Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1564
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: 81332
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:22015 original size:79 final size:81
Alignment explanation
Indices: 21879--22061 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
21869 TCGAATGATG
* *
21879 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
21943 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
21958 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
22020 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
22038 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
22062 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:22077 original size:40 final size:40
Alignment explanation
Indices: 21880--22063 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
21870 CGAATGATGT
* * * *
21880 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
21920 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
21960 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
21998 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
22039 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
22064 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:22085 original size:79 final size:79
Alignment explanation
Indices: 21932--22096 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
21922 GGACTAAGAT
* **
21932 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
21997 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
22011 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
22074 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
22090 CCGAAGG
1 CCGAAGG
22097 TACGTGATTC
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.65
80 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:30227 original size:40 final size:39
Alignment explanation
Indices: 30089--30220 Score: 167
Period size: 40 Copynumber: 3.3 Consensus size: 39
30079 GGACTAAGAT
* *
30089 CCGAAGGCATCTGTGCGAGTTACTAATTCCGGGCTAAG-C
1 CCGAAGGCATTTGTGCGAGTTACTAA-ACCGGGCTAAGTC
* * *
30128 CCGAAGGCATTGGTGCGAGTTACTAAATTCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAA-CCGGGCTAAGTC
*
30168 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTACTA-AACCGGGCTAAGTC
*
30208 TCGAAGGCATTTG
1 CCGAAGGCATTTG
30221 AACGAGTAGC
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 32 0.40
40 46 0.57
41 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGTTACTAAACCGGGCTAAGTC
Found at i:30242 original size:79 final size:79
Alignment explanation
Indices: 30089--30253 Score: 183
Period size: 79 Copynumber: 2.1 Consensus size: 79
30079 GGACTAAGAT
* **
30089 CCGAAGGCATCTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATCTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
* *
30154 ATTCGGGTTAAGTC
66 ATTCCGGTTAAATC
* * * *
30168 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCTCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATCTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
30231 TATA-TCCGGTTAAATT
63 TAAATTCCGGTTAAATC
30247 CCGAAGG
1 CCGAAGG
30254 TACGTGATTT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.03
79 50 0.69
80 20 0.28
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATCTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATTCCGGTTAAATC
Found at i:46686 original size:46 final size:46
Alignment explanation
Indices: 46551--46770 Score: 193
Period size: 46 Copynumber: 4.7 Consensus size: 46
46541 ACTTGTGTGA
* * * * *
46551 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCACATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCATGACGAGT
* * * * *
46597 GCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCATTGA-GACGAGT
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CTCATGACGAGT
*
46645 GCTAGTGTAAGACATGTCTGGGAGATGCATCGGCCTCGA-GACGTAAGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTC-ATGACG--AGT
46693 -C-AGTGTAAGACATGTCTGGGACATGCATCGG-CT-ATGA-GATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCATGACGA-GT
* *
46735 GTTAGTGTAAGACCATGTCTGGGGCATAGCATCGGC
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
46771 ACAAATATGC
Statistics
Matches: 142, Mismatches: 19, Indels: 25
0.76 0.10 0.13
Matches are distributed among these distances:
41 1 0.01
42 2 0.01
43 2 0.01
44 11 0.08
45 16 0.11
46 59 0.42
47 25 0.18
48 25 0.18
49 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCATGACGAGT
Found at i:48226 original size:21 final size:21
Alignment explanation
Indices: 48185--48226 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
48175 AAGAAAGGAA
* **
48185 ATAATAAAAGAAATACTAAGG
1 ATAATAAAAGAAAAAAAAAGG
48206 ATAATAAAAGAAAAAAAAAGG
1 ATAATAAAAGAAAAAAAAAGG
48227 GTTATTACCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.69, C:0.02, G:0.14, T:0.14
Consensus pattern (21 bp):
ATAATAAAAGAAAAAAAAAGG
Found at i:49733 original size:28 final size:28
Alignment explanation
Indices: 49668--49818 Score: 223
Period size: 28 Copynumber: 5.4 Consensus size: 28
49658 GAGATTGGCG
* * * *
49668 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
49697 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
49725 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
49753 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
49781 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
49808 CTGAGTGTGCG
1 CTAAGTGTGCG
49819 GACTTAATAT
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
27 24 0.21
28 76 0.66
29 15 0.13
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:59384 original size:27 final size:27
Alignment explanation
Indices: 59354--59531 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
59344 ATATTGAGCC
* * *
59354 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCTACACAATCAAAT
* **
59381 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACACAATCAAAT
* * * *
59408 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACACAATCA-AAT
** *** *
59436 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACACAATCAAAT
* * **
59463 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CACAATCAAAT
* * * *
59490 CGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTACACAATCAAAT
59517 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
59532 GTACAATTTA
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACACAATCAAAT
Found at i:59447 original size:55 final size:55
Alignment explanation
Indices: 59354--59531 Score: 204
Period size: 54 Copynumber: 3.3 Consensus size: 55
59344 ATATTGAGCC
* * *
59354 CGCACACTCAGTGCTATACA-A-TCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTAT-CATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
* * *
59408 CGCACACTTAGTGCTA-CATAGTT-AGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATCATA-TTCA-ACTCGCACACTTAGTGCCACATAGTCAAAT
** * *
59463 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
59517 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
59532 GTACAATTTA
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 56 0.54
55 45 0.43
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:59493 original size:82 final size:81
Alignment explanation
Indices: 59375--59530 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
59365 TGCTATACAA
* * *
59375 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAG-TAGAATCGCA
59440 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
59457 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCA
59521 CACTTAGTGC
65 CACTTAGTGC
59531 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 20 0.31
82 45 0.69
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCAC
ACTTAGTGCCGCATGG
Done.