Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold379
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: 429249
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 418 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:6616 original size:20 final size:20
Alignment explanation
Indices: 6563--6617 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
6553 AAATTCCCAG
**
6563 ATGTATCGATACAAAGATCA
1 ATGTATCGATACATTGATCA
*
6583 ATGTATTGATACATTGAAT-A
1 ATGTATCGATACATTG-ATCA
6603 ATGTATCGATACATT
1 ATGTATCGATACATT
6618 TCCTTGGCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTGATCA
Found at i:6688 original size:21 final size:19
Alignment explanation
Indices: 6641--6695 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
6631 GCAGGGCAAC
6641 TTTGTATCGATACAACACT
1 TTTGTATCGATACAACACT
*
6660 TATGTATCGATACATTA-ACT
1 TTTGTATCGATACA--ACACT
6680 GTTTGTATCGATACAA
1 -TTTGTATCGATACAA
6696 ATTGTTGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 14 0.45
20 3 0.10
21 14 0.45
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACAACACT
Found at i:7824 original size:20 final size:21
Alignment explanation
Indices: 7799--7839 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
7789 AAAAATTTCT
7799 AAATGTATCGATACAT-TGAG
1 AAATGTATCGATACATATGAG
*
7819 AAATGTATCTATACATATGAG
1 AAATGTATCGATACATATGAG
7840 TAAAACCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (21 bp):
AAATGTATCGATACATATGAG
Found at i:7978 original size:50 final size:50
Alignment explanation
Indices: 7799--7981 Score: 244
Period size: 50 Copynumber: 3.7 Consensus size: 50
7789 AAAAATTTCT
* * * *
7799 AAATGTATCGATACATTG-AGAAATGTATCTATACATATGAGTAAAACCCA
1 AAATGTATCGATACAATGAAG-AATGTATCGATACATCTGAGTAAAACACA
* * *
7849 TAATGTATCGATACAATGAAGAATGTATTGATACATCTGAGTAAAACTCA
1 AAATGTATCGATACAATGAAGAATGTATCGATACATCTGAGTAAAACACA
* *
7899 AAATATATCGATACAATGAAAAATGTATCGATACATCT-AGGTAAAACACA
1 AAATGTATCGATACAATGAAGAATGTATCGATACATCTGA-GTAAAACACA
*
7949 GAATGTATCGATACAATGAAGAATGTATCGATA
1 AAATGTATCGATACAATGAAGAATGTATCGATA
7982 TAAACTATAG
Statistics
Matches: 117, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
49 1 0.01
50 114 0.97
51 2 0.02
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (50 bp):
AAATGTATCGATACAATGAAGAATGTATCGATACATCTGAGTAAAACACA
Found at i:11363 original size:13 final size:13
Alignment explanation
Indices: 11342--11403 Score: 55
Period size: 13 Copynumber: 5.2 Consensus size: 13
11332 ATACAAAGAT
*
11342 CAATATATCGATA
1 CAATGTATCGATA
11355 CAATGTATCGATA
1 CAATGTATCGATA
11368 C-AT-T-T-GAGT-
1 CAATGTATCGA-TA
*
11377 -AATGTATTGATA
1 CAATGTATCGATA
11389 CAATGTATCGATA
1 CAATGTATCGATA
11402 CA
1 CA
11404 TTTGAGTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
9 4 0.10
10 3 0.08
11 3 0.08
12 4 0.10
13 26 0.65
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:11394 original size:34 final size:34
Alignment explanation
Indices: 11347--11424 Score: 147
Period size: 34 Copynumber: 2.3 Consensus size: 34
11337 AAGATCAATA
11347 TATCGATACAATGTATCGATACATTTGAGTAATG
1 TATCGATACAATGTATCGATACATTTGAGTAATG
*
11381 TATTGATACAATGTATCGATACATTTGAGTAATG
1 TATCGATACAATGTATCGATACATTTGAGTAATG
11415 TATCGATACA
1 TATCGATACA
11425 TTTCCTTGGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (34 bp):
TATCGATACAATGTATCGATACATTTGAGTAATG
Found at i:13993 original size:29 final size:28
Alignment explanation
Indices: 13920--14000 Score: 72
Period size: 29 Copynumber: 2.8 Consensus size: 28
13910 ATACATGTTT
* * *
13920 CAAAGATACCTATGTCAAAGTACTTATAC
1 CAAAGGTA-CTATGCCAAAGTACCTATAC
* *
13949 TAAAGGTACTTGTGCCAAAGTACCTATAC
1 CAAAGGTAC-TATGCCAAAGTACCTATAC
* *
13978 CGAAGGTAACTATGCCAAGGTAC
1 CAAAGGT-ACTATGCCAAAGTAC
14001 TTGTGTCAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
28 1 0.02
29 38 0.93
30 2 0.05
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (28 bp):
CAAAGGTACTATGCCAAAGTACCTATAC
Found at i:18607 original size:92 final size:92
Alignment explanation
Indices: 18436--18612 Score: 248
Period size: 92 Copynumber: 1.9 Consensus size: 92
18426 CAAGGACCCT
* * *
18436 CTACTTGAATTAAGGAACTTGGTCCTAGAGTCATTGGCAGCATCACCGTAGGTGTAAGCCTAACC
1 CTACTTAAATTAAGGAACTTGGTCCTAGAGTCATTGGCAGCATCACCATAGGTGCAAGCCTAACC
****
18501 TTTTGGCACAACCATGCCCCGTTTCCC
66 TTCCAACACAACCATGCCCCGTTTCCC
*
18528 CTACTTAAATT-AGAGAACTTGGTCCTAGAGTCATTGGTAGCATCACCATAGGTGCAAGCCTAAC
1 CTACTTAAATTAAG-GAACTTGGTCCTAGAGTCATTGGCAGCATCACCATAGGTGCAAGCCTAAC
**
18592 CTTCCAACATGACCATGCCCC
65 CTTCCAACACAACCATGCCCC
18613 ATTCCCCATA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
91 2 0.03
92 72 0.97
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (92 bp):
CTACTTAAATTAAGGAACTTGGTCCTAGAGTCATTGGCAGCATCACCATAGGTGCAAGCCTAACC
TTCCAACACAACCATGCCCCGTTTCCC
Found at i:19762 original size:28 final size:27
Alignment explanation
Indices: 19731--19822 Score: 98
Period size: 28 Copynumber: 3.3 Consensus size: 27
19721 GGTAATATAC
19731 ATGAGATAATATTTAGTAAGTATTACTT
1 ATGAGATAATATTTAGTAAGTATTA-TT
* *
19759 ATGAGAT-AT-TGTATGTAAAGTAATATT
1 ATGAGATAATATTTA-GT-AAGTATTATT
*
19786 CATGAGATAATATTCAGTAAGTATTATCT
1 -ATGAGATAATATTTAGTAAGTATTAT-T
19815 ATGAGATA
1 ATGAGATA
19823 TTATCTACCG
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
26 3 0.06
27 6 0.11
28 37 0.70
29 5 0.09
30 2 0.04
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.39
Consensus pattern (27 bp):
ATGAGATAATATTTAGTAAGTATTATT
Found at i:22475 original size:17 final size:18
Alignment explanation
Indices: 22453--22491 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
22443 AATATGAGTC
*
22453 TAATTATTA-TTTTATTT
1 TAATTAGTATTTTTATTT
22470 TAATTAGTATTTTTATTT
1 TAATTAGTATTTTTATTT
22488 TAAT
1 TAAT
22492 CTAAATAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
TAATTAGTATTTTTATTT
Found at i:22623 original size:20 final size:21
Alignment explanation
Indices: 22598--22645 Score: 89
Period size: 20 Copynumber: 2.3 Consensus size: 21
22588 TTTTTAAGAG
22598 TATATATCATATTGCTAATC-
1 TATATATCATATTGCTAATCT
22618 TATATATCATATTGCTAATCT
1 TATATATCATATTGCTAATCT
22639 TATATAT
1 TATATAT
22646 GTAGTTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.35, C:0.12, G:0.04, T:0.48
Consensus pattern (21 bp):
TATATATCATATTGCTAATCT
Found at i:35634 original size:22 final size:22
Alignment explanation
Indices: 35609--35662 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
35599 ATATATAATG
*
35609 AAATAATAAT-TTATCAGAAAGT
1 AAATAAT-ATCTTATCAAAAAGT
* *
35631 AAATTATATCTTATTAAAAAGT
1 AAATAATATCTTATCAAAAAGT
*
35653 AAATTATATC
1 AAATAATATC
35663 ATGAGCTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.37
Consensus pattern (22 bp):
AAATAATATCTTATCAAAAAGT
Found at i:36568 original size:15 final size:14
Alignment explanation
Indices: 36550--36662 Score: 59
Period size: 16 Copynumber: 7.2 Consensus size: 14
36540 GACAATATAT
36550 AATATTGTAATAATA
1 AATATT-TAATAATA
* *
36565 AATATTTAAAAATT
1 AATATTTAATAATA
36579 AAT-TTTATATAATA
1 AATATTTA-ATAATA
*
36593 AATTAATTTTATATATAA
1 AA-T-ATTTAATA-AT-A
36611 ATATAGATTTTAATAAATA
1 A-AT--A-TTTAAT-AATA
36630 AATATATTAATAATA
1 AATAT-TTAATAATA
36645 ACATATTATAATAA-A
1 A-ATATT-TAATAATA
36660 AAT
1 AAT
36663 TTACCTAAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 27
0.70 0.06 0.24
Matches are distributed among these distances:
13 4 0.05
14 17 0.22
15 16 0.21
16 19 0.24
17 5 0.06
18 5 0.06
19 4 0.05
20 7 0.09
21 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (14 bp):
AATATTTAATAATA
Found at i:36607 original size:20 final size:18
Alignment explanation
Indices: 36574--36632 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 18
36564 AAATATTTAA
36574 AAATTAATTTTATATAAT
1 AAATTAATTTTATATAAT
36592 AAATTAATTTTATAT-AT
1 AAATTAATTTTATATAAT
36609 AAATATAGATTTTA-ATAAAT
1 AAAT-TA-ATTTTATAT-AAT
36629 AAAT
1 AAAT
36633 ATATTAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.16
18 19 0.51
19 6 0.16
20 6 0.16
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AAATTAATTTTATATAAT
Found at i:36834 original size:32 final size:32
Alignment explanation
Indices: 36798--36881 Score: 111
Period size: 32 Copynumber: 2.6 Consensus size: 32
36788 ATTCGAACTT
*
36798 GAACTCGAAAAA-GCTTGAACTTGAAAAGGTTC
1 GAACTC-AAAAAGGCTCGAACTTGAAAAGGTTC
36830 GAACTCAAAAAGGCTCGAACTTGAAAAGGTTC
1 GAACTCAAAAAGGCTCGAACTTGAAAAGGTTC
36862 GAAC-CTAAATAA-GCTCGAAC
1 GAACTC-AAA-AAGGCTCGAAC
36882 CTAAAAAAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
31 6 0.12
32 40 0.83
33 2 0.04
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.19
Consensus pattern (32 bp):
GAACTCAAAAAGGCTCGAACTTGAAAAGGTTC
Found at i:36857 original size:16 final size:16
Alignment explanation
Indices: 36798--36865 Score: 73
Period size: 16 Copynumber: 4.2 Consensus size: 16
36788 ATTCGAACTT
* *
36798 GAACTCGAAAAAGCTT
1 GAACTCGAAAAGGCTC
* *
36814 GAACTTGAAAAGGTTC
1 GAACTCGAAAAGGCTC
*
36830 GAACTCAAAAAGGCTC
1 GAACTCGAAAAGGCTC
* *
36846 GAACTTGAAAAGGTTC
1 GAACTCGAAAAGGCTC
36862 GAAC
1 GAAC
36866 CTAAATAAGC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.19
Consensus pattern (16 bp):
GAACTCGAAAAGGCTC
Found at i:36951 original size:16 final size:16
Alignment explanation
Indices: 36915--36945 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36905 AGTCCGAATT
*
36915 TAAATAAATTCAAACC
1 TAAAAAAATTCAAACC
36931 TAAAAAAATTCAAAC
1 TAAAAAAATTCAAAC
36946 TCAAAATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.23
Consensus pattern (16 bp):
TAAAAAAATTCAAACC
Found at i:40211 original size:29 final size:28
Alignment explanation
Indices: 40169--40239 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
40159 CTTCATGGTC
*
40169 TATATATA-AT-TTATATTATTACA-ACTA
1 TATATATATATATTATATAATTA-ATAC-A
40196 TATATATATATATTATATAATTAATACA
1 TATATATATATATTATATAATTAATACA
*
40224 TATAT-TATATAATATA
1 TATATATATATATTATA
40240 CAATAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 18 0.46
28 9 0.23
29 12 0.31
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (28 bp):
TATATATATATATTATATAATTAATACA
Found at i:41409 original size:15 final size:15
Alignment explanation
Indices: 41389--41437 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
41379 GGAAAATCAA
41389 TTTGAAACAGCCAAT
1 TTTGAAACAGCCAAT
***
41404 TTTG-AA-ATTTAA-
1 TTTGAAACAGCCAAT
41416 TTTGAAACAGCCAAT
1 TTTGAAACAGCCAAT
41431 TTTGAAA
1 TTTGAAA
41438 TTCAATTTGA
Statistics
Matches: 25, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
12 4 0.16
13 5 0.20
14 5 0.20
15 11 0.44
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (15 bp):
TTTGAAACAGCCAAT
Found at i:41410 original size:27 final size:27
Alignment explanation
Indices: 41380--41452 Score: 128
Period size: 27 Copynumber: 2.7 Consensus size: 27
41370 CAGCTGGTAG
*
41380 GAAAATCAATTTGAAACAGCCAATTTT
1 GAAATTCAATTTGAAACAGCCAATTTT
*
41407 GAAATTTAATTTGAAACAGCCAATTTT
1 GAAATTCAATTTGAAACAGCCAATTTT
41434 GAAATTCAATTTGAAACAG
1 GAAATTCAATTTGAAACAG
41453 TGAAGGTTGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (27 bp):
GAAATTCAATTTGAAACAGCCAATTTT
Found at i:46119 original size:14 final size:14
Alignment explanation
Indices: 46100--46168 Score: 74
Period size: 14 Copynumber: 5.1 Consensus size: 14
46090 GGTAGGAAAA
46100 TCAATTTGAAACAG
1 TCAATTTGAAACAG
*
46114 TCAATTTTG-AA-AT
1 TCAA-TTTGAAACAG
46127 TCAATTTGAAACAG
1 TCAATTTGAAACAG
*
46141 TCAATTTTG-AA-AT
1 TCAA-TTTGAAACAG
46154 TCAATTTGAAACAG
1 TCAATTTGAAACAG
46168 T
1 T
46169 GAAGGTTGCA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
12 8 0.18
13 14 0.31
14 15 0.33
15 8 0.18
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (14 bp):
TCAATTTGAAACAG
Found at i:46132 original size:13 final size:12
Alignment explanation
Indices: 46095--46164 Score: 59
Period size: 13 Copynumber: 5.3 Consensus size: 12
46085 TAGCTGGTAG
*
46095 GAAAATCAATTT
1 GAAATTCAATTT
*
46107 GAAACAGTCAATTTT
1 G-AA-ATTCAA-TTT
46122 GAAATTCAATTT
1 GAAATTCAATTT
*
46134 GAAACAGTCAATTTT
1 G-AA-ATTCAA-TTT
46149 GAAATTCAATTT
1 GAAATTCAATTT
46161 GAAA
1 GAAA
46165 CAGTGAAGGT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
12 12 0.25
13 14 0.29
14 14 0.29
15 8 0.17
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.34
Consensus pattern (12 bp):
GAAATTCAATTT
Found at i:46133 original size:27 final size:27
Alignment explanation
Indices: 46095--46168 Score: 139
Period size: 27 Copynumber: 2.7 Consensus size: 27
46085 TAGCTGGTAG
*
46095 GAAAATCAATTTGAAACAGTCAATTTT
1 GAAATTCAATTTGAAACAGTCAATTTT
46122 GAAATTCAATTTGAAACAGTCAATTTT
1 GAAATTCAATTTGAAACAGTCAATTTT
46149 GAAATTCAATTTGAAACAGT
1 GAAATTCAATTTGAAACAGT
46169 GAAGGTTGCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (27 bp):
GAAATTCAATTTGAAACAGTCAATTTT
Found at i:51293 original size:15 final size:15
Alignment explanation
Indices: 51273--51324 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
51263 TTTTTATCAG
51273 ATTATATTTATAATA
1 ATTATATTTATAATA
* *
51288 ATTATAATCATAATA
1 ATTATATTTATAATA
*
51303 AATAT-TATTATAATTA
1 ATTATAT-TTATAA-TA
51319 ATTATA
1 ATTATA
51325 ATAAATTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 22 0.79
16 6 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATATTTATAATA
Found at i:51957 original size:21 final size:21
Alignment explanation
Indices: 51931--51970 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
51921 TGTATGATGC
* *
51931 TTCCATTAAGGTAATTATATG
1 TTCCATCAACGTAATTATATG
51952 TTCCATCAACGTAATTATA
1 TTCCATCAACGTAATTATA
51971 AAAATATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (21 bp):
TTCCATCAACGTAATTATATG
Found at i:53706 original size:2 final size:2
Alignment explanation
Indices: 53701--53729 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53691 ATATATATAT
53701 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
53730 TATAGTGTAT
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:56395 original size:10 final size:8
Alignment explanation
Indices: 56368--56401 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
56358 TACAATTTTT
56368 TATTTAAA
1 TATTTAAA
56376 TATTTAAA
1 TATTTAAA
56384 TATTAATAAA
1 TATT--TAAA
56394 TATTTAAA
1 TATTTAAA
56402 ATCTTTTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 16 0.67
10 8 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TATTTAAA
Found at i:56952 original size:203 final size:203
Alignment explanation
Indices: 56506--57896 Score: 2412
Period size: 203 Copynumber: 6.9 Consensus size: 203
56496 ATTAGGTGAA
* * * *
56506 CTTAATATCTACAAAAATTAAAATCAAAAACTTTGACTACTGAAAAACCTTGAA-GCTAGTTTCC
1 CTTAATATTTACAAAAATTAAAATCGAAAACTTTGGCTACTGGAAAACCTT-AAGGCTAGTTTCC
* * * ** *
56570 GTCATTTGTGTTAGACTCTTAAAAATTTTTCATATTTAGAAATTTTTAAAAATTGATCATTGGCA
65 GCCATTTGTGTTAGACTCCTAAAAATTTTTCATACTTAGAAATTTTTGGAAATTGATCATTGGTA
* *
56635 A-TTTTTTCGAAAATTTTCAAATTTAAGTATTATCATAAATTATGGAAACAAATTATGTAAATAC
130 ACTTTTTTAGAAAATTTTCAAATTTAAGTATTATCATAAATTATGGAGACAAATTATGTAAATAC
56699 AATAAAATT
195 AATAAAATT
* * * * * * *
56708 GTTAAAATTTTCAAAAATTTAAATCAAAAACTTTAGCTACTGAAAAACCTTAAGGCTAGTTTCCG
1 CTTAATATTTACAAAAATTAAAATCGAAAACTTTGGCTACTGGAAAACCTTAAGGCTAGTTTCCG
56773 CCATTTGTGTTAGACTCCTAAAAATTTTTCATACTTAGAAATTTTTGGAAATTGATCATTGGTAA
66 CCATTTGTGTTAGACTCCTAAAAATTTTTCATACTTAGAAATTTTTGGAAATTGATCATTGGTAA
56838 CTTTTTTAGAAAATTTTCAAATTTAAGTATTATCATAAATTATGGAGACAAATTATGTAAATACA
131 CTTTTTTAGAAAATTTTCAAATTTAAGTATTATCATAAATTATGGAGACAAATTATGTAAATACA
56903 ATAAAATT
196 ATAAAATT
*
56911 CTTAATATTTACAAAAATTAAAATCGAAAACTTTGGCTACTGGAAAACCTTAAGGTTAGTTTCCG
1 CTTAATATTTACAAAAATTAAAATCGAAAACTTTGGCTACTGGAAAACCTTAAGGCTAGTTTCCG
56976 CCATTTGTGTTAGACTCCTAAAAATTTTTCATACTTAGAAATTTTTGGAAATTGATCATTGGTAA
66 CCATTTGTGTTAGACTCCTAAAAATTTTTCATACTTAGAAATTTTTGGAAATTGATCATTGGTAA
57041 CTTTTTTAGAAAATTTTCAAATTTAAGTATTATCATAAATTATGGAGACAAATTATGTAAATACA
131 CTTTTTTAGAAAATTTTCAAATTTAAGTATTATCATAAATTATGGAGACAAATTATGTAAATACA
57106 ATAAAATT
196 ATAAAATT
57114 CTTAATATTTACAAAAATTAAAATCGAAAACTTTGGCTACTGGAAAACCTTAAGGCTAGTTTCCG
1 CTTAATATTTACAAAAATTAAAATCGAAAACTTTGGCTACTGGAAAACCTTAAGGCTAGTTTCCG
57179 CCATTTGTGTTAGACTCCTAAAAATTTTTCATACTTAGAAATTTTTGGAAATTGATCATTGGTAA
66 CCATTTGTGTTAGACTCCTAAAAATTTTTCATACTTAGAAATTTTTGGAAATTGATCATTGGTAA
*
57244 CTTTTTTAGAAAATTTTCAAATTTAAGTATTATTATAAATTATGGAGACAAATTATGTAAATACA
131 CTTTTTTAGAAAATTTTCAAATTTAAGTATTATCATAAATTATGGAGACAAATTATGTAAATACA
57309 ATAAAATT
196 ATAAAATT
57317 CTTAATATTTACAAAAATTAAAATCGAAAACTTTGGCTACTGGAAAACCTTAAGGCTAGTTTCCG
1 CTTAATATTTACAAAAATTAAAATCGAAAACTTTGGCTACTGGAAAACCTTAAGGCTAGTTTCCG
*
57382 CCATTTGTGTTAGACTCCTAAAAATGTTTCATACTTAGAAATTTTTGGAAATTGATCATTGGTAA
66 CCATTTGTGTTAGACTCCTAAAAATTTTTCATACTTAGAAATTTTTGGAAATTGATCATTGGTAA
57447 CTTTTTTAGAAAATTTTCAAATTTAAGTATTATCATAAATTATGGAGACAAATTATGTAAATACA
131 CTTTTTTAGAAAATTTTCAAATTTAAGTATTATCATAAATTATGGAGACAAATTATGTAAATACA
57512 ATAAAATT
196 ATAAAATT
57520 CTTAATATTTACAAAAATTAAAATCGAAAACTTTGGCTACTGGAAAACCTTAAGGCTAGTTTCCG
1 CTTAATATTTACAAAAATTAAAATCGAAAACTTTGGCTACTGGAAAACCTTAAGGCTAGTTTCCG
57585 CCATTTGTGTTAGACTCCTAAAAATTTTTCATACTTAGAAATTTTTGGAAATTGATCATTGGTAA
66 CCATTTGTGTTAGACTCCTAAAAATTTTTCATACTTAGAAATTTTTGGAAATTGATCATTGGTAA
* * *
57650 CTTTTTTCGAAAATTTTCAAATTTAAGTATTATCATAAATTATGGAAACAAATTATGTAAATATA
131 CTTTTTTAGAAAATTTTCAAATTTAAGTATTATCATAAATTATGGAGACAAATTATGTAAATACA
57715 ATAAAATT
196 ATAAAATT
* * *
57723 CTTAATATTTACAAAAATTAAAATCGAAAACTTTGGCTACCGGAAAACCTTAAGGCTAGTTTTCA
1 CTTAATATTTACAAAAATTAAAATCGAAAACTTTGGCTACTGGAAAACCTTAAGGCTAGTTTCCG
* * ** *
57788 CCATTTGTGTTAGACTCCTAAGAA-TTTTCGATACGTAGAAATTTTTTAAAAATTGATCATTTGT
66 CCATTTGTGTTAGACTCCTAAAAATTTTTC-ATACTTAGAAA-TTTTTGGAAATTGATCATTGGT
* *
57852 AACTTTTTCA-AAAATTTTCAAATTTAAGTATTATTATAAATTATG
129 AACTTTTTTAGAAAATTTTCAAATTTAAGTATTATCATAAATTATG
57897 TAAATACAAT
Statistics
Matches: 1143, Mismatches: 42, Indels: 7
0.96 0.04 0.01
Matches are distributed among these distances:
201 2 0.00
202 119 0.10
203 995 0.87
204 27 0.02
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (203 bp):
CTTAATATTTACAAAAATTAAAATCGAAAACTTTGGCTACTGGAAAACCTTAAGGCTAGTTTCCG
CCATTTGTGTTAGACTCCTAAAAATTTTTCATACTTAGAAATTTTTGGAAATTGATCATTGGTAA
CTTTTTTAGAAAATTTTCAAATTTAAGTATTATCATAAATTATGGAGACAAATTATGTAAATACA
ATAAAATT
Found at i:58169 original size:27 final size:25
Alignment explanation
Indices: 58099--58170 Score: 63
Period size: 27 Copynumber: 2.7 Consensus size: 25
58089 AAAAATTAGG
* *
58099 AAAACAAAAATTTAAAATATATTTAG
1 AAAACAGAAA-TTAAAATATATTTAA
**
58125 AAAATTGAAAATTAAAAATATATAATTAA
1 AAAACAG-AAATT-AAAATATAT--TTAA
58154 AAAACAGAAATTAAAAT
1 AAAACAGAAATTAAAAT
58171 TAAAACCAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
26 6 0.17
27 17 0.47
28 5 0.14
29 8 0.22
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (25 bp):
AAAACAGAAATTAAAATATATTTAA
Found at i:61745 original size:2 final size:2
Alignment explanation
Indices: 61738--61779 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
61728 TAGTTGTTCC
61738 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
61780 TTATTGAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67637 original size:116 final size:117
Alignment explanation
Indices: 67434--67668 Score: 314
Period size: 116 Copynumber: 2.0 Consensus size: 117
67424 ACTTGTAATC
* **
67434 TATAACAAATTCATCACAAATCATATTAATCGAGTAAATTACTTTTTGGGGATCATTTAGTTTTG
1 TATAACAAATTAATCACAAATCATATTAATCGAGTAAATTACTTTTTGGAAATCATTTAGTTTTG
* * *
67499 ATCATGTAACTTTGAAATAT-A-ATATTTTGATCACTAACATTTACAAATAA
66 ATCATGTAACTTTAAAAAATAATATATTTTCATCACTAACATTTACAAATAA
* * **
67549 TATAACAAATTAATCAC-AATCATATTAATTGAGTAAATTGCTTTTTTTGGAAATTTTTTAGTTT
1 TATAACAAATTAATCACAAATCATATTAATCGAGTAAATTAC--TTTTTGGAAATCATTTAGTTT
* * *
67613 TGATCATTTAATTTTAAAAAATAATATATTTTCATCACTAACATTTATAAATAA
64 TGATCATGTAACTTTAAAAAATAATATATTTTCATCACTAACATTTACAAATAA
67667 TA
1 TA
67669 ATCTTTTGAT
Statistics
Matches: 103, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
114 22 0.21
115 16 0.16
116 35 0.34
117 1 0.01
118 29 0.28
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (117 bp):
TATAACAAATTAATCACAAATCATATTAATCGAGTAAATTACTTTTTGGAAATCATTTAGTTTTG
ATCATGTAACTTTAAAAAATAATATATTTTCATCACTAACATTTACAAATAA
Found at i:67935 original size:2 final size:2
Alignment explanation
Indices: 67928--67977 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
67918 TCTTGTCTTT
67928 TA 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 TA
67970 TA TA TA TA
1 TA TA TA TA
67978 GAGAGAGAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:69380 original size:15 final size:14
Alignment explanation
Indices: 69361--69390 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
69351 TATTTTATAT
69361 ATTTTTATAATTAA
1 ATTTTTATAATTAA
*
69375 ATTTTTATTATTAA
1 ATTTTTATAATTAA
69389 AT
1 AT
69391 AATAATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTTTTATAATTAA
Found at i:69380 original size:24 final size:22
Alignment explanation
Indices: 69340--69386 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 22
69330 TTAGATACGC
69340 TTTTATATTAATATTTTATATAT
1 TTTTATATTAATATTTTAT-TAT
69363 TTTTATAATTAA-ATTTTTATTAT
1 TTTTAT-ATTAATA-TTTTATTAT
69386 T
1 T
69387 AAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTATATTAATATTTTATTAT
Found at i:70340 original size:18 final size:18
Alignment explanation
Indices: 70317--70387 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 18
70307 AAATTTTATT
*
70317 ATAACATAATAAAAATAA
1 ATAACAAAATAAAAATAA
* **
70335 ATAACAAAATAGAAATTC
1 ATAACAAAATAAAAATAA
***
70353 ATAATCACGCTAAAAATAA
1 ATAA-CAAAATAAAAATAA
*
70372 ATAATAAAATAAAAAT
1 ATAACAAAATAAAAAT
70388 TCACATCAGA
Statistics
Matches: 38, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
18 26 0.68
19 12 0.32
ACGTcount: A:0.66, C:0.08, G:0.03, T:0.23
Consensus pattern (18 bp):
ATAACAAAATAAAAATAA
Found at i:70539 original size:2 final size:2
Alignment explanation
Indices: 70527--70561 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
70517 AATTATCTAA
70527 AT AT A- 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
70562 CAAATCTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:72463 original size:33 final size:35
Alignment explanation
Indices: 72426--72491 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
72416 AATTTTAAAT
* * *
72426 ATTTTTAGTAAAC-AA-AATTTTTTAAATAATTTG
1 ATTTTTAGGAAACTAATAATTTGTTAAAAAATTTG
72459 ATTTTTAGGAAACTAATAATTTGTTAAAAAATT
1 ATTTTTAGGAAACTAATAATTTGTTAAAAAATT
72492 CTATCATCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 12 0.43
34 2 0.07
35 14 0.50
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (35 bp):
ATTTTTAGGAAACTAATAATTTGTTAAAAAATTTG
Found at i:75135 original size:160 final size:161
Alignment explanation
Indices: 74835--75151 Score: 393
Period size: 160 Copynumber: 2.0 Consensus size: 161
74825 GAAGCATACA
* * * ** * * *
74835 AAGATGGATAAGTGATCCAAAGAAGATTCATTACTCTTAATGACATTGGAGATGTATCTTGACTA
1 AAGATGCATAAATGATCCAAAAAAGATTCACCACTCCTAATAACATTGAAGATGTATCTTGACTA
** * * ** *
74900 TTCTCAGCTAGGGATTAATTGAATTAAAGTCTATGACCAAAGCAAGATGTATTTAGGAGAAATTG
66 TAATCAGCTAGGGATTAATTGAATTAAAGTCTATGACCAAAGCAAAATGAATTTAAAAGAAATTA
74965 TTTCTTTAAATTCATATCATTAATCATAAGT
131 TTTCTTTAAATTCATATCATTAATCATAAGT
*
74996 AAGATGCATAAATGATCCAAAAAAGATTCACCACTCCTAATAACATTGAAGATGTATCTTGTCTA
1 AAGATGCATAAATGATCCAAAAAAGATTCACCACTCCTAATAACATTGAAGATGTATCTTGACTA
** * * * * * *
75061 TAATTGGCTA-TGATTAATTGGATTAAAGTTTTTGGCCAAAGTAAAATGAATTTAAAAGAAATTA
66 TAATCAGCTAGGGATTAATTGAATTAAAGTCTATGACCAAAGCAAAATGAATTTAAAAGAAATTA
* *
75125 TTTTTTTAAATTCATATTATTAATCAT
131 TTTCTTTAAATTCATATCATTAATCAT
75152 GAGTTGCAAA
Statistics
Matches: 130, Mismatches: 26, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
160 68 0.52
161 62 0.48
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (161 bp):
AAGATGCATAAATGATCCAAAAAAGATTCACCACTCCTAATAACATTGAAGATGTATCTTGACTA
TAATCAGCTAGGGATTAATTGAATTAAAGTCTATGACCAAAGCAAAATGAATTTAAAAGAAATTA
TTTCTTTAAATTCATATCATTAATCATAAGT
Found at i:82024 original size:2 final size:2
Alignment explanation
Indices: 82019--82043 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
82009 GATATACTTT
82019 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 T
82044 GTGTGTGTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:82746 original size:13 final size:12
Alignment explanation
Indices: 82727--82763 Score: 65
Period size: 12 Copynumber: 3.0 Consensus size: 12
82717 AAAAATAATC
82727 ATTTTTATATTT
1 ATTTTTATATTT
82739 ATTTTTTATATTT
1 A-TTTTTATATTT
82752 ATTTTTATATTT
1 ATTTTTATATTT
82764 TAATTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTTTTATATTT
Found at i:82765 original size:13 final size:13
Alignment explanation
Indices: 82727--82765 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
82717 AAAAATAATC
82727 ATTTTTATA-TTT
1 ATTTTTATATTTT
82739 ATTTTT-TATATTT
1 ATTTTTATAT-TTT
82752 ATTTTTATATTTT
1 ATTTTTATATTTT
82765 A
1 A
82766 ATTAAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.08
12 6 0.25
13 13 0.54
14 3 0.12
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTTTTATATTTT
Found at i:83548 original size:2 final size:2
Alignment explanation
Indices: 83541--83568 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
83531 CGTTGTTTAA
83541 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
83569 CTAACCCATT
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):
AT
Found at i:83708 original size:28 final size:28
Alignment explanation
Indices: 83676--83732 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
83666 TTATCTTGTC
83676 TAAGTAAATTTTATTTAAATGTATTAGT
1 TAAGTAAATTTTATTTAAATGTATTAGT
*
83704 TAAGTTAATTTTATTTAAATGTATTAGT
1 TAAGTAAATTTTATTTAAATGTATTAGT
83732 T
1 T
83733 GTATCATGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (28 bp):
TAAGTAAATTTTATTTAAATGTATTAGT
Found at i:83793 original size:18 final size:19
Alignment explanation
Indices: 83765--83804 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
83755 TTTAAAAATA
* *
83765 AATATAAATAATTTTATTT
1 AATATAAATAATATCATTT
83784 AATA-AAATAATATCATTT
1 AATATAAATAATATCATTT
83802 AAT
1 AAT
83805 TCATTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
AATATAAATAATATCATTT
Found at i:84026 original size:22 final size:24
Alignment explanation
Indices: 83975--84027 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
83965 AAAAAAAATA
83975 ATATTTAATAAATCTTTAAAGTTTT
1 ATATTTAATAAA-CTTTAAAGTTTT
*
84000 ATATTTAATAAA-TTT-GAGTTTT
1 ATATTTAATAAACTTTAAAGTTTT
*
84022 TTATTT
1 ATATTT
84028 TATTATTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 11 0.42
23 3 0.12
25 12 0.46
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.57
Consensus pattern (24 bp):
ATATTTAATAAACTTTAAAGTTTT
Found at i:91258 original size:24 final size:27
Alignment explanation
Indices: 91185--91255 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
91175 AAACAAGCCT
* *
91185 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
91213 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
91240 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
91256 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:93177 original size:21 final size:22
Alignment explanation
Indices: 93139--93184 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
93129 ATTTGTTGAA
* **
93139 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
93160 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
93182 ACT
1 ACT
93185 TGTCTGAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:95795 original size:28 final size:27
Alignment explanation
Indices: 95745--95825 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 27
95735 TTTGACAAAT
* * *
95745 AAATAAGCCTCCATATTTGACAAATACA
1 AAATAA-CCACCATTTTTGACAAACACA
*
95773 AAGGA-AACCACCATTTTTAACAAACACA
1 AA--ATAACCACCATTTTTGACAAACACA
*
95801 AAATAATCACCATTTTTGACAAACA
1 AAATAACCACCATTTTTGACAAACA
95826 AATGGGTGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
26 1 0.02
27 19 0.43
28 21 0.48
29 2 0.05
30 1 0.02
ACGTcount: A:0.48, C:0.22, G:0.06, T:0.23
Consensus pattern (27 bp):
AAATAACCACCATTTTTGACAAACACA
Found at i:96251 original size:25 final size:25
Alignment explanation
Indices: 96192--96253 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 25
96182 AAGAAATATC
96192 AATT-CAATTAAGAAATGATAAAAA
1 AATTACAATTAAGAAATGATAAAAA
96216 AATTATCAATTAAGAAATGATAAAAA
1 AATTA-CAATTAAGAAATGATAAAAA
96242 AACTTA-AATTAA
1 AA-TTACAATTAA
96254 AATTATAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.11
25 6 0.17
26 22 0.63
27 3 0.09
ACGTcount: A:0.61, C:0.05, G:0.06, T:0.27
Consensus pattern (25 bp):
AATTACAATTAAGAAATGATAAAAA
Found at i:97314 original size:16 final size:17
Alignment explanation
Indices: 97288--97326 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
97278 ATGTTAGAAG
97288 AAAATATTTAAA-ATAAT
1 AAAA-ATTTAAAGATAAT
*
97305 AAAAATTTAAAGATATT
1 AAAAATTTAAAGATAAT
97322 AAAAA
1 AAAAA
97327 ATAAAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
AAAAATTTAAAGATAAT
Found at i:97375 original size:21 final size:21
Alignment explanation
Indices: 97345--97419 Score: 64
Period size: 22 Copynumber: 3.6 Consensus size: 21
97335 ATTTTATTAT
* *
97345 AAATTTAATTTTTAAATCATA
1 AAATTAAATTTTTAAATAATA
* **
97366 AAATTAAATTTTTTAAGTTTTA
1 AAATTAAA-TTTTTAAATAATA
97388 AAATTATAA-TTTT-AATAATA
1 AAATTA-AATTTTTAAATAATA
*
97408 AAAATAAATTTT
1 AAATTAAATTTT
97420 CACTATAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
19 2 0.05
20 12 0.28
21 11 0.26
22 16 0.37
23 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (21 bp):
AAATTAAATTTTTAAATAATA
Found at i:98079 original size:3 final size:3
Alignment explanation
Indices: 98071--98115 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
98061 TGAATATCTT
*
98071 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
98116 GCATGATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:98260 original size:4 final size:4
Alignment explanation
Indices: 98251--98277 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
98241 CGCTTCCTTG
98251 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
98278 TGGTATAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:99810 original size:19 final size:19
Alignment explanation
Indices: 99782--99819 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
99772 TACTATCACA
*
99782 ATCTTTTGAAGTTGAATCT
1 ATCTTCTGAAGTTGAATCT
99801 ATCTTCTGAAGTTGAATCT
1 ATCTTCTGAAGTTGAATCT
99820 TTCATTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (19 bp):
ATCTTCTGAAGTTGAATCT
Found at i:99897 original size:35 final size:35
Alignment explanation
Indices: 99851--99922 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
99841 ACACAATGAT
99851 ACCTTACATTGATATGCTTTGTTCTTACATTATAA
1 ACCTTACATTGATATGCTTTGTTCTTACATTATAA
* *
99886 ACCTTACATTGATATGCTTTGTTTTTGCATTATAA
1 ACCTTACATTGATATGCTTTGTTCTTACATTATAA
99921 AC
1 AC
99923 TTGGTACTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.46
Consensus pattern (35 bp):
ACCTTACATTGATATGCTTTGTTCTTACATTATAA
Found at i:103087 original size:11 final size:11
Alignment explanation
Indices: 103071--103095 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
103061 TTTTATATTC
103071 TTATTTTCTTT
1 TTATTTTCTTT
103082 TTATTTTCTTT
1 TTATTTTCTTT
103093 TTA
1 TTA
103096 GCTCATAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (11 bp):
TTATTTTCTTT
Found at i:104602 original size:13 final size:13
Alignment explanation
Indices: 104584--104610 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
104574 GCAATACATG
104584 ATTAAAAGTTAAA
1 ATTAAAAGTTAAA
104597 ATTAAAAGTTAAA
1 ATTAAAAGTTAAA
104610 A
1 A
104611 CATTAAAGAG
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:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (13 bp):
ATTAAAAGTTAAA
Found at i:108688 original size:25 final size:24
Alignment explanation
Indices: 108635--108690 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
108625 AGAATTTCAC
*
108635 GTGATGTAACATGTAGTATAAAAT
1 GTGATGTAACATGTAGTAGAAAAT
108659 GTGATGTAACATGTTA-TAGGAAAAT
1 GTGATGTAACATG-TAGTA-GAAAAT
*
108684 TTGATGT
1 GTGATGT
108691 GAATAATGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 15 0.54
25 13 0.46
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.36
Consensus pattern (24 bp):
GTGATGTAACATGTAGTAGAAAAT
Found at i:109941 original size:28 final size:29
Alignment explanation
Indices: 109885--109961 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 29
109875 GGAATAAAGT
* **
109885 CGGGGTTGGAGTATCCCC-TTGGAGGTAA
1 CGGGGTTGGAGTATCCCCGATGGAAATAA
109913 CGGGGTTGGAGTATCCCCGAT-GAAATAA
1 CGGGGTTGGAGTATCCCCGATGGAAATAA
** *
109941 CAAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
109962 TGTGAAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 41 0.98
29 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.25
Consensus pattern (29 bp):
CGGGGTTGGAGTATCCCCGATGGAAATAA
Found at i:110120 original size:52 final size:51
Alignment explanation
Indices: 109947--110120 Score: 179
Period size: 52 Copynumber: 3.3 Consensus size: 51
109937 ATAACAAGGT
* * * *
109947 TGGAGTATCCTCGATTGTGAAAAAATTGGTGTTTTTGGAAATAAAATCGGAGC
1 TGGAGTATCCCCGATTGTGGAAAAATTGGTG-TTTT-GAAATAAAATCAGAGA
* *** * *
110000 TGGAGTATCCCTGATTAAAGAAAAATTGGTGTTTTGAAAATAAAA-CCGGGA
1 TGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTG-AAATAAAATCAGAGA
* *
110051 TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAATCAGAGA
1 -TGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTT-GAAATAAAATCAGAGA
*
110104 TGGAATATCCCCGATTG
1 TGGAGTATCCCCGATTG
110121 CGGAGAATTG
Statistics
Matches: 99, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
51 4 0.04
52 65 0.66
53 30 0.30
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.30
Consensus pattern (51 bp):
TGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTGAAATAAAATCAGAGA
Found at i:112507 original size:20 final size:21
Alignment explanation
Indices: 112463--112517 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
112453 AAAATTCCCA
112463 AATGTATCGATACA-AAGATC
1 AATGTATCGATACATAAGATC
*
112483 CATGTATCGATACATGAA-AT-
1 AATGTATCGATACAT-AAGATC
112503 AATGTATCGATACAT
1 AATGTATCGATACAT
112518 TTCCTTGGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 27 0.87
21 2 0.06
22 2 0.06
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATAAGATC
Found at i:112560 original size:19 final size:18
Alignment explanation
Indices: 112536--112603 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
112526 CAGTAGCTAA
112536 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
112555 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
112570 -T-TGTATCGATACAACAC
1 TTATGTATCGATACAA-AC
112587 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
112604 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 2 0.05
19 27 0.63
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:112576 original size:13 final size:13
Alignment explanation
Indices: 112558--112582 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
112548 ACAATACTTA
112558 TGTATCGATACAT
1 TGTATCGATACAT
112571 TGTATCGATACA
1 TGTATCGATACA
112583 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:112580 original size:32 final size:32
Alignment explanation
Indices: 112539--112601 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
112529 TAGCTAATTA
*
112539 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
112571 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
112602 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:113267 original size:19 final size:18
Alignment explanation
Indices: 113225--113267 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
113215 TAATTAAAAA
* *
113225 AATATAAATTAAAATTAT
1 AATATAAAATAAAATGAT
113243 AGATATAAAATAAAATGAT
1 A-ATATAAAATAAAATGAT
113262 GAATAT
1 -AATAT
113268 GTAAATCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 19 0.90
20 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (18 bp):
AATATAAAATAAAATGAT
Found at i:113821 original size:21 final size:21
Alignment explanation
Indices: 113808--113859 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
113798 AATTCATATA
113808 TTTATAATTATAATTATATTAT
1 TTTAT-ATTATAATTATATTAT
* *
113830 TTTATATTATAAATATTTAATAT
1 TTTATATTAT-AAT-TATATTAT
113853 TTTATAT
1 TTTATAT
113860 ATTTATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 5 0.19
22 8 0.31
23 13 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTATATTATAATTATATTAT
Found at i:113846 original size:16 final size:16
Alignment explanation
Indices: 113827--113906 Score: 66
Period size: 16 Copynumber: 5.4 Consensus size: 16
113817 ATAATTATAT
113827 TATTTTATATTATAAA
1 TATTTTATATTATAAA
* *
113843 TATTTAATATT-T-TA
1 TATTTTATATTATAAA
*
113857 TATATT-TA-TATAAA
1 TATTTTATATTATAAA
*
113871 -ATTTTATA-TATTAA
1 TATTTTATATTATAAA
*
113885 TAATTTATATTATAAA
1 TATTTTATATTATAAA
113901 -ATTTTA
1 TATTTTA
113907 ATATATTTAT
Statistics
Matches: 49, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
12 1 0.02
13 7 0.14
14 13 0.27
15 13 0.27
16 15 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTTATATTATAAA
Found at i:113911 original size:13 final size:13
Alignment explanation
Indices: 113864--113911 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 13
113854 TTATATATTT
113864 ATATAAAATTTTA
1 ATATAAAATTTTA
113877 TATATTAATAATTTATA
1 -ATA-TAA-AATTT-TA
*
113894 TTATAAAATTTTA
1 ATATAAAATTTTA
113907 ATATA
1 ATATA
113912 TTTATGTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 6 0.21
14 8 0.28
15 6 0.21
16 7 0.24
17 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATATAAAATTTTA
Found at i:115926 original size:17 final size:18
Alignment explanation
Indices: 115874--115931 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 18
115864 TAATTATTTT
*
115874 AATATATAAATATATATTAA
1 AATATATAAA-A-AAATTAA
* *
115894 AATATTTAATAAAATTAA
1 AATATATAAAAAAATTAA
115912 AAT-TATAAAAAAATTAA
1 AATATATAAAAAAATTAA
115929 AAT
1 AAT
115932 CCCCAACATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
17 15 0.45
18 9 0.27
19 1 0.03
20 8 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATATATAAAAAAATTAA
Found at i:122631 original size:13 final size:13
Alignment explanation
Indices: 122613--122638 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
122603 CAATTTTTTG
122613 TGTATCGATACAT
1 TGTATCGATACAT
122626 TGTATCGATACAT
1 TGTATCGATACAT
122639 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:125202 original size:13 final size:13
Alignment explanation
Indices: 125184--125209 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
125174 ATAATCACCC
125184 TGTATCGATACAA
1 TGTATCGATACAA
125197 TGTATCGATACAA
1 TGTATCGATACAA
125210 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:127300 original size:15 final size:15
Alignment explanation
Indices: 127280--127310 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
127270 ATTTCGTTTG
*
127280 GAGCTTCTTCATTTT
1 GAGCTTCGTCATTTT
127295 GAGCTTCGTCATTTT
1 GAGCTTCGTCATTTT
127310 G
1 G
127311 GGCATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.48
Consensus pattern (15 bp):
GAGCTTCGTCATTTT
Found at i:129143 original size:21 final size:21
Alignment explanation
Indices: 129114--129158 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
129104 AAGTTTTCAT
*
129114 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
129134 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
129156 TTT
1 TTT
129159 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:131404 original size:13 final size:13
Alignment explanation
Indices: 131386--131411 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
131376 CAATTTTTTG
131386 TGTATCGATACAT
1 TGTATCGATACAT
131399 TGTATCGATACAT
1 TGTATCGATACAT
131412 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:133426 original size:22 final size:25
Alignment explanation
Indices: 133401--133449 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
133391 AGCGCATTAA
133401 TACTAA-TT-AAAAATTAT-TTTAT
1 TACTAATTTAAAAAATTATATTTAT
133423 TACTAATTTTAAAAAATTATATTTAT
1 TACTAA-TTTAAAAAATTATATTTAT
133449 T
1 T
133450 GTATTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.26
24 2 0.09
25 9 0.39
26 6 0.26
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (25 bp):
TACTAATTTAAAAAATTATATTTAT
Found at i:133679 original size:27 final size:28
Alignment explanation
Indices: 133644--133696 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
133634 TTTTAAAGTA
133644 TTTTTATTTATATTT-T-ATTAAATTAGT
1 TTTTTATTTAT-TTTATGATTAAATTAGT
133671 TTTTTATTTATTTTATGATTAAATTA
1 TTTTTATTTATTTTATGATTAAATTA
133697 TAAAATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 3 0.12
27 12 0.50
28 9 0.38
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (28 bp):
TTTTTATTTATTTTATGATTAAATTAGT
Found at i:134932 original size:21 final size:22
Alignment explanation
Indices: 134902--134942 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
134892 TATTTTAATA
*
134902 TTATA-ATTTTAATTTAATTTT
1 TTATATATTTTAATTAAATTTT
*
134923 TTATATTTTTTAATTAAATT
1 TTATATATTTTAATTAAATT
134943 GTGTCAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTATATATTTTAATTAAATTTT
Found at i:135330 original size:10 final size:9
Alignment explanation
Indices: 135310--135373 Score: 51
Period size: 9 Copynumber: 7.0 Consensus size: 9
135300 ATTTAATTTA
135310 ATTTTATAT
1 ATTTTATAT
135319 ATTTTATA-
1 ATTTTATAT
135327 ATATTTATAT
1 AT-TTTATAT
*
135337 GATTATT-TTT
1 -ATT-TTATAT
* *
135347 ATTTAATTT
1 ATTTTATAT
*
135356 AATTTATAT
1 ATTTTATAT
135365 ATTTTATAT
1 ATTTTATAT
135374 TTAATTTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
8 3 0.07
9 34 0.77
10 3 0.07
11 4 0.09
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (9 bp):
ATTTTATAT
Found at i:135361 original size:14 final size:15
Alignment explanation
Indices: 135327--135376 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 15
135317 ATATTTTATA
*
135327 ATATTTATATGA-TT
1 ATATTTATATAATTT
* *
135341 ATTTTTATTTAATTT
1 ATATTTATATAATTT
*
135356 A-ATTTATATATTTT
1 ATATTTATATAATTT
135370 ATATTTA
1 ATATTTA
135377 ATTTTTATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 20 0.71
15 8 0.29
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
ATATTTATATAATTT
Found at i:135391 original size:20 final size:20
Alignment explanation
Indices: 135352--135391 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
135342 TTTTTATTTA
**
135352 ATTTAATTTATATATTTTAT
1 ATTTAATTTATATAAATTAT
*
135372 ATTTAATTTTTATAAATTAT
1 ATTTAATTTATATAAATTAT
135392 TCATACAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTAATTTATATAAATTAT
Found at i:135392 original size:25 final size:24
Alignment explanation
Indices: 135338--135392 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
135328 TATTTATATG
*
135338 ATTATTTTTATTTAATTTAATTTAT
1 ATTATTTTTATTTAATTT-ATTTAA
135363 A-TATTTTATATTTAATTT-TTATAA
1 ATTATTTT-TATTTAATTTATT-TAA
135387 ATTATT
1 ATTATT
135393 CATACAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 2 0.08
24 9 0.35
25 15 0.58
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
ATTATTTTTATTTAATTTATTTAA
Found at i:135591 original size:16 final size:16
Alignment explanation
Indices: 135548--135591 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
135538 TTATTATTAA
*
135548 ATTAAAAAATAAATTT
1 ATTAAAAAATTAATTT
*
135564 ATTAAAATATTAA-TT
1 ATTAAAAAATTAATTT
135579 ATATAAAAAATTA
1 AT-TAAAAAATTA
135592 TATAAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTAAAAAATTAATTT
Found at i:137157 original size:3 final size:3
Alignment explanation
Indices: 137149--137187 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
137139 TAATTGGTTC
* *
137149 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTA CTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
137188 CTGCAGTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.03, C:0.03, G:0.31, T:0.64
Consensus pattern (3 bp):
TTG
Found at i:137937 original size:34 final size:33
Alignment explanation
Indices: 137893--138109 Score: 249
Period size: 34 Copynumber: 6.4 Consensus size: 33
137883 AAAAACCACT
*
137893 ATTTAATCAACAATGGCAACCTACCAAATCTACC
1 ATTTAATCAACAATGGTAACCTACCAAATC-ACC
*
137927 ATTTAGTCAACAATGGTAAGCC-ACCAAATCACCC
1 ATTTAATCAACAATGGTAA-CCTACCAAATCA-CC
* * **
137961 ATTTAATCAATAATGGTAAGCTACCAAATTTCTC
1 ATTTAATCAACAATGGTAACCTACCAAATCAC-C
* *
137995 ATTTAATCAACAATGGTAAGCTACCAAATCTCCC
1 ATTTAATCAACAATGGTAACCTACCAAATC-ACC
* *
138029 ATTTAGTCAACAATGGCAAACC-ACCAAATCACCC
1 ATTTAATCAACAATGG-TAACCTACCAAATCA-CC
* *
138063 ATTTAATCAATAATGGTAAACTACCAAATCACC
1 ATTTAATCAACAATGGTAACCTACCAAATCACC
138096 ATTTAATCAACAAT
1 ATTTAATCAACAAT
138110 TCTCCCACTT
Statistics
Matches: 156, Mismatches: 19, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
33 21 0.13
34 129 0.83
35 6 0.04
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (33 bp):
ATTTAATCAACAATGGTAACCTACCAAATCACC
Found at i:138005 original size:68 final size:67
Alignment explanation
Indices: 137893--138109 Score: 283
Period size: 68 Copynumber: 3.2 Consensus size: 67
137883 AAAAACCACT
* * *
137893 ATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAATCA
1 ATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAATCA
137958 CCC
65 CCC
* * * * *
137961 ATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAATCT
1 ATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAATCA
138026 CCC
65 CCC
* * * * *
138029 ATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAATAATGGTAAACTACCAAATCA
1 ATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAATCA
138094 -CC
65 CCC
138096 ATTTAATCAACAAT
1 ATTTAATCAACAAT
138110 TCTCCCACTT
Statistics
Matches: 129, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
67 17 0.13
68 111 0.86
69 1 0.01
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (67 bp):
ATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATCAC
CC
Found at i:138033 original size:102 final size:101
Alignment explanation
Indices: 137893--138109 Score: 353
Period size: 102 Copynumber: 2.1 Consensus size: 101
137883 AAAAACCACT
* *
137893 ATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAATCA
1 ATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAATCA
* **
137958 CCCATTTAATCAATAATGGTAAGCTACCAAATTTCTC
66 CCCATTTAATCAATAATGGTAAACTACCAAATCAC-C
* * *
137995 ATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATCA
1 ATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAATCA
138060 CCCATTTAATCAATAATGGTAAACTACCAAATCACC
66 CCCATTTAATCAATAATGGTAAACTACCAAATCACC
138096 ATTTAATCAACAAT
1 ATTTAATCAACAAT
138110 TCTCCCACTT
Statistics
Matches: 107, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
101 15 0.14
102 92 0.86
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (101 bp):
ATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAATCA
CCCATTTAATCAATAATGGTAAACTACCAAATCACC
Found at i:142202 original size:19 final size:19
Alignment explanation
Indices: 142175--142237 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
142165 TCACATGTAC
* *
142175 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
142194 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
142213 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
142232 AGTACC
1 AGTACC
142238 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:142588 original size:34 final size:33
Alignment explanation
Indices: 142540--142758 Score: 235
Period size: 34 Copynumber: 6.5 Consensus size: 33
142530 TGGTAAAAAC
*
142540 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
142573 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
142607 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** * *
142641 TTCTCATTTAATCAACAATGGTAAGCTACTAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
142675 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
* * *
142709 CACTCATTTAATTAATAATGGTAAACTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
142743 CACCATTTAATCAACA
1 CACCATTTAATCAACA
142759 TGAAAACCCA
Statistics
Matches: 154, Mismatches: 23, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
33 19 0.12
34 129 0.84
35 6 0.04
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:142656 original size:68 final size:68
Alignment explanation
Indices: 142542--142758 Score: 276
Period size: 68 Copynumber: 3.2 Consensus size: 68
142532 GTAAAAACCA
* * *
142542 CCATTTAATCAACAATGGCAACCTACCAAATCTAC-CATTTAGTCAACAATGGTAAGCCACCAAA
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACTCATTTAATCAACAATGGTAAGCTACCAAA
142606 TCAC
65 TCAC
* * * * *
142610 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACTAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCAAAT
*
142675 CTC
66 CAC
* * * * * *
142678 CCATTTAGTCAACAATGGCAAACCACCAAATCACTCATTTAATTAATAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCAAAT
142743 CA-
66 CAC
142745 CCATTTAATCAACA
1 CCATTTAATCAACA
142759 TGAAAACCCA
Statistics
Matches: 127, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
67 15 0.12
68 112 0.88
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.27
Consensus pattern (68 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCAAAT
CAC
Found at i:142684 original size:102 final size:101
Alignment explanation
Indices: 142540--142758 Score: 330
Period size: 102 Copynumber: 2.2 Consensus size: 101
142530 TGGTAAAAAC
* *
142540 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
*
142605 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
** * * * *
142641 TTCTCATTTAATCAACAATGGTAAGCTACTAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
* *
142706 AATCACTCATTTAATTAATAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
142743 CACCATTTAATCAACA
1 CACCATTTAATCAACA
142759 TGAAAACCCA
Statistics
Matches: 104, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 14 0.13
102 90 0.87
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
Found at i:143233 original size:21 final size:20
Alignment explanation
Indices: 143207--143250 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
143197 AATAAATAAG
143207 TATTATGTAATTA-TTTTAATT
1 TATTAT-TAA-TACTTTTAATT
143228 TATTATTAATACTTTTTAATT
1 TATTATTAATAC-TTTTAATT
143249 TA
1 TA
143251 AATAATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 2 0.10
20 3 0.14
21 16 0.76
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
TATTATTAATACTTTTAATT
Found at i:143301 original size:26 final size:26
Alignment explanation
Indices: 143263--143323 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
143253 TAATATTATT
143263 ATATTTA-ATATTTATAATTTA-TAAAA
1 ATATTTATAT-TTTAT-ATTTATTAAAA
*
143289 ATATTTATCATTTTATTTTTATTAAAA
1 ATATTTAT-ATTTTATATTTATTAAAA
*
143316 TTATTTAT
1 ATATTTAT
143324 TATAATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 11 0.37
27 17 0.57
28 2 0.07
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
ATATTTATATTTTATATTTATTAAAA
Found at i:144154 original size:17 final size:19
Alignment explanation
Indices: 144112--144156 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
144102 TTTATTTAAA
144112 TTTAATTATAAAAATATAAT
1 TTTAATTATAAAAATAT-AT
144132 TATTAATTA-AAAAATAT-T
1 T-TTAATTATAAAAATATAT
144150 TTTAATT
1 TTTAATT
144157 TTTTTATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 6 0.25
18 2 0.08
20 9 0.38
21 7 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTAATTATAAAAATATAT
Found at i:148328 original size:8 final size:8
Alignment explanation
Indices: 148317--148349 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
148307 TTTTTTTTTT
148317 GGGGGG-G
1 GGGGGGAG
*
148324 GGGGGGTG
1 GGGGGGAG
148332 GGGGGGAG
1 GGGGGGAG
148340 GGGGGGAG
1 GGGGGGAG
148348 GG
1 GG
148350 TTTGGAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.06, C:0.00, G:0.91, T:0.03
Consensus pattern (8 bp):
GGGGGGAG
Found at i:148335 original size:14 final size:15
Alignment explanation
Indices: 148316--148344 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
148306 TTTTTTTTTT
148316 TGGGGGGG-GGGGGG
1 TGGGGGGGAGGGGGG
148330 TGGGGGGGAGGGGGG
1 TGGGGGGGAGGGGGG
148345 GAGGGTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.03, C:0.00, G:0.90, T:0.07
Consensus pattern (15 bp):
TGGGGGGGAGGGGGG
Found at i:155110 original size:24 final size:24
Alignment explanation
Indices: 155078--155125 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
155068 TTATGGTTTC
155078 ATGCTCTCCAAAATGTGTTAATGT
1 ATGCTCTCCAAAATGTGTTAATGT
155102 ATGCTCTCCAAAATGTGTTAATGT
1 ATGCTCTCCAAAATGTGTTAATGT
155126 TATTTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (24 bp):
ATGCTCTCCAAAATGTGTTAATGT
Found at i:156528 original size:3 final size:3
Alignment explanation
Indices: 156522--156547 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
156512 AAAGAAGATG
156522 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
156548 TTATTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:161733 original size:13 final size:13
Alignment explanation
Indices: 161715--161797 Score: 67
Period size: 13 Copynumber: 5.5 Consensus size: 13
161705 ACAAAAATGT
161715 TGTATCGATACAA
1 TGTATCGATACAA
161728 TGTATCGATACATAA
1 TGTATCGATAC--AA
161743 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
161760 TGTATCGATACATAA
1 TGTATCGATAC--AA
161775 GTTTGTATCGATACAA
1 ---TGTATCGATACAA
161791 TGTATCG
1 TGTATCG
161798 CTACGAAGCT
Statistics
Matches: 59, Mismatches: 0, Indels: 22
0.73 0.00 0.27
Matches are distributed among these distances:
13 29 0.49
15 4 0.07
16 2 0.03
17 2 0.03
18 11 0.19
19 11 0.19
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:161738 original size:32 final size:32
Alignment explanation
Indices: 161696--161797 Score: 170
Period size: 32 Copynumber: 3.2 Consensus size: 32
161686 TTCAACGATT
* * *
161696 TGTATTGATACAAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
161728 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
161760 TGTATCGATACATAAGT-TTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
161791 TGTATCG
1 TGTATCG
161798 CTACGAAGCT
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
31 21 0.31
32 46 0.69
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:161860 original size:13 final size:13
Alignment explanation
Indices: 161842--161866 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
161832 ATTACTCAAA
161842 TGTATCGATACAT
1 TGTATCGATACAT
161855 TGTATCGATACA
1 TGTATCGATACA
161867 CTGATTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:161920 original size:52 final size:52
Alignment explanation
Indices: 161875--162004 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
161865 CACTGATTTT
*
161875 TGTATCGATACATGCAGGCAATTTTGCCCAGATGTATTGATACACTATGAAA
1 TGTATCGATACATGCAGGCAATTTTGCCCAGATGTATCGATACACTATGAAA
* * *
161927 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCAATACACTATGAAA
1 TGTATCGATACATGCAGGCAATTTTGCCCAGATGTATCGATACACTATGAAA
161979 TGTATCGATACATGCAGGCAAATTTT
1 TGTATCGATACATGCAGGC-AATTTT
162005 CATATTTCGG
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
52 66 0.93
53 5 0.07
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAATTTTGCCCAGATGTATCGATACACTATGAAA
Found at i:173619 original size:1 final size:1
Alignment explanation
Indices: 173609--173703 Score: 82
Period size: 1 Copynumber: 95.0 Consensus size: 1
173599 TGGCAATTGG
* * * ** * * * *
173609 AAAAAGAAAAAAACAAAACAAAAAAAAAGGAAAAAGAAAAAAAAAAAACAAAACAAAAAAAAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
173674 GAAAAAGAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
173704 GTGAAGATTT
Statistics
Matches: 74, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.87, C:0.05, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:173641 original size:30 final size:30
Alignment explanation
Indices: 173607--173702 Score: 129
Period size: 30 Copynumber: 3.0 Consensus size: 30
173597 CATGGCAATT
173607 GGAAAAAGAAAAAAACAAAACAAAAAAAAA
1 GGAAAAAGAAAAAAACAAAACAAAAAAAAA
173637 GGAAAAAGAAAAAAAAAAAACAAAACAAAAAAAAAA
1 GGAAAAAG-----AAAAAAACAAAAC-AAAAAAAAA
*
173673 GGAAAAAGAAAAAAAAAAAACAAAAAAAAA
1 GGAAAAAGAAAAAAACAAAACAAAAAAAAA
173703 AGTGAAGATT
Statistics
Matches: 59, Mismatches: 1, Indels: 12
0.82 0.01 0.17
Matches are distributed among these distances:
30 17 0.29
31 12 0.20
35 13 0.22
36 17 0.29
ACGTcount: A:0.85, C:0.05, G:0.09, T:0.00
Consensus pattern (30 bp):
GGAAAAAGAAAAAAACAAAACAAAAAAAAA
Found at i:173661 original size:35 final size:35
Alignment explanation
Indices: 173608--173703 Score: 167
Period size: 36 Copynumber: 2.7 Consensus size: 35
173598 ATGGCAATTG
173608 GAAAAAGAAAAAAACAAAACAAAAAAAAAGGAAAAA
1 GAAAAA-AAAAAAACAAAACAAAAAAAAAGGAAAAA
173644 GAAAAAAAAAAAACAAAACAAAAAAAAAAGGAAAAA
1 GAAAAAAAAAAAACAAAAC-AAAAAAAAAGGAAAAA
173680 GAAAAAAAAAAAACAAAA-AAAAAA
1 GAAAAAAAAAAAACAAAACAAAAAA
173704 GTGAAGATTT
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
34 6 0.10
35 13 0.22
36 40 0.68
ACGTcount: A:0.86, C:0.05, G:0.08, T:0.00
Consensus pattern (35 bp):
GAAAAAAAAAAAACAAAACAAAAAAAAAGGAAAAA
Found at i:178500 original size:20 final size:20
Alignment explanation
Indices: 178467--178533 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
178457 ATGAAAATTA
* *
178467 TGACGGAATGTCACAAGTTG
1 TGACGAAATATCACAAGTTG
* * *
178487 TGATGGAACT-TCACAAGTTA
1 TGA-CGAAATATCACAAGTTG
178507 TGACGAAATATCACAAGTTG
1 TGACGAAATATCACAAGTTG
178527 TGACGAA
1 TGACGAA
178534 TTCAATGATA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.11
20 31 0.82
21 3 0.08
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (20 bp):
TGACGAAATATCACAAGTTG
Found at i:184176 original size:18 final size:16
Alignment explanation
Indices: 184139--184185 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 16
184129 CGAGGGAAAG
184139 AAAAGAAAGAGAAAAA
1 AAAAGAAAGAGAAAAA
184155 AAAAGGAAAGAGAATGAAA
1 AAAA-GAAAGAGAA--AAA
184174 AAAAGAAAGAGA
1 AAAAGAAAGAGA
184186 GGAAAGGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.14
17 9 0.32
18 8 0.29
19 7 0.25
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (16 bp):
AAAAGAAAGAGAAAAA
Found at i:184293 original size:11 final size:11
Alignment explanation
Indices: 184263--184303 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
184253 ATTATTATAA
*
184263 ATTTATATAAT
1 ATTTATATATT
184274 ATTTAATATATT
1 ATTT-ATATATT
184286 ATTTATATATT
1 ATTTATATATT
184297 -TTTATAT
1 ATTTATAT
184304 TTGTATCGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 7 0.25
11 11 0.39
12 10 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTTATATATT
Found at i:184850 original size:17 final size:17
Alignment explanation
Indices: 184816--184862 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
184806 TAGGTTTGTA
*
184816 TTATATTTTAATTTATC
1 TTATATTTTAATTAATC
184833 TTATATTTT-ATATAATC
1 TTATATTTTAAT-TAATC
* *
184850 TGATATTGTAATT
1 TTATATTTTAATT
184863 CAATTTAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 2 0.08
17 21 0.84
18 2 0.08
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (17 bp):
TTATATTTTAATTAATC
Found at i:185004 original size:20 final size:21
Alignment explanation
Indices: 184956--185004 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
184946 TAATTTTTTA
*
184956 AAAATATTTTTATATTTATTT
1 AAAATATTTTTATATCTATTT
***
184977 ATGTTATTTTT-TATCTATTT
1 AAAATATTTTTATATCTATTT
184997 AAAATATT
1 AAAATATT
185005 ATAAATTTAT
Statistics
Matches: 21, Mismatches: 7, Indels: 1
0.72 0.24 0.03
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
AAAATATTTTTATATCTATTT
Found at i:189172 original size:2 final size:2
Alignment explanation
Indices: 189167--189217 Score: 79
Period size: 2 Copynumber: 26.0 Consensus size: 2
189157 TATCCATAAC
189167 AT AT AT -T AT AT A- AT CAT 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
189208 AT AT AT AT AT
1 AT AT AT AT AT
189218 GTGGATGTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.04
2 42 0.91
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:189428 original size:26 final size:26
Alignment explanation
Indices: 189396--189452 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
189386 TCTTAATCCA
* *
189396 ATTATTTTTGACATATATTACAAATT
1 ATTATTTTCGACATAGATTACAAATT
*
189422 ATTATTTTCGACCTAGATTACAAATT
1 ATTATTTTCGACATAGATTACAAATT
189448 ATTAT
1 ATTAT
189453 AATTGAACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (26 bp):
ATTATTTTCGACATAGATTACAAATT
Found at i:190621 original size:16 final size:16
Alignment explanation
Indices: 190584--190625 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
190574 AATTGAAAAG
*
190584 ATTTTTTTAA-ATTAA
1 ATTTTTTAAATATTAA
* *
190599 ATATTTTAAATATTTA
1 ATTTTTTAAATATTAA
190615 ATTTTTTAAAT
1 ATTTTTTAAAT
190626 TAATAAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTTTAAATATTAA
Found at i:197594 original size:16 final size:17
Alignment explanation
Indices: 197562--197594 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
197552 TATAATTGTG
*
197562 TAAATACTCGATTATAA
1 TAAATACTCGATGATAA
197579 TAAATA-TCGATGATAA
1 TAAATACTCGATGATAA
197595 ATGTTAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.33
Consensus pattern (17 bp):
TAAATACTCGATGATAA
Found at i:199439 original size:2 final size:2
Alignment explanation
Indices: 199434--199464 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
199424 ACAGACAGTC
199434 AT AT AT AT AT AT AT A- 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
199465 TGAAGTCCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:199454 original size:13 final size:13
Alignment explanation
Indices: 199436--199461 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
199426 AGACAGTCAT
199436 ATATATATATATA
1 ATATATATATATA
199449 ATATATATATATA
1 ATATATATATATA
199462 TATTGAAGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:199454 original size:15 final size:15
Alignment explanation
Indices: 199434--199463 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
199424 ACAGACAGTC
199434 ATATATATATATATA
1 ATATATATATATATA
199449 ATATATATATATATA
1 ATATATATATATATA
199464 TTGAAGTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:200206 original size:19 final size:19
Alignment explanation
Indices: 200182--200249 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
200172 AATTCAACAA
200182 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
200201 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
200216 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
200233 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
200250 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:200221 original size:13 final size:13
Alignment explanation
Indices: 200203--200227 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
200193 ACATAAGTTT
200203 TGTATCGATACAA
1 TGTATCGATACAA
200216 TGTATCGATACA
1 TGTATCGATACA
200228 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:200225 original size:32 final size:32
Alignment explanation
Indices: 200184--200246 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
200174 TTCAACAATT
*
200184 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
200216 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
200247 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:200307 original size:13 final size:13
Alignment explanation
Indices: 200289--200314 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
200279 CATTTTTCTG
200289 TGTATCGATACAT
1 TGTATCGATACAT
200302 TGTATCGATACAT
1 TGTATCGATACAT
200315 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Done.