Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014029.1 Kokia drynarioides strain JFW-HI SEQ_129060, 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: 171400
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 475 characters in sequence are not A, C, G, or T
Found at i:4016 original size:6 final size:6
Alignment explanation
Indices: 4005--4039 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
3995 AGAAATATTA
*
4005 TGAGAT TGAGAT TGAGAT TGAGAT TTA-AT TGAGAT
1 TGAGAT TGAGAT TGAGAT TGAGAT TGAGAT TGAGAT
4040 AATTAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (6 bp):
TGAGAT
Found at i:8838 original size:29 final size:28
Alignment explanation
Indices: 8806--9037 Score: 116
Period size: 29 Copynumber: 8.0 Consensus size: 28
8796 CGAACCTTTG
*
8806 GAAAATTTGAGGTCAAAAATGTGATTTTT
1 GAAAATTTGAGGTC-AAAATGTAATTTTT
* *
8835 GAAAATTTGAGGGCAAAATGGCAATTTTT
1 GAAAATTTGAGGTCAAAAT-GTAATTTTT
* ** * * *
8864 GGATGTTCG-GGGCAAAAATGTGATTTTT
1 GAAAATTTGAGGTC-AAAATGTAATTTTT
* **
8892 -AGAAGTTTG-GGAGAAAAATGTAAATTTTT
1 GA-AAATTTGAGG-TCAAAATGT-AATTTTT
* *
8921 GATAATATTAAGGGT-AAAATGTAATTTTT
1 GAAAAT-TTGA-GGTCAAAATGTAATTTTT
* *
8950 GGAAAGTTTG-GGTCAAAATATAATTTTT
1 -GAAAATTTGAGGTCAAAATGTAATTTTT
* *
8978 GGAAAGTTT-AGGGTTAAAATGTAATTTTT
1 -GAAAATTTGA-GGTCAAAATGTAATTTTT
* * *
9007 GAAAAGTTTAGTGGTTAAAATGTGATTTTT
1 GAAAA-TTT-GAGGTCAAAATGTAATTTTT
9037 G
1 G
9038 CGAAGTTTAT
Statistics
Matches: 160, Mismatches: 27, Indels: 31
0.73 0.12 0.14
Matches are distributed among these distances:
27 3 0.02
28 56 0.35
29 67 0.42
30 32 0.20
32 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.38
Consensus pattern (28 bp):
GAAAATTTGAGGTCAAAATGTAATTTTT
Found at i:9025 original size:30 final size:29
Alignment explanation
Indices: 8906--9046 Score: 153
Period size: 29 Copynumber: 4.8 Consensus size: 29
8896 GTTTGGGAGA
*
8906 AAAATGTAAATTTTTGATAATA-TTAAGGG-T
1 AAAATGT-AATTTTTGA-AA-AGTTTAGGGTT
* *
8936 AAAATGTAATTTTTGGAAAGTTT-GGGTC
1 AAAATGTAATTTTTGAAAAGTTTAGGGTT
* *
8964 AAAATATAATTTTTGGAAAGTTTAGGGTT
1 AAAATGTAATTTTTGAAAAGTTTAGGGTT
8993 AAAATGTAATTTTTGAAAAGTTTAGTGGTT
1 AAAATGTAATTTTTGAAAAGTTTAG-GGTT
* **
9023 AAAATGTGATTTTTGCGAAGTTTA
1 AAAATGTAATTTTTGAAAAGTTTA
9047 TAGGCCTTTT
Statistics
Matches: 97, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
27 4 0.04
28 26 0.27
29 35 0.36
30 32 0.33
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (29 bp):
AAAATGTAATTTTTGAAAAGTTTAGGGTT
Found at i:9326 original size:20 final size:19
Alignment explanation
Indices: 9292--9330 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
9282 TTGAAAATAA
*
9292 TTTAAAACAATTTAACAAAT
1 TTTAAAACAAATTAA-AAAT
*
9312 TTTAAAATAAATTAAAAAT
1 TTTAAAACAAATTAAAAAT
9331 GGCATTGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
TTTAAAACAAATTAAAAAT
Found at i:10071 original size:29 final size:30
Alignment explanation
Indices: 10030--10092 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
10020 ATGCTTAATA
*
10030 AATAAACAATAAATTATATATT-AATATA-T
1 AATAAACAATAAA-TAAATATTAAATATATT
*
10059 AATAAACAGTAAATAAATATTAAATATATT
1 AATAAACAATAAATAAATATTAAATATATT
10089 AATA
1 AATA
10093 TATATAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 7 0.23
29 18 0.60
30 5 0.17
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (30 bp):
AATAAACAATAAATAAATATTAAATATATT
Found at i:10100 original size:29 final size:27
Alignment explanation
Indices: 10030--10104 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 27
10020 ATGCTTAATA
*
10030 AATAAACAATAAATTATATATTAATATAT
1 AATAAAC-ATAAA-TAAATATTAATATAT
10059 AATAAACAGTAAATAAATATTAAATATATT
1 AATAAACA-TAAATAAATATT-AATATA-T
* *
10089 AATATATATAAATAAA
1 AATAAACATAAATAAA
10105 AAAACGCTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 8 0.20
29 25 0.62
30 7 0.17
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (27 bp):
AATAAACATAAATAAATATTAATATAT
Found at i:13369 original size:18 final size:18
Alignment explanation
Indices: 13339--13388 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 18
13329 CATTCTGACC
*
13339 TTTT-TTAAGTTTTTTTT
1 TTTTGTTAATTTTTTTTT
**
13356 TTTTGTTAATTTTTAATT
1 TTTTGTTAATTTTTTTTT
*
13374 TTTAGTT-ATTTTTTT
1 TTTTGTTAATTTTTTT
13389 AATTAAGAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (18 bp):
TTTTGTTAATTTTTTTTT
Found at i:13401 original size:34 final size:35
Alignment explanation
Indices: 13363--13439 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
13353 TTTTTTTGTT
* *
13363 AATTTTTAATTTTT-AGTTATTTTTTTAATTAAGA
1 AATTTTTAATTTTTAAGTTATCTTTTTAACTAAGA
* * *
13397 AATTTTTCATTTTTAATTTATCTTTTTAACTAATA
1 AATTTTTAATTTTTAAGTTATCTTTTTAACTAAGA
*
13432 ATTTTTTA
1 AATTTTTA
13440 TTTATATAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
34 13 0.37
35 22 0.63
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (35 bp):
AATTTTTAATTTTTAAGTTATCTTTTTAACTAAGA
Found at i:13522 original size:78 final size:77
Alignment explanation
Indices: 13419--13572 Score: 238
Period size: 78 Copynumber: 2.0 Consensus size: 77
13409 TTAATTTATC
* * *
13419 TTTTTAACTAATAATTTTTTATTTATATAAATAAAATAATAAATATGTAATTATATAATGAAAAT
1 TTTTTAACTAATAATTTTTTATTTATATAAACAAAATAATAAATATGTAATTATACAACGAAAAT
*
13484 ATATTTTATATG
66 ATATTATATATG
*
13496 TTTTTAA-TCAATAATTTATTTATTTATATAAACAAAATAATAAATATGTAATTATGCAACGAAA
1 TTTTTAACT-AATAATTT-TTTATTTATATAAACAAAATAATAAATATGTAATTATACAACGAAA
13560 ATATATTATATAT
64 ATATATTATATAT
13573 AATATTATAT
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
76 1 0.01
77 15 0.21
78 54 0.77
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.45
Consensus pattern (77 bp):
TTTTTAACTAATAATTTTTTATTTATATAAACAAAATAATAAATATGTAATTATACAACGAAAAT
ATATTATATATG
Found at i:13596 original size:78 final size:77
Alignment explanation
Indices: 13435--13598 Score: 211
Period size: 78 Copynumber: 2.1 Consensus size: 77
13425 ACTAATAATT
* * * * ** *
13435 TTTTATTTATATAAATAAAATAATAAATATGTAATTATATAATGAAAATATATTTTATATGTTTT
1 TTTTATTTATATAAACAAAATAATAAATATGTAATTATACAACGAAAATATATTATATATAATAT
* *
13500 TAATCAATAATT
66 TAATCAAAAATA
*
13512 TATTTATTTATATAAACAAAATAATAAATATGTAATTATGCAACGAAAATATATTATATATAATA
1 T-TTTATTTATATAAACAAAATAATAAATATGTAATTATACAACGAAAATATATTATATATAATA
*
13577 TTATATTAAAAATA
65 TTA-ATCAAAAATA
13591 TTTTATTT
1 TTTTATTT
13599 TTTTGAAGAG
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
77 1 0.01
78 65 0.88
79 8 0.11
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (77 bp):
TTTTATTTATATAAACAAAATAATAAATATGTAATTATACAACGAAAATATATTATATATAATAT
TAATCAAAAATA
Found at i:14006 original size:22 final size:21
Alignment explanation
Indices: 13970--14013 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
13960 AATTAAATTA
*
13970 AATATTAATTTTTTTATGAAT
1 AATATTAATTTTTTTATAAAT
13991 AATATTAATTTTTTTTATAAAT
1 AATATTAA-TTTTTTTATAAAT
14013 A
1 A
14014 CTAATTACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
AATATTAATTTTTTTATAAAT
Found at i:14010 original size:18 final size:20
Alignment explanation
Indices: 13970--14010 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 20
13960 AATTAAATTA
13970 AATATTAATTTTTTTATGAAT
1 AATATTAATTTTTTTAT-AAT
13991 AATATTAATTTTTTTTATAA
1 AATATTAA-TTTTTTTATAA
14011 ATACTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
AATATTAATTTTTTTATAAT
Found at i:14909 original size:20 final size:21
Alignment explanation
Indices: 14858--14909 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
14848 ATAAACTTTA
*
14858 TTTTATAATTTTTAATATTATT
1 TTTTATAA-ATTTAATATTATT
** *
14880 TGATACAAATTTAA-ATTATT
1 TTTTATAAATTTAATATTATT
14900 TTTTATAAAT
1 TTTTATAAAT
14910 ATTTTTAAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 13 0.57
21 5 0.22
22 5 0.22
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATAAATTTAATATTATT
Found at i:16063 original size:7 final size:7
Alignment explanation
Indices: 16022--16059 Score: 67
Period size: 7 Copynumber: 5.3 Consensus size: 7
16012 CGTATACCCT
16022 TGGCTGG
1 TGGCTGG
16029 TGGCTGG
1 TGGCTGG
16036 TGGCTGG
1 TGGCTGG
16043 TGGCTGG
1 TGGCTGG
16050 TGGTCTGG
1 TGG-CTGG
16058 TG
1 TG
16060 TCTGCTAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.00, C:0.13, G:0.55, T:0.32
Consensus pattern (7 bp):
TGGCTGG
Found at i:23078 original size:2 final size:2
Alignment explanation
Indices: 23065--23094 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
23055 AACGGTATGC
*
23065 AT AT AT AC 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
23095 CTTAACAAAG
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:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:25923 original size:20 final size:22
Alignment explanation
Indices: 25874--25936 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 22
25864 ATCATGATTG
*
25874 AATTAAATTTCAATAATAAAAAT
1 AATTAAATTT-AATTATAAAAAT
*
25897 AATTAAATTTAATTATAAATAT
1 AATTAAATTTAATTATAAAAAT
* *
25919 -A-TAAATTCATTTATAAAA
1 AATTAAATTTAATTATAAAA
25937 TTTAAAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 14 0.40
21 1 0.03
22 10 0.29
23 10 0.29
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTAAATTTAATTATAAAAAT
Found at i:29973 original size:32 final size:30
Alignment explanation
Indices: 29913--29988 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 30
29903 ATTGTAACAA
* * * *
29913 AATTGAAACAACAATTAATAGTTTATGGTATTG
1 AATTGAAA-AAAAATTAAGAATTGATGGTA--G
29946 AATTGAAAAAAAATTAAGAATTGATGGTAG
1 AATTGAAAAAAAATTAAGAATTGATGGTAG
29976 ATATTGAAAAAAA
1 A-ATTGAAAAAAA
29989 TGAAAAAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 2 0.05
31 11 0.29
32 17 0.45
33 8 0.21
ACGTcount: A:0.51, C:0.03, G:0.16, T:0.30
Consensus pattern (30 bp):
AATTGAAAAAAAATTAAGAATTGATGGTAG
Found at i:30308 original size:29 final size:29
Alignment explanation
Indices: 30240--30295 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
30230 TTCCACTAAA
30240 AAATAATTAGTTTTAATCTTAGTCAAACT
1 AAATAATTAGTTTTAATCTTAGTCAAACT
*
30269 AAATAATTAGTTTTAATTTTAGTCAAA
1 AAATAATTAGTTTTAATCTTAGTCAAA
30296 TAATTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (29 bp):
AAATAATTAGTTTTAATCTTAGTCAAACT
Found at i:32276 original size:13 final size:13
Alignment explanation
Indices: 32258--32305 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
32248 AGTAGATATG
32258 ATATTAAAAAAAT
1 ATATTAAAAAAAT
32271 ATATTAACAACAAA-
1 ATATTAA-AA-AAAT
32285 AT-TTAAAAAAAT
1 ATATTAAAAAAAT
32297 ATA-TAAAAA
1 ATATTAAAAA
32306 TTAAAAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
11 3 0.10
12 10 0.32
13 11 0.35
14 4 0.13
15 3 0.10
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (13 bp):
ATATTAAAAAAAT
Found at i:33414 original size:102 final size:102
Alignment explanation
Indices: 33209--33421 Score: 266
Period size: 102 Copynumber: 2.1 Consensus size: 102
33199 GAATTTGGGT
* * * * **
33209 GGAAATGAAATCCCGGAACCCGTTCCCCTGCAATTACCGACGAACGATGAAGTTCCTTTTGATAT
1 GGAAATGAAATCCCGGAACCAGTTCCCCAGAAATTACCGACGAACGATGAAGTTCCTATCAATAT
* ** *
33274 CGATAGTCTTTTAGTGGACCCGAGTGAAAATAAGTTG
66 CGATAGTCTTTTAGCGGACCAAAGAGAAAATAAGTTG
* * *
33311 GGAAATGAAATCCCGGAACCAGTTTCCCAGAAATTACCGATGAACGATGAATTTCCTATCAATAT
1 GGAAATGAAATCCCGGAACCAGTTCCCCAGAAATTACCGACGAACGATGAAGTTCCTATCAATAT
* * *
33376 TGATAGTCTTTTAGCGGATCAAAGAG-AAATGAATTTG
66 CGATAGTCTTTTAGCGGACCAAAGAGAAAAT-AAGTTG
33413 GGAAATGAA
1 GGAAATGAA
33422 TTCCGTGTAC
Statistics
Matches: 94, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
101 4 0.04
102 90 0.96
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (102 bp):
GGAAATGAAATCCCGGAACCAGTTCCCCAGAAATTACCGACGAACGATGAAGTTCCTATCAATAT
CGATAGTCTTTTAGCGGACCAAAGAGAAAATAAGTTG
Found at i:34926 original size:58 final size:56
Alignment explanation
Indices: 34842--35009 Score: 212
Period size: 58 Copynumber: 2.9 Consensus size: 56
34832 ATTATTTTTG
* * * *
34842 GGATTTGTTAGAAACGCAGTAAAAACTACATCCACAGTATTACTTTTGGGATTATTT
1 GGATTTGTTTGAAATGTAGTAAAAACTACATCCACACTATTA-TTTTGGGATTATTT
*
34899 CGGATTTGTTTGAAATGTAGTACAAACTACATCCACACTATTATTTTTGGGATTATTT
1 -GGATTTGTTTGAAATGTAGTAAAAACTACATCCACACTATTA-TTTTGGGATTATTT
* * * *
34957 GTTATTTGTTTGAATTGTTGTAAAAACTACATCCACATTATTATTTT-GGATTA
1 G-GATTTGTTTGAAATGTAGTAAAAACTACATCCACACTATTATTTTGGGATTA
35010 ATATTTTACT
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
56 6 0.06
57 5 0.05
58 87 0.89
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.41
Consensus pattern (56 bp):
GGATTTGTTTGAAATGTAGTAAAAACTACATCCACACTATTATTTTGGGATTATTT
Found at i:39572 original size:14 final size:15
Alignment explanation
Indices: 39543--39584 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
39533 GCTTTTTTTT
39543 TAATTTTTACTTAAT-A
1 TAATTTTT--TTAATAA
39559 TAATTTTTTTAATAA
1 TAATTTTTTTAATAA
*
39574 TATTTTTTTTA
1 TAATTTTTTTA
39585 CTCCATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 5 0.21
15 11 0.46
16 8 0.33
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
TAATTTTTTTAATAA
Found at i:46443 original size:32 final size:32
Alignment explanation
Indices: 46407--46476 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
46397 AGGATAATTT
*
46407 TTTTTTCCAA-AGGAAATGAAATTCAATTATTA
1 TTTTTT-CAATAGAAAATGAAATTCAATTATTA
* *
46439 TTTTTTTAATTGAAAATGAAATTCAATTATTA
1 TTTTTTCAATAGAAAATGAAATTCAATTATTA
46471 TTTTTT
1 TTTTTT
46477 AAAGTGTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 2 0.06
32 32 0.94
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.50
Consensus pattern (32 bp):
TTTTTTCAATAGAAAATGAAATTCAATTATTA
Found at i:47692 original size:2 final size:2
Alignment explanation
Indices: 47679--47708 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
47669 AAATACATAC
*
47679 AT AT AC 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
47709 TTGTCGTATC
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:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:56582 original size:39 final size:39
Alignment explanation
Indices: 56528--56606 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
56518 ATGCTGTTCC
56528 AAAGAACTTGGTGTGGGAAGCTGTCAACACACATGGGTG
1 AAAGAACTTGGTGTGGGAAGCTGTCAACACACATGGGTG
56567 AAAGAACTTGGTGTGGGAAGCTGTCAACACACATGGGTG
1 AAAGAACTTGGTGTGGGAAGCTGTCAACACACATGGGTG
56606 A
1 A
56607 CTACTATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.32, C:0.15, G:0.33, T:0.20
Consensus pattern (39 bp):
AAAGAACTTGGTGTGGGAAGCTGTCAACACACATGGGTG
Found at i:56636 original size:12 final size:12
Alignment explanation
Indices: 56615--56648 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
56605 GACTACTATT
56615 TTATGATTATGC
1 TTATGATTATGC
*
56627 TTATGCTTATGC
1 TTATGATTATGC
*
56639 TTATTATTAT
1 TTATGATTAT
56649 TATTATTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.56
Consensus pattern (12 bp):
TTATGATTATGC
Found at i:66236 original size:141 final size:141
Alignment explanation
Indices: 65964--66237 Score: 345
Period size: 141 Copynumber: 1.9 Consensus size: 141
65954 CTCCATGCAC
* * * * *
65964 AAGACTTGAACTCTAAACTTAGTTTAAAGGGTATTGAGCTCTTTATCACTATGGTTTTTGTCCCT
1 AAGACTAGAACTCTAAACTTAGCTTAAAGGGCATTGAGCTCTTTATCACTATGGTTTTAGCCCCT
* * * * * *
66029 CGATATTGGTAGTTACATTGGGCTCGAATTCCTAAATGAAGACAACGTTTTCTCGAACGTTATTT
66 CGATATTGGTAGTTACATTCGGCTCGAACTCCTAAATGAAGACAAAGCTCTCTCGAACATTATTT
66094 TCTCTGCTTAT
131 TCTCTGCTTAT
* * * *
66105 AAGACTAGAGCTCTTAACTTAGCTTAAAGGGCATTGAGTTCTTTATCATTAT-GTTTCTAGCCCC
1 AAGACTAGAACTCTAAACTTAGCTTAAAGGGCATTGAGCTCTTTATCACTATGGTTT-TAGCCCC
* * * *
66169 TCGATATCTGGTAGTTACATTCGGTTCGAACTCGTAAATGAGGACAAAGCTCTCTC-AACATTGT
65 TCGATAT-TGGTAGTTACATTCGGCTCGAACTCCTAAATGAAGACAAAGCTCTCTCGAACATTAT
66233 TTTCT
129 TTTCT
66238 TCGTTCCCAA
Statistics
Matches: 112, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
140 4 0.04
141 68 0.61
142 40 0.36
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (141 bp):
AAGACTAGAACTCTAAACTTAGCTTAAAGGGCATTGAGCTCTTTATCACTATGGTTTTAGCCCCT
CGATATTGGTAGTTACATTCGGCTCGAACTCCTAAATGAAGACAAAGCTCTCTCGAACATTATTT
TCTCTGCTTAT
Found at i:67718 original size:3 final size:3
Alignment explanation
Indices: 67710--67737 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
67700 GATATAACCC
67710 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
67738 TTGCATATAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:68951 original size:10 final size:10
Alignment explanation
Indices: 68931--68959 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
68921 TGTAGTTTAC
68931 TTTTC-TTTT
1 TTTTCTTTTT
68940 TTTTCTTTTT
1 TTTTCTTTTT
68950 TTTTCTTTTT
1 TTTTCTTTTT
68960 CAGATTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:76433 original size:22 final size:23
Alignment explanation
Indices: 76407--76450 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
76397 ATTTTTCTGT
76407 TTAAAAA-TTTCATCAATTTATG
1 TTAAAAATTTTCATCAATTTATG
*
76429 TTAAAAATTTTCATGAATTTAT
1 TTAAAAATTTTCATCAATTTAT
76451 ATTGTCAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (23 bp):
TTAAAAATTTTCATCAATTTATG
Found at i:78777 original size:132 final size:134
Alignment explanation
Indices: 78544--78795 Score: 323
Period size: 132 Copynumber: 1.9 Consensus size: 134
78534 ACTTCAGAAC
* * ** * *
78544 AAATATCCATACGAAAAACAAAAGCATCAAAGCTAAGAGCATCCACCTGCCACAAATTCTTCAAG
1 AAATATCCATACAAAAAACAAAAGCATCAAAGCTAAGAGCATCCAACTGAAACAAATTCTACAAA
* * * **
78609 CTATATAAATACACTTACCAAATGCAAACAATAAAAGCTTTACTGTAAAGCACGAGAACCTTCAA
66 C-ATATAAATACACTAACCAAACGCAAACAACAAAAGCTTTACCATAAAGCACGAGAACCTTCAA
78674 AAAAA
130 AAAAA
*
78679 AAATATCCATACAAAAAACACAAA-CTTCAAAG-TAAGAGCATCCAACTGAAACAAATTC-ACGA
1 AAATATCCATACAAAAAACA-AAAGCATCAAAGCTAAGAGCATCCAACTGAAACAAATTCTAC-A
**
78741 AAC-TATAAATACACTAATGAAACGCAAACAACAAAAGCTTTACCATAAAGCACGA
64 AACATATAAATACACTAACCAAACGCAAACAACAAAAGCTTTACCATAAAGCACGA
78796 ACCGGTAACA
Statistics
Matches: 101, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
132 45 0.45
133 1 0.01
134 26 0.26
135 26 0.26
136 3 0.03
ACGTcount: A:0.50, C:0.23, G:0.09, T:0.18
Consensus pattern (134 bp):
AAATATCCATACAAAAAACAAAAGCATCAAAGCTAAGAGCATCCAACTGAAACAAATTCTACAAA
CATATAAATACACTAACCAAACGCAAACAACAAAAGCTTTACCATAAAGCACGAGAACCTTCAAA
AAAA
Found at i:81365 original size:14 final size:14
Alignment explanation
Indices: 81348--81398 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
81338 AAATATTAAA
81348 TTATTTATATAATT
1 TTATTTATATAATT
81362 TTA-TTATATACATT
1 TTATTTATATA-ATT
* * *
81376 ATATTTTTAAAATT
1 TTATTTATATAATT
81390 TGTATTTAT
1 T-TATTTAT
81399 TATTATTGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
13 7 0.24
14 11 0.38
15 11 0.38
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (14 bp):
TTATTTATATAATT
Found at i:85720 original size:22 final size:24
Alignment explanation
Indices: 85688--85761 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 24
85678 ATCGAGATTC
85688 TTTTTC-C-AATTTGGTACTTAAA
1 TTTTTCTCTAATTTGGTACTTAAA
* *
85710 TTTTT-T-TAATTTGATACTTGAGGTA
1 TTTTTCTCTAATTTGGTACTT-A--AA
85735 TTTTTCTCTAATTTGGTACTTAAA
1 TTTTTCTCTAATTTGGTACTTAAA
85759 TTT
1 TTT
85762 GGCTTTAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
22 16 0.39
23 1 0.02
24 4 0.10
25 6 0.15
26 2 0.05
27 12 0.29
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.55
Consensus pattern (24 bp):
TTTTTCTCTAATTTGGTACTTAAA
Found at i:97249 original size:3 final size:3
Alignment explanation
Indices: 97241--97267 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
97231 ACTCTATATG
97241 GTT GTT GTT GTT GTT GTT GTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT
97268 ATAAGTGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
GTT
Found at i:103971 original size:7 final size:7
Alignment explanation
Indices: 103960--103992 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
103950 TTTGTCTCGT
*
103960 TGCTCAT
1 TGCTCAC
103967 TGCTCAC
1 TGCTCAC
103974 TGCTCAC
1 TGCTCAC
103981 TGCTCAC
1 TGCTCAC
103988 TGCTC
1 TGCTC
103993 TCCCCATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.39, G:0.15, T:0.33
Consensus pattern (7 bp):
TGCTCAC
Found at i:104307 original size:7 final size:7
Alignment explanation
Indices: 104295--104321 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
104285 ATTAAATGTG
104295 ATGTGTC
1 ATGTGTC
104302 ATGTGTC
1 ATGTGTC
104309 ATGTGTC
1 ATGTGTC
104316 ATGTGT
1 ATGTGT
104322 ACGTCATGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.11, G:0.30, T:0.44
Consensus pattern (7 bp):
ATGTGTC
Found at i:108809 original size:139 final size:140
Alignment explanation
Indices: 108544--108826 Score: 496
Period size: 139 Copynumber: 2.0 Consensus size: 140
108534 TGTGCAATTG
* *
108544 TATACATGAACTTTAATTTGGTGCAACTATACACGTGAAACTCTAATTGCGGTTCAAAGGTATAC
1 TATACATCAACTTTAATTTGGTGCAACTATACACGTGAAACTCTAATTACGGTTCAAAGGTATAC
108609 TTGAAACCTTAATTTTAATTTAATCATATACATCTAAAGAAATAAATACATCAATATATTTTTAA
66 TTGAAACCTTAATTTTAATTTAATCATATACATCTAAAGAAATAAATACATCAATATATTTTTAA
*
108674 TTTGGGTAAA
131 ATTGGGTAAA
* *
108684 TATACATCAA-TTTGATTTGGTGCAATTATACACGTGAAACTCTAATTACGGTTCAAAGGTATAC
1 TATACATCAACTTTAATTTGGTGCAACTATACACGTGAAACTCTAATTACGGTTCAAAGGTATAC
* *
108748 TTGAAACTTTAATTTTAATTTAATCATATACATTTAAAGAAATAAATACATCAATATATTTTTAA
66 TTGAAACCTTAATTTTAATTTAATCATATACATCTAAAGAAATAAATACATCAATATATTTTTAA
108813 ATTGGGTAAA
131 ATTGGGTAAA
108823 TATA
1 TATA
108827 ATTATTTATG
Statistics
Matches: 136, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
139 127 0.93
140 9 0.07
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (140 bp):
TATACATCAACTTTAATTTGGTGCAACTATACACGTGAAACTCTAATTACGGTTCAAAGGTATAC
TTGAAACCTTAATTTTAATTTAATCATATACATCTAAAGAAATAAATACATCAATATATTTTTAA
ATTGGGTAAA
Found at i:111165 original size:200 final size:203
Alignment explanation
Indices: 110764--111167 Score: 688
Period size: 200 Copynumber: 2.0 Consensus size: 203
110754 AAATAGATCT
* * *
110764 ACCTGTTTCTGCACATACGAGAAAATCAGATTGTATGTTTTCATTCTAGATGCTGAAATAAAAGC
1 ACCTGTTTCTGCACATACGAGAAAATCAGATTGTATGTCTTCATTCTACATGCCGAAATAAAAGC
* * *
110829 AATGGTGTTTTTTCCAGTATACATGCACACATCTATATGTTTATATATATGTGCATTAAGATGAA
66 AACGGTGTTTTTTCCAGTACACATG-ACACATCTATATGTTTATATATATGTGCATTAAGAAGAA
*
110894 ACATAGGTCCGACCTGTGCTTGAGGACTTACTTCGATTGCTGCATTGTTTGGTGCTGAGACAAAA
130 ACATAGGTCCGACCTGTGCTTGAGGACTTACTTCGATTACTGCATTGTTTGGTGCTGAGACAAAA
110959 GTTGCATCA
195 GTTGCATCA
110968 ACCTGTTTCTGCACATACGAGAAAATCAGATTGTATGTCTTCATTCTACATGCCGAAATAAAAGC
1 ACCTGTTTCTGCACATACGAGAAAATCAGATTGTATGTCTTCATTCTACATGCCGAAATAAAAGC
111033 AACGGTGTTTTTTCCAGTACACATG-CACA-C-ATATGTTTATATATATGTGCATTAAGAAGAAA
66 AACGGTGTTTTTTCCAGTACACATGACACATCTATATGTTTATATATATGTGCATTAAGAAGAAA
* * *
111095 CATAGGTCCGACCTGTGCTTGAGGACTTGCTTCGATTACTGCTTTGTTTGGTGCTGAGACAAAGG
131 CATAGGTCCGACCTGTGCTTGAGGACTTACTTCGATTACTGCATTGTTTGGTGCTGAGACAAAAG
111160 TTGCATCA
196 TTGCATCA
111168 GCAAATAGAT
Statistics
Matches: 190, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
200 100 0.53
201 1 0.01
202 4 0.02
204 85 0.45
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (203 bp):
ACCTGTTTCTGCACATACGAGAAAATCAGATTGTATGTCTTCATTCTACATGCCGAAATAAAAGC
AACGGTGTTTTTTCCAGTACACATGACACATCTATATGTTTATATATATGTGCATTAAGAAGAAA
CATAGGTCCGACCTGTGCTTGAGGACTTACTTCGATTACTGCATTGTTTGGTGCTGAGACAAAAG
TTGCATCA
Found at i:112108 original size:322 final size:313
Alignment explanation
Indices: 111523--112152 Score: 1046
Period size: 322 Copynumber: 2.0 Consensus size: 313
111513 GAGATAATTT
*
111523 TTTTTTGGGATCCTTGCTGCAAAACAACATTACCAAATGTGTGTGTGTGAGTGTTTAAACATGTT
1 TTTTTTGGGATCCTTGCTGCAAAACAACATTACCAAATGTGTGTGTGTGAGTGTTTAAACATGCT
** * *
111588 ACAGTAATAGAGGTTGAACTTCTATAATCAAGTTATTATGCATGGTGAAACACGAATCACCGTAT
66 ACAGTAATAGAGCCTGAACTTCCATAATCAAGTTATTATGCATGGTGAAACACGAATCACCATAT
*
111653 AGAATAAATGGATTCACAATGGTGATATGATTCCTAGAACCAAACATGGCATGCAGTGTATAATA
131 AGAATAAATGGATTCACAATGGTGATACGATTCCTAGAACCAAACATGGCATGCAGTGTATAATA
* *
111718 ACCCTGAAGTTGACAATCAACAATGTAAAACATAAACCTGCCATGACGTCTAGACTCCTTTTTGG
196 ACCCTGAAGTTGACAATCAACAATGTAAAACATAAACCTGCCATGACGTCTAGACTCCGTTGTGG
111783 AATTTGCTTGGCTCTCACTTGCAGTACTCCCTCGGCGTGGCTTCACGTTGGCA
261 AATTTGCTTGGCTCTCACTTGCAGTACTCCCTCGGCGTGGCTTCACGTTGGCA
111836 TTTTTT-GGATCCTTGCTGCAAAACAACATTACCAAATGTGTGTGTGTGTGTGTGTGAGTGTGTT
1 TTTTTTGGGATCCTTGCTGCAAAACAACATTACCAAA--------TGTGTGTGTGTGA--GTGTT
* *
111900 TAAACATGCTATAGTAATAGAGCCTGAACTTCCATGATCAAGTTATTATGCATGGTGAAACACGA
56 TAAACATGCTACAGTAATAGAGCCTGAACTTCCATAATCAAGTTATTATGCATGGTGAAACACGA
*
111965 ATCACCATATAGAATAAATGGATTCACGATGGTGATACGATTCCTAGAACCAAACATGGCATGCA
121 ATCACCATATAGAATAAATGGATTCACAATGGTGATACGATTCCTAGAACCAAACATGGCATGCA
*
112030 GTGTATAATAACCCTGGAGTTGACAATCAACAATGTAAAACATAAACCTGCCATGACGTCTAGAC
186 GTGTATAATAACCCTGAAGTTGACAATCAACAATGTAAAACATAAACCTGCCATGACGTCTAGAC
*
112095 TCCGTTGTGGAATTTGCTTGGCTCTCACTTGCAGTGCTCCCTCGGCGTGGCTTCACGT
251 TCCGTTGTGGAATTTGCTTGGCTCTCACTTGCAGTACTCCCTCGGCGTGGCTTCACGT
112153 AGGTATCTTT
Statistics
Matches: 294, Mismatches: 13, Indels: 11
0.92 0.04 0.03
Matches are distributed among these distances:
312 30 0.10
313 6 0.02
320 13 0.04
322 245 0.83
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (313 bp):
TTTTTTGGGATCCTTGCTGCAAAACAACATTACCAAATGTGTGTGTGTGAGTGTTTAAACATGCT
ACAGTAATAGAGCCTGAACTTCCATAATCAAGTTATTATGCATGGTGAAACACGAATCACCATAT
AGAATAAATGGATTCACAATGGTGATACGATTCCTAGAACCAAACATGGCATGCAGTGTATAATA
ACCCTGAAGTTGACAATCAACAATGTAAAACATAAACCTGCCATGACGTCTAGACTCCGTTGTGG
AATTTGCTTGGCTCTCACTTGCAGTACTCCCTCGGCGTGGCTTCACGTTGGCA
Found at i:123279 original size:20 final size:19
Alignment explanation
Indices: 123242--123281 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
123232 TATAAAATAT
*
123242 TTTAAAATTAATTAATTAA
1 TTTAAAATGAATTAATTAA
*
123261 TTTAAAATGAGTTATATTAA
1 TTTAAAATGAATTA-ATTAA
123281 T
1 T
123282 GTTATTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
TTTAAAATGAATTAATTAA
Found at i:125223 original size:22 final size:23
Alignment explanation
Indices: 125195--125245 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
125185 AAATTTATCA
125195 ATTTTAACTTG-TAT-TCAAAAAT
1 ATTTTAACTTGTTATATC-AAAAT
*
125217 ATTTTAATTTGTTATATCAAAAT
1 ATTTTAACTTGTTATATCAAAAT
125240 ATTTTA
1 ATTTTA
125246 TCAAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 10 0.38
23 14 0.54
24 2 0.08
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (23 bp):
ATTTTAACTTGTTATATCAAAAT
Found at i:125808 original size:18 final size:18
Alignment explanation
Indices: 125785--125827 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
125775 GAATAGGTTT
125785 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
125803 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
125821 TTAATTA
1 TTAATTA
125828 CAACTTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:140150 original size:59 final size:60
Alignment explanation
Indices: 140068--140197 Score: 174
Period size: 59 Copynumber: 2.2 Consensus size: 60
140058 GACAATATTG
* * *
140068 AAAAATTGAGTAATCATTCTGTAACTTTTCATACTTAGGTGACCA-AAAA-AATATTTACT
1 AAAAGTTGGGTAATCATTCTGTAACTTTTCATAATTAGGTGACCAGAAAAGAA-ATTTACT
* * *
140127 AAAAGTTGGGTAATCGTTTTGTAACTTTTCATAATTGGGTGACCAGAAAAGAAATTTACT
1 AAAAGTTGGGTAATCATTCTGTAACTTTTCATAATTAGGTGACCAGAAAAGAAATTTACT
*
140187 AATAGTTGGGT
1 AAAAGTTGGGT
140198 GACTACTAGT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
59 39 0.63
60 21 0.34
61 2 0.03
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (60 bp):
AAAAGTTGGGTAATCATTCTGTAACTTTTCATAATTAGGTGACCAGAAAAGAAATTTACT
Found at i:145662 original size:52 final size:52
Alignment explanation
Indices: 145584--145687 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
145574 AACTGGGGGG
145584 ATAGAGAAAAAAAGAGGGAGAACACAAACACATCATAATATTTGTTGCATTC
1 ATAGAGAAAAAAAGAGGGAGAACACAAACACATCATAATATTTGTTGCATTC
145636 ATAGAGAAAAAAAGAGGGAGAACACAAACACATCATAATATTTGTTGCATTC
1 ATAGAGAAAAAAAGAGGGAGAACACAAACACATCATAATATTTGTTGCATTC
145688 CAAGTGTCAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.21
Consensus pattern (52 bp):
ATAGAGAAAAAAAGAGGGAGAACACAAACACATCATAATATTTGTTGCATTC
Found at i:151219 original size:21 final size:21
Alignment explanation
Indices: 151178--151219 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
151168 ATATGTATGG
**
151178 ATAAATAAACAAATATTTAAA
1 ATAAATAAACAAATAAATAAA
*
151199 ATAAATAAATAAATAAATAAA
1 ATAAATAAACAAATAAATAAA
151220 CCAAAGGTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (21 bp):
ATAAATAAACAAATAAATAAA
Found at i:153035 original size:28 final size:28
Alignment explanation
Indices: 152977--153053 Score: 127
Period size: 28 Copynumber: 2.6 Consensus size: 28
152967 ACTTTGAAGT
152977 AAGGAATAGAATAAATATTTAAATATCAAGC
1 AAGGAATAGAAT-AA-A-TTAAATATCAAGC
153008 AAGGAATAGAATAAATTAAATATCAAGC
1 AAGGAATAGAATAAATTAAATATCAAGC
153036 AAGGAATAGAATAAATTA
1 AAGGAATAGAATAAATTA
153054 CTCTTAGAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
28 31 0.67
29 1 0.02
30 2 0.04
31 12 0.26
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.23
Consensus pattern (28 bp):
AAGGAATAGAATAAATTAAATATCAAGC
Found at i:158041 original size:32 final size:32
Alignment explanation
Indices: 158005--158066 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
157995 AGCTTTTGGT
* *
158005 TTTTTCATGTTATCAAAGAGTTGAATAATGGA
1 TTTTTCATGCTATCAAAGAGTTGAACAATGGA
* * *
158037 TTTTTCGTGCTGTCAAGGAGTTGAACAATG
1 TTTTTCATGCTATCAAAGAGTTGAACAATG
158067 AAAATATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.39
Consensus pattern (32 bp):
TTTTTCATGCTATCAAAGAGTTGAACAATGGA
Found at i:158420 original size:17 final size:17
Alignment explanation
Indices: 158400--158433 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
158390 TTGTATTACG
*
158400 CTTTATCTACTTGCTTT
1 CTTTATCTAATTGCTTT
*
158417 CTTTATGTAATTGCTTT
1 CTTTATCTAATTGCTTT
158434 GTATGACTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.18, G:0.09, T:0.59
Consensus pattern (17 bp):
CTTTATCTAATTGCTTT
Found at i:164648 original size:31 final size:30
Alignment explanation
Indices: 164611--164676 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 30
164601 TTTTATAATT
* * * *
164611 TAAAATTATATTTTAATTTTTTCAAAAATAA
1 TAAAATTATAATTTAATCTCTTAAAAAAT-A
*
164642 TAAAATTTTAATTTAATCTCTTAAAAAATA
1 TAAAATTATAATTTAATCTCTTAAAAAATA
164672 TAAAA
1 TAAAA
164677 AAATTAAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (30 bp):
TAAAATTATAATTTAATCTCTTAAAAAATA
Done.