Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009741.1 Kokia drynarioides strain JFW-HI SEQ_124460, 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: 30198
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Found at i:914 original size:6 final size:6
Alignment explanation
Indices: 899--1007 Score: 77
Period size: 6 Copynumber: 18.7 Consensus size: 6
889 TGTAATTGAT
* * *
899 TTTAAA TTTAAG TTTAAA ATT--A TTTCAAA TTTAAA -CTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
* * *
945 TTTAAA -ATAAA TTTAAA TTTAAAAA ATT-AA TTTAAA TATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTT--AAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
993 -GTAAA TTTAAT TTTA
1 TTTAAA TTTAAA TTTA
1008 GAAATAAATC
Statistics
Matches: 79, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
4 3 0.04
5 16 0.20
6 51 0.65
7 4 0.05
8 5 0.06
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:998 original size:17 final size:17
Alignment explanation
Indices: 901--992 Score: 104
Period size: 17 Copynumber: 5.6 Consensus size: 17
891 TAATTGATTT
*
901 TAAATTTAAGTTTAAAA
1 TAAATTTAAATTTAAAA
* *
918 T-TATTTCAAATTTAAAC
1 TAAATTT-AAATTTAAAA
935 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
952 TAAATTTAAATTT-AAA
1 TAAATTTAAATTTAAAA
968 -AAA-TT-AATTTAAATA
1 TAAATTTAAATTTAAA-A
983 TAAATTTAAA
1 TAAATTTAAA
993 GTAAATTTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
13 5 0.08
14 4 0.06
15 4 0.06
16 10 0.16
17 34 0.54
18 6 0.10
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:1007 original size:17 final size:16
Alignment explanation
Indices: 901--1021 Score: 87
Period size: 17 Copynumber: 7.6 Consensus size: 16
891 TAATTGATTT
*
901 TAAATTTAAGTTTAAA
1 TAAATTTAAATTTAAA
*
917 -ATTATTTCAAATTTAAA
1 TA-AATTT-AAATTTAAA
934 CTAAATTTAAATTTAAAA
1 -TAAATTTAAATTT-AAA
952 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
968 -AAA-TT-AATTTAAA
1 TAAATTTAAATTTAAA
981 T--A--TAAATTTAAA
1 TAAATTTAAATTTAAA
*
993 GTAAATTTAATTTTAGAAA
1 -TAAATTTAAATTT--AAA
*
1012 TAAATCTAAA
1 TAAATTTAAA
1022 ATCCATCTAA
Statistics
Matches: 85, Mismatches: 6, Indels: 26
0.73 0.05 0.22
Matches are distributed among these distances:
11 1 0.01
12 9 0.11
13 9 0.11
14 2 0.02
15 5 0.06
16 7 0.08
17 33 0.39
18 15 0.18
19 4 0.05
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:3248 original size:42 final size:42
Alignment explanation
Indices: 3189--3287 Score: 180
Period size: 42 Copynumber: 2.4 Consensus size: 42
3179 CACTACTGAG
*
3189 CTTGGATTTTCTTCATTGCTAGGGACGATTCTGATTACATAA
1 CTTGGATTTTCTTCATTGCTAGGGACAATTCTGATTACATAA
3231 CTTGGATTTTCTTCATTGCTAGGGACAATTCTGATTACATAA
1 CTTGGATTTTCTTCATTGCTAGGGACAATTCTGATTACATAA
*
3273 GTTGGATTTTCTTCA
1 CTTGGATTTTCTTCA
3288 ATGTTGCCGA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.42
Consensus pattern (42 bp):
CTTGGATTTTCTTCATTGCTAGGGACAATTCTGATTACATAA
Found at i:4413 original size:81 final size:82
Alignment explanation
Indices: 4297--4450 Score: 301
Period size: 81 Copynumber: 1.9 Consensus size: 82
4287 TGTTACAGTC
4297 GTATAAAAATCTGATTTTAGTTTTAGTTTTTTTTGTTTTTATTGTTTTTTTTTT-ATCTTTACAA
1 GTATAAAAATCTGATTTTAGTTTTAGTTTTTTTTGTTTTTATTGTTTTTTTTTTGATCTTTACAA
4361 AAGTTTTGGCGTTAGTT
66 AAGTTTTGGCGTTAGTT
4378 GTATAAAAATCTGATTTTAGTTTTAGTTTTTTTTGTTTTTATTGTTTTTTTTTTGATCTTTACAA
1 GTATAAAAATCTGATTTTAGTTTTAGTTTTTTTTGTTTTTATTGTTTTTTTTTTGATCTTTACAA
4443 AAGTTTTG
66 AAGTTTTG
4451 ACGTCACCCC
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 54 0.75
82 18 0.25
ACGTcount: A:0.21, C:0.05, G:0.13, T:0.61
Consensus pattern (82 bp):
GTATAAAAATCTGATTTTAGTTTTAGTTTTTTTTGTTTTTATTGTTTTTTTTTTGATCTTTACAA
AAGTTTTGGCGTTAGTT
Found at i:16206 original size:6 final size:6
Alignment explanation
Indices: 16197--16352 Score: 147
Period size: 6 Copynumber: 25.3 Consensus size: 6
16187 AATTAGTTCA
* * * *
16197 TTTATT TTTATT TTCATT TTCATT TTCATT TTT-TT TTCATT TTTCATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTT-ATT
16245 TTTCATT TTTCATT TTTCATT TTTCATT TTTCATT TTT-TT TATT-TT
1 TTT-ATT TTT-ATT TTT-ATT TTT-ATT TTT-ATT TTTATT T-TTATT
* * * *
16291 TTTATT TTTATT TTTATT TTTATT TTTAGT TTTAGT TTTAGT TTTAGT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
16339 TTTAGT TTTATT TT
1 TTTATT TTTATT TT
16353 ACTTTGAATT
Statistics
Matches: 140, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
5 9 0.06
6 90 0.64
7 41 0.29
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:16239 original size:7 final size:7
Alignment explanation
Indices: 16207--16317 Score: 122
Period size: 7 Copynumber: 17.6 Consensus size: 7
16197 TTTATTTTTA
16207 TTTTCA-
1 TTTTCAT
16213 TTTTCA-
1 TTTTCAT
16219 TTTTCA-
1 TTTTCAT
16225 TTTT--T
1 TTTTCAT
16230 TTTTCAT
1 TTTTCAT
16237 TTTTCAT
1 TTTTCAT
16244 TTTTCAT
1 TTTTCAT
16251 TTTTCAT
1 TTTTCAT
16258 TTTTCAT
1 TTTTCAT
16265 TTTTCAT
1 TTTTCAT
16272 TTTTCAT
1 TTTTCAT
16279 TTTT--T
1 TTTTCAT
16284 TTATT--T
1 TT-TTCAT
16290 TTTT-AT
1 TTTTCAT
16296 TTTT-AT
1 TTTTCAT
16302 TTTT-AT
1 TTTTCAT
16308 TTTT-AT
1 TTTTCAT
16314 TTTT
1 TTTT
16318 AGTTTTAGTT
Statistics
Matches: 100, Mismatches: 0, Indels: 10
0.91 0.00 0.09
Matches are distributed among these distances:
5 9 0.09
6 44 0.44
7 47 0.47
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTCAT
Found at i:17297 original size:12 final size:12
Alignment explanation
Indices: 17266--17299 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
17256 AAAAGTCAAA
17266 AAGAAAAAAATT
1 AAGAAAAAAATT
**
17278 AATTAAAAAATT
1 AAGAAAAAAATT
17290 AAGAAAAAAA
1 AAGAAAAAAA
17300 GAGAAAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (12 bp):
AAGAAAAAAATT
Found at i:17299 original size:32 final size:33
Alignment explanation
Indices: 17263--17341 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 33
17253 AAAAAAAGTC
* *
17263 AAAAAGAAAAAAATTAATT-AAAAAATTAAG-AA
1 AAAAAGAAAAAAATAAATTGAAAAAA-GAAGAAA
17295 AAAAAGAGAAAAAA-AAATTGAAAAAAGAAGAAA
1 AAAAAGA-AAAAAATAAATTGAAAAAAGAAGAAA
*
17328 AAAAAGATAAAAAT
1 AAAAAGAAAAAAAT
17342 GTGTTTGAGC
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
32 19 0.47
33 21 0.52
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (33 bp):
AAAAAGAAAAAAATAAATTGAAAAAAGAAGAAA
Found at i:17317 original size:22 final size:23
Alignment explanation
Indices: 17282--17332 Score: 70
Period size: 22 Copynumber: 2.2 Consensus size: 23
17272 AAAATTAATT
17282 AAAAAATTAAGAAAAAA-AGAGAAA
1 AAAAAATT-AGAAAAAAGA-AGAAA
17306 AAAAAATT-GAAAAAAGAAGAAA
1 AAAAAATTAGAAAAAAGAAGAAA
17328 AAAAA
1 AAAAA
17333 GATAAAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 17 0.65
23 1 0.04
24 8 0.31
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (23 bp):
AAAAAATTAGAAAAAAGAAGAAA
Found at i:17340 original size:22 final size:21
Alignment explanation
Indices: 17293--17340 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
17283 AAAAATTAAG
17293 AAAAAAAGAGAAAAAAAAATT
1 AAAAAAAGAGAAAAAAAAATT
*
17314 GAAAAAAGAAGAAAAAAAAGA-T
1 AAAAAAAG-AGAAAAAAAA-ATT
17336 AAAAA
1 AAAAA
17341 TGTGTTTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 7 0.30
22 15 0.65
23 1 0.04
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.06
Consensus pattern (21 bp):
AAAAAAAGAGAAAAAAAAATT
Found at i:21559 original size:2 final size:2
Alignment explanation
Indices: 21552--21578 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21542 GGATACTCGC
21552 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
21579 ACGATGCACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22524 original size:93 final size:94
Alignment explanation
Indices: 22416--22636 Score: 304
Period size: 93 Copynumber: 2.4 Consensus size: 94
22406 ACATACCAAT
* * *
22416 TTTGTCTTTTGTTTTTCTTATTTTTTCTTTAATTTTTGATAAAAAAAAATTGGTTTCCAAAAATC
1 TTTGCCTTTTGTTTTTCTTATTTTATCTTTAATTTTTGATAAAAAAAAACTGGTTTCCAAAAATC
22481 TTTCTGACCTTCTCCACACC-CCAACACA
66 TTTCTGACCTTCTCCACACCTCCAACACA
* * * * * *
22509 TTTGCCTTTTGTTTTTCTTATTCTATCTTTAATTTTTTATAGAAGAAAACTGGTTTTCAAAAATG
1 TTTGCCTTTTGTTTTTCTTATTTTATCTTTAATTTTTGATAAAAAAAAACTGGTTTCCAAAAATC
* * *
22574 TTTCTGACCTTTTCCACCCCTCCCACACA
66 TTTCTGACCTTCTCCACACCTCCAACACA
*
22603 TTTGCCTTTTGTTTTT-TTATTTTAT-TTTTATTTT
1 TTTGCCTTTTGTTTTTCTTATTTTATCTTTAATTTT
22637 ATTCTTCCTA
Statistics
Matches: 113, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
92 8 0.07
93 82 0.73
94 23 0.20
ACGTcount: A:0.23, C:0.19, G:0.07, T:0.51
Consensus pattern (94 bp):
TTTGCCTTTTGTTTTTCTTATTTTATCTTTAATTTTTGATAAAAAAAAACTGGTTTCCAAAAATC
TTTCTGACCTTCTCCACACCTCCAACACA
Found at i:23802 original size:42 final size:42
Alignment explanation
Indices: 23740--23822 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
23730 GGGTAGGATT
* *
23740 TGTGTATGCATTTGTTTCTGAATCTATG-TTTGCATCTGTATA
1 TGTGTATGCATTTGTATCTGAATCTA-GATATGCATCTGTATA
* *
23782 TGTGTCTGCATTTGTATCTGAGTCTAGATATGCATCTGTAT
1 TGTGTATGCATTTGTATCTGAATCTAGATATGCATCTGTAT
23823 TGGATTATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 35 0.97
ACGTcount: A:0.19, C:0.13, G:0.20, T:0.47
Consensus pattern (42 bp):
TGTGTATGCATTTGTATCTGAATCTAGATATGCATCTGTATA
Found at i:25298 original size:43 final size:43
Alignment explanation
Indices: 25244--25399 Score: 163
Period size: 43 Copynumber: 3.6 Consensus size: 43
25234 TTATGCTCCC
* * * * *
25244 ACCGAGTCATAAGTTCTTCCATTTACA-ATAATTTTATGCTCTT
1 ACCGAGACATAAG-TCTTCCATTTATACATAATCTCATGCTCAT
* *
25287 ACCGAGACATAAGTTCTTCGATTTATACATAATCTCATACTCAT
1 ACCGAGACATAAG-TCTTCCATTTATACATAATCTCATGCTCAT
* * *
25331 CCCGAGACATGAGTCTTCCATTTATATATAATCTCATGCTCAT
1 ACCGAGACATAAGTCTTCCATTTATACATAATCTCATGCTCAT
* *
25374 -CTTGAGACATGAGTCTTCCATTTATA
1 AC-CGAGACATAAGTCTTCCATTTATA
25400 TATCAAGTCT
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
42 1 0.01
43 74 0.76
44 23 0.23
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.37
Consensus pattern (43 bp):
ACCGAGACATAAGTCTTCCATTTATACATAATCTCATGCTCAT
Found at i:25400 original size:43 final size:43
Alignment explanation
Indices: 25288--25402 Score: 167
Period size: 43 Copynumber: 2.7 Consensus size: 43
25278 TATGCTCTTA
* * *
25288 CCGAGACATAAGTTCTTCGATTTATACATAATCTCATACTCATC
1 CCGAGACATGAG-TCTTCCATTTATATATAATCTCATACTCATC
*
25332 CCGAGACATGAGTCTTCCATTTATATATAATCTCATGCTCATC
1 CCGAGACATGAGTCTTCCATTTATATATAATCTCATACTCATC
**
25375 TTGAGACATGAGTCTTCCATTTATATAT
1 CCGAGACATGAGTCTTCCATTTATATAT
25403 CAAGTCTTTA
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
43 54 0.83
44 11 0.17
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.37
Consensus pattern (43 bp):
CCGAGACATGAGTCTTCCATTTATATATAATCTCATACTCATC
Found at i:29149 original size:19 final size:19
Alignment explanation
Indices: 29125--29164 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
29115 ACAAAAAAAT
*
29125 AATTTCCTTTTTGACTTTC
1 AATTTCCTTGTTGACTTTC
*
29144 AATTTCCTTGTTGATTTTC
1 AATTTCCTTGTTGACTTTC
29163 AA
1 AA
29165 CGATTTCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.55
Consensus pattern (19 bp):
AATTTCCTTGTTGACTTTC
Done.