Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold502
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: 762056
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 6
Found at i:215737 original size:2 final size:2
Alignment explanation
Indices: 215730--215758 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
215720 ATGTACAGAA
215730 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
215759 CACAATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:215848 original size:23 final size:23
Alignment explanation
Indices: 215822--215895 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
215812 TTAAGATTTA
215822 ATATAATGTTATTACTATAAATG
1 ATATAATGTTATTACTATAAATG
* * * * ** *
215845 ATATATTAGCTATT-TTACATTTA
1 ATATAAT-GTTATTACTATAAATG
215868 ATATAATGTTATTACTATAAATG
1 ATATAATGTTATTACTATAAATG
215891 ATATA
1 ATATA
215896 TTAGCTAAGT
Statistics
Matches: 35, Mismatches: 14, Indels: 4
0.66 0.26 0.08
Matches are distributed among these distances:
22 5 0.14
23 25 0.71
24 5 0.14
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (23 bp):
ATATAATGTTATTACTATAAATG
Found at i:218655 original size:11 final size:11
Alignment explanation
Indices: 218626--218661 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
218616 ATAAATTATA
*
218626 ATATATTAATT
1 ATATATTAAAT
218637 ATAT-TTAAAT
1 ATATATTAAAT
218647 ATATATTAAAT
1 ATATATTAAAT
218658 ATAT
1 ATAT
218662 CATATTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
ATATATTAAAT
Found at i:219171 original size:24 final size:24
Alignment explanation
Indices: 219121--219171 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
219111 TTATAAAAAC
* *
219121 ATAAAATACCTTAAACATAATATG
1 ATAAAATACCTTAAAAATAATAGG
*
219145 ATAAAATA-CTTAAAAATGATACGG
1 ATAAAATACCTTAAAAATAATA-GG
219169 ATA
1 ATA
219172 CATAAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (24 bp):
ATAAAATACCTTAAAAATAATAGG
Found at i:222234 original size:22 final size:22
Alignment explanation
Indices: 222204--222253 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
222194 AATAATATTT
*
222204 TTATTTAAAT-TTAATTATAAAA
1 TTATATAAATATTAA-TATAAAA
222226 TTATATAAATATTAATATAAAA
1 TTATATAAATATTAATATAAAA
*
222248 TAATAT
1 TTATAT
222254 TTAAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTATATAAATATTAATATAAAA
Found at i:222269 original size:24 final size:23
Alignment explanation
Indices: 222231--222275 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
222221 TAAAATTATA
* *
222231 TAAATATTAATATAAAATAATATT
1 TAAATAATAAAAT-AAATAATATT
222255 TAAATAATAAAATAAATAATA
1 TAAATAATAAAATAAATAATA
222276 AAATAAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAATAATAAAATAAATAATATT
Found at i:222270 original size:12 final size:12
Alignment explanation
Indices: 222255--222282 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
222245 AAATAATATT
222255 TAAATAATAAAA
1 TAAATAATAAAA
222267 TAAATAATAAAA
1 TAAATAATAAAA
222279 TAAA
1 TAAA
222283 CTTTAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
TAAATAATAAAA
Found at i:222880 original size:23 final size:23
Alignment explanation
Indices: 222819--222902 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 23
222809 AAATTTATGA
*
222819 TATATAATAA-AATATT--ATAT
1 TATATTATAATAATATTAAATAT
*
222839 TATTATTATTATAA-A--AAATAT
1 TA-TATTATAATAATATTAAATAT
222860 TATATTATAATAATATTAAATAT
1 TATATTATAATAATATTAAATAT
222883 TAAATATTAT-ATCAATATTA
1 T--ATATTATAAT-AATATTA
222903 TTTAATAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
20 12 0.24
21 14 0.27
22 2 0.04
23 7 0.14
24 2 0.04
25 14 0.27
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (23 bp):
TATATTATAATAATATTAAATAT
Found at i:222893 original size:25 final size:25
Alignment explanation
Indices: 222722--222902 Score: 70
Period size: 26 Copynumber: 7.1 Consensus size: 25
222712 AAAAATTAAA
* **
222722 TAAATATT-TATATTATAATTTTAT
1 TAAATATTAAATATTATAATAATAT
* * * *
222746 TAAAAAATAAATATTTTTATTAATAT
1 TAAATATTAAATA-TTATAATAATAT
222772 TATCAA-A-TAAATATTGAT-ATAATAT
1 TA--AATATTAAATATT-ATAATAATAT
* * *
222797 TTAATATTTAATAAATTTATGATATATAAT
1 TAAATA-TTAA-ATA-TTATAATA-AT-AT
* * * * *
222827 AAAATATTATATTATTATTATTATAA
1 TAAATATTA-AATATTATAATAATAT
*
222853 AAAATATT--ATATTATAATAATAT
1 TAAATATTAAATATTATAATAATAT
222876 TAAATATTAAATATTAT-ATCAATAT
1 TAAATATTAAATATTATAAT-AATAT
222901 TA
1 TA
222903 TTTAATAATA
Statistics
Matches: 117, Mismatches: 23, Indels: 33
0.68 0.13 0.19
Matches are distributed among these distances:
23 20 0.17
24 9 0.08
25 26 0.22
26 29 0.25
27 7 0.06
28 13 0.11
29 6 0.05
30 7 0.06
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (25 bp):
TAAATATTAAATATTATAATAATAT
Found at i:222909 original size:38 final size:34
Alignment explanation
Indices: 222862--222939 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 34
222852 AAAAATATTA
*
222862 TATTATAATAATATTAAATATTAAATATTATATCAATAT
1 TATT-TAATAATATT-AATATGAAATATT-TATC-AT-T
*
222901 TATTTAATAATATTAATGTGAAATATTTATCATT
1 TATTTAATAATATTAATATGAAATATTTATCATT
222935 TATTT
1 TATTT
222940 TGGTTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
34 6 0.16
35 2 0.05
36 4 0.11
37 11 0.30
38 10 0.27
39 4 0.11
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (34 bp):
TATTTAATAATATTAATATGAAATATTTATCATT
Found at i:228080 original size:2 final size:2
Alignment explanation
Indices: 228073--228109 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
228063 CGAAAATTAA
*
228073 AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
228110 CTTAATAAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:232787 original size:4 final size:4
Alignment explanation
Indices: 232778--232802 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
232768 ATTTCGATTG
232778 CTAT CTAT CTAT CTAT CTAT CTAT C
1 CTAT CTAT CTAT CTAT CTAT CTAT C
232803 AACCGCCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (4 bp):
CTAT
Found at i:233383 original size:21 final size:22
Alignment explanation
Indices: 233358--233415 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
233348 TAAAATTATA
*
233358 ATAATATATAATATAT-TAAAT
1 ATAATATATAATATATAAAAAT
233379 ATAAT-TATAATATATAAAAAT
1 ATAATATATAATATATAAAAAT
*
233400 ATATAAATATAATATA
1 ATA-ATATATAATATA
233416 ATTGTTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.31
21 12 0.38
22 1 0.03
23 9 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAATATATAATATATAAAAAT
Found at i:233385 original size:30 final size:29
Alignment explanation
Indices: 233342--233417 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 29
233332 TAAGTGATAA
* *
233342 ATAAATTAAAATTATAATA-ATATATAATAT
1 ATAAA-TATAATTATAATATATA-AAAATAT
233372 ATTAAATATAATTATAATATATAAAAATAT
1 A-TAAATATAATTATAATATATAAAAATAT
233402 ATAAATATAA-TATAAT
1 ATAAATATAATTATAAT
233418 TGTTTATAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
28 6 0.14
29 9 0.21
30 20 0.48
31 7 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
ATAAATATAATTATAATATATAAAAATAT
Found at i:233970 original size:27 final size:28
Alignment explanation
Indices: 233925--233977 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
233915 GGAAGACTCG
233925 ATAATTTGTATATAAATAT-ATTTTATT
1 ATAATTTGTATATAAATATAATTTTATT
* **
233952 ATAATTTTTATATTTATATAATTTTA
1 ATAATTTGTATATAAATATAATTTTA
233978 ATAAATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
ATAATTTGTATATAAATATAATTTTATT
Found at i:233973 original size:17 final size:19
Alignment explanation
Indices: 233941--233976 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
233931 TGTATATAAA
233941 TATATTTTATTATAATTTT
1 TATATTTTATTATAATTTT
233960 TATA-TTTA-TATAATTTT
1 TATATTTTATTATAATTTT
233977 AATAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATATTTTATTATAATTTT
Found at i:234064 original size:21 final size:23
Alignment explanation
Indices: 234005--234087 Score: 64
Period size: 26 Copynumber: 3.6 Consensus size: 23
233995 ATCACAAAAA
*
234005 ATTTTAAATATT-TATATATTTAT
1 ATTTTAATTATTATATATA-TTAT
** * *
234028 ATCATAATTAAATTATTTTTAATTAT
1 ATTTTAATT--ATTATATAT-ATTAT
234054 ATTTTAATTATTATATATATTAT
1 ATTTTAATTATTATATATATTAT
234077 A-TTTAA-TATTA
1 ATTTTAATTATTA
234088 AAAAAATATA
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
21 5 0.11
22 5 0.11
23 12 0.26
24 7 0.15
25 3 0.06
26 14 0.30
27 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTTAATTATTATATATATTAT
Found at i:234137 original size:32 final size:30
Alignment explanation
Indices: 234080--234151 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
234070 ATATTATATT
234080 TAATATTAAAAAAATATATAAAAATAAATTA
1 TAATATTAAAAAAATATATAAAAAT-AATTA
* * * *
234111 TAATATTAAAAAATTATTCTATAAATATTTA
1 TAATATTAAAAAAATA-TATAAAAATAATTA
234142 TAAATATTAA
1 T-AATATTAA
234152 TTAAATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 20 0.57
32 15 0.43
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (30 bp):
TAATATTAAAAAAATATATAAAAATAATTA
Found at i:234299 original size:28 final size:25
Alignment explanation
Indices: 234265--234325 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
234255 TTTTTACTTT
234265 AAATATTATCTTATTAATATTATTTTTA
1 AAATATTAT-TTATTAA-A-TATTTTTA
*
234293 AAATATTTATTTTTTAAATATTTTTA
1 AAATA-TTATTTATTAAATATTTTTA
*
234319 TAATATT
1 AAATATT
234326 TAAATAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 2 0.07
26 12 0.40
27 1 0.03
28 11 0.37
29 4 0.13
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
AAATATTATTTATTAAATATTTTTA
Found at i:234304 original size:15 final size:15
Alignment explanation
Indices: 234280--234315 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
234270 TTATCTTATT
234280 AATA-TTATTTTTAA
1 AATATTTATTTTTAA
*
234294 AATATTTATTTTTTA
1 AATATTTATTTTTAA
234309 AATATTT
1 AATATTT
234316 TTATAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
AATATTTATTTTTAA
Found at i:234346 original size:17 final size:17
Alignment explanation
Indices: 234324--234364 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
234314 TTTTATAATA
234324 TTTAAATAAATTTTTAT-
1 TTTAAATAAATTTTT-TG
*
234341 TTTAAAT-TATTTTTTG
1 TTTAAATAAATTTTTTG
234357 TTTAAATA
1 TTTAAATA
234365 TAAATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 1 0.05
16 13 0.62
17 7 0.33
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TTTAAATAAATTTTTTG
Found at i:234384 original size:53 final size:52
Alignment explanation
Indices: 234288--234389 Score: 125
Period size: 52 Copynumber: 1.9 Consensus size: 52
234278 TTAATATTAT
** * **
234288 TTTTAAAATATTTATTTTTTAAATATTTTTATAATATTTAAATAAATTTTTA
1 TTTTAAAATATTTATTTTTTAAATATAATTAAAATATAAAAATAAATTTTTA
*
234340 TTTTAAATTATTT-TTTGTTTAAATATAAATTAAAATATAAAAATAAATTT
1 TTTTAAAATATTTATTT-TTTAAATAT-AATTAAAATATAAAAATAAATTT
234390 CATAAATTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
51 3 0.07
52 21 0.50
53 18 0.43
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (52 bp):
TTTTAAAATATTTATTTTTTAAATATAATTAAAATATAAAAATAAATTTTTA
Found at i:235535 original size:56 final size:56
Alignment explanation
Indices: 235474--235586 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
235464 GTGTGCCATA
235474 GCCCTTATAATGTCTTGTTTCTTTTCTTTATCTACTTCGTGGCAGATCTGTGTTTG
1 GCCCTTATAATGTCTTGTTTCTTTTCTTTATCTACTTCGTGGCAGATCTGTGTTTG
235530 GCCCTTATAATGTCTTGTTTCTTTTCTTTATCTACTTCGTGGCAGATCTGTGTTTG
1 GCCCTTATAATGTCTTGTTTCTTTTCTTTATCTACTTCGTGGCAGATCTGTGTTTG
235586 G
1 G
235587 TGTTGGCATC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.50
Consensus pattern (56 bp):
GCCCTTATAATGTCTTGTTTCTTTTCTTTATCTACTTCGTGGCAGATCTGTGTTTG
Found at i:237799 original size:38 final size:38
Alignment explanation
Indices: 237737--237812 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
237727 ATCTATATGC
*
237737 TTCTTAATAGTTTCTTTTTATCTTGGGTAATTGCAAGA
1 TTCTTAATAGTTTCTTTTTATCTTGGATAATTGCAAGA
* *
237775 TTCTTAATAGTTTGTTTTCT-TCTTGGATCATTGCAAGA
1 TTCTTAATAGTTTCTTTT-TATCTTGGATAATTGCAAGA
237813 AGAATTTGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 33 0.97
39 1 0.03
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (38 bp):
TTCTTAATAGTTTCTTTTTATCTTGGATAATTGCAAGA
Found at i:241787 original size:3 final size:3
Alignment explanation
Indices: 241779--241817 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
241769 CCCCTTTAAT
241779 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
241818 AATGAGCTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TAC
Found at i:244052 original size:10 final size:10
Alignment explanation
Indices: 244037--244072 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
244027 ATAAATTATT
244037 TTTATATATA
1 TTTATATATA
244047 TTTATATATA
1 TTTATATATA
*
244057 TATATATATGA
1 TTTATATAT-A
244068 TTTAT
1 TTTAT
244073 TTAATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 18 0.78
11 5 0.22
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (10 bp):
TTTATATATA
Found at i:244054 original size:12 final size:12
Alignment explanation
Indices: 244024--244085 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
244014 TTAAGGAGTG
*
244024 TTTATAAAT-TA
1 TTTATATATATA
*
244035 TTTTTATATATA
1 TTTATATATATA
244047 TTTATATATATA
1 TTTATATATATA
* *
244059 TATATATGATTTA
1 TTTATAT-ATATA
*
244072 TTTA-ATATAAA
1 TTTATATATATA
244083 TTT
1 TTT
244086 TTTTTTGAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
11 13 0.32
12 21 0.51
13 7 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (12 bp):
TTTATATATATA
Found at i:245438 original size:28 final size:28
Alignment explanation
Indices: 245398--245451 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
245388 AAGAATTGAA
*
245398 TCACAGCCTACACCATTAACACTTCTAG
1 TCACAGCCTACACCATGAACACTTCTAG
245426 TCACAGCCTACACCATGAACACTTCT
1 TCACAGCCTACACCATGAACACTTCT
245452 CGTTGTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.31, C:0.37, G:0.07, T:0.24
Consensus pattern (28 bp):
TCACAGCCTACACCATGAACACTTCTAG
Found at i:249558 original size:2 final size:2
Alignment explanation
Indices: 249546--249586 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
249536 ACAACAAAGA
*
249546 AG AG TG AG AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
249587 GGGGGACTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.02
Consensus pattern (2 bp):
AG
Found at i:249937 original size:95 final size:95
Alignment explanation
Indices: 249780--249962 Score: 305
Period size: 95 Copynumber: 1.9 Consensus size: 95
249770 CTTTTGACCC
* *
249780 CATAAATACGAAAACAAAAATAATTAATTACGTTTTTTATAATTTATATTATATCAATTTTAATA
1 CATAAATAAGAAAACAAAAATAATTAATTACGTTTTTTATAATTTATATTATATAAATTTTAATA
*
249845 AATTTATATATTTATCTTATATTTTAACTT
66 AATTTATATATTTATATTATATTTTAACTT
* *
249875 CATACATAAGAAAACACAAAATAATTAATTA-TTTTTTTATAATTTATATTATATAAATTTTAAT
1 CATAAATAAGAAAACA-AAAATAATTAATTACGTTTTTTATAATTTATATTATATAAATTTTAAT
249939 AAATTTATATATTTATATTATATT
65 AAATTTATATATTTATATTATATT
249963 AATTTATATC
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
95 68 0.83
96 14 0.17
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.48
Consensus pattern (95 bp):
CATAAATAAGAAAACAAAAATAATTAATTACGTTTTTTATAATTTATATTATATAAATTTTAATA
AATTTATATATTTATATTATATTTTAACTT
Found at i:250769 original size:21 final size:21
Alignment explanation
Indices: 250704--250770 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
250694 ATATGTATTT
*
250704 ATAATTTAAATAATAATATT-
1 ATAATTTAAATAATAAAATTA
* *
250724 ATACATTT-AATAACAAAATAAA
1 ATA-ATTTAAATAATAAAAT-TA
*
250746 ATAATTTAAAAAATAAAATTA
1 ATAATTTAAATAATAAAATTA
250767 ATAA
1 ATAA
250771 AATGATATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
20 12 0.32
21 13 0.35
22 12 0.32
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAATTTAAATAATAAAATTA
Found at i:250771 original size:16 final size:16
Alignment explanation
Indices: 250730--250772 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
250720 TATTATACAT
250730 TTAATAACAAAATAAAA
1 TTAATAA-AAAATAAAA
250747 -TAATTTAAAAAATAAAA
1 TTAA--TAAAAAATAAAA
250764 TTAATAAAA
1 TTAATAAAA
250773 TGATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 8 0.35
17 9 0.39
18 6 0.26
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (16 bp):
TTAATAAAAAATAAAA
Found at i:250949 original size:18 final size:19
Alignment explanation
Indices: 250907--250942 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
250897 TAATTACTTT
250907 TATAAA-TATTAAATATAA
1 TATAAATTATTAAATATAA
*
250925 TATAAATTATTAATTATA
1 TATAAATTATTAAATATA
250943 TTTAAATACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TATAAATTATTAAATATAA
Found at i:251475 original size:23 final size:22
Alignment explanation
Indices: 251437--251480 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
251427 GAGATTGTTA
* *
251437 AATTTTTTTTTGTTTTTTTATT
1 AATTTTTTTTTATTTTCTTATT
251459 AATTTTTTTTATATTTTCTTAT
1 AATTTTTTTT-TATTTTCTTAT
251481 ATCAGTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (22 bp):
AATTTTTTTTTATTTTCTTATT
Found at i:251974 original size:29 final size:28
Alignment explanation
Indices: 251928--251983 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
251918 TTCTAAAAAT
* *
251928 AAAAAATATATAATTATTATATATTTAA
1 AAAAAATATAAAAATATTATATATTTAA
* *
251956 AAAAAATTATAAAAATATTTTATCTTTA
1 AAAAAA-TATAAAAATATTATATATTTA
251984 TAAACACTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (28 bp):
AAAAAATATAAAAATATTATATATTTAA
Found at i:252256 original size:27 final size:25
Alignment explanation
Indices: 252210--252259 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
252200 AAAAGTAATA
*
252210 AAATATAATTTTTATAATTAAATTT
1 AAATATAATTTATATAATTAAATTT
*
252235 AAATATATATTTATATTGATTAAAT
1 AAATATA-ATTTATA-TAATTAAAT
252260 AATCAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 6 0.29
27 8 0.38
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
AAATATAATTTATATAATTAAATTT
Found at i:253072 original size:2 final size:2
Alignment explanation
Indices: 253065--253105 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
253055 TTATGCGGGC
* * *
253065 AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
253106 AAAAAATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:253272 original size:28 final size:27
Alignment explanation
Indices: 253241--253329 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 27
253231 TAAAAAATTT
*
253241 ATTATAAATATTTTAATATATAATATAA
1 ATTATAAATATTTTAAAAT-TAATATAA
* *
253269 ATTATTAAT-TTATTAAAATTTATATAA
1 ATTATAAATATT-TTAAAATTAATATAA
253296 A--ATAAATATTTT-AAATTAATTATAA
1 ATTATAAATATTTTAAAATTAA-TATAA
*
253321 TATAATAAA
1 -ATTATAAA
253330 ATATAAATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
24 6 0.12
25 12 0.24
26 3 0.06
27 10 0.20
28 19 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATTATAAATATTTTAAAATTAATATAA
Found at i:255247 original size:15 final size:13
Alignment explanation
Indices: 255218--255256 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
255208 GATATGTATT
255218 TTTTAAAAAATTA
1 TTTTAAAAAATTA
*
255231 TTTTAAAAAATAA
1 TTTTAAAAAATTA
*
255244 TATTACAAAAATT
1 TTTTA-AAAAATT
255257 TTGATAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (13 bp):
TTTTAAAAAATTA
Found at i:255971 original size:16 final size:16
Alignment explanation
Indices: 255952--256004 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
255942 AAATATATAA
255952 ATAAATTAAATTTTAT
1 ATAAATTAAATTTTAT
*
255968 AT-AATAAAATTATTA-
1 ATAAATTAAATT-TTAT
*
255983 ATATATTAAATTTTAT
1 ATAAATTAAATTTTAT
255999 ATAAAT
1 ATAAAT
256005 ATATATTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 13 0.43
16 17 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAAATTAAATTTTAT
Found at i:255991 original size:31 final size:32
Alignment explanation
Indices: 255942--256002 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
255932 ATTATGAAAT
255942 AAATATATAAATAAATTAAATTTTATATAATA
1 AAATATATAAATAAATTAAATTTTATATAATA
* *
255974 AAAT-TATTAATATATTAAATTTTATATAA
1 AAATATATAAATAAATTAAATTTTATATAA
256003 ATATATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
AAATATATAAATAAATTAAATTTTATATAATA
Found at i:256007 original size:20 final size:19
Alignment explanation
Indices: 255945--256008 Score: 52
Period size: 20 Copynumber: 3.6 Consensus size: 19
255935 ATGAAATAAA
*
255945 TATATAAATAAATTAAATTT
1 TATAT-AATATATTAAATTT
255965 TATAT-A-ATA--AAA--T
1 TATATAATATATTAAATTT
255978 TAT-TAATATATTAAATTT
1 TATATAATATATTAAATTT
255996 TATATAAATATAT
1 TATAT-AATATAT
256009 ATTATTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 16
0.67 0.02 0.31
Matches are distributed among these distances:
12 1 0.03
13 5 0.14
14 3 0.09
15 3 0.09
16 3 0.09
17 2 0.06
18 5 0.14
19 1 0.03
20 12 0.34
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATATAATATATTAAATTT
Found at i:256041 original size:21 final size:20
Alignment explanation
Indices: 256017--256070 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
256007 ATATTATTTT
256017 AAAATATAATTATAATAT-ATA
1 AAAATATAA-TA-AATATAATA
256038 AAAATA-AATAAATATAATA
1 AAAATATAATAAATATAATA
*
256057 TAAATAT-ATAAATA
1 AAAATATAATAAATA
256071 AGTGTATCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 5 0.17
19 17 0.57
20 2 0.07
21 6 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATATAATAAATATAATA
Found at i:256067 original size:23 final size:23
Alignment explanation
Indices: 256022--256071 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
256012 ATTTTAAAAT
*
256022 ATAATTATAATATATAAAAATAA
1 ATAAATATAATATATAAAAATAA
*
256045 ATAAATATAATATA-AATATATAA
1 ATAAATATAATATATAA-AAATAA
256068 ATAA
1 ATAA
256072 GTGTATCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
ATAAATATAATATATAAAAATAA
Found at i:256698 original size:2 final size:2
Alignment explanation
Indices: 256691--256723 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
256681 ACACTCGAAT
256691 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
256724 GAAAATATTT
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:258137 original size:90 final size:91
Alignment explanation
Indices: 257984--258252 Score: 450
Period size: 90 Copynumber: 3.0 Consensus size: 91
257974 ATTTAATTGG
* *
257984 AGTCCATATTCCCATTTCCCAACATTGCTTTATAATTTATATTATCATCTAATTATTTTCATTAA
1 AGTCCATATACCCATTTCCCACCATTGCTTTATAATTTATATTATCATCTAATTATTTTCATTAA
* *
258049 TAAGTTCATATTTTCTAGTAAAAAA-
66 TGAGTTCATATTTTCTAGCAAAAAAT
* *
258074 AGTCCATATACACATTTCCCACCATTGCTTTATAATTTATATTATCATCTAACTATTTTCATTAA
1 AGTCCATATACCCATTTCCCACCATTGCTTTATAATTTATATTATCATCTAATTATTTTCATTAA
258139 TGAGTTCATATTTTCTAGCAAAAAAT
66 TGAGTTCATATTTTCTAGCAAAAAAT
*
258165 AGTCCATATACCCATTTCCCACCATTGCTTTATAATTTATATTATCATCTAATTATTTTCAATAA
1 AGTCCATATACCCATTTCCCACCATTGCTTTATAATTTATATTATCATCTAATTATTTTCATTAA
* *
258230 TGGGTTCATATTTTCTAACAAAA
66 TGAGTTCATATTTTCTAGCAAAA
258253 TGGTCAATAA
Statistics
Matches: 167, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
90 84 0.50
91 83 0.50
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.43
Consensus pattern (91 bp):
AGTCCATATACCCATTTCCCACCATTGCTTTATAATTTATATTATCATCTAATTATTTTCATTAA
TGAGTTCATATTTTCTAGCAAAAAAT
Found at i:258946 original size:18 final size:19
Alignment explanation
Indices: 258920--258957 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
258910 TAGTTGAATT
*
258920 ATTTGTTTAA-ATTTAAAA
1 ATTTATTTAATATTTAAAA
258938 ATTTATTTAATATTTAAAA
1 ATTTATTTAATATTTAAAA
258957 A
1 A
258958 ATTAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
ATTTATTTAATATTTAAAA
Found at i:258993 original size:26 final size:25
Alignment explanation
Indices: 258948--259018 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 25
258938 ATTTATTTAA
* *
258948 TATTTAAAAAATTAAATAAAAATAT-
1 TATTTAAAAAA-TAATTAAAAAAATC
258973 TATATTAAAAAATAAGTTAAAAAAATC
1 TAT-TTAAAAAATAA-TTAAAAAAATC
*
259000 TGTTTAAAAAATAAATTAA
1 TATTTAAAAAAT-AATTAA
259019 GTCAAGTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
25 6 0.15
26 29 0.74
27 4 0.10
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (25 bp):
TATTTAAAAAATAATTAAAAAAATC
Found at i:259018 original size:12 final size:13
Alignment explanation
Indices: 258951--258996 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
258941 TATTTAATAT
258951 TTAAAAAATTAAA
1 TTAAAAAATTAAA
*
258964 -TAAAAATATTATA
1 TTAAAAA-ATTAAA
*
258977 TTAAAAAA-TAAG
1 TTAAAAAATTAAA
258989 TTAAAAAA
1 TTAAAAAA
258997 ATCTGTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 16 0.57
13 6 0.21
14 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (13 bp):
TTAAAAAATTAAA
Found at i:259111 original size:25 final size:24
Alignment explanation
Indices: 259063--259111 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
259053 TTAATTTAAT
259063 ATATTTTAATTAGATAATATTATA
1 ATATTTTAATTAGATAATATTATA
*
259087 ATATTTTACATGTATAT-ATATTATA
1 ATATTTTA-AT-TAGATAATATTATA
259112 TAAAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 10 0.45
26 4 0.18
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (24 bp):
ATATTTTAATTAGATAATATTATA
Found at i:259186 original size:33 final size:32
Alignment explanation
Indices: 259106--259190 Score: 86
Period size: 33 Copynumber: 2.6 Consensus size: 32
259096 ATGTATATAT
* *
259106 ATTATATAAAAAATAAA-TATTATAATTTTAAT
1 ATTA-ATAAAAATTAAATTATTATAATTTTAAA
259138 ATTAA-AAAATTATTAAATTATT-TATATTTTAAA
1 ATTAATAAAA--ATTAAATTATTATA-ATTTTAAA
259171 ATTTAATAAAAATTAAATTA
1 A-TTAATAAAAATTAAATTA
259191 AAAAATTTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
30 4 0.09
31 1 0.02
32 11 0.24
33 21 0.47
34 4 0.09
35 4 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
ATTAATAAAAATTAAATTATTATAATTTTAAA
Found at i:259310 original size:25 final size:26
Alignment explanation
Indices: 259264--259354 Score: 100
Period size: 25 Copynumber: 3.6 Consensus size: 26
259254 CTGAATTATT
259264 TATTTATAAATTTAAATAAAATTTAA
1 TATTTATAAATTTAAATAAAATTTAA
* *
259290 TATTTAT-ATTTTAAATTAAATTTAA
1 TATTTATAAATTTAAATAAAATTTAA
*
259315 TATTTA-ATAATTATAAATAATA-TTAA
1 TATTTATA-AATT-TAAATAAAATTTAA
*
259341 TA-TTAAAAATTTAA
1 TATTTATAAATTTAA
259355 TTTAATTTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
24 3 0.05
25 29 0.52
26 17 0.30
27 7 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TATTTATAAATTTAAATAAAATTTAA
Found at i:259320 original size:32 final size:31
Alignment explanation
Indices: 259260--259329 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 31
259250 GAATCTGAAT
259260 TATTTAT-TTATAAATTTAAATAAAATTTAA
1 TATTTATATTATAAATTTAAATAAAATTTAA
* *
259290 TATTTATATTTTAAA-TTAAATTTAATATTTAA
1 TATTTATATTATAAATTTAAA--TAAAATTTAA
*
259322 TAATTATA
1 TATTTATA
259330 AATAATATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 12 0.35
31 6 0.18
32 16 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TATTTATATTATAAATTTAAATAAAATTTAA
Found at i:259354 original size:51 final size:50
Alignment explanation
Indices: 259264--259365 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 50
259254 CTGAATTATT
* * *
259264 TATTTATAAATTTAAATAAAATTTAATATTTATATTTTAAATTAAATTTAA
1 TATTTATAAATTTAAATAAAATTTAATATTAAAAATTT-AATTAAATTTAA
* *
259315 TATTTA-ATAATTATAAATAATA-TTAATATTAAAAATTTAATTTAATTTAA
1 TATTTATA-AATT-TAAATAAAATTTAATATTAAAAATTTAATTAAATTTAA
259365 T
1 T
259366 TTCACGTGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 13 0.30
51 23 0.52
52 8 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (50 bp):
TATTTATAAATTTAAATAAAATTTAATATTAAAAATTTAATTAAATTTAA
Found at i:259690 original size:17 final size:17
Alignment explanation
Indices: 259670--259713 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 17
259660 TATTAAAAAT
259670 ATTAATTTATATAATAG
1 ATTAATTTATATAATAG
259687 ATTAA---A-AT-ATAG
1 ATTAATTTATATAATAG
259699 ATTAATTTATATAAT
1 ATTAATTTATATAAT
259714 TTTATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 10
0.69 0.00 0.31
Matches are distributed among these distances:
12 9 0.41
13 2 0.09
14 1 0.05
15 1 0.05
16 2 0.09
17 7 0.32
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (17 bp):
ATTAATTTATATAATAG
Found at i:259749 original size:21 final size:21
Alignment explanation
Indices: 259709--259781 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 21
259699 ATTAATTTAT
*
259709 ATAATTTTATAATAATTTATAAA
1 ATAATTATAT-ATAA-TTATAAA
259732 ATAATTATATATAATTATAAA
1 ATAATTATATATAATTATAAA
*
259753 ATTAATTATTTA-AATTATAATA
1 A-TAATTATATATAATTATAA-A
*
259775 AAAATTA
1 ATAATTA
259782 AATTACATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
21 21 0.47
22 15 0.33
23 9 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAATTATATATAATTATAAA
Found at i:259792 original size:27 final size:27
Alignment explanation
Indices: 259733--259793 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
259723 ATTTATAAAA
*
259733 TAATTATA-TATAATTATAAAATTAAT
1 TAATTAAATTATAATTATAAAATTAAT
*
259759 TATTTAAATTATAA-TA-AAAATTAAAT
1 TAATTAAATTATAATTATAAAATT-AAT
259785 TACATTAAA
1 TA-ATTAAA
259794 AAATTTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 6 0.21
26 13 0.45
27 10 0.34
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (27 bp):
TAATTAAATTATAATTATAAAATTAAT
Found at i:259793 original size:17 final size:17
Alignment explanation
Indices: 259762--259795 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
259752 AATTAATTAT
*
259762 TTAAATTATAATAAAAA
1 TTAAATTACAATAAAAA
*
259779 TTAAATTACATTAAAAA
1 TTAAATTACAATAAAAA
259796 ATTTAATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAATTACAATAAAAA
Found at i:260814 original size:22 final size:23
Alignment explanation
Indices: 260771--260816 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
260761 TTTATTATTT
*
260771 ATTTTTAATAAAATATTAAATAA
1 ATTTATAATAAAATATTAAATAA
*
260794 ATTTATAATTAAAT-TTAAATAA
1 ATTTATAATAAAATATTAAATAA
260816 A
1 A
260817 AATATGTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTTATAATAAAATATTAAATAA
Found at i:267718 original size:2 final size:2
Alignment explanation
Indices: 267711--267735 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
267701 AGTCATATTA
267711 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
267736 AGAGAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:268762 original size:5 final size:6
Alignment explanation
Indices: 268747--268772 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
268737 GACATCGAGT
268747 TTTTTA TTTTTA TTTTTA TTTTTA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA TT
268773 GCTCTGTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:268914 original size:22 final size:22
Alignment explanation
Indices: 268889--268931 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
268879 GTTTTCCCGA
268889 GAAAGAGACAGAAAAG-AGAGAG
1 GAAAGAGACA-AAAAGAAGAGAG
*
268911 GAAAGAGAGAAAAAGAAGAGA
1 GAAAGAGACAAAAAGAAGAGA
268932 ATAGGAGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.63, C:0.02, G:0.35, T:0.00
Consensus pattern (22 bp):
GAAAGAGACAAAAAGAAGAGAG
Found at i:273156 original size:2 final size:2
Alignment explanation
Indices: 273149--273182 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
273139 TTATCCCAAT
273149 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
273183 GTCTAAGCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:273508 original size:22 final size:22
Alignment explanation
Indices: 273454--273519 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
273444 AAACATAAAT
* *
273454 ATTAAAATTTAAAAT-TATTAA
1 ATTAAAATTTTAAATCAATTAA
* *
273475 ATATTAATTTTTAAATCAATTAA
1 AT-TAAAATTTTAAATCAATTAA
273498 ATTAAAATTTTAAATCAATTAA
1 ATTAAAATTTTAAATCAATTAA
273520 CTTATATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 2 0.05
22 28 0.76
23 7 0.19
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTAAAATTTTAAATCAATTAA
Found at i:274063 original size:9 final size:9
Alignment explanation
Indices: 274038--274205 Score: 61
Period size: 9 Copynumber: 19.0 Consensus size: 9
274028 AAATAATTAA
274038 AATAT-TAT
1 AATATATAT
* *
274046 ATTAAATAT
1 AATATATAT
274055 AATATATAT
1 AATATATAT
274064 -A-ATATAT
1 AATATATAT
* *
274071 AATATTTTT
1 AATATATAT
*
274080 AAATTTATAT
1 -AATATATAT
*
274090 AATATAAAT
1 AATATATAT
*
274099 TAT-TAATAT
1 AATAT-ATAT
*
274108 AATTTTTATAT
1 AA--TATATAT
*
274119 AA-ATATAA
1 AATATATAT
*
274127 AATAT-TTT
1 AATATATAT
274135 AAT-TATGAT
1 AATATAT-AT
*
274144 AATATAAAT
1 AATATATAT
274153 AAATATAATAT
1 -AATAT-ATAT
*
274164 AA-ATTTAAT
1 AATATAT-AT
*
274173 AATTTATAT
1 AATATATAT
*
274182 TATAT-TAT
1 AATATATAT
274190 -ATATATAT
1 AATATATAT
274198 -ATATATAT
1 AATATATAT
274206 GTGTGTGTGT
Statistics
Matches: 117, Mismatches: 26, Indels: 34
0.66 0.15 0.19
Matches are distributed among these distances:
7 11 0.09
8 32 0.27
9 46 0.39
10 17 0.15
11 10 0.09
12 1 0.01
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (9 bp):
AATATATAT
Found at i:274162 original size:56 final size:57
Alignment explanation
Indices: 274057--274165 Score: 145
Period size: 56 Copynumber: 1.9 Consensus size: 57
274047 TTAAATATAA
* *
274057 TATATATAATATATAATATTTTTAAATTTATATAATATAAATTATTAATATAATTTT
1 TATATATAATATAAAATATTTTTAAATTTATATAATATAAATAATTAATATAATTTT
274114 TATATA-AATATAAAATA-TTTT-AA-TTATGATAATATAAATAAATATAATATAA
1 TATATATAATATAAAATATTTTTAAATTTAT-ATAATATAAAT-AAT-TAATATAA
274166 ATTTAATAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
53 4 0.09
54 13 0.28
55 6 0.13
56 18 0.38
57 6 0.13
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (57 bp):
TATATATAATATAAAATATTTTTAAATTTATATAATATAAATAATTAATATAATTTT
Found at i:282890 original size:26 final size:27
Alignment explanation
Indices: 282836--282908 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 27
282826 ATAAATGTAA
*
282836 TATATCTTAAATTATATTTTTAAATTTAT
1 TATAT-TTAAATTATA-TTTTAAAATTAT
*
282865 TATATTTATATTATA-TTTAAAATTAT
1 TATATTTAAATTATATTTTAAAATTAT
* *
282891 TAAATTTAATTTCATATT
1 TATATTTAAATT-ATATT
282909 CAAGGGAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
26 19 0.51
27 3 0.08
28 10 0.27
29 5 0.14
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.58
Consensus pattern (27 bp):
TATATTTAAATTATATTTTAAAATTAT
Found at i:282891 original size:15 final size:15
Alignment explanation
Indices: 282844--282899 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 15
282834 AATATATCTT
*
282844 AAATTA-TATTTTTA
1 AAATTATTATATTTA
*
282858 AATTTATTATATTT-
1 AAATTATTATATTTA
282872 --A-TATTATATTTA
1 AAATTATTATATTTA
*
282884 AAATTATTAAATTTA
1 AAATTATTATATTTA
282899 A
1 A
282900 TTTCATATTC
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
11 10 0.30
14 6 0.18
15 17 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AAATTATTATATTTA
Found at i:283193 original size:24 final size:24
Alignment explanation
Indices: 283166--283252 Score: 62
Period size: 21 Copynumber: 3.8 Consensus size: 24
283156 AATAAATTTA
283166 ATAATTTATATATTTAATTATATT
1 ATAATTTATATATTTAATTATATT
*
283190 ATAA--T-TATATTTAAATATATTT
1 ATAATTTATATATTTAATTATA-TT
*
283212 ATATCATATTAT-T-TTT-ATTATTTT
1 ATA--AT-TTATATATTTAATTATATT
*
283236 AT-ATATATATATTTAAT
1 ATAATTTATATATTTAAT
283253 ATTATAAGGT
Statistics
Matches: 49, Mismatches: 4, Indels: 21
0.66 0.05 0.28
Matches are distributed among these distances:
20 3 0.06
21 16 0.33
22 9 0.18
23 2 0.04
24 9 0.18
25 4 0.08
26 3 0.06
27 2 0.04
28 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (24 bp):
ATAATTTATATATTTAATTATATT
Found at i:283196 original size:11 final size:10
Alignment explanation
Indices: 283174--283212 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
283164 TAATAATTTA
283174 TATATTTAAT
1 TATATTTAAT
283184 TATATTATAAT
1 TATATT-TAAT
*
283195 TATATTTAAA
1 TATATTTAAT
283205 TATATTTA
1 TATATTTA
283213 TATCATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 17 0.63
11 10 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TATATTTAAT
Found at i:283240 original size:32 final size:31
Alignment explanation
Indices: 283170--283247 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 31
283160 AATTTAATAA
*
283170 TTTATATATTTA-ATTATATTATAATTATAT
1 TTTATATATTTATATCATATTATAATTATAT
* **
283200 TTAAATATATTTATATCATATTATTTTTATTAT
1 TT-TATATATTTATATCATATTATAATTA-TAT
*
283233 TTTATATATATATAT
1 TTTATATATTTATAT
283248 TTAATATTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 2 0.05
31 9 0.23
32 23 0.59
33 5 0.13
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (31 bp):
TTTATATATTTATATCATATTATAATTATAT
Found at i:283437 original size:2 final size:2
Alignment explanation
Indices: 283426--283454 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
283416 CATTCTTTTC
283426 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
283455 GTAATTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:284030 original size:12 final size:12
Alignment explanation
Indices: 284005--284041 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
283995 AGTCACCCCG
284005 TTCTCTG-C-CT
1 TTCTCTGTCTCT
*
284015 TTCTCTTTCTCT
1 TTCTCTGTCTCT
284027 TTCTCTGTCTCT
1 TTCTCTGTCTCT
284039 TTC
1 TTC
284042 CATCCCCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 6 0.26
11 1 0.04
12 16 0.70
ACGTcount: A:0.00, C:0.35, G:0.05, T:0.59
Consensus pattern (12 bp):
TTCTCTGTCTCT
Found at i:284403 original size:16 final size:15
Alignment explanation
Indices: 284382--284412 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
284372 ATTTAATATA
284382 TTATTTGTATTTTATT
1 TTATTTGT-TTTTATT
284398 TTATTTGTTTTTATT
1 TTATTTGTTTTTATT
284413 CTGTTTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.77
Consensus pattern (15 bp):
TTATTTGTTTTTATT
Found at i:284419 original size:15 final size:16
Alignment explanation
Indices: 284383--284421 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
284373 TTTAATATAT
*
284383 TATTTGTATTTTATTT
1 TATTTGTATTTTATTC
284399 TATTTGT-TTTTATTC
1 TATTTGTATTTTATTC
*
284414 TGTTTGTA
1 TATTTGTA
284422 ATTTCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.15, C:0.03, G:0.10, T:0.72
Consensus pattern (16 bp):
TATTTGTATTTTATTC
Found at i:289532 original size:31 final size:32
Alignment explanation
Indices: 289491--289554 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
289481 TTTGAAGAAA
289491 GGAAGACC-TGTGTGTTAGTCTGGGAACTGAT
1 GGAAGACCGTGTGTGTTAGTCTGGGAACTGAT
*
289522 GGAAGGCCTGTGTGTGTTAGTCTGGGAACTGAT
1 GGAAGACC-GTGTGTGTTAGTCTGGGAACTGAT
289555 TTTCGTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 7 0.23
33 23 0.77
ACGTcount: A:0.20, C:0.12, G:0.38, T:0.30
Consensus pattern (32 bp):
GGAAGACCGTGTGTGTTAGTCTGGGAACTGAT
Found at i:291819 original size:22 final size:24
Alignment explanation
Indices: 291794--291847 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
291784 TAATTATTCG
*
291794 AATTAAATTAAATTAA-ATTTTA-
1 AATTAAATTAAAATAATATTTTAT
**
291816 AATTATTTTAAAATAATATTTTAT
1 AATTAAATTAAAATAATATTTTAT
291840 AATATAAA
1 AAT-TAAA
291848 AATAAAAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 13 0.54
23 6 0.25
24 3 0.12
25 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AATTAAATTAAAATAATATTTTAT
Found at i:294369 original size:3 final size:3
Alignment explanation
Indices: 294361--294390 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
294351 TGAACAGTTA
294361 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
294391 TTTACTCAAG
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:295105 original size:2 final size:2
Alignment explanation
Indices: 295093--295144 Score: 70
Period size: 2 Copynumber: 26.0 Consensus size: 2
295083 AATAAAGATA
* *
295093 AT AT AT GT AT AT AT AT AT A- AT GT AT AT AT AT AT AT AT ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
295135 AT AT AT AT AT
1 AT AT AT AT AT
295145 GCAGTATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 41 0.93
3 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:295122 original size:17 final size:17
Alignment explanation
Indices: 295100--295144 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
295090 ATAATATATG
*
295100 TATATATATATA-AT-G
1 TATATATATATATATAC
295115 TATATATATATATATAC
1 TATATATATATATATAC
295132 TATATATATATAT
1 TATATATATATAT
295145 GCAGTATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 12 0.44
16 2 0.07
17 13 0.48
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
TATATATATATATATAC
Found at i:295122 original size:19 final size:19
Alignment explanation
Indices: 295090--295144 Score: 83
Period size: 19 Copynumber: 2.9 Consensus size: 19
295080 AAAAATAAAG
*
295090 ATAATATATGTATATATAT
1 ATAATATATATATATATAT
*
295109 ATAATGTATATATATATAT
1 ATAATATATATATATATAT
*
295128 ATACTATATATATATAT
1 ATAATATATATATATAT
295145 GCAGTATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (19 bp):
ATAATATATATATATATAT
Found at i:295144 original size:15 final size:14
Alignment explanation
Indices: 295093--295144 Score: 70
Period size: 15 Copynumber: 3.7 Consensus size: 14
295083 AATAAAGATA
*
295093 ATATATGTATATAT
1 ATATATATATATAT
*
295107 ATATA-ATGTATAT
1 ATATATATATATAT
295120 ATATATATATACTAT
1 ATATATATATA-TAT
295135 ATATATATAT
1 ATATATATAT
295145 GCAGTATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.33
14 9 0.27
15 13 0.39
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (14 bp):
ATATATATATATAT
Found at i:295915 original size:3 final size:3
Alignment explanation
Indices: 295907--295957 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
295897 AATAAAGCTG
295907 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
295955 TAT
1 TAT
295958 AATATACTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:296457 original size:18 final size:18
Alignment explanation
Indices: 296409--296457 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
296399 AGTAACGTAA
296409 ATTATTATTTTAAAAAATT
1 ATTATTATTTT-AAAAATT
* *
296428 A-AAATATTTTAAAAATT
1 ATTATTATTTTAAAAATT
*
296445 ATTATTATATTAA
1 ATTATTATTTTAA
296458 TATTTATATA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 8 0.33
18 15 0.62
19 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTATTATTTTAAAAATT
Found at i:297768 original size:23 final size:23
Alignment explanation
Indices: 297740--297790 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
297730 AAAAACTATT
297740 AGATTATAACTAATATTTAATTA
1 AGATTATAACTAATATTTAATTA
297763 AGATTATAACTAATATTTAATTA
1 AGATTATAACTAATATTTAATTA
*
297786 TGATT
1 AGATT
297791 TATTATGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (23 bp):
AGATTATAACTAATATTTAATTA
Found at i:303567 original size:2 final size:2
Alignment explanation
Indices: 303560--303589 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
303550 CTGTTCATAA
*
303560 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
303590 TTTACAAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:309547 original size:29 final size:29
Alignment explanation
Indices: 309505--309566 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
309495 TATTTCAACC
*
309505 AATTGAACTCTTGAATATTTGTTTTTATT
1 AATTAAACTCTTGAATATTTGTTTTTATT
309534 AATTAAACTCTTGAATATTTGTTTTTATT
1 AATTAAACTCTTGAATATTTGTTTTTATT
309563 AATT
1 AATT
309567 TAAGCCCTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.55
Consensus pattern (29 bp):
AATTAAACTCTTGAATATTTGTTTTTATT
Found at i:309597 original size:30 final size:30
Alignment explanation
Indices: 309563--309629 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
309553 TGTTTTTATT
*
309563 AATTTAAGCCCTTAAATACTTATTTTCATC
1 AATTTAAGCCCTTAAACACTTATTTTCATC
* *
309593 AATTTAAGCTCTTAAACATTTATTTTCATC
1 AATTTAAGCCCTTAAACACTTATTTTCATC
*
309623 AAATTAA
1 AATTTAA
309630 ACCAACGAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.37, C:0.16, G:0.03, T:0.43
Consensus pattern (30 bp):
AATTTAAGCCCTTAAACACTTATTTTCATC
Found at i:311328 original size:31 final size:29
Alignment explanation
Indices: 311293--311352 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
311283 TGATGATACC
**
311293 AAAGAATGATGTAAAATAAAAAAGTGAAATT
1 AAAGAATGATACAAAAT-AAAAA-TGAAATT
*
311324 AAAGAATGTTACAAAATAAAAATGAAATT
1 AAAGAATGATACAAAATAAAAATGAAATT
311353 CATATGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.27
30 5 0.19
31 14 0.54
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (29 bp):
AAAGAATGATACAAAATAAAAATGAAATT
Found at i:312055 original size:19 final size:18
Alignment explanation
Indices: 312022--312085 Score: 58
Period size: 19 Copynumber: 3.5 Consensus size: 18
312012 TTTATTTTTT
* *
312022 TATATATACAAATTAGAGA
1 TATATATATAAATTA-AAA
*
312041 TATATATATATATTAAAA
1 TATATATATAAATTAAAA
* *
312059 TCATATATATAAA-TATAC
1 T-ATATATATAAATTAAAA
312077 TATATATAT
1 TATATATAT
312086 GTATAATATA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
17 8 0.21
18 7 0.18
19 23 0.61
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (18 bp):
TATATATATAAATTAAAA
Found at i:312090 original size:15 final size:15
Alignment explanation
Indices: 312040--312096 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
312030 CAAATTAGAG
312040 ATATATATATATATTAA
1 ATATA-ATATATA-TAA
*
312057 A-ATCATATATATAA
1 ATATAATATATATAA
* *
312071 ATATACTATATATAT
1 ATATAATATATATAA
*
312086 GTATAATATAT
1 ATATAATATAT
312097 TGAATCAAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
14 4 0.12
15 26 0.79
16 2 0.06
17 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (15 bp):
ATATAATATATATAA
Found at i:312143 original size:24 final size:25
Alignment explanation
Indices: 312088--312144 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
312078 ATATATATGT
312088 ATAATATATTGAATCAAACTATTAAA
1 ATAAT-TATTGAATCAAACTATTAAA
* *
312114 AAAATTATTTAAT-AAACT-TTAAA
1 ATAATTATTGAATCAAACTATTAAA
312137 CATAATTA
1 -ATAATTA
312145 AAAATTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 5 0.19
24 11 0.41
25 7 0.26
26 4 0.15
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (25 bp):
ATAATTATTGAATCAAACTATTAAA
Found at i:312224 original size:3 final size:3
Alignment explanation
Indices: 312216--312250 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
312206 AACCAAAAAT
*
312216 ATA ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
312251 GTTGCACACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:321968 original size:23 final size:23
Alignment explanation
Indices: 321938--321993 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
321928 TTATTTGTTT
321938 AAAT-TTTAA-AAAATTTAAAAA
1 AAATATTTAATAAAATTTAAAAA
*
321959 ATAATATTTAATAAAATTTAAATA
1 A-AATATTTAATAAAATTTAAAAA
321983 AAATATTTAAT
1 AAATATTTAAT
321994 TTAAAAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 1 0.03
22 3 0.10
23 15 0.48
24 12 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATATTTAATAAAATTTAAAAA
Found at i:323012 original size:13 final size:13
Alignment explanation
Indices: 322989--323042 Score: 58
Period size: 13 Copynumber: 4.1 Consensus size: 13
322979 GTATTAAAAT
322989 TTATATAATATAAA
1 TTAT-TAATATAAA
*
323003 TTATTAATATGAA
1 TTATTAATATAAA
323016 TTATTAATTATTAAA
1 TTATTAA-TA-TAAA
323031 TT-TT-ATATAAA
1 TTATTAATATAAA
323042 T
1 T
323043 ATAAAATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
11 5 0.14
12 2 0.06
13 16 0.44
14 8 0.22
15 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (13 bp):
TTATTAATATAAA
Found at i:323014 original size:45 final size:45
Alignment explanation
Indices: 322963--323052 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 45
322953 AATTAATTAA
*
322963 AATATGATATAAAT-ATGTATTAAAATTTATAT-AATATAAATTATT
1 AATATGA-ATAAATAAT-TATTAAAATTTATATAAATATAAAATATT
* * *
323008 AATATGAATTATTAATTATTAAATTTTATATAAATATAAAATATT
1 AATATGAATAAATAATTATTAAAATTTATATAAATATAAAATATT
323053 TTAAAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
44 18 0.46
45 21 0.54
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (45 bp):
AATATGAATAAATAATTATTAAAATTTATATAAATATAAAATATT
Found at i:323764 original size:2 final size:2
Alignment explanation
Indices: 323757--323795 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
323747 GGAGTGAAGA
*
323757 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
323796 ATCTAAGGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:324074 original size:17 final size:17
Alignment explanation
Indices: 324043--324086 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
324033 TTTAAATCAG
324043 ATTAAATTT--AATTTA
1 ATTAAATTTAAAATTTA
324058 ATTAAATTTAAAATTTA
1 ATTAAATTTAAAATTTA
*
324075 AATAAATTTAAA
1 ATTAAATTTAAA
324087 TGTGTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 9 0.35
17 17 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTAAATTTAAAATTTA
Found at i:324322 original size:17 final size:17
Alignment explanation
Indices: 324300--324335 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
324290 CTCTACTTAT
324300 TTAAATATAAATAAATA
1 TTAAATATAAATAAATA
*
324317 TTAAATATAAATATATA
1 TTAAATATAAATAAATA
324334 TT
1 TT
324336 TATTTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAATATAAATAAATA
Found at i:329571 original size:2 final size:2
Alignment explanation
Indices: 329564--329595 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
329554 TGAACTTTTC
*
329564 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
329596 TTTTAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:332133 original size:40 final size:40
Alignment explanation
Indices: 332073--332158 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 40
332063 GATTCAACGT
332073 GAATATAACATTATAAAAAATATATGATTTAACAGATATG
1 GAATATAACATTATAAAAAATATATGATTTAACAGATATG
* * *
332113 GAATATAAGATTATAGAAAATATATGATTTAACTGATATG
1 GAATATAACATTATAAAAAATATATGATTTAACAGATATG
332153 GAATAT
1 GAATAT
332159 CATCATTTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.50, C:0.03, G:0.13, T:0.34
Consensus pattern (40 bp):
GAATATAACATTATAAAAAATATATGATTTAACAGATATG
Found at i:341312 original size:2 final size:2
Alignment explanation
Indices: 341305--341340 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
341295 TGGTTACATA
*
341305 AT AT AT AT AT AT AT AT AT GT 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
341341 GTTGCTATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:342241 original size:2 final size:2
Alignment explanation
Indices: 342234--342265 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
342224 CATTTAAATG
342234 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
342266 TTGACGCTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:348653 original size:25 final size:26
Alignment explanation
Indices: 348603--348653 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
348593 ACTTCATTAC
* *
348603 TTTTTAATTTATTATTTTTTAATATA
1 TTTTTAATTTATCATTTTGTAATATA
348629 TTTTTAA-TTATCA-TTTGTAACTATA
1 TTTTTAATTTATCATTTTGTAA-TATA
348654 AATTTTATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 6 0.27
25 9 0.41
26 7 0.32
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTTTAATTTATCATTTTGTAATATA
Found at i:348780 original size:2 final size:2
Alignment explanation
Indices: 348773--348800 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
348763 TAGTAAGACA
348773 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
348801 TACTAAGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:350116 original size:2 final size:2
Alignment explanation
Indices: 350109--350180 Score: 55
Period size: 2 Copynumber: 37.5 Consensus size: 2
350099 TGTCTACTTT
* * * *
350109 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TT TCA TG TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
350152 T- TA TA TA T- TA T- TA GTA TA T- TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA T
350181 TATTTTATTA
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
1 5 0.09
2 47 0.85
3 3 0.05
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (2 bp):
TA
Found at i:350438 original size:17 final size:19
Alignment explanation
Indices: 350389--350460 Score: 73
Period size: 17 Copynumber: 4.0 Consensus size: 19
350379 TTTATTTAAC
*
350389 ATAATATATATTA-ATTT-
1 ATAATTTATATTATATTTA
*
350406 ATACATATAT-TTATATTTA
1 ATA-ATTTATATTATATTTA
350425 A-AATTT-TATTATATTTA
1 ATAATTTATATTATATTTA
*
350442 ATAATTTATATTATTTTTA
1 ATAATTTATATTATATTTA
350461 TATTTTTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
16 1 0.02
17 19 0.40
18 16 0.34
19 11 0.23
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (19 bp):
ATAATTTATATTATATTTA
Found at i:352321 original size:2 final size:2
Alignment explanation
Indices: 352314--352351 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
352304 AGCAATGTAT
352314 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
352352 ATGGGTTTAA
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):
TA
Found at i:352610 original size:10 final size:10
Alignment explanation
Indices: 352597--352647 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
352587 TTAAAAAATT
352597 AATTAATAAA
1 AATTAATAAA
**
352607 AATTAAT-TC
1 AATTAATAAA
352616 AATTAATAAA
1 AATTAATAAA
*
352626 AATTTAAAAAA
1 AA-TTAATAAA
*
352637 AATTCATAAA
1 AATTAATAAA
352647 A
1 A
352648 CCATTTTAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
9 7 0.22
10 16 0.50
11 9 0.28
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (10 bp):
AATTAATAAA
Found at i:352621 original size:19 final size:18
Alignment explanation
Indices: 352593--352629 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
352583 TTTTTTAAAA
352593 AATTAATTAATAAAAATT
1 AATTAATTAATAAAAATT
352611 AATTCAATTAATAAAAATT
1 AATT-AATTAATAAAAATT
352630 TAAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAATTAATAAAAATT
Found at i:353103 original size:2 final size:2
Alignment explanation
Indices: 353096--353126 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
353086 ATGAACAAAT
353096 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 T
353127 TTGAAAACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:355935 original size:23 final size:22
Alignment explanation
Indices: 355888--355948 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
355878 TAATAAAATA
* *
355888 TAAATTTAAACTTAAACCTATT
1 TAAACTTAAACTAAAACCTATT
*
355910 TAAACTTAAACTAAAAGCTTATT
1 TAAACTTAAACTAAAA-CCTATT
355933 TAAACTTAAACTAAAA
1 TAAACTTAAACTAAAA
355949 ATCTAATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 14 0.40
23 21 0.60
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.34
Consensus pattern (22 bp):
TAAACTTAAACTAAAACCTATT
Found at i:357253 original size:32 final size:31
Alignment explanation
Indices: 357217--357305 Score: 128
Period size: 31 Copynumber: 2.9 Consensus size: 31
357207 TCAACATCTT
357217 AAAATTCAATAAAAATATAAAAATATAATCAC
1 AAAATTCAATAAAAA-ATAAAAATATAATCAC
*
357249 AAAATTCAATAAAAAATCAAAATATAATCAC
1 AAAATTCAATAAAAAATAAAAATATAATCAC
* *
357280 AAAATTCGAT--CAAATAAAAATATAAT
1 AAAATTCAATAAAAAATAAAAATATAAT
357306 AAGATTCAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
29 14 0.26
31 24 0.45
32 15 0.28
ACGTcount: A:0.64, C:0.10, G:0.01, T:0.25
Consensus pattern (31 bp):
AAAATTCAATAAAAAATAAAAATATAATCAC
Found at i:357713 original size:38 final size:38
Alignment explanation
Indices: 357640--357724 Score: 93
Period size: 38 Copynumber: 2.2 Consensus size: 38
357630 ATAAATAAGA
* *
357640 ATTATTTTGATTATTAATTTAAAAAAATTAATTAA-TAT
1 ATTATTTTAATTA-TAATTTAAAAAAAATAATTAATTAT
*
357678 ATTATTTTAATTA-AATTTAATAAAAAATATCTTAATTAT
1 ATTATTTTAATTATAATTTAA-AAAAAATA-ATTAATTAT
*
357717 ATTTTTTT
1 ATTATTTT
357725 TATAAATATT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
36 7 0.17
37 7 0.17
38 16 0.40
39 10 0.25
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (38 bp):
ATTATTTTAATTATAATTTAAAAAAAATAATTAATTAT
Found at i:357731 original size:38 final size:35
Alignment explanation
Indices: 357650--357731 Score: 83
Period size: 39 Copynumber: 2.2 Consensus size: 35
357640 ATTATTTTGA
* *
357650 TTATTAATTTAAAAAAATTAATTAATATATTATTT
1 TTATAAATTTAAAAAAAATAATTAATATATTATTT
* * *
357685 TAATTAAATTTAATAAAAAATATCTTAATTATATTTTTT
1 TTA-TAAATTTAA-AAAAAATA-ATTAA-TATATTATTT
357724 TTATAAAT
1 TTATAAAT
357732 ATTATCTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
35 2 0.05
36 8 0.22
37 7 0.19
38 9 0.24
39 11 0.30
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (35 bp):
TTATAAATTTAAAAAAAATAATTAATATATTATTT
Found at i:361578 original size:33 final size:33
Alignment explanation
Indices: 361536--361604 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
361526 CCTTGTTGCA
*
361536 TTTATCAACCCCAATTAATGGCTCAGCTAGCCT
1 TTTATCAACCCCAATTAATGGATCAGCTAGCCT
* *
361569 TTTATCAACCTCAATTAATGGATCAGCTTGCCT
1 TTTATCAACCCCAATTAATGGATCAGCTAGCCT
361602 TTT
1 TTT
361605 TATTTTTAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (33 bp):
TTTATCAACCCCAATTAATGGATCAGCTAGCCT
Found at i:365773 original size:186 final size:185
Alignment explanation
Indices: 365442--365780 Score: 421
Period size: 186 Copynumber: 1.8 Consensus size: 185
365432 CTGCCGAATT
* * * * *
365442 CTGCCGGATTTTAAAGACGCTGAATTCGAATCCAAACATGTTAGATACCACCTCTTAATAGTTTT
1 CTGCCAGATTTTAAAGACGCCGAATTCGAATCCAAACATGTTAGAAACCACCTCTTAAGAGTGTT
* * * *
365507 TACATACACATCCAAAATAAACCCCAGGTTTACATGCCTAAGCATTTCCATATACATTCTAATTC
66 AACATACACAACCAAAATAAACCCCAGGTTTACATGCCGAAGCAGTTCCATATACATTCTAATTC
365572 CTTGTAAGCAAAACACAAAAAAATTCATATCCGGAAATAGAGGGAAAAGGCTGCAG
131 CTTGTAA-CAAAACACAAAAAAATTCATATCCGGAAATAGAGGGAAAAGGCTGCAG
* * * * *
365628 CTGCCAGATTTTAAAGATGCCGTATTCGAATCTAGACATGTTAGAAACCATCTCTTAAGAGTGTT
1 CTGCCAGATTTTAAAGACGCCGAATTCGAATCCAAACATGTTAGAAACCACCTCTTAAGAGTGTT
* ** * * * *
365693 AAGATACACCAACTGAACTAAACCTC-GGATTTATATGCCGAAGCAGTTGCATATACATTCTAAT
66 AACATACA-CAACCAAAATAAACCCCAGG-TTTACATGCCGAAGCAGTTCCATATACATTCTAAT
365757 TCCTTTTGTAA-AAACACACAAAAA
129 TCC--TTGTAACAAA-ACACAAAAA
365781 TAAATAAATA
Statistics
Matches: 127, Mismatches: 21, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
186 63 0.50
187 49 0.39
188 9 0.07
189 6 0.05
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.27
Consensus pattern (185 bp):
CTGCCAGATTTTAAAGACGCCGAATTCGAATCCAAACATGTTAGAAACCACCTCTTAAGAGTGTT
AACATACACAACCAAAATAAACCCCAGGTTTACATGCCGAAGCAGTTCCATATACATTCTAATTC
CTTGTAACAAAACACAAAAAAATTCATATCCGGAAATAGAGGGAAAAGGCTGCAG
Found at i:367649 original size:2 final size:2
Alignment explanation
Indices: 367642--367666 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
367632 AAATCTGTAT
367642 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
367667 GAAAAGTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:372812 original size:18 final size:18
Alignment explanation
Indices: 372791--372831 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
372781 AAAGCCAGCC
*
372791 GAGAAGAAGCCGGCAGAG
1 GAGAAGAAGACGGCAGAG
* *
372809 GAGAAGAAGACGGTAGCG
1 GAGAAGAAGACGGCAGAG
372827 GAGAA
1 GAGAA
372832 AGCCCCGGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.12, G:0.44, T:0.02
Consensus pattern (18 bp):
GAGAAGAAGACGGCAGAG
Found at i:376081 original size:18 final size:16
Alignment explanation
Indices: 376054--376109 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 16
376044 ATTGACACTC
376054 AAATAAATATTTATTTT
1 AAATAAATATTTA-TTT
*
376071 AAATAAAATATTAATTT
1 AAAT-AAATATTTATTT
*
376088 AAATTAATGATTTATTT
1 AAATAAAT-ATTTATTT
376105 AAATA
1 AAATA
376110 TAAATTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 3 0.09
17 22 0.67
18 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
AAATAAATATTTATTT
Done.