Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011077.1 Kokia drynarioides strain JFW-HI SEQ_126050, 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: 3681
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.24
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:202 original size:29 final size:29
Alignment explanation
Indices: 136--197 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
126 CAATTTTCAA
* *
136 TTAATGATTGTTTCCTTTAATCCTCCTTT
1 TTAATAATTGTTTCCTTCAATCCTCCTTT
*
165 TTAATAATTGTTTCCTTCGATCCT-C-TT
1 TTAATAATTGTTTCCTTCAATCCTCCTTT
192 TTAATA
1 TTAATA
198 GAATTCTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 8 0.27
28 1 0.03
29 21 0.70
ACGTcount: A:0.21, C:0.19, G:0.06, T:0.53
Consensus pattern (29 bp):
TTAATAATTGTTTCCTTCAATCCTCCTTT
Found at i:910 original size:49 final size:49
Alignment explanation
Indices: 838--1041 Score: 189
Period size: 49 Copynumber: 4.4 Consensus size: 49
828 TGAACCAAAT
* *
838 TCGTCTTCCTGATGAGACACAGAGAAGCGGATTGAAACAAGCGACGCGG
1 TCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGCGACGCGG
887 TCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGCGACGCGG
1 TCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGCGACGCGG
** * * * * *
936 TAATTTTCCAGATGAGATACTGAG-A--AG--TGAACCAA---A----T
1 TCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGCGACGCGG
* * *
973 TTGTCTTCCTGATGGGATACAGAGAAGCAGATTGAAACAAACGACGCGG
1 TCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGCGACGCGG
* * *
1022 TCATTTTCCTGATAAGATAC
1 TCGTCTTCCTGATGAGATAC
1042 CAAGAAGAAG
Statistics
Matches: 121, Mismatches: 22, Indels: 24
0.72 0.13 0.14
Matches are distributed among these distances:
37 18 0.15
38 1 0.01
40 2 0.02
41 1 0.01
42 7 0.06
44 7 0.06
45 1 0.01
46 2 0.02
48 1 0.01
49 81 0.67
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.22
Consensus pattern (49 bp):
TCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGCGACGCGG
Found at i:1048 original size:86 final size:86
Alignment explanation
Indices: 889--1048 Score: 257
Period size: 86 Copynumber: 1.9 Consensus size: 86
879 CGACGCGGTC
* *
889 GTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGCGACGCGGTAATTTTCCAGATGAGAT
1 GTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAACGACGCGGTAATTTTCCAGATAAGAT
**
954 ACTGAGAAGTGAACCAAATTT
66 ACCAAGAAGTGAACCAAATTT
* * *
975 GTCTTCCTGATGGGATACAGAGAAGCAGATTGAAACAAACGACGCGGTCATTTTCCTGATAAGAT
1 GTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAACGACGCGGTAATTTTCCAGATAAGAT
1040 ACCAAGAAG
66 ACCAAGAAG
1049 AAGACCCAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
86 67 1.00
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (86 bp):
GTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAACGACGCGGTAATTTTCCAGATAAGAT
ACCAAGAAGTGAACCAAATTT
Found at i:1430 original size:86 final size:86
Alignment explanation
Indices: 1269--1430 Score: 243
Period size: 86 Copynumber: 1.9 Consensus size: 86
1259 AGTGACGCGA
* * *
1269 TCGTCTTCTTGATGAGATATAGAGAAGCAGATTGAAACAAGCGACACGGTAATTTTCCAGATAAG
1 TCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAACGACACGGTAATTTTCCAGATAAG
**
1334 ATACTGAGAAGTGAACCAAAT
66 ATACCAAGAAGTGAACCAAAT
* * * *
1355 TCGTCTTCCTGATGGGATACAGAGAAGCAGATTGAAACAAACGACGCGGTCATTTTCCTGATAAG
1 TCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAACGACACGGTAATTTTCCAGATAAG
1420 ATACCAAGAAG
66 ATACCAAGAAG
1431 AAGACCCAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
86 67 1.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (86 bp):
TCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAACGACACGGTAATTTTCCAGATAAG
ATACCAAGAAGTGAACCAAAT
Found at i:1501 original size:335 final size:335
Alignment explanation
Indices: 1109--1768 Score: 1104
Period size: 335 Copynumber: 2.0 Consensus size: 335
1099 NNNNNNNNNN
1109 GGCTCAAAGTAAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTAGAAG
1 GGCTCAAAGTAAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTAGAAG
*
1174 CAATAAAGGTTAGCTTCCTTATGAGATCCTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGACA
66 CAATAAAGGTTAGCTTCCTAATGAGATCCTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGACA
* *
1239 CAGAGAAGCGGATTGAAACAAGTGACGCGATCGTCTTCTTGATGAGATATAGAGAAGCAGATTGA
131 CAGAGAAGCGGATTGAAACAAGCGACGCGATCGTCTTCCTGATGAGATATAGAGAAGCAGATTGA
*
1304 AACAAGCGACACGGTAATTTTCCAGATAAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATG
196 AACAAGCGACACGGTAATTTTCCAGATAAGATACTGAGAAATGAACCAAATTCGTCTTCCTGATG
* * *
1369 GGATACAGAGAAGCAGATTGAAACAAACGACGCGGTCATTTTCCTGATAAGATACCAAGAAGAAG
261 GGATACAGAGAAGCAGATCGAAACAAACAACGCGGTCATTTTCCAGATAAGATACCAAGAAGAAG
1434 ACCCAAACGA
326 ACCCAAACGA
* *
1444 GGCTCAAAGTGAGCGAAATCTTCAAAACCCAGCTTTCTGATGAGACACTGAGAAGCAGGTAGAAG
1 GGCTCAAAGTAAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTAGAAG
* *
1509 CAATAAAGGTTAGCTTCCTAATGAGATCCTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
66 CAATAAAGGTTAGCTTCCTAATGAGATCCTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGACA
* * *
1574 TAGAGAAGCGGATTGAAACAAGCGACGCGGTTGTCTTCCTGATGAGATATAGAGAAGCAGATTGA
131 CAGAGAAGCGGATTGAAACAAGCGACGCGATCGTCTTCCTGATGAGATATAGAGAAGCAGATTGA
** * * *
1639 AACAAGCGATGCGGTCATTTTCCGGATGAGATACTGAGAAATGAACCAAATTCGTCTTCCTGATG
196 AACAAGCGACACGGTAATTTTCCAGATAAGATACTGAGAAATGAACCAAATTCGTCTTCCTGATG
* * * **
1704 GGATACAGAGAAGCGGATCGAAACAAGCAACGCGGTCATTTTCCAGATGAGATACTGAGAAGAAG
261 GGATACAGAGAAGCAGATCGAAACAAACAACGCGGTCATTTTCCAGATAAGATACCAAGAAGAAG
1769 GCCAAGTTAA
Statistics
Matches: 301, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
335 301 1.00
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.21
Consensus pattern (335 bp):
GGCTCAAAGTAAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTAGAAG
CAATAAAGGTTAGCTTCCTAATGAGATCCTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGACA
CAGAGAAGCGGATTGAAACAAGCGACGCGATCGTCTTCCTGATGAGATATAGAGAAGCAGATTGA
AACAAGCGACACGGTAATTTTCCAGATAAGATACTGAGAAATGAACCAAATTCGTCTTCCTGATG
GGATACAGAGAAGCAGATCGAAACAAACAACGCGGTCATTTTCCAGATAAGATACCAAGAAGAAG
ACCCAAACGA
Found at i:1629 original size:49 final size:49
Alignment explanation
Indices: 1555--1671 Score: 180
Period size: 49 Copynumber: 2.4 Consensus size: 49
1545 TGAACCAAAT
*
1555 TCGTCTTCCTGATGAGATATAGAGAAGCGGATTGAAACAAGCGACGCGG
1 TCGTCTTCCTGATGAGATATAGAGAAGCAGATTGAAACAAGCGACGCGG
* *
1604 TTGTCTTCCTGATGAGATATAGAGAAGCAGATTGAAACAAGCGATGCGG
1 TCGTCTTCCTGATGAGATATAGAGAAGCAGATTGAAACAAGCGACGCGG
* * *
1653 TCATTTTCCGGATGAGATA
1 TCGTCTTCCTGATGAGATA
1672 CTGAGAAATG
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 61 1.00
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (49 bp):
TCGTCTTCCTGATGAGATATAGAGAAGCAGATTGAAACAAGCGACGCGG
Found at i:1678 original size:49 final size:49
Alignment explanation
Indices: 1560--1765 Score: 161
Period size: 49 Copynumber: 4.4 Consensus size: 49
1550 CAAATTCGTC
* ** *
1560 TTCCTGATGAGATA-TAGAGAAGCGGATTGAAACAAGCGACGCGGTTGTC
1 TTCCTGATGAGATACT-GAGAAGCAGATTGAAACAAGCGACGCGGTCATT
*
1609 TTCCTGATGAGATA-TAGAGAAGCAGATTGAAACAAGCGATGCGGTCATT
1 TTCCTGATGAGATACT-GAGAAGCAGATTGAAACAAGCGACGCGGTCATT
* * **
1658 TTCCGGATGAGATACTGAG-A--A-A-TGAACCAA---ATTC-GTC---
1 TTCCTGATGAGATACTGAGAAGCAGATTGAAACAAGCGACGCGGTCATT
* * * * *
1695 TTCCTGATGGGATACAGAGAAGCGGATCGAAACAAGCAACGCGGTCATT
1 TTCCTGATGAGATACTGAGAAGCAGATTGAAACAAGCGACGCGGTCATT
*
1744 TTCCAGATGAGATACTGAGAAG
1 TTCCTGATGAGATACTGAGAAG
1766 AAGGCCAAGT
Statistics
Matches: 125, Mismatches: 19, Indels: 26
0.74 0.11 0.15
Matches are distributed among these distances:
37 16 0.13
38 1 0.01
40 3 0.02
41 4 0.03
42 6 0.05
44 7 0.06
45 3 0.02
46 4 0.03
48 1 0.01
49 79 0.63
50 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.22
Consensus pattern (49 bp):
TTCCTGATGAGATACTGAGAAGCAGATTGAAACAAGCGACGCGGTCATT
Found at i:1753 original size:86 final size:86
Alignment explanation
Indices: 1606--1764 Score: 255
Period size: 86 Copynumber: 1.8 Consensus size: 86
1596 CGACGCGGTT
* * * * *
1606 GTCTTCCTGATGAGATATAGAGAAGCAGATTGAAACAAGCGATGCGGTCATTTTCCGGATGAGAT
1 GTCTTCCTGATGAGATACAGAGAAGCAGATCGAAACAAGCAACGCGGTCATTTTCCAGATGAGAT
1671 ACTGAGAAATGAACCAAATTC
66 ACTGAGAAATGAACCAAATTC
* *
1692 GTCTTCCTGATGGGATACAGAGAAGCGGATCGAAACAAGCAACGCGGTCATTTTCCAGATGAGAT
1 GTCTTCCTGATGAGATACAGAGAAGCAGATCGAAACAAGCAACGCGGTCATTTTCCAGATGAGAT
1757 ACTGAGAA
66 ACTGAGAA
1765 GAAGGCCAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 66 1.00
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.23
Consensus pattern (86 bp):
GTCTTCCTGATGAGATACAGAGAAGCAGATCGAAACAAGCAACGCGGTCATTTTCCAGATGAGAT
ACTGAGAAATGAACCAAATTC
Done.