Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1600
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: 53433
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:103 original size:21 final size:21
Alignment explanation
Indices: 79--123 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
69 TCAGCTGCAA
* * *
79 TAAACACATTAAAAAAGTTAT
1 TAAACAAATGAAAAAACTTAT
*
100 TAAACAAATGAAAACACTTAT
1 TAAACAAATGAAAAAACTTAT
121 TAA
1 TAA
124 TTATAACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.58, C:0.11, G:0.04, T:0.27
Consensus pattern (21 bp):
TAAACAAATGAAAAAACTTAT
Found at i:12880 original size:30 final size:30
Alignment explanation
Indices: 12846--12942 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
12836 TAAACTAAAA
12846 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
12876 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
12906 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
12935 ATGAGCTA
1 -TGAGCTA
12943 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:15101 original size:12 final size:12
Alignment explanation
Indices: 15086--15116 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
15076 TTCTTTTTGC
15086 TTTTCAAAGGCT
1 TTTTCAAAGGCT
15098 TTTTCAAAGGCT
1 TTTTCAAAGGCT
15110 TTTTCAA
1 TTTTCAA
15117 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:15193 original size:6 final size:6
Alignment explanation
Indices: 15177--15226 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
15167 TTTCTTTTTA
*
15177 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
15226 T
1 T
15227 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:15209 original size:37 final size:37
Alignment explanation
Indices: 15166--15236 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
15156 CTTGCCTCTC
15166 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
15203 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
15237 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:15237 original size:16 final size:16
Alignment explanation
Indices: 15162--15222 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
15152 GCCTCTTGCC
*
15162 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
15178 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
15194 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
15210 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
15223 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:16167 original size:17 final size:17
Alignment explanation
Indices: 16147--16184 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
16137 TTTAACTCGA
16147 TTTTTTTGTC-ACTTTTT
1 TTTTTTTGTCGA-TTTTT
*
16164 TTTTTTTTTCGATTTTT
1 TTTTTTTGTCGATTTTT
16181 TTTT
1 TTTT
16185 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.05, C:0.08, G:0.05, T:0.82
Consensus pattern (17 bp):
TTTTTTTGTCGATTTTT
Found at i:16179 original size:12 final size:13
Alignment explanation
Indices: 16164--16204 Score: 59
Period size: 12 Copynumber: 3.2 Consensus size: 13
16154 GTCACTTTTT
16164 TTTTTTTTTCG-A
1 TTTTTTTTTCGAA
16176 TTTTTTTTT-GAA
1 TTTTTTTTTCGAA
16188 TTTTTTTTTCTGAA
1 TTTTTTTTTC-GAA
16202 TTT
1 TTT
16205 CTTCTCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.04
12 19 0.73
14 6 0.23
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:16193 original size:14 final size:14
Alignment explanation
Indices: 16164--16204 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 14
16154 GTCACTTTTT
16164 TTTTTTTTTC-G-A
1 TTTTTTTTTCTGAA
16176 -TTTTTTTT-TGAA
1 TTTTTTTTTCTGAA
16188 TTTTTTTTTCTGAA
1 TTTTTTTTTCTGAA
16202 TTT
1 TTT
16205 CTTCTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 8 0.32
14 7 0.28
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.76
Consensus pattern (14 bp):
TTTTTTTTTCTGAA
Found at i:17944 original size:30 final size:30
Alignment explanation
Indices: 17910--18006 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
17900 TAAACTAAAA
17910 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
17940 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
17970 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
17999 ATGAGCTA
1 -TGAGCTA
18007 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:20757 original size:9 final size:9
Alignment explanation
Indices: 20743--20770 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
20733 CAAAAAAATC
20743 AGTCAAAAA
1 AGTCAAAAA
20752 AGTCAAAAA
1 AGTCAAAAA
20761 AGTCAAAAA
1 AGTCAAAAA
20770 A
1 A
20771 TACGAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.68, C:0.11, G:0.11, T:0.11
Consensus pattern (9 bp):
AGTCAAAAA
Found at i:22050 original size:27 final size:27
Alignment explanation
Indices: 22020--22071 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
22010 ACAAGTGAGG
22020 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
22047 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
22072 AATTGAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:25740 original size:10 final size:10
Alignment explanation
Indices: 25725--25775 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
25715 TTGGGTTAAT
25725 ATTGAGCTGA
1 ATTGAGCTGA
25735 ATTGAGCTTGA
1 ATTGAGC-TGA
25746 A-TGAGCTGA
1 ATTGAGCTGA
*
25755 CTTGAGCTCG-
1 ATTGAGCT-GA
*
25765 AGTGAGCTGA
1 ATTGAGCTGA
25775 A
1 A
25776 CTAAGTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
9 4 0.12
10 25 0.74
11 5 0.15
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.27
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:25750 original size:20 final size:20
Alignment explanation
Indices: 25727--25775 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
25717 GGGTTAATAT
*
25727 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* *
25747 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
25767 TGAGCTGAA
1 TGAGCTGAA
25776 CTAAGTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.14, G:0.33, T:0.27
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:30782 original size:11 final size:10
Alignment explanation
Indices: 30766--30816 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 10
30756 TACGGTATTG
30766 TAAAAAAAA-
1 TAAAAAAAAT
*
30775 TATAAAAAACT
1 TA-AAAAAAAT
*
30786 TGAAAAAAAT
1 TAAAAAAAAT
30796 TCAAAAAAAAT
1 T-AAAAAAAAT
30807 TCAAAAAAAA
1 T-AAAAAAAA
30817 AGTTTGTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
9 2 0.06
10 14 0.40
11 19 0.54
ACGTcount: A:0.75, C:0.06, G:0.02, T:0.18
Consensus pattern (10 bp):
TAAAAAAAAT
Found at i:30783 original size:10 final size:10
Alignment explanation
Indices: 30768--30815 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
30758 CGGTATTGTA
30768 AAAAAAATAT-
1 AAAAAAAT-TC
* *
30778 AAAAAACTTG
1 AAAAAAATTC
30788 AAAAAAATTC
1 AAAAAAATTC
30798 AAAAAAAATTC
1 -AAAAAAATTC
30809 AAAAAAA
1 AAAAAAA
30816 AAGTTTGTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 1 0.03
10 22 0.67
11 10 0.30
ACGTcount: A:0.75, C:0.06, G:0.02, T:0.17
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:30817 original size:12 final size:11
Alignment explanation
Indices: 30788--30816 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
30778 AAAAAACTTG
30788 AAAAAAATTCA
1 AAAAAAATTCA
30799 AAAAAAATTCA
1 AAAAAAATTCA
30810 AAAAAAA
1 AAAAAAA
30817 AGTTTGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:31769 original size:21 final size:21
Alignment explanation
Indices: 31729--31788 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
31719 AATCTTGAAT
*
31729 GAAATTAAGAGAAGAA-AAAAA
1 GAAA-TAAGAGAAAAAGAAAAA
*
31750 GAAATGAGAGAAAAAGAAAAA
1 GAAATAAGAGAAAAAGAAAAA
*
31771 GAAATAAAAGAAAAAGAA
1 GAAATAAGAGAAAAAGAA
31789 CTAAAAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.26
21 25 0.74
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (21 bp):
GAAATAAGAGAAAAAGAAAAA
Found at i:31779 original size:15 final size:14
Alignment explanation
Indices: 31740--31799 Score: 66
Period size: 15 Copynumber: 4.1 Consensus size: 14
31730 AAATTAAGAG
31740 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
* *
31754 TGAGAGAAAAAGAAA
1 -AAGAAAAAAAGAAA
31769 AAGAAATAAAAGAAA
1 AAGAAA-AAAAGAAA
*
31784 AAGAACTAAAAGAAA
1 AAGAA-AAAAAGAAA
31799 A
1 A
31800 TGAGAGTGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
14 4 0.11
15 34 0.89
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.05
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:35478 original size:17 final size:18
Alignment explanation
Indices: 35441--35478 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
35431 GATTGAGAGT
* *
35441 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
35459 GAAAAGAAAT-TGAAAAA
1 GAAAAGAAATGTGAAAAA
35476 GAA
1 GAA
35479 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.63, C:0.03, G:0.24, T:0.11
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:35491 original size:13 final size:12
Alignment explanation
Indices: 35460--35514 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
35450 TGTGAAACAG
*
35460 AAAAGAAATTGA
1 AAAAGAAGTTGA
35472 AAAAGAAGTTGA
1 AAAAGAAGTTGA
*
35484 AGAAAGAAG-AGA
1 A-AAAGAAGTTGA
*
35496 AAATG-AGTTAGA
1 AAAAGAAGTT-GA
35508 AAAAGAA
1 AAAAGAA
35515 ACAAAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 21 0.62
13 8 0.24
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.13
Consensus pattern (12 bp):
AAAAGAAGTTGA
Found at i:40712 original size:40 final size:40
Alignment explanation
Indices: 40657--40737 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
40647 CCTTAGCTGC
*
40657 TGATAGGGGGTTGCGTGTGGACCAAGATCGAGTTGTCAAG
1 TGATACGGGGTTGCGTGTGGACCAAGATCGAGTTGTCAAG
40697 TGATACGGGGTTGCGTGTGGACCAAGATCGAGTTGTCAAG
1 TGATACGGGGTTGCGTGTGGACCAAGATCGAGTTGTCAAG
40737 T
1 T
40738 CACGAGAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.22, C:0.14, G:0.38, T:0.26
Consensus pattern (40 bp):
TGATACGGGGTTGCGTGTGGACCAAGATCGAGTTGTCAAG
Found at i:44166 original size:21 final size:21
Alignment explanation
Indices: 44140--44183 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
44130 AAAAGTTTTG
44140 AAAAAAAAATCGAAAAAAAAA
1 AAAAAAAAATCGAAAAAAAAA
* *
44161 AAAAAAAAATTGCAAAAAAAA
1 AAAAAAAAATCGAAAAAAAAA
44182 AA
1 AA
44184 TTGCATACGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.84, C:0.05, G:0.05, T:0.07
Consensus pattern (21 bp):
AAAAAAAAATCGAAAAAAAAA
Found at i:44177 original size:14 final size:14
Alignment explanation
Indices: 44160--44188 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
44150 CGAAAAAAAA
44160 AAAAAAAAAATTGC
1 AAAAAAAAAATTGC
44174 AAAAAAAAAATTGC
1 AAAAAAAAAATTGC
44188 A
1 A
44189 TACGGTCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAAAAAAAATTGC
Done.