Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold665
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: 27575
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1483 original size:15 final size:15
Alignment explanation
Indices: 1460--1490 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1450 TCAAAAATTA
1460 CAATACAAAACATAT
1 CAATACAAAACATAT
*
1475 CAATCCAAAACATAT
1 CAATACAAAACATAT
1490 C
1 C
1491 TTTCATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (15 bp):
CAATACAAAACATAT
Found at i:3140 original size:18 final size:18
Alignment explanation
Indices: 3117--3154 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
3107 CAAAATCACT
3117 TAACAA-AATACTTATAAA
1 TAACAACAATACTT-TAAA
3135 TAACAACTAATACTTTAAA
1 TAACAAC-AATACTTTAAA
3154 T
1 T
3155 TCATCATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 5 0.28
20 7 0.39
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (18 bp):
TAACAACAATACTTTAAA
Found at i:5615 original size:35 final size:35
Alignment explanation
Indices: 5575--5733 Score: 192
Period size: 35 Copynumber: 4.5 Consensus size: 35
5565 TTATGTACAT
5575 ATGTGATGATATATTGAACTTGTATATTTGGCCAC
1 ATGTGATGATATATTGAACTTGTATATTTGGCCAC
* * * * *
5610 ATGTGATGTTATATTAAACTTGAATATTTGACTAC
1 ATGTGATGATATATTGAACTTGTATATTTGGCCAC
* ** * *
5645 ATGTGATGTTATATTGAACTTGTATATTCAGTCAT
1 ATGTGATGATATATTGAACTTGTATATTTGGCCAC
* * *
5680 ATATGATGATATATTGTACTTGTATATTTGGCCAT
1 ATGTGATGATATATTGAACTTGTATATTTGGCCAC
*
5715 ATGTGATGATATAATGAAC
1 ATGTGATGATATATTGAAC
5734 CTTGAGTATT
Statistics
Matches: 102, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 102 1.00
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (35 bp):
ATGTGATGATATATTGAACTTGTATATTTGGCCAC
Found at i:9147 original size:55 final size:54
Alignment explanation
Indices: 9086--9265 Score: 279
Period size: 55 Copynumber: 3.3 Consensus size: 54
9076 ATATTAAGTC
* * *
9086 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCA-ACT
*
9141 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATC-AACT
* *
9196 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAATCAACT
9251 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
9266 GCACAATTTA
Statistics
Matches: 117, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
55 90 0.77
56 27 0.23
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAACT
Found at i:9150 original size:28 final size:27
Alignment explanation
Indices: 9086--9265 Score: 279
Period size: 28 Copynumber: 6.6 Consensus size: 27
9076 ATATTAAGTC
* * *
9086 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
9113 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCA-ACT
9141 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
9168 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
9196 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
* *
9224 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
9251 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
9266 GCACAATTTA
Statistics
Matches: 146, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.45
28 80 0.55
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:9206 original size:83 final size:82
Alignment explanation
Indices: 9086--9265 Score: 288
Period size: 83 Copynumber: 2.2 Consensus size: 82
9076 ATATTAAGTC
* * *
9086 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACTCGCACACTTA
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
9151 GTGCTACATAGTCAACT
66 GTGCTACATAGTCAACT
* *
9168 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTT
* *
9233 AGTGCTACATATTCAATT
65 AGTGCTACATAGTCAACT
9251 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
9266 GCACAATTTA
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
82 20 0.22
83 70 0.78
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (82 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
GTGCTACATAGTCAACT
Found at i:17339 original size:55 final size:55
Alignment explanation
Indices: 17278--17455 Score: 257
Period size: 55 Copynumber: 3.2 Consensus size: 55
17268 ATATTAAGTC
* * * *
17278 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
17333 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * *
17388 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAA-TCAAACT
17445 CGCACACTTAG
1 CGCACACTTAG
17456 CGCCAATCTC
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
55 73 0.66
56 22 0.20
57 16 0.14
ACGTcount: A:0.31, C:0.30, G:0.13, T:0.25
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:17342 original size:28 final size:27
Alignment explanation
Indices: 17278--17430 Score: 243
Period size: 28 Copynumber: 5.6 Consensus size: 27
17268 ATATTAAGTC
* * *
17278 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
17305 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCA-ACT
17333 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
17360 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
17388 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
17416 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
17431 GCACAATTTA
Statistics
Matches: 121, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
27 48 0.40
28 73 0.60
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:19868 original size:15 final size:15
Alignment explanation
Indices: 19850--19879 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
19840 GTATGCGAGA
19850 AATGGTTATGAAGCT
1 AATGGTTATGAAGCT
19865 AATGGTTATGAAGCT
1 AATGGTTATGAAGCT
19880 TACTTTGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (15 bp):
AATGGTTATGAAGCT
Found at i:22748 original size:74 final size:74
Alignment explanation
Indices: 22627--22773 Score: 240
Period size: 74 Copynumber: 2.0 Consensus size: 74
22617 GAGGAAAAAT
*
22627 CGATTCGTACTCTTGCTAATGAGATTAAAGAGTTACGAAATAAGAAAATTCCATTGGTTAAAGCA
1 CGATTCGTACTCTGGCTAATGAGATTAAAGAGTTACGAAATAAGAAAATTCCATTGGTTAAAGCA
22692 CTGTGGCAC
66 CTGTGGCAC
* * * * *
22701 CGATTTGTATTCTGGCTCATGAGATTAAAGAGTTACGAAATAAGAAAATTTCATTGGTTAAAGTA
1 CGATTCGTACTCTGGCTAATGAGATTAAAGAGTTACGAAATAAGAAAATTCCATTGGTTAAAGCA
22766 CTGTGGCA
66 CTGTGGCA
22774 TAAACACGGA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 67 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.31
Consensus pattern (74 bp):
CGATTCGTACTCTGGCTAATGAGATTAAAGAGTTACGAAATAAGAAAATTCCATTGGTTAAAGCA
CTGTGGCAC
Found at i:24424 original size:35 final size:35
Alignment explanation
Indices: 24384--24542 Score: 174
Period size: 35 Copynumber: 4.5 Consensus size: 35
24374 GTATGTACAT
24384 ATGTGATGATATATTGAACTTGTATATTTGGCCAC
1 ATGTGATGATATATTGAACTTGTATATTTGGCCAC
* * * * *
24419 ATGTGATGTTATATTAAACTTGAATATTTGACTAC
1 ATGTGATGATATATTGAACTTGTATATTTGGCCAC
* * * * * *
24454 ATTTGATGTTATATTGAGCTTGTATATTCGGTCAT
1 ATGTGATGATATATTGAACTTGTATATTTGGCCAC
* * * *
24489 ATATGATGATATATTGTACTTGTATTTTTGGCCAT
1 ATGTGATGATATATTGAACTTGTATATTTGGCCAC
*
24524 ATGTGATGATATAATGAAC
1 ATGTGATGATATATTGAAC
24543 ATTGAGTATT
Statistics
Matches: 100, Mismatches: 24, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 100 1.00
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (35 bp):
ATGTGATGATATATTGAACTTGTATATTTGGCCAC
Found at i:24531 original size:70 final size:70
Alignment explanation
Indices: 24381--24558 Score: 187
Period size: 70 Copynumber: 2.5 Consensus size: 70
24371 TTGGTATGTA
* * *
24381 CATATGTGATGATATATTGAACTTGTATATTTGGCCACATGTGATGTTATATTAAACTTGAATAT
1 CATATGTGATGATATATTGAACTTGTATATTCGGCCACATATGATGATATATTAAACTTGAATAT
24446 TTGAC
66 TTGAC
* * * * * * * ** * *
24451 TACATTTGATGTTATATTGAGCTTGTATATTCGGTCATATATGATGATATATTGTACTTGTATTT
1 CATATGTGATGATATATTGAACTTGTATATTCGGCCACATATGATGATATATTAAACTTGAATAT
*
24516 TTGGC
66 TTGAC
*
24521 CATATGTGATGATATAATGAACATTG-AGTATTCGGCCA
1 CATATGTGATGATATATTGAAC-TTGTA-TATTCGGCCA
24559 TACAAGTAAG
Statistics
Matches: 84, Mismatches: 22, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
70 72 0.86
71 12 0.14
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (70 bp):
CATATGTGATGATATATTGAACTTGTATATTCGGCCACATATGATGATATATTAAACTTGAATAT
TTGAC
Done.