Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015151.1 Kokia drynarioides strain JFW-HI SEQ_130195, 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: 336145
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 314 characters in sequence are not A, C, G, or T
Found at i:4609 original size:21 final size:21
Alignment explanation
Indices: 4576--4620 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
4566 TAACTATACT
*
4576 AAAATATTTTTAAAATAATAA
1 AAAATATTTTTAAAAAAATAA
4597 AAAAT-TTTATTAAAAAAATAA
1 AAAATATTT-TTAAAAAAATAA
4618 AAA
1 AAA
4621 TTAACCGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATATTTTTAAAAAAATAA
Found at i:14753 original size:18 final size:19
Alignment explanation
Indices: 14730--14767 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
14720 ATATATATAA
14730 TATAAA-ATTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
14748 TATAAATATTTTGAATTTT
1 TATAAATATTTGGAATTTT
14767 T
1 T
14768 TTGGTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:15056 original size:18 final size:16
Alignment explanation
Indices: 15020--15051 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
15010 TATTATAAAA
15020 GTAGAGAGACCAAATT
1 GTAGAGAGACCAAATT
15036 GTAGAGAGACCAAATT
1 GTAGAGAGACCAAATT
15052 ATGTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (16 bp):
GTAGAGAGACCAAATT
Found at i:16835 original size:6 final size:6
Alignment explanation
Indices: 16826--16863 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
16816 ATCATCATCA
16826 TCCTCT TCCTCT TCCTCT TCCTC- TCCATCT TCCTCT TC
1 TCCTCT TCCTCT TCCTCT TCCTCT TCC-TCT TCCTCT TC
16864 ATCGACAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 3 0.10
6 24 0.80
7 3 0.10
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (6 bp):
TCCTCT
Found at i:28687 original size:6 final size:6
Alignment explanation
Indices: 28678--28714 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
28668 TAATAATAAT
* *
28678 ATCAAC ATCAAC ATCAAC ATCAAC AACAAC AACAAC A
1 ATCAAC ATCAAC ATCAAC ATCAAC ATCAAC ATCAAC A
28715 ATAATAAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.57, C:0.32, G:0.00, T:0.11
Consensus pattern (6 bp):
ATCAAC
Found at i:32030 original size:22 final size:22
Alignment explanation
Indices: 32002--32043 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
31992 GCTACTGATG
32002 TCGCGACAACAAGACATGGAAT
1 TCGCGACAACAAGACATGGAAT
*
32024 TCGCGACAACAGGACATGGA
1 TCGCGACAACAAGACATGGA
32044 TGTCACAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.24, G:0.26, T:0.12
Consensus pattern (22 bp):
TCGCGACAACAAGACATGGAAT
Found at i:51354 original size:18 final size:17
Alignment explanation
Indices: 51333--51412 Score: 63
Period size: 17 Copynumber: 4.4 Consensus size: 17
51323 TAGATTAATT
51333 TTTAAATTTATTTCTAAA
1 TTTAAATTTATTT-TAAA
51351 TTTAAATTTACTTCATTTTAAA
1 TTTAAA--T--TT-ATTTTAAA
*
51373 TTTAAATTTAGTTTAAA
1 TTTAAATTTATTTTAAA
*
51390 TTTGAAA-TAATTTTAAA
1 TTT-AAATTTATTTTAAA
*
51407 CTTAAA
1 TTTAAA
51413 ACTTTAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
16 3 0.06
17 20 0.38
18 11 0.21
20 2 0.04
22 12 0.23
23 4 0.08
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:51404 original size:17 final size:17
Alignment explanation
Indices: 51321--51412 Score: 62
Period size: 17 Copynumber: 5.4 Consensus size: 17
51311 TATTTTTGAG
*
51321 TTTAGATTAATTTTTAAA
1 TTTAAATTAA-TTTTAAA
** *
51339 TTTATTTCTAAATTTAAA
1 TTTAAAT-TAATTTTAAA
* *
51357 TTT-ACTTCATTTTAAA
1 TTTAAATTAATTTTAAA
* *
51373 TTTAAATTTAGTTTAAA
1 TTTAAATTAATTTTAAA
51390 TTTGAAA-TAATTTTAAA
1 TTT-AAATTAATTTTAAA
*
51407 CTTAAA
1 TTTAAA
51413 ACTTTAAAAT
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
16 14 0.24
17 24 0.41
18 17 0.29
19 3 0.05
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTAAATTAATTTTAAA
Found at i:52132 original size:7 final size:7
Alignment explanation
Indices: 52120--52228 Score: 55
Period size: 7 Copynumber: 15.0 Consensus size: 7
52110 AGTAAGTATC
52120 ATTAATA
1 ATTAATA
52127 ATTAAT-
1 ATTAATA
52133 ATTAATA
1 ATTAATA
52140 ATAATAATA
1 AT--TAATA
* *
52149 AATAACAA
1 ATTAA-TA
*
52157 ATTTATA
1 ATTAATA
52164 A-TAATGA
1 ATTAAT-A
52171 TATTAATA
1 -ATTAATA
* *
52179 AGTATTA
1 ATTAATA
*
52186 ATAACAGTA
1 ATTA-A-TA
52195 ATTAATA
1 ATTAATA
*
52202 A-TACCT-
1 ATTA-ATA
52208 ATTAATA
1 ATTAATA
52215 ATTAATA
1 ATTAATA
52222 ATTAATA
1 ATTAATA
52229 TTTAGTAATA
Statistics
Matches: 76, Mismatches: 14, Indels: 24
0.67 0.12 0.21
Matches are distributed among these distances:
6 13 0.17
7 41 0.54
8 7 0.09
9 15 0.20
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.39
Consensus pattern (7 bp):
ATTAATA
Found at i:52237 original size:14 final size:14
Alignment explanation
Indices: 52120--52228 Score: 55
Period size: 15 Copynumber: 7.5 Consensus size: 14
52110 AGTAAGTATC
52120 ATTAATAATTAAT-
1 ATTAATAATTAATA
52133 ATTAATAATAATAATA
1 ATTAATAAT--TAATA
* * *
52149 AATAACAAATTTATA
1 ATTAA-TAATTAATA
52164 A-TAATGATATTAATA
1 ATTAAT-A-ATTAATA
* * *
52179 AGTATTAATAACAGTA
1 ATTAATAATTA-A-TA
*
52195 ATTAATAA-TACCT-
1 ATTAATAATTA-ATA
52208 ATTAATAATTAATA
1 ATTAATAATTAATA
52222 ATTAATA
1 ATTAATA
52229 TTTAGTAATA
Statistics
Matches: 73, Mismatches: 12, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
13 18 0.25
14 17 0.23
15 20 0.27
16 15 0.21
17 3 0.04
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.39
Consensus pattern (14 bp):
ATTAATAATTAATA
Found at i:53160 original size:30 final size:29
Alignment explanation
Indices: 53116--53287 Score: 111
Period size: 29 Copynumber: 5.8 Consensus size: 29
53106 GGAGGTCCCT
* *
53116 AAACTATCCAAAAATTCCATTTTTGACCTC
1 AAACT-TCTAAAAATTCCATTTTTAACCTC
* * **
53146 GAAACTTTTGAAAATTATATTTTTAACCTC
1 -AAACTTCTAAAAATTCCATTTTTAACCTC
* *
53176 AAACTTGC-AAAAATTCCTTTTTTAACCCC
1 AAACTT-CTAAAAATTCCATTTTTAACCTC
* *
53205 AAAAACTTCTAAAAATTCCA-TTTTGACCCC
1 --AAACTTCTAAAAATTCCATTTTTAACCTC
* *
53235 AAAAC-TCTCAAAAATTACCA-TTTTACCCCC
1 -AAACTTCT-AAAAATT-CCATTTTTAACCTC
*
53265 AAA-TGTCCAAAAATTCCATTTTT
1 AAACT-TCTAAAAATTCCATTTTT
53288 GATTCATTTT
Statistics
Matches: 115, Mismatches: 17, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
28 6 0.05
29 48 0.42
30 41 0.36
31 20 0.17
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCTAAAAATTCCATTTTTAACCTC
Found at i:53219 original size:31 final size:30
Alignment explanation
Indices: 53176--53267 Score: 100
Period size: 30 Copynumber: 3.0 Consensus size: 30
53166 TTTTAACCTC
*
53176 AAACTTGC-AAAAATTCCTTTTTTAACCCCAA
1 AAACTT-CTAAAAATTCC-ATTTTAACCCCAA
*
53207 AAACTTCTAAAAATTCCATTTTGACCCC-A
1 AAACTTCTAAAAATTCCATTTTAACCCCAA
*
53236 AAAC-TCTCAAAAATTACCATTTTACCCCCAA
1 AAACTTCT-AAAAATT-CCATTTTAACCCCAA
53267 A
1 A
53268 TGTCCAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
28 3 0.06
29 12 0.23
30 21 0.40
31 17 0.32
ACGTcount: A:0.40, C:0.28, G:0.02, T:0.29
Consensus pattern (30 bp):
AAACTTCTAAAAATTCCATTTTAACCCCAA
Found at i:53390 original size:27 final size:28
Alignment explanation
Indices: 53358--53418 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
53348 CCAAAATTTC
**
53358 CCAAAATTACCA-TTTGCCCTTGGGAAT
1 CCAAAATTACCATTTTGCCCCCGGGAAT
*
53385 CCAAAATTACCATTTTGCCCCCGGGTAT
1 CCAAAATTACCATTTTGCCCCCGGGAAT
53413 CCAAAA
1 CCAAAA
53419 AGTCTCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 12 0.40
28 18 0.60
ACGTcount: A:0.31, C:0.30, G:0.13, T:0.26
Consensus pattern (28 bp):
CCAAAATTACCATTTTGCCCCCGGGAAT
Found at i:53756 original size:96 final size:97
Alignment explanation
Indices: 53625--53817 Score: 257
Period size: 96 Copynumber: 2.0 Consensus size: 97
53615 AAAATTTTAA
* * * **
53625 AATCGAGGCAATATTCTTTCATTTCGAGTTTTGAAATTTTATGCCTTAACTTACTAGGTGCAATT
1 AATCGAGGCAATATTCTTTCATTTCGAGTTCTGAAAATTTACGCCTTAACTTACTAGGTGCAACC
*
53690 TTTCTTCAAATCGAAATAATCGAATA-CCTTT
66 TTTCTTCAAATCGAAATAATCAAATATCCTTT
* * *
53721 AATCGAGGCAATGTT-TTCTTATCTTCGA-TTCTGAAAATTTGCGCCTTAACTTACTAGGTGCAA
1 AATCGAGGCAATATTCTT-TCAT-TTCGAGTTCTGAAAATTTACGCCTTAACTTACTAGGTGCAA
*
53784 CCTTTCTTCAAATCGAGATAATCAAATATCCTTT
64 CCTTTCTTCAAATCGAAATAATCAAATATCCTTT
53818 TCCAAAATTC
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
95 2 0.02
96 72 0.86
97 10 0.12
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (97 bp):
AATCGAGGCAATATTCTTTCATTTCGAGTTCTGAAAATTTACGCCTTAACTTACTAGGTGCAACC
TTTCTTCAAATCGAAATAATCAAATATCCTTT
Found at i:57391 original size:18 final size:18
Alignment explanation
Indices: 57368--57424 Score: 114
Period size: 18 Copynumber: 3.2 Consensus size: 18
57358 GGTGGATAGT
57368 TTGGTATCAATGAATGTA
1 TTGGTATCAATGAATGTA
57386 TTGGTATCAATGAATGTA
1 TTGGTATCAATGAATGTA
57404 TTGGTATCAATGAATGTA
1 TTGGTATCAATGAATGTA
57422 TTG
1 TTG
57425 CTATATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.40
Consensus pattern (18 bp):
TTGGTATCAATGAATGTA
Found at i:61987 original size:23 final size:23
Alignment explanation
Indices: 61971--62014 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
61961 TTATTTTTTA
*
61971 TTCGTTTTTACTATTATTTTACT
1 TTCGTTTTTAATATTATTTTACT
*
61994 TTCTTTTTTAATATTATTTTA
1 TTCGTTTTTAATATTATTTTA
62015 ATATTGTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.68
Consensus pattern (23 bp):
TTCGTTTTTAATATTATTTTACT
Found at i:62121 original size:9 final size:9
Alignment explanation
Indices: 62082--62135 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 9
62072 AATATAAATA
62082 TTTTTAATGT
1 TTTTTAAT-T
*
62092 ATTTTAAATT
1 -TTTTTAATT
*
62102 TGTTT-ATT
1 TTTTTAATT
62110 TTTTTAATT
1 TTTTTAATT
62119 TTTTTAATGT
1 TTTTTAAT-T
62129 TTTTTAA
1 TTTTTAA
62136 GTGTATTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 7 0.19
9 14 0.38
10 9 0.24
11 7 0.19
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (9 bp):
TTTTTAATT
Found at i:67293 original size:41 final size:40
Alignment explanation
Indices: 67239--67324 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
67229 TTTATAAGAA
* * * *
67239 AAACGTCGTTAAAGGTCAGAGCATTAGCGGCGCTTTTCCAT
1 AAACATCGCTAAAGGTCA-AGCAATAACGGCGCTTTTCCAT
* * *
67280 AAACATCGCTAAAGGTTAAGTAATAACGGCGTTTTTCCAT
1 AAACATCGCTAAAGGTCAAGCAATAACGGCGCTTTTCCAT
67320 AAACA
1 AAACA
67325 CTGCTAATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 23 0.61
41 15 0.39
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (40 bp):
AAACATCGCTAAAGGTCAAGCAATAACGGCGCTTTTCCAT
Found at i:69387 original size:43 final size:43
Alignment explanation
Indices: 69291--69643 Score: 347
Period size: 43 Copynumber: 8.1 Consensus size: 43
69281 ATTAGCAACA
* * *
69291 TTTGTGGGAAAAGCGTCGCTAAAGACCATG-TATTTAGCAGCG
1 TTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCG
* * * **
69333 TTTGTGAGAAAAGCGCTGCTAAAGATCATGTTCTTTAGTAGCG
1 TTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCG
*
69376 TTTGTGGGAAAA--G-CGCTAAAGACCATGTTCTTTAGCGACG
1 TTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCG
*
69416 TTTGTGGGAAAAGCACCGCTAAAGACCATGTTCTTTAGCGGCG
1 TTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCG
* * ***
69459 TTTGTGGGAAAAGCGCCGTTAAAGACCATG-TCTTTAGTGAAA
1 TTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCG
* *
69501 TTTGTGAGAAAAGCGCCGCTAAGCCGCTAAAGATCATGTTCTTTAGCGGCG
1 TTTGTGGGAAAA-----GC---GCCGCTAAAGACCATGTTCTTTAGCGGCG
* *
69552 TTTGTGGGAAAAGAAGCACCGCTAAAGACCATGTTCTTTAGCGGCA
1 TTTGTGGG--AA-AAGCGCCGCTAAAGACCATGTTCTTTAGCGGCG
* * * * * *
69598 TTTGTGAGAAAAACGCCGCTAAAGACTATATTCTATAGCAGCG
1 TTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCG
69641 TTT
1 TTT
69644 TTCCTCATAA
Statistics
Matches: 256, Mismatches: 39, Indels: 31
0.79 0.12 0.10
Matches are distributed among these distances:
40 34 0.13
41 1 0.00
42 45 0.18
43 104 0.41
44 2 0.01
46 33 0.13
47 2 0.01
49 2 0.01
50 14 0.05
51 15 0.06
53 2 0.01
54 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (43 bp):
TTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCG
Found at i:69437 original size:83 final size:83
Alignment explanation
Indices: 69291--69622 Score: 335
Period size: 83 Copynumber: 3.8 Consensus size: 83
69281 ATTAGCAACA
* * * *
69291 TTTGTGGGAAAAGCGTCGCTAAAGACCATGTATTTAGC-AGCGTTTGTGAGAAAAGCGCTGCTAA
1 TTTGTGGGAAAAGC--CGCTAAAGACCATGTCTTTAGCGA-CATTTGTGAGAAAAGCACCGCTAA
**
69355 AGATCATGTTCTTTAGTAGCG
63 AGATCATGTTCTTTAGCGGCG
* *
69376 TTTGTGGGAAAAG-CGCTAAAGACCATGTTCTTTAGCGACGTTTGTGGGAAAAGCACCGCTAAAG
1 TTTGTGGGAAAAGCCGCTAAAGACCATG-TCTTTAGCGACATTTGTGAGAAAAGCACCGCTAAAG
*
69440 ACCATGTTCTTTAGCGGCG
65 ATCATGTTCTTTAGCGGCG
* * *
69459 TTTGTGGGAAAAGCGCCGTTAAAGACCATGTCTTTAGTGAAATTTGTGAGAAAAGCGCCGCTAAG
1 TTTGTGGGAAAA--GCCGCTAAAGACCATGTCTTTAGCGACATTTGTGAGAAAA-----GC--A-
69524 CCGCTAAAGATCATGTTCTTTAGCGGCG
56 CCGCTAAAGATCATGTTCTTTAGCGGCG
* * *
69552 TTTGTGGGAAAAGAAGCACCGCTAAAGACCATGTTCTTTAGCGGCATTTGTGAGAAAAACGCCGC
1 TTTGTGGG--AA-AAG--CCGCTAAAGACCATG-TCTTTAGCGACATTTGTGAGAAAAGCACCGC
69617 TAAAGA
60 TAAAGA
69623 CTATATTCTA
Statistics
Matches: 209, Mismatches: 19, Indels: 34
0.80 0.07 0.13
Matches are distributed among these distances:
82 14 0.07
83 58 0.28
84 1 0.00
85 34 0.16
86 13 0.06
89 10 0.05
90 2 0.01
92 2 0.01
93 35 0.17
94 1 0.00
95 2 0.01
96 16 0.08
97 21 0.10
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (83 bp):
TTTGTGGGAAAAGCCGCTAAAGACCATGTCTTTAGCGACATTTGTGAGAAAAGCACCGCTAAAGA
TCATGTTCTTTAGCGGCG
Found at i:69547 original size:93 final size:96
Alignment explanation
Indices: 69431--69619 Score: 285
Period size: 93 Copynumber: 2.0 Consensus size: 96
69421 GGGAAAAGCA
* *
69431 CCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGG-AA-AAGCGCCGTTAAAGACCATG-TCTT
1 CCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAGAAGCACCGCTAAAGACCATGTTCTT
* *
69493 TAGTGAAATTTGTGAGAAAAGCGCCGCTAAG
66 TAGCGAAATTTGTGAGAAAAACGCCGCTAAG
*
69524 CCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGAAAAGAAGCACCGCTAAAGACCATGTTCT
1 CCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGG-AAAGAAGCACCGCTAAAGACCATGTTCT
**
69589 TTAGCGGCATTTGTGAGAAAAACGCCGCTAA
65 TTAGCGAAATTTGTGAGAAAAACGCCGCTAA
69620 AGACTATATT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
93 35 0.41
95 2 0.02
96 18 0.21
97 30 0.35
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (96 bp):
CCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAGAAGCACCGCTAAAGACCATGTTCTT
TAGCGAAATTTGTGAGAAAAACGCCGCTAAG
Found at i:71954 original size:28 final size:28
Alignment explanation
Indices: 71910--71980 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
71900 GTGCGCTCTT
* **
71910 TATTCTGTTTAAGCACTTTAGTGCTT-TTC
1 TATTCTG-ATAAGCACTACAGTG-TTGTTC
71939 TATTCTGATAAGCACTACAGTGTTGTTC
1 TATTCTGATAAGCACTACAGTGTTGTTC
*
71967 TGTTCTGATAAGCA
1 TATTCTGATAAGCA
71981 TATTGGTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 2 0.05
28 28 0.76
29 7 0.19
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.44
Consensus pattern (28 bp):
TATTCTGATAAGCACTACAGTGTTGTTC
Found at i:71997 original size:28 final size:28
Alignment explanation
Indices: 71941--71999 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
71931 TGCTTTTCTA
*
71941 TTCTGATAAGCACTACAGTGTTGTTCTG
1 TTCTGATAAGCACTACAGTGTTGTACTG
**
71969 TTCTGATAAGCA-TATTGGTGTTGTACTG
1 TTCTGATAAGCACTA-CAGTGTTGTACTG
71997 TTC
1 TTC
72000 CGTTAACGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.42
Consensus pattern (28 bp):
TTCTGATAAGCACTACAGTGTTGTACTG
Found at i:83248 original size:23 final size:25
Alignment explanation
Indices: 83222--83267 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
83212 TCAATTAGGG
83222 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
83245 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
83268 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:99844 original size:22 final size:22
Alignment explanation
Indices: 99816--99882 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
99806 TTTTGGGCAT
99816 TATAAGACCTATATAAACCAGA
1 TATAAGACCTATATAAACCAGA
** *
99838 TATAAGA---A-A-AAGGCA-T
1 TATAAGACCTATATAAACCAGA
99854 TATAAGACCTATATAAACCAGA
1 TATAAGACCTATATAAACCAGA
99876 TATAAGA
1 TATAAGA
99883 AAAAGGGAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
16 7 0.21
17 4 0.12
18 1 0.03
19 2 0.06
20 1 0.03
21 4 0.12
22 14 0.42
ACGTcount: A:0.52, C:0.13, G:0.12, T:0.22
Consensus pattern (22 bp):
TATAAGACCTATATAAACCAGA
Found at i:99862 original size:38 final size:38
Alignment explanation
Indices: 99811--99888 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
99801 GGGTTTTTTG
99811 GGCATTATAAGACCTATATAAACCAGATATAAGAAAAA
1 GGCATTATAAGACCTATATAAACCAGATATAAGAAAAA
99849 GGCATTATAAGACCTATATAAACCAGATATAAGAAAAA
1 GGCATTATAAGACCTATATAAACCAGATATAAGAAAAA
99887 GG
1 GG
99889 GAGTAAGGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.51, C:0.13, G:0.15, T:0.21
Consensus pattern (38 bp):
GGCATTATAAGACCTATATAAACCAGATATAAGAAAAA
Found at i:103042 original size:3 final size:3
Alignment explanation
Indices: 103034--103070 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
103024 ATGCCGTCCA
103034 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC T
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC T
103071 AATCCCACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
TCC
Found at i:110519 original size:24 final size:24
Alignment explanation
Indices: 110503--110577 Score: 132
Period size: 24 Copynumber: 3.1 Consensus size: 24
110493 AGTTTGACTC
110503 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
110527 AAACAAATATACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
110551 AAACAATTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
110575 AAA
1 AAA
110578 GATTATTTCT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.53, C:0.08, G:0.12, T:0.27
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:121105 original size:23 final size:22
Alignment explanation
Indices: 121074--121134 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
121064 AATTTTAAAT
121074 AAATAAAAAAATTATTAAATATTA
1 AAAT-AAAAAATTA-TAAATATTA
*
121098 AAATAAAAAA-TATAAATATTT
1 AAATAAAAAATTATAAATATTA
*
121119 TAA-AAAAAATTA-AAAT
1 AAATAAAAAATTATAAAT
121135 CTAATATGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 10 0.29
21 12 0.35
22 2 0.06
23 6 0.18
24 4 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATAAAAAATTATAAATATTA
Found at i:121126 original size:21 final size:21
Alignment explanation
Indices: 121061--121128 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 21
121051 ATGACTATAT
*
121061 AAAAATTTTAAATA--AATAAA
1 AAAAATATTAAATATTAA-AAA
*
121081 AAAATTATTAAATATTAAAATA
1 AAAAATATTAAATATTAAAA-A
**
121103 AAAAATA-TAAATATTTTAAA
1 AAAAATATTAAATATTAAAAA
121123 AAAAAT
1 AAAAAT
121129 TAAAATCTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 19 0.47
21 12 0.30
22 9 0.22
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAAATATTAAATATTAAAAA
Found at i:122435 original size:18 final size:18
Alignment explanation
Indices: 122391--122437 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
122381 GTGTAACTTG
*
122391 TAACTAAAATAATTATGT
1 TAACTAAATTAATTATGT
122409 TAACTAAATTAATTATGT
1 TAACTAAATTAATTATGT
122427 TAACTAAATTA
1 TAACTAAATTA
122438 TAAGATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (18 bp):
TAACTAAATTAATTATGT
Found at i:123719 original size:16 final size:16
Alignment explanation
Indices: 123689--123731 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
123679 TGATAATTTT
*
123689 AAACATTATATAAAAAA
1 AAACA-TATAAAAAAAA
*
123706 GAACATATAAAAAAAA
1 AAACATATAAAAAAAA
*
123722 AAACTTATAA
1 AAACATATAA
123732 TGAAATTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.21
Consensus pattern (16 bp):
AAACATATAAAAAAAA
Found at i:133348 original size:6 final size:6
Alignment explanation
Indices: 133337--133362 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
133327 AAGGGAAGAG
133337 GATGAA GATGAA GATGAA GATGAA GA
1 GATGAA GATGAA GATGAA GATGAA GA
133363 AGAGAGGCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (6 bp):
GATGAA
Found at i:135109 original size:21 final size:20
Alignment explanation
Indices: 135083--135121 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
135073 AAAGATATAT
*
135083 ATTATTTATTTTAACATTTTC
1 ATTATTTAATTTAA-ATTTTC
135104 ATTATTTAATTTAAATTT
1 ATTATTTAATTTAAATTT
135122 AAATTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTATTTAATTTAAATTTTC
Found at i:142922 original size:21 final size:21
Alignment explanation
Indices: 142896--142949 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
142886 CTTGAATACT
142896 AAACCTTAAACCAT-AAATCTC
1 AAACCTTAAACC-TCAAATCTC
* *
142917 AAACCTTGAATCTCAAATCTC
1 AAACCTTAAACCTCAAATCTC
* *
142938 AAATCTCAAACC
1 AAACCTTAAACC
142950 CAATATTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.44, C:0.30, G:0.02, T:0.24
Consensus pattern (21 bp):
AAACCTTAAACCTCAAATCTC
Found at i:143065 original size:14 final size:14
Alignment explanation
Indices: 143046--143113 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
143036 TTTATGGGTT
143046 GAGTTCGAGGTTTA
1 GAGTTCGAGGTTTA
*
143060 GAGTTCGATGTTT-
1 GAGTTCGAGGTTTA
*
143073 GAGGTTTG-GGATTTA
1 GA-GTTCGAGG-TTTA
*
143088 -AGATTCGAGGTTTG
1 GAG-TTCGAGGTTTA
*
143102 GAGTTCAAGGTT
1 GAGTTCGAGGTT
143114 CAAAGGAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
13 4 0.10
14 34 0.81
15 4 0.10
ACGTcount: A:0.21, C:0.06, G:0.35, T:0.38
Consensus pattern (14 bp):
GAGTTCGAGGTTTA
Found at i:144964 original size:22 final size:21
Alignment explanation
Indices: 144913--144979 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
144903 CCGAGTTACT
*
144913 ATTTAATAAAAAAAATATTTTTTA
1 ATTTAAT--AAAAAAT-TTTATTA
* *
144937 ATTTAATTATAAATTTTATTA
1 ATTTAATAAAAAATTTTATTA
144958 ATATTAATAAAAAATATTTATT
1 AT-TTAATAAAAAAT-TTTATT
144980 TTTTAAATGG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
21 8 0.22
22 15 0.42
23 6 0.17
24 7 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTTAATAAAAAATTTTATTA
Found at i:152226 original size:22 final size:23
Alignment explanation
Indices: 152184--152230 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
152174 AATAAAAAGT
152184 TTTAAATTATATTCATGTTTATAA
1 TTTAAATTATATTCA-GTTTATAA
152208 TTTAAATTAT-TTCCA-TTTATAA
1 TTTAAATTATATT-CAGTTTATAA
152230 T
1 T
152231 ATTTAATTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 2 0.09
24 12 0.55
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTAAATTATATTCAGTTTATAA
Found at i:155819 original size:18 final size:18
Alignment explanation
Indices: 155796--155831 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
155786 TACATTAATA
*
155796 AAATTAACTAATAATTAT
1 AAATTAAATAATAATTAT
*
155814 AAATTAAATTATAATTAT
1 AAATTAAATAATAATTAT
155832 CACAATCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTAAATAATAATTAT
Found at i:160140 original size:18 final size:17
Alignment explanation
Indices: 160119--160168 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
160109 TTTTTAATTT
160119 TTTTCTTTTCATTTTCC
1 TTTTCTTTTCATTTTCC
* **
160136 ATTTTCTTCTGTTTTTCC
1 -TTTTCTTTTCATTTTCC
*
160154 TTTTGTTTTCATTTT
1 TTTTCTTTTCATTTT
160169 TTTAATGTAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.72
Consensus pattern (17 bp):
TTTTCTTTTCATTTTCC
Found at i:161864 original size:12 final size:11
Alignment explanation
Indices: 161847--161885 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
161837 TAAATTCACA
161847 ATAAAAAAAATT
1 ATAAAAAAAA-T
161859 ATAAAAAAAA-
1 ATAAAAAAAAT
161869 ATAAAAAAAAT
1 ATAAAAAAAAT
*
161880 AGAAAA
1 ATAAAA
161886 CAACAACCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 10 0.40
11 5 0.20
12 10 0.40
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (11 bp):
ATAAAAAAAAT
Found at i:166943 original size:22 final size:21
Alignment explanation
Indices: 166915--166959 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
166905 TTGCATTTAA
*
166915 TTTTTTTCTTCTATTTGTAGTT
1 TTTTTTTCTT-TATTTGTAATT
*
166937 TTTTTTTCTTTCTTTGTAATT
1 TTTTTTTCTTTATTTGTAATT
166958 TT
1 TT
166960 CCCATTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.09, C:0.09, G:0.07, T:0.76
Consensus pattern (21 bp):
TTTTTTTCTTTATTTGTAATT
Found at i:169768 original size:17 final size:17
Alignment explanation
Indices: 169748--169781 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
169738 TAATTTTTAA
* *
169748 TTAAAATTGTATTTTTT
1 TTAAAAATGAATTTTTT
169765 TTAAAAATGAATTTTTT
1 TTAAAAATGAATTTTTT
169782 AAAAATAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
TTAAAAATGAATTTTTT
Found at i:174547 original size:15 final size:16
Alignment explanation
Indices: 174527--174566 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
174517 TTGATAAATT
174527 AAAAAATTAAGT-CTG
1 AAAAAATTAAGTACTG
*
174542 AAAAAA-TAAGTATTG
1 AAAAAATTAAGTACTG
174557 -AAAAATTAAG
1 AAAAAATTAAG
174567 GGTTGAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.60, C:0.03, G:0.12, T:0.25
Consensus pattern (16 bp):
AAAAAATTAAGTACTG
Found at i:174660 original size:27 final size:27
Alignment explanation
Indices: 174630--174683 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
174620 AATTACAATT
174630 AGATTATTCGATAAAAGGATAATATAA
1 AGATTATTCGATAAAAGGATAATATAA
*
174657 AGATTGTTCGATAAAAGGATAATATAA
1 AGATTATTCGATAAAAGGATAATATAA
174684 TCTTAAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.50, C:0.04, G:0.17, T:0.30
Consensus pattern (27 bp):
AGATTATTCGATAAAAGGATAATATAA
Found at i:174845 original size:16 final size:18
Alignment explanation
Indices: 174819--174854 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
174809 GTGGGTGATC
174819 AAATGTGTTGAAAA-ATT
1 AAATGTGTTGAAAATATT
174836 AAAT-TGTTGAAAATATT
1 AAATGTGTTGAAAATATT
174853 AA
1 AA
174855 TTTTCAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (18 bp):
AAATGTGTTGAAAATATT
Found at i:175830 original size:16 final size:17
Alignment explanation
Indices: 175806--175852 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
175796 TCTAAATTAC
175806 ATAATATATAAAAATAAT
1 ATAA-ATATAAAAATAAT
* *
175824 AT-AATAT-AAAGTATT
1 ATAAATATAAAAATAAT
175839 ATAAATATAAAAAT
1 ATAAATATAAAAAT
175853 GGGTCAAGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 8 0.33
16 9 0.38
17 5 0.21
18 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
ATAAATATAAAAATAAT
Found at i:176744 original size:40 final size:41
Alignment explanation
Indices: 176678--176772 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 41
176668 AAACGCTGCA
* **
176678 AAAAGT-AGAGCAATAGCGGCGCTTATGGAAAAGCGCCACT
1 AAAAGTCAGAGCAATAACAACGCTTATGGAAAAGCGCCACT
* * *
176718 AAAAGTCAGAGCAATAACAACG-TTATGGGAAAGCGTCGCT
1 AAAAGTCAGAGCAATAACAACGCTTATGGAAAAGCGCCACT
*
176758 AAAGGTCAGAGCAAT
1 AAAAGTCAGAGCAAT
176773 TGCAGCGCTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 35 0.74
41 12 0.26
ACGTcount: A:0.40, C:0.18, G:0.26, T:0.16
Consensus pattern (41 bp):
AAAAGTCAGAGCAATAACAACGCTTATGGAAAAGCGCCACT
Found at i:188187 original size:20 final size:21
Alignment explanation
Indices: 188148--188193 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
188138 CATTAAATCA
188148 GATTTTATAATTCTTTTAAAT
1 GATTTTATAATTCTTTTAAAT
188169 GATTTTA-AATT-TTTATAAAT
1 GATTTTATAATTCTTT-TAAAT
*
188189 TATTT
1 GATTT
188194 ATTTGATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 3 0.13
20 13 0.57
21 7 0.30
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (21 bp):
GATTTTATAATTCTTTTAAAT
Found at i:189011 original size:9 final size:9
Alignment explanation
Indices: 188997--189024 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
188987 CTTCACCTGT
188997 GCAGCAGTA
1 GCAGCAGTA
189006 GCAGCAGTA
1 GCAGCAGTA
189015 GCAGCAGTA
1 GCAGCAGTA
189024 G
1 G
189025 ATGCTTTCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.36, T:0.11
Consensus pattern (9 bp):
GCAGCAGTA
Found at i:189979 original size:24 final size:24
Alignment explanation
Indices: 189934--189979 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
189924 CCTCACTGGA
*
189934 CTCTTCATCCTCAGCAGAACTACC
1 CTCTTCATCCTCAGCACAACTACC
* *
189958 CTCTTCATCCTCATCACTACTA
1 CTCTTCATCCTCAGCACAACTA
189980 TCGTCCTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.41, G:0.04, T:0.30
Consensus pattern (24 bp):
CTCTTCATCCTCAGCACAACTACC
Found at i:203503 original size:9 final size:8
Alignment explanation
Indices: 203464--203502 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
203454 AATAAAAATG
203464 TAATTTTA
1 TAATTTTA
*
203472 TCATTTTA
1 TAATTTTA
203480 TTAA-TTTA
1 -TAATTTTA
203488 TAATTTTA
1 TAATTTTA
203496 TAATTTT
1 TAATTTT
203503 TTGAAGGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 3 0.11
8 22 0.81
9 2 0.07
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (8 bp):
TAATTTTA
Found at i:205387 original size:15 final size:15
Alignment explanation
Indices: 205348--205388 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
205338 CTATTTGAAA
205348 ATATT-TTATATAAT
1 ATATTATTATATAAT
*
205362 ATA-TACATATATAAT
1 ATATTA-TTATATAAT
205377 ATATTATTATAT
1 ATATTATTATAT
205389 GTTATATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
13 1 0.05
14 3 0.14
15 16 0.73
16 2 0.09
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATTATTATATAAT
Found at i:206952 original size:14 final size:14
Alignment explanation
Indices: 206935--206968 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
206925 AGTCTGTTTA
206935 TATTTTGATAATTC
1 TATTTTGATAATTC
206949 TATTTTGATAATTC
1 TATTTTGATAATTC
*
206963 AATTTT
1 TATTTT
206969 AGAATGTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (14 bp):
TATTTTGATAATTC
Found at i:207852 original size:28 final size:28
Alignment explanation
Indices: 207821--207874 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
207811 TCTTTTAAAG
*
207821 AAAATATAAATT-ATAATATAATAAAATA
1 AAAATATAAATTAATAA-AAAATAAAATA
*
207849 AAAATATATATTAATAAAAAATAAAA
1 AAAATATAAATTAATAAAAAATAAAA
207875 AAATTAGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (28 bp):
AAAATATAAATTAATAAAAAATAAAATA
Found at i:207869 original size:23 final size:22
Alignment explanation
Indices: 207821--207875 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
207811 TCTTTTAAAG
*
207821 AAAATATAAATTATAATATAAT
1 AAAATAAAAATTATAATATAAT
*
207843 AAAATAAAAATATATATTAATAA-
1 AAAATAAAAAT-TATAAT-ATAAT
207866 AAAATAAAAA
1 AAAATAAAAA
207876 AATTAGGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 10 0.34
23 15 0.52
24 4 0.14
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAATAAAAATTATAATATAAT
Found at i:207877 original size:26 final size:26
Alignment explanation
Indices: 207816--207877 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 26
207806 TAAACTCTTT
* *
207816 TAAAGAAAATATAAATTATAATATAA
1 TAAAAAAAATATAAATTATAATAAAA
*
207842 TAAAATAAAAATATATATTAATAA-AAAA
1 T-AAA-AAAAATATAAATT-ATAATAAAA
207870 TAAAAAAA
1 TAAAAAAA
207878 TTAGGATTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 5 0.17
27 6 0.20
28 15 0.50
29 4 0.13
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (26 bp):
TAAAAAAAATATAAATTATAATAAAA
Found at i:211432 original size:10 final size:12
Alignment explanation
Indices: 211408--211436 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
211398 TAAATAGTAA
211408 ATATTTAATTAT
1 ATATTTAATTAT
211420 ATATTTAATTAT
1 ATATTTAATTAT
211432 ATATT
1 ATATT
211437 ACTTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATATTTAATTAT
Found at i:211633 original size:32 final size:33
Alignment explanation
Indices: 211561--211623 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
211551 CACAAAATTG
*
211561 TATTAATATGCAAAAATTTTATATAATATTAAT
1 TATTAATATACAAAAATTTTATATAATATTAAT
*
211594 TATTAATATACCAAAA-TTTATATAAATATT
1 TATTAATATACAAAAATTTTATAT-AATATT
211624 TAATATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 7 0.26
33 20 0.74
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (33 bp):
TATTAATATACAAAAATTTTATATAATATTAAT
Found at i:212313 original size:21 final size:21
Alignment explanation
Indices: 212289--212328 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
212279 AATTTAATTC
* *
212289 TTACCTATAAAATAAAAAATA
1 TTACCTAAAAAAAAAAAAATA
*
212310 TTACTTAAAAAAAAAAAAA
1 TTACCTAAAAAAAAAAAAA
212329 AAAGAGATGA
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:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (21 bp):
TTACCTAAAAAAAAAAAAATA
Found at i:216338 original size:17 final size:18
Alignment explanation
Indices: 216295--216341 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
216285 CAAAAATATG
* *
216295 TTTCACGTCAAATCAATT
1 TTTCATGTCAAATCAAAT
*
216313 TTTCGTGTCAAAT-AAAT
1 TTTCATGTCAAATCAAAT
216330 TTTCATGTCAAA
1 TTTCATGTCAAA
216342 AATACTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (18 bp):
TTTCATGTCAAATCAAAT
Found at i:218390 original size:63 final size:63
Alignment explanation
Indices: 218261--218382 Score: 158
Period size: 62 Copynumber: 2.0 Consensus size: 63
218251 CACTCTCAAC
* * **
218261 AATTATGTAGTTTTTATTCCCCAATGCGGGTTTAATTTCAAATTTGATCCCTTGTACTTTACA
1 AATTACGTAGTTTTTATTCCCCAATGCGGGTTCAATTTCAAATTCAATCCCTTGTACTTTACA
* ** *
218324 AATTACGTAGTTTTT-TTCCTCAATGTTGGTTCAATTTCCAATTCAATCCCTT-TACTTTA
1 AATTACGTAGTTTTTATTCCCCAATGCGGGTTCAATTTCAAATTCAATCCCTTGTACTTTA
218383 TGTAAATTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
61 7 0.14
62 30 0.59
63 14 0.27
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.46
Consensus pattern (63 bp):
AATTACGTAGTTTTTATTCCCCAATGCGGGTTCAATTTCAAATTCAATCCCTTGTACTTTACA
Found at i:221947 original size:13 final size:13
Alignment explanation
Indices: 221929--221961 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
221919 GGATAATTAC
*
221929 GAACTTTGAGTAT
1 GAACTTTGAATAT
221942 GAACTTTGAATAT
1 GAACTTTGAATAT
221955 GAACTTT
1 GAACTTT
221962 AAAATCAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (13 bp):
GAACTTTGAATAT
Found at i:226129 original size:71 final size:71
Alignment explanation
Indices: 226036--226179 Score: 234
Period size: 71 Copynumber: 2.0 Consensus size: 71
226026 GAGTGCACTG
* *
226036 AAGCGTATTTTATTATTGTTTATGGATTGAAAAGAGATTATGAATTGCAATAACACTAATCACAT
1 AAGCGTATTATATTATTATTTATGGATTGAAAAGAGATTATGAATTGCAATAACACTAATCACAT
226101 CATCAA
66 CATCAA
* * * *
226107 AAGCGTATTATCTTCTTATTTATGGATTGAAAAGAGATTATGGATTGCGATAACACTAATCACAT
1 AAGCGTATTATATTATTATTTATGGATTGAAAAGAGATTATGAATTGCAATAACACTAATCACAT
226172 CATCAA
66 CATCAA
226178 AA
1 AA
226180 CTTGACAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (71 bp):
AAGCGTATTATATTATTATTTATGGATTGAAAAGAGATTATGAATTGCAATAACACTAATCACAT
CATCAA
Found at i:226978 original size:171 final size:171
Alignment explanation
Indices: 226686--227247 Score: 851
Period size: 171 Copynumber: 3.3 Consensus size: 171
226676 ACAGAGCTTG
* * * * * *
226686 TTAATAACTGTTTGATTAAATTAATTGAGCAATGAATTTATAATTTAGTTTTAT-GCACTAA-TC
1 TTAATTACTGTTTAATTAAATTAATTTAGTAATGAATTTATAATTTAGCTTCATGGC-C-AATTC
* * *
226749 ACATCACTGATTTTTAGATTTGATTTAGTTTCGTTAATCTATGCAATAATCGCATCATTGAAACT
64 ACATCACTGATTTTTAGATCTGATTTAGTTTCGTTAATCTATGCAATGATCACATCATTGAAACT
*
226814 AGATCAATCTGAGTTGGAGGTTTTTACTGACGAGAAACCTTCT
129 AGATCAATCTGAGTTGAAGGTTTTTACTGACGAGAAACCTTCT
* *
226857 TTAATTACTGTTTAATTAGATTCATTTAGTAATGAATTTATAATTTAGCTTCATGGCCAATTCAC
1 TTAATTACTGTTTAATTAAATTAATTTAGTAATGAATTTATAATTTAGCTTCATGGCCAATTCAC
* *
226922 ATCACTGATTTTTAGATCCGATTTAGTTTCGTTGATCTATGCAATGATCACATCATTGAAACTAG
66 ATCACTGATTTTTAGATCTGATTTAGTTTCGTTAATCTATGCAATGATCACATCATTGAAACTAG
*
226987 ATCAATCTGAGTTGAAGGTTTTTACCGACGAGAAACCTTCT
131 ATCAATCTGAGTTGAAGGTTTTTACTGACGAGAAACCTTCT
* * *
227028 TTAATTACTGTTTGA-TAGATTAATTTAGTAAATGAATTTATAATTTAGCTTCATGGCCTATTCA
1 TTAATTACTGTTTAATTAAATTAATTTAGT-AATGAATTTATAATTTAGCTTCATGGCCAATTCA
* *
227092 CATGACTGATTTTTAGATCTGATTTAGTTTCGTTAATCTATGCAATGATCACATCACTGAAACTA
65 CATCACTGATTTTTAGATCTGATTTAGTTTCGTTAATCTATGCAATGATCACATCATTGAAACTA
* *
227157 GATTAATCTGAGTTGAAGGTTTTTACTAACGAGAAACCTTCT
130 GATCAATCTGAGTTGAAGGTTTTTACTGACGAGAAACCTTCT
*
227199 TTAATTACTGTTTTTAATTAAATTAATTTAGTAATGAATTTAGAATTTA
1 TTAATTACTG--TTTAATTAAATTAATTTAGTAATGAATTTATAATTTA
227248 AATCAATTGA
Statistics
Matches: 357, Mismatches: 28, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
170 15 0.04
171 307 0.86
172 2 0.01
173 20 0.06
174 13 0.04
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (171 bp):
TTAATTACTGTTTAATTAAATTAATTTAGTAATGAATTTATAATTTAGCTTCATGGCCAATTCAC
ATCACTGATTTTTAGATCTGATTTAGTTTCGTTAATCTATGCAATGATCACATCATTGAAACTAG
ATCAATCTGAGTTGAAGGTTTTTACTGACGAGAAACCTTCT
Found at i:236199 original size:12 final size:12
Alignment explanation
Indices: 236182--236212 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
236172 CATACCATAT
236182 TGATGATGCTGA
1 TGATGATGCTGA
*
236194 TGATGATGGTGA
1 TGATGATGCTGA
236206 TGATGAT
1 TGATGAT
236213 TCTCCATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.35, T:0.35
Consensus pattern (12 bp):
TGATGATGCTGA
Found at i:253324 original size:21 final size:22
Alignment explanation
Indices: 253295--253336 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
253285 GAGCACAGGG
*
253295 AAGCTCTAATTAGCTCCATTAA
1 AAGCTCTAATTAGCACCATTAA
*
253317 AAGC-CTAATTATCACCATTA
1 AAGCTCTAATTAGCACCATTA
253337 TTGACTGTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (22 bp):
AAGCTCTAATTAGCACCATTAA
Found at i:262854 original size:16 final size:18
Alignment explanation
Indices: 262833--262872 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
262823 ATTAACTAAT
262833 TAAACTAAGT-TA-ATAC
1 TAAACTAAGTATATATAC
*
262849 TAAACTAAGTATATATAT
1 TAAACTAAGTATATATAC
262867 TAAACT
1 TAAACT
262873 TGTGGAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
17 2 0.10
18 9 0.43
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (18 bp):
TAAACTAAGTATATATAC
Found at i:264964 original size:14 final size:14
Alignment explanation
Indices: 264875--264965 Score: 69
Period size: 14 Copynumber: 6.6 Consensus size: 14
264865 TTCTCGTAAA
*
264875 AGTCAATGATCAAT
1 AGTCAACGATCAAT
**
264889 AGTCAATTATCAAT
1 AGTCAACGATCAAT
* *
264903 AGTCAACTATCAAC
1 AGTCAACGATCAAT
*
264917 GGTCAAC-AGTCAA-
1 AGTCAACGA-TCAAT
* * *
264930 AGTTAATGATCAAC
1 AGTCAACGATCAAT
*
264944 GGTCAACGATCAAT
1 AGTCAACGATCAAT
264958 AGTCAACG
1 AGTCAACG
264966 GGTCAGGTCG
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
13 9 0.15
14 53 0.85
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (14 bp):
AGTCAACGATCAAT
Found at i:265080 original size:16 final size:16
Alignment explanation
Indices: 265059--265090 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
265049 TGGTTTGCGG
*
265059 TTTAGGTTTGGTTTAA
1 TTTAGGTTTGGGTTAA
265075 TTTAGGTTTGGGTTAA
1 TTTAGGTTTGGGTTAA
265091 AAGGTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.53
Consensus pattern (16 bp):
TTTAGGTTTGGGTTAA
Found at i:272002 original size:7 final size:7
Alignment explanation
Indices: 271990--272075 Score: 50
Period size: 7 Copynumber: 12.4 Consensus size: 7
271980 TCTCGAAAAA
271990 GTCAACG
1 GTCAACG
271997 GTCAACG
1 GTCAACG
* *
272004 GGCAA-A
1 GTCAACG
*
272010 GTCAATG
1 GTCAACG
*
272017 GTCAACA
1 GTCAACG
272024 GTCAACG
1 GTCAACG
*
272031 GTTAACG
1 GTCAACG
* *
272038 GGCAA-A
1 GTCAACG
**
272044 GTCAATA
1 GTCAACG
*
272051 GTCAATG
1 GTCAACG
*
272058 GTCAACA
1 GTCAACG
272065 GTCAACAG
1 GTCAAC-G
272073 GTC
1 GTC
272076 GGGTAGGGTT
Statistics
Matches: 60, Mismatches: 16, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
6 8 0.13
7 49 0.82
8 3 0.05
ACGTcount: A:0.35, C:0.22, G:0.26, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:272012 original size:20 final size:20
Alignment explanation
Indices: 271987--272048 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
271977 GTTTCTCGAA
271987 AAAGTCAACGGTCAACGGGC
1 AAAGTCAACGGTCAACGGGC
*
272007 AAAGTCAATGGTCAA----C
1 AAAGTCAACGGTCAACGGGC
*
272023 --AGTCAACGGTTAACGGGC
1 AAAGTCAACGGTCAACGGGC
272041 AAAGTCAA
1 AAAGTCAA
272049 TAGTCAATGG
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
14 11 0.33
16 1 0.03
18 1 0.03
20 20 0.61
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.15
Consensus pattern (20 bp):
AAAGTCAACGGTCAACGGGC
Found at i:272027 original size:34 final size:34
Alignment explanation
Indices: 271989--272070 Score: 119
Period size: 34 Copynumber: 2.4 Consensus size: 34
271979 TTCTCGAAAA
*
271989 AGTCAACGGTCAACGGGCAAAGTCAATGGTCAAC
1 AGTCAACGGTCAACGGGCAAAGTCAATAGTCAAC
* *
272023 AGTCAACGGTTAACGGGCAAAGTCAATAGTCAAT
1 AGTCAACGGTCAACGGGCAAAGTCAATAGTCAAC
* *
272057 GGTCAACAGTCAAC
1 AGTCAACGGTCAAC
272071 AGGTCGGGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (34 bp):
AGTCAACGGTCAACGGGCAAAGTCAATAGTCAAC
Found at i:272187 original size:16 final size:16
Alignment explanation
Indices: 272166--272197 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
272156 TGGTTTGGGG
*
272166 TTTAGGTTTGGTTTAA
1 TTTAGGTTTGGGTTAA
272182 TTTAGGTTTGGGTTAA
1 TTTAGGTTTGGGTTAA
272198 AAGGTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.53
Consensus pattern (16 bp):
TTTAGGTTTGGGTTAA
Found at i:273820 original size:37 final size:37
Alignment explanation
Indices: 273764--273956 Score: 194
Period size: 37 Copynumber: 5.2 Consensus size: 37
273754 GGACTACTGG
*
273764 CACAAAGCTTGCTAGGCACATAGCCCGAATACACC-A
1 CACAAAGCTTGCTAGGCACACAGCCCGAATACACCGA
* * * *
273800 GCATAAAGCCTGCTATGCACACAGCCTGAATACACCGA
1 -CACAAAGCTTGCTAGGCACACAGCCCGAATACACCGA
** **
273838 CACAAAGCTTGCTAGGCACACAGCTTGAATACATTGA
1 CACAAAGCTTGCTAGGCACACAGCCCGAATACACCGA
* * * *
273875 CACAAAG-TCTACTAGGTACATAGCCCGAATATACCGA
1 CACAAAGCT-TGCTAGGCACACAGCCCGAATACACCGA
* * *
273912 CACAAA-TTCTGCTAGGCACACAACCTGAATACACCGA
1 CACAAAGCT-TGCTAGGCACACAGCCCGAATACACCGA
273949 CACAAAGC
1 CACAAAGC
273957 CTGAATATTT
Statistics
Matches: 126, Mismatches: 26, Indels: 7
0.79 0.16 0.04
Matches are distributed among these distances:
36 1 0.01
37 124 0.98
38 1 0.01
ACGTcount: A:0.37, C:0.30, G:0.17, T:0.17
Consensus pattern (37 bp):
CACAAAGCTTGCTAGGCACACAGCCCGAATACACCGA
Found at i:278344 original size:21 final size:21
Alignment explanation
Indices: 278314--278358 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
278304 TCTTTTTTTG
*
278314 GTATCGATAGATG-CATGACTT
1 GTATCGATAGAAGTCAT-ACTT
*
278335 GTATCTATAGAAGTCATACTT
1 GTATCGATAGAAGTCATACTT
278356 GTA
1 GTA
278359 CTGGTAGAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (21 bp):
GTATCGATAGAAGTCATACTT
Found at i:285308 original size:25 final size:25
Alignment explanation
Indices: 285280--285329 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
285270 GGAGAAGAAG
285280 CAAGTTGGCTACAAATATAAGATAA
1 CAAGTTGGCTACAAATATAAGATAA
285305 CAAGTTGGCTACAAATATAAGATAA
1 CAAGTTGGCTACAAATATAAGATAA
285330 AAAAGAGAGG
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:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (25 bp):
CAAGTTGGCTACAAATATAAGATAA
Found at i:290996 original size:21 final size:20
Alignment explanation
Indices: 290972--291012 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
290962 ACTTGATCTC
290972 CAAATCTTAAAACTTGAAACT
1 CAAATC-TAAAACTTGAAACT
* *
290993 CAAATCTCAAACTTTAAACT
1 CAAATCTAAAACTTGAAACT
291013 TTGAACTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.29
Consensus pattern (20 bp):
CAAATCTAAAACTTGAAACT
Found at i:291006 original size:20 final size:22
Alignment explanation
Indices: 290959--291012 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
290949 ACCTCAAAAC
*
290959 CAAACTTG-ATCTCCAAATCTT
1 CAAACTTGAAACTCCAAATCTT
*
290980 AAAACTTGAAACT-CAAATC-T
1 CAAACTTGAAACTCCAAATCTT
*
291000 CAAACTTTAAACT
1 CAAACTTGAAACT
291013 TTGAACTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 12 0.43
21 13 0.46
22 3 0.11
ACGTcount: A:0.43, C:0.24, G:0.04, T:0.30
Consensus pattern (22 bp):
CAAACTTGAAACTCCAAATCTT
Found at i:292739 original size:20 final size:19
Alignment explanation
Indices: 292714--292762 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
292704 TTGATATATT
292714 TTATAATTAC-TATATTTTAA
1 TTATAATTACTTA-ATTTT-A
*
292734 TTATAATTTCTTAATTTTA
1 TTATAATTACTTAATTTTA
*
292753 TAATAATTAC
1 TTATAATTAC
292763 AATAATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 9 0.36
20 14 0.56
21 2 0.08
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATAATTACTTAATTTTA
Found at i:316888 original size:31 final size:29
Alignment explanation
Indices: 316847--316925 Score: 81
Period size: 31 Copynumber: 2.7 Consensus size: 29
316837 ATTTTTTAAA
*
316847 ATTTTAAAAAATTCAAAATAATTATAAAATT
1 ATTTTAAAAAATTAAAAATAA-T-TAAAATT
* *
316878 ATTTTTAAAAATTAAAAATCATTAAAATT
1 ATTTTAAAAAATTAAAAATAATTAAAATT
*
316907 A--TAAAAAAATATAAAAATA
1 ATTTTAAAAAAT-TAAAAATA
316926 TTTTTTTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
27 7 0.17
28 7 0.17
29 8 0.20
30 1 0.02
31 18 0.44
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (29 bp):
ATTTTAAAAAATTAAAAATAATTAAAATT
Found at i:323012 original size:78 final size:76
Alignment explanation
Indices: 322930--323078 Score: 183
Period size: 78 Copynumber: 1.9 Consensus size: 76
322920 GGAAAAGAAT
* *
322930 AAGAGTTTAAGTTCTCATTTCCGGTACAAAACAATC-GAGGAAAATTTGCTTGCACAAAAAATGT
1 AAGAGTTTAAGTTCTCATTTCAGGTACAAAACAATCAG-GGAAAA--TGCTTGCACAAAAAATAT
322994 AACATCAAACACAG
63 AACATCAAACACAG
* * ** * **
323008 AAGAGTTTAAGTTTTCATTTTATTTACAAAACAATCAGGGAAAATGTTTGCACAAAATGTATAAC
1 AAGAGTTTAAGTTCTCATTTCAGGTACAAAACAATCAGGGAAAATGCTTGCACAAAAAATATAAC
323073 ATCAAA
66 ATCAAA
323079 TATAGCTGAA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
76 23 0.38
78 37 0.61
79 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (76 bp):
AAGAGTTTAAGTTCTCATTTCAGGTACAAAACAATCAGGGAAAATGCTTGCACAAAAAATATAAC
ATCAAACACAG
Found at i:330847 original size:4 final size:4
Alignment explanation
Indices: 330822--330908 Score: 68
Period size: 4 Copynumber: 21.2 Consensus size: 4
330812 AAATAAACGG
* * * *
330822 GAAA GAAA AAAA GAAAA AAAA GAAA GAAA GGAA GAAG GAGAA GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
* * * *
330872 GGAA GAAG GAGAG GAAA GAAA G-AA GAAG GAAA GAAA G
1 GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G
330909 TTAATGTGTT
Statistics
Matches: 65, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
3 3 0.05
4 52 0.80
5 10 0.15
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:330856 original size:21 final size:21
Alignment explanation
Indices: 330822--330878 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
330812 AAATAAACGG
**
330822 GAAAGAAAAAAAGAAAAAAAA
1 GAAAGAAAGGAAGAAAAAAAA
** *
330843 GAAAGAAAGGAAGAAGGAGAA
1 GAAAGAAAGGAAGAAAAAAAA
330864 GAAAGAAAGGAAGAA
1 GAAAGAAAGGAAGAA
330879 GGAGAGGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGGAAGAAAAAAAA
Found at i:330859 original size:7 final size:7
Alignment explanation
Indices: 330849--330902 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
330839 AAAAGAAAGA
330849 AAGGAAG
1 AAGGAAG
330856 AAGG-AG
1 AAGGAAG
*
330862 AAGAAAG
1 AAGGAAG
330869 AAAGGAAG
1 -AAGGAAG
330877 AAGG-AG
1 AAGGAAG
330883 -AGGAAAG
1 AAGG-AAG
*
330890 AAAGAAG
1 AAGGAAG
330897 AAGGAA
1 AAGGAA
330903 AGAAAGTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
5 3 0.08
6 7 0.18
7 20 0.53
8 8 0.21
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (7 bp):
AAGGAAG
Found at i:330865 original size:17 final size:15
Alignment explanation
Indices: 330843--330908 Score: 70
Period size: 15 Copynumber: 4.6 Consensus size: 15
330833 AGAAAAAAAA
330843 GAAAGAAAGGAAGAAG
1 GAAAGAAAGG-AGAAG
330859 GAGAAGAAA-GA-AAG
1 GA-AAGAAAGGAGAAG
330873 G-AAG-AAGGAG-AG
1 GAAAGAAAGGAGAAG
*
330885 GAAAGAAAGAAGAAG
1 GAAAGAAAGGAGAAG
330900 GAAAGAAAG
1 GAAAGAAAG
330909 TTAATGTGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
11 2 0.05
12 8 0.19
13 3 0.07
14 9 0.21
15 12 0.28
16 3 0.07
17 6 0.14
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (15 bp):
GAAAGAAAGGAGAAG
Found at i:330879 original size:21 final size:21
Alignment explanation
Indices: 330841--330908 Score: 113
Period size: 21 Copynumber: 3.3 Consensus size: 21
330831 AAAGAAAAAA
330841 AAGAAAGAAAGGAAGAAGGAG
1 AAGAAAGAAAGGAAGAAGGAG
330862 AAGAAAGAAAGGAAGAAGGAG
1 AAGAAAGAAAGGAAGAAGGAG
*
330883 AGGAAAGAAA-GAAGAAGGA-
1 AAGAAAGAAAGGAAGAAGGAG
330902 AAGAAAG
1 AAGAAAG
330909 TTAATGTGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.13
20 9 0.20
21 30 0.67
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (21 bp):
AAGAAAGAAAGGAAGAAGGAG
Found at i:334068 original size:21 final size:21
Alignment explanation
Indices: 334042--334083 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
334032 TTAGGGTCTA
*
334042 TTTGCCCCG-GAGGAGTAGAGT
1 TTTG-CCCGAGAGGAATAGAGT
334063 TTTGCCCGAGAGGAATAGAGT
1 TTTGCCCGAGAGGAATAGAGT
334084 ATCGCGATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.24
Consensus pattern (21 bp):
TTTGCCCGAGAGGAATAGAGT
Found at i:336102 original size:16 final size:16
Alignment explanation
Indices: 336081--336130 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
336071 TGATGGGGAT
336081 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
336097 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
336112 A-TATTTTGATAATTA
1 ATTATTTTGATAATTA
336127 ATTA
1 ATTA
336131 GTTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Done.