Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012718.1 Kokia drynarioides strain JFW-HI SEQ_127729, 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: 5877
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Found at i:288 original size:152 final size:147
Alignment explanation
Indices: 1--290 Score: 343
Period size: 152 Copynumber: 1.9 Consensus size: 147
* *
1 TTTTTAGTTATTTTAAAGAAAAAGTTTAAATTGTCAACAAAGTTTTGATTTTTTTAACTATTTCG
1 TTTTTAGTTATTTTAAAGAAAAAGTTTAAATTGTCAACAAAATTTTGATTTTTTTAACTATTTCA
* * * **
66 AAATAAAAGTTTGGATTTTTAAGTAAAATGGTGATTTTCTTTAAGAGAGAGAAAGTTTAGATTTT
66 AAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTCTTTAACAAAGAGAAAGTTTAGA-TAA
*
131 TAAAAAATAAAAATCTAT
130 AAAAAAATAAAAATCTAT
*
149 TTTTTAGTTATTTTTAAAGAAAAAGTTTAAATT-TATAACAAAATTTTGATTTTTTTTTTAACTA
1 TTTTTAGTTA-TTTTAAAGAAAAAGTTTAAATTGT-CAACAAAATTTTGA---TTTTTTTAACTA
* * *
213 TTTCAAAATAAAAGTTT-GAGTTTTTAAGTAAAGTAGTGATTTTTGTTTAATCAAATGA-AAATT
61 TTTCAAAATAAAAGTTTGGA-TTTTTAAGTAAAATAGTGA-TTTTCTTTAA-CAAA-GAGAAAGT
* *
276 TTTGAAAAAAAAAAA
122 TTAGATAAAAAAAAA
291 AAGAAAAGAA
Statistics
Matches: 119, Mismatches: 14, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
148 11 0.09
149 34 0.29
151 2 0.02
152 45 0.38
153 15 0.13
154 10 0.08
155 2 0.02
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (147 bp):
TTTTTAGTTATTTTAAAGAAAAAGTTTAAATTGTCAACAAAATTTTGATTTTTTTAACTATTTCA
AAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTCTTTAACAAAGAGAAAGTTTAGATAAA
AAAAAATAAAAATCTAT
Found at i:1729 original size:81 final size:81
Alignment explanation
Indices: 1477--1729 Score: 191
Period size: 83 Copynumber: 3.1 Consensus size: 81
1467 TGAACACGTC
1477 TTAGTTAAGTTACAAGTAAATTAGATTAATGATAAAAGATTGAATAAGTTGTAGATGAATTTTAA
1 TTAGTTAAGTTACAAGTAAATTAGATTAATGATAAAAGATTGAATAAGTTGTAGATGAATTTTAA
1542 TATTTCTCTTAATTCA
66 TATTTCTCTTAATTCA
*** ** *
1558 TTAGTGATTTTTTTA-AAAAAAATTTAGGATT-CT-A-AAATAGAATT-AATTTTAAGGATTG-A
1 TTA--G-TTAAGTTACAAGTAAA-TTA-GATTAATGATAAA-AG-ATTGAA---TAA-G-TTGTA
* * * * * * **
1617 -AGGTATTTTACTAGAATTAT-TCACGTC-
54 GATGAATTTTA--ATATTTCTCTTAATTCA
1644 TTAGTTAAGTTACAAGTAAATTAGATTAATGATAAAAGATTGAATAAGTTGTAGATGAATTTTAA
1 TTAGTTAAGTTACAAGTAAATTAGATTAATGATAAAAGATTGAATAAGTTGTAGATGAATTTTAA
1709 TATTTCTCTTAATTCA
66 TATTTCTCTTAATTCA
1725 TTAGT
1 TTAGT
1730 GATTTTTTAA
Statistics
Matches: 121, Mismatches: 28, Indels: 46
0.62 0.14 0.24
Matches are distributed among these distances:
79 8 0.07
80 6 0.05
81 19 0.16
82 7 0.06
83 23 0.19
84 23 0.19
85 7 0.06
86 14 0.12
87 6 0.05
88 8 0.07
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42
Consensus pattern (81 bp):
TTAGTTAAGTTACAAGTAAATTAGATTAATGATAAAAGATTGAATAAGTTGTAGATGAATTTTAA
TATTTCTCTTAATTCA
Found at i:1747 original size:167 final size:167
Alignment explanation
Indices: 1471--1804 Score: 650
Period size: 167 Copynumber: 2.0 Consensus size: 167
1461 GTCTGGTGAA
1471 CACGTCTTAGTTAAGTTACAAGTAAATTAGATTAATGATAAAAGATTGAATAAGTTGTAGATGAA
1 CACGTCTTAGTTAAGTTACAAGTAAATTAGATTAATGATAAAAGATTGAATAAGTTGTAGATGAA
*
1536 TTTTAATATTTCTCTTAATTCATTAGTGATTTTTTTAAAAAAAATTTAGGATTCTAAAATAGAAT
66 TTTTAATATTTCTCTTAATTCATTAGTGATTTTTTAAAAAAAAATTTAGGATTCTAAAATAGAAT
1601 TAATTTTAAGGATTGAAGGTATTTTACTAGAATTATT
131 TAATTTTAAGGATTGAAGGTATTTTACTAGAATTATT
1638 CACGTCTTAGTTAAGTTACAAGTAAATTAGATTAATGATAAAAGATTGAATAAGTTGTAGATGAA
1 CACGTCTTAGTTAAGTTACAAGTAAATTAGATTAATGATAAAAGATTGAATAAGTTGTAGATGAA
*
1703 TTTTAATATTTCTCTTAATTCATTAGTGATTTTTTAAAAAAAAATTTAGGATTCTAAAATATAAT
66 TTTTAATATTTCTCTTAATTCATTAGTGATTTTTTAAAAAAAAATTTAGGATTCTAAAATAGAAT
1768 TAATTTTAAGGATTGAAGGTATTTTACTAGAATTATT
131 TAATTTTAAGGATTGAAGGTATTTTACTAGAATTATT
1805 TAGGTATCCT
Statistics
Matches: 165, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
167 165 1.00
ACGTcount: A:0.40, C:0.05, G:0.13, T:0.41
Consensus pattern (167 bp):
CACGTCTTAGTTAAGTTACAAGTAAATTAGATTAATGATAAAAGATTGAATAAGTTGTAGATGAA
TTTTAATATTTCTCTTAATTCATTAGTGATTTTTTAAAAAAAAATTTAGGATTCTAAAATAGAAT
TAATTTTAAGGATTGAAGGTATTTTACTAGAATTATT
Found at i:1761 original size:81 final size:81
Alignment explanation
Indices: 1509--1761 Score: 186
Period size: 79 Copynumber: 3.1 Consensus size: 81
1499 AGATTAATGA
*
1509 TAAAAGATTGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTGATTTTTTTAA
1 TAAAAGATTGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTGATTTTTTAAA
1574 AAAAAATTTAGGATTC
66 AAAAAATTTAGGATTC
* * * * * *
1590 T-AAA-ATAGAATTAA-TTTTA-A-GGA-TTGAAGGTATTT-TACTAGAATT-ATTCACGT-CTT
1 TAAAAGATTGAA-TAAGTTGTAGATGAATTTTAA--TATTTCT-CT-TAATTCATT-A-GTGATT
* ** *
1646 AGTTAAGTTACAAGTAAA-TTA-GATTAATGA
59 --TT---TTAAAAAAAAATTTAGGA-T--T-C
1676 TAAAAGATTGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTGATTTTTTAAA
1 TAAAAGATTGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTGATTTTTTAAA
1741 AAAAAATTTAGGATTC
66 AAAAAATTTAGGATTC
1757 TAAAA
1 TAAAA
1762 TATAATTAAT
Statistics
Matches: 124, Mismatches: 21, Indels: 54
0.62 0.11 0.27
Matches are distributed among these distances:
76 4 0.03
77 3 0.02
78 11 0.09
79 16 0.13
80 8 0.06
81 8 0.06
82 3 0.02
83 12 0.10
84 11 0.09
85 3 0.02
86 3 0.02
87 8 0.06
88 16 0.13
89 11 0.09
90 3 0.02
91 4 0.03
ACGTcount: A:0.40, C:0.05, G:0.13, T:0.42
Consensus pattern (81 bp):
TAAAAGATTGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTGATTTTTTAAA
AAAAAATTTAGGATTC
Found at i:5212 original size:4 final size:4
Alignment explanation
Indices: 5203--5237 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
5193 TTTGCCTCAT
* *
5203 ATTC ATTC ATTC ATTC ATTC ACTC ATTC ACTC ATT
1 ATTC ATTC ATTC ATTC ATTC ATTC ATTC ATTC ATT
5238 TGTTTATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.46
Consensus pattern (4 bp):
ATTC
Done.