Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012123.1 Kokia drynarioides strain JFW-HI SEQ_127122, 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: 67973
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:746 original size:21 final size:20
Alignment explanation
Indices: 722--772 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
712 TATCTCTTTG
**
722 TTATATTTTTATTATTTTATT
1 TTATATTTTTACAATTTT-TT
743 TTATAATTTTTACAATTTTTT
1 TTAT-ATTTTTACAATTTTTT
*
764 ATATATTTT
1 TTATATTTT
773 AAAATTTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 9 0.35
22 12 0.46
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (20 bp):
TTATATTTTTACAATTTTTT
Found at i:773 original size:19 final size:19
Alignment explanation
Indices: 741--780 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
731 TATTATTTTA
*
741 TTTTATAATTTTTACAATT
1 TTTTATAATTTTTAAAATT
760 TTTTAT-ATATTTTAAAATT
1 TTTTATAAT-TTTTAAAATT
779 TT
1 TT
781 CAAATGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTATAATTTTTAAAATT
Found at i:8392 original size:381 final size:381
Alignment explanation
Indices: 7689--8433 Score: 1454
Period size: 381 Copynumber: 2.0 Consensus size: 381
7679 GAAAAAACAA
7689 TTTTAACCTAAATCTTTGATCTTTCTGCTTGCAATTAGGATCAAGCGCTTCAGTTTCTTTATTTT
1 TTTTAACCTAAATCTTTGATCTTTCTGCTTGCAATTAGGATCAAGCGCTTCAGTTTCTTTATTTT
7754 TTATCGTAAGTCAAATTAACTGCTTATTTTTTTTGTTCTTCCCTTAATATGCTTTTTCTCCCAAT
66 TTATCGTAAGTCAAATTAACTGCTTATTTTTTTTGTTCTTCCCTTAATATGCTTTTTCTCCCAAT
7819 TTGTTTTCATTGACTTTACGATTGAAATGAAAAAAATAATTGGTTTTTGGTTTAAAGAATTAAAG
131 TTGTTTTCATTGACTTTACGATTGAAATGAAAAAAATAATTGGTTTTTGGTTTAAAGAATTAAAG
7884 CTTAAGGATTTTGAGGAGTTAAGTACCAAAAATATCTGTTTCATGTCAGAGCTTATATTGGAATC
196 CTTAAGGATTTTGAGGAGTTAAGTACCAAAAATATCTGTTTCATGTCAGAGCTTATATTGGAATC
7949 GTTGACTCTTTGCTCAACTGAATTGGAATTTCATTTATGGAGATTTTGTTTTTGCTTTACGACAA
261 GTTGACTCTTTGCTCAACTGAATTGGAATTTCATTTATGGAGATTTTGTTTTTGCTTTACGACAA
8014 TGATTTCATAAAGAAAAAAGTAGCATGCGTTGATTTTTGTTGAAAAAACAGTTTTT
326 TGATTTCATAAAGAAAAAAGTAGCATGCGTTGATTTTTGTTGAAAAAACAGTTTTT
*
8070 TTTTAACCTAAATCTTTGATCTTTCTGCTTGCAATTAGGATCAAGCGCTTTAGTTTCTTTATTTT
1 TTTTAACCTAAATCTTTGATCTTTCTGCTTGCAATTAGGATCAAGCGCTTCAGTTTCTTTATTTT
8135 TTATCGTAAGTCAAATTAACTGCTTATTTTTTTTGTTCTTCCCTTAATATGCTTTTTCTCCCAAT
66 TTATCGTAAGTCAAATTAACTGCTTATTTTTTTTGTTCTTCCCTTAATATGCTTTTTCTCCCAAT
*
8200 TTGTTTTCATTGGCTTTACGATTGAAATGAAAAAAATAATTGGTTTTTGGTTTAAAGAATTAAAG
131 TTGTTTTCATTGACTTTACGATTGAAATGAAAAAAATAATTGGTTTTTGGTTTAAAGAATTAAAG
*
8265 CTTAAGGATTTTGATGAGTTAAGTACCAAAAATATCTGTTTCATGTCAGAGCTTATATTGGAATC
196 CTTAAGGATTTTGAGGAGTTAAGTACCAAAAATATCTGTTTCATGTCAGAGCTTATATTGGAATC
8330 GTTGACTCTTTGCTCAACTGAATTGGAATTTCATTTATGGAGATTTTGTTTTTGCTTTACGACAA
261 GTTGACTCTTTGCTCAACTGAATTGGAATTTCATTTATGGAGATTTTGTTTTTGCTTTACGACAA
*
8395 TGATTTCATAAAGAAAAATGTAGCATGCGTTGATTTTTG
326 TGATTTCATAAAGAAAAAAGTAGCATGCGTTGATTTTTG
8434 GGTATTCATC
Statistics
Matches: 360, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
381 360 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (381 bp):
TTTTAACCTAAATCTTTGATCTTTCTGCTTGCAATTAGGATCAAGCGCTTCAGTTTCTTTATTTT
TTATCGTAAGTCAAATTAACTGCTTATTTTTTTTGTTCTTCCCTTAATATGCTTTTTCTCCCAAT
TTGTTTTCATTGACTTTACGATTGAAATGAAAAAAATAATTGGTTTTTGGTTTAAAGAATTAAAG
CTTAAGGATTTTGAGGAGTTAAGTACCAAAAATATCTGTTTCATGTCAGAGCTTATATTGGAATC
GTTGACTCTTTGCTCAACTGAATTGGAATTTCATTTATGGAGATTTTGTTTTTGCTTTACGACAA
TGATTTCATAAAGAAAAAAGTAGCATGCGTTGATTTTTGTTGAAAAAACAGTTTTT
Found at i:16678 original size:28 final size:28
Alignment explanation
Indices: 16642--16701 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
16632 TTAATATGAC
* *
16642 TATATAAAAATATTCAATAAATAAAA-AA
1 TATACAAAAATATTAAAT-AATAAAATAA
* *
16670 TATACAAAATTATTAAATATTAAAATAA
1 TATACAAAAATATTAAATAATAAAATAA
16698 TATA
1 TATA
16702 ATATAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (28 bp):
TATACAAAAATATTAAATAATAAAATAA
Found at i:21838 original size:21 final size:20
Alignment explanation
Indices: 21800--21863 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
21790 AATAATTATC
*
21800 TTAAT-AATATTCTATTAAT
1 TTAATAAATATTATATTAAT
21819 TTAATAAGAT-TTAATATTAAT
1 TTAATAA-ATATT-ATATTAAT
*
21840 CTTGATAAATATTATATTAAT
1 -TTAATAAATATTATATTAAT
21861 TTA
1 TTA
21864 CTATTAAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 5 0.14
20 5 0.14
21 19 0.51
22 8 0.22
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
TTAATAAATATTATATTAAT
Found at i:22180 original size:16 final size:18
Alignment explanation
Indices: 22146--22180 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
22136 CGTATAATAT
*
22146 AATAAGCATATTTTAAAA
1 AATAAGCATATTATAAAA
22164 AATAAGCAT-TTATAAAA
1 AATAAGCATATTATAAAA
22181 TTTTAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (18 bp):
AATAAGCATATTATAAAA
Found at i:22321 original size:12 final size:13
Alignment explanation
Indices: 22303--22344 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
22293 ATTTAATAAG
22303 ATTTAATATTAAT
1 ATTTAATATTAAT
22316 -TTTAATA-TAAT
1 ATTTAATATTAAT
22327 ATTT-ATATATAAT
1 ATTTAATAT-TAAT
22340 ATTTA
1 ATTTA
22345 TCTTGATAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
11 7 0.28
12 10 0.40
13 8 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTTAATATTAAT
Found at i:22330 original size:24 final size:25
Alignment explanation
Indices: 22298--22344 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
22288 TATTAATTTA
22298 ATAAGATTTA-ATATTAAT-TTTAAT
1 ATAAGATTTATATA-TAATATTTAAT
*
22322 ATAATATTTATATATAATATTTA
1 ATAAGATTTATATATAATATTTA
22345 TCTTGATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
ATAAGATTTATATATAATATTTAAT
Found at i:22345 original size:13 final size:12
Alignment explanation
Indices: 22298--22344 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
22288 TATTAATTTA
*
22298 ATAAGATTTAAT
1 ATAATATTTAAT
22310 ATTAAT-TTTAAT
1 A-TAATATTTAAT
22322 ATAATATTTATAT
1 ATAATATTTA-AT
22335 ATAATATTTA
1 ATAATATTTA
22345 TCTTGATAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
11 4 0.13
12 12 0.39
13 15 0.48
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
ATAATATTTAAT
Found at i:26186 original size:23 final size:23
Alignment explanation
Indices: 26178--26247 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
26168 TTTATTTAAC
26178 TTAATCGAACATGTTCACAAACA
1 TTAATCGAACATGTTCACAAACA
**
26201 TTAATCGAACATGTTCATGAACA
1 TTAATCGAACATGTTCACAAACA
* * *
26224 TATAATTGAACACGTTCACGAACA
1 T-TAATCGAACATGTTCACAAACA
26248 ATGTTAATGA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 22 0.54
24 19 0.46
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.27
Consensus pattern (23 bp):
TTAATCGAACATGTTCACAAACA
Found at i:26272 original size:4 final size:4
Alignment explanation
Indices: 26263--26288 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
26253 AATGAATAAT
26263 AAAC AAAC AAAC AAAC AAAC AAAC AA
1 AAAC AAAC AAAC AAAC AAAC AAAC AA
26289 TAAAAACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:26363 original size:12 final size:12
Alignment explanation
Indices: 26346--26381 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
26336 TAATTAATAA
26346 ATAAACGAGCTT
1 ATAAACGAGCTT
*
26358 ATAAACGATCTT
1 ATAAACGAGCTT
*
26370 TTAAACGAGCTT
1 ATAAACGAGCTT
26382 GTTCGTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.31
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:30134 original size:11 final size:11
Alignment explanation
Indices: 30085--30134 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
30075 GCTGTTTGTC
*
30085 ATTATTTTGGT
1 ATTATTTTGCT
* *
30096 ATCACTTTGCT
1 ATTATTTTGCT
*
30107 ATTATATTGCT
1 ATTATTTTGCT
*
30118 ATTATTTTGTT
1 ATTATTTTGCT
30129 ATTATT
1 ATTATT
30135 GTTTGAATAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.22, C:0.08, G:0.10, T:0.60
Consensus pattern (11 bp):
ATTATTTTGCT
Found at i:45274 original size:17 final size:18
Alignment explanation
Indices: 45254--45289 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
45244 AGTAAGTTCT
*
45254 ATATTTAAT-TTGAATTA
1 ATATTTAATGTTCAATTA
45271 ATATTTAATGTTCAATTA
1 ATATTTAATGTTCAATTA
45289 A
1 A
45290 CGGATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (18 bp):
ATATTTAATGTTCAATTA
Found at i:46635 original size:31 final size:30
Alignment explanation
Indices: 46580--46637 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
46570 GATTATGTAA
*
46580 TTCTTTAATATGGGTATAACATATATATTT
1 TTCTATAATATGGGTATAACATATATATTT
* *
46610 TTCTATAAGTATGTGTATAATATATATA
1 TTCTATAA-TATGGGTATAACATATATA
46638 ACATATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 7 0.29
31 17 0.71
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.48
Consensus pattern (30 bp):
TTCTATAATATGGGTATAACATATATATTT
Found at i:47240 original size:18 final size:19
Alignment explanation
Indices: 47217--47256 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
47207 ATGTTTTTGT
47217 TTATTTTTAAA-AAATTAA
1 TTATTTTTAAATAAATTAA
*
47235 TTATTTTTAAATAATTTAA
1 TTATTTTTAAATAAATTAA
47254 TTA
1 TTA
47257 AAGTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATTTTTAAATAAATTAA
Found at i:53043 original size:240 final size:240
Alignment explanation
Indices: 52615--53093 Score: 818
Period size: 240 Copynumber: 2.0 Consensus size: 240
52605 CGATTTCTTC
*
52615 CTCGCTCCACCTTATCTTCCTACCTTCTTATACTTGGTATCAATAAAATTCTTCTCTACATATTC
1 CTCGCTCCACCTTATCTTCCTACCTTCTTATACTTGGTATCAACAAAATTCTTCTCTACATATTC
*
52680 AACTTTTGATTAATCTTCGACCTCTGGCTAAATGCTAGTAACCTATGTATTGAAAGAAATTAGGT
66 AACTTTTGATTAATCTTCAACCTCTGGCTAAATGCTAGTAACCTATGTATTGAAAGAAATTAGGT
* *
52745 ATTTTACGTCTCATAAACTTCATCTCTATGTCCCAAATTTTAGGATCTATTTTTCAGATTTGCAA
131 ATTTTACATCTCATAAACTTCATCTCTATGTCCCAAATTTTAGGATCTATTTTTCAGATTTACAA
*
52810 CTATTCTTTTCAATAATTACATCTCTAAAATTTGATTTTGTGTTT
196 CTATTCCTTTCAATAATTACATCTCTAAAATTTGATTTTGTGTTT
*
52855 CTCGTTCCACCTTATCTTCCT-CCATTCTTATACTTGGTATCAACAAAATTCTTCTCTACATATT
1 CTCGCTCCACCTTATCTTCCTACC-TTCTTATACTTGGTATCAACAAAATTCTTCTCTACATATT
* *
52919 CAGCTTTTGATTAATCTTCAACCTCTGGCTAGATGCTAG-AAGCCTATGTATTGAAAGAAATTAG
65 CAACTTTTGATTAATCTTCAACCTCTGGCTAAATGCTAGTAA-CCTATGTATTGAAAGAAATTAG
* *
52983 GTATTTTACATCTCATAAACTTCATCTCTATGTCCTAAATTTTAGGATTTATTTTTCAGATTTAC
129 GTATTTTACATCTCATAAACTTCATCTCTATGTCCCAAATTTTAGGATCTATTTTTCAGATTTAC
* *
53048 AATTATTCCTTTCAATAATTACATCTTTAAAATTTGATTTTGTGTT
194 AACTATTCCTTTCAATAATTACATCTCTAAAATTTGATTTTGTGTT
53094 CACTCTTGAA
Statistics
Matches: 225, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
239 4 0.02
240 221 0.98
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.43
Consensus pattern (240 bp):
CTCGCTCCACCTTATCTTCCTACCTTCTTATACTTGGTATCAACAAAATTCTTCTCTACATATTC
AACTTTTGATTAATCTTCAACCTCTGGCTAAATGCTAGTAACCTATGTATTGAAAGAAATTAGGT
ATTTTACATCTCATAAACTTCATCTCTATGTCCCAAATTTTAGGATCTATTTTTCAGATTTACAA
CTATTCCTTTCAATAATTACATCTCTAAAATTTGATTTTGTGTTT
Found at i:59044 original size:23 final size:22
Alignment explanation
Indices: 59018--59063 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
59008 GTTTTTTAAT
59018 TTTTAATATATTATATCATGTTA
1 TTTTAATATATTATATCAT-TTA
* *
59041 TTTTTATATATTATGTCATTTA
1 TTTTAATATATTATATCATTTA
59063 T
1 T
59064 AACACAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (22 bp):
TTTTAATATATTATATCATTTA
Found at i:63497 original size:20 final size:20
Alignment explanation
Indices: 63472--63509 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
63462 AAAATGTGGT
63472 AGAAAAATAACAAAACAAAG
1 AGAAAAATAACAAAACAAAG
*
63492 AGAAAAATAACGAAACAA
1 AGAAAAATAACAAAACAA
63510 CATACCAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.11, G:0.11, T:0.05
Consensus pattern (20 bp):
AGAAAAATAACAAAACAAAG
Found at i:66947 original size:2 final size:2
Alignment explanation
Indices: 66940--66967 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
66930 TTAAAAATTA
66940 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66968 TAATGATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.