Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007400.1 Kokia drynarioides strain JFW-HI SEQ_122019, 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: 18365
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:692 original size:36 final size:35
Alignment explanation
Indices: 587--1176 Score: 542
Period size: 37 Copynumber: 16.3 Consensus size: 35
577 GCTTTATCTG
* *
587 AACCTTTTTAAGGTTGCCTTAGA-TGGTCTA-CCAT
1 AACCTTTTTAAGGTTGCCTTAGACAGGTCTATCC-C
* *
621 AACTTTTTTAAGGTTGCTTTAGAC-GAGTCTA-CCC
1 AACCTTTTTAAGGTTGCCTTAGACAG-GTCTATCCC
*
655 AAACCTTTTTAAGGATGCCTTAGACAGGTCTATCCC
1 -AACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCC
* *
691 AACCGTTTTTAAAGGTTACTTTAGACAAGGTCTATCCC
1 AACC-TTTTT-AAGGTTGCCTTAGAC-AGGTCTATCCC
* * * *
729 AACCTTTTTAAGGTTGCCTTAGATAGGTTTATACT
1 AACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCC
* *
764 AACCTTTTTTAAAGTTTGACTTAGACAAGGTCTATCCC
1 AACC-TTTTT-AAGGTTGCCTTAGAC-AGGTCTATCCC
* * * * * *
802 AATCTTTTTAAGGTTTCCCTAGACGGGTCAATTCC
1 AACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCC
**
837 AACCTTTTTTTATATTTTGCCTTAGACTAGGTCTATCCC
1 AACC--TTTTTA-AGGTTGCCTTAGAC-AGGTCTATCCC
* *
876 TACCTTTTTAAGGTTGCTTTAGACAGGTCTATCCC
1 AACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCC
* * * *
911 AACCTTTTTAAAGTTACCTTGGACAAGGTCTGTCCC
1 AACCTTTTTAAGGTTGCCTTAGAC-AGGTCTATCCC
* *
947 AACCTTTTTTAAAGTTGCCTTAGACAAGATCTATCCC
1 AACC-TTTTTAAGGTTGCCTTAGAC-AGGTCTATCCC
* *
984 AACCTTTTTTAAAGGTTGCCTTAGAGAATGTCTATCCC
1 AACC-TTTTT-AAGGTTGCCTTAGA-CAGGTCTATCCC
* *
1022 AACCTTTTTAAGGTTTCCTTAGACAAGGTCTATCCT
1 AACCTTTTTAAGGTTGCCTTAGAC-AGGTCTATCCC
1058 AACCTTTTTAAAGGTTGCCTTAGACAAGGTCTAT-CC
1 AACCTTTTT-AAGGTTGCCTTAGAC-AGGTCTATCCC
* ** *
1094 AACTTTTTTAAGGTTGCCTTAGATGGGTCTATCCT
1 AACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCC
* * * *
1129 AACCTTTCTTAAAAGGTTGTCTTAGACAAGATTTATCCT
1 AACCTTT-TT--AAGGTTGCCTTAGAC-AGGTCTATCCC
1168 AACCTTTTT
1 AACCTTTTT
1177 TAAAGGTCGA
Statistics
Matches: 459, Mismatches: 71, Indels: 48
0.79 0.12 0.08
Matches are distributed among these distances:
34 29 0.06
35 111 0.24
36 104 0.23
37 112 0.24
38 77 0.17
39 26 0.06
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.38
Consensus pattern (35 bp):
AACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCC
Found at i:747 original size:73 final size:72
Alignment explanation
Indices: 587--1176 Score: 636
Period size: 73 Copynumber: 8.1 Consensus size: 72
577 GCTTTATCTG
* * * * *
587 AACCTTTTTAAGGTTGCCTTAGA-TGGTCTA--CCATAACTTTTTTAAGGTTGCTTTAGACGA-G
1 AACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCCA-ACCTTTTTAAAGGTTGCCTTAGACAAGG
648 TCTA-CCC
65 TCTATCCC
* * *
655 AAACCTTTTTAAGGATGCCTTAGACAGGTCTATCCCAACCGTTTTTAAAGGTTACTTTAGACAAG
1 -AACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCCAACC-TTTTTAAAGGTTGCCTTAGACAAG
720 GTCTATCCC
64 GTCTATCCC
* * * * * *
729 AACCTTTTTAAGGTTGCCTTAGATAGGTTTATACTAACCTTTTTTAAAGTTTGACTTAGACAAGG
1 AACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCCAACC-TTTTTAAAGGTTGCCTTAGACAAGG
794 TCTATCCC
65 TCTATCCC
* * * * * * * ** *
802 AATCTTTTTAAGGTTTCCCTAGACGGGTCAATTCCAACCTTTTTTTATATTTTGCCTTAGACTAG
1 AACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCCAACC--TTTTTAAAGGTTGCCTTAGACAAG
867 GTCTATCCC
64 GTCTATCCC
* * * *
876 TACCTTTTTAAGGTTGCTTTAGACAGGTCTATCCCAACCTTTTTAAA-GTTACCTTGGACAAGGT
1 AACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGT
*
940 CTGTCCC
66 CTATCCC
* * *
947 AACCTTTTTTAAAGTTGCCTTAGACAAGATCTATCCCAACCTTTTTTAAAGGTTGCCTTAGAGAA
1 AACC-TTTTTAAGGTTGCCTTAGAC-AGGTCTATCCCAACC-TTTTTAAAGGTTGCCTTAGACAA
*
1012 TGTCTATCCC
63 GGTCTATCCC
* *
1022 AACCTTTTTAAGGTTTCCTTAGACAAGGTCTATCCTAACCTTTTTAAAGGTTGCCTTAGACAAGG
1 AACCTTTTTAAGGTTGCCTTAGAC-AGGTCTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGG
1087 TCTAT-CC
65 TCTATCCC
* ** * *
1094 AACTTTTTTAAGGTTGCCTTAGATGGGTCTATCCTAACCTTTCTTAAAAGGTTGTCTTAGACAAG
1 AACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCCAACCTTT-TT-AAAGGTTGCCTTAGACAAG
* * *
1159 ATTTATCCT
64 GTCTATCCC
1168 AACCTTTTT
1 AACCTTTTT
1177 TAAAGGTCGA
Statistics
Matches: 440, Mismatches: 67, Indels: 23
0.83 0.13 0.04
Matches are distributed among these distances:
69 22 0.05
70 6 0.01
71 41 0.09
72 73 0.17
73 162 0.37
74 113 0.26
75 23 0.05
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.38
Consensus pattern (72 bp):
AACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGT
CTATCCC
Found at i:6643 original size:37 final size:38
Alignment explanation
Indices: 6567--6660 Score: 118
Period size: 37 Copynumber: 2.5 Consensus size: 38
6557 AACACCACTT
* * *
6567 CATCCATCATACACACCATAATTGAGCTAAGGTAAGCC
1 CATCCACCCTACACACCACAATTGAGCTAAGGTAAGCC
* * * *
6605 CATCCACCTTGCACACCACAA-TGAGCTATGGTAGGCC
1 CATCCACCCTACACACCACAATTGAGCTAAGGTAAGCC
6642 CATCCACCCTACACACCAC
1 CATCCACCCTACACACCAC
6661 GATAGTGGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 31 0.65
38 17 0.35
ACGTcount: A:0.32, C:0.37, G:0.13, T:0.18
Consensus pattern (38 bp):
CATCCACCCTACACACCACAATTGAGCTAAGGTAAGCC
Found at i:9265 original size:76 final size:76
Alignment explanation
Indices: 9167--9320 Score: 299
Period size: 76 Copynumber: 2.0 Consensus size: 76
9157 GAATCTATTC
9167 TGTCATACTAGGCTCTTAGAGCTTGCTTAAGGCCATAAAGAGCCTTCTTAAGCTTATAAACTTTA
1 TGTCATACTAGGCTCTTAGAGCTTGCTTAAGGCCATAAAGAGCCTTCTTAAGCTTATAAACTTTA
9232 TGCTCATCTCT
66 TGCTCATCTCT
*
9243 TGTCATACTAGGCTCTTGGAGCTTGCTTAAGGCCATAAAGAGCCTTCTTAAGCTTATAAACTTTA
1 TGTCATACTAGGCTCTTAGAGCTTGCTTAAGGCCATAAAGAGCCTTCTTAAGCTTATAAACTTTA
9308 TGCTCATCTCT
66 TGCTCATCTCT
9319 TG
1 TG
9321 GAACTATAAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (76 bp):
TGTCATACTAGGCTCTTAGAGCTTGCTTAAGGCCATAAAGAGCCTTCTTAAGCTTATAAACTTTA
TGCTCATCTCT
Found at i:11485 original size:23 final size:23
Alignment explanation
Indices: 11455--11501 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
11445 CTTCTTCCCT
11455 TTGAAGTTGGAAGAAATTGGAAC
1 TTGAAGTTGGAAGAAATTGGAAC
11478 TTGAAGTTGGAAGAAATTGGAAC
1 TTGAAGTTGGAAGAAATTGGAAC
11501 T
1 T
11502 GACTTTCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.30, T:0.28
Consensus pattern (23 bp):
TTGAAGTTGGAAGAAATTGGAAC
Found at i:14163 original size:43 final size:43
Alignment explanation
Indices: 14115--14198 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
14105 TTCAGGAGAT
*
14115 ACAACTTGTTAATAATTGTCATCCAAATGTACATAGATAAGAA
1 ACAACTTGTTAATAATTGTCACCCAAATGTACATAGATAAGAA
14158 ACAACTTGTTAATAATTGTCACCCAAATGTACATAGATAAG
1 ACAACTTGTTAATAATTGTCACCCAAATGTACATAGATAAG
14199 CAGGTTACAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (43 bp):
ACAACTTGTTAATAATTGTCACCCAAATGTACATAGATAAGAA
Found at i:16794 original size:22 final size:24
Alignment explanation
Indices: 16750--16795 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
16740 TTATATTTTT
*
16750 ATTCAAAAAGTAAAAATGCTATTA
1 ATTCAAAAAGTAAAAATGATATTA
*
16774 ATTCAATAA-TAAAAA-GATATTA
1 ATTCAAAAAGTAAAAATGATATTA
16796 TATCTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 6 0.30
24 8 0.40
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (24 bp):
ATTCAAAAAGTAAAAATGATATTA
Done.