Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_283 ID=scaffold_283-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: 8894
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.30
Warning! 222 characters in sequence are not A, C, G, or T
Found at i:2220 original size:40 final size:40
Alignment explanation
Indices: 2176--2470 Score: 371
Period size: 40 Copynumber: 7.2 Consensus size: 40
2166 TTTTTTTTTG
*
2176 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
1 TCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGA
* **
2216 TCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTTTG-
1 TCTGCTCCACTATTGCTTAGGGAGATAAGA-CT-T-GATGCGA
* * * *
2258 TCCGCTCCGCTACTACTTAGGGAGATAAGACTTGATGCGA
1 TCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGA
* *
2298 TCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTCTG-
1 TCTGCTCCACTATTGCTTAGGGAGATAAGA-CT-TGATGC-GA
2340 TCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGA
1 TCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGA
* * *
2380 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTG-
1 TCTGCTCCACTATTGCTTAGGGAGATAAGA-CT-TGATGC-GA
2422 TCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGA
1 TCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGA
2462 TCTGCTCCA
1 TCTGCTCCA
2471 NNNNNNNNNN
Statistics
Matches: 218, Mismatches: 25, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
39 5 0.02
40 102 0.47
41 12 0.06
42 94 0.43
43 5 0.02
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (40 bp):
TCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGA
Found at i:2308 original size:82 final size:82
Alignment explanation
Indices: 2174--2470 Score: 531
Period size: 82 Copynumber: 3.6 Consensus size: 82
2164 GATTTTTTTT
2174 TGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGA
1 TGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGA
*
2239 GATAAGATCTGTGGTTT
66 GATAAGATCTGTGGTTC
* * *
2256 TGTCCGCTCCGCTACTACTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGA
1 TGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGA
2321 GATAAGATCTGTGGTTC
66 GATAAGATCTGTGGTTC
* *
2338 TGTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGA
1 TGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGA
2403 GATAAGATCTGTGGTTC
66 GATAAGATCTGTGGTTC
*
2420 TGTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCA
1 TGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCA
2471 NNNNNNNNNN
Statistics
Matches: 206, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 206 1.00
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (82 bp):
TGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGA
GATAAGATCTGTGGTTC
Found at i:3086 original size:95 final size:97
Alignment explanation
Indices: 2921--3102 Score: 314
Period size: 95 Copynumber: 1.9 Consensus size: 97
2911 AAGATCTGCA
*
2921 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGGCTTCAATGTACTCTACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTG
*
2986 TAGTCACAGGGAGGTAAAATCTACAATTTTTT
66 TAGTCACAAGGAGGTAAAATCTACAATTTTTT
* *
3018 ATCTTCAATCTATTCCACTGCC-AA-CCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTG
3081 TAGTCACAAGGAGGTAAAATCT
66 TAGTCACAAGGAGGTAAAATCT
3103 GCCATCTTCG
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
95 57 0.70
96 2 0.02
97 22 0.27
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (97 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTG
TAGTCACAAGGAGGTAAAATCTACAATTTTTT
Found at i:3173 original size:46 final size:46
Alignment explanation
Indices: 3123--3314 Score: 123
Period size: 46 Copynumber: 4.3 Consensus size: 46
3113 ATCTGCTTCG
3123 CTGCCAAATACAGGAAAGCAAGATCTGCAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGAAAGCAAGATCTGCAATCTTCAATCTATTCCA
* * * * *
3169 CTGCCAAATACAGG-GAG-ATAGAGT-TATCGA-CTTCAATGTACTCCA
1 CTGCCAAATACAGGAAAGCA-AGA-TCT-GCAATCTTCAATCTATTCCA
* * * * * * * ** * *
3214 CTG--TAGT-CAGGGAGGTAAAATCTGCCATCTTTGATCTGCTT-CG
1 CTGCCAAATACAGGAAAGCAAGATCTGCAATCTTCAATCT-ATTCCA
*
3257 CTGCCAAATGCA-GAAAGGCAAGATCTGCAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGAAA-GCAAGATCTGCAATCTTCAATCTATTCCA
3303 CTGCCAAATACA
1 CTGCCAAATACA
3315 TGGAGATAGA
Statistics
Matches: 103, Mismatches: 30, Indels: 26
0.65 0.19 0.16
Matches are distributed among these distances:
42 7 0.07
43 16 0.16
44 3 0.03
45 28 0.27
46 49 0.48
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (46 bp):
CTGCCAAATACAGGAAAGCAAGATCTGCAATCTTCAATCTATTCCA
Found at i:3219 original size:231 final size:231
Alignment explanation
Indices: 2786--3236 Score: 780
Period size: 231 Copynumber: 2.0 Consensus size: 231
2776 GATCTGGTTT
* *
2786 TCTTCACTCTATTCTACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGT
1 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGT
* * *
2851 AGTCACAGGGAGGTAAAATCTGCCATTTTCGATCTGCTTCGCTACCAAATACAGGAAGGCAAGAT
66 AGTCACAAGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTACCAAATACAGGAAAGCAAGAT
*
2916 CTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGGCTTCAATGTACTC
131 CTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGACTTCAATGTACTC
*
2981 TACTGTAGTCACAGGGAGGTAAAATCTACAATTTTTTA
196 CACTGTAGT--CAGGGAGGTAAAATCTACAATTTTTTA
*
3019 TCTTCAATCTATTCCACTGCC-AA-CCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGT
1 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGT
*
3082 AGTCACAAGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAAGCAAGAT
66 AGTCACAAGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTACCAAATACAGGAAAGCAAGAT
*
3147 CTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGACTTCAATGTACTC
131 CTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGACTTCAATGTACTC
3212 CACTGTAGTCAGGGAGGTAAAATCT
196 CACTGTAGTCAGGGAGGTAAAATCT
3237 GCCATCTTTG
Statistics
Matches: 208, Mismatches: 10, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
229 16 0.08
231 171 0.82
232 2 0.01
233 19 0.09
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (231 bp):
TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGT
AGTCACAAGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTACCAAATACAGGAAAGCAAGAT
CTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGACTTCAATGTACTC
CACTGTAGTCAGGGAGGTAAAATCTACAATTTTTTA
Found at i:3258 original size:134 final size:135
Alignment explanation
Indices: 3018--3428 Score: 663
Period size: 134 Copynumber: 3.1 Consensus size: 135
3008 ACAATTTTTT
*
3018 ATCTTCAATCTATTCCACTGCC-AA-CCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
* *
3081 TAGTCACAAGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAAGCAAGA
66 TAGT-ACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAAGCAAGA
3146 TCTGCA
130 TCTGCA
*
3152 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGACTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
3217 TAGT-CAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATGCA-GAAAGGCAAGA
66 TAGTACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAA-GCAAGA
3280 TCTGCA
130 TCTGCA
* *
3286 ATCTTCAATCTATTCCACTGCCAAATACATGGAGATAGAGTTATTGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
3351 TAGTCACAGGGAGGTAAAA-CTGCCAT-TTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAG
66 TAGT-ACAGGGAGGTAAAATCTGCCATCTTT-GATCTGCTTCGCTGCCAAATACAGGAAAGCAAG
3414 ATCTGCA
129 ATCTGCA
*
3421 ATCCTCAA
1 ATCTTCAA
3429 CCAGCTCTGC
Statistics
Matches: 259, Mismatches: 11, Indels: 13
0.92 0.04 0.05
Matches are distributed among these distances:
133 4 0.02
134 148 0.57
135 50 0.19
136 57 0.22
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (135 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
TAGTACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAAGCAAGAT
CTGCA
Found at i:3499 original size:42 final size:41
Alignment explanation
Indices: 3451--3671 Score: 130
Period size: 42 Copynumber: 5.2 Consensus size: 41
3441 CAATCGAGAG
3451 AGGCAAGGTTTGTCTTCGATCCGCTTCGCTGTTAATGTAGGA
1 AGGCAAGGTTTGTCTTCGATCCGCTTCGCTGTTAATG-AGGA
* * * ***
3493 AGGCAAGATCTGTTATCTTC-AACCAGC-TCTGCTACGAATGA-GA
1 AGGCAAG--GT-TTGTCTTCGATCC-GCTTC-GCTGTTAATGAGGA
* * *
3536 GAGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATACAGGA
1 -AGGCAAGGTTTGTCTTCGATCCGCTTCGCTGTTAAT-GAGGA
* * * ***
3579 AGGCAAGATCTGCTATCTTC-AACCAGC-TCTGCTACAAATGA-GA
1 AGGCAAGGT-T--TGTCTTCGATCC-GCTTC-GCTGTTAATGAGGA
3622 GAGGCAAGGTTTGTCTTCGATCCGCTTCGCTGTTAATGCAGGA
1 -AGGCAAGGTTTGTCTTCGATCCGCTTCGCTGTTAATG-AGGA
3665 AGGCAAG
1 AGGCAAG
3672 ATCTGCTATC
Statistics
Matches: 131, Mismatches: 28, Indels: 40
0.66 0.14 0.20
Matches are distributed among these distances:
41 30 0.23
42 34 0.26
43 10 0.08
44 27 0.21
45 30 0.23
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.28
Consensus pattern (41 bp):
AGGCAAGGTTTGTCTTCGATCCGCTTCGCTGTTAATGAGGA
Found at i:3524 original size:86 final size:86
Alignment explanation
Indices: 3378--3769 Score: 606
Period size: 86 Copynumber: 4.5 Consensus size: 86
3368 AACTGCCATT
* * * * *
3378 TTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCCTCAACCAGCTCTGCTAC-
1 TTCGATCCGCTTCGCTGTC-AATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTGCTACA
3442 AATCGAGAGAGGCAAGGTTTGTC
65 AAT-GAGAGAGGCAAGGTTTGTC
* * * *
3465 TTCGATCCGCTTCGCTGTTAATGTAGGAAGGCAAGATCTGTTATCTTCAACCAGCTCTGCTACGA
1 TTCGATCCGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTGCTACAA
3530 ATGAGAGAGGCAAGGTTTGTC
66 ATGAGAGAGGCAAGGTTTGTC
* *
3551 TTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTGCTACAA
1 TTCGATCCGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTGCTACAA
3616 ATGAGAGAGGCAAGGTTTGTC
66 ATGAGAGAGGCAAGGTTTGTC
*
3637 TTCGATCCGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTGCTACAA
1 TTCGATCCGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTGCTACAA
* *
3702 ACGAAAGAGGCAAGGTTTGTC
66 ATGAGAGAGGCAAGGTTTGTC
* * *
3723 TTCAATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCCATCTT
1 TTCGATCCGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTT
3770 TACTGATCTG
Statistics
Matches: 281, Mismatches: 23, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
86 262 0.93
87 19 0.07
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (86 bp):
TTCGATCCGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTGCTACAA
ATGAGAGAGGCAAGGTTTGTC
Found at i:3543 original size:44 final size:44
Alignment explanation
Indices: 3493--3715 Score: 128
Period size: 41 Copynumber: 5.2 Consensus size: 44
3483 TAATGTAGGA
*
3493 AGGCAAGATCTGTTATCTTCAACCAGCTCTGCTACGAATGAGAG
1 AGGCAAGATCTGTTATCTTCAACCAGCTCTGCTACAAATGAGAG
* * * * * * *
3537 AGGCAAG--GT-TTGTCTTCGATCTGCT-TCGCTGTC-AAT-ACAGG
1 AGGCAAGATCTGTTATCTTCAACCAGCTCT-GCT-ACAAATGAGA-G
*
3578 AAGGCAAGATCTGCTATCTTCAACCAGCTCTGCTACAAATGAGAG
1 -AGGCAAGATCTGTTATCTTCAACCAGCTCTGCTACAAATGAGAG
* * * ***
3623 AGGCAAG--GT-TTGTCTTCGATCC-GCT-TCGCTGTTAATGCAG-G
1 AGGCAAGATCTGTTATCTTC-AACCAGCTCT-GCTACAAATG-AGAG
* * *
3664 AAGGCAAGATCTGCTATCTTCAACCAGCTCTGCTACAAACGAAAG
1 -AGGCAAGATCTGTTATCTTCAACCAGCTCTGCTACAAATGAGAG
3709 AGGCAAG
1 AGGCAAG
3716 GTTTGTCTTC
Statistics
Matches: 128, Mismatches: 31, Indels: 40
0.64 0.16 0.20
Matches are distributed among these distances:
40 4 0.03
41 36 0.28
42 22 0.17
44 28 0.22
45 34 0.27
46 4 0.03
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (44 bp):
AGGCAAGATCTGTTATCTTCAACCAGCTCTGCTACAAATGAGAG
Found at i:4749 original size:12 final size:11
Alignment explanation
Indices: 4732--4774 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
4722 CCTCTCCTTT
4732 TTCTTTTTGTTA
1 TTCTTTTT-TTA
*
4744 TTCTTTTCTT-
1 TTCTTTTTTTA
4754 TTCTTTTTTTA
1 TTCTTTTTTTA
4765 TTTCTTTTTT
1 -TTCTTTTTT
4775 CAAGTGAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.33
11 2 0.07
12 16 0.59
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (11 bp):
TTCTTTTTTTA
Found at i:4755 original size:22 final size:22
Alignment explanation
Indices: 4730--4772 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4720 GGCCTCTCCT
4730 TTTTCTTTTTGTTA-TTCTTTTC
1 TTTTCTTTTT-TTATTTCTTTTC
4752 TTTTCTTTTTTTATTTCTTTT
1 TTTTCTTTTTTTATTTCTTTT
4773 TTCAAGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (22 bp):
TTTTCTTTTTTTATTTCTTTTC
Found at i:5252 original size:33 final size:29
Alignment explanation
Indices: 5215--5290 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 29
5205 TATTCTTTTA
*
5215 TTTTTGTTTTTTTTTGCTTTTGTTTTCTCGTT
1 TTTTTGTTTTTTTTTGC-TTT-TTTGCTC-TT
5247 TTTTT-TACTTTTTTTTGCTTTTTTGCTCTT
1 TTTTTGT--TTTTTTTTGCTTTTTTGCTCTT
5277 TTTTTGTTTTTTTT
1 TTTTTGTTTTTTTT
5291 ATTTTTGCCT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
29 7 0.17
30 7 0.17
31 8 0.20
32 8 0.20
33 10 0.25
ACGTcount: A:0.01, C:0.09, G:0.09, T:0.80
Consensus pattern (29 bp):
TTTTTGTTTTTTTTTGCTTTTTTGCTCTT
Done.