Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008402.1 Hibiscus syriacus cultivar Beakdansim tig00111171_pilon, 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: 226027
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1332 original size:16 final size:16
Alignment explanation
Indices: 1311--1341 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1301 TAATATTGAA
1311 ACTTGAACTCAAAAAG
1 ACTTGAACTCAAAAAG
1327 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
1342 AATTAGAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTCAAAAAG
Found at i:10286 original size:26 final size:26
Alignment explanation
Indices: 10257--10312 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
10247 TTCCATGAAA
10257 CAACCAATACTTTCTATAGCACGATT
1 CAACCAATACTTTCTATAGCACGATT
10283 CAACCAATACTTTCTATAGCACGATT
1 CAACCAATACTTTCTATAGCACGATT
10309 CAAC
1 CAAC
10313 AATCCTCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (26 bp):
CAACCAATACTTTCTATAGCACGATT
Found at i:12943 original size:79 final size:79
Alignment explanation
Indices: 12812--12970 Score: 291
Period size: 79 Copynumber: 2.0 Consensus size: 79
12802 CTATACGCCA
* *
12812 TACCTCTGTTTTCAATGTTTAGTTAAGACGGCTAGCACTCCATAAAGAGTTGCATACACATCCCA
1 TACCTCTGTTTTCAATGTTCAGTTAAGACGGCTAGCACTCCATAAACAGTTGCATACACATCCCA
12877 AGTCACAAGTATTG
66 AGTCACAAGTATTG
*
12891 TACCTCTGTTTTCATTGTTCAGTTAAGACGGCTAGCACTCCATAAACAGTTGCATACACATCCCA
1 TACCTCTGTTTTCAATGTTCAGTTAAGACGGCTAGCACTCCATAAACAGTTGCATACACATCCCA
12956 AGTCACAAGTATTG
66 AGTCACAAGTATTG
12970 T
1 T
12971 TAATTAATCT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.31
Consensus pattern (79 bp):
TACCTCTGTTTTCAATGTTCAGTTAAGACGGCTAGCACTCCATAAACAGTTGCATACACATCCCA
AGTCACAAGTATTG
Found at i:13672 original size:20 final size:22
Alignment explanation
Indices: 13636--13677 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
13626 ATTATTTATA
13636 TTTTATCTTTATGTTTA-TTTT
1 TTTTATCTTTATGTTTACTTTT
13657 TTTTAT-TTCTAT-TTTACTTTT
1 TTTTATCTT-TATGTTTACTTTT
13678 AGAAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTTATCTTTATGTTTACTTTT
Found at i:13678 original size:26 final size:26
Alignment explanation
Indices: 13621--13678 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
13611 AAACAATGCC
13621 CTTTTATTATTTATATTTTATCTTTA
1 CTTTTATTATTTATATTTTATCTTTA
* *
13647 -TGTTTATTTTTTTTATTTCTAT-TTTA
1 CT-TTTATTATTTATATTT-TATCTTTA
13673 CTTTTA
1 CTTTTA
13679 GAAAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
25 1 0.04
26 22 0.81
27 4 0.15
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (26 bp):
CTTTTATTATTTATATTTTATCTTTA
Found at i:15324 original size:19 final size:19
Alignment explanation
Indices: 15297--15336 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
15287 TATGCCGTAT
* * *
15297 ATATTAATTAATAATTTAA
1 ATATAAATTAAAAAATTAA
15316 ATATAAATTAAAAAATTAA
1 ATATAAATTAAAAAATTAA
15335 AT
1 AT
15337 TTATCAAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATAAATTAAAAAATTAA
Found at i:29084 original size:7 final size:7
Alignment explanation
Indices: 29072--29105 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
29062 GAGATAGTAT
29072 TTTAAAA
1 TTTAAAA
29079 TTTAAAA
1 TTTAAAA
29086 TTTAAAA
1 TTTAAAA
*
29093 TTTAAGA
1 TTTAAAA
29100 TTTAAA
1 TTTAAA
29106 TAGCTAGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (7 bp):
TTTAAAA
Found at i:32945 original size:33 final size:33
Alignment explanation
Indices: 32902--32993 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
32892 CCCATCTAAT
*
32902 TCATCTTCGCTATCATTAGCATCTCCTCTCTCC
1 TCATCCTCGCTATCATTAGCATCTCCTCTCTCC
32935 TCATCCTCGCTATCATTAGCATCTCCTCTCTCC
1 TCATCCTCGCTATCATTAGCATCTCCTCTCTCC
32968 TCATCCTCGCTATCATTAGCATCTCC
1 TCATCCTCGCTATCATTAGCATCTCC
32994 AGCAGCATCT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.16, C:0.40, G:0.07, T:0.37
Consensus pattern (33 bp):
TCATCCTCGCTATCATTAGCATCTCCTCTCTCC
Found at i:34307 original size:25 final size:25
Alignment explanation
Indices: 34261--34316 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
34251 TATATTTCTT
*
34261 TATATTTTTCATATATGAAATACATA
1 TATATTTTTCATATAT-AAATACACA
34287 TATATTTCTTCATATAT-AATACACA
1 TATATTT-TTCATATATAAATACACA
34312 TATAT
1 TATAT
34317 CATGCAAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 12 0.43
26 7 0.25
27 9 0.32
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.46
Consensus pattern (25 bp):
TATATTTTTCATATATAAATACACA
Found at i:40452 original size:21 final size:21
Alignment explanation
Indices: 40427--40467 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
40417 AAAGATTAAA
*
40427 AAATATTAATATTTTAAATAG
1 AAATAATAATATTTTAAATAG
40448 AAATAATAATATTTTAAATA
1 AAATAATAATATTTTAAATA
40468 ATTTTCTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AAATAATAATATTTTAAATAG
Found at i:42698 original size:18 final size:18
Alignment explanation
Indices: 42675--42711 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
42665 TGACCGATCA
42675 TAACCCGACCCGACCCGT
1 TAACCCGACCCGACCCGT
42693 TAACCCGACCCGACCCGT
1 TAACCCGACCCGACCCGT
42711 T
1 T
42712 GACCGTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.49, G:0.16, T:0.14
Consensus pattern (18 bp):
TAACCCGACCCGACCCGT
Found at i:45218 original size:24 final size:24
Alignment explanation
Indices: 45191--45281 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
45181 TCAAATTTGA
* *
45191 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* * *
45215 ATTCTGATCTGATA-TTCACATGG
1 ATTCTGATATGATACTTGACCTGG
* * *
45238 ATTCTGATCTGACACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
45262 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
45282 TTGAATTATG
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 19 0.35
24 35 0.65
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:45407 original size:35 final size:35
Alignment explanation
Indices: 45359--45433 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
45349 TGGAGGAAGA
* *
45359 TTACTTGGAGGTTCCTCAGTTGTATGCTCAGGGCC
1 TTACTTAGAGGTTCCTCAGCTGTATGCTCAGGGCC
* * *
45394 TTACTTAGCGGTTCCTCGGCTGTGTGCTCAGGGCC
1 TTACTTAGAGGTTCCTCAGCTGTATGCTCAGGGCC
45429 TTACT
1 TTACT
45434 GGACGTGAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.12, C:0.25, G:0.28, T:0.35
Consensus pattern (35 bp):
TTACTTAGAGGTTCCTCAGCTGTATGCTCAGGGCC
Found at i:52066 original size:18 final size:16
Alignment explanation
Indices: 52041--52080 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
52031 CCAACCTATT
*
52041 TTTAATTATATATTATA
1 TTTAATTACATATT-TA
52058 TTGTAATTACATATTTA
1 TT-TAATTACATATTTA
52075 TTTAAT
1 TTTAAT
52081 ATTTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 4 0.19
17 6 0.29
18 11 0.52
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (16 bp):
TTTAATTACATATTTA
Found at i:52108 original size:12 final size:12
Alignment explanation
Indices: 52077--52118 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
52067 CATATTTATT
*
52077 TAATATTTAAAA
1 TAATAATTAAAA
52089 T-A-AATTAAAA
1 TAATAATTAAAA
52099 TAATAATTAAAA
1 TAATAATTAAAA
52111 TAAATAAT
1 T-AATAAT
52119 AATATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 8 0.31
11 2 0.08
12 10 0.38
13 6 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAATAATTAAAA
Found at i:52130 original size:22 final size:22
Alignment explanation
Indices: 52077--52127 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
52067 CATATTTATT
52077 TAATATTTAAAATAAATTAAAA
1 TAATATTTAAAATAAATTAAAA
*
52099 TAATAATTAAAATAAA-TAATAA
1 TAATATTTAAAATAAATTAA-AA
52121 T-ATATTT
1 TAATATTT
52128 TAAGTCAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TAATATTTAAAATAAATTAAAA
Found at i:53770 original size:18 final size:18
Alignment explanation
Indices: 53731--53778 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
53721 AATATATTTA
*
53731 AAAACAATAAAAAAAATG
1 AAAACAATAAAATAAATG
*
53749 AAAACATATAAAATAACT-
1 AAAACA-ATAAAATAAATG
53767 AAAA-AATAAAAT
1 AAAACAATAAAAT
53779 TAAAAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 7 0.26
17 1 0.04
18 10 0.37
19 9 0.33
ACGTcount: A:0.75, C:0.06, G:0.02, T:0.17
Consensus pattern (18 bp):
AAAACAATAAAATAAATG
Found at i:53771 original size:19 final size:18
Alignment explanation
Indices: 53729--53771 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
53719 ACAATATATT
53729 TAAAAACAATAAAAAAAA
1 TAAAAACAATAAAAAAAA
* * *
53747 TGAAAACATATAAAATAAC
1 TAAAAACA-ATAAAAAAAA
53766 TAAAAA
1 TAAAAA
53772 ATAAAATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.16
Consensus pattern (18 bp):
TAAAAACAATAAAAAAAA
Found at i:55043 original size:3 final size:3
Alignment explanation
Indices: 55035--55137 Score: 145
Period size: 3 Copynumber: 34.7 Consensus size: 3
55025 TTAATATATT
* * *
55035 TAA TAA TAA -AA TAA TAA TAA AAA TAA TAA TAA AAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
55082 TAA TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55130 TAA TAA TA
1 TAA TAA TA
55138 TGGATAAAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
2 2 0.02
3 85 0.98
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:55499 original size:118 final size:118
Alignment explanation
Indices: 55292--55819 Score: 881
Period size: 118 Copynumber: 4.5 Consensus size: 118
55282 TTCTCCAGAT
* ** * *
55292 GAGTTCTTCTCATTACGAA--CTTTCTGCTGGGGATGATGTTCCATCAAATGATGAATTCAAGCA
1 GAGTTCTTCTCATTATGAACTCTTTCT-CTGGAAATGATGATCCATCAAGTGATGAATTCAAGCA
*
55355 AAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
65 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
55409 GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAA
1 GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAA
55474 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
66 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
*
55527 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAA
1 GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAA
55592 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
66 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
*
55645 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAA
1 GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAA
* *
55710 AAGGTTGAACAAGTTCTTCTCGTTATGAACTTCCTCTTCCTTCTTCAGAT---
66 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* *
55760 GAGTTCTTCTCATTATGAA--CTTTCTCTGGAAAAGAATGATCCATCAAGTGATGGATTCAA
1 GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATG-ATGATCCATCAAGTGATGAATTCAA
55820 ATCTTTGCTA
Statistics
Matches: 396, Mismatches: 12, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
113 13 0.03
114 24 0.06
115 19 0.05
117 18 0.05
118 316 0.80
119 6 0.02
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (118 bp):
GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAA
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
Found at i:56566 original size:83 final size:83
Alignment explanation
Indices: 56463--56835 Score: 667
Period size: 83 Copynumber: 4.5 Consensus size: 83
56453 CTTACCAAAA
56463 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
56528 TGATTGATTCTGTCCAAC
66 TGATTGATTCTGTCCAAC
* * *
56546 TATATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
56611 TGATTGATTCTGTCCAAC
66 TGATTGATTCTGTCCAAC
* *
56629 CATATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
*
56694 TGATTGGTTCTGTCCAAC
66 TGATTGATTCTGTCCAAC
56712 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
*
56777 TGATTGGTTCTG-CCAAAC
66 TGATTGATTCTGTCC-AAC
56795 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
56836 CTGTCTAACC
Statistics
Matches: 282, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
82 2 0.01
83 280 0.99
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
TGATTGATTCTGTCCAAC
Found at i:56939 original size:133 final size:133
Alignment explanation
Indices: 56701--57018 Score: 627
Period size: 133 Copynumber: 2.4 Consensus size: 133
56691 CAATGATTGG
*
56701 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCT
1 TTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCT
56766 TCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
66 TCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
56831 CTA
131 CTA
56834 TTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCT
1 TTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCT
56899 TCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
66 TCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
56964 CTA
131 CTA
56967 TTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 TTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
57019 CTGTCTAACC
Statistics
Matches: 184, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 184 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (133 bp):
TTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCT
TCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
CTA
Found at i:56979 original size:50 final size:50
Alignment explanation
Indices: 56925--57168 Score: 488
Period size: 50 Copynumber: 4.9 Consensus size: 50
56915 GGTTCTGCCA
56925 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
56975 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
57025 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
57075 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
57125 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
57169 AGTCTCTTTC
Statistics
Matches: 194, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 194 1.00
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.23
Consensus pattern (50 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
Found at i:58365 original size:17 final size:17
Alignment explanation
Indices: 58300--58383 Score: 57
Period size: 17 Copynumber: 4.8 Consensus size: 17
58290 CCTTGACCCT
*
58300 TTTCTTTTTCTATTATT-
1 TTTCTTTTTCT-TTTTTC
*
58317 TTTCTTCTTCTTTTTTTC
1 TTTCTTTTTC-TTTTTTC
***
58335 TTTTCCCCTT-TTTTTTC
1 -TTTCTTTTTCTTTTTTC
58352 TTTCTTTTTC-TTTTTC
1 TTTCTTTTTCTTTTTTC
58368 TCTTCTTCTTTCTTTT
1 T-TTCTT-TTTCTTTT
58384 CTTCAAGCAT
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
16 13 0.25
17 25 0.47
18 5 0.09
19 10 0.19
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTCTTTTTCTTTTTTC
Found at i:58379 original size:28 final size:28
Alignment explanation
Indices: 58300--58382 Score: 79
Period size: 27 Copynumber: 3.1 Consensus size: 28
58290 CCTTGACCCT
58300 TTTCTTTTTCTATTATT-T-TTCTTC-TTC
1 TTTCTTTTTCT-TT-TTCTCTTCTTCTTTC
* * *
58327 -TT-TTTTTCTTTTCCCCTT-TTTTTTC
1 TTTCTTTTTCTTTTTCTCTTCTTCTTTC
58352 TTTCTTTTTCTTTTTCTCTTCTTCTTTC
1 TTTCTTTTTCTTTTTCTCTTCTTCTTTC
58380 TTT
1 TTT
58383 TCTTCAAGCA
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
23 1 0.02
24 4 0.09
25 12 0.27
26 4 0.09
27 14 0.32
28 9 0.20
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (28 bp):
TTTCTTTTTCTTTTTCTCTTCTTCTTTC
Found at i:58384 original size:17 final size:16
Alignment explanation
Indices: 58298--58386 Score: 69
Period size: 16 Copynumber: 5.5 Consensus size: 16
58288 CACCTTGACC
58298 CTTTTCTTT-TTCTATT
1 CTTTTCTTTCTTCT-TT
*
58314 ATTTT-TCTTCTTCTTT
1 CTTTTCT-TTCTTCTTT
**
58330 -TTTTCTTTTCCCCTTT
1 CTTTTC-TTTCTTCTTT
*
58346 TTTTTCTTTCTT-TTT
1 CTTTTCTTTCTTCTTT
58361 CTTTTTCTCTTCTTCTTT
1 C-TTTTCT-TTCTTCTTT
58379 CTTTTCTT
1 CTTTTCTT
58387 CAAGCATAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
15 8 0.14
16 26 0.44
17 21 0.36
18 4 0.07
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.75
Consensus pattern (16 bp):
CTTTTCTTTCTTCTTT
Found at i:68933 original size:18 final size:18
Alignment explanation
Indices: 68910--68953 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
68900 AAAATGCTTG
68910 TAAATAAAATAAAACAT-A
1 TAAATAAAATAAAA-ATAA
**
68928 TAAATATTATAAAAATAA
1 TAAATAAAATAAAAATAA
68946 TAAATAAA
1 TAAATAAA
68954 TAATTTGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
TAAATAAAATAAAAATAA
Found at i:71057 original size:3 final size:3
Alignment explanation
Indices: 71049--71151 Score: 154
Period size: 3 Copynumber: 34.7 Consensus size: 3
71039 TTAATATATT
* *
71049 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA AAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
71096 TAA TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
71144 TAA TAA TA
1 TAA TAA TA
71152 TGGATAAAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
2 2 0.02
3 87 0.98
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:73476 original size:16 final size:16
Alignment explanation
Indices: 73452--73482 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
73442 TTAGTTCTCT
*
73452 ATTTTTGTTTTTTTTA
1 ATTTGTGTTTTTTTTA
73468 ATTTGTGTTTTTTTT
1 ATTTGTGTTTTTTTT
73483 CATTGGAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.81
Consensus pattern (16 bp):
ATTTGTGTTTTTTTTA
Found at i:81069 original size:19 final size:19
Alignment explanation
Indices: 81045--81087 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
81035 GCAACTATAC
81045 ACAGTTTGACAAGTCATCA
1 ACAGTTTGACAAGTCATCA
*
81064 ACAGTTTGACAAGTCGTCA
1 ACAGTTTGACAAGTCATCA
81083 ACAGT
1 ACAGT
81088 GAACATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (19 bp):
ACAGTTTGACAAGTCATCA
Found at i:84943 original size:65 final size:65
Alignment explanation
Indices: 84839--84968 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
84829 TGTTGTAGCA
84839 ACATGATTGATGTGTCTAGTATTAACTTAGCAGGTTATTCCTCTCGAAGGTATTCACCAAACAAC
1 ACATGATTGATGTGTCTAGTATTAACTTAGCAGGTTATTCCTCTCGAAGGTATTCACCAAACAAC
84904 ACATGATTGATGTGTCTAGTATTAACTTAGCAGGTTATTCCTCTCGAAGGTATTCACCAAACAAC
1 ACATGATTGATGTGTCTAGTATTAACTTAGCAGGTTATTCCTCTCGAAGGTATTCACCAAACAAC
84969 TTAAAAAAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (65 bp):
ACATGATTGATGTGTCTAGTATTAACTTAGCAGGTTATTCCTCTCGAAGGTATTCACCAAACAAC
Found at i:85867 original size:20 final size:20
Alignment explanation
Indices: 85825--85867 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
85815 TTAAAGTAAA
*
85825 TAAAATATAATTTATATATT
1 TAAAATATAATTTATATAAT
* * *
85845 TAAAATATATTTTTTTTAAT
1 TAAAATATAATTTATATAAT
85865 TAA
1 TAA
85868 TTCATAATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAAATATAATTTATATAAT
Found at i:89396 original size:2 final size:2
Alignment explanation
Indices: 89389--89424 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
89379 GAGTCTATTC
89389 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
89425 ACATTATCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:96341 original size:20 final size:20
Alignment explanation
Indices: 96313--96352 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
96303 TTAATCTTTA
*
96313 AATTTTTAAAATTATAAAAT
1 AATTATTAAAATTATAAAAT
* *
96333 AATTATTAAATTTATTAAAT
1 AATTATTAAAATTATAAAAT
96353 TGTTATATCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTATTAAAATTATAAAAT
Found at i:97336 original size:6 final size:6
Alignment explanation
Indices: 97325--97352 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
97315 TTGGGTTTGA
97325 TATGCG TATGCG TATGCG TATGCG TATG
1 TATGCG TATGCG TATGCG TATGCG TATG
97353 AACACTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.32, T:0.36
Consensus pattern (6 bp):
TATGCG
Found at i:101774 original size:24 final size:24
Alignment explanation
Indices: 101729--101778 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
101719 TGGTGGTTGA
* *
101729 TTTAATGGTTTCTTGAACTTTATT
1 TTTAATGGTATATTGAACTTTATT
* *
101753 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTGAACTTTATT
101777 TT
1 TT
101779 GGTTCTTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.04, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTGAACTTTATT
Found at i:102274 original size:16 final size:16
Alignment explanation
Indices: 102253--102285 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
102243 CACGTGAGGA
102253 TTATTTTC-TTTTCATT
1 TTATTTTCATTTT-ATT
102269 TTATTTTCATTTTATT
1 TTATTTTCATTTTATT
102285 T
1 T
102286 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCATTTTATT
Found at i:102275 original size:11 final size:11
Alignment explanation
Indices: 102255--102285 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
102245 CGTGAGGATT
*
102255 ATTTTCTTTTC
1 ATTTTATTTTC
102266 ATTTTATTTTC
1 ATTTTATTTTC
102277 ATTTTATTT
1 ATTTTATTT
102286 ACTGTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (11 bp):
ATTTTATTTTC
Found at i:106413 original size:18 final size:17
Alignment explanation
Indices: 106387--106429 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
106377 ATTTTATCGT
*
106387 TATAAATTTTGTTAAATA
1 TATATATTTT-TTAAATA
*
106405 TATATA-TTTTTAAATC
1 TATATATTTTTTAAATA
106421 TATATATTT
1 TATATATTT
106430 CGCATGATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 12 0.55
17 5 0.23
18 5 0.23
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
TATATATTTTTTAAATA
Found at i:106417 original size:16 final size:16
Alignment explanation
Indices: 106398--106429 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
106388 ATAAATTTTG
106398 TTAAATATATATATTT
1 TTAAATATATATATTT
*
106414 TTAAATCTATATATTT
1 TTAAATATATATATTT
106430 CGCATGATAG
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:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAAATATATATATTT
Found at i:109046 original size:169 final size:172
Alignment explanation
Indices: 108728--109075 Score: 650
Period size: 169 Copynumber: 2.0 Consensus size: 172
108718 GTACGAAAGG
108728 CATTATGGAATGAGGGCTTCAATGTCAAGGTGGTAAGGTGGGGTTATGCAAAAAAAGCATGTTTG
1 CATTA-GGAATGAGGGCTTCAATGTCAAGGTGGTAAGGTGGGGTTATGCAAAAAAAGCATGTTTG
108793 TTAGTTTTCCAGACAGTGGAGGATAAGAGGCAGCGATGGAAGATAAGTGGGAGGCTCTATCCTTC
65 TTAGTTTTCCAGACAGTGGAGGATAAGAGGCAGCGATGGAAGATAAGTGGGAGGCTCTATCCTTC
108858 TGGTTCGAAATGCTGGAGCCTGTTACGGAAGATGGGTGTGTTC
130 TGGTTCGAAATGCTGGAGCCTGTTACGGAAGATGGGTGTGTTC
108901 CATTAGGAATGAGGGCTTCAATGTCAAGGTGGTAA-G-GGGGTTATGC-AAAAAAGCATGTTTGT
1 CATTAGGAATGAGGGCTTCAATGTCAAGGTGGTAAGGTGGGGTTATGCAAAAAAAGCATGTTTGT
108963 TAGTTTTCCAGACAGTGGAGGATAAAGAGGCAGCGATGGAAGATAAGTGGGAGGCTCTATCCTTC
66 TAGTTTTCCAGACAGTGGAGGAT-AAGAGGCAGCGATGGAAGATAAGTGGGAGGCTCTATCCTTC
109028 T-GTTCGAAATGCTGGAGCCTGTTACGGAAGATGGGTGTGTTC
130 TGGTTCGAAATGCTGGAGCCTGTTACGGAAGATGGGTGTGTTC
109070 CATTAG
1 CATTAG
109076 CTTACTGTGC
Statistics
Matches: 174, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
169 86 0.49
170 52 0.30
171 1 0.01
172 30 0.17
173 5 0.03
ACGTcount: A:0.27, C:0.13, G:0.33, T:0.27
Consensus pattern (172 bp):
CATTAGGAATGAGGGCTTCAATGTCAAGGTGGTAAGGTGGGGTTATGCAAAAAAAGCATGTTTGT
TAGTTTTCCAGACAGTGGAGGATAAGAGGCAGCGATGGAAGATAAGTGGGAGGCTCTATCCTTCT
GGTTCGAAATGCTGGAGCCTGTTACGGAAGATGGGTGTGTTC
Found at i:124224 original size:43 final size:43
Alignment explanation
Indices: 124158--124276 Score: 184
Period size: 43 Copynumber: 2.8 Consensus size: 43
124148 ATATATATAT
* *
124158 ATTTAAATTAAATATATACATATTATATATATATTTTAATTTA
1 ATTTAAATTAAATTTATAAATATTATATATATATTTTAATTTA
* *
124201 ATTTAAATTTAATTTATAAATATTATATATATTTTTTAATTTA
1 ATTTAAATTAAATTTATAAATATTATATATATATTTTAATTTA
* *
124244 ATTTAAATTAAATTTATTAGTATTATATATATA
1 ATTTAAATTAAATTTATAAATATTATATATATA
124277 ATTATTATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 68 1.00
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.54
Consensus pattern (43 bp):
ATTTAAATTAAATTTATAAATATTATATATATATTTTAATTTA
Found at i:125197 original size:29 final size:30
Alignment explanation
Indices: 125160--125234 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 30
125150 AAAAAATTTA
* *
125160 AAATATTATAATATTATTTTGATATTATAAT
1 AAAT-TTATAATATTATTATAATATTATAAT
*
125191 -AATTTATAATATT-TTATAATATTTTAAT
1 AAATTTATAATATTATTATAATATTATAAT
*
125219 AAATTTA-AATAATATT
1 AAATTTATAATATTATT
125235 CAATAAATCA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
28 17 0.45
29 18 0.47
30 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (30 bp):
AAATTTATAATATTATTATAATATTATAAT
Found at i:125199 original size:10 final size:10
Alignment explanation
Indices: 125184--125231 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
125174 TATTTTGATA
125184 TTATAATAAT
1 TTATAATAAT
*
125194 TTATAATATT
1 TTATAATAAT
125204 TTATAAT-AT
1 TTATAATAAT
125213 TT-TAATAAAT
1 TTATAAT-AAT
125223 TTA-AATAAT
1 TTATAATAAT
125232 ATTCAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
8 4 0.12
9 6 0.18
10 23 0.70
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TTATAATAAT
Found at i:129941 original size:20 final size:21
Alignment explanation
Indices: 129903--129954 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
129893 ATGTCGATAC
*
129903 ATTTAATCAATTT-TATTTTA-
1 ATTTAATAAATTTAT-TTTTAT
129923 ATTTAATAAATTTACTTTTTAT
1 ATTTAATAAATTTA-TTTTTAT
129945 ATTTAA-AAAT
1 ATTTAATAAAT
129955 CAATCAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 12 0.43
21 9 0.32
22 7 0.25
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTAATAAATTTATTTTTAT
Found at i:131336 original size:107 final size:108
Alignment explanation
Indices: 131214--131431 Score: 420
Period size: 108 Copynumber: 2.0 Consensus size: 108
131204 TTAATTATTT
*
131214 AGAAGTGTTATTGTTTTTTTCAACCCATATGCAATTTTT-TCCGTCTTTTTTACATTTGAAATTG
1 AGAAGTGTTATTGTTTTTTTCAACCCATATGCAATTTTTGCCCGTCTTTTTTACATTTGAAATTG
131278 ATCATAAAATTATGTGACTGGGAATTGATGGTTTTTAAACCAC
66 ATCATAAAATTATGTGACTGGGAATTGATGGTTTTTAAACCAC
131321 AGAAGTGTTATTGTTTTTTTCAACCCATATGCAATTTTTGCCCGTCTTTTTTACATTTGAAATTG
1 AGAAGTGTTATTGTTTTTTTCAACCCATATGCAATTTTTGCCCGTCTTTTTTACATTTGAAATTG
131386 ATCATAAAATTATGTGACTGGGAATTGATGGTTTTTAAACCAC
66 ATCATAAAATTATGTGACTGGGAATTGATGGTTTTTAAACCAC
131429 AGA
1 AGA
131432 TGTTTCGCCT
Statistics
Matches: 109, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
107 39 0.36
108 70 0.64
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (108 bp):
AGAAGTGTTATTGTTTTTTTCAACCCATATGCAATTTTTGCCCGTCTTTTTTACATTTGAAATTG
ATCATAAAATTATGTGACTGGGAATTGATGGTTTTTAAACCAC
Found at i:133318 original size:20 final size:20
Alignment explanation
Indices: 133282--133319 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
133272 ATCCTATTCC
**
133282 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
133302 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
133320 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:137096 original size:184 final size:183
Alignment explanation
Indices: 136732--137102 Score: 516
Period size: 184 Copynumber: 2.0 Consensus size: 183
136722 TGAATGCTTA
* *
136732 TCTACATTCGATTTTGGCCTCCATTCTTTTTTTCCCCCTTAGATTTATTATTGGCTTGGTGTTTG
1 TCTACATTCGATTTTGGCCTCCACTCTTTTTTT--CCCTTAGATTTATTATTGGCTTGGGGTTTG
136797 GGATTGACAGTAGCTTCTGAAGTTGGCTTCTTGCCCTTGCTACATTTCTCACCCTTACATATACT
64 GGATTGACAGTAGCTTCTGAAGTTGGCTTCTTGCCCTTGCTACATTTCTCACCCTTACATATACT
* *
136862 CTCTTTCACACAACAATGGTGATCGGATTCCTAGGATATATGGGTTTCATCTTTT
129 CTCTTTCACACAACAATGGTCATCGGATTCCTAGGATACATGGGTTTCATCTTTT
* * *
136917 TCTACTTTCGATTTTTGGCCTCCACTCTTGTTTTT-TCTTAGATTTATTGTT-GCTTTGGGGTTT
1 TCTACATTCGA-TTTTGGCCTCCACTCTT-TTTTTCCCTTAGATTTATTATTGGC-TTGGGGTTT
* *
136980 GGGATT-ACCAGTAGCTTCTGAAGTTGGCTTCTTGCCCTTTCTACATTTCTCACCCTTACATCTA
63 GGGATTGA-CAGTAGCTTCTGAAGTTGGCTTCTTGCCCTTGCTACATTTCTCACCCTTACATATA
* * * * * *
137044 CTCTTTTTCACACCACAGTGGTCA-CAGGGTTCCTCGGATACATGGTTTTCATCTTTT
127 CTCTCTTTCACACAACAATGGTCATC-GGATTCCTAGGATACATGGGTTTCATCTTTT
137101 TC
1 TC
137103 CAAATAACGT
Statistics
Matches: 166, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
183 4 0.02
184 131 0.79
185 10 0.06
186 16 0.10
187 5 0.03
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (183 bp):
TCTACATTCGATTTTGGCCTCCACTCTTTTTTTCCCTTAGATTTATTATTGGCTTGGGGTTTGGG
ATTGACAGTAGCTTCTGAAGTTGGCTTCTTGCCCTTGCTACATTTCTCACCCTTACATATACTCT
CTTTCACACAACAATGGTCATCGGATTCCTAGGATACATGGGTTTCATCTTTT
Found at i:137485 original size:33 final size:34
Alignment explanation
Indices: 137447--137513 Score: 127
Period size: 33 Copynumber: 2.0 Consensus size: 34
137437 TTCCTAGATA
137447 TACCTAAAAAATACATC-AAATAACAATAAGCAT
1 TACCTAAAAAATACATCAAAATAACAATAAGCAT
137480 TACCTAAAAAATACATCAAAATAACAATAAGCAT
1 TACCTAAAAAATACATCAAAATAACAATAAGCAT
137514 GATCCAAACG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 17 0.52
34 16 0.48
ACGTcount: A:0.58, C:0.18, G:0.03, T:0.21
Consensus pattern (34 bp):
TACCTAAAAAATACATCAAAATAACAATAAGCAT
Found at i:140031 original size:27 final size:27
Alignment explanation
Indices: 140000--140055 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
139990 TTTGGGAAGG
140000 GTCTTGATTTACTTGTCGACTTGCTTT
1 GTCTTGATTTACTTGTCGACTTGCTTT
140027 GTCTTGATTTACTTGTCGACTTGCTTT
1 GTCTTGATTTACTTGTCGACTTGCTTT
140054 GT
1 GT
140056 AAAGAGCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.52
Consensus pattern (27 bp):
GTCTTGATTTACTTGTCGACTTGCTTT
Found at i:143942 original size:35 final size:36
Alignment explanation
Indices: 143903--143983 Score: 112
Period size: 35 Copynumber: 2.3 Consensus size: 36
143893 AACACATTCA
* * *
143903 TCAATTATATTCTAAA-CTCCAAATTC-CAAAATATT
1 TCAATTACATTCTAAACCT-CAAATTCTAAAAATACT
143938 TCAATTACATTCTAAACCTCAAATTCTAAAAATACT
1 TCAATTACATTCTAAACCTCAAATTCTAAAAATACT
143974 TCAATTACAT
1 TCAATTACAT
143984 GCCCAACCCA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
35 22 0.54
36 19 0.46
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (36 bp):
TCAATTACATTCTAAACCTCAAATTCTAAAAATACT
Found at i:143999 original size:36 final size:36
Alignment explanation
Indices: 143922--143995 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
143912 TTCTAAACTC
* * * *
143922 CAAATTC-CAAAATATTTCAATTACATTCTAAACCT
1 CAAATTCTAAAAATACTTCAATTACATGCCAAACCT
*
143957 CAAATTCTAAAAATACTTCAATTACATGCCCAACC-
1 CAAATTCTAAAAATACTTCAATTACATGCCAAACCT
143992 CAAA
1 CAAA
143996 ATTCATAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
35 11 0.33
36 22 0.67
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.28
Consensus pattern (36 bp):
CAAATTCTAAAAATACTTCAATTACATGCCAAACCT
Found at i:144739 original size:148 final size:148
Alignment explanation
Indices: 144469--144761 Score: 437
Period size: 148 Copynumber: 2.0 Consensus size: 148
144459 AAACTATTTA
* * * *
144469 AATTAGAATCAAATAATATTAGTGTATTATAAATATTTATAATTAAATTTAAACAGAAACTCGAG
1 AATTAGAATAAAATAATATTAGTATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
* *
144534 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAGATCGAAAAAAATTTGAGTCATCT
66 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTTGAGTCAACT
144599 ATTTTATAAAATGAACTG
131 ATTTTATAAAATGAACTG
*
144617 AATTAGAATAAAATAATATTA-TAATATGATCAATATTTATAATTAAATTTAAACAGAAACTCGA
1 AATTAGAATAAAATAATATTAGT-ATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGA
* * ***
144681 AAATTCAATTCAATTGGACTTGATTTCAATTTTATAAACTCAAATC-AAAATTTTTTTGAGTCAA
65 AAATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAA-AAATTTGAGTCAA
*
144745 CTATTTTATAAACTGAA
129 CTATTTTATAAAATGAA
144762 TTGAGTATTT
Statistics
Matches: 130, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
147 5 0.04
148 125 0.96
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (148 bp):
AATTAGAATAAAATAATATTAGTATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTTGAGTCAACT
ATTTTATAAAATGAACTG
Found at i:144852 original size:20 final size:20
Alignment explanation
Indices: 144795--144852 Score: 53
Period size: 22 Copynumber: 2.8 Consensus size: 20
144785 CCCTAAACCC
144795 AACATAATCACTTGTTTTTT
1 AACATAATCACTTGTTTTTT
*** * *
144815 TTTATAAGTGATTATGTTTTTT
1 AACATAA-TCACT-TGTTTTTT
144837 AACATAATCACTTGTT
1 AACATAATCACTTGTT
144853 GTTCACTTAT
Statistics
Matches: 26, Mismatches: 10, Indels: 4
0.65 0.25 0.10
Matches are distributed among these distances:
20 8 0.31
21 6 0.23
22 12 0.46
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.52
Consensus pattern (20 bp):
AACATAATCACTTGTTTTTT
Found at i:145014 original size:35 final size:35
Alignment explanation
Indices: 144975--145053 Score: 104
Period size: 35 Copynumber: 2.3 Consensus size: 35
144965 GGTTTAGGCG
* * *
144975 TGTAATTGAAGTATTTTTGAATTTGAAGTTTAGAA
1 TGTAATTGAAGCATTTTGGAATTTGAAGTTTAAAA
* **
145010 TGTAATTGAAGCATTTTGGATTTTGGGGTTTAAAA
1 TGTAATTGAAGCATTTTGGAATTTGAAGTTTAAAA
145045 TGTAATTGA
1 TGTAATTGA
145054 TGACTGTGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.32, C:0.01, G:0.23, T:0.44
Consensus pattern (35 bp):
TGTAATTGAAGCATTTTGGAATTTGAAGTTTAAAA
Found at i:145614 original size:6 final size:6
Alignment explanation
Indices: 145603--145645 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
145593 TTAATTAAAT
*
145603 ATTTAA ATTT-A ATTTCATA ATTTAA ATTTAT ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTT-A-A ATTTAA ATTTAA ATTTAA ATTTAA
145646 TTTTTTATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 5 0.16
6 21 0.66
7 1 0.03
8 5 0.16
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:145616 original size:18 final size:18
Alignment explanation
Indices: 145593--145645 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
145583 TACTTTTTAG
*
145593 TTAATTAAATATTTAAAT
1 TTAATTTAATATTTAAAT
*
145611 TTAATTTCATAATTTAAAT
1 TTAATTTAAT-ATTTAAAT
145630 TTATATTTAA-ATTTAA
1 TTA-ATTTAATATTTAA
145646 TTTTTTATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 14 0.47
19 11 0.37
20 5 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAATTTAATATTTAAAT
Found at i:145627 original size:19 final size:18
Alignment explanation
Indices: 145603--145645 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
145593 TTAATTAAAT
145603 ATTTAAATTTA-ATTTCATA
1 ATTTAAATTTATATTT-A-A
145622 ATTTAAATTTATATTTAA
1 ATTTAAATTTATATTTAA
145640 ATTTAA
1 ATTTAA
145646 TTTTTTATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.30
19 12 0.52
20 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTAAATTTATATTTAA
Found at i:145658 original size:18 final size:18
Alignment explanation
Indices: 145603--145658 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
145593 TTAATTAAAT
*
145603 ATTTAAATTTA-ATTTCATA
1 ATTTAAATTTATATCT-A-A
*
145622 ATTTAAATTTATATTTAA
1 ATTTAAATTTATATCTAA
* *
145640 ATTTAATTTTTTATCTAA
1 ATTTAAATTTATATCTAA
145658 A
1 A
145659 ATAACACTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 17 0.52
19 12 0.36
20 4 0.12
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTAAATTTATATCTAA
Found at i:148773 original size:17 final size:18
Alignment explanation
Indices: 148731--148774 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
148721 AGAAACTAAA
148731 GCTAAAAATGCGAATATG
1 GCTAAAAATGCGAATATG
148749 GCTAAAAATGCGAATATG
1 GCTAAAAATGCGAATATG
*
148767 GCCAAAAA
1 GCTAAAAA
148775 GTTCGAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.48, C:0.14, G:0.20, T:0.18
Consensus pattern (18 bp):
GCTAAAAATGCGAATATG
Found at i:158745 original size:29 final size:29
Alignment explanation
Indices: 158709--158784 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
158699 AACTAAATTG
158709 ATGTAAGCAATGACATCATTAATTAAATC
1 ATGTAAGCAATGACATCATTAATTAAATC
* *
158738 ATGTAAGCAATGACATCTTTAATTAAATG
1 ATGTAAGCAATGACATCATTAATTAAATC
*
158767 ATGTAAGTAATGACATCA
1 ATGTAAGCAATGACATCA
158785 ATTTAGTTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (29 bp):
ATGTAAGCAATGACATCATTAATTAAATC
Found at i:163512 original size:29 final size:29
Alignment explanation
Indices: 163476--163551 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
163466 AACTAAATTG
163476 ATGTAAGCAATGACATCATTAATTAAATC
1 ATGTAAGCAATGACATCATTAATTAAATC
* *
163505 ATGTAAGCAATGACATCTTTAATTAAATG
1 ATGTAAGCAATGACATCATTAATTAAATC
*
163534 ATGTAAGTAATGACATCA
1 ATGTAAGCAATGACATCA
163552 ATTTAGTTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (29 bp):
ATGTAAGCAATGACATCATTAATTAAATC
Found at i:164551 original size:31 final size:31
Alignment explanation
Indices: 164516--164580 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
164506 TTTGGTTCTT
164516 TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
1 TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
164547 TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
1 TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
164578 TGC
1 TGC
164581 TATGTATGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.03, C:0.29, G:0.32, T:0.35
Consensus pattern (31 bp):
TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
Found at i:164837 original size:20 final size:20
Alignment explanation
Indices: 164808--164846 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
164798 ACCTCTCCAT
164808 TGGCTCGTATGGCTCGTATA
1 TGGCTCGTATGGCTCGTATA
*
164828 TGGCTTGTATGGCTCGTAT
1 TGGCTCGTATGGCTCGTAT
164847 GTCACCCCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.18, G:0.31, T:0.38
Consensus pattern (20 bp):
TGGCTCGTATGGCTCGTATA
Found at i:164866 original size:9 final size:9
Alignment explanation
Indices: 164808--164847 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
164798 ACCTCTCCAT
164808 TGGCTCGTA
1 TGGCTCGTA
164817 TGGCTCGTATA
1 TGGCTCG--TA
*
164828 TGGCTTGTA
1 TGGCTCGTA
164837 TGGCTCGTA
1 TGGCTCGTA
164846 TG
1 TG
164848 TCACCCCGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 19 0.70
11 8 0.30
ACGTcount: A:0.12, C:0.17, G:0.33, T:0.38
Consensus pattern (9 bp):
TGGCTCGTA
Found at i:164877 original size:20 final size:21
Alignment explanation
Indices: 164834--164879 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
164824 TATATGGCTT
164834 GTATGGCTCGTATGTCACCCC
1 GTATGGCTCGTATGTCACCCC
*
164855 GTATGGCTCGTATGTC-TCCC
1 GTATGGCTCGTATGTCACCCC
164875 GTATG
1 GTATG
164880 TCGCCTGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.13, C:0.28, G:0.26, T:0.33
Consensus pattern (21 bp):
GTATGGCTCGTATGTCACCCC
Found at i:164922 original size:29 final size:29
Alignment explanation
Indices: 164880--164939 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
164870 CTCCCGTATG
164880 TCGCCTGGATTGCATGGCGTCCTACAAGA
1 TCGCCTGGATTGCATGGCGTCCTACAAGA
*
164909 TCGCCTGGATTGCATGGCGTCCTACGAGA
1 TCGCCTGGATTGCATGGCGTCCTACAAGA
164938 TC
1 TC
164940 ACTGTAGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.25
Consensus pattern (29 bp):
TCGCCTGGATTGCATGGCGTCCTACAAGA
Found at i:166782 original size:208 final size:209
Alignment explanation
Indices: 166197--166824 Score: 1224
Period size: 211 Copynumber: 3.0 Consensus size: 209
166187 CGCTAGTTAC
166197 AAGGCAAGTTGTTC-TTTTTTTTTGTTGAAAAAAATGCTTCTCAGTATCCATACTTTTGACACAC
1 AAGGCAAGTTGTTCTTTTTTTTTTGTTGAAAAAAATGCTTCTCAGTATCCATACTTTTGACACAC
166261 CATAAATCTCTCCAATCTAACAAAGATAGAATATCCCTAAAAACGATGGATTTTTGTGTATAATT
66 CATAAATCTCTCCAATCTAACAAAGATAGAATATCCCTAAAAACGATGGATTTTTGTGTATAATT
166326 TCGTGGATTTTAAAGAGGTTTCGAAAAAAATTAGACCAATAAAGTGATAGAGAACAAAAGGATAA
131 TCGTGGATTTTAAAGAGGTTTCGAAAAAAATTAGACCAATAAAGTGATAGAGAACAAAAGGATAA
166391 ATTCATCATTGTCT
196 ATTCATCATTGTCT
166405 AAGGCAAGTTGTTCTTTTTTTTTTTTGTTGAAAAAAATGCTTCTCAGTATCCATACTTTTGACAC
1 AAGGCAAGTTGTTC--TTTTTTTTTTGTTGAAAAAAATGCTTCTCAGTATCCATACTTTTGACAC
166470 ACCATAAATCTCTCCAATCTAACAAAGATAGAATATCCCTAAAAACGATGGATTTTTGTGTATAA
64 ACCATAAATCTCTCCAATCTAACAAAGATAGAATATCCCTAAAAACGATGGATTTTTGTGTATAA
166535 TTTCGTGGATTTTAAAGAGGTTTCGAAAAAAATTAGACCAATAAAGTGATAGAGAACAAAAGGAT
129 TTTCGTGGATTTTAAAGAGGTTTCGAAAAAAATTAGACCAATAAAGTGATAGAGAACAAAAGGAT
166600 AAATTCATCATTGTCT
194 AAATTCATCATTGTCT
166616 AAGGCAAGTTGTTCTTTTTTTTTTGTTGAAAAAAATGCTTCTCAGTATCCATACTTTTGACACAC
1 AAGGCAAGTTGTTCTTTTTTTTTTGTTGAAAAAAATGCTTCTCAGTATCCATACTTTTGACACAC
166681 CATAAATCTCTCCAATCTAACAAAGATAGAATATCCCTAAAAACGATGGA-TTTTGTGTATAATT
66 CATAAATCTCTCCAATCTAACAAAGATAGAATATCCCTAAAAACGATGGATTTTTGTGTATAATT
166745 TCGTGGATTTTAAAGAGGTTTCGAAAAAAATTAGACCAATAAAGTGATAGAGAACAAAAGGATAA
131 TCGTGGATTTTAAAGAGGTTTCGAAAAAAATTAGACCAATAAAGTGATAGAGAACAAAAGGATAA
166810 ATTCATCATTGTCT
196 ATTCATCATTGTCT
166824 A
1 A
166825 GGATGATTAT
Statistics
Matches: 417, Mismatches: 0, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
208 108 0.26
209 101 0.24
211 208 0.50
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.33
Consensus pattern (209 bp):
AAGGCAAGTTGTTCTTTTTTTTTTGTTGAAAAAAATGCTTCTCAGTATCCATACTTTTGACACAC
CATAAATCTCTCCAATCTAACAAAGATAGAATATCCCTAAAAACGATGGATTTTTGTGTATAATT
TCGTGGATTTTAAAGAGGTTTCGAAAAAAATTAGACCAATAAAGTGATAGAGAACAAAAGGATAA
ATTCATCATTGTCT
Found at i:178426 original size:13 final size:13
Alignment explanation
Indices: 178408--178434 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
178398 GGTTTGACTC
178408 TGAATATAACATG
1 TGAATATAACATG
178421 TGAATATAACATG
1 TGAATATAACATG
178434 T
1 T
178435 TTGATATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.33
Consensus pattern (13 bp):
TGAATATAACATG
Found at i:182340 original size:21 final size:21
Alignment explanation
Indices: 182311--182350 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
182301 AACATGCTTT
* *
182311 CAACCAAATTACCTTTTTTAA
1 CAACAAAATTACATTTTTTAA
*
182332 CAACAAAATTTCATTTTTT
1 CAACAAAATTACATTTTTT
182351 CCTACAATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (21 bp):
CAACAAAATTACATTTTTTAA
Found at i:186826 original size:277 final size:278
Alignment explanation
Indices: 186333--186885 Score: 1029
Period size: 277 Copynumber: 2.0 Consensus size: 278
186323 AGATTTGGAT
186333 TAGATCATTCAATTATTTAACTATTAATAAAAAAATGACGTGACGGTTTAATATTAATATGTACT
1 TAGATCATTCAATTATTTAACTATTAATAAAAAAATGACGTGACGGTTTAATATTAATATGTACT
186398 GACATTAAAGTCAAAAATTATTATTATCACGCCTCATCATTTTCTTCGTTAAAATTAAAATCATT
66 GACATTAAAGTCAAAAATTATTATTATCACGCCTCATCATTTTCTTCGTTAAAATTAAAATCATT
* *
186463 TCACTCATTTTCGATTGTTAAAAATTATCATTCTTCAACGATTTTTACTCTTATCATAAATATCA
131 TCACTCATTTCCGATTATTAAAAATTATCATTCTTCAACGATTTTTACTCTTATCATAAATATCA
186528 ATGAACTCGACTCATCGTCTTATGTTAATTTATCGGTTTAGATGTTCTAAAA-CTTTTTAAAACC
196 ATGAACTCGACTCATCGTCTTATGTTAATTTATCGGTTTAGATGTTCTAAAACCTTTTTAAAACC
186592 TATAGAAAA-ACAAAAAG
261 TATAGAAAACACAAAAAG
186609 TAGATCATTCAATTATTTAACTATTAATAAAAAAATGACGTGACGGTTTAATATTAATATGTACT
1 TAGATCATTCAATTATTTAACTATTAATAAAAAAATGACGTGACGGTTTAATATTAATATGTACT
*
186674 GACATTAAAGTCAAAAAATTATTGTTATCACGCCTCATCATTTTCTTCGTTAAAATTAAAATCAT
66 GACATTAAAGTC-AAAAATTATTATTATCACGCCTCATCATTTTCTTCGTTAAAATTAAAATCAT
* *
186739 TTCACTCATTTCCGATTATTAAAAATTATCATTCTTCAATGATTTTTACTGTTATCATAAATATC
130 TTCACTCATTTCCGATTATTAAAAATTATCATTCTTCAACGATTTTTACTCTTATCATAAATATC
*
186804 AATGAACTCGACTTATCGTCTTATGTTAATTTATCGGTTTAGATGTTCTAAAACCTTTTTAAAAC
195 AATGAACTCGACTCATCGTCTTATGTTAATTTATCGGTTTAGATGTTCTAAAACCTTTTTAAAAC
186869 CTATAGAAAACACAAAA
260 CTATAGAAAACACAAAA
186886 GATCCACTAT
Statistics
Matches: 268, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
276 77 0.29
277 164 0.61
278 21 0.08
279 6 0.02
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.39
Consensus pattern (278 bp):
TAGATCATTCAATTATTTAACTATTAATAAAAAAATGACGTGACGGTTTAATATTAATATGTACT
GACATTAAAGTCAAAAATTATTATTATCACGCCTCATCATTTTCTTCGTTAAAATTAAAATCATT
TCACTCATTTCCGATTATTAAAAATTATCATTCTTCAACGATTTTTACTCTTATCATAAATATCA
ATGAACTCGACTCATCGTCTTATGTTAATTTATCGGTTTAGATGTTCTAAAACCTTTTTAAAACC
TATAGAAAACACAAAAAG
Found at i:187595 original size:10 final size:10
Alignment explanation
Indices: 187580--187611 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
187570 TTATATATTG
187580 AATTTAATAA
1 AATTTAATAA
187590 AATTTAATAA
1 AATTTAATAA
187600 AA-TTAATAA
1 AATTTAATAA
187609 AAT
1 AAT
187612 AAAAGTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AATTTAATAA
Found at i:194565 original size:12 final size:13
Alignment explanation
Indices: 194542--194566 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
194532 TAACCCCCTA
194542 CCAAACCTTTTTG
1 CCAAACCTTTTTG
194555 CCAAACCTTTTT
1 CCAAACCTTTTT
194567 ATTCCAATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.32, G:0.04, T:0.40
Consensus pattern (13 bp):
CCAAACCTTTTTG
Found at i:204851 original size:2 final size:2
Alignment explanation
Indices: 204844--204886 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
204834 TCCCTAGTTT
204844 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
204886 T
1 T
204887 GAAAGATTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:207058 original size:21 final size:21
Alignment explanation
Indices: 207034--207074 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
207024 TTAACCGTTA
207034 ACCGACCGAATTAATTCGATG
1 ACCGACCGAATTAATTCGATG
207055 ACCGACCGAATTAATTCGAT
1 ACCGACCGAATTAATTCGAT
207075 TAATTCGATT
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:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (21 bp):
ACCGACCGAATTAATTCGATG
Found at i:210607 original size:13 final size:15
Alignment explanation
Indices: 210579--210608 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
210569 GCTTCAATCG
210579 TTAGTCCAATATATA
1 TTAGTCCAATATATA
210594 TTAGTCCAATATATA
1 TTAGTCCAATATATA
210609 CCGCTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (15 bp):
TTAGTCCAATATATA
Found at i:211809 original size:43 final size:44
Alignment explanation
Indices: 211761--211860 Score: 184
Period size: 44 Copynumber: 2.3 Consensus size: 44
211751 AGAAACTATC
211761 CACCTATAATAGTACAAAATACAAT-AAATTTGTAATTATAATT
1 CACCTATAATAGTACAAAATACAATAAAATTTGTAATTATAATT
211804 CACCTATAATAGTACAAAATACAATAAAATTTGTAATTATAATT
1 CACCTATAATAGTACAAAATACAATAAAATTTGTAATTATAATT
*
211848 CATCTATAATAGT
1 CACCTATAATAGT
211861 TACATATAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 25 0.45
44 30 0.55
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.35
Consensus pattern (44 bp):
CACCTATAATAGTACAAAATACAATAAAATTTGTAATTATAATT
Found at i:213654 original size:2 final size:2
Alignment explanation
Indices: 213649--213679 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
213639 TATGCGTGTG
*
213649 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
213680 TAAAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 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):
TA
Found at i:218104 original size:18 final size:17
Alignment explanation
Indices: 218075--218192 Score: 109
Period size: 17 Copynumber: 6.9 Consensus size: 17
218065 AAATAAGAAA
218075 AAGAAG-AGAAGAAAGG
1 AAGAAGAAGAAGAAAGG
218091 AAGGAAGAAGAAGAAA-G
1 AA-GAAGAAGAAGAAAGG
*
218108 AA-AAGAAGAAGAAGAAG
1 AAGAAGAAGAAGAA-AGG
*
218125 AAGAAGAAGAAGAAAAG
1 AAGAAGAAGAAGAAAGG
*
218142 AAGAAGGAAGGAAGAAAGT
1 AAGAA-GAA-GAAGAAAGG
*
218161 AAGAAGAAGGAA-AAAGA
1 AAGAAGAA-GAAGAAAGG
* *
218178 AAAAAAAAGAAGAAA
1 AAGAAGAAGAAGAAA
218193 TAAAGGAAGA
Statistics
Matches: 89, Mismatches: 5, Indels: 15
0.82 0.05 0.14
Matches are distributed among these distances:
15 11 0.12
16 6 0.07
17 31 0.35
18 29 0.33
19 12 0.13
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.01
Consensus pattern (17 bp):
AAGAAGAAGAAGAAAGG
Found at i:218197 original size:11 final size:11
Alignment explanation
Indices: 218095--218203 Score: 62
Period size: 11 Copynumber: 9.7 Consensus size: 11
218085 GAAAGGAAGG
*
218095 AAGAAG-AAGA
1 AAGAAGAAAAA
*
218105 AAGAA-AAGAAG
1 AAGAAGAA-AAA
*
218116 AAGAAGAAGAAG
1 AAGAAGAA-AAA
*
218128 AAGAAGAAGAA
1 AAGAAGAAAAA
**
218139 AAGAAGAAGGA
1 AAGAAGAAAAA
* **
218150 AGGAAGAAAGT
1 AAGAAGAAAAA
218161 AAGAAGAAGGAAA
1 AAGAAGAA--AAA
218174 AAGAA-AAAAA
1 AAGAAGAAAAA
218184 AAGAAGAAATAA
1 AAGAAGAAA-AA
*
218196 AGGAAGAA
1 AAGAAGAA
218204 GAGAAGGAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
10 14 0.17
11 35 0.44
12 25 0.31
13 6 0.08
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (11 bp):
AAGAAGAAAAA
Found at i:218205 original size:3 final size:3
Alignment explanation
Indices: 218069--218191 Score: 105
Period size: 3 Copynumber: 40.7 Consensus size: 3
218059 GAGATAAAAT
* *
218069 AAG AAA AAG AAG -AG AAG AA- AGG AAGG AAG AAG AAG AAAG AA- AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG -AAG AAG AAG
218113 AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG AAG AAGG AAGG AAG AAAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AA-G AAG -AAG
* *
218160 TAAG AAG AAGG AAA AAG AA- AA- AAA AAG AAG AA
1 -AAG AAG AA-G AAG AAG AAG AAG AAG AAG AAG AA
218192 ATAAAGGAAG
Statistics
Matches: 102, Mismatches: 8, Indels: 20
0.78 0.06 0.15
Matches are distributed among these distances:
2 11 0.11
3 69 0.68
4 22 0.22
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (3 bp):
AAG
Found at i:218440 original size:18 final size:19
Alignment explanation
Indices: 218417--218460 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
218407 GCGATGACTT
*
218417 TATTATTATT-TAATAAAA
1 TATTATTATTAGAATAAAA
*
218435 TATTATT-TTAGAATAAAT
1 TATTATTATTAGAATAAAA
218453 TATTATTA
1 TATTATTA
218461 AATGGTAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TATTATTATTAGAATAAAA
Found at i:220248 original size:18 final size:19
Alignment explanation
Indices: 220210--220249 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
220200 AAAATAATAT
*
220210 TAAAA-TAAC-AACATTAG
1 TAAAATTAACAAATATTAG
220227 TAAAATTAACAAATATTA-
1 TAAAATTAACAAATATTAG
220245 TAAAA
1 TAAAA
220250 ATAATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (19 bp):
TAAAATTAACAAATATTAG
Found at i:225543 original size:15 final size:16
Alignment explanation
Indices: 225511--225543 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
225501 AAAATCTTTC
225511 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
225527 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
225542 TT
1 TT
225544 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Done.