Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015255.1 Kokia drynarioides strain JFW-HI SEQ_130300, 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: 749686
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 917 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:302467 original size:116 final size:116
Alignment explanation
Indices: 302310--302540 Score: 358
Period size: 116 Copynumber: 2.0 Consensus size: 116
302300 CTCAAGTTGG
* *
302310 AATCATATTTCTTTCATTGGTCCTACACGCATTTGCTTTATTTTCATTGCTTTCTACTTTCTTTA
1 AATCATATTTCTTTCATTGGTCCTACACGCATCTGCTTTATTTTCATTGCATTCTACTTTCTTT-
*
302375 ACTT-TTTCCACGTACTTTATTG-CAGTAGTCAAAACATCGGTTCATATGCAC
65 ACTTCTTTCCACATACTTTATTGCCA-TAGTCAAAACATCGGTTCATATGCAC
* *
302426 AATCATATTTCTTTCATTGGTTCTACACGCATCTGCTTTATTTTCATTGCATTCTACTTTCTTTC
1 AATCATATTTCTTTCATTGGTCCTACACGCATCTGCTTTATTTTCATTGCATTCTACTTTCTTTA
* * *
302491 CTTCTTTCCACATACTTTATTGCCATTGTCAAAACTTTGGTTCATATGCA
66 CTTCTTTCCACATACTTTATTGCCATAGTCAAAACATCGGTTCATATGCA
302541 ATTATGCATA
Statistics
Matches: 105, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
115 3 0.03
116 100 0.95
117 2 0.02
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.46
Consensus pattern (116 bp):
AATCATATTTCTTTCATTGGTCCTACACGCATCTGCTTTATTTTCATTGCATTCTACTTTCTTTA
CTTCTTTCCACATACTTTATTGCCATAGTCAAAACATCGGTTCATATGCAC
Found at i:315988 original size:2 final size:2
Alignment explanation
Indices: 315976--316005 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
315966 GAGAATAATA
315976 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT A
316006 GTTGCTGACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:316857 original size:51 final size:51
Alignment explanation
Indices: 316796--316934 Score: 156
Period size: 51 Copynumber: 2.7 Consensus size: 51
316786 ATGTAAATGA
* * * *
316796 TGACAGAATGTGTAAATATTGA-GGGCTAAATTTGTTAAAT-AATGACCAAAT
1 TGACAAAATGTGTAAATATT-ATGAGCTAAATTTATTAAATCAA-AACCAAAT
* *
316847 TGACAAAATGTGTAAATATTATGAGTTATATTTATTAAATCAAAACCAAAT
1 TGACAAAATGTGTAAATATTATGAGCTAAATTTATTAAATCAAAACCAAAT
* * * *
316898 TGATAAAATGTGTAAATTTTAAGAACTAAATTTATTA
1 TGACAAAATGTGTAAATATTATGAGCTAAATTTATTA
316935 TTATATCAAC
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
50 1 0.01
51 71 0.96
52 2 0.03
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (51 bp):
TGACAAAATGTGTAAATATTATGAGCTAAATTTATTAAATCAAAACCAAAT
Found at i:325965 original size:82 final size:82
Alignment explanation
Indices: 325828--325993 Score: 314
Period size: 82 Copynumber: 2.0 Consensus size: 82
325818 AAAATTGGGG
*
325828 GGCATTGATTCGAAGGAAAACGTGGATTCCGCGGTTCAACATGTGGGCTTGGTAACCAATCCAAG
1 GGCATTGATTCGAAGGAAAACGTGGATTACGCGGTTCAACATGTGGGCTTGGTAACCAATCCAAG
325893 GTCAACAGAGTGTCTTT
66 GTCAACAGAGTGTCTTT
*
325910 GGCATTGATTCGAGGGAAAACGTGGATTACGCGGTTCAACATGTGGGCTTGGTAACCAATCCAAG
1 GGCATTGATTCGAAGGAAAACGTGGATTACGCGGTTCAACATGTGGGCTTGGTAACCAATCCAAG
325975 GTCAACAGAGTGTCTTT
66 GTCAACAGAGTGTCTTT
325992 GG
1 GG
325994 GTTTATTTCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.25
Consensus pattern (82 bp):
GGCATTGATTCGAAGGAAAACGTGGATTACGCGGTTCAACATGTGGGCTTGGTAACCAATCCAAG
GTCAACAGAGTGTCTTT
Found at i:326733 original size:30 final size:30
Alignment explanation
Indices: 326692--326772 Score: 144
Period size: 30 Copynumber: 2.7 Consensus size: 30
326682 ACCCATAATT
* *
326692 TTTCTCTTTTTCTTCATTGTTATTTTATAA
1 TTTCCCTTTTTCTTCATTATTATTTTATAA
326722 TTTCCCTTTTTCTTCATTATTATTTTATAA
1 TTTCCCTTTTTCTTCATTATTATTTTATAA
326752 TTTCCCTTTTTCTTCATTATT
1 TTTCCCTTTTTCTTCATTATT
326773 TCATATCATG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.16, C:0.17, G:0.01, T:0.65
Consensus pattern (30 bp):
TTTCCCTTTTTCTTCATTATTATTTTATAA
Found at i:340725 original size:24 final size:22
Alignment explanation
Indices: 340696--340739 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
340686 TCTTAGTACA
340696 AATTATTTTAACATTTCAAATTTT
1 AATTATTTTAA-ATTT-AAATTTT
340720 AATTATTTTAAATTTAAATT
1 AATTATTTTAAATTTAAATT
340740 ATTTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.25
23 4 0.20
24 11 0.55
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (22 bp):
AATTATTTTAAATTTAAATTTT
Found at i:340732 original size:16 final size:16
Alignment explanation
Indices: 340708--340744 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
340698 TTATTTTAAC
* *
340708 ATTTCAAATTTTAATT
1 ATTTTAAATTTAAATT
340724 ATTTTAAATTTAAATT
1 ATTTTAAATTTAAATT
340740 ATTTT
1 ATTTT
340745 TTAAATTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTAAATTTAAATT
Found at i:341066 original size:22 final size:25
Alignment explanation
Indices: 341018--341066 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 25
341008 TCGCTATAAG
*
341018 AATAATATTATATTTTAGATTATAA
1 AATAATATTATATTTTAGATTAAAA
*
341043 AATAA-ATTA-ATTTT-TATTAAAA
1 AATAATATTATATTTTAGATTAAAA
341065 AA
1 AA
341067 AATTTCATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 4 0.18
25 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
AATAATATTATATTTTAGATTAAAA
Found at i:346247 original size:20 final size:19
Alignment explanation
Indices: 346206--346245 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
346196 TTAATATTTT
*
346206 ATTTTAATAAAATATTTAA
1 ATTTTAATAAAACATTTAA
346225 ATTTTATATAAAACATATTAA
1 ATTTTA-ATAAAACAT-TTAA
346246 TTGTATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 8 0.44
21 4 0.22
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTTAATAAAACATTTAA
Found at i:355598 original size:10 final size:9
Alignment explanation
Indices: 355583--355609 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
355573 TTGACACGTG
355583 TTTTTTTAT
1 TTTTTTTAT
355592 TTTTTTTAT
1 TTTTTTTAT
355601 TTTTTTTAT
1 TTTTTTTAT
355610 ATATTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:359753 original size:18 final size:19
Alignment explanation
Indices: 359729--359772 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
359719 TCATTTATAA
* *
359729 AATTTTTAGTTATTTTTAT
1 AATTTTTAGGTAATTTTAT
*
359748 -ATTTTTTGGTAATTTTAT
1 AATTTTTAGGTAATTTTAT
359766 AATTTTT
1 AATTTTT
359773 TCTATTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (19 bp):
AATTTTTAGGTAATTTTAT
Found at i:359817 original size:30 final size:29
Alignment explanation
Indices: 359757--359815 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
359747 TATTTTTTGG
** *
359757 TAATTTTATAATTTTTTCTATTTTAAAAA
1 TAATTTTATAATTTTTTAAAATTTAAAAA
359786 TAATTTTAATAATTTTTGTAAAATTTAAAA
1 TAATTTT-ATAATTTTT-TAAAATTTAAAA
359816 TATTTTTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.28
30 9 0.36
31 9 0.36
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (29 bp):
TAATTTTATAATTTTTTAAAATTTAAAAA
Found at i:375092 original size:184 final size:183
Alignment explanation
Indices: 374775--375121 Score: 516
Period size: 184 Copynumber: 1.9 Consensus size: 183
374765 GAATATTGGT
* *
374775 ATCTAAGGTTCGTGATTGCACATGAAAAATATATATTAGATACCATATGACAATCAAACGGAACT
1 ATCTAAGGTTCGTGATTGCACATGAAAAATATACATTAGATACCATAGGACAATCAAACGGAACT
* * * *
374840 CGAGCCATAACGACCATAAACACAATTTATATGCACTTTTGAATCCCACAACAATCCAGCAGATA
66 AGAGCCATAACGAACATAAACACAATTTATATGCACTTTTGAATCCCACAACAAACCAGCAAATA
* *
374905 CTGCGTAAGTGCATAGTCACAAAGATCTTTAGGAAATATTTCAAGGAACCTGC
131 CTGCATAAGTGCATAGTCACAAACATCTTTAGGAAATATTTCAAGGAACCTGC
* * *
374958 ATCTAAGGTTCTTGATTGCACATGAAAAATATACATTAGATACCATAGGGA-AATGGAATCGGAA
1 ATCTAAGGTTCGTGATTGCACATGAAAAATATACATTAGATACCATA-GGACAAT-CAAACGGAA
* * * *
375022 CTAGAGCCATAACGAACATTAGCACAATTTATATGCACTTTTGTATCCCACAATAAACCAGCAAA
64 CTAGAGCCATAACGAACATAAACACAATTTATATGCACTTTTGAATCCCACAACAAACCAGCAAA
**
375087 TACTGCATAAGTGCATAGTCATTAACATCTTTAGG
129 TACTGCATAAGTGCATAGTCACAAACATCTTTAGG
375122 CCACTTACAC
Statistics
Matches: 145, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
183 48 0.33
184 97 0.67
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.26
Consensus pattern (183 bp):
ATCTAAGGTTCGTGATTGCACATGAAAAATATACATTAGATACCATAGGACAATCAAACGGAACT
AGAGCCATAACGAACATAAACACAATTTATATGCACTTTTGAATCCCACAACAAACCAGCAAATA
CTGCATAAGTGCATAGTCACAAACATCTTTAGGAAATATTTCAAGGAACCTGC
Found at i:377784 original size:22 final size:20
Alignment explanation
Indices: 377758--377798 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
377748 ATTAGGGACA
*
377758 ATATTTGGTAATTCATATTTGG
1 ATATTT-GTAAAT-ATATTTGG
377780 ATATTTGTAAATATATTTG
1 ATATTTGTAAATATATTTG
377799 ATTCATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.32, C:0.02, G:0.15, T:0.51
Consensus pattern (20 bp):
ATATTTGTAAATATATTTGG
Found at i:381031 original size:14 final size:14
Alignment explanation
Indices: 381009--381055 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
380999 GGGTTTAAAG
*
381009 TTCATGGTTCGAGA
1 TTCAGGGTTCGAGA
* *
381023 TTTAGGGTTCAAG-
1 TTCAGGGTTCGAGA
*
381036 TTCATGGTTCGAGA
1 TTCAGGGTTCGAGA
381050 TTCAGG
1 TTCAGG
381056 CTAAAAAATA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.21, C:0.13, G:0.30, T:0.36
Consensus pattern (14 bp):
TTCAGGGTTCGAGA
Found at i:384396 original size:6 final size:6
Alignment explanation
Indices: 384385--384415 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
384375 CTTGCAATGG
*
384385 TGGTGC TGGTGC TGGTGC TGGTGA TGGTGC T
1 TGGTGC TGGTGC TGGTGC TGGTGC TGGTGC T
384416 TCATTAATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.03, C:0.13, G:0.48, T:0.35
Consensus pattern (6 bp):
TGGTGC
Found at i:385221 original size:13 final size:13
Alignment explanation
Indices: 385203--385227 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
385193 TATTAATTAA
385203 AAAAACCATAATT
1 AAAAACCATAATT
385216 AAAAACCATAAT
1 AAAAACCATAAT
385228 AACTTATTTG
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:0.64, C:0.16, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAACCATAATT
Found at i:388141 original size:30 final size:29
Alignment explanation
Indices: 388056--388143 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 29
388046 ATATCAAAAC
* * *
388056 TATACATGAACTATGGTTTGATGTGCAATTG
1 TATACATGAAATTTGATTTGA--TGCAATTG
* * *
388087 TATACATGAACTTTGATTTTATGCAATTT
1 TATACATGAAATTTGATTTGATGCAATTG
388116 TATACATGAAATTTCGATTTGATGCAAT
1 TATACATGAAATTT-GATTTGATGCAAT
388144 CCTTGTAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
29 20 0.40
30 12 0.24
31 18 0.36
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (29 bp):
TATACATGAAATTTGATTTGATGCAATTG
Found at i:388365 original size:29 final size:28
Alignment explanation
Indices: 388324--388390 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 28
388314 GAGTTTCACT
*
388324 TGTATAATTGCACC-AAATTAAAATTTA
1 TGTATAATTGCACCTAAATCAAAATTTA
*
388351 TGTATACAGTTGCACCTTAAATCAAAGTTTA
1 TGTATA-A-TTGCACC-TAAATCAAAATTTA
388382 TGTATAATT
1 TGTATAATT
388391 TTGAGATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 6 0.18
28 1 0.03
29 9 0.26
30 1 0.03
31 17 0.50
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (28 bp):
TGTATAATTGCACCTAAATCAAAATTTA
Found at i:389553 original size:64 final size:64
Alignment explanation
Indices: 389485--389614 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
389475 ATTCAAAACC
389485 CTCAAATATACTTTTTAAACTTAATTAAAAATATTAAAAAATCGATGGCTGTGGAGTTTACGAA
1 CTCAAATATACTTTTTAAACTTAATTAAAAATATTAAAAAATCGATGGCTGTGGAGTTTACGAA
389549 CTCAAATATACTTTTTAAACTTAATTAAAAATATTAAAAAATCGATGGCTGTGGAGTTTACGAA
1 CTCAAATATACTTTTTAAACTTAATTAAAAATATTAAAAAATCGATGGCTGTGGAGTTTACGAA
389613 CT
1 CT
389615 GTAAGCTTAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (64 bp):
CTCAAATATACTTTTTAAACTTAATTAAAAATATTAAAAAATCGATGGCTGTGGAGTTTACGAA
Found at i:395571 original size:2 final size:2
Alignment explanation
Indices: 395564--395590 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
395554 TCAAACACCC
395564 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
395591 CTGTCTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:399830 original size:6 final size:7
Alignment explanation
Indices: 399814--399838 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
399804 CCCTCACCAA
399814 TTTTTCT
1 TTTTTCT
399821 TTTTTCT
1 TTTTTCT
399828 TTTTTCT
1 TTTTTCT
399835 TTTT
1 TTTT
399839 AAATTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:408840 original size:13 final size:13
Alignment explanation
Indices: 408822--408849 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
408812 CATAGAGATC
408822 TTTGTATTAAGAG
1 TTTGTATTAAGAG
408835 TTTGTATTAAGAG
1 TTTGTATTAAGAG
408848 TT
1 TT
408850 GGATTGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (13 bp):
TTTGTATTAAGAG
Found at i:409190 original size:19 final size:20
Alignment explanation
Indices: 409139--409190 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
409129 AAAAATACAA
409139 ATTTTGGAATTTTTAAAAAAT
1 ATTTT-GAATTTTTAAAAAAT
* *
409160 ATTTTGAA-TTTTGAAAATT
1 ATTTTGAATTTTTAAAAAAT
409179 ATTTT-AATTTTT
1 ATTTTGAATTTTT
409191 TTTTGTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 2 0.07
19 18 0.64
20 3 0.11
21 5 0.18
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.56
Consensus pattern (20 bp):
ATTTTGAATTTTTAAAAAAT
Found at i:415349 original size:10 final size:9
Alignment explanation
Indices: 415326--415350 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
415316 CAGTGTGAAG
415326 ATTTTTGCA
1 ATTTTTGCA
415335 ATTTTTGCA
1 ATTTTTGCA
415344 ATTTTTG
1 ATTTTTG
415351 TGCTTTGTAC
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:0.20, C:0.08, G:0.12, T:0.60
Consensus pattern (9 bp):
ATTTTTGCA
Found at i:422634 original size:10 final size:10
Alignment explanation
Indices: 422619--422651 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
422609 AGAAAAAGTC
*
422619 CTCTCTCTCT
1 CTCTCTCTGT
422629 CTCTCTCTGT
1 CTCTCTCTGT
422639 CTCTCTCTGT
1 CTCTCTCTGT
422649 CTC
1 CTC
422652 ACACATCAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.00, C:0.45, G:0.06, T:0.48
Consensus pattern (10 bp):
CTCTCTCTGT
Found at i:427311 original size:36 final size:36
Alignment explanation
Indices: 427264--427338 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
427254 TTCAATCAAT
427264 ATATATAAAGGGAGTTAATAGAGCAGTAATGTGATG
1 ATATATAAAGGGAGTTAATAGAGCAGTAATGTGATG
427300 ATATATAAAGGGAGTTAATAGAGCAGTAATGTGATG
1 ATATATAAAGGGAGTTAATAGAGCAGTAATGTGATG
427336 ATA
1 ATA
427339 AATGATTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.03, G:0.27, T:0.28
Consensus pattern (36 bp):
ATATATAAAGGGAGTTAATAGAGCAGTAATGTGATG
Found at i:431184 original size:25 final size:25
Alignment explanation
Indices: 431154--431203 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
431144 TAAATGGTGG
431154 TCATAAGAACAGCTGCATAAATTTA
1 TCATAAGAACAGCTGCATAAATTTA
431179 TCATAAGAACAGCTGCATAAATTTA
1 TCATAAGAACAGCTGCATAAATTTA
431204 ACTTACTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (25 bp):
TCATAAGAACAGCTGCATAAATTTA
Found at i:433362 original size:26 final size:24
Alignment explanation
Indices: 433327--433383 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 24
433317 TTTTTACTAC
* * *
433327 ATTATTATTTGAAAATATAAAAAA
1 ATTATAATTTAAAAAAATAAAAAA
433351 TATATATAATTTAAAAAAATAAAAAA
1 -AT-TATAATTTAAAAAAATAAAAAA
433377 ATTATAA
1 ATTATAA
433384 AGAACTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 5 0.18
25 4 0.14
26 19 0.68
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
ATTATAATTTAAAAAAATAAAAAA
Found at i:434483 original size:23 final size:23
Alignment explanation
Indices: 434456--434499 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
434446 GACTTAAATT
434456 TTAAAATCTAAAAAATAAAAAAA
1 TTAAAATCTAAAAAATAAAAAAA
* **
434479 TTAAAATTTTGAAAATAAAAA
1 TTAAAATCTAAAAAATAAAAA
434500 TATAGAGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (23 bp):
TTAAAATCTAAAAAATAAAAAAA
Found at i:438997 original size:47 final size:47
Alignment explanation
Indices: 438943--439037 Score: 113
Period size: 47 Copynumber: 2.0 Consensus size: 47
438933 AGGTTTGAAC
* *
438943 TAGGCAAC-GATTCCCGCATTAGGATTTGAA-TTTTTTTTTGTCCAAGT
1 TAGGCAACTG-TTCCCGCATTAGGACTTGAACTATTTTTTT-TCCAAGT
* * *
438990 TAGGCAACTGTTCTCGCTTTAGGGCTTGAACTATTTTTTTTCCAAGT
1 TAGGCAACTGTTCCCGCATTAGGACTTGAACTATTTTTTTTCCAAGT
439037 T
1 T
439038 CTAGGATTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
47 32 0.78
48 9 0.22
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (47 bp):
TAGGCAACTGTTCCCGCATTAGGACTTGAACTATTTTTTTTCCAAGT
Found at i:442662 original size:6 final size:6
Alignment explanation
Indices: 442640--442716 Score: 106
Period size: 6 Copynumber: 13.3 Consensus size: 6
442630 GCGTTCTCTT
* *
442640 TCCTTC TCCTT- T-C-TC TCCTTC TCCTTC TCCTTC TCCTTT TCCTTT
1 TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC
*
442685 TCCTTC TCCTTC TCTTTC TCCTTC TCCTTC TC
1 TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TC
442717 TTTACGCTTA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
3 1 0.02
4 2 0.03
5 2 0.03
6 59 0.92
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (6 bp):
TCCTTC
Found at i:454744 original size:16 final size:16
Alignment explanation
Indices: 454725--454813 Score: 97
Period size: 16 Copynumber: 5.4 Consensus size: 16
454715 GGGCCCCCTT
*
454725 TTTAAATTATTTTAAA
1 TTTAAATTAATTTAAA
* *
454741 TTTATATTTATTTTAAA
1 TTTA-AATTAATTTAAA
*
454758 TTTAAATTAATCTAAA
1 TTTAAATTAATTTAAA
*
454774 TTTAAATTAATTAAAA
1 TTTAAATTAATTTAAA
454790 TTTAAATTTAATTTCAAA
1 TTTAAA-TTAATTT-AAA
*
454808 ATTAAA
1 TTTAAA
454814 AAAGTCCAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
16 33 0.53
17 21 0.34
18 8 0.13
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTAAATTAATTTAAA
Found at i:454762 original size:6 final size:6
Alignment explanation
Indices: 454735--454813 Score: 62
Period size: 6 Copynumber: 14.0 Consensus size: 6
454725 TTTAAATTAT
* * *
454735 TTTAAA TTTATA TTT-AT TTTAAA TTTAAA -TT-AA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
454780 -TT-AA TTAAAA TTTAAA TTT-AA TTTCAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
454814 AAAGTCCAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
4 4 0.07
5 14 0.25
6 35 0.61
7 4 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:454801 original size:33 final size:33
Alignment explanation
Indices: 454725--454797 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
454715 GGGCCCCCTT
* * * * *
454725 TTTAAATTATTTTAAATTTATATTTATTTTAAA
1 TTTAAATTAATCTAAATTTATAATTAATTAAAA
454758 TTTAAATTAATCTAAATTTA-AATTAATTAAAA
1 TTTAAATTAATCTAAATTTATAATTAATTAAAA
454790 TTTAAATT
1 TTTAAATT
454798 TAATTTCAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
32 17 0.49
33 18 0.51
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (33 bp):
TTTAAATTAATCTAAATTTATAATTAATTAAAA
Found at i:454864 original size:25 final size:24
Alignment explanation
Indices: 454836--454915 Score: 56
Period size: 25 Copynumber: 3.2 Consensus size: 24
454826 ATAGCAATGT
454836 CCAATCACAAATGGCCCAAGTCAAC
1 CCAAT-ACAAATGGCCCAAGTCAAC
* *
454861 CCAAATAC--ATGACCCAAATGCCATAC
1 CC-AATACAAATGGCCC-AA-GTCA-AC
**
454887 TAAATTACAAATGGCCCAAGTCAAC
1 CCAA-TACAAATGGCCCAAGTCAAC
454912 CCAA
1 CCAA
454916 ATACCCTAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
23 6 0.15
24 2 0.05
25 13 0.32
26 11 0.28
27 2 0.05
28 6 0.15
ACGTcount: A:0.42, C:0.33, G:0.10, T:0.15
Consensus pattern (24 bp):
CCAATACAAATGGCCCAAGTCAAC
Found at i:456577 original size:30 final size:29
Alignment explanation
Indices: 456534--456946 Score: 285
Period size: 30 Copynumber: 13.9 Consensus size: 29
456524 GAGGTCCCCG
* *
456534 AACTTCCTAAAATCCCATTTTTGACCTCAA
1 AACTTCCAAAAATCCCATTTTT-ACCCCAA
* *
456564 AATTTCCAAAAATCCCATTTCTAACCCCAA
1 AACTTCCAAAAATCCCATTT-TTACCCCAA
* *
456594 AACTTCCAAAAATTCCGTTTTTACCCCTAA
1 AACTTCCAAAAATCCCATTTTTACCCC-AA
* *
456624 AACTTCCAAAAATTCTATTTTTACCCTC-A
1 AACTTCCAAAAATCCCATTTTTACCC-CAA
* * *
456653 AACTTCCCAAAATCTCATTTTTAACCTCAAA
1 AACTTCCAAAAATCCCATTTTT-ACC-CCAA
* * **
456684 AACTTTCAAAAATTCCATTTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTTACCCCAA
* * * *
456713 AACTTCCAGAAATCCCACTTCTAACCTCTAA
1 AACTTCCAAAAATCCCA-TTTTTACC-CCAA
* * * **
456744 AACTTTCAAAGATTCCATTTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTTACCCCAA
* * *
456773 AACTTCCCAAAATCCCATTTTTGACCTCGA
1 AACTTCCAAAAATCCCATTTTT-ACCCCAA
* *
456803 AACTTCCAAAAATTCCATTTTTACCCCCA
1 AACTTCCAAAAATCCCATTTTTACCCCAA
* * **
456832 AATTTCCAAAAATCCCATTTTCACCCCCG
1 AACTTCCAAAAATCCCATTTTTACCCCAA
* ** * * *
456861 AATTTTTAAAAATCCCATTTTCAACCTCGA
1 AACTTCCAAAAATCCCATTTT-TACCCCAA
**
456891 AACTTTTAAAAATACCC--TTTTACCCCCAA
1 AACTTCCAAAAAT-CCCATTTTTA-CCCCAA
* * *
456920 AA-GTCTAAAAATTCCATTTTTAACCCC
1 AACTTCCAAAAATCCCATTTTT-ACCCC
456947 GAATTTTCCC
Statistics
Matches: 301, Mismatches: 67, Indels: 31
0.75 0.17 0.08
Matches are distributed among these distances:
27 2 0.01
28 9 0.03
29 125 0.42
30 126 0.42
31 39 0.13
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (29 bp):
AACTTCCAAAAATCCCATTTTTACCCCAA
Found at i:456631 original size:60 final size:59
Alignment explanation
Indices: 456529--456852 Score: 371
Period size: 60 Copynumber: 5.4 Consensus size: 59
456519 CCGTGGAGGT
* * * * *
456529 CCCCGAACTTCCTAAAATCCCATTTTTGACCTCAAAATTTCCAAAAATCCCATTTCTAAC
1 CCCCAAACTTCCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATTCCATTT-TTAC
* * * * *
456589 CCCAAAACTTCCAAAAATTCCGTTTTT-ACCCCTAAAACTTCCAAAAATTCTATTTTTAC
1 CCCCAAACTTCCAAAAATCCCATTTTTGACCTC-AAAACTTCCAAAAATTCCATTTTTAC
* * * * *
456648 CCTCAAACTTCCCAAAATCTCATTTTTAACCTCAAAAACTTTCAAAAATTCCATTTTTAC
1 CCCCAAACTTCCAAAAATCCCATTTTTGACCTC-AAAACTTCCAAAAATTCCATTTTTAC
* * * * * * *
456708 CCCCGAACTTCCAGAAATCCCACTTCTAACCTCTAAAACTTTCAAAGATTCCATTTTTAC
1 CCCCAAACTTCCAAAAATCCCATTTTTGACCTC-AAAACTTCCAAAAATTCCATTTTTAC
* * *
456768 CCCCGAACTTCCCAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTAC
1 CCCCAAACTTCCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATTCCATTTTTAC
*
456827 CCCCAAATTTCCAAAAATCCCATTTT
1 CCCCAAACTTCCAAAAATCCCATTTT
456853 CACCCCCGAA
Statistics
Matches: 222, Mismatches: 40, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
59 74 0.33
60 148 0.67
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.32
Consensus pattern (59 bp):
CCCCAAACTTCCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATTCCATTTTTAC
Found at i:456971 original size:88 final size:89
Alignment explanation
Indices: 456750--456961 Score: 259
Period size: 88 Copynumber: 2.4 Consensus size: 89
456740 CTAAAACTTT
* * **
456750 CAAAGATTCCATTTTTACCCCCGAA-CTTCCCAAAATCCCATTTTTGACCTCGAAACTTCCAAAA
1 CAAAAATTCCATTTTTACCCCCGAATTTTCCCAAAATCCCATTTTCAACCTCGAAACTTCCAAAA
* * **
456814 ATTCCATTTTTACCCCCAAATTTC
66 ATACCACTTTTACCCCCAAAAGTC
* * ** **
456838 CAAAAATCCCATTTTCACCCCCGAATTTT-TAAAAATCCCATTTTCAACCTCGAAACTTTTAAAA
1 CAAAAATTCCATTTTTACCCCCGAATTTTCCCAAAATCCCATTTTCAACCTCGAAACTTCCAAAA
456902 ATACC-CTTTTACCCCCAAAAGTC
66 ATACCACTTTTACCCCCAAAAGTC
* *
456925 TAAAAATTCCATTTTTAACCCCGAATTTTCCCAAAAT
1 CAAAAATTCCATTTTTACCCCCGAATTTTCCCAAAAT
456962 TACTATTTCA
Statistics
Matches: 102, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
87 40 0.39
88 60 0.59
89 2 0.02
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.32
Consensus pattern (89 bp):
CAAAAATTCCATTTTTACCCCCGAATTTTCCCAAAATCCCATTTTCAACCTCGAAACTTCCAAAA
ATACCACTTTTACCCCCAAAAGTC
Found at i:456977 original size:88 final size:88
Alignment explanation
Indices: 456750--457004 Score: 227
Period size: 87 Copynumber: 2.9 Consensus size: 88
456740 CTAAAACTTT
* * * * *
456750 CAAAGATTCCATTTTTACCCCCGAA-CTTCCCAAAATCCCATTTTTGACCTCGAAACTTCCAAAA
1 CAAAAATTCCATTTTTACCCCCGAATTTTCCCAAAATTCC-TATTTCACCTCGAAACTTCCAAAA
* * **
456814 ATTCCATTTTTACCCCCAAATTTC
65 ATACCACTTTTACCCCCAAAAGTC
* * * * * **
456838 CAAAAATCCCATTTTCACCCCCGAATTTT--TAAAAATCCCATTTTCAACCTCGAAACTTTTAAA
1 CAAAAATTCCATTTTTACCCCCGAATTTTCCCAAAATTCCTA-TTTC-ACCTCGAAACTTCCAAA
456901 AATACC-CTTTTACCCCCAAAAGTC
64 AATACCACTTTTACCCCCAAAAGTC
* * *
456925 TAAAAATTCCATTTTTAACCCCGAATTTTCCCAAAATTACTATTTCACCCTCGAGAA--TCCAAA
1 CAAAAATTCCATTTTTACCCCCGAATTTTCCCAAAATTCCTATTTCA-CCTCGA-AACTTCCAAA
* *
456988 ATTACCA-TTTTGCCCCC
64 AATACCACTTTTACCCCC
457005 GAGTATCCAA
Statistics
Matches: 131, Mismatches: 28, Indels: 17
0.74 0.16 0.10
Matches are distributed among these distances:
87 68 0.52
88 52 0.40
89 11 0.08
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.31
Consensus pattern (88 bp):
CAAAAATTCCATTTTTACCCCCGAATTTTCCCAAAATTCCTATTTCACCTCGAAACTTCCAAAAA
TACCACTTTTACCCCCAAAAGTC
Found at i:456988 original size:28 final size:28
Alignment explanation
Indices: 456955--457016 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
456945 CCGAATTTTC
* *
456955 CCAAAATTACTATTTCACCCTCGAGAAT
1 CCAAAATTACCATTTCACCCCCGAGAAT
** *
456983 CCAAAATTACCATTTTGCCCCCGAGTAT
1 CCAAAATTACCATTTCACCCCCGAGAAT
457011 CCAAAA
1 CCAAAA
457017 GGTCTTATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.31, G:0.08, T:0.26
Consensus pattern (28 bp):
CCAAAATTACCATTTCACCCCCGAGAAT
Found at i:459135 original size:62 final size:62
Alignment explanation
Indices: 459038--459158 Score: 215
Period size: 62 Copynumber: 2.0 Consensus size: 62
459028 AGCATATTTT
459038 CAACCTTGCAAAATGAATTTTATATATAAAAATTGAAGTCTACTATTGAATTCAAAAGAAAA
1 CAACCTTGCAAAATGAATTTTATATATAAAAATTGAAGTCTACTATTGAATTCAAAAGAAAA
* * *
459100 CAACCTTGCAAAATGAATTTTATATATAAGAATTGAGGTCTACTATTGAATTCTAAAGA
1 CAACCTTGCAAAATGAATTTTATATATAAAAATTGAAGTCTACTATTGAATTCAAAAGA
459159 GTTTTCTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.32
Consensus pattern (62 bp):
CAACCTTGCAAAATGAATTTTATATATAAAAATTGAAGTCTACTATTGAATTCAAAAGAAAA
Found at i:461356 original size:32 final size:31
Alignment explanation
Indices: 461318--461398 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 31
461308 GAACCCCAAA
* *
461318 AAGTTTAAGTACCAACTTTA-AAAAAAAGTGTC
1 AAGTTTAAGTACCAA-ATCAGAAAAAAA-TGTC
* *
461350 AAGTTTAGGTATCAAATCAGGAAAAAAATGTC
1 AAGTTTAAGTACCAAATCA-GAAAAAAATGTC
*
461382 AAGTTTGAGTACCAAAT
1 AAGTTTAAGTACCAAAT
461399 TGGACAAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
31 2 0.05
32 31 0.77
33 7 0.17
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATCAGAAAAAAATGTC
Found at i:461436 original size:92 final size:91
Alignment explanation
Indices: 461263--461458 Score: 225
Period size: 92 Copynumber: 2.1 Consensus size: 91
461253 TAAAAAAAGA
* * ***
461263 TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTTAGGTACCAAATTGAACCCCAAAAAGTTTAAGT
1 TTAGGTACCAAATCAGGAAAAAAAGTCAAGTTTAGGTACCAAATTGAACAAAAAAAAGTTTAAGT
* *
461328 ACCAACTTTAAAAAAAAGTGTCAAGT
66 ACCAACATTAAAAAAAAGTGTCAAAT
* *
461354 TTAGGTATCAAATCAGGAAAAAAATGTCAAGTTT-GAGTACCAAATTGGACAAAAAAAAAGTTTA
1 TTAGGTACCAAATCAGGAAAAAAA-GTCAAGTTTAG-GTACCAAATTGAAC-AAAAAAAAGTTTA
* ** *
461418 TGTACCAA-ATTAGGAAAAAGTGTTAAAT
63 AGTACCAACATTAAAAAAAAGTGTCAAAT
*
461446 TCAGGTACCAAAT
1 TTAGGTACCAAAT
461459 GTTATATTAA
Statistics
Matches: 87, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
91 22 0.25
92 48 0.55
93 17 0.20
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (91 bp):
TTAGGTACCAAATCAGGAAAAAAAGTCAAGTTTAGGTACCAAATTGAACAAAAAAAAGTTTAAGT
ACCAACATTAAAAAAAAGTGTCAAAT
Found at i:462674 original size:2 final size:2
Alignment explanation
Indices: 462667--462695 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
462657 ATCGACTAAT
462667 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
462696 GTTAAGTATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:462796 original size:18 final size:19
Alignment explanation
Indices: 462759--462811 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
462749 TAATTATTTC
**
462759 AAATATTATTATTTTTAAT
1 AAATATTATTATTTGAAAT
462778 AAATATTA-TATTTGAAAT
1 AAATATTATTATTTGAAAT
*
462796 AATTAATTGATTATTT
1 AAAT-ATT-ATTATTT
462812 ATATTATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 11 0.39
19 11 0.39
20 1 0.04
21 5 0.18
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (19 bp):
AAATATTATTATTTGAAAT
Found at i:462942 original size:71 final size:71
Alignment explanation
Indices: 462790--462942 Score: 159
Period size: 71 Copynumber: 2.2 Consensus size: 71
462780 ATATTATATT
* * * * *
462790 TGAAATAATTAATTGATTATTTATATTATAATTTATCATACCTACAATGTAAGTGAAATAATAAT
1 TGAAAGAATTAATCGATTATTTATATTAGAATTTATCATACCCACAATGTAAGTGAAAAAATAAT
* * *
462855 GATATT
66 AACATA
* *
462861 TGAAAGAATTAATCGATTTTTTATATTAGAATTTATCGTACCCACAATGTACA-TGAAAAAAATA
1 TGAAAGAATTAATCGATTATTTATATTAGAATTTATCATACCCACAATGTA-AGTG-AAAAAATA
*
462925 TTTAACATA
64 -ATAACATA
462934 T-AAA-AATTA
1 TGAAAGAATTA
462943 TATATAAAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
71 52 0.76
72 11 0.16
73 5 0.07
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (71 bp):
TGAAAGAATTAATCGATTATTTATATTAGAATTTATCATACCCACAATGTAAGTGAAAAAATAAT
AACATA
Found at i:470923 original size:139 final size:139
Alignment explanation
Indices: 470664--470937 Score: 399
Period size: 139 Copynumber: 2.0 Consensus size: 139
470654 GTCCTATAAA
* *
470664 GGAAATGCCTCCTATGACTAAGAAGGGAAAGAAAACTAAATCTGTGAAGAAGGCTCGGAAAGTGA
1 GGAAATGCCTCCTATGACTAAGAAGGGAAAGAAAACTAAATCTGGGAAGAAGGCTCAGAAAGTGA
* * * * *
470729 TAAAGAGTATGTATCCTCTAGTCAAACGCACGAAAAAATTGAAATCTACGTCCTCTTAGCAGAGT
66 TAAAGAATATGTATCCTCTAGTCAAACGAACGAAAAAATTGAAATCCACGCCCTCTTAGCACAGT
470794 CTGCTCAAG
131 CTGCTCAAG
*
470803 GGAAATGCCTCCTATGTA-TAAGATGGTG-AAGAAAACTAAATCTGGGAAGAAGGCTCAGAAAGT
1 GGAAATGCCTCCTATG-ACTAAGAAGG-GAAAGAAAACTAAATCTGGGAAGAAGGCTCAGAAAGT
* * * * *
470866 GATAAAGAATGTGTATTCTCTCGTCAAACGAACGAAGAAATTGAAATCCATGCCCTCTTAGCACA
64 GATAAAGAATATGTATCCTCTAGTCAAACGAACGAAAAAATTGAAATCCACGCCCTCTTAGCACA
470931 GTCTGCT
129 GTCTGCT
470938 TTGTGAGTTT
Statistics
Matches: 120, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
139 118 0.98
140 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (139 bp):
GGAAATGCCTCCTATGACTAAGAAGGGAAAGAAAACTAAATCTGGGAAGAAGGCTCAGAAAGTGA
TAAAGAATATGTATCCTCTAGTCAAACGAACGAAAAAATTGAAATCCACGCCCTCTTAGCACAGT
CTGCTCAAG
Found at i:479492 original size:29 final size:29
Alignment explanation
Indices: 479458--479513 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
479448 ATGGTATCTA
479458 GATCAAATCAGTCTCTT-TATTATTAAATT
1 GATCAAATCAGTCT-TTATATTATTAAATT
* *
479487 GATCAATTTAGTCTTTATATTATTAAA
1 GATCAAATCAGTCTTTATATTATTAAA
479514 AGAAAACAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (29 bp):
GATCAAATCAGTCTTTATATTATTAAATT
Found at i:480987 original size:16 final size:16
Alignment explanation
Indices: 480962--481019 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
480952 TCGAACAGGT
*
480962 AACTCCAAATGACTCA
1 AACTCAAAATGACTCA
* *
480978 TACTCAAAATGATTCA
1 AACTCAAAATGACTCA
*
480994 AACTTAAAAT-AGCTCA
1 AACTCAAAATGA-CTCA
481010 AACTCAAAAT
1 AACTCAAAAT
481020 ATCTCGAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 1 0.03
16 33 0.97
ACGTcount: A:0.48, C:0.22, G:0.05, T:0.24
Consensus pattern (16 bp):
AACTCAAAATGACTCA
Found at i:486576 original size:111 final size:113
Alignment explanation
Indices: 486380--486602 Score: 315
Period size: 111 Copynumber: 2.0 Consensus size: 113
486370 TATTCTGTTA
* * *
486380 AATTAGGGATACATGTGACTGTGGATTCGGGGGAATTTTTTTAATTTCTGCTGGGTTTAAGGTTT
1 AATTAGGGATACAGGTGACTGTCGATTCGGGGGAATTTTTTTAATTTCTGCTAGGTTTAAGGTTT
* * * *
486445 CTAAGTCTCTTTATTTTCAATTCCAGTGGTATAATATTTCTAGGGTTG
66 CTAAGACTCCTTATTTTCAATTCCACTGGTATAATAGTTCTAGGGTTG
* * * * *
486493 AATTAGGGTTACAGGTGACTGTCGATT-TGTGGAA-TTTTTTAATTTCTGTTAGGTTTAGGGTTT
1 AATTAGGGATACAGGTGACTGTCGATTCGGGGGAATTTTTTTAATTTCTGCTAGGTTTAAGGTTT
*
486556 CTAAGACTCCTTGTTTTCAATTCCACTGGTATAATAGTTCTAGGGTT
66 CTAAGACTCCTTATTTTCAATTCCACTGGTATAATAGTTCTAGGGTT
486603 TTCGAGCTGT
Statistics
Matches: 97, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
111 68 0.70
112 5 0.05
113 24 0.25
ACGTcount: A:0.22, C:0.11, G:0.23, T:0.43
Consensus pattern (113 bp):
AATTAGGGATACAGGTGACTGTCGATTCGGGGGAATTTTTTTAATTTCTGCTAGGTTTAAGGTTT
CTAAGACTCCTTATTTTCAATTCCACTGGTATAATAGTTCTAGGGTTG
Found at i:488294 original size:2 final size:2
Alignment explanation
Indices: 488287--488323 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
488277 CGGCGGTGCT
*
488287 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
488324 TGTGTTTAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:490584 original size:25 final size:25
Alignment explanation
Indices: 490555--490609 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
490545 CTTTCTGTAA
* *
490555 AAAAATTTCATTTAT-TTCTATTGTT
1 AAAAATTTAATTTATATT-TACTGTT
490580 AAAAATTTAATTTATATTTACTGTT
1 AAAAATTTAATTTATATTTACTGTT
490605 AAAAA
1 AAAAA
490610 CTGGATTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 25 0.93
26 2 0.07
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (25 bp):
AAAAATTTAATTTATATTTACTGTT
Found at i:491906 original size:26 final size:26
Alignment explanation
Indices: 491871--491920 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
491861 AAAGTATACT
491871 TTTTGAAGCTTTTCTTTATTGCCTCC
1 TTTTGAAGCTTTTCTTTATTGCCTCC
491897 TTTTGAAGCTTTTCTTTATTGCCT
1 TTTTGAAGCTTTTCTTTATTGCCT
491921 TAGAATTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.20, G:0.12, T:0.56
Consensus pattern (26 bp):
TTTTGAAGCTTTTCTTTATTGCCTCC
Found at i:491986 original size:160 final size:162
Alignment explanation
Indices: 491606--492140 Score: 611
Period size: 161 Copynumber: 3.3 Consensus size: 162
491596 AAGCCTTAGA
* * * * * * * *
491606 ATATGTT-TCATCATGTTGTTCTTTGGCTTGCTGCTCTAGT-AATCTTCATATAATATTTTACCT
1 ATATGTTCT-ATCATATTGTT-TATGACTTGCTGGTCTAGTGAA-CCTCATATAATTTTTTATCA
* * * * * * *** * *
491669 TAGCCATGATTGTAAATCATAATTCT-TCGTCGAAGTATACCCAGTGAAGCTTTTTCTTT-GTCA
63 TACCCAGGATTGTTAATCAT-ACTCTGTCATCAAAGTATACCTTTTGAAGCTTTTTCTTTATTGA
491732 TCTCCTTTCAAAGCTTTTCTTTATTGCCTTAGAATTT
127 -CTCCTTTCAAAGCTTTTCTTTATTGCCTTAGAATTT
* * * *
491769 TTATGTT-TTTCATGTTGTTTATGACTTGCTGCTCTAGTGAACCTCATATAATTTTTTATCATAC
1 ATATGTTCTATCATATTGTTTATGACTTGCTGGTCTAGTGAACCTCATATAATTTTTTATCATAC
** * * *
491833 CCTTGATTGTTAATCATACTCCT-TCATTAAAGTATACTTTTTGAAGC-TTTTCTTTATTGCCTC
66 CCAGGATTGTTAATCATACT-CTGTCATCAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACTC
**
491896 CTTTTGAAGCTTTTCTTTATTGCCTTAGAATTT
130 CTTTCAAAGCTTTTCTTTATTGCCTTAGAATTT
* * *
491929 CTATGTTCTATCATATTG-TT-TGACTTGCTGGTCTAGTGTACCTCATGTAATTTTTTTATCATA
1 ATATGTTCTATCATATTGTTTATGACTTGCTGGTCTAGTGAACCTCATATAA-TTTTTTATCATA
*
491992 GCCAGGATTGTTAATCATACTCTGTCATCAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACTC
65 CCCAGGATTGTTAATCATACTCTGTCATCAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACTC
*
492057 CTTTCAAAGCTTTTCTTTATTACCTTAGAATTT
130 CTTTCAAAGCTTTTCTTTATTGCCTTAGAATTT
* *
492090 ATATTTTCTATCATATTGTTTATGACTTGCTGGTCTAGTGAACCACATATA
1 ATATGTTCTATCATATTGTTTATGACTTGCTGGTCTAGTGAACCTCATATA
492141 TATATTTATC
Statistics
Matches: 319, Mismatches: 44, Indels: 18
0.84 0.12 0.05
Matches are distributed among these distances:
159 29 0.09
160 104 0.33
161 139 0.44
162 14 0.04
163 33 0.10
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.47
Consensus pattern (162 bp):
ATATGTTCTATCATATTGTTTATGACTTGCTGGTCTAGTGAACCTCATATAATTTTTTATCATAC
CCAGGATTGTTAATCATACTCTGTCATCAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACTCC
TTTCAAAGCTTTTCTTTATTGCCTTAGAATTT
Found at i:498272 original size:2 final size:2
Alignment explanation
Indices: 498265--498292 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
498255 TTTCTTCCAT
498265 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
498293 ATTGTGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:499204 original size:2 final size:2
Alignment explanation
Indices: 499197--499227 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
499187 GAGTGCTTTG
499197 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
499228 TGTTTTCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:515871 original size:96 final size:96
Alignment explanation
Indices: 515683--515874 Score: 212
Period size: 96 Copynumber: 2.0 Consensus size: 96
515673 ATTTTTTAAA
* ** * *
515683 AAGGATATTCGATTATCTCGGTTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAATATTTCA
* *
515748 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAGAAACATTACCTCGATT
* * * *
515779 AAGGGTATTTGATTATTTCGATTTGAAGAAAAATTACGCCTAGTAAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAATA-TTTC
*
515843 -GAAACTCGAA-ATAAA-AGAATATTACCTCGATT
65 AG-AA-TCGAAGATAAAGA-AACATTACCTCGATT
515875 TTTTAAAACT
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
95 3 0.04
96 72 0.90
97 5 0.06
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAGAAACATTACCTCGATT
Found at i:516201 original size:29 final size:29
Alignment explanation
Indices: 516138--516366 Score: 273
Period size: 29 Copynumber: 7.8 Consensus size: 29
516128 TTTGGAAGTA
516138 AAAAATGGGATTTTTGGAAGTTTC-AGGGT
1 AAAAATGGGATTTTTGGAAG-TTCGAGGGT
*
516167 CAAAAATGGGATTTTTGGAAGTTCGAGTGT
1 -AAAAATGGGATTTTTGGAAGTTCGAGGGT
*
516197 AAAAATGGAATTTTTGGAAGTTTC-AGGGT
1 AAAAATGGGATTTTTGGAAG-TTCGAGGGT
* * *
516226 CAAAAATGAGATTTTTAGAAGTTTCGAGGTT
1 -AAAAATGGGATTTTTGGAAG-TTCGAGGGT
*
516257 AAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAAATGGGATTTTTGGAAGTTCGAGGGT
* **
516286 AAAAATGGAATTTTTGGAAGTTTTAGGGT
1 AAAAATGGGATTTTTGGAAGTTCGAGGGT
* *
516315 TAAAATGGGATTATTGGAAGTTCGAGGGT
1 AAAAATGGGATTTTTGGAAGTTCGAGGGT
* *
516344 AAAAGTGGAATTTTTGGACAGTT
1 AAAAATGGGATTTTTGGA-AGTT
516367 TAGGGACCTT
Statistics
Matches: 170, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
29 96 0.56
30 70 0.41
31 4 0.02
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (29 bp):
AAAAATGGGATTTTTGGAAGTTCGAGGGT
Found at i:516228 original size:59 final size:57
Alignment explanation
Indices: 516138--516366 Score: 266
Period size: 59 Copynumber: 3.9 Consensus size: 57
516128 TTTGGAAGTA
*
516138 AAAAATGGGATTTTTGGAAGTTTC-AGGGTCAAAAATGGGATTTTTGGAAGTTCGAGTGT
1 AAAAATGGGATTTTTGGAAG-TTCGAGGGT-AAAAATGGAATTTTTGGAAGTTCGAG-GT
* *
516197 AAAAATGGAATTTTTGGAAGTTTC-AGGGTCAAAAAT-GAGATTTTTAGAAGTTTCGAGGTT
1 AAAAATGGGATTTTTGGAAG-TTCGAGGGT-AAAAATGGA-ATTTTTGGAAG-TTCGAGG-T
* **
516257 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGT
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTCGA-GGT
* * *
516315 TAAAATGGGATTATTGGAAGTTCGAGGGTAAAAGTGGAATTTTTGGACAGTT
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGA-AGTT
516367 TAGGGACCTT
Statistics
Matches: 151, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
58 48 0.32
59 71 0.47
60 32 0.21
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (57 bp):
AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTCGAGGT
Found at i:516915 original size:13 final size:13
Alignment explanation
Indices: 516899--516923 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
516889 AAAAAAAACC
516899 AAAAAACCTCTCA
1 AAAAAACCTCTCA
516912 AAAAAACCTCTC
1 AAAAAACCTCTC
516924 GTCCCTCCTT
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:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAAACCTCTCA
Found at i:518165 original size:24 final size:23
Alignment explanation
Indices: 518138--518182 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
518128 GTACTTAGAC
518138 ATTTAAAATAAATTTTAAATTTAA
1 ATTTAAAATAAA-TTTAAATTTAA
*
518162 ATTTATAATAAATTTAAATTT
1 ATTTAAAATAAATTTAAATTT
518183 CAACCAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTAAAATAAATTTAAATTTAA
Found at i:518173 original size:17 final size:17
Alignment explanation
Indices: 518153--518235 Score: 87
Period size: 17 Copynumber: 4.9 Consensus size: 17
518143 AAATAAATTT
518153 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
*
518170 TAAATTTAAATTTCA-AC
1 TAAATTTAAATTT-ATAA
* *
518187 CAAATTTAAATTTAGAA
1 TAAATTTAAATTTATAA
* * *
518204 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAA
*
518221 TAAATTTAAGTTTAT
1 TAAATTTAAATTTAT
518236 TGGGCCCAGA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
16 1 0.02
17 52 0.96
18 1 0.02
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:518194 original size:34 final size:34
Alignment explanation
Indices: 518154--518235 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
518144 AATAAATTTT
* * *
518154 AAATTTAAATTTATAATAAATTTAAATTTCAACC
1 AAATTTAAATTTATAATAAACTTAAATTTAAAAC
* * *
518188 AAATTTAAATTTAGAATAAACTTAATTTTAAAAT
1 AAATTTAAATTTATAATAAACTTAAATTTAAAAC
*
518222 AAATTTAAGTTTAT
1 AAATTTAAATTTAT
518236 TGGGCCCAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (34 bp):
AAATTTAAATTTATAATAAACTTAAATTTAAAAC
Found at i:518406 original size:19 final size:19
Alignment explanation
Indices: 518370--518414 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
518360 AAATATATGA
* *
518370 AATAAATTCTTATAAAAAT
1 AATAAATTATAATAAAAAT
518389 AATAAATTATAATTAAAAAT
1 AATAAATTATAA-TAAAAAT
*
518409 AGTAAA
1 AATAAA
518415 AATAGTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AATAAATTATAATAAAAAT
Found at i:528300 original size:20 final size:19
Alignment explanation
Indices: 528254--528302 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
528244 TAAAACACAT
528254 TAAATA-ATAA-ATTTATAC
1 TAAATATATAATA-TTATAC
*
528272 TAAATATATAATATTATCC
1 TAAATATATAATATTATAC
528291 TAATATATATAA
1 TAA-ATATATAA
528303 AAACTTTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 6 0.22
19 12 0.44
20 9 0.33
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATATATAATATTATAC
Found at i:529198 original size:19 final size:17
Alignment explanation
Indices: 529174--529208 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
529164 ATTGTTTGGA
529174 TATTGTATAATTATTGTTT
1 TATTGT-TAATT-TTGTTT
529193 TATTGTTAATTTTGTT
1 TATTGTTAATTTTGTT
529209 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.66
Consensus pattern (17 bp):
TATTGTTAATTTTGTTT
Found at i:529214 original size:18 final size:19
Alignment explanation
Indices: 529174--529214 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
529164 ATTGTTTGGA
*
529174 TATTGTATAATTATTGTTT
1 TATTGTATAATTATTGTTC
529193 TATTGT-TAATT-TTGTTAC
1 TATTGTATAATTATTGTT-C
529211 TATT
1 TATT
529215 TTAGAGACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.63
Consensus pattern (19 bp):
TATTGTATAATTATTGTTC
Found at i:531898 original size:22 final size:22
Alignment explanation
Indices: 531870--531914 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
531860 GATTTAGGAA
*
531870 AGGTTGCTAAGGGGATCTCGTT
1 AGGTTGCTAAGCGGATCTCGTT
531892 AGGTTGCTAAGCGGATCTCGTT
1 AGGTTGCTAAGCGGATCTCGTT
531914 A
1 A
531915 CCTTGGTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.31
Consensus pattern (22 bp):
AGGTTGCTAAGCGGATCTCGTT
Found at i:544864 original size:31 final size:31
Alignment explanation
Indices: 544829--544891 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
544819 ATTTAGTCCT
*
544829 TATATTTT-AATCTGATCAATTTTAGTTCTTG
1 TATATTTTGAAT-TGATCAATTTAAGTTCTTG
**
544860 TATATTTTGAATTTCTCAATTTAAGTTCTTG
1 TATATTTTGAATTGATCAATTTAAGTTCTTG
544891 T
1 T
544892 TTTTTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 25 0.89
32 3 0.11
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.56
Consensus pattern (31 bp):
TATATTTTGAATTGATCAATTTAAGTTCTTG
Found at i:545352 original size:90 final size:89
Alignment explanation
Indices: 545190--545353 Score: 224
Period size: 90 Copynumber: 1.8 Consensus size: 89
545180 AACCCTGTGT
* *
545190 ATTTAATTAATTTATTTTAATTTGAAATTTTTTTCTCACATTAAAAGCTGGAAAATATTTCTTGG
1 ATTTAATTAATTTATTTTAATTTG-AATTTTTTTCTCACATTAAAAGCTGAAAAATATTTCTTAG
**
545255 GTTCCTTTCAGCTTTGGGTTTATGC
65 GACCCTTTCAGCTTTGGGTTTATGC
* *
545280 ATTTAATTAATTTATTTTAGTTTG-ATTTTTTTAC-CACATTAAAAGCTGAAAAAATATCTTTTT
1 ATTTAATTAATTTATTTTAATTTGAATTTTTTT-CTCACATTAAAAGCTG-AAAAATAT-TTCTT
545343 AGGACCCTTTC
63 AGGACCCTTTC
545354 CAATCCTAGG
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
88 22 0.34
89 8 0.12
90 35 0.54
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (89 bp):
ATTTAATTAATTTATTTTAATTTGAATTTTTTTCTCACATTAAAAGCTGAAAAATATTTCTTAGG
ACCCTTTCAGCTTTGGGTTTATGC
Found at i:553380 original size:22 final size:22
Alignment explanation
Indices: 553355--553399 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
553345 AAAATAAAAA
553355 AATATTCATAT-TATTTTTATTT
1 AATATTCATATAT-TTTTTATTT
**
553377 AATATTTTTATATTTTTTATTT
1 AATATTCATATATTTTTTATTT
553399 A
1 A
553400 TTTAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
AATATTCATATATTTTTTATTT
Found at i:556864 original size:30 final size:30
Alignment explanation
Indices: 556823--556905 Score: 78
Period size: 30 Copynumber: 2.7 Consensus size: 30
556813 GAAGGTTAAA
* *
556823 CTTTTTAAAATG-ATCAGATAAGAGCCAAAC
1 CTTTTTGAAATGTA-CAAATAAGAGCCAAAC
* **
556853 CTTTTTGAAATGTACAAATAAGGGTTAAAC
1 CTTTTTGAAATGTACAAATAAGAGCCAAAC
* *
556883 CTTTTTGAAGGTGTTCAAATAAG
1 CTTTTTGAA-ATGTACAAATAAG
556906 TGCTTCTCAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 32 0.73
31 12 0.27
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.33
Consensus pattern (30 bp):
CTTTTTGAAATGTACAAATAAGAGCCAAAC
Found at i:571322 original size:25 final size:23
Alignment explanation
Indices: 571291--571433 Score: 165
Period size: 23 Copynumber: 6.4 Consensus size: 23
571281 AGCACGTCTC
*
571291 GTGCTCTCTGATTAGCACTTTAT
1 GTGCTCTCTGATTAGCACTTTGT
571314 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* *
571337 GTGCTCTCTGTTATGAGCACTGTGT
1 GTGCTCTCTG--ATTAGCACTTTGT
571362 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
*
571385 GTG--CTC-----AGTACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* *
571401 GTACTCTCTGTTTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
571424 GTGCTCTCTG
1 GTGCTCTCTG
571434 TTGCCCAGCA
Statistics
Matches: 102, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
16 11 0.11
18 3 0.03
21 3 0.03
23 64 0.63
25 21 0.21
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTTTGT
Found at i:571371 original size:48 final size:46
Alignment explanation
Indices: 571291--571468 Score: 156
Period size: 48 Copynumber: 3.9 Consensus size: 46
571281 AGCACGTCTC
* *
571291 GTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATGAGCACTGTATGTGCTCTCTGATTAGCACTTTGT
*
571337 GTGCTCTCTGTTATGAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTG--ATGAGCACTGTATGTGCTCTCTGATTAGCACTTTGT
* * * * *
571385 GTG--CTC-----AGTACTTTGTGTACTCTCTGTTTAGCACTTTGT
1 GTGCTCTCTGATGAGCACTGTATGTGCTCTCTGATTAGCACTTTGT
* * *
571424 GTGCTCTCTGTTGCCCAGCACT-TATGTGCTCTCTGTTTAGTACTT
1 GTGCTCTCTGATG---AGCACTGTATGTGCTCTCTGATTAGCACTT
571469 CGGTACTCTC
Statistics
Matches: 109, Mismatches: 11, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
39 32 0.29
41 3 0.03
46 13 0.12
48 56 0.51
49 5 0.05
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (46 bp):
GTGCTCTCTGATGAGCACTGTATGTGCTCTCTGATTAGCACTTTGT
Found at i:571424 original size:23 final size:23
Alignment explanation
Indices: 571394--571483 Score: 87
Period size: 23 Copynumber: 3.9 Consensus size: 23
571384 TGTGCTCAGT
571394 ACTTTGTGTACTCTCTGTTTAGC
1 ACTTTGTGTACTCTCTGTTTAGC
* *
571417 ACTTTGTGTGCTCTCTGTTGCCCAGC
1 ACTTTGTGTACTCTCTGTT---TAGC
*
571443 ACTTATGTG--CTCTCTGTTTAGT
1 ACTT-TGTGTACTCTCTGTTTAGC
*
571465 ACTTCG-GTACTCTCTGTTT
1 ACTTTGTGTACTCTCTGTTT
571484 GTTTCGTTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.29
23 18 0.32
25 9 0.16
26 7 0.12
27 4 0.07
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (23 bp):
ACTTTGTGTACTCTCTGTTTAGC
Found at i:571453 original size:87 final size:87
Alignment explanation
Indices: 571307--571468 Score: 227
Period size: 87 Copynumber: 1.9 Consensus size: 87
571297 TCTGATTAGC
* ** *
571307 ACTTTATGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGTTATGAGCACTGTGTGTGCTCTCTG
1 ACTTTATGTACTCTCTGATTAGCACTTTGTGTGCTCTCTGTTACCAGCACTGTATGTGCTCTCTG
571372 ATTAGCACTTTGTGTGCTCAGT
66 ATTAGCACTTTGTGTGCTCAGT
* * *
571394 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCCAGCACT-TATGTGCTCTCT
1 ACTTTATGTACTCTCTGATTAGCACTTTGTGTGCTCTCTGTT-ACCAGCACTGTATGTGCTCTCT
* *
571458 GTTTAGTACTT
65 GATTAGCACTT
571469 CGGTACTCTC
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
87 59 0.91
88 6 0.09
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (87 bp):
ACTTTATGTACTCTCTGATTAGCACTTTGTGTGCTCTCTGTTACCAGCACTGTATGTGCTCTCTG
ATTAGCACTTTGTGTGCTCAGT
Found at i:585545 original size:32 final size:31
Alignment explanation
Indices: 585504--585571 Score: 127
Period size: 32 Copynumber: 2.2 Consensus size: 31
585494 ATGGCATGTG
585504 ATTGTGTATCTTCAGGATTACATCTAACTGT
1 ATTGTGTATCTTCAGGATTACATCTAACTGT
585535 AATTGTGTATCTTCAGGATTACATCTAACTGT
1 -ATTGTGTATCTTCAGGATTACATCTAACTGT
585567 ATTGT
1 ATTGT
585572 TCTCATCTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 5 0.14
32 31 0.86
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (31 bp):
ATTGTGTATCTTCAGGATTACATCTAACTGT
Found at i:587582 original size:189 final size:189
Alignment explanation
Indices: 587262--587643 Score: 764
Period size: 189 Copynumber: 2.0 Consensus size: 189
587252 TTTGCTGTGG
587262 AAAATTAATTACTTTTTCAGTTTTAATTTCTCACACTTTATGGGCTGAGATAATTCATACACAAG
1 AAAATTAATTACTTTTTCAGTTTTAATTTCTCACACTTTATGGGCTGAGATAATTCATACACAAG
587327 ATGCCCTTGTATATGTATATAGCCTTAGATATGATTAATTTTGTAACTTAGGTTTTTATACCATC
66 ATGCCCTTGTATATGTATATAGCCTTAGATATGATTAATTTTGTAACTTAGGTTTTTATACCATC
587392 AAATTGGAGCTAAAAATTGTTTATTTTTCCAATGTGTATATATTATATATGTGTATTTA
131 AAATTGGAGCTAAAAATTGTTTATTTTTCCAATGTGTATATATTATATATGTGTATTTA
587451 AAAATTAATTACTTTTTCAGTTTTAATTTCTCACACTTTATGGGCTGAGATAATTCATACACAAG
1 AAAATTAATTACTTTTTCAGTTTTAATTTCTCACACTTTATGGGCTGAGATAATTCATACACAAG
587516 ATGCCCTTGTATATGTATATAGCCTTAGATATGATTAATTTTGTAACTTAGGTTTTTATACCATC
66 ATGCCCTTGTATATGTATATAGCCTTAGATATGATTAATTTTGTAACTTAGGTTTTTATACCATC
587581 AAATTGGAGCTAAAAATTGTTTATTTTTCCAATGTGTATATATTATATATGTGTATTTA
131 AAATTGGAGCTAAAAATTGTTTATTTTTCCAATGTGTATATATTATATATGTGTATTTA
587640 AAAA
1 AAAA
587644 AAAATTGTCA
Statistics
Matches: 193, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
189 193 1.00
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (189 bp):
AAAATTAATTACTTTTTCAGTTTTAATTTCTCACACTTTATGGGCTGAGATAATTCATACACAAG
ATGCCCTTGTATATGTATATAGCCTTAGATATGATTAATTTTGTAACTTAGGTTTTTATACCATC
AAATTGGAGCTAAAAATTGTTTATTTTTCCAATGTGTATATATTATATATGTGTATTTA
Found at i:588158 original size:89 final size:90
Alignment explanation
Indices: 588002--588175 Score: 235
Period size: 89 Copynumber: 1.9 Consensus size: 90
587992 AAATCTAACT
* * * *
588002 TTATAACCATCTTTGAATGCTTGCAGACAGATTATACAAGCTTTGAAATAGCTTAGCATCTAGGG
1 TTATAACCATCTTTGAATGCTTACACACAGATTATACAAGCTTTGAAATAGCCTAGCATCTAAGG
*
588067 AGCATATTGG-TGTGGTGCTAGAGCC
66 AGCATA-TGGCTATGGTGCTAGAGCC
* ** * *
588092 TTATAATCATCTTTGTGTGCTTACACATAGA-TATACAATCTTTGAAATAGCCTAGCATCTAAGG
1 TTATAACCATCTTTGAATGCTTACACACAGATTATACAAGCTTTGAAATAGCCTAGCATCTAAGG
588156 AGCATATGGCTATGGTGCTA
66 AGCATATGGCTATGGTGCTA
588176 AGGTTAGTAG
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
88 3 0.04
89 45 0.62
90 25 0.34
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (90 bp):
TTATAACCATCTTTGAATGCTTACACACAGATTATACAAGCTTTGAAATAGCCTAGCATCTAAGG
AGCATATGGCTATGGTGCTAGAGCC
Found at i:590859 original size:18 final size:18
Alignment explanation
Indices: 590832--590867 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
590822 ACACAAATAG
*
590832 TATTATATGTAATACTAT
1 TATTACATGTAATACTAT
590850 TATTACATGTAATACTAT
1 TATTACATGTAATACTAT
590868 GAGACAAATA
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:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (18 bp):
TATTACATGTAATACTAT
Found at i:596248 original size:70 final size:67
Alignment explanation
Indices: 596122--596254 Score: 167
Period size: 70 Copynumber: 1.9 Consensus size: 67
596112 ATAAACAATA
* * *
596122 TAATAATTTTGCCTTTTAACTTAATGGGTAAACATTTATCAAAATGACATAATTTTACCTTTTAA
1 TAATAATTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTTTAA
596187 AT
66 AT
* * ** *
596189 TAATGATTTTGACTTTTAACTTTAGAAAGGGTAAGCATTTATCAAAACGATGTAGTTTTACCTTT
1 TAATAATTTTGACTTTTAAC-TT--AAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTT
596254 T
63 T
596255 CTTATTCGGA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
67 18 0.33
68 2 0.04
70 35 0.64
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (67 bp):
TAATAATTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTTTAA
AT
Found at i:600717 original size:23 final size:21
Alignment explanation
Indices: 600691--600736 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
600681 AATAACTTGA
600691 TTAACTCAAATAATTTGAACTAT
1 TTAACTCAAAT--TTTGAACTAT
* *
600714 TTAATTCAAATTTTGAATTAT
1 TTAACTCAAATTTTGAACTAT
600735 TT
1 TT
600737 TTCGAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
23 10 0.48
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (21 bp):
TTAACTCAAATTTTGAACTAT
Found at i:600757 original size:5 final size:5
Alignment explanation
Indices: 600747--600777 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
600737 TTCGAGTTTT
600747 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA T
600778 TTTGCTCACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:601622 original size:2 final size:2
Alignment explanation
Indices: 601615--601640 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
601605 TTATTAGGAA
601615 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
601641 GTGTATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:607464 original size:13 final size:13
Alignment explanation
Indices: 607443--607495 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
607433 AAAATTATTG
*
607443 ATTTGATTTAATA
1 ATTTAATTTAATA
607456 ATTTAATTTAATA
1 ATTTAATTTAATA
* *
607469 ATTATATTTTTATA
1 ATT-TAATTTAATA
* *
607483 ATGTAATTAAATA
1 ATTTAATTTAATA
607496 TGATTAAGAC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
13 22 0.69
14 10 0.31
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (13 bp):
ATTTAATTTAATA
Found at i:615166 original size:39 final size:40
Alignment explanation
Indices: 615100--615176 Score: 120
Period size: 39 Copynumber: 1.9 Consensus size: 40
615090 AAACTCAATG
*
615100 GACATCTTTTGAAGAGTCACAACCC-TTTCATATTGGATA
1 GACACCTTTTGAAGAGTCACAACCCTTTTCATATTGGATA
* *
615139 GACACCTTTTGAAGAGTTACAATCCTTTTCATATTGGA
1 GACACCTTTTGAAGAGTCACAACCCTTTTCATATTGGA
615177 CATACCTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 22 0.65
40 12 0.35
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (40 bp):
GACACCTTTTGAAGAGTCACAACCCTTTTCATATTGGATA
Found at i:615193 original size:39 final size:37
Alignment explanation
Indices: 615098--615189 Score: 107
Period size: 39 Copynumber: 2.5 Consensus size: 37
615088 ATAAACTCAA
615098 TGGACAT--CTTTTGAAGAGTCACAACCCTTTCATAT
1 TGGACATACCTTTTGAAGAGTCACAACCCTTTCATAT
* * * *
615133 TGGATAGACACCTTTTGAAGAGTTACAATCCTTTTCATAT
1 TGG--ACATACCTTTTGAAGAGTCACAA-CCCTTTCATAT
615173 TGGACATACCTTTTGAA
1 TGGACATACCTTTTGAA
615190 AGAGACTTGT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
35 3 0.07
37 2 0.04
38 12 0.26
39 16 0.35
40 13 0.28
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (37 bp):
TGGACATACCTTTTGAAGAGTCACAACCCTTTCATAT
Found at i:620105 original size:39 final size:40
Alignment explanation
Indices: 620047--620122 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 40
620037 CACTCAATGG
620047 ACACCTTTTGAAGAGTCACAAC-CCTTTCATATTGGATGA
1 ACACCTTTTGAAGAGTCACAACTCCTTTCATATTGGATGA
* * *
620086 ACACCTTTTGAAGATTCACAACTCTTTTTATATTGGA
1 ACACCTTTTGAAGAGTCACAACTCCTTTCATATTGGA
620123 CATACCTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 21 0.64
40 12 0.36
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (40 bp):
ACACCTTTTGAAGAGTCACAACTCCTTTCATATTGGATGA
Found at i:622432 original size:12 final size:12
Alignment explanation
Indices: 622415--622439 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
622405 GGGAAGGGGC
622415 GAGAGGATTTTG
1 GAGAGGATTTTG
622427 GAGAGGATTTTG
1 GAGAGGATTTTG
622439 G
1 G
622440 GTTTTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (12 bp):
GAGAGGATTTTG
Found at i:623073 original size:59 final size:60
Alignment explanation
Indices: 622970--623156 Score: 254
Period size: 60 Copynumber: 3.1 Consensus size: 60
622960 CCTCGAAGGT
* * *
622970 CCCCAAACTATCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTCGA-
1 CCCCAAACTTTCCAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTCGAC
* * *
623029 CCTCAAACTTTCCAAAAATTACCATTTTACCC-CAAAACTCCCAAAAATCCCATTTTTGAC
1 CCCCAAACTTTCCAAAAATTACCATTTTACCCTC-GAACTCCCAAAAATCCCATTTTCGAC
* *
623089 CCCCAATCCTTCCAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCCA-TTTCGAC
1 CCCCAAACTTTCCAAAAATTACCATTTTACCCTCGAACTCCCAAAAAT-CCCATTTTCGAC
*
623149 CCCGAAAC
1 CCCCAAAC
623157 ACCTTAAAAT
Statistics
Matches: 111, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
58 1 0.01
59 51 0.46
60 54 0.49
61 5 0.05
ACGTcount: A:0.35, C:0.36, G:0.03, T:0.26
Consensus pattern (60 bp):
CCCCAAACTTTCCAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTCGAC
Found at i:623119 original size:60 final size:59
Alignment explanation
Indices: 622970--623156 Score: 245
Period size: 59 Copynumber: 3.1 Consensus size: 59
622960 CCTCGAAGGT
* *
622970 CCCCAAA-CTATCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTCGA
1 CCCCAAACCT-TCCAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTCGA
* * * *
623029 CCTCAAACTTTCCAAAAATTACCATTTTACCC-CAAAACTCCCAAAAATCCCATTTTTGA
1 CCCCAAACCTTCCAAAAATTACCATTTTACCCTC-GAACTCCCAAAAATCCCATTTTCGA
*
623088 CCCCCAATCCTTCCAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCCA-TTTCGA
1 -CCCCAAACCTTCCAAAAATTACCATTTTACCCTCGAACTCCCAAAAAT-CCCATTTTCGA
623148 CCCCGAAAC
1 CCCC-AAAC
623157 ACCTTAAAAT
Statistics
Matches: 110, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
58 1 0.01
59 53 0.48
60 51 0.46
61 5 0.05
ACGTcount: A:0.35, C:0.36, G:0.03, T:0.26
Consensus pattern (59 bp):
CCCCAAACCTTCCAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTCGA
Found at i:623144 original size:29 final size:29
Alignment explanation
Indices: 622973--623136 Score: 149
Period size: 29 Copynumber: 5.5 Consensus size: 29
622963 CGAAGGTCCC
622973 CAAACTATCCAAAAATTACCATTTTACCCT
1 CAAACT-TCCAAAAATTACCATTTTACCCT
*
623003 CGAACTTCCAAAAA-T-CTCATTTT-CGACCT
1 CAAACTTCCAAAAATTAC-CATTTTAC--CCT
623032 CAAACTTTCCAAAAATTACCATTTTACCC-
1 CAAAC-TTCCAAAAATTACCATTTTACCCT
* * *
623061 CAAAACTCCCAAAAA-TCCCATTTTTGACCCC
1 C-AAACTTCCAAAAATTACCA-TTTT-ACCCT
*
623092 CAATCCTTCCAAAAATTACCATTTTACCCT
1 CAA-ACTTCCAAAAATTACCATTTTACCCT
* *
623122 CGAACTCCCAAAAAT
1 CAAACTTCCAAAAAT
623137 CCCCATTTCG
Statistics
Matches: 110, Mismatches: 11, Indels: 27
0.74 0.07 0.18
Matches are distributed among these distances:
27 2 0.02
28 11 0.10
29 38 0.35
30 32 0.29
31 21 0.19
32 6 0.05
ACGTcount: A:0.37, C:0.33, G:0.02, T:0.28
Consensus pattern (29 bp):
CAAACTTCCAAAAATTACCATTTTACCCT
Found at i:638289 original size:19 final size:20
Alignment explanation
Indices: 638251--638290 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
638241 TTTAAACTCA
638251 TTTTAAATTAGTTTATATTT
1 TTTTAAATTAGTTTATATTT
* *
638271 TTTTGAATTATTTTA-ATTT
1 TTTTAAATTAGTTTATATTT
638290 T
1 T
638291 AATTTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTAAATTAGTTTATATTT
Found at i:638355 original size:24 final size:25
Alignment explanation
Indices: 638328--638382 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 25
638318 TTATTAAAAA
638328 TTTTATATATGTGTA-A-TTTAATAT
1 TTTTATAT-TGTGTATATTTTAATAT
*
638352 TTTT-TATTGTTTATATTTTAATAT
1 TTTTATATTGTGTATATTTTAATAT
638376 TATTTAT
1 T-TTTAT
638383 TACTATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 5 0.19
23 4 0.15
24 13 0.50
25 3 0.12
26 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.65
Consensus pattern (25 bp):
TTTTATATTGTGTATATTTTAATAT
Found at i:638395 original size:24 final size:24
Alignment explanation
Indices: 638341--638397 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
638331 TATATATGTG
* * *
638341 TAATTTAATATTTTTTATTGTTTA
1 TAATTTAATATTATTTATTCTATA
*
638365 TATTTTAATATTATTTATTACTATA
1 TAATTTAATATTATTTATT-CTATA
638390 -AATTTAAT
1 TAATTTAAT
638398 TTTTATGTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 24 0.89
25 3 0.11
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
TAATTTAATATTATTTATTCTATA
Found at i:649402 original size:6 final size:6
Alignment explanation
Indices: 649391--649429 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
649381 GAAAATATGA
* *
649391 CTGTTG CTGTTG CTGTTG CTGTTG CTGCTG CTGCTG CTG
1 CTGTTG CTGTTG CTGTTG CTGTTG CTGTTG CTGTTG CTG
649430 CCTCCTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.23, G:0.33, T:0.44
Consensus pattern (6 bp):
CTGTTG
Found at i:655796 original size:2 final size:2
Alignment explanation
Indices: 655789--655816 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
655779 ACTTGAAATT
655789 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
655817 CATAAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:660465 original size:9 final size:9
Alignment explanation
Indices: 660451--660476 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
660441 ACTCAACAGT
660451 AAAAAGTTA
1 AAAAAGTTA
660460 AAAAAGTTA
1 AAAAAGTTA
660469 AAAAAGTT
1 AAAAAGTT
660477 TTTTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (9 bp):
AAAAAGTTA
Found at i:665295 original size:21 final size:21
Alignment explanation
Indices: 665257--665297 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
665247 GCATCAATAA
665257 TTTTATGTATTTTCTTATATG
1 TTTTATGTATTTTCTTATATG
*
665278 TTTT-TGTATTGTTGTTATAT
1 TTTTATGTATT-TTCTTATAT
665298 TTATGTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.17, C:0.02, G:0.12, T:0.68
Consensus pattern (21 bp):
TTTTATGTATTTTCTTATATG
Found at i:671612 original size:25 final size:27
Alignment explanation
Indices: 671583--671635 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 27
671573 TCATTCATCT
671583 AAAACTATCCAAAAT-A-AATATTAAA
1 AAAACTATCCAAAATAATAATATTAAA
*
671608 AAAACTATCCAAAGTAATAATATTAAA
1 AAAACTATCCAAAATAATAATATTAAA
671635 A
1 A
671636 TAAATAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 14 0.56
26 1 0.04
27 10 0.40
ACGTcount: A:0.62, C:0.11, G:0.02, T:0.25
Consensus pattern (27 bp):
AAAACTATCCAAAATAATAATATTAAA
Found at i:680013 original size:23 final size:21
Alignment explanation
Indices: 679969--680014 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
679959 ATTTTGTGCA
*
679969 TTAAATTTAAACATTGAATTT
1 TTAAATTTAAACATTCAATTT
*
679990 TTAAATTGTGAAACATTCATTTT
1 TTAAATT-T-AAACATTCAATTT
680013 TT
1 TT
680015 TTGGTAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 1 0.05
23 13 0.62
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (21 bp):
TTAAATTTAAACATTCAATTT
Found at i:681702 original size:30 final size:28
Alignment explanation
Indices: 681636--681704 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
681626 TTCGAATATC
* *
681636 TAAAATTTAATTCCTGTACTTTTAATTT
1 TAAAATTTAGTTCCTATACTTTTAATTT
681664 TAAGAATTTAGTTCCTATA-TTTTATATATT
1 TAA-AATTTAGTTCCTATACTTTTA-AT-TT
681694 TCAAAATTTAG
1 T-AAAATTTAG
681705 GTTTAACTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 8 0.23
29 15 0.43
30 10 0.29
31 2 0.06
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.51
Consensus pattern (28 bp):
TAAAATTTAGTTCCTATACTTTTAATTT
Found at i:699199 original size:102 final size:102
Alignment explanation
Indices: 699019--699226 Score: 400
Period size: 102 Copynumber: 2.0 Consensus size: 102
699009 TGTATTCCAT
*
699019 ATGC-AAATCTGCTTGTTGTAGTGTGATTCCTTTTGAAAGAGAATAGAGTAACCGACTTTAATTT
1 ATGCTAAATCTGCTTGCTGTAGTGTGATTCCTTTTGAAAGAGAATAGAGTAACCGACTTTAATTT
699083 GATCCGTTTCTTTCTATAATGTCATTAGTTATTCTGA
66 GATCCGTTTCTTTCTATAATGTCATTAGTTATTCTGA
699120 ATGCTAAATCTGCTTGCTGTAGTGTGATTCCTTTTGAAAGAGAATAGAGTAACCGACTTTAATTT
1 ATGCTAAATCTGCTTGCTGTAGTGTGATTCCTTTTGAAAGAGAATAGAGTAACCGACTTTAATTT
699185 GATCCGTTTCTTTCTATAATGTCATTAGTTATTCTGA
66 GATCCGTTTCTTTCTATAATGTCATTAGTTATTCTGA
699222 ATGCT
1 ATGCT
699227 GACGTACGTT
Statistics
Matches: 105, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
101 4 0.04
102 101 0.96
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.41
Consensus pattern (102 bp):
ATGCTAAATCTGCTTGCTGTAGTGTGATTCCTTTTGAAAGAGAATAGAGTAACCGACTTTAATTT
GATCCGTTTCTTTCTATAATGTCATTAGTTATTCTGA
Found at i:737675 original size:18 final size:18
Alignment explanation
Indices: 737635--737677 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
737625 ATTACTTTTA
*
737635 AATTTATTACTTGAATTT
1 AATTTATTACTTGAAATT
* * *
737653 CATTTATTCCTTTAAATT
1 AATTTATTACTTGAAATT
737671 AATTTAT
1 AATTTAT
737678 CATTTAATTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (18 bp):
AATTTATTACTTGAAATT
Found at i:739513 original size:29 final size:28
Alignment explanation
Indices: 739465--739533 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
739455 AAAAATGTAC
* * *
739465 TTTTTAATATTTTAATATTTAATATTATAG
1 TTTTTTATTTTTTAATATTTAA-ATT-TAA
739495 TTTTTTATTTTTTAA-ATTTAAATTTAA
1 TTTTTTATTTTTTAATATTTAAATTTAA
739522 TGTTTTTATTTT
1 T-TTTTTATTTT
739534 AATTGCCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 3 0.09
28 13 0.37
29 6 0.17
30 13 0.37
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (28 bp):
TTTTTTATTTTTTAATATTTAAATTTAA
Done.