Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold261
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: 750797
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 32985 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:708140 original size:6 final size:6
Alignment explanation
Indices: 708131--708182 Score: 86
Period size: 6 Copynumber: 8.7 Consensus size: 6
708121 AAAAAAGGAA
* *
708131 TTTGAT TTTGGT TTTGGT TTTGGT TTTGTT TTTGGT TTTGGT TTTGGT
1 TTTGGT TTTGGT TTTGGT TTTGGT TTTGGT TTTGGT TTTGGT TTTGGT
708179 TTTG
1 TTTG
708183 CAGTTCACTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.02, C:0.00, G:0.29, T:0.69
Consensus pattern (6 bp):
TTTGGT
Found at i:715987 original size:19 final size:20
Alignment explanation
Indices: 715965--716010 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
715955 AAAATAATAT
* *
715965 AAAATTGA-AAAAATTATTA
1 AAAATTGACAAAAAGTATAA
*
715984 AAAACT-ACAAAAAGTATAA
1 AAAATTGACAAAAAGTATAA
716003 AAAATTGA
1 AAAATTGA
716011 GAAAGAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
18 1 0.05
19 19 0.90
20 1 0.05
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.24
Consensus pattern (20 bp):
AAAATTGACAAAAAGTATAA
Found at i:716522 original size:4 final size:4
Alignment explanation
Indices: 716513--716538 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
716503 TCTTTAAGTA
716513 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
716539 TATGTTGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:717077 original size:22 final size:23
Alignment explanation
Indices: 717060--717102 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
717050 AAATCAAATC
717060 TCTAAGATTACAAAATCATATAT
1 TCTAAGATTACAAAATCATATAT
* *
717083 TCTAAGGTTAC-ATATCATAT
1 TCTAAGATTACAAAATCATAT
717103 CTGCGATTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (23 bp):
TCTAAGATTACAAAATCATATAT
Found at i:717088 original size:23 final size:22
Alignment explanation
Indices: 717047--717102 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
717037 GAAAGGTATC
717047 TACAAATCA-A-ATCTCTAAGAT
1 TACAAATCATATAT-TCTAAGAT
*
717068 TACAAAATCATATATTCTAAGGT
1 TAC-AAATCATATATTCTAAGAT
*
717091 TACATATCATAT
1 TACAAATCATAT
717103 CTGCGATTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 3 0.10
22 14 0.47
23 11 0.37
24 2 0.07
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (22 bp):
TACAAATCATATATTCTAAGAT
Found at i:722201 original size:22 final size:23
Alignment explanation
Indices: 722174--722218 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
722164 AGGTATCTAC
722174 AAATCAAATC-TCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
*
722196 AAATCATATCTTCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
722219 TATCATATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (23 bp):
AAATCAAATCTTCTAAGATTACA
Found at i:722222 original size:17 final size:17
Alignment explanation
Indices: 722200--722252 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 17
722190 ATTACAAAAT
722200 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
*
722217 CATATCATATCTACGATTA
1 CATATC-T-TCTAAGATTA
* *
722236 CATATCCTCGAAGATTA
1 CATATCTTCTAAGATTA
722253 TGTTTCCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 14 0.47
18 1 0.03
19 15 0.50
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.36
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:722223 original size:22 final size:22
Alignment explanation
Indices: 722171--722228 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
722161 GAAAGGTATC
*
722171 TACAAATCAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
722192 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
722215 TACATATCATATCT
1 TACAAATCATATCT
722229 ACGATTACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 3 0.09
22 19 0.58
23 11 0.33
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.34
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:724788 original size:24 final size:24
Alignment explanation
Indices: 724756--724805 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
724746 CTCATTGATT
724756 GTCTAAAGTTCAAACTGAAGATAA
1 GTCTAAAGTTCAAACTGAAGATAA
724780 GTCTAAAGTTCAAACTGAAGATAA
1 GTCTAAAGTTCAAACTGAAGATAA
724804 GT
1 GT
724806 GACATTGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (24 bp):
GTCTAAAGTTCAAACTGAAGATAA
Found at i:729264 original size:22 final size:22
Alignment explanation
Indices: 729236--729277 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
729226 GCAACAGGAA
729236 AGGATATTTCAAATCAAACTAC
1 AGGATATTTCAAATCAAACTAC
729258 AGGATATTTCAAATCAAACT
1 AGGATATTTCAAATCAAACT
729278 GCAAGGAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.29
Consensus pattern (22 bp):
AGGATATTTCAAATCAAACTAC
Found at i:734268 original size:15 final size:14
Alignment explanation
Indices: 734247--734282 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
734237 NNNGTCCTTA
*
734247 ATAATTATCTTAAT
1 ATAATTATCCTAAT
734261 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
734276 ATAATTA
1 ATAATTA
734283 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:741387 original size:46 final size:46
Alignment explanation
Indices: 741272--741391 Score: 174
Period size: 46 Copynumber: 2.7 Consensus size: 46
741262 CTCTGAAAAG
*
741272 ATTAAGGGATTTTAGCGTGCTCTCTG---ATTAGAACTATTAGGAT
1 ATTAAGGGAGTTTAGCGTGCTCTCTGATTATTAGAACTATTAGGAT
** *
741315 ATTAAGGGAGTTTAATGTGCTATCTGATTATTAGAACTATTAGGAT
1 ATTAAGGGAGTTTAGCGTGCTCTCTGATTATTAGAACTATTAGGAT
*
741361 ATTAAGGGAGTTTAGCGTACTCTCTGATTAT
1 ATTAAGGGAGTTTAGCGTGCTCTCTGATTAT
741392 CAGCACATCG
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
43 22 0.33
46 44 0.67
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (46 bp):
ATTAAGGGAGTTTAGCGTGCTCTCTGATTATTAGAACTATTAGGAT
Found at i:746807 original size:67 final size:67
Alignment explanation
Indices: 746699--746826 Score: 211
Period size: 67 Copynumber: 1.9 Consensus size: 67
746689 TTTCCAATTT
* * *
746699 AGAGAGCACACTCCTGCGAACCTTATTTCTTACAGCGGGATTACCAGTCTAGGCTAAATCCTCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCTCTG
746764 CA
66 CA
* *
746766 AGAGAGCACAGTCCCGTGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCC
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCC
746827 CTTGTAATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 56 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.23
Consensus pattern (67 bp):
AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCTCTG
CA
Found at i:747675 original size:28 final size:28
Alignment explanation
Indices: 747635--747694 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
747625 TCTTATTCAA
747635 TTGTACAGAATTCGAATAATGTTCCCGT
1 TTGTACAGAATTCGAATAATGTTCCCGT
*
747663 TTGTACAGAATTCGAATAATGTTTCCGT
1 TTGTACAGAATTCGAATAATGTTCCCGT
747691 TTGT
1 TTGT
747695 TTCTATTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (28 bp):
TTGTACAGAATTCGAATAATGTTCCCGT
Found at i:749065 original size:8 final size:8
Alignment explanation
Indices: 749052--749079 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
749042 TCCACTCTCC
749052 TCCTTCAT
1 TCCTTCAT
749060 TCCTTCAT
1 TCCTTCAT
749068 TCCTTCAT
1 TCCTTCAT
749076 TCCT
1 TCCT
749080 CTATCGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.39, G:0.00, T:0.50
Consensus pattern (8 bp):
TCCTTCAT
Done.