Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_277 ID=scaffold_277-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: 8848
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:613 original size:2 final size:2
Alignment explanation
Indices: 594--635 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
584 ATAAAGAAAA
* *
594 AT AT AT AA AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
635 A
1 A
636 ACATATGTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1542 original size:14 final size:14
Alignment explanation
Indices: 1523--1569 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
1513 GATTGCATAT
1523 CATATCTAAGATTA
1 CATATCTAAGATTA
*
1537 CATATC--ATATCTA
1 CATATCTAAGAT-TA
1550 CATATCTAAGATTA
1 CATATCTAAGATTA
1564 CATATC
1 CATATC
1570 ATATCTAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 3 0.11
13 8 0.29
14 14 0.50
15 3 0.11
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.36
Consensus pattern (14 bp):
CATATCTAAGATTA
Found at i:1553 original size:13 final size:13
Alignment explanation
Indices: 1535--1576 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1525 TATCTAAGAT
1535 TACATATCATATC
1 TACATATCATATC
*
1548 TACATATCTAAGAT-
1 TACATATC--ATATC
1562 TACATATCATATC
1 TACATATCATATC
1575 TA
1 TA
1577 AGATTTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
12 3 0.12
13 10 0.42
14 8 0.33
15 3 0.12
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (13 bp):
TACATATCATATC
Found at i:1555 original size:27 final size:27
Alignment explanation
Indices: 1523--1576 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1513 GATTGCATAT
1523 CATATCTAAGATTACATATCATATCTA
1 CATATCTAAGATTACATATCATATCTA
1550 CATATCTAAGATTACATATCATATCTA
1 CATATCTAAGATTACATATCATATCTA
1577 AGATTTCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.37
Consensus pattern (27 bp):
CATATCTAAGATTACATATCATATCTA
Found at i:1581 original size:19 final size:19
Alignment explanation
Indices: 1485--1549 Score: 76
Period size: 19 Copynumber: 3.2 Consensus size: 19
1475 AAATTAAATC
*
1485 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
*
1505 TCTTCTAAGATTGCATATCATA
1 ---TCTAAGATTACATATCATA
1527 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
1546 TCTA
1 TCTA
1550 CATATCTAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
19 22 0.56
22 7 0.18
23 10 0.26
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:1586 original size:19 final size:19
Alignment explanation
Indices: 1500--1588 Score: 74
Period size: 19 Copynumber: 4.4 Consensus size: 19
1490 GATTACAAAA
1500 TCATATC-T-TCTAAGATT
1 TCATATCATATCTAAGATT
*
1517 GCATATCATATCTAAGATTACAT
1 TCATATCATATCTAAGA-T---T
1540 ATCATATCTACATATCTAAGATT
1 -TCATA--T-CATATCTAAGATT
*
1563 ACATATCATATCTAAGATT
1 TCATATCATATCTAAGATT
1582 TCATATC
1 TCATATC
1589 CTTGAAGATT
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
17 6 0.10
18 1 0.02
19 26 0.45
20 2 0.03
22 4 0.07
23 2 0.03
24 4 0.07
26 2 0.03
27 11 0.19
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (19 bp):
TCATATCATATCTAAGATT
Found at i:2191 original size:45 final size:45
Alignment explanation
Indices: 2134--2475 Score: 183
Period size: 45 Copynumber: 7.8 Consensus size: 45
2124 TTGTTTATTT
* *
2134 AGTCTGCCCCACTGCAATTTCAGTGG-GATAAGACTTGATTTCTTG
1 AGTCTGCTCCACTGCAATTTCAG-GGAGATAAGACTCGATTTCTTG
* * *
2179 AGTCTGCTCCACTGCAACTTCAGGGAGATAATACTCGCTTTCTTG
1 AGTCTGCTCCACTGCAATTTCAGGGAGATAAGACTCGATTTCTTG
* * *
2224 GGTCTGCTCCACTGCAACTTT-AGGGAGATAAGACCCGA-TGC--G
1 AGTCTGCTCCACTGCAA-TTTCAGGGAGATAAGACTCGATTTCTTG
* ** * * *
2266 A-TATGCT-TTCTGCAACTTCAGAGAGATAAGATCTGTGA-TT-TT-
1 AGTCTGCTCCACTGCAATTTCAGGGAGATAAGA-CT-CGATTTCTTG
* ** * * * * *
2308 AATCCACTCCACTGCAAATTCAGGGAGATAGGA-T-TATTGGCTTT
1 AGTCTGCTCCACTGCAATTTCAGGGAGATAAGACTCGATT-TCTTG
* * * * *** *
2352 AATCTGCTCCACTACAACTTCAGGGAGATAAGATTCGCCATCTTC
1 AGTCTGCTCCACTGCAATTTCAGGGAGATAAGACTCGATTTCTTG
* * * * * *
2397 AGTCTG-TCTCACTACAACTTCA-GGAGGATAAGGCTTGCTTACTT-
1 AGTCTGCTC-CACTGCAATTTCAGGGA-GATAAGACTCGATTTCTTG
*
2441 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT
1 AGTCTGCTCCACTGCAATTTCAGGGAGATAAGACT
2476 AGATGCGATC
Statistics
Matches: 228, Mismatches: 50, Indels: 39
0.72 0.16 0.12
Matches are distributed among these distances:
39 2 0.01
40 18 0.08
41 7 0.03
42 6 0.03
43 5 0.02
44 82 0.36
45 106 0.46
46 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (45 bp):
AGTCTGCTCCACTGCAATTTCAGGGAGATAAGACTCGATTTCTTG
Found at i:2460 original size:44 final size:46
Alignment explanation
Indices: 2354--2472 Score: 142
Period size: 44 Copynumber: 2.7 Consensus size: 46
2344 TTGGCTTTAA
2354 TCTGCTCCACTACAACTTCAGGGAGATAA-GATTCGCCATCTTCAG
1 TCTGCTCCACTACAACTTCAGGGAGATAAGGATTCGCCATCTTCAG
* *
2399 TCTG-TCTCACTACAACTTCA-GGAGGATAAGGCTT-G-CTTACTT-AG
1 TCTGCTC-CACTACAACTTCAGGGA-GATAAGGATTCGCCAT-CTTCAG
*
2443 TCTGCTCCACTGCAACTTCAGGGAGATAAG
1 TCTGCTCCACTACAACTTCAGGGAGATAAG
2473 ACTAGATGCG
Statistics
Matches: 65, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
44 31 0.48
45 31 0.48
46 3 0.05
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (46 bp):
TCTGCTCCACTACAACTTCAGGGAGATAAGGATTCGCCATCTTCAG
Found at i:2483 original size:217 final size:217
Alignment explanation
Indices: 2225--2618 Score: 707
Period size: 217 Copynumber: 1.8 Consensus size: 217
2215 GCTTTCTTGG
* * *
2225 GTCTGCTCCACTGCAACTTTAGGGAGATAAGACCCGATGCGATATGCTTTCTGCAACTTCAGAGA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACCAGATGCGATATGCTCTCTGCAACTTCAGAGA
2290 GATAAGATCTGTGATTTTAATCCACTCCACTGCAAATTCAGGGAGATAGGATTATTGGCTTTAAT
66 GATAAGATCTGTGATTTTAATCCACTCCACTGCAAATTCAGGGAGATAGGATTATTGGCTTTAAT
2355 CTGCTCCACTACAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGTCTCACTACAACTTCAG
131 CTGCTCCACTACAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGTCTCACTACAACTTCAG
2420 GAGGATAAGGCTTGCTTACTTA
196 GAGGATAAGGCTTGCTTACTTA
* *
2442 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACCAGATGCGATATGCTCTCTGCAACTTCAGAGA
* * *
2507 GATAAGATCTGTGATTTTAATCCACTCCACTGCGACTTTAGGGAGATAGGATTATTGGCTTTAAT
66 GATAAGATCTGTGATTTTAATCCACTCCACTGCAAATTCAGGGAGATAGGATTATTGGCTTTAAT
*
2572 CTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCT
131 CTGCTCCACTACAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCT
2619 TTTAAATTGC
Statistics
Matches: 168, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
217 168 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (217 bp):
GTCTGCTCCACTGCAACTTCAGGGAGATAAGACCAGATGCGATATGCTCTCTGCAACTTCAGAGA
GATAAGATCTGTGATTTTAATCCACTCCACTGCAAATTCAGGGAGATAGGATTATTGGCTTTAAT
CTGCTCCACTACAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGTCTCACTACAACTTCAG
GAGGATAAGGCTTGCTTACTTA
Found at i:3017 original size:44 final size:44
Alignment explanation
Indices: 2967--3088 Score: 169
Period size: 44 Copynumber: 2.8 Consensus size: 44
2957 ATCTGCTATT
*
2967 TTCAACCTACTCCACTATTGCTCAGGGAGATAGGA-TTCACAATC
1 TTCAACCTATTCCACTATTGCTCAGGGAGATAGGACTT-ACAATC
*
3011 TTCAACCTATTCCACTGTTGAC-CAGGGAGATAGGACTTACAATC
1 TTCAACCTATTCCACTATTG-CTCAGGGAGATAGGACTTACAATC
*
3055 TTCAACCTATTCCACTACTG-TCTAGGGAGATAGG
1 TTCAACCTATTCCACTATTGCTC-AGGGAGATAGG
3089 GCTGGGGTCA
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
43 1 0.01
44 66 0.94
45 3 0.04
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (44 bp):
TTCAACCTATTCCACTATTGCTCAGGGAGATAGGACTTACAATC
Found at i:3218 original size:44 final size:44
Alignment explanation
Indices: 3088--3220 Score: 106
Period size: 44 Copynumber: 3.0 Consensus size: 44
3078 AGGGAGATAG
* *
3088 GGCTGGGGTCATCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAA
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAA
* * * * ** * * * **** *
3132 GATCTGCTATTTTTAACCTGCTCCGCT-ACAACCCAGGGAGGCAA
1 G-GCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAA
3176 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAA
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAA
3220 G
1 G
3221 ATCTACTATC
Statistics
Matches: 57, Mismatches: 30, Indels: 4
0.63 0.33 0.04
Matches are distributed among these distances:
43 17 0.30
44 25 0.44
45 15 0.26
ACGTcount: A:0.18, C:0.25, G:0.32, T:0.25
Consensus pattern (44 bp):
GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAA
Done.