Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 67 of 93
Found at i:25534995 original size:60 final size:59
Alignment explanation
Indices: 25534899--25535258 Score: 522
Period size: 60 Copynumber: 6.0 Consensus size: 59
25534889 TTTGATTTAA
* *
25534899 AAAGGGGGACCTAAAGCCCCGATTCATATTGGGTGGCGTGGGTAGTTCCCACAAGTAGGT
1 AAAGGGGGACCTGAAGCCCCGATTCATATT-GGTGGCGTGGGTAGTTCCCACGAGTAGGT
25534959 AAAGGGGGACCTGAAGCCCCGATTCATATTGAGTGGCGTGGGTAGTTCCCACGAGTAGGT
1 AAAGGGGGACCTGAAGCCCCGATTCATATTG-GTGGCGTGGGTAGTTCCCACGAGTAGGT
* * *
25535019 AATGGGGGACCTTAAACCCCGATTCATATTGAGTGGCGTGGGTAGTTCCCACGAGTAGGT
1 AAAGGGGGACCTGAAGCCCCGATTCATATTG-GTGGCGTGGGTAGTTCCCACGAGTAGGT
* * * *
25535079 AAAGGGGGACCTAAAGCCTCGATTCATATTGGGTGGCGTGGGTAGTTTCCACGACTAGGT
1 AAAGGGGGACCTGAAGCCCCGATTCATATT-GGTGGCGTGGGTAGTTCCCACGAGTAGGT
* *
25535139 AAAGGGGGACCTGAAGCCCCGATTTATATATGGTGGCGTGAGTAGTTCCCACGAGTAGGT
1 AAAGGGGGACCTGAAGCCCCGATTCATAT-TGGTGGCGTGGGTAGTTCCCACGAGTAGGT
* * * * *
25535199 AAAAGGGGACTTGAAGCCCCAATTTATGTATGGTGGCGTGGGTAGTTCCCACGAGTAGGT
1 AAAGGGGGACCTGAAGCCCCGATTCATAT-TGGTGGCGTGGGTAGTTCCCACGAGTAGGT
25535259 GATGATGTCT
Statistics
Matches: 275, Mismatches: 22, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
59 1 0.00
60 272 0.99
61 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (59 bp):
AAAGGGGGACCTGAAGCCCCGATTCATATTGGTGGCGTGGGTAGTTCCCACGAGTAGGT
Found at i:25538371 original size:30 final size:32
Alignment explanation
Indices: 25538308--25538374 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 32
25538298 AATAAATTTT
*
25538308 TAATTTCATATATTTCATTTTTATCTCTTATTA
1 TAATCTCATATATTTCATTTTTA-CTCTTATTA
25538341 TAATCTCATATATTTTC-TTTTTA-T-TTATTA
1 TAATCTCATATA-TTTCATTTTTACTCTTATTA
25538371 TAAT
1 TAAT
25538375 ACAAATTTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
30 10 0.31
31 1 0.03
33 17 0.53
34 4 0.12
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.61
Consensus pattern (32 bp):
TAATCTCATATATTTCATTTTTACTCTTATTA
Found at i:25538746 original size:22 final size:19
Alignment explanation
Indices: 25538721--25538766 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 19
25538711 GGGTAAATCC
25538721 ATTTTTATATTAATTAAAAATA
1 ATTTTTAT-TT-ATTAAAAA-A
*
25538743 ATTTTTATTTTTTAAAAAA
1 ATTTTTATTTATTAAAAAA
25538762 ATTTT
1 ATTTT
25538767 AAAATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.26
20 7 0.30
21 2 0.09
22 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTTATTTATTAAAAAA
Found at i:25538904 original size:34 final size:34
Alignment explanation
Indices: 25538810--25538905 Score: 95
Period size: 33 Copynumber: 2.8 Consensus size: 34
25538800 TTAAAGTTCT
25538810 TAAAAAATGAAAAATAGAAATGATTTTTTTAAAAAAA
1 TAAAAAAT-AAAAA-AGAAAT-ATTTTTTTAAAAAAA
* * * *
25538847 TAAAAAATCAAAAA-AAATTTTTTTTTGAAAAAT
1 TAAAAAATAAAAAAGAAATATTTTTTTAAAAAAA
** *
25538880 TTGAAAGTAAAAAAGAAATATTTTTT
1 TAAAAAATAAAAAAGAAATATTTTTT
25538906 ATTTTTTAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
33 22 0.45
34 14 0.29
35 1 0.02
36 4 0.08
37 8 0.16
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.34
Consensus pattern (34 bp):
TAAAAAATAAAAAAGAAATATTTTTTTAAAAAAA
Found at i:25539009 original size:26 final size:28
Alignment explanation
Indices: 25538980--25539035 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
25538970 AGCATAAAAA
*
25538980 AAATATCTTT-TATTTT-TCAAAA-TTCT
1 AAATATATTTATATTTTAT-AAAATTTCT
25539006 AAATATATTTATATTTTATAAAATTTCT
1 AAATATATTTATATTTTATAAAATTTCT
25539034 AA
1 AA
25539036 TCTCTTATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 9 0.35
27 10 0.38
28 7 0.27
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (28 bp):
AAATATATTTATATTTTATAAAATTTCT
Found at i:25540417 original size:19 final size:19
Alignment explanation
Indices: 25540393--25540448 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
25540383 TAATTATATT
25540393 AAAAATATATAAAAATTAA
1 AAAAATATATAAAAATTAA
* *
25540412 AAAAATATATAAAACTAAA
1 AAAAATATATAAAAATTAA
*
25540431 AAATAAT-TAAAAAAATTA
1 AAA-AATATATAAAAATTA
25540449 TTTGTTTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 28 0.90
20 3 0.10
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAAATATATAAAAATTAA
Found at i:25540435 original size:17 final size:19
Alignment explanation
Indices: 25540393--25540433 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
25540383 TAATTATATT
*
25540393 AAAAATATATAAAAATTAA
1 AAAAATATATAAAAACTAA
25540412 AAAAATATAT-AAAACTAA
1 AAAAATATATAAAAACTAA
25540430 AAAA
1 AAAA
25540434 TAATTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAAATATATAAAAACTAA
Found at i:25540441 original size:17 final size:18
Alignment explanation
Indices: 25540393--25540442 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
25540383 TAATTATATT
* *
25540393 AAAAATATATAAAAATTA
1 AAAAATATATTAAAACTA
25540411 AAAAA-ATATATAAAACTA
1 AAAAATATAT-TAAAACTA
25540429 AAAAATA-ATTAAAA
1 AAAAATATATTAAAA
25540443 AAATTATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 9 0.32
18 18 0.64
19 1 0.04
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAATATATTAAAACTA
Found at i:25542252 original size:90 final size:89
Alignment explanation
Indices: 25542090--25542268 Score: 241
Period size: 90 Copynumber: 2.0 Consensus size: 89
25542080 ATTTAAAATT
* * * *
25542090 CTGTAGCACGACTTATGGCCAAAAAACTAAAGTATATGCAAGCAGACTTTCGGGTCTTTTAACAT
1 CTGTAGCACGACTTATAGCCAAAAAACTAAAGTATATGCAAGCAAACTTTCGGGTCTTTCAACAC
*
25542155 CTCACTTTCCAAAATTAAGCCCAA
66 CTCACTTTCCAAAACTAAGCCCAA
* * * * *
25542179 NCTGTAGCTCGAGTTATAGCCAAAAAACTGAAGTATATGCAAGCAAACTTTTGGGTCTTTCAATA
1 -CTGTAGCACGACTTATAGCCAAAAAACTAAAGTATATGCAAGCAAACTTTCGGGTCTTTCAACA
* *
25542244 CCTTACTTTTCAAAACTAAGCCCAA
65 CCTCACTTTCCAAAACTAAGCCCAA
25542269 TTTCTTTAGT
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
90 77 1.00
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (89 bp):
CTGTAGCACGACTTATAGCCAAAAAACTAAAGTATATGCAAGCAAACTTTCGGGTCTTTCAACAC
CTCACTTTCCAAAACTAAGCCCAA
Found at i:25558870 original size:2 final size:2
Alignment explanation
Indices: 25558857--25558898 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
25558847 ATTGGCTATG
*
25558857 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25558899 CTATTATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25565134 original size:13 final size:14
Alignment explanation
Indices: 25565116--25565149 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
25565106 CTTCTATAAT
25565116 CATTTTT-TTTTTA
1 CATTTTTCTTTTTA
*
25565129 CATTTTTCTTTTTC
1 CATTTTTCTTTTTA
25565143 CATTTTT
1 CATTTTT
25565150 AGTTTTGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.74
Consensus pattern (14 bp):
CATTTTTCTTTTTA
Found at i:25580561 original size:19 final size:18
Alignment explanation
Indices: 25580533--25580571 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
25580523 ACCATAAAAA
*
25580533 TTTCTCTTAAAGTTTGTT
1 TTTCTCTTAAAGTTTCTT
*
25580551 TTTCTTCTTAATGTTTCTT
1 TTTC-TCTTAAAGTTTCTT
25580570 TT
1 TT
25580572 GTTAAACGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (18 bp):
TTTCTCTTAAAGTTTCTT
Found at i:25588080 original size:40 final size:40
Alignment explanation
Indices: 25588036--25588124 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
25588026 ATGTTAGTGC
* * * *
25588036 CTTTTCAAGAGGAGCAAGCACAAGCTCACAACGTCACTGT
1 CTTTTCAAGAGAAGCAAGCACAACCTCACAAAGTCACTAT
* *
25588076 CTTTTCAAAAGAAGCAAGCACAACCTCACAAAGTCATTAT
1 CTTTTCAAGAGAAGCAAGCACAACCTCACAAAGTCACTAT
25588116 CTTTTCAAG
1 CTTTTCAAG
25588125 GTTAAAGCAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.24
Consensus pattern (40 bp):
CTTTTCAAGAGAAGCAAGCACAACCTCACAAAGTCACTAT
Found at i:25588315 original size:208 final size:207
Alignment explanation
Indices: 25587925--25588343 Score: 524
Period size: 208 Copynumber: 2.0 Consensus size: 207
25587915 TTCTCCCTTG
* *
25587925 ATATCACAAGGAGTTTAAATCCACTATAAACTACCTTTTAAGGAGCAGACATAACCTTTCACAAA
1 ATATCACAAGGAATTTAAATCCACTATAAACTACCTTTTAAGGAACAGACATAACCTTTCACAAA
* * * * *
25587990 CATTTCCTTTTAAAAAAGAGCAAGCATAACCTTACAATGTTAGTGCCTTTTCAAGAGGAGCAAGC
66 CATTGCCTTTTAAAAAAGAGCAAGCATAACCTCACAACGTTAGTGCCTTTTCAAAAGAAGCAAGC
* * *
25588055 ACAAGCTCACAACGTCACTGTCTTTTCAAAAGAAGCAAGCACAACCTCACAAAGTCAT-TAT-CT
131 ACAACCTAACAACGTCACTGCCTTTTCAAAAGAA-CAAGCACAACCTCACAAAGT-ATCTATCCT
25588118 TTTCAAGGTTAAAGC
194 TTT-AAGGTTAAAGC
* * *
25588133 ATATCACAAGGAATTTAAATCCACTATAAATTGCCTTTTAAGGAATAGACATAACCTTTCACAAA
1 ATATCACAAGGAATTTAAATCCACTATAAACTACCTTTTAAGGAACAGACATAACCTTTCACAAA
* * * * *
25588198 CATTGCCTTTTCATAAGGAGCAAGCATAACCTCAGAACGTT-GTTGCCTTTTTAAAAGAAGCAAG
66 CATTGCCTTTTAAAAAAGAGCAAGCATAACCTCACAACGTTAG-TGCCTTTTCAAAAGAAGCAAG
* * * * * *
25588262 TACAACCTAACAATGTCATTGCCTTTTC-AAGGTTA-AAGCACAACCTTTCACAAAGTTTCTATC
130 CACAACCTAACAACGTCACTGCCTTTTCAAAAG-AACAAGCACAACC--TCACAAAGTATCTATC
25588325 CTTTTAAGGTTAAAGC
192 CTTTTAAGGTTAAAGC
25588341 ATA
1 ATA
25588344 ATTGTTCTAC
Statistics
Matches: 181, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
206 10 0.06
207 5 0.03
208 161 0.89
209 5 0.03
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.28
Consensus pattern (207 bp):
ATATCACAAGGAATTTAAATCCACTATAAACTACCTTTTAAGGAACAGACATAACCTTTCACAAA
CATTGCCTTTTAAAAAAGAGCAAGCATAACCTCACAACGTTAGTGCCTTTTCAAAAGAAGCAAGC
ACAACCTAACAACGTCACTGCCTTTTCAAAAGAACAAGCACAACCTCACAAAGTATCTATCCTTT
TAAGGTTAAAGC
Found at i:25597464 original size:35 final size:37
Alignment explanation
Indices: 25597411--25597492 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 37
25597401 AAACCCTCAT
* **
25597411 AATGGTTTTTCACAGGGAGTAAGCGGAACCCTT-AAC
1 AATGGTTTTTCACAGGGAGCAAGCAAAACCCTTCAAC
* * *
25597447 AATGCTTTTTCA-TGGGAGCAAGCAAAATCCTTCAAC
1 AATGGTTTTTCACAGGGAGCAAGCAAAACCCTTCAAC
25597483 AATGGTTTTT
1 AATGGTTTTT
25597493 AATAGGCTCA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 15 0.39
36 23 0.61
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (37 bp):
AATGGTTTTTCACAGGGAGCAAGCAAAACCCTTCAAC
Found at i:25600877 original size:35 final size:34
Alignment explanation
Indices: 25600838--25600944 Score: 110
Period size: 35 Copynumber: 3.1 Consensus size: 34
25600828 AGTTAGTTTT
25600838 AGGTTTTGGTTGATCCCATGAAAAACCATTGTTA
1 AGGTTTTGGTTGATCCCATGAAAAACCATTGTTA
* * ** *
25600872 CAGGTTATGGTTGAGCCTTTGAAAAGCCATT-TT-
1 -AGGTTTTGGTTGATCCCATGAAAAACCATTGTTA
* * *
25600905 GGGTTTTGGTTGATCCCGTGAAAAATCATTGTTAA
1 AGGTTTTGGTTGATCCCATGAAAAACCATTGTT-A
25600940 AGGTT
1 AGGTT
25600945 GTAGCTGAGC
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
32 23 0.41
33 2 0.04
34 2 0.04
35 29 0.52
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.36
Consensus pattern (34 bp):
AGGTTTTGGTTGATCCCATGAAAAACCATTGTTA
Found at i:25600917 original size:67 final size:67
Alignment explanation
Indices: 25600834--25600969 Score: 200
Period size: 67 Copynumber: 2.0 Consensus size: 67
25600824 GAAAAGTTAG
* * * *
25600834 TTTTAGGTTTTGGTTGATCCCATGAAAAACCATTGTTACAGGTTATGGTTGAGCCTTTGAAAAGC
1 TTTTAGGTTTTGGTTGATCCCATGAAAAACCATTGTTAAAGGTTATAGCTGAGCCTGTGAAAAGC
25600899 CA
66 CA
* * * *
25600901 TTTTGGGTTTTGGTTGATCCCGTGAAAAATCATTGTTAAAGGTTGTAGCTGAGCCTGTGAAAAGC
1 TTTTAGGTTTTGGTTGATCCCATGAAAAACCATTGTTAAAGGTTATAGCTGAGCCTGTGAAAAGC
25600966 CA
66 CA
25600968 TT
1 TT
25600970 GTAAAAGCTT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (67 bp):
TTTTAGGTTTTGGTTGATCCCATGAAAAACCATTGTTAAAGGTTATAGCTGAGCCTGTGAAAAGC
CA
Found at i:25600927 original size:32 final size:32
Alignment explanation
Indices: 25600834--25600934 Score: 103
Period size: 32 Copynumber: 3.1 Consensus size: 32
25600824 GAAAAGTTAG
25600834 TTTTAGGTTTTGGTTGATCCCATGAAAAACCA
1 TTTTAGGTTTTGGTTGATCCCATGAAAAACCA
* * ** *
25600866 TTGTTACAGGTTATGGTTGAGCCTTTGAAAAGCCA
1 TT-TT--AGGTTTTGGTTGATCCCATGAAAAACCA
* * *
25600901 TTTTGGGTTTTGGTTGATCCCGTGAAAAATCA
1 TTTTAGGTTTTGGTTGATCCCATGAAAAACCA
25600933 TT
1 TT
25600935 GTTAAAGGTT
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
32 25 0.46
33 2 0.04
34 2 0.04
35 25 0.46
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.39
Consensus pattern (32 bp):
TTTTAGGTTTTGGTTGATCCCATGAAAAACCA
Found at i:25600970 original size:35 final size:35
Alignment explanation
Indices: 25600838--25600976 Score: 104
Period size: 35 Copynumber: 4.1 Consensus size: 35
25600828 AGTTAGTTTT
* * ** *
25600838 AGGTTTTGGTTGATCCCATGAAAAACCATTGTTAC
1 AGGTTATGGTTGAGCCTGTGAAAAACCATTGTTAA
* *
25600873 AGGTTATGGTTGAGCCTTTGAAAAGCCATT-TT--
1 AGGTTATGGTTGAGCCTGTGAAAAACCATTGTTAA
* * * * *
25600905 GGGTTTTGGTTGATCCCGTGAAAAATCATTGTTAA
1 AGGTTATGGTTGAGCCTGTGAAAAACCATTGTTAA
* * * * *
25600940 AGGTTGTAGCTGAGCCTGTGAAAAGCCATTGTAAA
1 AGGTTATGGTTGAGCCTGTGAAAAACCATTGTTAA
25600975 AG
1 AG
25600977 CTTGGTGGAA
Statistics
Matches: 80, Mismatches: 21, Indels: 6
0.75 0.20 0.06
Matches are distributed among these distances:
32 23 0.29
33 2 0.03
34 2 0.03
35 53 0.66
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (35 bp):
AGGTTATGGTTGAGCCTGTGAAAAACCATTGTTAA
Found at i:25603697 original size:43 final size:43
Alignment explanation
Indices: 25603577--25603698 Score: 138
Period size: 43 Copynumber: 2.8 Consensus size: 43
25603567 TGACTCACCT
* * * **
25603577 ATGTGCGAGTAGGGAGTGTGCATAAGCCGATGATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGTCGATGATGACCCAGCC
* *
25603620 ATGTGC-AGGTAGGGAGTGCGCATAAATCGGTGATGACCCAGCC
1 ATGTGCGA-GTAGGGAGTGCGCATAAGTCGATGATGACCCAGCC
* * *
25603663 ATGTGCGAGTAGGGAGTGCACATGAGTTGATGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGTCGATGATGA
25603699 TGATAGGTGT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
42 1 0.02
43 63 0.97
44 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.37, T:0.22
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGTCGATGATGACCCAGCC
Found at i:25604232 original size:21 final size:21
Alignment explanation
Indices: 25604208--25604261 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
25604198 CTATTTATCA
25604208 CTGCAGCGAGAATGAACTTCG
1 CTGCAGCGAGAATGAACTTCG
25604229 CTGCAGCGAGAATGAACTTCG
1 CTGCAGCGAGAATGAACTTCG
25604250 CTGCAGCGAGAA
1 CTGCAGCGAGAA
25604262 ACATTCTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.24, G:0.30, T:0.17
Consensus pattern (21 bp):
CTGCAGCGAGAATGAACTTCG
Found at i:25621103 original size:19 final size:20
Alignment explanation
Indices: 25621071--25621108 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
25621061 AAATATCTTT
25621071 TTCTTCCAGCAGCTTCTTCA
1 TTCTTCCAGCAGCTTCTTCA
*
25621091 TTCTT-CAGTAGCTTCTTC
1 TTCTTCCAGCAGCTTCTTC
25621109 TCCTTCTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.13, C:0.32, G:0.11, T:0.45
Consensus pattern (20 bp):
TTCTTCCAGCAGCTTCTTCA
Found at i:25621969 original size:43 final size:43
Alignment explanation
Indices: 25621912--25622022 Score: 132
Period size: 43 Copynumber: 2.6 Consensus size: 43
25621902 GTAATGATAT
* * *
25621912 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTACGCATAAACCGATGA
* * * *
25621955 TGACCCGGTTATGTGCAAGTAGGGAGTACGCATAAACTGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTACGCATAAACCGATGA
** *
25621998 TGACCTAGCCATGTGCGAGTAGGGA
1 TGACCCGGCTATGTGCGAGTAGGGA
25622023 ATGCACGAGA
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.25, C:0.18, G:0.35, T:0.22
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTACGCATAAACCGATGA
Found at i:25626798 original size:2 final size:2
Alignment explanation
Indices: 25626791--25626832 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
25626781 ATGCTCTTAC
25626791 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25626833 CTTTTGTACC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25627262 original size:23 final size:22
Alignment explanation
Indices: 25627219--25627262 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
25627209 AAGTATAAAT
* **
25627219 ATATTTTTATTATAATTTAATA
1 ATATTTTTATTAAAAGATAATA
25627241 ATATTTTGTATTAAAAGATAAT
1 ATATTTT-TATTAAAAGATAAT
25627263 TAAACCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
ATATTTTTATTAAAAGATAATA
Found at i:25627300 original size:46 final size:44
Alignment explanation
Indices: 25627172--25627304 Score: 144
Period size: 46 Copynumber: 3.0 Consensus size: 44
25627162 AATAAAATCA
* *
25627172 AAAT-AACTTTTACTATAATTAAATAATATTTACA-TCAAAGTAT
1 AAATAAACTTTTATTATAATTAAATAATATTTACATTAAAAG-AT
* * * **
25627215 AAATATATTTTTATTATAATTTAATAATATTTTGTATTAAAAGAT
1 AAATAAACTTTTATTATAATTAAATAATA-TTTACATTAAAAGAT
*
25627260 AATTAAACCTTTTATTATAATTAAATAATATTTAACATTAAAAGA
1 AAATAAA-CTTTTATTATAATTAAATAATATTT-ACATTAAAAGA
25627305 CAAAATATAT
Statistics
Matches: 72, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
43 4 0.06
44 20 0.28
45 14 0.19
46 34 0.47
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (44 bp):
AAATAAACTTTTATTATAATTAAATAATATTTACATTAAAAGAT
Found at i:25627390 original size:10 final size:10
Alignment explanation
Indices: 25627375--25627437 Score: 51
Period size: 10 Copynumber: 6.4 Consensus size: 10
25627365 ATATTCAAAT
25627375 AATAATATTA
1 AATAATATTA
25627385 AATAATATT-
1 AATAATATTA
** *
25627394 TTTTATAGTTA
1 AATAATA-TTA
25627405 AATAATATT-
1 AATAATATTA
25627414 AAT-ATATTA
1 AATAATATTA
*
25627423 ATTAATATTTA
1 AATAATA-TTA
25627434 AATA
1 AATA
25627438 TTTTTATTTC
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
8 5 0.12
9 9 0.22
10 16 0.40
11 10 0.25
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (10 bp):
AATAATATTA
Found at i:25629961 original size:2 final size:2
Alignment explanation
Indices: 25629954--25629997 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
25629944 ACAAAAGGAT
* * * *
25629954 TA TA TA TA TA TG TA TA TA TG TA TA TA AA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25629996 TA
1 TA
25629998 CATGTGTGTG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:25646440 original size:35 final size:35
Alignment explanation
Indices: 25646401--25646670 Score: 240
Period size: 35 Copynumber: 7.7 Consensus size: 35
25646391 TAAGCCTAAT
** * *
25646401 TAACTTAATTATTTAATTTAAGCAATTAGGCCTAA
1 TAACTTAATTAAATAATTTAATCAATTAGGCCCAA
* * *
25646436 TAACTTAATTAAACAATTTAATTAATTAAGCCCAA
1 TAACTTAATTAAATAATTTAATCAATTAGGCCCAA
* * * *
25646471 CAATTTAATTAAACAATTTTAATCAACTAGGCCCAA
1 TAACTTAATTAAATAA-TTTAATCAATTAGGCCCAA
* *
25646507 TGACTTAATTAAACAAATTTAATCAATTAGGCCCAA
1 TAACTTAATTAAA-TAATTTAATCAATTAGGCCCAA
*** * *
25646543 TAACTTAATTGTTTAATTTAATTAATTAGGCTCAA
1 TAACTTAATTAAATAATTTAATCAATTAGGCCCAA
* * *
25646578 TGACTTAATTAAATAATTTAATTAATTAAGCCCAA
1 TAACTTAATTAAATAATTTAATCAATTAGGCCCAA
* * * * *
25646613 TGATTTAATTAAACAATTTAGTTAATTAGG--C-A
1 TAACTTAATTAAATAATTTAATCAATTAGGCCCAA
* *
25646645 CAACTTAATTAAACAATTTTAATCAA
1 TAACTTAATTAAATAA-TTTAATCAA
25646671 GTGCTTGAGA
Statistics
Matches: 193, Mismatches: 39, Indels: 8
0.80 0.16 0.03
Matches are distributed among these distances:
32 14 0.07
33 8 0.04
35 116 0.60
36 53 0.27
37 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.37
Consensus pattern (35 bp):
TAACTTAATTAAATAATTTAATCAATTAGGCCCAA
Found at i:25646545 original size:107 final size:105
Alignment explanation
Indices: 25646415--25646663 Score: 288
Period size: 107 Copynumber: 2.4 Consensus size: 105
25646405 TTAATTATTT
* * *
25646415 AATTTAAGCAATTAGGCCTAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAATTTAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAACTTAAT
*
25646480 TAAACAATTTTAATCAACTAGGCCCAATGACTTAATTAAAC
66 TAAACAA-TTTAATCAACTAAGCCCAATGACTTAATTAAAC
**** * * **
25646521 AAATTTAATCAATTAGGCCCAATAACTTAATTGTTTAATTTAATTAATTAGGCTCAATGACTTAA
1 -AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAACTTAA
* * * *
25646586 TTAAATAATTTAATTAATTAAGCCCAATGATTTAATTAAAC
65 TTAAACAATTTAATCAACTAAGCCCAATGACTTAATTAAAC
* * *
25646627 AATTTAGTTAATTAGG--C-ACAACTTAATTAAACAATTT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTT
25646664 TAATCAAGTG
Statistics
Matches: 119, Mismatches: 23, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
102 15 0.13
103 1 0.01
105 14 0.12
106 29 0.24
107 60 0.50
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (105 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAACTTAAT
TAAACAATTTAATCAACTAAGCCCAATGACTTAATTAAAC
Found at i:25646570 original size:142 final size:138
Alignment explanation
Indices: 25646401--25646670 Score: 380
Period size: 142 Copynumber: 1.9 Consensus size: 138
25646391 TAAGCCTAAT
25646401 TAACTTAATTATTTAATTTAAGCAATTAGGC-CTAATAACTTAATTAAACAATTTAATTAATTAA
1 TAACTTAATTATTTAATTTAAGCAATTAGGCTC-AATAACTTAATTAAACAATTTAATTAATTAA
*
25646465 GCCCAACAATTTAATTAAACAATTTTAATCAACTAGGCCCAATGACTTAATTAAACAAATTTAAT
65 GCCCAACAATTTAATTAAACAA-TTTAATCAACTAGGCAC-A--ACTTAATTAAACAAATTTAAT
25646530 CAATTAGGCCCAA
126 CAATTAGGCCCAA
* ** * *
25646543 TAACTTAATTGTTTAATTTAATTAATTAGGCTCAATGACTTAATTAAATAATTTAATTAATTAAG
1 TAACTTAATTATTTAATTTAAGCAATTAGGCTCAATAACTTAATTAAACAATTTAATTAATTAAG
** * * * *
25646608 CCCAATGATTTAATTAAACAATTTAGTTAATTAGGCACAACTTAATTAAACAATTTTAATCAA
66 CCCAACAATTTAATTAAACAATTTAATCAACTAGGCACAACTTAATTAAACAAATTTAATCAA
25646671 GTGCTTGAGA
Statistics
Matches: 115, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
138 23 0.20
140 1 0.01
141 13 0.11
142 77 0.67
143 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.37
Consensus pattern (138 bp):
TAACTTAATTATTTAATTTAAGCAATTAGGCTCAATAACTTAATTAAACAATTTAATTAATTAAG
CCCAACAATTTAATTAAACAATTTAATCAACTAGGCACAACTTAATTAAACAAATTTAATCAATT
AGGCCCAA
Found at i:25654571 original size:64 final size:61
Alignment explanation
Indices: 25654471--25654596 Score: 225
Period size: 64 Copynumber: 2.0 Consensus size: 61
25654461 TATCTCAAAT
25654471 TCCCTCTACATCTCTTTAGCAAAGTTCTTGCATAAAGCCTCATTAGTTGCACTAAACACAA
1 TCCCTCTACATCTCTTTAGCAAAGTTCTTGCATAAAGCCTCATTAGTTGCACTAAACACAA
25654532 TNCCCTCTACCATCTCTTTAGTCAAAGTTCTTGCATAAAGCCTCATTAGTTGCACTAAACACAA
1 T-CCCTCTA-CATCTCTTTAG-CAAAGTTCTTGCATAAAGCCTCATTAGTTGCACTAAACACAA
25654596 T
1 T
25654597 GTCATCCATA
Statistics
Matches: 62, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
61 1 0.02
62 7 0.11
63 11 0.18
64 43 0.69
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.32
Consensus pattern (61 bp):
TCCCTCTACATCTCTTTAGCAAAGTTCTTGCATAAAGCCTCATTAGTTGCACTAAACACAA
Found at i:25662561 original size:37 final size:37
Alignment explanation
Indices: 25662519--25662637 Score: 186
Period size: 37 Copynumber: 3.2 Consensus size: 37
25662509 TAATGTTTTG
*
25662519 TGATGATGTTGAAGTGTGCGAGTATGGAGTGCACACA
1 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
* * *
25662556 TGATGATGTT-AGAGTGTGTGAATAGGGAGTGCACACT
1 TGATGATGTTGA-AGTGTGCGAGTAGGGAGTGCACACA
25662593 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
1 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
25662630 TGATGATG
1 TGATGATG
25662638 ATATTGCATT
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
36 1 0.01
37 71 0.97
38 1 0.01
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.28
Consensus pattern (37 bp):
TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
Found at i:25667512 original size:43 final size:43
Alignment explanation
Indices: 25667455--25667573 Score: 177
Period size: 43 Copynumber: 2.8 Consensus size: 43
25667445 GTAATTATAT
* *
25667455 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
*
25667498 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
* *
25667541 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCAT
25667574 GAGCTGGTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.22, C:0.21, G:0.38, T:0.19
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
Found at i:25667583 original size:43 final size:43
Alignment explanation
Indices: 25667465--25667586 Score: 174
Period size: 43 Copynumber: 2.8 Consensus size: 43
25667455 TGACTCGGCT
* **
25667465 ATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCC
*
25667508 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
* *
25667551 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
25667587 TGATGATGGG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 70 0.99
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.19
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
Found at i:25673706 original size:29 final size:24
Alignment explanation
Indices: 25673639--25673709 Score: 63
Period size: 26 Copynumber: 2.7 Consensus size: 24
25673629 GGGGGTGTGA
25673639 AATTGTGAAAAAAAAGAAAAAAAG
1 AATTGTGAAAAAAAAGAAAAAAAG
25673663 AA-TGTTGAGAGAAAAAAGAAGAGAAAAG
1 AATTG-TGA-A-AAAAAAGAA-A-AAAAG
25673691 TTCAATTGTGAAAAAAAAG
1 ---AATTGTGAAAAAAAAG
25673710 GTGTACTTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
23 2 0.05
24 5 0.13
25 1 0.03
26 9 0.24
27 1 0.03
28 5 0.13
29 7 0.18
30 1 0.03
31 5 0.13
32 2 0.05
ACGTcount: A:0.62, C:0.01, G:0.21, T:0.15
Consensus pattern (24 bp):
AATTGTGAAAAAAAAGAAAAAAAG
Found at i:25677221 original size:105 final size:103
Alignment explanation
Indices: 25677088--25677390 Score: 448
Period size: 105 Copynumber: 2.9 Consensus size: 103
25677078 TGGTTATTTC
*
25677088 ATATAAGATATCAAATTATATTATAATAATCTTGTTATGAGATAACATGTTAGAATTATAACC-C
1 ATATAAGATATCAAATTGTATTATAATAAT-TTGTTATGAGATAACATGTTAGAATTAT-ACCAC
25677152 GTTAATATATATTTTGGTTAGTAGGAGTTTATACCTACTTG
64 -TTAATATATATTTTGGTTAGTAGGAGTTTATACCTACTTG
*
25677193 ATATAAGATATCAAACTGTATTATAATAATGTTGTTATGAGATAACATGTTAGAATTATACTCAC
1 ATATAAGATATCAAATTGTATTATAATAAT-TTGTTATGAGATAACATGTTAGAATTATAC-CAC
* * *
25677258 TTAGTATATATTTTGGTTAATAGGAGTTTATACCTATTTG
64 TTAATATATATTTTGGTTAGTAGGAGTTTATACCTACTTG
* * * *
25677298 ATATAAGATATCAAATTGTATTATAATAGTTTG-TATGAGATAACAAGTTAGAATTGTACCTACC
1 ATATAAGATATCAAATTGTATTATAATAATTTGTTATGAGATAACATGTTAGAATTATACC-ACT
25677362 TAATATATATTTCTGGTTAGTAGGAGTTT
65 TAATATATATTT-TGGTTAGTAGGAGTTT
25677391 TTACATTTTT
Statistics
Matches: 181, Mismatches: 13, Indels: 9
0.89 0.06 0.04
Matches are distributed among these distances:
102 1 0.01
103 37 0.20
104 20 0.11
105 122 0.67
106 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.41
Consensus pattern (103 bp):
ATATAAGATATCAAATTGTATTATAATAATTTGTTATGAGATAACATGTTAGAATTATACCACTT
AATATATATTTTGGTTAGTAGGAGTTTATACCTACTTG
Found at i:25678508 original size:15 final size:15
Alignment explanation
Indices: 25678438--25678508 Score: 81
Period size: 15 Copynumber: 4.7 Consensus size: 15
25678428 AAGAATAGTT
* *
25678438 GAGAAAGAAAAAAGAA
1 GAGAAAGGAAGAA-AA
*
25678454 GAGAAAGGAAAAAAA
1 GAGAAAGGAAGAAAA
*
25678469 GAGAAAGGAAGAAAG
1 GAGAAAGGAAGAAAA
*
25678484 GAGGAA-GAAGAAAA
1 GAGAAAGGAAGAAAA
25678498 GAGAAAGGAAG
1 GAGAAAGGAAG
25678509 GTTCGGCTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
14 12 0.25
15 24 0.50
16 12 0.25
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (15 bp):
GAGAAAGGAAGAAAA
Found at i:25680139 original size:81 final size:81
Alignment explanation
Indices: 25680048--25680211 Score: 276
Period size: 81 Copynumber: 2.0 Consensus size: 81
25680038 ATAGCTGGAG
* *
25680048 TCATCGTGTGCACCCCTACATCACGCACAACTAATGCCATCATGTGCTCCCCCCACATTGTGCAC
1 TCATCGTGTGCACCCCCACATCACGCACAACTAATGCCATCATGTGCTCCCCCCACATCGTGCAC
25680113 AT-GGCATATATCATCA
66 ATAGGCA-ATATCATCA
*
25680129 TCATCGTGTGCACCCCCACATCGCGCACAACTAATGCCATCATGTGCTCCCCCCACATCGTGCAC
1 TCATCGTGTGCACCCCCACATCACGCACAACTAATGCCATCATGTGCTCCCCCCACATCGTGCAC
*
25680194 ATAGGCAATCTCATCA
66 ATAGGCAATATCATCA
25680210 TC
1 TC
25680212 CACACTCCCT
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
81 74 0.95
82 4 0.05
ACGTcount: A:0.25, C:0.38, G:0.14, T:0.23
Consensus pattern (81 bp):
TCATCGTGTGCACCCCCACATCACGCACAACTAATGCCATCATGTGCTCCCCCCACATCGTGCAC
ATAGGCAATATCATCA
Found at i:25683815 original size:21 final size:21
Alignment explanation
Indices: 25683789--25683836 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
25683779 GCTATAAATA
* *
25683789 TCATTTTTTCCACCAGCTTCT
1 TCATTTTTTCCAACAACTTCT
*
25683810 TCA-TTTCTCCAACAACTTCT
1 TCATTTTTTCCAACAACTTCT
25683830 TC-TTTTT
1 TCATTTTT
25683837 CTTCCTCCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.17, C:0.31, G:0.02, T:0.50
Consensus pattern (21 bp):
TCATTTTTTCCAACAACTTCT
Found at i:25684571 original size:2 final size:2
Alignment explanation
Indices: 25684564--25684612 Score: 62
Period size: 2 Copynumber: 24.0 Consensus size: 2
25684554 TGTTATGTTG
* * *
25684564 AT AT AT AT AT AT AT AT AT AC AT AT AT GT AT CT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25684606 AT GAT AT
1 AT -AT AT
25684613 GTATTGATAG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:25690696 original size:27 final size:27
Alignment explanation
Indices: 25690639--25690697 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
25690629 TGGGTGGTGT
* * *
25690639 AAAATTACAATTTTACCCCTAGGTGGC
1 AAAATGACAATTTTACCCCTAGCTCGC
* *
25690666 AAAATGACTATTTTACCCCTATGCTCGA
1 AAAATGACAATTTTACCCCTA-GCTCGC
25690694 AAAA
1 AAAA
25690698 AGCCGAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (27 bp):
AAAATGACAATTTTACCCCTAGCTCGC
Found at i:25699480 original size:16 final size:16
Alignment explanation
Indices: 25699439--25699481 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
25699429 TTTCAAGACA
25699439 ATTTATAAAATCATTTT
1 ATTTATAAAA-CATTTT
25699456 ATTTA-AAAACATTTT
1 ATTTATAAAACATTTT
*
25699471 GTTTATAAAAC
1 ATTTATAAAAC
25699482 CTAAAAATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 10 0.42
16 9 0.38
17 5 0.21
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (16 bp):
ATTTATAAAACATTTT
Found at i:25705700 original size:19 final size:18
Alignment explanation
Indices: 25705678--25705736 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
25705668 TATGACACTG
*
25705678 AATAAAATATTAATTTTT
1 AATAAAATATTATTTTTT
25705696 --T--AATATTATTTTATT
1 AATAAAATATTATTTT-TT
25705711 AATAAAATATTATTTTTT
1 AATAAAATATTATTTTTT
*
25705729 AAAAAAAT
1 AATAAAAT
25705737 TTTCCACCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 10 0.29
15 2 0.06
16 1 0.03
17 1 0.03
18 9 0.26
19 11 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATAAAATATTATTTTTT
Found at i:25705735 original size:18 final size:19
Alignment explanation
Indices: 25705697--25705736 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
25705687 TTAATTTTTT
*
25705697 AATATTATTTTATTAATAA
1 AATATTATTTTATTAAAAA
25705716 AATATTATTTT-TTAAAAA
1 AATATTATTTTATTAAAAA
25705734 AAT
1 AAT
25705737 TTTCCACCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATATTATTTTATTAAAAA
Found at i:25709947 original size:43 final size:43
Alignment explanation
Indices: 25709880--25709972 Score: 159
Period size: 43 Copynumber: 2.2 Consensus size: 43
25709870 TTGTGTTATA
*
25709880 ATGAGGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
* *
25709923 ATGATGACCCAGCTATGTGTGGTGTGGGAGTGCACATGAGTTG
1 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
25709966 ATGATGA
1 ATGATGA
25709973 TGATATTGCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.23, C:0.15, G:0.38, T:0.25
Consensus pattern (43 bp):
ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
Found at i:25712568 original size:20 final size:19
Alignment explanation
Indices: 25712543--25712584 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
25712533 GCTTGTGATT
25712543 GATATGTCACATAGTATAAA
1 GATATGTCACA-AGTATAAA
**
25712563 GATATGTTGCAAGTATAAA
1 GATATGTCACAAGTATAAA
25712582 GAT
1 GAT
25712585 GCTTGGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (19 bp):
GATATGTCACAAGTATAAA
Found at i:25716036 original size:16 final size:15
Alignment explanation
Indices: 25716015--25716085 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
25716005 AGGAAGAGTT
25716015 GAGAAAGAAAGAAGAA
1 GAGAAAGAAAGAA-AA
* *
25716031 GAGAAAGGAAGAAAG
1 GAGAAAGAAAGAAAA
* *
25716046 GAGAAAGGAATAAATA
1 GAGAAAGAAAGAAA-A
* *
25716062 -AGGAAG-AATAAAA
1 GAGAAAGAAAGAAAA
25716075 GAGAAAGAAAG
1 GAGAAAGAAAG
25716086 GTTTGGCCTA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
13 1 0.02
14 11 0.24
15 21 0.47
16 12 0.27
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (15 bp):
GAGAAAGAAAGAAAA
Found at i:25717308 original size:25 final size:25
Alignment explanation
Indices: 25717279--25717328 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
25717269 ATGGTCTATG
*
25717279 ATTATACATAGCAAGGCCACGAGTT
1 ATTATACATAGCAAGGCCACAAGTT
* * *
25717304 ATTATATATGGCTAGGCCACAAGTT
1 ATTATACATAGCAAGGCCACAAGTT
25717329 GTGATACGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (25 bp):
ATTATACATAGCAAGGCCACAAGTT
Found at i:25719367 original size:28 final size:28
Alignment explanation
Indices: 25719306--25719534 Score: 199
Period size: 29 Copynumber: 7.9 Consensus size: 28
25719296 TTATGACAAC
* * *
25719306 TCTTGTCTTTAATTAAGATAAAACATATTA
1 TCTTGTC-TAAATTAAGA-CAAACATATTT
* *
25719336 TCTTGTCTAAATTGAGACAAATATATTT
1 TCTTGTCTAAATTAAGACAAACATATTT
* * *
25719364 TCTTGTCTAAAATAAGAAAAAATATATTTT
1 TCTTGTCTAAATTAAG-ACAAACATA-TTT
* *
25719394 TCTTTTCTTAAATTAAGACAAATATATTT
1 TCTTGTC-TAAATTAAGACAAACATATTT
* * * *
25719423 T-TTTTTTCAAATTATGACAAAACATGTTT
1 TCTTGTCT-AAATTAAGAC-AAACATATTT
*
25719452 TCTTGTCTAAATTAAGACAAACATGTTT
1 TCTTGTCTAAATTAAGACAAACATATTT
* *
25719480 TCTTCGTCTAAATTAAGATAAAACATGTTT
1 TCTT-GTCTAAATTAAGA-CAAACATATTT
*
25719510 TCTTGTCTAAATTAAGTCATAACAT
1 TCTTGTCTAAATTAAGACA-AACAT
25719535 GCCTAAAGCT
Statistics
Matches: 169, Mismatches: 21, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
27 1 0.01
28 50 0.30
29 68 0.40
30 42 0.25
31 8 0.05
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATATTT
Found at i:25719503 original size:58 final size:57
Alignment explanation
Indices: 25719306--25719534 Score: 244
Period size: 58 Copynumber: 3.9 Consensus size: 57
25719296 TTATGACAAC
* * * * *
25719306 TCTTGTCTTTAATTAAGATAAAACATATTATCTTGTCTAAATTGAGACAAATATATTT
1 TCTTGTC-TAAATTAAGATAAAACATGTTTTCTTGTCTAAATTAAGACAAACATATTT
* * * * * *
25719364 TCTTGTCTAAAATAAGAAAAAATATATTTTTCTTTTCTTAAATTAAGACAAATATATTT
1 TCTTGTCTAAATTAAGATAAAACAT-GTTTTCTTGTC-TAAATTAAGACAAACATATTT
* * * * *
25719423 T-TTTTTTCAAATTATGACAAAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTT
1 TCTTGTCT-AAATTAAGATAAAACATGTTTTCTTGTCTAAATTAAGACAAACATATTT
*
25719480 TCTTCGTCTAAATTAAGATAAAACATGTTTTCTTGTCTAAATTAAGTCATAACAT
1 TCTT-GTCTAAATTAAGATAAAACATGTTTTCTTGTCTAAATTAAGACA-AACAT
25719535 GCCTAAAGCT
Statistics
Matches: 142, Mismatches: 23, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
57 34 0.24
58 67 0.47
59 41 0.29
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (57 bp):
TCTTGTCTAAATTAAGATAAAACATGTTTTCTTGTCTAAATTAAGACAAACATATTT
Found at i:25723577 original size:35 final size:35
Alignment explanation
Indices: 25723538--25723618 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
25723528 ATCTTGATAG
*
25723538 AGGTTATGCCTGATCTTGAAAAAGACATGTTGTAA
1 AGGTTATGCCTGATCTTGAAAAAGACACGTTGTAA
* ** * *
25723573 AGGTTACGTTTGATCTTGTAAAAGGCACGTTGTAA
1 AGGTTATGCCTGATCTTGAAAAAGACACGTTGTAA
*
25723608 AAGTTATGCCT
1 AGGTTATGCCT
25723619 AACTCTATTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.33
Consensus pattern (35 bp):
AGGTTATGCCTGATCTTGAAAAAGACACGTTGTAA
Found at i:25725499 original size:2 final size:2
Alignment explanation
Indices: 25725492--25725524 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
25725482 TTTATGACAT
25725492 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25725525 CAACATCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25730317 original size:28 final size:29
Alignment explanation
Indices: 25730276--25730335 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
25730266 GTCTATGGGC
*
25730276 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
25730304 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
25730334 AA
1 AA
25730336 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:25732955 original size:40 final size:39
Alignment explanation
Indices: 25732911--25733012 Score: 125
Period size: 39 Copynumber: 2.6 Consensus size: 39
25732901 CCAGCTCATG
* *
25732911 TGCATCCCCCCACATCGTGCACATAGCAGAA-GTCATCGTC
1 TGCATCCCCCCACATCGTGCACA-A-AAGAATGCCATCGTC
* * *
25732951 TGCATCCCCACACATCGTGCACAAAATAATGCCATCGTG
1 TGCATCCCCCCACATCGTGCACAAAAGAATGCCATCGTC
*
25732990 TACATCCCCCCACATCGTGCACA
1 TGCATCCCCCCACATCGTGCACA
25733013 CGGGCCGTGT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.06
39 29 0.54
40 22 0.41
ACGTcount: A:0.27, C:0.38, G:0.15, T:0.20
Consensus pattern (39 bp):
TGCATCCCCCCACATCGTGCACAAAAGAATGCCATCGTC
Found at i:25733955 original size:35 final size:34
Alignment explanation
Indices: 25733872--25733980 Score: 146
Period size: 35 Copynumber: 3.1 Consensus size: 34
25733862 TTTCTCTTTC
* * *
25733872 AAATTTGCAGCAAAACTCTTTCTATTTCCTCTCA
1 AAATTTACAGCAAAACTCTTCCTATTTCCTCTAA
*
25733906 AAATTTACAGCAAAACTCCTCCTATTTCCTCTTAA
1 AAATTTACAGCAAAACTCTTCCTATTTCCTC-TAA
* *
25733941 AAATTTACAACAAAACTCTTCCTATTTCTTTCTAA
1 AAATTTACAGCAAAACTCTTCCTATTTC-CTCTAA
25733976 AAATT
1 AAATT
25733981 GTGCAGCACA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
34 28 0.42
35 36 0.55
36 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.38
Consensus pattern (34 bp):
AAATTTACAGCAAAACTCTTCCTATTTCCTCTAA
Found at i:25737361 original size:14 final size:14
Alignment explanation
Indices: 25737342--25737368 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25737332 ACATATACTC
25737342 ATATTTCAAAATAT
1 ATATTTCAAAATAT
25737356 ATATTTCAAAATA
1 ATATTTCAAAATA
25737369 ATTGGCAGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATTTCAAAATAT
Found at i:25748524 original size:21 final size:19
Alignment explanation
Indices: 25748488--25748528 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
25748478 ACATGTTGAG
25748488 TAGTTAATTTAAGTTATTT
1 TAGTTAATTTAAGTTATTT
*
25748507 TAGTTAAATTTTATGTTATTT
1 TAGTT-AA-TTTAAGTTATTT
25748528 T
1 T
25748529 GTTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (19 bp):
TAGTTAATTTAAGTTATTT
Found at i:25759417 original size:42 final size:43
Alignment explanation
Indices: 25759328--25759418 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
25759318 ACCATCCCAC
** * *
25759328 CATCATCAGTTCATGTGCATTCCCACACCGCACATAGCTGGGT
1 CATCATCAACTCATGTGCACTCCCACACCACACATAGCTGGGT
*
25759371 CATCATCAACTCATGTGCACTCCCACA-CACACATAGTTGGGT
1 CATCATCAACTCATGTGCACTCCCACACCACACATAGCTGGGT
25759413 CATCAT
1 CATCAT
25759419 TATCACACAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 19 0.44
43 24 0.56
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.25
Consensus pattern (43 bp):
CATCATCAACTCATGTGCACTCCCACACCACACATAGCTGGGT
Found at i:25760244 original size:22 final size:23
Alignment explanation
Indices: 25760219--25760268 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
25760209 GGAAGAAATA
*
25760219 AGAAGAAG-AAGAAGAAGCTGCT
1 AGAAGAAGTAAGAAAAAGCTGCT
* *
25760241 AGAA-ATGTGAGAAAAAGCTGCT
1 AGAAGAAGTAAGAAAAAGCTGCT
25760263 AGAAGA
1 AGAAGA
25760269 TGATATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.09
22 20 0.87
23 1 0.04
ACGTcount: A:0.50, C:0.08, G:0.30, T:0.12
Consensus pattern (23 bp):
AGAAGAAGTAAGAAAAAGCTGCT
Found at i:25761376 original size:21 final size:21
Alignment explanation
Indices: 25761293--25761368 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
25761283 TCTTGAAAAA
* *
25761293 ATGTATCAATACATTATGAAC
1 ATGTATCGATACATCATGAAC
* * *
25761314 ATTTATTGATA-A--ATGACC
1 ATGTATCGATACATCATGAAC
25761332 ATACGTATCGATACATCATGAAC
1 AT--GTATCGATACATCATGAAC
25761355 ATGTATCGATACAT
1 ATGTATCGATACAT
25761369 TTGAAACAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
18 7 0.16
20 8 0.19
21 21 0.49
23 7 0.16
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATCATGAAC
Found at i:25785613 original size:13 final size:13
Alignment explanation
Indices: 25785595--25785619 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25785585 TTTCAGAAAA
25785595 TTTATAAAATCAT
1 TTTATAAAATCAT
25785608 TTTATAAAATCA
1 TTTATAAAATCA
25785620 CAATTTCTCC
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:25787945 original size:72 final size:72
Alignment explanation
Indices: 25787790--25787971 Score: 197
Period size: 72 Copynumber: 2.5 Consensus size: 72
25787780 CTTCTTAGGG
* * * *
25787790 ATCAACCATTCATGC-TTGGAGGGTTGATCCTTTTCTTCCAAAGACTTAGCTTCTCTGTTTTGAC
1 ATCAACCTTTCATGCTTTGG-GGGTCGATCCTTTTCTTCCAAAAACTTAGCTTCTCTATTTTGAC
25787854 TTCCAAGA
65 TTCCAAGA
* * *
25787862 ATCAACTTTTCATGCTTTGGGGGTCGATCCTTTTCTTCCAAAAAGTTAGCTTTTCTATTTTGA-T
1 ATCAACCTTTCATGCTTTGGGGGTCGATCCTTTTCTTCCAAAAACTTAGCTTCTCTATTTTGACT
* *
25787926 GTCTAAGG
66 -TCCAAGA
** * * * *
25787934 ATTGACCTTTCATTCTTGGGGGGTCAAACCTTTTCTTC
1 ATCAACCTTTCATGCTTTGGGGGTCGATCCTTTTCTTC
25787972 TAGTAAGTGA
Statistics
Matches: 92, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
71 1 0.01
72 87 0.95
73 4 0.04
ACGTcount: A:0.20, C:0.21, G:0.18, T:0.41
Consensus pattern (72 bp):
ATCAACCTTTCATGCTTTGGGGGTCGATCCTTTTCTTCCAAAAACTTAGCTTCTCTATTTTGACT
TCCAAGA
Found at i:25789952 original size:50 final size:50
Alignment explanation
Indices: 25789893--25790008 Score: 171
Period size: 50 Copynumber: 2.3 Consensus size: 50
25789883 CACTATCAAC
* * * *
25789893 GATTCTTACTTTTTAACATGAAGCTATAACCCTTACACAAT-TCATAAAGG
1 GATTCTTACTTTTTAACAGGAAACGATAACCCTTACACAATCT-AGAAAGG
25789943 GATTCTTACTTTTTAACAGGAAACGATAACCCTTACACAATCTAGAAAGG
1 GATTCTTACTTTTTAACAGGAAACGATAACCCTTACACAATCTAGAAAGG
*
25789993 GCTTCTTACTTTTTAA
1 GATTCTTACTTTTTAA
25790009 TGGGATGAAG
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 59 0.98
51 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (50 bp):
GATTCTTACTTTTTAACAGGAAACGATAACCCTTACACAATCTAGAAAGG
Found at i:25795718 original size:42 final size:42
Alignment explanation
Indices: 25795669--25795776 Score: 137
Period size: 42 Copynumber: 2.6 Consensus size: 42
25795659 CCTTTTGTGT
25795669 GATGATGATGACCCAGCCATGTGCATGT-AGAAGTACACATGA
1 GATGATGATGACCCAGCCATGTGCATGTAAG-AGTACACATGA
* * * *
25795711 GCTGATGATGACCCAGCCATGTGCTTGTAAGAGTTCATATGA
1 GATGATGATGACCCAGCCATGTGCATGTAAGAGTACACATGA
* * *
25795753 GATGATGCTGACCCAACTATGTGC
1 GATGATGATGACCCAGCCATGTGC
25795777 GAGTGGGGAG
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 55 0.96
43 2 0.04
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (42 bp):
GATGATGATGACCCAGCCATGTGCATGTAAGAGTACACATGA
Found at i:25803310 original size:42 final size:42
Alignment explanation
Indices: 25803251--25803385 Score: 171
Period size: 42 Copynumber: 3.2 Consensus size: 42
25803241 TTTTGTGTGA
* *
25803251 TGATGATGACCCAGCCATGTGCGTGTAGAAGTTCACATGAGC
1 TGATGATGACCCAGCCATGTGCGTGTAGGAGTGCACATGAGC
* *
25803293 TGATGATGACCCAGCCATGTGCGTGTTGGAGTGCATATGAGC
1 TGATGATGACCCAGCCATGTGCGTGTAGGAGTGCACATGAGC
* * * * * *
25803335 TTATGCTGACCCAGCTATGTGAGAGTGGGGAGTGCACATGAGC
1 TGATGATGACCCAGCCATGTGCGTGT-AGGAGTGCACATGAGC
25803378 TGATGATG
1 TGATGATG
25803386 GTGGGATGGT
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 59 0.75
43 20 0.25
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.25
Consensus pattern (42 bp):
TGATGATGACCCAGCCATGTGCGTGTAGGAGTGCACATGAGC
Found at i:25825917 original size:5 final size:5
Alignment explanation
Indices: 25825904--25825943 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
25825894 CTATTAAATC
* *
25825904 TAACC TAACT TAACT TAACT TAACT TATCT TAACT TAACT
1 TAACT TAACT TAACT TAACT TAACT TAACT TAACT TAACT
25825944 GGACTTGGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (5 bp):
TAACT
Found at i:25829044 original size:2 final size:2
Alignment explanation
Indices: 25829037--25829074 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
25829027 ATGAAGAATA
25829037 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25829075 GAATAAGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25829396 original size:35 final size:35
Alignment explanation
Indices: 25829314--25829419 Score: 126
Period size: 36 Copynumber: 3.0 Consensus size: 35
25829304 CTTTTGCTGC
* *
25829314 TGATTTTGAAGGCTGAACGATATGGTTTT-TTTCT
1 TGATTTTGAAGGCTGAACGATATGGTTTTGGTTGT
25829348 ACTGATTTTGAAGGCTGAACGATATGGTTTTGGTTGT
1 --TGATTTTGAAGGCTGAACGATATGGTTTTGGTTGT
* * * *
25829385 TGATTTTGAAGGTTGAAAGTTGTGG-TTTGGTTGT
1 TGATTTTGAAGGCTGAACGATATGGTTTTGGTTGT
25829419 T
1 T
25829420 AATCTTCGTG
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
34 10 0.16
35 21 0.33
36 29 0.46
37 3 0.05
ACGTcount: A:0.20, C:0.06, G:0.29, T:0.45
Consensus pattern (35 bp):
TGATTTTGAAGGCTGAACGATATGGTTTTGGTTGT
Found at i:25829512 original size:34 final size:34
Alignment explanation
Indices: 25829440--25829519 Score: 85
Period size: 34 Copynumber: 2.4 Consensus size: 34
25829430 GCTTTGGTTG
* * *
25829440 CTGATTTTTGAAGGAGAATAGTACAGTTAAGTTG
1 CTGATTTTTGAAGGAGAATAGAACAGTTAAGCTA
*
25829474 CTGATTTTTG-AGGAGAAATAGAATAGCTTAA-CTA
1 CTGATTTTTGAAGGAG-AATAGAACAG-TTAAGCTA
25829508 CTGA-TTTTGAAG
1 CTGATTTTTGAAG
25829520 TCAATATGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
33 10 0.26
34 25 0.64
35 4 0.10
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.35
Consensus pattern (34 bp):
CTGATTTTTGAAGGAGAATAGAACAGTTAAGCTA
Found at i:25840662 original size:11 final size:11
Alignment explanation
Indices: 25840646--25840677 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
25840636 GAAAAATGAG
25840646 AAAAGAAAAAA
1 AAAAGAAAAAA
*
25840657 AAAAGAAAAGA
1 AAAAGAAAAAA
25840668 AAAAGAAAAA
1 AAAAGAAAAA
25840678 GAAAGAGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:25840678 original size:6 final size:6
Alignment explanation
Indices: 25840633--25840681 Score: 66
Period size: 6 Copynumber: 8.2 Consensus size: 6
25840623 ACGGTGAAAG
25840633 AAAGAA AAATGAGA AAAGAA AAA-AA AAAG-A AAAGAA AAAGAA AAAGAA
1 AAAGAA AAA-GA-A AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
25840681 A
1 A
25840682 GAGTGGGCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
5 10 0.26
6 21 0.54
7 4 0.10
8 4 0.10
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:25840683 original size:16 final size:16
Alignment explanation
Indices: 25840629--25840681 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 16
25840619 TTGAACGGTG
*
25840629 AAAGAAAGAAAAATGAGA
1 AAAGAAA-AAAAA-AAGA
25840647 AAAGAAAAAAAAAAGA
1 AAAGAAAAAAAAAAGA
25840663 AAAGAAAAAGAAAAAGA
1 AAAGAAAAA-AAAAAGA
25840680 AA
1 AA
25840682 GAGTGGGCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
16 12 0.36
17 14 0.42
18 7 0.21
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (16 bp):
AAAGAAAAAAAAAAGA
Found at i:25841861 original size:19 final size:19
Alignment explanation
Indices: 25841837--25841874 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
25841827 CCATTTGACT
25841837 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
25841856 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
25841875 GTTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:25850440 original size:22 final size:22
Alignment explanation
Indices: 25850412--25850454 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
25850402 CTCAAAGACT
25850412 GGTATATTTTATGTTCCTTACC
1 GGTATATTTTATGTTCCTTACC
25850434 GGTATATTTTATGTTCCTTAC
1 GGTATATTTTATGTTCCTTAC
25850455 TTTGGAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.51
Consensus pattern (22 bp):
GGTATATTTTATGTTCCTTACC
Found at i:25857725 original size:64 final size:61
Alignment explanation
Indices: 25857642--25857764 Score: 174
Period size: 64 Copynumber: 2.0 Consensus size: 61
25857632 CAACAGATAA
* * * *
25857642 TAACTGTTAGAAACAGACAAAAATAGATTCTGTCTGAAACAAGACACAATTGTGTTTATTGGTT
1 TAACTGCTAAAAACAGACAAAAATAGATT-TGTCTAAAAC-A-ACACAATTGTGTCTATTGGTT
*
25857706 TAACTGCTAAAAACAGACAAAAATCGATTTGTCTAAAACAACACAATTGTGTCTATTGG
1 TAACTGCTAAAAACAGACAAAAATAGATTTGTCTAAAACAACACAATTGTGTCTATTGG
25857765 AAAATTACCT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
61 18 0.33
62 1 0.02
63 9 0.17
64 26 0.48
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (61 bp):
TAACTGCTAAAAACAGACAAAAATAGATTTGTCTAAAACAACACAATTGTGTCTATTGGTT
Found at i:25889592 original size:43 final size:43
Alignment explanation
Indices: 25889531--25889649 Score: 177
Period size: 43 Copynumber: 2.8 Consensus size: 43
25889521 TAAGTCATGT
* * *
25889531 GCACTCCCTAC-TCGCACATGGCTAGGTCATCATCAGCTTATAC
1 GCACTCCC-ACATCGCACATAGCTGGGTCATCATCAGCTCATAC
**
25889574 GCACTCCCACATCGCACATAGCTGGGTCATCATCAGCTCATGT
1 GCACTCCCACATCGCACATAGCTGGGTCATCATCAGCTCATAC
25889617 GCACTCCCACATCGCACATAGCTGGGTCATCAT
1 GCACTCCCACATCGCACATAGCTGGGTCATCAT
25889650 TATCACACAA
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
42 2 0.03
43 68 0.97
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.24
Consensus pattern (43 bp):
GCACTCCCACATCGCACATAGCTGGGTCATCATCAGCTCATAC
Found at i:25889607 original size:21 final size:21
Alignment explanation
Indices: 25889583--25889649 Score: 50
Period size: 21 Copynumber: 3.1 Consensus size: 21
25889573 CGCACTCCCA
25889583 CATCGCACATAGCTGGGTCAT
1 CATCGCACATAGCTGGGTCAT
* **
25889604 CATCAGCTCAT-G-TGCACTCCCA-
1 CATC-GCACATAGCTG-GGT--CAT
25889626 CATCGCACATAGCTGGGTCAT
1 CATCGCACATAGCTGGGTCAT
25889647 CAT
1 CAT
25889650 TATCACACAA
Statistics
Matches: 33, Mismatches: 6, Indels: 14
0.62 0.11 0.26
Matches are distributed among these distances:
20 4 0.12
21 14 0.42
22 11 0.33
23 4 0.12
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (21 bp):
CATCGCACATAGCTGGGTCAT
Found at i:25901818 original size:11 final size:12
Alignment explanation
Indices: 25901790--25901830 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
25901780 ATGGTCAACC
*
25901790 ATAAG-GAGAAA
1 ATAAGAGAGGAA
25901801 ATAAGAGAGGAA
1 ATAAGAGAGGAA
25901813 AT-AGAGAGGAA
1 ATAAGAGAGGAA
25901824 ATGAAGA
1 AT-AAGA
25901831 AAAGAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 16 0.62
12 7 0.27
13 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.32, T:0.10
Consensus pattern (12 bp):
ATAAGAGAGGAA
Found at i:25916742 original size:26 final size:26
Alignment explanation
Indices: 25916682--25916743 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
25916672 ACCATATACC
*
25916682 CATCATCAACATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
25916708 CATCATCATCATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
25916734 CATCATCATC
1 CATCATCATC
25916744 TCATATGCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.32, C:0.42, G:0.03, T:0.23
Consensus pattern (26 bp):
CATCATCATCATGCACACCATCCCAT
Found at i:25921127 original size:20 final size:20
Alignment explanation
Indices: 25921102--25921139 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25921092 TTAGACAATA
25921102 TCTTTAA-ACCTTAATAAACT
1 TCTTTAAGA-CTTAATAAACT
25921122 TCTTTAAGACTTAATAAA
1 TCTTTAAGACTTAATAAA
25921140 AAATAATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (20 bp):
TCTTTAAGACTTAATAAACT
Found at i:25921998 original size:26 final size:26
Alignment explanation
Indices: 25921957--25922079 Score: 115
Period size: 26 Copynumber: 4.8 Consensus size: 26
25921947 GTGTCTATCA
*
25921957 ACTTTTGATGGTAAAATTATCCATTC
1 ACTTTTGGTGGTAAAATTATCCATTC
* * *
25921983 ACTTTTGGTGGCAAAATTATCTATCC
1 ACTTTTGGTGGTAAAATTATCCATTC
** *
25922009 ACTTTTGGTGACAAAATTATTC-TT-
1 ACTTTTGGTGGTAAAATTATCCATTC
* * *
25922033 AGATTTTGATGATAAAATTATCCATTC
1 A-CTTTTGGTGGTAAAATTATCCATTC
**
25922060 TTTTTTGGTGGTAAAATTAT
1 ACTTTTGGTGGTAAAATTAT
25922080 AATTAAAATA
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
24 1 0.01
25 18 0.23
26 59 0.76
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (26 bp):
ACTTTTGGTGGTAAAATTATCCATTC
Found at i:25925427 original size:17 final size:17
Alignment explanation
Indices: 25925405--25925439 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
25925395 GGAAGTTTTC
25925405 CTCCCCCTAAGTGTGTG
1 CTCCCCCTAAGTGTGTG
*
25925422 CTCCCCCTTAGTGTGTG
1 CTCCCCCTAAGTGTGTG
25925439 C
1 C
25925440 ATAGTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.09, C:0.37, G:0.23, T:0.31
Consensus pattern (17 bp):
CTCCCCCTAAGTGTGTG
Found at i:25937091 original size:2 final size:2
Alignment explanation
Indices: 25937084--25937145 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
25937074 NNNNGTGTTG
25937084 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
25937126 AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
25937146 TATTGTGTAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25937262 original size:43 final size:43
Alignment explanation
Indices: 25937172--25937274 Score: 111
Period size: 43 Copynumber: 2.4 Consensus size: 43
25937162 TGACTTGGCT
* **
25937172 ATGTGCGAGTAGGGAGTACACATAAGCCGAGGATGACCCGGTT
1 ATGTGCGAGTAGGGAGTACACATAAGCCGAGGATGACCCAGCC
* **
25937215 ATGTGTGAGTAGGGAGTACGTATAA-CTCG-GTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTACACATAAGC-CGAG-GATGACCCAGCC
*
25937258 ATGTGCGAGTTGGGAGT
1 ATGTGCGAGTAGGGAGT
25937275 GCGCATGAGC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
42 2 0.04
43 48 0.96
ACGTcount: A:0.25, C:0.17, G:0.36, T:0.22
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTACACATAAGCCGAGGATGACCCAGCC
Found at i:25943741 original size:63 final size:63
Alignment explanation
Indices: 25943642--25943886 Score: 400
Period size: 63 Copynumber: 3.9 Consensus size: 63
25943632 GAAATTGATG
*
25943642 CAACCGTGCATGTGTGGAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTGATAATTA
1 CAACCGTGCATGTGCGGAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTGATAATTA
25943705 CAACCGTGCATGTGCGGAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTGATAATTA
1 CAACCGTGCATGTGCGGAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTGATAATTA
** * *
25943768 TGACCGTGCATGTGCGAAGTGGGAAATGCAATGCCAGTTGAATGACAAAGGATGTGATAATTA
1 CAACCGTGCATGTGCGGAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTGATAATTA
* * * * *
25943831 CGACCGTGCATGTGCGGAGTGGGAAGTGCAATGCCGGTTTAATGATAAAGGTTGTG
1 CAACCGTGCATGTGCGGAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTG
25943887 GGGACGGCGA
Statistics
Matches: 170, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 170 1.00
ACGTcount: A:0.30, C:0.13, G:0.33, T:0.24
Consensus pattern (63 bp):
CAACCGTGCATGTGCGGAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTGATAATTA
Found at i:25947555 original size:61 final size:61
Alignment explanation
Indices: 25947457--25947621 Score: 240
Period size: 61 Copynumber: 2.7 Consensus size: 61
25947447 GGAGCCCAAC
* * * * *
25947457 CGTGCATGTGCGGAGTGGACAGTGCACATGCCGATAATGATGTTGTCATGATATTTATAAT
1 CGTGCATGTGCGGAGTGGGCAGTGCACATACCAATAATGATGCTATCATGATATTTATAAT
*
25947518 CGTGCATGTGCGGAGTGGGCAGTGCACATATCAATAATGATGCTATCATGATATTTATAAT
1 CGTGCATGTGCGGAGTGGGCAGTGCACATACCAATAATGATGCTATCATGATATTTATAAT
* * **
25947579 TGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATGC
1 CGTGCATGTGCGGAGTGGGCAGTGCACATACCAATAATGATGC
25947622 ACATCAGCTG
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 93 1.00
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (61 bp):
CGTGCATGTGCGGAGTGGGCAGTGCACATACCAATAATGATGCTATCATGATATTTATAAT
Found at i:25950657 original size:73 final size:73
Alignment explanation
Indices: 25950508--25950700 Score: 189
Period size: 73 Copynumber: 2.6 Consensus size: 73
25950498 GAATATTGAG
* * ** *
25950508 AAACAGAAAAGACTTAATCGACCAAGAAGTGGGTTAGTTGACTAAGAAGCTACTGCCAAAAATCT
1 AAACAGAAACGACTTAGTCGACCAAGAAGTAAGTTAGTCGACTAAGAAGCTACTGCCAAAAATCT
**
25950573 GGACTTCA
66 GGACTAAA
* *
25950581 AAACA-AAACTGACTTAGTCAACCAAGAAGTAAGTTAGTCGACTAAG-TGCTCACTGCCAAAAA-
1 AAACAGAAAC-GACTTAGTCGACCAAGAAGTAAGTTAGTCGACTAAGAAGCT-ACTGCCAAAAAT
25950643 CTGGAAAC-AAA
64 CTGG--ACTAAA
* * * *
25950654 AAACAGAGACAACTTAGTCGACTAAGACA-TAAGTTACTCGACTAAGA
1 AAACAGAAACGACTTAGTCGACCAAGA-AGTAAGTTAGTCGACTAAGA
25950701 GCATTCTGCT
Statistics
Matches: 99, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
72 10 0.10
73 83 0.84
74 6 0.06
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (73 bp):
AAACAGAAACGACTTAGTCGACCAAGAAGTAAGTTAGTCGACTAAGAAGCTACTGCCAAAAATCT
GGACTAAA
Found at i:25951184 original size:23 final size:21
Alignment explanation
Indices: 25951158--25951202 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
25951148 GGTTTTGGCT
25951158 AAGTTTGGTAAAAGCCATTGTAA
1 AAGTTTGGTAAAAG-C-TTGTAA
*
25951181 AAGTTTGGTGAAAGCTTGTAA
1 AAGTTTGGTAAAAGCTTGTAA
25951202 A
1 A
25951203 TTTCACCGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 1 0.05
23 13 0.62
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (21 bp):
AAGTTTGGTAAAAGCTTGTAA
Found at i:25954486 original size:20 final size:21
Alignment explanation
Indices: 25954449--25954488 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
25954439 TATTTTAATC
25954449 AAATTGATATTAATAATATTT
1 AAATTGATATTAATAATATTT
25954470 AAATT-ATATATAA-AATATT
1 AAATTGATAT-TAATAATATT
25954489 AATATTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
AAATTGATATTAATAATATTT
Found at i:25955818 original size:18 final size:18
Alignment explanation
Indices: 25955795--25955834 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
25955785 AGTTTCACAA
*
25955795 ATAATTCACAAGTAACAC
1 ATAATTCACAAATAACAC
* *
25955813 ATAATTCATAAATAACTC
1 ATAATTCACAAATAACAC
25955831 ATAA
1 ATAA
25955835 ATTAACAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.17, G:0.03, T:0.28
Consensus pattern (18 bp):
ATAATTCACAAATAACAC
Found at i:25957038 original size:9 final size:9
Alignment explanation
Indices: 25957026--25957054 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
25957016 TCCAAAACTC
25957026 AAAAAAATA
1 AAAAAAATA
25957035 AAAAAAAT-
1 AAAAAAATA
25957043 AAAAAAATA
1 AAAAAAATA
25957052 AAA
1 AAA
25957055 TTTGAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATA
Found at i:25957397 original size:16 final size:16
Alignment explanation
Indices: 25957367--25957404 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
25957357 ATTTATACTT
25957367 TTAAACAATAAATAAG
1 TTAAACAATAAATAAG
25957383 TTAAA-AATAAGATAAG
1 TTAAACAATAA-ATAAG
*
25957399 CTAAAC
1 TTAAAC
25957405 GGACACTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.61, C:0.08, G:0.08, T:0.24
Consensus pattern (16 bp):
TTAAACAATAAATAAG
Found at i:25964951 original size:31 final size:31
Alignment explanation
Indices: 25964913--25964990 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
25964903 TGTCATATGG
25964913 ACTAAATTGAACAAAAATATATAATACAGGC
1 ACTAAATTGAACAAAAATATATAATACAGGC
*
25964944 ACTAAATTGAACAAAAATATATAATACAGGG
1 ACTAAATTGAACAAAAATATATAATACAGGC
*
25964975 ATTAAATTGAACAAAA
1 ACTAAATTGAACAAAA
25964991 TTGAGATGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.23
Consensus pattern (31 bp):
ACTAAATTGAACAAAAATATATAATACAGGC
Found at i:25965898 original size:108 final size:108
Alignment explanation
Indices: 25965781--25965984 Score: 327
Period size: 108 Copynumber: 1.9 Consensus size: 108
25965771 AAATTTTGCA
* **
25965781 TAAATTTAAATAAAAGGTAAATTGGGTAAGAGTTGAATAATTTCATACCAATGTGTATTTGTAAA
1 TAAATTTAAATAAAAGGTAAATTGGGTAAGAGTTGAATAATTTCAAAAAAATGTGTATTTGTAAA
* * *
25965846 TTGTGAAAGTTGTAACTAAATAAACATATTTTGCTAATTTGAG
66 TTGTAAAAGGTATAACTAAATAAACATATTTTGCTAATTTGAG
* *
25965889 TAAATTTAAATCAAAGGTAAATTGGGTAAGAGTTGAATAATTTTAAAAAAATGTGTATTTGTAAA
1 TAAATTTAAATAAAAGGTAAATTGGGTAAGAGTTGAATAATTTCAAAAAAATGTGTATTTGTAAA
*
25965954 TTGTAAAAGGTATAACTAAATCAACATATTT
66 TTGTAAAAGGTATAACTAAATAAACATATTT
25965985 AGTTACTTTA
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
108 87 1.00
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (108 bp):
TAAATTTAAATAAAAGGTAAATTGGGTAAGAGTTGAATAATTTCAAAAAAATGTGTATTTGTAAA
TTGTAAAAGGTATAACTAAATAAACATATTTTGCTAATTTGAG
Found at i:25967025 original size:26 final size:26
Alignment explanation
Indices: 25966996--25967045 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
25966986 GTTGTTGTGC
* * *
25966996 TATATTTTGTTAGTCAATTGCATGAA
1 TATATTGTATTAGTCAACTGCATGAA
25967022 TATATTGTATTAGTCAACTGCATG
1 TATATTGTATTAGTCAACTGCATG
25967046 GATGCTTGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (26 bp):
TATATTGTATTAGTCAACTGCATGAA
Found at i:25967499 original size:18 final size:18
Alignment explanation
Indices: 25967478--25967515 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
25967468 AATTAATTAT
25967478 ATTAAGAATATATAA-AAA
1 ATTAA-AATATATAATAAA
*
25967496 ATTAAAATATTTAATAAA
1 ATTAAAATATATAATAAA
25967514 AT
1 AT
25967516 ATCTATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
ATTAAAATATATAATAAA
Found at i:25968268 original size:20 final size:21
Alignment explanation
Indices: 25968227--25968271 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
25968217 CCTAGGTGGA
*
25968227 AAAATTCAAAGGAAAAGTGTG
1 AAAATTCAAAGGAAAAGAGTG
25968248 AAAATTC-AAGGAAACA-AGTG
1 AAAATTCAAAGGAAA-AGAGTG
25968268 AAAA
1 AAAA
25968272 AGGTAAGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.58, C:0.07, G:0.20, T:0.16
Consensus pattern (21 bp):
AAAATTCAAAGGAAAAGAGTG
Found at i:25968272 original size:21 final size:20
Alignment explanation
Indices: 25968225--25968272 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
25968215 ACCCTAGGTG
25968225 GAAAAATTCAAAGGAAAAGT
1 GAAAAATTCAAAGGAAAAGT
*
25968245 GTGAAAATTC-AAGGAAACAAGT
1 G-AAAAATTCAAAGG-AA-AAGT
25968267 GAAAAA
1 GAAAAA
25968273 GGTAAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
20 5 0.22
21 13 0.57
22 5 0.22
ACGTcount: A:0.58, C:0.06, G:0.21, T:0.15
Consensus pattern (20 bp):
GAAAAATTCAAAGGAAAAGT
Found at i:25993220 original size:19 final size:18
Alignment explanation
Indices: 25993185--25993220 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25993175 CCACTGCAGT
*
25993185 ACCACCAATTGAGGCAAA
1 ACCACCAATTAAGGCAAA
25993203 ACCACCAATTAAAGGCAA
1 ACCACCAATT-AAGGCAA
25993221 GAAGACTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.47, C:0.28, G:0.14, T:0.11
Consensus pattern (18 bp):
ACCACCAATTAAGGCAAA
Found at i:25995145 original size:67 final size:67
Alignment explanation
Indices: 25995025--25995175 Score: 196
Period size: 67 Copynumber: 2.3 Consensus size: 67
25995015 TGATTGTTGT
* * * *
25995025 AGGTTGTGGTTGAGCCTTGGAAAAACCACTTTGGGTTTTAGTTTAGCTAGTGAAAAACTAGT-AT
1 AGGTTGTGGTTGAGCCTTGGAAAAACCACTTTGAGTTTTAGTTAAGCCAGTGAAAAACCAGTGAT
25995089 AAA
66 -AA
* * * * * *
25995092 AGGTTGTGGTTGAGCCTTTGAAAAACCACTTTGAGTTTTGGTTAATCCCGTGAAAAACCATTGCT
1 AGGTTGTGGTTGAGCCTTGGAAAAACCACTTTGAGTTTTAGTTAAGCCAGTGAAAAACCAGTGAT
25995157 AA
66 AA
25995159 AGGTTGTGGTTGAGCCT
1 AGGTTGTGGTTGAGCCT
25995176 ACGAAAAGCC
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
67 72 0.99
68 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (67 bp):
AGGTTGTGGTTGAGCCTTGGAAAAACCACTTTGAGTTTTAGTTAAGCCAGTGAAAAACCAGTGAT
AA
Found at i:26018899 original size:24 final size:23
Alignment explanation
Indices: 26018849--26018896 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
26018839 TTATTAGCTC
26018849 TTAATCTCATCAATCAAAAAGGT
1 TTAATCTCATCAATCAAAAAGGT
* *
26018872 TTAATCTCATTAATCGAAAAGGT
1 TTAATCTCATCAATCAAAAAGGT
26018895 TT
1 TT
26018897 TAACCTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (23 bp):
TTAATCTCATCAATCAAAAAGGT
Found at i:26020761 original size:127 final size:127
Alignment explanation
Indices: 26020535--26020790 Score: 397
Period size: 127 Copynumber: 2.0 Consensus size: 127
26020525 TAAAGTTCCT
*
26020535 ATCAATATAAAATAATTACGAATTTATAGTAGTATCTGTCTTTTATATATAAAATGAATGGTTAA
1 ATCAATATAAAATAATTACGAATTTATACTAGTATCTGTCTTTTATATATAAAATGAATGGTTAA
* * *
26020600 AGGTTGTCAAATTTAATTGATTTGTTTATTCAATGATGACTATGTGCTATT-TATATTGAGAA
66 AAGTTGTCAAATTCAATTGATTTGTTTATTCAATGATGACTATGTGCT-TTGTATATTGAAAA
* ** * *
26020662 ATCAATATAAAATAGTTATTAATTTCTACTAGTATCTGTCTTTTATATATAAAATGATTGGTTAA
1 ATCAATATAAAATAATTACGAATTTATACTAGTATCTGTCTTTTATATATAAAATGAATGGTTAA
* *
26020727 AAGTTGTCAAATTCAGTTGATTTGTTTATTCAATGATGACTGTGTGCTTTGTATATTGAAAA
66 AAGTTGTCAAATTCAATTGATTTGTTTATTCAATGATGACTATGTGCTTTGTATATTGAAAA
26020789 AT
1 AT
26020791 GAGTAAACCT
Statistics
Matches: 117, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
126 2 0.02
127 115 0.98
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (127 bp):
ATCAATATAAAATAATTACGAATTTATACTAGTATCTGTCTTTTATATATAAAATGAATGGTTAA
AAGTTGTCAAATTCAATTGATTTGTTTATTCAATGATGACTATGTGCTTTGTATATTGAAAA
Found at i:26021353 original size:25 final size:24
Alignment explanation
Indices: 26021299--26021355 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
26021289 AAGAGATAGT
*
26021299 AAAAATGATTATGTAATTAACTTAA
1 AAAAATTATTATGTAATTAAC-TAA
26021324 AAAAATTATTATGTAATTGAA-TAA
1 AAAAATTATTATGTAATT-AACTAA
26021348 ATAAAATT
1 A-AAAATT
26021356 TCATGGGCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 4 0.14
25 23 0.79
26 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (24 bp):
AAAAATTATTATGTAATTAACTAA
Found at i:26024483 original size:24 final size:23
Alignment explanation
Indices: 26024456--26024511 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
26024446 AAAAAAGACA
*
26024456 AAAAAAATTACAACAAAAGAAGT-T
1 AAAAAAATTAC--CAAAAAAAGTAT
*
26024480 AAAAAGATTACCAAAAAAAGTGAT
1 AAAAAAATTACCAAAAAAAGT-AT
26024504 AAAAAAAT
1 AAAAAAAT
26024512 AATAATTACC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 9 0.33
24 18 0.67
ACGTcount: A:0.68, C:0.07, G:0.09, T:0.16
Consensus pattern (23 bp):
AAAAAAATTACCAAAAAAAGTAT
Found at i:26025804 original size:25 final size:24
Alignment explanation
Indices: 26025766--26025812 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
26025756 TATTTAAAGA
26025766 ATATAATATGTTAATATATATATAC
1 ATATAATATGTTAA-ATATATATAC
*
26025791 ATATAATAAT-TTAAATTTATAT
1 ATATAAT-ATGTTAAATATATAT
26025813 TAATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 11 0.55
26 2 0.10
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
ATATAATATGTTAAATATATATAC
Found at i:26033675 original size:71 final size:71
Alignment explanation
Indices: 26033620--26033820 Score: 201
Period size: 71 Copynumber: 2.8 Consensus size: 71
26033610 GGAAGTCACG
* * *
26033620 CATTTTGGTCTAAGATAAACTATAGGCCCTCCATAGTTGATCTTATGAAGGAAAAATGGGAGAAA
1 CATTTTGGTCTAAGATAAACTATAGACCCTCCATAGTCGATCTTGTGAAGGAAAAATGGGAGAAA
26033685 TGCAAA
66 TGCAAA
* * * * * * *
26033691 CCTTTTGGTCTAAGATCAACTATAGACCCTTCATAGTCAATCTTGTGAAGGAAAATTGAGTAAAA
1 CATTTTGGTCTAAGATAAACTATAGACCCTCCATAGTCGATCTTGTGAAGGAAAAATG-G-GAGA
*
26033756 AAT--AGA
64 AATGCAAA
* ** * * * *
26033762 CATTCTGGTCTAAGATCGACTATAGACCCT-CATAGTCAATCCTATGAAGGGAAAATGGG
1 CATTTTGGTCTAAGATAAACTATAGACCCTCCATAGTCGATCTTGTGAAGGAAAAATGGG
26033821 TGAATCATAA
Statistics
Matches: 109, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
69 1 0.01
70 23 0.21
71 79 0.72
72 1 0.01
73 5 0.05
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27
Consensus pattern (71 bp):
CATTTTGGTCTAAGATAAACTATAGACCCTCCATAGTCGATCTTGTGAAGGAAAAATGGGAGAAA
TGCAAA
Found at i:26039405 original size:25 final size:24
Alignment explanation
Indices: 26039369--26039421 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
26039359 GTCAACCTAT
*
26039369 TTTTTAT-TTTTTTCAAAAAAATTA
1 TTTTTATATTTTAT-AAAAAAATTA
*
26039393 TTTTTATAATTTTATAATAAAATTA
1 TTTTTAT-ATTTTATAAAAAAATTA
26039418 TTTT
1 TTTT
26039422 ATGATTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.28
25 13 0.52
26 5 0.20
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTTATATTTTATAAAAAAATTA
Found at i:26039549 original size:22 final size:21
Alignment explanation
Indices: 26039507--26039557 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
26039497 ATATTATTGG
**
26039507 TAATTAAATTATTAATCTTAT
1 TAATTAAATTATTAAAATTAT
26039528 ATAATTAAA-TATATAAAATTAT
1 -TAATTAAATTAT-TAAAATTAT
26039550 TAAATTAA
1 T-AATTAA
26039558 TTAAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATTAAATTATTAAAATTAT
Found at i:26043896 original size:71 final size:70
Alignment explanation
Indices: 26043815--26043954 Score: 165
Period size: 71 Copynumber: 2.0 Consensus size: 70
26043805 TCAATCATAG
* * * *
26043815 GAAAGAAAAATGGGAGAA-ATGTAAATGTTCTGGTCTAGGATCAACTATAGACCTTCCATAGTCG
1 GAAAGAAAAATGGGAGAACAT-AAAAT-TTCTAGTCCAAGATCAACTATAGACCTTCCATAGTCG
26043879 ATCCTGT
64 ATCCTGT
* * * **
26043886 GAAAGGAAAATGGGTGAATCATAAAATTTCTAGTCCAAGATCGACTATAGATTTTCCATAGTCGA
1 GAAAGAAAAATGGGAGAA-CATAAAATTTCTAGTCCAAGATCAACTATAGACCTTCCATAGTCGA
26043951 TCCT
65 TCCT
26043955 AGGCTACCTA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
71 52 0.90
72 4 0.07
73 2 0.03
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.28
Consensus pattern (70 bp):
GAAAGAAAAATGGGAGAACATAAAATTTCTAGTCCAAGATCAACTATAGACCTTCCATAGTCGAT
CCTGT
Found at i:26057278 original size:143 final size:145
Alignment explanation
Indices: 26057004--26057301 Score: 528
Period size: 143 Copynumber: 2.1 Consensus size: 145
26056994 GTCTCTAAGT
*
26057004 ATCATTGATATCCAATCTCAATGATACATTGACCAGGAACATTTTGAGATTATGCTTTGATGCAT
1 ATCATT-ATATCCAATCTCAATGATACATTGACCAAGAACATTTTGAGATTATGCTTTGATGCAT
26057069 AAGAATCTTGTAACTGCAACCCATTTAGTTTTCTTGCAAGGCATATTAATCTCATGGATTTCATC
65 AAGAATCTTGTAACTGCAACCCATTTAGTTTTCTTGCAAGGCATATTAATCTCATGGATTTCATC
26057134 CAA-TTAGACTTATAA
130 CAATTTAGACTTATAA
* * * *
26057149 CTCATTATNTCCACTCTCATTGATACATTGACCAAGAACA-TTTGAGATTATGCTTTGATGCATA
1 ATCATTATATCCAATCTCAATGATACATTGACCAAGAACATTTTGAGATTATGCTTTGATGCATA
26057213 AGAATCTTGTAACTGCAACCCATTTAGTTTTCTTGCAAGGCATATTAATCTCATGGATTTCATCC
66 AGAATCTTGTAACTGCAACCCATTTAGTTTTCTTGCAAGGCATATTAATCTCATGGATTTCATCC
26057278 AATTTAGACTTATAA
131 AATTTAGACTTATAA
26057293 ATCATTATA
1 ATCATTATA
26057302 ATTAATGTCT
Statistics
Matches: 145, Mismatches: 7, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
143 91 0.63
144 49 0.34
145 5 0.03
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (145 bp):
ATCATTATATCCAATCTCAATGATACATTGACCAAGAACATTTTGAGATTATGCTTTGATGCATA
AGAATCTTGTAACTGCAACCCATTTAGTTTTCTTGCAAGGCATATTAATCTCATGGATTTCATCC
AATTTAGACTTATAA
Found at i:26060319 original size:22 final size:21
Alignment explanation
Indices: 26060270--26060320 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
26060260 ACCTGAGAGT
* * *
26060270 TTCTTGCTGTAGCGAGATTCA
1 TTCTCGCTGCAGCGAGATCCA
*
26060291 TTTTCGCTGCAGCGAGAATCCA
1 TTCTCGCTGCAGCGAG-ATCCA
26060313 TTCTCGCT
1 TTCTCGCT
26060321 ATAGTGAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (21 bp):
TTCTCGCTGCAGCGAGATCCA
Found at i:26060708 original size:43 final size:43
Alignment explanation
Indices: 26060598--26060808 Score: 240
Period size: 43 Copynumber: 5.0 Consensus size: 43
26060588 CCCGCCACAC
*
26060598 TCAGCTCATGTGCACTCCCTACA-CGCACA-ATG-TA-AT-ATCA
1 TCAGCTCATGTGCACTCCC-ACACCGCACATA-GCTAGGTCATCA
* * *
26060638 TCA--TCATGTGCATTCCCTAC-TCGCACATAGCTGGGTCATCA
1 TCAGCTCATGTGCACTCCC-ACACCGCACATAGCTAGGTCATCA
* * *
26060679 TCAACTCATGTGCACTCCCACACCACACATAGCTAGGTTATCA
1 TCAGCTCATGTGCACTCCCACACCGCACATAGCTAGGTCATCA
* * * *
26060722 TCAGCTCATGTGCACTCCCACACTGCACATACCTGGGTCATTA
1 TCAGCTCATGTGCACTCCCACACCGCACATAGCTAGGTCATCA
26060765 TCAGCTCATGTGCACTCCCACACCGCACATAGCTAGGTCATCA
1 TCAGCTCATGTGCACTCCCACACCGCACATAGCTAGGTCATCA
26060808 T
1 T
26060809 TATCACACAA
Statistics
Matches: 144, Mismatches: 19, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
38 23 0.16
39 2 0.01
40 4 0.03
41 7 0.05
42 2 0.01
43 106 0.74
ACGTcount: A:0.26, C:0.34, G:0.15, T:0.25
Consensus pattern (43 bp):
TCAGCTCATGTGCACTCCCACACCGCACATAGCTAGGTCATCA
Found at i:26061980 original size:2 final size:2
Alignment explanation
Indices: 26061968--26062006 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
26061958 ACATTATTCG
* *
26061968 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26062007 CAACACAGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26065958 original size:23 final size:23
Alignment explanation
Indices: 26065912--26065960 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
26065902 ATATATATCA
* * *
26065912 ATCATCATGTACACCATTCTATC
1 ATCATCATGCACACCATCCCATC
*
26065935 ATCATCATGCACATCATCCCATC
1 ATCATCATGCACACCATCCCATC
26065958 ATC
1 ATC
26065961 CCCAACTCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.35, G:0.04, T:0.31
Consensus pattern (23 bp):
ATCATCATGCACACCATCCCATC
Found at i:26066003 original size:43 final size:42
Alignment explanation
Indices: 26065969--26066078 Score: 130
Period size: 43 Copynumber: 2.6 Consensus size: 42
26065959 TCCCCAACTC
* ** **
26065969 ATGCGCACTCCCTACTTGCACATGGCTAGGTCATCACCGGGTT
1 ATGCGCACTCCCTACTCGCACATAACTAGGTCATCACC-GACT
* * *
26066012 ATGCGTACTCCTTACTCGCACATAACTAGGTCATCATCGACGT
1 ATGCGCACTCCCTACTCGCACATAACTAGGTCATCACCGAC-T
26066055 ATGCGCACTCCCTACTCGCACATA
1 ATGCGCACTCCCTACTCGCACATA
26066079 GCCGAGTCAA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 1 0.02
43 55 0.98
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.25
Consensus pattern (42 bp):
ATGCGCACTCCCTACTCGCACATAACTAGGTCATCACCGACT
Found at i:26080422 original size:21 final size:21
Alignment explanation
Indices: 26080380--26080422 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
26080370 CTTATACCGG
*
26080380 TGGTGGAACTAAAGGAGTAAC
1 TGGTGGAACTAAAGGAGAAAC
* * *
26080401 TGGTGGTACTATAGGTGAAAC
1 TGGTGGAACTAAAGGAGAAAC
26080422 T
1 T
26080423 TGACCAGCCT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.09, G:0.33, T:0.26
Consensus pattern (21 bp):
TGGTGGAACTAAAGGAGAAAC
Found at i:26087855 original size:97 final size:98
Alignment explanation
Indices: 26087700--26087951 Score: 303
Period size: 97 Copynumber: 2.6 Consensus size: 98
26087690 TACTAAATGT
* * * * *
26087700 GAGTGGTGACAACCCCAACTCAAAGCGAATAATGGAAAAAATCCCCATTATCTTGGATTCCTTGA
1 GAGTGGTGCCCACCCCAACTC-AAGCAAATAGT-GAATAAATCCCCATTATCTTGGATTCCTTGA
26087765 ACTATTT-TGAGTGACATTCAGCCTCACCCA-TATTA
64 ACT-TTTGTGAGTGACATTCAGCCTCACCCACT-TTA
* * * *
26087800 TAGTTGTGCCCACCCCAACTCAAGCAGATAGTGAAT-AATCCCCACTATCTTGGATTCCTTGAAC
1 GAGTGGTGCCCACCCCAACTCAAGCAAATAGTGAATAAATCCCCATTATCTTGGATTCCTTGAAC
* * * *
26087864 TTTTGTGAGTGGCATTTAGCCTCACTCACTTTC
66 TTTTGTGAGTGACATTCAGCCTCACCCACTTTA
* * *
26087897 GAGTGGTGCTCGCCCCAACTCAAGCAAATAGTGGATAAATCCCCATTATCTTGGA
1 GAGTGGTGCCCACCCCAACTCAAGCAAATAGTGAATAAATCCCCATTATCTTGGA
26087952 CTCTTTATGT
Statistics
Matches: 129, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
96 3 0.02
97 80 0.62
98 21 0.16
99 8 0.06
100 17 0.13
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (98 bp):
GAGTGGTGCCCACCCCAACTCAAGCAAATAGTGAATAAATCCCCATTATCTTGGATTCCTTGAAC
TTTTGTGAGTGACATTCAGCCTCACCCACTTTA
Found at i:26096382 original size:37 final size:37
Alignment explanation
Indices: 26096335--26096428 Score: 143
Period size: 37 Copynumber: 2.5 Consensus size: 37
26096325 TAATGTTGTG
** *
26096335 TGATGATAGAGTGTGCGAGTGGGGAGTGCACACATGA
1 TGATGATAGAGTGTGCGAGTAAGAAGTGCACACATGA
26096372 TGATGATAGAGTGTGCGAGTAAGAAGTGCACACATGA
1 TGATGATAGAGTGTGCGAGTAAGAAGTGCACACATGA
* *
26096409 TGATGTTAAAGTGTGCGAGT
1 TGATGATAGAGTGTGCGAGT
26096429 TGTTGGCTCC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.30, C:0.10, G:0.36, T:0.24
Consensus pattern (37 bp):
TGATGATAGAGTGTGCGAGTAAGAAGTGCACACATGA
Found at i:26109660 original size:14 final size:14
Alignment explanation
Indices: 26109641--26109670 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
26109631 TCCTAGATCA
26109641 GAGACTATCAGGGT
1 GAGACTATCAGGGT
26109655 GAGACTATCAGGGT
1 GAGACTATCAGGGT
26109669 GA
1 GA
26109671 AACTCACGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.37, T:0.20
Consensus pattern (14 bp):
GAGACTATCAGGGT
Done.