Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_85 ID=scaffold_85-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: 15152
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Found at i:458 original size:5 final size:5
Alignment explanation
Indices: 444--481 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
434 AATCATAAGC
* *
444 AAAT- AAATA AAATA AAATA AAATG AAATA AAAAA AAAT
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAAT
482 GTAAGCTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:1494 original size:9 final size:9
Alignment explanation
Indices: 1480--1509 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1470 TTCGACGTTC
1480 TTTTTGTTT
1 TTTTTGTTT
1489 TTTTTGTTT
1 TTTTTGTTT
*
1498 TTGTTGTTT
1 TTTTTGTTT
1507 TTT
1 TTT
1510 GTTTGCGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:1500 original size:15 final size:16
Alignment explanation
Indices: 1480--1513 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1470 TTCGACGTTC
1480 TTTTTGTT-TTTTTTG
1 TTTTTGTTGTTTTTTG
1495 TTTTTGTTGTTTTTTG
1 TTTTTGTTGTTTTTTG
1511 TTT
1 TTT
1514 GCGTGTGGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (16 bp):
TTTTTGTTGTTTTTTG
Found at i:2251 original size:132 final size:131
Alignment explanation
Indices: 2090--2534 Score: 646
Period size: 132 Copynumber: 3.4 Consensus size: 131
2080 ACAGGAAGAC
* * * **
2090 AAGATCCACATTCTTCAACCTACTCCACTGCTGCTCAGGGAGA-TAGGACCAGTGGCTTAAATCT
1 AAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGG-CTGGTGGCTTAAATCT
* *
2154 GCTTCCCTACTACATTGGGAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTATTGCTTAGGGA
65 GCTTCCCTACTAC-TTGGGAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGA
2219 GAT
129 GAT
*
2222 AAGATCTACAATCTTTC-ACCTACTCCACTGCTGCTCAGAGAGACAAGGCTGGTGGCTTAAATCT
1 AAGATCTACAATC-TTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGTGGCTTAAATCT
* *
2286 GCTTCCCTACTACCTT-GGAAGGATAAGATTTGTTGTCCTCGATCTGCTCCACTACTGCTTAGGG
65 GCTTCCCTACTA-CTTGGGAA-GATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGG
2350 AGAT
128 AGAT
*
2354 AAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGTTGGTGGCTTAAATCTG
1 AAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGTGGCTTAAATCTG
* * * * *
2419 C-TCCCCACTATCTTGGAAAGATAAGATTTGCCATCTTCGATCTGGTCCACTACTGCTTAGGGAG
66 CTTCCCTACTA-CTTGGGAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAG
2483 AT
130 AT
* *
2485 AAGATCTACAATCTTCAATCTACTCCACAGCTGCTCAGGGAGACAAGGCT
1 AAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCT
2535 TGGTTTCTTT
Statistics
Matches: 284, Mismatches: 23, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
131 107 0.38
132 170 0.60
133 7 0.02
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (131 bp):
AAGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGTGGCTTAAATCTG
CTTCCCTACTACTTGGGAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
T
Found at i:2380 original size:44 final size:44
Alignment explanation
Indices: 2327--2527 Score: 142
Period size: 44 Copynumber: 4.6 Consensus size: 44
2317 GTTGTCCTCG
*
2327 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCA
* * * * * ***** *
2371 ACCTACTCCACTGCTGCTCAGGGAGACAAGGT-TGGTGGCTTAA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCA
* * * * * *
2414 ATCTGCTCCCCACTA-T-CTT-GGAAAGATAAGATTTGCCATCTTCG
1 ATCTACT--CCACTACTGCTTAGG-GAGATAAGATCTACAATCTTCA
**
2458 ATCTGGTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCA
*
2502 ATCTACTCCAC-AGCTGCTCAGGGAGA
1 ATCTACTCCACTA-CTGCTTAGGGAGA
2528 CAAGGCTTGG
Statistics
Matches: 115, Mismatches: 34, Indels: 16
0.70 0.21 0.10
Matches are distributed among these distances:
42 8 0.07
43 21 0.18
44 79 0.69
45 7 0.06
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (44 bp):
ATCTACTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCA
Found at i:2675 original size:128 final size:129
Alignment explanation
Indices: 2519--2750 Score: 421
Period size: 128 Copynumber: 1.8 Consensus size: 129
2509 CCACAGCTGC
*
2519 TCAGGGAGACAAGGCTTGGTTTCTTTCGTCTGCTCCACTACTACTTAGGGAGATAAGACTTGATG
1 TCAGGGAGACAAGGATTGGTTTCTTTCGTCTGCTCCACTACTACTTAGGGAGATAAGACTTGATG
2584 CGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCACCACTGCAACT
66 CGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCACCACTGCAACT
* *
2648 TCAGGGAGA-TAGGATTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATG
1 TCAGGGAGACAAGGATTGGTTTCTTTCGTCTGCTCCACTACTACTTAGGGAGATAAGACTTGATG
*
2712 CGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGT
66 CGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGT
2751 AATCTTCGAC
Statistics
Matches: 99, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
128 90 0.91
129 9 0.09
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (129 bp):
TCAGGGAGACAAGGATTGGTTTCTTTCGTCTGCTCCACTACTACTTAGGGAGATAAGACTTGATG
CGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCACCACTGCAACT
Found at i:2685 original size:44 final size:42
Alignment explanation
Indices: 2519--2746 Score: 103
Period size: 44 Copynumber: 5.4 Consensus size: 42
2509 CCACAGCTGC
* * * *
2519 TCAGGGAGACAAGGCTTGGTTTCTTTCGTCTGCTCCACTACTACT
1 TCAGGGAGATAA-GATT-GTTT-TTTCGTCTGCTCCACTGCAACT
* * *
2564 T-AGGGAGATAAGACTTG---ATGCGATCTGCTCTACTGCAACT
1 TCAGGGAGATAAGA-TTGTTTTTTCG-TCTGCTCCACTGCAACT
* * ** * *
2604 TCAGAGAGATAAGATCTGTGGTTTTAATCCGCACCACTGCAACT
1 TCAGGGAGATAAGAT-TGT-TTTTTCGTCTGCTCCACTGCAACT
* * **
2648 TCAGGGAGATAGGATTGGTTTCTTTCGTCTGCTCCACTACTGCT
1 TCAGGGAGATAAGATT-GTTT-TTTCGTCTGCTCCACTGCAACT
* * * *
2692 T-AGGGAGATAAGACTTG---ATGCGATCTGCTCTACTGTAACT
1 TCAGGGAGATAAGA-TTGTTTTTTCG-TCTGCTCCACTGCAACT
*
2732 TCAGAGAGATAAGAT
1 TCAGGGAGATAAGAT
2747 CTGTAATCTT
Statistics
Matches: 136, Mismatches: 34, Indels: 31
0.68 0.17 0.15
Matches are distributed among these distances:
39 6 0.04
40 30 0.22
41 24 0.18
43 16 0.12
44 58 0.43
45 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (42 bp):
TCAGGGAGATAAGATTGTTTTTTCGTCTGCTCCACTGCAACT
Found at i:6067 original size:22 final size:22
Alignment explanation
Indices: 6039--6083 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
6029 AAATGGGGTC
6039 ACATTTCTCAGTTAGCTGTGAA
1 ACATTTCTCAGTTAGCTGTGAA
*
6061 ACATTTCTCAGTTATCTGTGAA
1 ACATTTCTCAGTTAGCTGTGAA
6083 A
1 A
6084 TGAACCTGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (22 bp):
ACATTTCTCAGTTAGCTGTGAA
Found at i:14471 original size:107 final size:107
Alignment explanation
Indices: 14082--14521 Score: 643
Period size: 107 Copynumber: 4.1 Consensus size: 107
14072 ATGACATGGA
* * *
14082 TTGAAA-TTTAAGAGGATA-TTTGGCTATTTGGTTC-AACGAGAAATCGAAACCCAGCACGTTAG
1 TTGAAATTTTAAAAGGATATTTTAGCTATTTGG-TCGAACGAAAAATCGAAACCCAGCACGTTAG
* *
14144 GGCACGTTTTCTCTAATTTCCAAACGCAAAATATTGCCTTATT
65 GGCACGTTTTCTCGAACTTCCAAACGCAAAATATTGCCTTATT
* *
14187 CTGAAATTTTAGAAGGATATTTTAGCTATTTGGTCGAACGAAAAAAAATCGAAACCCAGCACGTT
1 TTGAAATTTTAAAAGGATATTTTAGCTATTTGGTCGAACG---AAAAATCGAAACCCAGCACGTT
* * * **
14252 AGAGCACGTTTTCTCAAACTTCCAAATGTGAAATATTGCCTTATT
63 AGGGCACGTTTTCTCGAACTTCCAAACGCAAAATATTGCCTTATT
* *
14297 TTGAAAATTTAAAAGGATATTTTTGGCTATTTGGTCGAACGAAAAATCGAAACCCAGCACGTTAG
1 TTGAAATTTTAAAAGGATA-TTTTAGCTATTTGGTCGAACGAAAAATCGAAACCCAGCACGTTAG
* * *
14362 GGCATGTTTGCTCGAACTTCCAAACGTAAAATATTGCCTTATT
65 GGCACGTTTTCTCGAACTTCCAAACGCAAAATATTGCCTTATT
* *
14405 TTGAAATTTTAAAAGGATATTTTAGCTATTTGGTCAAACGAAAAATCGAAACCTAGCACGTTAGG
1 TTGAAATTTTAAAAGGATATTTTAGCTATTTGGTCGAACGAAAAATCGAAACCCAGCACGTTAGG
14470 GCACGTTTTCTCGAACTTCCAAACGCAAAATATTGCCTTATT
66 GCACGTTTTCTCGAACTTCCAAACGCAAAATATTGCCTTATT
14512 TTGAAATTTT
1 TTGAAATTTT
14522 TATTTGGATA
Statistics
Matches: 300, Mismatches: 28, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
105 5 0.02
106 12 0.04
107 108 0.36
108 79 0.26
110 76 0.25
111 20 0.07
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (107 bp):
TTGAAATTTTAAAAGGATATTTTAGCTATTTGGTCGAACGAAAAATCGAAACCCAGCACGTTAGG
GCACGTTTTCTCGAACTTCCAAACGCAAAATATTGCCTTATT
Done.