Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012060.1 Kokia drynarioides strain JFW-HI SEQ_127058, 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: 4229
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Found at i:968 original size:29 final size:29
Alignment explanation
Indices: 925--1297 Score: 232
Period size: 29 Copynumber: 12.8 Consensus size: 29
915 GGAGGTCCCT
* *
925 GAACTTTCTAAAAATTATCATTTTACCCCC
1 GAAC-TTCCAAAAATTACCATTTTACCCCC
* * *
955 GAACTTCCAAAAA-TCCCATTTTTAGCCCT
1 GAACTTCCAAAAATTACCA-TTTTACCCCC
* * *
984 GAACCTTCTAAAAATTACCATTTTACCACT
1 GAA-CTTCCAAAAATTACCATTTTACCCCC
* * ***
1014 AAACTTCCAAAAA-TCCCATTTTTGACCC
1 GAACTTCCAAAAATTACCATTTTACCCCC
* * * **
1042 TAA-ATCTAAAAATTACCATTTTACCCTT
1 GAACTTCCAAAAATTACCATTTTACCCCC
**
1070 GAACTTCCAAAAA-T-CTCATTTTTGGCCCC
1 GAACTTCCAAAAATTAC-CA-TTTTACCCCC
* *
1099 GAACCTTCTAAAAATTACCA-TTTACCCTC
1 GAA-CTTCCAAAAATTACCATTTTACCCCC
* *
1128 GAACTTCCAAAAA-TCCCATTTTTGA-CCCT
1 GAACTTCCAAAAATTACCA-TTTT-ACCCCC
*
1157 GAACTTTCTAAAAATTACCATTTTACCCCC
1 GAAC-TTCCAAAAATTACCATTTTACCCCC
* * *
1187 GAACTTCCAAAAA-TCCCAATTTTGA-TCCT
1 GAACTTCCAAAAATTACC-ATTTT-ACCCCC
*
1216 GAACCTTCTAAAAATTACCATTTTACCCCC
1 GAA-CTTCCAAAAATTACCATTTTACCCCC
*
1246 GAACTTCCAAAAA-TCCCATTTTTGA-CCCC
1 GAACTTCCAAAAATTACCA-TTTT-ACCCCC
* *
1275 TAACCTTCCAAAAA-TCCCATTTT
1 GAA-CTTCCAAAAATTACCATTTT
1298 CGACTCCGAA
Statistics
Matches: 264, Mismatches: 55, Indels: 49
0.72 0.15 0.13
Matches are distributed among these distances:
27 12 0.05
28 44 0.17
29 105 0.40
30 88 0.33
31 14 0.05
32 1 0.00
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.32
Consensus pattern (29 bp):
GAACTTCCAAAAATTACCATTTTACCCCC
Found at i:1019 original size:59 final size:59
Alignment explanation
Indices: 921--1297 Score: 534
Period size: 59 Copynumber: 6.5 Consensus size: 59
911 CCCCGGAGGT
* *
921 CCCTGAACTTTCTAAAAATTATCATTTTACCCCCGAACTTCCAAAAATCCCATTTTT-A
1 CCCTGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* **
979 GCCCTGAACCTTCTAAAAATTACCATTTTACCACTAAACTTCCAAAAATCCCATTTTTGA
1 -CCCTGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* ** * *
1039 CCCT-AA--ATCTAAAAATTACCATTTTACCCTTGAACTTCCAAAAATCTCATTTTTGG
1 CCCTGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* *
1095 CCCCGAACCTTCTAAAAATTACCA-TTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
1 CCCTGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* *
1153 CCCTGAACTTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCAATTTTGA
1 CCCTGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
*
1212 TCCTGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
1 CCCTGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* *
1271 CCCCT-AACCTTCCAAAAA-TCCCATTTT
1 -CCCTGAACCTTCTAAAAATTACCATTTT
1298 CGACTCCGAA
Statistics
Matches: 286, Mismatches: 26, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
56 47 0.16
57 2 0.01
58 63 0.22
59 170 0.59
60 4 0.01
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (59 bp):
CCCTGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
Found at i:1315 original size:30 final size:29
Alignment explanation
Indices: 943--1334 Score: 256
Period size: 30 Copynumber: 13.4 Consensus size: 29
933 TAAAAATTAT
943 CATTTT-ACCCCCGAA-CTTCCAAAAATCC
1 CATTTTGA-CCCCGAACCTTCCAAAAATCC
* * * *
971 CATTTTTAGCCCTGAACCTTCTAAAAATTAC
1 CATTTTGA-CCCCGAACCTTCCAAAAA-TCC
* * *
1002 CATTTT-ACCACTAAACTTCCAAAAATCC
1 CATTTTGACCCCGAACCTTCCAAAAATCC
* * * *
1030 CATTTTTGA-CCCTAA--ATCTAAAAATTAC
1 CA-TTTTGACCCCGAACCTTCCAAAAA-TCC
* *
1058 CATTTT-ACCCTTGAA-CTTCCAAAAATCT
1 CATTTTGACCC-CGAACCTTCCAAAAATCC
* * *
1086 CATTTTTGGCCCCGAACCTTCTAAAAATTAC
1 CA-TTTTGACCCCGAACCTTCCAAAAA-TCC
1117 CA-TTT-ACCCTCGAA-CTTCCAAAAATCC
1 CATTTTGACCC-CGAACCTTCCAAAAATCC
* * * *
1144 CATTTTTGACCCTGAACTTTCTAAAAATTAC
1 CA-TTTTGACCCCGAACCTTCCAAAAA-TCC
1175 CATTTT-ACCCCCGAA-CTTCCAAAAATCC
1 CATTTTGA-CCCCGAACCTTCCAAAAATCC
* * * *
1203 CAATTTTGATCCTGAACCTTCTAAAAATTAC
1 C-ATTTTGACCCCGAACCTTCCAAAAA-TCC
1234 CATTTT-ACCCCCGAA-CTTCCAAAAATCC
1 CATTTTGA-CCCCGAACCTTCCAAAAATCC
*
1262 CATTTTTGACCCCTAACCTTCCAAAAATCC
1 CA-TTTTGACCCCGAACCTTCCAAAAATCC
* * * *
1292 CATTTTCGACTCCGAACCCTCCAAAACTAC
1 CATTTT-GACCCCGAACCTTCCAAAAATCC
*
1322 CATTTTGCCCCCG
1 CATTTTGACCCCG
1335 TGCATCCGAA
Statistics
Matches: 283, Mismatches: 52, Indels: 57
0.72 0.13 0.15
Matches are distributed among these distances:
26 1 0.00
27 17 0.06
28 38 0.13
29 104 0.37
30 105 0.37
31 18 0.06
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.31
Consensus pattern (29 bp):
CATTTTGACCCCGAACCTTCCAAAAATCC
Found at i:1681 original size:96 final size:95
Alignment explanation
Indices: 1544--1726 Score: 235
Period size: 96 Copynumber: 1.9 Consensus size: 95
1534 ACTTTAAAAA
* * **
1544 CGAGGCAATATTCTTTATTTTGAATTTTGAAACTTTACGCCTTAACTTACTAGGTGCAATTTTTC
1 CGAGGCAATATTCCTTATTTTGAATTTTGAAACTTTACGCCTTAACTCACTAGGTGCAACCTTTC
1609 CTCAAATCAAAATAATCGAATACCCTTAAT
66 CTCAAATCAAAATAATCGAATACCCTTAAT
* *
1639 CGAGGCAATGTTTCCTTATCTTTG-ATTTTGAAA-TATTGCGCCTTAACTCACTAGGTGCAACCT
1 CGAGGCAAT-ATTCCTTAT-TTTGAATTTTGAAACT-TTACGCCTTAACTCACTAGGTGCAACCT
* ***
1702 TTCTTCAAATCGGGATAATCGAATA
63 TTCCTCAAATCAAAATAATCGAATA
1727 TCCTCTTCTC
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
95 10 0.13
96 61 0.81
97 4 0.05
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.37
Consensus pattern (95 bp):
CGAGGCAATATTCCTTATTTTGAATTTTGAAACTTTACGCCTTAACTCACTAGGTGCAACCTTTC
CTCAAATCAAAATAATCGAATACCCTTAAT
Found at i:3072 original size:23 final size:23
Alignment explanation
Indices: 3045--3095 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
3035 TTTTCGATTT
* * *
3045 ATTTTAAATTTGAATTTAAATTA
1 ATTTTAAAATTAAAATTAAATTA
*
3068 ATTTTAAAATTAAAATTAAATTT
1 ATTTTAAAATTAAAATTAAATTA
3091 ATTTT
1 ATTTT
3096 CAAGTTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTTTAAAATTAAAATTAAATTA
Found at i:3083 original size:18 final size:18
Alignment explanation
Indices: 3048--3091 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
3038 TCGATTTATT
* *
3048 TTAAATTT-GAATTTAAA
1 TTAAATTTAAAATTAAAA
*
3065 TTAATTTTAAAATTAAAA
1 TTAAATTTAAAATTAAAA
3083 TTAAATTTA
1 TTAAATTTA
3092 TTTTCAAGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TTAAATTTAAAATTAAAA
Found at i:3141 original size:14 final size:15
Alignment explanation
Indices: 3122--3150 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3112 TTATTATTAT
3122 AAAGTCC-AATTACA
1 AAAGTCCAAATTACA
3136 AAAGTCCAAATTACA
1 AAAGTCCAAATTACA
3151 TGTCCAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.21
Consensus pattern (15 bp):
AAAGTCCAAATTACA
Done.