Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015132.1 Kokia drynarioides strain JFW-HI SEQ_130176, 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: 328324
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 197 characters in sequence are not A, C, G, or T
Found at i:1813 original size:29 final size:28
Alignment explanation
Indices: 1711--1813 Score: 100
Period size: 29 Copynumber: 3.5 Consensus size: 28
1701 TTTCTTTGCA
1711 TTTGGAAGTTTAAGGGTAAAAATGTAATT
1 TTTGGAAGTTT-AGGGTAAAAATGTAATT
* * *
1740 TTTGAAAGTTTTTGGGTTAAAATAG-AATT
1 TTTGGAAG-TTTAGGGTAAAAAT-GTAATT
* * *
1769 TTTAGAAGTTCGAGGGTCAAAATGTAATT
1 TTTGGAAGTT-TAGGGTAAAAATGTAATT
1798 TTTGGATAGTTTAGGG
1 TTTGGA-AGTTTAGGG
1814 ACCTTCAGGG
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
28 3 0.05
29 48 0.81
30 8 0.14
ACGTcount: A:0.33, C:0.02, G:0.25, T:0.40
Consensus pattern (28 bp):
TTTGGAAGTTTAGGGTAAAAATGTAATT
Found at i:2464 original size:15 final size:14
Alignment explanation
Indices: 2444--2483 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
2434 AAAAAACTGC
2444 TTCTTTCGTTTTTT
1 TTCTTTCGTTTTTT
2458 ATTCTTTC-TTTTTT
1 -TTCTTTCGTTTTTT
2472 TTCTTT-GTTTTT
1 TTCTTTCGTTTTT
2484 AAGACCAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 11 0.46
14 6 0.25
15 7 0.29
ACGTcount: A:0.03, C:0.12, G:0.05, T:0.80
Consensus pattern (14 bp):
TTCTTTCGTTTTTT
Found at i:3659 original size:17 final size:17
Alignment explanation
Indices: 3618--3680 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
3608 TTAATTAATT
*
3618 TTAATTTTAAA-TTCAAA
1 TTAAATTTAAACTT-AAA
* *
3635 TTAGATTTAAACTTAAT
1 TTAAATTTAAACTTAAA
*
3652 TTAAATTTTAACTTAAA
1 TTAAATTTAAACTTAAA
*
3669 CTAAATTTAAAC
1 TTAAATTTAAAC
3681 CCAAAATGAA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
17 35 0.95
18 2 0.05
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (17 bp):
TTAAATTTAAACTTAAA
Found at i:9905 original size:29 final size:30
Alignment explanation
Indices: 9862--9920 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
9852 TGACATGATT
9862 GACTTAATTGATTTTT-ATCATTTTAAGAG
1 GACTTAATTGATTTTTAATCATTTTAAGAG
* *
9891 GACTTAATTGTTTTTTAATTATTTTAAGAG
1 GACTTAATTGATTTTTAATCATTTTAAGAG
9921 AGGTTGAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.51
Consensus pattern (30 bp):
GACTTAATTGATTTTTAATCATTTTAAGAG
Found at i:13093 original size:14 final size:14
Alignment explanation
Indices: 13074--13104 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13064 AGAATAGATT
13074 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
13088 TTTAATTAATTAAA
1 TTTAATTAAATAAA
13102 TTT
1 TTT
13105 TTTAAACCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:14459 original size:4 final size:4
Alignment explanation
Indices: 14450--14479 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
14440 TTAAGAGAGC
14450 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
14480 ATTATTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:17815 original size:21 final size:21
Alignment explanation
Indices: 17789--17832 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
17779 ATTGATATCT
17789 ATTTTAACAAAAATTTTAAAA
1 ATTTTAACAAAAATTTTAAAA
* * *
17810 ATTTTAATATAATTTTTAAAA
1 ATTTTAACAAAAATTTTAAAA
17831 AT
1 AT
17833 CCATATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTTAACAAAAATTTTAAAA
Found at i:22807 original size:2 final size:2
Alignment explanation
Indices: 22800--22825 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22790 GAAGATCCAA
22800 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
22826 TTTAGGATAT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27337 original size:160 final size:160
Alignment explanation
Indices: 27073--27391 Score: 566
Period size: 160 Copynumber: 2.0 Consensus size: 160
27063 CCAAAAAGGC
*
27073 AAGGGCAAATCTCTAAGCTCGACGTCTATAGAGAAAGTATCGATACAACTAGATACAAATTGTGT
1 AAGGGCAAATCTCTAAGCTCGACGTCTATAGACAAAGTATCGATACAACTAGATACAAATTGTGT
27138 TCTTTTAGAATAGATTTAGACCAATTAAACACCTTAATGATGGTTAACTGTAGTTCTGTGACTTA
66 TCTTTTAGAATAGATTTAGACCAATTAAACACCTTAATGATGGTTAACTGTAGTTCTGTGACTTA
27203 AAAGGTGGGTTCATAACCATTGTAGCAATT
131 AAAGGTGGGTTCATAACCATTGTAGCAATT
*
27233 AAGGGCAAATCTCTAAGCTCGACGTCTATAGACCAAGTATCGATACAACTAGATACAAATTGTGT
1 AAGGGCAAATCTCTAAGCTCGACGTCTATAGACAAAGTATCGATACAACTAGATACAAATTGTGT
* * *
27298 TCTTTTAGAATAGATTTAGATCAATTAAACACGTTAATGATGGTTAACTGTAGTTTTGTGACTTA
66 TCTTTTAGAATAGATTTAGACCAATTAAACACCTTAATGATGGTTAACTGTAGTTCTGTGACTTA
** *
27363 AAAGGTGGGTTTGTAACCATTGTTGCAAT
131 AAAGGTGGGTTCATAACCATTGTAGCAAT
27392 CTTTGCGTGA
Statistics
Matches: 151, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
160 151 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Consensus pattern (160 bp):
AAGGGCAAATCTCTAAGCTCGACGTCTATAGACAAAGTATCGATACAACTAGATACAAATTGTGT
TCTTTTAGAATAGATTTAGACCAATTAAACACCTTAATGATGGTTAACTGTAGTTCTGTGACTTA
AAAGGTGGGTTCATAACCATTGTAGCAATT
Found at i:35158 original size:20 final size:19
Alignment explanation
Indices: 35130--35167 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
35120 ACATAATATA
*
35130 TCCTTTGTGTTTTAATTACT
1 TCCTATGTGTTTT-ATTACT
35150 TCCTATGTGTTTTATTAC
1 TCCTATGTGTTTTATTAC
35168 ATAATCGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.16, C:0.16, G:0.11, T:0.58
Consensus pattern (19 bp):
TCCTATGTGTTTTATTACT
Found at i:36189 original size:29 final size:30
Alignment explanation
Indices: 36130--36193 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
36120 ATAGTTTATC
* *
36130 TTTATAATTTTTAAAAAATTAAATTAAAAT
1 TTTATAATTTTTAAAAAATCAAAATAAAAT
* * *
36160 TTTATCATTTTT-AAAAGTCAAAATATAAT
1 TTTATAATTTTTAAAAAATCAAAATAAAAT
36189 TTTAT
1 TTTAT
36194 TTTTACTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (30 bp):
TTTATAATTTTTAAAAAATCAAAATAAAAT
Found at i:37332 original size:100 final size:100
Alignment explanation
Indices: 37159--37360 Score: 404
Period size: 100 Copynumber: 2.0 Consensus size: 100
37149 AACTATGGGA
37159 TGTACTGGTCCTAAGTATGCTCTTTTGTTCCTAATTCTTCGCTACTACTATTTGTGTTTTGCATT
1 TGTACTGGTCCTAAGTATGCTCTTTTGTTCCTAATTCTTCGCTACTACTATTTGTGTTTTGCATT
37224 ACTTAGTAACAAAATCATCTAATTGTTCCTTCGTT
66 ACTTAGTAACAAAATCATCTAATTGTTCCTTCGTT
37259 TGTACTGGTCCTAAGTATGCTCTTTTGTTCCTAATTCTTCGCTACTACTATTTGTGTTTTGCATT
1 TGTACTGGTCCTAAGTATGCTCTTTTGTTCCTAATTCTTCGCTACTACTATTTGTGTTTTGCATT
37324 ACTTAGTAACAAAATCATCTAATTGTTCCTTCGTT
66 ACTTAGTAACAAAATCATCTAATTGTTCCTTCGTT
37359 TG
1 TG
37361 ATTTTATTCA
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 102 1.00
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.46
Consensus pattern (100 bp):
TGTACTGGTCCTAAGTATGCTCTTTTGTTCCTAATTCTTCGCTACTACTATTTGTGTTTTGCATT
ACTTAGTAACAAAATCATCTAATTGTTCCTTCGTT
Found at i:41286 original size:2 final size:2
Alignment explanation
Indices: 41273--41302 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
41263 TACTTTGAGA
*
41273 AT AT AG 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
41303 TTGTTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:43576 original size:20 final size:20
Alignment explanation
Indices: 43551--43589 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
43541 TAATATGTTC
43551 TAATGTGAT-TAATATAAAAT
1 TAATGT-ATATAATATAAAAT
*
43571 TAATGTATATAATTTAAAA
1 TAATGTATATAATATAAAA
43590 GCTATAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (20 bp):
TAATGTATATAATATAAAAT
Found at i:48926 original size:21 final size:21
Alignment explanation
Indices: 48891--48943 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
48881 AAATTATTAT
*
48891 AAATTTTTA-TTTAATAATAA
1 AAATCTTTAGTTTAATAATAA
48911 AAATCTTTAGTTTAATAATAA
1 AAATCTTTAGTTTAATAATAA
* *
48932 AGAGCTTTAGTT
1 AAATCTTTAGTT
48944 AATTAATCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (21 bp):
AAATCTTTAGTTTAATAATAA
Found at i:49598 original size:18 final size:19
Alignment explanation
Indices: 49575--49628 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
49565 ACAAAAAAAA
49575 ATATTATTTTCTTTTTA-T
1 ATATTATTTTCTTTTTACT
* *
49593 ATATTATTTCCCTTTTACTT
1 ATATTATTTTCTTTTTAC-T
49613 ATATT-TTCTTCTTTTT
1 ATATTATT-TTCTTTTT
49629 TTTTNNNNNN
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 15 0.52
19 2 0.07
20 12 0.41
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.69
Consensus pattern (19 bp):
ATATTATTTTCTTTTTACT
Found at i:49863 original size:19 final size:19
Alignment explanation
Indices: 49839--49881 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
49829 AAGCATAAAT
49839 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
49858 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
49877 TAAAT
1 TAAAT
49882 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:50489 original size:25 final size:25
Alignment explanation
Indices: 50455--50503 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
50445 ATCACCAACC
50455 CAATAACCCAAATCCTTTAAAAACT
1 CAATAACCCAAATCCTTTAAAAACT
*
50480 CAATAACCCAAATCCTTTTAAAAC
1 CAATAACCCAAATCCTTTAAAAAC
50504 CCAAACCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (25 bp):
CAATAACCCAAATCCTTTAAAAACT
Found at i:50514 original size:16 final size:17
Alignment explanation
Indices: 50484--50517 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
50474 AAAACTCAAT
50484 AACCCAAATCCTTTTAA
1 AACCCAAATCCTTTTAA
50501 AACCCAAA-CCTTTTAA
1 AACCCAAATCCTTTTAA
50517 A
1 A
50518 CCCTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.26
Consensus pattern (17 bp):
AACCCAAATCCTTTTAA
Found at i:50633 original size:11 final size:11
Alignment explanation
Indices: 50617--50655 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
50607 CAAGTCAAAC
50617 CGTTGACCGGT
1 CGTTGACCGGT
* *
50628 CGTTGATCGAT
1 CGTTGACCGGT
*
50639 CGTTGACCGGC
1 CGTTGACCGGT
50650 CGTTGA
1 CGTTGA
50656 TCGTGACTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.13, C:0.26, G:0.33, T:0.28
Consensus pattern (11 bp):
CGTTGACCGGT
Found at i:50645 original size:22 final size:22
Alignment explanation
Indices: 50617--50658 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
50607 CAAGTCAAAC
*
50617 CGTTGACCGGTCGTTGATCGAT
1 CGTTGACCGGCCGTTGATCGAT
50639 CGTTGACCGGCCGTTGATCG
1 CGTTGACCGGCCGTTGATCG
50659 TGACTTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.26, G:0.33, T:0.29
Consensus pattern (22 bp):
CGTTGACCGGCCGTTGATCGAT
Found at i:64644 original size:26 final size:26
Alignment explanation
Indices: 64564--64644 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
64554 TCTTGGTTTG
64564 CATGGTAGAAACATGTTATTGGCATA
1 CATGGTAGAAACATGTTATTGGCATA
* * * ** *
64590 CA-GATA-AAACTACT-ATCTTGGTTTG
1 CATGGTAGAAAC-A-TGTTATTGGCATA
64615 CATGGTAGAAACATGTTATTGGCATA
1 CATGGTAGAAACATGTTATTGGCATA
64641 CATG
1 CATG
64645 TATGCATGCA
Statistics
Matches: 38, Mismatches: 12, Indels: 10
0.63 0.20 0.17
Matches are distributed among these distances:
24 4 0.11
25 13 0.34
26 17 0.45
27 4 0.11
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (26 bp):
CATGGTAGAAACATGTTATTGGCATA
Found at i:64657 original size:16 final size:16
Alignment explanation
Indices: 64636--64674 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
64626 CATGTTATTG
**
64636 GCATACATGTATGCAT
1 GCATACATACATGCAT
64652 GCATACATACATGCAT
1 GCATACATACATGCAT
*
64668 ACATACA
1 GCATACA
64675 CACGTATACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (16 bp):
GCATACATACATGCAT
Found at i:64664 original size:12 final size:12
Alignment explanation
Indices: 64649--64674 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
64639 TACATGTATG
64649 CATGCATACATA
1 CATGCATACATA
64661 CATGCATACATA
1 CATGCATACATA
64673 CA
1 CA
64675 CACGTATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.27, G:0.08, T:0.23
Consensus pattern (12 bp):
CATGCATACATA
Found at i:69881 original size:6 final size:6
Alignment explanation
Indices: 69870--69896 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
69860 TTCAATTAAA
69870 TTTTGG TTTTGG TTTTGG TTTTGG TTT
1 TTTTGG TTTTGG TTTTGG TTTTGG TTT
69897 CCCACTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.30, T:0.70
Consensus pattern (6 bp):
TTTTGG
Found at i:74492 original size:23 final size:24
Alignment explanation
Indices: 74441--74493 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
74431 TTCTAGGTTG
74441 AATATGTTAAAAATGTTTTAATTAT
1 AATAT-TTAAAAATGTTTTAATTAT
74466 --TATTTAAGAAAT-TTTT-ATTAT
1 AATATTTAA-AAATGTTTTAATTAT
74487 AATATTT
1 AATATTT
74494 GAATTTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
21 5 0.20
22 8 0.32
23 12 0.48
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (24 bp):
AATATTTAAAAATGTTTTAATTAT
Found at i:76316 original size:36 final size:30
Alignment explanation
Indices: 76239--76317 Score: 131
Period size: 30 Copynumber: 2.6 Consensus size: 30
76229 TTAATATAAT
*
76239 ATTTGGTACTTGAACTTGACACTTTTTTTA
1 ATTTGGTACTTGAACTTGACACTTTTCTTA
76269 ATTTGGTACTTGAACTTGACACTTTTCTTA
1 ATTTGGTACTTGAACTTGACACTTTTCTTA
* *
76299 ATTTGGTACCTAAACTTGA
1 ATTTGGTACTTGAACTTGA
76318 TAAATTTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (30 bp):
ATTTGGTACTTGAACTTGACACTTTTCTTA
Found at i:76653 original size:58 final size:58
Alignment explanation
Indices: 76552--76736 Score: 212
Period size: 59 Copynumber: 3.2 Consensus size: 58
76542 ATAAATTTAT
* * * *
76552 GTACCAAATTGAATCTAAAAAAAGCTTAGGTACCAAATT-AGAAAAA-TGCCAAGTTCAG
1 GTACCAAATTG-A-GTAAAAAAAGTTTAAGTACCAAATTAAGAAAAAGTGTCAAGTTCAG
* * * *
76610 GTACCAAATTGAGTAAAAAAAGGTTTACGTACCAAATTAAGAAAAATTATCAAGTTTAG
1 GTACCAAATTGAGTAAAAAAA-GTTTAAGTACCAAATTAAGAAAAAGTGTCAAGTTCAG
* * *
76669 GTACTAAATTGGGTCAAAAAAAGTTTAAGTACCAAATTAAGAAAAAGTGTCAAGTTCAA
1 GTACCAAATTGAGT-AAAAAAAGTTTAAGTACCAAATTAAGAAAAAGTGTCAAGTTCAG
*
76728 ATACCAAAT
1 GTACCAAAT
76737 GTTATATTAA
Statistics
Matches: 108, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
56 8 0.07
57 15 0.14
58 18 0.17
59 60 0.56
60 7 0.06
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (58 bp):
GTACCAAATTGAGTAAAAAAAGTTTAAGTACCAAATTAAGAAAAAGTGTCAAGTTCAG
Found at i:76655 original size:28 final size:27
Alignment explanation
Indices: 76568--76714 Score: 89
Period size: 28 Copynumber: 5.1 Consensus size: 27
76558 AATTGAATCT
* *
76568 AAAAAAAGCTTAGGTACCAAATT-AGA
1 AAAAAAAGTTTAAGTACCAAATTAAGA
* * * *
76594 AAAATGCCAAGTTCAGGTACCAAATTGAGTA
1 AAAA---AAAGTTTAAGTACCAAATTAAG-A
* *
76625 AAAAAAGGTTTACGTACCAAATTAAGA
1 AAAAAAAGTTTAAGTACCAAATTAAGA
* * ** *
76652 AAAATTATCAAGTTTAGGTACTAAATTGGGTC
1 AAAA--A--AAGTTTAAGTACCAAATTAAG-A
76684 AAAAAAAGTTTAAGTACCAAATTAAGA
1 AAAAAAAGTTTAAGTACCAAATTAAGA
76711 AAAA
1 AAAA
76715 GTGTCAAGTT
Statistics
Matches: 92, Mismatches: 19, Indels: 19
0.71 0.15 0.15
Matches are distributed among these distances:
26 4 0.04
27 9 0.10
28 34 0.37
29 17 0.18
30 3 0.03
31 21 0.23
32 4 0.04
ACGTcount: A:0.50, C:0.11, G:0.16, T:0.24
Consensus pattern (27 bp):
AAAAAAAGTTTAAGTACCAAATTAAGA
Found at i:78165 original size:96 final size:96
Alignment explanation
Indices: 78030--78214 Score: 259
Period size: 96 Copynumber: 1.9 Consensus size: 96
78020 GAAAAGGATG
* ** **
78030 TTCGATTATCTCGATTTGAGGAAAGGTTGCACCTAGTAAGTTAAGGCGTAAATTTTC-AGAA-TC
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCGA-AACTC
78093 G-AATAAAAGGAAACATTGCCTCGATTAAGTGTA
65 GAAATAAAA-G-AACATTGCCTCGATTAAGTGTA
*
78126 TTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCGAAACTCG
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCGAAACTCG
*
78191 AAATAAAAGAATATTGCCTCGATT
66 AAATAAAAGAACATTGCCTCGATT
78215 TTAAAGTTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
96 67 0.85
97 5 0.06
98 7 0.09
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCGAAACTCG
AAATAAAAGAACATTGCCTCGATTAAGTGTA
Found at i:78472 original size:29 final size:29
Alignment explanation
Indices: 78440--78877 Score: 344
Period size: 29 Copynumber: 15.0 Consensus size: 29
78430 TGGATACCCG
* *
78440 GGGGT-AAAATGGTAATTTTGGGAAATTTT
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTT
* *
78469 GGGGTTAAAAATGGAATTTTTAGACA--TTG
1 GGGG-TAAAAATGGAATTTTTGGA-AGTTTT
* * *
78498 GGGGT-AAAAGGGTAA--TTTCGAGAGTTTC
1 GGGGTAAAAATGG-AATTTTTGGA-AGTTTT
* * ** * *
78526 GAGGTTGAAAATGGTGTTTTTGGACA-TCTG
1 G-GGGTAAAAATGGAATTTTTGGA-AGTTTT
* * *
78556 GGGGCAA-AATGGTAATTTTTGAAAGTTTC
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTT
* * *
78585 GGGGTCAAAAATGGAAATTTTGGAGGTTTG
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTT
*
78615 GGGGTAAAAATGGAATTTTTAG-AGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
*
78643 AGGGGTAAAATTGGAATTTTTGGAAGTTTT
1 -GGGGTAAAAATGGAATTTTTGGAAGTTTT
* * * *
78673 GTGGTCTAAAATGAAATTTTTGGAAGTTTG
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTT
*
78703 GGGGTAAAAATGTAATTTTTGGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
78732 GGGGTAAAAATGGAATTTTTGGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
* *
78761 GAGGTTAAAAAT-GAGATTTTTGGAAGTTTA
1 G-GGGTAAAAATGGA-ATTTTTGGAAGTTTT
78791 GGGGTAAAAATGGAATTTTTGGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
* * *
78820 GGGGTCTAAAATAGG-ATTTTTGGAAG-CTC
1 GGGGT-AAAAAT-GGAATTTTTGGAAGTTTT
*
78849 GAGGGTAAAAATGTAA-TTTTGGACAGTTT
1 G-GGGTAAAAATGGAATTTTTGGA-AGTTT
78878 AGGGACATTC
Statistics
Matches: 329, Mismatches: 54, Indels: 51
0.76 0.12 0.12
Matches are distributed among these distances:
26 6 0.02
27 6 0.02
28 24 0.07
29 158 0.48
30 114 0.35
31 21 0.06
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTT
Found at i:78571 original size:116 final size:118
Alignment explanation
Indices: 78412--78623 Score: 277
Period size: 116 Copynumber: 1.8 Consensus size: 118
78402 TGCAATCGGA
* * * *
78412 GTTGAAAATGAGACTTTTTGGATACCCGGGGGTAAAATGGTAATTTTGGGAAA-TTTTGGGGTTA
1 GTTGAAAATGAGACTTTTTGGACACCCGGGGGCAAAATGGTAATTTT-GGAAAGTTTCGGGGTCA
*
78476 AAAATGGAATTTTTAGA-CATTGGGGGTAAAAGGGTAATTTCGAGAGTTTCGAG
65 AAAATGGAAATTTTAGAGCATTGGGGGTAAAAGGGTAATTTCGAGAGTTTCGAG
** * * *
78529 GTTGAAAATG-GTGTTTTTGGACATCTGGGGGCAAAATGGTAATTTTTGAAAGTTTCGGGGTCAA
1 GTTGAAAATGAGACTTTTTGGACACCCGGGGGCAAAATGGTAATTTTGGAAAGTTTCGGGGTCAA
* **
78593 AAATGGAAATTTTGGAGGTTTGGGGGTAAAA
66 AAATGGAAATTTTAGAGCATTGGGGGTAAAA
78624 ATGGAATTTT
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
115 4 0.05
116 54 0.68
117 22 0.28
ACGTcount: A:0.30, C:0.06, G:0.32, T:0.33
Consensus pattern (118 bp):
GTTGAAAATGAGACTTTTTGGACACCCGGGGGCAAAATGGTAATTTTGGAAAGTTTCGGGGTCAA
AAATGGAAATTTTAGAGCATTGGGGGTAAAAGGGTAATTTCGAGAGTTTCGAG
Found at i:78606 original size:59 final size:58
Alignment explanation
Indices: 78439--78877 Score: 315
Period size: 59 Copynumber: 7.5 Consensus size: 58
78429 TTGGATACCC
* * *
78439 GGGGGTAAAATGGTAATTTTGGGAAA-TTTTGGGGTTAAAAATGGAATTTTTAGACA--TT
1 GGGGGAAAAATGG-AATTTT-TGAAAGTTTTGGGGTTAAAAATGGAATTTTTGGA-AGTTT
* * * * * * * ** *
78497 GGGGGTAAAAGGGTAA-TTTCGAGAGTTTCGAGGTTGAAAATGGTGTTTTTGGACA-TCT
1 GGGGGAAAAATGG-AATTTTTGAAAGTTTTGGGGTTAAAAATGGAATTTTTGGA-AGTTT
* * * * *
78555 GGGGGCAAAATGGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGAAATTTTGGAGGTTT
1 GGGGGAAAAATGG-AATTTTTGAAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTT
* *
78614 GGGGGTAAAAATGGAATTTTT-AGAGTTTTAGGGG-TAAAATTGGAATTTTTGGAAGTTTT
1 GGGGG-AAAAATGGAATTTTTGAAAGTTTT-GGGGTTAAAAATGGAATTTTTGGAAG-TTT
*** * * * *
78673 GTGGTCTAAAATGAAATTTTTGGAAG-TTTGGGGGTAAAAATGTAATTTTTGGAAGTTTT
1 G-GGGGAAAAATGGAATTTTTGAAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAG-TTT
* * *
78732 GGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAAT-GAGATTTTTGGAAGTTT
1 GGGGGAAAAATGGAATTTTTGAAAGTTTTGGGGTTAAAAATGGA-ATTTTTGGAAGTTT
* * * *
78790 AGGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCT-AAAATAGG-ATTTTTGGAAGCTC
1 -GGGGGAAAAATGGAATTTTTGAAAGTTTTGGGGT-TAAAAAT-GGAATTTTTGGAAGTTT
* * * *
78849 GAGGGTAAAAATGTAATTTTGGACAGTTT
1 G-GGGGAAAAATGGAATTTTTGAAAGTTT
78878 AGGGACATTC
Statistics
Matches: 313, Mismatches: 51, Indels: 33
0.79 0.13 0.08
Matches are distributed among these distances:
56 3 0.01
57 27 0.09
58 82 0.26
59 188 0.60
60 12 0.04
61 1 0.00
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36
Consensus pattern (58 bp):
GGGGGAAAAATGGAATTTTTGAAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTT
Found at i:78878 original size:88 final size:89
Alignment explanation
Indices: 78561--78881 Score: 374
Period size: 88 Copynumber: 3.6 Consensus size: 89
78551 ATCTGGGGGC
* * * *
78561 AAAATGGTAATTTTTGAAAGTTTCG-GGGTCAAAAATGGAAA-TTTTGGAGGTTTGGGGGTAAAA
1 AAAATGG-AATTTTTGGAAGTTTTGAGGGTCAAAAAT-GAAATTTTTGGAAGTTTAGGGGTAAAA
*
78624 ATGGAATTTTTAG-AGTTTTAGGGG-T
64 ATGGAATTTTTGGAAGTTTT-GGGGTT
* * *
78649 AAAATTGGAATTTTTGGAAGTTTTG-TGGTCTAAAATGAAATTTTTGGAAGTTTGGGGGTAAAAA
1 AAAA-TGGAATTTTTGGAAGTTTTGAGGGTCAAAAATGAAATTTTTGGAAGTTTAGGGGTAAAAA
* *
78713 TGTAATTTTTGGAAGTTTTGGGGTA
65 TGGAATTTTTGGAAGTTTTGGGGTT
* *
78738 AAAATGGAATTTTTGGAAGTTTTGA-GGTTAAAAATGAGATTTTTGGAAGTTTAGGGGTAAAAAT
1 AAAATGGAATTTTTGGAAGTTTTGAGGGTCAAAAATGAAATTTTTGGAAGTTTAGGGGTAAAAAT
78802 GGAATTTTTGGAAGTTTTGGGGTCT
66 GGAATTTTTGGAAGTTTTGGGGT-T
* * *
78827 AAAATAGG-ATTTTTGGAAG-CTCGAGGGT-AAAAATGTAA-TTTTGGACAGTTTAGGG
1 AAAAT-GGAATTTTTGGAAGTTTTGAGGGTCAAAAATGAAATTTTTGGA-AGTTTAGGG
78882 ACATTCAGGG
Statistics
Matches: 206, Mismatches: 18, Indels: 18
0.85 0.07 0.07
Matches are distributed among these distances:
87 11 0.05
88 161 0.78
89 32 0.16
90 2 0.01
ACGTcount: A:0.32, C:0.02, G:0.29, T:0.37
Consensus pattern (89 bp):
AAAATGGAATTTTTGGAAGTTTTGAGGGTCAAAAATGAAATTTTTGGAAGTTTAGGGGTAAAAAT
GGAATTTTTGGAAGTTTTGGGGTT
Found at i:79954 original size:3 final size:3
Alignment explanation
Indices: 79941--80026 Score: 57
Period size: 3 Copynumber: 27.7 Consensus size: 3
79931 CCTTTTTTAT
* * *
79941 TTA TTA TTTA TTA TTTA TTAA ATA TTA -TA GTTA TTA TCA ATA TTA TTA
1 TTA TTA -TTA TTA -TTA TT-A TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* * ** *
79989 TTA ATA TTA ATA TTA TTA TTA TTA AAA TAA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
80027 GCTGCTAATA
Statistics
Matches: 64, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
2 2 0.03
3 52 0.81
4 10 0.16
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:79968 original size:21 final size:18
Alignment explanation
Indices: 79942--80026 Score: 84
Period size: 18 Copynumber: 4.6 Consensus size: 18
79932 CTTTTTTATT
79942 TATTATTTATTATTTATTAAA
1 TATTA-TTATTA-TTATT-AA
*
79963 TATTA-TAGTTATTATCAA
1 TATTATTA-TTATTATTAA
*
79981 TATTATTATTAATATTAA
1 TATTATTATTATTATTAA
*
79999 TATTATTATTATTA-AAA
1 TATTATTATTATTATTAA
80016 TAATTATTATT
1 T-ATTATTATT
80027 GCTGCTAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
17 3 0.05
18 37 0.66
19 8 0.14
20 3 0.05
21 5 0.09
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (18 bp):
TATTATTATTATTATTAA
Found at i:80758 original size:17 final size:17
Alignment explanation
Indices: 80733--80775 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
80723 TTGTTTAATT
*
80733 TTAAATTTAAAATAAAC
1 TTAATTTTAAAATAAAC
*
80750 TTAATTTTAAAATAAAT
1 TTAATTTTAAAATAAAC
80767 TTAAATTTT
1 TT-AATTTT
80776 GTTGGGTCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAATTTTAAAATAAAC
Found at i:81292 original size:19 final size:20
Alignment explanation
Indices: 81260--81297 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
81250 CGTATATGTC
* *
81260 AAAATATAATTAAA-AGTTA
1 AAAATAAAAATAAACAGTTA
81279 AAAATAAAAATAAACAGTT
1 AAAATAAAAATAAACAGTT
81298 TCAACTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (20 bp):
AAAATAAAAATAAACAGTTA
Found at i:81820 original size:20 final size:20
Alignment explanation
Indices: 81775--81831 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
81765 ATATAAAAAT
* *
81775 ATTTAAAAATATATTTTTATA
1 ATTTTAAAATA-ATTTTAATA
* *
81796 CTTTTTAAATAATTTTAATA
1 ATTTTAAAATAATTTTAATA
81816 ATTTTAAAATAATTTT
1 ATTTTAAAATAATTTT
81832 TTATAATTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 22 0.73
21 8 0.27
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTTAAAATAATTTTAATA
Found at i:81826 original size:11 final size:10
Alignment explanation
Indices: 81798--81831 Score: 52
Period size: 9 Copynumber: 3.4 Consensus size: 10
81788 TTTTTATACT
81798 TTTTAAATAA
1 TTTTAAATAA
81808 TTTT-AATAA
1 TTTTAAATAA
81817 TTTTAAAATAA
1 TTTT-AAATAA
81828 TTTT
1 TTTT
81832 TTATAATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.41
10 4 0.18
11 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTTAAATAA
Found at i:81837 original size:21 final size:21
Alignment explanation
Indices: 81775--81840 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
81765 ATATAAAAAT
*
81775 ATTTAAAAAT-ATATTTTTATA
1 ATTTTAAAATAAT-TTTTTATA
* * *
81796 CTTTTTAAATAA-TTTTAATA
1 ATTTTAAAATAATTTTTTATA
81816 ATTTTAAAATAATTTTTTATA
1 ATTTTAAAATAATTTTTTATA
81837 ATTT
1 ATTT
81841 CTTTTTAACT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
20 17 0.47
21 18 0.50
22 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTAAAATAATTTTTTATA
Found at i:81839 original size:10 final size:10
Alignment explanation
Indices: 81782--81840 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
81772 AATATTTAAA
81782 AATATATTTTT
1 AATA-ATTTTT
*
81793 -ATACTTTTT
1 AATAATTTTT
81802 AAATAA-TTTT
1 -AATAATTTTT
*
81812 AATAATTTTAA
1 AATAATTTT-T
81823 AATAATTTTT
1 AATAATTTTT
*
81833 TATAATTT
1 AATAATTT
81841 CTTTTTAACT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
9 10 0.26
10 17 0.44
11 12 0.31
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (10 bp):
AATAATTTTT
Found at i:88104 original size:24 final size:21
Alignment explanation
Indices: 88070--88129 Score: 57
Period size: 24 Copynumber: 2.6 Consensus size: 21
88060 CGATTTTAGG
*
88070 TATTTTTTAATTCATTAAATAATA
1 TATTTTATAATTCA--AAA-AATA
88094 TATTTTATAATATCAAAAAATA
1 TATTTTATAAT-TCAAAAAATA
88116 TATTTATATTAATT
1 TATTT-TA-TAATT
88130 GTATAAGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
22 9 0.28
23 6 0.19
24 14 0.44
25 3 0.09
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTTTATAATTCAAAAAATA
Found at i:92807 original size:12 final size:13
Alignment explanation
Indices: 92787--92811 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
92777 TATTCAAGTT
92787 CTTATTTTTTTTC
1 CTTATTTTTTTTC
92800 CTTATTTTTTTT
1 CTTATTTTTTTT
92812 GAAAAAGTTT
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:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (13 bp):
CTTATTTTTTTTC
Found at i:104833 original size:16 final size:16
Alignment explanation
Indices: 104809--104845 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
104799 TTTTATTAAT
104809 ATTAATTAAATAAAAA
1 ATTAATTAAATAAAAA
* *
104825 ATTATTTAAATAATAA
1 ATTAATTAAATAAAAA
104841 ATTAA
1 ATTAA
104846 AAAAAATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTAATTAAATAAAAA
Found at i:104839 original size:30 final size:27
Alignment explanation
Indices: 104791--104851 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 27
104781 ATTCTGACAT
* *
104791 AAAAATAATTTTATTAATATTAATTAAATA
1 AAAAATAATTTAAATAATA--AATTAAA-A
*
104821 AAAAATTATTTAAATAATAAATTAAAA
1 AAAAATAATTTAAATAATAAATTAAAA
104848 AAAA
1 AAAA
104852 TATTGATACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 5 0.18
28 7 0.25
30 16 0.57
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
AAAAATAATTTAAATAATAAATTAAAA
Found at i:104940 original size:27 final size:27
Alignment explanation
Indices: 104909--104964 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
104899 TATTTTTGGG
*
104909 TGGTGCGTACATGATAGATGACACCAA
1 TGGTGCCTACATGATAGATGACACCAA
* *
104936 TGGTGCCTACCTGATAGATGACATCAA
1 TGGTGCCTACATGATAGATGACACCAA
104963 TG
1 TG
104965 ATGCTTACCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (27 bp):
TGGTGCCTACATGATAGATGACACCAA
Found at i:104973 original size:27 final size:27
Alignment explanation
Indices: 104920--104974 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
104910 GGTGCGTACA
*
104920 TGATAGATGACACCAATGGTGCCTACC
1 TGATAGATGACACCAATGATGCCTACC
* *
104947 TGATAGATGACATCAATGATGCTTACC
1 TGATAGATGACACCAATGATGCCTACC
104974 T
1 T
104975 ACCAGGCGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (27 bp):
TGATAGATGACACCAATGATGCCTACC
Found at i:105106 original size:3 final size:3
Alignment explanation
Indices: 105093--105124 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
105083 GAAGCAAAGA
105093 AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
105125 GGAAAGAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:105271 original size:17 final size:17
Alignment explanation
Indices: 105249--105282 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
105239 AAAAAATTTC
*
105249 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
105266 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
105283 TTATTGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:106073 original size:17 final size:17
Alignment explanation
Indices: 106035--106072 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
106025 AATTTAATTC
*
106035 ATTTGATATATTTAAAT
1 ATTTTATATATTTAAAT
106052 ATTTTATATA-TTAAAT
1 ATTTTATATATTTAAAT
106068 ATTTT
1 ATTTT
106073 TTAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTTTATATATTTAAAT
Found at i:106092 original size:12 final size:13
Alignment explanation
Indices: 106064--106091 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
106054 TTTATATATT
106064 AAATATTTTTTAA
1 AAATATTTTTTAA
106077 AAATATTTTTTAA
1 AAATATTTTTTAA
106090 AA
1 AA
106092 TGACAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATATTTTTTAA
Found at i:108504 original size:6 final size:6
Alignment explanation
Indices: 108493--108533 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
108483 TAGAATTAAA
*
108493 TATGTT TATGTT TATGTT TATGTT CT-TATT TATGTT TATGT
1 TATGTT TATGTT TATGTT TATGTT -TATGTT TATGTT TATGT
108534 ATGCAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.03
6 29 0.94
7 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.66
Consensus pattern (6 bp):
TATGTT
Found at i:111476 original size:25 final size:26
Alignment explanation
Indices: 111427--111478 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
111417 AACCTTCTGT
* *
111427 TTCCTTTTCTTCTTCAAAACTTTTGC
1 TTCCTTTCCTTCTTCAAAACATTTGC
111453 TTCCTTTCCTTCTTCAAAA-ATTTGC
1 TTCCTTTCCTTCTTCAAAACATTTGC
111478 T
1 T
111479 GTTAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.17, C:0.27, G:0.04, T:0.52
Consensus pattern (26 bp):
TTCCTTTCCTTCTTCAAAACATTTGC
Found at i:111964 original size:14 final size:14
Alignment explanation
Indices: 111921--111964 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
111911 ATTAATTTTA
111921 TTTTTTGTATTATAT
1 TTTTTTGTATTAT-T
** *
111936 TTTGGTGTATAATT
1 TTTTTTGTATTATT
111950 TTTTTTGTATTATT
1 TTTTTTGTATTATT
111964 T
1 T
111965 ATGTCAAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.18, C:0.00, G:0.11, T:0.70
Consensus pattern (14 bp):
TTTTTTGTATTATT
Found at i:113133 original size:24 final size:24
Alignment explanation
Indices: 113101--113146 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
113091 TTTATCAATT
*
113101 TTTTGAAATCTATGAATCTTGGGG
1 TTTTGAAATCTACGAATCTTGGGG
*
113125 TTTTGAAATCTACGGATCTTGG
1 TTTTGAAATCTACGAATCTTGG
113147 ACTTCCCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.41
Consensus pattern (24 bp):
TTTTGAAATCTACGAATCTTGGGG
Found at i:119408 original size:23 final size:22
Alignment explanation
Indices: 119357--119408 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
119347 TAAGGGACGA
* *
119357 AATT-AAATTGTAATTTTTACG
1 AATTAAAAATGTAATTTTTAAG
*
119378 ATAGTAAAAATGTAATTTTTAAAG
1 A-ATTAAAAATGTAATTTTT-AAG
119402 AATTAAA
1 AATTAAA
119409 TTAAAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 1 0.04
22 2 0.08
23 18 0.75
24 3 0.12
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (22 bp):
AATTAAAAATGTAATTTTTAAG
Found at i:119757 original size:17 final size:17
Alignment explanation
Indices: 119735--119775 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
119725 TCTTTTCCAG
119735 ATGCCCTAAATCGAAAT
1 ATGCCCTAAATCGAAAT
119752 ATGCCCTAAATCGAAAT
1 ATGCCCTAAATCGAAAT
*
119769 ATACCCT
1 ATGCCCT
119776 TCTCTTTCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (17 bp):
ATGCCCTAAATCGAAAT
Found at i:123095 original size:13 final size:13
Alignment explanation
Indices: 123079--123121 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
123069 TAAGTTCGAT
123079 ATGTGAACTCAAC
1 ATGTGAACTCAAC
*
123092 ATGTGAACTCATC
1 ATGTGAACTCAAC
* * *
123105 ATGCGAGCTTAAC
1 ATGTGAACTCAAC
123118 ATGT
1 ATGT
123122 AAACCGTGTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (13 bp):
ATGTGAACTCAAC
Found at i:128659 original size:23 final size:25
Alignment explanation
Indices: 128629--128683 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
128619 ACACTAGCGC
128629 GCTCTCTG-T-TTAGCAC-GTCTCGT
1 GCTCTCTGTTATTAGCACTGTCT-GT
*
128652 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTGTTATTAGCACTGTCTGT
128677 GCTCTCT
1 GCTCTCT
128684 AATTAGCANN
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 8 0.29
24 1 0.04
25 16 0.57
26 3 0.11
ACGTcount: A:0.09, C:0.27, G:0.22, T:0.42
Consensus pattern (25 bp):
GCTCTCTGTTATTAGCACTGTCTGT
Found at i:129309 original size:23 final size:21
Alignment explanation
Indices: 129279--129427 Score: 93
Period size: 23 Copynumber: 6.5 Consensus size: 21
129269 ACACTAGCGC
129279 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGTTTAGCACGT-T-GT
129302 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCAC-GT-TGT
* * *
129327 GCTTTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCAC-GT-TGT
* * *
129350 GCTCTCTGATTAGTACTTTGT
1 GCTCTCTGTTTAGCACGTTGT
129371 GTACTCTCTGTTTAGCACTGTATGT
1 G--CTCTCTGTTTAGCAC-GT-TGT
* *
129396 GCTCTCTG-TTAGTACTTTGGT
1 GCTCTCTGTTTAGCACGTT-GT
*
129417 ACTCTCTGTTT
1 GCTCTCTGTTT
129428 GTTTCGTATA
Statistics
Matches: 105, Mismatches: 12, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
20 1 0.01
21 14 0.13
22 10 0.10
23 55 0.52
24 2 0.02
25 20 0.19
26 3 0.03
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (21 bp):
GCTCTCTGTTTAGCACGTTGT
Found at i:129386 original size:46 final size:45
Alignment explanation
Indices: 129280--129427 Score: 165
Period size: 46 Copynumber: 3.2 Consensus size: 45
129270 CACTAGCGCG
* * * *
129280 CTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCACTGTGTGTG
1 CTCTCTGTTTAGCAC-TCTTGTGCTCTCTG--ATTAGTACTTTGTGTA
* * *
129328 CTTTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTTTGTGTA
1 CTCTCTGTTTAGCACTCT-TGTGCTCTCTGATTAGTACTTTGTGTA
*
129374 CTCTCTGTTTAGCACTGTATGTGCTCTCTG-TTAGTACTTTG-GTA
1 CTCTCTGTTTAGCACTCT-TGTGCTCTCTGATTAGTACTTTGTGTA
129418 CTCTCTGTTT
1 CTCTCTGTTT
129428 GTTTCGTATA
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
44 13 0.15
45 11 0.12
46 39 0.44
47 2 0.02
48 23 0.26
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (45 bp):
CTCTCTGTTTAGCACTCTTGTGCTCTCTGATTAGTACTTTGTGTA
Found at i:130965 original size:27 final size:28
Alignment explanation
Indices: 130920--130974 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
130910 AGCTTGAAAA
*
130920 TTTGAAAAAAGATACAAAAGATTATTTAT
1 TTTGAAAAAAGATACAAAACATT-TTTAT
*
130949 TTTGAAAATA-ATA-AAAACATTTTTAT
1 TTTGAAAAAAGATACAAAACATTTTTAT
130975 AAGTGTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.21
27 7 0.29
28 3 0.12
29 9 0.38
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (28 bp):
TTTGAAAAAAGATACAAAACATTTTTAT
Found at i:149032 original size:16 final size:16
Alignment explanation
Indices: 149011--149043 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
149001 AAATTCAAGA
*
149011 GAGATAGAGATAGAGG
1 GAGATAGAGAAAGAGG
149027 GAGATAGAGAAAGAGG
1 GAGATAGAGAAAGAGG
149043 G
1 G
149044 GGAGGAGCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.45, T:0.09
Consensus pattern (16 bp):
GAGATAGAGAAAGAGG
Found at i:151880 original size:8 final size:8
Alignment explanation
Indices: 151867--151892 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
151857 GAAGAAGATA
151867 TTGAATCT
1 TTGAATCT
151875 TTGAATCT
1 TTGAATCT
151883 TTGAATCT
1 TTGAATCT
151891 TT
1 TT
151893 AGGTTAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.54
Consensus pattern (8 bp):
TTGAATCT
Found at i:159852 original size:2 final size:2
Alignment explanation
Indices: 159845--159885 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
159835 CACTTTCAAC
159845 TA TA TA TA 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 TA TA TA TA T
159886 TACTTTTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:161352 original size:22 final size:21
Alignment explanation
Indices: 161327--161374 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
161317 CAAATATTGA
*
161327 TTAATAATAGGATAAATTAAGG
1 TTAATAAGAGGATAAATTAA-G
* * *
161349 TTAAAAAGATGATTAATTAAG
1 TTAATAAGAGGATAAATTAAG
161370 TTAAT
1 TTAAT
161375 TATGAAAGTC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (21 bp):
TTAATAAGAGGATAAATTAAG
Found at i:161463 original size:3 final size:3
Alignment explanation
Indices: 161455--161482 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
161445 CACATTTTCT
161455 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
161483 CTACAAGGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:162282 original size:41 final size:41
Alignment explanation
Indices: 162230--162345 Score: 196
Period size: 41 Copynumber: 2.8 Consensus size: 41
162220 TTGTATAAAT
162230 GGAAGACTCATGTCTCGAGATGAGAATGAGACTATGAATAA
1 GGAAGACTCATGTCTCGAGATGAGAATGAGACTATGAATAA
*
162271 GGAAGACTCATGTCTCAAGATGAGAATGAGACTATGAATAA
1 GGAAGACTCATGTCTCGAGATGAGAATGAGACTATGAATAA
* *
162312 GGAAGACTCGTGTCTCGAAATGAGAATGAAGACT
1 GGAAGACTCATGTCTCGAGATGAGAATG-AGACT
162346 CATGTCTCGA
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
41 65 0.93
42 5 0.07
ACGTcount: A:0.39, C:0.13, G:0.27, T:0.22
Consensus pattern (41 bp):
GGAAGACTCATGTCTCGAGATGAGAATGAGACTATGAATAA
Found at i:162344 original size:26 final size:26
Alignment explanation
Indices: 162313--162366 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
162303 TATGAATAAG
*
162313 GAAGACTCGTGTCTCGAAATGAGAAT
1 GAAGACTCATGTCTCGAAATGAGAAT
162339 GAAGACTCATGTCTCGAAATGAGAAT
1 GAAGACTCATGTCTCGAAATGAGAAT
162365 GA
1 GA
162367 GATTTTGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (26 bp):
GAAGACTCATGTCTCGAAATGAGAAT
Found at i:162380 original size:67 final size:67
Alignment explanation
Indices: 162272--162411 Score: 203
Period size: 67 Copynumber: 2.1 Consensus size: 67
162262 TATGAATAAG
*
162272 GAAGACTCATGTCTCAAGATGAGAATGAGACTATGAATAAGGAAGACTCGTGTCTCGAAATGAGA
1 GAAGACTCATGTCTCAAGATGAGAATGAGACTATGAATAAGGAAGACTCATGTCTCGAAATGAGA
162337 AT
66 AT
* * ** *
162339 GAAGACTCATGTCTCGAA-ATGAGAATGAGATTTTGCTTAAGGAAGACTCATGTCTCGAGATGAG
1 GAAGACTCATGTCTC-AAGATGAGAATGAGACTATGAATAAGGAAGACTCATGTCTCGAAATGAG
162403 AAT
65 AAT
162406 G-AGACT
1 GAAGACT
162412 ATGAATAAAG
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
66 5 0.08
67 59 0.89
68 2 0.03
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (67 bp):
GAAGACTCATGTCTCAAGATGAGAATGAGACTATGAATAAGGAAGACTCATGTCTCGAAATGAGA
AT
Found at i:162380 original size:108 final size:108
Alignment explanation
Indices: 162231--162448 Score: 364
Period size: 108 Copynumber: 2.0 Consensus size: 108
162221 TGTATAAATG
*
162231 GAAGACTCATGTCTCGAGATGAGAATGAGACTATGAATAAGGAAGACTCATGTCTCAAGATGAGA
1 GAAGACTCATGTCTCGAAATGAGAATGAGACTATGAATAAGGAAGACTCATGTCTCAAGATGAGA
* *
162296 ATGAGACTATGAATAAGGAAGACTCGTGTCTCGAAATGAGAAT
66 ATGAGACTATGAATAAAGAAGACTCATGTCTCGAAATGAGAAT
* * ** *
162339 GAAGACTCATGTCTCGAAATGAGAATGAGATTTTGCTTAAGGAAGACTCATGTCTCGAGATGAGA
1 GAAGACTCATGTCTCGAAATGAGAATGAGACTATGAATAAGGAAGACTCATGTCTCAAGATGAGA
162404 ATGAGACTATGAATAAAGAAGACTCATGTCTCGAAATGAGAAT
66 ATGAGACTATGAATAAAGAAGACTCATGTCTCGAAATGAGAAT
162447 GA
1 GA
162449 GATTTTGATT
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
108 102 1.00
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (108 bp):
GAAGACTCATGTCTCGAAATGAGAATGAGACTATGAATAAGGAAGACTCATGTCTCAAGATGAGA
ATGAGACTATGAATAAAGAAGACTCATGTCTCGAAATGAGAAT
Found at i:162384 original size:41 final size:41
Alignment explanation
Indices: 162339--162520 Score: 247
Period size: 41 Copynumber: 4.4 Consensus size: 41
162329 AAATGAGAAT
*
162339 GAAGACTCATGTCTCGAAATGAGAATGAGATTTTGCTTAAG
1 GAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAG
* * * * *
162380 GAAGACTCATGTCTCGAGATGAGAATGAGACTATGAATAAA
1 GAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAG
162421 GAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAG
1 GAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAG
* * *
162462 GAAGACTCATGTCTCGAGATGAGAATGAGAATATGATTAAAG
1 GAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATT-AAG
* * *
162504 AAAGACTTATGACTCGA
1 GAAGACTCATGTCTCGA
162521 TAGAGCATAA
Statistics
Matches: 123, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 106 0.86
42 17 0.14
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (41 bp):
GAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAG
Found at i:162476 original size:82 final size:82
Alignment explanation
Indices: 162339--162520 Score: 310
Period size: 82 Copynumber: 2.2 Consensus size: 82
162329 AAATGAGAAT
*
162339 GAAGACTCATGTCTCGAAATGAGAATGAGATTTTGCTTAAGGAAGACTCATGTCTCGAGATGAGA
1 GAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAGGAAGACTCATGTCTCGAGATGAGA
*
162404 ATGAGACTATGAATAAA
66 ATGAGAATATGAATAAA
162421 GAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAGGAAGACTCATGTCTCGAGATGAGA
1 GAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAGGAAGACTCATGTCTCGAGATGAGA
*
162486 ATGAGAATATGATTAAA
66 ATGAGAATATGAATAAA
* *
162503 GAAAGACTTATGACTCGA
1 G-AAGACTCATGTCTCGA
162521 TAGAGCATAA
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
82 80 0.85
83 14 0.15
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (82 bp):
GAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAGGAAGACTCATGTCTCGAGATGAGA
ATGAGAATATGAATAAA
Found at i:165817 original size:237 final size:237
Alignment explanation
Indices: 165402--165875 Score: 912
Period size: 237 Copynumber: 2.0 Consensus size: 237
165392 TTTCAAATTT
*
165402 ATAAGACATGATATATTAAAAGTTACTAAATGTCATGTGTAACCACATGTTACCCCTTTAAAAGT
1 ATAAGACATGATATATTAAAAGTTACTAAATATCATGTGTAACCACATGTTACCCCTTTAAAAGT
* *
165467 AACACATATTTTTGCATATTGTGACGAGCGACAAACACACGTGTCCTTGTTAAAAAATTGGAAAA
66 AACACAGATCTTTGCATATTGTGACGAGCGACAAACACACGTGTCCTTGTTAAAAAATTGGAAAA
165532 CAGACGAGCTGAGCGATGACAAGAAGTCTAGTCTTGGGCCAAACACACGGTCGAGTTACAGCGTG
131 CAGACGAGCTGAGCGATGACAAGAAGTCTAGTCTTGGGCCAAACACACGGTCGAGTTACAGCGTG
165597 CTCTTTATTTCACATATAACAATTTTGTATAAATTTTCAAAG
196 CTCTTTATTTCACATATAACAATTTTGTATAAATTTTCAAAG
*
165639 ATAAGACATGATATATTAAAGGTTACTAAATATCATGTGTAACCACATGTTACCCCTTTAAAAGT
1 ATAAGACATGATATATTAAAAGTTACTAAATATCATGTGTAACCACATGTTACCCCTTTAAAAGT
165704 AACACAGATCTTTGCATATTGTGACGAGCGACAAACACACGTGTCCTTGTTAAAAAATTGGAAAA
66 AACACAGATCTTTGCATATTGTGACGAGCGACAAACACACGTGTCCTTGTTAAAAAATTGGAAAA
165769 CAGACGAGCTGAGCGATGACAAGAAGTCTAGTCTTGGGCCAAACACACGGTCGAGTTACAGCGTG
131 CAGACGAGCTGAGCGATGACAAGAAGTCTAGTCTTGGGCCAAACACACGGTCGAGTTACAGCGTG
165834 CTCTTTATTTCACATATAACAATTTTGTATAAATTTTCAAAG
196 CTCTTTATTTCACATATAACAATTTTGTATAAATTTTCAAAG
165876 TAGACGAGCA
Statistics
Matches: 233, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
237 233 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (237 bp):
ATAAGACATGATATATTAAAAGTTACTAAATATCATGTGTAACCACATGTTACCCCTTTAAAAGT
AACACAGATCTTTGCATATTGTGACGAGCGACAAACACACGTGTCCTTGTTAAAAAATTGGAAAA
CAGACGAGCTGAGCGATGACAAGAAGTCTAGTCTTGGGCCAAACACACGGTCGAGTTACAGCGTG
CTCTTTATTTCACATATAACAATTTTGTATAAATTTTCAAAG
Found at i:171952 original size:24 final size:24
Alignment explanation
Indices: 171887--171957 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 24
171877 CGAAGTACTT
* *
171887 AACAGAAGCGCATAAGTGCTGGGGA
1 AACAGAAGCACATAAGTGCT-GAGA
171912 AACAGAAGCACATAAGTGCTGAGA
1 AACAGAAGCACATAAGTGCTGAGA
*
171936 AACAGTAGGCACA-AAGTGCTGA
1 AACAG-AAGCACATAAGTGCTGA
171958 ATAAAAGCAC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
24 17 0.40
25 25 0.60
ACGTcount: A:0.41, C:0.17, G:0.30, T:0.13
Consensus pattern (24 bp):
AACAGAAGCACATAAGTGCTGAGA
Found at i:185994 original size:16 final size:17
Alignment explanation
Indices: 185950--186003 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 17
185940 ACTTTTTCGA
185950 AAAAAACATAATTATTCT
1 AAAAAA-ATAATTATTCT
* *
185968 AAATACA-AATTATTC-
1 AAAAAAATAATTATTCT
*
185983 AAAAAAATAATTGTT-T
1 AAAAAAATAATTATTCT
185999 AAAAA
1 AAAAA
186004 TAATTATACT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 5 0.17
16 19 0.66
17 1 0.03
18 4 0.14
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.31
Consensus pattern (17 bp):
AAAAAAATAATTATTCT
Found at i:189835 original size:27 final size:27
Alignment explanation
Indices: 189764--189835 Score: 65
Period size: 27 Copynumber: 2.6 Consensus size: 27
189754 GAAAAAAATA
189764 ATATTCATACTTTTAAAATAATTTGTTTT
1 ATATT-ATA-TTTTAAAATAATTTGTTTT
* * ***
189793 ATGTT-TGTCAAAAAAATAATTTGTTTT
1 ATATTATAT-TTTAAAATAATTTGTTTT
189820 ATATTATATTTTAAAA
1 ATATTATATTTTAAAA
189836 ATATTATTTC
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
26 1 0.03
27 24 0.77
28 2 0.06
29 4 0.13
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (27 bp):
ATATTATATTTTAAAATAATTTGTTTT
Found at i:195285 original size:17 final size:17
Alignment explanation
Indices: 195263--195296 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
195253 CATTGGAGAG
195263 TGTGCTGTAGGAGATTT
1 TGTGCTGTAGGAGATTT
195280 TGTGCTGTAGGAGATTT
1 TGTGCTGTAGGAGATTT
195297 GAGTCTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.35, T:0.41
Consensus pattern (17 bp):
TGTGCTGTAGGAGATTT
Found at i:198602 original size:23 final size:21
Alignment explanation
Indices: 198559--198606 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
198549 CTTTTAAACC
198559 ATTTTTAGTTTTAGAATTTTA
1 ATTTTTAGTTTTAGAATTTTA
*
198580 TATTTTATAGTTTTCATAA-TTTA
1 -ATTTT-TAGTTTT-AGAATTTTA
198603 ATTT
1 ATTT
198607 AATTTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 9 0.39
23 11 0.48
24 3 0.13
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.62
Consensus pattern (21 bp):
ATTTTTAGTTTTAGAATTTTA
Found at i:198676 original size:33 final size:34
Alignment explanation
Indices: 198639--198705 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
198629 TGAGTTTTAT
* * *
198639 TTTTATAATTTTATAGTTTT-AATTTTTAAAATA
1 TTTTATAATTATAAAGTTTTGAATATTTAAAATA
*
198672 TTTTATAATTATAAATTTTTGAATATTTAAAATA
1 TTTTATAATTATAAAGTTTTGAATATTTAAAATA
198706 ATGATTGAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (34 bp):
TTTTATAATTATAAAGTTTTGAATATTTAAAATA
Found at i:198690 original size:25 final size:25
Alignment explanation
Indices: 198646--198699 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
198636 TATTTTTATA
* * *
198646 ATTTTATAGTTTTAATTTTTAAAAT
1 ATTTTATAATTATAAATTTTAAAAT
**
198671 ATTTTATAATTATAAATTTTTGAAT
1 ATTTTATAATTATAAATTTTAAAAT
198696 ATTT
1 ATTT
198700 AAAATAATGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (25 bp):
ATTTTATAATTATAAATTTTAAAAT
Found at i:204653 original size:100 final size:100
Alignment explanation
Indices: 204442--204645 Score: 399
Period size: 100 Copynumber: 2.0 Consensus size: 100
204432 AATGTGGACA
204442 CTTCAAGTTCTGCATCTACCAATGCATCTGAGAGCAATTCAGTTGAGTCAGGTACAGTTCTTTTA
1 CTTCAAGTTCTGCATCTACCAATGCATCTGAGAGCAATTCAGTTGAGTCAGGTACAGTTCTTTTA
*
204507 CATTCGTTCCAATCAACATTTTGTAGTTTTGCCTG
66 CACTCGTTCCAATCAACATTTTGTAGTTTTGCCTG
204542 CTTCAAGTTCTGCATCTACCAATGCATCTGAGAGCAATTCAGTTGAGTCAGGTACAGTTCTTTTA
1 CTTCAAGTTCTGCATCTACCAATGCATCTGAGAGCAATTCAGTTGAGTCAGGTACAGTTCTTTTA
204607 CACTCGTTCCAATCAACATTTTGTAGTTTTGCCTG
66 CACTCGTTCCAATCAACATTTTGTAGTTTTGCCTG
204642 CTTC
1 CTTC
204646 TATTTCTGAT
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 103 1.00
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.37
Consensus pattern (100 bp):
CTTCAAGTTCTGCATCTACCAATGCATCTGAGAGCAATTCAGTTGAGTCAGGTACAGTTCTTTTA
CACTCGTTCCAATCAACATTTTGTAGTTTTGCCTG
Found at i:205161 original size:218 final size:218
Alignment explanation
Indices: 204770--205424 Score: 1220
Period size: 218 Copynumber: 3.0 Consensus size: 218
204760 ATTATATCTT
* *
204770 TTGTTGGTAAGGATACATTGCAATCCGAGTCTAATGGAAAGCTGCCTACTTCTCAAAAAGATTCA
1 TTGTTGATAAGGATACATTGCAATCCGAGTCTAACGGAAAGCTGCCTACTTCTCAAAAAGATTCA
204835 CTTGATTCAAGAAAAAATGGGGTGCTGGAGAAACCTGGACAGCTTTCAGAATCATTGTCTAGACC
66 CTTGATTCAAGAAAAAATGGGGTGCTGGAGAAACCTGGACAGCTTTCAGAATCATTGTCTAGACC
*
204900 AACAGAAAAGAAGGTGGACACTTCCAGTTCTGCATCAAGCAATGCATCTAAGAACAATTCAGTTG
131 AACAGAAAAGAAGGTGGACACTTCCAGTTCTGCATCTAGCAATGCATCTAAGAACAATTCAGTTG
*
204965 ATTCAGGTAGTTTTCTTTTACTC
196 ATTCAGGTAGTATTCTTTTACTC
204988 TTGTTGATAAGGATACATTGCAATCCGAGTCTAACGGAAAGCTGCCTACTTCTCAAAAAGATTCA
1 TTGTTGATAAGGATACATTGCAATCCGAGTCTAACGGAAAGCTGCCTACTTCTCAAAAAGATTCA
*
205053 CTTGATTCAAGAGAAAATGGGGTGCTGGAGAAACCTGGACAGCTTTCAGAATCATTGTCTAGACC
66 CTTGATTCAAGAAAAAATGGGGTGCTGGAGAAACCTGGACAGCTTTCAGAATCATTGTCTAGACC
*
205118 AACAGAAAAGAAGGTGGACACTTCCAGTTCTGCATCTAGCAATGCATCTAAGAACACTTCAGTTG
131 AACAGAAAAGAAGGTGGACACTTCCAGTTCTGCATCTAGCAATGCATCTAAGAACAATTCAGTTG
205183 ATTCAGGTAGTATTCTTTTACTC
196 ATTCAGGTAGTATTCTTTTACTC
* *
205206 TTGTTGATAAGGATACATTGCAATCTGAGTCTAACGGAAAGATGCCTACTTCTCAAAAAGATTCA
1 TTGTTGATAAGGATACATTGCAATCCGAGTCTAACGGAAAGCTGCCTACTTCTCAAAAAGATTCA
*
205271 CTTGATTCAAGAAAAAAGGGGGTGCTGGAGAAACCTGGACAGCTTTCAGAATCATTGTCTAGACC
66 CTTGATTCAAGAAAAAATGGGGTGCTGGAGAAACCTGGACAGCTTTCAGAATCATTGTCTAGACC
*
205336 AACAGAAAAGAAGGTGGACACTTCCAGTTCTGCATCTAGCAATGCATCTAGGAACAATTCAGTTG
131 AACAGAAAAGAAGGTGGACACTTCCAGTTCTGCATCTAGCAATGCATCTAAGAACAATTCAGTTG
205401 ATTCAGGTAGTATTCTTTTACTC
196 ATTCAGGTAGTATTCTTTTACTC
205424 T
1 T
205425 CAGTTTGATG
Statistics
Matches: 425, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
218 425 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (218 bp):
TTGTTGATAAGGATACATTGCAATCCGAGTCTAACGGAAAGCTGCCTACTTCTCAAAAAGATTCA
CTTGATTCAAGAAAAAATGGGGTGCTGGAGAAACCTGGACAGCTTTCAGAATCATTGTCTAGACC
AACAGAAAAGAAGGTGGACACTTCCAGTTCTGCATCTAGCAATGCATCTAAGAACAATTCAGTTG
ATTCAGGTAGTATTCTTTTACTC
Found at i:206772 original size:202 final size:204
Alignment explanation
Indices: 206536--206949 Score: 778
Period size: 203 Copynumber: 2.0 Consensus size: 204
206526 TCAAAATATT
206536 AGAAAAATGGTAAGCTTTGTGATAGGCTCTTGTGGCTTAGAGGTTTCATATATTATTAGCATTAG
1 AGAAAAATGGTAAGCTTTGTGATAGGCTCTTGTGGCTTAGAGGTTTCATATATTATTAGCATTAG
* *
206601 T-AAAAAAAAAATTAGTAATTTTCTATCACTCTGTATTCTTCAAGTGTGAGAAACTAGATATGTA
66 TAAAAAAAAAAATTAGCAATTTTCTATCACTCTATATTCTTCAAGTGTGAGAAACTAGATATGTA
*
206665 CTGTGTGCACCTATTTTCATAATATAGATTGATCTTTTGGACTCTTTTGTACCTTAGTACCGGTT
131 CTGTGTGCACCTATTTTCATAATATAGATTGATCTTTTGGACTCTTTTCTACCTTAGTACCGGTT
206730 TCTCATGAA
196 TCTCATGAA
206739 AGAAAAATGGT-AGCTTTGTGATAGGCTCTTGTGGCTTAGAGGTTTCATATATTATTAGCATTAG
1 AGAAAAATGGTAAGCTTTGTGATAGGCTCTTGTGGCTTAGAGGTTTCATATATTATTAGCATTAG
206803 TAAAAAAAAAAATTAGCAATTTTCTATCACTCTATATTCTTCAAGTGTGAGAAACTAGATATGTA
66 TAAAAAAAAAAATTAGCAATTTTCTATCACTCTATATTCTTCAAGTGTGAGAAACTAGATATGTA
*
206868 CTGTGTGCACCTATTTTCATAATATAGATTGATCTTTTGGACTCTTTTCTACCTTAGTACTGGTT
131 CTGTGTGCACCTATTTTCATAATATAGATTGATCTTTTGGACTCTTTTCTACCTTAGTACCGGTT
206933 TCTCATGAA
196 TCTCATGAA
206942 AGAAAAAT
1 AGAAAAAT
206950 TAGGGATAAT
Statistics
Matches: 206, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
202 54 0.26
203 152 0.74
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.38
Consensus pattern (204 bp):
AGAAAAATGGTAAGCTTTGTGATAGGCTCTTGTGGCTTAGAGGTTTCATATATTATTAGCATTAG
TAAAAAAAAAAATTAGCAATTTTCTATCACTCTATATTCTTCAAGTGTGAGAAACTAGATATGTA
CTGTGTGCACCTATTTTCATAATATAGATTGATCTTTTGGACTCTTTTCTACCTTAGTACCGGTT
TCTCATGAA
Found at i:207980 original size:2 final size:2
Alignment explanation
Indices: 207973--208003 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
207963 GATAGCTTGC
207973 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
208004 TGATAGCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:208130 original size:25 final size:22
Alignment explanation
Indices: 208102--208148 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
208092 CATATCTTAG
208102 AATATGTTACATTATCTTGTTTGAT
1 AATAT-TT-CATTAT-TTGTTTGAT
*
208127 AATATTTTATTATTTGTTTGAT
1 AATATTTCATTATTTGTTTGAT
208149 GGGATGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 5 0.24
24 2 0.10
25 5 0.24
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.57
Consensus pattern (22 bp):
AATATTTCATTATTTGTTTGAT
Found at i:212688 original size:22 final size:21
Alignment explanation
Indices: 212660--212700 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
212650 TCTAATACTT
212660 GATATACATATATATAGTATTA
1 GATATACATATATAT-GTATTA
*
212682 GATATACATGTATATGTAT
1 GATATACATATATATGTAT
212701 CTATATTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.41
Consensus pattern (21 bp):
GATATACATATATATGTATTA
Found at i:230812 original size:63 final size:63
Alignment explanation
Indices: 230713--230883 Score: 306
Period size: 63 Copynumber: 2.7 Consensus size: 63
230703 ATAGGGACCG
*
230713 TATGCACAGTAAGAGGTCATCAAACAAACCAGAAGGTTCTGTATTAATGAGAGAAAGGAACAA
1 TATGCACAGTAAGAGGTCATCAAACAAACCAGAAGGTTCTGTATTAAAGAGAGAAAGGAACAA
*
230776 TATGCACAGTAAGAGGTCATCAAACAAACCAGAAGGTTCTGTATTAAAGAGAGAAAGGAACCA
1 TATGCACAGTAAGAGGTCATCAAACAAACCAGAAGGTTCTGTATTAAAGAGAGAAAGGAACAA
* *
230839 TATGCACAGTAAGAGGTCATCAAATAAACAAGAAGGTTCTGTATT
1 TATGCACAGTAAGAGGTCATCAAACAAACCAGAAGGTTCTGTATT
230884 TGCTATTTGC
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 104 1.00
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (63 bp):
TATGCACAGTAAGAGGTCATCAAACAAACCAGAAGGTTCTGTATTAAAGAGAGAAAGGAACAA
Found at i:232809 original size:2 final size:2
Alignment explanation
Indices: 232802--232841 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
232792 TTAGGTTCCC
232802 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
232842 TTATATATAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:244823 original size:21 final size:21
Alignment explanation
Indices: 244799--244841 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
244789 CTGCAATTCC
* *
244799 TCTATCAACTTCTTTTCCATG
1 TCTAGCAACTTCATTTCCATG
**
244820 TCTAGCTGCTTCATTTCCATG
1 TCTAGCAACTTCATTTCCATG
244841 T
1 T
244842 TACCCTGCCT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.28, G:0.09, T:0.47
Consensus pattern (21 bp):
TCTAGCAACTTCATTTCCATG
Found at i:244849 original size:21 final size:21
Alignment explanation
Indices: 244807--244845 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
244797 CCTCTATCAA
* *
244807 CTTCTTTTCCATGTCTAGCTG
1 CTTCATTTCCATGTCTACCTG
244828 CTTCATTTCCATGT-TACC
1 CTTCATTTCCATGTCTACC
244846 CTGCCTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 3 0.19
21 13 0.81
ACGTcount: A:0.13, C:0.31, G:0.10, T:0.46
Consensus pattern (21 bp):
CTTCATTTCCATGTCTACCTG
Found at i:245330 original size:4 final size:4
Alignment explanation
Indices: 245323--245350 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
245313 AATACGCATG
245323 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
245351 TACATTAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:266161 original size:188 final size:187
Alignment explanation
Indices: 265839--266177 Score: 493
Period size: 188 Copynumber: 1.8 Consensus size: 187
265829 TACATGCGAG
* * *
265839 ACTTCTGCATAAATTAGGTTAATTGCCTCTGTATGCTGTCTGGACTTTTAGCTTTTTTCCTTACC
1 ACTTCTGCATAAATTAGGTTAATTGCCTCTGAATGCTGTCTAGACTTCTAGCTTTTTTCCTTACC
** * * * *
265904 TTGAGATTTTTCTTGTATGCACCGGTACTTTAGCTTGGGTTGCTAAATTTATAACTGAAATGTAG
66 TTGAGATGCTTCTTGCATGCACCGGTACTTAAGCCTGAGTTGCTAAATTTATAACTGAAATGTAG
265969 TTTGTGGGAGTTCCTTCAACCCAAGATAGCAACACTGTTATCTCTGTCTTCATGTGGT
131 TTTGTGGGAGTTCCTT-AACCCAAGATAGCAACACTGTTATCTCTGTCTTCATGTGGT
* * *
266027 ACTTTTGCATAAATTAGGTTAGTTGCCTCTGAATGCTGT-TCAGACTTCTAGCTTTTTTCTTTAC
1 ACTTCTGCATAAATTAGGTTAATTGCCTCTGAATGCTGTCT-AGACTTCTAGCTTTTTTCCTTAC
* **
266091 TTTGAGATGCTTCTTGCATGCATTGGTACTTAAGCCTGAGTTGCTAAATTTATAACTTG-AATGT
65 CTTGAGATGCTTCTTGCATGCACCGGTACTTAAGCCTGAGTTGCTAAATTTATAAC-TGAAATGT
*
266155 AGTTTGTGGGTGTTCCTTAACCC
129 AGTTTGTGGGAGTTCCTTAACCC
266178 TTTTTCATTT
Statistics
Matches: 133, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
187 6 0.05
188 125 0.94
189 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (187 bp):
ACTTCTGCATAAATTAGGTTAATTGCCTCTGAATGCTGTCTAGACTTCTAGCTTTTTTCCTTACC
TTGAGATGCTTCTTGCATGCACCGGTACTTAAGCCTGAGTTGCTAAATTTATAACTGAAATGTAG
TTTGTGGGAGTTCCTTAACCCAAGATAGCAACACTGTTATCTCTGTCTTCATGTGGT
Found at i:270272 original size:6 final size:6
Alignment explanation
Indices: 270257--270289 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
270247 GATAAGGCCT
*
270257 CCTCAC CCTCAA CCTCAA CCTCAA CCTCAA CCT
1 CCTCAA CCTCAA CCTCAA CCTCAA CCTCAA CCT
270290 TCCATGGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.27, C:0.55, G:0.00, T:0.18
Consensus pattern (6 bp):
CCTCAA
Found at i:270883 original size:15 final size:15
Alignment explanation
Indices: 270863--270912 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
270853 ATTCCAGGAG
270863 AAGAAGGAGAAGAAA
1 AAGAAGGAGAAGAAA
** *
270878 AAGAAGTCGAAGAAG
1 AAGAAGGAGAAGAAA
* *
270893 AAGAAGGATAAGGAA
1 AAGAAGGAGAAGAAA
270908 AAGAA
1 AAGAA
270913 AAGAAAGGGG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.62, C:0.02, G:0.32, T:0.04
Consensus pattern (15 bp):
AAGAAGGAGAAGAAA
Found at i:277022 original size:9 final size:9
Alignment explanation
Indices: 277008--277033 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
276998 ATCACAAGAA
277008 ACATTTCAT
1 ACATTTCAT
277017 ACATTTCAT
1 ACATTTCAT
277026 ACATTTCA
1 ACATTTCA
277034 GACAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (9 bp):
ACATTTCAT
Found at i:279550 original size:55 final size:54
Alignment explanation
Indices: 279485--279597 Score: 181
Period size: 55 Copynumber: 2.1 Consensus size: 54
279475 TAATATTTTC
*
279485 TATTTTGATTCTTAGACATTGATAAGATGTAAAAAAAATTAGAAAGATAAAAAAA
1 TATTTTGATTCTTAGACATTGATAAGATGGAAAAAAAATTAGAAAGAT-AAAAAA
* * *
279540 TATTTTGATTCTTAGACTTTGATAGGATGGAAAGAAAATTAGAAAGATAAAAAA
1 TATTTTGATTCTTAGACATTGATAAGATGGAAAAAAAATTAGAAAGATAAAAAA
279594 TATT
1 TATT
279598 GAAGGGATGA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
54 10 0.19
55 44 0.81
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.33
Consensus pattern (54 bp):
TATTTTGATTCTTAGACATTGATAAGATGGAAAAAAAATTAGAAAGATAAAAAA
Found at i:297492 original size:15 final size:15
Alignment explanation
Indices: 297472--297525 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
297462 ATACTACAAA
297472 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
297487 ATATTTATAATTGAAAT
1 ATATTTATTATT--AAT
*
297504 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
297521 ATATT
1 ATATT
297526 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 16 0.50
17 5 0.16
19 11 0.34
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:297509 original size:34 final size:33
Alignment explanation
Indices: 297470--297534 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 33
297460 CTATACTACA
* *
297470 AAATATTTATTATTAATATATTTATAATTGAAAT
1 AAATATTTATTATTAAAATATTAAT-ATTGAAAT
297504 AAATATTTATTATTAAAATATTAATATTGAA
1 AAATATTTATTATTAAAATATTAATATTGAA
297535 TATTTTCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 6 0.21
34 23 0.79
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (33 bp):
AAATATTTATTATTAAAATATTAATATTGAAAT
Found at i:297511 original size:19 final size:19
Alignment explanation
Indices: 297487--297523 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
297477 TATTATTAAT
*
297487 ATATTTATAATTGAAATAA
1 ATATTTATAATTAAAATAA
*
297506 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
297524 TTAATATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:301956 original size:24 final size:24
Alignment explanation
Indices: 301909--301955 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
301899 TAATTAATTT
**
301909 TTTAAAATTTTTAAAAATATAAAA
1 TTTAAAATTACTAAAAATATAAAA
301933 TTTAAAATTACTAAAAAT-TAAAA
1 TTTAAAATTACTAAAAATATAAAA
301956 AACATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
TTTAAAATTACTAAAAATATAAAA
Found at i:312285 original size:30 final size:29
Alignment explanation
Indices: 312245--312313 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
312235 GATAATAATT
312245 TATAAGAATTAAATC-AAATCAAAATTTCATG
1 TATAA-AATTAAA-CAAAATCAAAATTT-ATG
* *
312276 TATAAAATTACACAAAATTAAAATTTATG
1 TATAAAATTAAACAAAATCAAAATTTATG
*
312305 TATACAATT
1 TATAAAATT
312314 GTATATTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 12 0.35
30 17 0.50
31 5 0.15
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.35
Consensus pattern (29 bp):
TATAAAATTAAACAAAATCAAAATTTATG
Found at i:320590 original size:36 final size:35
Alignment explanation
Indices: 320550--320661 Score: 111
Period size: 36 Copynumber: 3.2 Consensus size: 35
320540 ACTTTCAAAA
* * *
320550 AGAAGCACAAGTAGAAGTCCTGCAAGATCCTCTCGG
1 AGAAGCACAAGCAGAAGTCCTGTAAGAT-CTCTAGG
** * **
320586 AGAAGCATTAGCAGAAGCCCCATAAGA--TCTAGG
1 AGAAGCACAAGCAGAAGTCCTGTAAGATCTCTAGG
*
320619 AGAAGCACTAGCAGAAGTCCTGTAAGATCTTCTAGG
1 AGAAGCACAAGCAGAAGTCCTGTAAGATC-TCTAGG
320655 AGAAGCA
1 AGAAGCA
320662 TAAGTAGGAG
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
33 28 0.46
36 33 0.54
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (35 bp):
AGAAGCACAAGCAGAAGTCCTGTAAGATCTCTAGG
Found at i:320645 original size:33 final size:33
Alignment explanation
Indices: 320550--320648 Score: 99
Period size: 33 Copynumber: 2.9 Consensus size: 33
320540 ACTTTCAAAA
* * * *
320550 AGAAGCACAAGTAGAAGTCCTGCAAGATCCTCTCGG
1 AGAAGCACTAGCAGAAGTCCTGTAAGA---TCTAGG
* * **
320586 AGAAGCATTAGCAGAAGCCCCATAAGATCTAGG
1 AGAAGCACTAGCAGAAGTCCTGTAAGATCTAGG
320619 AGAAGCACTAGCAGAAGTCCTGTAAGATCT
1 AGAAGCACTAGCAGAAGTCCTGTAAGATCT
320649 TCTAGGAGAA
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
33 31 0.61
36 20 0.39
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.17
Consensus pattern (33 bp):
AGAAGCACTAGCAGAAGTCCTGTAAGATCTAGG
Found at i:321372 original size:36 final size:36
Alignment explanation
Indices: 321332--321415 Score: 141
Period size: 36 Copynumber: 2.3 Consensus size: 36
321322 ATGTGGTCAT
* *
321332 AGCCGTAGCCCTAGTCGAAGTCGAACCTCTATTCGC
1 AGCCGTAGCCCAAGTCGAAGTCGAACCCCTATTCGC
321368 AGCCGTAGCCCAAGTCGAAGTCGAACCCCTATTCGC
1 AGCCGTAGCCCAAGTCGAAGTCGAACCCCTATTCGC
*
321404 AGCCATAGCCCA
1 AGCCGTAGCCCA
321416 GTTGATTCTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.25, C:0.36, G:0.21, T:0.18
Consensus pattern (36 bp):
AGCCGTAGCCCAAGTCGAAGTCGAACCCCTATTCGC
Found at i:325842 original size:36 final size:36
Alignment explanation
Indices: 325795--325882 Score: 140
Period size: 36 Copynumber: 2.4 Consensus size: 36
325785 CAAACTCAGG
*
325795 GAATTTAAGTTAGTATAGATAAGCATAAATGCATAA
1 GAATTTAAGTTAGTATAGATAAGCACAAATGCATAA
* * *
325831 GAATTTAAGTTAGAATGGATAAGCACACATGCATAA
1 GAATTTAAGTTAGTATAGATAAGCACAAATGCATAA
325867 GAATTTAAGTTAGTAT
1 GAATTTAAGTTAGTAT
325883 CAGACATTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.31
Consensus pattern (36 bp):
GAATTTAAGTTAGTATAGATAAGCACAAATGCATAA
Found at i:326733 original size:84 final size:84
Alignment explanation
Indices: 326607--326768 Score: 254
Period size: 84 Copynumber: 1.9 Consensus size: 84
326597 AATGGCTGCA
* * * *
326607 AGATTCTCCTTTCTTTTAATATTTTAAAATTCAATTATTTCATGGTAATGATTTAAACAG-TGTA
1 AGATTCTCCTTTCTTTTAATATATTAAAATTCAATCAATTCATGGAAATGATTTAAAC-GTTGTA
326671 CTATTTGTGTTATGGGTACT
65 CTATTTGTGTTATGGGTACT
* *
326691 AGATTCTCCTTTCTTTTGATATATTAAAATTCAATCAATTCATGGAAATGTTTTAAACGTTGTAC
1 AGATTCTCCTTTCTTTTAATATATTAAAATTCAATCAATTCATGGAAATGATTTAAACGTTGTAC
326756 TATTTGTGTTATG
66 TATTTGTGTTATG
326769 CACATGCTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
83 1 0.01
84 70 0.99
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (84 bp):
AGATTCTCCTTTCTTTTAATATATTAAAATTCAATCAATTCATGGAAATGATTTAAACGTTGTAC
TATTTGTGTTATGGGTACT
Done.