Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002825.1 Kokia drynarioides strain JFW-HI SEQ_115182, 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: 76891
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 55 characters in sequence are not A, C, G, or T
Found at i:1698 original size:17 final size:17
Alignment explanation
Indices: 1676--1714 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1666 AGGTGGAGAA
* *
1676 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
1693 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
1710 CTTGT
1 CTTGT
1715 CAAGGTAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:8383 original size:2 final size:2
Alignment explanation
Indices: 8376--8405 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
8366 TCCAACAATG
*
8376 AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8406 GCAGAGACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11132 original size:18 final size:19
Alignment explanation
Indices: 11106--11141 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
11096 TTTGTGTTAT
*
11106 AAATTACATA-ATATATAA
1 AAATAACATACATATATAA
11124 AAATAACATACATATATA
1 AAATAACATACATATATA
11142 TATATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATAACATACATATATAA
Found at i:45710 original size:6 final size:6
Alignment explanation
Indices: 45699--45724 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
45689 TGCTTCTTTT
45699 CCACCG CCACCG CCACCG CCACCG CC
1 CCACCG CCACCG CCACCG CCACCG CC
45725 GAGAACCGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.69, G:0.15, T:0.00
Consensus pattern (6 bp):
CCACCG
Found at i:54300 original size:37 final size:37
Alignment explanation
Indices: 54209--54480 Score: 221
Period size: 37 Copynumber: 7.4 Consensus size: 37
54199 AATCGTATGT
* *
54209 CTTCCTTCAACCCTTCAAACTCCCCACTTTCTTCTTA
1 CTTCCTTCAACCCTTCAAGCTCCCTACTTTCTTCTTA
* * * *
54246 CTTCATTCCACACTTCAAGCTCCCTACGTTCTTCTTA
1 CTTCCTTCAACCCTTCAAGCTCCCTACTTTCTTCTTA
* * *
54283 CTTCCTTAAACCATTCAAGCT-CCTACTTTCTTCTCA
1 CTTCCTTCAACCCTTCAAGCTCCCTACTTTCTTCTTA
* * * ** * *
54319 ATTCCTTCAACCCTTAAACCTCCCTACAATCTACCGT-
1 CTTCCTTCAACCCTTCAAGCTCCCTACTTTCT-TCTTA
* * * * *
54356 CTTCCTTTAATCCTTAAAGCTCCTTAATTTCTTC-TA
1 CTTCCTTCAACCCTTCAAGCTCCCTACTTTCTTCTTA
* * * * * *
54392 GATTCATTCAACCCTTGAAGATCCCTACGTTCTTTCCT-
1 -CTTCCTTCAACCCTTCAAGCTCCCTACTTTC-TTCTTA
54430 CTTCCTTCAACCCTTCAAGCTCCCTACTTTCTTCGTTA
1 CTTCCTTCAACCCTTCAAGCTCCCTACTTTCTTC-TTA
*
54468 -TTCCTTGAACCCT
1 CTTCCTTCAACCCT
54481 ATTCATCCCA
Statistics
Matches: 179, Mismatches: 48, Indels: 16
0.74 0.20 0.07
Matches are distributed among these distances:
35 1 0.01
36 33 0.18
37 140 0.78
38 4 0.02
39 1 0.01
ACGTcount: A:0.21, C:0.37, G:0.04, T:0.38
Consensus pattern (37 bp):
CTTCCTTCAACCCTTCAAGCTCCCTACTTTCTTCTTA
Found at i:54479 original size:74 final size:73
Alignment explanation
Indices: 54208--54480 Score: 257
Period size: 74 Copynumber: 3.7 Consensus size: 73
54198 AAATCGTATG
* * * * *
54208 TCTTCCTTCAACCCTTCAAACTCCCCACTTTCTTCT-TACTTCATTCCACACTTCAAGCTCCCTA
1 TCTTCCTTCAACCCTTCAAGCTCCCTACTTTCTTCTATA-TTCATTCAACCCTTAAAGCTCCCTA
*
54272 CGTTCTTCT
65 CGTTCTTCC
* * * *
54281 TACTTCCTTAAACCATTCAAGCT-CCTACTTTCTTCTCA-ATTCCTTCAACCCTTAAACCTCCCT
1 T-CTTCCTTCAACCCTTCAAGCTCCCTACTTTCTTCT-ATATTCATTCAACCCTTAAAGCTCCCT
** *
54344 ACAATCTACC
64 ACGTTCTTCC
* * * * * * * *
54354 GTCTTCCTTTAATCCTTAAAGCTCCTTAATTTCTTCTAGATTCATTCAACCCTTGAAGATCCCTA
1 -TCTTCCTTCAACCCTTCAAGCTCCCTACTTTCTTCTATATTCATTCAACCCTTAAAGCTCCCTA
54419 CGTTCTTTCC
65 CGTTC-TTCC
* *
54429 TCTTCCTTCAACCCTTCAAGCTCCCTACTTTCTTCGT-TATTCCTTGAACCCT
1 TCTTCCTTCAACCCTTCAAGCTCCCTACTTTCTTC-TATATTCATTCAACCCT
54481 ATTCATCCCA
Statistics
Matches: 158, Mismatches: 34, Indels: 15
0.76 0.16 0.07
Matches are distributed among these distances:
73 56 0.35
74 98 0.62
75 4 0.03
ACGTcount: A:0.21, C:0.37, G:0.04, T:0.38
Consensus pattern (73 bp):
TCTTCCTTCAACCCTTCAAGCTCCCTACTTTCTTCTATATTCATTCAACCCTTAAAGCTCCCTAC
GTTCTTCC
Found at i:55476 original size:37 final size:37
Alignment explanation
Indices: 55427--55779 Score: 268
Period size: 37 Copynumber: 9.5 Consensus size: 37
55417 ATCGCATGCT
* *
55427 TTCCTTCCACCCTTCAAGCTCCCTACATTCTTCCTTC
1 TTCCTTCAACCCTTCAAGCTCCCTACTTTCTTCCTTC
* * * *
55464 TTCCTTCAACCCTTCAATCTCCCTATTTTCTTCTTTA
1 TTCCTTCAACCCTTCAAGCTCCCTACTTTCTTCCTTC
* *
55501 TTCCTTCAACACTTGAAGCTCCCTACTTTCTT-CTTGAC
1 TTCCTTCAACCCTTCAAGCTCCCTACTTTCTTCCTT--C
* * * * *
55539 -TCCTTTAACCGTTCAAGCTCCTTACGTTCTTCCCTC
1 TTCCTTCAACCCTTCAAGCTCCCTACTTTCTTCCTTC
* * ***
55575 TTCCTTCAACCCTTGAAGATTAATA-TGTTCTTCCCTTC
1 TTCCTTCAACCCTTCAAGCTCCCTACT-TTCTT-CCTTC
* * *
55613 TT-CTTCAACCATTTAAGCTTCCTACTTTCTTTCC-TC
1 TTCCTTCAACCCTTCAAGCTCCCTACTTTC-TTCCTTC
* **
55649 TTCCTTCAACCCTTGAAGCTCCCTACTTTCTTTCC-GA
1 TTCCTTCAACCCTTCAAGCTCCCTACTTTC-TTCCTTC
* * * * * *
55686 TTCATTCAACCCTTGAAGATCCATACCTTCTTCCCTC
1 TTCCTTCAACCCTTCAAGCTCCCTACTTTCTTCCTTC
* * *** **
55723 TTTCTTCAACCCTTTAAGCTTTTTACTTTCTTCCTGA
1 TTCCTTCAACCCTTCAAGCTCCCTACTTTCTTCCTTC
*
55760 TTCCTTCAATCCTTCAAGCT
1 TTCCTTCAACCCTTCAAGCT
55780 TTCTATTTTG
Statistics
Matches: 248, Mismatches: 58, Indels: 20
0.76 0.18 0.06
Matches are distributed among these distances:
36 11 0.04
37 226 0.91
38 11 0.04
ACGTcount: A:0.17, C:0.35, G:0.05, T:0.42
Consensus pattern (37 bp):
TTCCTTCAACCCTTCAAGCTCCCTACTTTCTTCCTTC
Found at i:55631 original size:111 final size:110
Alignment explanation
Indices: 55428--55779 Score: 327
Period size: 111 Copynumber: 3.2 Consensus size: 110
55418 TCGCATGCTT
* * * ** * *
55428 TCCTTCCACCCTTCAAGCTCCCTACATTCTTCCTTCTTCCTTCAACCCTTCAATCTCCCTATTTT
1 TCCTT-CAACCTTCAAGCTCCCTACATTCTTCCCTCTTCCTTCAACCCTTGAAGATCCATATCTT
* * * * *
55493 CTT-CTTTATTCCTTCAA-CACTTGAAGCTCCCTACTTTCTTCTTGAC
65 CTTCCCTTCTT-CTTCAACCA-TTTAAGCTTCCTACTTTCTTCCTGAC
* * * ** *
55539 TCCTTTAACCGTTCAAGCTCCTTACGTTCTTCCCTCTTCCTTCAACCCTTGAAGATTAATATGTT
1 TCCTTCAACC-TTCAAGCTCCCTACATTCTTCCCTCTTCCTTCAACCCTTGAAGATCCATATCTT
55604 CTTCCCTTCTTCTTCAACCATTTAAGCTTCCTACTTTCTTTCCT--C
65 CTTCCCTTCTTCTTCAACCATTTAAGCTTCCTACTTTC-TTCCTGAC
* * * ** * *
55649 TTCCTTCAACCCTTGAAGCTCCCTACTTTCTTTCCGATTCATTCAACCCTTGAAGATCCATACCT
1 -TCCTTCAA-CCTTCAAGCTCCCTACATTCTTCCCTCTTCCTTCAACCCTTGAAGATCCATATCT
* ** *
55714 TCTTCCC-TCTTTCTTCAACCCTTTAAGCTTTTTACTTTCTTCCTGAT
64 TCTTCCCTTC-TTCTTCAACCATTTAAGCTTCCTACTTTCTTCCTGAC
55761 TCCTTCAATCCTTCAAGCT
1 TCCTTCAA-CCTTCAAGCT
55780 TTCTATTTTG
Statistics
Matches: 197, Mismatches: 35, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
110 11 0.06
111 173 0.88
112 13 0.07
ACGTcount: A:0.17, C:0.36, G:0.05, T:0.42
Consensus pattern (110 bp):
TCCTTCAACCTTCAAGCTCCCTACATTCTTCCCTCTTCCTTCAACCCTTGAAGATCCATATCTTC
TTCCCTTCTTCTTCAACCATTTAAGCTTCCTACTTTCTTCCTGAC
Found at i:56693 original size:37 final size:37
Alignment explanation
Indices: 56652--56871 Score: 172
Period size: 37 Copynumber: 6.0 Consensus size: 37
56642 TTCAATATTC
* * *
56652 CAAGCTCCCTAATTTCTTCTCGCTTCCTTCAACCCTT
1 CAAGCTCCCTACTTTCTTCCCGATTCCTTCAACCCTT
* * * * **
56689 CAAGCTTCCTAATTTCATCCCGATTCATTCATTCCTT
1 CAAGCTCCCTACTTTCTTCCCGATTCCTTCAACCCTT
* * * ** * *
56726 GAAGATCTCTACGCTCTTCCCTATTCCTTTAACCCTT
1 CAAGCTCCCTACTTTCTTCCCGATTCCTTCAACCCTT
* * * * *
56763 CAAACCCCCTACCTTCTTCCCCATTCCTTTAACCCTT
1 CAAGCTCCCTACTTTCTTCCCGATTCCTTCAACCCTT
* * * *
56800 CAAACT-CCTATTTTCTTTCTGATTCCTTCAACCCTT
1 CAAGCTCCCTACTTTCTTCCCGATTCCTTCAACCCTT
* ** *
56836 CGAGCTCCCTACTTTCTTCCCTCTTTCTTCAACCCT
1 CAAGCTCCCTACTTTCTTCCCGATTCCTTCAACCCT
56872 CCTCATCCCA
Statistics
Matches: 139, Mismatches: 43, Indels: 2
0.76 0.23 0.01
Matches are distributed among these distances:
36 28 0.20
37 111 0.80
ACGTcount: A:0.18, C:0.39, G:0.05, T:0.39
Consensus pattern (37 bp):
CAAGCTCCCTACTTTCTTCCCGATTCCTTCAACCCTT
Found at i:59503 original size:3 final size:3
Alignment explanation
Indices: 59495--59520 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
59485 AAATGGACCT
59495 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
59521 GTATTTTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:59546 original size:3 final size:3
Alignment explanation
Indices: 59533--59564 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
59523 ATTTTGCAAG
59533 TTA TCTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA T
59565 AATGATTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:63852 original size:29 final size:28
Alignment explanation
Indices: 63806--63878 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
63796 TTTTTAATAA
63806 AAAAATATTAAAAGTTTATTAAAAATTAC
1 AAAAATATTAAAAGTTTA-TAAAAATTAC
* *
63835 AAAAAT-TGTAAAATTTTATAAAAATTGTAA
1 AAAAATAT-TAAAAGTTTATAAAAA-T-TAC
63865 AAAAATATATAAAA
1 AAAAATAT-TAAAA
63879 AATATATAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 7 0.19
29 16 0.43
30 8 0.22
31 6 0.16
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (28 bp):
AAAAATATTAAAAGTTTATAAAAATTAC
Found at i:63860 original size:11 final size:11
Alignment explanation
Indices: 63844--63918 Score: 50
Period size: 11 Copynumber: 7.2 Consensus size: 11
63834 CAAAAATTGT
*
63844 AAAATTTTATA
1 AAAATTATATA
*
63855 AAAATTGTA-A
1 AAAATTATATA
*
63865 AAAAATATATA
1 AAAATTATATA
*
63876 AAAAATATATA
1 AAAATTATATA
* *
63887 GAAA-TATAGA
1 AAAATTATATA
*
63897 AAAAATA-AT-
1 AAAATTATATA
*
63906 AAAATTTTATA
1 AAAATTATATA
63917 AA
1 AA
63919 CTAGAAAGAA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
9 5 0.10
10 19 0.37
11 27 0.53
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (11 bp):
AAAATTATATA
Found at i:63873 original size:19 final size:19
Alignment explanation
Indices: 63803--63878 Score: 55
Period size: 19 Copynumber: 3.8 Consensus size: 19
63793 GTCTTTTTAA
*
63803 TAAAAAAATATTAAAAGTT-
1 TAAAAAAATA-TAAAAATTG
* *
63822 TATTAAAAATTACAAAAATTG
1 TA--AAAAAATATAAAAATTG
***
63843 TAAAATTTTATAAAAATTG
1 TAAAAAAATATAAAAATTG
63862 TAAAAAAATATATAAAA
1 TAAAAAAATATA-AAAA
63879 AATATATAGA
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
19 25 0.57
20 10 0.23
21 9 0.20
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (19 bp):
TAAAAAAATATAAAAATTG
Found at i:63891 original size:21 final size:19
Alignment explanation
Indices: 63866--63910 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
63856 AAATTGTAAA
*
63866 AAAATATATAAAAAATATAT
1 AAAATATAGAAAAAATA-AT
63886 AGAAATATAGAAAAAATAAT
1 A-AAATATAGAAAAAATAAT
63906 AAAAT
1 AAAAT
63911 TTTATAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 4 0.17
20 4 0.17
21 15 0.65
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (19 bp):
AAAATATAGAAAAAATAAT
Found at i:65176 original size:18 final size:19
Alignment explanation
Indices: 65147--65189 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
65137 AAATTTAATT
65147 AAAATTTATAAAATTATC-A
1 AAAATTTAT-AAATTATCTA
*
65166 AAAATTT-TAAATTTTCTA
1 AAAATTTATAAATTATCTA
65184 AAAATT
1 AAAATT
65190 CATTATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
18 8 0.36
19 7 0.32
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATTTATAAATTATCTA
Found at i:70799 original size:2 final size:2
Alignment explanation
Indices: 70782--70816 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
70772 CAGATACAAG
*
70782 TA TA TG TA TGA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
70817 AGAAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
TA
Done.