Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold753
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: 27618
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Found at i:7296 original size:40 final size:40
Alignment explanation
Indices: 7216--7363 Score: 185
Period size: 40 Copynumber: 3.7 Consensus size: 40
7206 GATGATAACC
* **
7216 GGCTAAGT-CCGAAGGCATTT-TGCGCTAGTGACTAGTTCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTACATCCG
*
7256 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACATCCG
* *
7296 GGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACATCCG
* *
7336 GGCTATGTCCCGAAGGCA-TTGAGCGAGT
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGT
7364 AGCTATAGTC
Statistics
Matches: 96, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 8 0.08
40 72 0.75
41 12 0.12
42 4 0.04
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACATCCG
Found at i:12581 original size:38 final size:38
Alignment explanation
Indices: 12538--12613 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
12528 TTCATCCTTT
12538 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
12576 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
12614 GGAGTTCTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (38 bp):
TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
Found at i:13896 original size:40 final size:40
Alignment explanation
Indices: 13802--13946 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
13792 TACTCGAATG
*
13802 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* * *
13843 ACATCCGGACTAAGAT-CGGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
13883 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
13923 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
13947 CTTGTGCGAG
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.01
40 61 0.68
41 27 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:17577 original size:26 final size:26
Alignment explanation
Indices: 17548--17630 Score: 139
Period size: 26 Copynumber: 3.2 Consensus size: 26
17538 TGGTACAAAT
*
17548 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
17574 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
17600 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
17626 TGATA
1 TGATA
17631 GGCATTTCAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATGTTCCA
Found at i:20677 original size:25 final size:25
Alignment explanation
Indices: 20623--20680 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
20613 TTAATTTAAT
* *
20623 TTAATACTTATATTAATAGTATTTTA
1 TTAATA-TAATATTAATAGTATTATA
*
20649 TTAATATAATATTAA-AGTGATTATC
1 TTAATATAATATTAATAGT-ATTATA
20674 TTAATAT
1 TTAATAT
20681 TAAATTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 3 0.11
25 19 0.68
26 6 0.21
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.50
Consensus pattern (25 bp):
TTAATATAATATTAATAGTATTATA
Found at i:20758 original size:11 final size:11
Alignment explanation
Indices: 20744--20792 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 11
20734 ATAATATTAA
20744 ATTTATATAAT
1 ATTTATATAAT
20755 ATTTATATAAT
1 ATTTATATAAT
*
20766 AAATTTAATCTAAT
1 --ATTT-ATATAAT
20780 ATTTATATTAAT
1 ATTTATA-TAAT
20792 A
1 A
20793 AATATTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
11 13 0.41
12 9 0.28
13 4 0.12
14 6 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (11 bp):
ATTTATATAAT
Found at i:20761 original size:25 final size:25
Alignment explanation
Indices: 20733--20802 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
20723 ATTTTAATAA
*
20733 TATAATATTAAATTTATATAATATT
1 TATAATAATAAATTTATATAATATT
*
20758 TAT-ATAATAAATTTAATCTAATATT
1 TATAATAATAAATTT-ATATAATATT
*
20783 TATATTAATAAATATTATAT
1 TATAATAATAAAT-TTATAT
20803 TAATTTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
24 10 0.26
25 15 0.39
26 11 0.29
27 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (25 bp):
TATAATAATAAATTTATATAATATT
Found at i:20808 original size:25 final size:25
Alignment explanation
Indices: 20741--20816 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 25
20731 AATATAATAT
*
20741 TAAATTTATATAATATTTATA-TAA
1 TAAATTTATATTATATTTATATTAA
20765 TAAATTTA-ATCTAATATTTATATTAA
1 TAAATTTATAT-T-ATATTTATATTAA
20791 TAAATATTATATTA-ATTTAATATTAA
1 TAAAT-TTATATTATATTT-ATATTAA
20817 AGTGATTAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
23 2 0.04
24 8 0.18
25 13 0.29
26 16 0.36
27 4 0.09
28 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (25 bp):
TAAATTTATATTATATTTATATTAA
Found at i:21674 original size:33 final size:33
Alignment explanation
Indices: 21630--21702 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
21620 GGACATGCTT
* * *
21630 AACATGTGAATCAGATTTATAGTCAACATAGCC
1 AACATGCGAATCAAATTTATAGTCAACACAGCC
*
21663 AACATGCGAATCAAATTTATAGTCAACACAGTC
1 AACATGCGAATCAAATTTATAGTCAACACAGCC
21696 AACATGC
1 AACATGC
21703 TCAACATGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.25
Consensus pattern (33 bp):
AACATGCGAATCAAATTTATAGTCAACACAGCC
Found at i:26743 original size:39 final size:38
Alignment explanation
Indices: 26598--26751 Score: 152
Period size: 37 Copynumber: 4.0 Consensus size: 38
26588 ATTTGATGTG
* * ** *
26598 TATCCGGGCTTAAAGACCCGTAGGCTTTATGCTGGAATTA
1 TATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTATTA
26638 TATCCGGGTT-AATCCCGCAGGCTTCGTGCT-GTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
* *
26674 TATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
* * * *
26712 TATCTGAGTTTAAAGTCCC-TAGGCTTCGTGCTGGTGTTA
1 TATCCG-GGTTAAA-TCCCGCAGGCTTCGTGCTGGTATTA
26751 T
1 T
26752 GTTGGGTTTT
Statistics
Matches: 97, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
36 15 0.15
37 32 0.33
38 13 0.13
39 25 0.26
40 12 0.12
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.33
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
Done.