Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010653.1 Kokia drynarioides strain JFW-HI SEQ_125596, 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: 4353
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Found at i:1072 original size:30 final size:29
Alignment explanation
Indices: 1007--1366 Score: 166
Period size: 29 Copynumber: 12.3 Consensus size: 29
997 AAAAAAAAGA
* *
1007 GATTTTTGGAA-GTTCGAGGGT-AAAATAGT
1 GATTTTTGAAAGGTTCG-GGGTAAAAAT-GG
*
1036 AATTTTTGAAAGGTTCGGGGTCAAAAATGG
1 GATTTTTGAAAGGTTCGGGGT-AAAAATGG
* * *
1066 GGTTTTTGGAA-GTTCAAGGGT-AAAATGG
1 GATTTTTGAAAGGTTC-GGGGTAAAAATGG
*
1094 TAATTTTT-AGAAGGTTCGGGGTCAAAAATGG
1 -GATTTTTGA-AAGGTTCGGGGT-AAAAATGG
* * *
1125 GATTTTTGGAAGTTTGGGGGT-AAAATGG
1 GATTTTTGAAAGGTTCGGGGTAAAAATGG
* * *
1153 CAATTTTT-AGAAGGTTTGAGGTAAAAATGG
1 -GATTTTTGA-AAGGTTCGGGGTAAAAATGG
* * * * * *
1183 GGTTTTTGGAAGTTTAGGGG-CAAAATGTT
1 GATTTTTGAAAGGTTCGGGGTAAAAATG-G
* ***
1212 AATTTTTAGAAA-GTTTAAGGTCAAAAATGG
1 GATTTTT-GAAAGGTTCGGGGT-AAAAATGG
* * * * *
1242 GATTTTTGGAAGTTTTGGGGTAAAATTGT
1 GATTTTTGAAAGGTTCGGGGTAAAAATGG
* *
1271 AATTTTTGGAAA-GTTCGAGGTCAAAAATGG
1 GATTTTT-GAAAGGTTCGGGGT-AAAAATGG
* * *
1301 GATTTTTGGAAGTTTGGGGGT-AAAATGG
1 GATTTTTGAAAGGTTCGGGGTAAAAATGG
* * * * *
1329 TAATTTTTAAAATGTTCGAGGTTAAAATGG
1 -GATTTTTGAAAGGTTCGGGGTAAAAATGG
1359 GATTTTTG
1 GATTTTTG
1367 GAGATTTTGG
Statistics
Matches: 242, Mismatches: 65, Indels: 48
0.68 0.18 0.14
Matches are distributed among these distances:
28 27 0.11
29 109 0.45
30 88 0.36
31 18 0.07
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36
Consensus pattern (29 bp):
GATTTTTGAAAGGTTCGGGGTAAAAATGG
Found at i:1075 original size:59 final size:58
Alignment explanation
Indices: 1007--1453 Score: 494
Period size: 59 Copynumber: 7.6 Consensus size: 58
997 AAAAAAAAGA
* * *
1007 GATTTTTGGAAGTTCGAGGGTAAAATAGTAATTTTTGAAAGGTTCGGGGTCAAAAATGG
1 GATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGAAA-GTTCGAGGTCAAAAATGG
* ** * *
1066 GGTTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGG
1 GATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTT-GAAAGTTCGAGGTCAAAAATGG
* * * *
1125 GATTTTTGGAAGTTTGGGGGTAAAATGGCAATTTTTAGAAGGTTTGAGGT-AAAAATGG
1 GATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTT-GAAAGTTCGAGGTCAAAAATGG
* * * **
1183 GGTTTTTGGAAGTTT-AGGGGCAAAATGTTAATTTTTAGAAAGTTTAAGGTCAAAAATGG
1 GATTTTTGGAAGTTTGA-GGGTAAAATGGTAATTTTT-GAAAGTTCGAGGTCAAAAATGG
*
1242 GATTTTTGGAAGTTTTG-GGGTAAAATTGTAATTTTTGGAAAGTTCGAGGTCAAAAATGG
1 GATTTTTGGAAG-TTTGAGGGTAAAATGGTAATTTTT-GAAAGTTCGAGGTCAAAAATGG
* * *
1301 GATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAAAATGTTCGAGGT-TAAAATGG
1 GATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGAAA-GTTCGAGGTCAAAAATGG
* * * *
1359 GATTTTTGGAGATTTTG-GGGTAAAATAGTATTTTTTAGAAAGTT-TAGGGTCAAAAATGG
1 GATTTTTGGA-AGTTTGAGGGTAAAATGGTAATTTTT-GAAAGTTCGA-GGTCAAAAATGG
* * *
1418 GA-TTTTGGAAATTCGGGGGTAAAATGGTAATTTTTG
1 GATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTG
1454 GAGAGTTTAA
Statistics
Matches: 338, Mismatches: 38, Indels: 26
0.84 0.09 0.06
Matches are distributed among these distances:
57 6 0.02
58 121 0.36
59 205 0.61
60 6 0.02
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36
Consensus pattern (58 bp):
GATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGAAAGTTCGAGGTCAAAAATGG
Found at i:1218 original size:117 final size:118
Alignment explanation
Indices: 1007--1452 Score: 555
Period size: 117 Copynumber: 3.8 Consensus size: 118
997 AAAAAAAAGA
* * *
1007 GATTTTTGGAAGTTCGAGGGTAAAATAGTAATTTTT-GAAAGGTTCGGGGTCAAAAATGGGGTTT
1 GATTTTTGGAAGTTTGGGGGTAAAATAGTAATTTTTAGAAA-GTTCGAGGTCAAAAATGGGGTTT
* * *
1071 TTGGAAGTTCAAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGG
65 TTGGAAGTTCAGGGGTAAAATGGTAATTTTTAGAAAGTTCGAGGTCAAAAATGG
* * * *
1125 GATTTTTGGAAGTTTGGGGGTAAAATGGCAATTTTTAGAAGGTTTGAGGT-AAAAATGGGGTTTT
1 GATTTTTGGAAGTTTGGGGGTAAAATAGTAATTTTTAGAAAGTTCGAGGTCAAAAATGGGGTTTT
* * * **
1189 TGGAAGTTTAGGGGCAAAATGTTAATTTTTAGAAAGTTTAAGGTCAAAAATGG
66 TGGAAGTTCAGGGGTAAAATGGTAATTTTTAGAAAGTTCGAGGTCAAAAATGG
* * * *
1242 GATTTTTGGAAGTTTTGGGGTAAAATTGTAATTTTTGGAAAGTTCGAGGTCAAAAATGGGATTTT
1 GATTTTTGGAAGTTTGGGGGTAAAATAGTAATTTTTAGAAAGTTCGAGGTCAAAAATGGGGTTTT
** *
1307 TGGAAGTTTGGGGGTAAAATGGTAATTTTTA-AAATGTTCGAGGT-TAAAATGG
66 TGGAAGTTCAGGGGTAAAATGGTAATTTTTAGAAA-GTTCGAGGTCAAAAATGG
* * * *
1359 GATTTTTGG-AGATTTTGGGGTAAAATAGTATTTTTTAGAAAGTT-TAGGGTCAAAAAT-GGGAT
1 GATTTTTGGAAG-TTTGGGGGTAAAATAGTAATTTTTAGAAAGTTCGA-GGTCAAAAATGGGGTT
* *
1421 TTTGGAAATTCGGGGGTAAAATGGTAATTTTT
64 TTTGGAAGTTCAGGGGTAAAATGGTAATTTTT
1453 GGAGAGTTTA
Statistics
Matches: 287, Mismatches: 36, Indels: 12
0.86 0.11 0.04
Matches are distributed among these distances:
116 36 0.13
117 161 0.56
118 87 0.30
119 3 0.01
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36
Consensus pattern (118 bp):
GATTTTTGGAAGTTTGGGGGTAAAATAGTAATTTTTAGAAAGTTCGAGGTCAAAAATGGGGTTTT
TGGAAGTTCAGGGGTAAAATGGTAATTTTTAGAAAGTTCGAGGTCAAAAATGG
Found at i:1250 original size:176 final size:176
Alignment explanation
Indices: 1028--1452 Score: 588
Period size: 176 Copynumber: 2.4 Consensus size: 176
1018 GTTCGAGGGT
*** * *
1028 AAAATAGTAATTTTT-GAAAGGTTCGGGGTCAAAAATGGGGTTTTTGGAAGTTCAAGGGTAAAAT
1 AAAATAGTAATTTTTAGAAA-GTTTAAGGTCAAAAATGGGATTTTTGGAAGTTCAGGGGTAAAAT
* *
1092 GGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGCAAT
65 GGTAATTTTTAGAAAGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGCAAT
* * *
1157 TTTTAGAAGGTTTGAGGTAAAAATGGGGTTTTTGGA-AGTTTAGGGGC
130 TTTTAAAAGGTTCGAGGTAAAAATGGGATTTTTGGAGA-TTTAGGGGC
**
1204 AAAAT-GTTAATTTTTAGAAAGTTTAAGGTCAAAAATGGGATTTTTGGAAGTTTTGGGGTAAAAT
1 AAAATAG-TAATTTTTAGAAAGTTTAAGGTCAAAAATGGGATTTTTGGAAGTTCAGGGGTAAAAT
* * *
1268 TGTAATTTTTGGAAAGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAAT
65 GGTAATTTTTAGAAAGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGCAAT
* * * *
1333 TTTTAAAATGTTCGAGGTTAAAATGGGATTTTTGGAGATTTTGGGGT
130 TTTTAAAAGGTTCGAGGTAAAAATGGGATTTTTGGAGATTTAGGGGC
* * * *
1380 AAAATAGTATTTTTTAGAAAGTTTAGGGTCAAAAATGGGA-TTTTGGAAATTCGGGGGTAAAATG
1 AAAATAGTAATTTTTAGAAAGTTTAAGGTCAAAAATGGGATTTTTGGAAGTTCAGGGGTAAAATG
1444 GTAATTTTT
66 GTAATTTTT
1453 GGAGAGTTTA
Statistics
Matches: 220, Mismatches: 25, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
175 30 0.14
176 184 0.84
177 6 0.03
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (176 bp):
AAAATAGTAATTTTTAGAAAGTTTAAGGTCAAAAATGGGATTTTTGGAAGTTCAGGGGTAAAATG
GTAATTTTTAGAAAGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGCAATT
TTTAAAAGGTTCGAGGTAAAAATGGGATTTTTGGAGATTTAGGGGC
Done.