Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011009.1 Kokia drynarioides strain JFW-HI SEQ_125979, 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: 32335
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 306 characters in sequence are not A, C, G, or T
Found at i:659 original size:195 final size:191
Alignment explanation
Indices: 348--695 Score: 489
Period size: 195 Copynumber: 1.8 Consensus size: 191
338 CTAACGATAA
* *
348 TGCTCACACGAGCTGTCGAGAGTATGCATAAAGCATAGTCTCAGCCATCGTAGGGCCTATAATCC
1 TGCTCACACGAGCTGTCGAGAATATGCATAAAGCATAATCTCAGCCATCGTAGGGCCTATAATCC
* * *
413 ATTTAGGATCCATATCTCTTTTCAAAGTCATGATGCTACTCACACGAGCTGTCGAGGACTCGCAA
66 ATTTAGGATCCATATCTCTTTCCAAACTCACGATGCTACTCACACGAGCTGTCGAGGACTCGCAA
*
478 CATATGCGGTACCTCAGCCATCGATACTATATCTGTGCATATAATTGTTCCTTAATGATGC
131 CATATGCGGTACCTCAACCATCGATACTATATCTGTGCATATAATTGTTCCTTAATGATGC
* ***
539 TGCTCACACGAGCTGTTGAGAATATGCACTTCTGCATAAATCTCAGCCATCGTAGGGCCTATAAT
1 TGCTCACACGAGCTGTCGAGAATATGCA-TAAAGCAT-AATCTCAGCCATCGTAGGGCCTATAAT
* * * * * ** * *
604 CCATTCTTGTATTCTTTTCTCATTTCCCGACTCACGATGCTACTCACATGAGCTGTCGAGGACTT
64 CCATT-TAGGATCCATATCTC-TTTCCAAACTCACGATGCTACTCACACGAGCTGTCGAGGACTC
669 GCAACATATGCGGTACCTCAACCATCG
127 GCAACATATGCGGTACCTCAACCATCG
696 CGTCGGTTTC
Statistics
Matches: 134, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
191 26 0.19
192 5 0.04
193 31 0.23
194 10 0.07
195 62 0.46
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (191 bp):
TGCTCACACGAGCTGTCGAGAATATGCATAAAGCATAATCTCAGCCATCGTAGGGCCTATAATCC
ATTTAGGATCCATATCTCTTTCCAAACTCACGATGCTACTCACACGAGCTGTCGAGGACTCGCAA
CATATGCGGTACCTCAACCATCGATACTATATCTGTGCATATAATTGTTCCTTAATGATGC
Found at i:1651 original size:18 final size:18
Alignment explanation
Indices: 1628--1663 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1618 ATTTAAGGAC
1628 CTTAACTTACTTTTCAAT
1 CTTAACTTACTTTTCAAT
1646 CTTAACTTACTTTTCAAT
1 CTTAACTTACTTTTCAAT
1664 TTACATCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTAACTTACTTTTCAAT
Found at i:3520 original size:34 final size:34
Alignment explanation
Indices: 3477--3542 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
3467 TATGAAAGCA
*
3477 TAAGGAAGATGGAAGGTTAAAGGTCAAGGGAGGC
1 TAAGGAAGATGGAAGGTTAAAAGTCAAGGGAGGC
3511 TAAGGAAGATGGAAGGTTAAAAGTCAAGGGAG
1 TAAGGAAGATGGAAGGTTAAAAGTCAAGGGAG
3543 ATGAAAGGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.41, C:0.05, G:0.39, T:0.15
Consensus pattern (34 bp):
TAAGGAAGATGGAAGGTTAAAAGTCAAGGGAGGC
Found at i:11291 original size:18 final size:18
Alignment explanation
Indices: 11265--11325 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
11255 AGTAAAAGTA
*
11265 GTTACAAGAAGATGGAAG
1 GTTAAAAGAAGATGGAAG
** * *
11283 GTTAAAAGATCAAGGGAG
1 GTTAAAAGAAGATGGAAG
*
11301 GTT-AAGGAAGATGGAAG
1 GTTAAAAGAAGATGGAAG
11318 GTTAAAAG
1 GTTAAAAG
11326 TCAAGGGAGA
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
17 12 0.39
18 19 0.61
ACGTcount: A:0.44, C:0.03, G:0.34, T:0.18
Consensus pattern (18 bp):
GTTAAAAGAAGATGGAAG
Found at i:11321 original size:17 final size:16
Alignment explanation
Indices: 11270--11322 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
11260 AAGTAGTTAC
11270 AAGAAGATGGAAGGTT
1 AAGAAGATGGAAGGTT
*
11286 AA-AAGATCAAGGGAGGTT
1 AAGAAGAT---GGAAGGTT
11304 AAGGAAGATGGAAGGTT
1 AA-GAAGATGGAAGGTT
11321 AA
1 AA
11323 AAGTCAAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
15 5 0.17
16 2 0.07
17 9 0.30
18 9 0.30
20 5 0.17
ACGTcount: A:0.45, C:0.02, G:0.36, T:0.17
Consensus pattern (16 bp):
AAGAAGATGGAAGGTT
Found at i:14105 original size:89 final size:88
Alignment explanation
Indices: 13954--14141 Score: 322
Period size: 89 Copynumber: 2.1 Consensus size: 88
13944 TTAATGAATG
* * *
13954 TTTTTGGATTTGCTAACATATGAATTAATTACCATCTTAATCTCTACCAAGTGAGCTTAAAAACA
1 TTTTTGGATTTGCTAACATATGAATTAATTACCATCTTAATCCCTACAAAGTGAACTTAAAAACA
14019 AGTTTTAAAGTATTCTAATAAAGA
66 AGTTTTAAAGTATTCTAATAAA-A
*
14043 TTTTTGGATTTGCTAACATATGGATTAATTACCATCTTAATCCCTACAAAGTGAACTTAAAAACA
1 TTTTTGGATTTGCTAACATATGAATTAATTACCATCTTAATCCCTACAAAGTGAACTTAAAAACA
14108 AGTTTTAAAGTATTCTAATAAAA
66 AGTTTTAAAGTATTCTAATAAAA
14131 TTTTATGGATT
1 TTTT-TGGATT
14142 AATTACCATC
Statistics
Matches: 94, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
88 5 0.05
89 89 0.95
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (88 bp):
TTTTTGGATTTGCTAACATATGAATTAATTACCATCTTAATCCCTACAAAGTGAACTTAAAAACA
AGTTTTAAAGTATTCTAATAAAA
Found at i:14143 original size:73 final size:74
Alignment explanation
Indices: 14061--14203 Score: 245
Period size: 73 Copynumber: 1.9 Consensus size: 74
14051 TTTGCTAACA
14061 TATGGATTAATTACCATCTTAATCCCTA-CAAAGTGAACTT-AAAAACAAGTTTTAAAGTATTCT
1 TATGGATTAATTACCATCTTAATCCCTATC-AAGTGAACTTGAAAAACAAGTTTTAAAGTATTCT
14124 AATAAAATTT
65 AATAAAATTT
* *
14134 TATGGATTAATTACCATCTTAATCCCTATCAAGTGAGCTTGAAAAATAAGTTTTAAAGTATTCTA
1 TATGGATTAATTACCATCTTAATCCCTATCAAGTGAACTTGAAAAACAAGTTTTAAAGTATTCTA
14199 ATAAA
66 ATAAA
14204 GTTTAAAAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
73 37 0.56
74 29 0.44
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (74 bp):
TATGGATTAATTACCATCTTAATCCCTATCAAGTGAACTTGAAAAACAAGTTTTAAAGTATTCTA
ATAAAATTT
Found at i:15684 original size:240 final size:230
Alignment explanation
Indices: 15265--15700 Score: 570
Period size: 240 Copynumber: 1.9 Consensus size: 230
15255 AATTTATAAT
* *
15265 TATGTTTAAAAATAACATAAAATAAATAATGAAACTATGATTTGAAACTAATTAATAAAAACAAA
1 TATGTTTAAAAATAACATAAAATAAATAATAAAACTATGATTTGAAACTAATAAATAAAAACAAA
* * **
15330 TGAAATATGTACGGTATTAAAATAAAAAAGAATTAGATTAAATTATTTATCATGTTGTTGTCATC
66 CGAAATATATACAATATTAAAATAAAAAAGAATTAGATTAAATTATTTATCATGTTGTTGTCATC
* * * * *
15395 AATGTTGAGTTAACTCGTGACACCAATTTAATCAAATACATTGTTAATACTAGAAATTCTATCAC
131 AATGTTAAGTTAACTCATGACACCAACTCAATCAAATACATTATTAATACTAGAAATTCTATCAC
15460 ATGCACGTGGAAACCACAAATTTAGAACACAAATG
196 ATGCACGTGGAAACCACAAATTTAGAACACAAATG
* * *
15495 TATGTTTAAAAATAACATAAAATAAATAATAAAACATATGGTTTGAAACTAATAAATAATAACAC
1 TATGTTTAAAAATAACATAAAATAAATAATAAAAC-TATGATTTGAAACTAATAAATAAAAACAA
* *
15560 ACGAAATTTATACAATATTAAAAT-AAAAA-AATTAGATTAAATTGTTTATCATAGTATTGTTGT
65 ACGAAATATATACAATATTAAAATAAAAAAGAATTAGATTAAATTATTTATCAT-G--TTGTTGT
* * *
15623 CAATCTTGAGTCGTTTCCAAGTTAACTTATGACACCAACTCAATCAAATATATTATTAATACTAG
127 C-ATC---AAT-G-TT--AAGTTAACTCATGACACCAACTCAATCAAATACATTATTAATACTAG
*
15688 AAATTTTATCACA
184 AAATTCTATCACA
15701 CACGTATGCG
Statistics
Matches: 174, Mismatches: 20, Indels: 14
0.84 0.10 0.07
Matches are distributed among these distances:
229 22 0.13
230 40 0.23
231 44 0.25
232 8 0.05
233 3 0.02
236 2 0.01
237 1 0.01
238 2 0.01
240 52 0.30
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (230 bp):
TATGTTTAAAAATAACATAAAATAAATAATAAAACTATGATTTGAAACTAATAAATAAAAACAAA
CGAAATATATACAATATTAAAATAAAAAAGAATTAGATTAAATTATTTATCATGTTGTTGTCATC
AATGTTAAGTTAACTCATGACACCAACTCAATCAAATACATTATTAATACTAGAAATTCTATCAC
ATGCACGTGGAAACCACAAATTTAGAACACAAATG
Found at i:18398 original size:18 final size:16
Alignment explanation
Indices: 18367--18410 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
18357 GGTTTACGGT
*
18367 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
18384 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
18398 TTAAAAATTTATT
1 TTAAAAATTTATT
18411 CTTATTCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:22770 original size:18 final size:18
Alignment explanation
Indices: 22733--22771 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
22723 TTAATAATAC
* *
22733 TTTTATATCAAAAGTGTT
1 TTTTATATCAAAAATATT
*
22751 TTTTATCTCAAAAATATT
1 TTTTATATCAAAAATATT
22769 TTT
1 TTT
22772 GAAAAGCAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (18 bp):
TTTTATATCAAAAATATT
Found at i:26402 original size:28 final size:28
Alignment explanation
Indices: 26370--26500 Score: 163
Period size: 28 Copynumber: 4.7 Consensus size: 28
26360 TGGGCAAGCA
* *
26370 AAATGTCTCTATGGAGACCACTGTTACT
1 AAATGTCTCTACGGAGACCACTATTACT
*
26398 AAATGACTCTACGGAGACCACTATTACT
1 AAATGTCTCTACGGAGACCACTATTACT
*
26426 AAATGTCTCTACGGAGACCACCATTACT
1 AAATGTCTCTACGGAGACCACTATTACT
** * *
26454 AAATGTCTCTTTGGAGACCATTGTTACT
1 AAATGTCTCTACGGAGACCACTATTACT
** *
26482 TTATGTCTCTACAGAGACC
1 AAATGTCTCTACGGAGACC
26501 CTAGTGTGGT
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 88 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.31
Consensus pattern (28 bp):
AAATGTCTCTACGGAGACCACTATTACT
Done.