Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_7103
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: 4287
ACGTcount: A:0.20, C:0.28, G:0.30, T:0.23
Found at i:1699 original size:42 final size:42
Alignment explanation
Indices: 1595--1802 Score: 169
Period size: 42 Copynumber: 4.9 Consensus size: 42
1585 GAGCCTCCAT
*
1595 CACCTTGGTGGC-TCGGATGTGTGGGAGCCTC-AGCCACCATCGG
1 CACCTTGGT-GCAT-GGATGTGCGGGAGCCTCGAG-CACCATCGG
* * *
1638 TAACCTTGATGCTTGGATGTGCGGGAGCCTCGAGCACCATCGG
1 -CACCTTGGTGCATGGATGTGCGGGAGCCTCGAGCACCATCGG
* *
1681 CACCTTGGTGCATGGATGTGCGGGAGCATCG-GACACCACCGG
1 CACCTTGGTGCATGGATGTGCGGGAGCCTCGAG-CACCATCGG
* * ** * *
1723 CAAACTAGGCCCTTGGTTGTG-GGGAGCCTCGGAG-ACCATCGG
1 C-ACCTTGGTGCATGGATGTGCGGGAGCCTC-GAGCACCATCGG
*
1765 CACCTCGGTGCTAT-GATGTGCGGGAGCCTTC-AGCACCA
1 CACCTTGGTGC-ATGGATGTGCGGGAGCC-TCGAGCACCA
1803 AAGCTAAAGT
Statistics
Matches: 132, Mismatches: 22, Indels: 22
0.75 0.12 0.12
Matches are distributed among these distances:
41 14 0.11
42 64 0.48
43 43 0.33
44 11 0.08
ACGTcount: A:0.18, C:0.28, G:0.34, T:0.20
Consensus pattern (42 bp):
CACCTTGGTGCATGGATGTGCGGGAGCCTCGAGCACCATCGG
Found at i:2039 original size:24 final size:24
Alignment explanation
Indices: 2012--2090 Score: 106
Period size: 24 Copynumber: 3.3 Consensus size: 24
2002 CCGGTTAGGT
*
2012 TCCCGGTGGTGCTCCGGCGATCCG
1 TCCCGGTGGTGCTCCGGCGAACCG
*
2036 TCCCGGCGGTGCTCCGGCGAACCG
1 TCCCGGTGGTGCTCCGGCGAACCG
*
2060 TCCC-GTCGGTGCTCCGGTGAACCG
1 TCCCGGT-GGTGCTCCGGCGAACCG
*
2084 TTCCGGT
1 TCCCGGT
2091 AGCATAGGCC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
23 1 0.02
24 45 0.94
25 2 0.04
ACGTcount: A:0.06, C:0.38, G:0.35, T:0.20
Consensus pattern (24 bp):
TCCCGGTGGTGCTCCGGCGAACCG
Found at i:2243 original size:85 final size:85
Alignment explanation
Indices: 2095--2943 Score: 983
Period size: 85 Copynumber: 10.0 Consensus size: 85
2085 TCCGGTAGCA
* *
2095 TAGGCCCTTGGTCGTGCGGGAGCCTC-GGCACCATCGGCACCCT-GGTGCTAGGATGTGCAGGAG
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCA-CCTAGGTGCTTGGATGTGCGGGAG
* * *
2158 CCCCGGACACCATCGGCAAAC
65 CCTCGGGCACCATCGGCAACC
* ** * * * *
2179 TAAGCCCTTGGTATTGCAGGAGCCTCGGGCGCCATCGGCACCTCGGTGCTTCGATGTGCGGGAGC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGTGCTTGGATGTGCGGGAGC
2244 CTCGGGCACCATCGGCAACC
66 CTCGGGCACCATCGGCAACC
* *
2264 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTCGGTGCTAT-GATGGGCGGGAG
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGTGCT-TGGATGTGCGGGAG
* **
2328 CCTCGGACACTGTCGGCAACC
65 CCTCGGGCACCATCGGCAACC
* * * * *
2349 TAGGCCCTTGGTCGTGCGGGAGCCTCGAGCACCATCGGCACCTTGGTGCTTGGATGTCCGAGAAC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGTGCTTGGATGTGCGGGAGC
* *
2414 CTCGCGCACCATCGACAACC
66 CTCGGGCACCATCGGCAACC
* * * * **
2434 TAGGCCCTTGGTCGTGCGAGAGGCTCGGGCACCATCGGCAAACTAAGCCCTTGG-TCGTGCGGGA
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGTGCTTGGAT-GTGCGGGA
**
2498 GCCTCGGGCACCATCGGCAAAA
64 GCCTCGGGCACCATCGGCAACC
* * *
2520 TAGGCCCTTGGTCGTGCGGGAGCCTCGGCCACCATCGGCTCCTAGGTGCTGGGATGTGCGGGAGC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGTGCTTGGATGTGCGGGAGC
* *
2585 CTCGGACACCATCGGCAAAC
66 CTCGGGCACCATCGGCAACC
* * * * * *
2605 TAGGCCCTTTGTCGTGCGGGAGCCTCGTGCACCATCGACACCTTGGTGCTTGGATGTGCCGGAAC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGTGCTTGGATGTGCGGGAGC
2670 CTCGGGCACCATCGGCAACC
66 CTCGGGCACCATCGGCAACC
* * * ** ** *
2690 TAGACCCTTGGTCGTGCGAGAGGCTCGGGCACCATCGGCAAAATAGGCCCTTGG-TCGTGCGGGG
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGTGCTTGGAT-GTGCGGGA
*
2754 GCCTCGGCCACCATCGGC-ACC
64 GCCTCGGGCACCATCGGCAACC
* * *
2775 TCGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTTGGTGGCTCGGATGTGCGGGAG
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGT-GCTTGGATGTGCGGGAG
*
2840 CCTCGGGCAGCATCGGC-ACC
65 CCTCGGGCACCATCGGCAACC
* ** * ** * * *
2860 TCGGTGGCTAGGAGGTGCGGGAGCCTCGGACACCATCGGCAACTTGGTGCTTGGATGTGCGGGAG
1 TAGG-CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGTGCTTGGATGTGCGGGAG
2925 CCTCGGGCACCCATCGGCA
65 CCTCGGGCA-CCATCGGCA
2944 CCTTGGTGCC
Statistics
Matches: 646, Mismatches: 105, Indels: 25
0.83 0.14 0.03
Matches are distributed among these distances:
84 30 0.05
85 471 0.73
86 145 0.22
ACGTcount: A:0.16, C:0.32, G:0.34, T:0.18
Consensus pattern (85 bp):
TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGTGCTTGGATGTGCGGGAGC
CTCGGGCACCATCGGCAACC
Found at i:2555 original size:256 final size:254
Alignment explanation
Indices: 2095--2943 Score: 1082
Period size: 256 Copynumber: 3.3 Consensus size: 254
2085 TCCGGTAGCA
* * * *
2095 TAGGCCCTTGGTCGTGCGGGAGCCTCGGCACCATCGGCACCCTGGTGCTAGGATGTGC-AGGAGC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGCACCATCGGCACCTTGGTGCTTGGATGTCCGA-GAAC
* * * * ** * * *
2159 CCCGGACACCATCGGCAAACTAAGCCCTTGGTATTGC-AGGAGCCTCGGGCGCCATCGGC-ACCT
65 CTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGA-GAGGCTCGGGCACCATCGGCAAACT
* ** *
2222 CGGTGCTTCGAT-GTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAG
129 AGGCCCTT-GGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAG
* * * *
2286 CCTCGGGCACCATCGGCACCTCGGTGCTATGATGGGCGGGAGCCTCGGACACTGTCGGCAACC
193 CCTCGGGCACCATCGGCACCTAGGTGCTAGGATGTGCGGGAGCCTCGGACAC-ATCGGCAACC
2349 TAGGCCCTTGGTCGTGCGGGAGCCTCGAGCACCATCGGCACCTTGGTGCTTGGATGTCCGAGAAC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCG-GCACCATCGGCACCTTGGTGCTTGGATGTCCGAGAAC
* *
2414 CTCGCGCACCATCGACAACCTAGGCCCTTGGTCGTGCGAGAGGCTCGGGCACCATCGGCAAACTA
65 CTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGGCTCGGGCACCATCGGCAAACTA
* **
2479 AGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAAAATAGGCCCTTGGTCGTGCGGGAGCC
130 GGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCC
* * * *
2544 TCGGCCACCATCGGCTCCTAGGTGCTGGGATGTGCGGGAGCCTCGGACACCATCGGCAAAC
195 TCGGGCACCATCGGCACCTAGGTGCTAGGATGTGCGGGAGCCTCGGACA-CATCGGCAACC
* *
2605 TAGGCCCTTTGTCGTGCGGGAGCCTCGTGCACCATCGACACCTTGGTGCTTGGATGTGCCG-GAA
1 TAGGCCCTTGGTCGTGCGGGAGCCTCG-GCACCATCGGCACCTTGGTGCTTGGATGT-CCGAGAA
* *
2669 CCTCGGGCACCATCGGCAACCTAGACCCTTGGTCGTGCGAGAGGCTCGGGCACCATCGGCAAAAT
64 CCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGGCTCGGGCACCATCGGCAAACT
* * *
2734 AGGCCCTTGGTCGTGCGGGGGCCTCGGCCACCATCGGC-ACCTCGGCCCTTGGTCGTGCGGGAGC
129 AGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGC
* * *
2798 CTCGGGCACCATCGGCACCTTGGTGGCTCGGATGTGCGGGAGCCTCGGGCAGCATCGGC-ACC
194 CTCGGGCACCATCGGCACCTAGGT-GCTAGGATGTGCGGGAGCCTCGGACA-CATCGGCAACC
* ** * ** * * * *
2860 TCGGTGGCTAGGAGGTGCGGGAGCCTCGGACACCATCGGCAACTTGGTGCTTGGATGTGCGGGAG
1 TAGG-CCCTTGGTCGTGCGGGAGCCTCGG-CACCATCGGCACCTTGGTGCTTGGATGTCCGAGAA
2925 CCTCGGGCACCCATCGGCA
64 CCTCGGGCA-CCATCGGCA
2944 CCTTGGTGCC
Statistics
Matches: 522, Mismatches: 61, Indels: 21
0.86 0.10 0.03
Matches are distributed among these distances:
254 27 0.05
255 132 0.25
256 350 0.67
257 13 0.02
ACGTcount: A:0.16, C:0.32, G:0.34, T:0.18
Consensus pattern (254 bp):
TAGGCCCTTGGTCGTGCGGGAGCCTCGGCACCATCGGCACCTTGGTGCTTGGATGTCCGAGAACC
TCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGGCTCGGGCACCATCGGCAAACTAG
GCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCT
CGGGCACCATCGGCACCTAGGTGCTAGGATGTGCGGGAGCCTCGGACACATCGGCAACC
Found at i:2844 original size:43 final size:43
Alignment explanation
Indices: 2095--2966 Score: 683
Period size: 43 Copynumber: 20.5 Consensus size: 43
2085 TCCGGTAGCA
2095 TAGG-CCCTTGG-TCGTGCGGGAGCCTC-GGCACCATCGGCACCC
1 TAGGTCCCTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCA-CC
* * * * * *
2137 T-GGT-GCTAGGATGTGCAGGAGCCCCGGACACCATCGGCAAAC
1 TAGGTCCCTTGGATGTGCGGGAGCCTCGGGCACCATCGGC-ACC
* * *
2179 TAAG-CCCTTGGTAT-TGCAGGAGCCTCGGGCGCCATCGGCACC
1 TAGGTCCCTTGG-ATGTGCGGGAGCCTCGGGCACCATCGGCACC
* * *
2221 TCGGT-GCTTCGATGTGCGGGAGCCTCGGGCACCATCGGCAACC
1 TAGGTCCCTTGGATGTGCGGGAGCCTCGGGCACCATCGGC-ACC
2264 TAGG-CCCTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGCACC
1 TAGGTCCCTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCACC
* * * * **
2306 TCGGT-GCTAT-GATGGGCGGGAGCCTCGGACACTGTCGGCAACC
1 TAGGTCCCT-TGGATGTGCGGGAGCCTCGGGCACCATCGGC-ACC
*
2349 TAGG-CCCTTGG-TCGTGCGGGAGCCTCGAGCACCATCGGCACC
1 TAGGTCCCTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCACC
* * * * * * *
2391 TTGGT-GCTTGGATGTCCGAGAACCTCGCGCACCATCGACAACC
1 TAGGTCCCTTGGATGTGCGGGAGCCTCGGGCACCATCGGC-ACC
* * *
2434 TAGG-CCCTTGG-TCGTGCGAGAGGCTCGGGCACCATCGGCAAAC
1 TAGGTCCCTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGC-ACC
* **
2477 TAAG-CCCTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGCAAAA
1 TAGGTCCCTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGC-ACC
* *
2520 TAGG-CCCTTGG-TCGTGCGGGAGCCTCGGCCACCATCGGCTCC
1 TAGGTCCCTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCACC
* * * *
2562 TAGGT-GCTGGGATGTGCGGGAGCCTCGGACACCATCGGCAAAC
1 TAGGTCCCTTGGATGTGCGGGAGCCTCGGGCACCATCGGC-ACC
* * *
2605 TAGG-CCCTTTG-TCGTGCGGGAGCCTCGTGCACCATCGACACC
1 TAGGTCCCTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCACC
* * * *
2647 TTGGT-GCTTGGATGTGCCGGAACCTCGGGCACCATCGGCAACC
1 TAGGTCCCTTGGATGTGCGGGAGCCTCGGGCACCATCGGC-ACC
* * * **
2690 TA-GACCCTTGG-TCGTGCGAGAGGCTCGGGCACCATCGGCAAAA
1 TAGGTCCCTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGC-ACC
* *
2733 TAGG-CCCTTGG-TCGTGCGGGGGCCTCGGCCACCATCGGCACC
1 TAGGTCCCTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCACC
*
2775 TCGG-CCCTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGCACC
1 TAGGTCCCTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCACC
* ** * *
2817 TTGGTGGCTCGGATGTGCGGGAGCCTCGGGCAGCATCGGCACC
1 TAGGTCCCTTGGATGTGCGGGAGCCTCGGGCACCATCGGCACC
* ** * * * *
2860 TCGGTGGCTAGGAGGTGCGGGAGCCTCGGACACCATCGGCAAC
1 TAGGTCCCTTGGATGTGCGGGAGCCTCGGGCACCATCGGCACC
* *
2903 TTGGT-GCTTGGATGTGCGGGAGCCTCGGGCACCCATCGGCACC
1 TAGGTCCCTTGGATGTGCGGGAGCCTCGGGCA-CCATCGGCACC
* * *
2946 TTGGTGCCTGGGATGTGCGGG
1 TAGGTCCCTTGGATGTGCGGG
2967 CTAAAGAAGA
Statistics
Matches: 677, Mismatches: 114, Indels: 76
0.78 0.13 0.09
Matches are distributed among these distances:
41 19 0.03
42 246 0.36
43 395 0.58
44 17 0.03
ACGTcount: A:0.15, C:0.32, G:0.35, T:0.18
Consensus pattern (43 bp):
TAGGTCCCTTGGATGTGCGGGAGCCTCGGGCACCATCGGCACC
Done.