Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1311
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: 25851
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:2105 original size:20 final size:20
Alignment explanation
Indices: 2058--2105 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
2048 AAGTAAGCTC
2058 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
2078 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
2098 GTTGAGCT
1 GTTGAGCT
2106 GACGGTGCTC
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:3827 original size:18 final size:17
Alignment explanation
Indices: 3804--3895 Score: 62
Period size: 18 Copynumber: 5.2 Consensus size: 17
3794 GTTTTTCGCT
3804 TTTTCTTTTTCAATTTTC
1 TTTTCTTTTTC-ATTTTC
*
3822 TTTTCTTCATTTCTTTTTC
1 TTTTCTT--TTTCATTTTC
* ** *
3841 -TCTCACTTTGA-TTTC
1 TTTTCTTTTTCATTTTC
*
3856 TTTTCTTTTGCAATTTTC
1 TTTTCTTTTTC-ATTTTC
*
3874 TTTTTCTTTTTCGTTTTC
1 -TTTTCTTTTTCATTTTC
3892 TTTT
1 TTTT
3896 TGTTTCTTTC
Statistics
Matches: 55, Mismatches: 13, Indels: 13
0.68 0.16 0.16
Matches are distributed among these distances:
15 4 0.07
16 8 0.15
17 5 0.09
18 19 0.35
19 15 0.27
20 4 0.07
ACGTcount: A:0.08, C:0.18, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTCTTTTTCATTTTC
Found at i:3890 original size:7 final size:6
Alignment explanation
Indices: 3802--3896 Score: 50
Period size: 6 Copynumber: 15.0 Consensus size: 6
3792 CGGTTTTTCG
* * **
3802 CTTTTT CTTTTT CAATTTT C-TTTT CTTCATTT CTTTTT CTCTCA CTTTGATT
1 CTTTTT CTTTTT C-TTTTT CTTTTT CTT--TTT CTTTTT CTTTTT CTTT--TT
* * *
3854 -TCTTTT CTTTTG CAATTTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CT-TTTT CTTTTT C-TTTTT CTTTTT CTTTTT CTTTTT CTTTTT
3897 GTTTCTTTCA
Statistics
Matches: 67, Mismatches: 13, Indels: 18
0.68 0.13 0.18
Matches are distributed among these distances:
5 5 0.07
6 43 0.64
7 11 0.16
8 8 0.12
ACGTcount: A:0.07, C:0.19, G:0.03, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:5198 original size:10 final size:11
Alignment explanation
Indices: 5183--5211 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
5173 AACTTTAATT
5183 TTTTTTTTGA-
1 TTTTTTTTGAC
5193 TTTTTTTTGAC
1 TTTTTTTTGAC
5204 TTTTTTTT
1 TTTTTTTT
5212 TTCGTTACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAC
Found at i:6648 original size:20 final size:20
Alignment explanation
Indices: 6601--6648 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
6591 AGTAAGCTCG
6601 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
6621 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
6641 GTTGAGCT
1 GTTGAGCT
6649 AGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:9606 original size:186 final size:186
Alignment explanation
Indices: 9244--9610 Score: 537
Period size: 186 Copynumber: 2.0 Consensus size: 186
9234 GTCAACAACT
* *
9244 TCTATTGTTGGTTCATTCTCTGCCCTTAGCCAAATGTTTCCCTTCGTTGTTAAACCCATTTCCCT
1 TCTATTGTTGGTTCATTCTCTACCCTTAGCCAAATGTTTCCATTCGTTGTTAAACCCATTTCCCT
9309 TTTAAACGTTTGTTTGTAGCCTTTCTTCTATCTTGAAACAAACTTAGCCTTACTCAAATTCACGA
66 TTTAAACGTTTGTTTGTAGCCTTTCTTCTATCTTGAAACAAACTTAGCCTTACTCAAATTCACGA
* *
9374 TCGAGCAAACACTAACGACTCGAATCAATCACAAAACGAGTTCGTATCAAACAATC
131 TCGAGCAAACACTAACGACTCAAAACAATCACAAAACGAGTTCGTATCAAACAATC
*
9430 TCTATTGTTGGTTCATTCTCTACCCTTAGCCAAAT-TTTCCATTCGTTGTTAAACCTATTTCCCT
1 TCTATTGTTGGTTCATTCTCTACCCTTAGCCAAATGTTTCCATTCGTTGTTAAACCCATTTCCCT
* * *
9494 TTTAAAC-TATTGTTTGTAGCCTTTGTTCTATTTTGTAGAAACGAACTTAGCCTTACTCAAATTC
66 TTTAAACGT-TTGTTTGTAGCCTTTCTTCTA-TCT-T-GAAACAAACTTAGCCTTACTCAAATTC
* * * * *
9558 ACGATTGGGC-AACAC-ATACGACTCAAAAC-ATCACGAGATGAGTTCGTATCAAA
127 ACGATCGAGCAAACACTA-ACGACTCAAAACAATCACAAAACGAGTTCGTATCAAA
9611 TTAGTATCAG
Statistics
Matches: 163, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
184 1 0.01
185 54 0.33
186 58 0.36
187 16 0.10
188 34 0.21
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.36
Consensus pattern (186 bp):
TCTATTGTTGGTTCATTCTCTACCCTTAGCCAAATGTTTCCATTCGTTGTTAAACCCATTTCCCT
TTTAAACGTTTGTTTGTAGCCTTTCTTCTATCTTGAAACAAACTTAGCCTTACTCAAATTCACGA
TCGAGCAAACACTAACGACTCAAAACAATCACAAAACGAGTTCGTATCAAACAATC
Found at i:9693 original size:11 final size:11
Alignment explanation
Indices: 9677--9709 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
9667 TAGTAGTTTC
9677 TTCAAAAAAAA
1 TTCAAAAAAAA
9688 TTC-AAAAAAA
1 TTCAAAAAAAA
9698 TTCAAAAAAAA
1 TTCAAAAAAAA
9709 T
1 T
9710 GGTTTCCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:9696 original size:10 final size:10
Alignment explanation
Indices: 9681--9707 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
9671 AGTTTCTTCA
9681 AAAAAAATTC
1 AAAAAAATTC
9691 AAAAAAATTC
1 AAAAAAATTC
9701 AAAAAAA
1 AAAAAAA
9708 ATGGTTTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:9768 original size:18 final size:16
Alignment explanation
Indices: 9745--9803 Score: 75
Period size: 15 Copynumber: 3.6 Consensus size: 16
9735 GATATTAAGT
9745 TGAAAAAAAAAATTTTCG
1 TGAAAAAAAAAA--TTCG
9763 TGAAAAAAAAAATTCG
1 TGAAAAAAAAAATTCG
*
9779 T-CAAAAAAAAATTCG
1 TGAAAAAAAAAATTCG
*
9794 TCAAAAAAAA
1 TGAAAAAAAA
9804 GAAGAAGCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.37
16 12 0.32
18 12 0.32
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.20
Consensus pattern (16 bp):
TGAAAAAAAAAATTCG
Found at i:9784 original size:15 final size:15
Alignment explanation
Indices: 9766--9803 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
9756 ATTTTCGTGA
9766 AAAAAAAAATTCGTC
1 AAAAAAAAATTCGTC
9781 AAAAAAAAATTCGTC
1 AAAAAAAAATTCGTC
9796 AAAAAAAA
1 AAAAAAAA
9804 GAAGAAGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.68, C:0.11, G:0.05, T:0.16
Consensus pattern (15 bp):
AAAAAAAAATTCGTC
Found at i:10777 original size:18 final size:18
Alignment explanation
Indices: 10741--10790 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
10731 AAAAGAAACC
10741 GAAAAAGAAACGAAA-ATT-
1 GAAAAAGAAA--AAAGATTG
10759 GAAAAAGAGAAAAAGATTG
1 GAAAAAGA-AAAAAGATTG
*
10778 GAGAAAGAAAAAA
1 GAAAAAGAAAAAA
10791 AAGAGTGCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 3 0.11
18 16 0.57
19 9 0.32
ACGTcount: A:0.68, C:0.02, G:0.22, T:0.08
Consensus pattern (18 bp):
GAAAAAGAAAAAAGATTG
Found at i:13641 original size:46 final size:46
Alignment explanation
Indices: 13589--13682 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
13579 ATAGTGTGGC
*
13589 GTTCATCATATACCAAGGTTCTTATCA-TCATTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTC-TTGATAGTGGGTCGAG
13635 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
13681 GT
1 GT
13683 CTTTTCTTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 44 0.96
47 2 0.04
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (46 bp):
GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
Found at i:16763 original size:13 final size:13
Alignment explanation
Indices: 16745--16792 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
16735 TAGTTTCTCG
16745 AAAAAAACTCGAAA
1 AAAAAAACTCG-AA
*
16759 AAAAAAATTC-AA
1 AAAAAAACTCGAA
* *
16771 AAAAAAATTTGAA
1 AAAAAAACTCGAA
16784 AAAAAAACT
1 AAAAAAACT
16793 AGTTTCCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.37
13 10 0.33
14 9 0.30
ACGTcount: A:0.73, C:0.08, G:0.04, T:0.15
Consensus pattern (13 bp):
AAAAAAACTCGAA
Found at i:16772 original size:12 final size:13
Alignment explanation
Indices: 16756--16790 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
16746 AAAAAACTCG
*
16756 AAAAAAAAAATTC
1 AAAAAAAAATTTC
*
16769 AAAAAAAAATTTG
1 AAAAAAAAATTTC
16782 AAAAAAAAA
1 AAAAAAAAA
16791 CTAGTTTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (13 bp):
AAAAAAAAATTTC
Found at i:16852 original size:14 final size:14
Alignment explanation
Indices: 16828--16881 Score: 92
Period size: 14 Copynumber: 3.9 Consensus size: 14
16818 GGATATCAAG
16828 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
16842 TT-TGAAAAAAAAA
1 TTGTGAAAAAAAAA
*
16855 TTGTGAAAAAAAAT
1 TTGTGAAAAAAAAA
16869 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
16882 GAGCTAGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
13 13 0.34
14 25 0.66
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.24
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:16858 original size:27 final size:28
Alignment explanation
Indices: 16828--16881 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
16818 GGATATCAAG
16828 TTGTGAAAAAAAAATT-TGAAAAAAAAA
1 TTGTGAAAAAAAAATTGTGAAAAAAAAA
*
16855 TTGTGAAAAAAAATTTGTGAAAAAAAA
1 TTGTGAAAAAAAAATTGTGAAAAAAAA
16882 GAGCTAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.24
Consensus pattern (28 bp):
TTGTGAAAAAAAAATTGTGAAAAAAAAA
Found at i:20253 original size:21 final size:22
Alignment explanation
Indices: 20229--20274 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
20219 GTAAAACAAG
20229 TGAGGAAAAAG-AAAAAGAGAA
1 TGAGGAAAAAGCAAAAAGAGAA
* *
20250 TGA-GAAAGAGCAAAAAGAGAT
1 TGAGGAAAAAGCAAAAAGAGAA
20271 TGAG
1 TGAG
20275 AGTGAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.59, C:0.02, G:0.30, T:0.09
Consensus pattern (22 bp):
TGAGGAAAAAGCAAAAAGAGAA
Done.