Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010948.1 Kokia drynarioides strain JFW-HI SEQ_125916, 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: 50859
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
Found at i:1826 original size:29 final size:29
Alignment explanation
Indices: 1794--1955 Score: 87
Period size: 29 Copynumber: 5.5 Consensus size: 29
1784 ATTTTGTATC
1794 ATTTTGGTAAATAATATGATGGAGATATT
1 ATTTTGGTAAATAATATGATGGAGATATT
** * ** ** *
1823 ATTTTCATAATTAATTATTTTTTATAT-TAT
1 ATTTTGGTAAATAA-TATGATGGAGATAT-T
*
1853 ATTTTGGTCAATAATATGATGG-GAATATT
1 ATTTTGGTAAATAATATGATGGAG-ATATT
* ** ** *
1882 ATTTTGGTAATTAATTATTTTTTATAT-TAT
1 ATTTTGGTAAATAA-TATGATGGAGATAT-T
* *
1912 ATTTTGGTCAATAATATGATGGGGATATT
1 ATTTTGGTAAATAATATGATGGAGATATT
* *
1941 ATTTTGATAATTAAT
1 ATTTTGGTAAATAAT
1956 TATTTTTTAT
Statistics
Matches: 90, Mismatches: 35, Indels: 16
0.64 0.25 0.11
Matches are distributed among these distances:
29 51 0.57
30 39 0.43
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.51
Consensus pattern (29 bp):
ATTTTGGTAAATAATATGATGGAGATATT
Found at i:1866 original size:59 final size:58
Alignment explanation
Indices: 1794--1976 Score: 312
Period size: 59 Copynumber: 3.1 Consensus size: 58
1784 ATTTTGTATC
* *
1794 ATTTTGGTAAATAATATGATGGAGATATTATTTTCATAATTAATTATTTTTTATATTAT
1 ATTTTGGTCAATAATATGATGG-GATATTATTTTGATAATTAATTATTTTTTATATTAT
*
1853 ATTTTGGTCAATAATATGATGGGAATATTATTTTGGTAATTAATTATTTTTTATATTAT
1 ATTTTGGTCAATAATATGATGGG-ATATTATTTTGATAATTAATTATTTTTTATATTAT
1912 ATTTTGGTCAATAATATGATGGGGATATTATTTTGATAATTAATTATTTTTTATATTAT
1 ATTTTGGTCAATAATATGAT-GGGATATTATTTTGATAATTAATTATTTTTTATATTAT
1971 ATTTTG
1 ATTTTG
1977 AAAATTAATT
Statistics
Matches: 118, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
58 1 0.01
59 114 0.97
60 3 0.03
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.53
Consensus pattern (58 bp):
ATTTTGGTCAATAATATGATGGGATATTATTTTGATAATTAATTATTTTTTATATTAT
Found at i:1882 original size:31 final size:31
Alignment explanation
Indices: 1846--1942 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 31
1836 ATTATTTTTT
1846 ATATTATATTTTGGTCAATAATATGATGGGA
1 ATATTATATTTTGGTCAATAATATGATGGGA
****
1877 ATA-T-TATTTTGGT-AATTAAT-T-ATTTTTT
1 ATATTATATTTTGGTCAA-TAATATGA-TGGGA
*
1905 ATATTATATTTTGGTCAATAATATGATGGGG
1 ATATTATATTTTGGTCAATAATATGATGGGA
1936 ATATTAT
1 ATATTAT
1943 TTTGATAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
27 1 0.02
28 7 0.14
29 14 0.27
30 14 0.27
31 14 0.27
32 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.49
Consensus pattern (31 bp):
ATATTATATTTTGGTCAATAATATGATGGGA
Found at i:1917 original size:30 final size:30
Alignment explanation
Indices: 1830--1987 Score: 107
Period size: 30 Copynumber: 5.3 Consensus size: 30
1820 ATTATTTTCA
1830 TAATTAATTATTTTTTATATTATATTTTGG
1 TAATTAATTATTTTTTATATTATATTTTGG
* ***
1860 TCAA-TAA-TATGATGGGA-A-TATTATTTTGG
1 T-AATTAATTAT-TTTTTATATTA-TATTTTGG
1889 TAATTAATTATTTTTTATATTATATTTTGG
1 TAATTAATTATTTTTTATATTATATTTTGG
**** *
1919 TCAA-TAA-TATGATGGGGATA-T-TATTTTGA
1 T-AATTAATTAT--TTTTTATATTATATTTTGG
*
1948 TAATTAATTATTTTTTATATTATATTTTGA
1 TAATTAATTATTTTTTATATTATATTTTGG
*
1978 AAATTAATTA
1 TAATTAATTA
1988 GCCAAGTTTA
Statistics
Matches: 96, Mismatches: 18, Indels: 28
0.68 0.13 0.20
Matches are distributed among these distances:
28 10 0.10
29 33 0.34
30 43 0.45
31 10 0.10
ACGTcount: A:0.34, C:0.01, G:0.11, T:0.54
Consensus pattern (30 bp):
TAATTAATTATTTTTTATATTATATTTTGG
Found at i:1959 original size:16 final size:16
Alignment explanation
Indices: 1938--1987 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1928 TGATGGGGAT
1938 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
1954 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
1969 A-TATTTTGAAAATTA
1 ATTATTTTGATAATTA
1984 ATTA
1 ATTA
1988 GCCAAGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
14 9 0.33
15 5 0.19
16 13 0.48
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:2272 original size:20 final size:21
Alignment explanation
Indices: 2247--2289 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2237 TACTTACTAC
2247 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
2267 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
2288 TA
1 TA
2290 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:2647 original size:9 final size:9
Alignment explanation
Indices: 2633--2673 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
2623 TATTTTTTTT
2633 TTCTTCTCC
1 TTCTTCTCC
2642 TTCTTC-CC
1 TTCTTCTCC
2650 TTTCTTCTCC
1 -TTCTTCTCC
2660 TTC-T-TCC
1 TTCTTCTCC
2667 TTCTTCT
1 TTCTTCT
2674 TTCTTTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
7 6 0.21
8 4 0.14
9 16 0.57
10 2 0.07
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (9 bp):
TTCTTCTCC
Found at i:2655 original size:18 final size:18
Alignment explanation
Indices: 2632--2666 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2622 TTATTTTTTT
2632 TTTCTTCTCCTTCTTCCC
1 TTTCTTCTCCTTCTTCCC
2650 TTTCTTCTCCTTCTTCC
1 TTTCTTCTCCTTCTTCC
2667 TTCTTCTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTCTTCTCCTTCTTCCC
Found at i:2677 original size:4 final size:4
Alignment explanation
Indices: 2649--2712 Score: 62
Period size: 4 Copynumber: 16.2 Consensus size: 4
2639 TCCTTCTTCC
* *
2649 CTTT CTTCT CCTT C-TT CCTT C-TT CTTT CTTT CTTT CTTT CTTT CTCTT
1 CTTT CTT-T CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT-TT
*
2697 TTTT CTTT CTTT -TTT C
1 CTTT CTTT CTTT CTTT C
2713 CTTCATTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
3 9 0.17
4 37 0.71
5 6 0.12
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:2696 original size:25 final size:25
Alignment explanation
Indices: 2632--2712 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
2622 TTATTTTTTT
*
2632 TTTC-TTCTCCTTCTTCCCTTTCTTCTC
1 TTTCTTTCT-CTTCTT-TCTTTCTT-TC
* *
2659 CTTCTTCCTTCTTCTTTCTTTCTTTC
1 TTTCTTTC-TCTTCTTTCTTTCTTTC
*
2685 TTTCTTTCTCTTTTTTCTTTCTTT-
1 TTTCTTTCTCTTCTTTCTTTCTTTC
2709 TTTC
1 TTTC
2713 CTTCATTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
24 4 0.09
25 15 0.33
26 8 0.17
27 10 0.22
28 8 0.17
29 1 0.02
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTCTTTCTCTTCTTTCTTTCTTTC
Found at i:2709 original size:11 final size:11
Alignment explanation
Indices: 2667--2723 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
2657 TCCTTCTTCC
*
2667 TTCTTCTTTCT
1 TTCTTTTTTCT
2678 TTCTTTCTTTCTT
1 TTCTTT-TTTC-T
2691 TCTCTTTTTTCT
1 T-TCTTTTTTCT
*
2703 TTCTTTTTTCC
1 TTCTTTTTTCT
*
2714 TTCATTTTTC
1 TTCTTTTTTC
2724 ATTGGTCCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 23 0.57
12 6 0.15
13 6 0.15
14 5 0.12
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74
Consensus pattern (11 bp):
TTCTTTTTTCT
Found at i:3133 original size:15 final size:15
Alignment explanation
Indices: 3113--3141 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3103 TACCCATTAG
3113 TACCGCCATTTAGAA
1 TACCGCCATTTAGAA
3128 TACCGCCATTTAGA
1 TACCGCCATTTAGA
3142 GTTCTTCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (15 bp):
TACCGCCATTTAGAA
Found at i:14669 original size:23 final size:23
Alignment explanation
Indices: 14643--14741 Score: 110
Period size: 23 Copynumber: 4.3 Consensus size: 23
14633 ACTCGACCCG
14643 TTGACCGAATCAAA-TCGTTGACT
1 TTGACCGAATCAAACT-GTTGACT
* **
14666 TTGACTGAATTGAACTGTTGACT
1 TTGACCGAATCAAACTGTTGACT
* * *
14689 TTGATCAAATCAAACTATTGACT
1 TTGACCGAATCAAACTGTTGACT
* *
14712 TTGACCGAATCGAACCGTTGACT
1 TTGACCGAATCAAACTGTTGACT
14735 TTGACCG
1 TTGACCG
14742 TTGATTGTTG
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 60 0.98
24 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (23 bp):
TTGACCGAATCAAACTGTTGACT
Found at i:20352 original size:22 final size:21
Alignment explanation
Indices: 20327--20385 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
20317 TATCTAACTA
*
20327 TTAAATTATTATTCAAGATCAC
1 TTAAATTATTATTCAACA-CAC
*
20349 TT-AATTATTAATATCATCACAC
1 TTAAATTATT-AT-TCAACACAC
20371 TTAAATTATTATTCA
1 TTAAATTATTATTCA
20386 GTTTAATCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 10 0.31
22 11 0.34
23 11 0.34
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.44
Consensus pattern (21 bp):
TTAAATTATTATTCAACACAC
Found at i:20813 original size:2 final size:2
Alignment explanation
Indices: 20806--20836 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20796 CCATTTGCGC
20806 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20837 AGTGACGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23487 original size:10 final size:9
Alignment explanation
Indices: 23448--23511 Score: 51
Period size: 9 Copynumber: 7.0 Consensus size: 9
23438 AATTAATTTT
*
23448 TTAAAAATT
1 TTAAAAATA
23457 TTAAAAA-A
1 TTAAAAATA
*
23465 TCAAAAA-A
1 TTAAAAATA
23473 TTTAAAAATCA
1 -TTAAAAAT-A
*
23484 TTAAAATTA
1 TTAAAAATA
*
23493 TTTAAAATA
1 TTAAAAATA
23502 TATAAAAATA
1 T-TAAAAATA
23512 GTTTTTAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
8 7 0.16
9 22 0.50
10 14 0.32
11 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (9 bp):
TTAAAAATA
Found at i:23509 original size:20 final size:20
Alignment explanation
Indices: 23449--23510 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
23439 ATTAATTTTT
*
23449 TAAAAATT-TTAAAAAATC-
1 TAAAAATTATTTAAAAATCA
23467 -AAAAA--ATTTAAAAATCA
1 TAAAAATTATTTAAAAATCA
*
23484 TTAAAATTATTTAAAATAT-A
1 TAAAAATTATTTAAAA-ATCA
23504 TAAAAAT
1 TAAAAAT
23511 AGTTTTTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
16 9 0.26
17 5 0.14
18 4 0.11
20 15 0.43
21 2 0.06
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAATTATTTAAAAATCA
Found at i:26354 original size:23 final size:23
Alignment explanation
Indices: 26328--26377 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
26318 TAAATTTAAA
26328 GATGTAATTAAAATGATAATCAC
1 GATGTAATTAAAATGATAATCAC
26351 GATGTAATTAAAATGATAATCAC
1 GATGTAATTAAAATGATAATCAC
26374 GATG
1 GATG
26378 ATGTTTAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (23 bp):
GATGTAATTAAAATGATAATCAC
Found at i:27273 original size:21 final size:21
Alignment explanation
Indices: 27241--27294 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
27231 TCCCCTTCCT
27241 TTTGTA-ATATTACAATATAAA
1 TTTGTATA-ATTACAATATAAA
** *
27262 TTTGTATAATTACTTTTTAAA
1 TTTGTATAATTACAATATAAA
*
27283 GTTGTATAATTA
1 TTTGTATAATTA
27295 TTTTAAACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (21 bp):
TTTGTATAATTACAATATAAA
Found at i:27300 original size:19 final size:20
Alignment explanation
Indices: 27258--27301 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
27248 TATTACAATA
*
27258 TAAATTTGTATAATTACTTTT
1 TAAAGTTGTATAATTAC-TTT
27279 TAAAGTTGTATAATTA-TTT
1 TAAAGTTGTATAATTACTTT
27298 TAAA
1 TAAA
27302 CATTAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.32
21 15 0.68
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (20 bp):
TAAAGTTGTATAATTACTTT
Found at i:32902 original size:29 final size:28
Alignment explanation
Indices: 32847--32903 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
32837 AAAGAGAATT
32847 AAAACAATATTTAAAAAAAAAAAAAAAA
1 AAAACAATATTTAAAAAAAAAAAAAAAA
* * *
32875 AAAACAATATTTTAAAACAAAAAGAAAA
1 AAAACAATATTTAAAAAAAAAAAAAAAA
32903 A
1 A
32904 CTTACGTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (28 bp):
AAAACAATATTTAAAAAAAAAAAAAAAA
Found at i:36837 original size:18 final size:18
Alignment explanation
Indices: 36816--36850 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
36806 ATTTAGTAAA
36816 ATTTTATAATGATTTATG
1 ATTTTATAATGATTTATG
*
36834 ATTTTTTAATGATTTAT
1 ATTTTATAATGATTTAT
36851 TTAATAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (18 bp):
ATTTTATAATGATTTATG
Found at i:48173 original size:24 final size:24
Alignment explanation
Indices: 48146--48220 Score: 132
Period size: 24 Copynumber: 3.1 Consensus size: 24
48136 AGTTTGACTC
*
48146 AAACAAATAAACAGAGTTTAATTG
1 AAACAATTAAACAGAGTTTAATTG
48170 AAACAATTAAACAGAGTTTAATTG
1 AAACAATTAAACAGAGTTTAATTG
*
48194 AAACAATTAAACAGAGTTTAACTG
1 AAACAATTAAACAGAGTTTAATTG
48218 AAA
1 AAA
48221 TATTATTTGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.25
Consensus pattern (24 bp):
AAACAATTAAACAGAGTTTAATTG
Found at i:48381 original size:62 final size:62
Alignment explanation
Indices: 48306--48432 Score: 254
Period size: 62 Copynumber: 2.0 Consensus size: 62
48296 GCCAAAGCTC
48306 GTCACAGGCTTGCACACTATGCAGGGAATTAACTGAGTCGAATCTATGCTTAGAAGCTAGAA
1 GTCACAGGCTTGCACACTATGCAGGGAATTAACTGAGTCGAATCTATGCTTAGAAGCTAGAA
48368 GTCACAGGCTTGCACACTATGCAGGGAATTAACTGAGTCGAATCTATGCTTAGAAGCTAGAA
1 GTCACAGGCTTGCACACTATGCAGGGAATTAACTGAGTCGAATCTATGCTTAGAAGCTAGAA
48430 GTC
1 GTC
48433 TTCTAGCTTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (62 bp):
GTCACAGGCTTGCACACTATGCAGGGAATTAACTGAGTCGAATCTATGCTTAGAAGCTAGAA
Done.