Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011624.1 Kokia drynarioides strain JFW-HI SEQ_126615, 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: 80020
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 29 characters in sequence are not A, C, G, or T
Found at i:3116 original size:16 final size:16
Alignment explanation
Indices: 3076--3119 Score: 67
Period size: 14 Copynumber: 2.9 Consensus size: 16
3066 TAAATGATTT
3076 TAAAATTATTAAAA-A
1 TAAAATTATTAAAATA
3091 -AAAATT-TTAAAATA
1 TAAAATTATTAAAATA
3105 TAAAATTATTAAAAT
1 TAAAATTATTAAAAT
3120 TATTTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.23
14 7 0.27
15 6 0.23
16 7 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAAATTATTAAAATA
Found at i:3127 original size:29 final size:31
Alignment explanation
Indices: 3076--3144 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 31
3066 TAAATGATTT
3076 TAAAATTATTAAAAAAA-AATTTTAAAAT-A
1 TAAAATTATTAAAAAAATAATTTTAAAATAA
** ** *
3105 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATTAAAAAAATAATTTTAAAATAA
3136 TAAAATTAT
1 TAAAATTAT
3145 AGAATAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 15 0.45
30 8 0.24
31 10 0.30
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (31 bp):
TAAAATTATTAAAAAAATAATTTTAAAATAA
Found at i:3155 original size:30 final size:30
Alignment explanation
Indices: 3076--3155 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
3066 TAAATGATTT
***
3076 TAAAATTATTAAAA-AAAAATTTTAAAATA
1 TAAAATTATTAAAATAATTTTTTTAAAATA
* *
3105 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATTAAAATAATTTTTTTAAAAT-A
*
3136 TAAAATTA-TAGAATAATTTT
1 TAAAATTATTAAAATAATTTT
3156 AATTTCCAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 14 0.33
30 19 0.45
31 9 0.21
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (30 bp):
TAAAATTATTAAAATAATTTTTTTAAAATA
Found at i:8324 original size:28 final size:28
Alignment explanation
Indices: 8293--8430 Score: 116
Period size: 28 Copynumber: 5.2 Consensus size: 28
8283 CTGGCTAGTT
*
8293 TAAACGCATATGTATAAGCTGACAAGCG
1 TAAACGCATATGTATAAGCTGACGAGCG
* * *
8321 T-AA---ATGTGTACAAGCT-AGTGAGCG
1 TAAACGCATATGTATAAGCTGA-CGAGCG
*
8345 TAAACACATATGTATAAGCTGACGAGCG
1 TAAACGCATATGTATAAGCTGACGAGCG
**
8373 TAAACG----TGTGCAAGCT-AGCGAGCG
1 TAAACGCATATGTATAAGCTGA-CGAGCG
*
8397 TAAACGCATAAGTATAAGCTGACGAGCG
1 TAAACGCATATGTATAAGCTGACGAGCG
8425 TAAACG
1 TAAACG
8431 TGTGCAAGCT
Statistics
Matches: 85, Mismatches: 13, Indels: 24
0.70 0.11 0.20
Matches are distributed among these distances:
23 2 0.02
24 36 0.42
25 2 0.02
27 2 0.02
28 41 0.48
29 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.20
Consensus pattern (28 bp):
TAAACGCATATGTATAAGCTGACGAGCG
Found at i:8344 original size:24 final size:24
Alignment explanation
Indices: 8317--8457 Score: 106
Period size: 24 Copynumber: 5.5 Consensus size: 24
8307 TAAGCTGACA
* *
8317 AGCGTAAATGTGTACAAGCTAGTG
1 AGCGTAAACGTGTACAAGCTAGCG
* *
8341 AGCGTAAACACATATGTATAAGCT-GACG
1 AGCGT-AA-AC--GTGTACAAGCTAG-CG
*
8369 AGCGTAAACGTGTGCAAGCTAGCG
1 AGCGTAAACGTGTACAAGCTAGCG
*
8393 AGCGTAAACGCATAAGTATAAGCT-GACG
1 AGCGTAAACG--T--GTACAAGCTAG-CG
* *
8421 AGCGTAAACGTGTGCAAGCTAGTG
1 AGCGTAAACGTGTACAAGCTAGCG
8445 AGCGTAAACGTGT
1 AGCGTAAACGTGT
8458 GTTTATACAT
Statistics
Matches: 93, Mismatches: 12, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
24 46 0.49
25 4 0.04
26 5 0.05
27 4 0.04
28 34 0.37
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (24 bp):
AGCGTAAACGTGTACAAGCTAGCG
Found at i:8349 original size:52 final size:52
Alignment explanation
Indices: 8293--8454 Score: 270
Period size: 52 Copynumber: 3.1 Consensus size: 52
8283 CTGGCTAGTT
* * *
8293 TAAACGCATATGTATAAGCTGACAAGCGTAAATGTGTACAAGCTAGTGAGCG
1 TAAACGCATATGTATAAGCTGACGAGCGTAAACGTGTGCAAGCTAGTGAGCG
* *
8345 TAAACACATATGTATAAGCTGACGAGCGTAAACGTGTGCAAGCTAGCGAGCG
1 TAAACGCATATGTATAAGCTGACGAGCGTAAACGTGTGCAAGCTAGTGAGCG
*
8397 TAAACGCATAAGTATAAGCTGACGAGCGTAAACGTGTGCAAGCTAGTGAGCG
1 TAAACGCATATGTATAAGCTGACGAGCGTAAACGTGTGCAAGCTAGTGAGCG
8449 TAAACG
1 TAAACG
8455 TGTGTTTATA
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 102 1.00
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.20
Consensus pattern (52 bp):
TAAACGCATATGTATAAGCTGACGAGCGTAAACGTGTGCAAGCTAGTGAGCG
Found at i:10885 original size:16 final size:17
Alignment explanation
Indices: 10853--10885 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
10843 CACAATTAAG
10853 CTTAATTAACCTCTTTAC
1 CTTAATTAA-CTCTTTAC
10871 CTTAATTAA-TCTTTA
1 CTTAATTAACTCTTTA
10886 TTGTAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (17 bp):
CTTAATTAACTCTTTAC
Found at i:15580 original size:3 final size:3
Alignment explanation
Indices: 15572--15612 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
15562 GGATTTTAGT
15572 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
15613 GGGATTGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:18775 original size:3 final size:3
Alignment explanation
Indices: 18767--18822 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
18757 AAATAGATAC
18767 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
18815 ATA ATA AT
1 ATA ATA AT
18823 GTTAACATAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:28752 original size:24 final size:24
Alignment explanation
Indices: 28725--28773 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
28715 AGTCATATAA
28725 CTTAGTCATTCAACACAATTTAGT
1 CTTAGTCATTCAACACAATTTAGT
28749 CTTAGTCATTCAACACAATTTAGT
1 CTTAGTCATTCAACACAATTTAGT
28773 C
1 C
28774 CTTTTTGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (24 bp):
CTTAGTCATTCAACACAATTTAGT
Found at i:30389 original size:3 final size:3
Alignment explanation
Indices: 30376--30453 Score: 142
Period size: 3 Copynumber: 26.7 Consensus size: 3
30366 GGATTTCAGT
30376 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30422 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
30454 GGGATTGTAA
Statistics
Matches: 73, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 4 0.05
3 69 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:37980 original size:6 final size:6
Alignment explanation
Indices: 37969--37994 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
37959 CTTTTATGGG
37969 GTGGAA GTGGAA GTGGAA GTGGAA GT
1 GTGGAA GTGGAA GTGGAA GTGGAA GT
37995 TCATTTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.50, T:0.19
Consensus pattern (6 bp):
GTGGAA
Found at i:40041 original size:21 final size:19
Alignment explanation
Indices: 40001--40052 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
39991 AATTTTTTAT
*
40001 ATATTTATTTTATTATTTA
1 ATATTTATTTTATTAATTA
40020 ATATTTATTTTATAATAATTA
1 ATATTTATTTTAT--TAATTA
40041 AT-TTATATTTTA
1 ATATT-TATTTTA
40053 AGTGGTGTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 13 0.45
20 2 0.07
21 14 0.48
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATATTTATTTTATTAATTA
Found at i:40588 original size:2 final size:2
Alignment explanation
Indices: 40581--40613 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
40571 TATTCTTTTA
40581 AT 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 AT A
40614 ATTTCATAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45244 original size:24 final size:24
Alignment explanation
Indices: 45211--45256 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
45201 TTCGTAGGTC
*
45211 AAATAGATTATGCTAATAAATATA
1 AAATAGATTATACTAATAAATATA
* *
45235 AAATATATTATATTAATAAATA
1 AAATAGATTATACTAATAAATA
45257 CTAATTCTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATAGATTATACTAATAAATATA
Found at i:47433 original size:15 final size:15
Alignment explanation
Indices: 47413--47441 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
47403 AGTCATGGGA
47413 AATAATAATTAAATT
1 AATAATAATTAAATT
47428 AATAATAATTAAAT
1 AATAATAATTAAAT
47442 ATAAAAAAGA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATAATAATTAAATT
Found at i:49559 original size:50 final size:50
Alignment explanation
Indices: 49483--49744 Score: 308
Period size: 50 Copynumber: 5.2 Consensus size: 50
49473 AACTTTAGGT
*
49483 GTATAAGATTCGCCCTTGCGGCTTCAATCTGCCCCTCTACAGCTTCAGGA
1 GTATAAGATTCGCCATTGCGGCTTCAATCTGCCCCTCTACAGCTTCAGGA
* * * * * *
49533 GTACAAGATTGGCCATTGCAGTTTCAATCTGCCCCTTTATAGCTTCAGGA
1 GTATAAGATTCGCCATTGCGGCTTCAATCTGCCCCTCTACAGCTTCAGGA
* * * *
49583 GTATAAGATTCGCCATTGCGGCTTTAATCTACTCCTCTTCCAGCTTCAGGA
1 GTATAAGATTCGCCATTGCGGCTTCAATCTGCCCCTC-TACAGCTTCAGGA
* * * * * *
49634 GTATAAGATTCACCCTTGTGGCTTCAATCTGCCCCTCTACAACTTTAGGT
1 GTATAAGATTCGCCATTGCGGCTTCAATCTGCCCCTCTACAGCTTCAGGA
* * * * * *
49684 GTATGAGATTCACCATTGCGGCTTCAATCTGCTCGTCTACAGCTTTAGGG
1 GTATAAGATTCGCCATTGCGGCTTCAATCTGCCCCTCTACAGCTTCAGGA
49734 GTATAAGATTC
1 GTATAAGATTC
49745 ATTGTTTTGT
Statistics
Matches: 176, Mismatches: 35, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
50 134 0.76
51 42 0.24
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.32
Consensus pattern (50 bp):
GTATAAGATTCGCCATTGCGGCTTCAATCTGCCCCTCTACAGCTTCAGGA
Found at i:49660 original size:101 final size:100
Alignment explanation
Indices: 49451--49745 Score: 329
Period size: 101 Copynumber: 2.9 Consensus size: 100
49441 TCGCCTTCGT
* * * * * * *
49451 AGCTTCAATCTACCCTTCTTCCAACTTTAGGTGTATAAGATTCGCCCTTGCGGCTTCAATCTGCC
1 AGCTTCAATCTGCCCCTC-TACAACTTCAGGAGTATAAGATTCGCCATTGCGGCTTCAATCTGCT
* **
49516 CCTCTACAGCTTCAGGAGTACAAGATTGGCCATTGC
65 CCTCTACAGCTTCAGGAGTATAAGATTCACCATTGC
* * * * * *
49552 AGTTTCAATCTGCCCCTTTATAGCTTCAGGAGTATAAGATTCGCCATTGCGGCTTTAATCTACTC
1 AGCTTCAATCTGCCCCTCTACAACTTCAGGAGTATAAGATTCGCCATTGCGGCTTCAATCTGCTC
* * *
49617 CTCTTCCAGCTTCAGGAGTATAAGATTCACCCTTGT
66 CTC-TACAGCTTCAGGAGTATAAGATTCACCATTGC
* * * * *
49653 GGCTTCAATCTGCCCCTCTACAACTTTAGGTGTATGAGATTCACCATTGCGGCTTCAATCTGCTC
1 AGCTTCAATCTGCCCCTCTACAACTTCAGGAGTATAAGATTCGCCATTGCGGCTTCAATCTGCTC
* * *
49718 GTCTACAGCTTTAGGGGTATAAGATTCA
66 CTCTACAGCTTCAGGAGTATAAGATTCA
49746 TTGTTTTGTC
Statistics
Matches: 159, Mismatches: 34, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
100 63 0.40
101 96 0.60
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (100 bp):
AGCTTCAATCTGCCCCTCTACAACTTCAGGAGTATAAGATTCGCCATTGCGGCTTCAATCTGCTC
CTCTACAGCTTCAGGAGTATAAGATTCACCATTGC
Found at i:49712 original size:151 final size:151
Alignment explanation
Indices: 49452--49744 Score: 381
Period size: 151 Copynumber: 1.9 Consensus size: 151
49442 CGCCTTCGTA
* * *
49452 GCTTCAATCTACCCTTCTTCCAACTTTAGGTGTATAAGATTCGCCCTTGCGGCTTCAATCTGCCC
1 GCTTCAATCTACCCTTCTTCCAACTTCAGGAGTATAAGATTCACCCTTGCGGCTTCAATCTGCCC
* ** * * *
49517 CTCTACAGCTTCAGGAGTACAAGATTGGCCATTGCAGTTTCAATCTGCCCCTTTATAGCTTCAGG
66 CTCTACAACTTCAGGAGTACAAGATTCACCATTGCAGCTTCAATCTGCCCCTCTACAGCTTCAGG
49582 AGTATAAGATTCGCCATTGCG
131 AGTATAAGATTCGCCATTGCG
* * *
49603 GCTTTAATCTACTCC-TCTTCCAGCTTCAGGAGTATAAGATTCACCCTTGTGGCTTCAATCTGCC
1 GCTTCAATCTAC-CCTTCTTCCAACTTCAGGAGTATAAGATTCACCCTTGCGGCTTCAATCTGCC
* * ** * * * *
49667 CCTCTACAACTTTAGGTGTATGAGATTCACCATTGCGGCTTCAATCTGCTCGTCTACAGCTTTAG
65 CCTCTACAACTTCAGGAGTACAAGATTCACCATTGCAGCTTCAATCTGCCCCTCTACAGCTTCAG
*
49732 GGGTATAAGATTC
130 GAGTATAAGATTC
49745 ATTGTTTTGT
Statistics
Matches: 120, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
151 118 0.98
152 2 0.02
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (151 bp):
GCTTCAATCTACCCTTCTTCCAACTTCAGGAGTATAAGATTCACCCTTGCGGCTTCAATCTGCCC
CTCTACAACTTCAGGAGTACAAGATTCACCATTGCAGCTTCAATCTGCCCCTCTACAGCTTCAGG
AGTATAAGATTCGCCATTGCG
Found at i:49986 original size:50 final size:50
Alignment explanation
Indices: 49926--50028 Score: 170
Period size: 50 Copynumber: 2.1 Consensus size: 50
49916 TTATTTTTTA
* * *
49926 GTCCTTAGGTCGTCATTGATCGACTTTTGTCTAAGTTTTAACACTGATGT
1 GTCCTTAGGTCATCATTGATCGACTTTTGCCTAAGTTCTAACACTGATGT
*
49976 GTCCTTAGGTCATCATTGATCGTCTTTTGCCTAAGTTCTAACACTGATGT
1 GTCCTTAGGTCATCATTGATCGACTTTTGCCTAAGTTCTAACACTGATGT
50026 GTC
1 GTC
50029 ACCATGCCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.41
Consensus pattern (50 bp):
GTCCTTAGGTCATCATTGATCGACTTTTGCCTAAGTTCTAACACTGATGT
Found at i:60235 original size:87 final size:86
Alignment explanation
Indices: 60123--60296 Score: 330
Period size: 87 Copynumber: 2.0 Consensus size: 86
60113 CTAAAACCTT
60123 CTCAATGCCATCATCGAAGAAATTCAGAGATAGTGAAGTCCGAGGAGCAATCTATTTCGGCTTTT
1 CTCAATGCCATCATCGAAGAAATTCAGAGATAGTGAAGTCCGAGGAGCAATCTATTTCGGCTTTT
60188 TGAGTAGGAGCAGATCAAGAC
66 TGAGTAGGAGCAGATCAAGAC
*
60209 CNTCAATGCCATCATCGAAGAAATTCAGAGATAGTGAAGTCCGAGGAGCAGTCTATTTCGGCTTT
1 C-TCAATGCCATCATCGAAGAAATTCAGAGATAGTGAAGTCCGAGGAGCAATCTATTTCGGCTTT
60274 TTGAGTAGGAGCAGATCAAGAC
65 TTGAGTAGGAGCAGATCAAGAC
60296 C
1 C
60297 ACCGGAATCC
Statistics
Matches: 86, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
86 1 0.01
87 85 0.99
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (86 bp):
CTCAATGCCATCATCGAAGAAATTCAGAGATAGTGAAGTCCGAGGAGCAATCTATTTCGGCTTTT
TGAGTAGGAGCAGATCAAGAC
Done.