Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_410 ID=scaffold_410-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: 7830
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.30
Warning! 469 characters in sequence are not A, C, G, or T
Found at i:142 original size:46 final size:46
Alignment explanation
Indices: 90--398 Score: 167
Period size: 46 Copynumber: 6.8 Consensus size: 46
80 ATCTGCTTCG
*
90 CTGCCAAATACAGGAAGGCAAGATATGCAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGAAGGTAAGATATGCAATCTTCAATCTATTCCA
* * * * * *
136 CTGCCAAATACAGGGAGATAGAGTTATTG---GCTTCAATGTACTCCA
1 CTGCCAAATACAGGAAGGTA-AGATA-TGCAATCTTCAATCTATTCCA
* * * * * * * * *
181 CTG--TAGTCATAGGAAGGTAAAATCTGCCATCTTCGATCTGCTT-CG
1 CTGCCAAAT-ACAGGAAGGTAAGATATGCAATCTTCAATCT-ATTCCA
226 CTGCCAAATACAGGAAGGTAAGATATGCAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGAAGGTAAGATATGCAATCTTCAATCTATTCCA
* * * *
272 CTGCCAAATACAAGG-AGATAGAGTTATTG--A-CTTCAATGTACTCCA
1 CTGCCAAATAC-AGGAAGGTA-AGATA-TGCAATCTTCAATCTATTCCA
* * * * * * * * *
317 CTG--TAGTCACAGGGAGGTAAAATCTGCCATTTTCAATCTGCTT-CG
1 CTGCCAAAT-ACAGGAAGGTAAGATATGCAATCTTCAATCT-ATTCCA
* *
362 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAA
1 CTGCCAAATACAGGAAGGTAAGATATGCAATCTTCAA
399 CCAGCTCTGC
Statistics
Matches: 190, Mismatches: 52, Indels: 42
0.67 0.18 0.15
Matches are distributed among these distances:
42 4 0.02
43 11 0.06
44 15 0.08
45 56 0.29
46 85 0.45
47 15 0.08
48 4 0.02
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (46 bp):
CTGCCAAATACAGGAAGGTAAGATATGCAATCTTCAATCTATTCCA
Found at i:249 original size:136 final size:135
Alignment explanation
Indices: 1--398 Score: 699
Period size: 136 Copynumber: 2.9 Consensus size: 135
*
1 ACTGCCAAATACAGGGAGATAGAGTTATCGACTTCAATGTACTCCACTGTAGTC-AGGGAGGTAA
1 ACTGCCAAATACAGGGAGATAGAGTTATTGACTTCAATGTACTCCACTGTAGTCAAGGGAGGTAA
65 AATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATATGCAATCTTCAATCT
66 AATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATATGCAATCTTCAATCT
130 ATTCC
131 ATTCC
* *
135 ACTGCCAAATACAGGGAGATAGAGTTATTGGCTTCAATGTACTCCACTGTAGTCATAGGAAGGTA
1 ACTGCCAAATACAGGGAGATAGAGTTATTGACTTCAATGTACTCCACTGTAGTCA-AGGGAGGTA
*
200 AAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGTAAGATATGCAATCTTCAATC
65 AAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATATGCAATCTTCAATC
265 TATTCC
130 TATTCC
*
271 ACTGCCAAATACAAGGAGATAGAGTTATTGACTTCAATGTACTCCACTGTAGTCACAGGGAGGTA
1 ACTGCCAAATACAGGGAGATAGAGTTATTGACTTCAATGTACTCCACTGTAGTCA-AGGGAGGTA
* * *
336 AAATCTGCCATTTTCAATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAA
65 AAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATATGCAATCTTCAA
399 CCAGCTCTGC
Statistics
Matches: 250, Mismatches: 12, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
134 52 0.21
136 198 0.79
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (135 bp):
ACTGCCAAATACAGGGAGATAGAGTTATTGACTTCAATGTACTCCACTGTAGTCAAGGGAGGTAA
AATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATATGCAATCTTCAATCT
ATTCC
Found at i:520 original size:86 final size:86
Alignment explanation
Indices: 352--825 Score: 734
Period size: 86 Copynumber: 5.5 Consensus size: 86
342 GCCATTTTCA
* * *
352 ATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAACCAGCTCTGCTAC-AATC
1 ATCTGCTTCGCTGTC-AATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTGCTACAAAT-
*
416 GAGAGAGACAAGGTTTGTCTTCG
64 GAGAGAGGCAAGGTTTGTCTTCG
* * * *
439 ATCTGCTTCGTTGTCAATGCAAGAAGGCAAGATCTGCTATCTTCAACCAGCTCTGCTACGAATAA
1 ATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTGCTACAAATGA
*
504 GAGAGACAAGGTTTGTCTTCG
66 GAGAGGCAAGGTTTGTCTTCG
* * * *
525 ATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTGTTATCTTCAACCAGCTTTGCTACGAATGA
1 ATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTGCTACAAATGA
590 GAGAGGCAAGGTTTGTCTTCG
66 GAGAGGCAAGGTTTGTCTTCG
*
611 ATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTGCTACAAATGA
1 ATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTGCTACAAATGA
676 GAGAGGCAAGGTTTGTCTTCG
66 GAGAGGCAAGGTTTGTCTTCG
* * * *
697 ATCCGCTTCGCTGTTAATGTAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTGCTACAAACGA
1 ATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTGCTACAAATGA
* *
762 AAGAGGCAAGGTTTGTCTTCA
66 GAGAGGCAAGGTTTGTCTTCG
*
783 ATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCCATCTT
1 ATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTT
826 TACTAATCTG
Statistics
Matches: 357, Mismatches: 29, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
86 341 0.96
87 16 0.04
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (86 bp):
ATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTGCTACAAATGA
GAGAGGCAAGGTTTGTCTTCG
Found at i:1756 original size:9 final size:8
Alignment explanation
Indices: 1718--1747 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
1708 TGGCCTCTCC
1718 TTTTTCTT
1 TTTTTCTT
1726 TTTGTTCTT
1 TTT-TTCTT
1735 TTTTTCTT
1 TTTTTCTT
1743 TTTTT
1 TTTTT
1748 GTTTCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (8 bp):
TTTTTCTT
Found at i:2218 original size:8 final size:8
Alignment explanation
Indices: 2196--2298 Score: 74
Period size: 8 Copynumber: 13.5 Consensus size: 8
2186 TTATTTTTTA
*
2196 TTTTTTAT
1 TTTTTTGT
2204 TTTTTTGT
1 TTTTTTGT
2212 TTTTTTG-
1 TTTTTTGT
*
2219 -CTTTTGT
1 TTTTTTGT
* *
2226 TTTCTCGT
1 TTTTTTGT
2234 TTTTTT-T
1 TTTTTTGT
*
2241 TTTGCTT-T
1 TTT-TTTGT
*
2249 TTTTTTGC
1 TTTTTTGT
*
2257 TTTTTTGC
1 TTTTTTGT
2265 TTTTTTG-
1 TTTTTTGT
* *
2272 CTCTTT-T
1 TTTTTTGT
2279 TTTTTTGT
1 TTTTTTGT
2287 TTTTTTGT
1 TTTTTTGT
2295 TTTT
1 TTTT
2299 GCCTCTACTG
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
6 5 0.07
7 14 0.19
8 56 0.75
ACGTcount: A:0.01, C:0.08, G:0.10, T:0.82
Consensus pattern (8 bp):
TTTTTTGT
Found at i:2228 original size:11 final size:11
Alignment explanation
Indices: 2211--2262 Score: 59
Period size: 11 Copynumber: 4.4 Consensus size: 11
2201 TATTTTTTTG
2211 TTTTTTTGCTT
1 TTTTTTTGCTT
*
2222 TTGTTTTCTCGTTTT
1 TT-TTTT-T-G-CTT
2237 TTTTTTTGCTT
1 TTTTTTTGCTT
2248 TTTTTTTGCTT
1 TTTTTTTGCTT
2259 TTTT
1 TTTT
2263 GCTTTTTTGC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
11 19 0.54
12 5 0.14
13 2 0.06
14 5 0.14
15 4 0.11
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.81
Consensus pattern (11 bp):
TTTTTTTGCTT
Found at i:2253 original size:45 final size:40
Alignment explanation
Indices: 2189--2292 Score: 120
Period size: 45 Copynumber: 2.5 Consensus size: 40
2179 TTTTCTCTTA
* *
2189 TTTTTTATTTT-TTATTTTTTTGTTTTTTTGCTTTTGTTTTCTC
1 TTTTTT-TTTTGTT-TTTTTTTGCTTTTTTGC-TTT-TTTGCTC
2232 GTTTTTTTTTTTGCTTTTTTTTTGCTTTTTTGCTTTTTTGCTC
1 --TTTTTTTTTTG-TTTTTTTTTGCTTTTTTGCTTTTTTGCTC
2275 TTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTGTTTTTTT
2293 GTTTTTGCCT
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
40 7 0.13
41 11 0.20
43 6 0.11
44 7 0.13
45 22 0.40
46 2 0.04
ACGTcount: A:0.02, C:0.08, G:0.09, T:0.82
Consensus pattern (40 bp):
TTTTTTTTTTGTTTTTTTTTGCTTTTTTGCTTTTTTGCTC
Found at i:2279 original size:19 final size:20
Alignment explanation
Indices: 2237--2281 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
2227 TTCTCGTTTT
**
2237 TTTTTTTGCTTTTTTTTTGC
1 TTTTTTTGCTTTTTTGCTGC
2257 -TTTTTTGCTTTTTTGCT-C
1 TTTTTTTGCTTTTTTGCTGC
2275 TTTTTTT
1 TTTTTTT
2282 TTTGTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.00, C:0.11, G:0.09, T:0.80
Consensus pattern (20 bp):
TTTTTTTGCTTTTTTGCTGC
Done.