Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold401
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: 1910012
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 9 of 13
Found at i:1240703 original size:13 final size:14
Alignment explanation
Indices: 1240647--1240731 Score: 57
Period size: 15 Copynumber: 5.8 Consensus size: 14
1240637 TGATATGATA
*
1240647 AATATATAATGATATA
1 AATATA-AAT-ATATT
*
1240663 AATATAAATATA-A
1 AATATAAATATATT
*
1240676 AAAATTAAGATATATT
1 AATA-TAA-ATATATT
1240692 -ATATAAATATATAT
1 AATATAAATATAT-T
* *
1240706 AATATATACATATT
1 AATATAAATATATT
1240720 AAATATAAATAT
1 -AATATAAATAT
1240732 TTTTAGAATA
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
13 10 0.18
14 11 0.20
15 29 0.52
16 6 0.11
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (14 bp):
AATATAAATATATT
Found at i:1240718 original size:15 final size:15
Alignment explanation
Indices: 1240639--1240731 Score: 72
Period size: 13 Copynumber: 6.3 Consensus size: 15
1240629 AAAACATTTG
1240639 ATATGATAAATATATA
1 ATAT-ATAAATATATA
1240655 ATGATATAAATATA-A
1 AT-ATATAAATATATA
*
1240670 ATATA-AAAAAT-TA
1 ATATATAAATATATA
* *
1240683 AGATAT-ATTATATAA
1 ATATATAAATATAT-A
1240698 ATATATATAATATATA
1 ATATATA-AATATATA
1240714 CATAT-TAAATATA-A
1 -ATATATAAATATATA
1240728 ATAT
1 ATAT
1240732 TTTTAGAATA
Statistics
Matches: 63, Mismatches: 6, Indels: 19
0.72 0.07 0.22
Matches are distributed among these distances:
13 17 0.27
14 5 0.08
15 15 0.24
16 14 0.22
17 12 0.19
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (15 bp):
ATATATAAATATATA
Found at i:1244178 original size:2 final size:2
Alignment explanation
Indices: 1244171--1244210 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1244161 CAGGTATAGA
*
1244171 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1244211 GAGATGATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1250800 original size:14 final size:14
Alignment explanation
Indices: 1250783--1250809 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1250773 ATTATAAAAA
1250783 AAATAAAAAAATTT
1 AAATAAAAAAATTT
1250797 AAATAAAAAAATT
1 AAATAAAAAAATT
1250810 ATTATCTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATAAAAAAATTT
Found at i:1252822 original size:21 final size:22
Alignment explanation
Indices: 1252796--1252838 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
1252786 TGGGATAATT
1252796 TAATATTAA-TTAAATATATCA
1 TAATATTAAGTTAAATATATCA
1252817 TAATATTAAGTTTAAATATATC
1 TAATATTAAG-TTAAATATATC
1252839 TAGAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
23 11 0.55
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (22 bp):
TAATATTAAGTTAAATATATCA
Found at i:1252968 original size:18 final size:18
Alignment explanation
Indices: 1252942--1252988 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
1252932 ATATATATAT
1252942 ATTTAAATATCTCTTTTT-A
1 ATTT-AATATC-CTTTTTGA
*
1252961 ATTTAATAAACCTTTTTGA
1 ATTTAAT-ATCCTTTTTGA
1252980 ATTTAATAT
1 ATTTAATAT
1252989 AACGTATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (18 bp):
ATTTAATATCCTTTTTGA
Found at i:1255262 original size:7 final size:7
Alignment explanation
Indices: 1255251--1255283 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
1255241 TTTGAGTAAA
*
1255251 AATAATA
1 AATAATT
1255258 AATAATT
1 AATAATT
1255265 AATAATT
1 AATAATT
1255272 AATAATT
1 AATAATT
1255279 AATAA
1 AATAA
1255284 AAGAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AATAATT
Found at i:1255690 original size:20 final size:19
Alignment explanation
Indices: 1255667--1255704 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1255657 TTATTATTAA
1255667 ATAATAAAAATAATATTTTT
1 ATAAT-AAAATAATATTTTT
*
1255687 ATAATATAATAATATTTT
1 ATAATAAAATAATATTTT
1255705 AAAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATAATAAAATAATATTTTT
Found at i:1255791 original size:2 final size:2
Alignment explanation
Indices: 1255780--1255814 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1255770 CACGGTTTTA
*
1255780 AT AT -T AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1255815 GTACAAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1256240 original size:23 final size:23
Alignment explanation
Indices: 1256192--1256244 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1256182 GGCTTTTGAC
* * *
1256192 TTATAAATTAATTGATTTATATT
1 TTATATATTAATTGATGTATAAT
1256215 TTATATATTAATT-ATGTATAAAT
1 TTATATATTAATTGATGTAT-AAT
1256238 TTATATA
1 TTATATA
1256245 ATTTTTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (23 bp):
TTATATATTAATTGATGTATAAT
Found at i:1256381 original size:29 final size:29
Alignment explanation
Indices: 1256314--1256402 Score: 72
Period size: 29 Copynumber: 2.9 Consensus size: 29
1256304 AAAAATTTTA
* *
1256314 ATAAAATA-ATATTATTTAATTTATTTATGAT
1 ATAAAATATATATTA-TTAATATA-TTA-AAT
*
1256345 ATGTAAATATATATTATTAATATATTAAAT
1 AT-AAAATATATATTATTAATATATTAAAT
* * *
1256375 ATAAAATTTAAATTATTACTATTATTAA
1 ATAAAATATATATTATTAATA-TATTAA
1256403 TTATTAAACA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
29 15 0.31
30 10 0.21
31 5 0.10
32 12 0.25
33 6 0.12
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (29 bp):
ATAAAATATATATTATTAATATATTAAAT
Found at i:1258937 original size:25 final size:25
Alignment explanation
Indices: 1258908--1258989 Score: 82
Period size: 24 Copynumber: 3.4 Consensus size: 25
1258898 GAATATTTAT
*
1258908 ATTATATTTATATATTTTTATAATA
1 ATTATATTTATAAATTTTTATAATA
*
1258933 ATTATATTTA-AAATATTTATAAT-
1 ATTATATTTATAAATTTTTATAATA
* *
1258956 -TTATATTAAATAAATTTTAAT-ATA
1 ATTATATT-TATAAATTTTTATAATA
*
1258980 TTTATATTTA
1 ATTATATTTA
1258990 AATTATATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
22 7 0.15
23 3 0.06
24 20 0.43
25 17 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
ATTATATTTATAAATTTTTATAATA
Found at i:1258974 original size:47 final size:45
Alignment explanation
Indices: 1258899--1259001 Score: 111
Period size: 47 Copynumber: 2.2 Consensus size: 45
1258889 TAAAATTTTG
* *
1258899 AATATTTATATTATATTTATAT-ATTTTTATAATAATTATATTTAA
1 AATATTTATATTATATTAATATAATTTTAAT-ATAATTATATTTAA
*
1258944 AATATTTATAATTTATATTAA-ATAAATTTTAATATATTTATATTTAA
1 AATATTTAT-A-TTATATTAATAT-AATTTTAATATAATTATATTTAA
1258991 ATTATATTTAT
1 A--ATATTTAT
1259002 TTTACTTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
45 9 0.18
46 3 0.06
47 22 0.45
48 7 0.14
49 8 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (45 bp):
AATATTTATATTATATTAATATAATTTTAATATAATTATATTTAA
Found at i:1259047 original size:12 final size:12
Alignment explanation
Indices: 1258997--1259047 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
1258987 TTAAATTATA
*
1258997 TTTATTTTACTT
1 TTTATTTTATTT
* * *
1259009 TTTATGTGATGT
1 TTTATTTTATTT
*
1259021 TTTATTTTATAT
1 TTTATTTTATTT
1259033 TTTATTTTATTT
1 TTTATTTTATTT
1259045 TTT
1 TTT
1259048 GTATAATAGT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.75
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:1260453 original size:3 final size:3
Alignment explanation
Indices: 1260445--1260470 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1260435 CATGCATATG
1260445 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1260471 GTATCTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1261689 original size:21 final size:22
Alignment explanation
Indices: 1261665--1261728 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 22
1261655 ATTAAATTTT
1261665 TTATTTTAAT-TTAATTATAAA
1 TTATTTTAATATTAATTATAAA
* *
1261686 TTATATAAATATTAA-TATAAAA
1 TTATTTTAATATTAATTAT-AAA
* *
1261708 GTATTTT-TTATTAATTATAAA
1 TTATTTTAATATTAATTATAAA
1261729 AATAAATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 20 0.59
22 14 0.41
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TTATTTTAATATTAATTATAAA
Found at i:1261788 original size:15 final size:16
Alignment explanation
Indices: 1261753--1261789 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1261743 ATAAATTGAG
*
1261753 TAAAATAAAATAAATT
1 TAAAATTAAATAAATT
1261769 T-AAATTAAA-AAATT
1 TAAAATTAAATAAATT
1261783 TAAAATT
1 TAAAATT
1261790 TTTTTGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.32
15 12 0.63
16 1 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAAATTAAATAAATT
Found at i:1267218 original size:5 final size:5
Alignment explanation
Indices: 1267203--1267294 Score: 55
Period size: 5 Copynumber: 18.0 Consensus size: 5
1267193 ATCATTTTTA
* * *
1267203 TATAT TTTAT TATAT TATAAT TATAT T-TAA AATAGTT TATATT TATAT
1 TATAT TATAT TATAT TAT-AT TATAT TATAT TATA--T TATA-T TATAT
* * * *
1267251 TATATT TATAG TATTT TTTAT TATA- -ATAT TATTT TATAT TATAT
1 TATA-T TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1267295 GTTAATTAAT
Statistics
Matches: 66, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
3 3 0.05
4 2 0.03
5 42 0.64
6 16 0.24
7 3 0.05
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:1267272 original size:27 final size:26
Alignment explanation
Indices: 1267199--1267289 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 26
1267189 TTTTATCATT
1267199 TTTATATATTTTATTATATTATAATTATA
1 TTTATATATTTT-TTAT-TTAT-ATTATA
* * *
1267228 TTTAAAATAGTTTATATTTATATTATA
1 TTT-ATATATTTTTTATTTATATTATA
1267255 TTTATAGTATTTTTTATTATAATATTAT-
1 TTTATA-TATTTTTTATT-T-ATATTATA
1267283 TTTATAT
1 TTTATAT
1267290 TATATGTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
26 2 0.04
27 19 0.37
28 11 0.21
29 13 0.25
30 7 0.13
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTATATATTTTTTATTTATATTATA
Found at i:1268994 original size:27 final size:26
Alignment explanation
Indices: 1268964--1269025 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
1268954 ATAATTAAGT
*
1268964 AATATATACAATATAAAAATTAATCAA
1 AATATATACAATATAAAAA-TAATAAA
**
1268991 AATATAATTTAATATAAAAATAATAAA
1 AATAT-ATACAATATAAAAATAATAAA
1269018 AATATATA
1 AATATATA
1269026 AATTTTCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 2 0.07
27 16 0.53
28 12 0.40
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (26 bp):
AATATATACAATATAAAAATAATAAA
Found at i:1269280 original size:20 final size:20
Alignment explanation
Indices: 1269257--1269294 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1269247 TTAAATTTTT
* *
1269257 AAAATTTTATTTTTATATTA
1 AAAATTATATTATTATATTA
1269277 AAAATTATATTATTATAT
1 AAAATTATATTATTATAT
1269295 AAATATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AAAATTATATTATTATATTA
Found at i:1269310 original size:23 final size:23
Alignment explanation
Indices: 1269284--1269341 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1269274 TTAAAAATTA
1269284 TATT-ATTATATAAATATATTTTT
1 TATTAATTATAT-AATATATTTTT
* **
1269307 TATTAATTATATATTATATTTAA
1 TATTAATTATATAATATATTTTT
1269330 TATTAATT-TATA
1 TATTAATTATATA
1269342 GTTTTAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.13
23 20 0.65
24 7 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTAATTATATAATATATTTTT
Found at i:1269326 original size:16 final size:16
Alignment explanation
Indices: 1269279--1269326 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1269269 TTATATTAAA
1269279 AATTATATTATTATA-T
1 AATTATA-TATTATATT
* * *
1269295 AAATATATTTTTTATT
1 AATTATATATTATATT
1269311 AATTATATATTATATT
1 AATTATATATTATATT
1269327 TAATATTAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 5 0.20
16 20 0.80
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTATATATTATATT
Found at i:1269790 original size:20 final size:20
Alignment explanation
Indices: 1269762--1269901 Score: 68
Period size: 20 Copynumber: 7.2 Consensus size: 20
1269752 AATTTCATCA
* *
1269762 TTATCTTATTATTTATCTAT
1 TTATATTATTATTTATATAT
1269782 TTATATTA-TATTTATATAT
1 TTATATTATTATTTATATAT
1269801 TT-TATTA-TA-TTATA-AT
1 TTATATTATTATTTATATAT
* *
1269817 TATAAATATAATATTT-TATAT
1 T-TATAT-TATTATTTATATAT
** *
1269838 TTATAAAAATT-TTAATATAT
1 TTAT-ATTATTATTTATATAT
*
1269858 TAATAATT-TATATTATAATATAT
1 TTAT-ATTAT-TATT-T-ATATAT
1269881 TTATA-TATT-TTT-TATAT
1 TTATATTATTATTTATATAT
1269898 TTAT
1 TTAT
1269902 TGATAACTAA
Statistics
Matches: 94, Mismatches: 13, Indels: 29
0.69 0.10 0.21
Matches are distributed among these distances:
16 3 0.03
17 15 0.16
18 9 0.10
19 18 0.19
20 28 0.30
21 10 0.11
22 2 0.02
23 9 0.10
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATATTATTATTTATATAT
Found at i:1269793 original size:19 final size:18
Alignment explanation
Indices: 1269771--1269811 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
1269761 ATTATCTTAT
*
1269771 TATTTATCTATTTATATTA
1 TATTTATATATTT-TATTA
1269790 TATTTATATATTTTATTA
1 TATTTATATATTTTATTA
1269808 TATT
1 TATT
1269812 ATAATTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATATATTTTATTA
Found at i:1269841 original size:45 final size:48
Alignment explanation
Indices: 1269783--1269886 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 48
1269773 TTTATCTATT
* *
1269783 TATA-TTATATTTAT-ATATTTTATTATATT-ATAA-TTATAAATATAA
1 TATATTTATATTTATAAAATTTTAATATATTAATAATTTAT-AATATAA
*
1269828 TAT-TTTATATTTATAAAAATTTTAATATATTAATAATTTATATTATAA
1 TATATTTATATTTAT-AAAATTTTAATATATTAATAATTTATAATATAA
1269876 TATATTTATAT
1 TATATTTATAT
1269887 ATTTTTTATA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
45 13 0.26
47 13 0.26
48 13 0.26
49 11 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (48 bp):
TATATTTATATTTATAAAATTTTAATATATTAATAATTTATAATATAA
Found at i:1269842 original size:16 final size:16
Alignment explanation
Indices: 1269787--1269888 Score: 79
Period size: 16 Copynumber: 6.5 Consensus size: 16
1269777 TCTATTTATA
*
1269787 TTATATTTAT-ATATT
1 TTATATATATAATATT
* *
1269802 TTAT-TATATTATA-A
1 TTATATATATAATATT
*
1269816 TTATAAATATAATATT
1 TTATATATATAATATT
* *
1269832 TTATATTTATAAAAATT
1 TTATATATAT-AATATT
*
1269849 TTA-ATATATTAATAAT
1 TTATATATA-TAATATT
1269865 TTATAT-TATAATATAT
1 TTATATATATAATAT-T
1269881 TTATATAT
1 TTATATAT
1269889 TTTTTATATT
Statistics
Matches: 67, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
14 8 0.12
15 19 0.28
16 28 0.42
17 12 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATATATAATATT
Found at i:1270550 original size:3 final size:3
Alignment explanation
Indices: 1270542--1270567 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1270532 TTAATATTTA
1270542 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1270568 AAAGCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1272894 original size:38 final size:39
Alignment explanation
Indices: 1272811--1272930 Score: 117
Period size: 38 Copynumber: 3.1 Consensus size: 39
1272801 AGATCAGATC
*
1272811 TAAA-TTAATATAAAAAT-TTA-TTTTATTATTTATAA-AT
1 TAAATTTAA-ATAAAAATATTATTTTTATTATTTA-AATAA
1272848 TAAATTTAAATAAAAATATTATTTTTATTA-TTAAATAA
1 TAAATTTAAATAAAAATATTATTTTTATTATTTAAATAA
* * * *
1272886 TAATTTTAATTAAATTATATT-TTATTATTATTTAAATAAA
1 TAAATTTAAATAAA-AATATTATTTTTATTATTTAAAT-AA
1272926 TAAAT
1 TAAAT
1272931 AATTTAATTT
Statistics
Matches: 70, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
37 14 0.20
38 31 0.44
39 19 0.27
40 6 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (39 bp):
TAAATTTAAATAAAAATATTATTTTTATTATTTAAATAA
Found at i:1273459 original size:85 final size:84
Alignment explanation
Indices: 1273317--1273487 Score: 306
Period size: 85 Copynumber: 2.0 Consensus size: 84
1273307 TTGTCTCTTT
1273317 TAAAAATAAACACCTATAAAGTGGGAGTTTCTATTTCTAGAATTTGCAATTAAAAAAAAAAAGAA
1 TAAAAATAAACACCTATAAAGTGGGAGTTTCTATTTCTAGAATTTGCAATT-AAAAAAAAAAGAA
*
1273382 AAATATTAGTTGTTGTGGGG
65 AAATATTAATTGTTGTGGGG
**
1273402 TAAAAATCGACACCTATAAAGTGGGAGTTTCTATTTCTAGAATTTGCAATTAAAAAAAAAAGAAA
1 TAAAAATAAACACCTATAAAGTGGGAGTTTCTATTTCTAGAATTTGCAATTAAAAAAAAAAGAAA
1273467 AATATTAATTGTTGTGGGG
66 AATATTAATTGTTGTGGGG
1273486 TA
1 TA
1273488 CAGAGGTTTT
Statistics
Matches: 83, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
84 34 0.41
85 49 0.59
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.31
Consensus pattern (84 bp):
TAAAAATAAACACCTATAAAGTGGGAGTTTCTATTTCTAGAATTTGCAATTAAAAAAAAAAGAAA
AATATTAATTGTTGTGGGG
Found at i:1273675 original size:43 final size:42
Alignment explanation
Indices: 1273605--1273689 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 42
1273595 AGATAGTTGA
* * * *
1273605 GATTTAATTTTTTTATTATTTTATTAATGAAAATATTTTTAT
1 GATTTAATTTTATTAATATTTAATTAATAAAAATATTTTTAT
1273647 GATTTAATTTTGATTAATATTTAATTAATAAAAATATTTTTAT
1 GATTTAATTTT-ATTAATATTTAATTAATAAAAATATTTTTAT
1273690 TTAAATTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
42 11 0.29
43 27 0.71
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (42 bp):
GATTTAATTTTATTAATATTTAATTAATAAAAATATTTTTAT
Found at i:1274181 original size:3 final size:3
Alignment explanation
Indices: 1274173--1274199 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1274163 GAAACCAAGA
1274173 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1274200 TCAAACTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1276238 original size:24 final size:26
Alignment explanation
Indices: 1276184--1276238 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 26
1276174 TAATTTAAAA
1276184 TAAAAATAAATTATAATATTATGATT
1 TAAAAATAAATTATAATATTATGATT
** *
1276210 T-AAAATTTATTA-AATATTAT-TTT
1 TAAAAATAAATTATAATATTATGATT
1276233 TAAAAA
1 TAAAAA
1276239 ATAGTTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 3 0.12
24 12 0.48
25 9 0.36
26 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
TAAAAATAAATTATAATATTATGATT
Found at i:1276422 original size:12 final size:12
Alignment explanation
Indices: 1276394--1276432 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1276384 TTTTTTAACT
*
1276394 TTATAAA-TAAA
1 TTATAAATTTAA
*
1276405 TTATAAATTTAT
1 TTATAAATTTAA
1276417 TTATAAATTTAA
1 TTATAAATTTAA
1276429 TTAT
1 TTAT
1276433 TTTTTATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 7 0.29
12 17 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TTATAAATTTAA
Found at i:1276746 original size:18 final size:18
Alignment explanation
Indices: 1276702--1276792 Score: 66
Period size: 20 Copynumber: 5.1 Consensus size: 18
1276692 ATTAGTTTTA
1276702 AAAATTT-ATATTATATTAAT
1 AAAATTTAATATT-TA-T-AT
*
1276722 AATATTTAATATTTATAT
1 AAAATTTAATATTTATAT
1276740 AAAATTTAATA--TATA-
1 AAAATTTAATATTTATAT
* *
1276755 AATAGTTAATA-TTATAT
1 AAAATTTAATATTTATAT
*
1276772 AAATTTTAAAATATTTATAT
1 AAAATTT--AATATTTATAT
1276792 A
1 A
1276793 TTTATATTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
15 9 0.16
16 8 0.14
17 4 0.07
18 12 0.21
19 5 0.09
20 15 0.26
21 5 0.09
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (18 bp):
AAAATTTAATATTTATAT
Found at i:1276754 original size:14 final size:14
Alignment explanation
Indices: 1276735--1276777 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1276725 ATTTAATATT
1276735 TATATAAAATTTAA
1 TATATAAAATTTAA
*
1276749 TATATAAATAGTTAA
1 TATATAAA-ATTTAA
1276764 TATTATATAAATTT
1 TA-TATA-AAATTT
1276778 TAAAATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 8 0.33
15 7 0.29
16 7 0.29
17 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (14 bp):
TATATAAAATTTAA
Found at i:1276773 original size:32 final size:33
Alignment explanation
Indices: 1276722--1276785 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1276712 TTATATTAAT
* *
1276722 AATATTTAATATTTATATAAAATTTAATATATA
1 AATAGTTAATATTTATATAAAATTTAAAATATA
*
1276755 AATAGTTAATA-TTATATAAATTTTAAAATAT
1 AATAGTTAATATTTATATAAAATTTAAAATAT
1276786 TTATATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 18 0.64
33 10 0.36
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (33 bp):
AATAGTTAATATTTATATAAAATTTAAAATATA
Found at i:1276795 original size:18 final size:18
Alignment explanation
Indices: 1276697--1276795 Score: 51
Period size: 18 Copynumber: 5.2 Consensus size: 18
1276687 TTCAAATTAG
1276697 TTTTAAAA-ATTTATATTA
1 TTTTAAAATATTTATA-TA
*
1276715 TATTAATAATATTTA-ATA
1 TTTTAA-AATATTTATATA
1276733 TTTATATAAA-ATTTAATATA
1 TTT-TA-AAATATTT-ATATA
** * *
1276753 TAAATAGTTAATATTATATAAA
1 T-TTTA--AAATATT-TATATA
1276775 TTTTAAAATATTTATATA
1 TTTTAAAATATTTATATA
1276793 TTT
1 TTT
1276796 ATATTATATT
Statistics
Matches: 61, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
18 21 0.34
19 14 0.23
20 12 0.20
21 5 0.08
22 8 0.13
23 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (18 bp):
TTTTAAAATATTTATATA
Found at i:1276807 original size:18 final size:17
Alignment explanation
Indices: 1276705--1276811 Score: 62
Period size: 16 Copynumber: 6.2 Consensus size: 17
1276695 AGTTTTAAAA
1276705 ATTTATATTATATTAATAAT
1 ATTTATATTATA-T-AT-AT
*
1276725 ATTTAATATT-TATATAAA
1 ATTT-ATATTATATAT-AT
*
1276743 ATTTA-A-TATATAAAT
1 ATTTATATTATATATAT
* *
1276758 AGTTAATATTATATAAAT
1 A-TTTATATTATATATAT
* * *
1276776 -TTTAAAATATTTATAT
1 ATTTATATTATATATAT
1276792 ATTTATATTATAT-TAT
1 ATTTATATTATATATAT
1276808 ATTT
1 ATTT
1276812 TAATTATTTT
Statistics
Matches: 69, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
15 3 0.04
16 26 0.38
17 11 0.16
18 17 0.25
19 1 0.01
20 6 0.09
21 5 0.07
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (17 bp):
ATTTATATTATATATAT
Found at i:1276839 original size:19 final size:19
Alignment explanation
Indices: 1276804--1276853 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1276794 TTATATTATA
*
1276804 TTATATTTTAATTATTTTT
1 TTATATTTTAATAATTTTT
1276823 TTATA-TTTACATAATTTTT
1 TTATATTTTA-ATAATTTTT
*
1276842 TAAATATTTTAA
1 T-TATATTTTAA
1276854 CCCTCAAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 4 0.15
19 14 0.54
20 4 0.15
21 4 0.15
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATATTTTAATAATTTTT
Found at i:1277168 original size:18 final size:17
Alignment explanation
Indices: 1277145--1277214 Score: 61
Period size: 18 Copynumber: 4.0 Consensus size: 17
1277135 TTTTATTTTT
1277145 AATTTTATATTAAAATAA
1 AATTTTAT-TTAAAATAA
*
1277163 AATTTTATTTTAAATAAA
1 AATTTTATTTAAAAT-AA
* * * *
1277181 AAATTTATTCATATTAA
1 AATTTTATTTAAAATAA
1277198 AA-TTTATTTAAATATAA
1 AATTTTATTTAAA-ATAA
1277215 TTTAATTAAG
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
16 8 0.20
17 13 0.32
18 20 0.49
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTTATTTAAAATAA
Found at i:1277179 original size:17 final size:18
Alignment explanation
Indices: 1277145--1277181 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1277135 TTTTATTTTT
1277145 AATTTTATATTAAAATAA
1 AATTTTATATTAAAATAA
*
1277163 AATTTTAT-TTTAAATAA
1 AATTTTATATTAAAATAA
1277180 AA
1 AA
1277182 AATTTATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATTTTATATTAAAATAA
Found at i:1277263 original size:29 final size:29
Alignment explanation
Indices: 1277195--1277286 Score: 86
Period size: 29 Copynumber: 3.3 Consensus size: 29
1277185 TTATTCATAT
*
1277195 TAAAAT-TT-ATTTAAATATAATT--TAA
1 TAAAATATTAATTTAAATATAATTAAAAA
* * * *
1277220 TTAAGTATTTATTT-AATATTTATTAAAAA
1 TAAAATATTAATTTAAATA-TAATTAAAAA
1277249 TAAAATATTAATTTAAATATAATTAAAAA
1 TAAAATATTAATTTAAATATAATTAAAAA
*
1277278 TTAAATATT
1 TAAAATATT
1277287 TAACTCATTA
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
25 4 0.08
26 6 0.12
27 8 0.15
29 30 0.58
30 4 0.08
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (29 bp):
TAAAATATTAATTTAAATATAATTAAAAA
Found at i:1281738 original size:2 final size:2
Alignment explanation
Indices: 1281731--1281766 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1281721 CTATCTCATC
* *
1281731 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1281767 TGTTTGGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1283286 original size:17 final size:16
Alignment explanation
Indices: 1283257--1283288 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1283247 AAAAAATATA
1283257 TAAATATATTATAATT
1 TAAATATATTATAATT
1283273 TAAATATAATTATAAT
1 TAAATAT-ATTATAAT
1283289 AAAAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATATATTATAATT
Found at i:1286081 original size:15 final size:15
Alignment explanation
Indices: 1286061--1286092 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1286051 AATCTTAATC
*
1286061 ATAAATTTGTTACAA
1 ATAAATTTGCTACAA
1286076 ATAAATTTGCTACAA
1 ATAAATTTGCTACAA
1286091 AT
1 AT
1286093 GGAAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (15 bp):
ATAAATTTGCTACAA
Found at i:1286219 original size:2 final size:2
Alignment explanation
Indices: 1286214--1286241 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1286204 ATTTGCACAA
1286214 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
1286242 GGAAGTCTAA
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:1286287 original size:18 final size:21
Alignment explanation
Indices: 1286263--1286306 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
1286253 GGATAGGGTT
1286263 ATTTA-TTAAAATTT-AAAAG
1 ATTTATTTAAAATTTGAAAAG
*
1286282 -TTTATTTAATATTTGAAAAG
1 ATTTATTTAAAATTTGAAAAG
1286302 ATTTA
1 ATTTA
1286307 AATAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 4 0.19
19 8 0.38
20 5 0.24
21 4 0.19
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (21 bp):
ATTTATTTAAAATTTGAAAAG
Found at i:1286367 original size:22 final size:21
Alignment explanation
Indices: 1286337--1286377 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1286327 AAATTGAAGT
1286337 AAAAAAAATAAAATTTATTCA
1 AAAAAAAATAAAATTTATTCA
*
1286358 AAAAATAAATAGAATTTATT
1 AAAAA-AAATAAAATTTATT
1286378 TTTAACATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAAAAAATAAAATTTATTCA
Found at i:1286601 original size:15 final size:15
Alignment explanation
Indices: 1286581--1286627 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1286571 AATTTATATA
1286581 AAATTATATAAATTT
1 AAATTATATAAATTT
*
1286596 AAATTATAT-ATTTAT
1 AAATTATATAAATT-T
*
1286611 AAATATAAATAAATTT
1 AAAT-TATATAAATTT
1286627 A
1 A
1286628 TATTTTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 3 0.12
15 14 0.54
16 6 0.23
17 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATTATATAAATTT
Found at i:1301941 original size:27 final size:27
Alignment explanation
Indices: 1301911--1301998 Score: 113
Period size: 27 Copynumber: 3.3 Consensus size: 27
1301901 AAACGCCGGC
* *
1301911 GTGGAAGAGGGAGTGGCGAAGGCAGGA
1 GTGGAAGAAGGAGTGCCGAAGGCAGGA
* * * *
1301938 GTGGAAGAAGGAGTGCCAAATGCTGGC
1 GTGGAAGAAGGAGTGCCGAAGGCAGGA
*
1301965 GTGGAAGAAGGAGTGCCGAAGGCAGAA
1 GTGGAAGAAGGAGTGCCGAAGGCAGGA
1301992 GTGGAAG
1 GTGGAAG
1301999 CCTGAGCACC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.32, C:0.10, G:0.48, T:0.10
Consensus pattern (27 bp):
GTGGAAGAAGGAGTGCCGAAGGCAGGA
Found at i:1301948 original size:54 final size:54
Alignment explanation
Indices: 1301890--1301998 Score: 157
Period size: 54 Copynumber: 2.0 Consensus size: 54
1301880 CAAAATCGAG
* * *
1301890 GAAGGAGCT-CCAAACGCCGGCGTGGAAGAGGGAGTGGCGAAGGCAGGAGTGGAA
1 GAAGGAG-TGCCAAACGCCGGCGTGGAAGAAGGAGTGCCGAAGGCAGAAGTGGAA
* *
1301944 GAAGGAGTGCCAAATGCTGGCGTGGAAGAAGGAGTGCCGAAGGCAGAAGTGGAA
1 GAAGGAGTGCCAAACGCCGGCGTGGAAGAAGGAGTGCCGAAGGCAGAAGTGGAA
1301998 G
1 G
1301999 CCTGAGCACC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
53 1 0.02
54 48 0.98
ACGTcount: A:0.31, C:0.15, G:0.45, T:0.09
Consensus pattern (54 bp):
GAAGGAGTGCCAAACGCCGGCGTGGAAGAAGGAGTGCCGAAGGCAGAAGTGGAA
Found at i:1302436 original size:23 final size:24
Alignment explanation
Indices: 1302410--1302454 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1302400 TCAAATTTTA
1302410 TAAAAAATAAATAT-TTAAAATGT
1 TAAAAAATAAATATATTAAAATGT
* *
1302433 TAAATATTAAATATATTAAAAT
1 TAAAAAATAAATATATTAAAAT
1302455 ATACAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
TAAAAAATAAATATATTAAAATGT
Found at i:1302598 original size:16 final size:16
Alignment explanation
Indices: 1302577--1302661 Score: 54
Period size: 16 Copynumber: 5.5 Consensus size: 16
1302567 TAATTTTATA
1302577 ATCAATATCTAATTTT
1 ATCAATATCTAATTTT
*
1302593 ATCAATATAATAATTTT
1 ATCAATAT-CTAATTTT
* * * *
1302610 -TTAATTTTTTAATTTC
1 ATCAA-TATCTAATTTT
* *
1302626 ATTAAAAT-TAATTTT
1 ATCAATATCTAATTTT
1302641 AT---TATCTAATTTT
1 ATCAATATCTAATTTT
1302654 ATCAATAT
1 ATCAATAT
1302662 AATAATTTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
12 2 0.04
13 9 0.17
15 8 0.15
16 21 0.40
17 13 0.25
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (16 bp):
ATCAATATCTAATTTT
Found at i:1307109 original size:22 final size:21
Alignment explanation
Indices: 1307066--1307110 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
1307056 TTCCATTTGT
* **
1307066 AAATTTTTTATTATAATGTTA
1 AAATTTTTAATTATAACATTA
1307087 AAATTATTTAATTATAACATTA
1 AAATT-TTTAATTATAACATTA
1307109 AA
1 AA
1307111 TTGTCTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
AAATTTTTAATTATAACATTA
Found at i:1307514 original size:21 final size:21
Alignment explanation
Indices: 1307476--1307515 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1307466 ATTTTTTATT
*
1307476 TTTAAATTTTATATTGATTAA
1 TTTAAATTTTATACTGATTAA
1307497 TTTAAATATTTA-ACTGATT
1 TTTAAAT-TTTATACTGATT
1307516 TAAATATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTAAATTTTATACTGATTAA
Found at i:1309565 original size:29 final size:29
Alignment explanation
Indices: 1309542--1309596 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1309532 TTATTATTTA
1309542 AAATTATAAATTTAATTAATTATTTATAC
1 AAATTATAAATTTAATTAATTATTTATAC
* *
1309571 TAATTATAAAATTAATTAA--ATTTATA
1 AAATTATAAATTTAATTAATTATTTATA
1309597 TCACAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.29
29 17 0.71
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (29 bp):
AAATTATAAATTTAATTAATTATTTATAC
Found at i:1310607 original size:2 final size:2
Alignment explanation
Indices: 1310595--1310633 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1310585 TCATTTTAAT
* * *
1310595 TA TA GA TA TA TA TA TA TA TA TA TG TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1310634 TTCCTTCAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1311749 original size:9 final size:9
Alignment explanation
Indices: 1311735--1311765 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1311725 GAATTGTCTG
*
1311735 TTCTTCTGC
1 TTCTTCTCC
1311744 TTCTTCTCC
1 TTCTTCTCC
1311753 TTCTTCTCC
1 TTCTTCTCC
1311762 TTCT
1 TTCT
1311766 ATTGTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.39, G:0.03, T:0.58
Consensus pattern (9 bp):
TTCTTCTCC
Found at i:1312794 original size:2 final size:2
Alignment explanation
Indices: 1312787--1312812 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1312777 TCAAGATCAG
1312787 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
1312813 TGGAAATTTA
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):
AT
Found at i:1313989 original size:3 final size:3
Alignment explanation
Indices: 1313981--1314019 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1313971 CAAATTTTCA
1313981 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1314020 TTCCACGACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1318126 original size:16 final size:16
Alignment explanation
Indices: 1318105--1318139 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1318095 TAAGCTTATC
1318105 ATATTATA-AAATATAA
1 ATATTATATAAATA-AA
1318121 ATATTATATAAATAAA
1 ATATTATATAAATAAA
1318137 ATA
1 ATA
1318140 AAATATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATATTATATAAATAAA
Found at i:1318145 original size:16 final size:16
Alignment explanation
Indices: 1318126--1318158 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1318116 TATAAATATT
1318126 ATATAAATAA-AATAAA
1 ATATAAA-AATAATAAA
1318142 ATATAAAAATAATAAA
1 ATATAAAAATAATAAA
1318158 A
1 A
1318159 AAATTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 14 0.88
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
ATATAAAAATAATAAA
Found at i:1318178 original size:26 final size:24
Alignment explanation
Indices: 1318142--1318194 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
1318132 ATAAAATAAA
1318142 ATATAAAAATAATAAAAAAATTATAT
1 ATATAAAAAT-ATAAAAAAATT-TAT
* **
1318168 ATATATAAATATATTAAAATTTAT
1 ATATAAAAATATAAAAAAATTTAT
1318192 ATA
1 ATA
1318195 ATATTAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.25
25 9 0.38
26 9 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATAAAAATATAAAAAAATTTAT
Found at i:1318200 original size:17 final size:17
Alignment explanation
Indices: 1318178--1318231 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
1318168 ATATATAAAT
1318178 ATATTAAAATTTATATA
1 ATATTAAAATTTATATA
1318195 ATATT--AA-TTATGA-A
1 ATATTAAAATTTAT-ATA
*
1318209 TATATTAAAATTTACATA
1 -ATATTAAAATTTATATA
1318227 ATATT
1 ATATT
1318232 TTAAATAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 12
0.70 0.02 0.28
Matches are distributed among these distances:
14 5 0.17
15 8 0.27
17 13 0.43
18 4 0.13
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (17 bp):
ATATTAAAATTTATATA
Found at i:1319690 original size:29 final size:29
Alignment explanation
Indices: 1319643--1319720 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 29
1319633 AATTACATAA
1319643 ATATAATA-AAGATAAA-ATAATTAAAATATG
1 ATATAATATAA-ATAAATAT-ATTAAAAT-TG
* * *
1319673 ATATCATATAAATAAATATTTTAAAATTT
1 ATATAATATAAATAAATATATTAAAATTG
*
1319702 ATATAATATAAATTAATAT
1 ATATAATATAAATAAATAT
1319721 CTTATCAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 18 0.44
30 19 0.46
31 4 0.10
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (29 bp):
ATATAATATAAATAAATATATTAAAATTG
Found at i:1319736 original size:32 final size:29
Alignment explanation
Indices: 1319663--1319739 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 29
1319653 GATAAAATAA
* *
1319663 TTAAAATATGATATCATATAAATAAATATT
1 TTAAAAT-TTATATAATATAAATAAATATT
*
1319693 TTAAAATTTATATAATATAAATTAATATCT
1 TTAAAATTTATATAATATAAATAAATAT-T
1319723 TATCAAAATTTATATAA
1 T-T-AAAATTTATATAA
1319740 AGATAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
29 18 0.44
30 9 0.22
31 1 0.02
32 13 0.32
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (29 bp):
TTAAAATTTATATAATATAAATAAATATT
Found at i:1324069 original size:16 final size:15
Alignment explanation
Indices: 1324047--1324093 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
1324037 TATAAATATT
1324047 TTAAATTTTATATAA
1 TTAAATTTTATATAA
1324062 TATAAATTATTA-ATAGA
1 T-TAAATT-TTATATA-A
*
1324079 TTAAAATTTATATAA
1 TTAAATTTTATATAA
1324094 AAATAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
15 5 0.19
16 17 0.63
17 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:1326427 original size:120 final size:119
Alignment explanation
Indices: 1326215--1326448 Score: 423
Period size: 120 Copynumber: 2.0 Consensus size: 119
1326205 CTTCTAATAG
* * *
1326215 TTGCTTAGAGTTTACTGTATTCATTCTCGGTTGACGATTCTCTTACGCGTTCTTTTAGAGCGTGT
1 TTGCTTAGAGTTTACTATATTCATTCTCGGTTGACGATTCCCTCACGCGTTCTTTTAGAGCGTGT
*
1326280 TCTACAGATTCCGACCACTTTGGATCAAGTGCTCGGATGGGAGAACGTTATGTT
66 TCTACACATTCCGACCACTTTGGATCAAGTGCTCGGATGGGAGAACGTTATGTT
1326334 TTGCTTAGAGTTTACTATATTCATTCTCGGTTGACGATTCCCTACACGCGTTCTTTTAGAGCGTG
1 TTGCTTAGAGTTTACTATATTCATTCTCGGTTGACGATTCCCT-CACGCGTTCTTTTAGAGCGTG
1326399 TTCTACACATTCCGACCACTTTGGATCAAGTGCTCGGATGGGAGAACGTT
65 TTCTACACATTCCGACCACTTTGGATCAAGTGCTCGGATGGGAGAACGTT
1326449 CTGTGTCCAT
Statistics
Matches: 110, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
119 41 0.37
120 69 0.63
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (119 bp):
TTGCTTAGAGTTTACTATATTCATTCTCGGTTGACGATTCCCTCACGCGTTCTTTTAGAGCGTGT
TCTACACATTCCGACCACTTTGGATCAAGTGCTCGGATGGGAGAACGTTATGTT
Found at i:1327299 original size:2 final size:2
Alignment explanation
Indices: 1327288--1327322 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1327278 AATTTGGAAC
*
1327288 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1327323 AAGTTACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1329905 original size:16 final size:16
Alignment explanation
Indices: 1329877--1329933 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
1329867 AAACTTAATA
1329877 TAAAT-ATATTAAAATT
1 TAAATAATA-TAAAATT
1329893 TAAATAATAT-AAA-T
1 TAAATAATATAAAATT
*
1329907 T-ATTAATTATAAAATT
1 TAAATAA-TATAAAATT
*
1329923 TATATAATATA
1 TAAATAATATA
1329934 TAATAGTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
13 4 0.12
14 5 0.15
15 6 0.18
16 12 0.36
17 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATAATATAAAATT
Found at i:1329908 original size:21 final size:21
Alignment explanation
Indices: 1329856--1329908 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
1329846 ATATGATATA
*
1329856 ATAAA-AAAATAAAACTTAAT
1 ATAAATAAATTAAAACTTAAT
* *
1329876 ATAAATATATTAAAATTTAA-
1 ATAAATAAATTAAAACTTAAT
1329896 ATAATATAAATTA
1 ATAA-ATAAATTA
1329909 TTAATTATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAAATAAATTAAAACTTAAT
Found at i:1330224 original size:21 final size:22
Alignment explanation
Indices: 1330198--1330257 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
1330188 ATTAAAATTT
**
1330198 TATATAAATATAAATAATTTAA
1 TATATAAATATAAATAATAAAA
* *
1330220 -ATATAATTAT-AATTATAAAA
1 TATATAAATATAAATAATAAAA
1330240 TATATAAATATAATATAA
1 TATATAAATATAA-ATAA
1330258 ATGTAGGTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 7 0.24
21 18 0.62
22 1 0.03
23 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TATATAAATATAAATAATAAAA
Found at i:1330230 original size:27 final size:26
Alignment explanation
Indices: 1330199--1330259 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
1330189 TTAAAATTTT
*
1330199 ATATAAATAT-AAATAATTTAAATATA
1 ATATAAATATAAAAT-ATATAAATATA
*
1330225 ATTATAATTATAAAATATATAAATATA
1 A-TATAAATATAAAATATATAAATATA
1330252 ATATAAAT
1 ATATAAAT
1330260 GTAGGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 7 0.23
27 19 0.63
28 4 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
ATATAAATATAAAATATATAAATATA
Found at i:1330231 original size:17 final size:16
Alignment explanation
Indices: 1330200--1330259 Score: 63
Period size: 15 Copynumber: 3.8 Consensus size: 16
1330190 TAAAATTTTA
1330200 TATAAATATAAATAAT
1 TATAAATATAAATAAT
1330216 T-TAAATATAATTATAAT
1 TATAAATATAA--ATAAT
* *
1330233 TATAAA-ATATATAAA
1 TATAAATATAAATAAT
1330248 TAT-AATATAAAT
1 TATAAATATAAAT
1330260 GTAGGTATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 2 0.05
15 21 0.57
16 1 0.03
17 9 0.24
18 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TATAAATATAAATAAT
Found at i:1330984 original size:24 final size:25
Alignment explanation
Indices: 1330934--1330988 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
1330924 CATAAAATAA
* * *
1330934 TTTTATTATTTTCGTATCTTTAAAT
1 TTTTATTATTTTCATATATATAAAT
*
1330959 TTTTATTATTTT-ATATATATATAT
1 TTTTATTATTTTCATATATATAAAT
1330983 TTTTAT
1 TTTTAT
1330989 CGTTTTCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (25 bp):
TTTTATTATTTTCATATATATAAAT
Found at i:1337724 original size:17 final size:18
Alignment explanation
Indices: 1337702--1337751 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
1337692 ATTATTAGTT
1337702 ATAATTAAATTTAAAT-A
1 ATAATTAAATTTAAATCA
1337719 ATAATTAAGA-TTAAATCA
1 ATAATTAA-ATTTAAATCA
1337737 AT--TTAAATTATAAAT
1 ATAATTAAATT-TAAAT
1337752 TTTTTATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 1 0.03
16 5 0.17
17 19 0.66
18 4 0.14
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (18 bp):
ATAATTAAATTTAAATCA
Found at i:1340444 original size:28 final size:26
Alignment explanation
Indices: 1340395--1340459 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
1340385 CAATTATCAC
* * *
1340395 TAATTTTTTAAATAATAGTAATTAAT
1 TAATTTTTAAAAAAATAGTAATAAAT
1340421 TAATTTTTAAAAAAATAGTTTAATAAAT
1 TAATTTTTAAAAAAATAG--TAATAAAT
*
1340449 TTA-TTTTAAAA
1 TAATTTTTAAAA
1340460 TTAATATGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 16 0.48
27 8 0.24
28 9 0.27
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (26 bp):
TAATTTTTAAAAAAATAGTAATAAAT
Found at i:1340505 original size:16 final size:15
Alignment explanation
Indices: 1340484--1340517 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1340474 AATTAAAATA
1340484 TAATTTAATAATAATT
1 TAATTTAATAAT-ATT
*
1340500 TAATTTAATTATATT
1 TAATTTAATAATATT
1340515 TAA
1 TAA
1340518 AAATAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTTAATAATATT
Found at i:1353953 original size:12 final size:11
Alignment explanation
Indices: 1353932--1353981 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
1353922 AAAATTAAAG
1353932 TTAA-TTTAAT
1 TTAATTTTAAT
1353942 TATAATTTTAAT
1 T-TAATTTTAAT
**
1353954 TTAATAAATAAT
1 TTAAT-TTTAAT
1353966 TTAA-TTTAAT
1 TTAATTTTAAT
1353976 TTAATT
1 TTAATT
1353982 AAAATGTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
10 9 0.28
11 8 0.25
12 15 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTAATTTTAAT
Found at i:1353954 original size:17 final size:17
Alignment explanation
Indices: 1353932--1353981 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
1353922 AAAATTAAAG
1353932 TTAATTTAATTATAATT
1 TTAATTTAATTATAATT
*
1353949 TTAATTTAATAAATAA-T
1 TTAATTTAAT-TATAATT
1353966 TTAATTTAATT-TAATT
1 TTAATTTAATTATAATT
1353982 AAAATGTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 3 0.10
16 1 0.03
17 21 0.72
18 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAATTTAATTATAATT
Found at i:1353983 original size:4 final size:5
Alignment explanation
Indices: 1353932--1354000 Score: 57
Period size: 5 Copynumber: 12.8 Consensus size: 5
1353922 AAAATTAAAG
*
1353932 TTAAT TTAAT TATAATT TTAAT TTAAT AAATAAT TTAAT TTAAT TTAAT
1 TTAAT TTAAT T-TAA-T TTAAT TTAAT --TTAAT TTAAT TTAAT TTAAT
* * *
1353981 TAAAAT GTAAT TGAAT TTAA
1 T-TAAT TTAAT TTAAT TTAA
1354001 ATAGTAATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
5 36 0.71
6 9 0.18
7 6 0.12
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (5 bp):
TTAAT
Found at i:1353997 original size:16 final size:17
Alignment explanation
Indices: 1353972--1354009 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1353962 TAATTTAATT
*
1353972 TAATTTAATTAAAAT-G
1 TAATTGAATTAAAATAG
*
1353988 TAATTGAATTTAAATAG
1 TAATTGAATTAAAATAG
1354005 TAATT
1 TAATT
1354010 TATAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (17 bp):
TAATTGAATTAAAATAG
Found at i:1353997 original size:21 final size:22
Alignment explanation
Indices: 1353951--1354000 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1353941 TTATAATTTT
* *
1353951 AATTTAATAAATAATTTAATTT
1 AATTTAATAAATAATGTAATTG
*
1353973 AATTTAATTAA-AATGTAATTG
1 AATTTAATAAATAATGTAATTG
1353994 AATTTAA
1 AATTTAA
1354001 ATAGTAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (22 bp):
AATTTAATAAATAATGTAATTG
Found at i:1360232 original size:15 final size:17
Alignment explanation
Indices: 1360212--1360273 Score: 67
Period size: 16 Copynumber: 3.7 Consensus size: 17
1360202 TAAGTTTGTA
1360212 TTAATTT-AATT-TTAT
1 TTAATTTAAATTATTAT
1360227 TTAATTTAAATTATTAT
1 TTAATTTAAATTATTAT
* *
1360244 TTAATAAATAAAATATT-T
1 TTAAT--TTAAATTATTAT
1360262 TTAATTTAAATT
1 TTAATTTAAATT
1360274 TAATTATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 7 0.18
16 9 0.23
17 9 0.23
18 6 0.15
19 8 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAATTTAAATTATTAT
Found at i:1366729 original size:18 final size:17
Alignment explanation
Indices: 1366698--1366731 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1366688 AATTAAAATA
*
1366698 AAATATTTTAATTATAT
1 AAATATATTAATTATAT
1366715 AAATATATTATATTATA
1 AAATATATTA-ATTATA
1366732 ATCATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATATATTAATTATAT
Found at i:1369201 original size:16 final size:17
Alignment explanation
Indices: 1369172--1369216 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
1369162 AAAGTATCCG
*
1369172 TAATT-TATTTTTTAAA
1 TAATTATATTATTTAAA
1369188 -AATTATATTATTTAAA
1 TAATTATATTATTTAAA
*
1369204 TAA-AATATTATTT
1 TAATTATATTATTT
1369217 TTTATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 4 0.16
16 19 0.76
17 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATTATATTATTTAAA
Found at i:1369226 original size:19 final size:20
Alignment explanation
Indices: 1369176--1369226 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
1369166 TATCCGTAAT
1369176 TTATTT-TTTAAAAATTATA
1 TTATTTATTTAAAAATTATA
**
1369195 TTATTTAAATAAAATATTAT-
1 TTATTTATTTAAAA-ATTATA
1369215 TT-TTTATTTAAA
1 TTATTTATTTAAA
1369227 TTTAATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 14 0.54
20 7 0.27
21 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATTTATTTAAAAATTATA
Found at i:1369393 original size:27 final size:27
Alignment explanation
Indices: 1369329--1369416 Score: 69
Period size: 27 Copynumber: 3.3 Consensus size: 27
1369319 AATATCTTTT
* *
1369329 ATAATAAAATAAAATTATTT--TTAAA
1 ATAAAAAAATAAAATTATTTAAATAAA
**
1369354 GA-AAAAATTTAAAATTATTTAAATAAA
1 -ATAAAAAAATAAAATTATTTAAATAAA
1369381 ATAAAAAAAT-AAA-TATCGTTAAATAAA
1 ATAAAAAAATAAAATTAT--TTAAATAAA
1369408 AGTAAAAAA
1 A-TAAAAAA
1369417 TTTCTATTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
25 18 0.36
26 5 0.10
27 20 0.40
28 7 0.14
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (27 bp):
ATAAAAAAATAAAATTATTTAAATAAA
Found at i:1369775 original size:20 final size:21
Alignment explanation
Indices: 1369747--1369785 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1369737 CCCCCCCTCT
*
1369747 TTTACTTTTTTTT-TCTTTAA
1 TTTAATTTTTTTTCTCTTTAA
1369767 TTTAATTTTTTTTCTCTTT
1 TTTAATTTTTTTTCTCTTT
1369786 TTGAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTAATTTTTTTTCTCTTTAA
Found at i:1372914 original size:27 final size:26
Alignment explanation
Indices: 1372856--1372915 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 26
1372846 TTTGATATAA
1372856 AAATATTTTAAAAAATAATATCAAAT
1 AAATATTTTAAAAAATAATATCAAAT
*
1372882 ATAATATTTATAAAAAATAAT-TCATATT
1 A-AATATTT-TAAAAAATAATATCA-AAT
1372910 AAATAT
1 AAATAT
1372916 ATAGATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 1 0.03
27 15 0.50
28 14 0.47
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (26 bp):
AAATATTTTAAAAAATAATATCAAAT
Found at i:1372954 original size:12 final size:14
Alignment explanation
Indices: 1372905--1372976 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 14
1372895 AAAATAATTC
1372905 ATATTA-AATATATA
1 ATATTATAA-ATATA
*
1372919 GATTTTATATAATATA
1 -ATATTATA-AATATA
1372935 ATATTATAAATATA
1 ATATTATAAATATA
* *
1372949 ATTATAATAAA-AAA
1 A-TATTATAAATATA
1372963 ATAATTATAAATAT
1 AT-ATTATAAATAT
1372977 TATAAATACA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
13 1 0.02
14 17 0.37
15 21 0.46
16 6 0.13
17 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (14 bp):
ATATTATAAATATA
Found at i:1373351 original size:2 final size:2
Alignment explanation
Indices: 1373344--1373373 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1373334 TGAAAAGGAA
1373344 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
1373374 TAGAAAGAGA
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:1374551 original size:33 final size:35
Alignment explanation
Indices: 1374468--1374567 Score: 120
Period size: 33 Copynumber: 2.9 Consensus size: 35
1374458 TATATGATAT
1374468 AATAA-TATT-TATATTTATATTATATTATTTATTTA
1 AATAATTATTATATATTT-TATT-TATTATTTATTTA
*
1374503 AATTATTATCATATATATTTTATTT-TTATTTATTTA
1 AATAATTAT--TATATATTTTATTTATTATTTATTTA
1374539 AA-AATTATTATATATTTTATTTATT-TTTA
1 AATAATTATTATATATTTTATTTATTATTTA
1374568 AATACATATT
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
33 18 0.31
34 2 0.03
35 9 0.16
36 16 0.28
37 1 0.02
38 5 0.09
39 7 0.12
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (35 bp):
AATAATTATTATATATTTTATTTATTATTTATTTA
Found at i:1374705 original size:14 final size:14
Alignment explanation
Indices: 1374677--1374722 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1374667 ATTAAATTTA
*
1374677 ATAATTTTA-AAAT
1 ATAATTATATAAAT
1374690 ATAATTATATAAAT
1 ATAATTATATAAAT
*
1374704 ATAATATGTATAAA-
1 ATAAT-TATATAAAT
1374718 ATAAT
1 ATAAT
1374723 ATAAATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 8 0.28
14 14 0.48
15 7 0.24
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (14 bp):
ATAATTATATAAAT
Found at i:1374723 original size:14 final size:15
Alignment explanation
Indices: 1374686--1374724 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
1374676 AATAATTTTA
*
1374686 AAATATAAT-TATAT
1 AAATATAATATGTAT
1374700 AAATATAATATGTAT
1 AAATATAATATGTAT
1374715 AAA-ATAATAT
1 AAATATAATAT
1374725 AAATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
AAATATAATATGTAT
Found at i:1374802 original size:47 final size:48
Alignment explanation
Indices: 1374696--1374827 Score: 117
Period size: 47 Copynumber: 2.6 Consensus size: 48
1374686 AAATATAATT
* *
1374696 ATATAAATATAATATGTATAAAATAATATAAATATATATTTAAAAATTTTATAAC
1 ATATAATTATAATAT-AATAAAAT-ATATAAA-A-ATA---AAAAATTTTATAAC
* * *
1374751 ATAT-ATTATTAATATATTAATATTTATAAAAATAAAAAATATTT-TAA-
1 ATATAATTA-TAATATAATAAAATATATAAAAATAAAAAAT-TTTATAAC
1374798 ATATAATTATAATATAATAAAATATATAAA
1 ATATAATTATAATATAATAAAATATATAAA
1374828 TTATTAAATT
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
47 22 0.33
48 13 0.20
49 3 0.05
51 3 0.05
52 1 0.02
53 6 0.09
54 8 0.12
55 10 0.15
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.41
Consensus pattern (48 bp):
ATATAATTATAATATAATAAAATATATAAAAATAAAAAATTTTATAAC
Found at i:1375702 original size:21 final size:18
Alignment explanation
Indices: 1375657--1375702 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 18
1375647 TAAAATATAA
1375657 AAAATATTTTTATTTAAT
1 AAAATATTTTTATTTAAT
1375675 AATAATATTTTATAATTTAAT
1 AA-AATATTTT-T-ATTTAAT
1375696 ATAAATA
1 A-AAATA
1375703 AAATATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.08
19 8 0.33
20 1 0.04
21 12 0.50
22 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAAATATTTTTATTTAAT
Found at i:1375720 original size:21 final size:21
Alignment explanation
Indices: 1375657--1375723 Score: 59
Period size: 26 Copynumber: 3.0 Consensus size: 21
1375647 TAAAATATAA
1375657 AAAATATTTTTATT--T-AAT
1 AAAATATTTTTATTAATAAAT
1375675 AATAATATTTTATAATTTAATATAAAT
1 AA-AATATTTT-T-A-TT-A-ATAAAT
1375702 AAAATATTTTTATTAATAAAT
1 AAAATATTTTTATTAATAAAT
1375723 A
1 A
1375724 GTAATTCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 15
0.73 0.00 0.27
Matches are distributed among these distances:
18 2 0.05
19 8 0.20
20 1 0.03
21 8 0.20
22 3 0.08
23 2 0.05
24 1 0.03
25 1 0.03
26 9 0.22
27 5 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAATATTTTTATTAATAAAT
Found at i:1376315 original size:15 final size:16
Alignment explanation
Indices: 1376295--1376324 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1376285 TGATACTTCT
1376295 AATTAATA-TTAATTG
1 AATTAATATTTAATTG
1376310 AATTAATATTTAATT
1 AATTAATATTTAATT
1376325 AGATAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
AATTAATATTTAATTG
Found at i:1380199 original size:3 final size:3
Alignment explanation
Indices: 1380191--1380223 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1380181 CTATCCCCCC
1380191 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1380224 CATAAGCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1383118 original size:1 final size:1
Alignment explanation
Indices: 1383112--1383136 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1383102 GGCCTTCCTG
1383112 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
1383137 GGGTGCCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1384539 original size:2 final size:2
Alignment explanation
Indices: 1384534--1384568 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1384524 GAAGGCAAAG
1384534 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1384569 AAGCTGCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1385181 original size:13 final size:13
Alignment explanation
Indices: 1385165--1385195 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1385155 TTTTATTTAT
1385165 ATATTAAATATAA
1 ATATTAAATATAA
*
1385178 ATATCAAATATAA
1 ATATTAAATATAA
1385191 ATATT
1 ATATT
1385196 TTAAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATTAAATATAA
Found at i:1393096 original size:21 final size:21
Alignment explanation
Indices: 1393072--1393119 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1393062 TATATTATTT
*
1393072 TTATATTATATAGTATTT-TAA
1 TTATATTATATAATATTTAT-A
* *
1393093 TTATTTTTTATAATATTTATA
1 TTATATTATATAATATTTATA
1393114 TTATAT
1 TTATAT
1393120 CATTTTATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
TTATATTATATAATATTTATA
Found at i:1394902 original size:3 final size:3
Alignment explanation
Indices: 1394894--1394923 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1394884 TATTTTCATA
*
1394894 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1394924 TCAGGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1400546 original size:22 final size:22
Alignment explanation
Indices: 1400516--1400588 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
1400506 TTGATAATAA
*
1400516 AATATTAAAAATTATTTTTTAT
1 AATAATAAAAATTATTTTTTAT
1400538 AATAATAAAATTTATATATTTTTTAT
1 AATAATAAAA---AT-TATTTTTTAT
* *
1400564 -ATAA-ATTAAATTATTTTTTAA
1 AATAATA-AAAATTATTTTTTAT
1400585 AATA
1 AATA
1400589 TTAATTTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
21 9 0.21
22 14 0.33
24 1 0.02
25 8 0.19
26 10 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATAATAAAAATTATTTTTTAT
Found at i:1400547 original size:21 final size:21
Alignment explanation
Indices: 1400523--1400588 Score: 60
Period size: 24 Copynumber: 2.9 Consensus size: 21
1400513 TAAAATATTA
1400523 AAAATTATTTTTTATAATAAT
1 AAAATTATTTTTTATAATAAT
*
1400544 AAAATTTATATATTTTTTATATAAAT
1 AAAA-TTAT-T-TTTTATA-AT-AAT
* *
1400570 TAAATTATTTTTTAAAATA
1 AAAATTATTTTTTATAATA
1400589 TTAATTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
21 5 0.14
22 6 0.17
23 6 0.17
24 7 0.19
25 6 0.17
26 6 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAAATTATTTTTTATAATAAT
Found at i:1400777 original size:10 final size:10
Alignment explanation
Indices: 1400762--1400786 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1400752 TTATTCGATC
1400762 TAATAAAAGT
1 TAATAAAAGT
1400772 TAATAAAAGT
1 TAATAAAAGT
1400782 TAATA
1 TAATA
1400787 TTCAAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (10 bp):
TAATAAAAGT
Found at i:1402109 original size:18 final size:17
Alignment explanation
Indices: 1402057--1402109 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
1402047 GTTTGATATC
*
1402057 TTTTAAAAAAATTAATTT
1 TTTTAAAAATATT-ATTT
*
1402075 TCTTAAAAATGATTATTT
1 TTTTAAAAAT-ATTATTT
1402093 TTTTAAAAATATATATT
1 TTTTAAAAATAT-TATT
1402110 AATTATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 2 0.07
18 25 0.83
19 3 0.10
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTTAAAAATATTATTT
Found at i:1404119 original size:17 final size:17
Alignment explanation
Indices: 1404094--1404127 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1404084 ACAAACATTA
*
1404094 TTTAATAAAATTTAATT
1 TTTAATAAAAATTAATT
*
1404111 TTTATTAAAAATTAATT
1 TTTAATAAAAATTAATT
1404128 AAAAATATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAATAAAAATTAATT
Found at i:1404293 original size:28 final size:29
Alignment explanation
Indices: 1404238--1404293 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
1404228 TATTTTAAAT
**
1404238 ATAAAATTTAAATACATAATTATTATTTA
1 ATAAAATTTAAATACATAATTAAAATTTA
**
1404267 ATAAAATTT-AATTTATAATTAAAATTT
1 ATAAAATTTAAATACATAATTAAAATTT
1404294 TATTAATAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (29 bp):
ATAAAATTTAAATACATAATTAAAATTTA
Found at i:1404302 original size:18 final size:18
Alignment explanation
Indices: 1404268--1404302 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1404258 TATTATTTAA
*
1404268 TAAAATTTAATTTATAAT
1 TAAAATTTAATTAATAAT
*
1404286 TAAAATTTTATTAATAA
1 TAAAATTTAATTAATAA
1404303 CGACTAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAAATTTAATTAATAAT
Found at i:1404444 original size:20 final size:21
Alignment explanation
Indices: 1404407--1404446 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1404397 TATTCCTAAA
*
1404407 AAAAATTAACATTAATTTTTT
1 AAAAATAAACATTAATTTTTT
*
1404428 AAAAATAAATATT-ATTTTT
1 AAAAATAAACATTAATTTTT
1404447 GGTTAGCACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
AAAAATAAACATTAATTTTTT
Found at i:1407140 original size:18 final size:20
Alignment explanation
Indices: 1407104--1407140 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1407094 GATACAATGT
*
1407104 AGTTGCACTTTTGTGACTTA
1 AGTTGCACTTTGGTGACTTA
1407124 AGTTGC-CTTTGGT-ACTT
1 AGTTGCACTTTGGTGACTT
1407141 TGAAAACTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.25
19 6 0.38
20 6 0.38
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.46
Consensus pattern (20 bp):
AGTTGCACTTTGGTGACTTA
Found at i:1414580 original size:4 final size:4
Alignment explanation
Indices: 1414571--1414595 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1414561 CTCTATTTTC
1414571 TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT T
1414596 TTTTTTTACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:1414941 original size:4 final size:4
Alignment explanation
Indices: 1414924--1414959 Score: 63
Period size: 4 Copynumber: 8.8 Consensus size: 4
1414914 ATAATTTCCT
1414924 TTTA TTTCA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTT
1414960 GTTGTATACT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:1415814 original size:11 final size:12
Alignment explanation
Indices: 1415772--1415818 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
1415762 CAAAGTGGGT
1415772 TATTTTTTAAAA
1 TATTTTTTAAAA
*
1415784 AATTAATTTTAAAA
1 TATT--TTTTAAAA
1415798 TATTTTTTAAAA
1 TATTTTTTAAAA
1415810 T-TTTTTTAA
1 TATTTTTTAA
1415819 TTAATTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 8 0.26
12 12 0.39
14 11 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTTTTTAAAA
Found at i:1416137 original size:15 final size:15
Alignment explanation
Indices: 1416101--1416151 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1416091 TTTAATTTGT
1416101 ATATT-TTTATTAT-
1 ATATTATTTATTATA
*
1416114 ATTTATATTTATTATA
1 ATAT-TATTTATTATA
**
1416130 ATATTATTTAAAATA
1 ATATTATTTATTATA
1416145 ATATTAT
1 ATATTAT
1416152 AACATATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 3 0.10
14 1 0.03
15 24 0.77
16 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATTATTTATTATA
Found at i:1416193 original size:31 final size:33
Alignment explanation
Indices: 1416148--1416212 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
1416138 TAAAATAATA
1416148 TTATAACATATTAATAT-TTTAATAATTTATTT
1 TTATAACATATTAATATATTTAATAATTTATTT
* * *
1416180 TTATAA-ATTTTAATATATTTATTTATTTATTT
1 TTATAACATATTAATATATTTAATAATTTATTT
1416212 T
1 T
1416213 ATATTATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 9 0.31
32 20 0.69
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (33 bp):
TTATAACATATTAATATATTTAATAATTTATTT
Done.