Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2531
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: 24484
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Found at i:4071 original size:39 final size:40
Alignment explanation
Indices: 4013--4112 Score: 98
Period size: 40 Copynumber: 2.6 Consensus size: 40
4003 AATCAAGCAT
* * *
4013 CTTCGGGT-TT-AGCCGGATATAACCACTCGCA-CAAGGC
1 CTTCGGGTCTTAACCCGGATATAACCACTAGCATAAAGGC
*** *
4050 CTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAACCCGGATATAACCACTAGCATAAAGGC
* *
4090 CTTCGGGACTTAGCCCGGATATA
1 CTTCGGGTCTTAACCCGGATATA
4113 GTCTAGCACA
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
37 8 0.16
38 2 0.04
39 16 0.32
40 24 0.48
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAACCCGGATATAACCACTAGCATAAAGGC
Found at i:4128 original size:38 final size:39
Alignment explanation
Indices: 4048--4190 Score: 173
Period size: 38 Copynumber: 3.6 Consensus size: 39
4038 CTCGCACAAG
* * * *
4048 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTC-CTAGCACAAAT
4088 GCCTTCGGGACTTAGCCCGGATATAGT-CTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCCTAGCACAAAT
* * *
4126 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTC-C-TAGCACAAAT
4167 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
4191 CATTCGAGTA
Statistics
Matches: 89, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
37 3 0.03
38 31 0.35
40 25 0.28
41 27 0.30
42 3 0.03
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (39 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCCTAGCACAAAT
Found at i:16512 original size:22 final size:22
Alignment explanation
Indices: 16484--16605 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
16474 TTCCACATCC
16484 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
16506 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
16530 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
16553 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
16577 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
16600 ATCACA
1 ATCACA
16606 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:16629 original size:25 final size:25
Alignment explanation
Indices: 16600--16677 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
16590 ATTCGGCCTT
16600 ATCACACATACACATGTTCACATTC
1 ATCACACATACACATGTTCACATTC
* * *
16625 ATCACA-TTGGC-CA--TTCAGCCTT-
1 ATCACACAT-ACACATGTTCA-CATTC
16647 ATCACACATACACATGTTCACATTC
1 ATCACACATACACATGTTCACATTC
16672 ATCACA
1 ATCACA
16678 TTGGCCATTC
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 11 0.28
23 6 0.15
24 6 0.15
25 17 0.43
ACGTcount: A:0.33, C:0.32, G:0.06, T:0.28
Consensus pattern (25 bp):
ATCACACATACACATGTTCACATTC
Found at i:16852 original size:49 final size:47
Alignment explanation
Indices: 16456--17053 Score: 907
Period size: 47 Copynumber: 12.6 Consensus size: 47
16446 CCCTTCGGGA
* * *
16456 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
16503 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
16550 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
16597 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCAGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
16644 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
16691 CTTATCACATATATACACTTT-ACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* ** *
16737 CTTATCACATATATACACTTTCATATTCATCACACCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
16784 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
16831 CTTATCACATATGTATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATA--TATACACTTTCACATTCATCACATTGGCCATTCGGC
16880 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
16929 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
16978 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
17027 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
17054 TATTCAAATA
Statistics
Matches: 521, Mismatches: 23, Indels: 14
0.93 0.04 0.03
Matches are distributed among these distances:
46 47 0.09
47 288 0.55
48 1 0.00
49 182 0.35
51 3 0.01
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:18565 original size:56 final size:56
Alignment explanation
Indices: 18498--18617 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
18488 TATTAGTTTA
18498 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
18554 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
18610 TTGCCCAT
1 TTGCCCAT
18618 CATCCCTTGC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:21057 original size:46 final size:46
Alignment explanation
Indices: 21007--21182 Score: 175
Period size: 46 Copynumber: 3.8 Consensus size: 46
20997 TGGTTGAGCA
21007 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
21053 TCCGAACTCGTTGATTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
21098 TATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
21146 -CTC-AAGCTCGTTGAGTTGAGTCTGAGTTCGCTTATGG
1 TC-CGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
21183 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 13, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 6 0.06
46 57 0.54
47 27 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:21165 original size:93 final size:93
Alignment explanation
Indices: 21006--21175 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
20996 ATGGTTGAGC
* * *
21006 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGATTTG
1 ATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGTTG
21071 AGTCCGAGTTCGTGAGATGTAACTAGGT
66 AGTCCGAGTTCGTGAGATGTAACTAGGT
21099 ATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACG-CTC-AAGCTCGTTGAGT
1 ATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGTC-CGAA-CTCGTTGAGT
*
21162 TGAGTCTGAGTTCG
64 TGAGTCCGAGTTCG
21176 CTTATGGGCG
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
92 3 0.04
93 68 0.96
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (93 bp):
ATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGTTG
AGTCCGAGTTCGTGAGATGTAACTAGGT
Done.