Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011408.1 Kokia drynarioides strain JFW-HI SEQ_126390, 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: 40824
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:5087 original size:42 final size:42
Alignment explanation
Indices: 5040--5122 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
5030 AAAGGAGTTG
*
5040 TTTATGAGTGTTATTT-AGGAATAAAATTATATTTGGGTTTAA
1 TTTATGAGTGTT-TTTGAAGAATAAAATTATATTTGGGTTTAA
*
5082 TTTATGAGTGTTTTTGAAGAATGAAATTATATTTGGGTTTA
1 TTTATGAGTGTTTTTGAAGAATAAAATTATATTTGGGTTTA
5123 GTTTGTTGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 3 0.08
42 35 0.92
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.48
Consensus pattern (42 bp):
TTTATGAGTGTTTTTGAAGAATAAAATTATATTTGGGTTTAA
Found at i:6546 original size:30 final size:31
Alignment explanation
Indices: 6510--6581 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
6500 GTCACATTTA
* *
6510 ACAAAACAGTCACTCAACTT-T-GAAAATGTG
1 ACAAAACAGTCACTAAAATTATAGAAAA-GTG
6540 ACAAAACAGTCACTAAAATTATAGAAAAGTG
1 ACAAAACAGTCACTAAAATTATAGAAAAGTG
*
6571 ACAAAATAGTC
1 ACAAAACAGTC
6582 CTTTTCACCT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 18 0.49
31 14 0.38
32 5 0.14
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (31 bp):
ACAAAACAGTCACTAAAATTATAGAAAAGTG
Found at i:9359 original size:57 final size:56
Alignment explanation
Indices: 9280--9412 Score: 178
Period size: 57 Copynumber: 2.3 Consensus size: 56
9270 TTCCAGGTCA
* * *
9280 TTTTCATTTTTCA-TTTCATTTTCATTTTGGAGAAAACCACATTCATTTCCTAATG
1 TTTTCATTTTCCATTTTCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATG
* *
9335 TTTTCATTTCTCCATTTTTATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATG
1 TTTTCATTT-TCCATTTTCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATG
*
9392 TTTCCCATTTATCCATTTTCA
1 TTT-TCATTT-TCCATTTTCA
9413 CAATTTCTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
55 9 0.13
56 3 0.04
57 41 0.61
58 14 0.21
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.49
Consensus pattern (56 bp):
TTTTCATTTTCCATTTTCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATG
Found at i:10364 original size:28 final size:28
Alignment explanation
Indices: 10332--10388 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
10322 ATACCCATTA
10332 AAACCAAGGAAAACACCCAAAAACCTTC
1 AAACCAAGGAAAACACCCAAAAACCTTC
10360 AAACCAAGGAAAACACCCAAAAACCTTC
1 AAACCAAGGAAAACACCCAAAAACCTTC
10388 A
1 A
10389 TCTTCTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.54, C:0.32, G:0.07, T:0.07
Consensus pattern (28 bp):
AAACCAAGGAAAACACCCAAAAACCTTC
Found at i:12774 original size:49 final size:49
Alignment explanation
Indices: 12707--12853 Score: 285
Period size: 49 Copynumber: 3.0 Consensus size: 49
12697 AAAAATATAG
*
12707 CAAGATAATTAAGGGAAAAAAAGTTGTATGTGTAATAAAACACTAAAAT
1 CAAGATAATTAAGGGAAAAAAAGTTGCATGTGTAATAAAACACTAAAAT
12756 CAAGATAATTAAGGGAAAAAAAGTTGCATGTGTAATAAAACACTAAAAT
1 CAAGATAATTAAGGGAAAAAAAGTTGCATGTGTAATAAAACACTAAAAT
12805 CAAGATAATTAAGGGAAAAAAAGTTGCATGTGTAATAAAACACTAAAAT
1 CAAGATAATTAAGGGAAAAAAAGTTGCATGTGTAATAAAACACTAAAAT
12854 GAGGTAAGCA
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
49 97 1.00
ACGTcount: A:0.53, C:0.07, G:0.16, T:0.23
Consensus pattern (49 bp):
CAAGATAATTAAGGGAAAAAAAGTTGCATGTGTAATAAAACACTAAAAT
Found at i:12840 original size:27 final size:27
Alignment explanation
Indices: 12761--12840 Score: 62
Period size: 23 Copynumber: 3.1 Consensus size: 27
12751 AAAATCAAGA
12761 TAATTAAGGGAAAAAAAGTTGCATGTG
1 TAATTAAGGGAAAAAAAGTTGCATGTG
*** ** * *
12788 TAA-TAAAACACTAAAA--T-CAAG-A
1 TAATTAAGGGAAAAAAAGTTGCATGTG
12810 TAATTAAGGGAAAAAAAGTTGCATGTG
1 TAATTAAGGGAAAAAAAGTTGCATGTG
12837 TAAT
1 TAAT
12841 AAAACACTAA
Statistics
Matches: 34, Mismatches: 14, Indels: 10
0.59 0.24 0.17
Matches are distributed among these distances:
22 3 0.09
23 11 0.32
24 1 0.03
25 1 0.03
26 11 0.32
27 7 0.21
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (27 bp):
TAATTAAGGGAAAAAAAGTTGCATGTG
Found at i:15799 original size:79 final size:78
Alignment explanation
Indices: 15659--15879 Score: 264
Period size: 79 Copynumber: 2.8 Consensus size: 78
15649 ATAGTTATAA
* * ** *
15659 CACCCAGTGCCTAGCAGATAAACCGCAATTGTGAGTCCAGCTCTAGTTGGATT-AACCAACAATA
1 CACCCAGTGCCTAGCGGATAAACCGCAA-TGTGAGCCCAGCTCTAG-TCAATTAAACTAACAATA
* * *
15723 TTCGTCAAATCTTAG
64 TCCATCAAATCCTAG
* *
15738 CACCCAGTGCTTAGCGGATAAACCGCGAATGTGAGCCCAGCTCTAGTCAATTAAACTAACAACAT
1 CACCCAGTGCCTAGCGGATAAACCGC-AATGTGAGCCCAGCTCTAGTCAATTAAACTAACAATAT
*
15803 CCATCAAATCCTGG
65 CCATCAAATCCTAG
* * * *
15817 CACCCATTGCCTAGCGGATAAACCACAAATGTGAGCTCAGCTCTAGTCAGTTAAACTAACAAT
1 CACCCAGTGCCTAGCGGATAAACCGC-AATGTGAGCCCAGCTCTAGTCAATTAAACTAACAAT
15880 GTAAGTTATT
Statistics
Matches: 122, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
78 4 0.03
79 116 0.95
80 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (78 bp):
CACCCAGTGCCTAGCGGATAAACCGCAATGTGAGCCCAGCTCTAGTCAATTAAACTAACAATATC
CATCAAATCCTAG
Found at i:17239 original size:24 final size:24
Alignment explanation
Indices: 17206--17290 Score: 107
Period size: 24 Copynumber: 3.5 Consensus size: 24
17196 AGAAATAATA
17206 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAATTAAACTTTGTTTATTTG
* **
17230 TTTCATTTAAACCCTGTTTATTTG
1 TTTCAATTAAACTTTGTTTATTTG
* *
17254 TTTTAATTAAACTTTATTTATTTG
1 TTTCAATTAAACTTTGTTTATTTG
* *
17278 TTTTAGTTAAACT
1 TTTCAATTAAACT
17291 GTTATTAGTC
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.26, C:0.09, G:0.07, T:0.58
Consensus pattern (24 bp):
TTTCAATTAAACTTTGTTTATTTG
Found at i:19230 original size:24 final size:24
Alignment explanation
Indices: 19199--19251 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
19189 AGAAATAATC
*
19199 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAATTAAACTATGTTTATTTG
19223 TTTCAATTAAACTATGTTTATTTG
1 TTTCAATTAAACTATGTTTATTTG
19247 TTTCA
1 TTTCA
19252 GTAATTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.26, C:0.09, G:0.08, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTATGTTTATTTG
Found at i:20156 original size:16 final size:16
Alignment explanation
Indices: 20135--20165 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20125 AATTTAATCT
*
20135 AATATTTATCTTAATA
1 AATATTTATATTAATA
20151 AATATTTATATTAAT
1 AATATTTATATTAAT
20166 TTAAGATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
AATATTTATATTAATA
Found at i:29778 original size:51 final size:51
Alignment explanation
Indices: 29723--29822 Score: 164
Period size: 51 Copynumber: 2.0 Consensus size: 51
29713 TAAGTTTGTT
* *
29723 TTTGTGTTTTTGGCACATACCAGTAATTAATTTTTAAGACGGTTCATTTTG
1 TTTGTGTTTTTGGCAAATACCAGTAATTAATTTTTAAAACGGTTCATTTTG
* *
29774 TTTGTGTTTTTGGTAAATACCTGTAATTAATTTTTAAAACGGTTCATTT
1 TTTGTGTTTTTGGCAAATACCAGTAATTAATTTTTAAAACGGTTCATTT
29823 CGATAAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.49
Consensus pattern (51 bp):
TTTGTGTTTTTGGCAAATACCAGTAATTAATTTTTAAAACGGTTCATTTTG
Found at i:32372 original size:7 final size:7
Alignment explanation
Indices: 32360--32385 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
32350 TGGCAATTGA
32360 TTGATAG
1 TTGATAG
32367 TTGATAG
1 TTGATAG
32374 TTGATAG
1 TTGATAG
32381 TTGAT
1 TTGAT
32386 TGCAATGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (7 bp):
TTGATAG
Found at i:32425 original size:26 final size:26
Alignment explanation
Indices: 32395--32445 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
32385 TTGCAATGGT
*
32395 TGATTTGATTAGCTGAATT-TATTAAC
1 TGATTTGATCAGCTG-ATTCTATTAAC
32421 TGATTTGATCAGCTGATTCTATTAA
1 TGATTTGATCAGCTGATTCTATTAA
32446 TTATTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (26 bp):
TGATTTGATCAGCTGATTCTATTAAC
Found at i:32437 original size:13 final size:13
Alignment explanation
Indices: 32395--32438 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
32385 TTGCAATGGT
32395 TGATTTGATTAGC
1 TGATTTGATTAGC
*
32408 TGAATTT-ATTAAC
1 TG-ATTTGATTAGC
*
32421 TGATTTGATCAGC
1 TGATTTGATTAGC
32434 TGATT
1 TGATT
32439 CTATTAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 4 0.15
13 18 0.69
14 4 0.15
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.45
Consensus pattern (13 bp):
TGATTTGATTAGC
Found at i:32692 original size:26 final size:26
Alignment explanation
Indices: 32663--32713 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
32653 GCAGTGGTTG
* *
32663 ATTTGATCAACTGAA-TCTGTTAACTT
1 ATTTGACCAACT-AATTCTATTAACTT
32689 ATTTGACCAACTAATTCTATTAACT
1 ATTTGACCAACTAATTCTATTAACT
32714 GTTTATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (26 bp):
ATTTGACCAACTAATTCTATTAACTT
Found at i:36165 original size:15 final size:17
Alignment explanation
Indices: 36144--36184 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
36134 TAACCTTTTA
36144 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
*
36160 -AAATTATTAAAATGAT
1 AAAATTATAAAAATGAT
36176 AAAATTATA
1 AAAATTATA
36185 TTTTTACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:36211 original size:22 final size:22
Alignment explanation
Indices: 36139--36213 Score: 62
Period size: 24 Copynumber: 3.3 Consensus size: 22
36129 TGATTTAACC
*
36139 TTTTAAAAATTATAAAAATATAAA
1 TTTT-AAAATGATAAAAATAT-AA
* *
36163 TTATTAAAATGATAAAATTATAT
1 TT-TTAAAATGATAAAAATATAA
**
36186 TTTTACTATG-TAAAAATATACA
1 TTTTAAAATGATAAAAATATA-A
36208 TTTTAA
1 TTTTAA
36214 TTTCACGAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
21 9 0.22
22 11 0.27
23 3 0.07
24 16 0.39
25 2 0.05
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (22 bp):
TTTTAAAATGATAAAAATATAA
Found at i:39828 original size:12 final size:12
Alignment explanation
Indices: 39811--39836 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39801 ATTGAATTGA
39811 TTGTGATATTCT
1 TTGTGATATTCT
39823 TTGTGATATTCT
1 TTGTGATATTCT
39835 TT
1 TT
39837 TATCATTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (12 bp):
TTGTGATATTCT
Done.