Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 405 of 427
Found at i:117597878 original size:5 final size:5
Alignment explanation
Indices: 117597870--117597968 Score: 63
Period size: 5 Copynumber: 18.4 Consensus size: 5
117597860 AATATAATTT
* * * *
117597870 AAATG AAATG AAATGG TAATGG GAATGG AAATG AATTT AGAATG AAATG
1 AAATG AAATG AAAT-G AAAT-G AAAT-G AAATG AAATG A-AATG AAATG
* * * *
117597919 AAATTG GAATG AAATA AAATTA AAATG AAATG AAAATG AAAAG AAATG
1 AAA-TG AAATG AAATG AAA-TG AAATG AAATG -AAATG AAATG AAATG
117597967 AA
1 AA
117597969 GAAAAAAAAA
Statistics
Matches: 76, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
5 45 0.59
6 31 0.41
ACGTcount: A:0.57, C:0.00, G:0.21, T:0.22
Consensus pattern (5 bp):
AAATG
Found at i:117597918 original size:16 final size:16
Alignment explanation
Indices: 117597892--117597953 Score: 79
Period size: 16 Copynumber: 3.8 Consensus size: 16
117597882 ATGGTAATGG
*
117597892 GAATGGAAATGAATTTA
1 GAAT-GAAATGAAATTA
*
117597909 GAATGAAATGAAATTG
1 GAATGAAATGAAATTA
*
117597925 GAATGAAATAAAATTA
1 GAATGAAATGAAATTA
*
117597941 AAATGAAATGAAA
1 GAATGAAATGAAA
117597954 ATGAAAAGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
16 35 0.90
17 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.24
Consensus pattern (16 bp):
GAATGAAATGAAATTA
Found at i:117597964 original size:16 final size:16
Alignment explanation
Indices: 117597913--117597968 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
117597903 AATTTAGAAT
* * *
117597913 GAAATGAAATTGGAAT
1 GAAATGAAAATGAAAA
*
117597929 GAAAT-AAAATTAAAA
1 GAAATGAAAATGAAAA
117597944 TGAAATGAAAATGAAAA
1 -GAAATGAAAATGAAAA
117597961 GAAATGAA
1 GAAATGAA
117597969 GAAAAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
15 6 0.18
16 18 0.55
17 9 0.27
ACGTcount: A:0.62, C:0.00, G:0.18, T:0.20
Consensus pattern (16 bp):
GAAATGAAAATGAAAA
Found at i:117598198 original size:14 final size:14
Alignment explanation
Indices: 117598176--117598262 Score: 76
Period size: 14 Copynumber: 6.2 Consensus size: 14
117598166 GAAATGAGTT
*
117598176 AAAATAATAATATG
1 AAAAAAATAATATG
117598190 AAAAAAATAATAT-
1 AAAAAAATAATATG
117598203 ---AAAATGAAT-TG
1 AAAAAAAT-AATATG
117598214 AAAAAAATAATATG
1 AAAAAAATAATATG
*
117598228 AAAATAATATAAAAAATG
1 AAAA-AA-AT--AATATG
117598246 AAAAAAATAATATG
1 AAAAAAATAATATG
117598260 AAA
1 AAA
117598263 TGAATTGAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
10 6 0.10
11 3 0.05
13 3 0.05
14 31 0.52
15 2 0.03
16 4 0.07
17 2 0.03
18 9 0.15
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (14 bp):
AAAAAAATAATATG
Found at i:117598206 original size:11 final size:11
Alignment explanation
Indices: 117598192--117598242 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
117598182 ATAATATGAA
117598192 AAAAATAATAT
1 AAAAATAATAT
*
117598203 -AAAATGAATTGAA
1 AAAAAT-AA-T-AT
117598216 AAAAATAATAT
1 AAAAATAATAT
*
117598227 GAAAATAATAT
1 AAAAATAATAT
117598238 AAAAA
1 AAAAA
117598243 ATGAAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
10 5 0.16
11 17 0.53
12 2 0.06
13 3 0.09
14 5 0.16
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (11 bp):
AAAAATAATAT
Found at i:117598208 original size:37 final size:35
Alignment explanation
Indices: 117598161--117598262 Score: 111
Period size: 37 Copynumber: 2.9 Consensus size: 35
117598151 AATTTGATAA
*
117598161 AATATGAAATGAGTTAAAATAATAATATGAAAAAAAT
1 AATATAAAATGA-TTAAAA-AATAATATGAAAAAAAT
*
117598198 AATATAAAATGAATTGAAAAAAATAATATGAAAATAAT
1 AATATAAAATG-ATT--AAAAAATAATATGAAAAAAAT
*
117598236 -ATAAAAAATGA--AAAAAATAATATGAAA
1 AATATAAAATGATTAAAAAATAATATGAAA
117598263 TGAATTGAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
32 16 0.27
36 1 0.02
37 21 0.36
38 17 0.29
39 4 0.07
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.25
Consensus pattern (35 bp):
AATATAAAATGATTAAAAAATAATATGAAAAAAAT
Found at i:117598209 original size:19 final size:19
Alignment explanation
Indices: 117598182--117598266 Score: 77
Period size: 19 Copynumber: 4.5 Consensus size: 19
117598172 AGTTAAAATA
*
117598182 ATAATATGAAAAAAATAAT
1 ATAAAATGAAAAAAATAAT
*
117598201 ATAAAATGAATTGAAAA-AA-
1 ATAAAATGAA--AAAAATAAT
* *
117598220 ATAATATGAAAATAAT-AT
1 ATAAAATGAAAAAAATAAT
*
117598238 AAAAAATGAAAAAAATAAT
1 ATAAAATGAAAAAAATAAT
*
117598257 ATGAAATGAA
1 ATAAAATGAA
117598267 TTGAAAAAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
17 4 0.08
18 13 0.25
19 28 0.55
20 2 0.04
21 4 0.08
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (19 bp):
ATAAAATGAAAAAAATAAT
Found at i:117598241 original size:24 final size:24
Alignment explanation
Indices: 117598181--117598262 Score: 102
Period size: 24 Copynumber: 3.5 Consensus size: 24
117598171 GAGTTAAAAT
117598181 AATAATATGAAAAAAATAATATAA
1 AATAATATGAAAAAAATAATATAA
117598205 AATGAAT-TGAAAAAAATAATATGAA
1 AAT-AATATGAAAAAAATAATAT-AA
117598230 AATAATAT--AAAAAATGAA-A-AA
1 AATAATATGAAAAAAAT-AATATAA
117598251 AATAATATGAAA
1 AATAATATGAAA
117598263 TGAATTGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
21 10 0.19
23 10 0.19
24 23 0.44
25 9 0.17
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (24 bp):
AATAATATGAAAAAAATAATATAA
Found at i:117598253 original size:32 final size:32
Alignment explanation
Indices: 117598193--117598296 Score: 113
Period size: 35 Copynumber: 3.1 Consensus size: 32
117598183 TAATATGAAA
117598193 AAAATAATATAAAATGAATTGAAAAAAATAATATG
1 AAAATAATATAAAA--AA-TGAAAAAAATAATATG
117598228 AAAATAATATAAAAAATGAAAAAAATAATATG
1 AAAATAATATAAAAAATGAAAAAAATAATATG
* *
117598260 -AAATGAATTGAAAAAAAATGAAATGAAATAAT-TG
1 AAAAT-AA-T-ATAAAAAATGAAA-AAAATAATATG
117598294 AAA
1 AAA
117598297 TTAAATTAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
31 4 0.06
32 18 0.29
33 3 0.05
34 14 0.23
35 23 0.37
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (32 bp):
AAAATAATATAAAAAATGAAAAAAATAATATG
Found at i:117598271 original size:24 final size:23
Alignment explanation
Indices: 117598228--117598296 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 23
117598218 AAATAATATG
*
117598228 AAAATAATAT-AAA-AAATGAAA
1 AAAATAATATGAAATAATTGAAA
117598249 AAAATAATATGAAATGAATTGAAAA
1 AAAATAATATGAAAT-AATTG-AAA
117598274 AAAATGAA-ATGAAATAATTGAAA
1 AAAAT-AATATGAAATAATTGAAA
117598297 TTAAATTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
21 10 0.24
22 3 0.07
23 3 0.07
24 9 0.21
25 15 0.36
26 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (23 bp):
AAAATAATATGAAATAATTGAAA
Found at i:117598289 original size:56 final size:57
Alignment explanation
Indices: 117598154--117598291 Score: 174
Period size: 56 Copynumber: 2.4 Consensus size: 57
117598144 TCTAATTAAT
* * ** * *
117598154 TTGATAAAATATGAAATGAGTTAAAATAATAATATGAAAAAAATAATATAAAATGAA
1 TTGAAAAAAAATGAAATGAAATAATATAATAAAATGAAAAAAATAATATAAAATGAA
*
117598211 TTG-AAAAAAAT-AATATGAAAATAATATAA-AAAATGAAAAAAATAATATGAAATGAA
1 TTGAAAAAAAATGAA-ATG-AAATAATATAATAAAATGAAAAAAATAATATAAAATGAA
117598267 TTGAAAAAAAATGAAATGAAATAAT
1 TTGAAAAAAAATGAAATGAAATAAT
117598292 TGAAATTAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
55 2 0.03
56 44 0.63
57 22 0.31
58 2 0.03
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.25
Consensus pattern (57 bp):
TTGAAAAAAAATGAAATGAAATAATATAATAAAATGAAAAAAATAATATAAAATGAA
Found at i:117598313 original size:35 final size:34
Alignment explanation
Indices: 117598212--117598321 Score: 113
Period size: 34 Copynumber: 3.3 Consensus size: 34
117598202 TAAAATGAAT
*
117598212 TGAAAAAAATAATATGAAA-ATAA-T-ATAAAAAA
1 TGAAAAAAATAATATGAAATA-AATTGAAAAAAAA
*
117598244 TGAAAAAAATAATATGAAATGAATTGAAAAAAAA
1 TGAAAAAAATAATATGAAATAAATTGAAAAAAAA
* *
117598278 TGAAATGAAATAAT-TGAAATTAAATT-AAATTAAAA
1 TGAAA-AAAATAATATGAAA-TAAATTGAAA-AAAAA
117598313 TGAAAAAAA
1 TGAAAAAAA
117598322 GGTTGAAAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
32 21 0.32
33 1 0.02
34 23 0.35
35 21 0.32
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (34 bp):
TGAAAAAAATAATATGAAATAAATTGAAAAAAAA
Found at i:117603299 original size:3 final size:3
Alignment explanation
Indices: 117603293--117603406 Score: 83
Period size: 3 Copynumber: 38.7 Consensus size: 3
117603283 AGAAGACAAT
* * * * *
117603293 ATA ATA ATA ATA GTA GTA GTA AT- ACA ATA GTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
117603340 A-A ATA GA-A ATA ATA ATA GTG ATGA A-A ATA ATA ATA ATA GTA ATA
1 ATA ATA -ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA
* * *
117603384 ATT ACA ATA ATA ATT ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA AT
117603407 GAAACACATG
Statistics
Matches: 87, Mismatches: 18, Indels: 12
0.74 0.15 0.10
Matches are distributed among these distances:
2 6 0.07
3 79 0.91
4 2 0.02
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:117604289 original size:20 final size:19
Alignment explanation
Indices: 117604248--117604290 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
117604238 TTGAAATAGC
* **
117604248 AAATAAAAAAGGGAAATCG
1 AAATAAAAAAAGGAAAAAG
117604267 AAATGAAAAAAAGGAAAAAG
1 AAAT-AAAAAAAGGAAAAAG
117604287 AAAT
1 AAAT
117604291 CCAAGATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (19 bp):
AAATAAAAAAAGGAAAAAG
Found at i:117605156 original size:16 final size:17
Alignment explanation
Indices: 117605135--117605166 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
117605125 ATAAGATTAA
117605135 AATTATG-AAATAAAGT
1 AATTATGAAAATAAAGT
117605151 AATTATGAAAATAAAG
1 AATTATGAAAATAAAG
117605167 ATGTATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.28
Consensus pattern (17 bp):
AATTATGAAAATAAAGT
Found at i:117615125 original size:3 final size:3
Alignment explanation
Indices: 117615119--117615202 Score: 168
Period size: 3 Copynumber: 28.0 Consensus size: 3
117615109 TTGTTGTTAC
117615119 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
117615167 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
117615203 GTAATCTCTG
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:117615584 original size:3 final size:3
Alignment explanation
Indices: 117615576--117615622 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
117615566 TGGTGTGGAA
* * *
117615576 ATT ATT ATT ATT GTT ATT ATT ATT ATT TTT ATT ATT TTT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
117615623 GTAATCTCCG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:117615709 original size:21 final size:21
Alignment explanation
Indices: 117615680--117615729 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
117615670 CTGGTATATG
117615680 GTTAGTCAAGTAGTTAGTATTT
1 GTTA-TCAAGTAGTTAGTATTT
* *
117615702 GTTATCAAGTGGTTAGTGTTT
1 GTTATCAAGTAGTTAGTATTT
117615723 GTTATCA
1 GTTATCA
117615730 CTCACTAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.46
Consensus pattern (21 bp):
GTTATCAAGTAGTTAGTATTT
Found at i:117615959 original size:10 final size:10
Alignment explanation
Indices: 117615944--117615969 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
117615934 TCAAGTAAAT
117615944 ATTTCATGCG
1 ATTTCATGCG
117615954 ATTTCATGCG
1 ATTTCATGCG
117615964 ATTTCA
1 ATTTCA
117615970 AGTAAAGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.42
Consensus pattern (10 bp):
ATTTCATGCG
Found at i:117616460 original size:15 final size:15
Alignment explanation
Indices: 117616428--117616498 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 15
117616418 ATTTTATTGA
117616428 AAAT-TTTTAAT-AT
1 AAATATTTTAATAAT
*
117616441 TAATATTTTAATAAT
1 AAATATTTTAATAAT
*
117616456 AAATATTTACTACAATTAT
1 AAATATTT--T--AATAAT
*
117616475 AAATATATTAATAAT
1 AAATATTTTAATAAT
*
117616490 AAATGTTTT
1 AAATATTTT
117616499 GTAGTATAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
13 3 0.07
14 7 0.16
15 21 0.47
17 2 0.04
19 12 0.27
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (15 bp):
AAATATTTTAATAAT
Found at i:117617942 original size:27 final size:27
Alignment explanation
Indices: 117617912--117617969 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
117617902 AGATAATTAA
117617912 AATAA-AATCTTAA-ATTTGAATAATCCT
1 AATAATAATCTTAATA-TT-AATAATCCT
* *
117617939 AATAATTATCTTAATATTAATTATCCT
1 AATAATAATCTTAATATTAATAATCCT
117617966 AATA
1 AATA
117617970 GAATAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 17 0.63
28 9 0.33
29 1 0.04
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (27 bp):
AATAATAATCTTAATATTAATAATCCT
Found at i:117624222 original size:9 final size:9
Alignment explanation
Indices: 117624207--117624258 Score: 68
Period size: 9 Copynumber: 5.8 Consensus size: 9
117624197 TTTTGGTAAA
117624207 AAATTAACC
1 AAATTAACC
*
117624216 GAATTAACC
1 AAATTAACC
*
117624225 AAATTAACT
1 AAATTAACC
*
117624234 TAATTAACC
1 AAATTAACC
117624243 AAATTAACC
1 AAATTAACC
*
117624252 GAATTAA
1 AAATTAA
117624259 ATCACTGCAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.52, C:0.17, G:0.04, T:0.27
Consensus pattern (9 bp):
AAATTAACC
Found at i:117624230 original size:18 final size:18
Alignment explanation
Indices: 117624207--117624258 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
117624197 TTTTGGTAAA
117624207 AAATTAACCGAATTAACC
1 AAATTAACCGAATTAACC
**
117624225 AAATTAACTTAATTAACC
1 AAATTAACCGAATTAACC
117624243 AAATTAACCGAATTAA
1 AAATTAACCGAATTAA
117624259 ATCACTGCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.52, C:0.17, G:0.04, T:0.27
Consensus pattern (18 bp):
AAATTAACCGAATTAACC
Found at i:117624360 original size:17 final size:17
Alignment explanation
Indices: 117624301--117624361 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
117624291 TTTGAATCCC
*
117624301 TACATAATAAAAAACAT
1 TACATAATTAAAAACAT
** * *
117624318 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
117624338 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
117624355 TACATAA
1 TACATAA
117624362 GTCTTGAAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 20 0.62
20 12 0.38
ACGTcount: A:0.52, C:0.15, G:0.03, T:0.30
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:117624383 original size:37 final size:37
Alignment explanation
Indices: 117624258--117624366 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
117624248 AACCGAATTA
*
117624258 AATCACTGCATAATTAAAAACATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
* *
117624295 AATCCCTACATAATAAAAAACATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
117624332 AATCACTACATAATTAAAAACATTACATAAGTCTT
1 AATCACTACATAATTAAAAACATTACATAAGTCTT
117624367 GAAATTAACA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (37 bp):
AATCACTACATAATTAAAAACATTACATAAGTCTTTG
Found at i:117627104 original size:71 final size:71
Alignment explanation
Indices: 117627027--117627240 Score: 410
Period size: 71 Copynumber: 3.0 Consensus size: 71
117627017 TTACCCTTCG
*
117627027 ACAACAAATAAAAATAAGCAAAAATTACAACAATAAATCAATGAATCTTAAACTAAATAAAGTTA
1 ACAACAAATAAAAATAAGCAAAAATTACAACAATAAATCAATGAATCTTAAACTAAATAAATTTA
117627092 ATTAGA
66 ATTAGA
117627098 ACAACAAATAAAAATAAGCAAAAATTACAACAATAAATCAATGAATCTTAAACTAAATAAATTTA
1 ACAACAAATAAAAATAAGCAAAAATTACAACAATAAATCAATGAATCTTAAACTAAATAAATTTA
117627163 ATTAGA
66 ATTAGA
*
117627169 ACAACAAATAAAAATAAGTAAAAATTACAACAATAAATCAATGAATCTTAAACTAAATAAATTTA
1 ACAACAAATAAAAATAAGCAAAAATTACAACAATAAATCAATGAATCTTAAACTAAATAAATTTA
117627234 ATTAGA
66 ATTAGA
117627240 A
1 A
117627241 GATTGTAAAT
Statistics
Matches: 141, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 141 1.00
ACGTcount: A:0.61, C:0.11, G:0.05, T:0.24
Consensus pattern (71 bp):
ACAACAAATAAAAATAAGCAAAAATTACAACAATAAATCAATGAATCTTAAACTAAATAAATTTA
ATTAGA
Found at i:117627804 original size:20 final size:20
Alignment explanation
Indices: 117627779--117627820 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
117627769 TACAAATATG
* *
117627779 ATTAAATATCATTATAAAAT
1 ATTAAATAACATCATAAAAT
*
117627799 ATTAAATAAGATCATAAAAT
1 ATTAAATAACATCATAAAAT
117627819 AT
1 AT
117627821 CTCAAAAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (20 bp):
ATTAAATAACATCATAAAAT
Found at i:117628185 original size:13 final size:13
Alignment explanation
Indices: 117628148--117628204 Score: 66
Period size: 13 Copynumber: 4.6 Consensus size: 13
117628138 AATAAAAATT
*
117628148 ATTGGGTTGGGAA
1 ATTGGGTTGGGTA
*
117628161 ATTAGGTTGGGTA
1 ATTGGGTTGGGTA
117628174 ATTGGGTTGGG--
1 ATTGGGTTGGGTA
117628185 -TTGGGTTGGGTA
1 ATTGGGTTGGGTA
*
117628197 GTTGGGTT
1 ATTGGGTT
117628205 TAAATATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
10 10 0.26
13 28 0.74
ACGTcount: A:0.14, C:0.00, G:0.47, T:0.39
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:117637648 original size:46 final size:46
Alignment explanation
Indices: 117637581--117637755 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
117637571 TGTAACCCGC
117637581 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
117637627 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * ** *
117637677 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
117637720 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
117637756 ATGCTCAACC
Statistics
Matches: 109, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 63 0.58
47 26 0.24
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:117637701 original size:93 final size:93
Alignment explanation
Indices: 117637589--117637759 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
117637579 GCCCATAAGT
** *
117637589 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
117637654 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
*
117637682 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
117637747 CGAGTTCGGATGC
66 CGAGCTCGGATGC
117637760 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:117641416 original size:23 final size:23
Alignment explanation
Indices: 117641364--117641421 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
117641354 ATAGATATTT
* *
117641364 AATTATTATCATGGTTTATATAA
1 AATTATGATTATGGTTTATATAA
117641387 AATTATGATTATGGTTT-TATAA
1 AATTATGATTATGGTTTATATAA
*
117641409 TTATTATGATTAT
1 -AATTATGATTAT
117641422 TTAATGGATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 5 0.16
23 26 0.84
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (23 bp):
AATTATGATTATGGTTTATATAA
Found at i:117644767 original size:46 final size:46
Alignment explanation
Indices: 117644715--117645033 Score: 408
Period size: 46 Copynumber: 7.0 Consensus size: 46
117644705 AGTGTGCTCT
*
117644715 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
117644761 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
117644807 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGC-AC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
117644852 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** *** * *
117644898 ATGACGGGAAATAAATAAGACCATGGTTGACAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * **
117644944 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
117644990 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
117645034 TCATGTCAAA
Statistics
Matches: 246, Mismatches: 25, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
45 45 0.18
46 201 0.82
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:117644963 original size:137 final size:138
Alignment explanation
Indices: 117644715--117645054 Score: 427
Period size: 137 Copynumber: 2.5 Consensus size: 138
117644705 AGTGTGCTCT
* * * * ***
117644715 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACCTGATATGAAATGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATAAATAAG
* **
117644780 ACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAACGTGTAAGACCATGGTTGAAAGATACC
66 ACCATGGTTGAAAGATACCATGGCAGCCTGACATGAAACGAATAAGACCATGGTTGAAAGATACC
117644845 ATGGC-AC
131 ATGGCAAC
* *
117644852 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGAAATAAATAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATAAATAAG
* * *
117644917 ACCATGGTTGACAGATACCATGGCAGCGTGACATGAAATGAATAAGACCATGGTTGAAAGATACC
66 ACCATGGTTGAAAGATACCATGGCAGCCTGACATGAAACGAATAAGACCATGGTTGAAAGATACC
117644982 ATGGCAAC
131 ATGGCAAC
* * * * * * * *
117644990 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATGTCA--AAGATAAATA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAA-ATAAATA
117645052 AGA
64 AGA
117645055 TCGTGGATGG
Statistics
Matches: 175, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
136 2 0.01
137 131 0.75
138 42 0.24
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.21
Consensus pattern (138 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATAAATAAG
ACCATGGTTGAAAGATACCATGGCAGCCTGACATGAAACGAATAAGACCATGGTTGAAAGATACC
ATGGCAAC
Found at i:117648636 original size:3 final size:3
Alignment explanation
Indices: 117648628--117648676 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
117648618 CATTCTCATT
117648628 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
117648676 T
1 T
117648677 GCCCTTTTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:117653566 original size:18 final size:18
Alignment explanation
Indices: 117653543--117653579 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
117653533 TCTTGATATC
117653543 ACAGTCAAAGTTGTATTT
1 ACAGTCAAAGTTGTATTT
117653561 ACAGTCAAAGTTGTATTT
1 ACAGTCAAAGTTGTATTT
117653579 A
1 A
117653580 TCCTTGGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (18 bp):
ACAGTCAAAGTTGTATTT
Found at i:117654090 original size:21 final size:21
Alignment explanation
Indices: 117654061--117654112 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
117654051 TAAACCTTAA
117654061 AAATTATAAAAAAT-AAAAAT
1 AAATTATAAAAAATCAAAAAT
*
117654081 AAATATATAAAAATTCAAAAAT
1 AAAT-TATAAAAAATCAAAAAT
*
117654103 -ACTTATAAAA
1 AAATTATAAAA
117654113 GGAATTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 11 0.39
21 11 0.39
22 6 0.21
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATTATAAAAAATCAAAAAT
Found at i:117655200 original size:25 final size:25
Alignment explanation
Indices: 117655166--117655230 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 25
117655156 AGGCGCGACC
117655166 TATTTTTTTAATAATATAATT-TATT
1 TATTTTTTTAATAATATAATTAT-TT
*
117655191 TATTTTTTT-A-AATATTATTATTT
1 TATTTTTTTAATAATATAATTATTT
117655214 TATTATATTTTAATAAT
1 TATT-T-TTTTAATAAT
117655231 TTTTAAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
23 14 0.41
24 3 0.09
25 13 0.38
26 1 0.03
27 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TATTTTTTTAATAATATAATTATTT
Found at i:117655204 original size:26 final size:27
Alignment explanation
Indices: 117655166--117655224 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 27
117655156 AGGCGCGACC
117655166 TATTTTTTTAATAATA-TAATTTATT-
1 TATTTTTTTAATAATATTAATTTATTA
* *
117655191 TATTTTTTTAAATATTATTATTTTATTA
1 TATTTTTTT-AATAATATTAATTTATTA
117655219 TATTTT
1 TATTTT
117655225 AATAATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 9 0.31
26 6 0.21
27 8 0.28
28 6 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (27 bp):
TATTTTTTTAATAATATTAATTTATTA
Found at i:117655312 original size:27 final size:27
Alignment explanation
Indices: 117655282--117655341 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
117655272 GCCAGACCCG
117655282 GAGGCGCGACCAGTCGCTCCTGCTGCA
1 GAGGCGCGACCAGTCGCTCCTGCTGCA
117655309 GAGGCGCGACCAGTCGCTCCTGCTGCA
1 GAGGCGCGACCAGTCGCTCCTGCTGCA
117655336 GAGGCG
1 GAGGCG
117655342 TGACTCCCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.15, C:0.35, G:0.37, T:0.13
Consensus pattern (27 bp):
GAGGCGCGACCAGTCGCTCCTGCTGCA
Found at i:117659370 original size:24 final size:24
Alignment explanation
Indices: 117659341--117659389 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
117659331 CTCTGGCCCC
117659341 GCTCTGGGTCCGGCACTGCCTCCG
1 GCTCTGGGTCCGGCACTGCCTCCG
* * * *
117659365 GCTCTGGTTCTGGCTCTGGCTCCG
1 GCTCTGGGTCCGGCACTGCCTCCG
117659389 G
1 G
117659390 AGCTAGTGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.02, C:0.37, G:0.35, T:0.27
Consensus pattern (24 bp):
GCTCTGGGTCCGGCACTGCCTCCG
Found at i:117660461 original size:11 final size:11
Alignment explanation
Indices: 117660447--117660474 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
117660437 ACATTATATC
117660447 AAAATTACATT
1 AAAATTACATT
117660458 AAAATTACATT
1 AAAATTACATT
117660469 AAAATT
1 AAAATT
117660475 TCTTACTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (11 bp):
AAAATTACATT
Found at i:117661558 original size:3 final size:3
Alignment explanation
Indices: 117661531--117661598 Score: 68
Period size: 3 Copynumber: 22.7 Consensus size: 3
117661521 ACTAACATTT
* * * *
117661531 TTC TTC TTTC TCC TCC TTC TCC TTC TTC TTC TTC TTC TTT TTC TT-
1 TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
117661576 TTC TTC TTC TTC TT- TTC TCTC TT
1 TTC TTC TTC TTC TTC TTC T-TC TT
117661599 TGCTGCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
2 4 0.07
3 45 0.82
4 6 0.11
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:117661598 original size:23 final size:23
Alignment explanation
Indices: 117661553--117661599 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
117661543 CTCCTTCTCC
*
117661553 TTCTTCTTCTTCTTCTTTTTCTT
1 TTCTTCTTCTTCTTCTTTCTCTT
117661576 TTCTTCTTCTTCTT-TTCTCTCTT
1 TTCTTCTTCTTCTTCTT-TCTCTT
117661599 T
1 T
117661600 GCTGCTGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (23 bp):
TTCTTCTTCTTCTTCTTTCTCTT
Found at i:117661766 original size:27 final size:27
Alignment explanation
Indices: 117661728--117661791 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
117661718 CTGCAGGGGA
117661728 GTCGCGCCTCTGCAGCAGGAGCGACTG
1 GTCGCGCCTCTGCAGCAGGAGCGACTG
*
117661755 GTCGTGCCTCTGCAGCAGGAGCGACTG
1 GTCGCGCCTCTGCAGCAGGAGCGACTG
117661782 GTCGCGCCTC
1 GTCGCGCCTC
117661792 CGGGTCTGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.12, C:0.34, G:0.36, T:0.17
Consensus pattern (27 bp):
GTCGCGCCTCTGCAGCAGGAGCGACTG
Found at i:117661889 original size:26 final size:27
Alignment explanation
Indices: 117661849--117661907 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 27
117661839 AAAAATTATT
117661849 AAAATATAATAAAATAATAATATTTAAA
1 AAAATATAATAAAATAATAATA-TTAAA
* *
117661877 AAAATA-AAT-AAATTATATTATTAAA
1 AAAATATAATAAAATAATAATATTAAA
117661902 AAAATA
1 AAAATA
117661908 GGTCGCGCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 11 0.38
26 9 0.31
27 3 0.10
28 6 0.21
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (27 bp):
AAAATATAATAAAATAATAATATTAAA
Found at i:117662375 original size:9 final size:9
Alignment explanation
Indices: 117662358--117662403 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
117662348 TTAAAATTTT
*
117662358 AAATATAAA
1 AAATTTAAA
117662367 AAATTT-AA
1 AAATTTAAA
117662375 AAATTTAAA
1 AAATTTAAA
*
117662384 AAATTTTAA
1 AAATTTAAA
*
117662393 AAATATAAA
1 AAATTTAAA
117662402 AA
1 AA
117662404 TAAAAAGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
8 8 0.25
9 24 0.75
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
AAATTTAAA
Found at i:117662378 original size:17 final size:18
Alignment explanation
Indices: 117662350--117662403 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
117662340 GAAATTAATT
117662350 AAAATTTT--AAATATAA
1 AAAATTTTAAAAATATAA
*
117662366 AAAA-TTTAAAAATTTAA
1 AAAATTTTAAAAATATAA
117662383 AAAATTTTAAAAATATAA
1 AAAATTTTAAAAATATAA
117662401 AAA
1 AAA
117662404 TAAAAAGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 3 0.09
16 4 0.12
17 11 0.33
18 15 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATTTTAAAAATATAA
Found at i:117662405 original size:8 final size:8
Alignment explanation
Indices: 117662358--117662426 Score: 59
Period size: 8 Copynumber: 8.4 Consensus size: 8
117662348 TTAAAATTTT
117662358 AAATATAAA
1 AAATAT-AA
*
117662367 AAATTTAA
1 AAATATAA
*
117662375 AAATTTAAA
1 AAATAT-AA
*
117662384 AAATTTTAA
1 AAA-TATAA
117662393 AAATATAA
1 AAATATAA
117662401 AAATA-AA
1 AAATATAA
*
117662408 AAGTATAA
1 AAATATAA
*
117662416 AATTATAA
1 AAATATAA
117662424 AAA
1 AAA
117662427 AATTTTAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
7 6 0.12
8 28 0.54
9 15 0.29
10 3 0.06
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (8 bp):
AAATATAA
Found at i:117662407 original size:41 final size:41
Alignment explanation
Indices: 117662356--117662444 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 41
117662346 AATTAAAATT
* *
117662356 TTAAATATAAAAAATTTAAAAATT-T-AAAAAATTTTAAAAA
1 TTAAAAATAAAAAATAT-AAAATTATAAAAAAATTTTAAAAA
* *
117662396 TATAAAAATAAAAAGTATAAAATTATAAAAAAATTTTAAATA
1 T-TAAAAATAAAAAATATAAAATTATAAAAAAATTTTAAAAA
117662438 TTAAAAA
1 TTAAAAA
117662445 AATAATTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
40 7 0.17
41 20 0.48
42 15 0.36
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (41 bp):
TTAAAAATAAAAAATATAAAATTATAAAAAAATTTTAAAAA
Found at i:117662417 original size:33 final size:32
Alignment explanation
Indices: 117662350--117662417 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
117662340 GAAATTAATT
* *
117662350 AAAATTTTAAATATAAAAAATTTAAAAATTTAA
1 AAAATTTTAAAAATAAAAAA-TTAAAAATATAA
117662383 AAAATTTTAAAAATATAAAAA-TAAAAAGTATAA
1 AAAATTTTAAAAATA-AAAAATTAAAAA-TATAA
117662416 AA
1 AA
117662418 TTATAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 6 0.19
33 20 0.65
34 5 0.16
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (32 bp):
AAAATTTTAAAAATAAAAAATTAAAAATATAA
Found at i:117662423 original size:17 final size:16
Alignment explanation
Indices: 117662349--117662426 Score: 63
Period size: 17 Copynumber: 4.9 Consensus size: 16
117662339 AGAAATTAAT
* *
117662349 TAAAATTTTAAATATA
1 TAAAATTATAAAAATA
*
117662365 AAAAATT-TAAAAATTTA
1 TAAAATTATAAAAA--TA
* *
117662382 AAAAATTTTAAAAATA
1 TAAAATTATAAAAATA
117662398 TAAAA--ATAAAAAGTA
1 TAAAATTATAAAAA-TA
117662413 TAAAATTATAAAAA
1 TAAAATTATAAAAA
117662427 AATTTTAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
14 6 0.12
15 12 0.23
16 12 0.23
17 16 0.31
18 6 0.12
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (16 bp):
TAAAATTATAAAAATA
Found at i:117662453 original size:19 final size:18
Alignment explanation
Indices: 117662421--117662460 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
117662411 TATAAAATTA
*
117662421 TAAAAAAATTTTAAATAT
1 TAAAAAAATATTAAATAT
*
117662439 TAAAAAAATAATTAATTAT
1 TAAAAAAAT-ATTAAATAT
117662458 TAA
1 TAA
117662461 TGTGGTAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAAAAATATTAAATAT
Found at i:117669408 original size:26 final size:27
Alignment explanation
Indices: 117669380--117669434 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
117669370 GATTATTAAT
* *
117669380 AAAATAATATTTTATTTTAT-TTTCATA
1 AAAAT-ATATATTAATTTATATTTCATA
117669407 AAAATATATATTAATTTATATTTC-TA
1 AAAATATATATTAATTTATATTTCATA
117669433 AA
1 AA
117669435 GAAAATAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (27 bp):
AAAATATATATTAATTTATATTTCATA
Found at i:117674567 original size:25 final size:25
Alignment explanation
Indices: 117674513--117674567 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
117674503 AGCCAATGAT
117674513 TAAAAATAAAAAATATTAAATTATA
1 TAAAAATAAAAAATATTAAATTATA
* *
117674538 GAAAAA-ACAAAATGATTAAAATT-TA
1 TAAAAATAAAAAAT-ATT-AAATTATA
117674563 TAAAA
1 TAAAA
117674568 GAAGAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 6 0.24
25 14 0.56
26 5 0.20
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (25 bp):
TAAAAATAAAAAATATTAAATTATA
Found at i:117678314 original size:159 final size:159
Alignment explanation
Indices: 117678025--117678346 Score: 644
Period size: 159 Copynumber: 2.0 Consensus size: 159
117678015 AAAAAATCAT
117678025 ACAAAATTTAATTCTCAGGGAAGAGAGGTGGATCACATGGATCTCTTAAATACCAAGTCTTTCCT
1 ACAAAATTTAATTCTCAGGGAAGAGAGGTGGATCACATGGATCTCTTAAATACCAAGTCTTTCCT
117678090 TAGTCAGAATATTCCTTCTATAGTAATTTAATAGCACAATTAAATACTACTATTATACCCTCAAA
66 TAGTCAGAATATTCCTTCTATAGTAATTTAATAGCACAATTAAATACTACTATTATACCCTCAAA
117678155 TATTGAAAGAAAATAGGACAAGAAAAAAC
131 TATTGAAAGAAAATAGGACAAGAAAAAAC
117678184 ACAAAATTTAATTCTCAGGGAAGAGAGGTGGATCACATGGATCTCTTAAATACCAAGTCTTTCCT
1 ACAAAATTTAATTCTCAGGGAAGAGAGGTGGATCACATGGATCTCTTAAATACCAAGTCTTTCCT
117678249 TAGTCAGAATATTCCTTCTATAGTAATTTAATAGCACAATTAAATACTACTATTATACCCTCAAA
66 TAGTCAGAATATTCCTTCTATAGTAATTTAATAGCACAATTAAATACTACTATTATACCCTCAAA
117678314 TATTGAAAGAAAATAGGACAAGAAAAAAC
131 TATTGAAAGAAAATAGGACAAGAAAAAAC
117678343 ACAA
1 ACAA
117678347 GAGTTTTAAC
Statistics
Matches: 163, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 163 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (159 bp):
ACAAAATTTAATTCTCAGGGAAGAGAGGTGGATCACATGGATCTCTTAAATACCAAGTCTTTCCT
TAGTCAGAATATTCCTTCTATAGTAATTTAATAGCACAATTAAATACTACTATTATACCCTCAAA
TATTGAAAGAAAATAGGACAAGAAAAAAC
Found at i:117685215 original size:19 final size:17
Alignment explanation
Indices: 117685187--117685243 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 17
117685177 TTGATGGCTC
*
117685187 ATATTATTAAATAATAA
1 ATATTTTTAAATAATAA
*
117685204 ATTTATTTTTAAATGTAACAA
1 A--TATTTTTAAA--TAATAA
117685225 ATATTATTTAAATAATAA
1 ATATT-TTTAAATAATAA
117685243 A
1 A
117685244 AGCAGACTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
17 1 0.03
18 6 0.19
19 13 0.41
20 6 0.19
21 6 0.19
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
ATATTTTTAAATAATAA
Found at i:117700066 original size:29 final size:29
Alignment explanation
Indices: 117699983--117700067 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
117699973 TAATTTTAAT
*
117699983 TTAATTATATATATTTAAATAAATAAATATA
1 TTAATT-TATATATAT-AATAAATAAATATA
* * *
117700014 TTAATTTATTTTTATATTAAATAAATATTA
1 TTAATTTATATATATAATAAATAAATA-TA
* *
117700044 TT-ATTTATATATGTAATATATAAA
1 TTAATTTATATATATAATAAATAAA
117700068 CATAAAATGA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
29 28 0.64
30 10 0.23
31 6 0.14
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
TTAATTTATATATATAATAAATAAATATA
Found at i:117700224 original size:5 final size:5
Alignment explanation
Indices: 117700214--117700241 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
117700204 AAATTTTAAA
117700214 TATTT TATTT TATTT TATTT TATTT TAT
1 TATTT TATTT TATTT TATTT TATTT TAT
117700242 AGAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:117703610 original size:28 final size:28
Alignment explanation
Indices: 117703570--117703625 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
117703560 TATTTATCAG
117703570 TTTCATTTAAAGAATGTGATTGTGTTTT
1 TTTCATTTAAAGAATGTGATTGTGTTTT
117703598 TTTCATTTAAAGAATGTGATTGTGTTTT
1 TTTCATTTAAAGAATGTGATTGTGTTTT
117703626 CATTATTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.04, G:0.18, T:0.54
Consensus pattern (28 bp):
TTTCATTTAAAGAATGTGATTGTGTTTT
Found at i:117706705 original size:25 final size:25
Alignment explanation
Indices: 117706676--117706725 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
117706666 TTAAAAGAGA
117706676 ATATTAGTACTCTTATAACAATAAT
1 ATATTAGTACTCTTATAACAATAAT
117706701 ATATTAGTACTCTTATAACAATAAT
1 ATATTAGTACTCTTATAACAATAAT
117706726 TTAAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (25 bp):
ATATTAGTACTCTTATAACAATAAT
Found at i:117707012 original size:18 final size:18
Alignment explanation
Indices: 117706986--117707020 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
117706976 TATAATTATT
*
117706986 TTTAAAAAAATTAAAAAC
1 TTTAAAAAAAATAAAAAC
*
117707004 TTTATAAAAAATAAAAA
1 TTTAAAAAAAATAAAAA
117707021 TTATTAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
TTTAAAAAAAATAAAAAC
Found at i:117707844 original size:31 final size:31
Alignment explanation
Indices: 117707804--117707873 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
117707794 TTATAATTTG
* *
117707804 GTCACTAAATTATTTAAAAATTTTCATTGAA
1 GTCATTAAATTATCTAAAAATTTTCATTGAA
* * *
117707835 GTCATTAAATTATCTAAAAGTTTTTATTTAA
1 GTCATTAAATTATCTAAAAATTTTCATTGAA
117707866 GTCATTAA
1 GTCATTAA
117707874 GATGCTAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (31 bp):
GTCATTAAATTATCTAAAAATTTTCATTGAA
Found at i:117712145 original size:26 final size:26
Alignment explanation
Indices: 117712032--117712148 Score: 82
Period size: 27 Copynumber: 4.6 Consensus size: 26
117712022 AATTCCGGAT
* * * *
117712032 AGCCATATATCGTGAAGTTCAAG-CG
1 AGCCATATATCGGGAAGCTCACGAAG
*
117712057 AGCCA-ATATCGGGAAGCTC-CGGAG
1 AGCCATATATCGGGAAGCTCACGAAG
* * * *
117712081 AGTCAT-TAATCAGGAAGCTCATGAAAT
1 AGCCATAT-ATCGGGAAGCTCACG-AAG
*
117712108 AGCC-TTTAATCGGGAAGCTCACGAAG
1 AGCCATAT-ATCGGGAAGCTCACGAAG
117712134 AGCCATATATCGGGA
1 AGCCATATATCGGGA
117712149 CACTCATAAA
Statistics
Matches: 71, Mismatches: 14, Indels: 13
0.72 0.14 0.13
Matches are distributed among these distances:
23 1 0.01
24 18 0.25
25 16 0.23
26 15 0.21
27 21 0.30
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.21
Consensus pattern (26 bp):
AGCCATATATCGGGAAGCTCACGAAG
Found at i:117713342 original size:17 final size:17
Alignment explanation
Indices: 117713312--117713345 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
117713302 GACCTCAAAT
117713312 TTTGAATTCCATAGCTA
1 TTTGAATTCCATAGCTA
117713329 TTTG-ATTCCTATAGCTA
1 TTTGAATTCC-ATAGCTA
117713346 CTAGAACTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.44
Consensus pattern (17 bp):
TTTGAATTCCATAGCTA
Found at i:117716811 original size:47 final size:46
Alignment explanation
Indices: 117716703--117716871 Score: 230
Period size: 46 Copynumber: 3.7 Consensus size: 46
117716693 GTGTAAGACC
* *
117716703 ATAAGACCATAGTTGAAAGATACCATGGCAACGTGACATGAAATGT
1 ATAAGACCATAGTTGAAAGATACCATGGCAACGTGACAGGAAATGA
* *
117716749 GTAAGACCATGGTTGAAAGATACCATGGCAACGTGACAGGGAAATGA
1 ATAAGACCATAGTTGAAAGATACCATGGCAACGTGACA-GGAAATGA
* * * *
117716796 ATAAGACCATGGTTGAATGATACCATGGCAACATGACAGAAAATGA
1 ATAAGACCATAGTTGAAAGATACCATGGCAACGTGACAGGAAATGA
* * *
117716842 GTAAGACCATAGTTGAAAGACACTATGGCA
1 ATAAGACCATAGTTGAAAGATACCATGGCA
117716872 TCATGTCGAA
Statistics
Matches: 109, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
46 68 0.62
47 41 0.38
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (46 bp):
ATAAGACCATAGTTGAAAGATACCATGGCAACGTGACAGGAAATGA
Found at i:117716833 original size:93 final size:93
Alignment explanation
Indices: 117716703--117716871 Score: 259
Period size: 93 Copynumber: 1.8 Consensus size: 93
117716693 GTGTAAGACC
* * *
117716703 ATAAGACCATAGTTGAAAGATACCATGGCAACGTGACATG-AAATGTGTAAGACCATGGTTGAAA
1 ATAAGACCATAGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAAGACCATAGTTGAAA
*
117716767 GATACCATGGCAACGTGACAGGGAAATGA
65 GACACCATGGCAACGTGACAGGGAAATGA
* *
117716796 ATAAGACCATGGTTGAATGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAG
1 ATAAGACCATAGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAG
*
117716861 ACACTATGGCA
66 ACACCATGGCA
117716872 TCATGTCGAA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
92 1 0.01
93 67 0.99
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (93 bp):
ATAAGACCATAGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAG
ACACCATGGCAACGTGACAGGGAAATGA
Found at i:117721166 original size:26 final size:25
Alignment explanation
Indices: 117721123--117721171 Score: 89
Period size: 26 Copynumber: 1.9 Consensus size: 25
117721113 TCACTTTTTT
117721123 GAACTAAGAAAAAAAAAACAGGGGG
1 GAACTAAGAAAAAAAAAACAGGGGG
117721148 GAACTAAGGAAAAAAAAAACAGGG
1 GAACTAA-GAAAAAAAAAACAGGG
117721172 ATTTGGGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.61, C:0.08, G:0.27, T:0.04
Consensus pattern (25 bp):
GAACTAAGAAAAAAAAAACAGGGGG
Found at i:117724190 original size:7 final size:7
Alignment explanation
Indices: 117724178--117724202 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
117724168 AATTAAGGAA
117724178 ATGAAAT
1 ATGAAAT
117724185 ATGAAAT
1 ATGAAAT
117724192 ATGAAAT
1 ATGAAAT
117724199 ATGA
1 ATGA
117724203 TTGAACTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (7 bp):
ATGAAAT
Found at i:117724849 original size:13 final size:14
Alignment explanation
Indices: 117724831--117724862 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
117724821 TTATTTGTCC
117724831 TTATTTATTTATT-
1 TTATTTATTTATTA
117724844 TTATTTATTTATTA
1 TTATTTATTTATTA
117724858 TTATT
1 TTATT
117724863 GAATTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTATTTATTTATTA
Found at i:117726806 original size:6 final size:6
Alignment explanation
Indices: 117726795--117726828 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
117726785 CACCGCAACG
* *
117726795 GTAACA GTAACA GTAACA GTCACA GTAACG GTAA
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTAA
117726829 TGGTACACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.18
Consensus pattern (6 bp):
GTAACA
Found at i:117730981 original size:23 final size:21
Alignment explanation
Indices: 117730908--117730980 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 21
117730898 GTTTATTTTA
*
117730908 TTAAAAAATATATTTAATATT
1 TTAAAAAATATATTTAAAATT
* *
117730929 TAAAAAAATATATTATAAAACAT
1 TTAAAAAATATATT-TAAAA-TT
* *
117730952 TTCAAATATATATTTCAAAATT
1 TTAAAAAATATATTT-AAAATT
*
117730974 TTTAAAA
1 TTAAAAA
117730981 TTAATAATAA
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 13 0.32
22 11 0.28
23 16 0.40
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAAAAAATATATTTAAAATT
Found at i:117731093 original size:29 final size:29
Alignment explanation
Indices: 117731038--117731093 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
117731028 AAAAAAGTAA
*
117731038 TAAAAAACAAAGTAATATAAGACAAAACT
1 TAAAAAACAAAGTAATATAAGAAAAAACT
*
117731067 TAAAAAA-AAAGTAATAATAATAAAAAA
1 TAAAAAACAAAGTAAT-ATAAGAAAAAA
117731094 GAACAAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.18
Consensus pattern (29 bp):
TAAAAAACAAAGTAATATAAGAAAAAACT
Found at i:117731713 original size:20 final size:20
Alignment explanation
Indices: 117731688--117731727 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
117731678 GAGGCCGAAA
117731688 ACCATACCGTACAAGTTGAG
1 ACCATACCGTACAAGTTGAG
117731708 ACCATACCGTACAAGTTGAG
1 ACCATACCGTACAAGTTGAG
117731728 TTTATATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
ACCATACCGTACAAGTTGAG
Found at i:117735078 original size:13 final size:13
Alignment explanation
Indices: 117735051--117735113 Score: 65
Period size: 13 Copynumber: 4.9 Consensus size: 13
117735041 ACACTTAAAT
* *
117735051 TTTTTAAAAGTAC
1 TTTTCAAAAGCAC
*
117735064 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
117735077 TTTTCCAAATCAC
1 TTTTCAAAAGCAC
*
117735090 TTTTCAAAA-AAC
1 TTTTCAAAAGCAC
117735102 TTTTCAAAAGCA
1 TTTTCAAAAGCA
117735114 ATGAAGAACT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
12 11 0.28
13 29 0.73
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.35
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:117742212 original size:2 final size:2
Alignment explanation
Indices: 117742205--117742231 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
117742195 CTTATAAAAC
117742205 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 A
117742232 AAGCTAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:117744367 original size:23 final size:23
Alignment explanation
Indices: 117744317--117744368 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
117744307 AAATATGGAT
* * * *
117744317 TTTTTAAATTTATTTATTTATTA
1 TTTTTAAACTTATTAATATAATA
*
117744340 ATTTTAAACTTATTAATATAATA
1 TTTTTAAACTTATTAATATAATA
117744363 TTTTTA
1 TTTTTA
117744369 TATTTTTATT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTTAAACTTATTAATATAATA
Found at i:117744680 original size:29 final size:27
Alignment explanation
Indices: 117744627--117744684 Score: 64
Period size: 29 Copynumber: 2.0 Consensus size: 27
117744617 CAACTAAAAA
*
117744627 AAAATTATTTTTAAAAATTAAAAATCATT
1 AAAATTA-TTTTAAAAAATAAAAAT-ATT
117744656 AAAATTA-TTTAAAAAATAGATAAATATT
1 AAAATTATTTTAAAAAATA-A-AAATATT
117744684 A
1 A
117744685 GCGTGTCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
27 10 0.38
28 5 0.19
29 11 0.42
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (27 bp):
AAAATTATTTTAAAAAATAAAAATATT
Found at i:117748821 original size:46 final size:46
Alignment explanation
Indices: 117748771--117748946 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
117748761 TGGTTGAGCA
117748771 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
117748817 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
117748862 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
117748910 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
117748947 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:117748927 original size:93 final size:93
Alignment explanation
Indices: 117748768--117748939 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
117748758 GGATGGTTGA
* *
117748768 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
117748833 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
117748861 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
117748926 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
117748940 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:117756400 original size:46 final size:46
Alignment explanation
Indices: 117756350--117756525 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
117756340 TGGTTGAGCA
117756350 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
117756396 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
117756441 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
117756489 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
117756526 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:117756506 original size:93 final size:93
Alignment explanation
Indices: 117756347--117756518 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
117756337 GGATGGTTGA
* *
117756347 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
117756412 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
117756440 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
117756505 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
117756519 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:117766332 original size:39 final size:39
Alignment explanation
Indices: 117766248--117766400 Score: 225
Period size: 39 Copynumber: 3.9 Consensus size: 39
117766238 TATGGTAACC
** * *
117766248 CGCACAAAGGCCTTCGGGACTTAACCCGGATATCACAATT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
117766288 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
117766327 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
117766366 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
117766401 TCGAACATTC
Statistics
Matches: 103, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 88 0.85
40 15 0.15
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:117766373 original size:78 final size:79
Alignment explanation
Indices: 117766217--117766399 Score: 278
Period size: 78 Copynumber: 2.3 Consensus size: 79
117766207 TCGTTCAAAC
* * **
117766217 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATC
1 GCCTTCGGG-CTTAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATC
117766282 ACAATTTGCACAATT
65 ACAATTTGCACAATT
* ** *
117766297 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGG-CTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATCA
117766361 CAATTTGCACAATT
66 CAATTTGCACAATT
117766375 GCCTTCGGGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
117766400 CTCGAACATT
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
78 54 0.57
79 32 0.34
80 9 0.09
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (79 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATCA
CAATTTGCACAATT
Found at i:117775020 original size:5 final size:5
Alignment explanation
Indices: 117775010--117775039 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
117775000 GTTATTTTGC
117775010 ATTTT ATTTT ATTTT ATTTT ATTTAT ATTT
1 ATTTT ATTTT ATTTT ATTTT ATTT-T ATTT
117775040 ATGATTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:117776086 original size:24 final size:25
Alignment explanation
Indices: 117776039--117776095 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
117776029 TTTGTCCATA
*
117776039 TTATT-TTTAATATTTTGAAAATAT
1 TTATTATTTAATAATTTGAAAATAT
*
117776063 TTATTATTTAATAATTT-AATATAT
1 TTATTATTTAATAATTTGAAAATAT
117776087 TT-TTATTTA
1 TTATTATTTA
117776096 TTAAAATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 7 0.23
24 13 0.43
25 10 0.33
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TTATTATTTAATAATTTGAAAATAT
Found at i:117776107 original size:23 final size:24
Alignment explanation
Indices: 117776059--117776111 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
117776049 TATTTTGAAA
*
117776059 ATATTTATTATTTAATAATTTAAT
1 ATATTTATTATTTAATAAATTAAT
*
117776083 ATATTT-TTATTTATTAAAATTATAT
1 ATATTTATTATTTAAT-AAATTA-AT
117776108 ATAT
1 ATAT
117776112 AAACAACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.32
24 11 0.44
25 6 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATATTTATTATTTAATAAATTAAT
Found at i:117776960 original size:2 final size:2
Alignment explanation
Indices: 117776953--117776985 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
117776943 TACATTACAC
*
117776953 AT AT AT AT AT AT AT AT AT AT AT AT -T TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
117776986 TTAAGGTAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:117778260 original size:79 final size:79
Alignment explanation
Indices: 117778129--117778289 Score: 313
Period size: 79 Copynumber: 2.0 Consensus size: 79
117778119 AGGAATAAGC
117778129 TAAGCAACTATCACACCGACAGCACGATACCATATAATTATCATTTTAACATTTAATTTTATATA
1 TAAGCAACTATCACACCGACAGCACGATACCATATAATTATCATTTTAACATTTAATTTTATATA
117778194 TTATAAATAAATTA
66 TTATAAATAAATTA
*
117778208 TAAGCAACTATCACACCGACCGCACGATACCATATAATTATCATTTTAACATTTAATTTTATATA
1 TAAGCAACTATCACACCGACAGCACGATACCATATAATTATCATTTTAACATTTAATTTTATATA
117778273 TTATAAATAAATTA
66 TTATAAATAAATTA
117778287 TAA
1 TAA
117778290 ATCTATAATT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.35
Consensus pattern (79 bp):
TAAGCAACTATCACACCGACAGCACGATACCATATAATTATCATTTTAACATTTAATTTTATATA
TTATAAATAAATTA
Found at i:117785673 original size:42 final size:43
Alignment explanation
Indices: 117785623--117785707 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
117785613 AAAAAAGACA
117785623 AAGGATACGTATATGTGAAT-AAAAAAAAGTAAAAAAGACTGG
1 AAGGATACGTATATGTGAATAAAAAAAAAGTAAAAAAGACTGG
117785665 AAGGATACGTATATGTGAATAAAAAAAAAGTAAAAAAGACTGG
1 AAGGATACGTATATGTGAATAAAAAAAAAGTAAAAAAGACTGG
117785708 TTCGTGGGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 20 0.48
43 22 0.52
ACGTcount: A:0.55, C:0.05, G:0.21, T:0.19
Consensus pattern (43 bp):
AAGGATACGTATATGTGAATAAAAAAAAAGTAAAAAAGACTGG
Found at i:117786265 original size:16 final size:16
Alignment explanation
Indices: 117786240--117786271 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
117786230 TTTATCATAA
*
117786240 TAAACTATTTTTTTAT
1 TAAACAATTTTTTTAT
117786256 TAAACAATTTTTTTAT
1 TAAACAATTTTTTTAT
117786272 ACTTTTCATA
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:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (16 bp):
TAAACAATTTTTTTAT
Found at i:117792117 original size:12 final size:12
Alignment explanation
Indices: 117792086--117792124 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
117792076 AATCCTCAAA
*
117792086 TTTCCTT-TTTA
1 TTTCCTTCTTTC
*
117792097 TTTCTTTCTTTC
1 TTTCCTTCTTTC
117792109 TTTCCTTCTTTC
1 TTTCCTTCTTTC
117792121 TTTC
1 TTTC
117792125 TCACGTTTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 6 0.25
12 18 0.75
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTCCTTCTTTC
Found at i:117798526 original size:47 final size:47
Alignment explanation
Indices: 117798418--117798527 Score: 143
Period size: 47 Copynumber: 2.3 Consensus size: 47
117798408 CGGGATAAGT
*
117798418 ACATAGTGCTTCATCAGAACAAATCCGGAACTTTAACATTATAGTAC
1 ACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTAC
* * * *
117798465 ACAAAGTACTTCATCGGAACAAATCTGGAACTTTAACATTAGTCG-AC
1 ACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTA-TAGTAC
117798512 ACATAGTG-TCTCATCG
1 ACATAGTGCT-TCATCG
117798528 ACTCAATGTC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 51 0.94
48 2 0.04
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (47 bp):
ACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTAC
Found at i:117799382 original size:42 final size:43
Alignment explanation
Indices: 117799288--117799382 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 43
117799278 TATTTATTTA
* * *
117799288 TTTCT-TTCCTTCTTTCTTTCTCACGTTTGCTCTCTGTTAGTC
1 TTTCTATTCTTTCTTTCTTTCTCACGTTTGCTCTCTGTAACTC
117799330 TTTCTA-TCTTTCTTTCTTTCTCACGTTTGCTCTCTGTAACT-
1 TTTCTATTCTTTCTTTCTTTCTCACGTTTGCTCTCTGTAACTC
117799371 TTTCTATTCTTT
1 TTTCTATTCTTT
117799383 ACTCATTATA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
41 6 0.12
42 42 0.88
ACGTcount: A:0.07, C:0.26, G:0.07, T:0.59
Consensus pattern (43 bp):
TTTCTATTCTTTCTTTCTTTCTCACGTTTGCTCTCTGTAACTC
Found at i:117805481 original size:26 final size:26
Alignment explanation
Indices: 117805429--117805491 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
117805419 CTAAACAATT
*
117805429 TTAAATAAAT-AGTTAATAGAATCAA
1 TTAATTAAATCAGTTAATAGAATCAA
* * *
117805454 TTAATTAAATCAGTTAATGGATTTAA
1 TTAATTAAATCAGTTAATAGAATCAA
*
117805480 TTAATCAAATCA
1 TTAATTAAATCA
117805492 ACAACCACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 9 0.28
26 23 0.72
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (26 bp):
TTAATTAAATCAGTTAATAGAATCAA
Found at i:117805703 original size:3 final size:3
Alignment explanation
Indices: 117805695--117805730 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
117805685 GTGAAATGAA
117805695 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
117805731 GAATTTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:117805780 original size:17 final size:17
Alignment explanation
Indices: 117805758--117805793 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
117805748 CTTCATAAAT
117805758 TTTTTAATTTTTAATTA
1 TTTTTAATTTTTAATTA
* *
117805775 TTTTTATTTTTTAGTTA
1 TTTTTAATTTTTAATTA
117805792 TT
1 TT
117805794 AAATCTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTTTAATTTTTAATTA
Found at i:117810878 original size:23 final size:23
Alignment explanation
Indices: 117810835--117810890 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
117810825 TTAAATTTAA
*
117810835 AAATTAAAAA-TAAGAAAAATTTT
1 AAATAAAAAATTAAGAAAAA-TTT
*
117810858 AAATAAAAAATTAA-AACAATTT
1 AAATAAAAAATTAAGAAAAATTT
117810880 AAA-AAAAAATT
1 AAATAAAAAATT
117810891 GGATTGTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 8 0.27
22 6 0.20
23 13 0.43
24 3 0.10
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (23 bp):
AAATAAAAAATTAAGAAAAATTT
Found at i:117811057 original size:20 final size:18
Alignment explanation
Indices: 117811029--117811078 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 18
117811019 AAGAATTAGA
*
117811029 AAAAAATTAAAAATTACT
1 AAAATATTAAAAATTACT
* *
117811047 AAAAGTTATTAATAATTATT
1 AAAA--TATTAAAAATTACT
117811067 AAAATATTAAAA
1 AAAATATTAAAA
117811079 TAATACAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 11 0.42
20 15 0.58
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (18 bp):
AAAATATTAAAAATTACT
Found at i:117811385 original size:27 final size:27
Alignment explanation
Indices: 117811347--117811401 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
117811337 ATGTATGTAA
117811347 TGAAATTTGAACTCAAGCTAATTATAT
1 TGAAATTTGAACTCAAGCTAATTATAT
117811374 TGAAATTTGAACTCAAGCTAATTATAT
1 TGAAATTTGAACTCAAGCTAATTATAT
117811401 T
1 T
117811402 AGTAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (27 bp):
TGAAATTTGAACTCAAGCTAATTATAT
Found at i:117811503 original size:2 final size:2
Alignment explanation
Indices: 117811496--117811522 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
117811486 TCTCCATAGT
117811496 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 T
117811523 TTATTTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:117812010 original size:10 final size:10
Alignment explanation
Indices: 117811995--117812024 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
117811985 TTGATCTTGA
117811995 TTTAGGGTTT
1 TTTAGGGTTT
117812005 TTTAGGGTTT
1 TTTAGGGTTT
117812015 TTTAGGGTTT
1 TTTAGGGTTT
117812025 AAACTGAATT
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:0.10, C:0.00, G:0.30, T:0.60
Consensus pattern (10 bp):
TTTAGGGTTT
Found at i:117812325 original size:12 final size:12
Alignment explanation
Indices: 117812310--117812356 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
117812300 TTCAATCTTA
* *
117812310 ATTTTGATTCTG
1 ATTTCGATTTTG
117812322 ATTTCGATTTTG
1 ATTTCGATTTTG
117812334 ATTTCGATTTTG
1 ATTTCGATTTTG
*
117812346 ATTTCAATTTT
1 ATTTCGATTTT
117812357 AAACACTCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.19, C:0.09, G:0.13, T:0.60
Consensus pattern (12 bp):
ATTTCGATTTTG
Found at i:117812331 original size:18 final size:18
Alignment explanation
Indices: 117812310--117812349 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
117812300 TTCAATCTTA
117812310 ATTTTGA-TTCTGATTTCG
1 ATTTTGATTTC-GATTTCG
*
117812328 ATTTTGATTTCGATTTTG
1 ATTTTGATTTCGATTTCG
117812346 ATTT
1 ATTT
117812350 CAATTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.17, C:0.07, G:0.15, T:0.60
Consensus pattern (18 bp):
ATTTTGATTTCGATTTCG
Found at i:117812426 original size:36 final size:36
Alignment explanation
Indices: 117812371--117812440 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
117812361 ACTCACTGAT
*
117812371 TTTGATTCCAATTTTGATCTCAATTTAGATTTAGAA
1 TTTGATTCCAATTTAGATCTCAATTTAGATTTAGAA
** ** *
117812407 TTTGATTCTGATTTAGATCTGGATTTCGATTTAG
1 TTTGATTCCAATTTAGATCTCAATTTAGATTTAG
117812441 GGTTATTTCG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.49
Consensus pattern (36 bp):
TTTGATTCCAATTTAGATCTCAATTTAGATTTAGAA
Found at i:117812582 original size:47 final size:49
Alignment explanation
Indices: 117812475--117812588 Score: 171
Period size: 48 Copynumber: 2.4 Consensus size: 49
117812465 GCCATGTGCA
* * *
117812475 TGATGTTTATTGTTTGT-TTCTGCCATTGTATGAATGCTATTATCAAAT
1 TGATGTTTATTGTGTATATTCTGCCATTGTATGAATGCTATTATCAAAC
*
117812523 TGATGTGTATTGTGTATATT-TGCCATTGTATGAATGC-ATTATCAAAC
1 TGATGTTTATTGTGTATATTCTGCCATTGTATGAATGCTATTATCAAAC
117812570 TGATGTTTATTGTGTATAT
1 TGATGTTTATTGTGTATAT
117812589 CTGTCGTGAT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
47 27 0.45
48 31 0.52
49 2 0.03
ACGTcount: A:0.25, C:0.09, G:0.18, T:0.48
Consensus pattern (49 bp):
TGATGTTTATTGTGTATATTCTGCCATTGTATGAATGCTATTATCAAAC
Found at i:117812920 original size:15 final size:14
Alignment explanation
Indices: 117812900--117812941 Score: 68
Period size: 13 Copynumber: 3.0 Consensus size: 14
117812890 GAAGAAAACA
117812900 TGTCTGGTAGTGAT
1 TGTCTGGTAGTGAT
117812914 GTGTCTGGTAGTGA-
1 -TGTCTGGTAGTGAT
117812928 TGTCTGGTAGTGAT
1 TGTCTGGTAGTGAT
117812942 AGTGATGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.50
15 13 0.50
ACGTcount: A:0.14, C:0.07, G:0.38, T:0.40
Consensus pattern (14 bp):
TGTCTGGTAGTGAT
Found at i:117815816 original size:59 final size:59
Alignment explanation
Indices: 117815724--117815862 Score: 251
Period size: 59 Copynumber: 2.4 Consensus size: 59
117815714 TAATTGTTGT
*
117815724 CCAACTGTTAAGCAATTTGTATATCAACTGTTATCTTTTCTAACTAGCAGCCATGTATA
1 CCAACTGTTAAGCAATTTGTATATCAACTGTTATCTTTTCTAACCAGCAGCCATGTATA
*
117815783 CCAACTGTTAAGCAATTTGTATATCAATTGTTATCTTTTCTAACCAGCAGCCATGTATA
1 CCAACTGTTAAGCAATTTGTATATCAACTGTTATCTTTTCTAACCAGCAGCCATGTATA
*
117815842 CCAAGTGTTAAGCAATTTGTA
1 CCAACTGTTAAGCAATTTGTA
117815863 AATAACAACA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 77 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (59 bp):
CCAACTGTTAAGCAATTTGTATATCAACTGTTATCTTTTCTAACCAGCAGCCATGTATA
Found at i:117816453 original size:26 final size:26
Alignment explanation
Indices: 117816406--117816456 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
117816396 ATATCCATTT
* *
117816406 TTCCTCTTCTCCTTCTTTTTCTTCTC
1 TTCCTCTTCTCATTCTTCTTCTTCTC
117816432 TTCCTCTTCCTCATTC-TCTTCTTCT
1 TTCCTCTT-CTCATTCTTCTTCTTCT
117816457 TTTTCTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.02, C:0.39, G:0.00, T:0.59
Consensus pattern (26 bp):
TTCCTCTTCTCATTCTTCTTCTTCTC
Found at i:117818365 original size:37 final size:37
Alignment explanation
Indices: 117818323--117818397 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
117818313 TCTATTCTCC
117818323 TCTGTAAGTCCTTTCTTTCTCCATCTATTTTGTATCG
1 TCTGTAAGTCCTTTCTTTCTCCATCTATTTTGTATCG
117818360 TCTGTAAGTCCTTTCTTTCTCCATCTATTTTGTATCG
1 TCTGTAAGTCCTTTCTTTCTCCATCTATTTTGTATCG
117818397 T
1 T
117818398 TAATTTTCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.13, C:0.24, G:0.11, T:0.52
Consensus pattern (37 bp):
TCTGTAAGTCCTTTCTTTCTCCATCTATTTTGTATCG
Found at i:117820077 original size:11 final size:11
Alignment explanation
Indices: 117820061--117820085 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
117820051 TTTGATTTCC
117820061 TTTAAAATTAA
1 TTTAAAATTAA
117820072 TTTAAAATTAA
1 TTTAAAATTAA
117820083 TTT
1 TTT
117820086 CGTCACGACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTAAAATTAA
Found at i:117836943 original size:17 final size:16
Alignment explanation
Indices: 117836921--117836954 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
117836911 TAAATTTGAT
117836921 TTAAAAAAAAAGAAAAA
1 TTAAAAAAAAA-AAAAA
*
117836938 TTAAAAACAAAAAAAA
1 TTAAAAAAAAAAAAAA
117836954 T
1 T
117836955 CAAGATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (16 bp):
TTAAAAAAAAAAAAAA
Found at i:117837770 original size:29 final size:30
Alignment explanation
Indices: 117837736--117837797 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
117837726 ATTTATTTTA
117837736 TTGTTAA-TTTCTTATTATTTTA-AAGGCAT
1 TTGTTAATTTTCTTATTATTTTAGAA-GCAT
*
117837765 TTGTTAATTTTTTTATTATTTTAGAAGCAT
1 TTGTTAATTTTCTTATTATTTTAGAAGCAT
117837795 TTG
1 TTG
117837798 CTAGTTAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 7 0.23
30 21 0.70
31 2 0.07
ACGTcount: A:0.26, C:0.05, G:0.11, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTCTTATTATTTTAGAAGCAT
Found at i:117839807 original size:21 final size:20
Alignment explanation
Indices: 117839773--117839811 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
117839763 TTCGTATATA
117839773 TATATATATATATTGTTTTG
1 TATATATATATATTGTTTTG
*
117839793 TATATCATTTATATTGTTT
1 TATAT-ATATATATTGTTT
117839812 CGTTACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (20 bp):
TATATATATATATTGTTTTG
Found at i:117840689 original size:121 final size:121
Alignment explanation
Indices: 117840472--117840689 Score: 307
Period size: 121 Copynumber: 1.8 Consensus size: 121
117840462 AAAACAAGGA
* * * *
117840472 AATATTTCGTGTTTAGAAATTCGAGAAATCGTGTCCTAATGTGTTGGGTTTCGATTTTCCGTTTG
1 AATATTTCGTGTTTAGAAATTCGAGAAATCGTGTCCCAATGTGCTGGGTTTCGACTTACCGTTTG
* * *
117840537 GCCGAATAACTAAATATCCTTTTGAAGTTTCATCCATGTTTTCTTAAATTTGAGGC
66 ACCGAATAACCAAATATCCTTTTGAAATTTCATCCATGTTTTCTTAAATTTGAGGC
*
117840593 AATATTTTGTGTTT-GAAAATTCGAGAAATCGTG-CCCAATCGTGCTGGGTTTCGACTTACCGTT
1 AATATTTCGTGTTTAG-AAATTCGAGAAATCGTGTCCCAAT-GTGCTGGGTTTCGACTTACCGTT
*
117840656 TGACC-AGATAGCCAAATATCCTTTTGAAATTTCA
64 TGACCGA-ATAACCAAATATCCTTTTGAAATTTCA
117840690 AATGCATGAG
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
120 7 0.08
121 78 0.92
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (121 bp):
AATATTTCGTGTTTAGAAATTCGAGAAATCGTGTCCCAATGTGCTGGGTTTCGACTTACCGTTTG
ACCGAATAACCAAATATCCTTTTGAAATTTCATCCATGTTTTCTTAAATTTGAGGC
Found at i:117845693 original size:10 final size:10
Alignment explanation
Indices: 117845678--117845703 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
117845668 CAATCAGGTT
117845678 AAAATATTTG
1 AAAATATTTG
117845688 AAAATATTTG
1 AAAATATTTG
117845698 AAAATA
1 AAAATA
117845704 AAATTATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (10 bp):
AAAATATTTG
Found at i:117849270 original size:70 final size:70
Alignment explanation
Indices: 117849185--117849321 Score: 204
Period size: 70 Copynumber: 2.0 Consensus size: 70
117849175 ATTATTAACA
* * *
117849185 ATGTTGGCATCGTAATCTGCGTGGTAGTTCATATGTG-TTTCATGTTGACATGACATTATTTGTC
1 ATGTTGGCATCGTAATCTCCGTGGTAGTTCACATGTGCTTT-ATGCTGACATGACATTATTTGTC
117849249 TTAATG
65 TTAATG
* * *
117849255 ATGTTGGCATGGTAATTTCCGTGGTAGTTCACGTGTGCTTTATGCTGACATGACATTATTTGTCT
1 ATGTTGGCATCGTAATCTCCGTGGTAGTTCACATGTGCTTTATGCTGACATGACATTATTTGTCT
117849320 TA
66 TA
117849322 TATGTTACAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
70 57 0.95
71 3 0.05
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.42
Consensus pattern (70 bp):
ATGTTGGCATCGTAATCTCCGTGGTAGTTCACATGTGCTTTATGCTGACATGACATTATTTGTCT
TAATG
Found at i:117849372 original size:2 final size:2
Alignment explanation
Indices: 117849365--117849394 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
117849355 TTCAAAAATT
117849365 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
117849395 AAGCTCATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:117849545 original size:22 final size:20
Alignment explanation
Indices: 117849504--117849546 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
117849494 TTTGACTCTT
* *
117849504 TTTAAAAATTAATAATTAAA
1 TTTAAAAAATAAAAATTAAA
117849524 TTTAACAAAATAAAAATATAAA
1 TTTAA-AAAATAAAAAT-TAAA
117849546 T
1 T
117849547 ATCAAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
TTTAAAAAATAAAAATTAAA
Found at i:117849559 original size:22 final size:20
Alignment explanation
Indices: 117849507--117849559 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
117849497 GACTCTTTTT
* *
117849507 AAAAATTAATAATTAAATTT
1 AAAAATTAAAAATTAAATTC
*
117849527 AACAAAATAAAAATATAAATATC
1 AA-AAATTAAAAAT-TAAAT-TC
117849550 AAAAATTAAA
1 AAAAATTAAA
117849560 TTTATCAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 2 0.08
21 9 0.35
22 12 0.46
23 3 0.12
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAATTAAAAATTAAATTC
Found at i:117861948 original size:70 final size:71
Alignment explanation
Indices: 117861861--117862000 Score: 273
Period size: 70 Copynumber: 2.0 Consensus size: 71
117861851 TGAAACTGAA
117861861 AAAAACAAATTGAAAGTAACCATCATGAAAATTTGATAAAACATGGGACTATTTATGATTCTTTT
1 AAAAACAAATTGAAAGTAACCATCATGAAAATTTGATAAAACATGGGACTATTTATGATTCTTTT
117861926 TTTTTC
66 TTTTTC
117861932 AAAAA-AAATTGAAAGTAACCATCATGAAAATTTGATAAAACATGGGACTATTTATGATTCTTTT
1 AAAAACAAATTGAAAGTAACCATCATGAAAATTTGATAAAACATGGGACTATTTATGATTCTTTT
117861996 TTTTT
66 TTTTT
117862001 ATTCATTTTG
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 64 0.93
71 5 0.07
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.37
Consensus pattern (71 bp):
AAAAACAAATTGAAAGTAACCATCATGAAAATTTGATAAAACATGGGACTATTTATGATTCTTTT
TTTTTC
Done.