Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012771.1 Kokia drynarioides strain JFW-HI SEQ_127783, 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: 88657
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 207 characters in sequence are not A, C, G, or T
Found at i:2330 original size:2 final size:2
Alignment explanation
Indices: 2323--2351 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2313 TGCATGCGCA
2323 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2352 TTTTCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:9186 original size:11 final size:11
Alignment explanation
Indices: 9157--9190 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
9147 TCTGAATAAA
9157 TATT-TTTAAT
1 TATTATTTAAT
9167 TATTTATTTAAT
1 TA-TTATTTAAT
9179 TATTATTTAAT
1 TATTATTTAAT
9190 T
1 T
9191 GATAATCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.09
11 12 0.55
12 8 0.36
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTATTTAAT
Found at i:11660 original size:17 final size:17
Alignment explanation
Indices: 11638--11679 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
11628 TAACAAATAC
*
11638 TTATTTTT-GTAATTAA
1 TTATTTTTCATAATTAA
11654 TTTATTTTTCATAATTAA
1 -TTATTTTTCATAATTAA
11672 TTATTTTT
1 TTATTTTT
11680 TTATGTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (17 bp):
TTATTTTTCATAATTAA
Found at i:12630 original size:15 final size:15
Alignment explanation
Indices: 12610--12642 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
12600 CATCAACTTT
*
12610 CATATAAATCACAAA
1 CATATAAACCACAAA
12625 CATATAAACCACAAA
1 CATATAAACCACAAA
12640 CAT
1 CAT
12643 GTAAGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.00, T:0.18
Consensus pattern (15 bp):
CATATAAACCACAAA
Found at i:17564 original size:23 final size:22
Alignment explanation
Indices: 17511--17570 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
17501 AACTCGACTC
*
17511 TAATTCAAATTACTTATTCGAAT
1 TAATTCAAATAACTTATTC-AAT
*
17534 TAACTCAAATAACTTGATT-AAT
1 TAATTCAAATAACTT-ATTCAAT
*
17556 TCAATTCAATTAACT
1 T-AATTCAAATAACT
17571 CAAAATTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 4 0.13
23 24 0.77
24 3 0.10
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (22 bp):
TAATTCAAATAACTTATTCAAT
Found at i:29049 original size:21 final size:21
Alignment explanation
Indices: 28996--29056 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
28986 TTTTTTAGAT
28996 AATT-ATGT-TTATTTTCTTTA
1 AATTAATGTATTATTTT-TTTA
29016 AATTAA-G-AGTTATTTTTTTA
1 AATTAATGTA-TTATTTTTTTA
* *
29036 ATTTAATGTATTATTTATTTA
1 AATTAATGTATTATTTTTTTA
29057 TTTTTTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
20 14 0.41
21 19 0.56
22 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.61
Consensus pattern (21 bp):
AATTAATGTATTATTTTTTTA
Found at i:35016 original size:41 final size:41
Alignment explanation
Indices: 34971--35051 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
34961 CAAACTGTGT
* * *
34971 AACAATGGTTAAA-AAGAAAAACCATTTATACACAGTCCCGG
1 AACAATAG-TAAACAAGAAAAACCATGTACACACAGTCCCGG
35012 AACAATAGTAAACAAGAAAAACCATGTACACACAGTCCCG
1 AACAATAGTAAACAAGAAAAACCATGTACACACAGTCCCG
35052 AACTCCCTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 4 0.11
41 32 0.89
ACGTcount: A:0.48, C:0.22, G:0.14, T:0.16
Consensus pattern (41 bp):
AACAATAGTAAACAAGAAAAACCATGTACACACAGTCCCGG
Found at i:60230 original size:160 final size:160
Alignment explanation
Indices: 60055--60375 Score: 606
Period size: 160 Copynumber: 2.0 Consensus size: 160
60045 ATCAACGAGT
*
60055 AAATAACATACCTTAGATCCAAGTTTATTTGACGATCAATGTTAAAGATTGGTGAAGAAAGTAGT
1 AAATAACATACCTTAGATCCAAATTTATTTGACGATCAATGTTAAAGATTGGTGAAGAAAGTAGT
60120 TTGGATTTTAGTTTGCAAATTTATGACGTTTAAAGTAGTTTCATGAAAAACAATGCACTATATAA
66 TTGGATTTTAGTTTGCAAATTTATGACGTTTAAAGTAGTTTCATGAAAAACAATGCACTATATAA
*
60185 GAGAAAGGGGAATAAGAGCTTTCGATTTTA
131 GAGAAAGGGGAAGAAGAGCTTTCGATTTTA
60215 AAATAACATACCTTAGATCCAAATTTATTTGACGATCAATGTTAAAGATTGGTGAAGAAAGTAGT
1 AAATAACATACCTTAGATCCAAATTTATTTGACGATCAATGTTAAAGATTGGTGAAGAAAGTAGT
*
60280 TTGGATTTTAGTTTGCAAATTTATGACGTTTAAAGTAGTTTCATGAAAAACAATGTACTATATAA
66 TTGGATTTTAGTTTGCAAATTTATGACGTTTAAAGTAGTTTCATGAAAAACAATGCACTATATAA
*
60345 GCGAAAGGGGAAGAAGAGCTTTCGATTTTA
131 GAGAAAGGGGAAGAAGAGCTTTCGATTTTA
60375 A
1 A
60376 TATGTCGATG
Statistics
Matches: 157, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
160 157 1.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.33
Consensus pattern (160 bp):
AAATAACATACCTTAGATCCAAATTTATTTGACGATCAATGTTAAAGATTGGTGAAGAAAGTAGT
TTGGATTTTAGTTTGCAAATTTATGACGTTTAAAGTAGTTTCATGAAAAACAATGCACTATATAA
GAGAAAGGGGAAGAAGAGCTTTCGATTTTA
Found at i:63833 original size:2 final size:2
Alignment explanation
Indices: 63826--63858 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
63816 CAAGTTTATG
63826 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
63859 GGCAGTATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:66111 original size:22 final size:23
Alignment explanation
Indices: 66077--66131 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
66067 TTAACATGTT
* * *
66077 ATTTGTTAATTATTTTATTT-TA
1 ATTTATTATTTATATTATTTGTA
66099 ATTTATTATTTATATTATTTGTA
1 ATTTATTATTTATATTATTTGTA
66122 ATTATATTAT
1 ATT-TATTAT
66132 ATTAATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 17 0.61
23 5 0.18
24 6 0.21
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (23 bp):
ATTTATTATTTATATTATTTGTA
Found at i:66114 original size:6 final size:6
Alignment explanation
Indices: 66086--66169 Score: 58
Period size: 6 Copynumber: 14.8 Consensus size: 6
66076 TATTTGTTAA
66086 TTAT-T TTAT-T TTA-AT TTATTAT TTATA- TTAT-T TGTA-A- TTATA-
1 TTATAT TTATAT TTATAT TTA-TAT TTATAT TTATAT T-TATAT TTATAT
* * *
66128 TTATAT TAATAT AATATAT TTATAT TTATAT TTATCT TTATA
1 TTATAT TTATAT -TTATAT TTATAT TTATAT TTATAT TTATA
66170 ACAAGTATTA
Statistics
Matches: 64, Mismatches: 6, Indels: 17
0.74 0.07 0.20
Matches are distributed among these distances:
4 2 0.03
5 24 0.38
6 29 0.45
7 9 0.14
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (6 bp):
TTATAT
Found at i:66137 original size:37 final size:40
Alignment explanation
Indices: 66075--66153 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 40
66065 TTTTAACATG
* * *
66075 TTATTTGTTAATTATTTTATTTTAAT-TTAT-TATTTATA
1 TTATTTGTTAATTATATTATATTAATATAATATATTTATA
66113 TTATTTG-TAATTATATTATATTAATATAATATATTTATA
1 TTATTTGTTAATTATATTATATTAATATAATATATTTATA
66152 TT
1 TT
66154 TATATTTATC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 16 0.44
38 10 0.28
39 10 0.28
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (40 bp):
TTATTTGTTAATTATATTATATTAATATAATATATTTATA
Found at i:69482 original size:14 final size:14
Alignment explanation
Indices: 69463--69493 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
69453 TTAGCCGTAA
69463 TTTATTTGCTTTGT
1 TTTATTTGCTTTGT
*
69477 TTTATTTGTTTTGT
1 TTTATTTGCTTTGT
69491 TTT
1 TTT
69494 TCAATTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.03, G:0.13, T:0.77
Consensus pattern (14 bp):
TTTATTTGCTTTGT
Found at i:86951 original size:27 final size:27
Alignment explanation
Indices: 86919--86975 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
86909 TGACACCCAG
86919 TGGAGGAACACAAAGTGGCGGCACCAA
1 TGGAGGAACACAAAGTGGCGGCACCAA
** ** *
86946 TGGAGGATTATTAAGTGGCGGCACTAA
1 TGGAGGAACACAAAGTGGCGGCACCAA
86973 TGG
1 TGG
86976 GTGTTTTGCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.18
Consensus pattern (27 bp):
TGGAGGAACACAAAGTGGCGGCACCAA
Found at i:87226 original size:21 final size:22
Alignment explanation
Indices: 87172--87227 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 22
87162 AAGAGAAAGA
*
87172 AAGAAAGA-AAGAAGAAGAAGG
1 AAGAAAGAGAAGAAAAAGAAGG
*
87193 AAG-AAG-G-AGAAAAAG-GGG
1 AAGAAAGAGAAGAAAAAGAAGG
87211 AAGAAAGAGAAGAAAAA
1 AAGAAAGAGAAGAAAAA
87228 AAAAGACAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 5 0.17
19 10 0.34
20 4 0.14
21 10 0.34
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (22 bp):
AAGAAAGAGAAGAAAAAGAAGG
Found at i:87228 original size:22 final size:22
Alignment explanation
Indices: 87155--87233 Score: 63
Period size: 25 Copynumber: 3.5 Consensus size: 22
87145 ATTGAAGGAA
*
87155 AAAAAAAAAG-AGAAAGA-AAG
1 AAAAAAGAAGAAGAAAGAGAAG
*
87175 AAAGAAAGAAGAAGAAGGAAGAAGG
1 AAA-AAAGAAGAAGAAAG-AGAA-G
**
87200 AGAAAAAGGGGAAGAAAGAGAAG
1 A-AAAAAGAAGAAGAAAGAGAAG
*
87223 AAAAAAAAAGA
1 AAAAAAGAAGA
87234 CAATGTATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
20 3 0.07
21 6 0.13
22 12 0.27
23 3 0.07
24 6 0.13
25 13 0.29
26 2 0.04
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAGAAGAAAGAGAAG
Found at i:87432 original size:28 final size:27
Alignment explanation
Indices: 87400--87455 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
87390 TTAAGTATGA
87400 TTAATTTTAAAATATTTTAAT-TTGTTAG
1 TTAA-TTT-AAATATTTTAATGTTGTTAG
* *
87428 TTAATTTGATTATTTTAATGTTGTTAG
1 TTAATTTAAATATTTTAATGTTGTTAG
87455 T
1 T
87456 AAGTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.40
27 11 0.44
28 4 0.16
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (27 bp):
TTAATTTAAATATTTTAATGTTGTTAG
Found at i:87755 original size:16 final size:16
Alignment explanation
Indices: 87710--87759 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
87700 TAAACCTAGT
*
87710 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
87726 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
87740 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
87756 TAAT
1 TAAT
87760 ATCCCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Done.