Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 1 of 228
Found at i:97 original size:33 final size:35
Alignment explanation
Indices: 36--100 Score: 107
Period size: 33 Copynumber: 1.9 Consensus size: 35
26 CATCACAATC
36 CCACCGGGTCCTAGAACCAAAATCAAGCAACAACT
1 CCACCGGGTCCTAGAACCAAAATCAAGCAACAACT
*
71 CCACC-GGTTCTAGAACC-AAATCAAGCAACA
1 CCACCGGGTCCTAGAACCAAAATCAAGCAACA
101 CAATGCAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 13 0.45
34 11 0.38
35 5 0.17
ACGTcount: A:0.40, C:0.34, G:0.14, T:0.12
Consensus pattern (35 bp):
CCACCGGGTCCTAGAACCAAAATCAAGCAACAACT
Found at i:2864 original size:230 final size:230
Alignment explanation
Indices: 2458--2980 Score: 700
Period size: 230 Copynumber: 2.3 Consensus size: 230
2448 CATATTAGCA
* * * * * *
2458 AAAAGAAGCATATGTCAACTAAAAAC--AGAGGAATAGTATTCTGCTAAGCAGAAATTACAAAAA
1 AAAAGAAGAATATATCAACTAAAAACAGAGAGGAAAAGTATTCTGCTCAGCAGATATTAAAAAAA
* * * * * * * * *
2521 TATT-ATAAAGATACTATCCTGAGT-TCTGAGAGCAA-AGGAACTAGTGTAATGTTATTTGGAAA
66 TCTTAATATAGATATTTTCTTCAGTGT-TGGGAGGAATA-GAACTAGTGTAATGTTAATTGGAAA
* * **
2583 ATGAACTATAATGACAAAAATATAAATGATAAGCCGAAATCTAAGCGTGATTTGGGCCCAAAAAA
129 ATGAACTATAATGACAAAAATATAAATGAAAAGCCAAAATCTAAGCGTGATTCAGGCCCAAAAAA
*
2648 ACCAAACCACAAAATTATTCTACTAAGCAAAAACAAG
194 ACCAAACCACAAAATTACTCTACTAAGCAAAAACAAG
* *
2685 AAAAGAAGAATATATTAACTAAAAACAGAGAGGAAAATTATTCTGCTCAGC-GAATATTAAAAAA
1 AAAAGAAGAATATATCAACTAAAAACAGAGAGGAAAAGTATTCTGCTCAGCAG-ATATTAAAAAA
*
2749 ATCTTAATATAGATATTTTCTTCAGTGTTGGGAGGAATAGAACTAGTGTCATGTTAATTGGAAAA
65 ATCTTAATATAGATATTTTCTTCAGTGTTGGGAGGAATAGAACTAGTGTAATGTTAATTGGAAAA
* * *
2814 -GTAACTATAATGACAAAAATATAAATGAAAAGCCAAAATCTAATCGTGATTCAGGCTCAAAAAC
130 TG-AACTATAATGACAAAAATATAAATGAAAAGCCAAAATCTAAGCGTGATTCAGGCCCAAAAAA
* *
2878 ACCAAACCCCAAAATTACTCTGCTAAGCAAAAACAAG
194 ACCAAACCACAAAATTACTCTACTAAGCAAAAACAAG
*
2915 AAAAGAAGAATATATCAACTAAAAACAGAGAGGAAAAGTATTCTGCTCAGCAGATATTACAAAAA
1 AAAAGAAGAATATATCAACTAAAAACAGAGAGGAAAAGTATTCTGCTCAGCAGATATTAAAAAAA
2980 T
66 T
2981 TATTCTGCTA
Statistics
Matches: 257, Mismatches: 31, Indels: 13
0.85 0.10 0.04
Matches are distributed among these distances:
227 23 0.09
228 1 0.00
229 34 0.13
230 196 0.76
231 3 0.01
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.23
Consensus pattern (230 bp):
AAAAGAAGAATATATCAACTAAAAACAGAGAGGAAAAGTATTCTGCTCAGCAGATATTAAAAAAA
TCTTAATATAGATATTTTCTTCAGTGTTGGGAGGAATAGAACTAGTGTAATGTTAATTGGAAAAT
GAACTATAATGACAAAAATATAAATGAAAAGCCAAAATCTAAGCGTGATTCAGGCCCAAAAAAAC
CAAACCACAAAATTACTCTACTAAGCAAAAACAAG
Found at i:6467 original size:28 final size:29
Alignment explanation
Indices: 6414--6471 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
6404 TTTACATAAA
6414 TTTTAAAATTAAAAAAACTATAAAAATTAT
1 TTTTAAAATT-AAAAAACTATAAAAATTAT
* *
6444 TTTTAAAATT-AAAAATTATTAAAATTAT
1 TTTTAAAATTAAAAAACTATAAAAATTAT
6472 AAAATGTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 16 0.62
30 10 0.38
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (29 bp):
TTTTAAAATTAAAAAACTATAAAAATTAT
Found at i:11396 original size:21 final size:20
Alignment explanation
Indices: 11365--11423 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 20
11355 TCCATACGCA
11365 AAAAAATCTGAACCGGACACC
1 AAAAAATCTGAACCGGACA-C
11386 AAAACAA-CTGAACCGGACAC
1 AAAA-AATCTGAACCGGACAC
11406 AAAAAATTCTGAACCGGA
1 AAAAAA-TCTGAACCGGA
11424 ACGGAATTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 26 0.74
22 2 0.06
ACGTcount: A:0.49, C:0.25, G:0.15, T:0.10
Consensus pattern (20 bp):
AAAAAATCTGAACCGGACAC
Found at i:16122 original size:19 final size:20
Alignment explanation
Indices: 16086--16124 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
16076 ACCTTAAAAA
16086 TTTAAATTATATTAAATTTT
1 TTTAAATTATATTAAATTTT
16106 TTTAAACTTAT-TT-AATTTT
1 TTTAAA-TTATATTAAATTTT
16125 AAAACAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 8 0.44
21 4 0.22
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTAAATTATATTAAATTTT
Found at i:20209 original size:3 final size:3
Alignment explanation
Indices: 20201--20238 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
20191 CTCAATAAAT
*
20201 TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20239 TCTTCCTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:32072 original size:16 final size:17
Alignment explanation
Indices: 32038--32073 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
32028 ACCACAAAAT
32038 ATTTGAAAGAACATAAA
1 ATTTGAAAGAACATAAA
*
32055 ATTTGAAAG-ACTTAAA
1 ATTTGAAAGAACATAAA
32071 ATT
1 ATT
32074 AACTAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.53, C:0.06, G:0.11, T:0.31
Consensus pattern (17 bp):
ATTTGAAAGAACATAAA
Found at i:36116 original size:46 final size:45
Alignment explanation
Indices: 36046--36279 Score: 240
Period size: 36 Copynumber: 5.6 Consensus size: 45
36036 TTTGAGTACT
* *
36046 TCTGATCAAGAGACAAAGTAATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
36092 TCTGATCAAGTGACAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
36128 TCTGATCAA-TATACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGT-GACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
36174 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
36210 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
36255 TCTGATC-AGGGACAAA-TGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
36280 ATCATACGTA
Statistics
Matches: 160, Mismatches: 7, Indels: 45
0.75 0.03 0.21
Matches are distributed among these distances:
35 1 0.01
36 61 0.38
37 4 0.03
40 4 0.03
42 4 0.03
43 9 0.06
44 8 0.05
45 20 0.12
46 48 0.30
47 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:36144 original size:82 final size:81
Alignment explanation
Indices: 36046--36279 Score: 368
Period size: 82 Copynumber: 2.9 Consensus size: 81
36036 TTTGAGTACT
* *
36046 TCTGATCAAGAGACAAAGTAATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAATA-ACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
36111 GATAAGTGCTACACTTA
65 GATAAGTGCTACACTTA
*
36128 TCTGATCAATATACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAATA-ACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
36193 GATAAGTGCTACACTTA
65 GATAAGTGCTACACTTA
*
36210 TCTGATCAAGTGAA-AAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATC-AGGGACAAA-
1 TCTGATCAA-T-AACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAG
36271 TGATAAGTG
64 TGATAAGTG
36280 ATCATACGTA
Statistics
Matches: 144, Mismatches: 6, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
79 9 0.06
80 7 0.05
81 20 0.14
82 105 0.73
83 2 0.01
84 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.29
Consensus pattern (81 bp):
TCTGATCAATAACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTG
ATAAGTGCTACACTTA
Found at i:41664 original size:21 final size:21
Alignment explanation
Indices: 41638--41678 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41628 ATCTGCTCAA
* *
41638 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGATGTGGAGTAC
41659 ACTCCACCTGATGTGGAGTA
1 ACTCCACCTGATGTGGAGTA
41679 TTGCTTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGATGTGGAGTAC
Found at i:49686 original size:4 final size:4
Alignment explanation
Indices: 49677--49749 Score: 119
Period size: 4 Copynumber: 18.2 Consensus size: 4
49667 ATCTCCCTCA
* * *
49677 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTTT GTTT ATAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
49725 GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT G
49750 ACTGGATTCA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 65 1.00
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.52
Consensus pattern (4 bp):
GTAT
Found at i:52679 original size:24 final size:24
Alignment explanation
Indices: 52633--52697 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
52623 TTATCCCTCT
* * * *
52633 AATAATATAGTATTTCTTTTTTATA
1 AATAAT-TAATATTTATTGTTTAAA
52658 AATAATTAATATTTATTGTTTAAA
1 AATAATTAATATTTATTGTTTAAA
* *
52682 AATATTTAAAATTTAT
1 AATAATTAATATTTAT
52698 ATTTCATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 28 0.82
25 6 0.18
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (24 bp):
AATAATTAATATTTATTGTTTAAA
Found at i:57014 original size:22 final size:23
Alignment explanation
Indices: 56988--57030 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
56978 ATTTAGAATT
*
56988 TAAAC-TAAAATGATAAATTTTG
1 TAAACATAAAAGGATAAATTTTG
*
57010 TAAACATTAAAGGATAAATTT
1 TAAACATAAAAGGATAAATTT
57031 GTTGAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (23 bp):
TAAACATAAAAGGATAAATTTTG
Found at i:61848 original size:268 final size:261
Alignment explanation
Indices: 61362--61892 Score: 990
Period size: 268 Copynumber: 2.0 Consensus size: 261
61352 AGTTTAGTTG
61362 ATACATGGAAAAAAAGAGTTCAGGTTGAGTTGGATGCTAAATACGGTCCAAATCAGTCTGTTCCC
1 ATACATGGAAAAAAAGAGTTCAGGTTGAGTTGGATGCTAAATACGGTCCAAATCAGTCTGTTCCC
61427 TGGTCTGACGTTGCTAAATGTGGAATCAAGCACTATAGACCTTCTGAGGTGAAGAGTTCAGCAAC
66 TGGTCTGACGTTGCTAAATGTGGAATCAAGCACTATAGACCTTCTGAGGTGAAGAGTTCAGCAAC
61492 ACAATTCTCTGCAACTAAAACTGGTTTTGTTAAGCTTTTTCAAGGAGGGACTGCAACCAAGTCTG
131 ACAATTCTCTGCAACTAAAACTGGTTTTGTTAAGCTTTTTCAAGGAGGGACTGCAACCAAGTCTG
61557 CTTCTGCAATGCCGGTACCTATGAAGGCATCAACATTGCCTGCTTCAGCCAGAACAAAGGCGCGG
196 CTTCTGCAATGCCGGTACCTATGAAGGCATCAACATTGCCTGCTTCAGCCAGAACAAAGGCGCGG
61622 A
261 A
61623 ATACATGGAAAAAAAAGAGTTCAGGTTGAGTTGGATGCTAAATACGGTCCAAATCAGTCTGTTCC
1 ATACATGG-AAAAAAAGAGTTCAGGTTGAGTTGGATGCTAAATACGGTCCAAATCAGTCTGTTCC
*
61688 CTGGTCTGATGTTGCTAAATGTGGAATCAAGCACTATAGACCTTCTGAGGTTGCAGTGAAGAGTT
65 CTGGTCTGACGTTGCTAAATGTGGAATCAAGCACTATAGACCTTCTGA----G--GTGAAGAGTT
61753 CAGCAACACAATTCTCTGCAACTAAAACTGGTTTTGTTAAGCTTTTTCAAGGAGGGACTGCAACC
124 CAGCAACACAATTCTCTGCAACTAAAACTGGTTTTGTTAAGCTTTTTCAAGGAGGGACTGCAACC
61818 AAGTCTGCTTCTGCAATGCCGGTACCTATGAAGGCATCAACATTGCCTGCTTCAGCCAGAACAAA
189 AAGTCTGCTTCTGCAATGCCGGTACCTATGAAGGCATCAACATTGCCTGCTTCAGCCAGAACAAA
61883 GGCGCGGA
254 GGCGCGGA
61891 AT
1 AT
61893 GCTACTATTG
Statistics
Matches: 262, Mismatches: 1, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
261 8 0.03
262 103 0.39
266 1 0.00
268 150 0.57
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (261 bp):
ATACATGGAAAAAAAGAGTTCAGGTTGAGTTGGATGCTAAATACGGTCCAAATCAGTCTGTTCCC
TGGTCTGACGTTGCTAAATGTGGAATCAAGCACTATAGACCTTCTGAGGTGAAGAGTTCAGCAAC
ACAATTCTCTGCAACTAAAACTGGTTTTGTTAAGCTTTTTCAAGGAGGGACTGCAACCAAGTCTG
CTTCTGCAATGCCGGTACCTATGAAGGCATCAACATTGCCTGCTTCAGCCAGAACAAAGGCGCGG
A
Found at i:75356 original size:6 final size:6
Alignment explanation
Indices: 75347--75389 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
75337 TGGTCCTCAT
* * *
75347 CTCCAC CTCCAC CACCAC CACCAC CTCCAC CTCCTC C-CCAC CT
1 CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC CT
75390 TTCTCCAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.19, C:0.67, G:0.00, T:0.14
Consensus pattern (6 bp):
CTCCAC
Found at i:75367 original size:9 final size:9
Alignment explanation
Indices: 75349--75389 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
75339 GTCCTCATCT
75349 CCACCTCCA
1 CCACCTCCA
*
75358 CCACCACCA
1 CCACCTCCA
75367 CCACCTCCA
1 CCACCTCCA
*
75376 CCTCCTCC-
1 CCACCTCCA
75384 CCACCT
1 CCACCT
75390 TTCTCCAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
8 5 0.18
9 23 0.82
ACGTcount: A:0.20, C:0.68, G:0.00, T:0.12
Consensus pattern (9 bp):
CCACCTCCA
Found at i:76948 original size:13 final size:12
Alignment explanation
Indices: 76930--76963 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
76920 TAATATTGGC
76930 ATAAATTTTAATT
1 ATAAATTTTAA-T
*
76943 ATAAATATTAAT
1 ATAAATTTTAAT
76955 ATAAATTTT
1 ATAAATTTT
76964 TTTAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATAAATTTTAAT
Found at i:95552 original size:18 final size:18
Alignment explanation
Indices: 95508--95551 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
95498 TTTACTTCAC
95508 TTTCTTGTTTCTTTTCTTT
1 TTTCTT-TTTCTTTTCTTT
95527 TTTCTTTTTCTTTT-TTT
1 TTTCTTTTTCTTTTCTTT
95544 TTT-TTTTT
1 TTTCTTTTT
95552 TGGTTCTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.20
17 6 0.24
18 8 0.32
19 6 0.24
ACGTcount: A:0.00, C:0.11, G:0.02, T:0.86
Consensus pattern (18 bp):
TTTCTTTTTCTTTTCTTT
Found at i:99001 original size:26 final size:26
Alignment explanation
Indices: 98945--99001 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
98935 ACAAGTGGGA
*
98945 ATTTTAAGTAAAACGGAGAGTTTTGG
1 ATTTTAAGTAAAACGGAGAGTTTTGC
* * * * *
98971 GTTTTAAGTTATACGGGGCGTTTTGC
1 ATTTTAAGTAAAACGGAGAGTTTTGC
98997 ATTTT
1 ATTTT
99002 TGTTATAACT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.07, G:0.26, T:0.42
Consensus pattern (26 bp):
ATTTTAAGTAAAACGGAGAGTTTTGC
Found at i:104895 original size:115 final size:115
Alignment explanation
Indices: 104693--104927 Score: 470
Period size: 115 Copynumber: 2.0 Consensus size: 115
104683 CCTCTAAAAT
104693 AGGTATGCTAGAATATGTAACACTCGACCACCAATCAGTCATGTTTATTCAAGACGATAAATTTG
1 AGGTATGCTAGAATATGTAACACTCGACCACCAATCAGTCATGTTTATTCAAGACGATAAATTTG
104758 ACCCCTAGTCAATCTGATTTTAGTATCGACCTTCCCATTGTCCTATGTAA
66 ACCCCTAGTCAATCTGATTTTAGTATCGACCTTCCCATTGTCCTATGTAA
104808 AGGTATGCTAGAATATGTAACACTCGACCACCAATCAGTCATGTTTATTCAAGACGATAAATTTG
1 AGGTATGCTAGAATATGTAACACTCGACCACCAATCAGTCATGTTTATTCAAGACGATAAATTTG
104873 ACCCCTAGTCAATCTGATTTTAGTATCGACCTTCCCATTGTCCTATGTAA
66 ACCCCTAGTCAATCTGATTTTAGTATCGACCTTCCCATTGTCCTATGTAA
104923 AGGTA
1 AGGTA
104928 AACGACAGTG
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 120 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (115 bp):
AGGTATGCTAGAATATGTAACACTCGACCACCAATCAGTCATGTTTATTCAAGACGATAAATTTG
ACCCCTAGTCAATCTGATTTTAGTATCGACCTTCCCATTGTCCTATGTAA
Found at i:106975 original size:22 final size:22
Alignment explanation
Indices: 106949--107005 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
106939 TCAATGGTTT
106949 ATTTTGCACACC-CTTAGTTTGC
1 ATTTTGCA-ACCACTTAGTTTGC
* *
106971 GTTTTGCAACCAGTTTAGTTTGC
1 ATTTTGCAACCA-CTTAGTTTGC
106994 ATTTTGCAACCA
1 ATTTTGCAACCA
107006 GCTCAAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.10
22 7 0.23
23 20 0.67
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (22 bp):
ATTTTGCAACCACTTAGTTTGC
Found at i:106991 original size:23 final size:23
Alignment explanation
Indices: 106962--107006 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
106952 TTGCACACCC
*
106962 TTAGTTTGCGTTTTGCAACCAGT
1 TTAGTTTGCATTTTGCAACCAGT
106985 TTAGTTTGCATTTTGCAACCAG
1 TTAGTTTGCATTTTGCAACCAG
107007 CTCAAAATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (23 bp):
TTAGTTTGCATTTTGCAACCAGT
Found at i:108651 original size:5 final size:5
Alignment explanation
Indices: 108643--108668 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
108633 GTATCCTATC
108643 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
108669 GCTAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:109982 original size:93 final size:93
Alignment explanation
Indices: 109823--110008 Score: 354
Period size: 93 Copynumber: 2.0 Consensus size: 93
109813 TCAAATGTAA
109823 ACAGCATATGTTAAGTCAAAATGGAACTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
1 ACAGCATATGTTAAGTCAAAATGGAACTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
109888 TTAAGATTCATCAATTAAACAAAAATTC
66 TTAAGATTCATCAATTAAACAAAAATTC
*
109916 ACAGCATATGTTAAGTCAAAATGGATCTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
1 ACAGCATATGTTAAGTCAAAATGGAACTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
*
109981 TTGAGATTCATCAATTAAACAAAAATTC
66 TTAAGATTCATCAATTAAACAAAAATTC
110009 CAAGAAACTA
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 91 1.00
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.24
Consensus pattern (93 bp):
ACAGCATATGTTAAGTCAAAATGGAACTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
TTAAGATTCATCAATTAAACAAAAATTC
Found at i:113435 original size:10 final size:11
Alignment explanation
Indices: 113422--113451 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
113412 TTTTCATATG
113422 TTTTATTTTC-
1 TTTTATTTTCA
113432 TTTTATTTTCA
1 TTTTATTTTCA
113443 TTTTATTTT
1 TTTTATTTT
113452 GTTTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:114088 original size:19 final size:19
Alignment explanation
Indices: 114066--114108 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
114056 CGCATATTTT
114066 TATATGTAATATATATATG
1 TATATGTAATATATATATG
* * * *
114085 TATATTTTATTTTTATATG
1 TATATGTAATATATATATG
114104 TATAT
1 TATAT
114109 AATTTTAAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (19 bp):
TATATGTAATATATATATG
Found at i:117748 original size:17 final size:17
Alignment explanation
Indices: 117726--117760 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
117716 TAATTTTCTC
117726 TCTTTGATTTTAGTGTA
1 TCTTTGATTTTAGTGTA
117743 TCTTTGATTTTAGTGTA
1 TCTTTGATTTTAGTGTA
117760 T
1 T
117761 GACTCGGAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.06, G:0.17, T:0.60
Consensus pattern (17 bp):
TCTTTGATTTTAGTGTA
Found at i:128860 original size:22 final size:22
Alignment explanation
Indices: 128833--128876 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
128823 TAGATAACTT
128833 TGTTGAAGATAAAATTTTAAAA
1 TGTTGAAGATAAAATTTTAAAA
128855 TGTTGAAGATAAAATTTTAAAA
1 TGTTGAAGATAAAATTTTAAAA
128877 GTCAATACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (22 bp):
TGTTGAAGATAAAATTTTAAAA
Found at i:130197 original size:26 final size:26
Alignment explanation
Indices: 130163--130214 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
130153 CATACAATAC
*
130163 AAAAAAATTAACAAATATTAATATAT
1 AAAAAAATTAACAAATACTAATATAT
130189 AAAAAAATTAACAAATACTAATATAT
1 AAAAAAATTAACAAATACTAATATAT
130215 GTTTGGTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (26 bp):
AAAAAAATTAACAAATACTAATATAT
Found at i:141012 original size:4 final size:4
Alignment explanation
Indices: 140999--141028 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
140989 AGTTGATGTT
140999 TTTC -TTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
141029 TTTTTTACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:143847 original size:33 final size:33
Alignment explanation
Indices: 143805--143868 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
143795 TTTTATTTTG
143805 ACATTGTTTTGGACTGTAAATATGCTACTCTTA
1 ACATTGTTTTGGACTGTAAATATGCTACTCTTA
* *
143838 ACATTGTTTTGGACTTTAAATATTCTACTCT
1 ACATTGTTTTGGACTGTAAATATGCTACTCT
143869 CTTTTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (33 bp):
ACATTGTTTTGGACTGTAAATATGCTACTCTTA
Found at i:146943 original size:13 final size:13
Alignment explanation
Indices: 146925--146953 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
146915 TTTCTTTGTG
146925 TTAAATTCACTAA
1 TTAAATTCACTAA
146938 TTAAATTCACTAA
1 TTAAATTCACTAA
146951 TTA
1 TTA
146954 GGATCCTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAATTCACTAA
Found at i:148170 original size:13 final size:14
Alignment explanation
Indices: 148144--148173 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
148134 GTATTCTTCC
148144 TTTATTTTTCCTCA
1 TTTATTTTTCCTCA
148158 TTTATTTTT-CTCA
1 TTTATTTTTCCTCA
148171 TTT
1 TTT
148174 CTTTATTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATTTTTCCTCA
Found at i:166296 original size:10 final size:10
Alignment explanation
Indices: 166281--166314 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
166271 AATTTATTTT
166281 AAAAATTAAA
1 AAAAATTAAA
166291 AAAAATTAAA
1 AAAAATTAAA
166301 AAAAATTAAA
1 AAAAATTAAA
166311 AAAA
1 AAAA
166315 GTATTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:166325 original size:12 final size:11
Alignment explanation
Indices: 166310--166375 Score: 70
Period size: 11 Copynumber: 6.4 Consensus size: 11
166300 AAAAAATTAA
166310 AAAAAGTATTTT
1 AAAAA-TATTTT
166322 AAAAATATTTT
1 AAAAATATTTT
166333 --AAA-A--TT
1 AAAAATATTTT
* *
166339 AAAAAAAATTT
1 AAAAATATTTT
166350 AAAAATATTTT
1 AAAAATATTTT
166361 AAAAATATTTT
1 AAAAATATTTT
166372 AAAA
1 AAAA
166376 TTAAAAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
6 2 0.04
8 4 0.09
9 4 0.09
11 32 0.68
12 5 0.11
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:166366 original size:80 final size:80
Alignment explanation
Indices: 166275--166423 Score: 228
Period size: 80 Copynumber: 1.9 Consensus size: 80
166265 ACCAAAAATT
*
166275 TATTTTAAAAAT-TAAAAAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATT
1 TATTTTAAAAATAT-AAAAAAATTAAAAAAAATTAAAAAAAGTATTCTAAAAATATTTTAAAATT
166339 AAAAAAAATTTAAAAA
65 AAAAAAAATTTAAAAA
*** * *
166355 TATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAAAGTATTCTAAAAGTATTTTAAAATTA
1 TATTTTAAAAATATAAAAAAATTAAAAAAAATTAAAAAAAGTATTCTAAAAATATTTTAAAATTA
166420 AAAA
66 AAAA
166424 TTAAAAAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
80 61 0.98
81 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (80 bp):
TATTTTAAAAATATAAAAAAATTAAAAAAAATTAAAAAAAGTATTCTAAAAATATTTTAAAATTA
AAAAAAATTTAAAAA
Found at i:166394 original size:11 final size:11
Alignment explanation
Indices: 166281--166375 Score: 60
Period size: 11 Copynumber: 9.1 Consensus size: 11
166271 AATTTATTTT
166281 AAAAA-TTAAA
1 AAAAATTTAAA
166291 AAAAA-TTAAA
1 AAAAATTTAAA
166301 AAAAA-TTAAA
1 AAAAATTTAAA
*
166311 AAAAGTATTTTAA
1 AAAA--ATTTAAA
*
166324 AAATATTT---
1 AAAAATTTAAA
*
166332 TAAAA-TTAAA
1 AAAAATTTAAA
166342 AAAAATTTAAA
1 AAAAATTTAAA
* *
166353 AATATTTTAAA
1 AAAAATTTAAA
* *
166364 AATATTTTAAA
1 AAAAATTTAAA
166375 A
1 A
166376 TTAAAAAAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
7 2 0.03
8 3 0.04
10 28 0.39
11 30 0.42
12 1 0.01
13 7 0.10
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (11 bp):
AAAAATTTAAA
Found at i:166405 original size:41 final size:41
Alignment explanation
Indices: 166292--166439 Score: 207
Period size: 39 Copynumber: 3.7 Consensus size: 41
166282 AAAATTAAAA
*
166292 AAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAATATTTT
1 AAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAATATTTT
166333 AAAATTAAAAAAAATTT--AAAAA-TATTTTAAAAATATTTT
1 AAAATT-AAAAAAATTTAAAAAAAGTATTTTAAAAATATTTT
* *
166372 AAAATTAAAAAAATTTAAAAAAAGTATTCTAAAAGTATTTT
1 AAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAATATTTT
* *
166413 AAAATT--AAAAATTAAAAAAAAATATTT
1 AAAATTAAAAAAATTTAAAAAAAGTATTT
166440 ATTATATTCG
Statistics
Matches: 97, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
38 10 0.10
39 41 0.42
40 10 0.10
41 27 0.28
42 9 0.09
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (41 bp):
AAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAATATTTT
Found at i:180925 original size:3 final size:3
Alignment explanation
Indices: 180917--180967 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
180907 AGAACAAAAC
* * * *
180917 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCT TCG TCT TCA TCT TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
180965 TCA
1 TCA
180968 CCCAATTGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.25, C:0.33, G:0.02, T:0.39
Consensus pattern (3 bp):
TCA
Found at i:183827 original size:28 final size:28
Alignment explanation
Indices: 183779--183845 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
183769 TTTAAATAAG
* *
183779 TAAAAGTAA-AATTATACTTTAAACTCCT
1 TAAAAATAATAATTATAATTT-AACTCCT
* *
183807 TAAAAATAATAATT-TAATTTAATTCTT
1 TAAAAATAATAATTATAATTTAACTCCT
*
183834 TAAAAATTATAA
1 TAAAAATAATAA
183846 AATATAAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
27 16 0.48
28 13 0.39
29 4 0.12
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.40
Consensus pattern (28 bp):
TAAAAATAATAATTATAATTTAACTCCT
Found at i:183865 original size:6 final size:6
Alignment explanation
Indices: 183856--183882 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
183846 AATATAAATG
183856 ATTAAA ATTAAA ATTAAA ATTAAA ATT
1 ATTAAA ATTAAA ATTAAA ATTAAA ATT
183883 TAATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
ATTAAA
Found at i:191950 original size:30 final size:30
Alignment explanation
Indices: 191915--192004 Score: 171
Period size: 30 Copynumber: 3.0 Consensus size: 30
191905 TCCCACTTTG
191915 GTACTTAAACTATCATTTTTATCCTAGTTT
1 GTACTTAAACTATCATTTTTATCCTAGTTT
*
191945 GTACTTAAACTATCATTTTTACCCTAGTTT
1 GTACTTAAACTATCATTTTTATCCTAGTTT
191975 GTACTTAAACTATCATTTTTATCCTAGTTT
1 GTACTTAAACTATCATTTTTATCCTAGTTT
192005 ACCTCCCAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.49
Consensus pattern (30 bp):
GTACTTAAACTATCATTTTTATCCTAGTTT
Found at i:193061 original size:7 final size:7
Alignment explanation
Indices: 193040--193078 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
193030 GCCTGCTGTG
193040 TATATG-
1 TATATGA
*
193046 TAAATGA
1 TATATGA
193053 TATATGA
1 TATATGA
193060 TATATGA
1 TATATGA
193067 TATATGA
1 TATATGA
193074 TATAT
1 TATAT
193079 ATGAACATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (7 bp):
TATATGA
Found at i:205605 original size:3 final size:3
Alignment explanation
Indices: 205599--205623 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
205589 ACCATCAGAA
205599 CCG CCG CCG CCG CCG CCG CCG CCG C
1 CCG CCG CCG CCG CCG CCG CCG CCG C
205624 AACCACCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.32, T:0.00
Consensus pattern (3 bp):
CCG
Found at i:207264 original size:15 final size:15
Alignment explanation
Indices: 207241--207275 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
207231 CCTTCCATCC
*
207241 GATCCCTCGCATTTA
1 GATCTCTCGCATTTA
*
207256 GATCTCTCGGATTTA
1 GATCTCTCGCATTTA
207271 GATCT
1 GATCT
207276 GACCATAGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (15 bp):
GATCTCTCGCATTTA
Found at i:207758 original size:14 final size:14
Alignment explanation
Indices: 207741--207768 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
207731 TTCAACCCCG
207741 AAAATCAATGGCCT
1 AAAATCAATGGCCT
207755 AAAATCAATGGCCT
1 AAAATCAATGGCCT
207769 GGAAAGCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (14 bp):
AAAATCAATGGCCT
Found at i:215348 original size:12 final size:12
Alignment explanation
Indices: 215331--215363 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
215321 ATGTTGAGAT
215331 ACAGAAGAAAAG
1 ACAGAAGAAAAG
215343 ACAGAAGAAAAG
1 ACAGAAGAAAAG
215355 ACAGAAGAA
1 ACAGAAGAA
215364 TTTTAAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.67, C:0.09, G:0.24, T:0.00
Consensus pattern (12 bp):
ACAGAAGAAAAG
Found at i:216287 original size:23 final size:25
Alignment explanation
Indices: 216261--216310 Score: 77
Period size: 23 Copynumber: 2.1 Consensus size: 25
216251 ATTCAAAAAA
*
216261 TTTTATTTTTATGTA-TTTATG-AT
1 TTTTATTTTTATCTATTTTATGTAT
216284 TTTTATTTTTATCTATTTTATGTAT
1 TTTTATTTTTATCTATTTTATGTAT
216309 TT
1 TT
216311 ATGTGTATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 14 0.58
24 6 0.25
25 4 0.17
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.72
Consensus pattern (25 bp):
TTTTATTTTTATCTATTTTATGTAT
Found at i:216538 original size:30 final size:28
Alignment explanation
Indices: 216504--216576 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 28
216494 AGCCAGTGCT
*
216504 CAAATAAAACAATTTTGAAGCA-TTAATAAC
1 CAAATAAAAC-ATTTT-AA-AATTTAATAAC
*
216534 CAAATTATAACATTTTAAAATTTAATAAC
1 CAAA-TAAAACATTTTAAAATTTAATAAC
216563 CAAAATAAAA-ATTT
1 C-AAATAAAACATTT
216577 AAGTATGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
28 5 0.14
29 15 0.41
30 12 0.32
31 5 0.14
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.32
Consensus pattern (28 bp):
CAAATAAAACATTTTAAAATTTAATAAC
Found at i:217466 original size:21 final size:23
Alignment explanation
Indices: 217436--217478 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
217426 AATAAAATTT
*
217436 AAATATTAAA-TA-ATTTATTAA
1 AAATAATAAATTATATTTATTAA
217457 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
217479 TATTAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 2 0.11
23 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATAATAAATTATATTTATTAA
Found at i:218081 original size:29 final size:28
Alignment explanation
Indices: 218049--218109 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
218039 AAAGCCGTTT
218049 TTTTTTCAAAATTTACCAAAATGGGCCGA
1 TTTTTTCAAAATTTACCAAAATGGGCC-A
* ** * *
218078 TTTTTTGATTATTTACCAGAATGGTCCA
1 TTTTTTCAAAATTTACCAAAATGGGCCA
218106 TTTT
1 TTTT
218110 CCAGAAAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (28 bp):
TTTTTTCAAAATTTACCAAAATGGGCCA
Found at i:218553 original size:124 final size:124
Alignment explanation
Indices: 218328--218618 Score: 530
Period size: 124 Copynumber: 2.3 Consensus size: 124
218318 TTATTTTGAG
*
218328 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCGCCCTCGAGGATGCTAATTGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCGCCCTCGTGGATGCTAATTGAGAAGAAATTGT
*
218392 GAAATCGTGCCCTCGTGGATGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
65 GAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
*
218452 TTGATGTTTCTGAGCAAATAGTATAAAATCGCGCCCTCGTGGATGCTAATTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCGCCCTCGTGGATGCTAATTGAGAAGAAATTGTG
*
218517 AAATCGTGCCCTCGTGGACGCGATTTCGCTATAGTTGGTCATGTAAGAAATAATTTTTT
66 AAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
218576 TTGACGTTTCTGAGCAAATAGTATAAAATCGCGCCCTCGTGGA
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCGCCCTCGTGGA
218619 CGCGATTTTG
Statistics
Matches: 161, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
124 160 0.99
125 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.32
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCGCCCTCGTGGATGCTAATTGAGAAGAAATTGTG
AAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
Found at i:220493 original size:29 final size:29
Alignment explanation
Indices: 220451--220515 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
220441 GCCATTGATG
*
220451 AAAATATAAAAAAAA-TTAAAATTATTTTA
1 AAAAAATAAAAAAAATTTAAAATTA-TTTA
* *
220480 AAAAAATATAAAAAATTTGAAATTATTTA
1 AAAAAATAAAAAAAATTTAAAATTATTTA
220509 AAAAAAT
1 AAAAAAT
220516 GAAATTGAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 24 0.75
30 8 0.25
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (29 bp):
AAAAAATAAAAAAAATTTAAAATTATTTA
Found at i:220497 original size:20 final size:20
Alignment explanation
Indices: 220459--220497 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
220449 TGAAAATATA
*
220459 AAAAAAATTAAAATTATTTT
1 AAAAAAATTAAAATAATTTT
220479 AAAAAAATATAAAA-AATTT
1 AAAAAAAT-TAAAATAATTT
220498 GAAATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAAATTAAAATAATTTT
Found at i:220503 original size:30 final size:30
Alignment explanation
Indices: 220451--220515 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
220441 GCCATTGATG
220451 AAAATATAAAAAAAATTAAAATTATTTTAAA
1 AAAATATAAAAAAAATTAAAATTA-TTTAAA
* *
220482 AAAATAT-AAAAAATTTGAAATTATTTAAA
1 AAAATATAAAAAAAATTAAAATTATTTAAA
220511 AAAAT
1 AAAAT
220516 GAAATTGAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 11 0.34
30 14 0.44
31 7 0.22
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (30 bp):
AAAATATAAAAAAAATTAAAATTATTTAAA
Found at i:220574 original size:22 final size:21
Alignment explanation
Indices: 220549--220599 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 21
220539 TAATATGGAT
*
220549 TTGAGAGATTTTTGGAATGAAA
1 TTGAGAGA-TTTTGGAAGGAAA
220571 TTGAGAGGATTTTGGAAGGAAA
1 TTGAGA-GATTTTGGAAGGAAA
220593 TTGAGAG
1 TTGAGAG
220600 TTTAAGAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 24 0.89
23 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.31
Consensus pattern (21 bp):
TTGAGAGATTTTGGAAGGAAA
Found at i:220632 original size:22 final size:22
Alignment explanation
Indices: 220604--220650 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
220594 TGAGAGTTTA
220604 AGAGGATTTTGGAAGGAAATTG
1 AGAGGATTTTGGAAGGAAATTG
220626 AGAGGATTTTGGAAGGAAATTG
1 AGAGGATTTTGGAAGGAAATTG
220648 AGA
1 AGA
220651 TAGGATTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.36, T:0.26
Consensus pattern (22 bp):
AGAGGATTTTGGAAGGAAATTG
Found at i:221578 original size:21 final size:21
Alignment explanation
Indices: 221554--221594 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
221544 TTTATAATTC
*
221554 AATCAATTGAATTAATTAAAA
1 AATCAATTAAATTAATTAAAA
* *
221575 AATCGATTAAATTCATTAAA
1 AATCAATTAAATTAATTAAA
221595 TTCGTATTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (21 bp):
AATCAATTAAATTAATTAAAA
Found at i:241647 original size:4 final size:4
Alignment explanation
Indices: 241640--241682 Score: 70
Period size: 4 Copynumber: 10.8 Consensus size: 4
241630 AATGAATGAT
241640 TAAC TAAC TAAC TAAC TAAC TAAC -AGAC TAAC TAAC TAAC TAA
1 TAAC TAAC TAAC TAAC TAAC TAAC TA-AC TAAC TAAC TAAC TAA
241683 TATATCCACT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 1 0.03
4 35 0.95
5 1 0.03
ACGTcount: A:0.51, C:0.23, G:0.02, T:0.23
Consensus pattern (4 bp):
TAAC
Found at i:245971 original size:14 final size:14
Alignment explanation
Indices: 245948--245981 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
245938 TGGTATGAGT
245948 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
245961 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
245975 TTATAGG
1 TTATAGG
245982 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:246137 original size:24 final size:25
Alignment explanation
Indices: 246110--246157 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
246100 AGAAGAAAGT
246110 TTAAAGAACATAAAA-GAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAA
** *
246134 TTAAATTACTTAAAACGAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAA
246158 TGTGGGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (25 bp):
TTAAAGAACATAAAACGAAAAAAAA
Found at i:251374 original size:12 final size:12
Alignment explanation
Indices: 251350--251383 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
251340 ATTTCGAATA
251350 ATTAATGAATAAT
1 ATTAAT-AATAAT
251363 ATTAATAATAAT
1 ATTAATAATAAT
251375 ATTAATAAT
1 ATTAATAAT
251384 TATTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (12 bp):
ATTAATAATAAT
Found at i:252826 original size:37 final size:35
Alignment explanation
Indices: 252751--252826 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
252741 ATCATTGTGC
* * *
252751 CTTCATGTATTTTGTTGTGTTACTCTTGATCGTGT
1 CTTCATGTAGTTTGTTGTGTTACCCTTGATCGTAT
*
252786 CTTCATGTAGTTTGTTGTGCATTACCCTTGATTGTAT
1 CTTCATGTAGTTTGTTGTG--TTACCCTTGATCGTAT
252823 CTTC
1 CTTC
252827 GTTAATCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 18 0.51
37 17 0.49
ACGTcount: A:0.13, C:0.17, G:0.18, T:0.51
Consensus pattern (35 bp):
CTTCATGTAGTTTGTTGTGTTACCCTTGATCGTAT
Found at i:259078 original size:72 final size:70
Alignment explanation
Indices: 258876--259158 Score: 374
Period size: 72 Copynumber: 4.0 Consensus size: 70
258866 ATATAGTATT
* * * * * *
258876 TTAAACATGTAAAAAATTTAAAACTTTTTAAATTTATTTATACCAATTACACATTTAAAATA-TT
1 TTAAACATGCAAAAAATTAAAAACTTATTAAATTTATTCATACCAATCACACATTTTAAATATTT
258940 ATATA
66 ATATA
* *
258945 TTAAATATGCAAAAAAATTAAAAAC--ATTAAATTTATTCATACCTATCACACATTTTAAATATT
1 TTAAACATGC-AAAAAATTAAAAACTTATTAAATTTATTCATACCAATCACACATTTTAAATATT
259008 TATATA
65 TATATA
* * *
259014 TTAAACATGCAAAAAATTAAAAAAACTTATTGAATTTATTCATACCAACCACACATTTTTAATAT
1 TTAAACATGCAAAAAATT--AAAAACTTATTAAATTTATTCATACCAATCACACATTTTAAATAT
259079 TTATATA
64 TTATATA
* * *
259086 TTAAACATACAAAAAAAATTAAAAACTTATTAAATTTATTCAAACCAAGCACACATTTTAAATAT
1 TTAAACATGC--AAAAAATTAAAAACTTATTAAATTTATTCATACCAATCACACATTTTAAATAT
259151 TTATATA
64 TTATATA
259158 T
1 T
259159 ACATACATAC
Statistics
Matches: 188, Mismatches: 18, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
68 39 0.21
69 24 0.13
70 19 0.10
72 98 0.52
74 8 0.04
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (70 bp):
TTAAACATGCAAAAAATTAAAAACTTATTAAATTTATTCATACCAATCACACATTTTAAATATTT
ATATA
Found at i:259237 original size:27 final size:27
Alignment explanation
Indices: 259199--259252 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
259189 ATACATCGAG
259199 ACCTTTGTTTCATGTTTAAAGTTTAAT
1 ACCTTTGTTTCATGTTTAAAGTTTAAT
259226 ACCTTTGTTTCATGTTTAAAGTTTAAT
1 ACCTTTGTTTCATGTTTAAAGTTTAAT
259253 GATGACAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.52
Consensus pattern (27 bp):
ACCTTTGTTTCATGTTTAAAGTTTAAT
Found at i:265260 original size:31 final size:31
Alignment explanation
Indices: 265225--265286 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
265215 GAATTTTTTA
*
265225 AAAGGATAAACTTCAACTTGATTTAATCTAT
1 AAAGGATAAACTTCAACCTGATTTAATCTAT
265256 AAAGGATAAACTTCAACCTGATTTAATCTAT
1 AAAGGATAAACTTCAACCTGATTTAATCTAT
265287 GAACACCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.34
Consensus pattern (31 bp):
AAAGGATAAACTTCAACCTGATTTAATCTAT
Found at i:265313 original size:15 final size:15
Alignment explanation
Indices: 265293--265322 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
265283 CTATGAACAC
265293 CTTTAATCAATACAT
1 CTTTAATCAATACAT
265308 CTTTAATCAATACAT
1 CTTTAATCAATACAT
265323 GCAATTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (15 bp):
CTTTAATCAATACAT
Found at i:268211 original size:112 final size:107
Alignment explanation
Indices: 268015--268278 Score: 316
Period size: 112 Copynumber: 2.4 Consensus size: 107
268005 ACACAATTCA
* * *
268015 TTAACTTATCCAAAGTTCTATAAATATAAAATACCTTAAGCACAATACGAGAAGATACACAAATA
1 TTAACTTATCAAAAGTTCTATAAATATAAAATACCGTAAGCACAATACGAAAAGATACACAAATA
* *
268080 CGAAAAGAATACATGTAT-AACCAAATAAATCCAATCCACTG
66 CAAAAAGAATACATATATAAACCAAATAAATCCAATCCACTG
* * * *
268121 TTAACTTATCAAAAGTTCTTTAAATATAAAATATCGTAAGTACGATTATTATACGAAAATATACA
1 TTAACTTATCAAAAGTTCTATAAATATAAAATACCGTAAG--C-A-CA--ATACGAAAAGATACA
* *
268186 CAAATACAAAAAGAATACATATATAAACCAAGTAAATCCAATCGACTG
60 CAAATACAAAAAGAATACATATATAAACCAAATAAATCCAATCCACTG
* * * * *
268234 TTAACTTATCAAAAGTTGTA-AAACATAGAATACCTTAAGCGCAAT
1 TTAACTTATCAAAAGTTCTATAAATATAAAATACCGTAAGCACAAT
268279 TACAACACGA
Statistics
Matches: 132, Mismatches: 19, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
106 38 0.29
108 2 0.02
109 1 0.01
110 2 0.02
112 50 0.38
113 39 0.30
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.27
Consensus pattern (107 bp):
TTAACTTATCAAAAGTTCTATAAATATAAAATACCGTAAGCACAATACGAAAAGATACACAAATA
CAAAAAGAATACATATATAAACCAAATAAATCCAATCCACTG
Found at i:268310 original size:113 final size:113
Alignment explanation
Indices: 268056--268318 Score: 325
Period size: 112 Copynumber: 2.3 Consensus size: 113
268046 TACCTTAAGC
*
268056 ACAATACGAGAAGATACACAAATACG-AAAAGAATACATGTATAACCAAATAAATCCAATCCACT
1 ACAATACGAGAAGATACACAAATACGAAAAAGAATACATATATAACCAAATAAATCCAATCCACT
* * * * * *
268120 GTTAACTTATCAAAAGTTCTTTAAATATAAAATATCGTAAGTACGATT
66 GTTAACTTATCAAAAGTTCGTAAAACATAAAATACCGTAAGCACAATT
** * * * *
268168 ATTATACGAAAATATACACAAATAC-AAAAAGAATACATATATAAACCAAGTAAATCCAATCGAC
1 ACAATACGAGAAGATACACAAATACGAAAAAGAATACATATAT-AACCAAATAAATCCAATCCAC
* * *
268232 TGTTAACTTATCAAAAGTT-GTAAAACATAGAATACCTTAAGCGCAATT
65 TGTTAACTTATCAAAAGTTCGTAAAACATAAAATACCGTAAGCACAATT
* * *
268280 ACAACACGAGAAGATGCACAAATACGAAAAACAATACAT
1 ACAATACGAGAAGATACACAAATACGAAAAAGAATACAT
268319 GATAAGTTCT
Statistics
Matches: 125, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
112 75 0.60
113 50 0.40
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.23
Consensus pattern (113 bp):
ACAATACGAGAAGATACACAAATACGAAAAAGAATACATATATAACCAAATAAATCCAATCCACT
GTTAACTTATCAAAAGTTCGTAAAACATAAAATACCGTAAGCACAATT
Found at i:271947 original size:402 final size:403
Alignment explanation
Indices: 271178--271949 Score: 912
Period size: 402 Copynumber: 1.9 Consensus size: 403
271168 AAAAAAGGCT
* * * * * *
271178 AATTTTTTAAATTCGCTAACTGAGTTGGTGTTCGGTTGGCTCGTGACACCAACTCAGTAAAGGGT
1 AATTTTGTAAATTCGCTAACTGAGTTGGTGATCGATTGACTCATAACACCAACTCAGTAAAGGGT
* ** * * * *
271243 TTTATTAATAGTGTAAATGATATATAAGATGAAATAGTGGGTAAAGATATCATAGAGGCCTCTGT
66 TTTATTAATAGTATAAATGATATATAAGAAAAAATAGTGGCTAAAGATATCATAAAGGCATATGT
* * * * *
271308 ATTAGGAGTTAGATTGTGATATGCCCAATTTATTTAAAAATGGACAAATTAGTAATTGTACATTA
131 ATTAAGAGTTAAATTGTGATATGCCCAATTTATTAAAAAATGGACAAATAAATAATTGTACATTA
* ** *
271373 AATTAAAGAGTAAATTAGTCATTTCTGTTAAAAATTTTCCATCCATTTGTACGACTAAAAACTAA
196 AATCAAAGAGTAAACCAGTCATTTCTGTTAAAAATTTTCCATCCATTCGTACGACT----A-TAA
* *
271438 AAACTAAAAAGCTAATGGAATAACCAAGCAATGACACTTAACATGCCACGTGTATCTCATGATGA
256 AAACTAAAAAGCTAATGGAATAACCAAGCAATGACACATAACATGCCACGTGTACCTCATGATGA
* * *
271503 TGTGCAAGACTAGTTTTTAACAGTAGAAATAGATGGAATTTTTAACAAAAGGACCAATTCGCTCT
321 TGTGCAAGACCAATTTTTAACAGTAGAAATAGATGCAATTTTTAACAAAAGGACCAATTCGCTCT
271568 TTGATCTAACCTAAGGTC
386 TTGATCTAACCTAAGGTC
** * *
271586 AATTTTGTAAATTTTCTAACTGAGTTGGTGATCGATTGACTCATAACACTAACTCAGTCAAGGGT
1 AATTTTGTAAATTCGCTAACTGAGTTGGTGATCGATTGACTCATAACACCAACTCAGTAAAGGGT
* * * *
271651 TTTATTAATAGTATATATTATATATAAGACAAAAATAGTGGCTCAAGATATCATAAATGCATATG
66 TTTATTAATAGTATAAATGATATATAAGA-AAAAATAGTGGCTAAAGATATCATAAAGGCATATG
* * *
271716 TATTAAGAGTTAAATTGT-ATTTTG-CCACATTTATTCAAAAAATGGACAAATAAATCATTGTAT
130 TATTAAGAGTTAAATTGTGA-TATGCCCA-ATTTATT-AAAAAATGGACAAATAAATAATTGTAC
* * * *
271779 TTTAAATCAAAGAGTAAACCGGTTC-TTTCTGTTGAAAATTTT-CATTCATTCGTACGA-T-TAA
192 ATTAAATCAAAGAGTAAACCAG-TCATTTCTGTTAAAAATTTTCCATCCATTCGTACGACTATAA
* * ** * ** * * *
271840 AAATTGAAGGGCTAATGGAATAACCAAGCAGT-AGCACATGGCATGCCATGTGTACCTTATGTTG
256 AAACTAAAAAGCTAATGGAATAACCAAGCAATGA-CACATAACATGCCACGTGTACCTCATGATG
271904 ATGTGCAAGACCAATTTTTAACAGTAGAAAT-GAGTGCAATTTTTAA
320 ATGTGCAAGACCAATTTTTAACAGTAGAAATAGA-TGCAATTTTTAA
271950 TAGTAGAAAT
Statistics
Matches: 305, Mismatches: 52, Indels: 20
0.81 0.14 0.05
Matches are distributed among these distances:
401 3 0.01
402 93 0.30
408 86 0.28
409 66 0.22
410 55 0.18
411 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (403 bp):
AATTTTGTAAATTCGCTAACTGAGTTGGTGATCGATTGACTCATAACACCAACTCAGTAAAGGGT
TTTATTAATAGTATAAATGATATATAAGAAAAAATAGTGGCTAAAGATATCATAAAGGCATATGT
ATTAAGAGTTAAATTGTGATATGCCCAATTTATTAAAAAATGGACAAATAAATAATTGTACATTA
AATCAAAGAGTAAACCAGTCATTTCTGTTAAAAATTTTCCATCCATTCGTACGACTATAAAAACT
AAAAAGCTAATGGAATAACCAAGCAATGACACATAACATGCCACGTGTACCTCATGATGATGTGC
AAGACCAATTTTTAACAGTAGAAATAGATGCAATTTTTAACAAAAGGACCAATTCGCTCTTTGAT
CTAACCTAAGGTC
Found at i:271949 original size:25 final size:25
Alignment explanation
Indices: 271915--271977 Score: 108
Period size: 25 Copynumber: 2.5 Consensus size: 25
271905 TGTGCAAGAC
271915 CAATTTTTAACAGTAGAAATGAGTG
1 CAATTTTTAACAGTAGAAATGAGTG
*
271940 CAATTTTTAATAGTAGAAATGAGTG
1 CAATTTTTAACAGTAGAAATGAGTG
*
271965 AAATTTTTAACAG
1 CAATTTTTAACAG
271978 AAGGACCAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.35
Consensus pattern (25 bp):
CAATTTTTAACAGTAGAAATGAGTG
Found at i:272849 original size:21 final size:20
Alignment explanation
Indices: 272825--272881 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
272815 ATTATATTAT
272825 TTTTTAATTATTTAA-AACATA
1 TTTTTAA-TATTTAATAA-ATA
*
272846 TTTTTAATATATAATAAATA
1 TTTTTAATATTTAATAAATA
272866 TTATTTAATATTTAAT
1 TT-TTTAATATTTAAT
272882 TATTTAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTTAATATTTAATAAATA
Found at i:285970 original size:78 final size:77
Alignment explanation
Indices: 285804--286021 Score: 289
Period size: 78 Copynumber: 2.8 Consensus size: 77
285794 TTGTGTTATT
* * * *
285804 TTTGCATATTTTCATGTTATAGTAGTGTTAAAGGTGTTTTACATTTGGTATAAAGCTCGATATTG
1 TTTGTATATTTTCATGTTATAGTAGTGTTAAAGGTGTTTTACATTT-GTATAAAGTTTGATATCG
285869 GATAATTAGTACA
65 GATAATTAGTACA
*
285882 TTTGTATATTTTCATGTTATAGTAGTGTTAAAGGTGTTTTGCATTTGTATAAAGTTTGATATCGG
1 TTTGTATATTTTCATGTTATAGTAGTGTTAAAGGTGTTTTACATTTGTATAAAGTTTGATATCGG
285947 ATAATTAGTACA
66 ATAATTAGTACA
* *
285959 TTTGTGTTATTTT--TGTATATTTA-CATGTGTTAAAGGTGTTTTTACATTTGTATAAAGTTTGA
1 TTTGT-ATATTTTCATGT-TA--TAGTA-GTGTTAAAGGTG-TTTTACATTTGTATAAAGTTTGA
286021 T
60 T
286022 GTTGTAATAA
Statistics
Matches: 126, Mismatches: 8, Indels: 10
0.88 0.06 0.07
Matches are distributed among these distances:
76 3 0.02
77 35 0.28
78 51 0.40
79 14 0.11
80 23 0.18
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.48
Consensus pattern (77 bp):
TTTGTATATTTTCATGTTATAGTAGTGTTAAAGGTGTTTTACATTTGTATAAAGTTTGATATCGG
ATAATTAGTACA
Found at i:296946 original size:23 final size:23
Alignment explanation
Indices: 296920--296970 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
296910 GTTGGCATTT
296920 AAATATTCGTTTTAAATTGGTAA
1 AAATATTCGTTTTAAATTGGTAA
296943 AAATATTCGTTTTAAATTGGTAA
1 AAATATTCGTTTTAAATTGGTAA
296966 AAATA
1 AAATA
296971 CCTCTTCAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (23 bp):
AAATATTCGTTTTAAATTGGTAA
Found at i:305205 original size:18 final size:18
Alignment explanation
Indices: 305182--305218 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
305172 ATTAAAGTTG
305182 TGTATAATAAA-ATTAAAA
1 TGTATAA-AAATATTAAAA
305200 TGTATAAAAATATTAAAA
1 TGTATAAAAATATTAAAA
305218 T
1 T
305219 AAAATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
TGTATAAAAATATTAAAA
Found at i:316960 original size:30 final size:30
Alignment explanation
Indices: 316924--317024 Score: 175
Period size: 30 Copynumber: 3.4 Consensus size: 30
316914 TATGCTTGGA
* *
316924 ATGGGATATCCCCGACCCGCGTATCCCGCG
1 ATGGGATATCCCCGATCGGCGTATCCCGCG
316954 ATGGGATATCCCCGATCGGCGTATCCCGCG
1 ATGGGATATCCCCGATCGGCGTATCCCGCG
*
316984 ATGGGATATCCCCGATAGGCGTATCCCGCG
1 ATGGGATATCCCCGATCGGCGTATCCCGCG
317014 ATGGGATATCC
1 ATGGGATATCC
317025 TTCATCCGGA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.19, C:0.33, G:0.29, T:0.20
Consensus pattern (30 bp):
ATGGGATATCCCCGATCGGCGTATCCCGCG
Found at i:316963 original size:15 final size:15
Alignment explanation
Indices: 316945--317024 Score: 96
Period size: 15 Copynumber: 5.3 Consensus size: 15
316935 CCGACCCGCG
316945 TATCCCGCGATGGGA
1 TATCCCGCGATGGGA
316960 TATCCC-CGATCGGCG-
1 TATCCCGCGAT-GG-GA
316975 TATCCCGCGATGGGA
1 TATCCCGCGATGGGA
316990 TATCCC-CGATAGGCG-
1 TATCCCGCGAT-GG-GA
317005 TATCCCGCGATGGGA
1 TATCCCGCGATGGGA
317020 TATCC
1 TATCC
317025 TTCATCCGGA
Statistics
Matches: 57, Mismatches: 0, Indels: 16
0.78 0.00 0.22
Matches are distributed among these distances:
14 10 0.18
15 37 0.65
16 10 0.18
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.21
Consensus pattern (15 bp):
TATCCCGCGATGGGA
Found at i:317270 original size:29 final size:29
Alignment explanation
Indices: 317228--317296 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
317218 TGAATTGGAT
*
317228 ATAACCTAAGCCCAATAACACAGTAATCC
1 ATAAGCTAAGCCCAATAACACAGTAATCC
317257 ATAAGCTAAGCCCAATAACACAGTAATCC
1 ATAAGCTAAGCCCAATAACACAGTAATCC
317286 ATAAGCTAAGC
1 ATAAGCTAAGC
317297 AGTACACAGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.45, C:0.28, G:0.10, T:0.17
Consensus pattern (29 bp):
ATAAGCTAAGCCCAATAACACAGTAATCC
Found at i:326907 original size:34 final size:30
Alignment explanation
Indices: 326868--326930 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
326858 CAAAAATTAA
*
326868 TAAAATTTTAAGTATATATTTTATAATTAAATTT
1 TAAAATTTT-ACTAT-TA-TTTA-AATTAAATTT
326902 TAAAATTTTACTATTATTTAAATTAAATT
1 TAAAATTTTACTATTATTTAAATTAAATT
326931 CAGAGCGAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 9 0.32
31 4 0.14
32 2 0.07
33 4 0.14
34 9 0.32
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
TAAAATTTTACTATTATTTAAATTAAATTT
Found at i:336286 original size:22 final size:22
Alignment explanation
Indices: 336261--336303 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
336251 TAATAAAAAG
336261 AATATCTACAAAATATTCCTAA
1 AATATCTACAAAATATTCCTAA
* *
336283 AATATTTACAGAATATTCCTA
1 AATATCTACAAAATATTCCTA
336304 CACTCCCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (22 bp):
AATATCTACAAAATATTCCTAA
Found at i:340019 original size:22 final size:22
Alignment explanation
Indices: 339994--340036 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
339984 TAATAAAAAG
339994 AATATCTACAAAATATTCCTAA
1 AATATCTACAAAATATTCCTAA
* *
340016 AATATTTACAGAATATTCCTA
1 AATATCTACAAAATATTCCTA
340037 CATGTGTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (22 bp):
AATATCTACAAAATATTCCTAA
Found at i:346965 original size:15 final size:14
Alignment explanation
Indices: 346947--346980 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
346937 AGAGGAAAGG
346947 GAGAGGGAAAGAGAA
1 GAGAGGGAAAGAG-A
346962 GAGAGGGAAAGAGA
1 GAGAGGGAAAGAGA
346976 GAGAG
1 GAGAG
346981 AAAGAGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (14 bp):
GAGAGGGAAAGAGA
Found at i:346970 original size:27 final size:27
Alignment explanation
Indices: 346932--346987 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
346922 AAGGCGGAGG
* *
346932 GAAGAAGAGGAAAGGGAGAGGGAAAGA
1 GAAGAAGAGGAAAGAGAGAGAGAAAGA
346959 GAAG-AGAGGGAAAGAGAGAGAGAAAGA
1 GAAGAAGA-GGAAAGAGAGAGAGAAAGA
346986 GA
1 GA
346988 TTTCAATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (27 bp):
GAAGAAGAGGAAAGAGAGAGAGAAAGA
Found at i:346985 original size:12 final size:12
Alignment explanation
Indices: 346933--346987 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
346923 AGGCGGAGGG
346933 AAGA-AGAG-GA
1 AAGAGAGAGAGA
* *
346943 AAGGGAGAGGGA
1 AAGAGAGAGAGA
346955 AAGAGAAGAGAGGGA
1 AAGAG-AGAGA--GA
346970 AAGAGAGAGAGA
1 AAGAGAGAGAGA
346982 AAGAGA
1 AAGAGA
346988 TTTCAATGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 3 0.08
11 4 0.11
12 14 0.38
13 4 0.11
14 5 0.14
15 7 0.19
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (12 bp):
AAGAGAGAGAGA
Found at i:356419 original size:27 final size:27
Alignment explanation
Indices: 356381--356434 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
356371 CGAGACATGG
356381 ACTCGAGTATTTACCAATACAGTACGC
1 ACTCGAGTATTTACCAATACAGTACGC
356408 ACTCGAGTATTTACCAATACAGTACGC
1 ACTCGAGTATTTACCAATACAGTACGC
356435 TTAAATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (27 bp):
ACTCGAGTATTTACCAATACAGTACGC
Found at i:360113 original size:29 final size:31
Alignment explanation
Indices: 360075--360148 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
360065 AGTTTATATA
*
360075 TTTATAATTTTTAAAAA-TT-AAA-TCAAAAT
1 TTTATTATTTTTAAAAAGTTAAAAGT-AAAAT
*
360104 TTTATTATTTTTAAAAAGTTAAAAGTATAAT
1 TTTATTATTTTTAAAAAGTTAAAAGTAAAAT
*
360135 TTTATTATTATTAA
1 TTTATTATTTTTAA
360149 TTTAAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 16 0.41
30 2 0.05
31 20 0.51
32 1 0.03
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (31 bp):
TTTATTATTTTTAAAAAGTTAAAAGTAAAAT
Found at i:370835 original size:24 final size:24
Alignment explanation
Indices: 370808--370859 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
370798 TTAGTAAGTC
*
370808 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
370832 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
370856 AAAT
1 AAAT
370860 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:372805 original size:24 final size:24
Alignment explanation
Indices: 372778--372829 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
372768 TTAGTAAGTC
* *
372778 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACGAATAAATACT
* *
372802 AAATATATTATACGAATAAATACT
1 AAATAAACTATACGAATAAATACT
372826 AAAT
1 AAAT
372830 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.04, T:0.31
Consensus pattern (24 bp):
AAATAAACTATACGAATAAATACT
Found at i:384210 original size:60 final size:60
Alignment explanation
Indices: 384146--384284 Score: 165
Period size: 60 Copynumber: 2.3 Consensus size: 60
384136 TTTCAACCAA
* * * *
384146 AAAGCCAAGTTT-AGGTACCTAATCGAGCCAAAA-TAAACTTTAGGTATCAAATTAAACCTT
1 AAAGCCAA-TTTCAAGTACCTAAT-GAGACAAAAGAAAACTTTAGGTACCAAATTAAACCTT
* * *
384206 AAAGCCAATTTCAAGTACCTAATTAGACAAAAGAAAACTTTAGGTACCAATTTAAACTTT
1 AAAGCCAATTTCAAGTACCTAATGAGACAAAAGAAAACTTTAGGTACCAAATTAAACCTT
* *
384266 AAAGCCAAATACAAGTACC
1 AAAGCCAATTTCAAGTACC
384285 AAAATGTATA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 10 0.15
60 58 0.85
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.25
Consensus pattern (60 bp):
AAAGCCAATTTCAAGTACCTAATGAGACAAAAGAAAACTTTAGGTACCAAATTAAACCTT
Found at i:398799 original size:13 final size:13
Alignment explanation
Indices: 398781--398806 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
398771 TGACCGTTTT
398781 GTAGCTTTTTAAA
1 GTAGCTTTTTAAA
398794 GTAGCTTTTTAAA
1 GTAGCTTTTTAAA
398807 ATTGGTTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GTAGCTTTTTAAA
Found at i:414158 original size:6 final size:6
Alignment explanation
Indices: 414149--414184 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
414139 ATTATTATCA
*
414149 TTCTCT TTCTCT TTCTCC TTCTCT TTCTCT TTCTCT
1 TTCTCT TTCTCT TTCTCT TTCTCT TTCTCT TTCTCT
414185 AAGGAAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (6 bp):
TTCTCT
Found at i:414172 original size:18 final size:18
Alignment explanation
Indices: 414149--414183 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
414139 ATTATTATCA
414149 TTCTCTTTCTCTTTCTCC
1 TTCTCTTTCTCTTTCTCC
414167 TTCTCTTTCTCTTTCTC
1 TTCTCTTTCTCTTTCTC
414184 TAAGGAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (18 bp):
TTCTCTTTCTCTTTCTCC
Found at i:414925 original size:13 final size:13
Alignment explanation
Indices: 414907--414931 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
414897 GGTTTGGATA
414907 AAAATATAAGTTC
1 AAAATATAAGTTC
414920 AAAATATAAGTT
1 AAAATATAAGTT
414932 TCGGTAAAAA
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:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (13 bp):
AAAATATAAGTTC
Found at i:415065 original size:18 final size:17
Alignment explanation
Indices: 415030--415118 Score: 60
Period size: 17 Copynumber: 5.3 Consensus size: 17
415020 AATAAATATA
* *
415030 TTTATTTTTTAAATTTT
1 TTTAATTTTAAAATTTT
415047 TTTAATTTTAAAATATTT
1 TTTAATTTTAAAAT-TTT
* *
415065 TTTAA----ATACTTTT
1 TTTAATTTTAAAATTTT
*
415078 TTTATTATTTTTAAATTTT
1 TTTA--ATTTTAAAATTTT
* *
415097 TTTAATTTAAAAATATT
1 TTTAATTTTAAAATTTT
415114 TTTAA
1 TTTAA
415119 AATATTTTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
13 7 0.13
14 3 0.05
15 1 0.02
17 27 0.49
18 8 0.15
19 9 0.16
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTAATTTTAAAATTTT
Found at i:415092 original size:50 final size:48
Alignment explanation
Indices: 415030--415140 Score: 168
Period size: 50 Copynumber: 2.3 Consensus size: 48
415020 AATAAATATA
* * *
415030 TTTATTTTTTAAATTTTTTTAATTTTAAAATATTTTTTAAATACTTTTT
1 TTTAATTTTTAAATTTTTTTAATTTAAAAATATTTTTAAAATA-TTTTT
*
415079 TTATTATTTTTAAATTTTTTTAATTTAAAAATATTTTTAAAATATTTTT
1 TT-TAATTTTTAAATTTTTTTAATTTAAAAATATTTTTAAAATATTTTT
415128 TTTAATTTTTAAA
1 TTTAATTTTTAAA
415141 ATAAATTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
48 10 0.18
49 9 0.16
50 37 0.66
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (48 bp):
TTTAATTTTTAAATTTTTTTAATTTAAAAATATTTTTAAAATATTTTT
Found at i:415149 original size:21 final size:21
Alignment explanation
Indices: 415111--415150 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
415101 ATTTAAAAAT
**
415111 ATTTTTAAAATATTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
415132 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
415151 AGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:415157 original size:22 final size:22
Alignment explanation
Indices: 415110--415168 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
415100 AATTTAAAAA
**
415110 TATTTTTAAAAT--ATTTTTTT
1 TATTTTTAAAATAAATTTTTAG
415130 TAATTTTTAAAATAAATTTTTAG
1 T-ATTTTTAAAATAAATTTTTAG
415153 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
415169 AGCCGGGCCG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.33
22 8 0.24
23 13 0.39
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TATTTTTAAAATAAATTTTTAG
Found at i:415714 original size:21 final size:20
Alignment explanation
Indices: 415690--415751 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 20
415680 TATCTTATTC
*
415690 TAACATACAAAGACTATTTTT
1 TAACATA-AAAGACTAATTTT
*
415711 TAACAATAAAAAAGAATAATTTT
1 TAAC-AT--AAAAGACTAATTTT
415734 TAACA-AAAAGACTAATTT
1 TAACATAAAAGACTAATTT
415752 AATCTTTGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
19 12 0.34
21 4 0.11
22 3 0.09
23 15 0.43
24 1 0.03
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.32
Consensus pattern (20 bp):
TAACATAAAAGACTAATTTT
Found at i:416671 original size:24 final size:24
Alignment explanation
Indices: 416644--416689 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
416634 TAACTTTTAA
* *
416644 TCAATTTAATATCCAAAATTGATC
1 TCAAATTAATATACAAAATTGATC
* *
416668 TCAAATTACTATACAAATTTGA
1 TCAAATTAATATACAAAATTGA
416690 CTTCAATGTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.37
Consensus pattern (24 bp):
TCAAATTAATATACAAAATTGATC
Found at i:423212 original size:26 final size:31
Alignment explanation
Indices: 423149--423216 Score: 83
Period size: 33 Copynumber: 2.3 Consensus size: 31
423139 TTTGAATATT
423149 ATTAAGTTTGAATTTAATTAATTCGATTAATA
1 ATTAAGTTTGAATTTAATTAATTC-ATTAATA
423181 ATTTAAGTTTG-ATTTAA-TAATT-ATT-A-A
1 A-TTAAGTTTGAATTTAATTAATTCATTAATA
423208 ATTAAGTTT
1 ATTAAGTTT
423217 AAAATTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
26 8 0.23
27 2 0.06
28 1 0.03
29 3 0.09
31 5 0.14
32 7 0.20
33 9 0.26
ACGTcount: A:0.40, C:0.01, G:0.09, T:0.50
Consensus pattern (31 bp):
ATTAAGTTTGAATTTAATTAATTCATTAATA
Found at i:430305 original size:15 final size:15
Alignment explanation
Indices: 430282--430320 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
430272 TTATATGTTT
*
430282 TAATTTTTATTTTGA
1 TAATTTTTATTTTCA
*
430297 TATTTTTTATTTTCA
1 TAATTTTTATTTTCA
430312 TAATTTTTA
1 TAATTTTTA
430321 AATTTTTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (15 bp):
TAATTTTTATTTTCA
Found at i:431635 original size:24 final size:25
Alignment explanation
Indices: 431585--431637 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
431575 TCATTATGCC
**
431585 AATTTTAAATAAAAATAGTTTTGAA
1 AATTTTAAATAAAAATAAATTTGAA
431610 AATTTTAAATAAAAATAAATTT-AA
1 AATTTTAAATAAAAATAAATTTGAA
431634 AATT
1 AATT
431638 ATAGGGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (25 bp):
AATTTTAAATAAAAATAAATTTGAA
Found at i:444199 original size:23 final size:22
Alignment explanation
Indices: 444153--444199 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
444143 TTTCTTTCAA
* **
444153 TTGTTTTTTTTGGTGATATTGT
1 TTGTTTTTTTTGGTGAGAAAGT
444175 TTGTTTTTTTTGGTTGAGAAAGT
1 TTGTTTTTTTTGG-TGAGAAAGT
444198 TT
1 TT
444200 TGATATTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.13, C:0.00, G:0.23, T:0.64
Consensus pattern (22 bp):
TTGTTTTTTTTGGTGAGAAAGT
Found at i:456679 original size:136 final size:135
Alignment explanation
Indices: 456502--456769 Score: 500
Period size: 136 Copynumber: 2.0 Consensus size: 135
456492 GGGATAACTA
* *
456502 GCTGATGAGGCTATTTATAAAAAGCCAGGAGTATCCTTTCCTGACATGGAAAAGATATTTTGGAA
1 GCTGATGAGGCTATTTATAAAAAGCCAAGAGTATCCTTTCCTGAAATGGAAAAGATATTTTGGAA
456567 ATCAACGTGAATAATGTGATGCTTCCATTTTTTTAATAATTAATTTGTTGATATCGTACATTATC
66 ATCAACGTGAATAATGTGATGCTTCCATTTTTTTAATAATTAATTTGTTGATAT-GTACATTATC
456632 TGTCGT
130 TGTCGT
456638 GCTGATGAGGCTATTTATAAAAAGCCAAGAGTATCCTTTCCTGAAATGGAAAAGATATTTTGGAA
1 GCTGATGAGGCTATTTATAAAAAGCCAAGAGTATCCTTTCCTGAAATGGAAAAGATATTTTGGAA
*
456703 ATCTACGTGAATAATGTGATGCTTCCATTTTTTTAATAATTAATTTGTTGATATGTACATTATCT
66 ATCAACGTGAATAATGTGATGCTTCCATTTTTTTAATAATTAATTTGTTGATATGTACATTATCT
456768 GT
131 GT
456770 AGTGGTCCAT
Statistics
Matches: 129, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
135 13 0.10
136 116 0.90
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (135 bp):
GCTGATGAGGCTATTTATAAAAAGCCAAGAGTATCCTTTCCTGAAATGGAAAAGATATTTTGGAA
ATCAACGTGAATAATGTGATGCTTCCATTTTTTTAATAATTAATTTGTTGATATGTACATTATCT
GTCGT
Found at i:459135 original size:25 final size:25
Alignment explanation
Indices: 459113--459162 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
459103 TAAGAAAACT
*
459113 TAAAATAAATGATAATAAAAAAATC
1 TAAAATAAATAATAATAAAAAAATC
*
459138 TAATATAAATAATAATAACAAAAAT
1 TAAAATAAATAATAATAA-AAAAAT
459163 ATGAAACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (25 bp):
TAAAATAAATAATAATAAAAAAATC
Found at i:462531 original size:18 final size:18
Alignment explanation
Indices: 462504--462596 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
462494 TACGACCGTT
*
462504 TACGGTACTATTTACGTA
1 TACGGTACTATTCACGTA
*
462522 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
**
462540 TATAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
462558 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
462576 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
462594 TAC
1 TAC
462597 AGTAGTTGGG
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:472605 original size:14 final size:14
Alignment explanation
Indices: 472588--472615 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
472578 ACACATTACA
472588 CATTACATATAACT
1 CATTACATATAACT
472602 CATTACATATAACT
1 CATTACATATAACT
472616 GTCTGGTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (14 bp):
CATTACATATAACT
Found at i:475269 original size:21 final size:23
Alignment explanation
Indices: 475225--475269 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
475215 AATAAGTCAG
*
475225 ATAATATATCCAAATATTCGAATA
1 ATAATATATCCAAAGATTC-AATA
475249 ATAA-ATATCCAAAGATT-AATA
1 ATAATATATCCAAAGATTCAATA
475270 TCTGTATCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.31
Consensus pattern (23 bp):
ATAATATATCCAAAGATTCAATA
Found at i:481803 original size:21 final size:21
Alignment explanation
Indices: 481773--481822 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
481763 TGTTTCTAAC
* * *
481773 CTCACTGCTATATTATCCAAT
1 CTCACCGCTATAGTAACCAAT
*
481794 CTCACCGCTATAGTAACTAAT
1 CTCACCGCTATAGTAACCAAT
481815 CTCACCGC
1 CTCACCGC
481823 CACCGCTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.34, G:0.08, T:0.30
Consensus pattern (21 bp):
CTCACCGCTATAGTAACCAAT
Found at i:483599 original size:18 final size:18
Alignment explanation
Indices: 483578--483664 Score: 129
Period size: 18 Copynumber: 4.8 Consensus size: 18
483568 CGTTTACAGG
**
483578 ACTATTCACGTATACAAC
1 ACTATTCACGTATACGGC
*
483596 ACTATTCACGTATACGGT
1 ACTATTCACGTATACGGC
*
483614 ACTATTTACGTATACGGC
1 ACTATTCACGTATACGGC
*
483632 ACTATTCACGTATACGGT
1 ACTATTCACGTATACGGC
483650 ACTATTCACGTATAC
1 ACTATTCACGTATAC
483665 AGTAGTTGGG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (18 bp):
ACTATTCACGTATACGGC
Found at i:483625 original size:36 final size:36
Alignment explanation
Indices: 483578--483665 Score: 149
Period size: 36 Copynumber: 2.4 Consensus size: 36
483568 CGTTTACAGG
483578 ACTATTCACGTATACAACACTATTCACGTATACGGT
1 ACTATTCACGTATACAACACTATTCACGTATACGGT
* **
483614 ACTATTTACGTATACGGCACTATTCACGTATACGGT
1 ACTATTCACGTATACAACACTATTCACGTATACGGT
483650 ACTATTCACGTATACA
1 ACTATTCACGTATACA
483666 GTAGTTGGGA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (36 bp):
ACTATTCACGTATACAACACTATTCACGTATACGGT
Found at i:501488 original size:5 final size:5
Alignment explanation
Indices: 501465--501519 Score: 71
Period size: 5 Copynumber: 11.2 Consensus size: 5
501455 TTTTTATGTT
501465 TTATA -TATA TTAT- TT-TA TTATA TTATATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA -T-TATA TTATA TTATA TTATA TTATA
501514 TTATA T
1 TTATA T
501520 AAGTAAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.18
5 30 0.67
6 2 0.04
7 4 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:501490 original size:22 final size:23
Alignment explanation
Indices: 501465--501520 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 23
501455 TTTTTATGTT
*
501465 TTATATATAT-TATTTTATTATA
1 TTATATATATATATTATATTATA
501487 TTATATAT-TATATTATATTATA
1 TTATATATATATATTATATTATA
501509 TTATAT-TATATA
1 TTATATATATATA
501521 AGTAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 2 0.06
22 29 0.94
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTATATATATATATTATATTATA
Found at i:501497 original size:15 final size:16
Alignment explanation
Indices: 501465--501520 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 16
501455 TTTTTATGTT
*
501465 TTATATATATTATTTTA
1 TTATATATA-TATTATA
501482 TTATATTATATATTATA
1 TTATA-TATATATTATA
501499 TTATAT-TATATTATA
1 TTATATATATATTATA
501514 TTATATA
1 TTATATA
501521 AGTAAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
15 15 0.42
16 1 0.03
17 16 0.44
18 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATATATATATTATA
Found at i:503407 original size:3 final size:3
Alignment explanation
Indices: 503399--503442 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
503389 AATAAAAATT
* * *
503399 TTA TTA TTA TTA TTA TTG TTA ATA TAA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
503443 TTTAATGATT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:505420 original size:44 final size:43
Alignment explanation
Indices: 505370--505453 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 43
505360 AGTATAGGGG
505370 TAAAATAGAAATTTTGCCAGATATGTATTGAGTATGAATTGTAT
1 TAAAATAGAAATTTTGCCAGATATGTATTGAGT-TGAATTGTAT
* *
505414 TAAAATATAAATTTTTCCAGATATGTATTGAGTTGAATTG
1 TAAAATAGAAATTTTGCCAGATATGTATTGAGTTGAATTG
505454 AGTATGAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 7 0.18
44 31 0.82
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (43 bp):
TAAAATAGAAATTTTGCCAGATATGTATTGAGTTGAATTGTAT
Found at i:505959 original size:25 final size:25
Alignment explanation
Indices: 505799--505965 Score: 127
Period size: 25 Copynumber: 6.7 Consensus size: 25
505789 ACTCACCACA
* * *
505799 GCTCTTATGAGCATCCCGATATATG
1 GCTCTCATGAGCTTCCCGATAAATG
* * * **
505824 GCTCTCTTGAACTTCCCGTTATTTG
1 GCTCTCATGAGCTTCCCGATAAATG
* * * ** *
505849 GCTCTCACGAGCTTTCTGATACTTA
1 GCTCTCATGAGCTTCCCGATAAATG
** *
505874 GCTCTCACAAGCTTCCCGATATATG
1 GCTCTCATGAGCTTCCCGATAAATG
* * * *
505899 GCTCTTATAAGCTTCCTGATTAATG
1 GCTCTCATGAGCTTCCCGATAAATG
*
505924 GCTCTCTTGAGCTTCCCGATAAATG
1 GCTCTCATGAGCTTCCCGATAAATG
*
505949 GCTCGCATGAGCTTCCC
1 GCTCTCATGAGCTTCCC
505966 ATTATACAGA
Statistics
Matches: 110, Mismatches: 32, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 110 1.00
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (25 bp):
GCTCTCATGAGCTTCCCGATAAATG
Found at i:505962 original size:50 final size:50
Alignment explanation
Indices: 505799--505964 Score: 154
Period size: 50 Copynumber: 3.3 Consensus size: 50
505789 ACTCACCACA
* * * * * * *
505799 GCTCTTATGAGCATCCCGATATATGGCTCTCTTGAACTTCCCGTTATTTG
1 GCTCTCATGAGCTTCCTGATACATGGCTCTCTTGAGCTTCCCGATATATG
* * * * ***
505849 GCTCTCACGAGCTTTCTGATACTTAGCTCTCACAAGCTTCCCGATATATG
1 GCTCTCATGAGCTTCCTGATACATGGCTCTCTTGAGCTTCCCGATATATG
* * *
505899 GCTCTTATAAGCTTCCTGATTA-ATGGCTCTCTTGAGCTTCCCGATAAATG
1 GCTCTCATGAGCTTCCTGA-TACATGGCTCTCTTGAGCTTCCCGATATATG
*
505949 GCTCGCATGAGCTTCC
1 GCTCTCATGAGCTTCC
505965 CATTATACAG
Statistics
Matches: 88, Mismatches: 27, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
50 86 0.98
51 2 0.02
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (50 bp):
GCTCTCATGAGCTTCCTGATACATGGCTCTCTTGAGCTTCCCGATATATG
Found at i:509190 original size:39 final size:37
Alignment explanation
Indices: 509123--509215 Score: 89
Period size: 39 Copynumber: 2.5 Consensus size: 37
509113 ACCAGAATGG
* *
509123 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
509162 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* * *
509199 TACCTAGTACCTCATCG
1 CACCCAGTGCCTCATCG
509216 AATCTATCCG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
37 18 0.40
38 2 0.04
39 22 0.49
40 3 0.07
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.22
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:509899 original size:17 final size:16
Alignment explanation
Indices: 509867--509900 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
509857 TTGGCTATTC
*
509867 TGTTTCTTTCTTCTTT
1 TGTTTCTTTATTCTTT
509883 TGTTTCTTTTATTCTTT
1 TGTTTC-TTTATTCTTT
509900 T
1 T
509901 ATTTTAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTATTCTTT
Done.