Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012952.1 Kokia drynarioides strain JFW-HI SEQ_127970, 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: 82699
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 353 characters in sequence are not A, C, G, or T
Found at i:2113 original size:19 final size:19
Alignment explanation
Indices: 2091--2127 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2081 CAATCTCTAT
*
2091 ATTTTATTTTTGAAATAAA
1 ATTTTAATTTTGAAATAAA
*
2110 ATTTTAATTTTGACATAA
1 ATTTTAATTTTGAAATAA
2128 TTTGATATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (19 bp):
ATTTTAATTTTGAAATAAA
Found at i:3533 original size:17 final size:17
Alignment explanation
Indices: 3511--3544 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3501 TCTTTTTAAT
*
3511 TAAATTTAAATTTAAAA
1 TAAATTAAAATTTAAAA
3528 TAAATTAAAATTTAAAA
1 TAAATTAAAATTTAAAA
3545 ATTGGGTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTAAAATTTAAAA
Found at i:4106 original size:23 final size:22
Alignment explanation
Indices: 4071--4114 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
4061 TAATTTCATT
*
4071 ATTTATAGATAATATTCTAATC
1 ATTTATAAATAATATTCTAATC
4093 ATTTGATAAATAATATTCTAAT
1 ATTT-ATAAATAATATTCTAAT
4115 AACATTTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (22 bp):
ATTTATAAATAATATTCTAATC
Found at i:6254 original size:16 final size:16
Alignment explanation
Indices: 6235--6278 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
6225 TTTATTTTAA
6235 TATTTAATCATTTTTT
1 TATTTAATCATTTTTT
* *
6251 TATTTATTAAATTTTTT
1 TATTTAAT-CATTTTTT
*
6268 TATATAATCAT
1 TATTTAATCAT
6279 CTTAATATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTAATCATTTTTT
Found at i:17564 original size:2 final size:2
Alignment explanation
Indices: 17551--17588 Score: 51
Period size: 2 Copynumber: 18.5 Consensus size: 2
17541 GCCCTCCTAC
17551 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA -A TA GTA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T
17589 GATTTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 1 0.03
2 28 0.85
3 4 0.12
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:31671 original size:19 final size:20
Alignment explanation
Indices: 31647--31687 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
31637 TTAACGGTAT
31647 TTTATTA-ATTAATAATAAA
1 TTTATTATATTAATAATAAA
* *
31666 TTTATTATTTTAATATTAAA
1 TTTATTATATTAATAATAAA
31686 TT
1 TT
31688 AAATTTAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTATTATATTAATAATAAA
Found at i:31763 original size:61 final size:59
Alignment explanation
Indices: 31674--31790 Score: 146
Period size: 61 Copynumber: 1.9 Consensus size: 59
31664 AATTTATTAT
* ** * *
31674 TTTAATATTAAATTAAATTTAATGTTTATTTTG-TAGAGAATATTCTATTAATTTAATAAAA
1 TTTAATATTAAATTAAATCTAACATTTATCTTGATA-AG--TATTATATTAATTTAATAAAA
*
31735 TTTAATATTAAATTTAATCTAACATTTATCTTGATAAGTATTATATTAATTTAATA
1 TTTAATATTAAATTAAATCTAACATTTATCTTGATAAGTATTATATTAATTTAATA
31791 TTAGAGTGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 17 0.35
61 30 0.61
62 2 0.04
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (59 bp):
TTTAATATTAAATTAAATCTAACATTTATCTTGATAAGTATTATATTAATTTAATAAAA
Found at i:35489 original size:6 final size:6
Alignment explanation
Indices: 35478--35505 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
35468 ATCCAAAGAC
35478 TGCTAT TGCTAT TGCTAT TGCTAT TGCT
1 TGCTAT TGCTAT TGCTAT TGCTAT TGCT
35506 TGTACACCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.50
Consensus pattern (6 bp):
TGCTAT
Found at i:47062 original size:17 final size:18
Alignment explanation
Indices: 47036--47073 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
47026 GAGCAAACAT
*
47036 AAAAGGAAAA-GAGAAGA
1 AAAAGAAAAACGAGAAGA
*
47053 AAAAGAAAAACGAGAGGA
1 AAAAGAAAAACGAGAAGA
47071 AAA
1 AAA
47074 GAGAGGGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAACGAGAAGA
Found at i:50675 original size:21 final size:20
Alignment explanation
Indices: 50646--50689 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
50636 AACAATTATG
50646 TTTTTTTTTTTTTTTTTAAA
1 TTTTTTTTTTTTTTTTTAAA
*
50666 TTTNTTTTTTTTTTTTTTTAA
1 TTT-TTTTTTTTTTTTTTAAA
50687 TTT
1 TTT
50690 ATTATATCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.86
Consensus pattern (20 bp):
TTTTTTTTTTTTTTTTTAAA
Found at i:60115 original size:22 final size:22
Alignment explanation
Indices: 60087--60135 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
60077 TAAGAACCAA
60087 ATCCATCTTAAACTCGATCCAC
1 ATCCATCTTAAACTCGATCCAC
60109 ATCCATCTTAAACTCGATCCAC
1 ATCCATCTTAAACTCGATCCAC
60131 ATCCA
1 ATCCA
60136 ATCTCAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.33, C:0.37, G:0.04, T:0.27
Consensus pattern (22 bp):
ATCCATCTTAAACTCGATCCAC
Found at i:65924 original size:19 final size:19
Alignment explanation
Indices: 65879--65924 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
65869 GTATGATATC
*
65879 TTTTTAAAATCGTATTTTA
1 TTTTTAAAATCGTATTTAA
**
65898 TTTATTAAAATTTTATTTAA
1 TTT-TTAAAATCGTATTTAA
65918 TTTTTAA
1 TTTTTAA
65925 CAGATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTTAAAATCGTATTTAA
Found at i:69342 original size:45 final size:45
Alignment explanation
Indices: 69264--69388 Score: 151
Period size: 45 Copynumber: 2.8 Consensus size: 45
69254 GAGGAATAGT
* * * * * *
69264 GTATCGCGATGGCTCGTTAAACTTAGCCGGATATCCTTCCCTTGA
1 GTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTCCCTTGA
* * ***
69309 GTATTGCGGTGGCTCGTCAAATTGAGGTTGATATCCTTGGTTTGA
1 GTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTCCCTTGA
69354 GTATTGCGGTGGCTCGTCAAACTGAGGCTGATATC
1 GTATTGCGGTGGCTCGTCAAACTGAGGCTGATATC
69389 TTAGCTTAAT
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 67 1.00
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.33
Consensus pattern (45 bp):
GTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTCCCTTGA
Found at i:71675 original size:20 final size:21
Alignment explanation
Indices: 71650--71692 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
71640 TACTTACTTC
71650 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
71670 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
71691 TA
1 TA
71693 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:72079 original size:22 final size:22
Alignment explanation
Indices: 72053--72099 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
72043 TTTTTTTTCC
72053 TTTTCCTTCTTCC-TTCTTCTTT
1 TTTTCCTTCTTCCTTTC-TCTTT
* *
72075 TTTTCTTTCTTTCTTTCTCTTT
1 TTTTCCTTCTTCCTTTCTCTTT
72097 TTT
1 TTT
72100 CTTTCTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTCCTTCTTCCTTTCTCTTT
Found at i:72083 original size:4 final size:4
Alignment explanation
Indices: 72069--72107 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
72059 TTCTTCCTTC
* *
72069 TTCT TTTT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TT
72108 TTCCTTCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 27 0.90
5 3 0.10
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTCT
Found at i:72097 original size:21 final size:20
Alignment explanation
Indices: 72069--72107 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
72059 TTCTTCCTTC
72069 TTCTTTTTTTCTTTCTTTCT
1 TTCTTTTTTTCTTTCTTTCT
72089 TTCTCTTTTTTCTTTCTTT
1 TTCT-TTTTTTCTTTCTTT
72108 TTCCTTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TTCTTTTTTTCTTTCTTTCT
Found at i:73858 original size:19 final size:17
Alignment explanation
Indices: 73836--73881 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
73826 TTAAATTTTT
73836 TTAAAAAAATTAAAAATCA
1 TTAAAAAAATTAAAAA--A
**
73855 TTAAAAGTATTAAAAAA
1 TTAAAAAAATTAAAAAA
73872 TTAAAAAAAT
1 TTAAAAAAAT
73882 ATATTTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 9 0.39
19 14 0.61
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (17 bp):
TTAAAAAAATTAAAAAA
Done.