Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold210
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: 41299
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:4779 original size:104 final size:104
Alignment explanation
Indices: 4599--4822 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
4589 TGTATATAAA
** * *
4599 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
4664 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
4703 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
4767 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
4807 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
4823 GATATCCATT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:4887 original size:26 final size:26
Alignment explanation
Indices: 4852--4903 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
4842 AAATGAAAAG
* *
4852 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGATGATTCCCCGA
4878 GGGGTTGCTAAGTGATGATTCCCCGA
1 GGGGTTGCTAAGTGATGATTCCCCGA
4904 TTCAGTGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.15, C:0.21, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGATGATTCCCCGA
Found at i:4890 original size:70 final size:72
Alignment explanation
Indices: 4741--4891 Score: 243
Period size: 72 Copynumber: 2.1 Consensus size: 72
4731 TCATTGGTGG
* *
4741 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
4806 GAGGGGT
66 GAGGGGT
***
4813 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATT-CCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
4876 GAGGGGT
66 GAGGGGT
4883 TGCTAAGTG
1 TGCTAAGTG
4892 ATGATTCCCC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 20 0.27
71 24 0.32
72 30 0.41
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:12540 original size:40 final size:40
Alignment explanation
Indices: 12484--12707 Score: 261
Period size: 40 Copynumber: 5.5 Consensus size: 40
12474 TATTCGGATG
* *
12484 ATATCCGGGCTTAGTCCTGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
12524 ATATCCAGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
12567 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* ** * *
12607 ATATCCGGGCTAAGTCCTGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * * *
12647 ATATCCGGGCTAAGACCCGAAGGTATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
12687 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
12708 ATACTTGGGT
Statistics
Matches: 158, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 13 0.08
40 108 0.68
41 1 0.01
43 36 0.23
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:12629 original size:83 final size:79
Alignment explanation
Indices: 12488--12707 Score: 255
Period size: 83 Copynumber: 2.7 Consensus size: 79
12478 CGGATGATAT
* * * **
12488 CCGGGCTTAGTCCTGAAGGCATTTGTGCAAGTTACTATATCCAGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCC-GGCTAAGTCCCGAAGGCATTCA
12553 TGCGAGTAGTTG-CTATAC
65 TGC---TAG-TGACTATAC
* *
12571 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCTGAAGGCATTCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCC-GGCTAAGTCCCGAAGGCATTCA
*
12636 TGCTAGTGACTATAT
65 TGCTAGTGACTATAC
* * * *
12651 CCGGGCTAAGACCCGAAGGTATTTGTGCGAGTTG-CTATATCCGGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGCTAAGTCCCGAAG
12708 ATACTTGGGT
Statistics
Matches: 121, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
79 15 0.12
80 44 0.36
81 2 0.02
83 60 0.50
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGCTAAGTCCCGAAGGCATTCAT
GCTAGTGACTATAC
Found at i:12727 original size:123 final size:122
Alignment explanation
Indices: 12484--12708 Score: 312
Period size: 123 Copynumber: 1.9 Consensus size: 122
12474 TATTCGGATG
* ** * *
12484 ATATCCGGGCTTAGTCCTGAAGGCATTTGTGCAAGTTACTATATCCAGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGTCCTGAAGGCATTCATGCAAGTGACTATATCCAGGCTAAGACCCGAAGGCA
* * *
12549 TTTGTGCGAGTAGTTGCTATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
66 TTTGTGC-AGTAGTTGCTATACCCGGGCTAAATCCCGAAGACATTTGTGCAAGTGACT
* * *
12607 ATATCCGGGCTAAGTCCTGAAGGCATTCATGCTAGTGACTATATCCGGGCTAAGACCCGAAGGTA
1 ATATCCGGGCTAAGTCCTGAAGGCATTCATGCAAGTGACTATATCCAGGCTAAGACCCGAAGGCA
*
12672 TTTGTGC-G-AGTTGCTATATCC-GGCTAAATCCCGAAGA
66 TTTGTGCAGTAGTTGCTATACCCGGGCTAAATCCCGAAGA
12709 TACTTGGGTT
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
119 14 0.15
120 12 0.13
121 1 0.01
123 64 0.70
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.27
Consensus pattern (122 bp):
ATATCCGGGCTAAGTCCTGAAGGCATTCATGCAAGTGACTATATCCAGGCTAAGACCCGAAGGCA
TTTGTGCAGTAGTTGCTATACCCGGGCTAAATCCCGAAGACATTTGTGCAAGTGACT
Found at i:14728 original size:16 final size:16
Alignment explanation
Indices: 14707--14737 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
14697 ATTTGCAATA
14707 AGTACTGATTTTCATT
1 AGTACTGATTTTCATT
14723 AGTACTGATTTTCAT
1 AGTACTGATTTTCAT
14738 CCTCAAACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (16 bp):
AGTACTGATTTTCATT
Found at i:24114 original size:32 final size:32
Alignment explanation
Indices: 24028--24107 Score: 133
Period size: 32 Copynumber: 2.5 Consensus size: 32
24018 GTCTCAATTG
* *
24028 GGCCTAGCCCATCTCAGAATCAATATCAGTTG
1 GGCCTAGCCCATTTCAGAATCAATATCAGTTA
24060 GGCCTAGCCCATTTCAGAATCAATATCAGTTA
1 GGCCTAGCCCATTTCAGAATCAATATCAGTTA
*
24092 GGCCCAGCCCATTTCA
1 GGCCTAGCCCATTTCA
24108 ATATCAAACC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (32 bp):
GGCCTAGCCCATTTCAGAATCAATATCAGTTA
Found at i:31688 original size:28 final size:27
Alignment explanation
Indices: 31625--31776 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
31615 ATATTAAGTC
* * *
31625 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
31652 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
31680 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
31707 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
31735 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
31762 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31777 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:31709 original size:55 final size:55
Alignment explanation
Indices: 31625--31776 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
31615 ATATTAAGTC
* * *
31625 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
31680 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
31735 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
31777 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:39648 original size:29 final size:29
Alignment explanation
Indices: 39613--39686 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
39603 CAGTGCTATA
39613 ATAATCAACTCGCACAACGTTAGTGGCTAC
1 ATAATCAACTCGCACAAC-TTAGTGGCTAC
*
39643 A-AATCAAACTCGCATC-ACTTAGTTGCTAC
1 ATAATC-AACTCGCA-CAACTTAGTGGCTAC
*
39672 ATAGTCAA-TCGCACA
1 ATAATCAACTCGCACA
39687 CTTGCTACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
27 1 0.03
28 5 0.13
29 17 0.45
30 14 0.37
31 1 0.03
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (29 bp):
ATAATCAACTCGCACAACTTAGTGGCTAC
Found at i:39712 original size:23 final size:23
Alignment explanation
Indices: 39665--39712 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
39655 CATCACTTAG
* *
39665 TTGCTACATAGTCAATCGCACAC
1 TTGCTACATAGTCAACCGCAAAC
39688 TTGCTACATAGTCAAACCG-AAAC
1 TTGCTACATAGTC-AACCGCAAAC
39711 TT
1 TT
39713 AGTGCCACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (23 bp):
TTGCTACATAGTCAACCGCAAAC
Done.