Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1978
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: 46010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:10712 original size:70 final size:70
Alignment explanation
Indices: 10632--10820 Score: 317
Period size: 70 Copynumber: 2.7 Consensus size: 70
10622 TGAAATGCTT
10632 AACTTTAACTAGATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAAAAT
1 AACTTTAACTAGATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAAAAT
10697 GTATC
66 GTATC
10702 AACTTTAACTAGATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAAAAT
1 AACTTTAACTAGATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAAAAT
10767 GTATC
66 GTATC
* * * *
10772 AA-TATATTCATACATGTATCGATACATTGAAAAATATATCGATACATCT
1 AACTTTA-AC-TAGATGTATCGATACATTGAAAAATGTATCGATACATCT
10821 AGTTAAAAGA
Statistics
Matches: 113, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
69 3 0.03
70 73 0.65
71 37 0.33
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (70 bp):
AACTTTAACTAGATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAAAAT
GTATC
Found at i:10829 original size:70 final size:71
Alignment explanation
Indices: 10644--10865 Score: 299
Period size: 70 Copynumber: 3.2 Consensus size: 71
10634 CTTTAACTAG
*
10644 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAAAATGTATCAA-CT-T
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAAAATGTATCAATATAT
*
10707 TAACTAG
66 TAA-TAA
10714 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAAAATGTATCAATATAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAAAATGTATCAATATAT
* *
10779 TCATAC
66 TAATAA
* * * * * * *
10785 ATGTATCGATACATTGAAAAATATATCGATACATCT-AGTTAAAAGACATAATGTATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAAAATGTATCAATATAT
10849 TGAA-AA
66 T-AATAA
10855 ATGTATCGATA
1 ATGTATCGATA
10866 AATTTGGGCA
Statistics
Matches: 137, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
70 95 0.69
71 39 0.28
72 3 0.02
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (71 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAAAATGTATCAATATAT
TAATAA
Found at i:12933 original size:32 final size:33
Alignment explanation
Indices: 12875--12938 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
12865 CACACTCAGA
* *
12875 TGTATCGATACATATTGCTTAGTATCGATACAT
1 TGTACCGATACATATTGCATAGTATCGATACAT
*
12908 TGTACCGATACATGTT-CATAGTATCGATACA
1 TGTACCGATACATATTGCATAGTATCGATACA
12939 CCTTGAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (33 bp):
TGTACCGATACATATTGCATAGTATCGATACAT
Found at i:21392 original size:21 final size:20
Alignment explanation
Indices: 21347--21388 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
21337 TTGGATTTAA
21347 ATAAACTAAATTTAAAATCT
1 ATAAACTAAATTTAAAATCT
21367 ATAAATCTAAATTTAAAA-CT
1 ATAAA-CTAAATTTAAAATCT
21387 AT
1 AT
21389 TAAAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAAACTAAATTTAAAATCT
Found at i:22753 original size:20 final size:20
Alignment explanation
Indices: 22721--22759 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
22711 TAACAGATAA
*
22721 TTTTGAAACACGAGAATTAT
1 TTTTGAAACACGAAAATTAT
22741 TTTTGAATA-ACGAAAATTA
1 TTTTGAA-ACACGAAAATTA
22760 AAATCAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.36
Consensus pattern (20 bp):
TTTTGAAACACGAAAATTAT
Found at i:27437 original size:16 final size:16
Alignment explanation
Indices: 27411--27497 Score: 84
Period size: 16 Copynumber: 5.4 Consensus size: 16
27401 TTTTAAATCA
* *
27411 ATTTCGGGTTTGGATC
1 ATTTCGAGTTTGGGTC
*
27427 ATTTTGAGTTTGGGTC
1 ATTTCGAGTTTGGGTC
* *
27443 GTTTCGAGTTCGGGTC
1 ATTTCGAGTTTGGGTC
** *
27459 ATTTCGAGTTTGAATT
1 ATTTCGAGTTTGGGTC
* *
27475 ATTTCAAGTTCGGGTC
1 ATTTCGAGTTTGGGTC
27491 ATTTCGA
1 ATTTCGA
27498 ATTCGAGCCA
Statistics
Matches: 54, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 54 1.00
ACGTcount: A:0.16, C:0.13, G:0.28, T:0.44
Consensus pattern (16 bp):
ATTTCGAGTTTGGGTC
Found at i:27470 original size:48 final size:48
Alignment explanation
Indices: 27411--27502 Score: 112
Period size: 48 Copynumber: 1.9 Consensus size: 48
27401 TTTTAAATCA
* * ** * * *
27411 ATTTCGGGTTTGGATCATTTTGAGTTTGGGTCGTTTCGAGTTCGGGTC
1 ATTTCGAGTTTGAATCATTTCAAGTTCGGGTCATTTCGAATTCGGGTC
*
27459 ATTTCGAGTTTGAATTATTTCAAGTTCGGGTCATTTCGAATTCG
1 ATTTCGAGTTTGAATCATTTCAAGTTCGGGTCATTTCGAATTCG
27503 AGCCAATCGA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 36 1.00
ACGTcount: A:0.16, C:0.13, G:0.27, T:0.43
Consensus pattern (48 bp):
ATTTCGAGTTTGAATCATTTCAAGTTCGGGTCATTTCGAATTCGGGTC
Found at i:28398 original size:16 final size:16
Alignment explanation
Indices: 28379--28414 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
28369 AATTATCTCG
28379 AGTTTAAATCATTTTA
1 AGTTTAAATCATTTTA
*
28395 AGTTTAAATCATTTTG
1 AGTTTAAATCATTTTA
28411 AGTT
1 AGTT
28415 CAAGTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (16 bp):
AGTTTAAATCATTTTA
Found at i:28496 original size:21 final size:19
Alignment explanation
Indices: 28469--28513 Score: 54
Period size: 22 Copynumber: 2.2 Consensus size: 19
28459 TTTTTTTATC
*
28469 AATTTAAATTGAATCAAATTTA
1 AATTAAAATT-AATC-AA-TTA
28491 AATTAAAATTAATCAATTA
1 AATTAAAATTAATCAATTA
28510 AATT
1 AATT
28514 TTTTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 2 0.09
21 4 0.18
22 9 0.41
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (19 bp):
AATTAAAATTAATCAATTA
Found at i:30337 original size:18 final size:18
Alignment explanation
Indices: 30314--30370 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
30304 AATACTATTT
30314 TTAAAAAATTTTAAAATA
1 TTAAAAAATTTTAAAATA
* *
30332 TTAAAAAAATTTAAAAAA
1 TTAAAAAATTTTAAAATA
* *
30350 TAAAATAATATTTTTAAATA
1 TTAAA-AA-ATTTTAAAATA
30370 T
1 T
30371 AATATTGACA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
18 20 0.65
19 2 0.06
20 9 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAAAAATTTTAAAATA
Found at i:32135 original size:21 final size:21
Alignment explanation
Indices: 32086--32138 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
32076 ATAGCTATGT
*
32086 TATATGTA-AGTATTGTTATAT
1 TATATGTACA-TATTGTTATAC
* *
32107 TATGTGTACATATTGTTTTAC
1 TATATGTACATATTGTTATAC
32128 TATATGTACAT
1 TATATGTACAT
32139 TTAATTAGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.51
Consensus pattern (21 bp):
TATATGTACATATTGTTATAC
Found at i:33372 original size:37 final size:37
Alignment explanation
Indices: 33331--33440 Score: 197
Period size: 37 Copynumber: 3.0 Consensus size: 37
33321 AATAATGCCA
33331 ACTTTATAGAATATTGTAGTGCAAGAAACATTAGTGT
1 ACTTTATAGAATATTGTAGTGCAAGAAACATTAGTGT
*
33368 ACTTT-T-CAATATTGTAGTGCAAGAAACATTAGTGT
1 ACTTTATAGAATATTGTAGTGCAAGAAACATTAGTGT
33403 ACTTTATAGAATATTGTAGTGCAAGAAACATTAGTGT
1 ACTTTATAGAATATTGTAGTGCAAGAAACATTAGTGT
33440 A
1 A
33441 ATGATTAATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
35 33 0.48
36 2 0.03
37 34 0.49
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.35
Consensus pattern (37 bp):
ACTTTATAGAATATTGTAGTGCAAGAAACATTAGTGT
Found at i:36547 original size:18 final size:16
Alignment explanation
Indices: 36499--36548 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 16
36489 ATTTTAAGTC
36499 AATTTTTTTAAAAAA-
1 AATTTTTTTAAAAAAT
*
36514 AATTTATTTAATAAAAT
1 AATTTTTTTAA-AAAAT
36531 AATTTTTGTTACAAAAAT
1 AATTTTT-TTA-AAAAAT
36549 GAAATATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 10 0.34
16 4 0.14
17 6 0.21
18 8 0.28
19 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (16 bp):
AATTTTTTTAAAAAAT
Found at i:37789 original size:18 final size:18
Alignment explanation
Indices: 37740--37793 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
37730 TATATTCAAA
37740 TTTATATATAAAATAATTAT
1 TTTATATAT-AAATAA-TAT
* *
37760 TTT-TTTAAAAATAATAT
1 TTTATATATAAATAATAT
37777 TTTATATATAAATAATA
1 TTTATATATAAATAATA
37794 GATATAATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 6 0.21
18 17 0.59
19 3 0.10
20 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTATATATAAATAATAT
Found at i:38364 original size:2 final size:2
Alignment explanation
Indices: 38357--38392 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
38347 ATGGGTACTC
* *
38357 CT CT CT CT CT CT TT CT CT CT CT GT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
38393 GCAACACATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.44, G:0.03, T:0.53
Consensus pattern (2 bp):
CT
Found at i:42485 original size:2 final size:2
Alignment explanation
Indices: 42472--42515 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
42462 TATTGACCTC
*
42472 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42514 AT
1 AT
42516 TTATGTGTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.