Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1246
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: 64375
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:574 original size:3 final size:3
Alignment explanation
Indices: 566--599 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
556 TCTGAGTCAC
* *
566 CAT CAT CAT CAT TAT CAT CAT CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
600 CTTGATGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.38
Consensus pattern (3 bp):
CAT
Found at i:2228 original size:19 final size:20
Alignment explanation
Indices: 2183--2234 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2173 TTACAAGCCA
* *
2183 ATGTATCGATACATTTTGTG
1 ATGTATCGATACATATTATG
2203 ATGTATCGATACATATTATG
1 ATGTATCGATACATATTATG
2223 -TGTATCGATACA
1 ATGTATCGATACA
2235 AATTTAGCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATATTATG
Found at i:2293 original size:20 final size:20
Alignment explanation
Indices: 2268--2318 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2258 CCAATGACCT
**
2268 GTATCGATACATTTTTTCAA
1 GTATCGATACATTTAGTCAA
*
2288 GTATCGATACATTTAGTCAT
1 GTATCGATACATTTAGTCAA
2308 GTATCGATACA
1 GTATCGATACA
2319 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
GTATCGATACATTTAGTCAA
Found at i:2324 original size:13 final size:13
Alignment explanation
Indices: 2306--2330 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2296 ACATTTAGTC
2306 ATGTATCGATACA
1 ATGTATCGATACA
2319 ATGTATCGATAC
1 ATGTATCGATAC
2331 TGTGCAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5178 original size:15 final size:14
Alignment explanation
Indices: 5160--5188 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5150 TGTATCCTTC
5160 TTTTTCACTTGAAA
1 TTTTTCACTTGAAA
5174 TTTTTCACTTGAAA
1 TTTTTCACTTGAAA
5188 T
1 T
5189 GTTTAAGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTTTCACTTGAAA
Found at i:7801 original size:2 final size:2
Alignment explanation
Indices: 7794--7821 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7784 TGTGATAGAA
7794 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
7822 GCGCGCGCGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7989 original size:19 final size:19
Alignment explanation
Indices: 7958--7995 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
7948 TCACGTAATT
7958 TAAAATATTATTTATTTAA
1 TAAAATATTATTTATTTAA
7977 TAAAA-ATTAATTTATTTAA
1 TAAAATATT-ATTTATTTAA
7996 ATTTAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TAAAATATTATTTATTTAA
Found at i:8033 original size:21 final size:24
Alignment explanation
Indices: 8007--8052 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
7997 TTTAATTATA
8007 AAAATA-TATAA-ATA-TTAAAAT
1 AAAATATTATAATATATTTAAAAT
*
8028 AAAATATTTTAATATATTTAAAAT
1 AAAATATTATAATATATTTAAAAT
8052 A
1 A
8053 TTAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 4 0.19
23 3 0.14
24 8 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AAAATATTATAATATATTTAAAAT
Found at i:8060 original size:19 final size:19
Alignment explanation
Indices: 8027--8065 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
8017 AATATTAAAA
** *
8027 TAAAATATTTTAATATATT
1 TAAAATATTAAAATAAATT
8046 TAAAATATTAAAATAAATT
1 TAAAATATTAAAATAAATT
8065 T
1 T
8066 TTTAAAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAAATATTAAAATAAATT
Found at i:8080 original size:31 final size:32
Alignment explanation
Indices: 8006--8080 Score: 89
Period size: 31 Copynumber: 2.3 Consensus size: 32
7996 ATTTAATTAT
8006 AAAAATATATAAATATTAAAATAAAATATTTTAA
1 AAAAAT-TA-AAATATTAAAATAAAATATTTTAA
* * * *
8040 TATATTTAAAATATTAAAAT-AAATTTTTTAA
1 AAAAATTAAAATATTAAAATAAAATATTTTAA
8071 AAAAATTAAA
1 AAAAATTAAA
8081 TCTAAATCAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
31 17 0.50
32 12 0.35
33 2 0.06
34 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (32 bp):
AAAAATTAAAATATTAAAATAAAATATTTTAA
Found at i:8719 original size:23 final size:23
Alignment explanation
Indices: 8693--8736 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
8683 TATAATTATT
8693 AATAAAA-TAAAATATTTAATAAC
1 AATAAAATTAAAA-ATTTAATAAC
*
8716 AATAAAATTTAAAATTTAATA
1 AATAAAATTAAAAATTTAATA
8737 TTTATATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
AATAAAATTAAAAATTTAATAAC
Found at i:13085 original size:20 final size:17
Alignment explanation
Indices: 13043--13078 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
13033 TTCAAATCTC
*
13043 AACATTTAGACATAAAA
1 AACATCTAGACATAAAA
13060 AACATCTAGACATAAAA
1 AACATCTAGACATAAAA
13077 AA
1 AA
13079 ATACATCGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.61, C:0.14, G:0.06, T:0.19
Consensus pattern (17 bp):
AACATCTAGACATAAAA
Found at i:14066 original size:15 final size:14
Alignment explanation
Indices: 14040--14069 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
14030 ATAGCTCATT
14040 TTAAAATATAATAA
1 TTAAAATATAATAA
14054 TTAAAATTATAATAA
1 TTAAAA-TATAATAA
14069 T
1 T
14070 AAATATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TTAAAATATAATAA
Found at i:16257 original size:17 final size:17
Alignment explanation
Indices: 16213--16258 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
16203 TTTTGAGTCA
*
16213 TTTAGGGTTT-GAGTCAT
1 TTTA-GGTTTCGATTCAT
*
16230 TTT-GTTTTCGATTCAT
1 TTTAGGTTTCGATTCAT
16246 TTTAGGTTTCGAT
1 TTTAGGTTTCGAT
16259 CAATTGAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 4 0.17
16 9 0.38
17 11 0.46
ACGTcount: A:0.15, C:0.09, G:0.22, T:0.54
Consensus pattern (17 bp):
TTTAGGTTTCGATTCAT
Found at i:17084 original size:43 final size:43
Alignment explanation
Indices: 17023--17120 Score: 187
Period size: 43 Copynumber: 2.3 Consensus size: 43
17013 CACAAGCTTG
*
17023 TGTATCGATACAAATCCATGAGATGTGTCATTACCCATTATGA
1 TGTATCGATACAAATCCATGAGATGTATCATTACCCATTATGA
17066 TGTATCGATACAAATCCATGAGATGTATCATTACCCATTATGA
1 TGTATCGATACAAATCCATGAGATGTATCATTACCCATTATGA
17109 TGTATCGATACA
1 TGTATCGATACA
17121 TGGCCCTGGT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (43 bp):
TGTATCGATACAAATCCATGAGATGTATCATTACCCATTATGA
Found at i:17090 original size:23 final size:23
Alignment explanation
Indices: 17023--17094 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
17013 CACAAGCTTG
17023 TGTATCGATACAAATCCATGAGA
1 TGTATCGATACAAATCCATGAGA
* *
17046 TGTGTC-ATTAC----CCATTATGA
1 TGTATCGA-TACAAATCCATGA-GA
17066 TGTATCGATACAAATCCATGAGA
1 TGTATCGATACAAATCCATGAGA
17089 TGTATC
1 TGTATC
17095 ATTACCCATT
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
19 5 0.13
20 10 0.26
21 1 0.03
22 1 0.03
23 16 0.42
24 5 0.13
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (23 bp):
TGTATCGATACAAATCCATGAGA
Found at i:17112 original size:20 final size:20
Alignment explanation
Indices: 17044--17114 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 20
17034 AAATCCATGA
*
17044 GATGTGTCATTACCCATTAT
1 GATGTATCATTACCCATTAT
*
17064 GATGTATCGA-TACAAATCCATGA-
1 GATGTATC-ATTAC----CCATTAT
17087 GATGTATCATTACCCATTAT
1 GATGTATCATTACCCATTAT
17107 GATGTATC
1 GATGTATC
17115 GATACATGGC
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
19 5 0.12
20 18 0.44
21 1 0.02
22 1 0.02
23 11 0.27
24 5 0.12
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (20 bp):
GATGTATCATTACCCATTAT
Found at i:19634 original size:88 final size:88
Alignment explanation
Indices: 19514--19989 Score: 444
Period size: 88 Copynumber: 5.4 Consensus size: 88
19504 TCGATTTTGT
* * * * * *
19514 GGAAACTCTATCCCTATTATTCCAAGAAGATACTCTAACCTTATTCTAACAAAAATTTAAATCTT
1 GGAAACTCCATCCCTACTATTTCGAGAGGATACTCTAACCTTATTCTAACAAAAATTCAAATCTT
*
19579 TCTTCGTATAACTTTATCCTTAG
66 CCTTCGTATAACTTTATCCTTAG
* * *
19602 GGAAACTCCATCTCTACTATTTCGAGAGGATACTTCAAACC-CATTCTAACAAAAATTCAAATCT
1 GGAAACTCCATCCCTACTATTTCGAGAGGATAC-TCTAACCTTATTCTAACAAAAATTCAAATCT
* *
19666 TCCTTTGTATAACTTTATCTTTAG
65 TCCTTCGTATAACTTTATCCTTAG
* *
19690 GGAAACTCCATCCCAACTA-TTCTGAGGGGATACTCTAACCTTATTCTAACAAAAATTCAAATCT
1 GGAAACTCCATCCCTACTATTTC-GAGAGGATACTCTAACCTTATTCTAACAAAAATTCAAATCT
19754 TCCTTCGTATAACTTTATCCTTAG
65 TCCTTCGTATAACTTTATCCTTAG
* * * * * * *
19778 AGAAACTCTATCCCCACTATTTCAAG-GAGATACTCCAATCCTGT-TT-GAATAAAAATTCAAAT
1 GGAAACTCCATCCCTACTATTTCGAGAG-GATACTCTAA-CCT-TATTCTAACAAAAATTCAAAT
* * * * *
19840 TTTTCTTTGCATAATTTTATCCTTAG
63 CTTCCTTCGTATAACTTTATCCTTAG
* * * * * * **
19866 GGAAACTCCATCTCC-AATACTTCTAGGGGATATTCTAACCCTATTCTCCCAAAAATTTCAAAT-
1 GGAAACTCCATC-CCTACTATTTCGAGAGGATACTCTAACCTTATTCTAACAAAAA-TTCAAATC
* ** * *
19929 TTACCCTTCATATAGGTTTATCTTTGG
64 TT--CCTTCGTATAACTTTATCCTTAG
* * *
19956 GGAAACTGCATCCTTACTATTTTGAGAGGATACT
1 GGAAACTCCATCCCTACTATTTCGAGAGGATACT
19990 TCAACCATGT
Statistics
Matches: 314, Mismatches: 59, Indels: 28
0.78 0.15 0.07
Matches are distributed among these distances:
86 1 0.00
87 14 0.04
88 234 0.75
89 25 0.08
90 40 0.13
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (88 bp):
GGAAACTCCATCCCTACTATTTCGAGAGGATACTCTAACCTTATTCTAACAAAAATTCAAATCTT
CCTTCGTATAACTTTATCCTTAG
Found at i:19834 original size:176 final size:176
Alignment explanation
Indices: 19542--19928 Score: 512
Period size: 176 Copynumber: 2.2 Consensus size: 176
19532 ATTCCAAGAA
* * *
19542 GATACTCTAACCTTATTCTAACAAAAATTTAAATCTTTCTTCGTATAACTTTATCCTTAGGGAAA
1 GATACTCTAACCTTATTCTAACAAAAATTCAAATCTTCCTTCGTATAACTTTATCCTTAGAGAAA
* * * *
19607 CTCCATCTCTACTATTTCGAGAGGATACTTCAAACCCATTCTAACAAAAATTCAAATCTTCCTTT
66 CTCCATCCCCACTATTTCAAGAGGATACTCCAAACCCATTCTAACAAAAATTCAAATCTTCCTTT
* *
19672 GTATAACTTTATCTTTAGGGAAACTCCATC-CCAACTA-TTCTGAGGG
131 GCATAACTTTATCCTTAGGGAAACTCCATCTCCAA-TACTTCT-AGGG
19718 GATACTCTAACCTTATTCTAACAAAAATTCAAATCTTCCTTCGTATAACTTTATCCTTAGAGAAA
1 GATACTCTAACCTTATTCTAACAAAAATTCAAATCTTCCTTCGTATAACTTTATCCTTAGAGAAA
* * ** * * *
19783 CTCTATCCCCACTATTTCAAG-GAGATACTCCAATCCTGTT-TGAATAAAAATTCAAATTTTTCT
66 CTCCATCCCCACTATTTCAAGAG-GATACTCCAAACCCATTCT-AACAAAAATTCAAATCTTCCT
*
19846 TTGCATAATTTTATCCTTAGGGAAACTCCATCTCCAATACTTCTAGGG
129 TTGCATAACTTTATCCTTAGGGAAACTCCATCTCCAATACTTCTAGGG
* * **
19894 GATATTCTAACCCTATTCTCCCAAAAATTTCAAAT
1 GATACTCTAACCTTATTCTAACAAAAA-TTCAAAT
19929 TTACCCTTCA
Statistics
Matches: 185, Mismatches: 21, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
175 2 0.01
176 168 0.91
177 15 0.08
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (176 bp):
GATACTCTAACCTTATTCTAACAAAAATTCAAATCTTCCTTCGTATAACTTTATCCTTAGAGAAA
CTCCATCCCCACTATTTCAAGAGGATACTCCAAACCCATTCTAACAAAAATTCAAATCTTCCTTT
GCATAACTTTATCCTTAGGGAAACTCCATCTCCAATACTTCTAGGG
Found at i:28692 original size:19 final size:19
Alignment explanation
Indices: 28668--28777 Score: 118
Period size: 19 Copynumber: 6.4 Consensus size: 19
28658 CAAACAGAAA
*
28668 TTGTATCAATACATAAGTG
1 TTGTATCGATACATAAGTG
*
28687 TTGTATTGATACATAAGTG
1 TTGTATCGATACATAAGTG
28706 TTGTATCGAT--ATAA---
1 TTGTATCGATACATAAGTG
28720 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
28738 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
28752 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
28770 TTGTATCG
1 TTGTATCG
28778 CTACGAAGCT
Statistics
Matches: 76, Mismatches: 3, Indels: 24
0.74 0.03 0.23
Matches are distributed among these distances:
13 20 0.26
15 6 0.08
17 6 0.08
19 44 0.58
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:28730 original size:32 final size:32
Alignment explanation
Indices: 28688--28777 Score: 162
Period size: 32 Copynumber: 2.8 Consensus size: 32
28678 ACATAAGTGT
* *
28688 TGTATTGATACATAAGTGTTGTATCGATATAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
28720 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
28752 TGTATCGATACATAAGTGTTGTATCG
1 TGTATCGATACATAAGTGTTGTATCG
28778 CTACGAAGCT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:28762 original size:13 final size:13
Alignment explanation
Indices: 28707--28763 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
28697 ACATAAGTGT
*
28707 TGTATCGATATAA
1 TGTATCGATACAA
28720 TGTATCGATACATAA
1 TGTATCGATAC--AA
28735 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
28752 TGTATCGATACA
1 TGTATCGATACA
28764 TAAGTGTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 22 0.59
15 2 0.05
17 2 0.05
19 11 0.30
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:28840 original size:13 final size:13
Alignment explanation
Indices: 28822--28846 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28812 ATTACTCAAA
28822 TGTATCGATACAT
1 TGTATCGATACAT
28835 TGTATCGATACA
1 TGTATCGATACA
28847 CTGATCTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:28893 original size:52 final size:52
Alignment explanation
Indices: 28835--28983 Score: 212
Period size: 52 Copynumber: 2.9 Consensus size: 52
28825 ATCGATACAT
* * * *
28835 TGTATCGATACACTGAT-CTTTTTATTGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATAATATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
28887 TGTATCGATACACTATAATATGTATCGATACATACAGGCAAATTTGCCTAGA
1 TGTATCGATACACTATAATATGTATCGATACATGCAGGCAAATTTGCCCAGA
28939 TGTATCGATACACTATGAA-ATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTAT-AATATGTATCGATACATGCAGGCAAATTT
28984 TCATATTTTG
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (52 bp):
TGTATCGATACACTATAATATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:34239 original size:79 final size:79
Alignment explanation
Indices: 34149--34581 Score: 380
Period size: 80 Copynumber: 5.4 Consensus size: 79
34139 AAAACACCCT
* * * * * * *
34149 AACCCTACCATCTTCGAGAGAATACTCTAACCCCGTTTTTACTTTGAAAATGCCAAATTTTTTAT
1 AACCCCACCATCTTCGAGGGGATACTCCAACCCCGTTTTTACTTTCAAAATGTCAAATTTTTCAT
34214 CTCTAGGGATACTC
66 CTCTAGGGATACTC
* * * * * *
34228 AGCCCCACCATC-TCAGAGGGGATATTCCAAGCTCGTTTTTACTTCCAAAATGTTAAATTTTTCA
1 AACCCCACCATCTTC-GAGGGGATACTCCAACCCCGTTTTTACTTTCAAAATGTCAAATTTTTCA
34292 TC-C-ATGAGGATACTCC
65 TCTCTA-G-GGATACT-C
* * **
34308 AACCCCACCATCTTCGAGGGGTTACTGCAACCCCAATTTTACTTTCAAAACT-TCAAATTTTTCA
1 AACCCCACCATCTTCGAGGGGATACTCCAACCCCGTTTTTACTTTCAAAA-TGTCAAATTTTTCA
* * *
34372 TTTTTAGGGATAAGTC
65 TCTCTAGGGAT-ACTC
* * **
34388 AACCCCACCATCTCCGAGGGGATACTCCAACCCTGTTTTTAC-TTCTAAAA-CACTAAATTTTTC
1 AACCCCACCATCTTCGAGGGGATACTCCAACCCCGTTTTTACTTTC-AAAATGTC-AAATTTTTC
*
34451 ATCT-TTGGAGATATCTC
64 ATCTCTAGG-GATA-CTC
* * * *
34468 -ACCACCACCATCTTTGAGGGGATACTCCAACCCCATTTTTACTTCCAAAACGTCAAATTTTTCA
1 AACC-CCACCATCTTCGAGGGGATACTCCAACCCCGTTTTTACTTTCAAAATGTCAAATTTTTCA
*
34532 TCTC-GGGGCATACTCC
65 TCTCTAGGG-ATACT-C
* * * *
34548 AACCTCACAATCTCCAAGGGGATACTCCAACCCC
1 AACCCCACCATCTTCGAGGGGATACTCCAACCCC
34582 ACCATCTCTA
Statistics
Matches: 284, Mismatches: 49, Indels: 41
0.76 0.13 0.11
Matches are distributed among these distances:
77 1 0.00
78 4 0.01
79 71 0.25
80 195 0.69
81 12 0.04
82 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.31
Consensus pattern (79 bp):
AACCCCACCATCTTCGAGGGGATACTCCAACCCCGTTTTTACTTTCAAAATGTCAAATTTTTCAT
CTCTAGGGATACTC
Found at i:34478 original size:160 final size:160
Alignment explanation
Indices: 34149--34580 Score: 446
Period size: 160 Copynumber: 2.7 Consensus size: 160
34139 AAAACACCCT
* * * * ** * * *
34149 AACCCTACCATCTTCGAGAGAATACTCTAACCCCGTTTTTACTTTGAAAA-TGCCAAATTTTTTA
1 AACCCCACCATCTTCGAGGGGATACTCCAACCCCAATTTTACTTTCAAAACT-TCAAATTTTTCA
* * * * * *
34213 TCTCTAGGGATACTCAGCCCCACCATCTCAGAGGGGATATTCCAA-GCTCGTTTTTACTTCCAAA
65 TTTTTAGGGATACTCAACCCCACCATCTCCGAGGGGATACTCCAACCCTCGTTTTTACTTCCAAA
***
34277 ATGTTAAATTTTTCATCCATGAGGATACTCC
130 ACACTAAATTTTTCATCCATGAGGATACTCC
* *
34308 AACCCCACCATCTTCGAGGGGTTACTGCAACCCCAATTTTACTTTCAAAACTTCAAATTTTTCAT
1 AACCCCACCATCTTCGAGGGGATACTCCAACCCCAATTTTACTTTCAAAACTTCAAATTTTTCAT
* *
34373 TTTTAGGGATAAGTCAACCCCACCATCTCCGAGGGGATACTCCAACCCT-GTTTTTACTTCTAAA
66 TTTTAGGGAT-ACTCAACCCCACCATCTCCGAGGGGATACTCCAACCCTCGTTTTTACTTCCAAA
**
34437 ACACTAAATTTTTCATCTTTG-GAGATA-TCTC
130 ACACTAAATTTTTCATCCATGAG-GATACTC-C
* * * *
34468 -ACCACCACCATCTTTGAGGGGATACTCCAACCCCATTTTTACTTCCAAAACGTCAAATTTTTCA
1 AACC-CCACCATCTTCGAGGGGATACTCCAACCCCAATTTTACTTTCAAAACTTCAAATTTTTCA
* ** * * *
34532 -TCTCGGGGCATACTCCAACCTCACAATCTCCAAGGGGATACTCCAACCC
65 TTTTTAGGG-ATACT-CAACCCCACCATCTCCGAGGGGATACTCCAACCC
34581 CACCATCTCT
Statistics
Matches: 228, Mismatches: 37, Indels: 15
0.81 0.13 0.05
Matches are distributed among these distances:
159 73 0.32
160 153 0.67
161 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.31
Consensus pattern (160 bp):
AACCCCACCATCTTCGAGGGGATACTCCAACCCCAATTTTACTTTCAAAACTTCAAATTTTTCAT
TTTTAGGGATACTCAACCCCACCATCTCCGAGGGGATACTCCAACCCTCGTTTTTACTTCCAAAA
CACTAAATTTTTCATCCATGAGGATACTCC
Found at i:34581 original size:240 final size:238
Alignment explanation
Indices: 34149--34582 Score: 543
Period size: 240 Copynumber: 1.8 Consensus size: 238
34139 AAAACACCCT
* * * ** *
34149 AACCCTACCATCTTCGAGAGAATACTCTAACCCCGTTTTTACTTTGAAAATGCCAAATTTTTTAT
1 AACCCCACCATCTCCGAGAGAATACTCCAACCCCGTTTTTACTTTGAAAACACCAAATTTTTCAT
* * * * *
34214 CTCTAGGGATACTCAGCCCCACCATCTCAGAGGGGATATTCCAAGCTCGTTTTTACTTCCAAAAT
66 CTCTAGGGATACTCAGCCCCACCATCTCAGAGGGGATACTCCAACCCCATTTTTACTTCCAAAAC
* * * * * *
34279 GTTAAATTTTTCATCCATGAGGATACTCCAACCCCACCATCTTCGAGGGGTTACTGCAACCCCAA
131 GTCAAATTTTTCATCCA-GAGGATACTCCAACCCCACAATCTCCAAGGGGATACTCCAACCCCAA
34344 TTTTACTTTCAAAACTTCAAATTTTTCATTTTTAGGGATAAGTC
195 TTTTACTTTCAAAACTTCAAATTTTTCATTTTTAGGGATAAGTC
* * * *
34388 AACCCCACCATCTCCGAGGGGATACTCCAACCCTGTTTTTACTTCT-AAAACACTAAATTTTTCA
1 AACCCCACCATCTCCGAGAGAATACTCCAACCCCGTTTTTACTT-TGAAAACACCAAATTTTTCA
* **
34452 TCT-TTGGAGATATCTCA-CCACCACCATCTTTGAGGGGATACTCCAACCCCATTTTTACTTCCA
65 TCTCTAGG-GATA-CTCAGCC-CCACCATCTCAGAGGGGATACTCCAACCCCATTTTTACTTCCA
* *
34515 AAACGTCAAATTTTTCATCTC-GGGGCATACTCCAACCTCACAATCTCCAAGGGGATACTCCAAC
127 AAACGTCAAATTTTTCATC-CAGAGG-ATACTCCAACCCCACAATCTCCAAGGGGATACTCCAAC
34579 CCCA
190 CCCA
34583 CCATCTCTAA
Statistics
Matches: 163, Mismatches: 26, Indels: 11
0.81 0.13 0.05
Matches are distributed among these distances:
238 3 0.02
239 64 0.39
240 95 0.58
241 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.31
Consensus pattern (238 bp):
AACCCCACCATCTCCGAGAGAATACTCCAACCCCGTTTTTACTTTGAAAACACCAAATTTTTCAT
CTCTAGGGATACTCAGCCCCACCATCTCAGAGGGGATACTCCAACCCCATTTTTACTTCCAAAAC
GTCAAATTTTTCATCCAGAGGATACTCCAACCCCACAATCTCCAAGGGGATACTCCAACCCCAAT
TTTACTTTCAAAACTTCAAATTTTTCATTTTTAGGGATAAGTC
Found at i:34606 original size:27 final size:28
Alignment explanation
Indices: 34536--34607 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
34526 TTTTCATCTC
*
34536 GGGGCATACTCCAACCTCACAATCTCCAA
1 GGGG-ATACTCCAACCCCACAATCTCCAA
* *
34565 GGGGATACTCCAACCCCACCATCTCTAA
1 GGGGATACTCCAACCCCACAATCTCCAA
*
34593 -GGGATACTCTAACCC
1 GGGGATACTCCAACCC
34608 TATTTTTACT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 14 0.36
28 21 0.54
29 4 0.10
ACGTcount: A:0.29, C:0.38, G:0.15, T:0.18
Consensus pattern (28 bp):
GGGGATACTCCAACCCCACAATCTCCAA
Found at i:34678 original size:107 final size:109
Alignment explanation
Indices: 34472--34689 Score: 282
Period size: 107 Copynumber: 2.0 Consensus size: 109
34462 TATCTCACCA
* * *
34472 CCACCATCTTTGAGGGGATACTCCAACCCCATTTTTACTTCCAAAACGTCAAATTTTTCATCTCG
1 CCACCATCTCTGAAGGGATACTCCAACCCCATTTTTACTTCCAAAACATCAAATTTTTCATCTCG
* * *
34537 GGGCATACTCCAACCTCACAATCTCCAAGGGGATACTCC-AACC
66 GGGCATACTCAAACCCCACAATCTCCAAGAGGATACTCCAAACC
* * * *
34580 CCACCATCTCT-AAGGGATACTCTAACCCTATTTTTACTTCTAAAGCATCAAATTTTTCATCTCT
1 CCACCATCTCTGAAGGGATACTCCAACCCCATTTTTACTTCCAAAACATCAAATTTTTCATCTC-
* *
34644 GTGG-ATACTCAAACCCCAGC-ATCTCCGAGAGGATACTCCAAACC
65 GGGGCATACTCAAACCCCA-CAATCTCCAAGAGGATACTCCAAACC
34688 CC
1 CC
34690 TTTTTACTTC
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
107 75 0.79
108 20 0.21
ACGTcount: A:0.28, C:0.33, G:0.12, T:0.27
Consensus pattern (109 bp):
CCACCATCTCTGAAGGGATACTCCAACCCCATTTTTACTTCCAAAACATCAAATTTTTCATCTCG
GGGCATACTCAAACCCCACAATCTCCAAGAGGATACTCCAAACC
Found at i:34714 original size:80 final size:81
Alignment explanation
Indices: 34567--34761 Score: 195
Period size: 80 Copynumber: 2.4 Consensus size: 81
34557 ATCTCCAAGG
* ** * * *
34567 GGATACTCCAACCCCACCATCTCTAAG-GGATACT-CTAACCCTATTTTTACTTCTAAAGCATCA
1 GGATACTCAAACCCCACCATCTCCGAGAGGATACTCCAAACCCTATTTTTACTTCCAAAACATCA
* **
34630 AATTTTTCATCTCTGT
66 AATTTTACATCTCTAA
* *
34646 GGATACTCAAACCCCAGCATCTCCGAGAGGATACTCCAAACCC-CTTTTTACTTCCAAAACA-CT
1 GGATACTCAAACCCCACCATCTCCGAGAGGATACTCCAAACCCTATTTTTACTTCCAAAACATC-
* *
34709 GAATTTTACATTTCTAA
65 AAATTTTACATCTCTAA
*
34726 GGATATTCTAAA-CCCACCATCTCCGA-AGGTATACTC
1 GGATACTC-AAACCCCACCATCTCCGAGAGG-ATACTC
34762 TAACCTGGGC
Statistics
Matches: 96, Mismatches: 15, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
79 27 0.28
80 60 0.62
81 9 0.09
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (81 bp):
GGATACTCAAACCCCACCATCTCCGAGAGGATACTCCAAACCCTATTTTTACTTCCAAAACATCA
AATTTTACATCTCTAA
Found at i:38318 original size:74 final size:74
Alignment explanation
Indices: 38064--38888 Score: 859
Period size: 74 Copynumber: 11.2 Consensus size: 74
38054 GAGCAAGACA
* * * * * *
38064 CCTTTTCTTTGTCTTCAAAGCCCACATAAGCTGATCGCATCATTTATCTTTTTTAGCCCTCAAA-
1 CCTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTCAGTCCTCAAAG
* *
38128 A--AGCAAGG
66 ACTAG-GATG
* * * * *
38136 CAC-TTT-TTTTTCTTCAAAG-CCACATAAGTTAGTGGCATCATTTATCTTTTCCAGTCCTTAAA
1 C-CTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTCAGTCCTCAAA
* * * *
38198 AACCAAGACG
65 GACTAGGATG
* *
38208 CCTTTTCTTTTT-TTCAAAGCCCACATAAGTTGGTGGCATCATTTATCTTTTTCAGTCCTCAAAG
1 CCTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTCAGTCCTCAAAG
*
38272 ATTAGGATG
66 ACTAGGATG
** * * * *
38281 CCTTTTCTTTTTCTTCAAAGCCTGCATAAACTGGTGGCATCATTTATCTTTTCCAGTCCTCAAAA
1 CCTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTCAGTCCTCAAAG
* *
38346 ACCAAGATG
66 ACTAGGATG
* *
38355 CCTTTTTCTTTTTCTTCAAAGACCACACAAGCTGGTGGCATCATTTATCTTTTCCAGTCCTCAAA
1 CC-TTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTCAGTCCTCAAA
* *
38420 GAGTAAGATG
65 GACTAGGATG
* *
38430 CCTTTT-TTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTTATCTTTTCCAATCCTCAAA
1 CCTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCA-TTTATCTTTTTCAGTCCTCAAA
* ** *
38494 AAGAAAGATG
65 GACTAGGATG
* * * *
38504 CCTTTTCTTTTTTCTTCAAAGTCCACACAGGCTGATGGCATCATTTATCTTTTTTAGTCCTCAAA
1 CCTTTTC-TTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTCAGTCCTCAAA
*
38569 GAAC-AAGAT-
65 G-ACTAGGATG
*
38578 CCTTTTTCTTTTTCTTCAAAGCCCACACAAGC-GATGGCATCATTTATCTTTTTCAGTCCTCAAA
1 CC-TTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTCAGTCCTCAAA
* **
38642 CAAAAGGATG
65 GACTAGGATG
** ** * * * * *
38652 TTTTTTCTTTTT-TTTTAAGCCAACACAAGTTGGTGGTATTATTTATCTTTTAT-AGTCCTTAAA
1 CCTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTT-TCAGTCCTCAAA
*
38715 GACTAGGACG
65 GACTAGGATG
* * * *
38725 TCTTTTCTTTTTCTTTAAAGCCCACACAAGCTAGTGGCATCATTTATCTTCTTCAGTCCTCAAAG
1 CCTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTCAGTCCTCAAAG
** **
38790 TGTAGGGCG
66 ACTAGGATG
38799 CCTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTC-GCTCCTCAAA
1 CCTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTCAG-TCCTCAAA
*
38863 GAGTAGGATG
65 GACTAGGATG
* *
38873 CTTTTTATTTTTCTTC
1 CCTTTTCTTTTTCTTC
38889 TCATCATTTA
Statistics
Matches: 642, Mismatches: 90, Indels: 40
0.83 0.12 0.05
Matches are distributed among these distances:
70 35 0.05
71 14 0.02
72 32 0.05
73 188 0.29
74 245 0.38
75 95 0.15
76 33 0.05
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.38
Consensus pattern (74 bp):
CCTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTCAGTCCTCAAAG
ACTAGGATG
Found at i:38433 original size:149 final size:148
Alignment explanation
Indices: 38064--38888 Score: 924
Period size: 149 Copynumber: 5.6 Consensus size: 148
38054 GAGCAAGACA
* * * * * * *
38064 CCTTTTCTTTGTCTTCAAAGCCCACATAAGCTGATCGCATCATTTATCTTTTTTAGCCCTCAAAA
1 CCTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTCAGTCCTCAAAG
* * * *
38129 AGCAAG--GCAC-TTT-TTTTTCTTCAAAG-CCACATAAGTTAGTGGCATCATTTATCTTTTCCA
66 AGTAAGATGC-CTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTCCA
* *
38189 GTCCTTAAAAACCAAGACG
130 GTCCTCAAAAACCAAGATG
* *
38208 CCTTTTCTTTTT-TTCAAAGCCCACATAAGTTGGTGGCATCATTTATCTTTTTCAGTCCTCAAAG
1 CCTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTCAGTCCTCAAAG
* * ** * *
38272 ATTAGGATGCCTTTTCTTTTTCTTCAAAGCCTGCATAAACTGGTGGCATCATTTATCTTTTCCAG
66 AGTAAGATGCCTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTCCAG
38337 TCCTCAAAAACCAAGATG
131 TCCTCAAAAACCAAGATG
* *
38355 CCTTTTTCTTTTTCTTCAAAGACCACACAAGCTGGTGGCATCATTTATCTTTTCCAGTCCTCAAA
1 CC-TTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTCAGTCCTCAAA
38420 GAGTAAGATGCCTTTT-TTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTTATCTTTTCC
65 GAGTAAGATGCCTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCA-TTTATCTTTTCC
* **
38484 AATCCTCAAAAAGAAAGATG
129 AGTCCTCAAAAACCAAGATG
* * * *
38504 CCTTTTCTTTTTTCTTCAAAGTCCACACAGGCTGATGGCATCATTTATCTTTTTTAGTCCTCAAA
1 CCTTTTC-TTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTCAGTCCTCAAA
** * *
38569 GAACAAGAT-CCTTTTTCTTTTTCTTCAAAGCCCACACAAGC-GATGGCATCATTTATCTTTTTC
65 GAGTAAGATGCC-TTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTCC
38632 AGTCCTCAAACAA--AAGGATG
129 AGTCCTCAAA-AACCAA-GATG
** ** * * * * *
38652 TTTTTTCTTTTT-TTTTAAGCCAACACAAGTTGGTGGTATTATTTATCTTTTAT-AGTCCTTAAA
1 CCTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTT-TCAGTCCTCAAA
* * * * * *
38715 GACTAGGACGTCTTTTCTTTTTCTTTAAAGCCCACACAAGCTAGTGGCATCATTTATCTTCTT-C
65 GAGTAAGATGCCTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTT-TTCC
**** * **
38779 AGTCCTCAAAGTGTAGGGCG
129 AGTCCTCAAAAACCAAGATG
38799 CCTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTC-GCTCCTCAAA
1 CCTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTCAG-TCCTCAAA
* * *
38863 GAGTAGGATGCTTTTTATTTTTCTTC
65 GAGTAAGATGCCTTTTCTTTTTCTTC
38889 TCATCATTTA
Statistics
Matches: 579, Mismatches: 80, Indels: 40
0.83 0.11 0.06
Matches are distributed among these distances:
143 49 0.08
144 12 0.02
145 5 0.01
146 85 0.15
147 98 0.17
148 140 0.24
149 166 0.29
150 24 0.04
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.38
Consensus pattern (148 bp):
CCTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTCAGTCCTCAAAG
AGTAAGATGCCTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTCCAG
TCCTCAAAAACCAAGATG
Found at i:40156 original size:18 final size:19
Alignment explanation
Indices: 40120--40156 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
40110 TTTTTTGTAA
40120 AATGTATTGATACACAAGTT
1 AATGTATTGATA-ACAAGTT
40140 AATGTATTGAT-ACAAGT
1 AATGTATTGATAACAAGT
40157 CCAGAAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (19 bp):
AATGTATTGATAACAAGTT
Found at i:42671 original size:88 final size:87
Alignment explanation
Indices: 42529--42877 Score: 317
Period size: 88 Copynumber: 4.0 Consensus size: 87
42519 GGGAAACTCT
* ** * *
42529 ATCCCTACTATTTCGAGAGAATACTCCAACCCTGTTCGAACAAAAATTCAAATCTTCTTTCATAT
1 ATCCCTACTATTTCGAGAGGATACT-CAACCCCATTCTAACAAAAATTCAAATCTTCCTTCATAT
* *
42594 AACTTTATCTTTAGGAAAACTCC
65 AACTTTATCCTTAGGAAAACTTC
** * *
42617 ATCTTTACTATTTTGAGGGGATACTTCAACCCCATTCTAACAAAAATTCAAATCTTCCTTCATAT
1 ATCCCTACTATTTCGAGAGGATAC-TCAACCCCATTCTAACAAAAATTCAAATCTTCCTTCATAT
* * *
42682 TACTTTATCCTTAGGGAAGCTTC
65 AACTTTATCCTTAGGAAAACTTC
* * * ** * *** *
42705 ATCCCCATTATTTCGAGAGGATACTCTACCCTGTTTTATTGAAAATTCAAATCTTCCTTCATTTA
1 ATCCCTACTATTTCGAGAGGATACTCAACCCCATTCTAACAAAAATTCAAATCTTCCTTCATATA
*
42770 ACTTTATCCTT-GGAGAAACTTT
66 ACTTTATCCTTAGGA-AAACTTC
* * * * **
42792 ATCCCTACTA-TTCTGA-AGGGATACTCTAACTCCATTCTAACAAAAATTTAAATTTTTCTTCGC
1 ATCCCTACTATTTC-GAGA-GGATACTC-AACCCCATTCTAACAAAAATTCAAATCTTCCTTCAT
* * *
42855 ATAATTTTATCCTTGGGGAAACT
63 ATAACTTTATCCTTAGGAAAACT
42878 CTGTCCCTAT
Statistics
Matches: 205, Mismatches: 50, Indels: 12
0.77 0.19 0.04
Matches are distributed among these distances:
86 6 0.03
87 66 0.32
88 130 0.63
89 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.37
Consensus pattern (87 bp):
ATCCCTACTATTTCGAGAGGATACTCAACCCCATTCTAACAAAAATTCAAATCTTCCTTCATATA
ACTTTATCCTTAGGAAAACTTC
Found at i:45076 original size:30 final size:30
Alignment explanation
Indices: 45042--45098 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
45032 CTTTAAAATT
*
45042 GATTTTGATT-TGATTTTTTTAAAAATTTAA
1 GATTTTG-TTGTGATTTTTTAAAAAATTTAA
45072 GATTTTGTTGTGATTTTTTAAAAAATT
1 GATTTTGTTGTGATTTTTTAAAAAATT
45099 CTAGATTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (30 bp):
GATTTTGTTGTGATTTTTTAAAAAATTTAA
Found at i:45105 original size:30 final size:29
Alignment explanation
Indices: 45042--45111 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 29
45032 CTTTAAAATT
*
45042 GATTTTGATTTGATTTTTTTAAAAATTTAA
1 GATTTTG-TTTGATTTTTTAAAAAATTTAA
45072 GATTTTGTTGTGATTTTTTAAAAAATTCT-A
1 GATTTTGTT-TGATTTTTTAAAAAATT-TAA
*
45102 GATTATGTTT
1 GATTTTGTTT
45112 TAACACCTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 3 0.08
30 32 0.89
31 1 0.03
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.56
Consensus pattern (29 bp):
GATTTTGTTTGATTTTTTAAAAAATTTAA
Found at i:45469 original size:3 final size:3
Alignment explanation
Indices: 45463--45488 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
45453 TTAGCTAAAT
45463 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
45489 CAAGTATCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:46952 original size:14 final size:16
Alignment explanation
Indices: 46927--46959 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
46917 TATGTAATGA
46927 TAAAATTATT-AAAAT
1 TAAAATTATTAAAAAT
46942 TAAAA-TATTAAAAAT
1 TAAAATTATTAAAAAT
46957 TAA
1 TAA
46960 TAAATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAAATTATTAAAAAT
Found at i:48388 original size:50 final size:50
Alignment explanation
Indices: 48313--48476 Score: 240
Period size: 50 Copynumber: 3.3 Consensus size: 50
48303 AAGAATTGGT
48313 CGTAATTGTTGACTATTCTTCACCAACTTTTGACAATCGAGAAAGGTGGC
1 CGTAATTGTTGACTATTCTTCACCAACTTTTGACAATCGAGAAAGGTGGC
* * * *
48363 CGTAATTGTTGACTATTCTTCACCAA-TCTTTAATAATCGAGAGAGGTGGT
1 CGTAATTGTTGACTATTCTTCACCAACT-TTTGACAATCGAGAAAGGTGGC
* * * *
48413 CGTAATTGTTGACTATTTTTCACCAACCTTTGACAATAGAGAAAGGTGAC
1 CGTAATTGTTGACTATTCTTCACCAACTTTTGACAATCGAGAAAGGTGGC
48463 CGTAATTGTTGACT
1 CGTAATTGTTGACT
48477 TTAAGCATCT
Statistics
Matches: 100, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
49 1 0.01
50 99 0.99
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (50 bp):
CGTAATTGTTGACTATTCTTCACCAACTTTTGACAATCGAGAAAGGTGGC
Found at i:48741 original size:19 final size:19
Alignment explanation
Indices: 48717--48765 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
48707 TTGTCGAGGC
48717 ACTGTTCACGTATACGGGT
1 ACTGTTCACGTATACGGGT
** *
48736 ACTGTTCACACATACGGTT
1 ACTGTTCACGTATACGGGT
*
48755 ACTGTGCACGT
1 ACTGTTCACGT
48766 GAAACAGTGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.31
Consensus pattern (19 bp):
ACTGTTCACGTATACGGGT
Found at i:50296 original size:20 final size:21
Alignment explanation
Indices: 50271--50325 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
50261 GTATCGATAC
**
50271 AATGTATCGATACATGACCA-
1 AATGTATCGATACATGAAAAG
*
50291 AATGTATCGATACTTGAAAAG
1 AATGTATCGATACATGAAAAG
50312 AATGTATCGATACA
1 AATGTATCGATACA
50326 GGTTATTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAG
Found at i:50395 original size:13 final size:13
Alignment explanation
Indices: 50377--50402 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50367 ACACACAATA
50377 TGTATCGATACAT
1 TGTATCGATACAT
50390 TGTATCGATACAT
1 TGTATCGATACAT
50403 CCCAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:50418 original size:33 final size:32
Alignment explanation
Indices: 50357--50424 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
50347 GTAGCCAAAT
*
50357 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
50389 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
50422 TTG
1 TTG
50425 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:56591 original size:13 final size:13
Alignment explanation
Indices: 56573--56609 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
56563 AGCATTCTCA
*
56573 GTATCGATACATT
1 GTATCGATACAGT
56586 GTATCGATACAGT
1 GTATCGATACAGT
56599 GTATCGATACA
1 GTATCGATACA
56610 AGGGGTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (13 bp):
GTATCGATACAGT
Found at i:57971 original size:18 final size:18
Alignment explanation
Indices: 57948--57996 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
57938 CCTTCTCTTC
*
57948 AAAAAAAAAAGAGCAAAA
1 AAAAAAAAAAGAACAAAA
*
57966 AAAAAAAAAAAAACAAAA
1 AAAAAAAAAAGAACAAAA
57984 AAACAAAACAAAG
1 AAA-AAAA-AAAG
57997 GAAAAGAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 19 0.73
19 4 0.15
20 3 0.12
ACGTcount: A:0.86, C:0.08, G:0.06, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAGAACAAAA
Found at i:57992 original size:13 final size:13
Alignment explanation
Indices: 57947--57995 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
57937 GCCTTCTCTT
57947 CAAAA-AAAAAAGA
1 CAAAACAAAAAA-A
*
57960 GCAAAAAAAAAAAA
1 -CAAAACAAAAAAA
*
57974 AAAAACAAAAAAA
1 CAAAACAAAAAAA
57987 CAAAACAAA
1 CAAAACAAA
57996 GGAAAAGAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 19 0.61
14 6 0.19
15 6 0.19
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (13 bp):
CAAAACAAAAAAA
Found at i:59068 original size:55 final size:55
Alignment explanation
Indices: 58984--59936 Score: 1464
Period size: 55 Copynumber: 17.3 Consensus size: 55
58974 TCCGCTTTTT
***
58984 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCC
59039 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCC
59094 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
59149 AGTCCTCAAAGAGCAAGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
59204 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCC
59259 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
59314 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
59369 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
59424 AGTCCTTAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTGGTGGCATTTTCT
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
59479 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * *
59534 AGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTGGTGGCATTTTCT
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
59589 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* *
59644 AGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTCT
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
59699 AGTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
59754 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * * * *
59809 ATTCCCCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTGGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * *
59864 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-T
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* *
59919 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
59937 TACAATTTAT
Statistics
Matches: 840, Mismatches: 42, Indels: 32
0.92 0.05 0.04
Matches are distributed among these distances:
54 18 0.02
55 803 0.96
56 19 0.02
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:59864 original size:29 final size:29
Alignment explanation
Indices: 59717--59864 Score: 71
Period size: 29 Copynumber: 5.3 Consensus size: 29
59707 AAGAACAGGA
*
59717 CACCTTTCAAAGCCCACACAAGTTGGTGG
1 CACCTTTCAAAGCCCACACAAGTGGGTGG
* * * * * * *
59746 CA-TTTTC-CAGTCCTCA-AAGAGCAG-GA
1 CACCTTTCAAAGCCCACACAAGTG-GGTGG
*
59772 CACCTCTT-AAAGCCCACACAAGTTGGTGG
1 CACCT-TTCAAAGCCCACACAAGTGGGTGG
** * * *
59801 CACCTTTC-ATTCCC-CA-AAGAGCAG-GA
1 CACCTTTCAAAGCCCACACAAGTG-GGTGG
*
59827 CACTTTTCAAAGCCCACACAAGTGGGTGG
1 CACCTTTCAAAGCCCACACAAGTGGGTGG
59856 CACCTTTCA
1 CACCTTTCA
59865 GTCCTCAAAG
Statistics
Matches: 78, Mismatches: 29, Indels: 24
0.60 0.22 0.18
Matches are distributed among these distances:
26 17 0.22
27 15 0.19
28 22 0.28
29 24 0.31
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (29 bp):
CACCTTTCAAAGCCCACACAAGTGGGTGG
Found at i:60164 original size:19 final size:19
Alignment explanation
Indices: 60140--60207 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 19
60130 AATTCAACAA
60140 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
60159 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
*
60174 --CGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
* *
60191 ATTGTATCAATACATAA
1 TTTGTATCGATACATAA
60208 TTAGCTACTG
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
13 10 0.25
15 2 0.05
17 2 0.05
19 26 0.65
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:60179 original size:32 final size:32
Alignment explanation
Indices: 60143--60204 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
60133 TCAACAATTT
* *
60143 GTATCGATACATAAGTTTTGTATCGATACAAC
1 GTATCGATACATAAGTATTGTATCAATACAAC
60175 GTATCGATACATAAGTATTGTATCAATACA
1 GTATCGATACATAAGTATTGTATCAATACA
60205 TAATTAGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (32 bp):
GTATCGATACATAAGTATTGTATCAATACAAC
Found at i:60265 original size:13 final size:13
Alignment explanation
Indices: 60247--60272 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60237 CATTTTTCTG
60247 TGTATCGATACAT
1 TGTATCGATACAT
60260 TGTATCGATACAT
1 TGTATCGATACAT
60273 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:60266 original size:33 final size:33
Alignment explanation
Indices: 60227--60293 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
60217 GCCAAGGAAA
***
60227 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
60260 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
60293 T
1 T
60294 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:62695 original size:51 final size:52
Alignment explanation
Indices: 62639--62759 Score: 165
Period size: 51 Copynumber: 2.3 Consensus size: 52
62629 AATTCTCCAC
* * *
62639 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAA-ACACTAA-TTTTCTAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAGACACCAATTTTTC-AT
* *
62690 AATCGGGGATACTCTAACTCCGATTTTATTTCCAAAGATACCAATTTTTCAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAGACACCAATTTTTCAT
*
62742 AATCGAGGATACTCCAAC
1 AATCGGGGATACTCCAAC
62760 CTCGTTATCT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
51 33 0.54
52 23 0.38
53 5 0.08
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (52 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAGACACCAATTTTTCAT
Found at i:62805 original size:28 final size:27
Alignment explanation
Indices: 62748--62824 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 27
62738 TCATAATCGA
*
62748 GGATACTCCAACCTCGTTATCTCATCGG
1 GGATACTCCAACCCCGTTATCTCA-CGG
*
62776 GGATACTCCAACCCCGTTACTTTCGA-GG
1 GGATACTCCAACCCCGTTA-TCTC-ACGG
*
62804 GGATACTCCAATCCCGATTAT
1 GGATACTCCAACCCCG-TTAT
62825 TTTTTTTTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
28 36 0.84
29 6 0.14
30 1 0.02
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.27
Consensus pattern (27 bp):
GGATACTCCAACCCCGTTATCTCACGG
Done.