Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006472.1 Kokia drynarioides strain JFW-HI SEQ_121055, 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: 49922
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:7668 original size:18 final size:18
Alignment explanation
Indices: 7645--7682 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
7635 TAATATAGTT
*
7645 TTATTCG-GTTCATTCGAA
1 TTATTCGAGTT-AATCGAA
7663 TTATTCGAGTTAATCGAA
1 TTATTCGAGTTAATCGAA
7681 TT
1 TT
7683 TGAAAATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (18 bp):
TTATTCGAGTTAATCGAA
Found at i:28959 original size:30 final size:30
Alignment explanation
Indices: 28901--29188 Score: 238
Period size: 30 Copynumber: 9.7 Consensus size: 30
28891 AGAGGGTCGA
*
28901 AAAATG-AAGTTTTGAAGAA-TTT-AGGGTT
1 AAAATGTAATTTTTG-AGAAGTTTGAGGGTT
28929 AAAATGTAATTTTTGAGAAGTTTGAGGGTT
1 AAAATGTAATTTTTGAGAAGTTTGAGGGTT
*
28959 AAAATGTGAA-TTTGGAGAAGTTTGAGGGTT
1 AAAATGT-AATTTTTGAGAAGTTTGAGGGTT
* *
28989 AAAATGTGA-TTTTAAGAAGTTTGAGGGTT
1 AAAATGTAATTTTTGAGAAGTTTGAGGGTT
* *
29018 AAAATCTAATTTTT-AGATAGTTT-AGGGGTC
1 AAAATGTAATTTTTGAGA-AGTTTGA-GGGTT
* * *
29048 AAAGTGTGATTTTTAAGAAGTTT-AGGGGTT
1 AAAATGTAATTTTTGAGAAGTTTGA-GGGTT
* **
29078 AAAATGTGATTTTTG-GAAAGTACGAGGGTT
1 AAAATGTAATTTTTGAG-AAGTTTGAGGGTT
* * * *
29108 AAAATGTGATTTTTGAGAAGTTCGAGGATC
1 AAAATGTAATTTTTGAGAAGTTTGAGGGTT
* * *
29138 AAAATG-AGATTTTTAAAAAATTTGA-GGTT
1 AAAATGTA-ATTTTTGAGAAGTTTGAGGGTT
* * *
29167 AAAATGTGATTTTGGAAAAGTT
1 AAAATGTAATTTTTGAGAAGTT
29189 CGGGAACCTC
Statistics
Matches: 217, Mismatches: 30, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
28 10 0.05
29 60 0.28
30 140 0.65
31 7 0.03
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTTGAGAAGTTTGAGGGTT
Found at i:29021 original size:89 final size:89
Alignment explanation
Indices: 28910--29179 Score: 309
Period size: 89 Copynumber: 3.0 Consensus size: 89
28900 AAAAATGAAG
* * *
28910 TTTTGAAGAA-TTT-AGGGTTAAAATGTAATTTTTGAGAAGTTTGAGGGTTAAAATGTGAATTTG
1 TTTT-AAGAAGTTTGAGGGTTAAAATGTAATTTTTGAGAAGTTTGAGGGTCAAAATGTGATTTTT
*
28973 GAGAAGTTTGAGGGTTAAAATGTGA
65 AAGAAGTTTGAGGGTTAAAATGTGA
* *
28998 TTTTAAGAAGTTTGAGGGTTAAAATCTAATTTTT-AGATAGTTT-AGGGGTCAAAGTGTGATTTT
1 TTTTAAGAAGTTTGAGGGTTAAAATGTAATTTTTGAGA-AGTTTGA-GGGTCAAAATGTGATTTT
29061 TAAGAAGTTT-AGGGGTTAAAATGTGA
64 TAAGAAGTTTGA-GGGTTAAAATGTGA
** ** * * * *
29087 TTTTTGGAAAGTACGAGGGTTAAAATGTGATTTTTGAGAAGTTCGAGGATCAAAATGAGATTTTT
1 TTTTAAG-AAGTTTGAGGGTTAAAATGTAATTTTTGAGAAGTTTGAGGGTCAAAATGTGATTTTT
* *
29152 AAAAAATTTGA-GGTTAAAATGTGA
65 AAGAAGTTTGAGGGTTAAAATGTGA
29176 TTTT
1 TTTT
29180 GGAAAAGTTC
Statistics
Matches: 155, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
87 5 0.03
88 12 0.08
89 83 0.54
90 50 0.32
91 5 0.03
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (89 bp):
TTTTAAGAAGTTTGAGGGTTAAAATGTAATTTTTGAGAAGTTTGAGGGTCAAAATGTGATTTTTA
AGAAGTTTGAGGGTTAAAATGTGA
Found at i:30757 original size:21 final size:22
Alignment explanation
Indices: 30717--30759 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
30707 GGGGTATGGG
30717 TTTTAGTGTTTGTAATTTGGAC
1 TTTTAGTGTTTGTAATTTGGAC
30739 TTTTAGAT-TTTGT-ATTTGGAC
1 TTTTAG-TGTTTGTAATTTGGAC
30760 ATTCTGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
22 11 0.55
23 1 0.05
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.56
Consensus pattern (22 bp):
TTTTAGTGTTTGTAATTTGGAC
Found at i:30805 original size:17 final size:17
Alignment explanation
Indices: 30773--30828 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
30763 CTGTTTTTTT
30773 TTTAAA-TTTAAATAAA
1 TTTAAATTTTAAATAAA
*
30789 TTTAAATTTTGAATAAA
1 TTTAAATTTTAAATAAA
*
30806 TTTAAATTTAAAATAAA
1 TTTAAATTTTAAATAAA
*
30823 GTTAAA
1 TTTAAA
30829 CTTAAAATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
16 6 0.17
17 29 0.83
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (17 bp):
TTTAAATTTTAAATAAA
Found at i:30833 original size:17 final size:17
Alignment explanation
Indices: 30800--30836 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
30790 TTAAATTTTG
* *
30800 AATAAATTTAAATTTAA
1 AATAAAGTTAAACTTAA
30817 AATAAAGTTAAACTTAA
1 AATAAAGTTAAACTTAA
30834 AAT
1 AAT
30837 TGGGTTCGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (17 bp):
AATAAAGTTAAACTTAA
Found at i:31652 original size:13 final size:13
Alignment explanation
Indices: 31634--31661 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31624 AAAAATCTAG
31634 AGAAATGATGAAA
1 AGAAATGATGAAA
31647 AGAAATGATGAAA
1 AGAAATGATGAAA
31660 AG
1 AG
31662 CTATAAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.25, T:0.14
Consensus pattern (13 bp):
AGAAATGATGAAA
Found at i:34590 original size:48 final size:48
Alignment explanation
Indices: 34536--34771 Score: 143
Period size: 48 Copynumber: 5.3 Consensus size: 48
34526 TCTTCCTCTT
34536 TGTATCTCATCAGGAAGATGACCACCTCATTGATTTAATCCATTTCTC
1 TGTATCTCATCAGGAAGATGACCACCTCATTGATTTAATCCATTTCTC
* * * * * *
34584 TGTATCTCATCAAGAAGATG--GA--T-TTTGGTCT-A--C--TTCTT
1 TGTATCTCATCAGGAAGATGACCACCTCATTGATTTAATCCATTTCTC
* * *
34622 TATATCTCATCAGGAAGTTGACCGCCTCATTGATTTAATCCATTTCTC
1 TGTATCTCATCAGGAAGATGACCACCTCATTGATTTAATCCATTTCTC
* ** * ** * *
34670 TTTATCAAATCAGGAA-A--ACGA----A-T--TTTGGTCTACTTCTC
1 TGTATCTCATCAGGAAGATGACCACCTCATTGATTTAATCCATTTCTC
* **
34708 TGTATCTCATTAGGAAGATGACTGCCTCATTGATTTAATCCATTTCTC
1 TGTATCTCATCAGGAAGATGACCACCTCATTGATTTAATCCATTTCTC
*
34756 TATATCTCATCAGGAA
1 TGTATCTCATCAGGAA
34772 AATGGGGTTT
Statistics
Matches: 131, Mismatches: 37, Indels: 40
0.63 0.18 0.19
Matches are distributed among these distances:
38 44 0.34
39 1 0.01
40 2 0.02
41 3 0.02
42 2 0.02
43 10 0.08
44 2 0.02
45 3 0.02
46 3 0.02
48 61 0.47
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (48 bp):
TGTATCTCATCAGGAAGATGACCACCTCATTGATTTAATCCATTTCTC
Found at i:34601 original size:123 final size:123
Alignment explanation
Indices: 34329--34602 Score: 422
Period size: 123 Copynumber: 2.2 Consensus size: 123
34319 TTGCTTTGAC
* * *
34329 CCACTTCTCTGTATCTCATCAGGAAAATGGGGTTGGAAGTTTCACTCACATTGAGCTTTGCTTCA
1 CCACTTCTCTGTATCTCATCAGGAAGATAGGGTTGAAAGTTTCACTCACATTGAGCTTTGCTTCA
* *
34394 TTGAATTGGTCTTCTTCTCTGTATCTCATCAGGAAGATAACCGCATCATTGATTTAAT
66 TTGAATTGGTCTTCCTCTCTGTATCTCATCAGGAAGATAACCACATCATTGATTTAAT
* * * *
34452 CCACTTCCCTGTATTTCTTTAGGAAGATAGGGTTGAAAGTTTCACTCACATTGAGCTTTGCTTCA
1 CCACTTCTCTGTATCTCATCAGGAAGATAGGGTTGAAAGTTTCACTCACATTGAGCTTTGCTTCA
* * *
34517 TTGAATTGGTCTTCCTCTTTGTATCTCATCAGGAAGATGACCACCTCATTGATTTAAT
66 TTGAATTGGTCTTCCTCTCTGTATCTCATCAGGAAGATAACCACATCATTGATTTAAT
* *
34575 CCATTTCTCTGTATCTCATCAAGAAGAT
1 CCACTTCTCTGTATCTCATCAGGAAGAT
34603 GGATTTTGGT
Statistics
Matches: 133, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
123 133 1.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (123 bp):
CCACTTCTCTGTATCTCATCAGGAAGATAGGGTTGAAAGTTTCACTCACATTGAGCTTTGCTTCA
TTGAATTGGTCTTCCTCTCTGTATCTCATCAGGAAGATAACCACATCATTGATTTAAT
Found at i:34667 original size:86 final size:86
Alignment explanation
Indices: 34522--34776 Score: 366
Period size: 86 Copynumber: 3.0 Consensus size: 86
34512 CTTCATTGAA
* * * *
34522 TTGGTCTTCCTCTTTGTATCTCATCAGGAAGATGACCACCTCATTGATTTAATCCATTTCTCTGT
1 TTGGTCTACTTCTTTGTATCTCATCAGGAAGATGACCGCCTCATTGATTTAATCCATTTCTCTAT
* *
34587 ATCTCATCAAGAAGATGGATT
66 ATCTCATCAGGAAAATGGATT
* * *
34608 TTGGTCTACTTCTTTATATCTCATCAGGAAGTTGACCGCCTCATTGATTTAATCCATTTCTCTTT
1 TTGGTCTACTTCTTTGTATCTCATCAGGAAGATGACCGCCTCATTGATTTAATCCATTTCTCTAT
** * *
34673 ATCAAATCAGGAAAACGAATT
66 ATCTCATCAGGAAAATGGATT
* * *
34694 TTGGTCTACTTCTCTGTATCTCATTAGGAAGATGACTGCCTCATTGATTTAATCCATTTCTCTAT
1 TTGGTCTACTTCTTTGTATCTCATCAGGAAGATGACCGCCTCATTGATTTAATCCATTTCTCTAT
34759 ATCTCATCAGGAAAATGG
66 ATCTCATCAGGAAAATGG
34777 GGTTTTGAAA
Statistics
Matches: 147, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
86 147 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (86 bp):
TTGGTCTACTTCTTTGTATCTCATCAGGAAGATGACCGCCTCATTGATTTAATCCATTTCTCTAT
ATCTCATCAGGAAAATGGATT
Found at i:45833 original size:30 final size:30
Alignment explanation
Indices: 45799--46189 Score: 332
Period size: 30 Copynumber: 13.1 Consensus size: 30
45789 CGAAGAGTTA
* * *
45799 AGGGTCAAAATATAATTTTTGAGAAGTTTG
1 AGGGTCAAAATGTGATTTTTGAGAAGTTCG
* * *
45829 AGGGTCAAAATGTGATTTTGGAAAAGTTCA
1 AGGGTCAAAATGTGATTTTTGAGAAGTTCG
*
45859 AGGGTCAAAATGTGATTTTTGAAAAGTTCG
1 AGGGTCAAAATGTGATTTTTGAGAAGTTCG
* * * * *
45889 AAAGGTCAAAAAGTAATTTTTAAGAAGTTCA
1 -AGGGTCAAAATGTGATTTTTGAGAAGTTCG
* * *
45920 AGGGTTAAAATTTAATTTTTG-GAAAGTTCG
1 AGGGTCAAAATGTGATTTTTGAG-AAGTTCG
* * *
45950 AGGGT-TAAATATGATTTTTAAGAAGTTCG
1 AGGGTCAAAATGTGATTTTTGAGAAGTTCG
*
45979 AGGGTCAAAATGTGATTTTTGAGAAGTTTG
1 AGGGTCAAAATGTGATTTTTGAGAAGTTCG
** *
46009 -GGGATCAAAATAAGATTTTTG-GAAAGTTTG
1 AGGG-TCAAAATGTGATTTTTGAG-AAGTTCG
* * *
46039 A-GGTTAAAATGTAATTTTTGAGAAGTT-T
1 AGGGTCAAAATGTGATTTTTGAGAAGTTCG
* * *
46067 AGGAGTCAAAATGTGATTTTGGAAAAGTTTG
1 AGG-GTCAAAATGTGATTTTTGAGAAGTTCG
46098 AGGGTCAAAATGTGATTTTT-AGAAAGTTC-
1 AGGGTCAAAATGTGATTTTTGAG-AAGTTCG
* * * * *
46127 AAGGTAAAAATGTGATTTTGGAAAAGTT-T
1 AGGGTCAAAATGTGATTTTTGAGAAGTTCG
* * *
46156 AGGGGTTAAAACGTTATTTTTGAGAAGTTCG
1 A-GGGTCAAAATGTGATTTTTGAGAAGTTCG
46187 AGG
1 AGG
46190 ACCTCTTGAG
Statistics
Matches: 291, Mismatches: 54, Indels: 32
0.77 0.14 0.08
Matches are distributed among these distances:
28 1 0.00
29 71 0.24
30 191 0.66
31 28 0.10
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (30 bp):
AGGGTCAAAATGTGATTTTTGAGAAGTTCG
Found at i:46006 original size:59 final size:60
Alignment explanation
Indices: 45799--46189 Score: 338
Period size: 59 Copynumber: 6.5 Consensus size: 60
45789 CGAAGAGTTA
* * * *
45799 AGGGTCAAAATATAATTTTTGAGAAGTTTGAGGGTCAAAATGTGATTTTGGAAAAGTTCA
1 AGGGTCAAAATGTAATTTTTGAGAAGTTCGAGGGTCAAAATATGATTTTGGAAAAGTTCG
* * * * * *
45859 AGGGTCAAAATGTGATTTTTGAAAAGTTCGAAAGGTCAAAA-AGTAATTTT-TAAGAAGTTCA
1 AGGGTCAAAATGTAATTTTTGAGAAGTTCG-AGGGTCAAAATA-TGATTTTGGAA-AAGTTCG
* * * *
45920 AGGGTTAAAATTTAATTTTTG-GAAAGTTCGAGGGT-TAAATATGATTTT-TAAGAAGTTCG
1 AGGGTCAAAATGTAATTTTTGAG-AAGTTCGAGGGTCAAAATATGATTTTGGAA-AAGTTCG
* * * *
45979 AGGGTCAAAATGTGATTTTTGAGAAGTTTG-GGGATCAAAATAAGATTTTTGG-AAAGTTTG
1 AGGGTCAAAATGTAATTTTTGAGAAGTTCGAGGG-TCAAAATATGA-TTTTGGAAAAGTTCG
* * * *
46039 A-GGTTAAAATGTAATTTTTGAGAAGTT-TAGGAGTCAAAATGTGATTTTGGAAAAGTTTG
1 AGGGTCAAAATGTAATTTTTGAGAAGTTCGAGG-GTCAAAATATGATTTTGGAAAAGTTCG
* * * * *
46098 AGGGTCAAAATGTGATTTTT-AGAAAGTTC-AAGGTAAAAATGTGATTTTGGAAAAGTT-T
1 AGGGTCAAAATGTAATTTTTGAG-AAGTTCGAGGGTCAAAATATGATTTTGGAAAAGTTCG
* * *
46156 AGGGGTTAAAACGTTATTTTTGAGAAGTTCGAGG
1 A-GGGTCAAAATGTAATTTTTGAGAAGTTCGAGG
46190 ACCTCTTGAG
Statistics
Matches: 274, Mismatches: 38, Indels: 38
0.78 0.11 0.11
Matches are distributed among these distances:
58 10 0.04
59 136 0.50
60 76 0.28
61 52 0.19
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (60 bp):
AGGGTCAAAATGTAATTTTTGAGAAGTTCGAGGGTCAAAATATGATTTTGGAAAAGTTCG
Found at i:46137 original size:89 final size:88
Alignment explanation
Indices: 45794--46189 Score: 352
Period size: 89 Copynumber: 4.4 Consensus size: 88
45784 AGTTTCGAAG
* * *
45794 AGTTAAGGGTCAAAATATAATTTTTGAGAAGTTTGAGGGTCAAAATGTGA-TTTTGGAAAAGTTC
1 AGTTTAGGGTCAAAATGTAATTTTTGAAAAGTTTGAGGGTCAAAATGTGATTTTTGG-AAAGTTC
*
45858 AAGGGTCAAAATGTGATTTTTGAAA
65 AA-GGTAAAAATGTGATTTTTGAAA
* * * ** * * *
45883 AGTTCGAAAGGTCAAAAAGTAATTTTT-AAGAAGTTCAAGGGTTAAAATTTAATTTTTGGAAAGT
1 AGTT--TAGGGTCAAAATGTAATTTTTGAA-AAGTTTGAGGGTCAAAATGTGATTTTTGGAAAGT
* * *
45947 TCGAGGGT-TAAATATGATTTTT-AAGA
63 TC-AAGGTAAAAATGTGATTTTTGAA-A
* * * **
45973 AGTTCGAGGGTCAAAATGTGATTTTTGAGAAGTTTG-GGGATCAAAATAAGATTTTTGGAAAGTT
1 AGTT-TAGGGTCAAAATGTAATTTTTGAAAAGTTTGAGGG-TCAAAATGTGATTTTTGGAAAGTT
** * * *
46037 TGAGGTTAAAATGTAATTTTTGAGA
64 CAAGGTAAAAATGTGATTTTTGAAA
* * *
46062 AGTTTAGGAGTCAAAATGTGATTTTGGAAAAGTTTGAGGGTCAAAATGTGATTTTTAGAAAGTTC
1 AGTTTAGG-GTCAAAATGTAATTTTTGAAAAGTTTGAGGGTCAAAATGTGATTTTTGGAAAGTTC
*
46127 AAGGTAAAAATGTGATTTTGGAAA
65 AAGGTAAAAATGTGATTTTTGAAA
* * * * *
46151 AGTTTAGGGGTTAAAACGTTATTTTTGAGAAGTTCGAGG
1 AGTTTA-GGGTCAAAATGTAATTTTTGAAAAGTTTGAGG
46190 ACCTCTTGAG
Statistics
Matches: 245, Mismatches: 49, Indels: 26
0.77 0.15 0.08
Matches are distributed among these distances:
88 9 0.04
89 159 0.65
90 25 0.10
91 45 0.18
92 7 0.03
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (88 bp):
AGTTTAGGGTCAAAATGTAATTTTTGAAAAGTTTGAGGGTCAAAATGTGATTTTTGGAAAGTTCA
AGGTAAAAATGTGATTTTTGAAA
Found at i:49346 original size:17 final size:17
Alignment explanation
Indices: 49326--49358 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
49316 TTAAAAATGG
49326 TAAA-GATATAAATTATT
1 TAAATGATA-AAATTATT
49343 TAAATGATAAAATTAT
1 TAAATGATAAAATTAT
49359 ATTTTTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (17 bp):
TAAATGATAAAATTATT
Done.