Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4125
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: 15902
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2362 original size:44 final size:45
Alignment explanation
Indices: 2273--2885 Score: 520
Period size: 44 Copynumber: 14.2 Consensus size: 45
2263 GGAGTAGGTT
* * *
2273 GAAGATAACAGATCTTGTCTTCCTGTA-TGGACCGCAAAGTA-ATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGG-CAGCGAAGTAGATC
*
2317 GAAGATAGTA-ATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
2361 GAACATAGCAGATCTTGTCTT-CTGTATTGGCACCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
2405 -AAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*** * *
2449 GAAGACCTCAG--CGTTGTC-TCTCTG-A---GCAGCATGGAGTATG-TT
1 GAAGATAGCAGATC-TTGTCTTC-CTGTATTGGCAGC--GAAGTA-GATC
* * * *
2491 GAAAATAGTAGATCTTATCTTCCTGTATTGGCAGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * * * *
2536 GAAGAT-GACA-AGCCTGTCTCCCTG-AGTAGCAGTGGAGTAGATC
1 GAAGATAG-CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
2579 -AATATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
2623 GAAGAT-GACAGATCTTGTCTTCCTGTATTGGCAGTGATGTAGATC
1 GAAGATAG-CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
** * **
2668 -AATG-TAATAGATCTTGTCTTCCTTTACCGGCAGCGAAGTAGATC
1 GAA-GATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * *
2712 -AAGATAGTAGATCTTGTC-TCCTATA-TGGTAGCGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
2754 G-AGATA--AGATCTTGTCTTCCTGTATT-GCAGCGAAGTA-ATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * *
2794 AAAG-TAGCAGATCTAG-CTTTCT-T-TTGGTAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
2835 GAA-ACAGTAGATCTTATCTTCCTGTATTGGCAGCGAA-TAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
2878 GAAGATAG
1 GAAGATAG
2886 AAGTAACCAA
Statistics
Matches: 455, Mismatches: 74, Indels: 80
0.75 0.12 0.13
Matches are distributed among these distances:
39 2 0.00
40 30 0.07
41 36 0.08
42 50 0.11
43 99 0.22
44 167 0.37
45 67 0.15
47 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (45 bp):
GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
Found at i:2419 original size:88 final size:88
Alignment explanation
Indices: 2273--2885 Score: 522
Period size: 87 Copynumber: 7.1 Consensus size: 88
2263 GGAGTAGGTT
* * *
2273 GAAGATAACAGATCTTGTCTTCCTGTA-TGGACCGCAAAGTA-ATCGAAGATAGTA-ATCTTGTC
1 GAAGATAGCAGATCTTGTCTT-CTGTATTGG-CAGCGAAGTAGATC-AAGATAGTAGATCTTGTC
2335 TTCCTGTATTGGCAGCGAAGTAGATC
63 TTCCTGTATTGGCAGCGAAGTAGATC
* * *
2361 GAACATAGCAGATCTTGTCTTCTGTATTGGCACCGAAGTAGATCAAGATAGCAGATCTTGTCTTC
1 GAAGATAGCAGATCTTGTCTTCTGTATTGGCAGCGAAGTAGATCAAGATAGTAGATCTTGTCTTC
2426 CTGTATTGGCAGCGAAGTAGATC
66 CTGTATTGGCAGCGAAGTAGATC
*** * * * * *
2449 GAAGACCTCAG--CGTTGTCTCTCTG-A---GCAGCATGGAGTATGTTGAAAATAGTAGATCTTA
1 GAAGATAGCAGATC-TTGTCT-TCTGTATTGGCAGC--GAAGTA-GATCAAGATAGTAGATCTTG
*
2508 TCTTCCTGTATTGGCAGTGAAGTAGATC
61 TCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * * * * * *
2536 GAAGAT-GACA-AGCCTGTCTCCCTG-AGTAGCAGTGGAGTAGATCAATATAGCAGATCTTGTCT
1 GAAGATAG-CAGATCTTGTCT-TCTGTATTGGCAGCGAAGTAGATCAAGATAGTAGATCTTGTCT
* *
2598 TCCTATATTGGTAGCGAAGTAGATC
64 TCCTGTATTGGCAGCGAAGTAGATC
* * *
2623 GAAGAT-GACAGATCTTGTCTTCCTGTATTGGCAGTGATGTAGATCAATG-TAATAGATCTTGTC
1 GAAGATAG-CAGATCTTGTCTT-CTGTATTGGCAGCGAAGTAGATCAA-GATAGTAGATCTTGTC
* **
2686 TTCCTTTACCGGCAGCGAAGTAGATC
63 TTCCTGTATTGGCAGCGAAGTAGATC
* * * * **
2712 -AAGATAGTAGATCTTGTCTCCTATA-TGGTAGCGAAGTAGATTGAGATA--AGATCTTGTCTTC
1 GAAGATAGCAGATCTTGTCTTCTGTATTGGCAGCGAAGTAGATCAAGATAGTAGATCTTGTCTTC
2773 CTGTATT-GCAGCGAAGTA-ATC
66 CTGTATTGGCAGCGAAGTAGATC
* * * * *
2794 AAAG-TAGCAGATCTAG-CTTTCT-T-TTGGTAGCGAAGTAGATCGAA-ACAGTAGATCTTATCT
1 GAAGATAGCAGATCTTGTC-TTCTGTATTGGCAGCGAAGTAGATC-AAGATAGTAGATCTTGTCT
2854 TCCTGTATTGGCAGCGAA-TAGATC
64 TCCTGTATTGGCAGCGAAGTAGATC
2878 GAAGATAG
1 GAAGATAG
2886 AAGTAACCAA
Statistics
Matches: 432, Mismatches: 64, Indels: 61
0.78 0.11 0.11
Matches are distributed among these distances:
81 20 0.05
82 17 0.04
83 35 0.08
84 35 0.08
85 4 0.01
86 22 0.05
87 140 0.32
88 103 0.24
89 52 0.12
90 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (88 bp):
GAAGATAGCAGATCTTGTCTTCTGTATTGGCAGCGAAGTAGATCAAGATAGTAGATCTTGTCTTC
CTGTATTGGCAGCGAAGTAGATC
Found at i:3042 original size:44 final size:43
Alignment explanation
Indices: 2984--3093 Score: 132
Period size: 43 Copynumber: 2.5 Consensus size: 43
2974 ATCTAGTCTC
* *
2984 ATCT-CCTCGAGGTTGCAGTGGAGCAGATTGAATAAGCCAATCTT
1 ATCTCCCT-GAGGTTGCAGTGGAGCAGA-TGAAGAAACCAATCTT
* * *
3028 ATCTCCCTGGGGTTGCAGTGGAACAGATGAAGAAATCAATCTT
1 ATCTCCCTGAGGTTGCAGTGGAGCAGATGAAGAAACCAATCTT
* *
3071 ATCTCCCTGAAGTTGGAGTGGAG
1 ATCTCCCTGAGGTTGCAGTGGAG
3094 TGGATCAGAA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
43 32 0.57
44 21 0.38
45 3 0.05
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (43 bp):
ATCTCCCTGAGGTTGCAGTGGAGCAGATGAAGAAACCAATCTT
Found at i:3480 original size:44 final size:44
Alignment explanation
Indices: 3272--3480 Score: 122
Period size: 44 Copynumber: 4.8 Consensus size: 44
3262 GTACAAATCA
* ** * *
3272 TATCTCCCTGAGCAGTAGTGGAGTAGGTTTAAAATTGTAGATCC
1 TATCTCCCTGAGCAGTAGTGGAGTAGATCGAAGATTCTAGATCC
* * * ** * *
3316 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGA-ATCT
1 TATCTCCCTGAGCAGTAGTGGAGTAGATCGAAGA-TTCTAGATCC
* * * *** *
3360 TATCTTCCTGAG-A-TAGTAGGAAGCAGAGT-TAAGCCACCAG-TCC
1 TATCTCCCTGAGCAGTAGT-GG-AGTAGA-TCGAAGATTCTAGATCC
* * * *
3403 TATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAGATTCTAGATCC
1 TATCTCCCTGAGCAGTAGTGGAGTAGATCGAAGATTCTAGATCC
* *
3447 TGTCTCCCTAAGCAGTAGTGGAGTAGATCGAAGA
1 TATCTCCCTGAGCAGTAGTGGAGTAGATCGAAGA
3481 CGGCGAATCT
Statistics
Matches: 121, Mismatches: 35, Indels: 18
0.70 0.20 0.10
Matches are distributed among these distances:
42 5 0.04
43 29 0.24
44 82 0.68
45 5 0.04
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (44 bp):
TATCTCCCTGAGCAGTAGTGGAGTAGATCGAAGATTCTAGATCC
Found at i:3501 original size:44 final size:44
Alignment explanation
Indices: 3312--3518 Score: 122
Period size: 44 Copynumber: 4.7 Consensus size: 44
3302 AAAATTGTAG
* *
3312 ATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGA
1 ATCCTATCTTCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGA
* * * * *
3356 ATCTTATCTTCCTGAG-A-TAGTAGGAAGCAGAGT-TAAGCCA-CCA
1 ATCCTATCTTCCTAAGCAGTAGT-GG-AGCAGA-TCGAAGACAGCGA
* * * * * * ** *
3399 GTCCTATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAGA-TTCTA
1 ATCCTATCTTCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGA
* * * *
3442 GATCCTGTCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGCGA
1 -ATCCTATCTTCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGA
*
3487 ATCTTATCTTCCTAAG--GTAGTAGGAAGCAGAT
1 ATCCTATCTTCCTAAGCAGTAGT-GG-AGCAGAT
3519 TTAAGCCACC
Statistics
Matches: 122, Mismatches: 30, Indels: 22
0.70 0.17 0.13
Matches are distributed among these distances:
42 10 0.08
43 30 0.25
44 76 0.62
45 6 0.05
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.25
Consensus pattern (44 bp):
ATCCTATCTTCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGA
Found at i:3508 original size:131 final size:131
Alignment explanation
Indices: 3272--3661 Score: 627
Period size: 131 Copynumber: 3.0 Consensus size: 131
3262 GTACAAATCA
* *
3272 TATCTCCCTGAGCAGTAGTGGAGTAGGTTTAAAATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
* * * *
3337 AGCAGATCGAAGACAGCGAATCTTATCTTCCTGAGATAGTAGGAAGCAGAGTTAAGCCACCAGTC
66 AGCAGATCGAAGACGGCGAATCTTATCTTCCTAAGGTAGTAGGAAGCAGATTTAAGCCACCAGTC
3402 C
131 C
* * *
3403 TATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAGATTCTAGATCCTGTCTCCCTAAGCAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
*
3468 AGTAGATCGAAGACGGCGAATCTTATCTTCCTAAGGTAGTAGGAAGCAGATTTAAGCCACCAGTC
66 AGCAGATCGAAGACGGCGAATCTTATCTTCCTAAGGTAGTAGGAAGCAGATTTAAGCCACCAGTC
3533 C
131 C
* * *
3534 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAATATTGTAGATCCTGTCTCTCTAAGCAGTAGTAG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
* * *
3599 AGCAGATCAAAGACGGCGAGTCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCA
66 AGCAGATCGAAGACGGCGAATCTTATCTTCCTAAGGTAGTA-GGAAGCAGATTTAAGCCACCA
3662 ACCTTTTTCC
Statistics
Matches: 239, Mismatches: 19, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
131 218 0.91
132 21 0.09
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (131 bp):
TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
AGCAGATCGAAGACGGCGAATCTTATCTTCCTAAGGTAGTAGGAAGCAGATTTAAGCCACCAGTC
C
Found at i:4216 original size:22 final size:22
Alignment explanation
Indices: 4116--4203 Score: 146
Period size: 22 Copynumber: 4.1 Consensus size: 22
4106 AATCTTCAAG
4116 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
*
4135 GATATGCAATCTTAGAAGATAG
1 GATATGCAATCTTAGAAGATAT
4157 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
4179 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
4201 GAT
1 GAT
4204 TTTGTATCTT
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
19 13 0.20
22 51 0.80
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:4921 original size:30 final size:32
Alignment explanation
Indices: 4848--4923 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
4838 TAATTTATAT
*
4848 ACATACTTATATATATATATTTTTACATATTA
1 ACATACATATATATATATATTTTTACATATTA
* ** * *
4880 AAATATGTATATATATAT-TTTTTATA-ATTC
1 ACATACATATATATATATATTTTTACATATTA
4910 ACATACATATATAT
1 ACATACATATATAT
4924 TTTCTTATAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
30 14 0.39
31 7 0.19
32 15 0.42
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.49
Consensus pattern (32 bp):
ACATACATATATATATATATTTTTACATATTA
Found at i:4941 original size:20 final size:20
Alignment explanation
Indices: 4916--4953 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4906 ATTCACATAC
4916 ATATATAT-TTTCTTATATGT
1 ATATATATATTT-TTATATGT
4936 ATATATATATTTTTATAT
1 ATATATATATTTTTATAT
4954 TTTATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (20 bp):
ATATATATATTTTTATATGT
Done.