Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011702.1 Kokia drynarioides strain JFW-HI SEQ_126696, 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: 330312
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 3 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:313150 original size:98 final size:98
Alignment explanation
Indices: 313022--313211 Score: 229
Period size: 98 Copynumber: 1.9 Consensus size: 98
313012 TCCCTTCACA
* * * * *
313022 TCTCTAAGGTATAAGGTTCGTCGTTGCGGCTTAAACCTTTCTCTTCATATCT-TCATGGTACAAG
1 TCTCTAAGGTACAAGGTTCGTCGTTACGGCTTAAACCTTTCCCTCCATATCTCT-AGGGTACAAG
* * *
313086 ATTTATCGTTGCGGCTTCAATCTTTCCCATCATT
65 ATCTACCGTTGCGACTTCAATCTTTCCCATCATT
* * * * **
313120 TCTCTAAGGTACATGGTTTGTTGTTACGGCTTCAACCTTTCCCTCCATATCTCTAGGGTATTAGA
1 TCTCTAAGGTACAAGGTTCGTCGTTACGGCTTAAACCTTTCCCTCCATATCTCTAGGGTACAAGA
*
313185 TCTACCGTTGTGACTTCAATCTTTCCC
66 TCTACCGTTGCGACTTCAATCTTTCCC
313212 TTCAAACATG
Statistics
Matches: 76, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
98 75 0.99
99 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.39
Consensus pattern (98 bp):
TCTCTAAGGTACAAGGTTCGTCGTTACGGCTTAAACCTTTCCCTCCATATCTCTAGGGTACAAGA
TCTACCGTTGCGACTTCAATCTTTCCCATCATT
Found at i:313253 original size:21 final size:21
Alignment explanation
Indices: 313227--313270 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
313217 ACATGTAGAA
*
313227 TATGCTTTTATGGACCTCTGG
1 TATGCTTTTATAGACCTCTGG
313248 TATGCTTTTATAGACCTCTGG
1 TATGCTTTTATAGACCTCTGG
313269 TA
1 TA
313271 GGCCAGATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.43
Consensus pattern (21 bp):
TATGCTTTTATAGACCTCTGG
Found at i:314166 original size:7 final size:7
Alignment explanation
Indices: 314154--314197 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
314144 CGAGTTCTCA
314154 TTTTTCT
1 TTTTTCT
314161 TTTTTCT
1 TTTTTCT
314168 TTTTT-T
1 TTTTTCT
*
314174 TTTCTCT
1 TTTTTCT
*
314181 TTTCTCTT
1 TTTTTC-T
314189 TTTTTCT
1 TTTTTCT
314196 TT
1 TT
314198 CTTTTCCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 5 0.15
7 22 0.67
8 6 0.18
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:314178 original size:27 final size:28
Alignment explanation
Indices: 314148--314202 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
314138 TCACCTCGAG
*
314148 TTCTCATTTT-TC-TTTTTTCTTTTTTTT
1 TTCTC-TTTTCTCTTTTTTTCTTTCTTTT
314175 TTCTCTTTTCTCTTTTTTTCTTTCTTTT
1 TTCTCTTTTCTCTTTTTTTCTTTCTTTT
314203 CCTTTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 4 0.16
27 7 0.28
28 14 0.56
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (28 bp):
TTCTCTTTTCTCTTTTTTTCTTTCTTTT
Found at i:314183 original size:20 final size:20
Alignment explanation
Indices: 314154--314210 Score: 77
Period size: 18 Copynumber: 3.0 Consensus size: 20
314144 CGAGTTCTCA
314154 TTTTTCT-TTTT-TCTTTTT
1 TTTTTCTCTTTTCTCTTTTT
314172 TTTTTCTCTTTTCTCTTTTT
1 TTTTTCTCTTTTCTCTTTTT
*
314192 TTCTT-TCTTTTC-CTTTTT
1 TTTTTCTCTTTTCTCTTTTT
314210 T
1 T
314211 ATGTTTTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
18 14 0.39
19 11 0.31
20 11 0.31
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTCTCTTTTCTCTTTTT
Found at i:314209 original size:7 final size:6
Alignment explanation
Indices: 314154--314209 Score: 51
Period size: 7 Copynumber: 8.8 Consensus size: 6
314144 CGAGTTCTCA
* *
314154 TTTTTC TTTTTTC TTTTT- TTTTTC TCTTTTC TCTTTTT TTCTTTC TTTTCC
1 TTTTTC -TTTTTC TTTTTC TTTTTC T-TTTTC T-TTTTC TT-TTTC TTTTTC
314205 TTTTT
1 TTTTT
314210 TATGTTTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
5 5 0.12
6 14 0.33
7 23 0.55
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:314217 original size:27 final size:28
Alignment explanation
Indices: 314160--314218 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
314150 CTCATTTTTC
* * *
314160 TTTTTTCTTTTTTTTTTCTCTTTTCTCT
1 TTTTTTCTTTTCTTTTCCTCTTTTATCT
* *
314188 TTTTTTC-TTTCTTTTCCTTTTTTATGT
1 TTTTTTCTTTTCTTTTCCTCTTTTATCT
314215 TTTT
1 TTTT
314219 GGGTGAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (28 bp):
TTTTTTCTTTTCTTTTCCTCTTTTATCT
Found at i:319425 original size:15 final size:16
Alignment explanation
Indices: 319392--319426 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
319382 AAATTGATTA
*
319392 AAAATTAAATTTTAAT
1 AAAATTAAATTTAAAT
319408 AAAATTAAA-TTAAAT
1 AAAATTAAATTTAAAT
319423 AAAA
1 AAAA
319427 AGACTTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATTAAATTTAAAT
Found at i:319427 original size:16 final size:17
Alignment explanation
Indices: 319390--319427 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
319380 TAAAATTGAT
*
319390 TAAAAATTAAATTTTAA
1 TAAAAATTAAATTTAAA
319407 T-AAAATTAAA-TTAAA
1 TAAAAATTAAATTTAAA
319422 TAAAAA
1 TAAAAA
319428 GACTTGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 5 0.26
16 13 0.68
17 1 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAAATTAAATTTAAA
Found at i:323407 original size:29 final size:29
Alignment explanation
Indices: 323361--323510 Score: 151
Period size: 29 Copynumber: 5.1 Consensus size: 29
323351 AGCCTCTATT
* * *
323361 TTTTCCAAAATTATATTTTGATCCTAAAC
1 TTTTCTAAAATTAAATTTTGACCCTAAAC
323390 TTTTCTAAAATTAAATTTTGACCCTAAAC
1 TTTTCTAAAATTAAATTTTGACCCTAAAC
* * *
323419 TTCTCTAAAAGTAAATTTTAACCCCCT-AA-
1 TTTTCTAAAATTAAATTTTGA--CCCTAAAC
* *
323448 TTTTCTCAAAATTACATTTTAACCCTTAAAC
1 TTTTCT-AAAATTAAATTTTGACCC-TAAAC
* *
323479 TTTTCTAAAATTACATTTTGATCCTTAAAC
1 TTTTCTAAAATTAAATTTTGA-CCCTAAAC
323509 TT
1 TT
323511 CCCAAAGTTA
Statistics
Matches: 103, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
28 3 0.03
29 50 0.49
30 38 0.37
31 12 0.12
ACGTcount: A:0.35, C:0.19, G:0.03, T:0.43
Consensus pattern (29 bp):
TTTTCTAAAATTAAATTTTGACCCTAAAC
Found at i:323469 original size:30 final size:28
Alignment explanation
Indices: 323390--323497 Score: 101
Period size: 30 Copynumber: 3.7 Consensus size: 28
323380 GATCCTAAAC
*
323390 TTTTCTAAAATTAAATTTTGA-CCCTAAA
1 TTTTCTAAAATTAAATTTTAACCCCT-AA
* *
323418 CTTCTCTAAAAGTAAATTTTAACCCCCTAA
1 -TTTTCTAAAATTAAATTTTAA-CCCCTAA
* *
323448 TTTTCTCAAAATTACATTTTAACCCTTAAA
1 TTTTCT-AAAATTAAATTTTAACCCCT-AA
*
323478 CTTTTCTAAAATTACATTTT
1 -TTTTCTAAAATTAAATTTT
323498 GATCCTTAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
29 27 0.40
30 30 0.45
31 10 0.15
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.43
Consensus pattern (28 bp):
TTTTCTAAAATTAAATTTTAACCCCTAA
Found at i:329125 original size:9 final size:10
Alignment explanation
Indices: 329111--329147 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
329101 ATAAATAAAT
329111 AAAAAGAAA-
1 AAAAAGAAAG
329120 AAAAAGAAAG
1 AAAAAGAAAG
*
329130 AAAAA-AAAT
1 AAAAAGAAAG
329139 AAAAAGAAA
1 AAAAAGAAA
329148 AATAAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:329131 original size:13 final size:12
Alignment explanation
Indices: 329086--329157 Score: 54
Period size: 13 Copynumber: 5.2 Consensus size: 12
329076 GGATTCGATG
329086 AAGAAAAATAAATA
1 AAGAAAAA-AAA-A
*
329100 AATAAATAAATAAA
1 AAGAAA-AAA-AAA
329114 AAGAAAAAAAAGA
1 AAGAAAAAAAA-A
329127 AAGAAAAAAAATAAA
1 AAG--AAAAAA-AAA
329142 AAGAAAAATAAAA
1 AAGAAAAA-AAAA
329155 AAG
1 AAG
329158 GAATAAGAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
12 2 0.04
13 18 0.37
14 13 0.27
15 14 0.29
16 2 0.04
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (12 bp):
AAGAAAAAAAAA
Done.