Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004336.1 Kokia drynarioides strain JFW-HI SEQ_117664, 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: 2578
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Found at i:1674 original size:97 final size:97
Alignment explanation
Indices: 1506--1691 Score: 259
Period size: 97 Copynumber: 1.9 Consensus size: 97
1496 GAGAAGGATG
* *
1506 TTCGATTATCTCGATTTGAAGAAAAGTCGCACCTAGTAAGTTAATGCACAAATTTTCAGAATTAG
1 TTCGATTATCTCAATTTGAAGAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATTAG
* *
1571 AGATAAAGA-AACATTGTCTTGATTAAAGGGTA
66 AAATAAA-ACAACATTGCCTTGATTAAAGGGTA
* ** *
1603 TTCGATTATTTCAATTTGAAGAAAAGTCGTGCCTAGTAAGTTAAGGCACAAATTTTCA-ACATTC
1 TTCGATTATCTCAATTTGAAGAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCAGA-ATTA
*
1667 GAAATAAAACAATATTGCCTTGATT
65 GAAATAAAACAACATTGCCTTGATT
1692 TTAAAGTTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
96 2 0.03
97 76 0.97
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (97 bp):
TTCGATTATCTCAATTTGAAGAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATTAG
AAATAAAACAACATTGCCTTGATTAAAGGGTA
Found at i:1986 original size:26 final size:27
Alignment explanation
Indices: 1916--1988 Score: 103
Period size: 28 Copynumber: 2.7 Consensus size: 27
1906 TAAATATCCG
*
1916 AGGGCAAAATGGTAATTTTAAACACTT
1 AGGGGAAAATGGTAATTTTAAACACTT
* *
1943 GGGGGCAAAATGGTAATTTTAGACACTT
1 AGGGG-AAAATGGTAATTTTAAACACTT
1971 AGGGG-AAATGGTAATTTT
1 AGGGGAAAATGGTAATTTT
1989 GGGAAATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
26 13 0.32
27 3 0.07
28 25 0.61
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (27 bp):
AGGGGAAAATGGTAATTTTAAACACTT
Found at i:2018 original size:30 final size:31
Alignment explanation
Indices: 1976--2258 Score: 154
Period size: 30 Copynumber: 9.6 Consensus size: 31
1966 CACTTAGGGG
* *
1976 AAATGGTAATTTTGGGAAATTTCGGGGTCAA
1 AAATGGTAATTTTTGGAAAATTCGGGGTCAA
* *
2007 AAATGG-AATTTTTAG-ACATTCAGGGGT--A
1 AAATGGTAATTTTTGGAAAATTC-GGGGTCAA
* * * *
2035 AAATGATAGTTTTTGGAAAAATCGAGGTCAA
1 AAATGGTAATTTTTGGAAAATTCGGGGTCAA
* *
2066 AAATGG-AAATTTTGG-AAGTTCGAGGGT---
1 AAATGGTAATTTTTGGAAAATTCG-GGGTCAA
* *
2093 AAATGGTAATTTTTGGAAAAATCGGGATCAA
1 AAATGGTAATTTTTGGAAAATTCGGGGTCAA
* *
2124 AAATGG-AATTTTTGG-AAGTTCAGGGGT--T
1 AAATGGTAATTTTTGGAAAATTC-GGGGTCAA
* * **
2152 AAATGTTAATATTTGGAGAAA-TCAAGGTCAA
1 AAATGGTAATTTTTGGA-AAATTCGGGGTCAA
* * *
2183 AAA-GGGAATTTTTGG-AAGTTCAAGGGT--A
1 AAATGGTAATTTTTGGAAAATTC-GGGGTCAA
* * *
2211 AAATGATAATTTTTGGAAAAATCGAGGTCAA
1 AAATGGTAATTTTTGGAAAATTCGGGGTCAA
* *
2242 AAA-GGGAATTCTTGGAA
1 AAATGGTAATTTTTGGAA
2259 GTTTGGTGGC
Statistics
Matches: 185, Mismatches: 44, Indels: 47
0.67 0.16 0.17
Matches are distributed among these distances:
27 6 0.03
28 28 0.15
29 55 0.30
30 69 0.37
31 27 0.15
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.30
Consensus pattern (31 bp):
AAATGGTAATTTTTGGAAAATTCGGGGTCAA
Found at i:2068 original size:59 final size:58
Alignment explanation
Indices: 1971--2261 Score: 347
Period size: 59 Copynumber: 5.0 Consensus size: 58
1961 TTAGACACTT
* * ** * *
1971 AGGGG-AAATGGTAATTTTGGGAAATTTCGGGGTCAAAAATGGAATTTTTAGACA-TTC
1 AGGGGTAAATGATAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGA-AGTTC
* *
2028 AGGGGTAAAATGATAGTTTTTGGAAAAATCGAGGTCAAAAATGGAAATTTTGGAAGTTC
1 AGGGGT-AAATGATAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTC
*
2087 -GAGGGTAAATGGTAATTTTTGGAAAAATCG-GGATCAAAAATGGAATTTTTGGAAGTTC
1 AG-GGGTAAATGATAATTTTTGGAAAAATCGAGG-TCAAAAATGGAATTTTTGGAAGTTC
* * * * *
2145 AGGGGTTAAATGTTAATATTTGGAGAAATCAAGGTCAAAAAGGGAATTTTTGGAAGTTC
1 AGGGG-TAAATGATAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTC
* * *
2204 AAGGGTAAAATGATAATTTTTGGAAAAATCGAGGTCAAAAAGGGAATTCTTGGAAGTT
1 AGGGGT-AAATGATAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTT
2262 TGGTGGCTAA
Statistics
Matches: 203, Mismatches: 22, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
57 7 0.03
58 52 0.26
59 142 0.70
60 2 0.01
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.30
Consensus pattern (58 bp):
AGGGGTAAATGATAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTC
Found at i:2105 original size:117 final size:117
Alignment explanation
Indices: 1971--2261 Score: 377
Period size: 117 Copynumber: 2.5 Consensus size: 117
1961 TTAGACACTT
* * **
1971 AGGGGAAATGGTAATTTTGGGAAATTTCGGGGTCAAAAATGGAATTTTTAGACA-TTCAGGGGTA
1 AGGGTAAATGGTAATTTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTAGA-AGTTCAGGGGTA
* * * * *
2035 AAATGATAGTTTTTGGAAAAATCGAGGTCAAAAATGGAAATTTTGGAAGTTCG
65 AAATGATAATATTTGGAAAAATCAAGGTCAAAAAGGGAAATTTTGGAAGTTCA
* * *
2088 AGGGTAAATGGTAATTTTTGGAAAAATCGGGATCAAAAATGGAATTTTTGGAAGTTCAGGGGTTA
1 AGGGTAAATGGTAATTTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTAGAAGTTCAGGGGTAA
* * *
2153 AATGTTAATATTTGGAGAAATCAAGGTCAAAAAGGGAATTTTTGGAAGTTCA
66 AATGATAATATTTGGAAAAATCAAGGTCAAAAAGGGAAATTTTGGAAGTTCA
* * * * *
2205 AGGGTAAAATGATAATTTTTGGAAAAATCGAGGTCAAAAAGGGAATTCTTGGAAGTT
1 AGGGT-AAATGGTAATTTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTAGAAGTT
2262 TGGTGGCTAA
Statistics
Matches: 152, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
116 1 0.01
117 105 0.69
118 46 0.30
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.30
Consensus pattern (117 bp):
AGGGTAAATGGTAATTTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTAGAAGTTCAGGGGTAA
AATGATAATATTTGGAAAAATCAAGGTCAAAAAGGGAAATTTTGGAAGTTCA
Done.