Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011923.1 Kokia drynarioides strain JFW-HI SEQ_126921, 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: 142604
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 48 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--29 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30 GCAACAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7215 original size:21 final size:23
Alignment explanation
Indices: 7191--7235 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
7181 GGTTATTATT
*
7191 ATTTTTAAA-TAT-ACAATATAA
1 ATTTATAAATTATGACAATATAA
7212 ATTTATAAATTTATGACAATATAA
1 ATTTATAAA-TTATGACAATATAA
7236 GATTCTGTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
23 3 0.15
24 9 0.45
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (23 bp):
ATTTATAAATTATGACAATATAA
Found at i:7320 original size:19 final size:19
Alignment explanation
Indices: 7298--7351 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
7288 TAAAATTTTA
*
7298 TAATATATAATATATAAAT
1 TAATAAATAATATATAAAT
* *
7317 TAATAAAAAATTTATAAAAT
1 TAATAAATAATATAT-AAAT
7337 T-ATAAAT-ATATATAA
1 TAATAAATAATATATAA
7352 TAACTAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 2 0.07
18 5 0.17
19 17 0.59
20 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAATAAATAATATATAAAT
Found at i:7346 original size:33 final size:32
Alignment explanation
Indices: 7279--7361 Score: 85
Period size: 35 Copynumber: 2.4 Consensus size: 32
7269 TATTATTTTG
* *
7279 AAATATATATAAAATTTTATAATATATAATATAT
1 AAATA-ATA-AAAAATTTATAAAATATAATATAT
7313 AAATTAATAAAAAATTTATAAAATTATAAATATAT
1 AAA-TAATAAAAAATTTATAAAA-TAT-AATATAT
7348 ATAATAACTAAAAA
1 A-AATAA-TAAAAA
7362 GCACATTTAC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
33 12 0.29
34 9 0.21
35 13 0.31
36 8 0.19
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (32 bp):
AAATAATAAAAAATTTATAAAATATAATATAT
Found at i:7749 original size:20 final size:19
Alignment explanation
Indices: 7721--7769 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
7711 TAAATTAATT
* *
7721 ATTTTAATACGGAAATATCA
1 ATTTAAATAC-GAAATATAA
7741 ATTTAAATAACGAAATATAA
1 ATTTAAAT-ACGAAATATAA
*
7761 ATTCAAATA
1 ATTTAAATA
7770 TTAATTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 22 0.88
21 2 0.08
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (19 bp):
ATTTAAATACGAAATATAA
Found at i:9982 original size:2 final size:2
Alignment explanation
Indices: 9975--10022 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
9965 ACAAATTTAA
9975 AT AT AT 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 AT AT AT
10017 AT AT AT
1 AT AT AT
10023 GTTGTTTGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17455 original size:209 final size:209
Alignment explanation
Indices: 17089--17896 Score: 1206
Period size: 209 Copynumber: 3.9 Consensus size: 209
17079 GAGACAGATG
* * * * *
17089 AGTGAATCAAAACAAGTGATGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGATCAAATCAAA
1 AGTGGATCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAAT
* * * *
17154 GAAGCCAAAACTTAAAGTGAGCAAATCTTCGAACCCCAACTCCCTGATGAGATACTGAGAAGCAG
66 GAA-ACAAGACTCAAAGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAG
* * * *
17219 GTCGAAGCAATAAAGTGGTTACCTTCCTGATGAGATACAAAGAAGCGAACCAGATCTGTCTTCTT
130 GTCGAAGCAATAAAGCGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCTATCTTCTT
17284 GATGAGACACAGAGA
195 GATGAGACACAGAGA
* * *
17299 AGTGGATCAAAACAAGTAATGCGGTCATCTTCCTGGTGAGATACTGAGAAGTAGACCAAATCGAT
1 AGTGGATCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAAT
* * *
17364 GAAACAAGGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAG
66 GAAACAAGACTCAAAGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGG
*
17429 TCGAAGCAATAAAGCGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGAT-TCATCTTCCT
131 TCGAAGCAATAAAGCGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCT-ATCTTCTT
*
17493 GATGAGACACAAAGA
195 GATGAGACACAGAGA
* *
17508 AGTGGATCAAAACAAGTGATGCGGTCATCTTTCTGATGAGATACTGAGAAGTAGACCAAATTAAT
1 AGTGGATCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAAT
** * *
17573 GAAATTAGGCTCAAAGTGAGCAAATCTTCGAACCCCAACTTCCTGATAAGATACTGAGAAGCAGG
66 GAAACAAGACTCAAAGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGG
* * * * *
17638 TCAAAACAATAAAGCGATTACCTTCCTAATGAGATACAGAGAAGTGAACCAGGTCTATCTTCCTT
131 TCGAAGCAATAAAGCGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCTATCTT-CTT
17703 -ATGAGACACAGAGA
195 GATGAGACACAGAGA
* *
17717 AGTGGATCAAAAAAAGTGATGCGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAAT
1 AGTGGATCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAAT
* * * * *
17782 GAAACTAGACTCAAAGTGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGGAGTAGG
66 GAAACAAGACTCAAAGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGG
* *
17847 TCGAAGCAATAAACCGGTTACCTTCCTGATGAGATACAGAGAAGTAAACC
131 TCGAAGCAATAAAGCGGTTACCTTCCTGATGAGATACAGAGAAGTGAACC
17897 GAGAGATGAA
Statistics
Matches: 540, Mismatches: 55, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
208 1 0.00
209 476 0.88
210 63 0.12
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (209 bp):
AGTGGATCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAAT
GAAACAAGACTCAAAGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGG
TCGAAGCAATAAAGCGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCTATCTTCTTG
ATGAGACACAGAGA
Found at i:18285 original size:17 final size:17
Alignment explanation
Indices: 18263--18345 Score: 80
Period size: 17 Copynumber: 4.9 Consensus size: 17
18253 CAAACCCAAA
*
18263 TTTTAAATTTTAATTTT
1 TTTTAAATTTAAATTTT
* *
18280 TTTTAAGTTTAAATTTA
1 TTTTAAATTTAAATTTT
*
18297 TTATAAATTTAAATTATT
1 TTTTAAATTTAAATT-TT
*
18315 TTTT-AGTTT-AATTTT
1 TTTTAAATTTAAATTTT
* *
18330 TTTAAAATTTGAATTT
1 TTTTAAATTTAAATTT
18346 AATTAAAAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
15 5 0.09
16 8 0.15
17 36 0.68
18 4 0.08
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.63
Consensus pattern (17 bp):
TTTTAAATTTAAATTTT
Found at i:18305 original size:34 final size:33
Alignment explanation
Indices: 18266--18345 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 33
18256 ACCCAAATTT
*
18266 TAAATTTTAATTTTTTTTAAGTTTAAATTTATTA
1 TAAATTTAAATTTTTTTT-AGTTTAAATTTATTA
* *
18300 TAAATTTAAATTATTTTTTAGTTTAATTTTTTTA
1 TAAATTTAAATT-TTTTTTAGTTTAAATTTATTA
*
18334 -AAATTTGAATTT
1 TAAATTTAAATTT
18346 AATTAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
32 1 0.02
33 10 0.24
34 24 0.59
35 6 0.15
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (33 bp):
TAAATTTAAATTTTTTTTAGTTTAAATTTATTA
Found at i:20262 original size:29 final size:29
Alignment explanation
Indices: 20061--20363 Score: 194
Period size: 30 Copynumber: 10.3 Consensus size: 29
20051 TAATAATCAA
* **
20061 ATTTTAACCCTCGAACTTTTTAAAAATTAC
1 ATTTTTACCCTCGAAC-TTCCAAAAATTAC
* *
20091 ATTTTGACTCC-CGAACCTTCCAAAAATTAT
1 ATTTTTAC-CCTCGAA-CTTCCAAAAATTAC
* **
20121 ATTTTTAACCTCGAACTTCTTTAAAATTAC
1 ATTTTTACCCTCGAACTTC-CAAAAATTAC
* **
20151 ATTTTAACCCTTAAACTTCCCAAAAATTAC
1 ATTTTTACCCTCGAACTT-CCAAAAATTAC
* * * *
20181 ATTTTGAGCCTCGAACTTTCTAAAA-TAGC
1 ATTTTTACCCTCGAACTTCCAAAAATTA-C
* * *
20210 ATTTTTTACCCT-GTACTTTTCAAAAATTTC
1 A-TTTTTACCCTCGAAC-TTCCAAAAATTAC
* *
20240 ATTTTTACCCCCGAACTTCC-AAAATCAC
1 ATTTTTACCCTCGAACTTCCAAAAATTAC
* *
20268 TTTTTTATCCTCGAACTTCCAAAAATTACC
1 ATTTTTACCCTCGAACTTCCAAAAATTA-C
* *
20298 A-TTTTACCCTTGAA-TGT-CAAAAATCAC
1 ATTTTTACCCTCGAACT-TCCAAAAATTAC
*
20325 ACTTTTGT-CCC-CAAACTTCCAAAAATTACC
1 A-TTTT-TACCCTCGAACTTCCAAAAATTA-C
20355 A-TTTTACCC
1 ATTTTTACCC
20364 CTATATATAT
Statistics
Matches: 211, Mismatches: 42, Indels: 42
0.72 0.14 0.14
Matches are distributed among these distances:
27 3 0.01
28 43 0.20
29 61 0.29
30 99 0.47
31 5 0.02
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (29 bp):
ATTTTTACCCTCGAACTTCCAAAAATTAC
Found at i:20264 original size:28 final size:28
Alignment explanation
Indices: 20239--20348 Score: 80
Period size: 28 Copynumber: 3.9 Consensus size: 28
20229 TCAAAAATTT
20239 CATTTTTACCCCCGAACTTCCAAAATCA
1 CATTTTTACCCCCGAACTTCCAAAATCA
* * * *
20267 CTTTTTTATCCTCGAACTTCCAAAAATTA
1 CATTTTTACCCCCGAACTTCC-AAAATCA
** *
20296 CCA-TTTTACCCTTGAA-TGTCAAAAATCA
1 -CATTTTTACCCCCGAACT-TCCAAAATCA
* ** *
20324 CACTTTTGTCCCCAAACTTCCAAAA
1 CATTTTTACCCCCGAACTTCCAAAA
20349 ATTACCATTT
Statistics
Matches: 62, Mismatches: 15, Indels: 10
0.71 0.17 0.11
Matches are distributed among these distances:
27 2 0.03
28 39 0.63
29 20 0.32
30 1 0.02
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.33
Consensus pattern (28 bp):
CATTTTTACCCCCGAACTTCCAAAATCA
Found at i:20303 original size:57 final size:57
Alignment explanation
Indices: 20164--20364 Score: 160
Period size: 57 Copynumber: 3.5 Consensus size: 57
20154 TTAACCCTTA
* * * *
20164 AACTTCCCAAAAATTA-CATTTTGAGCCTCGAACTTTCTAAAAT-AGCATTTTTTACCCT-G
1 AACTT-CCAAAAATTACCATTTT-ACCCCCGAAC-TTCAAAAATCA-C-TTTTTTATCCTCG
* * * *
20223 TACTTTTCAAAAATT-TCATTTTTACCCCCGAACTTCCAAAATCACTTTTTTATCCTCG
1 AAC-TTCCAAAAATTACCA-TTTTACCCCCGAACTTCAAAAATCACTTTTTTATCCTCG
** ** * * *
20281 AACTTCCAAAAATTACCATTTTACCCTTGAA-TGTCAAAAATCACACTTTTGTCCCCA
1 AACTTCCAAAAATTACCATTTTACCCCCGAACT-TCAAAAATCACTTTTTTATCCTCG
20338 AACTTCCAAAAATTACCATTTTACCCC
1 AACTTCCAAAAATTACCATTTTACCCC
20365 TATATATATA
Statistics
Matches: 117, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
56 1 0.01
57 75 0.64
58 14 0.12
59 21 0.18
60 6 0.05
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.35
Consensus pattern (57 bp):
AACTTCCAAAAATTACCATTTTACCCCCGAACTTCAAAAATCACTTTTTTATCCTCG
Found at i:21237 original size:15 final size:16
Alignment explanation
Indices: 21217--21253 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
21207 ACACACGGAC
21217 GATTTTCCTCAAATA-
1 GATTTTCCTCAAATAG
21232 GATTTTCCTCAAATAG
1 GATTTTCCTCAAATAG
21248 GATTTT
1 GATTTT
21254 TGAAAATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (16 bp):
GATTTTCCTCAAATAG
Found at i:23490 original size:23 final size:23
Alignment explanation
Indices: 23464--23537 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
23454 TGAAAAAAAC
23464 CCCTTTATATGCACTTCTAAGGA
1 CCCTTTATATGCACTTCTAAGGA
* ** **
23487 CCCTCTT-TCTG-ACTTGAAAAAAA
1 CCCT-TTATATGCACTT-CTAAGGA
23510 CCCCTTTATATGCACTTCTAAGGA
1 -CCCTTTATATGCACTTCTAAGGA
23534 CCCT
1 CCCT
23538 CTTTAGGGGG
Statistics
Matches: 36, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
22 4 0.11
23 16 0.44
24 12 0.33
25 4 0.11
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (23 bp):
CCCTTTATATGCACTTCTAAGGA
Found at i:23494 original size:25 final size:24
Alignment explanation
Indices: 23462--23542 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 24
23452 CTTGAAAAAA
23462 ACCCCTTTATATGCACTTCTAAGG
1 ACCCCTTTATATGCACTTCTAAGG
* ** **
23486 A-CCCTCTT-TCTG-ACTTGAAAAAA
1 ACCCCT-TTATATGCACTT-CTAAGG
23509 ACCCCTTTATATGCACTTCTAAGG
1 ACCCCTTTATATGCACTTCTAAGG
23533 ACCCTCTTTA
1 ACCC-CTTTA
23543 GGGGGTATGA
Statistics
Matches: 41, Mismatches: 10, Indels: 11
0.66 0.16 0.18
Matches are distributed among these distances:
22 4 0.10
23 12 0.29
24 16 0.39
25 9 0.22
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (24 bp):
ACCCCTTTATATGCACTTCTAAGG
Found at i:23516 original size:47 final size:47
Alignment explanation
Indices: 23447--23541 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
23437 TGACCTAAAA
23447 TCTGACTTGAAAAAAACCCCTTTATATGCACTTCTAAGGACCCTCTT
1 TCTGACTTGAAAAAAACCCCTTTATATGCACTTCTAAGGACCCTCTT
23494 TCTGACTTGAAAAAAACCCCTTTATATGCACTTCTAAGGACCCTCTT
1 TCTGACTTGAAAAAAACCCCTTTATATGCACTTCTAAGGACCCTCTT
23541 T
1 T
23542 AGGGGGTATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (47 bp):
TCTGACTTGAAAAAAACCCCTTTATATGCACTTCTAAGGACCCTCTT
Found at i:24911 original size:2 final size:2
Alignment explanation
Indices: 24904--24934 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
24894 CATACTCACA
24904 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24935 CAAGCATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26270 original size:31 final size:32
Alignment explanation
Indices: 26219--26285 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 32
26209 CTTCAATCTT
*
26219 TCTTTTTTTTATTCTTAG-AAAGCATGTTGAA
1 TCTTTTTTTTATTCTTAGAAAAGCATCTTGAA
26250 TCTTTTTTTT-TT-TTAAAGAAAAAGCATCTTGAA
1 TCTTTTTTTTATTCTT--AG-AAAAGCATCTTGAA
26283 TCT
1 TCT
26286 ATACTGATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
29 2 0.06
30 2 0.06
31 12 0.39
33 15 0.48
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.51
Consensus pattern (32 bp):
TCTTTTTTTTATTCTTAGAAAAGCATCTTGAA
Found at i:30298 original size:13 final size:13
Alignment explanation
Indices: 30282--30307 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30272 AAGTGCACAT
30282 AATGTATGCATTC
1 AATGTATGCATTC
30295 AATGTATGCATTC
1 AATGTATGCATTC
30308 TGTCTCATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
AATGTATGCATTC
Found at i:44533 original size:82 final size:82
Alignment explanation
Indices: 44447--44618 Score: 326
Period size: 82 Copynumber: 2.1 Consensus size: 82
44437 ACAGTACAAT
*
44447 GTCATTGCTCCAAGCCAGATATCAAGGCAACAACAGATAAAAGAAAAGGGATGAGGCTGCCTCAC
1 GTCATTGCTCCAAGCCAGATATCAAGGCAACAACAGAAAAAAGAAAAGGGATGAGGCTGCCTCAC
44512 AAATTACACTGCTCTAA
66 AAATTACACTGCTCTAA
44529 GTCATTGCTCCAAGCCAGATATCAAGGCAACAACAGAAAAAAGAAAAGGGATGAGGCTGCCTCAC
1 GTCATTGCTCCAAGCCAGATATCAAGGCAACAACAGAAAAAAGAAAAGGGATGAGGCTGCCTCAC
44594 AAATTACACTGCTCTAA
66 AAATTACACTGCTCTAA
44611 GTTCATTG
1 G-TCATTG
44619 GTCACATTTA
Statistics
Matches: 88, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
82 82 0.93
83 6 0.07
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (82 bp):
GTCATTGCTCCAAGCCAGATATCAAGGCAACAACAGAAAAAAGAAAAGGGATGAGGCTGCCTCAC
AAATTACACTGCTCTAA
Found at i:54827 original size:47 final size:47
Alignment explanation
Indices: 54760--54867 Score: 193
Period size: 47 Copynumber: 2.3 Consensus size: 47
54750 CGGAAAAAAA
*
54760 AGGGGTTT-T-AGATAAAAGAAAGGATCGATAGATAAAAGGAGAGTT
1 AGGGGTTTGTAAGAGAAAAGAAAGGATCGATAGATAAAAGGAGAGTT
54805 AGGGGTTTGTAAGAGAAAAGAAAGGATCGATAGATAAAAGGAGAGTT
1 AGGGGTTTGTAAGAGAAAAGAAAGGATCGATAGATAAAAGGAGAGTT
54852 AGGGGTTTGTAAGAGA
1 AGGGGTTTGTAAGAGA
54868 GAGAAGAGAG
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
45 8 0.13
46 1 0.02
47 51 0.85
ACGTcount: A:0.43, C:0.02, G:0.34, T:0.21
Consensus pattern (47 bp):
AGGGGTTTGTAAGAGAAAAGAAAGGATCGATAGATAAAAGGAGAGTT
Found at i:58439 original size:21 final size:21
Alignment explanation
Indices: 58415--58463 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
58405 TATATGAATA
* *
58415 ATAAAAATTAAAATAAATATC
1 ATAAAAAATAAAACAAATATC
*
58436 ATAAAAAATAAAACGAATATC
1 ATAAAAAATAAAACAAATATC
*
58457 ACAAAAA
1 ATAAAAA
58464 CAATTGGGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.20
Consensus pattern (21 bp):
ATAAAAAATAAAACAAATATC
Found at i:58765 original size:18 final size:18
Alignment explanation
Indices: 58742--58794 Score: 52
Period size: 22 Copynumber: 2.7 Consensus size: 18
58732 TTGAAAGCTC
58742 ACCGAATAAATCAATTAA
1 ACCGAATAAATCAATTAA
*
58760 ACCGAACATGAAAATGAATTAA
1 ACCG-A-AT--AAATCAATTAA
*
58782 ATCGAATAAATCA
1 ACCGAATAAATCA
58795 TAAAATTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
18 9 0.32
19 1 0.04
20 4 0.14
21 1 0.04
22 13 0.46
ACGTcount: A:0.55, C:0.15, G:0.09, T:0.21
Consensus pattern (18 bp):
ACCGAATAAATCAATTAA
Found at i:60784 original size:19 final size:19
Alignment explanation
Indices: 60762--60809 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
60752 AAAAATATTT
60762 TAAAAAATAAAAAAAGTT-A
1 TAAAAAATAAAAAAA-TTCA
** *
60781 TAAAAGTTATAAAAATTCA
1 TAAAAAATAAAAAAATTCA
60800 TAAAAAATAA
1 TAAAAAATAA
60810 CATGAAATAC
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (19 bp):
TAAAAAATAAAAAAATTCA
Found at i:62493 original size:23 final size:21
Alignment explanation
Indices: 62467--62508 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
62457 TTTGATAAAG
62467 TTAAATTAAATTAATCATATTAA
1 TTAAATTAAA-TAAT-ATATTAA
62490 TTAAATTAAATAATATATT
1 TTAAATTAAATAATATATT
62509 TTTAGAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 4 0.21
23 10 0.53
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAAATTAAATAATATATTAA
Found at i:62950 original size:21 final size:20
Alignment explanation
Indices: 62909--62951 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
62899 TTTTATTAAT
*
62909 TTAATATTAAAATGATTATC
1 TTAATATTAAAATAATTATC
*
62929 TTAATATTAAATTAATTTATC
1 TTAATATTAAAATAA-TTATC
62950 TT
1 TT
62952 GTAGATAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (20 bp):
TTAATATTAAAATAATTATC
Found at i:62986 original size:53 final size:57
Alignment explanation
Indices: 62929--63036 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 57
62919 AATGATTATC
* *
62929 TTAATATTAA-ATTAAT-T-TATCT-TGTAGATAAGTATTCTATTAATTTAATAGAT
1 TTAATATTAATATTAATCTATATCTATCTAGATAAGTATTATATTAATTTAATAGAT
* *
62982 TTAATATTAATTTTAATCTAATATTTATCTAGATAAGTATTATATTAATTTAATA
1 TTAATATTAATATTAATCT-ATATCTATCTAGATAAGTATTATATTAATTTAATA
63037 TTAAAGTGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
53 10 0.22
54 5 0.11
55 1 0.02
57 4 0.09
58 26 0.57
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (57 bp):
TTAATATTAATATTAATCTATATCTATCTAGATAAGTATTATATTAATTTAATAGAT
Found at i:63975 original size:14 final size:15
Alignment explanation
Indices: 63949--63988 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
63939 ATGGAATGAG
63949 AATAAATTTTAATTA
1 AATAAATTTTAATTA
63964 AATAAA-TTTAATTA
1 AATAAATTTTAATTA
*
63978 ATTAAAATTTT
1 AAT-AAATTTT
63989 TAAACCCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 10 0.45
15 9 0.41
16 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAAATTTTAATTA
Found at i:64026 original size:3 final size:3
Alignment explanation
Indices: 64018--64052 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
64008 CACACACCTC
* *
64018 TCT TCT TCT TCT TCT TCT TCA TCT TCA TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
64053 CCTTTTGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.06, C:0.34, G:0.00, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:64133 original size:8 final size:8
Alignment explanation
Indices: 64120--64146 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
64110 TCCATTAACC
64120 CAAAGATT
1 CAAAGATT
64128 CAAAGATT
1 CAAAGATT
64136 CAAAGATT
1 CAAAGATT
64144 CAA
1 CAA
64147 TATCTTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (8 bp):
CAAAGATT
Found at i:70600 original size:17 final size:19
Alignment explanation
Indices: 70578--70612 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
70568 ATAAATATTC
70578 AGTTCATT-TT-TAATTTA
1 AGTTCATTATTATAATTTA
70595 AGTTCATTATTATAATTT
1 AGTTCATTATTATAATTT
70613 GTACTGAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (19 bp):
AGTTCATTATTATAATTTA
Found at i:78402 original size:18 final size:18
Alignment explanation
Indices: 78379--78420 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
78369 GAAGTATTTA
78379 TTTTAATGT-TTTTAGTAT
1 TTTTAATGTATTTTA-TAT
78397 TTTTAATGTATTTTATAT
1 TTTTAATGTATTTTATAT
*
78415 ATTTAA
1 TTTTAA
78421 AAATTATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (18 bp):
TTTTAATGTATTTTATAT
Found at i:78469 original size:24 final size:24
Alignment explanation
Indices: 78419--78470 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
78409 TTATATATTT
* * *
78419 AAAAATTATATAAAAATATTTACA
1 AAAAAATAAATAAAAATATATACA
*
78443 AAAAAATAAATAAAAATA-ATATA
1 AAAAAATAAATAAAAATATATACA
78466 AAAAA
1 AAAAA
78471 TTATTACGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAAAATAAATAAAAATATATACA
Found at i:83545 original size:22 final size:22
Alignment explanation
Indices: 83503--83545 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
83493 GAACACCATT
* *
83503 TATTATATATTTTTCATTTTAA
1 TATTATATATATTACATTTTAA
83525 TATTATA-ATATTACATATTTA
1 TATTATATATATTACAT-TTTA
83546 TAGTTTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTATATATATTACATTTTAA
Found at i:93180 original size:13 final size:13
Alignment explanation
Indices: 93148--93172 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
93138 TTTAAAAATT
93148 ATAAAAAATTTAA
1 ATAAAAAATTTAA
93161 ATAAAAAATTTA
1 ATAAAAAATTTA
93173 TCAAAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAAAAAATTTAA
Found at i:93239 original size:15 final size:16
Alignment explanation
Indices: 93209--93241 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
93199 ATTTTTCCCA
93209 AAAATAAAAATAAAAT
1 AAAATAAAAATAAAAT
*
93225 AAAAT-AAACTAAAAT
1 AAAATAAAAATAAAAT
93240 AA
1 AA
93242 TTTCTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAATAAAAATAAAAT
Found at i:104267 original size:31 final size:31
Alignment explanation
Indices: 104221--104291 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
104211 AAGTTTAAAA
104221 AATTCAATAACTTAAATGAAAACTTTTGAAT
1 AATTCAATAACTTAAATGAAAACTTTTGAAT
* *
104252 AGATT-AATAATTTAAATGAAAATTTTTGAAT
1 A-ATTCAATAACTTAAATGAAAACTTTTGAAT
104283 AATTCAATA
1 AATTCAATA
104292 TGAACAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
30 3 0.08
31 30 0.83
32 3 0.08
ACGTcount: A:0.49, C:0.06, G:0.07, T:0.38
Consensus pattern (31 bp):
AATTCAATAACTTAAATGAAAACTTTTGAAT
Found at i:107895 original size:2 final size:2
Alignment explanation
Indices: 107888--107913 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
107878 ACAAATACAC
107888 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
107914 ATGCCTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:131497 original size:20 final size:20
Alignment explanation
Indices: 131469--131508 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
131459 TTTATATACA
131469 AACAAAAGATAAAACTCTAT
1 AACAAAAGATAAAACTCTAT
*
131489 AACAGAAGATAAAACTCTAT
1 AACAAAAGATAAAACTCTAT
131509 GTTATATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.07, T:0.20
Consensus pattern (20 bp):
AACAAAAGATAAAACTCTAT
Found at i:134473 original size:41 final size:41
Alignment explanation
Indices: 134416--134511 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
134406 GAATTTTATT
* *
134416 TTAACAAT-AATTCTAGTCACCCGATTCTAACAATCTTCACC
1 TTAAC-ATGAATTCTAGTAACCCAATTCTAACAATCTTCACC
* *
134457 TTAACATGAATTCTAGTAATCTAATTCTAACAATCTTCACC
1 TTAACATGAATTCTAGTAACCCAATTCTAACAATCTTCACC
* *
134498 TTGACAAGAATTCT
1 TTAACATGAATTCT
134512 CTACGAACAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
40 2 0.04
41 46 0.96
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.34
Consensus pattern (41 bp):
TTAACATGAATTCTAGTAACCCAATTCTAACAATCTTCACC
Found at i:135351 original size:47 final size:47
Alignment explanation
Indices: 135282--135376 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
135272 CAAAAACAAC
135282 ATCTTTGCTAATCACAACTTTTCTATTTTCAGGACACCATAACTTAT
1 ATCTTTGCTAATCACAACTTTTCTATTTTCAGGACACCATAACTTAT
135329 ATCTTTGCTAATCACAACTTTTCTATTTTCAGGACACCATAACTTAT
1 ATCTTTGCTAATCACAACTTTTCTATTTTCAGGACACCATAACTTAT
135376 A
1 A
135377 CCCTTTTACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (47 bp):
ATCTTTGCTAATCACAACTTTTCTATTTTCAGGACACCATAACTTAT
Found at i:137913 original size:22 final size:21
Alignment explanation
Indices: 137888--137929 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
137878 TGAAAAATTA
*
137888 AAAAAATTAAGTATAAAAAATG
1 AAAAAA-TAAATATAAAAAATG
137910 AAAAAATAAATATAAAAAAT
1 AAAAAATAAATATAAAAAAT
137930 TAAGTGTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (21 bp):
AAAAAATAAATATAAAAAATG
Found at i:139125 original size:27 final size:27
Alignment explanation
Indices: 139076--139127 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
139066 TTATTCGGTA
* *
139076 GTGCCTACCTAACAGGCGACACCAATG
1 GTGCCAACCTAACACGCGACACCAATG
* *
139103 GTGCCAACCTGACACGCGGCACCAA
1 GTGCCAACCTAACACGCGACACCAA
139128 CTCCCAATGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.29, C:0.37, G:0.23, T:0.12
Consensus pattern (27 bp):
GTGCCAACCTAACACGCGACACCAATG
Found at i:139439 original size:17 final size:17
Alignment explanation
Indices: 139417--139450 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
139407 AAAAAAATCT
*
139417 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
139434 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
139451 TCATTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:142076 original size:72 final size:71
Alignment explanation
Indices: 141976--142118 Score: 268
Period size: 72 Copynumber: 2.0 Consensus size: 71
141966 GTTTGAGCTT
*
141976 GAGCTGCAGCACTATTCGGAGCTTGCGCTCGAGTCAGAGCGTAACATCGAGCCGACGCCTGAGTC
1 GAGCCGCAGCACTATTCGGAGCTTGCGCTCGAGTCAGAGCGTAACATCGAGCCGACGCCTGAGTC
142041 GTATCA
66 GTATCA
142047 NGAGCCGCAGCACTATTCGGAGCTTGCGCTCGAGTCAGAGCGTAACATCGAGCCGACGCCTGAGT
1 -GAGCCGCAGCACTATTCGGAGCTTGCGCTCGAGTCAGAGCGTAACATCGAGCCGACGCCTGAGT
142112 CGTATCA
65 CGTATCA
142119 TCCATGGTGG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.22, C:0.29, G:0.29, T:0.19
Consensus pattern (71 bp):
GAGCCGCAGCACTATTCGGAGCTTGCGCTCGAGTCAGAGCGTAACATCGAGCCGACGCCTGAGTC
GTATCA
Done.