Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014159.1 Kokia drynarioides strain JFW-HI SEQ_129192, 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: 462093
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 17 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:369392 original size:43 final size:43
Alignment explanation
Indices: 369330--369426 Score: 149
Period size: 43 Copynumber: 2.3 Consensus size: 43
369320 TGCTGCACAA
* *
369330 TTAATAACATGTCACGATATTAACAAGAGTCAAGTAATATAAT
1 TTAATAACATGCCACGATATTAACAAGAGTAAAGTAATATAAT
* * *
369373 TTAATAACATGCCATGATATTAACACGGGTAAAGTAATATAAT
1 TTAATAACATGCCACGATATTAACAAGAGTAAAGTAATATAAT
369416 TTAATAACATG
1 TTAATAACATG
369427 TCAATGAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.31
Consensus pattern (43 bp):
TTAATAACATGCCACGATATTAACAAGAGTAAAGTAATATAAT
Found at i:370785 original size:28 final size:28
Alignment explanation
Indices: 370751--370808 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
370741 ATTAATTAAT
*
370751 ATTACTTACTTACTACTAACAAAATAAA
1 ATTACTTACTAACTACTAACAAAATAAA
370779 ATTACTTACTAACTACTAACAAAATAAA
1 ATTACTTACTAACTACTAACAAAATAAA
370807 AT
1 AT
370809 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (28 bp):
ATTACTTACTAACTACTAACAAAATAAA
Found at i:370897 original size:12 final size:11
Alignment explanation
Indices: 370875--370908 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
370865 TACTAAATAA
370875 AAAAATTAAAT
1 AAAAATTAAAT
*
370886 AATAAATCAAAT
1 AA-AAATTAAAT
370898 AAAAATTAAAT
1 AAAAATTAAAT
370909 TAATCAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAAATTAAAT
Found at i:370905 original size:23 final size:24
Alignment explanation
Indices: 370875--370937 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 24
370865 TACTAAATAA
370875 AAAAATTAAATAATAAATC-AAAT
1 AAAAATTAAATAATAAATCAAAAT
370898 AAAAATTAAAT--T-AATCAAAAT
1 AAAAATTAAATAATAAATCAAAAT
370919 AAATAACTTAAAATAATAA
1 AAA-AA-TT-AAATAATAA
370938 TTACTAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
20 4 0.12
21 8 0.24
22 2 0.06
23 13 0.39
24 4 0.12
26 1 0.03
27 1 0.03
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (24 bp):
AAAAATTAAATAATAAATCAAAAT
Found at i:371211 original size:4 final size:4
Alignment explanation
Indices: 371202--371234 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
371192 CTTCTCCTCC
*
371202 TTCT TTCT TTTT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT T
371235 CTTCTTCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTCT
Found at i:373116 original size:2 final size:2
Alignment explanation
Indices: 373109--373133 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
373099 ACAGTTCACA
373109 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
373134 AGCAGTTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:373934 original size:15 final size:15
Alignment explanation
Indices: 373916--373950 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
373906 TCTCAACAAA
*
373916 TTCTTTCTTAGCATC
1 TTCTTTCTCAGCATC
373931 TTCTTTCTCAGCATC
1 TTCTTTCTCAGCATC
373946 TTCTT
1 TTCTT
373951 CCTTGTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.11, C:0.29, G:0.06, T:0.54
Consensus pattern (15 bp):
TTCTTTCTCAGCATC
Found at i:382339 original size:48 final size:46
Alignment explanation
Indices: 382286--382380 Score: 138
Period size: 46 Copynumber: 2.0 Consensus size: 46
382276 TCTATTTTAT
382286 TAAATGATACAATATTAA-AAGAATGTGTACAAAAAGATCCAAAAGAAC
1 TAAATGATACAA-A--AATAAGAATGTGTACAAAAAGATCCAAAAGAAC
* *
382334 TAAATGATACAAAAATTAGAATGTGTATAAAAAGATCCAAAAGAAC
1 TAAATGATACAAAAATAAGAATGTGTACAAAAAGATCCAAAAGAAC
382380 T
1 T
382381 TCTATTTTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
45 2 0.05
46 29 0.66
47 1 0.02
48 12 0.27
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (46 bp):
TAAATGATACAAAAATAAGAATGTGTACAAAAAGATCCAAAAGAAC
Found at i:382403 original size:105 final size:105
Alignment explanation
Indices: 382221--382438 Score: 391
Period size: 105 Copynumber: 2.1 Consensus size: 105
382211 ATTAGGATTT
* *
382221 AAAAGAACTAAATGATACAAAAATCAGAATGTGTATAAAAAGGTCTAAAAGAACTTCTATTTTAT
1 AAAAGAACTAAATGATACAAAAATCAGAATGTGTATAAAAAGATCCAAAAGAACTTCTATTTTAT
*
382286 TAAATGATACAATATTAAAAGAATGTGTACAAAAAGATCC
66 TAAATGATACAATATAAAAAGAATGTGTACAAAAAGATCC
*
382326 AAAAGAACTAAATGATACAAAAATTAGAATGTGTATAAAAAGATCCAAAAGAACTTCTATTTTAT
1 AAAAGAACTAAATGATACAAAAATCAGAATGTGTATAAAAAGATCCAAAAGAACTTCTATTTTAT
*
382391 TAAATGATACAATATAAAAAGAATGTGTACAAAAATATCC
66 TAAATGATACAATATAAAAAGAATGTGTACAAAAAGATCC
382431 AAAAGAAC
1 AAAAGAAC
382439 ATCAATGAAT
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 108 1.00
ACGTcount: A:0.53, C:0.10, G:0.11, T:0.26
Consensus pattern (105 bp):
AAAAGAACTAAATGATACAAAAATCAGAATGTGTATAAAAAGATCCAAAAGAACTTCTATTTTAT
TAAATGATACAATATAAAAAGAATGTGTACAAAAAGATCC
Found at i:392118 original size:17 final size:17
Alignment explanation
Indices: 392098--392130 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
392088 TTTAAGGACT
392098 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
392115 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
392131 TAAGTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:392409 original size:50 final size:50
Alignment explanation
Indices: 392325--392477 Score: 143
Period size: 50 Copynumber: 3.1 Consensus size: 50
392315 TGACATCCAT
* * * *
392325 TAACTCTCATGATTAGTTAAGTTTGCAGCATAAATAATGACATGCATTAAG
1 TAACTCACATG-TTAGTTAAATATGCATCATAAATAATGACATGCATTAAG
* ** *
392376 TAACTTACATGTTAGTTAAATATGCATCATAAATCCT-ATCATGCATTATG
1 TAACTCACATGTTAGTTAAATATGCATCATAAATAATGA-CATGCATTAAG
* * *
392426 TAACTCCCATGTTAGTT-AA-ATGCATCATTAAATCAA-GTCATGCATTTAG
1 TAACTCACATGTTAGTTAAATATGCATCA-TAAAT-AATGACATGCATTAAG
392475 TAA
1 TAA
392478 TCCCTTAGTT
Statistics
Matches: 83, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
48 8 0.10
49 20 0.24
50 46 0.55
51 9 0.11
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (50 bp):
TAACTCACATGTTAGTTAAATATGCATCATAAATAATGACATGCATTAAG
Found at i:392582 original size:37 final size:37
Alignment explanation
Indices: 392532--392605 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
392522 CATCTTGTAT
392532 GTTTAAACATGAGTTAGTGTGTTTATTTTTATTATAA
1 GTTTAAACATGAGTTAGTGTGTTTATTTTTATTATAA
392569 GTTTAAACATGAGTTAGTGTGTTTATTTTTATTATAA
1 GTTTAAACATGAGTTAGTGTGTTTATTTTTATTATAA
392606 ATAGGGTGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.51
Consensus pattern (37 bp):
GTTTAAACATGAGTTAGTGTGTTTATTTTTATTATAA
Found at i:400143 original size:19 final size:19
Alignment explanation
Indices: 400083--400136 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
400073 CGGAAGGAAT
400083 AGCATTACTGGCTCGTTTG
1 AGCATTACTGGCTCGTTTG
*
400102 AGCATTACTGACTCGTTTG
1 AGCATTACTGGCTCGTTTG
*
400121 AGCAATACTGGCTCGT
1 AGCATTACTGGCTCGT
400137 AAGAGCAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.33
Consensus pattern (19 bp):
AGCATTACTGGCTCGTTTG
Found at i:416464 original size:17 final size:17
Alignment explanation
Indices: 416438--416480 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
416428 AGTGAAAGAT
*
416438 ATGGGCATGAGTCCAGG
1 ATGGGTATGAGTCCAGG
*
416455 ATGGGTATGAGTCCGGG
1 ATGGGTATGAGTCCAGG
*
416472 ACGGGTATG
1 ATGGGTATG
416481 TAAATCTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.21, C:0.14, G:0.44, T:0.21
Consensus pattern (17 bp):
ATGGGTATGAGTCCAGG
Found at i:432973 original size:6 final size:6
Alignment explanation
Indices: 432962--432993 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
432952 TAGCGAACAC
432962 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT
432994 TTGTATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATAAAT
Found at i:438684 original size:108 final size:108
Alignment explanation
Indices: 438539--438744 Score: 322
Period size: 108 Copynumber: 1.9 Consensus size: 108
438529 ATAACAAAAT
* * **
438539 TGATGCAAAACTTAATTCAATGTAATTAAGGAGGATGGTTCAAACTAACACGAATGAAAGATTCA
1 TGATGCAAAACTTAATTAAATATAATTAAGGAGGATGGTTCAAACTAACACGAACCAAAGATTCA
438604 AAAGTTATTTGCCCAGCTTGCTCTAGCATTTGGAAAACAACAC
66 AAAGTTATTTGCCCAGCTTGCTCTAGCATTTGGAAAACAACAC
* * * * *
438647 TGATGCAAAACTTAATTAAATATAATTATGGATGATGGTTCAAACTAACATGAACCAATGCTTCA
1 TGATGCAAAACTTAATTAAATATAATTAAGGAGGATGGTTCAAACTAACACGAACCAAAGATTCA
*
438712 AAAGTTATTTGCTCAGCTTGCTCTAGCATTTGG
66 AAAGTTATTTGCCCAGCTTGCTCTAGCATTTGG
438745 CAATTTCTAT
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
108 88 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (108 bp):
TGATGCAAAACTTAATTAAATATAATTAAGGAGGATGGTTCAAACTAACACGAACCAAAGATTCA
AAAGTTATTTGCCCAGCTTGCTCTAGCATTTGGAAAACAACAC
Found at i:440287 original size:9 final size:9
Alignment explanation
Indices: 440269--440300 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
440259 TTATTTAGCT
*
440269 CAAAAAATA
1 CAAAATATA
440278 CAAAATATA
1 CAAAATATA
440287 CAAAATATA
1 CAAAATATA
440296 CAAAA
1 CAAAA
440301 AAAAATTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.72, C:0.12, G:0.00, T:0.16
Consensus pattern (9 bp):
CAAAATATA
Found at i:441575 original size:11 final size:11
Alignment explanation
Indices: 441561--441643 Score: 60
Period size: 11 Copynumber: 7.5 Consensus size: 11
441551 CACCACTTCT
441561 CCACCATAGCA
1 CCACCATAGCA
* *
441572 CCACCGTACCA
1 CCACCATAGCA
*
441583 CCACCCA-AGTA
1 CCA-CCATAGCA
* *
441594 TCACCATACCA
1 CCACCATAGCA
*
441605 CCAGCATAGCA
1 CCACCATAGCA
* *
441616 TCACCATATCA
1 CCACCATAGCA
* *
441627 CCACCCTTGCA
1 CCACCATAGCA
441638 CCACCA
1 CCACCA
441644 CAAAACTATT
Statistics
Matches: 51, Mismatches: 19, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
10 3 0.06
11 46 0.90
12 2 0.04
ACGTcount: A:0.33, C:0.47, G:0.07, T:0.13
Consensus pattern (11 bp):
CCACCATAGCA
Found at i:441586 original size:22 final size:22
Alignment explanation
Indices: 441561--441643 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 22
441551 CACCACTTCT
*
441561 CCACCATAGCACCACCGTACCA
1 CCACCATAGCACCACCATACCA
* *
441583 CCACCCA-AGTATCACCATACCA
1 CCA-CCATAGCACCACCATACCA
* * *
441605 CCAGCATAGCATCACCATATCA
1 CCACCATAGCACCACCATACCA
* *
441627 CCACCCTTGCACCACCA
1 CCACCATAGCACCACCA
441644 CAAAACTATT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
21 2 0.04
22 44 0.90
23 3 0.06
ACGTcount: A:0.33, C:0.47, G:0.07, T:0.13
Consensus pattern (22 bp):
CCACCATAGCACCACCATACCA
Found at i:442824 original size:24 final size:24
Alignment explanation
Indices: 442795--442844 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
442785 TCGCATTGAC
442795 ATAATCATGCATAAAAGTCTACAT
1 ATAATCATGCATAAAAGTCTACAT
442819 ATAATCATGCATAAAAGTCTACAT
1 ATAATCATGCATAAAAGTCTACAT
442843 AT
1 AT
442845 TTGATTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (24 bp):
ATAATCATGCATAAAAGTCTACAT
Found at i:443592 original size:14 final size:14
Alignment explanation
Indices: 443575--443604 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
443565 AAGATTGGTT
443575 AGAAAAGGATGTGA
1 AGAAAAGGATGTGA
443589 AGAAAAGGATGTGA
1 AGAAAAGGATGTGA
443603 AG
1 AG
443605 CATATCTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.37, T:0.13
Consensus pattern (14 bp):
AGAAAAGGATGTGA
Done.