Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_369 ID=scaffold_369-JGI_221_v2.0
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: 7806
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Found at i:977 original size:12 final size:12
Alignment explanation
Indices: 793--1040 Score: 247
Period size: 12 Copynumber: 20.8 Consensus size: 12
783 TCTTCTCACG
793 TTTCC-TCTCGC
1 TTTCCTTCTCGC
*
804 TTTCC-TCTCGA
1 TTTCCTTCTCGC
* *
815 TTTTCTTCTCAC
1 TTTCCTTCTCGC
*
827 TTTTCTTCTCGC
1 TTTCCTTCTCGC
*
839 TTTTCC-TCTTGC
1 -TTTCCTTCTCGC
*
851 TTTCCTTCTCGG
1 TTTCCTTCTCGC
863 TTTCCTTCTCGC
1 TTTCCTTCTCGC
875 TTTCCTTCTCGC
1 TTTCCTTCTCGC
*
887 TTTTCC-TCTCGA
1 -TTTCCTTCTCGC
* *
899 TTTTCTTCTCAC
1 TTTCCTTCTCGC
911 GTTT-CTTCTCGC
1 -TTTCCTTCTCGC
*
923 TTTTCC-TCTTGC
1 -TTTCCTTCTCGC
*
935 TTTTCTTCTCGC
1 TTTCCTTCTCGC
947 TTTCCTTCTCGC
1 TTTCCTTCTCGC
959 TTTCCTTCTCGC
1 TTTCCTTCTCGC
**
971 TTTCCTTCTCAA
1 TTTCCTTCTCGC
*
983 TTTCCTTCTAGC
1 TTTCCTTCTCGC
**
995 TTTCCTTCTCAA
1 TTTCCTTCTCGC
**
1007 TTTCCTTCTCAA
1 TTTCCTTCTCGC
1019 TTTCCTTCTCGC
1 TTTCCTTCTCGC
*
1031 TTTCCCTCTC
1 TTTCCTTCTC
1041 ACTGTTTTAC
Statistics
Matches: 198, Mismatches: 31, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
11 27 0.14
12 158 0.80
13 13 0.07
ACGTcount: A:0.04, C:0.37, G:0.07, T:0.52
Consensus pattern (12 bp):
TTTCCTTCTCGC
Found at i:2073 original size:10 final size:10
Alignment explanation
Indices: 2051--2280 Score: 214
Period size: 10 Copynumber: 23.9 Consensus size: 10
2041 CATTGTCGTA
*
2051 TTTTTC-TTA
1 TTTTTCTTTC
*
2060 TTTTTCTTCC
1 TTTTTCTTTC
2070 TTTTTCTTTC
1 TTTTTCTTTC
*
2080 CTTTTCTTTC
1 TTTTTCTTTC
* *
2090 CTTTTCCTTC
1 TTTTTCTTTC
*
2100 CTTTTCTTTC
1 TTTTTCTTTC
2110 TTTTTC-TTC
1 TTTTTCTTTC
2119 TTTTTCTTTC
1 TTTTTCTTTC
*
2129 GTTTTC-TTC
1 TTTTTCTTTC
*
2138 CTTTTCTTTC
1 TTTTTCTTTC
2148 TTTTTCTTTC
1 TTTTTCTTTC
2158 TTTTTCTTTC
1 TTTTTCTTTC
2168 TTTTTC-TTC
1 TTTTTCTTTC
2177 TTTTTCTTTC
1 TTTTTCTTTC
2187 TTTTT-TTTC
1 TTTTTCTTTC
2196 TTTTTC-TTC
1 TTTTTCTTTC
** *
2205 CGTAT-TTTC
1 TTTTTCTTTC
*
2214 TTTCTCTTTC
1 TTTTTCTTTC
2224 TTTTTCTTT-
1 TTTTTCTTTC
2233 TATTTTC-TTC
1 T-TTTTCTTTC
2243 TTTTGT-TTTC
1 TTTT-TCTTTC
* *
2253 ATTTTCCTT-
1 TTTTTCTTTC
*
2262 TGTTTCTTT-
1 TTTTTCTTTC
2271 TATTTTCTTT
1 T-TTTTCTTT
2281 TTCTTTTGTT
Statistics
Matches: 185, Mismatches: 23, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
9 65 0.35
10 120 0.65
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:2075 original size:19 final size:19
Alignment explanation
Indices: 2051--2246 Score: 225
Period size: 19 Copynumber: 10.2 Consensus size: 19
2041 CATTGTCGTA
* *
2051 TTTTTCTTATTTTTCTTCC
1 TTTTTCTTCTTTTTCTTTC
*
2070 TTTTTCTTTCCTTTTCTTTCC
1 TTTTTC-TTCTTTTTCTTT-C
* *
2091 TTTTCCTTCCTTTTCTTTC
1 TTTTTCTTCTTTTTCTTTC
2110 TTTTTCTTCTTTTTCTTTC
1 TTTTTCTTCTTTTTCTTTC
* *
2129 GTTTTCTTCCTTTTCTTTC
1 TTTTTCTTCTTTTTCTTTC
2148 TTTTTCTTTCTTTTTCTTTC
1 TTTTTC-TTCTTTTTCTTTC
2168 TTTTTCTTCTTTTTCTTTC
1 TTTTTCTTCTTTTTCTTTC
* *
2187 TTTTTTTTCTTTTTCTTCC
1 TTTTTCTTCTTTTTCTTTC
* * *
2206 GTATT-TTCTTTCTCTTTC
1 TTTTTCTTCTTTTTCTTTC
*
2224 TTTTTCTTTTATTTTC-TTC
1 TTTTTCTTCT-TTTTCTTTC
2243 TTTT
1 TTTT
2247 GTTTTCATTT
Statistics
Matches: 152, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
18 14 0.09
19 89 0.59
20 43 0.28
21 6 0.04
ACGTcount: A:0.02, C:0.22, G:0.01, T:0.75
Consensus pattern (19 bp):
TTTTTCTTCTTTTTCTTTC
Found at i:2244 original size:29 final size:27
Alignment explanation
Indices: 2051--2285 Score: 183
Period size: 29 Copynumber: 8.3 Consensus size: 27
2041 CATTGTCGTA
*
2051 TTTTTCTTATTTTTCTTCCTTTTTCTTTC
1 TTTTTCTTCTTTTTCTT-C-TTTTCTTTC
* *
2080 CTTTTCTTTCCTTTTCCTTCCTTTTCTTTC
1 TTTTTC-TT-CTTTTTCTT-CTTTTCTTTC
2110 TTTTTCTTCTTTTTCTTTCGTTTTC-TTC
1 TTTTTCTTCTTTTTC-TTC-TTTTCTTTC
*
2138 CTTTTCTTTCTTTTTCTTTCTTTTTCTTTC
1 TTTTTC-TTCTTTTTC-TTC-TTTTCTTTC
*
2168 TTTTTCTTCTTTTTCTTTCTTTTTTTTC
1 TTTTTCTTCTTTTTC-TTCTTTTCTTTC
* *
2196 TTTTTCTTCCGTATT-TTCTTTCTCTTTC
1 TTTTTCTT-CTTTTTCTTCTTT-TCTTTC
* *
2224 TTTTTCTTTTATTTTCTTCTTTTGTTTTC
1 TTTTTCTTCT-TTTTCTTCTTTT-CTTTC
* * *
2253 ATTTTC--CTTTGT-TTCTTTTATTTTC
1 TTTTTCTTCTTTTTCTTCTTTT-CTTTC
2278 TTTTTCTT
1 TTTTTCTT
2286 TTGTTTCCTA
Statistics
Matches: 172, Mismatches: 21, Indels: 28
0.78 0.10 0.13
Matches are distributed among these distances:
25 17 0.10
26 3 0.02
27 7 0.04
28 48 0.28
29 64 0.37
30 24 0.14
31 9 0.05
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (27 bp):
TTTTTCTTCTTTTTCTTCTTTTCTTTC
Found at i:2256 original size:19 final size:19
Alignment explanation
Indices: 2061--2280 Score: 169
Period size: 19 Copynumber: 11.4 Consensus size: 19
2051 TTTTTCTTAT
* *
2061 TTTTCTTCCTTTTTCTTTCC
1 TTTTCTTTCTTTTT-TTTCA
** *
2081 TTTTCTTTCCTTTTCCTTCC
1 TTTTCTTT-CTTTTTTTTCA
* *
2101 TTTTCTTTCTTTTTCTTCT
1 TTTTCTTTCTTTTTTTTCA
* * *
2120 TTTTCTTTCGTTTTCTTCC
1 TTTTCTTTCTTTTTTTTCA
*
2139 TTTTCTTTCTTTTTCTTTCT
1 TTTTCTTTCTTTTT-TTTCA
* *
2159 TTTTCTTTCTTTTTCTTCT
1 TTTTCTTTCTTTTTTTTCA
*
2178 TTTTCTTTCTTTTTTTTCT
1 TTTTCTTTCTTTTTTTTCA
** *
2197 TTTTC-TTCCGTATTTTC-
1 TTTTCTTTCTTTTTTTTCA
*
2214 TTTCTCTTTCTTTTTCTTTTA
1 TTT-TCTTTCTTTTT-TTTCA
2235 TTTTC-TTCTTTTGTTTTCA
1 TTTTCTTTCTTTT-TTTTCA
* *
2254 TTTTCCTTTGTTTCTTTT-A
1 TTTT-CTTTCTTTTTTTTCA
2273 TTTTCTTT
1 TTTTCTTT
2281 TTCTTTTGTT
Statistics
Matches: 169, Mismatches: 22, Indels: 20
0.80 0.10 0.09
Matches are distributed among these distances:
17 3 0.02
18 15 0.09
19 91 0.54
20 47 0.28
21 13 0.08
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTTCTTTCTTTTTTTTCA
Found at i:2288 original size:25 final size:25
Alignment explanation
Indices: 2240--2301 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
2230 TTTTATTTTC
*
2240 TTCTTTTGTTTTCATTTTCCTTTGT
1 TTCTTTTATTTTCATTTTCCTTTGT
* *
2265 TTCTTTTATTTTCTTTTTCTTTTGT
1 TTCTTTTATTTTCATTTTCCTTTGT
*
2290 TTCCTATTATTT
1 TT-CTTTTATTT
2302 CTTGCATTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 24 0.75
26 8 0.25
ACGTcount: A:0.06, C:0.15, G:0.05, T:0.74
Consensus pattern (25 bp):
TTCTTTTATTTTCATTTTCCTTTGT
Found at i:3672 original size:13 final size:13
Alignment explanation
Indices: 3654--3678 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3644 GTTGTAGTTG
3654 TATACCATCATTT
1 TATACCATCATTT
3667 TATACCATCATT
1 TATACCATCATT
3679 ATTGTTTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (13 bp):
TATACCATCATTT
Found at i:4586 original size:280 final size:278
Alignment explanation
Indices: 4038--4597 Score: 1012
Period size: 280 Copynumber: 2.0 Consensus size: 278
4028 ACTAACATGC
4038 AGAGTATAATGAGTTAATTGTGAGAATACTCTTTAAGTGAGCGAGGTGCAATATTTATGAGTTGA
1 AGAGTATAATGAGTTAATTGTGAGAATACTCTTTAAGTGAGCGAGGTGCAATATTTATGAGTTGA
*
4103 GTTGGAGGAGCTGTTATCTCATTAGCTTTATATAATTTAATGACAAAATTTTGGACTGTGCTGCA
66 GTTGGAGGAGCTGTTATCTCATTAGCTTTATATAATTTAATGACAAAATGTTGGACTGTGCTGCA
4168 CCATCGAGTTTATTTACTGGCAGAAATACAGCCTTTCGCTTATTTTTATGAAATGAAGTTTCGTA
131 CCATCGAGTTTATTTACTGGCAGAAATACAGCCTTTCGCTTATTTTTATGAAATGAAGTTTCGTA
*
4233 AAATATTGTAGAAAAAACGTCACCAAAGAACTTAGTATGTCATGAGACGCAAAGGAGAAGTAAAA
196 AAATATTGTAGAAAAAACGTCACCAAAGAACTTAGTATGTCATGAGACACAAAGGAGAAGTAAAA
4298 TATTAATTTTGAAATTTT
261 TATTAATTTTGAAATTTT
* *
4316 AGAGTATAATGAGTTAATTGTGAGACTATACTTTTTTAGTGAGCGAGGTGCAATATTTATGAGTT
1 AGAGTATAATGAGTTAATTGTGAGA--ATACTCTTTAAGTGAGCGAGGTGCAATATTTATGAGTT
*
4381 GAGTTGGAGGAGCTGTTATCTCATTAGGTTTATATAATTTAATGACAAAATGTTGGACTGTGCTG
64 GAGTTGGAGGAGCTGTTATCTCATTAGCTTTATATAATTTAATGACAAAATGTTGGACTGTGCTG
4446 CACCATCGAGTTTATTTACTGGCAGAAATACAGCCTTTCGCTTATTTTTATGAAATGAAGTTTCG
129 CACCATCGAGTTTATTTACTGGCAGAAATACAGCCTTTCGCTTATTTTTATGAAATGAAGTTTCG
* ** *
4511 TAAAATATTGTAGAAAAAACGTCACCAAAGAACTTAGTATGTTATGAGACACCTAGGAGAATTAA
194 TAAAATATTGTAGAAAAAACGTCACCAAAGAACTTAGTATGTCATGAGACACAAAGGAGAAGTAA
*
4576 AATCTTAATTTTGAAATTTT
259 AATATTAATTTTGAAATTTT
4596 AG
1 AG
4598 CCCAAAAAAA
Statistics
Matches: 270, Mismatches: 10, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
278 25 0.09
280 245 0.91
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (278 bp):
AGAGTATAATGAGTTAATTGTGAGAATACTCTTTAAGTGAGCGAGGTGCAATATTTATGAGTTGA
GTTGGAGGAGCTGTTATCTCATTAGCTTTATATAATTTAATGACAAAATGTTGGACTGTGCTGCA
CCATCGAGTTTATTTACTGGCAGAAATACAGCCTTTCGCTTATTTTTATGAAATGAAGTTTCGTA
AAATATTGTAGAAAAAACGTCACCAAAGAACTTAGTATGTCATGAGACACAAAGGAGAAGTAAAA
TATTAATTTTGAAATTTT
Done.