Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1903
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: 54939
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Found at i:6591 original size:17 final size:16
Alignment explanation
Indices: 6557--6603 Score: 62
Period size: 17 Copynumber: 3.0 Consensus size: 16
6547 AGGTTTTTTT
6557 AAATAATTT-A-ATTA
1 AAATAATTTAATATTA
6571 AAATAATTTAATATATA
1 AAATAATTTAATAT-TA
*
6588 AAATTATTTAATATTA
1 AAATAATTTAATATTA
6604 TCAAAAACAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 9 0.31
15 1 0.03
16 4 0.14
17 15 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATAATTTAATATTA
Found at i:7606 original size:2 final size:2
Alignment explanation
Indices: 7599--7635 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
7589 AGCTCAAGTC
7599 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7636 TAAAAATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7925 original size:25 final size:26
Alignment explanation
Indices: 7897--7989 Score: 86
Period size: 28 Copynumber: 3.5 Consensus size: 26
7887 ATTGTAATAA
*
7897 TTATTT-TAATATAGATTAATTTAAT
1 TTATTTATAAAATAGATTAATTTAAT
7922 TTATTATAATAAAATA-ATT-ATTTAAT
1 TTATT-T-ATAAAATAGATTAATTTAAT
*
7948 TTATCTTATAAAATAG-TTAATTTTTATT
1 TTAT-TTATAAAATAGATTAA--TTTAAT
7976 TTATTTCATAAAAT
1 TTATTT-ATAAAAT
7990 CTTCAAATAG
Statistics
Matches: 57, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
25 15 0.26
26 14 0.25
27 6 0.11
28 22 0.39
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
TTATTTATAAAATAGATTAATTTAAT
Found at i:7970 original size:26 final size:27
Alignment explanation
Indices: 7907--7970 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 27
7897 TTATTTTAAT
7907 ATAGATTAATTTAATTTATTATAATAAA
1 ATAG-TTAATTTAATTTATTATAATAAA
*
7935 ATAATT-ATTTAATTTATCT-T-ATAAA
1 ATAGTTAATTTAATTTAT-TATAATAAA
7960 ATAGTTAATTT
1 ATAGTTAATTT
7971 TTATTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 10 0.31
26 16 0.50
27 3 0.09
28 3 0.09
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (27 bp):
ATAGTTAATTTAATTTATTATAATAAA
Found at i:8189 original size:14 final size:14
Alignment explanation
Indices: 8172--8201 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
8162 TTCTCATAAA
8172 ATAATTATTTTATT
1 ATAATTATTTTATT
*
8186 ATAATTTTTTTATT
1 ATAATTATTTTATT
8200 AT
1 AT
8202 GATAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATAATTATTTTATT
Found at i:11767 original size:2 final size:2
Alignment explanation
Indices: 11762--11813 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
11752 GATATATGTG
11762 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11804 TA TA TA TA TA
1 TA TA TA TA TA
11814 ATCTTCTGGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14567 original size:20 final size:22
Alignment explanation
Indices: 14521--14569 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
14511 GAACATATCA
14521 AAATATATATAAAATAAATTAT
1 AAATATATATAAAATAAATTAT
* **
14543 TAATATAT-TAAAATTCA-TAT
1 AAATATATATAAAATAAATTAT
14563 AAATATA
1 AAATATA
14570 CAATACCTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 9 0.39
21 7 0.30
22 7 0.30
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATATATATAAAATAAATTAT
Found at i:16249 original size:54 final size:54
Alignment explanation
Indices: 16182--16291 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
16172 CTACGAGTGT
16182 TTAAAATATTGAACTTGTCTTCAACTATCTTGGAAACCATGATGCCTCGTATGA
1 TTAAAATATTGAACTTGTCTTCAACTATCTTGGAAACCATGATGCCTCGTATGA
16236 TTAAAATATTGAACTTGTCTTCAACTATCTTGGAAACCATGATGCCTCGTATGA
1 TTAAAATATTGAACTTGTCTTCAACTATCTTGGAAACCATGATGCCTCGTATGA
16290 TT
1 TT
16292 TATAATCTAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (54 bp):
TTAAAATATTGAACTTGTCTTCAACTATCTTGGAAACCATGATGCCTCGTATGA
Found at i:25068 original size:47 final size:47
Alignment explanation
Indices: 24999--25095 Score: 122
Period size: 47 Copynumber: 2.1 Consensus size: 47
24989 TAAATTTAAT
* * *
24999 AATTTAATAATATTTTTGTTTTATTGTTTATATTCAATAATAACTTA
1 AATTTAATAACATTTCTATTTTATTGTTTATATTCAATAATAACTTA
* * * * *
25046 AATTTAATTACATTTCTATTTTATTTTTTATATTTAATTATAATTTA
1 AATTTAATAACATTTCTATTTTATTGTTTATATTCAATAATAACTTA
25093 AAT
1 AAT
25096 CGACTTATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (47 bp):
AATTTAATAACATTTCTATTTTATTGTTTATATTCAATAATAACTTA
Found at i:26589 original size:24 final size:24
Alignment explanation
Indices: 26551--26628 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
26541 TTATTTTCAA
**
26551 ATTATAT-AATATATATTTTTTAT
1 ATTATATAAATATATATAATTTAT
26574 ATTTATATAAAT-TATATAATTTAT
1 A-TTATATAAATATATATAATTTAT
* * *
26598 ATCATATAAAAATATATTAAGTTAT
1 ATTATATAAATATATA-TAATTTAT
26623 -TTATAT
1 ATTATAT
26629 TTTAAAAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
23 9 0.20
24 26 0.58
25 10 0.22
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (24 bp):
ATTATATAAATATATATAATTTAT
Found at i:27399 original size:13 final size:14
Alignment explanation
Indices: 27368--27406 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
27358 AAAATTATTT
*
27368 AAATTTAATTTAATA
1 AAATTAAATTT-ATA
27383 TAAATTAAATTTATA
1 -AAATTAAATTTATA
27398 AAATTAAAT
1 AAATTAAAT
27407 AAATTACTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
15 3 0.14
16 10 0.45
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTAAATTTATA
Found at i:28707 original size:21 final size:21
Alignment explanation
Indices: 28651--28709 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
28641 CCCTTAATTA
* *
28651 TATCCATACAATTCT-ATCATG
1 TATCAATACAATCCTAAT-ATG
*
28672 TATCAATATAATCCTAATATG
1 TATCAATACAATCCTAATATG
* *
28693 TATCATTACACTCCTAA
1 TATCAATACAATCCTAA
28710 CATGCGTCGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.37
Consensus pattern (21 bp):
TATCAATACAATCCTAATATG
Found at i:30712 original size:20 final size:21
Alignment explanation
Indices: 30679--30720 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
30669 GTAAAGTTTG
*
30679 AGAAAATGAATTTAAAATTTA
1 AGAAAATGAATTTAAAAATTA
30700 AGAAAAT-AATTTAAAAATTA
1 AGAAAATGAATTTAAAAATTA
30720 A
1 A
30721 AAGCTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (21 bp):
AGAAAATGAATTTAAAAATTA
Found at i:30736 original size:25 final size:25
Alignment explanation
Indices: 30702--30762 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
30692 AAAATTTAAG
*
30702 AAAATAATTTAAAAATTAAAAGCTA
1 AAAATGATTTAAAAATTAAAAGCTA
*
30727 AAAATGATTTCAAAATTAAAAGCTA
1 AAAATGATTTAAAAATTAAAAGCTA
30752 AAAATGATTTA
1 AAAATGATTTA
30763 TTATTGAAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.30
Consensus pattern (25 bp):
AAAATGATTTAAAAATTAAAAGCTA
Found at i:34044 original size:21 final size:21
Alignment explanation
Indices: 34020--34129 Score: 166
Period size: 21 Copynumber: 5.2 Consensus size: 21
34010 AATTGTATTT
34020 ATACAATCTTGACATGTATCG
1 ATACAATCTTGACATGTATCG
*
34041 ATACCATCTTGACATGTATCG
1 ATACAATCTTGACATGTATCG
*
34062 ATACCATCTTGACATGTATCG
1 ATACAATCTTGACATGTATCG
* *
34083 ATACTATTTTGACATGTATCG
1 ATACAATCTTGACATGTATCG
* *
34104 ATACAATCTTGACATCTATTG
1 ATACAATCTTGACATGTATCG
34125 ATACA
1 ATACA
34130 CTTGGCTACA
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 82 1.00
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (21 bp):
ATACAATCTTGACATGTATCG
Found at i:35569 original size:25 final size:22
Alignment explanation
Indices: 35535--35595 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 22
35525 TGATTTATTT
35535 TTAAAT-AAAAATAATATAATATA
1 TTAAATCAAAAATAATAT-ATA-A
*
35558 TTAATATCAAAATTAATATATAA
1 TTAA-ATCAAAAATAATATATAA
*
35581 TTAAATTAAAAATAA
1 TTAAATCAAAAATAA
35596 ATTAAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 9 0.27
23 9 0.27
24 5 0.15
25 10 0.30
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
TTAAATCAAAAATAATATATAA
Found at i:35592 original size:23 final size:25
Alignment explanation
Indices: 35535--35593 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 25
35525 TGATTTATTT
35535 TTAAA-TAAAAA-TAATATAATATA
1 TTAAATTAAAAATTAATATAATATA
*
35558 TT-AATATCAAAATTAATAT-ATA-A
1 TTAAAT-TAAAAATTAATATAATATA
35581 TTAAATTAAAAAT
1 TTAAATTAAAAAT
35594 AAATTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
22 2 0.07
23 11 0.37
24 11 0.37
25 6 0.20
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
TTAAATTAAAAATTAATATAATATA
Found at i:35776 original size:11 final size:11
Alignment explanation
Indices: 35753--35805 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
35743 GAATTAAAAT
35753 ATAA-TTAA-A
1 ATAATTTAATA
*
35762 ATAATTTAATT
1 ATAATTTAATA
35773 ATAATTTAATA
1 ATAATTTAATA
35784 ATAA-TTAA-A
1 ATAATTTAATA
35793 GATAATTT-ATA
1 -ATAATTTAATA
35804 AT
1 AT
35806 TAAAAAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
9 5 0.14
10 15 0.41
11 17 0.46
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (11 bp):
ATAATTTAATA
Found at i:35791 original size:21 final size:22
Alignment explanation
Indices: 35744--35805 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 22
35734 TGTATACTTG
*
35744 AATTAAAATATAA-TTAA-AAT
1 AATTTAAATATAATTTAATAAT
*
35764 AATTTAATTATAATTTAATAAT
1 AATTTAAATATAATTTAATAAT
*
35786 AA-TTAAAGATAATTT-ATAAT
1 AATTTAAATATAATTTAATAAT
35806 TAAAAAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 16 0.44
21 15 0.42
22 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
AATTTAAATATAATTTAATAAT
Found at i:40913 original size:94 final size:94
Alignment explanation
Indices: 40738--40922 Score: 201
Period size: 94 Copynumber: 2.0 Consensus size: 94
40728 GCAAAATGAC
* * * * ** *
40738 ATGGCTAGTTGACTTTTCTGGTAATTACTGTAGATTTACATCTTTCAGATAGAATGATCCCCAAT
1 ATGGCTAATTGACTTTTCTGGTAACTACTGAAGATTTACATATACCAGATAGAATGATCCCCAAG
* * * * *
40803 TATGATAATAGTCAAGTCTGACAAAAAGT
66 TATAATAACAGGCAAGTATAACAAAAAGT
* * * * *
40832 ATGGCTAATTGACTTTTCTGGTAGCTACTGAAGATTTACATATACCCGTGTAGCATGATTCCC-A
1 ATGGCTAATTGACTTTTCTGGTAACTACTGAAGATTTACATATACCAG-ATAGAATGATCCCCAA
40896 GTATAATAACAGGCAAGTATAACAAAA
65 GTATAATAACAGGCAAGTATAACAAAA
40923 TGTAAGTCCG
Statistics
Matches: 73, Mismatches: 17, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
94 62 0.85
95 11 0.15
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Consensus pattern (94 bp):
ATGGCTAATTGACTTTTCTGGTAACTACTGAAGATTTACATATACCAGATAGAATGATCCCCAAG
TATAATAACAGGCAAGTATAACAAAAAGT
Done.