Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001432.1 Kokia drynarioides strain JFW-HI SEQ_112939, 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: 87056
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2959 original size:24 final size:24
Alignment explanation
Indices: 2913--2968 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
2903 GTAAATGAAT
* *
2913 TAAACGT-ATCATGCTGACGAGCG
1 TAAACGTAATCATGCTAACAAGCG
*
2936 TAAACGTAATTATGCTAACAAGCG
1 TAAACGTAATCATGCTAACAAGCG
2960 TAAACGTAA
1 TAAACGTAA
2969 AGAAGTCCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 7 0.24
24 22 0.76
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (24 bp):
TAAACGTAATCATGCTAACAAGCG
Found at i:3952 original size:70 final size:66
Alignment explanation
Indices: 3822--3953 Score: 158
Period size: 70 Copynumber: 1.9 Consensus size: 66
3812 ATAAACAACA
* * * *
3822 TAATAGTTTTGCTTTTAACTTAATGGGTAAACATTTATCAAAATGACATAATTTTACCTTTTAAC
1 TAATAGTTTTGCTTTTAACTTAAAGGGTAAAAATTTATCAAAACGACATAAGTTTACCTTTTAAC
3887 T
66 T
* *
3888 TAATGGTTTTGACTTTTAACTTTAGAAAGGGTAAAAATTTATCAAAACGACGT-AGTTTAGCCTT
1 TAATAGTTTTG-CTTTTAAC-TT--AAAGGGTAAAAATTTATCAAAACGACATAAGTTTA-CCTT
3952 TT
61 TT
3954 CTTATTCGGA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
66 10 0.18
67 8 0.15
68 2 0.04
69 5 0.09
70 30 0.55
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (66 bp):
TAATAGTTTTGCTTTTAACTTAAAGGGTAAAAATTTATCAAAACGACATAAGTTTACCTTTTAAC
T
Found at i:8339 original size:16 final size:16
Alignment explanation
Indices: 8318--8385 Score: 91
Period size: 16 Copynumber: 4.2 Consensus size: 16
8308 AGGTTCGTTC
*
8318 TAATGGAATAAAGCTG
1 TAATGGAATAGAGCTG
*
8334 TAATGGAATAGAGTTG
1 TAATGGAATAGAGCTG
**
8350 TAATAAAATAGAGCTG
1 TAATGGAATAGAGCTG
*
8366 TAATGGAATATAGCTG
1 TAATGGAATAGAGCTG
8382 TAAT
1 TAAT
8386 TAGTAATTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.43, C:0.04, G:0.24, T:0.29
Consensus pattern (16 bp):
TAATGGAATAGAGCTG
Found at i:9433 original size:20 final size:20
Alignment explanation
Indices: 9408--9487 Score: 79
Period size: 20 Copynumber: 4.0 Consensus size: 20
9398 ATTCTAAAAA
*
9408 GAATCGATTTAAACCACAAT
1 GAATCGATTTAAACAACAAT
* * *
9428 GAATCGATTCAAACAAGAGAA
1 GAATCGATTTAAACAACA-AT
*
9449 GAATCGATTTAAACAATAAT
1 GAATCGATTTAAACAACAAT
* * *
9469 GAATCCATTCAAATAACAA
1 GAATCGATTTAAACAACAA
9488 AACTATCGAT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 31 0.65
21 17 0.35
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.23
Consensus pattern (20 bp):
GAATCGATTTAAACAACAAT
Found at i:9496 original size:41 final size:41
Alignment explanation
Indices: 9404--9498 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 41
9394 ATCTATTCTA
* * * *
9404 AAAAGAATCGATTTAAACCACAATGAATCGATTCAAACAAG
1 AAAACAATCGATTTAAACAACAATGAATCCATTCAAACAAC
* * * *
9445 AGAAGAATCGATTTAAACAATAATGAATCCATTCAAATAAC
1 AAAACAATCGATTTAAACAACAATGAATCCATTCAAACAAC
*
9486 AAAACTATCGATT
1 AAAACAATCGATT
9499 AAAAGTAGAA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.51, C:0.16, G:0.11, T:0.23
Consensus pattern (41 bp):
AAAACAATCGATTTAAACAACAATGAATCCATTCAAACAAC
Found at i:19267 original size:24 final size:24
Alignment explanation
Indices: 19235--19283 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
19225 AGTTCATTAT
**
19235 GTTTACGCTCGTCTGCATGAATAC
1 GTTTACGCTCGTCAACATGAATAC
19259 GTTTACGCTCGTCAACATGAATAC
1 GTTTACGCTCGTCAACATGAATAC
19283 G
1 G
19284 AGAAACATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (24 bp):
GTTTACGCTCGTCAACATGAATAC
Found at i:20309 original size:21 final size:20
Alignment explanation
Indices: 20271--20309 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
20261 TTTCATAGCT
* *
20271 TCAAAATCTAACACTTTCTA
1 TCAAAATCGAACAATTTCTA
20291 TCAAAACTCGAACAATTTC
1 TCAAAA-TCGAACAATTTC
20310 ACTCTAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.31
Consensus pattern (20 bp):
TCAAAATCGAACAATTTCTA
Found at i:40637 original size:33 final size:33
Alignment explanation
Indices: 40599--40667 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
40589 AGACCATTGA
40599 TTTCTCCTTACTTAGGGTATAAATTGTTCCCAT
1 TTTCTCCTTACTTAGGGTATAAATTGTTCCCAT
*
40632 TTTCTCCTTACTTAGGGTATAAATTGTTCCTAT
1 TTTCTCCTTACTTAGGGTATAAATTGTTCCCAT
40665 TTT
1 TTT
40668 ATCATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.20, C:0.19, G:0.12, T:0.49
Consensus pattern (33 bp):
TTTCTCCTTACTTAGGGTATAAATTGTTCCCAT
Found at i:40717 original size:20 final size:21
Alignment explanation
Indices: 40692--40730 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40682 TGCATTTTTA
*
40692 GCATTTT-TAACTTAGTGACT
1 GCATTTTCTAACTCAGTGACT
40712 GCATTTTCTAACTCAGTGA
1 GCATTTTCTAACTCAGTGA
40731 TGCTCGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (21 bp):
GCATTTTCTAACTCAGTGACT
Found at i:61154 original size:21 final size:23
Alignment explanation
Indices: 61114--61159 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
61104 TTTCCCCTCA
*
61114 TTTTCTCTATTGCCAAACACCAT
1 TTTTCTCTATTGCAAAACACCAT
61137 TTTTCT-TATT-CAAAACACCAT
1 TTTTCTCTATTGCAAAACACCAT
61158 TT
1 TT
61160 ATAAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.55
22 4 0.18
23 6 0.27
ACGTcount: A:0.28, C:0.26, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTTCTCTATTGCAAAACACCAT
Found at i:63510 original size:13 final size:13
Alignment explanation
Indices: 63494--63532 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
63484 TGGTGAATGA
*
63494 TATTAATCTAAAG
1 TATTAATCTAAAC
63507 TATTAATCTAAAC
1 TATTAATCTAAAC
63520 TAAATTAATCTAA
1 T--ATTAATCTAA
63533 GTTAAGCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 13 0.57
15 10 0.43
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (13 bp):
TATTAATCTAAAC
Found at i:66703 original size:27 final size:28
Alignment explanation
Indices: 66671--66724 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
66661 GGAATCATAT
* * *
66671 TCACAAC-ATAGTTCTGGTGAACTTTCC
1 TCACAACGATAGTCCTGGAGAAATTTCC
66698 TCACAACGATAGTCCTGGAGAAATTTC
1 TCACAACGATAGTCCTGGAGAAATTTC
66725 TCCATGTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (28 bp):
TCACAACGATAGTCCTGGAGAAATTTCC
Found at i:66768 original size:28 final size:28
Alignment explanation
Indices: 66731--66823 Score: 86
Period size: 28 Copynumber: 3.4 Consensus size: 28
66721 TTTCTCCATG
66731 TTAGATAGTCCTGATAGACTTCCCAATT
1 TTAGATAGTCCTGATAGACTTCCCAATT
* *
66759 TTAGATAGTCTTG-TCGGAC-TCCCACA-T
1 TTAGATAGTCCTGAT-AGACTTCCCA-ATT
** *
66786 TTAGATTTTCCTGACAGACTT-CCAATAT
1 TTAGATAGTCCTGATAGACTTCCCAAT-T
66814 TTAGATAGTC
1 TTAGATAGTC
66824 TTGGCAATCC
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
26 1 0.02
27 23 0.46
28 26 0.52
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.37
Consensus pattern (28 bp):
TTAGATAGTCCTGATAGACTTCCCAATT
Found at i:69436 original size:22 final size:21
Alignment explanation
Indices: 69395--69436 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
69385 CAAAATTGGA
* *
69395 TGCTCTCAATTTTGTGTTGTT
1 TGCTCTCAATATGGTGTTGTT
69416 TGCTCTCAAATATGGTGTTGT
1 TGCTCTC-AATATGGTGTTGT
69437 ATTGATGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.50
Consensus pattern (21 bp):
TGCTCTCAATATGGTGTTGTT
Found at i:69730 original size:21 final size:21
Alignment explanation
Indices: 69706--69745 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
69696 AAATACCAAG
* *
69706 TAATATGGATAGTTTGGGCAT
1 TAATATGCACAGTTTGGGCAT
*
69727 TAATGTGCACAGTTTGGGC
1 TAATATGCACAGTTTGGGC
69746 TCCTTCCTCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.10, G:0.30, T:0.35
Consensus pattern (21 bp):
TAATATGCACAGTTTGGGCAT
Found at i:72986 original size:28 final size:28
Alignment explanation
Indices: 72954--73150 Score: 134
Period size: 28 Copynumber: 7.0 Consensus size: 28
72944 CCACAAGGCA
* *
72954 TCCTTTACCTAGTTAGCCACGAAGGCTT
1 TCCTTTACATAGTTAGCCACAAAGGCTT
***
72982 TCCTTTTTGTTA-TTAGCCACAAAGGC-T
1 TCC-TTTACATAGTTAGCCACAAAGGCTT
* *
73009 TCTTTTACATAGTTTTGCCACAAAGGCTT
1 TCCTTTACATAG-TTAGCCACAAAGGCTT
* * *
73038 TCCTTTCAGATA-TTCGCGACAAAGGCTT
1 TCCTTT-ACATAGTTAGCCACAAAGGCTT
* * *
73066 ACCTTTACAATATTTAGCCATAAAGG-TT
1 TCCTTTAC-ATAGTTAGCCACAAAGGCTT
* * * *
73094 TACTTTACAGAATTTAGCCACAATGGC-T
1 TCCTTTACA-TAGTTAGCCACAAAGGCTT
* *
73122 TCCTTTACAAAGTTTACCCACAAAGGCTT
1 TCCTTTACATAG-TTAGCCACAAAGGCTT
73151 CCATATCTAG
Statistics
Matches: 131, Mismatches: 27, Indels: 21
0.73 0.15 0.12
Matches are distributed among these distances:
26 5 0.04
27 7 0.05
28 93 0.71
29 22 0.17
30 4 0.03
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (28 bp):
TCCTTTACATAGTTAGCCACAAAGGCTT
Found at i:73040 original size:56 final size:55
Alignment explanation
Indices: 72944--73150 Score: 197
Period size: 56 Copynumber: 3.7 Consensus size: 55
72934 ATCATATTCA
* * * **
72944 CCAC-AAGGCATCCTTTACCTAG-TTAGCCACGAAGGCTTTCCTTTTTGTTATTAG
1 CCACAAAGGCTTCCTTTACATAGTTTAGCCACAAAGGCTTTCCTTTCAG-TATTAG
* * *
72998 CCACAAAGGCTTCTTTTACATAGTTTTGCCACAAAGGCTTTCCTTTCAGATATTCG
1 CCACAAAGGCTTCCTTTACATAGTTTAGCCACAAAGGCTTTCCTTTCAG-TATTAG
* * * *
73054 CGACAAAGGCTTACCTTTACAATA-TTTAGCCATAAAGG-TTTACTTTACAGAATTTAG
1 CCACAAAGGCTT-CCTTTAC-ATAGTTTAGCCACAAAGGCTTTCCTTT-CAGTA-TTAG
* * *
73111 CCACAATGGCTTCCTTTACAAAGTTTACCCACAAAGGCTT
1 CCACAAAGGCTTCCTTTACATAGTTTAGCCACAAAGGCTT
73151 CCATATCTAG
Statistics
Matches: 124, Mismatches: 21, Indels: 13
0.78 0.13 0.08
Matches are distributed among these distances:
54 4 0.03
55 17 0.14
56 64 0.52
57 36 0.29
58 3 0.02
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.33
Consensus pattern (55 bp):
CCACAAAGGCTTCCTTTACATAGTTTAGCCACAAAGGCTTTCCTTTCAGTATTAG
Found at i:73151 original size:28 final size:27
Alignment explanation
Indices: 72994--73152 Score: 149
Period size: 28 Copynumber: 5.7 Consensus size: 27
72984 CTTTTTGTTA
* *
72994 TTAGCCACAAAGGCTTCTTTTACATAGT
1 TTAGCCACAAAGGCTTCCTTTACA-AAT
* *
73022 TTTGCCACAAAGGCTTTCCTTT-CAGAT
1 TTAGCCACAAAGGC-TTCCTTTACAAAT
* *
73049 ATTCGCGACAAAGGCTTACCTTTACAATAT
1 -TTAGCCACAAAGGCTT-CCTTTACAA-AT
* * *
73079 TTAGCCATAAAGGTTTACTTTACAGAAT
1 TTAGCCACAAAGGCTTCCTTTACA-AAT
*
73107 TTAGCCACAATGGCTTCCTTTACAAAGT
1 TTAGCCACAAAGGCTTCCTTTACAAA-T
*
73135 TTACCCACAAAGGCTTCC
1 TTAGCCACAAAGGCTTCC
73153 ATATCTAGAG
Statistics
Matches: 106, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
27 5 0.05
28 78 0.74
29 21 0.20
30 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.33
Consensus pattern (27 bp):
TTAGCCACAAAGGCTTCCTTTACAAAT
Found at i:73738 original size:23 final size:22
Alignment explanation
Indices: 73712--73754 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
73702 ACTATTACAA
* *
73712 TTTCATGTAATTTATTCAATCTT
1 TTTCATGAAATTCATT-AATCTT
73735 TTTCATGAAATTCATTAATC
1 TTTCATGAAATTCATTAATC
73755 ATGCATTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTCATGAAATTCATTAATCTT
Found at i:83811 original size:28 final size:27
Alignment explanation
Indices: 83778--83974 Score: 110
Period size: 28 Copynumber: 7.0 Consensus size: 27
83768 CCACAAGGCA
*
83778 TCCTTTACCTAGTTAGCCATAAAGGCTT
1 TCCTTTACATA-TTAGCCATAAAGGCTT
*** * *
83806 TCCTTTTTGTTATCAGCCACAAAGGCTT
1 TCC-TTTACATATTAGCCATAAAGGCTT
* * *
83834 TCCTTTCAGATATTCGCCACAAAGGCTT
1 TCCTTT-ACATATTAGCCATAAAGGCTT
* * *
83862 TCCTTTAAGATATTCGCCACAAAGGCTT
1 TCCTTT-ACATATTAGCCATAAAGGCTT
* * *
83890 ACCTTTATAGAATTTAGCCATAAAGG-TT
1 TCCTTTACA-TA-TTAGCCATAAAGGCTT
* * *
83918 TACTTTACAGAATTTAGCCATAATGGC-T
1 TCCTTTACA-TA-TTAGCCATAAAGGCTT
* *
83946 TCCTTTACAAAGTTTACCCATAAAGGCTT
1 TCCTTTACATA--TTAGCCATAAAGGCTT
83975 CCATATTTAG
Statistics
Matches: 140, Mismatches: 22, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
27 7 0.05
28 116 0.83
29 17 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (27 bp):
TCCTTTACATATTAGCCATAAAGGCTT
Found at i:83924 original size:56 final size:56
Alignment explanation
Indices: 83790--83974 Score: 166
Period size: 56 Copynumber: 3.3 Consensus size: 56
83780 CTTTACCTAG
** *
83790 TTAGCCATAAAGGCTTTCCTTTTTGTTA-TCAGCCACAAAGGCTTTCCTTT-CAG-AT
1 TTAGCCATAAAGGCTTTCCTTTAAGATATTC-GCCACAAAGGC-TTCCTTTACAGAAT
* * *
83845 ATTCGCCACAAAGGCTTTCCTTTAAGATATTCGCCACAAAGGCTTACCTTTATAGAAT
1 -TTAGCCATAAAGGCTTTCCTTTAAGATATTCGCCACAAAGGCTT-CCTTTACAGAAT
* * * *
83903 TTAGCCATAAAGG-TTTACTTTACAGA-ATTTAGCCATAATGGCTTCCTTTACA-AAGT
1 TTAGCCATAAAGGCTTTCCTTTA-AGATA-TTCGCCACAAAGGCTTCCTTTACAGAA-T
*
83959 TTACCCATAAAGGCTT
1 TTAGCCATAAAGGCTT
83975 CCATATTTAG
Statistics
Matches: 107, Mismatches: 14, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
55 4 0.04
56 68 0.64
57 33 0.31
58 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (56 bp):
TTAGCCATAAAGGCTTTCCTTTAAGATATTCGCCACAAAGGCTTCCTTTACAGAAT
Found at i:83975 original size:28 final size:28
Alignment explanation
Indices: 83820--83976 Score: 135
Period size: 28 Copynumber: 5.6 Consensus size: 28
83810 TTTTGTTATC
*
83820 AGCCACAAAGGCTTTCCTTT-CAG-ATATT
1 AGCCATAAAGGC-TTCCTTTACAGAAT-TT
* *
83848 CGCCACAAAGGCTTTCCTTTA-AG-ATATT
1 AGCCATAAAGGC-TTCCTTTACAGAAT-TT
* * *
83876 CGCCACAAAGGCTTACCTTTATAGAATTT
1 AGCCATAAAGGCTT-CCTTTACAGAATTT
* *
83905 AGCCATAAAGGTTTACTTTACAGAATTT
1 AGCCATAAAGGCTTCCTTTACAGAATTT
*
83933 AGCCATAATGGCTTCCTTTACA-AAGTTT
1 AGCCATAAAGGCTTCCTTTACAGAA-TTT
*
83961 ACCCATAAAGGCTTCC
1 AGCCATAAAGGCTTCC
83977 ATATTTAGAG
Statistics
Matches: 113, Mismatches: 11, Indels: 10
0.84 0.08 0.07
Matches are distributed among these distances:
27 4 0.04
28 92 0.81
29 15 0.13
30 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.32
Consensus pattern (28 bp):
AGCCATAAAGGCTTCCTTTACAGAATTT
Done.