Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2661
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: 30282
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:9561 original size:130 final size:129
Alignment explanation
Indices: 9314--9561 Score: 327
Period size: 130 Copynumber: 1.9 Consensus size: 129
9304 ATTATACAGG
*
9314 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGATTA
1 TCTTATCTCCCTGAGATTACAGTAGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGATTA
* * *
9379 CAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAAGA
66 CAGCGGAGCAGATCAAAGACAGTAATCCTATCTCCCTGAGATTACAACGGAGCGGATTAAAAGA
* ** ** *
9443 TCTTATCTCTCTGAGGATTACAGTAGAGTAGACCGGAGAATTTCAGATCTTATCTCCCTGAGGTT
1 TCTTATCTCCCTGA-GATTACAGTAGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGATT
* ** * * *
9508 ACAGTGGAGCAGATTGAAGCCAG-AGATCTTATCTCCCTGAGATTACAGCGGAGC
65 ACAGCGGAGCAGATCAAAGACAGTA-ATCCTATCTCCCTGAGATTACAACGGAGC
9562 AGATCGAAGA
Statistics
Matches: 101, Mismatches: 16, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
129 14 0.14
130 87 0.86
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (129 bp):
TCTTATCTCCCTGAGATTACAGTAGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGATTA
CAGCGGAGCAGATCAAAGACAGTAATCCTATCTCCCTGAGATTACAACGGAGCGGATTAAAAGA
Found at i:9597 original size:87 final size:83
Alignment explanation
Indices: 9357--9693 Score: 263
Period size: 87 Copynumber: 3.9 Consensus size: 83
9347 AAAGAATTTC
* * * * *
9357 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTG-AGAT
1 AGATCTTATCTCCCTGAGATTACAGCAGAGCAGATCGAAGACACT-ATCCTATCTCCCTGAAG-T
* *
9421 TACAATGGAGCGGATTAA-A
64 TACAGTGGAGCAGATTAAGA
* * * * * * *
9440 AGATCTTATCTCTCTGAGGATTACAGTAGAGTAGACCGGAGA-ATTTCAGATCTTATCTCCCTGA
1 AGATCTTATCTCCCTGA-GATTACAGCAGAGCAGATCGAAGACA---C-TATCCTATCTCCCTGA
*
9504 GGTTACAGTGGAGCAGATTGAAGCCA
61 AGTTACAGTGGAGCAGATT-AAG--A
*
9530 GAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTT
1 -AGATCTTATCTCCCTGAGATTACAGCAGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTT
* *
9595 ACAGTGGAGCGGATTAAAATAA
65 ACAGTGGAGCAGATT--AA-GA
* * * * * *
9617 AGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCA-TCA--AGTCTTATCTCCCTGAAGT
1 A-GATCTTATCTCCCTGAGATTACAGCAGAGCAGATCGAAGACACTA-TCCTATCTCCCTGAAGT
*
9679 TGCAGTGGAGCAGAT
64 TACAGTGGAGCAGAT
9694 AGAAGAAACC
Statistics
Matches: 203, Mismatches: 35, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
83 17 0.08
84 19 0.09
85 29 0.14
86 30 0.15
87 68 0.33
88 3 0.01
90 20 0.10
91 17 0.08
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (83 bp):
AGATCTTATCTCCCTGAGATTACAGCAGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
CAGTGGAGCAGATTAAGA
Found at i:9640 original size:44 final size:42
Alignment explanation
Indices: 9314--9815 Score: 191
Period size: 44 Copynumber: 11.6 Consensus size: 42
9304 ATTATACAGG
* *
9314 TCTTATCTCCCTG-AGATTACAGTGGAACAGACCA-AAGAATTTCAGA
1 TCTTATCTCCCTGAAG-TTACAGTGGAGCAGA-TAGAAGAA----AGA
* *
9360 TCTTATCTCCCTG-AGATTACAGCGGAGCAGATCA-AAGATAGTAA
1 TCTTATCTCCCTGAAG-TTACAGTGGAGCAGAT-AGAAGAAAG--A
* * * * *
9404 TCCTATCTCCTTG-AGATTACAATGGAGCGGAT--TA-AAAGA
1 TCTTATCTCCCTGAAG-TTACAGTGGAGCAGATAGAAGAAAGA
* * * * ** *
9443 TCTTATCTCTCTGAGGATTACAGTAGAGTAGACCGGAGAATTTCAGA
1 TCTTATCTCCCTGAAG-TTACAGTGGAGCAGATAGAAGAA----AGA
* * *
9490 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATAGAAG--AAAGA
* * **
9534 TCTTATCTCCCTG-AGATTACAGCGGAGCAGATCGAAGACACTA
1 TCTTATCTCCCTGAAG-TTACAGTGGAGCAGATAGAAGA-AAGA
* * * *
9577 TCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGA-TAGAAGAAA-GA
* * ** * * * **
9621 TCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATCAAG-
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATAGAAGAAAGA
* *
9662 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAGAAGAAACCAA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATAGAAGAAA--GA
* * * * * * * *
9706 TCCTATCTCTCTGAAGTTGCAGTAGAGCGGATTAAAATCACAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGA-TAGAA-GAAAGA
* * * * * **
9750 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAG-
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATAGAAGAAAGA
* *
9791 TCTTATTTCCCTGAAG-TACAATGGA
1 TCTTATCTCCCTGAAGTTACAGTGGA
9816 TTGAAGCGAC
Statistics
Matches: 348, Mismatches: 85, Indels: 52
0.72 0.18 0.11
Matches are distributed among these distances:
39 11 0.03
40 19 0.05
41 47 0.14
42 8 0.02
43 37 0.11
44 151 0.43
45 4 0.01
46 52 0.15
47 18 0.05
48 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (42 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGATAGAAGAAAGA
Found at i:9739 original size:129 final size:128
Alignment explanation
Indices: 9487--9807 Score: 403
Period size: 129 Copynumber: 2.5 Consensus size: 128
9477 GGAGAATTTC
* * * * *
9487 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTG-AGAT
1 AGATCTTATCTCTCTGAGGTTACAGTAGAGCAGATCGCA-TCA-AG-TCTTATCTCCCTGAAG-T
* * * *
9551 TACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAT-
62 TACAGCGGAGCAGATAGAAGAAACAATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATC
9615 AA
127 AA
* * *
9617 AGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATCAAGTCTTATCTCCCTGAAGTTGC
1 A-GATCTTATCTCTCTGAGGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGTTAC
* * * *
9682 AGTGGAGCAGATAGAAGAAACCAATCCTATCTCTCTGAAGTTGCAGTAGAGCGGATTAAAATCAC
65 AGCGGAGCAGATAGAAGAAA-CAATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATCAA
* * *
9747 AGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTTATTTCCCTGAAGT
1 AGATCTTATCTCTCTGAGGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGT
9808 ACAATGGATT
Statistics
Matches: 166, Mismatches: 21, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
128 33 0.20
129 96 0.58
130 5 0.03
131 32 0.19
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (128 bp):
AGATCTTATCTCTCTGAGGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGTTACA
GCGGAGCAGATAGAAGAAACAATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATCAA
Found at i:10022 original size:15 final size:15
Alignment explanation
Indices: 10002--10053 Score: 104
Period size: 15 Copynumber: 3.5 Consensus size: 15
9992 TAACAAAGGG
10002 ACCCAATACCCACAA
1 ACCCAATACCCACAA
10017 ACCCAATACCCACAA
1 ACCCAATACCCACAA
10032 ACCCAATACCCACAA
1 ACCCAATACCCACAA
10047 ACCCAAT
1 ACCCAAT
10054 TACCATCCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.46, C:0.46, G:0.00, T:0.08
Consensus pattern (15 bp):
ACCCAATACCCACAA
Found at i:10035 original size:8 final size:8
Alignment explanation
Indices: 10009--10051 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
9999 GGGACCCAAT
10009 ACCCACAA
1 ACCCACAA
*
10017 ACCCA-AT
1 ACCCACAA
10024 ACCCACAA
1 ACCCACAA
*
10032 ACCCA-AT
1 ACCCACAA
10039 ACCCACAA
1 ACCCACAA
10047 ACCCA
1 ACCCA
10052 ATTACCATCC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 12 0.41
8 17 0.59
ACGTcount: A:0.47, C:0.49, G:0.00, T:0.05
Consensus pattern (8 bp):
ACCCACAA
Found at i:11284 original size:18 final size:18
Alignment explanation
Indices: 11263--11311 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
11253 TTATTATAAC
11263 TATTTATATATATCATCT
1 TATTTATATATATCATCT
*
11281 TATTATATATTTAT-ATCT
1 TATT-TATATATATCATCT
11299 TA-TTATATATATC
1 TATTTATATATATC
11312 CATATATCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.30
17 1 0.04
18 10 0.37
19 8 0.30
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTATATATATCATCT
Found at i:11284 original size:33 final size:35
Alignment explanation
Indices: 11247--11311 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
11237 CCTATTATTA
11247 TTATTAT-TA-TTATAAC-TATTTATATATATCATC
1 TTATTATATATTTATAACTTA-TTATATATATCATC
*
11280 TTATTATATATTTATATCTTATTATATATATC
1 TTATTATATATTTATAACTTATTATATATATC
11312 CATATATCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 7 0.25
34 2 0.07
35 17 0.61
36 2 0.07
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (35 bp):
TTATTATATATTTATAACTTATTATATATATCATC
Found at i:14017 original size:17 final size:19
Alignment explanation
Indices: 13995--14037 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
13985 TAAATACATA
13995 ATAAATAAAG-TTTAAG-T
1 ATAAATAAAGATTTAAGAT
14012 ATAAAT-AAGATTTAAGAAT
1 ATAAATAAAGATTTAAG-AT
14031 ATAAATA
1 ATAAATA
14038 GCAGAATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 12 0.55
19 7 0.32
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (19 bp):
ATAAATAAAGATTTAAGAT
Found at i:14265 original size:69 final size:69
Alignment explanation
Indices: 14186--14323 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
14176 AATTAAACTC
14186 TCTTAATTTTTTTTTAAAATTCTCATTAATCTC-AAAAAAATTTAAAATTTTAATTAGTCACCCA
1 TCTTAATTTTTTTTTAAAATTCTCATTAATCTCAAAAAAAATTTAAAATTTTAATTAGTCACCCA
14250 ATTT
66 ATTT
14254 TCTTAATTTTTTTTTAAAATTCTCATTAATCTCAAAAAAAATTTAAAATTTTAATTAGTCACCCA
1 TCTTAATTTTTTTTTAAAATTCTCATTAATCTCAAAAAAAATTTAAAATTTTAATTAGTCACCCA
14319 ATTT
66 ATTT
14323 T
1 T
14324 ATTTATTCTC
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
68 33 0.48
69 36 0.52
ACGTcount: A:0.38, C:0.13, G:0.01, T:0.47
Consensus pattern (69 bp):
TCTTAATTTTTTTTTAAAATTCTCATTAATCTCAAAAAAAATTTAAAATTTTAATTAGTCACCCA
ATTT
Found at i:14339 original size:68 final size:68
Alignment explanation
Indices: 14199--14339 Score: 221
Period size: 69 Copynumber: 2.1 Consensus size: 68
14189 TAATTTTTTT
* *
14199 TTAAAATTCTCATTAATCTCAAAAAAATTTAAAATTTTAATTAGTCACCCAATTTTCTTAATTTT
1 TTAAAATTCTCATTAATCTCAAAAAAATTTAAAATTTTAATTAGTCACCCAATTTTATTAATTTC
**
14264 TTT
66 TCA
*
14267 TTAAAATTCTCATTAATCTCAAAAAAAATTTAAAATTTTAATTAGTCACCCAATTTTATTTA-TT
1 TTAAAATTCTCATTAATCTC-AAAAAAATTTAAAATTTTAATTAGTCACCCAATTTTATTAATTT
14331 CTCA
65 CTCA
14335 TTAAA
1 TTAAA
14340 TTCCTATTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
68 28 0.42
69 39 0.58
ACGTcount: A:0.40, C:0.13, G:0.01, T:0.45
Consensus pattern (68 bp):
TTAAAATTCTCATTAATCTCAAAAAAATTTAAAATTTTAATTAGTCACCCAATTTTATTAATTTC
TCA
Found at i:21748 original size:19 final size:18
Alignment explanation
Indices: 21719--21760 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
21709 TTACAACACC
21719 AAAAAAGTATATAATTGATT
1 AAAAAAGTATAT--TTGATT
21739 AAAAAA-TATATTTGATT
1 AAAAAAGTATATTTGATT
21756 AAAAA
1 AAAAA
21761 TAAAAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.50
19 5 0.23
20 6 0.27
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (18 bp):
AAAAAAGTATATTTGATT
Found at i:23928 original size:14 final size:14
Alignment explanation
Indices: 23909--23939 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
23899 TTTAAAACAG
*
23909 GTGCGTTGATAATT
1 GTGCGTTGACAATT
23923 GTGCGTTGACAATT
1 GTGCGTTGACAATT
23937 GTG
1 GTG
23940 TGCTCTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.10, G:0.32, T:0.39
Consensus pattern (14 bp):
GTGCGTTGACAATT
Found at i:25384 original size:67 final size:67
Alignment explanation
Indices: 25286--25430 Score: 281
Period size: 67 Copynumber: 2.2 Consensus size: 67
25276 GCACTCAGTT
25286 TAATTTCACATTTTTCTTAAGAATTCTTAATCTAATCTTGGGTCAGATTGGTTTAAACCATTTGA
1 TAATTTCACATTTTTCTTAAGAATTCTTAATCTAATCTTGGGTCAGATTGGTTTAAACCATTTGA
25351 CC
66 CC
25353 TAATTTCACATTTTTCTTAAGAATTCTTAATCTAATCTTGGGTCAGATTGGTTTAAACCATTTGA
1 TAATTTCACATTTTTCTTAAGAATTCTTAATCTAATCTTGGGTCAGATTGGTTTAAACCATTTGA
25418 CC
66 CC
*
25420 AAATTTCACAT
1 TAATTTCACAT
25431 CACACTCTAT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 77 1.00
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.43
Consensus pattern (67 bp):
TAATTTCACATTTTTCTTAAGAATTCTTAATCTAATCTTGGGTCAGATTGGTTTAAACCATTTGA
CC
Found at i:25610 original size:24 final size:24
Alignment explanation
Indices: 25583--25631 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
25573 CTTTCATTCC
25583 ATTGTTTCAGTTAATGACTTCCCA
1 ATTGTTTCAGTTAATGACTTCCCA
25607 ATTGTTTCAGTTAATGACTTCCCA
1 ATTGTTTCAGTTAATGACTTCCCA
25631 A
1 A
25632 AAATGTACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (24 bp):
ATTGTTTCAGTTAATGACTTCCCA
Found at i:28683 original size:27 final size:25
Alignment explanation
Indices: 28629--28688 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 25
28619 TTTTAAAAAT
*
28629 TAAATA-AAAATATTTTAAAAATTA
1 TAAATATAAAATATTTCAAAAATTA
*
28653 TAAATATAAAAGTATTATCAAAATTTA
1 TAAATATAAAA-TATT-TCAAAAATTA
*
28680 TAAAAATAA
1 TAAATATAA
28689 TAAATAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.20
25 4 0.13
26 4 0.13
27 16 0.53
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (25 bp):
TAAATATAAAATATTTCAAAAATTA
Done.