Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1265
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: 436287
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
File 2 of 3
Found at i:191204 original size:21 final size:21
Alignment explanation
Indices: 191131--191216 Score: 99
Period size: 21 Copynumber: 4.2 Consensus size: 21
191121 TTTGATGAAT
*
191131 TTAATTTAAATAGATAATAAAA
1 TTAATTTTAATA-ATAATAAAA
191153 TTAATTTTAATAA-AATCAAAA
1 TTAATTTTAATAATAAT-AAAA
*
191174 ATAA---TAATAATAATAAAA
1 TTAATTTTAATAATAATAAAA
*
191192 TTAATTTTTATAATAATAAAA
1 TTAATTTTAATAATAATAAAA
191213 TTAA
1 TTAA
191217 AATTAATGAT
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
18 13 0.24
19 3 0.05
20 3 0.05
21 25 0.45
22 11 0.20
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (21 bp):
TTAATTTTAATAATAATAAAA
Found at i:191283 original size:13 final size:12
Alignment explanation
Indices: 191265--191314 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 12
191255 AAAATTAAAA
191265 TAAAAATGATTAT
1 TAAAAAT-ATTAT
*
191278 TAAAAATATTAA
1 TAAAAATATTAT
191290 TATAAAATA-TAT
1 TA-AAAATATTAT
*
191302 TAATAAT-TTAT
1 TAAAAATATTAT
191313 TA
1 TA
191315 TATATTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
11 9 0.28
12 10 0.31
13 13 0.41
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (12 bp):
TAAAAATATTAT
Found at i:191303 original size:15 final size:14
Alignment explanation
Indices: 191258--191306 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 14
191248 GGATAATAAA
*
191258 ATTAAAATAAAAAT
1 ATTAATATAAAAAT
191272 GATT-AT-TAAAAAT
1 -ATTAATATAAAAAT
191285 ATTAATATAAAATAT
1 ATTAATATAAAA-AT
191300 ATTAATA
1 ATTAATA
191307 ATTTATTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 3 0.10
13 9 0.30
14 6 0.20
15 12 0.40
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (14 bp):
ATTAATATAAAAAT
Found at i:191339 original size:18 final size:19
Alignment explanation
Indices: 191295--191339 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
191285 ATTAATATAA
*
191295 AATATATTAATAATTTATT
1 AATATTTTAATAATTTATT
191314 ATATATTTTAATAATTT-TT
1 A-ATATTTTAATAATTTATT
191333 AATATTT
1 AATATTT
191340 GAATTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.25
19 4 0.17
20 14 0.58
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
AATATTTTAATAATTTATT
Found at i:191391 original size:26 final size:25
Alignment explanation
Indices: 191349--191398 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
191339 TGAATTTAAA
*
191349 TATTTATATATTAAATATATAAATT
1 TATTTATATATTAAATAAATAAATT
191374 TATTTATTATATTAAATAAATAAAT
1 TATTTA-TATATTAAATAAATAAAT
191399 AATTTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TATTTATATATTAAATAAATAAATT
Found at i:191414 original size:26 final size:27
Alignment explanation
Indices: 191354--191419 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
191344 TTAAATATTT
* * **
191354 ATATATTAAATATATAAATTTATTTATT
1 ATAT-TTAAATAAATAAATTAATTTAAA
191382 ATA-TTAAATAAATAAA-TAATTTAAA
1 ATATTTAAATAAATAAATTAATTTAAA
191407 ATATTTAAATAAA
1 ATATTTAAATAAA
191420 ACATCAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 9 0.27
26 21 0.64
28 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
ATATTTAAATAAATAAATTAATTTAAA
Found at i:191705 original size:26 final size:25
Alignment explanation
Indices: 191682--191751 Score: 70
Period size: 27 Copynumber: 2.7 Consensus size: 25
191672 AAAAAAATTT
*
191682 AATATATATTTTATTAATATAAATAA
1 AATATA-ATTTTAATAATATAAATAA
*
191708 AATATAATTTTAATAATTTTAAAATATA
1 AATATAATTTTAATAA-TAT-AAATA-A
*
191736 AATATAA-ATTAATAAT
1 AATATAATTTTAATAAT
191752 TTTTAATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
25 9 0.24
26 9 0.24
27 12 0.32
28 8 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AATATAATTTTAATAATATAAATAA
Found at i:191757 original size:28 final size:27
Alignment explanation
Indices: 191702--191754 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
191692 TTATTAATAT
*
191702 AAATAAAATATAATTTTAATAATTTTA
1 AAATAAAATATAATATTAATAATTTTA
191729 AAATATAAATATAA-ATTAATAATTTT
1 AAATA-AAATATAATATTAATAATTTT
191755 TAATTATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
AAATAAAATATAATATTAATAATTTTA
Found at i:191777 original size:65 final size:65
Alignment explanation
Indices: 191707--191837 Score: 169
Period size: 65 Copynumber: 2.0 Consensus size: 65
191697 AATATAAATA
191707 AAATATAATTTTA-ATA-ATTTTAAAATATAAATATAAATTAATAATTTTTAATTA-TTATTTGA
1 AAATATAATTTTATATATATTTTAAAAT-TAAATATAAA-T-ATAATTTTTAATTATTTATTTGA
191769 TAT
63 TAT
* ** * *
191772 AAATATAATTTTATTTATATTTTATTATTTAATATAAATATAATTTTTAATTATTTATTTTATAT
1 AAATATAATTTTATATATATTTTAAAATTAAATATAAATATAATTTTTAATTATTTATTTGATAT
191837 A
1 A
191838 TTTTTTATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
64 14 0.24
65 25 0.43
66 11 0.19
67 8 0.14
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (65 bp):
AAATATAATTTTATATATATTTTAAAATTAAATATAAATATAATTTTTAATTATTTATTTGATAT
Found at i:191813 original size:23 final size:23
Alignment explanation
Indices: 191787--191852 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 23
191777 TAATTTTATT
191787 TATATTTTATTATTTAATATAAA
1 TATATTTTATTATTTAATATAAA
**
191810 TATAATTTTTAATTATTT-AT-TTTA
1 TAT-A-TTTT-ATTATTTAATATAAA
191834 TATATTTT-TTATTTAATAT
1 TATATTTTATTATTTAATAT
191853 TTTCAACGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
20 6 0.17
21 2 0.06
22 5 0.14
23 4 0.11
24 6 0.17
25 6 0.17
26 7 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TATATTTTATTATTTAATATAAA
Found at i:191820 original size:18 final size:18
Alignment explanation
Indices: 191768--191822 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 18
191758 TTATTATTTG
191768 ATATAAATATAA-TTTT-
1 ATATAAATATAATTTTTA
* * * *
191784 ATTTATATTTTATTATTTA
1 ATATAAATATAATT-TTTA
191803 ATATAAATATAATTTTTA
1 ATATAAATATAATTTTTA
191821 AT
1 AT
191823 TATTTATTTT
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
16 8 0.29
17 1 0.04
18 9 0.32
19 10 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATAAATATAATTTTTA
Found at i:191837 original size:30 final size:30
Alignment explanation
Indices: 191736--191837 Score: 107
Period size: 35 Copynumber: 3.2 Consensus size: 30
191726 TTAAAATATA
191736 AATATAAATTAATAATTTTTAATTA-TTATTT
1 AATATAAA-T-ATAATTTTTAATTATTTATTT
* *
191767 GATATAAATATAATTTTATTTATATTTTATTATTT
1 AATATAAATATAA--TT-TTTA-ATTAT-TTATTT
191802 AATATAAATATAATTTTTAATTATTTATTT
1 AATATAAATATAATTTTTAATTATTTATTT
*
191832 TATATA
1 AATATA
191838 TTTTTTATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
29 4 0.07
30 12 0.20
31 13 0.22
32 8 0.13
33 5 0.08
35 18 0.30
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (30 bp):
AATATAAATATAATTTTTAATTATTTATTT
Found at i:191838 original size:26 final size:23
Alignment explanation
Indices: 191779--191846 Score: 64
Period size: 26 Copynumber: 2.8 Consensus size: 23
191769 TATAAATATA
*
191779 ATTTTATTTATATTTTATTATTT
1 ATTTTATATATATTTTATTATTT
* * *
191802 AATATAAATATAATTTTTAATTATTT
1 ATTTTATATAT-A-TTTT-ATTATTT
*
191828 ATTTTATATATTTTTTATT
1 ATTTTATATATATTTTATT
191847 TAATATTTTC
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
23 10 0.29
24 5 0.15
25 4 0.12
26 15 0.44
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
ATTTTATATATATTTTATTATTT
Found at i:191853 original size:23 final size:23
Alignment explanation
Indices: 191787--191855 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
191777 TAATTTTATT
**
191787 TATATTTTATTATTTAATA-TAAA
1 TATATTTT-TTATTTAATATTTTA
* * *
191810 TATAATTTTTAATTATTTATTTTA
1 TATATTTTTTATTTA-ATATTTTA
191834 TATATTTTTTATTTAATATTTT
1 TATATTTTTTATTTAATATTTT
191856 CAACGATCAT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
22 6 0.17
23 15 0.42
24 15 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TATATTTTTTATTTAATATTTTA
Found at i:191958 original size:14 final size:14
Alignment explanation
Indices: 191941--191972 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
191931 AATAGTACCA
191941 TTATAATAACTAAC
1 TTATAATAACTAAC
191955 TTATAATAACTAAC
1 TTATAATAACTAAC
191969 TTAT
1 TTAT
191973 CTCTATTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (14 bp):
TTATAATAACTAAC
Found at i:192158 original size:17 final size:18
Alignment explanation
Indices: 192125--192161 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
192115 TGATAAATTA
*
192125 AATATTTTAATTGTATTT
1 AATATTTAAATTGTATTT
192143 AATATTTAAATT-TATTT
1 AATATTTAAATTGTATTT
192160 AA
1 AA
192162 AATAGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
AATATTTAAATTGTATTT
Found at i:194255 original size:21 final size:20
Alignment explanation
Indices: 194226--194264 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
194216 ACACATAATA
194226 TGATTATTT-ATTAAATTACT
1 TGATTATTTGA-TAAATTACT
194246 TGATCTATTTGATAAATTA
1 TGAT-TATTTGATAAATTA
194265 TGCATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 12 0.71
22 1 0.06
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (20 bp):
TGATTATTTGATAAATTACT
Found at i:194782 original size:8 final size:8
Alignment explanation
Indices: 194771--194798 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
194761 TTAATATAAA
194771 AATATTAT
1 AATATTAT
194779 AATATTAT
1 AATATTAT
194787 AATATTAT
1 AATATTAT
194795 AATA
1 AATA
194799 AATAATAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AATATTAT
Found at i:194783 original size:16 final size:16
Alignment explanation
Indices: 194749--194798 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
194739 TTAATTATAA
*
194749 AATATAAAGATA-T-T
1 AATATAAAAATATTAT
194763 AATATAAAAATATTAT
1 AATATAAAAATATTAT
* *
194779 AATATTATAATATTAT
1 AATATAAAAATATTAT
194795 AATA
1 AATA
194799 AATAATAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 11 0.35
15 1 0.03
16 19 0.61
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AATATAAAAATATTAT
Found at i:195217 original size:14 final size:14
Alignment explanation
Indices: 195190--195251 Score: 58
Period size: 13 Copynumber: 4.5 Consensus size: 14
195180 GTTGGCCTTG
*
195190 AAATTAAATAATATT
1 AAATAAAAT-ATATT
195205 AAATAAAATATATT
1 AAATAAAATATATT
*
195219 -AAGAAAATATA-T
1 AAATAAAATATATT
*
195231 AAATAAAA-ATTATA
1 AAATAAAATA-TATT
195245 AAATAAA
1 AAATAAA
195252 TAATATTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
12 2 0.05
13 18 0.45
14 12 0.30
15 8 0.20
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (14 bp):
AAATAAAATATATT
Found at i:195262 original size:26 final size:28
Alignment explanation
Indices: 195194--195262 Score: 65
Period size: 27 Copynumber: 2.5 Consensus size: 28
195184 GCCTTGAAAT
* *
195194 TAAATAATATTAAATAAAATATATTAAGA
1 TAAATAATATTATA-AAAATATATTAAAA
*
195223 -AAAT-ATATAAATAAAAAT-TA-TAAAA
1 TAAATAATAT-TATAAAAATATATTAAAA
195248 TAAATAATATTATAA
1 TAAATAATATTATAA
195263 GGTTAATGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
25 4 0.12
26 10 0.30
27 13 0.39
28 6 0.18
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (28 bp):
TAAATAATATTATAAAAATATATTAAAA
Found at i:200931 original size:16 final size:17
Alignment explanation
Indices: 200910--200948 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
200900 TGAAATTACG
*
200910 TATTTAT-AAATTTAAT
1 TATTTATGAAATTAAAT
*
200926 TATTTATGAACTTAAAT
1 TATTTATGAAATTAAAT
200943 TATTTA
1 TATTTA
200949 ATTAATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
TATTTATGAAATTAAAT
Found at i:201524 original size:26 final size:22
Alignment explanation
Indices: 201477--201518 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
201467 AAAACGACTG
201477 TATTTATATATATATATATTTT
1 TATTTATATATATATATATTTT
201499 TATTTAT-TATATTATATATT
1 TATTTATATATA-TATATATT
201519 AATTTTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTATATATATATATATTTT
Found at i:201529 original size:26 final size:25
Alignment explanation
Indices: 201480--201529 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
201470 ACGACTGTAT
*
201480 TTATATATATATATATTTTTATTTA
1 TTATATATATATATATTTTCATTTA
201505 TTATAT-TATATATTAATTTTCATTT
1 TTATATATATATA-T-ATTTTCATTT
201530 GATTTGATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 7 0.32
26 9 0.41
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (25 bp):
TTATATATATATATATTTTCATTTA
Found at i:202299 original size:2 final size:2
Alignment explanation
Indices: 202294--202321 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
202284 CACAACCCTA
202294 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
202322 TTCGTTCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:202654 original size:17 final size:17
Alignment explanation
Indices: 202632--202667 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
202622 TTAATTTTTT
202632 TTAAAAAAAA-CAGAAAA
1 TTAAAAAAAAGCA-AAAA
202649 TTAAAAAAAAGCAAAAA
1 TTAAAAAAAAGCAAAAA
202666 TT
1 TT
202668 TTTAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.17
Consensus pattern (17 bp):
TTAAAAAAAAGCAAAAA
Found at i:202657 original size:18 final size:17
Alignment explanation
Indices: 202634--202667 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
202624 AATTTTTTTT
202634 AAAAAAAACAGAAAATTA
1 AAAAAAAACA-AAAATTA
*
202652 AAAAAAAGCAAAAATT
1 AAAAAAAACAAAAATT
202668 TTTAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAAAAAACAAAAATTA
Found at i:202692 original size:26 final size:28
Alignment explanation
Indices: 202663--202721 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
202653 AAAAAAGCAA
202663 AAATTTTTA-AAATAAAT-ATATTATTT
1 AAATTTTTATAAATAAATGATATTATTT
* *
202689 AAA-TTTTATTAATAACTGATATTATTT
1 AAATTTTTATAAATAAATGATATTATTT
*
202716 TAATTT
1 AAATTT
202722 AATTAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 5 0.19
26 9 0.33
27 11 0.41
28 2 0.07
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (28 bp):
AAATTTTTATAAATAAATGATATTATTT
Found at i:202773 original size:33 final size:32
Alignment explanation
Indices: 202729--202790 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
202719 TTTAATTAAT
202729 TAAATTAAATTAAATAATTATTAA-AAAAATAAA
1 TAAATTAAATTAAAT--TTATTAATAAAAATAAA
*
202762 TAAATTTAATTAAATTTATTAATAAAAAT
1 TAAATTAAATTAAATTTATTAATAAAAAT
202791 TTAGTTCGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 7 0.26
32 6 0.22
33 14 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (32 bp):
TAAATTAAATTAAATTTATTAATAAAAATAAA
Found at i:202993 original size:9 final size:9
Alignment explanation
Indices: 202979--203047 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
202969 TGATATTATT
202979 TTAATTTAA
1 TTAATTTAA
*
202988 TTAATTAAA
1 TTAATTTAA
202997 TTAATTTAA
1 TTAATTTAA
* *
203006 ATAATTATTA
1 TTAATT-TAA
* * *
203016 TAAAATAAA
1 TTAATTTAA
*
203025 TAAATTTAA
1 TTAATTTAA
203034 TTAAATTT-A
1 TT-AATTTAA
203043 TTAAT
1 TTAAT
203048 AAAAATTTAA
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
8 3 0.07
9 33 0.72
10 10 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTAATTTAA
Found at i:202994 original size:18 final size:18
Alignment explanation
Indices: 202973--203014 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
202963 AATAACTGAT
*
202973 ATTATTTTAATTTAATTA
1 ATTATTTTAATTTAAATA
**
202991 ATTAAATTAATTTAAATA
1 ATTATTTTAATTTAAATA
203009 ATTATT
1 ATTATT
203015 ATAAAATAAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTATTTTAATTTAAATA
Found at i:203025 original size:28 final size:31
Alignment explanation
Indices: 202984--203051 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 31
202974 TTATTTTAAT
* * *
202984 TTAATTAATTAAATTAATTTAAAT-AA-TTA
1 TTAATAAAATAAATAAATTTAAATAAATTTA
*
203013 TT-ATAAAATAAATAAATTTAATTAAATTTA
1 TTAATAAAATAAATAAATTTAAATAAATTTA
203043 TTAATAAAA
1 TTAATAAAA
203052 ATTTAATTCG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 17 0.53
29 4 0.12
30 5 0.16
31 6 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
TTAATAAAATAAATAAATTTAAATAAATTTA
Found at i:203366 original size:15 final size:15
Alignment explanation
Indices: 203348--203393 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
203338 AATTGATTTT
*
203348 TAATATTAAATTTAA
1 TAATATTAAATATAA
203363 TAATATTAAATATAA
1 TAATATTAAATATAA
*
203378 TTATA-TAAATATAA
1 TAATATTAAATATAA
203392 TA
1 TA
203394 TAAATAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 10 0.36
15 18 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATATTAAATATAA
Found at i:203926 original size:18 final size:17
Alignment explanation
Indices: 203875--203928 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 17
203865 TCAATTCTCC
203875 TTAAAAATGTTAATTACTT
1 TTAAAAAT-TTAATTA-TT
*
203894 TTAAATAA-TCAATTATT
1 TTAAA-AATTTAATTATT
203911 TTAAAAATTTATATTATT
1 TTAAAAATTTA-ATTATT
203929 AACAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 2 0.07
17 9 0.30
18 12 0.40
19 5 0.17
20 2 0.07
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (17 bp):
TTAAAAATTTAATTATT
Found at i:204465 original size:31 final size:32
Alignment explanation
Indices: 204406--204465 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
204396 TTAAGTACTT
* * *
204406 TAAATTTATATTTTATTAATAAATTATCATGA
1 TAAATTAATATTTTAATAATAAAATATCATGA
*
204438 TAAATTAATGTTTTAAT-ATAAAATATCA
1 TAAATTAATATTTTAATAATAAAATATCA
204466 ATATAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 10 0.42
32 14 0.58
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (32 bp):
TAAATTAATATTTTAATAATAAAATATCATGA
Found at i:207428 original size:119 final size:120
Alignment explanation
Indices: 207250--207482 Score: 396
Period size: 119 Copynumber: 1.9 Consensus size: 120
207240 CAGGAACCGC
* *
207250 TCTGTGGTTCGTTTTCTGTATGCTATTAGTTTATTACTGAAATTGGTTCTACATCTGTT-GACAA
1 TCTGTGGTTCGTTTTCTATATGCTAGTAGTTTATTACTGAAATTGGTTCTACATCTGTTGGACAA
* *
207314 TTAGATTAATCTAGCAGACAGCAACTAGTTGTCTCTATCTGTTTGCAAAGTGCGA
66 TAAGATTAATCTAGCAGAAAGCAACTAGTTGTCTCTATCTGTTTGCAAAGTGCGA
* *
207369 TCTGTGGTTGGTTTTCTATATGCTAGTATTTTATTACTGAAATTGGTTCTACATCTGTTGGACAA
1 TCTGTGGTTCGTTTTCTATATGCTAGTAGTTTATTACTGAAATTGGTTCTACATCTGTTGGACAA
*
207434 TAATATTAATCTAGCAGAAAGCAACTAGTTGTCTCTATCTGTTTGCAAA
66 TAAGATTAATCTAGCAGAAAGCAACTAGTTGTCTCTATCTGTTTGCAAA
207483 TTGCAATTCT
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
119 55 0.52
120 51 0.48
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (120 bp):
TCTGTGGTTCGTTTTCTATATGCTAGTAGTTTATTACTGAAATTGGTTCTACATCTGTTGGACAA
TAAGATTAATCTAGCAGAAAGCAACTAGTTGTCTCTATCTGTTTGCAAAGTGCGA
Found at i:211927 original size:2 final size:2
Alignment explanation
Indices: 211922--211950 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
211912 ATATATATAT
211922 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
211951 TTTAAGGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:212002 original size:2 final size:2
Alignment explanation
Indices: 211995--212023 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
211985 ATTAAAGATT
211995 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
212024 TACTATTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:215565 original size:63 final size:63
Alignment explanation
Indices: 215470--215671 Score: 359
Period size: 63 Copynumber: 3.2 Consensus size: 63
215460 TATCGCCTTA
* *
215470 CCTAACTAGCATACAAGTGAATAACCCAAGTTATTACACATCCATGCTCTGATCATTTGATCG
1 CCTAACTAGCATACAAGCGAATAACCCAAGTTATTACACATACATGCTCTGATCATTTGATCG
215533 CCTAACTAGCATACAAGCGAATAACCCAAGTTATTACACATACATGCTCTGATCATTTGATCG
1 CCTAACTAGCATACAAGCGAATAACCCAAGTTATTACACATACATGCTCTGATCATTTGATCG
* *
215596 CCTAACTAGCATACAAGCAAATAACCCAAGTTATTACACATACATGCTCTGATCATTTGATCA
1 CCTAACTAGCATACAAGCGAATAACCCAAGTTATTACACATACATGCTCTGATCATTTGATCG
*
215659 CCTAGCTAGCATA
1 CCTAACTAGCATA
215672 TCATCTAATA
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 134 1.00
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.27
Consensus pattern (63 bp):
CCTAACTAGCATACAAGCGAATAACCCAAGTTATTACACATACATGCTCTGATCATTTGATCG
Found at i:215730 original size:87 final size:87
Alignment explanation
Indices: 215595--215758 Score: 229
Period size: 87 Copynumber: 1.9 Consensus size: 87
215585 TCATTTGATC
* * *
215595 GCCTAACTAGCATACAAGCAAATAACCCAAGTTATTACACATACATGCTCTGATCATTTGATCAC
1 GCCTAACTAGCATACAAGCAAATAACCCAAGTCATCACACATACATGCTCTGATCATATGATCAC
*
215660 CTAGCTAGCATATCATCTAATA
66 CTAACTAGCATATCATCTAATA
** * * * * *
215682 GCCTAACTAGCATACAAGGGAGTATCCTAAGTCATCACACATACATGCTCTGATCGTATGATCGC
1 GCCTAACTAGCATACAAGCAAATAACCCAAGTCATCACACATACATGCTCTGATCATATGATCAC
215747 CTAACTAGCATA
66 CTAACTAGCATA
215759 CAAGCAAATA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
87 66 1.00
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (87 bp):
GCCTAACTAGCATACAAGCAAATAACCCAAGTCATCACACATACATGCTCTGATCATATGATCAC
CTAACTAGCATATCATCTAATA
Found at i:215771 original size:213 final size:210
Alignment explanation
Indices: 215389--215793 Score: 533
Period size: 213 Copynumber: 1.9 Consensus size: 210
215379 TTCTTCGGCC
* * ** *
215389 AACTAACATATAAGCAAATAACCTGAATTATTGGACGTACATACTCTGATCATCTGATCACCTAA
1 AACTAACATACAAGCAAATAACCTCAATTATTACACATACATACTCTGATCATCTGATCACCTAA
* * * * *
215454 CAAGCATATCGCCTTACCTAACTAGCATACAAGTGAATAACCCAAGTTATTACACATCCATGCTC
66 CAAGCATATCACCTTACCTAACTAGCATACAAGGGAATAACCCAAGTCATCACACATACATGCTC
* * *
215519 TGATCATTTGATCGCCTAACTAGCATACAAGCGAATAACCCAAGTTATTACACATACATGCTCTG
131 TGATCATATGATCGCCTAACTAGCATACAAGCAAATAACCCAAGTTACTACACATACATGCTCTG
215584 ATCATTTGATCGCCT
196 ATCATTTGATCGCCT
* * *
215599 AACTAGCATACAAGCAAATAACC-CAAGTTATTACACATACATGCTCTGATCATTTGATCACCTA
1 AACTAACATACAAGCAAATAACCTCAA-TTATTACACATACATACTCTGATCATCTGATCACCTA
* * * * * *
215663 GCTAGCATATCATCTAATAGCCTAACTAGCATACAAGGGAGTATCCTAAGTCATCACACATACAT
65 ACAAGCATATCACCT--TA-CCTAACTAGCATACAAGGGAATAACCCAAGTCATCACACATACAT
* * * *
215728 GCTCTGATCGTATGATCGCCTAACTAGCATACAAGCAAATAACCCGAGTTACTACGCATGCATGC
127 GCTCTGATCATATGATCGCCTAACTAGCATACAAGCAAATAACCCAAGTTACTACACATACATGC
215793 T
192 T
215794 TTAATCGTCT
Statistics
Matches: 165, Mismatches: 26, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
209 2 0.01
210 64 0.39
212 2 0.01
213 97 0.59
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.26
Consensus pattern (210 bp):
AACTAACATACAAGCAAATAACCTCAATTATTACACATACATACTCTGATCATCTGATCACCTAA
CAAGCATATCACCTTACCTAACTAGCATACAAGGGAATAACCCAAGTCATCACACATACATGCTC
TGATCATATGATCGCCTAACTAGCATACAAGCAAATAACCCAAGTTACTACACATACATGCTCTG
ATCATTTGATCGCCT
Found at i:215810 original size:150 final size:150
Alignment explanation
Indices: 215532--215821 Score: 411
Period size: 150 Copynumber: 1.9 Consensus size: 150
215522 TCATTTGATC
* * *
215532 GCCTAACTAGCATACAAGCGAATAACCCAAGTTATTACACATACATGCTCTGATCATTTGATCGC
1 GCCTAACTAGCATACAAGCGAATAACCCAAGTCATCACACATACATGCTCTGATCATATGATCGC
* * *
215597 CTAACTAGCATACAAGCAAATAACCCAAGTTATTACACATACATGCTCTGATCATTTGATCACCT
66 CTAACTAGCATACAAGCAAATAACCCAAGTTACTACACATACATGCTCTAATCATTCGATCACCT
*
215662 AGCTAGCATATCATCTAATA
131 AACTAGCATATCATCTAATA
* * * * *
215682 GCCTAACTAGCATACAAGGGAGTATCCTAAGTCATCACACATACATGCTCTGATCGTATGATCGC
1 GCCTAACTAGCATACAAGCGAATAACCCAAGTCATCACACATACATGCTCTGATCATATGATCGC
* * * * *
215747 CTAACTAGCATACAAGCAAATAACCCGAGTTACTACGCATGCATGCTTTAATCGTCTCG-TCACC
66 CTAACTAGCATACAAGCAAATAACCCAAGTTACTACACATACATGCTCTAATCAT-TCGATCACC
215811 TAACTAGCATA
130 TAACTAGCATA
215822 AAAAAGTGAA
Statistics
Matches: 122, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
150 120 0.98
151 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.26
Consensus pattern (150 bp):
GCCTAACTAGCATACAAGCGAATAACCCAAGTCATCACACATACATGCTCTGATCATATGATCGC
CTAACTAGCATACAAGCAAATAACCCAAGTTACTACACATACATGCTCTAATCATTCGATCACCT
AACTAGCATATCATCTAATA
Found at i:216067 original size:48 final size:49
Alignment explanation
Indices: 215932--216130 Score: 162
Period size: 48 Copynumber: 4.2 Consensus size: 49
215922 TTGCAAGCTT
* * *
215932 GCATATAAGCAAGCAACTCAAGTGACTATGCATACATGC-CCTCCGAAT-
1 GCATATAAGCAAGCAACTCAGGTTACTATGCATACATGCTCATCC-AATA
** * * ** *
215980 GCATATAAGTGAGTACCTCAGGTTACTACACATAAATGCTCAT-CAATA
1 GCATATAAGCAAGCAACTCAGGTTACTATGCATACATGCTCATCCAATA
* *
216028 GCATATAAGCAAGCAACTCAGGTTACTATGTATGCATGCT-ATCCAA-A
1 GCATATAAGCAAGCAACTCAGGTTACTATGCATACATGCTCATCCAATA
* * * * *
216075 TGCATAT-A-CAAGCAACTCAGGTTAGCCAGGCAAACATGCTCA-CCGATT
1 -GCATATAAGCAAGCAACTCAGGTTA-CTATGCATACATGCTCATCCAATA
216123 GCATATAA
1 GCATATAA
216131 ATGAGTAACT
Statistics
Matches: 117, Mismatches: 26, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
46 16 0.14
47 26 0.22
48 73 0.62
49 2 0.02
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (49 bp):
GCATATAAGCAAGCAACTCAGGTTACTATGCATACATGCTCATCCAATA
Found at i:219686 original size:20 final size:20
Alignment explanation
Indices: 219661--219698 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
219651 AAGGATACTC
219661 AAAAAGAACAAAA-AAAAAAG
1 AAAAAGAA-AAAAGAAAAAAG
219681 AAAAAGAAAAAAGAAAAA
1 AAAAAGAAAAAAGAAAAA
219699 CCTTTCAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.87, C:0.03, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAAAGAAAAAAG
Found at i:219698 original size:14 final size:13
Alignment explanation
Indices: 219661--219698 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
219651 AAGGATACTC
219661 AAAAAGAACAAAAA
1 AAAAAGAA-AAAAA
*
219675 AAAAAGAAAAAGA
1 AAAAAGAAAAAAA
219688 AAAAAGAAAAA
1 AAAAAGAAAAA
219699 CCTTTCAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.87, C:0.03, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAA
Found at i:221386 original size:18 final size:18
Alignment explanation
Indices: 221342--221387 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
221332 AAATATGATA
221342 TTTATTTAAATATTTAAT
1 TTTATTTAAATATTTAAT
221360 TATTA-TTAAAT-TTTATAT
1 T-TTATTTAAATATTTA-AT
221378 TTTATTTAAA
1 TTTATTTAAA
221388 AAATTATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 7 0.28
18 15 0.60
19 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTATTTAAATATTTAAT
Found at i:222949 original size:22 final size:23
Alignment explanation
Indices: 222924--222967 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
222914 TAGTTATTCT
222924 AAATATAAATCAAT-TAGATTTA
1 AAATATAAATCAATCTAGATTTA
* * *
222946 AAATTTAAGTTAATCTAGATTT
1 AAATATAAATCAATCTAGATTT
222968 GGTTAAACAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.41
Consensus pattern (23 bp):
AAATATAAATCAATCTAGATTTA
Found at i:223065 original size:16 final size:16
Alignment explanation
Indices: 223037--223097 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
223027 TGGATTAATT
* *
223037 ATTTAAATAATTTTAG
1 ATTTAAATTATTTTAA
* *
223053 ATTTGAATTATTTTAT
1 ATTTAAATTATTTTAA
*
223069 ATTTTAA-TATTTTTAA
1 ATTTAAATTA-TTTTAA
223085 ATTTAAATTATTT
1 ATTTAAATTATTT
223098 CGAATTCGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
15 2 0.05
16 33 0.89
17 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
ATTTAAATTATTTTAA
Found at i:223083 original size:32 final size:32
Alignment explanation
Indices: 223036--223097 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
223026 TTGGATTAAT
* *
223036 TATTTAAATAATTTTAGATTTGAATTATTTTA
1 TATTTAAATAATTTTAAATTTAAATTATTTTA
* *
223068 TATTTTAATATTTTTAAATTTAAATTATTT
1 TATTTAAATAATTTTAAATTTAAATTATTT
223098 CGAATTCGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (32 bp):
TATTTAAATAATTTTAAATTTAAATTATTTTA
Found at i:223204 original size:20 final size:20
Alignment explanation
Indices: 223179--223241 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
223169 TTAAAAAATT
223179 AATTAAATTTTTTAAATATA
1 AATTAAATTTTTTAAATATA
* **
223199 AATTAAAATTTAAAAATAT-
1 AATTAAATTTTTTAAATATA
* * *
223218 ATTTAAATTATTTTTAATTTA
1 AATTAAATT-TTTTAAATATA
223239 AAT
1 AAT
223242 ATAATATAAT
Statistics
Matches: 31, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
19 7 0.23
20 22 0.71
21 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTAAATTTTTTAAATATA
Found at i:223262 original size:28 final size:28
Alignment explanation
Indices: 223205--223265 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
223195 TATAAATTAA
* *
223205 AATTTAAAAATATATTTAAATTATTTTT
1 AATTTAAAAATATATATAAATTATTATT
* *
223233 AATTTAAATATA-ATATAATTTAATTATT
1 AATTTAAAAATATATATAAATT-ATTATT
223261 AATTT
1 AATTT
223266 TTTTAATCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
AATTTAAAAATATATATAAATTATTATT
Found at i:231771 original size:15 final size:15
Alignment explanation
Indices: 231751--231792 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
231741 AGCAACTACT
*
231751 GCAACAACAGCAGCA
1 GCAACAACAACAGCA
*
231766 GCAACAACAACAGCG
1 GCAACAACAACAGCA
*
231781 GCAGCAACAACA
1 GCAACAACAACA
231793 ACAGTTGCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.48, C:0.33, G:0.19, T:0.00
Consensus pattern (15 bp):
GCAACAACAACAGCA
Found at i:231773 original size:18 final size:18
Alignment explanation
Indices: 231752--231796 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
231742 GCAACTACTG
231752 CAACAACAGCAGCAGCAA
1 CAACAACAGCAGCAGCAA
*
231770 CAACAACAGCGGCAGCAA
1 CAACAACAGCAGCAGCAA
231788 CAACAACAG
1 CAACAACAG
231797 TTGCACCAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.49, C:0.33, G:0.18, T:0.00
Consensus pattern (18 bp):
CAACAACAGCAGCAGCAA
Found at i:238035 original size:22 final size:24
Alignment explanation
Indices: 237974--238035 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 24
237964 TTTATATTTT
* *
237974 ATATTATTACTATTAATTTTTATGT
1 ATATTA-TATTATTAATTTTTATGC
* * *
237999 AAATTAAATTTTTAA-TTTTAT-C
1 ATATTATATTATTAATTTTTATGC
238021 ATATTATATTATTAA
1 ATATTATATTATTAA
238036 ATTTCTATTA
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
22 12 0.41
23 6 0.21
24 6 0.21
25 5 0.17
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (24 bp):
ATATTATATTATTAATTTTTATGC
Found at i:240449 original size:19 final size:17
Alignment explanation
Indices: 240427--240465 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
240417 TATATATATA
240427 TATATATATAACTTAATTT
1 TATATATATAA--TAATTT
*
240446 TATATTTATAATAATTT
1 TATATATATAATAATTT
240463 TAT
1 TAT
240466 TTATTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
19 10 0.53
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATATATAATAATTT
Found at i:242098 original size:17 final size:18
Alignment explanation
Indices: 242065--242101 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
242055 TGATAAATTA
*
242065 AATATTTTAATTGTATTT
1 AATATTTAAATTGTATTT
242083 AATATTTAAATT-TATTT
1 AATATTTAAATTGTATTT
242100 AA
1 AA
242102 AATAGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
AATATTTAAATTGTATTT
Found at i:243926 original size:27 final size:26
Alignment explanation
Indices: 243861--243927 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
243851 ACAAATTATT
243861 AATT-ATTATTTTTAATTAACTTAAA
1 AATTAATTATTTTTAATTAACTTAAA
* * *
243886 AAATAATAAATTTTTAATTTACTTATAA
1 AATTAAT-TATTTTTAATTAACTTA-AA
*
243914 AATTAATTTTTTTT
1 AATTAATTATTTTT
243928 GTCATCAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
25 3 0.09
26 2 0.06
27 20 0.61
28 8 0.24
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (26 bp):
AATTAATTATTTTTAATTAACTTAAA
Found at i:245448 original size:14 final size:14
Alignment explanation
Indices: 245421--245468 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
245411 GTTGGCCTTG
*
245421 AAATTAAATAATATT
1 AAATAAAAT-ATATT
245436 AAATAAAATATATT
1 AAATAAAATATATT
245450 -AA-AAAATATATAT
1 AAATAAAATATAT-T
245463 AAATAA
1 AAATAA
245469 TAAATCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 9 0.31
13 3 0.10
14 7 0.24
15 10 0.34
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATAAAATATATT
Found at i:245495 original size:27 final size:28
Alignment explanation
Indices: 245425--245495 Score: 69
Period size: 28 Copynumber: 2.5 Consensus size: 28
245415 GCCTTGAAAT
245425 TAAATAATATTA-AATAAAATATATTAAA
1 TAAATAATATTATAATAAAATATA-TAAA
*
245453 -AAATATATATAAATAAT-AAATCATA-AAA
1 TAAATA-ATAT-TATAATAAAAT-ATATAAA
245481 TAAATAATATTATAA
1 TAAATAATATTATAA
245496 GATTAATGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
27 9 0.25
28 11 0.31
29 10 0.28
30 6 0.17
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (28 bp):
TAAATAATATTATAATAAAATATATAAA
Found at i:245815 original size:14 final size:14
Alignment explanation
Indices: 245767--245816 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
245757 AAAATATTTA
245767 ATTA-AATTTAA-T
1 ATTATAATTTAATT
* *
245779 ATTATAAATTAAATG
1 ATTAT-AATTTAATT
*
245794 ATAATAATTTAATT
1 ATTATAATTTAATT
245808 ATTATAATT
1 ATTATAATT
245817 ATGAAAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
12 4 0.14
14 21 0.72
15 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
ATTATAATTTAATT
Found at i:245816 original size:28 final size:25
Alignment explanation
Indices: 245770--245836 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 25
245760 ATATTTAATT
245770 AAATTTAA-TATTATAAATTAAATGATA
1 AAATTTAATTATTATAAATT--ATGA-A
245797 ATAATTTAATTATTAT-AATTATGAA
1 A-AATTTAATTATTATAAATTATGAA
*
245822 AAATTAAATTATTAT
1 AAATTTAATTATTAT
245837 TAAAATATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
24 13 0.35
25 2 0.05
26 4 0.11
27 1 0.03
28 11 0.30
29 6 0.16
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (25 bp):
AAATTTAATTATTATAAATTATGAA
Found at i:247281 original size:110 final size:110
Alignment explanation
Indices: 247088--247309 Score: 435
Period size: 110 Copynumber: 2.0 Consensus size: 110
247078 ATAGGTGAAT
247088 TGTCAATAAAAGTCAGCTATTTGTTTGTCAAAAATAATGATTATTTTGTGTTTGTAAAAAATAGA
1 TGTCAATAAAAGTCAGCTATTTGTTTGTCAAAAATAATGATTATTTTGTGTTTGTAAAAAATAGA
247153 AACTTGTTTATTTGTCAAAATTTGTGGTTAATTTTTATTACAAAA
66 AACTTGTTTATTTGTCAAAATTTGTGGTTAATTTTTATTACAAAA
*
247198 TGTCAATAAAAGTCAGCTATTTGTTTGTCAAAAATAGTGATTATTTTGTGTTTGTAAAAAATAGA
1 TGTCAATAAAAGTCAGCTATTTGTTTGTCAAAAATAATGATTATTTTGTGTTTGTAAAAAATAGA
247263 AACTTGTTTATTTGTCAAAATTTGTGGTTAATTTTTATTACAAAA
66 AACTTGTTTATTTGTCAAAATTTGTGGTTAATTTTTATTACAAAA
247308 TG
1 TG
247310 GGAGAAAATG
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 111 1.00
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (110 bp):
TGTCAATAAAAGTCAGCTATTTGTTTGTCAAAAATAATGATTATTTTGTGTTTGTAAAAAATAGA
AACTTGTTTATTTGTCAAAATTTGTGGTTAATTTTTATTACAAAA
Found at i:248927 original size:12 final size:14
Alignment explanation
Indices: 248900--248958 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 14
248890 TATTCATGTC
248900 ATATTTATATAATT
1 ATATTTATATAATT
248914 ATATTTA-A-AATT
1 ATATTTATATAATT
248926 ATTAAGTTTAATATAATTT
1 A-T-A-TTT-ATATAA-TT
*
248945 ATATTTATTTAATT
1 ATATTTATATAATT
248959 TTTAAATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
12 5 0.14
13 2 0.05
14 10 0.27
15 8 0.22
16 4 0.11
17 2 0.05
18 3 0.08
19 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
ATATTTATATAATT
Found at i:249965 original size:13 final size:13
Alignment explanation
Indices: 249947--249987 Score: 82
Period size: 13 Copynumber: 3.2 Consensus size: 13
249937 ATTCATCATA
249947 TATCGATACAATG
1 TATCGATACAATG
249960 TATCGATACAATG
1 TATCGATACAATG
249973 TATCGATACAATG
1 TATCGATACAATG
249986 TA
1 TA
249988 CCATGTATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:249994 original size:33 final size:33
Alignment explanation
Indices: 249922--250003 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
249912 CCGTTACAAG
*
249922 CAATGTATCGATACAATTCATCATATATCGATA
1 CAATGTATCGATACAATTCATCATAAATCGATA
249955 CAATGTATCGATACAATGT-ATCGATACAAT-G-TA
1 CAATGTATCGATACAAT-TCATC-ATA-AATCGATA
*
249988 CCATGTATCGATACAA
1 CAATGTATCGATACAA
250004 ACAGTGGTAG
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
33 37 0.84
34 5 0.11
35 2 0.05
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (33 bp):
CAATGTATCGATACAATTCATCATAAATCGATA
Found at i:249995 original size:20 final size:20
Alignment explanation
Indices: 249924--250003 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 20
249914 GTTACAAGCA
*
249924 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
*
249944 ATATATCGATACAATGTATCGATAC
1 ATGTATCGATACAATGTA-C----C
249969 AATGTATCGATACAATGTACC
1 -ATGTATCGATACAATGTACC
249990 ATGTATCGATACAA
1 ATGTATCGATACAA
250004 ACAGTGGTAG
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
20 29 0.58
21 2 0.04
25 2 0.04
26 17 0.34
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:250076 original size:19 final size:19
Alignment explanation
Indices: 250031--250086 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
250021 ACTGTCAGTT
**
250031 TCATGTATCGATACAATTG
1 TCATGTATCGATACAATAA
*
250050 TCCATGTATCAATACAATAA
1 T-CATGTATCGATACAATAA
250070 TCATGTATCGATACAAT
1 TCATGTATCGATACAAT
250087 GTATCGATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (19 bp):
TCATGTATCGATACAATAA
Found at i:250090 original size:13 final size:13
Alignment explanation
Indices: 250072--250098 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
250062 TACAATAATC
250072 ATGTATCGATACA
1 ATGTATCGATACA
250085 ATGTATCGATACA
1 ATGTATCGATACA
250098 A
1 A
250099 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:261458 original size:119 final size:120
Alignment explanation
Indices: 261280--261512 Score: 396
Period size: 119 Copynumber: 1.9 Consensus size: 120
261270 CAGGAACCGC
* *
261280 TCTGTGGTTCGTTTTCTGTATGCTATTATTTTATTACTGAAATTGGTTCTACATCTGTT-GACAA
1 TCTGTGGTTCGTTTTCTATATGCTAGTATTTTATTACTGAAATTGGTTCTACATCTGTTGGACAA
*
261344 TTAGATTAATCTAGCAGACAGCAACTAGTTATCTCTATCTGTTTGCAAAGTGCGA
66 TTAGATTAATCTAGCAGAAAGCAACTAGTTATCTCTATCTGTTTGCAAAGTGCGA
* *
261399 TCTGTGGTTGGTTTTCTATATGCTAGTATTTTATTACTGAAATTGGTTCTACATCTGTTGGATAA
1 TCTGTGGTTCGTTTTCTATATGCTAGTATTTTATTACTGAAATTGGTTCTACATCTGTTGGACAA
* *
261464 TTATATTAATCTAGCAGAAAGCAACTAGTTGTCTCTATCTGTTTGCAAA
66 TTAGATTAATCTAGCAGAAAGCAACTAGTTATCTCTATCTGTTTGCAAA
261513 TTGCAATTCT
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
119 56 0.53
120 50 0.47
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.42
Consensus pattern (120 bp):
TCTGTGGTTCGTTTTCTATATGCTAGTATTTTATTACTGAAATTGGTTCTACATCTGTTGGACAA
TTAGATTAATCTAGCAGAAAGCAACTAGTTATCTCTATCTGTTTGCAAAGTGCGA
Found at i:264278 original size:2 final size:2
Alignment explanation
Indices: 264271--264297 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
264261 ACCACTTAAT
264271 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
264298 TTTTGTTGTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:268802 original size:63 final size:63
Alignment explanation
Indices: 268664--268863 Score: 350
Period size: 63 Copynumber: 3.2 Consensus size: 63
268654 TATCACCTTA
* *
268664 CCTAACTAGCATACAAGTGAATAACCCAAGTTATTACA-TTACA-GCTCTGATCATTTGATCG
1 CCTAACTAGCATACAAGCGAATAACCCAAGTTATTACACATACATGCTCTGATCATTTGATCG
268725 CCTAACTAGCATACAAGCGAATAACCCAAGTTATTACACATACATGCTCTGATCATTTGATCG
1 CCTAACTAGCATACAAGCGAATAACCCAAGTTATTACACATACATGCTCTGATCATTTGATCG
*
268788 CCTAACTAGCATACAAGCGAATAACCCAAGTTATTACACATACATGCTCTGATCATTTGATCA
1 CCTAACTAGCATACAAGCGAATAACCCAAGTTATTACACATACATGCTCTGATCATTTGATCG
*
268851 CCTAGCTAGCATA
1 CCTAACTAGCATA
268864 TCATCTAATA
Statistics
Matches: 133, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
61 37 0.28
62 4 0.03
63 92 0.69
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (63 bp):
CCTAACTAGCATACAAGCGAATAACCCAAGTTATTACACATACATGCTCTGATCATTTGATCG
Found at i:268922 original size:87 final size:87
Alignment explanation
Indices: 268787--268946 Score: 230
Period size: 87 Copynumber: 1.8 Consensus size: 87
268777 TCATTTGATC
* * *
268787 GCCTAACTAGCATACAAGCGAATAACCCAAGTTATTACACATACATGCTCTGATCATTTGATCAC
1 GCCTAACTAGCATACAAGCGAATAACCCAAGTCATCACACATACATGCTCTGATCATATGATCAC
*
268852 CTAGCTAGCATATCATCTAATA
66 CTAACTAGCATATCATCTAATA
* * * * * *
268874 GCCTAACTAGCATACAAGGGAGTATCCTAAGTCATCACACATACATGCTCTGATCGTATGATCGC
1 GCCTAACTAGCATACAAGCGAATAACCCAAGTCATCACACATACATGCTCTGATCATATGATCAC
268939 CTAACTAG
66 CTAACTAG
268947 AATACAAGCA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
87 63 1.00
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (87 bp):
GCCTAACTAGCATACAAGCGAATAACCCAAGTCATCACACATACATGCTCTGATCATATGATCAC
CTAACTAGCATATCATCTAATA
Found at i:269002 original size:150 final size:150
Alignment explanation
Indices: 268724--269010 Score: 378
Period size: 150 Copynumber: 1.9 Consensus size: 150
268714 TCATTTGATC
* * *
268724 GCCTAACTAGCATACAAGCGAATAACCCAAGTTATTACACATACATGCTCTGATCATTTGATCGC
1 GCCTAACTAGCATACAAGCGAATAACCCAAGTCATCACACATACATGCTCTGATCATATGATCGC
* * * * *
268789 CTAACTAGCATACAAGCGAATAACCCAAGTTATTACACATACATGCTCTGATCATTTGATCACCT
66 CTAACTAGAATACAAGCAAATAACCCAAGTTACTACACATACATGCTCTAATCATTCGATCACCT
*
268854 AGCTAGCATATCATCTAATA
131 AACTAGCATATCATCTAATA
* * * * *
268874 GCCTAACTAGCATACAAGGGAGTATCCTAAGTCATCACACATACATGCTCTGATCGTATGATCGC
1 GCCTAACTAGCATACAAGCGAATAACCCAAGTCATCACACATACATGCTCTGATCATATGATCGC
* * * * * *
268939 CTAACTAGAATACAAGCAAATAACCCGAGTTACTACGCATGCGTGCTTTAATCGTCTCG-TCACC
66 CTAACTAGAATACAAGCAAATAACCCAAGTTACTACACATACATGCTCTAATCAT-TCGATCACC
269003 TAACTAGC
130 TAACTAGC
269011 CTAAAAAAGT
Statistics
Matches: 116, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
150 114 0.98
151 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (150 bp):
GCCTAACTAGCATACAAGCGAATAACCCAAGTCATCACACATACATGCTCTGATCATATGATCGC
CTAACTAGAATACAAGCAAATAACCCAAGTTACTACACATACATGCTCTAATCATTCGATCACCT
AACTAGCATATCATCTAATA
Found at i:269007 original size:213 final size:211
Alignment explanation
Indices: 268620--269039 Score: 497
Period size: 213 Copynumber: 2.0 Consensus size: 211
268610 TTATTGCAGG
*
268620 TACATACTCTGATCATCTGATCACCTAACAAGCATATCACCTTACCTAACTAGCATACAAGTGAA
1 TACATACTCTGATCATCTGATCACCTAACAAGCATATCACCTTACCTAACTAGCATACAAGGGAA
* * * * * *
268685 TAACCCAAGTTATTACATTACAGCTCTGATCATTTGATCGCCTAACTAGCATACAAGCGAATAAC
66 TAACCCAAGTCATCACAATACAGCTCTGATCATATGATCGCCTAACTAGAATACAAGCAAATAAC
* * * * * *
268750 CCAAGTTATTACACATACATGCTCTGATCATTTGATCGCCTAACTAG-C-ATACAAGCGAATAAC
131 CCAAGTTACTACACATACATGCTCTAATCATTCGATCACCTAACTAGCCTAAAAAAGCGAATAAC
268813 CC-AAGTTATTACACA
196 CCAAAGTTATTACACA
* * * * *
268828 TACATGCTCTGATCATTTGATCACCTAGCTAGCATATCATCTAATAGCCTAACTAGCATACAAGG
1 TACATACTCTGATCATCTGATCACCTAACAAGCATATCACCT--TA-CCTAACTAGCATACAAGG
* * * *
268893 GAGTATCCTAAGTCATCACACATACATGCTCTGATCGTATGATCGCCTAACTAGAATACAAGCAA
63 GAATAACCCAAGTCATCACA-ATACA-GCTCTGATCATATGATCGCCTAACTAGAATACAAGCAA
* * * * * * *
268958 ATAACCCGAGTTACTACGCATGCGTGCTTTAATCGTCTCG-TCACCTAACTAGCCTAAAAAAGTG
126 ATAACCCAAGTTACTACACATACATGCTCTAATCAT-TCGATCACCTAACTAGCCTAAAAAAGCG
269022 AATAACCCAAAGTTATTA
190 AATAACCCAAAGTTATTA
269040 TGCAAACATG
Statistics
Matches: 174, Mismatches: 29, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
208 37 0.21
210 2 0.01
211 32 0.18
212 4 0.02
213 73 0.42
214 3 0.02
215 14 0.08
216 9 0.05
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (211 bp):
TACATACTCTGATCATCTGATCACCTAACAAGCATATCACCTTACCTAACTAGCATACAAGGGAA
TAACCCAAGTCATCACAATACAGCTCTGATCATATGATCGCCTAACTAGAATACAAGCAAATAAC
CCAAGTTACTACACATACATGCTCTAATCATTCGATCACCTAACTAGCCTAAAAAAGCGAATAAC
CCAAAGTTATTACACA
Found at i:269295 original size:46 final size:46
Alignment explanation
Indices: 269232--269333 Score: 195
Period size: 46 Copynumber: 2.2 Consensus size: 46
269222 ATATAAGCAG
*
269232 GCAACTCAGGTTACTATGTATGCATGCTATCCAAATGCATATACAA
1 GCAACTCAGGCTACTATGTATGCATGCTATCCAAATGCATATACAA
269278 GCAACTCAGGCTACTATGTATGCATGCTATCCAAATGCATATACAA
1 GCAACTCAGGCTACTATGTATGCATGCTATCCAAATGCATATACAA
269324 GCAACTCAGG
1 GCAACTCAGG
269334 TTAGCAGGCA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 55 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (46 bp):
GCAACTCAGGCTACTATGTATGCATGCTATCCAAATGCATATACAA
Found at i:269350 original size:46 final size:46
Alignment explanation
Indices: 269254--269351 Score: 135
Period size: 46 Copynumber: 2.1 Consensus size: 46
269244 ACTATGTATG
* * **
269254 CATGCTATCCAAATGCATATACAAGCAACTCAGGCTACTATGTATG
1 CATGCTATCCAAATGCATATACAAGCAACTCAGGCTACTAGGCAAA
*
269300 CATGCTATCCAAATGCATATACAAGCAACTCAGGTTAGC-AGGCAAA
1 CATGCTATCCAAATGCATATACAAGCAACTCAGGCTA-CTAGGCAAA
269346 CATGCT
1 CATGCT
269352 CACAGATTGC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.23
Consensus pattern (46 bp):
CATGCTATCCAAATGCATATACAAGCAACTCAGGCTACTAGGCAAA
Found at i:275985 original size:2 final size:2
Alignment explanation
Indices: 275978--276008 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
275968 TTTGATTATT
275978 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
276009 TCGACTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:276899 original size:2 final size:2
Alignment explanation
Indices: 276892--276921 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
276882 TATCCAAATG
276892 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
276922 TATTTTAATT
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):
AT
Found at i:277067 original size:29 final size:31
Alignment explanation
Indices: 277022--277081 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
277012 AATGTGTGAA
*
277022 AATATATTAAAATTTATATAATTAAATTATT
1 AATATATTAAAATTTATATAAATAAATTATT
* *
277053 AATATA-TAAAA-TTATTTAAATATATTATT
1 AATATATTAAAATTTATATAAATAAATTATT
277082 TTAAATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 15 0.58
30 5 0.19
31 6 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
AATATATTAAAATTTATATAAATAAATTATT
Found at i:293641 original size:26 final size:25
Alignment explanation
Indices: 293593--293653 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
293583 TTAATAAAAA
* * *
293593 TTAAATATAATTTTTATA-TTTAAT
1 TTAAATTTAATTTTTACACTTAAAT
293617 TTAAAATTTAATTATTTACACTTAAAT
1 TT-AAATTTAATT-TTTACACTTAAAT
293644 TTAAATTTAA
1 TTAAATTTAA
293654 ATTAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 2 0.06
25 9 0.29
26 13 0.42
27 7 0.23
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (25 bp):
TTAAATTTAATTTTTACACTTAAAT
Found at i:293663 original size:40 final size:40
Alignment explanation
Indices: 293619--293704 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
293609 TATTTAATTT
* * *
293619 AAAATTTAATT-ATTTACACTTAAATTTAAATTTAAATTAA
1 AAAATTTAATTCATTTAAAATAAAATTTAAA-TTAAATTAA
* * *
293659 AAAATTTCATTCATTTAAAATAAAATTTTAATTAAATTTA
1 AAAATTTAATTCATTTAAAATAAAATTTAAATTAAATTAA
293699 AAAATT
1 AAAATT
293705 ATTTAAATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 24 0.62
41 15 0.38
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (40 bp):
AAAATTTAATTCATTTAAAATAAAATTTAAATTAAATTAA
Found at i:293697 original size:23 final size:23
Alignment explanation
Indices: 293644--293726 Score: 71
Period size: 22 Copynumber: 3.6 Consensus size: 23
293634 ACACTTAAAT
* * *
293644 TTAAATTTAAATTAAAAAATTTCA
1 TTAAATTTAAAAT-AAAATTTTAA
*
293668 TT-CATTTAAAATAAAATTTTAA
1 TTAAATTTAAAATAAAATTTTAA
** *
293690 TTAAATTTAAAA-ATTATTTAAA
1 TTAAATTTAAAATAAAATTTTAA
293712 TTAAATATTAAAATA
1 TTAAAT-TTAAAATA
293727 TTTAAGGTGA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
22 23 0.48
23 22 0.46
24 3 0.06
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TTAAATTTAAAATAAAATTTTAA
Found at i:294484 original size:23 final size:22
Alignment explanation
Indices: 294421--294485 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 22
294411 TCTTTCAAAT
*
294421 AATTTATTTTAATAATGAAGAAA
1 AATTTATTTTAAAAAT-AAGAAA
*
294444 AATTAATTTATAAAAAATAA-AAA
1 AATTTATTT-T-AAAAATAAGAAA
294467 ACATTTATTTTATAAAATA
1 A-ATTTATTTTA-AAAATA
294486 CTAAAGCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
22 1 0.03
23 19 0.54
24 10 0.29
25 5 0.14
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (22 bp):
AATTTATTTTAAAAATAAGAAA
Found at i:295520 original size:7 final size:7
Alignment explanation
Indices: 295508--295533 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
295498 ACAATCATAT
295508 TAAAAAA
1 TAAAAAA
295515 TAAAAAA
1 TAAAAAA
295522 TAAAAAA
1 TAAAAAA
295529 TAAAA
1 TAAAA
295534 TAAAATATTG
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:295583 original size:2 final size:2
Alignment explanation
Indices: 295578--295623 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
295568 AATAACAACT
295578 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
295620 TA TA
1 TA TA
295624 CACACATACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:295877 original size:22 final size:22
Alignment explanation
Indices: 295851--295900 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
295841 TCAATGAAAG
*
295851 TTTTAGAATCATAA-ACAAATGT
1 TTTTA-AACCATAATACAAATGT
* *
295873 TTTTAAACCTTAATTCAAATGT
1 TTTTAAACCATAATACAAATGT
295895 TTTTAA
1 TTTTAA
295901 GTAAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (22 bp):
TTTTAAACCATAATACAAATGT
Found at i:296167 original size:33 final size:33
Alignment explanation
Indices: 296104--296168 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
296094 TACTATTGTT
* * *
296104 TGTATCGATACATGGTACATTGCATTGATACAA
1 TGTATCAATACATGATACATTGCATCGATACAA
*
296137 TGTATCAATACATGATGA-ATTGTATCGATACA
1 TGTATCAATACATGAT-ACATTGCATCGATACA
296169 TTGCTTCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (33 bp):
TGTATCAATACATGATACATTGCATCGATACAA
Found at i:301710 original size:21 final size:22
Alignment explanation
Indices: 301686--301728 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
301676 ATCAAATCTT
* *
301686 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
301707 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
301729 TCAATATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.28, C:0.21, G:0.00, T:0.51
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:311972 original size:2 final size:2
Alignment explanation
Indices: 311925--311955 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
311915 AAGTCTTCTG
311925 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 A
311956 CATGCATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:314325 original size:11 final size:11
Alignment explanation
Indices: 314309--314333 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
314299 TATTAAATCG
314309 TATTTTGATCA
1 TATTTTGATCA
314320 TATTTTGATCA
1 TATTTTGATCA
314331 TAT
1 TAT
314334 CTGATTTTAT
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:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (11 bp):
TATTTTGATCA
Found at i:316054 original size:20 final size:20
Alignment explanation
Indices: 316021--316061 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
316011 TTTTTTTATT
316021 TAAATTTAATTATAAAAATA
1 TAAATTTAATTATAAAAATA
316041 TAAATATTAA-TATAAAAATA
1 TAAAT-TTAATTATAAAAATA
316061 T
1 T
316062 TTTTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAATTTAATTATAAAAATA
Found at i:316099 original size:29 final size:28
Alignment explanation
Indices: 316045--316101 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
316035 AAAATATAAA
* *
316045 TATTAATATAAAAATATTTTTTAATTTT
1 TATTAATATAAAAATATATTTAAATTTT
316073 TATTAATTATAAATAATA-ATTTAAATTTT
1 TATTAA-TATAAA-AATATATTTAAATTTT
316102 CATATCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.24
29 15 0.60
30 4 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TATTAATATAAAAATATATTTAAATTTT
Found at i:319550 original size:5 final size:5
Alignment explanation
Indices: 319540--319586 Score: 76
Period size: 5 Copynumber: 9.4 Consensus size: 5
319530 AGCCACAACT
* *
319540 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AAGAA AAGAA AA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AA
319587 CGGTGAGTGG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (5 bp):
AATAA
Found at i:319905 original size:3 final size:3
Alignment explanation
Indices: 319897--319925 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
319887 ACGCACTCAC
319897 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
319926 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:320168 original size:3 final size:3
Alignment explanation
Indices: 320160--320196 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
320150 TAGATTTTCC
320160 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
320197 TTATTATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:321311 original size:19 final size:20
Alignment explanation
Indices: 321265--321311 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
321255 GTGTATAGTT
*
321265 ATTTTTTAAATATTATTTAA
1 ATTTTTTAAATATCATTTAA
* *
321285 ATTGTTTAATTATCATTT-A
1 ATTTTTTAAATATCATTTAA
321304 ATTTTTTA
1 ATTTTTTA
321312 GCATTTAGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTTTTAAATATCATTTAA
Found at i:321931 original size:23 final size:21
Alignment explanation
Indices: 321895--321937 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
321885 TATTATATTT
*
321895 TTATTTATTTAATAATTAAAA
1 TTATTTATTTAATAAATAAAA
321916 TTATTTATTTAAAATAAATAAA
1 TTATTTATTT--AATAAATAAA
321938 TAAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
23 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTATTTATTTAATAAATAAAA
Found at i:321967 original size:25 final size:25
Alignment explanation
Indices: 321889--321969 Score: 85
Period size: 25 Copynumber: 3.2 Consensus size: 25
321879 TAAATATATT
321889 ATATTTTTATTTATTTAATAATTAA
1 ATATTTTTATTTATTTAATAATTAA
* * *
321914 A-ATTATTTATTTAAAATAAATAAATAA
1 ATATT-TTTATTT--ATTTAATAATTAA
321941 ATATTTTTAATTTATTTAA-AATTAA
1 ATATTTTT-ATTTATTTAATAATTAA
321966 ATAT
1 ATAT
321970 ATATAATTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
24 3 0.07
25 17 0.38
26 4 0.09
27 14 0.31
28 7 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATATTTTTATTTATTTAATAATTAA
Found at i:322264 original size:2 final size:2
Alignment explanation
Indices: 322257--322290 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
322247 AAGACATTCC
322257 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
322291 TTCCTAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:330181 original size:26 final size:28
Alignment explanation
Indices: 330134--330186 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 28
330124 TTAAGTTAGC
*
330134 TTTTATTGTATTAAAATTATTT-TTTTA
1 TTTTATTGTATTAAAATAATTTATTTTA
**
330161 TTTT-TTGTATTTGAATAATTTATTTT
1 TTTTATTGTATTAAAATAATTTATTTT
330187 TTCAAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (28 bp):
TTTTATTGTATTAAAATAATTTATTTTA
Found at i:330437 original size:26 final size:27
Alignment explanation
Indices: 330407--330486 Score: 65
Period size: 32 Copynumber: 2.8 Consensus size: 27
330397 CACAATTATA
330407 TTTAAAATATTTTATATTCATAT-AAT
1 TTTAAAATATTTTATATTCATATAAAT
* *
330433 TTTAATATGTTAATAGTTTGTATT-ATATAAAT
1 TTT-A-A----AATATTTTATATTCATATAAAT
330465 TTTAAAATATTTGTATATTCAT
1 TTTAAAATATTT-TATATTCAT
330487 GTCATATTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 16
0.67 0.07 0.26
Matches are distributed among these distances:
26 9 0.22
27 6 0.15
28 3 0.07
30 1 0.02
31 5 0.12
32 17 0.41
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.54
Consensus pattern (27 bp):
TTTAAAATATTTTATATTCATATAAAT
Found at i:331586 original size:26 final size:27
Alignment explanation
Indices: 331510--331589 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
331500 AATCTAATCT
331510 TTTTTAATATAATTTAACAATTAAA-A
1 TTTTTAATATAATTTAACAATTAAATA
* * ** *
331536 TTTTATTATGTAAAATAATAATTAAATA
1 TTTT-TAATATAATTTAACAATTAAATA
331564 TTTTTAAT-TAATTTAA-AATTTAAATA
1 TTTTTAATATAATTTAACAA-TTAAATA
331590 CATGATTTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
25 2 0.05
26 17 0.40
27 19 0.44
28 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (27 bp):
TTTTTAATATAATTTAACAATTAAATA
Found at i:331759 original size:2 final size:2
Alignment explanation
Indices: 331699--331743 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
331689 TATTCTTAAG
331699 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
331741 TA T
1 TA T
331744 CACCATATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:331888 original size:143 final size:143
Alignment explanation
Indices: 331727--332029 Score: 588
Period size: 143 Copynumber: 2.1 Consensus size: 143
331717 TATATATATA
*
331727 TATATATATATATATATCACCATATTATATATAAGTGGATCAATGTAGCATTTACCATATTGCTT
1 TATATATATATATATATCACCATATAATATATAAGTGGATCAATGTAGCATTTACCATATTGCTT
331792 TTGGTTGGTGACATTAATTCACCAAAGTGAACTTAGACAATGGACAAAACCCAAATAGAAAAAGC
66 TTGGTTGGTGACATTAATTCACCAAAGTGAACTTAGACAATGGACAAAACCCAAATAGAAAAAGC
*
331857 CAATGTTTTGAGC
131 CAACGTTTTGAGC
331870 TATATATATATATATATCACCATATAATATATAAGTGGATCAATGTAGCATTTACCATATTGCTT
1 TATATATATATATATATCACCATATAATATATAAGTGGATCAATGTAGCATTTACCATATTGCTT
331935 TTGGTTGGTGACATTAATTCACCAAAGTGAACTTAGACAATGGACAAAACCCAAATAGAAAAAGC
66 TTGGTTGGTGACATTAATTCACCAAAGTGAACTTAGACAATGGACAAAACCCAAATAGAAAAAGC
332000 CAACGTTTTGAGC
131 CAACGTTTTGAGC
332013 TATATATATATATATAT
1 TATATATATATATATAT
332030 ATATATATAA
Statistics
Matches: 158, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
143 158 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (143 bp):
TATATATATATATATATCACCATATAATATATAAGTGGATCAATGTAGCATTTACCATATTGCTT
TTGGTTGGTGACATTAATTCACCAAAGTGAACTTAGACAATGGACAAAACCCAAATAGAAAAAGC
CAACGTTTTGAGC
Found at i:332020 original size:2 final size:2
Alignment explanation
Indices: 332013--332038 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
332003 CGTTTTGAGC
332013 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
332039 ATTCAAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:333928 original size:23 final size:22
Alignment explanation
Indices: 333902--333945 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
333892 AAATTTAACA
*
333902 TTTAAATTTTAATCTTTATTTTC
1 TTTAAATTATAAT-TTTATTTTC
* *
333925 TTTAGATTATAATTTTTTTTT
1 TTTAAATTATAATTTTATTTT
333946 ACCAAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTAAATTATAATTTTATTTTC
Found at i:334228 original size:29 final size:29
Alignment explanation
Indices: 334196--334278 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 29
334186 ATTAAATACA
334196 TTATATAATATAAATATATATTTTAAAAT
1 TTATATAATATAAATATATATTTTAAAAT
*
334225 TTATAAAATATAAAT-TATTAATTTATTAAAAT
1 TTATATAATATAAATATA-T-A-TT-TTAAAAT
334257 TTATATAAATATAAA-ATA-ATTT
1 TTATAT-AATATAAATATATATTT
334279 AAATATGATT
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
28 3 0.07
29 17 0.37
30 2 0.04
31 2 0.04
32 12 0.26
33 10 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TTATATAATATAAATATATATTTTAAAAT
Found at i:334235 original size:23 final size:23
Alignment explanation
Indices: 334207--334262 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
334197 TATATAATAT
334207 AAATATATATT-TTAAAATTTA-TA
1 AAATATATATTATT--AATTTATTA
*
334230 AAATATAAATTATTAATTTATTA
1 AAATATATATTATTAATTTATTA
*
334253 AAATTTATAT
1 AAATATATAT
334263 AAATATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 6 0.21
23 20 0.71
24 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATATATATTATTAATTTATTA
Found at i:334322 original size:28 final size:28
Alignment explanation
Indices: 334259--334329 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
334249 ATTAAAATTT
* *
334259 ATATAAATAT-AAAATAATTTAAATATG
1 ATATAAATATAAAAATAATATAAATATA
334286 AT-TATAATATAAAAAATAA-ATAAATATA
1 ATATA-AATAT-AAAAATAATATAAATATA
*
334314 ATATAAATATATAAAT
1 ATATAAATATAAAAAT
334330 TATTAAGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
26 2 0.05
27 12 0.32
28 14 0.38
29 9 0.24
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (28 bp):
ATATAAATATAAAAATAATATAAATATA
Found at i:335825 original size:27 final size:27
Alignment explanation
Indices: 335769--335826 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
335759 TTAGCATATG
** *
335769 TTTTTCTAAATTTTAAATGCTTTTATA
1 TTTTTCTAAATTTTAAATGAGTTTAGA
*
335796 TTTTTCTAAATTTTAAAATTAGTTT-GA
1 TTTTTCTAAATTTT-AAATGAGTTTAGA
335823 TTTT
1 TTTT
335827 ATAAATAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.60
Consensus pattern (27 bp):
TTTTTCTAAATTTTAAATGAGTTTAGA
Found at i:336623 original size:78 final size:79
Alignment explanation
Indices: 336479--336623 Score: 179
Period size: 78 Copynumber: 1.8 Consensus size: 79
336469 CTGGTTTCAG
* * ** *
336479 CCATGCCATCGATTTAGAATAGTAATTTTTGTTCTAACTCGTGCCACCTGTAAAAATAGTGGTTT
1 CCATGCCATCGAGTAAGAATAGTAATTTTTGTTCTAACTCGTGCCACCAATAAAAATAGTGATTT
336544 TTGTTTTAGTCCAC
66 TTGTTTTAGTCCAC
* * *
336558 CCATGCCATC-AGTAAGAATAGTAGTTTTTGTTCTAAAC-CGTGCCACCAAATTAGAATA-TGAT
1 CCATGCCATCGAGTAAGAATAGTAATTTTTGTTCT-AACTCGTGCCACC-AATAAAAATAGTGAT
336620 TTTT
64 TTTT
336624 ATTCTAACCT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
78 37 0.66
79 19 0.34
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (79 bp):
CCATGCCATCGAGTAAGAATAGTAATTTTTGTTCTAACTCGTGCCACCAATAAAAATAGTGATTT
TTGTTTTAGTCCAC
Found at i:341611 original size:28 final size:28
Alignment explanation
Indices: 341528--342985 Score: 860
Period size: 28 Copynumber: 50.2 Consensus size: 28
341518 TTTTTAAAAA
*
341528 AAAGG-TGCCACTAACTTCTGTGGGCTTT-
1 AAAGGATGCCACTGAC-T-TGTGGGCTTTG
* * *
341556 AAAGAAATGCCACTGACTTGTTGACTTTG
1 AAAG-GATGCCACTGACTTGTGGGCTTTG
* *
341585 AAAGGATGCCACTAACTTATGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * *
341613 GAAGGATGCCACTGAGTCGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * *
341641 AAAAGTTGCCACTGACTTGTGGGCTTGG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * *
341669 AAAAGATACCATTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* ** * * *
341697 AAAAGATGCCACCAACTTGTCGACATTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
341725 AAAGGATGCCACTGACTTGTAGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* ** *
341753 AAATGGGTTGCCACCAATTTGTGTGGGCTTTG
1 AAA--GGATGCCACTGA-CT-TGTGGGCTTTG
* * *
341785 AAATGAGTTGCCACCGA-TTGTGTGGTCTTTC
1 AAA-G-GATGCCACTGACTTGTG-GG-CTTTG
* **
341816 AAATGGGTTGCCACCAACTTGTGTGGGCTTTG
1 AAA--GGATGCCACTGAC-T-TGTGGGCTTTG
* **
341848 AAATGGGTTGCCACCAACTTGTGTGGGCTTTGG
1 AAA--GGATGCCACTGAC-T-TGTGGGCTTT-G
* *
341881 AAATAGGTTGCCAC-CAGCTTGTGTGGGCTTTG
1 -AA-AGGATGCCACTGA-C-T-TGTGGGCTTTG
* ** *
341913 AAATGGTTGCCACCAACTTGTGTGGGCTTTC
1 AAA-GGATGCCACTGAC-T-TGTGGGCTTTG
* *
341944 AAATGAGTGCCACTGACTTGCGTGGGCTTTA
1 AAAGGA-TGCCACTGACTT--GTGGGCTTTG
* **
341975 AAAGGATGCCACTAACTCATGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
342003 AAA-GAGTGCCACTGACTTGTGGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTG
* *
342031 AAAGGGTGCCACTGACTCGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * *
342059 AAAAGAGTGCTACTGACTCGTGGGCTTTGG
1 AAAGGA-TGCCACTGACTTGTGGGCTTT-G
* * *
342089 AAAAGATACCATTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
342117 AAAAGGGTTGCCA-TCGACTCGTGTGGGCTTTG
1 -AAA-GGATGCCACT-GACT--TGTGGGCTTTG
*
342149 AAAGGATGCCACTAACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
342177 AAAGGGTGCCACTAACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * *
342205 AAAAGTGTTGCCACCGACTCGTGGGCTTTG
1 -AAAG-GATGCCACTGACTTGTGGGCTTTG
*
342235 AAAGGATGCCACTGACTTGTAGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * *
342263 AAAAGGGTTGCCACCGGCTCGTGTGGGCTTTG
1 -AAA-GGATGCCACTGACT--TGTGGGCTTTG
* *
342295 AAAAGAGTGCCACTAACTTGTGGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTG
*
342324 AAAGGATGCCACTGACTTGTAGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
342352 AAAAGTGTTGCCACTGACTCGTGGGCTTTG
1 -AAAG-GATGCCACTGACTTGTGGGCTTTG
*
342382 AAAGGATGCCACTAACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
342410 AAAAGGGTTGCCACCGACTCATGTGGGCTTTG
1 -AAA-GGATGCCACTGACT--TGTGGGCTTTG
*
342442 AAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTG
* * *
342471 AAAGGGTGCCACTGATTTGTGGGCTTTA
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * * *
342499 AAAGGGTGCCACTAATTTGTGGGCTATG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
342527 AAATTGGTTGCCACTGACTTGTGTGGGCTTTC
1 AAA--GGATGCCACTGAC-T-TGTGGGCTTTG
* *
342559 AAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAA--GGATGCCACTGAC-T-TGTGGGCTTTG
* * *
342591 AAATAGGTTGCCACCGACTTGTGTGGGCTTTA
1 -AA-AGGATGCCACTGAC-T-TGTGGGCTTTG
* **
342623 AAAGGGTGCCACTGACTTGTGGGCTTAA
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* ** *
342651 AAAGGATGCCAC-GAAGTTGTGAAC-TTA
1 AAAGGATGCCACTG-ACTTGTGGGCTTTG
* * * *
342678 AAAGGGTGCCA-TGGAGTTGTGGACTTTA
1 AAAGGATGCCACT-GACTTGTGGGCTTTG
* * * *
342706 AAAGGGTGCCACGGAGTTGTGGACTTT-
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * * * *
342733 AAAGGGTGCCACGGAGTTGTGGAC-TTA
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * * *
342760 AAACGATGCCA-TGGAGTTGTGGACTTTA
1 AAAGGATGCCACT-GACTTGTGGGCTTTG
* * * * * *
342788 AAAGGGTGCCACGGAGTTATGGACTTTA
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * * * *
342816 AAAGGGTGCCACGGAGTTGTGGACTTTA
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * * * *
342844 AAAGGGTGCTACGGAGTTGTGGACTTT-
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * * * *
342871 AAAGGGTACCA-TGGAGTTGTGGAC-TTA
1 AAAGGATGCCACT-GACTTGTGGGCTTTG
* * * * *
342898 AAACGATGCCACGGAATTGTGGACTTTA
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * * * *
342926 AAAGGGTGCCACGGAGTTGTGGACTTTA
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * * *
342954 AAAGGGTGCCACGGAGTTGTGGACTTT-
1 AAAGGATGCCACTGACTTGTGGGCTTTG
342981 AAAGG
1 AAAGG
342986 GTACCACAGA
Statistics
Matches: 1206, Mismatches: 158, Indels: 133
0.81 0.11 0.09
Matches are distributed among these distances:
26 4 0.00
27 111 0.09
28 543 0.45
29 106 0.09
30 147 0.12
31 100 0.08
32 158 0.13
33 29 0.02
34 7 0.01
35 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (28 bp):
AAAGGATGCCACTGACTTGTGGGCTTTG
Found at i:342018 original size:58 final size:58
Alignment explanation
Indices: 341533--342648 Score: 767
Period size: 58 Copynumber: 18.8 Consensus size: 58
341523 AAAAAAAAGG
* * * * *
341533 TGCCACTAACTTCTGTGGGCTTT-AAAGAAATGCCACTGACTTGTTGACTTTGAAAG-GA
1 TGCCACTGACTT-TGTGGGCTTTAAAAG-GATGCCACTGACTTGTGGGCTTTGAAAGAGT
* * ** * *
341591 TGCCACTAAC-TTATGGGCTTTGGAAGGATGCCACTGAGTCGTGGGCTTTGAAA-AGT
1 TGCCACTGACTTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGT
* * * *
341647 TGCCACTGAC-TTGTGGGCTTGGAAAA-GATACCATTGACTTGTGGGCTTTGAAA-AGA
1 TGCCACTGACTTTGTGGGCTT-TAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGT
** * * * * * *
341703 TGCCACCAAC-TTGTCGACATTGAAAGGATGCCACTGACTTGTAGGCTTTGAAATGGGT
1 TGCCACTGACTTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAA-GAGT
** * * * * * *
341761 TGCCACCAATTTGTGTGGGCTTTGAAATGAGTTGCCACCGA-TTGTGTGGTCTTTCAAATGGGT
1 TGCCACTGACTT-TGTGGGCTTT-AAAAG-GATGCCACTGACTTGTG-GG-CTTTGAAA-GAGT
** * * ** *
341824 TGCCACCAACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGGAAATAGGT
1 TGCCACTGACTT-TGTGGGCTTT-AAA-AGGATGCCACTGAC-T-TGTGGGCTTT-GAAAGA-GT
* * * ** *
341889 TGCCAC-CAGCTTGTGTGGGCTTTGAAATGGTTGCCACCAACTTGTGTGGGCTTTCAAATGAG-
1 TGCCACTGA-CTT-TGTGGGCTTT-AAAAGGATGCCACTGAC-T-TGTGGGCTTTGAAA-GAGT
* * **
341951 TGCCACTGACTTGCGTGGGCTTTAAAAGGATGCCACTAACTCATGGGCTTTGAAAGAG-
1 TGCCACTGACTT-TGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGT
* * *
342009 TGCCACTGAC-TTGTGGGCTTTGAAAGGGTGCCACTGACTCGTGGGCTTTGAAAAGAG-
1 TGCCACTGACTTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTG-AAAGAGT
* * * * *
342066 TGCTACTGAC-TCGTGGGCTTTGGAAAA-GATACCATTGACTTGTGGGCTTTGAAAAGGGT
1 TGCCACTGACTTTGTGGGCTTT--AAAAGGATGCCACTGACTTGTGGGCTTTG-AAAGAGT
* * * *
342125 TGCCA-TCGACTCGTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAG-GG
1 TGCCACT-GACT-TTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGT
* * * * *
342183 TGCCACTAAC-TTGTGGGCTTTGAAAAGTGTTGCCACCGACTCGTGGGCTTTGAAAG-GA
1 TGCCACTGACTTTGTGGGCTTT-AAAAG-GATGCCACTGACTTGTGGGCTTTGAAAGAGT
* * * *
342241 TGCCACTGAC-TTGTAGGCTTTGAAAAGGGTTGCCACCGGCTCGTGTGGGCTTTGAAAAGAG-
1 TGCCACTGACTTTGTGGGCTTT-AAAA-GGATGCCACTGACT--TGTGGGCTTTG-AAAGAGT
* * * *
342302 TGCCACTAAC-TTGTGGGCTTTGAAAGGATGCCACTGACTTGTAGGCTTTGAAAAGTGT
1 TGCCACTGACTTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTG-AAAGAGT
* * * *
342360 TGCCACTGAC-TCGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGGT
1 TGCCACTGACTTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTG-AAAGAGT
* * *
342418 TGCCACCGACTCATGTGGGCTTTGAAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAG-GG
1 TGCCACTGACT-TTGTGGGCTTT-AAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGAGT
* * * *
342477 TGCCACTGA-TTTGTGGGCTTTAAAAGGGTGCCACTAATTTGTGGGCTATGAAATTG-GT
1 TGCCACTGACTTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAA--GAGT
* * * *
342535 TGCCACTGACTTGTGTGGGCTTTCAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATAGGT
1 TGCCACTGACTT-TGTGGGCTTT-AAA-AGGATGCCACTGAC-T-TGTGGGCTTTGAAAGA-GT
* *
342599 TGCCACCGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTT
1 TGCCACTGACTT-TGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTT
342649 AAAAAGGATG
Statistics
Matches: 877, Mismatches: 128, Indels: 104
0.79 0.12 0.09
Matches are distributed among these distances:
55 3 0.00
56 184 0.21
57 63 0.07
58 203 0.23
59 53 0.06
60 76 0.09
61 81 0.09
62 51 0.06
63 57 0.06
64 70 0.08
65 32 0.04
66 4 0.00
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (58 bp):
TGCCACTGACTTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGT
Found at i:342350 original size:147 final size:146
Alignment explanation
Indices: 341546--342662 Score: 1059
Period size: 147 Copynumber: 7.6 Consensus size: 146
341536 CACTAACTTC
* * * * * * *
341546 TGTGGGCTTT--AAAGAAATGCCACTGACTTGTTGACTTTGAAAGGATGCCACTAACTTATGGGC
1 TGTGGGCTTTGAAAAG-AGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * * * * *
341609 TTTG-GAAGGATGCCACTGAGTCGTGGGCTTTGAAAAGTTGCCACTGACTTGTGGGCTTGGAAAA
65 TTTGAAAAGGTTGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAA
* * **
341673 --GATACCATTGACT--
130 GGGTTGCCACCGACTCG
* * * * * *
341686 TGTGGGCTTTGAAAAGA-TGCCACCAACTTGTCGACATTGAAAGGATGCCACTGACTTGTAGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
* ** * * * *
341750 TTGAAATGGGTTGCCACCAATTTGTGTGGGCTTTGAAATGAGTTGCCACCGA-TTGTGTGGTCTT
66 TTGAAA-AGGTTGCCACTGA-CT-CGTGGGCTTTGAAA-G-GATGCCACTGACTTGTG-GG-CTT
* * * *
341814 TCAAATGGGTTGCCACCAACTTG
124 TGAAAAGGGTTGCCACCGACTCG
* * * * *
341837 TGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGGAAATAGGTTGCCAC-CAGCTT
1 TGTGGGCTTTGAAAAGAG-TGCCACTAAC-T-TGTGGGCTTT-G-AA-AGGGTGCCACTGA-C-T
* ** * * *
341901 GTGTGGGCTTTGAAATGGTTGCCACCAACTTGTGTGGGCTTTCAAATGAGTGCCACTGACTTGCG
58 -TGTGGGCTTTGAAAAGGTTGCCACTGAC-T-CGTGGGCTTTGAAAGGA-TGCCACTGACTT--G
* **
341966 TGGGCTTT-AAAA-GGATGCCACTAACTC-
117 TGGGCTTTGAAAAGGGTTGCCACCGACTCG
* * *
341993 -ATGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTCGTGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
* * * *
342056 TTGAAAAGAG-TGCTACTGACTCGTGGGCTTTGGAAAAGATACCATTGACTTGTGGGCTTTGAAA
66 TTGAAAAG-GTTGCCACTGACTCGTGGGCTTT-GAAAGGATGCCACTGACTTGTGGGCTTTGAAA
*
342120 AGGGTTGCCATCGACTCG
129 AGGGTTGCCACCGACTCG
* *
342138 TGTGGGCTTTGAAAGGA-TGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
* *
342202 TTGAAAAGTGTTGCCACCGACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTAGGCTTTGAAAA
66 TTGAAAAG-GTTGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAA
*
342267 GGGTTGCCACCGGCTCG
130 GGGTTGCCACCGACTCG
* *
342284 TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTAGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
*
342349 TTGAAAAGTGTTGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAA
66 TTGAAAAG-GTTGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAA
*
342414 GGGTTGCCACCGACTCA
130 GGGTTGCCACCGACTCG
* *
342431 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGATTTGTGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
* * * * * * *
342496 TT-AAAAGGGTGCCACTAATTTGTGGGCTATGAAATTGGTTGCCACTGACTTGTGTGGGCTTTCA
66 TTGAAAAGGTTGCCACTGACTCGTGGGCTTTGAAA--GGATGCCACTGAC-T-TGTGGGCTTTGA
* *
342560 AATGGGTTGCCACCGACTTG
127 AAAGGGTTGCCACCGACTCG
** *
342580 TGTGGGCTTTGAAATAG-GTTGCCACCGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTG
1 TGTGGGCTTTGAAA-AGAG-TGCCACTAAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTG
* *
342644 GGC-TTAAAAAGGATGCCAC
62 GGCTTTGAAAAGGTTGCCAC
342663 GAAGTTGTGA
Statistics
Matches: 824, Mismatches: 105, Indels: 84
0.81 0.10 0.08
Matches are distributed among these distances:
140 53 0.06
141 2 0.00
142 22 0.03
143 5 0.01
144 43 0.05
145 33 0.04
146 160 0.19
147 226 0.27
148 11 0.01
149 54 0.07
150 12 0.01
151 28 0.03
152 46 0.06
153 18 0.02
154 5 0.01
155 16 0.02
156 1 0.00
157 16 0.02
158 21 0.03
159 34 0.04
160 15 0.02
161 3 0.00
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (146 bp):
TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
TTGAAAAGGTTGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAG
GGTTGCCACCGACTCG
Found at i:342789 original size:110 final size:110
Alignment explanation
Indices: 342612--343020 Score: 577
Period size: 110 Copynumber: 3.7 Consensus size: 110
342602 CACCGACTTG
* * * * * * *
342612 TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTAAAAAGGATGCCACGAAGTTGTGAACTT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT-AAAAGGATACCACGGAGTTGTGGACTT
*
342677 AAAAGGGTGCCATGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
65 AAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
* * *
342723 TGTGGACTTT-AAAGGGTGCCACGGAGTTGTGGACTTAAAACGATGCCATGGAGTTGTGGACTTT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATACCACGGAGTTGTGGAC-TT
*
342787 AAAAGGGTGCCACGGAGTTATGGACTTTAAAAGGGTGCCACGGAGT
65 AAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
* * * *
342833 TGTGGACTTTAAAAGGGTGCTACGGAGTTGTGGACTTTAAAGGGTACCATGGAGTTGTGGACTTA
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATACCACGGAGTTGTGGACTTA
* * *
342898 AAACGATGCCACGGAATTGTGGACTTTAAAAGGGTGCCACGGAGT
66 AAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
* * *
342943 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTACCACAGAGTTGTGGACTTA
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATACCACGGAGTTGTGGACTTA
* *
343008 AAACGATGCCACG
66 AAAGGGTGCCACG
343021 TGTAGACACT
Statistics
Matches: 274, Mismatches: 22, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
109 21 0.08
110 198 0.72
111 55 0.20
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.25
Consensus pattern (110 bp):
TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATACCACGGAGTTGTGGACTTA
AAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
Found at i:342832 original size:138 final size:138
Alignment explanation
Indices: 342620--343020 Score: 599
Period size: 138 Copynumber: 2.9 Consensus size: 138
342610 TGTGTGGGCT
* * * * * * * * *
342620 TTAAAAGGGTGCCACTGACTTGTGGGCTTAAAAAGGATGCCACGAAGTTGTGAAC-TTAAAAGGG
1 TTAAAACGATGCCACGGAATTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
*
342684 TGCCATGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAG
66 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAG
342749 TTGTGGAC
131 TTGTGGAC
* * *
342757 TTAAAACGATGCCATGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTATGGACTTTAAAAGGG
1 TTAAAACGATGCCACGGAATTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
* * *
342822 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCTACGGAGTTGTGGACTTTAAAGGGTACCATGGAG
66 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAG
342887 TTGTGGAC
131 TTGTGGAC
342895 TTAAAACGATGCCACGGAATTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
1 TTAAAACGATGCCACGGAATTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
* * * * *
342960 TGCCACGGAGTTGTGGACTTT-AAAGGGTACCACAGAGTTGTGGACTTAAAACGATGCCACG
66 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACG
343021 TGTAGACACT
Statistics
Matches: 237, Mismatches: 26, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
137 76 0.32
138 161 0.68
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.25
Consensus pattern (138 bp):
TTAAAACGATGCCACGGAATTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAG
TTGTGGAC
Found at i:343275 original size:49 final size:49
Alignment explanation
Indices: 343130--343954 Score: 1032
Period size: 49 Copynumber: 17.4 Consensus size: 49
343120 GCGAAAATGG
*
343130 TGGCCTTGAATCAGCACATTGGCACC-TCATCTTTAAGTCTAATGTAGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
*
343178 TGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGACCAATGTAGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
*
343221 TGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
343270 TGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATGTAGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
* *
343313 TGGCCTTGACTCAGCACATTGGCACCATCATCTTTAAGTCCAATGTAGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
* *
343362 TGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
* * *
343405 TGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAACGTAGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
* *
343454 TGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
* *
343497 TGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
* *
343546 TGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
* * *
343589 TGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGTAGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
* * * * *
343638 TGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGCCCAATATAGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
* * *
343687 TGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATGTAGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
* * * *
343736 TGGCCTTGACTCAGCACATTGGCA-CTTGCACCATTAAGTCC-ATATAGC
1 TGGCCTTGAATCAGCACATTGGCACCTT-CATCTTTAAGTCCAATGTAGC
* *
343784 TGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
* * *
343833 TGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
* * *
343882 TGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTCAATGTAGC
1 TGGCCTTGAATCAGCACATTGGCACC--TT-CATCTTTAAGTCCAATGTAGC
343934 TGGCCTTGAATCAGCACATTG
1 TGGCCTTGAATCAGCACATTG
343955 ACATCCTTTT
Statistics
Matches: 673, Mismatches: 68, Indels: 68
0.83 0.08 0.08
Matches are distributed among these distances:
43 196 0.29
45 5 0.01
47 5 0.01
48 64 0.10
49 364 0.54
51 2 0.00
52 37 0.05
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (49 bp):
TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
Found at i:343286 original size:92 final size:92
Alignment explanation
Indices: 343130--343963 Score: 1186
Period size: 92 Copynumber: 8.8 Consensus size: 92
343120 GCGAAAATGG
* *
343130 TGGCCTTGAATCAGCACATTGGCACC-TCATCTTTAAGTCTAATGTAGCTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
* *
343194 CATTGGCACCTTTAAGACCAATGTAGC
66 CATTGGCACCTTTAAGTCCAATATAGC
* *
343221 TGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
*
343286 CATTGGCACCTTTAAGTCCAATGTAGC
66 CATTGGCACCTTTAAGTCCAATATAGC
* * *
343313 TGGCCTTGACTCAGCACATTGGCACCATCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
*
343378 CATTGGCACCTTTAAGTCCAATATCGC
66 CATTGGCACCTTTAAGTCCAATATAGC
* *
343405 TGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAACGTAGCTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
*
343470 CATTGGCACCTTTAAGTCCAATATCGC
66 CATTGGCACCTTTAAGTCCAATATAGC
*
343497 TGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
*
343562 CATTGGCACCTTTAAGTCCAATATCGC
66 CATTGGCACCTTTAAGTCCAATATAGC
* * *
343589 TGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCA
1 TGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
*
343654 CATTGGCACCTTCACCATTAAGCCCAATATAGC
66 CATTGGCACC-T-----TTAAGTCCAATATAGC
* * *
343687 TGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCA
1 TGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
*
343752 CATTGGCACTTGCACCATTAAGTCC-ATATAGC
66 CATT-G-----GCACCTTTAAGTCCAATATAGC
* *
343784 TGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCA
1 TGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
*
343849 CATTGGCACCTTCATCTTTAAGTCCAATATCGC
66 CATTGGCA----C--CTTTAAGTCCAATATAGC
* *
343882 TGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCA
1 TGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCA
*
343947 GCACATTGACATCCTTT
63 GCACATTGGCA-CCTTT
343964 TTCTCATCTT
Statistics
Matches: 690, Mismatches: 30, Indels: 41
0.91 0.04 0.05
Matches are distributed among these distances:
91 28 0.04
92 403 0.58
93 1 0.00
95 1 0.00
96 5 0.01
97 84 0.12
98 119 0.17
99 1 0.00
100 2 0.00
101 41 0.06
104 5 0.01
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (92 bp):
TGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
CATTGGCACCTTTAAGTCCAATATAGC
Found at i:343319 original size:22 final size:22
Alignment explanation
Indices: 343252--343319 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
343242 GCACCTTCAT
343252 CTTTAAGTCCAATGTAGCTGGC
1 CTTTAAGTCCAATGTAGCTGGC
* * *
343274 CTTGAA-TCAGCACAT-TGGC--AC
1 CTTTAAGTC--CA-ATGTAGCTGGC
343295 CTTTAAGTCCAATGTAGCTGGC
1 CTTTAAGTCCAATGTAGCTGGC
343317 CTT
1 CTT
343320 GACTCAGCAC
Statistics
Matches: 33, Mismatches: 6, Indels: 14
0.62 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 11 0.33
23 5 0.15
24 2 0.06
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.31
Consensus pattern (22 bp):
CTTTAAGTCCAATGTAGCTGGC
Found at i:343999 original size:55 final size:53
Alignment explanation
Indices: 343571--344001 Score: 174
Period size: 49 Copynumber: 8.6 Consensus size: 53
343561 ACATTGGCAC
* * *
343571 CTTTAAGTCC-AATATCGCTGGCCTTGAATCAGCATATTGGCA-----TCATCAT
1 CTTTAAG-CCTAATATCGCTGGCCTTGAATCAGCACATCGACACCTTTTC-TCAT
* * * * * *
343620 CTTTAAGTCC-AATGTAGCTGGCCTTGACTCAGCACATTGGCACC---T-TCAC
1 CTTTAAG-CCTAATATCGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * * * * *
343669 CATTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C-TTT-T-AT
1 CTTTAAGCCTAATATCGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * * * * * *
343718 CTTTAAGTCC-AATGTAGCTGGCCTTGACTCAGCACATTGGCA-C--TT-GCAC
1 CTTTAAG-CCTAATATCGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * * * *
343767 CATTAAGTCC--ATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-T-AT
1 CTTTAAG-CCTAATATCGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * * * *
343815 CTTTAAGTCC-AATGTAGCTGGCCTTGACTCAGCACATTGGCACC---T-TCAT
1 CTTTAAG-CCTAATATCGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* *
343864 CTTTAAGTCC-AATATCGCTGGCCTTGAATCAGCATATCGGCACCTTTTC-CAT
1 CTTTAAG-CCTAATATCGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * * *
343916 CTTTAAG-TTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGCCT-AATATCGCTGGCCTTGAATCAGCACATCGACA-CC-TTTTCTCAT
* *
343971 CTTTAAGCCTAATATCGTTGGCCGTGAATCA
1 CTTTAAGCCTAATATCGCTGGCCTTGAATCA
344002 ACATATTGGC
Statistics
Matches: 320, Mismatches: 42, Indels: 34
0.81 0.11 0.09
Matches are distributed among these distances:
48 45 0.14
49 197 0.62
50 4 0.01
51 1 0.00
52 38 0.12
53 2 0.01
54 5 0.02
55 27 0.08
56 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (53 bp):
CTTTAAGCCTAATATCGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
Done.