Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g00550.F2
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: 1843
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Found at i:1069 original size:44 final size:44
Alignment explanation
Indices: 808--1550 Score: 286
Period size: 44 Copynumber: 16.8 Consensus size: 44
798 ATCAAGCTTG
* * * *
808 ATCTGCTCCATTGCAACTTCAAGGAGATAAGATCTGCTATCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTCA
* * * * *
853 GTCTGCCCCACTGCAACTTTAGGGAGATAAGACTTGTAACTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCA
* * * * * *
897 A-CTTGCCCCACTGCAACTTTAGGGGGGTAAGGTTTGTGGCTTCA
1 ATC-TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCA
* * *** * **
941 ATCTACTCTACCATAACTTCAGGGAGATAAGATTCACCATGATAGGTTTG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-----TG-TAGCTTCA
* * * * * *
991 AT-T-CAACCTACTACAACTTCAGAGG-TATAGGATTTGTGGCTTTA
1 ATCTGC-TCC-ACTGCAACTTCAG-GGAGATAAGATTTGTAGCTTCA
* *
1035 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCAACTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCA
* * * ** **
1079 ATCTGCTCCACTGTAACTTCAGAGAGACAAGATTTGCGGCTTTG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCA
* * * *** *
1123 ATTTGCTCTACTGCAACTTCAGGGAGACAAGATCTACAATCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TTGTAGCTTCA
** * * ** * * * *
1168 GCCTACTCCACTACTGCTT-AGGGAGATAGGA-TGGTGGCTTAA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCA
**** * * *
1210 ATCTGCTCCACTATTGCTT-AGGGAGACAAGATTTGTTGTCTTCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAG-CTTCA
* * *** *
1254 ATCTGCTCCATTGCAACTTCAGGGAGACAAGATCTACAATCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TTGTAGCTTCA
** * * ** * * *
1299 GCCTACTCCACTACTGCTT-AGGGAGATAGGA-TGGTAGCTTAA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCA
* * * * * * *
1341 ATCTGCTTCACTGCAACTTCAGGAAGACAAGATTCGCCATCTTCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTCA
* * *
1386 ATCTGCTCCACTACAACTTCAGGGAGATAAGATTTGCA-ATCTCTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCT-TC-A
** * * * * * * *
1431 GCCTACTCCACTACAACTT-AAGGAGATAGGA-TGGTGGCTTAA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCA
* * * * * * *
1473 ATCTGCTTCACTGTAACTTCAGGAAGACAAGATTCGCTATCTTCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTCA
* * *
1518 ATCTGCTCTACTGCAACTTTAGGGAGACAAGAT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
1551 CTGCAATCTT
Statistics
Matches: 503, Mismatches: 167, Indels: 56
0.69 0.23 0.08
Matches are distributed among these distances:
42 62 0.12
43 28 0.06
44 218 0.43
45 162 0.32
46 2 0.00
48 1 0.00
49 4 0.01
50 24 0.05
51 2 0.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCA
Found at i:1269 original size:131 final size:132
Alignment explanation
Indices: 1078--1560 Score: 650
Period size: 132 Copynumber: 3.7 Consensus size: 132
1068 TTGCAACTTC
* ** * * *
1078 AATCTGCTCCACTGTAACTTCA-GAGAGACAAGATTTG-CGGCTTTGATTTGCTCTACTGCAACT
1 AATCTGCTCCACTGTAACTTCAGGA-AGACAAGATTCGCCATCTTCGATCTGCTCCACTGCAACT
1141 TCAGGGAGACAAGATCTACAATCTTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATGGTGGC
65 TCAGGGAGACAAGATCTACAATCTTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATGGTGGC
1206 TTA
130 TTA
* ** * * *** *
1209 AATCTGCTCCACTATTGCTT-AGGGAGACAAGATTTGTTGTCTTCGATCTGCTCCATTGCAACTT
1 AATCTGCTCCACTGTAACTTCAGGAAGACAAGATTCGCCATCTTCGATCTGCTCCACTGCAACTT
*
1273 CAGGGAGACAAGATCTACAATCTTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATGGTAGCT
66 CAGGGAGACAAGATCTACAATCTTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATGGTGGCT
1338 TA
131 TA
* * *
1340 AATCTGCTTCACTGCAACTTCAGGAAGACAAGATTCGCCATCTTCGATCTGCTCCACTACAACTT
1 AATCTGCTCCACTGTAACTTCAGGAAGACAAGATTCGCCATCTTCGATCTGCTCCACTGCAACTT
* * * ** *
1405 CAGGGAGATAAGATTTGCAATC-TCTAGCCTACTCCACTACAACTTAAGGAGATAGGATGGTGGC
66 CAGGGAGACAAGATCTACAATCTTC-AGCCTACTCCACTACTGCTTAGGGAGATAGGATGGTGGC
1469 TTA
130 TTA
* * *
1472 AATCTGCTTCACTGTAACTTCAGGAAGACAAGATTCGCTATCTTCGATCTGCTCTACTGCAACTT
1 AATCTGCTCCACTGTAACTTCAGGAAGACAAGATTCGCCATCTTCGATCTGCTCCACTGCAACTT
* *
1537 TAGGGAGACAAGATCTGCAATCTT
66 CAGGGAGACAAGATCTACAATCTT
1561 TAGTCTGCTT
Statistics
Matches: 310, Mismatches: 37, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
130 13 0.04
131 122 0.39
132 174 0.56
133 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (132 bp):
AATCTGCTCCACTGTAACTTCAGGAAGACAAGATTCGCCATCTTCGATCTGCTCCACTGCAACTT
CAGGGAGACAAGATCTACAATCTTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATGGTGGCT
TA
Found at i:1395 original size:87 final size:88
Alignment explanation
Indices: 1210--1419 Score: 219
Period size: 87 Copynumber: 2.4 Consensus size: 88
1200 GGTGGCTTAA
* * * * ** *
1210 ATCTGCTCCACTATTGCTTAGGGAGACAAGATTTGTTGTCTTCGATCTGCTCCATTGCAACTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATTGGTAGTCTTAAATCTGCTCCACTGCAACTTCA
*
1275 GGGAGACAAGATCTACAATCTTC
66 GGAAGACAAGATCTACAATCTTC
* * * *
1298 AGCCTACTCCACTACTGCTTAGGGAGATAGGA-TGGTAG-CTTAAATCTGCTTCACTGCAACTTC
1 A-TCTGCTCCACTACTGCTTAGGGAGATAAGATTGGTAGTCTTAAATCTGCTCCACTGCAACTTC
* *
1361 AGGAAGACAAGAT-TCGCCATCTTC
65 AGGAAGACAAGATCT-ACAATCTTC
**
1385 GATCTGCTCCACTACAACTTCAGGGAGATAAGATT
1 -ATCTGCTCCACTACTGCTT-AGGGAGATAAGATT
1420 TGCAATCTCT
Statistics
Matches: 98, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
86 1 0.01
87 54 0.55
88 17 0.17
89 26 0.27
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (88 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATTGGTAGTCTTAAATCTGCTCCACTGCAACTTCA
GGAAGACAAGATCTACAATCTTC
Found at i:1560 original size:45 final size:45
Alignment explanation
Indices: 1034--1569 Score: 283
Period size: 45 Copynumber: 12.2 Consensus size: 45
1024 TTGTGGCTTT
*
1034 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCAA-CTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
* * ** *
1078 AATCTGCTCCACTGTAACTTCAGAGAGACAAGATTTGC-GGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
* * * * *
1122 GATTTGCTCTACTGCAACTTCAGGGAGACAAGATCTACAATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
** * * ** * * * * *
1167 AGCCTACTCCACTACTGCTT-AGGGAGATAGGATGGTG---GCTTA
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGAT-TTGCAATCTTC
**** ***
1209 AATCTGCTCCACTATTGCTT-AGGGAGACAAGATTTGTTGTCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
* * * *
1253 GATCTGCTCCATTGCAACTTCAGGGAGACAAGATCTACAATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
** * * ** * * ** * *
1298 AGCCTACTCCACTACTGCTT-AGGGAGATAGGA--TGGTAGCTTA
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
* * * *
1340 AATCTGCTTCACTGCAACTTCAGGAAGACAAGATTCGCCATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
* * *
1385 GATCTGCTCCACTACAACTTCAGGGAGATAAGATTTGCAATC-TC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
** * * * * * * * *
1429 TAGCCTACTCCACTACAACTT-AAGGAGATAGGATGGTG---GCTTA
1 -AATCTGCTCCACTGCAACTTCAGGGAGACAAGAT-TTGCAATCTTC
* * * * *
1472 AATCTGCTTCACTGTAACTTCAGGAAGACAAGATTCGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
* * * * *
1517 GATCTGCTCTACTGCAACTTTAGGGAGACAAGATCTGCAATCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
*
1562 AGTCTGCT
1 AATCTGCT
1570 TCCTCGCTAC
Statistics
Matches: 353, Mismatches: 122, Indels: 33
0.69 0.24 0.06
Matches are distributed among these distances:
41 2 0.01
42 64 0.18
43 19 0.05
44 120 0.34
45 148 0.42
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (45 bp):
AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
Found at i:1823 original size:64 final size:64
Alignment explanation
Indices: 1707--1834 Score: 204
Period size: 64 Copynumber: 2.0 Consensus size: 64
1697 TCATGTATCT
* * *
1707 ATGCTTATGCCAAATAATTAGGATGCTATGATCGAAAGGAATCAAATGCTCCTAACTAGATGTG
1 ATGCTTATGCCAAATAATTAAGATGCTATGATCGAAAGAAATCAAATACTCCTAACTAGATGTG
*
1771 ATGCTTATGTCAAATAATTAAGATGCTATGATCGAAATGAAAT-AAATACTCCTAACTAGATGTG
1 ATGCTTATGCCAAATAATTAAGATGCTATGATCGAAA-GAAATCAAATACTCCTAACTAGATGTG
1835 TTATGAATG
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
64 55 0.93
65 4 0.07
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (64 bp):
ATGCTTATGCCAAATAATTAAGATGCTATGATCGAAAGAAATCAAATACTCCTAACTAGATGTG
Done.