGCTTT
* ** * * * *
737559 AAAAGGGTGCCACGGAGTTGTGGACTTT-AAAGGATGCCA-TAGAGTTGTGGGC-TTAAAAAGGT
1 AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACT-GACTTGTGGGCTTTGAAAAGGT
* ** *
737621 GCCACGGAGATGTGGAC-TT
65 GCCACTGACTTGTGGGCTTT
* ** * * * * * * * * *
737640 AAAAAGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACTAAGTTGTGGACATTAAAAAGGTG
1 AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGTG
* * * *
737705 ACACGGAGTTGTGGACTTT
66 CCACTGACTTGTGGGCTTT
* ** * * * *
737724 AAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCAC
1 AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCAC
737765 AGAGTTGTTG
Statistics
Matches: 884, Mismatches: 132, Indels: 72
0.81 0.12 0.07
Matches are distributed among these distances:
80 4 0.00
81 130 0.15
82 51 0.06
83 163 0.18
84 351 0.40
85 24 0.03
86 28 0.03
87 12 0.01
88 21 0.02
89 15 0.02
90 23 0.03
91 8 0.01
92 30 0.03
93 1 0.00
94 23 0.03
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.28
Consensus pattern (84 bp):
AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGTG
CCACTGACTTGTGGGCTTT
Found at i:737769 original size:28 final size:28
Alignment explanation
Indices: 736985--738030 Score: 726
Period size: 28 Copynumber: 37.6 Consensus size: 28
736975 TGCCACTAAC
* * * * * *
736985 TTGTGGGCTTTGAAATGATGCCACTGAC
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* ** *
737013 TTGTAGG-CTTTGAAAGGGTGCCACTCAC
1 TTGT-GGACTTTAAAAGGGTGCCACGGAG
* * * ** *
737041 TTGTGGGCTTTGAAATGGTGCCACTAAC
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* * * ** *
737069 TTGTGGGCTTTGAAAGGATGCCATTGAC
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* * * * *
737097 TTGTGGGC-TTAAAAAGATGCCACTGAC
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* * * * ** *
737124 TTGTGGGCTTTGAAATGATGCCACTAAC
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* * * **
737152 TTGTGGGCTTTGAAAGGGTGCCACTGTC
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* * * * *
737180 TTGTGGGCTTTGAAAGGATGCCACTGAC
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* * * *
737208 TTATGGGC-TTAAAAGGATGCCACGAAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* * * *
737235 TTGTGGGCTTTCAAATGGGTTGCCACCGACT
1 TTGTGGACTTT-AAAAGGG-TGCCACGGA-G
* * * * *
737266 TGTGTGGGCTTTCAAATGAGTTGCCACCGACT
1 T-TGTGGACTTT-AAAAG-GGTGCCACGGA-G
* * ** *
737298 TATGTGGGCTTTAAAATGAGTTGCCACCAAC
1 T-TGTGGACTTTAAAA-G-GGTGCCACGGAG
* * * * * *
737329 TTGTGGGCTTTGAAATGATGCCACTGAC
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* * * *
737357 TTGTGGGCTTTAAAATGGTGCCACTGAC
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* * * *
737385 TTGTGGGCTTTGAAAGGATGCCACGGAC
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* * * *
737413 TTGTGGGCTTTGAAAA-GATGCCATGGAC
1 TTGTGGACTTT-AAAAGGGTGCCACGGAG
737441 TTGTGGACTTT-AAAGGGTGCCACGGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
737468 TTGTGGAC-TTAAAAGGGTGCCACGGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
737495 TTGTGGAC-TTAAAAGGGTGCCACGGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* *
737522 TTGTGGAC-CTAAAAGGGTGCCACAGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* *
737549 TTGTGGGC-CTAAAAGGGTGCCACGGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* **
737576 TTGTGGACTTT-AAAGGATGCCATAGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* *
737603 TTGTGGGC-TTAAAAAGGTGCCACGGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* * *
737630 ATGTGGAC-TTAAAAAGATGCCACGGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
**
737657 TTGTGGACTTTAAAAGGGTGCCACTAAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* * *
737685 TTGTGGACATTAAAAAGGTGACACGGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
737713 TTGTGGACTTTAAAAGGGTGCCACGGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
*
737741 TTGTGGACTTTAAAAGGGTGCCACAGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* **
737769 TTGTTGAC-TTAAAAGAATGCCACGGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* *
737796 TTGTGGACTTTGAAAGGGTGCCACAGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* ***
737824 TTGTGGAC-TTAAAAGGATTTTACGGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
** *
737851 TTGTGGACTTTAAAAATGTGCCATGGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* *
737879 TTGTAGACTTT--AAGGGTGCCACGGAA
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* *
737905 TTGTGGACTTTAAAAGGATGCCATGGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* **
737933 TTGTAGAC-TTAAAAGGGTGCCGTGGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* * *
737960 TTGTGGAC-TTAAAAAGATACCACGGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* * * *
737987 TTATGGAC-TTCAAAGGTTGCCATGGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
*
738014 TTGTGGACTTAAAAAGG
1 TTGTGGACTTTAAAAGG
738031 AATACTACTG
Statistics
Matches: 863, Mismatches: 134, Indels: 42
0.83 0.13 0.04
Matches are distributed among these distances:
26 28 0.03
27 338 0.39
28 411 0.48
29 10 0.01
30 20 0.02
31 5 0.01
32 50 0.06
33 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.27
Consensus pattern (28 bp):
TTGTGGACTTTAAAAGGGTGCCACGGAG
Found at i:737851 original size:27 final size:27
Alignment explanation
Indices: 737347--738027 Score: 709
Period size: 27 Copynumber: 24.9 Consensus size: 27
737337 TTTGAAATGA
* * * *
737347 TGCCACTGACTTGTGGGCTTTAAAATGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * * * *
737375 TGCCACTGACTTGTGGGCTTTGAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * *
737403 TGCCACGGACTTGTGGGCTTTGAAAA-GA
1 TGCCACGGAGTTGTGGAC-TT-AAAAGGG
* * *
737431 TGCCATGGACTTGTGGACTTTAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
737458 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
737485 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
737512 TGCCACGGAGTTGTGGACCTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
737539 TGCCACAGAGTTGTGGGCCTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
737566 TGCCACGGAGTTGTGGACTTTAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
** * *
737593 TGCCATAGAGTTGTGGGCTTAAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
737620 TGCCACGGAGATGTGGACTTAAAAAGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
737647 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
** *
737675 TGCCACTAAGTTGTGGACATTAAAAAGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
*
737703 TGACACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
737731 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * **
737759 TGCCACAGAGTTGTTGACTTAAAAGAA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
737786 TGCCACGGAGTTGTGGACTTTGAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* *
737814 TGCCACAGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*** **
737841 TTTTACGGAGTTGTGGACTTTAAAAATG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * *
737869 TGCCATGGAGTTGTAGACTT-TAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
737895 TGCCACGGAATTGTGGACTTTAAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* *
737923 TGCCATGGAGTTGTAGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
** * *
737950 TGCCGTGGAGTTGTGGACTTAAAAAGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * * *
737977 TACCACGGAGTTATGGACTTCAAAGGT
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
738004 TGCCATGGAGTTGTGGACTTAAAA
1 TGCCACGGAGTTGTGGACTTAAAA
738028 AGGAATACTA
Statistics
Matches: 551, Mismatches: 95, Indels: 15
0.83 0.14 0.02
Matches are distributed among these distances:
26 21 0.04
27 306 0.56
28 221 0.40
29 3 0.01
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.26
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:741792 original size:34 final size:35
Alignment explanation
Indices: 741754--741820 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
741744 CCTTACAACA
741754 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
741788 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
741821 AGTCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:742391 original size:10 final size:10
Alignment explanation
Indices: 742372--742434 Score: 56
Period size: 10 Copynumber: 6.1 Consensus size: 10
742362 GTATCGATAC
742372 ATGAACAGTG
1 ATGAACAGTG
*
742382 ATGAATAGTG
1 ATGAACAGTG
* *
742392 ATGTATC-GATAC
1 ATG-AACAG-T-G
742404 ATGAACAGTG
1 ATGAACAGTG
*
742414 ATGAATAGTG
1 ATGAACAGTG
742424 ATGAACAGTG
1 ATGAACAGTG
742434 A
1 A
742435 AAATGAGATT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
10 32 0.78
11 5 0.12
12 4 0.10
ACGTcount: A:0.40, C:0.08, G:0.27, T:0.25
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:742397 original size:32 final size:32
Alignment explanation
Indices: 742356--742426 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
742346 CTCAATGTAC
742356 AGTGATGTATCGATACATGAACAGTGATGAAT
1 AGTGATGTATCGATACATGAACAGTGATGAAT
742388 AGTGATGTATCGATACATGAACAGTGATGAAT
1 AGTGATGTATCGATACATGAACAGTGATGAAT
742420 AGTGATG
1 AGTGATG
742427 AACAGTGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.28
Consensus pattern (32 bp):
AGTGATGTATCGATACATGAACAGTGATGAAT
Found at i:742480 original size:13 final size:13
Alignment explanation
Indices: 742462--742486 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
742452 TGCCAATGCT
742462 ATGTATCGATACA
1 ATGTATCGATACA
742475 ATGTATCGATAC
1 ATGTATCGATAC
742487 TTACCAAAAT
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):
ATGTATCGATACA
Found at i:744176 original size:20 final size:20
Alignment explanation
Indices: 744151--744217 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
744141 AATCCAGAAC
744151 TATCGATACTTTGAGTAAAG
1 TATCGATACTTTGAGTAAAG
*
744171 TATCGACACTTTGAGTAAAG
1 TATCGATACTTTGAGTAAAG
*
744191 TATCGATACTTTAAGTAAAG
1 TATCGATACTTTGAGTAAAG
744211 TATCGAT
1 TATCGAT
744218 TGGAATTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (20 bp):
TATCGATACTTTGAGTAAAG
Found at i:747347 original size:34 final size:35
Alignment explanation
Indices: 747309--747375 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
747299 CCTTACAACA
747309 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
747343 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
747376 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:747844 original size:22 final size:22
Alignment explanation
Indices: 747816--747858 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
747806 TTAAATAGTG
747816 TGAACAGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
747838 TGAACAGTGATGTATCGATAC
1 TGAACAGTGATGTATCGATAC
747859 TGTGATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (22 bp):
TGAACAGTGATGTATCGATACA
Found at i:747931 original size:22 final size:22
Alignment explanation
Indices: 747905--747961 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
747895 ATGTACAAAG
747905 ATGAATAGTGATGTATCGATAC
1 ATGAATAGTGATGTATCGATAC
* *
747927 ATGAACAGTGATGTATCGATAT
1 ATGAATAGTGATGTATCGATAC
747949 ATGAATAGTGATG
1 ATGAATAGTGATG
747962 AATAGTGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.32
Consensus pattern (22 bp):
ATGAATAGTGATGTATCGATAC
Found at i:753804 original size:543 final size:539
Alignment explanation
Indices: 752712--753775 Score: 1668
Period size: 543 Copynumber: 2.0 Consensus size: 539
752702 CACTCTATTT
*
752712 CATATGTTTTTTCTTTTTTTTTTTCTTCCTTTCTTCTTCATCTTCTTTCTTTCTTACCTAACTAG
1 CATATGTTTTTTCTTTTTTTTTTTCTTCCTTTCTTCTTCATCTTCTTTCTTTCTTACCTAACCAG
* * * * *
752777 GAAAGCAATCCAGAATCCGATGACCGGCCACCACGTCGGTCGTCGGCAACCACCGTCGGCCATCG
66 GAAAGCAATCCAAAATCCGACGACCGGCCACCACATCGGTCGTCGGCAACCACCGTCGGCCACCA
* * ** *
752842 CTCGTCGGTGGTCGTTGGCTACCAAATTTTACTTTTAGACTCTTTTTGACCTCCTTTTTTCAAAT
131 CTCCTCGGTGGTCATTGGCTACCAAATTTTACTTTTAGACTCTTTTCAACCTCCTCTTTTCAAAT
* *
752907 TCGGAGTCGGATTTTTTCAATTCTTTTTAGATCTTTTTAGATCTACAAGAGAAATTCGAATCTAA
196 CCGAAGTCGGATTTTTTCAATTCTTTTTAGATCTTTTTAGATCTACAAGAGAAATTCGAATCTAA
*
752972 TACCTCAAATTCAGTCACCGTCTATCGTCGGATCACTCCCAAAATCTAGTATGTTTTCCCCCTTG
261 TACCTCAAATTCAGTCACCGTCTATCGTCGGATCACTCCCAAAATCTAGTATGTTTTCCCCCTCG
* * *
753037 GTGTGAACTTCTTTTCACCGTTCGAATTTTTTAAATAATCATTGAAACCTCTTCAATCGAAAAAC
326 GTGTGAACTTCTTTTCACCGTTCGAAGTTTTCAAATAATCACTGAAACCTCTTCAATCGAAAAAC
*
753102 CCACGTTGATTTTTCTTTGGAAAGCTTTCTCTCCCTCTTTTTTTTTTACTCGACCTCTCCTCTTT
391 CCACGTTGATTTTTCTTTGGAAAGCTTTCTCTCCCTCTTTTTTTTTTACTCGACCTCTCCCCTTT
* *
753167 TTATCAAACATTTTCATCTTTGCTTTTTTTCTTTTTCCATTTTCGGCCAATTTGTCAGCCACCAA
456 TTATCAAACATTTTCATCTTTGCCTTTTTTCTTTCTCCATTTTCGGCCAATTTGTCAGCCACCAA
*** *
753232 ATCCCAGGCCACTCTATTT
521 ATCCCAGGCCACGAAATTG
753251 CATATGTTTTTTCTTTTTTTTCCTTTTTCTTCCTTTCTTCTTCATCTTCTTTCTTTCTTACCTAA
1 CATATGTTTTTTC--TTTTTT--TTTTTCTTCCTTTCTTCTTCATCTTCTTTCTTTCTTACCTAA
* *
753316 CCAGGAAAGCAATCCAAAATCCGACGACCGGCCACCACATCGGTCGTTGGCAACTACCGTCGGCC
62 CCAGGAAAGCAATCCAAAATCCGACGACCGGCCACCACATCGGTCGTCGGCAACCACCGTCGGCC
753381 ACCACTCACT-GGTGGTCATTGGCTACCAAATTTTACTTTTAGACTCTTTTCAACCTCCTCTTTT
127 ACCACTC-CTCGGTGGTCATTGGCTACCAAATTTTACTTTTAGACTCTTTTCAACCTCCTCTTTT
* *
753445 CAAATCCGAAGTCGGATTTTTTCAATTCTTTTTAGTTTTTTTTAGATCTACAAGAGAAATTCGAA
191 CAAATCCGAAGTCGGATTTTTTCAATTCTTTTTAGATCTTTTTAGATCTACAAGAGAAATTCGAA
* * **
753510 TCTTATACCTCAAATTCGGTCACCGTCTA-CTGTCGGATTGCTCCCAAAATCTAGTATGTTTTCC
256 TCTAATACCTCAAATTCAGTCACCGTCTATC-GTCGGATCACTCCCAAAATCTAGTATGTTTTCC
* * *
753574 CCCTCGGTGTGAACTTTTTTTCACCGTTCGGAGTTTTCAAATAATCACCTG-AATCTCTTCAATC
320 CCCTCGGTGTGAACTTCTTTTCACCGTTCGAAGTTTTCAAATAATCA-CTGAAACCTCTTCAATC
* *
753638 GAAAAACCCACTTTGATTTTTCTTTGGAAAGCTTTCTCTCCCTTTTTTTTTCTTTACTCGACCTC
384 GAAAAACCCACGTTGATTTTTCTTTGGAAAGCTTTCTCTCCCTCTTTTTTT-TTTACTCGACCTC
*
753703 TCCCCTTTTTATCAAACATTTTCATCTTTGCCTTTTTTCTTTCTCCATTTTTC-GTCAATTTGTC
448 TCCCCTTTTTATCAAACATTTTCATCTTTGCCTTTTTTCTTTCTCCA-TTTTCGGCCAATTTGTC
*
753767 GGCCACCAA
512 AGCCACCAA
753776 CTTTTTCCAC
Statistics
Matches: 481, Mismatches: 35, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
539 13 0.03
541 6 0.01
542 1 0.00
543 378 0.79
544 78 0.16
545 5 0.01
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.41
Consensus pattern (539 bp):
CATATGTTTTTTCTTTTTTTTTTTCTTCCTTTCTTCTTCATCTTCTTTCTTTCTTACCTAACCAG
GAAAGCAATCCAAAATCCGACGACCGGCCACCACATCGGTCGTCGGCAACCACCGTCGGCCACCA
CTCCTCGGTGGTCATTGGCTACCAAATTTTACTTTTAGACTCTTTTCAACCTCCTCTTTTCAAAT
CCGAAGTCGGATTTTTTCAATTCTTTTTAGATCTTTTTAGATCTACAAGAGAAATTCGAATCTAA
TACCTCAAATTCAGTCACCGTCTATCGTCGGATCACTCCCAAAATCTAGTATGTTTTCCCCCTCG
GTGTGAACTTCTTTTCACCGTTCGAAGTTTTCAAATAATCACTGAAACCTCTTCAATCGAAAAAC
CCACGTTGATTTTTCTTTGGAAAGCTTTCTCTCCCTCTTTTTTTTTTACTCGACCTCTCCCCTTT
TTATCAAACATTTTCATCTTTGCCTTTTTTCTTTCTCCATTTTCGGCCAATTTGTCAGCCACCAA
ATCCCAGGCCACGAAATTG
Found at i:756526 original size:13 final size:13
Alignment explanation
Indices: 756508--756533 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
756498 TACAGCAAGT
756508 ATGTATCGATACA
1 ATGTATCGATACA
756521 ATGTATCGATACA
1 ATGTATCGATACA
756534 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:758785 original size:21 final size:21
Alignment explanation
Indices: 758752--758796 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
758742 TTGCAAGTTG
*
758752 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
758774 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
758794 AAA
1 AAA
758797 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:760590 original size:15 final size:15
Alignment explanation
Indices: 760570--760600 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
760560 TAAAAATGTC
*
760570 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
760585 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
760600 C
1 C
760601 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:762677 original size:13 final size:13
Alignment explanation
Indices: 762659--762696 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
762649 GGAAATTCAA
762659 TGTATCGATACAT
1 TGTATCGATACAT
*
762672 TGTATCGATACCT
1 TGTATCGATACAT
762685 TGTATCGATACA
1 TGTATCGATACA
762697 GGGTGATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:762841 original size:21 final size:21
Alignment explanation
Indices: 762817--762863 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
762807 AAATCTTTTG
762817 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
762838 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
762858 CAAAAT
1 CAAAAT
762864 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:762860 original size:20 final size:19
Alignment explanation
Indices: 762819--762861 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
762809 ATCTTTTGCA
762819 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
762839 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
762859 AAA
1 AAA
762862 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:765259 original size:13 final size:13
Alignment explanation
Indices: 765241--765266 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
765231 TACAGCAAGT
765241 ATGTATCGATACA
1 ATGTATCGATACA
765254 ATGTATCGATACA
1 ATGTATCGATACA
765267 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:769521 original size:6 final size:7
Alignment explanation
Indices: 769485--769521 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
769475 ATATAAAAAA
769485 TTTATTT
1 TTTATTT
769492 TTTATTT
1 TTTATTT
769499 TTTACTTT
1 TTTA-TTT
*
769507 TTTCTTT
1 TTTATTT
769514 TTTATTT
1 TTTATTT
769521 T
1 T
769522 ATCATCTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTATTT
Found at i:769843 original size:20 final size:19
Alignment explanation
Indices: 769796--769844 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
769786 ATTTATAAAG
*
769796 AAGATAAAAATGAAAAAAA
1 AAGATAAAAAAGAAAAAAA
*
769815 AAGAGAAAAAAGTAAAGAAAA
1 AAGATAAAAAAG-AAA-AAAA
769836 AA-ATAAAAA
1 AAGATAAAAA
769845 TTAATTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 10 0.40
20 9 0.36
21 6 0.24
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (19 bp):
AAGATAAAAAAGAAAAAAA
Found at i:769900 original size:20 final size:21
Alignment explanation
Indices: 769875--769920 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
769865 TATGCTTATA
* *
769875 AATTAATT-ATATTTTAAAAT
1 AATTAATTCAAATTATAAAAT
769895 AATTAATTCAAATTATAAAAT
1 AATTAATTCAAATTATAAAAT
769916 AATTA
1 AATTA
769921 TTTTTTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTAATTCAAATTATAAAAT
Found at i:772635 original size:18 final size:17
Alignment explanation
Indices: 772587--772635 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
772577 CTATGGGTGA
772587 TTTAAAAAAAGTAATTT
1 TTTAAAAAAAGTAATTT
** *
772604 TTATAAAATGAGTAGTTT
1 TT-TAAAAAAAGTAATTT
772622 TTTAAATAAAAGTA
1 TTTAAA-AAAAGTA
772636 TGTGGTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (17 bp):
TTTAAAAAAAGTAATTT
Found at i:774859 original size:14 final size:15
Alignment explanation
Indices: 774842--774881 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
774832 AATTTTTTTT
774842 GAAAAAAATTT-GTA
1 GAAAAAAATTTAGTA
*
774856 GAAAAAAATTTATTA
1 GAAAAAAATTTAGTA
*
774871 GATAAAAATTT
1 GAAAAAAATTT
774882 CACAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (15 bp):
GAAAAAAATTTAGTA
Found at i:792208 original size:11 final size:11
Alignment explanation
Indices: 792194--792236 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
792184 TAAAAAGTAA
792194 AAAAAAAAACC
1 AAAAAAAAACC
**
792205 AAAAAAAAAAG
1 AAAAAAAAACC
792216 AAAAAAAAACC
1 AAAAAAAAACC
792227 AAAAAAAAAC
1 AAAAAAAAAC
792237 AATACAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACC
Found at i:792246 original size:22 final size:22
Alignment explanation
Indices: 792194--792235 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
792184 TAAAAAGTAA
792194 AAAAAAAAACCAAAAAAAAAAG
1 AAAAAAAAACCAAAAAAAAAAG
792216 AAAAAAAAACCAAAAAAAAA
1 AAAAAAAAACCAAAAAAAAA
792236 CAATACAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (22 bp):
AAAAAAAAACCAAAAAAAAAAG
Found at i:793672 original size:20 final size:21
Alignment explanation
Indices: 793647--793699 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
793637 TTACAAGCCA
793647 ATGTATCGATACAT-TTGGTC
1 ATGTATCGATACATCTTGGTC
* *
793667 ATGTATCGATATATCTTTGTC
1 ATGTATCGATACATCTTGGTC
793688 -TGTATCGATACA
1 ATGTATCGATACA
793700 AACAGTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTGGTC
Found at i:794377 original size:22 final size:22
Alignment explanation
Indices: 794350--794395 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
794340 TTTCCTTTTC
794350 TCTCCCCCTTAATAAAAAAATT
1 TCTCCCCCTTAATAAAAAAATT
*
794372 TCTCCCCCTTAATAAAACAATT
1 TCTCCCCCTTAATAAAAAAATT
794394 TC
1 TC
794396 CTTTAATCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (22 bp):
TCTCCCCCTTAATAAAAAAATT
Found at i:802449 original size:33 final size:33
Alignment explanation
Indices: 802403--802471 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
802393 CGTTACAAGC
802403 CAATGTATCGATACAT-TTGGTCATGTATCGATA
1 CAATGTATCGATACATCTTGGTC-TGTATCGATA
* *
802436 CAATGTATTGATACATCTTTGTCTGTATCGATA
1 CAATGTATCGATACATCTTGGTCTGTATCGATA
802469 CAA
1 CAA
802472 ACAGTTAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 28 0.85
34 5 0.15
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (33 bp):
CAATGTATCGATACATCTTGGTCTGTATCGATA
Found at i:808813 original size:161 final size:161
Alignment explanation
Indices: 808639--808938 Score: 478
Period size: 161 Copynumber: 1.9 Consensus size: 161
808629 ATGGGCAATG
* *
808639 AATCTTCTCGTCAAAGTCTTT-TATTAGGTTCAAAGGATTCAATTACATGACTATTAAAAATAAT
1 AATCTTCTCGTCAAAGT-TTTCTATTAAGTGCAAAGGATTCAATTACATGACTATTAAAAATAAT
* * * *
808703 A-GATATGAGACAAAAGATATACATTTCATCACTATGAAGATCCACTTATCAAAAAAGCCAAGTT
65 AGGATAAGAGACAAAAGATACACACTTCATCACTATGAAGATCCACTTATAAAAAAAGCCAAG-T
808767 TTTGCAACATAACAAAAAAAAGGGGGGACAACA
129 TTTGCAACATAACAAAAAAAAGGGGGGACAACA
*
808800 AATCTTCTCGTCAAAGTTTTCTATTAAGTGCAAAGGATTCAATTACATGACTGTTAAAAATAATA
1 AATCTTCTCGTCAAAGTTTTCTATTAAGTGCAAAGGATTCAATTACATGACTATTAAAAATAATA
* *
808865 GGATAAGAGACAAAAGATACACACTTCATCACTATTAAGATCTACTTATAAAAAAAGCCAAGTTT
66 GGATAAGAGACAAAAGATACACACTTCATCACTATGAAGATCCACTTATAAAAAAAGCCAAGTTT
*
808930 TGCATCATA
131 TGCAACATA
808939 GCTTTTAGAA
Statistics
Matches: 127, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
160 3 0.02
161 69 0.54
162 55 0.43
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.29
Consensus pattern (161 bp):
AATCTTCTCGTCAAAGTTTTCTATTAAGTGCAAAGGATTCAATTACATGACTATTAAAAATAATA
GGATAAGAGACAAAAGATACACACTTCATCACTATGAAGATCCACTTATAAAAAAAGCCAAGTTT
TGCAACATAACAAAAAAAAGGGGGGACAACA
Found at i:813950 original size:18 final size:18
Alignment explanation
Indices: 813927--813972 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
813917 TAAGATAACT
813927 TATTTTGTAATATGAATA
1 TATTTTGTAATATGAATA
813945 TATTTTGTAATATGAATA
1 TATTTTGTAATATGAATA
813963 TATTTTGTAA
1 TATTTTGTAA
813973 ATTGATAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (18 bp):
TATTTTGTAATATGAATA
Found at i:815591 original size:30 final size:30
Alignment explanation
Indices: 815555--815612 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
815545 AAAAGTCACA
*
815555 TTTTTACCCAGATGTATCGATACATTTTGT
1 TTTTTACCCAAATGTATCGATACATTTTGT
*
815585 TTTTTACCCAAATGTATCGGTACATTTT
1 TTTTTACCCAAATGTATCGATACATTTT
815613 TCAATGTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.47
Consensus pattern (30 bp):
TTTTTACCCAAATGTATCGATACATTTTGT
Found at i:815620 original size:20 final size:19
Alignment explanation
Indices: 815595--815662 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 19
815585 TTTTTACCCA
*
815595 AATGTATCGGTACATTTTT
1 AATGTATCGATACATTTTT
* *
815614 CAATGTATCGATACATGTATG
1 -AATGTATCGATACAT-TTTT
815635 AATGTATCGATACATTCTTT
1 AATGTATCGATACATT-TTT
815655 AATGTATC
1 AATGTATC
815663 AATAAATTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.02
20 38 0.93
21 2 0.05
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (19 bp):
AATGTATCGATACATTTTT
Found at i:815671 original size:20 final size:20
Alignment explanation
Indices: 815635--815672 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
815625 TACATGTATG
* *
815635 AATGTATCGATACATTCTTT
1 AATGTATCAATAAATTCTTT
815655 AATGTATCAATAAATTCT
1 AATGTATCAATAAATTCT
815673 GTCCTTTTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (20 bp):
AATGTATCAATAAATTCTTT
Found at i:828883 original size:21 final size:20
Alignment explanation
Indices: 828849--828901 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
828839 TTATAATAAA
*
828849 TAAAAAATAATTAATAATAT
1 TAAAAAATATTTAATAATAT
828869 TAAAAAATTATTT-A-AATAT
1 TAAAAAA-TATTTAATAATAT
828888 TAATAAAATATTTA
1 TAA-AAAATATTTA
828902 TGTGTTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 13 0.45
20 12 0.41
21 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAAAAATATTTAATAATAT
Found at i:828886 original size:19 final size:20
Alignment explanation
Indices: 828839--828902 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
828829 TTTTGTAAAA
* *
828839 TTATAATAAATAAAAAATAAT
1 TTATAAT-ATTAAAAAATTAT
*
828860 TAATAATATTAAAAAATTAT
1 TTATAATATTAAAAAATTAT
828880 TTA-AATATTAATAAAA-TAT
1 TTATAATATTAA-AAAATTAT
828899 TTAT
1 TTAT
828903 GTGTTATATG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 14 0.38
20 17 0.46
21 6 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTATAATATTAAAAAATTAT
Found at i:829101 original size:28 final size:29
Alignment explanation
Indices: 829068--829123 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
829058 TATTTTCTTA
829068 TAATTTTAAAAATAT-AAAATTAAAATAC
1 TAATTTTAAAAATATAAAAATTAAAATAC
*
829096 TAATTTTAATAATATAAAAATTAAAATA
1 TAATTTTAAAAATATAAAAATTAAAATA
829124 TTTTTTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
TAATTTTAAAAATATAAAAATTAAAATAC
Found at i:829123 original size:14 final size:13
Alignment explanation
Indices: 829076--829124 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
829066 TATAATTTTA
829076 AAAATATAAAATT
1 AAAATATAAAATT
**
829089 AAAATACTAATTTT
1 AAAATA-TAAAATT
829103 AATAATATAAAAATT
1 AA-AATAT-AAAATT
829118 AAAATAT
1 AAAATAT
829125 TTTTTAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 6 0.21
14 13 0.45
15 10 0.34
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (13 bp):
AAAATATAAAATT
Found at i:831126 original size:21 final size:21
Alignment explanation
Indices: 831100--831143 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
831090 TGCCAGTGAG
*
831100 TGCTAGTAATTTTTGTGTTAT
1 TGCTAGTAATTTTTGTCTTAT
*
831121 TGCTAGTAATTTTTTTCTTAT
1 TGCTAGTAATTTTTGTCTTAT
831142 TG
1 TG
831144 TGCGCAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.07, G:0.16, T:0.59
Consensus pattern (21 bp):
TGCTAGTAATTTTTGTCTTAT
Found at i:837741 original size:52 final size:52
Alignment explanation
Indices: 837656--837778 Score: 210
Period size: 52 Copynumber: 2.4 Consensus size: 52
837646 ATATGAAAAG
* * *
837656 TTGCCTGCATATATCAATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
837708 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
837760 TTGCCTGCATGTATCGATA
1 TTGCCTGCATGTATCGATA
837779 AAAAGATCAG
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:837793 original size:52 final size:52
Alignment explanation
Indices: 837681--837800 Score: 179
Period size: 52 Copynumber: 2.3 Consensus size: 52
837671 AATACATTTA
****
837681 ATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATTTT
1 ATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACAAAAG
*
837733 ATAATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATA-AAAAG
1 ATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACAAAAG
837784 ATCAGTGTATCGATACA
1 AT-AGTGTATCGATACA
837801 ATGTATCGAT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 3 0.05
52 58 0.95
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (52 bp):
ATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACAAAAG
Found at i:837807 original size:13 final size:13
Alignment explanation
Indices: 837789--837813 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
837779 AAAAGATCAG
837789 TGTATCGATACAA
1 TGTATCGATACAA
837802 TGTATCGATACA
1 TGTATCGATACA
837814 TTTGAGTAAT
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:837880 original size:19 final size:18
Alignment explanation
Indices: 837856--837953 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
837846 TAGCTTAAAT
837856 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
837875 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
837888 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
837907 TGTATCGATAC---C-T-
1 TGTATCGATACAAACTTA
837920 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
837940 TGTATCGATACAAA
1 TGTATCGATACAAA
837954 TCATTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
15 1 0.02
16 2 0.03
17 1 0.02
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:837893 original size:13 final size:13
Alignment explanation
Indices: 837875--837931 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
837865 ACAAAACTTA
837875 TGTATCGATACAT
1 TGTATCGATACAT
837888 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
*
837906 ATGTATCGATACCT
1 -TGTATCGATACAT
837920 TGTATCGATACA
1 TGTATCGATACA
837932 ACACTTTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 20 0.56
14 1 0.03
16 5 0.14
18 1 0.03
19 9 0.25
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:837895 original size:32 final size:32
Alignment explanation
Indices: 837854--837951 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
837844 AGTAGCTTAA
*
837854 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
837886 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
*
837918 CTTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
837951 A
1 A
837952 AATCATTGAA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 48 0.77
33 14 0.23
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:838719 original size:13 final size:13
Alignment explanation
Indices: 838701--838728 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
838691 TACAAAAGAT
838701 CAATGTATCGATA
1 CAATGTATCGATA
838714 CAATGTATCGATA
1 CAATGTATCGATA
838727 CA
1 CA
838729 TTTAAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:838808 original size:19 final size:18
Alignment explanation
Indices: 838780--838862 Score: 86
Period size: 19 Copynumber: 4.7 Consensus size: 18
838770 TAGCGATACA
838780 TTGTATCGATACAACACT
1 TTGTATCGATACAACACT
* *
838798 TATGTACCGATACAACAGT
1 T-TGTATCGATACAACACT
838817 GTTGTATCGAT---ACA--
1 -TTGTATCGATACAACACT
838831 TTGTATCGATACAACACT
1 TTGTATCGATACAACACT
838849 TATGTATCGATACA
1 T-TGTATCGATACA
838863 GTTACTGTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
13 10 0.19
16 6 0.11
18 2 0.04
19 35 0.65
20 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (18 bp):
TTGTATCGATACAACACT
Found at i:838836 original size:13 final size:13
Alignment explanation
Indices: 838818--838843 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
838808 TACAACAGTG
838818 TTGTATCGATACA
1 TTGTATCGATACA
838831 TTGTATCGATACA
1 TTGTATCGATACA
838844 ACACTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:838841 original size:32 final size:32
Alignment explanation
Indices: 838800--838862 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
838790 ACAACACTTA
*
838800 TGTACCGATACAACAGTGT-TGTATCGATACAT
1 TGTACCGATACAACACT-TATGTATCGATACAT
*
838832 TGTATCGATACAACACTTATGTATCGATACA
1 TGTACCGATACAACACTTATGTATCGATACA
838863 GTTACTGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (32 bp):
TGTACCGATACAACACTTATGTATCGATACAT
Found at i:839668 original size:49 final size:49
Alignment explanation
Indices: 839475--839855 Score: 284
Period size: 49 Copynumber: 8.1 Consensus size: 49
839465 ATATGCGGCT
* * ** * *
839475 AGCGATATTGGGCTTGAAGATGCGAAGAATGATAATGTGCTGATTCATGGCC
1 AGCGATATTGGACTTAAAGAT--GAAG-ATGCCAATATGCTGATTCAAGGCC
* * * * * **
839527 AGCGACATTAGACTTGAAGAAG-A-ATGCCAATGTGCTGAGACAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
* * * * * *
839574 AGCAACATTGGGCTTAGGAATGTTAAAGATGTCAATATGCTGATTCAAGGCC
1 AGCGATATTGGACTTA--AA-GATGAAGATGCCAATATGCTGATTCAAGGCC
* * * *
839626 AACGATATCGGACTTAAAGATGAAGATACCAATGTGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
* *
839675 GGCGACATTGGACTT-AA-A-G--G-TGCCAATATGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
*
839718 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
* * *
839767 AGCAACATT-G-CTTTAA-A-G--G-TGCCAATATGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
*
839809 AGCGATATTGG--TTTAA-A-G--G-TGCCAATATGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
839851 AGCGA
1 AGCGA
839856 ATTCGTCTCC
Statistics
Matches: 272, Mismatches: 45, Indels: 34
0.77 0.13 0.10
Matches are distributed among these distances:
42 65 0.24
43 36 0.13
44 3 0.01
45 2 0.01
46 3 0.01
47 37 0.14
48 4 0.01
49 69 0.25
50 4 0.01
51 1 0.00
52 48 0.18
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (49 bp):
AGCGATATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
Found at i:839753 original size:92 final size:91
Alignment explanation
Indices: 839596--839819 Score: 360
Period size: 92 Copynumber: 2.5 Consensus size: 91
839586 CTTAGGAATG
* * * *
839596 TTAAAGATGTCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGATACCAATGT
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATACCAATGT
* *
839661 GCTGATTCAAGGCCGGCGACATTGGAC-
66 GCTGATTCAAGGCCAGCAACATT-G-CT
*
839688 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGT
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATACCAATGT
839753 GCTGATTCAAGGCCAGCAACATTGCT
66 GCTGATTCAAGGCCAGCAACATTGCT
839779 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGG
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGG
839820 TTTAAAGGTG
Statistics
Matches: 124, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
90 1 0.01
91 42 0.34
92 81 0.65
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (91 bp):
TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATACCAATGT
GCTGATTCAAGGCCAGCAACATTGCT
Found at i:839806 original size:21 final size:21
Alignment explanation
Indices: 839782--839848 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
839772 CATTGCTTTA
839782 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
* *
839803 AA-G-GCCAGCGATAT--TGGTTTA
1 AAGGTGCCA---ATATGCT-GATTC
839824 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
839845 AAGG
1 AAGG
839849 CCAGCGAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 16
0.63 0.07 0.30
Matches are distributed among these distances:
19 4 0.12
20 6 0.18
21 14 0.41
22 6 0.18
23 4 0.12
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (21 bp):
AAGGTGCCAATATGCTGATTC
Found at i:839854 original size:42 final size:42
Alignment explanation
Indices: 839744--839855 Score: 188
Period size: 42 Copynumber: 2.7 Consensus size: 42
839734 AAGATGAAGA
* *
839744 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGCTTTAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGCTTTAAAGG
* *
839786 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTTTAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGCTTTAAAGG
839828 TGCCAATATGCTGATTCAAGGCCAGCGA
1 TGCCAATATGCTGATTCAAGGCCAGCGA
839856 ATTCGTCTCC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.26
Consensus pattern (42 bp):
TGCCAATATGCTGATTCAAGGCCAGCGACATTGCTTTAAAGG
Found at i:841382 original size:2 final size:2
Alignment explanation
Indices: 841375--841409 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
841365 AATCAAGAAT
841375 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 T
841410 TCAATGAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:842671 original size:4 final size:4
Alignment explanation
Indices: 842662--842714 Score: 83
Period size: 4 Copynumber: 13.8 Consensus size: 4
842652 ATGTGGTGGA
*
842662 AAAG AAAG AAAG -AAG AAAG AAAA AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
842709 -AAG AAA
1 AAAG AAA
842715 AAAAATTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 6 0.13
4 39 0.87
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Done.