Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011507.1 Kokia drynarioides strain JFW-HI SEQ_126492, 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: 43344
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 74 characters in sequence are not A, C, G, or T
Found at i:1087 original size:17 final size:17
Alignment explanation
Indices: 1036--1109 Score: 58
Period size: 17 Copynumber: 4.3 Consensus size: 17
1026 GTACTTGGAC
*
1036 ATTTAAAATAAATTTTAA
1 ATTTAAAATAAA-CTTAA
* ** *
1054 ATTTCAACCAAATTTAA
1 ATTTAAAATAAACTTAA
*
1071 ATTTAGAATAAACTTAA
1 ATTTAAAATAAACTTAA
* *
1088 TTTTAAAATAAATTTAA
1 ATTTAAAATAAACTTAA
*
1105 GTTTA
1 ATTTA
1110 TTGGGCCCAG
Statistics
Matches: 44, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
17 35 0.80
18 9 0.20
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (17 bp):
ATTTAAAATAAACTTAA
Found at i:3864 original size:24 final size:24
Alignment explanation
Indices: 3833--3883 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3823 CCAAACAAAA
* *
3833 TTAGCTCTCACGAGCTCAAGATGG
1 TTAGCTCTCACGAGCCCAAAATGG
* *
3857 TTAGCTCTTATGAGCCCAAAATGG
1 TTAGCTCTCACGAGCCCAAAATGG
3881 TTA
1 TTA
3884 ACCAATATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
TTAGCTCTCACGAGCCCAAAATGG
Found at i:8466 original size:43 final size:43
Alignment explanation
Indices: 8436--8626 Score: 238
Period size: 43 Copynumber: 4.4 Consensus size: 43
8426 GTAAAAACGT
* *
8436 CGCTAAAGGCCGTGTTCTTTAGCAGTGTTTGTGGGGAAAGCGC
1 CGCTAAAGACCGTGTTCTTTAGCAGAGTTTGTGGGGAAAGCGC
* ** * *
8479 CGCTAAAGACAGTGTTCTTTAGTGGCGTTTGTGGGGAAAGTGC
1 CGCTAAAGACCGTGTTCTTTAGCAGAGTTTGTGGGGAAAGCGC
*
8522 CGCTAAAGATCGTGTTCTTTAGCAGAGTTTGTGGGGAAAGCGC
1 CGCTAAAGACCGTGTTCTTTAGCAGAGTTTGTGGGGAAAGCGC
* * * ** * *
8565 CACTAAAGACCGTATTTTTTAGTGGCGTTTGTGGCGAAAGCGC
1 CGCTAAAGACCGTGTTCTTTAGCAGAGTTTGTGGGGAAAGCGC
*
8608 CGCTAAAGACCCTGTTCTT
1 CGCTAAAGACCGTGTTCTT
8627 GTAAGCACCG
Statistics
Matches: 124, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 124 1.00
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.29
Consensus pattern (43 bp):
CGCTAAAGACCGTGTTCTTTAGCAGAGTTTGTGGGGAAAGCGC
Found at i:8555 original size:86 final size:86
Alignment explanation
Indices: 8410--8626 Score: 308
Period size: 86 Copynumber: 2.5 Consensus size: 86
8400 AATCTGTTAA
** * * * *
8410 TTTAGTGGCGTTTGTGGTAAAAACGTCGCTAAAGGCCGTGTTCTTTAGCAGTGTTTGTGGGGAAA
1 TTTAGTGGCGTTTGTGGCGAAAGCGCCGCTAAAGACCGTGTTCTTTAGCAGAGTTTGTGGGGAAA
* *
8475 GCGCCGCTAAAGACAGTGTTC
66 GCGCCACTAAAGACAGTATTC
* * *
8496 TTTAGTGGCGTTTGTGGGGAAAGTGCCGCTAAAGATCGTGTTCTTTAGCAGAGTTTGTGGGGAAA
1 TTTAGTGGCGTTTGTGGCGAAAGCGCCGCTAAAGACCGTGTTCTTTAGCAGAGTTTGTGGGGAAA
* *
8561 GCGCCACTAAAGACCGTATTT
66 GCGCCACTAAAGACAGTATTC
*
8582 TTTAGTGGCGTTTGTGGCGAAAGCGCCGCTAAAGACCCTGTTCTT
1 TTTAGTGGCGTTTGTGGCGAAAGCGCCGCTAAAGACCGTGTTCTT
8627 GTAAGCACCG
Statistics
Matches: 115, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
86 115 1.00
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (86 bp):
TTTAGTGGCGTTTGTGGCGAAAGCGCCGCTAAAGACCGTGTTCTTTAGCAGAGTTTGTGGGGAAA
GCGCCACTAAAGACAGTATTC
Found at i:18359 original size:13 final size:13
Alignment explanation
Indices: 18341--18386 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
18331 AACCCTAAAC
18341 CCTAAAAACAAAA
1 CCTAAAAACAAAA
* *
18354 CCTAAAAACCTCAAC
1 CCTAAAAA-C-AAAA
18369 CCTAAAAACAAAA
1 CCTAAAAACAAAA
18382 CCTAA
1 CCTAA
18387 TAACCTCAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 15 0.56
14 2 0.07
15 10 0.37
ACGTcount: A:0.59, C:0.30, G:0.00, T:0.11
Consensus pattern (13 bp):
CCTAAAAACAAAA
Found at i:18369 original size:28 final size:28
Alignment explanation
Indices: 18338--18404 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
18328 TCCAACCCTA
18338 AACCCTAAAAACAAAACCTAAAAACCTC
1 AACCCTAAAAACAAAACCTAAAAACCTC
*
18366 AACCCTAAAAACAAAACCTAATAACCTC
1 AACCCTAAAAACAAAACCTAAAAACCTC
18394 AACCCTAAAAA
1 AACCCTAAAAA
18405 ATAAAAGGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.57, C:0.31, G:0.00, T:0.12
Consensus pattern (28 bp):
AACCCTAAAAACAAAACCTAAAAACCTC
Found at i:18374 original size:15 final size:15
Alignment explanation
Indices: 18354--18404 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
18344 AAAAACAAAA
18354 CCTAAAAACCTCAAC
1 CCTAAAAACCTCAAC
* *
18369 CCTAAAAA-C-AAAA
1 CCTAAAAACCTCAAC
*
18382 CCTAATAACCTCAAC
1 CCTAAAAACCTCAAC
18397 CCTAAAAA
1 CCTAAAAA
18405 ATAAAAGGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
13 9 0.32
14 2 0.07
15 17 0.61
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.14
Consensus pattern (15 bp):
CCTAAAAACCTCAAC
Found at i:19147 original size:23 final size:21
Alignment explanation
Indices: 19110--19192 Score: 69
Period size: 23 Copynumber: 3.7 Consensus size: 21
19100 ATAACACATA
19110 AATAACATAAATATAAAAAAAAT
1 AATAA-AT-AATATAAAAAAAAT
*
19133 AATAAATAATTTATAATAAAATAT
1 AATAAATAA--TATAA-AAAAAAT
* *
19157 AA-AAATAATATACATAAAAT
1 AATAAATAATATAAAAAAAAT
19177 AATAAACTATATATAA
1 AATAAA-TA-ATATAA
19193 CGTAAAATTG
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 7 0.14
21 9 0.18
22 4 0.08
23 21 0.43
24 8 0.16
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (21 bp):
AATAAATAATATAAAAAAAAT
Found at i:19179 original size:30 final size:31
Alignment explanation
Indices: 19100--19187 Score: 81
Period size: 33 Copynumber: 2.8 Consensus size: 31
19090 ATACCATTTC
* *
19100 ATAACACAT-AAATAACATAAATATAAAAAAA
1 ATAATACATAAAATAATA-AAATATAAAAAAA
* * *
19131 ATAATAAATAATTTATAATAAAATATAAAAATA
1 ATAATACATAA--AATAATAAAATATAAAAAAA
*
19164 AT-ATACATAAAATAATAAACTATA
1 ATAATACATAAAATAATAAAATATA
19188 TATAACGTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
30 12 0.26
31 7 0.15
32 8 0.17
33 14 0.30
34 5 0.11
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (31 bp):
ATAATACATAAAATAATAAAATATAAAAAAA
Found at i:19976 original size:13 final size:13
Alignment explanation
Indices: 19960--19984 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19950 AAATTAATTA
19960 ATAAAATATTATG
1 ATAAAATATTATG
19973 ATAAAATATTAT
1 ATAAAATATTAT
19985 AATATTCATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
ATAAAATATTATG
Found at i:30670 original size:22 final size:24
Alignment explanation
Indices: 30626--30671 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
30616 CAAAGTATAT
*
30626 TAATAATCCAAAATCAAATTAATAG
1 TAATAAT-CAAAATCAAAATAATAG
30651 TAATAAT-AAAAT-AAAATAATA
1 TAATAATCAAAATCAAAATAATA
30672 TAAATTTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 5 0.25
25 7 0.35
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (24 bp):
TAATAATCAAAATCAAAATAATAG
Found at i:31715 original size:7 final size:7
Alignment explanation
Indices: 31703--31741 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
31693 TTTGAAAAAA
31703 GTCAACG
1 GTCAACG
31710 GTCAACG
1 GTCAACG
*
31717 GTCAA-A
1 GTCAACG
31723 GTCAACG
1 GTCAACG
31730 GTCAACG
1 GTCAACG
*
31737 ATCAA
1 GTCAA
31742 ATTCAACAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:31725 original size:20 final size:20
Alignment explanation
Indices: 31700--31753 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
31690 TTTTTTGAAA
*
31700 AAAGTCAACGGTCAACGGTC
1 AAAGTCAACGGTCAACGATC
31720 AAAGTCAACGGTCAACGATC
1 AAAGTCAACGGTCAACGATC
* *
31740 AAATTCAACAGTCA
1 AAAGTCAACGGTCA
31754 GTCAAAGATC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.17
Consensus pattern (20 bp):
AAAGTCAACGGTCAACGATC
Found at i:31728 original size:13 final size:13
Alignment explanation
Indices: 31710--31734 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31700 AAAGTCAACG
31710 GTCAACGGTCAAA
1 GTCAACGGTCAAA
31723 GTCAACGGTCAA
1 GTCAACGGTCAA
31735 CGATCAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (13 bp):
GTCAACGGTCAAA
Found at i:31858 original size:23 final size:23
Alignment explanation
Indices: 31832--31888 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 23
31822 TGGGTTTGGG
31832 TTAAAGGGTTATTGGATTTAA-TT
1 TTAAAGGGTT-TTGGATTTAAGTT
* *
31855 TTAAA-GGATTTGGGTTTAAGTT
1 TTAAAGGGTTTTGGATTTAAGTT
31877 TTAAAAGGGTTT
1 TT-AAAGGGTTT
31889 GGGCTTAGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 9 0.32
22 7 0.25
23 8 0.29
24 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.46
Consensus pattern (23 bp):
TTAAAGGGTTTTGGATTTAAGTT
Found at i:31889 original size:23 final size:21
Alignment explanation
Indices: 31832--31891 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 21
31822 TGGGTTTGGG
*
31832 TTAAAGGGTTATTGGATTTAATT
1 TTAAAGGG-T-TTGGGTTTAATT
*
31855 TTAAAGGATTTGGGTTTAAGTT
1 TTAAAGGGTTTGGGTTTAA-TT
31877 TTAAAAGGGTTTGGG
1 TT-AAAGGGTTTGGG
31892 CTTAGGCACA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 9 0.28
22 5 0.16
23 18 0.56
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.43
Consensus pattern (21 bp):
TTAAAGGGTTTGGGTTTAATT
Found at i:32338 original size:3 final size:3
Alignment explanation
Indices: 32332--32361 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
32322 AGAAAGAGGG
32332 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
32362 GGAGAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:36382 original size:21 final size:20
Alignment explanation
Indices: 36349--36396 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
36339 ACATGAGTTA
* *
36349 AATTAAATATAAATAGGTTT
1 AATTAAATATAAAAAGGGTT
*
36369 AATTAAGATTTAAAAAGGGTT
1 AATTAA-ATATAAAAAGGGTT
36390 AATTAAA
1 AATTAAA
36397 GCTTAATGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.35
Consensus pattern (20 bp):
AATTAAATATAAAAAGGGTT
Found at i:37932 original size:26 final size:26
Alignment explanation
Indices: 37903--37955 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
37893 AGGAAGTATG
37903 ATAGGTTTTTAAAACTATGGAATGCA
1 ATAGGTTTTTAAAACTATGGAATGCA
*
37929 ATAGGTTTTTGAAACTATGGAATGCA
1 ATAGGTTTTTAAAACTATGGAATGCA
37955 A
1 A
37956 CAACCTTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.34
Consensus pattern (26 bp):
ATAGGTTTTTAAAACTATGGAATGCA
Found at i:40680 original size:21 final size:21
Alignment explanation
Indices: 40656--40701 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
40646 GGGTGTTACA
* * *
40656 AGAAGTATGACTTGTTTCGAT
1 AGAAGGATCACTTGTGTCGAT
*
40677 AGAAGGATCTCTTGTGTCGAT
1 AGAAGGATCACTTGTGTCGAT
40698 AGAA
1 AGAA
40702 CTTTCATTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (21 bp):
AGAAGGATCACTTGTGTCGAT
Done.