Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1262
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: 38962
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.36
Found at i:914 original size:2 final size:2
Alignment explanation
Indices: 907--931 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
897 CTTTGATGCT
907 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
932 TCCTTGAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1547 original size:22 final size:20
Alignment explanation
Indices: 1499--1556 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
1489 GAAAGTTAGA
*
1499 AAATTAAATTTAAATAATTT
1 AAATTTAATTTAAATAATTT
*
1519 AATATTTAATTTAAATAGTTTTT
1 AA-ATTTAATTTAAATA--ATTT
*
1542 AAATTTAATTAAAAT
1 AAATTTAATTTAAAT
1557 TTTAATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 2 0.06
21 13 0.41
22 12 0.38
23 5 0.16
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
AAATTTAATTTAAATAATTT
Found at i:6156 original size:3 final size:3
Alignment explanation
Indices: 6148--6177 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
6138 TGCCCTCTTC
6148 AAT AAT AAT AAT AAT AAT AAT AATT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AA
6178 AAGATAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6849 original size:8 final size:8
Alignment explanation
Indices: 6838--6919 Score: 78
Period size: 8 Copynumber: 9.8 Consensus size: 8
6828 ACCTCTCTTT
*
6838 CTCTATCC
1 CTCTATTC
6846 CTCTATTC
1 CTCTATTC
6854 CTCTATTC
1 CTCTATTC
6862 CTCTATTC
1 CTCTATTC
6870 CTCTATAT-
1 CTCTAT-TC
*
6878 ATCT-TTC
1 CTCTATTC
6885 TCTCTATCTTTC
1 -CTCTA---TTC
6897 TCTCTATTC
1 -CTCTATTC
6906 CTCTATTC
1 CTCTATTC
6914 CTCTAT
1 CTCTAT
6920 ATATCTTTCT
Statistics
Matches: 64, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
6 1 0.02
7 1 0.02
8 49 0.77
9 4 0.06
12 9 0.14
ACGTcount: A:0.13, C:0.35, G:0.00, T:0.51
Consensus pattern (8 bp):
CTCTATTC
Found at i:6894 original size:12 final size:12
Alignment explanation
Indices: 6877--6947 Score: 71
Period size: 12 Copynumber: 6.2 Consensus size: 12
6867 TTCCTCTATA
6877 TATCTTTCTCTC
1 TATCTTTCTCTC
6889 TATCTTTCTCTC
1 TATCTTTCTCTC
6901 TA---TTC-CTC
1 TATCTTTCTCTC
* * *
6909 TAT-TCCTCTATA
1 TATCT-TTCTCTC
6921 TATCTTTCTCTC
1 TATCTTTCTCTC
6933 TATCTTTCTCTC
1 TATCTTTCTCTC
6945 TAT
1 TAT
6948 TCCTCTATGC
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
8 5 0.10
9 3 0.06
11 2 0.04
12 37 0.77
13 1 0.02
ACGTcount: A:0.13, C:0.31, G:0.00, T:0.56
Consensus pattern (12 bp):
TATCTTTCTCTC
Found at i:6908 original size:44 final size:44
Alignment explanation
Indices: 6854--6961 Score: 207
Period size: 44 Copynumber: 2.5 Consensus size: 44
6844 CCCTCTATTC
6854 CTCTATTCCTCTATTCCTCTATATATCTTTCTCTCTATCTTTCT
1 CTCTATTCCTCTATTCCTCTATATATCTTTCTCTCTATCTTTCT
6898 CTCTATTCCTCTATTCCTCTATATATCTTTCTCTCTATCTTTCT
1 CTCTATTCCTCTATTCCTCTATATATCTTTCTCTCTATCTTTCT
*
6942 CTCTATTCCTCTATGCCTCT
1 CTCTATTCCTCTATTCCTCT
6962 CTCAAATGAC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 63 1.00
ACGTcount: A:0.13, C:0.33, G:0.01, T:0.53
Consensus pattern (44 bp):
CTCTATTCCTCTATTCCTCTATATATCTTTCTCTCTATCTTTCT
Found at i:6909 original size:10 final size:9
Alignment explanation
Indices: 6837--6955 Score: 62
Period size: 8 Copynumber: 13.8 Consensus size: 9
6827 TACCTCTCTT
6837 TCTCTA-TC
1 TCTCTATTC
*
6845 CCTCTATTC
1 TCTCTATTC
6854 -CTCTATTC
1 TCTCTATTC
6862 -CTCTATTC
1 TCTCTATTC
*
6870 -CTCTA-TA
1 TCTCTATTC
*
6877 TATCT-TTC
1 TCTCTATTC
6885 TCTCTATCTTTC
1 TCTCTA---TTC
6897 TCTCTATTC
1 TCTCTATTC
6906 -CTCTATTC
1 TCTCTATTC
*
6914 -CTCTA-TA
1 TCTCTATTC
*
6921 TATCT-TTC
1 TCTCTATTC
6929 TCTCTATCTTTC
1 TCTCTA---TTC
6941 TCTCTATTC
1 TCTCTATTC
6950 -CTCTAT
1 TCTCTAT
6956 GCCTCTCTCA
Statistics
Matches: 89, Mismatches: 9, Indels: 26
0.72 0.07 0.21
Matches are distributed among these distances:
7 2 0.02
8 61 0.69
9 8 0.09
12 18 0.20
ACGTcount: A:0.13, C:0.34, G:0.00, T:0.53
Consensus pattern (9 bp):
TCTCTATTC
Found at i:7211 original size:10 final size:10
Alignment explanation
Indices: 7196--7269 Score: 53
Period size: 10 Copynumber: 7.4 Consensus size: 10
7186 CTTCCCCATT
7196 ATTCTAGAAC
1 ATTCTAGAAC
7206 ATTCTAGAATC
1 ATTCTAGAA-C
* *
7217 -TTCCAGAGC
1 ATTCTAGAAC
* * *
7226 CTTCCACG-AT
1 ATTCTA-GAAC
*
7236 ATTCTAGAAT
1 ATTCTAGAAC
*
7246 ATTCCAGAAC
1 ATTCTAGAAC
7256 ATTCTAGAAC
1 ATTCTAGAAC
7266 ATTC
1 ATTC
7270 CAAAGTGTTC
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
9 2 0.04
10 47 0.92
11 2 0.04
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (10 bp):
ATTCTAGAAC
Found at i:8154 original size:8 final size:8
Alignment explanation
Indices: 8143--8196 Score: 99
Period size: 8 Copynumber: 6.8 Consensus size: 8
8133 ACCTCTCTTT
*
8143 CTCTATCC
1 CTCTATTC
8151 CTCTATTC
1 CTCTATTC
8159 CTCTATTC
1 CTCTATTC
8167 CTCTATTC
1 CTCTATTC
8175 CTCTATTC
1 CTCTATTC
8183 CTCTATTC
1 CTCTATTC
8191 CTCTAT
1 CTCTAT
8197 ATATCTTTCT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
8 45 1.00
ACGTcount: A:0.13, C:0.39, G:0.00, T:0.48
Consensus pattern (8 bp):
CTCTATTC
Found at i:8161 original size:24 final size:24
Alignment explanation
Indices: 8134--8196 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
8124 TCTTCTCTTA
* *
8134 CCTCTCTTTCTCTATCCCTCTATT
1 CCTCTATTCCTCTATCCCTCTATT
*
8158 CCTCTATTCCTCTATTCCTCTATT
1 CCTCTATTCCTCTATCCCTCTATT
8182 CCTCTATTCCTCTAT
1 CCTCTATTCCTCTAT
8197 ATATCTTTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.11, C:0.40, G:0.00, T:0.49
Consensus pattern (24 bp):
CCTCTATTCCTCTATCCCTCTATT
Found at i:8215 original size:12 final size:12
Alignment explanation
Indices: 8198--8260 Score: 83
Period size: 12 Copynumber: 5.2 Consensus size: 12
8188 TTCCTCTATA
8198 TATCTTTCTCTC
1 TATCTTTCTCTC
8210 TATCTTTCTCTC
1 TATCTTTCTCTC
* * *
8222 TAT-TCCTCTATA
1 TATCT-TTCTCTC
8234 TATCTTTCTCTC
1 TATCTTTCTCTC
8246 TATCTTTCTCTC
1 TATCTTTCTCTC
8258 TAT
1 TAT
8261 TCCTCTATGC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
11 1 0.02
12 41 0.95
13 1 0.02
ACGTcount: A:0.13, C:0.30, G:0.00, T:0.57
Consensus pattern (12 bp):
TATCTTTCTCTC
Found at i:8230 original size:36 final size:36
Alignment explanation
Indices: 8183--8268 Score: 172
Period size: 36 Copynumber: 2.4 Consensus size: 36
8173 TCCTCTATTC
8183 CTCTATTCCTCTATATATCTTTCTCTCTATCTTTCT
1 CTCTATTCCTCTATATATCTTTCTCTCTATCTTTCT
8219 CTCTATTCCTCTATATATCTTTCTCTCTATCTTTCT
1 CTCTATTCCTCTATATATCTTTCTCTCTATCTTTCT
8255 CTCTATTCCTCTAT
1 CTCTATTCCTCTAT
8269 GCCTCTCTCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.14, C:0.31, G:0.00, T:0.55
Consensus pattern (36 bp):
CTCTATTCCTCTATATATCTTTCTCTCTATCTTTCT
Found at i:8562 original size:10 final size:10
Alignment explanation
Indices: 8549--8582 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
8539 CTTCCACGAT
*
8549 ATTCTAGAAT
1 ATTCTAGAAC
*
8559 ATTCCAGAAC
1 ATTCTAGAAC
8569 ATTCTAGAAC
1 ATTCTAGAAC
8579 ATTC
1 ATTC
8583 CAAAGTGTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (10 bp):
ATTCTAGAAC
Found at i:11189 original size:26 final size:26
Alignment explanation
Indices: 11153--11205 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
11143 ATTTGTATTG
11153 GCTCATAAAATTATGTAATGCTACCA
1 GCTCATAAAATTATGTAATGCTACCA
11179 GCTCATAAAATTATGTAATGCTACCA
1 GCTCATAAAATTATGTAATGCTACCA
11205 G
1 G
11206 TGAGTTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (26 bp):
GCTCATAAAATTATGTAATGCTACCA
Found at i:16848 original size:19 final size:19
Alignment explanation
Indices: 16824--16864 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
16814 CTTAAAAACC
* *
16824 CTTGAAGCTAATTAAGGTT
1 CTTGAAGCTAAGTAAGATT
16843 CTTGAAGCTAAGTAAGATT
1 CTTGAAGCTAAGTAAGATT
16862 CTT
1 CTT
16865 AACGTTTGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (19 bp):
CTTGAAGCTAAGTAAGATT
Found at i:19220 original size:6 final size:6
Alignment explanation
Indices: 19211--19240 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
19201 AATCTGCTTC
*
19211 TATATT TATATT TATATT TATCTT TATATT
1 TATATT TATATT TATATT TATATT TATATT
19241 AATTCGAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:22008 original size:16 final size:13
Alignment explanation
Indices: 21969--22000 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
21959 TTAGGCTCCG
*
21969 TTTGCTTGTTAAT
1 TTTGTTTGTTAAT
21982 TTTGTTTGTTAAT
1 TTTGTTTGTTAAT
21995 TTTGTT
1 TTTGTT
22001 ATTTGTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.12, C:0.03, G:0.16, T:0.69
Consensus pattern (13 bp):
TTTGTTTGTTAAT
Found at i:23707 original size:2 final size:2
Alignment explanation
Indices: 23700--23742 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
23690 CATATTCTAG
23700 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
23742 A
1 A
23743 TATATATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:27572 original size:2 final size:2
Alignment explanation
Indices: 27567--27613 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
27557 TTTTTCCCAC
* *
27567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27609 AT AT A
1 AT AT A
27614 ACATTATTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28775 original size:3 final size:3
Alignment explanation
Indices: 28767--28799 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
28757 TATTATCTTA
*
28767 ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28800 TTGAGAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:28893 original size:4 final size:4
Alignment explanation
Indices: 28884--28909 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
28874 TGCCAACAAG
28884 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
28910 ATCAGAAATT
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):
AATA
Found at i:34000 original size:167 final size:167
Alignment explanation
Indices: 33724--34056 Score: 605
Period size: 167 Copynumber: 2.0 Consensus size: 167
33714 GGTTAAGGAT
* *
33724 TTCATCCTCAGGCTGGGCAGCCTCATGCTGAGCTAACCCCTATTCTCTTTTTTATCCATTTGTCT
1 TTCATCCTCAGGCCGGGCAGCCTCATGCTGAGCTAACCCCTACTCTCTTTTTTATCCATTTGTCT
*
33789 TCACTTGTAAATTGTATGATTTTCTAGCGTAATGAAGGAACTGACAAACTGGAATGGTAAGTGAA
66 TCACTTGTAAAATGTATGATTTTCTAGCGTAATGAAGGAACTGACAAACTGGAATGGTAAGTGAA
*
33854 ATCAAAGACAATAAATCAATGGATTAAGTTTGGTCTA
131 ATCAAAGAAAATAAATCAATGGATTAAGTTTGGTCTA
33891 TTCATCCTCAGGCCGGGCAGCCTCATGCTGAGCTAACCCCTACTCTCTTTTTTATCCATTTGTCT
1 TTCATCCTCAGGCCGGGCAGCCTCATGCTGAGCTAACCCCTACTCTCTTTTTTATCCATTTGTCT
*
33956 TCACTTGTAAAATGTATGATTTT-TGAGCGTACTGAAGGAACTGACAAACTGGAATGGTAAGTGA
66 TCACTTGTAAAATGTATGATTTTCT-AGCGTAATGAAGGAACTGACAAACTGGAATGGTAAGTGA
34020 AATCAAAGAAAATAAATCAATGGATTAAGTTTGGTCT
130 AATCAAAGAAAATAAATCAATGGATTAAGTTTGGTCT
34057 CCAGAGTGAG
Statistics
Matches: 160, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
166 1 0.01
167 159 0.99
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (167 bp):
TTCATCCTCAGGCCGGGCAGCCTCATGCTGAGCTAACCCCTACTCTCTTTTTTATCCATTTGTCT
TCACTTGTAAAATGTATGATTTTCTAGCGTAATGAAGGAACTGACAAACTGGAATGGTAAGTGAA
ATCAAAGAAAATAAATCAATGGATTAAGTTTGGTCTA
Done.