Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014314.1 Kokia drynarioides strain JFW-HI SEQ_129351, 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: 46907
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 156 characters in sequence are not A, C, G, or T
Found at i:1778 original size:23 final size:23
Alignment explanation
Indices: 1752--1798 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1742 GTAATAACTT
1752 AGTTCATTGGCTTAATCTTGAAA
1 AGTTCATTGGCTTAATCTTGAAA
1775 AGTTCATTGGCTTAATCTTGAAA
1 AGTTCATTGGCTTAATCTTGAAA
1798 A
1 A
1799 ACTATTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (23 bp):
AGTTCATTGGCTTAATCTTGAAA
Found at i:9172 original size:19 final size:18
Alignment explanation
Indices: 9144--9182 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
9134 ACTGTAAAAT
9144 AAAAATAAATAAT-TTAAA
1 AAAAATAAAT-ATCTTAAA
9162 AAAAATAAAATATCTTAAA
1 AAAAAT-AAATATCTTAAA
9181 AA
1 AA
9183 GTTATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATAAATATCTTAAA
Found at i:10524 original size:38 final size:36
Alignment explanation
Indices: 10481--10557 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
10471 ATATATTCTT
*
10481 TATAATTTTTTAAAAATTATTATATAT-TTTTAAAAATA
1 TATAA-TTTTTAAAAATT-TTATAAATATTTTAAAAA-A
**
10519 TATAATTTTTGGAAATTTTATAAATATTTTAAAAAA
1 TATAATTTTTAAAAATTTTATAAATATTTTAAAAAA
10555 TAT
1 TAT
10558 TTTTAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 11 0.31
37 19 0.54
38 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (36 bp):
TATAATTTTTAAAAATTTTATAAATATTTTAAAAAA
Found at i:10540 original size:18 final size:17
Alignment explanation
Indices: 10479--10552 Score: 58
Period size: 20 Copynumber: 3.9 Consensus size: 17
10469 TTATATATTC
10479 TTTATAATTTTTTAAAAAT
1 TTTATAA-TTTTT-AAAAT
*
10498 TATTATATATTTTTAAAAA
1 T-TTATA-ATTTTTAAAAT
* *
10517 TATATAATTTTTGGAAAT
1 TTTATAATTTTT-AAAAT
10535 TTTATAAATATTTTAAAA
1 TTTAT-AAT-TTTTAAAA
10553 AATATTTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
17 6 0.14
18 11 0.25
19 12 0.27
20 14 0.32
21 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTATAATTTTTAAAAT
Found at i:12445 original size:15 final size:15
Alignment explanation
Indices: 12427--12472 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
12417 TGATAATTTC
12427 AAAAATATAAAGATT
1 AAAAATATAAAGATT
*
12442 AAAAATATTAA-ATT
1 AAAAATATAAAGATT
* *
12456 -AAAGTATAAGGATT
1 AAAAATATAAAGATT
12470 AAA
1 AAA
12473 TTCACAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 7 0.28
14 6 0.24
15 12 0.48
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (15 bp):
AAAAATATAAAGATT
Found at i:14173 original size:30 final size:30
Alignment explanation
Indices: 14117--14173 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
14107 AAATTTTAAA
* * *
14117 TTAATAATAAAAAAAATTATATTTTAACCT
1 TTAAAAATAAAAAAAATAATAATTTAACCT
14147 TTAAAAATAAAAATAAA-AATAATTTAA
1 TTAAAAATAAAAA-AAATAATAATTTAA
14174 TTTAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 20 0.87
31 3 0.13
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (30 bp):
TTAAAAATAAAAAAAATAATAATTTAACCT
Found at i:14207 original size:15 final size:17
Alignment explanation
Indices: 14187--14224 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
14177 AATTTTTTAA
14187 AAATTATAAAAAT-AT-
1 AAATTATAAAAATGATG
*
14202 AAATTATTAAAATGATG
1 AAATTATAAAAATGATG
14219 AAATTA
1 AAATTA
14225 CATTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 2 0.10
17 6 0.30
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (17 bp):
AAATTATAAAAATGATG
Found at i:23673 original size:58 final size:58
Alignment explanation
Indices: 23534--23669 Score: 215
Period size: 58 Copynumber: 2.4 Consensus size: 58
23524 ATATTTAGAA
*
23534 TTACATTATAATTTTAACATTTTATGAGTGATCAAAATGCAATTTTCCCACACATTAAT
1 TTACATTATAA-TTTAACATTTTATGAGTGATCAAAATACAATTTTCCCACACATTAAT
*
23593 TTACATTATAATTTAACATTTTATGAGTGATCAAAATACAATTTTCTCACACATTAAT
1 TTACATTATAATTTAACATTTTATGAGTGATCAAAATACAATTTTCCCACACATTAAT
*
23651 TTATA-TAT-ATTTAA-ATTTT
1 TTACATTATAATTTAACATTTT
23670 TTTAAAGAGA
Statistics
Matches: 74, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
55 5 0.07
56 6 0.08
57 3 0.04
58 49 0.66
59 11 0.15
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.44
Consensus pattern (58 bp):
TTACATTATAATTTAACATTTTATGAGTGATCAAAATACAATTTTCCCACACATTAAT
Found at i:25337 original size:12 final size:13
Alignment explanation
Indices: 25320--25351 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
25310 AGATTGATAT
25320 TTTGGTAT-TTAA
1 TTTGGTATCTTAA
25332 TTTGGTATCTTAA
1 TTTGGTATCTTAA
25345 TTTGGTA
1 TTTGGTA
25352 AATGTGATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.22, C:0.03, G:0.19, T:0.56
Consensus pattern (13 bp):
TTTGGTATCTTAA
Found at i:38517 original size:406 final size:400
Alignment explanation
Indices: 37806--38584 Score: 987
Period size: 406 Copynumber: 1.9 Consensus size: 400
37796 AGCATCAATC
*
37806 ATCCTCATTCAATGATTCTATACAGTTTTCAAAAGATTGGTCACACAAGGCAGAATCAGATATCA
1 ATCCTCATTCAATGATTCTATACAGTTTTCAAAAGATTGGTCACACAAGGCAGAATCAGAAATCA
* * * * *
37871 GTCTCGGCTCATTAGTTCTAGCTTTGTTCAAACTCTATTCAATCAACTAGTTTTTAGGATTCCTT
66 GTCTCAGCTCACTAGTTCTAGCTTTGTTCAAACTCTATTCAATCAACTAATTTTCAGGATTCCTC
* * *
37936 TAGTTTCCTAAGCATGAAACTGATACGATCATATTCACGAGTGCTTAATTAAGCCCTTGCGAACA
131 TAGTTTCCTAAGCATGAAACTGATACGATCATATTCAAGAATGCTTAATTAAGCCCTCGCGAACA
* * * * *
38001 TGGTCGTATCGGAAAATTCATCCTCTGGTCACACATGACACAAGGTAGTATTGGAAATCAGTCTC
196 TGCTCATATCGGAAAATTCATCCTCCGGT-ACACAT---A-AAGGCAGTACTGGAAATCAGTCTC
* *
38066 AGTTCACTAGTTCTAGCTTGTTCAAACTTAATTCAATCGACTAATTATTAAGATTCCTCTAG-TA
256 AGTTCACTAGTTCTAGCTTGTTCAAACTTAATTCAATCAACTAATTATCAAGATTCCTCTAGTTA
**
38130 AGCATGAAACTGATATGATCATATTCAAGAACCCTTAAATTAAGCCGTCGTGCATATGATCATAT
321 AGCATGAAACTGATACAATCATATTCAAG-A-CCTTAAATTAAGCCGTCGTGCATATGATCATAT
38195 AGGAAACATCAAAATTG
384 AGGAAACATCAAAATTG
* * **
38212 ATCCTCATTCAATGATTCTATACGGTTTTCAAAAGATTGGTCACACAAGGCGGAATGGGAAATCA
1 ATCCTCATTCAATGATTCTATACAGTTTTCAAAAGATTGGTCACACAAGGCAGAATCAGAAATCA
* * * *
38277 GTCTCAGTTCACTAGTTCTAGC-TTGTTCAAACTCTATTCATTTAAC-AATTTGTCATGATTCCT
66 GTCTCAGCTCACTAGTTCTAGCTTTGTTCAAACTCTATTCAATCAACTAATTT-TCAGGATTCCT
* *
38340 CTAGTTTTCTAAGCATGAAACTGATATGATCATATTCAAGAATGCTTGAATTAAGCCCTCGCGAA
130 CTAGTTTCCTAAGCATGAAACTGATACGATCATATTCAAGAATGCTT-AATTAAGCCCTCGCGAA
38405 CATGCTCATATCGGAAACATTGAAATTCATCCTCCGGT-CACAT-AAGGCA-TGACTGGAAATCA
194 CATGCTCATATCGG----A---AAATTCATCCTCCGGTACACATAAAGGCAGT-ACTGGAAATCA
* * * * * *
38467 GTCTCGGTTCACTAGTTCTAGCTTGTTCAAACTCT-GTTCATTCAACTAATTGTCATGATTTCTC
251 GTCTCAGTTCACTAGTTCTAGCTTGTTCAAACT-TAATTCAATCAACTAATTATCAAGATTCCTC
* *
38531 TAGTTTTCTAAGCATGAAACTGATACAATCATTTTCAAGAGCTTAAATTAAGCC
315 TAG---T-TAAGCATGAAACTGATACAATCATATTCAAGACCTTAAATTAAGCC
38585 CTTGCGAACA
Statistics
Matches: 321, Mismatches: 36, Indels: 29
0.83 0.09 0.08
Matches are distributed among these distances:
404 4 0.01
405 74 0.23
406 179 0.56
407 1 0.00
409 13 0.04
410 2 0.01
411 33 0.10
413 15 0.05
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (400 bp):
ATCCTCATTCAATGATTCTATACAGTTTTCAAAAGATTGGTCACACAAGGCAGAATCAGAAATCA
GTCTCAGCTCACTAGTTCTAGCTTTGTTCAAACTCTATTCAATCAACTAATTTTCAGGATTCCTC
TAGTTTCCTAAGCATGAAACTGATACGATCATATTCAAGAATGCTTAATTAAGCCCTCGCGAACA
TGCTCATATCGGAAAATTCATCCTCCGGTACACATAAAGGCAGTACTGGAAATCAGTCTCAGTTC
ACTAGTTCTAGCTTGTTCAAACTTAATTCAATCAACTAATTATCAAGATTCCTCTAGTTAAGCAT
GAAACTGATACAATCATATTCAAGACCTTAAATTAAGCCGTCGTGCATATGATCATATAGGAAAC
ATCAAAATTG
Found at i:43544 original size:3 final size:3
Alignment explanation
Indices: 43536--43603 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
43526 CTGAACATCA
43536 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
43584 TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
43604 CTTCATAGGA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:45729 original size:27 final size:26
Alignment explanation
Indices: 45680--45731 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
45670 AAATTATCCA
*
45680 AATTCCAAACAATTTCATTATCAATG
1 AATTCCAAACAATTTCATAATCAATG
45706 AATTCCAAACAAATTATCA-AATCAAT
1 AATTCCAAAC-AATT-TCATAATCAAT
45732 TTCTGTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 10 0.43
27 10 0.43
28 3 0.13
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (26 bp):
AATTCCAAACAATTTCATAATCAATG
Done.