Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012966.1 Kokia drynarioides strain JFW-HI SEQ_127984, 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: 3746
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Found at i:1226 original size:30 final size:29
Alignment explanation
Indices: 1190--1292 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 29
1180 CCCCAGAGGT
*
1190 CCCTAAACTATCCAAAAATTATATTTTGAC
1 CCCTAAACT-TCCAAAAATTATATTTTAAC
*
1220 CCCTAAACTTCTCTAAAATTATATTTTAAC
1 CCCTAAACTTC-CAAAAATTATATTTTAAC
* ** * *
1250 ACCTAAACTTTTTAAAAATTACATTTTTAC
1 CCCTAAAC-TTCCAAAAATTATATTTTAAC
*
1280 CCCCAAACATTCC
1 CCCTAAAC-TTCC
1293 CAATTTCCAT
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
29 2 0.03
30 54 0.93
31 2 0.03
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.36
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTATATTTTAAC
Found at i:1363 original size:28 final size:29
Alignment explanation
Indices: 1263--1688 Score: 152
Period size: 29 Copynumber: 14.7 Consensus size: 29
1253 TAAACTTTTT
* *
1263 AAAAATTACATTTTTACCCCCAAACATTCC
1 AAAAATTCCATTTTTACCCTCAAAC-TTCC
* * ** ** *
1293 -CAATTTCCATTTTTGA-CCTTGATTTTCA
1 AAAAATTCCATTTTT-ACCCTCAAACTTCC
* * *
1321 AAAAATTGTCA-TTTTACCCTCAACCATCC
1 AAAAATT-CCATTTTTACCCTCAAACTTCC
* ***
1350 -AAAATTCCATTTTTAACCTCGATTTTTCC
1 AAAAATTCCATTTTTACCCTC-AAACTTCC
1379 AAAAATTACCA-TTTTA-CCTCAAACTTCC
1 AAAAATT-CCATTTTTACCCTCAAACTTCC
* **
1407 AAAAATTCCATTTTTGACCC-CGATTTATCC
1 AAAAATTCCATTTTT-ACCCTCAAACT-TCC
*
1437 -AAAATTACCA-TTTTACCCCCAAACTT-C
1 AAAAATT-CCATTTTTACCCTCAAACTTCC
* * ***
1464 AAAGATTTTCATTTTTA-CCTCGATTTTTCC
1 AAA-AATTCCATTTTTACCCTC-AAACTTCC
1494 AAAAATTACCA-TTTTACCC-CTAAACTTCC
1 AAAAATT-CCATTTTTACCCTC-AAACTTCC
* * **
1523 CAAAATTTCATTTTTGACCC-CGATTCTTCC
1 AAAAATTCCATTTTT-ACCCTC-AAACTTCC
* * *
1553 CAAAATTAC-TATTTTACCCCCAAACTTCC
1 AAAAATTCCAT-TTTTACCCTCAAACTTCC
* * **
1582 AAAAATTTCATTTTTTATCCC-GATTCTTTCC
1 AAAAATTCCA-TTTTTA-CCCTCAAAC-TTCC
* * *
1613 AAAAATACCA-TTTTACCCTCGAA-TGCC
1 AAAAATTCCATTTTTACCCTCAAACTTCC
* * *
1640 TAAAATTTCATTTTTAACCTCAAACTTTCC
1 AAAAATTCCATTTTTACCCTCAAAC-TTCC
*
1670 CAAAATTACCA-TTTTACCC
1 AAAAATT-CCATTTTTACCC
1689 CCCGATACCC
Statistics
Matches: 288, Mismatches: 74, Indels: 68
0.67 0.17 0.16
Matches are distributed among these distances:
27 16 0.06
28 63 0.22
29 111 0.39
30 77 0.27
31 21 0.07
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCTCAAACTTCC
Found at i:1571 original size:59 final size:59
Alignment explanation
Indices: 1264--1690 Score: 396
Period size: 58 Copynumber: 7.3 Consensus size: 59
1254 AAACTTTTTA
* **
1264 AAAATTA-CATTTTTACCCCCAAACATTCCC--AATTTCCATTTTTGACCTTGATT-TTCAA
1 AAAATTACCA-TTTTACCCCCAAAC-TTCCCAAAATTT-CATTTTTGACCTCGATTCTTCCC
** * * * * * * *
1322 AAAATTGTCATTTTACCCTCAACCAT-CCAAAATTCCATTTTTAACCTCGATTTTTCCA
1 AAAATTACCATTTTACCCCCAAACTTCCCAAAATTTCATTTTTGACCTCGATTCTTCCC
* * * *
1380 AAAATTACCATTTTA-CCTCAAACTTCCAAAAATTCCATTTTTGACCCCGATT-TAT-CC
1 AAAATTACCATTTTACCCCCAAACTTCCCAAAATTTCATTTTTGACCTCGATTCT-TCCC
* *
1437 AAAATTACCATTTTACCCCCAAACTT--CAAAGATTTTCATTTTT-ACCTCGATTTTTCCA
1 AAAATTACCATTTTACCCCCAAACTTCCCAAA-A-TTTCATTTTTGACCTCGATTCTTCCC
* *
1495 AAAATTACCATTTTACCCCTAAACTTCCCAAAATTTCATTTTTGACCCCGATTCTTCCC
1 AAAATTACCATTTTACCCCCAAACTTCCCAAAATTTCATTTTTGACCTCGATTCTTCCC
* * * *
1554 AAAATTACTATTTTACCCCCAAACTTCCAAAAATTTCATTTTTTATCC-CGATTCTTTCC
1 AAAATTACCATTTTACCCCCAAACTTCCCAAAATTTCATTTTTGA-CCTCGATTCTTCCC
* * * * * * **
1613 AAAAATACCATTTTACCCTCGAA-TGCCTAAAATTTCATTTTTAACCTC-AAACTTTCCC
1 AAAATTACCATTTTACCCCCAAACTTCCCAAAATTTCATTTTTGACCTCGATTC-TTCCC
1671 AAAATTACCATTTTACCCCC
1 AAAATTACCATTTTACCCCC
1691 CGATACCCAA
Statistics
Matches: 310, Mismatches: 42, Indels: 34
0.80 0.11 0.09
Matches are distributed among these distances:
56 5 0.02
57 55 0.18
58 159 0.51
59 85 0.27
60 6 0.02
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCAAACTTCCCAAAATTTCATTTTTGACCTCGATTCTTCCC
Found at i:1591 original size:117 final size:116
Alignment explanation
Indices: 1263--1690 Score: 464
Period size: 117 Copynumber: 3.7 Consensus size: 116
1253 TAAACTTTTT
* ** **
1263 AAAAATTA-CATTTTTACCCCCAAACATTCCC--AATTTCCATTTTTGACCTTGATTTTCAAAAA
1 AAAAATTACCA-TTTTACCCCTAAAC-TTCCCAAAATTT-CATTTTTGACCCCGATTTTCCCAAA
** * * * *
1325 ATTGTCATTTTACCCTCAACCATCC-AAAATTCCATTTTTAACCTCGATTTTTCC
63 ATTACCATTTTACCCCCAAACTTCCAAAAATTTCATTTTT-ACCTCGATTTTTCC
* * *
1379 AAAAATTACCATTTTACCTC-AAACTTCCAAAAATTCCATTTTTGACCCCGATTTAT-CCAAAAT
1 AAAAATTACCATTTTACCCCTAAACTTCCCAAAATTTCATTTTTGACCCCGATTT-TCCCAAAAT
*
1442 TACCATTTTACCCCCAAACTT-CAAAGATTTTCATTTTTACCTCGATTTTTCC
65 TACCATTTTACCCCCAAACTTCCAAA-AATTTCATTTTTACCTCGATTTTTCC
1494 AAAAATTACCATTTTACCCCTAAACTTCCCAAAATTTCATTTTTGACCCCGATTCTTCCCAAAAT
1 AAAAATTACCATTTTACCCCTAAACTTCCCAAAATTTCATTTTTGACCCCGATT-TTCCCAAAAT
*
1559 TACTATTTTACCCCCAAACTTCCAAAAATTTCATTTTTTATCC-CGATTCTTTCC
65 TACCATTTTACCCCCAAACTTCCAAAAATTTCA-TTTTTA-CCTCGATT-TTTCC
* * * * ** *
1613 AAAAA-TACCATTTTA-CCCTCGAA-TGCCTAAAATTTCATTTTTAACCTCAAACTTTCCCAAAA
1 AAAAATTACCATTTTACCCCT-AAACTTCCCAAAATTTCATTTTTGACC-CCGATTTTCCCAAAA
1675 TTACCATTTTACCCCC
64 TTACCATTTTACCCCC
1691 CGATACCCAA
Statistics
Matches: 270, Mismatches: 27, Indels: 29
0.83 0.08 0.09
Matches are distributed among these distances:
114 5 0.02
115 76 0.28
116 63 0.23
117 84 0.31
118 30 0.11
119 12 0.04
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (116 bp):
AAAAATTACCATTTTACCCCTAAACTTCCCAAAATTTCATTTTTGACCCCGATTTTCCCAAAATT
ACCATTTTACCCCCAAACTTCCAAAAATTTCATTTTTACCTCGATTTTTCC
Done.