Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold271
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: 492225
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
File 4 of 4
Found at i:429851 original size:155 final size:154
Alignment explanation
Indices: 429632--430009 Score: 401
Period size: 155 Copynumber: 2.4 Consensus size: 154
429622 AGGTTTGTTT
* * * **
429632 TTATCTTTTTTAAGTCTTTTAGAGGTATCAAGTACTTTTACAT-TGAAGATATCCCTTAAAGGCA
1 TTATCCTTTTTAAGTCTTTTAG-GGTATCAGGTACTTTTACGTCAAAAG-TATCCCTTAAAGGCA
* * * * * * *
429696 TTTTTGTAATTTT-TCAAAA-CTGAGTCCTAGGTTATCATC-GGGTCTGCTTTTATACCGAAGCT
64 -TTTTGTAATTTTCT-AAAATC-AAGTCCAAAGTTATCACCAGGTTC-ACTTTTATACCAAAGCT
* * *
429758 GGATATTTAGGATAGGTTTAT-CCCATCTA
125 AGATATTTAGAATAGGTTAATCCCCATCTA
*
429787 TTATCCTTTTTAAGTCTTTTAAGGGTATCAGGTACTTTTACGTCAAAAGTATCCCTTAAGGGCAT
1 TTATCCTTTTTAAGTCTTTT-AGGGTATCAGGTACTTTTACGTCAAAAGTATCCCTTAAAGGCAT
* * * *
429852 TTTGTAATTTTCTAAAATCAAGTCCAAAGTTTTCACCAGGTTCACTTTTATGCTAAAGGTAGATA
65 TTTGTAATTTTCTAAAATCAAGTCCAAAGTTATCACCAGGTTCACTTTTATACCAAAGCTAGATA
*
429917 TTTAGAATAGGTTAATCCCCATCTT
130 TTTAGAATAGGTTAATCCCCATCTA
* * *
429942 TTATCCTTTTTAAGTCTTTTAGGAGCATC-GAGTACTTTAACGTCAAAAGTAT-CTTCTAAAGGC
1 TTATCCTTTTTAAGTCTTTTAGG-GTATCAG-GTACTTTTACGTCAAAAGTATCCCT-TAAAGGC
430005 ATTTT
63 ATTTT
430010 CATAATATTC
Statistics
Matches: 189, Mismatches: 25, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
154 65 0.34
155 119 0.63
156 5 0.03
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (154 bp):
TTATCCTTTTTAAGTCTTTTAGGGTATCAGGTACTTTTACGTCAAAAGTATCCCTTAAAGGCATT
TTGTAATTTTCTAAAATCAAGTCCAAAGTTATCACCAGGTTCACTTTTATACCAAAGCTAGATAT
TTAGAATAGGTTAATCCCCATCTA
Found at i:431797 original size:43 final size:42
Alignment explanation
Indices: 431749--431833 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
431739 CCATACTTAC
* *
431749 TTTGAAACAATCACAAATGCTTATGTAAGAAAATAAGAGGAAA
1 TTTGAAACAATCACAAATG-TCATGCAAGAAAATAAGAGGAAA
*
431792 TTTGAAACAGTCACAAATGTCATGCAAGAAAATAAGAGGAAA
1 TTTGAAACAATCACAAATGTCATGCAAGAAAATAAGAGGAAA
431834 GTTAACTCAC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 21 0.54
43 18 0.46
ACGTcount: A:0.51, C:0.11, G:0.18, T:0.21
Consensus pattern (42 bp):
TTTGAAACAATCACAAATGTCATGCAAGAAAATAAGAGGAAA
Found at i:434190 original size:14 final size:13
Alignment explanation
Indices: 434165--434208 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 13
434155 CAATGGATCA
434165 AAAAATTA-TTTT
1 AAAAATTATTTTT
434177 AAAAATTATTTTTT
1 AAAAATTA-TTTTT
* *
434191 AAAAAATATATTT
1 AAAAATTATTTTT
434204 AAAAA
1 AAAAA
434209 ATTAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 8 0.29
13 9 0.32
14 11 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAAAATTATTTTT
Found at i:434209 original size:14 final size:14
Alignment explanation
Indices: 434164--434210 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 14
434154 TCAATGGATC
434164 AAAAAAT-TATTTT
1 AAAAAATATATTTT
* *
434177 AAAAATTATTTTTT
1 AAAAAATATATTTT
434191 AAAAAATATA-TTT
1 AAAAAATATATTTT
434204 AAAAAAT
1 AAAAAAT
434211 TAAAAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 16 0.55
14 13 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAAAATATATTTT
Found at i:435326 original size:2 final size:2
Alignment explanation
Indices: 435319--435344 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
435309 TCGAACTTTG
435319 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
435345 TTGTTTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:436685 original size:4 final size:4
Alignment explanation
Indices: 436676--436702 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
436666 TTAACAATGC
436676 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT
436703 ATACTTGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:441257 original size:6 final size:6
Alignment explanation
Indices: 441243--441276 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
441233 CTATCAGGCA
*
441243 TTTCGT TTTCAT TTTCAT TTTCAT TTTCAT TTTC
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTC
441277 GTTGTGCCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.12, C:0.18, G:0.03, T:0.68
Consensus pattern (6 bp):
TTTCAT
Found at i:445189 original size:13 final size:13
Alignment explanation
Indices: 445171--445199 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
445161 ATACAGATTG
445171 CATTGTATCGATA
1 CATTGTATCGATA
445184 CATTGTATCGATA
1 CATTGTATCGATA
445197 CAT
1 CAT
445200 GACCAAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:445234 original size:21 final size:21
Alignment explanation
Indices: 445187--445239 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
445177 ATCGATACAT
*
445187 TGTATCGATACATGACCAAAG
1 TGTATCGATACATGACAAAAG
*
445208 -GTATCGATACTTGA-AAAAG
1 TGTATCGATACATGACAAAAG
445227 ATGTATCGATACA
1 -TGTATCGATACA
445240 GGTCATTGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 4 0.15
20 13 0.48
21 10 0.37
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (21 bp):
TGTATCGATACATGACAAAAG
Found at i:445309 original size:13 final size:13
Alignment explanation
Indices: 445291--445315 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
445281 ACACACAATA
445291 TGTATCGATACAT
1 TGTATCGATACAT
445304 TGTATCGATACA
1 TGTATCGATACA
445316 CCCCAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:445312 original size:32 final size:33
Alignment explanation
Indices: 445271--445338 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
445261 GTAGCCAAAT
*
445271 TTGTATCGATACA-CACAATATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
* *
445303 TTGTATCGATACACCCCAAAATGTATTGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
445336 TTG
1 TTG
445339 GCTAGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCACAAAATGTATCGATACA
Found at i:447640 original size:21 final size:21
Alignment explanation
Indices: 447614--447664 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
447604 TCAGATAACC
* *
447614 AAATCAAAAGTAGAAATATTT
1 AAATCAAAAGAAAAAATATTT
447635 AAATCAAAAGAAAAAATATTT
1 AAATCAAAAGAAAAAATATTT
*
447656 CAATCAAAA
1 AAATCAAAA
447665 CAACATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.63, C:0.08, G:0.06, T:0.24
Consensus pattern (21 bp):
AAATCAAAAGAAAAAATATTT
Found at i:448060 original size:15 final size:14
Alignment explanation
Indices: 448036--448065 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
448026 TAATAAAATA
448036 TATATTTATTAATT
1 TATATTTATTAATT
448050 TATAGTTTATTAATT
1 TATA-TTTATTAATT
448065 T
1 T
448066 TTTTATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
TATATTTATTAATT
Found at i:448176 original size:19 final size:20
Alignment explanation
Indices: 448148--448189 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
448138 AATTAAGATG
448148 TATTTAATTATTATAT-ATT
1 TATTTAATTATTATATAATT
* *
448167 TATTTTATTATTTTATAATT
1 TATTTAATTATTATATAATT
448187 TAT
1 TAT
448190 ATTTGAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTAATTATTATATAATT
Found at i:448531 original size:12 final size:13
Alignment explanation
Indices: 448514--448585 Score: 73
Period size: 12 Copynumber: 5.9 Consensus size: 13
448504 ATGAATTTTT
448514 ATATTA-TATTAG
1 ATATTATTATTAG
448526 ATATTATTATTA-
1 ATATTATTATTAG
*
448538 TTATTATTATTA-
1 ATATTATTATTAG
*
448550 TTATTATTATTA-
1 ATATTATTATTAG
*
448562 TTATTATTATTA-
1 ATATTATTATTAG
*
448574 TTATTATTATTA
1 ATATTATTATTA
448586 TATAACACAT
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
12 53 0.91
13 5 0.09
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (13 bp):
ATATTATTATTAG
Found at i:448535 original size:3 final size:3
Alignment explanation
Indices: 448527--448586 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
448517 TTATATTAGA
448527 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
448575 TAT TAT TAT TAT
1 TAT TAT TAT TAT
448587 ATAACACATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:449870 original size:51 final size:51
Alignment explanation
Indices: 449794--449896 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
449784 ATGATTGAGT
449794 TAATAGATTGTAGGTGAATTGAAAAAAACTTAGTGCCACCTTAATTTGTGA
1 TAATAGATTGTAGGTGAATTGAAAAAAACTTAGTGCCACCTTAATTTGTGA
*
449845 TAATAGATTGTAGGTGAATTGAAAAAACCTTAGTGCCACCTTAATTTGTGA
1 TAATAGATTGTAGGTGAATTGAAAAAAACTTAGTGCCACCTTAATTTGTGA
449896 T
1 T
449897 GGTTGGAACA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (51 bp):
TAATAGATTGTAGGTGAATTGAAAAAAACTTAGTGCCACCTTAATTTGTGA
Found at i:450710 original size:1 final size:1
Alignment explanation
Indices: 450704--450728 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
450694 TTGATTTTGC
450704 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
450729 GCTTTGAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:453367 original size:40 final size:40
Alignment explanation
Indices: 453322--453447 Score: 164
Period size: 40 Copynumber: 3.1 Consensus size: 40
453312 TTTTTATATG
* *
453322 ATTTATATAC-ATTTGATCTTATTGTTATGATTTATGTTTT
1 ATTTATAT-CTATTTGATCTGATTGTTATAATTTATGTTTT
453362 ATTTATATCTATTTGATCTGATTGTTATAATTTATGTTTT
1 ATTTATATCTATTTGATCTGATTGTTATAATTTATGTTTT
* * * * * *
453402 ATTTATATTTATATGATTTGATTATTATAGTTTATGTTCT
1 ATTTATATCTATTTGATCTGATTGTTATAATTTATGTTTT
453442 ATTTAT
1 ATTTAT
453448 TTAAATCATG
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 76 0.99
ACGTcount: A:0.26, C:0.04, G:0.10, T:0.60
Consensus pattern (40 bp):
ATTTATATCTATTTGATCTGATTGTTATAATTTATGTTTT
Found at i:458226 original size:14 final size:14
Alignment explanation
Indices: 458207--458235 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
458197 GAGAGGAGTC
458207 TTTAGGATAGAAGT
1 TTTAGGATAGAAGT
458221 TTTAGGATAGAAGT
1 TTTAGGATAGAAGT
458235 T
1 T
458236 AAAATTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.38
Consensus pattern (14 bp):
TTTAGGATAGAAGT
Found at i:459041 original size:9 final size:9
Alignment explanation
Indices: 459026--459073 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
459016 AAATTAATAG
459026 AAAAAATTA
1 AAAAAATTA
*
459035 CAAAAATTA
1 AAAAAATTA
459044 AAAAAA-TA
1 AAAAAATTA
* *
459052 AATAAATGA
1 AAAAAATTA
*
459061 AAAAAATGA
1 AAAAAATTA
459070 AAAA
1 AAAA
459074 CGAAAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
8 7 0.21
9 26 0.79
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (9 bp):
AAAAAATTA
Found at i:461728 original size:19 final size:19
Alignment explanation
Indices: 461704--461766 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
461694 AAACAGTAAA
461704 TGTATCGATACATAAGTAT
1 TGTATCGATACATAAGTAT
461723 TGTATCGATAC---A--A-
1 TGTATCGATACATAAGTAT
*
461736 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTAT
461755 TGTATCGATACA
1 TGTATCGATACA
461767 ATGTATTGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
16 2 0.05
19 23 0.62
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATAAGTAT
Found at i:461739 original size:32 final size:32
Alignment explanation
Indices: 461702--461772 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
461692 ACAAACAGTA
461702 AATGTATCGATACATAAGTATTGTATCGATAC
1 AATGTATCGATACATAAGTATTGTATCGATAC
*
461734 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTATTGTATCGATAC
461766 AATGTAT
1 AATGTAT
461773 TGCTACAAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (32 bp):
AATGTATCGATACATAAGTATTGTATCGATAC
Found at i:461741 original size:13 final size:13
Alignment explanation
Indices: 461723--461747 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
461713 ACATAAGTAT
461723 TGTATCGATACAA
1 TGTATCGATACAA
461736 TGTATCGATACA
1 TGTATCGATACA
461748 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:465670 original size:15 final size:15
Alignment explanation
Indices: 465650--465679 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
465640 AATTTTAAGA
*
465650 TTAATTAAGTTTAAT
1 TTAATTAAATTTAAT
465665 TTAATTAAATTTAAT
1 TTAATTAAATTTAAT
465680 GTTTGAGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TTAATTAAATTTAAT
Found at i:465683 original size:22 final size:21
Alignment explanation
Indices: 465654--465698 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
465644 TTAAGATTAA
465654 TTAAGTTT-AATTTAATTAAAT
1 TTAAGTTTGAATTT-ATTAAAT
*
465675 TTAATGTTTGAGTTTATTAAAT
1 TTAA-GTTTGAATTTATTAAAT
465697 TT
1 TT
465699 GATCATTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 13 0.62
23 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTAAGTTTGAATTTATTAAAT
Found at i:465847 original size:16 final size:16
Alignment explanation
Indices: 465742--465850 Score: 62
Period size: 16 Copynumber: 6.8 Consensus size: 16
465732 ATTTCAAGAC
*
465742 TTAGATTATTTTG-AT
1 TTAGATCATTTTGAAT
* * *
465757 TTTGAATTATTTTGAGT
1 TTAG-ATCATTTTGAAT
* *
465774 TTAAATCATTTTAAAT
1 TTAGATCATTTTGAAT
**
465790 TTA-ATTCATTTCAAAT
1 TTAGA-TCATTTTGAAT
*
465806 TGAGAGTCATTTTGAAT
1 TTAGA-TCATTTTGAAT
* *
465823 TAATG-TCATTTTGAGT
1 TTA-GATCATTTTGAAT
465839 TTAGATCATTTT
1 TTAGATCATTTT
465851 TAGGTTTTTT
Statistics
Matches: 73, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
15 5 0.07
16 52 0.71
17 15 0.21
18 1 0.01
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (16 bp):
TTAGATCATTTTGAAT
Found at i:471772 original size:3 final size:3
Alignment explanation
Indices: 471764--471796 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
471754 TAAAGATCTA
471764 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
471797 TTGTGAGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:472103 original size:15 final size:17
Alignment explanation
Indices: 472083--472119 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
472073 AATCAATTTT
472083 AAATA-TAAATATT-AA
1 AAATATTAAATATTCAA
*
472098 AAATATTAAATGTTCAA
1 AAATATTAAATATTCAA
472115 AAATA
1 AAATA
472120 AAAAAAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 7 0.37
17 7 0.37
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (17 bp):
AAATATTAAATATTCAA
Found at i:472715 original size:15 final size:16
Alignment explanation
Indices: 472687--472723 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
472677 ATTTAAAACT
472687 ATTTAAACTTAAAATA
1 ATTTAAACTTAAAATA
472703 ATTTAAA-TTAAAATA
1 ATTTAAACTTAAAATA
472718 ATTTAA
1 ATTTAA
472724 CCCGTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTTAAACTTAAAATA
Found at i:473654 original size:16 final size:16
Alignment explanation
Indices: 473611--473667 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
473601 TTAAAAAATT
473611 TAAT-TTATA-TAAAA
1 TAATATTATATTAAAA
* *
473625 TAATATAAAATTAAAA
1 TAATATTATATTAAAA
*
473641 TAATATTATTTTAAAA
1 TAATATTATATTAAAA
473657 TAAGTATTATA
1 TAA-TATTATA
473668 AGTAATATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
14 4 0.12
15 3 0.09
16 21 0.62
17 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
TAATATTATATTAAAA
Found at i:473772 original size:35 final size:32
Alignment explanation
Indices: 473732--473804 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
473722 TAATCATAAG
* *
473732 ATTTAAAATTTTTAATTTTAAATTATTTATTATTT
1 ATTTAAAATATTTAA---TAAATTATATATTATTT
*
473767 ATTTAATATATTTAATAAATTATATATTATTT
1 ATTTAAAATATTTAATAAATTATATATTATTT
*
473799 TTTTAA
1 ATTTAA
473805 TTTTTTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 21 0.62
35 13 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
ATTTAAAATATTTAATAAATTATATATTATTT
Found at i:476591 original size:17 final size:17
Alignment explanation
Indices: 476545--476583 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
476535 GTTTCAACAT
476545 AAAAAAG-AAAA-AA-A
1 AAAAAAGAAAAAGAAGA
476559 AAAAAAGAAAAAGAAGA
1 AAAAAAGAAAAAGAAGA
476576 AAAAAAGA
1 AAAAAAGA
476584 GGAAGAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.32
15 4 0.18
16 2 0.09
17 9 0.41
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAGAAGA
Found at i:477187 original size:15 final size:15
Alignment explanation
Indices: 477169--477198 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
477159 TTAATAAATT
477169 TTTAAAATTTAAAAA
1 TTTAAAATTTAAAAA
477184 TTTAAAATTTAAAAA
1 TTTAAAATTTAAAAA
477199 GATTTATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTAAAATTTAAAAA
Found at i:477243 original size:15 final size:15
Alignment explanation
Indices: 477225--477278 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
477215 GTTCCTTCAA
*
477225 ATAAGTTAATTAAAT
1 ATAAATTAATTAAAT
**
477240 ATAAATTAAATTTTA-
1 ATAAATT-AATTAAAT
*
477255 ATAAGTTAATTAAAT
1 ATAAATTAATTAAAT
477270 ATAAATTAA
1 ATAAATTAA
477279 ATTTTATTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
14 5 0.17
15 20 0.67
16 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (15 bp):
ATAAATTAATTAAAT
Found at i:477248 original size:11 final size:11
Alignment explanation
Indices: 477232--477280 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
477222 CAAATAAGTT
477232 AATTAAATATA
1 AATTAAATATA
* *
477243 AATTAAATTTT
1 AATTAAATATA
*
477254 AA-TAAGT-T-
1 AATTAAATATA
477262 AATTAAATATA
1 AATTAAATATA
477273 AATTAAAT
1 AATTAAAT
477281 TTTATTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
8 2 0.06
9 5 0.16
10 5 0.16
11 19 0.61
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
AATTAAATATA
Found at i:477258 original size:30 final size:30
Alignment explanation
Indices: 477224--477284 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
477214 TGTTCCTTCA
477224 AATAAGTTAATTAAATATAAATTAAATTTT
1 AATAAGTTAATTAAATATAAATTAAATTTT
477254 AATAAGTTAATTAAATATAAATTAAATTTT
1 AATAAGTTAATTAAATATAAATTAAATTTT
477284 A
1 A
477285 TTAAAAGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (30 bp):
AATAAGTTAATTAAATATAAATTAAATTTT
Found at i:482550 original size:15 final size:15
Alignment explanation
Indices: 482530--482595 Score: 69
Period size: 16 Copynumber: 4.3 Consensus size: 15
482520 ATTTAAATTA
*
482530 TATTTTAGTTTTAAT
1 TATTTTAATTTTAAT
*
482545 TATTTTGAATATTAAT
1 TATTTT-AATTTTAAT
* *
482561 TATTTTAAATTTATGT
1 TATTTTAATTTTA-AT
*
482577 TATTTTAATTTAAAT
1 TATTTTAATTTTAAT
482592 TATT
1 TATT
482596 AATTTTTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
15 16 0.39
16 25 0.61
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (15 bp):
TATTTTAATTTTAAT
Found at i:483209 original size:16 final size:16
Alignment explanation
Indices: 483188--483218 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
483178 AAAAAGGCTA
*
483188 TAAGTTGTAGTTTTTG
1 TAAGTTATAGTTTTTG
483204 TAAGTTATAGTTTTT
1 TAAGTTATAGTTTTT
483219 TTTAGAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (16 bp):
TAAGTTATAGTTTTTG
Found at i:483286 original size:19 final size:19
Alignment explanation
Indices: 483249--483286 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
483239 GTGGATTAAC
*
483249 TTAAAAAAATATAATTTTA
1 TTAAAAAAATATAAATTTA
483268 TTAAAAAAA-AGTAAATTTA
1 TTAAAAAAATA-TAAATTTA
483287 GATAGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (19 bp):
TTAAAAAAATATAAATTTA
Found at i:483675 original size:15 final size:16
Alignment explanation
Indices: 483640--483677 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
483630 ACAAATATAA
483640 TTTTAAAATTATAAAT
1 TTTTAAAATTATAAAT
* *
483656 ATTTAATATT-TAAAT
1 TTTTAAAATTATAAAT
483671 TTTTAAA
1 TTTTAAA
483678 CATCAAATAA
Statistics
Matches: 18, Mismatches: 4, Indels: 1
0.78 0.17 0.04
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAAAATTATAAAT
Found at i:485250 original size:22 final size:22
Alignment explanation
Indices: 485225--485267 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
485215 TTCACTGTTC
485225 ATCACTGTTCATGTATCGATAA
1 ATCACTGTTCATGTATCGATAA
485247 ATCACTGTTCATGTATCGATA
1 ATCACTGTTCATGTATCGATA
485268 CATTGAGTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (22 bp):
ATCACTGTTCATGTATCGATAA
Found at i:486408 original size:19 final size:20
Alignment explanation
Indices: 486368--486410 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
486358 ATCAATTGAT
*
486368 TTTTTCTTAATTAATTTTTA
1 TTTTTCTTAATTAATTTATA
486388 TTTTT-TTAATT-ATTTAATA
1 TTTTTCTTAATTAATTT-ATA
486407 TTTT
1 TTTT
486411 GATGTGATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 12 0.57
20 5 0.24
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTCTTAATTAATTTATA
Found at i:486442 original size:22 final size:22
Alignment explanation
Indices: 486417--486471 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
486407 TTTTGATGTG
*
486417 ATTGAATTAAATGATTCGATCA
1 ATTGAATTAAATGATTCAATCA
*
486439 ATTGAATTAAATGATTTAATCA
1 ATTGAATTAAATGATTCAATCA
*
486461 ATTAAATTAAA
1 ATTGAATTAAA
486472 AATAAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.38
Consensus pattern (22 bp):
ATTGAATTAAATGATTCAATCA
Found at i:488239 original size:17 final size:17
Alignment explanation
Indices: 488217--488288 Score: 60
Period size: 17 Copynumber: 4.4 Consensus size: 17
488207 CATCAAACAC
488217 GGGGGAAAGGGAGAGGA
1 GGGGGAAAGGGAGAGGA
* *
488234 GGGGG-AGGCGGAAAGGA
1 GGGGGAAAG-GGAGAGGA
* * *
488251 GAGGGAGAGGGGGAGGA
1 GGGGGAAAGGGAGAGGA
*
488268 -GAGGAAAGGGAG-GGA
1 GGGGGAAAGGGAGAGGA
488283 GGGGGA
1 GGGGGA
488289 GGAAGCGGCA
Statistics
Matches: 40, Mismatches: 12, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
15 3 0.08
16 14 0.35
17 22 0.55
18 1 0.03
ACGTcount: A:0.32, C:0.01, G:0.67, T:0.00
Consensus pattern (17 bp):
GGGGGAAAGGGAGAGGA
Found at i:488254 original size:22 final size:23
Alignment explanation
Indices: 488220--488291 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 23
488210 CAAACACGGG
*
488220 GGAAAGG-GAGAGGAGGGGGAGGC
1 GGAAAGGAGAG-GGAGGGGGAGGA
488243 GGAAAGGAGAGGGAGAGGGGGAGGAGA
1 GGAAAGGAGA-GG-GAGGGGGA-G-GA
488270 GGAAAGG-GAGGGAGGGGGAGGA
1 GGAAAGGAGAGGGAGGGGGAGGA
488292 AGCGGCAAGA
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
22 2 0.05
23 8 0.19
24 11 0.26
25 11 0.26
26 3 0.07
27 8 0.19
ACGTcount: A:0.33, C:0.01, G:0.65, T:0.00
Consensus pattern (23 bp):
GGAAAGGAGAGGGAGGGGGAGGA
Done.