Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007821.1 Kokia drynarioides strain JFW-HI SEQ_122457, 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: 2655
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Found at i:925 original size:78 final size:77
Alignment explanation
Indices: 746--974 Score: 216
Period size: 78 Copynumber: 2.9 Consensus size: 77
736 TTGAAGATTC
* * * * * *
746 CGATCTCTTACCCCGAGCT-TGAGGCAGATCACTATTAGCCAATCTCTTATCCCGAGCTC-GGGG
1 CGATCTTTTACCCC-AACTATGGGGCAGATCACCATCAACCAATCTCTTA-CCCGAGC-CAGGGG
* *
809 CAGATGGTAGCCATT
63 CAGATTGTAGTCATT
** * *
824 CGATCTTTTACCCTGAGTCTGGGGCAGATCACCATCAACCAATCTCTTACCCCGAGCCAGGGGCA
1 CGATCTTTTACCCCAACTATGGGGCAGATCACCATCAACCAATCTCTTA-CCCGAGCCAGGGGCA
889 GATTGTAGTCA-T
65 GATTGTAGTCATT
* * * *
901 CTGATCTTTTACCCCAACTATGGGGTAGATCA-CAGCCATCCAATCTCTTACCCGA-TCATGGGG
1 C-GATCTTTTACCCCAACTATGGGGCAGATCACCA-TCAACCAATCTCTTACCCGAGCCA-GGGG
964 CAGATTGTAGT
63 CAGATTGTAGT
975 TATCGAAGCA
Statistics
Matches: 126, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
76 2 0.02
77 26 0.21
78 98 0.78
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (77 bp):
CGATCTTTTACCCCAACTATGGGGCAGATCACCATCAACCAATCTCTTACCCGAGCCAGGGGCAG
ATTGTAGTCATT
Found at i:1317 original size:172 final size:171
Alignment explanation
Indices: 1032--1409 Score: 596
Period size: 172 Copynumber: 2.2 Consensus size: 171
1022 GGACCAAATC
** *
1032 CGTCTTCCTGATGAGATACAGAGAAGTGGATGGAAACAGTGATGCAATCATCTTCTTGATGAGAT
1 CGTCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAGTGATGCAATCATCTTCCTGATGAGAT
* *
1097 ACAGAGAAGCATACCAAATTAATGAAACAAAGTTCAATGTGAGTGAAACTTCGAATCCCAGCTTC
66 ACAGAGAAGCATACCAAATTAATGAAACAAAGCTCAATGTGAGTGAAACTTCGAACCCCAGCTTC
1162 CGGATGAGATACTGAGA-AGCAGATCGAAGCAATAAAGCGGT
131 CGGATGAGATACTGAGAGA-CAGATCGAAGCAATAAAGCGGT
* ** *
1203 CGTCTTCTTGATGAGATACAGAGAAGTGGATTAAAACAAGTGATGCGGTCCTCTTCCTGATGAGA
1 CGTCTTCCTGATGAGATACAGAGAAGTGGATTAAAAC-AGTGATGCAATCATCTTCCTGATGAGA
*
1268 TACAGAGAAGTATACCAAATTAATGAAACAAAGCTCAATGTGAGTGAAACTTCGAACCCCAGCTT
65 TACAGAGAAGCATACCAAATTAATGAAACAAAGCTCAATGTGAGTGAAACTTCGAACCCCAGCTT
* * * *
1333 CCTGATGAGGTACTGAGAGACAGGTCGAAGCAATAAAGCTGT
130 CCGGATGAGATACTGAGAGACAGATCGAAGCAATAAAGCGGT
*
1375 CGTCTTCCTGATGAGATACAGAGAAGTGGACTAAA
1 CGTCTTCCTGATGAGATACAGAGAAGTGGATTAAA
1410 TCCGTCTTCC
Statistics
Matches: 189, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
171 34 0.18
172 154 0.81
173 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (171 bp):
CGTCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAGTGATGCAATCATCTTCCTGATGAGAT
ACAGAGAAGCATACCAAATTAATGAAACAAAGCTCAATGTGAGTGAAACTTCGAACCCCAGCTTC
CGGATGAGATACTGAGAGACAGATCGAAGCAATAAAGCGGT
Found at i:1769 original size:208 final size:207
Alignment explanation
Indices: 1202--1921 Score: 944
Period size: 209 Copynumber: 3.4 Consensus size: 207
1192 AATAAAGCGG
* * * *
1202 TCGTCTTCTTGATGAGATACAGAGAAGTGGATTAAAACAAGTGATGCGGTCCTCTTCCTGATGAG
1 TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGATCATCTTCCTGATGAG
* *
1267 ATACAGAGAAGTATACCAAATTAATGAAACAAAGCTCAATGTGAGTGAAACTTCGAACCCCAGCT
66 ATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATGTGAGCGAAACTTCGAACCCCAGCT
* * *
1332 TCCTGATGAGGTACTGAG-AGACAGGTCGAAGCAATAAAGCTGTCGTCTTCCTGATGAGATACAG
131 T-CTGATGAGATACTGAGAAG-CAGGTCGAAGCAATAAA-ATGTCATCTTCCTGATGAGATACAG
*
1396 AGAAGTGGACTAAAT
193 AGAAGTGGACCAAAT
* **
1411 CCGTCTTCCTGATGAGATACAGAGAAGTAGATTAAAACAAGTGA-G-GTAGTCATCTTCCTGATG
1 TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCG-A-TCATCTTCCTGATG
** * * *
1474 AGATATGGAGAAGTATACCAAATCAATGAAGCAAAGCTCGATGTGAGCGAAACTTCGAACCCTAG
64 AGATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATGTGAGCGAAACTTCGAACCCCAG
* ** *
1539 CTTACTGATGAGATACTGAGAAGCATGTTAAAGCAATAAAATGATCAACTTCCTGATGAGATACA
129 CTT-CTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATG-TCATCTTCCTGATGAGATACA
*
1604 GAGAAGTGAACCAAAT
192 GAGAAGTGGACCAAAT
* * *
1620 TCGTCTTCTTGATGAGATACAGAGAAGCGGATTGAAAC-AGTGATGCGATCATCTTCCTAATGAG
1 TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGATCATCTTCCTGATGAG
* * * * * * * *
1684 ATATAGAGAAGAATACCAAATCAACGAAATAAAGCTTAATATGAGCGAAACTCCAAACCCCAGCT
66 ATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATGTGAGCGAAACTTCGAACCCCAGCT
* ** *
1749 TCTTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAGCGGTCATCTTCCTGATGAGACACAGA
131 TC-TGATGAGATACTGAGAAGCAGGTCGAAGCAATAAA-ATGTCATCTTCCTGATGAGATACAGA
1814 GAAGTGGACCAAAT
194 GAAGTGGACCAAAT
* * *
1828 TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAAGAAGTAATGCGGTCATCTTCCTGATGAG
1 TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGATCATCTTCCTGATGAG
*
1893 ATACAGAGAAGTAGACCAAATCAAATGAA
66 ATACAGAGAAGTATACCAAATC-AATGAA
1922 GGAAAATGTG
Statistics
Matches: 443, Mismatches: 58, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
207 2 0.00
208 178 0.40
209 255 0.58
210 8 0.02
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (207 bp):
TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGATCATCTTCCTGATGAG
ATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATGTGAGCGAAACTTCGAACCCCAGCT
TCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGTCATCTTCCTGATGAGATACAGAGA
AGTGGACCAAAT
Found at i:1887 original size:86 final size:85
Alignment explanation
Indices: 1747--1913 Score: 237
Period size: 86 Copynumber: 2.0 Consensus size: 85
1737 CAAACCCCAG
* * **
1747 CTTCTTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAGCGGTCATCTTCCTGATGAGACACA
1 CTTCCTGATGAGATACAGAGAAGCGGGTAAAAGCAATAAAGCGGTCATCTTCCTGATGAGACACA
*
1812 GAGAAGTGGACCAAATTCGT
66 GAGAAGTAGACCAAATTCGT
* * *
1832 CTTCCTGATGAGATACAGAGAAGCGGATTAAAAG-AAGTAATGCGGTCATCTTCCTGATGAGATA
1 CTTCCTGATGAGATACAGAGAAGCGG-GTAAAAGCAA-TAAAGCGGTCATCTTCCTGATGAGACA
1896 CAGAGAAGTAGACCAAAT
64 CAGAGAAGTAGACCAAAT
1914 CAAATGAAGG
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
85 26 0.36
86 46 0.64
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (85 bp):
CTTCCTGATGAGATACAGAGAAGCGGGTAAAAGCAATAAAGCGGTCATCTTCCTGATGAGACACA
GAGAAGTAGACCAAATTCGT
Found at i:1990 original size:208 final size:205
Alignment explanation
Indices: 1202--2026 Score: 913
Period size: 209 Copynumber: 4.0 Consensus size: 205
1192 AATAAAGCGG
* * *
1202 TCGTCTTCTTGATGAGATACAGAGAAGTGGATTAAAACAAGTGATGCGGTCCTCTTCCTGATGAG
1 TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAG
* * * *
1267 ATACAGAGAAGTATACCAAAT-TAATGAAACAAAGCTCAATGTGAGTGAAACTTCGAACCCCAGC
66 ATACAGAGAAGTATACCAAATCAAATGAAGC-AA----AATGTGAGCGAAACTTCAAACCCCAGC
* *
1331 TTCCTGATGAGGTACTGAG-AGACAGGTCGAAGCAATAAAGCTG-TCGTCTTCCTGATGAGATAC
126 TTCCTGATGAGATACTGAGAAG-CAGGTCGAAGCAATAAAGC-GATCATCTTCCTGATGAGATAC
*
1394 AGAGAAGTGGACTAAAT
189 AGAGAAGTGGACCAAAT
* ** * **
1411 CCGTCTTCCTGATGAGATACAGAGAAGTAGATTAAAACAAGTGAGGTAGTCATCTTCCTGATGAG
1 TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAG
** * *
1476 ATATGGAGAAGTATACCAAATC-AATGAAGCAAAGCTCGATGTGAGCGAAACTTCGAACCCTAGC
66 ATACAGAGAAGTATACCAAATCAAATGAAGCAAA-----ATGTGAGCGAAACTTCAAACCCCAGC
* * ** ** *
1540 TTACTGATGAGATACTGAGAAGCATGTTAAAGCAATAAAATGATCAACTTCCTGATGAGATACAG
126 TTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGATCATCTTCCTGATGAGATACAG
*
1605 AGAAGTGAACCAAAT
191 AGAAGTGGACCAAAT
* * * *
1620 TCGTCTTCTTGATGAGATACAGAGAAGCGGATTGAAAC-AGTGATGCGATCATCTTCCTAATGAG
1 TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAG
* * * ** * *
1684 ATATAGAGAAGAATACCAAATCAACGAAATAAAGCTTAATATGAGCGAAACTCCAAACCCCAGCT
66 ATACAGAGAAGTATACCAAAT---C-AAATGAAGCAAAATGTGAGCGAAACTTCAAACCCCAGCT
* * * *
1749 TCTTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAGCGGTCATCTTCCTGATGAGACACAGA
127 TCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGATCATCTTCCTGATGAGATACAGA
1814 GAAGTGGACCAAAT
192 GAAGTGGACCAAAT
* *
1828 TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAAGAAGTAATGCGGTCATCTTCCTGATGAG
1 TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAG
* * * * **
1893 ATACAGAGAAGTAGACCAAATCAAATGAAGGAAAATGTGAGTGAAGCTTCAAAAACCCCTATTTT
66 ATACAGAGAAGTATACCAAATCAAATGAAGCAAAATGTGAGCGAAACTTC--AAACCCC-AGCTT
* * ** * * * *
1958 CCTGATAAGATACAGAGAAGTGGGTTGAAGCAATAAATCGATCATCTTCTTGGTGAGATACAGAG
128 CCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGATCATCTTCCTGATGAGATACAGAG
2023 AAGT
193 AAGT
2027 AGACTGAGAG
Statistics
Matches: 516, Mismatches: 83, Indels: 35
0.81 0.13 0.06
Matches are distributed among these distances:
204 1 0.00
205 20 0.04
206 1 0.00
207 7 0.01
208 230 0.45
209 246 0.48
210 2 0.00
211 1 0.00
213 8 0.02
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (205 bp):
TCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAG
ATACAGAGAAGTATACCAAATCAAATGAAGCAAAATGTGAGCGAAACTTCAAACCCCAGCTTCCT
GATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGATCATCTTCCTGATGAGATACAGAGAAG
TGGACCAAAT
Done.