Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1578
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: 17968
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.32
Found at i:1617 original size:29 final size:27
Alignment explanation
Indices: 1599--1668 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
1589 ATATTAAGTC
1599 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
1626 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
1654 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
1669 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:1662 original size:28 final size:28
Alignment explanation
Indices: 1599--1696 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
1589 ATATTAAGTC
*
1599 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
1626 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
1654 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
1683 CGCACACTTAGTGC
1 CGCACACTTAGTGC
1697 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:12184 original size:29 final size:27
Alignment explanation
Indices: 12166--12235 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
12156 ATATTAAGTC
12166 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
12193 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
12221 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
12236 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:12229 original size:28 final size:28
Alignment explanation
Indices: 12166--12263 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
12156 ATATTAAGTC
*
12166 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
12193 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
12221 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
12250 CGCACACTTAGTGC
1 CGCACACTTAGTGC
12264 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:14338 original size:46 final size:45
Alignment explanation
Indices: 14271--14439 Score: 196
Period size: 46 Copynumber: 3.7 Consensus size: 45
14261 GTAACCCGCC
* *
14271 CATAAGTGAACTCGGACTCAACTCAATGAGCTCAGGCGTTCGCATA
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGCATTCGCATA
* *
14317 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-ATGCCCAGTTA
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCA--TA
*** * * *
14363 CATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATC
1 CATAAGT-GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATA
14410 CATAAGTGAACTCGGACTCAACTCAACGAG
1 CATAAGTGAACTCGGACTCAACTCAACGAG
14440 TTCGAATGCC
Statistics
Matches: 103, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
44 4 0.04
45 2 0.02
46 61 0.59
47 32 0.31
49 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (45 bp):
CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATA
Found at i:14385 original size:93 final size:93
Alignment explanation
Indices: 14278--14451 Score: 269
Period size: 93 Copynumber: 1.9 Consensus size: 93
14268 GCCCATAAGT
* *
14278 GAACTCGGACTCAACTCAATGAGCTCAGG-CGTTCGCATACATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATACATAAGTGAACTCGGACTCAACTCA
*
14342 ACGAGCTCGGATGCCCAGTTACATCTCTC
65 ACGAGCTCGAATGCCCAGTTACATCTCTC
* * *
14371 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATACATAAGTGAACTCGGACTCAACTCAA
*
14436 CGAGTTCGAATGCCCA
66 CGAGCTCGAATGCCCA
14452 AACATCCTAG
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATACATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGAATGCCCAGTTACATCTCTC
Found at i:14464 original size:46 final size:46
Alignment explanation
Indices: 14321--14464 Score: 134
Period size: 46 Copynumber: 3.1 Consensus size: 46
14311 CGCATACATA
* *
14321 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGAATGCCCA--TACATC-CT
* *** * *
14370 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTC-GA-ATGCCCATACATCCT
*
14414 AGTGAACTCGGACTCAACTCAACGAGTTCGAATGCCCAAACATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGAATGCCCATACATCCT
14460 AGTGA
1 AGTGA
14465 CCACTTGTAT
Statistics
Matches: 74, Mismatches: 15, Indels: 15
0.71 0.14 0.14
Matches are distributed among these distances:
44 7 0.09
45 2 0.03
46 31 0.42
47 29 0.39
48 1 0.01
49 4 0.05
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGAATGCCCATACATCCT
Found at i:15990 original size:9 final size:9
Alignment explanation
Indices: 15976--16272 Score: 163
Period size: 9 Copynumber: 32.6 Consensus size: 9
15966 TATTTAAGTA
15976 TTATGTAAG
1 TTATGTAAG
15985 TTATGTAAG
1 TTATGTAAG
*
15994 TTATGATATG
1 TTATG-TAAG
* * *
16004 ATATAT-AT
1 TTATGTAAG
* *
16012 TTTTGTAAA
1 TTATGTAAG
* *
16021 TTATAT-AT
1 TTATGTAAG
*
16029 TTATCTAAG
1 TTATGTAAG
*
16038 TTATATAAG
1 TTATGTAAG
16047 TTATGTAAG
1 TTATGTAAG
*
16056 TTTTGTAAG
1 TTATGTAAG
*
16065 TTATGTAAA
1 TTATGTAAG
*
16074 TTATGATATAAAA
1 TTATG---T-AAG
*
16087 TATATTTAAG
1 T-TATGTAAG
16097 TATTATGTAAG
1 --TTATGTAAG
16108 TTATGTAAG
1 TTATGTAAG
*
16117 TTATGGTATG
1 TTAT-GTAAG
* * *
16127 ATATAT-AT
1 TTATGTAAG
16135 TTATGTAAG
1 TTATGTAAG
* *
16144 TTATAT-AT
1 TTATGTAAG
*
16152 TTATCTAAG
1 TTATGTAAG
*
16161 TTATATAAG
1 TTATGTAAG
*
16170 TTATATAAG
1 TTATGTAAG
*
16179 TTATGTATG
1 TTATGTAAG
*
16188 TTATATAAG
1 TTATGTAAG
*
16197 TTGTGTAAG
1 TTATGTAAG
* *
16206 TTATATAAA
1 TTATGTAAG
* *
16215 TTATAT-AT
1 TTATGTAAG
*
16223 TTATCTAAG
1 TTATGTAAG
*
16232 TTATATAAG
1 TTATGTAAG
*
16241 TTATGTACG
1 TTATGTAAG
*
16250 TTTTGTAAG
1 TTATGTAAG
*
16259 TTATGTAAA
1 TTATGTAAG
16268 TTATG
1 TTATG
16273 ATATCAAATA
Statistics
Matches: 220, Mismatches: 54, Indels: 28
0.73 0.18 0.09
Matches are distributed among these distances:
8 25 0.11
9 163 0.74
10 15 0.07
11 8 0.04
12 2 0.01
13 4 0.02
14 3 0.01
ACGTcount: A:0.36, C:0.01, G:0.14, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:15992 original size:43 final size:43
Alignment explanation
Indices: 15940--16137 Score: 182
Period size: 43 Copynumber: 4.7 Consensus size: 43
15930 TTCGTAAGCT
*
15940 AGTTATGTAAGATATGTTATGATATATATTTAAGTATTATGTA
1 AGTTATGTAAGATATGATATGATATATATTTAAGTATTATGTA
* ** *
15983 AGTTATGTAAGTTATGATATGATATATATTTTTGTAAATTATAT-
1 AGTTATGTAAGATATGATATGATATATATTTAAGT--ATTATGTA
* * *
16027 ATTTATCTAAG-T-T-ATAT-A-AGT-TATGTAAGT-TT-TGTA
1 AGTTATGTAAGATATGATATGATA-TATATTTAAGTATTATGTA
* *
16063 AGTTATGTAA-ATTATGATATAAAATATATTTAAGTATTATGTA
1 AGTTATGTAAGA-TATGATATGATATATATTTAAGTATTATGTA
* *
16106 AGTTATGTAAGTTATGGTATGATATATATTTA
1 AGTTATGTAAGATATGATATGATATATATTTA
16138 TGTAAGTTAT
Statistics
Matches: 123, Mismatches: 18, Indels: 28
0.73 0.11 0.17
Matches are distributed among these distances:
35 2 0.02
36 10 0.08
37 1 0.01
38 1 0.01
39 11 0.09
40 4 0.03
41 13 0.11
42 3 0.02
43 63 0.51
44 9 0.07
45 6 0.05
ACGTcount: A:0.37, C:0.01, G:0.15, T:0.47
Consensus pattern (43 bp):
AGTTATGTAAGATATGATATGATATATATTTAAGTATTATGTA
Found at i:16027 original size:17 final size:17
Alignment explanation
Indices: 16005--16044 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
15995 TATGATATGA
* *
16005 TATATATTTTTGTAAAT
1 TATATATTTATCTAAAT
*
16022 TATATATTTATCTAAGT
1 TATATATTTATCTAAAT
16039 TATATA
1 TATATA
16045 AGTTATGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (17 bp):
TATATATTTATCTAAAT
Found at i:16106 original size:123 final size:123
Alignment explanation
Indices: 15940--16196 Score: 408
Period size: 123 Copynumber: 2.1 Consensus size: 123
15930 TTCGTAAGCT
* * *
15940 AGTTATGTAAGATATGTTATGATATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGA
1 AGTTATGTAAGATATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGA
* * *
16005 TATATATTTTTGTAAATTATATATTTATCTAAGTTATATAAGTTATGTAAGTTTTGTA
66 TATATATTTATGTAAATTATATATTTATCTAAGTTATATAAGTTATATAAGTTATGTA
*
16063 AGTTATGTAA-ATTATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGGTATG
1 AGTTATGTAAGA-TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATG
*
16127 ATATATATTTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATATAAGTTATGTA
65 ATATATATTTATGTAAATTATATATTTATCTAAGTTATATAAGTTATATAAGTTATGTA
* *
16186 TGTTATATAAG
1 AGTTATGTAAG
16197 TTGTGTAAGT
Statistics
Matches: 122, Mismatches: 10, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
122 1 0.01
123 121 0.99
ACGTcount: A:0.37, C:0.01, G:0.14, T:0.47
Consensus pattern (123 bp):
AGTTATGTAAGATATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGA
TATATATTTATGTAAATTATATATTTATCTAAGTTATATAAGTTATATAAGTTATGTA
Found at i:16191 original size:71 final size:72
Alignment explanation
Indices: 16099--16263 Score: 208
Period size: 71 Copynumber: 2.3 Consensus size: 72
16089 TATTTAAGTA
* * * * *
16099 TTATGTAAGTTATGTAAGTTATGGTATGATATAT-ATTTATGTAAGTTATATATTTATCTAAGTT
1 TTATGTAAGTTATGTAAGTTATGATAAGATATATAAGTTATATAAATTATATATTTATCTAAGTT
16163 ATATAAG
66 ATATAAG
* * * * *
16170 TTATATAAGTTATGTATGTTAT-ATAAGTTGTGTAAGTTATATAAATTATATATTTATCTAAGTT
1 TTATGTAAGTTATGTAAGTTATGATAAGATATATAAGTTATATAAATTATATATTTATCTAAGTT
16234 ATATAAG
66 ATATAAG
* *
16241 TTATGTACGTTTTGTAAGTTATG
1 TTATGTAAGTTATGTAAGTTATG
16264 TAAATTATGA
Statistics
Matches: 78, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
70 6 0.08
71 72 0.92
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (72 bp):
TTATGTAAGTTATGTAAGTTATGATAAGATATATAAGTTATATAAATTATATATTTATCTAAGTT
ATATAAG
Found at i:16417 original size:28 final size:29
Alignment explanation
Indices: 16377--16445 Score: 106
Period size: 28 Copynumber: 2.4 Consensus size: 29
16367 AAGTTGCGGG
*
16377 ATTAAATAATATTTATAAAAA-TTA-TTTA
1 ATTAAATAATATTGA-AAAAATTTATTTTA
16405 ATTAAATAATATTGAAAAAATTTATTTTA
1 ATTAAATAATATTGAAAAAATTTATTTTA
16434 ATTAAATAATAT
1 ATTAAATAATAT
16446 ACATGTCGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
27 5 0.13
28 17 0.45
29 16 0.42
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (29 bp):
ATTAAATAATATTGAAAAAATTTATTTTA
Found at i:16650 original size:24 final size:24
Alignment explanation
Indices: 16618--16688 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
16608 TTAACTTAAA
*
16618 TGATAAAACGGGCGATAATATTTG
1 TGATAAAACGGACGATAATATTTG
* *
16642 TGATAAAACGAACAATAATATTTG
1 TGATAAAACGGACGATAATATTTG
16666 TGATAAAACGGACGATAATATTT
1 TGATAAAACGGACGATAATATTT
16689 CAATAATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (24 bp):
TGATAAAACGGACGATAATATTTG
Found at i:16843 original size:63 final size:64
Alignment explanation
Indices: 16736--16868 Score: 241
Period size: 63 Copynumber: 2.1 Consensus size: 64
16726 ATATTTTATT
* *
16736 AAATATTTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAATCGTGATAG
1 AAATATTTGTATATTAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCATGATAG
16800 AAATATTTGTATATTAGATGGGACATA-TATATCAATAAATAAATTTATTAAAAATCATGATAG
1 AAATATTTGTATATTAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCATGATAG
16863 AAATAT
1 AAATAT
16869 AGAAATATTA
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
63 40 0.60
64 27 0.40
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (64 bp):
AAATATTTGTATATTAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCATGATAG
Found at i:17433 original size:11 final size:11
Alignment explanation
Indices: 17419--17444 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17409 AATCTAAGGA
17419 TAAACAAGAAT
1 TAAACAAGAAT
17430 TAAACAAGAAT
1 TAAACAAGAAT
17441 TAAA
1 TAAA
17445 ACATAATCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.19
Consensus pattern (11 bp):
TAAACAAGAAT
Done.