Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000074.1 Hibiscus syriacus cultivar Beakdansim tig00000136_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1055225
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:273473 original size:36 final size:38
Alignment explanation
Indices: 273432--273529 Score: 134
Period size: 38 Copynumber: 2.7 Consensus size: 38
273422 AAATCAGAAA
273432 AAAGAGAAAAGAAACAAAGA-AAAA-CTAAAG-AAAAGC
1 AAAGAGAAAAGAAACAAAGAGAAAATC-AAAGAAAAAGC
273468 AAAGAG-AAAGAAACAAAGAGAAAATCAAAGAAAAAGC
1 AAAGAGAAAAGAAACAAAGAGAAAATCAAAGAAAAAGC
*
273505 AATAAAGAAAA-AAACAAAGAGAAAA
1 AA-AGAGAAAAGAAACAAAGAGAAAA
273530 AAGCACAGAA
Statistics
Matches: 56, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
35 13 0.23
36 14 0.25
37 9 0.16
38 17 0.30
39 3 0.05
ACGTcount: A:0.73, C:0.07, G:0.16, T:0.03
Consensus pattern (38 bp):
AAAGAGAAAAGAAACAAAGAGAAAATCAAAGAAAAAGC
Found at i:273496 original size:26 final size:26
Alignment explanation
Indices: 273460--273550 Score: 87
Period size: 26 Copynumber: 3.5 Consensus size: 26
273450 GAAAAACTAA
*
273460 AGAAAAGCAAAGAGAAAGAAACAAAG
1 AGAAAAACAAAGAGAAAGAAACAAAG
* * * *
273486 AGAAAATCAAAGAAAAAGCAATAAAG
1 AGAAAAACAAAGAGAAAGAAACAAAG
* *
273512 AAAAAAACAAAGAGAAA-AAAGCACAG
1 AGAAAAACAAAGAGAAAGAAA-CAAAG
273538 A-AAATAACAAAGA
1 AGAAA-AACAAAGA
273551 AGAAGCGAAG
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
25 5 0.09
26 48 0.91
ACGTcount: A:0.71, C:0.09, G:0.16, T:0.03
Consensus pattern (26 bp):
AGAAAAACAAAGAGAAAGAAACAAAG
Found at i:273530 original size:14 final size:14
Alignment explanation
Indices: 273462--273531 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 14
273452 AAAACTAAAG
*
273462 AAAAGCAAAGAGAA
1 AAAAACAAAGAGAA
*
273476 AGAAACAAAGAG--
1 AAAAACAAAGAGAA
*
273488 AAAATC-AA-AG-A
1 AAAAACAAAGAGAA
* *
273499 AAAAGCAATAAAGAA
1 AAAAACAA-AGAGAA
273514 AAAAACAAAGAGAA
1 AAAAACAAAGAGAA
273528 AAAA
1 AAAA
273532 GCACAGAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
10 2 0.05
11 7 0.16
12 5 0.11
13 1 0.02
14 21 0.48
15 8 0.18
ACGTcount: A:0.74, C:0.07, G:0.16, T:0.03
Consensus pattern (14 bp):
AAAAACAAAGAGAA
Found at i:273550 original size:52 final size:48
Alignment explanation
Indices: 273443--273565 Score: 119
Period size: 52 Copynumber: 2.5 Consensus size: 48
273433 AAGAGAAAAG
*
273443 AAACAAAGAAAAA-CTAAAGAAAAGCAAAGAGAAAGAAACAAAGAGAA
1 AAACAAAGAAAAAGCTAAAGAAAAACAAAGAGAAAGAAACAAAGAGAA
* *
273490 AATCAAAGAAAAAGCAATAAAGAAAAAAACAAAGAGAAA-AAAGCACAGA-AA
1 AAACAAAGAAAAAGC--TAAAG--AAAAACAAAGAGAAAGAAA-CAAAGAGAA
* *
273541 ATAACAAAGAAGAAGC-GAAGAAAAA
1 A-AACAAAGAAAAAGCTAAAGAAAAA
273566 GAGGACAAGA
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
47 17 0.27
48 1 0.02
49 3 0.05
50 5 0.08
51 6 0.10
52 31 0.49
ACGTcount: A:0.72, C:0.09, G:0.16, T:0.03
Consensus pattern (48 bp):
AAACAAAGAAAAAGCTAAAGAAAAACAAAGAGAAAGAAACAAAGAGAA
Found at i:273551 original size:12 final size:12
Alignment explanation
Indices: 273436--273551 Score: 78
Period size: 12 Copynumber: 9.3 Consensus size: 12
273426 CAGAAAAAAG
273436 AGAAAAGAAACAA
1 AGAAAA-AAACAA
273449 AG--AAAAACTAA
1 AGAAAAAAAC-AA
*
273460 AG--AAAAGCAA
1 AGAAAAAAACAA
273470 AGAGAAAGAAACAA
1 AGA-AAA-AAACAA
* *
273484 AGAGAAAATCAA
1 AGAAAAAAACAA
*
273496 AGAAAAAGCAATAA
1 AGAAAAA--AACAA
273510 AGAAAAAAACAA
1 AGAAAAAAACAA
*
273522 AGAGAAAAAAGCAC
1 AGA-AAAAAA-CAA
*
273536 AGAAAATAACAA
1 AGAAAAAAACAA
273548 AGAA
1 AGAA
273552 GAAGCGAAGA
Statistics
Matches: 83, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
10 8 0.10
11 11 0.13
12 24 0.29
13 17 0.20
14 23 0.28
ACGTcount: A:0.72, C:0.09, G:0.16, T:0.03
Consensus pattern (12 bp):
AGAAAAAAACAA
Found at i:274859 original size:63 final size:60
Alignment explanation
Indices: 274743--274902 Score: 157
Period size: 66 Copynumber: 2.6 Consensus size: 60
274733 TATCAGTATC
*
274743 CTTTGAGTTGTTTCTCTTGAAACAAATTTTGTCTCTCGAGACAGTTTCTTTTGA-AAAAT
1 CTTTGAGTTGTTTCTCTTGAAACAAATTTTGTCTCTCGAGACAATTTCTTTTGAGAAAAT
*
274802 CTTTGAGTATGTTTCT-TTGGAAATAAAGTTTTGTCTCTCTTGAGACAATTTGC-TTTGAGAAAA
1 CTTTGAGT-TGTTTCTCTT-GAAACAAA-TTTTGTCTCTC--GAGACAATTT-CTTTTGAG-AAA
*
274865 AA
59 AT
**
274867 CATTTGAGATCATTTC-CATTGAAACAAATTTTGTCT
1 C-TTTGAG-TTGTTTCTC-TTGAAACAAATTTTGTCT
274903 AATTTGAGGC
Statistics
Matches: 83, Mismatches: 6, Indels: 18
0.78 0.06 0.17
Matches are distributed among these distances:
59 10 0.12
60 14 0.17
61 11 0.13
63 14 0.17
64 1 0.01
65 13 0.16
66 17 0.20
67 3 0.04
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (60 bp):
CTTTGAGTTGTTTCTCTTGAAACAAATTTTGTCTCTCGAGACAATTTCTTTTGAGAAAAT
Found at i:274961 original size:31 final size:32
Alignment explanation
Indices: 274925--274991 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
274915 TTTTTTTTTT
* *
274925 AAACAAAA-AATCTTTGAGTCTCTTTCTATTG
1 AAACAAAATAATCTTTAAGTCACTTTCTATTG
* * *
274956 AAACAAAATCATCTTTAAGTCAGTTTCTCTTG
1 AAACAAAATAATCTTTAAGTCACTTTCTATTG
274988 AAAC
1 AAAC
274992 CATTATCCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 8 0.27
32 22 0.73
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (32 bp):
AAACAAAATAATCTTTAAGTCACTTTCTATTG
Found at i:275467 original size:134 final size:131
Alignment explanation
Indices: 275099--275483 Score: 328
Period size: 133 Copynumber: 2.9 Consensus size: 131
275089 ATAACAAGCT
* * * * * *
275099 ATCCTCATCACGTAGGAACCGTGTTATCTACACTTCCTAAAGATGGCTAAAAGTCTTTATCACGT
1 ATCCTCATCACGT-GTAACCGTGTTATC-ACCCCTCCTAAAGATGGCCAAAACTCTTCATCACGT
* * * * * *
275164 ATGAGTCGTGTCATCCCCGACCAGACCTCCTCATCACATAGGATCCATGTCACCCTTGATAACCA
64 ATGAGTAGTGTCATCCCCGACCAGAACTCCTCATCACGTAAGATCCATGTCACCATAGATAACCA
275229 TCC
129 TCC
* * * * * *
275232 ATTCTCATCACGTATGAACCGTGTTATCA-CCCTCCTAAAGATGGCC-TATCATCCTCATCGCGT
1 ATCCTCATCACGTGT-AACCGTGTTATCACCCCTCCTAAAGATGGCCAAAAC-TCTTCATCACGT
* *** * * *
275295 AGGAACGGTGCCATCCCCCGACCA-AACGTCTTTATCACGTAAGATCCATGTCATCCATAGATAA
64 ATGAGTAGTGTCAT-CCCCGACCAGAAC-TCCTCATCACGTAAGATCCATGTCA-CCATAGATAA
*
275359 CTAGT-C
126 CCA-TCC
* * * *
275365 GTCCTCATCGCGTCGTAACCATGTTATCACCCCTCCTAAAGATGGCCAGAACTCTTCATCACGTA
1 ATCCTCATCACGT-GTAACCGTGTTATCACCCCTCCTAAAGATGGCCAAAACTCTTCATCACGTA
* * * * * *
275430 TGAGTAGTGTAATCCCCTTACCAGATCTCCTCATCACGTAGGAGCCGTGTCACC
65 TGAGTAGTGTCATCCCC-GACCAGAACTCCTCATCACGTAAGATCCATGTCACC
275484 CTTTGACGAC
Statistics
Matches: 194, Mismatches: 47, Indels: 22
0.74 0.18 0.08
Matches are distributed among these distances:
130 1 0.01
131 34 0.18
132 31 0.16
133 63 0.32
134 61 0.31
135 4 0.02
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.26
Consensus pattern (131 bp):
ATCCTCATCACGTGTAACCGTGTTATCACCCCTCCTAAAGATGGCCAAAACTCTTCATCACGTAT
GAGTAGTGTCATCCCCGACCAGAACTCCTCATCACGTAAGATCCATGTCACCATAGATAACCATC
C
Found at i:275709 original size:3 final size:3
Alignment explanation
Indices: 275696--275725 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
275686 TATTTTAATA
275696 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
275726 TTTTGTTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:283359 original size:20 final size:21
Alignment explanation
Indices: 283334--283373 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
283324 TAATTTACTT
*
283334 TCAAAAGTAAATT-ATGATCA
1 TCAAAAGAAAATTGATGATCA
283354 TCAAAAGAAAATTGATGATC
1 TCAAAAGAAAATTGATGATC
283374 TTAAAGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (21 bp):
TCAAAAGAAAATTGATGATCA
Found at i:287080 original size:43 final size:43
Alignment explanation
Indices: 287000--287099 Score: 125
Period size: 43 Copynumber: 2.3 Consensus size: 43
286990 TTGTGCTTCA
*
287000 TGCATCGATACACTAGAGAGTGTACCGATGCATCCCTTGAATG
1 TGCATCGATACACTAGAGAGTGTACCGATGCAGCCCTTGAATG
*
287043 TGCATCGATACA-TCATGA-AGATGTACTGATGC-GCCCTTGAATG
1 TGCATCGATACACT-A-GAGAG-TGTACCGATGCAGCCCTTGAATG
*
287086 TGCATCGATTCACT
1 TGCATCGATACACT
287100 CTACTGTGCA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
42 1 0.02
43 36 0.72
44 13 0.26
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (43 bp):
TGCATCGATACACTAGAGAGTGTACCGATGCAGCCCTTGAATG
Found at i:287394 original size:15 final size:15
Alignment explanation
Indices: 287374--287404 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
287364 TATTGATTTT
287374 TGAACTTAGGACAAG
1 TGAACTTAGGACAAG
287389 TGAACTTAGGACAAG
1 TGAACTTAGGACAAG
287404 T
1 T
287405 TTTGATTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.23
Consensus pattern (15 bp):
TGAACTTAGGACAAG
Found at i:289838 original size:65 final size:64
Alignment explanation
Indices: 289763--289914 Score: 207
Period size: 65 Copynumber: 2.4 Consensus size: 64
289753 ACCCATTTCG
* *
289763 AATGCATTTTGTGTACCGATGCAGAAG-CCATGCATCGATGCACTCTTGAATATTTTGAATCATC
1 AATGCATTTTGTGTACCGATGCA-AAGACCATGCATCGATGCACTCTTGAAT-CTTTGAAACATC
289827 A
64 A
* * *
289828 AATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCTTGGATCTTTGAAACATCG
1 AATGCATTTTGTGTACCGATGCAAAGACCATGCATCGATGCACTCTTGAATCTTTGAAACATCA
* * *
289892 AATGTAATTAGTGTACCGATGCA
1 AATGCATTTTGTGTACCGATGCA
289915 CCCCTAGTGT
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
64 32 0.41
65 46 0.59
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (64 bp):
AATGCATTTTGTGTACCGATGCAAAGACCATGCATCGATGCACTCTTGAATCTTTGAAACATCA
Found at i:291141 original size:41 final size:41
Alignment explanation
Indices: 291075--291172 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 41
291065 TTAATAGTCA
* *
291075 TCCAATGTGAACAAAAGCAAGCATGTCTCCACATGGTGTCG
1 TCCAATGTGAACAAAAGAAAGCATGTCTCCAAATGGTGTCG
* * * * *
291116 TCCAATTTGAACACAAGAAATCATGTCTCCAAATGGT-ACC
1 TCCAATGTGAACAAAAGAAAGCATGTCTCCAAATGGTGTCG
291156 TCCAATGTGAACAAAAG
1 TCCAATGTGAACAAAAG
291173 CATGTTTAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
40 16 0.33
41 32 0.67
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.22
Consensus pattern (41 bp):
TCCAATGTGAACAAAAGAAAGCATGTCTCCAAATGGTGTCG
Found at i:291487 original size:29 final size:29
Alignment explanation
Indices: 291445--291503 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
291435 ATTTTCACCT
291445 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
291474 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
291503 A
1 A
291504 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:301442 original size:29 final size:28
Alignment explanation
Indices: 301410--301656 Score: 112
Period size: 29 Copynumber: 8.5 Consensus size: 28
301400 ATTGTCTCTT
301410 TTTATTATAATTTATAAAAGGTTTTATCC
1 TTTATTATAATTTATAAAA-GTTTTATCC
**
301439 TTTATTATAATTTATAAATAGTTTTATTT
1 TTTATTATAATTTATAAA-AGTTTTATCC
* * * *
301468 TATTTTATAGTAATTTATAAATGATTTTGTAC
1 T-TTAT-TA-TAATTTATAAAAG-TTTTATCC
* * *
301500 TCTATTGTAATTTATAAATAGTTGTGTAT-A
1 TTTATTATAATTTATAAA-AGTT-T-TATCC
* * *
301530 TAT-TTGTAATTTATGACAAA-TTGTATCC
1 TTTATTATAATTTAT-A-AAAGTTTTATCC
*
301558 TTTATTATAATTTATAAAA-TAATTT-TCA
1 TTTATTATAATTTATAAAAGT--TTTATCC
*
301586 TTTATTGTAAATTCTA-AAAAG-TTTATACC
1 TTTATTAT-AATT-TATAAAAGTTTTAT-CC
* * * * *
301615 TTTATTATAAATTCTAAAACTTTTTGTCT
1 TTTATTATAATTTATAAAA-GTTTTATCC
*
301644 TTTATTGTAATTT
1 TTTATTATAATTT
301657 GATGATTTTT
Statistics
Matches: 166, Mismatches: 30, Indels: 44
0.69 0.12 0.18
Matches are distributed among these distances:
27 11 0.07
28 20 0.12
29 92 0.55
30 17 0.10
31 9 0.05
32 17 0.10
ACGTcount: A:0.34, C:0.06, G:0.07, T:0.53
Consensus pattern (28 bp):
TTTATTATAATTTATAAAAGTTTTATCC
Found at i:301485 original size:61 final size:59
Alignment explanation
Indices: 301409--301575 Score: 162
Period size: 61 Copynumber: 2.8 Consensus size: 59
301399 AATTGTCTCT
* * *
301409 TTTTATTA-TAATTTATAAAAGGTTTTATCCTTTATTATAATTTATAAATAGTTTTATTTTA
1 TTTTA-TAGTAATTTATAAAA-GTTTTATCCTTTATTATAATTTATAAATAGTTGT-GTATA
* * * * *
301470 TTTTATAGTAATTTATAAATGATTTTGTACTCTATTGTAATTTATAAATAGTTGTGTATA
1 TTTTATAGTAATTTATAAAAG-TTTTATCCTTTATTATAATTTATAAATAGTTGTGTATA
* *
301530 TATT-T-GTAATTTATGACAAA-TTGTATCCTTTATTATAATTTATAAA
1 TTTTATAGTAATTTAT-A-AAAGTTTTATCCTTTATTATAATTTATAAA
301576 ATAATTTTCA
Statistics
Matches: 87, Mismatches: 15, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
58 30 0.34
59 2 0.02
60 11 0.13
61 44 0.51
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (59 bp):
TTTTATAGTAATTTATAAAAGTTTTATCCTTTATTATAATTTATAAATAGTTGTGTATA
Found at i:304779 original size:24 final size:24
Alignment explanation
Indices: 304752--304799 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
304742 TCCATTCCCA
304752 TAATAATATT-TGACTATGGACTTT
1 TAATAATATTATGA-TATGGACTTT
* *
304776 TAATAATGTTATTATATGGACTTT
1 TAATAATATTATGATATGGACTTT
304800 ATTATCTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.48
Consensus pattern (24 bp):
TAATAATATTATGATATGGACTTT
Found at i:307558 original size:127 final size:128
Alignment explanation
Indices: 307394--307651 Score: 491
Period size: 127 Copynumber: 2.0 Consensus size: 128
307384 ATCCACATAC
307394 ATCACTATGTATTAACCCCAATAAATCACTTGCTTGCTCACCTTTACTATTAAAAGGAGCATTAA
1 ATCACTATGTATTAACCCCAATAAATCACTTGCTTGCTCACCTTTACTATTAAAAGGAGCATTAA
* *
307459 TCATTTTTCCCAACAAGCAAGACTCACATACATCATATTGTTTGAAAACAAATGAATCTAATA
66 TCATTTTTCCCAACAAGCAAGACTCACATACATCATATTGTTCGAAAACAAATGAATCTAAAA
307522 ATCACT-TGTATTAACCCCAATAAATCACTTGCTTGCTCACCTTTACTATTAAAAGGAGCATTAA
1 ATCACTATGTATTAACCCCAATAAATCACTTGCTTGCTCACCTTTACTATTAAAAGGAGCATTAA
307586 TCATTTTTCCCAACAAGCAAGACTCACATACATCATATTGTTCGAAAACAAATGAATCTAAAA
66 TCATTTTTCCCAACAAGCAAGACTCACATACATCATATTGTTCGAAAACAAATGAATCTAAAA
307649 ATC
1 ATC
307652 CATCTTTATG
Statistics
Matches: 128, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
127 122 0.95
128 6 0.05
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (128 bp):
ATCACTATGTATTAACCCCAATAAATCACTTGCTTGCTCACCTTTACTATTAAAAGGAGCATTAA
TCATTTTTCCCAACAAGCAAGACTCACATACATCATATTGTTCGAAAACAAATGAATCTAAAA
Found at i:309351 original size:29 final size:29
Alignment explanation
Indices: 309318--309381 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
309308 TCCAAATATT
*
309318 TAACCTCTAGGTTTCTAATCCTATTAGAA
1 TAACCTCTAGGGTTCTAATCCTATTAGAA
309347 TAACCTCTAGGGTTCTAATCCTATTAGAA
1 TAACCTCTAGGGTTCTAATCCTATTAGAA
309376 TAACCT
1 TAACCT
309382 AGCTAAGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (29 bp):
TAACCTCTAGGGTTCTAATCCTATTAGAA
Found at i:314043 original size:24 final size:25
Alignment explanation
Indices: 314011--314057 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
314001 ATTTCCGAGA
314011 TTTTTTA-TTTTATTTTATTTTTCC
1 TTTTTTATTTTTATTTTATTTTTCC
*
314035 TTTTTTATTTTTTTTTTATTTTT
1 TTTTTTATTTTTATTTTATTTTT
314058 TTATTTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.11, C:0.04, G:0.00, T:0.85
Consensus pattern (25 bp):
TTTTTTATTTTTATTTTATTTTTCC
Found at i:314058 original size:11 final size:11
Alignment explanation
Indices: 314011--314059 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
314001 ATTTCCGAGA
314011 TTTTTTATTTT
1 TTTTTTATTTT
*
314022 ATTTTATT-TTTCC
1 -TTTT-TTATTT-T
314035 TTTTTTATTTT
1 TTTTTTATTTT
314046 TTTTTTATTTT
1 TTTTTTATTTT
314057 TTT
1 TTT
314060 ATTTTTGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
11 16 0.50
12 14 0.44
13 2 0.06
ACGTcount: A:0.10, C:0.04, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:314065 original size:19 final size:19
Alignment explanation
Indices: 314018--314065 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
314008 AGATTTTTTA
* *
314018 TTTTATTTTATTTTTCCTT
1 TTTTATTTTTTTTTTACTT
*
314037 TTTTATTTTTTTTTTATTT
1 TTTTATTTTTTTTTTACTT
314056 TTTTATTTTT
1 TTTTATTTTT
314066 GATGAAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.10, C:0.04, G:0.00, T:0.85
Consensus pattern (19 bp):
TTTTATTTTTTTTTTACTT
Found at i:315873 original size:4 final size:4
Alignment explanation
Indices: 315864--315890 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
315854 AAGTCAAACC
315864 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
315891 CATATTAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:322051 original size:24 final size:23
Alignment explanation
Indices: 322008--322052 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
321998 AAATTGATTT
* *
322008 TAAAATAAAAGATTAGAATAAAA
1 TAAAATAAAAGATAAAAATAAAA
322031 TAAAATATAAAGATAAAAATAA
1 TAAAATA-AAAGATAAAAATAA
322053 TAATTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (23 bp):
TAAAATAAAAGATAAAAATAAAA
Found at i:322945 original size:23 final size:23
Alignment explanation
Indices: 322919--322984 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
322909 TTAAACTATT
322919 TAAACTAAAATACTAAAAAAAGA
1 TAAACTAAAATACTAAAAAAAGA
* * * * **
322942 TAAAATAAAATTCTTAAAATATT
1 TAAACTAAAATACTAAAAAAAGA
*
322965 TAAACTAAAATCCTAAAAAA
1 TAAACTAAAATACTAAAAAA
322985 TGAGTTTGAC
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.26
Consensus pattern (23 bp):
TAAACTAAAATACTAAAAAAAGA
Found at i:325217 original size:31 final size:31
Alignment explanation
Indices: 325182--325242 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
325172 AACCATTCAC
* *
325182 AACTTTTCCAAAA-TTATTGAATTGGTCCCCT
1 AACTTTTCAAAAATTTATAGAA-TGGTCCCCT
325213 AACTTTTCAAAAATTTATAGAATGGTCCCC
1 AACTTTTCAAAAATTTATAGAATGGTCCCC
325243 AAATATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (31 bp):
AACTTTTCAAAAATTTATAGAATGGTCCCCT
Found at i:329858 original size:2 final size:2
Alignment explanation
Indices: 329851--329900 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
329841 AACATTCTTC
329851 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
329893 AT AT AT AT
1 AT AT AT AT
329901 TAAACATGAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:342736 original size:2 final size:2
Alignment explanation
Indices: 342731--342819 Score: 178
Period size: 2 Copynumber: 44.5 Consensus size: 2
342721 ACACACACAC
342731 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
342773 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
342815 AT AT A
1 AT AT A
342820 AATTCGTCTA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 87 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:345882 original size:43 final size:42
Alignment explanation
Indices: 345810--346081 Score: 185
Period size: 43 Copynumber: 6.3 Consensus size: 42
345800 TTGGGGTCAA
* ** *
345810 AAACGCCGCAATATGTAACGATATATAGCGGCGTTTTTACAGC
1 AAACGCCGCAATAGGTTTCGATATTTAGCGGCGTTTTTACA-C
* * * *
345853 AAATGTCGCAATATGATTT-GATATTTAGCGGCATTTTTTTA-AC
1 AAACGCCGCAATA-GGTTTCGATATTTAGCGGC--GTTTTTACAC
** * * *
345896 AAACGATGCAATAGGTTTGGATATTTAGCGACGTTTTTCTCAC
1 AAACGCCGCAATAGGTTTCGATATTTAGCGGCGTTTTT-ACAC
* * * *
345939 AAATGCCGCAATA-GTTATCGATATTTAGTGACGTTTTCAACAC
1 AAACGCCGCAATAGGTT-TCGATATTTAGCGGCGTTTT-TACAC
* *
345982 AAACGCCGCAATAGGTGTT-AATATTTAGCGGTGTTTTTCACAC
1 AAACGCCGCAATAGGT-TTCGATATTTAGCGGCGTTTTT-ACAC
* * ***
346025 AAACGCCGCAATAGGTAT-GTTATTTAATTGCGTTTATTCACAC
1 AAACGCCGCAATAGGTTTCGATATTTAGCGGCGTTT-TT-ACAC
*
346068 AAACGCCACAATAG
1 AAACGCCGCAATAG
346082 TTATGTTCTT
Statistics
Matches: 181, Mismatches: 36, Indels: 24
0.75 0.15 0.10
Matches are distributed among these distances:
41 5 0.03
42 19 0.10
43 145 0.80
44 5 0.03
45 7 0.04
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (42 bp):
AAACGCCGCAATAGGTTTCGATATTTAGCGGCGTTTTTACAC
Found at i:345962 original size:86 final size:85
Alignment explanation
Indices: 345829--346038 Score: 212
Period size: 86 Copynumber: 2.4 Consensus size: 85
345819 AATATGTAAC
* * * * **
345829 GATATATAGCGGCGTTTTT-ACAGCAAATGTCGCAATATGATTTGATATTTAGCGGCATTTTTTT
1 GATATTTAGCGGCGTTTTTCACA-CAAATGCCGCAATA-GATTTGATATTTAGCGAC-GTTTTCA
*
345893 A-ACAAACGATGCAATAGGT-TT
63 ACACAAACGACGCAATAGGTGTT
* * *
345914 GGATATTTAGCGACGTTTTTCTCACAAATGCCGCAATAG-TTATCGATATTTAGTGACGTTTTCA
1 -GATATTTAGCGGCGTTTTTCACACAAATGCCGCAATAGATT-T-GATATTTAGCGACGTTTTCA
*
345978 ACACAAACGCCGCAATAGGTGTT
63 ACACAAACGACGCAATAGGTGTT
* * *
346001 AATATTTAGCGGTGTTTTTCACACAAACGCCGCAATAG
1 GATATTTAGCGGCGTTTTTCACACAAATGCCGCAATAG
346039 GTATGTTATT
Statistics
Matches: 103, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
84 2 0.02
85 7 0.07
86 90 0.87
87 4 0.04
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (85 bp):
GATATTTAGCGGCGTTTTTCACACAAATGCCGCAATAGATTTGATATTTAGCGACGTTTTCAACA
CAAACGACGCAATAGGTGTT
Found at i:346068 original size:86 final size:86
Alignment explanation
Indices: 345894--346081 Score: 213
Period size: 86 Copynumber: 2.2 Consensus size: 86
345884 CATTTTTTTA
** * * * *
345894 ACAAACGATGCAATAGGTTTGGATATTTAGCGACGTTTTTCTCACAAATGCCGCAATAGTTATCG
1 ACAAACGCCGCAATAGGTTTGAATATTTAGCGACGTTTTTCACACAAACGCCGCAATAGGTATCG
345959 ATATTTAGTGACGTTTTCAAC
66 ATATTTAGTGACGTTTTCAAC
**
345980 ACAAACGCCGCAATAGGTGTT-AATATTTAGCGGTGTTTTTCACACAAACGCCGCAATAGGTAT-
1 ACAAACGCCGCAATAGGT-TTGAATATTTAGCGACGTTTTTCACACAAACGCCGCAATAGGTATC
* *
346043 GTTATTTAATTG-CGTTTATTC-AC
65 GATATTT-AGTGACG-TT-TTCAAC
*
346066 ACAAACGCCACAATAG
1 ACAAACGCCGCAATAG
346082 TTATGTTCTT
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
85 8 0.09
86 74 0.85
87 5 0.06
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Consensus pattern (86 bp):
ACAAACGCCGCAATAGGTTTGAATATTTAGCGACGTTTTTCACACAAACGCCGCAATAGGTATCG
ATATTTAGTGACGTTTTCAAC
Found at i:346087 original size:43 final size:42
Alignment explanation
Indices: 345927--346113 Score: 130
Period size: 43 Copynumber: 4.4 Consensus size: 42
345917 TATTTAGCGA
* * * * * *
345927 CGTTTTTCTCACAAATGCCGCAATAGTTATCGATATTT-AGTG
1 CGTTTTTCACACAAACGCCACAATAGGTAT-GTTATTTAATTG
* * ***
345969 ACG-TTTTCAACACAAACGCCGCAATAGGTGT-TAATATTTAGCGG
1 -CGTTTTTC-ACACAAACGCCACAATAGGTATGT--TATTTAATTG
* *
346013 TGTTTTTCACACAAACGCCGCAATAGGTATGTTATTTAATTG
1 CGTTTTTCACACAAACGCCACAATAGGTATGTTATTTAATTG
* * **
346055 CGTTTATTCACACAAACGCCACAATAGTTATGTTCTTTAACGG
1 CGTTT-TTCACACAAACGCCACAATAGGTATGTTATTTAATTG
346098 CGTTTTTGC-CACAAAC
1 CGTTTTT-CACACAAAC
346114 ATCGTAAAAT
Statistics
Matches: 117, Mismatches: 19, Indels: 17
0.76 0.12 0.11
Matches are distributed among these distances:
42 25 0.21
43 85 0.73
44 7 0.06
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.34
Consensus pattern (42 bp):
CGTTTTTCACACAAACGCCACAATAGGTATGTTATTTAATTG
Found at i:346488 original size:21 final size:22
Alignment explanation
Indices: 346463--346512 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
346453 ATTCTTCATA
*
346463 TCTCTGCTGATAT-GTTGCTTC
1 TCTCTGCTGATATCGCTGCTTC
*
346484 TCTCTG-TGATGTCGCTGCTTC
1 TCTCTGCTGATATCGCTGCTTC
346505 TCT-TGCTG
1 TCTCTGCTG
346513 CACTCTCAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.06, C:0.26, G:0.22, T:0.46
Consensus pattern (22 bp):
TCTCTGCTGATATCGCTGCTTC
Found at i:354279 original size:12 final size:14
Alignment explanation
Indices: 354248--354274 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
354238 AGGCAATGGC
354248 ATAATATATCTAGT
1 ATAATATATCTAGT
354262 ATAATATATCTAG
1 ATAATATATCTAG
354275 AAATAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
ATAATATATCTAGT
Found at i:355526 original size:23 final size:23
Alignment explanation
Indices: 355490--355538 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
355480 TAAAAAAACA
*
355490 TAACAACAATCATACATTTTAAT
1 TAACAACAAGCATACATTTTAAT
*
355513 TAACAACCAGCATACATTTTAAT
1 TAACAACAAGCATACATTTTAAT
355536 TAA
1 TAA
355539 GCCAGAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (23 bp):
TAACAACAAGCATACATTTTAAT
Found at i:357597 original size:16 final size:16
Alignment explanation
Indices: 357578--357608 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
357568 AAAATAAAAG
*
357578 TAAAAATATAAACATA
1 TAAAAACATAAACATA
357594 TAAAAACATAAACAT
1 TAAAAACATAAACAT
357609 CATTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (16 bp):
TAAAAACATAAACATA
Found at i:366352 original size:23 final size:23
Alignment explanation
Indices: 366325--366373 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
366315 AAATTGTTTT
* *
366325 TAAAATAGAAGAT-TAGAATAAAA
1 TAAAATAAAAGATAAAG-ATAAAA
366348 TAAAATAAAAGATAAAGATAAAA
1 TAAAATAAAAGATAAAGATAAAA
366371 TAA
1 TAA
366374 TTAATTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.20
Consensus pattern (23 bp):
TAAAATAAAAGATAAAGATAAAA
Found at i:366462 original size:63 final size:63
Alignment explanation
Indices: 366345--366463 Score: 177
Period size: 63 Copynumber: 1.9 Consensus size: 63
366335 GATTAGAATA
* * * *
366345 AAATAAAATAAAAGATAAAGATAAAATAATTAATTAATTAAATTAAATTAAATTAAATAGAGG
1 AAATAAAATAAAAGACAAAGATAAAATAAATAAATAATTAAATTAAAGTAAATTAAATAGAGG
*
366408 AAATAAAATAAAAGACAATGATAAAATAAATAAATAATTAAATTTAAAGT-AATTAA
1 AAATAAAATAAAAGACAAAGATAAAATAAATAAATAATTAAA-TTAAAGTAAATTAA
366464 GATAAAGAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
63 44 0.88
64 6 0.12
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.28
Consensus pattern (63 bp):
AAATAAAATAAAAGACAAAGATAAAATAAATAAATAATTAAATTAAAGTAAATTAAATAGAGG
Found at i:367117 original size:21 final size:21
Alignment explanation
Indices: 367070--367126 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
367060 AAAAATAAAA
367070 ATAAAAACAAAGAAAAACTTT
1 ATAAAAACAAAGAAAAACTTT
** *
367091 GGAAAAGA-AAAGAAAAATTTT
1 ATAAAA-ACAAAGAAAAACTTT
* *
367112 ATAAAACCAGAGAAA
1 ATAAAAACAAAGAAA
367127 TAAGAAGAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.65, C:0.07, G:0.12, T:0.16
Consensus pattern (21 bp):
ATAAAAACAAAGAAAAACTTT
Found at i:367310 original size:22 final size:23
Alignment explanation
Indices: 367271--367313 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
367261 AAAACAAAGA
*
367271 TAAAATAAAATTCTTAAAATATT
1 TAAAATAAAATGCTTAAAATATT
*
367294 TAAATTAAAATGC-TAAAATA
1 TAAAATAAAATGCTTAAAATA
367314 ATGAGTTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (23 bp):
TAAAATAAAATGCTTAAAATATT
Found at i:373146 original size:24 final size:24
Alignment explanation
Indices: 373102--373157 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
373092 ATATATTACC
* *
373102 TGAATTCTGTTATGATTTCTGATA
1 TGAATTCTGTTATAATATCTGATA
* * *
373126 TGGATTCTGTTCTAATATCTGATC
1 TGAATTCTGTTATAATATCTGATA
373150 TGAATTCT
1 TGAATTCT
373158 ATTTTGTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.23, C:0.12, G:0.16, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTATAATATCTGATA
Found at i:377534 original size:3 final size:3
Alignment explanation
Indices: 377528--377688 Score: 75
Period size: 3 Copynumber: 52.3 Consensus size: 3
377518 TATTCAATAA
* * *
377528 TAT TAT TAT TAT ATAA TAT GTAT TACT TAT TAT GAG T-T TAT TAT TCA-
1 TAT TAT TAT TAT -TAT TAT -TAT TA-T TAT TAT TAT TAT TAT TAT T-AT
* *
377575 TAT TAT TAT TAT ATAG TAT TAT T-T TA- TAT TAT CTAC TATT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT -TAT TA-T TAT TAT
* * * *
377621 TACA TAT CT-T TAA TAT TAT TAT CTAT TAT TA- TAT TTT TAC TAT TAT
1 TA-T TAT -TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
* *
377667 TAT T-T ATGT TAT TAA TAT TAT T
1 TAT TAT -TAT TAT TAT TAT TAT T
377689 TACTAATATT
Statistics
Matches: 119, Mismatches: 21, Indels: 36
0.68 0.12 0.20
Matches are distributed among these distances:
2 10 0.08
3 87 0.73
4 22 0.18
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:377536 original size:16 final size:17
Alignment explanation
Indices: 377515--377603 Score: 63
Period size: 16 Copynumber: 5.6 Consensus size: 17
377505 TCATTACTCC
377515 TATTATTCA-ATAATAT-
1 TATTATT-ATATAATATG
377531 TATTATTATATAATATG
1 TATTATTATATAATATG
377548 TATTACTTAT-T-ATGA-G
1 TATTA-TTATATAAT-ATG
*
377564 T-TTATTAT-TCATAT-
1 TATTATTATATAATATG
*
377578 TATTATTATATAGTAT-
1 TATTATTATATAATATG
377594 TATT-TTATAT
1 TATTATTATAT
377604 TATCTACTAT
Statistics
Matches: 63, Mismatches: 2, Indels: 17
0.77 0.02 0.21
Matches are distributed among these distances:
14 7 0.11
15 19 0.30
16 26 0.41
17 7 0.11
18 4 0.06
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.56
Consensus pattern (17 bp):
TATTATTATATAATATG
Found at i:377665 original size:17 final size:18
Alignment explanation
Indices: 377591--377673 Score: 70
Period size: 17 Copynumber: 4.8 Consensus size: 18
377581 TATTATATAG
*
377591 TATTATTTTA-TATTATC
1 TATTATTATATTATTATC
*
377608 TACTATT-TATTATTA-C
1 TATTATTATATTATTATC
377624 ATATCT-TTAATATTATTATC
1 -TAT-TATT-ATATTATTATC
*
377644 TATTATTATATTTTTA-C
1 TATTATTATATTATTATC
377661 TATTATTAT-TTAT
1 TATTATTATATTAT
377674 GTTATTAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
16 6 0.11
17 25 0.45
18 10 0.18
19 13 0.24
20 1 0.02
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTATTATATTATTATC
Found at i:377678 original size:9 final size:9
Alignment explanation
Indices: 377633--377724 Score: 53
Period size: 9 Copynumber: 9.8 Consensus size: 9
377623 CATATCTTTA
377633 ATATTATTAT
1 ATATTATT-T
*
377643 CTATTA-TT
1 ATATTATTT
*
377651 ATATTTTTACT
1 ATATTATT--T
377662 ATTATTATTT
1 A-TATTATTT
* *
377672 ATGTTATTA
1 ATATTATTT
377681 ATATTATTT
1 ATATTATTT
*
377690 ACTAATATTT
1 A-TATTATTT
* *
377700 GTATTA-CT
1 ATATTATTT
377708 ATATATATTT
1 ATAT-TATTT
377718 ATATTAT
1 ATATTAT
377725 CATACGTGTT
Statistics
Matches: 61, Mismatches: 14, Indels: 15
0.68 0.16 0.17
Matches are distributed among these distances:
8 9 0.15
9 25 0.41
10 19 0.31
11 2 0.03
12 6 0.10
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (9 bp):
ATATTATTT
Found at i:377685 original size:21 final size:20
Alignment explanation
Indices: 377515--377688 Score: 73
Period size: 20 Copynumber: 8.8 Consensus size: 20
377505 TCATTACTCC
*
377515 TATTATTCAATAATATTA-T-
1 TATTATT-AATATTATTATTA
*
377534 TATTATATAATATGTATTACT-
1 TATTAT-TAATAT-TATTATTA
* *
377555 TATTATGAGT-TTATTATTCA
1 TATTATTAATATTATTATT-A
* *
377575 TATTATTATTATATAGTATTA
1 TATTATTAATAT-TATTATTA
* * *
377596 TTTTA-TATTATCTACTATT-
1 TATTATTAATAT-TATTATTA
377615 TATTATTACATATCT-TTA--A
1 TATTATTA-ATAT-TATTATTA
*
377634 TATTATT-AT-CTATTATTA
1 TATTATTAATATTATTATTA
* *
377652 TATTTTTACTATTATTATTTA
1 TATTATTAATATTATTA-TTA
*
377673 TGTTATTAATATTATT
1 TATTATTAATATTATT
377689 TACTAATATT
Statistics
Matches: 119, Mismatches: 20, Indels: 30
0.70 0.12 0.18
Matches are distributed among these distances:
15 1 0.01
16 3 0.03
17 2 0.02
18 13 0.11
19 23 0.19
20 37 0.31
21 34 0.29
22 6 0.05
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (20 bp):
TATTATTAATATTATTATTA
Found at i:377784 original size:12 final size:12
Alignment explanation
Indices: 377737--377790 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
377727 TACGTGTTAT
*
377737 TATTTATTACTA
1 TATTTATTAATA
* *
377749 TA--TACTAATC
1 TATTTATTAATA
377759 TATTTATT-ATA
1 TATTTATTAATA
*
377770 TATTAATTAATA
1 TATTTATTAATA
377782 TATTTATTA
1 TATTTATTA
377791 TAAATATTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
10 7 0.22
11 9 0.28
12 16 0.50
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (12 bp):
TATTTATTAATA
Found at i:377785 original size:23 final size:21
Alignment explanation
Indices: 377737--377792 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 21
377727 TACGTGTTAT
*
377737 TATTTATTACTATATACTAATC
1 TATTTATTA-TATATACTAATA
*
377759 TATTTATTATATATTAATTAATA
1 TATTTATTATATA-T-ACTAATA
377782 TATTTATTATA
1 TATTTATTATA
377793 AATATTATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 4 0.13
22 10 0.33
23 16 0.53
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTTATTATATATACTAATA
Found at i:378233 original size:18 final size:18
Alignment explanation
Indices: 378210--378249 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
378200 ATTAAAAATA
*
378210 TTATTATTTTTAT-CGATT
1 TTATTATTATTATACG-TT
378228 TTATTATTATTATACGTT
1 TTATTATTATTATACGTT
378246 TTAT
1 TTAT
378250 CGGTTTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (18 bp):
TTATTATTATTATACGTT
Found at i:378354 original size:21 final size:19
Alignment explanation
Indices: 378329--378372 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
378319 AGAATTTTAA
*
378329 AAATATTAATATTTTAAGTAT
1 AAATAATAATATTTT-AG-AT
378350 AAATAATAATATTTTAGAT
1 AAATAATAATATTTTAGAT
378369 AAAT
1 AAAT
378373 TTTTATCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
20 2 0.09
21 14 0.64
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
AAATAATAATATTTTAGAT
Found at i:380043 original size:13 final size:14
Alignment explanation
Indices: 380025--380058 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
380015 CTTATTCGCG
380025 TTTTTTACT-TATT
1 TTTTTTACTATATT
380038 TTTTTTACTAATATT
1 TTTTTTACT-ATATT
380053 TTTTTT
1 TTTTTT
380059 TTCTTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.47
15 10 0.53
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTTACTATATT
Found at i:380371 original size:13 final size:13
Alignment explanation
Indices: 380348--380380 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
380338 TCAATTTGTT
380348 ATTTT-AATACAA
1 ATTTTGAATACAA
*
380360 ATTTTGAATACAC
1 ATTTTGAATACAA
380373 ATTTTGAA
1 ATTTTGAA
380381 GGGAAACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (13 bp):
ATTTTGAATACAA
Found at i:380786 original size:19 final size:19
Alignment explanation
Indices: 380762--380798 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
380752 ATGACCAACA
*
380762 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
380781 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
380799 CAGTATCGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:380928 original size:20 final size:20
Alignment explanation
Indices: 380905--380954 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
380895 GAATATGTAA
*
380905 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTATGACT
380925 ATCGCAACGCGATTATGACT
1 ATCGCAACGCGATTATGACT
*
380945 GTCGCAACGC
1 ATCGCAACGC
380955 TGAATTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATTATGACT
Found at i:381779 original size:24 final size:24
Alignment explanation
Indices: 381761--381807 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
381751 AGTCAGTATT
381761 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATCTTGGTCAATACC
* *
381785 CGGACTTTGATCTTGGTCAATAC
1 CGAAATTTGATCTTGGTCAATAC
381808 TCGGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTCAATACC
Found at i:381812 original size:24 final size:24
Alignment explanation
Indices: 381766--381819 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
381756 GTATTCGAAA
381766 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
381790 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
381814 TTTGAT
1 TTTGAT
381820 GATGTTTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:382038 original size:14 final size:14
Alignment explanation
Indices: 382019--382045 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
382009 GAATAAGAAA
382019 TCCCCGAAGAAAAG
1 TCCCCGAAGAAAAG
382033 TCCCCGAAGAAAA
1 TCCCCGAAGAAAA
382046 TGCCACGGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.30, G:0.19, T:0.07
Consensus pattern (14 bp):
TCCCCGAAGAAAAG
Found at i:387006 original size:20 final size:21
Alignment explanation
Indices: 386952--387014 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
386942 GATTCCCCTG
386952 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
386976 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
386996 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
387015 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:390864 original size:22 final size:21
Alignment explanation
Indices: 390822--390861 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
390812 GAGTTTGTTT
*
390822 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
390843 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
390862 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:393672 original size:18 final size:18
Alignment explanation
Indices: 393649--393683 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
393639 AGAAAAAGGC
*
393649 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
393667 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
393684 CAACCATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:393993 original size:140 final size:140
Alignment explanation
Indices: 393741--394023 Score: 512
Period size: 140 Copynumber: 2.0 Consensus size: 140
393731 GCAAACGTTG
*
393741 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTAAGT
* * *
393806 TTGAATATTGCTATGATTTATTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGTAACG
66 TTGAACATTGCTATGATCTATTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
393871 CGAATTTGAC
131 CGAATTTGAC
393881 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTAAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTAAGT
* *
393946 TTGAACATTGCTATGATCTGTTTAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTATTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
394011 CGAATTTGAC
131 CGAATTTGAC
394021 TAT
1 TAT
394024 CGCAACTCAA
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 137 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.45
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTAAGT
TTGAACATTGCTATGATCTATTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:394019 original size:20 final size:20
Alignment explanation
Indices: 393994--394145 Score: 112
Period size: 20 Copynumber: 8.2 Consensus size: 20
393984 TTACACATTC
*
393994 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
394014 ATTTGACTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
* *
394033 A----A-AATTGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
394048 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
394068 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
* *
394088 ATTTGACTATCACAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
394108 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
394122 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
394142 ATTT
1 ATTT
394146 ACTTTTGCGT
Statistics
Matches: 100, Mismatches: 20, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
14 17 0.17
15 3 0.03
16 1 0.01
18 1 0.01
19 3 0.03
20 75 0.75
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:394084 original size:74 final size:74
Alignment explanation
Indices: 393994--394145 Score: 207
Period size: 74 Copynumber: 2.1 Consensus size: 74
393984 TTACACATTC
* * * *
393994 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACTCA-AAAATTGCAACGCGAATTTGACTAT
1 ATTTGAATATCGCAACGCGAATTTGACTATCACAAC-CAGAAAATCGCAAAGCGAATTAGACTAT
*
394058 CGCAACGTGA
65 CGCAACGCGA
* * * *
394068 ATTTGATTATCGCAACGGGAATTTGACTATCACAACGAGAAAATCGCAAAGCGTATTAGACTATC
1 ATTTGAATATCGCAACGCGAATTTGACTATCACAACCAGAAAATCGCAAAGCGAATTAGACTATC
394133 GCAACGCGA
66 GCAACGCGA
394142 ATTT
1 ATTT
394146 ACTTTTGCGT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
73 1 0.01
74 67 0.99
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (74 bp):
ATTTGAATATCGCAACGCGAATTTGACTATCACAACCAGAAAATCGCAAAGCGAATTAGACTATC
GCAACGCGA
Found at i:394178 original size:20 final size:20
Alignment explanation
Indices: 394155--394220 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
394145 TACTTTTGCG
*
394155 TTGCGATTTTGGCTTTCGCA
1 TTGCGATTTTGACTTTCGCA
394175 TTGCGATTTTGACTTTCGCA
1 TTGCGATTTTGACTTTCGCA
* * *
394195 TTGCGATTTTGAGTTTAGCG
1 TTGCGATTTTGACTTTCGCA
394215 TTGCGA
1 TTGCGA
394221 AAGTGTACCT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.14, C:0.17, G:0.26, T:0.44
Consensus pattern (20 bp):
TTGCGATTTTGACTTTCGCA
Found at i:394219 original size:40 final size:39
Alignment explanation
Indices: 394138--394221 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 39
394128 CTATCGCAAC
* * *
394138 GCGAATTTACTTTTGCGTTGCGATTTTGGCTTTCGCATT
1 GCGAATTTACTTTCGCATTGCGATTTTGGCTTTAGCATT
* *
394177 GCGATTTTGACTTTCGCATTGCGATTTTGAG-TTTAGCGTT
1 GCGAATTT-ACTTTCGCATTGCGATTTTG-GCTTTAGCATT
394217 GCGAA
1 GCGAA
394222 AGTGTACCTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
39 7 0.19
40 29 0.78
41 1 0.03
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.43
Consensus pattern (39 bp):
GCGAATTTACTTTCGCATTGCGATTTTGGCTTTAGCATT
Found at i:394356 original size:27 final size:27
Alignment explanation
Indices: 394324--394433 Score: 94
Period size: 27 Copynumber: 3.7 Consensus size: 27
394314 ATAAGAATTA
*
394324 TTTACACATCAATTAAACAAATCAACT
1 TTTACAAATCAATTAAACAAATCAACT
* *
394351 TTTACAAATCAATTAAACAAGAACAAATAAGAATT
1 TTTACAAATCAATT-----A-AACAAAT--CAACT
*
394386 ATTTACACATCAATTAAACAAATCAACT
1 -TTTACAAATCAATTAAACAAATCAACT
*
394414 TTTATAAATCAATTAAACAA
1 TTTACAAATCAATTAAACAA
394434 GCAAAAAATG
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
27 31 0.47
28 3 0.05
30 7 0.11
31 1 0.02
32 1 0.02
33 7 0.11
35 3 0.05
36 13 0.20
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.29
Consensus pattern (27 bp):
TTTACAAATCAATTAAACAAATCAACT
Found at i:394384 original size:63 final size:64
Alignment explanation
Indices: 394272--394505 Score: 267
Period size: 63 Copynumber: 3.5 Consensus size: 64
394262 GATTGAAATC
* *
394272 AACAAATCAACTTTTACATTTCAATCAATTAAATAAGCACAAATAAGAATTATTTACACATCAAT
1 AACAAATCAACTTTTACA--T-AATCAATTAAACAAGAACAAATAAGAATTATTTACACATCAAT
394337 TA
63 TA
394339 AACAAATCAACTTTTACA-AATCAATTAAACAAGAACAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACATAATCAATTAAACAAGAACAAATAAGAATTATTTACACATCAATTA
* * * * *
394402 AACAAATCAACTTTTATA-AATCAATTAAACAAGCAAAAAATGCTAATAATTCTTATTTTCCTCA
1 AACAAATCAACTTTTACATAATCAATTAAACAAG-AACAAA---TAAGAA---TTA-TTTACACA
394466 TCAATTA
58 TCAATTA
*
394473 AACAAATCAGACTTTTA-AGAATCAATTAAACAA
1 AACAAATCA-ACTTTTACATAATCAATTAAACAA
394506 TCAAAAAAAG
Statistics
Matches: 150, Mismatches: 7, Indels: 15
0.87 0.04 0.09
Matches are distributed among these distances:
63 75 0.50
64 5 0.03
67 23 0.15
70 3 0.02
71 23 0.15
72 21 0.14
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACATAATCAATTAAACAAGAACAAATAAGAATTATTTACACATCAATTA
Found at i:394404 original size:36 final size:36
Alignment explanation
Indices: 394295--394406 Score: 116
Period size: 36 Copynumber: 3.4 Consensus size: 36
394285 TTACATTTCA
* *
394295 ATCAATTAAATAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAGAACAAATAAGAATTATTTACAC
* * *
394331 ATCAATT-----A-AACAAAT--CAACT-TTTACAA
1 ATCAATTAAACAAGAACAAATAAGAATTATTTACAC
394358 ATCAATTAAACAAGAACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAGAACAAATAAGAATTATTTACAC
394394 ATCAATTAAACAA
1 ATCAATTAAACAA
394407 ATCAACTTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
27 13 0.22
28 3 0.05
30 6 0.10
31 1 0.02
32 1 0.02
33 7 0.12
35 3 0.05
36 26 0.43
ACGTcount: A:0.54, C:0.15, G:0.04, T:0.27
Consensus pattern (36 bp):
ATCAATTAAACAAGAACAAATAAGAATTATTTACAC
Found at i:395856 original size:21 final size:21
Alignment explanation
Indices: 395832--395930 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 21
395822 GTGGGAAGGA
*
395832 CCTCTTCAACGATGATAGGGG
1 CCTCTTGAACGATGATAGGGG
* ** *
395853 CCTCTTGAACGGTGGGAGAGG
1 CCTCTTGAACGATGATAGGGG
* **
395874 ACTCTTGAGGGATGATAGGGG
1 CCTCTTGAACGATGATAGGGG
* * *
395895 CCTCTTGAATGAT-AGGAGAGG
1 CCTCTTGAACGATGA-TAGGGG
395916 CCTCTTGAACGATGA
1 CCTCTTGAACGATGA
395931 CAGGTGAGTC
Statistics
Matches: 58, Mismatches: 18, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
20 1 0.02
21 56 0.97
22 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.23
Consensus pattern (21 bp):
CCTCTTGAACGATGATAGGGG
Found at i:395879 original size:42 final size:42
Alignment explanation
Indices: 395812--395930 Score: 159
Period size: 42 Copynumber: 2.8 Consensus size: 42
395802 ATGAATCAGG
*
395812 CTCTTGAATGGTGGGA-AGGACCTCTTCAACGATGATAGGGGC
1 CTCTTGAATGGTGGGAGAGGA-CTCTTGAACGATGATAGGGGC
* **
395854 CTCTTGAACGGTGGGAGAGGACTCTTGAGGGATGATAGGGGC
1 CTCTTGAATGGTGGGAGAGGACTCTTGAACGATGATAGGGGC
* * *
395896 CTCTTGAATGATAGGAGAGGCCTCTTGAACGATGA
1 CTCTTGAATGGTGGGAGAGGACTCTTGAACGATGA
395931 CAGGTGAGTC
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.24
Consensus pattern (42 bp):
CTCTTGAATGGTGGGAGAGGACTCTTGAACGATGATAGGGGC
Found at i:396505 original size:20 final size:20
Alignment explanation
Indices: 396437--396503 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
396427 CGAAACTTAA
396437 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
396457 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
396477 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
396497 ATCGCAA
1 ATCGCAA
396504 TGGGATAATC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:396624 original size:33 final size:34
Alignment explanation
Indices: 396553--396628 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 34
396543 ACTAAATTCG
*
396553 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCA
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
* * *
396587 CGTTGCGATTTTTATTTT-GCATTGCTATTATCC
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
396620 CGTTGCGAT
1 CGTTGCGAT
396629 AGTCAAATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
33 21 0.55
34 17 0.45
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
Found at i:396645 original size:20 final size:20
Alignment explanation
Indices: 396620--396708 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
396610 GCTATTATCC
*
396620 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
396640 CGTTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
*
396660 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
*
396680 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
396700 CGTTGCGAT
1 CGTTGCGAT
396709 TTTTAAGTTT
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
19 3 0.05
20 59 0.91
21 3 0.05
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:396680 original size:40 final size:40
Alignment explanation
Indices: 396620--396708 Score: 151
Period size: 40 Copynumber: 2.2 Consensus size: 40
396610 GCTATTATCC
396620 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTCCG
** *
396660 CGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTCCG
396700 CGTTGCGAT
1 CGTTGCGAT
396709 TTTTAAGTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (40 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTCCG
Found at i:397165 original size:10 final size:10
Alignment explanation
Indices: 397150--397174 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
397140 TAAATGTCGT
397150 TATAGAGGTA
1 TATAGAGGTA
397160 TATAGAGGTA
1 TATAGAGGTA
397170 TATAG
1 TATAG
397175 TGTGGTCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (10 bp):
TATAGAGGTA
Found at i:398571 original size:20 final size:20
Alignment explanation
Indices: 398548--398588 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
398538 TCTGAAACTT
398548 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
398568 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
398588 A
1 A
398589 CTATCACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.20, G:0.15, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:398598 original size:20 final size:20
Alignment explanation
Indices: 398548--398603 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
398538 TCTGAAACTT
*
398548 AAAATCGCAACACGAAAATG
1 AAAATCACAACACGAAAATG
*
398568 AAAATCGCAACACGAAAATG
1 AAAATCACAACACGAAAATG
** *
398588 ACTATCACAACGCGAA
1 AAAATCACAACACGAA
398604 TTAAACTATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.52, C:0.23, G:0.14, T:0.11
Consensus pattern (20 bp):
AAAATCACAACACGAAAATG
Found at i:399007 original size:20 final size:21
Alignment explanation
Indices: 398982--399023 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
398972 TCTGAGAGAT
398982 GGAGAT-AGACGGATTTTGTC
1 GGAGATGAGACGGATTTTGTC
*
399002 GGAGATGGGGACGGATTTTGTC
1 GGAGAT-GAGACGGATTTTGTC
399024 AAAGATGGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
22 13 0.68
ACGTcount: A:0.21, C:0.10, G:0.40, T:0.29
Consensus pattern (21 bp):
GGAGATGAGACGGATTTTGTC
Found at i:399016 original size:22 final size:22
Alignment explanation
Indices: 398989--399039 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
398979 GATGGAGATA
**
398989 GACGGATTTTGTCGGAGATGGG
1 GACGGATTTTGTCAAAGATGGG
399011 GACGGATTTTGTCAAAGATGGG
1 GACGGATTTTGTCAAAGATGGG
399033 GACGGAT
1 GACGGAT
399040 GTCGCCGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.10, G:0.41, T:0.25
Consensus pattern (22 bp):
GACGGATTTTGTCAAAGATGGG
Found at i:399199 original size:21 final size:21
Alignment explanation
Indices: 399173--399329 Score: 107
Period size: 21 Copynumber: 7.6 Consensus size: 21
399163 GATAGTCAGA
*
399173 ATCGCGTTGCAATTATGAATT
1 ATCGCGTTGCGATTATGAATT
*
399194 ATCGCGTTGCGA-TAGTCAGA--
1 ATCGCGTTGCGATTA-TGA-ATT
*
399214 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGAATT
*
399235 ATCGCGTTGCGA-TAGTCAGA--
1 ATCGCGTTGCGATTA-TGA-ATT
* *
399255 ATCACGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGAATT
* * *
399276 ATCGTGTTGTGA-TAGTCAGA--
1 ATCGCGTTGCGATTA-TGA-ATT
*
399296 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGAATT
399317 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
399330 AGTCAGAATC
Statistics
Matches: 103, Mismatches: 18, Indels: 30
0.68 0.12 0.20
Matches are distributed among these distances:
19 3 0.03
20 42 0.41
21 55 0.53
22 3 0.03
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGAATT
Found at i:399212 original size:41 final size:41
Alignment explanation
Indices: 399155--399348 Score: 343
Period size: 41 Copynumber: 4.7 Consensus size: 41
399145 AAATAAAATA
* *
399155 CGCGTTGCGATAGTCAGAATCGCGTTGCAATTATGAATTAT
1 CGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTAT
399196 CGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTAT
1 CGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTAT
*
399237 CGCGTTGCGATAGTCAGAATCACGTTGCGATTATGTATTAT
1 CGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTAT
* *
399278 CGTGTTGTGATAGTCAGAATCGCGTTGCGATTATGTATTAT
1 CGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTAT
399319 CGCGTTGCGATAGTCAGAATCGCGTTGCGA
1 CGCGTTGCGATAGTCAGAATCGCGTTGCGA
399349 ATCTGGAAAC
Statistics
Matches: 145, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 145 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (41 bp):
CGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTAT
Found at i:399519 original size:18 final size:18
Alignment explanation
Indices: 399496--399534 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
399486 ATTTTCTCAA
399496 AAAAATATTATATGTATT
1 AAAAATATTATATGTATT
* *
399514 AAAAATATTTTTTGTATT
1 AAAAATATTATATGTATT
399532 AAA
1 AAA
399535 TATAATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (18 bp):
AAAAATATTATATGTATT
Found at i:400627 original size:19 final size:19
Alignment explanation
Indices: 400590--400627 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
400580 ATTAAAAGAC
*
400590 ATAATTAAAGTATAGAAAT
1 ATAATTAAAGTACAGAAAT
*
400609 ATAATTAAAGTACATAAAT
1 ATAATTAAAGTACAGAAAT
400628 GACACCACAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.32
Consensus pattern (19 bp):
ATAATTAAAGTACAGAAAT
Found at i:403676 original size:26 final size:26
Alignment explanation
Indices: 403647--403709 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
403637 AAGCAAGAGT
* *
403647 GGTAAAAGGCAAAAGTGAACATTAAG
1 GGTAAAAGCCAAAAGTGAACATCAAG
403673 GGTAAAAGCCAAAAGTGAACATCAAG
1 GGTAAAAGCCAAAAGTGAACATCAAG
403699 GGTAAAAGCCA
1 GGTAAAAGCCA
403710 TCCCGAGTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.49, C:0.13, G:0.25, T:0.13
Consensus pattern (26 bp):
GGTAAAAGCCAAAAGTGAACATCAAG
Found at i:404299 original size:21 final size:21
Alignment explanation
Indices: 404275--404314 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
404265 GAAACGAGAG
404275 TTGAAAA-AGACATTGAGAGCA
1 TTGAAAAGAGA-ATTGAGAGCA
404296 TTGAAAAGAGAATTGAGAG
1 TTGAAAAGAGAATTGAGAG
404315 TGAAAAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.47, C:0.05, G:0.28, T:0.20
Consensus pattern (21 bp):
TTGAAAAGAGAATTGAGAGCA
Found at i:409529 original size:60 final size:59
Alignment explanation
Indices: 409422--409576 Score: 161
Period size: 60 Copynumber: 2.6 Consensus size: 59
409412 AGAAAGTTTA
* * ***
409422 AAAAGTTTGGGGACCAATTTAGAATTGAT-GTCATAGTTTGAGAATGAAATTTAATTGTTC
1 AAAAGTTTGAGGA-CAATTTAGAA-TGATAGTCATAGTTTGAGAATGAAATTGAAACATTC
* *
409482 AAAAGTTTGAGGACTAATTTAGAATGATAGTCATAGTTT-AGGGATGAAATTGAAACATTT
1 AAAAGTTTGAGGAC-AATTTAGAATGATAGTCATAGTTTGA-GAATGAAATTGAAACATTC
* * *
409542 AAACGTTTAAGGAACAATTTAGAATGAGAGTCATA
1 AAAAGTTTGAGG-ACAATTTAGAATGATAGTCATA
409577 CTTTTAGGAC
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
59 6 0.07
60 73 0.90
61 2 0.02
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.33
Consensus pattern (59 bp):
AAAAGTTTGAGGACAATTTAGAATGATAGTCATAGTTTGAGAATGAAATTGAAACATTC
Found at i:417015 original size:14 final size:14
Alignment explanation
Indices: 416977--417030 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
416967 ATTTTAAATA
*
416977 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
416991 TTTTACATTTGCAT
1 ATTTACATTTGCAT
417005 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
417020 CTTTGCATTTG
1 ATTTACATTTG
417031 TATTGCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:422761 original size:115 final size:115
Alignment explanation
Indices: 422559--423014 Score: 781
Period size: 115 Copynumber: 4.0 Consensus size: 115
422549 AAGTGCCATG
422559 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
422624 TGGTTTGGTATGAACCCCAAAAACCAATCATTGAATTTTAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTTAAAGATGAATT
422674 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
422739 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTTAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTTAAAGATGAATT
422789 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
**
422854 TGGTTTGGTATGAACCCC-AAAACCAATCATTGGATTGAAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTTAAAGATGAATT
* *
422903 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * * * * *
422968 TGATTCGGTAGGAACCCC-AGAACCGATTATTGGAATTGAAAGATGAA
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTTAAAGATGAA
423015 CTGCATGATC
Statistics
Matches: 327, Mismatches: 14, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
114 130 0.40
115 197 0.60
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (115 bp):
TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTTAAAGATGAATT
Found at i:422985 original size:229 final size:229
Alignment explanation
Indices: 422559--423014 Score: 779
Period size: 229 Copynumber: 2.0 Consensus size: 229
422549 AAGTGCCATG
422559 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
**
422624 TGGTTTGGTATGAACCCCAAAAACCAATCATTGAATTTTAAAGATGAATTTGCTCATAGTAGAAA
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTGAATTGAAAAGATGAATTTGCTCATAGTAGAAA
* * * *
422689 TAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAC
131 TAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCGGTAGGAAC
* *
422754 CCCAAAAACCAATCATTGGATTTTAAAGATGAATT
196 CCC-AAAACCAATCATTGGAATTGAAAGATGAATT
422789 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
422854 TGGTTTGGTATGAACCCC-AAAACCAATCATTGGATTGAAAAGATGAATTTGCTCATAGTAGAAA
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTGAATTGAAAAGATGAATTTGCTCATAGTAGAAA
*
422918 TAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCGGTAGGAAC
131 TAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCGGTAGGAAC
* * *
422983 CCCAGAACCGATTATTGGAATTGAAAGATGAA
196 CCCAAAACCAATCATTGGAATTGAAAGATGAA
423015 CTGCATGATC
Statistics
Matches: 213, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
228 24 0.11
229 106 0.50
230 83 0.39
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (229 bp):
TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAAACCAATCATTGAATTGAAAAGATGAATTTGCTCATAGTAGAAA
TAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCGGTAGGAAC
CCCAAAACCAATCATTGGAATTGAAAGATGAATT
Found at i:425282 original size:54 final size:52
Alignment explanation
Indices: 425134--425334 Score: 239
Period size: 54 Copynumber: 3.8 Consensus size: 52
425124 AGAAATCTTG
* * *
425134 GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAACGCTTTATGAACGTCTGA
1 GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTA-CAAC-TCTGA
* *
425188 GCAAAACCCACA-AGAAAGGATGAATGTGTTGTCAAATGTTTTACAAACATCTGA
1 GCAGAAGCCACAGA-AAAGGATGAATGTGTTGTCAAATGTTTTAC-AAC-TCTGA
* *
425242 GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATCTC-GA
1 GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACAACTCTGA
* *
425293 -CAGAAACCACATGAAAA-GATGAATGTATTGTCAAATGTTTTA
1 GCAGAAGCCACA-GAAAAGGATGAATGTGTTGTCAAATGTTTTA
425335 TGAACCAGTG
Statistics
Matches: 130, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
50 33 0.25
51 7 0.05
52 2 0.02
53 3 0.02
54 84 0.65
55 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (52 bp):
GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACAACTCTGA
Found at i:425735 original size:22 final size:22
Alignment explanation
Indices: 425706--425760 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
425696 ATCTACACTC
*
425706 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
425728 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
425750 TTCAAAGATGA
1 TTCAAAGATGA
425761 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:426358 original size:113 final size:113
Alignment explanation
Indices: 426160--427172 Score: 1366
Period size: 113 Copynumber: 9.0 Consensus size: 113
426150 TAGCAAATAT
* *
426160 TCAAATCCATCA-TCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATTAGAAGAACTCACCTG
1 TCAAATCCATCACT-TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
*
426224 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
426273 TCAAATCCATCA-TCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACT-TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
*
426337 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
426386 TCAAATCCATCA-TCTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACT-TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
*
426450 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
426499 TCAAATCCATCA-TCTGATGGATCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATTTG
1 TCAAATCCATCACT-TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
* * *
426563 AAGAAGGAAGAAGAAATTTATAATGAGAAGAATTTGTTCAACTTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
426612 TCAAATCCATCACTTGATGGGTCAGCTTTTCCAG-AGAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * * *
426676 AGAAGGATGAAGAAGTTCATAACGAGAAAAATTTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * ****
426724 TCAAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
426789 AGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *** * ** *
426837 TCAAATCTATCACTTGATGGATTAAAATTTCCTGGTATAGTTCATAATGAGAAGAACTCATTACT
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCA-T-C-
* * * *
426902 TGAAGAAGGATGAAGAAGTTCATAACGAGAAAAATTTGTTCAACCTTTTGT
63 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * **** *
426953 TCAAATCTATCACTTGATGGA-CTATCTTTTCCAGTTCGATTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATC-AGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
* *
427017 AAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
427066 TCAAATCCACCACTTGATGGGTCAG-TTTTCCCAG-AGAAGTTCATAATGAGAAGAACTCATC--
1 TCAAATCCATCACTTGATGGATCAGCTTTT-CCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
* * ** *
427127 -AGGA-GAAGAAGAAGTTCATAATAAGAAGAGCTTATTCAACCTTTTG
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
427173 AATGACTCTA
Statistics
Matches: 824, Mismatches: 68, Indels: 21
0.90 0.07 0.02
Matches are distributed among these distances:
108 37 0.04
109 3 0.00
112 126 0.15
113 554 0.67
114 4 0.00
115 2 0.00
116 98 0.12
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:427154 original size:17 final size:17
Alignment explanation
Indices: 427100--427155 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
427090 GTTTTCCCAG
*
427100 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATAAGA
* *
427117 AGAA-CTCATCAGGAGAAGA
1 AGAAGTTCAT-A--ATAAGA
427136 AGAAGTTCATAATAAGA
1 AGAAGTTCATAATAAGA
427153 AGA
1 AGA
427156 GCTTATTCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
16 4 0.13
17 13 0.43
19 9 0.30
20 4 0.13
ACGTcount: A:0.50, C:0.09, G:0.23, T:0.18
Consensus pattern (17 bp):
AGAAGTTCATAATAAGA
Found at i:427403 original size:3 final size:3
Alignment explanation
Indices: 427397--427482 Score: 64
Period size: 3 Copynumber: 28.0 Consensus size: 3
427387 CATTTTAATG
* * * * * *
427397 TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TAA TTA TAA TAA TAA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
427445 TAA TAA TTA TTA TTA ATA TATA TTA TTTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA
427483 CAAAACCCGG
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
3 65 0.92
4 6 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (3 bp):
TTA
Found at i:432475 original size:16 final size:16
Alignment explanation
Indices: 432451--432481 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
432441 CCCCAAGGTG
432451 AAATACTCGATCTAAT
1 AAATACTCGATCTAAT
*
432467 AAATCCTCGATCTAA
1 AAATACTCGATCTAA
432482 CAGATCTTGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.23, G:0.06, T:0.29
Consensus pattern (16 bp):
AAATACTCGATCTAAT
Found at i:436012 original size:30 final size:31
Alignment explanation
Indices: 435953--436021 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
435943 AACCATTCAC
*
435953 AACTTTTCCAAAATTACCAAATTAGTCCCCA
1 AACTTTTCAAAAATTACCAAATTAGTCCCCA
*
435984 AACTTTTCAAAAATTA-TAGAATTA-TCCCCA
1 AACTTTTCAAAAATTACCA-AATTAGTCCCCA
*
436014 AATTTTTC
1 AACTTTTC
436022 TAAGGCTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 14 0.41
31 20 0.59
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (31 bp):
AACTTTTCAAAAATTACCAAATTAGTCCCCA
Found at i:437175 original size:29 final size:29
Alignment explanation
Indices: 437092--437181 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 29
437082 GGATAAATTG
* *
437092 TAACTTTTTAAAATTACCATTTTGGTC-TT
1 TAACTTTTAAAAATTA-CATTTTGGTCACT
* * *
437121 TAAACATTTTCAAAATTTATACTTTGGTCACT
1 T-AAC-TTTT-AAAAATTACATTTTGGTCACT
437153 TAACTTTTAAAAATTACATTTTGGTCACT
1 TAACTTTTAAAAATTACATTTTGGTCACT
437182 ATATAAAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
29 19 0.39
30 7 0.14
31 15 0.31
32 8 0.16
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.47
Consensus pattern (29 bp):
TAACTTTTAAAAATTACATTTTGGTCACT
Found at i:439663 original size:34 final size:34
Alignment explanation
Indices: 439625--439689 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
439615 AAGGAGTTTA
* *
439625 TATCTTTTTAATTGTTCAA-ATTAAAAGATATCAT
1 TATCTGTTTAAAT-TTCAATATTAAAAGATATCAT
*
439659 TATCTGTTTAAATTTGAATATTAAAAGATAT
1 TATCTGTTTAAATTTCAATATTAAAAGATAT
439690 TTAGTTAGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 4 0.15
34 23 0.85
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (34 bp):
TATCTGTTTAAATTTCAATATTAAAAGATATCAT
Found at i:440022 original size:5 final size:5
Alignment explanation
Indices: 440012--440051 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
440002 CAATAAAACA
440012 TTATT TTA-T TTA-T TTATT TCTA-T TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT T-TATT TTATT TTATT TTATT TT
440052 CTTATGAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 10 0.31
5 20 0.62
6 2 0.06
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTATT
Found at i:440575 original size:27 final size:27
Alignment explanation
Indices: 440536--440600 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
440526 GTCTTCTAGA
*
440536 GTTCTAGGGTCTTAGAGGTTCAAAAGT
1 GTTCTAGGATCTTAGAGGTTCAAAAGT
440563 GTTCTAGGATCTTAGAGGTTCAAAAGT
1 GTTCTAGGATCTTAGAGGTTCAAAAGT
440590 GTTCTAGGATC
1 GTTCTAGGATC
440601 CTCTAGTGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (27 bp):
GTTCTAGGATCTTAGAGGTTCAAAAGT
Found at i:445404 original size:3 final size:3
Alignment explanation
Indices: 445396--445458 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
445386 CAATATACAA
445396 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
445444 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
445459 GTAATTCATA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:445587 original size:13 final size:12
Alignment explanation
Indices: 445510--445588 Score: 63
Period size: 12 Copynumber: 6.5 Consensus size: 12
445500 ATGTTCATGC
445510 AAAATAAGTAAAT
1 AAAA-AAGTAAAT
*
445523 AAAAATATTAAAT
1 AAAAA-AGTAAAT
445536 AAATAAA-TAAAT
1 AAA-AAAGTAAAT
* ** *
445548 ATACCA-TGAAT
1 AAAAAAGTAAAT
*
445559 AAAAACGTAAAT
1 AAAAAAGTAAAT
445571 AAAAAAGTAAAT
1 AAAAAAGTAAAT
445583 AAAAAA
1 AAAAAA
445589 TATGTTTTAT
Statistics
Matches: 52, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
11 7 0.13
12 29 0.56
13 14 0.27
14 2 0.04
ACGTcount: A:0.70, C:0.04, G:0.05, T:0.22
Consensus pattern (12 bp):
AAAAAAGTAAAT
Found at i:447670 original size:134 final size:130
Alignment explanation
Indices: 447415--447685 Score: 300
Period size: 134 Copynumber: 2.1 Consensus size: 130
447405 TGAGCTCGAC
* * *
447415 ATCCTTCATCGTGAAGTGGAAATCTGACTCAAAATCTAGGTTGGAAAACATCTCCTCATTCTTGA
1 ATCCTTCATCGTGAAGTGGAAATCTGACTCAAAATATAGGATGGAAAAAATCTCCTCATTCTTGA
* * * *
447480 GTGCTAAATTGTGGTTGACTCATTCATCGTGAAGTTGAGTTGATTCTGAATGACTTGAGCATGAT
66 GTGCTAAATTATGGTTGACTCATTCATCATGAAGTTGAGTCGATTCTGAATAACTTGAGCATGAT
* * *
447545 ATCCTTCATTGTGAAGTTGAAATCGTG-CTCAAAATATAGGAT-GAAAAAATAGCTCCTCGA-TG
1 ATCCTTCATCGTGAAGTGGAAATC-TGACTCAAAATATAGGATGGAAAAAAT--CTCCTC-ATTC
* * *
447607 TTGAGTTAAGCTAAATTATTGTTGACT-ACTTCGTCATGAAGTTGAGTCGATAT-TGGATAACTT
62 TTGAG-T--GCTAAATTATGGTTGACTCA-TTCATCATGAAGTTGAGTCGAT-TCTGAATAACTT
*
447670 GAGTATGAT
122 GAGCATGAT
447679 ATCCTTC
1 ATCCTTC
447686 GCCTTGAAGT
Statistics
Matches: 118, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
129 7 0.06
130 35 0.30
131 14 0.12
132 2 0.02
133 1 0.01
134 58 0.49
135 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (130 bp):
ATCCTTCATCGTGAAGTGGAAATCTGACTCAAAATATAGGATGGAAAAAATCTCCTCATTCTTGA
GTGCTAAATTATGGTTGACTCATTCATCATGAAGTTGAGTCGATTCTGAATAACTTGAGCATGAT
Found at i:457615 original size:54 final size:54
Alignment explanation
Indices: 457533--457641 Score: 193
Period size: 54 Copynumber: 2.0 Consensus size: 54
457523 GTGATCTCTA
457533 TAGACAGGATTAAGGTGAAGCCTCACAAGGTAAAGGCTATAATGGACTGGGAAG
1 TAGACAGGATTAAGGTGAAGCCTCACAAGGTAAAGGCTATAATGGACTGGGAAG
*
457587 TAGACAGGATTAAGGT-AGATCCTCACAAGGTAAAGGCTATAATGGACTGGGAAG
1 TAGACAGGATTAAGGTGA-AGCCTCACAAGGTAAAGGCTATAATGGACTGGGAAG
457641 T
1 T
457642 TCCAAAGAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
53 1 0.02
54 52 0.98
ACGTcount: A:0.37, C:0.13, G:0.30, T:0.20
Consensus pattern (54 bp):
TAGACAGGATTAAGGTGAAGCCTCACAAGGTAAAGGCTATAATGGACTGGGAAG
Found at i:461152 original size:20 final size:21
Alignment explanation
Indices: 461115--461171 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
461105 GTCTACGCAG
*
461115 TCCTTTGGGACATATATG-TA
1 TCCTTTGGAACATATATGATA
* * *
461135 TCCTTTGGAACCTTTATGATG
1 TCCTTTGGAACATATATGATA
461156 TCCTTTGAGACACATA
1 TCCTTTG-GA-ACATA
461172 CTTGGTCCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 15 0.54
21 8 0.29
22 2 0.07
23 3 0.11
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.39
Consensus pattern (21 bp):
TCCTTTGGAACATATATGATA
Found at i:461306 original size:23 final size:23
Alignment explanation
Indices: 461239--461306 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
461229 CATTTTATAA
* *
461239 GGCACTTCGGTGCATTTCTACAT
1 GGCACTTCGATGCATTTCTACGT
* *
461262 GGCACTTC-ACTTCAATTCTACGT
1 GGCACTTCGA-TGCATTTCTACGT
*
461285 GGCACTTCGATGCATTTATACG
1 GGCACTTCGATGCATTTCTACG
461307 AGCCGTGGTG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (23 bp):
GGCACTTCGATGCATTTCTACGT
Found at i:462724 original size:3 final size:3
Alignment explanation
Indices: 462698--462750 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
462688 AAACAAAATC
* * * *
462698 ATG ATA ATG ATA ATG ATA ATG ATG ATG ATG ATG ATG ATG ATG ATA ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
462746 ATG AT
1 ATG AT
462751 CCAATTCATA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:466306 original size:17 final size:18
Alignment explanation
Indices: 466272--466307 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
466262 TTAAAAATTA
*
466272 AATAATAAATATATTTTT
1 AATAAAAAATATATTTTT
466290 AATAAAAAATA-ATTTTT
1 AATAAAAAATATATTTTT
466307 A
1 A
466308 TTATATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATAAAAAATATATTTTT
Found at i:467065 original size:2 final size:2
Alignment explanation
Indices: 467058--467100 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
467048 TAATTAATTC
467058 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
467100 A
1 A
467101 AAAATCTGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:467377 original size:6 final size:6
Alignment explanation
Indices: 467366--467390 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
467356 TCTCCTCTGT
467366 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
467391 GCCGAGCCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:471751 original size:90 final size:89
Alignment explanation
Indices: 471593--471769 Score: 300
Period size: 90 Copynumber: 2.0 Consensus size: 89
471583 CCTAACACAC
471593 CCTTTTATAGCCAAGTTAACCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATA
1 CCTTTTATAGCCAAGTTAACCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATA
* *
471658 TTTAATTAATTGGAATTTAATAAT
66 TTTAATTAATTGAAATTAAATAAT
* * *
471682 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATTTAT
1 CCTTTTATAGCCAAGTTAACCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATATAT
471747 ATTTAATTAATTGAAATTAAATA
65 ATTTAATTAATTGAAATTAAATA
471770 TTCGGGATTA
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 33 0.40
90 49 0.60
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTAACCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATA
TTTAATTAATTGAAATTAAATAAT
Found at i:475456 original size:18 final size:18
Alignment explanation
Indices: 475430--475465 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
475420 TTGAAAGGAC
475430 TGAAGTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
*
475448 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
475466 CGGATGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:480935 original size:2 final size:2
Alignment explanation
Indices: 480928--480956 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
480918 TATTTATGTA
480928 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
480957 ATGTATGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:481029 original size:87 final size:87
Alignment explanation
Indices: 480867--481029 Score: 245
Period size: 87 Copynumber: 1.9 Consensus size: 87
480857 GTGTTATAGA
* * * *
480867 TGTATGTGTGATTGTTTATGTGTGTATTTTGTTTGAGCATCAATAATTCGTTATTTATGTATGTG
1 TGTATGTATGATTGTTTATGTGTGTATTTTGTTTGAGCATCAATAATTCGTTATGTATGTATATA
* *
480932 TGTGTGTGTGTGTGTGTGTGTG
66 TATGTATGTGTGTGTGTGTGTG
* * *
480954 TGTATGTATGATTGTTTATGTGTGTCTTTTGTTTGAGCATCAGTAATTTGTTATGTATGTATATA
1 TGTATGTATGATTGTTTATGTGTGTATTTTGTTTGAGCATCAATAATTCGTTATGTATGTATATA
481019 TATGTATGTGT
66 TATGTATGTGT
481030 TTTGTATGAG
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 67 1.00
ACGTcount: A:0.18, C:0.04, G:0.26, T:0.52
Consensus pattern (87 bp):
TGTATGTATGATTGTTTATGTGTGTATTTTGTTTGAGCATCAATAATTCGTTATGTATGTATATA
TATGTATGTGTGTGTGTGTGTG
Found at i:481296 original size:46 final size:46
Alignment explanation
Indices: 481195--481326 Score: 142
Period size: 46 Copynumber: 2.9 Consensus size: 46
481185 CATCTTCTCT
* * *
481195 GGATGATAAATCCAATTATCGATATATAGGTTGGTGCATTTTTGCA
1 GGATGATAAATCCAATTATCGATATACAGGCTGGTGCATTTATGCA
* *
481241 TGATGATAAATCCAATTATCGATATACAGGCTAGTGCATCCTTAT-C-
1 GGATGATAAATCCAATTATCGATATACAGGCTGGTGCAT--TTATGCA
* * * * *
481287 GGATTATAAATCCATTTATTGATTTACAAGCTGGTGCATT
1 GGATGATAAATCCAATTATCGATATACAGGCTGGTGCATT
481327 ATTATAGAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
44 1 0.01
46 67 0.93
47 1 0.01
48 3 0.04
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.36
Consensus pattern (46 bp):
GGATGATAAATCCAATTATCGATATACAGGCTGGTGCATTTATGCA
Found at i:484353 original size:11 final size:11
Alignment explanation
Indices: 484337--484362 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
484327 TTTGACAAGC
484337 ATCATTTTACT
1 ATCATTTTACT
484348 ATCATTTTACT
1 ATCATTTTACT
484359 ATCA
1 ATCA
484363 AATAAATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (11 bp):
ATCATTTTACT
Found at i:486819 original size:19 final size:21
Alignment explanation
Indices: 486787--486825 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
486777 TTGGGCACAT
*
486787 AAAAATATTAAGA-GAAATAG
1 AAAAAAATTAAGAGGAAATAG
486807 AAAAAAATT-AGAGGAAATA
1 AAAAAAATTAAGAGGAAATA
486826 AATTACTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.18
Consensus pattern (21 bp):
AAAAAAATTAAGAGGAAATAG
Found at i:497622 original size:36 final size:36
Alignment explanation
Indices: 497582--497805 Score: 294
Period size: 36 Copynumber: 6.3 Consensus size: 36
497572 AAGTTTGCAT
*
497582 CGATTGAAGTCGAACGGAGGGAAGCATCGACACTTC
1 CGATTCAAGTCGAACGGAGGGAAGCATCGACACTTC
* * *
497618 CGATTCAAGTTGAACGGAGGGAAGCAACAACACTTC
1 CGATTCAAGTCGAACGGAGGGAAGCATCGACACTTC
*
497654 CGATTCAAGTCGAACGGATGGAAGCATC-AGCACTTC
1 CGATTCAAGTCGAACGGAGGGAAGCATCGA-CACTTC
* *
497690 CGATTCAAGTCGAACGGA-AGAAGCATCGGCACTTC
1 CGATTCAAGTCGAACGGAGGGAAGCATCGACACTTC
* * *
497725 CGATTCAAGT-GAATGGAAGGAAGCATCGACACTTT
1 CGATTCAAGTCGAACGGAGGGAAGCATCGACACTTC
* *
497760 CGATTCAAGTCGAAAGG-GAGGAAGCATTGACACTTC
1 CGATTCAAGTCGAACGGAG-GGAAGCATCGACACTTC
497796 CGATTCAAGT
1 CGATTCAAGT
497806 GTTCATCTTT
Statistics
Matches: 166, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
34 6 0.04
35 49 0.30
36 111 0.67
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (36 bp):
CGATTCAAGTCGAACGGAGGGAAGCATCGACACTTC
Found at i:497771 original size:106 final size:108
Alignment explanation
Indices: 497582--497805 Score: 312
Period size: 106 Copynumber: 2.1 Consensus size: 108
497572 AAGTTTGCAT
* * *
497582 CGATTGAAGTCGAACGGAGGGAAGCATCGACACTTCCGATTCAAGTTGAACGGAGGGAAGCAACA
1 CGATTCAAGTCGAACGGAGAGAAGCATCGACACTTCCGATTCAAGTTGAACGGAAGGAAGCAACA
497647 ACACTTCCGATTCAAGTCG-AACGGATGGAAGCATCAG-CACTTC
66 ACACTTCCGATTCAAGTCGAAACGGA-GGAAGCAT-AGACACTTC
* * * *
497690 CGATTCAAGTCGAACGGA-AGAAGCATCGGCACTTCCGATTCAAG-TGAATGGAAGGAAGCATCG
1 CGATTCAAGTCGAACGGAGAGAAGCATCGACACTTCCGATTCAAGTTGAACGGAAGGAAGCAACA
* * *
497753 ACACTTTCGATTCAAGTCGAAAGGGAGGAAGCATTGACACTTC
66 ACACTTCCGATTCAAGTCGAAACGGAGGAAGCATAGACACTTC
497796 CGATTCAAGT
1 CGATTCAAGT
497806 GTTCATCTTT
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
105 1 0.01
106 57 0.55
107 29 0.28
108 17 0.16
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (108 bp):
CGATTCAAGTCGAACGGAGAGAAGCATCGACACTTCCGATTCAAGTTGAACGGAAGGAAGCAACA
ACACTTCCGATTCAAGTCGAAACGGAGGAAGCATAGACACTTC
Done.