Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008902.1 Kokia drynarioides strain JFW-HI SEQ_123590, 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: 15208
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:2830 original size:59 final size:58
Alignment explanation
Indices: 2662--2937 Score: 306
Period size: 58 Copynumber: 4.7 Consensus size: 58
2652 GTAAAACGAT
* * * * * *
2662 AATTTTGGACACTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGTGGTCAAAAATAG
1 AATTTTGGACATTCGGGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGG
* * *
2720 -TTTTTAGACATTCGAGGGGTAAAATGGTAATTTTTGGAAG-TTTCGGGTCAAAAATGG
1 AATTTTGGACATTCG-GGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGG
* * *
2777 AATTTTTGGACATTAGGGGGTAAAATAGTAATTTTTAGAAGTTTTGGGGTCAAAAATGG
1 AA-TTTTGGACATTCGGGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGG
* * * * * * * *
2836 AATTCTGGATATTTGGGGGTAAAAATGATAATTTTTGAAAGTTTTAGGGTCAAAATTGT
1 AATTTTGGACATTCGGGGGT-AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGG
*
2895 AATTTTGGACA-TCCGGGGTAAAATGGTAATTTTTGGAAAGTTT
1 AATTTTGGACATTCGGGGGTAAAATGGTAATTTTTGG-AAGTTT
2938 AAGGTAAAAA
Statistics
Matches: 182, Mismatches: 30, Indels: 12
0.81 0.13 0.05
Matches are distributed among these distances:
57 39 0.21
58 74 0.41
59 69 0.38
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.36
Consensus pattern (58 bp):
AATTTTGGACATTCGGGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGG
Found at i:2979 original size:30 final size:30
Alignment explanation
Indices: 2852--2984 Score: 87
Period size: 30 Copynumber: 4.4 Consensus size: 30
2842 GGATATTTGG
* **
2852 GGGTAAAAATGATAATTTTTGAAAGTTTTA
1 GGGTAAAAATGATAATTTTGGAAAGTTCGA
* * *
2882 GGGTCAAAATTG-TAATTTTGGACA-TCCG-
1 GGGT-AAAAATGATAATTTTGGAAAGTTCGA
* *
2910 GGGT-AAAATGGTAATTTTTGGAAAGTT-TA
1 GGGTAAAAATGATAA-TTTTGGAAAGTTCGA
* * *
2939 AGGTAAAAAATGATATTTTTTGAAAGTTCGA
1 GGGT-AAAAATGATAATTTTGGAAAGTTCGA
2970 GGGTCAAAATATGAT
1 GGGT-AAAA-ATGAT
2985 TTCTAGACAT
Statistics
Matches: 77, Mismatches: 17, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
26 5 0.06
27 3 0.04
28 12 0.16
29 5 0.06
30 25 0.32
31 22 0.29
32 5 0.06
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (30 bp):
GGGTAAAAATGATAATTTTGGAAAGTTCGA
Found at i:5615 original size:11 final size:11
Alignment explanation
Indices: 5606--5668 Score: 81
Period size: 11 Copynumber: 5.7 Consensus size: 11
5596 AATTATTAGT
*
5606 TTTATATTAGA
1 TTTATATTATA
*
5617 TTTGTATTATA
1 TTTATATTATA
*
5628 CTTATATTATA
1 TTTATATTATA
* *
5639 TTTATTTTAGA
1 TTTATATTATA
5650 TTTATATTATA
1 TTTATATTATA
5661 TTTATATT
1 TTTATATT
5669 GCTGCCTTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 43 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.62
Consensus pattern (11 bp):
TTTATATTATA
Found at i:5643 original size:33 final size:33
Alignment explanation
Indices: 5606--5668 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
5596 AATTATTAGT
*
5606 TTTATATTAGATTTGTATTATACTTATATTATA
1 TTTATATTAGATTTATATTATACTTATATTATA
* *
5639 TTTATTTTAGATTTATATTATATTTATATT
1 TTTATATTAGATTTATATTATACTTATATT
5669 GCTGCCTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.62
Consensus pattern (33 bp):
TTTATATTAGATTTATATTATACTTATATTATA
Found at i:10633 original size:98 final size:97
Alignment explanation
Indices: 10457--10651 Score: 250
Period size: 98 Copynumber: 2.0 Consensus size: 97
10447 AACTTTGGAA
*
10457 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTCGCACCTAGTAAGTTAAGGCACAAACTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAACTTTCA
* * *
10522 GAATCAGAGATAAATA-AACATTGCCTCGATTT
66 AAATCAGAAATAAA-AGAACAATGCCTCGATTT
* * * * * *
10554 AAGGGTATTCGATTATTTCGATTTGAGGAAAAAATTGTACCTAGTAAGTTAAGGCACAAATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAG-AAAAATCGCACCTAGTAAGTTAAGGCACAAACTTTC
*
10619 AAAACTC-GAAATAAAAGAATAATGCCTCGATTT
65 AAAA-TCAGAAATAAAAGAACAATGCCTCGATTT
10652 TAAAGTTTTC
Statistics
Matches: 84, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
97 26 0.31
98 56 0.67
99 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAACTTTCA
AAATCAGAAATAAAAGAACAATGCCTCGATTT
Found at i:10969 original size:59 final size:57
Alignment explanation
Indices: 10908--11314 Score: 283
Period size: 60 Copynumber: 6.9 Consensus size: 57
10898 TTGGTCACTT
* * *
10908 GGGGATAAAATGGTACTTTTGGGAAATTTGAGGGTCAAAAATGGAATTTTTTGACA-TTTG
1 GGGG-TAAAATGGTACTTTTGGGAAA-TT-AGGGTCAAAAATTGAATTTTTGGA-AGTTTA
* * * *
10968 GGGGTAAAATGGAACTTTTGGAAGAATCAAGGTCAAAAATTGAATTTTTGGAAGTTTA
1 GGGGTAAAATGGTACTTTTGGGA-AATTAGGGTCAAAAATTGAATTTTTGGAAGTTTA
11026 GGGGTAAAATGGTTA-TTTTCGGAAGAAAATTAGGGTCAAAAATTGAATTTTTGGAAGTTTA
1 GGGGTAAAATGG-TACTTTT-GG--G-AAATTAGGGTCAAAAATTGAATTTTTGGAAGTTTA
* * ** * * * *
11087 GGGGTAAAATGGTAATTTTGGAAAAAAACTGGTGTCAAAAATGGAATTTTAGAAAG-TTC
1 GGGGTAAAATGGTACTTTTGGGAAATTA--GG-GTCAAAAATTGAATTTTTGGAAGTTTA
* ** * *
11146 GAGGG-AAAATGGTAATTTTCAAAGAAATTA-GGTC-AAAATGGAA-TTTTGGAAAG-TTC
1 G-GGGTAAAATGGTACTTTT--GGGAAATTAGGGTCAAAAATTGAATTTTTGG-AAGTTTA
* * ** *
11202 GAGGGTAAAATGGTAATTTTTAGAGAAATCGGGGTCAAAAAATGGAATTTTTGGAAGTTTA
1 G-GGGTAAAATGGT-ACTTTT-GGGAAATTAGGGTC-AAAAATTGAATTTTTGGAAGTTTA
* * ** *
11263 GGGGTAAAATGGTAATTTTTGGAAAATCGGGGTCAAAAATGGAA-TTTTGGAA
1 GGGGTAAAATGGT-ACTTTTGGGAAATTAGGGTCAAAAATTGAATTTTTGGAA
11315 AGCTCGGGGG
Statistics
Matches: 293, Mismatches: 32, Indels: 47
0.79 0.09 0.13
Matches are distributed among these distances:
55 4 0.01
56 20 0.07
57 31 0.11
58 60 0.20
59 52 0.18
60 64 0.22
61 61 0.21
62 1 0.00
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.31
Consensus pattern (57 bp):
GGGGTAAAATGGTACTTTTGGGAAATTAGGGTCAAAAATTGAATTTTTGGAAGTTTA
Found at i:11043 original size:29 final size:28
Alignment explanation
Indices: 11011--11109 Score: 92
Period size: 28 Copynumber: 3.4 Consensus size: 28
11001 CAAAAATTGA
11011 ATTTTTGGAAGTTTAGGGGTAAAATGGTT
1 ATTTTTGGAAGTTTAGGGGTAAAATGG-T
* * * *
11040 ATTTTCGGAAGAAAATTA-GGGTCAAAAATTGA
1 ATTTTTGGAAG---TTTAGGGGT--AAAATGGT
11072 ATTTTTGGAAGTTTAGGGGTAAAATGGT
1 ATTTTTGGAAGTTTAGGGGTAAAATGGT
*
11100 AATTTTGGAA
1 ATTTTTGGAA
11110 AAAAACTGGT
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
28 15 0.27
29 13 0.24
30 4 0.07
31 4 0.07
32 13 0.24
33 6 0.11
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.36
Consensus pattern (28 bp):
ATTTTTGGAAGTTTAGGGGTAAAATGGT
Found at i:11162 original size:28 final size:27
Alignment explanation
Indices: 11124--11221 Score: 94
Period size: 28 Copynumber: 3.5 Consensus size: 27
11114 ACTGGTGTCA
11124 AAAATGGAATTTTAGAAAGTTCGAGGG
1 AAAATGGAATTTTAGAAAGTTCGAGGG
*
11151 AAAATGGTAATTTTCAAAGAAA-TT--AGGTC
1 AAAATGG-AATTTT---AGAAAGTTCGAGG-G
*
11180 AAAATGGAATTTTGGAAAGTTCGAGGG
1 AAAATGGAATTTTAGAAAGTTCGAGGG
11207 TAAAATGGTAATTTT
1 -AAAATGG-AATTTT
11222 TAGAGAAATC
Statistics
Matches: 58, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
25 4 0.07
26 2 0.03
27 7 0.12
28 25 0.43
29 13 0.22
30 2 0.03
31 5 0.09
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.31
Consensus pattern (27 bp):
AAAATGGAATTTTAGAAAGTTCGAGGG
Found at i:11220 original size:29 final size:29
Alignment explanation
Indices: 11123--11385 Score: 151
Period size: 29 Copynumber: 9.1 Consensus size: 29
11113 AACTGGTGTC
*
11123 AAAAATGGAATTTTAGAAAGTTCGAGGG-
1 AAAAATGGAATTTTGGAAAGTTCGAGGGT
*
11151 -AAAATGGTAATTTT-CAAAGAAATT--A-GGT
1 AAAAATGG-AATTTTGGAAAG---TTCGAGGGT
*
11179 CAAAATGGAATTTTGGAAAGTTCGAGGGT
1 AAAAATGGAATTTTGGAAAGTTCGAGGGT
11208 -AAAATGGTAATTTTTAGAGAAA--TCG-GGGT
1 AAAAATGG-AA-TTTT-G-GAAAGTTCGAGGGT
*
11237 CAAAAAATGGAATTTTTGG-AAGTT-TAGGGGT
1 --AAAAATGGAA-TTTTGGAAAGTTCGA-GGGT
*
11268 -AAAATGGTAATTTTTGGAAA-ATCG-GGGT
1 AAAAATGG-AA-TTTTGGAAAGTTCGAGGGT
* *
11296 CAAAAATGGAATTTTGGAAAGCTCGGGGGT
1 -AAAAATGGAATTTTGGAAAGTTCGAGGGT
* ** ** *
11326 AAAAATGTAATTTTTTAAAAATCGAGGTT
1 AAAAATGGAATTTTGGAAAGTTCGAGGGT
* *
11355 AAAAATGAAATTTTGGAAAGTTCGGGGGT
1 AAAAATGGAATTTTGGAAAGTTCGAGGGT
11384 AA
1 AA
11386 TAATATAATT
Statistics
Matches: 187, Mismatches: 20, Indels: 55
0.71 0.08 0.21
Matches are distributed among these distances:
26 2 0.01
27 13 0.07
28 43 0.23
29 82 0.44
30 24 0.13
31 12 0.06
32 11 0.06
ACGTcount: A:0.39, C:0.05, G:0.27, T:0.30
Consensus pattern (29 bp):
AAAAATGGAATTTTGGAAAGTTCGAGGGT
Found at i:11263 original size:176 final size:175
Alignment explanation
Indices: 10992--11385 Score: 460
Period size: 176 Copynumber: 2.2 Consensus size: 175
10982 CTTTTGGAAG
* * * * *
10992 AATCAAGGTCAAAAATTGAATTTTTGG-AAGTT-TAGGGGTAAAATGGTTATTTTCGGAAGAAAA
1 AATCGAGGTC-AAAATGGAA-TTTTGGAAAGTTCGA-GGGTAAAATGGTAATTTTCAGAAGAAAA
* *
11055 TTAGGGTCAAAAATTGAATTTTTGGAAGTTTAGGGGTAAAATGGTAA-TTTTGGAAAAAAACTGG
63 TCAGGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGG--AAAAAC-GG
* *
11119 TGTCAAAAATGGAATTTTAGAAAGTTCGAGGG-AAAATGGTAATTTTCAAAGA
125 GGTCAAAAATGGAATTTTAGAAAGCTCGAGGGAAAAAT-GTAATTTTCAAA-A
* * *
11171 AAT-TAGGTCAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTAG-AG-AAATCG
1 AATCGAGGTCAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTCAGAAGAAAATCA
*
11233 GGGTCAAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAAATCGGGGTCA
66 GGGTC-AAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAAAACGGGGTCA
* * **
11298 AAAATGGAATTTTGGAAAGCTCGGGGGTAAAAATGTAATTTTTTAAA
130 AAAATGGAATTTTAGAAAGCTCGAGGG-AAAAATGTAATTTTCAAAA
* * *
11345 AATCGAGGTTAAAAATGAAATTTTGGAAAGTTCGGGGGTAA
1 AATCGAGG-TCAAAATGGAATTTTGGAAAGTTCGAGGGTAA
11386 TAATATAATT
Statistics
Matches: 187, Mismatches: 20, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
174 34 0.18
175 27 0.14
176 80 0.43
177 37 0.20
178 6 0.03
179 3 0.02
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.31
Consensus pattern (175 bp):
AATCGAGGTCAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTCAGAAGAAAATCA
GGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAAAACGGGGTCAA
AAATGGAATTTTAGAAAGCTCGAGGGAAAAATGTAATTTTCAAAA
Found at i:11331 original size:59 final size:59
Alignment explanation
Indices: 10908--11385 Score: 390
Period size: 58 Copynumber: 8.1 Consensus size: 59
10898 TTGGTCACTT
* * * * * * * *
10908 GGGGATAAAATGGTACTTTTGGGAAATTTGAGGGTCAAAAATGGAATTTTTTGACA-TTT
1 GGGGGTAAAATGGTAATTTTTGGAAAATCG-GGGTCAAAAATGGAATTTTTGGAAAGTTC
* ** * *
10967 GGGGGTAAAATGG-AACTTTTGGAAGAATCAAGGTCAAAAATTGAATTTTTGG-AAGTTT
1 GGGGGTAAAATGGTAATTTTTGGAA-AATCGGGGTCAAAAATGGAATTTTTGGAAAGTTC
* * * ** * *
11025 AGGGGTAAAATGGTTATTTTCGGAAGAAAATTAGGGTCAAAAATTGAATTTTTGG-AAGTTT
1 GGGGGTAAAATGGTAATTTT-TG--GAAAATCGGGGTCAAAAATGGAATTTTTGGAAAGTTC
* * * *
11086 AGGGGTAAAATGGTAA-TTTTGGAAAAAAACTGGTGTCAAAAATGGAA-TTTTAGAAAGTTC
1 GGGGGTAAAATGGTAATTTTTGG--AAAATC-GGGGTCAAAAATGGAATTTTTGGAAAGTTC
* *** **
11146 GAGGG-AAAATGGTAATTTTCAAAGAAAT-TAGGTC-AAAATGGAA-TTTTGGAAAGTTC
1 GGGGGTAAAATGGTAATTTTTGGA-AAATCGGGGTCAAAAATGGAATTTTTGGAAAGTTC
* * *
11202 GAGGGTAAAATGGTAATTTTTAGAGAAATCGGGGTCAAAAAATGGAATTTTTGG-AAGTTT
1 GGGGGTAAAATGGTAATTTTTGGA-AAATCGGGGTC-AAAAATGGAATTTTTGGAAAGTTC
* *
11262 AGGGGTAAAATGGTAATTTTTGGAAAATCGGGGTCAAAAATGGAA-TTTTGGAAAGCTC
1 GGGGGTAAAATGGTAATTTTTGGAAAATCGGGGTCAAAAATGGAATTTTTGGAAAGTTC
** * * *
11320 GGGGGTAAAAAT-GTAATTTTTTAAAAATCGAGGTTAAAAAT-GAAATTTTGGAAAGTTC
1 GGGGGT-AAAATGGTAATTTTTGGAAAATCGGGGTCAAAAATGGAATTTTTGGAAAGTTC
11378 GGGGGTAA
1 GGGGGTAA
11386 TAATATAATT
Statistics
Matches: 347, Mismatches: 52, Indels: 42
0.79 0.12 0.10
Matches are distributed among these distances:
56 26 0.07
57 37 0.11
58 109 0.31
59 57 0.16
60 63 0.18
61 52 0.15
62 3 0.01
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.31
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTTGGAAAATCGGGGTCAAAAATGGAATTTTTGGAAAGTTC
Found at i:12600 original size:16 final size:14
Alignment explanation
Indices: 12547--12629 Score: 60
Period size: 15 Copynumber: 5.6 Consensus size: 14
12537 GATTTCTTTT
*
12547 TTATTATTAATATTA
1 TTATTATTAAT-GTA
* *
12562 TTATTATTATTATCA
1 TTATTATTAATGT-A
12577 TTATTTATTAATGCTAA
1 TTA-TTATTAATG-T-A
*
12594 TTATTATTACTGT-
1 TTATTATTAATGTA
12607 TTATTATTAATGTTA
1 TTATTATTAATG-TA
*
12622 TTAATATT
1 TTATTATT
12630 TATTAAAACT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
13 11 0.20
14 2 0.04
15 22 0.40
16 15 0.27
17 5 0.09
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.59
Consensus pattern (14 bp):
TTATTATTAATGTA
Found at i:12602 original size:3 final size:3
Alignment explanation
Indices: 12547--12586 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
12537 GATTTCTTTT
* *
12547 TTA TTA TTA ATA TTA TTA TTA TTA TTA TCA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
12587 ATGCTAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:13480 original size:19 final size:17
Alignment explanation
Indices: 13447--13522 Score: 91
Period size: 17 Copynumber: 4.4 Consensus size: 17
13437 TATTTCAAAT
*
13447 TTTAAATTTAAAATAAA
1 TTTAAACTTAAAATAAA
13464 TTTAAACTTAAAAAATAAA
1 TTTAAACTT--AAAATAAA
*
13483 TTTAAATTTAAAAT-AA
1 TTTAAACTTAAAATAAA
*
13499 TTCTAAACTTAGAATAAA
1 TT-TAAACTTAAAATAAA
13517 TTTAAA
1 TTTAAA
13523 ATAAAGATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
16 4 0.08
17 27 0.53
18 4 0.08
19 16 0.31
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (17 bp):
TTTAAACTTAAAATAAA
Found at i:13494 original size:36 final size:34
Alignment explanation
Indices: 13447--13522 Score: 109
Period size: 36 Copynumber: 2.2 Consensus size: 34
13437 TATTTCAAAT
13447 TTTAAATTTAAAATAAATT-TAAACTTAAAAAATAAA
1 TTTAAATTTAAAAT-AATTCTAAACTT--AAAATAAA
*
13483 TTTAAATTTAAAATAATTCTAAACTTAGAATAAA
1 TTTAAATTTAAAATAATTCTAAACTTAAAATAAA
13517 TTTAAA
1 TTTAAA
13523 ATAAAGATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
34 13 0.34
35 4 0.11
36 21 0.55
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (34 bp):
TTTAAATTTAAAATAATTCTAAACTTAAAATAAA
Done.