Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1794
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: 27500
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Found at i:1817 original size:26 final size:27
Alignment explanation
Indices: 1781--1833 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1771 TGTCAGCTAG
* *
1781 TGAAATTTTAA-TGTTCGAATGTATGC
1 TGAAATTTTAAGTGTCCGAATGCATGC
*
1807 TGAATTTTTAAGTGTCCGAATGCATGC
1 TGAAATTTTAAGTGTCCGAATGCATGC
1834 CAGAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (27 bp):
TGAAATTTTAAGTGTCCGAATGCATGC
Found at i:3134 original size:48 final size:48
Alignment explanation
Indices: 3070--3217 Score: 224
Period size: 48 Copynumber: 3.1 Consensus size: 48
3060 TTGATGTACA
*
3070 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTAAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
*
3118 AGATATATATATGTGGTAAAGCCGAAAGGCTAATGTGAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
** ** * *
3166 AGCCATGCATATGTGGTAAAGCCAAATGGTTAATGTGAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
3214 AGAT
1 AGAT
3218 GTGTATATAT
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 89 1.00
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (48 bp):
AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
Found at i:8290 original size:21 final size:21
Alignment explanation
Indices: 8252--8291 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
8242 AAACTTGAGA
*
8252 AATTTTAGAATATTTTTGGTT
1 AATTTTAGAATATGTTTGGTT
8273 AATTTTGAGAATA-GTTTGG
1 AATTTT-AGAATATGTTTGG
8292 GGTGAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (21 bp):
AATTTTAGAATATGTTTGGTT
Found at i:14227 original size:43 final size:43
Alignment explanation
Indices: 14180--14316 Score: 143
Period size: 43 Copynumber: 3.2 Consensus size: 43
14170 AATGGCATAC
*
14180 CCCAAATATGGTCATACATATTATCACATATCAATGCCACTGT
1 CCCAAACATGGTCATACATATTATCACATATCAATGCCACTGT
* * ** * * * * *
14223 CCCAAACAGGGTCTTATTTGA-AATCGA-TTAACGATGCCAATGT
1 CCCAAACATGGTCATACAT-ATTATC-ACATATCAATGCCACTGT
*
14266 CCCAGACATGGTCATACATATTATCACATATCAATGCCACTGT
1 CCCAAACATGGTCATACATATTATCACATATCAATGCCACTGT
14309 CCCAAACA
1 CCCAAACA
14317 GGGACTTATA
Statistics
Matches: 69, Mismatches: 21, Indels: 8
0.70 0.21 0.08
Matches are distributed among these distances:
42 2 0.03
43 65 0.94
44 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.27
Consensus pattern (43 bp):
CCCAAACATGGTCATACATATTATCACATATCAATGCCACTGT
Found at i:14332 original size:86 final size:86
Alignment explanation
Indices: 14187--14386 Score: 337
Period size: 86 Copynumber: 2.3 Consensus size: 86
14177 TACCCCAAAT
* * *
14187 ATGGTCATACATATTATCACATATCAATGCCACTGTCCCAAACAGGGTCTTATTTGAAATCGATT
1 ATGGTCATACATATTATCACATATCAATGCCACTGTCCCAAACAGGGACTTATATGAAATCAATT
14252 AACGATGCCAATGTCCCAGAC
66 AACGATGCCAATGTCCCAGAC
14273 ATGGTCATACATATTATCACATATCAATGCCACTGTCCCAAACAGGGACTTATATGAAATCAATT
1 ATGGTCATACATATTATCACATATCAATGCCACTGTCCCAAACAGGGACTTATATGAAATCAATT
*
14338 AATGATGCCAATGTCCCAGAC
66 AACGATGCCAATGTCCCAGAC
* * *
14359 ATGGTCTTACATGTAATCACATATCAAT
1 ATGGTCATACATATTATCACATATCAAT
14387 AACCTAATGT
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 107 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.28
Consensus pattern (86 bp):
ATGGTCATACATATTATCACATATCAATGCCACTGTCCCAAACAGGGACTTATATGAAATCAATT
AACGATGCCAATGTCCCAGAC
Found at i:14346 original size:43 final size:43
Alignment explanation
Indices: 14213--14377 Score: 138
Period size: 43 Copynumber: 3.8 Consensus size: 43
14203 TCACATATCA
* * * *
14213 ATGCCACTGTCCCAAACAGGGTCTTATTTGAAATCGATTAACG
1 ATGCCAATGTCCCAAACAGGGTCTTATATGAAATCAATTAATG
* * * * * *
14256 ATGCCAATGTCCCAGACATGGTCATACAT-ATTATCACA-T-ATCA
1 ATGCCAATGTCCCAAACAGGGTCTTATATGA-AATCA-ATTAAT-G
* *
14299 ATGCCACTGTCCCAAACAGGGACTTATATGAAATCAATTAATG
1 ATGCCAATGTCCCAAACAGGGTCTTATATGAAATCAATTAATG
* * * *
14342 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCA
1 ATGCCAATGTCCCAAACAGGGTCTTATATGAAATCA
14378 CATATCAATA
Statistics
Matches: 92, Mismatches: 24, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
42 3 0.03
43 85 0.92
44 4 0.04
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (43 bp):
ATGCCAATGTCCCAAACAGGGTCTTATATGAAATCAATTAATG
Found at i:17237 original size:27 final size:26
Alignment explanation
Indices: 17220--17289 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 26
17210 ATATTAAGTC
17220 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
17247 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
17275 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
17290 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (26 bp):
CGCACACTCAGTGCTATATATCAACT
Found at i:17283 original size:28 final size:28
Alignment explanation
Indices: 17220--17315 Score: 131
Period size: 28 Copynumber: 3.4 Consensus size: 28
17210 ATATTAAGTC
*
17220 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
17247 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
17275 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
17304 CGCACACTTAGT
1 CGCACACTTAGT
17316 CCAATCTCAT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.35
28 23 0.37
29 17 0.27
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:17780 original size:12 final size:12
Alignment explanation
Indices: 17763--17789 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
17753 TGGGCATACT
17763 TATGTATATATA
1 TATGTATATATA
17775 TATGTATATATA
1 TATGTATATATA
17787 TAT
1 TAT
17790 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:25626 original size:27 final size:26
Alignment explanation
Indices: 25609--25678 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 26
25599 ATATTAAGTC
25609 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
25636 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
25664 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
25679 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (26 bp):
CGCACACTCAGTGCTATATATCAACT
Found at i:25672 original size:28 final size:28
Alignment explanation
Indices: 25609--25706 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
25599 ATATTAAGTC
*
25609 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
25636 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
25664 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
25693 CGCACACTTAGTGC
1 CGCACACTTAGTGC
25707 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Done.