Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001016.1 Kokia drynarioides strain JFW-HI SEQ_112227, 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: 16314
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1034 original size:60 final size:59
Alignment explanation
Indices: 963--1101 Score: 215
Period size: 60 Copynumber: 2.3 Consensus size: 59
953 ATGACACTCG
* * *
963 GGGGGTAAAATGGTAATTTTTGGAAGGCTTACAGTCAAAATCGGAATTTTTAGACATTT
1 GGGGGTAAAATGGTAATTTTTGGAAGGCTCACAGTCAAAATCGAAATTTTTAGACATTC
**
1022 GAGGGGTAAAATGGTAATTTTTGGAAGGCTCGGAGTCAAAATCGAAATTTTTAGACATTC
1 G-GGGGTAAAATGGTAATTTTTGGAAGGCTCACAGTCAAAATCGAAATTTTTAGACATTC
*
1082 GGGGGTAAAATGGCAATTTT
1 GGGGGTAAAATGGTAATTTT
1102 AGAGAATTTG
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
59 19 0.26
60 54 0.74
ACGTcount: A:0.32, C:0.09, G:0.27, T:0.32
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTTGGAAGGCTCACAGTCAAAATCGAAATTTTTAGACATTC
Found at i:1063 original size:30 final size:30
Alignment explanation
Indices: 969--1073 Score: 74
Period size: 30 Copynumber: 3.5 Consensus size: 30
959 CTCGGGGGGT
*
969 AAAATGGTAATTTTTGGAAGGCTTA-CAGTC
1 AAAATGGTAATTTTTGGAAGGC-TAGGAGTC
* ** *
999 AAAATCGG-AATTTTTAGACA-TTTGAGGGGT-
1 AAAAT-GGTAATTTTTGGA-AGGCT-AGGAGTC
*
1029 AAAATGGTAATTTTTGGAAGGCTCGGAGTC
1 AAAATGGTAATTTTTGGAAGGCTAGGAGTC
* *
1059 AAAATCGAAATTTTT
1 AAAATGGTAATTTTT
1074 AGACATTCGG
Statistics
Matches: 56, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
29 8 0.14
30 43 0.77
31 5 0.09
ACGTcount: A:0.34, C:0.09, G:0.24, T:0.33
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGAAGGCTAGGAGTC
Found at i:1162 original size:30 final size:30
Alignment explanation
Indices: 1126--1350 Score: 176
Period size: 30 Copynumber: 7.6 Consensus size: 30
1116 AAAAATGGTA
*
1126 TTTTGGAAAGTTTGGGGGTAAAAATGTAAT
1 TTTTGGAAAGTTTGAGGGTAAAAATGTAAT
* * **
1156 TTTTGGAAAATTTGAGGTTAAAAATGGGA-
1 TTTTGGAAAGTTTGAGGGTAAAAATGTAAT
1185 TTTTGGAAAGTTTGAGGGTGAAAAATGTAAT
1 TTTTGGAAAGTTTGAGGGT-AAAAATGTAAT
* * *
1216 TTTTAGAAAATTT-AGGGTAAAAAATGGAA-
1 TTTTGGAAAGTTTGAGGGT-AAAAATGTAAT
* * *
1245 TTTTGAAAAATTCT-AAGGTAAAAATGTAAT
1 TTTTGGAAAGTT-TGAGGGTAAAAATGTAAT
* * * *
1275 TTTTGGAAAATTCGA-AGTCAAAAATGGAA-
1 TTTTGGAAAGTTTGAGGGT-AAAAATGTAAT
* * * *
1304 TTTTGGAAAGTTTGGGGGTCAAAATATGAT
1 TTTTGGAAAGTTTGAGGGTAAAAATGTAAT
* *
1334 TTCTGGATAGTTT-AGGG
1 TTTTGGAAAGTTTGAGGG
1351 ACCTTCAAGA
Statistics
Matches: 155, Mismatches: 32, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
29 59 0.38
30 85 0.55
31 11 0.07
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (30 bp):
TTTTGGAAAGTTTGAGGGTAAAAATGTAAT
Found at i:1191 original size:59 final size:59
Alignment explanation
Indices: 1106--1328 Score: 281
Period size: 59 Copynumber: 3.8 Consensus size: 59
1096 AATTTTAGAG
* *
1106 AATTTG-GGTCAAAAATGGTATTTTGGAAAGTTTGGGGGTAAAAATGTAATTTTTGGAA
1 AATTTGAGGTCAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTGGAA
* * *
1164 AATTTGAGGTTAAAAATGGGATTTTGGAAAGTTTGAGGGTGAAAAATGTAATTTTTAGAA
1 AATTTGAGGTCAAAAATGGAATTTTGGAAAGTTTGAGGGT-AAAAATGTAATTTTTGGAA
* * * *
1224 AATTT-AGGGTAAAAAATGGAATTTTGAAAAATTCT-AAGGTAAAAATGTAATTTTTGGAA
1 AATTTGA-GGTCAAAAATGGAATTTTGGAAAGTT-TGAGGGTAAAAATGTAATTTTTGGAA
* * * *
1283 AATTCGAAGTCAAAAATGGAATTTTGGAAAGTTTGGGGGTCAAAAT
1 AATTTGAGGTCAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAAT
1329 ATGATTTCTG
Statistics
Matches: 141, Mismatches: 18, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
58 7 0.05
59 83 0.59
60 50 0.35
61 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (59 bp):
AATTTGAGGTCAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTGGAA
Found at i:1269 original size:119 final size:118
Alignment explanation
Indices: 1098--1327 Score: 318
Period size: 119 Copynumber: 1.9 Consensus size: 118
1088 AAAATGGCAA
* * * * * **
1098 TTTTAGAGAATTTGGGTCAAAAATGGTATTTTGGAAAGTTTGGGGGTAAAAATGTAATTTTTGGA
1 TTTTAGAAAATTTGGGTAAAAAATGGAATTTTGAAAAATTTGAAGGTAAAAATGTAATTTTTGGA
* * * * *
1163 AAATTTGAGGTTAAAAATGGGATTTTGGAAAGTTTGAGGGTGAAAAATGTAAT
66 AAATTCGAAGTCAAAAATGGAATTTTGGAAAGTTTGAGGGTCAAAAATGTAAT
1216 TTTTAGAAAATTTAGGGTAAAAAATGGAATTTTGAAAAATTCT-AAGGTAAAAATGTAATTTTTG
1 TTTTAGAAAATTT-GGGTAAAAAATGGAATTTTGAAAAATT-TGAAGGTAAAAATGTAATTTTTG
*
1280 GAAAATTCGAAGTCAAAAATGGAATTTTGGAAAGTTTGGGGGTCAAAA
64 GAAAATTCGAAGTCAAAAATGGAATTTTGGAAAGTTTGAGGGTCAAAA
1328 TATGATTTCT
Statistics
Matches: 97, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
118 12 0.12
119 84 0.87
120 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (118 bp):
TTTTAGAAAATTTGGGTAAAAAATGGAATTTTGAAAAATTTGAAGGTAAAAATGTAATTTTTGGA
AAATTCGAAGTCAAAAATGGAATTTTGGAAAGTTTGAGGGTCAAAAATGTAAT
Found at i:1665 original size:31 final size:30
Alignment explanation
Indices: 1626--1689 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
1616 ATGTATAATT
* * * *
1626 AATTAAAAATATAAAAAAGACGAAATTGTA
1 AATTAAAAAAAGAAAAAAGACCAAATGGTA
*
1656 AATTCAAAAAAAGAGAAAAGACCAAATGGTA
1 AATT-AAAAAAAGAAAAAAGACCAAATGGTA
1687 AAT
1 AAT
1690 ATACCCCTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.19
Consensus pattern (30 bp):
AATTAAAAAAAGAAAAAAGACCAAATGGTA
Found at i:3268 original size:23 final size:23
Alignment explanation
Indices: 3242--3287 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3232 ATTGGATATT
3242 ATTTA-AATAAATTTTAAATTTAA
1 ATTTATAATAAA-TTTAAATTTAA
*
3265 ATTTATAATAAATTTAATTTTAA
1 ATTTATAATAAATTTAAATTTAA
3288 GATAAATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTTATAATAAATTTAAATTTAA
Found at i:3276 original size:17 final size:17
Alignment explanation
Indices: 3256--3301 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
3246 AAATAAATTT
3256 TAAATTTAAATTTATA-A
1 TAAATTTAAATTTA-AGA
*
3273 TAAATTTAATTTTAAGA
1 TAAATTTAAATTTAAGA
*
3290 TAAATTCAAATT
1 TAAATTTAAATT
3302 CTGTTGGGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 1 0.04
17 24 0.96
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (17 bp):
TAAATTTAAATTTAAGA
Found at i:3834 original size:49 final size:49
Alignment explanation
Indices: 3729--4327 Score: 469
Period size: 49 Copynumber: 12.3 Consensus size: 49
3719 GCCATTGTGA
* * ** * * *
3729 CTTAAACCTTTCCCTTTTATGTCTTTTTGGTATTGGATTCGCCATTACGG
1 CTTAAATCTTTCCC-TTCATGTCTTCGTGGTACTGGATTCGCCGTTGCGG
* * * * *
3779 CTTAAATCTTTCCCTTCATGTTTTCGTGGTACTAGATTTGCCGTTACAG
1 CTTAAATCTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCGTTGCGG
** * * *** *
3828 CTTAAATCTTTCCCTTTTGTGTTTTCGTGGTATTGGATTTATCGTTGTGG
1 CTTAAATCTTTCCC-TTCATGTCTTCGTGGTACTGGATTCGCCGTTGCGG
3878 CTTAAATCTTTCCCTTCATG-CTTCGTGGTACTGGATTCGCCGTTGCGG
1 CTTAAATCTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCGTTGCGG
* * * *
3926 CTTAAATCTTTCCCTTCATG-CCTCTGAGGTA-TAAGG-TTCGTCGTTGTGG
1 CTTAAATCTTTCCCTTCATGTCTTC-GTGGTACT--GGATTCGCCGTTGCGG
* * *
3975 CTTAAA-CATTTCCCTTCATATCTTCGTGGTACTAGATTCGCTGTTGCGG
1 CTTAAATC-TTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCGTTGCGG
* * * * *
4024 GTTAAATCTTTCCCTTCATG-CTTCTGAGGTACAAGG-TTCGCCATTGCGA
1 CTTAAATCTTTCCCTTCATGTCTTC-GTGGTAC-TGGATTCGCCGTTGCGG
* * * *** **
4073 CTTAAACCTTTCCCTCCATATCTTCGTGGTACTGGATTCGTTATTGTAG
1 CTTAAATCTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCGTTGCGG
* * *
4122 CTTAAATCTTTCCCTTCATGTTTTAGTGGTACTGGATTCACCGTTGCGG
1 CTTAAATCTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCGTTGCGG
* * **
4171 CTTAAATCTTTCCCTTCATG-CTTCTGAGGTA-TAAGG-TTCACCGTTGCAA
1 CTTAAATCTTTCCCTTCATGTCTTC-GTGGTACT--GGATTCGCCGTTGCGG
* *
4220 CTTAAACCTTTCCC-T--T-T-TTCGTGGTACTGGATTCGTCGTTGCGG
1 CTTAAATCTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCGTTGCGG
* * *
4264 CTTAAATCTTTCCCTTCATG-CTTCTGAGGTA-TAAGG-TTCACCGTTGCGC
1 CTTAAATCTTTCCCTTCATGTCTTC-GTGGTACT--GGATTCGCCGTTGCGG
*
4313 CTTAAACCTTTCCCT
1 CTTAAATCTTTCCCT
4328 CCCTGTTTCG
Statistics
Matches: 437, Mismatches: 85, Indels: 55
0.76 0.15 0.10
Matches are distributed among these distances:
43 2 0.00
44 27 0.06
45 5 0.01
46 1 0.00
47 1 0.00
48 62 0.14
49 270 0.62
50 69 0.16
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.41
Consensus pattern (49 bp):
CTTAAATCTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCGTTGCGG
Found at i:3940 original size:147 final size:146
Alignment explanation
Indices: 3757--4283 Score: 516
Period size: 147 Copynumber: 3.6 Consensus size: 146
3747 ATGTCTTTTT
* * * * * * *
3757 GGTATTGGATTCGCCATTACGGCTTAAATCTTTCCCTTCATGTTTTCGTGGTACTAGATTTGCCG
1 GGTACTGG-TTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTCGTGGTACTAGATTCGTCG
* ** * * *
3822 TTACAGCTTAAATCTTTCCCTTTTGTGTTTTCGTGGTATTGGATTTATCGTTGTGGCTTAAATCT
65 TTGCAGCTTAAATCTTTCCC-TTCATGTTTTCGTGGTACTGGATTTACCGTTGCGGCTTAAATCT
*
3887 TTCCCTTCATGCTTC-GT
129 TTCCCTTCATGCTTCTGA
* * * * * *
3904 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG-CCTCTGAGGTA-TAAGGTTCGT
1 GGTACTGG-TTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTC-GTGGTACT-AGATTCGT
** * * * ** * *
3967 CGTTGTGGCTTAAA-CATTTCCCTTCATATCTTCGTGGTACTAGATTCGCTGTTGCGGGTTAAAT
63 CGTTGCAGCTTAAATC-TTTCCCTTCATGTTTTCGTGGTACTGGATTTACCGTTGCGGCTTAAAT
4031 CTTTCCCTTCATGCTTCTGA
127 CTTTCCCTTCATGCTTCTGA
* * * * **
4051 GGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTGGATTCGTTA
1 GGTAC-TGGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTCGTGGTACTAGATTCGTCG
* * *
4116 TTGTAGCTTAAATCTTTCCCTTCATGTTTTAGTGGTACTGGATTCACCGTTGCGGCTTAAATCTT
65 TTGCAGCTTAAATCTTTCCCTTCATGTTTTCGTGGTACTGGATTTACCGTTGCGGCTTAAATCTT
4181 TCCCTTCATGCTTCTGA
130 TCCCTTCATGCTTCTGA
* * * *
4198 GGTA-TAAGGTTCACCGTTGCAACTTAAACCTTTCCC-T--T-T-TTCGTGGTACTGGATTCGTC
1 GGTACT--GGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTCGTGGTACTAGATTCGTC
*
4257 GTTGCGGCTTAAATCTTTCCCTTCATG
64 GTTGCAGCTTAAATCTTTCCCTTCATG
4284 CTTCTGAGGT
Statistics
Matches: 316, Mismatches: 54, Indels: 25
0.80 0.14 0.06
Matches are distributed among these distances:
142 43 0.14
143 1 0.00
144 1 0.00
146 51 0.16
147 213 0.67
148 7 0.02
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40
Consensus pattern (146 bp):
GGTACTGGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTCGTGGTACTAGATTCGTCGT
TGCAGCTTAAATCTTTCCCTTCATGTTTTCGTGGTACTGGATTTACCGTTGCGGCTTAAATCTTT
CCCTTCATGCTTCTGA
Found at i:4270 original size:93 final size:93
Alignment explanation
Indices: 4142--4327 Score: 327
Period size: 93 Copynumber: 2.0 Consensus size: 93
4132 TCCCTTCATG
4142 TTTTAGTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGG
1 TTTTAGTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGG
4207 TTCACCGTTGCAACTTAAACCTTTCCCT
66 TTCACCGTTGCAACTTAAACCTTTCCCT
* **
4235 TTTTCGTGGTACTGGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGG
1 TTTTAGTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGG
**
4300 TTCACCGTTGCGCCTTAAACCTTTCCCT
66 TTCACCGTTGCAACTTAAACCTTTCCCT
4328 CCCTGTTTCG
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.38
Consensus pattern (93 bp):
TTTTAGTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGG
TTCACCGTTGCAACTTAAACCTTTCCCT
Found at i:16239 original size:60 final size:59
Alignment explanation
Indices: 16168--16306 Score: 215
Period size: 60 Copynumber: 2.3 Consensus size: 59
16158 ATGACACTCG
* * *
16168 GGGGGTAAAATGGTAATTTTTGGAAGGCTTACAGTCAAAATCGGAATTTTTAGACATTT
1 GGGGGTAAAATGGTAATTTTTGGAAGGCTCACAGTCAAAATCGAAATTTTTAGACATTC
**
16227 GAGGGGTAAAATGGTAATTTTTGGAAGGCTCGGAGTCAAAATCGAAATTTTTAGACATTC
1 G-GGGGTAAAATGGTAATTTTTGGAAGGCTCACAGTCAAAATCGAAATTTTTAGACATTC
*
16287 GGGGGTAAAATGGCAATTTT
1 GGGGGTAAAATGGTAATTTT
16307 AGAGAATT
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
59 19 0.26
60 54 0.74
ACGTcount: A:0.32, C:0.09, G:0.27, T:0.32
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTTGGAAGGCTCACAGTCAAAATCGAAATTTTTAGACATTC
Found at i:16268 original size:30 final size:30
Alignment explanation
Indices: 16174--16278 Score: 74
Period size: 30 Copynumber: 3.5 Consensus size: 30
16164 CTCGGGGGGT
*
16174 AAAATGGTAATTTTTGGAAGGCTTA-CAGTC
1 AAAATGGTAATTTTTGGAAGGC-TAGGAGTC
* ** *
16204 AAAATCGG-AATTTTTAGACA-TTTGAGGGGT-
1 AAAAT-GGTAATTTTTGGA-AGGCT-AGGAGTC
*
16234 AAAATGGTAATTTTTGGAAGGCTCGGAGTC
1 AAAATGGTAATTTTTGGAAGGCTAGGAGTC
* *
16264 AAAATCGAAATTTTT
1 AAAATGGTAATTTTT
16279 AGACATTCGG
Statistics
Matches: 56, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
29 8 0.14
30 43 0.77
31 5 0.09
ACGTcount: A:0.34, C:0.09, G:0.24, T:0.33
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGAAGGCTAGGAGTC
Done.