Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013413.1 Kokia drynarioides strain JFW-HI SEQ_128438, 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: 36892
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:1248 original size:53 final size:54
Alignment explanation
Indices: 1170--1273 Score: 167
Period size: 53 Copynumber: 1.9 Consensus size: 54
1160 GAAGGTCCCT
1170 AAACTGTCCAAAAATTCTATTTTTACACCCGAACTTCCAAAAATCCCATTTCTA
1 AAACTGTCCAAAAATTCTATTTTTACACCCGAACTTCCAAAAATCCCATTTCTA
* *
1224 AAACT-TCTAAAAATT-TCATTTTTACCCCCGAACTTCCAAAAATCCCATTT
1 AAACTGTCCAAAAATTCT-ATTTTTACACCCGAACTTCCAAAAATCCCATTT
1274 TTGACCCCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
52 1 0.02
53 41 0.87
54 5 0.11
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.33
Consensus pattern (54 bp):
AAACTGTCCAAAAATTCTATTTTTACACCCGAACTTCCAAAAATCCCATTTCTA
Found at i:1292 original size:30 final size:28
Alignment explanation
Indices: 1170--1629 Score: 421
Period size: 29 Copynumber: 15.8 Consensus size: 28
1160 GAAGGTCCCT
1170 AAACTGTCCAAAAAT-TCTATTTTTACACCC
1 AAACT-TCCAAAAATCTC-ATTTTTAC-CCC
* * *
1200 GAACTTCCAAAAATCCCATTTCTA----
1 AAACTTCCAAAAATCTCATTTTTACCCC
* *
1224 AAACTTCTAAAAATTTCATTTTTACCCCC
1 AAACTTCCAAAAATCTCATTTTTA-CCCC
* *
1253 GAACTTCCAAAAATCCCATTTTTGACCCC
1 AAACTTCCAAAAATCTCATTTTT-ACCCC
* *
1282 AAAACATCCAAAAATCTCATTTTTACCTC
1 -AAACTTCCAAAAATCTCATTTTTACCCC
1311 AAACTTCCAAAAATCTCATTTTTGACCCC
1 AAACTTCCAAAAATCTCATTTTT-ACCCC
* *
1340 GAAACTTCCAAAAATTTCAATTTTACCCTC
1 -AAACTTCCAAAAATCTCATTTTTACCC-C
** *
1370 AAACTTAAAAAAATCTCATTTTTGACCTCG
1 AAACTTCCAAAAATCTCATTTTT-ACC-CC
**
1400 AAACTTCCAAAAATCTTGTTTTTACCCCC
1 AAACTTCCAAAAATCTCATTTTTA-CCCC
* * *
1429 GAATTTCCAAAAATCTCATTTTTGATCCCT
1 AAACTTCCAAAAATCTCATTTTT-A-CCCC
*
1459 AAACTATCCAAAAATTTCATTTTTACCCC
1 AAACT-TCCAAAAATCTCATTTTTACCCC
* *
1488 TAAACTTCCAAAAATCCCATTTTTGACCCTA
1 -AAACTTCCAAAAATCTCATTTTT-ACCC-C
1519 AAACTTCCAAATAATC-CATTTTTACCCTC
1 AAACTTCCAAA-AATCTCATTTTTACCC-C
* *
1548 GAACTTCCAAAAATCCCATTTTTGACCCC
1 AAACTTCCAAAAATCTCATTTTT-ACCCC
1577 AAAACTTCCAAAAATC-CAATTTTTACCCC
1 -AAACTTCCAAAAATCTC-ATTTTTACCCC
* *
1606 TAAACTTTCAAAAATCCCATTTTT
1 -AAACTTCCAAAAATCTCATTTTT
1630 GACCTCGAAT
Statistics
Matches: 357, Mismatches: 48, Indels: 51
0.78 0.11 0.11
Matches are distributed among these distances:
24 19 0.05
28 26 0.07
29 158 0.44
30 132 0.37
31 22 0.06
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (28 bp):
AAACTTCCAAAAATCTCATTTTTACCCC
Found at i:1392 original size:59 final size:59
Alignment explanation
Indices: 1170--1633 Score: 506
Period size: 59 Copynumber: 7.9 Consensus size: 59
1160 GAAGGTCCCT
* *
1170 AAACTGTCCAAAAA-TTCTATTTTTACACC-CGAACTTCCAAAAATCCCA--TTT----CTA
1 AAACT-TCCAAAAATTTC-ATTTTTAC-CCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * *
1224 AAACTTCTAAAAATTTCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTTCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * * *
1283 AAACATCCAAAAATCTCATTTTTA-CCTCAAACTTCCAAAAATCTCATTTTTGACCCCG
1 AAACTTCCAAAAATTTCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
* ** * * *
1341 AAACTTCCAAAAATTTCAATTTTACCCTCAAACTTAAAAAAATCTCATTTTTGACCTCG
1 AAACTTCCAAAAATTTCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * * * * * *
1400 AAACTTCCAAAAATCTT-GTTTTTACCCCCGAATTTCCAAAAATCTCATTTTTGATCCCT
1 AAACTTCCAAAAAT-TTCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
*
1459 AAACTATCCAAAAATTTCATTTTTACCC-CTAAACTTCCAAAAATCCCATTTTTGACCCTA
1 AAACT-TCCAAAAATTTCATTTTTACCCTC-AAACTTCCAAAAATCCCATTTTTGACCCCA
* *
1519 AAACTTCCAAATAA-TCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAA-AATTTCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
* *
1578 AAACTTCCAAAAA-TCCAATTTTTACCC-CTAAACTTTCAAAAATCCCATTTTTGACC
1 AAACTTCCAAAAATTTC-ATTTTTACCCTC-AAACTTCCAAAAATCCCATTTTTGACC
1634 TCGAATTTTC
Statistics
Matches: 356, Mismatches: 37, Indels: 29
0.84 0.09 0.07
Matches are distributed among these distances:
52 2 0.01
53 34 0.10
54 8 0.02
55 3 0.01
58 57 0.16
59 200 0.56
60 52 0.15
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATTTCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
Found at i:1680 original size:28 final size:29
Alignment explanation
Indices: 1644--1701 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
1634 TCGAATTTTC
1644 CCAAAATTA-CGA-TTTTACCCCCGAGAAT
1 CCAAAATTATC-ATTTTTACCCCCGAGAAT
*
1672 CCAAAATTATCATTTTTGCCCCCGAGAAT
1 CCAAAATTATCATTTTTACCCCCGAGAAT
1701 C
1 C
1702 TGAAAAGTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.33, C:0.29, G:0.10, T:0.28
Consensus pattern (29 bp):
CCAAAATTATCATTTTTACCCCCGAGAAT
Found at i:1717 original size:30 final size:29
Alignment explanation
Indices: 1656--1717 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
1646 AAAATTACGA
*
1656 TTTTACCCCCGAGAATCCAAAATTATCAT
1 TTTTACCCCCGAGAATCCAAAAGTATCAT
* * *
1685 TTTTGCCCCCGAGAATCTGAAAAGTCTCAT
1 TTTTACCCCCGAGAATC-CAAAAGTATCAT
1715 TTT
1 TTT
1718 GAACTCCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (29 bp):
TTTTACCCCCGAGAATCCAAAAGTATCAT
Found at i:13770 original size:206 final size:206
Alignment explanation
Indices: 13401--14064 Score: 885
Period size: 206 Copynumber: 3.2 Consensus size: 206
13391 TGCGATACCC
* * *
13401 ACAAACGACGCGATCATCTTCCTAG-TGAGATACTGAGAAGAAGACCAAATCAGGCCCACGCTTA
1 ACAAGCGATGCGATCATCTTCCTAGATGAGATACTGAGAAGAAGACCAAATCAGGCCCA-GCTCA
* *
13465 AAGTGAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGACATCGAGAAGCAGGTCGAAGCAATAA
65 AAGCGAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAA
* *
13530 ACGGTTAGCTTCCAGATGAGATACTGAAAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
130 ACGGTTAGCTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAG
*
13595 AAGTTGATTGAA
195 AAGTAGATTGAA
13607 ACAAGCGATGCGATCATCTTCCTAG-TGAGATACTGAGAAGAAGACCAAATCAGGCCCATGCTCA
1 ACAAGCGATGCGATCATCTTCCTAGATGAGATACTGAGAAGAAGACCAAATCAGGCCCA-GCTCA
13671 AAGCGAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAA
65 AAGCGAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAA
13736 ACGGTTAGCTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAG
130 ACGGTTAGCTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAG
13801 AAGTAGATTGAA
195 AAGTAGATTGAA
* * * * ** *
13813 ACAAGCGATGCGGTCATCTT-CTTGATGAGATACTGAGAAGAAGGCCAAACCAAACCCA-CGC-A
1 ACAAGCGATGCGATCATCTTCCTAGATGAGATACTGAGAAGAAGACCAAATCAGGCCCAGCTCAA
* * * * * * *
13875 CGCTGA--ATAAACCTTCGAACTCCAGCTTCCTGATAAGATACTGAGAAGCAGGTCGAAGTAATA
66 AGC-GAGCA-AAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAAT-
* * * * * * * *
13938 AAACGGATAGCTCCCTGATGAGATACGGAGGAGTGAACCAAATCCGTCTTCCTGATGAAACACAA
128 AAACGGTTAGCTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAA
* * **
14003 AGAAATGGATCAAA
193 AGAAGTAGATTGAA
* ** *
14017 ACAAGTGATGCGGCCATCTTCCT-GATGAGATACTGAGAAGAAGGCCAA
1 ACAAGCGATGCGATCATCTTCCTAGATGAGATACTGAGAAGAAGACCAA
14065 GTCAACGAAA
Statistics
Matches: 416, Mismatches: 37, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
202 1 0.00
203 51 0.12
204 114 0.27
205 5 0.01
206 245 0.59
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (206 bp):
ACAAGCGATGCGATCATCTTCCTAGATGAGATACTGAGAAGAAGACCAAATCAGGCCCAGCTCAA
AGCGAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAA
CGGTTAGCTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGA
AGTAGATTGAA
Found at i:15076 original size:30 final size:29
Alignment explanation
Indices: 15033--15411 Score: 379
Period size: 30 Copynumber: 12.8 Consensus size: 29
15023 GAAGGTCCTT
* *
15033 AAACTGTCCAAAAATTCTATTTTTACCCCCG
1 AAACT-TCCAAAAATCCCATTTTTA-CCCCG
* * *
15064 AAACTTCTAAAAATCTCGTTTTTACCCCG
1 AAACTTCCAAAAATCCCATTTTTACCCCG
* *
15093 -AACTTCCAAAAATCCCATTTTTAACCTCA
1 AAACTTCCAAAAATCCCATTTTT-ACCCCG
* *
15122 AAACTTCTAAAAATTCCATTTTTACCCCTG
1 AAACTTCCAAAAATCCCATTTTTACCCC-G
*
15152 -AACTTCCAAAAATCCCATTTTTATCCCCA
1 AAACTTCCAAAAATCCCATTTTTA-CCCCG
15181 AAACTTCCAAAAATCCCATTTTTACCCCCG
1 AAACTTCCAAAAATCCCATTTTTA-CCCCG
* * *
15211 -AACTTACAAAAATCCCATTTTTAATCCCT
1 AAACTTCCAAAAATCCCATTTTT-ACCCCG
*** * * *
15240 AAACTATCCAAAAATTTAATTTTTATCTCA
1 AAACT-TCCAAAAATCCCATTTTTACCCCG
* * *
15270 AAACTTCTAAAATTCCCATTTTTGACCCAG
1 AAACTTCCAAAAATCCCATTTTT-ACCCCG
**
15300 AAACTTCCAAAAATTTCATTTTTACCCTCG
1 AAACTTCCAAAAATCCCATTTTTACCC-CG
*
15330 -AACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATCCCATTTTT-ACCCCG
*
15359 AAACTTCCAAAAATCCCATTTTTACCCCT
1 AAACTTCCAAAAATCCCATTTTTACCCCG
**
15388 AAACTTTTAAAAATCCCATTTTTA
1 AAACTTCCAAAAATCCCATTTTTA
15412 ACCTCGAATT
Statistics
Matches: 288, Mismatches: 48, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
28 19 0.07
29 123 0.43
30 127 0.44
31 19 0.07
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATCCCATTTTTACCCCG
Found at i:15174 original size:59 final size:59
Alignment explanation
Indices: 15034--15414 Score: 428
Period size: 59 Copynumber: 6.4 Consensus size: 59
15024 AAGGTCCTTA
* * * * * *
15034 AACTGTCCAAAAATTCTATTTTTACCCCCGAAACTTCTAAAAA-TCTCGTTTTTACCCC-G
1 AACT-TCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTC-CATTTTTACCCCTG
* *
15093 AACTTCCAAAAATCCCATTTTTAACCTCAAAACTTCTAAAAATTCCATTTTTACCCCTG
1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCTG
* * *
15152 AACTTCCAAAAATCCCATTTTTATCCCCAAAACTTCCAAAAATCCCATTTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCTG
* * * ** * * **
15211 AACTTACAAAAATCCCATTTTTAATCCCTAAACTATCCAAAAATTTAATTTTTATCTCAA
1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACT-TCCAAAAATTCCATTTTTACCCCTG
* * * *
15271 AACTTCTAAAATTCCCATTTTTGA-CCCAGAAACTTCCAAAAATTTCATTTTTA-CCCTCG
1 AACTTCCAAAAATCCCATTTTTAACCCCA-AAACTTCCAAAAATTCCATTTTTACCCCT-G
* * *
15330 AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATCCCATTTTTACCCCTA
1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCTG
**
15389 AACTTTTAAAAATCCCATTTTTAACC
1 AACTTCCAAAAATCCCATTTTTAACC
15415 TCGAATTTTC
Statistics
Matches: 276, Mismatches: 39, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
58 46 0.17
59 179 0.65
60 51 0.18
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (59 bp):
AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCTG
Found at i:18014 original size:18 final size:18
Alignment explanation
Indices: 17991--18027 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17981 AATTCGAATT
*
17991 AATTCGGTTAACCGATTG
1 AATTCGGTAAACCGATTG
*
18009 AATTCGGTAAATCGATTG
1 AATTCGGTAAACCGATTG
18027 A
1 A
18028 TTAATCGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (18 bp):
AATTCGGTAAACCGATTG
Found at i:24348 original size:11 final size:12
Alignment explanation
Indices: 24332--24360 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
24322 AATAATAATT
24332 TTATTTAGAT-A
1 TTATTTAGATAA
24343 TTATTTAGATAA
1 TTATTTAGATAA
24355 TTATTT
1 TTATTT
24361 TTTAGTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (12 bp):
TTATTTAGATAA
Found at i:36612 original size:6 final size:6
Alignment explanation
Indices: 36601--36678 Score: 67
Period size: 6 Copynumber: 13.5 Consensus size: 6
36591 ATTTGTTTAA
* *
36601 AAATTT AAATTT AAA-AT AAATTT AAATTT -AATTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* *
36647 -ATTTT CAAATTT AAAATT --ATTAT AAATTT AAA
1 AAATTT -AAATTT AAATTT AAATT-T AAATTT AAA
36679 ATAAAAAAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
4 2 0.04
5 14 0.25
6 34 0.60
7 7 0.12
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (6 bp):
AAATTT
Found at i:36627 original size:52 final size:52
Alignment explanation
Indices: 36569--36678 Score: 139
Period size: 52 Copynumber: 2.1 Consensus size: 52
36559 CCAAACTCAT
* * * *
36569 TTTAAATTTATTTTAGGATTAAATTTGTTTAAAAATTTAAATTTAAAATAAA
1 TTTAAATTTAATTTAAGATTAAATTTATTTAAAAATTTAAAATTAAAATAAA
* ** **
36621 TTTAAATTTAATTTAAGTTTAAATTTATTTTCAAATTTAAAATTATTATAAA
1 TTTAAATTTAATTTAAGATTAAATTTATTTAAAAATTTAAAATTAAAATAAA
36673 TTTAAA
1 TTTAAA
36679 ATAAAAAAAG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (52 bp):
TTTAAATTTAATTTAAGATTAAATTTATTTAAAAATTTAAAATTAAAATAAA
Found at i:36641 original size:11 final size:12
Alignment explanation
Indices: 36601--36678 Score: 67
Period size: 11 Copynumber: 6.8 Consensus size: 12
36591 ATTTGTTTAA
36601 AAATTTAAATTT
1 AAATTTAAATTT
*
36613 AAA-ATAAATTT
1 AAATTTAAATTT
36624 AAATTT-AATTT
1 AAATTTAAATTT
*
36635 AAGTTTAAATTT
1 AAATTTAAATTT
*
36647 -ATTTTCAAATTT
1 AAATTT-AAATTT
*
36659 AAAATT--ATTAT
1 AAATTTAAATT-T
36670 AAATTTAAA
1 AAATTTAAA
36679 ATAAAAAAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
10 3 0.06
11 30 0.58
12 15 0.29
13 4 0.08
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (12 bp):
AAATTTAAATTT
Found at i:36680 original size:17 final size:17
Alignment explanation
Indices: 36569--36678 Score: 89
Period size: 17 Copynumber: 6.4 Consensus size: 17
36559 CCAAACTCAT
* *
36569 TTTAAATTTATTTTAGGA
1 TTTAAATTTATTATA-AA
* *
36587 -TTAAATTTGTTTAAAAA
1 TTTAAATTT-ATTATAAA
**
36604 TTTAAATTTAAAATAAA
1 TTTAAATTTATTATAAA
*
36621 TTTAAATTTAATT-TAAG
1 TTTAAATTT-ATTATAAA
*
36638 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTAT-AAA
*
36656 TTTAAAATTATTATAAA
1 TTTAAATTTATTATAAA
36673 TTTAAA
1 TTTAAA
36679 ATAAAAAAAG
Statistics
Matches: 73, Mismatches: 14, Indels: 11
0.74 0.14 0.11
Matches are distributed among these distances:
16 3 0.04
17 44 0.60
18 26 0.36
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (17 bp):
TTTAAATTTATTATAAA
Done.