Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold824
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: 64916
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:10311 original size:21 final size:21
Alignment explanation
Indices: 10286--10326 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
10276 CATTGATTTA
10286 GTAAATTAGTTTATGAAATTC
1 GTAAATTAGTTTATGAAATTC
*
10307 GTAAATTAGTTTGTGAAATT
1 GTAAATTAGTTTATGAAATT
10327 AGAATATGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44
Consensus pattern (21 bp):
GTAAATTAGTTTATGAAATTC
Found at i:11070 original size:39 final size:39
Alignment explanation
Indices: 10952--11073 Score: 199
Period size: 39 Copynumber: 3.1 Consensus size: 39
10942 GTTCAATATT
10952 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
* * * **
10991 TAGAAACATATCCGAACTTGAGGACTACAGGCTACGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
11030 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
11069 TGGAA
1 TGGAA
11074 TATATCCAGG
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 73 1.00
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (39 bp):
TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
Found at i:18184 original size:21 final size:21
Alignment explanation
Indices: 18160--18200 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
18150 CATTGATTTA
18160 GTAAATTAGTTTATGAAATTC
1 GTAAATTAGTTTATGAAATTC
18181 GTAAATTAGTTTATGAAATT
1 GTAAATTAGTTTATGAAATT
18201 AGAATATGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.44
Consensus pattern (21 bp):
GTAAATTAGTTTATGAAATTC
Found at i:18902 original size:39 final size:38
Alignment explanation
Indices: 18848--18937 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
18838 ATGATATTTG
*
18848 GAAACATATCCGGACTTGAGGTCTGCAGGCTACGTGCT
1 GAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGCT
18886 AGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGCT
1 -GAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGCT
* *
18925 GGAATATATCCGG
1 GAAACATATCCGG
18938 GCCTAAAGTC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 11 0.23
39 37 0.77
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (38 bp):
GAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGCT
Found at i:18952 original size:39 final size:39
Alignment explanation
Indices: 18848--18965 Score: 112
Period size: 39 Copynumber: 3.0 Consensus size: 39
18838 ATGATATTTG
* * * *
18848 GAAACATATCCGGACTTGAGGTCTGCAGGCTACGTGCTA
1 GAAACATATCCGGACCTAAAGTCCGCAGGCTACGTGCTA
* * *
18887 GAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGCT-
1 GAAACATATCCGGACCTAAAGTCCGCAGGCTACGTGCTA
* * * **
18925 GGAATATATCCGGGCCTAAAGTCCCGCAGGCTTTGTGCTA
1 GAAACATATCCGGACCTAAAGT-CCGCAGGCTACGTGCTA
18965 G
1 G
18966 TAACTGGATT
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
38 16 0.24
39 51 0.75
40 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.29, T:0.23
Consensus pattern (39 bp):
GAAACATATCCGGACCTAAAGTCCGCAGGCTACGTGCTA
Found at i:25011 original size:358 final size:356
Alignment explanation
Indices: 24354--25406 Score: 1478
Period size: 358 Copynumber: 3.0 Consensus size: 356
24344 AGTTAAATTT
* *
24354 TAGCACT-ACGTTTCACCCTCGACTGATGGCCAACCAAAAAGAGTTATTCAGGTCTTAGAGGATA
1 TAGCACTGA-GTTTCACCCTCGACTGATGGCCAATCAAAAAAAGTTATTCAGGTCTTAGAGGATA
* * *
24418 TAATGCGTTCCTGTGTGATTGACTTTGGAATAAATTGGGAGAAGTATGTCCCTCTGGTTGAATTC
65 TAATGCGTTTCTGTGTGATTGATTTTGGAATAAACTGGGAGAAGTATGTCCCTCTGGTTGAATTC
* ** * *
24483 TCCTATAATAACAGTTACCATGTAAACCTGAAGATGTCTCCATTCGAAGCCTTGTATGGTAGAAG
130 TCCTATAATAATAGTTACCACATCAGCCTGAAGATGTCTCCATTCGAAGCCTTGTATGGTAGAAG
* * * *
24548 GTGTAGGACACCTGCCTATTTGATAGAATTGAGCGAAAGAAAGATAATGGATCCAAACATAGTAC
195 GTGTAGGACACCTACCTATTAGA-AGAATTGAGCGAAAGAAAGATAGTGGGTCCAAAC-TAGTAC
* * * *
24613 GTGAAATAGAAGAGAAAGCTGCCATCATCCATAGTCACTTAAAAACTACACAGGACCAACAGAAA
258 GTGAAACAGAAGAGAAAGTTGCCATCATCCATAGTCACTTAAAAACTATACAGGACCGACAGAAA
*
24678 TCATATACAAATTTAAAAATGACAGACAAAAATC
323 TCATATACAAATTTAAAAAAGACAGACAAAAATC
*
24712 TAGCACTGAGTTTCACCCTCGACTGAAGGCCAATCAAAAAAAGTTATTCAGGTCTTAGAGGATAT
1 TAGCACTGAGTTTCACCCTCGACTGATGGCCAATCAAAAAAAGTTATTCAGGTCTTAGAGGATAT
* *
24777 AATGCGTTTCTGTGTGATTGATTTTGGAATAAACTAGGAAAAGTATGTCCCTCTGGTTGAATTCT
66 AATGCGTTTCTGTGTGATTGATTTTGGAATAAACTGGGAGAAGTATGTCCCTCTGGTTGAATTCT
* * *
24842 CCTACAATAATAGTTACCACATCAGCCTGAAGATGTCTCCATTCGAGGCCTTGTATGGTAGAAGA
131 CCTATAATAATAGTTACCACATCAGCCTGAAGATGTCTCCATTCGAAGCCTTGTATGGTAGAAGG
* *
24907 TGTAGGACACCTA-CTCATTGGAAGTAATTGAGCGAAAGAAAGATAGTGGGTCCAAACTCAGTAT
196 TGTAGGACACCTACCT-ATTAGAAG-AATTGAGCGAAAGAAAGATAGTGGGTCCAAACT-AGTAC
* * * *
24971 GTTAAACAGAGGAGAAAGTTGTCATCATCCATAGTCACTTAAAAACTATACAGGACCGATAGAAA
258 GTGAAACAGAAGAGAAAGTTGCCATCATCCATAGTCACTTAAAAACTATACAGGACCGACAGAAA
* * * *
25036 TCATATACAGATTTAAAAAAGACTGCCAAAAATT
323 TCATATACAAATTTAAAAAAGACAGACAAAAATC
* * * *
25070 TAGCACTGCA-TTTCACCCTTGACTGATGGACAATCAGAAAAAGTTATTTAGGTCTTAGAGGATA
1 TAGCACTG-AGTTTCACCCTCGACTGATGGCCAATCAAAAAAAGTTATTCAGGTCTTAGAGGATA
*** * * * *
25134 TAACATGTTTCTGTGTGAGTGATTTAGGAATAAACTGGGAGAAGTATGTCCTTCTAGTTGAATTC
65 TAATGCGTTTCTGTGTGATTGATTTTGGAATAAACTGGGAGAAGTATGTCCCTCTGGTTGAATTC
25199 TCCTATAATAATTA-TTACCACATCAGCCTGAAGATGTCTCCATTCGAAGCC-----T-GTAGAA
130 TCCTATAATAA-TAGTTACCACATCAGCCTGAAGATGTCTCCATTCGAAGCCTTGTATGGTAGAA
* ** *
25257 GGTGTAGGACACCTACCTATTAGATGGAATTGAGAAAAAGAAAGATAGTGGGTCCAAACTTGGTA
194 GGTGTAGGACACCTACCTATTAGA-AGAATTGAGCGAAAGAAAGATAGTGGGTCCAAAC-TAGTA
* *
25322 CGTGAAACAGAAGAGAAAGTTGCCATCATCCATAGTCACTTAAAAACTATACATGACCGACATAA
257 CGTGAAACAGAAGAGAAAGTTGCCATCATCCATAGTCACTTAAAAACTATACAGGACCGACAGAA
25387 ATCATATACAAATTTAAAAA
322 ATCATATACAAATTTAAAAA
25407 GGAACTTGAG
Statistics
Matches: 622, Mismatches: 64, Indels: 24
0.88 0.09 0.03
Matches are distributed among these distances:
352 135 0.22
353 5 0.01
357 5 0.01
358 473 0.76
359 4 0.01
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (356 bp):
TAGCACTGAGTTTCACCCTCGACTGATGGCCAATCAAAAAAAGTTATTCAGGTCTTAGAGGATAT
AATGCGTTTCTGTGTGATTGATTTTGGAATAAACTGGGAGAAGTATGTCCCTCTGGTTGAATTCT
CCTATAATAATAGTTACCACATCAGCCTGAAGATGTCTCCATTCGAAGCCTTGTATGGTAGAAGG
TGTAGGACACCTACCTATTAGAAGAATTGAGCGAAAGAAAGATAGTGGGTCCAAACTAGTACGTG
AAACAGAAGAGAAAGTTGCCATCATCCATAGTCACTTAAAAACTATACAGGACCGACAGAAATCA
TATACAAATTTAAAAAAGACAGACAAAAATC
Found at i:28411 original size:64 final size:64
Alignment explanation
Indices: 28295--28414 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 64
28285 ATCTCCTTAG
* *
28295 AGGTTTTCTTAATTGATCCGCTACATCAGGAGGACCCTATGGCACATCAAGACCATTTCCCCAC
1 AGGTTATCTTAATTGATCCGCTACATCAGGAAGACCCTATGGCACATCAAGACCATTTCCCCAC
* * * *
28359 AGGTTATCTTAGTTGATTCGCTACATCATGAAGATCCTA-GGC-CATGCTAAGACCAT
1 AGGTTATCTTAATTGATCCGCTACATCAGGAAGACCCTATGGCACAT-C-AAGACCAT
28415 CCAAGTTGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
62 3 0.06
63 4 0.08
64 41 0.85
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (64 bp):
AGGTTATCTTAATTGATCCGCTACATCAGGAAGACCCTATGGCACATCAAGACCATTTCCCCAC
Found at i:28463 original size:13 final size:13
Alignment explanation
Indices: 28447--28481 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
28437 TCACCCTAGT
28447 CGATCATCTTTTA
1 CGATCATCTTTTA
28460 CGATCATCTTTTA
1 CGATCATCTTTTA
*
28473 CAATCATCT
1 CGATCATCT
28482 CAATGGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.43
Consensus pattern (13 bp):
CGATCATCTTTTA
Found at i:28743 original size:47 final size:48
Alignment explanation
Indices: 28670--28763 Score: 120
Period size: 47 Copynumber: 2.0 Consensus size: 48
28660 CCACCCTCAA
*
28670 AAAATATAATAAAATAAGAATAAAAACACATATTATATATACATAACT
1 AAAATATAAAAAAATAAGAATAAAAACACATATTATATATACATAACT
* ** *
28718 AAAATA-AAAAAAATGAA-AATGAAAACATGTATTATTTATACATAAC
1 AAAATATAAAAAAAT-AAGAATAAAAACACATATTATATATACATAAC
28764 CAATTGAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
47 32 0.80
48 8 0.20
ACGTcount: A:0.62, C:0.07, G:0.04, T:0.27
Consensus pattern (48 bp):
AAAATATAAAAAAATAAGAATAAAAACACATATTATATATACATAACT
Found at i:40354 original size:7 final size:7
Alignment explanation
Indices: 40339--40378 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
40329 CCTAGATGAA
40339 TTGGGCT
1 TTGGGCT
*
40346 TTAGGCT
1 TTGGGCT
40353 TTGGGCT
1 TTGGGCT
40360 TTGGGCT
1 TTGGGCT
40367 TTGGGCT
1 TTGGGCT
40374 TTGGG
1 TTGGG
40379 TTTCATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.03, C:0.12, G:0.42, T:0.42
Consensus pattern (7 bp):
TTGGGCT
Found at i:55733 original size:28 final size:29
Alignment explanation
Indices: 55701--55799 Score: 107
Period size: 28 Copynumber: 3.5 Consensus size: 29
55691 ATAATAAGCC
*
55701 CGCACACTTAGTGCTTA-ATAGTCGAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
*
55729 CGCACACTTAGTGC-TATATAATC-AACCT
1 CGCACACTTAGTGCTTACATAATCGAA-CT
* * *
55757 CGCACACTTAGTGCTATACA-ATTTGAACC
1 CGCACACTTAGTGCT-TACATAATCGAACT
55786 CGCACACTTAGTGC
1 CGCACACTTAGTGC
55800 CAATCTCATG
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
27 4 0.07
28 35 0.57
29 17 0.28
30 5 0.08
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCGAACT
Found at i:56508 original size:19 final size:19
Alignment explanation
Indices: 56484--56523 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
56474 TAATACCCAT
56484 TATAGCCATTCTCATAGTC
1 TATAGCCATTCTCATAGTC
56503 TATAGCCATTCTCATAGTC
1 TATAGCCATTCTCATAGTC
56522 TA
1 TA
56524 AATCTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.38
Consensus pattern (19 bp):
TATAGCCATTCTCATAGTC
Done.