Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_86 ID=scaffold_86-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: 15052
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.32
Found at i:35 original size:8 final size:9
Alignment explanation
Indices: 20--49 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
10 TTTAGCTAAG
20 TAAAAAAAA
1 TAAAAAAAA
29 TAAAAAAAA
1 TAAAAAAAA
38 TAAAAGAAAA
1 TAAAA-AAAA
48 TA
1 TA
50 TAGAATAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 14 0.70
10 6 0.30
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:962 original size:45 final size:45
Alignment explanation
Indices: 899--1194 Score: 224
Period size: 45 Copynumber: 6.7 Consensus size: 45
889 TATAGGCTTA
*
899 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCACCATTTTG
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATTTTG
** * * * **
944 GGTCTGCCCCACTGCAACTTCAGGGGGATAAGA-CCTG-C-TTATCC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTC-GCCATT-TTG
* * * *
988 AGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTAG--A---TG
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATTTTG
* * **
1028 AGATCTGCT-CTCTGCAACTTCAGAGAGATAAGA-TCTGTGATTTT-
1 A-ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTC-GCCATTTTG
**
1072 AATCCACTCCACTGCAACTTCAGGGAGATAAGATTCGCCATTTTG
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATTTTG
** * *
1117 GGTCTGC-CCTACTGCAACTTCAAGGG-GATAAGATTCGCCATCTTC
1 AATCTGCTCC-ACTGCAACTTC-AGGGAGATAAGATTCGCCATTTTG
*
1162 AATCTGCTCCACTGCAACTTTA-GGAGGATAAGA
1 AATCTGCTCCACTGCAACTTCAGGGA-GATAAGA
1195 CTTGTATCTT
Statistics
Matches: 196, Mismatches: 36, Indels: 38
0.73 0.13 0.14
Matches are distributed among these distances:
39 1 0.01
40 23 0.12
41 6 0.03
42 1 0.01
43 9 0.05
44 65 0.33
45 85 0.43
46 6 0.03
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (45 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATTTTG
Found at i:998 original size:89 final size:89
Alignment explanation
Indices: 899--1194 Score: 277
Period size: 89 Copynumber: 3.4 Consensus size: 89
889 TATAGGCTTA
899 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCACCATTTTGGGTCTGCCCCACTGCAACTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCACCATTTTGGGTCTGCCCCACTGCAACTT
*
964 CAGGGGGATAAGACCTGCTTA-TCC
66 CAGGGGGATAAGACCTG-TGATTCC
* * * * * * *
988 AGTCTGCTCCACTGCAACTTTAGGGAGATAAGACT-A-GA---TGAGATCTG-CTCTCTGCAACT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCACCATTTTG-GGTCTGCCCCACTGCAACT
* * * **
1047 TCAGAGAGATAAGATCTGTGATTTT
65 TCAGGGGGATAAGACCTGTGATTCC
** * *
1072 AATCCACTCCACTGCAACTTCAGGGAGATAAGATTCGCCATTTTGGGTCTGCCCTACTGCAACTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCACCATTTTGGGTCTGCCCCACTGCAACTT
* * ** *
1137 CAAGGGGATAAGA-TTCGCCATCTTC
66 CAGGGGGATAAGACCT-GTGAT-TCC
*
1162 AATCTGCTCCACTGCAACTTTA-GGAGGATAAGA
1 AATCTGCTCCACTGCAACTTCAGGGA-GATAAGA
1195 CTTGTATCTT
Statistics
Matches: 162, Mismatches: 34, Indels: 21
0.75 0.16 0.10
Matches are distributed among these distances:
83 2 0.01
84 58 0.36
85 5 0.03
86 1 0.01
87 1 0.01
88 7 0.04
89 60 0.37
90 28 0.17
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (89 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCACCATTTTGGGTCTGCCCCACTGCAACTT
CAGGGGGATAAGACCTGTGATTCC
Found at i:1284 original size:44 final size:44
Alignment explanation
Indices: 1229--1906 Score: 703
Period size: 44 Copynumber: 15.4 Consensus size: 44
1219 ACCAGTATGG
* * *
1229 GAAGACAAGATCTGCTATCTTTGATTTACTTCATGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
1273 GAAGACAAGATCTG-TCATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCT-ATCTTCGATCTACTTCACGCCAATACAT
1317 GAAGACAAGATCTG-TCATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCT-ATCTTCGATCTACTTCACGCCAATACAT
* * *
1361 GAAGACAAGATCTGCTA-CCTCTGATCTACTTCATGCCGATACAT
1 GAAGACAAGATCTGCTATCTTC-GATCTACTTCACGCCAATACAT
* * * * *
1405 GAAGAGAAGATCTACTTTTTTCGATCTAC-TC-CGCCACCAGTATGA-
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCA--A-TA-CAT
* * * *
1450 GAAGACAAGATCTGCTACCTTTGATCTACTTCATGCCGATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * ***
1494 GAAGACAAGATCTGCTTTCTTCGACCTA-TTC-CGCCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCA--A-TACAT
* * * *
1539 GAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATACAT
* * *
1582 GAAGACAGGATCTGCTATCTTCGATCTACTTCATGCTAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * * ***
1626 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACAT
*
1671 GAAGACAAGATTTGCTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* *
1715 GAAGACAAGATCTACTATCTTCGATCTACTTCATGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* *
1759 GAAGACAAGATCTGCTTTCTTCGATCTTCTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * * * * ***
1803 GAAGACAAGAT-TACTTTCTTAGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACAT
* *
1847 GAAGACGAGATCTACTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
1891 GAAGACAATATCTGCT
1 GAAGACAAGATCTGCT
1907 GCTTTTTAAC
Statistics
Matches: 523, Mismatches: 90, Indels: 42
0.80 0.14 0.06
Matches are distributed among these distances:
42 6 0.01
43 45 0.09
44 361 0.69
45 102 0.20
46 6 0.01
47 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (44 bp):
GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
Found at i:1481 original size:89 final size:88
Alignment explanation
Indices: 1273--1785 Score: 385
Period size: 89 Copynumber: 5.8 Consensus size: 88
1263 GCCAATACAT
* * * * * *
1273 GAAGACAAGATCTG-TCATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTCATCT
1 GAAGACAAGATCTGCT-ACCTTTGATCTACTTCATGCCGATACATGAAGACAAGATCTCT-TTCT
*
1337 TCGATCTACTTCACGCCA--A-TA-CA
64 TCGATCTAC-TC-CGCCACCAGTATGA
* * *
1360 TGAAGACAAGATCTGCTACCTCTGATCTACTTCATGCCGATACATGAAGAGAAGATCTACTTTTT
1 -GAAGACAAGATCTGCTACCTTTGATCTACTTCATGCCGATACATGAAGACAAGATCT-CTTTCT
1425 TCGATCTACTCCGCCACCAGTATGA
64 TCGATCTACTCCGCCACCAGTATGA
1450 GAAGACAAGATCTGCTACCTTTGATCTACTTCATGCCGATACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGCTACCTTTGATCTACTTCATGCCGATACATGAAGACAAGATCT-CTTTCTT
* * *
1515 CGACCTATTCCGCCACCAGTATGG
65 CGATCTACTCCGCCACCAGTATGA
* * * * * * * * * *
1539 GAAGACAAGATCTGC-ATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGATCTGCTATCTT
1 GAAGACAAGATCTGCTACCTTTGATCTACTTCATGCCGATACATGAAGACAAGATCT-CTTTCTT
* * *
1603 CGATCTACTTCATGCTA--A-TA-CA
65 CGATCTAC-TC-CGCCACCAGTATGA
** * * * *
1625 TGAAGACAAGATCTGCTTTCTTCGATCTACTTC--GCC-ACCAGTATGGGAAGACAAGATTTGCT
1 -GAAGACAAGATCTGCTACCTTTGATCTACTTCATGCCGA-TA-CAT--GAAGACAAGATCT-CT
* *
1687 ATCTTCGATCTACTTCACGCCA--A-TA-CA
60 TTCTTCGATCTAC-TC-CGCCACCAGTATGA
* * * *
1714 TGAAGACAAGATCTACTATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGCTTTCT
1 -GAAGACAAGATCTGCTACCTTTGATCTACTTCATGCCGATACATGAAGACAAGATCT-CTTTCT
1779 TCGATCT
64 TCGATCT
1786 TCTTCACGCC
Statistics
Matches: 360, Mismatches: 48, Indels: 34
0.81 0.11 0.08
Matches are distributed among these distances:
85 1 0.00
86 8 0.02
87 21 0.06
88 146 0.41
89 173 0.48
90 6 0.02
91 4 0.01
92 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (88 bp):
GAAGACAAGATCTGCTACCTTTGATCTACTTCATGCCGATACATGAAGACAAGATCTCTTTCTTC
GATCTACTCCGCCACCAGTATGA
Found at i:1588 original size:221 final size:221
Alignment explanation
Indices: 1201--1878 Score: 818
Period size: 221 Copynumber: 3.1 Consensus size: 221
1191 AAGACTTGTA
*
1201 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATTTACTTCATGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCATGCC
* *
1266 AATACATGAAGACAAGATCTG-TCATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
66 AATACATGAAGACAAGATCTGCT-ATCTTCGACCTACTTCACGCCAATACAGGAAGACAAGATCT
* * *
1330 GTCATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTACC-TCTGATCTACTTCA
130 GTCATCTTCGATCCACTTCACACCAATACAGGAAGACAAGATCTGCTACCTTC-GATCTACTTCA
* *
1394 TGCCGATACATGAAGAGAAGATCTACTT
194 TGCCAATACATGAAGACAAGATCTACTT
* * * *
1422 TTTTCGATCTACTCCGCCACCAGTATGAGAAGACAAGATCTGCTACCTTTGATCTACTTCATGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCATGCC
* * **
1487 GATACATGAAGACAAGATCTGCTTTCTTCGACCTA-TTC-CGCCACCAGTATGGGAAGACAAGAT
66 AATACATGAAGACAAGATCTGCTATCTTCGACCTACTTCACGCCA--A-TACAGGAAGACAAGAT
* * *
1550 CTG-CATCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTT
128 CTGTCATCTTCGATCCACTTCAC-ACCAATACAGGAAGACAAGATCTGCTACCTTCGATCTACTT
* *
1613 CATGCTAATACATGAAGACAAGATCTGCTT
192 CATGCCAATACATGAAGACAAGATCTACTT
* * *
1643 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATTTGCTATCTTCGATCTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCATGCC
* * * *
1708 AATACATGAAGACAAGATCTACTATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTG
66 AATACATGAAGACAAGATCTGCTATCTTCGACCTACTTCACGCCAATACAGGAAGACAAGATCTG
* ** * * * ** *
1773 -CTTTCTTCGATCTTCTTCACGCCAATACATGAAGACAAGAT-TACTTTCTTAGATCTACTTC--
131 TC-ATCTTCGATCCACTTCACACCAATACAGGAAGACAAGATCTGCTACCTTCGATCTACTTCAT
*** * *
1834 GCCACCAGTATGGGAAGACGAGATCTACTA
195 GCCA--A-TACATGAAGACAAGATCTACTT
1864 TCTTCGATCTACTTC
1 TCTTCGATCTACTTC
1879 ACGCCAATAC
Statistics
Matches: 391, Mismatches: 53, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
218 3 0.01
219 5 0.01
220 39 0.10
221 317 0.81
222 23 0.06
223 4 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (221 bp):
TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCATGCC
AATACATGAAGACAAGATCTGCTATCTTCGACCTACTTCACGCCAATACAGGAAGACAAGATCTG
TCATCTTCGATCCACTTCACACCAATACAGGAAGACAAGATCTGCTACCTTCGATCTACTTCATG
CCAATACATGAAGACAAGATCTACTT
Found at i:1721 original size:265 final size:263
Alignment explanation
Indices: 1229--1906 Score: 736
Period size: 265 Copynumber: 2.6 Consensus size: 263
1219 ACCAGTATGG
* * * * *
1229 GAAGACAAGATCTGCTATCTTTGAT-TTACTTCATGCCAATACATGAAGACAAGATCTGTCATCT
1 GAAGACAAGATCTGCTTTCTTCGATCCTA-TTCACGCCAATACAGGAAGACAAGATCTG-CATCT
* * * *
1293 TCGATCTACTTCACGCCAATACATGAAGACAAGATCTG-TCATCTTCGATCTACTTCACGCCAAT
64 TCGATCTACTTCACACCAATATAGGAAGACAGGATCTGCT-ATCTTCGATCTACTTCACGCCAAT
* *
1357 ACATGAAGACAAGATCTGC-TACCTCTGATCTACTTCATGCCGATACATGAAGAGAAGATCTACT
128 ACATGAAGACAAGATCTGCTTACCTCTGATCTACTTCA-GCCGACACATGAAGACAAGATCTACT
* * * * *
1421 TTTTTCGATCTACTCCGCCACCAGTATGAGAAGACAAGATCTGCTACCTTTGATCTACTTCATGC
192 ATCTTCGATCTACTCCGCCA-CAGTATCAGAAGACAAGATCTACTACCTTCGATCTACTTCATGC
*
1486 CGATACAT
256 CAATACAT
**
1494 GAAGACAAGATCTGCTTTCTTCGA-CCTATTC-CGCCACCAGTATGGGAAGACAAGATCTGCATC
1 GAAGACAAGATCTGCTTTCTTCGATCCTATTCACGCCA--A-TACAGGAAGACAAGATCTGCATC
* * *
1557 TTCGATCCACTTC-CTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCATGCTAA
63 TTCGATCTACTTCAC-ACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAA
* * * *
1621 TACATGAAGACAAGATCTGCTTTCTTC-GATCTACTTC-GCC-ACCAGTATGGGAAGACAAGATT
127 TACATGAAGACAAGATCTGCTTACCTCTGATCTACTTCAGCCGA-CA-CAT--GAAGACAAGATC
* *
1683 TGCTATCTTCGATCTACTTCACGCCA-A-TA-CATGAAGACAAGATCTACTATCTTCGATCTACT
188 TACTATCTTCGATCTAC-TC-CGCCACAGTATCA-GAAGACAAGATCTACTACCTTCGATCTACT
1745 TCATGCCAATACAT
250 TCATGCCAATACAT
* * * * *
1759 GAAGACAAGATCTGCTTTCTTCGATCTTCTTCACGCCAATACATGAAGACAAGAT-TACTTTCTT
1 GAAGACAAGATCTGCTTTCTTCGATCCTATTCACGCCAATACAGGAAGACAAGATCTGC-ATCTT
* * * * *
1823 AGATCTACTTCGCCACCAGTATGGGAAGAC-GAGATCTACTATCTTCGATCTACTTCACGCCAAT
65 CGATCTACTTC-ACACCAATATAGGAAGACAG-GATCTGCTATCTTCGATCTACTTCACGCCAAT
*
1887 ACATGAAGACAATATCTGCT
128 ACATGAAGACAAGATCTGCT
1907 GCTTTTTAAC
Statistics
Matches: 350, Mismatches: 43, Indels: 40
0.81 0.10 0.09
Matches are distributed among these distances:
262 1 0.00
263 10 0.03
264 34 0.10
265 241 0.69
266 52 0.15
267 7 0.02
268 5 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (263 bp):
GAAGACAAGATCTGCTTTCTTCGATCCTATTCACGCCAATACAGGAAGACAAGATCTGCATCTTC
GATCTACTTCACACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACA
TGAAGACAAGATCTGCTTACCTCTGATCTACTTCAGCCGACACATGAAGACAAGATCTACTATCT
TCGATCTACTCCGCCACAGTATCAGAAGACAAGATCTACTACCTTCGATCTACTTCATGCCAATA
CAT
Found at i:2811 original size:25 final size:26
Alignment explanation
Indices: 2773--2821 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
2763 GTGTCTTGAA
2773 AAGAAAAAGATATT-CAAGAACAATG
1 AAGAAAAAGATATTACAAGAACAATG
2798 AAGAATAAAG-TATTACAAGAACAA
1 AAGAA-AAAGATATTACAAGAACAA
2822 ACAAATTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.61, C:0.08, G:0.14, T:0.16
Consensus pattern (26 bp):
AAGAAAAAGATATTACAAGAACAATG
Found at i:4262 original size:18 final size:18
Alignment explanation
Indices: 4229--4263 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4219 AATTTCTTTA
*
4229 GCCTCCACAGCCTCCACG
1 GCCTCCACAGCATCCACG
*
4247 GCCTCCACAGTATCCAC
1 GCCTCCACAGCATCCAC
4264 ACATCTCAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.51, G:0.14, T:0.14
Consensus pattern (18 bp):
GCCTCCACAGCATCCACG
Done.