Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1086
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: 2869
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:557 original size:114 final size:114
Alignment explanation
Indices: 397--1756 Score: 1806
Period size: 115 Copynumber: 11.9 Consensus size: 114
387 GCATTAGCTA
* * * * * *
397 CGTTTTTCAAAAAGCCCCGC-AAAAAACCTAAGTCCAACGACGCCGTTTTCTGAGCATTCTGGGA
1 CGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
* * * * *
461 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAAAGCCCTGAGCATTAGCGG
66 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGG
* * * *
510 CGATTTTGAAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCATTCGAGGA
1 CGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
* * *
575 TTTAGCGGCGCTTTCT-A-AAAGTGCCGCTAATGCTCAAGGCTTTAGCGG
66 TTTAGCGGCG-TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGG
* * * * * *
623 TGTTTTTGAGAAAGCGCCGTAAAAAAACCGAATCCCAACGACGCCGTTTTCTGAGCCTTCGTGGA
1 CGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
*
688 TTTAGGGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGG
66 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGG
* ** *
737 CGTTTTTGAGAAAGCGACGCAAAAAAAACCTAAGCCCAACGATTCCGTTTTCTGTGCATCTT--G
1 CGTTTTTGAGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGC-T-TTCGG
* *
800 GGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCT-TGGGCTTTAGCGA
63 GGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGG
* * * *
851 CGTTTTTTAGAAAGTGCCGCAAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAG-TAGTCGGGG
1 CGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT-TTCGGGG
* * *
915 ATTTAGCGGTGTTTTTAAGAAAGCGCCGCTAATGCTCGGGGCTTTACCGG
65 ATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGG
* * *
965 CGTTTTTGAGAAAGCGCAGCAAAAAAACCTAAGCCCAACGATGCCGTTTTCTGAGCTTTCAGGGA
1 CGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
*
1030 TTTAGCAGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAG-GG
66 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGG
* * *
1078 CATTTTTGAGAAAGCGCCGCGAAAAAAACCTAAGCCCAACGATGCCGTTTTTTGAGCTTTCGGGG
1 CGTTTTTGAGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGG
*
1143 ATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTTAGGGCTTTA-CTGG
65 ATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGC-GG
* *
1193 CGTTTTTGAGAAAAGCGCCGTAAAAAAACCTAAGCCCAACGACGCCTTTTTCTGAGCTTTCGGGG
1 CGTTTTTGAG-AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGG
* * ** * * *
1258 ATTTAGCGGTGTTTTTGAGAAATTGCTGCTAATGCCCAGGGCTTTAGCAG
65 ATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGG
* * *
1308 CGTGTTTGAGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACGCAGTTTTCTAAGCTTTCGGGG
1 CGTTTTTGAGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGG
* *
1373 ATTTA-CGGGCGTTTTTAAGAAAGTGCTGCTAATGCTCAGGGCTTTAGCGG
65 ATTTAGC-GGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGG
* * *
1423 CGTTTTTGAGAAAGTGCCGCAAAAAAAACCTAAGCCCAACGATGCCATTTTCTGAGCTTTCGGGG
1 CGTTTTTGAGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGG
* * * *
1488 ATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTTAGGGCTTTACCGA
65 ATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGG
* *
1538 CGTTTTTGAGAAAGTGCCGCAAAAAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAGCTTTCGG
1 CGTTTTTGAGAAAGCGCCGC---AAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGG
* * * * * *
1603 GGATTTAGCGGCGTTTTTAAAAAAGCACCACTAATACTCAAGGCTTTACCGG
63 GGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGG
* *
1655 CGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCG-TTTCTGAGCTGTCGAGGA
1 CGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
* *
1719 TTTAGCAGCGTTTTTGAGAAAGCGCCGCTAATGCTCAG
66 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAG
1757 AGATTTAAAA
Statistics
Matches: 1102, Mismatches: 124, Indels: 42
0.87 0.10 0.03
Matches are distributed among these distances:
111 2 0.00
112 4 0.00
113 244 0.22
114 355 0.32
115 379 0.34
116 11 0.01
117 107 0.10
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (114 bp):
CGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGG
Found at i:901 original size:228 final size:227
Alignment explanation
Indices: 390--1753 Score: 1764
Period size: 228 Copynumber: 6.0 Consensus size: 227
380 AAAATAAGCA
* * * * * *
390 TTAGCTACGTTTTTCAAAAAGCCCCGC--AAAAAACCTAAGTCCAACGACGCCGTTTTCTGAGCA
1 TTAGCGACGTTTTTGAGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * * * * * *
453 TTCTGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAAAGCCCTGAGCATTAGCGGCGATTTTG
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
* *
518 AAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCATTCGAGGATTTAGCGG
131 AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCG-GGATTTAGCGG
* * *
583 CGCTTTCT-A-AAAGTGCCGCTAATGCTCAAGGCT
195 CG-TTTTTAAGAAAGCGCCGCTAATGCT-AGGGCT
** * * * *
616 TTAGCGGTGTTTTTGAGAAAGCGCCG-TAAAAAAACCGAATCCCAACGACGCCGTTTTCTGAGCC
1 TTAGCGACGTTTTTGAGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* *
680 TTCGTGGATTTAGGGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
* ** *
745 AGAAAGCGACGCAAAAAAAACCTAAGCCCAACGATTCCGTTTTCTGTGCATCTT-GGGATTTAGC
131 AGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGC-T-TTCGGGATTTAGC
*
809 GGCGTTTTTAAGAAAGCGCCGCTAATGCTTGGGCT
193 GGCGTTTTTAAGAAAGCGCCGCTAATGCTAGGGCT
* * *
844 TTAGCGACGTTTTTTAGAAAGTGCCGC-AAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAG-T
1 TTAGCGACGTTTTTGAGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * * *
907 AGTCGGGGATTTAGCGGTGTTTTTAAGAAAGCGCCGCTAATGCTCGGGGCTTTACCGGCGTTTTT
66 -TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTT
* * *
972 GAGAAAGCGCAGCAAAAAAACCTAAGCCCAACGATGCCGTTTTCTGAGCTTTCAGGGATTTAGCA
130 GAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTC-GGGATTTAGCG
1037 GCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
194 GCGTTTTTAAGAAAGCGCCGCTAATGCT-AGGGCT
* * * * *
1072 TTAG-GGCATTTTTGAGAAAGCGCCGCGAAAAAAACCTAAGCCCAACGATGCCGTTTTTTGAGCT
1 TTAGCGACGTTTTTGAGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
*
1136 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTTAGGGCTTTA-CTGGCGTTTTT
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGC-GGCGTTTTT
* *
1200 GAGAAAAGCGCCGTAAAAAAACCTAAGCCCAACGACGCCTTTTTCTGAGCTTTCGGGGATTTAGC
130 GAG-AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTC-GGGATTTAGC
* * ** * *
1265 GGTGTTTTTGAGAAATTGCTGCTAATGCCCAGGGCT
193 GGCGTTTTTAAGAAAGCGCCGCTAATG-CTAGGGCT
* * *
1301 TTAGC-AGCGTGTTTGAGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACGCAGTTTTCTAAGC
1 TTAGCGA-CGTTTTTGAGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGC
* *
1365 TTTCGGGGATTTA-CGGGCGTTTTTAAGAAAGTGCTGCTAATGCTCAGGGCTTTAGCGGCGTTTT
65 TTTCGGGGATTTAGC-GGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTT
* * *
1429 TGAGAAAGTGCCGCAAAAAAAACCTAAGCCCAACGATGCCATTTTCTGAGCTTTCGGGGATTTAG
129 TGAGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTC-GGGATTTAG
*
1494 CGGCGTTTTTAAGAAAGCGCCACTAATGCTTAGGGCT
192 CGGCGTTTTTAAGAAAGCGCCGCTAATGC-TAGGGCT
* * *
1531 TTACCGACGTTTTTGAGAAAGTGCCGCAAAAAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAG
1 TTAGCGACGTTTTTGAGAAAGCGCCGC--AAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAG
* * * * * *
1596 CTTTCGGGGATTTAGCGGCGTTTTTAAAAAAGCACCACTAATACTCAAGGCTTTACCGGCGTTTT
64 CTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTT
*
1661 TGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCG-TTTCTGAGCTGTCGAGGATTTAGC
129 TGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCG-GGATTTAGC
* *
1725 AGCGTTTTTGAGAAAGCGCCGCTAATGCT
193 GGCGTTTTTAAGAAAGCGCCGCTAATGCT
1754 CAGAGATTTA
Statistics
Matches: 995, Mismatches: 115, Indels: 53
0.86 0.10 0.05
Matches are distributed among these distances:
225 2 0.00
226 21 0.02
227 193 0.19
228 276 0.28
229 117 0.12
230 258 0.26
231 26 0.03
232 101 0.10
233 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (227 bp):
TTAGCGACGTTTTTGAGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGATTTAGCGGC
GTTTTTAAGAAAGCGCCGCTAATGCTAGGGCT
Found at i:2188 original size:14 final size:14
Alignment explanation
Indices: 2169--2202 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
2159 CTTTTAAGGT
2169 TTAGGGGTT-AGTAG
1 TTAGGGGTTAAG-AG
2183 TTAGGGGTTAAGAG
1 TTAGGGGTTAAGAG
2197 TTAGGG
1 TTAGGG
2203 ATTTAGGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (14 bp):
TTAGGGGTTAAGAG
Found at i:2208 original size:22 final size:22
Alignment explanation
Indices: 2183--2227 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2173 GGGTTAGTAG
2183 TTAGGGGTTAAGAGTTAGGGAT
1 TTAGGGGTTAAGAGTTAGGGAT
* *
2205 TTAGGGGTTAGGATTTAGGGAT
1 TTAGGGGTTAAGAGTTAGGGAT
2227 T
1 T
2228 CAAGGGTCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.40, T:0.36
Consensus pattern (22 bp):
TTAGGGGTTAAGAGTTAGGGAT
Found at i:2218 original size:14 final size:15
Alignment explanation
Indices: 2196--2224 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2186 GGGGTTAAGA
2196 GTTAGGGATTTAGGG
1 GTTAGGGATTTAGGG
2211 GTTA-GGATTTAGGG
1 GTTAGGGATTTAGGG
2225 ATTCAAGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.21, C:0.00, G:0.45, T:0.34
Consensus pattern (15 bp):
GTTAGGGATTTAGGG
Found at i:2234 original size:22 final size:22
Alignment explanation
Indices: 2187--2234 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
2177 TAGTAGTTAG
* *
2187 GGGTTAAGAGTTAGGGATTTAG
1 GGGTTAAGAGTTAGGGATTCAA
* *
2209 GGGTTAGGATTTAGGGATTCAA
1 GGGTTAAGAGTTAGGGATTCAA
2231 GGGT
1 GGGT
2235 CGGGTTAGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.25, C:0.02, G:0.42, T:0.31
Consensus pattern (22 bp):
GGGTTAAGAGTTAGGGATTCAA
Done.