Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2574
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: 72774
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:11447 original size:19 final size:21
Alignment explanation
Indices: 11394--11449 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
11384 AAAAAATTCA
11394 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
11415 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
*
11436 CA-GTAT-GATACATT
1 AATGTATCGATACATT
11450 CTCCAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.24
20 4 0.12
21 21 0.64
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.38
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:12403 original size:1 final size:1
Alignment explanation
Indices: 12397--12473 Score: 109
Period size: 1 Copynumber: 77.0 Consensus size: 1
12387 ACTCCAACCA
* * * *
12397 CCCCCCCCCCCCCCCACCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCACCCCCCCCCCCCCACC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
*
12462 CCCACCCCCCCC
1 CCCCCCCCCCCC
12474 GGGTACTTTC
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.06, C:0.94, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:12418 original size:14 final size:14
Alignment explanation
Indices: 12397--12473 Score: 122
Period size: 14 Copynumber: 5.6 Consensus size: 14
12387 ACTCCAACCA
12397 CCCCCCCC-CCCCC
1 CCCCCCCCACCCCC
*
12410 CCACCCCC-CCCCC
1 CCCCCCCCACCCCC
12423 CCCCCCCCACCCCC
1 CCCCCCCCACCCCC
12437 CCCCCCCCACCCCC
1 CCCCCCCCACCCCC
12451 CCCCCCCCACCCCC
1 CCCCCCCCACCCCC
12465 ACCCCCCCC
1 -CCCCCCCC
12474 GGGTACTTTC
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
13 19 0.32
14 33 0.55
15 8 0.13
ACGTcount: A:0.06, C:0.94, G:0.00, T:0.00
Consensus pattern (14 bp):
CCCCCCCCACCCCC
Found at i:12441 original size:33 final size:34
Alignment explanation
Indices: 12399--12473 Score: 143
Period size: 33 Copynumber: 2.2 Consensus size: 34
12389 TCCAACCACC
12399 CCCCCCCCCCCCCACCCCCCCCCCCCC-CCCCCA
1 CCCCCCCCCCCCCACCCCCCCCCCCCCACCCCCA
12432 CCCCCCCCCCCCCACCCCCCCCCCCCCACCCCCA
1 CCCCCCCCCCCCCACCCCCCCCCCCCCACCCCCA
12466 CCCCCCCC
1 CCCCCCCC
12474 GGGTACTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 27 0.66
34 14 0.34
ACGTcount: A:0.07, C:0.93, G:0.00, T:0.00
Consensus pattern (34 bp):
CCCCCCCCCCCCCACCCCCCCCCCCCCACCCCCA
Found at i:25064 original size:10 final size:10
Alignment explanation
Indices: 25049--25105 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 10
25039 CTTCTCTTCA
25049 AAAAAAAAAG
1 AAAAAAAAAG
25059 AAAAAAAAAG
1 AAAAAAAAAG
25069 AAACAAAACAAAG
1 -AA-AAAA-AAAG
* *
25082 AAAAAGGAGAG
1 AAAAA-AAAAG
25093 AAAAGAAAAAG
1 AAAA-AAAAAG
25104 AA
1 AA
25106 CCTGCTTAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
10 10 0.26
11 17 0.45
12 7 0.18
13 4 0.11
ACGTcount: A:0.81, C:0.04, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:26223 original size:59 final size:58
Alignment explanation
Indices: 26072--26828 Score: 705
Period size: 59 Copynumber: 13.3 Consensus size: 58
26062 TCCGCTTTTT
* **
26072 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACG-CTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C
* *
26133 AGACCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACG-CTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * **
26192 AGTCCTCAAAGAGCGGGACGTCTTTTCTTTTAAAGCCTACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACG-CTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C
* * *
26252 AGTCCTCAAAGAGCGGGATGCATTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGC-TTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
*
26311 AGTCCTCAAAGAGCGGGACGCATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGC-TTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
26370 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACG-CTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * *
26429 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCTACACAAGTTGGTGGCACCTTTT
1 AGTCCTCAAAGAGCAGGACGC-TTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACC-TTC
* * * * **
26490 AGTCCCCAAAGAGCAGGACCCCTTTC---GAAA-CCCACACAAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACGCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTC
* * ** * **
26545 AGTCCCCAAAGAGCAGGAC-C---CCTTTCGAAGCCTACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C
* * *
26600 AGTCCTCAAAGAGCAGGACAC----CTTTCAAAGCCCACACAAGTTGATGG------C
1 AGTCCTCAAAGAGCAGGACGCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
26648 A-TCCTCAAAGAGCAGGACAC----CTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTC
* * * **
26702 AGTCC-CAATGAGCAGGA--C--TCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C
* * * * * *
26756 AATCCTCAAAGAGCAGGACAC----CTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACGCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTC
*
26811 AGTCCTCAAAGAACAGGA
1 AGTCCTCAAAGAGCAGGA
26829 TACGCTTTAT
Statistics
Matches: 613, Mismatches: 55, Indels: 62
0.84 0.08 0.08
Matches are distributed among these distances:
47 42 0.07
48 2 0.00
51 1 0.00
52 1 0.00
53 2 0.00
54 51 0.08
55 156 0.25
56 7 0.01
57 1 0.00
58 1 0.00
59 196 0.32
60 111 0.18
61 42 0.07
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (58 bp):
AGTCCTCAAAGAGCAGGACGCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:26237 original size:119 final size:118
Alignment explanation
Indices: 26072--26822 Score: 745
Period size: 119 Copynumber: 6.6 Consensus size: 118
26062 TCCGCTTTTT
* * *
26072 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGAC
1 AGTCCTCAAAGAGCAGGACG-CTT-TTCTTTTAAAGCCTACACAAGTTGGTGGCATTTTCCAGTC
26137 CTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
64 CTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
*
26192 AGTCCTCAAAGAGCGGGACGTCTTTTCTTTTAAAGCCTACACAAGTTGGTGGCATTTTCCAGTCC
1 AGTCCTCAAAGAGCAGGACG-CTTTTCTTTTAAAGCCTACACAAGTTGGTGGCATTTTCCAGTCC
* * *
26257 TCAAAGAGCGGGATGCATTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTC
65 TCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * **
26311 AGTCCTCAAAGAGCGGGACGCATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCC
1 AGTCCTCAAAGAGCAGGACGC-TTTTCTTTTAAAGCCTACACAAGTTGGTGGCATTTTCCAGTCC
*
26375 TCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTC
65 TCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
*
26429 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCTACACAAGTTGGTGGCACCTTTT--AG
1 AGTCCTCAAAGAGCAGGACGC-TTTTCTTTT-AAAGCCTACACAAGTTGGTGGCA--TTTTCCAG
* * * * **
26492 TCCCCAAAGAGCAGGAC-CCCTTTC---GAAA-CCCACACAAGTTGGTGGCATTTTTC
62 TCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTC
* * **
26545 AGTCCCCAAAGAGCAGGAC-C---CCTTTCGAAGCCTACACAAGTTGGTGGCATTTTCCAGTCCT
1 AGTCCTCAAAGAGCAGGACGCTTTTCTTTTAAAGCCTACACAAGTTGGTGGCATTTTCCAGTCCT
* * *
26606 CAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGATGG------C
66 CAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * * *
26648 A-TCCTCAAAGAGCAGGACAC----CTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCC
1 AGTCCTCAAAGAGCAGGACGCTTTTCTTTTAAAGCCTACACAAGTTGGTGGCA-TTTTCCAGTCC
* * * **
26707 -CAATGAGCAGGACTCC-TTTC----AAAGCCCACACAAGTTGGTGGCATTTTCC
65 TCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C
* * * * * *
26756 AATCCTCAAAGAGCAGGACAC----CTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TAGTCC
1 AGTCCTCAAAGAGCAGGACGCTTTTCTTTTAAAGCCTACACAAGTTGGTGGCA-TTTTCCAGTCC
26816 TCAAAGA
65 TCAAAGA
26823 ACAGGATACG
Statistics
Matches: 563, Mismatches: 48, Indels: 50
0.85 0.07 0.08
Matches are distributed among these distances:
101 38 0.07
102 46 0.08
103 6 0.01
108 6 0.01
109 56 0.10
110 65 0.12
111 6 0.01
115 19 0.03
116 23 0.04
118 87 0.15
119 170 0.30
120 39 0.07
121 2 0.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (118 bp):
AGTCCTCAAAGAGCAGGACGCTTTTCTTTTAAAGCCTACACAAGTTGGTGGCATTTTCCAGTCCT
CAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:26399 original size:178 final size:176
Alignment explanation
Indices: 26072--26828 Score: 774
Period size: 178 Copynumber: 4.4 Consensus size: 176
26062 TCCGCTTTTT
* * ** *
26072 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGAC
1 AGTCCTCAAAGAGCAGGATGCATT-TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTC
* *
26137 CTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAA
64 CTCAAAGAGCAGGAC-CATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAA
* * *
26202 GAGCGGGACGTCTTTTCTTTTAAAGCCTACACAAGTTGGTGGCATTTTCC
128 GAGCAGGACG-CCTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
26252 AGTCCTCAAAGAGCGGGATGCATTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCT
1 AGTCCTCAAAGAGCAGGATGCATTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCT
*
26317 CAAAGAGCGGGACGCATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGA
66 CAAAGAGCAGGAC-CATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGA
* * **
26382 GCGGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTT-C
130 GCAGGACGCC-TTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* * * *
26429 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCTACACAAGTTGGTGGCACCTTTTAGTC
1 AGTCCTCAAAGAGCAGGATGCATTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACC-TTCAGTC
* ** * ** *
26494 CCCAAAGAGCAGGACCCCTTTC---GAAA-CCCACACAAGTTGGTGGCATTTTTCAGTCCCCAAA
64 CTCAAAGAGCAGGACCATTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTCAGTCCTCAAA
** *
26555 GAGCAGGAC-CC---CTTTCGAAGCCTACACAAGTTGGTGGCATTTTCC
128 GAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
26600 AGTCCTCAAAGAGCAGGA--CA---CCTTTCAAAGCCCACACAAGTTGATGG------CA-TCCT
1 AGTCCTCAAAGAGCAGGATGCATTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCT
* * *
26653 CAAAGAGCAGGA-CA---CCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC-CAATGA
66 CAAAGAGCAGGACCATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGA
*
26713 GCAGGACTCCTTTC----AAAGCCCACACAAGTTGGTGGCATTTTCC
130 GCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* * * * *
26756 AATCCTCAAAGAGCAGGA--CA---CCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCC
1 AGTCCTCAAAGAGCAGGATGCATTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCAGTCC
*
26816 TCAAAGAACAGGA
65 TCAAAGAGCAGGA
26829 TACGCTTTAT
Statistics
Matches: 501, Mismatches: 54, Indels: 60
0.81 0.09 0.10
Matches are distributed among these distances:
153 1 0.00
156 87 0.17
157 44 0.09
158 1 0.00
160 1 0.00
163 1 0.00
164 15 0.03
165 19 0.04
166 4 0.01
169 1 0.00
170 26 0.05
171 19 0.04
174 21 0.04
175 23 0.05
177 31 0.06
178 137 0.27
179 49 0.10
180 21 0.04
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (176 bp):
AGTCCTCAAAGAGCAGGATGCATTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCT
CAAAGAGCAGGACCATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAG
CAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:26552 original size:55 final size:55
Alignment explanation
Indices: 26067--26828 Score: 579
Period size: 55 Copynumber: 13.4 Consensus size: 55
26057 CTCCTTCCGC
*
26067 TTTTT-AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGA---C--C-CCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
26127 TTTTCCAGACCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGAC-CC----CTTTCAAAGCCCACACAAGTTGGTGGCA
** * * * *
26187 -CCTTCAGTCCTCAAAGAGCGGGACGTCTTTTCTTTTAAAGCCTACACAAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGAC--C---CCTTTCAAAGCCCACACAAGTTGGTGGCA
* * ** * *
26246 TTTTCCAGTCCTCAAAGAGCGGGATGCATTTTCTTTTAAAGCCCACCCAAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGA--C---CCCTTTCAAAGCCCACACAAGTTGGTGGCA
** * * *
26306 -CCTTCAGTCCTCAAAGAGCGGGACGCATTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGAC-C----CCTTTCAAAGCCCACACAAGTTGGTGGCA
** * * *
26365 -CCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGAC-CC----CTTTCAAAGCCCACACAAGTTGGTGGCA
** * * *
26424 -CCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCTACACAAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGA--C----CCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
26484 CCTTTT-AGTCCCCAAAGAGCAGGACCCCTTTCGAAA-CCCACACAAGTTGGTGGCA
1 -TTTTTCAGTCCTCAAAGAGCAGGACCCCTTTC-AAAGCCCACACAAGTTGGTGGCA
* * *
26539 TTTTTCAGTCCCCAAAGAGCAGGACCCCTTTCGAAGCCTACACAAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGACCCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
26594 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGATGG--
1 TTTTTCAGTCCTCAAAGAGCAGGACCCCTTTCAAAGCCCACACAAGTTGGTGGCA
*
26647 -----CA-TCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGACCCCT-TTCAAAGCCCACACAAGTTGGTGGCA
** * *
26696 CCTTTCAGTCC-CAATGAGCAGGACTCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGACCCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
26750 TTTTCCAATCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACGAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGACCCCTTTCAAAGCCCACACAAGTTGGTGGCA
*
26805 CTTTTT-AGTCCTCAAAGAACAGGA
1 -TTTTTCAGTCCTCAAAGAGCAGGA
26829 TACGCTTTAT
Statistics
Matches: 598, Mismatches: 61, Indels: 91
0.80 0.08 0.12
Matches are distributed among these distances:
47 41 0.07
48 4 0.01
53 2 0.00
54 53 0.09
55 173 0.29
56 8 0.01
57 2 0.00
58 1 0.00
59 171 0.29
60 104 0.17
61 34 0.06
62 3 0.01
63 1 0.00
64 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (55 bp):
TTTTTCAGTCCTCAAAGAGCAGGACCCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:26677 original size:47 final size:47
Alignment explanation
Indices: 26602--26804 Score: 194
Period size: 47 Copynumber: 4.0 Consensus size: 47
26592 CATTTTCCAG
26602 TCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGATGGCA
1 TCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGATGGCA
*
26649 TCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 TCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGATGGCA
* *
26696 -CCTTTCAGTCCCAATGAGCAGGACTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAA
1 TCC--TCA-----AA-GAGCAGGACACCTTTCAAAGCCCACACAAGTTGATGG-------C-A
* *
26758 TCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACGAGTTGGTGGCA
1 TCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGATGGCA
26805 CTTTTTAGTC
Statistics
Matches: 133, Mismatches: 4, Indels: 38
0.76 0.02 0.22
Matches are distributed among these distances:
46 2 0.02
47 44 0.33
48 6 0.05
53 4 0.03
54 33 0.25
55 35 0.26
56 2 0.02
61 4 0.03
62 1 0.01
63 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (47 bp):
TCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGATGGCA
Found at i:27600 original size:21 final size:21
Alignment explanation
Indices: 27574--27650 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
27564 AAAAAATTCA
27574 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
27595 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
27616 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
27637 AATGTATCGATACA
1 AATGTATCGATACA
27651 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:28644 original size:15 final size:15
Alignment explanation
Indices: 28624--28654 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28614 ATTTCGTTTG
*
28624 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
28639 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
28654 G
1 G
28655 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:30487 original size:21 final size:21
Alignment explanation
Indices: 30458--30502 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
30448 AAGTTTTCAT
*
30458 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
30478 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
30500 TTT
1 TTT
30503 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:32714 original size:13 final size:13
Alignment explanation
Indices: 32696--32721 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32686 CAATTTTTTG
32696 TGTATCGATACAT
1 TGTATCGATACAT
32709 TGTATCGATACAT
1 TGTATCGATACAT
32722 ACTTGCTGTA
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:33702 original size:27 final size:29
Alignment explanation
Indices: 33672--33746 Score: 102
Period size: 27 Copynumber: 2.7 Consensus size: 29
33662 TTTCTTCACA
33672 ATCGGGGATACTCCAACCCCATTA-AT-C
1 ATCGGGGATACTCCAACCCCATTATATCC
* *
33699 ATCGGGGATACTCCAACCCCGTTATTTCC
1 ATCGGGGATACTCCAACCCCATTATATCC
*
33728 A-AGGGGATACTCCAACCCC
1 ATCGGGGATACTCCAACCCC
33747 GGTTTTATTG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 23 0.53
28 18 0.42
29 2 0.05
ACGTcount: A:0.27, C:0.35, G:0.17, T:0.21
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCCATTATATCC
Found at i:33800 original size:52 final size:51
Alignment explanation
Indices: 33732--33900 Score: 189
Period size: 52 Copynumber: 3.3 Consensus size: 51
33722 ATTTCCAAGG
33732 GGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATCGA
1 GGATACTCCAACCCCGGTTTTATT-CTAAAACACTAATTTTTCCACAATCGA
* * ** *
33784 GGATACTCCAACCCCGGTTTTATTTTCAAAACGCTAA-TTTTCCTTTAATCGG
1 GGATACTCCAACCCCGGTTTTATTCT-AAAACACTAATTTTTCC-ACAATCGA
* * * * *
33836 GGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATCGA
1 GGATACTCCAACCCCGGTTTTA-TT-CTAAAACACTAATTTTTCCACAATCGA
33888 GGATACTCCAACC
1 GGATACTCCAACC
33901 TTGTTATTTC
Statistics
Matches: 96, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
51 7 0.07
52 75 0.78
53 10 0.10
54 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (51 bp):
GGATACTCCAACCCCGGTTTTATTCTAAAACACTAATTTTTCCACAATCGA
Found at i:33883 original size:104 final size:103
Alignment explanation
Indices: 33555--33900 Score: 324
Period size: 104 Copynumber: 3.3 Consensus size: 103
33545 TTGAGTTTCT
* * * * *
33555 CAATTTTCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAATACTAATTTT-CTATAA
1 CAATTTTTCACAATCGAGGATACTCCAACCCCG-TTTTATTTTCAAAACACTAATTTTCCTTTAA
33619 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACAC
65 TCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACAC
* * * ** * * * * ** *
33659 CAATTTCTTCACAATCGGGGATACTCCAACCCC-ATTAATCATCGGGGATACTCCAA--CCCCGT
1 CAATTT-TTCACAATCGAGGATACTCCAACCCCGTTTTATTTTC---AAAACACTAATTTTCCTT
* * * * *
33721 TATTTCCAAGGGGATACTCCAACCCCGGTTTTA-TTGCTAAAACAC
62 TA-AT-C--GGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
* *
33766 TAATTTTTCCACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACGCTAATTTTCCTTTA
1 CAATTTTT-CACAATCGAGGATACTCCAACCCC-GTTTTATTTTCAAAACACTAATTTTCCTTTA
*
33831 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATAC
64 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
33871 CAATTTTTCACAATCGAGGATACTCCAACC
1 CAATTTTTCACAATCGAGGATACTCCAACC
33901 TTGTTATTTC
Statistics
Matches: 185, Mismatches: 42, Indels: 30
0.72 0.16 0.12
Matches are distributed among these distances:
103 6 0.03
104 50 0.27
105 41 0.22
106 15 0.08
107 37 0.20
108 8 0.04
109 28 0.15
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.32
Consensus pattern (103 bp):
CAATTTTTCACAATCGAGGATACTCCAACCCCGTTTTATTTTCAAAACACTAATTTTCCTTTAAT
CGGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
Found at i:33925 original size:212 final size:212
Alignment explanation
Indices: 33558--34010 Score: 651
Period size: 212 Copynumber: 2.1 Consensus size: 212
33548 AGTTTCTCAA
* * *
33558 TTTTCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAATACTAATTTTCTATAATCGG
1 TTTTCCACAATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGG
*
33623 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAA
66 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
* * *
33688 CCCCATTAATCATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGGTTTT
131 CCCCATTAATCATCGGGGATACTCCAACCCCGGTACTTCCAAGGGGATACTCCAACCCCGGCTTT
*
33753 ATTGCTAAAACACTAAT
196 ATTCCTAAAACACTAAT
* * *
33770 TTTTCCACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACGCTAATTTTCCTTTAATCG
1 TTTTCCACAATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCG
*
33835 GGGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCA
65 GGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCA
*** * *
33898 ACCTTGTTATTTCATCGGGGATACTCCAACCCCGGTACTTCCGAGGGGATACTCCAACCCCGGCT
130 ACCCCATTA-ATCATCGGGGATACTCCAACCCCGGTACTTCCAAGGGGATACTCCAACCCCGGCT
* * *
33963 TTATTCCTAAAATATTGAT
194 TTATTCCTAAAACACTAAT
* * * *
33982 TTCT-CATAATTGGGGATACTCCAACCCCG
1 TTTTCCACAATCGAGGATACTCCAACCCCG
34011 TTATTTTCGA
Statistics
Matches: 215, Mismatches: 24, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
211 48 0.22
212 131 0.61
213 36 0.17
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (212 bp):
TTTTCCACAATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGG
GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
CCCCATTAATCATCGGGGATACTCCAACCCCGGTACTTCCAAGGGGATACTCCAACCCCGGCTTT
ATTCCTAAAACACTAAT
Found at i:34025 original size:107 final size:107
Alignment explanation
Indices: 33621--34033 Score: 285
Period size: 107 Copynumber: 3.9 Consensus size: 107
33611 TTCTATAATC
* * * *
33621 GGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACCCCGACTTTATTTCC-AAAAATACCAATTTC-TCACAATCGAGGATACTCC
* * * * *
33686 AACCCCATTA-ATCATCGGGGATACTCCAACCCCGTTATTTCCAA
64 AACCCCGTTATTTCA-CGGGGATACTCCAACCCCGGTACTTCCGA
** * * * * *
33730 GGGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAATTTTTCCACAATCGAGGATACTCCA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCT-CACAATCGAGGATACTCCA
* * * ** ** *
33794 ACCCCGGTTTTATTTTCA-----AAACGCTAATTTTCCTTTA-AT-C--
65 ACCCC-G--TTA-TTTCACGGGGATACTCCAA--CCCCGGTACTTCCGA
* * *
33834 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
**
33899 CCTTGTTATTTCATCGGGGATACTCCAACCCCGGTACTTCCGA
66 CCCCGTTATTTCA-CGGGGATACTCCAACCCCGGTACTTCCGA
* * *** * * *
33942 GGGGATACTCCAACCCCGGCTTTA-TTCCTAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
34006 CCCCGTTATTTTCGA-GGGGATACTCCAA
66 CCCCGTTA-TTTC-ACGGGGATACTCCAA
34034 TCCTGATTTT
Statistics
Matches: 238, Mismatches: 45, Indels: 44
0.73 0.14 0.13
Matches are distributed among these distances:
100 5 0.02
101 3 0.01
103 1 0.00
104 48 0.20
105 17 0.07
106 15 0.06
107 87 0.37
108 33 0.14
109 23 0.10
110 3 0.01
112 3 0.01
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTCACGGGGATACTCCAACCCCGGTACTTCCGA
Found at i:35231 original size:20 final size:20
Alignment explanation
Indices: 35208--35257 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
35198 TAAAGAAAAT
*
35208 TGTATCGATACATTTAGAAA
1 TGTATCGATACATTTACAAA
* **
35228 TGTATCGTTACATTTACTTA
1 TGTATCGATACATTTACAAA
35248 TGTATCGATA
1 TGTATCGATA
35258 TAATTTTTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTTACAAA
Found at i:35830 original size:2 final size:2
Alignment explanation
Indices: 35823--35850 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35813 TATAAACAAC
35823 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
35851 TGCGTAAATA
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:37025 original size:27 final size:27
Alignment explanation
Indices: 36974--37050 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 27
36964 TATATGGAAT
*
36974 AATATT-TTTATTAAAATAATAAATAATA
1 AATATTATTTATTATAA-AAT-AATAATA
37002 AATATTATTTATTATAAAATAATAATA
1 AATATTATTTATTATAAAATAATAATA
*
37029 AATATTATATATTATTAAAATA
1 AATATTATTTATTA-TAAAATA
37051 TAAATTTGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
27 20 0.44
28 16 0.36
29 9 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
AATATTATTTATTATAAAATAATAATA
Found at i:42113 original size:14 final size:14
Alignment explanation
Indices: 42096--42146 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
42086 AAATATTTGA
42096 ATATATAAAAATTT
1 ATATATAAAAATTT
42110 ATATA-AATTAAATTATT
1 ATATATAA--AAA-T-TT
42127 AATATATAAAAATTT
1 -ATATATAAAAATTT
42142 ATATA
1 ATATA
42147 AATATATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
13 2 0.06
14 10 0.32
15 5 0.16
16 2 0.06
17 5 0.16
18 5 0.16
19 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATATAAAAATTT
Found at i:42136 original size:32 final size:34
Alignment explanation
Indices: 42065--42169 Score: 126
Period size: 32 Copynumber: 3.1 Consensus size: 34
42055 AAGTTTTAAG
*
42065 ATAAAAATATAATATAAATAAAAATATTTGAATAT
1 ATAAAAAT-TTATATAAATAAAAATATTTGAATAT
* *
42100 ATAAAAATTTATATAAATTAAATTA-TT-AATAT
1 ATAAAAATTTATATAAATAAAAATATTTGAATAT
* *
42132 ATAAAAATTTATATAAATATATAATATTTTAA-AT
1 ATAAAAATTTATATAAATA-AAAATATTTGAATAT
42166 ATAA
1 ATAA
42170 TTATAATATT
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
32 23 0.38
33 6 0.10
34 22 0.36
35 10 0.16
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (34 bp):
ATAAAAATTTATATAAATAAAAATATTTGAATAT
Found at i:42167 original size:22 final size:22
Alignment explanation
Indices: 42075--42189 Score: 73
Period size: 20 Copynumber: 5.4 Consensus size: 22
42065 ATAAAAATAT
*
42075 AATATAAATA-AAAAT-ATTTGA
1 AATATAAATATATAATAATTT-A
* * *
42096 ATATATAAAAATTTATATAAATTA
1 A-ATATAAATATATA-ATAATTTA
* *
42120 AATTATTAATATATAAAAATTT-
1 AA-TATAAATATATAATAATTTA
*
42142 -ATATAAATATATAATATTTTA
1 AATATAAATATATAATAATTTA
42163 AATAT-AAT-TATAAT-ATTTA
1 AATATAAATATATAATAATTTA
*
42182 AAAATAAA
1 AATATAAA
42190 AAATTATTAT
Statistics
Matches: 72, Mismatches: 14, Indels: 17
0.70 0.14 0.17
Matches are distributed among these distances:
19 8 0.11
20 24 0.33
21 5 0.07
22 12 0.17
23 7 0.10
24 13 0.18
25 3 0.04
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (22 bp):
AATATAAATATATAATAATTTA
Found at i:45839 original size:26 final size:26
Alignment explanation
Indices: 45786--45839 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
45776 TTTTTCTTTC
* * **
45786 TTTCTTTTTCTTTCCATTTTTTCCAT
1 TTTCTTTCTCTCTCCATTCCTTCCAT
*
45812 TTTCTTTCTCTCTCCATTCCTTCTAT
1 TTTCTTTCTCTCTCCATTCCTTCCAT
45838 TT
1 TT
45840 CAACCTCACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTCTTTCTCTCTCCATTCCTTCCAT
Found at i:46525 original size:21 final size:22
Alignment explanation
Indices: 46499--46540 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
46489 TATAATTATT
46499 TTTATAAAATAATA-TTATAAC
1 TTTATAAAATAATATTTATAAC
**
46520 TTTATAATTTAATATTTATAA
1 TTTATAAAATAATATTTATAA
46541 ATATTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTATAAAATAATATTTATAAC
Found at i:47775 original size:4 final size:4
Alignment explanation
Indices: 47766--47796 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
47756 TCTGCCGGCC
47766 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
47797 TGTAATTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:54254 original size:14 final size:14
Alignment explanation
Indices: 54235--54262 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54225 ACCTTTTGGC
54235 AGGAGTTTATCAAT
1 AGGAGTTTATCAAT
54249 AGGAGTTTATCAAT
1 AGGAGTTTATCAAT
54263 CATTAAGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
AGGAGTTTATCAAT
Found at i:60685 original size:209 final size:209
Alignment explanation
Indices: 60325--60742 Score: 746
Period size: 209 Copynumber: 2.0 Consensus size: 209
60315 ACTTTACAAA
60325 TTATATTACTTTCAGATATGATTAATTTTAAGTTTAAAAATTACATATAATGTGAGTTTACTTAA
1 TTATATTACTTTCAGATATGATTAATTTTAAGTTTAAAAATTACATATAATGTGAGTTTACTTAA
**
60390 TTTTTCTCATAATTAAGATTGTTAAGTTTTGATATCTGGTTATTGAAACTAAAAGTATAGTATTC
66 TTTTTCTCATAATTAAGATTGTTAAGTTTTGATATCTGACTATTGAAACTAAAAGTATAGTATTC
*
60455 TATCAACAAATCACATAACTGTTGACAAATTTATTGAAAATTTACAAAAATGTTAAGTAATAAAA
131 TATCAACAAATCACATAACTGTTGACAAATTTATTGAAAATTTACAAAAACGTTAAGTAATAAAA
*
60520 CTTTTATATACTTT
196 CTTTTATACACTTT
* *
60534 TTATATTACTTTCAGATATGATTAATTTTAGGTTTAAAAATTACATATGATGTGAGTTTACTTAA
1 TTATATTACTTTCAGATATGATTAATTTTAAGTTTAAAAATTACATATAATGTGAGTTTACTTAA
* * *
60599 TTTTTTTTATAATTAAGCTTGTTAAGTTTTGATATCTGACTATTGAAACTAAAAGTATAGTATTC
66 TTTTTCTCATAATTAAGATTGTTAAGTTTTGATATCTGACTATTGAAACTAAAAGTATAGTATTC
*
60664 TATCAACAAATCACATAACTGTTGACAAATTTATTGAAAATTTACAAAAACGTTAGGTAATAAAA
131 TATCAACAAATCACATAACTGTTGACAAATTTATTGAAAATTTACAAAAACGTTAAGTAATAAAA
60729 CTTTTATACACTTT
196 CTTTTATACACTTT
60743 AATATTAAAT
Statistics
Matches: 199, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
209 199 1.00
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (209 bp):
TTATATTACTTTCAGATATGATTAATTTTAAGTTTAAAAATTACATATAATGTGAGTTTACTTAA
TTTTTCTCATAATTAAGATTGTTAAGTTTTGATATCTGACTATTGAAACTAAAAGTATAGTATTC
TATCAACAAATCACATAACTGTTGACAAATTTATTGAAAATTTACAAAAACGTTAAGTAATAAAA
CTTTTATACACTTT
Found at i:60772 original size:14 final size:14
Alignment explanation
Indices: 60755--60782 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
60745 TATTAAATCC
60755 TTAATAGATAACAT
1 TTAATAGATAACAT
60769 TTAATAGATAACAT
1 TTAATAGATAACAT
60783 GACAACCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
TTAATAGATAACAT
Found at i:64952 original size:6 final size:6
Alignment explanation
Indices: 64941--64971 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
64931 TTCGTCTCTT
64941 AGGCTC AGGCTC AGGCTC AGGCTC AGGCTC A
1 AGGCTC AGGCTC AGGCTC AGGCTC AGGCTC A
64972 ACTCATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.32, G:0.32, T:0.16
Consensus pattern (6 bp):
AGGCTC
Found at i:69443 original size:2 final size:2
Alignment explanation
Indices: 69436--69471 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
69426 ATGCAAATAC
69436 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
69472 GTTCGTATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70563 original size:2 final size:2
Alignment explanation
Indices: 70556--70594 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
70546 ATACATGTGA
70556 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
70595 AAAGGAGTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:71086 original size:20 final size:20
Alignment explanation
Indices: 71038--71108 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
71028 CATAAGTAAA
* *
71038 TGTATCGATACATTTACTATT
1 TGTATCGATAAATTTATTA-T
* *
71059 TATATCGATAAATTTTTTAT
1 TGTATCGATAAATTTATTAT
* * * *
71079 TGTATCGATATATTTCTCAA
1 TGTATCGATAAATTTATTAT
71099 TGTATCGATA
1 TGTATCGATA
71109 CATTCAAGCA
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.48
Consensus pattern (20 bp):
TGTATCGATAAATTTATTAT
Done.