Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006194.1 Kokia drynarioides strain JFW-HI SEQ_120763, 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: 64080
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 33 characters in sequence are not A, C, G, or T
Found at i:5595 original size:13 final size:14
Alignment explanation
Indices: 5577--5605 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5567 AAATTCACCT
5577 TTTTAGAA-TTGGG
1 TTTTAGAATTTGGG
5590 TTTTAGAATTTGGG
1 TTTTAGAATTTGGG
5604 TT
1 TT
5606 CATTTGGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.52
Consensus pattern (14 bp):
TTTTAGAATTTGGG
Found at i:12495 original size:49 final size:50
Alignment explanation
Indices: 12409--12515 Score: 137
Period size: 49 Copynumber: 2.2 Consensus size: 50
12399 TCAGCTGGGT
* * *
12409 TCCTGAGTTATACTCCAACTTGTTACTGCATACCCACTGTCAACTAGGAG
1 TCCTGAGTTATACTCCAACTTGTGACTGCATAACCACTATCAACTAGGAG
* * * *
12459 TCCT-AGTTATACTTCAACTTGTGATTGTATAACCACTATGAACTAGGAG
1 TCCTGAGTTATACTCCAACTTGTGACTGCATAACCACTATCAACTAGGAG
12508 T-CTGAGTT
1 TCCTGAGTT
12516 GTAATTTGAT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
48 2 0.04
49 43 0.88
50 4 0.08
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (50 bp):
TCCTGAGTTATACTCCAACTTGTGACTGCATAACCACTATCAACTAGGAG
Found at i:16697 original size:7 final size:7
Alignment explanation
Indices: 16685--16709 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16675 GTCAATTTCG
16685 ATTTTTT
1 ATTTTTT
16692 ATTTTTT
1 ATTTTTT
16699 ATTTTTT
1 ATTTTTT
16706 ATTT
1 ATTT
16710 ATCTAGGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
ATTTTTT
Found at i:18412 original size:21 final size:22
Alignment explanation
Indices: 18382--18424 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
18372 TCTTTATAAA
18382 ATTTTAATTTT-GAATGAGTTT
1 ATTTTAATTTTAGAATGAGTTT
* *
18403 ATTTTTATTTTAGATTGAGTTT
1 ATTTTAATTTTAGAATGAGTTT
18425 TAAATAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (22 bp):
ATTTTAATTTTAGAATGAGTTT
Found at i:19944 original size:19 final size:20
Alignment explanation
Indices: 19920--19958 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
19910 GTCTCCGCTT
19920 ATAATTGAATAAAA-GAAAA
1 ATAATTGAATAAAATGAAAA
*
19939 ATAATTGCATAAAATGAAAA
1 ATAATTGAATAAAATGAAAA
19959 TTGTGGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.64, C:0.03, G:0.10, T:0.23
Consensus pattern (20 bp):
ATAATTGAATAAAATGAAAA
Found at i:20257 original size:12 final size:11
Alignment explanation
Indices: 20231--20272 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
20221 CCAGACCCTT
*
20231 TTTAAATTTAA
1 TTTAAATTGAA
20242 TTTAAATCTGAA
1 TTTAAAT-TGAA
20254 TTTAAATT-AA
1 TTTAAATTGAA
20264 TCTTAAATT
1 T-TTAAATT
20273 TAAATTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 3 0.11
11 15 0.54
12 10 0.36
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (11 bp):
TTTAAATTGAA
Found at i:20258 original size:23 final size:23
Alignment explanation
Indices: 20231--20280 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
20221 CCAGACCCTT
*
20231 TTTAAATTTAAT-TTAAATCTGAA
1 TTTAAA-TTAATCTTAAATCTAAA
*
20254 TTTAAATTAATCTTAAATTTAAA
1 TTTAAATTAATCTTAAATCTAAA
20277 TTTA
1 TTTA
20281 TTTTCAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTAAATTAATCTTAAATCTAAA
Found at i:20272 original size:17 final size:18
Alignment explanation
Indices: 20232--20278 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
20222 CAGACCCTTT
*
20232 TTAAATTTAATTTAAATC
1 TTAAATTTAAATTAAATC
*
20250 -TGAATTTAAATT-AATC
1 TTAAATTTAAATTAAATC
20266 TTAAATTTAAATT
1 TTAAATTTAAATT
20279 TATTTTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (18 bp):
TTAAATTTAAATTAAATC
Found at i:20275 original size:6 final size:6
Alignment explanation
Indices: 20231--20280 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
20221 CCAGACCCTT
* *
20231 TTTAAA TTT-AA TTTAAA TCTGAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
20277 TTTA
1 TTTA
20281 TTTTCAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
4 2 0.06
5 7 0.19
6 24 0.67
7 3 0.08
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:21028 original size:3 final size:3
Alignment explanation
Indices: 21020--21052 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
21010 ATTAAATGGT
*
21020 TAA TAA TAA TAA TAA TAA TAC TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21053 AAAAGGGAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:22062 original size:29 final size:29
Alignment explanation
Indices: 22030--22221 Score: 215
Period size: 29 Copynumber: 6.5 Consensus size: 29
22020 TAAACTATCT
*
22030 AAAAATTACATTTTTACCCTTGAACTTCC
1 AAAAATTACATTTTTACCCTCGAACTTCC
22059 AAAAATTACATTTTTACCCTCGAACTTCC
1 AAAAATTACATTTTTACCCTCGAACTTCC
* *
22088 AAAAATTCCATTTTTTACCCTCAAACTTCC
1 AAAAATTACA-TTTTTACCCTCGAACTTCC
* * *
22118 AAAAATTCCATTTTTGA-TCTTGAAACTTCC
1 AAAAATTACATTTTT-ACCCTCG-AACTTCC
* *
22148 AAAAATTATATTTTTACCCCCGAACTTCC
1 AAAAATTACATTTTTACCCTCGAACTTCC
* * * *
22177 AAAAATTCCAATTTTAACCTTGAACTTTCC
1 AAAAATTACATTTTTACCCTCGAAC-TTCC
*
22207 CAAAATTATCATTTT
1 AAAAATTA-CATTTT
22222 GCCCCCCGAG
Statistics
Matches: 137, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
29 71 0.52
30 61 0.45
31 5 0.04
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAAATTACATTTTTACCCTCGAACTTCC
Found at i:22214 original size:59 final size:58
Alignment explanation
Indices: 22030--22230 Score: 224
Period size: 59 Copynumber: 3.4 Consensus size: 58
22020 TAAACTATCT
* ** * * *
22030 AAAAATTACATTTTTACCCTTGAACTTCCAAAAATTACATTTTTACCCTCGAACTTCC
1 AAAAATTATATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCTTGAACTTCC
* * * *
22088 AAAAATTCCAT-TTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGATCTTGAAACTTCC
1 AAAAATT--ATATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCTTG-AACTTCC
*
22148 AAAAATTATATTTTTACCCCCGAACTTCCAAAAATTCCAATTTTAACCTTGAACTTTCC
1 AAAAATTATATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCTTGAAC-TTCC
* **
22207 CAAAATTATCATTTTGCCCCCCGA
1 AAAAATTAT-ATTTTTACCCCCGA
22231 GAATCCAAAA
Statistics
Matches: 121, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
58 12 0.10
59 82 0.68
60 27 0.22
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (58 bp):
AAAAATTATATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCTTGAACTTCC
Found at i:22240 original size:89 final size:88
Alignment explanation
Indices: 22021--22196 Score: 205
Period size: 89 Copynumber: 2.0 Consensus size: 88
22011 GAAGGTCCCT
* * * *
22021 AAACTATCTAAAAATTACATTTTT-ACCCTTG-AACTTCCAAAAATTACATTTTTACCCTCGAAC
1 AAACT-TCCAAAAATTCCATTTTTGACCC-CGAAAC-TCCAAAAATTACATTTTTACCCCCGAAC
* *
22084 TTCCAAAAATTCCATTTTTTACCCTC
63 TTCCAAAAATTCCATATTTTAACCTC
* ** *
22110 AAACTTCCAAAAATTCCATTTTTGATCTTGAAACTTCCAAAAATTATATTTTTACCCCCGAACTT
1 AAACTTCCAAAAATTCCATTTTTGACCCCGAAAC-TCCAAAAATTACATTTTTACCCCCGAACTT
22175 CCAAAAATTCCA-ATTTTAACCT
65 CCAAAAATTCCATATTTTAACCT
22197 TGAACTTTCC
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
88 26 0.34
89 51 0.66
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (88 bp):
AAACTTCCAAAAATTCCATTTTTGACCCCGAAACTCCAAAAATTACATTTTTACCCCCGAACTTC
CAAAAATTCCATATTTTAACCTC
Found at i:22241 original size:59 final size:59
Alignment explanation
Indices: 22021--22250 Score: 173
Period size: 59 Copynumber: 3.9 Consensus size: 59
22011 GAAGGTCCCT
* * * ** * * * * *
22021 AAACTATCTAAAAATTACATTTTTACCCTTGAACTTCCAAAAATTACATTTTTACCCTCG
1 AAACT-TCCAAAAATTATATTTTGACCCCCGAACATCCAAAAATTCCAATTTTAACCTTG
* * * * * * *
22081 -AACTTCCAAAAATTCCAT-TTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGATCTTG
1 AAACTTCCAAAAATT--ATATTTTGACCCCCGAACATCCAAAAATTCCAATTTTAACCTTG
* *
22140 AAACTTCCAAAAATTATATTTTTACCCCCGAACTTCCAAAAATTCCAATTTTAACCTTG
1 AAACTTCCAAAAATTATATTTTGACCCCCGAACATCCAAAAATTCCAATTTTAACCTTG
* * *
22199 -AACTTTCCCAAAATTATCATTTTGCCCCCCGAGA-ATCC-AAAATTCCCATTTT
1 AAAC-TTCCAAAAATTAT-ATTTTGACCCCCGA-ACATCCAAAAATTCCAATTTT
22251 GCCCCCGGGT
Statistics
Matches: 144, Mismatches: 19, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
58 14 0.10
59 99 0.69
60 30 0.21
61 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (59 bp):
AAACTTCCAAAAATTATATTTTGACCCCCGAACATCCAAAAATTCCAATTTTAACCTTG
Found at i:26543 original size:20 final size:22
Alignment explanation
Indices: 26518--26558 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
26508 TTTAGTGTTA
26518 TTTATTATTAA-AAA-AAGCAG
1 TTTATTATTAACAAATAAGCAG
26538 TTTATTATTAACAAATAAGCA
1 TTTATTATTAACAAATAAGCA
26559 ATTACTCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 3 0.16
22 5 0.26
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (22 bp):
TTTATTATTAACAAATAAGCAG
Found at i:26785 original size:24 final size:24
Alignment explanation
Indices: 26763--26806 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
26753 TGTGGTGAAG
26763 AAATA-TTT-TATAAAAATAATGA
1 AAATACTTTCTATAAAAATAATGA
26785 AAATACTTTCTATAAAAATAAT
1 AAATACTTTCTATAAAAATAAT
26807 ATAAATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.25
23 3 0.15
24 12 0.60
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (24 bp):
AAATACTTTCTATAAAAATAATGA
Found at i:28508 original size:17 final size:18
Alignment explanation
Indices: 28473--28510 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
28463 ATTTTGTCAA
*
28473 ATTTTTATCTTATTAAAT
1 ATTTTTATCTAATTAAAT
*
28491 ATTTTTAT-TAATTTAAT
1 ATTTTTATCTAATTAAAT
28508 ATT
1 ATT
28511 ACAATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTTATCTAATTAAAT
Found at i:59774 original size:75 final size:75
Alignment explanation
Indices: 59659--59961 Score: 606
Period size: 75 Copynumber: 4.0 Consensus size: 75
59649 AGCTACTTCG
59659 AGTAATATTCTGAACAACAACATCACCTTCATTTTCGATATTAGCCAAAGCTTCAAAACTTTGTG
1 AGTAATATTCTGAACAACAACATCACCTTCATTTTCGATATTAGCCAAAGCTTCAAAACTTTGTG
59724 AAGAGCTAGA
66 AAGAGCTAGA
59734 AGTAATATTCTGAACAACAACATCACCTTCATTTTCGATATTAGCCAAAGCTTCAAAACTTTGTG
1 AGTAATATTCTGAACAACAACATCACCTTCATTTTCGATATTAGCCAAAGCTTCAAAACTTTGTG
59799 AAGAGCTAGA
66 AAGAGCTAGA
59809 AGTAATATTCTGAACAACAACATCACCTTCATTTTCGATATTAGCCAAAGCTTCAAAACTTTGTG
1 AGTAATATTCTGAACAACAACATCACCTTCATTTTCGATATTAGCCAAAGCTTCAAAACTTTGTG
59874 AAGAGCTAGA
66 AAGAGCTAGA
59884 AGTAATATTCTGAACAACAACATCACCTTCATTTTCGATATTAGCCAAAGCTTCAAAACTTTGTG
1 AGTAATATTCTGAACAACAACATCACCTTCATTTTCGATATTAGCCAAAGCTTCAAAACTTTGTG
59949 AAGAGCTAGA
66 AAGAGCTAGA
59959 AGT
1 AGT
59962 TGCATCGACT
Statistics
Matches: 228, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 228 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (75 bp):
AGTAATATTCTGAACAACAACATCACCTTCATTTTCGATATTAGCCAAAGCTTCAAAACTTTGTG
AAGAGCTAGA
Done.