Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013945.1 Kokia drynarioides strain JFW-HI SEQ_128975, 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: 32772
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1289 original size:26 final size:26
Alignment explanation
Indices: 1233--1290 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
1223 GATAAAATGG
* * *
1233 ATAACAATTTAATACCAATTCTGACA
1 ATAAAAATTTAATACCAATTCTAAAA
1259 A-AAAAATTTAAATACCAATT-TAAAA
1 ATAAAAATTT-AATACCAATTCTAAAA
1284 ATAAAAA
1 ATAAAAA
1291 CTAGTATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.28
Consensus pattern (26 bp):
ATAAAAATTTAATACCAATTCTAAAA
Found at i:5897 original size:26 final size:27
Alignment explanation
Indices: 5839--5899 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
5829 TCCTTTTTAA
* *
5839 AAAAATATTCATAAAAATTAAAAAGAT
1 AAAAATATTCATAAAAATTAAAAACAC
5866 AAAAAT-TTCA-AAAAATTAATAAACAC
1 AAAAATATTCATAAAAATTAA-AAACAC
*
5892 ATAAATAT
1 AAAAATAT
5900 AATAGTGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 9 0.31
26 13 0.45
27 7 0.24
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.26
Consensus pattern (27 bp):
AAAAATATTCATAAAAATTAAAAACAC
Found at i:9635 original size:16 final size:16
Alignment explanation
Indices: 9585--9646 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
9575 TGAAATACTG
9585 ATTACAAC-CATATTCC
1 ATTACAACTC-TATTCC
* ** * *
9601 ATTATATTTCTGTTAC
1 ATTACAACTCTATTCC
*
9617 ATTACAGCTCTATTCC
1 ATTACAACTCTATTCC
9633 ATTACAACTCTATT
1 ATTACAACTCTATT
9647 TTACTACAGC
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
16 33 0.97
17 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.42
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:11410 original size:59 final size:59
Alignment explanation
Indices: 11300--11856 Score: 382
Period size: 60 Copynumber: 9.3 Consensus size: 59
11290 GAAAAAAAAA
* * *
11300 TTTGTTGTTGGTCATTG-CATGGCCGACACCCCCCTTTTAATCTGAT--AAAAATCAAATTT
1 TTTGGTGTTGGCCA-TGCCATGGCCGACA--CCCCTTTTTATCTGATAAAAAAATCAAATTT
* * ** * *
11359 TTAGGTGTTGGCCATGCAATGGTTGACATCCCTATTTATCTGATAAAAAAATCAAATTT
1 TTTGGTGTTGGCCATGCCATGGCCGACACCCCTTTTTATCTGATAAAAAAATCAAATTT
** * * * * * *
11418 TTTTATGTTGACTATGCAATGGCCGACACCCCCTTTTTTTCAGATAAAAAAATTTCAATTTTT
1 TTTGGTGTTGGCCATGCCATGGCCGACA-CCCCTTTTTATCTGATAAAAAAA--TCAA-ATTT
* * *
11481 TTTGGTATTGGCCATTG-CATGGCCGACATCTCTTTTTATCTGA-ATAAAAAATCAAATTT
1 TTTGGTGTTGGCCA-TGCCATGGCCGACACCCCTTTTTATCTGATA-AAAAAATCAAATTT
** ** * * *
11540 TTAAGTGTTGGTAATACCATGGCCGACACCCCTTTTTGTC--ATATAAAAATTCAAATTATT
1 TTTGGTGTTGGCCATGCCATGGCCGACACCCCTTTTTATCTGATA-AAAAAATCAAA-T-TT
** * * * * *
11600 TTTTCTGTTAGCCATGCCATGGCCAACACCCCCTTTTTTATCTGGTAAAAAATTTTCAGATTT
1 TTTGGTGTTGGCCATGCCATGGCCGACA-CCCC-TTTTTATCTGATAAAAAA--ATCAAATTT
** * * *
11663 TTTGGAATTGGTCATTG-CATGACCGACACCCCTTTTTATCTGA-ATAAAAAATTAAA-TT
1 TTTGGTGTTGGCCA-TGCCATGGCCGACACCCCTTTTTATCTGATA-AAAAAATCAAATTT
* * * * *
11721 TTTGATGTGTTGGCCAT-CTCATGGTCGACACCCCTTTTT-TGTCAAATAAAAAATTAAATTTT
1 TTTG--GTGTTGGCCATGC-CATGGCCGACACCCCTTTTTATCTGATA-AAAAAATCAAA-TTT
* * * *
11783 TTTGGTGTTGGCCATACCATGACCGACATCCCTATTTATCTGATAAAAAAATCAAATTT
1 TTTGGTGTTGGCCATGCCATGGCCGACACCCCTTTTTATCTGATAAAAAAATCAAATTT
*
11842 TTTAGTGTTGGCCAT
1 TTTGGTGTTGGCCAT
11857 ACAATGACCG
Statistics
Matches: 387, Mismatches: 81, Indels: 60
0.73 0.15 0.11
Matches are distributed among these distances:
57 14 0.04
58 21 0.05
59 110 0.28
60 121 0.31
61 25 0.06
62 38 0.10
63 46 0.12
64 7 0.02
65 5 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (59 bp):
TTTGGTGTTGGCCATGCCATGGCCGACACCCCTTTTTATCTGATAAAAAAATCAAATTT
Found at i:11509 original size:122 final size:121
Alignment explanation
Indices: 11356--11588 Score: 285
Period size: 122 Copynumber: 1.9 Consensus size: 121
11346 AAAAATCAAA
* **
11356 TTTTTAGGTGTTGGCCATGCAATGGTTGACATCCCTATTTATCTG-ATAAAAAAATCAAATTTTT
1 TTTTTAGGTATTGGCCATGCAATGGCCGACATCCCTATTTATCTGAAT-AAAAAATCAAA-TTTT
* * *
11420 TTA-TGTTGACT-ATGCAATGGCCGACACCCCCTTTTTTTCAGATAAAAAAATTTCAATT
64 TAAGTGTTG-CTAATACAATGGCCGACA-CCCCTTTTTGTCAGATAAAAAAATTTCAATT
* * *
11478 TTTTTTGGTATTGGCCATTGC-ATGGCCGACATCTCTTTTTATCTGAATAAAAAATCAAATTTTT
1 TTTTTAGGTATTGGCCA-TGCAATGGCCGACATCCCTATTTATCTGAATAAAAAATCAAATTTTT
* * *
11542 AAGTGTTGGTAATACCATGGCCGACACCCCTTTTTGTCATATAAAAA
65 AAGTGTTGCTAATACAATGGCCGACACCCCTTTTTGTCAGATAAAAA
11589 TTCAAATTAT
Statistics
Matches: 95, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
121 26 0.27
122 64 0.67
123 5 0.05
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (121 bp):
TTTTTAGGTATTGGCCATGCAATGGCCGACATCCCTATTTATCTGAATAAAAAATCAAATTTTTA
AGTGTTGCTAATACAATGGCCGACACCCCTTTTTGTCAGATAAAAAAATTTCAATT
Found at i:11834 original size:182 final size:180
Alignment explanation
Indices: 11307--11834 Score: 559
Period size: 182 Copynumber: 2.9 Consensus size: 180
11297 AAATTTGTTG
* *
11307 TTGGTCATTGCATGGCCGACACCCCCCTTTTAATCTG-AT-AAAAATCAAATTTTTAGGTGTTGG
1 TTGGTCATTGCATGGCCGACA--CCCCTTTTTATCTGAATAAAAAATCAAATTTTTAAGTGTTGG
* * * * * * ** * * *
11370 CCATGCAATGGTTGACATCCCTATTTATCTGATAAAAAAATCAAATTTTTTTATGTTGACTATGC
64 CCATACCATGGTCGACACCCCTTTTTGTCAAAT-AAAAAATTAAATTTTTTTATGTTGGCCATGC
* * * *
11435 AATGGCCGACACCCCCTTTTTTTCAGATAAAAAAA-TTTCAATTTTTTTTGGTA
128 CATGGCCGACACCCCCTTTTTATCTGATAAAAAAATTTTCAA-TTTTTTTGGAA
* * * **
11488 TTGGCCATTGCATGGCCGACATCTCTTTTTATCTGAATAAAAAATCAAATTTTTAAGTGTTGGTA
1 TTGGTCATTGCATGGCCGACACCCCTTTTTATCTGAATAAAAAATCAAATTTTTAAGTGTTGGCC
* * * *
11553 ATACCATGGCCGACACCCCTTTTTGTCATAT-AAAAATTCAAATTATTTTTTCTGTTAGCCATGC
66 ATACCATGGTCGACACCCCTTTTTGTCAAATAAAAAATT-AAA-T-TTTTTTATGTTGGCCATGC
* *
11617 CATGGCCAACACCCCCTTTTTTATCTGGT-AAAAAATTTTCAGA-TTTTTTGGAA
128 CATGGCCGACACCCCC-TTTTTATCTGATAAAAAAATTTTCA-ATTTTTTTGGAA
* * *
11670 TTGGTCATTGCATGACCGACACCCCTTTTTATCTGAATAAAAAATTAAATTTTTGATGTGTTGGC
1 TTGGTCATTGCATGGCCGACACCCCTTTTTATCTGAATAAAAAATCAAATTTTT-AAGTGTTGGC
* *
11735 CAT-CTCATGGTCGACACCCCTTTTTTGTCAAATAAAAAATTAAATTTTTTTGGTGTTGGCCATA
65 CATAC-CATGGTCGACACCCC-TTTTTGTCAAATAAAAAATTAAATTTTTTT-ATGTTGGCCATG
* * *
11799 CCATGACCGACA-TCCCTATTTATCTGATAAAAAAAT
127 CCATGGCCGACACCCCCTTTTTATCTGATAAAAAAAT
11835 CAAATTTTTT
Statistics
Matches: 288, Mismatches: 45, Indels: 27
0.80 0.12 0.08
Matches are distributed among these distances:
179 17 0.06
180 5 0.02
181 76 0.26
182 110 0.38
183 58 0.20
184 15 0.05
185 7 0.02
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.37
Consensus pattern (180 bp):
TTGGTCATTGCATGGCCGACACCCCTTTTTATCTGAATAAAAAATCAAATTTTTAAGTGTTGGCC
ATACCATGGTCGACACCCCTTTTTGTCAAATAAAAAATTAAATTTTTTTATGTTGGCCATGCCAT
GGCCGACACCCCCTTTTTATCTGATAAAAAAATTTTCAATTTTTTTGGAA
Found at i:12707 original size:60 final size:60
Alignment explanation
Indices: 12643--12825 Score: 194
Period size: 60 Copynumber: 3.0 Consensus size: 60
12633 TTTAAAAAAA
* *
12643 TTTATCTGAAAAAAGGAGTGTCGATCATTGCATGGCCAACACCAAAAAATTTGATTTTTT
1 TTTATCTGAAAAAAGGGGTGTCGAACATTGCATGGCCAACACCAAAAAATTTGATTTTTT
* * * * ** * *
12703 TTTATCAGATAAATAGGGGTGTCGACCATGGCATGATCAACACTAAAATAA-TTGA--ATTT
1 TTTATCTGA-AAAAAGGGGTGTCGAACATTGCATGGCCAACACCAAAA-AATTTGATTTTTT
*
12762 TTTATCTGACAAAAAAGGGGTGTC-AACTATTGCATGGCCAACACCCAAAAATTTGATTTTTT
1 TTTATCTG--AAAAAAGGGGTGTCGAAC-ATTGCATGGCCAACACCAAAAAATTTGATTTTTT
12824 TT
1 TT
12826 ATCAAATTAA
Statistics
Matches: 97, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
59 14 0.14
60 40 0.41
61 36 0.37
62 7 0.07
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (60 bp):
TTTATCTGAAAAAAGGGGTGTCGAACATTGCATGGCCAACACCAAAAAATTTGATTTTTT
Found at i:12727 original size:61 final size:59
Alignment explanation
Indices: 12643--12829 Score: 191
Period size: 61 Copynumber: 3.1 Consensus size: 59
12633 TTTAAAAAAA
* * *
12643 TTTATCTGAAAAAAGGAGTGTCGATCATTGCATGGCCAACACCAAAAAATTTGATTTTTT
1 TTTATCAGAAAAAAGGGGTGTCGAACATTGCATGGCCAACACCAAAAAATTTGA-TTTTT
* * * ** * *
12703 TTTATCAGATAAATAGGGGTGTCGACCATGGCATGATCAACACTAAAATAA-TTGA-ATTT
1 TTTATCAGA-AAAAAGGGGTGTCGAACATTGCATGGCCAACACCAAAA-AATTTGATTTTT
* *
12762 TTTATCTGACAAAAAAGGGGTGTC-AACTATTGCATGGCCAACACCCAAAAATTTGATTTTT
1 TTTATC--AGAAAAAAGGGGTGTCGAAC-ATTGCATGGCCAACACCAAAAAATTTGATTTTT
12823 TTTATCA
1 TTTATCA
12830 AATTAAAAGA
Statistics
Matches: 102, Mismatches: 18, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
59 14 0.14
60 40 0.39
61 46 0.45
62 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Consensus pattern (59 bp):
TTTATCAGAAAAAAGGGGTGTCGAACATTGCATGGCCAACACCAAAAAATTTGATTTTT
Found at i:13445 original size:28 final size:28
Alignment explanation
Indices: 13414--13475 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
13404 TTAATTTATT
*
13414 ATTCTCGAT-TTGTTATTTTCAATTACCA
1 ATTCTCGATATT-TTATTTTAAATTACCA
*
13442 ATTCTCGATATTTTATTTTAAATTCCCA
1 ATTCTCGATATTTTATTTTAAATTACCA
13470 ATTCTC
1 ATTCTC
13476 AAATTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 29 0.94
29 2 0.06
ACGTcount: A:0.26, C:0.19, G:0.05, T:0.50
Consensus pattern (28 bp):
ATTCTCGATATTTTATTTTAAATTACCA
Found at i:21480 original size:21 final size:22
Alignment explanation
Indices: 21428--21482 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
21418 ATAAAAACTT
* * *
21428 AAGAAAAAACTTGAGTTTTTAC
1 AAGAAAAAATTTAAGGTTTTAC
*
21450 AAGCAAAAATTTAAGGTTTTAC
1 AAGAAAAAATTTAAGGTTTTAC
21472 -AGAAAAAATTT
1 AAGAAAAAATTT
21483 GAGTTTTGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.49, C:0.07, G:0.13, T:0.31
Consensus pattern (22 bp):
AAGAAAAAATTTAAGGTTTTAC
Found at i:23677 original size:15 final size:16
Alignment explanation
Indices: 23643--23682 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
23633 GAAAAGATAC
*
23643 TTAAAATTTGTGTAAG
1 TTAAAATTTGTATAAG
*
23659 TTAAATTTTGTATAA-
1 TTAAAATTTGTATAAG
23674 TTAAAATTT
1 TTAAAATTT
23683 CAATATATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (16 bp):
TTAAAATTTGTATAAG
Found at i:26283 original size:15 final size:15
Alignment explanation
Indices: 26263--26299 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
26253 GTCACCACTT
*
26263 TAAATTTATAAATAG
1 TAAATTTATAAACAG
26278 TAAATTTATAAACAG
1 TAAATTTATAAACAG
26293 TAAATTT
1 TAAATTT
26300 TTTAATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (15 bp):
TAAATTTATAAACAG
Found at i:29665 original size:21 final size:22
Alignment explanation
Indices: 29634--29678 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
29624 CATAAACACA
* *
29634 TATATTATTTTATATTTATATT
1 TATATTATTTTATAATTAAATT
29656 TATA-TATTTTATAATTAAATT
1 TATATTATTTTATAATTAAATT
29677 TA
1 TA
29679 AAATAAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATATTATTTTATAATTAAATT
Found at i:30356 original size:95 final size:94
Alignment explanation
Indices: 30182--30356 Score: 214
Period size: 95 Copynumber: 1.9 Consensus size: 94
30172 GTAATCCTTG
** *
30182 ATTTTGTGAAGTTATCTTTTATATTTTAAATTTGTTTATTTAAAATTGTTAATAAAAATTATTTA
1 ATTTTGTGAAAATATCTTTTATATTTCAAATTTGTTTATTTAAAATTGTT-ATAAAAATTATTTA
* **
30247 AAAGTTTGGTTATATATCTGTAATATTTTT
65 AAAATTTGAATATATATCTGTAATATTTTT
* *
30277 ATTTTGTGAAAATATTTTTTATATTTCAAATTTATTTTATTT-AAATTG-T-TAAAAATTATTTT
1 ATTTTGTGAAAATATCTTTTATATTTCAAATTT-GTTTATTTAAAATTGTTATAAAAATTA-TTT
30339 AAAAATTTGACA-ATATAT
64 AAAAATTTGA-ATATATAT
30357 TTTATTTTAC
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
92 9 0.13
93 17 0.25
94 1 0.01
95 35 0.51
96 7 0.10
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (94 bp):
ATTTTGTGAAAATATCTTTTATATTTCAAATTTGTTTATTTAAAATTGTTATAAAAATTATTTAA
AAATTTGAATATATATCTGTAATATTTTT
Found at i:32132 original size:4 final size:4
Alignment explanation
Indices: 32123--32188 Score: 62
Period size: 4 Copynumber: 16.2 Consensus size: 4
32113 AAATAAACGG
* * *
32123 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
* *
32173 G-AA GAAG GAGA GAAA G
1 GAAA GAAA GAAA GAAA G
32189 GTAATGTGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
3 3 0.06
4 40 0.78
5 8 0.16
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:32145 original size:17 final size:17
Alignment explanation
Indices: 32123--32155 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
32113 AAATAAACGG
32123 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
32140 GAAAGAAAGAAAGGAA
1 GAAAGAAAGAAAGGAA
32156 GAAGGAGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAGGAAA
Found at i:32168 original size:17 final size:16
Alignment explanation
Indices: 32130--32189 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 16
32120 CGGGAAAGAA
* *
32130 AGAAAGGAAAGAAAGAA
1 AGAAAGG-AAGAAGGAG
32147 AGAAAGGAAGAAGGAG
1 AGAAAGGAAGAAGGAG
32163 AGGAAAGAAAGAAGAAGGAG
1 A-GAAAG---GAAGAAGGAG
32183 AGAAAGG
1 AGAAAGG
32190 TAATGTGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
16 9 0.24
17 12 0.32
19 5 0.14
20 11 0.30
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
AGAAAGGAAGAAGGAG
Found at i:32189 original size:29 final size:30
Alignment explanation
Indices: 32125--32189 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
32115 ATAAACGGGA
32125 AAGAAA-GAAAGGAAAGAAAGAAAGAAAGG
1 AAGAAAGGAAAGGAAAGAAAGAAAGAAAGG
*
32154 AAG-AAGGAGAGGAAAGAAAG-AAG-AAGG
1 AAGAAAGGAAAGGAAAGAAAGAAAGAAAGG
32181 AGAGAAAGG
1 A-AGAAAGG
32190 TAATGTGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 5 0.16
28 7 0.22
29 20 0.62
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (30 bp):
AAGAAAGGAAAGGAAAGAAAGAAAGAAAGG
Done.