Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014990.1 Kokia drynarioides strain JFW-HI SEQ_130034, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 743029
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 631 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:1338 original size:18 final size:18
Alignment explanation
Indices: 1315--1350 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1305 TAGAACAAAA
1315 AAATTTAAAATATATTTT
1 AAATTTAAAATATATTTT
* *
1333 AAATTTTAAATTTATTTT
1 AAATTTAAAATATATTTT
1351 GGGTTATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATTTAAAATATATTTT
Found at i:6270 original size:21 final size:21
Alignment explanation
Indices: 6245--6285 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6235 TTTCATTTTT
*
6245 TTTCTTTTAAGTTTTTTTAAC
1 TTTCTTTTAAGTTCTTTTAAC
*
6266 TTTCTTTTATGTTCTTTTAA
1 TTTCTTTTAAGTTCTTTTAA
6286 TTTTTTCTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTCTTTTAAGTTCTTTTAAC
Found at i:8068 original size:21 final size:21
Alignment explanation
Indices: 8044--8084 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
8034 ATTTCCTTCT
* * *
8044 CTTTTTCTTATAAATTTGATC
1 CTTTTCCTGATAAATGTGATC
8065 CTTTTCCTGATAAATGTGAT
1 CTTTTCCTGATAAATGTGAT
8085 ATGGATATGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.10, T:0.51
Consensus pattern (21 bp):
CTTTTCCTGATAAATGTGATC
Found at i:16242 original size:29 final size:29
Alignment explanation
Indices: 16210--16275 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
16200 TTGGTCCTTA
16210 TACTTT-AATTTGATCAATCTTAGTCTCTT
1 TACTTTGAA-TTGATCAATCTTAGTCTCTT
* *
16239 TACTTTTTGAATTGATCAATTTTAGTCTTTT
1 TAC--TTTGAATTGATCAATCTTAGTCTCTT
16270 TACTTT
1 TACTTT
16276 TCGAGTTTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 6 0.19
31 24 0.75
32 2 0.06
ACGTcount: A:0.23, C:0.14, G:0.08, T:0.56
Consensus pattern (29 bp):
TACTTTGAATTGATCAATCTTAGTCTCTT
Found at i:19375 original size:20 final size:19
Alignment explanation
Indices: 19343--19385 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
19333 GTTTTACCCC
* *
19343 TAAAAAAAAATAATATTTT
1 TAAAAAAAAATAAAAATTT
*
19362 TAAAAAAATTATAAAAATTT
1 TAAAAAAA-AATAAAAATTT
19382 TAAA
1 TAAA
19386 CTTTAGAGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAAAAAATAAAAATTT
Found at i:27804 original size:2 final size:2
Alignment explanation
Indices: 27753--27787 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
27743 TAACCCTAAA
27753 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
27788 CTCCCAATTA
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:29483 original size:16 final size:16
Alignment explanation
Indices: 29462--29493 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29452 ATCTCTCCTA
29462 CCATCTCTTCAATTTT
1 CCATCTCTTCAATTTT
*
29478 CCATCTTTTCAATTTT
1 CCATCTCTTCAATTTT
29494 TTTCCACTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.28, G:0.00, T:0.53
Consensus pattern (16 bp):
CCATCTCTTCAATTTT
Found at i:36162 original size:2 final size:2
Alignment explanation
Indices: 36155--36179 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36145 TTGCAGAGTG
36155 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 T
36180 GCATGGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42645 original size:19 final size:18
Alignment explanation
Indices: 42623--42658 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
42613 ACAGAATTCC
*
42623 AAAATTTATATATTTTTTA
1 AAAAATTATA-ATTTTTTA
42642 AAAAATTATAATTTTTT
1 AAAAATTATAATTTTTT
42659 TTCAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAAAATTATAATTTTTTA
Found at i:45384 original size:24 final size:24
Alignment explanation
Indices: 45356--45430 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
45346 ATTTGACTCA
*
45356 AAACAACTAAACAGAGTTTAAATG
1 AAACAAATAAACAGAGTTTAAATG
* *
45380 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAAATG
*
45404 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAAATG
45428 AAA
1 AAA
45431 TATTATTTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.23
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAAATG
Found at i:53940 original size:9 final size:9
Alignment explanation
Indices: 53926--53968 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
53916 TTCACATCCT
53926 TCTCTCAAC
1 TCTCTCAAC
53935 TCTCTCAAAC
1 TCTCTC-AAC
* *
53945 CCTCTCAAG
1 TCTCTCAAC
53954 TCTCTCAAC
1 TCTCTCAAC
53963 TCTCTC
1 TCTCTC
53969 GTTCTGATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.21, C:0.44, G:0.02, T:0.33
Consensus pattern (9 bp):
TCTCTCAAC
Found at i:58108 original size:39 final size:39
Alignment explanation
Indices: 58051--58144 Score: 125
Period size: 39 Copynumber: 2.4 Consensus size: 39
58041 CTATTATAAC
* *
58051 TTAAGTTTATATATTTCATTTATCACAATACTAATGAAT
1 TTAAGTTTATATTTTTCATATATCACAATACTAATGAAT
* * *
58090 TTGAGTTTATATTTTTCATATATCATAATATTAATGAAT
1 TTAAGTTTATATTTTTCATATATCACAATACTAATGAAT
* *
58129 TTAAATATATATTTTT
1 TTAAGTTTATATTTTT
58145 TACTTCACAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.51
Consensus pattern (39 bp):
TTAAGTTTATATTTTTCATATATCACAATACTAATGAAT
Found at i:59150 original size:26 final size:27
Alignment explanation
Indices: 59090--59166 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 27
59080 TACATACAAC
* * *
59090 AAATTTAAAATATATATAATATATCAAAT
1 AAATTTAAAATACATA-AAAAAAT-AAAT
* *
59119 ATATTTAAAA-ACATTAAAAAATAAAT
1 AAATTTAAAATACATAAAAAAATAAAT
59145 AAATTTAAAATACATAAAAAAA
1 AAATTTAAAATACATAAAAAAA
59167 ATTATATTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 13 0.32
27 15 0.38
28 3 0.08
29 9 0.22
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (27 bp):
AAATTTAAAATACATAAAAAAATAAAT
Found at i:59302 original size:20 final size:21
Alignment explanation
Indices: 59279--59330 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
59269 AAAACGCATA
*
59279 AAAAATAACATCC-AAACAAC
1 AAAAATAACAACCAAAACAAC
59299 AAAAATAACAACCAAAACAAC
1 AAAAATAACAACCAAAACAAC
*
59320 AACAA-AACAAC
1 AAAAATAACAAC
59331 ATTAAAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.69, C:0.25, G:0.00, T:0.06
Consensus pattern (21 bp):
AAAAATAACAACCAAAACAAC
Found at i:59310 original size:12 final size:11
Alignment explanation
Indices: 59292--59371 Score: 65
Period size: 12 Copynumber: 7.1 Consensus size: 11
59282 AATAACATCC
59292 AAACAACAAAA
1 AAACAACAAAA
*
59303 ATAACAAC--CA
1 A-AACAACAAAA
*
59313 AAACAACAACA
1 AAACAACAAAA
*
59324 AAACAACATTAA
1 AAACAACA-AAA
59336 AAACAACAAAA
1 AAACAACAAAA
*
59347 ACAGCAACAAAA
1 A-AACAACAAAA
*
59359 ATAACAGCAAAA
1 A-AACAACAAAA
59371 A
1 A
59372 CGACACGAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
9 6 0.11
10 2 0.04
11 14 0.25
12 34 0.61
ACGTcount: A:0.71, C:0.21, G:0.03, T:0.05
Consensus pattern (11 bp):
AAACAACAAAA
Found at i:59341 original size:32 final size:32
Alignment explanation
Indices: 59292--59358 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
59282 AATAACATCC
*
59292 AAACAACAAAAATAACAACCAAAACAACAACA
1 AAACAACAAAAATAACAACAAAAACAACAACA
* *
59324 AAACAACATTAAA-AACAACAAAAACAGCAACA
1 AAACAACA-AAAATAACAACAAAAACAACAACA
59356 AAA
1 AAA
59359 ATAACAGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 28 0.90
33 3 0.10
ACGTcount: A:0.72, C:0.22, G:0.01, T:0.04
Consensus pattern (32 bp):
AAACAACAAAAATAACAACAAAAACAACAACA
Found at i:59394 original size:12 final size:12
Alignment explanation
Indices: 59379--59427 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
59369 AAACGACACG
59379 AAAACAGCAACC
1 AAAACAGCAACC
*
59391 AAAACAGTAA--
1 AAAACAGCAACC
* *
59401 AAAACAAC-ACA
1 AAAACAGCAACC
59412 AAAACAGCAACC
1 AAAACAGCAACC
59424 AAAA
1 AAAA
59428 TAGTAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
9 1 0.03
10 6 0.21
11 7 0.24
12 15 0.52
ACGTcount: A:0.67, C:0.24, G:0.06, T:0.02
Consensus pattern (12 bp):
AAAACAGCAACC
Found at i:59395 original size:56 final size:54
Alignment explanation
Indices: 59292--59421 Score: 129
Period size: 56 Copynumber: 2.4 Consensus size: 54
59282 AATAACATCC
* * **
59292 AAACAACAAAAATAACAACCAAAACAACAACAAAACAACATTAAAAACAACAAA
1 AAACAACAAAAATAACAGCAAAAACAACAACAAAACAACAACAAAAACAACAAA
* * * **
59346 AACAGCAACAAAAATAACAGCAAAAACGAC-ACGAAAACAGCAACCAAAACAGTAAA
1 AA-A-CAACAAAAATAACAGCAAAAACAACAAC-AAAACAACAACAAAAACAACAAA
*
59402 AAACAACACAAA-AACAGCAA
1 AAACAACAAAAATAACAGCAA
59422 CCAAAATAGT
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
53 8 0.13
54 10 0.16
55 4 0.06
56 41 0.65
ACGTcount: A:0.68, C:0.23, G:0.05, T:0.04
Consensus pattern (54 bp):
AAACAACAAAAATAACAGCAAAAACAACAACAAAACAACAACAAAAACAACAAA
Found at i:59404 original size:33 final size:33
Alignment explanation
Indices: 59334--59437 Score: 115
Period size: 33 Copynumber: 3.2 Consensus size: 33
59324 AAACAACATT
* *
59334 AAAAAC-A-ACAAAAACAGCAACAAAAATAACAG-C
1 AAAAACAACACAAAAACAGCAAC--CAA-AACAGTA
* *
59367 AAAAACGACACGAAAACAGCAACCAAAACAGTA
1 AAAAACAACACAAAAACAGCAACCAAAACAGTA
*
59400 AAAAACAACACAAAAACAGCAACCAAAATAGTA
1 AAAAACAACACAAAAACAGCAACCAAAACAGTA
59433 AAAAA
1 AAAAA
59438 AATAGCACCA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
32 5 0.08
33 43 0.69
34 1 0.02
35 13 0.21
ACGTcount: A:0.67, C:0.21, G:0.08, T:0.04
Consensus pattern (33 bp):
AAAAACAACACAAAAACAGCAACCAAAACAGTA
Found at i:61831 original size:23 final size:23
Alignment explanation
Indices: 61803--61852 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 23
61793 ACTATAATAC
*
61803 CAAAAAGTAATATCAACATTGCTA
1 CAAAAAGTAATATCAAAATTGC-A
61827 CAAAAAGTAATATCAAAATTGCA
1 CAAAAAGTAATATCAAAATTGCA
61850 CAA
1 CAA
61853 GCAAACAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.54, C:0.16, G:0.08, T:0.22
Consensus pattern (23 bp):
CAAAAAGTAATATCAAAATTGCA
Found at i:63339 original size:13 final size:13
Alignment explanation
Indices: 63310--63362 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
63300 CTTAAACCAA
**
63310 ACTTTTCAAAATT
1 ACTTTTCAAAAGC
*
63323 ACTTTTCCAAAGC
1 ACTTTTCAAAAGC
*
63336 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
*
63349 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
63362 A
1 A
63363 ATGCTAAACT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.34
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:72922 original size:20 final size:20
Alignment explanation
Indices: 72897--72966 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
72887 CTCCTGTGAG
72897 ACTTCTACCGGTAGAACTCC
1 ACTTCTACCGGTAGAACTCC
72917 ACTTCTACCGGTAGAACTCC
1 ACTTCTACCGGTAGAACTCC
* *
72937 ACTTCTACCGATACAACTCC
1 ACTTCTACCGGTAGAACTCC
72957 ACTTCTACCG
1 ACTTCTACCG
72967 ATACCTTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.26, C:0.37, G:0.11, T:0.26
Consensus pattern (20 bp):
ACTTCTACCGGTAGAACTCC
Found at i:73221 original size:20 final size:21
Alignment explanation
Indices: 73177--73231 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
73167 TAGAACTCCT
*
73177 CTTCTACTGATACAAATATAG
1 CTTCTACCGATACAAATATAG
*
73198 -TTCTACCGATACAAGTAT-G
1 CTTCTACCGATACAAATATAG
* *
73217 CTTCTATCGAAACAA
1 CTTCTACCGATACAA
73232 CTAAGTTGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (21 bp):
CTTCTACCGATACAAATATAG
Found at i:76288 original size:20 final size:21
Alignment explanation
Indices: 76244--76292 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
76234 TAGAACTCCT
* *
76244 CTTCTACTGATACAATTATAG
1 CTTCTACCGATACAAGTATAG
76265 -TTCTACCGATACAAGTAT-G
1 CTTCTACCGATACAAGTATAG
76284 CTTCTACCG
1 CTTCTACCG
76293 GAACAACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (21 bp):
CTTCTACCGATACAAGTATAG
Found at i:83260 original size:6 final size:6
Alignment explanation
Indices: 83249--83282 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
83239 ATACATACCT
83249 GTATGG GTATGG GTATGG GTATGG GTATGG GTAT
1 GTATGG GTATGG GTATGG GTATGG GTATGG GTAT
83283 ATGTCCTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.47, T:0.35
Consensus pattern (6 bp):
GTATGG
Found at i:89363 original size:29 final size:30
Alignment explanation
Indices: 89331--89401 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 30
89321 CGATCAAAGT
*
89331 TTCATGTATATAA-T-TACGTCAAATCAAAA
1 TTCATGTATA-AATTATACATCAAATCAAAA
*
89360 TTCATGTATCAAATTATACATTAAATCAAAA
1 TTCATGTAT-AAATTATACATCAAATCAAAA
89391 TTCATGTATAA
1 TTCATGTATAA
89402 TAGTAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
29 11 0.30
30 4 0.11
31 22 0.59
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.37
Consensus pattern (30 bp):
TTCATGTATAAATTATACATCAAATCAAAA
Found at i:90307 original size:15 final size:17
Alignment explanation
Indices: 90287--90318 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
90277 TGTATTTGAG
90287 TTTTGG-TT-TTTTCTC
1 TTTTGGATTATTTTCTC
90302 TTTTGGATTATTTTCTC
1 TTTTGGATTATTTTCTC
90319 CATATTGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.06, C:0.12, G:0.12, T:0.69
Consensus pattern (17 bp):
TTTTGGATTATTTTCTC
Found at i:122200 original size:17 final size:18
Alignment explanation
Indices: 122180--122217 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
122170 TTAGAATTTT
* *
122180 TTTAATTTTTATAAA-TA
1 TTTAAATTTTAAAAATTA
122197 TTTAAATTTTAAAAATTA
1 TTTAAATTTTAAAAATTA
122215 TTT
1 TTT
122218 TGTATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTAAATTTTAAAAATTA
Found at i:122709 original size:23 final size:23
Alignment explanation
Indices: 122669--122712 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
122659 AGTTAACAAA
*
122669 TTATCAATTTTACTAGTTAATCT
1 TTATCAATTTTACCAGTTAATCT
122692 TTATC-ATTTGTACCAGTTAAT
1 TTATCAATTT-TACCAGTTAAT
122713 TTTTTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.50
Consensus pattern (23 bp):
TTATCAATTTTACCAGTTAATCT
Found at i:131688 original size:22 final size:22
Alignment explanation
Indices: 131638--131716 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 22
131628 CTGGGGAAAT
*
131638 AGTAAGCACACACAGTGCAATCC
1 AGTAGGCACACACAGTGCAAT-C
131661 AGTAGGCACACACAGTGCAATC
1 AGTAGGCACACACAGTGCAATC
* *
131683 AGTAGG-AGCACATAGAGCAAATC
1 AGTAGGCA-CACACAGTGC-AATC
131706 AGTAGGCACAC
1 AGTAGGCACAC
131717 GAGGTGTGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
21 1 0.02
22 15 0.30
23 33 0.66
24 1 0.02
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.13
Consensus pattern (22 bp):
AGTAGGCACACACAGTGCAATC
Found at i:131731 original size:23 final size:23
Alignment explanation
Indices: 131705--131781 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
131695 TAGAGCAAAT
* * *
131705 CAGTAGGCACACGAGGTGTGAAA
1 CAGTAAGCACACGAAGTGCGAAA
131728 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
*
131751 TAGTAAGCACAC-ACAGTGCTG-AA
1 CAGTAAGCACACGA-AGTGC-GAAA
131774 CAGTAAGC
1 CAGTAAGC
131782 GCGCTAGCGT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
22 1 0.02
23 45 0.96
24 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.27, T:0.13
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Found at i:131882 original size:24 final size:26
Alignment explanation
Indices: 131844--131891 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
131834 TCTACATGGG
131844 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
131870 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
131892 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:131996 original size:15 final size:15
Alignment explanation
Indices: 131976--132007 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
131966 TTTATCATAA
131976 TTAAACACATAATAT
1 TTAAACACATAATAT
131991 TTAAACACATAATAT
1 TTAAACACATAATAT
132006 TT
1 TT
132008 CACATATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAAACACATAATAT
Found at i:133914 original size:18 final size:19
Alignment explanation
Indices: 133891--133931 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
133881 GCTAAGAGAT
*
133891 TGAAATGACTAA-AATATG
1 TGAAATGACGAAGAATATG
*
133909 TGAAATGAGGAAGAATATG
1 TGAAATGACGAAGAATATG
133928 TGAA
1 TGAA
133932 TTCATAACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.49, C:0.02, G:0.24, T:0.24
Consensus pattern (19 bp):
TGAAATGACGAAGAATATG
Found at i:140604 original size:2 final size:2
Alignment explanation
Indices: 140597--140625 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
140587 TTCTAAGAAC
140597 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
140626 AAATCACAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:144702 original size:19 final size:20
Alignment explanation
Indices: 144667--144704 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
144657 TCAATGATTG
144667 AATTAATTGGTTAAATTAAA
1 AATTAATTGGTTAAATTAAA
*
144687 AATTAA-TGGTTTAATTAA
1 AATTAATTGGTTAAATTAA
144705 TTTAATTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
AATTAATTGGTTAAATTAAA
Found at i:145284 original size:22 final size:22
Alignment explanation
Indices: 145259--145303 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
145249 ACATATATTG
145259 TAAAAGAAAAAATATTT-TTTTA
1 TAAAAGAAAAAAT-TTTATTTTA
* *
145281 TAAAATAATAAATTTTATTTTA
1 TAAAAGAAAAAATTTTATTTTA
145303 T
1 T
145304 TTTAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TAAAAGAAAAAATTTTATTTTA
Found at i:146165 original size:30 final size:31
Alignment explanation
Indices: 146104--146166 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 31
146094 TAGTAATGGT
* *
146104 AAAATTCAATTTGACCCCTTCATAAACAATA
1 AAAATTCAATTTGAACCCTTCAAAAACAATA
* * *
146135 AAAATTTAATTT-AACCCTTTAAAAATAATA
1 AAAATTCAATTTGAACCCTTCAAAAACAATA
146165 AA
1 AA
146167 TATATAAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.32
Consensus pattern (31 bp):
AAAATTCAATTTGAACCCTTCAAAAACAATA
Found at i:147312 original size:31 final size:29
Alignment explanation
Indices: 147260--147321 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
147250 TTTAGTCAAG
147260 ATTAAAAATTCAAAAATTAAAAAATATAAAA
1 ATTAAAAATTCAAAAATT--AAAATATAAAA
* *
147291 ATTAAAACTTCATCAAA-TAAAATATAAAA
1 ATTAAAAATTCA-AAAATTAAAATATAAAA
147320 AT
1 AT
147322 GAATTCCGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 13 0.46
31 12 0.43
32 3 0.11
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.27
Consensus pattern (29 bp):
ATTAAAAATTCAAAAATTAAAATATAAAA
Found at i:151421 original size:21 final size:22
Alignment explanation
Indices: 151397--151441 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
151387 AATCATCTTT
151397 TTATAAAAG-AAATTTTAAATC
1 TTATAAAAGAAAATTTTAAATC
151418 TTATAAAAGAAAATTTTAAATC
1 TTATAAAAGAAAATTTTAAATC
151440 TT
1 TT
151442 TTTAAGCGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (22 bp):
TTATAAAAGAAAATTTTAAATC
Found at i:156158 original size:20 final size:19
Alignment explanation
Indices: 156114--156170 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
156104 TAAATTTTAA
* * *
156114 AATTTTTATAAATTTTTTG
1 AATTTTTAAAAATATTTTC
156133 AA-TTTTAAAAACTATTTTC
1 AATTTTTAAAAA-TATTTTC
156152 AATTTTTGAAAAATATTTT
1 AATTTTT-AAAAATATTTT
156171 GGTTTTTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 8 0.25
19 9 0.28
20 10 0.31
21 5 0.16
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (19 bp):
AATTTTTAAAAATATTTTC
Found at i:160982 original size:23 final size:23
Alignment explanation
Indices: 160927--160975 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
160917 GAGAAACAAT
160927 TATTGTGTATTTAATATTCCTAG
1 TATTGTGTATTTAATATTCCTAG
160950 TATTGTGTATTTAATATTCCTAG
1 TATTGTGTATTTAATATTCCTAG
160973 TAT
1 TAT
160976 GATGTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.53
Consensus pattern (23 bp):
TATTGTGTATTTAATATTCCTAG
Found at i:161427 original size:16 final size:16
Alignment explanation
Indices: 161406--161439 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
161396 AATTTTTAAA
161406 CATAAAATATATTTTT
1 CATAAAATATATTTTT
161422 CATAAAATATATTTTT
1 CATAAAATATATTTTT
161438 CA
1 CA
161440 CTCACAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (16 bp):
CATAAAATATATTTTT
Found at i:163868 original size:24 final size:24
Alignment explanation
Indices: 163831--163891 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
163821 GTTTTGGTGC
*
163831 TTTTTTACTG-TTTTG-GTTGATG
1 TTTTTTATTGTTTTTGAGTTGATG
* *
163853 TTTTTTTGTTGTTTTTGAGTTGTTG
1 -TTTTTTATTGTTTTTGAGTTGATG
163878 TTTTTTATTGTTTT
1 TTTTTTATTGTTTT
163892 GATTGCTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 8 0.25
24 18 0.56
25 6 0.19
ACGTcount: A:0.07, C:0.02, G:0.20, T:0.72
Consensus pattern (24 bp):
TTTTTTATTGTTTTTGAGTTGATG
Found at i:163893 original size:23 final size:24
Alignment explanation
Indices: 163831--163893 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
163821 GTTTTGGTGC
*
163831 TTTTTTACTGTTTTG-GTTGATGT
1 TTTTTTATTGTTTTGAGTTGATGT
* *
163854 TTTTTTGTTGTTTTTGAGTTGTTG-
1 TTTTTTATTG-TTTTGAGTTGATGT
163878 TTTTTTATTGTTTTGA
1 TTTTTTATTGTTTTGA
163894 TTGCTATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 14 0.41
24 14 0.41
25 6 0.18
ACGTcount: A:0.08, C:0.02, G:0.21, T:0.70
Consensus pattern (24 bp):
TTTTTTATTGTTTTGAGTTGATGT
Found at i:163927 original size:24 final size:24
Alignment explanation
Indices: 163898--163953 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
163888 TTTTGATTGC
* * *
163898 TATTTTCGTGT-TATTTTTGGTGT
1 TATTTTTGTGTCTATTTTTGCTAT
*
163921 TATTTTTGTTTCTATTTTTGCTAT
1 TATTTTTGTGTCTATTTTTGCTAT
163945 TATTTTTGT
1 TATTTTTGT
163954 TGTTTTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.11, C:0.05, G:0.14, T:0.70
Consensus pattern (24 bp):
TATTTTTGTGTCTATTTTTGCTAT
Found at i:163928 original size:12 final size:12
Alignment explanation
Indices: 163900--163957 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
163890 TTGATTGCTA
*
163900 TTTTCGTGTTAT
1 TTTTGGTGTTAT
163912 TTTTGGTGTTAT
1 TTTTGGTGTTAT
*
163924 TTTT-GTTTCTAT
1 TTTTGGTGT-TAT
* *
163936 TTTTGCTATTAT
1 TTTTGGTGTTAT
*
163948 TTTTGTTGTT
1 TTTTGGTGTT
163958 TTTAATGTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
11 3 0.08
12 33 0.87
13 2 0.05
ACGTcount: A:0.09, C:0.05, G:0.16, T:0.71
Consensus pattern (12 bp):
TTTTGGTGTTAT
Found at i:163928 original size:36 final size:36
Alignment explanation
Indices: 163888--163957 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
163878 TTTTTTATTG
*
163888 TTTTGATTGCTATTTTCG-TGTTATTTTTGGTGTTAT
1 TTTTG-TTGCTATTTTCGCTATTATTTTTGGTGTTAT
* * *
163924 TTTTGTTTCTATTTTTGCTATTATTTTTGTTGTT
1 TTTTGTTGCTATTTTCGCTATTATTTTTGGTGTT
163958 TTTAATGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 10 0.34
36 19 0.66
ACGTcount: A:0.10, C:0.06, G:0.16, T:0.69
Consensus pattern (36 bp):
TTTTGTTGCTATTTTCGCTATTATTTTTGGTGTTAT
Found at i:163951 original size:68 final size:68
Alignment explanation
Indices: 163879--164008 Score: 156
Period size: 68 Copynumber: 1.9 Consensus size: 68
163869 GAGTTGTTGT
* * *
163879 TTTTTATTGTTTTGATTGCTATTTT-CGTGTTATTTTTGGTGTTATTTTTGTT-TCTATTTTTGC
1 TTTTTATTGTTTTGAATGCTATTTTAC-TGTTATTTTTGCTGTTATTTTGGTTGT-TATTTTTGC
163942 TATTA
64 TATTA
* * * * *
163947 TTTTTGTTGTTTTTAATGTTGTTTTACTGTTATTTTTGCTGTTGTTTTGGTTGTTATTTTTG
1 TTTTTATTGTTTTGAATGCTATTTTACTGTTATTTTTGCTGTTATTTTGGTTGTTATTTTTG
164009 TTGTTTGGAT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
68 50 0.96
69 2 0.04
ACGTcount: A:0.10, C:0.05, G:0.17, T:0.68
Consensus pattern (68 bp):
TTTTTATTGTTTTGAATGCTATTTTACTGTTATTTTTGCTGTTATTTTGGTTGTTATTTTTGCTA
TTA
Found at i:163966 original size:12 final size:12
Alignment explanation
Indices: 163951--163994 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
163941 CTATTATTTT
*
163951 TGTTGTTTTTAA
1 TGTTGTTTTTAC
163963 TGTTG-TTTTAC
1 TGTTGTTTTTAC
* *
163974 TGTTATTTTTGC
1 TGTTGTTTTTAC
163986 TGTTGTTTT
1 TGTTGTTTT
163995 GGTTGTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.09, C:0.05, G:0.18, T:0.68
Consensus pattern (12 bp):
TGTTGTTTTTAC
Found at i:164001 original size:24 final size:23
Alignment explanation
Indices: 163906--164013 Score: 78
Period size: 24 Copynumber: 4.7 Consensus size: 23
163896 GCTATTTTCG
* *
163906 TGTTATTTTTGGTGTTATTTTTGT
1 TGTTATTTTTGCTGTT-GTTTTGT
* *
163930 T-TCTATTTTTGCTATT-ATTT-T
1 TGT-TATTTTTGCTGTTGTTTTGT
* ** **
163951 TGTTGTTTTTAATGTTGTTTTAC
1 TGTTATTTTTGCTGTTGTTTTGT
163974 TGTTATTTTTGCTGTTGTTTTGGT
1 TGTTATTTTTGCTGTTGTTTT-GT
*
163998 TGTTATTTTTGTTGTT
1 TGTTATTTTTGCTGTT
164014 TGGATGCTAT
Statistics
Matches: 64, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
21 11 0.17
22 7 0.11
23 19 0.30
24 27 0.42
ACGTcount: A:0.09, C:0.04, G:0.18, T:0.69
Consensus pattern (23 bp):
TGTTATTTTTGCTGTTGTTTTGT
Found at i:164024 original size:20 final size:21
Alignment explanation
Indices: 163986--164036 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
163976 TTATTTTTGC
* *
163986 TGTTGTTTTGGTTGTTATTTT
1 TGTTGTTTTGGATGCTATTTT
164007 TGTTG-TTTGGATGCTATTTT
1 TGTTGTTTTGGATGCTATTTT
*
164027 TATGTGTTTT
1 TGT-TGTTTT
164037 TACCATTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 15 0.60
21 7 0.28
22 3 0.12
ACGTcount: A:0.08, C:0.02, G:0.24, T:0.67
Consensus pattern (21 bp):
TGTTGTTTTGGATGCTATTTT
Found at i:164025 original size:44 final size:44
Alignment explanation
Indices: 163932--164027 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 44
163922 ATTTTTGTTT
* *
163932 CTATTTTTGCTATTATTTTTGTTGTTTTTAATGTTGTTTTACTG
1 CTATTTTTGCTATTATTTTGGTTGTTTTTAATGTTGTTTGACTG
* * * *
163976 TTATTTTTGCTGTTGTTTTGGTTGTTATTT-TTGTTGTTTGGA-TG
1 CTATTTTTGCTATTATTTTGGTTGTT-TTTAATGTTGTTT-GACTG
164020 CTATTTTT
1 CTATTTTT
164028 ATGTGTTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
44 39 0.91
45 4 0.09
ACGTcount: A:0.10, C:0.05, G:0.18, T:0.67
Consensus pattern (44 bp):
CTATTTTTGCTATTATTTTGGTTGTTTTTAATGTTGTTTGACTG
Found at i:164027 original size:21 final size:22
Alignment explanation
Indices: 163977--164035 Score: 52
Period size: 21 Copynumber: 2.7 Consensus size: 22
163967 GTTTTACTGT
* * *
163977 TATTTTTGCTGTTGTTTTGGTTGT
1 TATTTTT-ATGTTG-TTTGGATGC
164001 TA-TTTT-TGTTGTTTGGATGC
1 TATTTTTATGTTGTTTGGATGC
164021 TATTTTTATG-TGTTT
1 TATTTTTATGTTGTTT
164036 TTACCATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 9 0.29
21 14 0.45
22 2 0.06
23 4 0.13
24 2 0.06
ACGTcount: A:0.08, C:0.03, G:0.22, T:0.66
Consensus pattern (22 bp):
TATTTTTATGTTGTTTGGATGC
Found at i:171483 original size:17 final size:17
Alignment explanation
Indices: 171461--171494 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
171451 CGTTGGGTTC
171461 CATGCCAAAGAAT-GATG
1 CATGCC-AAGAATAGATG
171478 CATGCCAAGAATAGATG
1 CATGCCAAGAATAGATG
171495 TGTGTAATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.18
Consensus pattern (17 bp):
CATGCCAAGAATAGATG
Found at i:172504 original size:16 final size:16
Alignment explanation
Indices: 172485--172536 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
172475 ATTACAATTT
172485 TATTTTATTAAAACTC
1 TATTTTATTAAAACTC
** *
172501 TATTTTATTATTACTT
1 TATTTTATTAAAACTC
*
172517 TATTTTATTACAACTC
1 TATTTTATTAAAACTC
172533 TATT
1 TATT
172537 CAGTGAACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTTATTAAAACTC
Found at i:192704 original size:18 final size:18
Alignment explanation
Indices: 192677--192714 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
192667 ACTCCAAGGC
192677 GACGACGAAGATGAAGAT
1 GACGACGAAGATGAAGAT
* *
192695 GACGATGAAGATGGAGAT
1 GACGACGAAGATGAAGAT
192713 GA
1 GA
192715 TGAAGATGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.08, G:0.37, T:0.13
Consensus pattern (18 bp):
GACGACGAAGATGAAGAT
Found at i:216439 original size:120 final size:120
Alignment explanation
Indices: 216230--216481 Score: 495
Period size: 120 Copynumber: 2.1 Consensus size: 120
216220 TCCTAAATAC
216230 AAATTTATTTTTATTTTTACCTCATTATATACGAATCTTATTTAAATTTATTTTGATTTACATCC
1 AAATTTATTTTTATTTTTACCTCATTATATACGAATCTTATTTAAATTTATTTTGATTTACATCC
216295 AAATATGTTTTGATTGTCAATTCAATCATGTTTATAATATTAATTATAATTATTT
66 AAATATGTTTTGATTGTCAATTCAATCATGTTTATAATATTAATTATAATTATTT
*
216350 AAATTTATTTTTATTTTTATCTCATTATATACGAATCTTATTTAAATTTATTTTGATTTACATCC
1 AAATTTATTTTTATTTTTACCTCATTATATACGAATCTTATTTAAATTTATTTTGATTTACATCC
216415 AAATATGTTTTGATTGTCAATTCAATCATGTTTATAATATTAATTATAATTATTT
66 AAATATGTTTTGATTGTCAATTCAATCATGTTTATAATATTAATTATAATTATTT
216470 AAATTTATTTTT
1 AAATTTATTTTT
216482 CTATAATTAT
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 131 1.00
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (120 bp):
AAATTTATTTTTATTTTTACCTCATTATATACGAATCTTATTTAAATTTATTTTGATTTACATCC
AAATATGTTTTGATTGTCAATTCAATCATGTTTATAATATTAATTATAATTATTT
Found at i:226349 original size:2 final size:2
Alignment explanation
Indices: 226344--226371 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
226334 AAAAAAGCAG
226344 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
226372 AACCTGCTCA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:230678 original size:33 final size:33
Alignment explanation
Indices: 230640--230705 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
230630 CATCGTTAAT
* *
230640 GGTAATAGAACAATCGTAAAATAATAAGAAAAA
1 GGTAATAGAACAATAGTAAAATAATAAAAAAAA
230673 GGTAATAGAACAATAGTAAAATAATAAAAAAAA
1 GGTAATAGAACAATAGTAAAATAATAAAAAAAA
230706 TAAAATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.64, C:0.05, G:0.14, T:0.18
Consensus pattern (33 bp):
GGTAATAGAACAATAGTAAAATAATAAAAAAAA
Found at i:231226 original size:15 final size:16
Alignment explanation
Indices: 231206--231241 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
231196 TTAATTTTTA
231206 AAATTATAAAAATA-T
1 AAATTATAAAAATATT
*
231221 AAATTATTAAAATATT
1 AAATTATAAAAATATT
231237 AAATT
1 AAATT
231242 TACATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATTATAAAAATATT
Found at i:237597 original size:6 final size:6
Alignment explanation
Indices: 237586--237631 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
237576 GGCAACCCAA
*
237586 TTATTT TTATTT TTATTT TTA--T TT-TTT TTATTT TTCTATT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTAT-TT TTATTT
237632 ATTTATTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
4 3 0.09
5 3 0.09
6 23 0.68
7 5 0.15
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (6 bp):
TTATTT
Found at i:237611 original size:13 final size:13
Alignment explanation
Indices: 237589--237640 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
237579 AACCCAATTA
237589 TTTTTATTTTTATT
1 TTTTTATTTTTA-T
*
237603 TTTATTTTTTTTAT
1 TTT-TTATTTTTAT
237617 TTTTCTA-TTTTAT
1 TTTT-TATTTTTAT
237630 TTATTTATTTT
1 TT-TTTATTTT
237641 ATTATATGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
13 11 0.34
14 13 0.41
15 8 0.25
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:237615 original size:9 final size:9
Alignment explanation
Indices: 237586--237643 Score: 57
Period size: 9 Copynumber: 6.6 Consensus size: 9
237576 GGCAACCCAA
237586 TTATTTTTAT
1 TTATTTTT-T
*
237596 TT-TTATTT
1 TTATTTTTT
237604 TTATTTTTT
1 TTATTTTTT
237613 TTA-TTTTT
1 TTATTTTTT
* *
237621 CTATTTTAT
1 TTATTTTTT
*
237630 TTATTTATT
1 TTATTTTTT
237639 TTATT
1 TTATT
237644 ATATGTGTCG
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
8 10 0.26
9 27 0.69
10 2 0.05
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (9 bp):
TTATTTTTT
Found at i:237615 original size:21 final size:21
Alignment explanation
Indices: 237589--237640 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
237579 AACCCAATTA
237589 TTTTTATTTTTAT-TTTTATTT
1 TTTTTATTTTTATATTTTA-TT
*
237610 TTTTTATTTTTCTATTTTATT
1 TTTTTATTTTTATATTTTATT
*
237631 TATTTATTTT
1 TTTTTATTTT
237641 ATTATATGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTTATTTTTATATTTTATT
Found at i:237619 original size:8 final size:8
Alignment explanation
Indices: 237595--237643 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
237585 ATTATTTTTA
237595 TTTTTATT
1 TTTTTATT
*
237603 TTTAT-TT
1 TTTTTATT
237610 TTTTTATT
1 TTTTTATT
*
237618 TTTCTATT
1 TTTTTATT
237626 TTATTTATT
1 TT-TTTATT
237635 TATTTTATT
1 T-TTTTATT
237644 ATATGTGTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
7 6 0.18
8 15 0.44
9 12 0.35
10 1 0.03
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTATT
Found at i:237625 original size:17 final size:16
Alignment explanation
Indices: 237595--237635 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
237585 ATTATTTTTA
237595 TTTTTA-TTTTTATTT
1 TTTTTATTTTTTATTT
237610 TTTTTATTTTTCTATTT
1 TTTTTATTTTT-TATTT
*
237627 TATTTATTT
1 TTTTTATTT
237636 ATTTTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.26
16 4 0.17
17 13 0.57
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTATTTTTTATTT
Found at i:237641 original size:13 final size:13
Alignment explanation
Indices: 237591--237643 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
237581 CCCAATTATT
237591 TTTATTT-TTATT-
1 TTTATTTATT-TTA
*
237603 TTTATTTTTTTTA
1 TTTATTTATTTTA
237616 TTT-TTCTATTTTA
1 TTTATT-TATTTTA
237629 TTTATTTATTTTA
1 TTTATTTATTTTA
237642 TT
1 TT
237644 ATATGTGTCG
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
12 11 0.31
13 23 0.64
14 2 0.06
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:237832 original size:16 final size:16
Alignment explanation
Indices: 237811--237845 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
237801 GATCTGGGGA
237811 AAAACAAAACTAAAAG
1 AAAACAAAACTAAAAG
* *
237827 AAAACAGAATTAAAAG
1 AAAACAAAACTAAAAG
237843 AAA
1 AAA
237846 TAGAAAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.74, C:0.09, G:0.09, T:0.09
Consensus pattern (16 bp):
AAAACAAAACTAAAAG
Found at i:238396 original size:12 final size:12
Alignment explanation
Indices: 238379--238405 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
238369 ATGAATGGGG
238379 AATGAATAATTC
1 AATGAATAATTC
238391 AATGAATAATTC
1 AATGAATAATTC
238403 AAT
1 AAT
238406 CACCCATCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (12 bp):
AATGAATAATTC
Found at i:240830 original size:3 final size:3
Alignment explanation
Indices: 240779--240819 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
240769 TATGAAAAAA
**
240779 ATT ATT ATT A-T AAA ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
240820 TTGATATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:251398 original size:33 final size:33
Alignment explanation
Indices: 251361--251438 Score: 156
Period size: 33 Copynumber: 2.4 Consensus size: 33
251351 CTCCTCCCGA
251361 TGCTTTTCACGTAGCAGCCTCTCCTCTTCCTTC
1 TGCTTTTCACGTAGCAGCCTCTCCTCTTCCTTC
251394 TGCTTTTCACGTAGCAGCCTCTCCTCTTCCTTC
1 TGCTTTTCACGTAGCAGCCTCTCCTCTTCCTTC
251427 TGCTTTTCACGT
1 TGCTTTTCACGT
251439 TCATGTCTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.37, G:0.13, T:0.41
Consensus pattern (33 bp):
TGCTTTTCACGTAGCAGCCTCTCCTCTTCCTTC
Found at i:254116 original size:68 final size:68
Alignment explanation
Indices: 254007--254146 Score: 262
Period size: 68 Copynumber: 2.1 Consensus size: 68
253997 TCCCCGCCAC
*
254007 TAATACCACCAGTCTCCATTTTTCAAGGTGAGAATAAAAATCCCAAGAAATTCAACAAAGGTGAA
1 TAATACCACCAGTCTCCATTTTTCAAGGTGAGAATAAAAATCCCAAAAAATTCAACAAAGGTGAA
254072 ACA
66 ACA
*
254075 TAATACCACCCGTCTCCATTTTTCAAGGTGAGAATAAAAATCCCAAAAAATTCAACAAAGGTGAA
1 TAATACCACCAGTCTCCATTTTTCAAGGTGAGAATAAAAATCCCAAAAAATTCAACAAAGGTGAA
254140 ACA
66 ACA
254143 TAAT
1 TAAT
254147 TTCACTCCCT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.23
Consensus pattern (68 bp):
TAATACCACCAGTCTCCATTTTTCAAGGTGAGAATAAAAATCCCAAAAAATTCAACAAAGGTGAA
ACA
Found at i:254925 original size:27 final size:28
Alignment explanation
Indices: 254895--254949 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
254885 TTCTCTCTCC
* *
254895 CTCTCACGATGCTGTTTTTCA-GTTTCT
1 CTCTCACAAAGCTGTTTTTCAGGTTTCT
*
254922 CTCTGACAAAGCTGTTTTTCAGGTTTCT
1 CTCTCACAAAGCTGTTTTTCAGGTTTCT
254950 TATTAGGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.15, C:0.24, G:0.16, T:0.45
Consensus pattern (28 bp):
CTCTCACAAAGCTGTTTTTCAGGTTTCT
Found at i:259236 original size:28 final size:28
Alignment explanation
Indices: 259205--259266 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
259195 CATTCTATTG
259205 ATTTAATTATTAAATAATTTTATTTT-TA
1 ATTTAATTATT-AATAATTTTATTTTCTA
*
259233 ATTTAATTATTAATATTTTTATTTTCTA
1 ATTTAATTATTAATAATTTTATTTTCTA
259261 ATTTAA
1 ATTTAA
259267 ACAGCTCGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 13 0.41
28 19 0.59
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (28 bp):
ATTTAATTATTAATAATTTTATTTTCTA
Found at i:259969 original size:17 final size:17
Alignment explanation
Indices: 259939--259974 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
259929 AGCAATTTAA
259939 TTTTTTTCCTTTTATATT
1 TTTTTTTCCTTTTAT-TT
259957 TTTTTTTCC-TTTATTT
1 TTTTTTTCCTTTTATTT
259973 TT
1 TT
259975 CATTCTCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 5 0.28
18 9 0.50
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTTCCTTTTATTT
Found at i:265437 original size:40 final size:40
Alignment explanation
Indices: 265382--265467 Score: 172
Period size: 40 Copynumber: 2.1 Consensus size: 40
265372 AACTGGGAAA
265382 CATTCTTAAAAATATCATTTGATATGATGGAATGGTTAAC
1 CATTCTTAAAAATATCATTTGATATGATGGAATGGTTAAC
265422 CATTCTTAAAAATATCATTTGATATGATGGAATGGTTAAC
1 CATTCTTAAAAATATCATTTGATATGATGGAATGGTTAAC
265462 CATTCT
1 CATTCT
265468 CCTTGTTTGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (40 bp):
CATTCTTAAAAATATCATTTGATATGATGGAATGGTTAAC
Found at i:277149 original size:22 final size:24
Alignment explanation
Indices: 277105--277150 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
277095 GAGATGATTT
* *
277105 GATTAAAAAATATGTAAATTTAAA
1 GATTAAAAAATATGAAAAATTAAA
277129 GATT-AAAAA-ATGAAAAATTAAA
1 GATTAAAAAATATGAAAAATTAAA
277151 TAAATAGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.55
23 5 0.25
24 4 0.20
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (24 bp):
GATTAAAAAATATGAAAAATTAAA
Found at i:277477 original size:20 final size:23
Alignment explanation
Indices: 277421--277479 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 23
277411 GTTGATGTAA
*
277421 AAAAATTATGATAATTATATATT
1 AAAAATTAAGATAATTATATATT
* *
277444 TAAAATTAATATAATT-TA-A-T
1 AAAAATTAAGATAATTATATATT
*
277464 AAAAATTAGGATAATT
1 AAAAATTAAGATAATT
277480 GTTATAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 14 0.47
21 1 0.03
22 2 0.07
23 13 0.43
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (23 bp):
AAAAATTAAGATAATTATATATT
Found at i:277498 original size:43 final size:44
Alignment explanation
Indices: 277421--277518 Score: 103
Period size: 43 Copynumber: 2.2 Consensus size: 44
277411 GTTGATGTAA
* *
277421 AAAAATTATGATAATTATATATTTAAAATTAATA-TAATTTAA-T
1 AAAAATTAGGATAATTATATAATTAAAA-TAATATTAATTTAATT
*
277464 AAAAATTAGGATAATTGTTATAAATTAAAA-AATATTGTAATTTAATT
1 AAAAATTAGGATAATT-ATAT-AATTAAAATAATA-T-TAATTTAATT
277511 AAAAATTA
1 AAAAATTA
277519 TTAGTTAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
43 19 0.41
44 3 0.07
45 7 0.15
46 8 0.17
47 9 0.20
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (44 bp):
AAAAATTAGGATAATTATATAATTAAAATAATATTAATTTAATT
Found at i:288898 original size:53 final size:53
Alignment explanation
Indices: 288818--288924 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
288808 AACCATTGGC
288818 AGGATGCAGTTGTAGATAGTTTTCGAATCAAGCTTGCAGTAGTCCTAGGTCAT
1 AGGATGCAGTTGTAGATAGTTTTCGAATCAAGCTTGCAGTAGTCCTAGGTCAT
288871 AGGATGCAGTTGTAGATAGTTTTCGAATCAAGCTTGCAGTAGTCCTAGGTCAT
1 AGGATGCAGTTGTAGATAGTTTTCGAATCAAGCTTGCAGTAGTCCTAGGTCAT
288924 A
1 A
288925 CCTGCAGAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (53 bp):
AGGATGCAGTTGTAGATAGTTTTCGAATCAAGCTTGCAGTAGTCCTAGGTCAT
Found at i:299789 original size:8 final size:8
Alignment explanation
Indices: 299764--299802 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
299754 ATTTTTGAAG
299764 TTTTTTTA
1 TTTTTTTA
*
299772 TGTTTTTA
1 TTTTTTTA
299780 TTTTTTTA
1 TTTTTTTA
299788 TTTTGTTT-
1 TTTT-TTTA
299796 TTTTTTT
1 TTTTTTT
299803 TGAATTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 3 0.11
8 22 0.79
9 3 0.11
ACGTcount: A:0.08, C:0.00, G:0.05, T:0.87
Consensus pattern (8 bp):
TTTTTTTA
Found at i:299809 original size:19 final size:19
Alignment explanation
Indices: 299772--299810 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
299762 AGTTTTTTTA
*
299772 TGTTTTTATTTTTTTATTT
1 TGTTTTTATTTTTTAATTT
299791 TGTTTTT-TTTTTTGAATTT
1 TGTTTTTATTTTTT-AATTT
299810 T
1 T
299811 TAAGAATCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.10, C:0.00, G:0.08, T:0.82
Consensus pattern (19 bp):
TGTTTTTATTTTTTAATTT
Found at i:300142 original size:16 final size:16
Alignment explanation
Indices: 300123--300164 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
300113 AATTACTAAA
300123 ATATAGATACATTA-TT
1 ATATAGATA-ATTAGTT
*
300139 ATATATATAATTAGTT
1 ATATAGATAATTAGTT
*
300155 ATATATATAA
1 ATATAGATAA
300165 CGCATATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (16 bp):
ATATAGATAATTAGTT
Found at i:300207 original size:9 final size:9
Alignment explanation
Indices: 300193--300256 Score: 51
Period size: 9 Copynumber: 6.8 Consensus size: 9
300183 GTTTATTTAT
300193 ATATTATTA
1 ATATTATTA
300202 ATATTATTTA
1 ATATTA-TTA
*
300212 TATATTATTCT
1 -ATATTATT-A
300223 ATATTATTA
1 ATATTATTA
*
300232 ATATATTTTA
1 ATAT-TATTA
300242 AT-TTATATA
1 ATATTAT-TA
300251 AT-TTAT
1 ATATTAT
300257 ATATATTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
8 2 0.04
9 19 0.41
10 19 0.41
11 6 0.13
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (9 bp):
ATATTATTA
Found at i:300210 original size:20 final size:20
Alignment explanation
Indices: 300185--300247 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
300175 CTTTATATGT
300185 TTATTTATATATTATTAATA
1 TTATTTATATATTATTAATA
*
300205 TTATTTATATATTATTCTATA
1 TTATTTATATATTATT-AATA
*
300226 TTATTAATATATT-TTAAT-
1 TTATTTATATATTATTAATA
300244 TTAT
1 TTAT
300248 ATAATTTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
18 4 0.10
19 2 0.05
20 18 0.46
21 15 0.38
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTATATATTATTAATA
Found at i:300236 original size:23 final size:21
Alignment explanation
Indices: 300185--300263 Score: 81
Period size: 23 Copynumber: 3.7 Consensus size: 21
300175 CTTTATATGT
*
300185 TTATT-TATATATTATTAATA
1 TTATTATATATATTATTTATA
300205 TTATT-TATATATTATTCTATA
1 TTATTATATATATTATT-TATA
*
300226 TTATTAATATATTTTAATTTATA
1 TTATT-ATATATATT-ATTTATA
*
300249 TAATTTATATATATT
1 TTA-TTATATATATT
300264 TAAATGATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
20 16 0.32
21 8 0.16
23 21 0.42
24 5 0.10
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATTATATATATTATTTATA
Found at i:300446 original size:21 final size:21
Alignment explanation
Indices: 300406--300444 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
300396 AAATCATGGA
*
300406 TAAATTCAAGCGACTCTTTCT
1 TAAATTCAAACGACTCTTTCT
300427 TAAATTCAAACGA-TCTTT
1 TAAATTCAAACGACTCTTT
300445 TCATAGACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (21 bp):
TAAATTCAAACGACTCTTTCT
Found at i:303990 original size:22 final size:21
Alignment explanation
Indices: 303974--304028 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 21
303964 AAAATACATA
303974 TTTAAAAAATAATAAATCAAT
1 TTTAAAAAATAATAAATCAAT
*
303995 TTTAAAAAATAAATTAA--AAT
1 TTTAAAAAAT-AATAAATCAAT
304015 TTTAAAAATATAAT
1 TTTAAAAA-ATAAT
304029 TTAAATTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 14 0.45
21 12 0.39
22 5 0.16
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TTTAAAAAATAATAAATCAAT
Found at i:304035 original size:20 final size:20
Alignment explanation
Indices: 303974--304033 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
303964 AAAATACATA
*
303974 TTTAAAAAAT-AATAAATCAAT
1 TTTAAAAAATAAATTAA--AAT
303995 TTTAAAAAATAAATTAAAAT
1 TTTAAAAAATAAATTAAAAT
*
304015 TTTAAAAATATAATTTAAA
1 TTTAAAAA-ATAAATTAAA
304034 TTAAATAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.31
21 19 0.54
22 5 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TTTAAAAAATAAATTAAAAT
Found at i:304060 original size:72 final size:71
Alignment explanation
Indices: 303907--304049 Score: 182
Period size: 73 Copynumber: 2.0 Consensus size: 71
303897 TTATGTTTGG
* *
303907 AAAAAAATAAATCAATTTAAAGCAATAAATTAAATTATAAAAATAGAACTTAATTACAAAATACA
1 AAAAAAATAAATCAATTTAAAGAAATAAATTAAATTATAAAAATAGAACTTAATTACAAAAGACA
303972 TATTTA
66 TATTTA
* * *
303978 AAAAATAATAAATCAATTTTAAA-AAATAAATTAAAATTTTAAAAATATAATTTAAATTA-AATA
1 AAAAA-AATAAATCAA-TTTAAAGAAATAAATT-AAATTATAAAAATAGAACTT-AATTACAA-A
304041 AGACATATT
61 AGACATATT
304050 AATTGAAATA
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
71 5 0.08
72 18 0.29
73 25 0.40
74 14 0.23
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (71 bp):
AAAAAAATAAATCAATTTAAAGAAATAAATTAAATTATAAAAATAGAACTTAATTACAAAAGACA
TATTTA
Found at i:304374 original size:55 final size:55
Alignment explanation
Indices: 304257--304419 Score: 190
Period size: 54 Copynumber: 3.0 Consensus size: 55
304247 TATTGACGCT
* * * *
304257 AATCATTAATTACTTCAAATC-CTAATTTTTTTTATATTTGATAAATTTGATGTC
1 AATCATCAATTACTTAAAATCTCGAATTTTTTTTATATTTGATAAAATTGATGTC
* *
304311 AATTATCAATTACTTAAAATCTC-AATTTTTTTTTATATTTGATAAAATTGGTGT-
1 AATCATCAATTACTTAAAATCTCGAA-TTTTTTTTATATTTGATAAAATTGATGTC
* * * *
304365 AGGTCATCAATTACTTTAAA-CTCGAATTATTTTTATATTTTATAAAATTGATGTC
1 A-ATCATCAATTACTTAAAATCTCGAATTTTTTTTATATTTGATAAAATTGATGTC
304420 TGATCATTAA
Statistics
Matches: 93, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
54 49 0.53
55 44 0.47
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.48
Consensus pattern (55 bp):
AATCATCAATTACTTAAAATCTCGAATTTTTTTTATATTTGATAAAATTGATGTC
Found at i:305398 original size:24 final size:24
Alignment explanation
Indices: 305370--305415 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
305360 AAAAAAAAAT
*
305370 AACATGATATCAAATTTTTTAATA
1 AACATGATATCAAAATTTTTAATA
* *
305394 AACATTATATTAAAATTTTTAA
1 AACATGATATCAAAATTTTTAA
305416 CAAGATATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (24 bp):
AACATGATATCAAAATTTTTAATA
Found at i:308705 original size:20 final size:19
Alignment explanation
Indices: 308677--308729 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
308667 TTTTTTATAG
308677 ATTTA-AATTTTTAATAATT
1 ATTTAGAATTTTTAAT-ATT
*
308696 -TATTAGAATTTTAAATATT
1 AT-TTAGAATTTTTAATATT
308715 ATTTAGAAGTTTTTA
1 ATTTAGAA-TTTTTA
308730 TGAACTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 1 0.04
19 12 0.43
20 15 0.54
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.55
Consensus pattern (19 bp):
ATTTAGAATTTTTAATATT
Found at i:308938 original size:8 final size:8
Alignment explanation
Indices: 308919--309019 Score: 53
Period size: 10 Copynumber: 11.5 Consensus size: 8
308909 TTTAAATATC
308919 TTTTATTAA
1 TTTTA-TAA
308928 TTTTATAA
1 TTTTATAA
*
308936 TTTTTTATAT
1 --TTTTATAA
308946 TTTTATAA
1 TTTTATAA
308954 TATTTATAA
1 T-TTTATAA
308963 GTTTATATCAA
1 -TTT-TAT-AA
308974 TTTTAATATA
1 TTTT-ATA-A
308984 TTTTA-AA
1 TTTTATAA
*
308991 TACTTAATAA
1 T--TTTATAA
*
309001 TTATAT-A
1 TTTTATAA
*
309008 TATTATAA
1 TTTTATAA
309016 TTTT
1 TTTT
309020 TCTTATTTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 25
0.69 0.08 0.24
Matches are distributed among these distances:
7 7 0.10
8 19 0.26
9 20 0.28
10 24 0.33
11 2 0.03
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (8 bp):
TTTTATAA
Found at i:309509 original size:3 final size:3
Alignment explanation
Indices: 309501--309530 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
309491 TTCAACTCTT
309501 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
309531 AAAGATGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:322547 original size:16 final size:16
Alignment explanation
Indices: 322500--322549 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
322490 TAAAATTAAA
322500 ATATTAAATAATTTATT
1 ATATT-AATAATTTATT
* *
322517 AGAATAATAA--T-TT
1 ATATTAATAATTTATT
322530 ATATTAATAATTTATT
1 ATATTAATAATTTATT
322546 ATAT
1 ATAT
322550 AACTAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 10 0.38
14 1 0.04
15 1 0.04
16 11 0.42
17 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:322559 original size:26 final size:26
Alignment explanation
Indices: 322498--322567 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 26
322488 AATAAAATTA
322498 AAATATTAAATAATTTATTAGAATAAT
1 AAATATT-AATAATTTATTAGAATAAT
*
322525 AATTTATATTAATAATTTATTA-TATAACT
1 AA---ATATTAATAATTTATTAGAATAA-T
*
322554 AAATATAAATAATT
1 AAATATTAATAATT
322568 AAATATGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
26 11 0.30
27 2 0.05
28 4 0.11
29 15 0.41
30 5 0.14
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (26 bp):
AAATATTAATAATTTATTAGAATAAT
Found at i:323202 original size:87 final size:86
Alignment explanation
Indices: 323076--323272 Score: 209
Period size: 87 Copynumber: 2.2 Consensus size: 86
323066 AAGTTTTTAA
* * * **
323076 TTTTTTACATTCAATTGGATATTTGAATTGTAAAAATGCATCAAAAAAATCCTCCAATTTTTTCA
1 TTTTTTACACTCAATTGGATACTTAAATTGTAAAAATGCAT-AAAAAAA-CCTCCAAACTTTT-A
*
323141 AAAAAA-CAATTAAGTCCCT-ACT
63 AAAAAAGCAATTAAGCCCCTGACT
* * * * *
323163 TTTTTTGCACTCAATTGGATGCTTAAATTTTCAAAATGCATAAAAAAACCTGCAAACTTTTAAAA
1 TTTTTTACACTCAATTGGATACTTAAATTGTAAAAATGCATAAAAAAACCTCCAAACTTTTAAAA
*
323228 AAAGCAATTAAGCCCCTGAGTTTT
66 AAAGCAATTAAGCCCCTGA---CT
*
323252 TTTTTTTCACTCAATTGGATA
1 TTTTTTACACTCAATTGGATA
323273 TTTGAACTGC
Statistics
Matches: 91, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
84 7 0.08
85 22 0.24
86 8 0.09
87 34 0.37
89 20 0.22
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (86 bp):
TTTTTTACACTCAATTGGATACTTAAATTGTAAAAATGCATAAAAAAACCTCCAAACTTTTAAAA
AAAGCAATTAAGCCCCTGACT
Found at i:323490 original size:40 final size:41
Alignment explanation
Indices: 323441--323533 Score: 118
Period size: 40 Copynumber: 2.3 Consensus size: 41
323431 AATTAGATTT
* *
323441 TTTTATAAAAATTTTAAAATATTAT-AAAAA-AACTGTAAAC
1 TTTTATAAAAATTATAAAAT-GTATCAAAAAGAACTGTAAAC
* * *
323481 TTTTATAAAAATTATAAAATGTATCAAAAAGACCTTTTAAC
1 TTTTATAAAAATTATAAAATGTATCAAAAAGAACTGTAAAC
323522 TTTTATAAAAAT
1 TTTTATAAAAAT
323534 CGTTAAAGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
39 3 0.07
40 24 0.52
41 19 0.41
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (41 bp):
TTTTATAAAAATTATAAAATGTATCAAAAAGAACTGTAAAC
Found at i:323498 original size:19 final size:19
Alignment explanation
Indices: 323441--323500 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
323431 AATTAGATTT
*
323441 TTTTATAAAAATTTTAAAA
1 TTTTATAAAAATTATAAAA
* * * *
323460 TATTATAAAAAAACTGTAAAC
1 T-TT-TATAAAAATTATAAAA
323481 TTTTATAAAAATTATAAAA
1 TTTTATAAAAATTATAAAA
323500 T
1 T
323501 GTATCAAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
19 14 0.45
20 4 0.13
21 13 0.42
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (19 bp):
TTTTATAAAAATTATAAAA
Found at i:324638 original size:29 final size:29
Alignment explanation
Indices: 324545--324647 Score: 95
Period size: 29 Copynumber: 3.5 Consensus size: 29
324535 AAATCCTTAC
*
324545 ATTTTCTATAATTTTCTTACGA-ATTTATAA
1 ATTTT-TATAATTTT-TTACGATTTTTATAA
* * * *
324575 AATTTTATAATTTTTT-CTATACTTCTATAT
1 ATTTTTATAATTTTTTACGAT--TTTTATAA
324605 A-TTTTATAATTTTTTACGATTTTTATAA
1 ATTTTTATAATTTTTTACGATTTTTATAA
*
324633 ATTTTTCTAATTTTT
1 ATTTTTATAATTTTT
324648 AATAAAACTA
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
27 2 0.03
28 9 0.15
29 35 0.59
30 13 0.22
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (29 bp):
ATTTTTATAATTTTTTACGATTTTTATAA
Found at i:324645 original size:19 final size:19
Alignment explanation
Indices: 324606--324653 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
324596 CTTCTATATA
324606 TTTTAT-AATTTTTTACGAT
1 TTTTATAAATTTTTTAC-AT
324625 TTTTATAAATTTTTCTA-AT
1 TTTTATAAATTTTT-TACAT
324644 TTTTAATAAA
1 TTTT-ATAAA
324654 ACTAGAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 12 0.46
20 12 0.46
21 2 0.08
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTATAAATTTTTTACAT
Found at i:337859 original size:12 final size:12
Alignment explanation
Indices: 337842--337871 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
337832 ATAAACCACA
337842 TCCTCTTTAATT
1 TCCTCTTTAATT
*
337854 TCCTCTTTTATT
1 TCCTCTTTAATT
337866 TCCTCT
1 TCCTCT
337872 ATCATATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.30, G:0.00, T:0.60
Consensus pattern (12 bp):
TCCTCTTTAATT
Found at i:344795 original size:12 final size:12
Alignment explanation
Indices: 344770--344820 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
344760 AATAACAATC
* *
344770 AAAACAGTAGCA
1 AAAACAATAACA
344782 AAAATC-ATAAC-
1 AAAA-CAATAACA
*
344793 AAAACAACAACA
1 AAAACAATAACA
344805 AAAACAATAACA
1 AAAACAATAACA
344817 AAAA
1 AAAA
344821 TAGCATCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 1 0.03
11 8 0.25
12 22 0.69
13 1 0.03
ACGTcount: A:0.71, C:0.18, G:0.04, T:0.08
Consensus pattern (12 bp):
AAAACAATAACA
Found at i:344844 original size:19 final size:19
Alignment explanation
Indices: 344816--344894 Score: 77
Period size: 21 Copynumber: 3.9 Consensus size: 19
344806 AAACAATAAC
*
344816 AAAAATAGCATCAAAACAGT
1 AAAAA-AGCACCAAAACAGT
*
344836 AAAAAAGCACCAAAACAGAA
1 AAAAAAGCACCAAAACAG-T
**
344856 AANAAAAAAACCAAAACAGT
1 AA-AAAAGCACCAAAACAGT
344876 AAAAAAAAGCACCAAAACA
1 --AAAAAAGCACCAAAACA
344895 ACAATATAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
19 12 0.25
20 7 0.15
21 27 0.56
22 2 0.04
ACGTcount: A:0.68, C:0.18, G:0.08, T:0.05
Consensus pattern (19 bp):
AAAAAAGCACCAAAACAGT
Found at i:355743 original size:2 final size:2
Alignment explanation
Indices: 355738--355766 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
355728 AATGGCGTGA
355738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
355767 GCACGTCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:364513 original size:1 final size:1
Alignment explanation
Indices: 364468--364497 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
364458 NNNNNNNNNN
364468 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
364498 CCTCGATGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:366715 original size:38 final size:38
Alignment explanation
Indices: 366664--366755 Score: 184
Period size: 38 Copynumber: 2.4 Consensus size: 38
366654 GGAACAGGGG
366664 AATTCCACCCAATCTCTTTTTTCTTTTATTGGATCTAA
1 AATTCCACCCAATCTCTTTTTTCTTTTATTGGATCTAA
366702 AATTCCACCCAATCTCTTTTTTCTTTTATTGGATCTAA
1 AATTCCACCCAATCTCTTTTTTCTTTTATTGGATCTAA
366740 AATTCCACCCAATCTC
1 AATTCCACCCAATCTC
366756 AATTTAAAGC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.25, C:0.27, G:0.04, T:0.43
Consensus pattern (38 bp):
AATTCCACCCAATCTCTTTTTTCTTTTATTGGATCTAA
Found at i:385190 original size:2 final size:2
Alignment explanation
Indices: 385183--385207 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
385173 TTTATTCAAA
385183 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
385208 ATAAGATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:385850 original size:42 final size:42
Alignment explanation
Indices: 385786--385899 Score: 149
Period size: 42 Copynumber: 2.7 Consensus size: 42
385776 AAGTATATAC
* * *
385786 TCTCAATGTTGATTAAAGTTTAGTTTAGTTAGCAAAGTTGTT
1 TCTCAATGTCGATTAAAATTTAGTTTAGTTAGCAAAGTTGGT
* **
385828 TCTCAATGTGGATTAAAATTTAGTTTAGTTAGCACGGTTGGT
1 TCTCAATGTCGATTAAAATTTAGTTTAGTTAGCAAAGTTGGT
* *
385870 T-TCAATTTCGATTAAATTTTAGTTTAGTTA
1 TCTCAATGTCGATTAAAATTTAGTTTAGTTA
385900 ACGCGTCTGA
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 26 0.41
42 38 0.59
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (42 bp):
TCTCAATGTCGATTAAAATTTAGTTTAGTTAGCAAAGTTGGT
Found at i:387240 original size:13 final size:14
Alignment explanation
Indices: 387222--387250 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
387212 ATAGTTGAAA
387222 TGCAAAGG-ATGGT
1 TGCAAAGGAATGGT
387235 TGCAAAGGAATGGT
1 TGCAAAGGAATGGT
387249 TG
1 TG
387251 GCTGAACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.31, C:0.07, G:0.38, T:0.24
Consensus pattern (14 bp):
TGCAAAGGAATGGT
Found at i:396891 original size:18 final size:17
Alignment explanation
Indices: 396863--396898 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
396853 TCAACAATCG
396863 AAATTTATTTTATAATA
1 AAATTTATTTTATAATA
396880 AAATTATATTTTATAATA
1 AAATT-TATTTTATAATA
396898 A
1 A
396899 TTAATACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTTATTTTATAATA
Found at i:397604 original size:16 final size:16
Alignment explanation
Indices: 397579--397617 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
397569 TAAAATTGTA
397579 ATATTAAATAATTAAGT
1 ATATT-AATAATTAAGT
* *
397596 ATATTAATAATTTATT
1 ATATTAATAATTAAGT
397612 ATATTA
1 ATATTA
397618 TTAAATATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
ATATTAATAATTAAGT
Found at i:397878 original size:19 final size:20
Alignment explanation
Indices: 397831--397879 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
397821 AAAAAAATAT
*
397831 ATTATTTTCTATTGACTTATAA
1 ATTATTTTCTATTGAC-T-CAA
*
397853 ATCATTTTCTATTGAC-CAA
1 ATTATTTTCTATTGACTCAA
397872 ATTATTTT
1 ATTATTTT
397880 TCATTAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 9 0.38
22 15 0.62
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.53
Consensus pattern (20 bp):
ATTATTTTCTATTGACTCAA
Found at i:404412 original size:17 final size:17
Alignment explanation
Indices: 404390--404423 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
404380 TGAATCTAGA
404390 CAACCATTCGATTAGGT
1 CAACCATTCGATTAGGT
*
404407 CAACCATTCGTTTAGGT
1 CAACCATTCGATTAGGT
404424 TCATTCCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (17 bp):
CAACCATTCGATTAGGT
Found at i:406021 original size:29 final size:29
Alignment explanation
Indices: 405891--406083 Score: 118
Period size: 29 Copynumber: 6.7 Consensus size: 29
405881 CAGTTGGGAT
405891 TAAAAT-GTAATTTTT-GA-ATGCTCGAGGG
1 TAAAATGGTAATTTTTGGACAT--TCGAGGG
* * *
405919 CAAAACGGTAA-TTTTGAACACTTCG-GGG
1 TAAAATGGTAATTTTTGGACA-TTCGAGGG
* * *
405947 CAAAATGATAA-TTTTGGACACTCAGGAGGAG
1 TAAAATGGTAATTTTTGGACATTC--GAGG-G
* * *
405978 -AATAT-GTATTTTTTTGGACATCCGAGGG
1 TAAAATGGTA-ATTTTTGGACATTCGAGGG
* *
406006 TAAAATGGTGATTTTTGGGA-ATTTCGAGGT
1 TAAAATGGTAATTTTT-GGACA-TTCGAGGG
*
406036 TAAAAAT-GAAATTTTTGGACATTCGAGGG
1 T-AAAATGGTAATTTTTGGACATTCGAGGG
406065 TAAAATGGTAATTTTTGGA
1 TAAAATGGTAATTTTTGGA
406084 AATTTTGAGG
Statistics
Matches: 127, Mismatches: 21, Indels: 33
0.70 0.12 0.18
Matches are distributed among these distances:
27 2 0.02
28 34 0.27
29 47 0.37
30 27 0.21
31 17 0.13
ACGTcount: A:0.33, C:0.09, G:0.25, T:0.33
Consensus pattern (29 bp):
TAAAATGGTAATTTTTGGACATTCGAGGG
Found at i:406051 original size:59 final size:59
Alignment explanation
Indices: 405988--406172 Score: 196
Period size: 59 Copynumber: 3.1 Consensus size: 59
405978 AATATGTATT
* * *
405988 TTTTTGGACATCCGAGGGTAAAATGGTGATTTTTGGGAATTTCGAGGTTAAAAATGAAA
1 TTTTTGGACATCCGAGGGTAAAATGGTAATTTTTGGAAATTTCGAGGTCAAAAATGAAA
* * *
406047 TTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAATTTTGAGGTCAAAAATGGAA
1 TTTTTGGACATCCGAGGGTAAAATGGTAATTTTTGGAAATTTCGAGGTCAAAAATGAAA
* * ** * * * *
406106 TTTTTTGAAACTTTG-GGGTCAAAAATGG-AATTTTTGAAAATTTAGGGGT-AAAAATGTAA
1 TTTTTGGACA-TCCGAGGGT--AAAATGGTAATTTTTGGAAATTTCGAGGTCAAAAATGAAA
406165 TTTTTGGA
1 TTTTTGGA
406173 AACTTTTAAG
Statistics
Matches: 109, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
59 81 0.74
60 21 0.19
61 7 0.06
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.37
Consensus pattern (59 bp):
TTTTTGGACATCCGAGGGTAAAATGGTAATTTTTGGAAATTTCGAGGTCAAAAATGAAA
Found at i:406109 original size:29 final size:30
Alignment explanation
Indices: 406007--406204 Score: 181
Period size: 30 Copynumber: 6.6 Consensus size: 30
405997 ATCCGAGGGT
* * * *
406007 AAAATGGTGATTTTTGGGAATTTCGAGGTTA
1 AAAATGG-AATTTTTGGAAATTTTGAGGTCA
* * *
406038 AAAATGAAATTTTTGGACA-TTCGAGGGT--
1 AAAATGGAATTTTTGGAAATTTTGA-GGTCA
406066 AAAATGGTAATTTTTGGAAATTTTGAGGTCA
1 AAAATGG-AATTTTTGGAAATTTTGAGGTCA
* * *
406097 AAAATGGAATTTTTTGAAACTTTGGGGTCA
1 AAAATGGAATTTTTGGAAATTTTGAGGTCA
* * *
406127 AAAATGGAATTTTTGAAAATTTAGGGGT-A
1 AAAATGGAATTTTTGGAAATTTTGAGGTCA
* *
406156 AAAATGTAATTTTTGGAAACTTTTAAGGTCA
1 AAAATGGAATTTTTGGAAA-TTTTGAGGTCA
*
406187 AAAATTGAA-TTTTGGAAA
1 AAAATGGAATTTTTGGAAA
406205 GTTCAGGGAC
Statistics
Matches: 139, Mismatches: 21, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
28 6 0.04
29 37 0.27
30 75 0.54
31 21 0.15
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAATTTTGAGGTCA
Found at i:407276 original size:6 final size:6
Alignment explanation
Indices: 407265--407308 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
407255 TTTCCTTTTT
*
407265 TATTAA TATTAA TATTAA TATTAA TATTAT TATTAA TA-TAA TAT
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TAT
407309 ATTTATTACT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TATTAA
Done.