Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold271
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: 858520
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 36313 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:205432 original size:128 final size:128
Alignment explanation
Indices: 205203--205437 Score: 348
Period size: 128 Copynumber: 1.8 Consensus size: 128
205193 TACTCTGCTG
* *
205203 CAACTTCAGAGAGATGAGATATGTGGTTTTAATCCACTCCATTGCAACTTCAAGGAGATAGGATT
1 CAACTTCAGAGAGATAAGATATGTGGTTTTAATCCACTCCACTGCAACTTCAAGGAGATAGGATT
* * ** *
205268 GGTTTCTTCTGTCTGCTCCACTGCAACTGCAGGGAGATAAGACTGGATGCGATCCGCCCTTTA
66 GATTGCTTCTACCTGCTCCACTGCAACTGCAAGGAGATAAGACTGGATGCGATCCGCCCTTTA
* *
205331 CAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATT
1 CAACTTCAGAGAGATAAGATATGTGGTTTTAATCCACTCCACTGCAACTTCAAGGAGATAGGATT
*
205396 -ATTAGCTT-TAACCTGCTCCACTGCAACTTCAAGGAGATAAGA
66 GATT-GCTTCT-ACCTGCTCCACTGCAACTGCAAGGAGATAAGA
205438 TTCGCCATCT
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
127 3 0.03
128 92 0.97
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (128 bp):
CAACTTCAGAGAGATAAGATATGTGGTTTTAATCCACTCCACTGCAACTTCAAGGAGATAGGATT
GATTGCTTCTACCTGCTCCACTGCAACTGCAAGGAGATAAGACTGGATGCGATCCGCCCTTTA
Found at i:205498 original size:43 final size:44
Alignment explanation
Indices: 205408--205512 Score: 119
Period size: 44 Copynumber: 2.4 Consensus size: 44
205398 TAGCTTTAAC
205408 CTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCCATCTTCAGT
1 CTGC-CCACTGCAACTTCAAGGAGATAAGATTCGCCATCTTCAGT
* *
205453 CTGCCCACTGTAACTTC-AGGAGGATAAGACTT-G-CTTCCTT-AGT
1 CTGCCCACTGCAACTTCAAGGA-GATAAGA-TTCGCCAT-CTTCAGT
205496 CTGCCCCACTGCAACTT
1 CTG-CCCACTGCAACTT
205513 TGATCTACTT
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
43 12 0.23
44 35 0.66
45 6 0.11
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (44 bp):
CTGCCCACTGCAACTTCAAGGAGATAAGATTCGCCATCTTCAGT
Found at i:206145 original size:133 final size:133
Alignment explanation
Indices: 205539--206139 Score: 815
Period size: 133 Copynumber: 4.5 Consensus size: 133
205529 CTAGGGAGAT
* * * * *
205539 AAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGG-AGATAGAATTACCGGCTTCAATGT
1 AAGATCTGAAATCTTTAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTTCTGGCTTCAATGT
* * * *
205603 ACTCCACTGTAACCTCAGGGAAGTAAAATCCGCCATCCTTGATCTGCT-CACTATCTATGCAGGA
65 ACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTGTCTATGCAGGA
205667 AGGC
130 AGGC
* *
205671 AAGATCTGTAA---TTAATCTATT-CAGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGT
1 AAGATCTGAAATCTTTAATCTATTCCA-CTGCTGCCCAGGGAAGTAGAATTTCTGGCTTCAATGT
* * *
205732 ACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCACTACTGCT-TG--G
65 ACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACT-GT-CTATGCAG
* *
205794 GGAGAC
128 GAAGGC
* * *
205800 AAGATCTAAAATCTTTTAATCTATTCCACTGCTGACCAGGAAAGTAGAATTTCTGGCTTCAATGT
1 AAGATCTGAAATC-TTTAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTTCTGGCTTCAATGT
* * * * *
205865 ACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTTCGCTGTCTATGCAAGA
65 ACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTGTCTATGCAGGA
205930 AGGC
130 AGGC
* *
205934 AAGATCTGAAATCTTTAATCTATTCCACTGCTGACCAGGAAAGTAGAATTTCTGGCTTCAATGTA
1 AAGATCTGAAATCTTTAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTTCTGGCTTCAATGTA
* * * *
205999 CTCCACTGCAACTTCAGGGAGGTAAAATCCACCAGCTTTGATCTGCTCCGCTGTCTATGCAGGAA
66 CTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTGTCTATGCAGGAA
206064 GGC
131 GGC
*
206067 AAGATCTAAAATCTTTAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTTCTGGCTTCAATGTA
1 AAGATCTGAAATCTTTAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTTCTGGCTTCAATGTA
206132 CTCCACTG
66 CTCCACTG
206140 CAACTTNNNN
Statistics
Matches: 423, Mismatches: 33, Indels: 25
0.88 0.07 0.05
Matches are distributed among these distances:
128 2 0.00
129 98 0.23
130 6 0.01
131 5 0.01
132 16 0.04
133 278 0.66
134 18 0.04
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (133 bp):
AAGATCTGAAATCTTTAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTTCTGGCTTCAATGTA
CTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTGTCTATGCAGGAA
GGC
Found at i:218462 original size:41 final size:41
Alignment explanation
Indices: 218404--218644 Score: 331
Period size: 41 Copynumber: 5.9 Consensus size: 41
218394 AAATATTTTT
*
218404 GCGGCGCTTCTTCAAAAACACCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
218445 ACGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* * ** *
218486 GTGGCGCTTCATGGAAAACGCCGCGAAAGATCTGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGATCTGAGCATTA
*
218527 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGATCTGAGCATTA
*
218568 GCGGCGCTTCTTCAAAAACGCCGCTAAAGATCTAAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* * * *
218609 GCGGTGCTTTTTTTC-CAAATGCCGCTAAAGATCTGA
1 GCGGCGC--TTCTTCAAAAACGCCGCTAAAGATCTGA
218645 AAGGTAGAAA
Statistics
Matches: 175, Mismatches: 23, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
41 152 0.87
42 18 0.10
43 5 0.03
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (41 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:218732 original size:39 final size:40
Alignment explanation
Indices: 218675--218810 Score: 121
Period size: 40 Copynumber: 3.4 Consensus size: 40
218665 TGGGCTTTGG
* *
218675 TTTTTTGCGGCGTTTTTCCAAAAAACGCCGCTAATGCTC-A
1 TTTTTAGCGGCG-TTTTCCAAAAAGCGCCGCTAATGCTCGA
* *** *
218715 TTTTTAGCGGCGCTTTCCTGGAAGCTCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTCCAAAAAGCGCCGCTAATGCTCGA
* * * * * *
218755 TCTTTAGCGGTGTTTTACATAAGGCGCCTCTAATGCTCGA
1 TTTTTAGCGGCGTTTTCCAAAAAGCGCCGCTAATGCTCGA
* *
218795 TTTTTAGTGACGTTTT
1 TTTTTAGCGGCGTTTT
218811 TTGTCCAAAC
Statistics
Matches: 74, Mismatches: 21, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
39 20 0.27
40 54 0.73
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTCCAAAAAGCGCCGCTAATGCTCGA
Found at i:219739 original size:20 final size:20
Alignment explanation
Indices: 219714--219755 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
219704 TTAAATTAAA
219714 AACTTACTAACGAAAGCAGT
1 AACTTACTAACGAAAGCAGT
219734 AACTTACTAACGAAAGCAGT
1 AACTTACTAACGAAAGCAGT
219754 AA
1 AA
219756 TTAAAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.19, G:0.14, T:0.19
Consensus pattern (20 bp):
AACTTACTAACGAAAGCAGT
Found at i:221222 original size:9 final size:9
Alignment explanation
Indices: 221208--221238 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
221198 GTTAAACGAA
221208 TCGAGTTAT
1 TCGAGTTAT
*
221217 TCGAGTTAA
1 TCGAGTTAT
221226 TCGAGTTAT
1 TCGAGTTAT
221235 TCGA
1 TCGA
221239 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:221316 original size:9 final size:9
Alignment explanation
Indices: 221292--221328 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
221282 TGAGTTTTCG
221292 AATTCGAAT
1 AATTCGAAT
**
221301 AGCTCGAAT
1 AATTCGAAT
221310 AATTCGAAT
1 AATTCGAAT
221319 AATTCGAAT
1 AATTCGAAT
221328 A
1 A
221329 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:225385 original size:27 final size:27
Alignment explanation
Indices: 225349--225416 Score: 111
Period size: 27 Copynumber: 2.5 Consensus size: 27
225339 AAATAAAAAA
*
225349 TTACCAAAATGT-TATAATTTTTTTTAT
1 TTACCAAAATATATATAA-TTTTTTTAT
225376 TTACCAAAATATATATAATTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTAT
225403 TTACCAAAATATAT
1 TTACCAAAATATAT
225417 CAAAAAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 34 0.87
28 5 0.13
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.50
Consensus pattern (27 bp):
TTACCAAAATATATATAATTTTTTTAT
Found at i:225442 original size:19 final size:19
Alignment explanation
Indices: 225418--225462 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
225408 AAAATATATC
225418 AAAAAAAAACAAAAAACAA
1 AAAAAAAAACAAAAAACAA
* *
225437 AAAAAAAAATAAAAAACAG
1 AAAAAAAAACAAAAAACAA
225456 AAAAAAA
1 AAAAAAA
225463 CCTGAACTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.89, C:0.07, G:0.02, T:0.02
Consensus pattern (19 bp):
AAAAAAAAACAAAAAACAA
Found at i:225533 original size:27 final size:27
Alignment explanation
Indices: 225503--225569 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
225493 AGGGAAGCAG
225503 GTTGGCGGCACCAAACAAGGGAACCCT
1 GTTGGCGGCACCAAACAAGGGAACCCT
*
225530 GTTGGCGGCACCAAACAAGGGATCCCT
1 GTTGGCGGCACCAAACAAGGGAACCCT
225557 GTTGGCGGCACCA
1 GTTGGCGGCACCA
225570 GTCCTACCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.25, C:0.30, G:0.31, T:0.13
Consensus pattern (27 bp):
GTTGGCGGCACCAAACAAGGGAACCCT
Found at i:225890 original size:3 final size:3
Alignment explanation
Indices: 225882--225916 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
225872 AATTTTATAG
225882 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
225917 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:226678 original size:14 final size:14
Alignment explanation
Indices: 226659--226691 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
226649 ACAATAACTA
226659 AAATTAGAATAATT
1 AAATTAGAATAATT
226673 AAATTAGAATAATT
1 AAATTAGAATAATT
226687 AAATT
1 AAATT
226692 GATACAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (14 bp):
AAATTAGAATAATT
Found at i:227680 original size:17 final size:17
Alignment explanation
Indices: 227658--227694 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
227648 AGTAAGATGT
227658 CATGAATATGACAATAG
1 CATGAATATGACAATAG
* *
227675 CATGAATATTAGAATAG
1 CATGAATATGACAATAG
227692 CAT
1 CAT
227695 CTTACCCCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (17 bp):
CATGAATATGACAATAG
Found at i:228914 original size:9 final size:9
Alignment explanation
Indices: 228897--228945 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
228887 AAATTTAGTG
228897 TGTTTTTTT
1 TGTTTTTTT
228906 CTGTTTTTTTT
1 -TG-TTTTTTT
*
228917 TATTTTTTT
1 TGTTTTTTT
228926 TGTTTTTTT
1 TGTTTTTTT
**
228935 TACTTTTTT
1 TGTTTTTTT
228944 TG
1 TG
228946 ATATATTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
9 23 0.70
10 3 0.09
11 7 0.21
ACGTcount: A:0.04, C:0.04, G:0.08, T:0.84
Consensus pattern (9 bp):
TGTTTTTTT
Found at i:228941 original size:19 final size:20
Alignment explanation
Indices: 228899--228944 Score: 69
Period size: 18 Copynumber: 2.4 Consensus size: 20
228889 ATTTAGTGTG
228899 TTTTTTTCTGTTTTTTTTTA
1 TTTTTTTCTGTTTTTTTTTA
228919 TTTTTTT-TG-TTTTTTTTA
1 TTTTTTTCTGTTTTTTTTTA
228937 CTTTTTTT
1 -TTTTTTT
228945 GATATATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.36
19 9 0.36
20 7 0.28
ACGTcount: A:0.04, C:0.04, G:0.04, T:0.87
Consensus pattern (20 bp):
TTTTTTTCTGTTTTTTTTTA
Found at i:228977 original size:28 final size:30
Alignment explanation
Indices: 228946--229012 Score: 113
Period size: 28 Copynumber: 2.3 Consensus size: 30
228936 ACTTTTTTTG
228946 ATATATTTTGGTAAATA-AAAAAAA-TTAT
1 ATATATTTTGGTAAATACAAAAAAAGTTAT
228974 ATATATTTTGGTAAATACAAAAAAAGTTAT
1 ATATATTTTGGTAAATACAAAAAAAGTTAT
229004 A-ATATTTTG
1 ATATATTTTG
229013 ACAATTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
28 17 0.46
29 15 0.41
30 5 0.14
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.40
Consensus pattern (30 bp):
ATATATTTTGGTAAATACAAAAAAAGTTAT
Found at i:229039 original size:13 final size:13
Alignment explanation
Indices: 229021--229046 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
229011 TGACAATTTT
229021 TTATTTTTTTATA
1 TTATTTTTTTATA
229034 TTATTTTTTTATA
1 TTATTTTTTTATA
229047 AAACCCATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTATTTTTTTATA
Found at i:229538 original size:10 final size:10
Alignment explanation
Indices: 229523--229623 Score: 79
Period size: 10 Copynumber: 10.5 Consensus size: 10
229513 NNCTCTTCTC
229523 CTTTCCTTTT
1 CTTTCCTTTT
229533 CTTTCCTTATT
1 CTTTCCTT-TT
229544 -TTT-C-TTT
1 CTTTCCTTTT
***
229551 CTTTCCTCCC
1 CTTTCCTTTT
229561 CTTTCCTTTT
1 CTTTCCTTTT
229571 CTTTCCTTCTT
1 CTTTCCTT-TT
229582 -TTT-C-TTT
1 CTTTCCTTTT
* *
229589 CTTTCCTCTC
1 CTTTCCTTTT
229599 CTTTCCTTTT
1 CTTTCCTTTT
* *
229609 CCTTCTTTTT
1 CTTTCCTTTT
229619 CTTTC
1 CTTTC
229624 TTCCTTTCTT
Statistics
Matches: 70, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
7 4 0.06
8 8 0.11
9 4 0.06
10 50 0.71
11 4 0.06
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.65
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:229553 original size:18 final size:18
Alignment explanation
Indices: 229530--229640 Score: 95
Period size: 18 Copynumber: 6.1 Consensus size: 18
229520 CTCCTTTCCT
*
229530 TTTCTTTCCTTATTTTTC
1 TTTCTTTCCTTCTTTTTC
* * *
229548 TTTCTTTCCTCCCCTTTCC
1 TTTCTTTCCT-TCTTTTTC
229567 TTTTCTTTCCTTCTTTTTC
1 -TTTCTTTCCTTCTTTTTC
*
229586 TTTCTTTCC-TCTCCTTTC
1 TTTCTTTCCTTCT-TTTTC
*
229604 -CT-TTTCCTTCTTTTTC
1 TTTCTTTCCTTCTTTTTC
229620 TTTC-TTCCTTTCTTTCTTC
1 TTTCTTTCC-TTCTTT-TTC
229639 TT
1 TT
229641 CTTCCCCTCT
Statistics
Matches: 74, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
16 9 0.12
17 12 0.16
18 29 0.39
19 14 0.19
20 10 0.14
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTCTTTCCTTCTTTTTC
Found at i:229573 original size:38 final size:38
Alignment explanation
Indices: 229522--229631 Score: 159
Period size: 38 Copynumber: 2.9 Consensus size: 38
229512 NNNCTCTTCT
229522 CCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCC
1 CCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCC
* *
229560 CCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCT
1 CCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCC
* * *
229598 CCTTTCCTTTTCCTT-CTTTTTCTTTCTTCCTTTC
1 CCTTTCCTTTTCTTTCCTTATT-TTTCTTTCTTTC
229632 TTTCTTCTTC
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
37 5 0.08
38 61 0.92
ACGTcount: A:0.01, C:0.35, G:0.00, T:0.65
Consensus pattern (38 bp):
CCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCC
Found at i:229584 original size:14 final size:14
Alignment explanation
Indices: 229567--229640 Score: 55
Period size: 14 Copynumber: 5.1 Consensus size: 14
229557 TCCCCTTTCC
229567 TTTTCTTTCCTTCT
1 TTTTCTTTCCTTCT
*
229581 TTTTCTTTCTTTCCT
1 TTTTCTTTCCTT-CT
229596 CTCCTTTCCTTTTCCTTCT
1 -T--TTT-C-TTTCCTTCT
229615 TTTTCTTT-CTTC-
1 TTTTCTTTCCTTCT
*
229627 CTTTCTTT-CTTCT
1 TTTTCTTTCCTTCT
229640 T
1 T
229641 CTTCCCCTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
12 11 0.22
13 4 0.08
14 14 0.29
15 3 0.06
16 4 0.08
18 4 0.08
19 3 0.06
20 6 0.12
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTCTTTCCTTCT
Found at i:229592 original size:28 final size:28
Alignment explanation
Indices: 229561--229640 Score: 85
Period size: 34 Copynumber: 2.8 Consensus size: 28
229551 CTTTCCTCCC
229561 CTTTCCTTTTCTTTCCTTCTTTTTCTTT
1 CTTTCCTTTTCTTTCCTTCTTTTTCTTT
229589 CTTTCCTCTCCTTTCCTTTTCCTTCTTTTTCTTT
1 CTTT-C-CT--TTT-C-TTTCCTTCTTTTTCTTT
229623 C-TTCC-TTTCTTT-CTTCTT
1 CTTTCCTTTTCTTTCCTTCTT
229641 CTTCCCCTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
25 6 0.13
26 3 0.07
27 1 0.02
28 7 0.15
29 1 0.02
30 2 0.04
31 1 0.02
32 4 0.09
33 3 0.07
34 18 0.39
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (28 bp):
CTTTCCTTTTCTTTCCTTCTTTTTCTTT
Found at i:229624 original size:10 final size:10
Alignment explanation
Indices: 229572--229643 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
229562 TTTCCTTTTC
*
229572 TTTCCTTCTT
1 TTTCTTTCTT
229582 TTTCTTTCTT
1 TTTCTTTCTT
*
229592 TCCTCTCCTTTCCT
1 T--T-T-CTTTCTT
*
229606 TTTCCTTCTT
1 TTTCTTTCTT
229616 TTTCTTTCTT
1 TTTCTTTCTT
229626 CCTTTCTTTCTT
1 --TTTCTTTCTT
*
229638 CTTCTT
1 TTTCTT
229644 CCCCTCTCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 29 0.58
11 1 0.02
12 12 0.24
13 1 0.02
14 7 0.14
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:229636 original size:22 final size:23
Alignment explanation
Indices: 229601--229643 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
229591 TTCCTCTCCT
*
229601 TTCCTTTTCCTTCTTTTTCTTTC
1 TTCCTTTTCCTTCTTCTTCTTTC
*
229624 TTCC-TTTCTTTCTTCTTCTT
1 TTCCTTTTCCTTCTTCTTCTT
229644 CCCCTCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (23 bp):
TTCCTTTTCCTTCTTCTTCTTTC
Found at i:229641 original size:28 final size:30
Alignment explanation
Indices: 229563--229644 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 30
229553 TTCCTCCCCT
*
229563 TTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCC
1 TTCC-TTTCTTT-CTTCTTCTTCTTTCTTTCC
*
229595 TCTCCTTTCCTTT-TCCTTCTT-TTTCTTT-C
1 T-TCCTTT-CTTTCTTCTTCTTCTTTCTTTCC
229624 TTCCTTTCTTTCTTCTTCTTC
1 TTCCTTTCTTTCTTCTTCTTC
229645 CCCTCTCCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
27 4 0.09
28 13 0.30
29 2 0.05
30 7 0.16
31 6 0.14
32 4 0.09
33 7 0.16
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (30 bp):
TTCCTTTCTTTCTTCTTCTTCTTTCTTTCC
Found at i:229654 original size:42 final size:40
Alignment explanation
Indices: 229542--229657 Score: 105
Period size: 42 Copynumber: 2.9 Consensus size: 40
229532 TCTTTCCTTA
* *
229542 TTTTTCTTTCTTTCCTCCCCTT-TCCT-T--TTCTTTCCTTC
1 TTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTT--TTC
* * *
229580 TTTTTCTTTCTTTCCTCTCCTTTCCTTTTCCTTCTTTTTC
1 TTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTTTTC
* *
229620 TTTCTTCCTTTCTTTCTTCTTCTTCCCCTCTCCTTCTT
1 TTT-TT-CTTTCTTTCCTCTCCTTCCCCTCTCCTTCTT
229658 CCCCCCACCA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
38 21 0.33
39 2 0.03
40 7 0.11
41 2 0.03
42 32 0.50
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (40 bp):
TTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTTTTC
Found at i:229731 original size:27 final size:27
Alignment explanation
Indices: 229693--229758 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
229683 ATTCAAGGGT
229693 GGTGCCGCCAACAAGGATCCCTTGTTC
1 GGTGCCGCCAACAAGGATCCCTTGTTC
* * *
229720 GGTGCCGCCAACAGGGTTCCCTTGTTT
1 GGTGCCGCCAACAAGGATCCCTTGTTC
229747 GGTGCCGCCAAC
1 GGTGCCGCCAAC
229759 CTACTTCCCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.15, C:0.33, G:0.29, T:0.23
Consensus pattern (27 bp):
GGTGCCGCCAACAAGGATCCCTTGTTC
Found at i:229766 original size:27 final size:27
Alignment explanation
Indices: 229693--229768 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
229683 ATTCAAGGGT
229693 GGTGCCGCCAACAAGGA--TCCCTTGTTC
1 GGTGCCGCCAAC-A-GACTTCCCTTGTTC
** *
229720 GGTGCCGCCAACAGGGTTCCCTTGTTT
1 GGTGCCGCCAACAGACTTCCCTTGTTC
**
229747 GGTGCCGCCAACCTACTTCCCT
1 GGTGCCGCCAACAGACTTCCCT
229769 CCACCCAAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 1 0.02
26 1 0.02
27 39 0.95
ACGTcount: A:0.14, C:0.36, G:0.25, T:0.25
Consensus pattern (27 bp):
GGTGCCGCCAACAGACTTCCCTTGTTC
Found at i:229872 original size:27 final size:28
Alignment explanation
Indices: 229837--229905 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
229827 TTTGTTTTTT
*
229837 TATATATTTTGGTAAATAAAAAAA-TTA
1 TATATATTTTGATAAATAAAAAAAGTTA
229864 TATATATTTTGATAAATAAAAAAAGTTA
1 TATATATTTTGATAAATAAAAAAAGTTA
*
229892 TA-ACATTTTGATAA
1 TATATATTTTGATAA
229906 TTTTTTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 34 0.87
28 5 0.13
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.41
Consensus pattern (28 bp):
TATATATTTTGATAAATAAAAAAAGTTA
Found at i:232615 original size:21 final size:20
Alignment explanation
Indices: 232578--232616 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
232568 TCATATTTCC
* *
232578 TTTATTTTTTTATGAATTTA
1 TTTATATTTTCATGAATTTA
232598 TTTATATTTTCATGGAATT
1 TTTATATTTTCAT-GAATT
232617 GCCAAGGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTATATTTTCATGAATTTA
Found at i:253152 original size:12 final size:12
Alignment explanation
Indices: 253137--253179 Score: 86
Period size: 12 Copynumber: 3.6 Consensus size: 12
253127 AATACAATAA
253137 AAATAACAAAAT
1 AAATAACAAAAT
253149 AAATAACAAAAT
1 AAATAACAAAAT
253161 AAATAACAAAAT
1 AAATAACAAAAT
253173 AAATAAC
1 AAATAAC
253180 TGCTTACCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.16
Consensus pattern (12 bp):
AAATAACAAAAT
Found at i:269192 original size:284 final size:284
Alignment explanation
Indices: 268682--269248 Score: 1125
Period size: 284 Copynumber: 2.0 Consensus size: 284
268672 TGTCAGCAAG
268682 TAAAAGCCGAGCATCAAGTACCATCTGGATTGCTTCAGCCGATCATGATACCTGAATGGAAATGG
1 TAAAAGCCGAGCATCAAGTACCATCTGGATTGCTTCAGCCGATCATGATACCTGAATGGAAATGG
268747 GACCGAGTTACGATGGATTTTGTATCCGGTTTACCGTTGACACCGAGCAAGAAAGATGCAATCTG
66 GACCGAGTTACGATGGATTTTGTATCCGGTTTACCGTTGACACCGAGCAAGAAAGATGCAATCTG
268812 AGTTATTGTTGATAGGTTGACAAAATCGGCACACTTTATTCTGATTCGCACGGATTTCCCACTCG
131 AGTTATTGTTGATAGGTTGACAAAATCGGCACACTTTATTCTGATTCGCACGGATTTCCCACTCG
268877 ATAAACTTGCTGAATTGTATGTTTCTCAAATTGTGAGATTGCATGGTGTGCCTATTTCTATTGTT
196 ATAAACTTGCTGAATTGTATGTTTCTCAAATTGTGAGATTGCATGGTGTGCCTATTTCTATTGTT
268942 TCAGACAGAGATCCGAGATTCACT
261 TCAGACAGAGATCCGAGATTCACT
*
268966 TAAAAGCTGAGCATCAAGTACCATCTGGATTGCTTCAGCCGATCATGATACCTGAATGGAAATGG
1 TAAAAGCCGAGCATCAAGTACCATCTGGATTGCTTCAGCCGATCATGATACCTGAATGGAAATGG
269031 GACCGAGTTACGATGGATTTTGTATCCGGTTTACCGTTGACACCGAGCAAGAAAGATGCAATCTG
66 GACCGAGTTACGATGGATTTTGTATCCGGTTTACCGTTGACACCGAGCAAGAAAGATGCAATCTG
269096 AGTTATTGTTGATAGGTTGACAAAATCGGCACACTTTATTCTGATTCGCACGGATTTCCCACTCG
131 AGTTATTGTTGATAGGTTGACAAAATCGGCACACTTTATTCTGATTCGCACGGATTTCCCACTCG
269161 ATAAACTTGCTGAATTGTATGTTTCTCAAATTGTGAGATTGCATGGTGTGCCTATTTCTATTGTT
196 ATAAACTTGCTGAATTGTATGTTTCTCAAATTGTGAGATTGCATGGTGTGCCTATTTCTATTGTT
269226 TCAGACAGAGATCCGAGATTCAC
261 TCAGACAGAGATCCGAGATTCAC
269249 ATCGCGATTT
Statistics
Matches: 282, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
284 282 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (284 bp):
TAAAAGCCGAGCATCAAGTACCATCTGGATTGCTTCAGCCGATCATGATACCTGAATGGAAATGG
GACCGAGTTACGATGGATTTTGTATCCGGTTTACCGTTGACACCGAGCAAGAAAGATGCAATCTG
AGTTATTGTTGATAGGTTGACAAAATCGGCACACTTTATTCTGATTCGCACGGATTTCCCACTCG
ATAAACTTGCTGAATTGTATGTTTCTCAAATTGTGAGATTGCATGGTGTGCCTATTTCTATTGTT
TCAGACAGAGATCCGAGATTCACT
Found at i:277213 original size:227 final size:228
Alignment explanation
Indices: 276919--277437 Score: 627
Period size: 227 Copynumber: 2.3 Consensus size: 228
276909 GCGCCACAAC
* * * *
276919 AACCAAAATGCATCGTTCTATTTTGAGGTATACGGGT-TTAGTGGCGCTTATATTAAAACGTCAC
1 AACCAAAACGCATCGTTCTATTTTGAGGTATACTGGTATTAGTGGCGCTTATATAAAAACGCCAC
* * * *
276983 TATATATCAAGCATTA-CTGGCGTTTGTTTAAAAGTGCCGCAAAAATGTTAACCAAAACGTATCG
66 TATACATCAAGCATTAGC-GGCGCTTGTTTAAAAGCGCCGCAAAAATGTTAACCAAAACGCATCG
* * * * * *
277047 TTTGATCTTAAGCTATAGTGATATTTGCGGCACTTATTTATAAACGCCACTA-A-AGC-ACACCA
130 TTCGATCTTAAGCTATAGTGACATTAGCGACACTTATTTAGAAACACCACTATATAGCTA-A-CA
**
277109 TTACCAGCGCTTATGTAAAAATGCCGCAAAGTTATT
193 TTACCAGCGCTTATGTAAAAATGCCGCAAAAATATT
* * *
277145 AACCAAAACGCATTGTTCTATCTTGAGGTGTACTGGTATTAGTGGCGCTTATATAAAAACGCCAC
1 AACCAAAACGCATCGTTCTATTTTGAGGTATACTGGTATTAGTGGCGCTTATATAAAAACGCCAC
277210 TATACATCAAGCATTAGCGGCGCTTGTTTAAAAGCGCCGCAAAAATGTTAACCAAAACGCATCGT
66 TATACATCAAGCATTAGCGGCGCTTGTTTAAAAGCGCCGCAAAAATGTTAACCAAAACGCATCGT
* * * * * * *
277275 TCGGTTTTGAGCTATTGTGGCATTAGCGACGCTTATTTAGAAACACCACTATATATCTAACATTA
131 TCGATCTTAAGCTATAGTGACATTAGCGACACTTATTTAGAAACACCACTATATAGCTAACATTA
* * * * *
277340 GCAGTGCTTTTTTAAAAATGCCGCAAAAATGTT
196 CCAGCGCTTATGTAAAAATGCCGCAAAAATATT
** * * * *
277373 AACCAAAACGCATCGTTCGGTTTTGAGATATAGTGGCATTAGTGGCGCGTT-TTTAAAAACGCCA
1 AACCAAAACGCATCGTTCTATTTTGAGGTATACTGGTATTAGTGGCGC-TTATATAAAAACGCCA
277437 C
65 C
277438 AAAATTGTTA
Statistics
Matches: 247, Mismatches: 40, Indels: 10
0.83 0.13 0.03
Matches are distributed among these distances:
226 32 0.13
227 123 0.50
228 86 0.35
229 5 0.02
230 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (228 bp):
AACCAAAACGCATCGTTCTATTTTGAGGTATACTGGTATTAGTGGCGCTTATATAAAAACGCCAC
TATACATCAAGCATTAGCGGCGCTTGTTTAAAAGCGCCGCAAAAATGTTAACCAAAACGCATCGT
TCGATCTTAAGCTATAGTGACATTAGCGACACTTATTTAGAAACACCACTATATAGCTAACATTA
CCAGCGCTTATGTAAAAATGCCGCAAAAATATT
Found at i:277265 original size:114 final size:114
Alignment explanation
Indices: 276919--277437 Score: 498
Period size: 114 Copynumber: 4.6 Consensus size: 114
276909 GCGCCACAAC
* * *
276919 AACCAAAATGCATCGTTCTATTTTGAGGTATACG-GGT-TTAGTGGCGCTTATATT-AAAACGTC
1 AACCAAAACGCATCGTTCTATTTTGAGCTATA-GTGGTATTAGTGGCGCTTAT-TTAAAAACGCC
* * *
276981 ACTATATATCAAGCATTA-CTGGCGTTTGTTTAAAAGTGCCGCAAAAATGTT
64 ACTATATATCAAGCATTAGC-AGCGCTTGTTTAAAAATGCCGCAAAAATGTT
* * * * * * * *
277032 AACCAAAACGTATCGTT-TGATCTTAAGCTATAGTGATATTTGCGGCACTTATTTATAAACGCCA
1 AACCAAAACGCATCGTTCT-ATTTTGAGCTATAGTGGTATTAGTGGCGCTTATTTAAAAACGCCA
* * * * * ** *
277096 CTA-A-AGCACACCATTACCAGCGCTTATGTAAAAATGCCGCAAAGTTATT
65 CTATATATCA-AGCATTAGCAGCGCTTGTTTAAAAATGCCGCAAAAATGTT
* * * * * *
277145 AACCAAAACGCATTGTTCTATCTTGAGGTGTACTGGTATTAGTGGCGCTTATATAAAAACGCCAC
1 AACCAAAACGCATCGTTCTATTTTGAGCTATAGTGGTATTAGTGGCGCTTATTTAAAAACGCCAC
* * **
277210 TATACATCAAGCATTAGCGGCGCTTGTTTAAAAGCGCCGCAAAAATGTT
66 TATATATCAAGCATTAGCAGCGCTTGTTTAAAAATGCCGCAAAAATGTT
** * * * * * *
277259 AACCAAAACGCATCGTTCGGTTTTGAGCTATTGTGGCATTAGCGACGCTTATTTAGAAACACCAC
1 AACCAAAACGCATCGTTCTATTTTGAGCTATAGTGGTATTAGTGGCGCTTATTTAAAAACGCCAC
* *
277324 TATATATCTAA-CATTAGCAGTGCTTTTTTAAAAATGCCGCAAAAATGTT
66 TATATATC-AAGCATTAGCAGCGCTTGTTTAAAAATGCCGCAAAAATGTT
** * *
277373 AACCAAAACGCATCGTTCGGTTTTGAGATATAGTGGCATTAGTGGCGCGTT-TTTAAAAACGCCA
1 AACCAAAACGCATCGTTCTATTTTGAGCTATAGTGGTATTAGTGGCGC-TTATTTAAAAACGCCA
277437 C
65 C
277438 AAAATTGTTA
Statistics
Matches: 325, Mismatches: 70, Indels: 21
0.78 0.17 0.05
Matches are distributed among these distances:
112 5 0.02
113 112 0.34
114 201 0.62
115 7 0.02
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (114 bp):
AACCAAAACGCATCGTTCTATTTTGAGCTATAGTGGTATTAGTGGCGCTTATTTAAAAACGCCAC
TATATATCAAGCATTAGCAGCGCTTGTTTAAAAATGCCGCAAAAATGTT
Found at i:278005 original size:21 final size:22
Alignment explanation
Indices: 277965--278011 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
277955 GGGTGTGGTC
277965 GTTTAGAGTTTAAGATTTAGG-
1 GTTTAGAGTTTAAGATTTAGGT
*
277986 GTTTAGAGTTTGAGGA-TTAGGT
1 GTTTAGAGTTT-AAGATTTAGGT
278008 GTTT
1 GTTT
278012 GTATTTAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (22 bp):
GTTTAGAGTTTAAGATTTAGGT
Found at i:280477 original size:9 final size:9
Alignment explanation
Indices: 280445--280811 Score: 174
Period size: 9 Copynumber: 42.3 Consensus size: 9
280435 AAAGTGATAT
280445 ACTTACATA
1 ACTTACATA
*
280454 ACTTATATATAA
1 AC-T-TACAT-A
280466 ACTTACATA
1 ACTTACATA
280475 ACTTACATA
1 ACTTACATA
*
280484 A-TAACATAATA
1 ACTTAC---ATA
280495 ACTTACATA
1 ACTTACATA
280504 A--TACATA
1 ACTTACATA
* *
280511 GCCTACATA
1 ACTTACATA
*
280520 ACTTACACA
1 ACTTACATA
280529 ACTTACATA
1 ACTTACATA
*
280538 A--TACACA
1 ACTTACATA
280545 ACTTACATA
1 ACTTACATA
*
280554 ACTTAAATA
1 ACTTACATA
280563 ACTTACATA
1 ACTTACATA
280572 A--TACATA
1 ACTTACATA
**
280579 ACTTTGATA
1 ACTTACATA
* *
280588 ACTAACATT
1 ACTTACATA
*
280597 A--TACACA
1 ACTTACATA
280604 ACTTACAATA
1 ACTTAC-ATA
280614 A--TACAT-
1 ACTTACATA
*
280620 TCTTACATA
1 ACTTACATA
* *
280629 ACTTGCATT
1 ACTTACATA
*
280638 A--TACACA
1 ACTTACATA
280645 ACTTACATA
1 ACTTACATA
280654 ACTTA-ATTAA
1 ACTTACA-T-A
*
280664 TATTATACATA
1 -ACT-TACATA
* *
280675 ACATGCATA
1 ACTTACATA
280684 A--TACATA
1 ACTTACATA
280691 ACTTACATA
1 ACTTACATA
280700 A--TACATA
1 ACTTACATA
* * *
280707 ACCTATATT
1 ACTTACATA
*
280716 GCTTACATA
1 ACTTACATA
280725 A--TACATA
1 ACTTACATA
280732 ACTTACATA
1 ACTTACATA
*
280741 ACTTATATA
1 ACTTACATA
280750 A--TACATA
1 ACTTACATA
280757 ACTTACATA
1 ACTTACATA
* *
280766 ATTTACCTA
1 ACTTACATA
280775 A--TACATA
1 ACTTACATA
* *
280782 A-ATATATA
1 ACTTACATA
* *
280790 TCATATCATA
1 ACTTA-CATA
280800 ACTTACATA
1 ACTTACATA
280809 ACT
1 ACT
280812 CATTTATAGT
Statistics
Matches: 268, Mismatches: 53, Indels: 74
0.68 0.13 0.19
Matches are distributed among these distances:
7 61 0.23
8 17 0.06
9 152 0.57
10 16 0.06
11 12 0.04
12 9 0.03
13 1 0.00
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.33
Consensus pattern (9 bp):
ACTTACATA
Found at i:280497 original size:20 final size:19
Alignment explanation
Indices: 280472--280510 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
280462 ATAAACTTAC
280472 ATAACTTACATAATAACATA
1 ATAACTTACATAAT-ACATA
280492 ATAACTTACATAATACATA
1 ATAACTTACATAATACATA
280511 GCCTACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAACTTACATAATACATA
Found at i:280537 original size:34 final size:34
Alignment explanation
Indices: 280494--280580 Score: 129
Period size: 34 Copynumber: 2.6 Consensus size: 34
280484 ATAACATAAT
* *
280494 AACTTACATAATACATAGCCTACATAACTTACAC
1 AACTTACATAATACATAACCTACATAACTTAAAC
* * *
280528 AACTTACATAATACACAACTTACATAACTTAAAT
1 AACTTACATAATACATAACCTACATAACTTAAAC
280562 AACTTACATAATACATAAC
1 AACTTACATAATACATAAC
280581 TTTGATAACT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.48, C:0.23, G:0.01, T:0.28
Consensus pattern (34 bp):
AACTTACATAATACATAACCTACATAACTTAAAC
Found at i:280542 original size:25 final size:25
Alignment explanation
Indices: 280445--280809 Score: 157
Period size: 25 Copynumber: 14.8 Consensus size: 25
280435 AAAGTGATAT
*
280445 ACTTACATAACTT--AT-ATATA-A
1 ACTTACATAACTTACATAATACATA
280466 ACTTACATAACTTACATAATAACATAATA
1 ACTTACATAACTTACATAAT-AC---ATA
*
280495 ACTTACATAA--TACATAGCCTACATA
1 ACTTACATAACTTACATA--ATACATA
* *
280520 ACTTACACAACTTACATAATACACA
1 ACTTACATAACTTACATAATACATA
*
280545 ACTTACATAACTTAAATAACTTACATA
1 ACTTACATAACTTACATAA--TACATA
** *
280572 A--TACATAACTTTGATAACTAACATT
1 ACTTACATAACTTACATAA-T-ACATA
*
280597 A--TACACAACTTACAATAATACAT-
1 ACTTACATAACTTAC-ATAATACATA
* * * *
280620 TCTTACATAACTTGCATTATACACA
1 ACTTACATAACTTACATAATACATA
280645 ACTTACATAACTTA-AT--TA-AT-
1 ACTTACATAACTTACATAATACATA
* * *
280665 ATTATACATAACATGCATAATACATA
1 ACT-TACATAACTTACATAATACATA
* *
280691 ACTTACATAA--TACATAACCTATATT
1 ACTTACATAACTTACATAA--TACATA
*
280716 GCTTACATAA--TACATAACTTACATA
1 ACTTACATAACTTACATAA--TACATA
*
280741 ACTTATATAA--TACATAACTTACATA
1 ACTTACATAACTTACATAA--TACATA
* * *
280766 ATTTACCTAA--TACATAAATATATA
1 ACTTACATAACTTACAT-AATACATA
* *
280790 TCATATCATAACTTACATAA
1 ACTTA-CATAACTTACATAA
280810 CTCATTTATA
Statistics
Matches: 269, Mismatches: 44, Indels: 57
0.73 0.12 0.15
Matches are distributed among these distances:
20 2 0.01
21 23 0.09
22 4 0.01
23 8 0.03
24 25 0.09
25 159 0.59
26 10 0.04
27 23 0.09
28 3 0.01
29 12 0.04
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (25 bp):
ACTTACATAACTTACATAATACATA
Found at i:280766 original size:16 final size:16
Alignment explanation
Indices: 280469--280767 Score: 150
Period size: 16 Copynumber: 18.1 Consensus size: 16
280459 TATATAAACT
280469 TACATAACTTACATAA
1 TACATAACTTACATAA
280485 TAACATAATAACTTACATAA
1 T-AC---ATAACTTACATAA
* *
280505 TACATAGCCTACATAA
1 TACATAACTTACATAA
*
280521 CTTACACAACTTACATAA
1 --TACATAACTTACATAA
*
280539 TACACAACTTACATAA
1 TACATAACTTACATAA
*
280555 CTTAAATAACTTACATAA
1 --TACATAACTTACATAA
**
280573 TACATAACTTTGATAA
1 TACATAACTTACATAA
* *
280589 CTAACATTA--TACACAA
1 -T-ACATAACTTACATAA
**
280605 CTTACAATAA--TACATTCT
1 --TAC-ATAACTTACA-TAA
* *
280623 TACATAACTTGCATTA
1 TACATAACTTACATAA
*
280639 TACACAACTTACAT-A
1 TACATAACTTACATAA
*
280654 -ACTTAA-TTA-ATATTA
1 TACATAACTTACATA--A
* *
280669 TACATAACATGCATAA
1 TACATAACTTACATAA
280685 TACATAACTTACATAA
1 TACATAACTTACATAA
* * **
280701 TACATAACCTATATTGCT
1 TACATAACTTACA-T-AA
280719 TACATAA--TACATAA
1 TACATAACTTACATAA
*
280733 CTTACATAACTTATATAA
1 --TACATAACTTACATAA
280751 TACATAACTTACATAA
1 TACATAACTTACATAA
280767 T
1 T
280768 TTACCTAATA
Statistics
Matches: 216, Mismatches: 40, Indels: 54
0.70 0.13 0.17
Matches are distributed among these distances:
12 2 0.01
13 3 0.01
14 4 0.02
15 7 0.03
16 120 0.56
17 16 0.07
18 48 0.22
19 2 0.01
20 14 0.06
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.32
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:282721 original size:36 final size:36
Alignment explanation
Indices: 282676--282745 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
282666 AGAAAAATGT
*
282676 TTGCGAGAACATTATCGGTACAATTTTGAATGTCGA
1 TTGCAAGAACATTATCGGTACAATTTTGAATGTCGA
*
282712 TTGCAAGAACATTATCGGTATAATTTTGAATGTC
1 TTGCAAGAACATTATCGGTACAATTTTGAATGTC
282746 AATGGAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (36 bp):
TTGCAAGAACATTATCGGTACAATTTTGAATGTCGA
Found at i:286256 original size:87 final size:87
Alignment explanation
Indices: 286143--286342 Score: 321
Period size: 87 Copynumber: 2.3 Consensus size: 87
286133 AACTTAAAGT
* *
286143 AGAGGCAGCATCGAGAGAAGCTGAGGTTCAAAGAAAATATGAAGAACTCCAGCTACAACTTAAAG
1 AGAGGCAGCATCGAGGGAAGCTGAGGTTCAAAGAAAATATGAAGAACTCCAGCTACAACTTAAAA
286208 CAAATGCAACAGCGAGGGAAGC
66 CAAATGCAACAGCGAGGGAAGC
* *
286230 GGAGGCAGCATCGAGGGAAGTTGAGGTTCAAAGAAAATATGAAGAACTCCAGCTACAACTTAAAA
1 AGAGGCAGCATCGAGGGAAGCTGAGGTTCAAAGAAAATATGAAGAACTCCAGCTACAACTTAAAA
*
286295 CAGATGCAACAGCGAGGGAAGC
66 CAAATGCAACAGCGAGGGAAGC
* *
286317 ACAGGCAGCAGT-GAGGGAAGCAGAGG
1 AGAGGCAGCA-TCGAGGGAAGCTGAGG
286343 CAGCAACGAG
Statistics
Matches: 103, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
87 102 0.99
88 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.30, T:0.12
Consensus pattern (87 bp):
AGAGGCAGCATCGAGGGAAGCTGAGGTTCAAAGAAAATATGAAGAACTCCAGCTACAACTTAAAA
CAAATGCAACAGCGAGGGAAGC
Found at i:286332 original size:21 final size:21
Alignment explanation
Indices: 286304--286380 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
286294 ACAGATGCAA
*
286304 CAGCGAGGGAAGCACAGGCAG
1 CAGCGAGGGAAGCAAAGGCAG
* *
286325 CAGTGAGGGAAGCAGAGGCAG
1 CAGCGAGGGAAGCAAAGGCAG
* * *
286346 CAACGAGAGAAGCAAAGGCTG
1 CAGCGAGGGAAGCAAAGGCAG
286367 CAGCGAGGGAAGCA
1 CAGCGAGGGAAGCA
286381 GAGTAGAGAA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.36, C:0.19, G:0.42, T:0.03
Consensus pattern (21 bp):
CAGCGAGGGAAGCAAAGGCAG
Found at i:287019 original size:43 final size:43
Alignment explanation
Indices: 286736--287008 Score: 343
Period size: 43 Copynumber: 6.4 Consensus size: 43
286726 AAAAAAGGCA
*
286736 CCGCTAAAAGTAATGATCTATAGCGGCGTTTGTGGGAAAAGCG
1 CCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAAAAGCG
* *
286779 CCGCTAAAAGTCATGA-CTTATAGCAGCGTTTGTTGGAAAAGCG
1 CCGCTAAAAGTCATGATC-TATAGCGGCGTTTGTGGGAAAAGCG
* * * * *
286822 CCGCTAAAAGTCATGATCTCTAGCGGCGATTGTTGGAGAAGTG
1 CCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAAAAGCG
* * ** *
286865 CCGCTAAAAGTCATGATCTATAGTGGCGTTCGTGAAAAAAACG
1 CCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAAAAGCG
* * * *
286908 CCGCTAAAAGTCATGATCTATAGCGGTGTTTAT-AGTAAAGCG
1 CCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAAAAGCG
* *
286950 CCGCTAAAAGTCATGACCTATAGCGGCGTTTGTGGGAGAAGCG
1 CCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAAAAGCG
*
286993 CCGCTAAAGGTCATGA
1 CCGCTAAAAGTCATGA
287009 CTTTTAGCGG
Statistics
Matches: 195, Mismatches: 32, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
42 37 0.19
43 157 0.81
44 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (43 bp):
CCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAAAAGCG
Found at i:287024 original size:26 final size:26
Alignment explanation
Indices: 286992--287097 Score: 203
Period size: 26 Copynumber: 4.1 Consensus size: 26
286982 TGGGAGAAGC
*
286992 GCCGCTAAAGGTCATGACTTTTAGCG
1 GCCGCTATAGGTCATGACTTTTAGCG
287018 GCCGCTATAGGTCATGACTTTTAGCG
1 GCCGCTATAGGTCATGACTTTTAGCG
287044 GCCGCTATAGGTCATGACTTTTAGCG
1 GCCGCTATAGGTCATGACTTTTAGCG
287070 GCCGCTATAGGTCATGACTTTTAGCG
1 GCCGCTATAGGTCATGACTTTTAGCG
287096 GC
1 GC
287098 GTTTATTTCT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (26 bp):
GCCGCTATAGGTCATGACTTTTAGCG
Found at i:291755 original size:23 final size:24
Alignment explanation
Indices: 291729--291780 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
291719 TGATTTTTAA
* *
291729 ATTTTGAATTA-TTTAGTGATAAT
1 ATTTAGAATTATTTTAGTAATAAT
291752 ATTTAGAATTATTTTAGTAATAAT
1 ATTTAGAATTATTTTAGTAATAAT
291776 -TTTAG
1 ATTTAG
291781 TGATAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.52
Consensus pattern (24 bp):
ATTTAGAATTATTTTAGTAATAAT
Found at i:291779 original size:12 final size:13
Alignment explanation
Indices: 291738--291793 Score: 64
Period size: 12 Copynumber: 4.5 Consensus size: 13
291728 AATTTTGAAT
*
291738 TATTTAGTGATAA
1 TATTTAGTAATAA
*
291751 TATTTAG-AATTA
1 TATTTAGTAATAA
291763 T-TTTAGTAATAA
1 TATTTAGTAATAA
*
291775 T-TTTAGTGATAA
1 TATTTAGTAATAA
291787 TATTTAG
1 TATTTAG
291794 GAAAAATCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
11 5 0.14
12 20 0.54
13 12 0.32
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (13 bp):
TATTTAGTAATAA
Found at i:298886 original size:19 final size:18
Alignment explanation
Indices: 298862--298904 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
298852 ATTACTACTT
298862 ATTTTTATAAATTTTATGA
1 ATTTTTATAAATTTTAT-A
* * *
298881 ATTTTTCTTATTTTTATA
1 ATTTTTATAAATTTTATA
298899 ATTTTT
1 ATTTTT
298905 TGAGAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
ATTTTTATAAATTTTATA
Found at i:298902 original size:9 final size:9
Alignment explanation
Indices: 298862--298918 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
298852 ATTACTACTT
298862 ATTTTTATA
1 ATTTTTATA
*
298871 AATTTTATGA
1 ATTTTTAT-A
* *
298881 ATTTTTCTT
1 ATTTTTATA
298890 ATTTTTATA
1 ATTTTTATA
*
298899 ATTTTTTGAGA
1 A-TTTTT-ATA
298910 ATTTTTATA
1 ATTTTTATA
298919 TAAACTTTAA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
9 17 0.46
10 17 0.46
11 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (9 bp):
ATTTTTATA
Found at i:298914 original size:28 final size:28
Alignment explanation
Indices: 298859--298914 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
298849 AAAATTACTA
*
298859 CTTATTTTTATAAATTTTATGAATTTTT
1 CTTATTTTTATAAATTTTATGAAATTTT
*
298887 CTTATTTTTAT-AATTTTTTGAGAATTTT
1 CTTATTTTTATAAATTTTATGA-AATTTT
298915 TATATAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.27, C:0.04, G:0.05, T:0.64
Consensus pattern (28 bp):
CTTATTTTTATAAATTTTATGAAATTTT
Found at i:299674 original size:11 final size:11
Alignment explanation
Indices: 299658--299686 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
299648 TTCAAAAATT
299658 CTCTTAAGTTC
1 CTCTTAAGTTC
299669 CTCTTAAGTTC
1 CTCTTAAGTTC
299680 CTCTTAA
1 CTCTTAA
299687 CTCTCTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.21, C:0.28, G:0.07, T:0.45
Consensus pattern (11 bp):
CTCTTAAGTTC
Found at i:299731 original size:12 final size:12
Alignment explanation
Indices: 299692--299735 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
299682 CTTAACTCTC
*
299692 TTTTTTTAAATA
1 TTTTTTAAAATA
* *
299704 ATTTTAAAAATA
1 TTTTTTAAAATA
299716 TTTTTTAAAAT-
1 TTTTTTAAAATA
299727 TTTTTTAAA
1 TTTTTTAAA
299736 CCGTAAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTTTTAAAATA
Found at i:304243 original size:9 final size:9
Alignment explanation
Indices: 304227--304262 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
304217 ATTCGAGTTG
304227 ATTCGAATA
1 ATTCGAATA
*
304236 ACTCGAATA
1 ATTCGAATA
*
304245 ATTTGAATA
1 ATTCGAATA
304254 ATTCGAATA
1 ATTCGAATA
304263 TCAAACTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (9 bp):
ATTCGAATA
Found at i:304504 original size:19 final size:20
Alignment explanation
Indices: 304464--304504 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
304454 CAAAAACCCT
*
304464 CAAAACTTTTTATTTTCCCC
1 CAAAACTTTTTATCTTCCCC
304484 CAAAA-TTTTTA-CTTCCTCC
1 CAAAACTTTTTATCTTCC-CC
304503 CA
1 CA
304505 CTTTTTCCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 4 0.21
19 10 0.53
20 5 0.26
ACGTcount: A:0.27, C:0.32, G:0.00, T:0.41
Consensus pattern (20 bp):
CAAAACTTTTTATCTTCCCC
Found at i:305039 original size:5 final size:5
Alignment explanation
Indices: 305029--305054 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
305019 GAACAAATAT
305029 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
305055 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:316656 original size:8 final size:8
Alignment explanation
Indices: 316649--316677 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
316639 AATTGGAATA
316649 AATAAA-T
1 AATAAATT
316656 AATAAATT
1 AATAAATT
316664 AATAAATT
1 AATAAATT
316672 AATAAA
1 AATAAA
316678 ACCTAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
AATAAATT
Found at i:316669 original size:19 final size:18
Alignment explanation
Indices: 316645--316694 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
316635 AAAAAATTGG
*
316645 AATAAATAAATAATAAATT
1 AATAAATAAATAA-AAACT
* *
316664 AATAAATTAATAAAACCT
1 AATAAATAAATAAAAACT
316682 AATAAATACAATA
1 AATAAATA-AATA
316695 TTGGACTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (18 bp):
AATAAATAAATAAAAACT
Found at i:329327 original size:13 final size:13
Alignment explanation
Indices: 329309--329334 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
329299 TAGGACATAG
329309 AAATTATTAAAAT
1 AAATTATTAAAAT
329322 AAATTATTAAAAT
1 AAATTATTAAAAT
329335 GTGTTTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATTATTAAAAT
Found at i:347877 original size:40 final size:40
Alignment explanation
Indices: 347818--347907 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
347808 AAAATTATTG
* * *
347818 CCTGAATGCACAAATGTGCCCCTGCTTGTGCTTTGGTACC
1 CCTGAATGCACAAACGTGCCCCTGCTTGTACTTCGGTACC
* *
347858 CCTGAATGCACAGACGTGCCCCTGTTTGTACTTCGGTACC
1 CCTGAATGCACAAACGTGCCCCTGCTTGTACTTCGGTACC
347898 CCTGAATGCA
1 CCTGAATGCA
347908 TTTACCTGCC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.19, C:0.31, G:0.22, T:0.28
Consensus pattern (40 bp):
CCTGAATGCACAAACGTGCCCCTGCTTGTACTTCGGTACC
Found at i:366202 original size:2 final size:2
Alignment explanation
Indices: 366195--366219 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
366185 ATGGTCAAAT
366195 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
366220 ATTCTAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:374136 original size:28 final size:28
Alignment explanation
Indices: 374081--374136 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
374071 GACCATAATG
*
374081 CCTCTAGAGGATAAATGCCTATTTTGCT
1 CCTCTAGAGGATAAATGACTATTTTGCT
374109 CCTCTAG-GG-TAAATGACTGATTTGTGCT
1 CCTCTAGAGGATAAATGACT-ATTT-TGCT
374137 ATGGTTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 8 0.32
27 6 0.24
28 11 0.44
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (28 bp):
CCTCTAGAGGATAAATGACTATTTTGCT
Found at i:376278 original size:47 final size:47
Alignment explanation
Indices: 376225--376319 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
376215 TGTAGAAAAA
*
376225 TACTATTTTGATAGATTTTTCTCTTTGAAGAGTGTTTTTGAGCTTAT
1 TACTATTTTGATAGATTTTTCTCTTTAAAGAGTGTTTTTGAGCTTAT
376272 TACTATTTTGATAGATTTTTCTCTTTAAAGAGTGTTTTTGAGCTTAT
1 TACTATTTTGATAGATTTTTCTCTTTAAAGAGTGTTTTTGAGCTTAT
376319 T
1 T
376320 TAGACACAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.22, C:0.08, G:0.16, T:0.54
Consensus pattern (47 bp):
TACTATTTTGATAGATTTTTCTCTTTAAAGAGTGTTTTTGAGCTTAT
Found at i:389704 original size:17 final size:17
Alignment explanation
Indices: 389682--389725 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
389672 TAGGAAATAA
389682 AAAATGTATATGTATAT
1 AAAATGTATATGTATAT
*
389699 AAAATGTAAATGTATAT
1 AAAATGTATATGTATAT
*
389716 -ATATGTATAT
1 AAAATGTATAT
389726 AAAAGTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAATGTATATGTATAT
Found at i:389859 original size:3 final size:3
Alignment explanation
Indices: 389851--389889 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
389841 GTATATATAG
* *
389851 TAA TAA TAA TAA TAA TGA TAA TAA TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
389890 CTTAATAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:390285 original size:21 final size:21
Alignment explanation
Indices: 390206--390284 Score: 97
Period size: 21 Copynumber: 3.7 Consensus size: 21
390196 AAATTAAATC
390206 TCTAAGATTAC-TAAATCATA
1 TCTAAGATTACATAAATCATA
*
390226 TCTTCTAAGATTGCATAAATCATA
1 ---TCTAAGATTACATAAATCATA
* *
390250 TCTAAGATTGCATATATCATA
1 TCTAAGATTACATAAATCATA
390271 TCTAAGATTACATA
1 TCTAAGATTACATA
390285 TCCTTGAAGA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
21 33 0.63
23 10 0.19
24 9 0.17
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.37
Consensus pattern (21 bp):
TCTAAGATTACATAAATCATA
Found at i:390791 original size:44 final size:42
Alignment explanation
Indices: 390729--390839 Score: 123
Period size: 44 Copynumber: 2.5 Consensus size: 42
390719 GATCTACTCT
** * *
390729 ACTGCAACTTCAGAGAGATAAGATATGTGGTTTTAATCTGCTTC
1 ACTGCAACTTCAG-GAGATAAGATAT-TGACTTTAATATGCTCC
* *
390773 ACTGTAACTTCATGGAGATAGGATTATTGACTTTAATATGCTCC
1 ACTGCAACTTCA-GGAGATAAGA-TATTGACTTTAATATGCTCC
*
390817 ACTACAACTTCAGGAGATAAGAT
1 ACTGCAACTTCAGGAGATAAGAT
390840 TCGCTATCTT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
42 1 0.02
43 9 0.16
44 42 0.75
45 4 0.07
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (42 bp):
ACTGCAACTTCAGGAGATAAGATATTGACTTTAATATGCTCC
Found at i:391455 original size:44 final size:44
Alignment explanation
Indices: 391314--391458 Score: 112
Period size: 44 Copynumber: 3.3 Consensus size: 44
391304 GCTATCGGTG
* * *
391314 CAGGAAGGTAAGATCTACTATTTTTAACCTACTCCGCTGCAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
* * * * * ** * * * ****
391358 CAGGGAGGCAAG-GCTGATGTCTTCGATCTGCTTCGTTGTCGGTG
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACC
391402 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
*
391446 CAGGGAGGCAAGA
1 CAGGAAGGCAAGA
391459 CTAGTGTCTT
Statistics
Matches: 67, Mismatches: 32, Indels: 4
0.65 0.31 0.04
Matches are distributed among these distances:
43 15 0.22
44 35 0.52
45 17 0.25
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (44 bp):
CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
Found at i:391506 original size:88 final size:88
Alignment explanation
Indices: 391292--391515 Score: 333
Period size: 88 Copynumber: 2.5 Consensus size: 88
391282 GTTGGGGTCA
* * *
391292 TCGATCTGCTTCGCTATCGGTGCAGGAAGGTAAGATCTACTATTTTTAACCTACTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCGCTGCAAC
*
391357 CCAGGGAGGCAAGGCTGATGTCT
66 CCAGGGAGGCAAGACTGATGTCT
* *
391380 TCGATCTGCTTCGTTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCGCTGCAAC
391445 CCAGGGAGGCAAGACT-AGTGTCT
66 CCAGGGAGGCAAGACTGA-TGTCT
* * * * *
391468 TCGATCTGCTTCACTGTCAGTGCATGAAGGCAAGATCTGTTATCTTTA
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
391516 CTGATCTGCT
Statistics
Matches: 123, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
87 1 0.01
88 122 0.99
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCGCTGCAAC
CCAGGGAGGCAAGACTGATGTCT
Found at i:397315 original size:21 final size:21
Alignment explanation
Indices: 397266--397363 Score: 121
Period size: 21 Copynumber: 4.7 Consensus size: 21
397256 AAATTAAATC
*
397266 TCTAAGATTACA-AAATCATA
1 TCTAAGATTGCATAAATCATA
397286 TCTTCTAAGATTGCATAAATCATA
1 ---TCTAAGATTGCATAAATCATA
*
397310 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATAAATCATA
397331 TCTAAGATTGCAT--ATCATA
1 TCTAAGATTGCATAAATCATA
*
397350 TCTAAGATTACATA
1 TCTAAGATTGCATA
397364 TCCTTGAAGA
Statistics
Matches: 70, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
19 18 0.26
21 33 0.47
23 11 0.16
24 8 0.11
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (21 bp):
TCTAAGATTGCATAAATCATA
Found at i:403017 original size:32 final size:32
Alignment explanation
Indices: 402979--403161 Score: 224
Period size: 32 Copynumber: 5.7 Consensus size: 32
402969 ATAAGTACAA
*
402979 TAATATGATTGGCACAAAGCCATCAGTAGTAG
1 TAATATGATCGGCACAAAGCCATCAGTAGTAG
* *
403011 TAATATGATCGGTACACAA-CCATCAGTAATAG
1 TAATATGATCGGCACA-AAGCCATCAGTAGTAG
* * *
403043 TAGTATGATCGGCACAAAGCCATAAGTAGTAA
1 TAATATGATCGGCACAAAGCCATCAGTAGTAG
* * * * *
403075 TACTATGATCGGTACACAGCCATCAATAATAG
1 TAATATGATCGGCACAAAGCCATCAGTAGTAG
* *
403107 TAGTATGATCGGCACAAAGCCATCAATAGTAG
1 TAATATGATCGGCACAAAGCCATCAGTAGTAG
*
403139 TAATATGATCGGTACAAAGCCAT
1 TAATATGATCGGCACAAAGCCAT
403162 AAATAGCATC
Statistics
Matches: 128, Mismatches: 21, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
31 2 0.02
32 124 0.97
33 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (32 bp):
TAATATGATCGGCACAAAGCCATCAGTAGTAG
Found at i:403083 original size:64 final size:64
Alignment explanation
Indices: 402982--403154 Score: 276
Period size: 64 Copynumber: 2.7 Consensus size: 64
402972 AGTACAATAA
* * *
402982 TATGATTGGCACAAAGCCATCAGTAGTAGTAATATGATCGGTACACAACCATCAGTAATAGTAG
1 TATGATCGGCACAAAGCCATAAGTAGTAGTAATATGATCGGTACACAACCATCAATAATAGTAG
* * *
403046 TATGATCGGCACAAAGCCATAAGTAGTAATACTATGATCGGTACACAGCCATCAATAATAGTAG
1 TATGATCGGCACAAAGCCATAAGTAGTAGTAATATGATCGGTACACAACCATCAATAATAGTAG
403110 TATGATCGGCACAAAGCCATCAA-TAGTAGTAATATGATCGGTACA
1 TATGATCGGCACAAAGCCAT-AAGTAGTAGTAATATGATCGGTACA
403155 AAGCCATAAA
Statistics
Matches: 100, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
64 98 0.98
65 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (64 bp):
TATGATCGGCACAAAGCCATAAGTAGTAGTAATATGATCGGTACACAACCATCAATAATAGTAG
Found at i:403130 original size:96 final size:95
Alignment explanation
Indices: 402964--403163 Score: 258
Period size: 96 Copynumber: 2.1 Consensus size: 95
402954 GAATGGCTAC
* * * *
402964 AAGCCATAAGTACAATAATATGATTGGCACAAAGCCATCAGTAGTAGTAATATGATCGGTACACA
1 AAGCCATAAGTACAATAATATGATCGGCACAAAGCCATCAATAATAGTAATATGATCGGCACACA
* *
403029 ACCATCAGTAATAGTAGTATGATCGGCACA
66 ACCATCAATAATAGTAATATGATCGGCACA
* * * * *
403059 AAGCCATAAGTAGTAATACTATGATCGGTACACAGCCATCAATAATAGTAGTATGATCGGCACA-
1 AAGCCATAAGTA-CAATAATATGATCGGCACAAAGCCATCAATAATAGTAATATGATCGGCACAC
* *
403123 AAGCCATCAATAGTAGTAATATGATCGGTACA
65 AA-CCATCAATAATAGTAATATGATCGGCACA
403155 AAGCCATAA
1 AAGCCATAA
403164 ATAGCATCGC
Statistics
Matches: 90, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
95 14 0.16
96 76 0.84
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (95 bp):
AAGCCATAAGTACAATAATATGATCGGCACAAAGCCATCAATAATAGTAATATGATCGGCACACA
ACCATCAATAATAGTAATATGATCGGCACA
Found at i:403198 original size:26 final size:26
Alignment explanation
Indices: 403169--403222 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
403159 CATAAATAGC
*
403169 ATCGCAACAAAGCTGCCAGCAACAGT
1 ATCGCAACAAAACTGCCAGCAACAGT
*
403195 ATCGCAACAAAACTGCCAGTAACAGT
1 ATCGCAACAAAACTGCCAGCAACAGT
403221 AT
1 AT
403223 ATATGGCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.41, C:0.28, G:0.17, T:0.15
Consensus pattern (26 bp):
ATCGCAACAAAACTGCCAGCAACAGT
Found at i:403244 original size:27 final size:27
Alignment explanation
Indices: 403210--403269 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
403200 AACAAAACTG
*
403210 CCAGTAACAGT-ATATATGGCCAAGCCA
1 CCAGTAACAGTGAT-TATGGCAAAGCCA
* *
403237 CCAGTAACAGTGATTGTGGCAAAGCTA
1 CCAGTAACAGTGATTATGGCAAAGCCA
403264 CCAGTA
1 CCAGTA
403270 TAGTACTTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (27 bp):
CCAGTAACAGTGATTATGGCAAAGCCA
Found at i:403396 original size:24 final size:24
Alignment explanation
Indices: 403338--403398 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
403328 CCATACACAG
** *
403338 AATCAGTCATACAAATCACAGACA
1 AATCAGTCATTTAAATCACAGAAA
403362 AATCAGTCATTTAAATCACAGAAA
1 AATCAGTCATTTAAATCACAGAAA
*
403386 AATTAGTCATTTA
1 AATCAGTCATTTA
403399 CATCTCGGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.48, C:0.18, G:0.08, T:0.26
Consensus pattern (24 bp):
AATCAGTCATTTAAATCACAGAAA
Found at i:427051 original size:17 final size:18
Alignment explanation
Indices: 427024--427057 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
427014 ATATTTGGTT
*
427024 GCTTGTTTAAAGCATAAG
1 GCTTGTTTAAAGAATAAG
427042 GCTT-TTTAAAGAATAA
1 GCTTGTTTAAAGAATAA
427058 CCAAAGCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (18 bp):
GCTTGTTTAAAGAATAAG
Found at i:432878 original size:9 final size:10
Alignment explanation
Indices: 432860--432887 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
432850 TATTATGATA
432860 ATCTTTTTTT
1 ATCTTTTTTT
432870 ATCTTTTTTT
1 ATCTTTTTTT
432880 ATCTTTTT
1 ATCTTTTT
432888 ATAATTAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (10 bp):
ATCTTTTTTT
Found at i:437502 original size:16 final size:16
Alignment explanation
Indices: 437481--437512 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
437471 GTTTTGTTGC
*
437481 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
437497 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
437513 CTTTCAATTA
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:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:437729 original size:44 final size:45
Alignment explanation
Indices: 437636--437734 Score: 123
Period size: 46 Copynumber: 2.2 Consensus size: 45
437626 AATAATAACA
*
437636 GATACACGGTGGATTCAGCACACACCAACCACCCTTTGTAATCAAT
1 GATAC-CGGTGGATTCAGCACACACCAACCACCCTTTATAATCAAT
* *
437682 GATATCCGGTGGGA-TCAGCACACAGCAACCA-CC-TTATAATTAAT
1 GATA-CCGGT-GGATTCAGCACACACCAACCACCCTTTATAATCAAT
437726 GATACCGGT
1 GATACCGGT
437735 TCACTTAGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
43 5 0.10
44 13 0.27
45 2 0.04
46 24 0.50
47 4 0.08
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.22
Consensus pattern (45 bp):
GATACCGGTGGATTCAGCACACACCAACCACCCTTTATAATCAAT
Found at i:437800 original size:51 final size:51
Alignment explanation
Indices: 437740--437930 Score: 230
Period size: 51 Copynumber: 3.8 Consensus size: 51
437730 CCGGTTCACT
* * * *
437740 TAGTAGCCTGCACATAGTTCTACACATGTGACCATCACTATCCAATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCAGTACACA
* * * *
437791 TAGTAGCCTGCACATAGTACTATACACGTGATCGA--AGCTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCAGTACACA
*
437842 TAGTAGCCTGCACATAGTACTACACATGTGACCTATCA-T-T-CAGGTACACA
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCA-GTACACA
437892 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
437931 TTCACTTTCA
Statistics
Matches: 119, Mismatches: 14, Indels: 15
0.80 0.09 0.10
Matches are distributed among these distances:
49 5 0.04
50 42 0.35
51 69 0.58
52 2 0.02
53 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCAGTACACA
Found at i:437946 original size:101 final size:102
Alignment explanation
Indices: 437730--437922 Score: 275
Period size: 102 Copynumber: 1.9 Consensus size: 102
437720 ATTAATGATA
* * *
437730 CCGGTTCACTTAGTAGCCTGCACATAGTTCTACACATGTGACCATCACTATCCAATACACGTAGT
1 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCAATACACATAGT
* *
437795 AGCCTGCACATAGTACTATACACGTGATCGAAGCTAT
66 AGCCTGCACATAGTACTACACACGTGATCCAAGCTAT
* * *
437832 CCGGTACGCATAGTAGCCTGCACATAGTACTACACATGTGACCTATCA-T-T-CAGGTACACATA
1 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACC-ATCACTATCCA-ATACACATA
437894 GTAGCCTGCACATAGTACTACACACGTGA
64 GTAGCCTGCACATAGTACTACACACGTGA
437923 CCATCACTTT
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
100 2 0.02
101 36 0.44
102 40 0.49
103 4 0.05
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (102 bp):
CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCAATACACATAGT
AGCCTGCACATAGTACTACACACGTGATCCAAGCTAT
Found at i:443504 original size:22 final size:22
Alignment explanation
Indices: 443465--443537 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 22
443455 TTTTGACATT
*
443465 GTTAGTTCCGGCATCAGATACGG
1 GTTAGTTCC-ACATCAGATACGG
443488 GTTAGTTCCACATCAGATACGG
1 GTTAGTTCCACATCAGATACGG
* *
443510 GTTAGTTCCAGCATCGGATACGA
1 GTTAGTTCCA-CATCAGATACGG
443533 GTTAG
1 GTTAG
443538 GGTGTTACAC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
22 22 0.48
23 24 0.52
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (22 bp):
GTTAGTTCCACATCAGATACGG
Found at i:450960 original size:26 final size:26
Alignment explanation
Indices: 450930--450983 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
450920 AACCATATAA
*
450930 ATGCGAACTGATGTATAAATATACAT
1 ATGCGAACTGATATATAAATATACAT
* * *
450956 ATGCGAACTGCTATATATATATATAT
1 ATGCGAACTGATATATAAATATACAT
450982 AT
1 AT
450984 ATATATGCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (26 bp):
ATGCGAACTGATATATAAATATACAT
Found at i:451779 original size:15 final size:15
Alignment explanation
Indices: 451755--451790 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
451745 TGATATGCGG
451755 TTTG-TTATATGTGA
1 TTTGTTTATATGTGA
451769 TTTGTTTATATGTGA
1 TTTGTTTATATGTGA
*
451784 GTTGTTT
1 TTTGTTT
451791 GGTATGTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.17, C:0.00, G:0.22, T:0.61
Consensus pattern (15 bp):
TTTGTTTATATGTGA
Found at i:453663 original size:19 final size:17
Alignment explanation
Indices: 453633--453677 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
453623 AAATTCTTAT
453633 ATATTTTTTAATTTTGAA
1 ATATTTTTTAATTTT-AA
453651 ATATTTTTATAATTTTAA
1 ATATTTTT-TAATTTTAA
*
453669 TTATTTTTT
1 ATATTTTTT
453678 GATCTGAGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 1 0.04
18 17 0.68
19 7 0.28
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
ATATTTTTTAATTTTAA
Found at i:463411 original size:28 final size:28
Alignment explanation
Indices: 463361--463415 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
463351 CAGAGTGTCT
*
463361 GATACTGTAACACCGATACAAAGTACTA
1 GATACTGTAACACCGATAAAAAGTACTA
*
463389 GATACTGTAACACCGTTAAAAAGTACT
1 GATACTGTAACACCGATAAAAAGTACT
463416 TGACATGCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.24
Consensus pattern (28 bp):
GATACTGTAACACCGATAAAAAGTACTA
Found at i:466474 original size:39 final size:39
Alignment explanation
Indices: 466430--466570 Score: 158
Period size: 39 Copynumber: 3.6 Consensus size: 39
466420 AACATGTTTT
* * *
466430 TGAGTATTCTGATTTATGCTTAAATGTTATATGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* **
466469 TGAGTACTGTGATATATGCTTAAATGTTATGTTTTTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * * *
466508 CGAGTATTGTGATATATGCTTGAGTGTTAGGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* *
466547 TGTGTAATAG-GATATATGCTTAAA
1 TGAGT-ATTGTGATATATGCTTAAA
466571 ATTGAATATG
Statistics
Matches: 83, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
39 80 0.96
40 3 0.04
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.45
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:482858 original size:13 final size:13
Alignment explanation
Indices: 482840--482875 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
482830 AGGCTCCTTC
482840 GCTTCTTTGCGTT
1 GCTTCTTTGCGTT
*
482853 GCTTCTCTGCGTT
1 GCTTCTTTGCGTT
482866 GCTTCTTTGC
1 GCTTCTTTGC
482876 TGATGGCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.00, C:0.28, G:0.22, T:0.50
Consensus pattern (13 bp):
GCTTCTTTGCGTT
Found at i:482999 original size:19 final size:19
Alignment explanation
Indices: 482975--483012 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
482965 CTAAAAGAGT
482975 TGAGAGAATGATGA-ATGAG
1 TGAGAG-ATGATGAGATGAG
482994 TGAGAGATGATGAGATGAG
1 TGAGAGATGATGAGATGAG
483013 GGATGATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.21
Consensus pattern (19 bp):
TGAGAGATGATGAGATGAG
Found at i:497286 original size:14 final size:15
Alignment explanation
Indices: 497261--497289 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
497251 ATTATCAATG
497261 TAAAATATAATTACA
1 TAAAATATAATTACA
497276 TAAAA-ATAATTACA
1 TAAAATATAATTACA
497290 AACTAATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAATATAATTACA
Found at i:506749 original size:21 final size:22
Alignment explanation
Indices: 506720--506766 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
506710 CAGAAGGAGT
*
506720 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
*
506742 GAGT-GTACTCCGCATCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
506763 GAGT
1 GAGT
506767 TTGAGCAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.23
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:516978 original size:15 final size:15
Alignment explanation
Indices: 516946--516975 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
516936 CTTTGTTGTA
516946 AATTTATTTATTTTT
1 AATTTATTTATTTTT
516961 AATTATATTTATTTT
1 AATT-TATTTATTTT
516976 AATAAATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
AATTTATTTATTTTT
Found at i:518005 original size:26 final size:26
Alignment explanation
Indices: 517976--518027 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
517966 AGTGATTTGG
* *
517976 TTTATATTCTAATGTTAGTTTCTTAT
1 TTTATATTCCAATGTTAATTTCTTAT
518002 TTTATATTCCAATGTTAATTTCTTAT
1 TTTATATTCCAATGTTAATTTCTTAT
518028 GTCCCATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.10, G:0.06, T:0.60
Consensus pattern (26 bp):
TTTATATTCCAATGTTAATTTCTTAT
Found at i:520711 original size:25 final size:25
Alignment explanation
Indices: 520626--520711 Score: 61
Period size: 25 Copynumber: 3.3 Consensus size: 25
520616 ATTAGAATTT
* * *
520626 TAGATTTTTAT-TTCAGATTTTATGG
1 TAGATTTTTATATT-AGAATTTAAGC
520651 TAGATTTTT-TAATTAG-ATTGTAAGATGC
1 TAGATTTTTAT-ATTAGAATT-T-A-A-GC
*
520679 TATATTTTTATATTAGAATTTAAGC
1 TAGATTTTTATATTAGAATTTAAGC
520704 TAGATTTT
1 TAGATTTT
520712 AGGATTTTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
24 3 0.06
25 21 0.44
26 4 0.08
27 1 0.02
28 15 0.31
29 4 0.08
ACGTcount: A:0.30, C:0.03, G:0.14, T:0.52
Consensus pattern (25 bp):
TAGATTTTTATATTAGAATTTAAGC
Found at i:520728 original size:6 final size:6
Alignment explanation
Indices: 520717--520742 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
520707 ATTTTAGGAT
520717 TTTATA TTTATA TTTATA TTTATA TT
1 TTTATA TTTATA TTTATA TTTATA TT
520743 AGAATTAGAT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTATA
Found at i:520946 original size:129 final size:131
Alignment explanation
Indices: 520734--521000 Score: 369
Period size: 129 Copynumber: 2.0 Consensus size: 131
520724 TTATATTTAT
* * * * *
520734 ATTTATATTAGAATTAGATTTTTAGAATTTAAGATTTTGTAGTAGTTTCTTTTAAATGGATTCTA
1 ATTT-TATTAGAATTAGATTTTTAGAATTTAAGAGTTTATAGTAGATTCTTTTAAATAGATTATA
* * * * * *
520799 GGATTTCATATTTTTATATTAGAATAGATTGTAGATCTTCGGAGTTTTATATT-GAAATTTAAGT
65 GGATTTCATATTTGTATATTAGAATAGAATCTAGACCTTAGGAGTTTTATATTAG-AATTTAAGC
520863 TAG
129 TAG
* *
520866 ATTTTATTAGAATTAGA-TTTTGGAATTTAAGAGTTTATAGTAGATT-TTTTAATTAGATTATAG
1 ATTTTATTAGAATTAGATTTTTAGAATTTAAGAGTTTATAGTAGATTCTTTTAAATAGATTATAG
*
520929 GATTTCATATTTGTATATTAGAATAGAATCTAGACCTTAGGATTTTTATATTAGAATTTAAGCTA
66 GATTTCATATTTGTATATTAGAATAGAATCTAGACCTTAGGAGTTTTATATTAGAATTTAAGCTA
520994 G
131 G
520995 ATTTTA
1 ATTTTA
521001 GAATTTTTTA
Statistics
Matches: 120, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
129 77 0.64
130 26 0.22
131 13 0.11
132 4 0.03
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (131 bp):
ATTTTATTAGAATTAGATTTTTAGAATTTAAGAGTTTATAGTAGATTCTTTTAAATAGATTATAG
GATTTCATATTTGTATATTAGAATAGAATCTAGACCTTAGGAGTTTTATATTAGAATTTAAGCTA
G
Found at i:520995 original size:33 final size:33
Alignment explanation
Indices: 520937--521012 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 33
520927 AGGATTTCAT
* * *
520937 ATTTGTATATTAGAATAGAATCTAGACCTTAGG
1 ATTTTTATATTAGAATAGAAGCTAGACCTTAGA
** **
520970 ATTTTTATATTAGAATTTAAGCTAGATTTTAGA
1 ATTTTTATATTAGAATAGAAGCTAGACCTTAGA
521003 ATTTTT-TATT
1 ATTTTTATATT
521013 TATATTAGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 4 0.11
33 32 0.89
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.47
Consensus pattern (33 bp):
ATTTTTATATTAGAATAGAAGCTAGACCTTAGA
Found at i:521122 original size:144 final size:143
Alignment explanation
Indices: 520866--521335 Score: 649
Period size: 144 Copynumber: 3.3 Consensus size: 143
520856 TTTAAGTTAG
* * * **
520866 ATTT-TATTAGAATTAGATTTTGGAATTTAAGAGTTTATAGTAGATTTTTTAATTAGATTATAGG
1 ATTTATATTAGAATTAAATTTTAGAATTTAAGATTTTATAGTAGA-TTTTTAATTAGATGCTAGG
* * * *
520930 ATTTCATATTTGTATATTAGAATAGAATCTAGACCTTAGGATTTTTATATTAGAATTTAAGCTAG
65 ATTTCATATTTTTATATTAGAATAGATTCTAGACTTTAGGA-TTTTATATTAGAATTTAAGATAG
*
520995 ATTTTAGAATTTTTT
129 ATTTTAGAATTTTAT
* * *
521010 ATTTATATTAGAATTAAATTTTAGAATTTAAGATTTTCTAGTAGATTTTAAATTAGATGCTAGGG
1 ATTTATATTAGAATTAAATTTTAGAATTTAAGATTTTATAGTAGATTTTTAATTAGATGCTAGGA
* * * *
521075 TTTCATTTTTTTATATTAGAATATATTCTAGACTTTAGGACATTTATATTAGAATTTAAGTTAGA
66 TTTCATATTTTTATATTAGAATAGATTCTAGACTTTAGGA-TTTTATATTAGAATTTAAGATAGA
*
521140 TTTTAGGATTTTAT
130 TTTTAGAATTTTAT
*
521154 ATTTATATTAGAATTATATTTTAGAATTTAAGATTTTTATAGTAGAATTTTTAATTAGATGCTAG
1 ATTTATATTAGAATTAAATTTTAGAATTTAAGA-TTTTATAGTAG-ATTTTTAATTAGATGCTAG
* * * *
521219 GATTTTATATTTTTATATTAGAATAGATTTTATACTTTAGGATTTTATATTAGAATTTAA-ATTG
64 GATTTCATATTTTTATATTAGAATAGATTCTAGACTTTAGGATTTTATATTAGAATTTAAGATAG
521283 ACTTTTAGGAA-TTTAT
129 A-TTTTA-GAATTTTAT
521299 ATTTATATTAGAATTAAATTTTAGAATTTAAGATTTT
1 ATTTATATTAGAATTAAATTTTAGAATTTAAGATTTT
521336 TATTTAAGAT
Statistics
Matches: 289, Mismatches: 32, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
144 128 0.44
145 105 0.36
146 56 0.19
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (143 bp):
ATTTATATTAGAATTAAATTTTAGAATTTAAGATTTTATAGTAGATTTTTAATTAGATGCTAGGA
TTTCATATTTTTATATTAGAATAGATTCTAGACTTTAGGATTTTATATTAGAATTTAAGATAGAT
TTTAGAATTTTAT
Found at i:521145 original size:33 final size:32
Alignment explanation
Indices: 521084--521156 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 32
521074 GTTTCATTTT
*
521084 TTTATATTAGAATATATTCTAGACTTTAGGACA
1 TTTATATTAGAATATAGTCTAGACTTTAGGA-A
* * *
521117 TTTATATTAGAATTTAAGT-TAGATTTTAGGAT
1 TTTATATTAGAATAT-AGTCTAGACTTTAGGAA
521149 TTTATATT
1 TTTATATT
521157 TATATTAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 8 0.23
33 25 0.71
34 2 0.06
ACGTcount: A:0.34, C:0.04, G:0.12, T:0.49
Consensus pattern (32 bp):
TTTATATTAGAATATAGTCTAGACTTTAGGAA
Found at i:521167 original size:38 final size:38
Alignment explanation
Indices: 521116--521341 Score: 138
Period size: 38 Copynumber: 6.1 Consensus size: 38
521106 ACTTTAGGAC
*
521116 ATTTATATTAGAATTTAAGTTAGATTTTAGGATTTTAT
1 ATTTATATTAGAATTTAATTTAGATTTTAGGATTTTAT
* * *
521154 ATTTATATTAGAATTATATTTTAGAATTTAAGA---T-T
1 ATTTATATTAGAATT-TAATTTAGATTTTAGGATTTTAT
* **
521189 -TTTATAGTAGAATTTTTAA-TTAGATGCTAGGATTTTAT
1 ATTTATATTAGAA--TTTAATTTAGATTTTAGGATTTTAT
** * * *
521227 ATTTTTATATTAGAATAGATTTTATACTTTAGG-----AT
1 A--TTTATATTAGAATTTAATTTAGATTTTAGGATTTTAT
* *
521262 -TTTATATTAGAATTTAAATT-GACTTTTAGGAATTTAT
1 ATTTATATTAGAATTTAATTTAGA-TTTTAGGATTTTAT
* * *
521299 ATTTATATTAGAATTAAATTTTAGAATTTAAGATTTT-T
1 ATTTATATTAGAATTTAA-TTTAGATTTTAGGATTTTAT
521337 ATTTA
1 ATTTA
521342 AGATTTTATA
Statistics
Matches: 139, Mismatches: 29, Indels: 40
0.67 0.14 0.19
Matches are distributed among these distances:
31 1 0.01
32 22 0.16
34 20 0.14
35 5 0.04
36 3 0.02
37 3 0.02
38 38 0.27
39 26 0.19
40 10 0.07
41 11 0.08
ACGTcount: A:0.36, C:0.01, G:0.11, T:0.52
Consensus pattern (38 bp):
ATTTATATTAGAATTTAATTTAGATTTTAGGATTTTAT
Found at i:521175 original size:32 final size:32
Alignment explanation
Indices: 521139--521327 Score: 85
Period size: 32 Copynumber: 5.4 Consensus size: 32
521129 TTTAAGTTAG
521139 ATTTTAGGATTTTATATTTATATTAGAATTAT
1 ATTTTAGGATTTTATATTTATATTAGAATTAT
* * * * *
521171 ATTTTAGAATTTAAGATTTTTATAGTAGAATTTTT
1 ATTTTAGGATTT--TATATTTATATTAGAA-TTAT
*
521206 AATTAGATGCTAGGATTTTATATTTTTATATTAGAA-TAG
1 -ATT---T--TAGGATTTTATA--TTTATATTAGAATTAT
* * *
521245 ATTTTA-TACTTTAGGATTTTATATTAGAATTTAAATT
1 ATTTTAGGATTTTA-TA-TTTATATTAGAA-TT--A-T
* *
521282 GACTTTTAGGAATTTATATTTATATTAGAATTAA
1 -A-TTTTAGGATTTTATATTTATATTAGAATTAT
*
521316 ATTTTAGAATTT
1 ATTTTAGGATTT
521328 AAGATTTTTA
Statistics
Matches: 116, Mismatches: 21, Indels: 40
0.66 0.12 0.23
Matches are distributed among these distances:
32 38 0.33
33 4 0.03
34 14 0.12
35 5 0.04
36 4 0.03
37 2 0.02
38 16 0.14
39 10 0.09
40 5 0.04
41 18 0.16
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.52
Consensus pattern (32 bp):
ATTTTAGGATTTTATATTTATATTAGAATTAT
Found at i:521350 original size:12 final size:13
Alignment explanation
Indices: 521324--521348 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
521314 AAATTTTAGA
521324 ATTTAAGATTTTT
1 ATTTAAGATTTTT
521337 ATTTAAGATTTT
1 ATTTAAGATTTT
521349 ATAGTAGCTT
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:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
ATTTAAGATTTTT
Found at i:527239 original size:55 final size:55
Alignment explanation
Indices: 527156--527263 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 55
527146 TAGCTTTTCT
* *
527156 TTTAAAAAAGAATAGATTTTAGACTTTAGGATTTTTTATTAGAATCTAAATTGTC
1 TTTAAAAAAGAATAGATTTTAGAATTTAGGATTTTATATTAGAATCTAAATTGTC
* *
527211 TTTAAAAAAGATTATATTTTAGAATTTAGGATTTTATATTAGAATCTAAATTG
1 TTTAAAAAAGAATAGATTTTAGAATTTAGGATTTTATATTAGAATCTAAATTG
527264 AATTTTAGGA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (55 bp):
TTTAAAAAAGAATAGATTTTAGAATTTAGGATTTTATATTAGAATCTAAATTGTC
Found at i:530923 original size:21 final size:21
Alignment explanation
Indices: 530888--530940 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
530878 TCATATCTTT
530888 CAAGATTGC--ATATCATATC
1 CAAGATTGCATATATCATATC
530907 CAAGATTGCATATATCATATC
1 CAAGATTGCATATATCATATC
*
530928 TAAGATTGCATAT
1 CAAGATTGCATAT
530941 CCTTGAAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 9 0.29
21 22 0.71
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (21 bp):
CAAGATTGCATATATCATATC
Found at i:531491 original size:44 final size:44
Alignment explanation
Indices: 531431--531594 Score: 256
Period size: 44 Copynumber: 3.7 Consensus size: 44
531421 ACCAGTATGG
*
531431 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
* *
531475 GAAGATAAGATTTGCTATCTTTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
* * *
531519 GAAGACAATATCTACTATCTTTGATCTACTTCACGCCAATATAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
* *
531563 GGAGACAAGATCTGCTTTCTTTGATCTACTTC
1 GAAGACAAGATCTGCTATCTTTGATCTACTTC
531595 GCCACCAGTA
Statistics
Matches: 108, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 108 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.33
Consensus pattern (44 bp):
GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
Found at i:531501 original size:118 final size:118
Alignment explanation
Indices: 531287--531505 Score: 314
Period size: 118 Copynumber: 1.9 Consensus size: 118
531277 GACTTGTATT
* * * * *
531287 TTCGATCTACTTCGCCACCAGTGTGGGAAGACAAGATCTGCTACCTTTGATCTATTTCATGCCTA
1 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTACCTTCGATCTACTTCACGCCAA
* *
531352 TACATGAGGACAAGATCTACTTTTTTCGATCTACTTTGCCAATACCTACTTTC
66 TACATGAAGACAAGATCTACTTCTTTCGATCTACTTTGCCAATACCTACTTTC
* *
531405 TTCGATCTACTTTGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAA
1 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTACCTTCGATCTACTTCACGCCAA
* * *
531470 TACATGAAGATAAGATTTGCTATCTTT-GATCTACTT
66 TACATGAAGACAAGATCTACT-TCTTTCGATCTACTT
531506 CACGCCAATA
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
118 84 0.95
119 4 0.05
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (118 bp):
TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTACCTTCGATCTACTTCACGCCAA
TACATGAAGACAAGATCTACTTCTTTCGATCTACTTTGCCAATACCTACTTTC
Found at i:531626 original size:88 final size:88
Alignment explanation
Indices: 531400--531628 Score: 289
Period size: 88 Copynumber: 2.6 Consensus size: 88
531390 CCAATACCTA
* *
531400 CTTTCTTCGATCTACTTTGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
1 CTTTCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG-TATCTTCGATCTACTTCAC
* *
531465 GCCAATACATGAAGATAAGATTTG
65 GCCAATACATGAAGACAAGATCTG
* * * * *** * * *
531489 CTATCTTTGATCTACTTC-ACGCCAATACATGAAGACAATATCTACTATCTTTGATCTACTTCAC
1 CTTTCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCT-GTATCTTCGATCTACTTCAC
* *
531553 GCCAATATATGGAGACAAGATCTG
65 GCCAATACATGAAGACAAGATCTG
531577 CTTTCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTATCTTC
1 CTTTCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTATCTTC
531629 AACCTGCTCC
Statistics
Matches: 112, Mismatches: 26, Indels: 5
0.78 0.18 0.03
Matches are distributed among these distances:
88 79 0.71
89 33 0.29
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.32
Consensus pattern (88 bp):
CTTTCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTATCTTCGATCTACTTCACG
CCAATACATGAAGACAAGATCTG
Found at i:531728 original size:88 final size:88
Alignment explanation
Indices: 531607--532341 Score: 1098
Period size: 88 Copynumber: 8.4 Consensus size: 88
531597 CACCAGTATG
* *
531607 GGAAGACAAGATCTG-TATCTTCAACCTGCTCCACTACGACCCAGGGAGGCAAGGCTGGTATCTT
1 GGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTT
*
531671 TGATCTGCTTCACTGTCGATACA
66 CGATCTGCTTCACTGTCGATACA
* *
531694 GTAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAGGCAAGGCTGGTATCTT
1 GGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTT
*
531759 TGATCTGCTTCACTGTCGATACA
66 CGATCTGCTTCACTGTCGATACA
*
531782 GTAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGAACCCAGGGA-GCAAGGCTGGTATCT
1 GGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC-AACCCAGGGAGGCAAGGCTGGTATCT
* * * *
531846 TTGATCTACTTCACTGTCGGTATA
65 TCGATCTGCTTCACTGTCGATACA
*
531870 GGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGTGAGGCAAGGCTGGTATCTT
1 GGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTT
* * **
531935 CGATCTGTTTCGCTGTCGATGTA
66 CGATCTGCTTCACTGTCGATACA
* * *
531958 AGAAGGCAAGATCTGTTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGACTGGTATCTT
1 GGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTT
532023 CGATCTGCTTCACTGTCGATACA
66 CGATCTGCTTCACTGTCGATACA
* * *
532046 GGAATGCAAGATCTGCTATTTTCAACCTGCTCCACTACAACTCAGGGAGGCAAGGCTGGTATCTT
1 GGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTT
* *
532111 CGATCTACTTCACTGTCGGTACA
66 CGATCTGCTTCACTGTCGATACA
* * *
532134 GGAAGGCAAGATCTGCTATCTTCAACCTGCTCAACTACAACCAAGGGAGGCTAGGCTGGTATCTT
1 GGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTT
* *
532199 CGATCTGCTTCGCTGTCGATGCA
66 CGATCTGCTTCACTGTCGATACA
* * *
532222 GGAAGGCAAGATTTACTATCTTCAACCTGCTCCACTACAACCCAAGGAGGCAAGGCTGGTATCTT
1 GGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTT
* *
532287 CGATCTGCTTCGCCGTC-AGTACA
66 CGATCTGCTTCACTGTCGA-TACA
* * *
532310 GGAAGGCAAAATCTGTTATTTTCAACCTGCTC
1 GGAAGGCAAGATCTGCTATCTTCAACCTGCTC
532342 TGCTGCAAAC
Statistics
Matches: 591, Mismatches: 53, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
87 23 0.04
88 559 0.95
89 9 0.02
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (88 bp):
GGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTT
CGATCTGCTTCACTGTCGATACA
Found at i:533954 original size:10 final size:9
Alignment explanation
Indices: 533939--533963 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
533929 CCTAGAAGAG
533939 TTTTTTTCT
1 TTTTTTTCT
533948 TTTTTTTCT
1 TTTTTTTCT
533957 TTTTTTT
1 TTTTTTT
533964 GCACCATCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:540885 original size:19 final size:19
Alignment explanation
Indices: 540814--540885 Score: 108
Period size: 19 Copynumber: 3.7 Consensus size: 19
540804 CATATCTTTC
* *
540814 AAGATTGCATATTATATCC
1 AAGATTGCATATCATATCT
540833 AAGATTGCATATATCATATCT
1 AAGATTGC--ATATCATATCT
540854 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCT
540873 AAGATTGCATATC
1 AAGATTGCATATC
540886 CTTGAAGATT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 32 0.65
21 17 0.35
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (19 bp):
AAGATTGCATATCATATCT
Found at i:541064 original size:20 final size:22
Alignment explanation
Indices: 541039--541078 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
541029 TTACAATTTG
541039 TATAATTA-A-AAAATATTTTA
1 TATAATTACATAAAATATTTTA
541059 TATAATTACATAAAATATTT
1 TATAATTACATAAAATATTT
541079 AAAAGATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (22 bp):
TATAATTACATAAAATATTTTA
Found at i:552385 original size:17 final size:17
Alignment explanation
Indices: 552363--552428 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
552353 AGAGCTTGCA
*
552363 GGTGAGCTCTCAAGTTT
1 GGTGAGCTCTCAATTTT
* *
552380 GGTGAGCTCACATTTTTT
1 GGTGAGCTCTCA-ATTTT
552398 GGTGAGCT-TGCAATTTT
1 GGTGAGCTCT-CAATTTT
*
552415 GGTGAGCTCGCAAT
1 GGTGAGCTCTCAAT
552429 CCGCAATTCG
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
17 27 0.68
18 13 0.32
ACGTcount: A:0.18, C:0.17, G:0.29, T:0.36
Consensus pattern (17 bp):
GGTGAGCTCTCAATTTT
Found at i:555781 original size:15 final size:15
Alignment explanation
Indices: 555761--555809 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
555751 CTTATTCAAA
555761 TTTCTTTGCATCCAT
1 TTTCTTTGCATCCAT
555776 TTTCTTTGCATCCAT
1 TTTCTTTGCATCCAT
* *
555791 TTTCTTTGCTTCAAT
1 TTTCTTTGCATCCAT
555806 TTTC
1 TTTC
555810 ATTAGTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.57
Consensus pattern (15 bp):
TTTCTTTGCATCCAT
Found at i:558302 original size:43 final size:43
Alignment explanation
Indices: 558241--558330 Score: 173
Period size: 43 Copynumber: 2.1 Consensus size: 43
558231 TGTTAAGTTT
558241 TAATTCTTTAAATACTTAGTTTTAATTTTAGGCTTTATGAATA
1 TAATTCTTTAAATACTTAGTTTTAATTTTAGGCTTTATGAATA
558284 TAATTCTTTAAATACTTAGTTTTAATTTTAGGCTTTATGAATA
1 TAATTCTTTAAATACTTAGTTTTAATTTTAGGCTTTATGAATA
558327 -AATT
1 TAATT
558331 TCTATGTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 4 0.09
43 43 0.91
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (43 bp):
TAATTCTTTAAATACTTAGTTTTAATTTTAGGCTTTATGAATA
Found at i:568597 original size:10 final size:10
Alignment explanation
Indices: 568582--568607 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
568572 TTTAATTCTT
568582 AAAAACCCTA
1 AAAAACCCTA
568592 AAAAACCCTA
1 AAAAACCCTA
568602 AAAAAC
1 AAAAAC
568608 AAAAGGATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.65, C:0.27, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAACCCTA
Found at i:586839 original size:31 final size:31
Alignment explanation
Indices: 586804--586890 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
586794 GATGAACTGA
* *
586804 CTATTCTGTGTTTATTGTCCTAACAGATTGT
1 CTATTCTGTGTTTACTATCCTAACAGATTGT
*
586835 CTATTCTGTGTTTACTATCCTAACGGATTGT
1 CTATTCTGTGTTTACTATCCTAACAGATTGT
* *
586866 CTGTTTTGTGTTTACTATCCTAACA
1 CTATTCTGTGTTTACTATCCTAACA
586891 AACTTACCTC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.47
Consensus pattern (31 bp):
CTATTCTGTGTTTACTATCCTAACAGATTGT
Found at i:588377 original size:38 final size:37
Alignment explanation
Indices: 588308--588393 Score: 95
Period size: 38 Copynumber: 2.3 Consensus size: 37
588298 CACACCAGAA
* *
588308 TGACACCCAGTGTCTTATCGGATAGTTCGAAGTAAAGT
1 TGACACCCAGTGTCTCATCGGATAGTCCGAAGT-AAGT
588346 TGACACCCAGTGTCTCATCGGCCA-AG-CCGAAGTAAGT
1 TGACACCCAGTGTCTCATCGG--ATAGTCCGAAGTAAGT
**
588383 TGGTACCCAGT
1 TGACACCCAGT
588394 ACCTTATCGA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
37 13 0.31
38 26 0.62
39 2 0.05
40 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (37 bp):
TGACACCCAGTGTCTCATCGGATAGTCCGAAGTAAGT
Found at i:589442 original size:17 final size:17
Alignment explanation
Indices: 589420--589452 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
589410 ATGGTCTCTG
*
589420 TTTCTTTTCTTCTTTTC
1 TTTCTTTTATTCTTTTC
589437 TTTCTTTTATTCTTTT
1 TTTCTTTTATTCTTTT
589453 ATTCTATTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCTTTTATTCTTTTC
Found at i:589507 original size:22 final size:24
Alignment explanation
Indices: 589477--589526 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
589467 ACGTATTAGT
*
589477 TAATAATAATAATAACAATATATTA
1 TAATAATCAT-ATAACAATATATTA
* *
589502 TAATAATCATATAATAATATTTTA
1 TAATAATCATATAACAATATATTA
589526 T
1 T
589527 TCACAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
TAATAATCATATAACAATATATTA
Done.