Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1153
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: 41596
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:5546 original size:40 final size:40
Alignment explanation
Indices: 5491--5713 Score: 374
Period size: 40 Copynumber: 5.6 Consensus size: 40
5481 GCATGCAATA
5491 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
5531 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
5571 ATACGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
5611 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* * *
5651 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* *
5691 ACCCGGGTTAAGACCCGAAGGCA
1 ATCCGGGCTAAGACCCGAAGGCA
5714 ATTGAGCTTG
Statistics
Matches: 172, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 172 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
Found at i:5732 original size:120 final size:120
Alignment explanation
Indices: 5491--5740 Score: 385
Period size: 120 Copynumber: 2.1 Consensus size: 120
5481 GCATGCAATA
*
5491 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
* * * * *
5556 TGTGCGAGTTGATATATACGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
66 CGTGCGAGTTGATATACACGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATAT
5611 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
* * * ** *
5676 CGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGAGCTTGTGGTTAT
66 CGTGCGAGTTGATATACACGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATAT
5731 ATCC-GGCTAA
1 ATCCGGGCTAA
5741 ATTCCAAAGA
Statistics
Matches: 118, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
119 6 0.05
120 112 0.95
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (120 bp):
ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
CGTGCGAGTTGATATACACGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATAT
Found at i:11402 original size:40 final size:39
Alignment explanation
Indices: 11343--11474 Score: 149
Period size: 40 Copynumber: 3.3 Consensus size: 39
11333 CATTTGAATG
* *
11343 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTG-TT
* * *
11383 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGTT
* * * *
11423 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGT-GTT
11463 ATATCC-GGCTAA
1 ATATCCGGGCTAA
11475 ATTCTGAAGA
Statistics
Matches: 76, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
39 6 0.08
40 68 0.89
41 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGTT
Found at i:16197 original size:40 final size:40
Alignment explanation
Indices: 16165--16428 Score: 376
Period size: 40 Copynumber: 6.7 Consensus size: 40
16155 CCAGCATGAT
* * * *
16165 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * *
16205 TGCTCTTCGGG-TTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
16244 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
16284 TGCTCTT-GGG-TTTAG-CCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
16321 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
16361 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
16401 TGCTCTTCGGGACTTAGCCCGGAT-CATC
1 TGCTCTTCGGGACTTAGCCCGGATACATC
16429 GTCGAGACCT
Statistics
Matches: 200, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
37 27 0.14
38 6 0.03
39 43 0.22
40 124 0.62
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:16330 original size:77 final size:78
Alignment explanation
Indices: 16165--16428 Score: 406
Period size: 77 Copynumber: 3.4 Consensus size: 78
16155 CCAGCATGAT
* * * * * *
16165 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGTTTAGCACGGATAT
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGTTTAGC-CGGATAT
16230 ATCACTAGCACGAA
65 ATCACTAGCACGAA
16244 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTT-GGGTTTAGCCGGATATA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGTTTAGCCGGATATA
16308 TCACTAGCACGAA
66 TCACTAGCACGAA
*
16321 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGG-TTTAG-CCGGATA
*
16386 CATCACTAGCACGAA
64 TATCACTAGCACGAA
*
16401 TGCTCTTCGGGACTTAGCCCGGAT-CATC
1 TGCTCTTCGGAACTTAGCCCGGATACATC
16429 GTCGAGACCT
Statistics
Matches: 173, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
77 68 0.39
78 12 0.07
79 49 0.28
80 44 0.25
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (78 bp):
TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGTTTAGCCGGATATA
TCACTAGCACGAA
Found at i:16362 original size:117 final size:116
Alignment explanation
Indices: 16183--16407 Score: 360
Period size: 117 Copynumber: 1.9 Consensus size: 116
16173 GGGACCTAGC
** *
16183 CCGGATATAACACCAGCACGAATGCTCTTCGGGTTTAGCACGGATATATCACTAGCACGAATGCT
1 CCGGATATAACACCAGCACGAATGCTCTTCGGACTTAGCACGGATACATCACTAGCACGAATGCT
*
16248 CTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTGGGTTTAG
66 CTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTTGGGTTTAG
* * * *
16299 CCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGC
1 CCGGATATAACACCAGCACGAATGCTCTTCGG-ACTTAGCACGGATACATCACTAGCACGAATGC
*
16364 TCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTT
65 TCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTT
16408 CGGGACTTAG
Statistics
Matches: 99, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
116 30 0.30
117 69 0.70
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (116 bp):
CCGGATATAACACCAGCACGAATGCTCTTCGGACTTAGCACGGATACATCACTAGCACGAATGCT
CTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTTGGGTTTAG
Found at i:19047 original size:47 final size:47
Alignment explanation
Indices: 18984--19287 Score: 430
Period size: 47 Copynumber: 6.4 Consensus size: 47
18974 CCCTTCGGGA
* * *
18984 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* * *
19031 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* *
19078 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* * *
19125 CTTATCACATATATACACTTTCACATTCATCACGTTGGTCACTCGAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* *
19172 CCTATCACATATATACACTTTCACATTCATCACGTTGGCCACTCGGAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGG-C
*
19220 C-TATCACATATATATATACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* *
19268 CCTATCACATATATATACTT
1 CTTATCACATATATACACTT
19288 GTACATCAAT
Statistics
Matches: 236, Mismatches: 17, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
47 190 0.81
48 4 0.02
49 42 0.18
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
Found at i:29998 original size:40 final size:40
Alignment explanation
Indices: 29800--30017 Score: 255
Period size: 40 Copynumber: 5.5 Consensus size: 40
29790 TGGATGATAA
* * *
29800 CCGGGCTAAGTCCCGAAGGAATTTGTGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
* ** * *
29840 CCGGGATAAGTTTCGAAGGCATTTGTGTGAGTTACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
29880 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
29920 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
29960 TCGGGCTATGTCCCGAAGGTATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
30000 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
30018 TACTTGGCTT
Statistics
Matches: 153, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
39 17 0.11
40 135 0.88
41 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:31890 original size:40 final size:40
Alignment explanation
Indices: 31842--32108 Score: 480
Period size: 40 Copynumber: 6.7 Consensus size: 40
31832 GCAAACACAT
* *
31842 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
31882 TTGCCTTCGGGTCTTAGCCCGGATATATCATCCCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
31922 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
31962 TTGCCTTCGGGTCTTAGCCCGGATATGTCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
32002 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
32042 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
32082 TTGCCTTCGGGTCTTAGCCCGGATATA
1 TTGCCTTCGGGTCTTAGCCCGGATATA
32109 ATCCAATGTT
Statistics
Matches: 217, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 217 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Done.