Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold508
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: 42746
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:10232 original size:51 final size:53
Alignment explanation
Indices: 10120--10219 Score: 132
Period size: 53 Copynumber: 1.9 Consensus size: 53
10110 TATGAAACTT
* **
10120 CCCCATTTCCTCAAAATCCAATCCATTTTTGCACTTTGTTCCAATCTTTATAA
1 CCCCATTTCCTCAAAATCCAATCCATTTTTCCACAATGTTCCAATCTTTATAA
* * *
10173 CCCCATTTCCTCAAAATCCCAT-CTTTTTTCCCCAATGTT-CAATCTTT
1 CCCCATTTCCTCAAAATCCAATCCATTTTTCCACAATGTTCCAATCTTT
10220 GAAATCTCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 8 0.20
52 12 0.29
53 21 0.51
ACGTcount: A:0.24, C:0.33, G:0.03, T:0.40
Consensus pattern (53 bp):
CCCCATTTCCTCAAAATCCAATCCATTTTTCCACAATGTTCCAATCTTTATAA
Found at i:21937 original size:27 final size:26
Alignment explanation
Indices: 21907--21957 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
21897 GTTCGTCAAA
*
21907 GGGCTAGGCAAGCTGGTATTCACTAAT
1 GGGCTAGGCAAGCT-GTAGTCACTAAT
* *
21934 GGGCTTGGCGAGCTGTAGTCACTA
1 GGGCTAGGCAAGCTGTAGTCACTA
21958 TTTTAGGTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 9 0.43
27 12 0.57
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.25
Consensus pattern (26 bp):
GGGCTAGGCAAGCTGTAGTCACTAAT
Found at i:22631 original size:16 final size:17
Alignment explanation
Indices: 22600--22632 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
22590 TATTTTATGT
22600 TTTGCGAGCTCTTTGTGA
1 TTTGCGAGC-CTTTGTGA
22618 TTTGCGAG-CTTTGTG
1 TTTGCGAGCCTTTGTG
22633 TTAAGTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.09, C:0.15, G:0.30, T:0.45
Consensus pattern (17 bp):
TTTGCGAGCCTTTGTGA
Found at i:24192 original size:39 final size:39
Alignment explanation
Indices: 24144--24283 Score: 244
Period size: 39 Copynumber: 3.6 Consensus size: 39
24134 GCTCTGATGA
*
24144 GCTTTAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
24183 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
*
24222 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
24261 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
24284 AGGTCACGAT
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 97 1.00
ACGTcount: A:0.11, C:0.26, G:0.25, T:0.38
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
Found at i:25116 original size:13 final size:13
Alignment explanation
Indices: 25098--25131 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
25088 AGGTAAAATG
25098 AATTAAAATACAA
1 AATTAAAATACAA
25111 AATTAAAATACAA
1 AATTAAAATACAA
25124 AATTAAAA
1 AATTAAAA
25132 GCCAATTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (13 bp):
AATTAAAATACAA
Found at i:26511 original size:49 final size:49
Alignment explanation
Indices: 26279--26516 Score: 305
Period size: 49 Copynumber: 4.8 Consensus size: 49
26269 TGAGGTCGCA
* ** *
26279 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCTAAAATTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTG-G-TCACG
* **
26330 TGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT-GGTCACG
* *
26380 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTCACG
* * * *
26429 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTCACG
* * *
26478 TATGTAGTACTATGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATA
26517 GCTTTGGCTA
Statistics
Matches: 167, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
49 88 0.53
50 42 0.25
51 36 0.22
52 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTCACG
Found at i:30262 original size:56 final size:56
Alignment explanation
Indices: 30201--30336 Score: 209
Period size: 56 Copynumber: 2.4 Consensus size: 56
30191 ATCATGGCAT
* *
30201 CGATATATATGTGCGAGTAAGACCACGTTTTATATGTTGGCATCGATATGTGACTC
1 CGATATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATCGATATGTGACTC
** * *
30257 CGATATATGTGTGTAAGTAAGACCGCGTTTTATACGTTGGCATCGATATGTGTCTC
1 CGATATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATCGATATGTGACTC
*
30313 CGATATATGTGTACGAGTAAGACC
1 CGATATATGTGTGCGAGTAAGACC
30337 CTGCCTGGGA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 71 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.33
Consensus pattern (56 bp):
CGATATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATCGATATGTGACTC
Found at i:31982 original size:40 final size:40
Alignment explanation
Indices: 31681--31978 Score: 429
Period size: 40 Copynumber: 7.5 Consensus size: 40
31671 AAGCCAAGTA
* * * * *
31681 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATA
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
31720 CCTTCGGGACATAGCCCGGATATTGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
31760 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
31800 CCTTCGGGACTTAGCCCGGATATGGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
31840 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * * *
31880 CCTTGGGGACTTAGCCCAGATATGGTAACTCACACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
31920 CCTTCGGGACTTAGCCCGGTTATTGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
31960 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
31979 TTATCATCCA
Statistics
Matches: 233, Mismatches: 24, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
39 12 0.05
40 221 0.95
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40185 original size:37 final size:39
Alignment explanation
Indices: 40005--40289 Score: 419
Period size: 37 Copynumber: 7.5 Consensus size: 39
39995 AAGCCAAGTA
* * * * *
40005 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATA
1 CCTTCGGGACTTAGCCCGGATAT-G-TAACTCGCACAAATG
*
40044 CCTTCGGGACATAGCCCGGATATGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATGTAACTCGCACAAATG
40083 CCTTC-GGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATAT-GTAACTCGCACAAATG
40122 CCTTCGGGACTTAGCCC-GATATGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATGTAACTCGCACAAATG
40160 CCTTC-GGACTTAGCCCGGATA-GTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATGTAACTCGCACAAATG
40197 CCTT-GGGACTTAGCCCGGATATGTAACTCGCAC-AATG
1 CCTTCGGGACTTAGCCCGGATATGTAACTCGCACAAATG
40234 CCTTCGGGACTTAGCCCGGA-ATGT-ACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATGTAACTCGCACAAATG
40271 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
40290 TTATCATCCA
Statistics
Matches: 230, Mismatches: 7, Indels: 20
0.89 0.03 0.08
Matches are distributed among these distances:
36 8 0.03
37 82 0.36
38 68 0.30
39 53 0.23
40 19 0.08
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGATATGTAACTCGCACAAATG
Found at i:40226 original size:75 final size:76
Alignment explanation
Indices: 40044--40289 Score: 412
Period size: 75 Copynumber: 3.2 Consensus size: 76
40034 CGCTCGAATA
*
40044 CCTTCGGGACATAGCCCGGATATGTAACTCGCACAAATGCCTTCGGACTTAGCCCGGATATAGTA
1 CCTTCGGGACTTAGCCCGGATATGTAACTCGCACAAATGCCTTCGGACTTAGCCCGG--ATAGTA
40109 ACTCGCACAAATG
64 ACTCGCACAAATG
40122 CCTTCGGGACTTAGCCC-GATATGTAACTCGCACAAATGCCTTCGGACTTAGCCCGGATAGTAAC
1 CCTTCGGGACTTAGCCCGGATATGTAACTCGCACAAATGCCTTCGGACTTAGCCCGGATAGTAAC
40186 TCGCACAAATG
66 TCGCACAAATG
40197 CCTT-GGGACTTAGCCCGGATATGTAACTCGCAC-AATGCCTTCGGGACTTAGCCCGGA-ATGT-
1 CCTTCGGGACTTAGCCCGGATATGTAACTCGCACAAATGCCTTC-GGACTTAGCCCGGATA-GTA
40258 ACTCGCACAAATG
64 ACTCGCACAAATG
40271 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
40290 TTATCATCCA
Statistics
Matches: 163, Mismatches: 1, Indels: 11
0.93 0.01 0.06
Matches are distributed among these distances:
74 39 0.24
75 69 0.42
77 39 0.24
78 16 0.10
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.22
Consensus pattern (76 bp):
CCTTCGGGACTTAGCCCGGATATGTAACTCGCACAAATGCCTTCGGACTTAGCCCGGATAGTAAC
TCGCACAAATG
Done.