Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002614.1 Kokia drynarioides strain JFW-HI SEQ_114829, 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, 895
Length: 1492
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Found at i:620 original size:30 final size:29
Alignment explanation
Indices: 577--802 Score: 176
Period size: 29 Copynumber: 7.7 Consensus size: 29
567 CTAGATTGTC
*
577 CAAAAATCTCATTTTTGACCCTGAAACTTT
1 CAAAAATCCCATTTTT-ACCCTGAAACTTT
* *
607 CAAAATTCCCATTTTTACCCTTG-AACTTC
1 CAAAAATCCCATTTTTACCC-TGAAACTTT
* **
636 CAAAAATCCCATTTTGACCCCAAAACTTT
1 CAAAAATCCCATTTTTACCCTGAAACTTT
* *
665 CAAAATTCCCA-TTTTACCCCT-AAACTTC
1 CAAAAATCCCATTTTTA-CCCTGAAACTTT
* *
693 CAAAAATCACATTTTTTACCCTCGAACCTTT
1 CAAAAATCCCA-TTTTTACCCT-GAAACTTT
* * * *
724 CGAAAAGTACCA-TTTTACACTCG-AACTTC
1 C-AAAAATCCCATTTTTACCCT-GAAACTTT
* *
753 CAAAAATCCCATTTTTGACCCCGAACCTTT
1 CAAAAATCCCATTTTT-ACCCTGAAACTTT
*
783 CAAAAATTACCA-TTTTACCC
1 CAAAAA-TCCCATTTTTACCC
803 CCGAACTTCC
Statistics
Matches: 155, Mismatches: 29, Indels: 25
0.74 0.14 0.12
Matches are distributed among these distances:
28 27 0.17
29 63 0.41
30 48 0.31
31 10 0.06
32 7 0.05
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.32
Consensus pattern (29 bp):
CAAAAATCCCATTTTTACCCTGAAACTTT
Found at i:782 original size:59 final size:58
Alignment explanation
Indices: 575--856 Score: 323
Period size: 59 Copynumber: 4.8 Consensus size: 58
565 CCCTAGATTG
* * * * **
575 TCCAAAAATCTCATTTTTGACCCTGAAACTTTCAAAATTCCCATTTTTACCCTTGAACT
1 TCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAATTACCA-TTTTACCCCCGAACT
* * * **
634 TCCAAAAATCCCA-TTTTGACCCCAAAACTTTCAAAATTCCCATTTTACCCCTAAACT
1 TCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAATTACCATTTTACCCCCGAACT
* * * * *
691 TCCAAAAATCACATTTTTTACCCTCGAACCTTTCGAAAAGTACCATTTTACACTCGAACT
1 TCCAAAAATCCCATTTTTGACCC-CGAACCTTTC-AAAATTACCATTTTACCCCCGAACT
751 TCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAAATTACCATTTTACCCCCGAACT
1 TCCAAAAATCCCATTTTTGACCCCGAACCTTTC-AAAATTACCATTTTACCCCCGAACT
*** * * *
810 TCCAAAAATTTGATTTTTGACTCCGAACCTTCCAAAACTACCATTTT
1 TCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAATTACCATTTT
857 GCCCTCGTGC
Statistics
Matches: 193, Mismatches: 27, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
57 25 0.13
58 48 0.25
59 80 0.41
60 40 0.21
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.33
Consensus pattern (58 bp):
TCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAATTACCATTTTACCCCCGAACT
Found at i:827 original size:29 final size:30
Alignment explanation
Indices: 575--856 Score: 171
Period size: 29 Copynumber: 9.6 Consensus size: 30
565 CCCTAGATTG
* *
575 TCCAAAAA-TCTCATTTTTGACCCTGAAACT
1 TCCAAAAATTC-CATTTTTGACCCCGAACCT
* *
605 TTC-AAAATTCCCATTTTT-ACCCTTGAA-CT
1 TCCAAAAATT-CCATTTTTGACCC-CGAACCT
* * *
634 TCCAAAAATCCCA-TTTTGACCCCAAAACT
1 TCCAAAAATTCCATTTTTGACCCCGAACCT
* * *
663 TTC-AAAATTCCCA-TTTT-ACCCCTAAACT
1 TCCAAAAATT-CCATTTTTGACCCCGAACCT
*
691 TCCAAAAA-TCACATTTTTTACCCTCGAACCTT
1 TCCAAAAATTC-CATTTTTGACCC-CGAACC-T
* * * *
723 TCGAAAAGTACCA-TTTT-ACACTCGAA-CT
1 TCCAAAAATTCCATTTTTGAC-CCCGAACCT
*
751 TCCAAAAATCCCATTTTTGACCCCGAACCT
1 TCCAAAAATTCCATTTTTGACCCCGAACCT
*
781 TTCAAAAATTACCA-TTTT-ACCCCCGAA-CT
1 TCCAAAAATT-CCATTTTTGA-CCCCGAACCT
** *
810 TCCAAAAATTTGATTTTTGACTCCGAACCT
1 TCCAAAAATTCCATTTTTGACCCCGAACCT
* *
840 TCCAAAACTACCATTTT
1 TCCAAAAATTCCATTTT
857 GCCCTCGTGC
Statistics
Matches: 200, Mismatches: 29, Indels: 46
0.73 0.11 0.17
Matches are distributed among these distances:
27 1 0.00
28 38 0.19
29 70 0.35
30 68 0.34
31 13 0.06
32 9 0.05
33 1 0.00
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.33
Consensus pattern (30 bp):
TCCAAAAATTCCATTTTTGACCCCGAACCT
Found at i:1226 original size:96 final size:96
Alignment explanation
Indices: 1080--1261 Score: 253
Period size: 96 Copynumber: 1.9 Consensus size: 96
1070 ATTTTAAAAA
* **
1080 AATCGAGGCAATATTCCTTTATTTCGATTTTTGAAAATTTATGCCTTAACTCACTAGGTGCATTC
1 AATCGAGGCAATATTCCTTTATTTCGATTTCTGAAAATTTATGCCTTAACTCACTAGGTGCAACC
1145 TTTCTTCAAATCGAAATAATCGAACACCCTT
66 TTTCTTCAAATCGAAATAATCGAACACCCTT
* *
1176 AATCGAGGCAATGTTTCC-TTATCTTCGA-TTCTGAAATATTT-TGCCTTAACTTACTAGGTGCA
1 AATCGAGGCAAT-ATTCCTTTAT-TTCGATTTCTGAAA-ATTTATGCCTTAACTCACTAGGTGCA
* *
1238 ACCTTTCTTCGAATCGAGATAATC
63 ACCTTTCTTCAAATCGAAATAATC
1262 AAATATCCTT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
96 63 0.83
97 13 0.17
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (96 bp):
AATCGAGGCAATATTCCTTTATTTCGATTTCTGAAAATTTATGCCTTAACTCACTAGGTGCAACC
TTTCTTCAAATCGAAATAATCGAACACCCTT
Done.