Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012751.1 Kokia drynarioides strain JFW-HI SEQ_127762, 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: 8393
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:4490 original size:26 final size:27
Alignment explanation
Indices: 4435--4490 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
4425 TAATTTGTAA
* *
4435 TTTTTAAACCTTTTTAAAAAAGAAATT
1 TTTTTAAACCTTTTTAAAAAACAAACT
*
4462 TTTTTAAACCTTTTT-AAAATCAAACT
1 TTTTTAAACCTTTTTAAAAAACAAACT
4488 TTT
1 TTT
4491 GGGTTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (27 bp):
TTTTTAAACCTTTTTAAAAAACAAACT
Found at i:5327 original size:36 final size:36
Alignment explanation
Indices: 5239--5327 Score: 96
Period size: 36 Copynumber: 2.5 Consensus size: 36
5229 TTATTTTTTG
*
5239 TTATTT-ATATATATT-TTTATTTGGTATTTAATTT
1 TTATTTAATTTATATTCTTTATTTGGTATTTAATTT
* * *
5273 TTATTTAATTTTTGTTCTTTATTTGTTATTT-ATTT
1 TTATTTAATTTATATTCTTTATTTGGTATTTAATTT
5308 TTATTGCT-ATTTATATTCTT
1 TTATT--TAATTTATATTCTT
5328 GCCTTCATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
34 6 0.13
35 15 0.33
36 23 0.51
37 1 0.02
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.70
Consensus pattern (36 bp):
TTATTTAATTTATATTCTTTATTTGGTATTTAATTT
Found at i:6292 original size:102 final size:101
Alignment explanation
Indices: 6110--6532 Score: 408
Period size: 101 Copynumber: 4.2 Consensus size: 101
6100 TAAAGATTTA
* *** * * *
6110 CTACTG-TAGTTTTAATCTGATTTCTGCAACTTTAGAGATATAGGATTTGG-GTTTGTAACTTC-
1 CTACTGTTAGCTTTAATCTGCCCTCTACAACTTAAGGGATATAGGATTTGGTG-TTGTAACTTCA
* * * *
6172 CTCAATTCCACTGCAACTTCAAGGAGATTGAGACCCG
65 CTCCATTCCACTACAACTTCAAGGAGATTGAGATCTG
* * * * * * **
6209 CTACTGTGAGCTTTAATCTGATCCACTACAACCTCAGGGATATAGGATTTGATGTTGTGGCTTCA
1 CTACTGTTAGCTTTAATCTG-CCCTCTACAACTTAAGGGATATAGGATTTGGTGTTGTAACTTCA
** * *
6274 CTCCATTCCACTGTAACTTTAGGGAGATTGAGATCTG
65 CTCCATTCCACTACAACTTCAAGGAGATTGAGATCTG
* * * *
6311 CTACTATTA-CTTCTAAACTGCCCTCTACAACTTTAGGGGTATAGGATTTGGTGTTGTAACTTCA
1 CTACTGTTAGCTT-TAATCTGCCCTCTACAACTTAAGGGATATAGGATTTGGTGTTGTAACTTCA
* * *
6375 CTCCATTCTACTACAACTTCAGGGAGATTGAGATCTA
65 CTCCATTCCACTACAACTTCAAGGAGATTGAGATCTG
* * *
6412 CTACTGTTAGTTTTAATCCGCCCCTCTACAACTTTAAGGG-TATAGAATTTGGTGTTGTAACTTC
1 CTACTGTTAGCTTTAATCTG-CCCTCTACAAC-TTAAGGGATATAGGATTTGGTGTTGTAACTTC
* *
6476 ACTCCATTCCACTACAACTTC-AGAGAGATTAAGATATG
64 ACTCCATTCCACTACAACTTCAAG-GAGATTGAGATCTG
* *
6514 TTACTTGTTAGTTTTAATC
1 CTAC-TGTTAGCTTTAATC
6533 CACCCCTTTG
Statistics
Matches: 267, Mismatches: 47, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
99 6 0.02
100 11 0.04
101 115 0.43
102 115 0.43
103 20 0.07
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.35
Consensus pattern (101 bp):
CTACTGTTAGCTTTAATCTGCCCTCTACAACTTAAGGGATATAGGATTTGGTGTTGTAACTTCAC
TCCATTCCACTACAACTTCAAGGAGATTGAGATCTG
Found at i:6376 original size:101 final size:101
Alignment explanation
Indices: 6022--6572 Score: 427
Period size: 102 Copynumber: 5.4 Consensus size: 101
6012 TCGTAAATTC
* ** * * * * * *
6022 AATCTGACCCACTGTAACTTTAGGGGTATAGGATTTGGTGTGGTAGCTTCATCTTGC-TT-TATT
1 AATCTGACCCTCTACAACTTTAGGGATATAGGATTTGGTGTTGTAACTTCA-C-TCCATTCCACT
* * ** * * *
6085 GCAACTTAAGAGAGATAAAGATTTACTACTG-TAGTTTT
64 GCAACTTCAGGGAGATTGAGATCTGCTACTGTTA-CTTT
** * * *
6123 AATCTGA-TTTCTGCAACTTTAGAGATATAGGATTTGG-GTTTGTAACTTC-CTCAATTCCACTG
1 AATCTGACCCTCTACAACTTTAGGGATATAGGATTTGGTG-TTGTAACTTCACTCCATTCCACTG
* * * *
6185 CAACTTCAAGGAGATTGAGACCCGCTACTGTGAGCTTT
65 CAACTTCAGGGAGATTGAGATCTGCTACTGTTA-CTTT
* * * * * ** *
6223 AATCTGATCCACTACAACCTCAGGGATATAGGATTTGATGTTGTGGCTTCACTCCATTCCACTGT
1 AATCTGACCCTCTACAACTTTAGGGATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTGC
* *
6288 AACTTTAGGGAGATTGAGATCTGCTACTATTACTTCT
66 AACTTCAGGGAGATTGAGATCTGCTACTGTTACTT-T
* * * *
6325 AAACTG-CCCTCTACAACTTTAGGGGTATAGGATTTGGTGTTGTAACTTCACTCCATTCTACTAC
1 AATCTGACCCTCTACAACTTTAGGGATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTGC
* *
6389 AACTTCAGGGAGATTGAGATCTACTACTGTTAGTTTT
66 AACTTCAGGGAGATTGAGATCTGCTACTGTTA-CTTT
* * * *
6426 AATCCGCCCCTCTACAACTTTAAGGG-TATAGAATTTGGTGTTGTAACTTCACTCCATTCCACTA
1 AATCTGACCCTCTACAACTTT-AGGGATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTG
* * * * *
6490 CAACTTCAGAGAGATTAAGATATGTTACTTGTTAGTTTT
65 CAACTTCAGGGAGATTGAGATCTGCTAC-TGTTA-CTTT
* * ** * * *
6529 AATC-CACCCCTTTGTAACTTTAGGGGTATAAGATTTGATGTTGT
1 AATCTGA-CCCTCTACAACTTTAGGGATATAGGATTTGGTGTTGT
6573 GGCTTTAATT
Statistics
Matches: 362, Mismatches: 74, Indels: 26
0.78 0.16 0.06
Matches are distributed among these distances:
97 1 0.00
98 3 0.01
99 25 0.07
100 44 0.12
101 121 0.33
102 124 0.34
103 44 0.12
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (101 bp):
AATCTGACCCTCTACAACTTTAGGGATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTGC
AACTTCAGGGAGATTGAGATCTGCTACTGTTACTTT
Found at i:6389 original size:50 final size:50
Alignment explanation
Indices: 6335--6495 Score: 119
Period size: 50 Copynumber: 3.2 Consensus size: 50
6325 AAACTGCCCT
6335 CTACAACTTTAGGGGTATAGGATTTGGTGTTGTAACTTCACTCCATTCTA
1 CTACAACTTTAGGGGTATAGGATTTGGTGTTGTAACTTCACTCCATTCTA
* * * ** ** ** * * ***
6385 CTACAACTTCAGGGAG-ATTGAGATCTACTACTGTTAGTTTTAATCCGCCCCT-
1 CTACAACTTTAGGG-GTATAG-GATTTGGTGTTG-TAACTTCACTCC-ATTCTA
* * *
6437 CTACAACTTTAAGGGTATAGAATTTGGTGTTGTAACTTCACTCCATTCCA
1 CTACAACTTTAGGGGTATAGGATTTGGTGTTGTAACTTCACTCCATTCTA
6487 CTACAACTT
1 CTACAACTT
6496 CAGAGAGATT
Statistics
Matches: 74, Mismatches: 31, Indels: 12
0.63 0.26 0.10
Matches are distributed among these distances:
49 1 0.01
50 33 0.45
51 15 0.20
52 23 0.31
53 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (50 bp):
CTACAACTTTAGGGGTATAGGATTTGGTGTTGTAACTTCACTCCATTCTA
Found at i:6849 original size:102 final size:102
Alignment explanation
Indices: 6590--6888 Score: 384
Period size: 102 Copynumber: 2.9 Consensus size: 102
6580 ATTTGATCCT
* * * *
6590 TGCAACTTCAGGGATATAAGATTTGGGTTTGAAACTTCACTCCATTCCACTGCAACTTCAGGGAG
1 TGCAACTTCAGGGATATAGGATTTGGGGTTGTAACTTCACTCCATTCCACTACAACTTCAGGGAG
* * *
6655 ATTGAGATCTGCTAATGATTAATTTTAATTCAATCCAC
66 ATTGAGATCTGCTACTG-TTAGTTTCAATTCAATCCAC
* * * * * *
6693 TGCAACTTTAGGGATATAGAATTTTGTGTTATAACATCACTCCATTCCACTACAACTTCAGGGAG
1 TGCAACTTCAGGGATATAGGATTTGGGGTTGTAACTTCACTCCATTCCACTACAACTTCAGGGAG
*
6758 ATTGAGATCTGCTACTGTTAGTTTCAA-TCTGATCCAC
66 ATTGAGATCTGCTACTGTTAGTTTCAATTC-AATCCAC
** * *
6795 TGCAACTTCAGGGATATAGGATTTGGGGTTGTGGCTTCACTCTATTCCATTACAACTTCAGGGAG
1 TGCAACTTCAGGGATATAGGATTTGGGGTTGTAACTTCACTCCATTCCACTACAACTTCAGGGAG
* * *
6860 ATTGAGATCTACTACGGTTAGTTTTAATT
66 ATTGAGATCTGCTACTGTTAGTTTCAATT
6889 AACCCCTTTA
Statistics
Matches: 167, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
101 2 0.01
102 93 0.56
103 72 0.43
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (102 bp):
TGCAACTTCAGGGATATAGGATTTGGGGTTGTAACTTCACTCCATTCCACTACAACTTCAGGGAG
ATTGAGATCTGCTACTGTTAGTTTCAATTCAATCCAC
Found at i:6915 original size:102 final size:101
Alignment explanation
Indices: 6590--6927 Score: 374
Period size: 102 Copynumber: 3.3 Consensus size: 101
6580 ATTTGATCCT
* * * *
6590 TGCAACTTCAGGGATATAAGATTTGG-GTTTGAAACTTCACTCCATTCCACTGCAACTTCAGGGA
1 TGCAACTTTAGGGATATAGGATTTGGTG-TTGTAACTTCACTCCATTCCACTACAACTTCAGGGA
* * *
6654 GATTGAGATCTGCTAATGATTAATTTTAATTCAATCCAC
65 GATTGAGATCTGCT-ACGGTTAGTTTTAATTCAA-CCAC
* * * *
6693 TGCAACTTTAGGGATATAGAATTTTGTGTTATAACATCACTCCATTCCACTACAACTTCAGGGAG
1 TGCAACTTTAGGGATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTACAACTTCAGGGAG
* * * *
6758 ATTGAGATCTGCTACTGTTAGTTTCAATCTGATCCAC
66 ATTGAGATCTGCTACGGTTAGTTTTAAT-TCAACCAC
* * ** * *
6795 TGCAACTTCAGGGATATAGGATTTGGGGTTGTGGCTTCACTCTATTCCATTACAACTTCAGGGAG
1 TGCAACTTTAGGGATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTACAACTTCAGGGAG
* *
6860 ATTGAGATCTACTACGGTTAGTTTTAATT-AACCCC
66 ATTGAGATCTGCTACGGTTAGTTTTAATTCAACCAC
** *
6895 TTTATAACTTTAGGGGTATAGGATTTGGTGTTG
1 --TGCAACTTTAGGGATATAGGATTTGGTGTTG
6928 CAGCTTTCAT
Statistics
Matches: 196, Mismatches: 35, Indels: 9
0.82 0.15 0.04
Matches are distributed among these distances:
100 4 0.02
101 1 0.01
102 120 0.61
103 70 0.36
104 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (101 bp):
TGCAACTTTAGGGATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTACAACTTCAGGGAG
ATTGAGATCTGCTACGGTTAGTTTTAATTCAACCAC
Found at i:6954 original size:50 final size:50
Alignment explanation
Indices: 6891--7014 Score: 151
Period size: 50 Copynumber: 2.5 Consensus size: 50
6881 TTTTAATTAA
* * *
6891 CCCCTTTATAACTTTAGGGGTATAGGATTTGGTGTTGCAGCTTTCAT-TCG
1 CCCCTTTACAACTTTAGGGGTATAGGATTTGATGTTGCAGCTTTAATCT-G
* * *
6941 CCCCTTTACAACTTCAGGGGTATAGGATTTGATTTTGTAGCTTTAATCTG
1 CCCCTTTACAACTTTAGGGGTATAGGATTTGATGTTGCAGCTTTAATCTG
** *
6991 CCTATTTGCAACTTTAGGGGTATA
1 CCCCTTTACAACTTTAGGGGTATA
7015 AAAGGTACAG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
50 62 0.98
51 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (50 bp):
CCCCTTTACAACTTTAGGGGTATAGGATTTGATGTTGCAGCTTTAATCTG
Found at i:6955 original size:357 final size:355
Alignment explanation
Indices: 6235--6972 Score: 908
Period size: 357 Copynumber: 2.1 Consensus size: 355
6225 TCTGATCCAC
* * * * *
6235 TACAACCTCAGGGATATAGGATTTGATGTTGTGGCTTCACTCCATTCCACTGTAACTTTAGGGAG
1 TACAACTTCAGGGATATAGGATTTGAGGTTGTGACTTCACTCCATTCCACTGCAACTTCAGGGAG
* * ** * * *
6300 ATTGAGATCTGCTACTATTACTTCTAAACTGCCCTCTACAACTTTAGGGGTATAGGATTTGGTGT
66 ATTGAGATCTGCTAATATTAATTCTAAACAACCCACTACAACTTTAGGGATATAGAATTTGGTGT
* * * *
6365 TGTAACTTCACTCCATTCTACTACAACTTCAGGGAGATTGAGATCTACTACTGTTAGTTTTAATC
131 TATAACATCACTCCATTCCACTACAACTTCAGGGAGATTGAGATCTACTACTGTTAGTTTCAATC
* * *
6430 CGCCCCTCTACAACTTTAAGGGTATAGAATTTGGTGTTGTAACTTCACTCCATTCCACTACAACT
196 CGACCCACTACAACTTTAAGGGTATAGAATTTGGGGTTGTAACTTCACTCCATTCCACTACAACT
** * * *
6495 TCAGAGAGATTAAGATATGTTACTTGTTAGTTTTAATCCACCCCTTTGTAACTTTAGGGGTATAA
261 TCAGAGAGATTAAGATATACTACTGGTTAGTTTTAATCAACCCCTTTATAACTTTAGGGGTATAA
** * *
6560 GATTTGATGTTGTGGCTTTAATTTGATCCT
326 GATTTGATGTTGCAGCTTTAATTCGACCCT
* *
6590 TGCAACTTCAGGGATATAAGATTTG-GGTT-TGAAACTTCACTCCATTCCACTGCAACTTCAGGG
1 TACAACTTCAGGGATATAGGATTTGAGGTTGTG--ACTTCACTCCATTCCACTGCAACTTCAGGG
* * * * *
6653 AGATTGAGATCTGCTAATGATTAATTTTAATTCAATCCACTGCAACTTTAGGGATATAGAATTTT
64 AGATTGAGATCTGCTAAT-ATTAATTCTAA-ACAACCCACTACAACTTTAGGGATATAGAATTTG
*
6718 GTGTTATAACATCACTCCATTCCACTACAACTTCAGGGAGATTGAGATCTGCTACTGTTAGTTTC
127 GTGTTATAACATCACTCCATTCCACTACAACTTCAGGGAGATTGAGATCTACTACTGTTAGTTTC
* * * * * ** * *
6783 AATCTGATCCACTGCAAC-TTCAGGGATATAGGATTTGGGGTTGTGGCTTCACTCTATTCCATTA
192 AATCCGACCCACTACAACTTTAAGGG-TATAGAATTTGGGGTTGTAACTTCACTCCATTCCACTA
* * * *
6847 CAACTTCAGGGAGATTGAGATCTACTAC-GGTTAGTTTTAATTAACCCCTTTATAACTTTAGGGG
256 CAACTTCAGAGAGATTAAGATATACTACTGGTTAGTTTTAATCAACCCCTTTATAACTTTAGGGG
* * * *
6911 TATAGGATTTGGTGTTGCAGCTTTCATTCGCCCCTT
321 TATAAGATTTGATGTTGCAGCTTTAATTCGACCC-T
*
6947 TACAACTTCAGGGGTATAGGATTTGA
1 TACAACTTCAGGGATATAGGATTTGA
6973 TTTTGTAGCT
Statistics
Matches: 320, Mismatches: 56, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
353 2 0.01
354 3 0.01
355 66 0.21
356 73 0.23
357 176 0.55
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (355 bp):
TACAACTTCAGGGATATAGGATTTGAGGTTGTGACTTCACTCCATTCCACTGCAACTTCAGGGAG
ATTGAGATCTGCTAATATTAATTCTAAACAACCCACTACAACTTTAGGGATATAGAATTTGGTGT
TATAACATCACTCCATTCCACTACAACTTCAGGGAGATTGAGATCTACTACTGTTAGTTTCAATC
CGACCCACTACAACTTTAAGGGTATAGAATTTGGGGTTGTAACTTCACTCCATTCCACTACAACT
TCAGAGAGATTAAGATATACTACTGGTTAGTTTTAATCAACCCCTTTATAACTTTAGGGGTATAA
GATTTGATGTTGCAGCTTTAATTCGACCCT
Found at i:7311 original size:88 final size:88
Alignment explanation
Indices: 7169--7333 Score: 240
Period size: 88 Copynumber: 1.9 Consensus size: 88
7159 CAACTTCAGG
* * *
7169 GAGATTGAGATCTACTACGGTTAGTTTTAATTAACCCCTTTATAACTTTAGGGGTAAAGGATTTG
1 GAGATTGAGATCTACTACAGTTAGTTTTAATCAACCCCTTTACAACTTTAGGGGTAAAGGATTTG
*
7234 GTGTTATAACTTCAATCTTCAAA
66 GTGTTACAACTTCAATCTTCAAA
* * ** * *
7257 GAGATTGAGATCTACTATATTTAGTTTTAATCCGCCCCTTTGCAACTTTAGGGGTATAGGATTTG
1 GAGATTGAGATCTACTACAGTTAGTTTTAATCAACCCCTTTACAACTTTAGGGGTAAAGGATTTG
7322 GTGTTACAACTT
66 GTGTTACAACTT
7334 TCATTCACCC
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
88 67 1.00
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (88 bp):
GAGATTGAGATCTACTACAGTTAGTTTTAATCAACCCCTTTACAACTTTAGGGGTAAAGGATTTG
GTGTTACAACTTCAATCTTCAAA
Found at i:8036 original size:19 final size:19
Alignment explanation
Indices: 8008--8062 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
7998 GAAGGAATTA
* *
8008 AAAATATCAAACATTGGTC
1 AAAATGTCAAACATTAGTC
8027 AAAATGTCAAACATTAGTC
1 AAAATGTCAAACATTAGTC
*
8046 AAAGATGGCAAACATTA
1 AAA-ATGTCAAACATTA
8063 AACAATGGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 20 0.62
20 12 0.38
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.24
Consensus pattern (19 bp):
AAAATGTCAAACATTAGTC
Done.