Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008083.1 Kokia drynarioides strain JFW-HI SEQ_122739, 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: 56040
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:994 original size:81 final size:79
Alignment explanation
Indices: 793--1077 Score: 302
Period size: 81 Copynumber: 3.5 Consensus size: 79
783 GACCCTTATA
* * * *
793 ATGGCTGAGATCCTAAATACGTTGCAGTTTCTTGATAGCTTGTGTGAGCAGCACTT-TGAGTGTG
1 ATGGCTGGGATCCTACATATGTTGCAGTTTCTTGACAGCTTGTGTGAGCAGCA-TTGTGAGTG-G
* * *
857 TAACACGGACCCTACG
64 TAATATGGACCGTACG
* * * * * * * * *
873 ATGGCTGAGATCTTGCATATGTTGCGGATTCTTGATAGCTTGTGTGAGTAGCTTTGTGACTAGGT
1 ATGGCTGGGATCCTACATATGTTGCAGTTTCTTGACAGCTTGTGTGAGCAGCATTGTGAGT-GGT
938 AATATGGACCGTATCG
65 AATATGGACCGTA-CG
* * *
954 ATGGTTGGGATCCTACATATGTCGCAGTTTCTTGACAGCTTGTGTGAGCAGCATCGTGAGTGGGT
1 ATGGCTGGGATCCTACATATGTTGCAGTTTCTTGACAGCTTGTGTGAGCAGCATTGTGAGT-GGT
*
1019 ATTATGGACCGTAGCG
65 AATATGGACCGTA-CG
* * *
1035 ATGGCTGGGATCCTACATATGTTACAGTTTCCTGACATCTTGT
1 ATGGCTGGGATCCTACATATGTTGCAGTTTCTTGACAGCTTGT
1078 CTGATTAGCA
Statistics
Matches: 170, Mismatches: 32, Indels: 5
0.82 0.15 0.02
Matches are distributed among these distances:
79 2 0.01
80 61 0.36
81 107 0.63
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (79 bp):
ATGGCTGGGATCCTACATATGTTGCAGTTTCTTGACAGCTTGTGTGAGCAGCATTGTGAGTGGTA
ATATGGACCGTACG
Found at i:1133 original size:26 final size:26
Alignment explanation
Indices: 1103--1155 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1093 TACTAGTTAT
1103 ACTCTATCTAG-GCTCGTAAGAGCTAA
1 ACTCTAT-TAGCGCTCGTAAGAGCTAA
* *
1129 ACTCTATTTGCGCTCGTATGAGCTAA
1 ACTCTATTAGCGCTCGTAAGAGCTAA
1155 A
1 A
1156 TTCTGGAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (26 bp):
ACTCTATTAGCGCTCGTAAGAGCTAA
Found at i:6869 original size:13 final size:14
Alignment explanation
Indices: 6846--6878 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6836 AGATCTACTT
6846 TAAACTCTAAAA-GA
1 TAAA-TCTAAAACGA
6860 TAAATCTAAAACGA
1 TAAATCTAAAACGA
6874 TAAAT
1 TAAAT
6879 AGAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.58, C:0.12, G:0.06, T:0.24
Consensus pattern (14 bp):
TAAATCTAAAACGA
Found at i:18386 original size:17 final size:17
Alignment explanation
Indices: 18340--18405 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 17
18330 ATATATATAG
**
18340 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* **
18357 AGATGCAGCGACAATAA
1 AAATGCAATGACAATAA
*
18374 AAATGCAATGACATTAA
1 AAATGCAATGACAATAA
* *
18391 TAATGCAAGGACAAT
1 AAATGCAATGACAAT
18406 TATACTACAG
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:18397 original size:34 final size:34
Alignment explanation
Indices: 18340--18405 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
18330 ATATATATAG
*
18340 AAATGCAATGACAATGTAGATGC-AGCGACAATAA
1 AAATGCAATGACAATATAGATGCAAG-GACAATAA
*
18374 AAATGCAATGACATTAATA-ATGCAAGGACAAT
1 AAATGCAATGACAAT-ATAGATGCAAGGACAAT
18406 TATACTACAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 24 0.86
35 4 0.14
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (34 bp):
AAATGCAATGACAATATAGATGCAAGGACAATAA
Found at i:22286 original size:22 final size:22
Alignment explanation
Indices: 22260--22302 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
22250 TAAGAACAAA
22260 ATAAATAAATAGAAAAATAAAT
1 ATAAATAAATAGAAAAATAAAT
* *
22282 ATAAATAAATATAAAATTAAA
1 ATAAATAAATAGAAAAATAAA
22303 AAAGAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (22 bp):
ATAAATAAATAGAAAAATAAAT
Found at i:25869 original size:14 final size:14
Alignment explanation
Indices: 25845--25878 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
25835 GAATCTACTT
25845 TAAACTCTAAAAAGA
1 TAAA-TCTAAAAAGA
*
25860 TAAATCTAAAAATA
1 TAAATCTAAAAAGA
25874 TAAAT
1 TAAAT
25879 ACAAATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.62, C:0.09, G:0.03, T:0.26
Consensus pattern (14 bp):
TAAATCTAAAAAGA
Found at i:27440 original size:22 final size:22
Alignment explanation
Indices: 27407--27467 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
27397 TATAAGAAAT
* *
27407 AAATAAAGAAATAGAAAATTAA
1 AAATAAAAAAATAGAAAAGTAA
* * *
27429 ATATAAATAAATATAAAAGTAA
1 AAATAAAAAAATAGAAAAGTAA
27451 AAATAAAAAAAT-GAAAA
1 AAATAAAAAAATAGAAAA
27468 AAAATTAGGT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 4 0.12
22 28 0.88
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (22 bp):
AAATAAAAAAATAGAAAAGTAA
Found at i:33598 original size:81 final size:80
Alignment explanation
Indices: 33333--33634 Score: 300
Period size: 80 Copynumber: 3.8 Consensus size: 80
33323 TAAAGACCCC
* * * * *
33333 TACGATGGCTGAGATCCTGCATACGTCGTAGTTTCTTGACAGCTTGTATGAGCAGCATTATGAGT
1 TACGATGGCTGAGATCCTGCATATGTTGCAGTTTCTTGACAGCTTGTGTGAGCAGCATTGTGAGT
* *
33398 GGGTAACATGGACTC
66 GGGTAATATGGACTA
* * * * * * *
33413 TACGATTGCTGAGATCTTGCATATGTTACGGATTCTTGATAGCTTGTGTGAGCAGCATTGTGACT
1 TACGATGGCTGAGATCCTGCATATGTTGCAGTTTCTTGACAGCTTGTGTGAGCAGCATTGTGAGT
*
33478 -GGTAATATGGACAA
66 GGGTAATATGGACTA
* * * * *
33492 TATCGATGGCTGGGATCCCGCATATGTTGCAGTTTCTTGACAGCTTGTGTTAGCAACATCGTGAG
1 TA-CGATGGCTGAGATCCTGCATATGTTGCAGTTTCTTGACAGCTTGTGTGAGCAGCATTGTGAG
** *
33557 TGGGTAATATGGTTTG
65 TGGGTAATATGGACTA
* * * * * * * *
33573 TAGCGATGGCTGGGATCTTGAATATGTTGCAGTTTCCTGATAACTTATGTGAGCGGCATTGT
1 TA-CGATGGCTGAGATCCTGCATATGTTGCAGTTTCTTGACAGCTTGTGTGAGCAGCATTGT
33635 ATATTGGTTA
Statistics
Matches: 177, Mismatches: 43, Indels: 3
0.79 0.19 0.01
Matches are distributed among these distances:
79 13 0.07
80 104 0.59
81 60 0.34
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (80 bp):
TACGATGGCTGAGATCCTGCATATGTTGCAGTTTCTTGACAGCTTGTGTGAGCAGCATTGTGAGT
GGGTAATATGGACTA
Found at i:38681 original size:80 final size:81
Alignment explanation
Indices: 38581--38755 Score: 219
Period size: 81 Copynumber: 2.2 Consensus size: 81
38571 CTTGATAGTG
* * *
38581 TGTGTGAGCAGCATTATGAGTGGGTAACATGGACCCTA-CGATGGCTGAGG-TCCTGCATATGTT
1 TGTGTGAGCAGCATCATGAGTGGGTAACATGGACCATATCGATGGCTG-GGATCCTACATATGTT
* *
38644 GCGGATTCTTCACAGCT
65 GCAGATTCTTCACAACT
* * *
38661 TGTGTGAGCAGCATCGTGAGTGGGTAATATGGAGCATATCGATGGCTGGGATCCTACATATGTTG
1 TGTGTGAGCAGCATCATGAGTGGGTAACATGGACCATATCGATGGCTGGGATCCTACATATGTTG
* * *
38726 TAGTTTCTTGACAACT
66 CAGATTCTTCACAACT
*
38742 TGTGTGAGTAGCAT
1 TGTGTGAGCAGCAT
38756 AGTATACTGG
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
80 35 0.43
81 46 0.57
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (81 bp):
TGTGTGAGCAGCATCATGAGTGGGTAACATGGACCATATCGATGGCTGGGATCCTACATATGTTG
CAGATTCTTCACAACT
Found at i:47202 original size:14 final size:15
Alignment explanation
Indices: 47172--47207 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
47162 ACAACTTCTT
47172 CTTCTTTTTCTTTTTC
1 CTTC-TTTTCTTTTTC
47188 CTTCTTTTC-TTTTC
1 CTTCTTTTCTTTTTC
47202 CTTCTT
1 CTTCTT
47208 CTTTTCTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 11 0.55
15 5 0.25
16 4 0.20
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (15 bp):
CTTCTTTTCTTTTTC
Found at i:47232 original size:27 final size:27
Alignment explanation
Indices: 47166--47232 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 27
47156 GTCGGGACAA
* *
47166 CTTCTTCTTCTTTTTCTTTTTCCTTCT
1 CTTCTTCTACTTCTTCTTTTTCCTTCT
* * * *
47193 TTTCTTTTCCTTCTTC-TTTTCTGTTCT
1 CTTCTTCTACTTCTTCTTTTTC-CTTCT
47220 CTTCTTCTACTTC
1 CTTCTTCTACTTC
47233 AATACCCTCA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
26 5 0.16
27 26 0.84
ACGTcount: A:0.01, C:0.30, G:0.01, T:0.67
Consensus pattern (27 bp):
CTTCTTCTACTTCTTCTTTTTCCTTCT
Done.