Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold803
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: 19995
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:4594 original size:23 final size:23
Alignment explanation
Indices: 4566--4612 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
4556 AGCCTTATGC
4566 CATCCGCGCACGAGAGGAGCCAT
1 CATCCGCGCACGAGAGGAGCCAT
*
4589 CATCCGCGCACGAGAGGAGGCAT
1 CATCCGCGCACGAGAGGAGCCAT
4612 C
1 C
4613 CTCCCTGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.34, G:0.32, T:0.09
Consensus pattern (23 bp):
CATCCGCGCACGAGAGGAGCCAT
Found at i:9896 original size:47 final size:47
Alignment explanation
Indices: 9825--10887 Score: 1787
Period size: 47 Copynumber: 22.6 Consensus size: 47
9815 CCCTTCGGGA
* * * * * *
9825 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
9872 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
9919 CTTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
9966 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10013 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
10060 CTTATCACATATATACACTTTCACATTCATTAAATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
10107 CTTATCACATATATATACCCTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
10156 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10203 CGTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10250 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10297 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
10346 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10393 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10440 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10487 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10534 CTTATCACATATATACACTTTCACATTCAT-A-ATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10579 CTTATCACATATATATACACTTTCACATTCATCACAT-GGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10627 CTTATCACATATATACACTTTCACATTCATCACAT-GGCCATT-GGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10672 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10719 CTTATCACATATATACACTTTCACATTCATCACATCGG-CATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
10765 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10814 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10861 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
10888 TATTCAAATA
Statistics
Matches: 970, Mismatches: 33, Indels: 26
0.94 0.03 0.03
Matches are distributed among these distances:
45 60 0.06
46 58 0.06
47 699 0.72
48 48 0.05
49 105 0.11
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:9903 original size:25 final size:25
Alignment explanation
Indices: 9875--9953 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
9865 ACTCGGCCCT
9875 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
9900 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
9922 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
9947 ATCACAT
1 ATCACAT
9954 CAGCCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:10238 original size:237 final size:235
Alignment explanation
Indices: 9825--10887 Score: 1841
Period size: 237 Copynumber: 4.5 Consensus size: 235
9815 CCCTTCGGGA
* * * * * *
9825 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACAC
9890 TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATC
*
9955 AGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
131 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
*
10020 CATATATACACTTTCACATTCATCACATCGGCTATTAGGC
196 CATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
10060 CTTATCACATATATACACTTTCACATTCATTAAATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCAC--ATATATAC
*
10125 CCTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
* * *
10190 TTGGCCATTCGGCCGTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
129 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
10255 CACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
194 CACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10297 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
10362 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
10427 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
129 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
10492 CACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
194 CACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10534 CTTATCACATATATACACTTTCACATTCAT-A-ATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCAC--ATATATAC
10597 ACTTTCACATTCATCACA-TGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
10661 T-GGCCATT-GGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
129 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
10724 CACATATATACACTTTCACATTCATCACATCGG-CATTAGGC
194 CACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10765 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
* *
10830 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATT
64 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATT
10888 TATTCAAATA
Statistics
Matches: 790, Mismatches: 27, Indels: 23
0.94 0.03 0.03
Matches are distributed among these distances:
231 16 0.02
232 88 0.11
233 76 0.10
234 86 0.11
235 114 0.14
237 366 0.46
239 44 0.06
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (235 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
CATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:15067 original size:40 final size:39
Alignment explanation
Indices: 14984--15192 Score: 373
Period size: 40 Copynumber: 5.3 Consensus size: 39
14974 ACTAGCACGA
* *
14984 GATATATCACTAGCACGAATGCTCTTCGGACTTAGTCCG
1 GATACATCACTAGCACGAATGCTCTTCGGACTTAGCCCG
15023 GATACATCACTAGCACGAATGCTCTTCGAGACTTAGCCCG
1 GATACATCACTAGCACGAATGCTCTTCG-GACTTAGCCCG
15063 GATACATCACTAGCACGAATGCTCTTCGAGACTTAGCCCG
1 GATACATCACTAGCACGAATGCTCTTCG-GACTTAGCCCG
15103 GATACATCACTAGCACGAATGCTCTTCGGACTTAGCCCG
1 GATACATCACTAGCACGAATGCTCTTCGGACTTAGCCCG
15142 GATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCG
1 GATACATCACTAGCACGAATGCTCTTC-GGACTTAGCCCG
15182 GATACATCACT
1 GATACATCACT
15193 CTCAATTCTC
Statistics
Matches: 166, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
39 65 0.39
40 101 0.61
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (39 bp):
GATACATCACTAGCACGAATGCTCTTCGGACTTAGCCCG
Found at i:15085 original size:79 final size:78
Alignment explanation
Indices: 14984--15192 Score: 373
Period size: 79 Copynumber: 2.6 Consensus size: 78
14974 ACTAGCACGA
* *
14984 GATATATCACTAGCACGAATGCTCTTCGGACTTAGTCCGGATACATCACTAGCACGAATGCTCTT
1 GATACATCACTAGCACGAATGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTT
15049 CGAGACTTAGCCCG
66 CG-GACTTAGCCCG
15063 GATACATCACTAGCACGAATGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
1 GATACATCACTAGCACGAATGCTCTTCG-GACTTAGCCCGGATACATCACTAGCACGAATGCTCT
15128 TCGGACTTAGCCCG
65 TCGGACTTAGCCCG
15142 GATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
1 GATACATCACTAGCACGAATGCTCTTC-GGACTTAGCCCGGATACATCACT
15193 CTCAATTCTC
Statistics
Matches: 126, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
79 87 0.69
80 39 0.31
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (78 bp):
GATACATCACTAGCACGAATGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTT
CGGACTTAGCCCG
Found at i:16676 original size:47 final size:47
Alignment explanation
Indices: 16605--16961 Score: 590
Period size: 47 Copynumber: 7.6 Consensus size: 47
16595 CCCTTCGGGA
* * * * * *
16605 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
16652 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
16699 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
16746 CTTATCACATATATACACTTTCACATTCATCACATCGG-CATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
16792 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
16839 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
16888 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
16935 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
16962 TATTCAAATA
Statistics
Matches: 295, Mismatches: 12, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
46 46 0.16
47 204 0.69
49 45 0.15
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:16683 original size:25 final size:25
Alignment explanation
Indices: 16655--16733 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
16645 ACTCGGCCCT
16655 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
16680 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
16702 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
16727 ATCACAT
1 ATCACAT
16734 CGGCCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:16923 original size:189 final size:187
Alignment explanation
Indices: 16605--16961 Score: 633
Period size: 189 Copynumber: 1.9 Consensus size: 187
16595 CCCTTCGGGA
* * * *
16605 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
16670 TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATC
16735 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCATTAGGC
131 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCATTAGGC
* * *
16792 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCAC--ATATATAC
16857 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
16922 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATT
129 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATT
16962 TATTCAAATA
Statistics
Matches: 161, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
187 48 0.30
189 113 0.70
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (187 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCATTAGGC
Done.