Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2095
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: 25403
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Found at i:1180 original size:40 final size:40
Alignment explanation
Indices: 1123--1372 Score: 249
Period size: 40 Copynumber: 6.3 Consensus size: 40
1113 CTAACGGGGT
* * * *
1123 TAAGTCCCGAAGACATTTGTGCTAGTGATTA-ATTCTGGGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTTACTATA-TCCGGGC
*
1163 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTTACTATATCCGGGC
* * *
1203 TAAGTCCTGAAGGCATTTAT-ATGAGTTACTA-ATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCT-AGTTACTATA-TCCGGGC
* *
1243 TAAGTCCCGAAGGCATTTGTACGAGTTACTATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTTACTATATCCGGGC
* * *
1283 TAAGTCTCGAAGGCATTTGTGCTAGTGACCATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTTACTATATCCGGGC
* * * * ***
1323 TAAGACCCGACGGC-CTTGTGCGAGTGGTTATATCC-GGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTTACTATATCCGGGC
*
1361 TAAATCCCGAAG
1 TAAGTCCCGAAG
1373 ATATTTGGGT
Statistics
Matches: 176, Mismatches: 29, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
38 12 0.07
39 17 0.10
40 145 0.82
41 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCTAGTTACTATATCCGGGC
Found at i:1320 original size:80 final size:79
Alignment explanation
Indices: 1123--1332 Score: 280
Period size: 80 Copynumber: 2.6 Consensus size: 79
1113 CTAACGGGGT
* * * *
1123 TAAGTCCCGAAGACATTTGTGCTAGTGATTAATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAG
1 TAAGT-CCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTACGAG
1188 TTACTATATCCGGGC
65 TTACTATATCCGGGC
* * *
1203 TAAGTCCTGAAGGCATTTAT-ATGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTACGA
1 TAAGTCC-GAAGGCATTTGTGCT-AGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTACGA
1267 GTTACTATATCCGGGC
64 GTTACTATATCCGGGC
* *
1283 TAAGTCTCGAAGGCATTTGTGCTAGTGAC-CATATCCGGGCTAAGACCCGA
1 TAAGTC-CGAAGGCATTTGTGCTAGTGACTAAT-TCCGGGCTAAGTCCCGA
1333 CGGCCTTGTG
Statistics
Matches: 113, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
79 5 0.04
80 106 0.94
81 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (79 bp):
TAAGTCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTACGAGT
TACTATATCCGGGC
Found at i:4097 original size:27 final size:27
Alignment explanation
Indices: 4067--4243 Score: 122
Period size: 27 Copynumber: 6.5 Consensus size: 27
4057 ATATTGAGCC
* * * *
4067 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCCACACAATCAAAT
**
4094 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCCACACAATCAAAT
* * **
4121 CGCACACTTAGTGCCACATAGTCCATCT
1 CGCACACTTAGTGCCACACAAT-CAAAT
*** *
4149 CGCACACTTAGTGCCACATGGTCAATT
1 CGCACACTTAGTGCCACACAATCAAAT
* * **
4176 CGCACACTTAGTG-CATCATATTCATTT
1 CGCACACTTAGTGCCA-CACAATCAAAT
* * * *
4203 CGCACACTGAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCCACACAATCAAAT
*
4230 CGCACCCTTAGTGC
1 CGCACACTTAGTGC
4244 TGTACAATTT
Statistics
Matches: 124, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
26 2 0.02
27 97 0.78
28 25 0.20
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.25
Consensus pattern (27 bp):
CGCACACTTAGTGCCACACAATCAAAT
Found at i:4159 original size:55 final size:55
Alignment explanation
Indices: 4067--4243 Score: 200
Period size: 54 Copynumber: 3.3 Consensus size: 55
4057 ATATTGAGCC
* * * * *
4067 CGCACACTCAGTGCTATACA-AT-CAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCCAT-CATATCCATCTCGCACACTTAGTGCCACATAGTCAAAT
* *
4121 CGCACACTTAGTGCCA-CATAGTCCATCTCGCACACTTAGTGCCACATGGTCAATT
1 CGCACACTTAGTGCCATCATA-TCCATCTCGCACACTTAGTGCCACATAGTCAAAT
* * * *
4176 CGCACACTTAGTG-CATCATATTCATTTCGCACACTGAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCCATCATATCCATCTCGCACACTTAGTGCCACATAGTCAAAT
*
4230 CGCACCCTTAGTGC
1 CGCACACTTAGTGC
4244 TGTACAATTT
Statistics
Matches: 104, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 57 0.55
55 44 0.42
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.25
Consensus pattern (55 bp):
CGCACACTTAGTGCCATCATATCCATCTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:4206 original size:82 final size:81
Alignment explanation
Indices: 4088--4243 Score: 197
Period size: 82 Copynumber: 1.9 Consensus size: 81
4078 TGCTATACAA
* * * **
4088 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCCACATAGTCCATCTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTGAGTGCAACATAGT-CAAATCGCA
4153 CACTTAGTGCCACATGG
65 CACTTAGTGCCACATGG
* * **
4170 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTGAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTGAGTGCAACATAGTCAAATCGCA
*
4234 CCCTTAGTGC
65 CACTTAGTGC
4244 TGTACAATTT
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
81 18 0.29
82 45 0.71
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTGAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCACATGG
Found at i:8553 original size:27 final size:26
Alignment explanation
Indices: 8517--8624 Score: 108
Period size: 27 Copynumber: 4.0 Consensus size: 26
8507 AGCGTCCTGC
*
8517 TGGCTATGCCACAATTATCTGATCTGG
1 TGGCTCTGCCAC-ATTATCTGATCTGG
*
8544 TGGCTCTGCCACATATATCTGTTCTGG
1 TGGCTCTGCCACAT-TATCTGATCTGG
* *
8571 TGGTTCTGCCACGATTATCTGTATTTGG
1 TGGCTCTGCCAC-ATTATCTG-ATCTGG
* * * *
8599 TGACTCTGTCATATTATCTGTTCTGG
1 TGGCTCTGCCACATTATCTGATCTGG
8625 CAGCCATGCT
Statistics
Matches: 67, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
26 6 0.09
27 47 0.70
28 14 0.21
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (26 bp):
TGGCTCTGCCACATTATCTGATCTGG
Found at i:16095 original size:24 final size:24
Alignment explanation
Indices: 16068--16113 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
16058 AACCCATTAC
*
16068 AGAATAAGAAACATTATCAGAACT
1 AGAATAAGAAACATAATCAGAACT
* *
16092 AGAATTAGAATCATAATCAGAA
1 AGAATAAGAAACATAATCAGAA
16114 TCAAAATCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.54, C:0.11, G:0.13, T:0.22
Consensus pattern (24 bp):
AGAATAAGAAACATAATCAGAACT
Found at i:16113 original size:12 final size:12
Alignment explanation
Indices: 16098--16153 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
16088 AACTAGAATT
*
16098 AGAATCATAATC
1 AGAATCAAAATC
16110 AGAATCAAAATC
1 AGAATCAAAATC
* *
16122 A-AGTGACAGAATC
1 AGAAT--CAAAATC
16135 AGAATCAAAATC
1 AGAATCAAAATC
*
16147 AGTATCA
1 AGAATCA
16154 GGTAACAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
11 2 0.06
12 24 0.69
13 7 0.20
14 2 0.06
ACGTcount: A:0.52, C:0.16, G:0.12, T:0.20
Consensus pattern (12 bp):
AGAATCAAAATC
Found at i:16162 original size:31 final size:31
Alignment explanation
Indices: 16098--16164 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
16088 AACTAGAATT
* * *
16098 AGAATCATAATCAGAATCAAAATCAAGTGAC
1 AGAATCAGAATCAAAATCAAAATCAAGTAAC
** *
16129 AGAATCAGAATCAAAATCAGTATCAGGTAAC
1 AGAATCAGAATCAAAATCAAAATCAAGTAAC
16160 AGAAT
1 AGAAT
16165 TAAAATTAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.19
Consensus pattern (31 bp):
AGAATCAGAATCAAAATCAAAATCAAGTAAC
Found at i:16600 original size:27 final size:27
Alignment explanation
Indices: 16570--16672 Score: 134
Period size: 27 Copynumber: 3.8 Consensus size: 27
16560 GGGGCAAAAT
* * *
16570 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
16597 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
16624 GATAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
16651 AGTAATTCTACCCTACAAGGGT
1 GGTAATTCTACCCTACAAGGGT
16673 TGTAACACCC
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.32
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:18357 original size:29 final size:29
Alignment explanation
Indices: 18323--18483 Score: 261
Period size: 29 Copynumber: 5.6 Consensus size: 29
18313 TAATCAACCG
* * *
18323 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTCAGTGCCATGCA-TTTCAAGCT
*
18352 CGCACACTTAGTGCCATGCATTTCAAGCT
1 CGCACACTCAGTGCCATGCATTTCAAGCT
18381 CGCACACTCAGTGCCATGCATTTCAAGCT
1 CGCACACTCAGTGCCATGCATTTCAAGCT
18410 CGCACACTCAGTGCCATGCATTTCAAGCT
1 CGCACACTCAGTGCCATGCATTTCAAGCT
*
18439 CGCACACTCAGTGACATGCATTTCAAGCT
1 CGCACACTCAGTGCCATGCATTTCAAGCT
18468 CGCACACTCAGTGCCA
1 CGCACACTCAGTGCCA
18484 ATCTCTCAAC
Statistics
Matches: 126, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
28 3 0.02
29 123 0.98
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (29 bp):
CGCACACTCAGTGCCATGCATTTCAAGCT
Done.