Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold103
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: 2633873
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 16636 characters in sequence are not A, C, G, or T
File 2 of 21
Found at i:125695 original size:66 final size:66
Alignment explanation
Indices: 125608--125742 Score: 243
Period size: 66 Copynumber: 2.0 Consensus size: 66
125598 GAAGTATTTG
* *
125608 TAAGTCTAATAATTGTTAAAAACATCCTTTCATGATCACATGTCTCCAATGAAGAGTTACAACTT
1 TAAGTCCAATAATTGTTAAAAACATCCTTTCATGATCACATGTCTCCAATGAAGACTTACAACTT
125673 T
66 T
*
125674 TAAGTCCAATAATTGTTAAAAACATCCTTTCATGATCACATGTCTCCAGTGAAGACTTACAACTT
1 TAAGTCCAATAATTGTTAAAAACATCCTTTCATGATCACATGTCTCCAATGAAGACTTACAACTT
125739 T
66 T
125740 TAA
1 TAA
125743 AATGAAAGAG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.34
Consensus pattern (66 bp):
TAAGTCCAATAATTGTTAAAAACATCCTTTCATGATCACATGTCTCCAATGAAGACTTACAACTT
T
Found at i:128340 original size:44 final size:45
Alignment explanation
Indices: 128292--128388 Score: 187
Period size: 44 Copynumber: 2.2 Consensus size: 45
128282 TTAAAAAAAT
128292 AAATTTTATAATTTTCATAAAAAATTAA-AAAAAGAAAATATAAA
1 AAATTTTATAATTTTCATAAAAAATTAAGAAAAAGAAAATATAAA
128336 AAATTTTATAATTTTCATAAAAAATTAAGAAAAAGAAAATATAAA
1 AAATTTTATAATTTTCATAAAAAATTAAGAAAAAGAAAATATAAA
128381 AAATTTTA
1 AAATTTTA
128389 CAAGGTAACT
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 28 0.54
45 24 0.46
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (45 bp):
AAATTTTATAATTTTCATAAAAAATTAAGAAAAAGAAAATATAAA
Found at i:128623 original size:15 final size:16
Alignment explanation
Indices: 128591--128630 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
128581 AAAAATCTAA
*
128591 TTAATAATGATAAAGT
1 TTAAAAATGATAAAGT
128607 TTAAAAATGAT-AAGT
1 TTAAAAATGATAAAGT
128622 TTAACAAAT
1 TTAA-AAAT
128631 TAAACATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.35
Consensus pattern (16 bp):
TTAAAAATGATAAAGT
Found at i:129335 original size:20 final size:21
Alignment explanation
Indices: 129294--129343 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
129284 TTATAACAAA
129294 TAAAAAATTTATTAACAGTAT
1 TAAAAAATTTATTAACAGTAT
129315 TAAAAAATTTATTTAA-A-TAT
1 TAAAAAATTTA-TTAACAGTAT
129335 TAATAAAAT
1 TAA-AAAAT
129344 ATTGACGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.22
21 17 0.63
22 4 0.15
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
TAAAAAATTTATTAACAGTAT
Found at i:130515 original size:2 final size:2
Alignment explanation
Indices: 130504--130534 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
130494 CGGTTTAAAG
130504 AT AT -T 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
130535 TAAAATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:130582 original size:39 final size:36
Alignment explanation
Indices: 130497--130613 Score: 103
Period size: 36 Copynumber: 3.1 Consensus size: 36
130487 TTTGCAACGG
* *
130497 TTTAAAGATATTAT-A-TATATATATATATATATATAT
1 TTTAAA-ATATTATAATTTTATTTATAT-TATATATAT
* *
130533 ATTAAAATATTAATAATTTATAATTTATATTATATAAAT
1 TTTAAAATATT-ATAATTT-T-ATTTATATTATATATAT
* * *
130572 TTTAACATATTTTTATTTTATTTATATTATATTATAT
1 TTTAAAATATTATAATTTTATTTATATTATA-TATAT
130609 TTTAA
1 TTTAA
130614 TTATTTTTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
35 5 0.08
36 19 0.29
37 11 0.17
38 6 0.09
39 18 0.27
40 7 0.11
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.55
Consensus pattern (36 bp):
TTTAAAATATTATAATTTTATTTATATTATATATAT
Found at i:130609 original size:21 final size:20
Alignment explanation
Indices: 130518--130631 Score: 80
Period size: 21 Copynumber: 5.8 Consensus size: 20
130508 TATATATATA
*
130518 TATATATATATATATATTAA-
1 TATAT-TATATATATTTTAAT
*
130538 AATATTA-ATA-ATTTATAATT
1 TATATTATATATATTT-TAA-T
*
130558 TATATTATATAAATTTTAA-
1 TATATTATATATATTTTAAT
* *
130577 CATATT-T-T-TATTTTATT
1 TATATTATATATATTTTAAT
130594 TATATTATATTATATTTTAAT
1 TATATTATA-TATATTTTAAT
* *
130615 TATTTTTTATATATTTT
1 TATATTATATATATTTT
130632 GTTGTATAGT
Statistics
Matches: 74, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
16 6 0.08
17 9 0.12
18 8 0.11
19 7 0.09
20 19 0.26
21 21 0.28
22 4 0.05
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (20 bp):
TATATTATATATATTTTAAT
Found at i:130630 original size:36 final size:35
Alignment explanation
Indices: 130549--130630 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 35
130539 ATATTAATAA
130549 TTTATA-ATTTATATTATATAAATTTTAACATATT
1 TTTATATATTTATATTATATAAATTTTAACATATT
* * *
130583 TTTATTTTATTTATATTATATTATATTTTAA-TTATTT
1 TTTA-TATATTTATATTATA-TAAATTTTAACATA-TT
130620 TTTATATATTT
1 TTTATATATTT
130631 TGTTGTATAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
34 4 0.10
35 1 0.03
36 20 0.50
37 15 0.38
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (35 bp):
TTTATATATTTATATTATATAAATTTTAACATATT
Found at i:132852 original size:2 final size:2
Alignment explanation
Indices: 132847--132879 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
132837 ATATTTCTTT
132847 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
132880 GCGTGTGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:135717 original size:2 final size:2
Alignment explanation
Indices: 135710--135751 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
135700 GTATAATCCT
135710 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
135752 CACACACACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:139386 original size:2 final size:2
Alignment explanation
Indices: 139379--139408 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
139369 CATGTACTTG
139379 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
139409 AGTGCATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:139842 original size:18 final size:19
Alignment explanation
Indices: 139798--139843 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
139788 TTGATGTATG
*
139798 ATATTATATAAATTTATATA
1 ATATTA-ATAAATTTAAATA
*
139818 TTATTAATAAA-TTAAATA
1 ATATTAATAAATTTAAATA
139836 ATATTAAT
1 ATATTAAT
139844 TTTTTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 13 0.57
19 5 0.22
20 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATTAATAAATTTAAATA
Found at i:140098 original size:2 final size:2
Alignment explanation
Indices: 140093--140117 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
140083 TCTCTCTCTC
140093 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
140118 CACCAGTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:140531 original size:18 final size:18
Alignment explanation
Indices: 140496--140533 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
140486 TTAACACATT
*
140496 TAATAATTTATATTTTAA
1 TAATAATTTATATATTAA
140514 TAAT-ATTTATATGATTAA
1 TAATAATTTATAT-ATTAA
140532 TA
1 TA
140534 TGAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TAATAATTTATATATTAA
Found at i:141216 original size:15 final size:15
Alignment explanation
Indices: 141196--141243 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
141186 AATTATTATC
141196 TTTTATTTTTTTCCT
1 TTTTATTTTTTTCCT
* *
141211 TTTTATCTTGTTT-AT
1 TTTTAT-TTTTTTCCT
141226 TTTTATTTTTTATCCT
1 TTTTATTTTTT-TCCT
141242 TT
1 TT
141244 CTTTGTGCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
14 4 0.15
15 14 0.54
16 8 0.31
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.77
Consensus pattern (15 bp):
TTTTATTTTTTTCCT
Found at i:141874 original size:22 final size:21
Alignment explanation
Indices: 141833--141876 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
141823 ATATTTTTAT
*
141833 TAAATTTAATTATAAGATATA
1 TAAATTTAATTATAAAATATA
141854 TAAATATTAA-TATAAAAATATA
1 TAAAT-TTAATTAT-AAAATATA
141876 T
1 T
141877 TTTTAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:143087 original size:6 final size:6
Alignment explanation
Indices: 143076--143100 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
143066 AGAAGATAAA
143076 TTAGGG TTAGGG TTAGGG TTAGGG T
1 TTAGGG TTAGGG TTAGGG TTAGGG T
143101 AAAGGTTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.36
Consensus pattern (6 bp):
TTAGGG
Found at i:143522 original size:2 final size:2
Alignment explanation
Indices: 143515--143544 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
143505 CCTCAAAGTT
143515 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
143545 TCATGAATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:144959 original size:2 final size:2
Alignment explanation
Indices: 144946--144980 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
144936 ATTATAAGGA
*
144946 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
144981 GAATTACGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:146678 original size:23 final size:23
Alignment explanation
Indices: 146633--146678 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
146623 GATTTGATTG
* *
146633 AAATATTTTTAAATATAAGTAAA
1 AAATAATTTTAAATATAAATAAA
146656 AAATAATTTT-AATATTAAATAAA
1 AAATAATTTTAAATA-TAAATAAA
146679 TAATGAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
AAATAATTTTAAATATAAATAAA
Found at i:148377 original size:14 final size:14
Alignment explanation
Indices: 148358--148389 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
148348 ATGGCAAAAC
*
148358 TAATTAAAAATTAT
1 TAATTAAAAAATAT
148372 TAATTAAAAAATAT
1 TAATTAAAAAATAT
148386 TAAT
1 TAAT
148390 CAACCTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATTAAAAAATAT
Found at i:150316 original size:2 final size:2
Alignment explanation
Indices: 150309--150344 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
150299 TTGACTTAGA
150309 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
150345 TCCATTAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:151727 original size:17 final size:19
Alignment explanation
Indices: 151705--151740 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
151695 TAATTATGAC
151705 ATGATA-AA-TATACGAAT
1 ATGATATAAGTATACGAAT
151722 ATGATATAAGTATACGAAT
1 ATGATATAAGTATACGAAT
151741 TATTAGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 9 0.53
ACGTcount: A:0.50, C:0.06, G:0.14, T:0.31
Consensus pattern (19 bp):
ATGATATAAGTATACGAAT
Found at i:151819 original size:19 final size:19
Alignment explanation
Indices: 151770--151821 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
151760 TTTAAATAAT
*
151770 AATAGTAATTTAATGTTAC
1 AATAGTAATTTTATGTTAC
*
151789 AATAGTGATTTTATGTTAC
1 AATAGTAATTTTATGTTAC
151808 AATAGTAATTTTAT
1 AATAGTAATTTTAT
151822 ATTTTTGACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (19 bp):
AATAGTAATTTTATGTTAC
Found at i:152893 original size:16 final size:16
Alignment explanation
Indices: 152860--152915 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
152850 TTTGGATTTA
* * *
152860 TTCGTGTTTGATCTTT
1 TTCGAGTTTGAGCCTT
152876 TTCGAGTTTGAGCCTT
1 TTCGAGTTTGAGCCTT
*
152892 TTC-AGGTTTAAGCCTT
1 TTCGA-GTTTGAGCCTT
152908 TTCGAGTT
1 TTCGAGTT
152916 CAAACTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 1 0.03
16 32 0.94
17 1 0.03
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.50
Consensus pattern (16 bp):
TTCGAGTTTGAGCCTT
Found at i:153066 original size:14 final size:14
Alignment explanation
Indices: 153039--153102 Score: 56
Period size: 16 Copynumber: 4.3 Consensus size: 14
153029 ATTTAAAAAG
*
153039 TAAATTATTATTTT
1 TAAATAATTATTTT
*
153053 TAAATAATTTTTTT
1 TAAATAATTATTTT
*
153067 TATAATATGTTATTTT
1 TA-AATA-ATTATTTT
*
153083 TAATATATTTATTTAT
1 TAA-ATAATTATTT-T
153099 TAAA
1 TAAA
153103 ATCTATATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
14 14 0.34
15 12 0.29
16 15 0.37
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (14 bp):
TAAATAATTATTTT
Found at i:155356 original size:24 final size:25
Alignment explanation
Indices: 155328--155377 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
155318 TTTCATATTG
155328 TATTCAA-AACTATC-AAATTTATAT
1 TATTCAATAA-TATCAAAATTTATAT
*
155352 TATTCAATAATTTCAAAATTTATAT
1 TATTCAATAATATCAAAATTTATAT
155377 T
1 T
155378 TAGTGTCGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (25 bp):
TATTCAATAATATCAAAATTTATAT
Found at i:157414 original size:26 final size:25
Alignment explanation
Indices: 157363--157414 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
157353 ATAAAAAATT
* *
157363 TTAAAAATATTTTTATAATGATTAA
1 TTAAAAATATTTTTATAATAAATAA
157388 TTAAAAAT-TTTTTATTTAATAAATAA
1 TTAAAAATATTTTTA--TAATAAATAA
157414 T
1 T
157415 AATTTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 6 0.26
25 8 0.35
26 9 0.39
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TTAAAAATATTTTTATAATAAATAA
Found at i:161345 original size:57 final size:58
Alignment explanation
Indices: 161216--161350 Score: 161
Period size: 58 Copynumber: 2.3 Consensus size: 58
161206 TAAATCTTTA
* *
161216 AAAATGCATGAAATGATA-AAAAAGTTTTCAGATCATAAAAAATGACTTCAATATCTCC
1 AAAATGCATGAAATGATATAAAAAGTTTTCAAATCATAAAAAATGACTTAAATATCT-C
* * *
161274 AAAATGCATAAAATGATATAACAA-TTTGT-AAATCATAAAAAATGATTTAAATATACT-
1 AAAATGCATGAAATGATATAAAAAGTTT-TCAAATCATAAAAAATGACTTAAATAT-CTC
*
161331 TAAATGCATGAAATGATATA
1 AAAATGCATGAAATGATATA
161351 GTAATCTTTA
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
57 18 0.27
58 42 0.63
59 7 0.10
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.30
Consensus pattern (58 bp):
AAAATGCATGAAATGATATAAAAAGTTTTCAAATCATAAAAAATGACTTAAATATCTC
Found at i:163546 original size:13 final size:13
Alignment explanation
Indices: 163528--163584 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
163518 CATAAAGTGT
163528 TGTATCGATACAA
1 TGTATCGATACAA
163541 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
163556 GTGTTGTATCGATATAA
1 ----TGTATCGATACAA
163573 TGTATCGATACA
1 TGTATCGATACA
163585 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
15 2 0.06
17 2 0.06
19 10 0.28
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:163563 original size:32 final size:32
Alignment explanation
Indices: 163508--163605 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
163498 TTCAACGATT
163508 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
*
163541 TGTATCGATACATAAGTGTTGTATCGATATAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
163573 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
163605 T
1 T
163606 ATAAGCTACT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 49 0.79
33 13 0.21
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:163565 original size:19 final size:18
Alignment explanation
Indices: 163506--163603 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
163496 ATTTCAACGA
163506 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
163525 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
163541 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
163557 TGTTGTATCGAT--ATAA-
1 T-TTGTATCGATACATAAG
163573 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
163589 TTTTGTATCGATACA
1 -TTTGTATCGATACA
163604 ATATAAGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 20 0.30
15 6 0.09
17 6 0.09
19 22 0.33
20 12 0.18
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:163643 original size:13 final size:13
Alignment explanation
Indices: 163625--163649 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
163615 TGTCAAAAAA
163625 TGTATCGATACAT
1 TGTATCGATACAT
163638 TGTATCGATACA
1 TGTATCGATACA
163650 CTGATCTTTG
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:163716 original size:52 final size:52
Alignment explanation
Indices: 163658--163786 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
163648 CACTGATCTT
163658 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
163710 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
163762 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
163787 TCATATTTCG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:169371 original size:17 final size:17
Alignment explanation
Indices: 169341--169393 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
169331 AATATAATAT
*
169341 AAAATATATATTATTAAA
1 AAAATTTAT-TTATTAAA
* *
169359 AAAATTTATTTATTTAT
1 AAAATTTATTTATTAAA
*
169376 AAAATTTCATATATTAAA
1 AAAATTT-ATTTATTAAA
169394 TATAAAGTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATTTATTTATTAAA
Found at i:170271 original size:26 final size:28
Alignment explanation
Indices: 170233--170309 Score: 70
Period size: 26 Copynumber: 2.8 Consensus size: 28
170223 ATTATTGTAT
*
170233 AATTAATTGATAAATATATATTTAATTAAA
1 AATTAA-T-ATAAATATATATTTAATAAAA
* * **
170263 AA-TAA-ATAATTAAATAAATAATAAAA
1 AATTAATATAAATATATATTTAATAAAA
170289 AATTAATATAAATATA-ATTTA
1 AATTAATATAAATATATATTTA
170310 CTAGCTTATA
Statistics
Matches: 36, Mismatches: 9, Indels: 7
0.69 0.17 0.13
Matches are distributed among these distances:
26 18 0.50
27 6 0.17
28 7 0.19
29 3 0.08
30 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (28 bp):
AATTAATATAAATATATATTTAATAAAA
Found at i:170279 original size:12 final size:12
Alignment explanation
Indices: 170262--170302 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
170252 ATTTAATTAA
170262 AAATAAATAATT
1 AAATAAATAATT
170274 AAATAAATAA-T
1 AAATAAATAATT
170285 AAA-AAATTAATAT
1 AAATAAA-TAAT-T
170298 AAATA
1 AAATA
170303 TAATTTACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 3 0.12
11 7 0.28
12 10 0.40
13 4 0.16
14 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATAAATAATT
Found at i:170287 original size:19 final size:19
Alignment explanation
Indices: 170254--170302 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
170244 AAATATATAT
* *
170254 TTAATTAAA-AATAAATAA
1 TTAAATAAATAATAAAAAA
170272 TTAAATAAATAATAAAAAA
1 TTAAATAAATAATAAAAAA
170291 TTAATATAAATA
1 TTAA-ATAAATA
170303 TAATTTACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 8 0.30
19 12 0.44
20 7 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TTAAATAAATAATAAAAAA
Found at i:170395 original size:21 final size:21
Alignment explanation
Indices: 170315--170395 Score: 56
Period size: 21 Copynumber: 3.7 Consensus size: 21
170305 ATTTACTAGC
*
170315 TTATAATTTAA-ATTTAATTTT
1 TTATAATTTAATATTT-ATATT
* *
170336 TTTTAATTTAAATTTGTTATTATT
1 TTATAATTT-AATAT-TTA-TATT
* * *
170360 TAACATATTTTATATTTATATT
1 TTATA-ATTTAATATTTATATT
170382 TTATAATTTAATAT
1 TTATAATTTAATAT
170396 AAATGTAATT
Statistics
Matches: 44, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
21 16 0.36
22 9 0.20
23 5 0.11
24 10 0.23
25 4 0.09
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (21 bp):
TTATAATTTAATATTTATATT
Found at i:170770 original size:18 final size:19
Alignment explanation
Indices: 170739--170849 Score: 68
Period size: 20 Copynumber: 5.8 Consensus size: 19
170729 ATATTATTTT
170739 TATATTATAATTATATATAA
1 TATATTAT-ATTATATATAA
*
170759 TATATTATTTATATATATAA
1 TATATTATAT-TATATATAA
* * *
170779 TTTAATATATTA-ATA-AT
1 TATATTATATTATATATAA
* *
170796 TA-ATTATATAAT-TTTAA
1 TATATTATATTATATATAA
*
170813 TATATTTATATATTTATATATA
1 TATA-TTATAT-TATATATA-A
* *
170835 TTTTTTATATTATAT
1 TATATTATATTATAT
170850 TTTATGTAAT
Statistics
Matches: 67, Mismatches: 16, Indels: 16
0.68 0.16 0.16
Matches are distributed among these distances:
16 8 0.12
17 5 0.07
18 4 0.06
19 9 0.13
20 29 0.43
21 9 0.13
22 3 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATTATATTATATATAA
Found at i:170833 original size:8 final size:8
Alignment explanation
Indices: 170723--170833 Score: 63
Period size: 8 Copynumber: 13.5 Consensus size: 8
170713 TATTTAATTA
170723 ATATTTAT
1 ATATTTAT
*
170731 ATTATTTTT
1 A-TATTTAT
170740 ATA-TTAT
1 ATATTTAT
170747 A-A-TTAT
1 ATATTTAT
*
170753 ATATAATAT
1 ATAT-TTAT
170762 ATTATTTAT
1 A-TATTTAT
170771 ATA--TAT
1 ATATTTAT
170777 A-ATTTAAT
1 ATATTT-AT
*
170785 ATATTAAT
1 ATATTTAT
*
170793 AATTAATTAT
1 -A-TATTTAT
170803 ATAATTTTAAT
1 AT-A-TTT-AT
170814 ATATTTAT
1 ATATTTAT
170822 ATATTTAT
1 ATATTTAT
170830 ATAT
1 ATAT
170834 ATTTTTTATA
Statistics
Matches: 81, Mismatches: 8, Indels: 28
0.69 0.07 0.24
Matches are distributed among these distances:
5 1 0.01
6 10 0.12
7 6 0.07
8 25 0.31
9 24 0.30
10 11 0.14
11 4 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
ATATTTAT
Found at i:170867 original size:75 final size:71
Alignment explanation
Indices: 170709--170868 Score: 159
Period size: 75 Copynumber: 2.2 Consensus size: 71
170699 TTTAGATCCA
* *
170709 GTAATA-TTTAATTAATATTTATATTATTTTTATATTATAATTATATATAATATATTATTTATAT
1 GTAATATTTTAA-TAATAATTATATAATTTTTATATTATAATTATATATAATATATTATTTATAT
170773 ATATAAT
65 ATATAAT
* *
170780 TTAATATATTAATAATTAATTATATAATTTTAATATATTTATATATT-TATAT-ATAT-TT-TTT
1 GTAATATTTTAATAA-TAATTATATAATTTT--TATA-TTATA-ATTATATATAATATATTATTT
*
170841 ATATTATATTTTAT
61 ATA-TATA--TAAT
170855 GTAATATTTTAATA
1 GTAATATTTTAATA
170869 TTTTAATTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
71 8 0.11
72 23 0.32
73 6 0.08
74 8 0.11
75 25 0.34
76 3 0.04
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (71 bp):
GTAATATTTTAATAATAATTATATAATTTTTATATTATAATTATATATAATATATTATTTATATA
TATAAT
Found at i:171052 original size:2 final size:2
Alignment explanation
Indices: 171045--171076 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
171035 ATAAAATTTC
*
171045 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
171077 ACTCCTGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:179743 original size:39 final size:39
Alignment explanation
Indices: 179686--179767 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 39
179676 AGCATTTAGA
* *
179686 TTTGAAAATTTTCCTTTTGTTTGTTC-AAATTTGATTCAG
1 TTTGAAAATTTTACTTTTGTTTG-TCAAAATTTGATTAAG
*
179725 TTTGAAAATTTTATTTTTGTTTGTCAAAATTTGATTAAG
1 TTTGAAAATTTTACTTTTGTTTGTCAAAATTTGATTAAG
179764 TTTG
1 TTTG
179768 GATGTAAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
38 2 0.05
39 37 0.95
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (39 bp):
TTTGAAAATTTTACTTTTGTTTGTCAAAATTTGATTAAG
Found at i:181467 original size:8 final size:8
Alignment explanation
Indices: 181444--181478 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
181434 TTGATAGCTC
181444 TTCTTCTTT
1 TTCTT-TTT
181453 TTCTTTTT
1 TTCTTTTT
*
181461 TTTTTTTT
1 TTCTTTTT
181469 TTCTTTTT
1 TTCTTTTT
181477 TT
1 TT
181479 ATAATTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 19 0.79
9 5 0.21
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTCTTTTT
Found at i:181900 original size:2 final size:2
Alignment explanation
Indices: 181893--181921 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
181883 AGGTCCTGAA
181893 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
181922 ATTCTTGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:182301 original size:20 final size:20
Alignment explanation
Indices: 182244--182307 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
182234 GTTGATAGGT
*
182244 AAAATTTATTTTTTTA-AAA
1 AAAATTTATTTTTTTACTAA
* **
182263 AAAATTTATATTTGAACTAA
1 AAAATTTATTTTTTTACTAA
** *
182283 ATTATTTATTTTTTTACTAC
1 AAAATTTATTTTTTTACTAA
182303 AAAAT
1 AAAAT
182308 ATGAGATATT
Statistics
Matches: 32, Mismatches: 12, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
19 13 0.41
20 19 0.59
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (20 bp):
AAAATTTATTTTTTTACTAA
Found at i:182432 original size:23 final size:24
Alignment explanation
Indices: 182382--182433 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
182372 TGTTAATAAA
182382 ATTAAAATTATAAAATGAATAATT
1 ATTAAAATTATAAAATGAATAATT
** *
182406 -TTAAAA-TATAAAATTTATAGTT
1 ATTAAAATTATAAAATGAATAATT
182428 ATTAAA
1 ATTAAA
182434 TAATACCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
ATTAAAATTATAAAATGAATAATT
Found at i:183584 original size:23 final size:24
Alignment explanation
Indices: 183540--183584 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
183530 TAAAAATAAA
*
183540 TAATTATATATTTAATATAATTTT
1 TAATTATATATTTAATAAAATTTT
*
183564 TAATTATCTA-TTAATAAAATT
1 TAATTATATATTTAATAAAATT
183585 ATTATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TAATTATATATTTAATAAAATTTT
Found at i:184951 original size:17 final size:18
Alignment explanation
Indices: 184914--184952 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
184904 TAAATTTTAA
*
184914 ATATATTAAATAATTATT
1 ATATATTAAATAATAATT
*
184932 ATATTTTAAA-AATAATT
1 ATATATTAAATAATAATT
184949 ATAT
1 ATAT
184953 GAATTAACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATATTAAATAATAATT
Found at i:186722 original size:2 final size:2
Alignment explanation
Indices: 186715--186745 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
186705 TAAGTTTTGC
186715 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
186746 ATGTTTGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:188445 original size:13 final size:13
Alignment explanation
Indices: 188424--188453 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
188414 CCTAACAAAG
*
188424 GATTGGCAATTTA
1 GATTCGCAATTTA
188437 GATTCGCAATTTA
1 GATTCGCAATTTA
188450 GATT
1 GATT
188454 TGGTTCTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (13 bp):
GATTCGCAATTTA
Found at i:193293 original size:17 final size:20
Alignment explanation
Indices: 193252--193293 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 20
193242 TTTTATTAAA
193252 TAATAAAATATAAATATTAT
1 TAATAAAATATAAATATTAT
193272 T-ATAAAA-AT-AATATT-T
1 TAATAAAATATAAATATTAT
193288 TAATAA
1 TAATAA
193294 TATAACGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.10
17 10 0.48
18 2 0.10
19 6 0.29
20 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAATAAAATATAAATATTAT
Found at i:195821 original size:20 final size:20
Alignment explanation
Indices: 195796--195834 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
195786 AAGACTAATA
195796 TAAATACAAACTAAAAGTTT
1 TAAATACAAACTAAAAGTTT
*
195816 TAAATACAAATTAAAAGTT
1 TAAATACAAACTAAAAGTT
195835 GAAGATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (20 bp):
TAAATACAAACTAAAAGTTT
Found at i:196109 original size:34 final size:34
Alignment explanation
Indices: 196042--196257 Score: 292
Period size: 34 Copynumber: 6.4 Consensus size: 34
196032 GAGAAAGGCA
* * *
196042 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
196075 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
196109 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
196142 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
196176 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
196210 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
196244 TGTTGATTAAATGG
1 TGTTGATTAAATGG
196258 TGGTTTTTTA
Statistics
Matches: 162, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 40 0.25
34 122 0.75
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:196223 original size:68 final size:67
Alignment explanation
Indices: 196042--196259 Score: 319
Period size: 67 Copynumber: 3.2 Consensus size: 67
196032 GAGAAAGGCA
* * * * *
196042 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
196107 AT
66 AT
* * * *
196109 TGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
196174 AT
66 AT
* * *
196176 TGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
196241 CAT
65 CAT
196244 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
196260 GTTTTTTACC
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 73 0.54
68 61 0.46
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (67 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
AT
Found at i:200744 original size:34 final size:34
Alignment explanation
Indices: 200675--200892 Score: 296
Period size: 34 Copynumber: 6.5 Consensus size: 34
200665 AAGTGGGAGA
* * *
200675 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
200708 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
200742 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
200775 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
200809 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
200843 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
200877 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
200893 TGGTTTTTTA
Statistics
Matches: 164, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 42 0.26
34 122 0.74
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:200858 original size:68 final size:67
Alignment explanation
Indices: 200675--200894 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
200665 AAGTGGGAGA
* * * * *
200675 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
200740 CC
66 CC
* * * *
200742 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
200807 CC
66 CC
* * *
200809 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
200874 GCC
65 GCC
200877 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
200895 GTTTTTTACC
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:205201 original size:12 final size:13
Alignment explanation
Indices: 205184--205218 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
205174 CCATTTCATA
205184 TTTTTTCTTTTT-
1 TTTTTTCTTTTTC
205196 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
205209 TTTCTTTCTT
1 TTT-TTTCTT
205219 CTTCATCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 3 0.14
14 6 0.29
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:206508 original size:32 final size:32
Alignment explanation
Indices: 206459--206869 Score: 644
Period size: 32 Copynumber: 12.8 Consensus size: 32
206449 AAAATGGTGA
* * *
206459 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
206491 TTTTAAATGGGTTGCCACCGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * * *
206523 TTTTAAATGGGTTGCCACCAACTTCTGGGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
**
206555 TTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
206587 TTTGAAATGGGTTGCCACCTACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
206619 TTT-AGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGA-AATGGGTTGCCACCGACTTGTGTGGGC
206651 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
206683 TTTGAAATGGCTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
206715 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
206747 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
206779 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
206811 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
206843 TTTGGAATGGGTTGCCACCGATTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
206870 AATTTAAAAG
Statistics
Matches: 356, Mismatches: 21, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
31 1 0.00
32 354 0.99
33 1 0.00
ACGTcount: A:0.16, C:0.19, G:0.34, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:206921 original size:27 final size:27
Alignment explanation
Indices: 206855--207646 Score: 1181
Period size: 27 Copynumber: 28.9 Consensus size: 27
206845 TGGAATGGGT
* * * *
206855 TGCCACCGATTTGTGAATTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
206882 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
206910 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
206937 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
206965 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
* *
206993 TGCCACAGAGTTGTGGACTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
207020 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * *
207048 TGCCACAGAGTTGTGGACTTAAAAAAGA
1 TGCCACGGAGTTGTGGACTT-AAAAGGG
* * *
207076 TGCCACAGAGTTATGGACTTAAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
207103 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
207130 TGCTACGGAGTTGTGGTCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
207157 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
207184 ATGCCATGGAGTTATGGACTTAAAAGAG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
207212 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
207239 TACCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
207266 TGCCACGGAGTTGTGGTA-TTAAAAGGAA
1 TGCCACGGAGTTGTGG-ACTTAAAAGG-G
*
207294 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
207321 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
207348 TGCCACGGAGTTGTGGACTTAAAAGGAA
1 TGCCACGGAGTTGTGGACTTAAAAGG-G
**
207376 TGCCATAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
207403 TGCCACGGAGTTGTAGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
207430 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
207457 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
207484 TGCCACGGAGTTGTGGACTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
207511 TACCACGGAGTTGTGGATTTTAAAAGGG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGG
*
207539 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
207566 TACCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* *
207594 TGCCACAGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
207621 TGCCACAGAGTTGTGGACTTTAAAAG
1 TGCCACGGAGTTGTGGAC-TTAAAAG
207647 AAAATGCCAC
Statistics
Matches: 701, Mismatches: 52, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
27 447 0.64
28 254 0.36
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.23
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:206924 original size:55 final size:54
Alignment explanation
Indices: 206855--207646 Score: 1181
Period size: 55 Copynumber: 14.5 Consensus size: 54
206845 TGGAATGGGT
* * * *
206855 TGCCACCGATTTGTGAATTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGG
206910 TGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGG
* *
206965 ATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
207020 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAAGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTT-AAAAGGG
* * *
207076 TGCCACAGAGTTATGGACTTAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
207130 TGCTACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
207184 ATGCCATGGAGTTATGGACTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
207239 TACCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGTA-TTAAAAGGAA
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGG-ACTTAAAAGG-G
*
207294 TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* **
207348 TGCCACGGAGTTGTGGACTTAAAAGGAATGCCATAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGG-GTGCCACGGAGTTGTGGACTTAAAAGGG
*
207403 TGCCACGGAGTTGTAGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
*
207457 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
207511 TACCACGGAGTTGTGGATTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
207566 TACCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
*
207621 TGCCACAGAGTTGTGGACTTTAAAAG
1 TGCCACGGAGTTGTGGAC-TTAAAAG
207647 AAAATGCCAC
Statistics
Matches: 676, Mismatches: 51, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
54 238 0.35
55 390 0.58
56 48 0.07
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.23
Consensus pattern (54 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:207066 original size:82 final size:81
Alignment explanation
Indices: 206855--207646 Score: 1181
Period size: 82 Copynumber: 9.6 Consensus size: 81
206845 TGGAATGGGT
* * * * *
206855 TGCCACCGATTTGTGAATTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
206920 TTGTGGACTTAAAAGGG
65 TTGTGGACTTAAAAGGG
* *
206937 ATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGA
1 -TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGA
*
207002 GTTGTGGACTAAAAAGGG
64 GTTGTGGACTTAAAAGGG
* * *
207020 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAAGATGCCACAGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTT-AAAAGGGTGCCACGGA
* *
207085 GTTATGGACTTAAAAAGG
64 GTTGTGGACTTAAAAGGG
* * *
207103 TGCCACGGAGTTGTGGACTTAAAAGGGTGCTACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
207168 TGTGGACTTAAAAGGG
66 TGTGGACTTAAAAGGG
* * * * *
207184 ATGCCATGGAGTTATGGACTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTACCACGGAG
1 -TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
207249 TTGTGGACTTAAAAGGG
65 TTGTGGACTTAAAAGGG
*
207266 TGCCACGGAGTTGTGGTA-TTAAAAGGAATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGA
1 TGCCACGGAGTTGTGG-ACTTAAAAGG-GTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGA
207330 GTTGTGGACTTAAAAGGG
64 GTTGTGGACTTAAAAGGG
* *
207348 TGCCACGGAGTTGTGGACTTAAAAGGAATGCCATAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGG-GTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
*
207413 TTGTAGACTTAAAAGGG
65 TTGTGGACTTAAAAGGG
*
207430 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
*
207495 TGTGGACTAAAAAGGG
66 TGTGGACTTAAAAGGG
* * *
207511 TACCACGGAGTTGTGGATTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTACCACGGAG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
207576 TTGTGGACTTTAAAAGGG
65 TTGTGGAC-TTAAAAGGG
* *
207594 TGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TTAAAAG
207647 AAAATGCCAC
Statistics
Matches: 652, Mismatches: 48, Indels: 18
0.91 0.07 0.03
Matches are distributed among these distances:
81 117 0.18
82 373 0.57
83 162 0.25
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.23
Consensus pattern (81 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
TGTGGACTTAAAAGGG
Found at i:214947 original size:24 final size:24
Alignment explanation
Indices: 214895--214947 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
214885 ATATTTTTTT
* * * *
214895 ATTTTTTAAAACAAATAAAGATCA
1 ATTTTTTAAAAAAAAAAAACATAA
*
214919 TTTTTTTAAAAAAAAAAAACATAA
1 ATTTTTTAAAAAAAAAAAACATAA
214943 ATTTT
1 ATTTT
214948 GAACTTTTCT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (24 bp):
ATTTTTTAAAAAAAAAAAACATAA
Found at i:215093 original size:2 final size:2
Alignment explanation
Indices: 215086--215122 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
215076 GATTTTCAAA
*
215086 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
215123 AATAAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:215509 original size:17 final size:17
Alignment explanation
Indices: 215487--215522 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
215477 CATTTCATAT
* *
215487 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTCTTTCTTC
215504 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
215521 TT
1 TT
215523 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:221000 original size:30 final size:29
Alignment explanation
Indices: 220960--221055 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 29
220950 AAAAAATTTA
220960 ATTTAGATAGAAATTAAAATTTAAGAGCTT
1 ATTTA-ATAGAAATTAAAATTTAAGAGCTT
* * *
220990 ATTTGAATAGAGGATTAAAATTGAAG-GTTT
1 ATTT-AATAGA-AATTAAAATTTAAGAGCTT
* **
221020 ATTTAAGGTAGAAATTAAAAATTAAGAATTT
1 ATTTAA--TAGAAATTAAAATTTAAGAGCTT
221051 ATTTA
1 ATTTA
221056 TTACAAACAA
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
29 2 0.04
30 27 0.50
31 25 0.46
ACGTcount: A:0.46, C:0.01, G:0.16, T:0.38
Consensus pattern (29 bp):
ATTTAATAGAAATTAAAATTTAAGAGCTT
Found at i:222062 original size:16 final size:16
Alignment explanation
Indices: 222043--222082 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
222033 TATTTTTGAG
*
222043 TTTAAATTATTTTAAA
1 TTTAAATCATTTTAAA
*
222059 TTTAACTCATTTTAAA
1 TTTAAATCATTTTAAA
*
222075 TTTGAATC
1 TTTAAATC
222083 GATTAGATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAAATCATTTTAAA
Found at i:222243 original size:15 final size:15
Alignment explanation
Indices: 222195--222244 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
222185 AATTTTAAAT
*
222195 TTAAATTAAATTTAA
1 TTAAAATAAATTTAA
* *
222210 AT-AAAT-TATTTAA
1 TTAAAATAAATTTAA
*
222223 TCAAAATAAATTTAA
1 TTAAAATAAATTTAA
222238 TTAAAAT
1 TTAAAAT
222245 TTTATTGAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
13 6 0.23
14 7 0.27
15 13 0.50
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
TTAAAATAAATTTAA
Found at i:222259 original size:28 final size:29
Alignment explanation
Indices: 222197--222270 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 29
222187 TTTTAAATTT
*
222197 AAAT-TAAATTTAAATAAATTATTTAATC
1 AAATATAAATTTAAATAAAATATTTAATC
* * *
222225 AAA-ATAAATTTAATTAAAAT-TTTATTG
1 AAATATAAATTTAAATAAAATATTTAATC
*
222252 AAATATAAATAATAAATAA
1 AAATATAAAT-TTAAATAA
222271 TAAATAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
27 8 0.22
28 23 0.62
29 6 0.16
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (29 bp):
AAATATAAATTTAAATAAAATATTTAATC
Found at i:222275 original size:14 final size:13
Alignment explanation
Indices: 222252--222300 Score: 52
Period size: 14 Copynumber: 4.0 Consensus size: 13
222242 AATTTTATTG
222252 AAATATAAATAAT
1 AAATATAAATAAT
222265 AAATAATAAATAAT
1 AAAT-ATAAATAAT
*
222279 --ATTTAAA-AAT
1 AAATATAAATAAT
222289 AAATAT-AATAAT
1 AAATATAAATAAT
222301 GATAATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 6 0.20
12 8 0.27
13 4 0.13
14 9 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATATAAATAAT
Found at i:222642 original size:17 final size:17
Alignment explanation
Indices: 222620--222652 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
222610 CAAAATCAGA
*
222620 AATTAATTTTAAGATCT
1 AATTAATTTCAAGATCT
222637 AATTAATTTCAAGATC
1 AATTAATTTCAAGATC
222653 CAAAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (17 bp):
AATTAATTTCAAGATCT
Found at i:222954 original size:42 final size:43
Alignment explanation
Indices: 222907--222992 Score: 104
Period size: 42 Copynumber: 2.0 Consensus size: 43
222897 AACTTCTTTA
* * *
222907 ATTTAAGTCGAATTA-AATTATTTATTAAT-TAAAAATATTTTT
1 ATTTAAATCGAATTATAA-AATATATTAATATAAAAATATTTTT
**
222949 ATTTAAATTTAATTATAAAATATATTAATATAAAAATATTTTT
1 ATTTAAATCGAATTATAAAATATATTAATATAAAAATATTTTT
222992 A
1 A
222993 AATTTTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
42 21 0.57
43 16 0.43
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (43 bp):
ATTTAAATCGAATTATAAAATATATTAATATAAAAATATTTTT
Found at i:222982 original size:27 final size:26
Alignment explanation
Indices: 222931--222982 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
222921 AAATTATTTA
* * *
222931 TTAATTAAAAATATTTTTATTTAAAT
1 TTAATTAAAAATATATTAATATAAAT
222957 TTAATTATAAAATATATTAATATAAA
1 TTAATTA-AAAATATATTAATATAAA
222983 AATATTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TTAATTAAAAATATATTAATATAAAT
Found at i:225975 original size:29 final size:28
Alignment explanation
Indices: 225921--225974 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
225911 CGATTTTAAG
**
225921 AAAAATTAATTTATAATTTTATTTTTCA
1 AAAAATTAATTTATAATAATATTTTTCA
225949 AAAAATTAATTTAATAATAA-ATTTTT
1 AAAAATTAATTT-ATAATAATATTTTT
225975 TATTTGTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (28 bp):
AAAAATTAATTTATAATAATATTTTTCA
Found at i:228779 original size:70 final size:69
Alignment explanation
Indices: 228667--228796 Score: 165
Period size: 70 Copynumber: 1.9 Consensus size: 69
228657 ACTTTTCAGC
* *
228667 TTTTCTATCAAAAAGAATCTAATTCTCAAGTACAATTAATGCATTAGTCTAATCCTTGCAGTCTT
1 TTTTCTATCAAAAAGAATCTAATTCTCAAGTACAATTAATGCATTAATCTAATCCATGCAGTCTT
228732 TCTT
66 TCTT
* * * *
228736 TTTTCCTAT-AAAAATGAATCTGATTCTC-AGATATAATTTATGCATTAATTTAATCCATGCA
1 TTTT-CTATCAAAAA-GAATCTAATTCTCAAG-TACAATTAATGCATTAATCTAATCCATGCA
228797 TTCTGACATT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
69 11 0.21
70 41 0.79
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (69 bp):
TTTTCTATCAAAAAGAATCTAATTCTCAAGTACAATTAATGCATTAATCTAATCCATGCAGTCTT
TCTT
Found at i:228858 original size:91 final size:91
Alignment explanation
Indices: 228725--229167 Score: 505
Period size: 91 Copynumber: 5.0 Consensus size: 91
228715 CTAATCCTTG
* * * * *
228725 CAGTCTTTCTTTTTTCCTATAAAAATGAATCTGATTCTCAGATATAATTTATGCATTAATTTAAT
1 CAGTCTTTCTTTTTTTCTATAAAAA-AAATCTGATTCTCAGATATAATTCATGCATTAGTCTAAT
* *
228790 CCATGCATTCTGACATTTACAATCAAT
65 CCTTGCAGTCTGACATTTACAATCAAT
* * * *
228817 CAGCCTTTCTTTTTTTCTATAAAAAAAATCTAATTCTCAGATGTAATTCATGCATTAGTCCAATC
1 CAGTCTTTCTTTTTTTCTATAAAAAAAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATC
* *
228882 CTTGTAGTTTGACATTTACAATCAAT
66 CTTGCAGTCTGACATTTACAATCAAT
* *
228908 CAGTCTTTC-TTTTTTCTATAAAAAAGAATCTGCTTCTCAGATATAATTCATGCATTAGTTTAAT
1 CAGTCTTTCTTTTTTTCTATAAAAAA-AATCTGATTCTCAGATATAATTCATGCATTAGTCTAAT
228972 CCTTGCAGTCTGACATTT---AT-AAT
65 CCTTGCAGTCTGACATTTACAATCAAT
** * * * *
228995 CAGTC-AAC-TTTTTTCTATAAAAAAAAATTTGATTCTTAGATGTAATTCATGCATTAGCCTAAT
1 CAGTCTTTCTTTTTTTCTAT-AAAAAAAATCTGATTCTCAGATATAATTCATGCATTAGTCTAAT
*
229058 CATTGCAGTCTGACATTT---A-CAAT
65 CCTTGCAGTCTGACATTTACAATCAAT
** * * *
229081 CAGTC-AACTTTTTTTCTATAAAAAAAAATCTGATTCTAAGATATAATTCATGCATTAATCTCAT
1 CAGTCTTTCTTTTTTTCTAT-AAAAAAAATCTGATTCTCAGATATAATTCATGCATTAGTCTAAT
* *
229145 CCTTGCAATATGACATTTACAAT
65 CCTTGCAGTCTGACATTTACAAT
229168 TGATTCTTAG
Statistics
Matches: 304, Mismatches: 39, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
86 72 0.24
87 78 0.26
88 2 0.01
90 17 0.06
91 112 0.37
92 23 0.08
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.40
Consensus pattern (91 bp):
CAGTCTTTCTTTTTTTCTATAAAAAAAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATC
CTTGCAGTCTGACATTTACAATCAAT
Found at i:229208 original size:57 final size:57
Alignment explanation
Indices: 229111--229224 Score: 156
Period size: 57 Copynumber: 2.0 Consensus size: 57
229101 AAAAAAAATC
* * *
229111 TGATTCTAAGATATAATTCATGCATTAATCTCATCCTTGCAATATGACATTTACAAT
1 TGATTCTAAGATATAATTCATACATTAATCTAATCCTTGCAATACGACATTTACAAT
* * * * *
229168 TGATTCTTAGATATAATTTATACATTAGTCTAATCTTTGCAATCCGACATTTACAAT
1 TGATTCTAAGATATAATTCATACATTAATCTAATCCTTGCAATACGACATTTACAAT
229225 CAATTAACAT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (57 bp):
TGATTCTAAGATATAATTCATACATTAATCTAATCCTTGCAATACGACATTTACAAT
Found at i:229332 original size:90 final size:89
Alignment explanation
Indices: 229165--229364 Score: 267
Period size: 90 Copynumber: 2.2 Consensus size: 89
229155 TGACATTTAC
* * * * *
229165 AATTGATTCTTAGATATAATTTATACATTAGTCTAATCTTTGCAATCCGACATTTACAATCAATT
1 AATTGATTCTTAGATATAATTCATACATTAATCTAATCTATGCAATCCAACATTTACAATCAATG
229230 AACATTTATTTTTTCTATAAAAAAG
66 AACATTTATTTTTTC-ATAAAAAAG
* * * *
229255 AATTGATTCTTAGATATAATTCATGCATTAATCTAATCTATGCAGTCTAACATTTACAATTAATG
1 AATTGATTCTTAGATATAATTCATACATTAATCTAATCTATGCAATCCAACATTTACAATCAATG
*
229320 AAC-TTCTTTTTTTTCATAAAAAAG
66 AACATT-TATTTTTTCATAAAAAAG
*
229344 AATCTGATTCTAAGATATAAT
1 AAT-TGATTCTTAGATATAAT
229365 CACATTTATT
Statistics
Matches: 97, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
89 14 0.14
90 83 0.86
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.41
Consensus pattern (89 bp):
AATTGATTCTTAGATATAATTCATACATTAATCTAATCTATGCAATCCAACATTTACAATCAATG
AACATTTATTTTTTCATAAAAAAG
Found at i:230176 original size:104 final size:104
Alignment explanation
Indices: 230057--230263 Score: 337
Period size: 105 Copynumber: 2.0 Consensus size: 104
230047 AAAAGGGTTT
* **
230057 ATTATTATTATTTTTAATAAAAT-TTAAAATAATATTTAATTAAGTTTAAAAAATTAAATTAACA
1 ATTATTATAATTTTTAATAAAATAAAAAAATAATATTTAATTAAGTTTAAAAAATTAAATTAACA
230121 AATCAAAAT-TTAATTATTATGTTTTTATAGAAATAAAAAA
66 AATCAAAATATTAATTATTATGTTTTT-TA-AAATAAAAAA
*
230161 ATTATTATAATTTTTAATAAAATAAAAAAATAATATTTAATTAAGTTTAAAAATTTAAATTAACA
1 ATTATTATAATTTTTAATAAAATAAAAAAATAATATTTAATTAAGTTTAAAAAATTAAATTAACA
*
230226 AATTAAAATATTAATTATTATGTTTTTTAAAATAAAAA
66 AATCAAAATATTAATTATTATGTTTTTTAAAATAAAAA
230264 TTTTTAAATT
Statistics
Matches: 96, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
104 31 0.32
105 48 0.50
106 17 0.18
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.43
Consensus pattern (104 bp):
ATTATTATAATTTTTAATAAAATAAAAAAATAATATTTAATTAAGTTTAAAAAATTAAATTAACA
AATCAAAATATTAATTATTATGTTTTTTAAAATAAAAAA
Found at i:230202 original size:30 final size:29
Alignment explanation
Indices: 230132--230191 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
230122 ATCAAAATTT
*
230132 AATTATTAT-GTTTTTATAGAAATAAAAA
1 AATTATTATAATTTTTATAGAAATAAAAA
230160 AATTATTATAATTTTTAATA-AAATAAAAA
1 AATTATTATAATTTTT-ATAGAAATAAAAA
230189 AAT
1 AAT
230192 AATATTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 9 0.31
29 17 0.59
30 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (29 bp):
AATTATTATAATTTTTATAGAAATAAAAA
Found at i:230269 original size:15 final size:15
Alignment explanation
Indices: 230249--230278 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
230239 ATTATTATGT
230249 TTTTTAAAATAAAAA
1 TTTTTAAAATAAAAA
*
230264 TTTTTAAATTAAAAA
1 TTTTTAAAATAAAAA
230279 AAGTTTTTTA
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTTTTAAAATAAAAA
Found at i:230908 original size:93 final size:92
Alignment explanation
Indices: 230806--231329 Score: 618
Period size: 93 Copynumber: 5.7 Consensus size: 92
230796 TAATCCTTGT
* * *
230806 AGTCTTTCTTTTTTCCTATAAAAAAAGAATCTGATTCTCAAATATAATTTATGCATTAGTCTAAT
1 AGTCTTTCTTTTTTTCTAT-AAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAAT
230871 TCTTTCAGCTTGACATTTACAATCAATC
65 TCTTTCAGCTTGACATTTACAATCAATC
* *
230899 AGTCTTTCTTTTTTTCTATAAAAAA-AA--TGATTCTCAGATATGATTCATGCATTAGTC-AAAT
1 AGTCTTTCTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATT
*
230960 CTTTGCAGCTTGACATTTACAATTAATC
66 CTTT-CAGCTTGACATTTACAATCAATC
* * * *
230988 AGTCTTTCTTTCTTTTTTATTAAAAAGAATCTGATTCTTAGATATAATTCATGCATTGGTCTAAT
1 AGTCTTTCTTT-TTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAAT
* * * *
231053 CCTTGCAGCCTGACATTTATAATCAATC
65 TCTTTCAGCTTGACATTTACAATCAATC
* * *
231081 AATCTTTCTTTTTTTTCTATTAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAA-
1 AGTCTTTC-TTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAAT
* *
231145 TCTTTGTAG-TCTGATATTTACAATCAATC
65 TCTTT-CAGCT-TGACATTTACAATCAATC
* *
231174 AGTCTTTCTTTTTTTCTATAAAAAAGAATCTGATTCTCATATATAATTCATGCATTAGTCTAATC
1 AGTCTTTCTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATT
* * *
231239 CTTGCA-ATCTGACATTTACAATCAGTC
66 CTTTCAGCT-TGACATTTACAATCAATC
* * *
231266 AACTTTTCTTTGCTTTTTTT-TATAAAAAA-AATATGATTCTTC-GATATAATTCATACATTAGT
1 -A---GTCTTT-CTTTTTTTCTATAAAAAAGAATCTGATTC-TCAGATATAATTCATGCATTAGT
231328 CT
60 CT
231330 CATCCTTGTA
Statistics
Matches: 373, Mismatches: 41, Indels: 32
0.84 0.09 0.07
Matches are distributed among these distances:
88 7 0.02
89 60 0.16
90 12 0.03
91 4 0.01
92 80 0.21
93 149 0.40
94 8 0.02
95 29 0.08
96 16 0.04
97 8 0.02
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (92 bp):
AGTCTTTCTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATT
CTTTCAGCTTGACATTTACAATCAATC
Found at i:231182 original size:182 final size:183
Alignment explanation
Indices: 230808--231451 Score: 703
Period size: 185 Copynumber: 3.5 Consensus size: 183
230798 ATCCTTGTAG
* *
230808 TCTTTCTTTTTTCCTATAAAAAAAGAATCTGATTCTCAAATATAATTTATGCATTAGTCTAATTC
1 TCTTTCTTTTTT-CTAT-AAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCC
* * *
230873 TTTCAGCTTGACATTTACAATCAATCAGTCTTTC-TTTTTTTCTA-TAAAAAAAATGATTCTCAG
64 TTGCAGCCTGACATTTACAATCAATCAATCTTTCTTTTTTTTCTATTAAAAAAAATGATTCTCAG
* * * * *
230936 ATATGATTCATGCATTAGTCAAATCTTTGCAG-CTTGACATTTACAATTAATCAG-
129 ATATAATTCATGCATTAGTCTAATCTTTGTAGTC-TGATATTTACAATCAATCAGT
* * * * *
230990 TCTTTCTTTCTTTTTTATTAAAAAGAATCTGATTCTTAGATATAATTCATGCATTGGTCTAATCC
1 TCTTTC-TT-TTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCC
* *
231055 TTGCAGCCTGACATTTATAATCAATCAATCTTTCTTTTTTTTCTATTAAAAAGAATCCGATTCTC
64 TTGCAGCCTGACATTTACAATCAATCAATCTTTCTTTTTTTTCTATTAAAAAAAAT--GATTCTC
231120 AGATATAATTCATGCATTAGTCTAATCTTTGTAGTCTGATATTTACAATCAATCAG-
127 AGATATAATTCATGCATTAGTCTAATCTTTGTAGTCTGATATTTACAATCAATCAGT
*
231176 TCTTTCTTTTTTTCTATAAAAAAGAATCTGATTCTCATATATAATTCATGCATTAGTCTAATCCT
1 TCTTTC-TTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCT
** * * *
231241 TGCAATCTGACATTTACAATCAGTCAA-CTTTTCTTTGCTTTTTTTTATAAAAAAAATATGATTC
65 TGCAGCCTGACATTTACAATCAATCAATC-TTTC-TT--TTTTTTCTATTAAAAAAA-ATGATTC
* * * * * *
231305 TTC-GATATAATTCATACATTAGTCTCATCCTTGTAATCTGATATTTACAATCAGTCAACTTTT
125 -TCAGATATAATTCATGCATTAGTCTAATCTTTGTAGTCTGATATTTACAATCAATC-A---GT
* * * * * * *
231368 TTTTTCCTTTTTT-TATAAAAAAAAAT-TTATTATCCAATATAATTCATACATTAGTCTCATCCT
1 TCTTT-CTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCT
* **
231431 TGTAGTATGACATTTACAATC
65 TGCAGCCTGACATTTACAATC
231452 GATTCTCAGA
Statistics
Matches: 397, Mismatches: 46, Indels: 30
0.84 0.10 0.06
Matches are distributed among these distances:
182 77 0.19
183 15 0.04
184 14 0.04
185 78 0.20
186 67 0.17
187 54 0.14
188 18 0.05
189 2 0.01
190 49 0.12
191 12 0.03
192 10 0.03
193 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.43
Consensus pattern (183 bp):
TCTTTCTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTT
GCAGCCTGACATTTACAATCAATCAATCTTTCTTTTTTTTCTATTAAAAAAAATGATTCTCAGAT
ATAATTCATGCATTAGTCTAATCTTTGTAGTCTGATATTTACAATCAATCAGT
Found at i:231335 original size:95 final size:93
Alignment explanation
Indices: 230808--231451 Score: 582
Period size: 93 Copynumber: 6.9 Consensus size: 93
230798 ATCCTTGTAG
* * * * *
230808 TCTTTCTTTTTTCCTATAAAAAAAGAATCTGATTCTCAAATATAATTTATGCATTAGTCTAATTC
1 TCTTTCTTTTTT-TTAT-AAAAAA-AATATGATTCTCAGATATAATTCATGCATTAGTCTAATCC
* * *
230873 TTTC-AGCTTGACATTTACAATCAATC-A--G
63 TTGCAATC-TGACATTTACAATCAATCAATTT
* * *
230901 TCTTTCTTTTTTTCTAT-AAAAAAA-ATGATTCTCAGATATGATTCATGCATTAGTCAAATCTTT
1 TCTTTCTTTTTTT-TATAAAAAAAATATGATTCTCAGATATAATTCATGCATTAGTCTAATCCTT
* * *
230964 GC-AGCTTGACATTTACAATTAATCAGTCTT
65 GCAATC-TGACATTTACAATCAATCAAT-TT
* * * * *
230994 TCTTTCTTTTTTAT-TAAAAAGAATCTGATTCTTAGATATAATTCATGCATTGGTCTAATCCTTG
1 TCTTTCTTTTTTTTATAAAAAAAATATGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTG
** *
231058 CAGCCTGACATTTATAATCAATCAATCTT
66 CAATCTGACATTTACAATCAATCAAT-TT
* * ** *
231087 TC-TT-TTTTTTCTATTAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCTTT
1 TCTTTCTTTTTTTTA-TAAAAAAAATATGATTCTCAGATATAATTCATGCATTAGTCTAATCCTT
* * * *
231150 GTAGTCTGATATTTACAATCAATC-A--G
65 GCAATCTGACATTTACAATCAATCAATTT
* *
231176 TCTTTCTTTTTTTCTATAAAAAAGAATCTGATTCTCATATATAATTCATGCATTAGTCTAATCCT
1 TCTTTCTTTTTTT-TATAAAAAA-AATATGATTCTCAGATATAATTCATGCATTAGTCTAATCCT
*
231241 TGCAATCTGACATTTACAATCAGTCAACTTT
64 TGCAATCTGACATTTACAATCAATCAA-TTT
* *
231272 TCTTTGCTTTTTTTTATAAAAAAAATATGATTCTTC-GATATAATTCATACATTAGTCTCATCCT
1 TCTTT-CTTTTTTTTATAAAAAAAATATGATTC-TCAGATATAATTCATGCATTAGTCTAATCCT
* * *
231336 TGTAATCTGATATTTACAATCAGTCAACTTTT
64 TGCAATCTGACATTTACAATCAATCAA--TTT
* * * * * *
231368 TTTTTCCTTTTTTTATAAAAAAAA-ATTTATTATCCA-ATATAATTCATACATTAGTCTCATCCT
1 TCTTTCTTTTTTTTATAAAAAAAATA-TGATTCT-CAGATATAATTCATGCATTAGTCTAATCCT
* * *
231431 TGTAGTATGACATTTACAATC
64 TGCAATCTGACATTTACAATC
231452 GATTCTCAGA
Statistics
Matches: 468, Mismatches: 59, Indels: 46
0.82 0.10 0.08
Matches are distributed among these distances:
89 56 0.12
90 4 0.01
91 25 0.05
92 71 0.15
93 151 0.32
94 3 0.01
95 127 0.27
96 23 0.05
97 8 0.02
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.43
Consensus pattern (93 bp):
TCTTTCTTTTTTTTATAAAAAAAATATGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTG
CAATCTGACATTTACAATCAATCAATTT
Found at i:232355 original size:16 final size:15
Alignment explanation
Indices: 232331--232361 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
232321 TGTTTTTATA
232331 AAAATAAAAAATTTT
1 AAAATAAAAAATTTT
*
232346 AAAATAAAAAAATTT
1 AAAATAAAAAATTTT
232361 A
1 A
232362 TAATTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATAAAAAATTTT
Found at i:232479 original size:116 final size:117
Alignment explanation
Indices: 232137--232486 Score: 423
Period size: 116 Copynumber: 3.0 Consensus size: 117
232127 TATTATTTTT
* * *
232137 AATAAAAA-AATATTCAATTAACTTTAACAGAAATTTATATTAATAAATTAAAATATT-A--ATT
1 AATAAAAATAATATTTAATTAAGTTT-A-A-AAATTTACATTAATAAATTAAAATATTAATTATT
* *
232198 A--TTTTTTAAAATAAAAAATTTAAATAAAAATAAAAAGAGTTTATTATTATTTTTTAATAA
63 ATGTTTTTTAAAATAAAAAATTT---T-AAAATAAAAA-A-ATTATTA-TAATTTTTAATAA
*
232258 AATTAAAAATAATATTTAATTAAGTTTAAAAAATTACATTAATAAATTAAAAT-TTAATTATTAT
1 AA-TAAAAATAATATTTAATTAAGTTTAAAAATTTACATTAATAAATTAAAATATTAATTATTAT
232322 GTTTTTATAAAAATAAAAAATTTTAAAATAAAAAAA-T-TTATAATTTTTAATAA
65 GTTTTT-T-AAAATAAAAAATTTTAAAATAAAAAAATTATTATAATTTTTAATAA
*
232375 AATAAAAATAATATTTAATTAAGTTTAAAAATTTACATTAACAAATTAAAATATTAATTATTATG
1 AATAAAAATAATATTTAATTAAGTTTAAAAATTTACATTAATAAATTAAAATATTAATTATTATG
* *
232440 TTTTTTATAAT-AAAAATTTTAAATTAAAAAAATTATTATAATATTTT
66 TTTTTTAAAATAAAAAATTTTAAAATAAAAAAATTATTATAAT-TTTT
232487 TTTATTTTTT
Statistics
Matches: 206, Mismatches: 10, Indels: 30
0.84 0.04 0.12
Matches are distributed among these distances:
114 20 0.10
115 5 0.02
116 56 0.27
117 35 0.17
118 3 0.01
119 3 0.01
120 23 0.11
121 4 0.02
122 21 0.10
123 16 0.08
124 5 0.02
125 1 0.00
126 14 0.07
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (117 bp):
AATAAAAATAATATTTAATTAAGTTTAAAAATTTACATTAATAAATTAAAATATTAATTATTATG
TTTTTTAAAATAAAAAATTTTAAAATAAAAAAATTATTATAATTTTTAATAA
Found at i:232814 original size:22 final size:23
Alignment explanation
Indices: 232770--232826 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
232760 TGAATAATAA
232770 TAAATTTTTTAATTCTTTAAATG
1 TAAATTTTTTAATTCTTTAAATG
* *
232793 TTATTTTTTTAATT-TGTT-AATG
1 TAAATTTTTTAATTCT-TTAAATG
232815 TAAATTTTTTAA
1 TAAATTTTTTAA
232827 ATTTAATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TAAATTTTTTAATTCTTTAAATG
Found at i:233049 original size:116 final size:110
Alignment explanation
Indices: 232799--233075 Score: 344
Period size: 110 Copynumber: 2.5 Consensus size: 110
232789 AATGTTATTT
* * *
232799 TTTTAATTTGTTAATGTAAATTTTTTAAATTTAATTAAATATCATTTTTTATTTTATTAAAAAAT
1 TTTTAATTTGTTAATGTAAATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAAT
232864 AATAATAATAAATACTTTTTATTTTTATAAAATATATAATTAATA
66 AATAATAATAAATACTTTTTATTTTTATAAAATATATAATTAATA
* *
232909 TTTTAATTTGTTAATATAATTTTTTTAAACTTAATTAAATATTTATTTTTAATTTTATTAAAAAA
1 TTTTAATTTGTTAATGTAAATTTTTTAAACTTAATTAAATA-TTATTTTTAATTTTATTAAAAAA
** **
232974 TAATAAT-ATACCCTTTTTAATTTAATTTTTTATTTTAAAA-A-ATAATTAATA
65 TAATAATAATA-AATACTT--TTT-A-TTTTTA---TAAAATATATAATTAATA
* *
233025 TTTTAATTTATTAATGTAAATTTTTTTAAAGTTAATTAAATATTATTTTTA
1 TTTTAATTTGTTAATGTAAA-TTTTTTAAACTTAATTAAATATTATTTTTA
233076 TTAAAAAATA
Statistics
Matches: 144, Mismatches: 13, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
110 41 0.28
111 31 0.22
113 3 0.02
114 1 0.01
115 6 0.04
116 36 0.25
117 21 0.15
118 5 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (110 bp):
TTTTAATTTGTTAATGTAAATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAAT
AATAATAATAAATACTTTTTATTTTTATAAAATATATAATTAATA
Found at i:233130 original size:67 final size:70
Alignment explanation
Indices: 233000--233130 Score: 180
Period size: 67 Copynumber: 1.9 Consensus size: 70
232990 TTAATTTAAT
** *
233000 TTTTTATTTTAAAAAATAATTAATATTTTAATTTATTAATGTAAATTTTTTTAAAGTTAATTAAA
1 TTTTTATTAAAAAAAATAATTAATATATTAATTTATTAATGTAAATTTTTTTAAAGTTAATTAAA
233065 TATTA
66 TATTA
* *
233070 TTTTTATTAAAAAATAATAATTAATATATT-A-TTATTTAT-TAAA-TTTTTTAAATTTAATTAA
1 TTTTTATTAAAAAA-AATAATTAATATATTAATTTATTAATGTAAATTTTTTTAAAGTTAATTAA
233131 TTTATAAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
67 17 0.31
68 4 0.07
69 7 0.13
70 13 0.24
71 14 0.25
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (70 bp):
TTTTTATTAAAAAAAATAATTAATATATTAATTTATTAATGTAAATTTTTTTAAAGTTAATTAAA
TATTA
Found at i:233132 original size:71 final size:70
Alignment explanation
Indices: 233000--233130 Score: 162
Period size: 71 Copynumber: 1.9 Consensus size: 70
232990 TTAATTTAAT
** * * *
233000 TTTTTATTTTAAAAAATAATTAATATTTTAATTTATTAATGTAAATTTTTTTAAAGTTAATTAAA
1 TTTTTATTAAAAAAAATAATTAATATATTAATTTATTAATGTAAATTTTTTAAAAATTAATTAAA
233065 TATTA
66 TATTA
* *
233070 TTTTTATTAAAAAATAATAATTAATATATT-A-TTATTTAT-TAAATTTTTT-AAATTTAATTAA
1 TTTTTATTAAAAAA-AATAATTAATATATTAATTTATTAATGTAAATTTTTTAAAAATTAATTAA
233131 TTTATAAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
67 11 0.20
68 10 0.18
69 7 0.13
70 13 0.24
71 14 0.25
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (70 bp):
TTTTTATTAAAAAAAATAATTAATATATTAATTTATTAATGTAAATTTTTTAAAAATTAATTAAA
TATTA
Found at i:233254 original size:13 final size:13
Alignment explanation
Indices: 233236--233273 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
233226 AACGAATTCG
233236 TAAAAAAAACTTT
1 TAAAAAAAACTTT
*
233249 TAAAAAATA-TTT
1 TAAAAAAAACTTT
233261 TATAAAAAAACTT
1 TA-AAAAAAACTT
233274 ATTTACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 5 0.24
13 14 0.67
14 2 0.10
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (13 bp):
TAAAAAAAACTTT
Found at i:239798 original size:22 final size:21
Alignment explanation
Indices: 239753--239794 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
239743 AAAATATTTT
*
239753 TATTTAAATTTAATTATAAAA
1 TATTTAAAATTAATTATAAAA
239774 TATTTAAAAATTAA-TATAAAA
1 TATTT-AAAATTAATTATAAAA
239795 ATATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATTTAAAATTAATTATAAAA
Found at i:240831 original size:20 final size:20
Alignment explanation
Indices: 240802--240839 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
240792 TTTTAGGTTA
*
240802 AATAAATAATAAATATAATT
1 AATAAATAATAAAAATAATT
*
240822 AATAATTAATAAAAATAA
1 AATAAATAATAAAAATAA
240840 GTATTTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AATAAATAATAAAAATAATT
Found at i:244251 original size:3 final size:3
Alignment explanation
Indices: 244243--244284 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
244233 TAGCCAACAT
244243 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
244285 AGCTTCTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:244847 original size:17 final size:17
Alignment explanation
Indices: 244825--244887 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 17
244815 CCACTCCAAA
244825 AAATTTAAAATATAATT
1 AAATTTAAAATATAATT
* *
244842 AAATTT-AAATTTAAAT
1 AAATTTAAAATATAATT
* * *
244858 AGATTATAAAAAATAATA
1 AAATT-TAAAATATAATT
244876 AAATTTTAAAAT
1 AAA-TTTAAAAT
244888 TTTATTTTTA
Statistics
Matches: 34, Mismatches: 9, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
16 12 0.35
17 7 0.21
18 13 0.38
19 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
AAATTTAAAATATAATT
Found at i:244917 original size:22 final size:21
Alignment explanation
Indices: 244888--244930 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
244878 ATTTTAAAAT
244888 TTTA-TTTTTAATTAATATTTA
1 TTTATTTTTTAATTAA-ATTTA
244909 TTTATTTTTTTAATTAAATTTA
1 TTTA-TTTTTTAATTAAATTTA
244931 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 5 0.25
23 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTATTTTTTAATTAAATTTA
Found at i:246897 original size:5 final size:5
Alignment explanation
Indices: 246882--246920 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
246872 ATAAAAATTA
*
246882 AAAATT AAAAT AAAAT AAAAT -TAAT AAAAT AAAAT AAAA
1 AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
246921 ATATATTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
4 3 0.10
5 23 0.77
6 4 0.13
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:246907 original size:14 final size:14
Alignment explanation
Indices: 246867--246916 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 14
246857 ACACTAATTT
246867 AATTAATAAAAATTAAA
1 AATTAAT-AAAA-T-AA
246884 AATTAAAATAAAATAA
1 AATT--AATAAAATAA
246900 AATTAATAAAATAA
1 AATTAATAAAATAA
246914 AAT
1 AAT
246917 AAAAATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
14 13 0.42
16 6 0.19
17 5 0.16
18 4 0.13
19 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AATTAATAAAATAA
Found at i:247317 original size:17 final size:17
Alignment explanation
Indices: 247295--247328 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
247285 AAATGACATA
247295 AAATTATACCTCTAACC
1 AAATTATACCTCTAACC
*
247312 AAATTATATCTCTAACC
1 AAATTATACCTCTAACC
247329 TTTGATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.26, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATTATACCTCTAACC
Found at i:247632 original size:2 final size:2
Alignment explanation
Indices: 247625--247663 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
247615 TTTATCAAAC
247625 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
247664 CTCAAACATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:252892 original size:20 final size:20
Alignment explanation
Indices: 252869--252922 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
252859 AATAATTTTC
252869 AATAAAAATATTAATACTTT
1 AATAAAAATATTAATACTTT
* * * *
252889 AATAAATATTTTTATATTTT
1 AATAAAAATATTAATACTTT
*
252909 ATTAATAAATATTA
1 AATAA-AAATATTA
252923 CTATATTAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AATAAAAATATTAATACTTT
Found at i:254647 original size:3 final size:3
Alignment explanation
Indices: 254641--254674 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
254631 TATTTTTTTA
254641 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
254675 TTATTATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:254679 original size:3 final size:3
Alignment explanation
Indices: 254673--254705 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
254663 ATAATAATAA
254673 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
254706 GTGCATTAAA
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):
TAT
Found at i:255421 original size:17 final size:17
Alignment explanation
Indices: 255375--255423 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 17
255365 AAGAAAAAAA
255375 TATATTTTTTATCTTTC
1 TATATTTTTTATCTTTC
*
255392 -A-ACTTTTCT-TCTTTC
1 TATA-TTTTTTATCTTTC
255407 TATATTTTTTATCTTTC
1 TATATTTTTTATCTTTC
255424 CAATTTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
15 7 0.27
16 12 0.46
17 7 0.27
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.67
Consensus pattern (17 bp):
TATATTTTTTATCTTTC
Found at i:255733 original size:17 final size:16
Alignment explanation
Indices: 255699--255737 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
255689 TACTTTATTT
*
255699 ATATTTAAATTATATA
1 ATATTTAAATAATATA
*
255715 ATTATTTAAATAATTTA
1 A-TATTTAAATAATATA
255732 ATATTT
1 ATATTT
255738 TTAAAGATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATATTTAAATAATATA
Found at i:257022 original size:29 final size:29
Alignment explanation
Indices: 256990--257051 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
256980 AAAAGTACAA
256990 AAATTAAAATATTAAATTTAATAAAATAT
1 AAATTAAAATATTAAATTTAATAAAATAT
** * *
257019 AAATTAAAATATTTTATTTATTATAATAT
1 AAATTAAAATATTAAATTTAATAAAATAT
257048 AAAT
1 AAAT
257052 ATGTTAGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
AAATTAAAATATTAAATTTAATAAAATAT
Found at i:258178 original size:4 final size:4
Alignment explanation
Indices: 258169--258195 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
258159 GTCTATCGAT
258169 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
258196 TCATTAGGAA
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:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:261283 original size:15 final size:15
Alignment explanation
Indices: 261258--261319 Score: 65
Period size: 15 Copynumber: 4.1 Consensus size: 15
261248 ATTAAAGTAT
261258 TAAATATATATAAATA
1 TAAA-ATATATAAATA
*
261274 TAAAATATATTAAT-
1 TAAAATATATAAATA
*
261288 TATAATTATAATAAA-A
1 TA-AAATAT-ATAAATA
261304 TAAAATATATAAATA
1 TAAAATATATAAATA
261319 T
1 T
261320 TATAAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
14 7 0.18
15 21 0.55
16 10 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAAATATATAAATA
Found at i:263682 original size:14 final size:14
Alignment explanation
Indices: 263663--263689 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
263653 TTGGAGCTAA
263663 ATTTAAAATTTAAG
1 ATTTAAAATTTAAG
263677 ATTTAAAATTTAA
1 ATTTAAAATTTAA
263690 TTCAAGTTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
ATTTAAAATTTAAG
Found at i:264250 original size:31 final size:33
Alignment explanation
Indices: 264215--264278 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
264205 CATTTTAATA
264215 AATATAAAAAAATAT-A-TAATATATATCATAT
1 AATATAAAAAAATATAATTAATATATATCATAT
***
264246 AATATATTTAAATATAATTAATATATATCATAT
1 AATATAAAAAAATATAATTAATATATATCATAT
264279 TCATATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 12 0.43
32 1 0.04
33 15 0.54
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (33 bp):
AATATAAAAAAATATAATTAATATATATCATAT
Found at i:268541 original size:22 final size:25
Alignment explanation
Indices: 268515--268567 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
268505 TATTTATGAA
268515 TATTA-GTT-AAAAATTATGT-ATT
1 TATTATGTTAAAAAATTATGTAATT
* *
268537 TATTATTTTAAAAAATTATTTAATT
1 TATTATGTTAAAAAATTATGTAATT
268562 TATTAT
1 TATTAT
268568 TTTTAATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 5 0.19
23 2 0.08
24 10 0.38
25 9 0.35
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (25 bp):
TATTATGTTAAAAAATTATGTAATT
Found at i:268579 original size:18 final size:18
Alignment explanation
Indices: 268558--268592 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
268548 AAAATTATTT
268558 AATTT-ATTATTTTTAATG
1 AATTTAATT-TTTTTAATG
268576 AATTTAATTTTTTTAAT
1 AATTTAATTTTTTTAAT
268593 ATAAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
AATTTAATTTTTTTAATG
Found at i:268585 original size:28 final size:25
Alignment explanation
Indices: 268523--268570 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
268513 AATATTAGTT
*
268523 AAAAATTATGT-ATTTATTATTTTA
1 AAAAATTATTTAATTTATTATTTTA
268547 AAAAATTATTTAATTTATTATTTT
1 AAAAATTATTTAATTTATTATTTT
268571 TAATGAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
AAAAATTATTTAATTTATTATTTTA
Found at i:268921 original size:17 final size:19
Alignment explanation
Indices: 268899--268936 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
268889 AATTTTAATA
268899 TAAAAAT-ATA-AATAGAT
1 TAAAAATGATATAATAGAT
*
268916 TAAAAATGATATAATATAT
1 TAAAAATGATATAATAGAT
268935 TA
1 TA
268937 TTATTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (19 bp):
TAAAAATGATATAATAGAT
Found at i:268964 original size:8 final size:8
Alignment explanation
Indices: 268951--269006 Score: 58
Period size: 8 Copynumber: 6.6 Consensus size: 8
268941 TATTAAAATT
268951 TATATAAA
1 TATATAAA
268959 TATATAATA
1 TATATAA-A
* *
268968 TTTATATA
1 TATATAAA
*
268976 TATAAAAA
1 TATATAAA
268984 TATATAAA
1 TATATAAA
268992 TAAATATAAA
1 T--ATATAAA
269002 TATAT
1 TATAT
269007 TAATTGTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
8 25 0.64
9 6 0.15
10 8 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TATATAAA
Found at i:269689 original size:2 final size:2
Alignment explanation
Indices: 269682--269734 Score: 72
Period size: 2 Copynumber: 26.5 Consensus size: 2
269672 CAATGACACT
* *
269682 TA TA TA TA TA TA TA TA TA TA TGA AA TA AA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
269724 TA TA TA TA TA T
1 TA TA TA TA TA T
269735 CAATGGATTG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 43 0.96
3 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:269988 original size:34 final size:33
Alignment explanation
Indices: 269905--269988 Score: 86
Period size: 34 Copynumber: 2.5 Consensus size: 33
269895 ATATAAAAAA
269905 TTATATAT-TTTATAAATTTTAATATATTAATAAT
1 TTATATATATTT-T-AATTTTAATATATTAATAAT
*
269939 TT-TATTTATTTTAATTTTAAT-T-TTAATTTATAT
1 TTATATATATTTTAATTTTAATATATTAA--TA-AT
269972 TTATATATATTTTAATT
1 TTATATATATTTTAATT
269989 ATTTTTATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
30 4 0.09
31 1 0.02
32 11 0.26
33 9 0.21
34 18 0.42
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (33 bp):
TTATATATATTTTAATTTTAATATATTAATAAT
Found at i:270003 original size:21 final size:22
Alignment explanation
Indices: 269929--270001 Score: 71
Period size: 21 Copynumber: 3.4 Consensus size: 22
269919 AATTTTAATA
*
269929 TATTAATAATTTTATTTATTTT
1 TATTAATAATTTTAATTATTTT
* * *
269951 AATT-TTAATTTTAATTTATATT
1 TATTAATAATTTTAA-TTATTTT
269973 TA-T-ATATATTTTAATTATTTT
1 TATTAATA-ATTTTAATTATTTT
269994 TATTAATA
1 TATTAATA
270002 TTATATATTG
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
21 19 0.47
22 18 0.45
23 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTAATAATTTTAATTATTTT
Found at i:270133 original size:3 final size:3
Alignment explanation
Indices: 270125--270150 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
270115 CTATTTGCTT
270125 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
270151 GATTTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.