Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012295.1 Kokia drynarioides strain JFW-HI SEQ_127296, 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: 8882
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Found at i:520 original size:23 final size:22
Alignment explanation
Indices: 490--532 Score: 77
Period size: 22 Copynumber: 1.9 Consensus size: 22
480 TAAGTTTTTA
490 AAAAAAAAGGGAAAAGAGAAGTT
1 AAAAAAAA-GGAAAAGAGAAGTT
513 AAAAAAAAGGAAAAGAGAAG
1 AAAAAAAAGGAAAAGAGAAG
533 GTTTTTACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.05
Consensus pattern (22 bp):
AAAAAAAAGGAAAAGAGAAGTT
Found at i:1327 original size:29 final size:28
Alignment explanation
Indices: 1282--1533 Score: 220
Period size: 29 Copynumber: 8.6 Consensus size: 28
1272 CCCTAATCTA
1282 TCCAAAAATTTCATTTTTACCTCCGAACT
1 TCCAAAAATTTCATTTTTACC-CCGAACT
*
1311 TCTAAAAATTTCATTTTTTGACCCCGAAACT
1 TCCAAAAATTTCA-TTTTT-ACCCCG-AACT
* ****
1342 TCAAAAAATTTCATTTTTAACTTTAAACT
1 TCCAAAAATTTCATTTTT-ACCCCGAACT
* *
1371 TCCAAAAAATTCATTTTTACCTCTGAACT
1 TCCAAAAATTTCATTTTTACC-CCGAACT
* * *
1400 TTCAAAAA-TCCTTTTTTGACCCCTGAACT
1 TCCAAAAATTTCATTTTT-ACCCC-GAACT
* *
1429 TCCAAAAATTCCATTTTCACCTCCGAACT
1 TCCAAAAATTTCATTTTTACC-CCGAACT
* * *
1458 TTCAAAAATTCCATTTTGACCCCGAAACT
1 TCCAAAAATTTCATTTTTACCCCG-AACT
* *
1487 TCCAAAAATTCCATTTTTACCCTCGAACC
1 TCCAAAAATTTCATTTTTACCC-CGAACT
1516 TCC-AAAATTTCCATTTTT
1 TCCAAAAATTT-CATTTTT
1534 GTCCCCAAAA
Statistics
Matches: 187, Mismatches: 25, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
28 19 0.10
29 123 0.66
30 26 0.14
31 19 0.10
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (28 bp):
TCCAAAAATTTCATTTTTACCCCGAACT
Found at i:1431 original size:58 final size:58
Alignment explanation
Indices: 1284--1563 Score: 241
Period size: 58 Copynumber: 4.8 Consensus size: 58
1274 CTAATCTATC
* * * *
1284 CAAAAATTTCATTTTTACCTCCG-AACTTCTAAAAATTTCATTTTTTGACC-CCGAAAC-TT
1 CAAAAATTCCATTTTGACC-CCGAAACTTCCAAAAATTCCA-TTTTT-ACCTCCG-AACTTT
* * * *** *
1343 CAAAAAATTTCATTTTTAACTTTAAACTTCCAAAAAATT-CATTTTTACCTCTGAACTTT
1 C-AAAAATTCCATTTTGACCCCGAAACTTCC-AAAAATTCCATTTTTACCTCCGAACTTT
* *
1402 CAAAAA-TCCTTTTTTGACCCCTG-AACTTCCAAAAATTCCATTTTCACCTCCGAACTTT
1 CAAAAATTCC-ATTTTGACCCC-GAAACTTCCAAAAATTCCATTTTTACCTCCGAACTTT
* *
1460 CAAAAATTCCATTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACC-CTCGAACCTC
1 CAAAAATTCCATTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCTC-CGAACTTT
* * * *
1518 CAAAATTTCCATTTTTGTCCCCAAAACTTTCAAAAATTACCATTTT
1 CAAAAATTCCA-TTTTGACCCCGAAACTTCCAAAAATT-CCATTTT
1564 GTCCTCAAAT
Statistics
Matches: 185, Mismatches: 23, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
57 11 0.06
58 98 0.53
59 37 0.20
60 32 0.17
61 7 0.04
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (58 bp):
CAAAAATTCCATTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCTCCGAACTTT
Found at i:1458 original size:87 final size:88
Alignment explanation
Indices: 1282--1532 Score: 255
Period size: 87 Copynumber: 2.9 Consensus size: 88
1272 CCCTAATCTA
* * *
1282 TCCAAAAATTTCATTTTTACCTCCGAAC-TTCTAAAAATTTCATTTTTTGACCCC-GAAACTTCA
1 TCCAAAAAATTCATTTTTACCTCCGAACTTTC-AAAAA-TTCCTTTTTTGACCCCTG-AACTTCC
* * **
1345 AAAAATTTCATTTTTAACTTTAAACT
63 AAAAATTCCATTTTCAACTCCAAACT
*
1371 TCCAAAAAATTCATTTTTACCTCTGAACTTTCAAAAA-TCCTTTTTTGACCCCTGAACTTCCAAA
1 TCCAAAAAATTCATTTTTACCTCCGAACTTTCAAAAATTCCTTTTTTGACCCCTGAACTTCCAAA
* *
1435 AATTCCATTTTCACCTCCGAACT
66 AATTCCATTTTCAACTCCAAACT
* * * * *
1458 TTC-AAAAATTCCATTTTGACC-CCGAAACTTCCAAAAATTCCATTTTT-A-CCCTCGAACCTCC
1 TCCAAAAAATT-CATTTTTACCTCCG-AACTTTCAAAAATTCCTTTTTTGACCCCT-GAACTTCC
*
1519 AAAATTTCCATTTT
63 AAAAATTCCATTTT
1533 TGTCCCCAAA
Statistics
Matches: 139, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
86 13 0.09
87 83 0.60
88 9 0.06
89 31 0.22
90 3 0.02
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (88 bp):
TCCAAAAAATTCATTTTTACCTCCGAACTTTCAAAAATTCCTTTTTTGACCCCTGAACTTCCAAA
AATTCCATTTTCAACTCCAAACT
Found at i:1564 original size:30 final size:29
Alignment explanation
Indices: 1396--1572 Score: 128
Period size: 29 Copynumber: 6.0 Consensus size: 29
1386 TTTACCTCTG
* * **
1396 AACTTTCAAAAA-TCCTTTTTTGACCCCTG
1 AACTTTCAAAAATTCC-ATTTTGTCCCCAA
* ** *
1425 AACTTCCAAAAATTCCATTTTCACCTCC-G
1 AACTTTCAAAAATTCCATTTTGTCC-CCAA
* *
1454 AACTTTCAAAAATTCCATTTTGACCCCGA
1 AACTTTCAAAAATTCCATTTTGTCCCCAA
* *
1483 AACTTCCAAAAATTCCATTTT-TACCCTC-G
1 AACTTTCAAAAATTCCATTTTGT-CCC-CAA
* * *
1512 AACCTCCAAAATTTCCATTTTTGTCCCCAA
1 AACTTTCAAAAATTCCA-TTTTGTCCCCAA
*
1542 AACTTTCAAAAATTACCATTTTGTCCTCAA
1 AACTTTCAAAAATT-CCATTTTGTCCCCAA
1572 A
1 A
1573 TGTCCGAAAA
Statistics
Matches: 123, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
28 2 0.02
29 81 0.66
30 36 0.29
31 4 0.03
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (29 bp):
AACTTTCAAAAATTCCATTTTGTCCCCAA
Found at i:2047 original size:96 final size:96
Alignment explanation
Indices: 1941--2132 Score: 273
Period size: 96 Copynumber: 2.0 Consensus size: 96
1931 AAAACTTTAA
*
1941 AATCGAGGCAATA-TTCTTTTAT-TTCGAGTT-TCGAAAATTTGCGCATTAACTTACTAGGTGCA
1 AATCGAGGCAATATTTC-CTTATCTTCGA-TTCT-GAAAATTTGCGCATTAACTTACTAGGTGCA
** *
2003 ATTTTTCTTCAAATCGAAATAATCGAATACCCTT
63 ACCTTTCTTCAAATCAAAATAATCGAATACCCTT
* *
2037 AATCGAGGCAATGTTTCCTTATCTTCGATTCTGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
1 AATCGAGGCAATATTTCCTTATCTTCGATTCTGAAAATTTGCGCATTAACTTACTAGGTGCAACC
*
2102 TTTCTTCAAATCAAAATAATCGAATATCCTT
66 TTTCTTCAAATCAAAATAATCGAATACCCTT
2133 TTCTCAAAAT
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
96 77 0.90
97 9 0.10
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (96 bp):
AATCGAGGCAATATTTCCTTATCTTCGATTCTGAAAATTTGCGCATTAACTTACTAGGTGCAACC
TTTCTTCAAATCAAAATAATCGAATACCCTT
Found at i:4843 original size:14 final size:15
Alignment explanation
Indices: 4824--4854 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4814 ACCATTTAAG
4824 TTTTATTTTTAT-TT
1 TTTTATTTTTATATT
4838 TTTTATTTTTATATT
1 TTTTATTTTTATATT
4853 TT
1 TT
4855 CGCAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTATTTTTATATT
Found at i:7436 original size:26 final size:26
Alignment explanation
Indices: 7369--7437 Score: 66
Period size: 26 Copynumber: 2.7 Consensus size: 26
7359 GGATCCTCTT
* *
7369 ATGCAGCGACAACTCTGGACAGATTC
1 ATGCAGCGACAATTCTGAACAGATTC
* * * * *
7395 ATGCATCGATACTTCTGAATAGGTTC
1 ATGCAGCGACAATTCTGAACAGATTC
*
7421 GTGCAGCGACAATTCTG
1 ATGCAGCGACAATTCTG
7438 GGCGTATTGC
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (26 bp):
ATGCAGCGACAATTCTGAACAGATTC
Found at i:7720 original size:17 final size:17
Alignment explanation
Indices: 7698--7795 Score: 53
Period size: 17 Copynumber: 5.7 Consensus size: 17
7688 AAACTCCCTT
7698 TAAATTTATTTTAAGAA
1 TAAATTTATTTTAAGAA
*
7715 TAAATTT-GTTT-AGAAA
1 TAAATTTATTTTAAG-AA
* *
7731 TTTAAATTTATATTAA-ATT
1 --TAAATTTATTTTAAGA-A
7750 TAAATTTATTTT--GAA
1 TAAATTTATTTTAAGAA
* **
7765 TTTAAATTTAATTTAAGTT
1 --TAAATTTATTTTAAGAA
7784 TAAATTTATTTT
1 TAAATTTATTTT
7796 CCAAATTTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 22
0.65 0.11 0.24
Matches are distributed among these distances:
15 2 0.03
16 6 0.10
17 40 0.67
18 8 0.13
19 3 0.05
20 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
TAAATTTATTTTAAGAA
Found at i:7739 original size:6 final size:6
Alignment explanation
Indices: 7728--7791 Score: 71
Period size: 6 Copynumber: 11.2 Consensus size: 6
7718 ATTTGTTTAG
* * *
7728 AAATTT AAATTT ATA-TT AAATTT AAATTT -ATTTT GAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
7774 -AATTT AAGTTT AAATTT A
1 AAATTT AAATTT AAATTT A
7792 TTTTCCAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
5 13 0.27
6 35 0.73
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:8586 original size:17 final size:16
Alignment explanation
Indices: 8566--8619 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
8556 CGGTTTTCAC
8566 AATATTTATTAATAAT
1 AATATTTATTAATAAT
*
8582 AAATATTTTCTTAATAAT
1 -AATA-TTTATTAATAAT
* *
8600 AATAATTTAATAATATT
1 AAT-ATTTATTAATAAT
8617 AAT
1 AAT
8620 GAATAATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 19 0.61
18 12 0.39
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATTTATTAATAAT
Done.