Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012139.1 Kokia drynarioides strain JFW-HI SEQ_127138, 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: 27655
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Warning! 106 characters in sequence are not A, C, G, or T
Found at i:2185 original size:54 final size:54
Alignment explanation
Indices: 2105--2211 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 54
2095 GAAAACACAA
* *
2105 ACAATGTGCCTTCTTCTTCCTTGTGCTAATGCCTTGTGATGTTGGCATTGGCAC
1 ACAATGTGCCTTCTTCTTCCTTGTGCTAATGCCTTCTAATGTTGGCATTGGCAC
* * *
2159 ACAATG-GGCTTCGTTCTTCTTTGTGCTAATGGCTTCTAATGTTGGCATTGGCA
1 ACAATGTGCCTTC-TTCTTCCTTGTGCTAATGCCTTCTAATGTTGGCATTGGCA
2212 TTCTCACTGG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
53 5 0.11
54 42 0.89
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.39
Consensus pattern (54 bp):
ACAATGTGCCTTCTTCTTCCTTGTGCTAATGCCTTCTAATGTTGGCATTGGCAC
Found at i:6956 original size:2 final size:2
Alignment explanation
Indices: 6949--6974 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6939 TAGAGTGTTG
6949 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6975 TTCCACCAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12586 original size:2 final size:2
Alignment explanation
Indices: 12579--12610 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12569 CTTCCCTTCA
12579 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12611 TTATCCAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14382 original size:29 final size:30
Alignment explanation
Indices: 14335--14391 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
14325 ATCGGAGTTC
*
14335 AAAATGAGACTTTTCGGATTCCCGGGGGAA
1 AAAATGAGAATTTTCGGATTCCCGGGGGAA
* *
14365 AAAATGATAATTTT-GGATTCTCGGGGG
1 AAAATGAGAATTTTCGGATTCCCGGGGG
14392 CGAAACGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.28
Consensus pattern (30 bp):
AAAATGAGAATTTTCGGATTCCCGGGGGAA
Found at i:14454 original size:29 final size:28
Alignment explanation
Indices: 14422--14829 Score: 311
Period size: 29 Copynumber: 13.6 Consensus size: 28
14412 ATTCGGAGTA
* * *
14422 AAAAATGGGATTTTTGAAAGTTTATGGGT
1 AAAAATAGAATTTTTGAAAGTTT-GGGGT
*
14451 AAAAATAGAATTTTTGAAAGTTTCGAGGTT
1 AAAAATAGAATTTTTGAAAGTTT-G-GGGT
* * *
14481 AAAAATGGGATTTTTGGAAGTTTGAGGGT
1 AAAAATAGAATTTTTGAAAGTTTG-GGGT
*
14510 AAAAAAAAAAAAAGAATTTTTGAAAGTTTTGGGGTT
1 ------AAAAATAGAATTTTTGAAAG-TTTGGGG-T
* *
14546 AAAAA-AGTGATTTTTGGAAGTTTGGGGT
1 AAAAATAG-AATTTTTGAAAGTTTGGGGT
14574 AAAAATAGAATTTTTTGAAAGTTTTGGGGTT
1 AAAAATAGAA-TTTTTGAAAG-TTTGGGG-T
* *
14605 AAAAA-ATGTGATTTTTGGAAGTTTGGGGGT
1 AAAAATA-G-AATTTTTGAAAGTTT-GGGGT
*
14635 AAAAATAGAATTTTTGAAAGTTTCGAGGTT
1 AAAAATAGAATTTTTGAAAGTTT-G-GGGT
*
14665 AAAAAT-GAGATTTTTGGAAGTTTGGGGGT
1 AAAAATAGA-ATTTTTGAAAGTTT-GGGGT
* *
14694 AAAATTAGAATTTTAGAAAGTTTCGGGGTT
1 AAAAATAGAATTTTTGAAAGTTT-GGGG-T
* * *
14724 AAAAATGGGATTTTTGGAAGTTTGGGGAT
1 AAAAATAGAATTTTTGAAAGTTTGGGG-T
* * * *
14753 GAAAGTATAATTTTTGAAAGTTCGGGGGT
1 AAAAATAGAATTTTTGAAAGTT-TGGGGT
14782 AAAAATAGAATTTTTGAAAGTTTTGGGGTT
1 AAAAATAGAATTTTTGAAAG-TTTGGGG-T
14812 AAAAAT-GAGATTTTTGAA
1 AAAAATAGA-ATTTTTGAA
14830 CAATTTAGGG
Statistics
Matches: 306, Mismatches: 47, Indels: 51
0.76 0.12 0.13
Matches are distributed among these distances:
28 7 0.02
29 131 0.43
30 122 0.40
31 21 0.07
32 1 0.00
35 19 0.06
36 5 0.02
ACGTcount: A:0.36, C:0.01, G:0.27, T:0.36
Consensus pattern (28 bp):
AAAAATAGAATTTTTGAAAGTTTGGGGT
Found at i:14486 original size:59 final size:58
Alignment explanation
Indices: 14413--14829 Score: 478
Period size: 59 Copynumber: 6.9 Consensus size: 58
14403 TTTTGGAAAA
* * * *
14413 TTCGGAGTAAAAAATGGGATTTTTGAAAGTTTATGGGTAAAAATAGAATTTTTGAAAGT
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGTTT-GGGGTAAAAATAGAATTTTTGAAAGT
* *
14472 TTCGAGGTTAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAAAAAAAAAAAGAATTTTTGAAAGT
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGTTTG-GGGT------AAAAATAGAATTTTTGAAAGT
* * *
14537 TTTGGGGTTAAAAAAGTGATTTTTGGAAGTTTGGGGTAAAAATAGAATTTTTTGAAAGT
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGTAAAAATAGAA-TTTTTGAAAGT
* *
14596 TTTGGGGTTAAAAAATGTGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTGAAAGT
1 TTCGGGGTT-AAAAATGGGATTTTTGGAAGTTT-GGGGTAAAAATAGAATTTTTGAAAGT
* * * *
14656 TTCGAGGTTAAAAATGAGATTTTTGGAAGTTTGGGGGTAAAATTAGAATTTTAGAAAGT
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGTTT-GGGGTAAAAATAGAATTTTTGAAAGT
* * *
14715 TTCGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGATGAAAGTATAATTTTTGAAAG-
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGG-TAAAAATAGAATTTTTGAAAGT
* * * *
14773 TTCGGGGGTAAAAATAGAATTTTTGAAAGTTTTGGGGTTAAAAAT-GAGATTTTTGAA
1 TTCGGGGTTAAAAATGGGATTTTTGGAAG-TTTGGGG-TAAAAATAGA-ATTTTTGAA
14830 CAATTTAGGG
Statistics
Matches: 314, Mismatches: 31, Indels: 26
0.85 0.08 0.07
Matches are distributed among these distances:
58 39 0.12
59 167 0.53
60 40 0.13
61 15 0.05
64 4 0.01
65 49 0.16
ACGTcount: A:0.36, C:0.01, G:0.27, T:0.36
Consensus pattern (58 bp):
TTCGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGTAAAAATAGAATTTTTGAAAGT
Found at i:15234 original size:17 final size:18
Alignment explanation
Indices: 15212--15245 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
15202 GAATCCTAGG
15212 TCGGGTCGGA-TCGGATT
1 TCGGGTCGGATTCGGATT
15229 TCGGGTCGGATTCGGAT
1 TCGGGTCGGATTCGGAT
15246 AATAGCTCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.12, C:0.18, G:0.41, T:0.29
Consensus pattern (18 bp):
TCGGGTCGGATTCGGATT
Found at i:15718 original size:14 final size:15
Alignment explanation
Indices: 15699--15728 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15689 AAAAAATCGT
15699 TTATTCG-ATTTTGA
1 TTATTCGTATTTTGA
15713 TTATTCGTATTTTGA
1 TTATTCGTATTTTGA
15728 T
1 T
15729 CTCCTCCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.60
Consensus pattern (15 bp):
TTATTCGTATTTTGA
Found at i:15935 original size:9 final size:9
Alignment explanation
Indices: 15904--15951 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
15894 AATATTATAT
*
15904 TTATTATTA
1 TTATTGTTA
* *
15913 ATATTATTA
1 TTATTGTTA
*
15922 CTATTGTTA
1 TTATTGTTA
15931 TTATTGTTA
1 TTATTGTTA
*
15940 TTAATGTTA
1 TTATTGTTA
15949 TTA
1 TTA
15952 AAGTCATTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.60
Consensus pattern (9 bp):
TTATTGTTA
Found at i:16692 original size:17 final size:15
Alignment explanation
Indices: 16651--16696 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
16641 AATAAACTTT
*
16651 AAATTTAAATTTAAT
1 AAATTTAAATTTAAC
*
16666 AAACTTAAATTTCAACC
1 AAATTTAAATTT-AA-C
16683 AAATTTAAATTTAA
1 AAATTTAAATTTAA
16697 AATAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 11 0.42
16 4 0.15
17 11 0.42
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATTTAAATTTAAC
Found at i:18586 original size:19 final size:20
Alignment explanation
Indices: 18542--18586 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
18532 AATTTTAAAT
18542 TTTAAAAATTCAAAATAATA
1 TTTAAAAATTCAAAATAATA
* *
18562 TATAAAAATTTAAAAT-ATA
1 TTTAAAAATTCAAAATAATA
18581 TTTAAA
1 TTTAAA
18587 TTTCAAGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTAAAAATTCAAAATAATA
Found at i:18797 original size:19 final size:19
Alignment explanation
Indices: 18731--18810 Score: 51
Period size: 19 Copynumber: 4.2 Consensus size: 19
18721 AAATTTTATT
*
18731 TTTATATTTTATATTTTTC
1 TTTATATTTTATATATTTC
18750 TAGATTATA-TTTAT-T-TTTC
1 T---TTATATTTTATATATTTC
** *
18769 TGAATGTTTTATATATTTC
1 TTTATATTTTATATATTTC
*
18788 TTTATATTTT-TCATATTTT
1 TTTATATTTTAT-ATATTTC
18807 TTTA
1 TTTA
18811 GTGTGTATAA
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
16 2 0.04
17 5 0.11
18 2 0.04
19 27 0.57
20 1 0.02
21 5 0.11
22 5 0.11
ACGTcount: A:0.24, C:0.05, G:0.04, T:0.68
Consensus pattern (19 bp):
TTTATATTTTATATATTTC
Found at i:21719 original size:15 final size:12
Alignment explanation
Indices: 21690--21729 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
21680 CAATTCGGTC
21690 TTTTTTTTTTCT
1 TTTTTTTTTTCT
*
21702 TTTTTTTTTTGCAG
1 TTTTTTTTTT-C-T
21716 TTTTTTTTTTCT
1 TTTTTTTTTTCT
21728 TT
1 TT
21730 ATAACATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 12 0.50
13 2 0.08
14 10 0.42
ACGTcount: A:0.03, C:0.07, G:0.05, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTTCT
Found at i:22595 original size:27 final size:29
Alignment explanation
Indices: 22551--22609 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
22541 ATAAATTTAA
* * *
22551 TTTTTAATATTTATATTT-ATTTTTAACT
1 TTTTTAATAATTAAATTTCATTTTCAACT
*
22579 TTTTTAA-AATTAAATTTCGTTTTCAACT
1 TTTTTAATAATTAAATTTCATTTTCAACT
22607 TTT
1 TTT
22610 AAAAAACAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.63
Consensus pattern (29 bp):
TTTTTAATAATTAAATTTCATTTTCAACT
Found at i:22702 original size:17 final size:19
Alignment explanation
Indices: 22680--22720 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
22670 AATTTATTTT
*
22680 TATTTTTAT-TTTTAAAA-
1 TATTTTTATAATTTAAAAC
22697 TATTTTTATAATTTAAAAC
1 TATTTTTATAATTTAAAAC
22716 TATTT
1 TATTT
22721 GTTGTTGTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
18 7 0.33
19 5 0.24
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTTTATAATTTAAAAC
Found at i:25993 original size:30 final size:28
Alignment explanation
Indices: 25946--26200 Score: 264
Period size: 30 Copynumber: 8.8 Consensus size: 28
25936 TAGGACATTC
* *
25946 GGGGT-AAAAGGGTAATTTTTGAAAGTTT
1 GGGGTAAAAATGG-AATTTTTGGAAGTTT
25974 CGGGGTTAAAAATGGAATTTTTGGAAGTTT
1 -GGGG-TAAAAATGGAATTTTTGGAAGTTT
*
26004 GAGGGTAAAAATGTAATTTTTGGAAGTTTT
1 G-GGGTAAAAATGGAATTTTTGGAAG-TTT
* *
26034 GAGGTCAAAAATGGAATTTTTGGAAGCTT
1 GGGGT-AAAAATGGAATTTTTGGAAGTTT
* *
26063 GAGAGTAAAAATGTAATTTTTGGAAGTTTT
1 G-GGGTAAAAATGGAATTTTTGGAAG-TTT
26093 GGGGTCAAAAATGGAATTTTTGGAAGTTT
1 GGGGT-AAAAATGGAATTTTTGGAAGTTT
*
26122 GGGGGT--AAATGTAATTTTTGGAAGTTTT
1 -GGGGTAAAAATGGAATTTTTGGAAG-TTT
* *
26150 GGGGGTCAAAATGGAATTTTTGGAAGTTCG
1 -GGGGTAAAAATGGAATTTTTGGAAGTT-T
* *
26180 GGGGTAAGAATGTAATTTTTG
1 GGGGTAAAAATGGAATTTTTG
26201 AATAGTTTAG
Statistics
Matches: 195, Mismatches: 18, Indels: 26
0.82 0.08 0.11
Matches are distributed among these distances:
27 17 0.09
28 9 0.05
29 76 0.39
30 87 0.45
31 6 0.03
ACGTcount: A:0.31, C:0.02, G:0.30, T:0.36
Consensus pattern (28 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTT
Found at i:26020 original size:59 final size:59
Alignment explanation
Indices: 25947--26200 Score: 370
Period size: 59 Copynumber: 4.3 Consensus size: 59
25937 AGGACATTCG
** * * *
25947 GGGTAAAAGGGTAATTTTTGAAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAGTTTGA
1 GGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTGA
* *
26006 GGGTAAAAATGTAATTTTTGGAAGTTTTGAGGTCAAAAATGGAATTTTTGGAAGCTTGA
1 GGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTGA
* *
26065 GAGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTGG
1 GGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTGA
* *
26124 GGGT--AAATGTAATTTTTGGAAGTTTTGGGGGTC-AAAATGGAATTTTTGGAAGTTCGG
1 GGGTAAAAATGTAATTTTTGGAAGTTTT-GGGGTCAAAAATGGAATTTTTGGAAGTTTGA
*
26181 GGGTAAGAATGTAATTTTTG
1 GGGTAAAAATGTAATTTTTG
26201 AATAGTTTAG
Statistics
Matches: 178, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
57 49 0.28
58 6 0.03
59 123 0.69
ACGTcount: A:0.31, C:0.02, G:0.30, T:0.37
Consensus pattern (59 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTGA
Found at i:27234 original size:21 final size:21
Alignment explanation
Indices: 27204--27266 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
27194 TTTCTTTTAT
27204 TATTATTAATGTTTTTATTAA
1 TATTATTAATGTTTTTATTAA
* *
27225 TATTAATAATATTTTTATTAA
1 TATTATTAATGTTTTTATTAA
*
27246 TACTTATTAATGCTATTTATT
1 TA-TTATTAATG-TTTTTATT
27267 GCTAATATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 21 0.60
22 7 0.20
23 7 0.20
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (21 bp):
TATTATTAATGTTTTTATTAA
Found at i:27253 original size:25 final size:25
Alignment explanation
Indices: 27225--27298 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 25
27215 TTTTTATTAA
27225 TATTAATAATATTTTTATTAATACT
1 TATTAATAATATTTTTATTAATACT
** ** *
27250 TATTAATGCTATTTATTGCTAATATT
1 TATTAATAATATTT-TTATTAATACT
* * *
27276 TATTATTAATGTTATTATTAATA
1 TATTAATAATATTTTTATTAATA
27299 ACAATATTTA
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
25 19 0.53
26 17 0.47
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (25 bp):
TATTAATAATATTTTTATTAATACT
Done.