Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005408.1 Kokia drynarioides strain JFW-HI SEQ_119419, 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: 44797
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:5933 original size:17 final size:17
Alignment explanation
Indices: 5868--5933 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 17
5858 AAGATTCAAC
*
5868 ATAAT-TAAATAATTTA
1 ATAATATAAATAATTCA
* *
5884 ATAATATAAATAGTACA
1 ATAATATAAATAATTCA
5901 A-AATATGAAATTTAATTCA
1 ATAATAT-AAA--TAATTCA
*
5920 ATATTATAAATAAT
1 ATAATATAAATAAT
5934 AGACATAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
16 10 0.26
17 16 0.41
19 9 0.23
20 4 0.10
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
ATAATATAAATAATTCA
Found at i:6103 original size:19 final size:19
Alignment explanation
Indices: 6064--6104 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
6054 GGGTTCGGGC
6064 AAGTAAAAATTTTTAGGGGG
1 AAGTAAAAA-TTTTAGGGGG
6084 AAGTAAAAA-TTTAGGAGGG
1 AAGTAAAAATTTTAGG-GGG
6103 AA
1 AA
6105 TATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.30
19 5 0.25
20 9 0.45
ACGTcount: A:0.46, C:0.00, G:0.29, T:0.24
Consensus pattern (19 bp):
AAGTAAAAATTTTAGGGGG
Found at i:6110 original size:20 final size:18
Alignment explanation
Indices: 6075--6113 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
6065 AGTAAAAATT
*
6075 TTTAGGGGGAAGTAAAAA
1 TTTAGGGGGAAATAAAAA
6093 TTTAGGAGGGAATATAAAAA
1 TTTAGG-GGGAA-ATAAAAA
6113 T
1 T
6114 AAAAAAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 5 0.28
20 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.28, T:0.26
Consensus pattern (18 bp):
TTTAGGGGGAAATAAAAA
Found at i:6688 original size:12 final size:12
Alignment explanation
Indices: 6671--6695 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6661 CTCCTATTTC
6671 TAAAAAAAAAAA
1 TAAAAAAAAAAA
6683 TAAAAAAAAAAA
1 TAAAAAAAAAAA
6695 T
1 T
6696 TAAATACGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (12 bp):
TAAAAAAAAAAA
Found at i:7219 original size:18 final size:20
Alignment explanation
Indices: 7182--7218 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7172 ACATCTAAAT
7182 TTTAAAAAAAATATATTTTA
1 TTTAAAAAAAATATATTTTA
*
7202 TTTAAAAAGAATA-ATTT
1 TTTAAAAAAAATATATTT
7219 ACAAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (20 bp):
TTTAAAAAAAATATATTTTA
Found at i:8749 original size:20 final size:20
Alignment explanation
Indices: 8726--8766 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
8716 AGTTAGCACA
8726 ATATGAATAATTCTATCAAG
1 ATATGAATAATTCTATCAAG
8746 ATATGAATAATTCTATCAAG
1 ATATGAATAATTCTATCAAG
8766 A
1 A
8767 AGAGAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (20 bp):
ATATGAATAATTCTATCAAG
Found at i:8773 original size:20 final size:20
Alignment explanation
Indices: 8730--8775 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
8720 AGCACAATAT
*
8730 GAATAATTCTATCAAGATAT
1 GAATAATTCTATCAAGATAA
8750 GAATAATTCTATCAAGA-AGA
1 GAATAATTCTATCAAGATA-A
8770 GAATAA
1 GAATAA
8776 ATACTTAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.28
Consensus pattern (20 bp):
GAATAATTCTATCAAGATAA
Found at i:13211 original size:18 final size:18
Alignment explanation
Indices: 13190--13232 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
13180 AAATTGAATG
*
13190 ATTTTCAACTTTTGATTT
1 ATTTGCAACTTTTGATTT
13208 ATTTGCAACTTTTGATTT
1 ATTTGCAACTTTTGATTT
13226 ATTTGCA
1 ATTTGCA
13233 TGTTAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.56
Consensus pattern (18 bp):
ATTTGCAACTTTTGATTT
Found at i:23276 original size:24 final size:23
Alignment explanation
Indices: 23249--23325 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 23
23239 ACAGACAGTA
23249 TTAGCCCATACGAGCCCAGAATGG
1 TTAGCCC-TACGAGCCCAGAATGG
* * * *
23273 TTAGCTCCTATGAGCCCAAAACGA
1 TTAGC-CCTACGAGCCCAGAATGG
*
23297 TTAGCTCTTACGAGCCCAGAATGG
1 TTAGC-CCTACGAGCCCAGAATGG
23321 TTAGC
1 TTAGC
23326 TTTTACGAGC
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
24 41 0.95
25 2 0.05
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (23 bp):
TTAGCCCTACGAGCCCAGAATGG
Found at i:23326 original size:24 final size:24
Alignment explanation
Indices: 23257--23342 Score: 109
Period size: 24 Copynumber: 3.6 Consensus size: 24
23247 TATTAGCCCA
*
23257 TACGAGCCCAGAATGGTTAGCTCC
1 TACGAGCCCAGAATGGTTAGCTCT
* * * *
23281 TATGAGCCCAAAACGATTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
*
23305 TACGAGCCCAGAATGGTTAGCTTT
1 TACGAGCCCAGAATGGTTAGCTCT
*
23329 TACGAGCGCAGAAT
1 TACGAGCCCAGAAT
23343 CAAAGTAACG
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.23
Consensus pattern (24 bp):
TACGAGCCCAGAATGGTTAGCTCT
Found at i:25467 original size:36 final size:36
Alignment explanation
Indices: 25366--25476 Score: 100
Period size: 36 Copynumber: 3.1 Consensus size: 36
25356 AAAGTTTACT
* * *
25366 TAAAAATAATATAATATATTATTAATTAATAAAATAAA
1 TAAAAATAATA-AATAT-TTAATATTTAATTAAATAAA
* * ** * *
25404 T-AAATTTATAAA-ATTATTGTATATAATTAGATAAA
1 TAAAAATAATAAATATT-TAATATTTAATTAAATAAA
25439 TAAAAATAATAAATATTTAATATTTAATTAAATAAA
1 TAAAAATAATAAATATTTAATATTTAATTAAATAAA
25475 TA
1 TA
25477 TACTTTATCT
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
34 1 0.02
35 16 0.29
36 28 0.50
37 10 0.18
38 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (36 bp):
TAAAAATAATAAATATTTAATATTTAATTAAATAAA
Found at i:26609 original size:14 final size:14
Alignment explanation
Indices: 26590--26620 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
26580 ATAATAAATC
26590 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
26604 TTTAATTAATTAAA
1 TTTAATTAAATAAA
26618 TTT
1 TTT
26621 TTAAACCCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:33054 original size:21 final size:21
Alignment explanation
Indices: 33013--33054 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 21
33003 ATTATTTCTA
* *
33013 TTTTCGTCATTTTAATTTTTT
1 TTTTCGTCAATTTAATGTTTT
33034 TTTTC-TCAATTTAATCGTTTT
1 TTTTCGTCAATTTAAT-GTTTT
33055 AAATAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTTCGTCAATTTAATGTTTT
Found at i:37392 original size:25 final size:24
Alignment explanation
Indices: 37332--37415 Score: 86
Period size: 25 Copynumber: 3.5 Consensus size: 24
37322 TGAAGTACTT
37332 AACAGAAG-AGCATAAGTGCTAGGGA
1 AACAGAAGCA-CATAAGTGCT-GGGA
37357 AACAGAAGCACATAAGTGCTGGGA
1 AACAGAAGCACATAAGTGCTGGGA
* *
37381 AACAGTAGGCACACACAGTGCT--G-
1 AACAG-AAGCACATA-AGTGCTGGGA
37404 AACAGAAGCACA
1 AACAGAAGCACA
37416 CACAATGCTG
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
22 6 0.11
23 5 0.09
24 10 0.19
25 25 0.47
26 7 0.13
ACGTcount: A:0.43, C:0.19, G:0.27, T:0.11
Consensus pattern (24 bp):
AACAGAAGCACATAAGTGCTGGGA
Found at i:37415 original size:22 final size:23
Alignment explanation
Indices: 37381--37435 Score: 85
Period size: 22 Copynumber: 2.4 Consensus size: 23
37371 AGTGCTGGGA
*
37381 AACAGTAGGCACACACAGTGCTG
1 AACAGTAAGCACACACAGTGCTG
*
37404 AACAG-AAGCACACACAATGCTG
1 AACAGTAAGCACACACAGTGCTG
37426 AACAGTAAGC
1 AACAGTAAGC
37436 GCGCTAATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.42, C:0.25, G:0.22, T:0.11
Consensus pattern (23 bp):
AACAGTAAGCACACACAGTGCTG
Found at i:43188 original size:96 final size:96
Alignment explanation
Indices: 43010--43195 Score: 227
Period size: 96 Copynumber: 1.9 Consensus size: 96
43000 GGAAAAGAAA
* ** * *
43010 ATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTTATAATTG
1 ATTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTTATAATCG
*
43075 AAGATAAGGAAACATTGCCTCGATTAAGATT
66 AAGATAAAGAAACATTGCCTCGATTAAGATT
* *
43106 ATTCGATTATTTCAATTTGAAGAAAAATTGCACTTAGTAAGTTAAGGCACAA-ATTTT-TGAAAC
1 ATTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTTAT--AA-
*
43169 TCGAA-ATAAA-AGAATATTGCCTCGATT
63 TCGAAGATAAAGA-AACATTGCCTCGATT
43196 TTAAAGATTT
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
94 1 0.01
95 6 0.08
96 66 0.86
97 4 0.05
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (96 bp):
ATTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTTATAATCG
AAGATAAAGAAACATTGCCTCGATTAAGATT
Found at i:43658 original size:90 final size:90
Alignment explanation
Indices: 43543--43715 Score: 222
Period size: 90 Copynumber: 1.9 Consensus size: 90
43533 ACATCCGAGG
* * * * *
43543 AAAAATGATAATTTTCGGATGTTCGAGGGTACAAATGGAGTTTTTAGAAGTCTCAGGGTTAAAAA
1 AAAAATGAGAATTTTCGGAAGTTCGAGGGTAAAAATAGAATTTTTAGAAGTCTCAGGGTTAAAAA
*
43608 TGAAATTTTTTTGAAGTTTCGAGGTC
66 TGAAA-TTTTTGGAAGTTTCGAGGTC
* * * **
43634 AAAAATG-GAATTTTTGGAAGTTCGAGGGTAAAAATAGAATTTTTGGAAGTTTTTGGGTTAAAAA
1 AAAAATGAGAATTTTCGGAAGTTCGAGGGTAAAAATAGAATTTTTAGAAGTCTCAGGGTTAAAAA
*
43698 TGGAATTTTTGGAAGTTT
66 TGAAATTTTTGGAAGTTT
43716 TAAGGTAAGA
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
89 12 0.17
90 51 0.73
91 7 0.10
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (90 bp):
AAAAATGAGAATTTTCGGAAGTTCGAGGGTAAAAATAGAATTTTTAGAAGTCTCAGGGTTAAAAA
TGAAATTTTTGGAAGTTTCGAGGTC
Found at i:43702 original size:59 final size:60
Alignment explanation
Indices: 43504--43714 Score: 174
Period size: 59 Copynumber: 3.6 Consensus size: 60
43494 TAATTTTGAG
* * * *
43504 AGTTTCGAGATCAAAAATGGAGTTTTTGGACA--TCCGAGG--AAAAATGATAA-TTTTCGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGA-AGTTCAG-GGTTAAAAATGA-AATTTTTTGGA
* * * * *
43562 TG-TTCGAGGGT-ACAAATGGAGTTTTTAGAAGTCTCAGGGTTAAAAATGAAATTTTTTTGA
1 AGTTTCGA-GGTCAAAAATGGAATTTTTGGAAGT-TCAGGGTTAAAAATGAAATTTTTTGGA
43622 AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGG-TAAAAAT-AGAA-TTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTC-AGGGTTAAAAATGA-AATTTTTTGGA
* *
43681 AGTTTTTG-GGTTAAAAATGGAATTTTTGGAAGTT
1 AG-TTTCGAGGTCAAAAATGGAATTTTTGGAAGTT
43715 TTAAGGTAAG
Statistics
Matches: 127, Mismatches: 14, Indels: 23
0.77 0.09 0.14
Matches are distributed among these distances:
56 1 0.01
57 21 0.17
58 5 0.04
59 40 0.31
60 33 0.26
61 27 0.21
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.35
Consensus pattern (60 bp):
AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCAGGGTTAAAAATGAAATTTTTTGGA
Found at i:43716 original size:29 final size:30
Alignment explanation
Indices: 43504--43715 Score: 161
Period size: 30 Copynumber: 7.2 Consensus size: 30
43494 TAATTTTGAG
* * *
43504 AGTTTCGAGATCAAAAATGGAGTTTTTGGA
1 AGTTTCGAGGTTAAAAATGGAATTTTTGGA
* * *
43534 CA--TCCGAGG--AAAAATGATAATTTTCGGA
1 -AGTTTCGAGGTTAAAAATG-GAATTTTTGGA
* * * * *
43562 TG-TTCGAGGGTACAAATGGAGTTTTTAGA
1 AGTTTCGAGGTTAAAAATGGAATTTTTGGA
* * *
43591 AGTCTC-AGGGTTAAAAATGAAATTTTTTTGA
1 AGTTTCGA-GGTTAAAAATGGAA-TTTTTGGA
*
43622 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
1 AGTTTCGAGGTTAAAAATGGAATTTTTGGA
* *
43652 AG-TTCGAGGGTAAAAATAGAATTTTTGGA
1 AGTTTCGAGGTTAAAAATGGAATTTTTGGA
*
43681 AGTTTTTG-GGTTAAAAATGGAATTTTTGGA
1 AG-TTTCGAGGTTAAAAATGGAATTTTTGGA
43711 AGTTT
1 AGTTT
43716 TAAGGTAAGA
Statistics
Matches: 142, Mismatches: 29, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
27 7 0.05
28 14 0.10
29 43 0.30
30 49 0.35
31 28 0.20
32 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.35
Consensus pattern (30 bp):
AGTTTCGAGGTTAAAAATGGAATTTTTGGA
Found at i:43716 original size:30 final size:30
Alignment explanation
Indices: 43575--43735 Score: 148
Period size: 30 Copynumber: 5.4 Consensus size: 30
43565 TCGAGGGTAC
* * * *
43575 AAATGGAGTTTTTAGAAGTCTCAGGGTTAA
1 AAATGGAATTTTTGGAAGTTTTAGGGTTAA
* * * *
43605 AAATGAAATTTTTTTGAAG-TTTCGAGGTCAA
1 AAATGGAA-TTTTTGGAAGTTTTAG-GGTTAA
**
43636 AAATGGAATTTTTGGAAGTTCGAGGG-TAA
1 AAATGGAATTTTTGGAAGTTTTAGGGTTAA
* *
43665 AAATAGAATTTTTGGAAGTTTTTGGGTTAA
1 AAATGGAATTTTTGGAAGTTTTAGGGTTAA
*
43695 AAATGGAATTTTTGGAAGTTTTAAGG-TAA
1 AAATGGAATTTTTGGAAGTTTTAGGGTTAA
* *
43724 GAATGTAATTTT
1 AAATGGAATTTT
43736 CAGATAGTTT
Statistics
Matches: 105, Mismatches: 22, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
29 37 0.35
30 45 0.43
31 23 0.22
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (30 bp):
AAATGGAATTTTTGGAAGTTTTAGGGTTAA
Found at i:44749 original size:19 final size:21
Alignment explanation
Indices: 44725--44770 Score: 78
Period size: 19 Copynumber: 2.3 Consensus size: 21
44715 TTCTTTTTAT
44725 TATTATTAATTA-TTAAT-AA
1 TATTATTAATTATTTAATAAA
44744 TATTATTAATTATTTAATAAA
1 TATTATTAATTATTTAATAAA
44765 TATTAT
1 TATTAT
44771 CTTTAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 12 0.48
20 5 0.20
21 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTATTAATTATTTAATAAA
Found at i:44777 original size:16 final size:15
Alignment explanation
Indices: 44756--44785 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
44746 TTATTAATTA
44756 TTTAATAAATATTATC
1 TTTAATAAA-ATTATC
44772 TTTAATAAAATTAT
1 TTTAATAAAATTAT
44786 TATTATCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAATAAAATTATC
Done.