Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1845
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: 57321
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:7858 original size:40 final size:39
Alignment explanation
Indices: 7774--7958 Score: 203
Period size: 40 Copynumber: 4.6 Consensus size: 39
7764 TCGAATGATG
* * * *
7774 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
7814 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
7854 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
7893 TCCGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCC-GAAGGCATTTGTGCGAGTTACTA-AA
*
7934 -CCGGGCTATGTCCTGAAGGCATTTG
1 TCCGGGCTAAGTCC-GAAGGCATTTG
7959 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
39 36 0.29
40 78 0.63
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:7912 original size:79 final size:81
Alignment explanation
Indices: 7774--7956 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 81
7764 TCGAATGATG
* *
7774 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
7838 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
7853 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCTGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCC-GAAGGCA
*
7915 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* * *
7933 ACCGGGCTATGTCCTGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
7957 TGAACGAGTA
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 56 0.64
80 29 0.33
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:7991 original size:79 final size:78
Alignment explanation
Indices: 7813--7991 Score: 184
Period size: 79 Copynumber: 2.3 Consensus size: 78
7803 AAGTGACCAT
* *
7813 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTG
1 ATCCGGATTAAG-TCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTG
**
7878 GTGCGAGTTACTAA
65 GAACGAGTTACTAA
* * * *
7892 ATCCGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCTGAAGGCAT
1 ATCCGGATTAAGTCC-GAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCAT
* *
7956 TTGAACGAG-TAGCTAT
63 TGGAACGAGTTA-CTAA
*
7972 ATCC-GATTAAATTCCGAAGG
1 ATCCGGATT-AAGTCCGAAGG
7992 TACGTGATTT
Statistics
Matches: 83, Mismatches: 12, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
78 5 0.06
79 50 0.60
80 28 0.34
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (78 bp):
ATCCGGATTAAGTCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGG
AACGAGTTACTAA
Found at i:9532 original size:136 final size:136
Alignment explanation
Indices: 9341--9611 Score: 499
Period size: 136 Copynumber: 2.0 Consensus size: 136
9331 GGGTGTTACA
*
9341 CCACATGTCCGTTAGGTGTCGACAGCCCATTTTTCGGCACTTATCGGCCCAATAGTAGGTCC-AC
1 CCACACGTCCGTTAGGTGTCGACAGCCCATTTTTCGGCACTTATCGGCCCAATAGTAGG-CCTAC
*
9405 AGTCGTCTTGGGCGACCCATGCAATCTTAATAGACAATTAGTGATAATGGGCCTATAACCCATAT
65 AGTCGTCTTGGGCGACCCATGCAATCTTAACAGACAATTAGTGATAATGGGCCTATAACCCATAT
9470 AGCAGGG
130 AGCAGGG
9477 CCACACGTCCGTTAGGTGTCGACAGCCCATTTTTCGGCACTTATCGGCCCAATAGTAGGCCTACA
1 CCACACGTCCGTTAGGTGTCGACAGCCCATTTTTCGGCACTTATCGGCCCAATAGTAGGCCTACA
*
9542 TTCGTCTTGGGCGACCCATGCAATCTTAACAGACAATTAGTGATAATGGGCCTATAACCCATATA
66 GTCGTCTTGGGCGACCCATGCAATCTTAACAGACAATTAGTGATAATGGGCCTATAACCCATATA
9607 GCAGG
131 GCAGG
9612 CCCATGTGGG
Statistics
Matches: 131, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
135 2 0.02
136 129 0.98
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (136 bp):
CCACACGTCCGTTAGGTGTCGACAGCCCATTTTTCGGCACTTATCGGCCCAATAGTAGGCCTACA
GTCGTCTTGGGCGACCCATGCAATCTTAACAGACAATTAGTGATAATGGGCCTATAACCCATATA
GCAGGG
Found at i:16168 original size:40 final size:40
Alignment explanation
Indices: 16109--16260 Score: 207
Period size: 40 Copynumber: 3.8 Consensus size: 40
16099 CATTTGAATG
* * *
16109 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
*
16149 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
*
16189 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
* * * *
16229 ATACCCGGGTTAAGACCCGAAGGTAATTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
16261 TTGTGGTTAT
Statistics
Matches: 101, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 98 0.97
41 3 0.03
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
Found at i:16272 original size:80 final size:80
Alignment explanation
Indices: 16109--16280 Score: 204
Period size: 80 Copynumber: 2.2 Consensus size: 80
16099 CATTTGAATG
* * * * *
16109 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
* *
16174 TTTGTGCGAGTTGAT
66 ATTGTGCGAGTGGAT
* * *
16189 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATACCCGGGTTAAGACCCGAAGGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAG-TGACTATACCCGGGCTAAGACCCGAAGGC
** *
16253 AATTGTGCTTGTGGTT
65 AATTGTGCGAGTGGAT
16269 ATATCC-GGCTAA
1 ATATCCGGGCTAA
16281 ATTCCGAAGA
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
79 6 0.08
80 70 0.90
81 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
ATTGTGCGAGTGGAT
Found at i:21869 original size:17 final size:17
Alignment explanation
Indices: 21847--21880 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21837 AGACAAGAAT
*
21847 TTCCGTTCAAATTTAAA
1 TTCCGTCCAAATTTAAA
21864 TTCCGTCCAAATTTAAA
1 TTCCGTCCAAATTTAAA
21881 ACTTTTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (17 bp):
TTCCGTCCAAATTTAAA
Found at i:22719 original size:16 final size:16
Alignment explanation
Indices: 22698--22753 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
22688 TTAGACTCAT
22698 TAACCATAAGCAACCA
1 TAACCATAAGCAACCA
* *** *
22714 TAACCACATTAAAGCA
1 TAACCATAAGCAACCA
*
22730 TAAACATAAGCAACCA
1 TAACCATAAGCAACCA
22746 TAACCATA
1 TAACCATA
22754 TTAAAGCATA
Statistics
Matches: 28, Mismatches: 12, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.52, C:0.27, G:0.05, T:0.16
Consensus pattern (16 bp):
TAACCATAAGCAACCA
Found at i:22738 original size:32 final size:32
Alignment explanation
Indices: 22702--22767 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
22692 ACTCATTAAC
22702 CATAAGCAACCATAACCACATTAAAGCATAAA
1 CATAAGCAACCATAACCACATTAAAGCATAAA
*
22734 CATAAGCAACCATAACCATATTAAAGCATAAA
1 CATAAGCAACCATAACCACATTAAAGCATAAA
22766 CA
1 CA
22768 CATTTGCATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.53, C:0.24, G:0.06, T:0.17
Consensus pattern (32 bp):
CATAAGCAACCATAACCACATTAAAGCATAAA
Found at i:22763 original size:16 final size:16
Alignment explanation
Indices: 22712--22764 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
22702 CATAAGCAAC
*
22712 CATAACCACATTAAAG
1 CATAACCATATTAAAG
* *** *
22728 CATAAACATAAGCAAC
1 CATAACCATATTAAAG
22744 CATAACCATATTAAAG
1 CATAACCATATTAAAG
22760 CATAA
1 CATAA
22765 ACACATTTGC
Statistics
Matches: 26, Mismatches: 11, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.53, C:0.23, G:0.06, T:0.19
Consensus pattern (16 bp):
CATAACCATATTAAAG
Found at i:23601 original size:45 final size:45
Alignment explanation
Indices: 23537--23624 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
23527 CCAAAACATG
* * *
23537 TGTCACATACATCATGAACTCAGACCATAACTCAATGAGTTCAAA
1 TGTCACAAACATCATGAACTCAAACCACAACTCAATGAGTTCAAA
* * *
23582 TGTCACAAATATCATGAACTTAAACCACAATTCAATGAGTTCA
1 TGTCACAAACATCATGAACTCAAACCACAACTCAATGAGTTCA
23625 GATCACAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.41, C:0.23, G:0.10, T:0.26
Consensus pattern (45 bp):
TGTCACAAACATCATGAACTCAAACCACAACTCAATGAGTTCAAA
Found at i:35876 original size:46 final size:46
Alignment explanation
Indices: 35823--35948 Score: 207
Period size: 46 Copynumber: 2.7 Consensus size: 46
35813 CGGTTGAGCA
*
35823 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
35869 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
35915 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
35949 AGGGCGGGTT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:39358 original size:33 final size:33
Alignment explanation
Indices: 39271--39372 Score: 105
Period size: 33 Copynumber: 3.1 Consensus size: 33
39261 TAATAGCTAG
* * * * *
39271 GGCCTTAGCCCATTTCAGTAACAGTAGCAATTT
1 GGCCTGAGCCCGTCTCAGTAACAGTAGCAGTCT
39304 GGGCCTGAGCCCGTCTCAGTAACAGTAGCAGTCT
1 -GGCCTGAGCCCGTCTCAGTAACAGTAGCAGTCT
* * * * *
39338 GGCTTGAGCTCGTTTTAGTAATAGTAGCAGTCT
1 GGCCTGAGCCCGTCTCAGTAACAGTAGCAGTCT
39371 GG
1 GG
39373 GCCGAAGCCC
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
33 30 0.52
34 28 0.48
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (33 bp):
GGCCTGAGCCCGTCTCAGTAACAGTAGCAGTCT
Found at i:42024 original size:79 final size:81
Alignment explanation
Indices: 41888--42070 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
41878 TCGAATGATG
* *
41888 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
41952 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
41967 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
42029 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
42047 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
42071 TGAACGAGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.65
80 30 0.34
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:42086 original size:40 final size:40
Alignment explanation
Indices: 41889--42072 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
41879 CGAATGATGT
* * * *
41889 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
41929 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
41969 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
42007 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
42048 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
42073 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 34 0.27
40 80 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:42094 original size:79 final size:79
Alignment explanation
Indices: 41941--42105 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
41931 GGACTAAGAT
* **
41941 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
42006 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
42020 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
42083 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
42099 CCGAAGG
1 CCGAAGG
42106 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.65
80 24 0.32
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:50135 original size:39 final size:40
Alignment explanation
Indices: 50035--50214 Score: 171
Period size: 39 Copynumber: 4.6 Consensus size: 40
50025 TCGAATGATG
* *
50035 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTA-AGTGAC-CATA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGA-T-ACTAATA
*
50074 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAATA
* * *
50114 TCCGGGCTAAGCCCGAAGGCATTGGTG-GAAGTTACTAA-A
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCG-AGATACTAATA
* *
50153 TCCGGGTTAAGT-CGAAGGCA-TTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAATA
* *
50190 ACCGGGCTATGTCCGAAGGCATTTG
1 TCCGGGCTAAGTCCGAAGGCATTTG
50215 AACGAGTAGT
Statistics
Matches: 118, Mismatches: 13, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
36 1 0.01
37 21 0.18
38 18 0.15
39 45 0.38
40 21 0.18
41 11 0.09
42 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:55385 original size:58 final size:56
Alignment explanation
Indices: 55294--55403 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 56
55284 TACATGTAAT
* *
55294 CCACATATCGATGCCACTATACCAGACAGGGTCTTACTCGTACACATATATATGAAAA
1 CCACATATCGATGCCACTATA-CAAACAGGGTCTTACTCGCACACAT-TATATGAAAA
55352 CCACATATCGATGCCAACATATA-AAAC-GTGGTCTTACTCGCACACATTATAT
1 CCACATATCGATGCC-AC-TATACAAACAG-GGTCTTACTCGCACACATTATAT
55404 TGATGCCCAT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
57 6 0.13
58 35 0.74
59 2 0.04
60 4 0.09
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.25
Consensus pattern (56 bp):
CCACATATCGATGCCACTATACAAACAGGGTCTTACTCGCACACATTATATGAAAA
Done.