Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: XM_021440386.1
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: 2520
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Found at i:720 original size:99 final size:96
Alignment explanation
Indices: 605--782 Score: 257
Period size: 96 Copynumber: 1.8 Consensus size: 96
595 ATGGGTCAAG
* * *
605 CTTCACGGGAGACCTTCAACCAAGCGTGCCGGCAGTTCAGAATCCTGGAGGACAGGATTGGACGT
1 CTTCACGGAAGACCTTCAAACAAGCGTG-C--CAGGTCAGAATCCTGGAGGACAGGATTGGACGT
* *
670 GGCAGGGTAATTTGCAGCCGAATGCTGTACCAAT
63 GGCAGAGTAATTGGCAGCCGAATGCTGTACCAAT
* * *
704 CTTCACGGAAGGCCTTCAAAGAGGCGTGCCAGGTCAGAATCCTGGAGGACAGGATTGGACGTGGC
1 CTTCACGGAAGACCTTCAAACAAGCGTGCCAGGTCAGAATCCTGGAGGACAGGATTGGACGTGGC
769 AGAGTAATTGGCAG
66 AGAGTAATTGGCAG
783 TCAAATATCT
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
96 47 0.66
98 1 0.01
99 23 0.32
ACGTcount: A:0.26, C:0.22, G:0.33, T:0.19
Consensus pattern (96 bp):
CTTCACGGAAGACCTTCAAACAAGCGTGCCAGGTCAGAATCCTGGAGGACAGGATTGGACGTGGC
AGAGTAATTGGCAGCCGAATGCTGTACCAAT
Found at i:1088 original size:63 final size:64
Alignment explanation
Indices: 1015--1178 Score: 183
Period size: 63 Copynumber: 2.6 Consensus size: 64
1005 ACCAAGATGG
* * * * * * *
1015 AGATGGAGAGGCTTTATGAAGAAAATAATGCACATAGAAAACTCGAGGCAGAGAATAAGGTC-A
1 AGATCGAGAGGCTTTGTAAAGAAAATGATGCACATAAAAAACTCGAAGAAGAGAATAAGGTCGA
* *
1078 AGATTGAGAGGCTTTGTAAAG-AAATCGACGCAC-TCAAAAAACTCGAAGAAGAGAATAAGGTCG
1 AGATCGAGAGGCTTTGTAAAGAAAAT-GATGCACAT-AAAAAACTCGAAGAAGAGAATAAGGTCG
1141 A
64 A
* *
1142 A-ATCGAAAGGCTTCGTAAAGAAAATGATGCACATAAA
1 AGATCGAGAGGCTTTGTAAAGAAAATGATGCACATAAA
1179 TTATTTCATC
Statistics
Matches: 84, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
62 5 0.06
63 72 0.86
64 7 0.08
ACGTcount: A:0.45, C:0.13, G:0.24, T:0.18
Consensus pattern (64 bp):
AGATCGAGAGGCTTTGTAAAGAAAATGATGCACATAAAAAACTCGAAGAAGAGAATAAGGTCGA
Found at i:1288 original size:63 final size:63
Alignment explanation
Indices: 1215--1830 Score: 521
Period size: 63 Copynumber: 9.8 Consensus size: 63
1205 TTGTGTCCAG
* * * ** *
1215 AAACTAGAGGAAAAGAACAAGATTGAGATCGAGAGGCTTTGCAAACTAAATGATGGACATAAA
1 AAACTCGAGGAAAAGAACAAGATTGAGATCGAGAGGCTTCGTAAAGAAAATGATGCACATAAA
* * * * *
1278 AAACTTGAGGAAGAGAAC-A-ATGTCACGATTGAAAGGCTTCGTAAAGAAAATGATGCACATAAA
1 AAACTCGAGGAAAAGAACAAGAT-TGA-GATCGAGAGGCTTCGTAAAGAAAATGATGCACATAAA
* * * *
1341 AGACTCGAGGAAGAGAACAAGATTGAGATCAAGAGGCTTCTTAAAGAAAATGATGCACATAAA
1 AAACTCGAGGAAAAGAACAAGATTGAGATCGAGAGGCTTCGTAAAGAAAATGATGCACATAAA
* * ** * * * * * * *
1404 GAACTCGA--AAAAGAGACAAAGGTCAAGGTGGAGAGGTTTCTTCAAGAAAGTAATGCACATAAA
1 AAACTCGAGGAAAAGA-AC-AAGATTGAGATCGAGAGGCTTCGTAAAGAAAATGATGCACATAAA
* * * * ** **
1467 GAACTTGAGGAAGAA-ACCAAGGTCAAGATCGAGAGGCTTCGTAAAGAAAATGATGCATTTAAA
1 AAACTCGAGGAA-AAGAACAAGATTGAGATCGAGAGGCTTCGTAAAGAAAATGATGCACATAAA
* * * * * ***
1530 AAACTTGAGGAAGAGAACAAGATCGAGATTGAGAGGCTTCGAAAAGAAAATGATGTGTATAAA
1 AAACTCGAGGAAAAGAACAAGATTGAGATCGAGAGGCTTCGTAAAGAAAATGATGCACATAAA
* * * *
1593 AAACTCGAGGAAGAA-AACAAGATCGAGATTGAGAGACTTCGTAAAGAAAATGATGCACACAAA
1 AAACTCGAGGAA-AAGAACAAGATTGAGATCGAGAGGCTTCGTAAAGAAAATGATGCACATAAA
* * * * * * *
1656 AAACT-GCAGGAAAAGACCAAGGTTAAGATCAAAAGGCTTCGTAAAGAAAATGACGCACATCAA
1 AAACTCG-AGGAAAAGAACAAGATTGAGATCGAGAGGCTTCGTAAAGAAAATGATGCACATAAA
* * * *
1719 AAACTCAAGGAAGAGAACAAGATTGAGATCGAGAGGCTTCGTAAAAAAAATGATGCACATGAA
1 AAACTCGAGGAAAAGAACAAGATTGAGATCGAGAGGCTTCGTAAAGAAAATGATGCACATAAA
* * ** * *
1782 AAACTC-ATGGAAAATACCAAGATCAAGAT-GAAAAGGCTTCGTGAAGAAA
1 AAACTCGA-GGAAAAGAACAAGATTGAGATCG-AGAGGCTTCGTAAAGAAA
1831 GGGATGCAAA
Statistics
Matches: 449, Mismatches: 88, Indels: 32
0.79 0.15 0.06
Matches are distributed among these distances:
61 7 0.02
62 11 0.02
63 419 0.93
64 5 0.01
65 5 0.01
66 2 0.00
ACGTcount: A:0.47, C:0.13, G:0.24, T:0.17
Consensus pattern (63 bp):
AAACTCGAGGAAAAGAACAAGATTGAGATCGAGAGGCTTCGTAAAGAAAATGATGCACATAAA
Found at i:1398 original size:225 final size:225
Alignment explanation
Indices: 987--1403 Score: 534
Period size: 225 Copynumber: 1.9 Consensus size: 225
977 GGCAAAAAAA
* * * * ** * *
987 CAGAAACTCGAGGAAAATACCAAGATGGAGATGGAGAGGCTTTATGAAGAAAATAATGCACATAG
1 CAGAAACTAGAGGAAAAGAACAAGATGGAGATCGAGAGGCTTTACAAACAAAATAATGCACATAA
* * * *
1052 AAAACTCGAGGCAGAGAATAAGGTCAAGATTGAGAGGCTTTGTAAAGAAATCGACGCACTCAAAA
66 AAAACTCGAGGAAGAGAACAAGGTCAAGATTGAAAGGCTTCGTAAAGAAATCGACGCACTCAAAA
* *
1117 AACTCGAAGAAGAGAATAAGGTCGAAATCGAAAGGCTTCGTAAAGAAAATGATGCACATAAATTA
131 AACTCGAAGAAGAGAACAAGATCGAAATCGAAAGGCTTCGTAAAGAAAATGATGCACATAAATTA
1182 TTTCATCTTTTTGATCTGACTTTTTGTGTC
196 TTTCATCTTTTTGATCTGACTTTTTGTGTC
* * * * *
1212 CAGAAACTAGAGGAAAAGAACAAGATTGAGATCGAGAGGCTTTGCAAACTAAATGATGGACATAA
1 CAGAAACTAGAGGAAAAGAACAAGATGGAGATCGAGAGGCTTTACAAACAAAATAATGCACATAA
* * * *
1277 AAAACTTGAGGAAGAGAACAATGTCACGATTGAAAGGCTTCGTAAAGAAAAT-GATGCACAT-AA
66 AAAACTCGAGGAAGAGAACAAGGTCAAGATTGAAAGGCTTCGTAAAG-AAATCGACGCAC-TCAA
* * * * *
1340 AAGACTCGAGGAAGAGAACAAGATTGAGATC-AAGAGGCTTCTTAAAGAAAATGATGCACATAAA
129 AAAACTCGAAGAAGAGAACAAGATCGAAATCGAA-AGGCTTCGTAAAGAAAATGATGCACATAAA
1404 GAACTCGAAA
Statistics
Matches: 161, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
224 2 0.01
225 154 0.96
226 5 0.03
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (225 bp):
CAGAAACTAGAGGAAAAGAACAAGATGGAGATCGAGAGGCTTTACAAACAAAATAATGCACATAA
AAAACTCGAGGAAGAGAACAAGGTCAAGATTGAAAGGCTTCGTAAAGAAATCGACGCACTCAAAA
AACTCGAAGAAGAGAACAAGATCGAAATCGAAAGGCTTCGTAAAGAAAATGATGCACATAAATTA
TTTCATCTTTTTGATCTGACTTTTTGTGTC
Found at i:1451 original size:126 final size:126
Alignment explanation
Indices: 1221--1830 Score: 581
Period size: 126 Copynumber: 4.8 Consensus size: 126
1211 CCAGAAACTA
* * * ** * *
1221 GAGGAAAAGAACAAGATTGAGATCGAGAGGCTTTGCAAACTAAATGATGGACATAAAAAACTTGA
1 GAGGAAGAGAACAAGATTGAGATCGAGAGGCTTCGTAAAGAAAATGATGCACATAAAAAACTCGA
* * *
1286 GGAAGAGAACAATGTCACGATTGAAAGGCTTCGTAAAGAAAATGATGCACATAAAAGACTC
66 GAAAGAGAACAAGGTCAAGATTGAAAGGCTTCGTAAAGAAAATGATGCACATAAAAGACTC
* * *
1347 GAGGAAGAGAACAAGATTGAGATCAAGAGGCTTCTTAAAGAAAATGATGCACATAAAGAACTCGA
1 GAGGAAGAGAACAAGATTGAGATCGAGAGGCTTCGTAAAGAAAATGATGCACATAAAAAACTCGA
* * * * * * * * * *
1412 AAAAGAG-ACAAAGGTCAAGGTGGAGAGGTTTCTTCAAGAAAGTAATGCACAT-AAAGAACTT
66 GAAAGAGAAC-AAGGTCAAGATTGAAAGGCTTCGTAAAGAAAATGATGCACATAAAAG-ACTC
* ** ** *
1473 GAGGAAGA-AACCAAGGTCAAGATCGAGAGGCTTCGTAAAGAAAATGATGCATTTAAAAAACTTG
1 GAGGAAGAGAA-CAAGATTGAGATCGAGAGGCTTCGTAAAGAAAATGATGCACATAAAAAACTCG
* * * * * *** *
1537 AGGAAGAGAACAAGATCGAGATTGAGAGGCTTCGAAAAGAAAATGATGTGTATAAAAAACTC
65 AGAAAGAGAACAAGGTCAAGATTGAAAGGCTTCGTAAAGAAAATGATGCACATAAAAGACTC
* * * * *
1599 GAGGAAGAAAACAAGATCGAGATTGAGAGACTTCGTAAAGAAAATGATGCACACAAAAAACT-GC
1 GAGGAAGAGAACAAGATTGAGATCGAGAGGCTTCGTAAAGAAAATGATGCACATAAAAAACTCG-
* * ** *
1663 AGGAAA-AGACCAAGGTTAAGATCAAAAGGCTTCGTAAAGAAAATGACGCACATCAAAA-ACTC
65 A-GAAAGAGAACAAGGTCAAGATTGAAAGGCTTCGTAAAGAAAATGATGCACAT-AAAAGACTC
* * *
1725 AAGGAAGAGAACAAGATTGAGATCGAGAGGCTTCGTAAAAAAAATGATGCACATGAAAAACTC-A
1 GAGGAAGAGAACAAGATTGAGATCGAGAGGCTTCGTAAAGAAAATGATGCACATAAAAAACTCGA
* * * *
1789 TGGAAA-ATACCAAGATCAAGA-TGAAAAGGCTTCGTGAAGAAA
66 --GAAAGAGAACAAGGTCAAGATTG-AAAGGCTTCGTAAAGAAA
1831 GGGATGCAAA
Statistics
Matches: 389, Mismatches: 83, Indels: 24
0.78 0.17 0.05
Matches are distributed among these distances:
125 10 0.03
126 365 0.94
127 14 0.04
ACGTcount: A:0.46, C:0.13, G:0.24, T:0.17
Consensus pattern (126 bp):
GAGGAAGAGAACAAGATTGAGATCGAGAGGCTTCGTAAAGAAAATGATGCACATAAAAAACTCGA
GAAAGAGAACAAGGTCAAGATTGAAAGGCTTCGTAAAGAAAATGATGCACATAAAAGACTC
Found at i:1600 original size:189 final size:189
Alignment explanation
Indices: 1262--1787 Score: 612
Period size: 189 Copynumber: 2.8 Consensus size: 189
1252 TTTGCAAACT
* * * * *
1262 AAATGATGGACATAAAAAACTTGAGGAAGAGAA-CAATGTCACGATTGAAAGGCTTCGTAAAGAA
1 AAATAATGCACATAAAAAACTTGAGGAAGA-AACCAAGGTCAAGATCGAAAGGCTTCGTAAAGAA
* * **
1326 AATGATGCACATAAAAGACTCGAGGAAGAGAACAAGATTGAGATCAAGAGGCTTCTTAAAGAAAA
65 AATGATGCACATAAAAAACTCGAGGAAGAGAACAAGATTGAGATCGAGAGGCTTCGAAAAGAAAA
* * * * ** * *
1391 TGATGCACATAAAGAACTCGAAAAAG-AGACAAAGGTCAAGGTGGAGAGGTTTCTTCAAGA
130 TGATGCACATAAAAAACTCGAAAAAGAAAAC-AAGATCAAGATGGAGAGACTTCGTAAAGA
* * *
1451 AAGTAATGCACATAAAGAACTTGAGGAAGAAACCAAGGTCAAGATCGAGAGGCTTCGTAAAGAAA
1 AAATAATGCACATAAAAAACTTGAGGAAGAAACCAAGGTCAAGATCGAAAGGCTTCGTAAAGAAA
** * * *
1516 ATGATGCATTTAAAAAACTTGAGGAAGAGAACAAGATCGAGATTGAGAGGCTTCGAAAAGAAAAT
66 ATGATGCACATAAAAAACTCGAGGAAGAGAACAAGATTGAGATCGAGAGGCTTCGAAAAGAAAAT
*** ** * *
1581 GATGTGTATAAAAAACTCGAGGAAGAAAACAAGATCGAGATTGAGAGACTTCGTAAAGA
131 GATGCACATAAAAAACTCGAAAAAGAAAACAAGATCAAGATGGAGAGACTTCGTAAAGA
* * * *
1640 AAATGATGCACACAAAAAAC-TGCAGGAA-AAGACCAAGGTTAAGATCAAAAGGCTTCGTAAAGA
1 AAATAATGCACATAAAAAACTTG-AGGAAGAA-ACCAAGGTCAAGATCGAAAGGCTTCGTAAAGA
* * *
1703 AAATGACGCACATCAAAAACTCAAGGAAGAGAACAAGATTGAGATCGAGAGGCTTCGTAAAA-AA
64 AAATGATGCACATAAAAAACTCGAGGAAGAGAACAAGATTGAGATCGAGAGGCTTCG-AAAAGAA
*
1767 AATGATGCACATGAAAAACTC
128 AATGATGCACATAAAAAACTC
1788 ATGGAAAATA
Statistics
Matches: 281, Mismatches: 51, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
188 6 0.02
189 268 0.95
190 7 0.02
ACGTcount: A:0.47, C:0.13, G:0.23, T:0.17
Consensus pattern (189 bp):
AAATAATGCACATAAAAAACTTGAGGAAGAAACCAAGGTCAAGATCGAAAGGCTTCGTAAAGAAA
ATGATGCACATAAAAAACTCGAGGAAGAGAACAAGATTGAGATCGAGAGGCTTCGAAAAGAAAAT
GATGCACATAAAAAACTCGAAAAAGAAAACAAGATCAAGATGGAGAGACTTCGTAAAGA
Done.