Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_209 ID=scaffold_209-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: 9303
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:1007 original size:44 final size:44
Alignment explanation
Indices: 896--1008 Score: 120
Period size: 44 Copynumber: 2.6 Consensus size: 44
886 GATTATCGAA
* * *
896 TTCAATCTGCTCCACTGCAACCTCAGGGAGTTAAGATTTGCTTC
1 TTCAGTCTGCTCCACTGCAACTTCAGGGAGTTAAGACTTGCTTC
* *** * *
940 TTCAGTCTGCCCCACTATGACTTCAGGGGGTTAAGACTTG-TTT
1 TTCAGTCTGCTCCACTGCAACTTCAGGGAGTTAAGACTTGCTTC
*
983 TCTCAGTCTGCTCCGCTGCAACTTCA
1 T-TCAGTCTGCTCCACTGCAACTTCA
1009 AAGAGATAAG
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
43 3 0.06
44 51 0.94
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.33
Consensus pattern (44 bp):
TTCAGTCTGCTCCACTGCAACTTCAGGGAGTTAAGACTTGCTTC
Found at i:1233 original size:43 final size:43
Alignment explanation
Indices: 1185--1320 Score: 118
Period size: 43 Copynumber: 3.2 Consensus size: 43
1175 CAACCGATGG
1185 AGGCAAGGCTTTGTTTTCGATCTGCTCCGTTGTTAATGCAGGA
1 AGGCAAGGCTTTGTTTTCGATCTGCTCCGTTGTTAATGCAGGA
* * ** * * ** * *
1228 AGGCAA-GATCTGCTTCTTTAACCAGCTCCACTG-CAA-CCGATGG-
1 AGGCAAGGCTTTG-TT-TTCGATCTGCTCCGTTGTTAATGC-A-GGA
1271 AGGCAAGGCTTTGTTTTCGATCTGCTCCGTTGTTAATGCAGGA
1 AGGCAAGGCTTTGTTTTCGATCTGCTCCGTTGTTAATGCAGGA
1314 AGGCAAG
1 AGGCAAG
1321 ATTTGCTTCT
Statistics
Matches: 65, Mismatches: 20, Indels: 16
0.64 0.20 0.16
Matches are distributed among these distances:
42 18 0.28
43 29 0.45
44 18 0.28
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.29
Consensus pattern (43 bp):
AGGCAAGGCTTTGTTTTCGATCTGCTCCGTTGTTAATGCAGGA
Found at i:1278 original size:86 final size:86
Alignment explanation
Indices: 1113--1934 Score: 1338
Period size: 86 Copynumber: 9.5 Consensus size: 86
1103 ACTTGTAATC
* ** * *
1113 TTCGATCTGCTTCACTGTCGATGCAGGAGGGCAAGATCTGCTATCTTCAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTGCAA
1178 CCGATGGAGGCAAGGCTTTGTT
65 CCGATGGAGGCAAGGCTTTGTT
* *
1200 TTCGATCTGCTCCGTTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
1265 CGATGGAGGCAAGGCTTTGTT
66 CGATGGAGGCAAGGCTTTGTT
* * * *
1286 TTCGATCTGCTCCGTTGTTAATGCAGGAAGGCAAGATTTGCTTCTTTAACCAGCTCCACTACAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
1351 CGATGGAGGCAAGGCTTTGTT
66 CGATGGAGGCAAGGCTTTGTT
*** *
1372 TTCGATCTGCTTCGCTGTTAGCACAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGTAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
1437 CGATGGAGGCAAGGCTTTGTT
66 CGATGGAGGCAAGGCTTTGTT
1458 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
1523 CGATGGAGGCAAGGCTTTGTT
66 CGATGGAGGCAAGGCTTTGTT
* * *
1544 TTGGATCTGTTTCGCTGTTAATGCAGGAAGGCAAGATCTACTTCTTTAACCAGCTCCACTGCAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
*
1609 CGATGGAGGCAATGCTTTGTT
66 CGATGGAGGCAAGGCTTTGTT
*
1630 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTACTTCTTTAACCAGCTCCACTGCAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
1695 CGATGGAGGCAAGGCTTTGTT
66 CGATGGAGGCAAGGCTTTGTT
* * * *
1716 TTCGATCTGTTTCGCTGTTAATGTAGAAAGACAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
*
1781 CAATGGAGGCAAGGCTTTGTT
66 CGATGGAGGCAAGGCTTTGTT
*
1802 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACTAGCTCCACTGCAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
*
1867 CGATGGAGGCAACGCTTTGTT
66 CGATGGAGGCAAGGCTTTGTT
* * ** *
1888 TTCGATCTACTTCGCTGTCAATAAAAGAAGGCAAGATCTGCTATCTT
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCT-TCTT
1935 CACTGATCTG
Statistics
Matches: 688, Mismatches: 46, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
86 648 0.94
87 40 0.06
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (86 bp):
TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
CGATGGAGGCAAGGCTTTGTT
Found at i:1361 original size:43 final size:43
Alignment explanation
Indices: 1228--1363 Score: 100
Period size: 43 Copynumber: 3.2 Consensus size: 43
1218 TAATGCAGGA
* *
1228 AGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGG
1 AGGCAAGATTTGCTTCTTTAACCAGCTCCACTACAACCGATGG
* ** * * ** ** *
1271 AGGCAAGGCTTTG-TT-TTCGATCTGCTCCGTTGTTAA-TGCA-GG
1 AGGCAA-GATTTGCTTCTTTAACCAGCTCCACT-ACAACCG-ATGG
1313 AAGGCAAGATTTGCTTCTTTAACCAGCTCCACTACAACCGATGG
1 -AGGCAAGATTTGCTTCTTTAACCAGCTCCACTACAACCGATGG
1357 AGGCAAG
1 AGGCAAG
1364 GCTTTGTTTT
Statistics
Matches: 64, Mismatches: 21, Indels: 16
0.63 0.21 0.16
Matches are distributed among these distances:
42 18 0.28
43 29 0.45
44 17 0.27
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (43 bp):
AGGCAAGATTTGCTTCTTTAACCAGCTCCACTACAACCGATGG
Found at i:1404 original size:43 final size:42
Alignment explanation
Indices: 1357--1492 Score: 107
Period size: 43 Copynumber: 3.2 Consensus size: 42
1347 CAACCGATGG
*
1357 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAGCACAGGA
1 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAAC-CAGGA
* * ** * * * *
1400 AGGCAA-GATCTGCTTCTTTAACCAGCTCCACTG-TAACCGATGG-
1 AGGCAAGGCTTTG-TT-TTCGATCTGCTTCGCTGTTAACC-A-GGA
*
1443 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGA
1 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAA-CCAGGA
1486 AGGCAAG
1 AGGCAAG
1493 ATCTGCTTCT
Statistics
Matches: 67, Mismatches: 18, Indels: 16
0.66 0.18 0.16
Matches are distributed among these distances:
42 18 0.27
43 31 0.46
44 18 0.27
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.29
Consensus pattern (42 bp):
AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACCAGGA
Found at i:4153 original size:32 final size:32
Alignment explanation
Indices: 4091--4153 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
4081 TTCATTTTCA
*
4091 TTTTGACCTTGATTTTTGATTTTTCTTTTTTG
1 TTTTGACCTTGATTTTTGATTTTGCTTTTTTG
* *
4123 TTTTGATCTTGA-TTTTGCTTTTGCTCTTTTT
1 TTTTGACCTTGATTTTTGATTTTGCT-TTTTT
4154 TTAATCTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 11 0.41
32 16 0.59
ACGTcount: A:0.08, C:0.11, G:0.13, T:0.68
Consensus pattern (32 bp):
TTTTGACCTTGATTTTTGATTTTGCTTTTTTG
Found at i:8962 original size:2 final size:2
Alignment explanation
Indices: 8957--8983 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8947 AAAAAGATAA
8957 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
8984 AACATATCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9061 original size:23 final size:23
Alignment explanation
Indices: 9012--9061 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
9002 ACAAATATGC
* *
9012 TAAATTTAAATAATGATACCTAG
1 TAAATTTAAATAATAATACATAG
9035 TAAATTTCAAATAATAATACATA-
1 TAAATTT-AAATAATAATACATAG
9058 TAAA
1 TAAA
9062 ACTTAAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.34
Consensus pattern (23 bp):
TAAATTTAAATAATAATACATAG
Done.