Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004444.1 Kokia drynarioides strain JFW-HI SEQ_117845, 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: 56732
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:507 original size:15 final size:15
Alignment explanation
Indices: 487--535 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
477 ATTTCTCTAA
487 AATTTATAAAATAAG
1 AATTTATAAAATAAG
* * *
502 AATTTACCAAAAAAAA
1 AATTTA-TAAAATAAG
518 AAGTTTATAAAATAAG
1 AA-TTTATAAAATAAG
534 AA
1 AA
536 ATATAAATGA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
15 6 0.23
16 16 0.62
17 4 0.15
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (15 bp):
AATTTATAAAATAAG
Found at i:1327 original size:23 final size:24
Alignment explanation
Indices: 1300--1365 Score: 93
Period size: 23 Copynumber: 2.9 Consensus size: 24
1290 TTTAATGTTC
*
1300 ACGAACATGTTCATTTAAC-TTAA
1 ACGAACATGTTCATTGAACATTAA
*
1323 TCGAACATGTTCA-TGAACATTAA
1 ACGAACATGTTCATTGAACATTAA
1346 ACGAACATGTTCA-TGAACAT
1 ACGAACATGTTCATTGAACAT
1366 ATAATTGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
22 4 0.10
23 35 0.90
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (24 bp):
ACGAACATGTTCATTGAACATTAA
Found at i:1343 original size:29 final size:24
Alignment explanation
Indices: 1300--1388 Score: 85
Period size: 23 Copynumber: 3.8 Consensus size: 24
1290 TTTAATGTTC
*
1300 ACGAACATGTTCATTTAAC--TTAA
1 ACGAACATGTTCA-TGAACATTTAA
*
1323 TCGAACATGTTCATGAACA-TTAA
1 ACGAACATGTTCATGAACATTTAA
*
1346 ACGAACATGTTCATGAACATATAA
1 ACGAACATGTTCATGAACATTTAA
** * *
1370 TTGAACACGTTCACGAACA
1 ACGAACATGTTCATGAACA
1389 ATGTTAATAA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
22 4 0.07
23 34 0.61
24 18 0.32
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (24 bp):
ACGAACATGTTCATGAACATTTAA
Found at i:1388 original size:47 final size:46
Alignment explanation
Indices: 1300--1388 Score: 117
Period size: 47 Copynumber: 1.9 Consensus size: 46
1290 TTTAATGTTC
* * *
1300 ACGAACATGTTCATTTAACTTAATCGAACATGTTCATGAACATTAA
1 ACGAACATGTTCATTGAACTTAATCGAACACGTTCACGAACATTAA
*
1346 ACGAACATGTTCA-TGAACATATAATTGAACACGTTCACGAACA
1 ACGAACATGTTCATTGAAC-T-TAATCGAACACGTTCACGAACA
1389 ATGTTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 4 0.11
46 14 0.38
47 19 0.51
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (46 bp):
ACGAACATGTTCATTGAACTTAATCGAACACGTTCACGAACATTAA
Found at i:1498 original size:12 final size:12
Alignment explanation
Indices: 1471--1517 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
1461 TCATTAATAA
*
1471 ATAAACGAAC-T
1 ATAAACGAGCTT
*
1482 ATAAACAAGCTT
1 ATAAACGAGCTT
*
1494 ATAAATGAGCTT
1 ATAAACGAGCTT
*
1506 TTAAACGAGCTT
1 ATAAACGAGCTT
1518 GTTCGTGAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
11 8 0.28
12 21 0.72
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.28
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:9651 original size:11 final size:11
Alignment explanation
Indices: 9635--9668 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
9625 ATGTACTTAC
9635 ATATTTTTTAT
1 ATATTTTTTAT
9646 ATA--TTTTAT
1 ATATTTTTTAT
9655 ATATTTTTTAT
1 ATATTTTTTAT
9666 ATA
1 ATA
9669 GAAAAATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.43
11 12 0.57
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
ATATTTTTTAT
Found at i:27120 original size:34 final size:34
Alignment explanation
Indices: 27081--27152 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
27071 TCAAGATCAT
*
27081 AAATCTAAAATAAGAAACAAAA-ATCATTCAGAAA
1 AAATCTAAAAGAAGAAACAAAATATCATTCA-AAA
27115 AAATCTAAAAGAAGAAACAAAATATCATTCAAAA
1 AAATCTAAAAGAAGAAACAAAATATCATTCAAAA
27149 AAAT
1 AAAT
27153 TTACCAGGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 28 0.78
35 8 0.22
ACGTcount: A:0.65, C:0.11, G:0.06, T:0.18
Consensus pattern (34 bp):
AAATCTAAAAGAAGAAACAAAATATCATTCAAAA
Found at i:32966 original size:30 final size:30
Alignment explanation
Indices: 32910--32978 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
32900 TCTCTTTAAT
* *
32910 TTTTAAATAAAAAGATAAACGCGTTTCAGC
1 TTTTAAATAAAAAGATAAACACGTTTCAAC
* * *
32940 TTTTAAATAAGAAGATAAATATGTTTCAAC
1 TTTTAAATAAAAAGATAAACACGTTTCAAC
32970 -TTTAAATAA
1 TTTTAAATAA
32979 TTTAATTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 9 0.26
30 25 0.74
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.35
Consensus pattern (30 bp):
TTTTAAATAAAAAGATAAACACGTTTCAAC
Found at i:34090 original size:24 final size:24
Alignment explanation
Indices: 34062--34112 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
34052 TAAAATATCA
*
34062 AAATAAATCTAAACACTTAGAATT
1 AAATAAACCTAAACACTTAGAATT
*
34086 AAATAAACCTAAAGACTTAGAATT
1 AAATAAACCTAAACACTTAGAATT
34110 AAA
1 AAA
34113 ATTGTCATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.57, C:0.12, G:0.06, T:0.25
Consensus pattern (24 bp):
AAATAAACCTAAACACTTAGAATT
Found at i:38343 original size:13 final size:13
Alignment explanation
Indices: 38325--38349 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38315 GCTAATTTGG
38325 AAAAGAAAAAAGA
1 AAAAGAAAAAAGA
38338 AAAAGAAAAAAG
1 AAAAGAAAAAAG
38350 GATACATGTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAGA
Found at i:41490 original size:18 final size:17
Alignment explanation
Indices: 41467--41501 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
41457 GGATAAATCT
41467 TTAATTAAATAAATTTAA
1 TTAATTAAA-AAATTTAA
41485 TTAATTAAAAAATTTAA
1 TTAATTAAAAAATTTAA
41502 ATCCTAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTAAAAAATTTAA
Found at i:45876 original size:35 final size:34
Alignment explanation
Indices: 45833--45898 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
45823 CATTTTGAAA
*
45833 TTAAAAAAA-TATATTAAATGTAAAAATATGATTT
1 TTAAAAAAATTATATTAAAGGT-AAAATATGATTT
*
45867 TTAATAAAAATTATTTTAAAGGTAAAATATGA
1 TTAA-AAAAATTATATTAAAGGTAAAATATGA
45899 AATTGATACC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 4 0.14
35 14 0.50
36 10 0.36
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.38
Consensus pattern (34 bp):
TTAAAAAAATTATATTAAAGGTAAAATATGATTT
Found at i:46002 original size:17 final size:17
Alignment explanation
Indices: 45960--46006 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
45950 AATTCAATTT
*
45960 TAATATAAAT-ATTTAA
1 TAATATAAATAATTCAA
45976 T-ATGATTAAATAATTCAA
1 TAAT-A-TAAATAATTCAA
45994 TAATATAAATAAT
1 TAATATAAATAAT
46007 ATAAAATGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 2 0.08
16 2 0.08
17 13 0.50
18 7 0.27
19 2 0.08
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TAATATAAATAATTCAA
Found at i:55045 original size:41 final size:41
Alignment explanation
Indices: 54998--55237 Score: 300
Period size: 41 Copynumber: 5.9 Consensus size: 41
54988 ACTTATGAGA
* **
54998 AAGCGCCGCTAAAGGTCAGAGCAATAGTGGTGCTTTTGTGC
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTTTGTGC
* ** * *
55039 AAGCGCCGCTAAAGGTTAGAGCAATAGCGACGCTTAGGGGA
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTTTGTGC
*
55080 AAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTTTGTTC
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTTTGTGC
* * * * *
55121 AAACGCTGCTAAAGGTTAGAGCAATAGCAATGCTTTTGTGC
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTTTGTGC
* *
55162 AAGCGCCGCTAAAGGTCAGAGCAATAGAGAAGCTTTTGTGC
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTTTGTGC
* * * *
55203 AAGCGTCGCTAAAGGTCAGAGTATTAGCGGCGCTT
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTT
55238 ATTTGAAAAA
Statistics
Matches: 167, Mismatches: 32, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 167 1.00
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.22
Consensus pattern (41 bp):
AAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTTTGTGC
Found at i:55067 original size:24 final size:23
Alignment explanation
Indices: 55040--55113 Score: 61
Period size: 24 Copynumber: 3.4 Consensus size: 23
55030 CTTTTGTGCA
*
55040 AGCGCCGCTAAAGGTTAGAGCAAT
1 AGCGACGCTAAAGG-TAGAGCAAT
*
55064 AGCGACGCT-TAGG--G-G-AA-
1 AGCGACGCTAAAGGTAGAGCAAT
*
55081 AGCGCCGCTAAAGGTCAGAGCAAT
1 AGCGACGCTAAAGGT-AGAGCAAT
55105 AGCGACGCT
1 AGCGACGCT
55114 TTTGTTCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 14
0.67 0.09 0.25
Matches are distributed among these distances:
17 8 0.21
18 5 0.13
19 1 0.03
20 1 0.03
21 1 0.03
22 1 0.03
23 5 0.13
24 16 0.42
ACGTcount: A:0.31, C:0.23, G:0.32, T:0.14
Consensus pattern (23 bp):
AGCGACGCTAAAGGTAGAGCAAT
Found at i:55155 original size:123 final size:123
Alignment explanation
Indices: 55005--55237 Score: 331
Period size: 123 Copynumber: 1.9 Consensus size: 123
54995 AGAAAGCGCC
*** * * *
55005 GCTAAAGGTCAGAGCAATAGTGGTGCTTTTGTGCAAGCGCCGCTAAAGGTTAGAGCAATAGCGAC
1 GCTAAAGGTCAGAGCAATAGCAATGCTTTTGTGCAAGCGCCGCTAAAGGTCAGAGCAATAGAGAA
55070 GCTTAGGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTTTGTTCAAACGCT
66 GCTTAGGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTTTGTTCAAACGCT
*
55128 GCTAAAGGTTAGAGCAATAGCAATGCTTTTGTGCAAGCGCCGCTAAAGGTCAGAGCAATAGAGAA
1 GCTAAAGGTCAGAGCAATAGCAATGCTTTTGTGCAAGCGCCGCTAAAGGTCAGAGCAATAGAGAA
** * * * * * *
55193 GCTTTTGTGCAAGCGTCGCTAAAGGTCAGAGTATTAGCGGCGCTT
66 GCTTAGGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTT
55238 ATTTGAAAAA
Statistics
Matches: 95, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
123 95 1.00
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (123 bp):
GCTAAAGGTCAGAGCAATAGCAATGCTTTTGTGCAAGCGCCGCTAAAGGTCAGAGCAATAGAGAA
GCTTAGGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTTTGTTCAAACGCT
Found at i:56071 original size:31 final size:31
Alignment explanation
Indices: 56036--56100 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
56026 GTTAGTCATG
56036 TTTATAACACCAACTATAAGAAGCTATCTTA
1 TTTATAACACCAACTATAAGAAGCTATCTTA
* *
56067 TTTATAACACCAACTATTAGAAGCTTTCTTA
1 TTTATAACACCAACTATAAGAAGCTATCTTA
56098 TTT
1 TTT
56101 TGCTTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.38
Consensus pattern (31 bp):
TTTATAACACCAACTATAAGAAGCTATCTTA
Done.