Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2155
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: 39412
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Found at i:894 original size:30 final size:26
Alignment explanation
Indices: 858--913 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 26
848 ATACTCATAT
858 ATTTTATTATTTCATAATCAAATTTAAATA
1 ATTTTA-TATTT-AT-AT-AAATTTAAATA
*
888 ATTTTATATTTATATAAATTTTAATA
1 ATTTTATATTTATATAAATTTAAATA
914 TATAATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 10 0.40
27 2 0.08
28 2 0.08
29 5 0.20
30 6 0.24
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTTTATATTTATATAAATTTAAATA
Found at i:904 original size:16 final size:16
Alignment explanation
Indices: 879--929 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
869 TCATAATCAA
*
879 ATTTAAATAATTTTAT
1 ATTTATATAATTTTAT
895 ATTTATATAAATTTTA-
1 ATTTATAT-AATTTTAT
*
911 ATATATAATAATTTT-T
1 ATTTAT-ATAATTTTAT
927 ATT
1 ATT
930 AAAATATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 20 0.69
17 9 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTATATAATTTTAT
Found at i:909 original size:17 final size:18
Alignment explanation
Indices: 887--928 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
877 AAATTTAAAT
*
887 AATTTTATATTTAT-ATA
1 AATTTTATATATATAATA
904 AATTTTA-ATATATAATA
1 AATTTTATATATATAATA
*
921 ATTTTTAT
1 AATTTTAT
929 TAAAATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTTTATATATATAATA
Found at i:964 original size:14 final size:14
Alignment explanation
Indices: 884--969 Score: 70
Period size: 14 Copynumber: 6.0 Consensus size: 14
874 ATCAAATTTA
884 AATAATTTTATATTT
1 AATAATTTTATA-TT
899 ATATAAATTTTAATATAT
1 A-AT-AATTTT-ATAT-T
917 AATAATTTT-TATT
1 AATAATTTTATATT
* **
930 AA-AATATTA-AAA
1 AATAATTTTATATT
942 AATAATTTTATATT
1 AATAATTTTATATT
*
956 AATATTTTTATATT
1 AATAATTTTATATT
970 TTTGTAATTA
Statistics
Matches: 57, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
12 8 0.14
13 9 0.16
14 17 0.30
15 1 0.02
16 8 0.14
17 9 0.16
18 5 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATAATTTTATATT
Found at i:1143 original size:62 final size:61
Alignment explanation
Indices: 1077--1198 Score: 167
Period size: 62 Copynumber: 2.0 Consensus size: 61
1067 ATATTTATAT
1077 GTAA-TTATTAATATTTTATATAATTACATTTACAAG-TAATATTATATGTAATTTATAAATAC
1 GTAATTTA-TAATATTTTATATAATTACATTTA-AAGATAATATTATATGTAATTTA-AAATAC
* * * *
1139 GTAATTTATAATATTTTATGTGATTATATTTAAAGATAATATTTTATGTAATTTAAAATA
1 GTAATTTATAATATTTTATATAATTACATTTAAAGATAATATTATATGTAATTTAAAATA
1199 TTTATATATA
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
61 8 0.15
62 43 0.80
63 3 0.06
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (61 bp):
GTAATTTATAATATTTTATATAATTACATTTAAAGATAATATTATATGTAATTTAAAATAC
Found at i:2769 original size:21 final size:19
Alignment explanation
Indices: 2743--2788 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
2733 ACAATTTGTT
2743 TCGATACAAATAGTAAATGTA
1 TCGATACAAA-AGT-AATGTA
* *
2764 TCGATACATAAGTATTGTA
1 TCGATACAAAAGTAATGTA
2783 TCGATA
1 TCGATA
2789 TAATGTATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 11 0.48
20 3 0.13
21 9 0.39
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (19 bp):
TCGATACAAAAGTAATGTA
Found at i:6824 original size:26 final size:28
Alignment explanation
Indices: 6776--6827 Score: 74
Period size: 26 Copynumber: 1.9 Consensus size: 28
6766 TTATTGAAAT
6776 TTTCAAATATATATAAAATATAATAAAG
1 TTTCAAATATATATAAAATATAATAAAG
6804 TTTC-AATAT-TAT-AAATAATAATAA
1 TTTCAAATATATATAAAAT-ATAATAA
6828 TAGGAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 4 0.17
26 10 0.43
27 5 0.22
28 4 0.17
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (28 bp):
TTTCAAATATATATAAAATATAATAAAG
Found at i:8203 original size:18 final size:18
Alignment explanation
Indices: 8180--8216 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
8170 AGATTTGGTT
8180 AACAAAATCTATTGAGAA
1 AACAAAATCTATTGAGAA
*
8198 AACAAAATCTGTTGAGAA
1 AACAAAATCTATTGAGAA
8216 A
1 A
8217 GTGACGTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.11, G:0.14, T:0.22
Consensus pattern (18 bp):
AACAAAATCTATTGAGAA
Found at i:9110 original size:20 final size:20
Alignment explanation
Indices: 9085--9125 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
9075 CCAAAAACAC
9085 TCTTTTTATTTAGAATTAGT
1 TCTTTTTATTTAGAATTAGT
9105 TCTTTTTATTTAGAATTAGT
1 TCTTTTTATTTAGAATTAGT
9125 T
1 T
9126 TAGAGTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.05, G:0.10, T:0.61
Consensus pattern (20 bp):
TCTTTTTATTTAGAATTAGT
Found at i:11705 original size:18 final size:18
Alignment explanation
Indices: 11660--11706 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
11650 ATTAGTTAAC
*
11660 AAAAGTTATAAAAGTAAT
1 AAAAGTTGTAAAAGTAAT
*
11678 -AAATTGTGTAAAAGTAAT
1 AAAAGT-TGTAAAAGTAAT
11696 AAAAGTTGTAA
1 AAAAGTTGTAA
11707 TATAATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 4 0.17
18 16 0.67
19 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (18 bp):
AAAAGTTGTAAAAGTAAT
Found at i:12720 original size:26 final size:26
Alignment explanation
Indices: 12691--12740 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
12681 ATGAAAAATT
*
12691 ATTTAATAAAATATTTATAAATAAGA
1 ATTTAATAAAATAGTTATAAATAAGA
**
12717 ATTTAATATTATAGTTATAAATAA
1 ATTTAATAAAATAGTTATAAATAA
12741 TATATAGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (26 bp):
ATTTAATAAAATAGTTATAAATAAGA
Found at i:12756 original size:18 final size:18
Alignment explanation
Indices: 12720--12757 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
12710 AATAAGAATT
*
12720 TAATATTATAGTTATAAA
1 TAATATTATAGTAATAAA
12738 TAATA-TATAGTAATCAAA
1 TAATATTATAGTAAT-AAA
12756 TA
1 TA
12758 TTTTAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (18 bp):
TAATATTATAGTAATAAA
Found at i:16591 original size:24 final size:23
Alignment explanation
Indices: 16558--16612 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
16548 ATTATTACAA
16558 TTATA-TAATTAATTAATT-TAGT
1 TTATATTAATTAATT-ATTATAGT
* *
16580 TTATAATTAATTTATTATTATATT
1 TTAT-ATTAATTAATTATTATAGT
16604 TTATATTAA
1 TTATATTAA
16613 AAAAATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 4 0.14
23 9 0.32
24 15 0.54
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TTATATTAATTAATTATTATAGT
Found at i:17081 original size:17 final size:18
Alignment explanation
Indices: 17053--17086 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
17043 TTTAATTAGT
17053 TATCATTTAATTATATTA
1 TATCATTTAATTATATTA
*
17071 TATCA-TTAATTTTATT
1 TATCATTTAATTATATT
17087 TTTTATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (18 bp):
TATCATTTAATTATATTA
Found at i:17426 original size:16 final size:16
Alignment explanation
Indices: 17392--17426 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
17382 CATATTTAGG
**
17392 ATATAATATGTCACGA
1 ATATAATATGTCAAAA
17408 ATATAATATGTCAAAA
1 ATATAATATGTCAAAA
17424 ATA
1 ATA
17427 ATTAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (16 bp):
ATATAATATGTCAAAA
Found at i:17450 original size:12 final size:12
Alignment explanation
Indices: 17433--17458 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17423 AATAATTAAA
17433 ATAAAAAATAAT
1 ATAAAAAATAAT
17445 ATAAAAAATAAT
1 ATAAAAAATAAT
17457 AT
1 AT
17459 GAACATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
ATAAAAAATAAT
Found at i:17794 original size:17 final size:17
Alignment explanation
Indices: 17768--17801 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17758 TCAAATATAT
*
17768 TAAATAAAAATTAAAAA
1 TAAATAAAAATGAAAAA
*
17785 TAAATTAAAATGAAAAA
1 TAAATAAAAATGAAAAA
17802 AATTAAGATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
TAAATAAAAATGAAAAA
Found at i:23549 original size:1 final size:1
Alignment explanation
Indices: 23545--23571 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
23535 TTCTTGTTTC
23545 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
23572 CTGGACGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:23765 original size:21 final size:19
Alignment explanation
Indices: 23740--23786 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
23730 GTATTAAAAC
23740 TTGTTTTTTTTGACTTTAAAT
1 TTGTTTTTTTT-A-TTTAAAT
*
23761 TTGTTAATTTTTATTTAAAT
1 TTGTT-TTTTTTATTTAAAT
23781 TT-TTTT
1 TTGTTTT
23787 AAAAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 1 0.04
19 2 0.09
20 9 0.39
21 6 0.26
22 5 0.22
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.70
Consensus pattern (19 bp):
TTGTTTTTTTTATTTAAAT
Found at i:31758 original size:51 final size:50
Alignment explanation
Indices: 31648--31781 Score: 180
Period size: 51 Copynumber: 2.7 Consensus size: 50
31638 ATTTGCCTGC
* * *
31648 ATGTATCGATACATTGAATG-ATGTATCGATACATTTGGGTAAAATCCAGA
1 ATGTATCGATATAATGAA-GAATGTATCGATACATTTGGGTAAAACCCAGA
***
31698 ATGTATCGATATAATGAAGAATGTATCGATACATTCTGGGTTTTACCCAGA
1 ATGTATCGATATAATGAAGAATGTATCGATACATT-TGGGTAAAACCCAGA
*
31749 ATGTATCGATATAATGAATAATGTATCGATACA
1 ATGTATCGATATAATGAAGAATGTATCGATACA
31782 AATAGTAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
49 1 0.01
50 31 0.41
51 43 0.57
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (50 bp):
ATGTATCGATATAATGAAGAATGTATCGATACATTTGGGTAAAACCCAGA
Found at i:34247 original size:153 final size:150
Alignment explanation
Indices: 34084--34686 Score: 552
Period size: 154 Copynumber: 4.0 Consensus size: 150
34074 TAAAATACAG
* *
34084 AGTTTTCTACTCCGTAAATTTTTCAGTAGGATTTTTTTAAGTTTATGATTTTCAAAATTC-TTAG
1 AGTTTTCTACTCCGTAAATTTTTCAGTAGGATTTTTCTAAGTTTATAATTTTCAAAATTCATTA-
* * * *
34148 AATATTATTGCTTAATTTACATTAAATTAATTTTGAAGAATTCAATTTATTTTATGATTTTTAGA
65 AATATTATT-CTTAATTCATATTAAATCAATTTTGAA-AATTCAATTTATTTTATGAGTTTTAGA
* *
34213 ATTTTTCCTATTACAAAAATACGA
128 ATTTTTTCTATTAC-AAAATATGA
* * * * *
34237 AATTTTCTACTTCGTAAATTTCTCCAGT-GAGATTTTTCTAAGTTTATAATTTTAAAAATTCTTT
1 AGTTTTCTACTCCGTAAATTT-TTCAGTAG-GATTTTTCTAAGTTTATAATTTTCAAAATTCATT
* * * * * *
34301 AAATATCATTGTTTAATTCATATTAAATCAGTTTTGAAAAAAT-AAGTTCATTTTATGAGTTGTA
64 AAATATTATT-CTTAATTCATATTAAATCAATTTTG-AAAATTCAA-TTTATTTTATGAGTTTTA
* *
34365 AAATTTTTTCTATTACTAAAATGTGA
126 GAATTTTTTCTATTAC-AAAATATGA
* * * * *
34391 AGTTTTCTATTCCGTAAATTTTTCTGAAGGATTTTTCTAAATTTATAA-TTTCTAAAATT-TTTC
1 AGTTTTCTACTCCGTAAATTTTTCAGTAGGATTTTTCTAAGTTTATAATTTTC-AAAATTCATT-
* * * * * * * *
34454 AAATATTATTTTTAGTTCTTATTAAATTATTTTTGAAAATTTAATATATTTTATGAGTTTTAGAT
64 AAATATTATTCTTAATTCATATTAAATCAATTTTGAAAATTCAATTTATTTTATGAGTTTTAGAA
* * * *
34519 TTTTTTCTGTTTTCAAGATATGG
129 TTTTTTCT-ATTACAAAATATGA
** * * * * *
34542 AGTTTTCTACTCCGTAAATTTTTTGGTAAGATTTTTTTGAGTTTATAATTTTTAGAATTCATTAA
1 AGTTTTCTACTCCGTAAATTTTTCAGTAGGATTTTTCTAAGTTTATAATTTTCAAAATTCATTAA
* * * *
34607 ATATT-TTCATTAGATCCATATTAAATCAATTTTTGTACATTCAATTTATTTTATGAGTTTTGGA
66 ATATTATTC-TTA-ATTCATATTAAATCAA-TTTTGAAAATTCAATTTATTTTATGAGTTTTAGA
* * *
34671 TTTTTTTATATAACAA
128 ATTTTTTCTATTACAA
34687 TTTTTCTCGG
Statistics
Matches: 364, Mismatches: 71, Indels: 31
0.78 0.15 0.07
Matches are distributed among these distances:
150 2 0.01
151 90 0.25
152 52 0.14
153 95 0.26
154 120 0.33
155 5 0.01
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.50
Consensus pattern (150 bp):
AGTTTTCTACTCCGTAAATTTTTCAGTAGGATTTTTCTAAGTTTATAATTTTCAAAATTCATTAA
ATATTATTCTTAATTCATATTAAATCAATTTTGAAAATTCAATTTATTTTATGAGTTTTAGAATT
TTTTCTATTACAAAATATGA
Found at i:36632 original size:153 final size:149
Alignment explanation
Indices: 36351--36797 Score: 412
Period size: 153 Copynumber: 3.0 Consensus size: 149
36341 TCCTCTGGGT
* * * *
36351 ACTTTCATGTCGAAGGTACCTAGGGGCATTTTCATAATTTTCATAT-AATCGAGTCTTAGGTTGT
1 ACTTTCATGTCGAAGGTACCCAAGGGCATTTTCGTAATTTT-ATTTGAATCGAGTCTTAGGTTGT
* * * * * * *
36415 CACCAGGATACTTTTATGTTGAAAGTGTGCATTTAAGATATGTTCATCCCATTTCTTATCATTTT
65 CACCGGGATACTTTTATGTCGAAGGTGTGCATTT-AGATAGGTT-ATCCCATTTATAATAATTTT
36480 AGTGTCCATTAGAGTTACTAGGAA
128 AGTGTCCATTAG-GTTACT-GGAA
* *
36504 ACTTTTATGTCGAAGGTACCCCAAGGGCATTTTCGT-ATTTTTTTTGAATCGAGTCTTAGGTTGT
1 ACTTTCATGTCGAAGGTA-CCCAAGGGCATTTTCGTAATTTTATTTGAATCGAGTCTTAGGTTGT
* * * *
36568 CACCGGGATACTTTTATGTCGAAGGTGTGCATTTAGTATAGGCTTATCGCAATTATGATTATTTT
65 CACCGGGATACTTTTATGTCGAAGGTGTGCATTTAG-ATAGG-TTATCCCATTTAT-AATAATTT
*
36633 TA-TGTCC------TT-C-GGAT
127 TAGTGTCCATTAGGTTACTGGAA
* * * * * * **
36647 ACTTTCACGTCAAAGGTATACCAATGGGTATTTTAGTAATTTTATTTGAATCGAGTGTTATTTTG
1 ACTTTCATGTCGAAGGTA-CCCAA-GGGCATTTTCGTAATTTTATTTGAATCGAGTCTTAGGTTG
* * * *
36712 TCATCGGGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTTATCCCATTTATAATAATTT
64 TCACCGGGATACTTTTATGTCGAAGGTGTGCATTTA-GATAGG-TTATCCCATTTATAATAATTT
*
36777 TAGTTTCCATTAGGGTTACTG
127 TAGTGTCCATTA-GGTTACTG
36798 AGATATTTTC
Statistics
Matches: 237, Mismatches: 39, Indels: 35
0.76 0.13 0.11
Matches are distributed among these distances:
143 22 0.09
144 18 0.08
145 76 0.32
146 3 0.01
152 6 0.03
153 89 0.38
154 23 0.10
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.41
Consensus pattern (149 bp):
ACTTTCATGTCGAAGGTACCCAAGGGCATTTTCGTAATTTTATTTGAATCGAGTCTTAGGTTGTC
ACCGGGATACTTTTATGTCGAAGGTGTGCATTTAGATAGGTTATCCCATTTATAATAATTTTAGT
GTCCATTAGGTTACTGGAA
Done.