Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2031
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: 365977
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 3 of 3
Found at i:321731 original size:28 final size:29
Alignment explanation
Indices: 321666--321963 Score: 260
Period size: 28 Copynumber: 10.5 Consensus size: 29
321656 CGCCAACTTG
*
321666 TGTGGGCTTTTGAAAGGGTT-ACA-TCAACT
1 TGTGGGCTTTTGAAA-GGTTGCCACT-AACT
* *
321695 CGTGTGCTTTTG-AAGGTTGCCACTAACT
1 TGTGGGCTTTTGAAAGGTTGCCACTAACT
* * *
321723 TGTGGGC-TTTGAAAGGATACCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTAACT
*
321751 TGTGGG--TTTGAAAGGGGTGCCACTAACT
1 TGTGGGCTTTTGAAA-GGTTGCCACTAACT
* * * *
321779 TGTGCGCTTTTG-AAGATTGCCATTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTAACT
* *
321807 TGTAGGCTTTT-AAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTAACT
* * *
321835 TGTGGGC-TTTGGAAGAGATGCCACTGACT
1 TGTGGGCTTTTGAAAG-GTTGCCACTAACT
* * *
321864 TGTGGGCTTTGGAAAAGATGCCACTGAA-T
1 TGTGGGCTTTTGAAAGGTTGCCACT-AACT
*
321893 TGTGGGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTAACT
* * *
321921 TGTGGGCTTTGGAAAAGATGCCACTAACT
1 TGTGGGCTTTTGAAAGGTTGCCACTAACT
321950 TGTGGGC-TTTGAAA
1 TGTGGGCTTTTGAAA
321964 AGGTGAGGAA
Statistics
Matches: 220, Mismatches: 36, Indels: 27
0.78 0.13 0.10
Matches are distributed among these distances:
27 19 0.09
28 118 0.54
29 73 0.33
30 10 0.05
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (29 bp):
TGTGGGCTTTTGAAAGGTTGCCACTAACT
Found at i:321865 original size:29 final size:29
Alignment explanation
Indices: 321712--321960 Score: 274
Period size: 28 Copynumber: 8.8 Consensus size: 29
321702 TTTTGAAGGT
* *
321712 TGCCACTAACTTGTGGGCTTTGAAAG-GA
1 TGCCACTGACTTGTGGGCTTTGGAAGAGA
* * * *
321740 TACCACTGACTTGTGGG-TTTGAAAGGGG
1 TGCCACTGACTTGTGGGCTTTGGAAGAGA
* * * *
321768 TGCCACTAACTTGTGCGCTTTTGAAGA-T
1 TGCCACTGACTTGTGGGCTTTGGAAGAGA
* * ** *
321796 TGCCATTGACTTGTAGGCTTTTAAAG-GT
1 TGCCACTGACTTGTGGGCTTTGGAAGAGA
321824 TGCCACTGACTTGTGGGCTTTGGAAGAGA
1 TGCCACTGACTTGTGGGCTTTGGAAGAGA
*
321853 TGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACTGACTTGTGGGCTTTGGAAGAGA
* * *
321882 TGCCACTGAATTGTGGGCTTTTGAAG-GT
1 TGCCACTGACTTGTGGGCTTTGGAAGAGA
*
321910 TGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACTGACTTGTGGGCTTTGGAAGAGA
*
321939 TGCCACTAACTTGTGGGCTTTG
1 TGCCACTGACTTGTGGGCTTTG
321961 AAAAGGTGAG
Statistics
Matches: 186, Mismatches: 30, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
27 8 0.04
28 98 0.53
29 80 0.43
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (29 bp):
TGCCACTGACTTGTGGGCTTTGGAAGAGA
Found at i:321866 original size:57 final size:56
Alignment explanation
Indices: 321703--321960 Score: 299
Period size: 57 Copynumber: 4.6 Consensus size: 56
321693 CTCGTGTGCT
* * *
321703 TTTG-AAGGTTGCCACTAACTTGTGGGCTTTGAAAGGATACCACTGACTTGTGGG-
1 TTTGAAAGGATGCCACTAACTTGTGGGCTTTGGAAGGATGCCACTGACTTGTGGGC
* * * * *
321757 TTTGAAAGGGGTGCCACTAACTTGTGCGCTTTTGAA-GATTGCCATTGACTTGTAGGC
1 TTTGAAA-GGATGCCACTAACTTGTGGGCTTTGGAAGGA-TGCCACTGACTTGTGGGC
* * *
321814 TTTTAAAGGTTGCCACTGACTTGTGGGCTTTGGAAGAGATGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTAACTTGTGGGCTTTGGAAG-GATGCCACTGACTTGTGGGC
* * *
321871 TTTGGAAAAGATGCCACTGAA-TTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGC
1 TTT-GAAAGGATGCCACT-AACTTGTGGGCTTTGGAAGGATGCCACTGACTTGTGGGC
*
321928 TTTGGAAAAGATGCCACTAACTTGTGGGCTTTG
1 TTT-GAAAGGATGCCACTAACTTGTGGGCTTTG
321961 AAAAGGTGAG
Statistics
Matches: 174, Mismatches: 21, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
54 4 0.02
55 4 0.02
56 64 0.37
57 73 0.42
58 28 0.16
59 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (56 bp):
TTTGAAAGGATGCCACTAACTTGTGGGCTTTGGAAGGATGCCACTGACTTGTGGGC
Found at i:323414 original size:1 final size:1
Alignment explanation
Indices: 323400--323494 Score: 55
Period size: 1 Copynumber: 95.0 Consensus size: 1
323390 CATCCGGACC
* * * * * * * * * *
323400 TTTTTTGTTGTTTTTTTTTGTTTTTTTTGTCTTTTTTTCTTCTTTTTTTTGTTTTTTTCTTCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
323465 TTTTTCTTCTTTCTTCTTCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
323495 GTGGAGAACG
Statistics
Matches: 64, Mismatches: 30, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (1 bp):
T
Found at i:323416 original size:11 final size:10
Alignment explanation
Indices: 323400--323469 Score: 72
Period size: 11 Copynumber: 6.8 Consensus size: 10
323390 CATCCGGACC
*
323400 TTTTTTGTTG
1 TTTTTTTTTG
323410 TTTTTTTTTG
1 TTTTTTTTTG
323420 -TTTTTTTTG
1 TTTTTTTTTG
323429 TCTTTTTTTCT-
1 T-TTTTTTT-TG
323440 TCTTTTTTTTG
1 T-TTTTTTTTG
*
323451 TTTTTTTCTTC
1 TTTTTTT-TTG
323462 TTTTTTTT
1 TTTTTTTT
323470 CTTCTTTCTT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
9 9 0.17
10 17 0.32
11 26 0.49
12 1 0.02
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:323418 original size:13 final size:12
Alignment explanation
Indices: 323400--323496 Score: 63
Period size: 13 Copynumber: 7.7 Consensus size: 12
323390 CATCCGGACC
323400 TTTTTTGTTGTTT
1 TTTTTTGTT-TTT
323413 TTTTTTGTTTTT
1 TTTTTTGTTTTT
323425 TTTGTCTT-TTTTT
1 TTT-T-TTGTTTTT
323438 CTTCTTTT-TTTTGT
1 -TT-TTTTGTTTT-T
* *
323452 TTTTTTCTTCTT
1 TTTTTTGTTTTT
*
323464 TTTTTTCTTCTTT
1 TTTTTTGTT-TTT
* * *
323477 CTTCTTCTTTTT
1 TTTTTTGTTTTT
323489 TTTTTTGT
1 TTTTTTGT
323497 GGAGAACGCC
Statistics
Matches: 70, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
12 28 0.40
13 35 0.50
14 6 0.09
15 1 0.01
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (12 bp):
TTTTTTGTTTTT
Found at i:323425 original size:20 final size:18
Alignment explanation
Indices: 323400--323469 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 18
323390 CATCCGGACC
*
323400 TTTTTTGTTGTTTTTTTT
1 TTTTTTTTTGTTTTTTTT
323418 TGTTTTTTTTGTCTTTTTTTCT
1 T-TTTTTTTTG--TTTTTTT-T
323440 TCTTTTTTTTGTTTTTTTCT
1 T-TTTTTTTTGTTTTTTT-T
323460 TCTTTTTTTT
1 T-TTTTTTTT
323470 CTTCTTTCTT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
18 1 0.02
19 8 0.17
20 19 0.41
21 7 0.15
22 11 0.24
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (18 bp):
TTTTTTTTTGTTTTTTTT
Found at i:323427 original size:22 final size:21
Alignment explanation
Indices: 323400--323491 Score: 114
Period size: 22 Copynumber: 4.3 Consensus size: 21
323390 CATCCGGACC
* *
323400 TTTTTTGTTGTTTTTTTTTGTT
1 TTTTTTGTT-TTTTTTCTTCTT
323422 TTTTTTGTCTTTTTTTCTTCTT
1 TTTTTTGT-TTTTTTTCTTCTT
323444 TTTTTTG-TTTTTTTCTTCTT
1 TTTTTTGTTTTTTTTCTTCTT
* *
323464 TTTTTTCTTCTTTCTTCTTCTT
1 TTTTTTGTT-TTTTTTCTTCTT
323486 TTTTTT
1 TTTTTT
323492 TTTGTGGAGA
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
20 19 0.30
21 1 0.02
22 42 0.67
23 1 0.02
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (21 bp):
TTTTTTGTTTTTTTTCTTCTT
Found at i:323466 original size:42 final size:41
Alignment explanation
Indices: 323399--323491 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 41
323389 TCATCCGGAC
*
323399 CTTTTTTGTTGTTTTTTTTTGTTTTTTTTGTCTT-TTT-TTCTT
1 CTTTTTT-TTGTTTTTTTTT-CTTTTTTT-TCTTCTTTCTTCTT
323441 CTTTTTTTTGTTTTTTTCTTCTTTTTTTTCTTCTTTCTTCTT
1 CTTTTTTTTGTTTTTTT-TTCTTTTTTTTCTTCTTTCTTCTT
323483 CTTTTTTTT
1 CTTTTTTTT
323492 TTTGTGGAGA
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
40 4 0.09
41 20 0.43
42 23 0.49
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (41 bp):
CTTTTTTTTGTTTTTTTTTCTTTTTTTTCTTCTTTCTTCTT
Found at i:323487 original size:20 final size:20
Alignment explanation
Indices: 323420--323489 Score: 79
Period size: 20 Copynumber: 3.4 Consensus size: 20
323410 TTTTTTTTTG
*
323420 TTTTTTTTGTCTTTTTTTCTTC
1 TTTTTTTTG-C-TTCTTTCTTC
* *
323442 TTTTTTTTGTTTTTTTCTTC
1 TTTTTTTTGCTTCTTTCTTC
323462 TTTTTTTT-CTTCTTTCTTC
1 TTTTTTTTGCTTCTTTCTTC
323481 TTCTTTTTT
1 TT-TTTTTT
323490 TTTTTGTGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 11 0.25
20 24 0.55
22 9 0.20
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (20 bp):
TTTTTTTTGCTTCTTTCTTC
Found at i:334157 original size:33 final size:33
Alignment explanation
Indices: 334115--334179 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
334105 TACCACTGCT
334115 TGTATCGATACATGA-CACATTGTATCGATACAA
1 TGTATCGATACATGATCA-ATTGTATCGATACAA
* *
334148 TGTATCGATATATGATGAATTGTATCGATACA
1 TGTATCGATACATGATCAATTGTATCGATACA
334180 TTGCTTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATGATCAATTGTATCGATACAA
Found at i:342224 original size:55 final size:53
Alignment explanation
Indices: 342068--342660 Score: 447
Period size: 53 Copynumber: 11.4 Consensus size: 53
342058 AATTAAACCC
* *
342068 TTTACATATAAAATAT-TTTTTAGTTTTTATTATTTTTAAATAGTAATTTGAGG-
1 TTTA-ATATAAAATATATTTTAAATTTTTATTATTTTTAAATAGTAATTTG-GGA
* * *
342121 TTTACTCTAAAATAT-TTTTTAATTTTTATTACTTTTTAAATAGTAATTTGGGA
1 TTTAATATAAAATATATTTTAAATTTTTATTA-TTTTTAAATAGTAATTTGGGA
* *
342174 TTTAATATAAAATATGATTTTAAAATTTTTATTATTTTTAAATAATAATTTGAGA
1 TTTAATATAAAATAT-ATTTT-AAATTTTTATTATTTTTAAATAGTAATTTGGGA
*
342229 TTTTATATAAAATATATTTTTAAATTTTTTATTATTTTTAAATAGTAATTT-GGA
1 TTTAATATAAAATATA-TTTTAAA-TTTTTATTATTTTTAAATAGTAATTTGGGA
* * **
342283 TCTTAATAT--AA-ATA---T---TTTTTATT-TTTCTAATTAGTAATTTGATA
1 T-TTAATATAAAATATATTTTAAATTTTTATTATTTTTAAATAGTAATTTGGGA
* * **
342327 TTTTATATAAAATATATTTTTTAAATTTTATATTATTTTTAAATAATAATTCAGGA
1 TTTAATATAAAATATA--TTTTAAATTTT-TATTATTTTTAAATAGTAATTTGGGA
* * *
342383 TTTAATAT-ATA-ATATTTTAAATTTTATTATTATTTTTAAATATTAATTTAGGA
1 TTTAATATAAAATATATTTTAAA-TTT-TTATTATTTTTAAATAGTAATTTGGGA
* * *
342436 TTTAATAT-AAATAT-TTTTAAATTTATTATTATTTTTTTAATAGTAATTCGAGA
1 TTTAATATAAAATATATTTTAAATTT-TTATTA-TTTTTAAATAGTAATTTGGGA
* ****
342489 TTTAATATAAAATAT-TTTT--A---TTA-T-TTTTTAAATATTAATTCAAAA
1 TTTAATATAAAATATATTTTAAATTTTTATTATTTTTAAATAGTAATTTGGGA
* * ****
342534 TTTAATATAAAATGT-TTTAAAATTTTTATTATTTTTTAAATAGTAATTCATAA
1 TTTAATATAAAATATATTTTAAATTTTTATTA-TTTTTAAATAGTAATTTGGGA
* * * *
342587 TTTAA-ATTAACAAT-TTTATTTAATTTTTTATTA-TTTTAAATCGTAATTTTTGGA
1 TTTAATA-TAA-AATATAT-TTTAAATTTTTATTATTTTTAAATAGTAA-TTTGGGA
*
342641 TTTAATATAAATTAT-TTTTA
1 TTTAATATAAAATATATTTTA
342661 TTTATTTTTT
Statistics
Matches: 448, Mismatches: 50, Indels: 85
0.77 0.09 0.15
Matches are distributed among these distances:
43 21 0.05
44 10 0.02
45 36 0.08
46 3 0.01
47 2 0.00
48 4 0.01
50 3 0.01
51 2 0.00
52 52 0.12
53 148 0.33
54 43 0.10
55 92 0.21
56 32 0.07
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (53 bp):
TTTAATATAAAATATATTTTAAATTTTTATTATTTTTAAATAGTAATTTGGGA
Found at i:342324 original size:98 final size:99
Alignment explanation
Indices: 342202--342581 Score: 368
Period size: 98 Copynumber: 3.8 Consensus size: 99
342192 TTTAAAATTT
*
342202 TTATTATTTTTAAATAATAATTTGAGATTTTATATAAAATATATTTTTAAATTTTTTATTA-TTT
1 TTATTATTTTTAAATATTAATTTGAGATTTTATATAAAA-ATATTTTTAAATTTTTTATTATTTT
*
342266 TTAAATAGTAATTTGGATCTTAATATAAATATTTT-
65 TTAAATAGTAATTAGGAT-TTAATATAAATATTTTA
* * * * *
342301 TTATT-TTTCTAATTAGTAATTTGATATTTTATATAAAATATATTTTTTAAATTTTATATTA-TT
1 TTATTATTTTTAAATATTAATTTGAGATTTTATATAAAA-ATA-TTTTTAAATTTTTTATTATTT
*
342364 TTTAAATAATAATTCAGGATTTAATATATAATATTTTAAATTTTA
64 TTTAAATAGTAATT-AGGATTT-A-ATATAA-A---T--ATTTTA
* *
342409 TTATTATTTTTAAATATTAATTT-AGGA-TTTA-ATATAAATATTTTTAAATTTATTATTATTTT
1 TTATTATTTTTAAATATTAATTTGA-GATTTTATATAAAAATATTTTTAAATTTTTTATTATTTT
* *
342471 TTTAATAGTAATTCGAGATTTAATATAAA-ATATTT-
65 TTAAATAGTAATTAG-GATTTAATATAAATAT-TTTA
** * * * *
342506 TTATTATTTTTTAAATATTAATTCAAAATTTAATAT-AAAAT-GTTTTAAAATTTTTATTATTTT
1 TTATTA-TTTTTAAATATTAATTTGAGATTTTATATAAAAATATTTTTAAATTTTTTATTATTTT
342569 TTAAATAGTAATT
65 TTAAATAGTAATT
342582 CATAATTTAA
Statistics
Matches: 236, Mismatches: 25, Indels: 41
0.78 0.08 0.14
Matches are distributed among these distances:
97 8 0.03
98 84 0.36
99 47 0.20
100 7 0.03
101 6 0.03
102 1 0.00
103 1 0.00
104 6 0.03
105 19 0.08
106 22 0.09
107 10 0.04
108 10 0.04
109 15 0.06
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (99 bp):
TTATTATTTTTAAATATTAATTTGAGATTTTATATAAAAATATTTTTAAATTTTTTATTATTTTT
TAAATAGTAATTAGGATTTAATATAAATATTTTA
Found at i:342335 original size:43 final size:45
Alignment explanation
Indices: 342252--342347 Score: 117
Period size: 43 Copynumber: 2.2 Consensus size: 45
342242 ATATTTTTAA
*
342252 ATTTTTTATTATTTTTAAATAGTAATTTGGATCTTAATAT-AAAT
1 ATTTTTTATTATTTCTAAATAGTAATTTGGATCTTAATATAAAAT
* * *
342296 ATTTTTTATT-TTTCTAATTAGTAATTT-GATATTTTATATAAAAT
1 ATTTTTTATTATTTCTAAATAGTAATTTGGAT-CTTAATATAAAAT
342340 ATATTTTT
1 AT-TTTTT
342348 TAAATTTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
42 3 0.07
43 21 0.47
44 16 0.36
45 5 0.11
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.58
Consensus pattern (45 bp):
ATTTTTTATTATTTCTAAATAGTAATTTGGATCTTAATATAAAAT
Found at i:342445 original size:152 final size:154
Alignment explanation
Indices: 342143--342453 Score: 429
Period size: 153 Copynumber: 2.0 Consensus size: 154
342133 TATTTTTTAA
* *
342143 TTTTTATTACTTTTTAAATAGTAATTTGGGATTTAATATAAAATATGATTTTAAAATTTTTATTA
1 TTTTTATTA-TTTCTAAATAGTAATTTGAGATTTAATATAAAATATGATTTTAAAATTTTTATTA
* *
342208 TTTTTAAATAATAATTTGAGATTTTATATAAAATATATTTTTAAATTTTTTATTATTTTTAAATA
65 TTTTTAAATAATAATTAGAGATTTAATATAAAATATATTTTTAAATTTTTTATTATTTTTAAATA
342273 GTAATTTGGATCTTAATATAAATAT
130 GTAATTTGGATCTTAATATAAATAT
* * * *
342298 TTTTTATT-TTTCTAATTAGTAATTTGATATTTTATATAAAATAT-ATTTTTTAAATTTTATATT
1 TTTTTATTATTTCTAAATAGTAATTTGAGATTTAATATAAAATATGA-TTTTAAAATTTT-TATT
*
342361 ATTTTTAAATAATAATTCAG-GATTTAATAT-ATA-ATA-TTTTAAATTTTATTATTATTTTTAA
64 ATTTTTAAATAATAATT-AGAGATTTAATATAAAATATATTTTTAAATTTT-TTATTATTTTTAA
*
342422 ATATTAATTTAGGAT-TTAATATAAATAT
127 ATAGTAATTT-GGATCTTAATATAAATAT
342450 TTTT
1 TTTT
342454 AAATTTATTA
Statistics
Matches: 141, Mismatches: 10, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
151 11 0.08
152 43 0.30
153 48 0.34
154 30 0.21
155 9 0.06
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.55
Consensus pattern (154 bp):
TTTTTATTATTTCTAAATAGTAATTTGAGATTTAATATAAAATATGATTTTAAAATTTTTATTAT
TTTTAAATAATAATTAGAGATTTAATATAAAATATATTTTTAAATTTTTTATTATTTTTAAATAG
TAATTTGGATCTTAATATAAATAT
Found at i:342515 original size:45 final size:45
Alignment explanation
Indices: 342456--342749 Score: 161
Period size: 53 Copynumber: 6.2 Consensus size: 45
342446 ATATTTTTAA
* * *
342456 ATTTATTATTATTTTTTTAATAGTAATTCGAGATTTAATATAAAAT
1 ATTT-TTATTATTTTTTAAATAGTAATTCAAAATTTAATATAAAAT
*
342502 ATTTTTATTATTTTTTAAATATTAATTCAAAATTTAATATAAAATGTTTT
1 ATTTTTATTATTTTTTAAATAGTAATTCAAAATTTAATATAAAA-----T
*
342552 AAAATTTTTATTATTTTTTAAATAGTAATTCATAATTTAA-ATTAACAATTTT
1 ---ATTTTTATTATTTTTTAAATAGTAATTCAAAATTTAATA-TAA-AA---T
* * **** *
342604 ATTTAATTTTTTATTATTTTAAATCGTAATTTTTGGATTTAATATAAATT
1 A-TT--TTTATTATT-TTTTAAATAGTAA-TTCAAAATTTAATATAAAAT
* * **
342654 ATTTTTATTTATTTTTTAAATAATAACTCAAAATTTATATATTTGCAAT
1 ATTTTTA-TTATTTTTTAAATAGTAATTCAAAATTTA-ATA--TAAAAT
* *
342703 A-TTTTATTA-TTTTTAAA-AATAACTT-AAGATTTAATAT-AAAT
1 ATTTTTATTATTTTTTAAATAGTAA-TTCAAAATTTAATATAAAAT
342744 -TTTTTA
1 ATTTTTA
342750 AGTTTTTGTT
Statistics
Matches: 199, Mismatches: 27, Indels: 49
0.72 0.10 0.18
Matches are distributed among these distances:
41 8 0.04
42 1 0.01
44 3 0.02
45 48 0.24
46 19 0.10
47 20 0.10
48 10 0.05
49 7 0.04
50 5 0.03
52 13 0.07
53 51 0.26
54 13 0.07
55 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (45 bp):
ATTTTTATTATTTTTTAAATAGTAATTCAAAATTTAATATAAAAT
Found at i:342552 original size:151 final size:146
Alignment explanation
Indices: 342351--342842 Score: 422
Period size: 151 Copynumber: 3.3 Consensus size: 146
342341 TATTTTTTAA
**
342351 ATTTTATATTA-TTTTTAAATAATAATTCAGGATTTAATATATAATATTTTAAATTTTATTATTA
1 ATTTT-TATTATTTTTTAAATAATAATTCAAAATTTAATATA-AAT-TTTTAAATTTT-TTATTA
* * *
342415 TTTTTAAATATTAATTTAGGATTTAATATAAATATTTTTAAATTTATTATTATTTTTTTAATAGT
62 TTTTTAAATAATAATTTAAGATTTAATATAAATATTTTTAAATTTATTATTA--TTTTAAATAGT
342480 AA-TTCGAGATTTAATATAAAAT
125 AATTTCG-GATTTAATATAAAAT
* *
342502 ATTTTTATTATTTTTTAAATATTAATTCAAAATTTAATATAAAATGTTTTAAAATTTTTATTATT
1 ATTTTTATTATTTTTTAAATAATAATTCAAAATTTAATAT-AAAT-TTTTAAATTTTTTATTA-T
* * * * *
342567 TTTTAAATAGTAATTCATA-ATTTAA-ATTAACA-ATTTTATTTAATTTTTTATTATTTTAAATC
63 TTTTAAATAATAATTTA-AGATTTAATA-TAA-ATA-TTT-TTAAATTTATTATTATTTTAAATA
* *
342629 GTAATTTTTGGATTTAATATAAATT
123 GTAA-TTTCGGATTTAATATAAAAT
* ** *
342654 ATTTTTATTTATTTTTTAAATAATAACTCAAAATTT-ATAT--A-TTTGCAATATTTTATTATTT
1 ATTTTTA-TTATTTTTTAAATAATAATTCAAAATTTAATATAAATTTTTAAATTTTTTATTATTT
* * * * *
342715 TTAAA-AATAACTTAAGATTTAATATAAAT-TTTTTAAGTTT-TTGTT-TTTTAAATAATTATTT
65 TTAAATAATAATTTAAGATTTAATATAAATATTTTTAAATTTATTATTATTTTAAATAGTAATTT
*
342776 -GAGA-TTAATATAAATT
130 CG-GATTTAATATAAAAT
* * * *
342792 ATTTTTAATTTTATTTTTAAAATAATAGTT-TAGATTTAATATAAATATTTT
1 ATTTTT-A--TTATTTTTTAAATAATAATTCAAAATTTAATATAAAT-TTTT
342843 TAATAGAAAA
Statistics
Matches: 284, Mismatches: 35, Indels: 51
0.77 0.09 0.14
Matches are distributed among these distances:
138 19 0.07
139 11 0.04
140 32 0.11
141 4 0.01
142 7 0.02
143 3 0.01
144 5 0.02
145 15 0.05
146 9 0.03
147 13 0.05
149 1 0.00
150 12 0.04
151 81 0.29
152 30 0.11
153 42 0.15
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (146 bp):
ATTTTTATTATTTTTTAAATAATAATTCAAAATTTAATATAAATTTTTAAATTTTTTATTATTTT
TAAATAATAATTTAAGATTTAATATAAATATTTTTAAATTTATTATTATTTTAAATAGTAATTTC
GGATTTAATATAAAAT
Found at i:342590 original size:98 final size:97
Alignment explanation
Indices: 342401--342614 Score: 269
Period size: 98 Copynumber: 2.2 Consensus size: 97
342391 ATAATATTTT
* **
342401 AAATTTTATTATTATTTTTAAATATTAATTTAGGATTTAATATAAATATTTTTAAATTTATTATT
1 AAATTTTATTATTATTTTTAAATATTAATTCAAAATTTAATATAAATATTTTTAAATTTATTATT
* *
342466 ATTTTTTTAATAGTAATTCGAGATTTAATATA
66 ATTTTTTAAATAGTAATTCGAAATTTAATATA
342498 AAATATTT-TTATTATTTTTTAAATATTAATTCAAAATTTAATATAAA-ATGTTTTAAAATTT-T
1 AAAT-TTTATTATTA-TTTTTAAATATTAATTCAAAATTTAATATAAATAT-TTTT-AAATTTAT
342560 TATTATTTTTTAAATAGTAATTC-ATAATTTAA-ATTA
62 TATTATTTTTTAAATAGTAATTCGA-AATTTAATA-TA
*
342596 ACAATTTTATT-TAATTTTT
1 A-AATTTTATTATTATTTTT
342615 TATTATTTTA
Statistics
Matches: 103, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
97 19 0.18
98 73 0.71
99 11 0.11
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (97 bp):
AAATTTTATTATTATTTTTAAATATTAATTCAAAATTTAATATAAATATTTTTAAATTTATTATT
ATTTTTTAAATAGTAATTCGAAATTTAATATA
Found at i:342762 original size:46 final size:46
Alignment explanation
Indices: 342639--342846 Score: 157
Period size: 47 Copynumber: 4.5 Consensus size: 46
342629 GTAATTTTTG
*
342639 GATTTAATATAAATTATTTTT-A-TTTATTTTTTAAATAATAACTCAA
1 GATTTAATATAAA-TATTTTTAATTTTATTTTTTAAA-AATAACTTAA
* *
342685 AATTTATATATTTGCAATA-TTTT-A--TTA-TTTTTAAAAATAACTTAA
1 GATTTA-ATA--T-AAATATTTTTAATTTTATTTTTTAAAAATAACTTAA
* * * *
342730 GATTTAATATAAAT-TTTTTAAGTTTTTGTTTTTTAAATAATTATTTGA
1 GATTTAATATAAATATTTTTAA--TTTTATTTTTTAAA-AATAACTTAA
* * *
342778 GA-TTAATATAAATTATTTTTAATTTTATTTTTAAAATAAT-AGTTTA
1 GATTTAATATAAA-TATTTTTAATTTTATTTTTTAAA-AATAACTTAA
342824 GATTTAATATAAATATTTTTAAT
1 GATTTAATATAAATATTTTTAAT
342847 AGAAAATTAG
Statistics
Matches: 134, Mismatches: 13, Indels: 30
0.76 0.07 0.17
Matches are distributed among these distances:
41 7 0.05
42 2 0.01
44 3 0.02
45 14 0.10
46 31 0.23
47 50 0.37
48 15 0.11
49 10 0.07
50 2 0.01
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (46 bp):
GATTTAATATAAATATTTTTAATTTTATTTTTTAAAAATAACTTAA
Found at i:344400 original size:2 final size:2
Alignment explanation
Indices: 344393--344430 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
344383 TATTCTGTGA
344393 AT AT 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
344431 CTTAGATGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:344875 original size:17 final size:17
Alignment explanation
Indices: 344855--344901 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
344845 TATTTTATTT
344855 AATATTATAATTAATTA
1 AATATTATAATTAATTA
344872 AATATTAT--TTAAATTA
1 AATATTATAATT-AATTA
*
344888 AAAATTA-AATTAAT
1 AATATTATAATTAAT
344902 AAAAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 2 0.08
16 14 0.54
17 10 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATATTATAATTAATTA
Found at i:350846 original size:33 final size:33
Alignment explanation
Indices: 350808--350873 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
350798 ATTTGCCTGC
* *
350808 ATGTATTGATACAAAGA-TCAGTGTATCGATACA
1 ATGTATCGATACAAAGAGT-AATGTATCGATACA
*
350841 ATGTATCGATACAATGAGTAATGTATCGATACA
1 ATGTATCGATACAAAGAGTAATGTATCGATACA
350874 TTTTCTTGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGAGTAATGTATCGATACA
Found at i:350847 original size:13 final size:13
Alignment explanation
Indices: 350829--350856 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
350819 CAAAGATCAG
350829 TGTATCGATACAA
1 TGTATCGATACAA
350842 TGTATCGATACAA
1 TGTATCGATACAA
350855 TG
1 TG
350857 AGTAATGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:350918 original size:19 final size:19
Alignment explanation
Indices: 350894--350959 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
350884 AGTAGCTTCA
350894 TATGTATCGATACAACACT
1 TATGTATCGATACAACACT
350913 TATGTATCGAT---ACA--
1 TATGTATCGATACAACACT
*
350927 T-TGTATCAATACAACACT
1 TATGTATCGATACAACACT
350945 TATGTATCGATACAA
1 TATGTATCGATACAA
350960 ATCGTTGACA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
13 8 0.21
14 1 0.03
16 6 0.15
18 1 0.03
19 23 0.59
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (19 bp):
TATGTATCGATACAACACT
Found at i:350939 original size:32 final size:32
Alignment explanation
Indices: 350896--350958 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
350886 TAGCTTCATA
*
350896 TGTATCGATACAACACTTATGTATCGATACAT
1 TGTATCAATACAACACTTATGTATCGATACAT
350928 TGTATCAATACAACACTTATGTATCGATACA
1 TGTATCAATACAACACTTATGTATCGATACA
350959 AATCGTTGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (32 bp):
TGTATCAATACAACACTTATGTATCGATACAT
Found at i:351525 original size:97 final size:97
Alignment explanation
Indices: 351360--351593 Score: 274
Period size: 97 Copynumber: 2.4 Consensus size: 97
351350 TATTTATCAG
* * * * *
351360 GGATACTCCAACCCTATTCCTCCGAAAGGATGCTCCAATCCCGCTTTTAAACCCATCAAACTTTA
1 GGATACTCCAACCCCATTCCTCCGAAGGGATACTCCAACCCCGCTTTTAAACCCATCAAACTTCA
* * * *
351425 AATCTTCTTTTTGCTTAAATTGTCATCATCGA
66 AATCTTATTCTCGCTTAAATCGTCATCATCGA
* * ***
351457 GGATACTCCAACCCCATTCCTCTGAAGGGATATTCCAACCCCGCTTTTAAACTTGTCAAGA-TTC
1 GGATACTCCAACCCCATTCCTCCGAAGGGATACTCCAACCCCGCTTTTAAACCCATCAA-ACTTC
* *
351521 AAATCTTATTCTCGCTTAAATCGTCATCATTGG
65 AAATCTTATTCTCGCTTAAATCGTCATCATCGA
* *
351554 GGACACTTCAACCCCATTCCTCCG-AGGGAATACTCCAACC
1 GGATACTCCAACCCCATTCCTCCGAAGGG-ATACTCCAACC
351594 TCATTTTTTT
Statistics
Matches: 115, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
96 4 0.03
97 110 0.96
98 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.30
Consensus pattern (97 bp):
GGATACTCCAACCCCATTCCTCCGAAGGGATACTCCAACCCCGCTTTTAAACCCATCAAACTTCA
AATCTTATTCTCGCTTAAATCGTCATCATCGA
Found at i:356559 original size:20 final size:21
Alignment explanation
Indices: 356534--356584 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
356524 ATTTCAAATA
*
356534 TATATCGATACATTCACTTA-
1 TATATCGATACATTAACTTAT
* *
356554 TGTATCGATATATTAACTTAT
1 TATATCGATACATTAACTTAT
356575 TATATCGATA
1 TATATCGATA
356585 TAAATTGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (21 bp):
TATATCGATACATTAACTTAT
Found at i:358432 original size:17 final size:17
Alignment explanation
Indices: 358412--358445 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
358402 ATCTTGATTG
358412 TTTTGAATCTAA-AATTT
1 TTTTGAAT-TAATAATTT
358429 TTTTGAATTAATAATTT
1 TTTTGAATTAATAATTT
358446 GAAGATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTTGAATTAATAATTT
Found at i:358721 original size:30 final size:30
Alignment explanation
Indices: 358685--358744 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
358675 GAGGATAGGG
358685 TCGGAGAATAAGAATATGAAACGTGATGAT
1 TCGGAGAATAAGAATATGAAACGTGATGAT
358715 TCGGAGAATAAGAATATGAAACGTGATGAT
1 TCGGAGAATAAGAATATGAAACGTGATGAT
358745 AGATTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.07, G:0.27, T:0.23
Consensus pattern (30 bp):
TCGGAGAATAAGAATATGAAACGTGATGAT
Found at i:360567 original size:17 final size:17
Alignment explanation
Indices: 360547--360623 Score: 63
Period size: 16 Copynumber: 4.7 Consensus size: 17
360537 TCAACAACTC
*
360547 AAATCTTAAAACAATCA
1 AAATCTTAAAATAATCA
* *
360564 AAAT-TGAAAAATAATTA
1 AAATCT-TAAAATAATCA
360581 AAATC-TAAAATAATCA
1 AAATCTTAAAATAATCA
* * *
360597 AAA-CATAAAATGATCC
1 AAATCTTAAAATAATCA
360613 AAA-CTTAAAAT
1 AAATCTTAAAAT
360624 GAACTGAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
15 1 0.02
16 32 0.65
17 16 0.33
ACGTcount: A:0.61, C:0.12, G:0.03, T:0.25
Consensus pattern (17 bp):
AAATCTTAAAATAATCA
Done.