Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015153.1 Kokia drynarioides strain JFW-HI SEQ_130197, whole genome shotgun sequence
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: 800050
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 392 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:38 original size:12 final size:12
Alignment explanation
Indices: 21--68 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
11 AAACATGTTC
21 ATTAATTTCCAA
1 ATTAATTTCCAA
33 ATTAATTTCAACTTAA
1 ATTAATTTC--C--AA
*
49 ATTAATTTTCAA
1 ATTAATTTCCAA
61 ATTAATTT
1 ATTAATTT
69 TTACACAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTAATTTCCAA
Found at i:67 original size:16 final size:16
Alignment explanation
Indices: 31--65 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
21 ATTAATTTCC
*
31 AAATTAATTTCAACTT
1 AAATTAATTTCAAATT
47 AAATTAATTTTCAAATT
1 AAATTAA-TTTCAAATT
64 AA
1 AA
66 TTTTTACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTAATTTCAAATT
Found at i:78 original size:28 final size:28
Alignment explanation
Indices: 21--78 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
11 AAACATGTTC
**
21 ATTAATTTCCAAATTAATTTCAACTTAA
1 ATTAATTTCCAAATTAATTTCAACACAA
* **
49 ATTAATTTTCAAATTAATTTTTACACAA
1 ATTAATTTCCAAATTAATTTCAACACAA
77 AT
1 AT
79 ATTTTTTCGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTAATTTCCAAATTAATTTCAACACAA
Found at i:4051 original size:37 final size:39
Alignment explanation
Indices: 3981--4053 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
3971 GCAATGGCCA
3981 ACACCCAAAAATGCAATATTTTTTTCGAAAAAATGGTCG
1 ACACCCAAAAATGCAATATTTTTTTCGAAAAAATGGTCG
*
4020 ACACCCAAAAATGCAAT-TTTTTTT-GAGAAAATGG
1 ACACCCAAAAATGCAATATTTTTTTCGAAAAAATGG
4054 GGTGTCGACC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
37 9 0.27
38 7 0.21
39 17 0.52
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (39 bp):
ACACCCAAAAATGCAATATTTTTTTCGAAAAAATGGTCG
Found at i:4058 original size:95 final size:94
Alignment explanation
Indices: 3939--4161 Score: 261
Period size: 97 Copynumber: 2.3 Consensus size: 94
3929 AAAATTTTGA
* * * *
3939 AATTTTTTTCGAGAAAAGAAGGTGTCGGCCATGCAATGGCCAACACCCAAAAA-TGCAATATTTT
1 AATTTTTTTCGAGAAAAG-GGGTGTCGGCCATGCAATGACCAACACCAAAAAATTGAAAT-TTTT
*
4003 TT-TCGAAAAAATGGTCGACACCCAAAAATGC
64 TTCTCG-AAAAATGGCCGACACCCAAAAATGC
* * ***
4034 AATTTTTTTTGAGAAAATGGGGTGTCGACCATTTGATGACCAACACCAAAAAATTTTGAAATTTT
1 AATTTTTTTCGAGAAAA-GGGGTGTCGGCCATGCAATGACCAACACCAAAAAA--TTGAAATTTT
*
4099 TTTCTCGAGAAATGGCCGACACCCAAAAATGC
63 TTTCTCGAAAAATGGCCGACACCCAAAAATGC
*
4131 AATTTTTTTCGAGAAAAGGGGGTGTCAGCCA
1 AATTTTTTTCGAGAAAA-GGGGTGTCGGCCA
4162 ACACCAAAAA
Statistics
Matches: 108, Mismatches: 15, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
95 43 0.40
96 1 0.01
97 56 0.52
98 8 0.07
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (94 bp):
AATTTTTTTCGAGAAAAGGGGTGTCGGCCATGCAATGACCAACACCAAAAAATTGAAATTTTTTT
CTCGAAAAATGGCCGACACCCAAAAATGC
Found at i:4265 original size:57 final size:56
Alignment explanation
Indices: 4158--4288 Score: 151
Period size: 57 Copynumber: 2.3 Consensus size: 56
4148 GGGGGTGTCA
4158 GCCAACACCAAAAAATTTTGAAATTTTTTTCTCAAAAAGGAGATGTCGGTCATGCAATG
1 GCCAACACCAAAAAA---TGAAATTTTTTTCTCAAAAAGGAGATGTCGGTCATGCAATG
* ***
4217 GCCAACACCAAAAAATGCAATTTTTTT-TCGAGAAAAGTGAG-TGTCGGTCATTTGATG
1 GCCAACACCAAAAAATGAAATTTTTTTCTC-A-AAAAG-GAGATGTCGGTCATGCAATG
4274 GCCAACA-CAAAAAAT
1 GCCAACACCAAAAAAT
4289 TGTATTTTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
55 2 0.03
56 20 0.31
57 25 0.38
58 3 0.05
59 15 0.23
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.27
Consensus pattern (56 bp):
GCCAACACCAAAAAATGAAATTTTTTTCTCAAAAAGGAGATGTCGGTCATGCAATG
Found at i:17847 original size:2 final size:2
Alignment explanation
Indices: 17836--17867 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
17826 TTAAATTTCC
17836 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17868 AAATATGAAT
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:18102 original size:33 final size:32
Alignment explanation
Indices: 18038--18105 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
18028 TCTATATTAT
*
18038 TTTTAATATTTAAAAATATTTATTTTATTTTA
1 TTTTAATATTTAAAAATATTTAATTTATTTTA
18070 TTTTAATATTTAATAAAT-TTATACATTT-TTTTA
1 TTTTAATATTTAA-AAATATT-TA-ATTTATTTTA
18103 TTT
1 TTT
18106 ATTGAAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
32 15 0.47
33 14 0.44
34 3 0.09
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (32 bp):
TTTTAATATTTAAAAATATTTAATTTATTTTA
Found at i:21631 original size:21 final size:21
Alignment explanation
Indices: 21607--21653 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
21597 ATATATAGGC
21607 CTTGAAATTGTAAACAAAACA
1 CTTGAAATTGTAAACAAAACA
**
21628 CTTGATTTTGTAAACAAAACA
1 CTTGAAATTGTAAACAAAACA
21649 CTTGA
1 CTTGA
21654 TTTTGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.30
Consensus pattern (21 bp):
CTTGAAATTGTAAACAAAACA
Found at i:21654 original size:21 final size:21
Alignment explanation
Indices: 21614--21658 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
21604 GGCCTTGAAA
21614 TTGTAAACAAAACACTTGATT
1 TTGTAAACAAAACACTTGATT
21635 TTGTAAACAAAACACTTGATT
1 TTGTAAACAAAACACTTGATT
21656 TTG
1 TTG
21659 ATTATTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (21 bp):
TTGTAAACAAAACACTTGATT
Found at i:27765 original size:24 final size:24
Alignment explanation
Indices: 27702--27767 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
27692 CTAAACAAAA
* *
27702 TTAGCTCATACAAGCCCAGATAGG
1 TTAGCTCATTCAAGCCCAGATAAG
* * *
27726 TTACCTC-TTACGAGCCTAGATAAG
1 TTAGCTCATT-CAAGCCCAGATAAG
27750 TTAGCTCATTCAAGCCCA
1 TTAGCTCATTCAAGCCCA
27768 AACAGAGTCT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
23 1 0.03
24 29 0.91
25 2 0.06
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (24 bp):
TTAGCTCATTCAAGCCCAGATAAG
Found at i:30801 original size:80 final size:80
Alignment explanation
Indices: 30657--30806 Score: 230
Period size: 80 Copynumber: 1.9 Consensus size: 80
30647 AGTAATTTCA
* * *
30657 TTTTAACTCTTGTAAGGAAGCTAATGAGTCATGTCTCTTCATTAGGATCCGATGTAGTTAAAAAG
1 TTTTAACTCTTGTAAGGAAGCCAATGAGTCATGTCTCTTCATTAAGATCCGATGTAGCTAAAAAG
*
30722 GCATGTCAATTTCGG
66 ACATGTCAATTTCGG
* *
30737 TTTTAACTCTTGT-AGGAAAGCCAATGAGTCATGTCTCTTCATTAAGATCTGATGTAGCTGAAAA
1 TTTTAACTCTTGTAAGG-AAGCCAATGAGTCATGTCTCTTCATTAAGATCCGATGTAGCTAAAAA
30801 GACATG
65 GACATG
30807 CCATTTCTCC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
79 3 0.05
80 60 0.95
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (80 bp):
TTTTAACTCTTGTAAGGAAGCCAATGAGTCATGTCTCTTCATTAAGATCCGATGTAGCTAAAAAG
ACATGTCAATTTCGG
Found at i:31296 original size:48 final size:47
Alignment explanation
Indices: 31258--31379 Score: 156
Period size: 48 Copynumber: 2.6 Consensus size: 47
31248 CAAGGCATTT
31258 AACAAAGATGCATTTAACAAACAAAACAATTAACAATGCAGATTACTA
1 AACAAAGATGCATTTAACAAACAAAACAATTAACAATGCAGATTA-TA
* * *
31306 AACAAAGATGCATTTAACAAATAAAACACTTAATC-ATGTAGATTATTA
1 AACAAAGATGCATTTAACAAACAAAACAATTAA-CAATGCAGATTA-TA
* * *
31354 AACAAAAATGCATCTAACAAAAAAAA
1 AACAAAGATGCATTTAACAAACAAAA
31380 ACACTTAATG
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
48 65 0.98
49 1 0.02
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (47 bp):
AACAAAGATGCATTTAACAAACAAAACAATTAACAATGCAGATTATA
Found at i:32338 original size:21 final size:21
Alignment explanation
Indices: 32314--32365 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
32304 TTGTGTTAGC
32314 TCTACCGATACAAGT-ATG-A
1 TCTACCGATACAAGTCATGCA
32333 TTTCTACCGATACAAGTCATGCA
1 --TCTACCGATACAAGTCATGCA
32356 TCTACCGATA
1 TCTACCGATA
32366 ACAAAAACTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 25 0.86
22 3 0.10
23 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (21 bp):
TCTACCGATACAAGTCATGCA
Found at i:36808 original size:24 final size:24
Alignment explanation
Indices: 36781--36843 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
36771 AGCTCATACA
*
36781 AGCCCAGATAAGTTAGC-TTTTACG
1 AGCCCAGATAAGTTAGCATATT-CG
*
36805 AGCCCAGATAAATTAGCATATTCG
1 AGCCCAGATAAGTTAGCATATTCG
*
36829 AGCCCTGATAGAGTT
1 AGCCCAGATA-AGTT
36844 TAACCAGTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 27 0.82
25 6 0.18
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (24 bp):
AGCCCAGATAAGTTAGCATATTCG
Found at i:40628 original size:24 final size:24
Alignment explanation
Indices: 40541--40629 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
40531 TTTCAAAAAT
* *
40541 TTAGCTCATACGAGCCCAGATAAAA
1 TTAGCTCATACGAGCCCAG-TTAAG
* * *
40566 TTAGCTCATACTAGCCCAGATAGG
1 TTAGCTCATACGAGCCCAGTTAAG
* *
40590 TTAGCTCTTATGAGCCCAGTTAAG
1 TTAGCTCATACGAGCCCAGTTAAG
*
40614 TTAGCTCATTCGAGCC
1 TTAGCTCATACGAGCC
40630 TAGACAATGT
Statistics
Matches: 51, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
24 33 0.65
25 18 0.35
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (24 bp):
TTAGCTCATACGAGCCCAGTTAAG
Found at i:48059 original size:51 final size:50
Alignment explanation
Indices: 47948--48165 Score: 230
Period size: 51 Copynumber: 4.3 Consensus size: 50
47938 TTTTATATTT
* * *
47948 AATAAAGTCATGCATTATGTAACTTTCATGTTATTTAAGTATACATCATA
1 AATAAAGTCATGCATTATGTAACTCTCATGTTAGTTAAGTATGCATCATA
* * *
47998 AATAATGACATGCATTATGTAAGTCTCATGATTAGTTAAGCT-TGCATCATA
1 AATAAAGTCATGCATTATGTAACTCTCATG-TTAGTTAAG-TATGCATCATA
* * *
48049 AATAAAGACATGCATTAAGTAACGT-ACATGTTAGTTAA-TATGCATCATA
1 AATAAAGTCATGCATTATGTAAC-TCTCATGTTAGTTAAGTATGCATCATA
* * *
48098 AATTATA-TCATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCATCATTA
1 AA-TAAAGTCATGCATTATGTAACTCTCATGTTAGTT-AAGTATGCATCA-TA
48150 AA-ATAAGTCATGCATT
1 AATA-AAGTCATGCATT
48166 TAGTAATCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
48 2 0.01
49 35 0.25
50 40 0.28
51 49 0.35
52 15 0.11
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (50 bp):
AATAAAGTCATGCATTATGTAACTCTCATGTTAGTTAAGTATGCATCATA
Found at i:48143 original size:100 final size:102
Alignment explanation
Indices: 47948--48171 Score: 287
Period size: 101 Copynumber: 2.2 Consensus size: 102
47938 TTTTATATTT
* * * *
47948 AATAAAGTCATGCATTATGTAACTTTCATGTTATTTAAGTATACATCATAAATAATGACATGCAT
1 AATAAAGTCATGCATTAAGTAACGTACATGTTAGTTAAGTATACATCATAAATAATGACATGCAT
* *
48013 TATGTAAGTCTCATGATTAGTTAAGCTTGCATCA-TA
66 TATGTAACTCCCATGATTAGTTAAGCTTGCATCATTA
* * *
48049 AATAAAGACATGCATTAAGTAACGTACATGTTAGTTAA-TATGCATCATAAATTAT-ATCATGCA
1 AATAAAGTCATGCATTAAGTAACGTACATGTTAGTTAAGTATACATCATAAATAATGA-CATGCA
*
48112 TTATGTAACTCCCATG-TTAGTTAAAGTTTGCATCATTA
65 TTATGTAACTCCCATGATTAGTT-AAGCTTGCATCATTA
*
48150 AA-ATAAGTCATGCATTTAGTAA
1 AATA-AAGTCATGCATTAAGTAA
48172 TCAATTAGTT
Statistics
Matches: 107, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
99 7 0.07
100 47 0.44
101 53 0.50
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (102 bp):
AATAAAGTCATGCATTAAGTAACGTACATGTTAGTTAAGTATACATCATAAATAATGACATGCAT
TATGTAACTCCCATGATTAGTTAAGCTTGCATCATTA
Found at i:48672 original size:36 final size:36
Alignment explanation
Indices: 48632--48746 Score: 117
Period size: 36 Copynumber: 3.2 Consensus size: 36
48622 AAGATGGAGA
48632 CCTTTAAACTA-TCCAAAGA-ATAATGAAAAGACATGC
1 CCTTTAAACTACT-CAAAGACA-AATGAAAAGACATGC
* * *
48668 CCTTTCATCTACTCAAAGACAAATGAAGAGACATGC
1 CCTTTAAACTACTCAAAGACAAATGAAAAGACATGC
* * * * *
48704 TCTTTCATCTCCTCAAAGACAAATGAAGAGACATGC
1 CCTTTAAACTACTCAAAGACAAATGAAAAGACATGC
*
48740 CTTTTAA
1 CCTTTAA
48747 GCTAGATAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
36 67 0.97
37 2 0.03
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (36 bp):
CCTTTAAACTACTCAAAGACAAATGAAAAGACATGC
Found at i:49283 original size:27 final size:27
Alignment explanation
Indices: 49243--49299 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
49233 AAAAAAAAGT
* *
49243 GAAAAAATTCAAAAAAAAAAGGACTTC
1 GAAAAAATTCAAAAAAAAAAGAAATTC
* *
49270 GAAAATATTGAAAAAAAAAAGAAATTC
1 GAAAAAATTCAAAAAAAAAAGAAATTC
49297 GAA
1 GAA
49300 TTTTAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.65, C:0.07, G:0.12, T:0.16
Consensus pattern (27 bp):
GAAAAAATTCAAAAAAAAAAGAAATTC
Found at i:49979 original size:17 final size:17
Alignment explanation
Indices: 49959--49991 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
49949 TTTAAGGACT
49959 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
49976 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
49992 TAAGTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:50469 original size:48 final size:48
Alignment explanation
Indices: 50417--50551 Score: 189
Period size: 48 Copynumber: 2.8 Consensus size: 48
50407 ATTATGCTTT
*
50417 ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATGATCTGCATC
1 ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATGATCTACATC
* * * * *
50465 ATTAAGTGTTTTGTTTATTAAATACATCTTTGTTTAGTAATCTACATT
1 ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATGATCTACATC
* * *
50513 ATTAAATGTTTTGTTTGTTAAATGCATCTCTGTTAAATG
1 ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATG
50552 CCTTGAATTA
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 74 1.00
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (48 bp):
ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATGATCTACATC
Found at i:53598 original size:83 final size:83
Alignment explanation
Indices: 53459--53627 Score: 320
Period size: 83 Copynumber: 2.0 Consensus size: 83
53449 GTTTACGCCC
53459 CTTGTTAGCTTTGTTGGAATTCATGTAATTTGTTTTGGCAAGCAGTTGTTTTGCCTTTTCATGCA
1 CTTGTTAGCTTTGTTGGAATTCATGTAATTTGTTTTGGCAAGCAGTTGTTTTGCCTTTTCATGCA
53524 TTGACTTAACCAATTCAG
66 TTGACTTAACCAATTCAG
* *
53542 CTTGTTAGCTTTGTTGGAATTCATGTAATTTGTTTTGGCAATCAGTTGTTTTGCCTTTTCATGTA
1 CTTGTTAGCTTTGTTGGAATTCATGTAATTTGTTTTGGCAAGCAGTTGTTTTGCCTTTTCATGCA
53607 TTGACTTAACCAATTCAG
66 TTGACTTAACCAATTCAG
53625 CTT
1 CTT
53628 TCTTATACCA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.20, C:0.15, G:0.18, T:0.46
Consensus pattern (83 bp):
CTTGTTAGCTTTGTTGGAATTCATGTAATTTGTTTTGGCAAGCAGTTGTTTTGCCTTTTCATGCA
TTGACTTAACCAATTCAG
Found at i:60961 original size:21 final size:21
Alignment explanation
Indices: 60937--60978 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
60927 AAAAGAGTGC
60937 AAGAGAGAAGAAA-AAGAAAGT
1 AAGAGAGAA-AAAGAAGAAAGT
**
60958 AAGATTGAAAAAGAAGAAAGT
1 AAGAGAGAAAAAGAAGAAAGT
60979 GATAAAGCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.64, C:0.00, G:0.26, T:0.10
Consensus pattern (21 bp):
AAGAGAGAAAAAGAAGAAAGT
Found at i:62190 original size:50 final size:49
Alignment explanation
Indices: 62050--62191 Score: 182
Period size: 47 Copynumber: 2.9 Consensus size: 49
62040 TTAATTAAGC
* * * *
62050 CATGCATTATGTAACTTTCATGTTAGTTAAGTATACATAATAAATAATGA
1 CATGCATTAAGTAAC-TTCATGTTAGTTAAATATGCATCATAAATAATGA
* *
62100 CATGCATTAACT--C-TCATGATTAGTTAAATTTGCATCATAAATAATGA
1 CATGCATTAAGTAACTTCATG-TTAGTTAAATATGCATCATAAATAATGA
62147 CATGCATTAAGTAACTTACATGTTAGTTAAATATGCATCATAAAT
1 CATGCATTAAGTAACTT-CATGTTAGTTAAATATGCATCATAAAT
62192 CATATCATGT
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
46 5 0.06
47 35 0.44
48 1 0.01
49 1 0.01
50 33 0.42
51 4 0.05
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (49 bp):
CATGCATTAAGTAACTTCATGTTAGTTAAATATGCATCATAAATAATGA
Found at i:62211 original size:50 final size:48
Alignment explanation
Indices: 62057--62238 Score: 165
Period size: 50 Copynumber: 3.7 Consensus size: 48
62047 AGCCATGCAT
* * *
62057 TATGTAACTTTCATGTTAGTTAAGTATACATAATAAATAATGACATG-C
1 TATGTAAC-TTCATGTTAGTTAAATATGCATCATAAATAATGACATGAC
* *
62105 -AT-TAACTCTCATGATTAGTTAAATTTGCATCATAAATAATGACATGCAT
1 TATGTAACT-TCATG-TTAGTTAAATATGCATCATAAATAATGACATG-AC
* *
62154 TAAGTAACTTACATGTTAGTTAAATATGCATCATAAATCAT-ATCATGTAC
1 TATGTAACTT-CATGTTAGTTAAATATGCATCATAAATAATGA-CATG-AC
* * *
62204 TATGTAACTCCCATGTTAGTTTAAGTTTGCATCAT
1 TATGTAACT-TCATGTTAG-TTAAATATGCATCAT
62239 TGAAACAAGT
Statistics
Matches: 110, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
45 1 0.01
46 9 0.08
47 30 0.27
49 1 0.01
50 47 0.43
51 22 0.20
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.38
Consensus pattern (48 bp):
TATGTAACTTCATGTTAGTTAAATATGCATCATAAATAATGACATGAC
Found at i:65157 original size:28 final size:28
Alignment explanation
Indices: 65117--65171 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
65107 GATATCTGAT
* *
65117 TTACTCCTTGTTGACCCAATGGTCATGC
1 TTACTCCCTGTTGACCCAAAGGTCATGC
*
65145 TTACTCCCTGTTGACCGAAAGGTCATG
1 TTACTCCCTGTTGACCCAAAGGTCATG
65172 TCTATTACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (28 bp):
TTACTCCCTGTTGACCCAAAGGTCATGC
Found at i:70486 original size:13 final size:13
Alignment explanation
Indices: 70468--70494 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
70458 ATTCGAATAT
70468 AATAAGACTGTAA
1 AATAAGACTGTAA
70481 AATAAGACTGTAA
1 AATAAGACTGTAA
70494 A
1 A
70495 TATTAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (13 bp):
AATAAGACTGTAA
Found at i:72979 original size:24 final size:25
Alignment explanation
Indices: 72952--73005 Score: 85
Period size: 24 Copynumber: 2.2 Consensus size: 25
72942 ACAAGTACAT
72952 AAACTAAT-GATAATCCGATGGGCA
1 AAACTAATCGATAATCCGATGGGCA
*
72976 AAACT-ATCGATACTCCGATGGGCA
1 AAACTAATCGATAATCCGATGGGCA
73000 AAACTA
1 AAACTA
73006 CCGATACTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (25 bp):
AAACTAATCGATAATCCGATGGGCA
Found at i:73010 original size:24 final size:24
Alignment explanation
Indices: 72960--73013 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
72950 ATAAACTAAT
* *
72960 GATAATCCGATGGGCAAAACTATC
1 GATACTCCGATGGGCAAAACTACC
72984 GATACTCCGATGGGCAAAACTACC
1 GATACTCCGATGGGCAAAACTACC
73008 GATACT
1 GATACT
73014 TATTATGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (24 bp):
GATACTCCGATGGGCAAAACTACC
Found at i:73675 original size:28 final size:28
Alignment explanation
Indices: 73631--73713 Score: 121
Period size: 28 Copynumber: 3.0 Consensus size: 28
73621 GATATTTGAT
*
73631 TTACTCCCTGTTGACCCATAGGTCATGC
1 TTACTCCCTGTTGACCCAAAGGTCATGC
* * *
73659 TTCCTCCCTGTTAACCCAAAGGTGATGC
1 TTACTCCCTGTTGACCCAAAGGTCATGC
*
73687 TTACTCTCTGTTGACCCAAAGGTCATG
1 TTACTCCCTGTTGACCCAAAGGTCATG
73714 ATGCTCATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.20, C:0.30, G:0.18, T:0.31
Consensus pattern (28 bp):
TTACTCCCTGTTGACCCAAAGGTCATGC
Found at i:78978 original size:31 final size:31
Alignment explanation
Indices: 78940--79067 Score: 87
Period size: 31 Copynumber: 4.3 Consensus size: 31
78930 TTAATATAAC
78940 ATTTGGTACCTGAA-TTTGACACTTTTTTCTA
1 ATTTGGTACCT-AACTTTGACACTTTTTTCTA
78971 ATTTGGTACCTAAACTTT-----TTTTGTTC-A
1 ATTTGGTACCT-AACTTTGACACTTTT-TTCTA
* * *
78998 ATTTGCTA-CTCAAGC-TTAACACTTTTTCCTA
1 ATTTGGTACCT-AA-CTTTGACACTTTTTTCTA
* *
79029 ATTTGGTACCTAA-ATTGACACTTTTTTTTA
1 ATTTGGTACCTAACTTTGACACTTTTTTCTA
*
79059 AGTTGGTAC
1 ATTTGGTAC
79068 TTAAATTTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 23
0.71 0.08 0.21
Matches are distributed among these distances:
26 6 0.08
27 13 0.17
28 3 0.04
30 23 0.30
31 27 0.35
32 5 0.06
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.47
Consensus pattern (31 bp):
ATTTGGTACCTAACTTTGACACTTTTTTCTA
Found at i:79415 original size:59 final size:61
Alignment explanation
Indices: 79303--79444 Score: 198
Period size: 59 Copynumber: 2.4 Consensus size: 61
79293 AATTAAATCT
** *
79303 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAAATGCCAAGTTCAGGTGTCAAATTGGGTCC
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAAATGCCAAGTTCAGGTACCAAATTGGGTCA
* * *
79364 AAAAAAA-TTTAGGTACCAAATTAGG-AAAAAGTGTCAAGTTTAGGTACCAAATTGGGTCA
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAAATGCCAAGTTCAGGTACCAAATTGGGTCA
* *
79423 AAAAAAATTTTAAGTACCAAAT
1 AAAAAAAGTTTAGGTACCAAAT
79445 GTTATATTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
59 35 0.48
60 31 0.42
61 7 0.10
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAAAAAGTTTAGGTACCAAATTAGGAAAAAAATGCCAAGTTCAGGTACCAAATTGGGTCA
Found at i:98278 original size:22 final size:22
Alignment explanation
Indices: 98247--98290 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
98237 TTGGTGCTTT
98247 TGTTACGACGTAAAGCATCCTA
1 TGTTACGACGTAAAGCATCCTA
*
98269 TGTTATGACGTAAAGCATCCTA
1 TGTTACGACGTAAAGCATCCTA
98291 AGTGATTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (22 bp):
TGTTACGACGTAAAGCATCCTA
Found at i:115206 original size:12 final size:12
Alignment explanation
Indices: 115191--115217 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
115181 AACATATGAT
115191 ACGTTTTATTTA
1 ACGTTTTATTTA
115203 ACGTTTTATTTA
1 ACGTTTTATTTA
115215 ACG
1 ACG
115218 GATTGTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.52
Consensus pattern (12 bp):
ACGTTTTATTTA
Found at i:116068 original size:11 final size:11
Alignment explanation
Indices: 116052--116083 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
116042 TCTTTGAACA
116052 ATTTCAAAGAG
1 ATTTCAAAGAG
116063 ATTTCAAAGAG
1 ATTTCAAAGAG
*
116074 AATTCAAAGA
1 ATTTCAAAGA
116084 CAACTGCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.25
Consensus pattern (11 bp):
ATTTCAAAGAG
Found at i:119643 original size:15 final size:15
Alignment explanation
Indices: 119620--119660 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
119610 ATCACTAGAT
119620 TGAACTGATTATATG
1 TGAACTGATTATATG
* *
119635 TGAATTGATTATGTG
1 TGAACTGATTATATG
119650 TGAACT-ATTAT
1 TGAACTGATTAT
119661 CTGCGATCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.44
Consensus pattern (15 bp):
TGAACTGATTATATG
Found at i:124671 original size:74 final size:74
Alignment explanation
Indices: 124550--124698 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
124540 AACAAGCTCC
124550 TAACTAATAAAGAGTGAGTTAGGCGAGGTATGTCTCAATCTCAATTTTGTGAATGATGTGGTAGC
1 TAACTAATAAAGAGTGAGTTAGGCGAGGTATGTCTCAATCTCAATTTTGTGAATGATGTGGTAGC
124615 ACTGTGGAG
66 ACTGTGGAG
124624 TAACTAATAAAGAGTGAGTTAGGCGAGGTATGTCTCAATCTCAATTTTGTGAATGATGTGGTAGC
1 TAACTAATAAAGAGTGAGTTAGGCGAGGTATGTCTCAATCTCAATTTTGTGAATGATGTGGTAGC
124689 ACTGTGGAG
66 ACTGTGGAG
124698 T
1 T
124699 CTACAATTTG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.32
Consensus pattern (74 bp):
TAACTAATAAAGAGTGAGTTAGGCGAGGTATGTCTCAATCTCAATTTTGTGAATGATGTGGTAGC
ACTGTGGAG
Found at i:127185 original size:3 final size:3
Alignment explanation
Indices: 127177--127202 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
127167 TTCTCAGTCT
127177 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
127203 TATAGAATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:127878 original size:51 final size:51
Alignment explanation
Indices: 127823--127926 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
127813 GAAATAAAGC
127823 TGAGATGATAGAGAAAGTTGAGACAGTTGAGGAGATTATTATGAATAAGGA
1 TGAGATGATAGAGAAAGTTGAGACAGTTGAGGAGATTATTATGAATAAGGA
*
127874 TGAGATGATAGAGAAGGTTGAGACAGTTGAGGAGATTATTATGAATAAGGA
1 TGAGATGATAGAGAAAGTTGAGACAGTTGAGGAGATTATTATGAATAAGGA
127925 TG
1 TG
127927 TAGAGACAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.39, C:0.02, G:0.33, T:0.26
Consensus pattern (51 bp):
TGAGATGATAGAGAAAGTTGAGACAGTTGAGGAGATTATTATGAATAAGGA
Found at i:135151 original size:28 final size:28
Alignment explanation
Indices: 135106--135164 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
135096 TAAGATGAGC
*
135106 ATATAAAAAAATTCAATAAATAAAA-AAT
1 ATATAAAAAAATTAAAT-AATAAAATAAT
** *
135134 ATATAAAATTATTAAATATTAAAATAAT
1 ATATAAAAAAATTAAATAATAAAATAAT
135162 ATA
1 ATA
135165 ATATAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (28 bp):
ATATAAAAAAATTAAATAATAAAATAAT
Found at i:135840 original size:25 final size:25
Alignment explanation
Indices: 135810--135860 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
135800 AGAAACTCTA
135810 AATTTTT-TCTCAAATTTTAAGAAT
1 AATTTTTATCTCAAATTTTAAGAAT
**
135834 AATTTTTATCTCAGGTTTTAAGAAT
1 AATTTTTATCTCAAATTTTAAGAAT
135859 AA
1 AA
135861 AAGAATTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (25 bp):
AATTTTTATCTCAAATTTTAAGAAT
Found at i:142239 original size:66 final size:66
Alignment explanation
Indices: 142133--142315 Score: 251
Period size: 66 Copynumber: 2.7 Consensus size: 66
142123 ATAGCAGAAC
* * * * *
142133 TGCATTCACGAGCAAGGAGTCCTCCTCCACACTTGTAGCATAAGCTAGATGATGCAGTACCAGTG
1 TGCATTCACGTGCAAAGTGTCCTCCTCCACACTTGTAGCATAAGCTAGATGATGCAGCACCAGTA
142198 G
66 G
**
142199 TGCATTCTTGTGCAAAGTGTCCTCCTCCACACTTGTAGCATAAGCTAGATGATGCAGCACCAGTA
1 TGCATTCACGTGCAAAGTGTCCTCCTCCACACTTGTAGCATAAGCTAGATGATGCAGCACCAGTA
142264 G
66 G
*
142265 TGCATTCACGTGCAAAGTG-CGCTCCTACAACACACTTGTAGCACAAGCTAG
1 TGCATTCACGTGCAAAGTGTC-CTCCT-C--CACACTTGTAGCATAAGCTAG
142316 GTGACTGATT
Statistics
Matches: 103, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
65 1 0.01
66 81 0.79
67 1 0.01
69 20 0.19
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (66 bp):
TGCATTCACGTGCAAAGTGTCCTCCTCCACACTTGTAGCATAAGCTAGATGATGCAGCACCAGTA
G
Found at i:144527 original size:2 final size:2
Alignment explanation
Indices: 144474--144513 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
144464 GAAGGTCAGA
*
144474 TC TC TC TC TC TC TC TC TC TC TC TC TC GC TC TC TC TAC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T-C TC T
144514 TCTTTCATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.03, C:0.47, G:0.03, T:0.47
Consensus pattern (2 bp):
TC
Found at i:145977 original size:18 final size:19
Alignment explanation
Indices: 145940--145980 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
145930 GGGAAAATGA
* *
145940 TTTTTGAAAAATTATTTAT
1 TTTTTGAAAAAATATATAT
145959 TTTTTGAAAAAATA-ATAT
1 TTTTTGAAAAAATATATAT
145977 TTTT
1 TTTT
145981 ATATTTGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
TTTTTGAAAAAATATATAT
Found at i:151908 original size:31 final size:31
Alignment explanation
Indices: 151865--151924 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
151855 AAGGACCTTT
* *
151865 AAATTAATTTGATTAGAATCAAATCAAATCG
1 AAATCAATTTGATTAGAATAAAATCAAATCG
*
151896 AAATCAATTTGATTTGAATAAAATCAAAT
1 AAATCAATTTGATTAGAATAAAATCAAAT
151925 TGAGATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (31 bp):
AAATCAATTTGATTAGAATAAAATCAAATCG
Found at i:153864 original size:21 final size:21
Alignment explanation
Indices: 153840--153879 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
153830 AAATCTTGAA
*
153840 TTTAACATGTCCTTGTTACGT
1 TTTAACATGTCATTGTTACGT
* *
153861 TTTACCATTTCATTGTTAC
1 TTTAACATGTCATTGTTAC
153880 TTCCAACAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.50
Consensus pattern (21 bp):
TTTAACATGTCATTGTTACGT
Found at i:156531 original size:3 final size:3
Alignment explanation
Indices: 156523--156557 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
156513 AAATCCTTTA
156523 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
156558 AAGATCGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:160043 original size:15 final size:13
Alignment explanation
Indices: 160019--160057 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 13
160009 TGCATATGCA
160019 TACATGCATTCAT
1 TACATGCATTCAT
160032 TAGCATTGCATTTCAT
1 TA-CA-TGCA-TTCAT
160048 TACATGCATT
1 TACATGCATT
160058 AAATTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 4 0.17
14 6 0.26
15 6 0.26
16 7 0.30
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (13 bp):
TACATGCATTCAT
Found at i:162725 original size:101 final size:99
Alignment explanation
Indices: 162592--163186 Score: 475
Period size: 101 Copynumber: 5.9 Consensus size: 99
162582 TTACAATAGT
* * *
162592 AAATCTTTATCTCCCTAAAGTTGCAGTGGAGCAAGATGGAGCTACGAATCAAATCCTATATCCCT
1 AAATCTTTATCTCTCTAAAGTTGAAGTGGAGCAAGATGAAGCTACGAATCAAATCCTATA-CCC-
* * *
162657 TGAAGGTGTAGTGGATTAGATTGAAGTTACGAAAGC
64 TGAAGTTATAGTGGATTAGATTGAAGCTACGAAAGC
* * * * * * * *
162693 AAATCCTTATCTCTCTGAAGTTGAAGTAGAGCAGGATAAAACTACAAAACCAAATCCTATACCCC
1 AAATCTTTATCTCTCTAAAGTTGAAGTGGAGCAAGATGAAGCTAC-GAATCAAATCCTATA-CCC
* * * * **
162758 TGAAGTTACAATGGGTCAGATTGAAGCTATAAAAGC
64 TGAAGTTATAGTGGATTAGATTGAAGCTACGAAAGC
* * * * *
162794 AAATCTTTGTCTCTCTAAAGTTGTAGTGGAGAAAGATGAAGCTATGACATCAAATCCTATAACCT
1 AAATCTTTATCTCTCTAAAGTTGAAGTGGAGCAAGATGAAGCTACGA-ATCAAATCCTAT-ACCC
*** *
162859 TGAAGTTATAGT-GAAGCGTATTGAAGTTACGAAAGC
64 TGAAGTTATAGTGGATTAG-ATTGAAGCTACGAAAGC
* * * ** * * *
162895 AAATCCTTCTCTCTCTAAAGTTGCAGTAAAGCAAGATGAAACTACAAAACCAAATCCTATACCCC
1 AAATCTTTATCTCTCTAAAGTTGAAGTGGAGCAAGATGAAGCTAC-GAATCAAATCCTATA-CCC
* * * * *
162960 TGAAGTTACAATGGA-TCGAATTGAAGCTACAAAAAC
64 TGAAGTTATAGTGGATTAG-ATTGAAGCTACGAAAGC
* *
162996 AAATATTTATCTCCCTAAAGTT-ATAGTGGAGCAAGATGAAGCTACGAAATCAAATCCTATATCC
1 AAATCTTTATCTCTCTAAAGTTGA-AGTGGAGCAAGATGAAGCTACG-AATCAAATCCTATA-CC
* * *
163060 CTGAAGTTGTAGTGGA-TCGAGTTGAAACTACAGAAA-C
63 CTGAAGTTATAGTGGATTAGA-TTGAAGCTAC-GAAAGC
* * * * *
163097 AAATCTTTATCTC-CATGAAGAT-ACAGTGGAGCAAGATGAAGTTACGACATTAAAACCTATATC
1 AAATCTTTATCTCTC-TAAAGTTGA-AGTGGAGCAAGATGAAGCTACGA-ATCAAATCCTATA-C
* * *
163160 CCTGAAATTGTAGTGGATCAGATTGAA
62 CCTGAAGTTATAGTGGATTAGATTGAA
163187 ACTATATTAG
Statistics
Matches: 393, Mismatches: 87, Indels: 28
0.77 0.17 0.06
Matches are distributed among these distances:
100 7 0.02
101 361 0.92
102 25 0.06
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (99 bp):
AAATCTTTATCTCTCTAAAGTTGAAGTGGAGCAAGATGAAGCTACGAATCAAATCCTATACCCTG
AAGTTATAGTGGATTAGATTGAAGCTACGAAAGC
Found at i:162995 original size:51 final size:49
Alignment explanation
Indices: 162931--163101 Score: 148
Period size: 50 Copynumber: 3.4 Consensus size: 49
162921 TAAAGCAAGA
* *
162931 TGAAACTACAAAACCAAATCCTATACCCCTGAAGTTACAATGGATCGAAT
1 TGAAACTACAAAA-CAAATCCTATACCCCTGAAGTTATAGTGGATCGAAT
* * * * * *
162981 TGAAGCTACAAAAACAAAT-ATTTATCTCCCTAAAGTTATAGTGGAGC-AAGA
1 TGAAACTAC-AAAACAAATCCTATA-C-CCCTGAAGTTATAGTGGATCGAA-T
* * * * *
163032 TGAAGCTACGAAATCAAATCCTATATCCCTGAAGTTGTAGTGGATCGAGT
1 TGAAACTAC-AAAACAAATCCTATACCCCTGAAGTTATAGTGGATCGAAT
163082 TGAAACTACAGAAACAAATC
1 TGAAACTACA-AAACAAATC
163102 TTTATCTCCA
Statistics
Matches: 94, Mismatches: 20, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
49 4 0.04
50 49 0.52
51 38 0.40
52 3 0.03
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (49 bp):
TGAAACTACAAAACAAATCCTATACCCCTGAAGTTATAGTGGATCGAAT
Found at i:163125 original size:51 final size:51
Alignment explanation
Indices: 162931--163126 Score: 152
Period size: 51 Copynumber: 3.9 Consensus size: 51
162921 TAAAGCAAGA
* * *
162931 TGAAACTACA-AAACCAAATC-CTATACCCCTGAAGTTACAATGGATCGAAT
1 TGAAACTACAGAAACCAAATCTTTAT-CCCCTGAAGTTACAGTGGATCGAGT
* * * * * * * *
162981 TGAAGCTACA-AAAACAAATATTTATCTCCCTAAAGTTATAGTGGAGCAAGA
1 TGAAACTACAGAAACCAAATCTTTATC-CCCTGAAGTTACAGTGGATCGAGT
* * * **
163032 TGAAGCTAC-GAAATCAAATCCTATAT-CCCTGAAGTTGTAGTGGATCGAGT
1 TGAAACTACAGAAACCAAAT-CTTTATCCCCTGAAGTTACAGTGGATCGAGT
* *
163082 TGAAACTACAGAAA-CAAATCTTTATCTCCATGAAGATACAGTGGA
1 TGAAACTACAGAAACCAAATCTTTATC-CCCTGAAGTTACAGTGGA
163127 GCAAGATGAA
Statistics
Matches: 114, Mismatches: 25, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
49 5 0.04
50 50 0.44
51 55 0.48
52 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (51 bp):
TGAAACTACAGAAACCAAATCTTTATCCCCTGAAGTTACAGTGGATCGAGT
Found at i:163165 original size:202 final size:202
Alignment explanation
Indices: 162592--163136 Score: 708
Period size: 202 Copynumber: 2.7 Consensus size: 202
162582 TTACAATAGT
* *
162592 AAATCTTTATCTCCCTAAAGTTGCAGTGGAGCAAGATGGAGCTACG-AATCAAATCCTATATCCC
1 AAATCTTTATCTCCCTAAAGTTGTAGTGGAGCAAGATGAAGCTACGAAATCAAATCCTATATCCC
* *
162656 TTGAAGGTGTAGTGGAT-TAGATTGAAGTTACGAAAGCAAATCCTTATCTCTCTGAAGTTGA-AG
66 -TGAAGTTGTAGTGGATCGAG-TTGAAGTTACGAAAGCAAATCCTTATCTCTCTGAAGTT-ACAG
* * *
162719 TAGAGCAGGATAAAACTACAAAACCAAATCCTATACCCCTGAAGTTACAATGGGTCAGATTGAAG
128 TAGAGCAAGATGAAACTACAAAACCAAATCCTATACCCCTGAAGTTACAATGGATCAGATTGAAG
* *
162784 CTATAAAAGC
193 CTACAAAAAC
* * * * * * *
162794 AAATCTTTGTCTCTCTAAAGTTGTAGTGGAGAAAGATGAAGCTATGACATCAAATCCTATAACCT
1 AAATCTTTATCTCCCTAAAGTTGTAGTGGAGCAAGATGAAGCTACGAAATCAAATCCTATATCCC
* * * * * *
162859 TGAAGTTATAGTGAAGCGTA-TTGAAGTTACGAAAGCAAATCCTTCTCTCTCTAAAGTTGCAGTA
66 TGAAGTTGTAGTGGATCG-AGTTGAAGTTACGAAAGCAAATCCTTATCTCTCTGAAGTTACAGTA
*
162923 AAGCAAGATGAAACTACAAAACCAAATCCTATACCCCTGAAGTTACAATGGATC-GAATTGAAGC
130 GAGCAAGATGAAACTACAAAACCAAATCCTATACCCCTGAAGTTACAATGGATCAG-ATTGAAGC
162987 TACAAAAAC
194 TACAAAAAC
* *
162996 AAATATTTATCTCCCTAAAGTTATAGTGGAGCAAGATGAAGCTACGAAATCAAATCCTATATCCC
1 AAATCTTTATCTCCCTAAAGTTGTAGTGGAGCAAGATGAAGCTACGAAATCAAATCCTATATCCC
** * *
163061 TGAAGTTGTAGTGGATCGAGTTGAAACTACAGAAA-CAAATCTTTATCTC-CATGAAGATACAGT
66 TGAAGTTGTAGTGGATCGAGTTGAAGTTAC-GAAAGCAAATCCTTATCTCTC-TGAAGTTACAGT
*
163124 GGAGCAAGATGAA
129 AGAGCAAGATGAA
163137 GTTACGACAT
Statistics
Matches: 291, Mismatches: 44, Indels: 16
0.83 0.13 0.05
Matches are distributed among these distances:
201 3 0.01
202 268 0.92
203 19 0.07
204 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.26
Consensus pattern (202 bp):
AAATCTTTATCTCCCTAAAGTTGTAGTGGAGCAAGATGAAGCTACGAAATCAAATCCTATATCCC
TGAAGTTGTAGTGGATCGAGTTGAAGTTACGAAAGCAAATCCTTATCTCTCTGAAGTTACAGTAG
AGCAAGATGAAACTACAAAACCAAATCCTATACCCCTGAAGTTACAATGGATCAGATTGAAGCTA
CAAAAAC
Found at i:165154 original size:27 final size:27
Alignment explanation
Indices: 165084--165159 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 27
165074 GTATCCTTTA
165084 TTATTT-TTTATTATTTTTGTATTTATT
1 TTATTTATTTATTA-TTTTGTATTTATT
165111 TTATATGCTATTATTATTATTTT-TATTTCATT
1 TTAT-T--TA-T-TTATTATTTTGTATTT-ATT
165143 TTATTTATTTATTATTT
1 TTATTTATTTATTATTT
165160 ATTTCTTATG
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
27 13 0.31
28 2 0.05
29 2 0.05
30 1 0.02
31 6 0.14
32 12 0.29
33 6 0.14
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (27 bp):
TTATTTATTTATTATTTTGTATTTATT
Found at i:165157 original size:11 final size:10
Alignment explanation
Indices: 165080--165168 Score: 60
Period size: 11 Copynumber: 8.5 Consensus size: 10
165070 CTTTGTATCC
165080 TTTA-TTATT
1 TTTATTTATT
165089 TTT-TATTATTT
1 TTTAT-TTA-TT
165100 TTGTATTTATT
1 TT-TATTTATT
*
165111 TTATATGCTATT
1 TT-TAT-TTATT
*
165123 ATTA-TTATT
1 TTTATTTATT
165132 TTTATTTCA-T
1 TTTATTT-ATT
165142 TTTATTTATT
1 TTTATTTATT
165152 TATTATTTATT
1 T-TTATTTATT
165163 TCTTAT
1 T-TTAT
165169 GTCATTTACA
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
9 11 0.17
10 15 0.23
11 28 0.44
12 9 0.14
13 1 0.02
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.72
Consensus pattern (10 bp):
TTTATTTATT
Found at i:165343 original size:9 final size:9
Alignment explanation
Indices: 165331--165398 Score: 52
Period size: 9 Copynumber: 7.9 Consensus size: 9
165321 TTATTATCCT
165331 TTTTATTAA
1 TTTTATTAA
165340 TTTTATTAA
1 TTTTATTAA
*
165349 -TTTATTTA
1 TTTTATTAA
*
165357 TGTTATTAA
1 TTTTATTAA
**
165366 TCATATT-A
1 TTTTATTAA
*
165374 -TTCATTAA
1 TTTTATTAA
* *
165382 TGTTATTTA
1 TTTTATTAA
165391 TTTTATTA
1 TTTTATTA
165399 TTCATGTATG
Statistics
Matches: 43, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
7 3 0.07
8 9 0.21
9 31 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTATTAA
Found at i:165354 original size:17 final size:18
Alignment explanation
Indices: 165333--165398 Score: 66
Period size: 17 Copynumber: 3.8 Consensus size: 18
165323 ATTATCCTTT
*
165333 TTATTAATTTTATTAAT-
1 TTATTTATTTTATTAATC
*
165350 TTATTTATGTTATTAATC
1 TTATTTATTTTATTAATC
* * *
165368 ATA-TTA-TTCATTAATG
1 TTATTTATTTTATTAATC
165384 TTATTTATTTTATTA
1 TTATTTATTTTATTA
165399 TTCATGTATG
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
16 9 0.24
17 21 0.55
18 8 0.21
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
TTATTTATTTTATTAATC
Found at i:165397 original size:25 final size:24
Alignment explanation
Indices: 165333--165409 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 24
165323 ATTATCCTTT
*
165333 TTATTAATTTTATTAATTTATTTATG
1 TTATTAATTTTATT-ATTCA-TTATG
**
165359 TTATTAATCATATTATTCATTAATG
1 TTATTAATTTTATTATTCATT-ATG
*
165384 TTATTTATTTTATTATTCATGTATG
1 TTATTAATTTTATTATTCAT-TATG
165409 T
1 T
165410 ATTTTTATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
24 2 0.05
25 28 0.65
26 13 0.30
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61
Consensus pattern (24 bp):
TTATTAATTTTATTATTCATTATG
Found at i:168164 original size:52 final size:52
Alignment explanation
Indices: 168086--168191 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
168076 ATTGCTGTCT
168086 AAGATAATTTATAGTTCAATGGGAGCTTTACAGACAAGTTATATATAGTCGC
1 AAGATAATTTATAGTTCAATGGGAGCTTTACAGACAAGTTATATATAGTCGC
168138 AAGATAATTTATAGTTCAATGGGAGCTTTACAGACAAGTTATATATAGTCGC
1 AAGATAATTTATAGTTCAATGGGAGCTTTACAGACAAGTTATATATAGTCGC
168190 AA
1 AA
168192 TGACATGACC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (52 bp):
AAGATAATTTATAGTTCAATGGGAGCTTTACAGACAAGTTATATATAGTCGC
Found at i:172409 original size:31 final size:31
Alignment explanation
Indices: 172373--172431 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
172363 ATAGGGCATA
*
172373 ATAGCCATAGGATTCAATTCCTCTATCTTGC
1 ATAGCCATAAGATTCAATTCCTCTATCTTGC
172404 ATAGCCATAAGATTCAATTCCTCTATCT
1 ATAGCCATAAGATTCAATTCCTCTATCT
172432 CACCAGTGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (31 bp):
ATAGCCATAAGATTCAATTCCTCTATCTTGC
Found at i:182489 original size:56 final size:56
Alignment explanation
Indices: 182416--182631 Score: 294
Period size: 56 Copynumber: 3.9 Consensus size: 56
182406 TTCGATTTGA
* *
182416 TATAACTCGGGTAGAGCTTTGGACTGCTTACGTCTCGATTATAGCATAATGCTATG
1 TATAGCTCGGGTAGAGCTTTGGACTGCTTACGTCTCGATTAGAGCATAATGCTATG
* * * * *
182472 TATAGCTTGGGTAGAGCTTTAGACTACTTATGTCTCGATTAGAGCGTAATGCTATG
1 TATAGCTCGGGTAGAGCTTTGGACTGCTTACGTCTCGATTAGAGCATAATGCTATG
* * * *
182528 TATAGCTCAGGTAAAGCTTTGGACTGGTTACGTCTCGATTAAAGCATAATGCTAT-
1 TATAGCTCGGGTAGAGCTTTGGACTGCTTACGTCTCGATTAGAGCATAATGCTATG
182583 TATAGCTCGGGTAGAGCTTTGGTA-TGCTTACGTCTC-AGTTAGAGCATAA
1 TATAGCTCGGGTAGAGCTTTGG-ACTGCTTACGTCTCGA-TTAGAGCATAA
182632 AGTTTTTTCA
Statistics
Matches: 138, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
54 1 0.01
55 41 0.30
56 96 0.70
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (56 bp):
TATAGCTCGGGTAGAGCTTTGGACTGCTTACGTCTCGATTAGAGCATAATGCTATG
Found at i:183397 original size:50 final size:51
Alignment explanation
Indices: 183329--183600 Score: 191
Period size: 50 Copynumber: 5.4 Consensus size: 51
183319 TGGAGCAAGA
* * * *
183329 TGAAGCTATAACATCAAATCCTATA-CCCTTGAAGTTACAGTGGATCGGAT
1 TGAAGCTACAAAAGCAAATCCTATATCCCTTAAAGTTACAGTGGATCGGAT
* * * * ** *
183379 TGAAGTTACAAAAGCAAATCCT-TATCTCTCCAAAGTTACAATAAAGCAGGA-
1 TGAAGCTACAAAAGCAAATCCTATATCCCT-TAAAGTTACAGTGGATC-GGAT
* * * * *
183430 TGAAACTACAAAACCAAATCCTATATCCC-TGAAGTTACGGTGGATCAGAT
1 TGAAGCTACAAAAGCAAATCCTATATCCCTTAAAGTTACAGTGGATCGGAT
* * * * * * * *
183480 TAAAGCTACAGAAGCAAAT-TTTTATCTCCCTAAAGTTACAATGGAGCAAGA-
1 TGAAGCTACAAAAGCAAATCCTATATC-CCTTAAAGTTACAGTGGATC-GGAT
* * *
183531 TGAAGCTACAAAATCAAATCCTATAT-CCTTAAAGTTGCAGTGGATCGGGT
1 TGAAGCTACAAAAGCAAATCCTATATCCCTTAAAGTTACAGTGGATCGGAT
*
183581 TGAAACTACAGAAA-CAAATC
1 TGAAGCTACA-AAAGCAAATC
183601 TTTATCTCCA
Statistics
Matches: 166, Mismatches: 45, Indels: 22
0.71 0.19 0.09
Matches are distributed among these distances:
49 10 0.06
50 79 0.48
51 62 0.37
52 15 0.09
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.25
Consensus pattern (51 bp):
TGAAGCTACAAAAGCAAATCCTATATCCCTTAAAGTTACAGTGGATCGGAT
Found at i:183439 original size:152 final size:153
Alignment explanation
Indices: 183140--183448 Score: 363
Period size: 152 Copynumber: 2.0 Consensus size: 153
183130 TTACAATAGT
* * * *
183140 AAATCTTTATCTCCCTAAAGTTGTAGTGGAGCAAGATGGAGCTACAACATCAAATCCTATATCCC
1 AAATATTTATCTCCCTAAAGTTGCAATGGAGCAAGATGAAGCTACAACATCAAATCCTATATCCC
** * * * * * ** * *
183205 TTGAAGGTGTAGTGGTTTAGATTGAAGTTGCGAAAGGAAATCCTTATCTCTCTGAAGTTGCAATG
66 TTGAAGGTACAGTGGATCAGATTGAAGTTACAAAAGCAAATCCTTATCTCTCCAAAGTTACAATA
* * * *
183270 GGTCAGATTGAAGCTACAGAAGC
131 AGTCAGATTGAAACTACAAAACC
* * *
183293 AAATATTTGTCTCCCTGAAGTTGCAATGGAGCAAGATGAAGCTATAACATCAAATCCTATA-CCC
1 AAATATTTATCTCCCTAAAGTTGCAATGGAGCAAGATGAAGCTACAACATCAAATCCTATATCCC
* *
183357 TTGAAGTTACAGTGGATCGGATTGAAGTTACAAAAGCAAATCCTTATCTCTCCAAAGTTACAATA
66 TTGAAGGTACAGTGGATCAGATTGAAGTTACAAAAGCAAATCCTTATCTCTCCAAAGTTACAAT-
183422 AAG-CAGGA-TGAAACTACAAAACC
130 AAGTCA-GATTGAAACTACAAAACC
183445 AAAT
1 AAAT
183449 CCTATATCCC
Statistics
Matches: 130, Mismatches: 24, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
152 73 0.56
153 57 0.44
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (153 bp):
AAATATTTATCTCCCTAAAGTTGCAATGGAGCAAGATGAAGCTACAACATCAAATCCTATATCCC
TTGAAGGTACAGTGGATCAGATTGAAGTTACAAAAGCAAATCCTTATCTCTCCAAAGTTACAATA
AGTCAGATTGAAACTACAAAACC
Found at i:183652 original size:202 final size:202
Alignment explanation
Indices: 183272--183659 Score: 512
Period size: 202 Copynumber: 1.9 Consensus size: 202
183262 TTGCAATGGG
* * * *
183272 TCAGATTGAAGCTACAGAAGCAAATATTTGTCTCCCTGAAGTTGCAATGGAGCAAGATGAAGCTA
1 TCAGATTAAAGCTACAGAAGCAAATATTTATCTCCCTAAAGTTACAATGGAGCAAGATGAAGCTA
* * * **
183337 TAACATCAAATCCTATACCCTTGAAGTTACAGTGGATCGGATTGAAGTTACAAAAGCAAATCCTT
66 CAAAATCAAATCCTATACCCTTAAAGTTACAGTGGATCGGATTGAAACTACAAAAGCAAATCCTT
* * *
183402 ATCTCTCCAAAGTTACAATAAAGCAGGATGAAACTACAAAACCAAATCCTATATCCCTGAAGTTA
131 ATATCTCCAAAGATACAATAAAGCAAGATGAAACTACAAAACCAAATCCTATATCCCTGAAGTTA
183467 CGGTGGA
196 CGGTGGA
*
183474 TCAGATTAAAGCTACAGAAGCAAATTTTTATCTCCCTAAAGTTACAATGGAGCAAGATGAAGCTA
1 TCAGATTAAAGCTACAGAAGCAAATATTTATCTCCCTAAAGTTACAATGGAGCAAGATGAAGCTA
* * *
183539 CAAAATCAAATCCTATATCCTTAAAGTTGCAGTGGATCGGGTTGAAACTACAGAAA-CAAAT-CT
66 CAAAATCAAATCCTATACCCTTAAAGTTACAGTGGATCGGATTGAAACTACA-AAAGCAAATCCT
* ** ** * * *
183602 T-TATCTCCATGAAGATACAGTGGAGCAAGATGAAGTTACGACATCAAATCCTATATCC
130 TATATCTCCA--AAGATACAATAAAGCAAGATGAAACTACAAAACCAAATCCTATATCC
183660 TAAAATTGTA
Statistics
Matches: 159, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
200 7 0.04
201 3 0.02
202 146 0.92
203 3 0.02
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (202 bp):
TCAGATTAAAGCTACAGAAGCAAATATTTATCTCCCTAAAGTTACAATGGAGCAAGATGAAGCTA
CAAAATCAAATCCTATACCCTTAAAGTTACAGTGGATCGGATTGAAACTACAAAAGCAAATCCTT
ATATCTCCAAAGATACAATAAAGCAAGATGAAACTACAAAACCAAATCCTATATCCCTGAAGTTA
CGGTGGA
Found at i:183657 original size:101 final size:101
Alignment explanation
Indices: 183242--183690 Score: 442
Period size: 101 Copynumber: 4.4 Consensus size: 101
183232 TTGCGAAAGG
* * * * * *
183242 AAATCCT-TATCTCTCTGAAGTTGCAATGGGTCAGATTGAAGCTACAGAAGCAAATATTTGTCTC
1 AAATCCTATATC-CT-TGAAGTTGCAGTGGATCAGATTGAAACTACAGAAACAAATCTTTATCTC
* * * *
183306 CCTGAAGTTGCAATGGAGCAAGATGAAGCTATAACATC
64 CATGAAGTTACAATGGAGCAAGATGAAGCTACAAAATC
* * * ** *
183344 AAATCCTATACCCTTGAAGTTACAGTGGATCGGATTGAAGTTACA-AAAGCAAATCCTTATCTCT
1 AAATCCTATATCCTTGAAGTTGCAGTGGATCAGATTGAAACTACAGAAA-CAAAT-CTT-TATCT
** * * *
183408 CCA--AAGTTACAATAAAGCAGGATGAAACTACAAAACC
63 CCATGAAGTTACAATGGAGCAAGATGAAGCTACAAAATC
* * * * *
183445 AAATCCTATATCCCTGAAGTTACGGTGGATCAGATT-AAAGCTACAGAAGCAAATTTTTATCTCC
1 AAATCCTATATCCTTGAAGTTGCAGTGGATCAGATTGAAA-CTACAGAAACAAATCTTTATCTCC
* *
183509 CTAAAGTTACAATGGAGCAAGATGAAGCTACAAAATC
65 ATGAAGTTACAATGGAGCAAGATGAAGCTACAAAATC
* * *
183546 AAATCCTATATCCTTAAAGTTGCAGTGGATCGGGTTGAAACTACAGAAACAAATCTTTATCTCCA
1 AAATCCTATATCCTTGAAGTTGCAGTGGATCAGATTGAAACTACAGAAACAAATCTTTATCTCCA
* * * * *
183611 TGAAGATACAGTGGAGCAAGATGAAGTTACGACATC
66 TGAAGTTACAATGGAGCAAGATGAAGCTACAAAATC
* * * *
183647 AAATCCTATATCC-TAAAATTGTAGTGGATCAAATTGAAACTACA
1 AAATCCTATATCCTTGAAGTTGCAGTGGATCAGATTGAAACTACA
183691 TTAGTAAGTA
Statistics
Matches: 285, Mismatches: 53, Indels: 20
0.80 0.15 0.06
Matches are distributed among these distances:
99 6 0.02
100 32 0.11
101 222 0.78
102 16 0.06
103 9 0.03
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (101 bp):
AAATCCTATATCCTTGAAGTTGCAGTGGATCAGATTGAAACTACAGAAACAAATCTTTATCTCCA
TGAAGTTACAATGGAGCAAGATGAAGCTACAAAATC
Found at i:185569 original size:11 final size:10
Alignment explanation
Indices: 185542--185627 Score: 61
Period size: 11 Copynumber: 8.0 Consensus size: 10
185532 TCCTTTATTA
185542 TTATTTTTA-
1 TTATTTTTAT
185551 TTATTTTTGTAT
1 TTA-TTTT-TAT
185563 TTATTTTATAT
1 TTATTTT-TAT
*
185574 GTTATTATTA-
1 -TTATTTTTAT
185584 TTATTTATTTAT
1 TTA-TT-TTTAT
185596 TTCA-TTTTAT
1 TT-ATTTTTAT
185606 TTATTTCTTAT
1 TTATTT-TTAT
185617 TTATTTCTTAT
1 TTATTT-TTAT
185628 GTCATTTACA
Statistics
Matches: 64, Mismatches: 3, Indels: 18
0.75 0.04 0.21
Matches are distributed among these distances:
9 7 0.11
10 15 0.23
11 30 0.47
12 11 0.17
13 1 0.02
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.72
Consensus pattern (10 bp):
TTATTTTTAT
Found at i:185579 original size:33 final size:34
Alignment explanation
Indices: 185542--185605 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
185532 TCCTTTATTA
*
185542 TTATTTTTATTATTT-TTGTATTT-ATTTTATATG
1 TTATTATTATTATTTATT-TATTTCATTTTATATG
185575 TTATTATTATTATTTATTTATTTCATTTTAT
1 TTATTATTATTATTTATTTATTTCATTTTAT
185606 TTATTTCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 19 0.68
34 9 0.32
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.72
Consensus pattern (34 bp):
TTATTATTATTATTTATTTATTTCATTTTATATG
Found at i:185604 original size:14 final size:15
Alignment explanation
Indices: 185560--185622 Score: 62
Period size: 14 Copynumber: 4.3 Consensus size: 15
185550 ATTATTTTTG
*
185560 TATTTATTTTATATGT
1 TATTTATTTCATAT-T
185576 TA-TTA-TT-ATTATT
1 TATTTATTTCA-TATT
185589 TATTTATTTCAT-TT
1 TATTTATTTCATATT
*
185603 TATTTATTTCTTATT
1 TATTTATTTCATATT
185618 TATTT
1 TATTT
185623 CTTATGTCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
13 4 0.10
14 21 0.51
15 13 0.32
16 3 0.07
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (15 bp):
TATTTATTTCATATT
Found at i:185803 original size:9 final size:9
Alignment explanation
Indices: 185791--185860 Score: 56
Period size: 9 Copynumber: 8.1 Consensus size: 9
185781 TTATTATCCT
185791 TTTTATTAA
1 TTTTATTAA
185800 TTTTATTAA
1 TTTTATTAA
*
185809 -TTTATTTA
1 TTTTATTAA
*
185817 TGTTATTAA
1 TTTTATTAA
**
185826 TCATATT-A
1 TTTTATTAA
*
185834 -TTCATTAA
1 TTTTATTAA
* *
185842 TGTTATTTA
1 TTTTATTAA
185851 TTTTATTAA
1 TTTTATTAA
185860 T
1 T
185861 CATGTATGTA
Statistics
Matches: 45, Mismatches: 13, Indels: 6
0.70 0.20 0.09
Matches are distributed among these distances:
7 3 0.07
8 9 0.20
9 33 0.73
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTATTAA
Found at i:185814 original size:17 final size:18
Alignment explanation
Indices: 185793--185861 Score: 72
Period size: 17 Copynumber: 4.0 Consensus size: 18
185783 ATTATCCTTT
*
185793 TTATTAATTTTATTAAT-
1 TTATTTATTTTATTAATC
*
185810 TTATTTATGTTATTAATC
1 TTATTTATTTTATTAATC
* * *
185828 ATA-TTA-TTCATTAATG
1 TTATTTATTTTATTAATC
185844 TTATTTATTTTATTAATC
1 TTATTTATTTTATTAATC
185862 ATGTATGTAT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
16 9 0.22
17 21 0.52
18 10 0.25
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (18 bp):
TTATTTATTTTATTAATC
Found at i:185857 original size:25 final size:24
Alignment explanation
Indices: 185793--185869 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 24
185783 ATTATCCTTT
*
185793 TTATTAATTTTATTAATTTATTTATG
1 TTATTAATTTTATT-ATTCA-TTATG
**
185819 TTATTAATCATATTATTCATTAATG
1 TTATTAATTTTATTATTCATT-ATG
* *
185844 TTATTTATTTTATTAATCATGTATG
1 TTATTAATTTTATTATTCAT-TATG
185869 T
1 T
185870 ATTTTTATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
24 2 0.05
25 27 0.64
26 13 0.31
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.60
Consensus pattern (24 bp):
TTATTAATTTTATTATTCATTATG
Found at i:186690 original size:45 final size:46
Alignment explanation
Indices: 186618--186709 Score: 105
Period size: 45 Copynumber: 2.0 Consensus size: 46
186608 CCTTTGATTT
* *
186618 TGTTAAACTACAGAATTAAAATTCTGAAACAAAATCAAATTAATTC
1 TGTTAAACGACAGAATTAAAATCCTGAAACAAAATCAAATTAATTC
* * * * **
186664 TGTTGAACGACAGGATT-AAATCCTGAAATAGAATTTAATTAATTC
1 TGTTAAACGACAGAATTAAAATCCTGAAACAAAATCAAATTAATTC
186709 T
1 T
186710 TTGTTTGGAA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
45 24 0.63
46 14 0.37
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.33
Consensus pattern (46 bp):
TGTTAAACGACAGAATTAAAATCCTGAAACAAAATCAAATTAATTC
Found at i:187668 original size:31 final size:31
Alignment explanation
Indices: 187618--187678 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
187608 CCTTTAAATT
*
187618 AATTTGATTAAAATCAAATCAAATCGAGATA
1 AATTTGATTAAAATAAAATCAAATCGAGATA
** * *
187649 AATTTGATTTGAATAAAATCATATTGAGAT
1 AATTTGATTAAAATAAAATCAAATCGAGAT
187679 GTTTTGTCCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.34
Consensus pattern (31 bp):
AATTTGATTAAAATAAAATCAAATCGAGATA
Found at i:189746 original size:29 final size:29
Alignment explanation
Indices: 189687--189747 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
189677 TAAACACAAC
* * * *
189687 AAAAAAGAATAGCTTTGTGGTGAATTCTG
1 AAAAAAGAATAGCTTTGTAGCGAACTATG
189716 AAAAAA-AATAGTCTTTGTAGCGAACTATG
1 AAAAAAGAATAG-CTTTGTAGCGAACTATG
189745 AAA
1 AAA
189748 GGTATGCCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (29 bp):
AAAAAAGAATAGCTTTGTAGCGAACTATG
Found at i:191048 original size:56 final size:56
Alignment explanation
Indices: 190973--191250 Score: 380
Period size: 56 Copynumber: 5.0 Consensus size: 56
190963 TTCGATCTGA
* *
190973 TATAACTCGGGTAGAGCTTTGGACTACTTACGTCTCGATTAGAGCATAATGCTATG
1 TATAGCTCGGGTAGAGCTTTGGACTGCTTACGTCTCGATTAGAGCATAATGCTATG
* *
191029 TATAGCTCAGGTAGAGCTTTAGACTGCTTACGTCTCGATTAGAGCATAATGCTATG
1 TATAGCTCGGGTAGAGCTTTGGACTGCTTACGTCTCGATTAGAGCATAATGCTATG
* * * * *
191085 TATAGCTTGGGTAGAGCTTTGGACTGCTTATGTCTTGGTTAGAGCGTAATGCTATG
1 TATAGCTCGGGTAGAGCTTTGGACTGCTTACGTCTCGATTAGAGCATAATGCTATG
* * *
191141 TATAGCTCGGGTAGAGCTGTGGACTACTTACGTCTCGATTAGAGCGTAATGCTAT-
1 TATAGCTCGGGTAGAGCTTTGGACTGCTTACGTCTCGATTAGAGCATAATGCTATG
** * * *
191196 TATAGCTCAAGTAGAGCTTTGGTCTGCTTACGTCTC-AGTTATAGCATAAAGCTAT
1 TATAGCTCGGGTAGAGCTTTGGACTGCTTACGTCTCGA-TTAGAGCATAATGCTAT
191251 TTCAACTTGG
Statistics
Matches: 196, Mismatches: 25, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
54 1 0.01
55 45 0.23
56 150 0.77
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (56 bp):
TATAGCTCGGGTAGAGCTTTGGACTGCTTACGTCTCGATTAGAGCATAATGCTATG
Found at i:191099 original size:28 final size:27
Alignment explanation
Indices: 191068--191158 Score: 71
Period size: 28 Copynumber: 3.3 Consensus size: 27
191058 ACGTCTCGAT
191068 TAGAGCATAATGCTATGTATAGCTTGGG
1 TAGAGC-TAATGCTATGTATAGCTTGGG
* * *
191096 TAGAGCT-TTG-GACTGCT-TATGTCTTGGT
1 TAGAGCTAATGCTA-TG-TATA-G-CTTGGG
*
191124 TAGAGCGTAATGCTATGTATAGCTCGGG
1 TAGAGC-TAATGCTATGTATAGCTTGGG
191152 TAGAGCT
1 TAGAGCT
191159 GTGGACTACT
Statistics
Matches: 48, Mismatches: 7, Indels: 17
0.67 0.10 0.24
Matches are distributed among these distances:
25 1 0.02
26 6 0.12
27 4 0.08
28 27 0.56
29 3 0.06
30 6 0.12
31 1 0.02
ACGTcount: A:0.23, C:0.13, G:0.30, T:0.34
Consensus pattern (27 bp):
TAGAGCTAATGCTATGTATAGCTTGGG
Found at i:195319 original size:53 final size:53
Alignment explanation
Indices: 195139--195429 Score: 284
Period size: 53 Copynumber: 5.5 Consensus size: 53
195129 TCATTTAGTT
* * * **
195139 CTCACAATGACACATAGTCATCGGACCTCACAATTCGTAAAGGATTCACCT-A
1 CTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAA
* ** * * *
195191 CACACGATGACATGTAGTCATCGAACCGCATAATCTGTAAAGGATTCATAT-A
1 CTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAA
*
195243 CTCACGATGATACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAA
1 CTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAA
* * * *
195296 CTCACGATGACACATAATCATCGGACCT-TTAATCCATGATAGGATTCATATAA
1 CTCACGATGACACATAGTCATCGGACCTCATAATCCGT-AAAGGATTCATATAA
* * * * * ** *
195349 ATCACGATGACACAGAGCCATCGGGCCT-TTAATCTATGATAGGATTCATATAA
1 CTCACGATGACACATAGTCATCGGACCTCATAATCCGT-AAAGGATTCATATAA
* ** *
195402 CTCACGATAACGTAGAGTCATCGGACCT
1 CTCACGATGACACATAGTCATCGGACCT
195430 TTAATCTTTG
Statistics
Matches: 202, Mismatches: 35, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
52 92 0.46
53 110 0.54
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (53 bp):
CTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAA
Found at i:211686 original size:13 final size:13
Alignment explanation
Indices: 211668--211700 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
211658 TAAAGCATAG
211668 TATAAATTCAAGA
1 TATAAATTCAAGA
211681 TATAAATTCAAGA
1 TATAAATTCAAGA
211694 TATAAAT
1 TATAAAT
211701 ACAAATGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (13 bp):
TATAAATTCAAGA
Found at i:235608 original size:21 final size:22
Alignment explanation
Indices: 235582--235630 Score: 91
Period size: 21 Copynumber: 2.3 Consensus size: 22
235572 CTTATTTTTT
235582 CAAATACGTCAAAAGATTATG-
1 CAAATACGTCAAAAGATTATGC
235603 CAAATACGTCAAAAGATTATGC
1 CAAATACGTCAAAAGATTATGC
235625 CAAATA
1 CAAATA
235631 GAGTTGACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.22
Consensus pattern (22 bp):
CAAATACGTCAAAAGATTATGC
Found at i:236112 original size:22 final size:21
Alignment explanation
Indices: 236087--236138 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
236077 AAAACTAATT
236087 ATTTTTTACAACTCTCATTACA
1 ATTTTTTACAACTC-CATTACA
* * **
236109 ATTTGTTACAATTCCATTTTA
1 ATTTTTTACAACTCCATTACA
236130 ATTTTTTAC
1 ATTTTTTAC
236139 TCTTATTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTTTTTACAACTCCATTACA
Found at i:236557 original size:17 final size:17
Alignment explanation
Indices: 236535--236598 Score: 110
Period size: 17 Copynumber: 3.8 Consensus size: 17
236525 AACCCATTTT
236535 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAG
236552 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAG
* *
236569 CTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAG
236586 TTTAAATTTATTT
1 TTTAAATTTATTT
236599 AAATTAATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTAAATTTATTTTAAG
Found at i:238722 original size:29 final size:29
Alignment explanation
Indices: 238400--238777 Score: 285
Period size: 30 Copynumber: 12.8 Consensus size: 29
238390 TTGACCCTCG
* **
238400 AACTTCTCCAAAATCCCATTTTAACACCT-
1 AACTTTTCCAAAATTACATTTTAAC-CCTA
* * ** *
238429 AACTTCTCTAAAATTGTATTTTGACCTCTA
1 AACTTTTCCAAAATTACATTTTAACC-CTA
* *
238459 AACTTTTTCAAAATTACATTTTGACCCCTA
1 AACTTTTCCAAAATTACATTTT-AACCCTA
* * *
238489 AATTTTTTCAAAATTACGTTTTAACTCCTA
1 AACTTTTCCAAAATTACATTTTAAC-CCTA
*
238519 AACTTTTCTAAAATTACATTTTAACCCCTA
1 AACTTTTCCAAAATTACATTTTAA-CCCTA
*
238549 AACTTTTCCAAAATTGCATTTTAACCCCTA
1 AACTTTTCCAAAATTACATTTTAA-CCCTA
* *
238579 AACTTTTCTAAAATTACATTTTAACCTTA
1 AACTTTTCCAAAATTACATTTTAACCCTA
** * * * *
238608 AACTCCTCTAAAATCACATTTTGA-CTTCA
1 AACTTTTCCAAAATTACATTTTAACCCT-A
* * *
238637 AACTTTGCTAAAATTGCATTTTAACCCCCTA
1 AACTTTTCCAAAATTACATTTTAA--CCCTA
* * * ** *
238668 AAC-ATTCTAAAATCATGTTTTGACCCTA
1 AACTTTTCCAAAATTACATTTTAACCCTA
* *
238696 AACTTCTCCAAAATTACATTTTAACCCTG
1 AACTTTTCCAAAATTACATTTTAACCCTA
* * *
238725 AGCTTTCCCAAAATTACATTTTCACCCTCTA
1 AACTTTTCCAAAATTACATTTT-AACC-CTA
* *
238756 AACTTTTCCAAATTTACGTTTT
1 AACTTTTCCAAAATTACATTTT
238778 GATTCCGTAT
Statistics
Matches: 278, Mismatches: 59, Indels: 22
0.77 0.16 0.06
Matches are distributed among these distances:
28 12 0.04
29 103 0.37
30 134 0.48
31 27 0.10
32 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.39
Consensus pattern (29 bp):
AACTTTTCCAAAATTACATTTTAACCCTA
Found at i:238738 original size:88 final size:89
Alignment explanation
Indices: 238409--238777 Score: 318
Period size: 88 Copynumber: 4.1 Consensus size: 89
238399 GAACTTCTCC
* * ** * **
238409 AAAATCCCATTTTAACACCT-AACTTCTCTAAAATTGTATTTTGACCTCTAAACTTTTTCAAAAT
1 AAAATCACGTTTTAAC-CCTAAACTTCTCTAAAATTACATTTTAACC-CTAAACTTTCCCAAAAT
* * * *
238473 TACATTTTGA-CCCCTAAA-TTTTTT
64 TGCATTTTAACCCCCTAAACTATTCT
* * *
238497 CAAAATTACGTTTTAACTCCTAAACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCCAAAA
1 -AAAATCACGTTTTAAC-CCTAAACTTCTCTAAAATTACATTTTAA-CCCTAAACTTTCCCAAAA
*
238562 TTGCATTTTAA-CCCCTAAACTTTTCT
63 TTGCATTTTAACCCCCTAAACTATTCT
* * * * * * * * *
238588 AAAATTACATTTTAACCTTAAACTCCTCTAAAATCACATTTTGA-CTTCAAACTTTGCTAAAATT
1 AAAATCACGTTTTAACCCTAAACTTCTCTAAAATTACATTTTAACCCT-AAACTTTCCCAAAATT
238652 GCATTTTAACCCCCTAAAC-ATTCT
65 GCATTTTAACCCCCTAAACTATTCT
* * * * * *
238676 AAAATCATGTTTTGACCCTAAACTTCTCCAAAATTACATTTTAACCCTGAGCTTTCCCAAAATTA
1 AAAATCACGTTTTAACCCTAAACTTCTCTAAAATTACATTTTAACCCTAAACTTTCCCAAAATTG
* * * *
238741 CATTTTCACCCTCTAAACTTTTCC
66 CATTTTAACCCCCTAAACTATTCT
* *
238765 AAATTTACGTTTT
1 AAAATCACGTTTT
238778 GATTCCGTAT
Statistics
Matches: 229, Mismatches: 44, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
87 2 0.01
88 90 0.39
89 63 0.28
90 67 0.29
91 7 0.03
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.39
Consensus pattern (89 bp):
AAAATCACGTTTTAACCCTAAACTTCTCTAAAATTACATTTTAACCCTAAACTTTCCCAAAATTG
CATTTTAACCCCCTAAACTATTCT
Found at i:250935 original size:78 final size:78
Alignment explanation
Indices: 250848--251016 Score: 239
Period size: 78 Copynumber: 2.2 Consensus size: 78
250838 AAACCATCCG
* * *
250848 ATCTTTTACCCCGAGCTTGGGGCAGATTGAAGCCATTCAATCTTTTACCCCGACCATGGGGTAGA
1 ATCTTTTACCCCAAGCTTGGGGCAGATTGAAGCCATTCAATCTTTTACCCCGACCATAGGGCAGA
*
250913 TCGCCATCAACCA
66 TCACCATCAACCA
* * * * *
250926 ATCTCTTACCCCAAGCTTGGGGCAGATTGAAGCCATTCGATCTTTTACCTCGAGCTTAGGGCAGA
1 ATCTTTTACCCCAAGCTTGGGGCAGATTGAAGCCATTCAATCTTTTACCCCGACCATAGGGCAGA
* *
250991 TCACCGTCAGCCA
66 TCACCATCAACCA
251004 ATCTTTTACCCCA
1 ATCTTTTACCCCA
251017 CGACAGGGGC
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.27
Consensus pattern (78 bp):
ATCTTTTACCCCAAGCTTGGGGCAGATTGAAGCCATTCAATCTTTTACCCCGACCATAGGGCAGA
TCACCATCAACCA
Found at i:250982 original size:39 final size:39
Alignment explanation
Indices: 250806--250991 Score: 185
Period size: 39 Copynumber: 4.8 Consensus size: 39
250796 TCACCATTAG
* * * *
250806 CCAATCTCTTACCCCAAGCATGGGGCAGATTGAAACCAT
1 CCAATCTTTTACCCCGAGCTTGGGGCAGATTGAAGCCAT
*
250845 CCGATCTTTTACCCCGAGCTTGGGGCAGATTGAAGCCAT
1 CCAATCTTTTACCCCGAGCTTGGGGCAGATTGAAGCCAT
* * * * * * * *
250884 TCAATCTTTTACCCCGACCATGGGGTAGATCGCCA-TCAA
1 CCAATCTTTTACCCCGAGCTTGGGGCAGATTG-AAGCCAT
* *
250923 CCAATCTCTTACCCCAAGCTTGGGGCAGATTGAAGCCAT
1 CCAATCTTTTACCCCGAGCTTGGGGCAGATTGAAGCCAT
* * * *
250962 TCGATCTTTTACCTCGAGCTTAGGGCAGAT
1 CCAATCTTTTACCCCGAGCTTGGGGCAGAT
250992 CACCGTCAGC
Statistics
Matches: 115, Mismatches: 30, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
38 1 0.01
39 113 0.98
40 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (39 bp):
CCAATCTTTTACCCCGAGCTTGGGGCAGATTGAAGCCAT
Found at i:251047 original size:117 final size:117
Alignment explanation
Indices: 250806--251049 Score: 296
Period size: 117 Copynumber: 2.1 Consensus size: 117
250796 TCACCATTAG
*
250806 CCAATCTCTTACCCCAAGCATGGGGCAGATTGAAACCATCCGATCTTTTACCCCGAGCTTGGGGC
1 CCAATCTCTTACCCCAAGCATGGGGCAGATTGAAACCATCCGATCTTTTACCCCGAGCTTAGGGC
* ** * * *
250871 AGATTGAAGCCATTCAATCTTTTACCCCGACCATGGGGTAGATCGCCATCAA
66 AGATTCAAGCCAGCCAATCTTTTACCCCGACCATGGGGCAGATCACCACCAA
* * * *
250923 CCAATCTCTTACCCCAAGCTTGGGGCAGATTGAAGCCATTCGATCTTTTACCTCGAGCTTAGGGC
1 CCAATCTCTTACCCCAAGCATGGGGCAGATTGAAACCATCCGATCTTTTACCCCGAGCTTAGGGC
* * * *
250988 AGA-TCACCGTCAGCCAATCTTTTACCCC-ACGACA-GGGGCAGATTACCACCAC
66 AGATTCA-AGCCAGCCAATCTTTTACCCCGAC--CATGGGGCAGATCACCACCAA
*
251040 CCCATCTCTT
1 CCAATCTCTT
251050 CTAAAAAAAA
Statistics
Matches: 108, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
116 4 0.04
117 102 0.94
118 2 0.02
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (117 bp):
CCAATCTCTTACCCCAAGCATGGGGCAGATTGAAACCATCCGATCTTTTACCCCGAGCTTAGGGC
AGATTCAAGCCAGCCAATCTTTTACCCCGACCATGGGGCAGATCACCACCAA
Found at i:251547 original size:17 final size:17
Alignment explanation
Indices: 251525--251597 Score: 119
Period size: 17 Copynumber: 4.3 Consensus size: 17
251515 TCATTTTTTA
*
251525 AAATTTATTTTAAGTTT
1 AAATTTATTTTAAATTT
251542 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
**
251559 AAATTTATTTTAAGCTT
1 AAATTTATTTTAAATTT
251576 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
251593 AAATT
1 AAATT
251598 AATAATGTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:251565 original size:34 final size:34
Alignment explanation
Indices: 251525--251597 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
251515 TCATTTTTTA
*
251525 AAATTTATTTTAAGTTTAAATTTATTTTAAATTT
1 AAATTTATTTTAAGCTTAAATTTATTTTAAATTT
251559 AAATTTATTTTAAGCTTAAATTTATTTTAAATTT
1 AAATTTATTTTAAGCTTAAATTTATTTTAAATTT
251593 AAATT
1 AAATT
251598 AATAATGTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (34 bp):
AAATTTATTTTAAGCTTAAATTTATTTTAAATTT
Found at i:251599 original size:5 final size:6
Alignment explanation
Indices: 251533--251597 Score: 55
Period size: 6 Copynumber: 11.3 Consensus size: 6
251523 TAAAATTTAT
* * * * *
251533 TTTAAG TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTAAG CTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
251579 TTT-AT TTTAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TT
251598 AATAATGTAT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
5 12 0.26
6 34 0.74
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:260569 original size:21 final size:24
Alignment explanation
Indices: 260522--260576 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 24
260512 AAGTATACAT
*
260522 ACTACCGATACATTAGTACTATAA
1 ACTACCGATACATTAGTAATATAA
260546 ACTACCGATAC-TT-GTAAT-TAA
1 ACTACCGATACATTAGTAATATAA
260567 ACTACCGATA
1 ACTACCGATA
260577 GAACCTAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 13 0.43
22 4 0.13
23 2 0.07
24 11 0.37
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (24 bp):
ACTACCGATACATTAGTAATATAA
Found at i:273612 original size:81 final size:81
Alignment explanation
Indices: 273504--273676 Score: 204
Period size: 81 Copynumber: 2.1 Consensus size: 81
273494 TCCTGACAAT
* * ** *
273504 TTGTGTGAGTAGCGTCGTGAGTGGGTAATATGGACCATAGCGATGGCTGAGGTCCT-ACATACAT
1 TTGTGTGAGTAGCATCGTAAGCAGGTAATATAGACCATAGCGATGGCTGAGGT-CTGACATACAT
*
273568 TACGGATTATCATCAGC
65 TACAGATTATCATCAGC
* ** * **
273585 TTGTGTGAGTAGCATCGTAAGCAGGTAATCTAGACCATATTGATGGCTGAGGTTTGACATATGTT
1 TTGTGTGAGTAGCATCGTAAGCAGGTAATATAGACCATAGCGATGGCTGAGGTCTGACATACATT
* *
273650 GCAGATTCTCATCAGC
66 ACAGATTATCATCAGC
273666 TTGTGTGAGTA
1 TTGTGTGAGTA
273677 TCATTGTATA
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
80 1 0.01
81 76 0.99
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (81 bp):
TTGTGTGAGTAGCATCGTAAGCAGGTAATATAGACCATAGCGATGGCTGAGGTCTGACATACATT
ACAGATTATCATCAGC
Found at i:273734 original size:26 final size:26
Alignment explanation
Indices: 273698--273772 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 26
273688 TAGTTAAACT
* *
273698 CTGAACTGGCTCGTAAGAACGATATA
1 CTGAATTGGCTCGTAAGAGCGATATA
* *
273724 CTGAATTGGCTCATAAGAGCGATATT
1 CTGAATTGGCTCGTAAGAGCGATATA
*
273750 CT-ATTTGGCTCGTAAGAGCGATA
1 CTGAATTGGCTCGTAAGAGCGATA
273773 CTCTGTTTGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
25 19 0.44
26 24 0.56
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (26 bp):
CTGAATTGGCTCGTAAGAGCGATATA
Found at i:273765 original size:25 final size:25
Alignment explanation
Indices: 273704--273782 Score: 95
Period size: 25 Copynumber: 3.1 Consensus size: 25
273694 AACTCTGAAC
* * *
273704 TGGCTCGTAAGAACGATATACTGAAT
1 TGGCTCGTAAGAGCGATATTCT-ATT
*
273730 TGGCTCATAAGAGCGATATTCTATT
1 TGGCTCGTAAGAGCGATATTCTATT
* *
273755 TGGCTCGTAAGAGCGATACTCTGTT
1 TGGCTCGTAAGAGCGATATTCTATT
273780 TGG
1 TGG
273783 GCTCATATGA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
25 27 0.59
26 19 0.41
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (25 bp):
TGGCTCGTAAGAGCGATATTCTATT
Found at i:273794 original size:26 final size:25
Alignment explanation
Indices: 273729--273794 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
273719 ATATACTGAA
*
273729 TTGGCTCATAAGAGCGATATTCTAT
1 TTGGCTCATAAGAGCGATACTCTAT
* *
273754 TTGGCTCGTAAGAGCGATACTCTGT
1 TTGGCTCATAAGAGCGATACTCTAT
*
273779 TTGGGCTCATATGAGC
1 TT-GGCTCATAAGAGC
273795 TAAATTTTGG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
25 24 0.69
26 11 0.31
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (25 bp):
TTGGCTCATAAGAGCGATACTCTAT
Found at i:273971 original size:135 final size:135
Alignment explanation
Indices: 273729--273999 Score: 497
Period size: 135 Copynumber: 2.0 Consensus size: 135
273719 ATATACTGAA
*
273729 TTGGCTCATAAGAGCGATATTCTATTTGGCTCGTAAGAGCGATACTCTGTTTGGGCTCATATGAG
1 TTGGCTCATAAGAGCGATATTCTATTTGGCTCGTAAGAGCGATACTCTGTCTGGGCTCATATGAG
*
273794 CTAAATTTTGGAAGACTCGTAGAGATCAACTTGACGCTAATGCCACGGGATAACAAAGATGTCTT
66 CTAAAATTTGGAAGACTCGTAGAGATCAACTTGACGCTAATGCCACGGGATAACAAAGATGTCTT
273859 ATTAC
131 ATTAC
*
273864 TTGGCTCATAAGAGTGATATTCTATTTGGCTCGTAAGAGCGATACTCTGTCTGGGCTCATATGAG
1 TTGGCTCATAAGAGCGATATTCTATTTGGCTCGTAAGAGCGATACTCTGTCTGGGCTCATATGAG
* *
273929 CTAAAATTTGGAAGACTCGTAGAGATCAACTTGATGCTAATGCCACGGGATAACGAAGATGTCTT
66 CTAAAATTTGGAAGACTCGTAGAGATCAACTTGACGCTAATGCCACGGGATAACAAAGATGTCTT
273994 ATTAC
131 ATTAC
273999 T
1 T
274000 CTTTCCGTAC
Statistics
Matches: 131, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
135 131 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (135 bp):
TTGGCTCATAAGAGCGATATTCTATTTGGCTCGTAAGAGCGATACTCTGTCTGGGCTCATATGAG
CTAAAATTTGGAAGACTCGTAGAGATCAACTTGACGCTAATGCCACGGGATAACAAAGATGTCTT
ATTAC
Found at i:279952 original size:47 final size:45
Alignment explanation
Indices: 279839--279964 Score: 135
Period size: 47 Copynumber: 2.7 Consensus size: 45
279829 ATTGTGAACA
279839 ATGTCACAGTAATGCAGATAAACTGCCACATAATCAAATCGTGGAT
1 ATGTCAC-GTAATGCAGATAAACTGCCACATAATCAAATCGTGGAT
* * ** * * **
279885 AAGCCACCACATATGTAGATATACTGCCACATAATTTAATCGTGGAT
1 ATGTCA-CGTA-ATGCAGATAAACTGCCACATAATCAAATCGTGGAT
279932 ATTGTCACGTTAATGCAGATAAACTGCCACATA
1 A-TGTCACG-TAATGCAGATAAACTGCCACATA
279965 CTTCCACCTT
Statistics
Matches: 62, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
46 5 0.08
47 53 0.85
48 4 0.06
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (45 bp):
ATGTCACGTAATGCAGATAAACTGCCACATAATCAAATCGTGGAT
Found at i:280316 original size:15 final size:16
Alignment explanation
Indices: 280288--280317 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
280278 CTCATCAAAC
280288 ATATTTTAAATAATAA
1 ATATTTTAAATAATAA
280304 ATATTTT-AATAATA
1 ATATTTTAAATAATA
280318 TAAAATATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATTTTAAATAATAA
Found at i:285028 original size:49 final size:49
Alignment explanation
Indices: 284902--285046 Score: 175
Period size: 49 Copynumber: 2.9 Consensus size: 49
284892 ACCGAAACAC
* * *
284902 CATTTGTGGACAAGCCACCACTAATTTGTAAATATACTACCACTTATAA
1 CATTTGTGGACAAGCCACCACTAATATGCAAATATACTACCACTTAAAA
* * *
284951 CATATTGTGGACAAGCCACCACTGATATGCATATATACTGCCAC-TAAAA
1 CAT-TTGTGGACAAGCCACCACTAATATGCAAATATACTACCACTTAAAA
* * * *
285000 CACTTTGTGGACAAACCACCACTTATATGCCAATAAACTACCACTTA
1 CA-TTTGTGGACAAGCCACCACTAATATGCAAATATACTACCACTTA
285047 CTTCCACCTT
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
49 43 0.53
50 38 0.47
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.27
Consensus pattern (49 bp):
CATTTGTGGACAAGCCACCACTAATATGCAAATATACTACCACTTAAAA
Found at i:291170 original size:6 final size:6
Alignment explanation
Indices: 291159--291183 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
291149 CTCAATTTTT
291159 AATCTC AATCTC AATCTC AATCTC A
1 AATCTC AATCTC AATCTC AATCTC A
291184 TGATATTGCA
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:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (6 bp):
AATCTC
Found at i:305240 original size:19 final size:20
Alignment explanation
Indices: 305193--305240 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
305183 TTGAAAATTC
305193 TTAA-TATTA-AATTATAAA
1 TTAATTATTATAATTATAAA
*
305211 TTAAATT-TTATAATT-TATA
1 TT-AATTATTATAATTATAAA
305230 TTAATTATTAT
1 TTAATTATTAT
305241 CAAGAGATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.24
19 14 0.56
20 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTATTATAATTATAAA
Found at i:305539 original size:97 final size:99
Alignment explanation
Indices: 305330--305706 Score: 372
Period size: 97 Copynumber: 3.7 Consensus size: 99
305320 ATTTTTTGAA
*
305330 TTTTGATAATTTTAATATTAATTATAAATTAAATTTTATAAATTATATTAATTATTATCAAAAGC
1 TTTTGATAATTTTAATATTAATTATAAATTAAATTTTATAATTTATATTAATTATTATCAAAAG-
** **
305395 TTGAATAAAGATTTTTCATTAAAATT-T-TTATTTTTCAAAG
65 TT---T-ATCA-TTTTCA--AATTTTATCTTATTTTTCAAAG
* * * *
305435 GTATGATAAGTCTTAATATTAATTATAAATTGAATTTTATAATTTATATTAATTATTATCAAAAG
1 TTTTGATAA-TTTTAATATTAATTATAAATTAAATTTTATAATTTATATTAATTATTATCAAAAG
305500 TTT-TCA-TTT-AAATGTTT-TCTTATTTTTCAAAG
65 TTTATCATTTTCAAAT-TTTATCTTATTTTTCAAAG
* * *
305532 TTTTGATAATTTTTAATATTAATTATAAATTAAATTTTATAATTTGTATTAATTATTAACAAGAG
1 TTTTGATAA-TTTTAATATTAATTATAAATTAAATTTTATAATTTATATTAATTATTATCAAAAG
* * * *
305597 TTTGAGATTATTTTTTCATATTTTAATTTTAATTTTTCAAAA
65 TTT---ATCA--TTTTCAAATTTT-ATCTT-ATTTTTCAAAG
*
305639 TTTTGATAATATTTATTATTAATTATAAATTAAATTTTATAATTTATATTAATTATTATTC-AAA
1 TTTTGATAAT-TTTAATATTAATTATAAATTAAATTTTATAATTTATATTAATTATTA-TCAAAA
305703 GTTT
64 GTTT
305707 GAATTAGGAT
Statistics
Matches: 231, Mismatches: 25, Indels: 30
0.81 0.09 0.10
Matches are distributed among these distances:
95 2 0.01
96 3 0.01
97 74 0.32
98 3 0.01
100 1 0.00
101 2 0.01
102 1 0.00
104 6 0.03
105 12 0.05
106 56 0.24
107 70 0.30
108 1 0.00
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.52
Consensus pattern (99 bp):
TTTTGATAATTTTAATATTAATTATAAATTAAATTTTATAATTTATATTAATTATTATCAAAAGT
TTATCATTTTCAAATTTTATCTTATTTTTCAAAG
Found at i:305636 original size:107 final size:106
Alignment explanation
Indices: 305521--305712 Score: 314
Period size: 107 Copynumber: 1.8 Consensus size: 106
305511 ATGTTTTCTT
* * *
305521 ATTTTTCAAAGTTTTGATAATTTTTAATATTAATTATAAATTAAATTTTATAATTTGTATTAATT
1 ATTTTTCAAAATTTTGATAATATTTAATATTAATTATAAATTAAATTTTATAATTTATATTAATT
305586 ATTA-ACAAGAGTTTGAGATTATTTTTTCATATTTTAATTTTA
66 ATTATACAA-AGTTTGA-ATTATTTTTTCATATTTTAATTTTA
*
305628 ATTTTTCAAAATTTTGATAATATTTATTATTAATTATAAATTAAATTTTATAATTTATATTAATT
1 ATTTTTCAAAATTTTGATAATATTTAATATTAATTATAAATTAAATTTTATAATTTATATTAATT
*
305693 ATTATTCAAAGTTTGAATTA
66 ATTATACAAAGTTTGAATTA
305713 GGATTTGTTT
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
106 4 0.05
107 72 0.91
108 3 0.04
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.54
Consensus pattern (106 bp):
ATTTTTCAAAATTTTGATAATATTTAATATTAATTATAAATTAAATTTTATAATTTATATTAATT
ATTATACAAAGTTTGAATTATTTTTTCATATTTTAATTTTA
Found at i:305689 original size:204 final size:201
Alignment explanation
Indices: 305304--305706 Score: 528
Period size: 204 Copynumber: 2.0 Consensus size: 201
305294 TTTAATTTGA
* **
305304 ATTTAATGTTATTTTTATTTTTTGAATTTTGATAATTTTAATATTAATTATAAATTAAATTTTAT
1 ATTTAATGTTATTCTTATTTTTCAAATTTTGATAATTTTAATATTAATTATAAATTAAATTTTAT
* *
305369 AAATTATATTAATTATTATCAAAAGCTTGAATAAAGATTTTTCATTAAAATTTTTATTTTTCAAA
66 AAATTATATTAATTATTAACAAAAGCTTGAATAAAGATTTTTCATTAAAATTTTAATTTTTCAAA
* *
305434 GGTATGATAAGTCTTAATATTAATTATAAATTGAATTTTATAATTTATATTAATTATTA-TCAAA
131 AGTATGATAAGTCTTAATATTAATTATAAATTAAATTTTATAATTTATATTAATTATTATTC-AA
305498 AGTTTTC
195 AGTTTTC
305505 ATTTAAATGTT-TTCTTATTTTTCAAAGTTTTGATAATTTTTAATATTAATTATAAATTAAATTT
1 ATTT-AATGTTATTCTTATTTTTCAAA-TTTTGATAA-TTTTAATATTAATTATAAATTAAATTT
* * * * * * **
305569 TATAATTTGTATTAATTATTAACAAGAGTTTGAGAT-TA-TTTTTTCATATTTTAATTTTAATTT
63 TATAAATTATATTAATTATTAACAAAAGCTTGA-ATAAAGATTTTTC--ATTAAAATTTTAATTT
* * * *
305632 TTCAAAATTTTGATAA-TATTTATTATTAATTATAAATTAAATTTTATAATTTATATTAATTATT
125 TTCAAAAGTATGATAAGT-CTTAATATTAATTATAAATTAAATTTTATAATTTATATTAATTATT
305696 ATTCAAAGTTT
189 ATTCAAAGTTT
305707 GAATTAGGAT
Statistics
Matches: 175, Mismatches: 19, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
201 16 0.09
202 21 0.12
203 57 0.33
204 79 0.45
205 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (201 bp):
ATTTAATGTTATTCTTATTTTTCAAATTTTGATAATTTTAATATTAATTATAAATTAAATTTTAT
AAATTATATTAATTATTAACAAAAGCTTGAATAAAGATTTTTCATTAAAATTTTAATTTTTCAAA
AGTATGATAAGTCTTAATATTAATTATAAATTAAATTTTATAATTTATATTAATTATTATTCAAA
GTTTTC
Found at i:307159 original size:18 final size:18
Alignment explanation
Indices: 307118--307160 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
307108 GATTTTGTTA
*
307118 AAGAAGAAGAAGATCCTG
1 AAGAAGAAGAAGATCCCG
307136 AAGAAGAAGAAGATCCCG
1 AAGAAGAAGAAGATCCCG
*
307154 AGGAAGA
1 AAGAAGA
307161 TCCTGTGGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.51, C:0.12, G:0.30, T:0.07
Consensus pattern (18 bp):
AAGAAGAAGAAGATCCCG
Found at i:308487 original size:16 final size:15
Alignment explanation
Indices: 308466--308496 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
308456 AAGTGAAATG
308466 AAAAAGAAAAAAGAGA
1 AAAAAG-AAAAAGAGA
308482 AAAAAGAAAAAGAGA
1 AAAAAGAAAAAGAGA
308497 GCATATGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAGAGA
Found at i:313878 original size:12 final size:12
Alignment explanation
Indices: 313861--313923 Score: 58
Period size: 12 Copynumber: 5.1 Consensus size: 12
313851 TTTTAATAAG
313861 ATTTAATATTAA
1 ATTTAATATTAA
313873 ATTTAATA-TAA
1 ATTTAATATTAA
* *
313884 TATTTATTAAGATAA
1 -ATTTAAT-A-TTAA
313899 ATATT-ATATTAA
1 AT-TTAATATTAA
313911 ATTTAATATTAA
1 ATTTAATATTAA
313923 A
1 A
313924 GTGATTAAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
11 5 0.12
12 27 0.64
13 2 0.05
14 3 0.07
15 5 0.12
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:314086 original size:25 final size:26
Alignment explanation
Indices: 314036--314083 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 26
314026 AGTTGTAAAG
314036 AGAAAATTCTCTGAAAAGATTATTTT
1 AGAAAATTCTCTGAAAAGATTATTTT
314062 AGAAAA-TCTCT--AAAGA-TATTTT
1 AGAAAATTCTCTGAAAAGATTATTTT
314084 TTTTACAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
25 5 0.23
26 6 0.27
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (26 bp):
AGAAAATTCTCTGAAAAGATTATTTT
Found at i:321798 original size:21 final size:20
Alignment explanation
Indices: 321759--321798 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
321749 TATTTAAAAA
* *
321759 AAATGAAAAACACATTTATC
1 AAATGAAAAAAAAATTTATC
321779 AAATGAAAATAAAAATTTAT
1 AAATGAAAA-AAAAATTTAT
321799 TTTTAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (20 bp):
AAATGAAAAAAAAATTTATC
Found at i:324555 original size:13 final size:13
Alignment explanation
Indices: 324537--324561 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
324527 ATAAGGCTAT
324537 TTAAAATGATTTG
1 TTAAAATGATTTG
324550 TTAAAATGATTT
1 TTAAAATGATTT
324562 TTTTGTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAAAATGATTTG
Found at i:324888 original size:30 final size:29
Alignment explanation
Indices: 324835--325107 Score: 224
Period size: 30 Copynumber: 9.1 Consensus size: 29
324825 CCCAATAGAT
* * * *
324835 CCCTAAACTTTTAAAAATCATATTTTGAC
1 CCCTAAACTTTTCAAAATTACATTTTAAC
* * *
324864 CCCTAAACTTCTTTAAAATTATATTTTGAC
1 CCCTAAACTT-TTCAAAATTACATTTTAAC
**
324894 CCCTAAACAATTCTAAAATTACATTTTAAC
1 CCCTAAACTTTTC-AAAATTACATTTTAAC
* *
324924 CCCTCAAACTTTCCAAAATTGCATTTTAAC
1 CCCT-AAACTTTTCAAAATTACATTTTAAC
**
324954 CTTTAAACTTTTTCTAAAATTACATTTTAAC
1 CCCTAAAC-TTTTC-AAAATTACATTTTAAC
* *
324985 CTCTAAACTTTTCCAAAATTACACTTTAAC
1 CCCTAAACTTTT-CAAAATTACATTTTAAC
*
325015 CCTTAAACTTTTCAAAATTACATTTTAA-
1 CCCTAAACTTTTCAAAATTACATTTTAAC
* * * * *
325043 CCCTCGAACTTCTCCAAAATCACGTTTTGAC
1 CCCT-AAACTT-TTCAAAATTACATTTTAAC
* * * *
325074 CCTTAAACCTTCTCAAAAATCACATTTTGAC
1 CCCTAAA-CTTTTC-AAAATTACATTTTAAC
325105 CCC
1 CCC
325108 ATTTTTTCCT
Statistics
Matches: 201, Mismatches: 32, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
28 3 0.01
29 36 0.18
30 110 0.55
31 52 0.26
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (29 bp):
CCCTAAACTTTTCAAAATTACATTTTAAC
Found at i:324978 original size:61 final size:60
Alignment explanation
Indices: 324838--325107 Score: 253
Period size: 61 Copynumber: 4.5 Consensus size: 60
324828 AATAGATCCC
* * * * ** * * *
324838 TAAACTTTT-AAAAATCATATTTTGACCCCT-AAACTTCTTTAAAATTATATTTTGACCCC
1 TAAACTTTTCTAAAATTACATTTTAACCCCTCAAACTT-TCCAAAATTACATTTTAACCCT
** * *
324897 TAAACAATTCTAAAATTACATTTTAACCCCTCAAACTTTCCAAAATTGCATTTTAACCTT
1 TAAACTTTTCTAAAATTACATTTTAACCCCTCAAACTTTCCAAAATTACATTTTAACCCT
* *
324957 TAAACTTTTTCTAAAATTACATTTTAACCTCT-AAACTTTTCCAAAATTACACTTTAACCCT
1 TAAAC-TTTTCTAAAATTACATTTTAACCCCTCAAAC-TTTCCAAAATTACATTTTAACCCT
* * * *
325018 TAAACTTTTC-AAAATTACATTTTAA-CCCTCGAACTTCTCCAAAATCACGTTTTGACCCT
1 TAAACTTTTCTAAAATTACATTTTAACCCCTCAAACTT-TCCAAAATTACATTTTAACCCT
* * * *
325077 TAAACCTTCTCAAAAATCACATTTTGACCCC
1 TAAA-CTTTTCTAAAATTACATTTTAACCCC
325108 ATTTTTTCCT
Statistics
Matches: 174, Mismatches: 28, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
58 5 0.03
59 47 0.27
60 51 0.29
61 68 0.39
62 3 0.02
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (60 bp):
TAAACTTTTCTAAAATTACATTTTAACCCCTCAAACTTTCCAAAATTACATTTTAACCCT
Found at i:325005 original size:91 final size:89
Alignment explanation
Indices: 324867--325044 Score: 239
Period size: 91 Copynumber: 2.0 Consensus size: 89
324857 TTTTGACCCC
* * * *
324867 TAAACTTCTTTAAAATTATATTTTGACCCCTAAACAATTCTAAAATTACATTTTAACCCCTCAAA
1 TAAACTTCTTTAAAATTACATTTTAACCCCTAAACAATTCCAAAATTACACTTTAA-CCCTCAAA
*
324932 CTTTCCAAAATTGCATTTTAACCTT
65 CTTTCCAAAATTACATTTTAACCTT
* * ** *
324957 TAAACTTTTTCTAAAATTACATTTTAACCTCTAAACTTTTCCAAAATTACACTTTAACCCTTAAA
1 TAAACTTCTT-TAAAATTACATTTTAACCCCTAAACAATTCCAAAATTACACTTTAACCCTCAAA
*
325022 CTTTTCAAAATTACATTTTAACC
65 CTTTCCAAAATTACATTTTAACC
325045 CTCGAACTTC
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
90 37 0.49
91 39 0.51
ACGTcount: A:0.37, C:0.22, G:0.01, T:0.40
Consensus pattern (89 bp):
TAAACTTCTTTAAAATTACATTTTAACCCCTAAACAATTCCAAAATTACACTTTAACCCTCAAAC
TTTCCAAAATTACATTTTAACCTT
Found at i:328826 original size:162 final size:161
Alignment explanation
Indices: 328652--329003 Score: 465
Period size: 162 Copynumber: 2.2 Consensus size: 161
328642 ATAAAGCGAT
*
328652 CATCTTCTTGATGAGATACAGAGAAGTGGACCAAAT-TCGTCTTCCTGATAAGATACAAAGAAGT
1 CATCTTCTTGATGAGATACAGAGAAGTGGACCAAATCT-GTCTTCCTGATAAGATACAAAGAAAT
* * * * * ** * * *
328716 GGATTAAAAGAAGTGATGCGGTCATCTTCCTGATGAGGTATGGAGAAGTAGACCAATTCAACGAA
65 GGATTAAAAGAAATGAGGCGATCATCTTCCTGATAAGATACAGAGAAGTAAACCAAATCAAAGAA
* * * *
328781 GTGAAA-CTCAGTGTGAGTGAAACTTTGAACCCC
130 G-CAAAGCTCAATGTGAGTGAAAC-TTCAAACCC
* *
328814 CATCTTCTTGATGAGATACAGAGAAGTGGACCAAATCTGTCTTCCTGATTAGATACAGAGAAATG
1 CATCTTCTTGATGAGATACAGAGAAGTGGACCAAATCTGTCTTCCTGATAAGATACAAAGAAATG
*
328879 GATTAAAATAAATGAGGCGATCATCTTCCTGATAAGATACAGAGAAGTAAACCAAATCAAAGAAG
66 GATTAAAAGAAATGAGGCGATCATCTTCCTGATAAGATACAGAGAAGTAAACCAAATCAAAGAAG
328944 CAAAGCTCAATGTGAGTGAAACTTCAAACCC
131 CAAAGCTCAATGTGAGTGAAACTTCAAACCC
* * * *
328975 TATCTTCCTGATAAGATACTGAGAAGTGG
1 CATCTTCTTGATGAGATACAGAGAAGTGG
329004 GTTAAAGCAA
Statistics
Matches: 166, Mismatches: 22, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
161 35 0.21
162 130 0.78
163 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (161 bp):
CATCTTCTTGATGAGATACAGAGAAGTGGACCAAATCTGTCTTCCTGATAAGATACAAAGAAATG
GATTAAAAGAAATGAGGCGATCATCTTCCTGATAAGATACAGAGAAGTAAACCAAATCAAAGAAG
CAAAGCTCAATGTGAGTGAAACTTCAAACCC
Found at i:329079 original size:209 final size:210
Alignment explanation
Indices: 328814--329257 Score: 631
Period size: 209 Copynumber: 2.1 Consensus size: 210
328804 TTTGAACCCC
* * * *
328814 CATCTTCTTGATGAGATACAGAGAAGTGGACCAAATCTGTCTTCCTGATTAGATACAGAGAAATG
1 CATCTTCTTGATGAGATACAGAGAAGTGCACCAAATCTATCTTCCTGATGAGATACAAAGAAATG
*
328879 GATTAAAATAAATGAGGCGATCATCTTCCTGATAAGATACAGAGAAGTAAACCAAATCAAAGAAG
66 GATTAAAACAAATGAGGCGATCATCTTCCTGATAAGATACAGAGAAGTAAACCAAATCAAAGAAG
* * * *
328944 CAAAGCTCAATGTGAGTGAAACTTC-AAACCCTATCTTCCTGATAAGATACTGAGAAGTGGGTTA
131 CAAAGCTCAATGTGAGTAAAACTTCGAAACCCCATCTTCCTGATAAGATACTAAGAAGTGGGTCA
*
329008 AAGCAATAAAACTGT
196 AAGCAATAAAACGGT
* * * * *
329023 CGTCTTCCTGGTGAGATATAGAGAAGTGCACCAAAT-TCATCTTCCTGATGAGATACAAAGAAGT
1 CATCTTCTTGATGAGATACAGAGAAGTGCACCAAATCT-ATCTTCCTGATGAGATACAAAGAAAT
* * * * * *
329087 GGATTAAAACAAATGAGGCGATCATCTTCCTGATGAGGTACATAGAAGTAGACCAAATCGATGAA
65 GGATTAAAACAAATGAGGCGATCATCTTCCTGATAAGATACAGAGAAGTAAACCAAATCAAAGAA
* * *
329152 GCGAAGCTCAATGTGAGTAAAACTTCGAACCCCCATCTTCCTGATGAGATACTAAGAAGTGGGTC
130 GCAAAGCTCAATGTGAGTAAAACTTCGAAACCCCATCTTCCTGATAAGATACTAAGAAGTGGGTC
* *
329217 AAAGCAGTAAAGCGGT
195 AAAGCAATAAAACGGT
329233 CATCTTCTTGATGAGATACAGAGAA
1 CATCTTCTTGATGAGATACAGAGAA
329258 AGAGACCAAT
Statistics
Matches: 203, Mismatches: 30, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
208 1 0.00
209 135 0.67
210 67 0.33
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.24
Consensus pattern (210 bp):
CATCTTCTTGATGAGATACAGAGAAGTGCACCAAATCTATCTTCCTGATGAGATACAAAGAAATG
GATTAAAACAAATGAGGCGATCATCTTCCTGATAAGATACAGAGAAGTAAACCAAATCAAAGAAG
CAAAGCTCAATGTGAGTAAAACTTCGAAACCCCATCTTCCTGATAAGATACTAAGAAGTGGGTCA
AAGCAATAAAACGGT
Found at i:329184 original size:371 final size:371
Alignment explanation
Indices: 328493--329213 Score: 1027
Period size: 371 Copynumber: 1.9 Consensus size: 371
328483 CTTCCAAATG
* * * * *
328493 AGATACAGAGAAGTGGATTAAAACAAGTGATGCGATCATCTTTCTGATGAGATACAGAGAAGAAG
1 AGATACAGAGAAATGGATTAAAACAAATGAGGCGATCATCTTCCTGATAAGATACAGAGAAGAAG
* ** * * *
328558 ACCAATTAAACGAAGTGAAGTTCAGTGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATAC
66 ACCAATCAAACGAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATAAGATAC
* * * *
328623 TGAGAAGTTGGTCAAAGCAATAAAGCGATCATCTTCTTGATGAGATACAGAGAAGTGGACCAAAT
131 TGAGAAGTGGGTCAAAGCAATAAAACGATCATCTTCCTGATGAGATACAGAGAAGTGCACCAAAT
* * * * *
328688 TCGTCTTCCTGATAAGATACAAAGAAGTGGATTAAAAGAAGTGATGCGGTCATCTTCCTGATGAG
196 TCATCTTCCTGATAAGATACAAAGAAGTGGATTAAAACAAATGAGGCGATCATCTTCCTGATGAG
** * * * * *
328753 GTATGGAGAAGTAGACCAATTCAACGAAGTGAAACTCAGTGTGAGTGAAACTTTGAACCCCCATC
261 GTACAGAGAAGTAGACCAAATCAACGAAGCGAAACTCAATGTGAGTAAAACTTCGAACCCCCATC
*
328818 TTCTTGATGAGATAC-AGAGAAGTGGACCAAATCTGTCTTCCTGATT
326 TTCCTGATGAGATACTA-AGAAGTGGACCAAATCTGTCTTCCTGATT
*
328864 AGATACAGAGAAATGGATTAAAATAAATGAGGCGATCATCTTCCTGATAAGATACAGAGAAGTAA
1 AGATACAGAGAAATGGATTAAAACAAATGAGGCGATCATCTTCCTGATAAGATACAGAGAAG-AA
*
328929 -ACCAAATCAAA-GAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCCTATCTTCCTGATAAGAT
65 GACC-AATCAAACGAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATAAGAT
* * * *
328992 ACTGAGAAGTGGGTTAAAGCAATAAAACTG-TCGTCTTCCTGGTGAGATATAGAGAAGTGCACCA
129 ACTGAGAAGTGGGTCAAAGCAATAAAAC-GATCATCTTCCTGATGAGATACAGAGAAGTGCACCA
*
329056 AATTCATCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAAATGAGGCGATCATCTTCCTGAT
193 AATTCATCTTCCTGATAAGATACAAAGAAGTGGATTAAAACAAATGAGGCGATCATCTTCCTGAT
* * * *
329121 GAGGTACATAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGTAAAACTTCGAACCCCC
258 GAGGTACAGAGAAGTAGACCAAATCAACGAAGCGAAACTCAATGTGAGTAAAACTTCGAACCCCC
329186 ATCTTCCTGATGAGATACTAAGAAGTGG
323 ATCTTCCTGATGAGATACTAAGAAGTGG
329214 GTCAAAGCAG
Statistics
Matches: 307, Mismatches: 39, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
371 297 0.97
372 10 0.03
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (371 bp):
AGATACAGAGAAATGGATTAAAACAAATGAGGCGATCATCTTCCTGATAAGATACAGAGAAGAAG
ACCAATCAAACGAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATAAGATAC
TGAGAAGTGGGTCAAAGCAATAAAACGATCATCTTCCTGATGAGATACAGAGAAGTGCACCAAAT
TCATCTTCCTGATAAGATACAAAGAAGTGGATTAAAACAAATGAGGCGATCATCTTCCTGATGAG
GTACAGAGAAGTAGACCAAATCAACGAAGCGAAACTCAATGTGAGTAAAACTTCGAACCCCCATC
TTCCTGATGAGATACTAAGAAGTGGACCAAATCTGTCTTCCTGATT
Found at i:329283 original size:124 final size:124
Alignment explanation
Indices: 329060--329391 Score: 400
Period size: 123 Copynumber: 2.7 Consensus size: 124
329050 GCACCAAATT
* * * * * * * *
329060 CATCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAAATGAGGCGATCATCTTCCTGATGAGG
1 CATCTTCCTGATGAGATACTAAGAAGTGGGTCAAAGC-AATAAAGCGGTCATCTTCCTGATGAGA
* * *
329125 TACATAG-AAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGTAAAACTTCGAACCCC
65 TACAGAGAAAGTAGACCAAATCAACGAAGCGAAGCTCAATGTGAGTAAAACTTCGAA-CCC
* *
329185 CATCTTCCTGATGAGATACTAAGAAGTGGGTCAAAGCAGTAAAGCGGTCATCTTCTTGATGAGAT
1 CATCTTCCTGATGAGATACTAAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTGATGAGAT
* * * *
329250 ACAGAGAAAG-AGACCAATTCAACGAAGTGAAGCTCAGTGTGAGTAAAACTTTGAACCC
66 ACAGAGAAAGTAGACCAAATCAACGAAGCGAAGCTCAATGTGAGTAAAACTTCGAACCC
* * * * * * *
329308 CAGCTTCTTGATGAGATACTGATAAGTGGGTCAAAGCAATAAAGTGGTCGTCTTCCTAATGAGAT
1 CATCTTCCTGATGAGATACTAAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTGATGAGAT
*
329373 ACAGAG-AAGTGGACCAAAT
66 ACAGAGAAAGTAGACCAAAT
329392 TCGTCTTCCT
Statistics
Matches: 177, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
122 3 0.02
123 72 0.41
124 66 0.37
125 36 0.20
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (124 bp):
CATCTTCCTGATGAGATACTAAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTGATGAGAT
ACAGAGAAAGTAGACCAAATCAACGAAGCGAAGCTCAATGTGAGTAAAACTTCGAACCC
Found at i:329360 original size:333 final size:334
Alignment explanation
Indices: 328899--329590 Score: 962
Period size: 333 Copynumber: 2.1 Consensus size: 334
328889 AATGAGGCGA
* *
328899 TCATCTTCCTGATAAGATACAGAG-AAGTAAACCAAATCAAAGAAGCAAAGCTCAATGTGAGTGA
1 TCATCTTCCTGATGAGATACAGAGAAAGTAAACCAAATCAAAGAAGCAAAGCTCAATGTGAGTAA
* * *
328963 AACTTCAAACCCTATCTTCCTGATAAGATACTGAGAAGTGGGTTAAAGCAATAAAACTGTCGTCT
66 AACTTCAAACCCCAGCTTCCTGATAAGATACTGAGAAGTGGGTCAAAGCAATAAAACTGTCGTCT
** *
329028 TCCTGGTGAGATATAGAGAAGTGCACCAAATTCATCTTCCTGATGAGATACAAAGAAGTGGATTA
131 TCCTAATGAGATACAGAGAAGTGCACCAAATTCATCTTCCTGATGAGATACAAAGAAGTGGATTA
* * * *
329093 AAACAAATGAGGCGATCATCTTCCTGATGAGGTACATAGAAGTAGACCAAATCGATGAAGCGAAG
196 AAACAAATGAGGCAATCATCTTCCTGATGAGGTACAAAGAAGTAGACCAAATCAACGAAGCGAAG
329158 CTCAATGTGAGTAAAAC-TTCGAACCCCCATCTTCCTGATGAGATACTA-AGAAGTGGGTCAAAG
261 CTCAATGTGAGTAAAACATT-GAACCCCCATCTTCCTGATGAGATAC-AGAGAAGTGGGTCAAAG
* *
329221 CAGTAAAGCGG
324 CAATAAAGAGG
* * * * ** *
329232 TCATCTTCTTGATGAGATACAGAGAAAG-AGACCAATTCAACGAAGTGAAGCTCAGTGTGAGTAA
1 TCATCTTCCTGATGAGATACAGAGAAAGTAAACCAAATCAAAGAAGCAAAGCTCAATGTGAGTAA
** * * * *
329296 AACTTTGAACCCCAGCTTCTTGATGAGATACTGATAAGTGGGTCAAAGCAAT-AAAGTGGTCGTC
66 AACTTCAAACCCCAGCTTCCTGATAAGATACTGAGAAGTGGGTCAAAGCAATAAAACT-GTCGTC
* * *
329360 TTCCTAATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGGATT
130 TTCCTAATGAGATACAGAGAAGTGCACCAAATTCATCTTCCTGATGAGATACAAAGAAGTGGATT
* * * *
329425 AAAACAAGTGATGCAATCATCTTCCTGATGAGGTACAAAGAAGTAGACCAATTCAACGAAGTGAA
195 AAAACAAATGAGGCAATCATCTTCCTGATGAGGTACAAAGAAGTAGACCAAATCAACGAAGCGAA
* * *
329490 GCTCAGTGTGAGTGAAACATTGAACCCCCATCTTCTTGATGAGATACAGAGAAGTGGGTCAAAGC
260 GCTCAATGTGAGTAAAACATTGAACCCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGC
*
329555 AATAACGAGG
325 AATAAAGAGG
* *
329565 TCACCTTCCTGATGAGATATAGAGAA
1 TCATCTTCCTGATGAGATACAGAGAA
329591 GTGGACCAAA
Statistics
Matches: 314, Mismatches: 41, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
332 5 0.02
333 304 0.97
334 5 0.02
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (334 bp):
TCATCTTCCTGATGAGATACAGAGAAAGTAAACCAAATCAAAGAAGCAAAGCTCAATGTGAGTAA
AACTTCAAACCCCAGCTTCCTGATAAGATACTGAGAAGTGGGTCAAAGCAATAAAACTGTCGTCT
TCCTAATGAGATACAGAGAAGTGCACCAAATTCATCTTCCTGATGAGATACAAAGAAGTGGATTA
AAACAAATGAGGCAATCATCTTCCTGATGAGGTACAAAGAAGTAGACCAAATCAACGAAGCGAAG
CTCAATGTGAGTAAAACATTGAACCCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCA
ATAAAGAGG
Found at i:329599 original size:210 final size:209
Alignment explanation
Indices: 329187--330637 Score: 1764
Period size: 209 Copynumber: 7.0 Consensus size: 209
329177 CGAACCCCCA
* * * * * * *
329187 TCTTCCTGATGAGATACTA-AGAAGTGGGTCAAAGC-AGTAAAGCGGTCATCTTCTTGATGAGAT
1 TCTTCCTGATGAGATAC-AGAGAAGTGGATTAAAACAAATGAGGCGGTCATCTTCCTGATGAGAT
* * * * * *
329250 ACAGAGAAAG-AGACCAATTCAACGAAGTGAAGCTCAGTGTGAGTAAAACTTTGAA-CCCCAGCT
65 ACAGAG-AAGTAGACCAAATCAATGAAGCGAAGCTCAATGTGAGTGAAAC-TTGAACCCCCATCT
* * *
329313 TCTTGATGAGATACTGATAAGTGGGTCAAAGCAATAAAGTGGTCGTCTTCCTAATGAGATACAGA
128 TCTTGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGCGGTCGTCTTCCTGATGAGATACAGA
*
329378 GAAGTGGACCAAATTCG
193 GAAGTGGACCAAATCCG
* * ** *
329395 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAAGTGATGCAATCATCTTCCTGATGAGGTA
1 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAAATGAGGCGGTCATCTTCCTGATGAGATA
* * * * *
329460 CAAAGAAGTAGACCAATTCAACGAAGTGAAGCTCAGTGTGAGTGAAACATTGAACCCCCATCTTC
66 CAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTGAGTGAAAC-TTGAACCCCCATCTTC
* * * ** *
329525 TTGATGAGATACAGAGAAGTGGGTCAAAGCAATAACGAGGTCACCTTCCTGATGAGATATAGAGA
130 TTGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGCGGTCGTCTTCCTGATGAGATACAGAGA
329590 AGTGGACCAAATCCG
195 AGTGGACCAAATCCG
* * * * * *
329605 TTTTCCTGATGAGATACAAAGAAATGGATTAAAATAAATTAGGCAGTCATCTTCCTGATGAGATA
1 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAAATGAGGCGGTCATCTTCCTGATGAGATA
* * * *
329670 CAGAGAAGTAAACCAAATC-----A---AAGCTCAATGTGAGTGAAACTTCAACCCCCGTCTTCC
66 CAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTGAGTGAAACTTGAACCCCCATCTTCT
* * * *
329727 TGATGAGATACTGAGAAGTAGGTCAAAGAAATAAAGCGGTTGTCTTCCTGATGAGATACAAAGAA
131 TGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGCGGTCGTCTTCCTGATGAGATACAGAGAA
*
329792 GTGGACCAAATTCG
196 GTGGACCAAATCCG
* * * *
329806 TCTTCCTGATTAGATACAAAGAAGTGGATTAAAACAAATGAGGCGATCATCTTCCTAATGAGATA
1 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAAATGAGGCGGTCATCTTCCTGATGAGATA
* * * * * * * *
329871 CAGAGAAGTAAACCAAATCAATAAAGCAAAGATCAATGTGAGTGAAACTTCAAACCCTATCTTCC
66 CAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTGAGTGAAACTTGAACCCCCATCTTCT
* * * *
329936 TGATGAGATACTGAGAAATGGGTCAAAGCAATAAAGCGATCGTCTTTCTGATGAGATACAGAAAA
131 TGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGCGGTCGTCTTCCTGATGAGATACAGAGAA
*
330001 GTGGACCAAATCTG
196 GTGGACCAAATCCG
* *
330015 TCTT-TTCGATGAGATACAGAGAAGTGGATTAAAACAAATGAGGCAGTCATCTTCCTGATGAGAT
1 TCTTCCT-GATGAGATACAGAGAAGTGGATTAAAACAAATGAGGCGGTCATCTTCCTGATGAGAT
* * * *
330079 ACAGAGAAGTAAACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTC
65 ACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTGAGTGAAACTTGAACCCCCATCTTC
* *
330144 TTGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGCGGTCGTCTCCCTGATGAGATACAAAGA
130 TTGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGCGGTCGTCTTCCTGATGAGATACAGAGA
*
330209 AGTAGG-CCAAATCCA
195 AGT-GGACCAAATCCG
* * * *
330224 TCTTCTTGATGAGATACAGAGAAGTGGATTAAAACAAATGAGACGGTCATCTTCCTAAAGAGATA
1 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAAATGAGGCGGTCATCTTCCTGATGAGATA
* * * *
330289 CAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATATGAGTAAAACTTCGAACCCTCATCTTC
66 CAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTGAGTGAAACTT-GAACCCCCATCTTC
* * * *
330354 CTGATGAGATATTGAGATGTGGGTCAAAGAAATAAAGCGGTCGTCTTCCTGATGAGATACAGAGA
130 TTGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGCGGTCGTCTTCCTGATGAGATACAGAGA
*
330419 AGTGGACCAAATCCA
195 AGTGGACCAAATCCG
* * * *
330434 TATTCTTGATGAGATACAGAGAAGTGGATTAAAACAAAAGAGGTGGTCATCTTCCTGATGAGATA
1 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAAATGAGGCGGTCATCTTCCTGATGAGATA
* * * * *
330499 CAGAGAAGTAGACCAAATCGATGAAGCGAACCTCAATGTTAGTAAAACTTCGAA-CCTCATCTTC
66 CAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTGAGTGAAACTT-GAACCCCCATCTTC
* * * * * * **
330563 TTGATGAGATA-TAGAGAAGTGGATCAAAACAATGAAGTGGTCATCTTCCTAATGAGATATTGAG
130 TTGATGAGATACT-GAGAAGTGGGTCAAAGCAATAAAGCGGTCGTCTTCCTGATGAGATACAGAG
*
330627 AAGTAGACCAA
194 AAGTGGACCAA
330638 GAAAAGAAGC
Statistics
Matches: 1097, Mismatches: 128, Indels: 35
0.87 0.10 0.03
Matches are distributed among these distances:
201 158 0.14
202 19 0.02
205 1 0.00
206 1 0.00
207 1 0.00
208 35 0.03
209 534 0.49
210 348 0.32
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.23
Consensus pattern (209 bp):
TCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAAATGAGGCGGTCATCTTCCTGATGAGATA
CAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTGAGTGAAACTTGAACCCCCATCTTCT
TGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGCGGTCGTCTTCCTGATGAGATACAGAGAA
GTGGACCAAATCCG
Found at i:331928 original size:30 final size:30
Alignment explanation
Indices: 331894--332250 Score: 342
Period size: 30 Copynumber: 12.0 Consensus size: 30
331884 AATAGATCCC
* * *
331894 TAAACTTTCCAAAAATCATATTTTAACCCT
1 TAAACTTTCCTAAAATTACATTTTAACCCT
*
331924 TAAAC-TTCTCTAAAATTATATTTTAACCCT
1 TAAACTTTC-CTAAAATTACATTTTAACCCT
331954 TAAA-TAATT-CTAAAATTACATTTTAACCCT
1 TAAACT--TTCCTAAAATTACATTTTAACCCT
* *
331984 TCAAACTTTTCTAAAATTGA-A-TTTAACCCC
1 T-AAACTTTCCTAAAATT-ACATTTTAACCCT
332014 TAAACTTTTCC-AAAATTACATTTTAACCCT
1 TAAAC-TTTCCTAAAATTACATTTTAACCCT
* *
332044 TAAACTTTTCTAAAATTACATTTCAACCCT
1 TAAACTTTCCTAAAATTACATTTTAACCCT
* *
332074 TAAAATTTTCTAAAATTACATTTTAACACC-
1 TAAACTTTCCTAAAATTACATTTTAAC-CCT
* * *
332104 TAAACTTTTCT-AAATTGCATTTCAACCCT
1 TAAACTTTCCTAAAATTACATTTTAACCCT
*
332133 TAAACTTTTCC-AAAATTACATTTTAACCCC
1 TAAAC-TTTCCTAAAATTACATTTTAACCCT
* * * *
332163 TAAACTTCTCC-AAAATCATATTTTTATCCT
1 TAAACTT-TCCTAAAATTACATTTTAACCCT
*
332193 TAAACCTTCC-AAAATTACATTTTAACCCT
1 TAAACTTTCCTAAAATTACATTTTAACCCT
** *
332222 CGAACTTCTCC-AAAATCACATTTTAACCC
1 TAAACTT-TCCTAAAATTACATTTTAACCC
332251 CGTATTCTCC
Statistics
Matches: 278, Mismatches: 31, Indels: 36
0.81 0.09 0.10
Matches are distributed among these distances:
28 3 0.01
29 60 0.22
30 197 0.71
31 14 0.05
32 4 0.01
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.38
Consensus pattern (30 bp):
TAAACTTTCCTAAAATTACATTTTAACCCT
Found at i:332148 original size:59 final size:60
Alignment explanation
Indices: 331894--332250 Score: 386
Period size: 59 Copynumber: 6.0 Consensus size: 60
331884 AATAGATCCC
* * * * *
331894 TAAAC-TTTCCAAAAATCATATTTTAACCCTTAAACTTCTCTAAAATTATATTTTAACCCT
1 TAAACTTTTCC-AAAATTACATTTTAACCCTTAAACTTTTCTAAAATTACATTTCAACCCT
* * *
331954 TAAA-TAATTCTAAAATTACATTTTAACCCTTCAAACTTTTCTAAAATTGA-ATTT-AACCCC
1 TAAACT-TTTCCAAAATTACATTTTAACCCTT-AAACTTTTCTAAAATT-ACATTTCAACCCT
332014 TAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCTAAAATTACATTTCAACCCT
1 TAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCTAAAATTACATTTCAACCCT
* * *
332074 TAAAATTTTCTAAAATTACATTTTAACACC-TAAACTTTTCT-AAATTGCATTTCAACCCT
1 TAAACTTTTCCAAAATTACATTTTAAC-CCTTAAACTTTTCTAAAATTACATTTCAACCCT
* * * * * ** *
332133 TAAACTTTTCCAAAATTACATTTTAACCCCTAAACTTCTCCAAAATCATATTTTTATCCT
1 TAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCTAAAATTACATTTCAACCCT
* ** * * * *
332193 TAAAC-CTTCCAAAATTACATTTTAACCCTCGAACTTCTCCAAAATCACATTTTAACCC
1 TAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCTAAAATTACATTTCAACCC
332251 CGTATTCTCC
Statistics
Matches: 258, Mismatches: 29, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
58 3 0.01
59 117 0.45
60 112 0.43
61 25 0.10
62 1 0.00
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.38
Consensus pattern (60 bp):
TAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCTAAAATTACATTTCAACCCT
Done.