Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007203.1 Kokia drynarioides strain JFW-HI SEQ_121817, 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: 1909
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Found at i:1112 original size:30 final size:28
Alignment explanation
Indices: 1055--1560 Score: 275
Period size: 30 Copynumber: 17.2 Consensus size: 28
1045 TAAACTATTC
**
1055 AAAAATTACCATTTTACCCCCAAACTTCT
1 AAAAA-TACCATTTTACCCTAAAACTTCT
1084 AAAAAT-CCAATTTTTAACCCTAAAACTTC-
1 AAAAATACC-A-TTTT-ACCCTAAAACTTCT
* **
1113 AAAAATTACCATTTTAGCCTCGAACTTCT
1 AAAAA-TACCATTTTACCCTAAAACTTCT
* * *
1142 AAAAATCCCAATTTTGACCCCAAAACTTCC
1 AAAAATACC-ATTTT-ACCCTAAAACTTCT
* **
1172 AAAATTACCATTTTACCCTTGAACTTCT
1 AAAAATACCATTTTACCCTAAAACTTCT
* *
1200 AAAAATCCCATTTTTGACCCCAAAACTTCT
1 AAAAATACCA-TTTT-ACCCTAAAACTTCT
* ** *
1230 AAGAATTACCATTTTACCCTTGAACTTTT
1 AA-AAATACCATTTTACCCTAAAACTTCT
* * *
1259 AAAAATCCCATTTTTGACCCCAAAACTTCA
1 AAAAATACCA-TTTT-ACCCTAAAACTTCT
* *
1289 AAAAATTACCATTTTACCCTTGAAACTTCC
1 AAAAA-TACCATTTTACCC-TAAAACTTCT
* *
1319 AAAAATTACCATTTTACCCCAAAACTTCC
1 AAAAA-TACCATTTTACCCTAAAACTTCT
* * *
1348 AAAAATCCCATTTTTTTGA-CCTCGAAACTTCC
1 AAAAATACCA---TTTT-ACCCT-AAAACTTCT
**
1380 AAAAATTACCATTTTACCCTCGAACTTC-
1 AAAAA-TACCATTTTACCCTAAAACTTCT
* * * *
1408 AAAAAAATCGATTTTTGA-CCTCGAAACTTCC
1 AAAAATA-CCA-TTTT-ACCCT-AAAACTTCT
*** *
1439 AAAAATACCATTTTACCCCCGAACTTCC
1 AAAAATACCATTTTACCCTAAAACTTCT
* * * * *
1467 AAAAGTCCCATTTTTTACCTTGAAACTTCC
1 AAAAATACCA--TTTTACCCTAAAACTTCT
* **
1497 AAAAATTATCATTTTACCCTCGAACTTCCT
1 AAAAA-TACCATTTTACCCTAAAACTT-CT
* ** *
1527 AAAATTACCATTTTACCCCCAAACTTCC
1 AAAAATACCATTTTACCCTAAAACTTCT
1555 AAAAAT
1 AAAAAT
1561 CTTATTTTTG
Statistics
Matches: 370, Mismatches: 75, Indels: 65
0.73 0.15 0.13
Matches are distributed among these distances:
27 3 0.01
28 72 0.19
29 121 0.33
30 129 0.35
31 27 0.07
32 14 0.04
33 4 0.01
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.32
Consensus pattern (28 bp):
AAAAATACCATTTTACCCTAAAACTTCT
Found at i:1266 original size:59 final size:58
Alignment explanation
Indices: 1052--1361 Score: 419
Period size: 58 Copynumber: 5.3 Consensus size: 58
1042 CCCTAAACTA
*** * * *
1052 TTCAAAAATTACCATTTTACCCCCAAACTTCTAAAAATCCAATTTTTAACCCTAAAAC
1 TTCAAAAATTACCATTTTACCCTTGAACTTCTAAAAATCCCATTTTTGACCCCAAAAC
* * *
1110 TTCAAAAATTACCATTTTAGCCTCGAACTTCTAAAAATCCCAATTTTGACCCCAAAAC
1 TTCAAAAATTACCATTTTACCCTTGAACTTCTAAAAATCCCATTTTTGACCCCAAAAC
*
1168 TTCCAAAATTACCATTTTACCCTTGAACTTCTAAAAATCCCATTTTTGACCCCAAAAC
1 TTCAAAAATTACCATTTTACCCTTGAACTTCTAAAAATCCCATTTTTGACCCCAAAAC
* *
1226 TTCTAAGAATTACCATTTTACCCTTGAACTTTTAAAAATCCCATTTTTGACCCCAAAAC
1 TTC-AAAAATTACCATTTTACCCTTGAACTTCTAAAAATCCCATTTTTGACCCCAAAAC
* *
1285 TTCAAAAAATTACCATTTTACCCTTGAAACTTCCAAAAATTACCA-TTTT-ACCCCAAAAC
1 TTC-AAAAATTACCATTTTACCCTTG-AACTTCTAAAAA-TCCCATTTTTGACCCCAAAAC
*
1344 TTCCAAAAA-TCCCATTTT
1 TT-CAAAAATTACCATTTT
1362 TTTGACCTCG
Statistics
Matches: 228, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
58 116 0.51
59 93 0.41
60 15 0.07
61 4 0.02
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.32
Consensus pattern (58 bp):
TTCAAAAATTACCATTTTACCCTTGAACTTCTAAAAATCCCATTTTTGACCCCAAAAC
Found at i:1480 original size:58 final size:59
Alignment explanation
Indices: 1310--1560 Score: 312
Period size: 58 Copynumber: 4.3 Consensus size: 59
1300 TTTTACCCTT
**
1310 GAAACTTCCAAAAATTACCATTTTACCCCAAAACTTCCAAAAATCCCATTTTTTTGACCTC
1 GAAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCA--TTTTTGACCTC
* * *
1371 GAAACTTCCAAAAATTACCATTTTACCCTCGAACTTCAAAAAAAT-CGATTTTTGACCTC
1 GAAACTTCCAAAAATTACCATTTTACCCCCGAACTTC-CAAAAATCCCATTTTTGACCTC
* * *
1430 GAAACTTCCAAAAA-TACCATTTTACCCCCGAACTTCCAAAAGTCCCATTTTTTACCTT
1 GAAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTC
* * * * *
1488 GAAACTTCCAAAAATTATCATTTTACCCTCGAACTTCCTAAAATTACCA-TTTT-ACCCC
1 GAAACTTCCAAAAATTACCATTTTACCCCCGAACTTCC-AAAAATCCCATTTTTGACCTC
*
1546 CAAACTTCCAAAAAT
1 GAAACTTCCAAAAAT
1561 CTTATTTTTG
Statistics
Matches: 168, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
57 5 0.03
58 63 0.38
59 50 0.30
60 8 0.05
61 36 0.21
62 6 0.04
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (59 bp):
GAAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTC
Found at i:1600 original size:59 final size:58
Alignment explanation
Indices: 1054--1606 Score: 408
Period size: 59 Copynumber: 9.4 Consensus size: 58
1044 CTAAACTATT
* * *
1054 CAAAAATTACCATTTTACCCCCAAACTTCTAAAAATCCAATTTTTAACCCTAAAACTT-
1 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTT-ACCCCAAAACTTC
* * * * *
1112 CAAAAATTACCATTTTAGCCTCGAACTTCTAAAAATCCCAATTTTGACCCCAAAACTTC
1 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCC-ATTTTTACCCCAAAACTTC
*** *
1171 C-AAAATTACCATTTTACCCTTGAACTTCTAAAAATCCCATTTTTGACCCCAAAACTTC
1 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTT-ACCCCAAAACTTC
* * *** **
1229 TAAGAATTACCATTTTACCCTTGAACTTTTAAAAATCCCATTTTTGACCCCAAAACTTC
1 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTT-ACCCCAAAACTTC
* ** *
1288 AAAAAATTACCATTTTACCCTTGAAACTTCCAAAAATTACCA-TTTTACCCCAAAACTTC
1 CAAAAATTACCATTTTACCC-CCAAACTTCCAAAAA-TCCCATTTTTACCCCAAAACTTC
* * * * *
1347 CAAAAA-TCCCATTTTTTTGACCTCGAAACTTCCAAAAATTACCA-TTTTACCCTC-GAACTTC
1 CAAAAATTACCA---TTTT-ACCCCCAAACTTCCAAAAA-TCCCATTTTTACCC-CAAAACTTC
* * * * * * **
1408 AAAAAAAT-CGATTTTTGACCTCGAAACTTCCAAAAATACCA-TTTTACCCCCGAACTTC
1 CAAAAATTACCA-TTTT-ACCCCCAAACTTCCAAAAATCCCATTTTTACCCCAAAACTTC
* * *** ** *
1466 C-AAAAGTCCCATTTTTTACCTTGAAACTTCCAAAAATTATCA-TTTTACCCTC-GAACTTC
1 CAAAAATTACCA--TTTTACCCCCAAACTTCCAAAAA-TCCCATTTTTACCC-CAAAACTTC
* ** * *
1525 CTAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTTATTTTTGACCCCGACACTTC
1 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTT-ACCCCAAAACTTC
*
1584 CAAAAATTACCATTTTACTCCCA
1 CAAAAATTACCATTTTACCCCCA
1607 GATGTCCGAA
Statistics
Matches: 432, Mismatches: 42, Indels: 41
0.84 0.08 0.08
Matches are distributed among these distances:
57 14 0.03
58 163 0.38
59 177 0.41
60 24 0.06
61 49 0.11
62 5 0.01
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTACCCCAAAACTTC
Done.