Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1560
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: 50739
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Found at i:2761 original size:20 final size:20
Alignment explanation
Indices: 2702--2761 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
2692 CTATGTTAGT
2702 TTATATATT-TATTATGTA-A
1 TTATAT-TTATATTATGTATA
**
2721 TT-TATTTATTTATTAAATATA
1 TTATATTTA--TATTATGTATA
2742 TTATATTTATATTATGTATA
1 TTATATTTATATTATGTATA
2762 AAATTATCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
17 2 0.06
18 3 0.09
19 2 0.06
20 16 0.50
21 3 0.09
22 6 0.19
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (20 bp):
TTATATTTATATTATGTATA
Found at i:3486 original size:46 final size:46
Alignment explanation
Indices: 3433--3520 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
3423 CTAAGTAATC
* *
3433 AAAATCTAATGAAACTCTAATTTTAAATTATTTTAAACACTAGACT
1 AAAATCTAATAAAACTCTAATTTTAAATTATTGTAAACACTAGACT
* **
3479 AAAATCTATTAAAACTCTAATTTTATTTTATTGTAAACACTA
1 AAAATCTAATAAAACTCTAATTTTAAATTATTGTAAACACTA
3521 TCAAAATAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.40
Consensus pattern (46 bp):
AAAATCTAATAAAACTCTAATTTTAAATTATTGTAAACACTAGACT
Found at i:5198 original size:42 final size:39
Alignment explanation
Indices: 5114--5335 Score: 143
Period size: 42 Copynumber: 5.5 Consensus size: 39
5104 ATATTTCCAG
* * **
5114 CTCAAACTGAAACCCAGA--ATCAAGAATCTAGGATTCAAC
1 CTCAAACTGAAGCCCAGATCATCAAGAA-C-ATGATTTTAC
* *
5153 CTCAAACTGAAGCACAGAATCATCAAGAACATGAGATTTTCC
1 CTCAAACTGAAGCCCAG-ATCATCAAGAACAT--GATTTTAC
* *
5195 CTCAAACTGAAACCCAGA--ATCAAGAATACTG-TTTTCCATCTC
1 CTCAAACTGAAGCCCAGATCATCAAGAACA-TGATTTT--A---C
* **
5237 CTCAAGCTGAAGCCCAGA--ATCAAGAACCCATGATTCAAC
1 CTCAAACTGAAGCCCAGATCATCAAGAA--CATGATTTTAC
5276 CTCAAACTGAAGCCCAGCATCATCAAGAACATGAGATTTTAC
1 CTCAAACTGAAGCCCAG-ATCATCAAGAACAT--GATTTTAC
*
5318 CTCAAACTGAAACCCAGA
1 CTCAAACTGAAGCCCAGA
5336 ATCAAGGATA
Statistics
Matches: 145, Mismatches: 19, Indels: 36
0.73 0.09 0.18
Matches are distributed among these distances:
37 4 0.03
38 1 0.01
39 41 0.28
40 7 0.05
41 3 0.02
42 84 0.58
43 2 0.01
44 3 0.02
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (39 bp):
CTCAAACTGAAGCCCAGATCATCAAGAACATGATTTTAC
Found at i:5333 original size:123 final size:123
Alignment explanation
Indices: 5114--5341 Score: 384
Period size: 123 Copynumber: 1.9 Consensus size: 123
5104 ATATTTCCAG
* *
5114 CTCAAACTGAAACCCAGAATCAAGAATCTAGGATTCAACCTCAAACTGAAGCACAGAATCATCAA
1 CTCAAACTGAAACCCAGAATCAAGAACCCAGGATTCAACCTCAAACTGAAGCACAGAATCATCAA
*
5179 GAACATGAGATTTTCCCTCAAACTGAAACCCAGAATCAAGAATACTGTTTTCCATCTC
66 GAACATGAGATTTTACCTCAAACTGAAACCCAGAATCAAGAATACTGTTTTCCATCTC
* * * * *
5237 CTCAAGCTGAAGCCCAGAATCAAGAACCCATGATTCAACCTCAAACTGAAGCCCAGCATCATCAA
1 CTCAAACTGAAACCCAGAATCAAGAACCCAGGATTCAACCTCAAACTGAAGCACAGAATCATCAA
5302 GAACATGAGATTTTACCTCAAACTGAAACCCAGAATCAAG
66 GAACATGAGATTTTACCTCAAACTGAAACCCAGAATCAAG
5342 GATATTGGAT
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
123 97 1.00
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (123 bp):
CTCAAACTGAAACCCAGAATCAAGAACCCAGGATTCAACCTCAAACTGAAGCACAGAATCATCAA
GAACATGAGATTTTACCTCAAACTGAAACCCAGAATCAAGAATACTGTTTTCCATCTC
Found at i:6177 original size:21 final size:21
Alignment explanation
Indices: 6147--6213 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
6137 TTTAAATAAT
*
6147 TTTTATTAAAATTTATTTATA
1 TTTTAATAAAATTTATTTATA
* *
6168 TTTGT-ATAAAAATAATTT-TA
1 TTT-TAATAAAATTTATTTATA
*
6188 TTTTAATTAAATTT-TTGTATA
1 TTTTAATAAAATTTATT-TATA
6209 TTTTA
1 TTTTA
6214 TTTTTTAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
19 3 0.08
20 12 0.33
21 20 0.56
22 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
TTTTAATAAAATTTATTTATA
Found at i:6612 original size:2 final size:2
Alignment explanation
Indices: 6605--6656 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
6595 AAAATACGTG
6605 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6647 TA TA TA TA TA
1 TA TA TA TA TA
6657 AGAAGGATCC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7720 original size:2 final size:2
Alignment explanation
Indices: 7713--7758 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
7703 AATTAATGAA
7713 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
7755 AT AT
1 AT AT
7759 TTCTGGTTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9131 original size:21 final size:22
Alignment explanation
Indices: 9107--9154 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
9097 TTACAAAATA
*
9107 ATATTTTTATAGT-ATAATTAT
1 ATATTTTTATAATAATAATTAT
9128 ATA-TTTTATAATAATAATTAT
1 ATATTTTTATAATAATAATTAT
9149 A-ATTTT
1 ATATTTT
9155 ATTTTACTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATTTTTATAATAATAATTAT
Found at i:9134 original size:20 final size:21
Alignment explanation
Indices: 9107--9156 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
9097 TTACAAAATA
*
9107 ATAT-TTTTATAGT-ATAATT
1 ATATATTTTATAATAATAATT
9126 ATATATTTTATAATAATAATT
1 ATATATTTTATAATAATAATT
9147 ATA-ATTTTAT
1 ATATATTTTAT
9157 TTTACTAGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 4 0.14
20 15 0.54
21 9 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATATATTTTATAATAATAATT
Found at i:10211 original size:42 final size:41
Alignment explanation
Indices: 10158--10379 Score: 162
Period size: 42 Copynumber: 5.4 Consensus size: 41
10148 TATCCTTGAT
10158 TCTGGGCTTCAGTTTGAGGTAAAATCCCGTGTTCTTGATGA
1 TCTGGGCTTCAGTTTGAGGTAAAATCCCGTGTTCTTGATGA
**
10199 TGCTGGGCTTCAGTTTGAGGTTGAATCCCG-GATTCTTGA--A
1 T-CTGGGCTTCAGTTTGAGGTAAAATCCCGTG-TTCTTGATGA
* * *
10239 TCTGGGCTTCAGCTTGAGGAGATGGAAAA--CAGTATTCTTGAT--
1 TCTGGGCTTCAGTTTGA-G-G-T--AAAATCCCGTGTTCTTGATGA
* *
10281 TCTGGG-TCTCAGTTTGAGGGAAAATCCCATGTTCTTGATGA
1 TCTGGGCT-TCAGTTTGAGGTAAAATCCCGTGTTCTTGATGA
* **
10322 TTCTGTGCTTCAGTTTGAGGTTGAAT-CC-TAGATTCTTGAT--
1 -TCTGGGCTTCAGTTTGAGGTAAAATCCCGT-G-TTCTTGATGA
*
10362 TCTGGGTTTCAGTTTGAG
1 TCTGGGCTTCAGTTTGAG
10380 CTGGAAATAT
Statistics
Matches: 145, Mismatches: 18, Indels: 38
0.72 0.09 0.19
Matches are distributed among these distances:
37 4 0.03
39 41 0.28
40 5 0.03
41 8 0.06
42 84 0.58
43 1 0.01
44 2 0.01
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (41 bp):
TCTGGGCTTCAGTTTGAGGTAAAATCCCGTGTTCTTGATGA
Found at i:10314 original size:123 final size:123
Alignment explanation
Indices: 10152--10379 Score: 359
Period size: 123 Copynumber: 1.9 Consensus size: 123
10142 ATCCAATATC
* *
10152 CTTGATTCTGGGCTTCAGTTTGAGGTAAAATCCCGTGTTCTTGATGATGCTGGGCTTCAGTTTGA
1 CTTGATTCTGGGCTTCAGTTTGAGGGAAAATCCCATGTTCTTGATGATGCTGGGCTTCAGTTTGA
*
10217 GGTTGAATCCCGGATTCTTGAATCTGGGCTTCAGCTTGAGGAGATGGAAAACAGTATT
66 GGTTGAATCCCAGATTCTTGAATCTGGGCTTCAGCTTGAGGAGATGGAAAACAGTATT
* *
10275 CTTGATTCTGGG-TCTCAGTTTGAGGGAAAATCCCATGTTCTTGATGATTCTGTGCTTCAGTTTG
1 CTTGATTCTGGGCT-TCAGTTTGAGGGAAAATCCCATGTTCTTGATGATGCTGGGCTTCAGTTTG
* * * *
10339 AGGTTGAATCCTAGATTCTTGATTCTGGGTTTCAGTTTGAG
65 AGGTTGAATCCCAGATTCTTGAATCTGGGCTTCAGCTTGAG
10380 CTGGAAATAT
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
122 1 0.01
123 94 0.99
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (123 bp):
CTTGATTCTGGGCTTCAGTTTGAGGGAAAATCCCATGTTCTTGATGATGCTGGGCTTCAGTTTGA
GGTTGAATCCCAGATTCTTGAATCTGGGCTTCAGCTTGAGGAGATGGAAAACAGTATT
Found at i:11905 original size:20 final size:21
Alignment explanation
Indices: 11868--11906 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11858 ACAGTTAATG
*
11868 TTTTTTTTCAATTATTCAATT
1 TTTTTTTTCAAATATTCAATT
*
11889 TTTTTTTTTAAAT-TTCAA
1 TTTTTTTTCAAATATTCAA
11907 CAAAAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTTTTTCAAATATTCAATT
Found at i:13582 original size:17 final size:18
Alignment explanation
Indices: 13545--13582 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
13535 AGAAAATAGT
13545 AATATTTTATGTTTTTCA
1 AATATTTTATGTTTTTCA
13563 AATATTTTTAT-TTTTT-A
1 AATA-TTTTATGTTTTTCA
13580 AAT
1 AAT
13583 TGGATTTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 9 0.47
19 6 0.32
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (18 bp):
AATATTTTATGTTTTTCA
Found at i:14746 original size:11 final size:12
Alignment explanation
Indices: 14687--14749 Score: 58
Period size: 11 Copynumber: 5.2 Consensus size: 12
14677 TTTAAATATG
*
14687 ATAATATTAAAT
1 ATAATATAAAAT
14699 ATAATTATATAAAT
1 ATAA-TATA-AAAT
* *
14713 ATTATATAAAAA
1 ATAATATAAAAT
14725 ATAAT-TAAAAT
1 ATAATATAAAAT
*
14736 ATGATAT-AAAT
1 ATAATATAAAAT
14747 ATA
1 ATA
14750 TGAATGTTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
11 15 0.37
12 12 0.29
13 7 0.17
14 7 0.17
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:14761 original size:28 final size:25
Alignment explanation
Indices: 14690--14790 Score: 68
Period size: 26 Copynumber: 4.0 Consensus size: 25
14680 AAATATGATA
* *
14690 ATATTAAATAT-AATTATATAAATATT
1 ATATAAAATATGAATTTTA-AAATA-T
*
14716 ATATAAAAAAT-AA--TTAAAATAT
1 ATATAAAATATGAATTTTAAAATAT
14738 GATATAAATATATGAATGTTTAAAA-AT
1 -ATATAAA-ATATGAAT-TTTAAAATAT
* *
14765 TTATATAATATGAATTTTAAACATAT
1 ATATAAAATATGAATTTTAAA-ATAT
14791 CAAAATTTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
22 1 0.02
23 12 0.20
24 11 0.18
25 11 0.18
26 18 0.30
27 2 0.03
28 6 0.10
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (25 bp):
ATATAAAATATGAATTTTAAAATAT
Found at i:14841 original size:30 final size:27
Alignment explanation
Indices: 14800--14855 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 27
14790 TCAAAATTTA
14800 TATAAATATAAAATACATTAAACATAAT
1 TATAAATATAAAATACATT-AACATAAT
*
14828 TATAATATGATAAAATATATTAACATAA
1 TATAA-AT-ATAAAATACATTAACATAA
14856 CTTAGATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 5 0.20
29 9 0.36
30 11 0.44
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (27 bp):
TATAAATATAAAATACATTAACATAAT
Found at i:16840 original size:46 final size:46
Alignment explanation
Indices: 16772--16860 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 46
16762 TTTAAGTAAT
*
16772 CAAAATCTACTGAAACTCTAATTTTAAATTATCT-TAAACACTAGAC
1 CAAAATCTACTAAAACTCTAATTTTAAATTAT-TGTAAACACTAGAC
* * * **
16818 CAAAATCTATTAAAATTTTAATTTTATTTTATTGTAAACACTA
1 CAAAATCTACTAAAACTCTAATTTTAAATTATTGTAAACACTA
16861 TCAAAATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
45 1 0.03
46 35 0.97
ACGTcount: A:0.43, C:0.15, G:0.03, T:0.39
Consensus pattern (46 bp):
CAAAATCTACTAAAACTCTAATTTTAAATTATTGTAAACACTAGAC
Found at i:18533 original size:42 final size:39
Alignment explanation
Indices: 18449--18670 Score: 143
Period size: 42 Copynumber: 5.5 Consensus size: 39
18439 ATATTTCCAG
* * **
18449 CTCAAACTGAAACCCAGA--ATCAAGAATCTAGGATTCAAC
1 CTCAAACTGAAGCCCAGATCATCAAGAA-C-ATGATTTTAC
* *
18488 CTCAAACTGAAGCACAGAATCATCAAGAACATGGGATTTTCC
1 CTCAAACTGAAGCCCAG-ATCATCAAGAACAT--GATTTTAC
* *
18530 CTCAAACTGAAACCCAGA--ATCAAGAATACTG-TTTTCCATCTC
1 CTCAAACTGAAGCCCAGATCATCAAGAACA-TGATTTT--A---C
* **
18572 CTCAAGCTGAAGCCCAGA--ATCAAGAACCCATGATTCAAC
1 CTCAAACTGAAGCCCAGATCATCAAGAA--CATGATTTTAC
18611 CTCAAACTGAAGCCCAGCATCATCAAGAACATGGGATTTTAC
1 CTCAAACTGAAGCCCAG-ATCATCAAGAACAT--GATTTTAC
*
18653 CTCAAACTGAAACCCAGA
1 CTCAAACTGAAGCCCAGA
18671 ATCAAGGATA
Statistics
Matches: 145, Mismatches: 19, Indels: 36
0.73 0.09 0.18
Matches are distributed among these distances:
37 4 0.03
38 1 0.01
39 41 0.28
40 7 0.05
41 3 0.02
42 84 0.58
43 2 0.01
44 3 0.02
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (39 bp):
CTCAAACTGAAGCCCAGATCATCAAGAACATGATTTTAC
Found at i:18668 original size:123 final size:123
Alignment explanation
Indices: 18449--18676 Score: 384
Period size: 123 Copynumber: 1.9 Consensus size: 123
18439 ATATTTCCAG
* *
18449 CTCAAACTGAAACCCAGAATCAAGAATCTAGGATTCAACCTCAAACTGAAGCACAGAATCATCAA
1 CTCAAACTGAAACCCAGAATCAAGAACCCAGGATTCAACCTCAAACTGAAGCACAGAATCATCAA
*
18514 GAACATGGGATTTTCCCTCAAACTGAAACCCAGAATCAAGAATACTGTTTTCCATCTC
66 GAACATGGGATTTTACCTCAAACTGAAACCCAGAATCAAGAATACTGTTTTCCATCTC
* * * * *
18572 CTCAAGCTGAAGCCCAGAATCAAGAACCCATGATTCAACCTCAAACTGAAGCCCAGCATCATCAA
1 CTCAAACTGAAACCCAGAATCAAGAACCCAGGATTCAACCTCAAACTGAAGCACAGAATCATCAA
18637 GAACATGGGATTTTACCTCAAACTGAAACCCAGAATCAAG
66 GAACATGGGATTTTACCTCAAACTGAAACCCAGAATCAAG
18677 GATATTGGAT
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
123 97 1.00
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (123 bp):
CTCAAACTGAAACCCAGAATCAAGAACCCAGGATTCAACCTCAAACTGAAGCACAGAATCATCAA
GAACATGGGATTTTACCTCAAACTGAAACCCAGAATCAAGAATACTGTTTTCCATCTC
Found at i:23258 original size:22 final size:24
Alignment explanation
Indices: 23216--23261 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
23206 TAACGATTTT
23216 ATAATTTATTTAGTTTAAAATTTAA
1 ATAATTTATTTAG-TTAAAATTTAA
23241 ATAATTT-TTTA-TTAAAATTTA
1 ATAATTTATTTAGTTAAAATTTA
23262 TTTATATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.48
24 4 0.19
25 7 0.33
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
ATAATTTATTTAGTTAAAATTTAA
Found at i:23606 original size:16 final size:16
Alignment explanation
Indices: 23568--23611 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
23558 ATGTTAGTTT
23568 ATATATTTATTATGTA
1 ATATATTTATTATGTA
*
23584 ATTTATTTATTAT-TAA
1 ATATATTTATTATGT-A
23600 ATATATTATATT
1 ATATATT-TATT
23612 TATATTATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 1 0.04
16 19 0.79
17 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
ATATATTTATTATGTA
Found at i:26048 original size:42 final size:39
Alignment explanation
Indices: 26001--26185 Score: 146
Period size: 42 Copynumber: 4.5 Consensus size: 39
25991 CTAGGATTCA
*
26001 ACCTCAAACTGAAGCACAGAATCATCAAGAACATGGGATTTT
1 ACCTCAAACTGAAGCCCAG-ATCATCAAGAACAT--GATTTT
* * *
26043 CCCTCAAACTGAAACCCAGA--ATCAAGAATACTG-TTTT
1 ACCTCAAACTGAAGCCCAGATCATCAAGAACA-TGATTTT
* **
26080 CCATCTCCTCAAGCTGAAGCCCAGA--ATCAAGAACCCATGATTCA
1 --A---CCTCAAACTGAAGCCCAGATCATCAAGAA--CATGATTTT
26124 ACCTCAAACTGAAGCCCAGCATCATCAAGAACATGGGATTTT
1 ACCTCAAACTGAAGCCCAG-ATCATCAAGAACAT--GATTTT
26166 ACCTCAAACTGAAGCCCAGA
1 ACCTCAAACTGAAGCCCAGA
26186 ATCAAGGATA
Statistics
Matches: 116, Mismatches: 13, Indels: 29
0.73 0.08 0.18
Matches are distributed among these distances:
37 4 0.03
38 1 0.01
39 26 0.22
40 5 0.04
41 2 0.02
42 73 0.63
43 2 0.02
44 3 0.03
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.20
Consensus pattern (39 bp):
ACCTCAAACTGAAGCCCAGATCATCAAGAACATGATTTT
Found at i:26184 original size:123 final size:123
Alignment explanation
Indices: 25964--26191 Score: 366
Period size: 123 Copynumber: 1.9 Consensus size: 123
25954 ATATTTCCAG
* * *
25964 CTCAAACTGAAACTCAGAATCAAGAATCTAGGATTCAACCTCAAACTGAAGCACAGAATCATCAA
1 CTCAAACTGAAACCCAGAATCAAGAACCCAGGATTCAACCTCAAACTGAAGCACAGAATCATCAA
*
26029 GAACATGGGATTTTCCCTCAAACTGAAACCCAGAATCAAGAATACTGTTTTCCATCTC
66 GAACATGGGATTTTACCTCAAACTGAAACCCAGAATCAAGAATACTGTTTTCCATCTC
* * * * *
26087 CTCAAGCTGAAGCCCAGAATCAAGAACCCATGATTCAACCTCAAACTGAAGCCCAGCATCATCAA
1 CTCAAACTGAAACCCAGAATCAAGAACCCAGGATTCAACCTCAAACTGAAGCACAGAATCATCAA
*
26152 GAACATGGGATTTTACCTCAAACTGAAGCCCAGAATCAAG
66 GAACATGGGATTTTACCTCAAACTGAAACCCAGAATCAAG
26192 GATATTGGAT
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
123 95 1.00
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (123 bp):
CTCAAACTGAAACCCAGAATCAAGAACCCAGGATTCAACCTCAAACTGAAGCACAGAATCATCAA
GAACATGGGATTTTACCTCAAACTGAAACCCAGAATCAAGAATACTGTTTTCCATCTC
Found at i:29914 original size:21 final size:22
Alignment explanation
Indices: 29890--29937 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
29880 TTACAAAATA
*
29890 ATATTTTTATAGT-ATAATTAT
1 ATATTTTTATAATAATAATTAT
29911 ATA-TTTTATAATAATAATTAT
1 ATATTTTTATAATAATAATTAT
29932 A-ATTTT
1 ATATTTT
29938 ATTTTACTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATTTTTATAATAATAATTAT
Found at i:29917 original size:20 final size:21
Alignment explanation
Indices: 29890--29939 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
29880 TTACAAAATA
*
29890 ATAT-TTTTATAGT-ATAATT
1 ATATATTTTATAATAATAATT
29909 ATATATTTTATAATAATAATT
1 ATATATTTTATAATAATAATT
29930 ATA-ATTTTAT
1 ATATATTTTAT
29940 TTTACTAGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 4 0.14
20 15 0.54
21 9 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATATATTTTATAATAATAATT
Found at i:30995 original size:42 final size:41
Alignment explanation
Indices: 30942--31163 Score: 162
Period size: 42 Copynumber: 5.4 Consensus size: 41
30932 TATCCTTGAT
30942 TCTGGGCTTCAGTTTGAGGTAAAATCCCGTGTTCTTGATGA
1 TCTGGGCTTCAGTTTGAGGTAAAATCCCGTGTTCTTGATGA
**
30983 TGCTGGGCTTCAGTTTGAGGTTGAATCCCG-GATTCTTGA--A
1 T-CTGGGCTTCAGTTTGAGGTAAAATCCCGTG-TTCTTGATGA
* * *
31023 TCTGGGCTTCAGCTTGAGGAGATGGAAAA--CAGTATTCTTGAT--
1 TCTGGGCTTCAGTTTGA-G-G-T--AAAATCCCGTGTTCTTGATGA
* *
31065 TCTGGG-TCTCAGTTTGAGGGAAAATCCCATGTTCTTGATGA
1 TCTGGGCT-TCAGTTTGAGGTAAAATCCCGTGTTCTTGATGA
* **
31106 TTCTGTGCTTCAGTTTGAGGTTGAAT-CC-TAGATTCTTGAT--
1 -TCTGGGCTTCAGTTTGAGGTAAAATCCCGT-G-TTCTTGATGA
*
31146 TCTGGGTTTCAGTTTGAG
1 TCTGGGCTTCAGTTTGAG
31164 CTGGAAATAT
Statistics
Matches: 145, Mismatches: 18, Indels: 38
0.72 0.09 0.19
Matches are distributed among these distances:
37 4 0.03
39 41 0.28
40 5 0.03
41 8 0.06
42 84 0.58
43 1 0.01
44 2 0.01
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (41 bp):
TCTGGGCTTCAGTTTGAGGTAAAATCCCGTGTTCTTGATGA
Found at i:31098 original size:123 final size:123
Alignment explanation
Indices: 30936--31163 Score: 359
Period size: 123 Copynumber: 1.9 Consensus size: 123
30926 ATCCAATATC
* *
30936 CTTGATTCTGGGCTTCAGTTTGAGGTAAAATCCCGTGTTCTTGATGATGCTGGGCTTCAGTTTGA
1 CTTGATTCTGGGCTTCAGTTTGAGGGAAAATCCCATGTTCTTGATGATGCTGGGCTTCAGTTTGA
*
31001 GGTTGAATCCCGGATTCTTGAATCTGGGCTTCAGCTTGAGGAGATGGAAAACAGTATT
66 GGTTGAATCCCAGATTCTTGAATCTGGGCTTCAGCTTGAGGAGATGGAAAACAGTATT
* *
31059 CTTGATTCTGGG-TCTCAGTTTGAGGGAAAATCCCATGTTCTTGATGATTCTGTGCTTCAGTTTG
1 CTTGATTCTGGGCT-TCAGTTTGAGGGAAAATCCCATGTTCTTGATGATGCTGGGCTTCAGTTTG
* * * *
31123 AGGTTGAATCCTAGATTCTTGATTCTGGGTTTCAGTTTGAG
65 AGGTTGAATCCCAGATTCTTGAATCTGGGCTTCAGCTTGAG
31164 CTGGAAATAT
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
122 1 0.01
123 94 0.99
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (123 bp):
CTTGATTCTGGGCTTCAGTTTGAGGGAAAATCCCATGTTCTTGATGATGCTGGGCTTCAGTTTGA
GGTTGAATCCCAGATTCTTGAATCTGGGCTTCAGCTTGAGGAGATGGAAAACAGTATT
Found at i:32689 original size:19 final size:20
Alignment explanation
Indices: 32652--32691 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
32642 ACAGTTAATG
*
32652 TTTTTTTTTCAATTATTCAA
1 TTTTTTTTTCAAATATTCAA
*
32672 TTTTTTTTTTAAAT-TTCAA
1 TTTTTTTTTCAAATATTCAA
32691 T
1 T
32692 AAAAATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTTTTTCAAATATTCAA
Found at i:34365 original size:17 final size:18
Alignment explanation
Indices: 34328--34365 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
34318 AGAAAATAGT
34328 AATATTTTATGTTTTTCA
1 AATATTTTATGTTTTTCA
34346 AATATTTTTAT-TTTTT-A
1 AATA-TTTTATGTTTTTCA
34363 AAT
1 AAT
34366 TGGATTTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 9 0.47
19 6 0.32
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (18 bp):
AATATTTTATGTTTTTCA
Found at i:35501 original size:11 final size:11
Alignment explanation
Indices: 35472--35530 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
35462 TAAATTTGAT
*
35472 AATATTAAATA
1 AATATTATATA
*
35483 TA-ATTATATA
1 AATATTATATA
35493 AATATTATATA
1 AATATTATATA
* *
35504 AAAATAAT-TAA
1 AATATTATAT-A
*
35515 AATATGATATA
1 AATATTATATA
35526 AATAT
1 AATAT
35531 ATGAATGTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
10 9 0.24
11 28 0.74
12 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
AATATTATATA
Found at i:35542 original size:28 final size:25
Alignment explanation
Indices: 35473--35572 Score: 68
Period size: 25 Copynumber: 4.0 Consensus size: 25
35463 AAATTTGATA
* *
35473 ATATTAAATAT-AATTATATAAATATT
1 ATATAAAATATGAATTTTA-AAATA-T
35499 ATATAAAA-AT-AA--TTAAAATAT
1 ATATAAAATATGAATTTTAAAATAT
35520 GATATAAATATATGAATGTTTAAAA-AT
1 -ATATAAA-ATATGAAT-TTTAAAATAT
* *
35547 TTATATAATATGAATTTTAAACATAT
1 ATATAAAATATGAATTTTAAA-ATAT
35573 CAAAATTTAT
Statistics
Matches: 61, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
21 1 0.02
22 12 0.20
23 3 0.05
24 8 0.13
25 15 0.25
26 14 0.23
27 2 0.03
28 6 0.10
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (25 bp):
ATATAAAATATGAATTTTAAAATAT
Found at i:35623 original size:30 final size:27
Alignment explanation
Indices: 35582--35637 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 27
35572 TCAAAATTTA
35582 TATAAATATAAAATACATTAAACATAAT
1 TATAAATATAAAATACATT-AACATAAT
*
35610 TATAATATGATAAAATATATTAACATAA
1 TATAA-AT-ATAAAATACATTAACATAA
35638 CTTAGATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 5 0.20
29 9 0.36
30 11 0.44
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (27 bp):
TATAAATATAAAATACATTAACATAAT
Found at i:39331 original size:42 final size:38
Alignment explanation
Indices: 39229--39456 Score: 158
Period size: 42 Copynumber: 5.6 Consensus size: 38
39219 ATATTTCCAG
**
39229 CTCAAACTGAAACCCAGAATCAAGAATC-TAGGATTCAAC
1 CTCAAACTGAAACCCAGAATCAAGAA-CAT-GGATTTTAC
* * * *
39268 CTCAAACTGAAGCACAAAATCATCAAGAACATGGGATTTTCC
1 CTCAAACTGAAAC-CCAGA--ATCAAGAACAT-GGATTTTAC
*
39310 CTCAAACTGAAACCCAGAATCAAGAATACT-G-TTTTCCATCTC
1 CTCAAACTGAAACCCAGAATCAAGAACA-TGGATTTT--A---C
* * **
39352 CTCAAGCTGAAGCCCAGAATCAAGAACCCAT-GATTCAAC
1 CTCAAACTGAAACCCAGAATCAAGAA--CATGGATTTTAC
*
39391 CTCAAACTGAAGCCCAGCATCATCAAGAACATGGGATTTTAC
1 CTCAAACTGAAACCCAG-A--ATCAAGAACAT-GGATTTTAC
39433 CTCAAACTGAAACCCAGAATCAAG
1 CTCAAACTGAAACCCAGAATCAAG
39457 GATATTGGAT
Statistics
Matches: 150, Mismatches: 21, Indels: 36
0.72 0.10 0.17
Matches are distributed among these distances:
37 4 0.03
38 1 0.01
39 44 0.29
40 8 0.05
41 5 0.03
42 83 0.55
43 2 0.01
44 3 0.02
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (38 bp):
CTCAAACTGAAACCCAGAATCAAGAACATGGATTTTAC
Found at i:39448 original size:123 final size:123
Alignment explanation
Indices: 39229--39456 Score: 375
Period size: 123 Copynumber: 1.9 Consensus size: 123
39219 ATATTTCCAG
* *
39229 CTCAAACTGAAACCCAGAATCAAGAATCTAGGATTCAACCTCAAACTGAAGCACAAAATCATCAA
1 CTCAAACTGAAACCCAGAATCAAGAACCCAGGATTCAACCTCAAACTGAAGCACAAAATCATCAA
*
39294 GAACATGGGATTTTCCCTCAAACTGAAACCCAGAATCAAGAATACTGTTTTCCATCTC
66 GAACATGGGATTTTACCTCAAACTGAAACCCAGAATCAAGAATACTGTTTTCCATCTC
* * * * **
39352 CTCAAGCTGAAGCCCAGAATCAAGAACCCATGATTCAACCTCAAACTGAAGCCCAGCATCATCAA
1 CTCAAACTGAAACCCAGAATCAAGAACCCAGGATTCAACCTCAAACTGAAGCACAAAATCATCAA
39417 GAACATGGGATTTTACCTCAAACTGAAACCCAGAATCAAG
66 GAACATGGGATTTTACCTCAAACTGAAACCCAGAATCAAG
39457 GATATTGGAT
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
123 96 1.00
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (123 bp):
CTCAAACTGAAACCCAGAATCAAGAACCCAGGATTCAACCTCAAACTGAAGCACAAAATCATCAA
GAACATGGGATTTTACCTCAAACTGAAACCCAGAATCAAGAATACTGTTTTCCATCTC
Found at i:40320 original size:38 final size:39
Alignment explanation
Indices: 40271--40345 Score: 111
Period size: 38 Copynumber: 1.9 Consensus size: 39
40261 TATATTAACG
40271 TATTATAAATTTATTTA-ATTTA-AAAAATAAGTAATTTTT
1 TATTATAAATTTATTTATATTTATAAAAA-AA-TAATTTTT
40310 TATTA-AAATTTATTTATATTTATAAAAAAATAATTT
1 TATTATAAATTTATTTATATTTATAAAAAAATAATTT
40346 AATTTTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
38 17 0.50
39 12 0.35
40 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (39 bp):
TATTATAAATTTATTTATATTTATAAAAAAATAATTTTT
Found at i:40350 original size:20 final size:20
Alignment explanation
Indices: 40283--40350 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
40273 TTATAAATTT
40283 ATTTAATTTA-AAAAATAAGTA
1 ATTTAATTTATAAAAA-AA-TA
* * *
40304 ATTT--TTTAT-TAAAATTT
1 ATTTAATTTATAAAAAAATA
40321 ATTTATATTTATAAAAAAATA
1 ATTTA-ATTTATAAAAAAATA
40342 ATTTAATTT
1 ATTTAATTT
40351 TATTTAAATC
Statistics
Matches: 36, Mismatches: 6, Indels: 11
0.68 0.11 0.21
Matches are distributed among these distances:
17 5 0.14
18 1 0.03
19 7 0.19
20 9 0.25
21 14 0.39
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (20 bp):
ATTTAATTTATAAAAAAATA
Found at i:40428 original size:15 final size:16
Alignment explanation
Indices: 40378--40429 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 16
40368 ATTTTACTTT
40378 TTAAATATATTTTTAA
1 TTAAATATATTTTTAA
* **
40394 TTTAAT-TATTAATAA
1 TTAAATATATTTTTAA
40409 TTAAATATATTTTTAA
1 TTAAATATATTTTTAA
40425 -TAAAT
1 TTAAAT
40430 TTTTTATTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTAAATATATTTTTAA
Found at i:40763 original size:2 final size:2
Alignment explanation
Indices: 40756--40781 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40746 AAAATACGTG
40756 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
40782 AAAGAAGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43654 original size:18 final size:18
Alignment explanation
Indices: 43606--43695 Score: 50
Period size: 17 Copynumber: 5.1 Consensus size: 18
43596 TCAATATACG
*
43606 AATATTTTAAAATTTAT-
1 AATATATTAAAATTTATA
43623 -ATA-A-TACAAA-TTATA
1 AATATATTA-AAATTTATA
43638 AATATATTAAAATTTATA
1 AATATATTAAAATTTATA
*
43656 TAA-ATA-TAAAATATATTA
1 -AATATATTAAAATTTA-TA
* *
43674 AACATAATTATAATATTATA
1 AATAT-ATTAAAAT-TTATA
43694 AA
1 AA
43696 ATACACCAAC
Statistics
Matches: 57, Mismatches: 4, Indels: 21
0.70 0.05 0.26
Matches are distributed among these distances:
14 6 0.11
15 3 0.05
16 6 0.11
17 14 0.25
18 14 0.25
19 3 0.05
20 9 0.16
21 2 0.04
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
AATATATTAAAATTTATA
Found at i:43668 original size:27 final size:28
Alignment explanation
Indices: 43577--43675 Score: 85
Period size: 32 Copynumber: 3.4 Consensus size: 28
43567 TTATATAAAA
* *
43577 AAATA-ATTAAAATATGATATCAATATAC
1 AAATATATTAAAAT-TTATATAAATATAC
* * * *
43605 GAATATTTTAAAATTTATATAATACAAATTAT
1 AAATATATTAAAATTTATAT-A-A-ATA-TAC
43637 AAATATATTAAAATTTATATAAATATA-
1 AAATATATTAAAATTTATATAAATATAC
43664 AAATATATTAAA
1 AAATATATTAAA
43676 CATAATTATA
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
27 12 0.21
28 11 0.19
29 9 0.16
30 2 0.04
31 3 0.05
32 20 0.35
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (28 bp):
AAATATATTAAAATTTATATAAATATAC
Found at i:46590 original size:39 final size:38
Alignment explanation
Indices: 46537--46657 Score: 118
Period size: 39 Copynumber: 3.0 Consensus size: 38
46527 TTTTCCATCT
*
46537 CCTCAAGCTGAAGCCCAGAATCAAGAACCCAT-GATTCAA
1 CCTCAAACTGAAGCCCAGAATCAAGAA--CATGGATTCAA
**
46576 CCTCAAACTGAAGCCCAGCATCATCAAGAACATGGGATTTTA
1 CCTCAAACTGAAGCCCAG-A--ATCAAGAACAT-GGATTCAA
* * *
46618 CCTCAAACTGAAACCCAGAATCAAGGATATTGGATTCAA
1 CCTCAAACTGAAGCCCAGAATCAAGAACA-TGGATTCAA
46657 C
1 C
46658 AGGAGACTCA
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
39 32 0.47
40 5 0.07
41 1 0.01
42 30 0.44
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.19
Consensus pattern (38 bp):
CCTCAAACTGAAGCCCAGAATCAAGAACATGGATTCAA
Found at i:47810 original size:42 final size:39
Alignment explanation
Indices: 47750--47977 Score: 155
Period size: 42 Copynumber: 5.6 Consensus size: 39
47740 ATCCAATATC
*
47750 CTTGATTCTGGGTTTCAGTTTGAGGTAAAATCCCATGTT
1 CTTGATTCTGGGCTTCAGTTTGAGGTAAAATCCCATGTT
**
47789 CTTGATGATGCTGGGCTTCAGTTTGAGGTTGAAT-CC-TGGATT
1 CTTGAT--T-CTGGGCTTCAGTTTGAGGTAAAATCCCAT-G-TT
* *
47831 CTTGATTCTGGGCTTCAGCTTGAGGAGATGGAAAA---CAGTATT
1 CTTGATTCTGGGCTTCAGTTTGA-G-G-T--AAAATCCCA-TGTT
* *
47873 CTTGATTCTGGGTTTCAGTTTGACGG-AAAATCCCATGTC
1 CTTGATTCTGGGCTTCAGTTTGA-GGTAAAATCCCATGTT
* ** *
47912 CTTGATGATTCTGTGCTTCAGTTTGAGGTTGAATCCTA-GATT
1 C-T--TGATTCTGGGCTTCAGTTTGAGGTAAAATCCCATG-TT
*
47954 CTTGATTCTGGGTTTCAGTTTGAG
1 CTTGATTCTGGGCTTCAGTTTGAG
47978 CTGGAAATAT
Statistics
Matches: 149, Mismatches: 20, Indels: 40
0.71 0.10 0.19
Matches are distributed among these distances:
37 4 0.03
39 44 0.30
40 6 0.04
41 10 0.07
42 82 0.55
44 3 0.02
ACGTcount: A:0.20, C:0.15, G:0.26, T:0.39
Consensus pattern (39 bp):
CTTGATTCTGGGCTTCAGTTTGAGGTAAAATCCCATGTT
Found at i:47916 original size:123 final size:123
Alignment explanation
Indices: 47750--47977 Score: 386
Period size: 123 Copynumber: 1.9 Consensus size: 123
47740 ATCCAATATC
*
47750 CTTGATTCTGGGTTTCAGTTTGAGGTAAAATCCCATGTTCTTGATGATGCTGGGCTTCAGTTTGA
1 CTTGATTCTGGGTTTCAGTTTGAGGTAAAATCCCATGTCCTTGATGATGCTGGGCTTCAGTTTGA
*
47815 GGTTGAATCCTGGATTCTTGATTCTGGGCTTCAGCTTGAGGAGATGGAAAACAGTATT
66 GGTTGAATCCTAGATTCTTGATTCTGGGCTTCAGCTTGAGGAGATGGAAAACAGTATT
* *
47873 CTTGATTCTGGGTTTCAGTTTGACGG-AAAATCCCATGTCCTTGATGATTCTGTGCTTCAGTTTG
1 CTTGATTCTGGGTTTCAGTTTGA-GGTAAAATCCCATGTCCTTGATGATGCTGGGCTTCAGTTTG
* *
47937 AGGTTGAATCCTAGATTCTTGATTCTGGGTTTCAGTTTGAG
65 AGGTTGAATCCTAGATTCTTGATTCTGGGCTTCAGCTTGAG
47978 CTGGAAATAT
Statistics
Matches: 98, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
123 96 0.98
124 2 0.02
ACGTcount: A:0.20, C:0.15, G:0.26, T:0.39
Consensus pattern (123 bp):
CTTGATTCTGGGTTTCAGTTTGAGGTAAAATCCCATGTCCTTGATGATGCTGGGCTTCAGTTTGA
GGTTGAATCCTAGATTCTTGATTCTGGGCTTCAGCTTGAGGAGATGGAAAACAGTATT
Found at i:49733 original size:28 final size:25
Alignment explanation
Indices: 49701--49762 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
49691 TAAAAAATAA
49701 TTAAAATATGATATAAATATACGAATGT
1 TTAAAATAT-ATATAAA-ATACGAAT-T
* *
49729 TTAAAA-ATTTATATAATACGAATT
1 TTAAAATATATATAAAATACGAATT
49753 TTAAACATAT
1 TTAAA-ATAT
49763 CAAAACTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 6 0.20
25 9 0.30
26 7 0.23
27 2 0.07
28 6 0.20
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.39
Consensus pattern (25 bp):
TTAAAATATATATAAAATACGAATT
Found at i:49811 original size:29 final size:27
Alignment explanation
Indices: 49772--49826 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
49762 TCAAAACTTA
49772 TATAAATAT-AAATGCATTAAACATAAT
1 TATAAATATAAAATGCATT-AACATAAT
*
49799 TATAATATGATAAAATGTATTAACATAA
1 TATAA-AT-ATAAAATGCATTAACATAA
49827 CTTAGATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 5 0.21
28 2 0.08
29 9 0.38
30 8 0.33
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (27 bp):
TATAAATATAAAATGCATTAACATAAT
Done.