Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2156
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: 15577
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.28
Found at i:12254 original size:8 final size:8
Alignment explanation
Indices: 12241--12282 Score: 66
Period size: 8 Copynumber: 5.0 Consensus size: 8
12231 TCCTTTACAC
12241 CAAAAAAA
1 CAAAAAAA
12249 CAAAAAAA
1 CAAAAAAA
12257 CAAAAAAA
1 CAAAAAAA
12265 CAAAAAACAA
1 C-AAAAA-AA
12275 CAAAAAAA
1 CAAAAAAA
12283 ATAGCAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 19 0.59
9 10 0.31
10 3 0.09
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:12262 original size:16 final size:18
Alignment explanation
Indices: 12241--12282 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
12231 TCCTTTACAC
12241 CAAAAAAAC-AAAAA-AA
1 CAAAAAAACAAAAAACAA
12257 CAAAAAAACAAAAAACAA
1 CAAAAAAACAAAAAACAA
12275 CAAAAAAA
1 CAAAAAAA
12283 ATAGCAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 9 0.38
17 5 0.21
18 10 0.42
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (18 bp):
CAAAAAAACAAAAAACAA
Found at i:12263 original size:15 final size:15
Alignment explanation
Indices: 12241--12293 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
12231 TCCTTTACAC
12241 CAAAAAAACAAAAAAA
1 CAAAAAAAC-AAAAAA
12257 CAAAAAAACAAAAAA
1 CAAAAAAACAAAAAA
* *
12272 CAACAAAAA-AAATAG
1 CAA-AAAAACAAAAAA
12287 CAAAAAA
1 CAAAAAA
12294 TAGAAGGGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 4 0.12
15 16 0.47
16 14 0.41
ACGTcount: A:0.83, C:0.13, G:0.02, T:0.02
Consensus pattern (15 bp):
CAAAAAAACAAAAAA
Found at i:13571 original size:29 final size:29
Alignment explanation
Indices: 13513--14359 Score: 1001
Period size: 28 Copynumber: 29.6 Consensus size: 29
13503 AATGTTCATC
13513 CCTTTCAAAGCCCACAAAGTCAGTGGCACT
1 CCTTTCAAAGCCCAC-AAGTCAGTGGCACT
13543 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
**
13572 ATTTTCAAAGCCCACAA-TCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
13600 CTTTTTAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
13629 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
13658 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
13687 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
13716 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
13744 CCTTTCGAAGCCCACAAGTTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAG-TCAGTGGCACT
* *
13773 CCTTGCGAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
13802 -CTTTCAAAGCCCACAAGTTAGT-GCTC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
13828 CCTTTCAAAGCCCACACAAGTCAGTGGCACT
1 CCTTTCAAAG-CC-CACAAGTCAGTGGCACT
* *
13859 CCTTTTAAAGCCCACGCAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
* *
13889 CTTTTCAAAGCCCACGAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
13918 -CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
13945 CCTTTC-AAGCCCACGAGTCAGTGGTAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
13972 CTTTTCAAAGCCCACGAGTTAGTGGCA--
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
13999 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
14028 -CTTTCAAAGCCCACGAGTCAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
14055 CCTTTC-AAGCCCACAAGTCAATAGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
14082 CCTTTCAAAGCCCACACAAGTTAGTGGCACT
1 CCTTTCAAAG-CC-CACAAGTCAGTGGCACT
14113 CCTTTCAAAGCCCACGCAAGTCAGTGGCA--
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
*
14142 CCTTTCAAAGCCCCCGAAGTCAGTGGCACT
1 CCTTTCAAAGCCCAC-AAGTCAGTGGCACT
*
14172 -CTTTCAAAGCCCACAAGTCAGTGGAAAC-
1 CCTTTCAAAGCCCACAAGTCAGTGG-CACT
*
14200 CCTTTC-AAGCCCACAAGTCAGTTGGTAC-
1 CCTTTCAAAGCCCACAAGTCAG-TGGCACT
* *
14228 CTTTTCAAAGCCCACAAGTCAGTGGCGCT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
14257 -CTTTCAAAGCCCACGAGTCAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
14284 CCTTTCAAAGCCCACGCAAGTCCGTGGCAC-
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
* **
14314 CCTTTTAAAGCCCACGCAA-TCAGTAACACT
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
*
14344 CTTTTCAAAGCCCACA
1 CCTTTCAAAGCCCACA
14360 TGTGTCAGTG
Statistics
Matches: 721, Mismatches: 60, Indels: 74
0.84 0.07 0.09
Matches are distributed among these distances:
27 86 0.12
28 252 0.35
29 251 0.35
30 88 0.12
31 44 0.06
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (29 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:13604 original size:28 final size:29
Alignment explanation
Indices: 13515--14359 Score: 990
Period size: 29 Copynumber: 29.5 Consensus size: 29
13505 TGTTCATCCC
*
13515 TTTCAAAGCCCACAAAGTCAGTGGCACTCC
1 TTTCAAAGCCCAC-AAGTCAGTGGCACTCT
*
13545 TTTCAAAGCCCACAAGTCAGTGGCACTAT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
13574 TTTCAAAGCCCACAA-TCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
13602 TTTTAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
13631 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
13660 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
13689 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
13718 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
13746 TTTCGAAGCCCACAAGTTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAG-TCAGTGGCACTCT
* *
13775 TTGCGAAGCCCACAAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
13803 TTTCAAAGCCCACAAGTTAGT-GCTC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
13830 TTTCAAAGCCCACACAAGTCAGTGGCACTCCT
1 TTTCAAAG-CC-CACAAGTCAGTGGCACT-CT
*
13862 TTT-AAAGCCCACGCAAGTTAGTGGCAC-CT
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCT
*
13891 TTTCAAAGCCCACGAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
13919 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
13947 TTTC-AAGCCCACGAGTCAGTGGTAC-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
13974 TTTCAAAGCCCACGAGTTAGTGGCAC-C-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
14001 TTTCAAAGCCCACAAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
14029 TTTCAAAGCCCACGAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
14057 TTTC-AAGCCCACAAGTCAATAGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
14084 TTTCAAAGCCCACACAAGTTAGTGGCACTCC
1 TTTCAAAG-CC-CACAAGTCAGTGGCACTCT
14115 TTTCAAAGCCCACGCAAGTCAGTGGCAC-C-
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCT
*
14144 TTTCAAAGCCCCCGAAGTCAGTGGCACTC-
1 TTTCAAAGCCCAC-AAGTCAGTGGCACTCT
* *
14173 TTTCAAAGCCCACAAGTCAGTGGAAAC-CC
1 TTTCAAAGCCCACAAGTCAGTGG-CACTCT
*
14202 TTTC-AAGCCCACAAGTCAGTTGGTAC-CT
1 TTTCAAAGCCCACAAGTCAG-TGGCACTCT
*
14230 TTTCAAAGCCCACAAGTCAGTGGCGCTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
14258 TTTCAAAGCCCACGAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
14286 TTTCAAAGCCCACGCAAGTCCGTGGCACCCT
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCT
**
14317 TTT-AAAGCCCACGCAA-TCAGTAACACTCT
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCT
14346 TTTCAAAGCCCACA
1 TTTCAAAGCCCACA
14360 TGTGTCAGTG
Statistics
Matches: 724, Mismatches: 55, Indels: 74
0.85 0.06 0.09
Matches are distributed among these distances:
26 1 0.00
27 88 0.12
28 252 0.35
29 261 0.36
30 74 0.10
31 44 0.06
32 4 0.01
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCT
Found at i:13710 original size:144 final size:142
Alignment explanation
Indices: 13512--14359 Score: 1003
Period size: 144 Copynumber: 5.9 Consensus size: 142
13502 GAATGTTCAT
**
13512 CCCTTTCAAAGCCCACAAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTATTTT
1 CCCTTTCAAAGCCCAC-AAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTT
* *
13577 CAAAGCCCACAA-TCAGTGGCACTCTTTTTAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCC
65 CAAAGCCCACAAGTCAGTGGCAC-C-TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCC
*
13641 CACAAATCAGTGGCA
128 CACAAGTCAGTGGCA
* * * *
13656 CTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTT
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTT
* * *
13721 CAAAGCCCACAAGTCAGTGGCACCCTTTCGAAGCCCACAAGTTCAGTGGCAC-CCTTGCGAAGCC
65 CAAAGCCCACAAGTCAGTGGCA-CCTTTCAAAGCCCACAAG-TCAGTGGCACTCCTTTCAAAGCC
13785 CACAAGTCAGTGGCA
128 CACAAGTCAGTGGCA
* * *
13800 CTCTTTCAAAGCCCACAAGTTAGT-GCTC-CCTTTCAAAGCCCACACAAGTCAGTGGCACTCCTT
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG-CC-CACAAGTCAGTGGCACTCCTT
* * *
13863 TTAAAGCCCACGCAAGTTAGTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACT-CTTTCAAAG
64 TCAAAGCCCA--CAAGTCAGTGGCACC-TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG
13927 CCCACAAGTCAGTGGCA
126 CCCACAAGTCAGTGGCA
* * * * *
13944 CCCTTTC-AAGCCCACGAGTCAGTGGTAC-CTTTTCAAAGCCCACGAGTTAGTGGCA--CCTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
*
14005 AAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACGAGTCAGTGGCA-TCCTTTC-AAGCCCA
66 AAAGCCCACAAGTCAGTGGCAC-CTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCA
* *
14068 CAAGTCAATAGCA
130 CAAGTCAGTGGCA
*
14081 CCCTTTCAAAGCCCACACAAGTTAGTGGCACTCCTTTCAAAGCCCACGCAAGTCAGTGGCA--CC
1 CCCTTTCAAAG-CC-CACAAGTCAGTGGCACTCCTTTCAAAGCCCA--CAAGTCAGTGGCACTCC
* *
14144 TTTCAAAGCCCCCGAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGAAAC-CCTTTC-A
62 TTTCAAAGCCCAC-AAGTCAGTGGCAC-CTTTCAAAGCCCACAAGTCAGTGG-CACTCCTTTCAA
*
14207 AGCCCACAAGTCAGTTGGTA
124 AGCCCACAAGTCAG-TGGCA
* * *
14227 CCTTTTCAAAGCCCACAAGTCAGTGGCGCT-CTTTCAAAGCCCACGAGTCAGTGGCA-TCCTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
* * ** *
14290 AAAGCCCACGCAAGTCCGTGGCACCCTTTTAAAGCCCACGCAA-TCAGTAACACTCTTTTCAAAG
66 AAAGCCCA--CAAGTCAGTGGCA-CCTTTCAAAGCCCA--CAAGTCAGTGGCACTCCTTTCAAAG
14354 CCCACA
126 CCCACA
14360 TGTGTCAGTG
Statistics
Matches: 615, Mismatches: 58, Indels: 61
0.84 0.08 0.08
Matches are distributed among these distances:
137 26 0.04
138 46 0.07
139 3 0.00
140 26 0.04
141 34 0.06
142 31 0.05
143 127 0.21
144 213 0.35
145 95 0.15
146 14 0.02
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.22
Consensus pattern (142 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
AAAGCCCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCAC
AAGTCAGTGGCA
Found at i:15012 original size:20 final size:19
Alignment explanation
Indices: 14966--15041 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 19
14956 TCATACCTTG
* *
14966 ATGTATCGATACATTTTTCA
1 ATGTATCGATACA-TTATGA
*
14986 ATATATCGATACATGTATGA
1 ATGTATCGATACAT-TATGA
*
15006 ATGTATCGATA-TTCTAT-A
1 ATGTATCGATACAT-TATGA
15024 ATGTATCGATACATTATG
1 ATGTATCGATACATTATG
15042 TCTTTTTACC
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
18 15 0.33
19 6 0.13
20 25 0.54
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (19 bp):
ATGTATCGATACATTATGA
Done.