Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 1 of 344
Found at i:837 original size:16 final size:15
Alignment explanation
Indices: 793--846 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
783 TCCGCAGGGT
*
793 GGGATATACCTCAGC
1 GGGATATACCTAAGC
*
808 CGGACTAT-CCTAAGTC
1 GGGA-TATACCTAAG-C
824 GGGATATACCTAAGCC
1 GGGATATACCTAAG-C
840 GGGATAT
1 GGGATAT
847 CCTCGGAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
15 11 0.34
16 21 0.66
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (15 bp):
GGGATATACCTAAGC
Found at i:1061 original size:42 final size:43
Alignment explanation
Indices: 967--1081 Score: 135
Period size: 42 Copynumber: 2.7 Consensus size: 43
957 TGAACCGGGA
* * * *
967 TGGGATATCAGAGGGATATCCCCGGAATTGATTATTCTAAGAG
1 TGGGATATGAGAGGGATATCCCTGGAATAGATTATTCCAAGAG
*
1010 -GGGAAATGAGAGGGATATCCCTGGAATAGATTATTCCAAG-G
1 TGGGATATGAGAGGGATATCCCTGGAATAGATTATTCCAAGAG
* * * *
1051 TGGGATATGAGCGGTATTTTCCTGGAATAGA
1 TGGGATATGAGAGGGATATCCCTGGAATAGA
1082 AAAGAGAATG
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.02
42 60 0.98
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.27
Consensus pattern (43 bp):
TGGGATATGAGAGGGATATCCCTGGAATAGATTATTCCAAGAG
Found at i:7612 original size:30 final size:30
Alignment explanation
Indices: 7577--7634 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
7567 ATTTTTTTAA
7577 TAATTTTGTTATTATTTTAAAGAAATTTGT
1 TAATTTTGTTATTATTTTAAAGAAATTTGT
* *
7607 TAATTTTGTTATTATTTTAGAGATATTT
1 TAATTTTGTTATTATTTTAAAGAAATTT
7635 ACTTATTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (30 bp):
TAATTTTGTTATTATTTTAAAGAAATTTGT
Found at i:18991 original size:44 final size:45
Alignment explanation
Indices: 18926--19016 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
18916 ACCTCTATTC
* * *
18926 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
18970 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
19015 CA
1 CA
19017 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:19018 original size:16 final size:16
Alignment explanation
Indices: 18997--19065 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
18987 GATTAGCTAT
18997 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
19013 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
19030 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
19046 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
19062 TACA
1 TACA
19066 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:19039 original size:33 final size:32
Alignment explanation
Indices: 18997--19065 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
18987 GATTAGCTAT
18997 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
19030 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
19062 TACA
1 TACA
19066 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:21815 original size:52 final size:52
Alignment explanation
Indices: 21677--21849 Score: 186
Period size: 52 Copynumber: 3.3 Consensus size: 52
21667 CTATGGTCTT
* * *
21677 ACACAGATCACATTACACACCGATGCCATATCCCAGATATGATCTTATAC-GGA
1 ACACATATCACA-T-CACACCGATGCCATAGCCCAGATATGGTCTTATACAGGA
** *
21730 ATCACATTATCATGTCACACCGATGTCATAGCCCAGATATGGTCTTATACAGGA
1 A-CACA-TATCACATCACACCGATGCCATAGCCCAGATATGGTCTTATACAGGA
** * * **
21784 ACACATATCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACAGCC
1 ACACATATCACATCACACCGATGCCATAGCCCAGATATGGTCTTATACAGGA
*
21836 GCACATATCACATC
1 ACACATATCACATC
21850 TTTTTCGTCG
Statistics
Matches: 100, Mismatches: 17, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
52 50 0.50
53 37 0.37
54 9 0.09
55 4 0.04
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (52 bp):
ACACATATCACATCACACCGATGCCATAGCCCAGATATGGTCTTATACAGGA
Found at i:25053 original size:54 final size:54
Alignment explanation
Indices: 24971--25129 Score: 180
Period size: 54 Copynumber: 3.0 Consensus size: 54
24961 GGCAACAAGT
* *
24971 GATAAGCGATATT-CGTATAAGACCATAGCTGGGCTATAGCATCGGAAAATAAAA
1 GATAAGTGAT-TTCCGTATAAGACCATAGCTGGGCTATGGCATCGGAAAATAAAA
* * ***
25025 GATAAGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCTTCGGATTAATGTGA
1 GATAAGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGA-AAATAAAA
* * * *
25080 TACAAGTGA--TCCGTATAAGACCATAGCTGGGCTATGGCATCAGAGAATAA
1 GATAAGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGAAAATAA
25130 TTATAAGTGC
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
52 3 0.03
53 35 0.39
54 40 0.45
55 11 0.12
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.25
Consensus pattern (54 bp):
GATAAGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGAAAATAAAA
Found at i:25115 original size:53 final size:53
Alignment explanation
Indices: 24984--25129 Score: 177
Period size: 53 Copynumber: 2.7 Consensus size: 53
24974 AAGCGATATT
* *
24984 CGTATAAGACCATAGCTGGGCTATAGCATCGGAAAATAAAAGATAAGTGATTTC
1 CGTATAAGACCATAGCTGGGCTATGGCATCGGAAAATAAAAGACAAGTGA-TTC
* * *** *
25038 CGTATAAGACCATAGCTGGGCTATGGCTTCGGATTAATGTGATACAAGTGA-TC
1 CGTATAAGACCATAGCTGGGCTATGGCATCGGA-AAATAAAAGACAAGTGATTC
* *
25091 CGTATAAGACCATAGCTGGGCTATGGCATCAGAGAATAA
1 CGTATAAGACCATAGCTGGGCTATGGCATCGGAAAATAA
25130 TTATAAGTGC
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
52 3 0.04
53 33 0.42
54 31 0.40
55 11 0.14
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (53 bp):
CGTATAAGACCATAGCTGGGCTATGGCATCGGAAAATAAAAGACAAGTGATTC
Found at i:27772 original size:22 final size:22
Alignment explanation
Indices: 27747--27820 Score: 123
Period size: 22 Copynumber: 3.4 Consensus size: 22
27737 AAATATCTTT
*
27747 ACTCCACTAAACCACTCCAACC
1 ACTCCACTAAACCACCCCAACC
27769 ACTCCACTAAACCACCCCAACC
1 ACTCCACTAAACCACCCCAACC
27791 AC-CCTACTAAACCACCCCAACC
1 ACTCC-ACTAAACCACCCCAACC
27813 ACTCCACT
1 ACTCCACT
27821 TGCCTAGAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
21 2 0.04
22 45 0.92
23 2 0.04
ACGTcount: A:0.35, C:0.53, G:0.00, T:0.12
Consensus pattern (22 bp):
ACTCCACTAAACCACCCCAACC
Found at i:28226 original size:3 final size:3
Alignment explanation
Indices: 28215--28294 Score: 53
Period size: 3 Copynumber: 26.3 Consensus size: 3
28205 TTTATTTTTT
* *
28215 TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
28258 TCTCA TGTA TATA TTA TTA TT- TATA TTA TTA -TA TTA T
1 T-T-A T-TA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA T
28295 ATATGCCCTC
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
2 7 0.11
3 46 0.74
4 7 0.11
5 2 0.03
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:28272 original size:21 final size:18
Alignment explanation
Indices: 28219--28294 Score: 82
Period size: 18 Copynumber: 4.1 Consensus size: 18
28209 TTTTTTTTAT
* *
28219 TTTATTATTTTTACTATTA
1 TTTA-TATTATTATTATTA
28238 TTTATATTATTATTATTA
1 TTTATATTATTATTATTA
*
28256 TTTCTCATGTATATATTATTA
1 TTTAT-AT-TAT-TATTATTA
28277 TTTATATTATTA-TATTA
1 TTTATATTATTATTATTA
28294 T
1 T
28295 ATATGCCCTC
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
17 6 0.12
18 18 0.36
19 9 0.18
20 5 0.10
21 12 0.24
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (18 bp):
TTTATATTATTATTATTA
Found at i:28295 original size:27 final size:26
Alignment explanation
Indices: 28206--28298 Score: 82
Period size: 26 Copynumber: 3.6 Consensus size: 26
28196 GAGCTTTGTT
* * * *
28206 TTATTTTTTTTATTTTATTATTTTTA
1 TTATTATTTATATATTATTATTTATA
*
28232 CTATTATTTATATTATTATTA-TTAT-
1 TTATTATTTATA-TATTATTATTTATA
* * *
28257 TTCTCATGTATATATTATTATTTATA
1 TTATTATTTATATATTATTATTTATA
28283 TTATTATATTATATAT
1 TTATTAT-TTATATAT
28299 GCCCTCTCCA
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
24 8 0.16
25 12 0.24
26 17 0.33
27 14 0.27
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (26 bp):
TTATTATTTATATATTATTATTTATA
Found at i:28375 original size:3 final size:3
Alignment explanation
Indices: 28369--28419 Score: 50
Period size: 3 Copynumber: 16.0 Consensus size: 3
28359 TTCTGACTAC
*
28369 TAT TAT TAT ATAT ATAT GTAT TAT TGT T-T GTAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT -TAT -TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
28417 TAT
1 TAT
28420 CACCCCTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 1 0.02
3 31 0.72
4 11 0.26
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:32008 original size:19 final size:18
Alignment explanation
Indices: 31984--32025 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
31974 TGGTATTAGT
*
31984 AATAATAATAATAATAGAA
1 AATAATAACAATAATA-AA
*
32003 AATAATAACAATATTAAA
1 AATAATAACAATAATAAA
32021 AATAA
1 AATAA
32026 CACTCTCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (18 bp):
AATAATAACAATAATAAA
Found at i:32428 original size:13 final size:13
Alignment explanation
Indices: 32395--32507 Score: 108
Period size: 13 Copynumber: 9.6 Consensus size: 13
32385 TTTGTAGGCA
32395 AGTGGAGTGG-TT
1 AGTGGAGTGGTTT
32407 -G-GG-GTGGTTT
1 AGTGGAGTGGTTT
32417 AGTGGAGTGGTTT
1 AGTGGAGTGGTTT
32430 AGTAGG-GTGG-TT
1 AGT-GGAGTGGTTT
32442 -G-GG-GTGGTTT
1 AGTGGAGTGGTTT
*
32452 AGTGAAGTGGTTT
1 AGTGGAGTGGTTT
*
32465 AGTGTAGTGGTTT
1 AGTGGAGTGGTTT
32478 AGTGGAGTGG--T
1 AGTGGAGTGGTTT
32489 --TGGAGTGGTTT
1 AGTGGAGTGGTTT
32500 AGTGGAGT
1 AGTGGAGT
32508 AAAGATATTT
Statistics
Matches: 85, Mismatches: 3, Indels: 25
0.75 0.03 0.22
Matches are distributed among these distances:
9 18 0.21
10 6 0.07
11 6 0.07
12 5 0.06
13 48 0.56
14 2 0.02
ACGTcount: A:0.14, C:0.00, G:0.49, T:0.37
Consensus pattern (13 bp):
AGTGGAGTGGTTT
Found at i:32447 original size:35 final size:35
Alignment explanation
Indices: 32401--32467 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
32391 GGCAAGTGGA
*
32401 GTGGTTGGGGTGGTTTAGTGGAGTGGTTTAGTAGG
1 GTGGTTGGGGTGGTTTAGTGAAGTGGTTTAGTAGG
32436 GTGGTTGGGGTGGTTTAGTGAAGTGGTTTAGT
1 GTGGTTGGGGTGGTTTAGTGAAGTGGTTTAGT
32468 GTAGTGGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.12, C:0.00, G:0.49, T:0.39
Consensus pattern (35 bp):
GTGGTTGGGGTGGTTTAGTGAAGTGGTTTAGTAGG
Found at i:32463 original size:48 final size:48
Alignment explanation
Indices: 32410--32503 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
32400 AGTGGTTGGG
*
32410 GTGGTTTAGTGGAGTGGTTTAGTAGG-GTGGTTGGGGTGGTTTAGTGAA
1 GTGGTTTAGTGGAGTGGTTTAGT-GGAGTGGTTGGAGTGGTTTAGTGAA
*
32458 GTGGTTTAGTGTAGTGGTTTAGTGGAGTGGTTGGAGTGGTTTAGTG
1 GTGGTTTAGTGGAGTGGTTTAGTGGAGTGGTTGGAGTGGTTTAGTG
32504 GAGTAAAGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
47 2 0.05
48 41 0.95
ACGTcount: A:0.14, C:0.00, G:0.47, T:0.39
Consensus pattern (48 bp):
GTGGTTTAGTGGAGTGGTTTAGTGGAGTGGTTGGAGTGGTTTAGTGAA
Found at i:32475 original size:35 final size:34
Alignment explanation
Indices: 32399--32476 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 34
32389 TAGGCAAGTG
*
32399 GAGTGGTTGGGGTGGTTTAGTGGAGTGGTTTAGT
1 GAGTGGTTGGGGTGGTTTAGTGAAGTGGTTTAGT
*
32433 AGGGTGGTTGGGGTGGTTTAGTGAAGTGGTTTAGT
1 -GAGTGGTTGGGGTGGTTTAGTGAAGTGGTTTAGT
32468 GTAGTGGTT
1 G-AGTGGTT
32477 TAGTGGAGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
34 1 0.03
35 38 0.97
ACGTcount: A:0.13, C:0.00, G:0.49, T:0.38
Consensus pattern (34 bp):
GAGTGGTTGGGGTGGTTTAGTGAAGTGGTTTAGT
Found at i:32503 original size:22 final size:22
Alignment explanation
Indices: 32419--32507 Score: 108
Period size: 22 Copynumber: 3.9 Consensus size: 22
32409 GGTGGTTTAG
32419 TGGAGTGGTTTAGTAGG-GTGGT
1 TGGAGTGGTTTAGT-GGAGTGGT
* *
32441 TGGGGTGGTTTAGTGAAGTGGTT
1 TGGAGTGGTTTAGTGGAGTGG-T
32464 TAGTGTAGTGGTTTAGTGGAGTGGT
1 T-G-G-AGTGGTTTAGTGGAGTGGT
32489 TGGAGTGGTTTAGTGGAGT
1 TGGAGTGGTTTAGTGGAGT
32508 AAAGATATTT
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
21 1 0.02
22 33 0.57
23 3 0.05
24 2 0.03
25 3 0.05
26 16 0.28
ACGTcount: A:0.15, C:0.00, G:0.47, T:0.38
Consensus pattern (22 bp):
TGGAGTGGTTTAGTGGAGTGGT
Found at i:36382 original size:33 final size:33
Alignment explanation
Indices: 36337--36404 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
36327 AAAAAGATAG
* *
36337 GAAAAAAAGGATTATGGTTGCGAAACTGAACAT
1 GAAAAAAAGGATTATGGCTGCAAAACTGAACAT
* * *
36370 GAAAAAAGGGATTATGGCTGTAAAACTGGACAT
1 GAAAAAAAGGATTATGGCTGCAAAACTGAACAT
36403 GA
1 GA
36405 GTAATGCATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (33 bp):
GAAAAAAAGGATTATGGCTGCAAAACTGAACAT
Found at i:39145 original size:47 final size:47
Alignment explanation
Indices: 39075--39245 Score: 170
Period size: 47 Copynumber: 3.6 Consensus size: 47
39065 TCAGAGAGGC
*
39075 GTGATTATGTGCTTCCGTATAAGACCATATCTGGGATATGGCATCGGT
1 GTGATTATGTGCTACCGTATAAGACCATAT-TGGGATATGGCATCGGT
* *
39123 GTGA-TATGTGCTACTGTATAAGACCATATTTGGGATATGGCATCAGT
1 GTGATTATGTGCTACCGTATAAGACCATA-TTGGGATATGGCATCGGT
* * * * * *
39170 GTGA-TATGTGAT-CCGTGTAAGACCATGGTTGGGCTATGGCTTTGGT
1 GTGATTATGTGCTACCGTATAAGACCAT-ATTGGGATATGGCATCGGT
* *
39216 GTGTATTATGTGACTA-TGTGTAAGACCATA
1 GTG-ATTATGTG-CTACCGTATAAGACCATA
39246 GTTTTACTAT
Statistics
Matches: 103, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
46 29 0.28
47 50 0.49
48 11 0.11
49 13 0.13
ACGTcount: A:0.24, C:0.13, G:0.28, T:0.35
Consensus pattern (47 bp):
GTGATTATGTGCTACCGTATAAGACCATATTGGGATATGGCATCGGT
Found at i:53949 original size:22 final size:23
Alignment explanation
Indices: 53924--53969 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
53914 CAACCAAATC
53924 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
53946 AATTCATACATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
53969 A
1 A
53970 CGTCATCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 15 0.68
24 1 0.05
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:53975 original size:23 final size:24
Alignment explanation
Indices: 53930--53982 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
53920 AATCAATTCA
*
53930 ACATATTTTCAAGATAAATTCAT-
1 ACATATTTTCAAGATAAAGTCATC
*
53953 ACATATTTAT-AAGATAACGTCATC
1 ACATATTT-TCAAGATAAAGTCATC
53977 ACATAT
1 ACATAT
53983 CTAAAACCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (24 bp):
ACATATTTTCAAGATAAAGTCATC
Found at i:57569 original size:22 final size:22
Alignment explanation
Indices: 57543--57588 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
57533 AATCACATAT
57543 TTACATGTCATGATAAATATCA
1 TTACATGTCATGATAAATATCA
57565 TTACATGTCATGATAAATATCA
1 TTACATGTCATGATAAATATCA
57587 TT
1 TT
57589 CTCTTGTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (22 bp):
TTACATGTCATGATAAATATCA
Found at i:59350 original size:2 final size:2
Alignment explanation
Indices: 59345--59369 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59335 TTTTTTCCAT
59345 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
59370 TATATATACT
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:59725 original size:30 final size:30
Alignment explanation
Indices: 59670--59727 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
59660 TATTTGTACT
* *
59670 TTTAGTCCCTTAAATTTTTTATATTTACAC
1 TTTAATCCCTTAAATTTTTGATATTTACAC
59700 TTTAATCCCTTAAA-TTTTGAGTATTTAC
1 TTTAATCCCTTAAATTTTTGA-TATTTAC
59728 TCTTGGTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.28, C:0.16, G:0.05, T:0.52
Consensus pattern (30 bp):
TTTAATCCCTTAAATTTTTGATATTTACAC
Found at i:78138 original size:12 final size:12
Alignment explanation
Indices: 78121--78164 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
78111 TTTACTTCAC
78121 TTTCTTGTTTCT
1 TTTCTTGTTTCT
*
78133 TTTCTTTTTTCT
1 TTTCTTGTTTCT
*
78145 TTT-TTTTTTCT
1 TTTCTTGTTTCT
*
78156 TTTTTTGTT
1 TTTCTTGTT
78165 CTCTAAATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 11 0.38
12 18 0.62
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (12 bp):
TTTCTTGTTTCT
Found at i:78151 original size:11 final size:11
Alignment explanation
Indices: 78128--78166 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
78118 CACTTTCTTG
78128 TTTCTTTTCTTT
1 TTTCTTTT-TTT
78140 TTTCTTTTTTT
1 TTTCTTTTTTT
78151 TTTCTTTTTTT
1 TTTCTTTTTTT
*
78162 GTTCT
1 TTTCT
78167 CTAAATCAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:78742 original size:60 final size:60
Alignment explanation
Indices: 78667--78787 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
78657 TTTTACACAA
78667 ATTTGAACCTTTCAAGCACCACTATGTTACCAATGCTATAATATTTGTTACCCAAAGTCT
1 ATTTGAACCTTTCAAGCACCACTATGTTACCAATGCTATAATATTTGTTACCCAAAGTCT
78727 ATTTGAACCTTTCAAGCACCACTATGTTACCAATGCTATAATATTTGTTACCCAAAGTCT
1 ATTTGAACCTTTCAAGCACCACTATGTTACCAATGCTATAATATTTGTTACCCAAAGTCT
78787 A
1 A
78788 AATTAGACAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (60 bp):
ATTTGAACCTTTCAAGCACCACTATGTTACCAATGCTATAATATTTGTTACCCAAAGTCT
Found at i:78915 original size:49 final size:49
Alignment explanation
Indices: 78843--78941 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
78833 CTATAAAAGA
78843 AAGTGATACATTGTAAATATTTCTAAATATTCACGAGGCATTCTTACTT
1 AAGTGATACATTGTAAATATTTCTAAATATTCACGAGGCATTCTTACTT
78892 AAGTGATACATTGTAAATATTTCTAAATATTCACGAGGCATTCTTACTT
1 AAGTGATACATTGTAAATATTTCTAAATATTCACGAGGCATTCTTACTT
78941 A
1 A
78942 GATCAAGTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (49 bp):
AAGTGATACATTGTAAATATTTCTAAATATTCACGAGGCATTCTTACTT
Found at i:80417 original size:18 final size:18
Alignment explanation
Indices: 80394--80442 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
80384 AAGCATTTAC
80394 ATTAAGATTGCAATTAAA
1 ATTAAGATTGCAATTAAA
* ** *
80412 ATTAAGAATGCGTTTACA
1 ATTAAGATTGCAATTAAA
*
80430 ACTAAGATTGCAA
1 ATTAAGATTGCAA
80443 AATTTTGCAC
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (18 bp):
ATTAAGATTGCAATTAAA
Found at i:89826 original size:14 final size:13
Alignment explanation
Indices: 89807--89836 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
89797 TTTCTAAATT
89807 AATTTTTTAATAA
1 AATTTTTTAATAA
*
89820 AATTTTTTAATCA
1 AATTTTTTAATAA
89833 AATT
1 AATT
89837 CTCTAGTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
AATTTTTTAATAA
Found at i:91811 original size:26 final size:25
Alignment explanation
Indices: 91763--91817 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 25
91753 TGGTACAAAT
*
91763 TGATAATGGGTAGTTAAATGTTCCA
1 TGATAATGGGTAGGTAAATGTTCCA
*
91788 TGATAATGGATTAGGTAAATGTTCCA
1 TGATAATGG-GTAGGTAAATGTTCCA
91814 TGAT
1 TGAT
91818 GGACATTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (25 bp):
TGATAATGGGTAGGTAAATGTTCCA
Found at i:107590 original size:19 final size:20
Alignment explanation
Indices: 107566--107608 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
107556 GGTTTTTTCG
* *
107566 TGAAATTTAATGCACATG-A
1 TGAAATGTAATGCAAATGAA
107585 TGAAATGTAATGCAAATGAA
1 TGAAATGTAATGCAAATGAA
107605 TGAA
1 TGAA
107609 TGCAAAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.28
Consensus pattern (20 bp):
TGAAATGTAATGCAAATGAA
Found at i:115102 original size:17 final size:16
Alignment explanation
Indices: 115060--115104 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
115050 TTTCTTTCTC
115060 TTTTTTTTTTTT-ACT
1 TTTTTTTTTTTTGACT
*
115075 TTTTTACTTTTTTGACT
1 TTTTT-TTTTTTTGACT
115092 TTTGTTTTTTTTT
1 TTT-TTTTTTTTT
115105 TTATGTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 5 0.20
16 6 0.24
17 12 0.48
18 2 0.08
ACGTcount: A:0.07, C:0.07, G:0.04, T:0.82
Consensus pattern (16 bp):
TTTTTTTTTTTTGACT
Found at i:115113 original size:19 final size:20
Alignment explanation
Indices: 115091--115128 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
115081 CTTTTTTGAC
*
115091 TTTTGT-TTTTTTTTTTATG
1 TTTTGTCTTTTTTCTTTATG
115110 TTTTGTCTTTTTTCTTTAT
1 TTTTGTCTTTTTTCTTTAT
115129 TTTATTCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.05, C:0.05, G:0.08, T:0.82
Consensus pattern (20 bp):
TTTTGTCTTTTTTCTTTATG
Found at i:115347 original size:21 final size:23
Alignment explanation
Indices: 115323--115379 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 23
115313 TTTATAATAA
115323 TTTAAATATTATTTAATT-TG-T
1 TTTAAATATTATTTAATTATGAT
*
115344 TTTATAATATT-TTAAATTATGAT
1 TTTA-AATATTATTTAATTATGAT
115367 TTTAAA-ATTATTT
1 TTTAAATATTATTT
115380 TTAAAGATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 13 0.43
22 12 0.40
23 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTAAATATTATTTAATTATGAT
Found at i:115494 original size:15 final size:16
Alignment explanation
Indices: 115470--115506 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
115460 AATAAAAAAT
115470 AAAAAA-TATTT-TTA
1 AAAAAATTATTTGTTA
115484 AAAAAATTATTTGTTA
1 AAAAAATTATTTGTTA
115500 AAAAAAT
1 AAAAAAT
115507 GAGTTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.29
15 5 0.24
16 10 0.48
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AAAAAATTATTTGTTA
Found at i:115625 original size:19 final size:18
Alignment explanation
Indices: 115601--115644 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
115591 TCACATCATA
115601 TTTTTTAACAAATAAATAT
1 TTTTTTAACAAATAAAT-T
*
115620 TTTTTTAACAAATATATT
1 TTTTTTAACAAATAAATT
115638 TTTTTTA
1 TTTTTTA
115645 TTTTTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTTTAACAAATAAATT
Found at i:115756 original size:13 final size:13
Alignment explanation
Indices: 115740--115783 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
115730 TTTTTCTTAT
*
115740 TTTATTTTGTTTA
1 TTTATTTTATTTA
115753 TTTATTTTATTTA
1 TTTATTTTATTTA
* *
115766 TTTTTTGTTATTAA
1 TTTATT-TTATTTA
115780 TTTA
1 TTTA
115784 AAAAATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 17 0.65
14 9 0.35
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:115777 original size:10 final size:9
Alignment explanation
Indices: 115736--115769 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
115726 ACATTTTTTC
115736 TTATTTTAT
1 TTATTTTAT
115745 TT-TGTTTAT
1 TTAT-TTTAT
115754 TTATTTTAT
1 TTATTTTAT
115763 TTATTTT
1 TTATTTT
115770 TTGTTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.04
9 21 0.91
10 1 0.04
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (9 bp):
TTATTTTAT
Found at i:115843 original size:23 final size:22
Alignment explanation
Indices: 115784--115851 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 22
115774 TATTAATTTA
* *
115784 AAAAATTTAAA-ATGTATATTTG
1 AAAATTTTAAATAT-TATTTTTG
*
115806 AAATATTTTATAATATATATTTTTT
1 AAA-ATTTTA-AATAT-TATTTTTG
115831 AAAATTTTAAATATTATTTTT
1 AAAATTTTAAATATTATTTTT
115852 AAATTATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 10 0.26
23 10 0.26
24 8 0.21
25 11 0.28
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (22 bp):
AAAATTTTAAATATTATTTTTG
Found at i:115853 original size:13 final size:12
Alignment explanation
Indices: 115789--115868 Score: 53
Period size: 11 Copynumber: 6.8 Consensus size: 12
115779 ATTTAAAAAA
*
115789 TTTAAAATGTATA
1 TTTAAAAT-TATT
*
115802 TTTGAAA-TATT
1 TTTAAAATTATT
*
115813 TTATAATATATATT
1 TT-TAAAAT-TATT
*
115827 TTTTAAA--A-T
1 TTTAAAATTATT
115836 TTTAAATATTATT
1 TTTAAA-ATTATT
115849 TTT-AAATTATT
1 TTTAAAATTATT
115860 TTTAAAATT
1 TTTAAAATT
115869 TTGAGTATTA
Statistics
Matches: 52, Mismatches: 7, Indels: 17
0.68 0.09 0.22
Matches are distributed among these distances:
9 6 0.12
10 2 0.04
11 14 0.27
12 11 0.21
13 13 0.25
14 6 0.12
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (12 bp):
TTTAAAATTATT
Found at i:115860 original size:23 final size:25
Alignment explanation
Indices: 115806--115861 Score: 75
Period size: 23 Copynumber: 2.4 Consensus size: 25
115796 TGTATATTTG
115806 AAATATTTTATAATATATATTTTTT
1 AAATATTTTATAATATATATTTTTT
115831 AAA-ATTTTA-AATAT-TA-TTTTT
1 AAATATTTTATAATATATATTTTTT
115852 AAATTATTTT
1 AAA-TATTTT
115862 TAAAATTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 8 0.28
22 2 0.07
23 10 0.34
24 6 0.21
25 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
AAATATTTTATAATATATATTTTTT
Found at i:115920 original size:14 final size:14
Alignment explanation
Indices: 115903--115978 Score: 59
Period size: 14 Copynumber: 5.5 Consensus size: 14
115893 GTCTTATAAA
115903 TTTTAAAAATATAT
1 TTTTAAAAATATAT
* *
115917 TTTTTAAACT-TAT
1 TTTTAAAAATATAT
** * *
115930 TTTTCTGAATTTTAAT
1 TTTT-AAAAATAT-AT
115946 TTTT--AAATATAT
1 TTTTAAAAATATAT
115958 TTTTAAAAATATAT
1 TTTTAAAAATATAT
115972 TTTTAAA
1 TTTTAAA
115979 CAAAATAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
12 6 0.12
13 11 0.22
14 27 0.53
15 1 0.02
16 6 0.12
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (14 bp):
TTTTAAAAATATAT
Found at i:116025 original size:20 final size:22
Alignment explanation
Indices: 115990--116035 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
115980 AAAATAAAAT
115990 AATTTCAAAAATATATATTT-A
1 AATTTCAAAAATATATATTTGA
*
116011 AATTT-AAATATATATATTTGA
1 AATTTCAAAAATATATATTTGA
116032 AATT
1 AATT
116036 ATTTCTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
AATTTCAAAAATATATATTTGA
Found at i:116223 original size:34 final size:34
Alignment explanation
Indices: 116132--116229 Score: 101
Period size: 33 Copynumber: 2.8 Consensus size: 34
116122 AAAATATTTC
116132 AAATATATATTAAAAAAATAATATTTAAAATTTTAAA
1 AAATATATATT--AAAAA-AATATTTAAAATTTTAAA
* * *
116169 AAGTA-AT-TTCAAATATATATTTAAAATTTTAAA
1 AAATATATATT-AAAAAAATATTTAAAATTTTAAA
* *
116202 AAATATATATTAATAAAATATTTTAAAT
1 AAATATATATTAAAAAAATATTTAAAAT
116230 ATATATTTCA
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
33 21 0.42
34 19 0.38
35 4 0.08
36 2 0.04
37 4 0.08
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (34 bp):
AAATATATATTAAAAAAATATTTAAAATTTTAAA
Found at i:116242 original size:22 final size:21
Alignment explanation
Indices: 116174--116250 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 21
116164 TTAAAAAGTA
*
116174 ATTTCAAATATATATTTAAA-
1 ATTTTAAATATATATTTAAAT
116194 ATTTTAAAAAATATATATTAATAAAAT
1 ATTTT---AAATATATATT--T-AAAT
116221 ATTTTAAATATATATTTCAAAT
1 ATTTTAAATATATATTT-AAAT
*
116243 TTTTTAAA
1 ATTTTAAA
116251 GTTAATAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
20 4 0.09
22 12 0.26
23 11 0.23
24 11 0.23
25 1 0.02
26 3 0.06
27 5 0.11
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTTAAATATATATTTAAAT
Found at i:116265 original size:47 final size:47
Alignment explanation
Indices: 116080--116245 Score: 164
Period size: 47 Copynumber: 3.5 Consensus size: 47
116070 AAAATTAATT
* *
116080 TTTCAAAATATGTATTTAAAATTTTAAAAAATATATATTAATAAAATA
1 TTTC-AAATATATATTTAAAATTTTAAAAAATATATAATAATAAAATA
* *
116128 TTTCAAATATATA-TTAAAA----AAATAATATTTAA-AATTTTAAAAAGTAA
1 TTTCAAATATATATTTAAAATTTTAAAAAATATATAATAA---T-AAAA-T-A
*
116175 TTTCAAATATATATTTAAAATTTTAAAAAATATATATTAATAAAATA
1 TTTCAAATATATATTTAAAATTTTAAAAAATATATAATAATAAAATA
* *
116222 TTTTAAATATATATTTCAAATTTT
1 TTTCAAATATATATTTAAAATTTT
116246 TTAAAGTTAA
Statistics
Matches: 97, Mismatches: 9, Indels: 25
0.74 0.07 0.19
Matches are distributed among these distances:
41 2 0.02
42 10 0.10
44 1 0.01
45 4 0.04
46 7 0.07
47 45 0.46
48 11 0.11
49 4 0.04
50 1 0.01
52 10 0.10
53 2 0.02
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (47 bp):
TTTCAAATATATATTTAAAATTTTAAAAAATATATAATAATAAAATA
Found at i:116316 original size:15 final size:14
Alignment explanation
Indices: 116271--116318 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
116261 ATAAATTAAT
*
116271 AAAATAAAATAAAA
1 AAAACAAAATAAAA
*
116285 AAAGACAAAACATAAA
1 AAA-ACAAAATA-AAA
116301 AAAACAAAAGTAAAA
1 AAAACAAAA-TAAAA
116316 AAA
1 AAA
116319 GTAAAAAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 3 0.11
15 18 0.64
16 7 0.25
ACGTcount: A:0.81, C:0.06, G:0.04, T:0.08
Consensus pattern (14 bp):
AAAACAAAATAAAA
Found at i:116316 original size:22 final size:21
Alignment explanation
Indices: 116271--116326 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 21
116261 ATAAATTAAT
116271 AAAATAAAATAAAAAAAGACAA
1 AAAATAAAA-AAAAAAAGACAA
*
116293 AACATAAAAAAACAAAAGTA-AA
1 AAAATAAAAAAA-AAAAG-ACAA
116315 AAAAGTAAAAAA
1 AAAA-TAAAAAA
116327 GTAAGGGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 3 0.10
22 18 0.62
23 8 0.28
ACGTcount: A:0.80, C:0.05, G:0.05, T:0.09
Consensus pattern (21 bp):
AAAATAAAAAAAAAAAGACAA
Found at i:141871 original size:49 final size:49
Alignment explanation
Indices: 141809--141908 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
141799 TTTATAAAGT
141809 TAAACTAATTTTATTGGCATCTCAATAATATCAAAATAATATTTACTAC
1 TAAACTAATTTTATTGGCATCTCAATAATATCAAAATAATATTTACTAC
*
141858 TAAACTAATTTTATTGGCATCTTAATAATATCAAAATAATATTTACTAC
1 TAAACTAATTTTATTGGCATCTCAATAATATCAAAATAATATTTACTAC
141907 TA
1 TA
141909 TGAAAGTTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (49 bp):
TAAACTAATTTTATTGGCATCTCAATAATATCAAAATAATATTTACTAC
Found at i:148064 original size:8 final size:8
Alignment explanation
Indices: 148051--148078 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
148041 TAGGTCATTT
148051 AGCTCCAA
1 AGCTCCAA
148059 AGCTCCAA
1 AGCTCCAA
148067 AGCTCCAA
1 AGCTCCAA
148075 AGCT
1 AGCT
148079 TATCATTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.36, C:0.36, G:0.14, T:0.14
Consensus pattern (8 bp):
AGCTCCAA
Found at i:153219 original size:543 final size:543
Alignment explanation
Indices: 152192--153282 Score: 2173
Period size: 543 Copynumber: 2.0 Consensus size: 543
152182 TGCTGCTACT
152192 GCTTTATGTATGTATGTATAAAATCCATAACAGATTAACAGAAGATTTTATATTATACAACAGAT
1 GCTTTATGTATGTATGTATAAAATCCATAACAGATTAACAGAAGATTTTATATTATACAACAGAT
152257 AGACACAACAATACAAAAAAAGCGTAAGCATGACATAGAATACACAAATTAACATATATGAGCAC
66 AGACACAACAATACAAAAAAAGCGTAAGCATGACATAGAATACACAAATTAACATATATGAGCAC
*
152322 CATCTGGATCTTGTAATGAAAATATGGAAAGTGAACCTTAGCTGATCCATTAGGAATAATGGAAA
131 CATCTGGATCTTGTAATGAAAATATGGAAAGTGAACCTTAGCTGATCCATAAGGAATAATGGAAA
152387 TAAAAAATCAATAGCTTGACCCAGACCAGAAACAATTTGCTCCTGTCCAAATTTCCCAGGTGCCA
196 TAAAAAATCAATAGCTTGACCCAGACCAGAAACAATTTGCTCCTGTCCAAATTTCCCAGGTGCCA
152452 TAGATACGTCCTAAATTCAATCACTACCTTTCTACTGTGGATGGATCTACAAAACCAAATCAAAA
261 TAGATACGTCCTAAATTCAATCACTACCTTTCTACTGTGGATGGATCTACAAAACCAAATCAAAA
152517 TTCCCACTTGTTACTGCTCAGGATTTTCTACCTCGGCCTCGGCTTCGTCCATACGAAGCCTTTTC
326 TTCCCACTTGTTACTGCTCAGGATTTTCTACCTCGGCCTCGGCTTCGTCCATACGAAGCCTTTTC
152582 GGACTTGATTTCAGTTTACAATCCTCCACATTGGGAGCTTTATACTTTGATGGTAGAGATGTTGG
391 GGACTTGATTTCAGTTTACAATCCTCCACATTGGGAGCTTTATACTTTGATGGTAGAGATGTTGG
152647 TGACTCGGTTTTGGACTCACAAGGCTCGGTTTCTGATGCAATCCTTGATGGCAGTTCGGAGTTTG
456 TGACTCGGTTTTGGACTCACAAGGCTCGGTTTCTGATGCAATCCTTGATGGCAGTTCGGAGTTTG
152712 GGTTCGGAACTAAGGCATTGCCA
521 GGTTCGGAACTAAGGCATTGCCA
152735 GCTTTATGTATGTATGTATAAAATCCATAACAGATTAACAGAAGATTTTATATTATACAACAGAT
1 GCTTTATGTATGTATGTATAAAATCCATAACAGATTAACAGAAGATTTTATATTATACAACAGAT
152800 AGACACAACAATACAAAAAAAGCGTAAGCATGACATAGAATACACAAATTAACATATATGAGCAC
66 AGACACAACAATACAAAAAAAGCGTAAGCATGACATAGAATACACAAATTAACATATATGAGCAC
152865 CATCTGGATCTTGTAATGAAAATATGGAAAGTGAACCTTAGCTGATCCATAAGGAATAATGGAAA
131 CATCTGGATCTTGTAATGAAAATATGGAAAGTGAACCTTAGCTGATCCATAAGGAATAATGGAAA
152930 TAAAAAATCAATAGCTTGACCCAGACCAGAAACAATTTGCTCCTGTCCAAATTTCCCAGGTGCCA
196 TAAAAAATCAATAGCTTGACCCAGACCAGAAACAATTTGCTCCTGTCCAAATTTCCCAGGTGCCA
152995 TAGATACGTCCTAAATTCAATCACTACCTTTCTACTGTGGATGGATCTACAAAACCAAATCAAAA
261 TAGATACGTCCTAAATTCAATCACTACCTTTCTACTGTGGATGGATCTACAAAACCAAATCAAAA
153060 TTCCCACTTGTTACTGCTCAGGATTTTCTACCTCGGCCTCGGCTTCGTCCATACGAAGCCTTTTC
326 TTCCCACTTGTTACTGCTCAGGATTTTCTACCTCGGCCTCGGCTTCGTCCATACGAAGCCTTTTC
153125 GGACTTGATTTCAGTTTACAATCCTCCACATTGGGAGCTTTATACTTTGATGGTAGAGATGTTGG
391 GGACTTGATTTCAGTTTACAATCCTCCACATTGGGAGCTTTATACTTTGATGGTAGAGATGTTGG
153190 TGACTCGGTTTTGGACTCACAAGGCTCGGTTTCTGATGCAATCCTTGATGGCAGTTCGGAGTTTG
456 TGACTCGGTTTTGGACTCACAAGGCTCGGTTTCTGATGCAATCCTTGATGGCAGTTCGGAGTTTG
153255 GGTTCGGAACTAAGGCATTGCCA
521 GGTTCGGAACTAAGGCATTGCCA
153278 GCTTT
1 GCTTT
153283 CTGCTGTTCC
Statistics
Matches: 547, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
543 547 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Consensus pattern (543 bp):
GCTTTATGTATGTATGTATAAAATCCATAACAGATTAACAGAAGATTTTATATTATACAACAGAT
AGACACAACAATACAAAAAAAGCGTAAGCATGACATAGAATACACAAATTAACATATATGAGCAC
CATCTGGATCTTGTAATGAAAATATGGAAAGTGAACCTTAGCTGATCCATAAGGAATAATGGAAA
TAAAAAATCAATAGCTTGACCCAGACCAGAAACAATTTGCTCCTGTCCAAATTTCCCAGGTGCCA
TAGATACGTCCTAAATTCAATCACTACCTTTCTACTGTGGATGGATCTACAAAACCAAATCAAAA
TTCCCACTTGTTACTGCTCAGGATTTTCTACCTCGGCCTCGGCTTCGTCCATACGAAGCCTTTTC
GGACTTGATTTCAGTTTACAATCCTCCACATTGGGAGCTTTATACTTTGATGGTAGAGATGTTGG
TGACTCGGTTTTGGACTCACAAGGCTCGGTTTCTGATGCAATCCTTGATGGCAGTTCGGAGTTTG
GGTTCGGAACTAAGGCATTGCCA
Found at i:164351 original size:11 final size:11
Alignment explanation
Indices: 164335--164360 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
164325 TTTGTCTAGT
164335 GGTGTGCTGAA
1 GGTGTGCTGAA
164346 GGTGTGCTGAA
1 GGTGTGCTGAA
164357 GGTG
1 GGTG
164361 GTAGGCTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.08, G:0.50, T:0.27
Consensus pattern (11 bp):
GGTGTGCTGAA
Found at i:166883 original size:18 final size:18
Alignment explanation
Indices: 166860--166895 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
166850 AACTTTCTTA
166860 GCTTCCATAATAGATGTT
1 GCTTCCATAATAGATGTT
166878 GCTTCCATAATAGATGTT
1 GCTTCCATAATAGATGTT
166896 TATGATTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (18 bp):
GCTTCCATAATAGATGTT
Found at i:178336 original size:21 final size:21
Alignment explanation
Indices: 178312--178364 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
178302 CATTGTTTTT
*
178312 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
* *
178333 AATCTCACTGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
178354 AATCTCACCGC
1 AATCTCACCGC
178365 CACCGCTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.36, G:0.09, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:179470 original size:10 final size:10
Alignment explanation
Indices: 179455--179480 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
179445 AGCTTCTCAT
179455 GAATTTACAA
1 GAATTTACAA
179465 GAATTTACAA
1 GAATTTACAA
179475 GAATTT
1 GAATTT
179481 GATGCACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (10 bp):
GAATTTACAA
Found at i:179686 original size:3 final size:3
Alignment explanation
Indices: 179678--179725 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
179668 AGAACAGAAC
* * * *
179678 TCA TCA TCA TCA TCA TCA TCT TCA TCT TCA TCT TCA TCT TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
179726 CCCAATTGTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.25, C:0.33, G:0.00, T:0.42
Consensus pattern (3 bp):
TCA
Found at i:183484 original size:30 final size:31
Alignment explanation
Indices: 183430--183491 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 31
183420 TGGGGTGATT
*
183430 TGATAAAAAAATATAAATTTAAGGACTACAAA
1 TGATAAAAAAATATAAATTAAAGGACTA-AAA
183462 TGATAAAAAAAT-TAAA-TAAAGGACTAAAA
1 TGATAAAAAAATATAAATTAAAGGACTAAAA
183491 T
1 T
183492 AAAAATTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 4 0.14
30 9 0.31
31 4 0.14
32 12 0.41
ACGTcount: A:0.61, C:0.05, G:0.10, T:0.24
Consensus pattern (31 bp):
TGATAAAAAAATATAAATTAAAGGACTAAAA
Found at i:191800 original size:7 final size:7
Alignment explanation
Indices: 191780--191817 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
191770 GCCTGCTGTG
191780 TATATG-
1 TATATGA
191786 TA-ATGA
1 TATATGA
191792 TATATGA
1 TATATGA
191799 TATATGA
1 TATATGA
191806 TATATGA
1 TATATGA
191813 TATAT
1 TATAT
191818 ATGAACATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 3 0.10
6 4 0.13
7 23 0.77
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (7 bp):
TATATGA
Found at i:200103 original size:29 final size:30
Alignment explanation
Indices: 200080--200141 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
200070 TTATAGAATT
*
200080 ACATCAAATCAAAATTTATATATAATATTA
1 ACATCAAATCAAAATTAATATATAATATTA
* *
200110 CACATTAAATCAAAATTAATATATAATTTTA
1 -ACATCAAATCAAAATTAATATATAATATTA
200141 A
1 A
200142 GATTTATCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (30 bp):
ACATCAAATCAAAATTAATATATAATATTA
Found at i:200683 original size:5 final size:5
Alignment explanation
Indices: 200673--200697 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
200663 AGAATTTATG
200673 ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA
200698 TTTTTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTTA
Found at i:200977 original size:42 final size:42
Alignment explanation
Indices: 200930--201014 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
200920 TCATCTTAGA
200930 AAGTTCAGCTAAGCAAGTGAAATAAATAAATGAGTGAACTAC
1 AAGTTCAGCTAAGCAAGTGAAATAAATAAATGAGTGAACTAC
*
200972 AAGTTCGGCTAAGCAAGTGAAATAAATAAATGAGTGAACTAC
1 AAGTTCAGCTAAGCAAGTGAAATAAATAAATGAGTGAACTAC
201014 A
1 A
201015 TAAGAATAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.21
Consensus pattern (42 bp):
AAGTTCAGCTAAGCAAGTGAAATAAATAAATGAGTGAACTAC
Found at i:206226 original size:15 final size:15
Alignment explanation
Indices: 206203--206237 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
206193 CCCTCCATCC
*
206203 GATCCCTCGCATTTA
1 GATCTCTCGCATTTA
*
206218 GATCTCTCGGATTTA
1 GATCTCTCGCATTTA
206233 GATCT
1 GATCT
206238 GACCATAGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (15 bp):
GATCTCTCGCATTTA
Found at i:215292 original size:17 final size:17
Alignment explanation
Indices: 215270--215319 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
215260 AAAAAATTTT
215270 ATTTTTATGTATTTATG
1 ATTTTTATGTATTTATG
* *
215287 ATTTTTAT-TTTTTATCC
1 ATTTTTATGTATTTAT-G
215304 A-TTTTATGTATTTATG
1 ATTTTTATGTATTTATG
215320 TGTATAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.22, C:0.04, G:0.08, T:0.66
Consensus pattern (17 bp):
ATTTTTATGTATTTATG
Found at i:215307 original size:24 final size:25
Alignment explanation
Indices: 215266--215316 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
215256 TTCAAAAAAA
**
215266 TTTTATTTTTATGTA-TTTATG-AT
1 TTTTATTTTTATCCATTTTATGTAT
215289 TTTTATTTTTTATCCATTTTATGTAT
1 TTTTA-TTTTTATCCATTTTATGTAT
215315 TT
1 TT
215317 ATGTGTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 5 0.22
24 8 0.35
25 6 0.26
26 4 0.17
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.71
Consensus pattern (25 bp):
TTTTATTTTTATCCATTTTATGTAT
Found at i:217491 original size:16 final size:16
Alignment explanation
Indices: 217470--217534 Score: 85
Period size: 16 Copynumber: 4.1 Consensus size: 16
217460 TTCGCTGTAT
217470 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
217486 TGGAATAAAGGCGTAA
1 TGGAATAGAGGCGTAA
* *
217502 TGGAATAGAAGTGTAA
1 TGGAATAGAGGCGTAA
* *
217518 TGGATTAGAGGTGTAA
1 TGGAATAGAGGCGTAA
217534 T
1 T
217535 AGCAAATCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.38, C:0.03, G:0.34, T:0.25
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:217572 original size:45 final size:43
Alignment explanation
Indices: 217512--217622 Score: 124
Period size: 45 Copynumber: 2.6 Consensus size: 43
217502 TGGAATAGAA
*
217512 GTGTAATGGATTAGAGGTGTAATAGCAAATCAAT-TGTTTGGTT
1 GTGTAATGGAATAGAGGTGTAATAGCAAATC-ATGTGTTTGGTT
* * *
217555 GAATGTAATGGAATAGAGGCGTAATAG-TATTCATGTGTTTGGTT
1 G--TGTAATGGAATAGAGGTGTAATAGCAAATCATGTGTTTGGTT
217599 G-G--ATGGAATAGAGGTGTAATAGCA
1 GTGTAATGGAATAGAGGTGTAATAGCA
217623 TAATGGAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
39 19 0.33
41 1 0.02
43 3 0.05
44 13 0.22
45 22 0.38
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.33
Consensus pattern (43 bp):
GTGTAATGGAATAGAGGTGTAATAGCAAATCATGTGTTTGGTT
Found at i:217785 original size:16 final size:16
Alignment explanation
Indices: 217748--217789 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
217738 TTAATCATAT
*
217748 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
217764 TT-AAATATATTATAA
1 TTAAAATATATTATAA
217779 TTAAAATATAT
1 TTAAAATATAT
217790 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:217796 original size:14 final size:15
Alignment explanation
Indices: 217757--217798 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
217747 TTTAAACATA
*
217757 ATTATTATTAAATAT
1 ATTATAATTAAATAT
217772 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
217786 A-TATAATTTAATA
1 ATTATAATTAAATA
217799 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:217916 original size:14 final size:15
Alignment explanation
Indices: 217867--217918 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
217857 ATAAAATATA
217867 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
217882 TATTAAATATATTAT
1 AATTAAATATATTAT
217897 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
217910 AATTTAATA
1 AATTAAATA
217919 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:218035 original size:14 final size:15
Alignment explanation
Indices: 217986--218037 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
217976 TATAAATATA
217986 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
218001 TATTAAATATATTAT
1 AATTAAATATATTAT
218016 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
218029 AATTTAATA
1 AATTAAATA
218038 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:218071 original size:119 final size:120
Alignment explanation
Indices: 217751--218153 Score: 763
Period size: 120 Copynumber: 3.4 Consensus size: 120
217741 ATCATATTTA
217751 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
217816 TATTCTTATATGAATTTACTGAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTGAAATCATAATATATGATACTATAAAATATAAATT
217871 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
217936 TATTCTTATATGAATTTACTGAAATCATAATATATGATACTAT-AAATATAAATT
66 TATTCTTATATGAATTTACTGAAATCATAATATATGATACTATAAAATATAAATT
*
217990 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
* *
218055 TATTCTTATATGAATTTACTCAAATAATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTGAAATCATAATATATGATACTATAAAATATAAATT
*
218110 AACATAATTATTATTAAATATATTATAATTAAAATATATTATTT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTT
218154 TTCATATTAT
Statistics
Matches: 278, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
119 116 0.42
120 162 0.58
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
TATTCTTATATGAATTTACTGAAATCATAATATATGATACTATAAAATATAAATT
Found at i:218146 original size:16 final size:16
Alignment explanation
Indices: 218106--218151 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
218096 ATAAAATATA
*
218106 AATTAACATA-ATTAT
1 AATTAAAATATATTAT
*
218121 TATT-AAATATATTAT
1 AATTAAAATATATTAT
218136 AATTAAAATATATTAT
1 AATTAAAATATATTAT
218152 TTTTCATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 4 0.15
15 11 0.42
16 11 0.42
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTAAAATATATTAT
Found at i:218162 original size:12 final size:11
Alignment explanation
Indices: 218144--218183 Score: 62
Period size: 12 Copynumber: 3.5 Consensus size: 11
218134 ATAATTAAAA
218144 TATATTATTTT
1 TATATTATTTT
218155 TCATATTATTTT
1 T-ATATTATTTT
218167 TGATATTATTTT
1 T-ATATTATTTT
218179 TATAT
1 TATAT
218184 CATGTATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 5 0.19
12 22 0.81
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (11 bp):
TATATTATTTT
Found at i:223261 original size:7 final size:8
Alignment explanation
Indices: 223218--223242 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
223208 ATAGAATTTC
223218 ATATTTTT
1 ATATTTTT
223226 ATATTTTT
1 ATATTTTT
223234 ATATTTTT
1 ATATTTTT
223242 A
1 A
223243 AAATGCTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
ATATTTTT
Found at i:240284 original size:4 final size:4
Alignment explanation
Indices: 240277--240315 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
240267 AATGAATGAT
* * *
240277 TAAC TAAC TAAC TAAC AAAC AAAC TAAC AAAC TAAC TAA
1 TAAC TAAC TAAC TAAC TAAC TAAC TAAC TAAC TAAC TAA
240316 TATATCCACT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.59, C:0.23, G:0.00, T:0.18
Consensus pattern (4 bp):
TAAC
Found at i:250591 original size:37 final size:35
Alignment explanation
Indices: 250516--250591 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
250506 ATCATTGTGC
* * * *
250516 CTTCATGTATTTTGTTGTGTTACTCTTGATCGTGT
1 CTTCATATAGTTTGTTGTGTTACCCTTGATCGTAT
*
250551 CTTCATATAGTTTGTTGTGCATTACCCTTGATTGTAT
1 CTTCATATAGTTTGTTGTG--TTACCCTTGATCGTAT
250588 CTTC
1 CTTC
250592 CTTAATCAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 17 0.50
37 17 0.50
ACGTcount: A:0.14, C:0.17, G:0.17, T:0.51
Consensus pattern (35 bp):
CTTCATATAGTTTGTTGTGTTACCCTTGATCGTAT
Found at i:254307 original size:25 final size:26
Alignment explanation
Indices: 254267--254316 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
254257 TTGGACTTAT
* * *
254267 TTGATCCTTTTTAATAGTATAGGGAA
1 TTGATCCTATTTAATAATAGAGGGAA
254293 TTGATCC-ATTTAATAATAGAGGGA
1 TTGATCCTATTTAATAATAGAGGGA
254317 CTAATTTGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (26 bp):
TTGATCCTATTTAATAATAGAGGGAA
Found at i:256685 original size:70 final size:71
Alignment explanation
Indices: 256595--256881 Score: 377
Period size: 71 Copynumber: 4.1 Consensus size: 71
256585 ATCGAATATG
* * * * * *
256595 ATATTTTAAACATG-TAAAAAATTTATAACTT-TTAAAATTTATTTAAACCAATCACACATTTAA
1 ATATATTAAACATGCAAAAAAATTAAAAACTTATT-AAATTTATTCAAACCAATCACACATTTTA
256658 AATATTT
65 AATATTT
* * *
256665 ATATATTAAACATGCAAAAAAATTAAAAAC--ATTAAATTTATTTATACCGATCACACATTTTAA
1 ATATATTAAACATGCAAAAAAATTAAAAACTTATTAAATTTATTCAAACCAATCACACATTTTAA
256728 ATATTT
66 ATATTT
* *
256734 ATATATTAAACATGCAAAAAAATTAAAAAACTTATTGAATTTATTCATA-CAATCACACATTTTA
1 ATATATTAAACATGCAAAAAAATT-AAAAACTTATTAAATTTATTCAAACCAATCACACATTTTA
256798 AATATTT
65 AATATTT
* * * *
256805 ATATATTAAACATACAAAAAATTTAAAAACTTATTAAATTTATTCAAACTAAGCACACATTTTAA
1 ATATATTAAACATGCAAAAAAATTAAAAACTTATTAAATTTATTCAAACCAATCACACATTTTAA
256870 ATATTT
66 ATATTT
*
256876 GTATAT
1 ATATAT
256882 ACATACATAC
Statistics
Matches: 194, Mismatches: 17, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
69 57 0.29
70 43 0.22
71 80 0.41
72 14 0.07
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (71 bp):
ATATATTAAACATGCAAAAAAATTAAAAACTTATTAAATTTATTCAAACCAATCACACATTTTAA
ATATTT
Found at i:262538 original size:17 final size:18
Alignment explanation
Indices: 262518--262552 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
262508 TTTTCCAAGA
262518 ATAAT-TTAATTTTTTAT
1 ATAATGTTAATTTTTTAT
*
262535 ATAATGTTCATTTTTTAT
1 ATAATGTTAATTTTTTAT
262553 CCATAATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (18 bp):
ATAATGTTAATTTTTTAT
Found at i:262647 original size:9 final size:9
Alignment explanation
Indices: 262621--262650 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
262611 ATGTTTTCTT
*
262621 AATTGCTGT
1 AATTGCTGC
262630 AATTGCTGC
1 AATTGCTGC
262639 AATTGCTGC
1 AATTGCTGC
262648 AAT
1 AAT
262651 AACGATCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (9 bp):
AATTGCTGC
Found at i:266103 original size:113 final size:112
Alignment explanation
Indices: 265808--266111 Score: 338
Period size: 112 Copynumber: 2.8 Consensus size: 112
265798 ACACAATTCA
* * *
265808 TTAACTTATCCAAAGTTCTATAAATATAAAATACCTTAAG-C----ACAATACGAGAAGATACAC
1 TTAACTTATCAAAAGTTCTATAAACATAAAATACCGTAAGACGAATACAATACGAGAAGATACAC
* *
265868 AAATACG-AAAAGAATACATGTATATCCAAATAAATCCAATCCACTG
66 AAATACGAAAAAGAATACATATATAACCAAATAAATCCAATCCACTG
* * ** * * *
265914 TTAACTTATCAAAAGTTCTATAAATATAAAATATCGTAAGTACGAATATTATACGAAAAAATATA
1 TTAACTTATCAAAAGTTCTATAAACATAAAATACCGTAAG-ACGAATACAATACGAGAAGATACA
* *
265979 CAAATAC-AAAAAGAATACATATATAAACCAAGTAAATCCAATCGACTG
65 CAAATACGAAAAAGAATACATATAT-AACCAAATAAATCCAATCCACTG
* * * * *
266027 TTAACTTATCAAAAGTTGTA-AAACATAGAATACCTTAAG-CGCAATTACAACACGAGAAGATGC
1 TTAACTTATCAAAAGTTCTATAAACATAAAATACCGTAAGACG-AA-TACAATACGAGAAGATAC
266090 ACAAATACGAAAAAGAATACAT
64 ACAAATACGAAAAAGAATACAT
266112 GATAAGTTCT
Statistics
Matches: 163, Mismatches: 24, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
106 37 0.23
108 1 0.01
110 2 0.01
111 2 0.01
112 69 0.42
113 52 0.32
ACGTcount: A:0.50, C:0.16, G:0.10, T:0.24
Consensus pattern (112 bp):
TTAACTTATCAAAAGTTCTATAAACATAAAATACCGTAAGACGAATACAATACGAGAAGATACAC
AAATACGAAAAAGAATACATATATAACCAAATAAATCCAATCCACTG
Found at i:271247 original size:22 final size:22
Alignment explanation
Indices: 271222--271287 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
271212 GACTTTATAT
271222 TATATTTTTTAATTATTTAAAA
1 TATATTTTTTAATTATTTAAAA
*
271244 TATA-TTTTTAA-TATATAATAAA
1 TATATTTTTTAATTAT-TTA-AAA
* *
271266 TATTTTTTTTAATGATTTAAAA
1 TATATTTTTTAATTATTTAAAA
271288 ATTGATTCGG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
20 3 0.08
21 9 0.25
22 13 0.36
23 9 0.25
24 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TATATTTTTTAATTATTTAAAA
Found at i:271268 original size:20 final size:21
Alignment explanation
Indices: 271222--271272 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
271212 GACTTTATAT
*
271222 TATATTTTTTAATTATTTAAAA
1 TATA-TTTTTAATTATATAAAA
271244 TATATTTTTAA-TATATAATAA
1 TATATTTTTAATTATATAA-AA
271265 -ATATTTTT
1 TATATTTTT
271273 TTTAATGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 14 0.52
21 9 0.33
22 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATATTTTTAATTATATAAAA
Found at i:273247 original size:24 final size:23
Alignment explanation
Indices: 273220--273285 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 23
273210 TTTATGTTAG
273220 ATTAAAAACTAAACTAGTCTTTCT
1 ATTAAAAA-TAAACTAGTCTTTCT
* * *
273244 ATTAAAAATTATA-TA-TATTTTT
1 ATTAAAAA-TAAACTAGTCTTTCT
273266 ATTAAAAATAAACTTAGTCT
1 ATTAAAAATAAAC-TAGTCT
273286 AATATTGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
21 3 0.09
22 13 0.39
23 4 0.12
24 13 0.39
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.42
Consensus pattern (23 bp):
ATTAAAAATAAACTAGTCTTTCT
Found at i:284958 original size:78 final size:78
Alignment explanation
Indices: 284791--284950 Score: 232
Period size: 78 Copynumber: 2.1 Consensus size: 78
284781 TTGTGTTATT
* **
284791 TTTGCATATTTTCATGTTATAGTAGTGTTAAAGGTGTTTTACATTTGGTATAAAGCTCGATATTT
1 TTTGTATATTTTCATGTTATAGTAGTGTTAAAGGTGTTTTACATTTGGTATAAAGCTCGATATCG
284856 GATAATTAGTACA
66 GATAATTAGTACA
* * * * *
284869 TTTGTATATTTTCATGTTATAGTAGTGTTAAAGGTGTTTTGCATTT-GTTTAAAGTTTGATGTCG
1 TTTGTATATTTTCATGTTATAGTAGTGTTAAAGGTGTTTTACATTTGGTATAAAGCTCGATATCG
*
284933 GATACTTAGTACA
66 GATAATTAGTACA
284946 TTTGT
1 TTTGT
284951 GTTATTTTTG
Statistics
Matches: 73, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
77 29 0.40
78 44 0.60
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.47
Consensus pattern (78 bp):
TTTGTATATTTTCATGTTATAGTAGTGTTAAAGGTGTTTTACATTTGGTATAAAGCTCGATATCG
GATAATTAGTACA
Found at i:286506 original size:21 final size:21
Alignment explanation
Indices: 286480--286520 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
286470 TTGATTTGTT
286480 AATTTTATGCGAAATTGATCA
1 AATTTTATGCGAAATTGATCA
286501 AATTTTATGCGAAATTGATC
1 AATTTTATGCGAAATTGATC
286521 TTGAATTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.39
Consensus pattern (21 bp):
AATTTTATGCGAAATTGATCA
Found at i:297042 original size:23 final size:23
Alignment explanation
Indices: 296999--297042 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
296989 TGTGTAAAAT
*
296999 AAATAAATTCATTTTTCAAAACC
1 AAATAAATTCAATTTTCAAAACC
297022 AAATAAATTCAAATTTT-AAAA
1 AAATAAATTC-AATTTTCAAAA
297043 TAATTATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (23 bp):
AAATAAATTCAATTTTCAAAACC
Found at i:297140 original size:9 final size:9
Alignment explanation
Indices: 297094--297148 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
297084 CAATATTTAG
297094 TTTCAAATT
1 TTTCAAATT
**
297103 TGACAAATT
1 TTTCAAATT
*
297112 TTTCACATT
1 TTTCAAATT
* *
297121 TTTTAATTT
1 TTTCAAATT
297130 TTTCAAATT
1 TTTCAAATT
*
297139 TTACAAATT
1 TTTCAAATT
297148 T
1 T
297149 GACAATTCTT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.55
Consensus pattern (9 bp):
TTTCAAATT
Found at i:303828 original size:18 final size:18
Alignment explanation
Indices: 303798--303832 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
303788 TAAAGGTGTT
303798 TATAATAAAATTAAAATG
1 TATAATAAAATTAAAATG
303816 TATAA-AAATATTAAAAT
1 TATAATAAA-ATTAAAAT
303833 AAAATTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
TATAATAAAATTAAAATG
Found at i:327393 original size:22 final size:20
Alignment explanation
Indices: 327363--327404 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
327353 ACAATTTGTA
327363 AATAATAAATTTATATATTAAT
1 AATAATAAA--TATATATTAAT
*
327385 AATATTAAATATATATTAAT
1 AATAATAAATATATATTAAT
327405 TTTATTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAATAAATATATATTAAT
Found at i:341021 original size:18 final size:17
Alignment explanation
Indices: 340983--341044 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 17
340973 CGAAAGGGAG
340983 AGGGAAAGAGAAGAG--
1 AGGGAAAGAGAAGAGAA
340998 AGGGAAAGAGAGAGAGAA
1 AGGGAAAGAGA-AGAGAA
* *
341016 AGGGAAAGGGAAAGGGAA
1 AGGGAAAGAG-AAGAGAA
*
341034 AGAGAAAGAGA
1 AGGGAAAGAGA
341045 TTTCAATGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 11 0.28
16 4 0.10
17 1 0.03
18 22 0.56
19 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (17 bp):
AGGGAAAGAGAAGAGAA
Found at i:341022 original size:6 final size:6
Alignment explanation
Indices: 340974--341041 Score: 55
Period size: 6 Copynumber: 10.8 Consensus size: 6
340964 GGAAGAAGAC
* * * * *
340974 GAAAGG GAGAGG GAAAGAG AAGAGAGG GAAAGA GAGAGA GAAAGG GAAAGG
1 GAAAGG GAAAGG GAAAG-G --GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG
*
341025 GAAAGG GAAAGA GAAAG
1 GAAAGG GAAAGG GAAAG
341042 AGATTTCAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
6 44 0.88
7 1 0.02
8 1 0.02
9 4 0.08
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (6 bp):
GAAAGG
Found at i:353111 original size:18 final size:18
Alignment explanation
Indices: 353088--353124 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
353078 AATTTATTGT
*
353088 ATAAAATAATAA-ATTTA
1 ATAAAAAAATAATATTTA
353105 ATAAAAAAATAATATTTA
1 ATAAAAAAATAATATTTA
353123 AT
1 AT
353125 GAGTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAAAAAAATAATATTTA
Found at i:365709 original size:25 final size:25
Alignment explanation
Indices: 365679--365728 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
365669 ATGAGTAAAC
365679 AAATAAACTCAAGCTCTTCTTTCTT
1 AAATAAACTCAAGCTCTTCTTTCTT
365704 AAATAAACTCAAGCTCTTCTTTCTT
1 AAATAAACTCAAGCTCTTCTTTCTT
365729 TTTTTGCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (25 bp):
AAATAAACTCAAGCTCTTCTTTCTT
Found at i:367918 original size:30 final size:31
Alignment explanation
Indices: 367884--367944 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
367874 TTTTGTGATA
*
367884 AATATTAAATTT-ATACAT-AATCTTTGATTT
1 AATATGAAATTTAATACATAAAT-TTTGATTT
* *
367914 AATATGCAATTTAATACGTAAATTTTGATTT
1 AATATGAAATTTAATACATAAATTTTGATTT
367945 GATGCAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 10 0.38
31 13 0.50
32 3 0.12
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (31 bp):
AATATGAAATTTAATACATAAATTTTGATTT
Found at i:369707 original size:38 final size:39
Alignment explanation
Indices: 369623--369757 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
369613 ACCAATATGG
*
369623 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
369662 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
369700 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
369741 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
369758 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
38 19 0.25
39 36 0.48
40 4 0.05
41 16 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:374421 original size:31 final size:31
Alignment explanation
Indices: 374369--374427 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
374359 TTAAAGGAGC
* * *
374369 AAATTAAAATTTTCAACAAATTTCAAGAAAA
1 AAATAAAAAATTTCAAAAAATTTCAAGAAAA
*
374400 AAATAAAAAATTTCAAAAAATTTGAAGA
1 AAATAAAAAATTTCAAAAAATTTCAAGA
374428 CCAAGATCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.27
Consensus pattern (31 bp):
AAATAAAAAATTTCAAAAAATTTCAAGAAAA
Found at i:375986 original size:15 final size:16
Alignment explanation
Indices: 375966--376002 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
375956 GGTACTTGAT
375966 GAATAATGAAGAATC-
1 GAATAATGAAGAATCG
375981 GAATAATGAAGAATCG
1 GAATAATGAAGAATCG
375997 GAATAA
1 GAATAA
376003 CATAGACCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.54, C:0.05, G:0.22, T:0.19
Consensus pattern (16 bp):
GAATAATGAAGAATCG
Found at i:378795 original size:11 final size:11
Alignment explanation
Indices: 378727--378817 Score: 56
Period size: 11 Copynumber: 7.6 Consensus size: 11
378717 AAAATACCTT
* *
378727 TAAAATAGTAG
1 TAAAATAATAA
*
378738 TAAAATCAACAA
1 TAAAAT-AATAA
378750 TAAAATAATAA
1 TAAAATAATAA
*
378761 TTATACAATATCTAAA
1 -TA-A-AATA-AT-AA
378777 TAATAATAATAA
1 TAA-AATAATAA
*
378789 TAAAATAATAG
1 TAAAATAATAA
* *
378800 CAACATAATAA
1 TAAAATAATAA
378811 TAAAATA
1 TAAAATA
378818 TACTAAACAA
Statistics
Matches: 61, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
11 30 0.49
12 15 0.25
13 2 0.03
14 9 0.15
15 3 0.05
16 2 0.03
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:379513 original size:60 final size:60
Alignment explanation
Indices: 379435--379587 Score: 150
Period size: 60 Copynumber: 2.5 Consensus size: 60
379425 ATTAAATGTG
* ** * *
379435 CCAATTTAAATCAAAAAGCCAAGTTT-AGGTACCGAATCAAACCAAAA-TAAACTTTAGATA
1 CCAAATTAAATCTTAAAGCCAA-TTTCAAGTACCGAATCAAA-CAAAAGAAAACTTTAGATA
* * * *
379495 TCAAATTAAATCTTAAAGCCAATTTCAAGTACCTAATTAGACAAAAGAAAACTTTAGATA
1 CCAAATTAAATCTTAAAGCCAATTTCAAGTACCGAATCAAACAAAAGAAAACTTTAGATA
* * *
379555 CCAATTTAAA-CTTTAAAGCCAAATGCAAGTACC
1 CCAAATTAAATC-TTAAAGCCAATTTCAAGTACC
379588 AAAATGTATA
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
59 9 0.12
60 68 0.88
ACGTcount: A:0.47, C:0.18, G:0.09, T:0.25
Consensus pattern (60 bp):
CCAAATTAAATCTTAAAGCCAATTTCAAGTACCGAATCAAACAAAAGAAAACTTTAGATA
Found at i:382044 original size:33 final size:33
Alignment explanation
Indices: 381997--382061 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
381987 ATCTTATCTG
*
381997 GCATTATCAATGGTGATTTAATGCTT-TTTTTTA
1 GCATGATCAATGGTGATTTAATG-TTGTTTTTTA
382030 GCATGATCAATGGTGATTTAATGTTGTTTTTT
1 GCATGATCAATGGTGATTTAATGTTGTTTTTT
382062 CCACCCTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 2 0.07
33 28 0.93
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.51
Consensus pattern (33 bp):
GCATGATCAATGGTGATTTAATGTTGTTTTTTA
Found at i:384986 original size:16 final size:16
Alignment explanation
Indices: 384965--385004 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
384955 AGAAAGTCTT
384965 TTTAAAAATAAATTTA
1 TTTAAAAATAAATTTA
**
384981 TTT-AAAATATTTTTA
1 TTTAAAAATAAATTTA
384996 TTTAAAAAT
1 TTTAAAAAT
385005 TTGGTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTAAAAATAAATTTA
Found at i:397191 original size:19 final size:19
Alignment explanation
Indices: 397167--397204 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
397157 ACCCTGATTG
*
397167 TCTTCCACAAATGTTTTGA
1 TCTTCCACAAATGTCTTGA
*
397186 TCTTCCACGAATGTCTTGA
1 TCTTCCACAAATGTCTTGA
397205 CATTAGGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (19 bp):
TCTTCCACAAATGTCTTGA
Found at i:409339 original size:12 final size:12
Alignment explanation
Indices: 409322--409346 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
409312 AGCAAACCAG
409322 GAAATTTGCTTC
1 GAAATTTGCTTC
409334 GAAATTTGCTTC
1 GAAATTTGCTTC
409346 G
1 G
409347 TAAAAAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (12 bp):
GAAATTTGCTTC
Found at i:411166 original size:48 final size:49
Alignment explanation
Indices: 411110--411207 Score: 180
Period size: 48 Copynumber: 2.0 Consensus size: 49
411100 TGGGCTAAAG
411110 TTAGATTCGATCCTGAATTTTGTTTTATTTTCTA-TTTTTTATGTTAAT
1 TTAGATTCGATCCTGAATTTTGTTTTATTTTCTATTTTTTTATGTTAAT
*
411158 TTAGATTCGATCCTGAATTTTGTTTTATTTTCTATTTTTTTATTTTAAT
1 TTAGATTCGATCCTGAATTTTGTTTTATTTTCTATTTTTTTATGTTAAT
411207 T
1 T
411208 AAAAAAACAT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 34 0.71
49 14 0.29
ACGTcount: A:0.20, C:0.08, G:0.09, T:0.62
Consensus pattern (49 bp):
TTAGATTCGATCCTGAATTTTGTTTTATTTTCTATTTTTTTATGTTAAT
Found at i:426895 original size:11 final size:11
Alignment explanation
Indices: 426879--426911 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
426869 ATTTTAAATA
426879 ATTTAATAATT
1 ATTTAATAATT
426890 ATTTAATAATT
1 ATTTAATAATT
*
426901 TTTTAA-AATT
1 ATTTAATAATT
426911 A
1 A
426912 AGTGACTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTTAATAATT
Found at i:431576 original size:22 final size:22
Alignment explanation
Indices: 431560--431605 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
431550 TATAAGTACA
431560 ATTAGGATTAATAATAAATAAT
1 ATTAGGATTAATAATAAATAAT
431582 ATTAGGATTAATAATAAATAAT
1 ATTAGGATTAATAATAAATAAT
431604 AT
1 AT
431606 ACATTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (22 bp):
ATTAGGATTAATAATAAATAAT
Found at i:439341 original size:23 final size:21
Alignment explanation
Indices: 439294--439342 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
439284 TCTTTCAATT
* **
439294 GTTTTTTTTTTTGGTGATATT
1 GTTTTTTTTTTTGGTGAGAAA
439315 GTTTGTTTTTTTTGGTTGAGAAA
1 GTTT-TTTTTTTTGG-TGAGAAA
439338 GTTTT
1 GTTTT
439343 GATATTTGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 4 0.17
22 11 0.48
23 8 0.35
ACGTcount: A:0.12, C:0.00, G:0.22, T:0.65
Consensus pattern (21 bp):
GTTTTTTTTTTTGGTGAGAAA
Found at i:446556 original size:45 final size:45
Alignment explanation
Indices: 446492--446581 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
446482 AAAAAAAGGT
446492 GAGGAATGATATAGTAAATTTCTTTAAATTGTTCTTCATGAGTTA
1 GAGGAATGATATAGTAAATTTCTTTAAATTGTTCTTCATGAGTTA
446537 GAGGAATGATATAGTAAATTTCTTTAAATTGTTCTTCATGAGTTA
1 GAGGAATGATATAGTAAATTTCTTTAAATTGTTCTTCATGAGTTA
446582 ATATTTAGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (45 bp):
GAGGAATGATATAGTAAATTTCTTTAAATTGTTCTTCATGAGTTA
Found at i:446896 original size:12 final size:12
Alignment explanation
Indices: 446879--446906 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
446869 TTTTAAAACA
446879 TTATATTTATTT
1 TTATATTTATTT
446891 TTATATTTATTT
1 TTATATTTATTT
446903 TTAT
1 TTAT
446907 TTAATAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
TTATATTTATTT
Found at i:458567 original size:17 final size:17
Alignment explanation
Indices: 458535--458569 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
458525 CAAAAATTAA
458535 ATTATTTATATAATTTT
1 ATTATTTATATAATTTT
458552 ATTATTTAT-TATATTTT
1 ATTATTTATATA-ATTTT
458569 A
1 A
458570 AAATTTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTATTTATATAATTTT
Found at i:459117 original size:3 final size:3
Alignment explanation
Indices: 459109--459150 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
459099 TTTAGGGAAC
*
459109 TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
459151 CAGGGGCGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:462737 original size:21 final size:21
Alignment explanation
Indices: 462711--462751 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
462701 ATCTGCTCAA
* *
462711 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
462732 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
462752 TTGCTCATCT
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:481647 original size:12 final size:12
Alignment explanation
Indices: 481630--481654 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
481620 GGTGTTCAGT
481630 CGGTTAACCGAC
1 CGGTTAACCGAC
481642 CGGTTAACCGAC
1 CGGTTAACCGAC
481654 C
1 C
481655 CGAAATTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:481829 original size:9 final size:9
Alignment explanation
Indices: 481815--481951 Score: 202
Period size: 9 Copynumber: 14.6 Consensus size: 9
481805 TTTGGTTAAA
481815 AATTACCCG
1 AATTACCCG
481824 AATTACCCG
1 AATTACCCG
481833 AATTACCCG
1 AATTACCCG
*
481842 ACTTACCCG
1 AATTACCCG
481851 AATTACCCG
1 AATTACCCG
481860 AATTACCCG
1 AATTACCCG
481869 AATTACCCG
1 AATTACCCG
481878 AATTACCCG
1 AATTACCCG
*
481887 AAAATTACCCA
1 --AATTACCCG
481898 AATTACCCG
1 AATTACCCG
481907 AATTACCCG
1 AATTACCCG
481916 AAAATTACCCG
1 --AATTACCCG
481927 AAAATTACCCG
1 --AATTACCCG
481938 AATTACCCG
1 AATTACCCG
481947 AATTA
1 AATTA
481952 AATCACTACA
Statistics
Matches: 120, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
9 92 0.77
11 28 0.23
ACGTcount: A:0.37, C:0.31, G:0.09, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:481980 original size:17 final size:17
Alignment explanation
Indices: 481958--482018 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
481948 ATTAAATCAC
481958 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
481975 TACATAAATCTTTGAATCAC
1 TACAT-AA--TTAAAAACAT
*
481995 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
482012 TACATAA
1 TACATAA
482019 GTCTTTGAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 17 0.53
18 2 0.06
19 2 0.06
20 11 0.34
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Done.