Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014051.1 Kokia drynarioides strain JFW-HI SEQ_129082, 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: 3694
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1011 original size:30 final size:30
Alignment explanation
Indices: 975--1071 Score: 76
Period size: 30 Copynumber: 3.3 Consensus size: 30
965 AGAAATCATA
*
975 TTTTGACCCCTGAACTTTCTTAAATTCCAT
1 TTTTGACCCCTGAACTTTCATAAATTCCAT
* * * *
1005 TTTTGA-CCTTG-ATTTTCCCAAAAATTACAT
1 TTTTGACCCCTGAACTTT--CATAAATTCCAT
* *
1035 TTTT-TCCCC-GAACTTTCCTAAATTCCAT
1 TTTTGACCCCTGAACTTTCATAAATTCCAT
*
1063 TTTTTACCC
1 TTTTGACCC
1072 TATTTTTTTC
Statistics
Matches: 50, Mismatches: 12, Indels: 11
0.68 0.16 0.15
Matches are distributed among these distances:
28 17 0.34
29 8 0.16
30 25 0.50
ACGTcount: A:0.24, C:0.27, G:0.05, T:0.44
Consensus pattern (30 bp):
TTTTGACCCCTGAACTTTCATAAATTCCAT
Found at i:1089 original size:59 final size:58
Alignment explanation
Indices: 974--1130 Score: 192
Period size: 59 Copynumber: 2.7 Consensus size: 58
964 TAGAAATCAT
* *
974 ATTTTGACCCCTGAACTTTCTTAAATTCCATTTTTGACCTTGATTTTCCCAAAAATTAC
1 ATTTTTACCCC-GAACTTTCCTAAATTCCATTTTTGACCTTGATTTTCCCAAAAATTAC
* * * *
1033 ATTTTTTCCCCGAACTTTCCTAAATTCCATTTTTTACCCTAT-TTTTTTCCAAAAATTAC
1 ATTTTTACCCCGAACTTTCCTAAATTCCATTTTTGA-CCT-TGATTTTCCCAAAAATTAC
* *
1092 ATTTTTACCCTC-AACTTTCCAAAATTCCATTTTTAACCT
1 ATTTTTACCC-CGAACTTTCCTAAATTCCATTTTTGACCT
1131 CGAATTTAAA
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
58 26 0.30
59 58 0.67
60 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.03, T:0.45
Consensus pattern (58 bp):
ATTTTTACCCCGAACTTTCCTAAATTCCATTTTTGACCTTGATTTTCCCAAAAATTAC
Found at i:1111 original size:29 final size:29
Alignment explanation
Indices: 1022--1248 Score: 112
Period size: 29 Copynumber: 7.7 Consensus size: 29
1012 CTTGATTTTC
*
1022 CCAAAAATTACATTTTTTCCC-CGAACTTT
1 CCAAAAATTACATTTTTACCCTC-AACTTT
* * **
1051 CC-TAAATTCCATTTTTTACCCT-ATTTTTTT
1 CCAAAAATTACA-TTTTTACCCTCA--ACTTT
1081 CCAAAAATTACATTTTTACCCTCAACTTT
1 CCAAAAATTACATTTTTACCCTCAACTTT
* *
1110 CC-AAAATTCCATTTTTAACCTCGAA-TTT
1 CCAAAAATTACATTTTTACCCTC-AACTTT
** * **
1138 AAAAAAAAATACCA-TTTTACCCTCAAAATT
1 -CCAAAAATTA-CATTTTTACCCTCAACTTT
* * *
1168 CCAAAAATTTCATTTTTAACCTCGA-TTCCT
1 CCAAAAATTACATTTTTACCCTCAACTT--T
* **
1198 CCAAAAATGACCA-TTTTACACCGGAAC-TT
1 CCAAAAATTA-CATTTTTAC-CCTCAACTTT
*
1227 CCAAAAATTCCATTTTTGACCC
1 CCAAAAATTACATTTTT-ACCC
1249 GAATTTTTCA
Statistics
Matches: 147, Mismatches: 32, Indels: 38
0.68 0.15 0.18
Matches are distributed among these distances:
28 34 0.23
29 50 0.34
30 47 0.32
31 16 0.11
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (29 bp):
CCAAAAATTACATTTTTACCCTCAACTTT
Found at i:1126 original size:28 final size:28
Alignment explanation
Indices: 1025--1131 Score: 92
Period size: 28 Copynumber: 3.7 Consensus size: 28
1015 GATTTTCCCA
*
1025 AAAATTACATTTTTTCCC-CGAACTTTCC
1 AAAATTACATTTTTACCCTC-AACTTTCC
* * **
1053 TAAATTCCATTTTTTACCCT-ATTTTTTTCC
1 AAAATTACA-TTTTTACCCTCA--ACTTTCC
1083 AAAAATTACATTTTTACCCTCAACTTTCC
1 -AAAATTACATTTTTACCCTCAACTTTCC
* *
1112 AAAATTCCATTTTTAACCTC
1 AAAATTACATTTTTACCCTC
1132 GAATTTAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
28 26 0.42
29 13 0.21
30 15 0.24
31 8 0.13
ACGTcount: A:0.29, C:0.26, G:0.01, T:0.44
Consensus pattern (28 bp):
AAAATTACATTTTTACCCTCAACTTTCC
Found at i:1143 original size:28 final size:28
Alignment explanation
Indices: 1082--1254 Score: 88
Period size: 28 Copynumber: 6.0 Consensus size: 28
1072 TATTTTTTTC
* *
1082 CAAAAATTACATTTTTACCCTC-AACTTT
1 CAAAAATTCCATTTTTAACCTCGAA-TTT
*
1110 CCAAAATTCCATTTTTAACCTCGAATTT
1 CAAAAATTCCATTTTTAACCTCGAATTT
* * * * *
1138 AAAAAAAAATACCA-TTTTACCCTCAAAATTC
1 ---CAAAAATTCCATTTTTAACCTC-GAATTT
*
1169 CAAAAATTTCATTTTTAACCTCG-ATTCCT
1 CAAAAATTCCATTTTTAACCTCGAATT--T
* * *
1198 CCAAAAATGACCA-TTTTACACC-GGAACTTC
1 -CAAAAAT-TCCATTTTTA-ACCTCGAA-TTT
*
1228 CAAAAATTCCATTTTTGACC-CGAATTT
1 CAAAAATTCCATTTTTAACCTCGAATTT
1255 TTCAAAAAAA
Statistics
Matches: 108, Mismatches: 23, Indels: 29
0.68 0.14 0.18
Matches are distributed among these distances:
27 5 0.05
28 39 0.36
29 22 0.20
30 22 0.20
31 18 0.17
32 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (28 bp):
CAAAAATTCCATTTTTAACCTCGAATTT
Found at i:1146 original size:59 final size:60
Alignment explanation
Indices: 1024--1193 Score: 170
Period size: 59 Copynumber: 2.9 Consensus size: 60
1014 TGATTTTCCC
* * * * * ****
1024 AAAAATTACATTTTTTCCC-CGAACTTTCCTAAATTCCATTTTTTACC-CTATTTTTTTCC
1 AAAAATTACATTTTTACCCTC-AACTTTCCAAAATTCCATTTTTAACCTCGATATTTAAAA
1083 AAAAATTACATTTTTACCCTCAACTTTCCAAAATTCCATTTTTAACCTCGA-ATTTAAAA
1 AAAAATTACATTTTTACCCTCAACTTTCCAAAATTCCATTTTTAACCTCGATATTTAAAA
** *
1142 AAAAA-TACCA-TTTTACCCTCAAAATTCCAAAAATTTCATTTTTAACCTCGAT
1 AAAAATTA-CATTTTTACCCTCAACTTTCC-AAAATTCCATTTTTAACCTCGAT
1194 TCCTCCAAAA
Statistics
Matches: 94, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
58 18 0.19
59 73 0.78
60 3 0.03
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.40
Consensus pattern (60 bp):
AAAAATTACATTTTTACCCTCAACTTTCCAAAATTCCATTTTTAACCTCGATATTTAAAA
Found at i:1204 original size:59 final size:59
Alignment explanation
Indices: 1054--1337 Score: 249
Period size: 59 Copynumber: 4.8 Consensus size: 59
1044 GAACTTTCCT
* * * * *
1054 AAATTCCATTTTTTACCCTATTTTTTTCCAAAAATTA-CATTTTTACCCTC-AACTTTCC-A
1 AAATTCCATTTTTAACCCGA-ATTCTTCCAAAAAATACCA-TTTTACCCTCAAAC-TTCCAA
*** *
1113 AAATTCCATTTTTAACCTCGAATT-TAAAAAAAAATACCATTTTACCCTCAAAATTCCAA
1 AAATTCCATTTTTAACC-CGAATTCTTCCAAAAAATACCATTTTACCCTCAAACTTCCAA
* * **
1172 AAATTTCATTTTTAACCTCG-ATTCCTCC-AAAAATGACCATTTTACACC-GGAACTTCCAA
1 AAATTCCATTTTTAACC-CGAATTCTTCCAAAAAAT-ACCATTTTAC-CCTCAAACTTCCAA
* * * *
1231 AAATTCCATTTTTGACCCGAATTTTTCAAAAAAATGACCATTTTACCCCCAAACTTCCAA
1 AAATTCCATTTTTAACCCGAATTCTTCCAAAAAAT-ACCATTTTACCCTCAAACTTCCAA
* * * * *
1291 AAAATCCATTTTTGACCCTAATTCTTCCAAAAAGTACCATATTACCC
1 AAATTCCATTTTTAACCCGAATTCTTCCAAAAAATACCATTTTACCC
1338 CCGAATGTCT
Statistics
Matches: 186, Mismatches: 29, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
58 33 0.18
59 93 0.50
60 60 0.32
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.35
Consensus pattern (59 bp):
AAATTCCATTTTTAACCCGAATTCTTCCAAAAAATACCATTTTACCCTCAAACTTCCAA
Found at i:1318 original size:30 final size:30
Alignment explanation
Indices: 1224--1323 Score: 98
Period size: 30 Copynumber: 3.3 Consensus size: 30
1214 TACACCGGAA
* *
1224 CTTCCAAAAATTCCATTTTTGACCCGAATT
1 CTTCCAAAAAATCCATTTTTGACCCCAATT
* * *
1254 TTTCAAAAAAATGACCA-TTTT-ACCCCCAA-A
1 CTTCCAAAAAAT--CCATTTTTGA-CCCCAATT
*
1284 CTTCCAAAAAATCCATTTTTGACCCTAATT
1 CTTCCAAAAAATCCATTTTTGACCCCAATT
1314 CTTCCAAAAA
1 CTTCCAAAAA
1324 GTACCATATT
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
28 3 0.05
29 9 0.16
30 31 0.56
31 9 0.16
32 3 0.05
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.32
Consensus pattern (30 bp):
CTTCCAAAAAATCCATTTTTGACCCCAATT
Found at i:1352 original size:119 final size:118
Alignment explanation
Indices: 1108--1364 Score: 290
Period size: 119 Copynumber: 2.2 Consensus size: 118
1098 ACCCTCAACT
* *
1108 TTCC-AAAATTCCATTTTTAACCTCGAATTTAAAAAAAAATACCATTTTACCCTCAAAATTCCAA
1 TTCCAAAAATTCCATTTTTGACCTCGAATTTAAAAAAAAATACCATTTTACCCCCAAAATTCCAA
* * * * *
1172 AAATTTCATTTTTAACCTCGATTCCTCCAAAAATGACCATTTTACACCGGAAC
66 AAAATCCATTTTTAACCTCAATTCCTCCAAAAATGACCATATTACACCCGAAC
** *
1225 TTCCAAAAATTCCATTTTTGACC-CGAATTTTTCAAAAAAATGACCATTTTACCCCCAAACTTCC
1 TTCCAAAAATTCCATTTTTGACCTCGAA-TTTAAAAAAAAAT-ACCATTTTACCCCCAAAATTCC
* * *
1289 AAAAAATCCATTTTTGACC-CTAATTCTTCCAAAAA-GTACCATATTACCCCCGAA-
64 AAAAAATCCATTTTTAACCTC-AATTCCTCCAAAAATG-ACCATATTACACCCGAAC
* * *
1343 TGTCTAAAAATTTCTTTTTTGA
1 T-TCCAAAAATTCCATTTTTGA
1365 TATCGAACTT
Statistics
Matches: 118, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
117 8 0.07
118 31 0.26
119 79 0.67
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (118 bp):
TTCCAAAAATTCCATTTTTGACCTCGAATTTAAAAAAAAATACCATTTTACCCCCAAAATTCCAA
AAAATCCATTTTTAACCTCAATTCCTCCAAAAATGACCATATTACACCCGAAC
Found at i:1439 original size:28 final size:28
Alignment explanation
Indices: 1377--1437 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
1367 TCGAACTTTC
*
1377 CCAAAATTACCATTTTACCTCCAAGTGT
1 CCAAAATTACCATTTTACCTCCAAGTAT
* *
1405 CCAAAATTACTATTTTACCT-CGAGTAT
1 CCAAAATTACCATTTTACCTCCAAGTAT
1432 CCAAAA
1 CCAAAA
1438 ATCTCATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 11 0.37
28 19 0.63
ACGTcount: A:0.36, C:0.26, G:0.07, T:0.31
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCTCCAAGTAT
Found at i:1446 original size:27 final size:29
Alignment explanation
Indices: 1377--1447 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
1367 TCGAACTTTC
* *
1377 CCAAAATTAC-CATTTTACCTCCAAGTGT
1 CCAAAAATACTCATTTTACCTCCAAGTAT
* *
1405 CCAAAATTACT-ATTTTACCT-CGAGTAT
1 CCAAAAATACTCATTTTACCTCCAAGTAT
1432 CCAAAAAT-CTCATTTT
1 CCAAAAATACTCATTTT
1448 CAACTCCGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
26 2 0.05
27 17 0.45
28 19 0.50
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.35
Consensus pattern (29 bp):
CCAAAAATACTCATTTTACCTCCAAGTAT
Found at i:2526 original size:17 final size:17
Alignment explanation
Indices: 2501--2534 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2491 AATAACTTCG
*
2501 CATGGTTTTTCAAAAAT
1 CATGGTTTTTAAAAAAT
*
2518 CATGTTTTTTAAAAAAT
1 CATGGTTTTTAAAAAAT
2535 GTCCGTGCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (17 bp):
CATGGTTTTTAAAAAAT
Found at i:3445 original size:30 final size:30
Alignment explanation
Indices: 3383--3691 Score: 263
Period size: 30 Copynumber: 10.3 Consensus size: 30
3373 AAAGTCAATC
* * * *
3383 TTTTGGAAAA-TTTGAGGTTGAAAATGTGA
1 TTTTGGAAAAGTTTAAGGGTCAAAATGTAA
* * *
3412 TTTTGGAGAAGTTTAACGGTCAAAATGCAA
1 TTTTGGAAAAGTTTAAGGGTCAAAATGTAA
*
3442 TTTTGGAAAAGTTTAAGGGTAAAAAT-TCAA
1 TTTTGGAAAAGTTTAAGGGTCAAAATGT-AA
*
3472 TTTTGGAAAAGTTTGAA-GGTTAAAATGTAA
1 TTTTGGAAAAGTTT-AAGGGTCAAAATGTAA
* * * **
3502 TTTTAGAGAAGTTT-AGAGGTTAAAAAATAA
1 TTTTGGAAAAGTTTAAG-GGTCAAAATGTAA
* *
3532 TTTTGGAAAAGTTTATGGGTTAAAATGTAA
1 TTTTGGAAAAGTTTAAGGGTCAAAATGTAA
*
3562 TTTTAGAAAAGTTTAAGGGTTC-AAATGTAA
1 TTTTGGAAAAGTTTAAGGG-TCAAAATGTAA
*
3592 TTTTAGAAAAGTTT-AGGTGTCAAAATGTAA
1 TTTTGGAAAAGTTTAAGG-GTCAAAATGTAA
* * * * **
3622 TTTT-TAGAAATTTTAGGGGTTAAAACATAA
1 TTTTGGA-AAAGTTTAAGGGTCAAAATGTAA
* * *
3652 TTTTGGACAATTTTAAGGGTTAAAATGTAA
1 TTTTGGAAAAGTTTAAGGGTCAAAATGTAA
*
3682 TTTTTGAAAA
1 TTTTGGAAAA
3692 ATT
Statistics
Matches: 230, Mismatches: 37, Indels: 25
0.79 0.13 0.09
Matches are distributed among these distances:
28 1 0.00
29 15 0.07
30 206 0.90
31 8 0.03
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.37
Consensus pattern (30 bp):
TTTTGGAAAAGTTTAAGGGTCAAAATGTAA
Found at i:3475 original size:60 final size:59
Alignment explanation
Indices: 3411--3691 Score: 300
Period size: 60 Copynumber: 4.7 Consensus size: 59
3401 TGAAAATGTG
* * * * *
3411 ATTTTGGAGAAGTTTAACGGTCAAAATGCAATTTTGGAAAAGTTTAAGGGTAAAAATTCA
1 ATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTAGAAAAGTTTAAGGGTAAAAATT-A
* * *
3471 ATTTTGGAAAAGTTTGAA-GGTTAAAATGTAATTTTAGAGAAGTTTAGAGGTTAAAAAATA
1 ATTTTGGAAAAGTTT-AAGGGTTAAAATGTAATTTTAGAAAAGTTTA-AGGGTAAAAATTA
* **
3531 ATTTTGGAAAAGTTTATGGGTTAAAATGTAATTTTAGAAAAGTTTAAGGGTTCAAATGTA
1 ATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTAGAAAAGTTTAAGGGTAAAAAT-TA
* * * *
3591 ATTTTAGAAAAGTTT-AGGTGTCAAAATGTAATTTTTAG-AAATTTTAGGGGTTAAAACA-TA
1 ATTTTGGAAAAGTTTAAGG-GTTAAAATGTAA-TTTTAGAAAAGTTTAAGGG-TAAAA-ATTA
* * *
3651 ATTTTGGACAATTTTAAGGGTTAAAATGTAATTTTTGAAAA
1 ATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTAGAAAA
3692 ATT
Statistics
Matches: 186, Mismatches: 25, Indels: 20
0.81 0.11 0.09
Matches are distributed among these distances:
59 15 0.08
60 146 0.78
61 24 0.13
62 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (59 bp):
ATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTAGAAAAGTTTAAGGGTAAAAATTA
Found at i:3487 original size:90 final size:88
Alignment explanation
Indices: 3383--3685 Score: 306
Period size: 90 Copynumber: 3.4 Consensus size: 88
3373 AAAGTCAATC
* * *
3383 TTTTGGAAAA-TTTGAGGTTGAAAATGTGATTTTGGAGAAGTTTAACGGTCAAAATGCAATTTTG
1 TTTTGGAAAAGTTTGAGGTT-AAAATGTAATTTTAGAGAAGTTTAA-GGTCAAAATGTAATTTTG
3447 GAAAAGTTTAAGGGTAAAAAT-TCAA
64 GAAAAGTTTAAGGGTAAAAATGT-AA
* **
3472 TTTTGGAAAAGTTTGAAGGTTAAAATGTAATTTTAGAGAAGTTTAGAGGTTAAAAAATAATTTTG
1 TTTTGGAAAAGTTTG-AGGTTAAAATGTAATTTTAGAGAAGTTTA-AGGTCAAAATGTAATTTTG
* *
3537 GAAAAGTTTATGGGTTAAAATGTAA
64 GAAAAGTTTAAGGGTAAAAATGTAA
* * * * *
3562 TTTTAGAAAAGTTTAAGGGTTCAAATGTAATTTTAGAAAAGTTTAGGTGTCAAAATGTAATTTT-
1 TTTTGGAAAAGTTTGA-GGTTAAAATGTAATTTTAGAGAAGTTTAAG-GTCAAAATGTAATTTTG
* * * * **
3626 TAGAAATTTTAGGGGTTAAAACATAA
64 GA-AAAGTTTAAGGGTAAAAATGTAA
* * *
3652 TTTTGGACAATTTTAAGGGTTAAAATGTAATTTT
1 TTTTGGAAAAGTTTGA-GGTTAAAATGTAATTTT
3686 TGAAAAATT
Statistics
Matches: 182, Mismatches: 25, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
89 13 0.07
90 162 0.89
91 7 0.04
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.37
Consensus pattern (88 bp):
TTTTGGAAAAGTTTGAGGTTAAAATGTAATTTTAGAGAAGTTTAAGGTCAAAATGTAATTTTGGA
AAAGTTTAAGGGTAAAAATGTAA
Done.