Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1745
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: 9870
ACGTcount: A:0.20, C:0.33, G:0.30, T:0.17
Found at i:900 original size:400 final size:395
Alignment explanation
Indices: 119--911 Score: 926
Period size: 401 Copynumber: 2.0 Consensus size: 395
109 ATTTTGTAAT
* * * * * * *
119 CGAGAGGGACATCTGCCGGGCGCTAACCATGCCAGGCTCATGGATCGCAATCCCCGACAGGCAAC
1 CGAGAGGGACATCTGCCGGGCGCGAACAATGCCAGGCGCATCGAGCACAATCCCCGACAGACAAC
* * * *
184 CTGCATGACGTGCCCACCGTTGCCGATGCAATGGGCCACGAGACTGCCCCTGCTCGAGGGCATGG
66 CGGCAGGACGAGCCCACCGTTGCCGAAGCAATGGGCCACGAGACTGCCCCTGCTCGAGGGCATGG
*
249 CCAGGCCAAGCCCTCACCTGCAGCCTCTGCCCACGCCACAACCGGGACTACCGACTCGATTCGGA
131 CCAGGCCAAGCCCTCACCTGCAGCCTCTGCCCACGCCACAACCGGGACTACCAACTCGATTCGGA
* * * * *
314 ACTTGGCAGCATCACCGCAGGTGCGAGCCTTGCCTTCTGGCACGACCACGCCCCGTTACCCGCAC
196 ACTTGGCAGAATCACCGCAGGTGCGAGCCTTCCCTACTGGCACGACCACGCCCCGTGACCCACAC
* *
379 ACGCTGCCAACCGATCGCGCACGCAGAGACCGACGGCCTCACCACGGATCACTTGGACCGCGAAG
261 ACGCTGCCAACCGATCGCGCACACAGAGACCGACGGCCTCACCACGGATCACCTGGACCGCGAAG
* ** * *
444 GGTCCCGTCACCGCAGCTGGGCATCCGGCCACCGAAAACCACGATCGCAAGGCACGCGCGACCTG
326 GGTCCCATCACCGCAGCAAGGCATCCAGCCACCGAAAA-CAC-A-CG-AAGGCACGCACGACCTG
509 GATCTTAAC
387 GATCTTAAC
*
518 CGAGAGGGACACTCTGCCGGGGCGCGATCAATGCCAGGCGCATCGAGCACAATCCCCGACAGACA
1 CGAGAGGGACA-TCTGCC-GGGCGCGAACAATGCCAGGCGCATCGAGCACAATCCCCGACAGACA
* *
583 ACCGGCGGGACGAGCCCACCGTTGCCGAAGCAA-GGGCCGCGAGACTGCCCCTGCTC-ACGGGGC
64 ACCGGCAGGACGAGCCCACCGTTGCCGAAGCAATGGGCCACGAGACTGCCCCTGCTCGA--GGGC
*
646 ATGGCCAGGCCAAGCCC-CACCTGCAGCTTCTGCCCACGCCACAACCGGGACTACCAACTCGAAT
127 ATGGCCAGGCCAAGCCCTCACCTGCAGCCTCTGCCCACGCCACAACCGGGACTACCAACTCG-AT
*
710 TCGGGAACTTGGCAGAATCAGCGCAGGTG-GAAG-CTTAACCCTAC-GGCACGACCACGCCCCTT
191 TC-GGAACTTGGCAGAATCACCGCAGGTGCG-AGCCTT--CCCTACTGGCACGACCACGCCCC--
* ** * * * * **
772 GTGCCCCACACACGCGTGCCATGCGATCGGCAGCATACGGCGACCG-GGGACCTTGCCACGGATC
250 GTGACCCACACACGC-TGCCAACCGATC-GC-GCACACAGAGACCGACGG-CCTCACCACGGATC
* ** *
836 ACCTGGACCGCGCAGGGTCTCCATCACCGC-GACAAGGTTTCCAGCCACC-AAAA-AC-CG-GGG
311 ACCTGGACCGCGAAGGGTC-CCATCACCGCAG-CAAGGCATCCAGCCACCGAAAACACACGAAGG
*
896 CACGCATGACCTGGAT
374 CACGCACGACCTGGAT
912 TTCACCCGAG
Statistics
Matches: 334, Mismatches: 43, Indels: 33
0.81 0.10 0.08
Matches are distributed among these distances:
399 12 0.04
400 86 0.26
401 95 0.28
402 44 0.13
403 4 0.01
404 12 0.04
405 12 0.04
406 4 0.01
407 44 0.13
408 21 0.06
ACGTcount: A:0.22, C:0.37, G:0.28, T:0.13
Consensus pattern (395 bp):
CGAGAGGGACATCTGCCGGGCGCGAACAATGCCAGGCGCATCGAGCACAATCCCCGACAGACAAC
CGGCAGGACGAGCCCACCGTTGCCGAAGCAATGGGCCACGAGACTGCCCCTGCTCGAGGGCATGG
CCAGGCCAAGCCCTCACCTGCAGCCTCTGCCCACGCCACAACCGGGACTACCAACTCGATTCGGA
ACTTGGCAGAATCACCGCAGGTGCGAGCCTTCCCTACTGGCACGACCACGCCCCGTGACCCACAC
ACGCTGCCAACCGATCGCGCACACAGAGACCGACGGCCTCACCACGGATCACCTGGACCGCGAAG
GGTCCCATCACCGCAGCAAGGCATCCAGCCACCGAAAACACACGAAGGCACGCACGACCTGGATC
TTAAC
Found at i:2028 original size:103 final size:101
Alignment explanation
Indices: 1876--2064 Score: 297
Period size: 103 Copynumber: 1.9 Consensus size: 101
1866 CGGCCCGGGG
*
1876 GCGCCCTTCCCGCCCCCGTGGTGGGGGCGGCCGGGGCGCACACCACGCGGAGCGCCGGTGCGCGC
1 GCGCCCTTCCCGCCCCCGGGGTGGGGGCGGCCGGGGCGCACACCACGCGGAGCGCCGGTGCGCGC
1941 CTCGCCCACCCTCGGGTGCGGCCAGGAGCACGGTGC
66 CTCGCCCACCCTCGGGTGCGGCCAGGAGCACGGTGC
* * * *
1977 GCGCCCTTCCCGCCCCCTGGGGTGGGGGGCGGTCGGGGCGCCCACCTCGCGGGGCGCCGGTGCGC
1 GCGCCCTTCCCGCCCCC-GGGGT-GGGGGCGGCCGGGGCGCACACCACGCGGAGCGCCGGTGCGC
* *
2042 GCCTCGCCCGCCCTCTGGTGCGG
64 GCCTCGCCCACCCTCGGGTGCGG
2065 GCGGCCGCGG
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 17 0.22
102 4 0.05
103 58 0.73
ACGTcount: A:0.05, C:0.43, G:0.42, T:0.11
Consensus pattern (101 bp):
GCGCCCTTCCCGCCCCCGGGGTGGGGGCGGCCGGGGCGCACACCACGCGGAGCGCCGGTGCGCGC
CTCGCCCACCCTCGGGTGCGGCCAGGAGCACGGTGC
Found at i:2304 original size:64 final size:64
Alignment explanation
Indices: 2225--2346 Score: 199
Period size: 64 Copynumber: 1.9 Consensus size: 64
2215 CGTTTGGTTG
*
2225 GGGGGGAGGGACGGATGCTGGGGAGGGACTCGTTGCGCACGCTTGGCCCTCCGCATGTTAGAGA
1 GGGGGGAGGGACGGATGCTGGGGAGGGACTCGTTGCCCACGCTTGGCCCTCCGCATGTTAGAGA
* * * *
2289 GGGGGGAGGGCCGGATGGTTGGGAGGGACTCGTTGCCCACGCTTGGGCCTCCGCATGT
1 GGGGGGAGGGACGGATGCTGGGGAGGGACTCGTTGCCCACGCTTGGCCCTCCGCATGT
2347 GCTATCGGTG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.13, C:0.23, G:0.46, T:0.18
Consensus pattern (64 bp):
GGGGGGAGGGACGGATGCTGGGGAGGGACTCGTTGCCCACGCTTGGCCCTCCGCATGTTAGAGA
Found at i:2854 original size:102 final size:102
Alignment explanation
Indices: 2685--2871 Score: 315
Period size: 102 Copynumber: 1.8 Consensus size: 102
2675 GGCCAGGTGC
* *
2685 ACGGTGCGCGCCCTGCCCGCCCCCTGGTGTGGGGGCGGTCGGGGCGCACACCATGCGGAGCACCG
1 ACGGTGCGCGCCCTGCCCGCCCCCTGGGGTGGGGGCGGGCGGGGCGCACACCATGCGGAGCACCG
2750 GTGCGCGCCTCGCCCACCCTCGGCTGCGGGCGGGAGA
66 GTGCGCGCCTCGCCCACCCTCGGCTGCGGGCGGGAGA
*
2787 ACGGTGCGCGCCCAT-CCCGCCCCCTGGGGTCGGGGGCGGGCGGGGCGCACGCCATGCGGAGCA-
1 ACGGTGCGCGCCC-TGCCCGCCCCCTGGGGT-GGGGGCGGGCGGGGCGCACACCATGCGGAGCAC
2850 CGGTGCGCGCCTCGCCCACCCT
64 CGGTGCGCGCCTCGCCCACCCT
2872 GGGGGGTGCG
Statistics
Matches: 80, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
102 49 0.61
103 31 0.39
ACGTcount: A:0.09, C:0.41, G:0.41, T:0.10
Consensus pattern (102 bp):
ACGGTGCGCGCCCTGCCCGCCCCCTGGGGTGGGGGCGGGCGGGGCGCACACCATGCGGAGCACCG
GTGCGCGCCTCGCCCACCCTCGGCTGCGGGCGGGAGA
Found at i:2942 original size:64 final size:62
Alignment explanation
Indices: 2782--2957 Score: 168
Period size: 64 Copynumber: 2.8 Consensus size: 62
2772 GCTGCGGGCG
* ** *
2782 GGAGAACGGTGCGCGCCCATCCCGCCCCCTGGGGT-CGGGGGCGG-GCGGGGCGCACGCCATGC
1 GGAGCACGGTGCGCGCCC-TCCCGCCCCCTGGGGTGC-GGGGCGGCGCGGCACGCACGCCAGGC
*
2844 GGAGCACGGTGCGCG-CCTCGCC-CACCCTGGGGGGTGCGGGGCGGCCGCGGCACGCAC-CC-GG
1 GGAGCACGGTGCGCGCCCTC-CCGCCCCCT--GGGGTGCGGGGCGG-CGCGGCACGCACGCCAGG
2905 CC
62 -C
2907 AGGAGCACGGTGCGCGCCCTTCCCGCCCCCTGGGGTG-GGGGCGGTCGCGGC
1 -GGAGCACGGTGCGCGCCC-TCCCGCCCCCTGGGGTGCGGGGCGG-CGCGGC
2958 GCACACCGTG
Statistics
Matches: 96, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
60 7 0.07
61 4 0.04
62 27 0.28
63 17 0.18
64 30 0.31
65 4 0.04
66 7 0.07
ACGTcount: A:0.08, C:0.39, G:0.45, T:0.09
Consensus pattern (62 bp):
GGAGCACGGTGCGCGCCCTCCCGCCCCCTGGGGTGCGGGGCGGCGCGGCACGCACGCCAGGC
Found at i:3035 original size:819 final size:811
Alignment explanation
Indices: 1214--3121 Score: 2339
Period size: 819 Copynumber: 2.3 Consensus size: 811
1204 GCGCGCGCAA
* * *** * *
1214 CGCCCGCCCTCGGGTGCGGACGGCCGCGGCACCCGCA-AAAGCCACGAGCATGGTGCGCGCCCTT
1 CGCCCACCCTCGGGTGCGGGCGGCCGCGGCA--CGCACCCGGCCAGGAGCACGGTGCGCGCCCTT
* * * * ** *
1278 CCCGCCCCC-AGGGTGGGAGCGGTCGGGGCGCGCACCATGCGGCGCAATGGGTGCGCACCCTTGC
64 CCCGCCCCCTGGGGTGGGGGCGGTCGGGGCGCACACC-TG-GGGGCACCGGGTGCGCACCGTTGC
* * *
1342 CGGGGTACCCAACCGACCGATGCAACGGTAAGGGACGAACACGTTTGGAGAGGGGAGGGACAGAT
127 CGGGGTACCCAACCGACCGACGCAACGCTAAGGGACGAACACGTTTGGAGAGGGGAGGGACGGAT
* * *
1407 GCCGGGGAGGGACTCGTTGCACACGCTCGGCCCTACGCATGCTTGGAGGGGGGAGGGACGGATGC
192 GCCGGGGAGGGACTCGTTGCGCACGCTTGGCCCTCCGCATGCTTGGAGGGGGGAGGGACGGATGC
*
1472 TTGGGGAGGGACTCGTTGCACACGCGTGGGCCTCCGCATGTGCTATCGGTGCCGAATTCGGGGTC
257 TTGGGGAGGGACTCGTTGCACACGCGTGGGCCTCCGCATGTGCTATCGGTGCCGAATTCGCGGTC
*
1537 GTCGGCACCGTCGCCGGAGCACCGCCGGAGAACCTGACCGGCGGTGGGGGGGAGCCCCGGCGAAT
322 CTCGGCACCGT----------CCGCCGGAGAACCTGACCGGCGGTGGGGGGGAGCCCCGGCGAA-
* *
1602 GGGGGAGGGGTGTGGGCGACGGCACGCGATGGGTGCAGGGTGGCAGCCCCGCAGGGCACCCCACT
376 -GGGGAGCGGTGT----G--GGCACGCGACGGGTGCAGGGTGGCAGCCCCGCAGGGCACCCCACT
* * * **
1667 GCCCCCCCCCTTGGTTGCTCAAGTATCACACCCCCTATAGAGCTTAAGATGGATTTCTTTGTTGT
434 G-CCCCCCCCTAGGTTGCTCAAGTATCACACCCCCTATAGAGCTTAAGAGGGATTTCTATGCCGT
* * * *
1732 CACCAGTGGAGGTGCCCACGTTCGAAACAGGGACAGTTTTTCTCCCGCACCGAGGGTGGGCCGAG
498 CACCAGCGGAAGTGACCACGTTCGAAACAGGGACAGTTTTTCTCCCGCACCGAGGGTGGGCCAAG
* * * *
1797 ACCCCACCACCTCGGGCACCCGGTGCGCGCCACGCCCACCCTCGGGTGCGCGGGGCCGAGGCTCG
563 ACCCCACCACCTCGGGCACCCGGCGCGCGCCACGCCCACCCTCGGGCGCGCGGGGCCGAGGCACA
* *
1862 CACCCGGCCCGGGGGCGCCCTTCCCGCCCCCGTGGTGGGGGCGGCCGGGGCGCACACCACGCGGA
628 CACCCGGCCCGGGCGCGCCCTGCCCGCCCCCGTGGTGGGGGCGGCCGGGGCGCACACCACGCGGA
* * * *
1927 GCGCCGGTGCGCGCCTCGCCCACCCTCGGGTGCGGCCAGGAGCACGGTGCGCGCCCTTCCCGCCC
693 GCACCGGTGCGCGCCTCGCCCACCCTCGGCTGCGGCCAGGAGAACGGTGCGCGCCCATCCCGCCC
* * * * *
1992 CCTGGGGTGGGGGGCGGTCGGGGCGCCCACCTCGCGGGGCGCCGGTGCGCGCCT
758 CCTGGGGTCGGGGGCGGGCGGGGCGCACACCTCGCGGAGCGACGGTGCGCGCCT
* * * * * *
2046 CGCCCGCCCTCTGGTGCGGGCGGCCGCGGCACGGACCCGGGCGGGAGCACGGGGCGCGCCCTTCC
1 CGCCCACCCTCGGGTGCGGGCGGCCGCGGCACGCACCCGGCCAGGAGCACGGTGCGCGCCCTTCC
*
2111 CGCCCCCTGGGGTGGGGGCGGTCGGGGCGCACACCTCGCGGGGCACCGGGTGCGCACCGTTGTCG
66 CGCCCCCTGGGGTGGGGGCGGTCGGGGCGCACACCT-G-GGGGCACCGGGTGCGCACCGTTGCCG
* *
2176 GGGTACCCAACCGACCGACGCAACGCTAAGGGACGAACACGTTTGGTTGGGGGGGAGGGACGGAT
129 GGGTACCCAACCGACCGACGCAACGCTAAGGGACGAACACGTTTGG--AGAGGGGAGGGACGGAT
* *
2241 GCTGGGGAGGGACTCGTTGCGCACGCTTGGCCCTCCGCATG-TTAGAGAGGGGGGAGGGCCGGAT
192 GCCGGGGAGGGACTCGTTGCGCACGCTTGGCCCTCCGCATGCTT-G-GAGGGGGGAGGGACGGAT
* * *
2305 GGTT-GGGAGGGACTCGTTGCCCACGCTTGGGCCTCCGCATGTGCTATCGGTGCCGAATTCGCGG
255 GCTTGGGGAGGGACTCGTTGCACACGCGTGGGCCTCCGCATGTGCTATCGGTGCCGAATTCGCGG
*
2369 TCCTCGGCACCGT-CGCCGGAGAACCTGACCGGCGGT-GGGGGGAGCCCCGGCG-A-GTG-GCGG
320 TCCTCGGCACCGTCCGCCGGAGAACCTGACCGGCGGTGGGGGGGAGCCCCGGCGAAGGGGAGCGG
* * *
2429 -GT-GGCACGCGACGGGTGCTGGGTGGCAGCCCCGCGGGGCACCCCCAGTG-CCCCCCCTAGGTT
385 TGTGGGCACGCGACGGGTGCAGGGTGGCAGCCCCGCAGGGCA-CCCCACTGCCCCCCCCTAGGTT
*
2491 GCTCAAGTATCACACCCCCTATAGAGCTTAAG-GGGCATTTCATAT-CCGTTACCAGCGGACAG-
449 GCTCAAGTATCACACCCCCTATAGAGCTTAAGAGGG-ATTTC-TATGCCGTCACCAGCGGA-AGT
* * * *
2553 GACCACGTTCGAAACAGGGTCGGTTTTTCTGCCGCACCTAGGGT-GGCGCAAG-CCCGCACCACC
511 GACCACGTTCGAAACAGGGACAGTTTTTCTCCCGCACCGAGGGTGGGC-CAAGACCC-CACCACC
* * *
2616 TCGGGCAGCCGGCGCGCGCCTCGCCCACCCTCGGGCGCG-GGCGGCCGAGGCACACCCCCGGCCA
574 TCGGGCACCCGGCGCGCGCCACGCCCACCCTCGGGCGCGCGG-GGCCGAGGCACACACCCGG-C-
* *
2680 GGTGCACGGTGCGCGCCCTGCCCGCCCCC-TGGTGTGGGGGCGGTCGGGGCGCACACCATGCGGA
636 ----C-CGG-GCGCGCCCTGCCCGCCCCCGT-G-GTGGGGGCGGCCGGGGCGCACACCACGCGGA
* *
2744 GCACCGGTGCGCGCCTCGCCCACCCTCGGCTGCGGGCGGGAGAACGGTGCGCGCCCATCCCGCCC
693 GCACCGGTGCGCGCCTCGCCCACCCTCGGCTGCGGCCAGGAGAACGGTGCGCGCCCATCCCGCCC
*
2809 CCTGGGGTCGGGGGCGGGCGGGGCGCACGCCAT-GCGGAGC-ACGGTGCGCGCCT
758 CCTGGGGTCGGGGGCGGGCGGGGCGCACACC-TCGCGGAGCGACGGTGCGCGCCT
*
2862 CGCCCACCCTGGGGGGTGCGGGGCGGCCGCGGCACGCACCCGGCCAGGAGCACGGTGCGCGCCCT
1 CGCCCACCCT--CGGGTGC-GGGCGGCCGCGGCACGCACCCGGCCAGGAGCACGGTGCGCGCCCT
* *
2927 TCCCGCCCCCTGGGGTGGGGGCGGTCGCGGCGCACACCGTGGGGAGCACCGGGTGCGCACAGTTG
63 TCCCGCCCCCTGGGGTGGGGGCGGTCGGGGCGCACACC-TGGGG-GCACCGGGTGCGCACCGTTG
* * * *
2992 CCGGGGTACCCAACCGACCGGCGCAACGCTAAGGGAAGAACACGTTCGGAGCGGGGAGGGACGGA
126 CCGGGGTACCCAACCGACCGACGCAACGCTAAGGGACGAACACGTTTGGAGAGGGGAGGGACGGA
* ** * * *
3057 TGGCCGGGGGAGGGACTCGTTGCGCATGCGTTGG-CCTCCGCCCGTTTGGTGTGGGGAGGGACGG
191 T-GCC-GGGGAGGGACTCGTTGCGCACGC-TTGGCCCTCCGCATGCTTGGAGGGGGGAGGGACGG
3121 A
253 A
3122 CGGCCTATGT
Statistics
Matches: 943, Mismatches: 99, Indels: 82
0.84 0.09 0.07
Matches are distributed among these distances:
807 10 0.01
808 159 0.17
809 39 0.04
810 7 0.01
814 1 0.00
815 4 0.00
816 41 0.04
817 139 0.15
818 27 0.03
819 174 0.18
820 7 0.01
821 1 0.00
822 16 0.02
823 23 0.02
830 3 0.00
831 29 0.03
832 120 0.13
833 2 0.00
834 121 0.13
835 20 0.02
ACGTcount: A:0.13, C:0.34, G:0.40, T:0.13
Consensus pattern (811 bp):
CGCCCACCCTCGGGTGCGGGCGGCCGCGGCACGCACCCGGCCAGGAGCACGGTGCGCGCCCTTCC
CGCCCCCTGGGGTGGGGGCGGTCGGGGCGCACACCTGGGGGCACCGGGTGCGCACCGTTGCCGGG
GTACCCAACCGACCGACGCAACGCTAAGGGACGAACACGTTTGGAGAGGGGAGGGACGGATGCCG
GGGAGGGACTCGTTGCGCACGCTTGGCCCTCCGCATGCTTGGAGGGGGGAGGGACGGATGCTTGG
GGAGGGACTCGTTGCACACGCGTGGGCCTCCGCATGTGCTATCGGTGCCGAATTCGCGGTCCTCG
GCACCGTCCGCCGGAGAACCTGACCGGCGGTGGGGGGGAGCCCCGGCGAAGGGGAGCGGTGTGGG
CACGCGACGGGTGCAGGGTGGCAGCCCCGCAGGGCACCCCACTGCCCCCCCCTAGGTTGCTCAAG
TATCACACCCCCTATAGAGCTTAAGAGGGATTTCTATGCCGTCACCAGCGGAAGTGACCACGTTC
GAAACAGGGACAGTTTTTCTCCCGCACCGAGGGTGGGCCAAGACCCCACCACCTCGGGCACCCGG
CGCGCGCCACGCCCACCCTCGGGCGCGCGGGGCCGAGGCACACACCCGGCCCGGGCGCGCCCTGC
CCGCCCCCGTGGTGGGGGCGGCCGGGGCGCACACCACGCGGAGCACCGGTGCGCGCCTCGCCCAC
CCTCGGCTGCGGCCAGGAGAACGGTGCGCGCCCATCCCGCCCCCTGGGGTCGGGGGCGGGCGGGG
CGCACACCTCGCGGAGCGACGGTGCGCGCCT
Done.