Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015134.1 Kokia drynarioides strain JFW-HI SEQ_130178, 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: 177399
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 41 characters in sequence are not A, C, G, or T
Found at i:17938 original size:12 final size:12
Alignment explanation
Indices: 17919--17948 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
17909 TGAAGACGGA
17919 GATGATGGTGAT
1 GATGATGGTGAT
*
17931 GGTGATGGTGAT
1 GATGATGGTGAT
17943 GATGAT
1 GATGAT
17949 TCGTTTTGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.43, T:0.33
Consensus pattern (12 bp):
GATGATGGTGAT
Found at i:18783 original size:18 final size:17
Alignment explanation
Indices: 18740--18776 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
18730 AATTCAATCC
18740 TTTT-ATTTTTTTTTCA
1 TTTTGATTTTTTTTTCA
*
18756 TTTTGATTTTTTTTTTA
1 TTTTGATTTTTTTTTCA
18773 TTTT
1 TTTT
18777 AGCTTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.11, C:0.03, G:0.03, T:0.84
Consensus pattern (17 bp):
TTTTGATTTTTTTTTCA
Found at i:19249 original size:82 final size:82
Alignment explanation
Indices: 19122--19272 Score: 241
Period size: 82 Copynumber: 1.8 Consensus size: 82
19112 AAGTGAATAA
* * * *
19122 TTTTCAGTTTTGGTTATTCTAATTTGCTTAAATTTGGTATTTAATCCTTATATTTTAATTTCTAA
1 TTTTCAGTTTCGGTTATTCTAATATGATTAAATTTGGTATTTAATCCTTATATTTTAAATTCTAA
19187 CATATAAAAGTGGTTAT
66 CATATAAAAGTGGTTAT
*
19204 TTTTTAGTTTCGGTTATTCTAATATGATTAAATTTGAG-ATTTAATCCTTATATTTTAAATTCTA
1 TTTTCAGTTTCGGTTATTCTAATATGATTAAATTTG-GTATTTAATCCTTATATTTTAAATTCTA
19268 ACATA
65 ACATA
19273 ATTTGGTCTC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
82 62 0.98
83 1 0.02
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.52
Consensus pattern (82 bp):
TTTTCAGTTTCGGTTATTCTAATATGATTAAATTTGGTATTTAATCCTTATATTTTAAATTCTAA
CATATAAAAGTGGTTAT
Found at i:24882 original size:11 final size:11
Alignment explanation
Indices: 24861--24893 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
24851 TAGGTTTGTT
24861 TGTCAAAATTGA
1 TGTC-AAATTGA
24873 TGTCAAATTGA
1 TGTCAAATTGA
24884 TGTCAAATTG
1 TGTCAAATTG
24894 GAGGATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (11 bp):
TGTCAAATTGA
Found at i:30242 original size:25 final size:25
Alignment explanation
Indices: 30191--30243 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
30181 ATACATCATC
* *
30191 TTTGATATACTTTGTAATGTTATAA
1 TTTGATATACTTTGTAATATTAAAA
*
30216 TTTGGTATA-TTTGTATATATTAAAA
1 TTTGATATACTTTGTA-ATATTAAAA
30241 TTT
1 TTT
30244 AATTTTGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (25 bp):
TTTGATATACTTTGTAATATTAAAA
Found at i:58636 original size:23 final size:23
Alignment explanation
Indices: 58604--58776 Score: 122
Period size: 23 Copynumber: 7.4 Consensus size: 23
58594 ACGCTAGTGC
*
58604 GCTTACTGTTTCGTACTTTGTGT
1 GCTTACTGTTTCGCACTTTGTGT
*
58627 GTTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTTCGCACTTTGTGT
* *
58650 GCTTACTGTTTCACACTTCGTGT
1 GCTTACTGTTTCGCACTTTGTGT
* * * *
58673 GCTTACTAATTT-GCGCTATGTGC
1 GCTTACT-GTTTCGCACTTTGTGT
* *
58696 G-TCTACTGATT-GCACTGTGTGT
1 GCT-TACTGTTTCGCACTTTGTGT
* * *
58718 GCCTACTGGATT-GCACTGTGTGT
1 GCTTACT-GTTTCGCACTTTGTGT
*
58741 GCTTATTGTTTTTC-CAGCATTTGTGT
1 GCTTACTG--TTTCGCA-C-TTTGTGT
58767 GCTTACTGTT
1 GCTTACTGTT
58777 AAGTACTTCG
Statistics
Matches: 119, Mismatches: 22, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
22 17 0.14
23 79 0.66
24 9 0.08
25 1 0.01
26 13 0.11
ACGTcount: A:0.12, C:0.20, G:0.23, T:0.46
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTTGTGT
Found at i:60622 original size:23 final size:24
Alignment explanation
Indices: 60595--60649 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 24
60585 ATGGGTCAAA
* *
60595 TTATTGTTTT-AATAATATATAAT
1 TTATTATTTTGAATAATATAGAAT
60618 TTATTATTTTGGAAATAATATAGAAT
1 TTATTATTTT-G-AATAATATAGAAT
60644 TTATTA
1 TTATTA
60650 AAATGTTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 9 0.33
26 18 0.67
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (24 bp):
TTATTATTTTGAATAATATAGAAT
Found at i:60776 original size:5 final size:5
Alignment explanation
Indices: 60753--60794 Score: 59
Period size: 5 Copynumber: 8.4 Consensus size: 5
60743 ACCGCGTAAG
*
60753 AAAG- AAAGA GAAGGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
1 AAAGA AAAGA -AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
60795 GGATTTAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
4 4 0.12
5 26 0.76
6 4 0.12
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:76051 original size:14 final size:14
Alignment explanation
Indices: 76029--76064 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
76019 TTCATCCAAA
*
76029 TTTAAATTTTAATT
1 TTTAAATTTCAATT
*
76043 TTTATATTTCAATT
1 TTTAAATTTCAATT
76057 TTTAAATT
1 TTTAAATT
76065 ATTTAATACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTAAATTTCAATT
Found at i:76079 original size:24 final size:23
Alignment explanation
Indices: 76035--76094 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
76025 CAAATTTAAA
*
76035 TTTT-AATT-TTTATATTTCAAT
1 TTTTAAATTATTTATACTTCAAT
76056 TTTTAAATTATTTAATACTTCAAT
1 TTTTAAATTATTT-ATACTTCAAT
76080 TCTTATAATATTATT
1 T-TT-TAA-ATTATT
76095 GGTTAATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 4 0.12
22 4 0.12
23 3 0.09
24 10 0.31
25 2 0.06
26 3 0.09
27 6 0.19
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTAAATTATTTATACTTCAAT
Found at i:77775 original size:29 final size:29
Alignment explanation
Indices: 77743--77798 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
77733 AACCATTAAT
* * *
77743 ATTTTATAAATTTTATTAATTTAATTTTA
1 ATTTTAAAAATTTAATAAATTTAATTTTA
77772 ATTTTAAAAATTTAATAAATTTAATTT
1 ATTTTAAAAATTTAATAAATTTAATTT
77799 ACAATATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
ATTTTAAAAATTTAATAAATTTAATTTTA
Found at i:79274 original size:8 final size:9
Alignment explanation
Indices: 79246--79285 Score: 55
Period size: 10 Copynumber: 4.3 Consensus size: 9
79236 AATATTTTAG
79246 AAAATGACAA
1 AAAATGA-AA
79256 AAAAGTGAAA
1 AAAA-TGAAA
79266 AAAAT-AAA
1 AAAATGAAA
79274 AAAATGAAA
1 AAAATGAAA
79283 AAA
1 AAA
79286 GGAAAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.29
9 7 0.25
10 10 0.36
11 3 0.11
ACGTcount: A:0.78, C:0.03, G:0.10, T:0.10
Consensus pattern (9 bp):
AAAATGAAA
Found at i:82220 original size:80 final size:80
Alignment explanation
Indices: 82087--82241 Score: 247
Period size: 80 Copynumber: 1.9 Consensus size: 80
82077 CCAATAATGA
* *
82087 CCATAAATTCCCTCTAATAGTGGTTCTATTGTTAATATTGAGTTATTCTAGAACATCTTTTTGCC
1 CCATAAATCCCCTCTAATAGTGGTTCTATAGTTAATATTGAGTTATTCTAGAACATCTTTTTGCC
82152 AAATATACTTATTCC
66 AAATATACTTATTCC
* * * *
82167 CCATAAATCCCCTCTATTAGTGGTTCTGTAGTTGATATTGAGTTATTCTAGAACATCTTTTTGGC
1 CCATAAATCCCCTCTAATAGTGGTTCTATAGTTAATATTGAGTTATTCTAGAACATCTTTTTGCC
*
82232 AAATTTACTT
66 AAATATACTT
82242 TCAGATATAA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (80 bp):
CCATAAATCCCCTCTAATAGTGGTTCTATAGTTAATATTGAGTTATTCTAGAACATCTTTTTGCC
AAATATACTTATTCC
Found at i:85388 original size:21 final size:22
Alignment explanation
Indices: 85364--85408 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
85354 ATCAAAAAAA
* *
85364 TTTATGTAT-AAATTTTGATTT
1 TTTATATATAAAATTTTAATTT
85385 TTTATATATAAAATTTTAATTT
1 TTTATATATAAAATTTTAATTT
85407 TT
1 TT
85409 ATTCCATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (22 bp):
TTTATATATAAAATTTTAATTT
Found at i:85409 original size:21 final size:21
Alignment explanation
Indices: 85364--85410 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
85354 ATCAAAAAAA
* *
85364 TTTATGTATAAATTTTGATTT
1 TTTATATATAAATTTTGAATT
85385 TTTATATATAAAATTTT-AATT
1 TTTATATAT-AAATTTTGAATT
85406 TTTAT
1 TTTAT
85411 TCCATCTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTATATATAAATTTTGAATT
Found at i:92862 original size:6 final size:6
Alignment explanation
Indices: 92851--92878 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
92841 ACATTTCCAA
92851 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
92879 TTATAGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:95453 original size:16 final size:15
Alignment explanation
Indices: 95425--95462 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
95415 AGATAATTAA
*
95425 AAAAATAAAAATATT
1 AAAAATAAAAATAAT
95440 AAAAATAAATAATAAT
1 AAAAATAAA-AATAAT
95456 AAAAATA
1 AAAAATA
95463 TATCATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATAAAAATAAT
Found at i:117762 original size:32 final size:32
Alignment explanation
Indices: 117719--117781 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
117709 ATAAATAGTA
* *
117719 TGTGATGAAATACGTTTTATGGATTGCTTGTC
1 TGTGATAAAATAAGTTTTATGGATTGCTTGTC
*
117751 TGTGATAAAATAAGTTTTATGGGTTGCTTGT
1 TGTGATAAAATAAGTTTTATGGATTGCTTGT
117782 TATGTTCTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.24, C:0.06, G:0.25, T:0.44
Consensus pattern (32 bp):
TGTGATAAAATAAGTTTTATGGATTGCTTGTC
Found at i:131330 original size:32 final size:32
Alignment explanation
Indices: 131284--131347 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
131274 AAGCTAAATA
* *
131284 GTCTGTGATGAAATACGTTTTAT-GGATTGCTT
1 GTCTGTGATAAAATAAGTTTTATAGG-TTGCTT
131316 GTCTGTGATAAAATAAGTTTTATAGGTTGCTT
1 GTCTGTGATAAAATAAGTTTTATAGGTTGCTT
131348 TTTATGTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 27 0.93
33 2 0.07
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (32 bp):
GTCTGTGATAAAATAAGTTTTATAGGTTGCTT
Found at i:131428 original size:96 final size:97
Alignment explanation
Indices: 131263--131454 Score: 332
Period size: 96 Copynumber: 2.0 Consensus size: 97
131253 GACTGCCTGC
**
131263 TTACATCTCTTAAGCTAAATAGTCTGTGATGAAATACGTTTTATGGATTGCTTGTCTGTGATAAA
1 TTACATCTCTTAAGCTAAATAGAATGTGATGAAATACGTTTTATGGATTGCTTGTCTGTGATAAA
*
131328 ATAAGTTTTATAGGTTGCTTTTTATGTTCTGA
66 ATAAGTTTTATAGGTTGCTTGTTATGTTCTGA
*
131360 TTACATCTCTTAAGCT-AATAGAATGTTATGAAATACGTTTTATGGATTGCTTGTCTGTGATAAA
1 TTACATCTCTTAAGCTAAATAGAATGTGATGAAATACGTTTTATGGATTGCTTGTCTGTGATAAA
*
131424 ATAAGTTTTATGGGTTGCTTGTTATGTTCTG
66 ATAAGTTTTATAGGTTGCTTGTTATGTTCTG
131455 TTTATGGATA
Statistics
Matches: 90, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
96 74 0.82
97 16 0.18
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (97 bp):
TTACATCTCTTAAGCTAAATAGAATGTGATGAAATACGTTTTATGGATTGCTTGTCTGTGATAAA
ATAAGTTTTATAGGTTGCTTGTTATGTTCTGA
Found at i:133506 original size:503 final size:505
Alignment explanation
Indices: 132557--133530 Score: 1844
Period size: 503 Copynumber: 1.9 Consensus size: 505
132547 GATGATTAAA
132557 GTATTACATACACTAGATACTGCCAGCTGGCTTTACAACATTGACACTCCATTTGGTAGAAAGGA
1 GTATTACATACACTAGATACTGCCAGCTGGCTTTACAACATTGACACTCCATTTGGTAGAAAGGA
* *
132622 TGGAAAGAATCAAGGAAAAAAGTTTACCATAAAAATAGAGTTACAGAATAGCAAATGTGGTTATG
66 TGGAAAGAATCAAGGAAAAAAGTTTACCACAAAAATAGAGTTACAGAATAGAAAATGTGGTTATG
132687 AATATCAACCATCAGACTAAATTTTTTTTTTGTTCTCCCTACTAAAGAAAGCCTTATTGGCTAGC
131 AATATCAACCATCAGACTAAATTTTTTTTTTGTTCTCCCTACTAAAGAAAGCCTTATTGGCTAGC
132752 AATTGTAAGCTATTTGGAGTTTTTTTTTTTTGTTTTGACAAAATAAGCTATTTGGAATTAAATTC
196 AATTGTAAGCTATTTGGAGTTTTTTTTTTTTGTTTTGACAAAATAAGCTATTTGGAATTAAATTC
132817 ATAGGTAGGGGCTGTTTGTGAAGGCAATTCAATGTTTATAAAGTTTTGGGATTGAACAGCATTCT
261 ATAGGTAGGGGCTGTTTGTGAAGGCAATTCAATGTTTATAAAGTTTTGGGATTGAACAGCATTCT
132882 ACCAGCTGAAGTGTATTATAAATGCTGTACTAGTCAGGTCTCTACATGGTTCCTCTTTTGCGCCT
326 ACCAGCTGAAGTGTATTATAAATGCTGTACTAGTCAGGTCTCTACATGGTTCCTCTTTTGCGCCT
* * *
132947 GCATTAGAACCTTGCTTTGTTTAAACTTTGTCAAACATGTAATATATTTGGCTTTATGATGATTA
391 GCATTAGAAACTTGCTTTCTTTAAACTTCGTCAAACATGTAATATATTTGGCTTTATGATGATTA
133012 AAGTATTTATGACATACAGTTGGGTGTTAAAACCTGCTCTTCTGGGCTTT
456 AAGTATTTATGACATACAGTTGGGTGTTAAAACCTGCTCTTCTGGGCTTT
133062 GTATTACATACACTAGATACTGCCAGCTGGCTTTACAACATTGACACTCCATTTGGTAGAAAGGA
1 GTATTACATACACTAGATACTGCCAGCTGGCTTTACAACATTGACACTCCATTTGGTAGAAAGGA
* *
133127 TGGAAAGAGTCAAGGAAAAAAGTTTACCACAAAAATAGAGTTACAGACTAGAAAATGTGGTTATG
66 TGGAAAGAATCAAGGAAAAAAGTTTACCACAAAAATAGAGTTACAGAATAGAAAATGTGGTTATG
*
133192 AATATCAACCATCAGACTAATTTTTTTTTTTGTTCTCCCTACTAAAGAAAGCCTTATTGGCTAGC
131 AATATCAACCATCAGACTAAATTTTTTTTTTGTTCTCCCTACTAAAGAAAGCCTTATTGGCTAGC
133257 AATTGTAAGCTATTTGGAG-TTTTTTTTTTT-TTTTGACAAAATAAGCTATTTGGAATTAAATTC
196 AATTGTAAGCTATTTGGAGTTTTTTTTTTTTGTTTTGACAAAATAAGCTATTTGGAATTAAATTC
*
133320 ATAGGTAGGGGCTGTTTGTGAAGGCAATTTAATGTTTATAAAGTTTTGGGATTGAACAGCATTCT
261 ATAGGTAGGGGCTGTTTGTGAAGGCAATTCAATGTTTATAAAGTTTTGGGATTGAACAGCATTCT
133385 ACCAGCTGAAGTGTATTATAAATGCTGTACTAGTCAGGTCTCTACATGGTTCCTCTTTTGCGCCT
326 ACCAGCTGAAGTGTATTATAAATGCTGTACTAGTCAGGTCTCTACATGGTTCCTCTTTTGCGCCT
*
133450 GCGTTAGAAACTTGCTTTCTTTAAACTTCGTCAAACATGTAATATATTTGGCTTTATGATGATTA
391 GCATTAGAAACTTGCTTTCTTTAAACTTCGTCAAACATGTAATATATTTGGCTTTATGATGATTA
133515 AAGTATTTATGACATA
456 AAGTATTTATGACATA
133531 GGGTTCTGTT
Statistics
Matches: 459, Mismatches: 10, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
503 239 0.52
504 11 0.02
505 209 0.46
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.36
Consensus pattern (505 bp):
GTATTACATACACTAGATACTGCCAGCTGGCTTTACAACATTGACACTCCATTTGGTAGAAAGGA
TGGAAAGAATCAAGGAAAAAAGTTTACCACAAAAATAGAGTTACAGAATAGAAAATGTGGTTATG
AATATCAACCATCAGACTAAATTTTTTTTTTGTTCTCCCTACTAAAGAAAGCCTTATTGGCTAGC
AATTGTAAGCTATTTGGAGTTTTTTTTTTTTGTTTTGACAAAATAAGCTATTTGGAATTAAATTC
ATAGGTAGGGGCTGTTTGTGAAGGCAATTCAATGTTTATAAAGTTTTGGGATTGAACAGCATTCT
ACCAGCTGAAGTGTATTATAAATGCTGTACTAGTCAGGTCTCTACATGGTTCCTCTTTTGCGCCT
GCATTAGAAACTTGCTTTCTTTAAACTTCGTCAAACATGTAATATATTTGGCTTTATGATGATTA
AAGTATTTATGACATACAGTTGGGTGTTAAAACCTGCTCTTCTGGGCTTT
Found at i:135241 original size:34 final size:35
Alignment explanation
Indices: 135175--135243 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
135165 GCGCTGGACA
* *
135175 ACCTATATAATGTAAGCTTGATCTGTTTTTTGTCT
1 ACCTATATAATGTAAGCTTAATCTGTTCTTTGTCT
* * *
135210 ACCTTTATAAT-TTAGCTTAATGTGTTCTTTGTCT
1 ACCTATATAATGTAAGCTTAATCTGTTCTTTGTCT
135244 GTTTGTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 19 0.66
35 10 0.34
ACGTcount: A:0.22, C:0.14, G:0.13, T:0.51
Consensus pattern (35 bp):
ACCTATATAATGTAAGCTTAATCTGTTCTTTGTCT
Found at i:149308 original size:6 final size:6
Alignment explanation
Indices: 149295--149329 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
149285 CTGTCCCTGT
149295 TCCC-A TCCCTA TCCCTA TCCCTA TCCCTA TCCCTA
1 TCCCTA TCCCTA TCCCTA TCCCTA TCCCTA TCCCTA
149330 ACCTCTACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.17, C:0.51, G:0.00, T:0.31
Consensus pattern (6 bp):
TCCCTA
Found at i:150532 original size:30 final size:30
Alignment explanation
Indices: 150498--150579 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 30
150488 TATTAAAAAA
*
150498 AAATTAGGTACCAAATTAGGAAAAA-GAGTC
1 AAATTAGGTACCAAATTA-AAAAAACGAGTC
* *
150528 AAATTCAGGTATCAAATTAAAAAAACGTGTC
1 AAATT-AGGTACCAAATTAAAAAAACGAGTC
* *
150559 AAGTTTGAGTACCAAATTAAA
1 AAATTAG-GTACCAAATTAAA
150580 CCCAAAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
30 11 0.26
31 32 0.74
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (30 bp):
AAATTAGGTACCAAATTAAAAAAACGAGTC
Found at i:152519 original size:13 final size:13
Alignment explanation
Indices: 152501--152528 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
152491 CTTAAATCTG
152501 CTATATCCAGCTT
1 CTATATCCAGCTT
152514 CTATATCCAGCTT
1 CTATATCCAGCTT
152527 CT
1 CT
152529 GATACACATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.32, G:0.07, T:0.39
Consensus pattern (13 bp):
CTATATCCAGCTT
Found at i:158130 original size:81 final size:84
Alignment explanation
Indices: 157514--158147 Score: 713
Period size: 84 Copynumber: 7.6 Consensus size: 84
157504 TAGTTGCTTC
* * * * ***
157514 TGCTTTAGCGATCTCAAAATCGGCACATTTTCTTGCTTCAACAGCCTTCTTCTTGGTTTCTTCTG
1 TGCTTTAGCCATCTCCAAATCAGCACATTTTCTTTCTTCAACAGCCTTCTTCTTCAATTCTTCTG
* * *
157579 CAATCTTCCTTTGCGCCTC
66 CAATCTTCCTCTGCTCCTG
* ** ** * *
157598 TGCTTCAGCCATCTGTAAATCAGCATGTTTTCTTTTTTCAACTGCCTTCTTCTT-AATCTCTTCT
1 TGCTTTAGCCATCTCCAAATCAGCACATTTTCTTTCTTCAACAGCCTTCTTCTTCAAT-TCTTCT
*
157662 GCAATCTTCTTCTGCTCCTG
65 GCAATCTTCCTCTGCTCCTG
* * ** * * * *
157682 TGCTTTAGCCATCTCCAAAGCCGCATGTTTTCTTTCTTCAACAACCTTCTTCTTCGACTCTTCGG
1 TGCTTTAGCCATCTCCAAATCAGCACATTTTCTTTCTTCAACAGCCTTCTTCTTCAATTCTTCTG
*
157747 CAATCTTCTTCTGCTCCTG
66 CAATCTTCCTCTGCTCCTG
* ** *
157766 TGCTTTAGCCATCTCCAAAGCAGCATGTTTTCTTTCTTCAAAAGCCTTCTTCTTCAATTCTTCTG
1 TGCTTTAGCCATCTCCAAATCAGCACATTTTCTTTCTTCAACAGCCTTCTTCTTCAATTCTTCTG
* *
157831 CAGTCTTCCTCTTCTCCTG
66 CAATCTTCCTCTGCTCCTG
* * *
157850 TGCTTCAGCAATCTCCAAATCAGCACATTTTCTTTCTTCAACAGCTTTCTTCTTCAATTCTTCTG
1 TGCTTTAGCCATCTCCAAATCAGCACATTTTCTTTCTTCAACAGCCTTCTTCTTCAATTCTTCTG
* *
157915 CAGTCTTCCTTTGCTCCTG
66 CAATCTTCCTCTGCTCCTG
*
157934 TGCTTTAGCAATCTCCAAATCAGCACATTTTCTTTCTTCAACAGCCTTCTTCTTC-ATCTCTTCT
1 TGCTTTAGCCATCTCCAAATCAGCACATTTTCTTTCTTCAACAGCCTTCTTCTTCAAT-TCTTCT
* *
157998 GCAACCTTCCTCTCCTCCTG
65 GCAATCTTCCTCTGCTCCTG
* * * * *
158018 TGCCTTAGCCATCTCCAGATCAGCACATTTTCTATCTTCAACA-CC-T-TTCAT-AGATTTTTCT
1 TGCTTTAGCCATCTCCAAATCAGCACATTTTCTTTCTTCAACAGCCTTCTTCTTCA-ATTCTTCT
* * * *
158079 ACAAACTTTCTCTGCTCCTT
65 GCAATCTTCCTCTGCTCCTG
* * * *
158099 TGCTTTAGCCATCTCCGAATCAGCACCTTTTCTTTCTTTAACGGCCTTC
1 TGCTTTAGCCATCTCCAAATCAGCACATTTTCTTTCTTCAACAGCCTTC
158148 CTTGTTTCTT
Statistics
Matches: 473, Mismatches: 69, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
81 60 0.13
82 5 0.01
83 6 0.01
84 401 0.85
85 1 0.00
ACGTcount: A:0.17, C:0.32, G:0.10, T:0.41
Consensus pattern (84 bp):
TGCTTTAGCCATCTCCAAATCAGCACATTTTCTTTCTTCAACAGCCTTCTTCTTCAATTCTTCTG
CAATCTTCCTCTGCTCCTG
Found at i:160701 original size:12 final size:12
Alignment explanation
Indices: 160680--160709 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
160670 AATAATTTTT
*
160680 TTAATGAAAATA
1 TTAATTAAAATA
160692 TTAATTAAAATA
1 TTAATTAAAATA
160704 TTAATT
1 TTAATT
160710 TTTTTAACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (12 bp):
TTAATTAAAATA
Found at i:165889 original size:13 final size:13
Alignment explanation
Indices: 165871--165901 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
165861 CCNNNCCCTC
165871 CTTTTAATATATT
1 CTTTTAATATATT
*
165884 CTTTTATTATATT
1 CTTTTAATATATT
165897 CTTTT
1 CTTTT
165902 CAATCTACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (13 bp):
CTTTTAATATATT
Found at i:168382 original size:29 final size:29
Alignment explanation
Indices: 168321--168387 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
168311 ATTTTAAGGG
* *
168321 TTTAGGATTTAGGTTTTTAGTGTTCATGT
1 TTTAGGATTTAGGTTTTTAGTGTTCAAGA
* *
168350 TTTAGGGTTTATGGTTTTT-GTGTTTAAGA
1 TTTAGGATTTA-GGTTTTTAGTGTTCAAGA
*
168379 TTTAAGATT
1 TTTAGGATT
168388 CAGGGTTTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 24 0.77
30 7 0.23
ACGTcount: A:0.19, C:0.01, G:0.24, T:0.55
Consensus pattern (29 bp):
TTTAGGATTTAGGTTTTTAGTGTTCAAGA
Found at i:168417 original size:14 final size:14
Alignment explanation
Indices: 168400--168510 Score: 66
Period size: 14 Copynumber: 7.8 Consensus size: 14
168390 GGGTTTATAT
*
168400 TTTAGTGTTTA-TGG
1 TTTAGGGTTTAGT-G
* *
168414 TTTAGGATTT-GTT
1 TTTAGGGTTTAGTG
*
168427 TTTAGGGTTTTAGTA
1 TTTAGGG-TTTAGTG
* *
168442 TTTATGGTTTTAGAG
1 TTTA-GGGTTTAGTG
* * **
168457 TTCATGGTTTAGAC
1 TTTAGGGTTTAGTG
168471 TTTAGGGTTTGAGTG
1 TTTAGGGTTT-AGTG
168486 TTTAGGGTTT-GTG
1 TTTAGGGTTTAGTG
168499 TTATAGGGTTTA
1 TT-TAGGGTTTA
168511 AGTATCTAGT
Statistics
Matches: 74, Mismatches: 16, Indels: 13
0.72 0.16 0.13
Matches are distributed among these distances:
13 11 0.15
14 35 0.47
15 26 0.35
16 2 0.03
ACGTcount: A:0.17, C:0.02, G:0.29, T:0.52
Consensus pattern (14 bp):
TTTAGGGTTTAGTG
Found at i:168491 original size:15 final size:13
Alignment explanation
Indices: 168471--168509 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
168461 TGGTTTAGAC
168471 TTTAGGGTTTGAGTG
1 TTTAGGGTTT--GTG
168486 TTTAGGGTTTGTG
1 TTTAGGGTTTGTG
168499 TTATAGGGTTT
1 TT-TAGGGTTT
168510 AAGTATCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.22
14 8 0.35
15 10 0.43
ACGTcount: A:0.13, C:0.00, G:0.36, T:0.51
Consensus pattern (13 bp):
TTTAGGGTTTGTG
Found at i:168494 original size:29 final size:29
Alignment explanation
Indices: 168427--168509 Score: 71
Period size: 29 Copynumber: 2.8 Consensus size: 29
168417 AGGATTTGTT
* *
168427 TTTAGGGTTTTAGTATTTATGGTTTTAGAG
1 TTTAGGG-TTTAGTATTTAGGGTTTGAGAG
* * *
168457 TTCATGGTTTAG-ACTTTAGGGTTTGAGTG
1 TTTAGGGTTTAGTA-TTTAGGGTTTGAGAG
*
168486 TTTAGGGTTT-GTGTTATAGGGTTT
1 TTTAGGGTTTAGTATT-TAGGGTTT
168510 AAGTATCTAG
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
28 4 0.10
29 33 0.79
30 5 0.12
ACGTcount: A:0.17, C:0.02, G:0.30, T:0.51
Consensus pattern (29 bp):
TTTAGGGTTTAGTATTTAGGGTTTGAGAG
Found at i:168598 original size:21 final size:20
Alignment explanation
Indices: 168567--168635 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 20
168557 AGTTTGTTGT
168567 TTTTGGTTTTAGGGTTTATGGG
1 TTTT-GTTTTAGGGTTTA-GGG
* *
168589 TTTTGTTTTAGTGTTTAGCG
1 TTTTGTTTTAGGGTTTAGGG
168609 TTTATGTTTTCAGGGTTTAGGG
1 TTT-TGTTTT-AGGGTTTAGGG
168631 TTTTG
1 TTTTG
168636 GTATTTATGG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 5 0.12
21 20 0.49
22 16 0.39
ACGTcount: A:0.10, C:0.03, G:0.30, T:0.57
Consensus pattern (20 bp):
TTTTGTTTTAGGGTTTAGGG
Found at i:173205 original size:12 final size:12
Alignment explanation
Indices: 173188--173242 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
173178 GGATTCAAAG
*
173188 ATGGGAGAGAGA
1 ATGGGAAAGAGA
*
173200 ATGGGAAAGGGA
1 ATGGGAAAGAGA
* *
173212 ATGGGAATGGGA
1 ATGGGAAAGAGA
* *
173224 ATGGGAATGGGA
1 ATGGGAAAGAGA
173236 ATGGGAA
1 ATGGGAA
173243 TTGAAAGAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.38, C:0.00, G:0.49, T:0.13
Consensus pattern (12 bp):
ATGGGAAAGAGA
Found at i:173217 original size:6 final size:6
Alignment explanation
Indices: 173198--173243 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
173188 ATGGGAGAGA
*
173198 GAATGG GAAAGG GAATGG GAATGG GAATGG GAATGG GAATGG GAAT
1 GAATGG GAATGG GAATGG GAATGG GAATGG GAATGG GAATGG GAAT
173244 TGAAAGAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.37, C:0.00, G:0.48, T:0.15
Consensus pattern (6 bp):
GAATGG
Done.