Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015190.1 Kokia drynarioides strain JFW-HI SEQ_130234, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 593296
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 12 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:981 original size:13 final size:13
Alignment explanation
Indices: 963--990 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
953 TCCTTCTTCC
963 TTTATTTCTTTCT
1 TTTATTTCTTTCT
976 TTTATTTCTTTCT
1 TTTATTTCTTTCT
989 TT
1 TT
991 CCCGTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATTTCTTTCT
Found at i:2457 original size:12 final size:12
Alignment explanation
Indices: 2442--2475 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2432 GGGAAAAAGT
2442 AAAAATAAAAAC
1 AAAAATAAAAAC
*
2454 AAAAAGAAAAAC
1 AAAAATAAAAAC
2466 AAAGAATAAA
1 AAA-AATAAA
2476 GGTAAAGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.82, C:0.06, G:0.06, T:0.06
Consensus pattern (12 bp):
AAAAATAAAAAC
Found at i:9570 original size:4 final size:4
Alignment explanation
Indices: 9561--9591 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
9551 AAATTATGCA
*
9561 TATG TATG TATG TACG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
9592 TGCTAACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:24245 original size:21 final size:21
Alignment explanation
Indices: 24221--24289 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
24211 ATTTACCTTG
24221 ATTGACATCAATAACCTCTTT
1 ATTGACATCAATAACCTCTTT
* * ** *
24242 ATTGGCTACCAA-AATTTACCTTG
1 ATTGAC-ATCAATAACCT--CTTT
24265 ATTGACATCAATAACCTCTTT
1 ATTGACATCAATAACCTCTTT
24286 ATTG
1 ATTG
24290 GCTACCAATT
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
21 15 0.44
22 8 0.24
23 11 0.32
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.38
Consensus pattern (21 bp):
ATTGACATCAATAACCTCTTT
Found at i:24271 original size:44 final size:44
Alignment explanation
Indices: 24208--24297 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
24198 AATTAAAGAA
24208 AAAATTTACCTTGATTGACATCAATAACCTCTTTATTGGCTACC
1 AAAATTTACCTTGATTGACATCAATAACCTCTTTATTGGCTACC
24252 AAAATTTACCTTGATTGACATCAATAACCTCTTTATTGGCTACC
1 AAAATTTACCTTGATTGACATCAATAACCTCTTTATTGGCTACC
24296 AA
1 AA
24298 TTCAAATGTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (44 bp):
AAAATTTACCTTGATTGACATCAATAACCTCTTTATTGGCTACC
Found at i:24298 original size:22 final size:22
Alignment explanation
Indices: 24229--24298 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
24219 TGATTGACAT
24229 CAATAACCTCTTTATTGGCTAC
1 CAATAACCTCTTTATTGGCTAC
** * * *
24251 CAA-AATTTACCTTGATTGAC-AT
1 CAATAACCT--CTTTATTGGCTAC
24273 CAATAACCTCTTTATTGGCTAC
1 CAATAACCTCTTTATTGGCTAC
24295 CAAT
1 CAAT
24299 TCAAATGTCA
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
21 11 0.32
22 12 0.35
23 11 0.32
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (22 bp):
CAATAACCTCTTTATTGGCTAC
Found at i:26087 original size:13 final size:13
Alignment explanation
Indices: 26069--26093 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26059 TAAATCTCCT
26069 TATTTTATTTTTA
1 TATTTTATTTTTA
26082 TATTTTATTTTT
1 TATTTTATTTTT
26094 TTAACAAGTG
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TATTTTATTTTTA
Found at i:34997 original size:183 final size:184
Alignment explanation
Indices: 34680--35013 Score: 480
Period size: 183 Copynumber: 1.8 Consensus size: 184
34670 ATGGGGTCTC
* * *
34680 TGTATAGGAAATGAGTTTTGTAGGGGTGTGAGGAAGAGTTTGGTAAAATATTGGGTTAATGGGGT
1 TGTAAAGGAAATGAGTTTTGTAGGGGTGTGAGGAAGAGTTTGGTAAAATATCGGGTTAATGGGAT
* * * ** *
34745 AAAATGTATTTCAATTGTTTAAACCTAGGGAGCATAGAAAACTGCTCTTGTTTTTGGGCTCGAGT
66 AAAATGGATTTCAATTGGTTAAACCTAGGGAACATAGAAAACTGAGCATGTTTTTGGGCTCGAGT
34810 TTAGTGCTTGTCTATTGGGTGCGAGGAAGAGTTTGGTAATTTCTGTGGCATCTT
131 TTAGTGCTTGTCTATTGGGTGCGAGGAAGAGTTTGGTAATTTCTGTGGCATCTT
*
34864 TGTAAAGG-AATGAGTTTTGTA-GGGTCGTGAGGAAGAGTTTGGTAAAATGTCGGGTTAATGGGA
1 TGTAAAGGAAATGAGTTTTGTAGGGGT-GTGAGGAAGAGTTTGGTAAAATATCGGGTTAATGGGA
* *
34927 T-AAA-GGGTTTCCATGTGGTTAAACCTAGGGAACATAGAAAACTGAGCATGTTTTTGGGGCTC-
65 TAAAATGGATTTCAAT-TGGTTAAACCTAGGGAACATAGAAAACTGAGCATGTTTTT-GGGCTCG
*
34989 AGGTTTAGTGTTTGTCTATTGGGTG
128 A-GTTTAGTGCTTGTCTATTGGGTG
35014 TTTTGACCTC
Statistics
Matches: 133, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
181 7 0.05
182 43 0.32
183 76 0.57
184 7 0.05
ACGTcount: A:0.25, C:0.08, G:0.32, T:0.35
Consensus pattern (184 bp):
TGTAAAGGAAATGAGTTTTGTAGGGGTGTGAGGAAGAGTTTGGTAAAATATCGGGTTAATGGGAT
AAAATGGATTTCAATTGGTTAAACCTAGGGAACATAGAAAACTGAGCATGTTTTTGGGCTCGAGT
TTAGTGCTTGTCTATTGGGTGCGAGGAAGAGTTTGGTAATTTCTGTGGCATCTT
Found at i:36976 original size:33 final size:33
Alignment explanation
Indices: 36934--37012 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
36924 ATTAACCCAT
36934 TTCAGTGGCATGCGTCCAATAAACATAGTGTGA
1 TTCAGTGGCATGCGTCCAATAAACATAGTGTGA
36967 TTCAGTGGCATGCGTCCAATAAACATAGTGTGA
1 TTCAGTGGCATGCGTCCAATAAACATAGTGTGA
37000 TTCAGTGGCATGC
1 TTCAGTGGCATGC
37013 TTATTCATGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (33 bp):
TTCAGTGGCATGCGTCCAATAAACATAGTGTGA
Found at i:39355 original size:6 final size:6
Alignment explanation
Indices: 39344--39379 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
39334 TTTATCATGT
39344 TGGTAG TGGTAG TGGTAG TGGTAG TGGTAG TGGTAG
1 TGGTAG TGGTAG TGGTAG TGGTAG TGGTAG TGGTAG
39380 AGGTTGATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (6 bp):
TGGTAG
Found at i:42234 original size:2 final size:2
Alignment explanation
Indices: 42229--42261 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
42219 ATATTAAAAA
42229 AT AT 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 AT AT A
42262 AATTAATAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42326 original size:3 final size:3
Alignment explanation
Indices: 42318--42351 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
42308 CACATCAAAC
42318 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
42352 ACACTTCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:43915 original size:15 final size:16
Alignment explanation
Indices: 43882--43913 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
43872 CACATTAAAA
*
43882 TACATTAAAAAATATT
1 TACATTAAAAAACATT
43898 TACATTAAAAAACATT
1 TACATTAAAAAACATT
43914 ACCGTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.34
Consensus pattern (16 bp):
TACATTAAAAAACATT
Found at i:52193 original size:65 final size:65
Alignment explanation
Indices: 52118--52247 Score: 206
Period size: 65 Copynumber: 2.0 Consensus size: 65
52108 ACAACGATAG
* * *
52118 CTGTTTAATTCTATGTACATAGGGGCGCTTTTCTAGCAGTGAATTTTAGTATGGGAGACGTTTGA
1 CTGTTTAATTCTATGTACATAGGGACACTTTTCTAGCACTGAATTTTAGTATGGGAGACGTTTGA
* * *
52183 CTGTTTAATTCTATGTACATAGGGATACTTTTCTAGCACTGAATTTTTGTATGGGAGATGTTTGA
1 CTGTTTAATTCTATGTACATAGGGACACTTTTCTAGCACTGAATTTTAGTATGGGAGACGTTTGA
52248 TATAATGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.41
Consensus pattern (65 bp):
CTGTTTAATTCTATGTACATAGGGACACTTTTCTAGCACTGAATTTTAGTATGGGAGACGTTTGA
Found at i:59736 original size:40 final size:40
Alignment explanation
Indices: 59670--59752 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
59660 TTTCAGCATG
* *
59670 AGTTTGACTTGGAACCGGAAGTTGTATACTAAATAAATAA
1 AGTTTGACTTGGAACCAGAAGATGTATACTAAATAAATAA
* * *
59710 AGTTTGACTT-GACACCAGAGGATGTATACTGAATAAATGA
1 AGTTTGACTTGGA-ACCAGAAGATGTATACTAAATAAATAA
59750 AGT
1 AGT
59753 GCTGTGGGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 2 0.05
40 35 0.95
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.29
Consensus pattern (40 bp):
AGTTTGACTTGGAACCAGAAGATGTATACTAAATAAATAA
Found at i:69650 original size:27 final size:27
Alignment explanation
Indices: 69596--69655 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
69586 ATCATAAAAT
*
69596 AATTTAAAATAATTTTCAAAAATTCAA
1 AATTTAAAATAATTTTCAAAAATCCAA
*
69623 ATTTTAAAAT-ATTTAT-AAAAACTCCAA
1 AATTTAAAATAATTT-TCAAAAA-TCCAA
69650 AATTTA
1 AATTTA
69656 TATTTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 9 0.32
27 19 0.68
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.38
Consensus pattern (27 bp):
AATTTAAAATAATTTTCAAAAATCCAA
Found at i:69685 original size:34 final size:34
Alignment explanation
Indices: 69590--69685 Score: 86
Period size: 34 Copynumber: 2.7 Consensus size: 34
69580 CAAATAATCA
*
69590 TAAAATAATTTAAAATAATTTTCAAAAATTCAAATTT
1 TAAAATAA-TTATAA-AATTTTC-AAAATTCAAATTT
* ** * * *
69627 TAAAATATTTATAAAAACTCCAAAATTTATATTTT
1 TAAAATAATTATAAAATTTTCAAAATTCA-AATTT
69662 TAAAA-AATTATAAAATTTTCAAAA
1 TAAAATAATTATAAAATTTTCAAAA
69686 AAAATCTAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
34 22 0.47
35 13 0.28
36 5 0.11
37 7 0.15
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (34 bp):
TAAAATAATTATAAAATTTTCAAAATTCAAATTT
Found at i:71275 original size:16 final size:17
Alignment explanation
Indices: 71239--71281 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
71229 CTGTGGGTTT
71239 AAAATCACTTGATCCTA
1 AAAATCACTTGATCCTA
71256 AAAATCACTTGATCCTA
1 AAAATCACTTGATCCTA
71273 AAAATCACT
1 AAAATCACT
71282 CTGTGGTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.44, C:0.23, G:0.05, T:0.28
Consensus pattern (17 bp):
AAAATCACTTGATCCTA
Found at i:105429 original size:4 final size:4
Alignment explanation
Indices: 105415--105459 Score: 51
Period size: 4 Copynumber: 11.5 Consensus size: 4
105405 TAATTGACTT
105415 TTAA TTAAA TTAA TT-- TTAA -TAA TTAA TTAA TTAA TTAAA TTAA TT
1 TTAA TT-AA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT-AA TTAA TT
105460 CGATTCGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
2 2 0.06
3 3 0.08
4 23 0.64
5 8 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
TTAA
Found at i:105429 original size:9 final size:8
Alignment explanation
Indices: 105415--105459 Score: 51
Period size: 9 Copynumber: 5.8 Consensus size: 8
105405 TAATTGACTT
105415 TTAATTAAA
1 TTAATT-AA
105424 TTAATT--
1 TTAATTAA
105430 TTAA-TAA
1 TTAATTAA
105437 TTAATTAA
1 TTAATTAA
105445 TTAATTAAA
1 TTAATT-AA
105454 TTAATT
1 TTAATT
105460 CGATTCGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 1 0.03
6 4 0.12
7 4 0.12
8 9 0.28
9 14 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
TTAATTAA
Found at i:106124 original size:84 final size:82
Alignment explanation
Indices: 106018--106181 Score: 258
Period size: 84 Copynumber: 2.0 Consensus size: 82
106008 AAATTATTGA
* *
106018 TTTTACTTTTGTCCCCAGCAGAGACAAAGAAAATATACAGAGGAAAAAGAGAAAAAAACTTCGAA
1 TTTTACTTTTGTCCCCACCAGAGACAAAGAAAATATACAGAGGAAAAA-A-AAAAAAACTTAGAA
106083 CGAGCTTCGTGGGTGGAGC
64 CGAGCTTCGTGGGTGGAGC
* *
106102 TTTTACTTTTG-CCCCTACCAGAGAGAAAGAAAATATACAGAGGAAAAAAAAGAAAACTTAGAAC
1 TTTTACTTTTGTCCCC-ACCAGAGACAAAGAAAATATACAGAGGAAAAAAAAAAAAACTTAGAAC
106166 GAGCTTCGTGGGTGGA
65 GAGCTTCGTGGGTGGA
106182 ACTTGTTTTC
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
82 29 0.39
83 5 0.07
84 41 0.55
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (82 bp):
TTTTACTTTTGTCCCCACCAGAGACAAAGAAAATATACAGAGGAAAAAAAAAAAAACTTAGAACG
AGCTTCGTGGGTGGAGC
Found at i:125208 original size:17 final size:17
Alignment explanation
Indices: 125186--125218 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
125176 CAAATTTTAA
125186 TATAAA-AATATTAAAAT
1 TATAAAGAA-ATTAAAAT
125203 TATAAAGAAATTAAAA
1 TATAAAGAAATTAAAA
125219 AAAAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
TATAAAGAAATTAAAAT
Found at i:126057 original size:22 final size:22
Alignment explanation
Indices: 126019--126076 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
126009 TTGTACTTTT
126019 TATA-ATTAT-ATTAAAAAATAA
1 TATATATTATAATT-AAAAATAA
126040 TATATATTATAATTAAAAATAA
1 TATATATTATAATTAAAAATAA
126062 -A-AGTATT-TAATTAAA
1 TATA-TATTATAATTAAA
126077 GTTATTCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
20 9 0.26
21 9 0.26
22 13 0.38
23 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TATATATTATAATTAAAAATAA
Found at i:129828 original size:3 final size:3
Alignment explanation
Indices: 129820--129919 Score: 83
Period size: 3 Copynumber: 36.0 Consensus size: 3
129810 CCTAGGAAAT
* * *
129820 AGA AGA AGA AG- AGA AAA AG- AGA AGTA AG- AGA AGA A-A TGG AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA
*
129862 AGA AGA AGA A-A AGA AGA AG- AGA AGA AGA A-A A-A AAA AGA AGA AG-
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
129905 AGG AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA
129920 GAAAATGGAA
Statistics
Matches: 80, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
2 17 0.21
3 60 0.75
4 3 0.04
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:129850 original size:9 final size:8
Alignment explanation
Indices: 129823--129922 Score: 89
Period size: 8 Copynumber: 12.5 Consensus size: 8
129813 AGGAAATAGA
129823 AGAAGAAG
1 AGAAGAAG
*
129831 AGAAAAAG
1 AGAAGAAG
129839 AGAAGTAAG
1 AGAAG-AAG
129848 AGAAGAA-
1 AGAAGAAG
*
129855 ATGGAGAAG
1 A-GAAGAAG
*
129864 AAGAAGAAA
1 -AGAAGAAG
129873 AGAAGAAG
1 AGAAGAAG
129881 AGAAGAAG
1 AGAAGAAG
* * *
129889 AAAAAAAA
1 AGAAGAAG
129897 AGAAGAAG
1 AGAAGAAG
*
129905 AGGAG-A-
1 AGAAGAAG
129911 AGAAGAAG
1 AGAAGAAG
129919 AGAA
1 AGAA
129923 AATGGAAGGA
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
6 4 0.06
7 3 0.04
8 51 0.71
9 13 0.18
10 1 0.01
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (8 bp):
AGAAGAAG
Found at i:132501 original size:206 final size:206
Alignment explanation
Indices: 132145--132554 Score: 712
Period size: 206 Copynumber: 2.0 Consensus size: 206
132135 TTGAACAACC
* * * *
132145 TCTCTCCTACCTTGTATTTCTACCGATACAACCAAGGGTTCTACTAGAACAAGTATGCAGAATTC
1 TCTCTCCTACCCTGTACTTCTACCGATACAACCAAGGGTTCTACCAAAACAAGTATGCAGAATTC
*
132210 AAATATTCACACAAGTTCTCATGCTCAGCCAACAATTCTCATTTCAAAACATAAGGTACAAAAGA
66 AAATATTCACACAAGTTCTCATGCACAGCCAACAATTCTCATTTCAAAACATAAGGTACAAAAGA
* *
132275 CAATTATTCTTAAAGTTCAAAACACATTTTATAATACATTTCATTTCATTGTAAGCATACTTTCA
131 CAATTATTCTTAAAGTTCAAAACACATTTGATAATACATTTCATTTCATTGTAAGCATAATTTCA
132340 CCCATAGTACA
196 CCCATAGTACA
*
132351 TCTCTCCTACCCTGTACTTCTATCGATACAACCAAGGGTTCTACCAAAACAAGTATGCAGAATTC
1 TCTCTCCTACCCTGTACTTCTACCGATACAACCAAGGGTTCTACCAAAACAAGTATGCAGAATTC
* *
132416 AAATATTCACACAAGTTTTCATGCACAGCCAACAATTCTGATTTCAAAACATAAGGTACAAAAGA
66 AAATATTCACACAAGTTCTCATGCACAGCCAACAATTCTCATTTCAAAACATAAGGTACAAAAGA
* *
132481 CAATTATTCTTAACGTTCAAAACACATTTGATAATACATTTCATTTCATTGTAAGCCTAATTTCA
131 CAATTATTCTTAAAGTTCAAAACACATTTGATAATACATTTCATTTCATTGTAAGCATAATTTCA
132546 CCCATAGTA
196 CCCATAGTA
132555 ACATGAAAAA
Statistics
Matches: 192, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
206 192 1.00
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.31
Consensus pattern (206 bp):
TCTCTCCTACCCTGTACTTCTACCGATACAACCAAGGGTTCTACCAAAACAAGTATGCAGAATTC
AAATATTCACACAAGTTCTCATGCACAGCCAACAATTCTCATTTCAAAACATAAGGTACAAAAGA
CAATTATTCTTAAAGTTCAAAACACATTTGATAATACATTTCATTTCATTGTAAGCATAATTTCA
CCCATAGTACA
Found at i:134103 original size:48 final size:48
Alignment explanation
Indices: 134030--134126 Score: 140
Period size: 48 Copynumber: 2.0 Consensus size: 48
134020 TAATTATTCT
134030 TCATTAAGTGTTTGGTTTGTTAAATGCATATTTATTTAATAATATGCA
1 TCATTAAGTGTTTGGTTTGTTAAATGCATATTTATTTAATAATATGCA
* * * * * *
134078 TCATTAAGTGTTTTGTTTGTTAAATGTATCTTTGTTTAGTAATCTGCA
1 TCATTAAGTGTTTGGTTTGTTAAATGCATATTTATTTAATAATATGCA
134126 T
1 T
134127 TATTGAATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51
Consensus pattern (48 bp):
TCATTAAGTGTTTGGTTTGTTAAATGCATATTTATTTAATAATATGCA
Found at i:134142 original size:48 final size:48
Alignment explanation
Indices: 134030--134143 Score: 115
Period size: 48 Copynumber: 2.4 Consensus size: 48
134020 TAATTATTCT
*
134030 TCATTAAGTGT-TTGGTTTGTTAAATGCATATTTATTTAATAATATGCA
1 TCATTAAGTATGTT-GTTTGTTAAATGCATATTTATTTAATAATATGCA
* * * * * * *
134078 TCATTAAGTGTTTTGTTTGTTAAATGTATCTTTGTTTAGTAATCTGCA
1 TCATTAAGTATGTTGTTTGTTAAATGCATATTTATTTAATAATATGCA
*
134126 TTATTGAA-TATGTTGTTT
1 TCATT-AAGTATGTTGTTT
134144 TTATGAGTGT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
48 52 0.93
49 4 0.07
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.52
Consensus pattern (48 bp):
TCATTAAGTATGTTGTTTGTTAAATGCATATTTATTTAATAATATGCA
Found at i:134510 original size:79 final size:78
Alignment explanation
Indices: 134405--134560 Score: 206
Period size: 79 Copynumber: 2.0 Consensus size: 78
134395 AGCCAATAAA
* * * * *
134405 CACACTAAGGTTACATAAGTCTTCATTAAGGA-AGAATACCATGCCTTTTCAGCTACATCATATC
1 CACACTAAGGATACATAAGTCTTCATTAACGACA-AATACCATGCCTTTTCAACTAAATCAGATC
*
134469 CTAATGAAGAGACT
65 CTAATAAAGAGACT
* **
134483 CACATTAAGGATACAATAAGTCTTCATTAACGACAAATGTCATGCCTTTTCAACTAAATCAGATC
1 CACACTAAGGATAC-ATAAGTCTTCATTAACGACAAATACCATGCCTTTTCAACTAAATCAGATC
134548 CTAATAAAGAGAC
65 CTAATAAAGAGAC
134561 ATGACTCATT
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
78 12 0.18
79 54 0.81
80 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (78 bp):
CACACTAAGGATACATAAGTCTTCATTAACGACAAATACCATGCCTTTTCAACTAAATCAGATCC
TAATAAAGAGACT
Found at i:142055 original size:21 final size:21
Alignment explanation
Indices: 142031--142080 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
142021 CCAATAAACA
142031 CATTAAGGTTACATAAGTCTT
1 CATTAAGGTTACATAAGTCTT
142052 CATTAAGGTTACATAAGTCTT
1 CATTAAGGTTACATAAGTCTT
142073 CATTAAGG
1 CATTAAGG
142081 AGAAATATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (21 bp):
CATTAAGGTTACATAAGTCTT
Found at i:142199 original size:79 final size:78
Alignment explanation
Indices: 142052--142206 Score: 247
Period size: 79 Copynumber: 2.0 Consensus size: 78
142042 CATAAGTCTT
* *
142052 CATTAAGGTTACATAAGTCTTCATTAAGGAGAAATATCATGCCTTTTCAGCTACATCAGATCCCA
1 CATTAAGGATACATAAGTCTTCATTAAGGAGAAATATCATGCCTTTTCAACTACATCAGATCCCA
142117 ATGAAGAGACACA
66 ATGAAGAGACACA
* * * *
142130 CATTAAGGATACAATAAGTCTTCATTAAGGAGAAATGTCATGTCTTTTGAACTACATCAGATCCT
1 CATTAAGGATAC-ATAAGTCTTCATTAAGGAGAAATATCATGCCTTTTCAACTACATCAGATCCC
142195 AATGAAGAGACA
65 AATGAAGAGACA
142207 TGACTCATTG
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
78 11 0.16
79 59 0.84
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (78 bp):
CATTAAGGATACATAAGTCTTCATTAAGGAGAAATATCATGCCTTTTCAACTACATCAGATCCCA
ATGAAGAGACACA
Found at i:152203 original size:4 final size:4
Alignment explanation
Indices: 152196--152226 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
152186 TATATATATA
152196 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
152227 ATGTATAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:155477 original size:51 final size:51
Alignment explanation
Indices: 155415--155518 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 51
155405 GTTATTTTTT
* *
155415 TAAAATGAAACTCAGATGACTGTTTTGTCAACTATCCCAAAATTGAGTAAC
1 TAAAATAAAACTCAGATAACTGTTTTGTCAACTATCCCAAAATTGAGTAAC
*
155466 TAAAATAAAACTCAGATAACTGTTTTGTCAACTATCCCAAAATTGAGTTAC
1 TAAAATAAAACTCAGATAACTGTTTTGTCAACTATCCCAAAATTGAGTAAC
155517 TA
1 TA
155519 TTGGTATAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (51 bp):
TAAAATAAAACTCAGATAACTGTTTTGTCAACTATCCCAAAATTGAGTAAC
Found at i:156048 original size:29 final size:30
Alignment explanation
Indices: 155983--156048 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
155973 TTCTCAATTC
*
155983 TCAAATAATAGAATTCAAAATCCATCAAAAT
1 TCAAA-AATAGAATTCAAAATCCATAAAAAT
*
156014 TAAAAAATA-AATATCAAAATCC-TAAAAAT
1 TCAAAAATAGAAT-TCAAAATCCATAAAAAT
156043 TCAAAA
1 TCAAAA
156049 TAATCAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 14 0.45
30 13 0.42
31 4 0.13
ACGTcount: A:0.61, C:0.14, G:0.02, T:0.24
Consensus pattern (30 bp):
TCAAAAATAGAATTCAAAATCCATAAAAAT
Found at i:160293 original size:31 final size:31
Alignment explanation
Indices: 160258--160337 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 31
160248 ATAGCCAGTG
*
160258 ACTTAAATTAAACCTTTTAAATAGTTCAATA
1 ACTTAAATTAAACATTTTAAATAGTTCAATA
* * * * *
160289 ACTTAAATAAAAAATTTTGAATAGTTTAATG
1 ACTTAAATTAAACATTTTAAATAGTTCAATA
*
160320 A-TTAAATTATAACTTTTT
1 ACTTAAATTA-AACATTTT
160338 TAATTAAATT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 7 0.18
31 32 0.82
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (31 bp):
ACTTAAATTAAACATTTTAAATAGTTCAATA
Found at i:164818 original size:14 final size:15
Alignment explanation
Indices: 164792--164821 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
164782 TATAATATAA
164792 TGATAAGATGAACAG
1 TGATAAGATGAACAG
164807 TGATAA-ATGAACAG
1 TGATAAGATGAACAG
164821 T
1 T
164822 AAAACACAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.47, C:0.07, G:0.23, T:0.23
Consensus pattern (15 bp):
TGATAAGATGAACAG
Found at i:174244 original size:70 final size:70
Alignment explanation
Indices: 174131--174270 Score: 262
Period size: 70 Copynumber: 2.0 Consensus size: 70
174121 AGAAAGTTTG
174131 GTTGAGCCTCTCTTAAAATTGAAGAACCATTAAGGTTAGTTCTAATGATTTTCATGTTTTTCTTA
1 GTTGAGCCTCTCTTAAAATTGAAGAACCATTAAGGTTAGTTCTAATGATTTTCATGTTTTTCTTA
174196 AGTTA
66 AGTTA
* *
174201 GTTGAGCCTCTCTTAAATTTGAAGAACTATTAAGGTTAGTTCTAATGATTTTCATGTTTTTCTTA
1 GTTGAGCCTCTCTTAAAATTGAAGAACCATTAAGGTTAGTTCTAATGATTTTCATGTTTTTCTTA
174266 AGTTA
66 AGTTA
174271 TTCTAGCTCG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (70 bp):
GTTGAGCCTCTCTTAAAATTGAAGAACCATTAAGGTTAGTTCTAATGATTTTCATGTTTTTCTTA
AGTTA
Found at i:183406 original size:15 final size:15
Alignment explanation
Indices: 183386--183415 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
183376 ATGTACAGAC
183386 CATCTTCAACCTCAT
1 CATCTTCAACCTCAT
*
183401 CATCTTCTACCTCAT
1 CATCTTCAACCTCAT
183416 ATCATACCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.40, G:0.00, T:0.37
Consensus pattern (15 bp):
CATCTTCAACCTCAT
Found at i:188115 original size:12 final size:12
Alignment explanation
Indices: 188098--188122 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
188088 GAGTAGAAGT
188098 TATGATAAAGGG
1 TATGATAAAGGG
188110 TATGATAAAGGG
1 TATGATAAAGGG
188122 T
1 T
188123 CTTGGTCTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (12 bp):
TATGATAAAGGG
Found at i:188200 original size:29 final size:29
Alignment explanation
Indices: 188147--188202 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
188137 AGATACAGAC
* *
188147 TAAAGAAGAATATTTACTATTTGCTTTAA
1 TAAAGAAGAATATTCACTATGTGCTTTAA
* *
188176 TAAAGAAGAATCTTCACTGTGTGCTTT
1 TAAAGAAGAATATTCACTATGTGCTTT
188203 TACTTTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (29 bp):
TAAAGAAGAATATTCACTATGTGCTTTAA
Found at i:189653 original size:29 final size:29
Alignment explanation
Indices: 189620--189678 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
189610 ATAAATTTAA
* * *
189620 TAAATAAATTTAAAGTTTCAATTTTTCTT
1 TAAATAAATTCAAAGTTTAAAATTTTCTT
*
189649 TAAATAAATTCAAGGTTTAAAATTTTCTT
1 TAAATAAATTCAAAGTTTAAAATTTTCTT
189678 T
1 T
189679 TCTTTCAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (29 bp):
TAAATAAATTCAAAGTTTAAAATTTTCTT
Found at i:191984 original size:29 final size:29
Alignment explanation
Indices: 191927--191987 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 29
191917 TGCAGTGGTG
* *
191927 AAATTAAAATTT-T-CTTTTAGGAAATTA
1 AAATTAAAATTTATATTTTTACGAAATTA
*
191954 AAATTAAAATTTATATTTTTACGATAATAA
1 AAATTAAAATTTATATTTTTACGA-AATTA
191984 AAAT
1 AAAT
191988 ATAATTTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 12 0.43
28 1 0.04
29 7 0.25
30 8 0.29
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (29 bp):
AAATTAAAATTTATATTTTTACGAAATTA
Found at i:192018 original size:15 final size:17
Alignment explanation
Indices: 191988--192026 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
191978 TAATAAAAAT
191988 ATAATTTCATTATTTTA
1 ATAATTTCATTATTTTA
*
192005 ATAATTT-A-TATTTTT
1 ATAATTTCATTATTTTA
192020 ATAATTT
1 ATAATTT
192027 TTAATTAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 1 0.05
17 7 0.33
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
ATAATTTCATTATTTTA
Found at i:193735 original size:12 final size:12
Alignment explanation
Indices: 193718--193743 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
193708 AAATTAAAAT
193718 GATGAAGAAGAA
1 GATGAAGAAGAA
193730 GATGAAGAAGAA
1 GATGAAGAAGAA
193742 GA
1 GA
193744 AAAAATTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.35, T:0.08
Consensus pattern (12 bp):
GATGAAGAAGAA
Found at i:194087 original size:19 final size:22
Alignment explanation
Indices: 194063--194105 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
194053 AAAATAATTT
194063 AAAATAA-TTT-AT-ATTTTAA
1 AAAATAATTTTAATAATTTTAA
194082 AAAATAATTTTAATAATTTTAA
1 AAAATAATTTTAATAATTTTAA
194104 AA
1 AA
194106 TCATTTGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 3 0.14
21 2 0.10
22 9 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAATAATTTTAATAATTTTAA
Found at i:194093 original size:13 final size:13
Alignment explanation
Indices: 194046--194094 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 13
194036 ATAATTTTAT
194046 ATTTTAAAAAATA
1 ATTTTAAAAAATA
194059 A-TTTAAAATAATTTA
1 ATTTTAAAA-AA--TA
194074 TATTTTAAAAAATA
1 -ATTTTAAAAAATA
194088 ATTTTAA
1 ATTTTAA
194095 TAATTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
12 7 0.23
13 10 0.32
14 2 0.06
15 2 0.06
16 3 0.10
17 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTTTAAAAAATA
Found at i:194102 original size:29 final size:29
Alignment explanation
Indices: 194029--194102 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
194019 TATTCATAAC
194029 AATTTTAATAATTTTATATTTTAAAAAAT
1 AATTTTAATAATTTTATATTTTAAAAAAT
*
194058 AATTTAAAATAA-TTTATATTTTAAAAAAT
1 AATTT-TAATAATTTTATATTTTAAAAAAT
194087 AATTTTAATAATTTTA
1 AATTTTAATAATTTTA
194103 AAATCATTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 5 0.12
29 31 0.76
30 5 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
AATTTTAATAATTTTATATTTTAAAAAAT
Found at i:198741 original size:49 final size:49
Alignment explanation
Indices: 198607--198741 Score: 182
Period size: 50 Copynumber: 2.7 Consensus size: 49
198597 GCTCTTGTAT
* * **
198607 TTTGAAGTAGAAAAAATATCTTCATGCAATGAAACGTCCATGCTAATGTA
1 TTTGAAGTAGAAAAAACATCTT-ATGCATTGAAACGTCCATGCTAACATA
*
198657 TTTGAAGTAGAAAAAACATCCCTATGCATTGAAACGTCCATGCTAACATA
1 TTTGAAGTAGAAAAAACAT-CTTATGCATTGAAACGTCCATGCTAACATA
*
198707 TTTGAAGT-GAGAAAACATCATTATGCATTGAAACG
1 TTTGAAGTAGAAAAAACATC-TTATGCATTGAAACG
198742 ACCAACCATG
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
48 1 0.01
49 23 0.30
50 50 0.66
51 2 0.03
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (49 bp):
TTTGAAGTAGAAAAAACATCTTATGCATTGAAACGTCCATGCTAACATA
Found at i:198826 original size:22 final size:24
Alignment explanation
Indices: 198798--198841 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
198788 TATAAATACC
198798 TTGTAA-CATCC-AAACTTGAAAA
1 TTGTAACCATCCAAAACTTGAAAA
198820 TTGTAACCATCCAAAACTTGAA
1 TTGTAACCATCCAAAACTTGAA
198842 GACTTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 5 0.25
24 9 0.45
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.27
Consensus pattern (24 bp):
TTGTAACCATCCAAAACTTGAAAA
Found at i:200499 original size:38 final size:38
Alignment explanation
Indices: 200445--200534 Score: 128
Period size: 38 Copynumber: 2.4 Consensus size: 38
200435 CTTCGTCATG
200445 ACATAGCATGCCTATGTTGA-AACAAACCCTATGTCGCA
1 ACATAGCATGCCTATGTT-ACAACAAACCCTATGTCGCA
* * **
200483 ACATAGCATGCTTATGTTACAACAAACCTTATGTCGTG
1 ACATAGCATGCCTATGTTACAACAAACCCTATGTCGCA
200521 ACATAGCATGCCTA
1 ACATAGCATGCCTA
200535 CATCGTGACA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 1 0.02
38 45 0.98
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (38 bp):
ACATAGCATGCCTATGTTACAACAAACCCTATGTCGCA
Found at i:202934 original size:10 final size:10
Alignment explanation
Indices: 202906--202936 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
202896 GATTTTGTAA
*
202906 AGTAATTTCT
1 AGTAATTTTT
202916 AGTAATTTTT
1 AGTAATTTTT
202926 AGTAATTTTT
1 AGTAATTTTT
202936 A
1 A
202937 TGTTAAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.55
Consensus pattern (10 bp):
AGTAATTTTT
Found at i:203310 original size:29 final size:29
Alignment explanation
Indices: 203277--203334 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
203267 GGTAAGTTCG
203277 TAATAACTATTTATAACTGTCTTTCTTAT
1 TAATAACTATTTATAACTGTCTTTCTTAT
203306 TAATAACTATTTATAACTGTCTTTCTTAT
1 TAATAACTATTTATAACTGTCTTTCTTAT
203335 GTTTATTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.52
Consensus pattern (29 bp):
TAATAACTATTTATAACTGTCTTTCTTAT
Found at i:210506 original size:21 final size:21
Alignment explanation
Indices: 210468--210507 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
210458 TACCCTGTAA
* *
210468 TTCTACCGATACATGTATGAG
1 TTCTACCGAAACAAGTATGAG
*
210489 TTCTACTGAAACAAGTATG
1 TTCTACCGAAACAAGTATG
210508 TAAAATCTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (21 bp):
TTCTACCGAAACAAGTATGAG
Found at i:215953 original size:14 final size:14
Alignment explanation
Indices: 215934--215963 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
215924 GTGCGTTTCG
215934 GAATTCTAGACTCT
1 GAATTCTAGACTCT
215948 GAATTCTAGACTCT
1 GAATTCTAGACTCT
215962 GA
1 GA
215964 CGGCCCTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (14 bp):
GAATTCTAGACTCT
Found at i:242942 original size:7 final size:7
Alignment explanation
Indices: 242930--242955 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
242920 TCACAATCAC
242930 AGAGAAG
1 AGAGAAG
242937 AGAGAAG
1 AGAGAAG
242944 AGAGAAG
1 AGAGAAG
242951 AGAGA
1 AGAGA
242956 GTGGCTATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (7 bp):
AGAGAAG
Found at i:249062 original size:29 final size:29
Alignment explanation
Indices: 249020--249078 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
249010 ATAGAATATC
249020 CTTAATCTTTTTGGTAACCATTACTTCTT
1 CTTAATCTTTTTGGTAACCATTACTTCTT
249049 CTTAATCTTTTTGGTAACCATTACTTCTT
1 CTTAATCTTTTTGGTAACCATTACTTCTT
249078 C
1 C
249079 CTTCATGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.20, C:0.22, G:0.07, T:0.51
Consensus pattern (29 bp):
CTTAATCTTTTTGGTAACCATTACTTCTT
Found at i:250514 original size:11 final size:10
Alignment explanation
Indices: 250500--250529 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
250490 TTAAAAATTC
250500 AAAAAAATAA
1 AAAAAAATAA
250510 AAAAAAATAA
1 AAAAAAATAA
250520 AAAAAAATAA
1 AAAAAAATAA
250530 TAATTTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:251278 original size:21 final size:19
Alignment explanation
Indices: 251244--251293 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
251234 TTAGTTATGA
*
251244 ATATTTTCATAACTTTGCAT
1 ATATTTTTATAACTTT-CAT
* *
251264 GTATTTTTATAAACTTTTAT
1 ATATTTTTAT-AACTTTCAT
251284 ATATTTTTAT
1 ATATTTTTAT
251294 TAAAAATGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.30, C:0.08, G:0.04, T:0.58
Consensus pattern (19 bp):
ATATTTTTATAACTTTCAT
Found at i:252566 original size:59 final size:59
Alignment explanation
Indices: 252494--252605 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 59
252484 AATTGAATCT
* * * * *
252494 AAAAAAAGCTTAGGTGTCC-AATTAGGAAAAAATGTTAAGTTCAGGTATCAAATTGGGTA
1 AAAAAAAGCTTAGGT-ACCAAATTAAGAAAAAATATTAAGTTCAGATACCAAATTGGGTA
* *
252553 AAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTATTAAGTTCAGATACCAAAT
1 AAAAAAAGCTTAGGTACCAAATTAAGAAAAAATATTAAGTTCAGATACCAAAT
252606 GCTATATTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
58 2 0.04
59 43 0.96
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (59 bp):
AAAAAAAGCTTAGGTACCAAATTAAGAAAAAATATTAAGTTCAGATACCAAATTGGGTA
Found at i:255612 original size:28 final size:29
Alignment explanation
Indices: 255581--255664 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
255571 AGTTTTGGAT
*
255581 CCCTTAAAAGTTGGAAATTTTTTTTA-AG
1 CCCTTAAAAGTTGGAAATTTTTTTTAGAC
* **
255609 CCCTTAAAAGTTGCAAAAAATTTTTTAGAC
1 CCCTTAAAAGTTG-GAAATTTTTTTTAGAC
* *
255639 CCCTTAAAAGCTAGAAATTTTTTTTA
1 CCCTTAAAAGTTGGAAATTTTTTTTA
255665 TGTCTCTTAA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
28 13 0.29
29 20 0.44
30 12 0.27
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (29 bp):
CCCTTAAAAGTTGGAAATTTTTTTTAGAC
Found at i:255643 original size:30 final size:28
Alignment explanation
Indices: 255581--255648 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
255571 AGTTTTGGAT
* ** *
255581 CCCTTAAAAGTTGGAAATTTTTTTTAAG
1 CCCTTAAAAGTTGAAAAAATTTTTTAAC
255609 CCCTTAAAAGTTGCAAAAAATTTTTTAGAC
1 CCCTTAAAAGTTG-AAAAAATTTTTTA-AC
255639 CCCTTAAAAG
1 CCCTTAAAAG
255649 CTAGAAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 13 0.38
29 10 0.29
30 11 0.32
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (28 bp):
CCCTTAAAAGTTGAAAAAATTTTTTAAC
Found at i:257286 original size:9 final size:8
Alignment explanation
Indices: 257265--257309 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
257255 TTAAATAAAA
257265 AAATATAT
1 AAATATAT
257273 AAATATATT
1 AAATATA-T
257282 AAATAT-T
1 AAATATAT
257289 AAA-ATA-
1 AAATATAT
257295 AAATAATAT
1 AAAT-ATAT
257304 AAATAT
1 AAATAT
257310 TTTTAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
6 5 0.16
7 4 0.12
8 12 0.38
9 11 0.34
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAATATAT
Found at i:258572 original size:74 final size:74
Alignment explanation
Indices: 258451--258601 Score: 302
Period size: 74 Copynumber: 2.0 Consensus size: 74
258441 ATTCGAATTC
258451 ATACTATTTCATGCCAAATAAATCACCTAACCAATTCCAAATCAAAACCAACTTAAACATGAGCT
1 ATACTATTTCATGCCAAATAAATCACCTAACCAATTCCAAATCAAAACCAACTTAAACATGAGCT
258516 CAACCCTCA
66 CAACCCTCA
258525 ATACTATTTCATGCCAAATAAATCACCTAACCAATTCCAAATCAAAACCAACTTAAACATGAGCT
1 ATACTATTTCATGCCAAATAAATCACCTAACCAATTCCAAATCAAAACCAACTTAAACATGAGCT
258590 CAACCCTCA
66 CAACCCTCA
258599 ATA
1 ATA
258602 TCAATTTCCA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 77 1.00
ACGTcount: A:0.44, C:0.29, G:0.04, T:0.23
Consensus pattern (74 bp):
ATACTATTTCATGCCAAATAAATCACCTAACCAATTCCAAATCAAAACCAACTTAAACATGAGCT
CAACCCTCA
Found at i:259710 original size:17 final size:17
Alignment explanation
Indices: 259688--259721 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
259678 TACTCTTAAC
259688 TAAATCTAGCCAATTTG
1 TAAATCTAGCCAATTTG
259705 TAAATCTAGCCAATTTG
1 TAAATCTAGCCAATTTG
259722 CACACAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (17 bp):
TAAATCTAGCCAATTTG
Found at i:280386 original size:16 final size:17
Alignment explanation
Indices: 280367--280399 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
280357 TGTAACTCCT
280367 TAAACTACGAA-CTTAC
1 TAAACTACGAAGCTTAC
*
280383 TAAACTATGAAGCTTAC
1 TAAACTACGAAGCTTAC
280400 CACAGGTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27
Consensus pattern (17 bp):
TAAACTACGAAGCTTAC
Found at i:284810 original size:15 final size:15
Alignment explanation
Indices: 284792--284840 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
284782 CAACACTAGT
284792 GCTCGCATCTTCCAA
1 GCTCGCATCTTCCAA
* *** *
284807 GCTCGTAAGGTCCAT
1 GCTCGCATCTTCCAA
284822 GCTCGCATCTTCCAA
1 GCTCGCATCTTCCAA
284837 GCTC
1 GCTC
284841 ACAAGGTCCA
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.18, C:0.37, G:0.18, T:0.27
Consensus pattern (15 bp):
GCTCGCATCTTCCAA
Found at i:284811 original size:30 final size:30
Alignment explanation
Indices: 284777--284859 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
284767 CAGCATGATT
*
284777 GCTCGCAA-CACTAGTGCTCGCATCTTCCAA
1 GCTCGCAAGCACCA-TGCTCGCATCTTCCAA
* **
284807 GCTCGTAAGGTCCATGCTCGCATCTTCCAA
1 GCTCGCAAGCACCATGCTCGCATCTTCCAA
* **
284837 GCTCACAAGGTCCATGCTCGCAT
1 GCTCGCAAGCACCATGCTCGCAT
284860 TATTCGTGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 44 0.96
31 2 0.04
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (30 bp):
GCTCGCAAGCACCATGCTCGCATCTTCCAA
Found at i:287836 original size:3 final size:3
Alignment explanation
Indices: 287828--287865 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
287818 AATACAACAT
287828 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
287866 TTTAATGACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:290304 original size:12 final size:12
Alignment explanation
Indices: 290283--290311 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
290273 GAGATGAAGG
290283 TTTT-GGAGTGT
1 TTTTGGGAGTGT
290294 TTTTGGGAGTGT
1 TTTTGGGAGTGT
290306 TTTTGG
1 TTTTGG
290312 ATGCACGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.07, C:0.00, G:0.38, T:0.55
Consensus pattern (12 bp):
TTTTGGGAGTGT
Found at i:303036 original size:50 final size:47
Alignment explanation
Indices: 302972--303099 Score: 123
Period size: 47 Copynumber: 2.7 Consensus size: 47
302962 GCACCATTTT
* *
302972 TGGACATGCTACCACTAAGTTGCAGATAAACTGCCACTGATAACACTTGG
1 TGGACAAGCCACCACT-A-TTGCAGATAAACTGCCACTGA-AACACTTGG
* * * * *
303022 TGGACAAGCCACCACT-TATGCAGATATATTACCATTGAAACACTTTG
1 TGGACAAGCCACCACTAT-TGCAGATAAACTGCCACTGAAACACTTGG
* * *
303069 TGAACAAGCCACAACTTTTGCAGATAAACTG
1 TGGACAAGCCACCACTATTGCAGATAAACTG
303100 TCACATACTT
Statistics
Matches: 64, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
47 33 0.52
48 17 0.27
50 14 0.22
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.25
Consensus pattern (47 bp):
TGGACAAGCCACCACTATTGCAGATAAACTGCCACTGAAACACTTGG
Found at i:317441 original size:18 final size:19
Alignment explanation
Indices: 317409--317445 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
317399 AACCCACAAA
*
317409 ATATTTTTTTATTTTTCTC
1 ATATTTTTCTATTTTTCTC
317428 ATATTTTTCT-TTTTTCTC
1 ATATTTTTCTATTTTTCTC
317446 GACTTTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (19 bp):
ATATTTTTCTATTTTTCTC
Found at i:320967 original size:25 final size:25
Alignment explanation
Indices: 320890--321051 Score: 153
Period size: 25 Copynumber: 6.4 Consensus size: 25
320880 GTACATAGTA
* * *
320890 CCTGCTAAACATTCACCAGCTCGAAT
1 CCTGCTAAA-AATCACCGGCTCGAAG
* *
320916 CCTGCTAAATAATCATCGGCTCAAAG
1 CCTGCTAAA-AATCACCGGCTCGAAG
* *
320942 CCTGCGAAAAATCACCGACTCGAAG
1 CCTGCTAAAAATCACCGGCTCGAAG
* *
320967 CTTGCAAAAAATCACCGGCTCGAAG
1 CCTGCTAAAAATCACCGGCTCGAAG
* * *
320992 CCTGCTAATTAGTCACCGGCTCAAAG
1 CCTGCTAA-AAATCACCGGCTCGAAG
* * *
321018 CTTGCTAAAAATCACCAGCTTGAAG
1 CCTGCTAAAAATCACCGGCTCGAAG
*
321043 CTTGCTAAA
1 CCTGCTAAA
321052 GTCATTGACT
Statistics
Matches: 111, Mismatches: 24, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
25 62 0.56
26 49 0.44
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (25 bp):
CCTGCTAAAAATCACCGGCTCGAAG
Found at i:321028 original size:51 final size:50
Alignment explanation
Indices: 320918--321051 Score: 151
Period size: 51 Copynumber: 2.6 Consensus size: 50
320908 GCTCGAATCC
* * * *
320918 TGCTAAATAATCATCGGCTCAAAGCCTGCGAAAAATCACCGACTCGAAGCT
1 TGCTAAA-AATCACCGGCTCGAAGCCTGCTAAAAATCACCGACTCAAAGCT
* * * *
320969 TGCAAAAAATCACCGGCTCGAAGCCTGCTAATTAGTCACCGGCTCAAAGCT
1 TGCTAAAAATCACCGGCTCGAAGCCTGCTAA-AAATCACCGACTCAAAGCT
* * *
321020 TGCTAAAAATCACCAGCTTGAAGCTTGCTAAA
1 TGCTAAAAATCACCGGCTCGAAGCCTGCTAAA
321052 GTCATTGACT
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
50 21 0.30
51 48 0.70
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (50 bp):
TGCTAAAAATCACCGGCTCGAAGCCTGCTAAAAATCACCGACTCAAAGCT
Found at i:321028 original size:76 final size:76
Alignment explanation
Indices: 320902--321047 Score: 204
Period size: 76 Copynumber: 1.9 Consensus size: 76
320892 TGCTAAACAT
* *
320902 TCACCAGCTCGAATCCTGCTAAATAATCATCGGCTCAAAGCCTGCGAAAAATCACC-GACTCGAA
1 TCACCAGCTCGAAGCCTGCTAAATAATCACCGGCTCAAAGCCTGCGAAAAATCACCAG-CTCGAA
320966 GCTTGCAAAAAA
65 GCTTGCAAAAAA
* * * * * *
320978 TCACCGGCTCGAAGCCTGCTAATTAGTCACCGGCTCAAAGCTTGCTAAAAATCACCAGCTTGAAG
1 TCACCAGCTCGAAGCCTGCTAAATAATCACCGGCTCAAAGCCTGCGAAAAATCACCAGCTCGAAG
321043 CTTGC
66 CTTGC
321048 TAAAGTCATT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
76 60 0.98
77 1 0.02
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (76 bp):
TCACCAGCTCGAAGCCTGCTAAATAATCACCGGCTCAAAGCCTGCGAAAAATCACCAGCTCGAAG
CTTGCAAAAAA
Found at i:322014 original size:15 final size:16
Alignment explanation
Indices: 321994--322028 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
321984 TACCTAAGTA
*
321994 CATTAGTT-TTTATTT
1 CATTAGTTATTTACTT
322009 CATTAGTTATTTACTT
1 CATTAGTTATTTACTT
322025 CATT
1 CATT
322029 TAACTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.23, C:0.11, G:0.06, T:0.60
Consensus pattern (16 bp):
CATTAGTTATTTACTT
Found at i:327386 original size:268 final size:272
Alignment explanation
Indices: 326874--327415 Score: 950
Period size: 268 Copynumber: 2.0 Consensus size: 272
326864 AACACTTTAA
*
326874 ACCCGTAACTGTCATTGTTCTAGAGTCTTGACGTATTAAAAAATAATTTATAACAATCATTCAAA
1 ACCCGTAACTGTCATTGTTCTAGAGTCTTGACGTATTAAAAAATAAATTATAACAATCATTCAAA
326939 TGTTCACGAACATACATACATATATATATATATACTCAAAACATATATTAAACAAGTTACTAATC
66 TGTTCAC-AACATACATACATATATATATATATACTCAAAACATATATTAAACAAGTTACTAATC
** **
327004 ACGTTTAGTATTTAATTTAATTTACATTAGCATATAATAATGATACTTGTAATTAGAGATCAAAT
130 ACAATTAGTATTTAATTTAATTTACATTAGCATATAATAATGATACAAGTAATTAGAGATCAAAT
*
327069 TAAAACACATTGAGTCCTTTAAATGAAAATAAAAAATTTAAACAAAACAAGGGTCACACGGTCGT
195 TAAAACACATTGAGTCCTTTAAATGAAAATAAAAAATTTAAACAAAACAAGGGTCACACGGCCGT
327134 GTGTCTTTAACAC
260 GTGTCTTTAACAC
* *
327147 ACCCGTAACTGTCATTGTTCTAGATTCTTGACGTATTACAAAATAAATTATAACAATCATTCAAA
1 ACCCGTAACTGTCATTGTTCTAGAGTCTTGACGTATTAAAAAATAAATTATAACAATCATTCAAA
327212 TGTTCAC-A-A-ACATACATATATATATATATACTCAAAACATATATTAAACAAGTTACTAATCA
66 TGTTCACAACATACATACATATATATATATATACTCAAAACATATATTAAACAAGTTACTAATCA
327274 CAATTAGTATTTAATTT-ATTTACATTAGCATATAATAATGATACAAGTAATTAGAGATCAAATT
131 CAATTAGTATTTAATTTAATTTACATTAGCATATAATAATGATACAAGTAATTAGAGATCAAATT
*
327338 AAAACACATTGAGTCCTTTAAATGAAAATAAAAAAATTT-AACAAAACAAGTGTCACACGGCCGT
196 AAAACACATTGAGTCCTTTAAATGAAAAT-AAAAAATTTAAACAAAACAAGGGTCACACGGCCGT
327402 GTGTCTTTAACAC
260 GTGTCTTTAACAC
327415 A
1 A
327416 TGCCCTGTAC
Statistics
Matches: 259, Mismatches: 9, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
268 111 0.43
269 77 0.30
270 1 0.00
271 1 0.00
273 69 0.27
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (272 bp):
ACCCGTAACTGTCATTGTTCTAGAGTCTTGACGTATTAAAAAATAAATTATAACAATCATTCAAA
TGTTCACAACATACATACATATATATATATATACTCAAAACATATATTAAACAAGTTACTAATCA
CAATTAGTATTTAATTTAATTTACATTAGCATATAATAATGATACAAGTAATTAGAGATCAAATT
AAAACACATTGAGTCCTTTAAATGAAAATAAAAAATTTAAACAAAACAAGGGTCACACGGCCGTG
TGTCTTTAACAC
Found at i:328401 original size:26 final size:26
Alignment explanation
Indices: 328372--328629 Score: 145
Period size: 26 Copynumber: 10.1 Consensus size: 26
328362 TACTAAACAT
* *
328372 TCACTGGCTCAAAGCCTGCTAAATAA
1 TCACCGGCTCAAAGCCTGCTAAATAG
* * * *
328398 TCACCAGCTCGAAGCCTACTAAATCG
1 TCACCGGCTCAAAGCCTGCTAAATAG
* *
328424 TCACTC-ACTCAAAGCTTGCTAACA-A-
1 TCAC-CGGCTCAAAGCCTGCTAA-ATAG
** * **
328449 TCACCGGCTTGAATCCTGCTACTTAG
1 TCACCGGCTCAAAGCCTGCTAAATAG
*** *
328475 TCTTTGGCTCAAAGCGTGCTAAA-AG
1 TCACCGGCTCAAAGCCTGCTAAATAG
* *
328500 TCACCAGCT-AGAATCCTGCTAAATAG
1 TCACCGGCTCA-AAGCCTGCTAAATAG
* *
328526 TCACC-ACTCAAAGCCTGCTAAA-AA
1 TCACCGGCTCAAAGCCTGCTAAATAG
* * * **
328550 TCACTGGCTCGAAGCTTATTAAATAG
1 TCACCGGCTCAAAGCCTGCTAAATAG
* *
328576 TCACCGCCTCAAAGCCTGCTAAA-AA
1 TCACCGGCTCAAAGCCTGCTAAATAG
* ** *
328601 TCACCGACTCAAAGATTGCTAAATGG
1 TCACCGGCTCAAAGCCTGCTAAATAG
328627 TCA
1 TCA
328630 ACTCAAATTT
Statistics
Matches: 166, Mismatches: 55, Indels: 22
0.68 0.23 0.09
Matches are distributed among these distances:
24 7 0.04
25 78 0.47
26 79 0.48
27 2 0.01
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.24
Consensus pattern (26 bp):
TCACCGGCTCAAAGCCTGCTAAATAG
Found at i:328519 original size:25 final size:24
Alignment explanation
Indices: 328482--328623 Score: 97
Period size: 25 Copynumber: 5.7 Consensus size: 24
328472 TAGTCTTTGG
*
328482 CTCAAAGCGTGCTAAAAGTCACCA
1 CTCAAAGCCTGCTAAAAGTCACCA
*
328506 GCT-AGAATCCTGCTAAATAGTCACCA
1 -CTCA-AAGCCTGCTAAA-AGTCACCA
* **
328532 CTCAAAGCCTGCTAAAAATCACTGG
1 CTCAAAGCCTGCTAAAAGTCAC-CA
* * ** *
328557 CTCGAAGCTTATTAAATAGTCACCGC
1 CTCAAAGCCTGCTAAA-AGTCACC-A
*
328583 CTCAAAGCCTGCTAAAAATCACCGA
1 CTCAAAGCCTGCTAAAAGTCACC-A
**
328608 CTCAAAGATTGCTAAA
1 CTCAAAGCCTGCTAAA
328624 TGGTCAACTC
Statistics
Matches: 90, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
24 6 0.07
25 58 0.64
26 26 0.29
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.21
Consensus pattern (24 bp):
CTCAAAGCCTGCTAAAAGTCACCA
Found at i:328527 original size:51 final size:50
Alignment explanation
Indices: 328372--328605 Score: 182
Period size: 51 Copynumber: 4.6 Consensus size: 50
328362 TACTAAACAT
* * * *
328372 TCACTGGCTCAAAGCCTGCTAAATAATCACCAGCTCGAAGCCTACTAAATCG
1 TCACTGGCTCAAAGCCTGCT-AA-AATCACCAGCTAGAATCCTGCTAAATAG
** * * * **
328424 TCACTCACTCAAAGCTTGCTAACAATCACCGGCTTGAATCCTGCTACTTAG
1 TCACTGGCTCAAAGCCTGCTAA-AATCACCAGCTAGAATCCTGCTAAATAG
** *
328475 TCTTTGGCTCAAAGCGTGCTAAAAGTCACCAGCTAGAATCCTGCTAAATAG
1 TCACTGGCTCAAAGCCTGCTAAAA-TCACCAGCTAGAATCCTGCTAAATAG
** ** * * * **
328526 TCAC-CACTCAAAGCCTGCTAAAAATCACTGGCTCGAAGCTTATTAAATAG
1 TCACTGGCTCAAAGCCTGCT-AAAATCACCAGCTAGAATCCTGCTAAATAG
* *
328576 TCACCGCCTCAAAGCCTGCTAAAAATCACC
1 TCACTGGCTCAAAGCCTGCT-AAAATCACC
328606 GACTCAAAGA
Statistics
Matches: 144, Mismatches: 35, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
50 37 0.26
51 90 0.62
52 17 0.12
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (50 bp):
TCACTGGCTCAAAGCCTGCTAAAATCACCAGCTAGAATCCTGCTAAATAG
Found at i:328577 original size:101 final size:102
Alignment explanation
Indices: 328360--328605 Score: 278
Period size: 101 Copynumber: 2.4 Consensus size: 102
328350 GTACATAGTA
* * * *
328360 CCTACTAAACATTCACTGGCTCAAAGCCTGCTAAATAATCACCAGCTCGAAGCCTACTAAATCGT
1 CCTACTAAATAGTCACTGGCTCAAAGCCTGCTAAA-AATCACCAGCTAGAAGCCTACTAAATAGT
* * * *
328425 CACTCACTCAAAGCTTGCTAACAATCACCGGCTTGAAT
65 CACTCACTCAAAGCCTGCTAAAAATCACCGGCTCGAAG
* ** ** * * * *
328463 CCTGCTACTTAGTCTTTGGCTCAAAGCGTGCTAAAAGTCACCAGCTAGAATCCTGCTAAATAGTC
1 CCTACTAAATAGTCACTGGCTCAAAGCCTGCTAAAAATCACCAGCTAGAAGCCTACTAAATAGTC
*
328528 AC-CACTCAAAGCCTGCTAAAAATCACTGGCTCGAAG
66 ACTCACTCAAAGCCTGCTAAAAATCACCGGCTCGAAG
* * * *
328564 CTTATTAAATAGTCACCGCCTCAAAGCCTGCTAAAAATCACC
1 CCTACTAAATAGTCACTGGCTCAAAGCCTGCTAAAAATCACC
328606 GACTCAAAGA
Statistics
Matches: 114, Mismatches: 29, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
101 60 0.53
102 27 0.24
103 27 0.24
ACGTcount: A:0.33, C:0.30, G:0.14, T:0.24
Consensus pattern (102 bp):
CCTACTAAATAGTCACTGGCTCAAAGCCTGCTAAAAATCACCAGCTAGAAGCCTACTAAATAGTC
ACTCACTCAAAGCCTGCTAAAAATCACCGGCTCGAAG
Found at i:328624 original size:51 final size:50
Alignment explanation
Indices: 328516--328636 Score: 147
Period size: 51 Copynumber: 2.4 Consensus size: 50
328506 GCTAGAATCC
* * * *
328516 TGCTAAATAGTCACCACTCAAAGCCTGCTAAAAATCACTGGCTCGAAGCT
1 TGCTAAATAGTCACCACTCAAAGCCTGCTAAAAATCACCGACTCAAAGAT
** *
328566 TATTAAATAGTCACCGCCTCAAAGCCTGCTAAAAATCACCGACTCAAAGAT
1 TGCTAAATAGTCACC-ACTCAAAGCCTGCTAAAAATCACCGACTCAAAGAT
*
328617 TGCTAAATGGTCA--ACTCAAA
1 TGCTAAATAGTCACCACTCAAA
328637 TTTCTATTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
48 6 0.10
50 13 0.22
51 40 0.68
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.22
Consensus pattern (50 bp):
TGCTAAATAGTCACCACTCAAAGCCTGCTAAAAATCACCGACTCAAAGAT
Found at i:331711 original size:17 final size:17
Alignment explanation
Indices: 331689--331729 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
331679 TAACATTACA
331689 AGCAATGAGTGACATCT
1 AGCAATGAGTGACATCT
*
331706 AGCAATAAGTGACATCT
1 AGCAATGAGTGACATCT
331723 AGCAATG
1 AGCAATG
331730 CACCATTGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (17 bp):
AGCAATGAGTGACATCT
Found at i:349838 original size:18 final size:18
Alignment explanation
Indices: 349817--349858 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
349807 ATATAGACTG
349817 TTGTGGTTGTAATCGTGA
1 TTGTGGTTGTAATCGTGA
349835 TTGTGGTTGTAATCGTGA
1 TTGTGGTTGTAATCGTGA
349853 TATGTG
1 T-TGTG
349859 ACTGCATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.17, C:0.05, G:0.33, T:0.45
Consensus pattern (18 bp):
TTGTGGTTGTAATCGTGA
Found at i:355208 original size:44 final size:44
Alignment explanation
Indices: 355144--355260 Score: 225
Period size: 44 Copynumber: 2.7 Consensus size: 44
355134 TATAACACTA
*
355144 TGAAAATAGAAGAAATATATCTGCTACAAAGCGTAAACATGCGT
1 TGAAAATAGAAGAAAGATATCTGCTACAAAGCGTAAACATGCGT
355188 TGAAAATAGAAGAAAGATATCTGCTACAAAGCGTAAACATGCGT
1 TGAAAATAGAAGAAAGATATCTGCTACAAAGCGTAAACATGCGT
355232 TGAAAATAGAAGAAAGATATCTGCTACAA
1 TGAAAATAGAAGAAAGATATCTGCTACAA
355261 CGTTGAGCAA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
44 72 1.00
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (44 bp):
TGAAAATAGAAGAAAGATATCTGCTACAAAGCGTAAACATGCGT
Found at i:366524 original size:22 final size:21
Alignment explanation
Indices: 366499--366567 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 21
366489 TGATCATGCG
366499 AGAAAATGAGAGGAAAATAAAA
1 AGAAAATGAGA-GAAAATAAAA
** *
366521 AGAATTTGAGAGAAGAA-ACAA
1 AGAAAATGAGAGAA-AATAAAA
* *
366542 AG-AAATGAGAGAAAATGAGA
1 AGAAAATGAGAGAAAATAAAA
366562 AGAAAA
1 AGAAAA
366568 AAAGAAAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
19 2 0.06
20 12 0.33
21 11 0.31
22 11 0.31
ACGTcount: A:0.64, C:0.01, G:0.25, T:0.10
Consensus pattern (21 bp):
AGAAAATGAGAGAAAATAAAA
Found at i:370137 original size:24 final size:25
Alignment explanation
Indices: 370104--370150 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
370094 ACAGAATATT
370104 TTTTTATTTTT-TATTTTTCTCGTA
1 TTTTTATTTTTCTATTTTTCTCGTA
* *
370128 TTTTTCTTTTTCTTTTTTTCTCG
1 TTTTTATTTTTCTATTTTTCTCG
370151 ACTTTTTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.06, C:0.13, G:0.04, T:0.77
Consensus pattern (25 bp):
TTTTTATTTTTCTATTTTTCTCGTA
Found at i:372837 original size:50 final size:50
Alignment explanation
Indices: 372783--372924 Score: 162
Period size: 51 Copynumber: 2.8 Consensus size: 50
372773 CCATGATATA
* *
372783 ATTTATGATGTATATTTAACTAACACATAAGTTACATAATGCATGTCATT
1 ATTTATGATGCATACTTAACTAACACATAAGTTACATAATGCATGTCATT
* * * *
372833 ATTTATGATGCAAACTTAGCTAA-TCATGAGATTTACATAATGCATGTCATT
1 ATTTATGATGCATACTTAACTAACACAT-A-AGTTACATAATGCATGTCATT
* * *
372884 ATTTATGATACATACATAACTAACATGA-AAGTTACATAATG
1 ATTTATGATGCATACTTAACTAACA-CATAAGTTACATAATG
372925 TATGACTTTA
Statistics
Matches: 75, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
49 3 0.04
50 31 0.41
51 40 0.53
53 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (50 bp):
ATTTATGATGCATACTTAACTAACACATAAGTTACATAATGCATGTCATT
Found at i:372874 original size:51 final size:50
Alignment explanation
Indices: 372811--372924 Score: 165
Period size: 51 Copynumber: 2.3 Consensus size: 50
372801 ACTAACACAT
* * *
372811 AAGTTACATAATGCATGTCATTATTTATGATGCAAACTTAGCTAATCATGA
1 AAGTTACATAATGCATGTCATTATTTATGATACAAACATAACTAA-CATGA
* * *
372862 GATTTACATAATGCATGTCATTATTTATGATACATACATAACTAACATGA
1 AAGTTACATAATGCATGTCATTATTTATGATACAAACATAACTAACATGA
372912 AAGTTACATAATG
1 AAGTTACATAATG
372925 TATGACTTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 16 0.29
51 39 0.71
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.35
Consensus pattern (50 bp):
AAGTTACATAATGCATGTCATTATTTATGATACAAACATAACTAACATGA
Found at i:373886 original size:21 final size:21
Alignment explanation
Indices: 373844--373887 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
373834 TTTCAACTTC
*
373844 TTTTTTTTACAAACACTTTCT
1 TTTTTTTTACAAACACTATCT
* * *
373865 TTTTTTTTTCAACCTCTATCT
1 TTTTTTTTACAAACACTATCT
373886 TT
1 TT
373888 CTTTCTTCTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.18, C:0.20, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTTTTTACAAACACTATCT
Found at i:376011 original size:23 final size:22
Alignment explanation
Indices: 375985--376054 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 22
375975 ATATTTTCTT
375985 TTCGAATCTTTCTTTTTTTTTAA
1 TTCGAAT-TTTCTTTTTTTTTAA
* *
376008 TTCGATTTTTTTTCTTTTTTTAAA
1 TTCGAATTTTCTT-TTTTTTT-AA
*
376032 TTTGAA-TTTCTTTTTTTTCTAA
1 TTCGAATTTTCTTTTTTTT-TAA
376054 T
1 T
376055 ATTTTCGAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 14 0.36
23 19 0.49
24 6 0.15
ACGTcount: A:0.17, C:0.10, G:0.04, T:0.69
Consensus pattern (22 bp):
TTCGAATTTTCTTTTTTTTTAA
Found at i:376045 original size:26 final size:26
Alignment explanation
Indices: 375993--376076 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 26
375983 TTTTCGAATC
* *
375993 TTTCTTTTTTTTTAATTCG-ATTT-TT
1 TTTC-TTTTTTTAAATTTGAATTTCTT
376018 TTTCTTTTTTTAAATTTGAATTTC--
1 TTTCTTTTTTTAAATTTGAATTTCTT
*
376042 TTT-TTTTTCTAATATTTTCGAATTTCTT
1 TTTCTTTTTTTAA-A-TTT-GAATTTCTT
376070 TTTCTTT
1 TTTCTTT
376077 AAATTTTTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
23 8 0.17
24 16 0.33
25 11 0.23
26 7 0.15
28 3 0.06
29 3 0.06
ACGTcount: A:0.15, C:0.10, G:0.04, T:0.71
Consensus pattern (26 bp):
TTTCTTTTTTTAAATTTGAATTTCTT
Found at i:376085 original size:26 final size:26
Alignment explanation
Indices: 376035--376098 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
376025 TTTTAAATTT
*
376035 GAATTTCTTTTTTTTCTAATATTTTC
1 GAATTTCTTTTTTTTCAAATATTTTC
*
376061 GAATTTCTTTTTCTTT-AAAT-TTTTT
1 GAATTTCTTTTT-TTTCAAATATTTTC
*
376086 GAGTTT-TTTTTTT
1 GAATTTCTTTTTTT
376099 ATTTTTTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 2 0.06
24 5 0.15
25 9 0.26
26 15 0.44
27 3 0.09
ACGTcount: A:0.17, C:0.08, G:0.06, T:0.69
Consensus pattern (26 bp):
GAATTTCTTTTTTTTCAAATATTTTC
Found at i:377337 original size:51 final size:50
Alignment explanation
Indices: 377194--377341 Score: 190
Period size: 50 Copynumber: 2.9 Consensus size: 50
377184 TGTTTTAATT
* **
377194 ATGCAAACTTTAACTGACATGGGAGTTACATAATGCATGAT-ATAATTTATG
1 ATGCAAAC-TTAACTAACATGAAAGTTACATAATGCATG-TCATAATTTATG
* * * * *
377245 ATGCATATTTAACTAACATGTAAGTTACATAATGCTTGTCATTATTTATG
1 ATGCAAACTTAACTAACATGAAAGTTACATAATGCATGTCATAATTTATG
377295 ATGCAAACTTAACTAATCATGAAAGTTACATAATGCATGTCATAATT
1 ATGCAAACTTAACTAA-CATGAAAGTTACATAATGCATGTCATAATT
377342 AAAAGATCTA
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
49 1 0.01
50 49 0.59
51 33 0.40
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.36
Consensus pattern (50 bp):
ATGCAAACTTAACTAACATGAAAGTTACATAATGCATGTCATAATTTATG
Found at i:381132 original size:25 final size:25
Alignment explanation
Indices: 381104--381171 Score: 120
Period size: 25 Copynumber: 2.7 Consensus size: 25
381094 AATTAATAAT
381104 AATT-CTCTTTGAGTTTTTCTTCAAG
1 AATTGCTC-TTGAGTTTTTCTTCAAG
381129 AATTGCTCTTGAGTTTTTCTTCAAG
1 AATTGCTCTTGAGTTTTTCTTCAAG
381154 AATTGCTCTTGAGTTTTT
1 AATTGCTCTTGAGTTTTT
381172 TTTTTTTTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 39 0.93
26 3 0.07
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.51
Consensus pattern (25 bp):
AATTGCTCTTGAGTTTTTCTTCAAG
Found at i:381500 original size:47 final size:47
Alignment explanation
Indices: 381446--381542 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
381436 GTTCTCCTAC
381446 CTTGATCCATCAAGGAACACATCAAAAATTAAGAGATTCAATATTTT
1 CTTGATCCATCAAGGAACACATCAAAAATTAAGAGATTCAATATTTT
381493 CTTGATCCATCAAGGAACACATCAAAAATTAAGAGATTCAATATTTT
1 CTTGATCCATCAAGGAACACATCAAAAATTAAGAGATTCAATATTTT
381540 CTT
1 CTT
381543 TCTTTTTCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (47 bp):
CTTGATCCATCAAGGAACACATCAAAAATTAAGAGATTCAATATTTT
Found at i:385904 original size:24 final size:24
Alignment explanation
Indices: 385872--385926 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
385862 TATAGGGTTC
**
385872 ACACAGGATGACACACGTCCTATG
1 ACACAGGATGACACACAACCTATG
*
385896 ACACAGGATGACACCCAACCTATG
1 ACACAGGATGACACACAACCTATG
385920 ACA-AGGA
1 ACACAGGA
385927 CGTGTGGGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.38, C:0.29, G:0.20, T:0.13
Consensus pattern (24 bp):
ACACAGGATGACACACAACCTATG
Found at i:388072 original size:16 final size:17
Alignment explanation
Indices: 388051--388083 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
388041 AATCCGAACA
388051 TTAAAA-CATAAGTTAT
1 TTAAAAGCATAAGTTAT
388067 TTAAAATGCATAAGTTA
1 TTAAAA-GCATAAGTTA
388084 AGAATGAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (17 bp):
TTAAAAGCATAAGTTAT
Found at i:393029 original size:9 final size:9
Alignment explanation
Indices: 393015--393048 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
393005 TTTTTTTTTA
393015 TTTAAATTT
1 TTTAAATTT
393024 TTTAAATTT
1 TTTAAATTT
*
393033 TTTAAA-AT
1 TTTAAATTT
393041 TTTAAATT
1 TTTAAATT
393049 AAAAAAAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTAAATTT
Found at i:394534 original size:50 final size:50
Alignment explanation
Indices: 394457--394608 Score: 180
Period size: 50 Copynumber: 3.0 Consensus size: 50
394447 TGTCAACGAA
* * *
394457 ATAACATAAATATAATATATTTATATAAAACACAAGAGCTGAAA-AAAGCAAT
1 ATAA-ATAAATAT-TTATATTTATATAAAACACAAAAGCT-AAATAAAACAAT
*
394509 ATAAATAAATATTTATATTTATATAAAACACAAAATCTAAATAAAACAAT
1 ATAAATAAATATTTATATTTATATAAAACACAAAAGCTAAATAAAACAAT
* * * * *
394559 ATAAATAAATATTTATATTTTTGTAAAAGCACAAAATCTGAACAAAACAA
1 ATAAATAAATATTTATATTTATATAAAA-CACAAAAGCTAAATAAAACAA
394609 AAAAAGGAAT
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
49 3 0.03
50 56 0.62
51 27 0.30
52 4 0.04
ACGTcount: A:0.57, C:0.09, G:0.05, T:0.29
Consensus pattern (50 bp):
ATAAATAAATATTTATATTTATATAAAACACAAAAGCTAAATAAAACAAT
Found at i:397555 original size:24 final size:24
Alignment explanation
Indices: 397528--397578 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
397518 ATCATGGATA
397528 TCAAGTCCCTTGCCTGTTGGGGAC
1 TCAAGTCCCTTGCCTGTTGGGGAC
397552 TCAAGTCCCTTGCCTGTTGGGGAC
1 TCAAGTCCCTTGCCTGTTGGGGAC
397576 TCA
1 TCA
397579 TATTAACTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.14, C:0.29, G:0.27, T:0.29
Consensus pattern (24 bp):
TCAAGTCCCTTGCCTGTTGGGGAC
Found at i:398898 original size:16 final size:17
Alignment explanation
Indices: 398877--398909 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
398867 AGGAACTTGA
398877 CTCTAGT-CAACCGTCT
1 CTCTAGTGCAACCGTCT
*
398893 CTCTAGTGGAACCGTCT
1 CTCTAGTGCAACCGTCT
398910 TACACTAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.18, C:0.33, G:0.18, T:0.30
Consensus pattern (17 bp):
CTCTAGTGCAACCGTCT
Found at i:400917 original size:107 final size:107
Alignment explanation
Indices: 400731--400945 Score: 430
Period size: 107 Copynumber: 2.0 Consensus size: 107
400721 TGAATGAGCC
400731 AAGAAAAGTAGGTTTATATACATTTGATTTTGAAAGAACTCATTAATAGTTTAAGACATGTAATT
1 AAGAAAAGTAGGTTTATATACATTTGATTTTGAAAGAACTCATTAATAGTTTAAGACATGTAATT
400796 AAGCATGTGATGAGTCATGAATTGATGTCAAATTATGTTTGT
66 AAGCATGTGATGAGTCATGAATTGATGTCAAATTATGTTTGT
400838 AAGAAAAGTAGGTTTATATACATTTGATTTTGAAAGAACTCATTAATAGTTTAAGACATGTAATT
1 AAGAAAAGTAGGTTTATATACATTTGATTTTGAAAGAACTCATTAATAGTTTAAGACATGTAATT
400903 AAGCATGTGATGAGTCATGAATTGATGTCAAATTATGTTTGT
66 AAGCATGTGATGAGTCATGAATTGATGTCAAATTATGTTTGT
400945 A
1 A
400946 TGACCAAGAA
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 108 1.00
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.37
Consensus pattern (107 bp):
AAGAAAAGTAGGTTTATATACATTTGATTTTGAAAGAACTCATTAATAGTTTAAGACATGTAATT
AAGCATGTGATGAGTCATGAATTGATGTCAAATTATGTTTGT
Found at i:401250 original size:24 final size:24
Alignment explanation
Indices: 401223--401272 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
401213 AAGATTTTAC
401223 AAAGGATTTGAAAAGGTGTTACAA
1 AAAGGATTTGAAAAGGTGTTACAA
401247 AAAGGATTTGAAAAGGTGTTACAA
1 AAAGGATTTGAAAAGGTGTTACAA
401271 AA
1 AA
401273 TTGCATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.04, G:0.24, T:0.24
Consensus pattern (24 bp):
AAAGGATTTGAAAAGGTGTTACAA
Found at i:408115 original size:16 final size:18
Alignment explanation
Indices: 408096--408129 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
408086 TTTAACATTC
408096 TTTTTTAT-T-AAAAATA
1 TTTTTTATGTCAAAAATA
408112 TTTTTTATGTCAAAAATA
1 TTTTTTATGTCAAAAATA
408130 CTTATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 1 0.06
18 7 0.44
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTTTTATGTCAAAAATA
Found at i:408381 original size:19 final size:21
Alignment explanation
Indices: 408344--408382 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
408334 ATAATGAAAA
*
408344 ATATATTTAAAGAATTAATTG
1 ATATATTTAAAGAAATAATTG
408365 ATAT-TTTAAA-AAATAATT
1 ATATATTTAAAGAAATAATT
408383 ACATATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 6 0.35
21 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
ATATATTTAAAGAAATAATTG
Found at i:411655 original size:73 final size:73
Alignment explanation
Indices: 411563--411708 Score: 274
Period size: 73 Copynumber: 2.0 Consensus size: 73
411553 TACAGGAGAA
411563 AGCATTCTTCTCTTATTTGCAAATTTAAGGATTGTCTAATTGAAATGATTATGTCGGGTCCTAGG
1 AGCATTCTTCTCTTATTTGCAAATTTAAGGATTGTCTAATTGAAATGATTATGTCGGGTCCTAGG
411628 TTTTTATT
66 TTTTTATT
* *
411636 AGCATTTTTCTCTTATTTGCAAATTTAAGGATTGTCTAATTGAAATGATTGTGTCGGGTCCTAGG
1 AGCATTCTTCTCTTATTTGCAAATTTAAGGATTGTCTAATTGAAATGATTATGTCGGGTCCTAGG
411701 TTTTTATT
66 TTTTTATT
411709 TGAACTTATG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.46
Consensus pattern (73 bp):
AGCATTCTTCTCTTATTTGCAAATTTAAGGATTGTCTAATTGAAATGATTATGTCGGGTCCTAGG
TTTTTATT
Found at i:414754 original size:16 final size:16
Alignment explanation
Indices: 414733--414765 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
414723 GGATATGCTC
414733 TATCAATGTTGTTTGT
1 TATCAATGTTGTTTGT
414749 TATCAATGTTGTTTGT
1 TATCAATGTTGTTTGT
414765 T
1 T
414766 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.18, T:0.58
Consensus pattern (16 bp):
TATCAATGTTGTTTGT
Found at i:416774 original size:23 final size:23
Alignment explanation
Indices: 416699--416814 Score: 69
Period size: 23 Copynumber: 4.9 Consensus size: 23
416689 ACCCTACTAT
* *
416699 TTTTATTTTATTTAATTTGATCCCA
1 TTTT-TTTTATTTAATTTTAT-TCA
* *
416724 -TGTTTTTATTT-ATTTGAATT-A
1 TTTTTTTTATTTAATTT-TATTCA
416745 TTATTTTTTATTTAATTTTATTCA
1 TT-TTTTTTATTTAATTTTATTCA
* *
416769 -TTTTTTTATTTAGTCATTTATTTA
1 TTTTTTTTATTTAAT--TTTATTCA
*
416793 TTTATTTGTTATTTATTTTTAT
1 TTT-TTT-TTATTTAATTTTAT
416815 GTTATTTATA
Statistics
Matches: 73, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
21 1 0.01
22 17 0.23
23 23 0.32
24 14 0.19
25 7 0.10
26 3 0.04
27 8 0.11
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (23 bp):
TTTTTTTTATTTAATTTTATTCA
Found at i:416806 original size:15 final size:15
Alignment explanation
Indices: 416786--416823 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
416776 ATTTAGTCAT
416786 TTATTTATTTATT-TG
1 TTATTTATTT-TTATG
416801 TTATTTATTTTTATG
1 TTATTTATTTTTATG
416816 TTATTTAT
1 TTATTTAT
416824 ATTCCTGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 2 0.09
15 20 0.91
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (15 bp):
TTATTTATTTTTATG
Found at i:416840 original size:4 final size:4
Alignment explanation
Indices: 416728--416823 Score: 67
Period size: 4 Copynumber: 24.2 Consensus size: 4
416718 ATCCCATGTT
* * *
416728 TTTA TTTA TTTGA ATTA -TTA TTT- TTTA TTTAA TTTTA TTCA TTTT TTTA
1 TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTT-A -TTTA TTTA TTTA TTTA
* * *
416777 TTTA GTCA TTTA TTTA TTTA TTT- GTTA TTTA -TT- TTTA TGTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA
416823 T
1 T
416824 ATTCCTGCTT
Statistics
Matches: 72, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
3 12 0.17
4 48 0.67
5 9 0.12
6 3 0.04
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:417117 original size:21 final size:21
Alignment explanation
Indices: 417093--417149 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
417083 ATTGCCATGA
417093 TTATTATTGTTATTTTATTTG
1 TTATTATTGTTATTTTATTTG
* * *
417114 TTATCATTATTTTTTTATTTG
1 TTATTATTGTTATTTTATTTG
417135 -TATTATTTGTTATTT
1 TTATTA-TTGTTATTT
417150 ATTGTATATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.72
Consensus pattern (21 bp):
TTATTATTGTTATTTTATTTG
Found at i:417152 original size:20 final size:20
Alignment explanation
Indices: 417094--417162 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
417084 TTGCCATGAT
417094 TATTA-TTGTTATTTTATTTG
1 TATTATTTGTTA-TTTATTTG
* *
417114 TTATCATTAT-TTTTTTATTTG
1 -TATTATT-TGTTATTTATTTG
417135 TATTATTTGTTATTTA-TTG
1 TATTATTTGTTATTTATTTG
417154 TATATATTT
1 TAT-TATTT
417163 ATTTTACTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
19 7 0.17
20 17 0.43
21 12 0.30
22 3 0.08
23 1 0.03
ACGTcount: A:0.22, C:0.01, G:0.07, T:0.70
Consensus pattern (20 bp):
TATTATTTGTTATTTATTTG
Found at i:435606 original size:27 final size:27
Alignment explanation
Indices: 435575--435627 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
435565 AAATTTAATG
435575 AATGAAATAAAAGTAATA-AAA-ATAAAT
1 AATG-AATAAAA-TAATATAAACATAAAT
435602 AATGAATAAAATAATATAAACATAAA
1 AATGAATAAAATAATATAAACATAAA
435628 AAAAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 5 0.21
26 10 0.42
27 9 0.38
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.23
Consensus pattern (27 bp):
AATGAATAAAATAATATAAACATAAAT
Found at i:442305 original size:9 final size:9
Alignment explanation
Indices: 442286--442327 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
442276 TTGGTATAAA
*
442286 AATTATCCG
1 AATTAACCG
*
442295 AATTAATCG
1 AATTAACCG
*
442304 AATTACCCG
1 AATTAACCG
442313 AATTAACCG
1 AATTAACCG
442322 AATTAA
1 AATTAA
442328 AGTATTGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:442307 original size:18 final size:18
Alignment explanation
Indices: 442286--442326 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
442276 TTGGTATAAA
* *
442286 AATTATCCGAATTAATCG
1 AATTACCCGAATTAACCG
442304 AATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
442322 AATTA
1 AATTA
442327 AAGTATTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (18 bp):
AATTACCCGAATTAACCG
Found at i:442725 original size:36 final size:36
Alignment explanation
Indices: 442674--442743 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
442664 AAGACAACTT
* *
442674 ACTTACACCGGTGTAAGTATGTTTACTTTAATCATG
1 ACTTACACCGATGTAAGTATGATTACTTTAATCATG
*
442710 ACTTACATCGATGTAAGTATGATTACTTTAATCA
1 ACTTACACCGATGTAAGTATGATTACTTTAATCA
442744 AGTTTGGGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (36 bp):
ACTTACACCGATGTAAGTATGATTACTTTAATCATG
Found at i:454445 original size:27 final size:24
Alignment explanation
Indices: 454403--454452 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
454393 CCTCTCTAAT
*
454403 AACAACACCACCATCACCACCTCG
1 AACAACACCACCATCAACACCTCG
454427 AACAACACCACACTGATCAACACCTC
1 AACAACACCAC-C--ATCAACACCTC
454453 TACCACCATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 11 0.50
25 1 0.05
27 10 0.45
ACGTcount: A:0.40, C:0.46, G:0.04, T:0.10
Consensus pattern (24 bp):
AACAACACCACCATCAACACCTCG
Found at i:457209 original size:40 final size:41
Alignment explanation
Indices: 457083--457221 Score: 165
Period size: 42 Copynumber: 3.4 Consensus size: 41
457073 AAGCTACGAT
*
457083 TTAGCAGGCTATAAGTTGGTGTAAAAGAATTCAAG-TTACGGC
1 TTAGCAGGCTATAAGTTGGTGTAAAA-AACTCAAGCTT-CGGC
** ** *
457125 TTAGCAGGCTATGTGCCGGTGTAATAAAACTCAAGCTACGGC
1 TTAGCAGGCTATAAGTTGGTGTAA-AAAACTCAAGCTTCGGC
* *
457167 TTAGCAGGCTACAAGTTGGTGT-AAAAACTCAAGCTTCAGC
1 TTAGCAGGCTATAAGTTGGTGTAAAAAACTCAAGCTTCGGC
457207 TTAGCAGGCTATAAG
1 TTAGCAGGCTATAAG
457222 CCGATGTATT
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
40 29 0.36
41 1 0.01
42 48 0.59
43 3 0.04
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (41 bp):
TTAGCAGGCTATAAGTTGGTGTAAAAAACTCAAGCTTCGGC
Found at i:457239 original size:40 final size:40
Alignment explanation
Indices: 457083--457240 Score: 129
Period size: 42 Copynumber: 3.9 Consensus size: 40
457073 AAGCTACGAT
** * *
457083 TTAGCAGGCTATAAGTTGGTGTAAAAGAATTCAAG-TTACGGC
1 TTAGCAGGCTATAAGCCGGTGT-ATA-AACTCAAGCTT-CGGC
** *
457125 TTAGCAGGCTATGTGCCGGTGTAATAAAACTCAAGCTACGGC
1 TTAGCAGGCTATAAGCCGGTGT-AT-AAACTCAAGCTTCGGC
* ** * *
457167 TTAGCAGGCTACAAGTTGGTGTAAAAACTCAAGCTTCAGC
1 TTAGCAGGCTATAAGCCGGTGTATAAACTCAAGCTTCGGC
* * *
457207 TTAGCAGGCTATAAGCCGATGTATTAATTCAAGC
1 TTAGCAGGCTATAAGCCGGTGTATAAACTCAAGC
457241 CAAACTATAG
Statistics
Matches: 92, Mismatches: 22, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
40 41 0.45
41 1 0.01
42 48 0.52
43 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.27
Consensus pattern (40 bp):
TTAGCAGGCTATAAGCCGGTGTATAAACTCAAGCTTCGGC
Found at i:463353 original size:21 final size:21
Alignment explanation
Indices: 463329--463378 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
463319 CCTATGACAG
* * *
463329 TTCTACCGATACAAGTGAAGC
1 TTCTACCGAAACAAATCAAGC
*
463350 TTCTACCGAAACAAATCATGC
1 TTCTACCGAAACAAATCAAGC
463371 TTCTACCG
1 TTCTACCG
463379 GTACTAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (21 bp):
TTCTACCGAAACAAATCAAGC
Done.