Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014639.1 Kokia drynarioides strain JFW-HI SEQ_129678, 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: 42195
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:12883 original size:2 final size:2
Alignment explanation
Indices: 12878--12910 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12868 TCAACCGAAG
*
12878 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12911 TCCCTTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:20318 original size:17 final size:17
Alignment explanation
Indices: 20272--20318 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
20262 CAGATAGACC
*
20272 AAATTCAAATCA-TTTT
1 AAATTTAAATCATTTTT
20288 AAATTTAAAT-ATTTTT
1 AAATTTAAATCATTTTT
*
20304 AAATTTTAATCATTT
1 AAATTTAAATCATTT
20319 GAGCTCGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 1 0.04
16 22 0.81
17 4 0.15
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (17 bp):
AAATTTAAATCATTTTT
Found at i:20490 original size:12 final size:12
Alignment explanation
Indices: 20473--20497 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20463 CCACATTCAT
20473 TGCCTGCAAGCC
1 TGCCTGCAAGCC
20485 TGCCTGCAAGCC
1 TGCCTGCAAGCC
20497 T
1 T
20498 CTTCTGTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.40, G:0.24, T:0.20
Consensus pattern (12 bp):
TGCCTGCAAGCC
Found at i:29013 original size:197 final size:197
Alignment explanation
Indices: 28671--29098 Score: 608
Period size: 197 Copynumber: 2.2 Consensus size: 197
28661 AAGCATACAT
* * * *
28671 AAACCAAGAAAAAAACTTCATTCCTCTACTGGTC--ATTCTAAACAGTAATAATTGATGTCATTA
1 AAACCGAGAAAAAAACTTCATTCCTCTACTGATCATATTCTAAACACTAATAATCGATGTCATTA
* * * * * *
28734 TTGACCAGAATTACCATATGGTTGATATGCTTAGACCAACAAACGAACTGTATAGTTACAGCAAA
66 TTAACCAGAATTACCACATGGTTGATATGCTTAAAACAACAAACGAACTATATAATTACAGCAAA
* *
28799 TAACTTCAACATAAACACACAAGAACAAAACTCCTTATAGCAGCCCTGACAAGGTGAAATGAAGC
131 TAACTTCAACATAAACACACAAGAACAAAACTCCTTATAGCAGCCCTGACAAGGTAAAACGAAGC
28864 AC
196 AC
* * * **
28866 AAACCGAGCAAAAAACTTCATTTCTCTACTGATCATATTCTAAACTCTAATAATCGATGTTGTTA
1 AAACCGAGAAAAAAACTTCATTCCTCTACTGATCATATTCTAAACACTAATAATCGATGTCATTA
* * * *
28931 TTAACCAGGATTACCACATGGTTGATATGCTTAAAACAATAAATGAACTATATAATTACAGCATA
66 TTAACCAGAATTACCACATGGTTGATATGCTTAAAACAACAAACGAACTATATAATTACAGCAAA
* **
28996 TAACTTCAACATAAACACAGAAGAACGGAACTCCTTATAGCAGCCCTGACAAGGTAAAACGAAGC
131 TAACTTCAACATAAACACACAAGAACAAAACTCCTTATAGCAGCCCTGACAAGGTAAAACGAAGC
29061 AC
196 AC
* *
29063 AAACCGAGTAAAAAACTTCATTCCTCTATTGATCAT
1 AAACCGAGAAAAAAACTTCATTCCTCTACTGATCAT
29099 TTAATCACTA
Statistics
Matches: 204, Mismatches: 27, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
195 30 0.15
197 174 0.85
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (197 bp):
AAACCGAGAAAAAAACTTCATTCCTCTACTGATCATATTCTAAACACTAATAATCGATGTCATTA
TTAACCAGAATTACCACATGGTTGATATGCTTAAAACAACAAACGAACTATATAATTACAGCAAA
TAACTTCAACATAAACACACAAGAACAAAACTCCTTATAGCAGCCCTGACAAGGTAAAACGAAGC
AC
Found at i:29220 original size:140 final size:142
Alignment explanation
Indices: 28968--29254 Score: 398
Period size: 140 Copynumber: 2.0 Consensus size: 142
28958 TGCTTAAAAC
* * * ** *
28968 AATAAATGAACTATATAATTACAGCATATAACTTCAACATAAACACAGAAGAACGGAACTCCTTA
1 AATAAATGAACTATATAATTACAACAAATAACTTCAACATAAACACACAAGAACAAAACTACTTA
* * * * * *
29033 TAGCAGCCCTGACAAGGTAAAACGAAGCACAAACCGAGTAAAAAACTTCATTCCTCTATTGATCA
66 TAGCAGCCCTCACAAGGTAAAACAAAGCACAAACCAAGCAAAAAACTTCATGCCTCTATCGATCA
*
29098 TT-T-AATCACT
131 TTCTAAAACACT
* * *
29108 AATAAATGAACTATATAGTTACAATAAATAACTTCAACATAAATACACAAGAACAAAACTACTTA
1 AATAAATGAACTATATAATTACAACAAATAACTTCAACATAAACACACAAGAACAAAACTACTTA
* *
29173 TAGCAGCCCTCAGAAGGTACAACAAAGCACAAACCAAGCAAAAAACTTCATGCCTCTATCGATCA
66 TAGCAGCCCTCACAAGGTAAAACAAAGCACAAACCAAGCAAAAAACTTCATGCCTCTATCGATCA
29238 TTCTAAAACACT
131 TTCTAAAACACT
29250 AATAA
1 AATAA
29255 CTGATGATGT
Statistics
Matches: 127, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
140 115 0.91
141 1 0.01
142 11 0.09
ACGTcount: A:0.46, C:0.22, G:0.10, T:0.22
Consensus pattern (142 bp):
AATAAATGAACTATATAATTACAACAAATAACTTCAACATAAACACACAAGAACAAAACTACTTA
TAGCAGCCCTCACAAGGTAAAACAAAGCACAAACCAAGCAAAAAACTTCATGCCTCTATCGATCA
TTCTAAAACACT
Found at i:31501 original size:21 final size:23
Alignment explanation
Indices: 31452--31521 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 23
31442 TTAAAAAAAG
*
31452 TATTAAA-ATAATTATATATAA-A
1 TATTAAATAAAATTA-ATATAATA
* * *
31474 AATTTAATAAAATTAA-ATATTA
1 TATTAAATAAAATTAATATAATA
*
31496 TATTAAATTAAATTAATATAATA
1 TATTAAATAAAATTAATATAATA
31519 TAT
1 TAT
31522 ATTTTAAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
21 3 0.08
22 20 0.54
23 14 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATTAAATAAAATTAATATAATA
Found at i:31511 original size:22 final size:23
Alignment explanation
Indices: 31483--31534 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
31473 AAATTTAATA
*
31483 AAATTAAATATTATAT-TAAATT
1 AAATTAAATATAATATATAAATT
**
31505 AAATT-AATATAATATATATTTT
1 AAATTAAATATAATATATAAATT
31527 AAATTAAA
1 AAATTAAA
31535 AATGTATGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 9 0.36
22 14 0.56
23 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATTAAATATAATATATAAATT
Found at i:41663 original size:30 final size:30
Alignment explanation
Indices: 41564--41937 Score: 299
Period size: 29 Copynumber: 12.6 Consensus size: 30
41554 TTCGAGGTCG
*
41564 AAAATGGAGTTTTTGG-A-TATTCAGGGG-TA
1 AAAATGGAATTTTTGGAAGT-TTC-GGGGATA
** *
41593 AAAATGGAATTTTTGGAAGTTTTAGGG-TC
1 AAAATGGAATTTTTGGAAGTTTCGGGGATA
* *
41622 AAAACGGAATTTTTGGAAGTTTCGGGGCTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGATA
* *
41652 AAAATGGAATTTTTGGAAGTTTTGGGGTCAAA
1 AAAATGGAATTTTTGGAAGTTTCGGGG--ATA
* *
41684 AAAAT-GAGATTTTTAGAAGTTT-GGGGGTA
1 AAAATGGA-ATTTTTGGAAGTTTCGGGGATA
* *
41713 AAAATGGAATTTTTAGAAGTTTC-GTGATAA
1 AAAATGGAATTTTTGGAAGTTTCGGGGAT-A
* * *
41743 AAAATGGGATTTTTAGAAGTTT-GGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGATA
*
41772 AAAATGGAATTATTGGAAGTTTCGGGG-TCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGAT-A
* *
41802 AAAAT-GAGATTTTTAGAAG-TTCGGGTATA
1 AAAATGGA-ATTTTTGGAAGTTTCGGGGATA
* * * * *
41831 AAAATGAAATGTTTAGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGATA
* *
41861 AAAAT-GAGATTTTTAGAAG-TTCGAGGATA
1 AAAATGGA-ATTTTTGGAAGTTTCGGGGATA
* * * *
41890 AAAACGAAATTTTTGAAAGTTTCGAGGATA
1 AAAATGGAATTTTTGGAAGTTTCGGGGATA
41920 AAAAT-GAGATTTTTGGAA
1 AAAATGGA-ATTTTTGGAA
41938 ATTCAAGGGC
Statistics
Matches: 282, Mismatches: 43, Indels: 39
0.77 0.12 0.11
Matches are distributed among these distances:
29 133 0.47
30 123 0.44
31 7 0.02
32 19 0.07
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGATA
Found at i:41664 original size:59 final size:60
Alignment explanation
Indices: 41587--41933 Score: 384
Period size: 59 Copynumber: 5.8 Consensus size: 60
41577 TGGATATTCA
* ** *
41587 GGGG-TAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAACGGA-ATTTTTGGAAGTTTC
1 GGGGATAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTAGAAGTTTC
*
41645 GGGGCTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAAAATGAGATTTTTAGAAGTTT-
1 GGGGATAAAAATGGAATTTTTGGAAGTTTTGGGGTC--AAAAATGAGATTTTTAGAAGTTTC
* * * * * * *
41706 GGGGGTAAAAATGGAATTTTTAGAAGTTTCGTGATAAAAAATGGGATTTTTAGAAGTTT-
1 GGGGATAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTAGAAGTTTC
* * *
41765 GGGGGTAAAAATGGAATTATTGGAAGTTTCGGGGTCAAAAATGAGATTTTTAGAAG-TTC
1 GGGGATAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTAGAAGTTTC
* * * * *
41824 GGGTATAAAAATGAAATGTTTAGAAGTTTTGGGGTTAAAAATGAGATTTTTAGAAG-TTC
1 GGGGATAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTAGAAGTTTC
* * * * * *
41883 GAGGATAAAAACGAAATTTTTGAAAGTTTCGAGGAT-AAAAATGAGATTTTT
1 GGGGATAAAAATGGAATTTTTGGAAGTTTTG-GGGTCAAAAATGAGATTTTT
41934 GGAAATTCAA
Statistics
Matches: 250, Mismatches: 33, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
58 6 0.02
59 192 0.77
60 3 0.01
61 36 0.14
62 13 0.05
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (60 bp):
GGGGATAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTAGAAGTTTC
Done.