Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009177.1 Kokia drynarioides strain JFW-HI SEQ_123882, 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: 134489
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
Found at i:1433 original size:22 final size:23
Alignment explanation
Indices: 1395--1447 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1385 GCAAATCTAT
1395 CACAAAGGTAGACGAAAA-CGTGC
1 CACAAA-GTAGACGAAAAGCGTGC
*
1418 CACAAAGTAGATGAAAAGCGTGC
1 CACAAAGTAGACGAAAAGCGTGC
*
1441 CGCAAAG
1 CACAAAG
1448 ACAGATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.43, C:0.21, G:0.26, T:0.09
Consensus pattern (23 bp):
CACAAAGTAGACGAAAAGCGTGC
Found at i:1457 original size:23 final size:22
Alignment explanation
Indices: 1408--1458 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
1398 AAAGGTAGAC
*
1408 GAAAACGTGCCACAAAGTAGAT
1 GAAAACGTGCCACAAAGCAGAT
*
1430 GAAAAGCGTGCCGCAAAGACAGAT
1 GAAAA-CGTGCCACAAAG-CAGAT
*
1454 AAAAA
1 GAAAA
1459 TCAGAACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 11 0.46
24 8 0.33
ACGTcount: A:0.49, C:0.18, G:0.24, T:0.10
Consensus pattern (22 bp):
GAAAACGTGCCACAAAGCAGAT
Found at i:3720 original size:95 final size:95
Alignment explanation
Indices: 3556--3745 Score: 353
Period size: 95 Copynumber: 2.0 Consensus size: 95
3546 TCAAGAGCGG
3556 AGAGAGCAAAAATGGATTTGTGTCCGAAGCTGGGAATGCTAAAAGTGGATATAGCTATAGTTACC
1 AGAGAGCAAAAATGGATTTGTGTCCGAAGCTGGGAATGCTAAAAGTGGATATAGCTATAGTTACC
3621 CTTACCCACAAAATCTCTAGAGGTTTCGTT
66 CTTACCCACAAAATCTCTAGAGGTTTCGTT
* * *
3651 AGAGAGCAAAAATGGATTTGTGTCCGAAGCTGGGATTGCTAAAAGTGGATATATCTATAGTTACT
1 AGAGAGCAAAAATGGATTTGTGTCCGAAGCTGGGAATGCTAAAAGTGGATATAGCTATAGTTACC
3716 CTTACCCACAAAATCTCTAGAGGTTTCGTT
66 CTTACCCACAAAATCTCTAGAGGTTTCGTT
3746 TAGTCGGCCT
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 92 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (95 bp):
AGAGAGCAAAAATGGATTTGTGTCCGAAGCTGGGAATGCTAAAAGTGGATATAGCTATAGTTACC
CTTACCCACAAAATCTCTAGAGGTTTCGTT
Found at i:4361 original size:18 final size:15
Alignment explanation
Indices: 4317--4366 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 15
4307 ACACTTTCAT
4317 CAAATCTATCAAAAAAA
1 CAAAT-TAT-AAAAAAA
4334 CAAATTATAAAAAAA
1 CAAATTATAAAAAAA
4349 CAAAAGTTGATAAAAAAA
1 C-AAA-TT-ATAAAAAAA
4367 AAACTCAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.27
16 6 0.20
17 7 0.23
18 9 0.30
ACGTcount: A:0.68, C:0.10, G:0.04, T:0.18
Consensus pattern (15 bp):
CAAATTATAAAAAAA
Found at i:23513 original size:27 final size:27
Alignment explanation
Indices: 23461--23513 Score: 63
Period size: 29 Copynumber: 1.9 Consensus size: 27
23451 ATTTTGATAC
* *
23461 TTTTTTTTTAATATGGTACGTGTGTAAT
1 TTTTTTTTTAATATGATACG-ATGTAAT
23489 TTTTTTTTCTAATATGATAC-ATGTA
1 TTTTTTTT-TAATATGATACGATGTA
23514 TTTGACAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 4 0.18
28 8 0.36
29 10 0.45
ACGTcount: A:0.25, C:0.06, G:0.13, T:0.57
Consensus pattern (27 bp):
TTTTTTTTTAATATGATACGATGTAAT
Found at i:30271 original size:2 final size:2
Alignment explanation
Indices: 30266--30298 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
30256 TTTTATAATT
*
30266 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30299 TGATTATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:43986 original size:18 final size:17
Alignment explanation
Indices: 43965--43998 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
43955 TTAAATTTTT
43965 TCAAAAATGCCTTTTTGC
1 TCAAAAATG-CTTTTTGC
*
43983 TCAAAAGTGCTTTTTG
1 TCAAAAATGCTTTTTG
43999 GCTAAAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (17 bp):
TCAAAAATGCTTTTTGC
Found at i:44006 original size:18 final size:17
Alignment explanation
Indices: 43975--44008 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
43965 TCAAAAATGC
*
43975 CTTTTTGCTCAAAAGTG
1 CTTTTTGCTAAAAAGTG
43992 CTTTTTGGCTAAAAAGT
1 CTTTTT-GCTAAAAAGT
44009 TATTTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (17 bp):
CTTTTTGCTAAAAAGTG
Found at i:50863 original size:23 final size:24
Alignment explanation
Indices: 50837--50884 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
50827 ATTATTACAA
50837 ATATTTA-AAAACT-ATAAAAATAT
1 ATATTTATAAAA-TGATAAAAATAT
50860 ATATTTATTAAAATGATAAAAATAT
1 ATATTTA-TAAAATGATAAAAATAT
50885 TTAAATTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 7 0.32
24 1 0.05
25 14 0.64
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
ATATTTATAAAATGATAAAAATAT
Found at i:53142 original size:18 final size:18
Alignment explanation
Indices: 53111--53145 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
53101 TTAATGTTTG
53111 ATTTATTCGAATTTAAAA
1 ATTTATTCGAATTTAAAA
53129 ATTTAATTCG-ATTTAAA
1 ATTT-ATTCGAATTTAAA
53146 CTTGAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (18 bp):
ATTTATTCGAATTTAAAA
Found at i:53194 original size:14 final size:15
Alignment explanation
Indices: 53171--53206 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
53161 AAAAATTGAT
53171 TTAATT-AATTC-GA
1 TTAATTCAATTCAGA
53184 TTAATTCAATTCAGA
1 TTAATTCAATTCAGA
53199 -TAATTCAA
1 TTAATTCAA
53207 AATTCGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.29
14 13 0.62
15 2 0.10
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.42
Consensus pattern (15 bp):
TTAATTCAATTCAGA
Found at i:60435 original size:5 final size:5
Alignment explanation
Indices: 60389--60434 Score: 76
Period size: 5 Copynumber: 9.2 Consensus size: 5
60379 ACGCACAAAT
60389 ATAATA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A-AAA A
1 ATAA-A ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
60435 ACTCAAATCT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.10
5 32 0.80
6 4 0.10
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:84949 original size:82 final size:79
Alignment explanation
Indices: 84803--84958 Score: 231
Period size: 82 Copynumber: 1.9 Consensus size: 79
84793 GCCATCGTGA
* * *
84803 CATTGTTTGGTAAAGCAGAAAAATGAGAAAAGGGAAGAAAGCGGATGGAAAAGAGAAAAAAAAAT
1 CATTGTTTGGTAAAGCAGAAAAATGAAAAAAGAGAAGAAAGCCGATGGAAAAGAGAAAAAAAAAT
84868 GTTTTTATTTGCGG
66 GTTTTTATTTGCGG
* * *
84882 CATTGTTTGGTAAAGCGGAAAAATGAAAAAACAAGAGAATAAAGCCGATGGAAAAGAGAAAAGAA
1 CATTGTTTGGTAAAGCAGAAAAATG--AAAA-AAGAGAAGAAAGCCGATGGAAAAGAGAAAAAAA
84947 AATGTTTTTATT
63 AATGTTTTTATT
84959 AATGTCAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
79 24 0.35
81 3 0.04
82 41 0.60
ACGTcount: A:0.47, C:0.06, G:0.25, T:0.22
Consensus pattern (79 bp):
CATTGTTTGGTAAAGCAGAAAAATGAAAAAAGAGAAGAAAGCCGATGGAAAAGAGAAAAAAAAAT
GTTTTTATTTGCGG
Found at i:86493 original size:33 final size:35
Alignment explanation
Indices: 86451--86522 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
86441 TCAAACTCAC
* * *
86451 TAAATTAGAGCACCTTTCTTCTAT-AAAATTAAAA
1 TAAATTAGAGAACCTTTCTTATATGAAAAATAAAA
*
86485 TAAA-TAGAGAACTTTTCTTATATGAAAAATAAAA
1 TAAATTAGAGAACCTTTCTTATATGAAAAATAAAA
86519 TAAA
1 TAAA
86523 AAATAAAGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 16 0.48
34 17 0.52
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (35 bp):
TAAATTAGAGAACCTTTCTTATATGAAAAATAAAA
Found at i:91312 original size:29 final size:29
Alignment explanation
Indices: 91249--91359 Score: 122
Period size: 30 Copynumber: 3.8 Consensus size: 29
91239 GGGATTTAAA
91249 AAAATTATTTTTT-AACTTTTAA-AGGT-C
1 AAAATT-TTTTTTCAACTTTTAAGAGGTCC
*
91276 AAATATTTTTTTTCAACTTTTAAGGGGTCC
1 AAA-ATTTTTTTTCAACTTTTAAGAGGTCC
* *
91306 AAAATTTTTTTACCAATTTTTAAGAGG-CC
1 AAAATTTTTTT-TCAACTTTTAAGAGGTCC
91335 AAAATTTTTTTTTTCAACTTTTAAG
1 AAAA--TTTTTTTTCAACTTTTAAG
91360 TAACCTAAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
27 9 0.13
28 12 0.17
29 17 0.24
30 26 0.37
31 7 0.10
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (29 bp):
AAAATTTTTTTTCAACTTTTAAGAGGTCC
Found at i:96738 original size:23 final size:23
Alignment explanation
Indices: 96706--96776 Score: 97
Period size: 23 Copynumber: 3.1 Consensus size: 23
96696 ACGCTAGCGC
* *
96706 GCTTACTGTTTCGCACTTTGTGT
1 GCTTATTGTTTCGCACTTCGTGT
*
96729 GCTTATTGTTTTGCACTTCGTGT
1 GCTTATTGTTTCGCACTTCGTGT
* *
96752 GCTTATTGTTTCGCACCTCTTGT
1 GCTTATTGTTTCGCACTTCGTGT
96775 GC
1 GC
96777 CTACTGATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.08, C:0.23, G:0.21, T:0.48
Consensus pattern (23 bp):
GCTTATTGTTTCGCACTTCGTGT
Found at i:96790 original size:23 final size:23
Alignment explanation
Indices: 96738--96812 Score: 57
Period size: 23 Copynumber: 3.3 Consensus size: 23
96728 TGCTTATTGT
* * * *
96738 TTTGCACTTCGTGTGCTTATTG-
1 TTTGCACCTCTTGTGCCTACTGA
96760 TTTCGCACCTCTTGTGCCTACTGA
1 TTT-GCACCTCTTGTGCCTACTGA
* *
96784 TTTGCA-CTATGTGCGCCTACTGA
1 TTTGCACCTCT-TGTGCCTACTGA
96807 -TTGCAC
1 TTTGCAC
96813 TGTGTGTGCT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
22 11 0.26
23 29 0.67
24 3 0.07
ACGTcount: A:0.13, C:0.27, G:0.20, T:0.40
Consensus pattern (23 bp):
TTTGCACCTCTTGTGCCTACTGA
Found at i:96813 original size:22 final size:22
Alignment explanation
Indices: 96775--96841 Score: 80
Period size: 23 Copynumber: 3.0 Consensus size: 22
96765 CACCTCTTGT
*
96775 GCCTACTGATTTGCACTATGTGC
1 GCCTACTGA-TTGCACTGTGTGC
*
96798 GCCTACTGATTGCACTGTGTGT
1 GCCTACTGATTGCACTGTGTGC
* *
96820 GCTTGCTGGATTGCACTGTGTG
1 GCCTACT-GATTGCACTGTGTG
96842 TGCTTACTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.41
23 23 0.59
ACGTcount: A:0.13, C:0.22, G:0.28, T:0.36
Consensus pattern (22 bp):
GCCTACTGATTGCACTGTGTGC
Found at i:103978 original size:23 final size:23
Alignment explanation
Indices: 103944--104024 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
103934 ACGCTAGCGC
*
103944 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTATTTCGCACTTCGTGT
103967 GCTTACTATTTCGCACTTCGTGT
1 GCTTACTATTTCGCACTTCGTGT
* * *
103990 GCTTACTGTTTCGTACCTCGTGT
1 GCTTACTATTTCGCACTTCGTGT
*
104013 GCCTACTGATTT
1 GCTTACT-ATTT
104025 GCGCTATGTG
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 48 0.94
24 3 0.06
ACGTcount: A:0.11, C:0.26, G:0.20, T:0.43
Consensus pattern (23 bp):
GCTTACTATTTCGCACTTCGTGT
Found at i:104043 original size:46 final size:46
Alignment explanation
Indices: 103942--104047 Score: 126
Period size: 46 Copynumber: 2.3 Consensus size: 46
103932 GAACGCTAGC
* *
103942 GCGCTTACTGTTTCGCACTTCGTGTGCTTACTATTTCGCACTTCGT
1 GCGCTTACTGTTTCGCACCTCGTGTGCCTACTATTTCGCACTTCGT
* * *
103988 GTGCTTACTGTTTCGTACCTCGTGTGCCTACTGATTT-GCGCTAT-GT
1 GCGCTTACTGTTTCGCACCTCGTGTGCCTACT-ATTTCGCACT-TCGT
*
104034 GCGCCTACTGTTTC
1 GCGCTTACTGTTTC
104048 CCCAGCACTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
46 46 0.90
47 5 0.10
ACGTcount: A:0.10, C:0.27, G:0.22, T:0.41
Consensus pattern (46 bp):
GCGCTTACTGTTTCGCACCTCGTGTGCCTACTATTTCGCACTTCGT
Found at i:104095 original size:26 final size:28
Alignment explanation
Indices: 104039--104099 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
104029 TATGTGCGCC
104039 TACTGTTTCCCCAGCACTTGTGTGTGCT
1 TACTGTTTCCCCAGCACTTGTGTGTGCT
104067 TACTGTTTCCCCAGCAC-T-TGTGTGCT
1 TACTGTTTCCCCAGCACTTGTGTGTGCT
104093 TACTGTT
1 TACTGTT
104100 AAGTACTTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 15 0.45
27 1 0.03
28 17 0.52
ACGTcount: A:0.11, C:0.28, G:0.20, T:0.41
Consensus pattern (28 bp):
TACTGTTTCCCCAGCACTTGTGTGTGCT
Found at i:118720 original size:3 final size:3
Alignment explanation
Indices: 118705--118748 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
118695 TGAGAAACTT
* * * *
118705 TAC TAC TAA TAC TAC TAG TAC TAG TAC TAA TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
118749 TTATTTCTCG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:128631 original size:15 final size:15
Alignment explanation
Indices: 128585--128631 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
128575 CTATATGCAA
* *
128585 TATTTATTTAATTTT
1 TATTTTTTTATTTTT
*
128600 TACTCTTTTTATTTTT
1 TA-TTTTTTTATTTTT
128616 TATTTTTTTATTTTT
1 TATTTTTTTATTTTT
128631 T
1 T
128632 TTTACTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (15 bp):
TATTTTTTTATTTTT
Done.