Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold377.1
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: 1197438
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 15558 characters in sequence are not A, C, G, or T
File 1 of 4
Found at i:364 original size:26 final size:24
Alignment explanation
Indices: 334--382 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
324 AAATAAAAAT
*
334 TTTAAAAATATAATAAATCAAATATA
1 TTTAAAAACATAA-AAA-CAAATATA
360 TTTAAAAACATAAAAACAAATAT
1 TTTAAAAACATAAAAACAAATAT
383 TAAAACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (24 bp):
TTTAAAAACATAAAAACAAATATA
Found at i:402 original size:21 final size:21
Alignment explanation
Indices: 353--411 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
343 ATAATAAATC
*
353 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
373 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
395 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
412 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:7174 original size:38 final size:38
Alignment explanation
Indices: 7104--7254 Score: 194
Period size: 38 Copynumber: 4.0 Consensus size: 38
7094 TATCATGTAA
* ** * *
7104 AATAGTAGACATGTTTAACATGTATTCAGTTCAATAGT
1 AATAGTAGACATGCTTAACATGTATTTGGTTCAACAGC
** *
7142 AGCATTAGACATGCTTAACATGTATTTGGTTCAACAGC
1 AATAGTAGACATGCTTAACATGTATTTGGTTCAACAGC
* *
7180 AATAGTAGACATGCTTAACATTTATTTGGTTCAACAAC
1 AATAGTAGACATGCTTAACATGTATTTGGTTCAACAGC
* *
7218 AATAGTAGACATGCTTAACATGTATTTAGTTTAACAG
1 AATAGTAGACATGCTTAACATGTATTTGGTTCAACAG
7255 TATCAGTAGG
Statistics
Matches: 96, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 96 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (38 bp):
AATAGTAGACATGCTTAACATGTATTTGGTTCAACAGC
Found at i:8592 original size:123 final size:123
Alignment explanation
Indices: 8373--8620 Score: 496
Period size: 123 Copynumber: 2.0 Consensus size: 123
8363 GGAAAAAAAG
8373 TGGCTCAAACCTAAGGTCACTTAGGGGAAAAGTTAACTCTTAACCATTAGGCCTAAAACATATTT
1 TGGCTCAAACCTAAGGTCACTTAGGGGAAAAGTTAACTCTTAACCATTAGGCCTAAAACATATTT
8438 ATTGTCTAGTTTATATTTCTAATCGCATATATTTGGTGTAGCTTTTATCCTAGATTGT
66 ATTGTCTAGTTTATATTTCTAATCGCATATATTTGGTGTAGCTTTTATCCTAGATTGT
8496 TGGCTCAAACCTAAGGTCACTTAGGGGAAAAGTTAACTCTTAACCATTAGGCCTAAAACATATTT
1 TGGCTCAAACCTAAGGTCACTTAGGGGAAAAGTTAACTCTTAACCATTAGGCCTAAAACATATTT
8561 ATTGTCTAGTTTATATTTCTAATCGCATATATTTGGTGTAGCTTTTATCCTAGATTGT
66 ATTGTCTAGTTTATATTTCTAATCGCATATATTTGGTGTAGCTTTTATCCTAGATTGT
8619 TG
1 TG
8621 AAAATTAAAA
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 125 1.00
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (123 bp):
TGGCTCAAACCTAAGGTCACTTAGGGGAAAAGTTAACTCTTAACCATTAGGCCTAAAACATATTT
ATTGTCTAGTTTATATTTCTAATCGCATATATTTGGTGTAGCTTTTATCCTAGATTGT
Found at i:12432 original size:27 final size:29
Alignment explanation
Indices: 12379--12432 Score: 67
Period size: 27 Copynumber: 1.9 Consensus size: 29
12369 GAGAAGTTTC
* **
12379 ATTATTATTATAAATATTAAATTAATAAA
1 ATTATTATTATAAAAATTAAAAAAATAAA
12408 ATTATT-TTA-AAAAATTAAAAAAATA
1 ATTATTATTATAAAAATTAAAAAAATA
12433 TACATTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 13 0.59
28 3 0.14
29 6 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
ATTATTATTATAAAAATTAAAAAAATAAA
Found at i:15816 original size:15 final size:16
Alignment explanation
Indices: 15796--15831 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
15786 AATAATATTG
15796 AATATATATAT-ACAT
1 AATATATATATAACAT
15811 AATATATATATAACAT
1 AATATATATATAACAT
15827 AATAT
1 AATAT
15832 TAAAAACACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
AATATATATATAACAT
Found at i:15853 original size:22 final size:24
Alignment explanation
Indices: 15825--15877 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
15815 TATATATAAC
* *
15825 ATAATAT-TAAAAACACA-TATAT
1 ATAATATGAAAAAACAAATTATAT
*
15847 ATAATATGAAAAAAGAAATTATAT
1 ATAATATGAAAAAACAAATTATAT
15871 ATAATAT
1 ATAATAT
15878 AATACATAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 7 0.27
23 7 0.27
24 12 0.46
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (24 bp):
ATAATATGAAAAAACAAATTATAT
Found at i:16567 original size:12 final size:12
Alignment explanation
Indices: 16550--16580 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
16540 ACGTATGAGT
16550 AGAAAAAAAAGA
1 AGAAAAAAAAGA
*
16562 AGAAAAAGAAGA
1 AGAAAAAAAAGA
16574 AGAAAAA
1 AGAAAAA
16581 TAACAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAAGA
Found at i:19092 original size:14 final size:15
Alignment explanation
Indices: 19073--19104 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
19063 ATTAGATTTC
19073 TTTTTTT-TTCTT-T
1 TTTTTTTCTTCTTAT
19086 TTTTTTTCTTCTTAT
1 TTTTTTTCTTCTTAT
19101 TTTT
1 TTTT
19105 AGATTAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 5 0.29
15 5 0.29
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTTTCTTCTTAT
Found at i:20146 original size:16 final size:16
Alignment explanation
Indices: 20127--20161 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
20117 TTACATATCT
20127 ATCAATTTCAATTTGG
1 ATCAATTTCAATTTGG
20143 ATCAATTTCAATTTGG
1 ATCAATTTCAATTTGG
20159 ATC
1 ATC
20162 CGTGTCAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (16 bp):
ATCAATTTCAATTTGG
Found at i:35234 original size:70 final size:70
Alignment explanation
Indices: 35157--35293 Score: 222
Period size: 70 Copynumber: 2.0 Consensus size: 70
35147 TGGACTCAGA
*
35157 TTCATGGTTCAAATAAGTCACTTACCTTTTAAGTACTAAATTGGAC-AAAAATCTAAATTCAGGT
1 TTCATGGTTCAAATAAGTCACTTACC-TTTAAGTACTAAATTGGACAAAAAATCTAAATTCAAGT
35221 GTTAGG
65 GTTAGG
* * *
35227 TTCATGGTTTAAATAAGTCATTTACCTTTAAGTACTAATTTGGACAAAAAATCTAAATTCAAGTG
1 TTCATGGTTCAAATAAGTCACTTACCTTTAAGTACTAAATTGGACAAAAAATCTAAATTCAAGTG
35292 TT
66 TT
35294 GATTTAAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
69 18 0.29
70 44 0.71
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (70 bp):
TTCATGGTTCAAATAAGTCACTTACCTTTAAGTACTAAATTGGACAAAAAATCTAAATTCAAGTG
TTAGG
Found at i:40331 original size:15 final size:17
Alignment explanation
Indices: 40304--40338 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
40294 AATTTCAGTA
40304 ATTATTGTTATTTC-TC
1 ATTATTGTTATTTCTTC
40320 ATTATT-TTATTTCTTC
1 ATTATTGTTATTTCTTC
40336 ATT
1 ATT
40339 TATCTTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.20, C:0.11, G:0.03, T:0.66
Consensus pattern (17 bp):
ATTATTGTTATTTCTTC
Found at i:54932 original size:26 final size:24
Alignment explanation
Indices: 54898--54959 Score: 79
Period size: 26 Copynumber: 2.5 Consensus size: 24
54888 AATTTTTGAA
54898 ATTTTAAAATTGAAAAATTAAGAATT
1 ATTTTAAAATT-AAAAATT-AGAATT
*
54924 ATTTTAAAAATTAAAAATTATAATT
1 ATTTT-AAAATTAAAAATTAGAATT
*
54949 TTTTTAAAATT
1 ATTTTAAAATT
54960 TAAGTAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 6 0.18
25 9 0.27
26 12 0.36
27 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (24 bp):
ATTTTAAAATTAAAAATTAGAATT
Found at i:54939 original size:25 final size:25
Alignment explanation
Indices: 54898--54962 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
54888 AATTTTTGAA
54898 ATTTT-AAAATTGAAAAATTAAGAATT
1 ATTTTAAAAATT-AAAAATT-AGAATT
*
54924 ATTTTAAAAATTAAAAATTATAATT
1 ATTTTAAAAATTAAAAATTAGAATT
* *
54949 TTTTTAAAATTTAA
1 ATTTTAAAAATTAA
54963 GTAATTATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
25 17 0.49
26 12 0.34
27 6 0.17
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (25 bp):
ATTTTAAAAATTAAAAATTAGAATT
Found at i:56720 original size:32 final size:32
Alignment explanation
Indices: 56683--56759 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
56673 ATGCATGTGT
* * **
56683 GTAACTTTTCATCTTCAAGTCTCTTTGCATTA
1 GTAACTTTTCATATTCAAGCCTCTTCACATTA
* * *
56715 TTAACTCTTCATATTCAAGCCTCTTCACATTC
1 GTAACTTTTCATATTCAAGCCTCTTCACATTA
56747 GTAACTTTTCATA
1 GTAACTTTTCATA
56760 ATTTATTTTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (32 bp):
GTAACTTTTCATATTCAAGCCTCTTCACATTA
Found at i:61268 original size:32 final size:32
Alignment explanation
Indices: 61193--61269 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 32
61183 ATGCATGTGT
** * **
61193 GTAACTTTTCACCTTCAAGTCTCTTTGCATTA
1 GTAACTTTTCATATTCAAGCCTCTTCACATTA
* * *
61225 TTAACTCTTCATATTCAAGCCTCTTCACATTC
1 GTAACTTTTCATATTCAAGCCTCTTCACATTA
61257 GTAACTTTTCATA
1 GTAACTTTTCATA
61270 ATTTATTTTA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.25, C:0.26, G:0.06, T:0.43
Consensus pattern (32 bp):
GTAACTTTTCATATTCAAGCCTCTTCACATTA
Found at i:95336 original size:2 final size:2
Alignment explanation
Indices: 95329--95373 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
95319 CTCTTAAATT
95329 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
95371 TC T
1 TC T
95374 ATATATATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:99948 original size:5 final size:6
Alignment explanation
Indices: 99933--99957 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
99923 TACTTTTTCA
99933 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
99958 TGTAGATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:106480 original size:18 final size:19
Alignment explanation
Indices: 106457--106504 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
106447 ATTTTAAAAA
106457 TATAAATTTTGGA-ATTTT
1 TATAAATTTTGGATATTTT
* *
106475 TATAAATATTTTGATTTTTT
1 TATAAAT-TTTGGATATTTT
*
106495 TTTAAATTTT
1 TATAAATTTT
106505 TGTTGAGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 7 0.28
19 8 0.32
20 10 0.40
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (19 bp):
TATAAATTTTGGATATTTT
Found at i:112650 original size:16 final size:17
Alignment explanation
Indices: 112620--112652 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
112610 ATATAATTAA
*
112620 AATATATTAATTTATTT
1 AATATATTAAATTATTT
112637 AATA-ATTAAATTATTT
1 AATATATTAAATTATTT
112653 GTACAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATATATTAAATTATTT
Found at i:113017 original size:22 final size:22
Alignment explanation
Indices: 112990--113033 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
112980 TTAACTTAAA
*
112990 TTTAATACTTAATTACTTAATT
1 TTTAATACCTAATTACTTAATT
113012 TTTAATACCTAATTACTTAATT
1 TTTAATACCTAATTACTTAATT
113034 ATTGTGTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTAATACCTAATTACTTAATT
Found at i:114338 original size:3 final size:3
Alignment explanation
Indices: 114330--114356 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
114320 TTAAATATTT
114330 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
114357 TCTTTTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:120768 original size:29 final size:30
Alignment explanation
Indices: 120704--120770 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
120694 AATCCCAAAA
120704 CTATACATGAATTATATTTTAATGTGAAATT
1 CTATACATGAATTATATTTTAATGT-AAATT
* *
120735 CTATACATTAATTTTGATTTT-ATGT-AATT
1 CTATACATGAATTAT-ATTTTAATGTAAATT
*
120764 TTATACA
1 CTATACA
120771 GGGAATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 10 0.31
31 17 0.53
32 5 0.16
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.49
Consensus pattern (30 bp):
CTATACATGAATTATATTTTAATGTAAATT
Found at i:122213 original size:16 final size:16
Alignment explanation
Indices: 122192--122222 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
122182 TAGAAACACG
122192 AATAGCTGTCCACCAA
1 AATAGCTGTCCACCAA
122208 AATAGCTGTCCACCA
1 AATAGCTGTCCACCA
122223 GAGCAGAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.32, G:0.13, T:0.19
Consensus pattern (16 bp):
AATAGCTGTCCACCAA
Found at i:137743 original size:12 final size:12
Alignment explanation
Indices: 137726--137769 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
137716 ATAATAAGAG
137726 AAGAAGAAAAAA
1 AAGAAGAAAAAA
137738 AAGAAGAAAAAA
1 AAGAAGAAAAAA
137750 AAGAAGAAAAAA
1 AAGAAGAAAAAA
*
137762 AAGGAGAA
1 AAGAAGAA
137770 GAGAAAAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAAAA
Found at i:137744 original size:15 final size:15
Alignment explanation
Indices: 137724--137778 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
137714 GAATAATAAG
137724 AGAAGAAGAAAAAA-A
1 AGAAGAA-AAAAAAGA
137739 AGAAGAAAAAAAAGA
1 AGAAGAAAAAAAAGA
*
137754 AGAA-AAAAAAGGAGA
1 AGAAGAAAAAA-AAGA
137769 AG-AGAAAAAA
1 AGAAGAAAAAA
137779 CGGAGATTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
14 13 0.36
15 23 0.64
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AGAAGAAAAAAAAGA
Found at i:139992 original size:39 final size:39
Alignment explanation
Indices: 139946--140163 Score: 292
Period size: 39 Copynumber: 5.6 Consensus size: 39
139936 GCTCTGGTGA
* *
139946 GCTTCAGTTAGCCTTTGGGCTTCCATTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
*
139985 GCTTCAGTCAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
140024 GTTTCAGTCAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* * * *
140063 GCTTCAGTTAGCCTCCGAGCTTCCGCTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* ** *
140102 GCTTCAGCTAAACTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* **
140141 GCTTCAGCTAAACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
140164 AGATCACGAA
Statistics
Matches: 163, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 163 1.00
ACGTcount: A:0.14, C:0.27, G:0.23, T:0.36
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
Found at i:140106 original size:21 final size:21
Alignment explanation
Indices: 140042--140145 Score: 67
Period size: 21 Copynumber: 5.2 Consensus size: 21
140032 CAGCCTTCGG
* *
140042 GCTTCCGTTTAGCACTTGTGT
1 GCTTCCGCTTAGCACTTATGT
* ** *
140063 GCTTCAG-TTAGC-C-TCCGA
1 GCTTCCGCTTAGCACTTATGT
140081 GCTTCCGCTTAGCACTTATGT
1 GCTTCCGCTTAGCACTTATGT
* * * *
140102 GCTTCAGC-TA-AACTT-CGG
1 GCTTCCGCTTAGCACTTATGT
*
140120 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGCTTAGCACTTATGT
140141 GCTTC
1 GCTTC
140146 AGCTAAACTT
Statistics
Matches: 60, Mismatches: 17, Indels: 12
0.67 0.19 0.13
Matches are distributed among these distances:
18 15 0.25
19 12 0.20
20 12 0.20
21 21 0.35
ACGTcount: A:0.14, C:0.28, G:0.21, T:0.37
Consensus pattern (21 bp):
GCTTCCGCTTAGCACTTATGT
Found at i:140164 original size:18 final size:18
Alignment explanation
Indices: 140102--140165 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
140092 GCACTTATGT
140102 GCTTCAGCTAAACTTCGG
1 GCTTCAGCTAAACTTCGG
* * * * *
140120 GCTTCCGTTTAGCACTTATGT
1 GCTTCAG-CTA-AACTT-CGG
140141 GCTTCAGCTAAACTTCGG
1 GCTTCAGCTAAACTTCGG
140159 GCTTCAG
1 GCTTCAG
140166 ATCACGAATG
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
18 14 0.42
19 6 0.18
20 6 0.18
21 7 0.21
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.33
Consensus pattern (18 bp):
GCTTCAGCTAAACTTCGG
Found at i:141420 original size:49 final size:49
Alignment explanation
Indices: 141348--141443 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 49
141338 GTTAGACTTT
* *
141348 AATTTTCCCTTTCATAAATCTTTGGGTTTTTATGGAGGAAATCAATTTC
1 AATTTCCCCTTTCATAAATCTTTGGGTTTTCATGGAGGAAATCAATTTC
141397 AATTTCCCCTTTCATAAATCTTTGGGTTTTCATGGAGGAAATCAATT
1 AATTTCCCCTTTCATAAATCTTTGGGTTTTCATGGAGGAAATCAATT
141444 GGGATACCCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.43
Consensus pattern (49 bp):
AATTTCCCCTTTCATAAATCTTTGGGTTTTCATGGAGGAAATCAATTTC
Found at i:142916 original size:9 final size:9
Alignment explanation
Indices: 142904--142928 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
142894 TATTATATTT
142904 ATTATTATC
1 ATTATTATC
142913 ATTATTATC
1 ATTATTATC
142922 ATTATTA
1 ATTATTA
142929 ACTATTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTATTATC
Found at i:142990 original size:14 final size:13
Alignment explanation
Indices: 142957--142998 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
142947 ATAAGATATA
142957 AAAGAAATGAAAG-
1 AAAGAAA-GAAAGC
142970 AAAGAAAGAAAGC
1 AAAGAAAGAAAGC
142983 ACAAGAAAGAATAGC
1 A-AAGAAAGAA-AGC
142998 A
1 A
142999 GAAGCCATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.19
13 8 0.31
14 9 0.35
15 4 0.15
ACGTcount: A:0.67, C:0.07, G:0.21, T:0.05
Consensus pattern (13 bp):
AAAGAAAGAAAGC
Found at i:143533 original size:15 final size:14
Alignment explanation
Indices: 143497--143536 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
143487 ATTTGATTGG
143497 AAAATGAATT-AAA
1 AAAATGAATTAAAA
*
143510 AATATGAATTAAATA
1 AAAATGAATTAAA-A
143525 AAAATGAATTAA
1 AAAATGAATTAA
143537 TTTATGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 9 0.39
14 2 0.09
15 12 0.52
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (14 bp):
AAAATGAATTAAAA
Found at i:143908 original size:23 final size:23
Alignment explanation
Indices: 143878--143988 Score: 124
Period size: 23 Copynumber: 5.0 Consensus size: 23
143868 GGCTTTGCCG
*
143878 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
*
143901 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
* **
143924 TTCAGGCACCTCGTGTGTCG--T
1 ATCAGGCACCTTATGTGTCGTAT
**
143945 ATCAGGCACCTCGTGTGTCGT-T
1 ATCAGGCACCTTATGTGTCGTAT
143967 -TCAGGCA-CTTATGTGTCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
143988 A
1 A
143989 CTGATCAGGT
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.13
21 28 0.36
22 1 0.01
23 39 0.50
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (23 bp):
ATCAGGCACCTTATGTGTCGTAT
Found at i:143963 original size:44 final size:41
Alignment explanation
Indices: 143879--143987 Score: 110
Period size: 44 Copynumber: 2.5 Consensus size: 41
143869 GCTTTGCCGA
* * *
143879 TCAGGCACTTTATGTGTCGTATATCAGGCACTTTATGTGTCGTATT
1 TCAGGCAC-TCATGTGTCG--TATCAGGCACCTCATGTGTCG--TT
* *
143925 TCAGGCACCTCGTGTGTCGTATCAGGCACCTCGTGTGTCGTT
1 TCAGGCA-CTCATGTGTCGTATCAGGCACCTCATGTGTCGTT
*
143967 TCAGGCACTTATGTGTCGTAT
1 TCAGGCACTCATGTGTCGTAT
143988 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
41 12 0.22
42 9 0.16
44 18 0.33
46 15 0.27
47 1 0.02
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.37
Consensus pattern (41 bp):
TCAGGCACTCATGTGTCGTATCAGGCACCTCATGTGTCGTT
Found at i:145225 original size:21 final size:21
Alignment explanation
Indices: 145201--145241 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
145191 CAACGTGGCA
145201 AGTTAA-TTGGCCACATCAGCT
1 AGTTAACTT-GCCACATCAGCT
145222 AGTTAACTTGCCACATCAGC
1 AGTTAACTTGCCACATCAGC
145242 AGTCCTGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (21 bp):
AGTTAACTTGCCACATCAGCT
Found at i:145738 original size:21 final size:21
Alignment explanation
Indices: 145714--145754 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
145704 CAACGTGGCA
145714 AGTTAA-TTGGCCACATCAGCT
1 AGTTAACTT-GCCACATCAGCT
145735 AGTTAACTTGCCACATCAGC
1 AGTTAACTTGCCACATCAGC
145755 AGTCCTGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (21 bp):
AGTTAACTTGCCACATCAGCT
Found at i:145768 original size:513 final size:513
Alignment explanation
Indices: 144801--145826 Score: 1980
Period size: 513 Copynumber: 2.0 Consensus size: 513
144791 CTCAGCGTAC
*
144801 GGTTTGTTTCCGTGCGCAGATTAGGTACAAAAATTTTGAAGAGTTGTATTTGAGATTACGAGTCT
1 GGTTTGTTTCCGTGAGCAGATTAGGTACAAAAATTTTGAAGAGTTGTATTTGAGATTACGAGTCT
144866 TCATCTCATCACATCTTCAAGCAACAAGAGGGTATGTTTTAAAATTTTGAATAGAATGACATGTA
66 TCATCTCATCACATCTTCAAGCAACAAGAGGGTATGTTTTAAAATTTTGAATAGAATGACATGTA
*
144931 CTTAAGGAAGAATTAAGTATGTCCCAAGTAGTAGTAATGGATTTAAATATAAATTATTTAAATTT
131 CTTAAGGAAAAATTAAGTATGTCCCAAGTAGTAGTAATGGATTTAAATATAAATTATTTAAATTT
144996 ATGATTTGTCTGTTTTTATGTTCAAATATAATAGTAATTAGCCAAGAATTACTTGGGCACCAAAT
196 ATGATTTGTCTGTTTTTATGTTCAAATATAATAGTAATTAGCCAAGAATTACTTGGGCACCAAAT
145061 GTACTATTCCTATATCAAGTTCCTCGAGTCGAACATGGTATAGGGGTGTTACAGTTTTGCCCTAA
261 GTACTATTCCTATATCAAGTTCCTCGAGTCGAACATGGTATAGGGGTGTTACAGTTTTGCCCTAA
*
145126 ACCAACATAACCCTTCAGATTTTTTCCCTAAACCTACCCCAAACCTTGACCGATCAGCTGCTTCA
326 ACCAACATAACCCTTCAGATTTTTTCCCTAAACCCACCCCAAACCTTGACCGATCAGCTGCTTCA
145191 CAACGTGGCAAGTTAATTGGCCACATCAGCTAGTTAACTTGCCACATCAGCAGTCCTGCTAGTGT
391 CAACGTGGCAAGTTAATTGGCCACATCAGCTAGTTAACTTGCCACATCAGCAGTCCTGCTAGTGT
145256 CTTAATGGAAATTGTTAATCAGTGACTGTTTTGTCACTTTTTTATAACGCTAGTGACT
456 CTTAATGGAAATTGTTAATCAGTGACTGTTTTGTCACTTTTTTATAACGCTAGTGACT
145314 GGTTTGTTTCCGTGAGCAGATTAGGTACAAAAATTTTGAAGAGTTGTATTTGAGATTACGAGTCT
1 GGTTTGTTTCCGTGAGCAGATTAGGTACAAAAATTTTGAAGAGTTGTATTTGAGATTACGAGTCT
*
145379 TCATCTCATCACATCTTCAAGCAACAAGGGGGTATGTTTTAAAATTTTGAATAGAATGACATGTA
66 TCATCTCATCACATCTTCAAGCAACAAGAGGGTATGTTTTAAAATTTTGAATAGAATGACATGTA
145444 CTTAAGGAAAAATTAAGTATGTCCCAAGTAGTAGTAATGGATTTAAATATAAATTATTTAAATTT
131 CTTAAGGAAAAATTAAGTATGTCCCAAGTAGTAGTAATGGATTTAAATATAAATTATTTAAATTT
145509 ATGATTTGTCTGTTTTTATGTTCAAATATAATAGTAATTAGCCAAGAATTACTTGGGCACCAAAT
196 ATGATTTGTCTGTTTTTATGTTCAAATATAATAGTAATTAGCCAAGAATTACTTGGGCACCAAAT
*
145574 GTACTATTCCTATATCAGGTTCCTCGAGTCGAACATGGTATAGGGGTGTTACAGTTTTGCCCTAA
261 GTACTATTCCTATATCAAGTTCCTCGAGTCGAACATGGTATAGGGGTGTTACAGTTTTGCCCTAA
* * *
145639 ACCAACGTAACCTTTCAGATTTTTTCCTTAAACCCACCCCAAACCTTGACCGATCAGCTGCTTCA
326 ACCAACATAACCCTTCAGATTTTTTCCCTAAACCCACCCCAAACCTTGACCGATCAGCTGCTTCA
145704 CAACGTGGCAAGTTAATTGGCCACATCAGCTAGTTAACTTGCCACATCAGCAGTCCTGCTAGTGT
391 CAACGTGGCAAGTTAATTGGCCACATCAGCTAGTTAACTTGCCACATCAGCAGTCCTGCTAGTGT
145769 CTTAATGGAAATTGTTAATCAGTGACTGTTTTGTCACTTTTTTATAACGCTAGTGACT
456 CTTAATGGAAATTGTTAATCAGTGACTGTTTTGTCACTTTTTTATAACGCTAGTGACT
145827 ATTTTGTTAT
Statistics
Matches: 505, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
513 505 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (513 bp):
GGTTTGTTTCCGTGAGCAGATTAGGTACAAAAATTTTGAAGAGTTGTATTTGAGATTACGAGTCT
TCATCTCATCACATCTTCAAGCAACAAGAGGGTATGTTTTAAAATTTTGAATAGAATGACATGTA
CTTAAGGAAAAATTAAGTATGTCCCAAGTAGTAGTAATGGATTTAAATATAAATTATTTAAATTT
ATGATTTGTCTGTTTTTATGTTCAAATATAATAGTAATTAGCCAAGAATTACTTGGGCACCAAAT
GTACTATTCCTATATCAAGTTCCTCGAGTCGAACATGGTATAGGGGTGTTACAGTTTTGCCCTAA
ACCAACATAACCCTTCAGATTTTTTCCCTAAACCCACCCCAAACCTTGACCGATCAGCTGCTTCA
CAACGTGGCAAGTTAATTGGCCACATCAGCTAGTTAACTTGCCACATCAGCAGTCCTGCTAGTGT
CTTAATGGAAATTGTTAATCAGTGACTGTTTTGTCACTTTTTTATAACGCTAGTGACT
Found at i:146119 original size:13 final size:13
Alignment explanation
Indices: 146096--146131 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
146086 TATAAAGATT
146096 TTTTAAA-ATTTA
1 TTTTAAATATTTA
146108 TTTTAAATATTTA
1 TTTTAAATATTTA
146121 TTTT-AATATTT
1 TTTTAAATATTT
146132 TTAGTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTAAATATTTA
Found at i:149490 original size:40 final size:40
Alignment explanation
Indices: 149435--149516 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
149425 TATTACAATT
149435 GTGGATTGCTTGGCCAAGTTGGGTTTTAAATGGAATTCAA
1 GTGGATTGCTTGGCCAAGTTGGGTTTTAAATGGAATTCAA
* *
149475 GTGGATTGCTTGGCCAAGTTGGGTTTTACATGGAATTTAA
1 GTGGATTGCTTGGCCAAGTTGGGTTTTAAATGGAATTCAA
149515 GT
1 GT
149517 CTTCAAATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.10, G:0.30, T:0.37
Consensus pattern (40 bp):
GTGGATTGCTTGGCCAAGTTGGGTTTTAAATGGAATTCAA
Found at i:150332 original size:4 final size:4
Alignment explanation
Indices: 150323--150355 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
150313 GATTTTGAAT
*
150323 TTTA TTTA TTTA TTTA TTTA TTT- TTTC TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
150356 CTTTTCGGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:150338 original size:12 final size:11
Alignment explanation
Indices: 150322--150360 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
150312 TGATTTTGAA
150322 TTTTATTTATT
1 TTTTATTTATT
150333 TATTTATTTATT
1 T-TTTATTTATT
*
150345 TTTTCTTTATT
1 TTTTATTTATT
150356 CTTTT
1 -TTTT
150361 CGGTTGAGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTATTTATT
Found at i:152317 original size:43 final size:43
Alignment explanation
Indices: 152261--152344 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
152251 ACAATGGTTA
* * *
152261 TTAAATAAGGTTATTTGTATTTTGAGTATATTGTTTCATATTG
1 TTAAACAAAGTTATTTGTATTTTGAGTATATTGCTTCATATTG
152304 TTAAACAAAGTTATTTGTATTTTGAGTATATTGCTTCATAT
1 TTAAACAAAGTTATTTGTATTTTGAGTATATTGCTTCATAT
152345 GTTTTTTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (43 bp):
TTAAACAAAGTTATTTGTATTTTGAGTATATTGCTTCATATTG
Found at i:153898 original size:11 final size:11
Alignment explanation
Indices: 153879--153911 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
153869 TGTATTAAGC
*
153879 TAAATAATAAT
1 TAAAAAATAAT
153890 TAAAAAATAAT
1 TAAAAAATAAT
153901 TAAAAAATAAT
1 TAAAAAATAAT
153912 CTGGTATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAAAAAATAAT
Found at i:154204 original size:15 final size:16
Alignment explanation
Indices: 154174--154207 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
154164 TTTTATATGA
*
154174 AATTTTAATTTAATTT
1 AATTTTAATATAATTT
154190 AATTTT-ATATAATTT
1 AATTTTAATATAATTT
154205 AAT
1 AAT
154208 ATATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AATTTTAATATAATTT
Found at i:159048 original size:24 final size:24
Alignment explanation
Indices: 159021--159101 Score: 90
Period size: 24 Copynumber: 3.2 Consensus size: 24
159011 TAATCTACAT
159021 TATTTAAATTACTTGTGATCTTTA
1 TATTTAAATTACTTGTGATCTTTA
* * *
159045 TATTTAAGTTAGGTCTCTCTACATCTTTA
1 TATTTAAATTA---CT-TGT-GATCTTTA
159074 TATTTAAATTACTTGTGATCTTTA
1 TATTTAAATTACTTGTGATCTTTA
159098 TATT
1 TATT
159102 ATTCCACCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
24 21 0.46
25 2 0.04
26 2 0.04
27 2 0.04
28 2 0.04
29 17 0.37
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.53
Consensus pattern (24 bp):
TATTTAAATTACTTGTGATCTTTA
Found at i:162225 original size:18 final size:18
Alignment explanation
Indices: 162202--162237 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
162192 CTTTTAAATG
*
162202 ATATTTTATTAAGTAATA
1 ATATTTTAATAAGTAATA
*
162220 ATATTTTAATAATTAATA
1 ATATTTTAATAAGTAATA
162238 TTATAATACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
ATATTTTAATAAGTAATA
Found at i:164261 original size:18 final size:18
Alignment explanation
Indices: 164238--164279 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
164228 TATTAATAAT
164238 ATTTATATTCATGC-TTTA
1 ATTTATATTCAT-CATTTA
* *
164256 ATTTATTTTTATCATTTA
1 ATTTATATTCATCATTTA
164274 ATTTAT
1 ATTTAT
164280 GATCAATACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (18 bp):
ATTTATATTCATCATTTA
Found at i:167435 original size:18 final size:18
Alignment explanation
Indices: 167412--167449 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
167402 GAAGAAATAT
*
167412 GATAAT-AATTAAAGGTAA
1 GATAATGAACTAAA-GTAA
167430 GATAATGAACTAAAGTAA
1 GATAATGAACTAAAGTAA
167448 GA
1 GA
167450 ATGATTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.55, C:0.03, G:0.18, T:0.24
Consensus pattern (18 bp):
GATAATGAACTAAAGTAA
Found at i:173784 original size:7 final size:7
Alignment explanation
Indices: 173772--173816 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
173762 TAGTATTTTC
*
173772 TTATAAT
1 TTATTAT
*
173779 TTATAAT
1 TTATTAT
173786 TTATTAT
1 TTATTAT
173793 TTATTA-
1 TTATTAT
173799 TTATTAT
1 TTATTAT
*
173806 CTATTAT
1 TTATTAT
173813 TTAT
1 TTAT
173817 AAAAATGATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
6 6 0.18
7 28 0.82
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (7 bp):
TTATTAT
Found at i:182724 original size:3 final size:3
Alignment explanation
Indices: 182718--182747 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
182708 CTACTACTAC
182718 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
182748 AAGATGTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:183669 original size:14 final size:15
Alignment explanation
Indices: 183638--183672 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
183628 TGATGACATT
*
183638 AATAATAGATATTAA
1 AATAATAGATACTAA
183653 AATAATA-ATACTAA
1 AATAATAGATACTAA
183667 AATAAT
1 AATAAT
183673 TAACTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATAATAGATACTAA
Found at i:186323 original size:23 final size:23
Alignment explanation
Indices: 186297--186340 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
186287 GTTATATTAT
*
186297 GAAAT-GTTGGATTTTTTGTCATG
1 GAAATAGTT-GATTTATTGTCATG
186320 GAAATAGTTGATTTATTGTCA
1 GAAATAGTTGATTTATTGTCA
186341 CAAAATATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.27, C:0.05, G:0.23, T:0.45
Consensus pattern (23 bp):
GAAATAGTTGATTTATTGTCATG
Found at i:188136 original size:24 final size:24
Alignment explanation
Indices: 188102--188150 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
188092 GTTTTGTTCA
*
188102 TGACATTCCTTGCTGGTGAGAGTG
1 TGACATCCCTTGCTGGTGAGAGTG
188126 TGACATCCCTTGCTGGTGAGAGTG
1 TGACATCCCTTGCTGGTGAGAGTG
188150 T
1 T
188151 AACACCCCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.16, C:0.18, G:0.33, T:0.33
Consensus pattern (24 bp):
TGACATCCCTTGCTGGTGAGAGTG
Found at i:191545 original size:75 final size:75
Alignment explanation
Indices: 191417--191568 Score: 268
Period size: 75 Copynumber: 2.0 Consensus size: 75
191407 TATGAGATTA
* *
191417 AAGAAACCCCATCAGTTCATCAACGGAGAGAACTGAAAGGTCTTTGGATTCTTCTATAGCAGCCA
1 AAGAAACCCCATCAGTTCATCAACGGAGAGAACTGAAAGGTCTTTGGATTCTTCTATAACAACCA
191482 CAACATGATC
66 CAACATGATC
* *
191492 AAGAGACCCCATCATTTCATCAACGGAGAGAACTGAAAGGTCTTTGGATTCTTCTATAACAACCA
1 AAGAAACCCCATCAGTTCATCAACGGAGAGAACTGAAAGGTCTTTGGATTCTTCTATAACAACCA
191557 CAACATGATC
66 CAACATGATC
191567 AA
1 AA
191569 ATTTTATCGT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (75 bp):
AAGAAACCCCATCAGTTCATCAACGGAGAGAACTGAAAGGTCTTTGGATTCTTCTATAACAACCA
CAACATGATC
Found at i:192595 original size:380 final size:380
Alignment explanation
Indices: 191894--192654 Score: 1369
Period size: 380 Copynumber: 2.0 Consensus size: 380
191884 TTGGTTTCTT
*
191894 TCAATCTTTTTTCTTCTTCTTCATCAAGTTCAAGTATGTCAGCGAACCAGTACTCGACCAAGTCC
1 TCAATCTTTTTTCTTCTTCTTCATCAAGTTCAAGTATGTCAGCGAACCAGTACTCGACCAAATCC
*
191959 CATAGCTCTTGTAATTTGAGCAATGTCTTCACCTTGATGCTTCACCACTCATATTTCTCACCATT
66 CATAGCTCTTGTAATTTGAGCAATGTCTTCACCTTGATGCTCCACCACTCATATTTCTCACCATT
* * *
192024 AAAAATGGGTATGAGTGGTTGAGAGGAAGAAAAACCAGTTGATGCTATTCCAAGAACACACACTC
131 AAAAATGGGTATGAGTGGTTGAGAGGAAAAAAAACCAGCTGATACTATTCCAAGAACACACACTC
** * *
192089 TCTTTTCTCGTGTTTCCCAAAGACCCAAAAAGGTGTTTCTCTCAAATACCTAATGGACCCAAACC
196 TCTCCTCTCGTATTTCCCAAAGACCCAAAAAGGTGTTTCTCTCAAATACCCAATGGACCCAAACC
192154 TAACTTTCACTCAATTGCCTAAGAGATCGAACCTTGCTCTGATACCAAATTTATTGAAGAAGGAA
261 TAACTTTCACTCAATTGCCTAAGAGATCGAACCTTGCTCTGATACCAAATTTATTGAAGAAGGAA
* *
192219 ACTTGAAAGAGACAATTATAATATGCATCAAAGTTATTCTATTATTGATAAACAC
326 ACGTGAAAGAGACAATTACAATATGCATCAAAGTTATTCTATTATTGATAAACAC
* * *
192274 TCAATCTTTTTTCTTCTTCTTCATCAGGTTCAAGTATGTCAGCGAACCCGTACTCGACCAAATCT
1 TCAATCTTTTTTCTTCTTCTTCATCAAGTTCAAGTATGTCAGCGAACCAGTACTCGACCAAATCC
192339 CATAGCTCTTGTAATTTGAGCAATGTCTTCACCTTGATGCTCCACCACTCATATTTCTCACCATT
66 CATAGCTCTTGTAATTTGAGCAATGTCTTCACCTTGATGCTCCACCACTCATATTTCTCACCATT
*
192404 GAAAATGGGTATGAGTGGTTGAGAGGAAAAAAAACCAGCTGATACTATTCCAAGAACACACACTC
131 AAAAATGGGTATGAGTGGTTGAGAGGAAAAAAAACCAGCTGATACTATTCCAAGAACACACACTC
*
192469 TCTCCTCTCGTATTTTCCAAAGACCCAAAAAGGTGTTTCTCTCAAATACCCAATGGACCCAAACC
196 TCTCCTCTCGTATTTCCCAAAGACCCAAAAAGGTGTTTCTCTCAAATACCCAATGGACCCAAACC
192534 TAACTTTCACTCAATTGCCTAAGAGATCGAACCTTGCTCTGATACCAAATTTATTGAAGAAGGAA
261 TAACTTTCACTCAATTGCCTAAGAGATCGAACCTTGCTCTGATACCAAATTTATTGAAGAAGGAA
*
192599 ACGTGAAAGAGATAATTACAATATGCATCAAAGTTATTCTATTATTGATAAACAC
326 ACGTGAAAGAGACAATTACAATATGCATCAAAGTTATTCTATTATTGATAAACAC
192654 T
1 T
192655 GAATTGCTAA
Statistics
Matches: 364, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
380 364 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.30
Consensus pattern (380 bp):
TCAATCTTTTTTCTTCTTCTTCATCAAGTTCAAGTATGTCAGCGAACCAGTACTCGACCAAATCC
CATAGCTCTTGTAATTTGAGCAATGTCTTCACCTTGATGCTCCACCACTCATATTTCTCACCATT
AAAAATGGGTATGAGTGGTTGAGAGGAAAAAAAACCAGCTGATACTATTCCAAGAACACACACTC
TCTCCTCTCGTATTTCCCAAAGACCCAAAAAGGTGTTTCTCTCAAATACCCAATGGACCCAAACC
TAACTTTCACTCAATTGCCTAAGAGATCGAACCTTGCTCTGATACCAAATTTATTGAAGAAGGAA
ACGTGAAAGAGACAATTACAATATGCATCAAAGTTATTCTATTATTGATAAACAC
Found at i:204558 original size:101 final size:101
Alignment explanation
Indices: 204430--204634 Score: 383
Period size: 101 Copynumber: 2.0 Consensus size: 101
204420 ATAATTCAAT
*
204430 AAATTTAACCCTTCACATTTACAAATTCTATCAATTTGATTATCAAACTTCTTAATCAAAGCTTT
1 AAATTTAACCCTTCACATTTACAAATTCTATCAATTTGATTATCAAACTTCCTAATCAAAGCTTT
204495 CAACTTTTAAAACGGAAGTATTTGTAAGCAATACTC
66 CAACTTTTAAAACGGAAGTATTTGTAAGCAATACTC
*
204531 AAATTTAACCCTTCACATTTACAAATTCTATCAATTTGATTATCAAACTTCCTAATCAAATCTTT
1 AAATTTAACCCTTCACATTTACAAATTCTATCAATTTGATTATCAAACTTCCTAATCAAAGCTTT
*
204596 CAACTTTTAAAATGGAAGTATTTGTAAGCAATACTC
66 CAACTTTTAAAACGGAAGTATTTGTAAGCAATACTC
204632 AAA
1 AAA
204635 CTTCTATTTG
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.37
Consensus pattern (101 bp):
AAATTTAACCCTTCACATTTACAAATTCTATCAATTTGATTATCAAACTTCCTAATCAAAGCTTT
CAACTTTTAAAACGGAAGTATTTGTAAGCAATACTC
Found at i:207500 original size:16 final size:16
Alignment explanation
Indices: 207451--207500 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
207441 ATTACTTTTC
207451 CCTCAAAACTTTTACT
1 CCTCAAAACTTTTACT
**
207467 CCTTC-CCA-TTTT-CT
1 CC-TCAAAACTTTTACT
207481 CCTCAAAACTTTTACT
1 CCTCAAAACTTTTACT
207497 CCTC
1 CCTC
207501 TTCCATCCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
13 2 0.08
14 5 0.19
15 8 0.31
16 9 0.35
17 2 0.08
ACGTcount: A:0.22, C:0.38, G:0.00, T:0.40
Consensus pattern (16 bp):
CCTCAAAACTTTTACT
Found at i:207659 original size:30 final size:30
Alignment explanation
Indices: 207610--207668 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
207600 AACTTTTTAT
207610 TTTCCCCCAAAATTCTTAC-TCCCTCCCAC
1 TTTCCCCCAAAATTCTTACTTCCCTCCCAC
* *
207639 TTTCCCCCTAAAATTTTTACTTCCTTCCCA
1 TTTCCCCC-AAAATTCTTACTTCCCTCCCA
207669 TCCCCCCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 10 0.38
31 8 0.31
ACGTcount: A:0.20, C:0.42, G:0.00, T:0.37
Consensus pattern (30 bp):
TTTCCCCCAAAATTCTTACTTCCCTCCCAC
Found at i:211255 original size:30 final size:30
Alignment explanation
Indices: 211214--211339 Score: 189
Period size: 30 Copynumber: 4.2 Consensus size: 30
211204 CTAGCCTTTG
211214 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* *
211244 CCCCCAACAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* *
211274 CCACTACCTACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* * *
211304 CCACCACCTACTCCATTAACCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
211334 CCACCA
1 CCACCA
211340 TCACTTGCCT
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 87 1.00
ACGTcount: A:0.26, C:0.49, G:0.06, T:0.19
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:211277 original size:18 final size:18
Alignment explanation
Indices: 211254--211307 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
211244 CCCCCAACAA
211254 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
*
211272 CTCCACT----AC-C-TA
1 CTCCACTAGCCACACTTG
211284 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
211302 CTCCAC
1 CTCCAC
211308 CACCTACTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 8 0.29
13 1 0.04
14 2 0.07
16 2 0.07
17 1 0.04
18 14 0.50
ACGTcount: A:0.22, C:0.48, G:0.07, T:0.22
Consensus pattern (18 bp):
CTCCACTAGCCACACTTG
Found at i:213912 original size:15 final size:15
Alignment explanation
Indices: 213892--213926 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
213882 TAACTAATTT
*
213892 AATAAATTAAAATAA
1 AATAAATAAAAATAA
213907 AATAAATAAAAATAA
1 AATAAATAAAAATAA
213922 AATAA
1 AATAA
213927 TATCTTCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AATAAATAAAAATAA
Found at i:218795 original size:61 final size:61
Alignment explanation
Indices: 218725--218848 Score: 178
Period size: 61 Copynumber: 2.0 Consensus size: 61
218715 TTGTCCTACT
* * * * *
218725 AATTAATTTTCTATATTATTTCAACGGATT-TTTTACAAGTATTTTATATTCATCATTTTTA
1 AATTAATTTTCTATATTATTTCAACAGATTCTTCT-CAAGTATTATATATACATAATTTTTA
*
218786 AATTAATTTTCTGTATTATTTCAACAGATTCTTCTCAAGTATTATATATACATAATTTTTA
1 AATTAATTTTCTATATTATTTCAACAGATTCTTCTCAAGTATTATATATACATAATTTTTA
218847 AA
1 AA
218849 ATTTATTCAA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
61 53 0.95
62 3 0.05
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (61 bp):
AATTAATTTTCTATATTATTTCAACAGATTCTTCTCAAGTATTATATATACATAATTTTTA
Found at i:218887 original size:16 final size:16
Alignment explanation
Indices: 218866--218899 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
218856 CAAAAACAAG
218866 TTTTATATATACATTA
1 TTTTATATATACATTA
* *
218882 TTTTATATGTGCATTA
1 TTTTATATATACATTA
218898 TT
1 TT
218900 ATATTTACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (16 bp):
TTTTATATATACATTA
Found at i:221177 original size:17 final size:17
Alignment explanation
Indices: 221155--221198 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
221145 TTTTTTTAAT
221155 TTTTTTTC-TGTCTCTTA
1 TTTTTTTCATG-CTCTTA
*
221172 TTTTTTTCAATGGTCTTA
1 TTTTTTTC-ATGCTCTTA
221190 TTTTTTTCA
1 TTTTTTTCA
221199 ATGGGTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 9 0.38
18 13 0.54
19 2 0.08
ACGTcount: A:0.11, C:0.14, G:0.07, T:0.68
Consensus pattern (17 bp):
TTTTTTTCATGCTCTTA
Found at i:221212 original size:19 final size:18
Alignment explanation
Indices: 221167--221214 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
221157 TTTTTCTGTC
221167 TCTTATTTTTTTCAATGG
1 TCTTATTTTTTTCAATGG
221185 TCTTATTTTTTTCAATGG
1 TCTTATTTTTTTCAATGG
*
221203 -GTT-TTTTTTTCA
1 TCTTATTTTTTTCA
221215 TTTGACAGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 9 0.31
17 2 0.07
18 18 0.62
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.65
Consensus pattern (18 bp):
TCTTATTTTTTTCAATGG
Found at i:223910 original size:105 final size:105
Alignment explanation
Indices: 223801--223997 Score: 349
Period size: 105 Copynumber: 1.9 Consensus size: 105
223791 ATAAAAAAAA
223801 TTACCTTATAGATTAAATTAATTTATAAAATTAAAATTTAAAATATAAAAATAACGTGTAGAAAT
1 TTACCTTATAGATTAAATTAATTTATAAAATTAAAATTTAAAATATAAAAATAACGTGTAGAAAT
* *
223866 TACGTCTATAAATTAAATTTATAAATATACTACTCGTTAT
66 AACATCTATAAATTAAATTTATAAATATACTACTCGTTAT
* *
223906 TTACCTTATAGATTAAATTAATTTATAAAATTAAATTTTAAAATATAAAAATAATGTGTAGAAAT
1 TTACCTTATAGATTAAATTAATTTATAAAATTAAAATTTAAAATATAAAAATAACGTGTAGAAAT
*
223971 AACATTTATAAATTAAATTTATAAATA
66 AACATCTATAAATTAAATTTATAAATA
223998 ATTTTTTTGG
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 87 1.00
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.40
Consensus pattern (105 bp):
TTACCTTATAGATTAAATTAATTTATAAAATTAAAATTTAAAATATAAAAATAACGTGTAGAAAT
AACATCTATAAATTAAATTTATAAATATACTACTCGTTAT
Found at i:236139 original size:13 final size:13
Alignment explanation
Indices: 236121--236150 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
236111 ACTCACTCTC
*
236121 TTCTTTTTTCTTT
1 TTCTTTTTCCTTT
236134 TTCTTTTTCCTTT
1 TTCTTTTTCCTTT
236147 TTCT
1 TTCT
236151 AGTTTCGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTCTTTTTCCTTT
Found at i:240717 original size:33 final size:33
Alignment explanation
Indices: 240675--240740 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
240665 CATATGCAAC
240675 TTTATGAATTAAGTATACCTGAGTTGGATTACA
1 TTTATGAATTAAGTATACCTGAGTTGGATTACA
240708 TTTATGAATTAAGTATACCTGAGTTGGATTACA
1 TTTATGAATTAAGTATACCTGAGTTGGATTACA
240741 AAATGTTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (33 bp):
TTTATGAATTAAGTATACCTGAGTTGGATTACA
Found at i:250545 original size:16 final size:16
Alignment explanation
Indices: 250524--250559 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
250514 TATTTATTAT
250524 AAATATTTACGAAGTA
1 AAATATTTACGAAGTA
250540 AAATATTTACGAAGTA
1 AAATATTTACGAAGTA
250556 AAAT
1 AAAT
250560 GAGTGGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.53, C:0.06, G:0.11, T:0.31
Consensus pattern (16 bp):
AAATATTTACGAAGTA
Found at i:250767 original size:8 final size:8
Alignment explanation
Indices: 250754--250782 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
250744 TTATGTTTAG
250754 TATATTAT
1 TATATTAT
250762 TATATTAT
1 TATATTAT
250770 TATATTAT
1 TATATTAT
250778 TATAT
1 TATAT
250783 AATAAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:250815 original size:5 final size:5
Alignment explanation
Indices: 250805--250840 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
250795 TTATGTTTTA
*
250805 ATTAT ATTAT ATTAT ATTAT ACTAT ATTAT A-TAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
250841 AAACTAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (5 bp):
ATTAT
Found at i:252131 original size:15 final size:15
Alignment explanation
Indices: 252111--252167 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
252101 CGATGAATTT
252111 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
252126 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
252141 ATTGAATTTATATTG
1 ATTGAATTTATATTG
252156 ATTGAA-TTATAT
1 ATTGAATTTATAT
252168 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:252569 original size:23 final size:23
Alignment explanation
Indices: 252539--252625 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
252529 GCTTTATCGA
* *
252539 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
252562 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
252583 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
252605 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
252626 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:256814 original size:113 final size:113
Alignment explanation
Indices: 256616--256855 Score: 462
Period size: 113 Copynumber: 2.1 Consensus size: 113
256606 TATATACATT
* *
256616 ATAACTTAAACTTTTTACTTTCATAATCTTAATAGTTTCACCCCTTACATTCATTTTACATCTCT
1 ATAACTTAAACATTTTACTGTCATAATCTTAATAGTTTCACCCCTTACATTCATTTTACATCTCT
256681 TCCCTGTAGTTAAGCAATTCATATATATTTCTATCTTCATATTATTCG
66 TCCCTGTAGTTAAGCAATTCATATATATTTCTATCTTCATATTATTCG
256729 ATAACTTAAACATTTTACTGTCATAATCTTAATAGTTTCACCCCTTACATTCATTTTACATCTCT
1 ATAACTTAAACATTTTACTGTCATAATCTTAATAGTTTCACCCCTTACATTCATTTTACATCTCT
256794 TCCCTGTAGTTAAGCAATTCATATATATTTCTATCTTCATATTATTCG
66 TCCCTGTAGTTAAGCAATTCATATATATTTCTATCTTCATATTATTCG
256842 ATAACTTAAACATT
1 ATAACTTAAACATT
256856 CGTAAATCAG
Statistics
Matches: 125, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 125 1.00
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.45
Consensus pattern (113 bp):
ATAACTTAAACATTTTACTGTCATAATCTTAATAGTTTCACCCCTTACATTCATTTTACATCTCT
TCCCTGTAGTTAAGCAATTCATATATATTTCTATCTTCATATTATTCG
Found at i:258162 original size:23 final size:23
Alignment explanation
Indices: 258132--258175 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
258122 ATTGTAAAAG
258132 GTGTAAAAATTGCTAAAATGAAT
1 GTGTAAAAATTGCTAAAATGAAT
* *
258155 GTGTAAAAGTTGCTAGAATGA
1 GTGTAAAAATTGCTAAAATGA
258176 TTAAATAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.23, T:0.30
Consensus pattern (23 bp):
GTGTAAAAATTGCTAAAATGAAT
Found at i:260620 original size:14 final size:14
Alignment explanation
Indices: 260601--260630 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
260591 TATCTTATAA
260601 ATATGCGTGAATCT
1 ATATGCGTGAATCT
*
260615 ATATGCGTTAATCT
1 ATATGCGTGAATCT
260629 AT
1 AT
260631 CTTGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (14 bp):
ATATGCGTGAATCT
Found at i:262937 original size:22 final size:23
Alignment explanation
Indices: 262898--262946 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 23
262888 AGTATTTTCG
*
262898 TTATTTTATTTCACTTT-AAATA
1 TTATTTGATTTCACTTTAAAATA
262920 TTATTTGATTATCA-TTTACAAATA
1 TTATTTGATT-TCACTTTA-AAATA
262944 TTA
1 TTA
262947 GTGTATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 12 0.52
23 3 0.13
24 8 0.35
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (23 bp):
TTATTTGATTTCACTTTAAAATA
Found at i:263103 original size:3 final size:3
Alignment explanation
Indices: 263090--263165 Score: 64
Period size: 3 Copynumber: 24.7 Consensus size: 3
263080 TTTTCTTTTG
* ** **
263090 TAT TTT TAT TAT TAT TGC TAT TAT TAT TGC TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
263138 TATT TAT TA- TATT TAT ATAA TAT TAT TA
1 TA-T TAT TAT TA-T TAT -TAT TAT TAT TA
263166 ATAGGTACTT
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
2 2 0.04
3 48 0.84
4 7 0.12
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:263333 original size:22 final size:21
Alignment explanation
Indices: 263292--263333 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
263282 TACACTTTGT
* *
263292 AATACTATTAGTATATATTTC
1 AATACCATTAGTATACATTTC
263313 AATACCATTAGTTATACATTT
1 AATACCATTAG-TATACATTT
263334 TTGTACTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (21 bp):
AATACCATTAGTATACATTTC
Found at i:263427 original size:24 final size:22
Alignment explanation
Indices: 263400--263457 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
263390 TAGTGTGTTT
263400 TATTATATGTATATATACTCTCAA
1 TATTATAT-TAT-TATACTCTCAA
* *
263424 TATTATATTCTTATACTCTTAA
1 TATTATATTATTATACTCTCAA
**
263446 TACCATATTATT
1 TATTATATTATT
263458 CTTATTATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 19 0.66
23 2 0.07
24 8 0.28
ACGTcount: A:0.34, C:0.14, G:0.02, T:0.50
Consensus pattern (22 bp):
TATTATATTATTATACTCTCAA
Found at i:267723 original size:17 final size:18
Alignment explanation
Indices: 267693--267730 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
267683 CCTCCCTCTC
*
267693 TTTTCCTCTCGTTTTTCT
1 TTTTCCTCTCGTTTTCCT
*
267711 TTTTCTTCT-GTTTTCCT
1 TTTTCCTCTCGTTTTCCT
267728 TTT
1 TTT
267731 ATGTTTGCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.00, C:0.24, G:0.05, T:0.71
Consensus pattern (18 bp):
TTTTCCTCTCGTTTTCCT
Found at i:275288 original size:26 final size:24
Alignment explanation
Indices: 275239--275293 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
275229 TATTATGTAA
* *
275239 TTTTTTTAAATTTTTAATAAAATT
1 TTTTTTTAAAATTATAATAAAATT
*
275263 TATTTTTTAAAATTATATATATAATT
1 T-TTTTTTAAAATTATA-ATAAAATT
275289 TTTTT
1 TTTTT
275294 AAATAATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 17 0.65
26 8 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTTTTTAAAATTATAATAAAATT
Found at i:275292 original size:24 final size:24
Alignment explanation
Indices: 275218--275293 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 24
275208 TGGTGTAGTA
* *
275218 TTTTAAGATTATATTATGTAA-TTT
1 TTTTAAAATTATA-TATATAATTTT
* * *
275242 TTTTAAATTTTTA-ATAAAATTTATT
1 TTTTAAAATTATATATATAA-TT-TT
275267 TTTTAAAATTATATATATAATTTT
1 TTTTAAAATTATATATATAATTTT
275291 TTT
1 TTT
275294 AAATAATTTC
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
22 4 0.10
24 16 0.40
25 15 0.38
26 5 0.12
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (24 bp):
TTTTAAAATTATATATATAATTTT
Found at i:275301 original size:25 final size:25
Alignment explanation
Indices: 275225--275301 Score: 63
Period size: 24 Copynumber: 3.1 Consensus size: 25
275215 GTATTTTAAG
*
275225 ATTATATTATGTAATTTTTTTAAAT-
1 ATTATA-TATATAATTTTTTTAAATA
* * *
275250 -TTTTA-ATAAAATTTATTTTTTAA-A
1 ATTATATATATAA-TT-TTTTTAAATA
275274 ATTATATATATAATTTTTTTAAATA
1 ATTATATATATAATTTTTTTAAATA
275299 ATT
1 ATT
275302 TCATTATAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
22 4 0.10
23 2 0.05
24 18 0.46
25 10 0.26
26 5 0.13
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (25 bp):
ATTATATATATAATTTTTTTAAATA
Found at i:275461 original size:41 final size:41
Alignment explanation
Indices: 275383--275462 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 41
275373 GGAGGATAAT
* * * *
275383 ACGCTTCATCACAATTTAACCTATATATTCCTGTATTGAAA
1 ACGCTTCAGCACAATCTAACCCATATATTCCTATATTGAAA
* * *
275424 ACGCTTCAGCACAGTCTAACCCATATCTTCTTATATTGA
1 ACGCTTCAGCACAATCTAACCCATATATTCCTATATTGA
275463 CATTTGACAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.35
Consensus pattern (41 bp):
ACGCTTCAGCACAATCTAACCCATATATTCCTATATTGAAA
Found at i:288056 original size:25 final size:26
Alignment explanation
Indices: 288027--288084 Score: 79
Period size: 23 Copynumber: 2.4 Consensus size: 26
288017 AAATTAATGA
288027 AATATTTAAAATATATTTTT-TAATT
1 AATATTTAAAATATATTTTTATAATT
*
288052 AATATTT--TATATATTTTTATAATT
1 AATATTTAAAATATATTTTTATAATT
288076 AA-ATTTAAA
1 AATATTTAAA
288085 TAATAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 14 0.50
24 7 0.25
25 7 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
AATATTTAAAATATATTTTTATAATT
Found at i:288810 original size:15 final size:16
Alignment explanation
Indices: 288790--288819 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
288780 AGGTATAATA
288790 AAATAT-TAAAAAAAT
1 AAATATATAAAAAAAT
288805 AAATATATAAAAAAA
1 AAATATATAAAAAAA
288820 GAGAGAGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATATATAAAAAAAT
Found at i:296331 original size:20 final size:20
Alignment explanation
Indices: 296306--296355 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
296296 TGGCTTAAAA
296306 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
296326 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
296343 GTGGTAGTGGATT
1 TTGGTAGTGGATT
296356 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:300970 original size:20 final size:20
Alignment explanation
Indices: 300945--300994 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
300935 TGGCTTAAAA
300945 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
300965 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
300982 GTGGTAGTGGATT
1 TTGGTAGTGGATT
300995 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:308996 original size:21 final size:21
Alignment explanation
Indices: 308972--309018 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
308962 CTTTTTAGGT
* *
308972 TTTTAAAT-TTGTTTTTCTTTA
1 TTTTAAATATTCTTTTT-TTGA
*
308993 TTTTCAATATTCTTTTTTTGA
1 TTTTAAATATTCTTTTTTTGA
309014 TTTTA
1 TTTTA
309019 TTTTTTATAC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTAAATATTCTTTTTTTGA
Found at i:310573 original size:16 final size:18
Alignment explanation
Indices: 310542--310574 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
310532 TATATATTAT
310542 TAATAAGAATTAAATATG
1 TAATAAGAATTAAATATG
310560 TAATAA-AA-TAAATAT
1 TAATAAGAATTAAATAT
310575 TTATTGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (18 bp):
TAATAAGAATTAAATATG
Found at i:311410 original size:29 final size:30
Alignment explanation
Indices: 311377--311437 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
311367 ATAATGAAAC
*
311377 AATTAACTAAAATAAT-TATTTAA-AAAGTA
1 AATTAAAT-AAATAATCTATTTAATAAAGTA
* *
311406 AATTAAATCAATAATCTATTTAATAAATTA
1 AATTAAATAAATAATCTATTTAATAAAGTA
311436 AA
1 AA
311438 AACACTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.22
29 14 0.52
30 7 0.26
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (30 bp):
AATTAAATAAATAATCTATTTAATAAAGTA
Found at i:312195 original size:27 final size:32
Alignment explanation
Indices: 312138--312200 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 32
312128 AAGCAATATT
*
312138 TTTTATTTAATTATAATATATATTTTTTAAAA
1 TTTTATTTAATTATAATATATATTTTATAAAA
312170 TTTTATTT-ATT-TAA-A-ATA-TTTATAAAA
1 TTTTATTTAATTATAATATATATTTTATAAAA
312197 TTTT
1 TTTT
312201 GCAAATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 12 0.40
28 3 0.10
29 1 0.03
30 3 0.10
31 3 0.10
32 8 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
TTTTATTTAATTATAATATATATTTTATAAAA
Found at i:312739 original size:26 final size:26
Alignment explanation
Indices: 312698--312772 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 26
312688 CCTTTAAAAA
* *
312698 AAAAGAGTCAAGCTTAATTTTTTTTAT
1 AAAA-AGTCAAACTTAATTTTTTTGAT
312725 AAAAAGTCAAACTTAA-TTTTTTGAT
1 AAAAAGTCAAACTTAATTTTTTTGAT
* *
312750 ACAGAAGGTCAAACTTAGTTTTT
1 A-A-AAAGTCAAACTTAATTTTT
312773 GATTCTTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 9 0.22
26 12 0.29
27 16 0.39
28 4 0.10
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (26 bp):
AAAAAGTCAAACTTAATTTTTTTGAT
Found at i:315203 original size:20 final size:20
Alignment explanation
Indices: 315178--315227 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
315168 TGGCTTAAAA
315178 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
315198 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
315215 GTGGTAGTGGATT
1 TTGGTAGTGGATT
315228 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:319842 original size:20 final size:20
Alignment explanation
Indices: 319817--319866 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
319807 TGGCTTAAAA
319817 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
319837 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
319854 GTGGTAGTGGATT
1 TTGGTAGTGGATT
319867 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:320402 original size:5 final size:5
Alignment explanation
Indices: 320387--320525 Score: 269
Period size: 5 Copynumber: 27.6 Consensus size: 5
320377 TAATAATAAA
320387 TATACT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATA-T TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
320438 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
320488 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
320526 TCTTAATATA
Statistics
Matches: 133, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 129 0.97
6 4 0.03
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:325250 original size:20 final size:20
Alignment explanation
Indices: 325225--325274 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
325215 TGGCTTAAAA
325225 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
325245 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
325262 GTGGTAGTGGATT
1 TTGGTAGTGGATT
325275 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:328569 original size:52 final size:53
Alignment explanation
Indices: 328512--328614 Score: 199
Period size: 53 Copynumber: 2.0 Consensus size: 53
328502 GCCAGCGACG
328512 TATTATTAAAAAAAAT-AAAAAAAGTTACCTTTTGAACTTCCGGCCACCATAA
1 TATTATTAAAAAAAATAAAAAAAAGTTACCTTTTGAACTTCCGGCCACCATAA
328564 TATTATTAAAAAAAATAAAAAAAAGTTACCTTTTGAACTTCCGGCCACCAT
1 TATTATTAAAAAAAATAAAAAAAAGTTACCTTTTGAACTTCCGGCCACCAT
328615 GTGCGGTGGC
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 16 0.32
53 34 0.68
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (53 bp):
TATTATTAAAAAAAATAAAAAAAAGTTACCTTTTGAACTTCCGGCCACCATAA
Found at i:332792 original size:13 final size:13
Alignment explanation
Indices: 332774--332798 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
332764 CCTTCTTTTA
332774 TTTTTAATTAATG
1 TTTTTAATTAATG
332787 TTTTTAATTAAT
1 TTTTTAATTAAT
332799 AAATATATTA
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:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:333114 original size:20 final size:22
Alignment explanation
Indices: 333075--333114 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
333065 TGCTAATACA
*
333075 TTAAAAACATTAATTAAAAATT
1 TTAAAAACATTAACTAAAAATT
333097 TTAAAAA-A-TAACTAAAAA
1 TTAAAAACATTAACTAAAAA
333115 AATATAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 1 0.06
22 7 0.41
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (22 bp):
TTAAAAACATTAACTAAAAATT
Found at i:333572 original size:21 final size:21
Alignment explanation
Indices: 333535--333575 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
333525 TAAGATAACA
*
333535 ATAATAATATTTATAAAATAG
1 ATAATAATATATATAAAATAG
333556 ATAA-AATATATAGTAAAATA
1 ATAATAATATATA-TAAAATA
333576 TTGGTGCTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (21 bp):
ATAATAATATATATAAAATAG
Found at i:335611 original size:25 final size:26
Alignment explanation
Indices: 335582--335632 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
335572 AAAAGTAGAA
335582 AAGGAATTATTTAGG-TTTTTTTTAC
1 AAGGAATTATTTAGGCTTTTTTTTAC
335607 AAGGAATTATTTAGGCTTTTTTTTAC
1 AAGGAATTATTTAGGCTTTTTTTTAC
335633 TTAAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.27, C:0.06, G:0.16, T:0.51
Consensus pattern (26 bp):
AAGGAATTATTTAGGCTTTTTTTTAC
Found at i:336810 original size:26 final size:26
Alignment explanation
Indices: 336774--336828 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
336764 CCTTTGCACG
336774 AGATTAATTACTTTTGGGTTAGATAT
1 AGATTAATTACTTTTGGGTTAGATAT
336800 AGATTAATTACTTTTGGGTTAGATAT
1 AGATTAATTACTTTTGGGTTAGATAT
336826 AGA
1 AGA
336829 GTAAAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.44
Consensus pattern (26 bp):
AGATTAATTACTTTTGGGTTAGATAT
Found at i:340217 original size:28 final size:30
Alignment explanation
Indices: 340175--340232 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
340165 GAATTGGATC
340175 AAATCAAAATTTTATGTAT-GAATTACACA
1 AAATCAAAATTTTATGTATAGAATTACACA
*
340204 AAATCAAAA-TTTATGTATATAATTACACA
1 AAATCAAAATTTTATGTATAGAATTACACA
340233 TTCATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.34
Consensus pattern (30 bp):
AAATCAAAATTTTATGTATAGAATTACACA
Found at i:340912 original size:18 final size:17
Alignment explanation
Indices: 340891--340924 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
340881 AAAGATTAAA
340891 ATATA-TTTTAATTTTT
1 ATATATTTTTAATTTTT
*
340907 ATATATTTTTTATTTTT
1 ATATATTTTTAATTTTT
340924 A
1 A
340925 AAATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
ATATATTTTTAATTTTT
Found at i:341319 original size:37 final size:37
Alignment explanation
Indices: 341230--341327 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 37
341220 GATATCGAAG
*
341230 GTCGCAATTTTAAATCAAGCGAACCATAAAAATAACA
1 GTCGCAATATTAAATCAAGCGAACCATAAAAATAACA
** ** * * *
341267 GTCGTGATACCAAATCAAGCGAATCATAAAAATGATA
1 GTCGCAATATTAAATCAAGCGAACCATAAAAATAACA
* *
341304 GTCGCAATGTTAAATCAAGTGAAC
1 GTCGCAATATTAAATCAAGCGAAC
341328 TGGTGAAATG
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.22
Consensus pattern (37 bp):
GTCGCAATATTAAATCAAGCGAACCATAAAAATAACA
Found at i:341377 original size:40 final size:37
Alignment explanation
Indices: 341230--341378 Score: 95
Period size: 37 Copynumber: 3.9 Consensus size: 37
341220 GATATCGAAG
* * ***
341230 GTCGCAATTTTAAATCAAGCGAACCATAAAAATAACA
1 GTCGCAATCTTAAATCAAGTGAACCATAAAAATGTTA
** * * * *
341267 GTCGTGATAC-CAAATCAAGCGAATCATAAAAATGATA
1 GTCGCAAT-CTTAAATCAAGTGAACCATAAAAATGTTA
* ** *
341304 GTCGCAATGTTAAATCAAGTGAACTGGT-GAAATGTTGAA
1 GTCGCAATCTTAAATCAAGTGAAC-CATAAAAATGTT--A
*
341343 GATCGCGATCTTAAATCAAGTGAACCATAAAAATGT
1 G-TCGCAATCTTAAATCAAGTGAACCATAAAAATGT
341379 CATTTATGAT
Statistics
Matches: 83, Mismatches: 22, Indels: 11
0.72 0.19 0.09
Matches are distributed among these distances:
37 52 0.63
38 1 0.01
39 3 0.04
40 27 0.33
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.24
Consensus pattern (37 bp):
GTCGCAATCTTAAATCAAGTGAACCATAAAAATGTTA
Found at i:341508 original size:37 final size:36
Alignment explanation
Indices: 341385--341519 Score: 117
Period size: 37 Copynumber: 3.6 Consensus size: 36
341375 ATGTCATTTA
* *
341385 TGATGTTAAATCAAGCGAACTATTAAAAGATCAAATGTCG
1 TGATGTTAAATCAAGCGAATTA-TAAAA-ATAAAAT-T-G
* * * * * * *
341425 TAATCTTAAATCAAGTGAATTGTAAAAATGACAAGTA
1 TGATGTTAAATCAAGCGAATTATAAAAAT-AAAATTG
* *
341462 CGATATTAAATCAAGCGAATTATAAAAATAAAAATTG
1 TGATGTTAAATCAAGCGAATTATAAAAAT-AAAATTG
341499 TGATGTTAAATCAAGCGAATT
1 TGATGTTAAATCAAGCGAATT
341520 GTCAGAATAT
Statistics
Matches: 74, Mismatches: 20, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
37 47 0.64
38 3 0.04
39 7 0.09
40 17 0.23
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.29
Consensus pattern (36 bp):
TGATGTTAAATCAAGCGAATTATAAAAATAAAATTG
Found at i:342243 original size:18 final size:18
Alignment explanation
Indices: 342213--342248 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
342203 TTCATATATT
342213 AAATTACATAATAAATAA
1 AAATTACATAATAAATAA
342231 AAATT-CATAAATAAATAA
1 AAATTACAT-AATAAATAA
342249 TTTTATGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATTACATAATAAATAA
Found at i:342812 original size:17 final size:17
Alignment explanation
Indices: 342764--342814 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
342754 GAAATATTTA
*
342764 TTTTAATATTTTTATTAT
1 TTTTAATTTTTTTA-TAT
* * *
342782 TTTTGA-TGTATTATAT
1 TTTTAATTTTTTTATAT
342798 TTTTAATTTTTTTATAT
1 TTTTAATTTTTTTATAT
342815 AAAAAAACAA
Statistics
Matches: 25, Mismatches: 7, Indels: 3
0.71 0.20 0.09
Matches are distributed among these distances:
16 8 0.32
17 12 0.48
18 5 0.20
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (17 bp):
TTTTAATTTTTTTATAT
Found at i:346974 original size:21 final size:21
Alignment explanation
Indices: 346948--346988 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
346938 AGACGAGCAA
* *
346948 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
346969 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
346989 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:350771 original size:2 final size:2
Alignment explanation
Indices: 350764--350790 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
350754 TCACTCGACA
350764 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
350791 TATATATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:358408 original size:12 final size:11
Alignment explanation
Indices: 358384--358413 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
358374 CATTTTGTTA
358384 TTTAGTTTCTTT
1 TTTA-TTTCTTT
358396 TTTATTTCTTT
1 TTTATTTCTTT
358407 TTTATTT
1 TTTATTT
358414 TTGTTTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTATTTCTTT
Found at i:360446 original size:132 final size:132
Alignment explanation
Indices: 360102--360452 Score: 358
Period size: 132 Copynumber: 2.7 Consensus size: 132
360092 TAGATGTTTG
* * * *
360102 GCAATTCGGGAAATCGTACCCTATCGTGCTGGGTTGCAATTTCCTATTTGTTCGAAACAATCGAA
1 GCAATTCGGGGAATCGTACCCTATCGTGCTGGGTTGCAATTTCCTATTTGCTCAAAATAATCGAA
** *
360167 TAT-TCCTTCGGTGTTCCACTCATGTCTTTTAAAAAATTTTATTAAAACGAAAGAAATGTTCGAT
66 TATCT-CTTCGGAATTTCACTCATGTCTTTTAAAAAATTTTATTAAAACG--AGAAATGTTCGAT
360231 ATTTA
128 ATTTA
** * * * * *
360236 GCAATTCATGGAATCGTGCCCTAACGTGTTGGG-TGCAATTT-CTCGTTTGCTCAAAATAATCAA
1 GCAATTCGGGGAATCGTACCCTATCGTGCTGGGTTGCAATTTCCT-ATTTGCTCAAAATAATCGA
* ** *
360299 ATGTCTCTTTAGAATTTCATTCATGT-TTTCTAAAAAAAAAATTTTA-T-AAA-G-GAAATGTTC
65 ATATCTCTTCGGAATTTCACTCATGTCTTT-T----AAAAAATTTTATTAAAACGAGAAATGTTC
*
360359 GGTATTTA
125 GATATTTA
* * *
360367 GCAGTTCGGGGAATAGTACCCTATCGTGCTGGGTTACAATTTCCTATTTGCTCAAAATAATCGAA
1 GCAATTCGGGGAATCGTACCCTATCGTGCTGGGTTGCAATTTCCTATTTGCTCAAAATAATCGAA
*
360432 TATCTCTCCGGAATTTCACTC
66 TATCTCTTCGGAATTTCACTC
360453 GTATCTTCCA
Statistics
Matches: 174, Mismatches: 34, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
131 42 0.24
132 46 0.26
133 42 0.24
134 29 0.17
135 3 0.02
136 1 0.01
137 11 0.06
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.36
Consensus pattern (132 bp):
GCAATTCGGGGAATCGTACCCTATCGTGCTGGGTTGCAATTTCCTATTTGCTCAAAATAATCGAA
TATCTCTTCGGAATTTCACTCATGTCTTTTAAAAAATTTTATTAAAACGAGAAATGTTCGATATT
TA
Found at i:362132 original size:2 final size:2
Alignment explanation
Indices: 362117--362183 Score: 116
Period size: 2 Copynumber: 33.5 Consensus size: 2
362107 GGGATGTATT
* *
362117 TG TG TG TT TA TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
362159 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
362184 AACAACCTAA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.01, C:0.00, G:0.46, T:0.52
Consensus pattern (2 bp):
TG
Found at i:364318 original size:20 final size:18
Alignment explanation
Indices: 364293--364329 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
364283 ATTGCTAAGT
364293 TGTAAAATGAGTTGTAAATG
1 TGTAAAAT-AGTTG-AAATG
364313 TGTAAAATAGTTGAAAT
1 TGTAAAATAGTTGAAAT
364330 TATGAGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
TGTAAAATAGTTGAAATG
Found at i:364934 original size:46 final size:46
Alignment explanation
Indices: 364867--364963 Score: 167
Period size: 46 Copynumber: 2.1 Consensus size: 46
364857 AAGTGACATG
*
364867 TCACTAGGATGGTTGAGCATCCGAACTTGTTGAGTTGAGAACGAGT
1 TCACTAGGATGGTTGAGCATCCGAACTCGTTGAGTTGAGAACGAGT
**
364913 TCACTAGGATGGTTGAGCATCCGAACTCGTTGAGTTGAGTCCGAGT
1 TCACTAGGATGGTTGAGCATCCGAACTCGTTGAGTTGAGAACGAGT
364959 TCACT
1 TCACT
364964 TATGGATGCG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (46 bp):
TCACTAGGATGGTTGAGCATCCGAACTCGTTGAGTTGAGAACGAGT
Found at i:364984 original size:46 final size:46
Alignment explanation
Indices: 364934--365107 Score: 160
Period size: 46 Copynumber: 3.8 Consensus size: 46
364924 GTTGAGCATC
*
364934 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTT
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGAT
* * *
364980 CGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--GA--CGTAACTAGGCAT
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-AA-T--G-AT
* * **
365026 CTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCC
1 C-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGAT
* * *
365073 CGAGCTCGTTGAGTTGAGTTCGAGTTCATTTATGG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
365108 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 13, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
41 2 0.02
42 2 0.02
43 3 0.03
45 3 0.03
46 60 0.58
47 25 0.24
48 3 0.03
50 2 0.02
51 2 0.02
52 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGAT
Done.