Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold234
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: 616507
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 5 of 5
Found at i:595505 original size:43 final size:43
Alignment explanation
Indices: 595395--595529 Score: 171
Period size: 43 Copynumber: 3.0 Consensus size: 43
595385 CTTAAAGGTG
** *
595395 AAGGTGCCAATGTACTGATTCAAGGCCAGCAACATTGGACTCAAAGGTG
1 AAGGTGCCAATGTGTTGATTCAAGGCCAGCAACATTGGACT------TA
595444 AAGGTGCCAATGTGTTGATTCAAGGCCAGCAACATTGGACTTA
1 AAGGTGCCAATGTGTTGATTCAAGGCCAGCAACATTGGACTTA
* *
595487 AAGGTGCCAATATGTTGATTCAAGGCCAGCAATATTGGACTTA
1 AAGGTGCCAATGTGTTGATTCAAGGCCAGCAACATTGGACTTA
595530 GAAGAAGATG
Statistics
Matches: 81, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
43 42 0.52
49 39 0.48
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (43 bp):
AAGGTGCCAATGTGTTGATTCAAGGCCAGCAACATTGGACTTA
Found at i:595511 original size:21 final size:21
Alignment explanation
Indices: 595444--595511 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
595434 CTCAAAGGTG
*
595444 AAGGTGCCAATGTGTTGATTC
1 AAGGTGCCAATATGTTGATTC
* * * *
595465 AAGG-CCAGCAACAT-TGGACTTA
1 AAGGTGC--CAATATGTTGA-TTC
595487 AAGGTGCCAATATGTTGATTC
1 AAGGTGCCAATATGTTGATTC
595508 AAGG
1 AAGG
595512 CCAGCAATAT
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
20 1 0.03
21 18 0.55
22 13 0.39
23 1 0.03
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.26
Consensus pattern (21 bp):
AAGGTGCCAATATGTTGATTC
Found at i:595519 original size:22 final size:22
Alignment explanation
Indices: 595451--595521 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
595441 GTGAAGGTGC
*
595451 CAATGTGTTGATTCAAGGCCAG
1 CAATATGTTGATTCAAGGCCAG
* * * *
595473 CAACAT-TGGACTTAAAGG--TG
1 CAATATGTTGA-TTCAAGGCCAG
595493 CCAATATGTTGATTCAAGGCCAG
1 -CAATATGTTGATTCAAGGCCAG
595516 CAATAT
1 CAATAT
595522 TGGACTTAGA
Statistics
Matches: 35, Mismatches: 9, Indels: 10
0.65 0.17 0.19
Matches are distributed among these distances:
20 1 0.03
21 14 0.40
22 19 0.54
23 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (22 bp):
CAATATGTTGATTCAAGGCCAG
Found at i:595817 original size:139 final size:139
Alignment explanation
Indices: 595588--595842 Score: 465
Period size: 139 Copynumber: 1.8 Consensus size: 139
595578 CTTGTATGCT
*
595588 TTTGAAGGTTGCCACTACTTTGTGGGCTTTGAAGGTTGCCACTAACTTGTGGGTTTTTGAAAAGA
1 TTTGAAGGTTGCCACTACTTTGTGGGCTTTGAAGGTTGCCACTAACTTATGGGTTTTTGAAAAGA
* * *
595653 TGCCCCTGACTTGTGGGCTTTTGAAAAGATTCCACTGACTTGTGGGCTTTGAAGGTTGCCACTAA
66 TGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTAGGCTTTGAAGGTTGCCACTAA
595718 CTTATGGGC
131 CTTATGGGC
*
595727 TTTGAAGGTTGCGACTACTTTGTGGGCTTTGAAGGTTGCCACTAACTTATGGGTTTTTGAAAAGA
1 TTTGAAGGTTGCCACTACTTTGTGGGCTTTGAAGGTTGCCACTAACTTATGGGTTTTTGAAAAGA
595792 TGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTAGGCTTTG
66 TGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTAGGCTTTG
595843 GAAAGTGAGG
Statistics
Matches: 111, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
139 111 1.00
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (139 bp):
TTTGAAGGTTGCCACTACTTTGTGGGCTTTGAAGGTTGCCACTAACTTATGGGTTTTTGAAAAGA
TGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTAGGCTTTGAAGGTTGCCACTAA
CTTATGGGC
Found at i:595839 original size:29 final size:28
Alignment explanation
Indices: 595585--595841 Score: 249
Period size: 29 Copynumber: 9.2 Consensus size: 28
595575 CAACTTGTAT
595585 GCTTTTGAAGGTTGCCACT-ACTTTGTGG
1 GCTTTTGAAGGTTGCCACTGAC-TTGTGG
*
595613 GC-TTTGAAGGTTGCCACTAACTTGTGG
1 GCTTTTGAAGGTTGCCACTGACTTGTGG
* * * *
595640 GTTTTTGAAAAGATGCCCCTGACTTGTGG
1 GCTTTTG-AAGGTTGCCACTGACTTGTGG
*
595669 GCTTTTGAAAAGATT-CCACTGACTTGTGG
1 GCTTTTG--AAGGTTGCCACTGACTTGTGG
* *
595698 GC-TTTGAAGGTTGCCACTAACTTATGG
1 GCTTTTGAAGGTTGCCACTGACTTGTGG
*
595725 GC-TTTGAAGGTTGCGACT-ACTTTGTGG
1 GCTTTTGAAGGTTGCCACTGAC-TTGTGG
* *
595752 GC-TTTGAAGGTTGCCACTAACTTATGG
1 GCTTTTGAAGGTTGCCACTGACTTGTGG
* * *
595779 GTTTTTGAAAAGATGCCACTGACTTGTGG
1 GCTTTTG-AAGGTTGCCACTGACTTGTGG
* * *
595808 GCTTTTGAAAAGATGCCACTGACTTGTAG
1 GCTTTTG-AAGGTTGCCACTGACTTGTGG
595837 GCTTT
1 GCTTT
595842 GGAAAGTGAG
Statistics
Matches: 196, Mismatches: 24, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.04
27 80 0.41
28 18 0.09
29 87 0.44
30 4 0.02
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (28 bp):
GCTTTTGAAGGTTGCCACTGACTTGTGG
Found at i:597274 original size:1 final size:1
Alignment explanation
Indices: 597270--597322 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
597260 TGTTTGTTTG
* * * * * *
597270 TTTTTGTTTTTTTTTTTGTTTTTTTTTTGTTTGTTGTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
597323 AGCGAAGGAC
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:597294 original size:37 final size:36
Alignment explanation
Indices: 597253--597322 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
597243 ATCCGGACCC
597253 TTTTTGTTGTTTGTTTGTTTTTGTTT-TTTTTTTTGTT
1 TTTTTGTTGTTTG-TTGTTTTT-TTTGTTTTTTTTGTT
*
597290 TTTTTTTTGTTTGTTGTTTTTTTTGTTTTTTTT
1 TTTTTGTTGTTTGTTGTTTTTTTTGTTTTTTTT
597323 AGCGAAGGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
35 3 0.10
36 16 0.52
37 12 0.39
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (36 bp):
TTTTTGTTGTTTGTTGTTTTTTTTGTTTTTTTTGTT
Found at i:597298 original size:29 final size:27
Alignment explanation
Indices: 597253--597322 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
597243 ATCCGGACCC
* * * *
597253 TTTTTGTTGTTTGTTTGTT-TTTGTTT
1 TTTTTTTTGTTTTTTTTTTGTTTGTTG
597279 TTTTTTTTGTTTTTTTTTTGTTTGTTG
1 TTTTTTTTGTTTTTTTTTTGTTTGTTG
597306 TTTTTTTTGTTTTTTTT
1 TTTTTTTTGTTTTTTTT
597323 AGCGAAGGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 16 0.41
27 23 0.59
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (27 bp):
TTTTTTTTGTTTTTTTTTTGTTTGTTG
Found at i:611375 original size:13 final size:13
Alignment explanation
Indices: 611357--611382 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
611347 AGGGTAGCTT
611357 TTGTATCGATACA
1 TTGTATCGATACA
611370 TTGTATCGATACA
1 TTGTATCGATACA
611383 ACACTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:612268 original size:5 final size:5
Alignment explanation
Indices: 612268--612302 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
612258 ATAAAATAAA
612268 AAAT- AAATT AAATT AAATT AAATT AAATT AAATT A
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT A
612303 CTATAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AAATT
Found at i:613682 original size:30 final size:30
Alignment explanation
Indices: 613635--613713 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 30
613625 TTTGTTTTTG
* *
613635 TTTTAAGATTTTTTATTTT-TCTTTAAAAA
1 TTTTAAAATTTTCTATTTTATCTTTAAAAA
*
613664 TTTTAAAATTTATCTATTTTATTTTTAAAAA
1 TTTTAAAATTT-TCTATTTTATCTTTAAAAA
*
613695 TTTTTAGAATTTT-TATTTT
1 -TTTTAAAATTTTCTATTTT
613714 CTATTTGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
29 10 0.23
30 13 0.30
31 10 0.23
32 10 0.23
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (30 bp):
TTTTAAAATTTTCTATTTTATCTTTAAAAA
Found at i:613719 original size:32 final size:31
Alignment explanation
Indices: 613635--613698 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
613625 TTTGTTTTTG
* * *
613635 TTTTAAGATTT-TTTATTTT-TCTTTAAAAA
1 TTTTAAAATTTATCTATTTTATTTTTAAAAA
613664 TTTTAAAATTTATCTATTTTATTTTTAAAAA
1 TTTTAAAATTTATCTATTTTATTTTTAAAAA
613695 TTTT
1 TTTT
613699 TAGAATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 10 0.33
30 7 0.23
31 13 0.43
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (31 bp):
TTTTAAAATTTATCTATTTTATTTTTAAAAA
Found at i:614764 original size:11 final size:11
Alignment explanation
Indices: 614748--614824 Score: 56
Period size: 11 Copynumber: 7.4 Consensus size: 11
614738 ATTAATTAAC
*
614748 ATAATATGAAT
1 ATAATATAAAT
*
614759 ATAATATAAAAA
1 ATAATAT-AAAT
*
614771 ATAATATGAAT
1 ATAATATAAAT
*
614782 ATGATAT-AA-
1 ATAATATAAAT
614791 AT-ATATAAAT
1 ATAATATAAAT
*
614801 ATATTA-AAAT
1 ATAATATAAAT
*
614811 AT-ATATAAAA
1 ATAATATAAAT
614821 ATAA
1 ATAA
614825 ATTATTATGT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
8 4 0.08
9 6 0.12
10 15 0.29
11 18 0.35
12 9 0.17
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:614778 original size:23 final size:23
Alignment explanation
Indices: 614748--614791 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
614738 ATTAATTAAC
614748 ATAATATGAATATAATATAAAAA
1 ATAATATGAATATAATATAAAAA
*
614771 ATAATATGAATATGATATAAA
1 ATAATATGAATATAATATAAA
614792 TATATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (23 bp):
ATAATATGAATATAATATAAAAA
Found at i:614793 original size:29 final size:28
Alignment explanation
Indices: 614750--614825 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
614740 TAATTAACAT
*
614750 AATATGA-ATATAATATAAAAAATAATATG
1 AATATGATATA-AATATAAAAAATAATA-A
* *
614779 AATATGATATAAATATATAAATATATTAA
1 AATATGATATAAATATA-AAAAATAATAA
*
614808 AATAT-ATATAAAAATAAA
1 AATATGATATAAATATAAA
614826 TTATTATGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 2 0.05
28 10 0.24
29 18 0.44
30 11 0.27
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (28 bp):
AATATGATATAAATATAAAAAATAATAA
Found at i:615240 original size:38 final size:40
Alignment explanation
Indices: 615190--615291 Score: 113
Period size: 38 Copynumber: 2.6 Consensus size: 40
615180 CATGTAATCT
* * * *
615190 ATTA-AAAATTAAAAAATTTACTAAATATAT-TAATTTTA
1 ATTATAAATTTAAAAAATTTAATAAATAAATATAAATTTA
*
615228 ATT-TAAATTTAAAAAATTTAATTAATAAATATAAATTTA
1 ATTATAAATTTAAAAAATTTAATAAATAAATATAAATTTA
*
615267 ATTAT-AATTTATAAAAAATTAATAA
1 ATTATAAATTTA-AAAAATTTAATAA
615292 TTTAAAATTA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
38 25 0.47
39 16 0.30
40 12 0.23
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (40 bp):
ATTATAAATTTAAAAAATTTAATAAATAAATATAAATTTA
Found at i:615247 original size:15 final size:15
Alignment explanation
Indices: 615227--615267 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
615217 TATTAATTTT
615227 AATTTAAATTTAAAA
1 AATTTAAATTTAAAA
*
615242 AATTT-AA-TTAATA
1 AATTTAAATTTAAAA
*
615255 AATATAAATTTAA
1 AATTTAAATTTAA
615268 TTATAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.41
14 4 0.18
15 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTTAAATTTAAAA
Found at i:615279 original size:19 final size:19
Alignment explanation
Indices: 615245--615306 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 19
615235 TTTAAAAAAT
*
615245 TTAATTAATAA-ATATAAA
1 TTAATTAATAATTTATAAA
615263 TTTAATT-ATAATTTATAAA
1 -TTAATTAATAATTTATAAA
*
615282 -AAATTAATAATTTA-AAA
1 TTAATTAATAATTTATAAA
615299 TTAATTAA
1 TTAATTAA
615307 CTTACACCCT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
17 7 0.19
18 18 0.49
19 12 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAATTAATAATTTATAAA
Found at i:616372 original size:13 final size:13
Alignment explanation
Indices: 616354--616380 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
616344 TGTATATATA
616354 TGTGTGTTGTGTG
1 TGTGTGTTGTGTG
616367 TGTGTGTTGTGTG
1 TGTGTGTTGTGTG
616380 T
1 T
616381 ATATTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.44, T:0.56
Consensus pattern (13 bp):
TGTGTGTTGTGTG
Done.