Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015074.1 Kokia drynarioides strain JFW-HI SEQ_130118, 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: 89674
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:16101 original size:11 final size:11
Alignment explanation
Indices: 16085--16158 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
16075 AAAAAAATTG
*
16085 TTATTTTTTTA
1 TTATTTTGTTA
*
16096 TTATTTTGCTA
1 TTATTTTGTTA
*
16107 TTTATTATTATTA
1 -TTATT-TTGTTA
* *
16120 TTATGTTGCTA
1 TTATTTTGTTA
*
16131 TTATTTTATTA
1 TTATTTTGTTA
* *
16142 TTCTATTGTTA
1 TTATTTTGTTA
16153 TTATTT
1 TTATTT
16159 GAATATTGTA
Statistics
Matches: 46, Mismatches: 15, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
11 33 0.72
12 9 0.20
13 4 0.09
ACGTcount: A:0.22, C:0.04, G:0.05, T:0.69
Consensus pattern (11 bp):
TTATTTTGTTA
Found at i:16326 original size:21 final size:20
Alignment explanation
Indices: 16279--16326 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
16269 ATTGGGAAAC
16279 ATTTATTTTTAATTTTTTGA
1 ATTTATTTTTAATTTTTTGA
* * *
16299 GTATTATTTATTTATTTTTTTA
1 AT-TTATTT-TTAATTTTTTGA
16321 ATTTAT
1 ATTTAT
16327 ATAAAAATAG
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 10 0.45
22 11 0.50
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (20 bp):
ATTTATTTTTAATTTTTTGA
Found at i:29668 original size:7 final size:7
Alignment explanation
Indices: 29658--29682 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29648 AAGAAAGATG
29658 AAAGGTT
1 AAAGGTT
29665 AAAGGTT
1 AAAGGTT
29672 AAAGGTT
1 AAAGGTT
29679 AAAG
1 AAAG
29683 AAGATGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (7 bp):
AAAGGTT
Found at i:29692 original size:24 final size:24
Alignment explanation
Indices: 29665--29719 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
29655 ATGAAAGGTT
*
29665 AAAGGTTAAAGGTTAAAGAAGATG
1 AAAGGTGAAAGGTTAAAGAAGATG
* *
29689 AAAGGTGGAAGGTTAAAGGAGATG
1 AAAGGTGAAAGGTTAAAGAAGATG
29713 AAAGGTG
1 AAAGGTG
29720 TCAAGTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.18
Consensus pattern (24 bp):
AAAGGTGAAAGGTTAAAGAAGATG
Found at i:32064 original size:16 final size:17
Alignment explanation
Indices: 32036--32069 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
32026 TGATAATTCA
*
32036 TTCCAATCTATTTCTTT
1 TTCCAATCTATTTATTT
32053 TTCCAA-CTATTTATTT
1 TTCCAATCTATTTATTT
32069 T
1 T
32070 CTCTCCCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (17 bp):
TTCCAATCTATTTATTT
Found at i:48761 original size:24 final size:23
Alignment explanation
Indices: 48734--48783 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
48724 TTGTTGATTA
* *
48734 ATTTCATTCTAATAATTTTATTTT
1 ATTTCATTATAATAATTCT-TTTT
*
48758 ATTTCATTATATTAATTCTTTTT
1 ATTTCATTATAATAATTCTTTTT
48781 ATT
1 ATT
48784 ATTTATCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (23 bp):
ATTTCATTATAATAATTCTTTTT
Found at i:50382 original size:18 final size:17
Alignment explanation
Indices: 50359--50393 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
50349 ACATGCTCGA
50359 GTGCTTTATTTATCTTGT
1 GTGCTTTATTTAT-TTGT
*
50377 GTGCTTTCTTTATTTGT
1 GTGCTTTATTTATTTGT
50394 CTTTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.09, C:0.11, G:0.17, T:0.63
Consensus pattern (17 bp):
GTGCTTTATTTATTTGT
Found at i:56234 original size:51 final size:51
Alignment explanation
Indices: 56153--56343 Score: 256
Period size: 51 Copynumber: 3.7 Consensus size: 51
56143 CTATAAACGA
* * *
56153 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGTATT
1 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGAATT
*
56204 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGAATT
* * * * *
56255 AAAGGTCCGATGACTAAGTGTTATCATGAGTAAATGAATCCATGATGAACT
1 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGAATT
* * * * *
56306 ATAGGTCCGATAACTCAGTGTCATCGTGAGTATATGAA
1 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAA
56344 CTTGTATACG
Statistics
Matches: 125, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 125 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.30
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGAATT
Found at i:58270 original size:21 final size:21
Alignment explanation
Indices: 58246--58293 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
58236 ACGATCTGAG
58246 CACATGAGCATGAGGGGTAGC
1 CACATGAGCATGAGGGGTAGC
* *
58267 CACACGAGCATGTGGGGTAGC
1 CACATGAGCATGAGGGGTAGC
58288 CACATG
1 CACATG
58294 GTCTAGCTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.23, G:0.35, T:0.15
Consensus pattern (21 bp):
CACATGAGCATGAGGGGTAGC
Found at i:61175 original size:30 final size:30
Alignment explanation
Indices: 60992--61169 Score: 184
Period size: 30 Copynumber: 6.0 Consensus size: 30
60982 TAAAATCGGA
60992 TCAAATTTGAATTTTTA-AAAACTTT-AGGGG
1 TCAAATTTGAATTTTTAGAAAA-TTTGA-GGG
* * *
61022 TCAAATTAGAATTTTTAGAAAGTTTAAGGG
1 TCAAATTTGAATTTTTAGAAAATTTGAGGG
* * * *
61052 TTAAATTGGAATTTTTTGAAAATTTGATGG
1 TCAAATTTGAATTTTTAGAAAATTTGAGGG
* * *
61082 TCAAATTGGAATTTTTTGAAAATTTGATGG
1 TCAAATTTGAATTTTTAGAAAATTTGAGGG
*
61112 TCAAATTTGAATTTTT-GGAAATTTGAGGG
1 TCAAATTTGAATTTTTAGAAAATTTGAGGG
* * *
61141 TTAAATTTGAATTTTTGGAAAGTTT-AGGG
1 TCAAATTTGAATTTTTAGAAAATTTGAGGG
61170 GTTAAAACAT
Statistics
Matches: 130, Mismatches: 15, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
29 30 0.23
30 96 0.74
31 4 0.03
ACGTcount: A:0.34, C:0.03, G:0.21, T:0.42
Consensus pattern (30 bp):
TCAAATTTGAATTTTTAGAAAATTTGAGGG
Found at i:61184 original size:30 final size:29
Alignment explanation
Indices: 61030--61186 Score: 88
Period size: 30 Copynumber: 5.3 Consensus size: 29
61020 GGTCAAATTA
* * *
61030 GAATTTTTAGAAAGTTTAAGGGTTAAA-TT
1 GAATTTTTGGAAA-TTTGAGGGTTAAACAT
* * * *
61059 GGAATTTTTTGAAAATTTGATGGTCAAA-TT
1 -GAA-TTTTTGGAAATTTGAGGGTTAAACAT
* * * **
61089 GGAATTTTTTGAAAATTTGATGGTCAAATTT
1 -GAA-TTTTTGGAAATTTGAGGGTTAAACAT
**
61120 GAATTTTTGGAAATTTGAGGGTTAAATTT
1 GAATTTTTGGAAATTTGAGGGTTAAACAT
61149 GAATTTTTGGAAAGTTT-AGGGGTTAAAACAT
1 GAATTTTTGGAAA-TTTGA-GGGTT-AAACAT
61180 -AATTTTT
1 GAATTTTT
61187 TAATAGTTTA
Statistics
Matches: 112, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
29 37 0.33
30 61 0.54
31 14 0.12
ACGTcount: A:0.34, C:0.02, G:0.21, T:0.43
Consensus pattern (29 bp):
GAATTTTTGGAAATTTGAGGGTTAAACAT
Found at i:62801 original size:40 final size:39
Alignment explanation
Indices: 62717--63083 Score: 236
Period size: 39 Copynumber: 9.3 Consensus size: 39
62707 ATAGCTTTAG
* * * *
62717 GGGTAAAAGAT-TGGATTGT-TTCAATTTGCCCCATAGTCA
1 GGGTAAAAGATCT-GATTGTCTTCAATCTGCCTC-TGGTTA
* * * *
62756 AGGTAAGAGATCTGATAGTCTTCAATCTGCGCTCTTGTTA
1 GGGTAAAAGATCTGATTGTCTTCAATCTGC-CTCTGGTTA
* **
62796 GGGTAAAAGAT-TGGATTG-CTTCAATCTGCCTGATGGTCG
1 GGGTAAAAGATCT-GATTGTCTTCAATCTGCCT-CTGGTTA
* * *
62835 GGGTAACAA-ATCGGATGGTCTTCAATCTGCCCTCTAGTTA
1 GGGTAA-AAGATCTGATTGTCTTCAATCTG-CCTCTGGTTA
* *
62875 GGGTAAAAGAT-TGGATTG-CTTCAATCTGCCCCATGG-TC
1 GGGTAAAAGATCT-GATTGTCTTCAATCTGCCTC-TGGTTA
* * *
62913 GGGTTAAGAGATCGGATAGTCTTCAATCTGCCCTCTGGTTA
1 GGG-TAAAAGATCTGATTGTCTTCAATCTG-CCTCTGGTTA
* *
62954 GGGTATAAGAT-TGGATTG-CTTCAATCTGCCTCATGGTCA
1 GGGTAAAAGATCT-GATTGTCTTCAATCTGCCTC-TGGTTA
* * * * *
62993 GGTTAAGAGATCAGATGGTCTTCAATCTACCCTCTGGTTA
1 GGGTAAAAGATCTGATTGTCTTCAATCT-GCCTCTGGTTA
* * *
63033 GGGTAAAAGAT-TAGATT-ACTTCAATCTGCCCCATGGTCA
1 GGGTAAAAGATCT-GATTGTCTTCAATCTGCCTC-TGGTTA
*
63072 GGGTAACAGATC
1 GGGTAAAAGATC
63084 AAATGGTATC
Statistics
Matches: 252, Mismatches: 51, Indels: 49
0.72 0.14 0.14
Matches are distributed among these distances:
38 16 0.06
39 117 0.46
40 103 0.41
41 16 0.06
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (39 bp):
GGGTAAAAGATCTGATTGTCTTCAATCTGCCTCTGGTTA
Found at i:62856 original size:79 final size:79
Alignment explanation
Indices: 62717--63156 Score: 567
Period size: 79 Copynumber: 5.6 Consensus size: 79
62707 ATAGCTTTAG
* * * * * *
62717 GGGTAAAAGATTGGATTGTTTCAATTTGCCCCATAGTCAAGGTAAGAGATCTGATAGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATCAGATGGTCTTCAAT
* *
62782 CTGCGCTCTTGTTA
66 CTGCCCTCTGGTTA
** * * * *
62796 GGGTAAAAGATTGGATTGCTTCAATCTGCCTGATGGTCGGGGTAACAAATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATCAGATGGTCTTCAAT
*
62861 CTGCCCTCTAGTTA
66 CTGCCCTCTGGTTA
* *
62875 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTC-GGGTTAAGAGATCGGATAGTCTTCAA
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCAGGG-TAAGAGATCAGATGGTCTTCAA
62939 TCTGCCCTCTGGTTA
65 TCTGCCCTCTGGTTA
* * *
62954 GGGTATAAGATTGGATTGCTTCAATCTGCCTCATGGTCAGGTTAAGAGATCAGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATCAGATGGTCTTCAAT
*
63019 CTACCCTCTGGTTA
66 CTGCCCTCTGGTTA
* * * * * *
63033 GGGTAAAAGATTAGATTACTTCAATCTGCCCCATGGTCAGGGTAACAGATCAAATGGTATCCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATCAGATGGTCTTCAAT
* * **
63098 TTGCCCTTTAATTA
66 CTGCCCTCTGGTTA
* *
63112 GGGTAAAAGATTGGATTGCTTTAATCTGCCCCATGGTCGGGGTAA
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCAGGGTAA
63157 AAGACTCGAG
Statistics
Matches: 316, Mismatches: 43, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
78 3 0.01
79 311 0.98
80 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (79 bp):
GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATCAGATGGTCTTCAAT
CTGCCCTCTGGTTA
Found at i:63140 original size:237 final size:237
Alignment explanation
Indices: 62717--63152 Score: 640
Period size: 237 Copynumber: 1.8 Consensus size: 237
62707 ATAGCTTTAG
* * *
62717 GGGTAAAAGATTGGATTGTTTCAATTTGCCCCATAGTCAAGGTAAGAGATCTGATAGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATAGTCAAGGTAAGAGATCAGATAGTCTTCAAT
* * * * * ** *
62782 CTGCGCTCTTGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCCTGATGGTCGGGGTAACAAATC
66 CTACCCTCTGGTTAGGGTAAAAGATTAGATTACTTCAATCTGCCCCATGGTCAGGGTAACAAATC
** * * *
62847 GGATGGTCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGT
131 AAATGGTATCCAATCTGCCCTCTAATTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGT
62912 CGGGTTAAGAGATCGGATAGTCTTCAATCTGCCCTCTGGTTA
196 CGGGTTAAGAGATCGGATAGTCTTCAATCTGCCCTCTGGTTA
* * * *
62954 GGGTATAAGATTGGATTGCTTCAATCTGCCTCATGGTC-AGGTTAAGAGATCAGATGGTCTTCAA
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATAGTCAAGG-TAAGAGATCAGATAGTCTTCAA
*
63018 TCTACCCTCTGGTTAGGGTAAAAGATTAGATTACTTCAATCTGCCCCATGGTCAGGGTAACAGAT
65 TCTACCCTCTGGTTAGGGTAAAAGATTAGATTACTTCAATCTGCCCCATGGTCAGGGTAACAAAT
* * *
63083 CAAATGGTATCCAATTTGCCCTTTAATTAGGGTAAAAGATTGGATTGCTTTAATCTGCCCCATGG
130 CAAATGGTATCCAATCTGCCCTCTAATTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGG
63148 TCGGG
195 TCGGG
63153 GTAAAAGACT
Statistics
Matches: 174, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
236 3 0.02
237 171 0.98
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (237 bp):
GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATAGTCAAGGTAAGAGATCAGATAGTCTTCAAT
CTACCCTCTGGTTAGGGTAAAAGATTAGATTACTTCAATCTGCCCCATGGTCAGGGTAACAAATC
AAATGGTATCCAATCTGCCCTCTAATTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGT
CGGGTTAAGAGATCGGATAGTCTTCAATCTGCCCTCTGGTTA
Found at i:63256 original size:50 final size:50
Alignment explanation
Indices: 63202--63346 Score: 184
Period size: 50 Copynumber: 2.9 Consensus size: 50
63192 CAGGAGTATA
** *
63202 AGATTCGTCCTTGCTACTTCAATCTGCCCCTCTACAGCTTTAGGTGAATG
1 AGATTCGTCCTTGCGGCTTCAATTTGCCCCTCTACAGCTTTAGGTGAATG
* * *
63252 AGATTCG-CCATTACGGCTTCAATTTGCCCCTTTACAGCTTTAGGTGTATG
1 AGATTCGTCC-TTGCGGCTTCAATTTGCCCCTCTACAGCTTTAGGTGAATG
* * *
63302 AGATTTGTCATTGAGGCTTCAAATTTGCCCCTCTACAGCTTTAGG
1 AGATTCGTCCTTGCGGCTTC-AATTTGCCCCTCTACAGCTTTAGG
63347 GGTATAGGAC
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
49 2 0.02
50 55 0.68
51 24 0.30
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (50 bp):
AGATTCGTCCTTGCGGCTTCAATTTGCCCCTCTACAGCTTTAGGTGAATG
Found at i:63972 original size:112 final size:112
Alignment explanation
Indices: 63770--63988 Score: 348
Period size: 112 Copynumber: 2.0 Consensus size: 112
63760 CCTTATATCG
*
63770 TTAGACCACTAACCGTCATTTCAATGCAAAAATGCTTGAACAAGGTTGTAAAGTGGATAAAATTG
1 TTAGACCACTAACCGTCATTTCAATGCAAAAATGCTTGAACAAGGTTGTAAAGTGGATAAAATTA
*
63835 AATTTGATTACAGGCAAAGCTCGCATGAATGAAAAGATTAAAAATCA
66 AATTTGATTACAGGCAAAGCTCGCATGAATGAAAAAATTAAAAATCA
* * ** * *
63882 TTAGTCCACTAACCGTCATTTCAATGCAAAAATGTTTGAACGGGGTTGTGAGGTGGATAAAATTA
1 TTAGACCACTAACCGTCATTTCAATGCAAAAATGCTTGAACAAGGTTGTAAAGTGGATAAAATTA
* *
63947 AATTTTATTAGAGGCAAAGCTCGCATGAATGAAAAAATTAAA
66 AATTTGATTACAGGCAAAGCTCGCATGAATGAAAAAATTAAA
63989 CATTGATCAA
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
112 97 1.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (112 bp):
TTAGACCACTAACCGTCATTTCAATGCAAAAATGCTTGAACAAGGTTGTAAAGTGGATAAAATTA
AATTTGATTACAGGCAAAGCTCGCATGAATGAAAAAATTAAAAATCA
Found at i:64322 original size:20 final size:20
Alignment explanation
Indices: 64297--64353 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
64287 CCTCCCCTTT
64297 TTCTTTTTCTTTTTCTTTTC
1 TTCTTTTTCTTTTTCTTTTC
*
64317 TTCTTTTTTCCTTTT-TTTTC
1 TTC-TTTTTCTTTTTCTTTTC
*
64337 TCCTTTTCTCTTTTTCT
1 TTCTTTT-TCTTTTTCT
64354 CTTTTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 4 0.13
20 16 0.52
21 11 0.35
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (20 bp):
TTCTTTTTCTTTTTCTTTTC
Found at i:64330 original size:28 final size:25
Alignment explanation
Indices: 64293--64364 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 25
64283 TTGACCTCCC
64293 CTTTTT-CTTTTTCTTTTTCTTTTCTT
1 CTTTTTCCTTTTT-TTTTTCTTTTC-T
*
64319 CTTTTTTCCTTTTTTTTCTCCTTTTCT
1 C-TTTTTCCTTTTTTTT-TTCTTTTCT
64346 CTTTTTCTCTTTTTTTTTT
1 CTTTTTC-CTTTTTTTTTT
64365 GGTGAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 8 0.20
27 19 0.47
28 13 0.32
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (25 bp):
CTTTTTCCTTTTTTTTTTCTTTTCT
Found at i:64351 original size:8 final size:8
Alignment explanation
Indices: 64300--64359 Score: 54
Period size: 8 Copynumber: 7.5 Consensus size: 8
64290 CCCCTTTTTC
64300 TTTT-TCT
1 TTTTCTCT
64307 TTTTCT-T
1 TTTTCTCT
64314 TTCTTCT-T
1 TT-TTCTCT
*
64322 TTTTCCTTTT
1 TTTT-C-TCT
*
64332 TTTTCTCC
1 TTTTCTCT
64340 TTTTCTCT
1 TTTTCTCT
64348 TTTTCTCT
1 TTTTCTCT
64356 TTTT
1 TTTT
64360 TTTTTGGTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
7 9 0.20
8 29 0.64
9 2 0.04
10 5 0.11
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTCTCT
Found at i:68685 original size:60 final size:61
Alignment explanation
Indices: 68617--68767 Score: 182
Period size: 61 Copynumber: 2.5 Consensus size: 61
68607 CATTAAAATT
68617 GGGTCAAATTTGAATTTTT-GAAAACTTTAAGGGCTAAA-TCAAATTTTTTGG-AAAGTTTAG
1 GGGTCAAATTTGAATTTTTAGAAAA-TTTAAGGGCTAAATTCAAA-TTTTTGGAAAAGTTTAG
* * * * * ** *
68677 GGGTCAAATTGGAATTTTTGGAAGATTTGAGGGTTAAATTTGAATTTTTGGAAAATTTTAG
1 GGGTCAAATTTGAATTTTTAGAAAATTTAAGGGCTAAATTCAAATTTTTGGAAAAGTTTAG
*
68738 GGGTCAAATTTGAATTTTTAGAAATTTTAA
1 GGGTCAAATTTGAATTTTTAGAAAATTTAA
68768 AGGTCAAAAC
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
60 36 0.47
61 40 0.53
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (61 bp):
GGGTCAAATTTGAATTTTTAGAAAATTTAAGGGCTAAATTCAAATTTTTGGAAAAGTTTAG
Found at i:68750 original size:31 final size:31
Alignment explanation
Indices: 68617--68775 Score: 150
Period size: 30 Copynumber: 5.3 Consensus size: 31
68607 CATTAAAATT
*
68617 GGGTCAAATTTGAATTTTT-GAAAACTTTAA
1 GGGTCAAATTTGAATTTTTGGAAAATTTTAA
** * *
68647 GGG-CTAAA-TCAAATTTTTTGG-AAAGTTTAG
1 GGGTC-AAATTTGAA-TTTTTGGAAAATTTTAA
* * *
68677 GGGTCAAATTGGAATTTTTGGAAGA-TTTGA
1 GGGTCAAATTTGAATTTTTGGAAAATTTTAA
* *
68707 GGGTTAAATTTGAATTTTTGGAAAATTTTAG
1 GGGTCAAATTTGAATTTTTGGAAAATTTTAA
*
68738 GGGTCAAATTTGAATTTTTAG-AAATTTTAA
1 GGGTCAAATTTGAATTTTTGGAAAATTTTAA
*
68768 AGGTCAAA
1 GGGTCAAA
68776 ACATAATTTT
Statistics
Matches: 104, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
29 4 0.04
30 71 0.68
31 29 0.28
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (31 bp):
GGGTCAAATTTGAATTTTTGGAAAATTTTAA
Found at i:68784 original size:61 final size:57
Alignment explanation
Indices: 68617--68786 Score: 146
Period size: 61 Copynumber: 2.8 Consensus size: 57
68607 CATTAAAATT
* *
68617 GGGTCAAATTTGAATTTTTGAAAACTTTAAGGGCTAAATCA-AATTTTTTGGAAAGTTTAG
1 GGGTCAAATTTGAATTTTTG-AAA-TTTAAGGTC-AAAACATAA-TTTTTGGAAAGTTTAG
* * * ** *
68677 GGGTCAAATTGGAATTTTTGGAAGATTTGAGGGT-TAAATTTGAATTTTTGGAAAATTTTAG
1 GGGTCAAATTTGAATTTTT-GAA-ATTT-AAGGTCAAAACAT-AATTTTTGG-AAAGTTTAG
68738 GGGTCAAATTTGAATTTTTAGAAATTTTAAAGGTCAAAACATAATTTTT
1 GGGTCAAATTTGAATTTTT-GAAA-TTT-AAGGTCAAAACATAATTTTT
68787 AAATAGTTTG
Statistics
Matches: 87, Mismatches: 15, Indels: 15
0.74 0.13 0.13
Matches are distributed among these distances:
59 2 0.02
60 31 0.36
61 50 0.57
62 4 0.05
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.40
Consensus pattern (57 bp):
GGGTCAAATTTGAATTTTTGAAATTTAAGGTCAAAACATAATTTTTGGAAAGTTTAG
Found at i:88442 original size:13 final size:12
Alignment explanation
Indices: 88398--88454 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 12
88388 ATATAATAAG
88398 ATAATATTAATT
1 ATAATATTAATT
**
88410 A-AATAACAATTT
1 ATAATATTAA-TT
*
88422 ATATTATTATATT
1 ATAATATTA-ATT
88435 ATAATATTAATT
1 ATAATATTAATT
88447 AATAATAT
1 -ATAATAT
88455 CTTAAATTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
11 6 0.17
12 7 0.20
13 21 0.60
14 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
ATAATATTAATT
Done.