Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009664.1 Kokia drynarioides strain JFW-HI SEQ_124382, 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: 2745
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37
Found at i:747 original size:57 final size:57
Alignment explanation
Indices: 694--915 Score: 193
Period size: 57 Copynumber: 3.8 Consensus size: 57
684 CAATTTTTTT
* *
694 GTGTTGG-CTATCAAATGGTCGACACCCCCTTTTCTTGAAAAAAAATTGTATTTTTGG
1 GTGTTGGTC-ATCAAATGGCCGACACCCCCTTTTCTCGAAAAAAAATTGTATTTTTGG
*** * * *
751 GTGTTGGTCATTGCATGGTCGACACCCCCTTTT-TGAGAAAAAAAATT-TCAAAAATTTTT-T
1 GTGTTGGTCATCAAATGGCCGACACCCCCTTTTCT-CGAAAAAAAATTGT-----ATTTTTGG
* *
811 GTGTTGGTCATCAAATGGCCGATACCGCCC-TTTCTCGAAAAAAAATTGCATTTTTGG
1 GTGTTGGTCATCAAATGGCCGACACC-CCCTTTTCTCGAAAAAAAATTGTATTTTTGG
* *** *
868 GTGTTGGCCATTGCATGGCCGACATCCCCTTTTCTCGAGAAAAAAATT
1 GTGTTGGTCATCAAATGGCCGACACCCCCTTTTCTCGA-AAAAAAATT
916 TCAAAATTCC
Statistics
Matches: 133, Mismatches: 19, Indels: 25
0.75 0.11 0.14
Matches are distributed among these distances:
56 11 0.08
57 67 0.50
58 10 0.08
60 35 0.26
61 10 0.08
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (57 bp):
GTGTTGGTCATCAAATGGCCGACACCCCCTTTTCTCGAAAAAAAATTGTATTTTTGG
Found at i:824 original size:117 final size:118
Alignment explanation
Indices: 688--921 Score: 350
Period size: 117 Copynumber: 2.0 Consensus size: 118
678 AAAATACAAT
* * *
688 TTTTTTGTGTTGGCTATCAAATGGTCGACACC-CCCTTTTCTTGAAAAAAAATTGTATTTTTGGG
1 TTTTTTGTGTTGGCTATCAAATGGCCGACACCGCCC-TTTCTCGAAAAAAAATTGCATTTTTGGG
* *
752 TGTTGGTCATTGCATGGTCGACACCCCCTTTT-T-GAGAAAAAAAATTTCAAAAA
65 TGTTGGCCATTGCATGGCCGACACCCCCTTTTCTCGAG-AAAAAAATTTCAAAAA
*
805 TTTTTTGTGTTGG-TCATCAAATGGCCGATACCGCCCTTTCTCGAAAAAAAATTGCATTTTTGGG
1 TTTTTTGTGTTGGCT-ATCAAATGGCCGACACCGCCCTTTCTCGAAAAAAAATTGCATTTTTGGG
*
869 TGTTGGCCATTGCATGGCCGACATCCCCTTTTCTCGAGAAAAAAATTTCAAAA
65 TGTTGGCCATTGCATGGCCGACACCCCCTTTTCTCGAGAAAAAAATTTCAAAA
922 TTCCTTTTTC
Statistics
Matches: 106, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
116 1 0.01
117 83 0.78
118 19 0.18
119 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.35
Consensus pattern (118 bp):
TTTTTTGTGTTGGCTATCAAATGGCCGACACCGCCCTTTCTCGAAAAAAAATTGCATTTTTGGGT
GTTGGCCATTGCATGGCCGACACCCCCTTTTCTCGAGAAAAAAATTTCAAAAA
Found at i:989 original size:88 final size:89
Alignment explanation
Indices: 848--1009 Score: 265
Period size: 88 Copynumber: 1.8 Consensus size: 89
838 CCCTTTCTCG
* *
848 AAAAAAAATTGCATTTTTGGGTGTTGGCCATTGCATGGCCGACATCCCCTTTTCTC-GAGAAAAA
1 AAAAAAAATTACATTTTTGGGTGTTGGCCATTGCATGACCGACATCCCCTTTTCTCGGAGAAAAA
*
912 AATTTCAAAATTCCTTTTTCTCCA
66 AATTACAAAATTCCTTTTTCTCCA
*
936 AAAAAAAATTACATTTTTGGGTGTTGGCCATTGCATGACCGACA-CCCCATTTTCTCGGATAAAA
1 AAAAAAAATTACATTTTTGGGTGTTGGCCATTGCATGACCGACATCCCC-TTTTCTCGGAGAAAA
1000 AAATTACAAA
65 AAATTACAAA
1010 TTTTTTTGGT
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
87 4 0.06
88 49 0.72
89 15 0.22
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (89 bp):
AAAAAAAATTACATTTTTGGGTGTTGGCCATTGCATGACCGACATCCCCTTTTCTCGGAGAAAAA
AATTACAAAATTCCTTTTTCTCCA
Found at i:1079 original size:120 final size:117
Alignment explanation
Indices: 927--1288 Score: 507
Period size: 120 Copynumber: 3.0 Consensus size: 117
917 CAAAATTCCT
* *
927 TTTTCTCCAAAAAAAAATTACATTTTTGGGTGTTGGCCATTGCATGACCGACACCCCATTTTCTC
1 TTTTCT-CAAAAAAAAATT-CATTTTTTGGTGTTGGCCATTGCATGGCCGACACCCCATTTTCTC
992 GGATAAAAAAATTACAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC
64 -GATAAAAAAATTACAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC
1047 TTTTCTCAAAAAAAAAATTGCATTTTTTGGTGTTGGCCATTGCATGGCCGACACCCCATTTTCTC
1 TTTTCTC-AAAAAAAAATT-CATTTTTTGGTGTTGGCCATTGCATGGCCGACACCCCATTTTCTC
* *
1112 -A-AGAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC
64 GATA-AAAAAATTACAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC
* * * * *
1165 TTTT-TCGAAAAAAAATTCAAAATTTTTTGGTGTTGGTCA-TGCAATGGCCTACACCCCCTTTTT
1 TTTTCTCAAAAAAAAATTC---ATTTTTTGGTGTTGGCCATTGC-ATGGCCGACACCCCATTTTC
*
1228 TCGAATAAAAAAATTACAAATTTTTTTGATGTTGGCCATCAAATGGCCGACACCCCC
62 TCG-ATAAAAAAATTACAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC
1285 TTTT
1 TTTT
1289 TATTTGGTAA
Statistics
Matches: 220, Mismatches: 13, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
115 1 0.00
116 10 0.05
117 6 0.03
118 89 0.40
119 1 0.00
120 112 0.51
121 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (117 bp):
TTTTCTCAAAAAAAAATTCATTTTTTGGTGTTGGCCATTGCATGGCCGACACCCCATTTTCTCGA
TAAAAAAATTACAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC
Found at i:1086 original size:58 final size:58
Alignment explanation
Indices: 927--1288 Score: 390
Period size: 58 Copynumber: 6.1 Consensus size: 58
917 CAAAATTCCT
* *** * *
927 TTTTCTCCAAAAAAAAATTAC-ATTTTTGGGTGTTGGCCATTGCATGACCGACACCCCA
1 TTTTCT-CAAAAAAAAATTACAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC
*
985 TTTTCTCGGATAAAAAAATTACAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC
1 TTTTCTC--AAAAAAAAATTAC-AA-TTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC
* *** *
1047 TTTTCTCAAAAAAAAAATTGC-ATTTTTTGGTGTTGGCCATTGCATGGCCGACACCCCA
1 TTTTCTC-AAAAAAAAATTACAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC
* *
1105 TTTTCTCAAGAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC
1 TTTTCTCAA-AAAAAAATT-ACAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC
* * * *
1165 TTTT-TCGAAAAAAAATTCAAAATTTTTTGGTGTTGGTCATGC-AATGGCCTACACCCCC
1 TTTTCTCAAAAAAAAATT-ACAATTTTTTGGTGTTGGCCAT-CAAATGGCCGACACCCCC
* *
1223 TTTTTTCGAATAAAAAAATTACAAATTTTTTTGATGTTGGCCATCAAATGGCCGACACCCCC
1 TTTTCTC-AA-AAAAAAATTAC-AA-TTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC
1285 TTTT
1 TTTT
1289 TATTTGGTAA
Statistics
Matches: 259, Mismatches: 30, Indels: 26
0.82 0.10 0.08
Matches are distributed among these distances:
57 3 0.01
58 102 0.39
59 19 0.07
60 39 0.15
61 24 0.09
62 72 0.28
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (58 bp):
TTTTCTCAAAAAAAAATTACAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC
Found at i:1338 original size:59 final size:58
Alignment explanation
Indices: 938--1340 Score: 348
Period size: 62 Copynumber: 6.8 Consensus size: 58
928 TTTCTCCAAA
* * *** * * *
938 AAAAAATTACA-TTTTTGGGTGTTGGCCATTGCATGACCGACACCCCATTTTCTCGGAT
1 AAAAAATTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTTTC-GAT
* * *
996 AAAAAAATTACAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTCAAAA
1 -AAAAAATT--AAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTTTC-GAT
** *** * * * *
1058 AAAAAATTGCA-TTTTTTGGTGTTGGCCATTGCATGGCCGACACCCCATTTTCTCAAG
1 AAAAAATTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTTTCGAT
* *
1115 AAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC-TTTTTCGAA
1 AAAAAA-TT-AAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTTTCGAT
* * *
1174 AAAAAATTCAAAATTTTTTGGTGTTGGTCATGC-AATGGCCTACACCCCCTTTTTTCGAAT
1 AAAAAATT-AAATTTTTTTGGTGTTGGCCAT-CAAATGGCCGACACCCCCTTTTTTCG-AT
* * *
1234 AAAAAAATTACAAATTTTTTTGATGTTGGCCATCAAATGGCCGACACCCCCTTTTTATTTGGT
1 -AAAAAATT--AAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC-TTTT-TTCGAT
* ** *
1297 AAAAAATT-AATTTTTTTGGTGTTGGTCATGTAATGTCCGACACC
1 AAAAAATTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACC
1341 AACTTCCCCT
Statistics
Matches: 290, Mismatches: 40, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
57 8 0.03
58 80 0.28
59 61 0.21
60 33 0.11
61 19 0.07
62 81 0.28
63 5 0.02
64 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (58 bp):
AAAAAATTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTTTCGAT
Found at i:2738 original size:89 final size:87
Alignment explanation
Indices: 2526--2745 Score: 272
Period size: 84 Copynumber: 2.6 Consensus size: 87
2516 AATTTAACAT
* * * * * *
2526 TATTTAAATAAAAAA-GATTATTATTATATTATAATTTATATCAAATATTGTGTTAATTTGACAA
1 TATTTAAATAAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTATTAATTTAACAA
2590 TACATTATTTATCAAATTTTCA
66 TACATTATTTATCAAATTTTCA
* *
2612 TATTTAAA-ATACAAATTATTATTA--A-ATTACAATTTTTATCAAATAATGTATTGATTTAACA
1 TATTTAAATA-AAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTATTAATTTAACA
* *
2673 ATACATTATTTAT-TAATTTTATA
65 ATACATTATTTATCAAATTTT-CA
2696 TATTTAAATAAAAATTATTATTATTATTATATTACAATTTTTATCAAATA
1 TATTTAAATAAAAA--ATTATTATTATTATATTACAATTTTTATCAAATA
Statistics
Matches: 114, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
83 6 0.05
84 55 0.48
85 3 0.03
86 22 0.19
87 7 0.06
88 1 0.01
89 20 0.18
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (87 bp):
TATTTAAATAAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTATTAATTTAACAA
TACATTATTTATCAAATTTTCA
Done.