Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3399
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: 49255
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Found at i:2249 original size:28 final size:27
Alignment explanation
Indices: 2184--2335 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
2174 ATATTAAGTC
* * *
2184 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
2211 CGCACAGTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
2239 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
2266 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
2294 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
2321 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
2336 GCACAATTTA
Statistics
Matches: 117, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
27 65 0.56
28 52 0.44
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:2268 original size:55 final size:55
Alignment explanation
Indices: 2184--2335 Score: 250
Period size: 55 Copynumber: 2.8 Consensus size: 55
2174 ATATTAAGTC
* * * *
2184 CGCACACTCAGTGCTATATAATCAACTCGCACAGTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
2239 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
2294 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
2336 GCACAATTTA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 91 1.00
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:10212 original size:28 final size:27
Alignment explanation
Indices: 10149--10300 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
10139 ATATTAAGTC
* * *
10149 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
10176 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
10204 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
10231 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
10259 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
10286 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
10301 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:10233 original size:55 final size:55
Alignment explanation
Indices: 10149--10300 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
10139 ATATTAAGTC
* * *
10149 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
10204 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
10259 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
10301 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:16105 original size:16 final size:16
Alignment explanation
Indices: 16051--16113 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
16041 CACTGTAACA
* *
16051 GAATAGGGCTATAATT
1 GAATAGAGCTGTAATT
* * *
16067 GAATAGGGTTGTAAAT
1 GAATAGAGCTGTAATT
16083 GAATAGAGCTGTAATT
1 GAATAGAGCTGTAATT
*
16099 GAATAGAACTGTAAT
1 GAATAGAGCTGTAAT
16114 CAGTAATTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30
Consensus pattern (16 bp):
GAATAGAGCTGTAATT
Found at i:16112 original size:32 final size:32
Alignment explanation
Indices: 16042--16112 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
16032 CGTTTGATTC
* *
16042 ACTGTAACAGAATAGGGCTATAATTGAATAGG
1 ACTGTAACAGAATAGAGCTATAATTGAATAGA
** *
16074 GTTGTAA-ATGAATAGAGCTGTAATTGAATAGA
1 ACTGTAACA-GAATAGAGCTATAATTGAATAGA
16106 ACTGTAA
1 ACTGTAA
16113 TCAGTAATTC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
31 1 0.03
32 30 0.97
ACGTcount: A:0.41, C:0.07, G:0.24, T:0.28
Consensus pattern (32 bp):
ACTGTAACAGAATAGAGCTATAATTGAATAGA
Found at i:16183 original size:43 final size:45
Alignment explanation
Indices: 16099--16187 Score: 128
Period size: 43 Copynumber: 2.0 Consensus size: 45
16089 AGCTGTAATT
16099 GAATAGAACTGTAATCAGTAATTCAACTGTTTGGTTGAATGGAATG
1 GAATAGAACTGTAATCAG-AATTCAACTGTTTGGTTGAATGGAATG
***
16145 GAATAGAACTGTAAT-AG-ATTCTTGTGTTTGGTTGAATGGAATG
1 GAATAGAACTGTAATCAGAATTCAACTGTTTGGTTGAATGGAATG
16188 ATGTTGTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
43 23 0.57
45 2 0.05
46 15 0.38
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.35
Consensus pattern (45 bp):
GAATAGAACTGTAATCAGAATTCAACTGTTTGGTTGAATGGAATG
Found at i:16918 original size:33 final size:33
Alignment explanation
Indices: 16881--16947 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
16871 GATTAAACCA
16881 ACCAATTTGATCAAATCCAAACATCCATGATGG
1 ACCAATTTGATCAAATCCAAACATCCATGATGG
* *
16914 ACCAATTTGATCAAGTTCAAACATCCATGATGG
1 ACCAATTTGATCAAATCCAAACATCCATGATGG
16947 A
1 A
16948 AACAAGGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.25
Consensus pattern (33 bp):
ACCAATTTGATCAAATCCAAACATCCATGATGG
Found at i:20119 original size:72 final size:73
Alignment explanation
Indices: 20029--20184 Score: 224
Period size: 72 Copynumber: 2.2 Consensus size: 73
20019 GGATAAAAGC
* * *
20029 ATGAAAAAGAGGGAGAAGGTTTGAAGAAAATGGGAAGAAGAATG-AAAAAAAGAAGATGCTTCAG
1 ATGAAAAAGAGAGAGAAGGTTGGAAGAAAATGGGAAGAAGAATGAAAAAAAAAAAGATGCTTCAG
*
20093 ACGTGAAA
66 ACATGAAA
* * **
20101 ATGAAAAAGAGAGTGAAGGTTGGAAGGACTTGGGAAGAAGAATGAAAAAAAAAAAGATGCTTCAG
1 ATGAAAAAGAGAGAGAAGGTTGGAAGAAAATGGGAAGAAGAATGAAAAAAAAAAAGATGCTTCAG
*
20166 ACATGAGA
66 ACATGAAA
20174 ATGAAAAAGAG
1 ATGAAAAAGAG
20185 GGACAAGGGT
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
72 38 0.51
73 36 0.49
ACGTcount: A:0.51, C:0.04, G:0.30, T:0.14
Consensus pattern (73 bp):
ATGAAAAAGAGAGAGAAGGTTGGAAGAAAATGGGAAGAAGAATGAAAAAAAAAAAGATGCTTCAG
ACATGAAA
Found at i:23716 original size:54 final size:53
Alignment explanation
Indices: 23584--23704 Score: 131
Period size: 54 Copynumber: 2.2 Consensus size: 53
23574 TGTAGTATTC
* * *
23584 ACACGGCCATGTA-ACACGCTCGTGTCCAAGGCCGTGTCAACCACACGCTAAGAC
1 ACACGACCATGTACACAC-C-CGTGTCCAAGGCCGTGTCAACCACACACTAAGAA
*
23638 ACACGACCGTGTAACACACCCGTGTCCACA-GCCGTGTCAACCACACAACTAAGAA
1 ACACGACCATGT-ACACACCCGTGTCCA-AGGCCGTGTCAACCACAC-ACTAAGAA
23693 ACAC-ACCCATGT
1 ACACGA-CCATGT
23705 CTCTACCCGT
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
54 35 0.61
55 18 0.32
56 4 0.07
ACGTcount: A:0.31, C:0.36, G:0.18, T:0.14
Consensus pattern (53 bp):
ACACGACCATGTACACACCCGTGTCCAAGGCCGTGTCAACCACACACTAAGAA
Found at i:24824 original size:18 final size:18
Alignment explanation
Indices: 24801--24836 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
24791 ATATATCATC
24801 TCACACAAATCAACTCAA
1 TCACACAAATCAACTCAA
* *
24819 TCACACAATTCAATTCAA
1 TCACACAAATCAACTCAA
24837 GCATAATAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (18 bp):
TCACACAAATCAACTCAA
Found at i:25934 original size:14 final size:14
Alignment explanation
Indices: 25915--25941 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25905 CAAAATCGAT
25915 AAAATTTTCATATC
1 AAAATTTTCATATC
25929 AAAATTTTCATAT
1 AAAATTTTCATAT
25942 GACCTTCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAATTTTCATATC
Found at i:31788 original size:39 final size:39
Alignment explanation
Indices: 31584--31806 Score: 232
Period size: 40 Copynumber: 5.6 Consensus size: 39
31574 TTGAATGCTG
* * * * * *
31584 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * *
31624 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
*
31664 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* **
31704 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACTAAA
* *
31744 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
31783 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
31807 TGAACGAGGA
Statistics
Matches: 158, Mismatches: 20, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
39 39 0.25
40 109 0.69
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:31826 original size:79 final size:80
Alignment explanation
Indices: 31659--31841 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
31649 GTGCGAGATA
* * *
31659 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
31724 CAGTCGTGCGAGTTG
66 CAGTCGAACGAGGAG
* * * *
31739 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
* *
31803 CATTTGAACGAGGAG
66 CAGTCGAACGAGGAG
* *
31818 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
31842 TACGTGATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 45 0.52
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CAGTCGAACGAGGAG
Found at i:39536 original size:40 final size:39
Alignment explanation
Indices: 39491--39707 Score: 172
Period size: 39 Copynumber: 5.5 Consensus size: 39
39481 AAGTGAATAT
* *
39491 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAA
1 ATCCGG-TTAAG-TCCCGAAGGCATTCGTGCGAGATACTAA
* * *
39531 TTCCGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
1 ATCCGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAA
* * **
39570 ATCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAA
1 ATCC-GGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAA
* *
39610 ATCCGGGTT-AGTCCCGAAGGCATT-GTGTGAGTTACTAA
1 ATCC-GGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAA
* * * * ** * *
39648 AACCGGGCTATGTCCCGAAGGCATTTGAACGAGGA-GCTAT
1 ATCC-GGTTAAGTCCCGAAGGCATTCGTGCGA-GATACTAA
*
39688 ATCCGGTTAAATCCCGAAGG
1 ATCCGGTTAAGTCCCGAAGG
39708 TACGTGATTT
Statistics
Matches: 147, Mismatches: 25, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
38 19 0.13
39 71 0.48
40 56 0.38
41 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (39 bp):
ATCCGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAA
Found at i:39590 original size:79 final size:79
Alignment explanation
Indices: 39452--39674 Score: 227
Period size: 79 Copynumber: 2.8 Consensus size: 79
39442 TTGAATGCTG
* * * * * * *
39452 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGATTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTAATAAATCCGGGTTAAG-TCCCGAAGGCATT
*
39516 TGTGCGAGATACTAAT
64 TGTGCGAGATACTAAA
* * *
39532 TCC-GGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTAATAAATCCGGGTTAAGTCCCGAAGGCATTT
* **
39596 GTGCGAGTTGTTAAA
65 GTGCGAGATACTAAA
* * * * *
39611 TCCGGGTT-AGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGTTAAGTCCCGAAGGCATTTG
39675 AACGAGGAGC
Statistics
Matches: 119, Mismatches: 21, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
78 35 0.29
79 73 0.61
80 11 0.09
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGTTAAGTCCCGAAGGCATTTG
TGCGAGATACTAAA
Found at i:39663 original size:39 final size:38
Alignment explanation
Indices: 39452--39672 Score: 185
Period size: 40 Copynumber: 5.6 Consensus size: 38
39442 TTGAATGCTG
* * * * * *
39452 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGG-TTAGTCCCGAAGGCATTGTGC-GAGTTATTAAA
* * * * *
39492 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTT-AG-TCCCGAAGG-CATTGTGCGAGTTATTAAA
39532 TCC-GGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTT-AGTCCCGAAGGCATT-GTGCGAGTTATTAAA
* *
39571 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTT-AGTCCCGAAGGCA-TTGTGCGAGTTATTAAA
* *
39611 TCCGGGTTAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAGTCCCGAAGGCATTGTGCGAGTTATTAAA
* *
39649 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTA-GTCCCGAAGGCATT
39673 TGAACGAGGA
Statistics
Matches: 152, Mismatches: 21, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
38 24 0.16
39 56 0.37
40 62 0.41
41 10 0.07
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (38 bp):
TCCGGGTTAGTCCCGAAGGCATTGTGCGAGTTATTAAA
Found at i:39692 original size:78 final size:79
Alignment explanation
Indices: 39527--39707 Score: 204
Period size: 78 Copynumber: 2.3 Consensus size: 79
39517 GTGCGAGATA
* * * *
39527 CTAATTCCGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGC
1 CTAAATCCGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
** **
39592 AGTCGTGCGAGTTG
66 AGTCGAACGAGGAG
* * *
39606 TTAAATCCGGGTT-AGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCC-GGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
* *
39669 CATTTGAACGAGGAG
65 CAGTCGAACGAGGAG
* *
39684 CTATATCCGGTTAAATCCCGAAGG
1 CTAAATCCGGTTAAGTCCCGAAGG
39708 TACGTGATTT
Statistics
Matches: 84, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
77 4 0.05
78 55 0.65
79 21 0.25
80 4 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CTAAATCCGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
AGTCGAACGAGGAG
Done.