Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold124
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: 1034113
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 25 characters in sequence are not A, C, G, or T
File 5 of 7
Found at i:567264 original size:57 final size:57
Alignment explanation
Indices: 567150--567377 Score: 201
Period size: 57 Copynumber: 3.9 Consensus size: 57
567140 GCTTACAAAA
* * * * * *
567150 GAAAAA-GAGTGCCACGGAGTTGTCGACTTTGGAAAAGATGCCACCGACTTGTGGGCTT
1 GAAAAAGGA-TGCCACTGACTTGTGGGCTTT-GAAAAGTTGCCACTGACTTGTGGGCTT
* * *
567208 CGAAAAAGGGTGCCACTGATTTGTGGGCTTTG-AAGGTTGCCACTGACTTGTGGGCTTTT
1 -GAAAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGTTGCCACTGACTTGTGGGC--TT
** * *
567267 GAAAAAAAATGCCACTGACTTGTGGGCTTTGAAAAAGATGCCATTGACTTGTGGGCTT
1 GAAAAAGGATGCCACTGACTTGTGGGCTTTG-AAAAGTTGCCACTGACTTGTGGGCTT
** * * * *
567325 -TTAAAGGTTGCTACTAACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGG
1 GAAAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGT-TGCCACTGACTTGTGG
567378 ACTTTTGAAG
Statistics
Matches: 138, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
56 4 0.03
57 58 0.42
58 30 0.22
59 25 0.18
60 21 0.15
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (57 bp):
GAAAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGTTGCCACTGACTTGTGGGCTT
Found at i:567332 original size:88 final size:86
Alignment explanation
Indices: 567176--567382 Score: 272
Period size: 88 Copynumber: 2.4 Consensus size: 86
567166 GAGTTGTCGA
* * * * * * *
567176 CTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGAAAAAGGGTGCCACTGATTTGTGGGCTTTGA
1 CTTTGAAAAAAATGCCACTGACTTGTGGGCTTTGAAAAAGGATGCCACTGACTTGTGGGCTTTAA
*
567241 AGGTTGCCACTGACTTGTGGG
66 AGGTTGCCACTAACTTGTGGG
*
567262 CTTTTGAAAAAAAATGCCACTGACTTGTGGGCTTTGAAAAA-GATGCCATTGACTTGTGGGCTTT
1 C-TTTG-AAAAAAATGCCACTGACTTGTGGGCTTTGAAAAAGGATGCCACTGACTTGTGGGC-TT
*
567326 TAAAGGTTGCTACTAACTTGTGGG
63 TAAAGGTTGCCACTAACTTGTGGG
* *
567350 CTTTGAAAAATATGCCACTGACTTGTGGACTTT
1 CTTTGAAAAAAATGCCACTGACTTGTGGGCTTT
567383 TGAAGGGTGA
Statistics
Matches: 106, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
86 27 0.25
87 25 0.24
88 54 0.51
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (86 bp):
CTTTGAAAAAAATGCCACTGACTTGTGGGCTTTGAAAAAGGATGCCACTGACTTGTGGGCTTTAA
AGGTTGCCACTAACTTGTGGG
Found at i:567366 original size:117 final size:116
Alignment explanation
Indices: 567176--567386 Score: 280
Period size: 117 Copynumber: 1.8 Consensus size: 116
567166 GAGTTGTCGA
* * *
567176 CTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGAAAAAGGGTGCCACTGATTTGTGGGCTTTGA
1 CTTTGAAAAAGATGCCACCGACTTGTGGGCTTC-AAAAAGGGTGCCACTAACTTGTGGGCTTTGA
** *
567241 AGGTTGCCACTGACTTGTGGGCTTTTGAAAAAAAATGCCACTGACTTGTGGG
65 AAATTGCCACTGACTTGTGGACTTTTGAAAAAAAATGCCACTGACTTGTGGG
** ** * *
567293 CTTTGAAAAAGATGCCATTGACTTGTGGGCTT-TTAAAGGTTGCTACTAACTTGTGGGCTTTGAA
1 CTTTGAAAAAGATGCCACCGACTTGTGGGCTTCAAAAAGGGTGCCACTAACTTGTGGGCTTTG-A
567357 AAATATGCCACTGACTTGTGGACTTTTGAA
65 AAAT-TGCCACTGACTTGTGGACTTTTGAA
567387 GGGTGAGGAA
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
115 24 0.30
116 3 0.04
117 53 0.66
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (116 bp):
CTTTGAAAAAGATGCCACCGACTTGTGGGCTTCAAAAAGGGTGCCACTAACTTGTGGGCTTTGAA
AATTGCCACTGACTTGTGGACTTTTGAAAAAAAATGCCACTGACTTGTGGG
Found at i:568829 original size:1 final size:1
Alignment explanation
Indices: 568823--568920 Score: 79
Period size: 1 Copynumber: 98.0 Consensus size: 1
568813 TCCGAACCCC
* * * * * * * * *
568823 TTTTTTTTGTTTTTTTTTTGTTTGTTTTTGTTTGTTTTTTTTTGTTTTTGTTTTGTTTTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
568888 TTTTTTTTTTGTTTTGTTTTGTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
568921 GTGGAGGACG
Statistics
Matches: 71, Mismatches: 26, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (1 bp):
T
Found at i:568838 original size:10 final size:10
Alignment explanation
Indices: 568825--568918 Score: 116
Period size: 11 Copynumber: 8.9 Consensus size: 10
568815 CGAACCCCTT
*
568825 TTTTTTGTTTT
1 TTTTTT-TTTG
568836 TTTTTTGTTTG
1 TTTTTT-TTTG
*
568847 TTTTTGTTTG
1 TTTTTTTTTG
568857 TTTTTTTTTG
1 TTTTTTTTTG
568867 TTTTTGTTTTG
1 TTTTT-TTTTG
568878 TTTTTTTTTG
1 TTTTTTTTTG
568888 TTTTTTTTTTG
1 -TTTTTTTTTG
*
568899 TTTTGTTTTG
1 TTTTTTTTTG
568909 TTTGTTTTTT
1 TTT-TTTTTT
568919 TTGTGGAGGA
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
10 35 0.47
11 40 0.53
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:568852 original size:21 final size:20
Alignment explanation
Indices: 568826--568920 Score: 124
Period size: 21 Copynumber: 4.7 Consensus size: 20
568816 GAACCCCTTT
568826 TTTTTGTTTTTTTTTTGTTTG
1 TTTTTGTTTTTTTTTT-TTTG
*
568847 TTTTTGTTTGTTTTTTTTTG
1 TTTTTGTTTTTTTTTTTTTG
568867 TTTTTGTTTTGTTTTTTTTTG
1 TTTTTGTTTT-TTTTTTTTTG
568888 TTTTT-TTTTTGTTTTGTTTTG
1 TTTTTGTTTTT-TTTT-TTTTG
568909 --TTTGTTTTTTTT
1 TTTTTGTTTTTTTT
568921 GTGGAGGACG
Statistics
Matches: 68, Mismatches: 2, Indels: 10
0.85 0.03 0.12
Matches are distributed among these distances:
19 7 0.10
20 26 0.38
21 35 0.51
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (20 bp):
TTTTTGTTTTTTTTTTTTTG
Found at i:575992 original size:21 final size:21
Alignment explanation
Indices: 575968--576024 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
575958 AAAAAATTTA
575968 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
* *
575989 AATGTTTCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
576010 AATGTATCGATACAT
1 AATGTATCGATACAT
576025 CCTACAACTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.39
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:576104 original size:19 final size:19
Alignment explanation
Indices: 576080--576147 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
576070 AATTCAACAA
576080 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
576099 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
576114 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
576131 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
576148 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:576119 original size:13 final size:13
Alignment explanation
Indices: 576101--576125 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
576091 ACATAAGTTT
576101 TGTATCGATACAA
1 TGTATCGATACAA
576114 TGTATCGATACA
1 TGTATCGATACA
576126 TAAGTATTGT
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:576123 original size:32 final size:32
Alignment explanation
Indices: 576082--576144 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
576072 TTCAACAATT
*
576082 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
576114 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
576145 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:576205 original size:13 final size:13
Alignment explanation
Indices: 576187--576212 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
576177 CATTTTTCTG
576187 TGTATCGATACAT
1 TGTATCGATACAT
576200 TGTATCGATACAT
1 TGTATCGATACAT
576213 GGATCTTTGT
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):
TGTATCGATACAT
Found at i:576209 original size:33 final size:33
Alignment explanation
Indices: 576167--576233 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
576157 GCCAAGGAAA
***
576167 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
576200 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
576233 T
1 T
576234 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:578754 original size:28 final size:27
Alignment explanation
Indices: 578687--578759 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
578677 CTTCACAATC
* *
578687 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
578714 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
578742 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
578760 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:578804 original size:51 final size:51
Alignment explanation
Indices: 578742--578912 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
578732 TTATTTCTGA
* * *
578742 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
578793 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
578846 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
578898 GAGGATACTCCAACC
1 GGGGATACTCCAACC
578913 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:578905 original size:105 final size:105
Alignment explanation
Indices: 578573--578912 Score: 273
Period size: 105 Copynumber: 3.2 Consensus size: 105
578563 CTCAATTCTC
* * * * ** *
578573 CACAATCGAGGATATTCCAACTCCGATTTTACTTTCAAAACATTAATTT-T-CTATAATCGGGGA
1 CACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTCCTTTAATCGGGGA
*
578636 TACTCCAACTCCGATTTTATTTCCAAAAAAAACACCAATTTCTT
66 TACTCCAACTCCGATTTTATTTCC---AAAAATACCAATTT-TT
* * * ** * * * * * *
578680 CACAATCGGGGACACTCCAACCCC-G-TTAATCATCGGGGATACTCCAA---CCCCGTTATTTCT
1 CACAATCGAGGATACTCCAACCCCGGTTTTATTTTC---AAAACACCAATTTCTCCTTTA-ATC-
* * * * *
578740 GAGGGGATACTCCAACCCCGACTTTATTTTC-AAAATATCGATTTTT
61 --GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
* * *
578786 CATAATCGGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATCGGGGA
1 CACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTCCTTTAATCGGGGA
*
578851 TACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTT
66 TACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
578891 CACAATCGAGGATACTCCAACC
1 CACAATCGAGGATACTCCAACC
578913 TCGTTATTTC
Statistics
Matches: 174, Mismatches: 44, Indels: 32
0.70 0.18 0.13
Matches are distributed among these distances:
104 25 0.14
105 44 0.25
106 24 0.14
107 36 0.21
108 19 0.11
111 26 0.15
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (105 bp):
CACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTCCTTTAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
Found at i:578931 original size:28 final size:28
Alignment explanation
Indices: 578895--578976 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
578885 ATTTTTCACA
*
578895 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
578923 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
578951 --CGAAGGAACACTCCAACCTCGTTATT
1 ATCG--GGGATACTCCAACCTCGTTATT
578977 ATCTCCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 2 0.04
28 43 0.96
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:588380 original size:52 final size:51
Alignment explanation
Indices: 588302--588450 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 51
588292 CGAAATATGA
*
588302 AAATTTTCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
588354 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
* **
588406 AAATTTGCCTACATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
588451 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.95
53 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:588457 original size:13 final size:13
Alignment explanation
Indices: 588439--588463 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
588429 CAAAGATCAG
588439 TGTATCGATACAA
1 TGTATCGATACAA
588452 TGTATCGATACA
1 TGTATCGATACA
588464 TTTAAGTGAT
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:588543 original size:13 final size:13
Alignment explanation
Indices: 588525--588549 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
588515 ACAAAAAAAA
588525 TGTATCGATACAT
1 TGTATCGATACAT
588538 TGTATCGATACA
1 TGTATCGATACA
588550 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:590289 original size:20 final size:20
Alignment explanation
Indices: 590264--590341 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 20
590254 AATGTCCAAA
590264 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATGTTTCT
* *
590284 ATGTATCGATACATCTGGAAATTCA
1 ATGTATCGATACA--T-G--TTTCT
*
590309 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATGTTTCT
*
590329 TTGTATCGATACA
1 ATGTATCGATACA
590342 GGGTGATTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 28 0.60
22 1 0.02
23 2 0.04
25 16 0.34
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATGTTTCT
Found at i:590505 original size:20 final size:20
Alignment explanation
Indices: 590462--590507 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
590452 AAATCTTTTG
590462 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
590483 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
590503 CAAAA
1 CAAAA
590508 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:594788 original size:97 final size:97
Alignment explanation
Indices: 594648--594840 Score: 264
Period size: 97 Copynumber: 2.0 Consensus size: 97
594638 TCTCTCAGAG
* *
594648 GAATGGGGTTGGAGTATCCCCAACGATGACAATTTGGGTGAAAATAAGATTTAAATCTT-AACAT
1 GAATGGGGTTGGAGTATCCCCAACGATGACAATTTAGGCGAAAATAAGATTTAAATCTTGAACA-
* *
594712 GTTTAAAAAAAGGGTT-GGAGTATCCCCTTGAAA
65 GTTTAAAAAAAGAGTTAGG-GTATCCCCGTGAAA
* * * * *
594745 GAATGGGGTTGTAGTATCCTCGATGATGACAATTTAGGCGAAAATAAGATTTAAATCTTGACCAG
1 GAATGGGGTTGGAGTATCCCCAACGATGACAATTTAGGCGAAAATAAGATTTAAATCTTGAACAG
*
594810 TTTAAAAATAGAGTTAGGGTATCCCCGTGAA
66 TTTAAAAAAAGAGTTAGGGTATCCCCGTGAA
594841 TAAAACTTTG
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
97 79 0.94
98 5 0.06
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.28
Consensus pattern (97 bp):
GAATGGGGTTGGAGTATCCCCAACGATGACAATTTAGGCGAAAATAAGATTTAAATCTTGAACAG
TTTAAAAAAAGAGTTAGGGTATCCCCGTGAAA
Found at i:595888 original size:52 final size:52
Alignment explanation
Indices: 595821--596048 Score: 174
Period size: 52 Copynumber: 4.4 Consensus size: 52
595811 GGTAAGGCTA
* * * *
595821 CCAATATGCTTATTCAAGGTCAACGATATCGGACTTAAAGATAATAAAGGTG
1 CCAATATACTGATTCAAGGCCAACGATATCAGACTTAAAGATAATAAAGGTG
* * * * * * *
595873 CCAATATACTGATTCATGGCTAGCGATATCAGACTTTAAGATCATAAGGGCTA
1 CCAATATACTGATTCAAGGCCAACGATATCAGACTTAAAGATAATAAAGG-TG
* * ** * * * *
595926 CTAATCTACTGATTCAAGGCCAGTGACATTAGACTTAAAGATGA-CAAGAGTG
1 CCAATATACTGATTCAAGGCCAACGATATCAGACTTAAAGATAATAAAG-GTG
* * * * * *
595978 CCAATATATTGATTTAAAGCCAACAATATTAGAATTAAAGATAATAGAA--TG
1 CCAATATACTGATTCAAGGCCAACGATATCAGACTTAAAGATAATA-AAGGTG
*
596029 GCAATATACTGATTCAAGGC
1 CCAATATACTGATTCAAGGC
596049 TAGTGACATT
Statistics
Matches: 133, Mismatches: 39, Indels: 9
0.73 0.22 0.05
Matches are distributed among these distances:
51 18 0.14
52 76 0.57
53 37 0.28
54 2 0.02
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (52 bp):
CCAATATACTGATTCAAGGCCAACGATATCAGACTTAAAGATAATAAAGGTG
Found at i:596312 original size:31 final size:32
Alignment explanation
Indices: 596252--596588 Score: 287
Period size: 31 Copynumber: 10.6 Consensus size: 32
596242 GATGCCAACA
* * * *
596252 ACTTGTTTGAGCTTTTGAGAAAGGTTGCCACTA
1 ACTTGTGTGGGCTTTTGA-AAGGGTTGCCACTG
* * *
596285 ACTTGTATGGG-TTTTGGAAGGGTTGCCATTG
1 ACTTGTGTGGGCTTTTGAAAGGGTTGCCACTG
*
596316 ACTTGTGTGGGCTTTTGAAAGGGGTTGCCACCG
1 ACTTGTGTGGGCTTTTGAAA-GGGTTGCCACTG
*
596349 ACTTGTGTGGG-TTTTGAAAGGGTTACCA-TCG
1 ACTTGTGTGGGCTTTTGAAAGGGTTGCCACT-G
* *
596380 ACTTGTGTGGGCTTTTAAAAGGGTTGCCATTG
1 ACTTGTGTGGGCTTTTGAAAGGGTTGCCACTG
* * *
596412 AGTTATGTGGGCTTTTGAAAGGGTTGCCACCG
1 ACTTGTGTGGGCTTTTGAAAGGGTTGCCACTG
* * *
596444 ACTTATATGGGCTTTTGAAA-GGTTGCCATTG
1 ACTTGTGTGGGCTTTTGAAAGGGTTGCCACTG
** * **
596475 ACTTGCATGAGCTTTTGAAAAGGGTTGCCACCA
1 ACTTGTGTGGGCTTTTG-AAAGGGTTGCCACTG
* * * * *
596508 ATTTATGTGGGCTTTTG-AAGTGTTACCAAC-A
1 ACTTGTGTGGGCTTTTGAAAGGGTTGCC-ACTG
*
596539 ACTTGTGTGGGC-TTTAAAAGGGTTGCCA-TCG
1 ACTTGTGTGGGCTTTTGAAAGGGTTGCCACT-G
* *
596570 ACTTATATGGGC-TTTGAAA
1 ACTTGTGTGGGCTTTTGAAA
596589 ATGGGTGCCA
Statistics
Matches: 248, Mismatches: 45, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
30 4 0.02
31 107 0.43
32 86 0.35
33 51 0.21
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (32 bp):
ACTTGTGTGGGCTTTTGAAAGGGTTGCCACTG
Found at i:596330 original size:64 final size:62
Alignment explanation
Indices: 596252--596598 Score: 275
Period size: 64 Copynumber: 5.5 Consensus size: 62
596242 GATGCCAACA
* * * * *
596252 ACTTGTTTGAGCTTTTGAGAAAGGTTGCCACTAACTTGTATGGGTTTTGGAAGGGTTGCCATTG
1 ACTTGTGTGGGCTTTT-A-AAAGGTTGCCACTGACTTGTATGGGTTTTGAAAGGGTTGCCATCG
* * * *
596316 ACTTGTGTGGGCTTTTGAAAGGGGTTGCCACCGACTTGTGTGGGTTTTGAAAGGGTTACCATCG
1 ACTTGTGTGGGCTTTT-AAA-AGGTTGCCACTGACTTGTATGGGTTTTGAAAGGGTTGCCATCG
* * * * *
596380 ACTTGTGTGGGCTTTTAAAAGGGTTGCCATTGAGTTATGTGGGCTTTTGAAAGGGTTGCCACCG
1 ACTTGTGTGGGCTTTTAAAA-GGTTGCCACTGACTTGTATGGG-TTTTGAAAGGGTTGCCATCG
* * * * * * * *
596444 ACTTATATGGGCTTTTGAAAGGTTGCCATTGACTTGCATGAGCTTTTGAAAAGGGTTGCCACCA
1 ACTTGTGTGGGCTTTTAAAAGGTTGCCACTGACTTGTATG-GGTTTTG-AAAGGGTTGCCATCG
* * * * * * * *
596508 ATTTATGTGGGCTTTT-GAAGTGTTACCAAC-AACTTGTGTGGGCTTTAAAAGGGTTGCCATCG
1 ACTTGTGTGGGCTTTTAAAAG-GTTGCC-ACTGACTTGTATGGGTTTTGAAAGGGTTGCCATCG
* * * *
596570 ACTTATATGGGCTTTGAAAATGGGTGCCA
1 ACTTGTGTGGGCTTTTAAAA-GGTTGCCA
596599 TGGAGTTATG
Statistics
Matches: 230, Mismatches: 44, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
62 27 0.12
63 57 0.25
64 145 0.63
65 1 0.00
ACGTcount: A:0.21, C:0.15, G:0.30, T:0.34
Consensus pattern (62 bp):
ACTTGTGTGGGCTTTTAAAAGGTTGCCACTGACTTGTATGGGTTTTGAAAGGGTTGCCATCG
Found at i:596573 original size:95 final size:96
Alignment explanation
Indices: 596285--596598 Score: 336
Period size: 95 Copynumber: 3.3 Consensus size: 96
596275 GTTGCCACTA
* *** * *
596285 ACTTGTATGGG-TTTTG-GAAGGGTTGCCATTGACTTGTGTGGGCTTTTGAAAGGGGTTGCCACC
1 ACTTGTATGGGCTTTTGAAAAGGGTTGCCACCAAGTTATGTGGGCTTTTGAAA-GGGTTGCCACC
* *
596348 GACTTGTGTGGGTTTTGAAAGGGTTACCATCG
65 GACTTGTGTGGGCTTTGAAAGGGTTGCCATCG
* ***
596380 ACTTGTGTGGGCTTTT-AAAAGGGTTGCCATTGAGTTATGTGGGCTTTTGAAAGGGTTGCCACCG
1 ACTTGTATGGGCTTTTGAAAAGGGTTGCCACCAAGTTATGTGGGCTTTTGAAAGGGTTGCCACCG
* * *
596444 ACTTATATGGGCTTTTGAAA-GGTTGCCATTG
66 ACTTGTGTGGGC-TTTGAAAGGGTTGCCATCG
* * * * * * *
596475 ACTTGCATGAGCTTTTGAAAAGGGTTGCCACCAATTTATGTGGGCTTTTG-AAGTGTTACCAACA
1 ACTTGTATGGGCTTTTGAAAAGGGTTGCCACCAAGTTATGTGGGCTTTTGAAAGGGTTGCCACCG
*
596539 ACTTGTGTGGGCTTTAAAAGGGTTGCCATCG
66 ACTTGTGTGGGCTTTGAAAGGGTTGCCATCG
*
596570 ACTTATATGGGC-TTTGAAAATGGG-TGCCA
1 ACTTGTATGGGCTTTTGAAAA-GGGTTGCCA
596599 TGGAGTTATG
Statistics
Matches: 186, Mismatches: 27, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
94 19 0.10
95 95 0.51
96 72 0.39
ACGTcount: A:0.21, C:0.15, G:0.30, T:0.34
Consensus pattern (96 bp):
ACTTGTATGGGCTTTTGAAAAGGGTTGCCACCAAGTTATGTGGGCTTTTGAAAGGGTTGCCACCG
ACTTGTGTGGGCTTTGAAAGGGTTGCCATCG
Found at i:596615 original size:30 final size:29
Alignment explanation
Indices: 596581--597396 Score: 624
Period size: 29 Copynumber: 27.9 Consensus size: 29
596571 CTTATATGGG
* *
596581 CTTTGAAAATGGGTGCCATGGAGTTATGGA
1 CTTTGAAAA-GGGTGCCACGGAGTTGTGGA
*
596611 CTTTGAAAAGGGTGCCACGCG-GTTATGGA
1 CTTTGAAAAGGGTGCCACG-GAGTTGTGGA
** * ** **
596640 CTTTGCGAAGGGTGCTACTTAGTCATGGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
* * ** * **
596669 CTTTGACAAGGGGTCCCATAGAATCCTGGA
1 CTTTGA-AAAGGGTGCCACGGAGTTGTGGA
* * * *
596699 TTTTGAAAAGGGTGCCACGAAGGTGTGAA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
**
596728 CTTTGAAAAGGGGTGCCACGGAGTCATGGA
1 CTTTGAAAA-GGGTGCCACGGAGTTGTGGA
* *
596758 CTTTGAAAAGAGTGCCACGAAGTTGTGGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
* * *
596787 CTTTGAAAAGGGTGCCATGAAGTCGTGGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
* *
596816 CTTTGAAAAGGGTGCCACGGAATTATGGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
* *
596845 CTTT-AAAAAGGTGCCACGGAGTTGTAGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
*
596873 CTTT-AAGAAGGGTGCCACGGAGTTATGGA
1 CTTTGAA-AAGGGTGCCACGGAGTTGTGGA
** * * *
596902 CTTT-AAACAAAGTACCACGGAGCTATGGA
1 CTTTGAAA-AGGGTGCCACGGAGTTGTGGA
* * *
596931 CTTTAAAAAAAGAGTGCCACGAAGTTGTGGA
1 CTTT--GAAAAGGGTGCCACGGAGTTGTGGA
* ** *
596962 CTTTAAAAATAGTGCCACAGAGTTGTGGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
* *
596991 CTTTGAAAAATGGGTGCTAAGGAGTTGTGGA
1 CTTTG-AAAA-GGGTGCCACGGAGTTGTGGA
* * *
597022 CTTTGAGAAAGGATGCCATGGAGTTATGGA
1 CTTTGA-AAAGGGTGCCACGGAGTTGTGGA
* *
597052 CTTTGAGAAGGGGTGCCACAGAGTTGTGGA
1 CTTTGA-AAAGGGTGCCACGGAGTTGTGGA
* * *
597082 GTTTAAAAAAGGTGCCACGGAGTTGTGGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
* * * *
597111 CATTAGAAAATGGGTGTCACAGAGTTATGGA
1 C-TTTGAAAA-GGGTGCCACGGAGTTGTGGA
* * * *
597142 CTTTGAAAAAGGTTGCCATGGAATTGTTGA
1 CTTTG-AAAAGGGTGCCACGGAGTTGTGGA
* *
597172 CTTTGAAAAAGGTGCCACAGAGTTGTGGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
* * * *
597201 CTTTGAAAAAGTTGCTACGGAGTTGTGGG
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
* * *
597230 CTTTGAAAAGGTTTCCACAGAGTTGTGGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
* *
597259 CTTT-AAAAGGGTGTCACGAAGTTGTGGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
** * *
597287 CTTTGAAAAGGGTGCCACAAAGTTATAGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
* *
597316 CTTT-AAAAGGCTGCCAC--AG-AGTGGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
* * ** * *
597341 CTTTGAAAAGGATGTCACTAAGTCGTAGA
1 CTTTGAAAAGGGTGCCACGGAGTTGTGGA
* * * *
597370 CTTTAAAAAAGGTGCAATGGAGTTGTG
1 CTTTGAAAAGGGTGCCACGGAGTTGTG
597397 TAGTTTGAGG
Statistics
Matches: 624, Mismatches: 142, Indels: 41
0.77 0.18 0.05
Matches are distributed among these distances:
25 7 0.01
26 13 0.02
28 64 0.10
29 343 0.55
30 130 0.21
31 64 0.10
32 3 0.00
ACGTcount: A:0.30, C:0.13, G:0.31, T:0.26
Consensus pattern (29 bp):
CTTTGAAAAGGGTGCCACGGAGTTGTGGA
Found at i:596831 original size:58 final size:58
Alignment explanation
Indices: 596581--597396 Score: 607
Period size: 59 Copynumber: 14.0 Consensus size: 58
596571 CTTATATGGG
* * * *
596581 CTTTGAAAATGGGTGCCATGGAGTTATGGACTTTGAAAAGGGTGCCACGCG-GTTATGGA
1 CTTTGAAAA-GGGTGCCACGAAGTTGTGGACTTTGAAAAGGGTGCCACG-GAGTTGTGGA
** * ** ** * * ** * **
596640 CTTTGCGAAGGGTGCTACTTAGTCATGGACTTTGACAAGGGGTCCCATAGAATCCTGGA
1 CTTTGAAAAGGGTGCCACGAAGTTGTGGACTTTGA-AAAGGGTGCCACGGAGTTGTGGA
* * * **
596699 TTTTGAAAAGGGTGCCACGAAGGTGTGAACTTTGAAAAGGGGTGCCACGGAGTCATGGA
1 CTTTGAAAAGGGTGCCACGAAGTTGTGGACTTTGAAAA-GGGTGCCACGGAGTTGTGGA
* * * *
596758 CTTTGAAAAGAGTGCCACGAAGTTGTGGACTTTGAAAAGGGTGCCATGAAGTCGTGGA
1 CTTTGAAAAGGGTGCCACGAAGTTGTGGACTTTGAAAAGGGTGCCACGGAGTTGTGGA
* * *
596816 CTTTGAAAAGGGTGCCACGGAA-TTATGGACTTT-AAAAAGGTGCCACGGAGTTGTAGA
1 CTTTGAAAAGGGTGCCAC-GAAGTTGTGGACTTTGAAAAGGGTGCCACGGAGTTGTGGA
* * ** * * *
596873 CTTT-AAGAAGGGTGCCACGGAGTTATGGACTTT-AAACAAAGTACCACGGAGCTATGGA
1 CTTTGAA-AAGGGTGCCACGAAGTTGTGGACTTTGAAA-AGGGTGCCACGGAGTTGTGGA
* * * ** *
596931 CTTTAAAAAAAGAGTGCCACGAAGTTGTGGACTTTAAAAATAGTGCCACAGAGTTGTGGA
1 CTTT--GAAAAGGGTGCCACGAAGTTGTGGACTTTGAAAAGGGTGCCACGGAGTTGTGGA
* * * * * *
596991 CTTTGAAAAATGGGTGCTAAGGAGTTGTGGACTTTGAGAAAGGATGCCATGGAGTTATGGA
1 CTTTG-AAAA-GGGTGCCACGAAGTTGTGGACTTTGA-AAAGGGTGCCACGGAGTTGTGGA
* * * *
597052 CTTTGAGAAGGGGTGCCAC-AGAGTTGTGGAGTTTAAAAAAGGTGCCACGGAGTTGTGGA
1 CTTTGA-AAAGGGTGCCACGA-AGTTGTGGACTTTGAAAAGGGTGCCACGGAGTTGTGGA
* * * * * * *
597111 CATTAGAAAATGGGTGTCAC-AGAGTTATGGACTTTGAAAAAGGTTGCCATGGAATTGTTGA
1 C-TTTGAAAA-GGGTGCCACGA-AGTTGTGGACTTTG-AAAAGGGTGCCACGGAGTTGTGGA
* * * * *
597172 CTTTGAAAAAGGTGCCAC-AGAGTTGTGGACTTTGAAAAAGTTGCTACGGAGTTGTGGG
1 CTTTGAAAAGGGTGCCACGA-AGTTGTGGACTTTGAAAAGGGTGCCACGGAGTTGTGGA
* * * *
597230 CTTTGAAAAGGTTTCCAC-AGAGTTGTGGACTTT-AAAAGGGTGTCACGAAGTTGTGGA
1 CTTTGAAAAGGGTGCCACGA-AGTTGTGGACTTTGAAAAGGGTGCCACGGAGTTGTGGA
* * * * *
597287 CTTTGAAAAGGGTGCCACAAAGTTATAGACTTT-AAAAGGCTGCCAC--AG-AGTGGA
1 CTTTGAAAAGGGTGCCACGAAGTTGTGGACTTTGAAAAGGGTGCCACGGAGTTGTGGA
* * * * * * * * *
597341 CTTTGAAAAGGATGTCACTAAGTCGTAGACTTTAAAAAAGGTGCAATGGAGTTGTG
1 CTTTGAAAAGGGTGCCACGAAGTTGTGGACTTTGAAAAGGGTGCCACGGAGTTGTG
597397 TAGTTTGAGG
Statistics
Matches: 606, Mismatches: 127, Indels: 49
0.77 0.16 0.06
Matches are distributed among these distances:
54 33 0.05
55 11 0.02
56 4 0.01
57 106 0.17
58 140 0.23
59 146 0.24
60 117 0.19
61 49 0.08
ACGTcount: A:0.30, C:0.13, G:0.31, T:0.26
Consensus pattern (58 bp):
CTTTGAAAAGGGTGCCACGAAGTTGTGGACTTTGAAAAGGGTGCCACGGAGTTGTGGA
Found at i:602186 original size:33 final size:33
Alignment explanation
Indices: 602149--602215 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
602139 TTCAACGATT
602149 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
602182 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
602215 T
1 T
602216 TTAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:602187 original size:13 final size:13
Alignment explanation
Indices: 602169--602193 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
602159 CATAAAATGT
602169 TGTATCGATACAA
1 TGTATCGATACAA
602182 TGTATCGATACA
1 TGTATCGATACA
602194 TATTTTTTTG
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:602274 original size:13 final size:13
Alignment explanation
Indices: 602256--602280 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
602246 ATTACTCACA
602256 TGTATCGATACAT
1 TGTATCGATACAT
602269 TGTATCGATACA
1 TGTATCGATACA
602281 CTGATCTTTG
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:602345 original size:52 final size:52
Alignment explanation
Indices: 602289--602409 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
602279 CACTGATCTT
*
602289 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
602341 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
602393 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
602410 ATAAATTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:606555 original size:27 final size:28
Alignment explanation
Indices: 606506--606575 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
606496 ATAAAACCGT
* *
606506 GGTTAGAGTATCCCCTCGAAAATAA-AA
1 GGTTGGAGTATCCCCTAGAAAATAACAA
**
606533 GGTTGGAGTATCCCCTTAG-AAATAACGG
1 GGTTGGAGTATCCCC-TAGAAAATAACAA
606561 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
606576 GATTGTGGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 20 0.54
28 17 0.46
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (28 bp):
GGTTGGAGTATCCCCTAGAAAATAACAA
Found at i:606573 original size:106 final size:107
Alignment explanation
Indices: 606452--606654 Score: 239
Period size: 106 Copynumber: 1.9 Consensus size: 107
606442 GAAATAAAAT
* * * **
606452 CGGGGTTGAAGTATCCCTAATTGTGAAAAATCAGAATTTTGGAAATAAAACCGTGGTT-AGAGTA
1 CGGGGTTGAAGTATCCCCAATTGTGAAAAATCAGAATTGTGGAAACAAAACCAAGGTTGA-AGTA
606516 TCCCCTCGAAAATAA-AAGGTTGGAGTATCCCCTTAGAAATAA
65 TCCCCTCGAAAATAACAAGGTTGGAGTATCCCCTTAGAAATAA
* * ** ** ** * *
606558 CGGGGTTGGAGTATCCCCGATTGTGGGAAATTGGTGTTGTGGAGACAAAATCAAGGTTGAAGTAT
1 CGGGGTTGAAGTATCCCCAATTGTGAAAAATCAGAATTGTGGAAACAAAACCAAGGTTGAAGTAT
*
606623 CCCCTCGAAAATAACGAGGTTGGAGTATCCCC
66 CCCCTCGAAAATAACAAGGTTGGAGTATCCCC
606655 GATTGTGAAA
Statistics
Matches: 79, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
106 62 0.78
107 17 0.22
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (107 bp):
CGGGGTTGAAGTATCCCCAATTGTGAAAAATCAGAATTGTGGAAACAAAACCAAGGTTGAAGTAT
CCCCTCGAAAATAACAAGGTTGGAGTATCCCCTTAGAAATAA
Found at i:608096 original size:120 final size:120
Alignment explanation
Indices: 607882--608124 Score: 468
Period size: 120 Copynumber: 2.0 Consensus size: 120
607872 CAACAAACAC
607882 AACATATGTCATGGAGGACAAAAATGCATGAACCAAGATGACATTTTTATGGGAAGAAAAGAAAA
1 AACATATGTCATGGAGGACAAAAATGCATGAACCAAGATGACATTTTTATGGGAAGAAAAGAAAA
*
607947 GAAAGAAAAAATGCATGGTGATGGCAAGTTATCATTAACATAAACATGTTAAAAA
66 GAAAGAAAAAATGCATGGTGATGGAAAGTTATCATTAACATAAACATGTTAAAAA
608002 AACATATGTCATGGAGGACAAAAATGCATGAACCAAGATGACATTTTTATGGGAAGAAAAGAAAA
1 AACATATGTCATGGAGGACAAAAATGCATGAACCAAGATGACATTTTTATGGGAAGAAAAGAAAA
*
608067 GAAAGAACAAATGCATGGTGATGGAAAGTTATCATTAACATAAACATGTTAAAAA
66 GAAAGAAAAAATGCATGGTGATGGAAAGTTATCATTAACATAAACATGTTAAAAA
608122 AAC
1 AAC
608125 TTGTTTATTT
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 121 1.00
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.21
Consensus pattern (120 bp):
AACATATGTCATGGAGGACAAAAATGCATGAACCAAGATGACATTTTTATGGGAAGAAAAGAAAA
GAAAGAAAAAATGCATGGTGATGGAAAGTTATCATTAACATAAACATGTTAAAAA
Found at i:610237 original size:23 final size:22
Alignment explanation
Indices: 610194--610242 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
610184 TAAAACAAAG
**
610194 AAAATAACAGACAAATTTACAC
1 AAAATAACAGACAAAAATACAC
* *
610216 AAAATAAACATACAAAAATACAT
1 AAAAT-AACAGACAAAAATACAC
610239 AAAA
1 AAAA
610243 AAGAGGGACG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.67, C:0.14, G:0.02, T:0.16
Consensus pattern (22 bp):
AAAATAACAGACAAAAATACAC
Found at i:610572 original size:51 final size:51
Alignment explanation
Indices: 610510--610627 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 51
610500 AGAAATAACA
* * * *
610510 GGGTTGAAGTATCCCC-ATTGGTGGAAAATTGATGTTTTAGAAATAAAA-TCG
1 GGGTTGGAGTATCCCCGATT-GTGAAAAATCGATATTTTAGAAATAAAACT-G
* *
610561 GGGTTGGAGTATCCCCGATTGTGAAAAATCGGTATTTTGGAAATAAAACTG
1 GGGTTGGAGTATCCCCGATTGTGAAAAATCGATATTTTAGAAATAAAACTG
610612 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
610628 TCAAAAATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
51 55 0.93
52 4 0.07
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.30
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCGATTGTGAAAAATCGATATTTTAGAAATAAAACTG
Found at i:610683 original size:28 final size:28
Alignment explanation
Indices: 610611--610683 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
610601 AAATAAAACT
*
610611 GGGGTTGGAGTATCCCCTCAAAAATAAC
1 GGGGTTGGAGTATCCCTTCAAAAATAAC
* *
610639 GGGGTTGGAGTATCCCTTTAGAAATAAC
1 GGGGTTGGAGTATCCCTTCAAAAATAAC
*
610667 GGGGTTAGAGTATCCCT
1 GGGGTTGGAGTATCCCT
610684 GATTGTGGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCTTCAAAAATAAC
Found at i:610696 original size:107 final size:109
Alignment explanation
Indices: 610545--610761 Score: 294
Period size: 107 Copynumber: 2.0 Consensus size: 109
610535 AAATTGATGT
* * *
610545 TTTAGAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGAAAAATCGGTATTTTGGAAATAAAAC
1 TTTAGAAAT-AAATCGGGGTTAGAGTATCCCCGATTGTGAAAAATCGGTATTGTGGAAAGAAAAC
* * *
610610 TGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCC
65 TGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTCGAAGTATCCC
* * * * *
610655 TTTAGAAAT-AA-CGGGGTTAGAGTATCCCTGATTGTGGAAAATTGTTGTTGTGGAAAGAAAACT
1 TTTAGAAATAAATCGGGGTTAGAGTATCCCCGATTGTGAAAAATCGGTATTGTGGAAAGAAAACT
**
610718 GGGGTTGGAGTATCCCCTTGAAAATAACAGGGTCGAAGTATCCC
66 GGGGTTGGAGTATCCCCTCAAAAATAACAGGGTCGAAGTATCCC
610762 CGATTGTGGA
Statistics
Matches: 94, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
107 83 0.88
108 2 0.02
110 9 0.10
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (109 bp):
TTTAGAAATAAATCGGGGTTAGAGTATCCCCGATTGTGAAAAATCGGTATTGTGGAAAGAAAACT
GGGGTTGGAGTATCCCCTCAAAAATAACAGGGTCGAAGTATCCC
Found at i:618188 original size:13 final size:13
Alignment explanation
Indices: 618170--618195 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
618160 ACAATTTTTG
618170 TGTATCGATACAT
1 TGTATCGATACAT
618183 TGTATCGATACAT
1 TGTATCGATACAT
618196 ACTTTGGTGT
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):
TGTATCGATACAT
Found at i:618192 original size:32 final size:33
Alignment explanation
Indices: 618151--618214 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
618141 TACAAGCCAA
* *
618151 TGTATCGATACA-ATTTTTGTGTATCGATACAT
1 TGTATCGATACATACTTTGGTGTATCGATACAT
*
618183 TGTATCGATACATACTTTGGTGTATTGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
618215 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:618291 original size:20 final size:20
Alignment explanation
Indices: 618245--618318 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
618235 ATCCCAATGA
***
618245 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGAAT
618266 CATGTATCGATACATTGCAA-
1 CATGTATCGATACATTG-AAT
*
618286 CATGTATCGATACTTTGAAT
1 CATGTATCGATACATTGAAT
*
618306 TATGTATCGATAC
1 CATGTATCGATAC
618319 TTTTAAGGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 29 0.63
21 15 0.33
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:618916 original size:39 final size:39
Alignment explanation
Indices: 618841--618931 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 39
618831 TTTTCTTTCT
618841 CCCTTAATTAAAGTAATTTTAACAAATTCGTACATTCTCC
1 CCCTTAATTAAAGTAATTTTAACAAATTCG-ACATTCTCC
* *
618881 CCCTTAA-TAAGGTAATTTTAGCAAATTTACG-CATTCTCC
1 CCCTTAATTAAAGTAATTTTAACAAA-TT-CGACATTCTCC
* *
618920 CCTTTTATTAAA
1 CCCTTAATTAAA
618932 AAAATCTCCC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
39 29 0.67
40 12 0.28
41 2 0.05
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (39 bp):
CCCTTAATTAAAGTAATTTTAACAAATTCGACATTCTCC
Found at i:620311 original size:21 final size:20
Alignment explanation
Indices: 620282--620324 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
620272 GGCTAGTATG
*
620282 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
620303 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
620323 GG
1 GG
620325 TGGTGCTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.30, G:0.44, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:620783 original size:13 final size:13
Alignment explanation
Indices: 620765--620880 Score: 178
Period size: 13 Copynumber: 8.9 Consensus size: 13
620755 ATAATCCCCC
*
620765 TGTATCGATACAG
1 TGTATCGATACAA
620778 TGTATCGATACAA
1 TGTATCGATACAA
* *
620791 TGTATCAATACAG
1 TGTATCGATACAA
620804 TGTATCGATACAA
1 TGTATCGATACAA
*
620817 TGTATCGATACAG
1 TGTATCGATACAA
620830 TGTATCGATACAA
1 TGTATCGATACAA
* *
620843 TGTATAGATACAG
1 TGTATCGATACAA
620856 TGTATCGATACAA
1 TGTATCGATACAA
620869 TGTATCGATACA
1 TGTATCGATACA
620881 TTGAATTTCC
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 92 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:620794 original size:26 final size:26
Alignment explanation
Indices: 620765--620880 Score: 214
Period size: 26 Copynumber: 4.5 Consensus size: 26
620755 ATAATCCCCC
620765 TGTATCGATACAGTGTATCGATACAA
1 TGTATCGATACAGTGTATCGATACAA
*
620791 TGTATCAATACAGTGTATCGATACAA
1 TGTATCGATACAGTGTATCGATACAA
620817 TGTATCGATACAGTGTATCGATACAA
1 TGTATCGATACAGTGTATCGATACAA
*
620843 TGTATAGATACAGTGTATCGATACAA
1 TGTATCGATACAGTGTATCGATACAA
620869 TGTATCGATACA
1 TGTATCGATACA
620881 TTGAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 86 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (26 bp):
TGTATCGATACAGTGTATCGATACAA
Found at i:622953 original size:15 final size:15
Alignment explanation
Indices: 622933--622973 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
622923 GTTCATCGAT
622933 TTCATTTGGAGCTTC
1 TTCATTTGGAGCTTC
*
622948 TTCATTTTGAGCTTC
1 TTCATTTGGAGCTTC
*
622963 CTCAATTTGGA
1 TTC-ATTTGGA
622974 CATTTTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (15 bp):
TTCATTTGGAGCTTC
Found at i:624590 original size:13 final size:13
Alignment explanation
Indices: 624572--624597 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
624562 TACACCAAGT
624572 ATGTATCGATACA
1 ATGTATCGATACA
624585 ATGTATCGATACA
1 ATGTATCGATACA
624598 CCAAAAATTG
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:624595 original size:32 final size:33
Alignment explanation
Indices: 624554--624617 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
624544 TAGCCAAACT
**
624554 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
624586 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
624618 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:628102 original size:19 final size:19
Alignment explanation
Indices: 628078--628127 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
628068 TACAAGCCAA
628078 TGTATCGATACAATTTTTG
1 TGTATCGATACAATTTTTG
628097 TGTATCGATACAATTTTTG
1 TGTATCGATACAATTTTTG
628116 TGTATCGATACA
1 TGTATCGATACA
628128 TTGTATCGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (19 bp):
TGTATCGATACAATTTTTG
Found at i:628134 original size:13 final size:13
Alignment explanation
Indices: 628116--628141 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
628106 ACAATTTTTG
628116 TGTATCGATACAT
1 TGTATCGATACAT
628129 TGTATCGATACAT
1 TGTATCGATACAT
628142 ACTTTGGTGT
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):
TGTATCGATACAT
Found at i:628138 original size:32 final size:33
Alignment explanation
Indices: 628097--628160 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
628087 ACAATTTTTG
* *
628097 TGTATCGATACA-ATTTTTGTGTATCGATACAT
1 TGTATCGATACATACTTTGGTGTATCGATACAT
628129 TGTATCGATACATACTTTGGTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
628161 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:628613 original size:12 final size:12
Alignment explanation
Indices: 628596--628621 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
628586 CACAATTGTC
628596 CATGTATCGATA
1 CATGTATCGATA
628608 CATGTATCGATA
1 CATGTATCGATA
628620 CA
1 CA
628622 AAGCATAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (12 bp):
CATGTATCGATA
Found at i:636087 original size:18 final size:18
Alignment explanation
Indices: 636066--636100 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
636056 TCCAAGTCAC
636066 CATCATCATCATCATTAT
1 CATCATCATCATCATTAT
*
636084 CATCTTCATCATCATTA
1 CATCATCATCATCATTA
636101 ATGGTTGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (18 bp):
CATCATCATCATCATTAT
Found at i:637765 original size:20 final size:20
Alignment explanation
Indices: 637740--637794 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
637730 CTACCAGTTT
**
637740 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
637760 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
*
637779 CAAGTATCGATACAAT
1 CATGTATCGATACAAT
637795 GTCTCGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:638554 original size:34 final size:34
Alignment explanation
Indices: 638507--638575 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
638497 AGAATAACAA
*
638507 AAACTTACGTATTTCATTAGTCTTCTAATAGGGT
1 AAACTTACATATTTCATTAGTCTTCTAATAGGGT
638541 AAACTTACATATTTCATTAGTCTTCTAATAGGGT
1 AAACTTACATATTTCATTAGTCTTCTAATAGGGT
638575 A
1 A
638576 CATAAGAGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (34 bp):
AAACTTACATATTTCATTAGTCTTCTAATAGGGT
Found at i:640727 original size:25 final size:25
Alignment explanation
Indices: 640693--640743 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
640683 CAAATTCCCT
*
640693 AGGGGAAAAAACATCTAGCTTTTTA
1 AGGGGAAAAAACATCTAGCTCTTTA
640718 AGGGGAAAAAACATCTAGCTCTTTA
1 AGGGGAAAAAACATCTAGCTCTTTA
640743 A
1 A
640744 AAATAACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (25 bp):
AGGGGAAAAAACATCTAGCTCTTTA
Found at i:640821 original size:21 final size:19
Alignment explanation
Indices: 640788--640830 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
640778 CCTACTTCCA
640788 AGAAGATTTTCGA-CATTTT
1 AGAAGATTTTCGAGC-TTTT
640807 AGAAGATGCTTTCGAGCTTTT
1 AGAAGAT--TTTCGAGCTTTT
640828 AGA
1 AGA
640831 GTTCAGGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 7 0.33
21 13 0.62
22 1 0.05
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (19 bp):
AGAAGATTTTCGAGCTTTT
Found at i:641288 original size:46 final size:45
Alignment explanation
Indices: 641122--641403 Score: 227
Period size: 45 Copynumber: 6.3 Consensus size: 45
641112 ATACTTGATT
* * *
641122 AAACTCTTTTCATTC-TGATTTGATGTGATGGTTCTCACCTTGGTC
1 AAACTCTTTTCATTCTTG-TTTGACGTGATGGTTCTCGCCCTGGTC
* * * * * *
641167 AAACTCTTTCCATTATTGCTTGATGTGATGGTTCTTGCCCTAGTC
1 AAACTCTTTTCATTCTTGTTTGACGTGATGGTTCTCGCCCTGGTC
* * *
641212 AAAGT-TTTCTCATTCTCGTTTGACTTGATGGTTCTCGCCCTGGTC
1 AAACTCTTT-TCATTCTTGTTTGACGTGATGGTTCTCGCCCTGGTC
* *
641257 AAACATCTTTTCATTCTTGTTTGACATGATGGTTCTCGCCCTGGTT
1 AAAC-TCTTTTCATTCTTGTTTGACGTGATGGTTCTCGCCCTGGTC
* * * * *
641303 AAACTCTTTTTATTC--GACTTGACGTGATGGTTCTTGCCTTGATC
1 AAACTCTTTTCATTCTTG-TTTGACGTGATGGTTCTCGCCCTGGTC
* ** * * *
641347 AAACT-TCGTTCACTT-TCATTTGACGTGATAGTT-TAGCCCTAGTC
1 AAACTCT-TTTCA-TTCTTGTTTGACGTGATGGTTCTCGCCCTGGTC
*
641391 AAACCCTTTTCAT
1 AAACTCTTTTCAT
641404 CCTCAGTCAC
Statistics
Matches: 189, Mismatches: 38, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
43 3 0.02
44 47 0.25
45 96 0.51
46 40 0.21
47 3 0.02
ACGTcount: A:0.18, C:0.22, G:0.17, T:0.42
Consensus pattern (45 bp):
AAACTCTTTTCATTCTTGTTTGACGTGATGGTTCTCGCCCTGGTC
Found at i:642807 original size:21 final size:20
Alignment explanation
Indices: 642766--642822 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 20
642756 AGCAAGTGGA
*
642766 AGAAAAAAGAAAAAGAAGAG
1 AGAAAAAAGAAAAAAAAGAG
642786 A-AAATAAAGAAAGAAAAAGAG
1 AGAAA-AAAGAAA-AAAAAGAG
642807 AGAAAAAAGAAAAAAA
1 AGAAAAAAGAAAAAAA
642823 CTAAGCCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 3 0.09
20 12 0.36
21 15 0.45
22 3 0.09
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (20 bp):
AGAAAAAAGAAAAAAAAGAG
Found at i:642821 original size:9 final size:9
Alignment explanation
Indices: 642768--642822 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 9
642758 CAAGTGGAAG
642768 AAAAAAGAA
1 AAAAAAGAA
642777 AAAGAAGAGAA
1 AAA-AA-AGAA
*
642788 AATAAAGAA
1 AAAAAAGAA
642797 AGAAAAAGAGA
1 A-AAAAAGA-A
642808 GAAAAAAGAA
1 -AAAAAAGAA
642818 AAAAA
1 AAAAA
642823 CTAAGCCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 13 0.33
10 11 0.28
11 14 0.36
12 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:642892 original size:29 final size:28
Alignment explanation
Indices: 642843--642901 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
642833 CTCTTGCATC
*
642843 TTTGATTTCTTCTTAGGTAATCATCTTAT
1 TTTGATTTCTTCTTAGCTAAT-ATCTTAT
* *
642872 TTTGCATTTTTTCTT-GCTAATTTCTTAT
1 TTTG-ATTTCTTCTTAGCTAATATCTTAT
642900 TT
1 TT
642902 ATCTCTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 8 0.31
29 9 0.35
30 9 0.35
ACGTcount: A:0.17, C:0.14, G:0.08, T:0.61
Consensus pattern (28 bp):
TTTGATTTCTTCTTAGCTAATATCTTAT
Found at i:644119 original size:109 final size:109
Alignment explanation
Indices: 643983--644197 Score: 349
Period size: 109 Copynumber: 2.0 Consensus size: 109
643973 AAATGTATTA
* * * * * *
643983 ATACCTTTTTCATTTTGTCGATACATTCTGGGTTTTAACCTAAATGTGTTGATACATTATTCATT
1 ATACATTTTTCATTGTATCGATACATTCTGGGTTTTAACCCAAATGTATTGATACATTATTCACT
*
644048 GTATCGATACATTCTAGGTTTTTGACCCAAATGTATCGATATCG
66 GTATCAATACATTCTAGGTTTTTGACCCAAATGTATCGATATCG
644092 ATACATTTTTCATTGTATCGATACATTCTGGGTTTTAACCCAAATGTATTGATACATTATTCACT
1 ATACATTTTTCATTGTATCGATACATTCTGGGTTTTAACCCAAATGTATTGATACATTATTCACT
* *
644157 GTATCAATACATTCTGGGTTTTTTACCCAAATGTATCGATA
66 GTATCAATACATTCTAGGTTTTTGACCCAAATGTATCGATA
644198 CATTCTTCAA
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
109 97 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.42
Consensus pattern (109 bp):
ATACATTTTTCATTGTATCGATACATTCTGGGTTTTAACCCAAATGTATTGATACATTATTCACT
GTATCAATACATTCTAGGTTTTTGACCCAAATGTATCGATATCG
Found at i:644212 original size:52 final size:51
Alignment explanation
Indices: 643973--644217 Score: 256
Period size: 51 Copynumber: 4.6 Consensus size: 51
643963 TCTGGAAAGA
** * * * * *
643973 AAATGTATTAATACCTTTTTCATTTTGTCGATACATTCTGGGTTTTAACCT
1 AAATGTATCGATACATTATTCATTGTATCGATACATTCTGGGTTTTAACCC
* * * *
644024 AAATGTGTTGATACATTATTCATTGTATCGATACATTCTAGGTTTTTGACCC
1 AAATGTATCGATACATTATTCATTGTATCGATACATTCT-GGGTTTTAACCC
*
644076 AAATGTATCGATATCGATACATTTTTCATTGTATCGATACATTCTGGGTTTTAACCC
1 -AA---AT-G-TATCGATACATTATTCATTGTATCGATACATTCTGGGTTTTAACCC
* * * *
644133 AAATGTATTGATACATTATTCACTGTATCAATACATTCTGGGTTTTTTACCC
1 AAATGTATCGATACATTATTCATTGTATCGATACATTCTGGG-TTTTAACCC
* *
644185 AAATGTATCGATACATTCTTCAATGTATCGATA
1 AAATGTATCGATACATTATTCATTGTATCGATA
644218 TATACAGCCA
Statistics
Matches: 163, Mismatches: 23, Indels: 15
0.81 0.11 0.07
Matches are distributed among these distances:
51 66 0.40
52 47 0.29
53 4 0.02
56 4 0.02
57 11 0.07
58 31 0.19
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (51 bp):
AAATGTATCGATACATTATTCATTGTATCGATACATTCTGGGTTTTAACCC
Found at i:644302 original size:45 final size:45
Alignment explanation
Indices: 644238--644371 Score: 241
Period size: 45 Copynumber: 3.0 Consensus size: 45
644228 ATTTTGAACA
*
644238 TTTTGAGTTACTTTCCAACCTGCTCATTGCATATTCAAAAATTAG
1 TTTTGAGTCACTTTCCAACCTGCTCATTGCATATTCAAAAATTAG
644283 TTTTGAGTCACTTTCCAACCTGCTCATTGCATATTCAAAAATTAG
1 TTTTGAGTCACTTTCCAACCTGCTCATTGCATATTCAAAAATTAG
* *
644328 TTTTGAGTCACTTTCCAACCTTCTCATTGCACATTCAAAAATTA
1 TTTTGAGTCACTTTCCAACCTGCTCATTGCATATTCAAAAATTA
644372 ATTTCAACAC
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 86 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (45 bp):
TTTTGAGTCACTTTCCAACCTGCTCATTGCATATTCAAAAATTAG
Found at i:648331 original size:21 final size:20
Alignment explanation
Indices: 648309--648356 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
648299 ATTTTTAATA
*
648309 AAATAAAATAAAAATTAAAT
1 AAATAAAATAAAAATAAAAT
* *
648329 AAATAATAATCATAATAAAAT
1 AAATAA-AATAAAAATAAAAT
648350 AAATAAA
1 AAATAAA
648357 TATAGCCTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (20 bp):
AAATAAAATAAAAATAAAAT
Found at i:648333 original size:25 final size:25
Alignment explanation
Indices: 648305--648358 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
648295 AATGATTTTT
648305 AATAA-AAT-AAAATAAAAATTAAATA
1 AATAATAATCAAAAT-AAAA-TAAATA
*
648330 AATAATAATCATAATAAAATAAATA
1 AATAATAATCAAAATAAAATAAATA
648355 AATA
1 AATA
648359 TAGCCTTCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 15 0.58
26 7 0.27
27 4 0.15
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (25 bp):
AATAATAATCAAAATAAAATAAATA
Found at i:649260 original size:3 final size:3
Alignment explanation
Indices: 649254--649293 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
649244 TAATAAAAGT
649254 ATA ATA ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
649294 TAAGAAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:649378 original size:17 final size:17
Alignment explanation
Indices: 649356--649389 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
649346 TTAGGTGGCG
*
649356 TTTCATTCATGCTTTCA
1 TTTCATGCATGCTTTCA
*
649373 TTTCATGCATGTTTTCA
1 TTTCATGCATGCTTTCA
649390 CACATGAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.21, G:0.09, T:0.53
Consensus pattern (17 bp):
TTTCATGCATGCTTTCA
Found at i:651893 original size:16 final size:16
Alignment explanation
Indices: 651869--651902 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
651859 AAATCATCCA
*
651869 TCTAGGGTAAAAATCT
1 TCTAAGGTAAAAATCT
651885 TCTAAGGTAAAAATCT
1 TCTAAGGTAAAAATCT
651901 TC
1 TC
651903 ATTACTTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (16 bp):
TCTAAGGTAAAAATCT
Found at i:652211 original size:153 final size:154
Alignment explanation
Indices: 651952--652553 Score: 553
Period size: 153 Copynumber: 3.9 Consensus size: 154
651942 CTTCTACATC
* *
651952 AAAGATATCCCTTGGGGGCATTTTCATAATTTTTCTT-GAACCAAGTCTTAGGTCATCACCAGGT
1 AAAG-TATCCCTTAGGGGCATTTTCATAATTTTT-TTAGAACCAAGTCCTAGGTCATCACCAGGT
* *
652016 TTGCTTTTATG-CAAAAGGTGGACATTTAGGATAGGTTCATCCCATCT-AATC-CTTTTAAATCC
64 CTGCTTTTATGCCAAAA-GTAGACATTTAGGATAGGTTCATCCCATCTAAATCTCTTTTAAATCC
652078 TTTAGGGGTATCGGCCACTTTCAAGTTG
128 TTTAGGGGTATCGG-CACTTTCAAGTTG
* *
652106 AAAGTATCCCTTAGGGGCATTTTCATAATTTTTTTAGAACCAAGTCTTAGGTCATCACCGGGTCT
1 AAAGTATCCCTTAGGGGCATTTTCATAATTTTTTTAGAACCAAGTCCTAGGTCATCACCAGGTCT
* * *
652171 GCTTTTATGCCAAAAGTGGACATTTGGGATAGGTTCATCCCATCT-AATC-CTTTTAAATCTTTT
66 GCTTTTATGCCAAAAGTAGACATTTAGGATAGGTTCATCCCATCTAAATCTCTTTTAAATCCTTT
* * * * *
652234 ACGGGTATTGGGCATTTTCACG-TC
131 AGGGGTA-TCGGCACTTTCAAGTTG
* * * * ** *
652258 AAAGGTATCCCTTAGGGGTATTTTCGTAATTTTTTTAGAACCGAGTCCTAGATTGTCA-CTGAGT
1 AAA-GTATCCCTTAGGGGCATTTTCATAATTTTTTTAGAACCAAGTCCTAGGTCATCACCAG-GT
* * ** * * * * * *
652322 CTACTTTTATGCCGATGGTAGATATTTAGGATAGGTTCACCCCTTTTAAAATCTTTTTTAAGTCC
64 CTGCTTTTATGCCAAAAGTAGACATTTAGGATAGGTTCATCCCATCT-AAATCTCTTTTAAATCC
* * * *
652387 TTTAGGGGCATCAGGTACTTTTACA-TCG
128 TTTAGGGGTATC-GGCACTTTCA-AGTTG
* * * * * * **
652415 AAGGTATCCCCTAGAGACATTTT-AGTAA-TTTTTTATAACCGAA-TCCTAAGTTGTCACCAGGT
1 AAAGTATCCCTTAGGGGCATTTTCA-TAATTTTTTTAGAACC-AAGTCCTAGGTCATCACCAGGT
* * * * * * *
652477 CTGCTTTTATGCTAAAACTAGATATTTAGGATAGGTTCATCCCTTTTAAAATCTTTTTTAAGTCC
64 CTGCTTTTATGCCAAAAGTAGACATTTAGGATAGGTTCATCCCATCT-AAATCTCTTTTAAATCC
652542 TTTAGGGGTATC
128 TTTAGGGGTATC
652554 AGGTACTTCT
Statistics
Matches: 375, Mismatches: 59, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
152 8 0.02
153 210 0.56
154 12 0.03
155 98 0.26
156 45 0.12
157 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (154 bp):
AAAGTATCCCTTAGGGGCATTTTCATAATTTTTTTAGAACCAAGTCCTAGGTCATCACCAGGTCT
GCTTTTATGCCAAAAGTAGACATTTAGGATAGGTTCATCCCATCTAAATCTCTTTTAAATCCTTT
AGGGGTATCGGCACTTTCAAGTTG
Found at i:652485 original size:155 final size:156
Alignment explanation
Indices: 652259--652561 Score: 423
Period size: 155 Copynumber: 1.9 Consensus size: 156
652249 TTTCACGTCA
* * ** * * *
652259 AAGGTATCCCTTAGGGGTATTTTCGTAATTTTTTTAGAACCGAGTCCTAGATTGTCACTGAGTCT
1 AAGGTATCCCCTAGAGACATTTTAGTAATTTTTTTAGAACCGAATCCTAGATTGTCACAGAGTCT
* ***
652324 ACTTTTATGCCGATGGTAGATATTTAGGATAGGTTCACCCCTTTTAAAATCTTTTTTAAGTCCTT
66 ACTTTTATGCCAAAACTAGATATTTAGGATAGGTTCACCCCTTTTAAAATCTTTTTTAAGTCCTT
652389 TAGGGGCATCAGGTACTTTTACATCG
131 TAGGGGCATCAGGTACTTTTACATCG
*
652415 AAGGTATCCCCTAGAGACATTTTAGTAA-TTTTTTATAACCGAATCCTA-AGTTGTCACCAG-GT
1 AAGGTATCCCCTAGAGACATTTTAGTAATTTTTTTAGAACCGAATCCTAGA-TTGTCA-CAGAGT
* * *
652477 CTGCTTTTATGCTAAAACTAGATATTTAGGATAGGTTCATCCCTTTTAAAATCTTTTTTAAGTCC
64 CTACTTTTATGCCAAAACTAGATATTTAGGATAGGTTCACCCCTTTTAAAATCTTTTTTAAGTCC
*
652542 TTTAGGGGTATCAGGTACTT
129 TTTAGGGGCATCAGGTACTT
652562 CTACGTCAAA
Statistics
Matches: 129, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
154 1 0.01
155 103 0.80
156 25 0.19
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (156 bp):
AAGGTATCCCCTAGAGACATTTTAGTAATTTTTTTAGAACCGAATCCTAGATTGTCACAGAGTCT
ACTTTTATGCCAAAACTAGATATTTAGGATAGGTTCACCCCTTTTAAAATCTTTTTTAAGTCCTT
TAGGGGCATCAGGTACTTTTACATCG
Found at i:659184 original size:52 final size:51
Alignment explanation
Indices: 659113--659251 Score: 174
Period size: 52 Copynumber: 2.7 Consensus size: 51
659103 AATTGCCTGC
* **
659113 ATGTATCGATACATTAAAGAATGTATCGATACATTTGGGACAAAAACCCAAA
1 ATGTATAGATACAAAAAAGAATGTATCGATACATTTGGGAC-AAAACCCAAA
* * *
659165 ATGTATAGATACAAAAAAGAATATATCAATACATTTGGGTCAAAACCCAAA
1 ATGTATAGATACAAAAAAGAATGTATCGATACATTTGGGACAAAACCCAAA
*
659216 ATGTA-ACGATACAATGAAA-AATGTATCGATACATTT
1 ATGTATA-GATACAA-AAAAGAATGTATCGATACATTT
659252 TCATTCCAGA
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
50 1 0.01
51 37 0.49
52 38 0.50
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.26
Consensus pattern (51 bp):
ATGTATAGATACAAAAAAGAATGTATCGATACATTTGGGACAAAACCCAAA
Found at i:659248 original size:51 final size:53
Alignment explanation
Indices: 659113--659251 Score: 180
Period size: 51 Copynumber: 2.7 Consensus size: 53
659103 AATTGCCTGC
* *
659113 ATGTATCGATAC-ATTAAAGAATGTATCGATACATTTGGGACAAAAACCCAAA
1 ATGTAACGATACAATAAAAGAATGTATCGATACATTTGGGACAAAAACCCAAA
* * *
659165 ATGTATA-GATACAA-AAAAGAATATATCAATACATTTGGGTC-AAAACCCAAA
1 ATGTA-ACGATACAATAAAAGAATGTATCGATACATTTGGGACAAAAACCCAAA
*
659216 ATGTAACGATACAATGAAA-AATGTATCGATACATTT
1 ATGTAACGATACAATAAAAGAATGTATCGATACATTT
659252 TCATTCCAGA
Statistics
Matches: 75, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
50 1 0.01
51 37 0.49
52 36 0.48
53 1 0.01
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.26
Consensus pattern (53 bp):
ATGTAACGATACAATAAAAGAATGTATCGATACATTTGGGACAAAAACCCAAA
Found at i:659337 original size:26 final size:25
Alignment explanation
Indices: 659308--659367 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 25
659298 ATTTTTGACA
*
659308 TGTATCAATACAATACATTACCCTAT
1 TGTATCGATACAAT-CATTACCCTAT
659334 TGTATCGAT----TCATTACCCTAT
1 TGTATCGATACAATCATTACCCTAT
659355 TGTATCGATACAA
1 TGTATCGATACAA
659368 ATTGTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
21 20 0.69
22 1 0.03
26 8 0.28
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (25 bp):
TGTATCGATACAATCATTACCCTAT
Found at i:659349 original size:21 final size:21
Alignment explanation
Indices: 659323--659363 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
659313 CAATACAATA
659323 CATTACCCTATTGTATCGATT
1 CATTACCCTATTGTATCGATT
659344 CATTACCCTATTGTATCGAT
1 CATTACCCTATTGTATCGAT
659364 ACAAATTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.41
Consensus pattern (21 bp):
CATTACCCTATTGTATCGATT
Found at i:664744 original size:28 final size:28
Alignment explanation
Indices: 664712--664769 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
664702 CTTGTACTTT
664712 TTAAACTCTTTAAATCTTTTATTTTAGG
1 TTAAACTCTTTAAATCTTTTATTTTAGG
664740 TTAAACTCTTTAAATCTTTTATTTTAGG
1 TTAAACTCTTTAAATCTTTTATTTTAGG
664768 TT
1 TT
664770 GTTTTTCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (28 bp):
TTAAACTCTTTAAATCTTTTATTTTAGG
Found at i:667057 original size:13 final size:13
Alignment explanation
Indices: 667039--667063 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
667029 ATTATGCCTA
667039 GTATTGATACATT
1 GTATTGATACATT
667052 GTATTGATACAT
1 GTATTGATACAT
667064 GCTCATTGTA
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:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
GTATTGATACATT
Found at i:667093 original size:20 final size:20
Alignment explanation
Indices: 667049--667143 Score: 174
Period size: 20 Copynumber: 4.8 Consensus size: 20
667039 GTATTGATAC
*
667049 ATTGTATTGATACATGCTC-
1 ATTGTATCGATACATGCTCA
667068 ATTGTATCGATACATGCTCA
1 ATTGTATCGATACATGCTCA
667088 ATTGTATCGATACATGCTCA
1 ATTGTATCGATACATGCTCA
667108 ATTGTATCGATACATGCTCA
1 ATTGTATCGATACATGCTCA
667128 ATTGTATCGATACATG
1 ATTGTATCGATACATG
667144 AAATTGACAG
Statistics
Matches: 74, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
19 18 0.24
20 56 0.76
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (20 bp):
ATTGTATCGATACATGCTCA
Found at i:667202 original size:13 final size:13
Alignment explanation
Indices: 667184--667213 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
667174 TATACATAGG
667184 ACATTGTATCGAT
1 ACATTGTATCGAT
667197 ACATTGTATCGAT
1 ACATTGTATCGAT
667210 ACAT
1 ACAT
667214 GACCAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:667292 original size:19 final size:20
Alignment explanation
Indices: 667268--667305 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
667258 TAAATTTCAA
667268 ATGAA-TGTATCGATACATT
1 ATGAATTGTATCGATACATT
667287 ATGAATTGTATCGATACAT
1 ATGAATTGTATCGATACAT
667306 AGTAATAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (20 bp):
ATGAATTGTATCGATACATT
Found at i:667530 original size:21 final size:22
Alignment explanation
Indices: 667489--667536 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
667479 TTTTATTTTC
667489 TCATTTTCAAGAGCTTTTAAAT
1 TCATTTTCAAGAGCTTTTAAAT
667511 TCATTTTCAAGAGC-TTTAAAT
1 TCATTTTCAAGAGCTTTTAAAT
667532 TCATT
1 TCATT
667537 GTTGTTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (22 bp):
TCATTTTCAAGAGCTTTTAAAT
Found at i:670022 original size:16 final size:16
Alignment explanation
Indices: 670001--670031 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
669991 TGTAATAATG
*
670001 ATAAATGTGGTGAACA
1 ATAAATGGGGTGAACA
670017 ATAAATGGGGTGAAC
1 ATAAATGGGGTGAAC
670032 TATTCCCGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (16 bp):
ATAAATGGGGTGAACA
Found at i:670777 original size:24 final size:24
Alignment explanation
Indices: 670740--670785 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
670730 CTATAAATAA
*
670740 ATTATAACATTTTAATA-ATTTAT
1 ATTATAAAATTTTAATACATTTAT
670763 ATTATACAAATTTTAATACATTT
1 ATTATA-AAATTTTAATACATTT
670786 GTGCATTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 10 0.50
25 4 0.20
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTATAAAATTTTAATACATTTAT
Found at i:671373 original size:17 final size:17
Alignment explanation
Indices: 671351--671398 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
671341 ATTCAAATCG
671351 GTTATTTTTGGATTCGA
1 GTTATTTTTGGATTCGA
* * *
671368 GTTATTTTGGGTTTAGA
1 GTTATTTTTGGATTCGA
*
671385 TTTA-TTTTGGATTC
1 GTTATTTTTGGATTC
671399 AGATCATCTG
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.17, C:0.04, G:0.23, T:0.56
Consensus pattern (17 bp):
GTTATTTTTGGATTCGA
Found at i:671402 original size:17 final size:17
Alignment explanation
Indices: 671356--671402 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
671346 AATCGGTTAT
*
671356 TTTTGGATTC-GAGTTA
1 TTTTGGATTCAGATTTA
* *
671372 TTTTGGGTTTAGATTTA
1 TTTTGGATTCAGATTTA
671389 TTTTGGATTCAGAT
1 TTTTGGATTCAGAT
671403 CATCTGGGGC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 8 0.32
17 17 0.68
ACGTcount: A:0.19, C:0.04, G:0.23, T:0.53
Consensus pattern (17 bp):
TTTTGGATTCAGATTTA
Found at i:673982 original size:13 final size:13
Alignment explanation
Indices: 673964--673988 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
673954 ATTTTACTTA
673964 GTATCGATACATT
1 GTATCGATACATT
673977 GTATCGATACAT
1 GTATCGATACAT
673989 AAAACTAGTA
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):
GTATCGATACATT
Found at i:674057 original size:22 final size:22
Alignment explanation
Indices: 674024--674076 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
674014 TTTCACTGTT
* *
674024 CATCACTATTCATATATCGATA
1 CATCACTGTTCATATATCAATA
* *
674046 TATCACTGTTCATGTATCAATA
1 CATCACTGTTCATATATCAATA
674068 CATCACTGT
1 CATCACTGT
674077 ACATCACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATATATCAATA
Found at i:674136 original size:73 final size:73
Alignment explanation
Indices: 674049--674186 Score: 213
Period size: 73 Copynumber: 1.9 Consensus size: 73
674039 ATCGATATAT
* *
674049 CACTGTTCATGTATCAATACATCACTGTACATCACTATACATTGAGCCCAACGACCATAATTTCA
1 CACTGTTCATGTATCAATACATCACTATACATCACTATACATTAAGCCCAACGACCATAATTTCA
674114 CTGTTCAG
66 CTGTTCAG
* * * * *
674122 CACTGTTCATGTATCGATACATCACTATTCATCACTATACATTAAGCCCAGCGGCTATAATTTCA
1 CACTGTTCATGTATCAATACATCACTATACATCACTATACATTAAGCCCAACGACCATAATTTCA
674187 AATGCATGTA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 58 1.00
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (73 bp):
CACTGTTCATGTATCAATACATCACTATACATCACTATACATTAAGCCCAACGACCATAATTTCA
CTGTTCAG
Found at i:676275 original size:21 final size:21
Alignment explanation
Indices: 676251--676302 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
676241 GAACCAGAGG
* *
676251 AGAAAATGAATGAGTTGGAAA
1 AGAAAATGAATAAGTTGCAAA
676272 AGAAAA-GAAATAAGTTGCAAA
1 AGAAAATG-AATAAGTTGCAAA
676293 ATGAAAATGA
1 A-GAAAATGA
676303 TTAGTTAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.04
21 18 0.69
22 6 0.23
23 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.23, T:0.17
Consensus pattern (21 bp):
AGAAAATGAATAAGTTGCAAA
Found at i:680281 original size:27 final size:27
Alignment explanation
Indices: 680243--680308 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
680233 TTAAAATGCG
* * *
680243 GTTGGAGTATCCCTTCGAAGGAGTAGA
1 GTTGGAGTATCCCCTCGAAGAAATAGA
* *
680270 GTTGGAGTATCCCCTCGGAGAAATAGG
1 GTTGGAGTATCCCCTCGAAGAAATAGA
680297 GTTGGAGTATCC
1 GTTGGAGTATCC
680309 TAATAAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (27 bp):
GTTGGAGTATCCCCTCGAAGAAATAGA
Found at i:683033 original size:22 final size:22
Alignment explanation
Indices: 683008--683064 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
682998 TTTCACTGTT
*
683008 CATCACTGTTCATATATCGGTA
1 CATCACTGTTCATATATCGATA
*
683030 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATATATCGATA
683052 CATCACTGTTCAT
1 CATCACTGTTCAT
683065 CACTATACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (22 bp):
CATCACTGTTCATATATCGATA
Found at i:683157 original size:73 final size:73
Alignment explanation
Indices: 683033--683170 Score: 231
Period size: 73 Copynumber: 1.9 Consensus size: 73
683023 ATCGGTACAT
* *
683033 CACTGTTCATGTATCGATACATCACTGTTCATCACTATACATTGAGCCCAACGACCATAATTTCA
1 CACTGTTCATGTATAGATACATCACTGTTCATCACTATACATTAAGCCCAACGACCATAATTTCA
683098 CTGTTTAG
66 CTGTTTAG
* * *
683106 CACTGTTCATGTATAGATACATCACTGTTCATCACTATACATTAAGTCCAACGGCTATAATTTCA
1 CACTGTTCATGTATAGATACATCACTGTTCATCACTATACATTAAGCCCAACGACCATAATTTCA
683171 AATGCATGTA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 60 1.00
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (73 bp):
CACTGTTCATGTATAGATACATCACTGTTCATCACTATACATTAAGCCCAACGACCATAATTTCA
CTGTTTAG
Found at i:688165 original size:157 final size:156
Alignment explanation
Indices: 687909--688761 Score: 777
Period size: 157 Copynumber: 5.5 Consensus size: 156
687899 TAAGTTTAAC
* * * * * * * *
687909 AAAAATTACGAAAATGCC-CCTAAAGGT-TACCTTCGACATAAAAGTACCT-AATACCCCCAAAG
1 AAAAATTACCAAAAT-CCTCCTAAGGGTATACCTTCGACGTAAAAGTATCTCGATAACCCTAAAA
* * *
687971 GACTTAAAAAAGA-CTATAAAATGGATGAACCTCTCCTAAATGTCCACCTTCAGCATAAAAGCAA
65 GACTT-AAAAAGATC-ATAAAAGGGATGAACCTATCCTAAATGCCCACCTTCAGCATAAAAGCAA
* * * *
688035 ACTCGGTGACGACCTAGAAGTTTATTTTA
128 ACCCGGTGACGACCTAGGAGTTGATTCTA
*
688064 AAAAATTACCAAAATACCT-CT-AGGGTTATACCTTCGACGTAAAAGTATCTCGATAACCTTAAA
1 AAAAATTACCAAAAT-CCTCCTAAGGG-TATACCTTCGACGTAAAAGTATCTCGATAACCCTAAA
* * *
688127 AGACTTAAAAAGATGCATAAAAGGGATGAACCGATCCTAAATGCCCTCCTTCAGCATGAAAA-CG
64 AGACTTAAAAAGAT-CATAAAAGGGATGAACCTATCCTAAATGCCCACCTTCAGCAT-AAAAGCA
* * *
688191 ACCCCGGTGATGACCTAGGAGTTGGTTCTA
127 AACCCGGTGACGACCTAGGAGTTGATTCTA
* * *
688221 AAAAATTACCAAAATGCTCCTAAGGGTATACCTTCGACGTAAAAGTATCTTGACAACCCTAAAAG
1 AAAAATTACCAAAATCCTCCTAAGGGTATACCTTCGACGTAAAAGTATCTCGATAACCCTAAAAG
* ** *
688286 ACTTAAAAAGACTCATAAAAGGGATGAACCTATCCTAAATGCCTACCTTTGGCATAAAAGCAGAC
66 ACTTAAAAAGA-TCATAAAAGGGATGAACCTATCCTAAATGCCCACCTTCAGCATAAAAGCAAAC
*
688351 CCGGTGACGACCTAGGAGTTGGTTCTA
130 CCGGTGACGACCTAGGAGTTGATTCTA
* * * * * *
688378 AGAAAATTACTAAAATGCTCCTAAGGGTATACCTTCGACGTAAAAATACCT-GATACCCCTAAAG
1 A-AAAATTACCAAAATCCTCCTAAGGGTATACCTTCGACGTAAAAGTATCTCGATAACCCTAAAA
* * * * *
688442 GACTCAAAAAGGATTATAAAAGGGGTGAACCTATCCTAAATACCCACCTTC-GACGTAAAAGGC-
65 GACTTAAAAA-GATCATAAAAGGGATGAACCTATCCTAAATGCCCACCTTCAG-CATAAAA-GCA
** * * *
688505 --CTTGGTGACGACCTAGGACTCGATTATA
127 AACCCGGTGACGACCTAGGAGTTGATTCTA
* * *
688533 AAAAATTACAAAAATGCC-CCT-AGGGGATACCTTCGACGTAAAAGTATC-CTGATACCCCTAAA
1 AAAAATTACCAAAAT-CCTCCTAAGGGTATACCTTCGACGTAAAAGTATCTC-GATAACCCTAAA
* * * * ** ** * **
688595 GGACTGAAAAGGA-CTATAAAAGGGGTGAACCTATCCTAAATATCCACCTTTGGCATGAAAGCGG
64 AGACTTAAAAAGATC-ATAAAAGGGATGAACCTATCCTAAATGCCCACCTTCAGCATAAAAGCAA
* * *
688659 ACCCGATGACAACCTAGGACTTGATTCTA
128 ACCCGGTGACGACCTAGGAGTTGATTCTA
* ** * * * * * ** *
688688 GAAAAATTACGAAAATGTTCAT-AGGGGATACCTTCGACGTGAAAGTATCCCGGTAGTCCTAAAG
1 -AAAAATTACCAAAATCCTCCTAAGGGTATACCTTCGACGTAAAAGTATCTCGATAACCCTAAAA
688752 GACTTAAAAA
65 GACTTAAAAA
688762 TGATAAGTAA
Statistics
Matches: 589, Mismatches: 83, Indels: 51
0.81 0.11 0.07
Matches are distributed among these distances:
152 2 0.00
153 65 0.11
154 41 0.07
155 65 0.11
156 94 0.16
157 262 0.44
158 60 0.10
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.23
Consensus pattern (156 bp):
AAAAATTACCAAAATCCTCCTAAGGGTATACCTTCGACGTAAAAGTATCTCGATAACCCTAAAAG
ACTTAAAAAGATCATAAAAGGGATGAACCTATCCTAAATGCCCACCTTCAGCATAAAAGCAAACC
CGGTGACGACCTAGGAGTTGATTCTA
Found at i:690374 original size:18 final size:20
Alignment explanation
Indices: 690351--690395 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
690341 TGTTGTTGCC
*
690351 GTTGCT-TGTTGCTT-ATTT
1 GTTGCTATGTTGCTTCAGTT
690369 GTTGCTGATGTTGCTTCAGTT
1 GTTGCT-ATGTTGCTTCAGTT
690390 GTTGCT
1 GTTGCT
690396 GGTGTTATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
20 8 0.35
21 9 0.39
ACGTcount: A:0.07, C:0.13, G:0.27, T:0.53
Consensus pattern (20 bp):
GTTGCTATGTTGCTTCAGTT
Found at i:690393 original size:21 final size:20
Alignment explanation
Indices: 690357--690401 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
690347 TGCCGTTGCT
*
690357 TGTTGCTTATTTGTTGCTGA
1 TGTTGCTTAGTTGTTGCTGA
*
690377 TGTTGCTTCAGTTGTTGCTGG
1 TGTTGCTT-AGTTGTTGCTGA
690398 TGTT
1 TGTT
690402 ATTGTTGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.07, C:0.11, G:0.29, T:0.53
Consensus pattern (20 bp):
TGTTGCTTAGTTGTTGCTGA
Found at i:690893 original size:18 final size:18
Alignment explanation
Indices: 690861--690916 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
690851 AACCATCTTT
*
690861 TTTTTCATTCATCTTTTCC
1 TTTTTCTTTC-TCTTTTCC
*
690880 TTTTTCTTTCTC-TTTCTT
1 TTTTTCTTTCTCTTTTC-C
*
690898 TTTTTCTTTCTCTCTTCC
1 TTTTTCTTTCTCTTTTCC
690916 T
1 T
690917 CCCCTCTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 4 0.13
18 15 0.48
19 12 0.39
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTCTTTCTCTTTTCC
Found at i:691228 original size:16 final size:17
Alignment explanation
Indices: 691202--691240 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
691192 AAAATTTAAC
691202 AAAAAAGATC-AAATTGT
1 AAAAAAGATCAAAATT-T
691219 AAAAAA-ATCAAAATTT
1 AAAAAAGATCAAAATTT
691235 AAAAAA
1 AAAAAA
691241 TAAGATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (17 bp):
AAAAAAGATCAAAATTT
Found at i:691252 original size:19 final size:18
Alignment explanation
Indices: 691190--691254 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 18
691180 AAATTATATT
691190 ATAAAATTTAACAAAAAAG
1 ATAAAATTTAA-AAAAAAG
*
691209 ATCAAATTGT--AAAAAA-
1 ATAAAATT-TAAAAAAAAG
691225 ATCAAAATTTAAAAAATAAG
1 AT-AAAATTTAAAAAA-AAG
691245 ATAAAATTTA
1 ATAAAATTTA
691255 TGTGATCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
16 3 0.08
17 11 0.29
18 4 0.11
19 17 0.45
20 3 0.08
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (18 bp):
ATAAAATTTAAAAAAAAG
Found at i:691620 original size:164 final size:164
Alignment explanation
Indices: 691391--691786 Score: 415
Period size: 164 Copynumber: 2.4 Consensus size: 164
691381 AAATCAAAAA
* * *
691391 ATAAGAAATAAATTAAATTTTGAAAAACTGATTTAATGGGAATCAAATAACAATA-TTAGATGAA
1 ATAA-AAAT-AATTAAATTTT-TAAAACTGATTTAATGTGAATCAAATAATAATATTTA-ATGAA
* * * **
691455 TTTTAAAAATTTTAAATCAAGAAAAATCCT-TCTAAAAAATTTACGGAGAAGAAAACTTGGT-TT
62 TTTTAAAAATTTTAAATCAAGAAAAATCCTCACGAAAAAATTTACGGAGAAAAAAACTCCGTATT
* * * **
691518 CTCGAAA-AATAGGACTTCAAAGGAAAAAATTCAAAACTC
127 CTAGAAACAAGAGAACTTCAAA-G-AAAAATGAAAAACTC
* * *
691557 ATAAAAATGAATTAAATTTTTAAAACTGAATTAATGTGAATTAAATAATAATATTTAATGAATTA
1 ATAAAAAT-AATTAAATTTTTAAAACTGATTTAATGTGAATCAAATAATAATATTTAATGAATTT
** *** *
691622 TAAAAATTTTGGATCGTTAAAAATCCTCACGAAAAAATTTACGGAGAAAAAAACTCCGTATTTTA
65 TAAAAATTTTAAATCAAGAAAAATCCTCACGAAAAAATTTACGGAGAAAAAAACTCCGTATTCTA
*
691687 GAAACAAGAGAATTTCAAAGAAAAATGAAAAACTC
130 GAAACAAGAGAACTTCAAAGAAAAATGAAAAACTC
* *** * * *
691722 ATGAAAATAAAGGAATTTTTAGAAACT-ATTTAATGTGAACCAAATGATAATATTTGATGAATTT
1 ATAAAAATAATTAAATTTTTA-AAACTGATTTAATGTGAATCAAATAATAATATTTAATGAATTT
691786 T
65 T
691787 GATATTTTAA
Statistics
Matches: 191, Mismatches: 34, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
164 99 0.52
165 69 0.36
166 12 0.06
167 11 0.06
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.30
Consensus pattern (164 bp):
ATAAAAATAATTAAATTTTTAAAACTGATTTAATGTGAATCAAATAATAATATTTAATGAATTTT
AAAAATTTTAAATCAAGAAAAATCCTCACGAAAAAATTTACGGAGAAAAAAACTCCGTATTCTAG
AAACAAGAGAACTTCAAAGAAAAATGAAAAACTC
Found at i:695144 original size:52 final size:52
Alignment explanation
Indices: 695079--695279 Score: 305
Period size: 52 Copynumber: 3.9 Consensus size: 52
695069 CAATGTTAGA
* * * * *
695079 GTGACTTGTTGTCACT-AGTAATGATGATGCCCTGATGGCAAACAGGATCGAG
1 GTGACTTGGTGTCACTGA-TAATGATGATGCCATGGTGGCAATCAAGATCGAG
* *
695131 GTGACTTGGTGTCACTAATAATGATGATGCCATGGTGGCGATCAAGATCGAG
1 GTGACTTGGTGTCACTGATAATGATGATGCCATGGTGGCAATCAAGATCGAG
* *
695183 GTGACTTGGTGTTACTGATAATGATGATGCCATGGGGGCAATCAAGATCGAG
1 GTGACTTGGTGTCACTGATAATGATGATGCCATGGTGGCAATCAAGATCGAG
695235 GTGACTTGGTGTCACTGATAATGATGATGCCATGGTGGCAATCAA
1 GTGACTTGGTGTCACTGATAATGATGATGCCATGGTGGCAATCAA
695280 CAGTAATGAG
Statistics
Matches: 136, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
52 135 0.99
53 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (52 bp):
GTGACTTGGTGTCACTGATAATGATGATGCCATGGTGGCAATCAAGATCGAG
Found at i:699758 original size:18 final size:18
Alignment explanation
Indices: 699732--699767 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
699722 GTGAGTGCGT
*
699732 ATTTCAAGTGTTTGTGTC
1 ATTTCAAGTGTCTGTGTC
*
699750 ATTTTAAGTGTCTGTGTC
1 ATTTCAAGTGTCTGTGTC
699768 GCACTCTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.11, G:0.22, T:0.50
Consensus pattern (18 bp):
ATTTCAAGTGTCTGTGTC
Found at i:701552 original size:15 final size:15
Alignment explanation
Indices: 701523--701563 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
701513 GATAAGGACC
701523 TTAAAATTATACAAAA
1 TTAAAATT-TACAAAA
701539 TTAAAATTTACAAAA
1 TTAAAATTTACAAAA
701554 TTAAAATTTA
1 TTAAAATTTA
701564 ACTTTCTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.68
16 8 0.32
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (15 bp):
TTAAAATTTACAAAA
Found at i:701706 original size:2 final size:2
Alignment explanation
Indices: 701693--701736 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
701683 ATAGAAAGAA
*
701693 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
701736 A
1 A
701737 CTATTGGTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:705989 original size:18 final size:18
Alignment explanation
Indices: 705966--706001 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
705956 AAGGATCATT
*
705966 TACATTGCGATTATTGTA
1 TACATTGCGATAATTGTA
*
705984 TACATTGTGATAATTGTA
1 TACATTGCGATAATTGTA
706002 GGAAGCCAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
TACATTGCGATAATTGTA
Found at i:711279 original size:2 final size:2
Alignment explanation
Indices: 711274--711305 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
711264 CACACAAAAG
711274 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
711306 ACAGATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:711378 original size:2 final size:2
Alignment explanation
Indices: 711371--711402 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
711361 TGGAATATTT
711371 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
711403 GACACACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:711428 original size:2 final size:2
Alignment explanation
Indices: 711423--711459 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
711413 CAAACACAAG
711423 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
711460 TACAAGGCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:712455 original size:16 final size:18
Alignment explanation
Indices: 712420--712460 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
712410 TTTAAAATAT
712420 TTAAAATATATATTTAAA
1 TTAAAATATATATTTAAA
712438 TTAAAATATA-ATTT-AA
1 TTAAAATATATATTTAAA
712454 TTAAAAT
1 TTAAAAT
712461 TTAAATTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 9 0.39
17 4 0.17
18 10 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAAATATATATTTAAA
Found at i:716002 original size:20 final size:20
Alignment explanation
Indices: 715977--716027 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
715967 TTTTCATAAT
* *
715977 TTGTATCGATACCTTATTCA
1 TTGTATCGATACATGATTCA
* *
715997 TTGTATTGATACATGGTTCA
1 TTGTATCGATACATGATTCA
*
716017 TTATATCGATA
1 TTGTATCGATA
716028 AATTGTATCG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (20 bp):
TTGTATCGATACATGATTCA
Found at i:718429 original size:50 final size:50
Alignment explanation
Indices: 718370--718495 Score: 162
Period size: 50 Copynumber: 2.5 Consensus size: 50
718360 ATTAAATTTC
* * *
718370 TTGATTTTTCATCTCGGGGATACTCCAACCCTAGCTTTATTTCTAAAATA
1 TTGATTTTTCATCTCGGGGATACTCCAACCCCAGCTTTATTTCCAAAACA
* * *
718420 TTGATTTTTCATCTCGGGGATACTCTAACCCCGGTTTTATTTCCAAAACA
1 TTGATTTTTCATCTCGGGGATACTCCAACCCCAGCTTTATTTCCAAAACA
** *
718470 TCAATTTTTCATAATCGGGGATACTC
1 TTGATTTTTCAT-CTCGGGGATACTC
718496 TAATCTCGTT
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 54 0.82
51 12 0.18
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.39
Consensus pattern (50 bp):
TTGATTTTTCATCTCGGGGATACTCCAACCCCAGCTTTATTTCCAAAACA
Found at i:718618 original size:79 final size:79
Alignment explanation
Indices: 718535--718766 Score: 204
Period size: 79 Copynumber: 2.9 Consensus size: 79
718525 AATCCCAGCT
* * * * * * *
718535 TTATTTCTAAA-ATATTGA-TTTCTCACAATTGGGGATACTCCAGCCCTGTTATTTTGGCGGGGA
1 TTATTTCTAAAGAT-TCGATTTTC-CACAATCGGAGATACTCCAACCCCGTTATTTTCGAGGGGA
718598 TACTCCAACCTCGGGC
64 TACTCCAACCTCGGGC
*
718614 TTATTTCTAAAGCTTCGATTTTCCACAATCGGAGATACTCCAACCCCGTTATTTTCGAGGGGATA
1 TTATTTCTAAAGATTCGATTTTCCACAATCGGAGATACTCCAACCCCGTTATTTTCGAGGGGATA
* * ***
718679 CTGCAACCCCGATT
66 CTCCAACCTCGGGC
* * * * * *
718693 TTATTT-TCAAA-ACGTCGATTTTCTATAATCAGG-GATGCTCCAACCCTGTTATTTTCAAGGGG
1 TTATTTCT-AAAGA-TTCGATTTTCCACAATC-GGAGATACTCCAACCCCGTTATTTTCGAGGGG
*
718755 ATGCTCCAACCT
63 ATACTCCAACCT
718767 TGTTATTTCC
Statistics
Matches: 125, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
78 1 0.01
79 117 0.94
80 7 0.06
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.34
Consensus pattern (79 bp):
TTATTTCTAAAGATTCGATTTTCCACAATCGGAGATACTCCAACCCCGTTATTTTCGAGGGGATA
CTCCAACCTCGGGC
Found at i:718762 original size:28 final size:27
Alignment explanation
Indices: 718723--718793 Score: 115
Period size: 28 Copynumber: 2.6 Consensus size: 27
718713 TTCTATAATC
*
718723 AGGGATGCTCCAACCCTGTTATTTTCA
1 AGGGATGCTCCAACCCTGTTATTTCCA
*
718750 AGGGGATGCTCCAACCTTGTTATTTCCA
1 A-GGGATGCTCCAACCCTGTTATTTCCA
718778 AGGGATGCTCCAACCC
1 AGGGATGCTCCAACCC
718794 CGATTTTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 15 0.38
28 25 0.62
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (27 bp):
AGGGATGCTCCAACCCTGTTATTTCCA
Found at i:724336 original size:28 final size:28
Alignment explanation
Indices: 724296--724391 Score: 133
Period size: 28 Copynumber: 3.4 Consensus size: 28
724286 ATAAAGCCGG
724296 GGTTGGAGTATCCCCTCGGAGGTAACGA
1 GGTTGGAGTATCCCCTCGGAGGTAACGA
*
724324 GGTTGGAGTATCCCCTCGGAGGTAACGG
1 GGTTGGAGTATCCCCTCGGAGGTAACGA
**
724352 GGTTGGAGTAT--CCTCGATGAAATAACGA
1 GGTTGGAGTATCCCCTCG--GAGGTAACGA
724380 GGTTGGAGTATC
1 GGTTGGAGTATC
724392 ATCAATTGTG
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
26 5 0.08
28 56 0.92
ACGTcount: A:0.23, C:0.18, G:0.35, T:0.24
Consensus pattern (28 bp):
GGTTGGAGTATCCCCTCGGAGGTAACGA
Found at i:724535 original size:51 final size:52
Alignment explanation
Indices: 724415--724549 Score: 166
Period size: 51 Copynumber: 2.6 Consensus size: 52
724405 AATTGGTGTT
* * * *
724415 TTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTGT
1 TTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGGAAAATTAGTGA
* ** *
724467 TTTGAAAATAAAGCCGGGGTTGGAGTATCCCCGATT-GTGGAAAA-TCGCTGA
1 TTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGGAAAATTAG-TGA
*
724518 TTTGAAAATAAAACCGGGGTTGAAGTATCCCC
1 TTTGAAAATAAAACCGGGGTTGGAGTATCCCC
724550 TCGGAGATAA
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
50 2 0.03
51 38 0.53
52 32 0.44
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (52 bp):
TTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGGAAAATTAGTGA
Found at i:724614 original size:79 final size:79
Alignment explanation
Indices: 724482--724739 Score: 331
Period size: 79 Copynumber: 3.3 Consensus size: 79
724472 AAATAAAGCC
* ** * * *
724482 GGGGTTGGAGTATCCCCGATTGTG-GAAAATCGCTGATTTGA-AAATAAAACCGGGGTTGAAGTA
1 GGGGTTGGAGTATCCCCGATTATGAG-AAATCAAT-ATTTTAGAAATAAAGCCGGGGTTGGAGTA
* * *
724545 TCCCCTCGGAGATAAC
64 TCCCCTCGAAAATAAT
** *
724561 GGGGTTGGAGTATCCTTGATTATGAGAAATTAATATTTTAGAAATAAAGCCGGGGTTGGAGTATC
1 GGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATC
724626 CCCTCGAAAATAAT
66 CCCTCGAAAATAAT
* *
724640 AGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGGAATAAAGCCGGGGGTTGGAGTAT
1 GGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAGCC-GGGGTTGGAGTAT
*
724705 CCCCTCAAAAATAAT
65 CCCCTCGAAAATAAT
*
724720 GAGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
724740 AATTAACGGG
Statistics
Matches: 156, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
78 5 0.03
79 105 0.67
80 46 0.29
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (79 bp):
GGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATC
CCCTCGAAAATAAT
Found at i:724760 original size:27 final size:27
Alignment explanation
Indices: 724692--724766 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
724682 AATAAAGCCG
* * *
724692 GGGGTTGGAGTATCCCCTCAAAAATAAT
1 GGGGTTGGAGTATCCCC-GATAAATAAC
* *
724720 GAGGTTGGAGTATCCCCGATAATTAAC
1 GGGGTTGGAGTATCCCCGATAAATAAC
724747 GGGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
724767 GAAAAATTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 25 0.61
28 16 0.39
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCCGATAAATAAC
Found at i:724840 original size:51 final size:48
Alignment explanation
Indices: 724754--724867 Score: 135
Period size: 51 Copynumber: 2.3 Consensus size: 48
724744 AACGGGGTTG
724754 GAGTATCCCCGA-TGAAAAATTGATGTTTTAGAAATAAAATCGGAGTT
1 GAGTATCCCCGATTGAAAAATTGATGTTTTAGAAATAAAATCGGAGTT
*
724801 AGAGTATCCCCGATTATAGAAAATT-AGTGTTTT-GAAAATAAAATCGGAGTT
1 -GAGTATCCCCGATT-GA-AAAATTGA-TGTTTTAG-AAATAAAATCGGAGTT
*
724852 GGGATATCCCCGATTG
1 GAG-TATCCCCGATTG
724868 TGGAGAATTG
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
48 12 0.21
49 1 0.02
50 5 0.09
51 39 0.68
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (48 bp):
GAGTATCCCCGATTGAAAAATTGATGTTTTAGAAATAAAATCGGAGTT
Found at i:727253 original size:33 final size:33
Alignment explanation
Indices: 727211--727276 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
727201 AACTTCCTAG
*
727211 ATGTATCGATACAAAGAATAGATGTAT-GATACA
1 ATGTATCGATACAAAGAA-AAATGTATCGATACA
*
727244 ATGTATCGATACACAGAAAAATGTATCGATACA
1 ATGTATCGATACAAAGAAAAATGTATCGATACA
727277 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 7 0.23
33 23 0.77
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATGTATCGATACA
Found at i:735640 original size:52 final size:52
Alignment explanation
Indices: 735492--735620 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
735482 CAAAATATAA
735492 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
* *
735544 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
*
735596 AAATTTGCTTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
735621 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Done.