Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CCACVL1_21438
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: 4638
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Found at i:1211 original size:15 final size:15
Alignment explanation
Indices: 1191--1220 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1181 AAACTGATAA
1191 AGGAGGTGAAAAAGG
1 AGGAGGTGAAAAAGG
1206 AGGAGGTGAAAAAGG
1 AGGAGGTGAAAAAGG
1221 CGAGGGCTCA
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:0.47, C:0.00, G:0.47, T:0.07
Consensus pattern (15 bp):
AGGAGGTGAAAAAGG
Found at i:1225 original size:14 final size:15
Alignment explanation
Indices: 1193--1225 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1183 ACTGATAAAG
*
1193 GAGGTGAAAAAGGAG
1 GAGGTGAAAAAGGAC
1208 GAGGTGAAAAAGG-C
1 GAGGTGAAAAAGGAC
1222 GAGG
1 GAGG
1226 GCTCATCAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.42, C:0.03, G:0.48, T:0.06
Consensus pattern (15 bp):
GAGGTGAAAAAGGAC
Found at i:3782 original size:333 final size:333
Alignment explanation
Indices: 3176--3916 Score: 1130
Period size: 333 Copynumber: 2.2 Consensus size: 333
3166 AAGGATTCTA
** *
3176 ATTGGAACTCAGGACCTGGAGATGCAAGCCAGAATTCAGGTTGGGGCAAGAAAAGCAATTGGAAC
1 ATTGGAACTCAGGACCTGGAGATGCAAGCCAGGGTTCAGGTTGGGGCCAGAAAAGCAATTGGAAC
* * *
3241 TCAGGG-AGTGCAAACCAGGATCCAGGTTGCGGTAAGAAAAATGATTCAAACTTTGGATCTGATA
66 T-AGGGAAGTGCAAACCAGGATCAAGGTTGCGGCAAGAAAAATAATTCAAACTTTGGATCTGATA
** * *
3305 ATGCAACCGAAGATTCTAGTTGGGGAAGGAAAAATGACTGGAAATCAGGATCTGCAGATGCAAAT
130 ATGCAACAAAAGATTCTAGTTGGGGAAAGAAAAATGACTGGAAATCAGGAACTGCAGATGCAAAT
* * *
3370 CAGAATTCAAACTGGGGTAAGAAAAGTAGTTGGGGTGCTGGAACCGGTGATTCTGGCCAAGACTC
195 CAGAATTCAAACTGGGGCAAGAAAAGTAGCTGGGGTGCTGGAACCAGTGATTCTGGCCAAGACTC
*
3435 TGGGGGTAAAAAGGGGAATTGGAACTCTGGTTCTGGTGGTGCAGGCCATGATTCAGGGTGGGGCA
260 TGGGGGTAAAAAGGGGAATTGGAACTCTGGTTCTGGTGGTGCAGGCCAGGATTCAGGGTGGGGCA
3500 AGAAAAGCG
325 AGAAAAGCG
* * * * *
3509 ATTGGAAATCAGAAGCTGGAGATGCAAGCCAGGGGTCGGGTTGGGGCCAGAAAAGCAATTGGAAC
1 ATTGGAACTCAGGACCTGGAGATGCAAGCCAGGGTTCAGGTTGGGGCCAGAAAAGCAATTGGAAC
* * * *
3574 TTGGGAAGTGCAAACCAGGATCAAGGTTG-GGCCAAGAAAAATAATTCAGATTTTGGATCTGATG
66 TAGGGAAGTGCAAACCAGGATCAAGGTTGCGG-CAAGAAAAATAATTCAAACTTTGGATCTGATA
* * *
3638 ATGCAACAAAAGATTCTAGTTGGGGAAAGAAAAATGACTCTG-ATTCAGGAACTGGAGATGCAAA
130 ATGCAACAAAAGATTCTAGTTGGGGAAAGAAAAATGACT-GGAAATCAGGAACTGCAGATGCAAA
3702 TCAGAATTCAAACTGGGGCACA-AAAAGTAGCTGGGGTGCTGGAACCAGTGATTCTGGCCAAGAC
194 TCAGAATTCAAACTGGGGCA-AGAAAAGTAGCTGGGGTGCTGGAACCAGTGATTCTGGCCAAGAC
* *
3766 TCTTGGGGTAAAAAGGGGAATTGGAACTCTGGTTCTGGTGGTGCAGGCCAGGATTCAGGTTGGGG
258 TCTGGGGGTAAAAAGGGGAATTGGAACTCTGGTTCTGGTGGTGCAGGCCAGGATTCAGGGTGGGG
3831 CAAGAAAAGCG
323 CAAGAAAAGCG
* * *
3842 ACTGGAACTCGGGACCTGGAGGTGCAAGCCAGGGTTCAGGTTGGGGCCAGAAAAGCAATTGGAAC
1 ATTGGAACTCAGGACCTGGAGATGCAAGCCAGGGTTCAGGTTGGGGCCAGAAAAGCAATTGGAAC
*
3907 TCGGGAAGTG
66 TAGGGAAGTG
3917 GAAATGAAGA
Statistics
Matches: 367, Mismatches: 37, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
332 5 0.01
333 360 0.98
334 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.33, T:0.20
Consensus pattern (333 bp):
ATTGGAACTCAGGACCTGGAGATGCAAGCCAGGGTTCAGGTTGGGGCCAGAAAAGCAATTGGAAC
TAGGGAAGTGCAAACCAGGATCAAGGTTGCGGCAAGAAAAATAATTCAAACTTTGGATCTGATAA
TGCAACAAAAGATTCTAGTTGGGGAAAGAAAAATGACTGGAAATCAGGAACTGCAGATGCAAATC
AGAATTCAAACTGGGGCAAGAAAAGTAGCTGGGGTGCTGGAACCAGTGATTCTGGCCAAGACTCT
GGGGGTAAAAAGGGGAATTGGAACTCTGGTTCTGGTGGTGCAGGCCAGGATTCAGGGTGGGGCAA
GAAAAGCG
Found at i:3848 original size:57 final size:57
Alignment explanation
Indices: 3800--3912 Score: 172
Period size: 57 Copynumber: 2.0 Consensus size: 57
3790 AACTCTGGTT
* * *
3800 CTGGTGGTGCAGGCCAGGATTCAGGTTGGGGCAAGAAAAGCGACTGGAACTCGGGAC
1 CTGGAGGTGCAAGCCAGGATTCAGGTTGGGGCAAGAAAAGCAACTGGAACTCGGGAC
* * *
3857 CTGGAGGTGCAAGCCAGGGTTCAGGTTGGGGCCAGAAAAGCAATTGGAACTCGGGA
1 CTGGAGGTGCAAGCCAGGATTCAGGTTGGGGCAAGAAAAGCAACTGGAACTCGGGA
3913 AGTGGAAATG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.26, C:0.19, G:0.40, T:0.16
Consensus pattern (57 bp):
CTGGAGGTGCAAGCCAGGATTCAGGTTGGGGCAAGAAAAGCAACTGGAACTCGGGAC
Found at i:4100 original size:30 final size:30
Alignment explanation
Indices: 4066--4137 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
4056 TGGTTTTGGC
*
4066 GGTAGAGATGGCGATGGAGAAAGCTATGGA
1 GGTAGAGGTGGCGATGGAGAAAGCTATGGA
4096 GGTAGAGGTGGCGATGGAGAAAGCTATGGA
1 GGTAGAGGTGGCGATGGAGAAAGCTATGGA
4126 GGTAGAGGTGGC
1 GGTAGAGGTGGC
4138 TACAGAGGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.29, C:0.07, G:0.47, T:0.17
Consensus pattern (30 bp):
GGTAGAGGTGGCGATGGAGAAAGCTATGGA
Found at i:4177 original size:30 final size:30
Alignment explanation
Indices: 4142--4271 Score: 224
Period size: 30 Copynumber: 4.3 Consensus size: 30
4132 GGTGGCTACA
* *
4142 GAGGTAGAGGTGGTGACAGGGGAGGATTTA
1 GAGGTAGAGGTGGCGACAGGGGAGGATTTG
4172 GAGGTAGAGGTGGCGACAGGGGAGGATTTG
1 GAGGTAGAGGTGGCGACAGGGGAGGATTTG
*
4202 GAGGTAGAGGTGGTGACAGGGGAGGATTTG
1 GAGGTAGAGGTGGCGACAGGGGAGGATTTG
*
4232 GAGGTAGAGGTGGCGACGGGGGAGGATTTG
1 GAGGTAGAGGTGGCGACAGGGGAGGATTTG
4262 GAGGTAGAGG
1 GAGGTAGAGG
4272 ACGTGGAAGG
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 95 1.00
ACGTcount: A:0.24, C:0.05, G:0.54, T:0.18
Consensus pattern (30 bp):
GAGGTAGAGGTGGCGACAGGGGAGGATTTG
Found at i:4467 original size:36 final size:36
Alignment explanation
Indices: 4426--4533 Score: 207
Period size: 36 Copynumber: 3.0 Consensus size: 36
4416 GAAGGACCAA
4426 GGACAGAGCTCTGGTGGAGGTTGGGGTAGCCAAGGT
1 GGACAGAGCTCTGGTGGAGGTTGGGGTAGCCAAGGT
*
4462 GGACAGAGCTCTGGTGGAGGTTGGGGTAGCCAAGGC
1 GGACAGAGCTCTGGTGGAGGTTGGGGTAGCCAAGGT
4498 GGACAGAGCTCTGGTGGAGGTTGGGGTAGCCAAGGT
1 GGACAGAGCTCTGGTGGAGGTTGGGGTAGCCAAGGT
4534 TCTGGAGATC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 70 1.00
ACGTcount: A:0.19, C:0.15, G:0.47, T:0.19
Consensus pattern (36 bp):
GGACAGAGCTCTGGTGGAGGTTGGGGTAGCCAAGGT
Done.