Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011844.1 Kokia drynarioides strain JFW-HI SEQ_126840, 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: 15854
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Warning! 61 characters in sequence are not A, C, G, or T
Found at i:1126 original size:29 final size:29
Alignment explanation
Indices: 1094--1471 Score: 319
Period size: 29 Copynumber: 12.9 Consensus size: 29
1084 ACCCCGGAGT
* *
1094 TTCCAAAATTTCCATGTTTACCCTCGAAC
1 TTCCAAAAATTCCATTTTTACCCTCGAAC
* * * *
1123 TTCCAAATATTTCGTGTTTAACCC-CGAAAC
1 TTCCAAAAATTCCAT-TTTTACCCTCG-AAC
**
1153 TT-CAAAATATTCCATTTTTACCCTTAAAC
1 TTCCAAAA-ATTCCATTTTTACCCTCGAAC
** *
1182 TTTTAAAAATTCCATTTTTGACCC-CAAAAC
1 TTCCAAAAATTCCATTTTT-ACCCTC-GAAC
* *
1212 TTCTAAAAATTACATTTTTACCCTCGAA-
1 TTCCAAAAATTCCATTTTTACCCTCGAAC
1240 TTCCCAAAAATTCCATTTTTGA-CCTCGAAAC
1 TT-CCAAAAATTCCATTTTT-ACCCTCG-AAC
1271 TTCCAAAAAATT-CATTTTTA-CCTCCGAAC
1 TTCC-AAAAATTCCATTTTTACCCT-CGAAC
*
1300 TTCC-AAAATTCTATTTTTAACCC-CGAAAC
1 TTCCAAAAATTCCATTTTT-ACCCTCG-AAC
* *
1329 TTCTAAAAATTCCATTTTTACCCCCGAAC
1 TTCCAAAAATTCCATTTTTACCCTCGAAC
* **
1358 TTCCAAAAATTCCATTTTCAACCCTAAAAC
1 TTCCAAAAATTCCATTTT-TACCCTCGAAC
1388 TTCCAAAAATTCCATTTTTACCCTCGAAC
1 TTCCAAAAATTCCATTTTTACCCTCGAAC
* * *
1417 CTCCAAAATTTCCATTTTTGACCC-CAAAAC
1 TTCCAAAAATTCCATTTTT-ACCCTC-GAAC
* *
1447 TTTCAAAATTTACCA-TTTTACCCTC
1 TTCCAAAAATT-CCATTTTTACCCTC
1472 AAAAATTCAA
Statistics
Matches: 289, Mismatches: 35, Indels: 49
0.77 0.09 0.13
Matches are distributed among these distances:
27 6 0.02
28 10 0.03
29 138 0.48
30 123 0.43
31 12 0.04
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTTACCCTCGAAC
Found at i:1176 original size:59 final size:58
Alignment explanation
Indices: 1097--1471 Score: 400
Period size: 59 Copynumber: 6.4 Consensus size: 58
1087 CCGGAGTTTC
* * * * * * *
1097 CAAAATTTCCATGTTTACCCTCGAACTTCCAAATATTTCGTGTTTAACCCCGAAACTT
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCAAAACTT
** ** *
1155 CAAAATATTCCATTTTTACCCTTAAACTTTTAAAAATTCCATTTTTGACCCCAAAACTT
1 CAAAA-ATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCAAAACTT
* * * *
1214 CTAAAAATTACATTTTTACCCTCGAA-TTCCCAAAAATTCCATTTTTGACCTCGAAACTT
1 C-AAAAATTCCATTTTTACCCTCGAACTT-CCAAAAATTCCATTTTTAACCCCAAAACTT
* *
1273 CCAAAAAATT-CATTTTTA-CCTCCGAACTTCC-AAAATTCTATTTTTAACCCCGAAACTT
1 -C-AAAAATTCCATTTTTACCCT-CGAACTTCCAAAAATTCCATTTTTAACCCCAAAACTT
* * *
1331 CTAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTCAACCCTAAAACTT
1 C-AAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCAAAACTT
* * *
1390 CCAAAAATTCCATTTTTACCCTCGAACCTCCAAAATTTCCATTTTTGACCCCAAAACTTT
1 -CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCAAAAC-TT
*
1450 CAAAATTTACCA-TTTTACCCTC
1 CAAAAATT-CCATTTTTACCCTC
1472 AAAAATTCAA
Statistics
Matches: 269, Mismatches: 36, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
57 8 0.03
58 51 0.19
59 190 0.71
60 20 0.07
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (58 bp):
CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCAAAACTT
Found at i:1481 original size:29 final size:29
Alignment explanation
Indices: 1420--1498 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 29
1410 CTCGAACCTC
*
1420 CAAAATTT-CCATTTTTGACCCCAAAACTTT
1 CAAAATTTACCA-TTTT-ACCCCAAAACATT
1450 CAAAATTTACCATTTTACCCTCAAAA-ATT
1 CAAAATTTACCATTTTACCC-CAAAACATT
1479 CAAAA-TTACCATTTTACCCC
1 CAAAATTTACCATTTTACCCC
1499 TCGGGTATCC
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
27 1 0.02
28 14 0.30
29 11 0.24
30 17 0.37
31 3 0.07
ACGTcount: A:0.37, C:0.28, G:0.01, T:0.34
Consensus pattern (29 bp):
CAAAATTTACCATTTTACCCCAAAACATT
Found at i:13748 original size:205 final size:205
Alignment explanation
Indices: 13396--13999 Score: 850
Period size: 205 Copynumber: 2.9 Consensus size: 205
13386 CCAACTCAAG
* * * * * *
13396 GCTCGATGTGAGCAAATCTTCGAATCCCAGCTTCTTGATGAGATATTGAGAAGCAGGGCGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCTTGATTAGACACTAAGAAGCAGGTCGAAGCA
* * * * *
13461 ATAAAAAGTTAGCTTCTTGATGAGATATTGAGAAGTGGACAAAATTCGTCTTCCTAATGAGATAC
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
* * *
13526 AGAGAAGCAAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
131 AGAGAAGCGAATTGAAACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
*
13591 TCAAACCCAT
196 TCAAACCCAC
13601 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCTTGATTAGACACTAAGAAGCAGGTCGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCTTGATTAGACACTAAGAAGCAGGTCGAAGCA
* *
13666 ATAAAAGGTTAGCTTCCTAATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
13731 AGAGAAGCGAATTGAAACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
131 AGAGAAGCGAATTGAAACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
*
13796 TCAAATCCAC
196 TCAAACCCAC
* * *
13806 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCTTAATTAGACACTAAGAAGCAGGTCAAAGTA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCTTGATTAGACACTAAGAAGCAGGTCGAAGCA
* * * * * * * *
13871 ATACAAGGTTAGCTTCCTGATGAAATAC-GAGGAGATGAACCAAAATCATCTTCCTGATGAAACA
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAG-TGGACCAAATTCGTCTTCCTGATGAGATA
* * ** ** * * *
13935 CAGAGAAGTGGATCAAAACAAGTGATACGGTCGTCTTCCTGATGAGATACTGAGAAGAAGGCCAA
130 CAGAGAAGCGAATTGAAACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
14000 GTTAATGAAA
Statistics
Matches: 358, Mismatches: 40, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
204 4 0.01
205 354 0.99
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (205 bp):
GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCTTGATTAGACACTAAGAAGCAGGTCGAAGCA
ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
AGAGAAGCGAATTGAAACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
TCAAACCCAC
Found at i:14078 original size:6 final size:6
Alignment explanation
Indices: 14067--14134 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
14057 TCAAATTTAT
** **
14067 TTTAAA TTTAAA TTTATCT TTTAAAA TTTAAA TTT-GC TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
14116 TTT-AA TTAAAA TTAAAA TT
1 TTTAAA TTTAAA TTTAAA TT
14135 GATTTAAAAC
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
5 7 0.14
6 35 0.71
7 6 0.12
8 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:14081 original size:17 final size:17
Alignment explanation
Indices: 14059--14139 Score: 81
Period size: 17 Copynumber: 4.6 Consensus size: 17
14049 GAATTGATTC
14059 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
14076 AAATTTATCTTTTAAAATTT
1 AAATTTA--TTTT-AAATTT
**
14096 AAATTTGCTTTAAATTT
1 AAATTTATTTTAAATTT
* * *
14113 AAATTTAATTAAAATTA
1 AAATTTATTTTAAATTT
*
14130 AAATTGATTT
1 AAATTTATTT
14140 AAAACTTAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
17 34 0.64
18 3 0.06
19 4 0.08
20 12 0.23
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:14141 original size:17 final size:18
Alignment explanation
Indices: 14086--14148 Score: 51
Period size: 17 Copynumber: 3.7 Consensus size: 18
14076 AAATTTATCT
* * *
14086 TTTAAAATTTAAATTTGC
1 TTTAAAACTTAAAATTGA
* *
14104 TTT-AAA-TTTAAATTTA
1 TTTAAAACTTAAAATTGA
*
14120 ATTAAAA-TTAAAATTGA
1 TTTAAAACTTAAAATTGA
14137 TTTAAAACTTAA
1 TTTAAAACTTAA
14149 TTAAATTAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
16 8 0.23
17 20 0.57
18 7 0.20
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (18 bp):
TTTAAAACTTAAAATTGA
Found at i:14141 original size:33 final size:34
Alignment explanation
Indices: 14067--14159 Score: 91
Period size: 33 Copynumber: 2.7 Consensus size: 34
14057 TCAAATTTAT
* * *
14067 TTTAAATTTAAATTTATCTTTTAAAATTTAAATTTGC
1 TTTAAATTTAAATTTA---ATTAAAATTTAAAATTGA
14104 TTTAAATTTAAATTTAATTAAAA-TTAAAATTGA
1 TTTAAATTTAAATTTAATTAAAATTTAAAATTGA
* *
14137 TTTAAAACTT-AATTAAATTAAAA
1 TTT-AAATTTAAATTTAATTAAAA
14160 GTCCAAAAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
33 23 0.46
34 11 0.22
37 16 0.32
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (34 bp):
TTTAAATTTAAATTTAATTAAAATTTAAAATTGA
Found at i:15205 original size:17 final size:17
Alignment explanation
Indices: 15165--15237 Score: 67
Period size: 17 Copynumber: 4.4 Consensus size: 17
15155 AATTTATCTT
**
15165 TTAAAATTTAAATTTGC
1 TTAAAATTTAAATTTAA
*
15182 TTTAAATTTAAATTTAA
1 TTAAAATTTAAATTTAA
* * *
15199 TTAAAATTAAAATTGAT
1 TTAAAATTTAAATTTAA
* *
15216 TTAAAACTT-AATTAAA
1 TTAAAATTTAAATTTAA
15232 TTAAAA
1 TTAAAA
15238 GTTCAAAAAC
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
16 11 0.24
17 34 0.76
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
TTAAAATTTAAATTTAA
Found at i:15219 original size:33 final size:34
Alignment explanation
Indices: 15165--15237 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
15155 AATTTATCTT
* * * *
15165 TTAAAATTTAAATTTGCTTT-AAATTTAAATTTAA
1 TTAAAATTTAAAATTGATTTAAAACTT-AATTAAA
15199 TTAAAA-TTAAAATTGATTTAAAACTTAATTAAA
1 TTAAAATTTAAAATTGATTTAAAACTTAATTAAA
15232 TTAAAA
1 TTAAAA
15238 GTTCAAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 23 0.68
34 11 0.32
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (34 bp):
TTAAAATTTAAAATTGATTTAAAACTTAATTAAA
Done.