Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold139
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: 1720190
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 4798 characters in sequence are not A, C, G, or T
File 2 of 11
Found at i:159840 original size:32 final size:32
Alignment explanation
Indices: 159811--159873 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
159801 AGGTACCATT
* *
159811 AACTTGTGTGGGCTTTGAAAAGAGTTACCACC
1 AACTCGTGTAGGCTTTGAAAAGAGTTACCACC
*
159843 GACTCGTGTAGGCTTTGAAAAGAGTTACCAC
1 AACTCGTGTAGGCTTTGAAAAGAGTTACCAC
159874 TGGCTTGTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (32 bp):
AACTCGTGTAGGCTTTGAAAAGAGTTACCACC
Found at i:159934 original size:28 final size:28
Alignment explanation
Indices: 159870--160395 Score: 629
Period size: 28 Copynumber: 18.5 Consensus size: 28
159860 AAAAGAGTTA
*
159870 CCACTGGCTTGTGGGCTTTGAAAGGGGTG
1 CCACTGACTTGTGGGCTTTGAAA-GGGTG
*
159899 CCACTGACTTGTGGGCGTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* *
159927 CCACTGACTTGTGGGTTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* **
159955 CCACTAACTTGTGGGCTTTGAAAATGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
*
159983 CCACTGATTTGTGGGCTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* **
160011 CCACTGACTTATGGGCTTTGAAAAGAATG
1 CCACTGACTTGTGGGCTTTG-AAAGGGTG
* * * *
160040 CAACTGACTGGTGGACTTTGAAAAGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
*
160068 CCACTGACTTGCGTGGGCTTCGAAAGGGTG
1 CCACTGACTT--GTGGGCTTTGAAAGGGTG
* *
160098 CCACTAACTTGTGGGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* * *
160126 CTACTAACTTGTGGGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* * *
160154 CCACTAACTTGTGGGATTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
*
160182 CCACTGACTTGTGGGCTTTGAAAAGAGTTG
1 CCACTGACTTGTGGGCTTTG-AAAG-GGTG
* *
160212 CCACTGACTCGTGGGCTTTGAAAAGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
*
160240 CCACTGACTTGTGGGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
*
160268 CCACTAACTTGTGGGCTTTGAATAGGGTTG
1 CCACTGACTTGTGGGCTTTGAA-AGGG-TG
* * * * *
160298 CCGCTAACTCGTAGGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* * *
160326 CCACTGACTTGTGAGCTTTAAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
160354 CCACTGACTTGTGGGCTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* *
160382 CCACTAATTTGTGG
1 CCACTGACTTGTGG
160396 TGCCACTAAC
Statistics
Matches: 428, Mismatches: 62, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
28 305 0.71
29 56 0.13
30 67 0.16
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (28 bp):
CCACTGACTTGTGGGCTTTGAAAGGGTG
Found at i:159977 original size:56 final size:56
Alignment explanation
Indices: 159870--160694 Score: 918
Period size: 56 Copynumber: 14.9 Consensus size: 56
159860 AAAAGAGTTA
* * *
159870 CCACTGGCTTGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCGTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAA-GGATGCCACTGACTTGTGGGCTTTGAAAGGGTG
* * **
159927 CCACTGACTTGTGGGTTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAATGTG
1 CCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTG
* * * **
159983 CCACTGATTTGTGGGCTTTGAAAGGGTGCCACTGACTTATGGGCTTTGAAAAGAATG
1 CCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG-AAAGGGTG
* * * *
160040 CAACTGACTGGTGGACTTTGAAAAGG-TGCCACTGACTTGCGTGGGCTTCGAAAGGGTG
1 CCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTT--GTGGGCTTTGAAAGGGTG
* * * *
160098 CCACTAACTTGTGGGCTTTGAAAGGATGCTACTAACTTGTGGGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTG
* * *
160154 CCACTAACTTGTGGGATTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTG
1 CCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG-AAAG-GGTG
* *
160212 CCACTGACTCGTGGGCTTTGAAAAGG-TGCCACTGACTTGTGGGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTG
* * * * * * *
160268 CCACTAACTTGTGGGCTTTGAATAGGGTTGCCGCTAACTCGTAGGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAA-A-GGATGCCACTGACTTGTGGGCTTTGAAAGGGTG
* *
160326 CCACTGACTTGTGAGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTG
* * *
160382 CCACT-AATT-T--G---T----GG-TGCCACTAACTTGTGGGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTG
* * * * *
160426 CCATTGACTTATGGGCTTTAAAAAGG-TGCCATTGACTTGTGGGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTT-GAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTG
*
160482 CCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAA-GG-G
1 CCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTG
**
160536 ---CTGACTTGTGGGCTTCAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTG
* * * *
160589 CCACTGACTTATGGGCTTTGAAAGGATGCCATTGACTTGTGGGCTTTAAAAAGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTG
* * * *
160645 CTACTGACTTGTGGGCTTTAAAAAGG-TGCCACTAACTTATGGGCTTTGAA
1 CCACTGACTTGTGGGCTTT-GAAAGGATGCCACTGACTTGTGGGCTTTGAA
160695 GAGATGAACG
Statistics
Matches: 656, Mismatches: 82, Indels: 61
0.82 0.10 0.08
Matches are distributed among these distances:
44 32 0.05
45 5 0.01
46 1 0.00
48 1 0.00
49 1 0.00
51 46 0.07
52 3 0.00
53 1 0.00
54 2 0.00
55 11 0.02
56 341 0.52
57 75 0.11
58 124 0.19
59 13 0.02
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (56 bp):
CCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTG
Found at i:160399 original size:16 final size:16
Alignment explanation
Indices: 160378--160411 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
160368 GCTTTGAAAG
*
160378 GGTGCCACTAATTTGT
1 GGTGCCACTAACTTGT
160394 GGTGCCACTAACTTGT
1 GGTGCCACTAACTTGT
160410 GG
1 GG
160412 GCTTTGAAAG
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:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (16 bp):
GGTGCCACTAACTTGT
Found at i:160428 original size:28 final size:27
Alignment explanation
Indices: 160394--160694 Score: 367
Period size: 28 Copynumber: 11.0 Consensus size: 27
160384 ACTAATTTGT
*
160394 GGTGCCACTAACTTGTGGGCTTTGAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAA
* * *
160421 GGATGCCATTGACTTATGGGCTTTAAAAA
1 GG-TGCCACTGACTTGTGGGCTTT-GAAA
*
160450 GGTGCCATTGACTTGTGGGCTTTGAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAA
160477 GGATGCCACTGACTTGTGGGCTTTGAAA
1 GG-TGCCACTGACTTGTGGGCTTTGAAA
160505 GGGTGCCACTGACTTGTGGGCTTTGAAA
1 -GGTGCCACTGACTTGTGGGCTTTGAAA
**
160533 GG-G---CTGACTTGTGGGCTTCAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAA
160556 GGATGCCACTGACTTGTGGGCTTTGAAA
1 GG-TGCCACTGACTTGTGGGCTTTGAAA
*
160584 GGGTGCCACTGACTTATGGGCTTTGAAA
1 -GGTGCCACTGACTTGTGGGCTTTGAAA
* *
160612 GGATGCCATTGACTTGTGGGCTTTAAAAA
1 GG-TGCCACTGACTTGTGGGCTTT-GAAA
* *
160641 GGTGCTACTGACTTGTGGGCTTTAAAAA
1 GGTGCCACTGACTTGTGGGCTTT-GAAA
* *
160669 GGTGCCACTAACTTATGGGCTTTGAA
1 GGTGCCACTGACTTGTGGGCTTTGAA
160695 GAGATGAACG
Statistics
Matches: 241, Mismatches: 21, Indels: 24
0.84 0.07 0.08
Matches are distributed among these distances:
23 20 0.08
25 1 0.00
26 1 0.00
27 13 0.05
28 192 0.80
29 14 0.06
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.30
Consensus pattern (27 bp):
GGTGCCACTGACTTGTGGGCTTTGAAA
Found at i:160474 original size:100 final size:104
Alignment explanation
Indices: 160296--160694 Score: 372
Period size: 107 Copynumber: 3.8 Consensus size: 104
160286 TGAATAGGGT
* * * *
160296 TGCCGCTAACTCGTAGGCTTTGAAAGGATGCCACTGACTTGTGAGCTTTAAAAGGATGCCACTGA
1 TGCCACTAACTTGTGGGCTTTGAAAGGATGCCA-TGACTTGTGGGCTTTAAAAGGATGCCACTGA
160361 CTTGTGGGCTTTGAAAGGGTGCCACT-AATT-T-G-T-GG
65 CTTGTGGGCTTTGAAAGGGTGCCACTGAATTGTGGTTAGG
* *
160396 TGCCACTAACTTGTGGGCTTTGAAAGGATGCCATTGACTTATGGGCTTTAAAAAGG-TGCCATTG
1 TGCCACTAACTTGTGGGCTTTGAAAGGATGCCA-TGACTTGTGGGCTTT-AAAAGGATGCCACTG
* *
160460 ACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGG
64 ACTTGTGGGCTTTGAAAGGGTGCCACTGAATTGT-GG--TT---A-GG
* *
160508 TGCCACTGACTTGTGGGCTTTGAAAGG--G-C-TGACTTGTGGGCTTCAAAAGGATGCCACTGAC
1 TGCCACTAACTTGTGGGCTTTGAAAGGATGCCATGACTTGTGGGCTTTAAAAGGATGCCACTGAC
* *
160569 TTGTGGGCTTTGAAAGGGTGCCACTGACTTATGGGCTTTGAAAGG
66 TTGTGGGCTTTGAAAGGGTGCCACTGAATTGT-GG--TT---AGG
* * * *
160614 ATGCCATTGACTTGTGGGCTTTAAAAAGG-TGCTACTGACTTGTGGGCTTTAAAAAGG-TGCCAC
1 -TGCCACTAACTTGTGGGCTTT-GAAAGGATGCCA-TGACTTGTGGGCTTT-AAAAGGATGCCAC
* *
160677 TAACTTATGGGCTTTGAA
62 TGACTTGTGGGCTTTGAA
160695 GAGATGAACG
Statistics
Matches: 257, Mismatches: 21, Indels: 30
0.83 0.07 0.10
Matches are distributed among these distances:
100 76 0.30
101 9 0.04
102 1 0.00
104 1 0.00
106 8 0.03
107 84 0.33
108 5 0.02
109 2 0.01
110 1 0.00
112 64 0.25
113 6 0.02
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (104 bp):
TGCCACTAACTTGTGGGCTTTGAAAGGATGCCATGACTTGTGGGCTTTAAAAGGATGCCACTGAC
TTGTGGGCTTTGAAAGGGTGCCACTGAATTGTGGTTAGG
Found at i:161932 original size:9 final size:9
Alignment explanation
Indices: 161909--161986 Score: 63
Period size: 9 Copynumber: 8.6 Consensus size: 9
161899 TTTTTTGCTA
161909 TTTTTTCTTG
1 TTTTTT-TTG
*
161919 GTTTTTTTG
1 TTTTTTTTG
161928 TTTTTTTTG
1 TTTTTTTTG
161937 TTTTGTTTT-
1 TTTT-TTTTG
*
161946 TTTCTGGTTT-
1 TTT-T-TTTTG
*
161956 TTTGTTTTG
1 TTTTTTTTG
*
161965 TTGTTTTTG
1 TTTTTTTTG
161974 TTTTTTTT-
1 TTTTTTTTG
161982 TTTTT
1 TTTTT
161987 GGGGTATGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
8 8 0.14
9 32 0.56
10 17 0.30
ACGTcount: A:0.00, C:0.03, G:0.14, T:0.83
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:161935 original size:23 final size:22
Alignment explanation
Indices: 161898--161985 Score: 88
Period size: 22 Copynumber: 3.9 Consensus size: 22
161888 CCCCTTTCTA
* * *
161898 TTTTTTTGCTATTTTTTCTTGG
1 TTTTTTTGTTTTTTTTTTTTGG
*
161920 TTTTTTTGTTTTTTTTGTTTTGT
1 TTTTTTTGTTTTTTTT-TTTTGG
* *
161943 TTTTTTCTGGTTTTTTGTTTT-G
1 TTTTTT-TGTTTTTTTTTTTTGG
161965 TTGTTTTTGTTTTTTTTTTTT
1 TT-TTTTTGTTTTTTTTTTTT
161986 TGGGGTATGA
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
22 28 0.52
23 18 0.33
24 8 0.15
ACGTcount: A:0.01, C:0.03, G:0.14, T:0.82
Consensus pattern (22 bp):
TTTTTTTGTTTTTTTTTTTTGG
Found at i:161940 original size:14 final size:14
Alignment explanation
Indices: 161923--161987 Score: 69
Period size: 16 Copynumber: 4.4 Consensus size: 14
161913 TTCTTGGTTT
161923 TTTTGTTTTTTTTG
1 TTTTGTTTTTTTTG
161937 TTTTGTTTTTTTCTGG
1 TTTTGTTTTTTT-T-G
161953 TTTT-TTGTTTTGTTG
1 TTTTGTT-TTTT-TTG
*
161968 TTTTTGTTTTTTTTT
1 -TTTTGTTTTTTTTG
161983 TTTTG
1 TTTTG
161988 GGGTATGAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
14 17 0.39
15 6 0.14
16 18 0.41
17 3 0.07
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (14 bp):
TTTTGTTTTTTTTG
Found at i:161979 original size:32 final size:33
Alignment explanation
Indices: 161900--161980 Score: 103
Period size: 32 Copynumber: 2.4 Consensus size: 33
161890 CCTTTCTATT
*
161900 TTTTTGCTATTTTTTCTTGGTTTTTTTGTTTTTTT
1 TTTTTG-T-TTTTTTCTTGGTTTTTTTGTTTTTTG
161935 TGTTTTGTTTTTTTC-TGG-TTTTTTGTTTTGTTG
1 T-TTTTGTTTTTTTCTTGGTTTTTTTGTTTT-TTG
161968 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
161981 TTTTTTGGGG
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
32 23 0.53
33 6 0.14
34 7 0.16
35 2 0.05
36 5 0.12
ACGTcount: A:0.01, C:0.04, G:0.15, T:0.80
Consensus pattern (33 bp):
TTTTTGTTTTTTTCTTGGTTTTTTTGTTTTTTG
Found at i:161986 original size:23 final size:22
Alignment explanation
Indices: 161919--161987 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 22
161909 TTTTTTCTTG
161919 GTTTTTTTGTTTTTTTTGTTTT
1 GTTTTTTTGTTTTTTTTGTTTT
* *
161941 GTTTTTTTCTGGTTTTTTGTTTT
1 GTTTTTTTGT-TTTTTTTGTTTT
*
161964 GTTGTTTTTGTTTTTTTTTTTTT
1 GTT-TTTTTGTTTTTTTTGTTTT
161987 G
1 G
161988 GGGTATGAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
22 9 0.22
23 25 0.62
24 6 0.15
ACGTcount: A:0.00, C:0.01, G:0.16, T:0.83
Consensus pattern (22 bp):
GTTTTTTTGTTTTTTTTGTTTT
Found at i:171373 original size:19 final size:19
Alignment explanation
Indices: 171349--171387 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
171339 AACAGTAAAT
*
171349 ATAAGTTTTGTATCGATAC
1 ATAAGTGTTGTATCGATAC
171368 ATAAGTGTTGTATCGATAC
1 ATAAGTGTTGTATCGATAC
171387 A
1 A
171388 ATGTATCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (19 bp):
ATAAGTGTTGTATCGATAC
Found at i:171442 original size:20 final size:20
Alignment explanation
Indices: 171417--171471 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
171407 CTGCCAAGGA
171417 AATGTATCGATACATT-ACTC
1 AATGTATCGATACATTGA-TC
171437 AATGTATCGATACATTGATC
1 AATGTATCGATACATTGATC
**
171457 TTTGTATCGATACAT
1 AATGTATCGATACAT
171472 GCAGGCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (20 bp):
AATGTATCGATACATTGATC
Found at i:179395 original size:20 final size:20
Alignment explanation
Indices: 179370--179443 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
179360 TTTTAACTAG
179370 ATGTATCGATACATT-AAAGA
1 ATGTATCGATACATTCAAA-A
* * *
179390 ATGTATCGAGACATTCATAC
1 ATGTATCGATACATTCAAAA
* *
179410 ATATATCGATACATTGAAAA
1 ATGTATCGATACATTCAAAA
*
179430 ATGAATCGATACAT
1 ATGTATCGATACAT
179444 CTGGTTACTT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATTCAAAA
Found at i:180281 original size:72 final size:72
Alignment explanation
Indices: 180174--180319 Score: 283
Period size: 72 Copynumber: 2.0 Consensus size: 72
180164 GGCATGTTCA
*
180174 ATCAAGCATTTTCATTCATGAAAATAAAAAAATAAACCATGTAAGAACATAATTTCATGAAAGCA
1 ATCAAGCATTTTCATTCATGAAAATAAAAAAATAAACCATGTAAGAAAATAATTTCATGAAAGCA
180239 TGAATTT
66 TGAATTT
180246 ATCAAGCATTTTCATTCATGAAAATAAAAAAATAAACCATGTAAGAAAATAATTTCATGAAAGCA
1 ATCAAGCATTTTCATTCATGAAAATAAAAAAATAAACCATGTAAGAAAATAATTTCATGAAAGCA
180311 TGAATTT
66 TGAATTT
180318 AT
1 AT
180320 TAATCATTCA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (72 bp):
ATCAAGCATTTTCATTCATGAAAATAAAAAAATAAACCATGTAAGAAAATAATTTCATGAAAGCA
TGAATTT
Found at i:180342 original size:72 final size:71
Alignment explanation
Indices: 180174--180343 Score: 216
Period size: 72 Copynumber: 2.4 Consensus size: 71
180164 GGCATGTTCA
** * *
180174 ATCAAGCATTTTCATTCATGAAAATAAAAAAATAAACCATGTAAGAACATAATTTCATGAAAGCA
1 ATCAAGCA-TTTCATAAATAAAAATAAAAAAATAAACCATGTAAGAAAATAATTTCATGAAAGCA
180239 TGAATTT
65 TGAATTT
** *
180246 ATCAAGCATTTTCATTCATGAAAATAAAAAAATAAACCATGTAAGAAAATAATTTCATGAAAGCA
1 ATCAAGCA-TTTCATAAATAAAAATAAAAAAATAAACCATGTAAGAAAATAATTTCATGAAAGCA
180311 TGAATTT
65 TGAATTT
* *
180318 ATTAATCA-TTCATGAAAATAAAAATA
1 ATCAAGCATTTCAT--AAATAAAAATA
180344 TTTAAGAAAT
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
70 5 0.06
72 85 0.94
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (71 bp):
ATCAAGCATTTCATAAATAAAAATAAAAAAATAAACCATGTAAGAAAATAATTTCATGAAAGCAT
GAATTT
Found at i:182004 original size:21 final size:21
Alignment explanation
Indices: 181979--182023 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
181969 CACTTGTAAC
*
181979 TCATTTCTTTTCTCCTCTAAT
1 TCATTTATTTTCTCCTCTAAT
**
182000 TCATTTATTTTCTTTTCTAAT
1 TCATTTATTTTCTCCTCTAAT
182021 TCA
1 TCA
182024 CTTAATTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.22, G:0.00, T:0.60
Consensus pattern (21 bp):
TCATTTATTTTCTCCTCTAAT
Found at i:182036 original size:21 final size:21
Alignment explanation
Indices: 181994--182037 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
181984 TCTTTTCTCC
* * *
181994 TCTAATTCATTTATTTTCTTT
1 TCTAATTCACTTAATTTATTT
182015 TCTAATTCACTTAATTTATTT
1 TCTAATTCACTTAATTTATTT
182036 TC
1 TC
182038 AAGAATATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (21 bp):
TCTAATTCACTTAATTTATTT
Found at i:183684 original size:36 final size:35
Alignment explanation
Indices: 183602--183699 Score: 109
Period size: 36 Copynumber: 2.9 Consensus size: 35
183592 CCTTACAACA
*
183602 CTATC-TTTC-AAGACTAAGATAGAAACCTC-CT--
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCC
* *
183633 -TATCTTTTCACAGGCTAAGATAGAGCCTCTCTCC
1 CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCC
183667 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
183700 AATCACTTAG
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
30 4 0.07
31 9 0.16
32 13 0.24
35 4 0.07
36 25 0.45
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.32
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCC
Found at i:184954 original size:18 final size:18
Alignment explanation
Indices: 184931--184966 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
184921 CAAAAGCTAG
*
184931 CTTGGTGTTTGTTGCTTT
1 CTTGGTGTTAGTTGCTTT
184949 CTTGGTGTTAGTTGCTTT
1 CTTGGTGTTAGTTGCTTT
184967 TCTTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.03, C:0.11, G:0.28, T:0.58
Consensus pattern (18 bp):
CTTGGTGTTAGTTGCTTT
Found at i:185009 original size:24 final size:24
Alignment explanation
Indices: 184964--185010 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
184954 TGTTAGTTGC
* *
184964 TTTTCTTTTTCTTTTTTGGTTGTG
1 TTTTCTTTTTATTTCTTGGTTGTG
184988 TTTTCTTCTTTATTTCTT-GTTGT
1 TTTTCTT-TTTATTTCTTGGTTGT
185011 TTCATTTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.02, C:0.11, G:0.13, T:0.74
Consensus pattern (24 bp):
TTTTCTTTTTATTTCTTGGTTGTG
Found at i:188520 original size:14 final size:13
Alignment explanation
Indices: 188501--188531 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
188491 ATTCTTCTTA
188501 TTTTCCATTTTTGT
1 TTTTCCATTTTT-T
188515 TTTTCCATTTTTT
1 TTTTCCATTTTTT
188528 TTTT
1 TTTT
188532 GCTGTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.06, C:0.13, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTTCCATTTTTT
Found at i:189420 original size:37 final size:38
Alignment explanation
Indices: 189335--189436 Score: 102
Period size: 37 Copynumber: 2.7 Consensus size: 38
189325 TAAATTAGTA
* *
189335 TTTCAAAATTCTTTTTGTTTCTTG-AGTTTTTCATTTTTCT
1 TTTC-AAA-TCTTTTTGTTT-TCGAAATTTTTCATTTTTCT
* *
189375 TGTGAAATCTTTTTGTTTTCGAAATTTTTC-TTTTTCT
1 TTTCAAATCTTTTTGTTTTCGAAATTTTTCATTTTTCT
*
189412 TTTCAAATCCTCTTT-TTTTCGAAAT
1 TTTCAAAT-CTTTTTGTTTTCGAAAT
189437 ACAAAGTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
37 25 0.47
38 23 0.43
39 3 0.06
40 2 0.04
ACGTcount: A:0.18, C:0.14, G:0.08, T:0.61
Consensus pattern (38 bp):
TTTCAAATCTTTTTGTTTTCGAAATTTTTCATTTTTCT
Found at i:194748 original size:51 final size:49
Alignment explanation
Indices: 194704--194809 Score: 124
Period size: 49 Copynumber: 2.1 Consensus size: 49
194694 TACATTGAAA
*
194704 AATGTGTCAATAAATTTAGGTCAAAACCTAGAATGTATAGATACAATAAAT
1 AATGTATCAATAAATTTAGGT-AAAACC-AGAATGTATAGATACAATAAAT
* * * * * *
194755 AATGTATCGATATATTTGGGTAAATCCAGAATGTATCGATACAATAGA-
1 AATGTATCAATAAATTTAGGTAAAACCAGAATGTATAGATACAATAAAT
194803 AATGTAT
1 AATGTAT
194810 AGATACATTC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
48 7 0.15
49 19 0.40
50 5 0.10
51 17 0.35
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.31
Consensus pattern (49 bp):
AATGTATCAATAAATTTAGGTAAAACCAGAATGTATAGATACAATAAAT
Found at i:196640 original size:12 final size:12
Alignment explanation
Indices: 196623--196653 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
196613 CTTGGCAAGT
196623 GAGAAAAAAAGA
1 GAGAAAAAAAGA
196635 GAGAAAAAAAGA
1 GAGAAAAAAAGA
196647 GAAGAAA
1 G-AGAAA
196654 GGAAATAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
GAGAAAAAAAGA
Found at i:197125 original size:21 final size:21
Alignment explanation
Indices: 197100--197146 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
197090 CCCCTTGCTA
197100 TTTTGAGT-TGATTTGAAGGAT
1 TTTTGAGTGTGATTTG-AGGAT
* *
197121 TTTTG-GTGTGTTTTGATGAT
1 TTTTGAGTGTGATTTGAGGAT
197141 TTTTGA
1 TTTTGA
197147 TTAGTAGGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.55
Consensus pattern (21 bp):
TTTTGAGTGTGATTTGAGGAT
Found at i:197733 original size:142 final size:143
Alignment explanation
Indices: 197571--197877 Score: 349
Period size: 142 Copynumber: 2.2 Consensus size: 143
197561 TTTTCTTATT
* * *
197571 TTTTTCAATATTTCTAATATTCCT-ATGCTTAAACGT-AGGGGTCT-AGAAATTTTCAAAA-TGT
1 TTTTTCAAGATTTCTAATATTCCTCATGCGTAAACGTGA-GGGTATGA-AAATTTTCAAAACT-T
197632 TTCATATCTTTTTGGTTCTCCATTAAGGTACGAAATGAAGT-TTTTGAGAAATAAAAAATTAAAT
63 TTCATATCTTTTTGGTTCTCCATTAAGGTACGAAATGAAGTCTTTTGA-AAATAAAAAATTAAAT
* * *
197696 GAAAATTATTATCTCAA
127 AAAAATTACTACCTCAA
* * * *** *
197713 TTTTTC-AGAATTTCTAATATT-TTCGTGGGTATTTGTGAGGGTATGAAAATTTTTAAAACTTTT
1 TTTTTCAAG-ATTTCTAATATTCCTCATGCGTAAACGTGAGGGTATGAAAATTTTCAAAACTTTT
** * * *
197776 TGTATCTTTTTGGTTCTCCATTAAGGTACGAAATGAATTCTTTTGAAATTAAAAATTTAAATAAA
65 CATATCTTTTTGGTTCTCCATTAAGGTACGAAATGAAGTCTTTTGAAAATAAAAAATTAAATAAA
*
197841 AATTACTACCTTAA
130 AATTACTACCTCAA
197855 TTTTTCAAGATTTCTAATATTCC
1 TTTTTCAAGATTTCTAATATTCC
197878 AATGGTTTTC
Statistics
Matches: 137, Mismatches: 20, Indels: 15
0.80 0.12 0.09
Matches are distributed among these distances:
141 2 0.01
142 124 0.91
143 11 0.08
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.43
Consensus pattern (143 bp):
TTTTTCAAGATTTCTAATATTCCTCATGCGTAAACGTGAGGGTATGAAAATTTTCAAAACTTTTC
ATATCTTTTTGGTTCTCCATTAAGGTACGAAATGAAGTCTTTTGAAAATAAAAAATTAAATAAAA
ATTACTACCTCAA
Found at i:197896 original size:142 final size:142
Alignment explanation
Indices: 197609--197923 Score: 390
Period size: 142 Copynumber: 2.2 Consensus size: 142
197599 TTAAACGTAG
* *
197609 GGGTCTAGAAATTTTCAAAA-TGTTTCATATCTTTTTGGTTCTCCATTAAGGTACGAAATGAAGT
1 GGGTATAGAAATTTTCAAAACT-TTTCGTATCTTTTTGGTTCTCCATTAAGGTACGAAATGAAGT
* * * * *
197673 TTTTGAGAAATAAAAAATTAAATGAAAATTATTATCTCAATTTTTCAGAATTTCTAATATTTTCG
65 TTTTGAGAAATAAAAAATTAAATAAAAATTACTACCTCAATTTTTCAGAATTTCTAATATTTCCA
* *
197738 TGGGTATTTGTGA
130 TGGGTATTTATAA
* * *
197751 GGGTAT-GAAAATTTTTAAAACTTTTTGTATCTTTTTGGTTCTCCATTAAGGTACGAAATGAATT
1 GGGTATAG-AAATTTTCAAAACTTTTCGTATCTTTTTGGTTCTCCATTAAGGTACGAAATGAAGT
* * *
197815 CTTTTGA-AATTAAAAATTTAAATAAAAATTACTACCTTAATTTTTCA-AGATTTCTAATA-TTC
65 -TTTTGAGAAATAAAAAATTAAATAAAAATTACTACCTCAATTTTTCAGA-ATTTCTAATATTTC
*
197877 CAAT-GGTTTTCTATAA
128 C-ATGGGTATT-TATAA
197893 GGGTATAGAAATTTTCAAAACTTTTCGTATC
1 GGGTATAGAAATTTTCAAAACTTTTCGTATC
197924 CCTTGATTTT
Statistics
Matches: 148, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
141 10 0.07
142 130 0.88
143 8 0.05
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.42
Consensus pattern (142 bp):
GGGTATAGAAATTTTCAAAACTTTTCGTATCTTTTTGGTTCTCCATTAAGGTACGAAATGAAGTT
TTTGAGAAATAAAAAATTAAATAAAAATTACTACCTCAATTTTTCAGAATTTCTAATATTTCCAT
GGGTATTTATAA
Found at i:198467 original size:148 final size:149
Alignment explanation
Indices: 198241--198510 Score: 427
Period size: 148 Copynumber: 1.8 Consensus size: 149
198231 TGGTGGTAGG
* *
198241 CCTTAGAGACCTTTTAGCCTTTTTCTTGAAACCTAGTCCTATAAAACTACCGGGTCTGCTATTAT
1 CCTTAGAGACCTTTTAGCCTTTTTCTCGAAACCTAGTCCTATAAAACTACCGGGTCTACTATTAT
* **
198306 GCTGAAGGTATGAATTAGGAGTAGGTTT-TTTTCATCTTCTTAAGTCCTCTAGGATCATCGGGTA
66 GCCGAAGGTATGAATTAGGAGTACATTTGTTTTCATCTTCTTAAGTCCTCTAGGATCATCGGGTA
198370 CTTCTTAGTCGATGGTGGA
131 CTTCTTAGTCGATGGTGGA
* *
198389 CCTTAGGGACCTTTTAGCCTTTTTCTCGAAACCTAGTCCTATAAAACTATCGGGTCTACT-TCTA
1 CCTTAGAGACCTTTTAGCCTTTTTCTCGAAACCTAGTCCTATAAAACTACCGGGTCTACTAT-TA
* * *
198453 TGCCGAAGGTATGAATTAGGAGTACATTTGTTTTCATCTTTTTAAGTCTTTTAGGATC
65 TGCCGAAGGTATGAATTAGGAGTACATTTGTTTTCATCTTCTTAAGTCCTCTAGGATC
198511 TCCAGCCACT
Statistics
Matches: 110, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
147 1 0.01
148 84 0.76
149 25 0.23
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (149 bp):
CCTTAGAGACCTTTTAGCCTTTTTCTCGAAACCTAGTCCTATAAAACTACCGGGTCTACTATTAT
GCCGAAGGTATGAATTAGGAGTACATTTGTTTTCATCTTCTTAAGTCCTCTAGGATCATCGGGTA
CTTCTTAGTCGATGGTGGA
Found at i:208760 original size:13 final size:13
Alignment explanation
Indices: 208742--208781 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
208732 ACAATGTTCT
*
208742 TTGTATCAATACA
1 TTGTATCGATACA
*
208755 TTGTATCGATATA
1 TTGTATCGATACA
*
208768 ATGTATCGATACA
1 TTGTATCGATACA
208781 T
1 T
208782 GGGTTACTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:210262 original size:28 final size:28
Alignment explanation
Indices: 210222--210293 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
210212 TGGTCTGAGA
*
210222 GTTGATCACTTCACTTTCGCAGCGCATG
1 GTTGAGCACTTCACTTTCGCAGCGCATG
*
210250 GTTGAGCACTTCACTTTTGCAGCGCATG
1 GTTGAGCACTTCACTTTCGCAGCGCATG
* *
210278 GATGAGCACTTTACTT
1 GTTGAGCACTTCACTT
210294 CACTTAACTG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.33
Consensus pattern (28 bp):
GTTGAGCACTTCACTTTCGCAGCGCATG
Found at i:211286 original size:19 final size:18
Alignment explanation
Indices: 211214--211285 Score: 81
Period size: 20 Copynumber: 3.7 Consensus size: 18
211204 AACCCATGTA
*
211214 TGTATCGATACACTTTCAGA
1 TGTATCGATACA-TTTCA-T
*
211234 TGTATCGATACATTATGCTT
1 TGTATCGATACATT-T-CAT
211254 TGTATCGATACATGTTCAT
1 TGTATCGATACAT-TTCAT
211273 TGTATCGATACAT
1 TGTATCGATACAT
211286 GAACAAATGT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
19 17 0.37
20 27 0.59
21 2 0.04
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (18 bp):
TGTATCGATACATTTCAT
Found at i:211361 original size:20 final size:20
Alignment explanation
Indices: 211335--211388 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
211325 CTACCACTCT
*
211335 TTGTATCGATACATGGCACAA
1 TTGTATCGATACAT-GAACAA
*
211356 -TGTATCGATACATGAAGAA
1 TTGTATCGATACATGAACAA
211375 TTGTATCGATACAT
1 TTGTATCGATACAT
211389 TGCCTCAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 4 0.13
20 26 0.87
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (20 bp):
TTGTATCGATACATGAACAA
Found at i:213241 original size:12 final size:12
Alignment explanation
Indices: 213224--213249 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
213214 CTTATTTTGC
213224 TTTCTTTCTTGT
1 TTTCTTTCTTGT
213236 TTTCTTTCTTGT
1 TTTCTTTCTTGT
213248 TT
1 TT
213250 ATTTCTTTAT
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:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (12 bp):
TTTCTTTCTTGT
Found at i:213244 original size:16 final size:17
Alignment explanation
Indices: 213213--213245 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
213203 TAGGTAATCA
213213 TCTTATTTTGCTTTCTT
1 TCTTATTTTGCTTTCTT
*
213230 TCTTGTTTT-CTTTCTT
1 TCTTATTTTGCTTTCTT
213246 GTTTATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.03, C:0.18, G:0.06, T:0.73
Consensus pattern (17 bp):
TCTTATTTTGCTTTCTT
Found at i:216452 original size:34 final size:34
Alignment explanation
Indices: 216381--216444 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
216371 GTGTTTGTGA
216381 AAAGAATAAGCACAAAGGAATACAAATGAGCTTTG
1 AAAGAATAAGCACAAAGGAATACAAA-GAGCTTTG
216416 AAAGAATAA-CAACAAA-GAATACAAA-AGCT
1 AAAGAATAAGC-ACAAAGGAATACAAAGAGCT
216445 CTATGAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 4 0.14
34 10 0.36
35 14 0.50
ACGTcount: A:0.58, C:0.12, G:0.16, T:0.14
Consensus pattern (34 bp):
AAAGAATAAGCACAAAGGAATACAAAGAGCTTTG
Found at i:216732 original size:20 final size:20
Alignment explanation
Indices: 216718--216756 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
216708 TGATACATTT
216718 CACCATGTATCGATACAATC
1 CACCATGTATCGATACAATC
**
216738 CTTCATGTATCGATACAAT
1 CACCATGTATCGATACAAT
216757 GTGATCTTTA
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:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (20 bp):
CACCATGTATCGATACAATC
Found at i:217494 original size:16 final size:17
Alignment explanation
Indices: 217473--217515 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 17
217463 AATTTTTAAT
217473 ATAAAATTCT-CCCTTA
1 ATAAAATTCTCCCCTTA
217489 ATAAAATTTTCTCCCCCTTA
1 ATAAAA--TTCT-CCCCTTA
217509 ATAAAAT
1 ATAAAAT
217516 ATTTAATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 6 0.26
18 5 0.22
20 12 0.52
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAAAATTCTCCCCTTA
Found at i:217500 original size:18 final size:19
Alignment explanation
Indices: 217479--217515 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
217469 TAATATAAAA
217479 TTCT-CCCTTAATAAAATT
1 TTCTCCCCTTAATAAAATT
217497 TTCTCCCCCTTAATAAAAT
1 TTCT-CCCCTTAATAAAAT
217516 ATTTAATGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
20 13 0.76
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.41
Consensus pattern (19 bp):
TTCTCCCCTTAATAAAATT
Found at i:226624 original size:155 final size:155
Alignment explanation
Indices: 226342--226652 Score: 622
Period size: 155 Copynumber: 2.0 Consensus size: 155
226332 TTTAGGGTAC
226342 CACAATCCTAAGTTGGGAATGTCTCGTAAGTACTTAAAGATTCTCTTTACGGCAAGTAAGTGAGA
1 CACAATCCTAAGTTGGGAATGTCTCGTAAGTACTTAAAGATTCTCTTTACGGCAAGTAAGTGAGA
226407 CTCCTTTGATGAGGATTGGAAACAGGCACAAAGGCAAAAACTAAACATAATATCTGGTCTGTTAG
66 CTCCTTTGATGAGGATTGGAAACAGGCACAAAGGCAAAAACTAAACATAATATCTGGTCTGTTAG
226472 CAGTAAGATATAAAAAAGAACCTAT
131 CAGTAAGATATAAAAAAGAACCTAT
226497 CACAATCCTAAGTTGGGAATGTCTCGTAAGTACTTAAAGATTCTCTTTACGGCAAGTAAGTGAGA
1 CACAATCCTAAGTTGGGAATGTCTCGTAAGTACTTAAAGATTCTCTTTACGGCAAGTAAGTGAGA
226562 CTCCTTTGATGAGGATTGGAAACAGGCACAAAGGCAAAAACTAAACATAATATCTGGTCTGTTAG
66 CTCCTTTGATGAGGATTGGAAACAGGCACAAAGGCAAAAACTAAACATAATATCTGGTCTGTTAG
226627 CAGTAAGATATAAAAAAGAACCTAT
131 CAGTAAGATATAAAAAAGAACCTAT
226652 C
1 C
226653 GTAGACCTAT
Statistics
Matches: 156, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
155 156 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (155 bp):
CACAATCCTAAGTTGGGAATGTCTCGTAAGTACTTAAAGATTCTCTTTACGGCAAGTAAGTGAGA
CTCCTTTGATGAGGATTGGAAACAGGCACAAAGGCAAAAACTAAACATAATATCTGGTCTGTTAG
CAGTAAGATATAAAAAAGAACCTAT
Found at i:229689 original size:93 final size:92
Alignment explanation
Indices: 229570--229737 Score: 210
Period size: 93 Copynumber: 1.8 Consensus size: 92
229560 TGGCTGTATC
* * * * *
229570 GAAGACTTATTTTGAAATTTTCTTAAATGTTTTAGATCCCACCACCAATTATCATTTTGTAAAAG
1 GAAGACTTATTTTGAAACTTTCTTAAATGCTTTAGATACCACCACCAATAACCATTTTGTAAAAG
*
229635 TCTTTAAATGCTTCAAATGCCTCCATT
66 TCTCTAAATGCTTCAAATGCCTCCATT
* * * * ***
229662 GAAGATTTTTTTTGAAAACTTTCTTAAATGCTTTGGATATCACCATTGATAACCATTTTGTAAAA
1 GAAGACTTATTTTG-AAACTTTCTTAAATGCTTTAGATACCACCACCAATAACCATTTTGTAAAA
229727 GTCTCTAAATG
65 GTCTCTAAATG
229738 TTTTGGATAC
Statistics
Matches: 62, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
92 12 0.19
93 50 0.81
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.40
Consensus pattern (92 bp):
GAAGACTTATTTTGAAACTTTCTTAAATGCTTTAGATACCACCACCAATAACCATTTTGTAAAAG
TCTCTAAATGCTTCAAATGCCTCCATT
Found at i:229739 original size:185 final size:186
Alignment explanation
Indices: 229387--229877 Score: 476
Period size: 186 Copynumber: 2.6 Consensus size: 186
229377 CATCGCTGAT
* * * * * *
229387 GACTTGTTTTGACAGTTTTCTTAACTGTTATGGATTTCACCACCAATGATCATTTTGTAAAAATC
1 GACTTATTTTGACAATTTTCTTAAATGTTTTAGATTCCACCACCAATGATCATTTTGTAAAAATC
* * *** ** * *
229452 CTTAAATGTTTTGGATGTTTCCATTGAAAACTTGTTTTGAAAATTTTCTTGAAA--ATTTGGATT
66 TTTAAATGCTTCAAATGCCTCCATTG-AAATTTTTTTTGAAAATTTTCTT-AAATGATTTGGATT
* ** * ** * *
229515 CAACCATTGATGATTATTTTGAAAAAATCTTTAAAATGTTTTAGATGGCTGTATCGAA
129 CAACCATTGATAACCATTTTGAAAAAATCTCTAAAATGTTTTAGATACCTGTACCAAA
* * *
229573 GACTTATTTTGA-AATTTTCTTAAATGTTTTAGATCCCACCACCAATTATCATTTTGTAAAAGTC
1 GACTTATTTTGACAATTTTCTTAAATGTTTTAGATTCCACCACCAATGATCATTTTGTAAAAATC
* *
229637 TTTAAATGCTTCAAATGCCTCCATTGAAGATTTTTTTTGAAAACTTTCTTAAATGCTTTGGATAT
66 TTTAAATGCTTCAAATGCCTCCATTGAA-ATTTTTTTTGAAAATTTTCTTAAATGATTTGGAT-T
* * * *
229702 C-ACCATTGATAACCATTTTGTAAAAGTCTCT-AAATGTTTTGGATACCTTTACCAAA
129 CAACCATTGATAACCATTTTGAAAAAATCTCTAAAATGTTTTAGATACCTGTACCAAA
* * * * ***
229758 GACTTATTTTGAGAATTTT-TTGAAATGCTTCAGATTCTACCACTGGTGATCATTTTGTAAAAAT
1 GACTTATTTTGACAATTTTCTT-AAATGTTTTAGATTCCACCACCAATGATCATTTTGTAAAAAT
* * *
229822 ATTTAAATGC-TCTAAATGCCTCTATTGAAAGTTTGTTTTT-AAAATTTTATTAAATG
65 CTTTAAATGCTTC-AAATGCCTCCATTGAAA-TTT-TTTTTGAAAATTTTCTTAAATG
229878 TCTCAAATTT
Statistics
Matches: 251, Mismatches: 45, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
184 5 0.02
185 117 0.47
186 122 0.49
187 7 0.03
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (186 bp):
GACTTATTTTGACAATTTTCTTAAATGTTTTAGATTCCACCACCAATGATCATTTTGTAAAAATC
TTTAAATGCTTCAAATGCCTCCATTGAAATTTTTTTTGAAAATTTTCTTAAATGATTTGGATTCA
ACCATTGATAACCATTTTGAAAAAATCTCTAAAATGTTTTAGATACCTGTACCAAA
Found at i:234144 original size:13 final size:13
Alignment explanation
Indices: 234126--234151 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
234116 CAATTTTTGG
234126 TGTATCGATACAT
1 TGTATCGATACAT
234139 TGTATCGATACAT
1 TGTATCGATACAT
234152 ACTTGGTGTA
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:234163 original size:32 final size:33
Alignment explanation
Indices: 234106--234169 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
234096 TACAAGCCAA
**
234106 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
234139 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
234170 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:234176 original size:19 final size:18
Alignment explanation
Indices: 234106--234176 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
234096 TACAAGCCAA
234106 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
234126 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
234139 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
234158 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
234177 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:234891 original size:21 final size:21
Alignment explanation
Indices: 234850--234893 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
234840 CTCCCCTTTA
* *
234850 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
234871 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
234892 TC
1 TC
234894 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:236714 original size:13 final size:13
Alignment explanation
Indices: 236696--236721 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
236686 ATAATCACCC
236696 TGTATCGATACAA
1 TGTATCGATACAA
236709 TGTATCGATACAA
1 TGTATCGATACAA
236722 AGAAAAATGT
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):
TGTATCGATACAA
Found at i:238820 original size:15 final size:15
Alignment explanation
Indices: 238800--238830 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
238790 ATTTCGTTTG
*
238800 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
238815 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
238830 G
1 G
238831 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:240661 original size:21 final size:21
Alignment explanation
Indices: 240632--240676 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
240622 AAGTTTTCAT
*
240632 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
240652 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
240674 TTT
1 TTT
240677 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:242911 original size:20 final size:20
Alignment explanation
Indices: 242886--242937 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
242876 TACAAGCGAA
**
242886 TGTATCGATACAATTTTTGG
1 TGTATCGATACAATACTTGG
242906 TGTATCGATAC-ATACTTGG
1 TGTATCGATACAATACTTGG
242925 TGTATCGATACAA
1 TGTATCGATACAA
242938 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.38
Consensus pattern (20 bp):
TGTATCGATACAATACTTGG
Found at i:242943 original size:19 final size:18
Alignment explanation
Indices: 242886--242943 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 18
242876 TACAAGCGAA
242886 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
*
242906 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
242925 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
242944 CTACTGCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 1 0.03
19 20 0.59
20 12 0.35
21 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:245600 original size:166 final size:166
Alignment explanation
Indices: 245378--245677 Score: 435
Period size: 166 Copynumber: 1.8 Consensus size: 166
245368 CACCAAATGT
* * *
245378 TAAATCAGTTTTGAAATAATCATTTTATTTCATAAGTTTTTCATTTTTTTCTTGAAATTCTCTTG
1 TAAATCAGTTTTGAAAGAATCATTATATTTCATAAGTTTTTCATTTTTTCCTTGAAATTCTCTTG
* * *
245443 TTTCTGAAATACTAAGTTTTCTATTCCATAAATATTTTCGGGAGAGTTTTTCTC-GATTCAAAAT
66 TTTCTGAAAAACTAAGTTTTCTAATCCATAAATATTTTCGGGAGAATTTTTCTCAG-TTCAAAAT
245507 TTTTAATATTCTTTAAATATCATCACTTAAATCATAG
130 TTTTAATATTCTTTAAATATCATCACTTAAATCATAG
* *
245544 TAAATCAGTTTTGAAAGATTCATCTAT-TTTCATGAGTTTTT-ATTTTTTCCCTTGAAATTCTCT
1 TAAATCAGTTTTGAAAGAATCAT-TATATTTCATAAGTTTTTCATTTTTT-CCTTGAAATTCTCT
* * * * *
245607 TGTTTTTGAAAAACTGAGTTTTTTAATCTATAAATATTTTCGGGAGAATTTTTCTCAGTTTAAAA
64 TGTTTCTGAAAAACTAAGTTTTCTAATCCATAAATATTTTCGGGAGAATTTTTCTCAGTTCAAAA
245672 TTTTTA
129 TTTTTA
245678 GAATTCATCT
Statistics
Matches: 118, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
165 7 0.06
166 108 0.92
167 3 0.03
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.49
Consensus pattern (166 bp):
TAAATCAGTTTTGAAAGAATCATTATATTTCATAAGTTTTTCATTTTTTCCTTGAAATTCTCTTG
TTTCTGAAAAACTAAGTTTTCTAATCCATAAATATTTTCGGGAGAATTTTTCTCAGTTCAAAATT
TTTAATATTCTTTAAATATCATCACTTAAATCATAG
Found at i:245747 original size:166 final size:164
Alignment explanation
Indices: 245401--245758 Score: 373
Period size: 166 Copynumber: 2.2 Consensus size: 164
245391 AAATAATCAT
* * *
245401 TTTATTTCATAAGTTTTTCATTTTTTTCTTGAAATTCTCTTGTTTCTGAAATACTAAGTTTTCTA
1 TTTATTTCATGAGTTTTT-ATTTTTTCCTTGAAATTCTCTTGTTTCTGAAAAACTAAGTTTTCTA
* * *
245466 TTCCATAAATATTTTCGGGAGAGTTTTTCTCGATTCAAAATTTTTAATATTCTTTAAATATCATC
65 ATCCATAAATATTTTCGGGAGAATTTTTCTCGATTCAAAATTTTTAATATTCTCTAAATATCATC
* * ** * *
245531 ACTTAAATCATAGTAAATCAGTTTTGAAAGATTCA
130 ACTTAAATCACAGTAAATCACTTTCAAAAAATTAA
* * * *
245566 TCTATTTTCATGAGTTTTTATTTTTTCCCTTGAAATTCTCTTGTTTTTGAAAAACTGAGTTTTTT
1 TTTA-TTTCATGAGTTTTTATTTTTT-CCTTGAAATTCTCTTGTTTCTGAAAAACTAAGTTTTCT
* *
245631 AATCTATAAATATTTTCGGGAGAATTTTTCTC-AGTTTAAAATTTTTAGA-ATTCATCT-AATAT
64 AATCCATAAATATTTTCGGGAGAATTTTTCTCGA-TTCAAAATTTTTA-ATATTC-TCTAAATAT
** * * * *
245693 TGTCA-TTGAATTCCCATTAAATTACTTTCAAAAAATTTAA
126 CATCACTT-AAATCACAGTAAATCACTTTCAAAAAA-TTAA
* *
245733 TTTATTTAATGAGTTTTGAATTTTTT
1 TTTATTTCATGAGTTTT-TATTTTTT
245759 TGTATTTATT
Statistics
Matches: 158, Mismatches: 27, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
165 13 0.08
166 129 0.82
167 16 0.10
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.49
Consensus pattern (164 bp):
TTTATTTCATGAGTTTTTATTTTTTCCTTGAAATTCTCTTGTTTCTGAAAAACTAAGTTTTCTAA
TCCATAAATATTTTCGGGAGAATTTTTCTCGATTCAAAATTTTTAATATTCTCTAAATATCATCA
CTTAAATCACAGTAAATCACTTTCAAAAAATTAA
Found at i:246271 original size:13 final size:13
Alignment explanation
Indices: 246251--246298 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
246241 TTTGGCAAGT
246251 GAGAAAAAAAAGA
1 GAGAAAAAAAAGA
*
246264 GTGAAAAAAAAGA
1 GAGAAAAAAAAGA
*
246277 AAGAAAAAAAAGA
1 GAGAAAAAAAAGA
246290 GAGAAAAAA
1 GAGAAAAAA
246299 GAAAAACCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (13 bp):
GAGAAAAAAAAGA
Found at i:246296 original size:24 final size:25
Alignment explanation
Indices: 246252--246302 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 25
246242 TTGGCAAGTG
246252 AGAAAAAAAAGAGTGAAAAAAAAGAA
1 AGAAAAAAAAGAG-GAAAAAAAAGAA
*
246278 AGAAAAAAAAGA-GAGAAAAAAGAA
1 AGAAAAAAAAGAGGAAAAAAAAGAA
246302 A
1 A
246303 AACCTAGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 12 0.50
26 12 0.50
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (25 bp):
AGAAAAAAAAGAGGAAAAAAAAGAA
Found at i:249794 original size:12 final size:12
Alignment explanation
Indices: 249777--249811 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
249767 ATATTATACA
*
249777 TACATACACTTG
1 TACATACACATG
249789 TACATACACATG
1 TACATACACATG
*
249801 TACATGCACAT
1 TACATACACAT
249812 ACACTCCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.09, T:0.29
Consensus pattern (12 bp):
TACATACACATG
Found at i:251233 original size:311 final size:311
Alignment explanation
Indices: 250665--251888 Score: 2148
Period size: 311 Copynumber: 3.9 Consensus size: 311
250655 TGGTACAACA
*
250665 ATCTAAATCGCTCATAAATCAAATGTTGGGCTGACTTGGCAAGTGCTTTTCTCCAGCAATACAAG
1 ATCTGAATCGCTCATAAATCAAATGTTGGGCTGACTTGGCAAGTGCTTTTCTCCAGCAATACAAG
* *
250730 AATATGGCAGAATGGGTACCCAACAGGTTGACCTTCTAAAATTTAGG-GAAAAAGTCAACCGAAT
66 AATATGGCAGAGTGGGTACCCAACAGGTTGACCCTCTAAAATTT-GGAGAAAAAGTCAACCGAAT
*
250794 CTTTCAAAGAATATGCTTAACGATGAAGAGACCCAACTTCTCAAGTCCAACTGCCCTTGACTGAG
130 CTTTCAAAGAATATGCTTAACGATGAAGAGACCCAACTTCTCAGGTCCAACTGCCCTTGACTGAG
250859 AAGGAGATGATGATGTTATTCATGAATACTCTGCATCCACCCTATTATGACAAGTTAGTAGGGAA
195 AAGGAGATGATGATGTTATTCATGAATACTCTGCATCCACCCTATTATGACAAGTTAGTAGGGAA
*
250924 TGCGACAAAGAATTTTTTCGATCTTGTAATCTTTGAAGAAGGAGAATTTATG
260 TGCGACAAAGAATTTTTTCGATCTTGTAATCTTTGGAGAAGGAGAATTTATG
* ** *
250976 ATCTGAATCGCTCATAAATCAAATGTTAGGCTGTTTTGGCAAGTGCTTTTCTCCAGTAATACAAG
1 ATCTGAATCGCTCATAAATCAAATGTTGGGCTGACTTGGCAAGTGCTTTTCTCCAGCAATACAAG
*
251041 AATATGGCAGAGTGGGTAACCAACAGGTTGACCCTCTAAAATTTGGAGAAAAAGTCAACCGAATC
66 AATATGGCAGAGTGGGTACCCAACAGGTTGACCCTCTAAAATTTGGAGAAAAAGTCAACCGAATC
*
251106 TTTCAAAGAATATGCTTAACGATGAA-AGGACCCAACTTCTTAGGTCCAACTGCCCTTGACTGAG
131 TTTCAAAGAATATGCTTAACGATGAAGA-GACCCAACTTCTCAGGTCCAACTGCCCTTGACTGAG
**
251170 AAGGAGATGATGATGTTATTTGTGAATACTCTGCATCCACCCTATTATGACAAGTTAGTAGGGAA
195 AAGGAGATGATGATGTTATTCATGAATACTCTGCATCCACCCTATTATGACAAGTTAGTAGGGAA
251235 TGCGACAAAGAATTTTTTCGATCTTGTAATCTTTGGAGAAGGAGAATTTATG
260 TGCGACAAAGAATTTTTTCGATCTTGTAATCTTTGGAGAAGGAGAATTTATG
251287 ATCTGAATCGCTCATAAATCAAATGTTGGGCTGACTTGGCAAGTGCTTTTCTCCAGCAATACAAG
1 ATCTGAATCGCTCATAAATCAAATGTTGGGCTGACTTGGCAAGTGCTTTTCTCCAGCAATACAAG
* *
251352 AATATGGCGGAGTGGGTACCCAACAGGTTGACCCTCTAAAATTTGGAGAAAAAGTTAACCGAATC
66 AATATGGCAGAGTGGGTACCCAACAGGTTGACCCTCTAAAATTTGGAGAAAAAGTCAACCGAATC
* *
251417 TTTCAAAGAATATGCTTAACGATGATGTGACCCAACTTCTCAGGTCCAACTGCCCTTGACTGAGA
131 TTTCAAAGAATATGCTTAACGATGAAGAGACCCAACTTCTCAGGTCCAACTGCCCTTGACTGAGA
251482 AGGAGATGATGATGTTATTCATGAATACTCTGCATCCACCCTATTATGACAAGTTAGTAGGGAAT
196 AGGAGATGATGATGTTATTCATGAATACTCTGCATCCACCCTATTATGACAAGTTAGTAGGGAAT
*
251547 GCGACAAAGAATTTTTTCGATCTTGTAATCTCTGGAGAAGGAGAATTTATG
261 GCGACAAAGAATTTTTTCGATCTTGTAATCTTTGGAGAAGGAGAATTTATG
*
251598 ATTTGAATCGCTCATAAATCAAATGTTGGGCTGACTTGGCAAGTGCTTTTCTCCAGCAATACAAG
1 ATCTGAATCGCTCATAAATCAAATGTTGGGCTGACTTGGCAAGTGCTTTTCTCCAGCAATACAAG
* * * *
251663 AATATGGC-GAAGTTGGTACCCAATAGGTTGACCCTCTAAAATTTGGAGAAAAAGTTAACTGAAT
66 AATATGGCAG-AGTGGGTACCCAACAGGTTGACCCTCTAAAATTTGGAGAAAAAGTCAACCGAAT
* *
251727 CTTTCAAAGAATATGCTTAACGATGAAGGGACCCAACTTCTCAGGTCCAACTGCCCTTGATTGAG
130 CTTTCAAAGAATATGCTTAACGATGAAGAGACCCAACTTCTCAGGTCCAACTGCCCTTGACTGAG
*
251792 AAGGAGATGATGATGTTATTCGTGAATACTCTGCATCCACCCTATTATGACAAGTTAGTAGGGAA
195 AAGGAGATGATGATGTTATTCATGAATACTCTGCATCCACCCTATTATGACAAGTTAGTAGGGAA
* *
251857 TGCGACAAAGAATTTTTTTGTTCTTGTAATCT
260 TGCGACAAAGAATTTTTTCGATCTTGTAATCT
251889 CTAGAGAAAT
Statistics
Matches: 873, Mismatches: 36, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
310 4 0.00
311 869 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (311 bp):
ATCTGAATCGCTCATAAATCAAATGTTGGGCTGACTTGGCAAGTGCTTTTCTCCAGCAATACAAG
AATATGGCAGAGTGGGTACCCAACAGGTTGACCCTCTAAAATTTGGAGAAAAAGTCAACCGAATC
TTTCAAAGAATATGCTTAACGATGAAGAGACCCAACTTCTCAGGTCCAACTGCCCTTGACTGAGA
AGGAGATGATGATGTTATTCATGAATACTCTGCATCCACCCTATTATGACAAGTTAGTAGGGAAT
GCGACAAAGAATTTTTTCGATCTTGTAATCTTTGGAGAAGGAGAATTTATG
Found at i:252631 original size:8 final size:8
Alignment explanation
Indices: 252618--252654 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
252608 TCTTTTTGTT
252618 AAAAATAA
1 AAAAATAA
*
252626 AAAAATTA
1 AAAAATAA
252634 AAAAAT-A
1 AAAAATAA
252641 AAAAATAA
1 AAAAATAA
252649 AAAAAT
1 AAAAAT
252655 GTAAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (8 bp):
AAAAATAA
Found at i:252634 original size:15 final size:16
Alignment explanation
Indices: 252618--252664 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
252608 TCTTTTTGTT
252618 AAAAATAAAAAAATTA
1 AAAAATAAAAAAATTA
*
252634 AAAAAT-AAAAAATAA
1 AAAAATAAAAAAATTA
**
252649 AAAAATGTAAAAATTA
1 AAAAATAAAAAAATTA
252665 TTATTTGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (16 bp):
AAAAATAAAAAAATTA
Found at i:252652 original size:7 final size:7
Alignment explanation
Indices: 252618--252652 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
252608 TCTTTTTGTT
252618 AAAAATAA
1 AAAAAT-A
252626 AAAAATTA
1 AAAAA-TA
252634 AAAAATA
1 AAAAATA
252641 AAAAATA
1 AAAAATA
252648 AAAAA
1 AAAAA
252653 ATGTAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 14 0.54
8 11 0.42
9 1 0.04
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:254110 original size:79 final size:79
Alignment explanation
Indices: 254011--254440 Score: 429
Period size: 79 Copynumber: 5.4 Consensus size: 79
254001 TATTTTGGAG
* * * * * *
254011 ATAAAACCTGGGATTAGAGTATCTCCTCGAAAATAACAGGGTCGGAGTATCCTTGATTGTGTAAA
1 ATAAAA-CTGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGATTGTGAAAA
*
254076 ATCGATGTTTTGAAA
65 ATCGGTGTTTTGAAA
* * *
254091 ATAAAACTGGGGTTGGAGTATCCCCTCGAAAATAAC-GGGTTTGGAGTATCTTCGATTATGGAAA
1 ATAAAACTGGGGTTGGAGTATCCCCTCGAAAATAACAGGG-TTGGAGTATCCTCGATTGTGAAAA
*
254155 ATCGGTGTTTTGGAA
65 ATCGGTGTTTTGAAA
* * * * * *
254170 ATAAATC-AGGGTTGGAGTATCCCCTCGGAAATAACAGGGTTGGAGTGTCCACAATTGTGAAAAA
1 ATAAAACTGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGATTGTGAAAAA
*
254234 TTGGTGTTTTCG-AA
66 TCGGTGTTTT-GAAA
* * * * *
254248 ATAAAA-TCGGGGTTAGAGTATCCCCTCGAAAATAATAGGGTAGGAGTATCCTCGATTATGGAAA
1 ATAAAACT-GGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGATTGTGAAAA
** *
254312 ATCTATGTTTTGGAA
65 ATCGGTGTTTTGAAA
* * * * * * * * *
254327 ATAAAACCGAGGTTGGAGTAACTCCTTGGAGATAACGGGGTTGGAGTATCCTAGATTGTGAAAAA
1 ATAAAACTGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGATTGTGAAAAA
*
254392 TCGGTGCTTTGGAAA
66 TCGGTG-TTTTGAAA
* * *
254407 A-AAAACCGAGGTTGGAGTATCCCCTCGGAAATAA
1 ATAAAACTGGGGTTGGAGTATCCCCTCGAAAATAA
254441 AAACATGAAT
Statistics
Matches: 286, Mismatches: 56, Indels: 17
0.80 0.16 0.05
Matches are distributed among these distances:
78 65 0.23
79 208 0.73
80 13 0.05
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (79 bp):
ATAAAACTGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGATTGTGAAAAA
TCGGTGTTTTGAAA
Found at i:254196 original size:157 final size:158
Alignment explanation
Indices: 254027--254440 Score: 516
Period size: 157 Copynumber: 2.6 Consensus size: 158
254017 CCTGGGATTA
* * * * *
254027 GAGTATCTCCTCGAAAATAACAGGGTCGGAGTATCCTTGATTGTGTAAAATCGATGTTTTGAAAA
1 GAGTATCTCCTCGGAAATAACAGGGTTGGAGTATCCTAGATTGTGAAAAATCGGTGTTTTGAAAA
* * *
254092 TAAAACTGGGGTTGGAGTATCCCCTCGAAAATAA-CGGGTTTGGAGTATCTTCGATTATGGAAAA
66 TAAAACTGGGGTTGGAGTATCCCCTCGAAAATAATAGGG-TAGGAGTATCCTCGATTATGGAAAA
* *
254156 TCGGTGTTTTGGAAATAAATCAG-GGTTG
130 TCGATGTTTTGGAAATAAAACAGAGGTTG
* * * *
254184 GAGTATCCCCTCGGAAATAACAGGGTTGGAGTGTCC-ACAATTGTGAAAAATTGGTGTTTTCG-A
1 GAGTATCTCCTCGGAAATAACAGGGTTGGAGTATCCTA-GATTGTGAAAAATCGGTGTTTT-GAA
*
254247 AATAAAA-TCGGGGTTAGAGTATCCCCTCGAAAATAATAGGGTAGGAGTATCCTCGATTATGGAA
64 AATAAAACT-GGGGTTGGAGTATCCCCTCGAAAATAATAGGGTAGGAGTATCCTCGATTATGGAA
* *
254311 AATCTATGTTTTGGAAATAAAACCGAGGTTG
128 AATCGATGTTTTGGAAATAAAACAGAGGTTG
* * * * *
254342 GAGTAACTCCTTGGAGATAACGGGGTTGGAGTATCCTAGATTGTGAAAAATCGGTGCTTTGGAAA
1 GAGTATCTCCTCGGAAATAACAGGGTTGGAGTATCCTAGATTGTGAAAAATCGGTG-TTTTGAAA
* * *
254407 A-AAAACCGAGGTTGGAGTATCCCCTCGGAAATAA
65 ATAAAACTGGGGTTGGAGTATCCCCTCGAAAATAA
254441 AAACATGAAT
Statistics
Matches: 218, Mismatches: 30, Indels: 17
0.82 0.11 0.06
Matches are distributed among these distances:
156 1 0.00
157 126 0.58
158 84 0.39
159 7 0.03
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (158 bp):
GAGTATCTCCTCGGAAATAACAGGGTTGGAGTATCCTAGATTGTGAAAAATCGGTGTTTTGAAAA
TAAAACTGGGGTTGGAGTATCCCCTCGAAAATAATAGGGTAGGAGTATCCTCGATTATGGAAAAT
CGATGTTTTGGAAATAAAACAGAGGTTG
Found at i:254472 original size:236 final size:236
Alignment explanation
Indices: 254024--254451 Score: 545
Period size: 236 Copynumber: 1.8 Consensus size: 236
254014 AAACCTGGGA
* * * * *
254024 TTAGAGTATCTCCTCGAAAATAACAGGGTCGGAGTATCCTTGATTGTGTAAAATCGATGTTTTGA
1 TTAGAGTATCCCCTCGAAAATAACAGGGTAGGAGTATCCTCGATTATGGAAAATCGATGTTTTGA
* * * * * * *
254089 AAATAAAACTGGGGTTGGAGTATCCCCTCGAAAATAACGGGTTTGGAGTATCTTCGATTATGGAA
66 AAATAAAACCGAGGTTGGAGTAACCCCTCGAAAATAACGGGGTTGGAGTATCCTAGATTATGAAA
* * * **** * *
254154 AATCGGTGTTTTGGAAATAAATCAGGGTTGGAGTATCCCCTCGGAAATAACAGGGTTGGAGTGTC
131 AATCGGTGCTTTGGAAAAAAAACAGGGTTGGAGTATCCCCTCGGAAATAACAAACATGGAATGTA
* *
254219 CACAATTGTGAAAAATTGGTGTTTTCGAAATAAAATCGGGG
196 AACAATTATGAAAAATTGGTGTTTTCGAAATAAAATCGGGG
* * *
254260 TTAGAGTATCCCCTCGAAAATAATAGGGTAGGAGTATCCTCGATTATGGAAAATCTATGTTTTGG
1 TTAGAGTATCCCCTCGAAAATAACAGGGTAGGAGTATCCTCGATTATGGAAAATCGATGTTTTGA
* * * * *
254325 AAATAAAACCGAGGTTGGAGTAACTCCTTGGAGATAACGGGGTTGGAGTATCCTAGATTGTGAAA
66 AAATAAAACCGAGGTTGGAGTAACCCCTCGAAAATAACGGGGTTGGAGTATCCTAGATTATGAAA
*
254390 AATCGGTGCTTTGGAAAAAAAACCGAGGTTGGAGTATCCCCTCGGAAATAA-AAACAT-GAATG
131 AATCGGTGCTTTGGAAAAAAAACAG-GGTTGGAGTATCCCCTCGGAAATAACAAACATGGAATG
254452 AAAGTTTTAT
Statistics
Matches: 162, Mismatches: 29, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
235 4 0.02
236 133 0.82
237 25 0.15
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (236 bp):
TTAGAGTATCCCCTCGAAAATAACAGGGTAGGAGTATCCTCGATTATGGAAAATCGATGTTTTGA
AAATAAAACCGAGGTTGGAGTAACCCCTCGAAAATAACGGGGTTGGAGTATCCTAGATTATGAAA
AATCGGTGCTTTGGAAAAAAAACAGGGTTGGAGTATCCCCTCGGAAATAACAAACATGGAATGTA
AACAATTATGAAAAATTGGTGTTTTCGAAATAAAATCGGGG
Found at i:258543 original size:20 final size:21
Alignment explanation
Indices: 258512--258550 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
258502 AGGTCAAAAC
258512 CCTAGAAAGTATCGATACAAG
1 CCTAGAAAGTATCGATACAAG
258533 CCTAG-AAGTATCGATACA
1 CCTAGAAAGTATCGATACA
258551 TATTGCTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21
Consensus pattern (21 bp):
CCTAGAAAGTATCGATACAAG
Found at i:258576 original size:13 final size:13
Alignment explanation
Indices: 258558--258584 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
258548 ACATATTGCT
258558 TTGTATCGATACA
1 TTGTATCGATACA
258571 TTGTATCGATACA
1 TTGTATCGATACA
258584 T
1 T
258585 GTTCATTGTA
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:258582 original size:33 final size:32
Alignment explanation
Indices: 258540--258603 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
258530 AAGCCTAGAA
*
258540 GTATCGATACATATTGCTTTGTATCGATACATT
1 GTATCGATACATATT-CATTGTATCGATACATT
*
258573 GTATCGATACATGTTCATTGTATCGATACAT
1 GTATCGATACATATTCATTGTATCGATACAT
258604 GAAGAATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (32 bp):
GTATCGATACATATTCATTGTATCGATACATT
Found at i:258614 original size:20 final size:20
Alignment explanation
Indices: 258570--258626 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
258560 GTATCGATAC
***
258570 ATTGTATCGATACATG-TTC
1 ATTGTATCGATACATGAAGA
258589 ATTGTATCGATACATGAAGA
1 ATTGTATCGATACATGAAGA
*
258609 ATTGTATCGAAACATGAA
1 ATTGTATCGATACATGAA
258627 TAGTAGTAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (20 bp):
ATTGTATCGATACATGAAGA
Found at i:259677 original size:14 final size:15
Alignment explanation
Indices: 259646--259678 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
259636 TTTTGTAATA
259646 AAAAAAATCTAAAAT
1 AAAAAAATCTAAAAT
*
259661 AAAAAAATC-AAATT
1 AAAAAAATCTAAAAT
259675 AAAA
1 AAAA
259679 TAAAAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAAAAATCTAAAAT
Found at i:259725 original size:22 final size:21
Alignment explanation
Indices: 259697--259737 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
259687 AAACTAATAA
259697 AAGAAAAGAAAAATGAAAAATC
1 AAGAAAAGAAAAA-GAAAAATC
*
259719 AAGAAAAGATAAAGAAAAA
1 AAGAAAAGAAAAAGAAAAA
259738 GGGCCATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (21 bp):
AAGAAAAGAAAAAGAAAAATC
Found at i:260735 original size:13 final size:13
Alignment explanation
Indices: 260717--260741 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
260707 ATTACTCAAA
260717 TGTATCGATACAT
1 TGTATCGATACAT
260730 TGTATCGATACA
1 TGTATCGATACA
260742 CCAATCTTTG
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:260806 original size:52 final size:52
Alignment explanation
Indices: 260750--260878 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
260740 CACCAATCTT
*
260750 TGTATCGATACATGCAGGTAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGTAAATTTGCCCAGATGTATCGATACACTATAAAA
* * *
260802 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGTAAATTTGCCCAGATGTATCGATACACTATAAAA
*
260854 TGTATCGATACATGCAGATAAATTT
1 TGTATCGATACATGCAGGTAAATTT
260879 TCATATTTCG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGTAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:264675 original size:61 final size:59
Alignment explanation
Indices: 264497--264678 Score: 199
Period size: 57 Copynumber: 3.1 Consensus size: 59
264487 CTCTTCACCA
* * ** * *
264497 AAATCCACCCTTGCTTCACTATATTCGGTCAAGCCTTTCCTCATTTAA--TATTAT-TTC
1 AAATCCACCCTCGCTTAACTGCATTCGGTTAAGCCTTTCCTCATTTAACTTATT-TGATC
* * * *
264554 AAATCCACCCTTGCTTAACTGTATTCGGTTAAGCCTTTCCTCTTTTAACTATATTCGATC
1 AAATCCACCCTCGCTTAACTGCATTCGGTTAAGCCTTTCCTCATTTAACT-TATTTGATC
* *
264614 AAATCCACCCTCGCTTAAATTGCATTTGGTTAAGCCTTTCCTCATTTAACTGTATTTGATC
1 AAATCCACCCTCGCTT-AACTGCATTCGGTTAAGCCTTTCCTCATTTAACT-TATTTGATC
264675 AAAT
1 AAAT
264679 TCTACTCTTA
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
57 44 0.41
60 21 0.20
61 42 0.39
ACGTcount: A:0.25, C:0.26, G:0.09, T:0.40
Consensus pattern (59 bp):
AAATCCACCCTCGCTTAACTGCATTCGGTTAAGCCTTTCCTCATTTAACTTATTTGATC
Found at i:264787 original size:60 final size:60
Alignment explanation
Indices: 264497--264844 Score: 282
Period size: 61 Copynumber: 5.8 Consensus size: 60
264487 CTCTTCACCA
* *
264497 AAATCCACCCTTGCTTCACTA-TATTCGGTCAAGCCTTTCCTCATTTAA-TATTATT---TC
1 AAATCCACCCTTGCTTAAC-AGTATTCGGTCAAGCCTTTCCTTATTTAACTA-TATTCGATC
* *
264554 AAATCCACCCTTGCTTAACTGTATTCGGTTAAGCCTTTCCTCT-TTTAACTATATTCGATC
1 AAATCCACCCTTGCTTAACAGTATTCGGTCAAGCCTTTCCT-TATTTAACTATATTCGATC
* * * * * * *
264614 AAATCCACCCTCGCTTAA-ATTGCATTTGGTTAAGCCTTTCCTCATTTAACTGTATTTGATC
1 AAATCCACCCTTGCTTAACA--GTATTCGGTCAAGCCTTTCCTTATTTAACTATATTCGATC
* * ** * * ** *
264675 AAATTCTACTCTTAATTGACTA-TATGCAATCAAG-CTTTCCCTTATTTGACTATATTCGATC
1 AAA-TCCACCCTTGCTTAAC-AGTATTCGGTCAAGCCTTT-CCTTATTTAACTATATTCGATC
* * * *
264736 AAATCCACTCTTGCTTAACAGTATTTGGTTAAGCCTTTCTTTATTTAACTATATTCGATC
1 AAATCCACCCTTGCTTAACAGTATTCGGTCAAGCCTTTCCTTATTTAACTATATTCGATC
* ** *
264796 AAATTTCACACCCTTACTTAATTGTATTCGGTCAAGCCTTTCTTTATTT
1 AAA--TC-CACCCTTGCTTAACAGTATTCGGTCAAGCCTTTCCTTATTT
264845 GATTGTACTT
Statistics
Matches: 229, Mismatches: 44, Indels: 30
0.76 0.15 0.10
Matches are distributed among these distances:
57 46 0.20
58 2 0.01
59 1 0.00
60 65 0.28
61 68 0.30
62 11 0.05
63 35 0.15
64 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (60 bp):
AAATCCACCCTTGCTTAACAGTATTCGGTCAAGCCTTTCCTTATTTAACTATATTCGATC
Found at i:264948 original size:60 final size:59
Alignment explanation
Indices: 264818--265067 Score: 193
Period size: 60 Copynumber: 4.2 Consensus size: 59
264808 CTTACTTAAT
* * ** * * **
264818 TGTATTCGGTCAAGCCTTTCTTTATTTGATTGTACTTGATCAAAT-TT--CCCTCTAAAC
1 TGTATTCGGTCAAGTCTTTCTTCATTT-AAAGTACTCGGTCAAATCTTACCCCTCTTGAC
* *
264875 TATATTCGGTCAAGTCTTTCTTCATTTAAACATACTCGGTCAAATCTTACCCCTCTTGAC
1 TGTATTCGGTCAAGTCTTTCTTCATTTAAA-GTACTCGGTCAAATCTTACCCCTCTTGAC
* * * * ** * * *
264935 TGTATTCGATCAAGACTATCCTCATTTGTTAGTGCTCGATCAAATCTTACCTCGT-TTGAC
1 TGTATTCGGTCAAGTCTTTCTTCATTT-AAAGTACTCGGTCAAATCTTACC-CCTCTTGAC
* * ** * *
264995 TGTATTTGGTTAAGTCTTTCTTCATTTGATTGTACTCAGTGAAATCTTACCCCTCTTGAC
1 TGTATTCGGTCAAGTCTTTCTTCATTT-AAAGTACTCGGTCAAATCTTACCCCTCTTGAC
*
265055 TGTATTTGGTCAA
1 TGTATTCGGTCAA
265068 TACAACCCTT
Statistics
Matches: 151, Mismatches: 35, Indels: 11
0.77 0.18 0.06
Matches are distributed among these distances:
56 1 0.01
57 35 0.23
58 2 0.01
59 2 0.01
60 108 0.72
61 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.42
Consensus pattern (59 bp):
TGTATTCGGTCAAGTCTTTCTTCATTTAAAGTACTCGGTCAAATCTTACCCCTCTTGAC
Found at i:265087 original size:60 final size:60
Alignment explanation
Indices: 264907--265163 Score: 189
Period size: 60 Copynumber: 4.3 Consensus size: 60
264897 CATTTAAACA
* ** * * * * *
264907 TACTCGGTCAAATCTTACCCCTCTTGACTGTATTCGATCAAGACTATCCTCATTT-GTTAG
1 TACTCAGTCAAATCTTACCCCTCTAAACTGTATTTGGTCAAGACAACCCTCATTTCATT-G
* * ** * * *** * *
264967 TGCTC-GATCAAATCTTACCTCGT-TTGACTGTATTTGGTTAAGTCTTTCTTCATTTGATTG
1 TACTCAG-TCAAATCTTACC-CCTCTAAACTGTATTTGGTCAAGACAACCCTCATTTCATTG
* ** * *
265027 TACTCAGTGAAATCTTACCCCTCTTGACTGTATTTGGTCAATACAACCCTTATTTCATTG
1 TACTCAGTCAAATCTTACCCCTCTAAACTGTATTTGGTCAAGACAACCCTCATTTCATTG
* * *
265087 TACTCTA-TCAAATCTTACCCCTCTAAACTGTATTTGGTCAAGACTACTCTCATTTCATTA
1 TACTC-AGTCAAATCTTACCCCTCTAAACTGTATTTGGTCAAGACAACCCTCATTTCATTG
* *
265147 TATTCGGTCAAATCTTA
1 TACTCAGTCAAATCTTA
265164 GTTTGCTTGA
Statistics
Matches: 159, Mismatches: 31, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
59 3 0.02
60 150 0.94
61 6 0.04
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (60 bp):
TACTCAGTCAAATCTTACCCCTCTAAACTGTATTTGGTCAAGACAACCCTCATTTCATTG
Found at i:265160 original size:120 final size:119
Alignment explanation
Indices: 264839--265163 Score: 329
Period size: 120 Copynumber: 2.7 Consensus size: 119
264829 AAGCCTTTCT
* *
264839 TTATTTGATTGTACT-TGATCAAAT-TT--CCCTCTAAACTATATTCGGTCAAGTCTTTCTTCAT
1 TTATTT-ATTGTACTCT-ATCAAATCTTACCCCTCTAAACTGTATTTGGTCAAGTCTTTCTTCAT
** * *
264900 TTAAACATACTCGGTCAAATCTTACCCCTCTTGACTGTATTCGATCAAGACTATCC
64 TTAATTATACTCGGTCAAATCTTACCCCTCTTGACTGTATTCGATCAAGACAACCC
* * * * * ** *
264956 TCATTTGTTAGTGCTCGATCAAATCTTACCTCGT-TTGACTGTATTTGGTTAAGTCTTTCTTCAT
1 TTATTTATT-GTACTCTATCAAATCTTACC-CCTCTAAACTGTATTTGGTCAAGTCTTTCTTCAT
* * * * * * *
265020 TTGATTGTACTCAGTGAAATCTTACCCCTCTTGACTGTATTTGGTCAATACAACCC
64 TTAATTATACTCGGTCAAATCTTACCCCTCTTGACTGTATTCGATCAAGACAACCC
* *
265076 TTATTTCATTGTACTCTATCAAATCTTACCCCTCTAAACTGTATTTGGTCAAGAC-TACTCTCAT
1 TTATTT-ATTGTACTCTATCAAATCTTACCCCTCTAAACTGTATTTGGTCAAGTCTTTCT-TCAT
* *
265140 TTCATTATATTCGGTCAAATCTTA
64 TTAATTATACTCGGTCAAATCTTA
265164 GTTTGCTTGA
Statistics
Matches: 163, Mismatches: 36, Indels: 15
0.76 0.17 0.07
Matches are distributed among these distances:
116 2 0.01
117 16 0.10
118 2 0.01
119 5 0.03
120 134 0.82
121 4 0.02
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (119 bp):
TTATTTATTGTACTCTATCAAATCTTACCCCTCTAAACTGTATTTGGTCAAGTCTTTCTTCATTT
AATTATACTCGGTCAAATCTTACCCCTCTTGACTGTATTCGATCAAGACAACCC
Found at i:265235 original size:180 final size:180
Alignment explanation
Indices: 264914--265241 Score: 410
Period size: 180 Copynumber: 1.8 Consensus size: 180
264904 ACATACTCGG
** * *
264914 TCAAATCTTACCCCTCTTGACTGTATTCGATCAAGACTATCCTCATTTGTTAGTGCTCGATCAAA
1 TCAAATCTTACCCCTCTAAACTGTATTCGATCAAGACTATCCTCATTTATTAGTACTCGATCAAA
* * * * * *
264979 TCTTACCTCGTTTGACTGTATTTGGTTAAGTCTTTCTTCATTTGATTGTACTCAGTGAAATCTTA
66 TCTTACCTCGCTTGACTATATTCGATGAAGTCTTTCTTCATTTGATTGTACTCAGTGAAATCCTA
*
265044 CCCCTCTTGACTGTATTTGGTCAATACAACCCTTATTTCATTGTACTCTA
131 CCCCTCTTGACTATATTTGGTCAATACAACCCTTATTTCATTGTACTCTA
* * * *
265094 TCAAATCTTACCCCTCTAAACTGTATTTGGTCAAGACTA-CTCTCATTTCATTA-TATTCGGTCA
1 TCAAATCTTACCCCTCTAAACTGTATTCGATCAAGACTATC-CTCATTT-ATTAGTACTCGATCA
** * * * *
265157 AATCTTAGTTTGCTTGACTATATTCGATGAAGTCTTTCTTTATTTGATTGTACTCGGTTAAATCC
64 AATCTTACCTCGCTTGACTATATTCGATGAAGTCTTTCTTCATTTGATTGTACTCAGTGAAATCC
*
265222 TA-CCTTGCTTGACTATATTT
129 TACCCCT-CTTGACTATATTT
265242 AATCAAGTCT
Statistics
Matches: 123, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
179 4 0.03
180 116 0.94
181 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.42
Consensus pattern (180 bp):
TCAAATCTTACCCCTCTAAACTGTATTCGATCAAGACTATCCTCATTTATTAGTACTCGATCAAA
TCTTACCTCGCTTGACTATATTCGATGAAGTCTTTCTTCATTTGATTGTACTCAGTGAAATCCTA
CCCCTCTTGACTATATTTGGTCAATACAACCCTTATTTCATTGTACTCTA
Found at i:265277 original size:30 final size:30
Alignment explanation
Indices: 265143--265278 Score: 92
Period size: 30 Copynumber: 4.5 Consensus size: 30
265133 CTCTCATTTC
* ** *
265143 ATTATATTCGGTCAAATCTTAGTTTGCTTG
1 ATTATATTCGATCAAATCTTACCTTACTTG
* * * * * *
265173 ACTATATTCGATGAAGTCTTTCTTTATTTG
1 ATTATATTCGATCAAATCTTACCTTACTTG
* * * * * *
265203 ATTGTACTCGGTTAAATCCTACCTTGCTTG
1 ATTATATTCGATCAAATCTTACCTTACTTG
* ** *
265233 ACTATATTTAATCAAGTCTTACCTTACTTG
1 ATTATATTCGATCAAATCTTACCTTACTTG
265263 ATTATATTCGATCAAA
1 ATTATATTCGATCAAA
265279 CCTTTCCTCA
Statistics
Matches: 73, Mismatches: 33, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
30 73 1.00
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.44
Consensus pattern (30 bp):
ATTATATTCGATCAAATCTTACCTTACTTG
Found at i:266523 original size:62 final size:64
Alignment explanation
Indices: 266449--266636 Score: 229
Period size: 65 Copynumber: 2.9 Consensus size: 64
266439 ATGTAATTAG
* *
266449 AAAATGATAGCAACAAGAAGAA-ACAA-AAAAAAGTAATTAAGCTGCTGAAAATAAATAAG-AAA
1 AAAATGACAGCAACAAGAAGAAGA-AACAAAAAAGTAATTAAGCTGCTGAAAACAAATAAGAAAA
* * * *
266511 GAAATGACAGCAACAAGAAGAAGAAACGAAAAAAGCAATTAAGCTGCTGAAAACCAATAGGAAAA
1 AAAATGACAGCAACAAGAAGAAGAAAC-AAAAAAGTAATTAAGCTGCTGAAAACAAATAAGAAAA
* * * * *
266576 AAAATGGCAACAAGAAGAAGAAGAAATAGAAAAAGTAATTAAGTTGCTGAAAACAAATAAG
1 AAAATGACAGCAACAAGAAGAAGAAACA-AAAAAGTAATTAAGCTGCTGAAAACAAATAAG
266637 TAATAGCAAA
Statistics
Matches: 106, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
62 22 0.21
63 1 0.01
64 30 0.28
65 53 0.50
ACGTcount: A:0.60, C:0.10, G:0.18, T:0.13
Consensus pattern (64 bp):
AAAATGACAGCAACAAGAAGAAGAAACAAAAAAGTAATTAAGCTGCTGAAAACAAATAAGAAAA
Found at i:266920 original size:20 final size:22
Alignment explanation
Indices: 266872--266943 Score: 60
Period size: 22 Copynumber: 3.1 Consensus size: 22
266862 TCAAAACAGT
266872 AAAGAAACAATTAGCAAAAACATCAAC
1 AAAG-AACAA-TAGC-AAAA-A-CAAC
266899 AAAG-ACACA-AGC-AAAACAAC
1 AAAGAACA-ATAGCAAAAACAAC
266919 AAAAGAACAATAGCAAAAACAAC
1 -AAAGAACAATAGCAAAAACAAC
266942 AA
1 AA
266944 GCTTGACACT
Statistics
Matches: 40, Mismatches: 0, Indels: 15
0.73 0.00 0.27
Matches are distributed among these distances:
20 4 0.10
21 6 0.15
22 11 0.28
23 8 0.20
24 3 0.08
25 3 0.08
26 1 0.03
27 4 0.10
ACGTcount: A:0.67, C:0.19, G:0.08, T:0.06
Consensus pattern (22 bp):
AAAGAACAATAGCAAAAACAAC
Found at i:266937 original size:23 final size:23
Alignment explanation
Indices: 266872--266943 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 23
266862 TCAAAACAGT
*
266872 AAAGAAACAATTAGCAAAAACATCA
1 AAAG-AACAA-TAGCAAAAACAACA
266897 ACAA-AGACACA-AGC-AAAACAACA
1 A-AAGA-ACA-ATAGCAAAAACAACA
266920 AAAGAACAATAGCAAAAACAACA
1 AAAGAACAATAGCAAAAACAACA
266943 A
1 A
266944 GCTTGACACT
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
21 1 0.03
22 8 0.20
23 20 0.50
24 4 0.10
25 4 0.10
26 3 0.08
ACGTcount: A:0.67, C:0.19, G:0.08, T:0.06
Consensus pattern (23 bp):
AAAGAACAATAGCAAAAACAACA
Found at i:267046 original size:23 final size:23
Alignment explanation
Indices: 267003--267048 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
266993 TCTCCATTTT
*
267003 GAGTTGCATGAGAAATGGATTAA
1 GAGTTGCATGAGAAATCGATTAA
267026 GAGTTGCATGATG-AATCGATTAA
1 GAGTTGCATGA-GAAATCGATTAA
267049 TGGAGAATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.37, C:0.07, G:0.28, T:0.28
Consensus pattern (23 bp):
GAGTTGCATGAGAAATCGATTAA
Found at i:272050 original size:21 final size:20
Alignment explanation
Indices: 272017--272064 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 20
272007 AGCTAGATGT
272017 TGGACAT-G-TTAAAATGCA
1 TGGACATGGCTTAAAATGCA
272035 TGGTACATGGCTTAAAATGCA
1 TGG-ACATGGCTTAAAATGCA
272056 TGGACATGG
1 TGGACATGG
272065 GCTATTTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.11
19 4 0.15
20 7 0.26
21 13 0.48
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.27
Consensus pattern (20 bp):
TGGACATGGCTTAAAATGCA
Found at i:272984 original size:51 final size:50
Alignment explanation
Indices: 272927--273041 Score: 149
Period size: 51 Copynumber: 2.3 Consensus size: 50
272917 AATTAACTAG
* * ** *
272927 ATGTATCGATACCTTGAAAAATGTATTGATACATCTGGGTAAAAAAACAAA
1 ATGTATCGATACATTGAAAAATATATCAATACATCTAGGT-AAAAAACAAA
** *
272978 ATGTATCGATACATTGAAAAATATATCAATACATCTAGGTAAAAATTAGA
1 ATGTATCGATACATTGAAAAATATATCAATACATCTAGGTAAAAAACAAA
273028 ATGTATCGATACAT
1 ATGTATCGATACAT
273042 GTACTAGTCA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 21 0.38
51 35 0.62
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (50 bp):
ATGTATCGATACATTGAAAAATATATCAATACATCTAGGTAAAAAACAAA
Found at i:277313 original size:34 final size:34
Alignment explanation
Indices: 277267--277492 Score: 197
Period size: 34 Copynumber: 7.3 Consensus size: 34
277257 TCTCTAAAGC
* *
277267 CCACAATTCCGTGGCACTCTTTTTCCTTCTAAGT
1 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
* **
277301 CCACAACCCCGTGGCA--C-----CCTTTTAACC
1 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
*
277328 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGT
1 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
* **
277362 CCACAACTCCATGGCA--C-----CCTTTTAACC
1 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
*
277389 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGT
1 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
* *
277423 CCACAACTCTGTGGCA--C-----CCTTTTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
277450 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
1 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
277484 CCACAACTC
1 CCACAACTC
277493 TATGGCACCC
Statistics
Matches: 149, Mismatches: 22, Indels: 42
0.70 0.10 0.20
Matches are distributed among these distances:
27 67 0.45
29 3 0.02
32 3 0.02
34 76 0.51
ACGTcount: A:0.20, C:0.38, G:0.11, T:0.31
Consensus pattern (34 bp):
CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
Found at i:277331 original size:27 final size:27
Alignment explanation
Indices: 277301--277472 Score: 119
Period size: 27 Copynumber: 5.9 Consensus size: 27
277291 CCTTCTAAGT
*
277301 CCACAACCCCGTGGCACCCTTTTAACC
1 CCACAACTCCGTGGCACCCTTTTAACC
* **
277328 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGT
1 CCACAACTCCGTGGCA--C-----CCTTTTAACC
*
277362 CCACAACTCCATGGCACCCTTTTAACC
1 CCACAACTCCGTGGCACCCTTTTAACC
* **
277389 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGT
1 CCACAACTCCGTGGCA--C-----CCTTTTAACC
* *
277423 CCACAACTCTGTGGCACCCTTTTAAGC
1 CCACAACTCCGTGGCACCCTTTTAACC
*
277450 CCACAACTCCGTGGCACTCTTTT
1 CCACAACTCCGTGGCACCCTTTT
277473 TCCTTTTAAG
Statistics
Matches: 114, Mismatches: 17, Indels: 28
0.72 0.11 0.18
Matches are distributed among these distances:
27 66 0.58
29 2 0.02
32 2 0.02
34 44 0.39
ACGTcount: A:0.20, C:0.40, G:0.12, T:0.28
Consensus pattern (27 bp):
CCACAACTCCGTGGCACCCTTTTAACC
Found at i:277499 original size:34 final size:34
Alignment explanation
Indices: 277440--277505 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
277430 TCTGTGGCAC
* *
277440 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
1 CCTTTTAAGCCCACAACTCCATGGCACCCTTTTT
* *
277474 CCTTTTAAGTCCACAACTCTATGGCACCCTTT
1 CCTTTTAAGCCCACAACTCCATGGCACCCTTT
277506 AAAGCCCACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.20, C:0.35, G:0.11, T:0.35
Consensus pattern (34 bp):
CCTTTTAAGCCCACAACTCCATGGCACCCTTTTT
Found at i:277531 original size:26 final size:27
Alignment explanation
Indices: 277474--277528 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
277464 CACTCTTTTT
* *
277474 CCTTTTAAGTCCACAACTCTATGGCAC
1 CCTTTAAAGCCCACAACTCTATGGCAC
277501 CCTTTAAAGCCCACAACTCCT-TGGCAC
1 CCTTTAAAGCCCACAACT-CTATGGCAC
277528 C
1 C
277529 TTTCCCTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.25, C:0.38, G:0.11, T:0.25
Consensus pattern (27 bp):
CCTTTAAAGCCCACAACTCTATGGCAC
Found at i:277549 original size:61 final size:61
Alignment explanation
Indices: 277263--277531 Score: 432
Period size: 61 Copynumber: 4.4 Consensus size: 61
277253 CTTTTCTCTA
* * *
277263 AAGCCCACAATTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACCCCGTGGCACCCTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCATGGCACCCTTTT
*
277324 AACCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCATGGCACCCTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCATGGCACCCTTTT
* **
277385 AACCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCCTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCATGGCACCCTTTT
* * *
277446 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTATGGCACCCTTTA
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCATGGCACCCTTTT
*
277507 AAGCCCACAACTCCTTGGCAC-CTTT
1 AAGCCCACAACTCCGTGGCACTCTTT
277532 CCCTTCTCAA
Statistics
Matches: 197, Mismatches: 11, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
60 4 0.02
61 193 0.98
ACGTcount: A:0.21, C:0.38, G:0.12, T:0.30
Consensus pattern (61 bp):
AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCATGGCACCCTTTT
Found at i:277618 original size:32 final size:33
Alignment explanation
Indices: 277534--277660 Score: 150
Period size: 33 Copynumber: 3.8 Consensus size: 33
277524 GCACCTTTCC
*
277534 CTTCTCAAAGCCCACATAAGTTGGTGGCAACCTT
1 CTTCT-AAAGCCCACACAAGTTGGTGGCAACCTT
* * *
277568 TTTCTAAAGCCCAAACAAGTTGGTGGCAATCC-C
1 CTTCTAAAGCCCACACAAGTTGGTGGCAA-CCTT
* *
277601 CTT-TAAAGCCCACACAAGTCGATGGCAACCTT
1 CTTCTAAAGCCCACACAAGTTGGTGGCAACCTT
* *
277633 CTTCAAAAGCCCACACAAGATGGTGGCA
1 CTTCTAAAGCCCACACAAGTTGGTGGCA
277661 TCTTCTTTTA
Statistics
Matches: 77, Mismatches: 13, Indels: 7
0.79 0.13 0.07
Matches are distributed among these distances:
31 2 0.03
32 25 0.32
33 44 0.57
34 6 0.08
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (33 bp):
CTTCTAAAGCCCACACAAGTTGGTGGCAACCTT
Found at i:277824 original size:92 final size:92
Alignment explanation
Indices: 277667--278956 Score: 1948
Period size: 92 Copynumber: 14.0 Consensus size: 92
277657 GGCATCTTCT
* *
277667 TTTAAGTCCAATATAGCTGGCCTTAAATCAGCATATTGGCACCTTCATCTTTAAATCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
* *
277732 CTAGCCTTGAATCAACACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* *
277759 TTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTAAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
* *
277824 CTAGCCTTGAATCAACACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* * *
277851 TTTAAGTCTAATATAACTGGCCTTTAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
** *
277916 CTGGCCTTGAAT-TTCACATTGGTACC
66 CTGGCCTTGAATCAGCACATTGGCACC
*
277942 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATCTTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
* *
278007 CTAGCCTTGAATCAGCAAATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
*
278034 TTTAAATCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
278099 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* * *
278126 TTTAAATCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGCAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
278191 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* *
278218 TTTAAATCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGCAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
* *
278283 CTAGCCTTGAATCAGCACTTTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* *
278310 TTTAAATCCAATATAGCTGGCCTTGAATCAGCATATTGTCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
278375 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
*
278402 TTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
* *
278467 CTGGCCTTGAATTAGCACATTAGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* * * *
278494 TTTATGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAA
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
278559 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
278586 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
* *
278651 CTAGCCTTGAATTAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* * * *
278678 TTTAAGTCCAGTATTGCTGGTCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
278743 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* * * * *
278770 TTTAAGTCCAATGTAGCTAGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
* *
278829 CTGGCCTTGAATTAGCATATTGGCACCTTTTTC
66 CTGGCCTTGAATCAGCACATTGGCA-C-----C
* * * * * *
278862 TTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCAGCTTCATCTTTAAGTCCAATATCA
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT-A
* * * *
278927 -CTAGCCTTGAATTAGCATATTGGCGCC
65 GCTGGCCTTGAATCAGCACATTGGCACC
278954 TTT
1 TTT
278957 GTCATCTTTA
Statistics
Matches: 1110, Mismatches: 74, Indels: 28
0.92 0.06 0.02
Matches are distributed among these distances:
86 38 0.03
87 1 0.00
91 83 0.07
92 948 0.85
96 1 0.00
97 1 0.00
98 38 0.03
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (92 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
CTGGCCTTGAATCAGCACATTGGCACC
Found at i:278078 original size:21 final size:21
Alignment explanation
Indices: 278011--278078 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
278001 ATGTAGCTAG
*
278011 CCTTGAATCAGCAAATTGGCA
1 CCTTGAATCAGCATATTGGCA
* ** *
278032 CCTTTAAATCCAATATAGCTGG--
1 CC-TTGAAT-CAGCATA-TTGGCA
278054 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCATATTGGCA
278075 CCTT
1 CCTT
278079 CATCTTTAAG
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 3 0.09
20 5 0.15
21 11 0.33
22 7 0.21
23 4 0.12
24 3 0.09
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (21 bp):
CCTTGAATCAGCATATTGGCA
Found at i:278170 original size:21 final size:21
Alignment explanation
Indices: 278103--278170 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
278093 ATGTAGCTGG
*
278103 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCATATTGGCA
* *
278124 CCTTTAAATC--CAATATT-GCTGG
1 CC-TTGAATCAGC-ATATTGGC--A
278146 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCATATTGGCA
278167 CCTT
1 CCTT
278171 CATCTTTAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 14
0.65 0.09 0.26
Matches are distributed among these distances:
20 3 0.09
21 16 0.46
22 13 0.37
23 3 0.09
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (21 bp):
CCTTGAATCAGCATATTGGCA
Found at i:278262 original size:21 final size:21
Alignment explanation
Indices: 278195--278262 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
278185 ATGCAGCTGG
*
278195 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCATATTGGCA
* ** *
278216 CCTTTAAATCCAATATAGCTGG--
1 CC-TTGAAT-CAGCATA-TTGGCA
278238 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCATATTGGCA
278259 CCTT
1 CCTT
278263 CATCTTTAAG
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 3 0.09
20 5 0.15
21 11 0.33
22 7 0.21
23 4 0.12
24 3 0.09
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.29
Consensus pattern (21 bp):
CCTTGAATCAGCATATTGGCA
Found at i:278403 original size:21 final size:20
Alignment explanation
Indices: 278379--278446 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 20
278369 ATGTAGCTGG
278379 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCA-ATTGGCA
* *
278400 CCTTTAAGTC--CAATATAGCTA
1 CCTTGAA-TCAGCAAT-TGGC-A
278421 GCCTTGAATCAGCATATTGGCA
1 -CCTTGAATCAGCA-ATTGGCA
278443 CCTT
1 CCTT
278447 CATCTTTAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 13 0.36
22 9 0.25
23 5 0.14
24 2 0.06
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.29
Consensus pattern (20 bp):
CCTTGAATCAGCAATTGGCA
Found at i:278771 original size:21 final size:21
Alignment explanation
Indices: 278747--278814 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
278737 ATGTAGCTGG
278747 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* *
278768 CCTTTAAGTC--CA-ATGTAGCTA
1 CCTTGAA-TCAGCACAT-TGGC-A
278789 GCCTTGAATCAGCACATTGGCA
1 -CCTTGAATCAGCACATTGGCA
278811 CCTT
1 CCTT
278815 TAAGTCCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 13 0.36
22 9 0.25
23 5 0.14
24 2 0.06
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:279781 original size:32 final size:32
Alignment explanation
Indices: 279745--279815 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
279735 ACAAAAATGT
279745 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
279777 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
279809 TGTATCG
1 TGTATCG
279816 CTACGAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:279782 original size:13 final size:13
Alignment explanation
Indices: 279764--279788 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
279754 ACATAAGTGT
279764 TGTATCGATACAA
1 TGTATCGATACAA
279777 TGTATCGATACA
1 TGTATCGATACA
279789 TAAGTTTTGT
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:279801 original size:19 final size:19
Alignment explanation
Indices: 279725--279807 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
279715 TTTCAACGAT
* *
279725 TTGTATCGATACAAAAATG
1 TTGTATCGATACATAAGTG
279744 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
279763 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
*
279777 -TGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
279795 TTGTATCGATACA
1 TTGTATCGATACA
279808 ATGTATCGCT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.20
15 2 0.04
17 2 0.04
19 41 0.73
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:279878 original size:13 final size:13
Alignment explanation
Indices: 279860--279884 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
279850 ATTACTCAAA
279860 TGTATCGATACAT
1 TGTATCGATACAT
279873 TGTATCGATACA
1 TGTATCGATACA
279885 CTGATATTTG
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:279935 original size:52 final size:52
Alignment explanation
Indices: 279873--280013 Score: 203
Period size: 52 Copynumber: 2.7 Consensus size: 52
279863 ATCGATACAT
** *
279873 TGTATCGATACACTGAT-ATTTGTATCGATACATGCAGGCAAATTCGCCCAGA
1 TGTATCGATACACT-ATAAAATGTATCGATACATGCAGGCAAATTCGCCAAGA
* *
279925 TGTATCGATACACTATAAAATGTATCGATACATACAGGCAAATTTGCCAAGA
1 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTCGCCAAGA
* *
279977 TATATCGATACACTATGAAATGTATCGATACATGCAG
1 TGTATCGATACACTATAAAATGTATCGATACATGCAG
280014 AAAATTTTCA
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 2 0.03
52 78 0.98
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTCGCCAAGA
Found at i:280913 original size:20 final size:19
Alignment explanation
Indices: 280869--280914 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
280859 GTTAACAGCC
* *
280869 CATGATTCATGCATTTGAG
1 CATGTTTCATGCATTTCAG
280888 CTATGTTTCATGCATTTACAG
1 C-ATGTTTCATGCATTT-CAG
280909 CATGTT
1 CATGTT
280915 CAGCACCTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 19 0.83
21 3 0.13
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (19 bp):
CATGTTTCATGCATTTCAG
Found at i:284854 original size:156 final size:156
Alignment explanation
Indices: 284562--284881 Score: 400
Period size: 156 Copynumber: 2.1 Consensus size: 156
284552 TATTCACCAG
* * *
284562 ATATCATCATTTAAATCATGTTAAATCACTTTTGAAAAATTCATTTTCTTTCATGAGTTTTTCAT
1 ATATCATCACTTAAATCATGGTAAATCAATTTTGAAAAATTCATTTTCTTTCATGAGTTTTTCAT
* * *
284627 TTTTTACTTGAAATTCTCTTATTTCCAAAATATAGAGTTTTTTATTCTATAAATATTTTCGAAAA
66 TTTTTACTTGAAATTCTCCTATTTCCAAAATACAGAGTTTTCTATTCTATAAATATTTTCGAAAA
*
284692 GGTTTTTCTCGGTTCAAAATTTTTA-A
131 -GTTTTTCTCGATTCAAAATTTTTAGA
* * * *
284718 ATATCATTACTTAAATCATGGTAAATCAATTTTGAAAATTTTATTTAT-TTTCATGAGTTTTTCT
1 ATATCATCACTTAAATCATGGTAAATCAATTTTGAAAAATTCATTT-TCTTTCATGAGTTTTTCA
* * **
284782 TTTTTTCCCTTGAAATTTTCCTATTTTTTAAAAT-CA-AGTTTTCTATTCTATAAATATTTTCGA
65 TTTTTT-ACTTGAAATTCTCCTA-TTTCCAAAATACAGAGTTTTCTATTCTATAAATATTTTCGA
*
284845 GAGAA-TTTTTCTCGATTTAAAATTTTTAGA
128 -A-AAGTTTTTCTCGATTCAAAATTTTTAGA
284875 AT-TCATC
1 ATATCATC
284882 TAATATTGTT
Statistics
Matches: 141, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
156 112 0.79
157 19 0.13
158 10 0.07
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (156 bp):
ATATCATCACTTAAATCATGGTAAATCAATTTTGAAAAATTCATTTTCTTTCATGAGTTTTTCAT
TTTTTACTTGAAATTCTCCTATTTCCAAAATACAGAGTTTTCTATTCTATAAATATTTTCGAAAA
GTTTTTCTCGATTCAAAATTTTTAGA
Found at i:292930 original size:30 final size:30
Alignment explanation
Indices: 292894--292972 Score: 122
Period size: 31 Copynumber: 2.6 Consensus size: 30
292884 TGCATAGTAC
292894 ATGTATCGATACATTTTGTTTTTTACCCAG
1 ATGTATCGATACATTTTGTTTTTTACCCAG
* * *
292924 ATGTATCGATAGATTCTAGTTTTTTACCTAG
1 ATGTATCGATACATT-TTGTTTTTTACCCAG
292955 ATGTATCGATACATTTTG
1 ATGTATCGATACATTTTG
292973 AGCATTTCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 16 0.37
31 27 0.63
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (30 bp):
ATGTATCGATACATTTTGTTTTTTACCCAG
Found at i:295145 original size:24 final size:26
Alignment explanation
Indices: 295113--295163 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
295103 TATCAAAATT
295113 CTATTCAT-C-GGGGATACTCCAACC
1 CTATTCATCCAGGGGATACTCCAACC
*
295137 CTATTCATCCGAGGGGATGCTCCAACC
1 CTATTCATCC-AGGGGATACTCCAACC
295164 TCGTTTGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 8 0.35
25 1 0.04
27 14 0.61
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.24
Consensus pattern (26 bp):
CTATTCATCCAGGGGATACTCCAACC
Found at i:296021 original size:20 final size:20
Alignment explanation
Indices: 295974--296011 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
295964 ACATTTAATT
295974 GTATCGATACATGTTGCACA
1 GTATCGATACATGTTGCACA
*
295994 GTATCGATACCTGTTGCA
1 GTATCGATACATGTTGCA
296012 TTATATCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCACA
Found at i:297256 original size:20 final size:20
Alignment explanation
Indices: 297231--297284 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
297221 AAAATCCTTA
297231 AAAGTATCGATACACAATTC
1 AAAGTATCGATACACAATTC
297251 AAAGTATCGATACACAATTC
1 AAAGTATCGATACACAATTC
297271 AAAGTATCGATACA
1 AAAGTATCGATACA
297285 TGTTGCAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.24
Consensus pattern (20 bp):
AAAGTATCGATACACAATTC
Found at i:297394 original size:13 final size:13
Alignment explanation
Indices: 297376--297401 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
297366 TACACAAAGT
297376 ATGTATCGATACA
1 ATGTATCGATACA
297389 ATGTATCGATACA
1 ATGTATCGATACA
297402 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:297399 original size:32 final size:33
Alignment explanation
Indices: 297358--297421 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
297348 TAGCCAAACT
**
297358 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
297390 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
297422 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:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:305473 original size:33 final size:33
Alignment explanation
Indices: 305431--305494 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
305421 CACATTTAAT
*
305431 TGTATCGATACATGTTGCACAGTATCGATACAC
1 TGTATCGATACATATTGCACAGTATCGATACAC
* **
305464 TGTATCGATACCTATTGCATTGTATCGATAC
1 TGTATCGATACATATTGCACAGTATCGATAC
305495 TTCAAAAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATATTGCACAGTATCGATACAC
Found at i:305586 original size:13 final size:13
Alignment explanation
Indices: 305568--305592 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
305558 ACACACAGTA
305568 TGTATCGATACAC
1 TGTATCGATACAC
305581 TGTATCGATACA
1 TGTATCGATACA
305593 ACATAAAATG
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:305609 original size:33 final size:32
Alignment explanation
Indices: 305549--305612 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
305539 TAGCCAAACT
**
305549 TGTATCGATACACACAGTATGTATCGATACAC
1 TGTATCGATACACACAAAATGTATCGATACAC
*
305581 TGTATCGATACAACATAAAATGTATCGATACA
1 TGTATCGATAC-ACACAAAATGTATCGATACA
305613 TTGGCCTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAC
Found at i:307317 original size:20 final size:20
Alignment explanation
Indices: 307292--307329 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
307282 TATTCATAAT
307292 TAAATTGTATCGATACATGG
1 TAAATTGTATCGATACATGG
*
307312 TAAATTGTATCGGTACAT
1 TAAATTGTATCGATACAT
307330 TAAGCCCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (20 bp):
TAAATTGTATCGATACATGG
Found at i:307843 original size:31 final size:31
Alignment explanation
Indices: 307768--307893 Score: 162
Period size: 31 Copynumber: 3.9 Consensus size: 31
307758 GATTTAGAGA
*
307768 TTCTATCTTAGCCTTTGAAAAAGATATGGAGAAAGG
1 TTCTATCTTAGCCTGTG-AAAAGATA-GG-G--AGG
* *
307804 TTCCATCTTAGCTTGTGAAAAGATAGGGAGG
1 TTCTATCTTAGCCTGTGAAAAGATAGGGAGG
*
307835 TTCTATCTTAGCCTATGAAAAGATAGGGAGG
1 TTCTATCTTAGCCTGTGAAAAGATAGGGAGG
*
307866 TTCTATCTTAGCCTGTTAAAAGATAGGG
1 TTCTATCTTAGCCTGTGAAAAGATAGGG
307894 TTGTAAGGTT
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
31 57 0.70
33 1 0.01
34 2 0.02
35 8 0.10
36 14 0.17
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.31
Consensus pattern (31 bp):
TTCTATCTTAGCCTGTGAAAAGATAGGGAGG
Found at i:307903 original size:67 final size:66
Alignment explanation
Indices: 307768--307893 Score: 179
Period size: 62 Copynumber: 2.0 Consensus size: 66
307758 GATTTAGAGA
* *
307768 TTCTATCTTAGCCTTTGAAAAAGATATGGAGAAAGGTTCCATCTTAGCTTGTGAAAAGATAGGGA
1 TTCTATCTTAGCCTATGAAAAAGATATGGAG-AAGGTTCCATCTTAGCCTGTGAAAAGATAGGGA
307833 GG
65 GG
* *
307835 TTCTATCTTAGCCTATG-AAAAGATA-GG-G-AGGTTCTATCTTAGCCTGTTAAAAGATAGGG
1 TTCTATCTTAGCCTATGAAAAAGATATGGAGAAGGTTCCATCTTAGCCTGTGAAAAGATAGGG
307894 TTGTAAGGTT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
62 28 0.51
64 1 0.02
65 2 0.04
66 8 0.15
67 16 0.29
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.31
Consensus pattern (66 bp):
TTCTATCTTAGCCTATGAAAAAGATATGGAGAAGGTTCCATCTTAGCCTGTGAAAAGATAGGGAG
G
Found at i:313211 original size:71 final size:69
Alignment explanation
Indices: 313135--313627 Score: 448
Period size: 71 Copynumber: 7.0 Consensus size: 69
313125 CGCCTTTTCT
* * * * *
313135 TCACTTATCTACTCTATTCCTCAAAGTACACAATGCTTTTTCTTTTTCAAAGCTCACACAAGCTG
1 TCACTTATCTTCTCTAGTCCTCAAAG-ACAGAATGCTTTTT-TTCTTCAAAGCCCACACAAGCTG
313200 GTGGCA
64 GTGGCA
* * *
313206 TCACTTATTTTCTCTAGTCCTCAAAGAGCAGGATGTCATTTTTTCTTCAAAGCCCACACAAGCTG
1 TCACTTATCTTCTCTAGTCCTCAAAGA-CAGAATG-CTTTTTTTCTTCAAAGCCCACACAAGCTG
313271 GTGGCA
64 GTGGCA
* * * * *
313277 TCACTTATTTTCTCTAGTCCTCAAAGAGCATAATGTCATTTTTTCTTCAAAGCCCACACAAGATT
1 TCACTTATCTTCTCTAGTCCTCAAAGA-CAGAATG-CTTTTTTTCTTCAAAGCCCACACAAGCTG
*
313342 GTAGCA
64 GTGGCA
* * * * * *
313348 TCATTTAT-TTCTTTAATCTTCCAAA-AGCA-ACATGCTTTTTCTTCTTCAAAGCCCATACAAGT
1 TCACTTATCTTCTCTAGTCCT-CAAAGA-CAGA-ATGCTTTTT-TTCTTCAAAGCCCACACAAGC
*
313410 TGATGGCA
62 TGGTGGCA
* * * *
313418 TCATTTATCTTCTTTAGTCCTCAAAGAGTAGAA--CATTTTTTTATTCAAAGCCCACACAAGCTG
1 TCACTTATCTTCTCTAGTCCTCAAAGA-CAGAATGC-TTTTTTTCTTCAAAGCCCACACAAGCTG
*
313481 GTGCCA
64 GTGGCA
* * * *
313487 TCATTTATCTAT-TCTAGTCCTCAAAGAATAGGATAT-CTTTTCTTCTTCAAAGCCCACACAAGT
1 TCACTTATCT-TCTCTAGTCCTCAAAG-ACA-GA-ATGCTTTTTTTCTTCAAAGCCCACACAAGC
313550 TGGTGGCA
62 TGGTGGCA
* *
313558 TCGCTTATCTTTTCTAGTCCTCAAA-A-AGTATGATGCTTTTTTTTCTTCAAAGCCCACACAAGC
1 TCACTTATCTTCTCTAGTCCTCAAAGACAG-A--ATGC-TTTTTTTCTTCAAAGCCCACACAAGC
313621 T-GTGGCA
62 TGGTGGCA
313628 CCTACCCACC
Statistics
Matches: 362, Mismatches: 41, Indels: 39
0.82 0.09 0.09
Matches are distributed among these distances:
67 1 0.00
68 2 0.01
69 59 0.16
70 70 0.19
71 223 0.62
72 7 0.02
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.35
Consensus pattern (69 bp):
TCACTTATCTTCTCTAGTCCTCAAAGACAGAATGCTTTTTTTCTTCAAAGCCCACACAAGCTGGT
GGCA
Found at i:313250 original size:33 final size:33
Alignment explanation
Indices: 313213--313322 Score: 80
Period size: 33 Copynumber: 3.2 Consensus size: 33
313203 GCATCACTTA
313213 TTTTCTCTAGTCCTCAAAGAGCAGGATGTCATT
1 TTTTCTCTAGTCCTCAAAGAGCAGGATGTCATT
* * * * *
313246 TTTTCTTCAAAGCCCACACA-AGCTGG-TGGCATCACTT
1 TTTTC-TC-TAGTCCTCAAAGAGCAGGAT-G--TCA-TT
**
313283 ATTTTCTCTAGTCCTCAAAGAGCATAATGTCATT
1 -TTTTCTCTAGTCCTCAAAGAGCAGGATGTCATT
313317 TTTTCT
1 TTTTCT
313323 TCAAAGCCCA
Statistics
Matches: 56, Mismatches: 12, Indels: 18
0.65 0.14 0.21
Matches are distributed among these distances:
33 12 0.21
34 10 0.18
35 10 0.18
36 10 0.18
37 8 0.14
38 6 0.11
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.37
Consensus pattern (33 bp):
TTTTCTCTAGTCCTCAAAGAGCAGGATGTCATT
Found at i:313535 original size:210 final size:210
Alignment explanation
Indices: 313167--313627 Score: 551
Period size: 210 Copynumber: 2.2 Consensus size: 210
313157 AAAGTACACA
* * *
313167 ATGCTTTTTCTTTTTCAAAGCTCACACAAGCTGGTGGCATCACTTATTTTCTCTAGTCCTCAAAG
1 ATGCTTTTTCTTCTTCAAAGCCCACACAAGCT-GTGGCATCACTTATCTTCTCTAGTCCTCAAAG
* * * *
313232 AGCAGGATGTCATTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCACTTATTTTCTCTAGTCC
65 AGCAGGA-GACATTTTTTATTCAAAGCCCACACAAGCTGGTGCCATCACTTATTATCTCTAGTCC
* *
313297 TCAAAGAGCATAATGTCATTTTTTCTTCAAAGCCCACACAAGATT-GTAGCATCATTTAT-TTCT
129 TCAAAGA-CATAATATCATTTTTTCTTCAAAGCCCACACAAG-TTGGTAGCATCACTTATCTT-T
* *
313360 T-TAATCTTCCAAAAGCAAC
191 TCTAATCCTCAAAAAGCAAC
* * * *
313379 ATGCTTTTTCTTCTTCAAAGCCCATACAAGTTGATGGCATCATTTATCTTCTTTAGTCCTCAAAG
1 ATGCTTTTTCTTCTTCAAAGCCCACACAAGCTG-TGGCATCACTTATCTTCTCTAGTCCTCAAAG
* *
313444 AGTA-GA-ACATTTTTTTATTCAAAGCCCACACAAGCTGGTGCCATCATTTATCTAT-TCTAGTC
65 AGCAGGAGACA-TTTTTTATTCAAAGCCCACACAAGCTGGTGCCATCACTTAT-TATCTCTAGTC
* *
313506 CTCAAAGA-ATAGGATATC-TTTTCTTCTTCAAAGCCCACACAAGTTGGTGGCATCGCTTATCTT
128 CTCAAAGACATA--ATATCATTTT-TTCTTCAAAGCCCACACAAGTTGGTAGCATCACTTATCTT
* * **
313569 TTCTAGTCCTCAAAAAGTATG
190 TTCTAATCCTCAAAAAGCAAC
*
313590 ATGCTTTTTTTTCTTCAAAGCCCACACAAGCTGTGGCA
1 ATGCTTTTTCTTCTTCAAAGCCCACACAAGCTGTGGCA
313628 CCTACCCACC
Statistics
Matches: 214, Mismatches: 26, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
208 3 0.01
209 8 0.04
210 95 0.44
211 49 0.23
212 59 0.28
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.36
Consensus pattern (210 bp):
ATGCTTTTTCTTCTTCAAAGCCCACACAAGCTGTGGCATCACTTATCTTCTCTAGTCCTCAAAGA
GCAGGAGACATTTTTTATTCAAAGCCCACACAAGCTGGTGCCATCACTTATTATCTCTAGTCCTC
AAAGACATAATATCATTTTTTCTTCAAAGCCCACACAAGTTGGTAGCATCACTTATCTTTTCTAA
TCCTCAAAAAGCAAC
Found at i:317036 original size:88 final size:86
Alignment explanation
Indices: 316877--317227 Score: 346
Period size: 88 Copynumber: 4.0 Consensus size: 86
316867 GATTTTAGGA
** * * * * * * *
316877 AAACTCTATCCTTACTATTTCGAGGGGATATTCTAA-CCTGTTCTAACAAAAATTCAAAGTTTCC
1 AAACTCTATCCCCACTATTCCGAGAGGATACTCCAACCCTATTCTATCAAAAATTCAAA-TTTTC
*
316941 TTTGTATAATTCTATCCTTGGG
65 TTTGTATAATTTTATCCTTGGG
* * **
316963 CAAACTCTATCCCCATTATTCCGAGAGGATATTCCAACCCCGTTCTATCAAAAATTCAAATTTTC
1 -AAACTCTATCCCCACTATTCCGAGAGGATACTCCAACCCTATTCTATCAAAAATTCAAATTTTC
317028 TTTCGTATAATTTTATCCTTGGGG
65 TTT-GTATAATTTTATCCTT-GGG
* * *
317052 AAACTCGATCCCCACTATTCC-AAAGGGATACTCTAACCCTATTCTATCAAAAATTCAAATTTTC
1 AAACTCTATCCCCACTATTCCGAGA-GGATACTCCAACCCTATTCTATCAAAAATTCAAATTTTC
317116 TTTCGTATAATTTTATCCTTGGAG
65 TTT-GTATAATTTTATCCTTGG-G
* ** * ** * * * * *
317140 AAACTCCATCCTTATTCCTCGGAGGGGATACTCCAATCCTATTTTACCAAAAATTTCAAATTTTA
1 AAACTCTATCCCCACTATTCCGAGAGGATACTCCAACCCTATTCTATCAAAAA-TTCAAATTTT-
*
317205 CTTTATATAATTTTATCCTTGGG
64 CTTTGTATAATTTTATCCTTGGG
317228 GGAAACTCCC
Statistics
Matches: 225, Mismatches: 31, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
87 41 0.18
88 149 0.66
89 31 0.14
90 4 0.02
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.37
Consensus pattern (86 bp):
AAACTCTATCCCCACTATTCCGAGAGGATACTCCAACCCTATTCTATCAAAAATTCAAATTTTCT
TTGTATAATTTTATCCTTGGG
Found at i:325215 original size:21 final size:22
Alignment explanation
Indices: 325191--325232 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
325181 TTCAGGCTTT
*
325191 AATAA-TGTTTAAAAATGTTTA
1 AATAATTGATTAAAAATGTTTA
*
325212 AATAATTGATTAAAATTGTTT
1 AATAATTGATTAAAAATGTTT
325233 TAAAAGGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (22 bp):
AATAATTGATTAAAAATGTTTA
Done.