Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015217.1 Kokia drynarioides strain JFW-HI SEQ_130261, whole genome shotgun sequence
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: 264354
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 343 characters in sequence are not A, C, G, or T
Found at i:1760 original size:28 final size:28
Alignment explanation
Indices: 1729--1782 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1719 TACTTTTATA
*
1729 AGTTCAAACTCCGGCACCCTTTAATCGT
1 AGTTCAAACTCCGACACCCTTTAATCGT
**
1757 AGTTCCTACTCCGACACCCTTTAATC
1 AGTTCAAACTCCGACACCCTTTAATC
1783 TCTTGCTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.24, C:0.35, G:0.11, T:0.30
Consensus pattern (28 bp):
AGTTCAAACTCCGACACCCTTTAATCGT
Found at i:16582 original size:25 final size:24
Alignment explanation
Indices: 16540--16588 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
16530 TTGTTTTCAA
16540 TTTTATTTAATTAAAAAAACAAATT
1 TTTTATTTAATTAAAAAAA-AAATT
* **
16565 TTTTATTTTATTTTAAAAAAAATT
1 TTTTATTTAATTAAAAAAAAAATT
16589 CATGGAACTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTTATTTAATTAAAAAAAAAATT
Found at i:28123 original size:51 final size:51
Alignment explanation
Indices: 28047--28200 Score: 308
Period size: 51 Copynumber: 3.0 Consensus size: 51
28037 AACACTTAAG
28047 TTGCAAGCATAAATGTTACAATACATCATATTGAATAGTTTCAAATGACAA
1 TTGCAAGCATAAATGTTACAATACATCATATTGAATAGTTTCAAATGACAA
28098 TTGCAAGCATAAATGTTACAATACATCATATTGAATAGTTTCAAATGACAA
1 TTGCAAGCATAAATGTTACAATACATCATATTGAATAGTTTCAAATGACAA
28149 TTGCAAGCATAAATGTTACAATACATCATATTGAATAGTTTCAAATGACAA
1 TTGCAAGCATAAATGTTACAATACATCATATTGAATAGTTTCAAATGACAA
28200 T
1 T
28201 CAAGGCAACC
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 103 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.32
Consensus pattern (51 bp):
TTGCAAGCATAAATGTTACAATACATCATATTGAATAGTTTCAAATGACAA
Found at i:30782 original size:23 final size:23
Alignment explanation
Indices: 30756--30806 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
30746 AAAAATATAT
* *
30756 TAATTTTTTTAATAGTTCAAATA
1 TAATTATTTTAATAATTCAAATA
*
30779 TAATTATTTTGATAATTCAAATA
1 TAATTATTTTAATAATTCAAATA
30802 TAATT
1 TAATT
30807 CTAACTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (23 bp):
TAATTATTTTAATAATTCAAATA
Found at i:31123 original size:16 final size:16
Alignment explanation
Indices: 31087--31125 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
31077 CTCATATTTG
*
31087 ATTTTT-TTTAAATTA
1 ATTTTTATTTAAAATA
31102 ATTTTTTATTTAAAATA
1 A-TTTTTATTTAAAATA
31119 ATTTTTA
1 ATTTTTA
31126 AGAAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 11 0.52
17 9 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTTTATTTAAAATA
Found at i:31124 original size:18 final size:16
Alignment explanation
Indices: 31088--31124 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
31078 TCATATTTGA
*
31088 TTTTTTTTAAATTAAT
1 TTTTTTTTAAAATAAT
31104 TTTTTATTTAAAATAAT
1 TTTTT-TTTAAAATAAT
31121 TTTT
1 TTTT
31125 AAGAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTTTTAAAATAAT
Found at i:31253 original size:43 final size:41
Alignment explanation
Indices: 31206--31297 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 41
31196 AAAAAAGTAT
* *
31206 TTATATTAAAAAAAACACAACTATAAATATAATAAATCTTTCA
1 TTATATTAAAAAAAACACAA--ATAAATAAAATAAATATTTCA
* *
31249 TTATA--ATAAAAAACACAAATAAATAAAATAAATATTTTA
1 TTATATTAAAAAAAACACAAATAAATAAAATAAATATTTCA
31288 TTATATTAAA
1 TTATATTAAA
31298 CATAATTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
39 23 0.55
41 14 0.33
43 5 0.12
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.34
Consensus pattern (41 bp):
TTATATTAAAAAAAACACAAATAAATAAAATAAATATTTCA
Found at i:32611 original size:21 final size:24
Alignment explanation
Indices: 32573--32616 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
32563 TTTAACAAAA
*
32573 AAAAAAGAAATTTTAAAA-TATTC
1 AAAAAAGAAATTTAAAAACTATTC
32596 AAAAAA-AAA-TTAAAAACTATT
1 AAAAAAGAAATTTAAAAACTATT
32617 TAGTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 7 0.37
23 6 0.32
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (24 bp):
AAAAAAGAAATTTAAAAACTATTC
Found at i:34139 original size:31 final size:31
Alignment explanation
Indices: 34091--34157 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
34081 TAAAGTCCTT
* *
34091 TGAACTTAGTAATTATT-CTAACATTGTAGCA
1 TGAACTTAGTAACTATTCCT-ACATTGAAGCA
*
34122 TGAA-TTAGTTAACTATTCCTACATTGAAGCT
1 TGAACTTAG-TAACTATTCCTACATTGAAGCA
34153 TGAAC
1 TGAAC
34158 CTTTTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
30 4 0.13
31 24 0.80
32 2 0.07
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.37
Consensus pattern (31 bp):
TGAACTTAGTAACTATTCCTACATTGAAGCA
Found at i:40731 original size:30 final size:30
Alignment explanation
Indices: 40695--40765 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
40685 GGACCCCAAA
*
40695 AAGTTTAAGTACCAACTTA-AAACAAGTGTC
1 AAGTTTAAGTACCAAATTAGAAA-AAGTGTC
* *
40725 AAGTTTAGGTACCAAATTAGGAAAAGTGTC
1 AAGTTTAAGTACCAAATTAGAAAAAGTGTC
*
40755 AAGTTTGAGTA
1 AAGTTTAAGTA
40766 TTAAATTGGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 33 0.94
31 2 0.06
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (30 bp):
AAGTTTAAGTACCAAATTAGAAAAAGTGTC
Found at i:40809 original size:28 final size:28
Alignment explanation
Indices: 40725--40809 Score: 66
Period size: 28 Copynumber: 3.0 Consensus size: 28
40715 AACAAGTGTC
* ***
40725 AAGTTTAGGTACCAAATTAGGAAAAGTGTC
1 AAGTTTAGGTATCAAATTAGGAAAA--AAA
* *
40755 AAGTTT-GAGTATTAAATT-GGACCAAAAA
1 AAGTTTAG-GTATCAAATTAGGA-AAAAAA
40783 AAGTTTAGGTATCAAATTAGGAAAAAA
1 AAGTTTAGGTATCAAATTAGGAAAAAA
40810 TATCAAGTTC
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
28 19 0.44
29 8 0.19
30 16 0.37
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.27
Consensus pattern (28 bp):
AAGTTTAGGTATCAAATTAGGAAAAAAA
Found at i:40818 original size:89 final size:89
Alignment explanation
Indices: 40640--40830 Score: 217
Period size: 89 Copynumber: 2.1 Consensus size: 89
40630 TAAAAAAAAA
**
40640 TTAGGTACCAAATTAGGAAAAATAGTCAAGTTCAGGTACCAAATTGGACCCCAAAAAGTTTAAGT
1 TTAGGTACCAAATTAGGAAAAATAGTCAAGTTCAGGTACCAAATTGGACCAAAAAAAGTTTAAGT
* * *
40705 ACCAACTTAAAACAAGTGTCAAGT
66 ACCAAATTAAAACAAATATCAAGT
* * ** *
40729 TTAGGTACCAAATTAGGAAAAGT-GTCAAGTT-TGAGTATTAAATTGGACCAAAAAAAGTTTAGG
1 TTAGGTACCAAATTAGGAAAAATAGTCAAGTTCAG-GTACCAAATTGGACCAAAAAAAGTTTAAG
*
40792 TATCAAATTAGGAAA-AAATATCAAGT
65 TACCAAATTA--AAACAAATATCAAGT
* *
40818 TCAAGTACCAAAT
1 TTAGGTACCAAAT
40831 GTTATATTAA
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
87 1 0.01
88 40 0.47
89 42 0.49
90 3 0.03
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (89 bp):
TTAGGTACCAAATTAGGAAAAATAGTCAAGTTCAGGTACCAAATTGGACCAAAAAAAGTTTAAGT
ACCAAATTAAAACAAATATCAAGT
Found at i:40988 original size:18 final size:16
Alignment explanation
Indices: 40956--40994 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
40946 TTGGTCTTTA
40956 AAATTAAAAAATATAT
1 AAATTAAAAAATATAT
*
40972 GAATTAAAAAAATTATAT
1 AAATT-AAAAAA-TATAT
40990 AAATT
1 AAATT
40995 TTCAATGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 4 0.21
17 6 0.32
18 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
AAATTAAAAAATATAT
Found at i:46366 original size:20 final size:21
Alignment explanation
Indices: 46318--46366 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
46308 TTCGACAGAA
46318 TTAATA-TTTATTATTTGAAAG
1 TTAATATTTTATTATTT-AAAG
*
46339 -T-ATCTTTTATTATTT-AAG
1 TTAATATTTTATTATTTAAAG
46357 TTAATATTTT
1 TTAATATTTT
46367 GAAGTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 7
0.72 0.06 0.22
Matches are distributed among these distances:
18 3 0.13
19 3 0.13
20 17 0.74
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (21 bp):
TTAATATTTTATTATTTAAAG
Found at i:46895 original size:19 final size:19
Alignment explanation
Indices: 46852--46901 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
46842 TTGAAAAAAA
*
46852 TATTAATTTAATAAAATAG
1 TATTAATTAAATAAAATAG
*
46871 -ACTTAATTAAATAATATAG
1 TA-TTAATTAAATAAAATAG
46890 TATTAATCTAAA
1 TATTAAT-TAAA
46902 ATATAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 1 0.04
19 20 0.77
20 5 0.19
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (19 bp):
TATTAATTAAATAAAATAG
Found at i:46911 original size:5 final size:5
Alignment explanation
Indices: 46901--46925 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
46891 ATTAATCTAA
46901 AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT
46926 TTTTATGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:47516 original size:2 final size:2
Alignment explanation
Indices: 47504--47536 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
47494 TAACATAATG
47504 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47537 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:60912 original size:16 final size:17
Alignment explanation
Indices: 60891--60927 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
60881 ATTTAGATGC
60891 AATTTTTA-GAAAAAAA
1 AATTTTTAGGAAAAAAA
60907 AATTTTTAGGAAAAAAA
1 AATTTTTAGGAAAAAAA
60924 AATT
1 AATT
60928 ATTATTGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (17 bp):
AATTTTTAGGAAAAAAA
Found at i:70382 original size:104 final size:103
Alignment explanation
Indices: 70251--70523 Score: 291
Period size: 105 Copynumber: 2.6 Consensus size: 103
70241 TGAACCGGAT
* *
70251 TAAAACC-TGAGTTCAT-AGGTCAAAACCGCTAAACATCATAAAAGATATGATATTTGAATCCAA
1 TAAAACCTTGAGTTCATAAGG-CAAAACCGCTAAATATCATAAAAGATATGAAATTTGAATCCAA
* ** **
70314 TGCCGGTAATATATGACCTCAGGTAACCGCATGATTAGAAC
65 T-CCAGTAA-ATACCACCTCAGGTAACCGCATGAACAGAAC
* * *
70355 T-AAACCTTGAGTTCATAAGGCAAAACCGCAAAATATCATTAAAAAATATGAGATTTGAATCCAA
1 TAAAACCTTGAGTTCATAAGGCAAAACCGCTAAATATCA-TAAAAGATATGAAATTTGAATCC-A
* * * * *
70419 ATCCAGTAAATACCACTTCGGGTAACCGCATGAACCGGAT
64 ATCCAGTAAATACCACCTCAGGTAACCGCATGAACAGAAC
* * * * *
70459 TAAAACCTAGAGTTCATAAGTCAAATCCGCTAAATATTATACAAGATATCGAAATTTGAATCCAA
1 TAAAACCTTGAGTTCATAAGGCAAAACCGCTAAATATCATAAAAGATAT-GAAATTTGAATCCAA
70524 ATCCGCTAAA
Statistics
Matches: 141, Mismatches: 22, Indels: 12
0.81 0.13 0.07
Matches are distributed among these distances:
103 5 0.04
104 59 0.42
105 74 0.52
106 3 0.02
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (103 bp):
TAAAACCTTGAGTTCATAAGGCAAAACCGCTAAATATCATAAAAGATATGAAATTTGAATCCAAT
CCAGTAAATACCACCTCAGGTAACCGCATGAACAGAAC
Found at i:70475 original size:105 final size:102
Alignment explanation
Indices: 70199--70565 Score: 330
Period size: 104 Copynumber: 3.5 Consensus size: 102
70189 AAGGTCTGCG
* * * ** **
70199 ATTTGAATCCAAATCAGCTAAATATCAACTCAATTAACCAAATGAACCGGATTAAAACCTGAGTT
1 ATTTGAATCCAAATCCG-TAAATACCACCTCAGGTAACCGCATGAACCGGATTAAAACCTGAGTT
* *
70264 CAT-AGGTCAAAACCGCTAAACATCATAAAAGATATGAT
65 CATAAGG-CAAAACCGCTAAATATCATAAAAGATATGAA
** *** * *
70302 ATTTGAATCC-AATGCCGGTAATATATGACCTCAGGTAACCGCATGATTAGAACT-AAACCTTGA
1 ATTTGAATCCAAAT-CC-GTAA-ATACCACCTCAGGTAACCGCATGAACCGGATTAAAACC-TGA
* * *
70365 GTTCATAAGGCAAAACCGCAAAATATCATTAAAAAATATGAG
62 GTTCATAAGGCAAAACCGCTAAATATCA-TAAAAGATATGAA
* *
70407 ATTTGAATCCAAATCCAGTAAATACCACTTCGGGTAACCGCATGAACCGGATTAAAACCTAGAGT
1 ATTTGAATCCAAATCC-GTAAATACCACCTCAGGTAACCGCATGAACCGGATTAAAACCT-GAGT
* * * *
70472 TCATAAGTCAAATCCGCTAAATATTATACAAGATATCGAA
64 TCATAAGGCAAAACCGCTAAATATCATAAAAGATAT-GAA
*** *
70512 ATTTGAATCCAAATCCGCTAAATATTGCCTC-GGCTAACC-TATGAACCGGATTAA
1 ATTTGAATCCAAATCCG-TAAATACCACCTCAGG-TAACCGCATGAACCGGATTAA
70566 GCTTCGAGTT
Statistics
Matches: 214, Mismatches: 38, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
102 3 0.01
103 19 0.09
104 96 0.45
105 93 0.43
106 3 0.01
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (102 bp):
ATTTGAATCCAAATCCGTAAATACCACCTCAGGTAACCGCATGAACCGGATTAAAACCTGAGTTC
ATAAGGCAAAACCGCTAAATATCATAAAAGATATGAA
Found at i:80118 original size:13 final size:13
Alignment explanation
Indices: 80100--80126 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
80090 TAACCCTTTG
80100 ACCTTGCACACAC
1 ACCTTGCACACAC
80113 ACCTTGCACACAC
1 ACCTTGCACACAC
80126 A
1 A
80127 GGCACTCGAA
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:0.33, C:0.44, G:0.07, T:0.15
Consensus pattern (13 bp):
ACCTTGCACACAC
Found at i:81967 original size:69 final size:69
Alignment explanation
Indices: 81856--81994 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
81846 TCATGATTCC
81856 TGTGATAACTGATATATAGAAGCTAGTTTTATTGATTTGAAGAAATAATCTTATCTGGTTGTTTA
1 TGTGATAACTGATATATAGAAGCTAGTTTTATTGATTTGAAGAAATAATCTTATCTGGTTGTTTA
81921 TGTG
66 TGTG
*
81925 TGTGATAACTGATATATAGATGCTAGTTTTATTGATTTGAAGAAATAATCTTATCTGGTTGTTTA
1 TGTGATAACTGATATATAGAAGCTAGTTTTATTGATTTGAAGAAATAATCTTATCTGGTTGTTTA
81990 TGTG
66 TGTG
81994 T
1 T
81995 TTAAGTTTTA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.45
Consensus pattern (69 bp):
TGTGATAACTGATATATAGAAGCTAGTTTTATTGATTTGAAGAAATAATCTTATCTGGTTGTTTA
TGTG
Found at i:81990 original size:34 final size:34
Alignment explanation
Indices: 81883--81990 Score: 94
Period size: 34 Copynumber: 3.1 Consensus size: 34
81873 AGAAGCTAGT
81883 TTTATTGATTTGAAGAAATAATCTTATCTGGTTG
1 TTTATTGATTTGAAGAAATAATCTTATCTGGTTG
* * * * * ** * *
81917 TTTATGTG-TGTG-ATAACTGATATATAGATGCTAG
1 TTTAT-TGATTTGAAGAAATAATCT-TATCTGGTTG
81951 TTTTATTGATTTGAAGAAATAATCTTATCTGGTTG
1 -TTTATTGATTTGAAGAAATAATCTTATCTGGTTG
81986 TTTAT
1 TTTAT
81991 GTGTTTAAGT
Statistics
Matches: 51, Mismatches: 18, Indels: 10
0.65 0.23 0.13
Matches are distributed among these distances:
33 7 0.14
34 21 0.41
35 16 0.31
36 7 0.14
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.47
Consensus pattern (34 bp):
TTTATTGATTTGAAGAAATAATCTTATCTGGTTG
Found at i:84280 original size:2 final size:2
Alignment explanation
Indices: 84273--84320 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
84263 TGAAGTATGC
84273 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
84315 AT AT AT
1 AT AT AT
84321 GAAATTTTGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84538 original size:15 final size:17
Alignment explanation
Indices: 84496--84543 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 17
84486 ATTAATTTAA
*
84496 ATCAAAATTT--TATGT
1 ATCAAAATTTCATATAT
84511 AT-AAAATTTCATA-AT
1 ATCAAAATTTCATATAT
84526 ATCAAAA-TTCATATAT
1 ATCAAAATTTCATATAT
84542 AT
1 AT
84544 AATTACATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 7 0.25
15 11 0.39
16 10 0.36
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (17 bp):
ATCAAAATTTCATATAT
Found at i:84573 original size:29 final size:29
Alignment explanation
Indices: 84475--84576 Score: 79
Period size: 29 Copynumber: 3.5 Consensus size: 29
84465 TTGTATTAAT
*
84475 AATTTATG-AAAATTA-AT-TTAAATCAA
1 AATTTATGTATAATTACATATTAAATCAA
* *
84501 AATTTTATGTATAAAATTTCATA--ATATCAA
1 AA-TTTATGTAT--AATTACATATTAAATCAA
* *
84531 AATTCATATATATAATTACATATTAAATTAA
1 AATT--TATGTATAATTACATATTAAATCAA
84562 AATTTATGTATAATT
1 AATTTATGTATAATT
84577 TTAATATTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
26 2 0.03
27 6 0.10
28 1 0.02
29 20 0.34
30 12 0.21
31 17 0.29
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (29 bp):
AATTTATGTATAATTACATATTAAATCAA
Found at i:87583 original size:14 final size:15
Alignment explanation
Indices: 87554--87582 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
87544 TTGGATCACC
87554 ATAAAACGTTTTTTT
1 ATAAAACGTTTTTTT
87569 ATAAAACGTTTTTT
1 ATAAAACGTTTTTT
87583 AAAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (15 bp):
ATAAAACGTTTTTTT
Found at i:87588 original size:14 final size:15
Alignment explanation
Indices: 87556--87588 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
87546 GGATCACCAT
*
87556 AAAACGTTTTTTTAT
1 AAAACGTTTTTTTAA
87571 AAAACG-TTTTTTAA
1 AAAACGTTTTTTTAA
87585 AAAA
1 AAAA
87589 AAAAAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (15 bp):
AAAACGTTTTTTTAA
Found at i:87589 original size:15 final size:15
Alignment explanation
Indices: 87556--87589 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
87546 GGATCACCAT
* *
87556 AAAACGTTTTTTTAT
1 AAAACGTTTTTTAAA
87571 AAAACGTTTTTTAAA
1 AAAACGTTTTTTAAA
87586 AAAA
1 AAAA
87590 AAAAAAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (15 bp):
AAAACGTTTTTTAAA
Found at i:88486 original size:57 final size:59
Alignment explanation
Indices: 88391--88549 Score: 164
Period size: 58 Copynumber: 2.7 Consensus size: 59
88381 TGGATTCTCG
* * * * *
88391 AGGGTGAAATGGTAATTTTGGGAAA-ATTCGAGGTTAAAAATGGAAATTTT-AACAT-TA
1 AGGGTAAAAGGGTAATTTT-TGAAAGTTTCGAGGTTAAAAATGGAAATTTTGAACATCCA
* ** *
88448 AGGGGTAAAAGGGTAA-TTTTGAGAGTTTCGAGGTTAAAAATGGAGTTTTTGGACATCCA
1 A-GGGTAAAAGGGTAATTTTTGAAAGTTTCGAGGTTAAAAATGGAAATTTTGAACATCCA
* * *
88507 AGGGTAAAATGGTAATTTTTGAAAGTTTCAAGGTCAAAAATGG
1 AGGGTAAAAGGGTAATTTTTGAAAGTTTCGAGGTTAAAAATGG
88550 GATTTTGGAA
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
56 3 0.04
57 26 0.31
58 29 0.35
59 26 0.31
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.31
Consensus pattern (59 bp):
AGGGTAAAAGGGTAATTTTTGAAAGTTTCGAGGTTAAAAATGGAAATTTTGAACATCCA
Found at i:88515 original size:58 final size:59
Alignment explanation
Indices: 88417--88558 Score: 175
Period size: 59 Copynumber: 2.5 Consensus size: 59
88407 TTTGGGAAAA
* * * *
88417 TTCGAGGTTAAAAATGGAAATTTT-AACATTAAGGGGTAAAAGGGTAA-TTTTGAGAGT
1 TTCGAGGTTAAAAATGGAGATTTTGGACATCAAGGGGTAAAAGGGTAATTTTTGAAAGT
* *
88474 TTCGAGGTTAAAAATGGAGTTTTTGGACATCCAA-GGGTAAAATGGTAATTTTTGAAAGT
1 TTCGAGGTTAAAAATGGAGATTTTGGACAT-CAAGGGGTAAAAGGGTAATTTTTGAAAGT
* *
88533 TTCAAGGTCAAAAATGG-GATTTTGGA
1 TTCGAGGTTAAAAATGGAGATTTTGGA
88559 AGTTCGGGGG
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
57 22 0.30
58 25 0.34
59 26 0.36
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (59 bp):
TTCGAGGTTAAAAATGGAGATTTTGGACATCAAGGGGTAAAAGGGTAATTTTTGAAAGT
Found at i:88546 original size:59 final size:59
Alignment explanation
Indices: 88450--88882 Score: 254
Period size: 59 Copynumber: 7.3 Consensus size: 59
88440 TAACATTAAG
* * *
88450 GGGTAAAAGGGTAA-TTTTGAGAGTTTCGAGGTTAAAAATGGAGTTTTTGGACA-TCCAA
1 GGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTCAAAAATGGAGTTTTTGGA-AGTCCAA
* * * **
88508 GGGTAAAATGGTAATTTTTGAAAGTTTCAAGGTCAAAAATGG-GATTTTGGAAGTTCGG
1 GGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTCAAAAATGGAGTTTTTGGAAGTCCAA
* * * * *
88566 GGGTAAAAATGG-AATTTTTGGAAGCTTCGGGGTCAAAAATAGGA-TTTTTGGAAGTTTCGA
1 GGGT-AAAATGGTAATTTTTGAAAGTTTCGAGGTCAAAAAT-GGAGTTTTTGGAAG-TCCAA
* * * * *
88626 -GGTCAAAAATAGG-ATTTTTTG-AAGTTTTGGGGT-AAAAATGGAATTTTTGGAAGCTTCAA
1 GGGT--AAAAT-GGTAATTTTTGAAAGTTTCGAGGTCAAAAATGGAGTTTTTGGAAG-TCCAA
* * * * ***
88685 -GGTCAAAAATAGG--ATTTTTGGAAGTTTTGAGGTCAAAAATATGA-TTTTTTGAAGTTCGGG
1 GGGT--AAAAT-GGTAATTTTTGAAAGTTTCGAGGTCAAAAAT-GGAGTTTTTGGAAG-TCCAA
* * * * *
88745 GGGTAAAATGG-AATTTTTGGAAGTTTTGAGGTCGAAAATGG-GATTTTTGGAAGTTCGA
1 GGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTCAAAAATGGAG-TTTTTGGAAGTCCAA
* * * * * *
88803 GGGAAAAAATGG-AATTTTGGGGAAGTTTCGAGGTCAAAAAT-AAGATTTTTGGAAGTTCAG
1 GGG-TAAAATGGTAATTTT-TGAAAGTTTCGAGGTCAAAAATGGAG-TTTTTGGAAGTCCAA
88863 GGGTAAAAATGG-AATTTTTG
1 GGGT-AAAATGGTAATTTTTG
88883 GACAGTTTAG
Statistics
Matches: 312, Mismatches: 43, Indels: 39
0.79 0.11 0.10
Matches are distributed among these distances:
57 1 0.00
58 68 0.22
59 143 0.46
60 86 0.28
61 14 0.04
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTCAAAAATGGAGTTTTTGGAAGTCCAA
Found at i:88555 original size:30 final size:30
Alignment explanation
Indices: 88512--88890 Score: 342
Period size: 30 Copynumber: 12.7 Consensus size: 30
88502 ATCCAAGGGT
* * *
88512 AAAATGGTAATTTTTGAAAGTTTCAAGGTCA
1 AAAATGG-GATTTTTGGAAGTTTCGAGGTCA
*
88543 AAAATGGGA-TTTTGGAAG-TTCGGGGGT-A
1 AAAATGGGATTTTTGGAAGTTTC-GAGGTCA
* * *
88571 AAAATGGAATTTTTGGAAGCTTCGGGGTCA
1 AAAATGGGATTTTTGGAAGTTTCGAGGTCA
*
88601 AAAATAGGATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGGATTTTTGGAAGTTTCGAGGTCA
* * * *
88631 AAAATAGGATTTTTTGAAGTTTTGGGGT-A
1 AAAATGGGATTTTTGGAAGTTTCGAGGTCA
* * *
88660 AAAATGGAATTTTTGGAAGCTTCAAGGTCA
1 AAAATGGGATTTTTGGAAGTTTCGAGGTCA
* *
88690 AAAATAGGATTTTTGGAAGTTTTGAGGTCA
1 AAAATGGGATTTTTGGAAGTTTCGAGGTCA
** * * ***
88720 AAAATATGATTTTTTGAAG-TTCGGGGGGT
1 AAAATGGGATTTTTGGAAGTTTCGAGGTCA
* * *
88749 AAAATGGAATTTTTGGAAGTTTTGAGGTCG
1 AAAATGGGATTTTTGGAAGTTTCGAGGTCA
**
88779 AAAATGGGATTTTTGGAAG-TTCGAGGGAA
1 AAAATGGGATTTTTGGAAGTTTCGAGGTCA
* *
88808 AAAATGGAATTTTGGGGAAGTTTCGAGGTCA
1 AAAATGGGATTTT-TGGAAGTTTCGAGGTCA
** *
88839 AAAATAAGATTTTTGGAAG-TTCAGGGGT-A
1 AAAATGGGATTTTTGGAAGTTTC-GAGGTCA
*
88868 AAAATGGAATTTTTGGACAGTTT
1 AAAATGGGATTTTTGGA-AGTTT
88891 AGGGACCCTC
Statistics
Matches: 280, Mismatches: 57, Indels: 22
0.78 0.16 0.06
Matches are distributed among these distances:
28 12 0.04
29 103 0.37
30 138 0.49
31 27 0.10
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (30 bp):
AAAATGGGATTTTTGGAAGTTTCGAGGTCA
Found at i:88674 original size:89 final size:89
Alignment explanation
Indices: 88521--88890 Score: 405
Period size: 89 Copynumber: 4.2 Consensus size: 89
88511 TAAAATGGTA
* * * *
88521 ATTTTTGAAAGTTTCAAGGTCAAAAATGGGA-TTTTGGAAGTTCGGGGGTAAAAATGGAATTTTT
1 ATTTTTGGAAGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTT
*
88585 GGAAGCTTCGGGGTCAAAAATAGG
66 GGAAGCTTCGAGGTCAAAAATAGG
* *
88609 ATTTTTGGAAGTTTCGAGGTCAAAAATAGGATTTTTTGAAGTTTTGGGGTAAAAATGGAATTTTT
1 ATTTTTGGAAGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTT
*
88674 GGAAGCTTCAAGGTCAAAAATAGG
66 GGAAGCTTCGAGGTCAAAAATAGG
* * * *
88698 ATTTTTGGAAGTTTTGAGGTCAAAAATATGATTTTTTGAAGTTCGGGGGGT-AAAATGGAATTTT
1 ATTTTTGGAAGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTT-TGGGGGTAAAAATGGAATTTT
* * * *
88762 TGGAAGTTTTGAGGTCGAAAATGGG
65 TGGAAGCTTCGAGGTCAAAAATAGG
** * * * *
88787 ATTTTTGGAAG-TTCGAGGGAAAAAAT-GGAATTTTGGGGAAGTTTCGAGGTCAAAAAT-AAGAT
1 ATTTTTGGAAGTTTCGAGGTCAAAAATAGG-ATTTT-TGGAAGTTTGGGGGT-AAAAATGGA-AT
*
88849 TTTTGGAAG-TTCAGGGGT-AAAAAT-GG
62 TTTTGGAAGCTTC-GAGGTCAAAAATAGG
88875 AATTTTTGGACAGTTT
1 -ATTTTTGGA-AGTTT
88891 AGGGACCCTC
Statistics
Matches: 241, Mismatches: 30, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
87 1 0.00
88 51 0.21
89 160 0.66
90 27 0.11
91 2 0.01
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (89 bp):
ATTTTTGGAAGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTT
GGAAGCTTCGAGGTCAAAAATAGG
Found at i:90802 original size:2 final size:2
Alignment explanation
Indices: 90795--90830 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
90785 TTTTATTTCT
90795 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
90831 CTAGTTAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:93546 original size:33 final size:32
Alignment explanation
Indices: 93509--93579 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
93499 TTAATTTTTC
* *
93509 ATTTTAAAAT-TTTAAAAATATTTTTTATTTCAA
1 ATTTTAAAATATTCAAAAATATATTTT-TTT-AA
*
93542 ATTTT-TAATATTCAAAAATATATTTTTTTAA
1 ATTTTAAAATATTCAAAAATATATTTTTTTAA
93573 ATTTTAA
1 ATTTTAA
93580 TATAGTAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
31 7 0.22
32 6 0.19
33 19 0.59
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (32 bp):
ATTTTAAAATATTCAAAAATATATTTTTTTAA
Found at i:98160 original size:15 final size:15
Alignment explanation
Indices: 98140--98187 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 15
98130 TATATTTTTA
98140 AAAATTAAAAAAATT
1 AAAATTAAAAAAATT
98155 AAAATTAATAAAAAAATT
1 AAAA-T--TAAAAAAATT
98173 ATAAA-TAAAAAAATT
1 A-AAATTAAAAAAATT
98188 TATAAAGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 14 0.48
16 1 0.03
18 11 0.38
19 3 0.10
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATTAAAAAAATT
Found at i:98185 original size:18 final size:18
Alignment explanation
Indices: 98146--98185 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
98136 TTTAAAAATT
*
98146 AAAAAAATTAAAATTAAT
1 AAAAAAATTAAAATTAAA
98164 AAAAAAATTATAAA-TAAA
1 AAAAAAATTA-AAATTAAA
98182 AAAA
1 AAAA
98186 TTTATAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAAAATTAAAATTAAA
Found at i:98185 original size:27 final size:26
Alignment explanation
Indices: 98139--98193 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 26
98129 ATATATTTTT
98139 AAAAATTAAAAAAATTAAAATTAATAA
1 AAAAATTAAAAAAA-TAAAATTAATAA
*
98166 AAAAATTATAAATAAA-AAAATTTATAA
1 AAAAATTA-AAA-AAATAAAATTAATAA
98193 A
1 A
98194 GTATTTGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 19 0.76
28 3 0.12
29 3 0.12
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (26 bp):
AAAAATTAAAAAAATAAAATTAATAA
Found at i:98190 original size:16 final size:15
Alignment explanation
Indices: 98161--98193 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 15
98151 AATTAAAATT
98161 AATAAAAAAATTATA
1 AATAAAAAAATTATA
98176 AATAAAAAAATTTATA
1 AATAAAAAAA-TTATA
98192 AA
1 AA
98194 GTATTTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAAAAAAATTATA
Found at i:100106 original size:53 final size:54
Alignment explanation
Indices: 99948--100106 Score: 189
Period size: 54 Copynumber: 3.0 Consensus size: 54
99938 TTTGATTTGT
* *
99948 AGACCACGAGATTCGTAAAATCTCGTAAGTAGAAAGTTGTGATCGTAAATC-TG
1 AGACCACGAGATTCGTAAAATCTCGTAAGTAGAAGGTTGTGATCGTAAATCATC
*** * *
100001 AGGACTGTGAGATTTGTAAAATAC-CGAAAGTAGAAGGTTGTGATCGTAAATCATC
1 A-GACCACGAGATTCGTAAAAT-CTCGTAAGTAGAAGGTTGTGATCGTAAATCATC
* * *
100056 AGACCACGAGATTCAT-AAATCTCGTAAGAAGAAGGTCGTGATCGTAAATCA
1 AGACCACGAGATTCGTAAAATCTCGTAAGTAGAAGGTTGTGATCGTAAATCA
100107 ACTGAATCTT
Statistics
Matches: 87, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
52 1 0.01
53 31 0.36
54 52 0.60
55 3 0.03
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.25
Consensus pattern (54 bp):
AGACCACGAGATTCGTAAAATCTCGTAAGTAGAAGGTTGTGATCGTAAATCATC
Found at i:100631 original size:54 final size:54
Alignment explanation
Indices: 100540--100724 Score: 140
Period size: 54 Copynumber: 3.4 Consensus size: 54
100530 ATCCCGTAAA
* * * **
100540 TAAAAGGTCCTGATCGTAAATCA-TCGGATCGTAAGATTAGTAAAATCTCGA-AAG
1 TAAAAGGTCATGATCGAAAATCAGT-GGACCGCGAGATTAGTAAAATC-CGACAAG
* * * * ** * *
100594 TATATGGTCGTGATTGAAAATCAGTGGATTGCGAGATTTGTAAAATCCTACAAG
1 TAAAAGGTCATGATCGAAAATCAGTGGACCGCGAGATTAGTAAAATCCGACAAG
* * * * *
100648 TAAAAGGTCATGGTCGTAAATCAGTGGACCGCGAGATTCGTAAAATCCTATAAG
1 TAAAAGGTCATGATCGAAAATCAGTGGACCGCGAGATTAGTAAAATCCGACAAG
* ** *
100702 TAGATTGTCATGATCGTAAATCA
1 TAAAAGGTCATGATCGAAAATCA
100725 ACTGAAGCTT
Statistics
Matches: 105, Mismatches: 24, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
53 2 0.02
54 102 0.97
55 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (54 bp):
TAAAAGGTCATGATCGAAAATCAGTGGACCGCGAGATTAGTAAAATCCGACAAG
Found at i:101301 original size:54 final size:54
Alignment explanation
Indices: 101140--101338 Score: 186
Period size: 54 Copynumber: 3.7 Consensus size: 54
101130 CAATATTTAA
* * * * * * *
101140 TAAAATCCCGTAAGTAGAAGGTCACGGTCGTAAATCAGC-AAATCGTGAGATTTG
1 TAAAATCCCGTAAGTAGAAGGTCATGATCGTAAATCAACTGACT-GCGAGATTCG
* * * * * * * * *
101194 TAAAATCTCGAAACTAGAAGATCATGATCATAAATC-AGTAGACCGCAAAATTCG
1 TAAAATCCCGTAAGTAGAAGGTCATGATCGTAAATCAACT-GACTGCGAGATTCG
* *
101248 TAAAATCCCGCAAGTAAAAGGTCATGATCGTAAATCAACTGACTGCGAGATTCG
1 TAAAATCCCGTAAGTAGAAGGTCATGATCGTAAATCAACTGACTGCGAGATTCG
**
101302 TAAAATCCCGTAAGTAGATTGTCATGATCGTAAATCA
1 TAAAATCCCGTAAGTAGAAGGTCATGATCGTAAATCA
101339 TTTGAAGCGT
Statistics
Matches: 112, Mismatches: 30, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
54 109 0.97
55 3 0.03
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (54 bp):
TAAAATCCCGTAAGTAGAAGGTCATGATCGTAAATCAACTGACTGCGAGATTCG
Found at i:101329 original size:108 final size:108
Alignment explanation
Indices: 101140--101338 Score: 240
Period size: 108 Copynumber: 1.8 Consensus size: 108
101130 CAATATTTAA
* * * * * * *
101140 TAAAATCCCGTAAGTAGAAGGTCACGGTCGTAAATCAGCAAATCGTGAGATTTGTAAAATCTCGA
1 TAAAATCCCGCAAGTAAAAGGTCACGATCGTAAATCAACAAATCGCGAGATTCGTAAAATCCCGA
101205 AACTAGAAGATCATGATCATAAATCAGTAGACCGCAAAATTCG
66 AACTAGAAGATCATGATCATAAATCAGTAGACCGCAAAATTCG
* **
101248 TAAAATCCCGCAAGTAAAAGGTCATGATCGTAAATCAACTGA-CTGCGAGATTCGTAAAATCCCG
1 TAAAATCCCGCAAGTAAAAGGTCACGATCGTAAATCAACAAATC-GCGAGATTCGTAAAATCCCG
* * * *
101312 TAAGTAGATTG-TCATGATCGTAAATCA
65 AAACTAGA-AGATCATGATCATAAATCA
101339 TTTGAAGCGT
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
107 1 0.01
108 73 0.97
109 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (108 bp):
TAAAATCCCGCAAGTAAAAGGTCACGATCGTAAATCAACAAATCGCGAGATTCGTAAAATCCCGA
AACTAGAAGATCATGATCATAAATCAGTAGACCGCAAAATTCG
Found at i:101763 original size:619 final size:616
Alignment explanation
Indices: 100016--101797 Score: 2175
Period size: 614 Copynumber: 2.9 Consensus size: 616
100006 TGTGAGATTT
* * * ** * * * * *
100016 GTAAAATACCGAAAGTAGAAGGTTGTGATCGTAAATCATCAGACCACGAGATTCAT-AAATCTCG
1 GTAAAATCCCGCAAGTAAAAGGTCATGATCGTAAATCAACTGACCGCGAGATTCGTAAAATCCCG
* ** * * *
100080 TAAGAAGAAGGTCGTGATCGTAAATCAACTGAATCTTTTTAGAAACTTCTTTGTTTTTTTGAGCA
66 TAAGTAGATTGTCATGATCGTAAATCAACTGAAGC-TTTTAGAAAGTTCTTTGTTTTTTTGAGCA
* * *
100145 TATCGATCCGTTTCAAGCTTCATTTCAATTGCATGGTGAAGAGAAGTAGCTTCAG--GCTCACGA
130 TATTGATCCATTTCAAGCTTCATTTCAATT--ATGGTGAAGAGAAGTAGCTTTAGAAGCTCACGA
*
100208 AGGCAATGTAACAAAATTGATTCCTCTATCC-CTCTTCTTTCAAGGTCAATTTT-AGGTTCTTCC
193 AGACAATGTAACAAAATTGATTCCTCTATCCTCTCTTCTTTCAAGGTC-ATTTTGA-GTTCTTCC
** * * *
100271 TCAACATGTCTATATTCATCATTTCTAGCATCTAACATGCACTGAAGAGCAGAGAGGTTAGAATT
256 TCAACA-CACTATATTCATCATCTCTAGCATCTAACATGCTCTGAAGGGCAGAGAGGTTAGAATT
** *
100336 AACTAGTTGAAAATCATCT-TTGTTCATTCTTAGAACTAGTTCAGAAAATTTACATTCCTTTTGA
320 AACTAGTTGAAAATCATCTCAAG-TCATTCTTAGAACTAGTTCAGAAAATTTACATTTCTTTTGA
* * * *
100400 ACTAAGAAAACCAACATATCCACACTAGTATCGGAGCAATTATTAGCCACACCCATTGCATGGTC
384 ACCAAGAAAACCAACATATCCAAACTAGTATCGGAGCAATTATTAGCCGCACTCATTGCATGGTC
* * * *
100465 AACCAATTTTCTCAACATCTTCTGATAATTCTCATCATCAAACAATCTAAACAAGATTGAATTAA
449 AACCAATTTTCTCAACATCTTCTAATAATTCTCATCATCAAACAGTCTAAACAATATTGAATAAA
* * * ** *
100530 ATCCCGTAAATAAAAGGTC-CTGATCGTAAATCATCGGATCGTAAGATTAGTAAAATCTCGAAAG
514 ATCCCGTAAGTAGAAGGTCAC-GATCGTAAATCAGCAAATCGTAAGATTAGTAAAATCTCGAAAC
* * * * * * ** * * *
100594 TATATGGTCGTGATTGAAAATCAGTGGATTGCGAGATTT
578 TAGAAGATCATGATTCAAAATCAGTAGACCGCAAAATTC
** * * *
100633 GTAAAATCCTACAAGTAAAAGGTCATGGTCGTAAATC-AGTGGACCGCGAGATTCGTAAAATCCT
1 GTAAAATCCCGCAAGTAAAAGGTCATGATCGTAAATCAACT-GACCGCGAGATTCGTAAAATCCC
* * *
100697 ATAAGTAGATTGTCATGATCGTAAATCAACTGAAGCTTTTCAAAAAGTAC-----TTTTTTGAGC
65 GTAAGTAGATTGTCATGATCGTAAATCAACTGAAGCTTTT-AGAAAGTTCTTTGTTTTTTTGAGC
* * * * *
100757 ATATTGATCCATTTCGAGCTTCATTTCAAACGTACGGTGAAGAGAAGTAGC-TT-CAAGCTCACA
129 ATATTGATCCATTTCAAGCTTCATTTC-AA-TTATGGTGAAGAGAAGTAGCTTTAGAAGCTCACG
*
100820 AAGACAATATAACAAAATTGATTCCTCTATCCT-TCTTCTTTCAAGGTCAGTTTTGAGTTCTTCC
192 AAGACAATGTAACAAAATTGATTCCTCTATCCTCTCTTCTTTCAAGGTCA-TTTTGAGTTCTTCC
* * * *
100884 TCGACACACCTATATTAATCATCTCTAGCATCTAACTTGCTCTGAAGGGCAAAGAGGTTAGAATT
256 TCAACACA-CTATATTCATCATCTCTAGCATCTAACATGCTCTGAAGGGCAGAGAGGTTAGAATT
* ** * * *
100949 AACTAGTTGAAAAATCATCTCTAA-TCATTCCTATTACTAGTTTAGAATATTTAAATTTCTTTTG
320 AACTAGTTG-AAAATCATCTC-AAGTCATTCTTAGAACTAGTTCAGAAAATTTACATTTCTTTTG
* *
101013 AACCAAGAAAACCAACATATCAAAACTAGTATCGGAGAAATTATTAGCCGCACTCATTGCATGGT
383 AACCAAGAAAACCAACATATCCAAACTAGTATCGGAGCAATTATTAGCCGCACTCATTGCATGGT
** * * * * *
101078 CAACCAAACTTCTCAACATCTTCTAATAATTCTAATAATCAAATAGACTAAACAATATTTAATAA
448 CAACCAATTTTCTCAACATCTTCTAATAATTCTCATCATCAAACAGTCTAAACAATATTGAATAA
* * *
101143 AATCCCGTAAGTAGAAGGTCACGGTCGTAAATCAGCAAATCGTGAGATTTGTAAAATCTCGAAAC
513 AATCCCGTAAGTAGAAGGTCACGATCGTAAATCAGCAAATCGTAAGATTAGTAAAATCTCGAAAC
101208 TAGAAGATCATGA-TCATAAATCAGTAGACCGCAAAATTC
578 TAGAAGATCATGATTCA-AAATCAGTAGACCGCAAAATTC
*
101247 GTAAAATCCCGCAAGTAAAAGGTCATGATCGTAAATCAACTGACTGCGAGATTCGTAAAATCCCG
1 GTAAAATCCCGCAAGTAAAAGGTCATGATCGTAAATCAACTGACCGCGAGATTCGTAAAATCCCG
**
101312 TAAGTAGATTGTCATGATCGTAAATCATTTGAAGCGTTTTAGAAAGTTCTTTGTTTTTCTTG-GC
66 TAAGTAGATTGTCATGATCGTAAATCAACTGAAGC-TTTTAGAAAGTTCTTTGTTTTT-TTGAGC
* * * *
101376 AGATT-AGTCCATTTCAATCTTCATTTCAGATTATGATCAAGAGAAGTAGCTTTAGAAGCTCACG
129 ATATTGA-TCCATTTCAAGCTTCATTTCA-ATTATGGTGAAGAGAAGTAGCTTTAGAAGCTCACG
* *
101440 AAGACAATGTAACAAAATTTATTCCTTTATCCTCT-TTCTTTCAAGGTCGATTTTGAGTTCTTCC
192 AAGACAATGTAACAAAATTGATTCCTCTATCCTCTCTTCTTTCAAGGTC-ATTTTGAGTTCTTCC
* * *
101504 TCAACACACGTATATTCATCATCTCTAGCATCTAACATACTCTGAAGGGTAGAGAGTTTAGAATT
256 TCAACACAC-TATATTCATCATCTCTAGCATCTAACATGCTCTGAAGGGCAGAGAGGTTAGAATT
* * * *
101569 AGCTAGTTGAAAATCATCTCAAGCCATTCTTAGAACTAGTTCAAAAAATTTTCATTTCTTTTGAA
320 AACTAGTTGAAAATCATCTCAAGTCATTCTTAGAACTAGTTCAGAAAATTTACATTTCTTTTGAA
* *
101634 CCAAGAAAACCAACATATCCAGACTAGTATTGGAGCAATTATTAGCCGCACTCATTGCATGGTCA
385 CCAAGAAAACCAACATATCCAAACTAGTATCGGAGCAATTATTAGCCGCACTCATTGCATGGTCA
* * * * * *
101699 ACTAATTTTCTCCACATCTTTTCATAATTCTCATCATCGAACAGTCTAAATAATATTGAATAAAA
450 ACCAATTTTCTCAACATCTTCTAATAATTCTCATCATCAAACAGTCTAAACAATATTGAATAAAA
* *
101764 TCCCGTAAGTAGAAGGTAACGATTGTAAATCAGC
515 TCCCGTAAGTAGAAGGTCACGATCGTAAATCAGC
101798 GGACTGTGAG
Statistics
Matches: 984, Mismatches: 149, Indels: 62
0.82 0.12 0.05
Matches are distributed among these distances:
612 2 0.00
613 180 0.18
614 333 0.34
615 8 0.01
617 46 0.05
618 61 0.06
619 220 0.22
620 132 0.13
621 2 0.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (616 bp):
GTAAAATCCCGCAAGTAAAAGGTCATGATCGTAAATCAACTGACCGCGAGATTCGTAAAATCCCG
TAAGTAGATTGTCATGATCGTAAATCAACTGAAGCTTTTAGAAAGTTCTTTGTTTTTTTGAGCAT
ATTGATCCATTTCAAGCTTCATTTCAATTATGGTGAAGAGAAGTAGCTTTAGAAGCTCACGAAGA
CAATGTAACAAAATTGATTCCTCTATCCTCTCTTCTTTCAAGGTCATTTTGAGTTCTTCCTCAAC
ACACTATATTCATCATCTCTAGCATCTAACATGCTCTGAAGGGCAGAGAGGTTAGAATTAACTAG
TTGAAAATCATCTCAAGTCATTCTTAGAACTAGTTCAGAAAATTTACATTTCTTTTGAACCAAGA
AAACCAACATATCCAAACTAGTATCGGAGCAATTATTAGCCGCACTCATTGCATGGTCAACCAAT
TTTCTCAACATCTTCTAATAATTCTCATCATCAAACAGTCTAAACAATATTGAATAAAATCCCGT
AAGTAGAAGGTCACGATCGTAAATCAGCAAATCGTAAGATTAGTAAAATCTCGAAACTAGAAGAT
CATGATTCAAAATCAGTAGACCGCAAAATTC
Found at i:119684 original size:102 final size:103
Alignment explanation
Indices: 119508--119713 Score: 360
Period size: 102 Copynumber: 2.0 Consensus size: 103
119498 TAGACAAAAG
*
119508 AATGAGCAAGCCAGAAGGTGTGGGCGCGACCCTGACATACCAGCTGACCAAGAAAACACAATATT
1 AATGAGCAAGCCAGAAGGTGTGGGCGCGACCCTGACATACCAGCTAACCAAGAAAACACAATATT
119573 ACAACAAGAGCCTAATATTCTCCAATC-TTTACAAGAA
66 ACAACAAGAGCCTAATATTCTCCAATCTTTTACAAGAA
* * * *
119610 AATGAGCAAGTCAGAAGGTGTGGGCGCTACCCTGTCATACCAGCTAACCAGGAAAACACAATATT
1 AATGAGCAAGCCAGAAGGTGTGGGCGCGACCCTGACATACCAGCTAACCAAGAAAACACAATATT
119675 ACAACAAGAGCCTAATATTCTCCAATCTTTTACAAGAA
66 ACAACAAGAGCCTAATATTCTCCAATCTTTTACAAGAA
119713 A
1 A
119714 CCGACTTCTT
Statistics
Matches: 98, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
102 87 0.89
103 11 0.11
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (103 bp):
AATGAGCAAGCCAGAAGGTGTGGGCGCGACCCTGACATACCAGCTAACCAAGAAAACACAATATT
ACAACAAGAGCCTAATATTCTCCAATCTTTTACAAGAA
Found at i:124090 original size:31 final size:30
Alignment explanation
Indices: 124047--124113 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 30
124037 ACCTAATTTT
124047 TTTTATCCAATTTGGTA-CTCAAACTTGACAC
1 TTTT-TCCAATTTGGTACCT-AAACTTGACAC
124078 TTTTTCCTAATTTGGTACCTAAACTTGACAC
1 TTTTTCC-AATTTGGTACCTAAACTTGACAC
124109 TTTTT
1 TTTTT
124114 TTTAAGTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 3 0.09
31 29 0.85
32 2 0.06
ACGTcount: A:0.25, C:0.21, G:0.09, T:0.45
Consensus pattern (30 bp):
TTTTTCCAATTTGGTACCTAAACTTGACAC
Found at i:124113 original size:88 final size:89
Alignment explanation
Indices: 123999--124188 Score: 240
Period size: 88 Copynumber: 2.1 Consensus size: 89
123989 TTAATATAAC
** * * **
123999 ATTTGGTATTTAAACTTGATACTTTTTTTCAATTTGATACCT-AA-TTTTTTTTATCCAATTTGG
1 ATTTGGTACCTAAACTTGACACTTTTTTTCAAGTTGATACCTAAACTTTTTTGGATCCAATTTGG
124062 TACTCAAACTTGACACTTTTTCCTA
66 TACTCAAACTTGACAC-TTTTCCTA
* *
124087 ATTTGGTACCTAAACTTGACACTTTTTTTTAAGTTGATACTTAAACTTTTTTGGATCCAATTTGG
1 ATTTGGTACCTAAACTTGACACTTTTTTTCAAGTTGATACCTAAACTTTTTTGGATCCAATTTGG
* * *
124152 TACTCGAACTTGACTCTTTTCCTG
66 TACTCAAACTTGACACTTTTCCTA
* *
124176 ACTTGATACCTAA
1 ATTTGGTACCTAA
124189 TGTTTTTTAA
Statistics
Matches: 87, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
88 36 0.41
89 20 0.23
90 31 0.36
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (89 bp):
ATTTGGTACCTAAACTTGACACTTTTTTTCAAGTTGATACCTAAACTTTTTTGGATCCAATTTGG
TACTCAAACTTGACACTTTTCCTA
Found at i:124132 original size:31 final size:31
Alignment explanation
Indices: 124062--124134 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
124052 TCCAATTTGG
* * *
124062 TACTCAAACTTGACACTTTTTCCTAATTTGG
1 TACTTAAACTTGACACTTTTTCCTAAGTTGA
* **
124093 TACCTAAACTTGACACTTTTTTTTAAGTTGA
1 TACTTAAACTTGACACTTTTTCCTAAGTTGA
124124 TACTTAAACTT
1 TACTTAAACTT
124135 TTTTGGATCC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (31 bp):
TACTTAAACTTGACACTTTTTCCTAAGTTGA
Found at i:124455 original size:60 final size:59
Alignment explanation
Indices: 124355--124528 Score: 138
Period size: 60 Copynumber: 2.9 Consensus size: 59
124345 AATTGAATCT
* * * * *
124355 AAAAAAAGCTTAGGTACCAAATTAGGAAAAAATACCAAGTTTAGGT-TCCAATTTGGGTC
1 AAAAAAAGTTTAGATACCAAATTAGGAAAAAATACCAAGTTCAAGTAT-CAAATTGGGTC
* * *** *
124414 AAAAAAAAGTTTAGATATCAAATTAGGAAAAAGTGTGAAGTTCAAGTATCAAATTGTGTC
1 -AAAAAAAGTTTAGATACCAAATTAGGAAAAAATACCAAGTTCAAGTATCAAATTGGGTC
** * *
124474 AAAAAAAGTTTAAGGAT--CAAATTTAAAAAAAAAGAGTCAAGTTCAAGTATCAAAT
1 AAAAAAAGTTT-A-GATACCAAA-TTAGGAAAAAATA-CCAAGTTCAAGTATCAAAT
124529 GTTATATTAA
Statistics
Matches: 92, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
59 15 0.16
60 55 0.60
61 22 0.24
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (59 bp):
AAAAAAAGTTTAGATACCAAATTAGGAAAAAATACCAAGTTCAAGTATCAAATTGGGTC
Found at i:124493 original size:59 final size:61
Alignment explanation
Indices: 124415--124528 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
124405 ATTTGGGTCA
* ** * *
124415 AAAAAAAGTTTAGATATCAAA-TT-AGGAAAAAGTGTGAAGTTCAAGTATCAAATTGTGTC
1 AAAAAAAGTTTAGAGATCAAATTTAAAAAAAAAGAGTCAAGTTCAAGTATCAAATTGTGTC
124474 AAAAAAAGTTTA-AGGATCAAATTTAAAAAAAAAGAGTCAAGTTCAAGTATCAAAT
1 AAAAAAAGTTTAGA-GATCAAATTTAAAAAAAAAGAGTCAAGTTCAAGTATCAAAT
124529 GTTATATTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 1 0.02
59 18 0.38
60 2 0.04
61 26 0.55
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.26
Consensus pattern (61 bp):
AAAAAAAGTTTAGAGATCAAATTTAAAAAAAAAGAGTCAAGTTCAAGTATCAAATTGTGTC
Found at i:144805 original size:21 final size:25
Alignment explanation
Indices: 144781--144830 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 25
144771 TACGGACTTT
*
144781 GATAAGTTTAT-TTT-ATT-ATA-A
1 GATAAATTTATATTTGATTAATAGA
144802 GATAAATTTATATTTGATTAATAGA
1 GATAAATTTATATTTGATTAATAGA
144827 GATA
1 GATA
144831 TTATACAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 10 0.42
22 3 0.12
23 3 0.12
24 3 0.12
25 5 0.21
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (25 bp):
GATAAATTTATATTTGATTAATAGA
Found at i:159575 original size:23 final size:23
Alignment explanation
Indices: 159527--159577 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
159517 ATCTACCGAG
* * *
159527 TATTTTCCAATATTATGAAATTT
1 TATTTTCCAATATAAGGAAATCT
159550 TATTTTCCAA-ATAAGGATAATCT
1 TATTTTCCAATATAAGGA-AATCT
159573 TATTT
1 TATTT
159578 CTAAAAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49
Consensus pattern (23 bp):
TATTTTCCAATATAAGGAAATCT
Found at i:160493 original size:20 final size:19
Alignment explanation
Indices: 160448--160499 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
160438 TAGATAAAAG
* *
160448 TATTAATGTTATATCTTGTA
1 TATTAAT-TTATATCATATA
160468 TAATTAATTTATATCATATCA
1 T-ATTAATTTATATCATAT-A
*
160489 TATTATTTTAT
1 TATTAATTTAT
160500 TTATGTATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.56
Consensus pattern (19 bp):
TATTAATTTATATCATATA
Found at i:167416 original size:17 final size:17
Alignment explanation
Indices: 167384--167432 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
167374 CGTGATAAAA
167384 AAAATTATAAAAATATT
1 AAAATTATAAAAATATT
167401 AAAA-TATAAAACATATT
1 AAAATTATAAAA-ATATT
167418 AAATATTATTAAAAA
1 AAA-ATTA-TAAAAA
167433 GTTAGAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 7 0.25
17 12 0.43
18 1 0.04
19 3 0.11
20 5 0.18
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTATAAAAATATT
Found at i:167939 original size:21 final size:21
Alignment explanation
Indices: 167915--167958 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
167905 TTTATAGTCT
* *
167915 TTTTTGTATATTTTA-AACAAA
1 TTTTTGCATAATTTATAA-AAA
167936 TTTTTGCATAATTTATAAAAA
1 TTTTTGCATAATTTATAAAAA
167957 TT
1 TT
167959 AGTTAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (21 bp):
TTTTTGCATAATTTATAAAAA
Found at i:175019 original size:2 final size:2
Alignment explanation
Indices: 175012--175041 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
175002 ATGCATGCTA
175012 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
175042 GTGGCCTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:183775 original size:60 final size:61
Alignment explanation
Indices: 183650--183765 Score: 166
Period size: 61 Copynumber: 1.9 Consensus size: 61
183640 TTAATATAAC
* *
183650 ATTTGATACTTGAACTTACCATTTTTCTTCTAATTTAGTATCTAAACTTTTTTTTGACCCA
1 ATTTGATACTTGAACTTACCATTTTTCTTCTAATTTAGTACCTAAACTTTTTTTTAACCCA
* *
183711 ATTTGATACTTGAACTTGA-CATTTTT-TTCTAATTTGGTACCT-AAGTTTTTTTTAA
1 ATTTGATACTTGAACTT-ACCATTTTTCTTCTAATTTAGTACCTAAACTTTTTTTTAA
183766 ATTCAATTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
59 11 0.22
60 14 0.28
61 24 0.48
62 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.51
Consensus pattern (61 bp):
ATTTGATACTTGAACTTACCATTTTTCTTCTAATTTAGTACCTAAACTTTTTTTTAACCCA
Found at i:184034 original size:30 final size:30
Alignment explanation
Indices: 183998--184072 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
183988 ACTAACTTAA
*
183998 AAAAAAAATGTCAAGTTTAGATATCAAATT
1 AAAAAAAATATCAAGTTTAGATATCAAATT
184028 AAAAAAAATATCAAGTTTAGATATCAAATT
1 AAAAAAAATATCAAGTTTAGATATCAAATT
*
184058 AAGAAAAAGTATCAA
1 AA-AAAAAATATCAA
184073 ATTCGAATAC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
30 31 0.74
31 11 0.26
ACGTcount: A:0.57, C:0.07, G:0.09, T:0.27
Consensus pattern (30 bp):
AAAAAAAATATCAAGTTTAGATATCAAATT
Found at i:184087 original size:31 final size:30
Alignment explanation
Indices: 183998--184087 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 30
183988 ACTAACTTAA
* * * *
183998 AAAAAAAATGTCAAGTTTAGATATCAAATT
1 AAAAAAAATATCAAATTGAGATACCAAATT
* * *
184028 AAAAAAAATATCAAGTTTAGATATCAAATT
1 AAAAAAAATATCAAATTGAGATACCAAATT
*
184058 AAGAAAAAGTATCAAATTCGA-ATACCAAAT
1 AA-AAAAAATATCAAATT-GAGATACCAAAT
184088 ATTATATTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
30 31 0.58
31 21 0.40
32 1 0.02
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.27
Consensus pattern (30 bp):
AAAAAAAATATCAAATTGAGATACCAAATT
Found at i:187584 original size:18 final size:18
Alignment explanation
Indices: 187561--187602 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
187551 TTTGGTGTTG
187561 TTTTTTACTGTTTTGATA
1 TTTTTTACTGTTTTGATA
*
187579 TTTTTTACTGTTTTGATG
1 TTTTTTACTGTTTTGATA
187597 TTTTTT
1 TTTTTT
187603 TTATTGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.12, C:0.05, G:0.12, T:0.71
Consensus pattern (18 bp):
TTTTTTACTGTTTTGATA
Found at i:187602 original size:20 final size:20
Alignment explanation
Indices: 187550--187616 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
187540 TATATTGTTT
*
187550 TTTTGGTGTTGTTTTTTACTG
1 TTTTGATGTT-TTTTTTACTG
*
187571 TTTTGA--TATTTTTTACTG
1 TTTTGATGTTTTTTTTACTG
*
187589 TTTTGATGTTTTTTTTATTG
1 TTTTGATGTTTTTTTTACTG
187609 TTTTGATG
1 TTTTGATG
187617 CTGTTATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
18 16 0.40
19 1 0.03
20 18 0.45
21 5 0.12
ACGTcount: A:0.10, C:0.03, G:0.18, T:0.69
Consensus pattern (20 bp):
TTTTGATGTTTTTTTTACTG
Found at i:187629 original size:20 final size:20
Alignment explanation
Indices: 187559--187630 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 20
187549 TTTTTGGTGT
* * *
187559 TGTTTTTTACTGTTTTGATA
1 TGTTATTTATTGTTTTGATG
*
187579 T-TT-TTTACTGTTTTGATG
1 TGTTATTTATTGTTTTGATG
* *
187597 TTTTTTTTATTGTTTTGATG
1 TGTTATTTATTGTTTTGATG
187617 CTGTTATTT-TTGTT
1 -TGTTATTTATTGTT
187631 GTTGTTTTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
18 15 0.33
19 4 0.09
20 20 0.44
21 6 0.13
ACGTcount: A:0.11, C:0.04, G:0.15, T:0.69
Consensus pattern (20 bp):
TGTTATTTATTGTTTTGATG
Found at i:187638 original size:12 final size:12
Alignment explanation
Indices: 187618--187708 Score: 89
Period size: 12 Copynumber: 7.8 Consensus size: 12
187608 GTTTTGATGC
187618 TGTTATTTTTGT
1 TGTTATTTTTGT
*
187630 TGTTGTTTTTGT
1 TGTTATTTTTGT
*
187642 TGCTATTTTTGT
1 TGTTATTTTTGT
*
187654 TGCTATTTTTGT
1 TGTTATTTTTGT
*
187666 TGTT-TTTCTGT
1 TGTTATTTTTGT
* *
187677 TATT-TTTTT-A
1 TGTTATTTTTGT
* *
187687 TGCTATTTTGGT
1 TGTTATTTTTGT
187699 TGTTATTTTT
1 TGTTATTTTT
187709 ATGTATTTTT
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
10 2 0.03
11 17 0.27
12 44 0.70
ACGTcount: A:0.08, C:0.04, G:0.16, T:0.71
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:187671 original size:33 final size:33
Alignment explanation
Indices: 187629--187702 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
187619 GTTATTTTTG
*
187629 TTGTTGTTTTTGTTGCTATTTTTGT-TGCTATTT
1 TTGTTGTTTTT-CTGCTATTTTTGTATGCTATTT
* *
187662 TTGTTGTTTTTCTGTTATTTTTTTATGCTATTT
1 TTGTTGTTTTTCTGCTATTTTTGTATGCTATTT
*
187695 TGGTTGTT
1 TTGTTGTT
187703 ATTTTTATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
32 10 0.28
33 26 0.72
ACGTcount: A:0.07, C:0.05, G:0.18, T:0.70
Consensus pattern (33 bp):
TTGTTGTTTTTCTGCTATTTTTGTATGCTATTT
Found at i:191002 original size:26 final size:27
Alignment explanation
Indices: 190973--191026 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
190963 CGTTCATGTT
*
190973 AATTATTTTT-TAACTTATAGTTGTAC
1 AATTATTTTTCAAACTTATAGTTGTAC
* *
190999 AATTCTTTTTCAAACTTATATTTGTAC
1 AATTATTTTTCAAACTTATAGTTGTAC
191026 A
1 A
191027 TTGATGATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.52
Consensus pattern (27 bp):
AATTATTTTTCAAACTTATAGTTGTAC
Found at i:193918 original size:20 final size:18
Alignment explanation
Indices: 193893--193972 Score: 79
Period size: 20 Copynumber: 4.1 Consensus size: 18
193883 TTTTTTTAAA
193893 AATTATTTAAATCGTTTTTT
1 AATTATTTAAAT--TTTTTT
* *
193913 AATTATTTTAATTTAATTAT
1 AATTATTTAAATTT--TTTT
*
193933 AATTTTTTAAATTATGTTTT
1 AATTATTTAAATT-T-TTTT
193953 AATTATTTAAATTTTTTT
1 AATTATTTAAATTTTTTT
193971 AA
1 AA
193973 AAATTTTGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
18 8 0.16
19 1 0.02
20 40 0.80
21 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (18 bp):
AATTATTTAAATTTTTTT
Found at i:193925 original size:29 final size:28
Alignment explanation
Indices: 193893--193972 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 28
193883 TTTTTTTAAA
193893 AATTATTTAAATCGTTTTTTAATTA-TTTT
1 AATTATTTAAAT--TTTTTTAATTAGTTTT
* *
193922 AATTTAATTATAATTTTTTAAATTATGTTTT
1 AA-TTATTTA-AATTTTTTTAATTA-GTTTT
193953 AATTATTTAAATTTTTTTAA
1 AATTATTTAAATTTTTTTAA
193973 AAATTTTGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
29 22 0.51
30 12 0.28
31 9 0.21
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (28 bp):
AATTATTTAAATTTTTTTAATTAGTTTT
Found at i:194066 original size:58 final size:57
Alignment explanation
Indices: 193981--194184 Score: 200
Period size: 58 Copynumber: 3.6 Consensus size: 57
193971 AAAAATTTTG
* *
193981 AAAATATGATGTAAGTCATT-GGATGGCAAACACTAAAAAAAATTATTTTTAAATCTGA
1 AAAATATGATGTAAGCCATTAGG-TGGCAAACACTAAAAAAAA-TATTTTTAAATCTAA
* * *
194039 AAAATATGATGTAGGCCATTAGGTGGCAAACA--AAAAAAAATATTTTTAAATTTAG
1 AAAATATGATGTAAGCCATTAGGTGGCAAACACTAAAAAAAATATTTTTAAATCTAA
* * * * * * *
194094 GAAATGTGGTGTAGGCCATTAGATGACAAACACTCAAAAAAAA-AATTTTAAATCTAAA
1 AAAATATGATGTAAGCCATTAGGTGGCAAACACT-AAAAAAAATATTTTTAAATCT-AA
* * * *
194152 AAAAAATGGTGTAAGCCATTGGGTGGCAGACAC
1 AAAATATGATGTAAGCCATTAGGTGGCAAACAC
194185 CCACAAAACT
Statistics
Matches: 120, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
55 39 0.32
56 8 0.07
57 10 0.08
58 61 0.51
59 2 0.02
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (57 bp):
AAAATATGATGTAAGCCATTAGGTGGCAAACACTAAAAAAAATATTTTTAAATCTAA
Found at i:194107 original size:55 final size:57
Alignment explanation
Indices: 193981--194154 Score: 178
Period size: 55 Copynumber: 3.1 Consensus size: 57
193971 AAAAATTTTG
* * *
193981 AAAATATGATGTAAGTCATTGGATGGCAAACACTAAAAAAAATTATTTTTAAATCTGA
1 AAAATATGATGTAGGCCATTAGATGGCAAACAC-AAAAAAAATTATTTTTAAATCTGA
* *
194039 AAAATATGATGTAGGCCATTAGGTGGCAAACA-AAAAAAAA-TATTTTTAAAT-TTA
1 AAAATATGATGTAGGCCATTAGATGGCAAACACAAAAAAAATTATTTTTAAATCTGA
* * * * * *
194093 GGAAATGTGGTGTAGGCCATTAGATGACAAACACTCAAAAAAAA--AATTTTAAATCTAA
1 -AAAATATGATGTAGGCCATTAGATGGCAAACA--CAAAAAAAATTATTTTTAAATCTGA
194151 AAAA
1 AAAA
194155 AAATGGTGTA
Statistics
Matches: 98, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
54 2 0.02
55 38 0.39
56 8 0.08
57 12 0.12
58 38 0.39
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.28
Consensus pattern (57 bp):
AAAATATGATGTAGGCCATTAGATGGCAAACACAAAAAAAATTATTTTTAAATCTGA
Found at i:201949 original size:71 final size:72
Alignment explanation
Indices: 201832--201973 Score: 223
Period size: 71 Copynumber: 2.0 Consensus size: 72
201822 ATTTTTAAAA
** *
201832 AGATGTAATTGTAAATGTTAGAGAATTTTTAATTAGGAATGCAAATGAATTTAACTTGAACGAAT
1 AGATGTAATTGTAAATGTTAGAGAATTTTTAATTAGGAATGCAAATGAATCGAACTTGAACAAAT
201897 AAATCTC
66 AAATCTC
* * *
201904 AGATGTAATTGTAATTGTT-GAGAATTTTTTATTAGGAATGTAAATGAATCGAACTTGAACAAAT
1 AGATGTAATTGTAAATGTTAGAGAATTTTTAATTAGGAATGCAAATGAATCGAACTTGAACAAAT
201968 AAATCT
66 AAATCT
201974 TTGTTCGTGT
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
71 46 0.72
72 18 0.28
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.36
Consensus pattern (72 bp):
AGATGTAATTGTAAATGTTAGAGAATTTTTAATTAGGAATGCAAATGAATCGAACTTGAACAAAT
AAATCTC
Found at i:202115 original size:12 final size:12
Alignment explanation
Indices: 202092--202151 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
202082 TTCATTTAAC
202092 TTAATCGAACATA
1 TTAAT-GAACATA
*
202105 TTCATGAACATA
1 TTAATGAACATA
*
202117 -TAATTGAACATG
1 TTAA-TGAACATA
*
202129 TTTATGAACATA
1 TTAATGAACATA
202141 -TAATTGAACAT
1 TTAA-TGAACAT
202152 GTTTACGAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
11 4 0.11
12 28 0.74
13 6 0.16
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (12 bp):
TTAATGAACATA
Found at i:202125 original size:24 final size:24
Alignment explanation
Indices: 202075--202151 Score: 95
Period size: 24 Copynumber: 3.2 Consensus size: 24
202065 TAATGCTCAC
* *
202075 GAACATATTCATTTAAC-T-TAATC
1 GAACATATTCA-TGAACATATAATT
202098 GAACATATTCATGAACATATAATT
1 GAACATATTCATGAACATATAATT
* *
202122 GAACATGTTTATGAACATATAATT
1 GAACATATTCATGAACATATAATT
202146 GAACAT
1 GAACAT
202152 GTTTACGAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
22 4 0.08
23 12 0.25
24 32 0.67
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (24 bp):
GAACATATTCATGAACATATAATT
Found at i:202152 original size:24 final size:24
Alignment explanation
Indices: 202093--202162 Score: 104
Period size: 24 Copynumber: 2.9 Consensus size: 24
202083 TCATTTAACT
* * *
202093 TAATCGAACATATTCATGAACATA
1 TAATTGAACATGTTTATGAACATA
202117 TAATTGAACATGTTTATGAACATA
1 TAATTGAACATGTTTATGAACATA
*
202141 TAATTGAACATGTTTACGAACA
1 TAATTGAACATGTTTATGAACA
202163 ATGTTAATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (24 bp):
TAATTGAACATGTTTATGAACATA
Found at i:204851 original size:17 final size:17
Alignment explanation
Indices: 204809--204852 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
204799 TAAAATTAAT
**
204809 AATATTTTAAAATTTTA
1 AATATTTTAAAAAATTA
* *
204826 AAAAATTTAAAAAATTA
1 AATATTTTAAAAAATTA
204843 AATATTTTAA
1 AATATTTTAA
204853 TATATATTTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATATTTTAAAAAATTA
Found at i:208492 original size:22 final size:22
Alignment explanation
Indices: 208467--208517 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
208457 AAAATCTTTT
208467 ATTTTTAATTTTTTTAAAAAAC
1 ATTTTTAATTTTTTTAAAAAAC
**
208489 ATTTATT--TTTTTTTTCAAAAC
1 ATTT-TTAATTTTTTTAAAAAAC
208510 -TTTTTAAT
1 ATTTTTAAT
208518 GTAGCTCTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
19 2 0.08
20 3 0.12
21 13 0.54
22 4 0.17
23 2 0.08
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTTTAATTTTTTTAAAAAAC
Found at i:236489 original size:20 final size:21
Alignment explanation
Indices: 236464--236509 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
236454 GAATTATGTA
236464 ATTTGAATTTATAA-CTTTAT
1 ATTTGAATTTATAATCTTTAT
* *
236484 ATTTGAATTTTTAATTTTTAT
1 ATTTGAATTTATAATCTTTAT
236505 ATTTG
1 ATTTG
236510 GATTATACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (21 bp):
ATTTGAATTTATAATCTTTAT
Found at i:236667 original size:16 final size:16
Alignment explanation
Indices: 236646--236685 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
236636 CCGATTATTA
236646 CGGGTACCCAAAATTC
1 CGGGTACCCAAAATTC
*
236662 CGGGTACCAAAAATTC
1 CGGGTACCCAAAATTC
236678 C-GGTACCC
1 CGGGTACCC
236686 CATATTCAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.17
Consensus pattern (16 bp):
CGGGTACCCAAAATTC
Found at i:259738 original size:155 final size:155
Alignment explanation
Indices: 259475--259785 Score: 577
Period size: 155 Copynumber: 2.0 Consensus size: 155
259465 GGGTCAGTGG
* *
259475 GTGGGTTCCATTCGCTTTTAGAGCCTTATGCCACAAGTCACAACTTAACTTGTCTTGTTTCTGAG
1 GTGGGTTCCATTCGCTTTTAGAACCTTATGCCACAAGGCACAACTTAACTTGTCTTGTTTCTGAG
259540 GAGCTTCCATATAAATAAAATACTTCACTCTCTGCTCTTGCAACTCACCACCAACACATTATCAT
66 GAGCTTCCATATAAATAAAATACTTCACTCTCTGCTCTTGCAACTCACCACCAACACATTATCAT
259605 CCTCACTTCTCTCACCACTACTCTT
131 CCTCACTTCTCTCACCACTACTCTT
* * *
259630 GTGGGTTCCATTCGCTTTTAGAATCTTGTGCCACAAGGCACAACTTAAGTTGTCTTGTTTCTGAG
1 GTGGGTTCCATTCGCTTTTAGAACCTTATGCCACAAGGCACAACTTAACTTGTCTTGTTTCTGAG
259695 GAGCTTCCATATAAATAAAATACTTCACTCTCTGCTCTTGCAACTCACCACCAACACATTATCAT
66 GAGCTTCCATATAAATAAAATACTTCACTCTCTGCTCTTGCAACTCACCACCAACACATTATCAT
259760 CCTCACTTCTCTCACCACTACTCTT
131 CCTCACTTCTCTCACCACTACTCTT
259785 G
1 G
259786 CTTTCTTTAG
Statistics
Matches: 151, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
155 151 1.00
ACGTcount: A:0.25, C:0.30, G:0.12, T:0.33
Consensus pattern (155 bp):
GTGGGTTCCATTCGCTTTTAGAACCTTATGCCACAAGGCACAACTTAACTTGTCTTGTTTCTGAG
GAGCTTCCATATAAATAAAATACTTCACTCTCTGCTCTTGCAACTCACCACCAACACATTATCAT
CCTCACTTCTCTCACCACTACTCTT
Found at i:264217 original size:4 final size:4
Alignment explanation
Indices: 264208--264293 Score: 77
Period size: 4 Copynumber: 21.2 Consensus size: 4
264198 AAATAAACGG
* * *
264208 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
* * *
264258 -AAA GAAG GAGA GTAAA GAAA G-AA GAAG GAAA GAAA G
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA G
264294 GTAATGTGTT
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
3 6 0.09
4 50 0.75
5 11 0.16
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:264230 original size:17 final size:17
Alignment explanation
Indices: 264208--264293 Score: 83
Period size: 17 Copynumber: 5.3 Consensus size: 17
264198 AAATAAACGG
264208 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
264225 GAAAGAAAGAAAGG-AA
1 GAAAGAAAGAAAGGAAA
* *
264241 GAAGGAGAGGAAA-GAAA
1 GAAAGA-AAGAAAGGAAA
* * *
264258 -AAAGAAGGAGAGTAAA
1 GAAAGAAAGAAAGGAAA
264274 GAAAG-AAG-AAGGAAA
1 GAAAGAAAGAAAGGAAA
264289 GAAAG
1 GAAAG
264294 GTAATGTGTT
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
15 15 0.26
16 17 0.30
17 25 0.44
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (17 bp):
GAAAGAAAGAAAGGAAA
Found at i:264264 original size:20 final size:21
Alignment explanation
Indices: 264207--264286 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
264197 CAAATAAACG
*
264207 GGAAAGAAAGAAAGGAAAGA-A
1 GGAAAGAAAGAAA-GAAGGAGA
* *
264228 AGAAAGAAAGGAAGAAGGAGA
1 GGAAAGAAAGAAAGAAGGAGA
264249 GGAAAGAAA-AAAGAAGGAGA
1 GGAAAGAAAGAAAGAAGGAGA
*
264269 GTAAAGAAAG-AAGAAGGA
1 GGAAAGAAAGAAAGAAGGA
264287 AAGAAAGGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
20 31 0.61
21 20 0.39
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.01
Consensus pattern (21 bp):
GGAAAGAAAGAAAGAAGGAGA
Done.