Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007175.1 Kokia drynarioides strain JFW-HI SEQ_121787, 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: 84402
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Warning! 97 characters in sequence are not A, C, G, or T
Found at i:1344 original size:25 final size:25
Alignment explanation
Indices: 1295--1344 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1285 AAATTAAAAG
* * *
1295 TTTCTTTTATATTTTAATAGTATTT
1 TTTCTCTTATATTTTAAAAGGATTT
1320 TTTCTCTTATATTTTAAAAGGATTT
1 TTTCTCTTATATTTTAAAAGGATTT
1345 ATTTATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (25 bp):
TTTCTCTTATATTTTAAAAGGATTT
Found at i:4737 original size:20 final size:20
Alignment explanation
Indices: 4708--4751 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
4698 AATATTATTT
* * * *
4708 TTATTTATTTTTATTTTAAG
1 TTATTAATTTATAATTTAAA
4728 TTATTAATTTATAATTTAAA
1 TTATTAATTTATAATTTAAA
4748 TTAT
1 TTAT
4752 ATTAAAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TTATTAATTTATAATTTAAA
Found at i:8440 original size:14 final size:14
Alignment explanation
Indices: 8395--8445 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 14
8385 ATTTTAACGT
*
8395 TACTTTTG-AGAAG
1 TACTTTTGAAAAAG
8408 TACTTTT-AAAAAG
1 TACTTTTGAAAAAG
*
8421 T-GTTTTGAAAAAG
1 TACTTTTGAAAAAG
*
8434 TATTTTTGAAAA
1 TACTTTTGAAAA
8446 GTTTAGTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
12 4 0.12
13 19 0.59
14 9 0.28
ACGTcount: A:0.39, C:0.04, G:0.16, T:0.41
Consensus pattern (14 bp):
TACTTTTGAAAAAG
Found at i:18741 original size:11 final size:11
Alignment explanation
Indices: 18725--18750 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
18715 CTTATATATG
18725 AAAAAAGAAAA
1 AAAAAAGAAAA
18736 AAAAAAGAAAA
1 AAAAAAGAAAA
18747 AAAA
1 AAAA
18751 GAAAAGGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:19420 original size:18 final size:18
Alignment explanation
Indices: 19380--19431 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
19370 TTTTCAGTTG
*
19380 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAATTTATT
*
19398 CAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
19416 TAATTAA--AAATTTATT
1 TAATTAATTAAATTTATT
19432 ATCATCCCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 7 0.23
18 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:32102 original size:29 final size:29
Alignment explanation
Indices: 32060--32126 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
32050 TTAGGACCTT
32060 CTAAATTCCTAGAAATAAAAATATAGGGA
1 CTAAATTCCTAGAAATAAAAATATAGGGA
**
32089 CTAAATTTTTAGAAATAAAAATATAGGGA
1 CTAAATTCCTAGAAATAAAAATATAGGGA
32118 CTAAATTCC
1 CTAAATTCC
32127 AAATTTGGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.28
Consensus pattern (29 bp):
CTAAATTCCTAGAAATAAAAATATAGGGA
Found at i:35539 original size:26 final size:26
Alignment explanation
Indices: 35510--35560 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
35500 TACCAAGTTC
35510 CATAGTATACATTAACCCTTTTAAAT
1 CATAGTATACATTAACCCTTTTAAAT
35536 CATAGTATACATTAACCCTTTTAAA
1 CATAGTATACATTAACCCTTTTAAA
35561 GTATATTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (26 bp):
CATAGTATACATTAACCCTTTTAAAT
Found at i:43311 original size:22 final size:22
Alignment explanation
Indices: 43267--43313 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
43257 TCACAATTTA
** *
43267 AAATTTTAAAAATAGGAGGATT
1 AAATTTTAAAAATACAAGAATT
*
43289 AAATTTTAAAATTACAAGAATT
1 AAATTTTAAAAATACAAGAATT
43311 AAA
1 AAA
43314 GAATTATGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.55, C:0.02, G:0.11, T:0.32
Consensus pattern (22 bp):
AAATTTTAAAAATACAAGAATT
Found at i:58455 original size:20 final size:21
Alignment explanation
Indices: 58432--58471 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
58422 TAATCAAATT
*
58432 TAAAATAATAT-AAATTTTAA
1 TAAAAAAATATAAAATTTTAA
*
58452 TAAAAAAATCTAAAATTTTA
1 TAAAAAAATATAAAATTTTA
58472 TATTTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAAAAATATAAAATTTTAA
Found at i:70590 original size:4 final size:4
Alignment explanation
Indices: 70573--70612 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
70563 TTGGAAAGGT
*
70573 TGTA TGTA TATA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
70613 ACTATTCAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:81251 original size:30 final size:30
Alignment explanation
Indices: 81210--81274 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
81200 GTTGGATTTA
*
81210 AAAAAAATTT-AATAGTGCAGTGATTTAAAT
1 AAAAAAATTTAAATAGT-CAGTGACTTAAAT
* *
81240 AAAAAATTTTAAATAGTTAGTGACTTAAAT
1 AAAAAAATTTAAATAGTCAGTGACTTAAAT
*
81270 GAAAA
1 AAAAA
81275 CTTTCGAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 24 0.80
31 6 0.20
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.32
Consensus pattern (30 bp):
AAAAAAATTTAAATAGTCAGTGACTTAAAT
Found at i:81285 original size:30 final size:30
Alignment explanation
Indices: 81211--81287 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
81201 TTGGATTTAA
* *
81211 AAAAAATTT--AATAGTGCAGTGATTTAAAT
1 AAAAAATTTCAAATAGT-TAGTGACTTAAAT
*
81240 AAAAAATTTTAAATAGTTAGTGACTTAAAT
1 AAAAAATTTCAAATAGTTAGTGACTTAAAT
* * *
81270 GAAAACTTTCGAATAGTT
1 AAAAAATTTCAAATAGTT
81288 CAATAATTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 9 0.22
30 25 0.62
31 6 0.15
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.35
Consensus pattern (30 bp):
AAAAAATTTCAAATAGTTAGTGACTTAAAT
Found at i:83844 original size:19 final size:20
Alignment explanation
Indices: 83805--83855 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
83795 AATTAAAAAT
*
83805 AATATTTTATTAAAATGTTA
1 AATATTTTAATAAAATGTTA
* *
83825 AA-ATTTTAATAATATTTTA
1 AATATTTTAATAAAATGTTA
83844 AATATTGTTAAT
1 AATATT-TTAAT
83856 TATAATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 16 0.62
20 5 0.19
21 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
AATATTTTAATAAAATGTTA
Found at i:84038 original size:17 final size:18
Alignment explanation
Indices: 84016--84059 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
84006 ATAATACATA
84016 ATATATTAATTA-TTATC
1 ATATATTAATTATTTATC
*
84033 ATATATT-ATTATTTATT
1 ATATATTAATTATTTATC
84050 ATATAATTAA
1 ATAT-ATTAA
84060 AATATGCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 4 0.17
17 15 0.65
18 3 0.13
19 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATATTAATTATTTATC
Done.