Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold304
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: 1004668
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 49120 characters in sequence are not A, C, G, or T
File 1 of 4
Found at i:33 original size:3 final size:3
Alignment explanation
Indices: 25--56 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
15 TATGAGTAAT
25 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
57 CCAATTGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3158 original size:20 final size:21
Alignment explanation
Indices: 3116--3158 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3106 GATTATTTTA
*
3116 AAAACTCAATTGACTTAATCC
1 AAAACTCAATTGACTTAACCC
3137 AAAA-TCAACTTGACTT-ACCC
1 AAAACTCAA-TTGACTTAACCC
3157 AA
1 AA
3159 TTGATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.44, C:0.26, G:0.05, T:0.26
Consensus pattern (21 bp):
AAAACTCAATTGACTTAACCC
Found at i:7924 original size:25 final size:25
Alignment explanation
Indices: 7896--7945 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
7886 TACAGAATAT
7896 TTTAAATTT-TGTAATATT-TTTTAAA
1 TTTAAATTTGTG-AAT-TTATTTTAAA
7921 TTTAAATTTGTGAATTTATTTTAAA
1 TTTAAATTTGTGAATTTATTTTAAA
7946 ATTTTAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 2 0.09
25 19 0.83
26 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (25 bp):
TTTAAATTTGTGAATTTATTTTAAA
Found at i:10187 original size:20 final size:21
Alignment explanation
Indices: 10154--10202 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
10144 ATTAATTACA
* * *
10154 TTAAACATTTTAAAATTA-TT
1 TTAAATATTCTAAAATGATTT
*
10174 TTAAATATTCTAAAGTGATTT
1 TTAAATATTCTAAAATGATTT
10195 TTAAATAT
1 TTAAATAT
10203 AAAATGTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (21 bp):
TTAAATATTCTAAAATGATTT
Found at i:16104 original size:25 final size:24
Alignment explanation
Indices: 16048--16104 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
16038 TGTTTCATAT
*
16048 AACTCACCGTTTAGCTTAATATAA
1 AACTCACCATTTAGCTTAATATAA
*
16072 AACGCACCATATTA-CTTAATACTAA
1 AACTCACCAT-TTAGCTTAATA-TAA
16097 AACTCACC
1 AACTCACC
16105 GTTTGGAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 15 0.54
25 13 0.46
ACGTcount: A:0.40, C:0.26, G:0.05, T:0.28
Consensus pattern (24 bp):
AACTCACCATTTAGCTTAATATAA
Found at i:25262 original size:29 final size:29
Alignment explanation
Indices: 25216--25272 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
25206 CGGTGCTTTT
*
25216 GAACCAATAACTCAGATA-TCACTTGGTTC
1 GAACCAACAACTCAGATACT-ACTTGGTTC
* *
25245 GAACCAACAGCTCGGATACTACTTGGTT
1 GAACCAACAACTCAGATACTACTTGGTT
25273 TAAACCTTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (29 bp):
GAACCAACAACTCAGATACTACTTGGTTC
Found at i:27153 original size:53 final size:53
Alignment explanation
Indices: 27095--27201 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
27085 TGTTTCTAGG
27095 TACTGAAGTTAAATTAATCTCAGAACAGACCAAATTAAGAATTATACCTTTCT
1 TACTGAAGTTAAATTAATCTCAGAACAGACCAAATTAAGAATTATACCTTTCT
27148 TACTGAAGTTAAATTAATCTCAGAACAGACCAAATTAAGAATTATACCTTTCT
1 TACTGAAGTTAAATTAATCTCAGAACAGACCAAATTAAGAATTATACCTTTCT
27201 T
1 T
27202 TGCACGTCAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (53 bp):
TACTGAAGTTAAATTAATCTCAGAACAGACCAAATTAAGAATTATACCTTTCT
Found at i:37844 original size:5 final size:5
Alignment explanation
Indices: 37821--37873 Score: 76
Period size: 5 Copynumber: 11.2 Consensus size: 5
37811 TTTTTATGTT
*
37821 TTATA -TATA TTAT- TT-TA TTATA TTATA TTATA TTATA TTGTA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
37868 TTATA T
1 TTATA T
37874 AAGTAAAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
3 1 0.02
4 8 0.19
5 34 0.79
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:37908 original size:16 final size:16
Alignment explanation
Indices: 37874--37906 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
37864 TATATTATAT
37874 AAGTAAAAATAAAAAA
1 AAGTAAAAATAAAAAA
37890 AAGT-AAAATAAAAAA
1 AAGTAAAAATAAAAAA
37905 AA
1 AA
37907 AGATGACAAA
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:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
AAGTAAAAATAAAAAA
Found at i:38907 original size:5 final size:5
Alignment explanation
Indices: 38899--38955 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
38889 TTAGTTTATT
* *
38899 TAATA TAATA TAATA TAACA TAATA TATTATA TTATA TAATA -AA-A TAATA
1 TAATA TAATA TAATA TAATA TAATA TA--ATA TAATA TAATA TAATA TAATA
38949 T-ATA TAA
1 TAATA TAA
38956 AACATAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.19
5 30 0.70
7 4 0.09
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:39701 original size:40 final size:40
Alignment explanation
Indices: 39639--39775 Score: 95
Period size: 40 Copynumber: 3.3 Consensus size: 40
39629 GAAGGAGATG
* *
39639 AAAAATGAAA-GAGAGCACAAATGGATGAACAAAAAAGGAA
1 AAAAATGAAAGGAAAACA-AAATGGATGAACAAAAAAGGAA
39679 AAAAATGAAAGGAAAACAAAAT-GA-GAACGAAAGAGACAGGAA
1 AAAAATGAAAGGAAAACAAAATGGATGAAC-AAA-A-A-AGGAA
* * *
39721 ACGAAGAAGGGAAAGGAAAA-AACACATGGATGAACAAAAGAGG-G
1 A--AA-AA-TGAAAGGAAAACAA-A-ATGGATGAACAAAAAAGGAA
39765 AAAAATGAAAG
1 AAAAATGAAAG
39776 AAATGGTAGA
Statistics
Matches: 78, Mismatches: 6, Indels: 26
0.71 0.05 0.24
Matches are distributed among these distances:
38 4 0.05
39 5 0.06
40 20 0.26
41 8 0.10
42 8 0.10
44 3 0.04
45 7 0.09
46 11 0.14
47 3 0.04
48 5 0.06
49 4 0.05
ACGTcount: A:0.61, C:0.07, G:0.26, T:0.06
Consensus pattern (40 bp):
AAAAATGAAAGGAAAACAAAATGGATGAACAAAAAAGGAA
Found at i:49459 original size:5 final size:5
Alignment explanation
Indices: 49449--49473 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
49439 TAAAGAAACC
49449 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
49474 AGCACAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:54772 original size:43 final size:43
Alignment explanation
Indices: 54722--54803 Score: 164
Period size: 43 Copynumber: 1.9 Consensus size: 43
54712 TGTCAACAAG
54722 AAAGTTTAGTTTAAAACTACTTCTTGTTTAGATTAATCAGAAT
1 AAAGTTTAGTTTAAAACTACTTCTTGTTTAGATTAATCAGAAT
54765 AAAGTTTAGTTTAAAACTACTTCTTGTTTAGATTAATCA
1 AAAGTTTAGTTTAAAACTACTTCTTGTTTAGATTAATCA
54804 TAATTCTAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.43
Consensus pattern (43 bp):
AAAGTTTAGTTTAAAACTACTTCTTGTTTAGATTAATCAGAAT
Found at i:54810 original size:22 final size:22
Alignment explanation
Indices: 54742--54810 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
54732 TTAAAACTAC
*
54742 TTCTTGTTTAGATTAATCAGAA
1 TTCTTGTTTAGATTAATCATAA
*** * * *
54764 -TAAAGTTTAGTTTAA-AACTAC
1 TTCTTGTTTAGATTAATCA-TAA
54785 TTCTTGTTTAGATTAATCATAA
1 TTCTTGTTTAGATTAATCATAA
54807 TTCT
1 TTCT
54811 AGTATACTTA
Statistics
Matches: 31, Mismatches: 13, Indels: 6
0.62 0.26 0.12
Matches are distributed among these distances:
20 1 0.03
21 12 0.39
22 17 0.55
23 1 0.03
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (22 bp):
TTCTTGTTTAGATTAATCATAA
Found at i:57622 original size:35 final size:34
Alignment explanation
Indices: 57584--57733 Score: 131
Period size: 35 Copynumber: 4.3 Consensus size: 34
57574 ATATGAGAAT
*
57584 TTTTTTTAAAACACGATAA-TTTTGAAACACAATA
1 TTTTTTTAAAACACGA-AACTTTTGAAACACAAGA
* * * * *
57618 TTTTTTGAAGACATGGAAATTTTTGAAAACACAGGA
1 TTTTTTTAAAACA-CGAAACTTTTG-AAACACAAGA
* * *
57654 ATTTTTTGAAACACGAAACTTTTGAAACACGAAAA
1 TTTTTTTAAAACACGAAACTTTTGAAACAC-AAGA
* * * * *
57689 ATTTTTGAAAACACAAAAATTTTGAAACACGAGA
1 TTTTTTTAAAACACGAAACTTTTGAAACACAAGA
57723 TTTTTTTAAAA
1 TTTTTTTAAAA
57734 GGACGTATCG
Statistics
Matches: 91, Mismatches: 21, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
34 30 0.33
35 44 0.48
36 17 0.19
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (34 bp):
TTTTTTTAAAACACGAAACTTTTGAAACACAAGA
Found at i:57641 original size:19 final size:19
Alignment explanation
Indices: 57617--57664 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
57607 GAAACACAAT
* *
57617 ATTTTTTGAAGACA-TGGA
1 ATTTTTTGAAAACACAGGA
*
57635 AATTTTTGAAAACACAGGA
1 ATTTTTTGAAAACACAGGA
57654 ATTTTTTGAAA
1 ATTTTTTGAAA
57665 CACGAAACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.38
Consensus pattern (19 bp):
ATTTTTTGAAAACACAGGA
Found at i:57727 original size:16 final size:16
Alignment explanation
Indices: 57586--57727 Score: 108
Period size: 16 Copynumber: 8.3 Consensus size: 16
57576 ATGAGAATTT
*
57586 TTTTTAAAACACGATAA
1 TTTTTGAAACACGA-AA
57603 -TTTTGAAACAC-AATA
1 TTTTTGAAACACGAA-A
*
57618 TTTTTTGAAGACATGGAAA
1 -TTTTTGAA-ACA-CGAAA
*
57637 TTTTTGAAAACACAGGAAT
1 TTTTTG-AAACAC--GAAA
57656 TTTTTGAAACACGAAA
1 TTTTTGAAACACGAAA
*
57672 CTTTTGAAACACGAAAAA
1 TTTTTGAAACACG--AAA
*
57690 TTTTTGAAAACACAAAA
1 TTTTTG-AAACACGAAA
* *
57707 ATTTTGAAACACGAGA
1 TTTTTGAAACACGAAA
57723 TTTTT
1 TTTTT
57728 TTAAAAGGAC
Statistics
Matches: 101, Mismatches: 12, Indels: 25
0.73 0.09 0.18
Matches are distributed among these distances:
14 1 0.01
15 2 0.02
16 37 0.37
17 15 0.15
18 26 0.26
19 18 0.18
20 2 0.02
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (16 bp):
TTTTTGAAACACGAAA
Found at i:58221 original size:14 final size:14
Alignment explanation
Indices: 58204--58245 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
58194 ATTTTTCCTT
58204 TTTCTTTTTTTTTC
1 TTTCTTTTTTTTTC
58218 TTTC-TTTTTTTTC
1 TTTCTTTTTTTTTC
* *
58231 TTGCTCTTTTTTTC
1 TTTCTTTTTTTTTC
58245 T
1 T
58246 GGACTGCTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (14 bp):
TTTCTTTTTTTTTC
Found at i:58238 original size:15 final size:13
Alignment explanation
Indices: 58204--58245 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
58194 ATTTTTCCTT
58204 TTTCTTTTTTTTTC
1 TTTC-TTTTTTTTC
58218 TTTCTTTTTTTTC
1 TTTCTTTTTTTTC
*
58231 TTGCTCTTTTTTTC
1 TTTCT-TTTTTTTC
58245 T
1 T
58246 GGACTGCTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 13 0.50
14 13 0.50
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (13 bp):
TTTCTTTTTTTTC
Found at i:58507 original size:4 final size:4
Alignment explanation
Indices: 58500--58581 Score: 65
Period size: 4 Copynumber: 22.0 Consensus size: 4
58490 TTTTTATTTT
*
58500 TTTC TTTCC CTTTC -TTC -TTC TTCC T-TC T-TC TT-C TTT- TTTC -TTC
1 TTTC TTT-C -TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
58543 TTTC TTTC TTTC -TTC TCTT- TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC T-TTC TTTC TTTC TTTC TTTC TTTC
58582 ACGATCAGCG
Statistics
Matches: 66, Mismatches: 2, Indels: 20
0.75 0.02 0.23
Matches are distributed among these distances:
3 25 0.38
4 34 0.52
5 4 0.06
6 3 0.05
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTC
Found at i:58527 original size:13 final size:13
Alignment explanation
Indices: 58511--58579 Score: 70
Period size: 13 Copynumber: 5.2 Consensus size: 13
58501 TTCTTTCCCT
*
58511 TTCTTCTTCTTCC
1 TTCTTCTTCTTTC
*
58524 TTCTTCTTCTTTT
1 TTCTTCTTCTTTC
58537 TTCTTCTTTCTTTC
1 TTCTTC-TTCTTTC
58551 TTTCTTC-TCTTT-
1 -TTCTTCTTCTTTC
58563 TTCTTTCTTTCTTTC
1 TTC-TTC-TTCTTTC
58578 TT
1 TT
58580 TCACGATCAG
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
11 3 0.06
12 3 0.06
13 22 0.47
14 11 0.23
15 8 0.17
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
TTCTTCTTCTTTC
Found at i:58561 original size:27 final size:27
Alignment explanation
Indices: 58510--58581 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
58500 TTTCTTTCCC
*
58510 TTTCTTC-TTC-TTCCTTCTTCTTCTTT
1 TTTCTTCTTTCTTTCTTTCTTCTTC-TT
58536 TTTCTTCTTTCTTTCTTTCTTC-TCTT
1 TTTCTTCTTTCTTTCTTTCTTCTTCTT
58562 TTTCTTTCTTTCTTTCTTTC
1 TTTC-TTCTTTCTTTCTTTC
58582 ACGATCAGCG
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
26 13 0.31
27 20 0.48
28 9 0.21
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTCTTCTTTCTTTCTTTCTTCTTCTT
Found at i:59159 original size:30 final size:29
Alignment explanation
Indices: 59092--59226 Score: 128
Period size: 30 Copynumber: 4.6 Consensus size: 29
59082 AAAATTTTTG
* ** * *
59092 GGGT-AAAGTGTAATTTTGGGAAATTTTA
1 GGGTCAAAATGTAATTTTAAGAAAGTTAA
* *
59120 GGGTCAAAATGTAATTCTAGGAAAGTTCAA
1 GGGTCAAAATGTAATTTTAAGAAAGTT-AA
* * *
59150 GGGTTAAAATGCAATTTTAAGAAAGTTGAG
1 GGGTCAAAATGTAATTTTAAGAAAGTT-AA
* * *
59180 GGGTTAAAATGTAATTTTAAAAAAGTTAG
1 GGGTCAAAATGTAATTTTAAGAAAGTTAA
59209 GGGTCAAAATGTAATTTT
1 GGGTCAAAATGTAATTTT
59227 TTTTAAAAAA
Statistics
Matches: 91, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
28 4 0.04
29 37 0.41
30 50 0.55
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTAAGAAAGTTAA
Found at i:61745 original size:27 final size:27
Alignment explanation
Indices: 61715--61793 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
61705 TTGCCAATTA
* * *
61715 GTTTGGCAAGCTGGAGTTCACCAGTTG
1 GTTTGGCGAGCTGGGGTTCACCAGTAG
*
61742 GTTTGGCGAGTTGGGGTTCACCAGTAG
1 GTTTGGCGAGCTGGGGTTCACCAGTAG
*
61769 GTTTTGCGAGCTGGGGTTCACCAGT
1 GTTTGGCGAGCTGGGGTTCACCAGT
61794 CTAAGTCGAG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.15, C:0.18, G:0.37, T:0.30
Consensus pattern (27 bp):
GTTTGGCGAGCTGGGGTTCACCAGTAG
Found at i:65438 original size:25 final size:25
Alignment explanation
Indices: 65390--65438 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
65380 CATAATTGAA
* * *
65390 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
65415 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
65439 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:65902 original size:43 final size:43
Alignment explanation
Indices: 65834--65919 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
65824 TACGTGATTG
*
65834 ATATTGAAATGACAAAGATGGGAAATGAATATGAGATGAGAAA
1 ATATTGAAATGACAAAGATGAGAAATGAATATGAGATGAGAAA
* *
65877 ATATTGAAATGACAAATATGAGAAATGATTATGAGATGAGAAA
1 ATATTGAAATGACAAAGATGAGAAATGAATATGAGATGAGAAA
65920 TGAAATATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.51, C:0.02, G:0.23, T:0.23
Consensus pattern (43 bp):
ATATTGAAATGACAAAGATGAGAAATGAATATGAGATGAGAAA
Found at i:66849 original size:30 final size:30
Alignment explanation
Indices: 66804--66878 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
66794 CATGGCTTGG
* *
66804 ACACACGGGCATGTGTCACACACGGGCAAC
1 ACACATGGGCATGTGTCACACACAGGCAAC
*
66834 ACACATGGGCTTGTGTCACACACAGGCAAC
1 ACACATGGGCATGTGTCACACACAGGCAAC
*
66864 ACACATAGGCATGTG
1 ACACATGGGCATGTG
66879 ACCCAAGTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.31, C:0.29, G:0.25, T:0.15
Consensus pattern (30 bp):
ACACATGGGCATGTGTCACACACAGGCAAC
Found at i:82267 original size:44 final size:43
Alignment explanation
Indices: 82066--83265 Score: 292
Period size: 44 Copynumber: 27.7 Consensus size: 43
82056 TCGGTGGGCA
* * * *
82066 ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACC
1 ATAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCC
* * * * * *
82109 TTAGATCTTATCTCTCTATGAAGTTGCAG-AGAGCAGATCACA-TC
1 ATA-ATCTTATCT-TC-CTGAAGTTGCAGTGGAGCAGATTAAAGCC
* * * *
82153 -TAGTCTTATCCTCCTGAAGTTGCAGT-GATGCAGACTGAAGATGGC
1 ATAATCTTATCTTCCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCC
82198 A-AATCTTATC-TCCTTGAAGTTGCAGTGGAGCAGATTAAAGCC
1 ATAATCTTATCTTCC-TGAAGTTGCAGTGGAGCAGATTAAAGCC
* * **
82240 GATAATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAATC
1 -ATAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCC
* * *
82284 ACAGATCTTATC-TCTCTGAAGTTGCA---AAG-AGA--AAATCGC
1 ATA-ATCTTATCTTC-CTGAAGTTGCAGTGGAGCAGATTAAAGC-C
* * * *
82323 ATCTAGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTAAGTAAG-C
1 A--TAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGA-TTA--AAGCC
* * ** *
82370 A-AGTCTTATCCTCCTGAAGTTATAGT-GAGGCAGACTGAAGATAG-C
1 ATAATCTTATCTTCCTGAAGTTGCAGTGGA-GCAGA-T-TA-A-AGCC
* * *
82415 A-AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACC
1 ATAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCC
* * *** *
82457 -TCAAATCTTATC-TCTCTGAAGTTGCAG-AGAGTAGATCGCA-TC
1 AT--AATCTTATCTTC-CTGAAGTTGCAGTGGAGCAGATTAAAGCC
* * * * * ** *
82499 -TAGTCTTATATCCCTGAATTTACAGCAGAGCAGACTAAGTAAG-C
1 ATAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGA-TTA--AAGCC
* * *
82543 A-AGTCTTATCCTT-TTGAAGTTGCAGT-GAGGCAGACTGAAGATAG-C
1 ATAATCTTAT-CTTCCTGAAGTTGCAGTGGA-GCAGA-T-TA-A-AGCC
* *
82588 A-AATCTTATC-TCCGTGAAGTTGCAGTGGAG-TGAATTAAAACC
1 ATAATCTTATCTTCC-TGAAGTTGCAGTGGAGCAG-ATTAAAGCC
* ** * *** *
82630 TTAGATCTTATCTCTTTATGAAGTTGCAG-AGAGCAGATCGCA-TC
1 ATA-ATCTTA--TCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCC
* * * *
82674 -TAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGTAAG-C
1 ATAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGA-TTA--AAGCC
* * * * *
82718 A-AGTCTTATCCTCTTGAAGTTGCAGT-GAGGCAGACTGAAGATGAC
1 ATAATCTTATCTTCCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCC
* * *
82763 A-AATCTTATCTCCCTGAAGTAGCAGTGGAACAGATTAAAGCC
1 ATAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCC
* * *
82805 GATAATCCTATC-TCTCTGAAGTTGCAGTAGAGCGGATTAAA---
1 -ATAATCTTATCTTC-CTGAAGTTGCAGTGGAGCAGATTAAAGCC
* * *** *
82846 ATTAGATCTTATCTTTCTGAAGTTGCAG-AGAGCAGATCGCA-TC
1 A-TA-ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCC
* * *
82889 -TAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAG-C
1 ATAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGA-TTA--AAGCC
* * * * *
82933 A-AGTCTTATCCTCCTAAAGTTGCAGT-GAGGCAGACTGAAGATGGC
1 ATAATCTTATCTTCCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCC
*
82978 A-AATC-T-TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC
1 ATAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCC
* * **
83018 GATAATCCTAT-TTCCCTGAAGTTGCAGTGGAGCGGATTAAAATC
1 -ATAATCTTATCTT-CCTGAAGTTGCAGTGGAGCAGATTAAAGCC
* ** * *** *
83062 ACAGATCTTATC-TCTCTGAAGTTGCA-AAGAGCAAATCGCA-TC
1 ATA-ATCTTATCTTC-CTGAAGTTGCAGTGGAGCAGATTAAAGCC
* * * * *
83104 -TAGTCTTATCTCCCTGAAGTTACAGCGGAGCAGACTAAGTAAG-C
1 ATAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGA-TTA--AAGCC
* * * *
83148 A-AGTCTTATCCTCCTGAAGTTGTAGT-GAGGCAGACTGAAGATAG-C
1 ATAATCTTATCTTCCTGAAGTTGCAGTGGA-GCAGA-T-TA-A-AGCC
* * * *
83193 A-AATCTTATCTCCCTGAAGTTGTAGTGGAGCCGATTAAAGCT
1 ATAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCC
83235 ATAAGTCTTATC-TCCTTGAAGTTGCAGTGGA
1 ATAA-TCTTATCTTCC-TGAAGTTGCAGTGGA
83266 ATATATTGAA
Statistics
Matches: 870, Mismatches: 173, Indels: 227
0.69 0.14 0.18
Matches are distributed among these distances:
38 3 0.00
39 2 0.00
40 103 0.12
41 60 0.07
42 60 0.07
43 80 0.09
44 355 0.41
45 166 0.19
46 35 0.04
47 4 0.00
49 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (43 bp):
ATAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCC
Found at i:82433 original size:173 final size:173
Alignment explanation
Indices: 82068--82959 Score: 985
Period size: 173 Copynumber: 5.2 Consensus size: 173
82058 GGTGGGCAAT
*
82068 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTATGAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTC--TGAAGT
* *
82133 TGCAGAGAGCAGATCACATCTAGTCTTATC-CTCCTGAAGTTGCAG-TGATGCAGACTGAAG-AT
64 TGCAGAGAGCAGATCGCATCTAGTCTTATCTC-CCTGAAGTTGCAGCGGA-GCAGACT-AAGTA-
* * * * **
82195 GGCAAATCTTAT-CTCCTTGAAGTTGCAGTG-GAGCAGATTAAAG-CCG-A
125 AGCAAGTCTTATCCTCC-TGAAGTTGCAGTGAG-GCAGACTGAAGATAGCA
* * * **
82242 TAATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTT
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTT
* * *
82307 GCAAAGAGAAAATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTAAGTAAGCAA
65 GCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTAAGTAAGCAA
**
82372 GTCTTATCCTCCTGAAGTTATAGTGAGGCAGACTGAAGATAGCA
130 GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATAGCA
* *
82416 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAAATCTTATCTCTCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTG
* * * * *
82481 CAGAGAGTAGATCGCATCTAGTCTTATATCCCTGAATTTACAGCAGAGCAGACTAAGTAAGCAAG
66 CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTAAGTAAGCAAG
**
82546 TCTTATCCTTTTGAAGTTGCAGTGAGGCAGACTGAAGATAGCA
131 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATAGCA
* * * *
82589 AATCTTATCTCCGTGAAGTTGCAGTGGAGTGAATTAAAACCTTAGATCTTATCTCTTTATGAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTC--TCTGAAGT
* *
82654 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGTAAGCA
64 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTAAGTAAGCA
*
82719 AGTCTTATCCTCTTGAAGTTGCAGTGAGGCAGACTGAAGAT-GACA
129 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATAG-CA
* * * * * *
82764 AATCTTATCTCCCTGAAGTAGCAGTGGAACAGATTAAAGCCGATA-ATCCTATCTCTCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACC-TTAGATCTTATCTCTCTGAAGTT
* *** ** * * * *
82828 GCAGTAGAGCGGATTAAAAT-TAGATCTTATCTTTCTGAAGTTGCAG-AGAGCAGA-T-CG-CAT
65 GCAG-AGAGCAGA-TCGCATCTAG-TCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTAAGTAAG
*
82888 CTAGTCTTAT-CTCCCTGAAGTTGCAGTG-GAGCAGACT-AAG-TAAGCA
127 CAAGTCTTATCCT-CCTGAAGTTGCAGTGAG-GCAGACTGAAGAT-AGCA
* *
82934 AGTCTTATC-CTCCTAAAGTTGCAGTG
1 AATCTTATCTC-CCTGAAGTTGCAGTG
82960 AGGCAGACTG
Statistics
Matches: 625, Mismatches: 73, Indels: 43
0.84 0.10 0.06
Matches are distributed among these distances:
169 2 0.00
170 29 0.05
171 32 0.05
172 34 0.05
173 279 0.45
174 22 0.04
175 225 0.36
176 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (173 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTG
CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTAAGTAAGCAAG
TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATAGCA
Found at i:82550 original size:217 final size:218
Alignment explanation
Indices: 82154--82614 Score: 467
Period size: 217 Copynumber: 2.1 Consensus size: 218
82144 GATCACATCT
* * * *
82154 AGTCTTATCCTCCTGAAGTTGCAGTGATGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTT
1 AGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATAGCAAATCTTATCTCCCTGAAGTT
* * * *
82219 GCAGTGGAGCAGATTAAAGCCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAATC
66 GCAGTGGAGCAGATTAAAACCCATAATCCTATCTTCCTGAAGTTGCAGTAGAGCAGATTAAAATC
* * * * * * *
82284 ACAGATCTTATCTCTCTGAAGTTGCAAAGAGAAAATCGCATCTAGTCTTAT-CTCCCTGAAGTTG
131 ACAGATCTTATATCCCTGAAGTTACAAAGAGAAAATAGAAGCAAGTCTTATCCT-CCTGAAGTTG
82348 CAGCGGA-GCAGACT-AAG-TAAGCA
195 CAG-GGAGGCAGACTGAAGAT-AGCA
*
82371 AGTCTTATCCTCCTGAAGTTATAGTGAGGCAGACTGAAGATAGCAAATCTTATCTCCCTGAAGTT
1 AGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATAGCAAATCTTATCTCCCTGAAGTT
* * * ***
82436 GCAGTGGAGCGGATTAAAACCTCA-AATCTTATC-TCTCTGAAGTTGCAG-AGAGTAGA-TCGCA
66 GCAGTGGAGCAGATTAAAACC-CATAATCCTATCTTC-CTGAAGTTGCAGTAGAGCAGATTAAAA
* * * * * **
82497 TC-TAG-TCTTATATCCCTGAATTTACAGCAGAGCAGACTAAGTAAGCAAGTCTTATCCTTTTGA
129 TCACAGATCTTATATCCCTGAAGTTACA-AAGAG-AAAAT-AG-AAGCAAGTCTTATCCTCCTGA
*
82560 AGTTGCAGTGAGGCAGACTGAAGATAGCA
190 AGTTGCAGGGAGGCAGACTGAAGATAGCA
* *
82589 AATCTTAT-CTCCGTGAAGTTGCAGTG
1 AGTCTTATCCTCC-TGAAGTTACAGTG
82615 GAGTGAATTA
Statistics
Matches: 200, Mismatches: 33, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
213 17 0.09
214 6 0.03
215 7 0.04
216 10 0.05
217 131 0.65
218 28 0.14
219 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (218 bp):
AGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATAGCAAATCTTATCTCCCTGAAGTT
GCAGTGGAGCAGATTAAAACCCATAATCCTATCTTCCTGAAGTTGCAGTAGAGCAGATTAAAATC
ACAGATCTTATATCCCTGAAGTTACAAAGAGAAAATAGAAGCAAGTCTTATCCTCCTGAAGTTGC
AGGGAGGCAGACTGAAGATAGCA
Found at i:82710 original size:348 final size:346
Alignment explanation
Indices: 82068--82926 Score: 1014
Period size: 348 Copynumber: 2.5 Consensus size: 346
82058 GGTGGGCAAT
* * *
82068 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTATGAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAAATCTTATCTCTC--TGAAGT
* * *
82133 TGCAGAGAGCAGATCACATCTAGTCTTATCCTCCTGAAGTTGCAGTGATGCAGACTGAAGATGGC
64 TGCAGAGAGCAGATCACATCTAGTCTTATCCTCCTGAAGTTACAGAGATGCAGACTGAAGATAGC
* *
82198 AAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTTCCTGAAGTT
129 AAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAAGCAGATAATCCTATCTTCCTGAAGTT
* * *
82263 GCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAAAGAGAAAATCGCATCTA
194 GCAGTGGAGCGAATTAAAACCACAGATCTTATCTCTATGAAGTTGCAAAGAGAAAATCGCATCTA
* *
82328 GTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTAT
259 GTCTTATCTCCCTAAAGTTGCAGCGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTAC
82393 AGTGAGGCAGACTGAAGAT-AGCA
324 AGTGAGGCAGACTGAAGATGA-CA
82416 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAAATCTTATCTCTCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAAATCTTATCTCTCTGAAGTTG
* * * *
82481 CAGAGAGTAGATCGCATCTAGTCTTAT-ATCCCTGAATTTACAGCAGA-GCAGACT-AAG-TAAG
66 CAGAGAGCAGATCACATCTAGTCTTATCCT-CCTGAAGTTACAG-AGATGCAGACTGAAGAT-AG
* * * * *
82542 CAAGTCTTATC-CTTTTGAAGTTGCAGT-GAGGCAGACTGAAGATAGCA-AATCTTATC-TCCGT
128 CAAATCTTATCTC-CTTGAAGTTGCAGTGGA-GCAGACTAAAG-CAG-ATAATCCTATCTTCC-T
* ** * * *
82603 GAAGTTGCAGTGGAGTGAATTAAAACCTTAGATCTTATCTCTTTATGAAGTTGCAGAGAGCAGAT
188 GAAGTTGCAGTGGAGCGAATTAAAACCACAGATCTTATCTC--TATGAAGTTGCAAAGAGAAAAT
* *
82668 CGCATCTAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCTT
251 CGCATCTAGTCTTATCTCCCTAAAGTTGCAGCGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCT
*
82733 GAAGTTGCAGTGAGGCAGACTGAAGATGACA
316 GAAGTTACAGTGAGGCAGACTGAAGATGACA
* * * * * *
82764 AATCTTATCTCCCTGAAGTAGCAGTGGAACAGATTAAAGCC-GATAATCCTATCTCTCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTCA-AATCTTATCTCTCTGAAGTT
* * * * * * *
82828 GCAGTAGAGCGGATTAAAAT-TAGATCTTATCTTTCTGAAGTTGCAGAGA-GCAGA-TCG--CAT
65 GCAG-AGAGCAGA-TCACATCTAG-TCTTATCCTCCTGAAGTTACAGAGATGCAGACT-GAAGAT
* * *
82888 --CTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
126 AGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAA
82927 GTAAGCAAGT
Statistics
Matches: 439, Mismatches: 51, Indels: 44
0.82 0.10 0.08
Matches are distributed among these distances:
344 4 0.01
345 40 0.09
346 127 0.29
347 7 0.02
348 222 0.51
349 19 0.04
350 19 0.04
351 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (346 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAAATCTTATCTCTCTGAAGTTG
CAGAGAGCAGATCACATCTAGTCTTATCCTCCTGAAGTTACAGAGATGCAGACTGAAGATAGCAA
ATCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAAGCAGATAATCCTATCTTCCTGAAGTTGC
AGTGGAGCGAATTAAAACCACAGATCTTATCTCTATGAAGTTGCAAAGAGAAAATCGCATCTAGT
CTTATCTCCCTAAAGTTGCAGCGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAG
TGAGGCAGACTGAAGATGACA
Found at i:82878 original size:215 final size:215
Alignment explanation
Indices: 82589--83265 Score: 1013
Period size: 215 Copynumber: 3.1 Consensus size: 215
82579 GAAGATAGCA
* * * *
82589 AATCTTATCTCCGTGAAGTTGCAGTGGAGTGAATTAAAACCTTAGATCTTATCTCTTTATGAAGT
1 AATCCTATCTCCGTGAAGTTGCAGTGGAGCGGATTAAAA--TTAGATCTTA--TCTTTCTGAAGT
*
82654 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGTAAGCA
62 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
* *
82719 AGTCTTATCCTCTTGAAGTTGCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTGAAGTA
127 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTGAAGTT
*
82784 GCAGTGGAACAGATTAAAGCCGAT
192 GCAGTGGAGCAGATTAAAGCCGAT
*
82808 AATCCTATCTCTC-TGAAGTTGCAGTAGAGCGGATTAAAATTAGATCTTATCTTTCTGAAGTTGC
1 AATCCTATCTC-CGTGAAGTTGCAGTGGAGCGGATTAAAATTAGATCTTATCTTTCTGAAGTTGC
82872 AGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGT
65 AGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGT
* *
82937 CTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATC-T-TCTCCCTGAAGTTGCA
130 CTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTGAAGTTGCA
83000 GTGGAGCAGATTAAAGCCGAT
195 GTGGAGCAGATTAAAGCCGAT
* * * *
83021 AATCCTATTTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCGTGAAGTTGCAGTGGAGCGGATTAAAAT--TAGATCTTATCTTTCTGAAGTTG
* * * *
83086 CAAAGAGCAAATCGCATCTAGTCTTATCTCCCTGAAGTTACAGCGGAGCAGACTAAGTAAGCAAG
64 CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAG
*
83151 TCTTATCCTCCTGAAGTTGTAGTGAGGCAGACTGAAGAT-AGCAAATCTTATCTCCCTGAAGTTG
129 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGA-CAAATCTTATCTCCCTGAAGTTG
* * *
83215 TAGTGGAGCCGATTAAAG-CTAT
193 CAGTGGAGCAGATTAAAGCCGAT
* *
83237 AAGTCTTATCTCCTTGAAGTTGCAGTGGA
1 AA-TCCTATCTCCGTGAAGTTGCAGTGGA
83266 ATATATTGAA
Statistics
Matches: 422, Mismatches: 28, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
212 1 0.00
213 71 0.17
214 1 0.00
215 246 0.58
216 6 0.01
217 63 0.15
219 33 0.08
220 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (215 bp):
AATCCTATCTCCGTGAAGTTGCAGTGGAGCGGATTAAAATTAGATCTTATCTTTCTGAAGTTGCA
GAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTC
TTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTGAAGTTGCAG
TGGAGCAGATTAAAGCCGAT
Found at i:83073 original size:390 final size:389
Alignment explanation
Indices: 82154--83261 Score: 1275
Period size: 390 Copynumber: 2.8 Consensus size: 389
82144 GATCACATCT
* *
82154 AGTCTTATCCTCCTGAAGTTGCAGTGATGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
82219 GCAGTGGAGCAGATTAAAGCCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAATC
66 GCAGTGGAGCAGATTAAAGCCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAATC
* * * *
82284 ACAGATCTTATCTCTCTGAAGTTGCAAAGAGAAAATCGCATCTAGTCTTATCTCCCTGAAGTTGC
131 ACAGATCTTATCTCTCTGAAGTTGCAAAGAGAAAATAGAAGCAAGTCTTATCTCCCTGAAGTTGC
* * * * *
82349 AGCGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTATAGTGAGGCAGACTGAAGATAG
196 AGCGGAGCAGACTAAGTAAGCAAATCTTATCCTCCTGAAGTTACAGTGAGACAGACTAAAGACAG
* *
82414 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAAATCTTATCTCTCTGAAGT
261 CAAATCCTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAA-CTCAAATCTTATCTCTCTGAAGT
* *
82479 TGCAGAGAGTAGATCGCATCTAGTCTTATATCCCTGAATTTACAGCAGAGCAGACTAAGTAAGCA
325 TGCAGAGAGCAGATCGCATCTAGTCTTATATCCCTGAAGTTACAGCAGAGCAGACTAAGTAAGCA
** * *
82544 AGTCTTATCCTTTTGAAGTTGCAGTGAGGCAGACTGAAGATAGCAAATCTTATCTCCGTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
* * * * ** * * **
82609 GCAGTGGAG-TGAATTAAAACC-TTAGATCTTATCTCTTTATGAAGTTGCAG-AGAGCAGA-TCG
66 GCAGTGGAGCAG-ATTAAAGCCGATA-ATCCTA--TCTTCCTGAAGTTGCAGTGGAGCGGATTAA
* * * * ** * * *
82670 CATC-TAG-TCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATC-CTCT
127 AATCACAGATCTTATCTCTCTGAAGTTGCA-AAGAG-AAAAT-AG-AAGCAAGTCTTATCTC-CC
* *
82732 TGAAGTTGCAG-TGAGGCAGACTGAAG-ATGACAAATCTTAT-CTCCCTGAAG-TAGCAGTG-GA
187 TGAAGTTGCAGCGGA-GCAGACT-AAGTAAG-CAAATCTTATCCT-CCTGAAGTTA-CAGTGAG-
* * * * *
82792 ACAGATTAAAG-CCG-ATAATCCTATCTCTCTGAAGTTGCAGTAGAGCGGATTAAAA-TTAGATC
246 ACAGACTAAAGACAGCA-AATCCTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAACTCAAATC
* * * **
82854 TTATCTTTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAG
310 TTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATATCCCTGAAGTTACAGCAGAG
82919 CAGACTAAGTAAGCA
375 CAGACTAAGTAAGCA
*
82934 AGTCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATC-T-TCTCCCTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
82997 GCAGTGGAGCAGATTAAAGCCGATAATCCTAT-TTCCCTGAAGTTGCAGTGGAGCGGATTAAAAT
66 GCAGTGGAGCAGATTAAAGCCGATAATCCTATCTT-CCTGAAGTTGCAGTGGAGCGGATTAAAAT
* * * * * *
83061 CACAGATCTTATCTCTCTGAAGTTGCAAAGAGCAAATCGCATCTAGTCTTATCTCCCTGAAGTTA
130 CACAGATCTTATCTCTCTGAAGTTGCAAAGAGAAAATAGAAGCAAGTCTTATCTCCCTGAAGTTG
* ** * * *
83126 CAGCGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGTAGTGAGGCAGACTGAAGATA
195 CAGCGGAGCAGACTAAGTAAGCAAATCTTATCCTCCTGAAGTTACAGTGAGACAGACTAAAGACA
* * * * *
83191 GCAAATCTTATCTCCCTGAAGTTGTAGTGGAGCCGATTAAAGCT-ATAAGTCTTATCTC-CTTGA
260 GCAAATCCTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAACTCA-AA-TCTTATCTCTC-TGA
83254 AGTTGCAG
322 AGTTGCAG
83262 TGGAATATAT
Statistics
Matches: 586, Mismatches: 97, Indels: 72
0.78 0.13 0.10
Matches are distributed among these distances:
385 33 0.06
386 82 0.14
387 14 0.02
388 78 0.13
389 17 0.03
390 231 0.39
391 11 0.02
392 89 0.15
393 31 0.05
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (389 bp):
AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
GCAGTGGAGCAGATTAAAGCCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAATC
ACAGATCTTATCTCTCTGAAGTTGCAAAGAGAAAATAGAAGCAAGTCTTATCTCCCTGAAGTTGC
AGCGGAGCAGACTAAGTAAGCAAATCTTATCCTCCTGAAGTTACAGTGAGACAGACTAAAGACAG
CAAATCCTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAACTCAAATCTTATCTCTCTGAAGTT
GCAGAGAGCAGATCGCATCTAGTCTTATATCCCTGAAGTTACAGCAGAGCAGACTAAGTAAGCA
Found at i:84679 original size:13 final size:14
Alignment explanation
Indices: 84649--84684 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
84639 ATTATAATTA
*
84649 TTATTTATTTTCAT
1 TTATTTATTCTCAT
84663 TTATTTATTCT-AT
1 TTATTTATTCTCAT
84676 TTATTTATT
1 TTATTTATT
84685 GATTANNNNN
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (14 bp):
TTATTTATTCTCAT
Found at i:90958 original size:43 final size:43
Alignment explanation
Indices: 90910--91328 Score: 352
Period size: 43 Copynumber: 9.8 Consensus size: 43
90900 AGACCAAAAC
* *
90910 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTGAAGTCCATGGT
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGTCCATGAT
* * * *
90953 CTTTAGCGGCCCTTTTCCCACAAACGCCGCTGAAGGCCATGGT
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGTCCATGAT
* *
90996 CTTTAGCGGCCCTTTTCCCACAAACGCCGCTAAAGGT-CATGGT
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA-GTCCATGAT
* * * *
91039 CTTCAGCGGCACTTTTCCCACAAACGTCGCTAAAGGT-CATGCT
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA-GTCCATGAT
* * * *
91082 CTTTAGCGGCGCTTTTACGAAAAACGCCGCTAAAGGT-CATGGT
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA-GTCCATGAT
* * * ** * * * *
91125 CTTTAACGACGC-TTACAAAACAAACGCCACTAACA-ACAATGAC
1 CTTTAGCGGCGCTTTTC-CCACAAACGCCGCTAA-AGTCCATGAT
* * * * *
91168 CTTTAGAGGCGCTTCT-CTAGAAAACGCCACTAAA-TACC-TGAT
1 CTTTAGCGGCGCTTTTCCCA-CAAACGCCGCTAAAGT-CCATGAT
* * *
91210 CATTAGCGGCGCCTTTCCAACAAACGCCGCTAAAGTTCC-TGAT
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAG-TCCATGAT
* * * *
91253 CTTTAGCGGCGTTTTTCTCTCAAACGCCGCTAAAGACCATGAT
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGTCCATGAT
* *
91296 CTTTAGCAGCGCTTTTCCCACAAACGCCACTAA
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAA
91329 TTTTGGCAGA
Statistics
Matches: 308, Mismatches: 57, Indels: 22
0.80 0.15 0.06
Matches are distributed among these distances:
42 33 0.11
43 271 0.88
44 4 0.01
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.25
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGTCCATGAT
Found at i:91739 original size:21 final size:21
Alignment explanation
Indices: 91710--91760 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
91700 TTTTACGTTG
91710 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
91731 CTCTACTTCCCTCGTTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
91752 CTCTGCTTC
1 CTCTGCTTC
91761 TCTCACTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.06, C:0.45, G:0.16, T:0.33
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:91913 original size:66 final size:65
Alignment explanation
Indices: 91742--91921 Score: 193
Period size: 66 Copynumber: 2.7 Consensus size: 65
91732 TCTACTTCCC
* * * *
91742 TCGTTGCAGCCTCTGCTTCTCTC-ACTGTTGCATCTACTTTAAGCTGCTGCTGGAGTTCTTCATA
1 TCGTTG-AACCTCAGCTTCTCTCGA-TGTTGCATCTGCTTTAAGTTG-TGCTGGAGTTCTTCATA
91806 CTT
63 CTT
* * * * *
91809 TCGTTGAACCTCAGCTTCTCTCGCTGCTGTATTTGCTTTAAGTTGTAGCTGGAGTTCTTTATATC
1 TCGTTGAACCTCAGCTTCTCTCGATGTTGCATCTGCTTTAAGTTGT-GCTGGAGTTCTTCATA-C
91874 TT
64 TT
* * *
91876 T-TTTGAACCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTTGTG
1 TCGTTGAACCTCAGCTTCTCTCGATGTTGCATCTGCTTTAAGTTGTG
91922 TAATTTGCTC
Statistics
Matches: 94, Mismatches: 16, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
65 2 0.02
66 82 0.87
67 10 0.11
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (65 bp):
TCGTTGAACCTCAGCTTCTCTCGATGTTGCATCTGCTTTAAGTTGTGCTGGAGTTCTTCATACTT
Found at i:103259 original size:8 final size:8
Alignment explanation
Indices: 103246--103314 Score: 81
Period size: 8 Copynumber: 8.9 Consensus size: 8
103236 ACCCTTGACA
103246 CCCTAAAC
1 CCCTAAAC
103254 CCCTAAAC
1 CCCTAAAC
103262 CCCT-AAC
1 CCCTAAAC
*
103269 ACCTAAATC
1 CCCTAAA-C
103278 CCCTAAAC
1 CCCTAAAC
*
103286 CCCTAAAT
1 CCCTAAAC
103294 CCCT-AAC
1 CCCTAAAC
*
103301 CTCT-AAC
1 CCCTAAAC
103308 CCCTAAA
1 CCCTAAA
103315 TCTCGATCCC
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
7 17 0.33
8 28 0.54
9 7 0.13
ACGTcount: A:0.36, C:0.46, G:0.00, T:0.17
Consensus pattern (8 bp):
CCCTAAAC
Found at i:103482 original size:21 final size:21
Alignment explanation
Indices: 103441--103483 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
103431 GATCTCGAAT
*
103441 CTCTAAACCCTAAATCACTAA
1 CTCTAAACCCCAAATCACTAA
*
103462 CTCTTAACCCCAAACTC-CTAA
1 CTCTAAACCCCAAA-TCACTAA
103483 C
1 C
103484 CCCTAAACGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.37, C:0.40, G:0.00, T:0.23
Consensus pattern (21 bp):
CTCTAAACCCCAAATCACTAA
Found at i:103658 original size:14 final size:15
Alignment explanation
Indices: 103641--103673 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
103631 CTTAAATCAG
103641 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
*
103655 AATCCTTAATTCCAT
1 AATCCCTAATTCCAT
103670 AATC
1 AATC
103674 TATAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.33
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:104119 original size:41 final size:41
Alignment explanation
Indices: 104060--104416 Score: 347
Period size: 41 Copynumber: 8.7 Consensus size: 41
104050 AAATGTTTTT
* ** *
104060 GCGGCGCTTTTTCAAAAACGCCGCTAAATCTCGGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
104101 GTGGCGCTTTACCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGATCTGAGCATTA
* * * * * * *
104142 GCTGCACTTTTCTATAAACGCCACTAAAGATTTGAGCA-TC
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGATCTGAGCATTA
* ** * *
104182 GCGGCGATTTTGGAAAAACGCCGATAAAGATCTGAGCTTTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGATCTGAGCATTA
* * * *
104223 GCGGCGCTTCTACAAAAACGCCCCTAAATATCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGATCTGAGCATTA
* * *
104264 CCGGCGCTTTTTTCAAAAACGCCGCTAAAGATCTGAACATTA
1 GCGGCGC-TTTTCCAAAAACGCCGCTAAAGATCTGAGCATTA
* * * * *
104306 GCAGCGCTTCTCAAAAAACGCCGCTAATGATTTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGATCTGAGCATTA
* * * *
104347 GCGGCGATTTTACAAAAACGCCGCTAAAGATCTGGGAATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGATCTGAGCATTA
* ***
104388 GCGGTGCTTTTTTTTAAAACGCCGCTAAA
1 GCGGCGC-TTTTCCAAAAACGCCGCTAAA
104417 TCCCCAAAAG
Statistics
Matches: 251, Mismatches: 62, Indels: 5
0.79 0.19 0.02
Matches are distributed among these distances:
40 29 0.12
41 170 0.68
42 52 0.21
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (41 bp):
GCGGCGCTTTTCCAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:104361 original size:124 final size:121
Alignment explanation
Indices: 104073--104416 Score: 355
Period size: 124 Copynumber: 2.8 Consensus size: 121
104063 GCGCTTTTTC
* ** * * *
104073 AAAAACGCCGCTAAATCTCGGAGCATTAGTGGCGCTTTACCAAAAACGCCGCTAAAGATCTGAGC
1 AAAAACGCCGATAAAGATCTGAGCATTAGCGGCGTTTTA-CAAAAACGCCGCTAAAGATCTGAGC
* * * * * * * * * * **
104138 ATTAGCTGCACTTTTCTATAAACGCCACTAAAGATTTGAGCATCGCGGCGATTTTGG
65 ATTAGCGGCGCTTTTTTAAAAACGCCGCTAAAGATCTGAACATAGCAGCGATTCTCA
* * * *
104195 AAAAACGCCGATAAAGATCTGAGCTTTAGCGGCGCTTCTACAAAAACGCCCCTAAATATCTGAGC
1 AAAAACGCCGATAAAGATCTGAGCATTAGCGGCG-TTTTACAAAAACGCCGCTAAAGATCTGAGC
* *
104260 ATTACCGGCGCTTTTTTCAAAAACGCCGCTAAAGATCTGAACATTAGCAGCGCTTCTCA
65 ATTAGCGGCGCTTTTTT-AAAAACGCCGCTAAAGATCTGAACA-TAGCAGCGATTCTCA
* * * * *
104319 AAAAACGCCGCTAATGATTTGAGCATTAGCGGCGATTTTACAAAAACGCCGCTAAAGATCTGGGA
1 AAAAACGCCGATAAAGATCTGAGCATTAGCGGCG-TTTTACAAAAACGCCGCTAAAGATCTGAGC
* *
104384 ATTAGCGGTGCTTTTTTTTAAAACGCCGCTAAA
65 ATTAGCGGCGC-TTTTTTAAAAACGCCGCTAAA
104417 TCCCCAAAAG
Statistics
Matches: 181, Mismatches: 37, Indels: 6
0.81 0.17 0.03
Matches are distributed among these distances:
122 64 0.35
123 24 0.13
124 87 0.48
125 6 0.03
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (121 bp):
AAAAACGCCGATAAAGATCTGAGCATTAGCGGCGTTTTACAAAAACGCCGCTAAAGATCTGAGCA
TTAGCGGCGCTTTTTTAAAAACGCCGCTAAAGATCTGAACATAGCAGCGATTCTCA
Found at i:104407 original size:83 final size:82
Alignment explanation
Indices: 104060--104415 Score: 323
Period size: 83 Copynumber: 4.3 Consensus size: 82
104050 AAATGTTTTT
* * * *
104060 GCGGCGCTTTTTCAAAAACGCCGCTAA--ATCTCGGAGCATTAGTGGCG-CTTTACCAAAAACGC
1 GCGGCGCTTCTTCAAAAACGCCGCTAATGAT-T-TGAGCATTAGCGGCGATTTTA-CAAAAACGC
*
104122 CGCTAAAGATCTGAGCATTA
63 CGCTAAAGATCTGAGAATTA
* * * * * * **
104142 GCTGCACTT-TTCTATAAACGCCACTAAAGATTTGAGCA-TCGCGGCGATTTTGGAAAAACGCCG
1 GCGGCGCTTCTTC-AAAAACGCCGCTAATGATTTGAGCATTAGCGGCGATTTTACAAAAACGCCG
* **
104205 ATAAAGATCTGAGCTTTA
65 CTAAAGATCTGAGAATTA
* * * * * *
104223 GCGGCGCTTCTACAAAAACGCCCCTAAAT-ATCTGAGCATTACCGGCGCTTTTTTCAAAAACGCC
1 GCGGCGCTTCTTCAAAAACGCCGCT-AATGATTTGAGCATTAGCGGCG-ATTTTACAAAAACGCC
104287 GCTAAAGATCTGA-ACATTA
64 GCTAAAGATCTGAGA-ATTA
*
104306 GCAGCGCTTC-TCAAAAAACGCCGCTAATGATTTGAGCATTAGCGGCGATTTTACAAAAACGCCG
1 GCGGCGCTTCTTC-AAAAACGCCGCTAATGATTTGAGCATTAGCGGCGATTTTACAAAAACGCCG
*
104370 CTAAAGATCTGGGAATTA
65 CTAAAGATCTGAGAATTA
* * **
104388 GCGGTGCTTTTTTTTAAAACGCCGCTAA
1 GCGGCGC-TTCTTCAAAAACGCCGCTAA
104416 ATCCCCAAAA
Statistics
Matches: 220, Mismatches: 40, Indels: 27
0.77 0.14 0.09
Matches are distributed among these distances:
81 60 0.27
82 76 0.35
83 81 0.37
84 3 0.01
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (82 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAATGATTTGAGCATTAGCGGCGATTTTACAAAAACGCCGC
TAAAGATCTGAGAATTA
Found at i:109323 original size:101 final size:102
Alignment explanation
Indices: 109148--109352 Score: 403
Period size: 101 Copynumber: 2.0 Consensus size: 102
109138 AAGTCCTTAA
109148 ATGTTTTAAAAATTTTAAAATAGTAAAGATAAAATTATACTTTAGCTTTTCTAAAATTATAAAAA
1 ATGTTTTAAAAATTTTAAAATAGTAAAGATAAAATTATACTTTAGCTTTTCTAAAATTATAAAAA
109213 TTTAATTTAATTCTTTAAAAATTAT-AAATATAGATT
66 TTTAATTTAATTCTTTAAAAATTATAAAATATAGATT
109249 ATGTTTTAAAAATTTTAAAATAGTAAAGATAAAATTATACTTTAGCTTTTCTAAAATTATAAAAA
1 ATGTTTTAAAAATTTTAAAATAGTAAAGATAAAATTATACTTTAGCTTTTCTAAAATTATAAAAA
109314 TTTAATTTAATTCTTTAAAAATTATAAAATATAGATT
66 TTTAATTTAATTCTTTAAAAATTATAAAATATAGATT
109351 AT
1 AT
109353 AAAAATTAAA
Statistics
Matches: 103, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
101 90 0.87
102 13 0.13
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (102 bp):
ATGTTTTAAAAATTTTAAAATAGTAAAGATAAAATTATACTTTAGCTTTTCTAAAATTATAAAAA
TTTAATTTAATTCTTTAAAAATTATAAAATATAGATT
Found at i:114907 original size:166 final size:166
Alignment explanation
Indices: 114633--114967 Score: 589
Period size: 166 Copynumber: 2.0 Consensus size: 166
114623 AAGTATTGAG
114633 TAAGGAAATGGTCATAACTTGATGTTTAATGGTGTGGGAATAAAATCTTCATTTCAGATGACTTT
1 TAAGGAAATGGTCATAACTTGATGTTTAATGGTGTGGGAATAAAATCTTCATTTCAGATGACTTT
* *
114698 CAGGATCTTATGACTCTGTTGTGTTCTTCTTTTAGGAAATCTTTGAGCATTTTCATGTGATCATT
66 CAGGATCTTATGACTCTGTTGTGTTCTTCTTTTAGGAAATCTTTCAGCATTTTCATGTAATCATT
114763 GCGATTGTCTAGTTGTCTTCCCTAATTTCTTTTAAT
131 GCGATTGTCTAGTTGTCTTCCCTAATTTCTTTTAAT
* * **
114799 TAAGGAACTGGTCATAACTTGATGTTTAATGGTGTGGGAATAAAATCTTTATTTTTGATGACTTT
1 TAAGGAAATGGTCATAACTTGATGTTTAATGGTGTGGGAATAAAATCTTCATTTCAGATGACTTT
*
114864 GAGGATCTTATGACTCTGTTGTGTTCTTCTTTTAGGAAATCTTTCAGCATTTTCATGTAATCATT
66 CAGGATCTTATGACTCTGTTGTGTTCTTCTTTTAGGAAATCTTTCAGCATTTTCATGTAATCATT
* *
114929 GTGATTGTCTAGTTGTCTTCTCTAATTTCTTTTAAT
131 GCGATTGTCTAGTTGTCTTCCCTAATTTCTTTTAAT
114965 TAA
1 TAA
114968 TGTTAATTTT
Statistics
Matches: 160, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
166 160 1.00
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (166 bp):
TAAGGAAATGGTCATAACTTGATGTTTAATGGTGTGGGAATAAAATCTTCATTTCAGATGACTTT
CAGGATCTTATGACTCTGTTGTGTTCTTCTTTTAGGAAATCTTTCAGCATTTTCATGTAATCATT
GCGATTGTCTAGTTGTCTTCCCTAATTTCTTTTAAT
Found at i:122776 original size:6 final size:6
Alignment explanation
Indices: 122765--122789 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
122755 ATATCAAAGA
122765 ACCTGC ACCTGC ACCTGC ACCTGC A
1 ACCTGC ACCTGC ACCTGC ACCTGC A
122790 ACTCCAAGAT
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:0.20, C:0.48, G:0.16, T:0.16
Consensus pattern (6 bp):
ACCTGC
Found at i:124605 original size:81 final size:81
Alignment explanation
Indices: 124470--124639 Score: 315
Period size: 81 Copynumber: 2.1 Consensus size: 81
124460 ACTGGCAACG
124470 AAGTGCATTACCAGATAAATCAGAATAGGGTAAACTGGCATGTAAGTGCATACTAGCGCATACAA
1 AAGTGCATTACCAGATAAATCAGAATAGGGTAAACTGGCATGTAAGTGCATACTAGCGCATACAA
124535 CGCATCCTGGCGCACA
66 CGCATCCTGGCGCACA
124551 AAGTGCATTACCAGATAAATC-GAAATAGGGTAAACTGGCATGTAAGTGCATACTAGCGCATACA
1 AAGTGCATTACCAGATAAATCAG-AATAGGGTAAACTGGCATGTAAGTGCATACTAGCGCATACA
*
124615 ACGCATCCTGGCTCACA
65 ACGCATCCTGGCGCACA
124632 AAGTGCAT
1 AAGTGCAT
124640 ATTTGGCACA
Statistics
Matches: 87, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
80 1 0.01
81 86 0.99
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.21
Consensus pattern (81 bp):
AAGTGCATTACCAGATAAATCAGAATAGGGTAAACTGGCATGTAAGTGCATACTAGCGCATACAA
CGCATCCTGGCGCACA
Found at i:124639 original size:19 final size:19
Alignment explanation
Indices: 124617--124665 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
124607 CGCATACAAC
* *
124617 GCATCCTGGCTCACAAAGT
1 GCATCTTGGCACACAAAGT
*
124636 GCATATTTGGCACACAAAGT
1 GCAT-CTTGGCACACAAAGT
124656 GCATCTTGGC
1 GCATCTTGGC
124666 GTATAAGCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (19 bp):
GCATCTTGGCACACAAAGT
Found at i:127570 original size:10 final size:10
Alignment explanation
Indices: 127555--127583 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
127545 TTAAATTCTA
127555 AAAGATAAAT
1 AAAGATAAAT
127565 AAAGATAAAT
1 AAAGATAAAT
127575 AAAGATAAA
1 AAAGATAAA
127584 AGCTAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:132324 original size:10 final size:10
Alignment explanation
Indices: 132309--132337 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
132299 TTAAATTCTA
132309 AAAGATAAAT
1 AAAGATAAAT
132319 AAAGATAAAT
1 AAAGATAAAT
132329 AAAGATAAA
1 AAAGATAAA
132338 AGCTAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:136016 original size:27 final size:27
Alignment explanation
Indices: 135978--136030 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
135968 ATTGAATTAA
*
135978 AAGGGGTTGCTAAGTGCTGATTCCCTC
1 AAGGGGTTGCTAAGTACTGATTCCCTC
136005 AAGGGGTTGCTAAGTACTGATTCCCT
1 AAGGGGTTGCTAAGTACTGATTCCCT
136031 GAATCATTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (27 bp):
AAGGGGTTGCTAAGTACTGATTCCCTC
Found at i:136051 original size:33 final size:33
Alignment explanation
Indices: 135982--136325 Score: 169
Period size: 33 Copynumber: 9.7 Consensus size: 33
135972 AATTAAAAGG
*
135982 GGTTGCTAAGTGCTGATT-CCC---TCA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
136009 GGTTGCTAAGTACTGATTCCCTGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
136042 GGTTGCTAAGTGCTGATTCCACCGTAACTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-AA--T-CAT-TG---GT
* *
136084 GGTTGCTAAGTTCTGATTCCCGGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* **
136117 AGTTGCTAAGTTTTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
** * *
136150 GGTTGCTAAGTGCTGATTTCGTCGTATCTTAAATGTGAAAGA
1 GGTTGCTAAGTGCTGA-TTCCCCGAATC----AT-TG---GT
* * *
136192 GGTTGCTAATTGATGATTCCTCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * *
136225 GGCTGCTAAGTGCTGATTCCACCGTATCTTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGAATC-----AT-TG---GT
* *
136268 GGTTGCTAAATGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
136301 GGTTGCCAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
136326 TAACGGATAA
Statistics
Matches: 242, Mismatches: 40, Indels: 63
0.70 0.12 0.18
Matches are distributed among these distances:
27 17 0.07
28 2 0.01
31 3 0.01
32 2 0.01
33 99 0.41
34 19 0.08
35 2 0.01
36 6 0.02
37 6 0.02
38 5 0.02
39 6 0.02
40 4 0.02
41 11 0.05
42 41 0.17
43 19 0.08
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:136160 original size:108 final size:108
Alignment explanation
Indices: 136010--136244 Score: 321
Period size: 108 Copynumber: 2.2 Consensus size: 108
136000 CCCTCAAGGG
* *
136010 GTTGCTAAGTACTGATTCCCTGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAACTTGAA
1 GTTGCTAAGTACTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAACTTAAA
* *
136075 TGTGAAAGGGGTTGCTAAGTT-CTGATTCC-CGGAATCATTGGTA
66 TGTGAAAGAGGTTGCTAA-TTGATGATTCCTC-GAATCATTGGTA
** * ** *
136118 GTTGCTAAGTTTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTTCGTCGTATCTTAAA
1 GTTGCTAAGTACTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAACTTAAA
*
136183 TGTGAAAGAGGTTGCTAATTGATGATTCCTCGAATCATTGGTG
66 TGTGAAAGAGGTTGCTAATTGATGATTCCTCGAATCATTGGTA
* *
136226 GCTGCTAAGTGCTGATTCC
1 GTTGCTAAGTACTGATTCC
136245 ACCGTATCTT
Statistics
Matches: 111, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
107 2 0.02
108 108 0.97
109 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (108 bp):
GTTGCTAAGTACTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAACTTAAA
TGTGAAAGAGGTTGCTAATTGATGATTCCTCGAATCATTGGTA
Found at i:136210 original size:75 final size:76
Alignment explanation
Indices: 136130--136324 Score: 275
Period size: 76 Copynumber: 2.6 Consensus size: 76
136120 TGCTAAGTTT
* **
136130 TGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTTCGTCGTATC-TTAAATGTGAAAGAGG
1 TGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTGAAAGAGG
*
136194 TTGCTAATTGA
66 TTGCTAAATGA
* * * *
136205 TGATTCCTCGAATCATTGGTGGCTGCTAAGTGCTGATTCCACCGTATCTTTGAATGTGAAAGGGG
1 TGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTGAAAGAGG
*
136270 TTGCTAAATGC
66 TTGCTAAATGA
* * *
136281 TGATTCCCCGAATCACTGGTGGTTGCCAAGTGCTGAATCCACCG
1 TGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCG
136325 ATAACGGATA
Statistics
Matches: 105, Mismatches: 14, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
75 43 0.41
76 62 0.59
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (76 bp):
TGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTGAAAGAGG
TTGCTAAATGA
Found at i:138031 original size:20 final size:20
Alignment explanation
Indices: 138006--138146 Score: 90
Period size: 20 Copynumber: 7.0 Consensus size: 20
137996 ATAGTTGCGT
138006 AACAGAGGCACCGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
** *
138026 AACAGAGGCA-CGATTTTACA
1 AACAGAGGCACCGA-AGTGCA
** *
138046 ATTAGAGGCA-CGATTGTGCA
1 AACAGAGGCACCGA-AGTGCA
** **
138066 ATTAGAGGCACCGCTGTGCA
1 AACAGAGGCACCGAAGTGCA
* * *
138086 AACAGAGACACTGAAGTGTA
1 AACAGAGGCACCGAAGTGCA
* *
138106 AATAGAGGCACTGAAGTGCGA
1 AACAGAGGCACCGAAGTGC-A
*
138127 AA-AGAGGCACTGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
138146 A
1 A
138147 TCCCGTAAAA
Statistics
Matches: 100, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
19 5 0.05
20 90 0.90
21 5 0.05
ACGTcount: A:0.38, C:0.18, G:0.28, T:0.16
Consensus pattern (20 bp):
AACAGAGGCACCGAAGTGCA
Found at i:138112 original size:40 final size:40
Alignment explanation
Indices: 138068--138143 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
138058 ATTGTGCAAT
**
138068 TAGAGGCACCGCTGTGC-AAACAGAGACACTGAAGTGTAAA
1 TAGAGGCACCGAAGTGCGAAA-AGAGACACTGAAGTGTAAA
* *
138108 TAGAGGCACTGAAGTGCGAAAAGAGGCACTGAAGTG
1 TAGAGGCACCGAAGTGCGAAAAGAGACACTGAAGTG
138144 CAATCCCGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 28 0.90
41 3 0.10
ACGTcount: A:0.37, C:0.17, G:0.32, T:0.14
Consensus pattern (40 bp):
TAGAGGCACCGAAGTGCGAAAAGAGACACTGAAGTGTAAA
Found at i:141534 original size:40 final size:40
Alignment explanation
Indices: 141420--141520 Score: 157
Period size: 40 Copynumber: 2.5 Consensus size: 40
141410 TGACTCAGAA
* * *
141420 CACCGACATTAAGCCTGCTAGACATTAAGTCTGTAAAGTT
1 CACCGGCATTAAGCCTGCTAGACATTAAGTCTGAAAAATT
*
141460 CACCGGCATTAAGCCTGCTAGAAATTAAGTCTGAAAAATT
1 CACCGGCATTAAGCCTGCTAGACATTAAGTCTGAAAAATT
*
141500 CACCGGGATTAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
141521 GCATAGAACC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACATTAAGTCTGAAAAATT
Found at i:144603 original size:11 final size:11
Alignment explanation
Indices: 144587--144644 Score: 59
Period size: 11 Copynumber: 5.4 Consensus size: 11
144577 GATAACCATT
144587 TTAATATTAAA
1 TTAATATTAAA
144598 TTAATA--AAA
1 TTAATATTAAA
*
144607 -TACTATTAAGA
1 TTAATATTAA-A
*
144618 TAAATATTAAA
1 TTAATATTAAA
144629 TTAATATTAATA
1 TTAATATTAA-A
144641 TTAA
1 TTAA
144645 ACAATTAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
8 4 0.11
9 3 0.08
10 2 0.05
11 17 0.45
12 12 0.32
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:149299 original size:37 final size:37
Alignment explanation
Indices: 149257--149328 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
149247 TGACCTTTAT
* * *
149257 ACTGTTTACACGGTGTCGCCTCAAGGACCAGTAGATA
1 ACTGTTTACACGGTGTCGCCCCAAGAACCACTAGATA
*
149294 ACTGTTTACACGGTGTTGCCCCAAGAACCACTAGA
1 ACTGTTTACACGGTGTCGCCCCAAGAACCACTAGA
149329 CCGAAGGCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (37 bp):
ACTGTTTACACGGTGTCGCCCCAAGAACCACTAGATA
Found at i:156875 original size:6 final size:6
Alignment explanation
Indices: 156855--156904 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
156845 GAAGAAAAAC
* *
156855 AAATAA CAATAAA AAATAA AAGA-AA AAATAA AAATAA AAATAA AATTAA
1 AAATAA AAAT-AA AAATAA AA-ATAA AAATAA AAATAA AAATAA AAATAA
156904 A
1 A
156905 TAAAAGATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
5 1 0.03
6 31 0.82
7 6 0.16
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:156876 original size:31 final size:31
Alignment explanation
Indices: 156841--156899 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
156831 ATAAATCCAA
* *
156841 AAAAGAAGAAAA-ACAAATAACAATAAAAAAT
1 AAAAGAA-AAAATAAAAATAAAAATAAAAAAT
156872 AAAAGAAAAAATAAAAATAAAAATAAAA
1 AAAAGAAAAAATAAAAATAAAAATAAAA
156900 TTAAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.81, C:0.03, G:0.05, T:0.10
Consensus pattern (31 bp):
AAAAGAAAAAATAAAAATAAAAATAAAAAAT
Found at i:156882 original size:12 final size:11
Alignment explanation
Indices: 156839--156899 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 11
156829 ATATAAATCC
*
156839 AAAAAAGAAGAA
1 AAAAAATAA-AA
156851 AAACAAATAACAA
1 AAA-AAATAA-AA
156864 TAAAAAATAAAA
1 -AAAAAATAAAA
156876 GAAAAAATAAAA
1 -AAAAAATAAAA
156888 ATAAAAATAAAA
1 A-AAAAATAAAA
156900 TTAAATAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
11 1 0.02
12 26 0.60
13 13 0.30
14 3 0.07
ACGTcount: A:0.82, C:0.03, G:0.05, T:0.10
Consensus pattern (11 bp):
AAAAAATAAAA
Found at i:156887 original size:18 final size:18
Alignment explanation
Indices: 156866--156911 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
156856 AATAACAATA
156866 AAAAATAAAAGAAAAAAT
1 AAAAATAAAAGAAAAAAT
*
156884 AAAAATAAAA-ATAAAAT
1 AAAAATAAAAGAAAAAAT
*
156901 -TAAATAAAAGA
1 AAAAATAAAAGA
156912 TAATTGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 8 0.32
17 7 0.28
18 10 0.40
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.15
Consensus pattern (18 bp):
AAAAATAAAAGAAAAAAT
Found at i:163741 original size:20 final size:20
Alignment explanation
Indices: 163703--163741 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
163693 AACATTAAAA
*
163703 ATACCGTAATCACAACCAAG
1 ATACCATAATCACAACCAAG
163723 ATACCATAA-CACAAGCCAA
1 ATACCATAATCACAA-CCAA
163742 ACCATATGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.49, C:0.31, G:0.08, T:0.13
Consensus pattern (20 bp):
ATACCATAATCACAACCAAG
Found at i:168391 original size:34 final size:34
Alignment explanation
Indices: 168323--168398 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
168313 TTATAACATT
* *
168323 CATTAACTTTAAATTTTTACCATTGATATCATTAA
1 CATTAA-TATAAATTTTTACCATTGACATCATTAA
** *
168358 CATTAATATAAATTTTTACTTTTGACATTATTAA
1 CATTAATATAAATTTTTACCATTGACATCATTAA
*
168392 CTTTAAT
1 CATTAAT
168399 GAAAAAATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
34 29 0.83
35 6 0.17
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.49
Consensus pattern (34 bp):
CATTAATATAAATTTTTACCATTGACATCATTAA
Found at i:171217 original size:9 final size:9
Alignment explanation
Indices: 171192--171236 Score: 63
Period size: 9 Copynumber: 5.0 Consensus size: 9
171182 TGATTCAATC
171192 CGGTTAATT
1 CGGTTAATT
*
171201 CGGGTAATT
1 CGGTTAATT
*
171210 TGGTTAATT
1 CGGTTAATT
*
171219 CGTTTAATT
1 CGGTTAATT
171228 CGGTTAATT
1 CGGTTAATT
171237 TTTAACCAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.22, C:0.09, G:0.22, T:0.47
Consensus pattern (9 bp):
CGGTTAATT
Found at i:171594 original size:18 final size:19
Alignment explanation
Indices: 171563--171598 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
171553 TTAATTAATT
171563 TGATTTTGATTTTTGTTCC
1 TGATTTTGATTTTTGTTCC
171582 TGATTTT-ATTTTTGTTC
1 TGATTTTGATTTTTGTTC
171599 AAATTTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.11, C:0.08, G:0.14, T:0.67
Consensus pattern (19 bp):
TGATTTTGATTTTTGTTCC
Found at i:172831 original size:22 final size:21
Alignment explanation
Indices: 172781--172833 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 21
172771 AGAGGGTTTT
*
172781 CAATCAAA-AAAAGTAAAAAG
1 CAATCAAATAAAAGCAAAAAG
* *
172801 TAGTCCAAATAAACAGCAAAAAG
1 CAAT-CAAATAAA-AGCAAAAAG
172824 CAATCAAATA
1 CAATCAAATA
172834 TTCAAAACTC
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 2 0.08
21 4 0.16
22 9 0.36
23 10 0.40
ACGTcount: A:0.62, C:0.15, G:0.09, T:0.13
Consensus pattern (21 bp):
CAATCAAATAAAAGCAAAAAG
Found at i:180413 original size:27 final size:27
Alignment explanation
Indices: 180375--180428 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
180365 ATAAAAATCC
*
180375 TTGTCTAAACCCCATCCAAGTGGGGTT
1 TTGTCTAAACCCCATCCAAGTCGGGTT
*
180402 TTGTCTAAACCCCATTCAAGTCGGGTT
1 TTGTCTAAACCCCATCCAAGTCGGGTT
180429 GGGTGGGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.31
Consensus pattern (27 bp):
TTGTCTAAACCCCATCCAAGTCGGGTT
Found at i:181376 original size:21 final size:21
Alignment explanation
Indices: 181352--181421 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
181342 AATGTTCTTT
181352 AAATATAATTATAAAAAATTA
1 AAATATAATTATAAAAAATTA
*
181373 AAATAATTAA-GATAAAAATATTA
1 AAAT-A-TAATTATAAAAA-ATTA
*
181396 CAAAT-TAATT-TAAAATATTA
1 -AAATATAATTATAAAAAATTA
181416 AAATAT
1 AAATAT
181422 TGTACTAACT
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
19 4 0.10
20 5 0.12
21 12 0.30
22 8 0.20
23 7 0.17
24 4 0.10
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (21 bp):
AAATATAATTATAAAAAATTA
Found at i:181823 original size:18 final size:18
Alignment explanation
Indices: 181777--181839 Score: 53
Period size: 18 Copynumber: 3.5 Consensus size: 18
181767 CCGAGATAAT
181777 GAAAAAT-ATTAAATTTAAA
1 GAAAAATAATT-AA-TTAAA
181796 -AATAAA-AATTAATTAAA
1 GAA-AAATAATTAATTAAA
181813 GAAAAATAATTTAA-TAAA
1 GAAAAATAA-TTAATTAAA
*
181831 TAAAAATAA
1 GAAAAATAA
181840 ACTAAAAAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
17 8 0.21
18 20 0.53
19 10 0.26
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
GAAAAATAATTAATTAAA
Found at i:181826 original size:19 final size:18
Alignment explanation
Indices: 181804--181839 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
181794 AAAATAAAAA
181804 TTAATTAAAGAAAAATAAT
1 TTAA-TAAAGAAAAATAAT
*
181823 TTAATAAATAAAAATAA
1 TTAATAAAGAAAAATAA
181840 ACTAAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
TTAATAAAGAAAAATAAT
Found at i:185619 original size:2 final size:2
Alignment explanation
Indices: 185612--185643 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
185602 ATAGTATAAG
185612 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
185644 GATAATGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:185813 original size:41 final size:41
Alignment explanation
Indices: 185753--185894 Score: 196
Period size: 41 Copynumber: 3.5 Consensus size: 41
185743 TATAATTGGT
* * * *
185753 TTTCAGGCTTAATGCCTAGCGGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTA
* *
185794 TTTCAGATTTTATGTCTAGCAGGCTTGATGCTGGTGAATTA
1 TTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTA
* *
185835 CTTCAGACTTTATGTCTAGCAGGCTTGATGCCGATGAATTA
1 TTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTA
185876 TTTCAGAC-TTATTGTCTAG
1 TTTCAGACTTTA-TGTCTAG
185895 TAGGTTTCAT
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
40 3 0.03
41 86 0.97
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (41 bp):
TTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTA
Found at i:185928 original size:82 final size:81
Alignment explanation
Indices: 185754--185928 Score: 196
Period size: 82 Copynumber: 2.1 Consensus size: 81
185744 ATAATTGGTT
* * * *
185754 TTCAG-GCTTAATGCCTAGCGGGCTTGATGCCGGTGAATTATTTCAGATTTTATGTCTAGCAGGC
1 TTCAGAGCTTTATGCCTAGCAGGCTTGATGCCGATGAATTATTTCAGATTATATGTCTAGCAGGC
* *
185818 TTGATGCTGGTGAATTAC
66 TTCATGCTAGTG-A-TAC
* *
185836 TTCAGA-CTTTATGTCTAGCAGGCTTGATGCCGATGAATTATTTCAGACTTAT-TGTCTAGTAGG
1 TTCAGAGCTTTATGCCTAGCAGGCTTGATGCCGATGAATTATTTCAGA-TTATATGTCTAGCAGG
*
185899 TTTCATGCTAGTG-TAC
65 CTTCATGCTAGTGATAC
185915 TTCAGTAAGCTTTA
1 TTCAG--AGCTTTA
185929 GACTTAACAG
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
79 8 0.10
81 1 0.01
82 67 0.85
83 3 0.04
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (81 bp):
TTCAGAGCTTTATGCCTAGCAGGCTTGATGCCGATGAATTATTTCAGATTATATGTCTAGCAGGC
TTCATGCTAGTGATAC
Found at i:188272 original size:11 final size:12
Alignment explanation
Indices: 188249--188296 Score: 50
Period size: 11 Copynumber: 4.3 Consensus size: 12
188239 AGTTCAAGTA
188249 AGATGTAGA-AC
1 AGATGTAGATAC
188260 AGAT-TAGATAC
1 AGATGTAGATAC
* *
188271 AGATGCAGATGC
1 AGATGTAGATAC
188283 AGA-GTAGAT-C
1 AGATGTAGATAC
188293 AGAT
1 AGAT
188297 ACAGATGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
10 8 0.26
11 15 0.48
12 8 0.26
ACGTcount: A:0.42, C:0.10, G:0.27, T:0.21
Consensus pattern (12 bp):
AGATGTAGATAC
Found at i:188295 original size:22 final size:23
Alignment explanation
Indices: 188259--188305 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
188249 AGATGTAGAA
* *
188259 CAGATTAGATACAGATGCAGATG
1 CAGAGTAGATACAGATACAGATG
188282 CAGAGTAGAT-CAGATACAGATG
1 CAGAGTAGATACAGATACAGATG
188304 CA
1 CA
188306 AAACAAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.19
Consensus pattern (23 bp):
CAGAGTAGATACAGATACAGATG
Found at i:189051 original size:63 final size:63
Alignment explanation
Indices: 188968--189162 Score: 196
Period size: 62 Copynumber: 3.1 Consensus size: 63
188958 CCTTCACATG
* * *
188968 GCCTAGACACACACCCGTGTCACTGGCCCGTGTGACCTTAAATCCAAAACAGTAAGTTACACA
1 GCCTGGACACACGCCCGTGTCCCTGGCCCGTGTGACCTTAAATCCAAAACAGTAAGTTACACA
* * * * ** * * * *
189031 GCCTGGACACACGCCTGTGTCCCTGACCTGAGTGACC-T-AATGTAAAAACAATGAGTTATACG
1 GCCTGGACACACGCCCGTGTCCCTGGCCCGTGTGACCTTAAAT-CCAAAACAGTAAGTTACACA
* * *
189093 GCCTGGACACACGCCCGTGTCCCTCGCTCGTGTGACCTTAAATCCATAAACAGTGAGAGTTACAT
1 GCCTGGACACACGCCCGTGTCCCTGGCCCGTGTGACCTTAAATCCA-AAACAGT-A-AGTTACAC
189158 A
63 A
189159 GCCT
1 GCCT
189163 ACCACACAGC
Statistics
Matches: 100, Mismatches: 26, Indels: 9
0.74 0.19 0.07
Matches are distributed among these distances:
61 3 0.03
62 46 0.46
63 32 0.32
64 9 0.09
66 10 0.10
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.22
Consensus pattern (63 bp):
GCCTGGACACACGCCCGTGTCCCTGGCCCGTGTGACCTTAAATCCAAAACAGTAAGTTACACA
Found at i:189722 original size:22 final size:21
Alignment explanation
Indices: 189699--189743 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
189689 TGCGAAATAG
189699 AAAGAAAGAATAAAAGAAAAAGA
1 AAAG-AAGAA-AAAAGAAAAAGA
*
189722 AAAGAAGAAGAAA-AAAAAGA
1 AAAGAAGAAAAAAGAAAAAGA
189742 AA
1 AA
189744 CGATAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 3 0.14
22 5 0.24
23 4 0.19
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (21 bp):
AAAGAAGAAAAAAGAAAAAGA
Found at i:190395 original size:18 final size:18
Alignment explanation
Indices: 190374--190408 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
190364 TTTTTAAACC
*
190374 TTTTTTT-ATTTTTTACA
1 TTTTTTTCAATTTTTACA
190391 TTTTTTTCAATTTTTACA
1 TTTTTTTCAATTTTTACA
190409 ATATTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTTTCAATTTTTACA
Found at i:190415 original size:18 final size:19
Alignment explanation
Indices: 190383--190425 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
190373 CTTTTTTTAT
* * *
190383 TTTTTACATTTTTTTCAA-
1 TTTTTACAATATTTTAAAC
190401 TTTTTACAATATTTTAAAC
1 TTTTTACAATATTTTAAAC
190420 TTTTTA
1 TTTTTA
190426 ATAACATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTACAATATTTTAAAC
Found at i:190941 original size:30 final size:30
Alignment explanation
Indices: 190907--190969 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
190897 ACTTATTTTA
*
190907 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTGTAGAGGCAT
*
190937 TTGTTAATTTTGTTATTATTGTAGAGTCAT
1 TTGTTAATTTTGTTATTATTGTAGAGGCAT
190967 TTG
1 TTG
190970 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.22, C:0.03, G:0.17, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTGTAGAGGCAT
Found at i:191116 original size:12 final size:11
Alignment explanation
Indices: 191083--191122 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
191073 GATATATTGT
*
191083 ATAATTTAAAA
1 ATAATATAAAA
*
191094 ATTATATAAAA
1 ATAATATAAAA
191105 ATAATATAAAA
1 ATAATATAAAA
191116 ATTAATA
1 A-TAATA
191123 CGAACGTGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 20 0.80
12 5 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:192043 original size:19 final size:21
Alignment explanation
Indices: 192005--192060 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
191995 AAAAAAAGAA
192005 TCAAAATAATTATCAAAAA-T
1 TCAAAATAATTATCAAAAATT
*
192025 TCAAAATATTTAT-AAAAATT
1 TCAAAATAATTATCAAAAATT
*
192045 TCAAAAAAATT-TCAAA
1 TCAAAATAATTATCAAA
192061 TTTTATATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (21 bp):
TCAAAATAATTATCAAAAATT
Found at i:196184 original size:11 final size:11
Alignment explanation
Indices: 196170--196195 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
196160 ATTTTTTTAA
196170 TTTTAAAATAC
1 TTTTAAAATAC
196181 TTTTAAAATAC
1 TTTTAAAATAC
196192 TTTT
1 TTTT
196196 TTAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:196207 original size:39 final size:39
Alignment explanation
Indices: 196153--196263 Score: 177
Period size: 39 Copynumber: 2.8 Consensus size: 39
196143 ATATTTTTAT
196153 TTTTTTTATTTTTTTAATTTTAAAATACTTTTAAAATAC
1 TTTTTTTATTTTTTTAATTTTAAAATACTTTTAAAATAC
* * *
196192 TTTTTTAATTTTTTTAATTTTAAATTATTTTTAAAATAC
1 TTTTTTTATTTTTTTAATTTTAAAATACTTTTAAAATAC
*
196231 TTTTTTTATTTTTTTATTTTTAAAATACATTTT
1 TTTTTTTATTTTTTTAATTTTAAAATAC-TTTT
196264 TGGTGTTTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 60 0.94
40 4 0.06
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.66
Consensus pattern (39 bp):
TTTTTTTATTTTTTTAATTTTAAAATACTTTTAAAATAC
Found at i:198940 original size:25 final size:25
Alignment explanation
Indices: 198904--199043 Score: 127
Period size: 25 Copynumber: 5.6 Consensus size: 25
198894 GTTTTGACCC
*
198904 ACAGCTCATGTGAGCATACCGATTT
1 ACAGCTCGTGTGAGCATACCGATTT
* * *
198929 ATAGCTCGTGTGAGCATACCAATCT
1 ACAGCTCGTGTGAGCATACCGATTT
* ** *
198954 ACAGATCGTGTGAGCATATAGGTTT
1 ACAGCTCGTGTGAGCATACCGATTT
* * * * *
198979 ATAGCTTGTGAGAGCATATCGATCT
1 ACAGCTCGTGTGAGCATACCGATTT
* * *
199004 ACAGCTCGAGTGAACATACCGATTC
1 ACAGCTCGTGTGAGCATACCGATTT
*
199029 ACAGCTCGTATGAGC
1 ACAGCTCGTGTGAGC
199044 GTACATGTAC
Statistics
Matches: 86, Mismatches: 29, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
25 86 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (25 bp):
ACAGCTCGTGTGAGCATACCGATTT
Found at i:198970 original size:50 final size:50
Alignment explanation
Indices: 198912--199043 Score: 147
Period size: 50 Copynumber: 2.6 Consensus size: 50
198902 CCACAGCTCA
198912 TGTGAGCATACCGATTTATAGCTCGTGTGAGCATACCAATCTACAGATCG
1 TGTGAGCATACCGATTTATAGCTCGTGTGAGCATACCAATCTACAGATCG
** * * * * * *
198962 TGTGAGCATATAGGTTTATAGCTTGTGAGAGCATATCGATCTACAGCTCG
1 TGTGAGCATACCGATTTATAGCTCGTGTGAGCATACCAATCTACAGATCG
* * * * *
199012 AGTGAACATACCGATTCACAGCTCGTATGAGC
1 TGTGAGCATACCGATTTATAGCTCGTGTGAGC
199044 GTACATGTAC
Statistics
Matches: 64, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
50 64 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (50 bp):
TGTGAGCATACCGATTTATAGCTCGTGTGAGCATACCAATCTACAGATCG
Found at i:200176 original size:20 final size:20
Alignment explanation
Indices: 200143--200181 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
200133 GTCGTATGGT
200143 TTGGCTTGTGTTATGGTATA
1 TTGGCTTGTGTTATGGTATA
200163 TTGG-TTGTGATTATGGTAT
1 TTGGCTTGTG-TTATGGTAT
200182 TTTGAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.15, C:0.03, G:0.31, T:0.51
Consensus pattern (20 bp):
TTGGCTTGTGTTATGGTATA
Found at i:206272 original size:36 final size:36
Alignment explanation
Indices: 206148--206282 Score: 137
Period size: 37 Copynumber: 3.7 Consensus size: 36
206138 AGCTCTTCGA
* * * * *
206148 AGCATTTGTCATGTTATTGGTTGGACTAGCTCTACGG
1 AGCATTTGGCGTGTTATCGGTTGGATTAGCTCTA-TG
*
206185 AGCATTTGGCGTGTTATCGGTTGGATTAGCTCTTTGG
1 AGCATTTGGCGTGTTATCGGTTGGATTAGCTCTAT-G
* * *
206222 AACATATGGTGTGTT-TCGGTTGGATTAGCTCTCATG
1 AGCATTTGGCGTGTTATCGGTTGGATTAGCTCT-ATG
* *
206258 AGCATTTGACGTGTTTTCGGTTGGA
1 AGCATTTGGCGTGTTATCGGTTGGA
206283 CTATTGTGCT
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
36 29 0.36
37 52 0.64
ACGTcount: A:0.17, C:0.14, G:0.30, T:0.39
Consensus pattern (36 bp):
AGCATTTGGCGTGTTATCGGTTGGATTAGCTCTATG
Found at i:212681 original size:40 final size:40
Alignment explanation
Indices: 212625--212708 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
212615 TGTATAAGCC
*
212625 TTCAGGAGTACCGAAGTACAAACAGAGACATATATGTGCA
1 TTCAGGAGTACCGAAGTACAAACAGAGACACATATGTGCA
* * * * *
212665 TTCAGGGGTACTGAAGTACAAACATAGGCACGTATGTGCA
1 TTCAGGAGTACCGAAGTACAAACAGAGACACATATGTGCA
212705 TTCA
1 TTCA
212709 TAGAACAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.23
Consensus pattern (40 bp):
TTCAGGAGTACCGAAGTACAAACAGAGACACATATGTGCA
Found at i:214717 original size:14 final size:14
Alignment explanation
Indices: 214698--214725 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
214688 GATAATGTTT
214698 TTGAATTTGATAAA
1 TTGAATTTGATAAA
214712 TTGAATTTGATAAA
1 TTGAATTTGATAAA
214726 CAAAGGAAAG
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:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (14 bp):
TTGAATTTGATAAA
Found at i:224568 original size:28 final size:29
Alignment explanation
Indices: 224537--224610 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 29
224527 ATCAAAAAAA
*
224537 TTTTCTTCTCTCAATTTCT-CCAACATCT
1 TTTTCTTCTCTCAATTTCTCCCAACATAT
* *
224565 TTTTCTTCTCTTATTTTCTCCCAACATAT
1 TTTTCTTCTCTCAATTTCTCCCAACATAT
* *
224594 TTTTTTTCACTC-ATTTC
1 TTTTCTTCTCTCAATTTC
224611 CTTTCCAACA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 21 0.55
29 17 0.45
ACGTcount: A:0.16, C:0.28, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTTCTTCTCTCAATTTCTCCCAACATAT
Found at i:224609 original size:29 final size:28
Alignment explanation
Indices: 224537--224609 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 28
224527 ATCAAAAAAA
* *
224537 TTTTCTTCTCTCAATTTCTCCAACATCT
1 TTTTCTTCTCTCATTTTCTCCAACATAT
*
224565 TTTTCTTCTCTTATTTTCTCCCAACATAT
1 TTTTCTTCTCTCATTTTCT-CCAACATAT
* *
224594 TTTTTTTCACTCATTT
1 TTTTCTTCTCTCATTT
224610 CCTTTCCAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
28 17 0.45
29 21 0.55
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTTCTTCTCTCATTTTCTCCAACATAT
Found at i:227437 original size:16 final size:16
Alignment explanation
Indices: 227413--227451 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
227403 ATGAAATAAC
* *
227413 TAAAGTAAATAAACAA
1 TAAAATAAACAAACAA
227429 TAAAATAAACAAACAA
1 TAAAATAAACAAACAA
*
227445 TTAAATA
1 TAAAATA
227452 GGTTAAACCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.69, C:0.08, G:0.03, T:0.21
Consensus pattern (16 bp):
TAAAATAAACAAACAA
Found at i:234169 original size:25 final size:25
Alignment explanation
Indices: 234141--234373 Score: 164
Period size: 25 Copynumber: 9.3 Consensus size: 25
234131 ATTATATAGG
* *
234141 AAGCCTTCGTGGTGAGTCATCTGTA
1 AAGCCTTTGTGGCGAGTCATCTGTA
* * * * *
234166 AAGCCTTTGTGGCAAATTATTTGCA
1 AAGCCTTTGTGGCGAGTCATCTGTA
** *
234191 AAGTTTTTGTGGCGAGTCATCTATA
1 AAGCCTTTGTGGCGAGTCATCTGTA
* * * * *
234216 AAGCTTTTGTGGTGAAT--TGTTTAA
1 AAGCCTTTGTGGCGAGTCATCTGT-A
*
234240 TAAGCCTTTGTGGCGAGTCATCTCTA
1 -AAGCCTTTGTGGCGAGTCATCTGTA
* * ** **
234266 AAGCCTTTGTGTCGAATTGTCTGGG
1 AAGCCTTTGTGGCGAGTCATCTGTA
* *
234291 AAGCCTTTGTGGCAAGTCATCTATA
1 AAGCCTTTGTGGCGAGTCATCTGTA
* * * **
234316 AAGCCTTTGTGGTGAATTATCTGGG
1 AAGCCTTTGTGGCGAGTCATCTGTA
*
234341 AAGCCTTTGCGGCGAGTCATCTGTA
1 AAGCCTTTGTGGCGAGTCATCTGTA
234366 AAGCCTTT
1 AAGCCTTT
234374 TTAGCGAATT
Statistics
Matches: 151, Mismatches: 53, Indels: 8
0.71 0.25 0.04
Matches are distributed among these distances:
23 3 0.02
24 1 0.01
25 143 0.95
26 1 0.01
27 3 0.02
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (25 bp):
AAGCCTTTGTGGCGAGTCATCTGTA
Found at i:234173 original size:50 final size:50
Alignment explanation
Indices: 234116--234612 Score: 304
Period size: 50 Copynumber: 9.9 Consensus size: 50
234106 AAACCAAACC
* * * *
234116 AAGCCTTTGTGGTGAATTATATAGGAAGCCTTCGTGGTGAGTCATCTGTA
1 AAGCCTTTGTGGTGAATTATCTAGGAAGCCTTTGTGGCGAGTCATCTATA
** * * **
234166 AAGCCTTTGTGGCAAATTAT-TTGCAAAGTTTTTGTGGCGAGTCATCTATA
1 AAGCCTTTGTGGTGAATTATCTAG-GAAGCCTTTGTGGCGAGTCATCTATA
* * * ** *
234216 AAGCTTTTGTGGTGAATTGTTTAATAAGCCTTTGTGGCGAGTCATCTCTA
1 AAGCCTTTGTGGTGAATTATCTAGGAAGCCTTTGTGGCGAGTCATCTATA
* * *
234266 AAGCCTTTGT-GTCGAATTGTCTGGGAAGCCTTTGTGGCAAGTCATCTATA
1 AAGCCTTTGTGGT-GAATTATCTAGGAAGCCTTTGTGGCGAGTCATCTATA
* * *
234316 AAGCCTTTGTGGTGAATTATCTGGGAAGCCTTTGCGGCGAGTCATCTGTA
1 AAGCCTTTGTGGTGAATTATCTAGGAAGCCTTTGTGGCGAGTCATCTATA
* * * * * * * * * *
234366 AAGCCTTTTTAGCGAATTGT-TGGGGAAGCTTTTGTGGCAATTCATATGTA
1 AAGCCTTTGTGGTGAATTATCT-AGGAAGCCTTTGTGGCGAGTCATCTATA
* * * * * * * *
234416 AATCCTTTGTGCCT-AATTGTCTGGGAAGCTTTTGCGACGAGTCTTCTATA
1 AAGCCTTTGTG-GTGAATTATCTAGGAAGCCTTTGTGGCGAGTCATCTATA
* * * * * * * * ** * *
234466 AGGCCTTTGGGGCGAATTGTTTGGGAAGCCTTTGTGGTGAATGTTTTGGT-
1 AAGCCTTTGTGGTGAATTATCTAGGAAGCCTTTGTGGCGAGTCATCT-ATA
* * * ** * ** *
234516 ATGCCTTTGT-GTCGAGTCATCTATAAAGCCTTTATGATGAGTCATCTGTA
1 AAGCCTTTGTGGT-GAATTATCTAGGAAGCCTTTGTGGCGAGTCATCTATA
* * * **
234566 AAGCCTTTATGGTGAATTATTTAGGAAGCCCTAATGGCGAGTCATCT
1 AAGCCTTTGTGGTGAATTATCTAGGAAGCCTTTGTGGCGAGTCATCT
234613 TGGAAGCCTA
Statistics
Matches: 343, Mismatches: 92, Indels: 24
0.75 0.20 0.05
Matches are distributed among these distances:
49 8 0.02
50 328 0.96
51 7 0.02
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.36
Consensus pattern (50 bp):
AAGCCTTTGTGGTGAATTATCTAGGAAGCCTTTGTGGCGAGTCATCTATA
Found at i:234300 original size:100 final size:100
Alignment explanation
Indices: 234116--234502 Score: 416
Period size: 100 Copynumber: 3.9 Consensus size: 100
234106 AAACCAAACC
* * * * *
234116 AAGCCTTTGTGGTGAATTATATAGGAAGCCTTCGTGGTGAGTCATCTGTAAAGCCTTTGTGGCAA
1 AAGCCTTTGTGGTGAATTATCTAGGAAGCCTTTGCGGCGAGTCATCTGTAAAGCCTTTGTGGCGA
* ** ** *
234181 ATTATTTGCAAAGTTTTTGTGGCGAGTCATCTATA
66 ATTGTTTGGGAAGCCTTTGTGGCAAGTCATCTATA
* * * ** * * *
234216 AAGCTTTTGTGGTGAATTGTTTAATAAGCCTTTGTGGCGAGTCATCTCTAAAGCCTTTGTGTCGA
1 AAGCCTTTGTGGTGAATTATCTAGGAAGCCTTTGCGGCGAGTCATCTGTAAAGCCTTTGTGGCGA
*
234281 ATTGTCTGGGAAGCCTTTGTGGCAAGTCATCTATA
66 ATTGTTTGGGAAGCCTTTGTGGCAAGTCATCTATA
* * *
234316 AAGCCTTTGTGGTGAATTATCTGGGAAGCCTTTGCGGCGAGTCATCTGTAAAGCCTTTTTAGCGA
1 AAGCCTTTGTGGTGAATTATCTAGGAAGCCTTTGCGGCGAGTCATCTGTAAAGCCTTTGTGGCGA
* * * * *
234381 ATTGTTGGGGAAGCTTTTGTGGCAATTCATATGTA
66 ATTGTTTGGGAAGCCTTTGTGGCAAGTCATCTATA
* * * * * * * * * *
234416 AATCCTTTGTGCCT-AATTGTCTGGGAAGCTTTTGCGACGAGTCTTCTATAAGGCCTTTGGGGCG
1 AAGCCTTTGTG-GTGAATTATCTAGGAAGCCTTTGCGGCGAGTCATCTGTAAAGCCTTTGTGGCG
234480 AATTGTTTGGGAAGCCTTTGTGG
65 AATTGTTTGGGAAGCCTTTGTGG
234503 TGAATGTTTT
Statistics
Matches: 239, Mismatches: 47, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
100 238 1.00
101 1 0.00
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.36
Consensus pattern (100 bp):
AAGCCTTTGTGGTGAATTATCTAGGAAGCCTTTGCGGCGAGTCATCTGTAAAGCCTTTGTGGCGA
ATTGTTTGGGAAGCCTTTGTGGCAAGTCATCTATA
Found at i:234356 original size:150 final size:150
Alignment explanation
Indices: 234116--234499 Score: 403
Period size: 150 Copynumber: 2.6 Consensus size: 150
234106 AAACCAAACC
* * * * * * *
234116 AAGCCTTTGTGGT-GAATTATATAGGAAGCCTTCGTGGTGAGTCATCTGTAAAGCCTTTGTGGCA
1 AAGCCTTTGT-GTCGAATTGTCTGGGAAGCCTTTGTGGCGAGTCATCTATAAAGCCTTTGTGGCG
** ** * * * * *
234180 AATTATTTGCAAAGTTTTTGTGGCGAGTCATCTATAAAG-CTTTTGTGGTGAATTGTTTAATAAG
65 AATTATTTGGGAAGCCTTTGCGGCGAGTCATCTATAAAGCCTTTT-TAGCGAATTGTTGAAGAAG
* *
234244 CCTTTGTGGCGAGTCATCTCTA
129 CCTTTGTGGCAAGTCATATCTA
* *
234266 AAGCCTTTGTGTCGAATTGTCTGGGAAGCCTTTGTGGCAAGTCATCTATAAAGCCTTTGTGGTGA
1 AAGCCTTTGTGTCGAATTGTCTGGGAAGCCTTTGTGGCGAGTCATCTATAAAGCCTTTGTGGCGA
* * ** *
234331 ATTATCTGGGAAGCCTTTGCGGCGAGTCATCTGTAAAGCCTTTTTAGCGAATTGTTGGGGAAGCT
66 ATTATTTGGGAAGCCTTTGCGGCGAGTCATCTATAAAGCCTTTTTAGCGAATTGTTGAAGAAGCC
* *
234396 TTTGTGGCAATTCATATGTA
131 TTTGTGGCAAGTCATATCTA
* * * * * * * * *
234416 AATCCTTTGTGCCTAATTGTCTGGGAAGCTTTTGCGACGAGTCTTCTATAAGGCCTTTGGGGCGA
1 AAGCCTTTGTGTCGAATTGTCTGGGAAGCCTTTGTGGCGAGTCATCTATAAAGCCTTTGTGGCGA
*
234481 ATTGTTTGGGAAGCCTTTG
66 ATTATTTGGGAAGCCTTTG
234500 TGGTGAATGT
Statistics
Matches: 192, Mismatches: 40, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
149 2 0.01
150 185 0.96
151 5 0.03
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.36
Consensus pattern (150 bp):
AAGCCTTTGTGTCGAATTGTCTGGGAAGCCTTTGTGGCGAGTCATCTATAAAGCCTTTGTGGCGA
ATTATTTGGGAAGCCTTTGCGGCGAGTCATCTATAAAGCCTTTTTAGCGAATTGTTGAAGAAGCC
TTTGTGGCAAGTCATATCTA
Found at i:234507 original size:25 final size:25
Alignment explanation
Indices: 234468--234526 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
234458 CTTCTATAAG
*
234468 GCCTTTGGGGCGAAT-TGTTTGGGAA
1 GCCTTTGTGGCGAATGT-TTTGGGAA
* * *
234493 GCCTTTGTGGTGAATGTTTTGGTAT
1 GCCTTTGTGGCGAATGTTTTGGGAA
234518 GCCTTTGTG
1 GCCTTTGTG
234527 TCGAGTCATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 28 0.97
26 1 0.03
ACGTcount: A:0.12, C:0.12, G:0.36, T:0.41
Consensus pattern (25 bp):
GCCTTTGTGGCGAATGTTTTGGGAA
Found at i:234546 original size:25 final size:25
Alignment explanation
Indices: 234529--234576 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
234519 CCTTTGTGTC
234529 GAGTCATCTATAAAGCCTTTATGAT
1 GAGTCATCTATAAAGCCTTTATGAT
*
234554 GAGTCATCTGTAAAGCCTTTATG
1 GAGTCATCTATAAAGCCTTTATG
234577 GTGAATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (25 bp):
GAGTCATCTATAAAGCCTTTATGAT
Found at i:239523 original size:5 final size:5
Alignment explanation
Indices: 239502--239559 Score: 66
Period size: 5 Copynumber: 11.4 Consensus size: 5
239492 TTACTTTATT
239502 TAATA TATATAA TAATA TAATA TAATA TAAT- TAATA TAATA T-ATAA
1 TAATA TA-AT-A TAATA TAATA TAATA TAATA TAATA TAATA TAAT-A
*
239548 TAAAA TAATA TA
1 TAATA TAATA TA
239560 CATAACATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
4 6 0.13
5 32 0.70
6 5 0.11
7 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:239536 original size:31 final size:29
Alignment explanation
Indices: 239501--239559 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
239491 TTTACTTTAT
239501 TTAATAT-ATATAATAATATAATATAATATAA
1 TTAATATAATAT-ATAATA-AA-ATAATATAA
239532 TTAATATAATATATAATAAAATAATATA
1 TTAATATAATATATAATAAAATAATATA
239560 CATAACATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 8 0.30
30 2 0.07
31 13 0.48
32 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
TTAATATAATATATAATAAAATAATATAA
Found at i:239538 original size:19 final size:18
Alignment explanation
Indices: 239502--239559 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 18
239492 TTACTTTATT
239502 TAATAT-ATATAATAATA
1 TAATATAATATAATAATA
239519 TAATATAATATAATTAATA
1 TAATATAATATAA-TAATA
*
239538 TAATATATAATAAAATAATA
1 T-A-ATATAATATAATAATA
239558 TA
1 TA
239560 CATAACATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
17 6 0.17
18 6 0.17
19 7 0.19
20 7 0.19
21 10 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATATAATATAATAATA
Found at i:239569 original size:14 final size:13
Alignment explanation
Indices: 239502--239559 Score: 68
Period size: 12 Copynumber: 4.5 Consensus size: 13
239492 TTACTTTATT
239502 TAATAT-ATATAA
1 TAATATAATATAA
239514 TAATATAATATAA
1 TAATATAATATAA
239527 T-ATAATTAATATAA
1 TAAT-A-TAATATAA
*
239541 T-ATATAATAAAA
1 TAATATAATATAA
239553 TAATATA
1 TAATATA
239560 CATAACATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
12 16 0.39
13 14 0.34
14 11 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATATAATATAA
Found at i:241007 original size:15 final size:15
Alignment explanation
Indices: 240987--241017 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
240977 ACATCTACTG
240987 AAATAGATGAATTAC
1 AAATAGATGAATTAC
241002 AAATAGATGAATTAC
1 AAATAGATGAATTAC
241017 A
1 A
241018 TACAACATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.26
Consensus pattern (15 bp):
AAATAGATGAATTAC
Found at i:241984 original size:21 final size:21
Alignment explanation
Indices: 241960--242015 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
241950 CGGAACAATT
*
241960 AAGAAAAAGA-GAAATACAAAA
1 AAGAAAAAGATCAAAT-CAAAA
*
241981 AAG-AATAGATCAAATCAAAA
1 AAGAAAAAGATCAAATCAAAA
*
242001 AAGAAATAGAATCAA
1 AAGAAAAAG-ATCAA
242016 CAATTTGTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 13 0.43
21 12 0.40
22 5 0.17
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.11
Consensus pattern (21 bp):
AAGAAAAAGATCAAATCAAAA
Found at i:242001 original size:20 final size:23
Alignment explanation
Indices: 241971--242015 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
241961 AGAAAAAGAG
241971 AAATACAAAAAAG-AATAG-ATC
1 AAATACAAAAAAGAAATAGAATC
241992 AAAT-CAAAAAAGAAATAGAATC
1 AAATACAAAAAAGAAATAGAATC
242014 AA
1 AA
242016 CAATTTGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.13
Consensus pattern (23 bp):
AAATACAAAAAAGAAATAGAATC
Found at i:244881 original size:34 final size:33
Alignment explanation
Indices: 244843--244972 Score: 118
Period size: 34 Copynumber: 3.8 Consensus size: 33
244833 AAAATATGTG
*
244843 TGAATAGGAAAGATTCCTTGCAA-AGAATGATGCA
1 TGAATAGGAAAGATTCCCTGCAAGA-AATGATG-A
* * * *
244877 TGAATAGAAAAGATTCCCTACAAGAAAAGACGA
1 TGAATAGGAAAGATTCCCTGCAAGAAATGATGA
* * *
244910 GGTGAACAGGAAAGATTCCTTGCAAGAAATGATGTG
1 --TGAATAGGAAAGATTCCCTGCAAGAAATGATG-A
* *
244946 TGAATAGGACATATTCCCTGCAAGAAA
1 TGAATAGGAAAGATTCCCTGCAAGAAA
244973 AGACAAGAAA
Statistics
Matches: 76, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
33 1 0.01
34 48 0.63
35 27 0.36
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (33 bp):
TGAATAGGAAAGATTCCCTGCAAGAAATGATGA
Found at i:244924 original size:69 final size:69
Alignment explanation
Indices: 244842--244976 Score: 191
Period size: 69 Copynumber: 2.0 Consensus size: 69
244832 GAAAATATGT
*
244842 GTGAATAGGAAAGATTCCTTGCAA-AGAATGATGCATGAATAGAAAAGATTCCCTACAAGAAAAG
1 GTGAACAGGAAAGATTCCTTGCAAGA-AATGATGCATGAATAGAAAAGATTCCCTACAAGAAAAG
244906 ACGAG
65 ACGAG
** * * * *
244911 GTGAACAGGAAAGATTCCTTGCAAGAAATGATGTGTGAATAGGACATATTCCCTGCAAGAAAAGA
1 GTGAACAGGAAAGATTCCTTGCAAGAAATGATGCATGAATAGAAAAGATTCCCTACAAGAAAAGA
244976 C
66 C
244977 AAGAAAAAAG
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
69 57 0.98
70 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (69 bp):
GTGAACAGGAAAGATTCCTTGCAAGAAATGATGCATGAATAGAAAAGATTCCCTACAAGAAAAGA
CGAG
Found at i:244927 original size:35 final size:34
Alignment explanation
Indices: 244827--244976 Score: 104
Period size: 34 Copynumber: 4.4 Consensus size: 34
244817 GAAGAAATGA
* * * * *
244827 TGCAAGAAAATATGTGTGAATAGGAAAGATTCCT
1 TGCAAGAAAAGACGGGTGAACAGGAAAGATTCCC
* * ** * *
244861 TGCAA-AGAATGATGCATGAATAGAAAAGATTCCC
1 TGCAAGA-AAAGACGGGTGAACAGGAAAGATTCCC
* *
244895 TACAAGAAAAGACGAGGTGAACAGGAAAGATTCCT
1 TGCAAGAAAAGACG-GGTGAACAGGAAAGATTCCC
* * * * * *
244930 TGCAAGAAATGATGTGTGAATAGGACATATTCCC
1 TGCAAGAAAAGACGGGTGAACAGGAAAGATTCCC
244964 TGCAAGAAAAGAC
1 TGCAAGAAAAGAC
244977 AAGAAAAAAG
Statistics
Matches: 89, Mismatches: 24, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
33 1 0.01
34 61 0.69
35 27 0.30
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (34 bp):
TGCAAGAAAAGACGGGTGAACAGGAAAGATTCCC
Found at i:245040 original size:19 final size:19
Alignment explanation
Indices: 245016--245056 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
245006 CTGTAATTTG
245016 TATTTTTGTAATCAGAGAA
1 TATTTTTGTAATCAGAGAA
245035 TATTTTTGTAATCAGAGAA
1 TATTTTTGTAATCAGAGAA
245054 TAT
1 TAT
245057 ATTCTCTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (19 bp):
TATTTTTGTAATCAGAGAA
Found at i:245223 original size:21 final size:23
Alignment explanation
Indices: 245190--245232 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
245180 CATTTGAGTT
245190 GTTTCTCCAAATTTTC-CAAAAA
1 GTTTCTCCAAATTTTCTCAAAAA
245212 GTTTCT-CAAATTTTCTCAAAA
1 GTTTCTCCAAATTTTCTCAAAA
245233 TTTTTAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.40
Consensus pattern (23 bp):
GTTTCTCCAAATTTTCTCAAAAA
Found at i:245233 original size:11 final size:11
Alignment explanation
Indices: 245191--245236 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
245181 ATTTGAGTTG
*
245191 TTTCTCCAAAT
1 TTTCTCAAAAT
*
245202 TTTC-CAAAAAG
1 TTTCTC-AAAAT
245213 TTTCTC-AAAT
1 TTTCTCAAAAT
245223 TTTCTCAAAAT
1 TTTCTCAAAAT
245234 TTT
1 TTT
245237 TAAGTTTACA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
10 10 0.34
11 18 0.62
12 1 0.03
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.46
Consensus pattern (11 bp):
TTTCTCAAAAT
Found at i:245289 original size:13 final size:13
Alignment explanation
Indices: 245271--245308 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
245261 ATTTTCCAAA
245271 TTTTCAAATTAAG
1 TTTTCAAATTAAG
245284 TTTTCAAACTTAAG
1 TTTTCAAA-TTAAG
*
245298 CTTTCAAATTA
1 TTTTCAAATTA
245309 CAAATATCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (13 bp):
TTTTCAAATTAAG
Found at i:248155 original size:34 final size:34
Alignment explanation
Indices: 248107--248250 Score: 155
Period size: 34 Copynumber: 4.2 Consensus size: 34
248097 TTTTTTGTCT
* * *
248107 TTTCTTTCAAGGAATATTTCCTGTTCACACATCA
1 TTTCTTGCAGGGAATCTTTCCTGTTCACACATCA
* * * *
248141 TTTCTTGCAGGGAATCTTTTCTGTTCACCTCGTCT
1 TTTCTTGCAGGGAATCTTTCCTGTTCA-CACATCA
* **
248176 TTTCTTGCAGGGAATCTTTCATGTTCATGCATCA
1 TTTCTTGCAGGGAATCTTTCCTGTTCACACATCA
* *
248210 -TTCTTTGCAGGGAATCTTTCCTATTCACACATCT
1 TTTC-TTGCAGGGAATCTTTCCTGTTCACACATCA
248244 TTTCTTG
1 TTTCTTG
248251 TATCATTTCT
Statistics
Matches: 89, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
33 3 0.03
34 54 0.61
35 32 0.36
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.44
Consensus pattern (34 bp):
TTTCTTGCAGGGAATCTTTCCTGTTCACACATCA
Found at i:248190 original size:69 final size:68
Alignment explanation
Indices: 248103--248250 Score: 181
Period size: 69 Copynumber: 2.2 Consensus size: 68
248093 TCTTTTTTTT
* * * *
248103 GTCTTTTCTTTCAAGGAATATTTCCTGTTCACACATCATT-TCTTGCAGGGAATCTTTTCTGTTC
1 GTCTTTTCTTGCAAGGAATATTTCATGTTCACACATCATTCT-TTGCAGGGAATCTTTCCTATTC
*
248167 ACCTC
65 A-CAC
* * **
248172 GTCTTTTCTTGCAGGGAATCTTTCATGTTCATGCATCATTCTTTGCAGGGAATCTTTCCTATTCA
1 GTCTTTTCTTGCAAGGAATATTTCATGTTCACACATCATTCTTTGCAGGGAATCTTTCCTATTCA
248237 CAC
66 CAC
*
248240 ATCTTTTCTTG
1 GTCTTTTCTTG
248251 TATCATTTCT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
68 12 0.18
69 55 0.81
70 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.14, T:0.44
Consensus pattern (68 bp):
GTCTTTTCTTGCAAGGAATATTTCATGTTCACACATCATTCTTTGCAGGGAATCTTTCCTATTCA
CAC
Found at i:250986 original size:15 final size:15
Alignment explanation
Indices: 250966--250996 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
250956 AGATGTTGTA
250966 TGTAATTCATCTATT
1 TGTAATTCATCTATT
250981 TGTAATTCATCTATT
1 TGTAATTCATCTATT
250996 T
1 T
250997 CAGTAGATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.06, T:0.55
Consensus pattern (15 bp):
TGTAATTCATCTATT
Found at i:254298 original size:13 final size:13
Alignment explanation
Indices: 254280--254317 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
254270 GAAATATTTG
254280 TAAGTTGAAAACT
1 TAAGTTGAAAACT
254293 TAAGTTTGAAAACT
1 TAAG-TTGAAAACT
*
254307 TAATTTGAAAA
1 TAAGTTGAAAA
254318 TTTGGTAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.34
Consensus pattern (13 bp):
TAAGTTGAAAACT
Found at i:254301 original size:14 final size:14
Alignment explanation
Indices: 254280--254317 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
254270 GAAATATTTG
254280 TAAG-TTGAAAACT
1 TAAGTTTGAAAACT
254293 TAAGTTTGAAAACT
1 TAAGTTTGAAAACT
254307 TAA-TTTGAAAA
1 TAAGTTTGAAAA
254318 TTTGGTAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.34
Consensus pattern (14 bp):
TAAGTTTGAAAACT
Done.