Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold412
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: 4645160
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 1 of 32
Found at i:731 original size:37 final size:40
Alignment explanation
Indices: 643--742 Score: 143
Period size: 37 Copynumber: 2.5 Consensus size: 40
633 AATTTTAAAT
*
643 GATAATAAAGTTTTCTAAAATAATTATCCAAAAACAAAAAA
1 GATAATATAGTTTTCTAAAATAATTATCC-AAAACAAAAAA
* *
684 GATAATATAGTTTTCTAAAATAATTA-CC-CAAC-AGAAA
1 GATAATATAGTTTTCTAAAATAATTATCCAAAACAAAAAA
721 GATAATATAGTTTTCTAAAATA
1 GATAATATAGTTTTCTAAAATA
743 TTTTAAAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
37 26 0.46
38 3 0.05
40 2 0.04
41 25 0.45
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (40 bp):
GATAATATAGTTTTCTAAAATAATTATCCAAAACAAAAAA
Found at i:2138 original size:5 final size:5
Alignment explanation
Indices: 2128--2170 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
2118 TTCTAAACAT
* **
2128 ATATA ATATA ATATA ATGTA ATATA ATATA GGATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATA
2171 CGCAGTAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:2713 original size:2 final size:2
Alignment explanation
Indices: 2700--2735 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2690 CACTGTCATG
*
2700 TC TC TA TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2736 ATAATTGTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4407 original size:2 final size:2
Alignment explanation
Indices: 4400--4437 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
4390 CATGGAGATA
*
4400 AT AT AT AT CT 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
4438 CTCCAATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5769 original size:23 final size:23
Alignment explanation
Indices: 5734--5858 Score: 78
Period size: 24 Copynumber: 5.3 Consensus size: 23
5724 CATCATCATC
*
5734 AATATAATATATAACTTTTATATA
1 AATAAAAT-TATAACTTTTATATA
* * *
5758 GATAAAATTATAAATTATCCT-TTTA
1 AATAAAATTATAACTT-T--TATATA
* *
5783 AAT-AATTTATAATTTTTATATA
1 AATAAAATTATAACTTTTATATA
*
5805 AATAAAATTATAAGCCTTTTTTATA
1 AATAAAATTATAA--CTTTTATATA
*
5830 AAT--AATTCATAACTTTTACATA
1 AATAAAATT-ATAACTTTTATATA
*
5852 GATAAAA
1 AATAAAA
5859 CTGTAAATTT
Statistics
Matches: 77, Mismatches: 14, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
21 1 0.01
22 16 0.21
23 20 0.26
24 23 0.30
25 16 0.21
26 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.44
Consensus pattern (23 bp):
AATAAAATTATAACTTTTATATA
Found at i:5794 original size:47 final size:45
Alignment explanation
Indices: 5737--5880 Score: 146
Period size: 47 Copynumber: 3.1 Consensus size: 45
5727 CATCATCAAT
*
5737 ATAATATATAACTTTTATATAGATAAAATTATAAATTATCCTTT-TAA
1 ATAATTTATAACTTTTATATAGATAAAATTATAAATT-T--TTTATAA
* * *
5784 ATAATTTATAATTTTTATATAAATAAAATTATAAGCCTTTTTTATAA
1 ATAATTTATAACTTTTATATAGATAAAATTATAA--ATTTTTTATAA
* * * * *
5831 ATAATTCATAACTTTTACATAGATAAAACTGTAAATTTCTTTATTA
1 ATAATTTATAACTTTTATATAGATAAAATTATAAATTT-TTTATAA
5877 ATAA
1 ATAA
5881 GATTACACAA
Statistics
Matches: 81, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
45 3 0.04
46 13 0.16
47 62 0.77
48 1 0.01
49 2 0.02
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (45 bp):
ATAATTTATAACTTTTATATAGATAAAATTATAAATTTTTTATAA
Found at i:5809 original size:22 final size:22
Alignment explanation
Indices: 5781--5856 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
5771 ATTATCCTTT
5781 TAAATAATTTATAATTTTTATA
1 TAAATAATTTATAATTTTTATA
*
5803 TAAATAAAATTATAAGCCTTTTT-TA
1 TAAAT-AATTTATAA---TTTTTATA
* * *
5828 TAAATAATTCATAACTTTTACA
1 TAAATAATTTATAATTTTTATA
*
5850 TAGATAA
1 TAAATAA
5857 AACTGTAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
21 4 0.09
22 12 0.28
23 8 0.19
24 7 0.16
25 7 0.16
26 5 0.12
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.45
Consensus pattern (22 bp):
TAAATAATTTATAATTTTTATA
Found at i:7304 original size:6 final size:6
Alignment explanation
Indices: 7293--7318 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
7283 GAGAAGTGAT
7293 AGAAAG AGAAAG AGAAAG AGAAAG AG
1 AGAAAG AGAAAG AGAAAG AGAAAG AG
7319 TGCTGCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (6 bp):
AGAAAG
Found at i:7618 original size:12 final size:12
Alignment explanation
Indices: 7601--7643 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
7591 ATTAACAATT
*
7601 GGGAAAGGGAAA
1 GGGAAAAGGAAA
7613 GGGAAAAGGAAA
1 GGGAAAAGGAAA
* *
7625 AGGAAAAGCAAA
1 GGGAAAAGGAAA
*
7637 GAGAAAA
1 GGGAAAA
7644 AAAGATAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.60, C:0.02, G:0.37, T:0.00
Consensus pattern (12 bp):
GGGAAAAGGAAA
Found at i:8067 original size:2 final size:2
Alignment explanation
Indices: 8060--8091 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8050 AATAAAAACT
8060 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
8092 CACCCTATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11096 original size:2 final size:2
Alignment explanation
Indices: 11089--11122 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
11079 CCTTTGAAAC
11089 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
11123 TAGTATTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12615 original size:25 final size:25
Alignment explanation
Indices: 12565--12617 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
12555 TATTAAAAAA
* *
12565 ATTTTAAAAATTATAAATAATTTTT
1 ATTTTAAAAAATATAAATAATATTT
*
12590 ATTTTAATAAAATATTAA-AATATTT
1 ATTTTAA-AAAATATAAATAATATTT
12615 ATT
1 ATT
12618 AATAATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTTTAAAAAATATAAATAATATTT
Found at i:12627 original size:23 final size:24
Alignment explanation
Indices: 12593--12671 Score: 67
Period size: 23 Copynumber: 3.4 Consensus size: 24
12583 AATTTTTATT
* *
12593 TTAATAAAATATTAAA-ATATTTA
1 TTAATAATATATTAAAGATATATA
*
12616 TTAATAATATA-TAAAGTTATATA
1 TTAATAATATATTAAAGATATATA
* *
12639 TTATTAATAAATTAAATG-TATATAA
1 TTAATAATATATTAAA-GATATAT-A
12664 TT-ATAATA
1 TTAATAATA
12672 ATACGAGAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
22 4 0.09
23 24 0.52
24 14 0.30
25 4 0.09
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (24 bp):
TTAATAATATATTAAAGATATATA
Found at i:13305 original size:1 final size:1
Alignment explanation
Indices: 13299--13325 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
13289 TCTTTTCTCT
13299 CCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCC
13326 GGTTTTTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:16189 original size:20 final size:20
Alignment explanation
Indices: 16164--16204 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
16154 TATGATTCAT
16164 TTACAAGGCATAGGATGAAG
1 TTACAAGGCATAGGATGAAG
16184 TTACAAGGCATAGGATGAAG
1 TTACAAGGCATAGGATGAAG
16204 T
1 T
16205 GTCATGCGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.10, G:0.29, T:0.22
Consensus pattern (20 bp):
TTACAAGGCATAGGATGAAG
Found at i:19699 original size:33 final size:35
Alignment explanation
Indices: 19652--19716 Score: 91
Period size: 33 Copynumber: 1.9 Consensus size: 35
19642 TAAGATATCA
19652 TAAAAATAATATATAAATTA-ATTA-AAATATAATT
1 TAAAAATAATATATAAA-TACATTATAAATATAATT
*
19686 TAAAAA-ATTATATAAATACATTATAAATATA
1 TAAAAATAATATATAAATACATTATAAATATA
19717 TAAATATGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 2 0.07
33 13 0.46
34 13 0.46
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (35 bp):
TAAAAATAATATATAAATACATTATAAATATAATT
Found at i:19774 original size:23 final size:23
Alignment explanation
Indices: 19726--19774 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
19716 ATAAATATGG
*
19726 TTAATTTTATATAAAATAAATTA
1 TTAATTTTATATAAAATAAATAA
19749 TTAATATTT-TATAAAATTAAA-AA
1 TTAAT-TTTATATAAAA-TAAATAA
19772 TTA
1 TTA
19775 TTTAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTAATTTTATATAAAATAAATAA
Found at i:21829 original size:87 final size:87
Alignment explanation
Indices: 21738--21943 Score: 251
Period size: 87 Copynumber: 2.4 Consensus size: 87
21728 GTGGAGTTGA
21738 AGTGTCTCCT-TCAAGATAGTGGGGATGGAGTTTCCCCAA-GAGCAAAATTGTACGAAGGAAAAT
1 AGTGTCTCCTCTCAA-ATAGTGGGGATGGAGTTTCCCCAAGGA-CAAAATTGTACGAAGGAAAAT
* *
21801 TTAATTTTTGAAGAATGAGATTGG
64 TTAATTTTTAAAGAACGAGATTGG
** * * *
21825 AGTGTC-CCTCTCAAAATAGTAAGGATGGTGTTTCCCCAAGGACAAATTTGTATGAAGGAAAATT
1 AGTGTCTCCTCTC-AAATAGTGGGGATGGAGTTTCCCCAAGGACAAAATTGTACGAAGGAAAATT
* *
21889 TAATTTTTAAAGAGCGAGGTTGG
65 TAATTTTTAAAGAACGAGATTGG
*
21912 AGTG--TCCTCTCGAAATAGTGGGGATAGAGTTT
1 AGTGTCTCCTCTC-AAATAGTGGGGATGGAGTTT
21944 TCCCGGATAT
Statistics
Matches: 101, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
86 25 0.25
87 72 0.71
88 4 0.04
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (87 bp):
AGTGTCTCCTCTCAAATAGTGGGGATGGAGTTTCCCCAAGGACAAAATTGTACGAAGGAAAATTT
AATTTTTAAAGAACGAGATTGG
Found at i:26475 original size:52 final size:52
Alignment explanation
Indices: 26394--26514 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
26384 GAAAAGTTGT
*
26394 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
* *
26446 CTGCATATATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
26498 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
26515 AAGATCAGTG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:26527 original size:52 final size:51
Alignment explanation
Indices: 26394--26534 Score: 203
Period size: 52 Copynumber: 2.7 Consensus size: 51
26384 GAAAAGTTGT
26394 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* * *
26446 CTGCATATATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
26498 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
26535 ATGTATCGAT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.03
52 78 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:26541 original size:13 final size:13
Alignment explanation
Indices: 26523--26547 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26513 CAAAGATCAG
26523 TGTATCGATACAA
1 TGTATCGATACAA
26536 TGTATCGATACA
1 TGTATCGATACA
26548 TTTGAGTAAT
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):
TGTATCGATACAA
Found at i:29332 original size:96 final size:97
Alignment explanation
Indices: 29207--29403 Score: 208
Period size: 97 Copynumber: 2.0 Consensus size: 97
29197 TTCGATTGAC
*
29207 AAACAAGATTGGAGTATCTCCTCGAAAGAATAGAGTTTG-AGT-GTCCTCGAGGACGA-AATTTA
1 AAACAAGATTGGAGTATCTCCTCGAAAGAAT-GAGGTTGAAGTAGTCC-CGAGGACGACAATTTA
* *
29269 AGCAAAAATAAGATTTAAAT-TGTGACAAGTTTAA
64 AGCAAAAACAAGATTTAAATCT-TAACAAGTTTAA
* * * * * *
29303 AAACAAGGTTGGAGTATC-CTTTC-AGAAGAATGGGGTTGAAGTATTCCCGATGATGACAATTTA
1 AAACAAGATTGGAGTATCTC-CTCGA-AAGAATGAGGTTGAAGTAGTCCCGAGGACGACAATTTA
* *
29366 GGCAAAAACCAGATTTAAATCTTAACAAGTTTAA
64 AGCAAAAACAAGATTTAAATCTTAACAAGTTTAA
29400 AAAC
1 AAAC
29404 GGGGTTAAAG
Statistics
Matches: 84, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
95 7 0.08
96 35 0.42
97 41 0.49
98 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (97 bp):
AAACAAGATTGGAGTATCTCCTCGAAAGAATGAGGTTGAAGTAGTCCCGAGGACGACAATTTAAG
CAAAAACAAGATTTAAATCTTAACAAGTTTAA
Found at i:31789 original size:19 final size:21
Alignment explanation
Indices: 31765--31817 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
31755 AGCGATACAT
31765 TGTATCGATACAA-CACT-TA
1 TGTATCGATACAATCACTGTA
* *
31784 TGTATCGATACAATTACTGTT
1 TGTATCGATACAATCACTGTA
31805 TGTATCGATACAA
1 TGTATCGATACAA
31818 ATTGTTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (21 bp):
TGTATCGATACAATCACTGTA
Found at i:35060 original size:16 final size:15
Alignment explanation
Indices: 35035--35065 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
35025 ATGTTAAACT
35035 CAATTGACTCGAATC
1 CAATTGACTCGAATC
35050 CAATATGACTCGAATC
1 CAAT-TGACTCGAATC
35066 TGATTAACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (15 bp):
CAATTGACTCGAATC
Found at i:35373 original size:2 final size:2
Alignment explanation
Indices: 35366--35391 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35356 TTAAATTTAT
35366 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
35392 AATAAGACTT
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:37169 original size:28 final size:27
Alignment explanation
Indices: 37115--37171 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
37105 CAAGTTTAAA
*
37115 AATGGGGTTAGAGTATCCCCTCAGAAT
1 AATGGGGTTAGAGTATCCCCTAAGAAT
*
37142 AATGGGAGTTGGAGTATCCCC-AATGAAT
1 AATGGG-GTTAGAGTATCCCCTAA-GAAT
37170 AA
1 AA
37172 AATTTCGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (27 bp):
AATGGGGTTAGAGTATCCCCTAAGAAT
Found at i:38871 original size:12 final size:13
Alignment explanation
Indices: 38846--38875 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
38836 GAAATGAGGA
38846 GTTTTTGTTGAGT
1 GTTTTTGTTGAGT
38859 GTTTTTGTT-AGT
1 GTTTTTGTTGAGT
38871 GTTTT
1 GTTTT
38876 GGCTAAGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.07, C:0.00, G:0.27, T:0.67
Consensus pattern (13 bp):
GTTTTTGTTGAGT
Found at i:40089 original size:13 final size:13
Alignment explanation
Indices: 40071--40104 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
40061 AATGAGAGGC
40071 GCGGGGGGCGGGG
1 GCGGGGGGCGGGG
*
40084 GCGGGGGGGGGGG
1 GCGGGGGGCGGGG
*
40097 GAGGGGGG
1 GCGGGGGG
40105 GTGTTTGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.03, C:0.09, G:0.88, T:0.00
Consensus pattern (13 bp):
GCGGGGGGCGGGG
Found at i:40294 original size:2 final size:2
Alignment explanation
Indices: 40287--40313 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40277 AGGAAGTAGA
40287 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
40314 ACAACAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40410 original size:44 final size:45
Alignment explanation
Indices: 40330--40419 Score: 164
Period size: 44 Copynumber: 2.0 Consensus size: 45
40320 ACATTTAAAT
40330 ATTTTATTCCAAATTCTGGGCAAAGTTTGCATCCGCACAACACAA
1 ATTTTATTCCAAATTCTGGGCAAAGTTTGCATCCGCACAACACAA
*
40375 ATTTTATTCCAAATTCT-GGCAAAGTTTGCATCCGCACTACACAA
1 ATTTTATTCCAAATTCTGGGCAAAGTTTGCATCCGCACAACACAA
40419 A
1 A
40420 ACTCTTGATA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 27 0.61
45 17 0.39
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.30
Consensus pattern (45 bp):
ATTTTATTCCAAATTCTGGGCAAAGTTTGCATCCGCACAACACAA
Found at i:42609 original size:2 final size:2
Alignment explanation
Indices: 42597--42633 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
42587 TAAGATCAGT
*
42597 TG TG CG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
42634 AATATATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.03, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:50567 original size:11 final size:11
Alignment explanation
Indices: 50551--50599 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
50541 TTTGGATTTA
50551 GGGTTTGGGTT
1 GGGTTTGGGTT
*
50562 GGGTTTGGGTC
1 GGGTTTGGGTT
50573 GGGTTTGGGGTT
1 GGGTTT-GGGTT
50585 GAGG-TTGAGGTT
1 G-GGTTTG-GGTT
50597 GGG
1 GGG
50600 GGCTTATGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 19 0.58
12 12 0.36
13 2 0.06
ACGTcount: A:0.04, C:0.02, G:0.57, T:0.37
Consensus pattern (11 bp):
GGGTTTGGGTT
Found at i:52808 original size:23 final size:22
Alignment explanation
Indices: 52737--52808 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 22
52727 TAATAAAATA
* *
52737 TAAATTTAAACTTAAA-CCCATT
1 TAAA-TTAAACTAAAAGCCCAAT
*
52759 TAAATCTAAACTAAAAGCTC-AT
1 TAAAT-TAAACTAAAAGCCCAAT
52781 CTAAACTTAAACTAAAAGCCCAAT
1 -TAAA-TTAAACTAAAAGCCCAAT
52805 TAAA
1 TAAA
52809 ACCAAAAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
21 1 0.02
22 14 0.34
23 23 0.56
24 3 0.07
ACGTcount: A:0.50, C:0.19, G:0.03, T:0.28
Consensus pattern (22 bp):
TAAATTAAACTAAAAGCCCAAT
Found at i:53093 original size:20 final size:20
Alignment explanation
Indices: 53064--53111 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
53054 ATCCTACCTA
* *
53064 AGATAGCAACTTGGCATAGT
1 AGATAACAACTTGGCAGAGT
53084 AGATAACAACTTGGCAGAGT
1 AGATAACAACTTGGCAGAGT
53104 AGATAACA
1 AGATAACA
53112 GCTTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.21
Consensus pattern (20 bp):
AGATAACAACTTGGCAGAGT
Found at i:58336 original size:52 final size:52
Alignment explanation
Indices: 58258--58459 Score: 246
Period size: 52 Copynumber: 3.9 Consensus size: 52
58248 ACTATCTTTG
*
58258 ATCGCCACCATGACATCATTATTATCAGTGACACCAAGTCACCCTAACTCTA
1 ATCGCCACCATGGCATCATTATTATCAGTGACACCAAGTCACCCTAACTCTA
* * *
58310 ATCGCCACCATGGTATCATTATTATCAGTGACACCAAGTCATCCTAACTCTG
1 ATCGCCACCATGGCATCATTATTATCAGTGACACCAAGTCACCCTAACTCTA
* * **
58362 ATCGCCACCATAGCATCATTATTATCAATGACACCAAGTCA-CCTAAACTCCG
1 ATCGCCACCATGGCATCATTATTATCAGTGACACCAAGTCACCCT-AACTCTA
* * * * * *
58414 ATAAG-CACTATGGCATCATCATGATCAGTAACACCAGGTCACCCTA
1 AT-CGCCACCATGGCATCATTATTATCAGTGACACCAAGTCACCCTA
58460 TTGAGCACCA
Statistics
Matches: 131, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
51 3 0.02
52 124 0.95
53 4 0.03
ACGTcount: A:0.33, C:0.31, G:0.12, T:0.25
Consensus pattern (52 bp):
ATCGCCACCATGGCATCATTATTATCAGTGACACCAAGTCACCCTAACTCTA
Found at i:72938 original size:21 final size:21
Alignment explanation
Indices: 72914--72984 Score: 63
Period size: 25 Copynumber: 3.1 Consensus size: 21
72904 TAAAATATTA
72914 TATTTAAATTTAAAAATTAAT
1 TATTTAAATTTAAAAATTAAT
*
72935 TATTTAATTAAATTTTAAAATT-AT
1 TA--T--TTAAATTTAAAAATTAAT
*
72959 TATTTAAAATTTAAAATTTATAT
1 TATTT-AAATTTAAAAATTA-AT
72982 TAT
1 TAT
72985 CTATATTTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
20 2 0.05
21 13 0.32
22 1 0.03
23 6 0.15
24 4 0.10
25 14 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTTAAATTTAAAAATTAAT
Found at i:72965 original size:24 final size:25
Alignment explanation
Indices: 72917--72965 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
72907 AATATTATAT
72917 TTAAATTTAAAAATTAATTATTTAA
1 TTAAATTTAAAAATTAATTATTTAA
*
72942 TTAAATTTTAAAATT-ATTATTTAA
1 TTAAATTTAAAAATTAATTATTTAA
72966 AATTTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TTAAATTTAAAAATTAATTATTTAA
Found at i:72971 original size:20 final size:20
Alignment explanation
Indices: 72904--72976 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 20
72894 TTAATCTGAA
*
72904 TAAAA-TATTATATTTAAATT
1 TAAAATTATTAT-TTAAAATT
72924 TAAAAATTAATTATTTAATTAAATTT
1 T-AAAATT-ATTATTT-A--AAA-TT
72950 TAAAATTATTATTTAAAATT
1 TAAAATTATTATTTAAAATT
72970 TAAAATT
1 TAAAATT
72977 TATATTATCT
Statistics
Matches: 45, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
20 10 0.22
21 7 0.16
22 3 0.07
23 6 0.13
24 7 0.16
25 9 0.20
26 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAAATTATTATTTAAAATT
Found at i:72982 original size:20 final size:21
Alignment explanation
Indices: 72904--73052 Score: 69
Period size: 21 Copynumber: 7.0 Consensus size: 21
72894 TTAATCTGAA
72904 TAAAATATTA-TATTT-AAATT
1 TAAAAT-TTATTATTTAAAATT
*
72924 TAAAAATTAATTATTTAATTAAATTT
1 T-AAAATTTATTATTT-A--AAA-TT
72950 TAAAA-TTATTATTTAAAATT
1 TAAAATTTATTATTTAAAATT
* * *
72970 TAAAATTTATATTATCTATATTT
1 TAAAA-TT-TATTATTTAAAATT
* *
72993 TGAGAATTTA-TATTTAAATTT
1 T-AAAATTTATTATTTAAAATT
* **
73014 TAAATTTTAAAATTT-AAA--
1 TAAAATTTATTATTTAAAATT
* *
73032 TAAATTTTATTTTTTAAAATT
1 TAAAATTTATTATTTAAAATT
73053 GATTCAAATT
Statistics
Matches: 99, Mismatches: 15, Indels: 29
0.69 0.10 0.20
Matches are distributed among these distances:
18 12 0.12
19 3 0.03
20 18 0.18
21 27 0.27
22 3 0.03
23 15 0.15
24 11 0.11
25 7 0.07
26 3 0.03
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (21 bp):
TAAAATTTATTATTTAAAATT
Found at i:73016 original size:44 final size:44
Alignment explanation
Indices: 72910--73040 Score: 124
Period size: 44 Copynumber: 3.0 Consensus size: 44
72900 TGAATAAAAT
* *
72910 ATTATATTTAAATTTAAAAATTAATTATTTAATTAAATTTTAAA
1 ATTATATTTAAATTTTAAAATTTATTATTTAATTAAATTTTAAA
* *
72954 ATTATTATTTAAAATTTAAAATTTA-TA-TT-ATCTATATTTTGAGAA
1 ATTA-TATTTAAATTTTAAAATTTATTATTTAAT-TAAATTTT-A-AA
* * ** *
72999 TTTATATTTAAATTTTAAATTTTAAAATTTAAATAAATTTTA
1 ATTATATTTAAATTTTAAAATTTATTATTTAATTAAATTTTA
73041 TTTTTTAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
42 2 0.03
43 9 0.13
44 25 0.36
45 24 0.34
46 9 0.13
47 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.52
Consensus pattern (44 bp):
ATTATATTTAAATTTTAAAATTTATTATTTAATTAAATTTTAAA
Found at i:73024 original size:14 final size:14
Alignment explanation
Indices: 72942--73032 Score: 53
Period size: 14 Copynumber: 6.4 Consensus size: 14
72932 AATTATTTAA
72942 TTAAATTTTAAAA-
1 TTAAATTTTAAAAT
*
72955 TT-ATTATTTAAAAT
1 TTAAAT-TTTAAAAT
**
72969 TTAAAATTTATATTAT
1 TT-AAATTT-TAAAAT
* * *
72985 CTATATTTTGAGAAT
1 TTAAATTTT-AAAAT
* *
73000 TTATA-TTTAAATT
1 TTAAATTTTAAAAT
73013 TTAAATTTTAAAAT
1 TTAAATTTTAAAAT
73027 TTAAAT
1 TTAAAT
73033 AAATTTTATT
Statistics
Matches: 58, Mismatches: 13, Indels: 13
0.69 0.15 0.15
Matches are distributed among these distances:
12 2 0.03
13 16 0.28
14 19 0.33
15 14 0.24
16 7 0.12
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (14 bp):
TTAAATTTTAAAAT
Found at i:73368 original size:23 final size:23
Alignment explanation
Indices: 73327--73374 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
73317 ATAATTTTTT
*
73327 TTATATTTTTATGTATTTAATTA
1 TTATATTTTTATGTATTTAAATA
*
73350 TTATA-TTTTATTTATTTTAAATA
1 TTATATTTTTATGTA-TTTAAATA
73373 TT
1 TT
73375 TACATATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTATATTTTTATGTATTTAAATA
Found at i:76704 original size:16 final size:16
Alignment explanation
Indices: 76649--76717 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
76639 ACTAATATAA
76649 ATAAAGTAATTTATAAAT
1 ATAAA-TAATTTA-AAAT
*
76667 -TATATAAATTT--AAT
1 ATAAAT-AATTTAAAAT
76681 AT-AATAATATTAAAAT
1 ATAAATAAT-TTAAAAT
76697 -TAAATAATTTAAAAT
1 ATAAATAATTTAAAAT
76712 ATAAAT
1 ATAAAT
76718 TATCTTCCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 16
0.70 0.03 0.27
Matches are distributed among these distances:
13 3 0.07
14 7 0.17
15 9 0.21
16 15 0.36
17 8 0.19
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (16 bp):
ATAAATAATTTAAAAT
Found at i:76719 original size:21 final size:21
Alignment explanation
Indices: 76642--76717 Score: 57
Period size: 22 Copynumber: 3.4 Consensus size: 21
76632 TAACAAAACT
*
76642 AATATAAATAAAGTAATTTATA
1 AATATAAATAAATTAATTTA-A
* *
76664 AAT-TATATAAATTTAATATAA
1 AATATAAATAAA-TTAATTTAA
76685 TAATATTAAAATTAAA-TAATTTAA
1 -AATA-T-AAA-TAAATTAATTTAA
76709 AATATAAAT
1 AATATAAAT
76718 TATCTTCCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
20 1 0.02
21 11 0.26
22 13 0.30
23 4 0.09
24 8 0.19
25 2 0.05
26 4 0.09
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (21 bp):
AATATAAATAAATTAATTTAA
Found at i:78380 original size:3 final size:3
Alignment explanation
Indices: 78366--78410 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
78356 AGCAAAAGGA
*
78366 AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
78411 GCTTCACAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:85013 original size:4 final size:4
Alignment explanation
Indices: 85004--85037 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
84994 AACAAAAAAG
85004 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
85038 TTATCTTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:87735 original size:20 final size:19
Alignment explanation
Indices: 87710--87748 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
87700 ACCAGTATTA
87710 GTAAATCGTAAATGTAAAAT
1 GTAAATCGTAAAT-TAAAAT
*
87730 GTAAATTGTAAATTAAAAT
1 GTAAATCGTAAATTAAAAT
87749 TTTGACGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.51, C:0.03, G:0.13, T:0.33
Consensus pattern (19 bp):
GTAAATCGTAAATTAAAAT
Found at i:88413 original size:15 final size:15
Alignment explanation
Indices: 88393--88424 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
88383 TTCTACATTG
88393 TCTGCATCATCATCA
1 TCTGCATCATCATCA
*
88408 TCTGCATCATTATCA
1 TCTGCATCATCATCA
88423 TC
1 TC
88425 ATCTTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.31, G:0.06, T:0.38
Consensus pattern (15 bp):
TCTGCATCATCATCA
Found at i:88424 original size:21 final size:21
Alignment explanation
Indices: 88398--88443 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
88388 CATTGTCTGC
88398 ATCATCATCATCTGCATCATT
1 ATCATCATCATCTGCATCATT
* **
88419 ATCATCATCTTCTTTATCATT
1 ATCATCATCATCTGCATCATT
88440 ATCA
1 ATCA
88444 GCTGTAGTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.26, G:0.02, T:0.43
Consensus pattern (21 bp):
ATCATCATCATCTGCATCATT
Found at i:91727 original size:3 final size:3
Alignment explanation
Indices: 91719--91746 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
91709 AAAACTTAAC
91719 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
91747 TTCAAGGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:93005 original size:12 final size:12
Alignment explanation
Indices: 92988--93026 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
92978 TTACTTTCTT
92988 GGTTTGGGTTTG
1 GGTTTGGGTTTG
93000 GGTTTGGGGTTTG
1 GGTTT-GGGTTTG
*
93013 GGATTGGG-TTG
1 GGTTTGGGTTTG
93024 GGT
1 GGT
93027 GTGGAAGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 5 0.21
12 8 0.33
13 11 0.46
ACGTcount: A:0.03, C:0.00, G:0.54, T:0.44
Consensus pattern (12 bp):
GGTTTGGGTTTG
Found at i:93011 original size:7 final size:6
Alignment explanation
Indices: 92988--93026 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
92978 TTACTTTCTT
*
92988 GGTTTG GGTTTG GGTTTGG GGTTTG GGATTG GG-TTG GGT
1 GGTTTG GGTTTG GGTTT-G GGTTTG GGTTTG GGTTTG GGT
93027 GTGGAAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 5 0.17
6 19 0.63
7 6 0.20
ACGTcount: A:0.03, C:0.00, G:0.54, T:0.44
Consensus pattern (6 bp):
GGTTTG
Found at i:93283 original size:6 final size:6
Alignment explanation
Indices: 93267--93306 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
93257 TAAGGTTCGA
* *
93267 TTTTTC TTTTTTC TTTTTC TTTTTC TTTTTG TATTTC TTT
1 TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTT
93307 GATCCTTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:94850 original size:39 final size:39
Alignment explanation
Indices: 94807--94881 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
94797 GAATGTCTCT
*
94807 TCAATGGATTGCCACTAGCAAACGACCCTGATGTGCATC
1 TCAATGGATTGCCACTAGCAAACGACCCTCATGTGCATC
* * *
94846 TCAATGGATTGCCAGTAGCAAATGACTCTCATGTGC
1 TCAATGGATTGCCACTAGCAAACGACCCTCATGTGC
94882 CTCCTTTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.25
Consensus pattern (39 bp):
TCAATGGATTGCCACTAGCAAACGACCCTCATGTGCATC
Found at i:96217 original size:48 final size:48
Alignment explanation
Indices: 96146--96243 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
96136 AAGTAGACAA
*
96146 CACTGATGTCCCAACCTATAATCCTACATCTTCATCCGTGAGTTATCC
1 CACTGATGTCCCAACCCATAATCCTACATCTTCATCCGTGAGTTATCC
* *
96194 CACTGGTGTCCCAACCCATAATCCTACGTCTTCATCCGTGAGTTATCC
1 CACTGATGTCCCAACCCATAATCCTACATCTTCATCCGTGAGTTATCC
96242 CA
1 CA
96244 TTGTCGAACA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.23, C:0.35, G:0.12, T:0.30
Consensus pattern (48 bp):
CACTGATGTCCCAACCCATAATCCTACATCTTCATCCGTGAGTTATCC
Found at i:96866 original size:3 final size:3
Alignment explanation
Indices: 96858--96885 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
96848 TTACGTGAAG
96858 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
96886 GTTCTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:97189 original size:13 final size:13
Alignment explanation
Indices: 97173--97199 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
97163 TTACTGTAAT
97173 AAATTATAATAAA
1 AAATTATAATAAA
97186 AAATTATAATAAA
1 AAATTATAATAAA
97199 A
1 A
97200 GTAAGGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATTATAATAAA
Found at i:97254 original size:21 final size:23
Alignment explanation
Indices: 97228--97284 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 23
97218 ATTGAGATAT
97228 AAAATAAATAAATAT-TAA-AAA
1 AAAATAAATAAATATATAATAAA
*
97249 ATAAT-AA-AAATATATAATAAA
1 AAAATAAATAAATATATAATAAA
97270 AAAATAAATATAATA
1 AAAATAAATA-AATA
97285 ATTTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
19 6 0.21
20 5 0.17
21 11 0.38
22 2 0.07
23 1 0.03
24 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (23 bp):
AAAATAAATAAATATATAATAAA
Found at i:97282 original size:17 final size:17
Alignment explanation
Indices: 97226--97285 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 17
97216 AAATTGAGAT
97226 ATAAAATAAATAAATATTA
1 ATAAAA-AAATAAATA-TA
* *
97245 AAAAATAATAAAAATATATA
1 ATAAA-AA-AATAA-ATATA
97265 ATAAAAAAATAAATATA
1 ATAAAAAAATAAATATA
97282 ATAA
1 ATAA
97286 TTTTTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 9 0.26
18 4 0.12
19 7 0.21
20 11 0.32
21 3 0.09
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
ATAAAAAAATAAATATA
Found at i:101346 original size:33 final size:33
Alignment explanation
Indices: 101294--101357 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
101284 TGACGCCTTA
*
101294 AATTTAATAATATTAAAAATAAATATTATTTAT
1 AATTTAATAATATTAAAAATAAATAATATTTAT
*
101327 AATTTAATCAATA-TGAAAATAAATAATATTT
1 AATTTAAT-AATATTAAAAATAAATAATATTT
101358 TTAAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 24 0.86
34 4 0.14
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (33 bp):
AATTTAATAATATTAAAAATAAATAATATTTAT
Found at i:102635 original size:2 final size:2
Alignment explanation
Indices: 102628--102660 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
102618 CTAGGCTATT
102628 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
102661 TAATTAAGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:103127 original size:2 final size:2
Alignment explanation
Indices: 103120--103152 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
103110 GCGGGAAGGA
103120 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 A
103153 AGATTACCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:105266 original size:3 final size:3
Alignment explanation
Indices: 105258--105292 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
105248 TCCATTTTAC
105258 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
105293 CCCGACAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:105635 original size:22 final size:23
Alignment explanation
Indices: 105603--105662 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
105593 TGATATTTAA
*
105603 TAATTAAAAAATTATTTAAAT-T
1 TAATTATAAAATTATTTAAATAT
**
105625 TAATTATAAAA-TAAATAAATAT
1 TAATTATAAAATTATTTAAATAT
*
105647 TAA-TATAAAATAATTT
1 TAATTATAAAATTATTT
105663 TTTAAATTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATTATAAAATTATTTAAATAT
Found at i:105653 original size:21 final size:21
Alignment explanation
Indices: 105619--105659 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
105609 AAAAATTATT
105619 TAAATTTAATTATAAAATAAA
1 TAAATTTAATTATAAAATAAA
105640 TAAATATTAA-TATAAAATAA
1 TAAAT-TTAATTATAAAATAA
105660 TTTTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAATTTAATTATAAAATAAA
Found at i:106716 original size:3 final size:3
Alignment explanation
Indices: 106708--106737 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
106698 TTAATTAATC
106708 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
106738 CGGAGAGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:106835 original size:2 final size:2
Alignment explanation
Indices: 106828--106854 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
106818 ATTCTCCAAT
106828 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
106855 TTGCACACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:106975 original size:2 final size:2
Alignment explanation
Indices: 106970--106996 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
106960 TCTCTCTCTC
106970 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
106997 CAAAAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:108841 original size:39 final size:39
Alignment explanation
Indices: 108766--108849 Score: 96
Period size: 39 Copynumber: 2.2 Consensus size: 39
108756 GAAGATGAGA
* * **
108766 AGGAATCTGATTTTGATGTCTCGTATGATGTATATGAAG
1 AGGAATCTGATTGTGATGTCTCATATGAAATATATGAAG
* * *
108805 AGGAATCTGATTGTGGTGTCTTATATGAAATCTATGAAG
1 AGGAATCTGATTGTGATGTCTCATATGAAATATATGAAG
*
108844 ATGAAT
1 AGGAAT
108850 GTGAAGATGT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.37
Consensus pattern (39 bp):
AGGAATCTGATTGTGATGTCTCATATGAAATATATGAAG
Found at i:108887 original size:69 final size:69
Alignment explanation
Indices: 108805--109098 Score: 437
Period size: 69 Copynumber: 4.3 Consensus size: 69
108795 GTATATGAAG
* * *
108805 AGGAATCTGATTGTGGTGTCTTATATGAAATCTATGAAGATGAATGTGAAGATGTATACGAAGAT
1 AGGAATCTGATTGTGGTGTCTCATATGAAATCTATGAAGATGGATGTGAAGATGTATATGAAGAT
108870 GAGA
66 GAGA
* * * * *
108874 AGGAATCTAATTGTGGTGTCCCATTTGAAATCTATGAAGATGGATGTGAAGATGTATATAAAGAA
1 AGGAATCTGATTGTGGTGTCTCATATGAAATCTATGAAGATGGATGTGAAGATGTATATGAAGAT
108939 GAGA
66 GAGA
* * *
108943 AGGAATCTGATTGTGGTGTCGCATATGAAATCAATGAAGATGGATGTGAGGATGTATATGAAGAT
1 AGGAATCTGATTGTGGTGTCTCATATGAAATCTATGAAGATGGATGTGAAGATGTATATGAAGAT
*
109008 GGGA
66 GAGA
**
109012 AGGAATCTGATTGTGAG-GTCTCATATGAAATCTATGAAGACCGATGTGAAGATGTATATGAAGA
1 AGGAATCTGATTGTG-GTGTCTCATATGAAATCTATGAAGATGGATGTGAAGATGTATATGAAGA
109076 TGAGA
65 TGAGA
*
109081 AGGAATCTGACTGTGGTG
1 AGGAATCTGATTGTGGTG
109099 AAGGTAAGAG
Statistics
Matches: 200, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
68 1 0.00
69 198 0.99
70 1 0.00
ACGTcount: A:0.35, C:0.07, G:0.29, T:0.29
Consensus pattern (69 bp):
AGGAATCTGATTGTGGTGTCTCATATGAAATCTATGAAGATGGATGTGAAGATGTATATGAAGAT
GAGA
Found at i:108912 original size:108 final size:106
Alignment explanation
Indices: 108699--108913 Score: 286
Period size: 108 Copynumber: 2.0 Consensus size: 106
108689 GGGTGTAAGA
* *
108699 AGGAATCTGATTGTGATGTCTCATATGAAATCTATGAATATATGCGAAGATGTATATGAAGATGA
1 AGGAATCTGATTGTGATGTCTCATATGAAATCTATGAAGATATGCGAAGATGTATACGAAGATGA
* * * * **
108764 GAAGGAATCTGATTTTGATGTCTCGTATGATGTATATGAAG
66 GAAGGAATCTAATTGTGATGTCCCATATGAAATATATGAAG
* * *
108805 AGGAATCTGATTGTGGTGTCTTATATGAAATCTATGAAGATGAATGTGAAGATGTATACGAAGAT
1 AGGAATCTGATTGTGATGTCTCATATGAAATCTATGAAGAT--ATGCGAAGATGTATACGAAGAT
* * *
108870 GAGAAGGAATCTAATTGTGGTGTCCCATTTGAAATCTATGAAG
64 GAGAAGGAATCTAATTGTGATGTCCCATATGAAATATATGAAG
108913 A
1 A
108914 TGGATGTGAA
Statistics
Matches: 93, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
106 38 0.41
108 55 0.59
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.33
Consensus pattern (106 bp):
AGGAATCTGATTGTGATGTCTCATATGAAATCTATGAAGATATGCGAAGATGTATACGAAGATGA
GAAGGAATCTAATTGTGATGTCCCATATGAAATATATGAAG
Found at i:109029 original size:36 final size:35
Alignment explanation
Indices: 108985--109095 Score: 97
Period size: 36 Copynumber: 3.2 Consensus size: 35
108975 AATGAAGATG
*
108985 GATGTGAGGATGTATATGAAGATGGGAAGGAATCT
1 GATGTGAGGATGTATATGAAGATGAGAAGGAATCT
* * *
109020 GATTGTGAGG-TCTCATATGAA-ATCTATGAA-G-A-CC
1 GA-TGTGAGGATGT-ATATGAAGAT-GA-GAAGGAATCT
*
109054 GATGTGAAGATGTATATGAAGATGAGAAGGAATCT
1 GATGTGAGGATGTATATGAAGATGAGAAGGAATCT
109089 GACTGTG
1 GA-TGTG
109096 GTGAAGGTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 19
0.68 0.09 0.22
Matches are distributed among these distances:
32 3 0.05
33 15 0.26
34 8 0.14
35 10 0.17
36 19 0.33
37 3 0.05
ACGTcount: A:0.34, C:0.07, G:0.32, T:0.27
Consensus pattern (35 bp):
GATGTGAGGATGTATATGAAGATGAGAAGGAATCT
Found at i:115577 original size:12 final size:12
Alignment explanation
Indices: 115562--115587 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
115552 GCTTTGGGCG
115562 ATAGAAATGGAA
1 ATAGAAATGGAA
115574 ATAGAAATGGAA
1 ATAGAAATGGAA
115586 AT
1 AT
115588 GGGAGAGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.23, T:0.19
Consensus pattern (12 bp):
ATAGAAATGGAA
Found at i:115685 original size:6 final size:6
Alignment explanation
Indices: 115674--115703 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
115664 TCAATAAGGG
115674 CTTGGC CTTGGC CTTGGC CTTGGC CTTGGC
1 CTTGGC CTTGGC CTTGGC CTTGGC CTTGGC
115704 TAATAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (6 bp):
CTTGGC
Found at i:123608 original size:112 final size:112
Alignment explanation
Indices: 123432--123633 Score: 325
Period size: 112 Copynumber: 1.8 Consensus size: 112
123422 AAATACTATG
* *
123432 TGTTGTATCTTTAAAGGATTGTGCAGTCTCTTGTTAGAAGGTCAGTGCCAAAAGTCTGGAGTCTT
1 TGTTGTATCTTTAAAGGATTGCGCAGTCTCTCGTTAGAAGGTCAGTGCCAAAAGTCTGGAGTCTT
* *
123497 GGAAGGTGGTTCAATGGATGGCTTAGAAAATACCTAAAAATGTTACA
66 GGAAGATGGTTCAATAGATGGCTTAGAAAATACCTAAAAATGTTACA
* * *
123544 TGTTGTATCTTTAAATGATTGCGC-GCTCTCTCGTTAGAAGTTCAGTGCCAAAATTCTGGAGTCT
1 TGTTGTATCTTTAAAGGATTGCGCAG-TCTCTCGTTAGAAGGTCAGTGCCAAAAGTCTGGAGTCT
123608 TGGAAGATGGTTCAATAGATGGCTTA
65 TGGAAGATGGTTCAATAGATGGCTTA
123634 TTTAGACTTT
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
111 1 0.01
112 81 0.99
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (112 bp):
TGTTGTATCTTTAAAGGATTGCGCAGTCTCTCGTTAGAAGGTCAGTGCCAAAAGTCTGGAGTCTT
GGAAGATGGTTCAATAGATGGCTTAGAAAATACCTAAAAATGTTACA
Found at i:125034 original size:3 final size:3
Alignment explanation
Indices: 125026--125050 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
125016 TGGGTATGGT
125026 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
125051 TCAATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:125281 original size:2 final size:2
Alignment explanation
Indices: 125274--125301 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
125264 GCCCAGACAA
125274 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
125302 CCCCTTACCT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:127171 original size:39 final size:39
Alignment explanation
Indices: 127097--127331 Score: 213
Period size: 39 Copynumber: 6.0 Consensus size: 39
127087 ATTCCCCATC
* * * * *
127097 CCACATTGCTGCCGTCTACAAGTGCTAGTTTCCTGAACT
1 CCACACTGCTTCCATCTTCAAGTGCTAGTTCCCTGAACT
* * * *
127136 CTACACTGCTTCCATATTCAAGTGCTAGTGCCCTGAGCT
1 CCACACTGCTTCCATCTTCAAGTGCTAGTTCCCTGAACT
* * *
127175 CTACGCTGCTTCCATCTTCAAGTGCTAGTTCCCCGAACT
1 CCACACTGCTTCCATCTTCAAGTGCTAGTTCCCTGAACT
** * * *
127214 CCATGCTGCTCCCATCTTCAAGTGCTAGCTCCCGGAACT
1 CCACACTGCTTCCATCTTCAAGTGCTAGTTCCCTGAACT
* * * * * *
127253 CCACAAC-CCTACCACCTTCAAGTTCTAGCTCCCAGAACT
1 CCAC-ACTGCTTCCATCTTCAAGTGCTAGTTCCCTGAACT
* *
127292 CCACGA-TGCTGCCACCTTCAAGTGCTAGTTCCCTGAACT
1 CCAC-ACTGCTTCCATCTTCAAGTGCTAGTTCCCTGAACT
127331 C
1 C
127332 TACATTGTTA
Statistics
Matches: 162, Mismatches: 32, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
39 161 0.99
40 1 0.01
ACGTcount: A:0.21, C:0.36, G:0.16, T:0.27
Consensus pattern (39 bp):
CCACACTGCTTCCATCTTCAAGTGCTAGTTCCCTGAACT
Found at i:127246 original size:20 final size:20
Alignment explanation
Indices: 127186--127246 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
127176 TACGCTGCTT
*
127186 CCATCTTCAAGTGCTAGTTCC
1 CCATCTTCAAGTGCTAGCT-C
* *
127207 CCGAAC-TCCA-TGCT-GCTC
1 CC-ATCTTCAAGTGCTAGCTC
127225 CCATCTTCAAGTGCTAGCTC
1 CCATCTTCAAGTGCTAGCTC
127245 CC
1 CC
127247 GGAACTCCAC
Statistics
Matches: 31, Mismatches: 5, Indels: 9
0.69 0.11 0.20
Matches are distributed among these distances:
17 2 0.06
18 6 0.19
19 6 0.19
20 10 0.32
21 5 0.16
22 2 0.06
ACGTcount: A:0.18, C:0.39, G:0.15, T:0.28
Consensus pattern (20 bp):
CCATCTTCAAGTGCTAGCTC
Found at i:130638 original size:127 final size:126
Alignment explanation
Indices: 130406--130649 Score: 321
Period size: 127 Copynumber: 1.9 Consensus size: 126
130396 TTAGATAAGA
* * * *
130406 TCATTCTTCCATTCTCTATCTCTTTTTGTATTATTTGTAGATGCATATTGAGGGGGATTGATCAT
1 TCATTCTTCCATTCTCTATCTCCTTGTATATTATTTGTAGATGCATATTGAGGGGGATAGATCAT
* *
130471 TCTCTAAATATAAGTGTAGCTATGACAATCGCTAATTGTTTGTTTTGTAGATAAGATCATT
66 TCTCTAAATATAAGTGTAGCTATGACAATCGCTAATTGTTTGCTTTATAGATAAGATCATT
* * *
130532 TCATTCTTCCAGTTCTCTTTCTCCTTGTATGTTA-TTGATAGATGCCTATTGAGGGGGATAGAAT
1 TCATTCTTCCA-TTCTCTATCTCCTTGTATATTATTTG-TAGATGCATATTGAGGGGGATAG-AT
* ** * *
130596 CATTCTCTAAATTTGTGTGTAGCTATGAGAATTGCTAA-TGTTTGCTTTATAGAT
63 CATTCTCTAAATATAAGTGTAGCTATGACAATCGCTAATTGTTTGCTTTATAGAT
130650 TTCACACTAT
Statistics
Matches: 101, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
126 14 0.14
127 52 0.51
128 35 0.35
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44
Consensus pattern (126 bp):
TCATTCTTCCATTCTCTATCTCCTTGTATATTATTTGTAGATGCATATTGAGGGGGATAGATCAT
TCTCTAAATATAAGTGTAGCTATGACAATCGCTAATTGTTTGCTTTATAGATAAGATCATT
Found at i:132106 original size:26 final size:26
Alignment explanation
Indices: 132070--132125 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
132060 ATCTATTAAG
*
132070 GTCATATGTCACACAAAGGTTTAGTA
1 GTCATATGTCACACAAAGGTTTAATA
132096 GTCATATGTCACACAAAGGTTTAATA
1 GTCATATGTCACACAAAGGTTTAATA
132122 GTCA
1 GTCA
132126 ATTAGTGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (26 bp):
GTCATATGTCACACAAAGGTTTAATA
Found at i:137997 original size:2 final size:2
Alignment explanation
Indices: 137990--138016 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
137980 AAGTGGCAAC
137990 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
138017 GTAAAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:139884 original size:2 final size:2
Alignment explanation
Indices: 139877--139906 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
139867 GCATATTATT
139877 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
139907 GTTAGGTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:140501 original size:3 final size:3
Alignment explanation
Indices: 140493--140522 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
140483 TGCATTCAAT
140493 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
140523 TATTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:140529 original size:3 final size:3
Alignment explanation
Indices: 140523--140558 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
140513 AATAATAATA
*
140523 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
140559 AAACAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:142425 original size:2 final size:2
Alignment explanation
Indices: 142413--142441 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
142403 TGGAGAAAGC
142413 AT AT AT A- 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
142442 TGAATTCCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:144474 original size:2 final size:2
Alignment explanation
Indices: 144467--144506 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
144457 TTTTGGGCTG
*
144467 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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
144507 TAGCTAAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:149074 original size:5 final size:5
Alignment explanation
Indices: 149064--149091 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
149054 AGCATTTGCC
149064 GTGGT GTGGT GTGGT GTGGT GTGGT GTG
1 GTGGT GTGGT GTGGT GTGGT GTGGT GTG
149092 TGGTCACAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.61, T:0.39
Consensus pattern (5 bp):
GTGGT
Found at i:150101 original size:3 final size:3
Alignment explanation
Indices: 150093--150130 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
150083 TATAATTGGC
150093 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
150131 AATTTCGAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:154905 original size:51 final size:50
Alignment explanation
Indices: 154841--154937 Score: 131
Period size: 51 Copynumber: 1.9 Consensus size: 50
154831 ACAATTTCAC
* * * *
154841 AATTCTCAATTGTGATTGAAGTTTTCGTTTAATTAATAGTAAAACCATCCA
1 AATTCTCAATTGTGATCGAAGTTTGCATTTAACT-ATAGTAAAACCATCCA
* *
154892 AATTCTCAGTTGTGATCGAAGTTTGCATTTAACTATTGTAAAACCA
1 AATTCTCAATTGTGATCGAAGTTTGCATTTAACTATAGTAAAACCA
154938 AATCACACTA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
50 11 0.28
51 29 0.73
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.38
Consensus pattern (50 bp):
AATTCTCAATTGTGATCGAAGTTTGCATTTAACTATAGTAAAACCATCCA
Found at i:156748 original size:2 final size:2
Alignment explanation
Indices: 156741--156773 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
156731 TAGTAACAGT
156741 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
156774 AGGGTCTCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:158893 original size:12 final size:12
Alignment explanation
Indices: 158876--158900 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
158866 CAAGAGATTT
158876 AAAAAAAATGAA
1 AAAAAAAATGAA
158888 AAAAAAAATGAA
1 AAAAAAAATGAA
158900 A
1 A
158901 TTTGATACGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAAAAATGAA
Found at i:168905 original size:2 final size:2
Alignment explanation
Indices: 168898--168922 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
168888 CAACAAAGGC
168898 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 A
168923 ACACAGCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:172178 original size:2 final size:2
Alignment explanation
Indices: 172173--172205 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
172163 ATATGTATGT
172173 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
172206 TGGATTCGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:172723 original size:22 final size:21
Alignment explanation
Indices: 172686--172733 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
172676 TATAAAATTA
172686 ATTTTAATAATATTTAAGA-T
1 ATTTTAATAATATTTAAGATT
* *
172706 ATTTTAAATTAATTTTTATGATT
1 ATTTT-AA-TAATATTTAAGATT
172729 ATTTT
1 ATTTT
172734 TAAAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 2 0.09
22 10 0.43
23 6 0.26
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
ATTTTAATAATATTTAAGATT
Found at i:173016 original size:25 final size:26
Alignment explanation
Indices: 172982--173032 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
172972 TTTTAAAAAT
172982 ATAATAATTATAAATTAATAAGAATA
1 ATAATAATTATAAATTAATAAGAATA
173008 ATAAT-ATTATAAATTAATAAGAATA
1 ATAATAATTATAAATTAATAAGAATA
173033 TAAATTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (26 bp):
ATAATAATTATAAATTAATAAGAATA
Found at i:173027 original size:16 final size:17
Alignment explanation
Indices: 173015--173069 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
173005 ATAATAATAT
173015 TATAAA-TTAATAAGAA
1 TATAAATTTAATAAGAA
*
173031 TATAAATTTAATAAAAAA
1 TATAAATTTAAT-AAGAA
* * *
173049 TACAAACTTAATAAGCA
1 TATAAATTTAATAAGAA
173066 TATA
1 TATA
173070 TTTTTTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
16 6 0.19
17 11 0.35
18 14 0.45
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (17 bp):
TATAAATTTAATAAGAA
Found at i:184426 original size:14 final size:15
Alignment explanation
Indices: 184401--184429 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
184391 CCTCTCACCT
184401 CCCCCTGATTTTTCA
1 CCCCCTGATTTTTCA
184416 CCCCCTG-TTTTTCA
1 CCCCCTGATTTTTCA
184430 TTTATTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.10, C:0.41, G:0.07, T:0.41
Consensus pattern (15 bp):
CCCCCTGATTTTTCA
Found at i:184981 original size:2 final size:2
Alignment explanation
Indices: 184968--184997 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
184958 AAGCTGCTCG
*
184968 AT AT AA 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
184998 CACCTTACAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:185237 original size:6 final size:6
Alignment explanation
Indices: 185226--185260 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
185216 TGGGTATTAT
185226 ATATAA ATATAA ATATAA ATATAA ATATAA ATATA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATA
185261 TGTATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:186701 original size:2 final size:2
Alignment explanation
Indices: 186694--186732 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
186684 CCTACATTAC
186694 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
186733 AGAAATTACA
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:197610 original size:2 final size:2
Alignment explanation
Indices: 197598--197629 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
197588 TGTAGTTGTC
*
197598 AT AT AT GT 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
197630 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:202617 original size:2 final size:2
Alignment explanation
Indices: 202612--202641 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
202602 ATTTTTGAAG
202612 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
202642 GCGGTTGTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:205065 original size:16 final size:16
Alignment explanation
Indices: 205046--205080 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
205036 TATTTTTTAA
*
205046 AATTTTAATTTAATTT
1 AATTTTAATATAATTT
*
205062 AATTTTTATATAATTT
1 AATTTTAATATAATTT
205078 AAT
1 AAT
205081 ACTAGTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTTAATATAATTT
Found at i:206735 original size:15 final size:17
Alignment explanation
Indices: 206715--206755 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
206705 ATTTATATAT
206715 TTATATTAT-ATT-TTA
1 TTATATTATAATTATTA
206730 TTATATTATAATTATTA
1 TTATATTATAATTATTA
206747 TTATTATTA
1 TTA-TATTA
206756 AAATATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.39
16 3 0.13
17 6 0.26
18 5 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTATATTATAATTATTA
Found at i:207782 original size:12 final size:12
Alignment explanation
Indices: 207765--207790 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
207755 GTGCGTATCA
207765 TTGATTATTTAT
1 TTGATTATTTAT
207777 TTGATTATTTAT
1 TTGATTATTTAT
207789 TT
1 TT
207791 ATCATCCTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGATTATTTAT
Found at i:233870 original size:21 final size:20
Alignment explanation
Indices: 233845--233887 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
233835 TTTTATCATA
233845 ATTTAATT-TAATATTAAATTT
1 ATTTAATTAT-ATATT-AATTT
233866 ATTTAATTATATATTAATTT
1 ATTTAATTATATATTAATTT
233886 AT
1 AT
233888 AAATATGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 13 0.62
22 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTAATTATATATTAATTT
Found at i:233880 original size:12 final size:10
Alignment explanation
Indices: 233847--233888 Score: 50
Period size: 11 Copynumber: 4.0 Consensus size: 10
233837 TTATCATAAT
233847 TTAATTTAATA
1 TTAATTT-ATA
233858 TTAAATTTAT-
1 TT-AATTTATA
233868 TTAATTATATA
1 TTAATT-TATA
233879 TTAATTTATA
1 TTAATTTATA
233889 AATATGATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
9 4 0.14
10 9 0.32
11 10 0.36
12 5 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TTAATTTATA
Found at i:234460 original size:2 final size:2
Alignment explanation
Indices: 234453--234487 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
234443 ATCATCCACT
234453 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
234488 TTTTCTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:235038 original size:2 final size:2
Alignment explanation
Indices: 235031--235057 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
235021 TGAGTCATTG
235031 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 A
235058 GCTCTTATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:239099 original size:41 final size:41
Alignment explanation
Indices: 239042--239125 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
239032 CTACTTCCTC
239042 AAAATAATGTTCCTCCATTATTTTGGGTTGCTTCACCTTGT
1 AAAATAATGTTCCTCCATTATTTTGGGTTGCTTCACCTTGT
*
239083 AAAATAATGTTCCTCCATTATTTTGGTTTGCTTCACCTTGT
1 AAAATAATGTTCCTCCATTATTTTGGGTTGCTTCACCTTGT
239124 AA
1 AA
239126 TGTTCTCTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (41 bp):
AAAATAATGTTCCTCCATTATTTTGGGTTGCTTCACCTTGT
Found at i:250158 original size:15 final size:16
Alignment explanation
Indices: 250138--250170 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
250128 GTTTGGATTT
250138 TTATTTTCTTTTT-TG
1 TTATTTTCTTTTTCTG
250153 TTATTTTCTTTTTCTG
1 TTATTTTCTTTTTCTG
250169 TT
1 TT
250171 TTATATAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.79
Consensus pattern (16 bp):
TTATTTTCTTTTTCTG
Found at i:254887 original size:3 final size:3
Alignment explanation
Indices: 254879--254927 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
254869 CTGCTACCTA
254879 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
254927 A
1 A
254928 TTGTTGCATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:257110 original size:3 final size:3
Alignment explanation
Indices: 257104--257131 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
257094 GTCGTCGTAT
257104 CTG CTG CTG CTG CTG CTG CTG CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG C
257132 CTATGGAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.32, T:0.32
Consensus pattern (3 bp):
CTG
Found at i:258557 original size:2 final size:2
Alignment explanation
Indices: 258550--258582 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
258540 GAGGAAGTCA
258550 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 A
258583 AGGTTTCCGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:262208 original size:2 final size:2
Alignment explanation
Indices: 262201--262233 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
262191 CAGCTTAATG
262201 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 A
262234 AGAAGGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:263191 original size:6 final size:6
Alignment explanation
Indices: 263180--263204 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
263170 CAAGGAGGGG
263180 TCAAAC TCAAAC TCAAAC TCAAAC T
1 TCAAAC TCAAAC TCAAAC TCAAAC T
263205 GGACAGGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (6 bp):
TCAAAC
Found at i:269022 original size:14 final size:14
Alignment explanation
Indices: 269005--269033 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
268995 ATTGATTAAA
269005 TATTATTTTTATTT
1 TATTATTTTTATTT
269019 TATTATTTTTATTT
1 TATTATTTTTATTT
269033 T
1 T
269034 TAATAATATT
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:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TATTATTTTTATTT
Found at i:270007 original size:16 final size:15
Alignment explanation
Indices: 269978--270032 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 15
269968 AAATGAATTG
269978 TATTTAAATATATTA
1 TATTTAAATATATTA
269993 TATTTAAAT-TA-TA
1 TATTTAAATATATTA
270006 T-TTT--ATATATT-
1 TATTTAAATATATTA
270017 TA-TTAAATATATTA
1 TATTTAAATATATTA
270031 TA
1 TA
270033 CTTTCGTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
10 2 0.06
11 5 0.15
12 4 0.12
13 10 0.29
14 4 0.12
15 9 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTTAAATATATTA
Found at i:270642 original size:2 final size:2
Alignment explanation
Indices: 270629--270658 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
270619 GGGCAGTTTG
*
270629 TA TA TG 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
270659 AGGCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Done.