Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_224 ID=scaffold_224-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: 9188
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Found at i:1100 original size:13 final size:12
Alignment explanation
Indices: 1075--1120 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
1065 TAGTAGAAAC
1075 TAAAAAAAT--A
1 TAAAAAAATAAA
*
1085 TAATAAAATATAA
1 TAAAAAAATA-AA
1098 TAAAAAAATGAAA
1 TAAAAAAAT-AAA
1111 TAAAAAAATA
1 TAAAAAAATA
1121 CAAGAACTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 8 0.27
12 1 0.03
13 20 0.67
14 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (12 bp):
TAAAAAAATAAA
Found at i:1991 original size:44 final size:44
Alignment explanation
Indices: 1943--2335 Score: 168
Period size: 44 Copynumber: 9.1 Consensus size: 44
1933 CAAAGGTATT
* *
1943 GGATTCATCGTTTTAATCCGCTCCACTGCAACTTTAGGGAGATA
1 GGATTCATCGTTTTAATCCACTCCACTGCAACTTCAGGGAGATA
*** * ** *
1987 GGATT-AGTAACTTCAATCTGCTCCACTGCAACTTCAGAGAGATAA
1 GGATTCA-TCGTTTTAATCCACTCCACTGCAACTTCAGGGAGAT-A
* ** * * *
2032 GGCTGGATGCG-----ATCTACTCTACTGCAACTTCAGAGAGATA
1 GGATTCAT-CGTTTTAATCCACTCCACTGCAACTTCAGGGAGATA
* * * *
2072 AGA-TCTGTTGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
1 GGATTC-ATCGTTTTAATCCACTCCACTGCAACTTCAGGGAGATA
** * * * ** * * *
2116 GGATTTGTAGCTTCAATCTTCTTCGCAGCAACTTCAGGG-GTATA
1 GGATTCATCGTTTTAATCCACTCCACTGCAACTTCAGGGAG-ATA
* * * *
2160 GAATTCATCATTTTAATCCACTCCACTGCAACTTTAGGGAGACA
1 GGATTCATCGTTTTAATCCACTCCACTGCAACTTCAGGGAGATA
* **
2204 GGATT-AGC-TTCTTCTGTCCACTCCACTGCAACTTCAGGGAGATAA
1 GGATTCATCGTT-TT-AATCCACTCCACTGCAACTTCAGGGAGAT-A
* * ** * * * *
2249 GG---C-TGGATGCAATCTACTCTACTGCAACTTTAGAGAGATA
1 GGATTCATCGTTTTAATCCACTCCACTGCAACTTCAGGGAGATA
* * * *
2289 AGA-TCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
1 GGATTC-ATCGTTTTAATCCACTCCACTGCAACTTCAGGGAGATA
2333 GGA
1 GGA
2336 ATGGCTTATT
Statistics
Matches: 253, Mismatches: 74, Indels: 44
0.68 0.20 0.12
Matches are distributed among these distances:
39 1 0.00
40 5 0.02
41 49 0.19
42 3 0.01
43 7 0.03
44 177 0.70
45 10 0.04
46 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (44 bp):
GGATTCATCGTTTTAATCCACTCCACTGCAACTTCAGGGAGATA
Found at i:2195 original size:217 final size:217
Alignment explanation
Indices: 1926--2335 Score: 660
Period size: 217 Copynumber: 1.9 Consensus size: 217
1916 CTGACCCTCT
* * * * *
1926 GCAACTTCAAAGGTATTGGATTCATCGTTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGAT
1 GCAACTTCAAAGGTATAGAATTCATCATTTTAATCCACTCCACTGCAACTTTAGGGAGACAGGAT
** *
1991 TAG-TAACTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGGCTGGATGCGATCTACTCTACT
66 TAGCT-ACTTCAATCCACTCCACTGCAACTTCAGAGAGATAAGGCTGGATGCAATCTACTCTACT
*
2055 GCAACTTCAGAGAGATAAGATCTGTTGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGAT
130 GCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGAT
2120 TTGTAGCTTCAATCTTCTTCGCA
195 TTGTAGCTTCAATCTTCTTCGCA
**
2143 GCAACTTCAGGGGTATAGAATTCATCATTTTAATCCACTCCACTGCAACTTTAGGGAGACAGGAT
1 GCAACTTCAAAGGTATAGAATTCATCATTTTAATCCACTCCACTGCAACTTTAGGGAGACAGGAT
* ** *
2208 TAGCTTCTTCTGTCCACTCCACTGCAACTTCAGGGAGATAAGGCTGGATGCAATCTACTCTACTG
66 TAGCTACTTCAATCCACTCCACTGCAACTTCAGAGAGATAAGGCTGGATGCAATCTACTCTACTG
*
2273 CAACTTTAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGA
131 CAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGA
2336 ATGGCTTATT
Statistics
Matches: 176, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
217 175 0.99
218 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (217 bp):
GCAACTTCAAAGGTATAGAATTCATCATTTTAATCCACTCCACTGCAACTTTAGGGAGACAGGAT
TAGCTACTTCAATCCACTCCACTGCAACTTCAGAGAGATAAGGCTGGATGCAATCTACTCTACTG
CAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATT
TGTAGCTTCAATCTTCTTCGCA
Found at i:2481 original size:100 final size:99
Alignment explanation
Indices: 2344--2855 Score: 542
Period size: 100 Copynumber: 5.1 Consensus size: 99
2334 GAATGGCTTA
* * * ** * * *
2344 TTCAATCTGTTTAACTGTAATGTCGGGGAAGTAAGATTCGCCATCGTAGCTTCAGTCTATTCCAC
1 TTCAATCT-TTTAATTGCAATGTCAGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCAC
* *
2409 TGCACCGCCTGGAAAGTAAGATTTGTCGTTGTAGC
65 TGCACCGCCTGGAAAGTAAGATTTGCCGTTGTGGC
* *
2444 CTCAATCTTTTAAATTGTAATGTCAGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCAC
1 TTCAATCTTTT-AATTGCAATGTCAGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCAC
* * *
2509 TGCACTGCCTGGGAAGTAAGATTTACCGTTGTGGC
65 TGCACCGCCTGGAAAGTAAGATTTGCCGTTGTGGC
* * *
2544 TTCAATCTTTTAAATTGCAATGTCAGGGAAGCGAGGTTCGCCGTTGTAGCTTCAATCTGTTCCAT
1 TTCAATCTTTT-AATTGCAATGTCAGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCAC
* * * * * * ** * *
2609 TACATCGCCAGGGAAGTGAGGTTCACTGTTGTAGC
65 TGCACCGCCTGGAAAGTAAGATTTGCCGTTGTGGC
* * * * *
2644 TTCAATCTATTTGACTGCAATGT-TGAGGAAGCAAGATTCGCCATCGTAGCTTCAATCTGTTCCA
1 TTCAATCT-TTTAATTGCAATGTCAG-GGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
* *
2708 CTGCATCGCCTGGGAAGGTAAGATTCT-CCGTTGTGGC
64 CTGCACCGCCT-GGAAAGTAAGATT-TGCCGTTGTGGC
* * * * *
2745 CTCAATCTTTTAATTGCAATGTCAGGGAAGCGAGATTTGCCGTTGTGGCTTCAATCTATTCCACT
1 TTCAATCTTTTAATTGCAATGTCAGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACT
* * * *
2810 GCACCACCTGAGAGAGTAAGATTCGCCATTGTGGC
66 GCACCGCCTG-GAAAGTAAGATTTGCCGTTGTGGC
2845 TTCAATCTTTT
1 TTCAATCTTTT
2856 TGACTGCAAT
Statistics
Matches: 343, Mismatches: 61, Indels: 16
0.82 0.15 0.04
Matches are distributed among these distances:
99 5 0.01
100 310 0.90
101 28 0.08
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (99 bp):
TTCAATCTTTTAATTGCAATGTCAGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACT
GCACCGCCTGGAAAGTAAGATTTGCCGTTGTGGC
Found at i:2523 original size:50 final size:50
Alignment explanation
Indices: 2377--2812 Score: 270
Period size: 50 Copynumber: 8.7 Consensus size: 50
2367 CGGGGAAGTA
* * * ** * * **
2377 AGATTCGCCATCGTAGCTTCAGTCTATTCCACTGCACCGCCTGGAAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCAATGCCAGGGAAGCG
* * * * ** * * *
2427 AGATTTGTCGTTGTAGCCTCAATCTTTTAAATTGTAATGTCAGGGAAGCG
1 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCAATGCCAGGGAAGCG
* * * * **
2477 AGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCCTGGGAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCAATGCCAGGGAAGCG
** * * ** * *
2527 AGATTTACCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAGCG
1 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCAATGCCAGGGAAGCG
* * * * *
2577 AGGTTCGCCGTTGTAGCTTCAATCTGTTCCATTAC-ATCGCCAGGGAAGTG
1 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCAAT-GCCAGGGAAGCG
* * * ** ** *
2627 AGGTTCACTGTTGTAGCTTCAATCTATTTGACTGCAATG-TTGAGGAAGCA
1 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCAATGCCAG-GGAAGCG
* * * *
2677 AGATTCGCCATCGTAGCTTCAATCTGTTCCACTGC-ATCGCCTGGGAAG-G
1 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCAAT-GCCAGGGAAGCG
* * * ** * *
2726 TAAGATTCTCCGTTGTGGCCTCAATCT-TTTAATTGCAATGTCAGGGAAGCG
1 --AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCAATGCCAGGGAAGCG
* *
2777 AGATTTGCCGTTGTGGCTTCAATCTATTCCACTGCA
1 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCA
2813 CCACCTGAGA
Statistics
Matches: 284, Mismatches: 92, Indels: 20
0.72 0.23 0.05
Matches are distributed among these distances:
49 27 0.10
50 230 0.81
51 27 0.10
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.31
Consensus pattern (50 bp):
AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCAATGCCAGGGAAGCG
Found at i:2723 original size:150 final size:149
Alignment explanation
Indices: 2344--2801 Score: 384
Period size: 150 Copynumber: 3.1 Consensus size: 149
2334 GAATGGCTTA
* * *
2344 TTCAATCTGTTTAACTGTAATGTCGGGGAAGTAAGATTCGCCATCGTAGCTTCAGTCTATTCCAC
1 TTCAATCTGTTTAACTGCAATGT-TGGGAAGTAAGATTCGCCATCGTAGCTTCAATCTATTCCAC
* * * * * * *
2409 TGCACCGCCTGGAAAGTAAGATTTGTCGTTGTAGCCTCAATCTTTTAAATTGTAATGTCAGGGAA
65 TGCATCGCCTGGGAAGCAAGATTCGCCGTTGTAGCCTCAATCTGTTAAATTGTAATGCCAGGGAA
*
2474 GCGAGATTCGCCGTCGTAGC
130 GCGAGATTCACCGTCGTAGC
** * * ** * * * * ** *
2494 TTCAATCTGTTCCACTGCACTGCCTGGGAAGTAAGATTTACCGTTGTGGCTTCAATCTTTTAAAT
1 TTCAATCTGTTTAACTGCAATG-TTGGGAAGTAAGATTCGCCATCGTAGCTTCAATCTATTCCAC
* * * * * **
2559 TGCAAT-GTCAGGGAAGCGAGGTTCGCCGTTGTAGCTTCAATCTGTTCCA-T-TACATCGCCAGG
65 TGC-ATCGCCTGGGAAGCAAGATTCGCCGTTGTAGCCTCAATCTGTTAAATTGTA-AT-GCCAGG
* * * *
2621 GAAGTGAGGTTCACTGTTGTAGC
127 GAAGCGAGATTCACCGTCGTAGC
* * * *
2644 TTCAATCTATTTGACTGCAATGTTGAGGAAGCAAGATTCGCCATCGTAGCTTCAATCTGTTCCAC
1 TTCAATCTGTTTAACTGCAATGTTG-GGAAGTAAGATTCGCCATCGTAGCTTCAATCTATTCCAC
* * * * * *
2709 TGCATCGCCTGGGAAGGTAAGATTCTCCGTTGTGGCCTCAATCT-TTTAATTGCAATGTCAGGGA
65 TGCATCGCCTGGGAA-GCAAGATTCGCCGTTGTAGCCTCAATCTGTTAAATTGTAATGCCAGGGA
** * *
2773 AGCGAGATTTGCCGTTGTGGC
129 AGCGAGATTCACCGTCGTAGC
2794 TTCAATCT
1 TTCAATCT
2802 ATTCCACTGC
Statistics
Matches: 231, Mismatches: 68, Indels: 18
0.73 0.21 0.06
Matches are distributed among these distances:
148 2 0.01
149 7 0.03
150 195 0.84
151 26 0.11
152 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (149 bp):
TTCAATCTGTTTAACTGCAATGTTGGGAAGTAAGATTCGCCATCGTAGCTTCAATCTATTCCACT
GCATCGCCTGGGAAGCAAGATTCGCCGTTGTAGCCTCAATCTGTTAAATTGTAATGCCAGGGAAG
CGAGATTCACCGTCGTAGC
Found at i:4248 original size:10 final size:9
Alignment explanation
Indices: 4226--4292 Score: 98
Period size: 10 Copynumber: 7.0 Consensus size: 9
4216 TTGGCCTCTC
4226 CTTTTTCTTT
1 CTTTTT-TTT
4236 CTTATTTTTT
1 CTT-TTTTTT
4246 CTTTTTTTT
1 CTTTTTTTT
4255 CTTTCTTTTT
1 CTTT-TTTTT
4265 CTTTCTTTTT
1 CTTT-TTTTT
4275 CTTTTTTTT
1 CTTTTTTTT
4284 CTTTTTTTT
1 CTTTTTTTT
4293 TTAATTTTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
9 24 0.44
10 28 0.51
11 3 0.05
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:4273 original size:29 final size:29
Alignment explanation
Indices: 4233--4300 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
4223 CTCCTTTTTC
4233 TTTCTTATTTTTTCTTTTTTTTCTTTCTT
1 TTTCTTATTTTTTCTTTTTTTTCTTTCTT
4262 TTTCTT-TCTTTTTCTTTTTTTTCTTT-TT
1 TTTCTTAT-TTTTTCTTTTTTTTCTTTCTT
*
4290 TTT-TTAATTTT
1 TTTCTTATTTTT
4301 ATTGAATCTG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
27 6 0.17
28 6 0.17
29 24 0.67
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (29 bp):
TTTCTTATTTTTTCTTTTTTTTCTTTCTT
Found at i:4300 original size:19 final size:18
Alignment explanation
Indices: 4226--4292 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 18
4216 TTGGCCTCTC
4226 CTTTTTCTTTCTTATTTTTT
1 CTTTTT-TTTCTT-TTTTTT
4246 CTTTTTTTTCTTTCTTTTT
1 CTTTTTTTTCTTT-TTTTT
4265 CTTTCTTTTTCTTTTTTTT
1 CTTT-TTTTTCTTTTTTTT
4284 CTTTTTTTT
1 CTTTTTTTT
4293 TTAATTTTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.13
19 24 0.53
20 15 0.33
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (18 bp):
CTTTTTTTTCTTTTTTTT
Done.