Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009439.1 Kokia drynarioides strain JFW-HI SEQ_124146, 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: 11554
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4256 original size:28 final size:27
Alignment explanation
Indices: 4225--4319 Score: 64
Period size: 28 Copynumber: 3.3 Consensus size: 27
4215 AAGGCTAAAT
*
4225 GGTAATTTTAGACACTTGAGGGCAAAAC
1 GGTAATTTTAGACA-TTAAGGGCAAAAC
* * * *
4253 GGTATTTTTGGAAAGTTCAGGGTCAAAAAC
1 GGTAATTTTAGACA-TTAAGGG-C-AAAAC
** * *
4283 GAAAATTTTAGACATCTAAGGGTAAAAT
1 GGTAATTTTAGACAT-TAAGGGCAAAAC
4311 GGTAATTTT
1 GGTAATTTT
4320 TAGAAAAATA
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
28 28 0.57
29 2 0.04
30 19 0.39
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.31
Consensus pattern (27 bp):
GGTAATTTTAGACATTAAGGGCAAAAC
Found at i:4365 original size:59 final size:58
Alignment explanation
Indices: 4301--4703 Score: 370
Period size: 59 Copynumber: 6.9 Consensus size: 58
4291 TAGACATCTA
* * *
4301 AGGGTAAAATGGTAATTTTTAGAAAAATAGGGGTTAAAAATGGAATTTTTGGAAGTTTG
1 AGGGTAAAATGGTAATTTTTAGAGAAATCGGGGTTAAAAATGGAA-TTTTGGAAGTTCG
* ** * *
4360 TGGGTAAAATAATAAATTTTT-GAGAAATTGAGGTTAAAAATGGAATTTTGGAAGTTCG
1 AGGGTAAAATGGT-AATTTTTAGAGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCG
* * * * *
4418 AGGGAAAAAATGGTAATTTTTGGAGAAATCGGGGTTAGAAATGGGATTTTGAAAGTTCG
1 AGGG-TAAAATGGTAATTTTTAGAGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCG
** ** *
4477 -GAGGTAAAATTTTAATTTTT-GAGAAATCGGGGTTAAAAATTAAATATTGGAAGTTCG
1 AG-GGTAAAATGGTAATTTTTAGAGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCG
* * * *
4534 AGAGTAAAATGGTAATTTTTGGAGAAATCGAGG-TCAAAATGGAATTTTGGAAAGTTCG
1 AGGGTAAAATGGTAATTTTTAGAGAAATCGGGGTTAAAAATGGAATTTTGG-AAGTTCG
* * * * * * * * * *
4592 AGGGTAAAATGGTAATTTTAAAAAAAATCAGAGTCAAATATGGATTTTTGAAAAGTT-A
1 AGGGTAAAATGGTAATTTTTAGAGAAATCGGGGTTAAAAATGGAATTTTG-GAAGTTCG
* *
4650 AGGGGTAAAAAT-GTAATTTTTAGA-AAGTTCGGGGTTGAAAATGGAATTTTGGAA
1 A-GGGT-AAAATGGTAATTTTTAGAGAA-ATCGGGGTTAAAAATGGAATTTTGGAA
4704 AAGTTCAATA
Statistics
Matches: 275, Mismatches: 57, Indels: 25
0.77 0.16 0.07
Matches are distributed among these distances:
57 59 0.21
58 85 0.31
59 119 0.43
60 12 0.04
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (58 bp):
AGGGTAAAATGGTAATTTTTAGAGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCG
Found at i:4441 original size:30 final size:28
Alignment explanation
Indices: 4336--4441 Score: 99
Period size: 30 Copynumber: 3.6 Consensus size: 28
4326 AATAGGGGTT
*
4336 AAAAATGGAATTTTTGGAAGTTTGTGGGTA
1 AAAAATGGAATTTTTGGAAG-TTGAGGG-A
* * **
4366 AAATAAT-AAATTTTTGAGAAATTGAGGTT
1 AAA-AATGGAATTTTTG-GAAGTTGAGGGA
4395 AAAAATGGAA-TTTTGGAAGTTCGAGGGA
1 AAAAATGGAATTTTTGGAAGTT-GAGGGA
4423 AAAAATGGTAATTTTTGGA
1 AAAAATGG-AATTTTTGGA
4442 GAAATCGGGG
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
27 5 0.08
28 20 0.33
29 7 0.11
30 23 0.38
31 6 0.10
ACGTcount: A:0.40, C:0.01, G:0.25, T:0.34
Consensus pattern (28 bp):
AAAAATGGAATTTTTGGAAGTTGAGGGA
Found at i:4506 original size:29 final size:28
Alignment explanation
Indices: 4477--4573 Score: 72
Period size: 28 Copynumber: 3.4 Consensus size: 28
4467 TGAAAGTTCG
*
4477 GAGGTAAAATTTTAATTTTTGAGAAATC
1 GAGGTAAAATATTAATTTTTGAGAAATC
* * * *
4505 GGGGTTAAAA-ATTAAATATTG-GAAGTTC
1 GAGG-TAAAATATTAATTTTTGAGAA-ATC
**
4533 GAGAGTAAAATGGTAATTTTTGGAGAAATC
1 GAG-GTAAAATATTAATTTTT-GAGAAATC
4563 GAGGTCAAAAT
1 GAGGT-AAAAT
4574 GGAATTTTGG
Statistics
Matches: 51, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
27 3 0.06
28 20 0.39
29 14 0.27
30 11 0.22
31 3 0.06
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.32
Consensus pattern (28 bp):
GAGGTAAAATATTAATTTTTGAGAAATC
Found at i:4573 original size:57 final size:57
Alignment explanation
Indices: 4304--4610 Score: 321
Period size: 58 Copynumber: 5.3 Consensus size: 57
4294 ACATCTAAGG
* * * * * *
4304 GTAAAATGGTAATTTTTAGAAAAATAGGGGTTAAAAATGGAATTTTTGGAAGTTTGTGG
1 GTAAAATGGTAATTTTT-GAGAAATCGAGGTTAAAAATGGAA-TTTTGGAAGTTCGAGA
** * *
4363 GTAAAATAATAAATTTTTGAGAAATTGAGGTTAAAAATGGAATTTTGGAAGTTCGAGG
1 GTAAAATGGT-AATTTTTGAGAAATCGAGGTTAAAAATGGAATTTTGGAAGTTCGAGA
* * * * *
4421 GAAAAAATGGTAATTTTTGGAGAAATCGGGGTTAGAAATGGGATTTTGAAAGTTCG-GA
1 G-TAAAATGGTAATTTTT-GAGAAATCGAGGTTAAAAATGGAATTTTGGAAGTTCGAGA
** * ** *
4479 GGTAAAATTTTAATTTTTGAGAAATCGGGGTTAAAAATTAAATATTGGAAGTTCGAGA
1 -GTAAAATGGTAATTTTTGAGAAATCGAGGTTAAAAATGGAATTTTGGAAGTTCGAGA
* *
4537 GTAAAATGGTAATTTTTGGAGAAATCGAGG-TCAAAATGGAATTTTGGAAAGTTCGAGG
1 GTAAAATGGTAATTTTT-GAGAAATCGAGGTTAAAAATGGAATTTTGG-AAGTTCGAGA
4595 GTAAAATGGTAATTTT
1 GTAAAATGGTAATTTT
4611 AAAAAAAATC
Statistics
Matches: 208, Mismatches: 33, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
57 59 0.28
58 74 0.36
59 68 0.33
60 7 0.03
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (57 bp):
GTAAAATGGTAATTTTTGAGAAATCGAGGTTAAAAATGGAATTTTGGAAGTTCGAGA
Found at i:4707 original size:30 final size:28
Alignment explanation
Indices: 4396--4709 Score: 109
Period size: 30 Copynumber: 10.8 Consensus size: 28
4386 ATTGAGGTTA
*
4396 AAAATGGAATTTTGG--AAGTTCGAGGGAA
1 AAAATGGAATTTTGGAAAAGTTCG-GGG-T
4424 AAAATGGTAATTTTTGGAGAAA--TCGGGGTT
1 AAAATGG-AA-TTTTGGA-AAAGTTCGGGG-T
*
4454 AGAAATGGGATTTT-G-AAAGTTCGGAGGT
1 A-AAATGGAATTTTGGAAAAGTTCGG-GGT
** *
4482 AAAATTTTAATTTTTGAGAAA--TCGGGGTT
1 AAAA-TGGAATTTTGGA-AAAGTTCGGGG-T
** * *
4511 AAAAATTAAATATTGG--AAGTTCGAGAGT
1 -AAAATGGAATTTTGGAAAAGTTCG-GGGT
*
4539 AAAATGGTAATTTTTGGAGAAA--TCGAGGT
1 AAAATGG-AA-TTTTGGA-AAAGTTCGGGGT
4568 CAAAATGGAATTTTGG-AAAGTTCGAGGGT
1 -AAAATGGAATTTTGGAAAAGTTCG-GGGT
** ** * *
4597 AAAATGGTAATTTTAAAAAAAATCAGAGT
1 AAAATGG-AATTTTGGAAAAGTTCGGGGT
* *
4626 CAAATATGG-ATTTTTGAAAAGTTAAGGGGT
1 -AAA-ATGGAATTTTGGAAAAGTT-CGGGGT
* *
4656 AAAAATGTAATTTT-TAGAAAGTTCGGGGTT
1 -AAAATGGAATTTTGGA-AAAGTTCGGGG-T
4686 GAAAATGGAATTTTGGAAAAGTTC
1 -AAAATGGAATTTTGGAAAAGTTC
4710 AATAGTCAAA
Statistics
Matches: 214, Mismatches: 36, Indels: 70
0.67 0.11 0.22
Matches are distributed among these distances:
26 8 0.04
27 8 0.04
28 44 0.21
29 63 0.29
30 70 0.33
31 17 0.08
32 2 0.01
33 2 0.01
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.31
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAAGTTCGGGGT
Found at i:5718 original size:3 final size:3
Alignment explanation
Indices: 5710--5809 Score: 74
Period size: 3 Copynumber: 32.0 Consensus size: 3
5700 TCATTTTTAT
* * * * *
5710 TTA TTA TTA ATA TTAA TTA TTA TTA TTA ATA ATA TTT TTA TTAA TAA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
* * * * *
5757 TTA TTA ATG TTA TTA TTA TCA TTA TTTA TTA TTTA TCA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TTA TTA TTA TTA
5804 TTA TTA
1 TTA TTA
5810 ATATATAACC
Statistics
Matches: 75, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
3 64 0.85
4 11 0.15
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:5770 original size:25 final size:24
Alignment explanation
Indices: 5713--5811 Score: 76
Period size: 25 Copynumber: 4.0 Consensus size: 24
5703 TTTTTATTTA
*
5713 TTATTAATATTAATTATTATTATTAAT
1 TTATTATTATTAA-TA--ATTATTAAT
* *
5740 AATATTTTTATTAATAATTATTAAT
1 -TTATTATTATTAATAATTATTAAT
* * *
5765 GTTATTATTATCATTATTTATT-AT
1 -TTATTATTATTAATAATTATTAAT
*
5789 TTATCATTATTAAT-ATTATTAAT
1 TTATTATTATTAATAATTATTAAT
5812 ATATAACCTT
Statistics
Matches: 57, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
22 5 0.09
23 13 0.23
24 2 0.04
25 25 0.44
27 2 0.04
28 10 0.18
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (24 bp):
TTATTATTATTAATAATTATTAAT
Found at i:5773 original size:28 final size:28
Alignment explanation
Indices: 5710--5811 Score: 75
Period size: 28 Copynumber: 3.7 Consensus size: 28
5700 TCATTTTTAT
* *
5710 TTATTATTAATATTAATTATTATTATTA
1 TTATTATTAATATTAATAATTATTAATA
* * ** *
5738 ATAATATTTTTATTAATAATTATTAATG
1 TTATTATTAATATTAATAATTATTAATA
* *
5766 TTATTATT-ATCATTATTTATTATT--TA
1 TTATTATTAAT-ATTAATAATTATTAATA
* *
5792 TCATTATTAATATTATTAAT
1 TTATTATTAATATTAATAAT
5812 ATATAACCTT
Statistics
Matches: 57, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
26 16 0.28
27 3 0.05
28 38 0.67
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (28 bp):
TTATTATTAATATTAATAATTATTAATA
Found at i:5794 original size:17 final size:16
Alignment explanation
Indices: 5766--5809 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
5756 ATTATTAATG
5766 TTATTATTATCATTAT
1 TTATTATTATCATTAT
5782 TTATTATTTATCATTAT
1 TTATTA-TTATCATTAT
5799 TAATATTATTA
1 T--TATTATTA
5810 ATATATAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.24
17 11 0.44
18 3 0.12
19 5 0.20
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATTATTATCATTAT
Found at i:5798 original size:13 final size:13
Alignment explanation
Indices: 5706--5809 Score: 63
Period size: 13 Copynumber: 8.0 Consensus size: 13
5696 GGCTTCATTT
5706 TTATTTATTATTA
1 TTATTTATTATTA
* *
5719 ATATTAATTATTA
1 TTATTTATTATTA
* *
5732 TTA-TTAATAATA
1 TTATTTATTATTA
*
5744 TT-TTTATTAATAA
1 TTATTTATT-ATTA
*
5757 TTATTAATGTTATTA
1 TTATT--TATTATTA
*
5772 TTA-TCATTATTTA
1 TTATTTATTA-TTA
*
5785 TTATTTATCATTA
1 TTATTTATTATTA
*
5798 TTA-ATATTATTA
1 TTATTTATTATTA
5810 ATATATAACC
Statistics
Matches: 67, Mismatches: 17, Indels: 15
0.68 0.17 0.15
Matches are distributed among these distances:
12 22 0.33
13 29 0.43
14 7 0.10
15 6 0.09
16 3 0.04
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.60
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:5810 original size:9 final size:9
Alignment explanation
Indices: 5711--5813 Score: 86
Period size: 9 Copynumber: 11.3 Consensus size: 9
5701 CATTTTTATT
5711 TATTATTAA
1 TATTATTAA
*
5720 TATTAATTAT
1 TATT-ATTAA
5730 TATTATTAA
1 TATTATTAA
*
5739 TAATATT--
1 TATTATTAA
5746 T-TTATTAA
1 TATTATTAA
5754 TAATTATTAA
1 T-ATTATTAA
* *
5764 TGTTATTAT
1 TATTATTAA
* *
5773 TATCATTATT
1 TATTATTA-A
*
5783 TATTATTTA
1 TATTATTAA
5792 TCATTATTAA
1 T-ATTATTAA
5802 TATTATTAA
1 TATTATTAA
5811 TAT
1 TAT
5814 ATAACCTTAT
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
6 4 0.05
7 1 0.01
8 1 0.01
9 38 0.51
10 31 0.41
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (9 bp):
TATTATTAA
Done.