Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1748
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: 17837
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Found at i:1931 original size:47 final size:47
Alignment explanation
Indices: 1814--2259 Score: 774
Period size: 47 Copynumber: 9.6 Consensus size: 47
1804 CCCTTCGGGA
* * * * * *
1814 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1861 C-TGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1907 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1954 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2001 CTTATCACATATATACACTTTCACATTCATCACAT-GGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2047 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
2094 CTTATCACATATATACACTTTCACATTCATCACAT-GGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2140 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2187 CTTATCACATATATACACTTTCACATTCATCACAT-GGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2233 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
2260 TATTCAAATA
Statistics
Matches: 383, Mismatches: 13, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
46 167 0.44
47 216 0.56
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:2066 original size:140 final size:141
Alignment explanation
Indices: 1814--2259 Score: 819
Period size: 140 Copynumber: 3.2 Consensus size: 141
1804 CCCTTCGGGA
* * * * *
1814 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCC-TGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1878 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
1943 GGCCATTAGGC
131 GGCCATTAGGC
1954 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
2019 TTTCACATTCATCACAT-GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
2083 GGCCATTAGGC
131 GGCCATTAGGC
2094 CTTATCACATATATACACTTTCACATTCATCACA-TGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
2158 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT-
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
2222 GGCCATTAGGC
131 GGCCATTAGGC
2233 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
2260 TATTCAAATA
Statistics
Matches: 299, Mismatches: 5, Indels: 5
0.97 0.02 0.02
Matches are distributed among these distances:
139 85 0.28
140 182 0.61
141 32 0.11
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:2087 original size:93 final size:93
Alignment explanation
Indices: 1814--2259 Score: 786
Period size: 93 Copynumber: 4.8 Consensus size: 93
1804 CCCTTCGGGA
* * * * * *
1814 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCC-TGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCAC-ATGGCCATTAGGCCTTATCACATATATACAC
1878 TTTCACATTCATCACATCGGCCATTAGGC
65 TTTCACATTCATCACATCGGCCATTAGGC
1907 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACAT-GGCCATTAGGCCTTATCACATATATACAC
* *
1972 TTTCACATTCATCACATTGGCCATTCGGC
65 TTTCACATTCATCACATCGGCCATTAGGC
2001 CTTATCACATATATACACTTTCACATTCATCACATGGCCATTAGGCCTTATCACATATATACACT
1 CTTATCACATATATACACTTTCACATTCATCACATGGCCATTAGGCCTTATCACATATATACACT
2066 TTCACATTCATCACATCGGCCATTAGGC
66 TTCACATTCATCACATCGGCCATTAGGC
*
2094 CTTATCACATATATACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATATACACT
1 CTTATCACATATATACACTTTCACATTCATCACATGGCCATTAGGCCTTATCACATATATACACT
2159 TTCACATTCATCACATCGGCCATTAGGC
66 TTCACATTCATCACATCGGCCATTAGGC
2187 CTTATCACATATATACACTTTCACATTCATCACATGGCCATTAGGCCTTATCACATATATACACT
1 CTTATCACATATATACACTTTCACATTCATCACATGGCCATTAGGCCTTATCACATATATACACT
2252 TTCACATT
66 TTCACATT
2260 TATTCAAATA
Statistics
Matches: 339, Mismatches: 12, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
92 1 0.00
93 261 0.77
94 77 0.23
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (93 bp):
CTTATCACATATATACACTTTCACATTCATCACATGGCCATTAGGCCTTATCACATATATACACT
TTCACATTCATCACATCGGCCATTAGGC
Found at i:5728 original size:40 final size:40
Alignment explanation
Indices: 5683--6000 Score: 482
Period size: 40 Copynumber: 8.1 Consensus size: 40
5673 CGAATACACG
* * * *
5683 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* * * * * *
5723 ACACCAGCACGAATGCTCTTCGGG-TTTAGCACGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
5762 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
5802 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
5842 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
5882 TCACTAGCA-GAATGCTCTTC-GGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
5920 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
5960 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT-CA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
5999 TC
1 TC
6001 GTCGAGACCT
Statistics
Matches: 258, Mismatches: 17, Indels: 7
0.91 0.06 0.02
Matches are distributed among these distances:
38 26 0.10
39 59 0.23
40 173 0.67
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:5946 original size:118 final size:119
Alignment explanation
Indices: 5683--6000 Score: 498
Period size: 118 Copynumber: 2.7 Consensus size: 119
5673 CGAATACACG
* * * * * * **
5683 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGT
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAC
* *
5748 TTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
66 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
5802 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGG-A
5867 CTTAGCCCGGATACATCACTAGCA-GAATGCTCTTCGG-ACTTAGCCCGGATACA
65 CTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
*
5920 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTC-GGA
5985 CTTAGCCCGGAT-CATC
65 CTTAGCCCGGATACATC
6001 GTCGAGACCT
Statistics
Matches: 186, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
117 4 0.02
118 89 0.48
119 72 0.39
120 21 0.11
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (119 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAC
TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
Found at i:6098 original size:35 final size:38
Alignment explanation
Indices: 6053--6162 Score: 156
Period size: 38 Copynumber: 3.0 Consensus size: 38
6043 GAATTTTAAT
6053 CCGGACATAATCTCTGTACATAGCCATC-GGT-TTTA-
1 CCGGACATAATCTCTGTACATAGCCATCGGGTCTTTAC
6088 CCGGACATAATCTCTGTACATAGCCATCGGGTCTTTAC
1 CCGGACATAATCTCTGTACATAGCCATCGGGTCTTTAC
* * *
6126 CCGGACATAATCTCT-TCATATAGTCAGCGGGTCTTTA
1 CCGGACATAATCTCTGT-ACATAGCCATCGGGTCTTTA
6163 AACTCGGATT
Statistics
Matches: 68, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
35 28 0.41
36 3 0.04
37 5 0.07
38 32 0.47
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (38 bp):
CCGGACATAATCTCTGTACATAGCCATCGGGTCTTTAC
Found at i:8685 original size:47 final size:47
Alignment explanation
Indices: 8582--8985 Score: 665
Period size: 47 Copynumber: 8.6 Consensus size: 47
8572 CCCTTCGGGA
* * * * *
8582 CTTATCACATTTATACACTTTCACATCCAT--CATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8627 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8674 CTTATCACATATATACACTTTCACATTCATCACATCGG-CATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8720 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8767 CTTATCACATATATATACACTTTCACATTCATCACAT-GGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8815 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8862 CTTATCACATATATATACACTTTCACATTCATCACAT-GGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8910 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8957 CTTATCACATATATATACACTTTCACATT
1 CTTATCAC--ATATATACACTTTCACATT
8986 TATTCAAATA
Statistics
Matches: 341, Mismatches: 7, Indels: 18
0.93 0.02 0.05
Matches are distributed among these distances:
45 28 0.08
46 100 0.29
47 103 0.30
48 37 0.11
49 73 0.21
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:8811 original size:95 final size:95
Alignment explanation
Indices: 8582--8985 Score: 712
Period size: 95 Copynumber: 4.3 Consensus size: 95
8572 CCCTTCGGGA
* * * *
8582 CTTATCACAT-T-TATACACTTTCACATCCATCA-TTGGCCACTCGGCCTTATCACATATATACA
1 CTTATCACATATATATACACTTTCACATTCATCACATGGCCATTAGGCCTTATCACATATATACA
8644 CTTTCACATTCATCACATCGGCCATTAGGC
66 CTTTCACATTCATCACATCGGCCATTAGGC
8674 CTTATCAC--ATATATACACTTTCACATTCATCACATCGG-CATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACAT-GGCCATTAGGCCTTATCACATATATAC
8736 ACTTTCACATTCATCACATCGGCCATTAGGC
65 ACTTTCACATTCATCACATCGGCCATTAGGC
8767 CTTATCACATATATATACACTTTCACATTCATCACATGGCCATTAGGCCTTATCACATATATACA
1 CTTATCACATATATATACACTTTCACATTCATCACATGGCCATTAGGCCTTATCACATATATACA
8832 CTTTCACATTCATCACATCGGCCATTAGGC
66 CTTTCACATTCATCACATCGGCCATTAGGC
*
8862 CTTATCACATATATATACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATATACA
1 CTTATCACATATATATACACTTTCACATTCATCACATGGCCATTAGGCCTTATCACATATATACA
8927 CTTTCACATTCATCACATCGGCCATTAGGC
66 CTTTCACATTCATCACATCGGCCATTAGGC
8957 CTTATCACATATATATACACTTTCACATT
1 CTTATCACATATATATACACTTTCACATT
8986 TATTCAAATA
Statistics
Matches: 300, Mismatches: 5, Indels: 11
0.95 0.02 0.03
Matches are distributed among these distances:
91 1 0.00
92 28 0.09
93 62 0.21
94 4 0.01
95 205 0.68
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (95 bp):
CTTATCACATATATATACACTTTCACATTCATCACATGGCCATTAGGCCTTATCACATATATACA
CTTTCACATTCATCACATCGGCCATTAGGC
Found at i:12458 original size:40 final size:40
Alignment explanation
Indices: 12413--12732 Score: 482
Period size: 40 Copynumber: 8.1 Consensus size: 40
12403 CGAATACACG
* * * *
12413 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* * * ** * *
12453 ACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
12493 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
12533 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
12573 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
*
12613 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
12653 TCACTAGCATGAATGCTCTTC-GGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
12692 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT-CA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
12731 TC
1 TC
12733 GTCGAGACCT
Statistics
Matches: 259, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
39 42 0.16
40 217 0.84
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:12855 original size:38 final size:38
Alignment explanation
Indices: 12786--12860 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
12776 GAATTTTAAT
*
12786 CCGGACATAATCTCTGTACATAGCCATCGGGTCTTTAC
1 CCGGACATAATCTCTGTACATAGCCAGCGGGTCTTTAC
* *
12824 CCGGACATAATCTCT-TCATATAGTCAGCGGGTCTTTA
1 CCGGACATAATCTCTGT-ACATAGCCAGCGGGTCTTTA
12861 AACTCGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (38 bp):
CCGGACATAATCTCTGTACATAGCCAGCGGGTCTTTAC
Found at i:15357 original size:47 final size:47
Alignment explanation
Indices: 15279--15682 Score: 684
Period size: 47 Copynumber: 8.6 Consensus size: 47
15269 CCCTTCGGGA
* * * * * *
15279 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
15326 CTTGTCACATATATACACTTTCACATTCATCACAT-GGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
15372 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
15419 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
15466 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
15513 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
15560 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
15607 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
15654 CTTATCACATATATATACACTTTCACATT
1 CTTATCAC--ATATATACACTTTCACATT
15683 TATTCAAATA
Statistics
Matches: 339, Mismatches: 15, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
46 43 0.13
47 277 0.82
49 19 0.06
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Done.