Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014966.1 Kokia drynarioides strain JFW-HI SEQ_130010, 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: 330293
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 105 characters in sequence are not A, C, G, or T
Found at i:2275 original size:6 final size:6
Alignment explanation
Indices: 2264--2288 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2254 TTCTTGTCAT
2264 TGCTAG TGCTAG TGCTAG TGCTAG T
1 TGCTAG TGCTAG TGCTAG TGCTAG T
2289 TTTGCAAGCG
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:0.16, C:0.16, G:0.32, T:0.36
Consensus pattern (6 bp):
TGCTAG
Found at i:2823 original size:58 final size:62
Alignment explanation
Indices: 2686--2847 Score: 192
Period size: 62 Copynumber: 2.7 Consensus size: 62
2676 GTCAATTTTT
* * * * *
2686 AAAGACAAAATTATATTATTATATTTGA-AACGTAAATTGATCGGTCGATTAGTCGATCTATA
1 AAAGACAAAATGATATTATCATATTT-ATAAAGTAAATTGATCGATCGATTACTCGATCTATA
* *
2748 AAAGACAAAATGGTATTATCATATTTATAAAGTAAATTGATCGATC-A-T-CT-GATCTTTA
1 AAAGACAAAATGATATTATCATATTTATAAAGTAAATTGATCGATCGATTACTCGATCTATA
* *
2806 AAAGACAAAATGATATTATCGTA-TTGTAAAGTAAATTGATCG
1 AAAGACAAAATGATATTATCATATTTATAAAGTAAATTGATCG
2848 GTCTTTTAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
57 18 0.20
58 28 0.31
59 1 0.01
60 1 0.01
61 2 0.02
62 39 0.44
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (62 bp):
AAAGACAAAATGATATTATCATATTTATAAAGTAAATTGATCGATCGATTACTCGATCTATA
Found at i:28043 original size:7 final size:7
Alignment explanation
Indices: 28031--28057 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
28021 TATAAATCTA
28031 ATTTATG
1 ATTTATG
28038 ATTTATG
1 ATTTATG
28045 ATTTATG
1 ATTTATG
28052 ATTTAT
1 ATTTAT
28058 ACGGTAAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (7 bp):
ATTTATG
Found at i:30451 original size:17 final size:17
Alignment explanation
Indices: 30406--30464 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
30396 CTAAAAATAA
*
30406 AAAAAATA-ATTTTATT
1 AAAAAATATATTTTAAT
* *
30422 AAAAGACT-TTTTTTAA-
1 AAAA-AATATATTTTAAT
*
30438 AATAAATATATTTTAAT
1 AAAAAATATATTTTAAT
30455 AAAAAATATA
1 AAAAAATATA
30465 AAGTTAATCT
Statistics
Matches: 32, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
15 2 0.06
16 14 0.44
17 16 0.50
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
AAAAAATATATTTTAAT
Found at i:37239 original size:44 final size:44
Alignment explanation
Indices: 37191--37282 Score: 184
Period size: 44 Copynumber: 2.1 Consensus size: 44
37181 ATAAAAGAAA
37191 AAAATATATAATGCAGTAATATATATAATTTTTAAATGTTAATT
1 AAAATATATAATGCAGTAATATATATAATTTTTAAATGTTAATT
37235 AAAATATATAATGCAGTAATATATATAATTTTTAAATGTTAATT
1 AAAATATATAATGCAGTAATATATATAATTTTTAAATGTTAATT
37279 AAAA
1 AAAA
37283 AACAAATATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (44 bp):
AAAATATATAATGCAGTAATATATATAATTTTTAAATGTTAATT
Found at i:37542 original size:20 final size:20
Alignment explanation
Indices: 37514--37580 Score: 52
Period size: 20 Copynumber: 3.4 Consensus size: 20
37504 TCACATCATC
*
37514 AAATGATTTTAAAATTTTTA
1 AAATTATTTTAAAATTTTTA
*
37534 AAATTATTTTTTAAAA--TATA
1 AAATTA--TTTTAAAATTTTTA
37554 AAATTA--TTAAAATTATTTTA
1 AAATTATTTTAAAA-T-TTTTA
37574 AAATTAT
1 AAATTAT
37581 AACCATCATC
Statistics
Matches: 37, Mismatches: 3, Indels: 13
0.70 0.06 0.25
Matches are distributed among these distances:
16 6 0.16
20 23 0.62
22 8 0.22
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (20 bp):
AAATTATTTTAAAATTTTTA
Found at i:51133 original size:49 final size:49
Alignment explanation
Indices: 51080--51179 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
51070 TAAACTATGG
51080 AGTATCCAGTAAAACTTGATTAGTCTACTTGCTTCGGATAAAAAACTCT
1 AGTATCCAGTAAAACTTGATTAGTCTACTTGCTTCGGATAAAAAACTCT
51129 AGTATCCAGTAAAACTTGATTAGTCTACTTGCTTCGGATAAAAAACTCT
1 AGTATCCAGTAAAACTTGATTAGTCTACTTGCTTCGGATAAAAAACTCT
51178 AG
1 AG
51180 GAAGTTTACA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (49 bp):
AGTATCCAGTAAAACTTGATTAGTCTACTTGCTTCGGATAAAAAACTCT
Found at i:62824 original size:6 final size:6
Alignment explanation
Indices: 62813--62838 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
62803 AATTAATTAG
62813 AATGAA AATGAA AATGAA AATGAA AA
1 AATGAA AATGAA AATGAA AATGAA AA
62839 GAATTATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AATGAA
Found at i:66823 original size:23 final size:21
Alignment explanation
Indices: 66792--66836 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
66782 AATAACTTGA
66792 TTAACTCAAATAACTTGAATTAT
1 TTAACTC-AA-AACTTGAATTAT
* *
66815 TTAATTCAAAATTTGAATTAT
1 TTAACTCAAAACTTGAATTAT
66836 T
1 T
66837 CTTCGAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 2 0.10
23 6 0.30
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.44
Consensus pattern (21 bp):
TTAACTCAAAACTTGAATTAT
Found at i:81398 original size:124 final size:124
Alignment explanation
Indices: 81178--81426 Score: 480
Period size: 124 Copynumber: 2.0 Consensus size: 124
81168 GCCCCTTAGA
*
81178 ACCTGGATGATTTTAAAATCCAAACCACAATCATACCAGAAGCACCTCTAAACTATATGTACGAA
1 ACCTGGATGATTTTAAAATCCAAACCACAATCATACCAGAAGCACCTCTAAACTATATATACGAA
*
81243 AGAAATGAGCATATACATGTATCCAACACTCCTACTATTCTGAGTAGCAGTAAGACTAT
66 AGAAATGAGCACATACATGTATCCAACACTCCTACTATTCTGAGTAGCAGTAAGACTAT
81302 ACCTGGATGATTTTAAAATCCAAACCACAATCATACCAGAAGCACCTCTAAACTATATATACGAA
1 ACCTGGATGATTTTAAAATCCAAACCACAATCATACCAGAAGCACCTCTAAACTATATATACGAA
81367 AGAAATGAGCACATACATGTATCCAACACTCCTACTATTCTGAGTAGCAGTAAGACTAT
66 AGAAATGAGCACATACATGTATCCAACACTCCTACTATTCTGAGTAGCAGTAAGACTAT
81426 A
1 A
81427 TGCTGATGCA
Statistics
Matches: 123, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 123 1.00
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.24
Consensus pattern (124 bp):
ACCTGGATGATTTTAAAATCCAAACCACAATCATACCAGAAGCACCTCTAAACTATATATACGAA
AGAAATGAGCACATACATGTATCCAACACTCCTACTATTCTGAGTAGCAGTAAGACTAT
Found at i:99994 original size:2 final size:2
Alignment explanation
Indices: 99987--100012 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
99977 ACAAATAACT
99987 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
100013 ATCAGACGGA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:101451 original size:21 final size:21
Alignment explanation
Indices: 101425--101466 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
101415 GGTGCTGAAT
*
101425 GGCTTTCACAATACCCTTTCA
1 GGCTTTCAAAATACCCTTTCA
* *
101446 GGCTTTGAAAATACTCTTTCA
1 GGCTTTCAAAATACCCTTTCA
101467 ATTCAACATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (21 bp):
GGCTTTCAAAATACCCTTTCA
Found at i:101555 original size:52 final size:53
Alignment explanation
Indices: 101493--101594 Score: 145
Period size: 53 Copynumber: 1.9 Consensus size: 53
101483 AACAAAGCAG
101493 CACTGAAATGATTCAACAAG-CAACGAA-GTAAAATGCAAAACAATTAAAACAA
1 CACTGAAATGATTCAACAAGCCAAC-AATGTAAAATGCAAAACAATTAAAACAA
* * * *
101545 CACTGGAATGATTCAGCAGGCCAACAATGTAAAATGGAAAACAATTAAAA
1 CACTGAAATGATTCAACAAGCCAACAATGTAAAATGCAAAACAATTAAAA
101595 GAGAGAAAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
52 19 0.43
53 25 0.57
ACGTcount: A:0.52, C:0.17, G:0.15, T:0.17
Consensus pattern (53 bp):
CACTGAAATGATTCAACAAGCCAACAATGTAAAATGCAAAACAATTAAAACAA
Found at i:107295 original size:23 final size:23
Alignment explanation
Indices: 107221--107411 Score: 127
Period size: 23 Copynumber: 8.5 Consensus size: 23
107211 TATATGGAAC
*
107221 AAACAGAGAGTAC-CAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
107243 AAACAGAGAG-A-ACATAAGTGCT
1 AAACAGAGAGCACACA-AAGTGCT
* * *
107265 GGGCAACAGAGAGGACACACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
107291 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
* *
107311 --AC--TGAGCACACAAAATGCT
1 AAACAGAGAGCACACAAAGTGCT
*
107330 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
107353 AATA-ACGAAGAGCACGA-GACGTGCT
1 AA-ACA-G-AGAGCAC-ACAAAGTGCT
*
107378 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
107401 AAACAGAGAGC
1 AAACAGAGAGC
107412 GCGCTAAAGT
Statistics
Matches: 133, Mismatches: 16, Indels: 39
0.71 0.09 0.21
Matches are distributed among these distances:
16 10 0.08
18 3 0.02
19 1 0.01
20 1 0.01
21 5 0.04
22 18 0.14
23 56 0.42
24 3 0.02
25 25 0.19
26 8 0.06
27 3 0.02
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:116985 original size:26 final size:26
Alignment explanation
Indices: 116956--117006 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
116946 TTTAAGAAAA
*
116956 ATTGT-AAGAATTATTATAATTTTTAG
1 ATTGTAAAAAATTATTAT-ATTTTTAG
116982 ATTGTAAAAAATTATTATATTTTTA
1 ATTGTAAAAAATTATTATATTTTTA
117007 CAATTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (26 bp):
ATTGTAAAAAATTATTATATTTTTAG
Found at i:117530 original size:20 final size:22
Alignment explanation
Indices: 117507--117550 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
117497 TTTTACCAGC
*
117507 TTTTTAC-A-TTTTAAAATGTT
1 TTTTTACAATTTTTAAAATATT
117527 TTTTTACAATTTTTAAAATATT
1 TTTTTACAATTTTTAAAATATT
117549 TT
1 TT
117551 AATAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 1 0.05
22 13 0.62
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTTACAATTTTTAAAATATT
Found at i:124512 original size:29 final size:29
Alignment explanation
Indices: 124488--124573 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
124478 ACTAAATTCC
*
124488 TTTTTAAATTTAAATT-TGTTTTAAATTTA
1 TTTTTAAATTTAAATTAAG-TTTAAATTTA
**
124517 AATTTAAATTTAAATTAAGTTTAAATTTA
1 TTTTTAAATTTAAATTAAGTTTAAATTTA
* * *
124546 TTTTTAAAATTAAAAT-ATTTTAAATTTA
1 TTTTTAAATTTAAATTAAGTTTAAATTTA
124574 AAAAGTCTCA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
28 11 0.23
29 36 0.75
30 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (29 bp):
TTTTTAAATTTAAATTAAGTTTAAATTTA
Found at i:124516 original size:23 final size:23
Alignment explanation
Indices: 124490--124575 Score: 77
Period size: 23 Copynumber: 3.8 Consensus size: 23
124480 TAAATTCCTT
***
124490 TTTAAATTTAAATTTGTTTTAAA
1 TTTAAATTTAAATTTAAATTAAA
*
124513 TTTAAATTTAAATTTAAATTAAG
1 TTTAAATTTAAATTTAAATTAAA
**
124536 TTTAAATTTATTTTTAAAATTAAA
1 TTTAAATTTAAATTT-AAATTAAA
* *
124560 -AT-ATTTTAAATTTAAA
1 TTTAAATTTAAATTTAAA
124576 AAGTCTCATT
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
21 3 0.06
22 8 0.16
23 33 0.65
24 7 0.14
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTAAATTTAAATTTAAATTAAA
Found at i:124534 original size:11 final size:11
Alignment explanation
Indices: 124508--124543 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
124498 TAAATTTGTT
124508 TTAAATTTAAA
1 TTAAATTTAAA
124519 TTTAAATTTAAA
1 -TTAAATTTAAA
*
124531 TTAAGTTTAAA
1 TTAAATTTAAA
124542 TT
1 TT
124544 TATTTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:124534 original size:17 final size:18
Alignment explanation
Indices: 124490--124559 Score: 72
Period size: 17 Copynumber: 4.0 Consensus size: 18
124480 TAAATTCCTT
**
124490 TTTAAATTTAAATTT-GT
1 TTTAAATTTAAATTTAAA
124507 TTTAAATTTAAATTTAAA
1 TTTAAATTTAAATTTAAA
*
124525 TTTAAA-TTAAGTTTAAA
1 TTTAAATTTAAATTTAAA
** *
124542 TTTATTTTTAAAATTAAA
1 TTTAAATTTAAATTTAAA
124560 ATATTTTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
17 29 0.66
18 15 0.34
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTAAATTTAAATTTAAA
Found at i:124575 original size:6 final size:6
Alignment explanation
Indices: 124490--124559 Score: 72
Period size: 6 Copynumber: 12.0 Consensus size: 6
124480 TAAATTCCTT
** *
124490 TTTAAA TTTAAA TTT-GT TTTAAA TTTAAA TTTAAA TTTAAA -TTAAG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** *
124536 TTTAAA TTTATT TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
124560 ATATTTTAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
5 7 0.14
6 44 0.86
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:125256 original size:3 final size:3
Alignment explanation
Indices: 125248--125313 Score: 55
Period size: 3 Copynumber: 22.0 Consensus size: 3
125238 TAAAGAGTAT
* * *
125248 TAA TAA TAA TTAA TAA TAA TAG TAA TAA TAA TAA -ATA TAA CAT TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
**
125294 TAA TTT TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
125314 AAAATAAAGA
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
2 3 0.06
3 42 0.86
4 4 0.08
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:126514 original size:29 final size:29
Alignment explanation
Indices: 126481--126721 Score: 161
Period size: 29 Copynumber: 8.1 Consensus size: 29
126471 AAACTGTCCG
*
126481 AAAATTACATTTTT-ACCCTCAAACTTCAA
1 AAAATTCCATTTTTGACCC-CAAACTTCAA
*
126510 AAAA-TCCATTTTTGACCCCAAAACTTCCA
1 AAAATTCCATTTTTGACCCC-AAACTTCAA
* *
126539 AAAATTCCATTTTT-ACCCAAGAACTTCCA
1 AAAATTCCATTTTTGACCCCA-AACTTCAA
* *
126568 AAAATTCCAATTTTTGACCTCGAAACTTCCA
1 AAAATTCC-ATTTTTGACC-CCAAACTTCAA
* * *
126599 AAATTTCCATTTTT-ACCCCCGAACCTCAA
1 AAAATTCCATTTTTGA-CCCCAAACTTCAA
* * * *
126628 AAATTTTCATTTTTAATCCCGAAACTTTCAA
1 AAAATTCCATTTTTGA-CCCCAAAC-TTCAA
* * ** *
126659 AAAATACCATTTTT-CCCCCGGA-TGTCTA
1 AAAATTCCATTTTTGACCCCAAACT-TCAA
* *
126687 AAAACTCCATTTTTGACCTCGAAACTCTCAA
1 AAAATTCCATTTTTGACC-CCAAACT-TCAA
126718 AAAA
1 AAAA
126722 AATACCCTTT
Statistics
Matches: 168, Mismatches: 30, Indels: 26
0.75 0.13 0.12
Matches are distributed among these distances:
27 1 0.01
28 25 0.15
29 67 0.40
30 32 0.19
31 41 0.24
32 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.32
Consensus pattern (29 bp):
AAAATTCCATTTTTGACCCCAAACTTCAA
Found at i:126548 original size:30 final size:29
Alignment explanation
Indices: 126471--126677 Score: 170
Period size: 29 Copynumber: 7.0 Consensus size: 29
126461 GGAGGTTCCT
* *
126471 AAACTGTCCGAAAATTACATTTTTACCCTC-
1 AAACT-TCCAAAAATTCCATTTTTACCC-CA
*
126501 AAACTT-CAAAAAATCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
126530 AAACTTCCAAAAATTCCATTTTTA-CCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* *
126558 AGAACTTCCAAAAATTCCAATTTTTGACCTCG
1 A-AACTTCCAAAAATTCC-ATTTTT-ACCCCA
* *
126590 AAACTTCCAAAATTTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* * * * *
126619 GAACCT-CAAAAATTTTCATTTTTAATCCCG
1 AAACTTCCAAAAA-TTCCATTTTT-ACCCCA
* * *
126649 AAACTTTCAAAAAATACCATTTTTCCCCC
1 AAAC-TTCCAAAAATTCCATTTTTACCCC
126678 GGATGTCTAA
Statistics
Matches: 144, Mismatches: 22, Indels: 22
0.77 0.12 0.12
Matches are distributed among these distances:
28 24 0.17
29 45 0.31
30 42 0.29
31 25 0.17
32 8 0.06
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCA
Found at i:126640 original size:59 final size:58
Alignment explanation
Indices: 126471--126721 Score: 238
Period size: 60 Copynumber: 4.2 Consensus size: 58
126461 GGAGGTTCCT
* * * * * * *
126471 AAACTGTCCGAAAATTACATTTTTACCCTCAAACTTCAAAAAATCCATTTTTGACCCCA
1 AAACT-TCCAAAAATTCCATTTTTACCCCCGAACTTCAAAAATTCCATTTTTGACCTCG
**
126530 AAACTTCCAAAAATTCCATTTTTACCCAAGAACTTCCAAAAATTCCAATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTT-CAAAAATTCC-ATTTTTGACCTCG
* * * *
126590 AAACTTCCAAAATTTCCATTTTTACCCCCGAACCTCAAAAATTTTCATTTTTAATCC-CG
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCAAAAA-TTCCATTTTTGA-CCTCG
* * * *
126649 AAACTTTCAAAAAATACCATTTTT-CCCCCGGA-TGTCTAAAAACTCCATTTTTGACCTCG
1 AAAC-TTCCAAAAATTCCATTTTTACCCCCGAACT-TC-AAAAATTCCATTTTTGACCTCG
*
126708 AAACTCTCAAAAAA
1 AAACT-TCCAAAAA
126722 AATACCCTTT
Statistics
Matches: 161, Mismatches: 22, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
58 28 0.17
59 65 0.40
60 68 0.42
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.31
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCAAAAATTCCATTTTTGACCTCG
Found at i:126669 original size:60 final size:58
Alignment explanation
Indices: 126488--126775 Score: 206
Period size: 60 Copynumber: 4.8 Consensus size: 58
126478 CCGAAAATTA
* * * * * * *
126488 CATTTTTACCCTCAAACTTCAAAAAATCCATTTTTGACCCCAAAAC-TTCCAAAAATTC
1 CATTTTTACCCCCGAACGTCAAAAATTCCATTTTTGA-CCCGAAACTTTCAAAAAATAC
** * * * *
126546 CATTTTTACCCAAGAACTTCCAAAAATTCCAATTTTTGACCTCGAAAC-TTCCAAAATTTC
1 CATTTTTACCCCCGAACGT-CAAAAATTCC-ATTTTTGACC-CGAAACTTTCAAAAAATAC
* * *
126606 CATTTTTACCCCCGAACCTCAAAAATTTTCATTTTTAATCCCGAAACTTTCAAAAAATAC
1 CATTTTTACCCCCGAACGTCAAAAA-TTCCATTTTTGA-CCCGAAACTTTCAAAAAATAC
* * * *
126666 CATTTTT-CCCCCGGATGTCTAAAAACTCCATTTTTGACCTCGAAACTCTCAAAAAAAATAC
1 CATTTTTACCCCCGAACGTC-AAAAATTCCATTTTTGACC-CGAAACTTTC--AAAAAATAC
* * * ** * *
126727 C-CTTTTACCCCCAAATGTCTAAAAATTTTATTTTTAACCCCAAACTTTC
1 CATTTTTACCCCCGAACGTC-AAAAATTCCATTTTTGACCCGAAACTTTC
126776 CCAAAATTAC
Statistics
Matches: 189, Mismatches: 30, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
58 18 0.10
59 57 0.30
60 78 0.41
61 36 0.19
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (58 bp):
CATTTTTACCCCCGAACGTCAAAAATTCCATTTTTGACCCGAAACTTTCAAAAAATAC
Found at i:126760 original size:61 final size:59
Alignment explanation
Indices: 126609--126800 Score: 165
Period size: 59 Copynumber: 3.2 Consensus size: 59
126599 AAATTTCCAT
** *
126609 TTTTACCCCCGAACCTC-AAAAATTTTCATTTTTAATCCCGAAACTTTCAAAAAATACCA
1 TTTTACCCCCGAATGTCTAAAAATTTT-ATTTTTAATCCCGAAACTCTCAAAAAATACCA
* * * ** * *
126668 TTTTTCCCCCGGATGTCTAAAAACTCCATTTTTGA-CCTCGAAACTCTCAAAAAAAATACCC
1 TTTTACCCCCGAATGTCTAAAAATTTTATTTTTAATCC-CGAAACTCTC--AAAAAATACCA
* * * * *
126729 TTTTACCCCCAAATGTCTAAAAATTTTATTTTTAA-CCCCAAACTTTCCCAAAATTACCA
1 TTTTACCCCCGAATGTCTAAAAATTTTATTTTTAATCCCGAAACTCT-CAAAAAATACCA
* *
126788 TGTTGCCCCCGAA
1 TTTTACCCCCGAA
126801 AATCCAAAAT
Statistics
Matches: 103, Mismatches: 25, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
58 2 0.02
59 47 0.46
60 13 0.13
61 41 0.40
ACGTcount: A:0.34, C:0.29, G:0.06, T:0.32
Consensus pattern (59 bp):
TTTTACCCCCGAATGTCTAAAAATTTTATTTTTAATCCCGAAACTCTCAAAAAATACCA
Found at i:130781 original size:6 final size:6
Alignment explanation
Indices: 130770--130802 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
130760 ATAACAAGTC
130770 GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAG
1 GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAG
130803 AGAGCAGACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
GAGGGA
Found at i:131013 original size:2 final size:2
Alignment explanation
Indices: 131008--131037 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
130998 CAAAAAGGGG
131008 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
131038 AGGTTATGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:134527 original size:22 final size:21
Alignment explanation
Indices: 134488--134532 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
134478 AAAAATAGTG
134488 AAAATTAAAAAAACTATAAAA
1 AAAATTAAAAAAACTATAAAA
* * *
134509 AAAATTCAAGAAAATTATATAA
1 AAAATT-AAAAAAACTATAAAA
134531 AA
1 AA
134533 TTTAATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (21 bp):
AAAATTAAAAAAACTATAAAA
Found at i:134542 original size:20 final size:20
Alignment explanation
Indices: 134509--134570 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
134499 AACTATAAAA
* *
134509 AAAATTCAAGAAAATTATAT
1 AAAATTTAATAAAATTATAT
134529 AAAATTTAATAAAA-TAT-T
1 AAAATTTAATAAAATTATAT
*
134547 AAAAATT-ATAAAACTTATA-
1 AAAATTTAATAAAA-TTATAT
134566 AAAAT
1 AAAAT
134571 AATGTGAGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
17 6 0.17
18 7 0.20
19 10 0.29
20 12 0.34
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (20 bp):
AAAATTTAATAAAATTATAT
Found at i:134558 original size:9 final size:9
Alignment explanation
Indices: 134519--134570 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
134509 AAAATTCAAG
134519 AAAATTATA
1 AAAATTATA
134528 TAAAATT-TA
1 -AAAATTATA
*
134537 ATAAAATATTA
1 A-AAATTA-TA
134548 AAAATTATA
1 AAAATTATA
*
134557 AAACTTATA
1 AAAATTATA
134566 AAAAT
1 AAAAT
134571 AATGTGAGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
8 1 0.03
9 20 0.57
10 11 0.31
11 3 0.09
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAATTATA
Found at i:136064 original size:14 final size:14
Alignment explanation
Indices: 136023--136064 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
136013 ACTTAAAATT
136023 AATTATAGAATTATA
1 AATTATAGAATT-TA
*
136038 AA-TATAGATTTTA
1 AATTATAGAATTTA
*
136051 AATTATAAAATTTA
1 AATTATAGAATTTA
136065 TATTTTACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 4 0.17
14 17 0.74
15 2 0.09
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (14 bp):
AATTATAGAATTTA
Found at i:151112 original size:9 final size:9
Alignment explanation
Indices: 151093--151131 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
151083 ATTTAATTAT
151093 TAAATTCGAA
1 TAAA-TCGAA
*
151103 TAACTCGAA
1 TAAATCGAA
*
151112 TAATTCGAA
1 TAAATCGAA
151121 TAAATCGAA
1 TAAATCGAA
151130 TA
1 TA
151132 CAAACTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 23 0.88
10 3 0.12
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (9 bp):
TAAATCGAA
Found at i:151116 original size:18 final size:18
Alignment explanation
Indices: 151095--151131 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
151085 TTAATTATTA
*
151095 AATTCGAATAACTCGAAT
1 AATTCGAATAAATCGAAT
151113 AATTCGAATAAATCGAAT
1 AATTCGAATAAATCGAAT
151131 A
1 A
151132 CAAACTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.27
Consensus pattern (18 bp):
AATTCGAATAAATCGAAT
Found at i:151538 original size:12 final size:13
Alignment explanation
Indices: 151521--151549 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
151511 CTTTATAATG
151521 AAAAATTT-AAGA
1 AAAAATTTAAAGA
151533 AAAAATTTAAAGA
1 AAAAATTTAAAGA
151546 AAAA
1 AAAA
151550 TATATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (13 bp):
AAAAATTTAAAGA
Found at i:158028 original size:18 final size:19
Alignment explanation
Indices: 157984--158030 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
157974 AATTAATATA
157984 AATATAAATATATAATAATT
1 AATAT-AATATATAATAATT
*
158004 -ATTTAATATATAA-AATT
1 AATATAATATATAATAATT
158021 AATATAATAT
1 AATATAATAT
158031 TTTTATAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 4 0.17
18 17 0.71
19 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATATAATATATAATAATT
Found at i:159017 original size:23 final size:22
Alignment explanation
Indices: 158983--159037 Score: 60
Period size: 25 Copynumber: 2.4 Consensus size: 22
158973 AATGTATTAT
158983 ATATATTT-AAAAATTATATAGAA
1 ATAT-TTTAAAAAATTATATA-AA
159006 ATATTTTCAAAAAAATTATATAAA
1 ATATTTT--AAAAAATTATATAAA
159030 AT-TTTTAA
1 ATATTTTAA
159038 TACGAGCGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
21 2 0.07
22 3 0.10
23 8 0.28
24 4 0.14
25 12 0.41
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
ATATTTTAAAAAATTATATAAA
Found at i:159287 original size:2 final size:2
Alignment explanation
Indices: 159280--159319 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
159270 TTCGACCATT
159280 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
159320 ACTTGAGTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:160662 original size:12 final size:12
Alignment explanation
Indices: 160647--160671 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
160637 TTTAAAATCG
160647 TTTTTTTTTTTC
1 TTTTTTTTTTTC
160659 TTTTTTTTTTTC
1 TTTTTTTTTTTC
160671 T
1 T
160672 AATTTAACTG
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:166677 original size:26 final size:26
Alignment explanation
Indices: 166648--166780 Score: 117
Period size: 26 Copynumber: 4.9 Consensus size: 26
166638 AAAACTGACT
166648 GTACAGGACTGATAACAAAATTTAAA
1 GTACAGGACTGATAACAAAATTTAAA
166674 GTACAGGACTGATAACAAAATTTACTTTAAA
1 GTACAGGACTGATAAC-AAA---A-TTTAAA
*
166705 GTACAGGACTGATAACAAAATTTTAA
1 GTACAGGACTGATAACAAAATTTAAA
* * *** *
166731 CT-CATGATCTTTGA-AATGTACTTTAAA
1 GTACAGGA-C--TGATAACAAAATTTAAA
166758 GTACAGGACTGATAACAAAATTT
1 GTACAGGACTGATAACAAAATTT
166781 CATCATTAAA
Statistics
Matches: 83, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
25 7 0.08
26 29 0.35
27 14 0.17
28 7 0.08
30 4 0.05
31 22 0.27
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (26 bp):
GTACAGGACTGATAACAAAATTTAAA
Found at i:166706 original size:31 final size:30
Alignment explanation
Indices: 166648--166727 Score: 123
Period size: 31 Copynumber: 2.8 Consensus size: 30
166638 AAAACTGACT
166648 GTACAGGACTGATAAC-AAA---ATTTAAA
1 GTACAGGACTGATAACAAAATTTATTTAAA
166674 GTACAGGACTGATAACAAAATTTACTTTAAA
1 GTACAGGACTGATAACAAAATTTA-TTTAAA
166705 GTACAGGACTGATAACAAAATTT
1 GTACAGGACTGATAACAAAATTT
166728 TAACTCATGA
Statistics
Matches: 49, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
26 16 0.33
27 3 0.06
30 1 0.02
31 29 0.59
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.26
Consensus pattern (30 bp):
GTACAGGACTGATAACAAAATTTATTTAAA
Found at i:166977 original size:16 final size:16
Alignment explanation
Indices: 166956--166989 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
166946 TATATTTATA
166956 TATTTAAATTTTATTT
1 TATTTAAATTTTATTT
*
166972 TATTTATATTTTATTT
1 TATTTAAATTTTATTT
166988 TA
1 TA
166990 ATATCGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTAAATTTTATTT
Found at i:167241 original size:16 final size:16
Alignment explanation
Indices: 167214--167252 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
167204 TATACATTTA
167214 AATTTCATTTTACTCAC
1 AATTT-ATTTTACTCAC
167231 AATTTATTTTACTCAC
1 AATTTATTTTACTCAC
167247 AATTTA
1 AATTTA
167253 ATCTATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTTATTTTACTCAC
Found at i:178542 original size:25 final size:25
Alignment explanation
Indices: 178490--178542 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
178480 ATAGTAATCA
*
178490 TTTACTTTCATTAGTTTTCCTCTCT
1 TTTACTTTCATTAGTTTTCCTCTAT
* *
178515 TTTACTTTCTTTTA-TTTTCCTTTAT
1 TTTACTTTC-ATTAGTTTTCCTCTAT
178540 TTT
1 TTT
178543 CCTTCACTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 21 0.88
26 3 0.12
ACGTcount: A:0.11, C:0.19, G:0.02, T:0.68
Consensus pattern (25 bp):
TTTACTTTCATTAGTTTTCCTCTAT
Found at i:198055 original size:9 final size:9
Alignment explanation
Indices: 198031--198167 Score: 67
Period size: 10 Copynumber: 15.4 Consensus size: 9
198021 TTTGACAATT
198031 ATTTTTATTA
1 ATTTTTA-TA
*
198041 AATTTTATA
1 ATTTTTATA
198050 ATTTTTAT-
1 ATTTTTATA
198058 A-TTTT-T-
1 ATTTTTATA
198064 ATTTTTATA
1 ATTTTTATA
198073 ATTTTTTATA
1 A-TTTTTATA
** *
198083 AAATATATCA
1 ATTTTTAT-A
*
198093 A-CTTTATA
1 ATTTTTATA
198101 ATTTTTTATGA
1 A-TTTTTAT-A
198112 ATTTTTATA
1 ATTTTTATA
*
198121 ATGTTTAATA
1 AT-TTTTATA
* *
198131 AATTTTATT
1 ATTTTTATA
*
198140 A-GTTTAT-
1 ATTTTTATA
198147 -TTTTT-TA
1 ATTTTTATA
198154 ATATTTTATA
1 AT-TTTTATA
198164 ATTT
1 ATTT
198168 CTATTAAAAA
Statistics
Matches: 99, Mismatches: 14, Indels: 29
0.70 0.10 0.20
Matches are distributed among these distances:
6 3 0.03
7 11 0.11
8 10 0.10
9 33 0.33
10 40 0.40
11 2 0.02
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (9 bp):
ATTTTTATA
Found at i:198069 original size:14 final size:15
Alignment explanation
Indices: 198029--198078 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 15
198019 ATTTTGACAA
198029 TTATTTTTATTAAATTT
1 TTATTTTTA-T-AATTT
198046 TATAATTTTTAT-ATTT
1 T-T-ATTTTTATAATTT
198062 TTATTTTTATAATTT
1 TTATTTTTATAATTT
198077 TT
1 TT
198079 TATAAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
14 8 0.27
15 7 0.23
16 5 0.17
17 1 0.03
18 2 0.07
19 7 0.23
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATTTTTATAATTT
Found at i:199100 original size:19 final size:18
Alignment explanation
Indices: 199076--199114 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
199066 CATTGTTTAC
199076 TTTTAAACACATATTTATA
1 TTTTAAACA-ATATTTATA
* *
199095 TTTTAAATAATTTTTATA
1 TTTTAAACAATATTTATA
199113 TT
1 TT
199115 AATATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAAACAATATTTATA
Found at i:201015 original size:7 final size:7
Alignment explanation
Indices: 201003--201030 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
200993 AATTTTAAAA
201003 ATATTTT
1 ATATTTT
201010 ATATTTT
1 ATATTTT
201017 ATATTTT
1 ATATTTT
201024 ATATTTT
1 ATATTTT
201031 TATAATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATATTTT
Found at i:201081 original size:29 final size:29
Alignment explanation
Indices: 201016--201092 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 29
201006 TTTTATATTT
*
201016 TATATTTTATATTTTT-ATAATAATTTTAA
1 TATATTTTAT-TTTTTAAAAATAATTTTAA
*
201045 TGAT-TTTTATTTTTTAAAAATAATTTTTA
1 T-ATATTTTATTTTTTAAAAATAATTTTAA
201074 TATATTTTGATTTTTTAAA
1 TATATTTT-ATTTTTTAAA
201093 TTTCAAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 7 0.17
29 23 0.55
30 12 0.29
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (29 bp):
TATATTTTATTTTTTAAAAATAATTTTAA
Found at i:214787 original size:38 final size:38
Alignment explanation
Indices: 214744--214829 Score: 88
Period size: 38 Copynumber: 2.3 Consensus size: 38
214734 TCATACATAT
214744 TTAATTATTTAT-ATTTAGTCA-TATAATAAATTATTAAC
1 TTAATTATTTATAATTTA-TCATTATAATAAATT-TTAAC
* *
214782 TTAATTCA-TTATAATTTATTATTTTAATAAATTTTAAC
1 TTAATT-ATTTATAATTTATCATTATAATAAATTTTAAC
* *
214820 ATAATAATTT
1 TTAATTATTT
214830 TAAATAATCT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
37 1 0.03
38 23 0.57
39 16 0.40
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.52
Consensus pattern (38 bp):
TTAATTATTTATAATTTATCATTATAATAAATTTTAAC
Found at i:214891 original size:15 final size:15
Alignment explanation
Indices: 214871--214928 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
214861 ATTCAATATT
214871 AATATTTTAATAATA
1 AATATTTTAATAATA
* *
214886 AATATTTATTACAGTTACA
1 AATA-TT-TTA-A-TAATA
*
214905 AATATATTAATAATA
1 AATATTTTAATAATA
214920 AATATTTTA
1 AATATTTTA
214929 TAGTATAAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 15 0.45
16 3 0.09
17 6 0.18
18 2 0.06
19 7 0.21
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:215313 original size:18 final size:20
Alignment explanation
Indices: 215282--215319 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
215272 TCTAAACATT
*
215282 AAAAAATATTAATT-TTTTC
1 AAAAAATATGAATTATTTTC
215301 AAAAAA-ATGAATTATTTTC
1 AAAAAATATGAATTATTTTC
215320 CGAAACTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (20 bp):
AAAAAATATGAATTATTTTC
Found at i:215797 original size:15 final size:15
Alignment explanation
Indices: 215773--215820 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
215763 TATTTCAAGT
*
215773 TTATAATATTTTATA
1 TTATATTATTTTATA
215788 TTATATTATTTTTATA
1 TTATATTA-TTTTATA
*
215804 TATAATATAATTTTATA
1 T-T-ATATTATTTTATA
215821 ACTCATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 7 0.25
16 8 0.29
17 8 0.29
18 5 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATATTATTTTATA
Found at i:215811 original size:18 final size:16
Alignment explanation
Indices: 215774--215817 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
215764 ATTTCAAGTT
215774 TATAATATTTTATATTA
1 TATAAT-TTTTATATTA
*
215791 TATTATTTTTATATATAA
1 TATAATTTTTATAT-T-A
215809 TATAATTTT
1 TATAATTTT
215818 ATAACTCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 8 0.35
17 6 0.26
18 9 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATAATTTTTATATTA
Found at i:215928 original size:16 final size:17
Alignment explanation
Indices: 215894--215926 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
215884 AGATTACTGT
215894 ATAAAATATTATAATAA
1 ATAAAATATTATAATAA
215911 ATAAAA-ATTAT-ATAA
1 ATAAAATATTATAATAA
215926 A
1 A
215927 ATTATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 5 0.31
17 6 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAAATATTATAATAA
Found at i:225716 original size:19 final size:19
Alignment explanation
Indices: 225656--225725 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
225646 ATTACAAAGG
*
225656 AAATTCAAAATAAATTTCAA
1 AAATTCAAAAT-AATTTTAA
* *
225676 AAATTCAAATTAATTTTTA
1 AAATTCAAAATAATTTTAA
225695 AAATTCAAAAT-ATTTATAA
1 AAATTCAAAATAATTT-TAA
225714 AAATTTCAAAAT
1 AAA-TTCAAAAT
225726 TTATATTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
18 4 0.09
19 21 0.49
20 18 0.42
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATTCAAAATAATTTTAA
Found at i:225722 original size:39 final size:41
Alignment explanation
Indices: 225656--225737 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 41
225646 ATTACAAAGG
225656 AAATTCAAAATAAATTTCAAAAATTC-AAA-TTA-ATTTTTA
1 AAATTCAAAAT-AATTTCAAAAATTCAAAATTTATATTTTTA
*
225695 AAATTCAAAAT-ATTTATAAAAATTTCAAAATTTATATTTTTA
1 AAATTCAAAATAATTT-CAAAAA-TTCAAAATTTATATTTTTA
225737 A
1 A
225738 TTCTTTTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
37 4 0.11
38 5 0.14
39 14 0.38
40 3 0.08
41 3 0.08
42 8 0.22
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.41
Consensus pattern (41 bp):
AAATTCAAAATAATTTCAAAAATTCAAAATTTATATTTTTA
Found at i:226487 original size:6 final size:6
Alignment explanation
Indices: 226476--226514 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
226466 AGCTATCATT
226476 CAAAAG CAAAAG CAAAAG CAAAAG CAAAAG CAAAAG CAA
1 CAAAAG CAAAAG CAAAAG CAAAAG CAAAAG CAAAAG CAA
226515 GAAGATAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.67, C:0.18, G:0.15, T:0.00
Consensus pattern (6 bp):
CAAAAG
Found at i:236605 original size:2 final size:2
Alignment explanation
Indices: 236598--236630 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
236588 AGTTTTGCAT
236598 TA 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 TA T
236631 TCTTACACTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:247042 original size:20 final size:21
Alignment explanation
Indices: 247004--247042 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
246994 CATATATGTA
247004 CAAAACACATTATCATATAAT
1 CAAAACACATTATCATATAAT
247025 CAAATACAC-TTA-CATATA
1 CAAA-ACACATTATCATATA
247043 GTAGGATCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (21 bp):
CAAAACACATTATCATATAAT
Found at i:252187 original size:17 final size:18
Alignment explanation
Indices: 252160--252193 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
252150 TCATAAGATG
*
252160 AATTATTAAATATATTAA
1 AATTATTAAATAAATTAA
252178 AATT-TTAAATAAATTA
1 AATTATTAAATAAATTA
252194 TTTTATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTATTAAATAAATTAA
Found at i:257370 original size:2 final size:2
Alignment explanation
Indices: 257365--257393 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
257355 AGCTTTAATT
257365 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
257394 TTCATTAATA
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:261847 original size:18 final size:19
Alignment explanation
Indices: 261817--261853 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
261807 AAATGATGAT
261817 TTAACGTGTCACC-TTAAC
1 TTAACGTGTCACCGTTAAC
261835 TTAACGT-TACACCGTTAAC
1 TTAACGTGT-CACCGTTAAC
261854 GGTAATTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.06
18 11 0.65
19 5 0.29
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (19 bp):
TTAACGTGTCACCGTTAAC
Found at i:266659 original size:30 final size:31
Alignment explanation
Indices: 266625--266705 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 31
266615 AAAATTTGGA
*
266625 CCCTTAAAAGCTAAATTTTTTTTTTTGA-AT
1 CCCTTAAAAGTTAAATTTTTTTTTTTGACAT
*
266655 CCCTTAAAAGTTATACTTTTTTTTTTTGACAT
1 CCCTTAAAAGTTA-AATTTTTTTTTTTGACAT
266687 ---TTAAAAGTTAAATTTTTTT
1 CCCTTAAAAGTTAAATTTTTTT
266706 AAACTCTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
28 8 0.17
29 10 0.22
30 12 0.26
31 14 0.30
32 2 0.04
ACGTcount: A:0.30, C:0.11, G:0.06, T:0.53
Consensus pattern (31 bp):
CCCTTAAAAGTTAAATTTTTTTTTTTGACAT
Found at i:284626 original size:56 final size:55
Alignment explanation
Indices: 284451--284642 Score: 187
Period size: 56 Copynumber: 3.5 Consensus size: 55
284441 TAAAAAAATT
** *
284451 TATTTTTTTGATATTTGTCATCCAATGGCATA-ACCACCTTTAT-TAGATTTAAAAA
1 TATTTTTTTGATATTTGTCATCCAATGGTTTACACCA-CTTT-TCCAGATTTAAAAA
* ** * * *
284506 TA-TTTTTTGAGTATTTGTCATCTAAAAGTTTACATCACTTATCTCAAATTTAAAAA
1 TATTTTTTTGA-TATTTGTCATCCAATGGTTTACACCACTTTTC-CAGATTTAAAAA
* *
284562 TATTTTTTTGATATTAGTCATCCAATGGTTTACACCATCTTTTCCAGATATAAAAA
1 TATTTTTTTGATATTTGTCATCCAATGGTTTACACCA-CTTTTCCAGATTTAAAAA
*
284618 TATTTTTTT-ATGTTTG-CTATCCAAT
1 TATTTTTTTGATATTTGTC-ATCCAAT
284643 AACCTACACC
Statistics
Matches: 111, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
54 10 0.09
55 33 0.30
56 55 0.50
57 13 0.12
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (55 bp):
TATTTTTTTGATATTTGTCATCCAATGGTTTACACCACTTTTCCAGATTTAAAAA
Found at i:284909 original size:58 final size:57
Alignment explanation
Indices: 284836--285197 Score: 304
Period size: 58 Copynumber: 6.3 Consensus size: 57
284826 GGATAGTAAG
* *
284836 CACTCAAAAAAATATTTTTAAATTTGAAAAAGATGATGTAGGCTATTAAGTGGCAAA
1 CACTCAAAAAAATATTTTTAAATTTGAAAAAGATGGTGTAGGCCATTAAGTGGCAAA
* * * * * ** **
284893 CACTCCAAAAAAATATTTTT-AATCTGAGAAATATGGTGTAAGTCATTGGGTGATAAA
1 CACT-CAAAAAAATATTTTTAAATTTGAAAAAGATGGTGTAGGCCATTAAGTGGCAAA
* * * *
284950 TC-CT-AAAAATATTATTTTTATATTTGGAAAATG-TGGTGTAGGCCATTGAGTGGCAAA
1 -CACTCAAAAA-AATATTTTTAAATTT-GAAAAAGATGGTGTAGGCCATTAAGTGGCAAA
* * * *
285007 CAC-CCAAAAAATATTTTTAAATTTGGAAAAGATGGTGTAGGCCATTAGGTGACAAA
1 CACTCAAAAAAATATTTTTAAATTTGAAAAAGATGGTGTAGGCCATTAAGTGGCAAA
**** * * * * *
285063 CACTCAAATTTTTTTTTTTTAAATTTGGAAAATATGATGTAGGCCATTGAGTGGCAAA
1 CACTCAAA-AAAATATTTTTAAATTTGAAAAAGATGGTGTAGGCCATTAAGTGGCAAA
* ** *
285121 CACTCAAAATAAATATTTTTAAATTTGGAAAAA-ATGGTGTGGGTAATTAGGTGGCAAA
1 CACTCAAAA-AAATATTTTTAAATTT-GAAAAAGATGGTGTAGGCCATTAAGTGGCAAA
* **
285179 CATTTTAAAAAATATTTTT
1 CACTCAAAAAAATATTTTT
285198 TTATTCGTAT
Statistics
Matches: 237, Mismatches: 56, Indels: 24
0.75 0.18 0.08
Matches are distributed among these distances:
55 10 0.04
56 46 0.19
57 72 0.30
58 104 0.44
59 5 0.02
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (57 bp):
CACTCAAAAAAATATTTTTAAATTTGAAAAAGATGGTGTAGGCCATTAAGTGGCAAA
Found at i:284934 original size:114 final size:114
Alignment explanation
Indices: 284793--285144 Score: 371
Period size: 114 Copynumber: 3.1 Consensus size: 114
284783 TAATTTTAAT
* * *
284793 TTTTTAAATCTGAGAAATATGGTGTAAGTCATCGGAT-AGTAAGCACTCAAAAAAATATTTTTAA
1 TTTTTAAATCTGAGAAATATGGTGTAAGTCATAGG-TGA-TAAACACTCAAAAAATTATTTTTAA
* *
284857 ATTTGAAAAAGATGATGTAGGCTATTAAGTGGCAAACACTCCAAAAAAATA
64 ATTTGAAAAAGATGATGTAGGCCATTGAGTGGCAAACACTCCAAAAAAATA
*
284908 TTTTT-AATCTGAGAAATATGGTGTAAGTCATTGGGTGATAAATC-CT-AAAAATATTATTTTTA
1 TTTTTAAATCTGAGAAATATGGTGTAAGTCA-TAGGTGATAAA-CACTCAAAAA-ATTATTTTTA
* * *
284970 TATTTGGAAAATG-TGGTGTAGGCCATTGAGTGGCAAACAC-CC-AAAAAATA
63 AATTT-GAAAAAGATGATGTAGGCCATTGAGTGGCAAACACTCCAAAAAAATA
* * * * * *** *
285020 TTTTTAAATTTG-GAAAAGATGGTGTAGGCCATTAGGTGACAAACACTCAAATTTTTTTTTTTTA
1 TTTTTAAATCTGAG-AAATATGGTGTAAGTCA-TAGGTGATAAACACTCAAA-AAATTATTTTTA
* *
285084 AATTTGGAAAATATGATGTAGGCCATTGAGTGGCAAACACT-CAAAATAAATA
63 AATTTGAAAAAGATGATGTAGGCCATTGAGTGGCAAACACTCCAAAA-AAATA
285136 TTTTTAAAT
1 TTTTTAAAT
285145 TTGGAAAAAA
Statistics
Matches: 200, Mismatches: 23, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
112 15 0.08
113 42 0.21
114 110 0.55
115 19 0.09
116 14 0.07
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.34
Consensus pattern (114 bp):
TTTTTAAATCTGAGAAATATGGTGTAAGTCATAGGTGATAAACACTCAAAAAATTATTTTTAAAT
TTGAAAAAGATGATGTAGGCCATTGAGTGGCAAACACTCCAAAAAAATA
Found at i:288637 original size:19 final size:19
Alignment explanation
Indices: 288608--288650 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
288598 TGATTCTTAT
288608 ATTTT-TCTAATACTCATC
1 ATTTTCTCTAATACTCATC
288626 ATTTTCTCTAATACTCATC
1 ATTTTCTCTAATACTCATC
288645 ATTTTC
1 ATTTTC
288651 ACCCTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTTCTCTAATACTCATC
Found at i:289614 original size:37 final size:35
Alignment explanation
Indices: 289556--289637 Score: 101
Period size: 37 Copynumber: 2.3 Consensus size: 35
289546 TTTAAATTCG
* **
289556 TTTAAATTTATTTTTAGATTTAAATTTATGTCAAA
1 TTTAAATTTATTTTTAAATTTAAATTTACCTCAAA
* *
289591 TTTAAATTTATCTTTTTAAATTTAAATTTGCCTTAAA
1 TTTAAATTTA--TTTTTAAATTTAAATTTACCTCAAA
289628 TTTAAATTTA
1 TTTAAATTTA
289638 ATTAAATTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 10 0.25
37 30 0.75
ACGTcount: A:0.37, C:0.05, G:0.04, T:0.55
Consensus pattern (35 bp):
TTTAAATTTATTTTTAAATTTAAATTTACCTCAAA
Found at i:290372 original size:30 final size:30
Alignment explanation
Indices: 290338--290394 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
290328 TATTGGCAAT
* * *
290338 AATAATAATAATATCACTAATATCATTAAC
1 AATAATAATAACATCAATAATAACATTAAC
*
290368 AATAATAATGACATCAATAATAACATT
1 AATAATAATAACATCAATAATAACATT
290395 TAATAATAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (30 bp):
AATAATAATAACATCAATAATAACATTAAC
Found at i:291573 original size:57 final size:58
Alignment explanation
Indices: 291470--291669 Score: 278
Period size: 59 Copynumber: 3.4 Consensus size: 58
291460 CCCTAAACTA
*
291470 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCTTTTTTGACCCCGAACCT
1 TCCAAAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
** * *
291529 TCTTAAAATTACCATTTTA-CCCAAACTTCCAAAAATTCCATTTTTGACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* *
291586 TCCAAAAATTACCATTTTACCCCTGGACTTCCAAAAATCCCATTTTTGACCCCGAGA-CA
1 TCCAAAAATTACCATTTTACCCC-GAACTTCCAAAAATCCCATTTTTGACCCCGA-ACCT
*
291645 TCCAAAAATTACTATTTTACTCCCG
1 TCCAAAAATTACCATTTTAC-CCCG
291670 GATGTCCAAA
Statistics
Matches: 125, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
57 52 0.42
58 3 0.02
59 66 0.53
60 4 0.03
ACGTcount: A:0.32, C:0.32, G:0.06, T:0.30
Consensus pattern (58 bp):
TCCAAAAATTACCATTTTACCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
Found at i:291677 original size:29 final size:27
Alignment explanation
Indices: 291470--291679 Score: 113
Period size: 29 Copynumber: 7.2 Consensus size: 27
291460 CCCTAAACTA
*
291470 TCCAAAAATTACCATTTTACCCCCGAACT
1 TCCAAAAATTACCATTTTA-CCCCGGA-T
* * *
291499 TCCAAAAA-TCCCTTTTTTGACCCCGAACCT
1 TCCAAAAATTACC-ATTTT-ACCCCGGA--T
** **
291529 TCTTAAAATTACCATTTTA-CCCAAACT
1 TCCAAAAATTACCATTTTACCCCGGA-T
*
291556 TCCAAAAATT-CCATTTTTGACCCCGAACCT
1 TCCAAAAATTACCA-TTTT-ACCCCGGA--T
291586 TCCAAAAATTACCATTTTACCCCTGGACT
1 TCCAAAAATTACCATTTTACCCC-GGA-T
* *
291615 TCCAAAAA-TCCCATTTTTGACCCCGAGACA
1 TCCAAAAATTACCA-TTTT-ACCCCG-GA-T
*
291645 TCCAAAAATTACTATTTTACTCCCGGAT
1 TCCAAAAATTACCATTTTAC-CCCGGAT
291673 GTCCAAA
1 -TCCAAA
291680 GACTCCGTTT
Statistics
Matches: 149, Mismatches: 16, Indels: 32
0.76 0.08 0.16
Matches are distributed among these distances:
26 3 0.02
27 14 0.09
28 13 0.09
29 55 0.37
30 55 0.37
31 9 0.06
ACGTcount: A:0.32, C:0.31, G:0.06, T:0.30
Consensus pattern (27 bp):
TCCAAAAATTACCATTTTACCCCGGAT
Found at i:291758 original size:28 final size:31
Alignment explanation
Indices: 291703--291778 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 31
291693 ACTTCGAAAC
* * * *
291703 TCTCAAAATTATCGTTTTTACCCCCGAATGT
1 TCTCTAAATTACCATTTTTAACCCCGAATGT
* *
291734 T-T-TAAATT-CCATTTTTAACCTCGAATTT
1 TCTCTAAATTACCATTTTTAACCCCGAATGT
291762 TCTCTAAATTACCATTT
1 TCTCTAAATTACCATTT
291779 GGCCCCGTGC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
28 16 0.44
29 6 0.17
30 7 0.19
31 7 0.19
ACGTcount: A:0.28, C:0.22, G:0.05, T:0.45
Consensus pattern (31 bp):
TCTCTAAATTACCATTTTTAACCCCGAATGT
Found at i:295442 original size:2 final size:2
Alignment explanation
Indices: 295435--295496 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
295425 TTTGTTTTTC
295435 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
295477 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
295497 TGAATTTACA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:295925 original size:84 final size:83
Alignment explanation
Indices: 295807--296049 Score: 310
Period size: 84 Copynumber: 2.9 Consensus size: 83
295797 TTAAGGGGAT
* *
295807 CAAAGTGCAATTTTACTATATATTAATTTATAATTTCTTTATTTATAAGAGGGTTGAATTGAAAA
1 CAAAGTGCAATTTTACTATATATTAATTTATAATTTATTTATTTATAAGAGGATTGAATT-AAAA
*
295872 TTTTTCATTTT-AGGA-GA
65 TTTTTCATTTTGAGAAGGA
* * **
295889 CTAAAGTGTAATTTTACTATAATATTAATTTGTAATTTATCCATTTATAAGAGGATTGAATTAAA
1 C-AAAGTGCAATTTTACTAT-ATATTAATTTATAATTTATTTATTTATAAGAGGATTGAATTAAA
*
295954 ATTTTTAATTATTGAGAAGGA
64 ATTTTTCATT-TTGAGAAGGA
** * * * *
295975 CAAAGTGCAATTTTACTATATATTAATTTATAAACTATTTATTTATAGGAGGACTAAATTAAAAA
1 CAAAGTGCAATTTTACTATATATTAATTTATAATTTATTTATTTATAAGAGGATTGAATTAAAAT
296040 TTTTCATTTT
66 TTTTCATTTT
296050 TGAGGCCAAG
Statistics
Matches: 137, Mismatches: 19, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
82 1 0.01
83 31 0.23
84 82 0.60
85 20 0.15
86 3 0.02
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (83 bp):
CAAAGTGCAATTTTACTATATATTAATTTATAATTTATTTATTTATAAGAGGATTGAATTAAAAT
TTTTCATTTTGAGAAGGA
Found at i:297469 original size:13 final size:13
Alignment explanation
Indices: 297451--297477 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
297441 CTCTCTCTCT
297451 CTCGTGTATGAAC
1 CTCGTGTATGAAC
297464 CTCGTGTATGAAC
1 CTCGTGTATGAAC
297477 C
1 C
297478 AGTTTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (13 bp):
CTCGTGTATGAAC
Found at i:314542 original size:4 final size:4
Alignment explanation
Indices: 314535--314566 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
314525 CTCTCTCTCT
314535 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC
1 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC
314567 ATATATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.00, C:0.75, G:0.00, T:0.25
Consensus pattern (4 bp):
CTCC
Found at i:316869 original size:23 final size:25
Alignment explanation
Indices: 316840--316899 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
316830 TAAGACAAAT
* * *
316840 TTTTTTTAAAAGTGTTGAAATTATA
1 TTTTTATATAAGTGTAGAAATTATA
316865 TTTTTATATAAGTGTAGAAATTATA
1 TTTTTATATAAGTGTAGAAATTATA
*
316890 TTTCTATATA
1 TTTTTATATA
316900 TATTCTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.52
Consensus pattern (25 bp):
TTTTTATATAAGTGTAGAAATTATA
Found at i:319511 original size:28 final size:28
Alignment explanation
Indices: 319348--319714 Score: 217
Period size: 29 Copynumber: 12.6 Consensus size: 28
319338 GGATACCCGA
* * *
319348 GGGTAAAACGATAA-TTTTGGACACTTCGG
1 GGGTAAAATG-TAATTTTTGGA-AGTTTGG
* *
319377 GGGTAAAATAGTAATTTTTAGAGGTTT-G
1 GGGTAAAAT-GTAATTTTTGGAAGTTTGG
* *
319405 AGGTCAAAAAATAG-AATTTTTGGACA-TTCGG
1 GGGT---AAAAT-GTAATTTTTGGA-AGTTTGG
*
319436 GGGTAAAAAGGTAATTTTTGGAAAGTTT-G
1 GGGT-AAAATGTAATTTTTGG-AAGTTTGG
*
319465 GGGTCAAAAATGGAATTTTTGGAAGTTTGG
1 GGGT--AAAATGTAATTTTTGGAAGTTTGG
319495 GGGTAAAATGTAATTTTTGAGAAGTTTGG
1 GGGTAAAATGTAATTTTTG-GAAGTTTGG
* *
319524 GGTTAAAATGGAATTTTTGGAAGTTTGG
1 GGGTAAAATGTAATTTTTGGAAGTTTGG
* * *
319552 GGATAAAGTGGTAA-TTTTGGAGAATTT-G
1 GGGTAAAAT-GTAATTTTTGGA-AGTTTGG
* * * ***
319580 GGGTCAAAATGGAATTTTTTGAAATTCAA
1 GGGT-AAAATGTAATTTTTGGAAGTTTGG
*
319609 GGGTAAAATGTAATTTTTGAAAGTTTGAG
1 GGGTAAAATGTAATTTTTGGAAGTTTG-G
** ** *
319638 GGCAAAAATGTAATTTTTAAAATTTTGAAG
1 GGGTAAAATGTAATTTTTGGAAGTTTG--G
* * *
319668 GGTTAAAATGTAATTTTTAGAAAGTTAGG
1 GGGTAAAATGTAATTTTT-GGAAGTTTGG
* * *
319697 GGTTAAAATATCATTTTT
1 GGGTAAAATGTAATTTTT
319715 AAAAAGTTTG
Statistics
Matches: 272, Mismatches: 45, Indels: 42
0.76 0.13 0.12
Matches are distributed among these distances:
28 70 0.26
29 126 0.46
30 59 0.22
31 17 0.06
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.36
Consensus pattern (28 bp):
GGGTAAAATGTAATTTTTGGAAGTTTGG
Found at i:319548 original size:57 final size:57
Alignment explanation
Indices: 319375--319705 Score: 305
Period size: 57 Copynumber: 5.7 Consensus size: 57
319365 TGGACACTTC
* * * *
319375 GGGGGTAAAATAGTAATTTTT-AGAGGTTTGAGGTCAAAAAATAGAATTTTTGGACA-TTC
1 GGGGGTAAAAT-GTAATTTTTGAGAAGTTTGGGGT--AAAAATGGAATTTTTGGA-AGTTT
*
319434 GGGGGTAAAAAGGTAATTTTTG-GAAAGTTTGGGGTCAAAAATGGAATTTTTGGAAGTTT
1 GGGGGT-AAAATGTAATTTTTGAG-AAGTTTGGGGT-AAAAATGGAATTTTTGGAAGTTT
*
319493 GGGGGTAAAATGTAATTTTTGAGAAGTTTGGGGTTAAAATGGAATTTTTGGAAGTTT
1 GGGGGTAAAATGTAATTTTTGAGAAGTTTGGGGTAAAAATGGAATTTTTGGAAGTTT
* * * * * * *
319550 GGGGATAAAGTGGTAATTTTGGAGAA-TTTGGGGTCAAAATGGAATTTTTTGAAATTC
1 GGGGGTAAAAT-GTAATTTTTGAGAAGTTTGGGGTAAAAATGGAATTTTTGGAAGTTT
** * * ** *
319607 AAGGGTAAAATGTAATTTTTGA-AAGTTTGAGGGCAAAAATGTAATTTTTAAAATTTT
1 GGGGGTAAAATGTAATTTTTGAGAAGTTTG-GGGTAAAAATGGAATTTTTGGAAGTTT
* * *
319664 GAAGGGTTAAAATGTAATTTTT-AGAAAGTTAGGGGTTAAAAT
1 G--GGGGTAAAATGTAATTTTTGAG-AAGTTTGGGGTAAAAAT
319706 ATCATTTTTA
Statistics
Matches: 227, Mismatches: 33, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
55 2 0.01
56 14 0.06
57 85 0.37
58 40 0.18
59 67 0.30
60 19 0.08
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (57 bp):
GGGGGTAAAATGTAATTTTTGAGAAGTTTGGGGTAAAAATGGAATTTTTGGAAGTTT
Found at i:319700 original size:29 final size:28
Alignment explanation
Indices: 319435--319729 Score: 245
Period size: 29 Copynumber: 10.2 Consensus size: 28
319425 TGGACATTCG
* *
319435 GGGGTAAAAAGGTAATTTTTGGAAAGTTT
1 GGGGTTAAAATGTAATTTTT-GAAAGTTT
* * *
319464 GGGGTCAAAAATGGAATTTTTGGAAGTTT
1 GGGGT-TAAAATGTAATTTTTGAAAGTTT
*
319493 GGGGGTAAAATGTAATTTTTGAGAAGTTT
1 GGGGTTAAAATGTAATTTTTGA-AAGTTT
* *
319522 GGGGTTAAAATGGAATTTTTGGAAGTTT
1 GGGGTTAAAATGTAATTTTTGAAAGTTT
* * *
319550 GGGGATAAAGTGGTAATTTTGGAGAA-TTT
1 GGGGTTAAAAT-GTAATTTTTGA-AAGTTT
* * *
319579 GGGGTCAAAATGGAATTTTTTGAAA-TTCA
1 GGGGTTAAAATGTAA-TTTTTGAAAGTT-T
*
319608 AGGG-TAAAATGTAATTTTTGAAAGTTT
1 GGGGTTAAAATGTAATTTTTGAAAGTTT
** * *
319635 GAGGGCAAAAATGTAATTTTTAAAATTTT
1 G-GGGTTAAAATGTAATTTTTGAAAGTTT
*
319664 GAAGGGTTAAAATGTAATTTTTAGAAAGTTA
1 G--GGGTTAAAATGTAATTTTT-GAAAGTTT
* * *
319695 GGGGTTAAAATATCATTTTTAAAAAGTTT
1 GGGGTTAAAATGTAATTTTT-GAAAGTTT
319724 GAGGGT
1 G-GGGT
319730 CTGCTCTTTT
Statistics
Matches: 216, Mismatches: 38, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
27 9 0.04
28 49 0.23
29 115 0.53
30 37 0.17
31 6 0.03
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.37
Consensus pattern (28 bp):
GGGGTTAAAATGTAATTTTTGAAAGTTT
Found at i:319729 original size:59 final size:59
Alignment explanation
Indices: 319607--319729 Score: 153
Period size: 59 Copynumber: 2.1 Consensus size: 59
319597 TTTGAAATTC
* * *
319607 AAGGG-TAAAATGTAATTTTTGAAAGTTTGAGGGCAAAAATGTAATTTTTAAAATTTTG
1 AAGGGTTAAAATGTAATTTTTGAAAGTTAGAGGGCAAAAATATAATTTTTAAAAGTTTG
** *
319665 AAGGGTTAAAATGTAATTTTTAGAAAGTTAG-GGGTTAAAATATCATTTTTAAAAAGTTTG
1 AAGGGTTAAAATGTAATTTTT-GAAAGTTAGAGGGCAAAAATATAATTTTT-AAAAGTTTG
319725 -AGGGT
1 AAGGGT
319730 CTGCTCTTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
58 5 0.09
59 35 0.62
60 16 0.29
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (59 bp):
AAGGGTTAAAATGTAATTTTTGAAAGTTAGAGGGCAAAAATATAATTTTTAAAAGTTTG
Found at i:325629 original size:21 final size:22
Alignment explanation
Indices: 325590--325641 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
325580 ATTGATTTAA
*
325590 AAATATATAAAAATGAAATCAT
1 AAATATATAAAAATAAAATCAT
* *
325612 AAATATTTAAAAA-AAAATTAT
1 AAATATATAAAAATAAAATCAT
*
325633 AAAAATATA
1 AAATATATA
325642 TAATAGAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (22 bp):
AAATATATAAAAATAAAATCAT
Found at i:326819 original size:2 final size:2
Alignment explanation
Indices: 326812--326848 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
326802 GTGTTGAAAT
*
326812 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
326849 TCTATTTATT
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:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:326849 original size:6 final size:6
Alignment explanation
Indices: 326814--326874 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
326804 GTTGAAATTA
* * * * *
326814 TATATA TATATA TATATA TATATA TATATT TATA-T TCTATT TAT-TT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
326860 TACTATT TATATT TA
1 TA-TATT TATATT TA
326875 AAATTTGTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
5 8 0.16
6 37 0.76
7 4 0.08
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (6 bp):
TATATT
Found at i:328871 original size:18 final size:18
Alignment explanation
Indices: 328786--328871 Score: 72
Period size: 17 Copynumber: 4.8 Consensus size: 18
328776 TTCATTTTGG
*
328786 GTTT-AAATTTAGTTTAAA
1 GTTTAAAATTTAATTT-AA
* **
328804 GTTTAAACTTTTCTTTTAA
1 GTTTAAA-ATTTAATTTAA
*
328823 GTTT-AAATTTAAATTAA
1 GTTTAAAATTTAATTTAA
328840 GTTTAAAA-TTAATTTGAA
1 GTTTAAAATTTAATTT-AA
328858 -TTTAAAATTTAATT
1 GTTTAAAATTTAATT
328872 ATTTAAAATG
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
17 24 0.44
18 17 0.31
19 8 0.15
20 6 0.11
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (18 bp):
GTTTAAAATTTAATTTAA
Found at i:329596 original size:3 final size:3
Alignment explanation
Indices: 329588--329614 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
329578 TAACATTAAT
329588 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
329615 GTAAAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Done.