Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_630 ID=scaffold_630-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: 6238
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.27
Warning! 1099 characters in sequence are not A, C, G, or T
Found at i:137 original size:10 final size:10
Alignment explanation
Indices: 122--172 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
112 CATTTATATC
*
122 TTTAATTTCA
1 TTTAATTTTA
*
132 TTTAATTTAA
1 TTTAATTTTA
*
142 TTCAATTTTTA
1 TTTAA-TTTTA
153 TTTAATTTTA
1 TTTAATTTTA
*
163 TTTTATTTTA
1 TTTAATTTTA
173 AATACTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
10 27 0.77
11 8 0.23
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTAATTTTA
Found at i:142 original size:15 final size:15
Alignment explanation
Indices: 122--170 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
112 CATTTATATC
*
122 TTTAATTTCATTTAA
1 TTTAATTTCATTTTA
137 TTTAA-TTCAATTTTTA
1 TTTAATTTC-A-TTTTA
*
153 TTTAATTTTATTTTA
1 TTTAATTTCATTTTA
168 TTT
1 TTT
171 TAAATACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 3 0.10
15 14 0.48
16 10 0.34
17 2 0.07
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTAATTTCATTTTA
Found at i:170 original size:21 final size:21
Alignment explanation
Indices: 113--171 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
103 ATATTTTGGC
*
113 ATTTATATCTTTAATTTCATTTA
1 ATTT-TAT-TTTATTTTCATTTA
* ** *
136 ATTTAATTCAATTTTTATTTA
1 ATTTTATTTTATTTTCATTTA
157 ATTTTATTTTATTTT
1 ATTTTATTTTATTTT
172 AAATACTTTT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 22 0.79
22 2 0.07
23 4 0.14
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTTTATTTTATTTTCATTTA
Found at i:172 original size:16 final size:16
Alignment explanation
Indices: 122--173 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
112 CATTTATATC
*
122 TTTAATTTCA-TTTAA
1 TTTAATTTTATTTTAA
** *
137 TTTAATTCAATTTTTA
1 TTTAATTTTATTTTAA
*
153 TTTAATTTTATTTTAT
1 TTTAATTTTATTTTAA
169 TTTAA
1 TTTAA
174 ATACTTTTAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTAATTTTATTTTAA
Found at i:367 original size:22 final size:21
Alignment explanation
Indices: 334--376 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
324 TCGCGTTTCG
334 AAATTTTCGTGTCTTCAAAAA
1 AAATTTTCGTGTCTTCAAAAA
*
355 AAATTTCTCGTGTTTTCAAAAA
1 AAATTT-TCGTGTCTTCAAAAA
377 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (21 bp):
AAATTTTCGTGTCTTCAAAAA
Found at i:375 original size:20 final size:20
Alignment explanation
Indices: 334--376 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
324 TCGCGTTTCG
334 AAATTTTCGTGTCTTCAAAAA
1 AAATTTTCGTGTCTTC-AAAA
*
355 AAATTTCTCGTGTTTTCAAAA
1 AAATTT-TCGTGTCTTCAAAA
376 A
1 A
377 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (20 bp):
AAATTTTCGTGTCTTCAAAA
Found at i:532 original size:17 final size:19
Alignment explanation
Indices: 492--537 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
482 AAATTTTTCG
*
492 TGTTTTC-AAAAATTCTCA
1 TGTTTTCAAAAAAATCTCA
510 TGTTTTCAAAAAAATC-CA
1 TGTTTTCAAAAAAATCTCA
528 T-TTTTCAAAA
1 TGTTTTCAAAA
538 TTTTTTGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 9 0.35
18 10 0.38
19 7 0.27
ACGTcount: A:0.39, C:0.15, G:0.04, T:0.41
Consensus pattern (19 bp):
TGTTTTCAAAAAAATCTCA
Found at i:564 original size:36 final size:36
Alignment explanation
Indices: 510--593 Score: 95
Period size: 36 Copynumber: 2.4 Consensus size: 36
500 AAAATTCTCA
*
510 TGTTTTCAAAAAAATCCATTTTTC-AAAATTTTTTG
1 TGTTTTCAAAAAAATCCATATTTCTAAAATTTTTTG
** *
545 TGTTTTCTAAAAATTTCCATATTTCTAAAA-TTTTCG
1 TGTTTTC-AAAAAAATCCATATTTCTAAAATTTTTTG
581 TG-TTT-AAAAAAAT
1 TGTTTTCAAAAAAAT
594 TTCGTATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
33 6 0.15
35 10 0.24
36 21 0.51
37 4 0.10
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.48
Consensus pattern (36 bp):
TGTTTTCAAAAAAATCCATATTTCTAAAATTTTTTG
Found at i:776 original size:19 final size:18
Alignment explanation
Indices: 625--978 Score: 191
Period size: 17 Copynumber: 19.6 Consensus size: 18
615 TTTTTATTTT
* *
625 TTTTCAACAATTCTCGAG
1 TTTTCAAAAATTCTCGTG
*
643 -TTTCACAAATTCTCGTG
1 TTTTCAAAAATTCTCGTG
* * **
660 TTTT-AAAATTTTTTATG
1 TTTTCAAAAATTCTCGTG
*
677 TTTTAAAAAATAAATTTCTCGTG
1 TTTT---CAA-AAA-TTCTCGTG
*
700 -TTTCAAAAAATTGTCGTG
1 TTTTC-AAAAATTCTCGTG
* *
718 TTTT-AAAAATTTTCATG
1 TTTTCAAAAATTCTCGTG
*
735 -TTTCTAAAATGT-TCGT-
1 TTTTCAAAAAT-TCTCGTG
* *
751 ATTTCAAAAAATCCTCGTG
1 TTTTC-AAAAATTCTCGTG
*
770 TTTTCAAAAATTCTCATG
1 TTTTCAAAAATTCTCGTG
788 -TTTCAAAAA-TCTTCGTG
1 TTTTCAAAAATTC-TCGTG
*
805 TTTTC-AAAATTCTAGTG
1 TTTTCAAAAATTCTCGTG
* *
822 -TTTCAAAAATTTTCATG
1 TTTTCAAAAATTCTCGTG
* *
839 TTTTCAAAAATTTCCCCTG
1 TTTTCAAAAA-TTCTCGTG
*
858 TTTTCAAAAATTCTCGTA
1 TTTTCAAAAATTCTCGTG
* * *
876 TTTT-GAAAATTTTCTTG
1 TTTTCAAAAATTCTCGTG
893 TTTTCAAAAAAAAAACTT-TCGTG
1 TTTTC-----AAAAA-TTCTCGTG
*
916 TTTT-ATAAA-TCTCCGTG
1 TTTTCAAAAATTCT-CGTG
933 TTTTCAAAAAATTCTCGT-
1 TTTTC-AAAAATTCTCGTG
* *
951 CTTTCAAAAATTTTCGTG
1 TTTTCAAAAATTCTCGTG
969 TTTTCAAAAA
1 TTTTCAAAAA
979 ATTGACCTTG
Statistics
Matches: 257, Mismatches: 45, Indels: 68
0.69 0.12 0.18
Matches are distributed among these distances:
15 1 0.00
16 10 0.04
17 115 0.45
18 68 0.26
19 32 0.12
20 5 0.02
21 2 0.01
22 5 0.02
23 17 0.07
24 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (18 bp):
TTTTCAAAAATTCTCGTG
Found at i:827 original size:16 final size:16
Alignment explanation
Indices: 771--829 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 16
761 ATCCTCGTGT
771 TTTCAAAAATTCTCA-TG
1 TTTC-AAAATTCT-AGTG
* *
788 TTTCAAAAATCTTCGTG
1 TTTCAAAATTC-TAGTG
805 TTTTCAAAATTCTAGTG
1 -TTTCAAAATTCTAGTG
822 TTTCAAAA
1 TTTCAAAA
830 ATTTTCATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 14 0.40
17 11 0.31
18 10 0.29
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (16 bp):
TTTCAAAATTCTAGTG
Found at i:901 original size:35 final size:36
Alignment explanation
Indices: 643--978 Score: 164
Period size: 35 Copynumber: 9.2 Consensus size: 36
633 AATTCTCGAG
* *
643 TTTCACAAATTCTCGTGTTTT--AAAATTTTTTATGT
1 TTTCAAAAATTCTCGTGTTTTCAAAAATTTTCT-TGT
* * *
678 TTTAAAAAATAAATTTCTCGTG-TTTCAAAAAATTGTCGTGT
1 TTT---CAA-AAA-TTCTCGTGTTTTC-AAAAATTTTCTTGT
* * * *
719 TTT-AAAAATTTTCATG-TTTCTAAAATGTTC--GT
1 TTTCAAAAATTCTCGTGTTTTCAAAAATTTTCTTGT
* * *
751 ATTTCAAAAAATCCTCGTGTTTTCAAAAATTCTCATG-
1 -TTTC-AAAAATTCTCGTGTTTTCAAAAATTTTCTTGT
*
788 TTTCAAAAA-TCTTCGTGTTTTC-AAAA--TTCTAGT
1 TTTCAAAAATTC-TCGTGTTTTCAAAAATTTTCTTGT
* * * *
821 GTTTCAAAAATTTTCATGTTTTCAAAAATTTCCCCTGT
1 -TTTCAAAAATTCTCGTGTTTTCAAAAATTT-TCTTGT
* *
859 TTTCAAAAATTCTCGTATTTT-GAAAATTTTCTTGT
1 TTTCAAAAATTCTCGTGTTTTCAAAAATTTTCTTGT
* * * *
894 TTTCAAAAAAAAAACTT-TCGTGTTTT-ATAAATCTCCGTGT
1 TTTC-----AAAAA-TTCTCGTGTTTTCAAAAATTTTCTTGT
* *
934 TTTCAAAAAATTCTCGT-CTTTCAAAAATTTTCGTGT
1 TTTC-AAAAATTCTCGTGTTTTCAAAAATTTTCTTGT
970 TTTCAAAAA
1 TTTCAAAAA
979 ATTGACCTTG
Statistics
Matches: 230, Mismatches: 41, Indels: 60
0.69 0.12 0.18
Matches are distributed among these distances:
32 5 0.02
33 3 0.01
34 30 0.13
35 61 0.27
36 50 0.22
37 21 0.09
38 5 0.02
39 6 0.03
40 34 0.15
41 8 0.03
42 7 0.03
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (36 bp):
TTTCAAAAATTCTCGTGTTTTCAAAAATTTTCTTGT
Done.