Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013910.1 Kokia drynarioides strain JFW-HI SEQ_128939, 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: 8303
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:1695 original size:17 final size:17
Alignment explanation
Indices: 1673--1738 Score: 78
Period size: 17 Copynumber: 3.9 Consensus size: 17
1663 TGGAGTTGTT
*
1673 TTTTAAATTTTAATTTA
1 TTTTAAATTTAAATTTA
*
1690 TTTTAAATTTAAACTTA
1 TTTTAAATTTAAATTTA
* * *
1707 CTTTGAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
*
1724 TTTTAAATTAAAATT
1 TTTTAAATTTAAATT
1739 AAAAGTGTCC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:1763 original size:13 final size:13
Alignment explanation
Indices: 1745--1769 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1735 AATTAAAAGT
1745 GTCCAATTACAAA
1 GTCCAATTACAAA
1758 GTCCAATTACAA
1 GTCCAATTACAA
1770 TTGAGCCCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (13 bp):
GTCCAATTACAAA
Found at i:2436 original size:3 final size:3
Alignment explanation
Indices: 2411--2492 Score: 85
Period size: 3 Copynumber: 26.7 Consensus size: 3
2401 TAAATTAGTT
* * *
2411 TAA TAAA TAA AAA TAA TAT TAA TAA TAA TAA -ATA TAA TAC TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
* *
2457 CAT TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2493 GTAACAAAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
2 1 0.02
3 57 0.88
4 7 0.11
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3481 original size:29 final size:28
Alignment explanation
Indices: 3398--3777 Score: 127
Period size: 29 Copynumber: 13.1 Consensus size: 28
3388 GCCTGAAGGT
* * * *
3398 CCCTAAACTATCCAAAAATCATATTTTGA
1 CCCTAAACTTTTCAAAAATTACATTTT-A
* * * *
3427 CCCTTGAACGTTTCCAAAATTCCATTTTGA
1 CCC-TAAACTTTTCAAAAATTACATTTT-A
3457 CCCTAAACTTTTCAAAAATTACATTTTA
1 CCCTAAACTTTTCAAAAATTACATTTTA
** * *
3485 CCCCCGAAC-TTTCCAAAATTCCATTTTTA
1 -CCCTAAACTTTTCAAAAATTACA-TTTTA
** ** *
3514 ATCTCGATTTTTCCAAAAATTACCATTTTA
1 CCCTAAACTTTT-CAAAAATTA-CATTTTA
* * * *
3544 CCTTCGAAC--TTCCAAAATTCCATTTTTGA
1 CCCT-AAACTTTTCAAAAATTACA-TTTT-A
*
3573 -CCTAGAA-TTTTCCAAAATTACCATTTTA
1 CCCTA-AACTTTTCAAAAATTA-CATTTTA
* * *
3601 CCCGTGATC-TTTCAAAAATTCCATTTTTA
1 CCC-TAAACTTTTCAAAAATTACA-TTTTA
** *
3630 -CCTCGATTTTTCCAAAAATTACATTTTA
1 CCCTAAACTTTT-CAAAAATTACATTTTA
* * *
3658 CCCCTAAAC--TTCCAAATTTCCATTTTTAA
1 -CCCTAAACTTTTCAAAAATTACA-TTTT-A
* *
3687 CCTTGAA-TTTTCCAAAAATTACATTTTTAA
1 CCCTAAACTTTT-CAAAAATTACA-TTTT-A
* * *
3717 CCCCAAAC-TTTCTAAAATTCCATATTTA
1 CCCTAAACTTTTCAAAAATTACAT-TTTA
*
3745 ACCTCAAA-TTTTCAAAAATTACCATTTTA
1 CCCT-AAACTTTTCAAAAATTA-CATTTTA
3774 CCCT
1 CCCT
3778 CGAACTTCCA
Statistics
Matches: 255, Mismatches: 65, Indels: 62
0.67 0.17 0.16
Matches are distributed among these distances:
27 11 0.04
28 58 0.23
29 117 0.46
30 66 0.26
31 3 0.01
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.38
Consensus pattern (28 bp):
CCCTAAACTTTTCAAAAATTACATTTTA
Found at i:3526 original size:57 final size:58
Alignment explanation
Indices: 3432--3838 Score: 398
Period size: 58 Copynumber: 7.0 Consensus size: 58
3422 TTTGACCCTT
* * ** *
3432 GAACGTTTCCAAAATTCCATTTTGACCCTAAACTTTTCAAAAATTA-CATTTTACCCCC
1 GAAC-TTTCCAAAATTCCATTTTTAACCTCGATTTTTCAAAAATTACCATTTTACCCCC
* **
3490 GAACTTTCCAAAATTCCATTTTTAATCTCGATTTTTCCAAAAATTACCATTTTACCTTC
1 GAACTTTCCAAAATTCCATTTTTAACCTCGATTTTT-CAAAAATTACCATTTTACCCCC
* * * * **
3549 GAAC-TTCCAAAATTCCATTTTTGACCTAGAATTTTCCAAAATTACCATTTTACCCGT
1 GAACTTTCCAAAATTCCATTTTTAACCTCGATTTTTCAAAAATTACCATTTTACCCCC
* * *
3606 GATCTTTCAAAAATTCCATTTTT-ACCTCGATTTTTCCAAAAATTA-CATTTTACCCCT
1 GAACTTTCCAAAATTCCATTTTTAACCTCGATTTTT-CAAAAATTACCATTTTACCCCC
* * * * *
3663 AAAC-TTCCAAATTTCCATTTTTAACCTTGAATTTTCCAAAAATTA-CATTTTTAACCCC
1 GAACTTTCCAAAATTCCATTTTTAACCTCG-ATTTTTCAAAAATTACCA-TTTTACCCCC
* * * * * *
3721 AAACTTTCTAAAATTCCATATTTAACCTCAAATTTTCAAAAATTACCATTTTACCCTC
1 GAACTTTCCAAAATTCCATTTTTAACCTCGATTTTTCAAAAATTACCATTTTACCCCC
* * ** *
3779 GAAC-TTCCAAAATTCCATTTTTGATCC-CGAACTTACCCAAAATTACCATTTTACCCCC
1 GAACTTTCCAAAATTCCATTTTT-AACCTCG-ATTTTTCAAAAATTACCATTTTACCCCC
3837 GA
1 GA
3839 GTATCCAAAA
Statistics
Matches: 289, Mismatches: 49, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
56 16 0.06
57 103 0.36
58 134 0.46
59 36 0.12
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.38
Consensus pattern (58 bp):
GAACTTTCCAAAATTCCATTTTTAACCTCGATTTTTCAAAAATTACCATTTTACCCCC
Found at i:3560 original size:58 final size:58
Alignment explanation
Indices: 3432--3835 Score: 427
Period size: 57 Copynumber: 7.0 Consensus size: 58
3422 TTTGACCCTT
* * *
3432 GAACGTTTCCAAAATTCCATTTTGACCCT-AAACTTTT-CAAAAATTA-CATTTTACCCCC
1 GAAC-TTTCCAAAATTCCATTTTTAACCTCGAA-TTTTCCAAAAATTACCATTTTA-CCCC
* * *
3490 GAACTTTCCAAAATTCCATTTTTAATCTCGATTTTTCCAAAAATTACCATTTTACCTTC
1 GAACTTTCCAAAATTCCATTTTTAACCTCGAATTTTCCAAAAATTACCATTTTACC-CC
* * *
3549 GAAC-TTCCAAAATTCCATTTTTGACCTAGAATTTTCC-AAAATTACCATTTTACCCGT
1 GAACTTTCCAAAATTCCATTTTTAACCTCGAATTTTCCAAAAATTACCATTTTACCC-C
* * *
3606 GATCTTTCAAAAATTCCATTTTT-ACCTCGATTTTTCCAAAAATTA-CATTTTACCCC
1 GAACTTTCCAAAATTCCATTTTTAACCTCGAATTTTCCAAAAATTACCATTTTACCCC
* * *
3662 TAAAC-TTCCAAATTTCCATTTTTAACCTTGAATTTTCCAAAAATTA-CATTTTTAACCCC
1 -GAACTTTCCAAAATTCCATTTTTAACCTCGAATTTTCCAAAAATTACCA-TTTT-ACCCC
* * * *
3721 AAACTTTCTAAAATTCCATATTTAACCTCAAATTTT-CAAAAATTACCATTTTACCCTC
1 GAACTTTCCAAAATTCCATTTTTAACCTCGAATTTTCCAAAAATTACCATTTTACCC-C
* * * *
3779 GAAC-TTCCAAAATTCCATTTTTGATCC-CGAACTTACCCAAAATTACCATTTTACCCC
1 GAACTTTCCAAAATTCCATTTTT-AACCTCGAATTTTCCAAAAATTACCATTTTACCCC
3836 CGAGTATCCA
Statistics
Matches: 294, Mismatches: 36, Indels: 33
0.81 0.10 0.09
Matches are distributed among these distances:
56 16 0.05
57 117 0.40
58 116 0.39
59 45 0.15
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.38
Consensus pattern (58 bp):
GAACTTTCCAAAATTCCATTTTTAACCTCGAATTTTCCAAAAATTACCATTTTACCCC
Found at i:3778 original size:29 final size:28
Alignment explanation
Indices: 3437--3799 Score: 222
Period size: 29 Copynumber: 12.6 Consensus size: 28
3427 CCCTTGAACG
* *
3437 TTTCCAAAATTCCATTTTGACCCT-AAACT
1 TTTCAAAAATTCCATTTT-ACCCTCGAA-T
* * *
3466 TTTCAAAAATTACATTTTACCCCCGAAC
1 TTTCAAAAATTCCATTTTACCCTCGAAT
* ** *
3494 TTTCCAAAATTCCATTTTTAATCTCGATT
1 TTTCAAAAATTCCA-TTTTACCCTCGAAT
*
3523 TTTCCAAAAATTACCATTTTACCTTCGAA-
1 TTT-CAAAAATT-CCATTTTACCCTCGAAT
* * *
3552 CTTCCAAAATTCCATTTTTGA-CCTAGAAT
1 TTTCAAAAATTCCA-TTTT-ACCCTCGAAT
*
3581 TTTCCAAAATTACCATTTTACCCGT-G-AT
1 TTTCAAAAATT-CCATTTTACCC-TCGAAT
*
3609 CTTTCAAAAATTCCATTTTTA-CCTCGATT
1 -TTTCAAAAATTCCA-TTTTACCCTCGAAT
* * *
3638 TTTCCAAAAATTACATTTTACCC-CTAAA
1 TTT-CAAAAATTCCATTTTACCCTCGAAT
* * * * *
3666 CTTCCAAATTTCCATTTTTAACCTTGAAT
1 TTTCAAAAATTCCA-TTTTACCCTCGAAT
* * *
3695 TTTCCAAAAATTACATTTTTAACCC-CAAAC
1 TTT-CAAAAATTCCA-TTTT-ACCCTCGAAT
* * *
3725 TTTCTAAAATTCCATATTTAACCTCAAAT
1 TTTCAAAAATTCCAT-TTTACCCTCGAAT
3754 TTTCAAAAATTACCATTTTACCCTCGAA-
1 TTTCAAAAATT-CCATTTTACCCTCGAAT
* *
3782 CTTCCAAAATTCCATTTT
1 TTTCAAAAATTCCATTTT
3800 TGATCCCGAA
Statistics
Matches: 258, Mismatches: 53, Indels: 48
0.72 0.15 0.13
Matches are distributed among these distances:
27 19 0.07
28 73 0.28
29 118 0.46
30 42 0.16
31 6 0.02
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (28 bp):
TTTCAAAAATTCCATTTTACCCTCGAAT
Found at i:3838 original size:30 final size:28
Alignment explanation
Indices: 3471--3838 Score: 148
Period size: 29 Copynumber: 12.8 Consensus size: 28
3461 AAACTTTTCA
3471 AAAATTA-CATTTTACCCCCGAACTTTCC
1 AAAATTACCATTTTACCCCCGAAC-TTCC
** * **
3499 AAAATT-CCATTTTTAATCTCGATTTTTCC
1 AAAATTACCA-TTTTACCCCCGA-ACTTCC
**
3528 AAAAATTACCATTTTACCTTCGAACTTCC
1 -AAAATTACCATTTTACCCCCGAACTTCC
** *
3557 AAAATT-CCATTTTTGA-CCTAGAATTTTCC
1 AAAATTACCA-TTTT-ACCCCCGAA-CTTCC
** * *
3586 AAAATTACCATTTTACCCGTGATCTTTCA
1 AAAATTACCATTTTACCCCCGAAC-TTCC
* **
3615 AAAATT-CCATTTTTA-CCTCGATTTTTCC
1 AAAATTACCA-TTTTACCCCCGA-ACTTCC
**
3643 AAAAATTA-CATTTTACCCCTAAACTTCC
1 -AAAATTACCATTTTACCCCCGAACTTCC
* * ** *
3671 -AAATTTCCATTTTTAACCTTGAATTTTCC
1 AAAATTACCA-TTTTACCCCCGAA-CTTCC
* * *
3700 AAAAATTA-CATTTTTAACCCCAAACTTTCT
1 -AAAATTACCA-TTTTACCCCCGAAC-TTCC
* * * * *
3730 AAAATT-CCATATTTAACCTCAAATTTTCA
1 AAAATTACCAT-TTTACCCCCGAA-CTTCC
*
3759 AAAATTACCATTTTACCCTCGAACTTCC
1 AAAATTACCATTTTACCCCCGAACTTCC
*
3787 AAAATT-CCATTTTTGA-TCCCGAACTTACCC
1 AAAATTACCA-TTTT-ACCCCCGAACTT--CC
3817 AAAATTACCATTTTACCCCCGA
1 AAAATTACCATTTTACCCCCGA
3839 GTATCCAAAA
Statistics
Matches: 260, Mismatches: 48, Indels: 62
0.70 0.13 0.17
Matches are distributed among these distances:
26 5 0.02
27 8 0.03
28 75 0.29
29 106 0.41
30 55 0.21
31 11 0.04
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.38
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCCGAACTTCC
Done.