Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4618.1
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: 51248
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Warning! 267 characters in sequence are not A, C, G, or T
Found at i:5619 original size:28 final size:28
Alignment explanation
Indices: 5556--5653 Score: 171
Period size: 28 Copynumber: 3.5 Consensus size: 28
5546 ATATTAAGTC
*
5556 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
5583 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
5611 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
5639 CGCACACCTAGTGCT
1 CGCACACTTAGTGCT
5654 GTACAATTTA
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 22 0.32
28 46 0.68
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:5953 original size:28 final size:28
Alignment explanation
Indices: 5890--6155 Score: 446
Period size: 28 Copynumber: 9.5 Consensus size: 28
5880 ATATTAAGTC
* *
5890 CGCACACTCAGTGTTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
5917 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
5945 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
5973 CGCACACTTAGTGCTATATAATCAAAC-
1 CGCACACTTAGTGCTATATAATCAAACT
6000 CGGCACACTTAGTGCTATATAATCAAACT
1 C-GCACACTTAGTGCTATATAATCAAACT
6029 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
6057 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
6085 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
6113 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
6142 CGCACACTTAGTGC
1 CGCACACTTAGTGC
6156 CAATCTCATG
Statistics
Matches: 229, Mismatches: 6, Indels: 6
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.10
28 187 0.82
29 20 0.09
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:9217 original size:46 final size:46
Alignment explanation
Indices: 9164--9254 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
9154 TATATATACA
* * *
9164 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATCTCACATTAACCATTCGGCTTTACCACATATC
* * *
9210 CATCTCATACACATTTCGCATTAACCATTCGGCTTTCCCACATAT
1 CATCTCATACACATCTCACATTAACCATTCGGCTTTACCACATAT
9255 ATACACTTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.27, C:0.32, G:0.07, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATCTCACATTAACCATTCGGCTTTACCACATATC
Found at i:9299 original size:47 final size:47
Alignment explanation
Indices: 9234--9700 Score: 630
Period size: 47 Copynumber: 9.9 Consensus size: 47
9224 TTCGCATTAA
* ** * *
9234 CCATTCGGCTTTCCCACATATATACACT-TCCACGTTCATCACATTGG
1 CCATTCGGCCTTATCACATATATACA-TGTTCACATTCATCACATTGG
* * *
9281 CCATTCTGCCTTATCACATATATGCATGTTCACATTTATCACATTGG
1 CCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGG
* * * * *
9328 CCATTCTGCCTTATCACATATATGCATGCTCATATTTATCACATTGG
1 CCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGG
* * * *
9375 CCATTTGGCCTTATCACATATGTGCATGTTCATATTCATCACATTGG
1 CCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGG
* *
9422 CCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTGG
1 CCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGG
*
9469 CCATTCGGCCTTATCACATATGTACATGTTCACATTCATCACATTGG
1 CCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGG
*
9516 CCATTCGGCCTTATCACATATGTACATGTTCACATTCATCACATTGG
1 CCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGG
*
9563 CCATTCGGCCTTATCACATATGTACATGTTCACATTCATCACATTGG
1 CCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGG
* * * *
9610 CCATTCGGCCTTATCACACAAATGCATGTTCACATTCATCACATTTG
1 CCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGG
* * ** * *
9657 CCATTCGGCCTTAGCTCATATATACACATTGACATCCATCACAT
1 CCATTCGGCCTTATCACATATATACATGTTCACATTCATCACAT
9701 AAAATCCTAA
Statistics
Matches: 383, Mismatches: 36, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
46 1 0.00
47 382 1.00
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.34
Consensus pattern (47 bp):
CCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGG
Found at i:11364 original size:26 final size:25
Alignment explanation
Indices: 11334--11392 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
11324 TTTATGTCAT
*
11334 TAAATAAAAAAAGTTTAAAAATATAA
1 TAAATAAAAAAA-TTTAAAAACATAA
* *
11360 TAAATCAAATATATTTAAAAACATAA
1 TAAAT-AAAAAAATTTAAAAACATAA
11386 -AAATAAA
1 TAAATAAA
11393 TATTAAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 3 0.10
25 4 0.14
26 17 0.59
27 5 0.17
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (25 bp):
TAAATAAAAAAATTTAAAAACATAA
Found at i:11407 original size:22 final size:22
Alignment explanation
Indices: 11366--11424 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
11356 ATAATAAATC
* *
11366 AAATATAT-TTAAAA-ACATAA
1 AAATAAATATTAAAACAAATAA
11386 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
*
11408 AAAT-AATACTAAAACAA
1 AAATAAATATTAAAACAA
11425 TTCTTAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 18 0.53
22 9 0.26
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:11501 original size:15 final size:16
Alignment explanation
Indices: 11471--11503 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
11461 AAATGGTTAT
11471 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
11488 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
11503 A
1 A
11504 AAAATATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:16587 original size:93 final size:93
Alignment explanation
Indices: 16472--16642 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
16462 GCCCATAAGT
* *
16472 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
16537 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
16565 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
16630 CGAGTTCGGATGC
66 CGAGTTCGGATGC
16643 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:16639 original size:46 final size:46
Alignment explanation
Indices: 16464--16639 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
16454 TGTAACCCGC
* * *
16464 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
16510 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* * *
16560 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
16603 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
16640 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 64 0.58
47 29 0.26
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:23649 original size:5 final size:5
Alignment explanation
Indices: 23639--23667 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
23629 TTTTTCTTGC
23639 AATTT AATTT AATTT AATTT AATTT AATT
1 AATTT AATTT AATTT AATTT AATTT AATT
23668 ATTTATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
AATTT
Found at i:31941 original size:40 final size:40
Alignment explanation
Indices: 31769--31934 Score: 237
Period size: 40 Copynumber: 4.2 Consensus size: 40
31759 AACCCAAGTA
* * * *
31769 CCTTCGGGATTTAG-CTGGATATAG-CAACTCGGACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* * *
31808 CCTTTGGGACTTAGCCCGGATATAGTAACTAGCACAGATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
31848 CCTTCGGGACTTAGCCTGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
31888 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
31928 CCTTCGG
1 CCTTCGG
31935 ATCTTAGTCC
Statistics
Matches: 113, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
39 12 0.11
40 101 0.89
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:34142 original size:27 final size:27
Alignment explanation
Indices: 34112--34289 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
34102 ATATTGAGTC
* * * *
34112 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
34139 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
34166 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
34194 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
34221 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
34248 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
34275 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
34290 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:34251 original size:82 final size:81
Alignment explanation
Indices: 34133--34288 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
34123 TGCTATATAA
* *
34133 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
34198 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
34215 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
34279 CACTTAGTGC
65 CACTTAGTGC
34289 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:36710 original size:13 final size:13
Alignment explanation
Indices: 36692--36717 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36682 ATTTTTATTT
36692 TTAACATAAAATA
1 TTAACATAAAATA
36705 TTAACATAAAATA
1 TTAACATAAAATA
36718 ATTATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACATAAAATA
Found at i:41095 original size:10 final size:11
Alignment explanation
Indices: 41053--41095 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
41043 TAGAAAAGCG
41053 AAAGGAGCCAA
1 AAAGGAGCCAA
*
41064 AAACGAGCCAA
1 AAAGGAGCCAA
*
41075 AAAGG-GACAA
1 AAAGGAGCCAA
41085 AAAGGA-CCAA
1 AAAGGAGCCAA
41095 A
1 A
41096 TTGAGAAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 13 0.48
11 14 0.52
ACGTcount: A:0.58, C:0.19, G:0.23, T:0.00
Consensus pattern (11 bp):
AAAGGAGCCAA
Found at i:46043 original size:39 final size:39
Alignment explanation
Indices: 45879--46061 Score: 170
Period size: 40 Copynumber: 4.6 Consensus size: 39
45869 TTGAATGCTG
* * * * * * *
45879 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTATGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * * *
45919 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTATG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
* **
45959 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTATGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
45999 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
46038 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTATGTCCCGAAGGCATT
46062 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.31
40 74 0.61
41 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:46081 original size:79 final size:80
Alignment explanation
Indices: 45915--46096 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 80
45905 GCTAAGTGAA
* * * *
45915 TATATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGG
1 TATATCCGGGTTAAG-TCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGG
** ** *
45979 CATTCGTGCGAGTTGT
65 CATTCGAACGAGGAGC
* * * * *
45995 TAAATCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
*
46059 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
*
46074 TATATCC-GGTTAAATCCCGAAGG
1 TATATCCGGGTTAAGTCCCGAAGG
46097 TACGTGATTT
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
78 14 0.17
79 50 0.60
80 19 0.23
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Done.