Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000941.1 Kokia drynarioides strain JFW-HI SEQ_112101, 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: 15278
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Found at i:501 original size:3 final size:3
Alignment explanation
Indices: 495--533 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
485 ACCCTAAAAA
* * *
495 AAT AAT AAG AAT AAG AAT AAT AAT GAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
534 TTGGGCCCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:947 original size:42 final size:42
Alignment explanation
Indices: 880--1100 Score: 254
Period size: 42 Copynumber: 5.3 Consensus size: 42
870 CTACGCCTAG
* *
880 GCCTCTAAATGCAATAAAAACTAAATGAGCCTCCACACCTGA
1 GCCTCTAAATGCAATGAAAAGTAAATGAGCCTCCACACCTGA
* * *
922 GCCTTTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTGG
1 GCCTCTAAATGCAATGAAAAGTAAATGAGCCTCCACACCTGA
*
964 GCCTC-AAATGCAATGAAAAGTAAATG-GACCTCCACACCTGG
1 GCCTCTAAATGCAATGAAAAGTAAATGAG-CCTCCACACCTGA
* * *
1005 GCCTCTGAATGCAAAT-AAAAGTAAATGAACCTCCACA-CTTA
1 GCCTCTAAATGC-AATGAAAAGTAAATGAGCCTCCACACCTGA
* * *
1046 GGCCTCTAAATGTAATGAAAAGTAAAT-AGGCCTCCACACTTGG
1 -GCCTCTAAATGCAATGAAAAGTAAATGA-GCCTCCACACCTGA
1089 GCCTCTGAAATG
1 GCCTCT-AAATG
1101 AACCTCAACA
Statistics
Matches: 154, Mismatches: 16, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
40 1 0.01
41 45 0.29
42 99 0.64
43 9 0.06
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.21
Consensus pattern (42 bp):
GCCTCTAAATGCAATGAAAAGTAAATGAGCCTCCACACCTGA
Found at i:1001 original size:83 final size:84
Alignment explanation
Indices: 861--1100 Score: 290
Period size: 83 Copynumber: 2.9 Consensus size: 84
851 AAAATAAATG
* * * *
861 AATGGACCTCTACGCCTAGGCCTCTAAATGCAATAAAAACTAAAT-GAGCCTCCACACCTGAGCC
1 AATGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGA-CCTCCACACCTGAGCC
*
925 TTTAAATGC-AATGAAAAGTA
65 TCTAAATGCAAAT-AAAAGTA
* * *
945 AATGGGCCTCCACACCTGGGCCTC-AAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCT
1 AATGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGAGCCT
*
1009 CTGAATGCAAATAAAAGTA
66 CTAAATGCAAATAAAAGTA
* * * * *
1028 AATGAACCTCCACACTTAGGCCTCTAAATGTAATGAAAAGTAAATAGG-CCTCCACACTTGGGCC
1 AATGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAAT-GGACCTCCACACCTGAGCC
1092 TCTGAAATG
65 TCT-AAATG
1101 AACCTCAACA
Statistics
Matches: 135, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
83 67 0.50
84 62 0.46
85 6 0.04
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (84 bp):
AATGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGAGCCT
CTAAATGCAAATAAAAGTA
Found at i:1008 original size:125 final size:122
Alignment explanation
Indices: 861--1217 Score: 371
Period size: 125 Copynumber: 3.0 Consensus size: 122
851 AAAATAAATG
* * * *
861 AATGGACCTCTACGCCTAGGCCTCTAAATGCAATAAAAACTAAATGAGCCTCCACACCTGAGCCT
1 AATGGACCTCAACACCTAGGCCTCTGAATGCAATAAAAAGTAAATGAGCCTCCACACCTGAGCCT
*
926 TTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCAAATGCAATGAAAAGTA
66 CTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCAAATGCAATG--AAG-A
* * * *
986 AATGGACCTCCACACCTGGGCCTCTGAATGCAA-ATAAAAGTAAATGAACCTCCACA-CTTAGGC
1 AATGGACCTCAACACCTAGGCCTCTGAATGCAATA-AAAAGTAAATGAGCCTCCACACCTGA-GC
* * *
1049 CTCTAAATGTAATGAAAAGTAAATAGGCCTCCACACTTGGG-C-C---T-C--T---GA
64 CTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCAAATGCAATGAAGA
* * * * * *
1097 AATGAACCTCAACACCTCGACCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACCTGGGCCT
1 AATGGACCTCAACACCTAGGCCTCTGAATGCAATAAAAAGTAAATGAGCCTCCACACCTGAGCCT
* * * *
1162 CTGAATGCGATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGTAATGAA
66 CTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTGGGCCTC-AAATGCAATGAA
1218 TGCTTTCCTT
Statistics
Matches: 189, Mismatches: 27, Indels: 34
0.76 0.11 0.14
Matches are distributed among these distances:
111 86 0.46
112 4 0.02
113 1 0.01
117 2 0.01
119 1 0.01
120 2 0.01
123 1 0.01
124 5 0.03
125 87 0.46
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (122 bp):
AATGGACCTCAACACCTAGGCCTCTGAATGCAATAAAAAGTAAATGAGCCTCCACACCTGAGCCT
CTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCAAATGCAATGAAGA
Found at i:1121 original size:69 final size:69
Alignment explanation
Indices: 1027--1166 Score: 208
Period size: 69 Copynumber: 2.0 Consensus size: 69
1017 AAATAAAAGT
* * * * *
1027 AAATGAACCTCCACACTTAGGCCTCTAAATGTAATGAAAAGTAAATAGGCCTCCACACTTGGGCC
1 AAATGAACCTCAACACCTAGACCTCTAAATGCAATGAAAAGTAAATAGGCCTCCACACCTGGGCC
1092 TCTG
66 TCTG
* * *
1096 AAATGAACCTCAACACCTCGACCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACCTGGGCC
1 AAATGAACCTCAACACCTAGACCTCTAAATGCAATGAAAAGTAAATAGGCCTCCACACCTGGGCC
1161 TCTG
66 TCTG
1165 AA
1 AA
1167 TGCGATGAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.21
Consensus pattern (69 bp):
AAATGAACCTCAACACCTAGACCTCTAAATGCAATGAAAAGTAAATAGGCCTCCACACCTGGGCC
TCTG
Found at i:1155 original size:42 final size:42
Alignment explanation
Indices: 1096--1217 Score: 172
Period size: 42 Copynumber: 2.9 Consensus size: 42
1086 TGGGCCTCTG
* * * *
1096 AAATGAACCTCAACACCTCGACCTCTGAATGCAATGAAAAGT
1 AAATGGACCTCCACACCTGGGCCTCTGAATGCAATGAAAAGT
* *
1138 AAATGGGCCTCCACACCTGGGCCTCTGAATGCGATGAAAAGT
1 AAATGGACCTCCACACCTGGGCCTCTGAATGCAATGAAAAGT
* *
1180 AAATGGACCTCCACACCTGGGCCTCTAAATGTAATGAA
1 AAATGGACCTCCACACCTGGGCCTCTGAATGCAATGAA
1218 TGCTTTCCTT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (42 bp):
AAATGGACCTCCACACCTGGGCCTCTGAATGCAATGAAAAGT
Found at i:1161 original size:111 final size:110
Alignment explanation
Indices: 984--1210 Score: 305
Period size: 111 Copynumber: 2.1 Consensus size: 110
974 CAATGAAAAG
* * * * *
984 TAAATGGACCTCCACACCTGGGCCTCTGAATGCAAATAAAAGTAAATGAACCTCCACACTTAGGC
1 TAAATGAACCTCAACACCTCGACCTCTGAATGCAAATAAAAGTAAATGAACCTCCACACCTAGGC
* *
1049 CTCTAAATGTAATGAAAAGTAAATAGG-CCTCCACACTTGGGCCTC
66 CTCTAAATGCAATGAAAAGTAAAT-GGACCTCCACACCTGGGCCTC
** *
1094 TGAAATGAACCTCAACACCTCGACCTCTGAATGC-AATGAAAAGTAAATGGGCCTCCACACCTGG
1 T-AAATGAACCTCAACACCTCGACCTCTGAATGCAAAT-AAAAGTAAATGAACCTCCACACCTAG
* *
1158 GCCTCTGAATGCGATGAAAAGTAAATGGACCTCCACACCTGGGCCTC
64 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTC
1205 TAAATG
1 TAAATG
1211 TAATGAATGC
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
110 11 0.11
111 91 0.89
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (110 bp):
TAAATGAACCTCAACACCTCGACCTCTGAATGCAAATAAAAGTAAATGAACCTCCACACCTAGGC
CTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTC
Found at i:1656 original size:9 final size:8
Alignment explanation
Indices: 1620--1655 Score: 63
Period size: 8 Copynumber: 4.4 Consensus size: 8
1610 TTGCTCTCTC
1620 TTTCTATTT
1 TTTCTA-TT
1629 TTTCTATT
1 TTTCTATT
1637 TTTCTATT
1 TTTCTATT
1645 TTTCTATT
1 TTTCTATT
1653 TTT
1 TTT
1656 TTGTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 21 0.78
9 6 0.22
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTCTATT
Found at i:15021 original size:150 final size:149
Alignment explanation
Indices: 14688--15207 Score: 733
Period size: 150 Copynumber: 3.4 Consensus size: 149
14678 TGATTAAATA
*
14688 AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* * *
14753 GTTAAAAGTTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTATTTTTTTTTTAAAAATC
66 GTAAAAAATTT--ACTTTTTCTTTAAAATAACTAAAAAACAGA-TTT-TTATTTTTTT-AAAATC
14818 TAAACTTTCTTTTTTTTTT-AAAG
126 TAAACTTTCTTTTTTTTTTAAAAG
*
14841 AAAATCACTATTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAGAAAAAATCAAAACTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTA-AAAAAATCAAAACTT
* * * *
14906 TGTCAAAAATTTTCTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTTTAAACTCTAAA
65 TGTAAAAAATTTACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTTAAAATCTAAA
14971 CTTTCTTTTTTTTTTAAAAG
130 CTTTCTTTTTTTTTTAAAAG
*
14991 AAAATCACTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAATAGTTAGAAAAAATCAAAACTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTA-AAAAAATCAAAACTT
* * *
15056 TGTTAAAAAATTAAAATTTTTCTTTAAAATAACT-AAAAACAGATTTTTATTTTTTAAAAATCTA
65 TG-TAAAAAATT-TACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTTAAAATCTA
*
15120 AATTTTCTGTTTTTTTTTTTAAAAG
128 AACTTTC---TTTTTTTTTTAAAAG
* *
15145 AAAATCACTATTTTGCTTAAAAAAT-CAAAGCTTTTATTTCGAAATTGTTTAAAAAAA-CAAAAC
1 AAAATCACTATTTTACTT-AAAAATCCAAA-CTTTTATTTCGAAATAG-TTAAAAAAATCAAAAC
15208 ATTTCCCAAA
Statistics
Matches: 338, Mismatches: 19, Indels: 19
0.90 0.05 0.05
Matches are distributed among these distances:
149 24 0.07
150 78 0.23
151 44 0.13
152 46 0.14
153 47 0.14
154 68 0.20
155 28 0.08
156 3 0.01
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.42
Consensus pattern (149 bp):
AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
GTAAAAAATTTACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTTAAAATCTAAAC
TTTCTTTTTTTTTTAAAAG
Done.