Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011025.1 Kokia drynarioides strain JFW-HI SEQ_125996, 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: 81323
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1566 original size:59 final size:59
Alignment explanation
Indices: 1520--1761 Score: 439
Period size: 59 Copynumber: 4.1 Consensus size: 59
1510 ATTTTGTACC
*
1520 ATTTTGGTAAATAATATGATGAGGATATTATTTTGATAATTAATTATTTTTTATATTAT
1 ATTTTGGTCAATAATATGATGAGGATATTATTTTGATAATTAATTATTTTTTATATTAT
*
1579 ATTTTGGTCAATAATATGATGGGGATATTATTTTGATAATTAATTATTTTTTATATTAT
1 ATTTTGGTCAATAATATGATGAGGATATTATTTTGATAATTAATTATTTTTTATATTAT
* *
1638 ATTTTGGTCAATAATATGATGGGGATATTATTTTGATAATTAATTATGTTTTATATTAT
1 ATTTTGGTCAATAATATGATGAGGATATTATTTTGATAATTAATTATTTTTTATATTAT
*
1697 ATTTTAGTCAATAATATGATGAGGATATTATTTTGATAATTAATTATTTTTTATATTAT
1 ATTTTGGTCAATAATATGATGAGGATATTATTTTGATAATTAATTATTTTTTATATTAT
1756 ATTTTG
1 ATTTTG
1762 AAAATTAATT
Statistics
Matches: 176, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 176 1.00
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.52
Consensus pattern (59 bp):
ATTTTGGTCAATAATATGATGAGGATATTATTTTGATAATTAATTATTTTTTATATTAT
Found at i:1744 original size:16 final size:16
Alignment explanation
Indices: 1723--1772 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1713 TGATGAGGAT
1723 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
1739 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
1754 A-TATTTTGAAAATTA
1 ATTATTTTGATAATTA
1769 ATTA
1 ATTA
1773 GCCAAGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
14 9 0.33
15 5 0.19
16 13 0.48
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:2484 original size:17 final size:17
Alignment explanation
Indices: 2459--2491 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2449 CCTTCTTCCT
2459 TCTTCTTTCTTTCTTTC
1 TCTTCTTTCTTTCTTTC
*
2476 TCTTTTTTCTTTCTTT
1 TCTTCTTTCTTTCTTT
2492 TTTCCTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TCTTCTTTCTTTCTTTC
Found at i:2486 original size:13 final size:13
Alignment explanation
Indices: 2462--2494 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2452 TCTTCCTTCT
2462 TCTTTCTTTCTTTC
1 TCTTT-TTTCTTTC
2476 TCTTTTTTCTTTC
1 TCTTTTTTCTTTC
2489 T-TTTTT
1 TCTTTTT
2495 CCTTCATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 9 0.47
14 5 0.26
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TCTTTTTTCTTTC
Found at i:2490 original size:11 final size:11
Alignment explanation
Indices: 2461--2506 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
2451 TTCTTCCTTC
2461 TTCTTTCTTTCT
1 TTCTTTCTTT-T
2473 TTC--TCTTTT
1 TTCTTTCTTTT
2482 TTCTTTCTTTT
1 TTCTTTCTTTT
* *
2493 TTCCTTCATTT
1 TTCTTTCTTTT
2504 TTC
1 TTC
2507 GTTGGTCCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 4 0.13
10 5 0.17
11 18 0.60
12 3 0.10
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (11 bp):
TTCTTTCTTTT
Found at i:22079 original size:13 final size:13
Alignment explanation
Indices: 22056--22086 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
22046 TAATTTGATA
22056 CTTGA-GTTTTTC
1 CTTGATGTTTTTC
22068 CTTGATGTTTTTC
1 CTTGATGTTTTTC
22081 CTTGAT
1 CTTGAT
22087 CCAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.10, C:0.16, G:0.16, T:0.58
Consensus pattern (13 bp):
CTTGATGTTTTTC
Found at i:23884 original size:19 final size:21
Alignment explanation
Indices: 23849--23889 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
23839 AAAAAAATAT
23849 TTTTAAAAATATAAATT-ATA
1 TTTTAAAAATATAAATTCATA
*
23869 TTTTAAACAT-TAAATTCATA
1 TTTTAAAAATATAAATTCATA
23889 T
1 T
23890 AATTGACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTTAAAAATATAAATTCATA
Found at i:27083 original size:18 final size:19
Alignment explanation
Indices: 27052--27090 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
27042 TCACATCAAT
27052 AAATAATTTGAAAATTATAA
1 AAATAATTTGAAAATT-TAA
27072 AAAT-ATTT-AAAATTTAA
1 AAATAATTTGAAAATTTAA
27089 AA
1 AA
27091 TAAAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 6 0.32
19 4 0.21
20 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
AAATAATTTGAAAATTTAA
Found at i:27605 original size:3 final size:3
Alignment explanation
Indices: 27597--27622 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
27587 ATGCATTGCT
27597 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
27623 GCTAAGCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:29170 original size:34 final size:35
Alignment explanation
Indices: 29131--29205 Score: 91
Period size: 36 Copynumber: 2.2 Consensus size: 35
29121 ATTAAATTGT
* *
29131 TGTTTTGGTG-T-TGTGTTTTTACTGTTTTGGTTGC
1 TGTTTTGGTGCTATGTGTTTTTACTATTTT-GATGC
* *
29165 TGTTTTGGTGCTATTTTTTTTTACTATTTTGATGC
1 TGTTTTGGTGCTATGTGTTTTTACTATTTTGATGC
29200 TGTTTT
1 TGTTTT
29206 TATTGTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 10 0.29
35 11 0.31
36 14 0.40
ACGTcount: A:0.07, C:0.07, G:0.23, T:0.64
Consensus pattern (35 bp):
TGTTTTGGTGCTATGTGTTTTTACTATTTTGATGC
Found at i:29194 original size:11 final size:11
Alignment explanation
Indices: 29180--29247 Score: 57
Period size: 12 Copynumber: 6.0 Consensus size: 11
29170 TGGTGCTATT
*
29180 TTTTTTTACTA
1 TTTTTTTGCTA
** *
29191 TTTTGATGCTG
1 TTTTTTTGCTA
*
29202 TTTTTATTGTTA
1 TTTTT-TTGCTA
29214 TTTTTGTTGCTA
1 TTTTT-TTGCTA
29226 TTTTTTT-CTA
1 TTTTTTTGCTA
29236 TTATTTTTGCTA
1 TT-TTTTTGCTA
29248 CTGTTTTGGT
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
10 5 0.11
11 18 0.41
12 21 0.48
ACGTcount: A:0.13, C:0.07, G:0.10, T:0.69
Consensus pattern (11 bp):
TTTTTTTGCTA
Found at i:29194 original size:24 final size:23
Alignment explanation
Indices: 29167--29242 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 23
29157 TTGGTTGCTG
*
29167 TTTTGGTGCTATTTTTTTTTACTA
1 TTTTGATGCTATTTTTTTTTA-TA
*
29191 TTTTGATGCTGTTTTTATTGTTAT-
1 TTTTGATGCTATTTTT-TT-TTATA
* *
29215 TTTTGTTGCTATTTTTTTCTATTA
1 TTTTGATGCTATTTTTTTTTA-TA
29239 TTTT
1 TTTT
29243 TGCTACTGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
22 2 0.05
23 3 0.07
24 32 0.74
25 3 0.07
26 3 0.07
ACGTcount: A:0.12, C:0.07, G:0.12, T:0.70
Consensus pattern (23 bp):
TTTTGATGCTATTTTTTTTTATA
Found at i:29252 original size:49 final size:48
Alignment explanation
Indices: 29150--29271 Score: 138
Period size: 49 Copynumber: 2.5 Consensus size: 48
29140 GTTGTGTTTT
* * * * *
29150 TACTGTTTTGGTTGCT-GTTTTGGTGCTATTTTTTTTTACTATTTTGA
1 TACTGTTTTGATTGTTATTTTTGTTGCTATTTTTTTCTACTATTTTGA
* * * *
29197 TGCTGTTTTTATTGTTATTTTTGTTGCTATTTTTTTCTATTATTTTTGC
1 TACTGTTTTGATTGTTATTTTTGTTGCTATTTTTTTCTACTA-TTTTGA
*
29246 TACTGTTTTGGTTGTTATTTTTGTTG
1 TACTGTTTTGATTGTTATTTTTGTTG
29272 TTTGGATGTT
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
47 12 0.20
48 21 0.34
49 28 0.46
ACGTcount: A:0.10, C:0.07, G:0.17, T:0.66
Consensus pattern (48 bp):
TACTGTTTTGATTGTTATTTTTGTTGCTATTTTTTTCTACTATTTTGA
Found at i:29254 original size:22 final size:22
Alignment explanation
Indices: 29212--29254 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
29202 TTTTTATTGT
* *
29212 TATTTTTGTTGCTATTTTTTTC
1 TATTTTTGTTGCTACTGTTTTC
29234 TATTATTT-TTGCTACTGTTTT
1 TATT-TTTGTTGCTACTGTTTT
29255 GGTTGTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.70
Consensus pattern (22 bp):
TATTTTTGTTGCTACTGTTTTC
Found at i:38254 original size:31 final size:31
Alignment explanation
Indices: 38218--38285 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
38208 CTTAACAATG
38218 CAATGACTTAAATAAAAACTTTT-GAATAATT
1 CAATGACTTAAATAAAAA-TTTTCGAATAATT
*
38249 CAATGACTTAAATGAAAATTTTCGAATAATT
1 CAATGACTTAAATAAAAATTTTCGAATAATT
*
38280 TAATGA
1 CAATGA
38286 TTATTTTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 4 0.12
31 30 0.88
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (31 bp):
CAATGACTTAAATAAAAATTTTCGAATAATT
Found at i:41675 original size:17 final size:16
Alignment explanation
Indices: 41652--41692 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
41642 ATAGTAAGAA
41652 TATAATTTTAT-TATT
1 TATAATTTTATATATT
41667 T-TAATAATTTATATATT
1 TATAAT--TTTATATATT
41684 TATAATTTT
1 TATAATTTT
41693 TAAAGGAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
14 4 0.18
15 1 0.05
16 8 0.36
17 5 0.23
18 4 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATAATTTTATATATT
Found at i:42933 original size:74 final size:74
Alignment explanation
Indices: 42821--43025 Score: 365
Period size: 74 Copynumber: 2.8 Consensus size: 74
42811 CTTTTTTAAA
*
42821 GCATCGTGGTAATTTGCTATTGTTGTATTCGGGTGTTGCGTTGCTTTTGCTAGATTGATCTGCTA
1 GCATCGTGGTAATTTGCTATTGTTGTATTCGGGTGTTGCGTTGCTTTTGCTAGATTGATCTACTA
*
42886 TTTTTGCAG
66 TTTTGGCAG
42895 GCATCGTGGTAATTTGCTATTGTTGTATTCGGGTGTTGCGTTGCTTTTGCTAGATTGATCTACTA
1 GCATCGTGGTAATTTGCTATTGTTGTATTCGGGTGTTGCGTTGCTTTTGCTAGATTGATCTACTA
42960 TTTTGGCAG
66 TTTTGGCAG
* * *
42969 GCATCGTGGTAATTTGCTATTATTGTATTCGAGTGTTGTGTTGCTTTTGCTAGATTG
1 GCATCGTGGTAATTTGCTATTGTTGTATTCGGGTGTTGCGTTGCTTTTGCTAGATTG
43026 GTCTCCTGTT
Statistics
Matches: 126, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 126 1.00
ACGTcount: A:0.15, C:0.13, G:0.27, T:0.46
Consensus pattern (74 bp):
GCATCGTGGTAATTTGCTATTGTTGTATTCGGGTGTTGCGTTGCTTTTGCTAGATTGATCTACTA
TTTTGGCAG
Found at i:44919 original size:25 final size:25
Alignment explanation
Indices: 44873--44954 Score: 73
Period size: 24 Copynumber: 3.4 Consensus size: 25
44863 TACGGAAATT
**
44873 AAATTATAA-TTT-TTATGATAATA
1 AAATTATAATTTTATTATTTTAATA
44896 AAATTATAATTTTATTATTTTAAT-
1 AAATTATAATTTTATTATTTTAATA
* * * * *
44920 AATTTATATTTTTATAAATTTAAAA
1 AAATTATAATTTTATTATTTTAATA
44945 AAATTA-AATT
1 AAATTATAATT
44955 AAATTTTTAT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
23 9 0.19
24 25 0.53
25 13 0.28
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (25 bp):
AAATTATAATTTTATTATTTTAATA
Found at i:44939 original size:16 final size:17
Alignment explanation
Indices: 44899--44941 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
44889 GATAATAAAA
*
44899 TTATAATTTTATTATTT
1 TTATAAATTTATTATTT
*
44916 TAAT-AATTTA-TATTT
1 TTATAAATTTATTATTT
44931 TTATAAATTTA
1 TTATAAATTTA
44942 AAAAAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 8 0.36
16 11 0.50
17 3 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTATAAATTTATTATTT
Found at i:59557 original size:2 final size:2
Alignment explanation
Indices: 59550--59576 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59540 GTATATTTGA
59550 AT 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 AT A
59577 AACTAGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:63734 original size:79 final size:79
Alignment explanation
Indices: 63603--63762 Score: 311
Period size: 79 Copynumber: 2.0 Consensus size: 79
63593 GGCTTTGTTC
*
63603 TTTGAGGGAATTCAGGGAATGAAATTCGTACTCCTTCAGATGGAAGAGAACCTTTTTGCTGTCTT
1 TTTGAGGGAATTCAGGGAATGAAATTCGTACTCCTTCAGATGGAAGAGAACCTTTCTGCTGTCTT
63668 ATGGATGGAAATAA
66 ATGGATGGAAATAA
63682 TTTGAGGGAATTCAGGGAATGAAATTCGTACTCCTTCAGATGGAAGAGAACCTTTCTGCTGTCTT
1 TTTGAGGGAATTCAGGGAATGAAATTCGTACTCCTTCAGATGGAAGAGAACCTTTCTGCTGTCTT
63747 ATGGATGGAAATAA
66 ATGGATGGAAATAA
63761 TT
1 TT
63763 CTACAGTTTC
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (79 bp):
TTTGAGGGAATTCAGGGAATGAAATTCGTACTCCTTCAGATGGAAGAGAACCTTTCTGCTGTCTT
ATGGATGGAAATAA
Found at i:72788 original size:39 final size:39
Alignment explanation
Indices: 72734--72811 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
72724 TATGAACATA
*
72734 ATTTCAAGTGAGAGATGACCTTTTGACTATTTTAGTTTT
1 ATTTCAAGTGAGAGATGACCTTTTGACTATTTTAATTTT
*
72773 ATTTCAAGTGAGAGATGAGCTTTTGACTATTTTAATTTT
1 ATTTCAAGTGAGAGATGACCTTTTGACTATTTTAATTTT
72812 TTCTTTGGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.46
Consensus pattern (39 bp):
ATTTCAAGTGAGAGATGACCTTTTGACTATTTTAATTTT
Found at i:73199 original size:22 final size:24
Alignment explanation
Indices: 73174--73228 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
73164 TTTTCCATTT
* *
73174 TTTAATATAAT-ATATTTA-TATA
1 TTTAATATAATCATAATAAGTATA
73196 TTTAATATAATCATAATAAGTATA
1 TTTAATATAATCATAATAAGTATA
73220 TTT-ATATAA
1 TTTAATATAA
73229 GACAAGCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 11 0.38
23 11 0.38
24 7 0.24
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
TTTAATATAATCATAATAAGTATA
Found at i:81194 original size:21 final size:20
Alignment explanation
Indices: 81141--81195 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
81131 AAATCGTATG
*
81141 TAATTTTATTT-TTATATAA
1 TAATATTATTTATTATATAA
*
81160 -AAAATTAATATTATTATATTAA
1 TAATATT-AT-TTATTATA-TAA
81182 TAATATTATTTATT
1 TAATATTATTTATT
81196 TTAATTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
18 4 0.14
19 2 0.07
20 2 0.07
21 10 0.36
22 5 0.18
23 5 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TAATATTATTTATTATATAA
Done.