Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1852
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: 32567
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:3584 original size:27 final size:27
Alignment explanation
Indices: 3554--3731 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
3544 ATATTGAGTC
* * * *
3554 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
3581 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
3608 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
3636 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
3663 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
3690 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
3717 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
3732 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:3693 original size:82 final size:81
Alignment explanation
Indices: 3575--3730 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
3565 TGCTATATAA
* *
3575 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
3640 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
3657 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
3721 CACTTAGTGC
65 CACTTAGTGC
3731 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:7967 original size:40 final size:40
Alignment explanation
Indices: 7923--8144 Score: 237
Period size: 40 Copynumber: 5.6 Consensus size: 40
7913 GCTCCTCGTT
*
7923 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
7963 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
*
8003 CAAATGCCTTCGGGACTTAACCCGGATT-TAGGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATA-GTAACTCGCA
* * *
8044 CCAATGCCTTCGGG-CTTAGCCCGG-AATTAGTATCTCG--
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* * * *
8081 CAAATGCCTTC-GGATCTTAGTCCGGATATGGT-ACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
8121 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
8145 ACATCATTCA
Statistics
Matches: 158, Mismatches: 13, Indels: 23
0.81 0.07 0.12
Matches are distributed among these distances:
36 2 0.01
37 11 0.07
38 14 0.09
39 23 0.15
40 83 0.53
41 25 0.16
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:8027 original size:80 final size:78
Alignment explanation
Indices: 7923--8145 Score: 267
Period size: 80 Copynumber: 2.8 Consensus size: 78
7913 GCTCCTCGTT
* *
7923 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
7988 ATTTAGTAACTCG
66 AATTAGTAACTCG
* *
8001 CACAAATGCCTTCGGGACTTAACCCGGATT-TAGGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 --CAAATGCCTTCGGGACTTAGCCCGG-TTATA-GTAACTCGCACAAATGCCTTCGGGACTTAGC
*
8064 CCGGAATTAGTATCTCG
62 CCGGAATTAGTAACTCG
* * * *
8081 CAAATGCCTTC-GGATCTTAGTCCGGATATGGT-ACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCC
8143 GGA
64 GGA
8146 CATCATTCAA
Statistics
Matches: 125, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
76 11 0.09
77 24 0.19
78 20 0.16
80 45 0.36
81 25 0.20
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
AATTAGTAACTCG
Found at i:8123 original size:118 final size:119
Alignment explanation
Indices: 7925--8145 Score: 281
Period size: 118 Copynumber: 1.9 Consensus size: 119
7915 TCCTCGTTCA
*
7925 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCG-ACAAATGCCTTCGGGACTTAACCCGGAT
* *
7990 TTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGGTAACTCGCACC
65 ATAGTAACTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGGTAACTCGCACC
* * **
8046 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCG-CAAATGCCTTC-GGATCTTAGTCCGGA
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGACAAATGCCTTCGGGA-CTTAACCCGGA
* *
8107 TATGGT-ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 TATAGTAAC-TAGCACAAAGCCTTCGGGACTTAACCCGGA
8146 CATCATTCAA
Statistics
Matches: 88, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
117 25 0.28
118 32 0.36
119 1 0.01
120 18 0.20
121 12 0.14
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGACAAATGCCTTCGGGACTTAACCCGGATA
TAGTAACTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGGTAACTCGCACC
Found at i:18407 original size:40 final size:40
Alignment explanation
Indices: 18354--18545 Score: 255
Period size: 40 Copynumber: 4.8 Consensus size: 40
18344 GGATATAGCT
* * *
18354 ACTCGCTCGAATGCCTTTGGGACTTAGCCCGG-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
** *
18394 GTTCGCACAAATGCCTTCGGAACTTAGCCCGG-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
18434 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* *
18474 ACTCGCA-ACAATGCCTTCGGGACCTAGCCCGGAATTAGTC
1 ACTCGCACA-AATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
18514 ACTAGCACAAATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
18546 TTATCATCCG
Statistics
Matches: 136, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
39 1 0.01
40 132 0.97
41 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:23732 original size:26 final size:26
Alignment explanation
Indices: 23703--23752 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
23693 GCAAATGATG
*
23703 TGAATGAATGAACACCAATGGGCAGA
1 TGAATGAATAAACACCAATGGGCAGA
*
23729 TGAATGAATAAACTCCAATGGGCA
1 TGAATGAATAAACACCAATGGGCA
23753 TACAATGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (26 bp):
TGAATGAATAAACACCAATGGGCAGA
Found at i:25826 original size:46 final size:46
Alignment explanation
Indices: 25776--25951 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
25766 TGATTGAGCA
25776 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
25822 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
25867 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
25915 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
25952 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 61 0.55
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:25932 original size:93 final size:93
Alignment explanation
Indices: 25773--25944 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
25763 GGATGATTGA
*
25773 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
25838 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
25866 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
25930 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
25945 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Done.