Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020167.1 Corchorus olitorius cultivar O-4 contig20200, 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: 150408
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1666 original size:27 final size:27
Alignment explanation
Indices: 1624--1684 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
1614 TCTTCATTAT
* *
1624 AGGGGTAAAATCGTAATTTTATCAATC
1 AGGGGTAAAATAGTAAATTTATCAATC
* * *
1651 AGGGGTAACATAGTAAATTTGTCCATC
1 AGGGGTAAAATAGTAAATTTATCAATC
*
1678 ACGGGTA
1 AGGGGTA
1685 TTTTTGGTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (27 bp):
AGGGGTAAAATAGTAAATTTATCAATC
Found at i:6482 original size:19 final size:17
Alignment explanation
Indices: 6429--6483 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 17
6419 TTTAAACTAT
6429 TAATAAAAAAATAAAACA
1 TAATAAAAAAATAAAA-A
*
6447 TAAGTAAAAAAA-GAAAA
1 TAA-TAAAAAAATAAAAA
6464 TGAATAAATAAAATAAAAA
1 T-AATAAA-AAAATAAAAA
6483 T
1 T
6484 CCACTAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 6 0.19
18 12 0.39
19 13 0.42
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (17 bp):
TAATAAAAAAATAAAAA
Found at i:6579 original size:118 final size:108
Alignment explanation
Indices: 6455--6689 Score: 353
Period size: 118 Copynumber: 2.1 Consensus size: 108
6445 CATAAGTAAA
6455 AAAAGAAAATGAATAAATAAAATAAAAATCCACTAATAATATAAATATATATATAAATAAAATAA
1 AAAAGAAAATGAATAAATAAAATAAAAATCCA-T--TAAT-T--ATATATATATAAAT-AAATAA
6520 AAGTAGAAAAAGTTAAAAGAAAGAGAGAGAGAGAAAAAAAAGAGAGAATAACC
59 AAGTAGAAAAAGTTAAAAG--AGAGAGAGAGAGAAAAAAAAGAGAGAATAA-C
6573 AAAAGAAAATGAATAAATAAAATAAAAATCCATTAATTATATATATATAAATAAATAAAAGTAGA
1 AAAAGAAAATGAATAAATAAAATAAAAATCCATTAATTATATATATATAAATAAATAAAAGTAGA
* *
6638 AAAAGTTAAAAGAGAGAGAGAGAGAGAGAAAAGAGAGAATAAC
66 AAAAGTTAAAAGAGAGAGAGAGAGAAAAAAAAGAGAGAATAAC
*
6681 AAAAAAAAA
1 AAAAGAAAA
6690 GGGTCAGAAG
Statistics
Matches: 114, Mismatches: 3, Indels: 10
0.90 0.02 0.08
Matches are distributed among these distances:
108 9 0.08
109 28 0.25
111 25 0.22
112 14 0.12
114 1 0.01
115 4 0.04
117 1 0.01
118 32 0.28
ACGTcount: A:0.66, C:0.03, G:0.14, T:0.17
Consensus pattern (108 bp):
AAAAGAAAATGAATAAATAAAATAAAAATCCATTAATTATATATATATAAATAAATAAAAGTAGA
AAAAGTTAAAAGAGAGAGAGAGAGAAAAAAAAGAGAGAATAAC
Found at i:7276 original size:2 final size:2
Alignment explanation
Indices: 7263--7293 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
7253 TTTAAGCATG
*
7263 AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7294 AATGTATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:8263 original size:49 final size:50
Alignment explanation
Indices: 8204--8302 Score: 146
Period size: 49 Copynumber: 2.0 Consensus size: 50
8194 AGTCATTCAA
* *
8204 AAGCTCGAGGCATTTTGTTGATC-TCTAGTCTTCCGAATCAATCTAGCTT
1 AAGCTCGAGGCATTTTGTTGATCATCTAGTATTCAGAATCAATCTAGCTT
* * *
8253 AAGCTTGAGGCATTTTGTTGATCATCTTGTATTCATAATCAATCTAGCTT
1 AAGCTCGAGGCATTTTGTTGATCATCTAGTATTCAGAATCAATCTAGCTT
8303 GACCCTTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
49 22 0.50
50 22 0.50
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.39
Consensus pattern (50 bp):
AAGCTCGAGGCATTTTGTTGATCATCTAGTATTCAGAATCAATCTAGCTT
Found at i:31631 original size:19 final size:19
Alignment explanation
Indices: 31607--31649 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
31597 CCAATTATTA
31607 AAGTTAAGGTCCTAAATTC
1 AAGTTAAGGTCCTAAATTC
31626 AAGTTAAGGTCCTAAATTC
1 AAGTTAAGGTCCTAAATTC
31645 AAGTT
1 AAGTT
31650 TTAAAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (19 bp):
AAGTTAAGGTCCTAAATTC
Found at i:32087 original size:28 final size:28
Alignment explanation
Indices: 32055--32110 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
32045 TGCTATGAGA
32055 TTTCAATTGTATTCCTTGGGGAAGGGGT
1 TTTCAATTGTATTCCTTGGGGAAGGGGT
32083 TTTCAATTGTATTCCTTGGGGAAGGGGT
1 TTTCAATTGTATTCCTTGGGGAAGGGGT
32111 CATGTAGCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.18, C:0.11, G:0.32, T:0.39
Consensus pattern (28 bp):
TTTCAATTGTATTCCTTGGGGAAGGGGT
Found at i:34993 original size:178 final size:178
Alignment explanation
Indices: 34689--35018 Score: 486
Period size: 178 Copynumber: 1.9 Consensus size: 178
34679 TAAGCTCAAA
* * *
34689 TTATGTAATATTAAGTAAACCGTCTATTTCCGTTAACCGAAACAACTAATTATTTGGAAGCATTT
1 TTATATAATATTAAGTAAACCATCTATTTCCGTTAACCGAAACAACAAATTATTTGGAAGCATTT
* * **
34754 TTTATACCTTAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAAC
66 TTGATACCTTAAACATTAAATTTAGTTTTCGAGTCCTTAATGAAAACTGTAGATCATGGAACAAC
* *
34819 CTTTCAAGAGACATTTGAATCATCTCAATCAGACATCTAGAACAAAAG
131 CTTTCAAGAGACACTTAAATCATCTCAATCAGACATCTAGAACAAAAG
**
34867 TTATATAATATTAAGTGGACCATCTA-TTCTCGTTAACCGAAACAACAAATT-TTTCGGAAGCAT
1 TTATATAATATTAAGTAAACCATCTATTTC-CGTTAACCGAAACAACAAATTATTT-GGAAGCAT
34930 TTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTAATGAAAACTGTAGATCATGGAAC
64 TTTTGATACCTT-AAACATTAAATTTAGTTTTCGAGTCCTTAATGAAAACTGTAGATCATGGAAC
* * *
34994 AATCTTTTAATAGACACTTAAATCA
128 AACCTTTCAAGAGACACTTAAATCA
35019 CCTTAATTGG
Statistics
Matches: 135, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
177 9 0.07
178 126 0.93
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (178 bp):
TTATATAATATTAAGTAAACCATCTATTTCCGTTAACCGAAACAACAAATTATTTGGAAGCATTT
TTGATACCTTAAACATTAAATTTAGTTTTCGAGTCCTTAATGAAAACTGTAGATCATGGAACAAC
CTTTCAAGAGACACTTAAATCATCTCAATCAGACATCTAGAACAAAAG
Found at i:35179 original size:18 final size:19
Alignment explanation
Indices: 35156--35201 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
35146 TTTTTATTTT
*
35156 ATATATATACATGTAT-AC
1 ATATATATACACGTATGAC
35174 ATATATATACACGTATGAC
1 ATATATATACACGTATGAC
*
35193 GTATATATA
1 ATATATATA
35202 TAGTTTATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (19 bp):
ATATATATACACGTATGAC
Found at i:37778 original size:20 final size:19
Alignment explanation
Indices: 37766--37818 Score: 88
Period size: 20 Copynumber: 2.7 Consensus size: 19
37756 ATATCGATAA
37766 ATATCGACGGATAAACGGAT
1 ATATCGACGGAT-AACGGAT
37786 ATATCGACGGATACACGGAT
1 ATATCGACGGATA-ACGGAT
37806 ATATCGACGGATA
1 ATATCGACGGATA
37819 TCCCGTGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.21
Consensus pattern (19 bp):
ATATCGACGGATAACGGAT
Found at i:37797 original size:12 final size:12
Alignment explanation
Indices: 37780--37819 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
37770 CGACGGATAA
37780 ACGGATATATCG
1 ACGGATATATCG
37792 ACGG--ATA-C-
1 ACGGATATATCG
37800 ACGGATATATCG
1 ACGGATATATCG
37812 ACGGATAT
1 ACGGATAT
37820 CCCGTGACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
8 4 0.17
9 1 0.04
10 6 0.25
11 1 0.04
12 12 0.50
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (12 bp):
ACGGATATATCG
Found at i:37887 original size:12 final size:12
Alignment explanation
Indices: 37870--37908 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
37860 GTACAGATAT
37870 CGGATATATCGA
1 CGGATATATCGA
37882 CGGATATATCGA
1 CGGATATATCGA
37894 --G--ATATCGA
1 CGGATATATCGA
37902 CGGATAT
1 CGGATAT
37909 TTAATTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.30
10 2 0.09
12 14 0.61
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (12 bp):
CGGATATATCGA
Found at i:43559 original size:56 final size:56
Alignment explanation
Indices: 43489--43644 Score: 287
Period size: 56 Copynumber: 2.8 Consensus size: 56
43479 GTATATCTTA
*
43489 TAAATCTAGAATTGGGTATTTTGATTTGTTCTAATAAAATCATAATACATGTAATG
1 TAAATCTAGAATTGGGTATTTTGATTTGTTCTAATAAAATCATAATACATGAAATG
43545 TAAATCTAGAATTGGGTATTTTGATTTGTTCTAATAAAATCATAATACATGAAATG
1 TAAATCTAGAATTGGGTATTTTGATTTGTTCTAATAAAATCATAATACATGAAATG
*
43601 TAATTCTAGAATTGGGTATTTTGATTTGTT-TAATAAAATCATAA
1 TAAATCTAGAATTGGGTATTTTGATTTGTTCTAATAAAATCATAA
43645 AATCATAATA
Statistics
Matches: 98, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
55 14 0.14
56 84 0.86
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (56 bp):
TAAATCTAGAATTGGGTATTTTGATTTGTTCTAATAAAATCATAATACATGAAATG
Found at i:45114 original size:29 final size:29
Alignment explanation
Indices: 45082--45186 Score: 111
Period size: 29 Copynumber: 3.3 Consensus size: 29
45072 ACTTAATTTT
45082 TTTTATTTTGATCAAAACGTACCCTAAAATTTTA
1 TTTTATTTTGATCAAAACGTACCCT-AAA----A
45116 TTTTTTTTATTTTGATCAAAACGTACCCTAAAA
1 ---TTT-TATTTTGATCAAAACGTACCCTAAAA
* *
45149 TTTTATTTTCATCAAAACGTACTCTAAAA
1 TTTTATTTTGATCAAAACGTACCCTAAAA
45178 TTTTATTTT
1 TTTTATTTT
45187 TTACAGTATA
Statistics
Matches: 65, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
29 33 0.51
30 3 0.05
33 1 0.02
37 6 0.09
38 22 0.34
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (29 bp):
TTTTATTTTGATCAAAACGTACCCTAAAA
Found at i:45121 original size:37 final size:38
Alignment explanation
Indices: 45077--45157 Score: 162
Period size: 38 Copynumber: 2.1 Consensus size: 38
45067 TTTGTACTTA
45077 ATTTTTTTTATTTTGATCAAAACGTACCCTAAAATTTT
1 ATTTTTTTTATTTTGATCAAAACGTACCCTAAAATTTT
45115 ATTTTTTTTATTTTGATCAAAACGTACCCTAAAATTTT
1 ATTTTTTTTATTTTGATCAAAACGTACCCTAAAATTTT
45153 ATTTT
1 ATTTT
45158 CATCAAAACG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.31, C:0.12, G:0.05, T:0.52
Consensus pattern (38 bp):
ATTTTTTTTATTTTGATCAAAACGTACCCTAAAATTTT
Found at i:45400 original size:31 final size:31
Alignment explanation
Indices: 45362--45510 Score: 154
Period size: 31 Copynumber: 4.6 Consensus size: 31
45352 TGTCCGACAT
* *
45362 GCCACGTGTACCAAAAAACAACATGTGGCAC
1 GCCACGTGTACCAAAAAGCGACATGTGGCAC
45393 GCCACGTGTCAAGTGTACCAAAAAGCGACATGTGGCAC
1 GCCA-----C--GTGTACCAAAAAGCGACATGTGGCAC
45431 GCCACGTGTACCAAAAAGCGACATGTGGCAC
1 GCCACGTGTACCAAAAAGCGACATGTGGCAC
* * * *
45462 GCCACATGTACCAAAAAGTGACACGTGGCAT
1 GCCACGTGTACCAAAAAGCGACATGTGGCAC
* **
45493 GCCATGTGTTTCAAAAAG
1 GCCACGTGTACCAAAAAG
45511 TGATACGTGA
Statistics
Matches: 101, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
31 71 0.70
33 1 0.01
36 1 0.01
38 28 0.28
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.16
Consensus pattern (31 bp):
GCCACGTGTACCAAAAAGCGACATGTGGCAC
Found at i:45403 original size:136 final size:132
Alignment explanation
Indices: 45149--45393 Score: 350
Period size: 136 Copynumber: 1.8 Consensus size: 132
45139 TACCCTAAAA
**
45149 TTTTATTTTCATCAAAACGTACTCTAAAATTTTATTTTTTACAGTATAACAAACGGTTCTATTAC
1 TTTTATTTTCATCAAAACGTACTCTAAAATTTTATTTTTTACAGTATAACAAACGACTCTATTAC
* *
45214 GATGTCCGACGTGATATGCCACGTGTACCAAAAAGCGACAAGTGGCACGTGTCACGTTTGCACCC
66 GATGTCCGAC--G--ATGCCACGTGTACCAAAAAACAACAAGTGGCACGTGTCACGTTTGCACCC
45279 AACTTT
127 AACTTT
* * * *
45285 TTTTATTTTGATCAAAATGTA-TCCTAAAATTTTATTTTTTACGGTATGACAAACGACTCTATTA
1 TTTTATTTTCATCAAAACGTACT-CTAAAATTTTATTTTTTACAGTATAACAAACGACTCTATTA
*
45349 CGATGTCCGAC-ATGCCACGTGTACCAAAAAACAACATGTGGCACG
65 CGATGTCCGACGATGCCACGTGTACCAAAAAACAACAAGTGGCACG
45394 CCACGTGTCA
Statistics
Matches: 99, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
131 31 0.31
135 1 0.01
136 67 0.68
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33
Consensus pattern (132 bp):
TTTTATTTTCATCAAAACGTACTCTAAAATTTTATTTTTTACAGTATAACAAACGACTCTATTAC
GATGTCCGACGATGCCACGTGTACCAAAAAACAACAAGTGGCACGTGTCACGTTTGCACCCAACT
TT
Found at i:50138 original size:45 final size:47
Alignment explanation
Indices: 50048--50139 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 47
50038 TAGATTCCAC
50048 AACAAAAACAAAAAGCAAAGCCACAATATAAAAAATGGAAGAAATTA
1 AACAAAAACAAAAAGCAAAGCCACAATATAAAAAATGGAAGAAATTA
* * * *
50095 AACAAAAACAAGAATCACAGCCAC-A-GTAAAAAATGGAAGAAATTA
1 AACAAAAACAAAAAGCAAAGCCACAATATAAAAAATGGAAGAAATTA
50140 GATAAAACGT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 19 0.46
46 1 0.02
47 21 0.51
ACGTcount: A:0.63, C:0.14, G:0.12, T:0.11
Consensus pattern (47 bp):
AACAAAAACAAAAAGCAAAGCCACAATATAAAAAATGGAAGAAATTA
Found at i:52751 original size:111 final size:107
Alignment explanation
Indices: 52427--52843 Score: 364
Period size: 107 Copynumber: 3.7 Consensus size: 107
52417 ATCTTTATTA
* * * * *
52427 TAGGGTTTAAGAAATGAAATTTCAAACAATTTATCACGAAGTTTAGCCTCTAATTCA-AGAAAAG
1 TAGGGTTTTAGAAATAAAATATCAAACAAATTATCAC-AAGTTTAGCCACTAATTCATAG-AAA-
*
52491 TTATTTAATAGGGTAAGTTTTAAA--TTTAATATATTAATTATAG
63 TTATTTTATAGGGTAAGTTTTAAATTTTTAATATATTAATTATAG
* * * * * * * *
52534 TATGGATTTAGAAATAAAATATCAAAAAAAAATGCATCATAAAGTTTAACCACAAATTCATTATA
1 TAGGGTTTTAGAAATAAAATATC--AAACAAAT-TATCA-CAAGTTTAGCCACTAATTCA-TAGA
52599 AATTATTTTATAGGGTAAGTTTT-AATATTTTAA-ATATTAATTATAG
61 AATTATTTTATAGGGTAAGTTTTAAAT-TTTTAATATATTAATTATAG
* *
52645 TAGGGTTTTAGAAATAAAATCTCAAACAAATTATCACAAGGTTTAGCAACTAA-TCACTAGAAAT
1 TAGGGTTTTAGAAATAAAATATCAAACAAATTATCACAA-GTTTAGCCACTAATTCA-TAGAAAT
52709 TATTTTATAGGGTAAGTTTTAAATTTTATAATATTATATAATTATATAG
64 TATTTTATAGGGTAAGTTTTAAATTTT-TAATA-TAT-TAA-T-TATAG
* *
52758 TAGGATTATAGAAAT--AATATCAAACAATTATAATTTATCACAATGTTTAGCCACTAATTCATT
1 TAGGGTTTTAGAAATAAAATATCAAAC----A-AA-TTATCACAA-GTTTAGCCACTAATTCA-T
*
52821 AAAAATTACTATTTTATAGGGTA
58 AGAAA-T--TATTTTATAGGGTA
52844 TTTCATATAT
Statistics
Matches: 251, Mismatches: 32, Indels: 40
0.78 0.10 0.12
Matches are distributed among these distances:
107 52 0.21
108 20 0.08
109 16 0.06
110 43 0.17
111 48 0.19
112 7 0.03
113 18 0.07
115 1 0.00
116 2 0.01
117 21 0.08
118 8 0.03
119 1 0.00
121 14 0.06
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (107 bp):
TAGGGTTTTAGAAATAAAATATCAAACAAATTATCACAAGTTTAGCCACTAATTCATAGAAATTA
TTTTATAGGGTAAGTTTTAAATTTTTAATATATTAATTATAG
Found at i:55941 original size:35 final size:34
Alignment explanation
Indices: 55885--55957 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 34
55875 GCTTTGAGGT
*
55885 GGTTTGGGTTTTGGTTTGATGGGTT-ATGTAGTTG
1 GGTTTGGGCTTTGGTTTGATGGGTTAAT-TAGTTG
*
55919 GGTTTGGGCTTTGATTTTGATGGGTTAATTAGTTG
1 GGTTTGGGCTTTG-GTTTGATGGGTTAATTAGTTG
55954 GGTT
1 GGTT
55958 AGTTTTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
34 12 0.34
35 21 0.60
36 2 0.06
ACGTcount: A:0.11, C:0.01, G:0.38, T:0.49
Consensus pattern (34 bp):
GGTTTGGGCTTTGGTTTGATGGGTTAATTAGTTG
Found at i:56634 original size:35 final size:35
Alignment explanation
Indices: 56585--56725 Score: 203
Period size: 35 Copynumber: 4.0 Consensus size: 35
56575 GAATTTCATC
*
56585 AAGTTTTTTTAATTGGGAAAGTTCCCACCAGTTTT
1 AAGTTTTTTAAATTGGGAAAGTTCCCACCAGTTTT
56620 AAGTTTTTTAAATTGGGAAAGTTCCCACCAGTTTT
1 AAGTTTTTTAAATTGGGAAAGTTCCCACCAGTTTT
* * *
56655 AAGTCTTTTAAATTGGGAAAGTCCCCATCAGCTTTT
1 AAGTTTTTTAAATTGGGAAAGTTCCCACCAG-TTTT
* *
56691 AAG-TTTTCAAATTGGGAAAGTTCCCATTCAGTTTT
1 AAGTTTTTTAAATTGGGAAAGTTCCCA-CCAGTTTT
56726 TCAAAGTTCC
Statistics
Matches: 97, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
35 86 0.89
36 11 0.11
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.40
Consensus pattern (35 bp):
AAGTTTTTTAAATTGGGAAAGTTCCCACCAGTTTT
Found at i:56744 original size:21 final size:21
Alignment explanation
Indices: 56707--56746 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
56697 TCAAATTGGG
*
56707 AAAGTTCCCATTCAGTTTTTC
1 AAAGTTCCCATCCAGTTTTTC
56728 AAAGTTCCCA-CCAAGTTTT
1 AAAGTTCCCATCC-AGTTTT
56747 AGTTTTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.38
Consensus pattern (21 bp):
AAAGTTCCCATCCAGTTTTTC
Found at i:57394 original size:14 final size:14
Alignment explanation
Indices: 57375--57419 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
57365 TGATTCAATG
*
57375 CTAACTCCTAAGTT
1 CTAACTCCTAAGTC
*
57389 CTAACTCCTAAATC
1 CTAACTCCTAAGTC
*
57403 CTAA-TCCTAAGGC
1 CTAACTCCTAAGTC
57416 CTAA
1 CTAA
57420 GCTATAAAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.33, C:0.31, G:0.07, T:0.29
Consensus pattern (14 bp):
CTAACTCCTAAGTC
Found at i:58698 original size:14 final size:13
Alignment explanation
Indices: 58679--58801 Score: 85
Period size: 14 Copynumber: 9.2 Consensus size: 13
58669 CTGAATTACT
58679 GAATTACAAAAACA
1 GAATTA-AAAAACA
58693 GAATTAAAAAAACA
1 GAATT-AAAAAACA
*
58707 GAATTTCAAAAACA
1 GAA-TTAAAAAACA
*
58721 GAA-T----AACT
1 GAATTAAAAAACA
58729 GAATTACAAAAACA
1 GAATTA-AAAAACA
58743 GAATTGAAAAAACA
1 GAATT-AAAAAACA
* * *
58757 AAATTACAGAAATA
1 GAATTA-AAAAACA
*
58771 GAGTTGAACAAAACA
1 GAATT-AA-AAAACA
58786 GAATTAAAAAACA
1 GAATTAAAAAACA
58799 GAA
1 GAA
58802 ATATAGAACC
Statistics
Matches: 86, Mismatches: 11, Indels: 25
0.70 0.09 0.20
Matches are distributed among these distances:
8 6 0.07
9 1 0.01
12 1 0.01
13 10 0.12
14 55 0.64
15 13 0.15
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.16
Consensus pattern (13 bp):
GAATTAAAAAACA
Found at i:58710 original size:28 final size:28
Alignment explanation
Indices: 58679--58801 Score: 116
Period size: 28 Copynumber: 4.6 Consensus size: 28
58669 CTGAATTACT
58679 GAATTACAAAAACAGAATTAAAAAAACA
1 GAATTACAAAAACAGAATTAAAAAAACA
* *
58707 GAATTTCAAAAACAGAA-T-----AACT
1 GAATTACAAAAACAGAATTAAAAAAACA
*
58729 GAATTACAAAAACAGAATTGAAAAAACA
1 GAATTACAAAAACAGAATTAAAAAAACA
* * * * *
58757 AAATTACAGAAATAGAGTTGAACAAAACA
1 GAATTACAAAAACAGAATT-AAAAAAACA
58786 GAATTA-AAAAACAGAA
1 GAATTACAAAAACAGAA
58802 ATATAGAACC
Statistics
Matches: 74, Mismatches: 14, Indels: 14
0.73 0.14 0.14
Matches are distributed among these distances:
22 19 0.26
23 1 0.01
27 1 0.01
28 41 0.55
29 12 0.16
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.16
Consensus pattern (28 bp):
GAATTACAAAAACAGAATTAAAAAAACA
Found at i:58737 original size:50 final size:50
Alignment explanation
Indices: 58665--58761 Score: 158
Period size: 50 Copynumber: 1.9 Consensus size: 50
58655 ACCTAAAATC
* * *
58665 AAAACTGAATTACTGAATTACAAAAACAGAATTAAAAAAACAGAATTTCA
1 AAAACAGAATAACTGAATTACAAAAACAGAATTAAAAAAACAAAATTTCA
*
58715 AAAACAGAATAACTGAATTACAAAAACAGAATTGAAAAAACAAAATT
1 AAAACAGAATAACTGAATTACAAAAACAGAATTAAAAAAACAAAATT
58762 ACAGAAATAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.61, C:0.11, G:0.08, T:0.20
Consensus pattern (50 bp):
AAAACAGAATAACTGAATTACAAAAACAGAATTAAAAAAACAAAATTTCA
Found at i:58738 original size:22 final size:22
Alignment explanation
Indices: 58665--58746 Score: 74
Period size: 22 Copynumber: 3.5 Consensus size: 22
58655 ACCTAAAATC
* *
58665 AAAACTGAATTACTGAATTACA
1 AAAACAGAATAACTGAATTACA
* *
58687 AAAACAGAATTAAAAAAACAGAATTTCA
1 AAAACAGAA-T-----AACTGAATTACA
58715 AAAACAGAATAACTGAATTACA
1 AAAACAGAATAACTGAATTACA
58737 AAAACAGAAT
1 AAAACAGAAT
58747 TGAAAAAACA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
22 28 0.58
23 1 0.02
27 1 0.02
28 18 0.38
ACGTcount: A:0.60, C:0.12, G:0.09, T:0.20
Consensus pattern (22 bp):
AAAACAGAATAACTGAATTACA
Found at i:61307 original size:13 final size:13
Alignment explanation
Indices: 61285--61332 Score: 87
Period size: 13 Copynumber: 3.7 Consensus size: 13
61275 CTCATTTCTC
*
61285 AAGCATTACAGGT
1 AAGCACTACAGGT
61298 AAGCACTACAGGT
1 AAGCACTACAGGT
61311 AAGCACTACAGGT
1 AAGCACTACAGGT
61324 AAGCACTAC
1 AAGCACTAC
61333 TAGTATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.17
Consensus pattern (13 bp):
AAGCACTACAGGT
Found at i:62219 original size:2 final size:2
Alignment explanation
Indices: 62212--62236 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
62202 AATAACTTAA
62212 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
62237 AGTACGAATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73217 original size:3 final size:3
Alignment explanation
Indices: 73211--73242 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
73201 AAGATCATCA
73211 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
73243 TTTAGAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:73617 original size:16 final size:16
Alignment explanation
Indices: 73596--73627 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
73586 AAAGAGAAAC
73596 AGAAAAATGAGTAAAA
1 AGAAAAATGAGTAAAA
73612 AGAAAAATGAGTAAAA
1 AGAAAAATGAGTAAAA
73628 TCCAGAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (16 bp):
AGAAAAATGAGTAAAA
Found at i:74068 original size:3 final size:3
Alignment explanation
Indices: 74060--74090 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
74050 TACATAAGCT
74060 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA C
74091 TCTCACTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:78003 original size:2 final size:2
Alignment explanation
Indices: 77996--78031 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
77986 AAACCTTACC
77996 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
78032 TCTTGTCTCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85085 original size:26 final size:27
Alignment explanation
Indices: 85031--85085 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
85021 CAAAAAAAAA
* *
85031 AAAAAACTGAACTAACTCAACTGACTC
1 AAAAAACTGAACTAACCCAACAGACTC
85058 AAAAAACTG-ACTAAACCCAACAGA-TC
1 AAAAAACTGAACT-AACCCAACAGACTC
85084 AA
1 AA
85086 TAGATTTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.53, C:0.25, G:0.07, T:0.15
Consensus pattern (27 bp):
AAAAAACTGAACTAACCCAACAGACTC
Found at i:91492 original size:8 final size:8
Alignment explanation
Indices: 91479--91503 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
91469 AAGGAAATTT
91479 AAAAAATA
1 AAAAAATA
91487 AAAAAATA
1 AAAAAATA
91495 AAAAAATA
1 AAAAAATA
91503 A
1 A
91504 TGGCAGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAATA
Found at i:93874 original size:42 final size:45
Alignment explanation
Indices: 93823--93914 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
93813 AGTGCATTAC
* *
93823 CTAA-ATTCTACT-C-C-ATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCAATCTCTAGATAATTCATCAAAATAAAA
93864 CTAATATTCTACTCCTCAATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTACTCCTCAATCTCTAGATAATTCATCAAAATAAAA
93909 CTAATA
1 CTAATA
93915 CTAATTGTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.18
43 1 0.02
44 1 0.02
45 31 0.69
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.33
Consensus pattern (45 bp):
CTAATATTCTACTCCTCAATCTCTAGATAATTCATCAAAATAAAA
Found at i:94521 original size:295 final size:292
Alignment explanation
Indices: 93989--94575 Score: 930
Period size: 295 Copynumber: 2.0 Consensus size: 292
93979 AATCTTGATT
*
93989 GCAATTGTTAAATTAATGAACTCGAGTAGACACATTTACAGCACTAATCCTTTGGAATTCCGGAA
1 GCAATTGTTAAATTAATGAACTCGAGTAGACACATTTACAGCACCAATCCTTTGGAATTCCGGAA
**
94054 GAGGAGTTGAACCGGCAAATCCTAATATCCACACACAATCAATATGTAATTAAAACACACTTAAT
66 GAGGAGTTGAACCGGCAAATCCTAATATCCACACACAATCAATACATAATTAAAACACACTTAAT
* *
94119 CATAAATATAAAAATAGTAAATTACAAAAAAGACAGCATAAAAAGTAAGGGAGGAAATTCATCGA
131 CATAAATACAAAAATAGTAAATTACAAAAAAGACAGCATAAAAAGTAAGGGAGGAAATTCATCAA
* *
94184 GGCCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAAAGCCAAAAGGAGGCACCAGAT
196 GGCCCTTTTTAGTCACCCGAAAAGTGAGAAAAGAC--AAAAAAAAGCCAAAAGGAGACACCACAT
94249 TAATCCTCAATTTGGCCTTTTAAGTAATTTCCATA
259 TAATCCTCAATTTGGCC-TTTAAGTAATTTCCATA
* * *
94284 GCAATTGTTAAATTAATGAACTCGGGTAGATACATTTATAGCACCAATCCTTTGGAATT-CGGCA
1 GCAATTGTTAAATTAATGAACTCGAGTAGACACATTTACAGCACCAATCCTTTGGAATTCCGG-A
* * *
94348 A-AGGAGTTGAACCGGTAAATCCTAATATCCACTCACAATTAATACATAATTAAAACACACTTAA
65 AGAGGAGTTGAACCGGCAAATCCTAATATCCACACACAATCAATACATAATTAAAACACACTTAA
* *
94412 TCATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGGAGT-AAAAGTAAGGGAGGAAATTCAT
130 TCATAAATACAAAAATAGTAAATTACAAAAAA-GACAGCA-TAAAAAGTAAGGGAGGAAATTCAT
*
94476 CAAGAG-CCTTTTTAGTCACCCGAAAAGTGAGAAAAGACCAAAAAAAGCCAAAAGGAGACACCAC
193 CAAG-GCCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAGCCAAAAGGAGACACCAC
*
94540 ATTAATCCTCAATTTGGCCTTTAAGTACTTTCCATA
257 ATTAATCCTCAATTTGGCCTTTAAGTAATTTCCATA
94576 ATCACTAAAA
Statistics
Matches: 271, Mismatches: 17, Indels: 11
0.91 0.06 0.04
Matches are distributed among these distances:
292 16 0.06
293 42 0.15
294 92 0.34
295 119 0.44
296 2 0.01
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.24
Consensus pattern (292 bp):
GCAATTGTTAAATTAATGAACTCGAGTAGACACATTTACAGCACCAATCCTTTGGAATTCCGGAA
GAGGAGTTGAACCGGCAAATCCTAATATCCACACACAATCAATACATAATTAAAACACACTTAAT
CATAAATACAAAAATAGTAAATTACAAAAAAGACAGCATAAAAAGTAAGGGAGGAAATTCATCAA
GGCCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAGCCAAAAGGAGACACCACATTA
ATCCTCAATTTGGCCTTTAAGTAATTTCCATA
Found at i:98687 original size:41 final size:40
Alignment explanation
Indices: 98594--98714 Score: 215
Period size: 41 Copynumber: 3.0 Consensus size: 40
98584 AAATAGTTGC
*
98594 AAAATCATGTCTTTTTAAGAATTGAATGTTTGATGCTTCTT
1 AAAATCATGTC-TTTTAAGAATTGAATGTTTGATGTTTCTT
98635 AAAATCATGTCTTTTAAGAATTGAATGTTTGATGTTTCTT
1 AAAATCATGTCTTTTAAGAATTGAATGTTTGATGTTTCTT
98675 AAAATCATTGTCTTTTAAGAATTGAATGTTTGATGTTTCT
1 AAAATCA-TGTCTTTTAAGAATTGAATGTTTGATGTTTCT
98715 AGGTAACTTT
Statistics
Matches: 78, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
40 35 0.45
41 43 0.55
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (40 bp):
AAAATCATGTCTTTTAAGAATTGAATGTTTGATGTTTCTT
Found at i:102297 original size:22 final size:23
Alignment explanation
Indices: 102252--102297 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
102242 ATAATGGAAG
*
102252 ACACTTAAAGCCTTTAAATACTAA
1 ACACTTAAA-CCTTAAAATACTAA
*
102276 ACACTTAAA-CTTAAAATCCTAA
1 ACACTTAAACCTTAAAATACTAA
102298 TTCTAATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.55
24 9 0.45
ACGTcount: A:0.48, C:0.22, G:0.02, T:0.28
Consensus pattern (23 bp):
ACACTTAAACCTTAAAATACTAA
Found at i:102908 original size:17 final size:17
Alignment explanation
Indices: 102888--102926 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
102878 CTAGTAATTT
102888 AAGATCACCAGTGATGC
1 AAGATCACCAGTGATGC
*
102905 AAGATCACCGGTGATGC
1 AAGATCACCAGTGATGC
102922 AAGAT
1 AAGAT
102927 TACATGGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.18
Consensus pattern (17 bp):
AAGATCACCAGTGATGC
Found at i:103886 original size:42 final size:42
Alignment explanation
Indices: 103822--103904 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
103812 TAGCTAAGTC
103822 TTGAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCA
1 TTGAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCA
* *
103864 TTGAAAATTCTTTGTAACTTAAGAAATACTCAACTCAAATC
1 TTGAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
103905 CTAATCCTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (42 bp):
TTGAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCA
Found at i:104042 original size:56 final size:56
Alignment explanation
Indices: 103970--104079 Score: 211
Period size: 56 Copynumber: 2.0 Consensus size: 56
103960 TTTATTTTGT
*
103970 AGAATAATTAAGTAGAGATAGGGGGATATGATTTATTATAACATTTATTGTGTGGA
1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGGA
104026 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTG
1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTG
104080 AAAGGAAAAG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.35
Consensus pattern (56 bp):
AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGGA
Found at i:110732 original size:4 final size:4
Alignment explanation
Indices: 110717--110758 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
110707 ACAAATCATG
* * *
110717 AAGA ATGA AAGA AAGA AAGA AAGA AAGA AAGG AAGG AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
110759 AGATCTAGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:112748 original size:2 final size:2
Alignment explanation
Indices: 112743--112777 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
112733 ATTTTTTTAA
112743 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
112778 GTATTGAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:118762 original size:39 final size:39
Alignment explanation
Indices: 118719--118801 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 39
118709 CATCAAGAGG
* * *
118719 AAGAAGAACAGAAACA-AGTTCAACAACATCAA-AAACATC
1 AAGAAGAACAAAAACAGA-ATCAACAACAACAACAAA-ATC
*
118758 AAGAAGAAGAAAAACAGAATCAACAACAACAACAAAATC
1 AAGAAGAACAAAAACAGAATCAACAACAACAACAAAATC
118797 AAGAA
1 AAGAA
118802 CATGAAGAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
39 34 0.89
40 4 0.11
ACGTcount: A:0.64, C:0.18, G:0.11, T:0.07
Consensus pattern (39 bp):
AAGAAGAACAAAAACAGAATCAACAACAACAACAAAATC
Found at i:118788 original size:45 final size:46
Alignment explanation
Indices: 118709--118815 Score: 117
Period size: 45 Copynumber: 2.3 Consensus size: 46
118699 AACCCAACAT
* * ***
118709 CATCAAGAGGAAGAAGAACAGAAACAAGTTCAACAAC-ATCAAAAA
1 CATCAAGAAGAAGAAAAACAGAAACAACAACAACAACAATCAAAAA
* *
118754 CATCAAGAAGAAGAAAAACAGAATCAACAACAACAACAAAATCAAGAA
1 CATCAAGAAGAAGAAAAACAGAAACAACAACAACAAC--AATCAAAAA
*
118802 CATGAAGAAGAAGA
1 CATCAAGAAGAAGA
118816 GAATCATCAT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
45 31 0.61
48 20 0.39
ACGTcount: A:0.61, C:0.17, G:0.15, T:0.07
Consensus pattern (46 bp):
CATCAAGAAGAAGAAAAACAGAAACAACAACAACAACAATCAAAAA
Found at i:118837 original size:3 final size:3
Alignment explanation
Indices: 118831--118891 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
118821 ATCATCAATT
118831 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
118879 AGA AGA AGC AGA A
1 AGA AGA AGA AGA A
118892 AATAAGCAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.02, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:128136 original size:437 final size:436
Alignment explanation
Indices: 127307--128358 Score: 1251
Period size: 439 Copynumber: 2.4 Consensus size: 436
127297 TTTATATTTG
* * *
127307 TATTTTTTTTTCTATTTGTCCGATTAAGGTGATTCAAGTGTTTATTAAAAAGTAATTTCATGATC
1 TATTTTTTTTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTAATGATC
* * ** * *
127372 TACAATTTTCATTAAGAACTCAAAAGTCAA-TTTTACTGTTTTGATTCTACAAAATACTTCCGAA
66 TACAACTTTCATGAAG-ACTCAAAAG-CAATTTTTA-TGTTTCAATTCTAAAAAATGCTTCCGAA
* * * * *
127436 ATTTTGTGGTTTTGATTGCCGGTTAATTTAATATCGTATAATTTTTTGTCCACATATCCAATTGA
128 ATTTTGTGGTTTTGATTGCCAGTTAATTTAATACCATATAA-TTTTCGTCCACATATCCAATTAA
* * * * * *
127501 AGTTATTGAAGTGTCGGTTAAAAGGTTATTGCATGATTTACGACTTTCATGAAGGACCCGAAAGC
192 AGTTATTCAAGTGTCGGTTAAAAGGTTACTGCATAATCTACGACTTTCATAAAGAACCCGAAAGC
* *
127566 TAAATTTGATCTATAAGTTTCGTGAAGGGTTCAAAAGGGAATTTTTAAGATTCAAAATCCCCATT
257 TAAATTTGATCTACAAGTTTCATGAAGGGTTCAAAAGGGAATTTTTAAGATTCAAAATCCCCATT
* * * * * *
127631 AACAAACATTTTCTTATTTGGATTATTTATCAAATGACCCTCATAGTTTTCTACTTTATACTACT
322 AACAAACATTTTCTTATTTGAATTAGTTACCAAATCACCCTCATACTTTTCTACTTTATACCACT
* *
127696 TAGTTCTTTACAAATTCTATCTTTATCTAACG-TTTAA-GC-T-TTATTTTTTT
387 TAGTCCTTTACAAATTCTATC-TTA-CT--CGATTTAACACTTATTATTTTTTT
* * *
127746 TATTCTTTTTTCTATTTGTCCGATTAAGTTGATTCATGTGTCTATTAAAAGGTAATTTAATGATC
1 TATTTTTTTTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTAATGATC
* *
127811 TACAACTTTCATGAATGACTCAAAAGCAAATTTTTATGTTTCAATTCAAAAAAATGCTTCCTAAA
66 TACAACTTTCATGAA-GACTCAAAAGC-AATTTTTATGTTTCAATTCTAAAAAATGCTTCCGAAA
* ** *
127876 -TTTGTTTGTTTTGATTGTTAGTCT-ATTTAATACCATATAA-TTTCGATCCACATGTCCAATTA
129 TTTTG-TGGTTTTGATTGCCAGT-TAATTTAATACCATATAATTTTCG-TCCACATATCCAATTA
*
127938 AAGTTATTCAAGTGTCGGTTAAAAGGTTACTGTATAATCTACGACTTTCATAAAGAACCCGAAAG
191 AAGTTATTCAAGTGTCGGTTAAAAGGTTACTGCATAATCTACGACTTTCATAAAGAACCCGAAAG
* * * * *
128003 -TTAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAAATCTCCAT
256 CTAAATTTGATCTACAAGTTTCATGAAGGGTTCAAAAGGGAATTTTTAAGATTCAAAATCCCCAT
* * *
128067 TAACAAATATTTTCTTATTTGAATTAGTTACCAAATCACCCTCATACTTTTCTATTTTATGCCAC
321 TAACAAACATTTTCTTATTTGAATTAGTTACCAAATCACCCTCATACTTTTCTACTTTATACCAC
* * *
128132 TTAGTCCTTTCCAAATTTTATCTTACTCGATTTAACACTTCATTTTTTTTTT
386 TTAGTCCTTTACAAATTCTATCTTACTCGATTTAACACTT-ATTATTTTTTT
* * * * *
128184 TATTTTTTTTGTTCTATTTGTCCAATTAAGGTAATTCAGGTGTCTATTAGAAGGTAATTTTATGA
1 TA-TTTTTTT-TTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTAATGA
* ** **
128249 TCTACAACTTTCATGAAAGACTCAAAAACTAATTTTTATAATTCAATTCTAAAAAATGCTTTTGA
64 TCTACAACTTTCATG-AAGACTCAAAAGC-AATTTTTATGTTTCAATTCTAAAAAATGCTTCCGA
* * * * * * *
128314 AGTTTTGTGATTTCGATTGACAATCT-ATTTAATAACATATTATTT
127 AATTTTGTGGTTTTGATTGCCAGT-TAATTTAATACCATATAATTT
128359 GTGATCCAGA
Statistics
Matches: 522, Mismatches: 75, Indels: 30
0.83 0.12 0.05
Matches are distributed among these distances:
433 2 0.00
434 5 0.01
435 3 0.01
436 4 0.01
437 136 0.26
438 88 0.17
439 139 0.27
440 137 0.26
441 8 0.02
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (436 bp):
TATTTTTTTTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTAATGATC
TACAACTTTCATGAAGACTCAAAAGCAATTTTTATGTTTCAATTCTAAAAAATGCTTCCGAAATT
TTGTGGTTTTGATTGCCAGTTAATTTAATACCATATAATTTTCGTCCACATATCCAATTAAAGTT
ATTCAAGTGTCGGTTAAAAGGTTACTGCATAATCTACGACTTTCATAAAGAACCCGAAAGCTAAA
TTTGATCTACAAGTTTCATGAAGGGTTCAAAAGGGAATTTTTAAGATTCAAAATCCCCATTAACA
AACATTTTCTTATTTGAATTAGTTACCAAATCACCCTCATACTTTTCTACTTTATACCACTTAGT
CCTTTACAAATTCTATCTTACTCGATTTAACACTTATTATTTTTTT
Found at i:128346 original size:440 final size:435
Alignment explanation
Indices: 127307--128358 Score: 1249
Period size: 440 Copynumber: 2.4 Consensus size: 435
127297 TTTATATTTG
* * *
127307 TATTTTTTTTTCTATTTGTCCGATTAAGGTGATTCAAGTGTTTATTAAAAAGTAATTTCATGATC
1 TATTTTTTTTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTAATGATC
* * * ** * * *
127372 TACAATTTTCAT-TAAGAACTC-AAAAGTCAA-TTTTACTGTTTTGATTCTACAAAATACTTCCG
66 TACAACTTTCATGAAAG-ACTCAAAAACT-AATTTTTA-TGTTTCAATTCTAAAAAATGCTTCTG
* * * * *
127434 AAATTTTGTGGTTTTGATTGCCGGT-TAATTTAATATCGTATAATTTTTTGTCCACATATCCAAT
128 AAATTTTGT-GTTTTGATTGACAGTCT-ATTTAATAACATATAA--TTTCGTCCACATATCCAAT
* * * * * * *
127498 TGAAGTTATTGAAGTGTCGGTTAAAAGGTTATTGCATGATTTACGACTTTCATGAAGGACCCGAA
189 TAAAGTTATTCAAGTGTCGGTTAAAAGGTTACTGCATAATCTACGACTTTCATAAAGAACCCGAA
* *
127563 AGCTAAATTTGATCTATAAGTTTCGTGAAGGGTTCAAAAGGGAATTTTTAAGATTCAAAATCCCC
254 AGCTAAATTTGATCTACAAGTTTCATGAAGGGTTCAAAAGGGAATTTTTAAGATTCAAAATCCCC
* * * * * *
127628 ATTAACAAACATTTTCTTATTTGGATTATTTATCAAATGACCCTCATAGTTTTCTACTTTATACT
319 ATTAACAAACATTTTCTTATTTGAATTAGTTACCAAATCACCCTCATACTTTTCTACTTTATACC
* *
127693 ACTTAGTTCTTTACAAATTCTATCTTTATCTAACGTTTAAGCTTTATTTTTTT
384 ACTTAGTCCTTTACAAATTCTATCTTTATCT-ACGTTTAAACTTTATTTTTTT
* * *
127746 TATTCTTTTTTCTATTTGTCCGATTAAGTTGATTCATGTGTCTATTAAAAGGTAATTTAATGATC
1 TATTTTTTTTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTAATGATC
* * * *
127811 TACAACTTTCATGAATGACTCAAAAGCAAATTTTTATGTTTCAATTCAAAAAAATGCTTCCT-AA
66 TACAACTTTCATGAAAGACTCAAAAACTAATTTTTATGTTTCAATTCTAAAAAATGCTT-CTGAA
* ** * *
127875 ATTTGTTTGTTTTGATTGTTAGTCTATTTAATACCATATAATTTCGATCCACATGTCCAATTAAA
130 ATTT-TGTGTTTTGATTGACAGTCTATTTAATAACATATAATTTCG-TCCACATATCCAATTAAA
*
127940 GTTATTCAAGTGTCGGTTAAAAGGTTACTGTATAATCTACGACTTTCATAAAGAACCCGAAAG-T
193 GTTATTCAAGTGTCGGTTAAAAGGTTACTGCATAATCTACGACTTTCATAAAGAACCCGAAAGCT
* * * * *
128004 TAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAAATCTCCATTA
258 AAATTTGATCTACAAGTTTCATGAAGGGTTCAAAAGGGAATTTTTAAGATTCAAAATCCCCATTA
* * *
128069 ACAAATATTTTCTTATTTGAATTAGTTACCAAATCACCCTCATACTTTTCTATTTTATGCCACTT
323 ACAAACATTTTCTTATTTGAATTAGTTACCAAATCACCCTCATACTTTTCTACTTTATACCACTT
* * *
128134 AGTCCTTTCCAAATTTTATC-TTA-CT-CGATTTAACACTTCATTTTTTTTTT
388 AGTCCTTTACAAATTCTATCTTTATCTACG-TTTAA-AC-T--TTATTTTTTT
* * * * *
128184 TATTTTTTTTGTTCTATTTGTCCAATTAAGGTAATTCAGGTGTCTATTAGAAGGTAATTTTATGA
1 TA-TTTTTTT-TTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTAATGA
** *
128249 TCTACAACTTTCATGAAAGACTCAAAAACTAATTTTTATAATTCAATTCTAAAAAATGCTTTTGA
64 TCTACAACTTTCATGAAAGACTCAAAAACTAATTTTTATGTTTCAATTCTAAAAAATGCTTCTGA
* * * *
128314 AGTTTTGTGATTTCGATTGACAATCTATTTAATAACATATTATTT
129 AATTTTGTG-TTTTGATTGACAGTCTATTTAATAACATATAATTT
128359 GTGATCCAGA
Statistics
Matches: 520, Mismatches: 77, Indels: 31
0.83 0.12 0.05
Matches are distributed among these distances:
433 2 0.00
434 5 0.01
435 3 0.01
436 4 0.01
437 136 0.26
438 83 0.16
439 136 0.26
440 151 0.29
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (435 bp):
TATTTTTTTTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTAATGATC
TACAACTTTCATGAAAGACTCAAAAACTAATTTTTATGTTTCAATTCTAAAAAATGCTTCTGAAA
TTTTGTGTTTTGATTGACAGTCTATTTAATAACATATAATTTCGTCCACATATCCAATTAAAGTT
ATTCAAGTGTCGGTTAAAAGGTTACTGCATAATCTACGACTTTCATAAAGAACCCGAAAGCTAAA
TTTGATCTACAAGTTTCATGAAGGGTTCAAAAGGGAATTTTTAAGATTCAAAATCCCCATTAACA
AACATTTTCTTATTTGAATTAGTTACCAAATCACCCTCATACTTTTCTACTTTATACCACTTAGT
CCTTTACAAATTCTATCTTTATCTACGTTTAAACTTTATTTTTTT
Found at i:128652 original size:34 final size:34
Alignment explanation
Indices: 128612--128677 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
128602 TTTGAAATGA
*
128612 AACCAAAATCAGTATGAAAATTACATAATACACC
1 AACCAAAATCAGTATGAAAATTACACAATACACC
*
128646 AACCAAAATCAGTATGAAAATTATACAATACA
1 AACCAAAATCAGTATGAAAATTACACAATACA
128678 TCATCAGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.55, C:0.18, G:0.06, T:0.21
Consensus pattern (34 bp):
AACCAAAATCAGTATGAAAATTACACAATACACC
Found at i:130586 original size:33 final size:33
Alignment explanation
Indices: 130549--130617 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
130539 ACTCGACAAA
*
130549 CTGAACTAACTCAAACATTCAAGATCTAAAGAT
1 CTGAACTAACTCAAACATCCAAGATCTAAAGAT
130582 CTGAACTAACTCAAACATCCAAGATCTAAAGAT
1 CTGAACTAACTCAAACATCCAAGATCTAAAGAT
130615 CTG
1 CTG
130618 GAGACTCATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.43, C:0.23, G:0.10, T:0.23
Consensus pattern (33 bp):
CTGAACTAACTCAAACATCCAAGATCTAAAGAT
Found at i:131061 original size:18 final size:19
Alignment explanation
Indices: 131022--131061 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
131012 GTGCTCCCGT
131022 TGTGATGCTCCCACTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
131043 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
131061 T
1 T
131062 TCTGACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Found at i:131464 original size:31 final size:29
Alignment explanation
Indices: 131425--131510 Score: 104
Period size: 31 Copynumber: 2.9 Consensus size: 29
131415 AGTAGTTGAT
131425 AAAA-AATAAAAATAAAAATAAAAAGCCAG
1 AAAAGAATAAAAATAAAAATAAAAAG-CAG
**
131454 AAAACGAATAAAAA-AAAGAATAAAAAAGGTG
1 AAAA-GAATAAAAATAAA-AAT-AAAAAGCAG
131485 AAAAGAATAAAAATAAAAATAAAAAG
1 AAAAGAATAAAAATAAAAATAAAAAG
131511 TTAAGAGAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
29 10 0.20
30 15 0.30
31 19 0.38
32 6 0.12
ACGTcount: A:0.76, C:0.03, G:0.10, T:0.10
Consensus pattern (29 bp):
AAAAGAATAAAAATAAAAATAAAAAGCAG
Found at i:142593 original size:33 final size:33
Alignment explanation
Indices: 142556--142621 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
142546 TTTGACTTCA
*
142556 ATTAATAGTGTTCCCACCTTTTAAAATTGCATG
1 ATTAATAGTGTTCCCACCTTTCAAAATTGCATG
* * *
142589 ATTAATGGTGTTCCTACCTTTCCAAATTGCATG
1 ATTAATAGTGTTCCCACCTTTCAAAATTGCATG
142622 CCATTAGGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (33 bp):
ATTAATAGTGTTCCCACCTTTCAAAATTGCATG
Found at i:145359 original size:12 final size:13
Alignment explanation
Indices: 145339--145371 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
145329 GTTGGGTTAA
145339 TAGTTTGTTTATT
1 TAGTTTGTTTATT
*
145352 TA-TTTGTTTGTT
1 TAGTTTGTTTATT
145364 TAGTTTGT
1 TAGTTTGT
145372 AATTAGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.12, C:0.00, G:0.18, T:0.70
Consensus pattern (13 bp):
TAGTTTGTTTATT
Found at i:145534 original size:61 final size:60
Alignment explanation
Indices: 145437--145554 Score: 182
Period size: 61 Copynumber: 1.9 Consensus size: 60
145427 GAGCATATAA
* *
145437 GGAATTATTCTGATTGTAACGAAATTTCAATGTTACCTATTAAAAAAAATTGAATTTTTGG
1 GGAATTATTCTAATTGTAACGAAATTTCAATATTACCTATT-AAAAAAATTGAATTTTTGG
* * *
145498 GGAATTATTCTAATTGTAATGAGATTTCAATATTACCTATTACAAAAATTGAATTTT
1 GGAATTATTCTAATTGTAACGAAATTTCAATATTACCTATTAAAAAAATTGAATTTT
145555 CGGTACTTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
60 15 0.29
61 37 0.71
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (60 bp):
GGAATTATTCTAATTGTAACGAAATTTCAATATTACCTATTAAAAAAATTGAATTTTTGG
Found at i:146812 original size:24 final size:24
Alignment explanation
Indices: 146785--146834 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
146775 AGATTTCCTC
*
146785 CTGAGTACATCTAATTCCTCTTGG
1 CTGAGTACATCCAATTCCTCTTGG
*
146809 CTGAGTTCATCCAATTCCTCTTGG
1 CTGAGTACATCCAATTCCTCTTGG
146833 CT
1 CT
146835 TGTAGCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.18, C:0.28, G:0.16, T:0.38
Consensus pattern (24 bp):
CTGAGTACATCCAATTCCTCTTGG
Found at i:149576 original size:31 final size:31
Alignment explanation
Indices: 149540--149603 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
149530 AGAGTTTGTC
*
149540 TTTATTTTCTTA-TTTAGATTATTATTAGGCT
1 TTTATTTTCTTATTTTAG-TTAGTATTAGGCT
*
149571 TTTATTTTCTTATTTTAGTTAGTATTGGGCT
1 TTTATTTTCTTATTTTAGTTAGTATTAGGCT
149602 TT
1 TT
149604 ATTGGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (31 bp):
TTTATTTTCTTATTTTAGTTAGTATTAGGCT
Done.