Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold222
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: 33758
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Found at i:1813 original size:56 final size:55
Alignment explanation
Indices: 1752--1906 Score: 184
Period size: 52 Copynumber: 2.9 Consensus size: 55
1742 TTATTGCCCA
*
1752 TCTTCTTATTATTCTTCCATTAACACAACAT-TTCAATGACATGTTATGCCCATTCT
1 TCTTCTTATTATTCTTCCATTAACACAACATGTTC-ATGACATGTT-TGCCCATGCT
1808 TCTTCTTATTATTCTTCCA--AACACAAC-TGTTCATGAACATGTTT-CCCATGCT
1 TCTTCTTATTATTCTTCCATTAACACAACATGTTCATG-ACATGTTTGCCCATGCT
*
1860 TCTTATT-TT-TTC--CCATTAAACACAACATGTTCATGACCATGTTTGCC
1 TCTTCTTATTATTCTTCCATT-AACACAACATGTTCATGA-CATGTTTGCC
1907 ATCATCCCTG
Statistics
Matches: 89, Mismatches: 2, Indels: 19
0.81 0.02 0.17
Matches are distributed among these distances:
48 3 0.03
50 3 0.03
51 11 0.12
52 28 0.31
53 7 0.08
54 18 0.20
56 19 0.21
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.41
Consensus pattern (55 bp):
TCTTCTTATTATTCTTCCATTAACACAACATGTTCATGACATGTTTGCCCATGCT
Found at i:8137 original size:42 final size:40
Alignment explanation
Indices: 7999--8292 Score: 301
Period size: 41 Copynumber: 7.4 Consensus size: 40
7989 TGACAACCGC
* *
7999 GGCTAAAGTCCCGAAGGCATTTGT-CTAG-TACTA-ATTTCG
1 GGCT-AAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCG
*
8038 GGCT-AGT-CCGATGGCA-TTGTGCGAGTTACTATATACCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT-CCG
8076 GGCTAAGTCCCGAAGGGCATTTTGTGCGAGTTACTATATCCG
1 GGCTAAGTCCCGAA-GGCA-TTTGTGCGAGTTACTATATCCG
*
8118 GGCTTAGGGTCCCG-AGGCA-TTGTGCGAGTTTACTATAT-CG
1 GGC-TA-AGTCCCGAAGGCATTTGTGCGAG-TTACTATATCCG
8158 GGCTAAGTCCCGAAGGCATTTGTTGCCGAGTTACTATGATCCG
1 GGCTAAGTCCCGAAGGCATTTG-TG-CGAGTTACTAT-ATCCG
*
8201 GGC-AGGTCCCGAAGGCA-TTGTGCG-GTTACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
*
8238 GGCT-AGTCCCGAAGGCATTTGTGCGAGTTTACTTATAACC-
1 GGCTAAGTCCCGAAGGCATTTGTGCGAG-TTAC-TATATCCG
* *
8278 GGCTAAATTCCGAAG
1 GGCTAAGTCCCGAAG
8293 TTTACTGGTT
Statistics
Matches: 220, Mismatches: 11, Indels: 46
0.79 0.04 0.17
Matches are distributed among these distances:
35 4 0.02
36 11 0.05
37 29 0.13
38 28 0.13
39 17 0.08
40 31 0.14
41 39 0.18
42 29 0.13
43 26 0.12
44 6 0.03
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
Found at i:8170 original size:82 final size:78
Alignment explanation
Indices: 7999--8266 Score: 322
Period size: 79 Copynumber: 3.4 Consensus size: 78
7989 TGACAACCGC
* *
7999 GGCTAAAGTCCCGAAGGCATTTGT-CTAG-TACTA--ATTTCGGGCTA-GT-CCGATGGCATTGT
1 GGCT-AAGTCCCGAAGGCATTTGTGCGAGTTACTATGA-TCCGGGC-AGGTCCCGA-GGCATTGT
8058 GCGAGTTACTATATACCG
62 GCGAGTTACTATAT-CCG
8076 GGCTAAGTCCCGAAGGGCATTTTGTGCGAGTTACTAT-ATCCGGGCTTAGGGTCCCGAGGCATTG
1 GGCTAAGTCCCGAA-GGCA-TTTGTGCGAGTTACTATGATCCGGGC--A-GGTCCCGAGGCATTG
8140 TGCGAGTTTACTATAT-CG
61 TGCGAG-TTACTATATCCG
8158 GGCTAAGTCCCGAAGGCATTTGTTGCCGAGTTACTATGATCCGGGCAGGTCCCGAAGGCATTGTG
1 GGCTAAGTCCCGAAGGCATTTG-TG-CGAGTTACTATGATCCGGGCAGGTCCCG-AGGCATTGTG
8223 CG-GTTACTATATCCG
63 CGAGTTACTATATCCG
8238 GGCT-AGTCCCGAAGGCATTTGTGCGAGTT
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTT
8267 TACTTATAAC
Statistics
Matches: 174, Mismatches: 2, Indels: 30
0.84 0.01 0.15
Matches are distributed among these distances:
76 10 0.06
77 14 0.08
78 7 0.04
79 29 0.17
80 29 0.17
81 22 0.13
82 27 0.16
83 23 0.13
84 13 0.07
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (78 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATGATCCGGGCAGGTCCCGAGGCATTGTGCGA
GTTACTATATCCG
Found at i:14733 original size:39 final size:38
Alignment explanation
Indices: 14662--14791 Score: 160
Period size: 39 Copynumber: 3.4 Consensus size: 38
14652 TCCTCGTTCA
*
14662 AATGCCTTCGGAC--AAGCCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGACTTAA-CCC-GATTTAATAACTCGCACG
14700 AATGCCTTCGGGACTTAACCCGATTTAATAACTCGCACG
1 AATGCCTTC-GGACTTAACCCGATTTAATAACTCGCACG
* *
14739 AATGCCTTCGGACTTAACCCGA-TTAGTATCTCGCAC-
1 AATGCCTTCGGACTTAACCCGATTTAATAACTCGCACG
*
14775 AAAGCCTTCGGATCTTA
1 AATGCCTTCGGA-CTTA
14792 TCCGGATATA
Statistics
Matches: 84, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
36 11 0.13
37 16 0.19
38 22 0.26
39 30 0.36
40 3 0.04
41 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (38 bp):
AATGCCTTCGGACTTAACCCGATTTAATAACTCGCACG
Found at i:22491 original size:40 final size:40
Alignment explanation
Indices: 22447--22630 Score: 201
Period size: 40 Copynumber: 4.6 Consensus size: 40
22437 TCCTCGTTCA
* * *
22447 AATGCCTTCGGGACATAGCCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
22487 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
22527 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
22567 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
22607 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
22631 CAGCATTCAA
Statistics
Matches: 125, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
39 3 0.02
40 114 0.91
41 8 0.06
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:22639 original size:41 final size:41
Alignment explanation
Indices: 22562--22639 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
22552 TTAGTATCTC
* * *
22562 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
22603 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
22640 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:27226 original size:40 final size:40
Alignment explanation
Indices: 27171--27388 Score: 350
Period size: 40 Copynumber: 5.5 Consensus size: 40
27161 CGGATGATAA
* *
27171 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
27211 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
27251 CCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
27291 CTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
27331 CCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
27371 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
27389 TACTTGGGCT
Statistics
Matches: 167, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
39 14 0.08
40 152 0.91
41 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:27944 original size:56 final size:56
Alignment explanation
Indices: 27858--27977 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
27848 ACAAGGGATG
27858 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
27914 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
27970 ATGGGCAA
1 ATGGGCAA
27978 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:28989 original size:80 final size:80
Alignment explanation
Indices: 28837--29015 Score: 222
Period size: 80 Copynumber: 2.2 Consensus size: 80
28827 TCGAATGATG
* * *
28837 TCCGGGCTAAGTCCCGAAGGCTTTGGTGCGAGTTACTAAATCCGGGTTAAGTTCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
**
28902 GTGCGAGTTA-CTAAA
66 GAACGAG-TAGCTAAA
*
28917 TCCGGGTTAAGTCCCGAAGGCATTT-GTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCAT
*
28980 TTGAACGAGTAGCTATA
64 TTGAACGAGTAGCTAAA
* *
28997 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
29016 TACGTGATTT
Statistics
Matches: 87, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
79 16 0.18
80 66 0.76
81 5 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
GAACGAGTAGCTAAA
Found at i:28996 original size:40 final size:40
Alignment explanation
Indices: 28837--28982 Score: 224
Period size: 40 Copynumber: 3.6 Consensus size: 40
28827 TCGAATGATG
28837 TCCGGGCTAAGTCCCGAAGGC-TTTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTT-GTGCGAGTTACTAAA
* *
28877 TCCGGGTTAAGTTCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28917 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
28958 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28983 AACGAGTAGC
Statistics
Matches: 99, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
40 94 0.95
41 5 0.05
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Done.