Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010797.1 Kokia drynarioides strain JFW-HI SEQ_125764, 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: 48590
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:333 original size:103 final size:102
Alignment explanation
Indices: 148--352 Score: 374
Period size: 103 Copynumber: 2.0 Consensus size: 102
138 TGACAATAGG
148 TATTCCACACCAAATATGCCACCCTCACTACTTCGCTTACATTCAATGTCAAACCATTTGACCAA
1 TATTCCACACCAAATATGCCACCCTCACTACTTCGCTTACATTCAATGTCAAACCATTTGACCAA
213 GTTGACCCGACAAAAACACATGACGTAACCCTATCTA
66 GTTGACCCGACAAAAACACATGACGTAACCCTATCTA
*
250 NTATTCCACACCAGATATGCCACCCTCACTACTTCGCTTACATTCAATGTCAAACCATTTGACCA
1 -TATTCCACACCAAATATGCCACCCTCACTACTTCGCTTACATTCAATGTCAAACCATTTGACCA
* *
315 AGTTGACCCGATAGAAACACATGACGTAACCCTATCTA
65 AGTTGACCCGACAAAAACACATGACGTAACCCTATCTA
353 GCACCCGCAG
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 99 1.00
ACGTcount: A:0.33, C:0.32, G:0.10, T:0.25
Consensus pattern (102 bp):
TATTCCACACCAAATATGCCACCCTCACTACTTCGCTTACATTCAATGTCAAACCATTTGACCAA
GTTGACCCGACAAAAACACATGACGTAACCCTATCTA
Found at i:9998 original size:42 final size:41
Alignment explanation
Indices: 9939--10017 Score: 131
Period size: 42 Copynumber: 1.9 Consensus size: 41
9929 CGACTTGCTT
9939 CAAAATATGAGTTAATAATTAAAAAAATTAAATAGGAGGCTC
1 CAAAATATGAGTTAATAATT-AAAAAATTAAATAGGAGGCTC
* *
9981 CAAAATATGAGTTAATAATTTAAGAATTAAATAGGAG
1 CAAAATATGAGTTAATAATTAAAAAATTAAATAGGAG
10018 ATGTGATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 15 0.43
42 20 0.57
ACGTcount: A:0.52, C:0.05, G:0.15, T:0.28
Consensus pattern (41 bp):
CAAAATATGAGTTAATAATTAAAAAATTAAATAGGAGGCTC
Found at i:18084 original size:28 final size:27
Alignment explanation
Indices: 18053--18113 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
18043 AAAATGCGAT
*
18053 TTTTGGATATCCAGGGGCAAAATGGTAA
1 TTTTGGACAT-CAGGGGCAAAATGGTAA
**
18081 TTTTGGACATTTGGGGCAAAATGGTAA
1 TTTTGGACATCAGGGGCAAAATGGTAA
18108 TTTTGG
1 TTTTGG
18114 GAAAGTTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 21 0.70
28 9 0.30
ACGTcount: A:0.28, C:0.08, G:0.30, T:0.34
Consensus pattern (27 bp):
TTTTGGACATCAGGGGCAAAATGGTAA
Found at i:18169 original size:28 final size:27
Alignment explanation
Indices: 18066--18172 Score: 101
Period size: 27 Copynumber: 3.8 Consensus size: 27
18056 TGGATATCCA
*
18066 GGGGCAAAATGGTAATTTTGGACATTT
1 GGGGTAAAATGGTAATTTTGGACATTT
* *
18093 GGGGCAAAATGGTAATTTTGGGAAAGTTT
1 GGGGTAAAATGGTAATTTT-GGACA-TTT
* *
18122 GGGGTTAATAGTGG-AATTTTAGG-CATTC
1 GGGG-TAA-AATGGTAATTTT-GGACATTT
18150 GAGGGTAAAATGGTAATTTTGGA
1 G-GGGTAAAATGGTAATTTTGGA
18173 AGAATCGGGA
Statistics
Matches: 66, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
27 25 0.38
28 16 0.24
29 11 0.17
30 10 0.15
31 4 0.06
ACGTcount: A:0.30, C:0.05, G:0.33, T:0.33
Consensus pattern (27 bp):
GGGGTAAAATGGTAATTTTGGACATTT
Found at i:18255 original size:30 final size:30
Alignment explanation
Indices: 18213--18378 Score: 96
Period size: 30 Copynumber: 5.6 Consensus size: 30
18203 AGTTCGAGGT
18213 AAAATGGCAATTTTTGGAAAAATTGAGGTTA
1 AAAATGG-AATTTTTGGAAAAATTGAGGTTA
* * * *
18244 AAAATGGAATTTTAGG--AAGTTTAGGGGT-
1 AAAATGGAATTTTTGGAAAAATTGA-GGTTA
* * ** *
18272 AATATGATAAATTTTTAAAAAAATTAAGGTTA
1 AAAATG--GAATTTTTGGAAAAATTGAGGTTA
** *
18304 AAAATATAA-TTTTGG--AAGTTCGAGG-T-
1 AAAATGGAATTTTTGGAAAAATT-GAGGTTA
* *
18330 AAAATGGTAATTTTTTGAAAAATCGAGGTTA
1 AAAATGG-AATTTTTGGAAAAATTGAGGTTA
18361 AAAATGGAATTTTTGGAA
1 AAAATGGAATTTTTGGAA
18379 GTTTGGGGGT
Statistics
Matches: 97, Mismatches: 25, Indels: 27
0.65 0.17 0.18
Matches are distributed among these distances:
26 5 0.05
27 7 0.07
28 18 0.19
29 11 0.11
30 30 0.31
31 17 0.18
32 9 0.09
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.34
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAAAATTGAGGTTA
Found at i:18257 original size:57 final size:58
Alignment explanation
Indices: 18098--18381 Score: 272
Period size: 57 Copynumber: 4.9 Consensus size: 58
18088 CATTTGGGGC
* ** * * * *
18098 AAAATGGTAATTTTGGGAAAGTTTGGGGTTAATAGTGGAATTTTAGGCA-TTCGAGGGT
1 AAAATGGTAATTTTTGGAAAAATTGAGGTTAAAAATGGAATTTTAGGAAGTTCGA-GGT
* * * *
18156 AAAATGGTAA-TTTTGGAAGAATCG-GGATCAAAAATGAAATTTTTA-GAAGTTCGAGGT
1 AAAATGGTAATTTTTGGAAAAATTGAGG-TTAAAAATGGAA-TTTTAGGAAGTTCGAGGT
* * *
18213 AAAATGGCAATTTTTGGAAAAATTGAGGTTAAAAATGGAATTTTAGGAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGAAAAATTGAGGTTAAAAATGGAATTTTAGGAAG-TTCGAGGT
* * ** * **
18272 AATATGATAAATTTTTAAAAAAATTAAGGTTAAAAATATAATTTT-GGAAGTTCGAGGT
1 AAAATGGT-AATTTTTGGAAAAATTGAGGTTAAAAATGGAATTTTAGGAAGTTCGAGGT
* * *
18330 AAAATGGTAATTTTTTGAAAAATCGAGGTTAAAAATGGAATTTTTGGAAGTT
1 AAAATGGTAATTTTTGGAAAAATTGAGGTTAAAAATGGAATTTTAGGAAGTT
18382 TGGGGGTAAA
Statistics
Matches: 182, Mismatches: 35, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
56 2 0.01
57 66 0.36
58 65 0.36
59 18 0.10
60 31 0.17
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGAAAAATTGAGGTTAAAAATGGAATTTTAGGAAGTTCGAGGT
Found at i:18375 original size:58 final size:58
Alignment explanation
Indices: 18098--18381 Score: 261
Period size: 58 Copynumber: 4.9 Consensus size: 58
18088 CATTTGGGGC
* ** * * * * * *
18098 AAAATGGTAATTTTGGGAAAGTTTGGGGTTAATAGTGGAATTTTAGGCA-TTCGAGGGT
1 AAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTTGGAAGTTCGA-GGT
* * * *
18156 AAAATGGTAA-TTTTGGAAGAATCG-GGATCAAAAATGAAATTTTTAGAAGTTCGAGGT
1 AAAATGGTAATTTTTGGAAAAATCGAGG-TTAAAAATGGAATTTTTGGAAGTTCGAGGT
* * * * *
18213 AAAATGGCAATTTTTGGAAAAATTGAGGTTAAAAATGGAATTTTAGGAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTTGGAAG-TTCGAGGT
* * ** ** **
18272 AATATGATAAATTTTTAAAAAAATTAAGGTTAAAAATATAA-TTTTGGAAGTTCGAGGT
1 AAAATGGT-AATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTTGGAAGTTCGAGGT
*
18330 AAAATGGTAATTTTTTGAAAAATCGAGGTTAAAAATGGAATTTTTGGAAGTT
1 AAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTTGGAAGTT
18382 TGGGGGTAAA
Statistics
Matches: 179, Mismatches: 40, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
56 2 0.01
57 61 0.34
58 68 0.38
59 21 0.12
60 27 0.15
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTTGGAAGTTCGAGGT
Found at i:18391 original size:29 final size:27
Alignment explanation
Indices: 18359--18445 Score: 93
Period size: 30 Copynumber: 3.0 Consensus size: 27
18349 AAATCGAGGT
*
18359 TAAAAATGGAATTTTTGGAAGTTTGGGGG
1 TAAAAAT--AATTTTTGGAAGTTTAGGGG
*
18388 TAAAATATAATTTTGGAGAAGTTTAGGGG
1 TAAAA-ATAATTTTTG-GAAGTTTAGGGG
18417 TCAAAATATAATTTTTGGATAGTTTAGGG
1 T-AAAA-ATAATTTTTGGA-AGTTTAGGG
18446 ACCTTCAGGG
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
28 7 0.14
29 19 0.37
30 25 0.49
ACGTcount: A:0.34, C:0.01, G:0.28, T:0.37
Consensus pattern (27 bp):
TAAAAATAATTTTTGGAAGTTTAGGGG
Found at i:18425 original size:30 final size:29
Alignment explanation
Indices: 18368--18445 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 29
18358 TTAAAAATGG
* *
18368 AATTTTTG-GAAGTTTGGGGGTAAAATAT
1 AATTTTGGAGAAGTTTAGGGGTAAAATAT
18396 AATTTTGGAGAAGTTTAGGGGTCAAAATAT
1 AATTTTGGAGAAGTTTAGGGGT-AAAATAT
*
18426 AATTTTTGGA-TAGTTTAGGG
1 AA-TTTTGGAGAAGTTTAGGG
18446 ACCTTCAGGG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 7 0.16
29 12 0.27
30 18 0.41
31 7 0.16
ACGTcount: A:0.32, C:0.01, G:0.28, T:0.38
Consensus pattern (29 bp):
AATTTTGGAGAAGTTTAGGGGTAAAATAT
Found at i:21114 original size:3 final size:3
Alignment explanation
Indices: 21106--21147 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
21096 GCCATCCTTT
21106 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
21148 CACTCTTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:21212 original size:24 final size:24
Alignment explanation
Indices: 21185--21232 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
21175 TACTTGATGT
*
21185 TTATCAGAGTAATAGTAAACTTAA
1 TTATCAGAGTAATACTAAACTTAA
*
21209 TTATCAGAGTAATACTAAATTTAA
1 TTATCAGAGTAATACTAAACTTAA
21233 CAGTTTACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.35
Consensus pattern (24 bp):
TTATCAGAGTAATACTAAACTTAA
Found at i:40121 original size:11 final size:11
Alignment explanation
Indices: 40094--40132 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
40084 ATTAGAATCT
*
40094 ATAATAAAATTA
1 ATAA-AAAATAA
40106 ATAAAAAATAA
1 ATAAAAAATAA
*
40117 TTAAAAAATAA
1 ATAAAAAATAA
40128 ATAAA
1 ATAAA
40133 TAGCTAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 20 0.83
12 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
ATAAAAAATAA
Done.