Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold196
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: 7488280
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 125249 characters in sequence are not A, C, G, or T
File 1 of 47
Found at i:7825 original size:2 final size:2
Alignment explanation
Indices: 7818--7867 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
7808 ACTGAGAATG
7818 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
7860 A- AT AT AT A
1 AT AT AT AT A
7868 ATCCAAGGCT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9791 original size:18 final size:20
Alignment explanation
Indices: 9768--9808 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
9758 TATAATACAG
*
9768 AAATATA-TATAAT-CTTTT
1 AAATATATTAAAATACTTTT
9786 AAATATATTAAAATACTTTT
1 AAATATATTAAAATACTTTT
9806 AAA
1 AAA
9809 AAAATTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 5 0.25
20 8 0.40
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATATATTAAAATACTTTT
Found at i:10008 original size:2 final size:2
Alignment explanation
Indices: 10003--10064 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
9993 AGAAAAATAA
*
10003 AT AT AT AG 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
10045 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
10065 TGCTGCCTAG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12322 original size:14 final size:14
Alignment explanation
Indices: 12300--12335 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
12290 AAGATTATAA
*
12300 TAAATTTTAAATAT
1 TAAAATTTAAATAT
12314 TAAAATTTAAATAT
1 TAAAATTTAAATAT
12328 T-AAATTTA
1 TAAAATTTA
12336 TCAAATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAAATTTAAATAT
Found at i:17544 original size:51 final size:51
Alignment explanation
Indices: 17487--17589 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
17477 ATGTGTTACT
*
17487 TCATTTTATTATTTTCATAATTTGAAAAAGAAAAAAAATAAAAGTAAAAAA
1 TCATTTTATTATTTTCATAATTGGAAAAAGAAAAAAAATAAAAGTAAAAAA
17538 TCATTTTATTATTTTCATAATTGGAAAAAGAAAAAAAATAAAAGTAAAAAA
1 TCATTTTATTATTTTCATAATTGGAAAAAGAAAAAAAATAAAAGTAAAAAA
17589 T
1 T
17590 GCACTGACAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (51 bp):
TCATTTTATTATTTTCATAATTGGAAAAAGAAAAAAAATAAAAGTAAAAAA
Found at i:20140 original size:14 final size:15
Alignment explanation
Indices: 20121--20149 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20111 CTAATTTGAA
20121 ATGATTT-TCTTTTT
1 ATGATTTATCTTTTT
20135 ATGATTTATCTTTTT
1 ATGATTTATCTTTTT
20150 TCTTATCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.69
Consensus pattern (15 bp):
ATGATTTATCTTTTT
Found at i:33674 original size:22 final size:22
Alignment explanation
Indices: 33649--33696 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
33639 ATCTGAAACA
* *
33649 AAATTTTAATATAATCTCTAAT
1 AAATTTTAACATAATCTCCAAT
*
33671 AAATTTTAACATAATTTCCAAT
1 AAATTTTAACATAATCTCCAAT
33693 AAAT
1 AAAT
33697 ATACAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATTTTAACATAATCTCCAAT
Found at i:36432 original size:51 final size:51
Alignment explanation
Indices: 36369--36484 Score: 180
Period size: 51 Copynumber: 2.3 Consensus size: 51
36359 AAATAGCAGG
* * *
36369 GTTGGAGTATCCCCGATTGTGAGAAA-TTAGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAACTTAGTATTTTAGAAATAAAATCGGA
36420 GTTGGAGTATCCCCGATTATGAAAACTTAGTATTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAACTTAGTATTTTAGAAATAAAATCGGA
*
36471 GTTTGAGTATCCCC
1 GTTGGAGTATCCCC
36485 TCAAAAATAA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 3 0.05
51 57 0.95
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAACTTAGTATTTTAGAAATAAAATCGGA
Found at i:36613 original size:109 final size:107
Alignment explanation
Indices: 36420--36628 Score: 258
Period size: 109 Copynumber: 1.9 Consensus size: 107
36410 TAAAATCGGA
* ** * * *
36420 GTTGGAGTATCCCCGATTATGAAAACTTAGTATTTTAGAAATAAAATCGGAGTTTGAGTATCCCC
1 GTTGGAGTACCCCCGATTATGAAAAAATAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCC
* *
36485 TCAAAAATAACGATATTGGAGTATCCCTGATGAAATAACAAG
66 TCAAAAATAACGAGATTGGAGTATCCCCGATGAAATAACAAG
* *
36527 GTTGGAGTACCCCCGATTATGAAAAAAATAATATTTTTA-AATATAAAGCCGGGGTTGGAGTATC
1 GTTGGAGTACCCCCGATTATG-AAAAAATAATA-TTTTAGAA-ATAAAACCGGAGTTGGAGTATC
** * *
36591 CCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAA
63 CCCTCAAAAATAACGAGATTGGAGTATCCCCGATGAAA
36629 AATTGATGTT
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
107 20 0.24
108 10 0.12
109 55 0.65
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (107 bp):
GTTGGAGTACCCCCGATTATGAAAAAATAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCC
TCAAAAATAACGAGATTGGAGTATCCCCGATGAAATAACAAG
Found at i:37592 original size:19 final size:19
Alignment explanation
Indices: 37568--37606 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
37558 GGCCAAGACT
37568 ATCCTACATCTATTGGACA
1 ATCCTACATCTATTGGACA
37587 ATCCTACATCTATTGGACA
1 ATCCTACATCTATTGGACA
37606 A
1 A
37607 AAGAGACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (19 bp):
ATCCTACATCTATTGGACA
Found at i:39075 original size:13 final size:13
Alignment explanation
Indices: 39057--39082 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39047 ACAAAGATCG
39057 ATGTATCGATACA
1 ATGTATCGATACA
39070 ATGTATCGATACA
1 ATGTATCGATACA
39083 CTTCCTTAAT
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:39093 original size:21 final size:21
Alignment explanation
Indices: 39069--39110 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
39059 GTATCGATAC
*
39069 AATGTATCGATACACTTCCTT
1 AATGTATCCATACACTTCCTT
*
39090 AATGTATCCATACATTTCCTT
1 AATGTATCCATACACTTCCTT
39111 GGCAGTAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (21 bp):
AATGTATCCATACACTTCCTT
Found at i:39143 original size:13 final size:13
Alignment explanation
Indices: 39121--39178 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
39111 GGCAGTAGCT
*
39121 TTGTAGCGATACA
1 TTGTATCGATACA
39134 TTGTATCGATACAAAA
1 TTGTATCGATAC---A
39150 TTCATGTATCGATACA
1 -T--TGTATCGATACA
39166 TTGTATCGATACA
1 TTGTATCGATACA
39179 ACATTTATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
15 1 0.03
16 2 0.05
17 1 0.03
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:39168 original size:32 final size:32
Alignment explanation
Indices: 39122--39195 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
39112 GCAGTAGCTT
*
39122 TGTAGCGATACATTGTATCGATACAAAATTCA
1 TGTATCGATACATTGTATCGATACAAAATTCA
* *
39154 TGTATCGATACATTGTATCGATACAACATTTA
1 TGTATCGATACATTGTATCGATACAAAATTCA
39186 TGTATCGATA
1 TGTATCGATA
39196 TATTTACTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAAAATTCA
Found at i:39191 original size:19 final size:19
Alignment explanation
Indices: 39135--39195 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
39125 AGCGATACAT
* *
39135 TGTATCGATACAAAATTCA
1 TGTATCGATACAACATTTA
39154 TGTATCGAT---ACA--T-
1 TGTATCGATACAACATTTA
39167 TGTATCGATACAACATTTA
1 TGTATCGATACAACATTTA
39186 TGTATCGATA
1 TGTATCGATA
39196 TATTTACTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
13 9 0.26
16 5 0.15
18 1 0.03
19 19 0.56
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (19 bp):
TGTATCGATACAACATTTA
Found at i:39227 original size:19 final size:19
Alignment explanation
Indices: 39166--39227 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
39156 TATCGATACA
39166 TTGTATCGATACAACATT-T
1 TTGTATCGATACAA-ATTGT
* * * *
39185 ATGTATCGATATATTTACTGT
1 TTGTATCGATACA--AATTGT
39206 TTGTATCGATACAAATTGT
1 TTGTATCGATACAAATTGT
39225 TTG
1 TTG
39228 AAATTCGAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
19 18 0.56
20 2 0.06
21 12 0.38
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (19 bp):
TTGTATCGATACAAATTGT
Found at i:39289 original size:20 final size:21
Alignment explanation
Indices: 39257--39311 Score: 103
Period size: 20 Copynumber: 2.7 Consensus size: 21
39247 GTTGGGACCT
39257 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATTCTAGAAA
39278 TGTATC-ATACATTCTAGAAA
1 TGTATCGATACATTCTAGAAA
39298 TGTATCGATACATT
1 TGTATCGATACATT
39312 TGGATAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 20 0.61
21 13 0.39
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTCTAGAAA
Found at i:40042 original size:42 final size:42
Alignment explanation
Indices: 39996--40081 Score: 104
Period size: 42 Copynumber: 2.0 Consensus size: 42
39986 CCCATTTTTC
* *
39996 GAGGAC-AAAGGAAAAAGGGAAATGAAA-TACGTCCTGCTCTTT
1 GAGGACGAAA-GAAAAAGGAAAAT-AAAGTACATCCTGCTCTTT
* *
40038 GAGGACGAAAGAAAGAGGAAAATAAAGTGCATCCTGCTCTTT
1 GAGGACGAAAGAAAAAGGAAAATAAAGTACATCCTGCTCTTT
40080 GA
1 GA
40082 ACACTAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
41 3 0.08
42 32 0.84
43 3 0.08
ACGTcount: A:0.41, C:0.14, G:0.27, T:0.19
Consensus pattern (42 bp):
GAGGACGAAAGAAAAAGGAAAATAAAGTACATCCTGCTCTTT
Found at i:40157 original size:61 final size:61
Alignment explanation
Indices: 40069--40676 Score: 657
Period size: 61 Copynumber: 10.4 Consensus size: 61
40059 ATAAAGTGCA
** * * * * ***
40069 TCCTGCTCTTTGAACACTAAAAAGTGCCAACAACTCGTGTGGGCTTTGAAAAGGAAATATG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCG
* *
40130 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAA-GCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAG-GAAAGGCG
* *
40191 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT---AA-G--AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCG
* *
40246 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCG
* * * *
40307 TTCTGCCCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCG
* * * *
40368 TCCTGCCCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCG
*
40429 TCCTG-TCCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAGAAGGCG
1 TCCTGCT-CTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGA-AAGGCG
* * *
40490 TCTTGCTCTTTAAGGACTG-AAGGTGCCACCAGCTTGTGTGGGCTTT----A--AAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCG
* * *
40544 TCTTGATCTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTG---A--AAA-GCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCG
* * *
40599 TCATGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGCCTTT------GAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCG
40654 TCCTGCTCTTTGAGGACT-AAAGG
1 TCCTGCTCTTTGAGGACTGAAAGG
40677 GTGAAAGGAA
Statistics
Matches: 488, Mismatches: 42, Indels: 41
0.85 0.07 0.07
Matches are distributed among these distances:
54 30 0.06
55 138 0.28
56 5 0.01
57 1 0.00
58 4 0.01
60 34 0.07
61 267 0.55
62 9 0.02
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26
Consensus pattern (61 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCG
Found at i:40274 original size:177 final size:175
Alignment explanation
Indices: 40069--40676 Score: 703
Period size: 177 Copynumber: 3.5 Consensus size: 175
40059 ATAAAGTGCA
** * * ***
40069 TCCTGCTCTTTGAACACTAAAAAGTGCCAACAACTCGTGTGGGCTTTGAAAAGGAAATATGTCCT
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGCGTCCT
*
40134 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCCTGCTC
66 GCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTG-AAAGAGAAAGCGTCCTGCTC
*
40199 TTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
129 TTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAGAGGCG
* * *
40246 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGCGTTCT
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGCGTCCT
* *
40311 GCCCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGAAA-AGAAAAGGCGTCCTGCC
66 GCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAG-AAA-GCGTCCTGCT
40375 CTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCG
128 CTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTT--AAAG---AGGCG
*
40429 TCCTG-TCCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAGAAGGCGTC
1 TCCTGCT-CTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGGA-AAGGCGTC
* * * * *
40492 TTGCTCTTTAAGGACTGAAGGTGCCACCAGCTTGTGTGGGCTTT-AAA-AG---GCGTCTTGATC
64 CTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAGAAAGCGTCCTGCTC
* *
40552 TTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA-A-GCG
129 TTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAAGAGGCG
* * *
40599 TCATGCTCTTTGAGGACTG-AAAGATGCCACCAACTTGTGTGGCCTTT------GAAAGGCGTCC
1 TCCTGCTCTTTGAGGACTGAAAAG-TGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGCGTCC
*
40657 TGCTCTTTGAGGACTAAAGG
65 TGCTCTTTGAGGACTGAAGG
40677 GTGAAAGGAA
Statistics
Matches: 383, Mismatches: 33, Indels: 43
0.83 0.07 0.09
Matches are distributed among these distances:
164 26 0.07
165 2 0.01
169 4 0.01
170 41 0.11
171 2 0.01
175 5 0.01
176 55 0.14
177 138 0.36
178 1 0.00
180 3 0.01
181 5 0.01
182 34 0.09
183 67 0.17
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26
Consensus pattern (175 bp):
TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGCGTCCT
GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAGAAAGCGTCCTGCTCTT
TGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAAGAGGCG
Found at i:40758 original size:61 final size:60
Alignment explanation
Indices: 40680--40948 Score: 354
Period size: 61 Copynumber: 4.5 Consensus size: 60
40670 CTAAAGGGTG
40680 AAAGGAAAGAGCGTCCTGCTCTTTGAGGACTAGGAA-GTGCCACCAACTTGTGTGGGCTTTA
1 AAAGGAAAG-GCGTCCTGCTCTTTGAGGACT-GGAAGGTGCCACCAACTTGTGTGGGCTTTA
* * *
40741 AAAGGAGAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAGCTTATGTGGGCTTTA
1 AAAGGA-AAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTA
* * * *
40801 AAAGAAAAAGGCGTCCTGCTCTTTGAGGACTGGAGGGTGCCATCAACTCGTGTGGGCTTT-
1 AAAG-GAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTA
* *
40861 --A--AAAGGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
1 AAAGGAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTA
*
40917 AAAGGAAAAGGCATCCTGCTCTTTGAGGACTG
1 AAAGG-AAAGGCGTCCTGCTCTTTGAGGACTG
40949 AAAAGTGGAA
Statistics
Matches: 183, Mismatches: 15, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
55 49 0.27
58 2 0.01
59 2 0.01
60 51 0.28
61 76 0.42
62 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (60 bp):
AAAGGAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTA
Found at i:40943 original size:116 final size:117
Alignment explanation
Indices: 40680--40948 Score: 375
Period size: 116 Copynumber: 2.3 Consensus size: 117
40670 CTAAAGGGTG
*
40680 AAAGG-AAAGAGCGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAA
1 AAAGGAAAAG-GCGTCCTGCTCTTTGAGGACT-GGAAGTGCCACCAACTCGTGTGGGCTTT--AA
* *
40744 GGAGAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAGCTTATGTGGGCTTTA
62 -GAGAAGGCATCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTATGTGGGCTTTA
* * *
40801 AAAGAAAAAGGCGTCCTGCTCTTTGAGGACTGGAGGGTGCCATCAACTCGTGTGGGCTTT-A-A-
1 AAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGA-AGTGCCACCAACTCGTGTGGGCTTTAAGAG
*
40863 AAGGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
65 AAGGCATCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTATGTGGGCTTTA
*
40917 AAAGGAAAAGGCATCCTGCTCTTTGAGGACTG
1 AAAGGAAAAGGCGTCCTGCTCTTTGAGGACTG
40949 AAAAGTGGAA
Statistics
Matches: 136, Mismatches: 9, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
115 23 0.17
116 58 0.43
118 1 0.01
120 3 0.02
121 47 0.35
122 4 0.03
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (117 bp):
AAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAGTGCCACCAACTCGTGTGGGCTTTAAGAGA
AGGCATCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTATGTGGGCTTTA
Found at i:45148 original size:20 final size:20
Alignment explanation
Indices: 45120--45193 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
45110 TTTTACCCAG
45120 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
45140 ATATATCGATACATGTTTGA
1 ATGTATCGATACATTTTTCA
* *
45160 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
45180 ATGTATCGATACAT
1 ATGTATCGATACAT
45194 CTAGTTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:52109 original size:15 final size:16
Alignment explanation
Indices: 52085--52126 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
52075 TCAAAAGCAG
52085 AAGCACAAAAAATG-AA
1 AAGCA-AAAAAATGCAA
*
52101 AAG-AAAAAAGTGCAA
1 AAGCAAAAAAATGCAA
52116 AAGCAAAAAAA
1 AAGCAAAAAAA
52127 AAGGGAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 7 0.32
15 6 0.27
16 9 0.41
ACGTcount: A:0.71, C:0.10, G:0.14, T:0.05
Consensus pattern (16 bp):
AAGCAAAAAAATGCAA
Found at i:53495 original size:27 final size:27
Alignment explanation
Indices: 53432--53882 Score: 408
Period size: 27 Copynumber: 16.4 Consensus size: 27
53422 TGACCTCTTC
53432 AAAGTCCACAACTCCGTGGCACTCTTTT
1 AAAGTCCACAACTCCGTGGCAC-CTTTT
* *
53460 AAAGTCCACAACTCCATGGCACCCTTT
1 AAAGTCCACAACTCCGTGGCACCTTTT
53487 AAAGTCCACAACTCCGTGGCACTCTTTT
1 AAAGTCCACAACTCCGTGGCAC-CTTTT
* *
53515 AAAGTCCACAACTCCATGGCACCCTTT
1 AAAGTCCACAACTCCGTGGCACCTTTT
53542 AAAGTCCACAACTCCGTGGCACCTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTT
*
53569 TAAGTCCACAACTCCGTGGCACCTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTT
* * * *
53596 TAAGTCCACAATTCTGTGGTACCTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTT
*
53623 TAAGTCCACAA-TCCCGTGGCACCCTTTT
1 AAAGTCCACAACT-CCGTGGCA-CCTTTT
* *
53651 -AAGTCCACAACTCTGTGGTACTCTTTT
1 AAAGTCCACAACTCCGTGGCAC-CTTTT
53678 GAAA-TCCACAACTCCGTGGCATCCTTTT
1 -AAAGTCCACAACTCCGTGGCA-CCTTTT
*
53706 -AAGTCCACAACTCCGTGGCACCTTTC
1 AAAGTCCACAACTCCGTGGCACCTTTT
* * ** *
53732 AAAGCCCACAAGTTAGTGGCATCCCTTTC
1 AAAGTCCACAACTCCGTGGCA--CCTTTT
* * * * *
53761 AGAGCCCACAAGTCAGTGGCATCTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTT
* * *
53788 CAAAG-CTCACAAGTCAGTGGCATCCTTTC
1 -AAAGTC-CACAACTCCGTGGCA-CCTTTT
* * ** *
53817 AAAGCCCACAAGTCAATGGCACCATTTC
1 AAAGTCCACAACTCCGTGGCACC-TTTT
* * ** *
53845 AAAGCCCACAAGTTAGTGGCATCTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTT
*
53872 CAAAGCCCACA
1 -AAAGTCCACA
53883 CAAGTCGGTG
Statistics
Matches: 370, Mismatches: 35, Indels: 36
0.84 0.08 0.08
Matches are distributed among these distances:
26 9 0.02
27 185 0.50
28 143 0.39
29 33 0.09
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.27
Consensus pattern (27 bp):
AAAGTCCACAACTCCGTGGCACCTTTT
Found at i:53563 original size:82 final size:82
Alignment explanation
Indices: 53432--53742 Score: 405
Period size: 82 Copynumber: 3.8 Consensus size: 82
53422 TGACCTCTTC
* *
53432 AAAGTCCACAACTCCGTGGCACTCTTTTAAAGTCCACAACTCCATGGCACCCTTTAAAGTCCACA
1 AAAGTCCACAACTCCGTGGCAC-CCTTTAAAGTCCACAACTCCGTGGCACCCTTTAAAGTCCACA
53497 ACTCCGTGGCACTCTTTT
65 ACTCCGTGGCACTCTTTT
* * *
53515 AAAGTCCACAACTCCATGGCACCCTTTAAAGTCCACAACTCCGTGGCACCTTTTTAAGTCCACAA
1 AAAGTCCACAACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTAAAGTCCACAA
53580 CTCCGTGGCAC-CTTTT
66 CTCCGTGGCACTCTTTT
* * * * * * *
53596 TAAGTCCACAATTCTGTGGTACCTTTTTAAGTCCACAA-TCCCGTGGCACCCTTTTAAGTCCACA
1 AAAGTCCACAACTCCGTGGCACCCTTTAAAGTCCACAACT-CCGTGGCACCCTTTAAAGTCCACA
* *
53660 ACTCTGTGGTACTCTTTT
65 ACTCCGTGGCACTCTTTT
* * *
53678 GAAA-TCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCA-CCTTTCAAAGCCCAC
1 -AAAGTCCACAACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTT-AAAGTCCAC
53741 AA
64 AA
53743 GTTAGTGGCA
Statistics
Matches: 200, Mismatches: 23, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
80 1 0.00
81 74 0.37
82 101 0.50
83 24 0.12
ACGTcount: A:0.26, C:0.33, G:0.14, T:0.28
Consensus pattern (82 bp):
AAAGTCCACAACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTAAAGTCCACAA
CTCCGTGGCACTCTTTT
Found at i:53601 original size:54 final size:55
Alignment explanation
Indices: 53433--53815 Score: 438
Period size: 55 Copynumber: 7.0 Consensus size: 55
53423 GACCTCTTCA
* *
53433 AAGTCCACAACTCCGTGGCACTCTTTTAAAGTCCACAACTCCATGGCACCCTTTA
1 AAGTCCACAACTCCGTGGCACTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT
* *
53488 AAGTCCACAACTCCGTGGCACTCTTTTAAAGTCCACAACTCCATGGCACCCTTTA
1 AAGTCCACAACTCCGTGGCACTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT
* *
53543 AAGTCCACAACTCCGTGGCAC-CTTTTTAAGTCCACAACTCCGTGGCACCTTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT
* * * *
53597 AAGTCCACAATTCTGTGGTAC-CTTTTTAAGTCCACAA-TCCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTAAAGTCCACAACT-CCGTGGCACCCTTTT
* * *
53651 AAGTCCACAACTCTGTGGTACTCTTTTGAAA-TCCACAACTCCGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTT-AAAGTCCACAACTCCGTGGCACCCTTTT
* * * ** *
53706 AAGTCCACAACTCCGTGGCAC-CTTTCAAAGCCCACAAGTTAGTGGCATCCCTTTC
1 AAGTCCACAACTCCGTGGCACTCTTTTAAAGTCCACAACTCCGTGGCA-CCCTTTT
* * * * * *
53761 AGAGCCCACAAGTCAGTGGCA-TCTTTTCAAAG-CTCACAAGTCAGTGGCATCCTTT
1 A-AGTCCACAACTCCGTGGCACTCTTTT-AAAGTC-CACAACTCCGTGGCACCCTTT
53816 CAAAGCCCAC
Statistics
Matches: 292, Mismatches: 26, Indels: 19
0.87 0.08 0.06
Matches are distributed among these distances:
53 4 0.01
54 114 0.39
55 127 0.43
56 29 0.10
57 18 0.06
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (55 bp):
AAGTCCACAACTCCGTGGCACTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT
Found at i:53798 original size:28 final size:28
Alignment explanation
Indices: 53429--54497 Score: 516
Period size: 28 Copynumber: 37.1 Consensus size: 28
53419 CTGTGACCTC
* * *
53429 TTCAAAGTCCACAACTCCGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCTT
* * * *
53458 TT-AAAGTCCACAACTCCA-TGGCACCCT
1 TTCAAAGCCCACAAGT-CAGTGGCATCTT
* * *
53485 TT-AAAGTCCACAACTCCGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCTT
* * * *
53513 TT-AAAGTCCACAACTCCA-TGGCACCCT
1 TTCAAAGCCCACAAGT-CAGTGGCATCTT
* * * *
53540 TT-AAAGTCCACAACTCCGTGGCACCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* * * * *
53567 TT-TAAGTCCACAACTCCGTGGCACCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* * * * * *
53594 TT-TAAGTCCACAATTCTGTGGTACCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* * * *
53621 TT-TAAGTCCACAA-TCCCGTGGCACCCTT
1 TTCAAAGCCCACAAGT-CAGTGGCA-TCTT
* * * *
53649 TT--AAGTCCACAACTCTGTGGTACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCTT
* * * *
53676 TTGAAA-TCCACAACTCCGTGGCATCCTT
1 TTCAAAGCCCACAAGTCAGTGGCAT-CTT
* * * *
53704 TT--AAGTCCACAACTCCGTGGCA-CCT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* *
53729 TTCAAAGCCCACAAGTTAGTGGCATCCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT-CTT
*
53758 TTCAGAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* *
53786 TTCAAAGCTCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* * *
53814 TTCAAAGCCCACAAGTCAATGGCACCAT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
*
53842 TTCAAAGCCCACAAGTTAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* *
53870 TTCAAAGCCCACACAAGTCGGTGGCAGCTCAT
1 TTCAAAG-CC-CACAAGTCAGTGGCA--TCTT
* * * *
53902 TTCAAAGCCCACACAAGTCGGTGGAAGCCCAT
1 TTCAAAG-CC-CACAAGTCAGTGGCA--TCTT
*
53934 TTCAAAGCCCACAAGTCGGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* ** * * *
53962 TCCAAAGCCCACACAAGTTGGTGACACCCT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCTT
* *
53992 TTCAAAGCCCACACAAGTCAGTGGCAACCCAT
1 TTCAAAG-CC-CACAAGTCAGTGGC-A-TCTT
* * * *
54024 TTGAAAGCCCACATAAGTCGGTGGCAACCCAT
1 TTCAAAGCCCAC--AAGTCAGTGGC-A-TCTT
** *
54056 TTCAAAGCCCACACAAGTTGGTGGCAACCTAT
1 TTCAAAG-CC-CACAAGTCAGTGGC-ATCT-T
* * * *
54088 TTCAAAGCCCACATAAG-CTGGTGACAACCCAT
1 TTCAAAGCCCAC--AAGTC-AGTGGC-A-TCTT
* * *
54120 TTGAAAGCCCACACAAGTCGGTGGCAACTCAT
1 TTCAAAG-CC-CACAAGTCAGTGGC-A-TCTT
** * *
54152 TTCAAAGCCCACACAAGTTGGTGGCAACCCAT
1 TTCAAAG-CC-CACAAGTCAGTGGC-A-TCTT
*
54184 TTCAAAGCCCACACAAGTCGGTGGCATCTT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCTT
* * * *
54214 TTCAAAGCCCATAAGTTAGTGGTATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
*
54242 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* * *
54270 TTCAATGTCCACAAGTCGGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* *
54298 TTCAAAGCCCACAAGTCAATGGTATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* * * *
54326 TTCCAAGCCCACAAGTTAGAGGCAACTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* * ** *
54354 TTCGAAGCCTATGAGTCAGTGGCAACTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* * *
54382 TTCAAAGCCCACGAGTCAGTAGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* *
54410 TCCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
** * *
54438 TTCAAAAACCACAAGTCAGTGACATCTC
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* * *
54466 TGCAAAGCCCACAGAAGTTAGTGGCACCTT
1 TTCAAAGCCCAC--AAGTCAGTGGCATCTT
54496 TT
1 TT
54498 TTTTAAAAAA
Statistics
Matches: 874, Mismatches: 128, Indels: 75
0.81 0.12 0.07
Matches are distributed among these distances:
25 4 0.00
26 5 0.01
27 172 0.20
28 365 0.42
29 38 0.04
30 91 0.10
31 10 0.01
32 176 0.20
33 7 0.01
34 6 0.01
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCTT
Found at i:53815 original size:56 final size:56
Alignment explanation
Indices: 53429--54497 Score: 595
Period size: 56 Copynumber: 18.5 Consensus size: 56
53419 CTGTGACCTC
* * * * * *
53429 TTCAAAGTCCACAACTCCGTGGCACTCTTTT-AAAGTCCACAACTCCA-TGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCTTTTCAAAGCCCACAAGT-CAGTGGCATCCT
* * * * * *
53485 TT-AAAGTCCACAACTCCGTGGCACTCTTTT-AAAGTCCACAACTCCA-TGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCTTTTCAAAGCCCACAAGT-CAGTGGCATCCT
* * * * * * * *
53540 TT-AAAGTCCACAACTCCGTGGCACCTTTT-TAAGTCCACAACTCCGTGGCA-CCT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCT
** * * * * * * * * *
53593 TTTTAAGTCCACAATTCTGTGGTACCTTTT-TAAGTCCACAA-TCCCGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGT-CAGTGGCATCCT
* * * * * * * * *
53648 TT-TAAGTCCACAACTCTGTGGTACTCTTTTGAAA-TCCACAACTCCGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCTTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * * * * *
53703 TT-TAAGTCCACAACTCCGTGGCA-CCTTTCAAAGCCCACAAGTTAGTGGCATCCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCAT-CCT
* *
53758 TTCAGAGCCCACAAGTCAGTGGCATCTTTTCAAAGCTCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * * * *
53814 TTCAAAGCCCACAAGTCAATGGCACCATTTCAAAGCCCACAAGTTAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * * * *
53870 TTCAAAGCCCACACAAGTCGGTGGCAGCTCATTTCAAAGCCCACACAAGTCGGTGGAAGCCCAT
1 TTCAAAG-CC-CACAAGTCAGTGGCA--TCTTTTCAAAG-CC-CACAAGTCAGTGGCA-TCC-T
* * ** * *
53934 TTCAAAGCCCACAAGTCGGTGGCATCTTTCCAAAGCCCACACAAGTTGGTGACACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAG-CC-CACAAGTCAGTGGCATCCT
* * * * *
53992 TTCAAAGCCCACACAAGTCAGTGGCAACCCATTTGAAAGCCCACATAAGTCGGTGGCAACCCAT
1 TTCAAAG-CC-CACAAGTCAGTGGC-A-TCTTTTCAAAGCCCAC--AAGTCAGTGGC-ATCC-T
** * * * *
54056 TTCAAAGCCCACACAAGTTGGTGGCAACCTATTTCAAAGCCCACATAAG-CTGGTGACAACCCAT
1 TTCAAAG-CC-CACAAGTCAGTGGC-ATCT-TTTCAAAGCCCAC--AAGTC-AGTGGC-ATCC-T
* * * ** *
54120 TTGAAAGCCCACACAAGTCGGTGGCAACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCCAT
1 TTCAAAG-CC-CACAAGTCAGTGGC-A-TCTTTTCAAAG-CC-CACAAGTCAGTGGC-ATCC-T
* * * *
54184 TTCAAAGCCCACACAAGTCGGTGGCATCTTTTCAAAGCCCATAAGTTAGTGGTATCCT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * * * *
54242 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAATGTCCACAAGTCGGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * * * * * *
54298 TTCAAAGCCCACAAGTCAATGGTATCTTTTCCAAGCCCACAAGTTAGAGGCAACTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * ** * * *
54354 TTCGAAGCCTATGAGTCAGTGGCAACTTTTCAAAGCCCACGAGTCAGTAGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * ** *
54410 TCCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAAACCACAAGTCAGTGACAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
54465 CTGCAAAGCCCACAGAAGTTAGTGGCACCTTTT
1 -TTCAAAGCCCAC--AAGTCAGTGGCATCTTTT
54498 TTTTAAAAAA
Statistics
Matches: 857, Mismatches: 120, Indels: 70
0.82 0.11 0.07
Matches are distributed among these distances:
53 14 0.02
54 98 0.11
55 132 0.15
56 258 0.30
57 29 0.03
58 44 0.05
59 8 0.01
60 62 0.07
61 7 0.01
62 53 0.06
63 11 0.01
64 135 0.16
65 3 0.00
66 3 0.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (56 bp):
TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:53910 original size:32 final size:31
Alignment explanation
Indices: 53711--54310 Score: 458
Period size: 32 Copynumber: 20.1 Consensus size: 31
53701 CTTTTAAGTC
* *
53711 CACAACTCCGTGGCAC-C-TTTCAAAG-CC-
1 CACAAGTCGGTGGCACTCATTTCAAAGCCCA
** * *
53738 CACAAGTTAGTGGCA-TCCCTTTCAGAG-CC-
1 CACAAGTCGGTGGCACT-CATTTCAAAGCCCA
* * *
53767 CACAAGTCAGTGGCA-TCTTTTCAAAG--CT
1 CACAAGTCGGTGGCACTCATTTCAAAGCCCA
* *
53795 CACAAGTCAGTGGCA-TCCTTTCAAAG-CC-
1 CACAAGTCGGTGGCACTCATTTCAAAGCCCA
**
53823 CACAAGTCAATGGCAC-CATTTCAAAG-CC-
1 CACAAGTCGGTGGCACTCATTTCAAAGCCCA
** *
53851 CACAAGTTAGTGGCA-TCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCACTCATTTCAAAGCCCA
53881 CACAAGTCGGTGGCAGCTCATTTCAAAGCCCA
1 CACAAGTCGGTGGCA-CTCATTTCAAAGCCCA
* *
53913 CACAAGTCGGTGGAAGCCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCA-CTCATTTCAAAGCCCA
53943 CACAAGTCGGTGGCA-TC-TTTCCAAAGCCCA
1 CACAAGTCGGTGGCACTCATTT-CAAAGCCCA
* * *
53973 CACAAGTTGGTGACAC-CCTTTCAAAGCCCA
1 CACAAGTCGGTGGCACTCATTTCAAAGCCCA
* * *
54003 CACAAGTCAGTGGCAACCCATTTGAAAGCCCA
1 CACAAGTCGGTGGC-ACTCATTTCAAAGCCCA
* *
54035 CATAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGC-ACTCATTTCAAAGCCCA
*
54067 CACAAGTTGGTGGCAAC-CTATTTCAAAGCCCA
1 CACAAGTCGGTGGC-ACTC-ATTTCAAAGCCCA
* * * *
54099 CATAAG-CTGGTGACAACCCATTTGAAAGCCCA
1 CACAAGTC-GGTGGC-ACTCATTTCAAAGCCCA
54131 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
1 CACAAGTCGGTGGC-ACTCATTTCAAAGCCCA
* *
54163 CACAAGTTGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGC-ACTCATTTCAAAGCCCA
*
54195 CACAAGTCGGTGGCA-TCTTTTCAAAG-CC-
1 CACAAGTCGGTGGCACTCATTTCAAAGCCCA
* ** * *
54223 CATAAGTTAGTGGTA-TCCTTTCAAAG-CC-
1 CACAAGTCGGTGGCACTCATTTCAAAGCCCA
* * * *
54251 CACAAGTCAGTGGCA-TCCTTTCAATG-TC-
1 CACAAGTCGGTGGCACTCATTTCAAAGCCCA
*
54279 CACAAGTCGGTGGCA-TCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCACTCATTTCAAAGCCCA
54309 CA
1 CA
54311 AGTCAATGGT
Statistics
Matches: 490, Mismatches: 59, Indels: 45
0.82 0.10 0.08
Matches are distributed among these distances:
27 16 0.03
28 156 0.32
29 32 0.07
30 72 0.15
31 9 0.02
32 203 0.41
33 2 0.00
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.21
Consensus pattern (31 bp):
CACAAGTCGGTGGCACTCATTTCAAAGCCCA
Found at i:54633 original size:45 final size:45
Alignment explanation
Indices: 54569--54784 Score: 204
Period size: 45 Copynumber: 4.7 Consensus size: 45
54559 TCTTAAAATC
* * * * *
54569 CAATATCGTTGGCATTGAATCAGCATATTGGCATCTTTATTAGCT
1 CAATGTCGCTGGCCTTGAATCAGCACATTGCCATCTTTATTAGCT
* *
54614 CAATGTCGCTGGCCTTGAATCAGCACATTATCCAT-TTTCCCTTAGCT
1 CAATGTCGCTGGCCTTGAATCAGCACATT-GCCATCTTT--ATTAGCT
* *
54661 CAATGTCGCTAGCCTTGAATCAGCACATTGTCCA-CTTTATTAGCC
1 CAATGTCGCTGGCCTTGAATCAGCACATTG-CCATCTTTATTAGCT
* *
54706 CAATGTCGCTGGCCTTGAATCAGCACATTGGTCCA-CTTTTCCCTTAGTT
1 CAATGTCGCTGGCCTTGAATCAGCACATT-G-CCATC-TTT--ATTAGCT
* **
54755 CAATGTCGTTGGCCTTGAATTGGCACATTG
1 CAATGTCGCTGGCCTTGAATCAGCACATTG
54785 GCAATCCTCT
Statistics
Matches: 144, Mismatches: 18, Indels: 15
0.81 0.10 0.08
Matches are distributed among these distances:
45 61 0.42
46 9 0.06
47 43 0.30
48 1 0.01
49 30 0.21
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.34
Consensus pattern (45 bp):
CAATGTCGCTGGCCTTGAATCAGCACATTGCCATCTTTATTAGCT
Found at i:54665 original size:47 final size:47
Alignment explanation
Indices: 54608--54784 Score: 241
Period size: 47 Copynumber: 3.8 Consensus size: 47
54598 GGCATCTTTA
*
54608 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTATCCATTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCATTTTCCC
* * *
54655 TTAGCTCAATGTCGCTAGCCTTGAATCAGCACATTGTCCACTTT--A
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCATTTTCCC
*
54700 TTAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATT-GTCCA-TTTTCCC
* * **
54749 TTAGTTCAATGTCGTTGGCCTTGAATTGGCACATTG
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTG
54785 GCAATCCTCT
Statistics
Matches: 113, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
45 33 0.29
46 5 0.04
47 44 0.39
48 1 0.01
49 30 0.27
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (47 bp):
TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCATTTTCCC
Found at i:55190 original size:20 final size:20
Alignment explanation
Indices: 55162--55232 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
55152 TTTTACCCAG
55162 ATGTATCGATATATTTTTCA
1 ATGTATCGATATATTTTTCA
* * * *
55182 ATATATCGATACATGTTTGA
1 ATGTATCGATATATTTTTCA
*
55202 ATGTATCGATATATTCTTCA
1 ATGTATCGATATATTTTTCA
55222 ATGTATCGATA
1 ATGTATCGATA
55233 CATCTAGTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (20 bp):
ATGTATCGATATATTTTTCA
Found at i:67356 original size:51 final size:50
Alignment explanation
Indices: 67290--67405 Score: 160
Period size: 51 Copynumber: 2.3 Consensus size: 50
67280 AAAATAGCAA
* * * *
67290 GGTTGGAGTATCCCCGATCGTGAGAAATTGGTGTTTTGGAAATAAAATTG
1 GGTTGAAGTATCCCCGATCGTGAAAAATTGGTATTTTAGAAATAAAATTG
* *
67340 GATTTGAAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAATTG
1 G-GTTGAAGTATCCCCGATCGTGAAAAATTGGTATTTTAGAAATAAAATTG
*
67391 GGTTGCAGTATCCCC
1 GGTTGAAGTATCCCC
67406 TCGAAAATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 13 0.23
51 44 0.77
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (50 bp):
GGTTGAAGTATCCCCGATCGTGAAAAATTGGTATTTTAGAAATAAAATTG
Found at i:70011 original size:21 final size:21
Alignment explanation
Indices: 69972--70013 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
69962 GTATCGATAC
*
69972 AATGTATCAATACACTTCCTT
1 AATGTATCAACACACTTCCTT
* *
69993 AATGTATCGACACATTTCCTT
1 AATGTATCAACACACTTCCTT
70014 GGCAGTAGCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (21 bp):
AATGTATCAACACACTTCCTT
Found at i:70062 original size:19 final size:19
Alignment explanation
Indices: 70038--70110 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
70028 AGCGATACAT
*
70038 TGTATCAATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
70057 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
** *
70076 TGTATCGATACATTTACTGTT
1 TGTATCGATACA-AAACT-TA
70097 TGTATCGATACAAA
1 TGTATCGATACAAA
70111 TTGTTTGAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
19 29 0.64
20 3 0.07
21 13 0.29
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:77262 original size:15 final size:16
Alignment explanation
Indices: 77242--77282 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
77232 TGTAAAGAAT
77242 AAATTAGTGGA-CAAG
1 AAATTAGTGGAGCAAG
* *
77257 AAATTAATGGAGTAAG
1 AAATTAGTGGAGCAAG
77273 AAATTAGTGG
1 AAATTAGTGG
77283 CTACTTACCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.46, C:0.02, G:0.27, T:0.24
Consensus pattern (16 bp):
AAATTAGTGGAGCAAG
Found at i:78400 original size:13 final size:12
Alignment explanation
Indices: 78382--78481 Score: 54
Period size: 11 Copynumber: 8.5 Consensus size: 12
78372 GAGTTAAAAT
78382 TAAATAATTATAA
1 TAAATAA-TATAA
78395 TAAATAATATAA
1 TAAATAATATAA
78407 -AATATAA-ATGAA
1 TAA-ATAATAT-AA
* *
78419 TTAA-GATATAA
1 TAAATAATATAA
*
78430 -AAATAACATAA
1 TAAATAATATAA
78441 -AAATAAT-TAA
1 TAAATAATATAA
78451 -AATATAATATTATA
1 TAA-ATAATA-TA-A
*
78465 TAAA-AATAAAA
1 TAAATAATATAA
78476 TAAATA
1 TAAATA
78482 CAATATAAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 23
0.70 0.07 0.23
Matches are distributed among these distances:
10 7 0.10
11 28 0.41
12 16 0.23
13 14 0.20
14 2 0.03
15 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (12 bp):
TAAATAATATAA
Found at i:78429 original size:28 final size:26
Alignment explanation
Indices: 78383--78499 Score: 81
Period size: 27 Copynumber: 4.1 Consensus size: 26
78373 AGTTAAAATT
*
78383 AAATAATTATAATAAATAATATAAAATAT
1 AAATAATTA-AAT--ATAATATAAAATAA
* *
78412 AAATGAATTAAGATATAAAAATAACATAA
1 AAAT-AATTAA-ATAT-AATATAAAATAA
* *
78441 AAATAATTAAAATATAATATTATATAA
1 AAATAATT-AAATATAATATAAAATAA
* *
78468 AAATAAAATAAATACAATATAAATATACA
1 AAAT-AATTAAATATAATATAAA-ATA-A
78497 AAA
1 AAA
78500 ATATTTTCTC
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
27 24 0.34
28 16 0.23
29 24 0.34
30 7 0.10
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.29
Consensus pattern (26 bp):
AAATAATTAAATATAATATAAAATAA
Found at i:78487 original size:22 final size:23
Alignment explanation
Indices: 78448--78490 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
78438 TAAAAATAAT
**
78448 TAAAATATAATATTATATAAAAA
1 TAAAATATAATACAATATAAAAA
78471 TAAAATA-AATACAATATAAA
1 TAAAATATAATACAATATAAA
78491 TATACAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAAATATAATACAATATAAAAA
Found at i:78487 original size:32 final size:30
Alignment explanation
Indices: 78440--78502 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 30
78430 AAATAACATA
* *
78440 AAAATAATTAAAATATAATATTATATAAAAAT
1 AAAATAAATAAAATATAA-A-TATACAAAAAT
*
78472 AAAATAAATACAATATAAATATACAAAAAT
1 AAAATAAATAAAATATAAATATACAAAAAT
78502 A
1 A
78503 TTTTCTCCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 11 0.39
31 1 0.04
32 16 0.57
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (30 bp):
AAAATAAATAAAATATAAATATACAAAAAT
Found at i:78698 original size:24 final size:24
Alignment explanation
Indices: 78654--78706 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
78644 AGAACTTGTT
*
78654 TTATTTGAAACTATCAAATTATTA
1 TTATTTGAAACTATCAAATTAGTA
* *
78678 TTATTTGAAACTGT-ATTATTAGTA
1 TTATTTGAAACTATCA-AATTAGTA
78702 TTATT
1 TTATT
78707 ACTATTGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.51
Consensus pattern (24 bp):
TTATTTGAAACTATCAAATTAGTA
Found at i:79161 original size:16 final size:18
Alignment explanation
Indices: 79140--79174 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
79130 GTAAAAATTA
79140 ATTAAAT-AAT-TTTAAT
1 ATTAAATAAATATTTAAT
79156 ATTAAATAAATATTTAAT
1 ATTAAATAAATATTTAAT
79174 A
1 A
79175 AAATATGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 3 0.18
18 7 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTAAATAAATATTTAAT
Found at i:80496 original size:17 final size:21
Alignment explanation
Indices: 80456--80501 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
80446 AATTAATTTA
80456 ATTTTATATAGATATAAAATT
1 ATTTTATATAGATATAAAATT
*
80477 ATTTTATAT-G-TAAAAATATT
1 ATTTTATATAGATATAAA-ATT
80497 ATTTT
1 ATTTT
80502 CTATTTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 5 0.22
20 9 0.39
21 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (21 bp):
ATTTTATATAGATATAAAATT
Found at i:80499 original size:20 final size:20
Alignment explanation
Indices: 80456--80521 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
80446 AATTAATTTA
*
80456 ATTTTATATAGATATAAA-ATT
1 ATTTTATAT-G-TAAAAATATT
80477 ATTTTATATGTAAAAATATT
1 ATTTTATATGTAAAAATATT
* * *
80497 ATTTTCTATTTAATTAATATT
1 ATTTTATATGTAA-AAATATT
80518 ATTT
1 ATTT
80522 CACTAATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.13
20 15 0.38
21 19 0.49
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTTTATATGTAAAAATATT
Found at i:82713 original size:2 final size:2
Alignment explanation
Indices: 82708--82736 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
82698 TCTCTCCCTT
82708 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
82737 TTTAAGACGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:83011 original size:29 final size:32
Alignment explanation
Indices: 82962--83021 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 32
82952 AAATATCTTA
82962 TTTAAATAAAATATATAATTATAAA-AATAAT
1 TTTAAATAAAATATATAATTATAAACAATAAT
*
82993 TTTAAA-AAATTAT-TAATTATAAACAATAA
1 TTTAAATAAAATATATAATTATAAACAATAA
83022 AAATAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 10 0.37
30 11 0.41
31 6 0.22
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (32 bp):
TTTAAATAAAATATATAATTATAAACAATAAT
Found at i:83543 original size:23 final size:23
Alignment explanation
Indices: 83524--83570 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
83514 GATAATTTTT
*
83524 TAATATTTAAATATTAAATTTAA
1 TAATATATAAATATTAAATTTAA
* *
83547 TATTATATAAATATTAAATATAA
1 TAATATATAAATATTAAATTTAA
83570 T
1 T
83571 TAAAATTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TAATATATAAATATTAAATTTAA
Found at i:92252 original size:22 final size:22
Alignment explanation
Indices: 92214--92272 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 22
92204 ATTAAAATTT
* * *
92214 TAAATTTTTTAAT-AATAAATA
1 TAAAATTTTAAATAAATAAAAA
92235 TAAAATTTTAAATAAATAAAAA
1 TAAAATTTTAAATAAATAAAAA
**
92257 TATTA-TTTAAATAAAT
1 TAAAATTTTAAATAAAT
92273 TAACGCTTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 22 0.69
22 10 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAATTTTAAATAAATAAAAA
Found at i:95084 original size:2 final size:2
Alignment explanation
Indices: 95077--95103 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
95067 ACCTCTTTAA
95077 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
95104 TTTTTCCCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:95636 original size:3 final size:3
Alignment explanation
Indices: 95630--95662 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
95620 ATAGATGTAG
95630 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
95663 TTGCTTGCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:97044 original size:12 final size:12
Alignment explanation
Indices: 97027--97051 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
97017 AATCAAAACT
97027 TATGATAATAGA
1 TATGATAATAGA
97039 TATGATAATAGA
1 TATGATAATAGA
97051 T
1 T
97052 TTTGATACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (12 bp):
TATGATAATAGA
Found at i:97813 original size:28 final size:28
Alignment explanation
Indices: 97782--97842 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
97772 ATGGAAAAGG
97782 GAGAAAATAATGGAAAAATAAGAAAAAT
1 GAGAAAATAATGGAAAAATAAGAAAAAT
** ** *
97810 GAGAGTATTTTTGAAAAATAAGAAAAAT
1 GAGAAAATAATGGAAAAATAAGAAAAAT
97838 GAGAA
1 GAGAA
97843 TAATTTTAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.61, C:0.00, G:0.20, T:0.20
Consensus pattern (28 bp):
GAGAAAATAATGGAAAAATAAGAAAAAT
Found at i:97849 original size:28 final size:28
Alignment explanation
Indices: 97794--97849 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
97784 GAAAATAATG
* *
97794 GAAAAATAAGAAAAATGAGAGTATTTTT
1 GAAAAATAAGAAAAATGAGAATAATTTT
97822 GAAAAATAAGAAAAATGAGAATAATTTT
1 GAAAAATAAGAAAAATGAGAATAATTTT
97850 AAGATTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.16, T:0.27
Consensus pattern (28 bp):
GAAAAATAAGAAAAATGAGAATAATTTT
Found at i:97894 original size:19 final size:18
Alignment explanation
Indices: 97859--97896 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
97849 TAAGATTTAA
97859 ATTAATTTTTAAATAAAT
1 ATTAATTTTTAAATAAAT
*
97877 ATTAATTTATTTAATAAAT
1 ATTAATTT-TTAAATAAAT
97896 A
1 A
97897 CGTAACATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTAATTTTTAAATAAAT
Found at i:98230 original size:21 final size:23
Alignment explanation
Indices: 98189--98233 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
98179 TAAATTAGAA
98189 TTTAACTAATTAAAAATTAATTT
1 TTTAACTAATTAAAAATTAATTT
98212 TTTAA-TAATTAAAAA-TAATTT
1 TTTAACTAATTAAAAATTAATTT
98233 T
1 T
98234 AAAGTAACCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 7 0.32
22 10 0.45
23 5 0.23
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTAACTAATTAAAAATTAATTT
Found at i:98567 original size:31 final size:31
Alignment explanation
Indices: 98532--98609 Score: 79
Period size: 34 Copynumber: 2.4 Consensus size: 31
98522 AATAATTATT
98532 TTAAAATATTAAAAT-TTATATATTTTTATAA
1 TTAAAATATTAAAATATTATATA-TTTTATAA
* *
98563 TTAAAAATAAATAAAAATATTATTTATTTTATAA
1 TT-AAAAT--ATTAAAATATTATATATTTTATAA
98597 TTAATAAT-TTAAA
1 TTAA-AATATTAAA
98610 TTAAATTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
31 6 0.15
32 5 0.13
33 2 0.05
34 20 0.51
35 6 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
TTAAAATATTAAAATATTATATATTTTATAA
Found at i:100963 original size:16 final size:16
Alignment explanation
Indices: 100944--100974 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
100934 TATTAAAAAT
100944 AATTAATAAAATTATC
1 AATTAATAAAATTATC
*
100960 AATTAATAAATTTAT
1 AATTAATAAAATTAT
100975 ATAAAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTAATAAAATTATC
Found at i:105509 original size:23 final size:22
Alignment explanation
Indices: 105483--105542 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 22
105473 AAGTTATTTT
105483 TTAAATAATAAAAAATTAATAAA
1 TTAAATAATAAAAAATTAA-AAA
105506 TTAAACT-ATAAAAAGA-TAAAAA
1 TTAAA-TAATAAAAA-ATTAAAAA
105528 -T-AATAATATAAAAAT
1 TTAAATAATA-AAAAAT
105543 ATTTTTAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
19 1 0.03
20 6 0.19
21 5 0.16
22 3 0.09
23 15 0.47
24 2 0.06
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (22 bp):
TTAAATAATAAAAAATTAAAAA
Found at i:107459 original size:22 final size:21
Alignment explanation
Indices: 107425--107508 Score: 65
Period size: 22 Copynumber: 4.2 Consensus size: 21
107415 ACGAATATAT
* *
107425 TTAAGATACTATTTAAAATAAA
1 TTAATATATTATTTAAAAT-AA
*
107447 TTAATATATTATTTATAATAA
1 TTAATATATTATTTAAAATAA
107468 -T-A-ATA-TA-TT-AAATAA
1 TTAATATATTATTTAAAATAA
107483 -TAATAGTATTATTTAAAATATA
1 TTAATA-TATTATTTAAAATA-A
107505 TTAA
1 TTAA
107509 CTTGATATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
15 6 0.12
16 3 0.06
17 3 0.06
18 5 0.10
19 3 0.06
20 3 0.06
21 7 0.14
22 17 0.34
23 3 0.06
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (21 bp):
TTAATATATTATTTAAAATAA
Found at i:107483 original size:15 final size:15
Alignment explanation
Indices: 107463--107508 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
107453 TATTATTTAT
107463 AATAATAATATATTA
1 AATAATAATATATTA
107478 AATAATAATAGTATTA
1 AATAATAATA-TATTA
**
107494 TTTAA-AATATATTA
1 AATAATAATATATTA
107508 A
1 A
107509 CTTGATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 5 0.19
15 14 0.52
16 8 0.30
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
AATAATAATATATTA
Found at i:107502 original size:18 final size:17
Alignment explanation
Indices: 107443--107502 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
107433 CTATTTAAAA
*
107443 TAAATTAATATATTATT
1 TAAAATAATATATTATT
*
107460 TATAATAATA-ATATATT
1 TAAAATAATATAT-TATT
*
107477 AAATAATAATAGTATTATT
1 TAA-AATAATA-TATTATT
107496 TAAAATA
1 TAAAATA
107503 TATTAACTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
16 2 0.06
17 13 0.38
18 11 0.32
19 6 0.18
20 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
TAAAATAATATATTATT
Found at i:107548 original size:24 final size:24
Alignment explanation
Indices: 107516--107564 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
107506 TAACTTGATA
* *
107516 TATTATTTATAGTATTAAAAATAT
1 TATTATTTATAATAATAAAAATAT
*
107540 TATTATTTATAATAATAATAATAT
1 TATTATTTATAATAATAAAAATAT
107564 T
1 T
107565 GTTAATAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TATTATTTATAATAATAAAAATAT
Found at i:108655 original size:21 final size:21
Alignment explanation
Indices: 108588--108658 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 21
108578 TAGCTCATTA
*
108588 TTAATGTATAAAATTTTTATATT
1 TTAATG-ATAAAAATTTTATA-T
* * *
108611 ATTAAT-ATAAAAAATATAAAAT
1 -TTAATGAT-AAAAATTTTATAT
108633 TTAATGATAAAAATTTTATAT
1 TTAATGATAAAAATTTTATAT
108654 TTAAT
1 TTAAT
108659 ATATTATTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
21 20 0.53
22 5 0.13
23 8 0.21
24 5 0.13
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (21 bp):
TTAATGATAAAAATTTTATAT
Found at i:108671 original size:44 final size:45
Alignment explanation
Indices: 108588--108687 Score: 111
Period size: 44 Copynumber: 2.3 Consensus size: 45
108578 TAGCTCATTA
*
108588 TTAATGTATAAAATTTTTATATTATTAATATAAAAAATATA-AAAT
1 TTAATG-ATAAAAATTTTATATTATTAATATAAAAAATATATAAAT
**
108633 TTAATGATAAAAATTTTATA-T-TTAATATATTATTAATATATAAAT
1 TTAATGATAAAAATTTTATATTATTAATATA--AAAAATATATAAAT
108678 TT-AT-ATAAAA
1 TTAATGATAAAA
108688 TAAATATATT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
42 8 0.16
43 7 0.14
44 22 0.45
45 12 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (45 bp):
TTAATGATAAAAATTTTATATTATTAATATAAAAAATATATAAAT
Found at i:109567 original size:31 final size:31
Alignment explanation
Indices: 109506--109567 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
109496 TGCTGCTCAA
* *
109506 CTTCAAAGCCAGCTTGCCTAACCAATCCCTT
1 CTTCAAAGCCAGCTTGCCCAACCAAACCCTT
**
109537 CTTCAAAGCTGGCTT-CCCAACCAAGACCCTT
1 CTTCAAAGCCAGCTTGCCCAACCAA-ACCCTT
109568 GTAATTTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.26, C:0.39, G:0.11, T:0.24
Consensus pattern (31 bp):
CTTCAAAGCCAGCTTGCCCAACCAAACCCTT
Found at i:115152 original size:2 final size:2
Alignment explanation
Indices: 115145--115171 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
115135 TCCTTTTACT
115145 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
115172 TTTTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:115613 original size:30 final size:30
Alignment explanation
Indices: 115578--115643 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
115568 ATATCTAGAC
*
115578 TTTTAAGTTACA-CTCAAAAAAATTTTTAAT
1 TTTTAAATTACATCTC-AAAAAATTTTTAAT
** *
115608 TTTTAAATTGTATCTCAATAAATTTTTAAT
1 TTTTAAATTACATCTCAAAAAATTTTTAAT
115638 TTTTAA
1 TTTTAA
115644 TTTATATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (30 bp):
TTTTAAATTACATCTCAAAAAATTTTTAAT
Found at i:120974 original size:22 final size:21
Alignment explanation
Indices: 120922--120987 Score: 73
Period size: 20 Copynumber: 3.1 Consensus size: 21
120912 TTTGATAAAA
*
120922 AATTTTAGATAATATTTTATGT
1 AATTTTA-ATAATATTTTATAT
120944 AA--TTAATAATATTTTTATAT
1 AATTTTAATAATA-TTTTATAT
* *
120964 AATTTTAATAATACTTTATGT
1 AATTTTAATAATATTTTATAT
120985 AAT
1 AAT
120988 ACTATTTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 6 0.16
20 12 0.32
21 9 0.24
22 11 0.29
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (21 bp):
AATTTTAATAATATTTTATAT
Found at i:121059 original size:20 final size:19
Alignment explanation
Indices: 121012--121061 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
121002 TTTTTAAGTT
*
121012 ATATTTTATATAACTTATA
1 ATATTTTATGTAACTTATA
121031 ATATTTTTATGTAA-TATAGTA
1 ATA-TTTTATGTAACT-TA-TA
121052 ATATTTTATG
1 ATATTTTATG
121062 CAATTTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 4 0.15
20 18 0.67
21 5 0.19
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (19 bp):
ATATTTTATGTAACTTATA
Found at i:121860 original size:20 final size:21
Alignment explanation
Indices: 121809--121864 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
121799 AATTCTTAAA
121809 TAATATTTTATGTAA-CTCAG
1 TAATATTTTATGTAATCTCAG
* *
121829 -AATGTTTATATGTAATGTC-G
1 TAATATTT-TATGTAATCTCAG
121849 TAATATTTTATGTAAT
1 TAATATTTTATGTAAT
121865 TCTGATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 6 0.20
20 16 0.53
21 8 0.27
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.48
Consensus pattern (21 bp):
TAATATTTTATGTAATCTCAG
Found at i:122963 original size:25 final size:24
Alignment explanation
Indices: 122935--123014 Score: 65
Period size: 28 Copynumber: 3.1 Consensus size: 24
122925 CTAACAATAA
122935 TTATTATTTAATAATAAAAAAAATT
1 TTATTATTTAAT-ATAAAAAAAATT
* *
122960 TTATTTAAATTCAATTATAAAAAATATAT
1 TTA-TT--ATTTAA-TATAAAAAAAAT-T
122989 TTA-TA-TTAATATAAAAATAAATT
1 TTATTATTTAATATAAAAA-AAATT
123012 TTA
1 TTA
123015 AATTTTTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
23 12 0.27
24 6 0.13
25 4 0.09
26 2 0.04
27 1 0.02
28 15 0.33
29 5 0.11
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (24 bp):
TTATTATTTAATATAAAAAAAATT
Found at i:123005 original size:23 final size:23
Alignment explanation
Indices: 122933--123005 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 23
122923 CCCTAACAAT
*
122933 AATTATTATTTAA-TAATAAAAAA
1 AATTA-TATTTAATTAATATAAAA
*
122956 AATTTTATTTAAATTCAATTATAAAA
1 AATTATATTT-AATT-AA-TATAAAA
122982 AA-TATATTTATATTAATATAAAA
1 AATTATATTTA-ATTAATATAAAA
123005 A
1 A
123006 TAAATTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
22 5 0.12
23 14 0.33
24 4 0.10
25 11 0.26
26 8 0.19
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (23 bp):
AATTATATTTAATTAATATAAAA
Found at i:123845 original size:16 final size:16
Alignment explanation
Indices: 123807--123845 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
123797 TTAATTTTTA
123807 TTGATAATTTTTAAAT
1 TTGATAATTTTTAAAT
* * *
123823 ATAATAATTTTTTAAT
1 TTGATAATTTTTAAAT
123839 TTGATAA
1 TTGATAA
123846 CATAAAAACA
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (16 bp):
TTGATAATTTTTAAAT
Found at i:125108 original size:17 final size:17
Alignment explanation
Indices: 125083--125117 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
125073 TTATAACGAC
* *
125083 ACTTCTAATAACTCCTA
1 ACTTATAATAACACCTA
125100 ACTTATAATAACACCTA
1 ACTTATAATAACACCTA
125117 A
1 A
125118 AATTTAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.31
Consensus pattern (17 bp):
ACTTATAATAACACCTA
Found at i:126270 original size:12 final size:12
Alignment explanation
Indices: 126253--126295 Score: 68
Period size: 12 Copynumber: 3.4 Consensus size: 12
126243 TTAAGATTTG
126253 ATAAAAAATAAT
1 ATAAAAAATAAT
126265 ATAAAAAATATAAT
1 AT-AAAAA-ATAAT
126279 ATAAAAAATAAT
1 ATAAAAAATAAT
126291 ATAAA
1 ATAAA
126296 CATGCTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.41
13 10 0.34
14 7 0.24
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
ATAAAAAATAAT
Found at i:126277 original size:14 final size:14
Alignment explanation
Indices: 126255--126288 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
126245 AAGATTTGAT
126255 AAAAA-ATAATATA
1 AAAAATATAATATA
126268 AAAAATATAATATA
1 AAAAATATAATATA
126282 AAAAATA
1 AAAAATA
126289 ATATAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAAATATAATATA
Found at i:127165 original size:2 final size:2
Alignment explanation
Indices: 127152--127191 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
127142 CCGGGAAGAA
*
127152 CT CT CA CT CT 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 CT CT CT CT CT
127192 ATATATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:128602 original size:18 final size:18
Alignment explanation
Indices: 128563--128611 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
128553 GGAAAAATAC
* *
128563 TTTTAAAAAATATTATAT
1 TTTTAAAAAATAATATAA
128581 TTTTAAAAAATTAATA-AA
1 TTTTAAAAAA-TAATATAA
*
128599 TTTTAAAATATAA
1 TTTTAAAAAATAA
128612 GTGAATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 3 0.11
18 20 0.74
19 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTTAAAAAATAATATAA
Found at i:128872 original size:11 final size:11
Alignment explanation
Indices: 128856--128895 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
128846 TATATTTTTT
128856 AATTAAATTTA
1 AATTAAATTTA
128867 AATTAAATTTA
1 AATTAAATTTA
*
128878 ATTTAAAATTTTA
1 AATT-AAA-TTTA
128891 AATTA
1 AATTA
128896 TTATTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 14 0.56
12 4 0.16
13 7 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AATTAAATTTA
Found at i:129773 original size:18 final size:18
Alignment explanation
Indices: 129666--129773 Score: 52
Period size: 18 Copynumber: 6.2 Consensus size: 18
129656 TTATTTATTA
129666 AAATATTAAAATTTATAT
1 AAATATTAAAATTTATAT
* *
129684 AAATA-TATAATATCATA-
1 AAATATTAAAAT-TTATAT
* *
129701 AATATATTTATAATATATA-
1 AA-ATA-TTAAAATTTATAT
*
129720 AAATCATTTAAAATTAAT-T
1 AAAT-A-TTAAAATTTATAT
**
129739 TTATATT---ATTTAT-T
1 AAATATTAAAATTTATAT
129753 AAATATTAAAATTTATAT
1 AAATATTAAAATTTATAT
129771 AAA
1 AAA
129774 CATATAATAT
Statistics
Matches: 68, Mismatches: 12, Indels: 20
0.68 0.12 0.20
Matches are distributed among these distances:
14 11 0.16
17 15 0.22
18 19 0.28
19 17 0.25
20 6 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATATTAAAATTTATAT
Found at i:131219 original size:32 final size:32
Alignment explanation
Indices: 131178--131263 Score: 136
Period size: 32 Copynumber: 2.7 Consensus size: 32
131168 AAGATAGGTA
*
131178 TTTATAAGAATTTAAGCTCTAAAATATAAGTG
1 TTTACAAGAATTTAAGCTCTAAAATATAAGTG
* *
131210 TTTACAAGAATTTAGGCTCTAAAATATAGGTG
1 TTTACAAGAATTTAAGCTCTAAAATATAAGTG
*
131242 TTTACAAAAATTTAAGCTCTAA
1 TTTACAAGAATTTAAGCTCTAA
131264 GTATGATAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (32 bp):
TTTACAAGAATTTAAGCTCTAAAATATAAGTG
Found at i:132392 original size:21 final size:23
Alignment explanation
Indices: 132337--132393 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 23
132327 TATTTTTTAT
132337 TTCTC-TTCTTT-CTCTTTATCCC
1 TTCTCTTTCTTTCCTCTTTAT-CC
* *
132359 TTCTTTTTTTTTCCTCTTT-T-C
1 TTCTCTTTCTTTCCTCTTTATCC
132380 TTCTCTTTCTTTCC
1 TTCTCTTTCTTTCC
132394 ATTATCTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 13 0.45
22 4 0.14
23 6 0.21
24 6 0.21
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.67
Consensus pattern (23 bp):
TTCTCTTTCTTTCCTCTTTATCC
Found at i:133085 original size:51 final size:51
Alignment explanation
Indices: 133007--133104 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
132997 CATGCTATAA
* *
133007 GTAGATATTAAAATTTATCACTGTACTTTATTTTTATTAATACTTGACATT
1 GTAGATATTAAAATTTATCAATATACTTTATTTTTATTAATACTTGACATT
* * *
133058 GTAGATATTGAAATTTGTCAATATACTTTATTTTTATTAATATTTGA
1 GTAGATATTAAAATTTATCAATATACTTTATTTTTATTAATACTTGA
133105 TCTTAAACTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (51 bp):
GTAGATATTAAAATTTATCAATATACTTTATTTTTATTAATACTTGACATT
Found at i:134088 original size:21 final size:22
Alignment explanation
Indices: 134054--134096 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
134044 CAAAACCAAT
*
134054 TCATTTCCTTCTTGTGATTGCA
1 TCATTGCCTTCTTGTGATTGCA
134076 TCATTGCC-TCTTGTGATTGCA
1 TCATTGCCTTCTTGTGATTGCA
134097 CTACAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.47
Consensus pattern (22 bp):
TCATTGCCTTCTTGTGATTGCA
Found at i:135511 original size:2 final size:2
Alignment explanation
Indices: 135504--135533 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
135494 TAAAAATGGA
135504 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
135534 ACATATATAT
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:135905 original size:3 final size:3
Alignment explanation
Indices: 135899--135923 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
135889 AAATATCATC
135899 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
135924 AACTATTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:136174 original size:2 final size:2
Alignment explanation
Indices: 136167--136209 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
136157 TCACTAAAAG
*
136167 AT AT AT AT GT 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
136209 A
1 A
136210 GAAAATACCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:137705 original size:27 final size:26
Alignment explanation
Indices: 137657--137710 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
137647 ATCGAAAAAG
137657 GATATTGCAACTATAACCTGTTCTAAA
1 GATATTGCAACTATAACCTGTTC-AAA
* * **
137684 GATATTTCAGCTATAAGTTGTTCAAA
1 GATATTGCAACTATAACCTGTTCAAA
137710 G
1 G
137711 CTTGAATGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (26 bp):
GATATTGCAACTATAACCTGTTCAAA
Found at i:141925 original size:13 final size:13
Alignment explanation
Indices: 141907--141931 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
141897 TACATGACAG
141907 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
141920 AAAAAAAAAGAA
1 AAAAAAAAAGAA
141932 GGGAACATAG
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAA
Found at i:143315 original size:2 final size:2
Alignment explanation
Indices: 143308--143342 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
143298 CTTTCTCTTT
143308 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
143343 GTTAAAAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:147593 original size:50 final size:50
Alignment explanation
Indices: 147534--147706 Score: 240
Period size: 50 Copynumber: 3.5 Consensus size: 50
147524 AATTGCTTAG
** * * *
147534 AGTCAACAATTACGATCACCTCTCTCTATTATCAAAGATTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGATTGATGAAGAAT
*
147584 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGATGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGATTGATGAAGAAT
* * * *
147634 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAA-AGTCGTTAAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGA-TTGATGAAGAAT
147684 AGTCAACAATTACGGCCACCTCT
1 AGTCAACAATTACGGCCACCTCT
147707 TTTGCACCCA
Statistics
Matches: 110, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
50 110 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (50 bp):
AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGATTGATGAAGAAT
Found at i:148626 original size:25 final size:25
Alignment explanation
Indices: 148598--148660 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 25
148588 ATACAAAATT
148598 AAAAATAAAT-TAAAACAGAATATAA
1 AAAAATAAATATAAAACA-AATATAA
*
148623 AAAAATAAATATAAAATAAATATACA
1 AAAAATAAATATAAAACAAATATA-A
148649 AATAAA-AAATAT
1 AA-AAATAAATAT
148661 TTATAAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
25 16 0.47
26 15 0.44
27 3 0.09
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.22
Consensus pattern (25 bp):
AAAAATAAATATAAAACAAATATAA
Found at i:148633 original size:14 final size:15
Alignment explanation
Indices: 148616--148644 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
148606 ATTAAAACAG
148616 AATATAAAA-AAATA
1 AATATAAAATAAATA
148630 AATATAAAATAAATA
1 AATATAAAATAAATA
148645 TACAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AATATAAAATAAATA
Found at i:148654 original size:31 final size:31
Alignment explanation
Indices: 148565--148657 Score: 82
Period size: 31 Copynumber: 3.0 Consensus size: 31
148555 TTTAATACTT
* * *
148565 TAAATATATAAA-AAATAATACGAATACAAAAT
1 TAAATATA-AAATAAAT-ATACAAATAAAAAAA
* * * *
148597 TAAAAATAAATTAAA-ACAGAATATAAAAAAA
1 TAAATATAAAATAAATATACAA-ATAAAAAAA
148628 TAAATATAAAATAAATATACAAATAAAAAA
1 TAAATATAAAATAAATATACAAATAAAAAA
148658 TATTTATAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
30 3 0.06
31 30 0.64
32 14 0.30
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (31 bp):
TAAATATAAAATAAATATACAAATAAAAAAA
Found at i:148803 original size:34 final size:32
Alignment explanation
Indices: 148735--148844 Score: 98
Period size: 34 Copynumber: 3.3 Consensus size: 32
148725 TTTCTCATAT
* *
148735 ATAAAATA-ATAAATACATAAAAATATACACAAA
1 ATAAAATATATTAATAC-TAAAAATATATA-AAA
148768 ATAAAATATATTAATACGTCAAAAATATATAAAA
1 ATAAAATATATTAATAC-T-AAAAATATATAAAA
* * * *
148802 ATATAATATTTTTAATA-TAAAAAAATATAAAT
1 ATAAAATA-TATTAATACTAAAAATATATAAAA
148834 ATAAATATATA
1 ATAAA-ATATA
148845 ATTATTTTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
32 17 0.27
33 12 0.19
34 18 0.28
35 17 0.27
ACGTcount: A:0.64, C:0.05, G:0.01, T:0.31
Consensus pattern (32 bp):
ATAAAATATATTAATACTAAAAATATATAAAA
Found at i:148981 original size:14 final size:14
Alignment explanation
Indices: 148964--149005 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 14
148954 TATAGATAAT
148964 AATGTGAAAAAGGA
1 AATGTGAAAAAGGA
*
148978 AA--TGAAAAA-AA
1 AATGTGAAAAAGGA
148989 AATGTGAAAAAGGA
1 AATGTGAAAAAGGA
149003 AAT
1 AAT
149006 TTAAACTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
11 3 0.13
12 7 0.30
13 7 0.30
14 6 0.26
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.14
Consensus pattern (14 bp):
AATGTGAAAAAGGA
Found at i:149262 original size:182 final size:182
Alignment explanation
Indices: 148983--149350 Score: 532
Period size: 182 Copynumber: 2.0 Consensus size: 182
148973 AAGGAAATGA
* *
148983 AAAAAAAATGTGAAAAAGGAAATTTAAACTATCACACCCGACAATCATATTTTTCCCCCTAGCAT
1 AAAAAAAATGTGAAAAAGGAAATTTAAACCATCACACCCGACAATCATATTTTT-CCCCAAGCAT
149048 TTTCATTTTCAACAGTTTCTTTCTGTGTATAATAATTAAATTAATTTTCTTTTTTTCTACAGTTT
65 TTTCATTTTCAACAGTTTCTTTCTGTGTATAATAATTAAATTAATTTTCTTTTTTTCTACAG-TT
149113 CTTTTTTAAAAAAAATAAGAAAAATATCTAA-GGTAATGATGATGAATCTTGGGTTGC
129 CTTTTTTAAAAAAAA-AA-AAAAATATC-AAGGGTAATGATGATGAATCTTGGG-TGC
* * * * *
149170 AAAAAAATTGTGAAAAAGGAAA-TTATACCATGCAC-CCC-AGAATCATATTTTT-TCCAATCAT
1 AAAAAAAATGTGAAAAAGGAAATTTAAACCAT-CACACCCGACAATCATATTTTTCCCCAAGCAT
*
149231 TTTCATTTTCAACA-TTTCTTTCTGTGTATAATAATTAAATTAATTTTCTTTTTTTTTACAGTTC
65 TTTCATTTTCAACAGTTTCTTTCTGTGTATAATAATTAAATTAATTTTCTTTTTTTCTACAGTTC
* * *
149295 TTTTTTTAAAAAAAGAAAAAATATCAAGGGTAATGATTATGAATCTTGGGTGC
130 TTTTTTAAAAAAAAAAAAAAATATCAAGGGTAATGATGATGAATCTTGGGTGC
149348 AAA
1 AAA
149351 TCTATCCTCT
Statistics
Matches: 168, Mismatches: 11, Indels: 13
0.88 0.06 0.07
Matches are distributed among these distances:
178 8 0.05
179 30 0.18
180 1 0.01
181 16 0.10
182 46 0.27
183 20 0.12
185 13 0.08
186 10 0.06
187 24 0.14
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (182 bp):
AAAAAAAATGTGAAAAAGGAAATTTAAACCATCACACCCGACAATCATATTTTTCCCCAAGCATT
TTCATTTTCAACAGTTTCTTTCTGTGTATAATAATTAAATTAATTTTCTTTTTTTCTACAGTTCT
TTTTTAAAAAAAAAAAAAAATATCAAGGGTAATGATGATGAATCTTGGGTGC
Found at i:150456 original size:15 final size:15
Alignment explanation
Indices: 150419--150463 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
150409 ATCATATATT
150419 TTTAAT-TTAATTAAA
1 TTTAATATT-ATTAAA
150434 -TT-ATATTATTAAA
1 TTTAATATTATTAAA
*
150447 TTTAATATTAATAAA
1 TTTAATATTATTAAA
150462 TT
1 TT
150464 AAGTCATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 8 0.31
14 6 0.23
15 12 0.46
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAATATTATTAAA
Found at i:151759 original size:11 final size:11
Alignment explanation
Indices: 151743--151799 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
151733 TTAACAACCA
151743 AATATATATTT
1 AATATATATTT
* *
151754 AATATAAATAT
1 AATATATATTT
*
151765 AATTAAATATTT
1 AA-TATATATTT
*
151777 AATAAATATTT
1 AATATATATTT
*
151788 TATATAT-TTT
1 AATATATATTT
151798 AA
1 AA
151800 AAAATTATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
10 4 0.11
11 25 0.68
12 8 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
AATATATATTT
Found at i:151783 original size:21 final size:21
Alignment explanation
Indices: 151748--151835 Score: 58
Period size: 21 Copynumber: 4.2 Consensus size: 21
151738 AACCAAATAT
151748 ATATTTAATATAAATATAATTAA
1 ATATTT-A-ATAAATATAATTAA
* *
151771 ATATTTAATAAATAT-TTTAT
1 ATATTTAATAAATATAATTAA
* **
151791 ATATTTTAAAAAAT-TATATTTT
1 ATA-TTTAATAAATATA-ATTAA
*
151813 ATATTTAA-ATATA-AATTAA
1 ATATTTAATAAATATAATTAA
151832 ATAT
1 ATAT
151836 AAATATTTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
19 7 0.13
20 11 0.21
21 22 0.42
22 7 0.13
23 6 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATATTTAATAAATATAATTAA
Found at i:151818 original size:22 final size:21
Alignment explanation
Indices: 151774--151818 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
151764 TAATTAAATA
*
151774 TTTAATAAATATTTTATATAT
1 TTTAAAAAATATTTTATATAT
151795 TTTAAAAAATTATATTT-TATAT
1 TTTAAAAAA-TAT-TTTATATAT
151817 TT
1 TT
151819 AAATATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 10 0.48
23 3 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTAAAAAATATTTTATATAT
Found at i:152550 original size:17 final size:18
Alignment explanation
Indices: 152524--152567 Score: 72
Period size: 17 Copynumber: 2.5 Consensus size: 18
152514 AAATATAGCA
*
152524 ATATACATACAGATATAT
1 ATATATATACAGATATAT
152542 -TATATATACAGATATAT
1 ATATATATACAGATATAT
152559 ATATATATA
1 ATATATATA
152568 TATTAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.39
Consensus pattern (18 bp):
ATATATATACAGATATAT
Found at i:152556 original size:29 final size:29
Alignment explanation
Indices: 152516--152572 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
152506 CAAAAAAGAA
152516 ATATAGCAATATACATACAGATATATTAT
1 ATATAGCAATATACATACAGATATATTAT
* * *
152545 ATATA-CAGATATATATATATATATATTA
1 ATATAGCA-ATATACATACAGATATATTA
152573 ATTAAACTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (29 bp):
ATATAGCAATATACATACAGATATATTAT
Found at i:152673 original size:35 final size:36
Alignment explanation
Indices: 152608--152676 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 36
152598 TCTTTCATTG
*
152608 GATTATGATTTAAAATTTTTAATTAAATTTAAATTA
1 GATTATGATTTAAAATTTTAAATTAAATTTAAATTA
*
152644 GATT-TGATTTAAAA-TTTAAATTATTATTTAAAT
1 GATTATGATTTAAAATTTTAAATTA-AATTTAAAT
152677 ATTAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 8 0.27
35 18 0.60
36 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (36 bp):
GATTATGATTTAAAATTTTAAATTAAATTTAAATTA
Found at i:152900 original size:31 final size:30
Alignment explanation
Indices: 152863--152943 Score: 110
Period size: 31 Copynumber: 2.7 Consensus size: 30
152853 ATAGTGATGA
* *
152863 AATTAAAATTAGTAGTAAGATATGCATTTG
1 AATTAAAATTAGTAGTAAAATATGAATTTG
* *
152893 AATTTAAAATTAATAATAAAATATGAATTTG
1 AA-TTAAAATTAGTAGTAAAATATGAATTTG
152924 -ATTAAAATTAGTAGTAAAAT
1 AATTAAAATTAGTAGTAAAAT
152944 TAAAATTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 17 0.39
30 3 0.07
31 24 0.55
ACGTcount: A:0.51, C:0.01, G:0.11, T:0.37
Consensus pattern (30 bp):
AATTAAAATTAGTAGTAAAATATGAATTTG
Found at i:153634 original size:27 final size:28
Alignment explanation
Indices: 153604--153665 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
153594 ATTATGCTAG
153604 ATTTTATATTCGATAATATATA-TTTAT
1 ATTTTATATTCGATAATATATATTTTAT
** * *
153631 ATTTTAT-TTTTATATTTTATATTTTAT
1 ATTTTATATTCGATAATATATATTTTAT
153658 ATTTTATA
1 ATTTTATA
153666 ATTATTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 10 0.34
27 19 0.66
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (28 bp):
ATTTTATATTCGATAATATATATTTTAT
Found at i:153648 original size:7 final size:7
Alignment explanation
Indices: 153620--153754 Score: 82
Period size: 7 Copynumber: 18.1 Consensus size: 7
153610 TATTCGATAA
153620 TATATATT
1 TATAT-TT
153628 TATATTT
1 TATATTT
153635 TAT-TTT
1 TATATTT
153641 TATATTT
1 TATATTT
153648 TATATTT
1 TATATTT
153655 TATATTT
1 TATATTT
*
153662 TATA-AT
1 TATATTT
153668 TAT-TTT
1 TATATTT
* *
153674 AAAAATATTA
1 ---TATATTT
153684 TATATTT
1 TATATTT
153691 ATATAAATTT
1 -TAT--ATTT
153701 TAATATTT
1 T-ATATTT
153709 TATAATTAAT
1 TAT-ATT--T
153719 TAT-TTT
1 TATATTT
153725 TATTATTT
1 TA-TATTT
*
153733 TATATTA
1 TATATTT
153740 TAT-TTT
1 TATATTT
153746 TATTATTT
1 TA-TATTT
153754 T
1 T
153755 TTATATAATA
Statistics
Matches: 102, Mismatches: 8, Indels: 34
0.71 0.06 0.24
Matches are distributed among these distances:
6 18 0.18
7 42 0.41
8 27 0.26
9 3 0.03
10 12 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (7 bp):
TATATTT
Found at i:153670 original size:27 final size:26
Alignment explanation
Indices: 153620--153738 Score: 86
Period size: 27 Copynumber: 4.5 Consensus size: 26
153610 TATTCGATAA
**
153620 TATATATTTATATTTTATTTTTATATTT
1 TATAT-TTTATATTTTATAATTAT-TTT
153648 TATATTTTATATTTTATAATTATTTT
1 TATATTTTATATTTTATAATTATTTT
* *
153674 AAAAATATTATATATTTATATAA--ATTTT
1 ---TATATTTTATATTT-TATAATTATTTT
* *
153702 AATATTTTATA--AT-TAATTATTTT
1 TATATTTTATATTTTATAATTATTTT
153725 TATTATTTTATATT
1 TA-TATTTTATATT
153739 ATATTTTTAT
Statistics
Matches: 75, Mismatches: 7, Indels: 20
0.74 0.07 0.20
Matches are distributed among these distances:
21 3 0.04
22 1 0.01
23 6 0.08
24 9 0.12
25 10 0.13
26 3 0.04
27 16 0.21
28 10 0.13
29 12 0.16
30 5 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TATATTTTATATTTTATAATTATTTT
Found at i:153691 original size:62 final size:60
Alignment explanation
Indices: 153620--153734 Score: 151
Period size: 61 Copynumber: 1.9 Consensus size: 60
153610 TATTCGATAA
** * * *
153620 TATATATTTATATTTTATTTTTATATTTTATATTTTA-TATTTTATAATTATTTTAAAAATAT
1 TATATATTTATA-TAAATTTTAATATTTTATAATTAATTATTTT-T-ATTATTTTAAAAATAT
153682 TATATATTTATATAAATTTTAATATTTTATAATTAATTATTTTTATTATTTTA
1 TATATATTTATATAAATTTTAATATTTTATAATTAATTATTTTTATTATTTTA
153735 TATTATATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 9 0.19
61 20 0.43
62 18 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (60 bp):
TATATATTTATATAAATTTTAATATTTTATAATTAATTATTTTTATTATTTTAAAAATAT
Found at i:153700 original size:28 final size:28
Alignment explanation
Indices: 153649--153703 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
153639 TTTATATTTT
*
153649 ATATTTTATATTTTATAATTATTTTAAAA
1 ATATTATATATTTTATAA-TATTTTAAAA
153678 ATATTATATATTTATATAA-ATTTTAA
1 ATATTATATATTT-TATAATATTTTAA
153704 TATTTTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 7 0.29
29 12 0.50
30 5 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
ATATTATATATTTTATAATATTTTAAAA
Found at i:153755 original size:10 final size:10
Alignment explanation
Indices: 153717--153758 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
153707 TTTATAATTA
153717 ATTA-TTTTT
1 ATTATTTTTT
*
153726 ATTATTTTAT
1 ATTATTTTTT
153736 ATTATATTTTT
1 ATTAT-TTTTT
153747 ATTATTTTTT
1 ATTATTTTTT
153757 AT
1 AT
153759 ATAATATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 4 0.14
10 16 0.55
11 9 0.31
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTATTTTTT
Found at i:153765 original size:23 final size:23
Alignment explanation
Indices: 153679--153766 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 23
153669 ATTTTAAAAA
*
153679 TATTATATATTTATATAA-A-TTT
1 TATTAT-TTTTTATATAATATTTT
* *
153701 TAATATTTTATA-ATTAATTATTTT
1 TATTATTTTTTATA-TAA-TATTTT
*
153725 TATTA--TTTTATATTATATTTT
1 TATTATTTTTTATATAATATTTT
153746 TATTATTTTTTATATAATATT
1 TATTATTTTTTATATAATATT
153767 AAATCGTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
20 1 0.02
21 18 0.35
22 11 0.21
23 15 0.29
24 7 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TATTATTTTTTATATAATATTTT
Found at i:154977 original size:16 final size:15
Alignment explanation
Indices: 154945--154999 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 15
154935 AATTAAAAAA
154945 ATTAAAATAA-T-AT
1 ATTAAAATAATTAAT
154958 ATTAAAATATATTAAT
1 ATTAAAATA-ATTAAT
* *
154974 ATTAATACACATTAAT
1 ATTAAAATA-ATTAAT
154990 ATTAAAATAA
1 ATTAAAATAA
155000 AATCAAGACA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
13 9 0.26
14 1 0.03
15 2 0.06
16 22 0.65
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTAAAATAATTAAT
Found at i:159960 original size:2 final size:2
Alignment explanation
Indices: 159953--160060 Score: 155
Period size: 2 Copynumber: 54.5 Consensus size: 2
159943 AATGCTTGGA
*
159953 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT 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
* * * * *
159995 TT AT AT AT AC AT AT AT AT AT AT AT TT AT AT AT TT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
160037 AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
160061 ATTGTATTAG
Statistics
Matches: 93, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
1 1 0.01
2 92 0.99
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:160181 original size:16 final size:16
Alignment explanation
Indices: 160160--160194 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
160150 AGAAGTACAC
160160 ATAATTAATTTGATTT
1 ATAATTAATTTGATTT
* *
160176 ATAATTTATTTGGTTT
1 ATAATTAATTTGATTT
160192 ATA
1 ATA
160195 TGAAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (16 bp):
ATAATTAATTTGATTT
Found at i:160421 original size:32 final size:31
Alignment explanation
Indices: 160343--160472 Score: 104
Period size: 32 Copynumber: 4.2 Consensus size: 31
160333 ATATTATTGG
* *
160343 ATTTTAATACATTTAATGAATTGAAAATATTG
1 ATTTTGATACATTTAATGAATTG-AAATATTA
** * * *
160375 GGTTTGGTAGATTTAGTGAATTGAAATATTCA
1 ATTTTGATACATTTAATGAATTGAAATATT-A
* *
160407 ATTTTGATACATTTAATAAATTAAAATATTTA
1 ATTTTGATACATTTAATGAATTGAAATA-TTA
* *
160439 ATTTT-AGTACATTTAAT-AATTTAAA-ATTG
1 ATTTTGA-TACATTTAATGAATTGAAATATTA
160468 ATTTT
1 ATTTT
160473 AATTAATTGG
Statistics
Matches: 79, Mismatches: 16, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
29 7 0.09
30 1 0.01
31 15 0.19
32 54 0.68
33 2 0.03
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (31 bp):
ATTTTGATACATTTAATGAATTGAAATATTA
Found at i:161733 original size:21 final size:19
Alignment explanation
Indices: 161698--161750 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
161688 AAACTGATTA
*
161698 AATAAA-ATGTTTGTTAAC
1 AATAAATATATTTGTTAAC
*
161716 AATAAATTAATATTTGTTAAT
1 AATAAA-T-ATATTTGTTAAC
161737 AATAAATATATTTG
1 AATAAATATATTTG
161751 AAAAATGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 6 0.20
19 7 0.23
20 1 0.03
21 16 0.53
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (19 bp):
AATAAATATATTTGTTAAC
Found at i:162788 original size:21 final size:20
Alignment explanation
Indices: 162764--162817 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 20
162754 AAAATATAAA
162764 AAAATAATATAATTAATTTT-T
1 AAAATAATATAA--AATTTTGT
162785 AAAA-AAT-TAAAATTTTGT
1 AAAATAATATAAAATTTTGT
162803 ACAAATCAATATAAA
1 A-AAAT-AATATAAA
162818 TTTATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
17 6 0.21
18 2 0.07
19 6 0.21
20 3 0.11
21 7 0.25
22 4 0.14
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATATAAAATTTTGT
Found at i:164340 original size:23 final size:23
Alignment explanation
Indices: 164309--164439 Score: 72
Period size: 23 Copynumber: 5.6 Consensus size: 23
164299 TACACTAATA
164309 ATTAGTATTATATTTTAACATATT
1 ATTA-TATTATATTTTAACATATT
* * *
164333 AATATATTTCTATTATGT-TCA-ATT
1 ATTATA-TTATATT-T-TAACATATT
* * * *
164357 ATTTTTTTATATTATATCATATT
1 ATTATATTATATTTTAACATATT
* *
164380 -TTATATAATATTTTAATTATATT
1 ATTATATTATATTTTAA-CATATT
* *
164403 -TTATATTATATTTATAATATATA
1 ATTATATTATATTT-TAACATATT
*
164426 ATAATATTATATTT
1 ATTATATTATATTT
164440 AAAATTATCA
Statistics
Matches: 82, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
21 1 0.01
22 14 0.17
23 33 0.40
24 30 0.37
25 3 0.04
26 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (23 bp):
ATTATATTATATTTTAACATATT
Done.