Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold29
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: 5511024
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 57772 characters in sequence are not A, C, G, or T
File 2 of 34
Found at i:194954 original size:40 final size:39
Alignment explanation
Indices: 194887--194964 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
194877 TCATACCCTG
* *
194887 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
194927 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
194965 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:199198 original size:14 final size:14
Alignment explanation
Indices: 199174--199209 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
199164 TTTCTTTGTG
199174 CTTTTTC-TTTTTT
1 CTTTTTCATTTTTT
199187 CTTTTTCATTTTTT
1 CTTTTTCATTTTTT
*
199201 GTTTTTCAT
1 CTTTTTCAT
199210 AGAAGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.06, C:0.14, G:0.03, T:0.78
Consensus pattern (14 bp):
CTTTTTCATTTTTT
Found at i:236623 original size:33 final size:33
Alignment explanation
Indices: 236585--236651 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
236575 GTTACAAGCT
*
236585 ATGTATCGATACATT-TCTTCATGTATCGATACA
1 ATGTATCGATACATTGT-ATCATGTATCGATACA
*
236618 ATGTATTGATACATTGTATCATGTATCGATACA
1 ATGTATCGATACATTGTATCATGTATCGATACA
236651 A
1 A
236652 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (33 bp):
ATGTATCGATACATTGTATCATGTATCGATACA
Found at i:236725 original size:19 final size:20
Alignment explanation
Indices: 236680--236728 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
236670 CTGCCAGTTT
**
236680 CATGTATCGATACAATTTGGC
1 CATGTATCGATACAA-TTGAA
236701 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
236720 CATGTATCG
1 CATGTATCG
236729 CTATAATGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 11 0.42
21 15 0.58
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:242516 original size:4 final size:4
Alignment explanation
Indices: 242507--242536 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
242497 ACAATTGAAC
242507 AATT AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AATT AA
242537 AGTAGGGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
AATT
Found at i:247632 original size:78 final size:77
Alignment explanation
Indices: 247549--247791 Score: 199
Period size: 78 Copynumber: 3.1 Consensus size: 77
247539 TTTTATAAAA
247549 TAATATTTTAATTGTAGAAATATTAATAAAATAATAAATTGTAACATTATCAATATTTTAAATTT
1 TAATATTTTAATTGTA-AAATATTAATAAAATAATAAATTGTAACATTATCAATATTTTAAATTT
247614 TAAATAGTATTTT
65 TAAATAGTATTTT
* * * * * * **** * *
247627 TAATATTTT-GTTAATAAATGTTTTTATATAAATTAGGCTTTATAA-ATATAT-AATA--ATAAA
1 TAATATTTTAATT-GTAAA-ATATTAATA-AAATAATAAATTGTAACAT-TATCAATATTTTAAA
* ** * **
247687 TTTTTATTATAAAAATAA
62 -TTTTA-AATAGTATTTT
*
247705 TAATATTTTAATAGTATAAATATTAATAAAATAATAAATTGTAACATTATCAATATTTTAAATTT
1 TAATATTTTAATTGTA-AAATATTAATAAAATAATAAATTGTAACATTATCAATATTTTAAATTT
*
247770 TAGATAGTATTTT
65 TAAATAGTATTTT
247783 TAATATTTT
1 TAATATTTT
247792 GTTAATAAAT
Statistics
Matches: 116, Mismatches: 37, Indels: 24
0.66 0.21 0.14
Matches are distributed among these distances:
76 4 0.03
77 22 0.19
78 65 0.56
79 21 0.18
80 4 0.03
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (77 bp):
TAATATTTTAATTGTAAAATATTAATAAAATAATAAATTGTAACATTATCAATATTTTAAATTTT
AAATAGTATTTT
Found at i:247673 original size:149 final size:154
Alignment explanation
Indices: 247500--247811 Score: 508
Period size: 156 Copynumber: 2.0 Consensus size: 154
247490 TAATAATAAA
* * *
247500 TTTATATAAATTATGCTTTATAAATATTTAA-AA-ATATTTTT-TTAT-AA-AATAATATTTTAA
1 TTTATATAAATTAGGCTTTATAAATATATAATAATAAATTTTTATTATAAATAATAATATTTTAA
*
247560 TTGTAGAAATATTAATAAAATAATAAATTGTAACATTATCAATATTTTAAATTTTAAATAGTATT
66 TAGTAGAAATATTAATAAAATAATAAATTGTAACATTATCAATATTTTAAATTTTAAATAGTATT
*
247625 TTTAATATTTTGTTAATAAATGTT
131 TTTAATATTTTGTTAATAAATGTC
247649 TTTATATAAATTAGGCTTTATAAATATATAATAATAAATTTTTATTATAAAAATAATAATATTTT
1 TTTATATAAATTAGGCTTTATAAATATATAATAATAAATTTTTATTAT--AAATAATAATATTTT
* *
247714 AATAGTATAAATATTAATAAAATAATAAATTGTAACATTATCAATATTTTAAATTTTAGATAGTA
64 AATAGTAGAAATATTAATAAAATAATAAATTGTAACATTATCAATATTTTAAATTTTAAATAGTA
247779 TTTTTAATATTTTGTTAATAAATGTC
129 TTTTTAATATTTTGTTAATAAATGTC
247805 TTTATAT
1 TTTATAT
247812 GACTATGTTA
Statistics
Matches: 149, Mismatches: 7, Indels: 7
0.91 0.04 0.04
Matches are distributed among these distances:
149 29 0.19
150 2 0.01
151 7 0.05
152 4 0.03
155 2 0.01
156 105 0.70
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (154 bp):
TTTATATAAATTAGGCTTTATAAATATATAATAATAAATTTTTATTATAAATAATAATATTTTAA
TAGTAGAAATATTAATAAAATAATAAATTGTAACATTATCAATATTTTAAATTTTAAATAGTATT
TTTAATATTTTGTTAATAAATGTC
Found at i:247722 original size:25 final size:23
Alignment explanation
Indices: 247676--247734 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 23
247666 TTATAAATAT
*
247676 ATAATAATAAATTTTTATTATAA
1 ATAATAATAAATTTTTAGTATAA
247699 A-AATAATAATATTTTAATAGTATAA
1 ATAATAATAA-ATTTT--TAGTATAA
*
247724 ATATTAATAAA
1 ATAATAATAAA
247735 ATAATAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 8 0.27
23 6 0.20
25 9 0.30
26 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
ATAATAATAAATTTTTAGTATAA
Found at i:247725 original size:23 final size:23
Alignment explanation
Indices: 247671--247732 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
247661 AGGCTTTATA
247671 AATATAT-AATAATAA-ATTTTT
1 AATATATAAATAATAATATTTTT
* *
247692 ATTATAAAAATAATAATA-TTTT
1 AATATATAAATAATAATATTTTT
*
247714 AATAGTATAAATATTAATA
1 AATA-TATAAATAATAATA
247733 AAATAATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
21 5 0.15
22 15 0.45
23 13 0.39
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
AATATATAAATAATAATATTTTT
Found at i:248851 original size:27 final size:26
Alignment explanation
Indices: 248819--248908 Score: 110
Period size: 28 Copynumber: 3.4 Consensus size: 26
248809 CACCCATTTG
248819 TTTGTCAAAAATGGTGGTTATTTTGTA
1 TTTGTCAAAAATGGTGGTT-TTTTGTA
248846 TTTGTCAAAAATGGTGGTTTCCTTTGTA
1 TTTGTCAAAAATGGTGGTTT--TTTGTA
* * * *
248874 TTTGTCAAATATGGAGGCTTGTT-TA
1 TTTGTCAAAAATGGTGGTTTTTTGTA
248899 TTTGTCAAAA
1 TTTGTCAAAA
248909 TTTATGGCTA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
25 11 0.20
26 3 0.05
27 19 0.34
28 23 0.41
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.46
Consensus pattern (26 bp):
TTTGTCAAAAATGGTGGTTTTTTGTA
Found at i:253446 original size:28 final size:27
Alignment explanation
Indices: 253393--253456 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 27
253383 CACCCATTTG
253393 TTTGTCAAAAATGGTGATTATTTTGTA
1 TTTGTCAAAAATGGTGATTATTTTGTA
*
253420 TTTGTCAAAAATGGTGGTT-TCCTTTGTA
1 TTTGTCAAAAATGGTGATTAT--TTTGTA
253448 TTTGTCAAA
1 TTTGTCAAA
253457 TATGAAGGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 1 0.03
27 18 0.53
28 15 0.44
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.47
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGATTATTTTGTA
Found at i:254098 original size:18 final size:19
Alignment explanation
Indices: 254075--254115 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
254065 TGATCCAATT
254075 TATTTTTTAATTATATA-A
1 TATTTTTTAATTATATATA
*
254093 TATTTTTTATTTATATATA
1 TATTTTTTAATTATATATA
254112 TATT
1 TATT
254116 ATGTGATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TATTTTTTAATTATATATA
Found at i:254283 original size:25 final size:24
Alignment explanation
Indices: 254236--254283 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
254226 AATAAAAATT
** *
254236 AAATTAAAAAAATATTTTGTAAAA
1 AAATTAAAAAAATATAATATAAAA
254260 AAATTAAAACAAATATAATATAAA
1 AAATTAAAA-AAATATAATATAAA
254284 TAGATTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (24 bp):
AAATTAAAAAAATATAATATAAAA
Found at i:254527 original size:3 final size:3
Alignment explanation
Indices: 254519--254559 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
254509 GTGTCTGTGC
254519 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
254560 TATACAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:254694 original size:26 final size:26
Alignment explanation
Indices: 254665--254718 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
254655 GGACATTTCA
254665 ACATTTTAATTTCTAATTTGTACTGC
1 ACATTTTAATTTCTAATTTGTACTGC
254691 ACATTTTAATTTCTAATTTGTACTGC
1 ACATTTTAATTTCTAATTTGTACTGC
254717 AC
1 AC
254719 GACCATAGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (26 bp):
ACATTTTAATTTCTAATTTGTACTGC
Found at i:255154 original size:31 final size:32
Alignment explanation
Indices: 255116--255179 Score: 112
Period size: 31 Copynumber: 2.0 Consensus size: 32
255106 TATTATATAT
255116 TTTATATAAATTTTAATATATTAATA-ATTTA
1 TTTATATAAATTTTAATATATTAATATATTTA
*
255147 TTTATATAAATTTTAATATATTTATATATTTA
1 TTTATATAAATTTTAATATATTAATATATTTA
255179 T
1 T
255180 ATTTTTATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
TTTATATAAATTTTAATATATTAATATATTTA
Found at i:255166 original size:14 final size:14
Alignment explanation
Indices: 255118--255167 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
255108 TTATATATTT
255118 TATATAAATTTTAA
1 TATATAAATTTTAA
* *
255132 TATATTAATAATTTATT
1 TATA-TAA-ATTTTA-A
255149 TATATAAATTTTAA
1 TATATAAATTTTAA
255163 TATAT
1 TATAT
255168 TTATATATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 9 0.31
15 8 0.28
16 8 0.28
17 4 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:255186 original size:8 final size:8
Alignment explanation
Indices: 255076--255187 Score: 59
Period size: 8 Copynumber: 13.1 Consensus size: 8
255066 GTATTAGCAT
255076 TATATTTA
1 TATATTTA
255084 TATTATTTAA
1 TA-TATTT-A
255094 TTATATTTA
1 -TATATTTA
*
255103 GAGTA-TTA
1 TA-TATTTA
255111 TATATTTTA
1 TATA-TTTA
255120 TATAAATTTTAA
1 TAT--A-TTT-A
*
255132 TATATTAA
1 TATATTTA
255140 TA-ATTTA
1 TATATTTA
* *
255147 TTTATATA
1 TATATTTA
*
255155 AAT-TTTAA
1 TATATTT-A
255163 TATATTTA
1 TATATTTA
255171 TATATTTA
1 TATATTTA
*
255179 TATTTTTA
1 TATATTTA
255187 T
1 T
255188 TCATGTTGTA
Statistics
Matches: 81, Mismatches: 11, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
7 9 0.11
8 35 0.43
9 19 0.23
10 7 0.09
11 7 0.09
12 4 0.05
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (8 bp):
TATATTTA
Found at i:255219 original size:13 final size:13
Alignment explanation
Indices: 255075--255223 Score: 51
Period size: 13 Copynumber: 10.8 Consensus size: 13
255065 AGTATTAGCA
255075 TTATATTTATATTAT
1 TTATA-TTATATT-T
255090 TTA-ATTATATTT
1 TTATATTATATTT
**
255102 AGAGTATTATATATT
1 TTA-TATTATAT-TT
*
255117 TTATA-TAAATTT
1 TTATATTATATTT
255129 TAATATATTAATAATTT
1 T--TATATT-AT-ATTT
*
255146 ATT-TA-TATAAATT
1 -TTATATTAT-ATTT
255159 TTA-A-TATATTT
1 TTATATTATATTT
*
255170 ATATATTTATATTT
1 TTATA-TTATATTT
*
255184 TTATTCATGT-TGTATT
1 TTA-T-AT-TATAT-TT
255200 TTATATTATATTT
1 TTATATTATATTT
*
255213 TTTTATTATAT
1 TTATATTATAT
255224 AATTATATTG
Statistics
Matches: 103, Mismatches: 13, Indels: 38
0.67 0.08 0.25
Matches are distributed among these distances:
11 5 0.05
12 12 0.12
13 30 0.29
14 28 0.27
15 14 0.14
16 9 0.09
17 4 0.04
18 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.61
Consensus pattern (13 bp):
TTATATTATATTT
Found at i:257756 original size:23 final size:23
Alignment explanation
Indices: 257726--257770 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
257716 ATATTAATAA
*
257726 TAAAAATAT-TTATAATAATAATT
1 TAAAAATATAATA-AATAATAATT
257749 TAAAAATATAATAAATAATAAT
1 TAAAAATATAATAAATAATAAT
257771 GACTATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAAAATATAATAAATAATAATT
Found at i:258396 original size:21 final size:22
Alignment explanation
Indices: 258356--258402 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
258346 ATTTTAAAAG
258356 ATTTGAATTATTTATGATGATAA
1 ATTTGAATTATTTATGATGA-AA
258379 ATTTGAA-TATTT-TGATGAAA
1 ATTTGAATTATTTATGATGAAA
258399 ATTT
1 ATTT
258403 CAAACTCACC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 6 0.25
21 6 0.25
22 5 0.21
23 7 0.29
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (22 bp):
ATTTGAATTATTTATGATGAAA
Found at i:259884 original size:15 final size:16
Alignment explanation
Indices: 259864--259894 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
259854 TTTTATATTA
259864 ATAATTGT-TTGTAAT
1 ATAATTGTGTTGTAAT
259879 ATAATTGTGTTGTAAT
1 ATAATTGTGTTGTAAT
259895 TATTAACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (16 bp):
ATAATTGTGTTGTAAT
Found at i:261351 original size:16 final size:16
Alignment explanation
Indices: 261330--261361 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
261320 TTTCAAGTTT
*
261330 GAGTTATTTTGGGTTC
1 GAGTTATTTCGGGTTC
261346 GAGTTATTTCGGGTTC
1 GAGTTATTTCGGGTTC
261362 AGATCATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.09, G:0.31, T:0.47
Consensus pattern (16 bp):
GAGTTATTTCGGGTTC
Found at i:261387 original size:16 final size:16
Alignment explanation
Indices: 261351--261381 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
261341 GGTTCGAGTT
261351 ATTTCGGGTTCAGATC
1 ATTTCGGGTTCAGATC
*
261367 ATTTCTGGTTCAGAT
1 ATTTCGGGTTCAGAT
261382 TGTTTCGAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (16 bp):
ATTTCGGGTTCAGATC
Found at i:262466 original size:10 final size:11
Alignment explanation
Indices: 262434--262458 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
262424 TGAAAAATTA
262434 AATAATTATTT
1 AATAATTATTT
262445 AATAATTATTT
1 AATAATTATTT
262456 AAT
1 AAT
262459 GATATTTACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AATAATTATTT
Found at i:264967 original size:33 final size:32
Alignment explanation
Indices: 264923--264987 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
264913 ACACACCCAG
264923 ATGTATCGATACATATTGC-TTAGTATCGATACA
1 ATGTATCGATACATATT-CATTA-TATCGATACA
* *
264956 ATGTATTGATACATGTTCATTATATCGATACA
1 ATGTATCGATACATATTCATTATATCGATACA
264988 TCATGAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 11 0.38
33 18 0.62
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (32 bp):
ATGTATCGATACATATTCATTATATCGATACA
Found at i:267234 original size:21 final size:21
Alignment explanation
Indices: 267210--267267 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
267200 TAATATTCTT
* *
267210 GAAAAGAAATTAAGTGAATTA
1 GAAAAGAAAATAAATGAATTA
267231 GAAAAGAAAATAAATGAATTA
1 GAAAAGAAAATAAATGAATTA
**
267252 GAGGAGAAAA-AAATGA
1 GAAAAGAAAATAAATGA
267268 GTTGCAAGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
20 6 0.18
21 27 0.82
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (21 bp):
GAAAAGAAAATAAATGAATTA
Found at i:270519 original size:33 final size:32
Alignment explanation
Indices: 270477--270541 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
270467 ACACACCCAG
270477 ATGTATCGATACATATTGC-TTAGTATCGATACA
1 ATGTATCGATACATATT-CATTA-TATCGATACA
*
270510 ATGTATCGATACATGTTCATTATATCGATACA
1 ATGTATCGATACATATTCATTATATCGATACA
270542 TTATGAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 11 0.37
33 19 0.63
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (32 bp):
ATGTATCGATACATATTCATTATATCGATACA
Found at i:271151 original size:36 final size:33
Alignment explanation
Indices: 271106--271198 Score: 109
Period size: 36 Copynumber: 2.8 Consensus size: 33
271096 CTAAGTGATT
271106 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGGGA
1 GAGAGGTTCTATCTTAGCC-TTGAAAAAGATA--GA
*
271142 GAGAGGTTCTATCTTAGCCCGTG-AAAAGATAGA
1 GAGAGGTTCTATCTTAG-CCTTGAAAAAGATAGA
* *
271175 GAG-GTTTCTATCTTAACCTTGAAA
1 GAGAGGTTCTATCTTAGCCTTGAAA
271199 GATAGTGTAG
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
31 4 0.08
32 13 0.25
33 5 0.10
35 8 0.16
36 19 0.37
37 2 0.04
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (33 bp):
GAGAGGTTCTATCTTAGCCTTGAAAAAGATAGA
Found at i:284776 original size:16 final size:17
Alignment explanation
Indices: 284746--284790 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
284736 TTATGCCTAC
*
284746 AAATAAAAAATAATAAA-
1 AAATCAAAAA-AATAAAG
284763 AAATCAAAAAAATAAAG
1 AAATCAAAAAAATAAAG
284780 AAA-CAAAAAAA
1 AAATCAAAAAAA
284791 ATCGAATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.82, C:0.04, G:0.02, T:0.11
Consensus pattern (17 bp):
AAATCAAAAAAATAAAG
Found at i:285510 original size:76 final size:76
Alignment explanation
Indices: 285397--285602 Score: 252
Period size: 76 Copynumber: 2.7 Consensus size: 76
285387 GAATTTTAGA
** * * * * * ** *
285397 AACCACATATTCCTTATCATGTTCTTTTACTTTAGCTTATTACCAATTTGTTTTGGTTGTTGATG
1 AACCACATATTCCCCATCATGATCTTCTACTTTAGCTTGTTATCAATTTGTTTCGACTGTTAATG
*
285462 GAAAATTGCA-
66 GAAAATTACAG
* *
285472 TACTCATATATTCCCCATCATGATCTTCTACTTTAGCTTGTTATCAATTTGTTTCGACTGTTAAT
1 AAC-CACATATTCCCCATCATGATCTTCTACTTTAGCTTGTTATCAATTTGTTTCGACTGTTAAT
*
285537 GGAAAATTATAG
65 GGAAAATTACAG
* *
285549 AACCACATATTCCCCATCAGGATCTTCTACTTTAGCTTGTTATCAGTTTGTTTC
1 AACCACATATTCCCCATCATGATCTTCTACTTTAGCTTGTTATCAATTTGTTTC
285603 CGCCATTAAT
Statistics
Matches: 111, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
75 2 0.02
76 107 0.96
77 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.43
Consensus pattern (76 bp):
AACCACATATTCCCCATCATGATCTTCTACTTTAGCTTGTTATCAATTTGTTTCGACTGTTAATG
GAAAATTACAG
Found at i:285638 original size:76 final size:76
Alignment explanation
Indices: 285476--285639 Score: 215
Period size: 76 Copynumber: 2.2 Consensus size: 76
285466 ATTGCATACT
* **
285476 CATATATTCCCCATCATGATCTTCTACTTTAGCTTGTTATCAATTTGTTTCGACTGTTAATGGAA
1 CATATATTCCCCATCAGGATCTTCTACTTTAGCTTGTTATCAATTTGTTTCGACCATTAATGGAA
* *
285541 AATTATAGAAC
66 AATGATAAAAC
* *
285552 CACATATTCCCCATCAGGATCTTCTACTTTAGCTTGTTATCAGTTTGTTTCCG-CCATTAATGGA
1 CATATATTCCCCATCAGGATCTTCTACTTTAGCTTGTTATCAATTTGTTT-CGACCATTAATGGA
*
285616 AAGTGA-AAAAC
65 AAATGATAAAAC
* *
285627 TATATATTTCCCA
1 CATATATTCCCCA
285640 ATCAAGTTCT
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
75 14 0.18
76 60 0.79
77 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (76 bp):
CATATATTCCCCATCAGGATCTTCTACTTTAGCTTGTTATCAATTTGTTTCGACCATTAATGGAA
AATGATAAAAC
Found at i:286196 original size:41 final size:40
Alignment explanation
Indices: 286151--286245 Score: 102
Period size: 41 Copynumber: 2.4 Consensus size: 40
286141 CAATTAGCCC
* * * *
286151 TTTTTCATCTATTGACTTTTCGATTTTGTCTTAATCATCAT
1 TTTTTCATCTATTAACTTGTCAATTTCGTCTTAATCATC-T
* * *
286192 TTTTTTATTTATTAACTTGTCAATTTCGTCTTGATCATCT
1 TTTTTCATCTATTAACTTGTCAATTTCGTCTTAATCATCT
*
286232 TCTTTCATCT-TTAA
1 TTTTTCATCTATTAA
286246 TTTATCGTTT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
39 4 0.09
40 8 0.18
41 32 0.73
ACGTcount: A:0.20, C:0.17, G:0.06, T:0.57
Consensus pattern (40 bp):
TTTTTCATCTATTAACTTGTCAATTTCGTCTTAATCATCT
Found at i:287542 original size:33 final size:33
Alignment explanation
Indices: 287500--287565 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
287490 TTTGGGATAA
* **
287500 TGTATCGATACAATTTGTTATGTATCAATACAT
1 TGTATCGATACAATGTGCCATGTATCAATACAT
*
287533 TGTATCGATACAATGTGCCATGTATCGATACAT
1 TGTATCGATACAATGTGCCATGTATCAATACAT
287566 ATAGTGGTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (33 bp):
TGTATCGATACAATGTGCCATGTATCAATACAT
Found at i:287628 original size:20 final size:20
Alignment explanation
Indices: 287603--287648 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
287593 TCATTTATTA
**
287603 ATACAATTGTGCATGTATCG
1 ATACAATTGAACATGTATCG
287623 ATACAA-TGAACATGTATCG
1 ATACAATTGAACATGTATCG
*
287642 AAACAAT
1 ATACAAT
287649 GTATCTATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
ATACAATTGAACATGTATCG
Found at i:289903 original size:19 final size:18
Alignment explanation
Indices: 289858--289915 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 18
289848 ACTACCAGTT
289858 TCATGTATCGATACAATTG
1 TCATGTATCGATACAA-TG
289877 TCCATGTATCGATACAATG
1 T-CATGTATCGATACAATG
289896 ATCATGTATCGATACAATG
1 -TCATGTATCGATACAATG
289915 T
1 T
289916 ATCGATACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.03
19 20 0.54
20 16 0.43
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (18 bp):
TCATGTATCGATACAATG
Found at i:289917 original size:13 final size:13
Alignment explanation
Indices: 289899--289925 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
289889 TACAATGATC
289899 ATGTATCGATACA
1 ATGTATCGATACA
289912 ATGTATCGATACA
1 ATGTATCGATACA
289925 A
1 A
289926 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:289941 original size:33 final size:32
Alignment explanation
Indices: 289880--289944 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
289870 ACAATTGTCC
* *
289880 ATGTATCGATACAATGATCATGTATCGATACA
1 ATGTATCGATACAAAGATAATGTATCGATACA
289912 ATGTATCGATACAAAGCATAATGTATCGATACA
1 ATGTATCGATACAAAG-ATAATGTATCGATACA
289945 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (32 bp):
ATGTATCGATACAAAGATAATGTATCGATACA
Found at i:292473 original size:13 final size:13
Alignment explanation
Indices: 292455--292481 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
292445 ATAGTAACCC
292455 ATGTATCGATACA
1 ATGTATCGATACA
292468 ATGTATCGATACA
1 ATGTATCGATACA
292481 A
1 A
292482 GGAATGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:297303 original size:41 final size:40
Alignment explanation
Indices: 297238--297373 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 40
297228 CTCCTAAAAC
* * *
297238 GATCAACCCTTCATTTTTAGTTGACTTGTTAATTTTGTCCT
1 GATCAACCATTCATCTTTA-TTGACTTGTTAGTTTTGTCCT
297279 GATCAACCATTCACTCTTTATTGACTTGTTAGTTTTGTCCT
1 GATCAACCATTCA-TCTTTATTGACTTGTTAGTTTTGTCCT
* * * * * *
297320 GGTCAACCTCTTTTAT-TCTATTAACTTGTTAGTTTTGTCCC
1 GATCAA-C-CATTCATCTTTATTGACTTGTTAGTTTTGTCCT
*
297361 AATCAACCATTCA
1 GATCAACCATTCA
297374 CTCATAGTTG
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
39 4 0.05
40 1 0.01
41 63 0.80
42 7 0.09
43 4 0.05
ACGTcount: A:0.21, C:0.22, G:0.11, T:0.46
Consensus pattern (40 bp):
GATCAACCATTCATCTTTATTGACTTGTTAGTTTTGTCCT
Found at i:301168 original size:13 final size:13
Alignment explanation
Indices: 301150--301175 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
301140 ACATTTTGTG
301150 ATGTATCGATACA
1 ATGTATCGATACA
301163 ATGTATCGATACA
1 ATGTATCGATACA
301176 TTGGCTTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:301243 original size:20 final size:20
Alignment explanation
Indices: 301218--301270 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
301208 TTAAATGCAT
**
301218 GTATCGATACATTTTTTCAA
1 GTATCGATACATTTAGTCAA
*
301238 GTATCGATACATTTAGTCAT
1 GTATCGATACATTTAGTCAA
301258 GTATCGATACATT
1 GTATCGATACATT
301271 GTATCGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (20 bp):
GTATCGATACATTTAGTCAA
Found at i:301866 original size:22 final size:22
Alignment explanation
Indices: 301836--301880 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
301826 TTTTCTTTTC
*
301836 TCTCTCCCTTAATCAAAA-AATT
1 TCTCCCCCTTAAT-AAAATAATT
301858 TCTCCCCCTTAATAAAATAATT
1 TCTCCCCCTTAATAAAATAATT
301880 T
1 T
301881 AACAATTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.38
Consensus pattern (22 bp):
TCTCCCCCTTAATAAAATAATT
Found at i:301927 original size:25 final size:25
Alignment explanation
Indices: 301899--301971 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
301889 CGCACATTAA
301899 AAAATTCTTTCTCCCCCTTAATCAT
1 AAAATTCTTTCTCCCCCTTAATCAT
* * *
301924 AAAA---TTTC-GCACATT-A--A-
1 AAAATTCTTTCTCCCCCTTAATCAT
301941 AAAATTCTTTCTCCCCCTTAATCAT
1 AAAATTCTTTCTCCCCCTTAATCAT
301966 AAAATT
1 AAAATT
301972 ATTTACACAA
Statistics
Matches: 34, Mismatches: 6, Indels: 16
0.61 0.11 0.29
Matches are distributed among these distances:
17 4 0.12
18 1 0.03
20 5 0.15
21 8 0.24
22 5 0.15
24 1 0.03
25 10 0.29
ACGTcount: A:0.36, C:0.26, G:0.01, T:0.37
Consensus pattern (25 bp):
AAAATTCTTTCTCCCCCTTAATCAT
Found at i:301930 original size:50 final size:48
Alignment explanation
Indices: 301856--301971 Score: 154
Period size: 42 Copynumber: 2.5 Consensus size: 48
301846 AATCAAAAAA
*
301856 TTTCTCCCCCTTAATAAAATAATTTAACAATTTCGCACATTAAAAAATTC
1 TTTCTCCCCCTTAATCAAA-AATTTAA-AATTTCGCACATTAAAAAATTC
301906 TTTCTCCCCCTTAATC----A--TAAAATTTCGCACATTAAAAAATTC
1 TTTCTCCCCCTTAATCAAAAATTTAAAATTTCGCACATTAAAAAATTC
301948 TTTCTCCCCCTTAATCATAAAATT
1 TTTCTCCCCCTTAATCA-AAAATT
301972 ATTTACACAA
Statistics
Matches: 58, Mismatches: 1, Indels: 15
0.78 0.01 0.20
Matches are distributed among these distances:
42 38 0.66
43 3 0.05
45 1 0.02
47 1 0.02
50 15 0.26
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (48 bp):
TTTCTCCCCCTTAATCAAAAATTTAAAATTTCGCACATTAAAAAATTC
Found at i:301931 original size:42 final size:42
Alignment explanation
Indices: 301884--301971 Score: 176
Period size: 42 Copynumber: 2.1 Consensus size: 42
301874 ATAATTTAAC
301884 AATTTCGCACATTAAAAAATTCTTTCTCCCCCTTAATCATAA
1 AATTTCGCACATTAAAAAATTCTTTCTCCCCCTTAATCATAA
301926 AATTTCGCACATTAAAAAATTCTTTCTCCCCCTTAATCATAA
1 AATTTCGCACATTAAAAAATTCTTTCTCCCCCTTAATCATAA
301968 AATT
1 AATT
301972 ATTTACACAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.36
Consensus pattern (42 bp):
AATTTCGCACATTAAAAAATTCTTTCTCCCCCTTAATCATAA
Found at i:303826 original size:13 final size:13
Alignment explanation
Indices: 303804--303841 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
303794 ATAAATCCCT
*
303804 TGTATCGATACAC
1 TGTATCGATACAA
*
303817 TGTCTCGATACAA
1 TGTATCGATACAA
303830 TGTATCGATACA
1 TGTATCGATACA
303842 GAGAATGCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:309998 original size:13 final size:13
Alignment explanation
Indices: 309980--310004 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
309970 GTTACAAGCA
309980 AATGTATCGATAT
1 AATGTATCGATAT
309993 AATGTATCGATA
1 AATGTATCGATA
310005 CATATTGTGT
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:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
AATGTATCGATAT
Found at i:310084 original size:20 final size:20
Alignment explanation
Indices: 310059--310111 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
310049 CCAATGACTT
**
310059 GTATCGATACATTTTTTCAA
1 GTATCGATACATTTAGTCAA
*
310079 GTATCGATACATTTAGTCAT
1 GTATCGATACATTTAGTCAA
*
310099 GTATCGTTACATT
1 GTATCGATACATT
310112 GTATCGATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (20 bp):
GTATCGATACATTTAGTCAA
Found at i:312732 original size:18 final size:18
Alignment explanation
Indices: 312709--312745 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
312699 TGTTAAATGC
*
312709 ATGCAATGAATGACATAT
1 ATGCAATGAATGAAATAT
*
312727 ATGCAATGTATGAAATAT
1 ATGCAATGAATGAAATAT
312745 A
1 A
312746 GATATCATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (18 bp):
ATGCAATGAATGAAATAT
Found at i:313671 original size:20 final size:20
Alignment explanation
Indices: 313629--313674 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
313619 ATTACAAGCA
* *
313629 ATGTATCGTTACAATTCATC
1 ATGTATCGATACAATTCACC
313649 ATGTATCGATACAATGT-ACC
1 ATGTATCGATACAAT-TCACC
313669 ATGTAT
1 ATGTAT
313675 TAATACAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:313755 original size:19 final size:19
Alignment explanation
Indices: 313711--313766 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
313701 TTACCAGTTT
**
313711 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
313731 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
313750 CATGTATCGATACAATG
1 CATGTATCGATACAATG
313767 TATCAATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:321510 original size:13 final size:13
Alignment explanation
Indices: 321492--321522 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
321482 ACAATTCATC
321492 ATGTATCAATACA
1 ATGTATCAATACA
*
321505 ATGTATCGATACA
1 ATGTATCAATACA
321518 ATGTA
1 ATGTA
321523 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:321510 original size:33 final size:33
Alignment explanation
Indices: 321470--321538 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
321460 CCGTTACAAG
*
321470 CAATGTATCGATACAAT-TCATCATGTATCAATA
1 CAATGTATCGATACAATGT-ACCATGTATCAATA
*
321503 CAATGTATCGATACAATGTACCATGTATCGATA
1 CAATGTATCGATACAATGTACCATGTATCAATA
321536 CAA
1 CAA
321539 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (33 bp):
CAATGTATCGATACAATGTACCATGTATCAATA
Found at i:321591 original size:19 final size:21
Alignment explanation
Indices: 321567--321619 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 21
321557 CTACCAGTTT
*
321567 CATGTATCGATACAATG-A-A
1 CATGTATCGATACAAAGCATA
321586 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAAAGCATA
321607 -ATGTATCGATACA
1 CATGTATCGATACA
321620 TCTGGGTGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 16 0.52
20 14 0.45
21 1 0.03
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (21 bp):
CATGTATCGATACAAAGCATA
Found at i:323728 original size:18 final size:18
Alignment explanation
Indices: 323705--323742 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
323695 TGAGCACAAT
323705 AAAAAGAACAAAAAAGAA
1 AAAAAGAACAAAAAAGAA
* *
323723 AAAAAGAAGAACAAAGAA
1 AAAAAGAACAAAAAAGAA
323741 AA
1 AA
323743 TGACTAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (18 bp):
AAAAAGAACAAAAAAGAA
Found at i:325153 original size:24 final size:24
Alignment explanation
Indices: 325125--325183 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
325115 TATTATGCCA
325125 AAAATCATATTATAAGAACAAAAT
1 AAAATCATATTATAAGAACAAAAT
* * *
325149 AAAATCATATCATAAGCACATAAT
1 AAAATCATATTATAAGAACAAAAT
*
325173 AAAATCTTATT
1 AAAATCATATT
325184 TGCATAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.29
Consensus pattern (24 bp):
AAAATCATATTATAAGAACAAAAT
Found at i:325377 original size:18 final size:18
Alignment explanation
Indices: 325354--325392 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
325344 TTACTTTCCA
325354 AAAATTAATATT-TTCAAG
1 AAAATTAA-ATTCTTCAAG
*
325372 AAAATTAAATTCTTTAAG
1 AAAATTAAATTCTTCAAG
325390 AAA
1 AAA
325393 CCTAAATGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (18 bp):
AAAATTAAATTCTTCAAG
Found at i:326140 original size:138 final size:139
Alignment explanation
Indices: 325915--326167 Score: 375
Period size: 138 Copynumber: 1.8 Consensus size: 139
325905 CACACCCATG
* *
325915 TTAAGTGCACAATCAATAAGAAATTAGTGCAAAAGATTTCCAATACTAAGTTATCTTCAAGTCAA
1 TTAAGTGCACAATCAATAAGAAATTAATGCAAAAAATTTCCAATACTAAGTTATCTTCAAGTCAA
* * * * *
325980 GGGCAAGATTTATATTCTTTAAAGTCTTATGAATCTAAATCAATTTTGAATTGTGGAACAATTCC
66 GGCCAACATTGATATTCTTTAAAGTCCTATGAATCCAAATCAATTTTGAATTGTGGAACAATTCC
326045 AAAGCCCTA
131 AAAGCCCTA
* * * *
326054 TTAAGTGCACAATCAAT-AGAAATTAATGCAAAAAATTTCCAACT-TTAGGTTATTTTTAAGTCA
1 TTAAGTGCACAATCAATAAGAAATTAATGCAAAAAATTTCCAA-TACTAAGTTATCTTCAAGTCA
*
326117 AGGCCAACATTGATTTTCTTTAAAGTCCTATGAATCCAAATCAATTTTGAA
65 AGGCCAACATTGATATTCTTTAAAGTCCTATGAATCCAAATCAATTTTGAA
326168 ACTTTAAGTG
Statistics
Matches: 101, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
138 83 0.82
139 18 0.18
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.34
Consensus pattern (139 bp):
TTAAGTGCACAATCAATAAGAAATTAATGCAAAAAATTTCCAATACTAAGTTATCTTCAAGTCAA
GGCCAACATTGATATTCTTTAAAGTCCTATGAATCCAAATCAATTTTGAATTGTGGAACAATTCC
AAAGCCCTA
Found at i:329379 original size:39 final size:39
Alignment explanation
Indices: 329336--329439 Score: 111
Period size: 39 Copynumber: 2.7 Consensus size: 39
329326 TAAGCACGTC
329336 AATTTTCATAAAATATAAGCTACTATAACTAAAAACCTT
1 AATTTTCATAAAATATAAGCTACTATAACTAAAAACCTT
** * **
329375 AA-TTTCTATAAAATATAAATTGCTATAACTAAGCACCTT
1 AATTTTC-ATAAAATATAAGCTACTATAACTAAAAACCTT
* * * *
329414 AATTTTTATAAGATACAAGCTCCTAT
1 AATTTTCATAAAATATAAGCTACTAT
329440 GGATTTTAGC
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
38 4 0.08
39 45 0.87
40 3 0.06
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (39 bp):
AATTTTCATAAAATATAAGCTACTATAACTAAAAACCTT
Found at i:332278 original size:3 final size:3
Alignment explanation
Indices: 332270--332300 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
332260 TCAACCATCA
332270 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
332301 AGAAGTTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:332771 original size:15 final size:16
Alignment explanation
Indices: 332731--332772 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
332721 TAATAAATCA
332731 AAAATTGTTGAAAATG
1 AAAATTGTTGAAAATG
*
332747 -AAATTCTTGAAAA-G
1 AAAATTGTTGAAAATG
*
332761 AAAATAGTTGAA
1 AAAATTGTTGAA
332773 CTAGAAAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 1 0.05
15 21 0.95
ACGTcount: A:0.52, C:0.02, G:0.17, T:0.29
Consensus pattern (16 bp):
AAAATTGTTGAAAATG
Found at i:333552 original size:90 final size:90
Alignment explanation
Indices: 333389--333574 Score: 239
Period size: 90 Copynumber: 2.1 Consensus size: 90
333379 AGAAGGCTCA
* * * * * * * *
333389 ACAC-AAATGCTTATAGAGGTTCGGTCCAAACATGGCACCTACGTCCTCTCTCCTTAACATTTTC
1 ACACGAAATGCTTAGAAAGGTTCGGTCAAAACACGACACCTACGTCCTCTCTCCTCAACACTTCC
* *
333453 TTCTTGAGTGCTATCAAAATTCACT
66 TTCTCGAGTGCTACCAAAATTCACT
* *
333478 ACACGAAATGCTTAGAAAGGTTGGGTCAAAACACGACACCTACGTCCTCTCTCCTCGACACTTCC
1 ACACGAAATGCTTAGAAAGGTTCGGTCAAAACACGACACCTACGTCCTCTCTCCTCAACACTTCC
* *
333543 TTGTCGAGTGTTACCAAAATTCACT
66 TTCTCGAGTGCTACCAAAATTCACT
333568 ACACGAA
1 ACACGAA
333575 TTGATTACCT
Statistics
Matches: 82, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
89 4 0.05
90 78 0.95
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (90 bp):
ACACGAAATGCTTAGAAAGGTTCGGTCAAAACACGACACCTACGTCCTCTCTCCTCAACACTTCC
TTCTCGAGTGCTACCAAAATTCACT
Found at i:334153 original size:33 final size:33
Alignment explanation
Indices: 334089--334154 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
334079 ATTGGATATG
* *
334089 ATGTATCGATACAATTCCTCATTTATTGATACA
1 ATGTATCGATACAATTCCTCATGTATCGATACA
*
334122 ATGTATCGATACATTGTCC-CATGTATCGATACA
1 ATGTATCGATACAAT-TCCTCATGTATCGATACA
334155 TTTCACTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (33 bp):
ATGTATCGATACAATTCCTCATGTATCGATACA
Found at i:339733 original size:16 final size:17
Alignment explanation
Indices: 339698--339736 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
339688 CTTTTATTTC
*
339698 TTTCTTGTTTTCTAACT
1 TTTCTTGTATTCTAACT
339715 TTTCTTGTATT-TAACT
1 TTTCTTGTATTCTAACT
339731 TTTCTT
1 TTTCTT
339737 AATGAACGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.13, C:0.15, G:0.05, T:0.67
Consensus pattern (17 bp):
TTTCTTGTATTCTAACT
Found at i:343731 original size:20 final size:19
Alignment explanation
Indices: 343688--343741 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
343678 ACATTATGCT
**
343688 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGGACA
*
343707 TTGTATTGATACATGGACAA
1 TTGTATCGATACATGGAC-A
343727 TTGTATCGATACATG
1 TTGTATCGATACATG
343742 AAACTAGCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.39
Consensus pattern (19 bp):
TTGTATCGATACATGGACA
Found at i:352414 original size:13 final size:13
Alignment explanation
Indices: 352396--352422 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
352386 ACATTATGCT
352396 TTGTATCGATACA
1 TTGTATCGATACA
352409 TTGTATCGATACA
1 TTGTATCGATACA
352422 T
1 T
352423 GGACAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:352497 original size:20 final size:20
Alignment explanation
Indices: 352472--352525 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
352462 CTACCACTGT
*
352472 TTGTATCGATACATGGT-ATA
1 TTGTATCGATACATGATGA-A
352492 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
352512 TTGTATCGATACAT
1 TTGTATCGATACAT
352526 TGCTTGTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:358535 original size:21 final size:21
Alignment explanation
Indices: 358502--358542 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
358492 CTAAGTAAAA
358502 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
358523 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
358543 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:358608 original size:21 final size:20
Alignment explanation
Indices: 358579--358635 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
358569 AAAACCCTGA
**
358579 AAAGTATCGATACACATTTT
1 AAAGTATCGATACACATTGC
*
358599 AAATGTATCGATACAGATTGC
1 AAA-GTATCGATACACATTGC
*
358620 ATAGTATCGATACACA
1 AAAGTATCGATACACA
358636 CAAATATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (20 bp):
AAAGTATCGATACACATTGC
Found at i:358721 original size:53 final size:53
Alignment explanation
Indices: 358623--358759 Score: 213
Period size: 53 Copynumber: 2.6 Consensus size: 53
358613 AGATTGCATA
*
358623 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
* * *
358677 GTATCGATACACACAATATGTATCGATATAGGTCACTGGTAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
358730 GTATCGATACACA-ACATATGTATCGATACA
1 GTATCGATACACACA-ATATGTATCGATACA
358760 TTGGTAGTAG
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 62 0.81
54 14 0.18
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
Found at i:358834 original size:21 final size:22
Alignment explanation
Indices: 358801--358856 Score: 96
Period size: 21 Copynumber: 2.6 Consensus size: 22
358791 CATCACTATT
*
358801 CATCAATGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
358823 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
358844 CATCACTGTTCAT
1 CATCACTGTTCAT
358857 AGGTCACTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:358945 original size:13 final size:13
Alignment explanation
Indices: 358927--358965 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
358917 TCACTATTCA
358927 TGTATCGATACAT
1 TGTATCGATACAT
*
358940 TGTATCGATACAG
1 TGTATCGATACAT
358953 TGTATCGATACAT
1 TGTATCGATACAT
358966 CATAAATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:361473 original size:18 final size:18
Alignment explanation
Indices: 361437--361474 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
361427 GAGATTTATG
*
361437 AATGCATGAAGCATGGAA
1 AATGCATGAAGCATAGAA
361455 AATGCATGGAA-CATAGAA
1 AATGCAT-GAAGCATAGAA
361473 AA
1 AA
361475 AAAGCATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.50, C:0.11, G:0.24, T:0.16
Consensus pattern (18 bp):
AATGCATGAAGCATAGAA
Found at i:362392 original size:52 final size:51
Alignment explanation
Indices: 362322--362460 Score: 174
Period size: 51 Copynumber: 2.7 Consensus size: 51
362312 ATTCGCCTAC
* * *
362322 ATGTATTGATACATTAAAGAATGTATCGATATATTT-GGTTCAAAAACCC-AGA
1 ATGTATCGATACAATAAAGAATGTATCGATACATTTAGGTT---AAACCCTAGA
* *
362374 ATGTTTCGATACAGTAAAGAATGTATCGATACATTTAGGTTAAACCCTAGA
1 ATGTATCGATACAATAAAGAATGTATCGATACATTTAGGTTAAACCCTAGA
* *
362425 ATGTATCGATACAATAAAAAATATATCGATACATTT
1 ATGTATCGATACAATAAAGAATGTATCGATACATTT
362461 CATTCCAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
50 6 0.08
51 35 0.45
52 32 0.42
53 4 0.05
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.32
Consensus pattern (51 bp):
ATGTATCGATACAATAAAGAATGTATCGATACATTTAGGTTAAACCCTAGA
Found at i:362567 original size:21 final size:20
Alignment explanation
Indices: 362515--362568 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
362505 CATTTCAAAC
362515 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
**
362535 ATGTATTAATACATTCACTT
1 ATGTATCGATACATTCACTT
362555 ATTGTATCGATACA
1 A-TGTATCGATACA
362569 AATTATTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:365233 original size:17 final size:18
Alignment explanation
Indices: 365211--365249 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
365201 AAGAAAATTT
365211 ATTTTAAT-AAA-CAACTA
1 ATTTTAATGAAATCAA-TA
365228 ATTTTAATGAAATCAATA
1 ATTTTAATGAAATCAATA
365246 ATTT
1 ATTT
365250 AAGATGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 9 0.45
19 3 0.15
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTTTAATGAAATCAATA
Found at i:365457 original size:21 final size:21
Alignment explanation
Indices: 365410--365467 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
365400 AAAAATTATC
*
365410 CAAATGTATCGATACATTTGT
1 CAAATGTATCGATACATTTGA
**
365431 GGAATGTATCGATACATTCT-A
1 CAAATGTATCGATACATT-TGA
365452 CAAATGTATCGATACA
1 CAAATGTATCGATACA
365468 GGGTCCCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (21 bp):
CAAATGTATCGATACATTTGA
Found at i:365527 original size:19 final size:19
Alignment explanation
Indices: 365503--365557 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
365493 AATTCAACAA
365503 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
365522 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
365541 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
365558 TTAGCTACTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:365615 original size:13 final size:13
Alignment explanation
Indices: 365597--365623 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
365587 CATTTTTCTG
365597 TGTATCGATACAT
1 TGTATCGATACAT
365610 TGTATCGATACAT
1 TGTATCGATACAT
365623 T
1 T
365624 TGAAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:368015 original size:51 final size:51
Alignment explanation
Indices: 367955--368071 Score: 147
Period size: 51 Copynumber: 2.4 Consensus size: 51
367945 AATTCTCCGC
367955 AATCGGGGATA-TCCCAACTCCGATTTCATTT-TCAAAACA-CTAATTTTCTAT
1 AATCGGGGATACT-CCAACTCCGATTTCATTTCT-AAAACATC-AATTTTCTAT
*
368006 AATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAA-TTT-T-T
1 AATCGGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTCTAT
*
368054 CATCGGGGATACTCCAAC
1 AATCGGGGATACTCCAAC
368072 CCCGTTAATC
Statistics
Matches: 61, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
48 18 0.30
49 1 0.02
50 3 0.05
51 36 0.59
52 3 0.05
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (51 bp):
AATCGGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTCTAT
Found at i:368125 original size:28 final size:27
Alignment explanation
Indices: 368053--368129 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 27
368043 CATCAATTTT
368053 TCATCGGGGATACTCCAACCCCGTTAA
1 TCATCGGGGATACTCCAACCCCGTTAA
*
368080 TCATCGGGGATACTCCAACCCTGTT-A
1 TCATCGGGGATACTCCAACCCCGTTAA
**
368106 TTTTCGAGGGGATACTCCAACCCC
1 TCATC--GGGGATACTCCAACCCC
368130 CGGCTTTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 4 0.09
27 24 0.55
28 16 0.36
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.25
Consensus pattern (27 bp):
TCATCGGGGATACTCCAACCCCGTTAA
Found at i:368336 original size:187 final size:183
Alignment explanation
Indices: 368010--368407 Score: 546
Period size: 187 Copynumber: 2.2 Consensus size: 183
368000 TTCTATAATC
* * * **
368010 GGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCC
1 GGGGATACTCCAACTCCGATTTTATTTCTAAAACACCAATTTTACAACGAAGATACTCCAACCCC
* * ** * *
368075 GTTAATCATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCCGGCTTTATT
66 GTTAATCATCAGGGATACTCCAACCCCGTTACCTCCGAGGAGATACTCCAACCCCCGGCTTTATT
* * * *
368140 TCTAAAATATTAATTTCTCATAATCGGGGATACTCTAACCCCGTTATCTCCGA
131 CCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGTTACCTCCGA
*
368193 GGGGACACTCCAACTCCGATTTTATTTCTAAAAACACCAAATTTTCACAACTGAAGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATTTCT-AAAACACC-AATTTT-ACAAC-GAAGATACTCCAA
* *
368258 CCTCGTTATTTCATCAGGGATACTCCAACCCCGTTACCTCCGAGGAGATACTCCAA-CCCCGGCT
62 CCCCGTTA-ATCATCAGGGATACTCCAACCCCGTTACCTCCGAGGAGATACTCCAACCCCCGGCT
* *
368322 TTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCGTTACCTCCGA
126 TTATTCCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGTTACCTCCGA
* *
368380 GGGGATACTCCAATTTCGATTTTATTTC
1 GGGGATACTCCAACTCCGATTTTATTTC
368408 CTAATCATCG
Statistics
Matches: 187, Mismatches: 23, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
183 28 0.15
184 7 0.04
185 6 0.03
186 3 0.02
187 103 0.55
188 40 0.21
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (183 bp):
GGGGATACTCCAACTCCGATTTTATTTCTAAAACACCAATTTTACAACGAAGATACTCCAACCCC
GTTAATCATCAGGGATACTCCAACCCCGTTACCTCCGAGGAGATACTCCAACCCCCGGCTTTATT
CCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGTTACCTCCGA
Found at i:368405 original size:79 final size:79
Alignment explanation
Indices: 368274--368446 Score: 213
Period size: 79 Copynumber: 2.2 Consensus size: 79
368264 TATTTCATCA
* *
368274 GGGATACTCCAACCCCGTTACCTCCGAGGAGATACTCCAACCCCGGCTTTATTCCCAAAAT-ATT
1 GGGATACTCCAACCCCGTTACCTCCGAGGAGATACTCCAACCCCGACTTTATTCCC-AAATCATC
* **
368338 GATTTCTCATAATTG
65 GATTTCTCACAACCG
* *** * * *
368353 GGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAATTTCGATTTTATTTCCTAATCATCG
1 GGGATACTCCAACCCCGTTACCTCCGAGGAGATACTCCAACCCCGACTTTATTCCCAAATCATCG
*
368418 ATTTTTCACAACCG
66 ATTTCTCACAACCG
368432 GGGATACTCCAACCC
1 GGGATACTCCAACCC
368447 TGTTGTTTTC
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
78 3 0.04
79 77 0.96
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.28
Consensus pattern (79 bp):
GGGATACTCCAACCCCGTTACCTCCGAGGAGATACTCCAACCCCGACTTTATTCCCAAATCATCG
ATTTCTCACAACCG
Found at i:370401 original size:20 final size:19
Alignment explanation
Indices: 370377--370429 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
370367 CACACCCAGA
370377 TGTATCGATACATATTGC-T
1 TGTATCGATACATATT-CAT
* *
370396 TGGTATCGACACATGTTCAT
1 T-GTATCGATACATATTCAT
370416 TGTATCGATACATA
1 TGTATCGATACATA
370430 CAAGAAACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATATTCAT
Found at i:370800 original size:34 final size:34
Alignment explanation
Indices: 370768--370833 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 34
370758 TACATTTCAA
370768 AAAGCT-TTTGTATT-CTTTGTTG-TTATTCTTTC
1 AAAGCTATTTGTATTCCTTTG-TGCTTATTCTTTC
370800 AAAGCTCATTTGTATTCCTTTGTGCTTATTCTTT
1 AAAGCT-ATTTGTATTCCTTTGTGCTTATTCTTT
370834 TCACAAACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
32 6 0.20
34 10 0.33
35 14 0.47
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.56
Consensus pattern (34 bp):
AAAGCTATTTGTATTCCTTTGTGCTTATTCTTTC
Found at i:377233 original size:32 final size:30
Alignment explanation
Indices: 377197--377255 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
377187 GAAATCAAAT
377197 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
377229 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
377256 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:377578 original size:32 final size:34
Alignment explanation
Indices: 377515--377581 Score: 111
Period size: 32 Copynumber: 2.0 Consensus size: 34
377505 TACAAGCCAA
*
377515 TGTATCGATACATATTTTATGTGTATTGATACAT
1 TGTATCGATACATATTTTATGTGTATCGATACAT
377549 TGTATCGATACATA-TTT-TGTGTATCGATACAT
1 TGTATCGATACATATTTTATGTGTATCGATACAT
377581 T
1 T
377582 TTGGACATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 15 0.47
33 3 0.09
34 14 0.44
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.46
Consensus pattern (34 bp):
TGTATCGATACATATTTTATGTGTATCGATACAT
Found at i:377582 original size:17 final size:18
Alignment explanation
Indices: 377549--377584 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
377539 ATTGATACAT
377549 TGTATCGATACATATTTTG
1 TGTATCGATACA-ATTTTG
377568 TGTATCGATAC-ATTTTG
1 TGTATCGATACAATTTTG
377585 GACATTTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
19 11 0.65
ACGTcount: A:0.25, C:0.11, G:0.17, T:0.47
Consensus pattern (18 bp):
TGTATCGATACAATTTTG
Found at i:381433 original size:21 final size:21
Alignment explanation
Indices: 381404--381448 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
381394 AAGTTTTTAT
*
381404 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
381424 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
381446 TTT
1 TTT
381449 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:383687 original size:13 final size:13
Alignment explanation
Indices: 383669--383694 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
383659 ATATTTTATG
383669 TGTATCGATACAT
1 TGTATCGATACAT
383682 TGTATCGATACAT
1 TGTATCGATACAT
383695 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:383706 original size:19 final size:19
Alignment explanation
Indices: 383648--383712 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
383638 TACAAGCCAA
383648 TGTATCGATACATATTTTATG
1 TGTATCGATACATA-TTT-TG
383669 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
383682 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
383701 TGTATCGATACA
1 TGTATCGATACA
383713 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:383708 original size:32 final size:34
Alignment explanation
Indices: 383648--383712 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 34
383638 TACAAGCCAA
383648 TGTATCGATACATATTTTATGTGTATCGATACAT
1 TGTATCGATACATATTTTATGTGTATCGATACAT
383682 TGTATCGATACATA-TTT-TGTGTATCGATACA
1 TGTATCGATACATATTTTATGTGTATCGATACA
383713 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 14 0.45
33 3 0.10
34 14 0.45
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.43
Consensus pattern (34 bp):
TGTATCGATACATATTTTATGTGTATCGATACAT
Found at i:388279 original size:15 final size:15
Alignment explanation
Indices: 388255--388286 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
388245 ACATGTTTGA
388255 TTCAAAATGAAACGT
1 TTCAAAATGAAACGT
*
388270 TTCAAGATGAAACGT
1 TTCAAAATGAAACGT
388285 TT
1 TT
388287 GTTAAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (15 bp):
TTCAAAATGAAACGT
Found at i:389497 original size:15 final size:15
Alignment explanation
Indices: 389474--389519 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
389464 TCGATCAATC
*
389474 AATTTAATTTATATA
1 AATTAAATTTATATA
389489 AATTAAA--T-TATA
1 AATTAAATTTATATA
*
389501 AATAAAATTTATATA
1 AATTAAATTTATATA
389516 AATT
1 AATT
389520 TTAATTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
12 10 0.40
13 1 0.04
14 1 0.04
15 13 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTAAATTTATATA
Found at i:389633 original size:20 final size:19
Alignment explanation
Indices: 389589--389640 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
389579 AATTTAATTA
389589 TAAAATAT-ATAAATA--T
1 TAAAATATAATAAATAGTT
*
389605 TAAAATATAATTAATAGTT
1 TAAAATATAATAAATAGTT
389624 TAATAATATAATAAATA
1 TAA-AATATAATAAATA
389641 ATAAAAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 8 0.27
17 6 0.20
19 4 0.13
20 12 0.40
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
TAAAATATAATAAATAGTT
Found at i:389963 original size:16 final size:16
Alignment explanation
Indices: 389944--389977 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
389934 ATGATTAGAC
* *
389944 CTTAAAATGATTTAAA
1 CTTAAAATAACTTAAA
389960 CTTAAAATAACTTAAA
1 CTTAAAATAACTTAAA
389976 CT
1 CT
389978 CGAGATTAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (16 bp):
CTTAAAATAACTTAAA
Found at i:391656 original size:9 final size:9
Alignment explanation
Indices: 391642--391674 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
391632 CTTTAAGTTG
391642 TTTTTTCTT
1 TTTTTTCTT
391651 TTTTTTCTT
1 TTTTTTCTT
391660 TTTTTTCTT
1 TTTTTTCTT
391669 TCTTTT
1 T-TTTT
391675 GTATTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:391681 original size:18 final size:18
Alignment explanation
Indices: 391642--391683 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
391632 CTTTAAGTTG
* *
391642 TTTTTTCTTTTTTTTCTT
1 TTTTTTCTTTCTTTTCTA
*
391660 TTTTTTCTTTCTTTTGTA
1 TTTTTTCTTTCTTTTCTA
391678 TTTTTT
1 TTTTTT
391684 AAGACAAGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.86
Consensus pattern (18 bp):
TTTTTTCTTTCTTTTCTA
Found at i:393146 original size:104 final size:104
Alignment explanation
Indices: 392966--393155 Score: 371
Period size: 104 Copynumber: 1.8 Consensus size: 104
392956 CCAACGATCA
392966 AAAATCTTAAATTTTCACAATTTGTATCGATATGAACAGTACATATATCGATACATTCTTTTTTT
1 AAAATCTTAAATTTTCACAATTTGTATCGATATGAACAGTACATATATCGATACATTCTTTTTTT
*
393031 ACCCAGATGTATCGATACATTGAAAGGTCCTAACAGTCG
66 ACCCAAATGTATCGATACATTGAAAGGTCCTAACAGTCG
393070 AAAATCTTAAATTTTCACAATTTGTATCGATATGAACAGTACATATATCGATACATTCTTTTTTT
1 AAAATCTTAAATTTTCACAATTTGTATCGATATGAACAGTACATATATCGATACATTCTTTTTTT
393135 ACCCAAATGTATCGATACATT
66 ACCCAAATGTATCGATACATT
393156 TTTCAATGTA
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 85 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (104 bp):
AAAATCTTAAATTTTCACAATTTGTATCGATATGAACAGTACATATATCGATACATTCTTTTTTT
ACCCAAATGTATCGATACATTGAAAGGTCCTAACAGTCG
Found at i:393151 original size:50 final size:50
Alignment explanation
Indices: 392988--393151 Score: 149
Period size: 50 Copynumber: 3.2 Consensus size: 50
392978 TTTCACAATT
*
392988 TGTATCGATATGAACAGTACATATATCGATACATTCTTTTTTTACCCAGA
1 TGTATCGATATGAACAGTACATATATCGATACATTCTTTTTTTACCCAAA
* * * * * *
393038 TGTATCGATACATTGAA-AGGT-CCTAACAGTCGA-A-AATCTTAAATTTT-CACAATT
1 TGTATCGAT--A-TGAACA-GTACAT-ATA-TCGATACATTCTT--TTTTTACCCAA-A
393092 TGTATCGATATGAACAGTACATATATCGATACATTCTTTTTTTACCCAAA
1 TGTATCGATATGAACAGTACATATATCGATACATTCTTTTTTTACCCAAA
393142 TGTATCGATA
1 TGTATCGATA
393152 CATTTTTCAA
Statistics
Matches: 87, Mismatches: 13, Indels: 28
0.68 0.10 0.22
Matches are distributed among these distances:
50 27 0.31
51 13 0.15
52 18 0.21
53 12 0.14
54 17 0.20
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (50 bp):
TGTATCGATATGAACAGTACATATATCGATACATTCTTTTTTTACCCAAA
Found at i:396646 original size:18 final size:18
Alignment explanation
Indices: 396623--396658 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
396613 ATTAAATATT
* *
396623 TAACAATTTGATTTTATA
1 TAACAAATTAATTTTATA
396641 TAACAAATTAATTTTATA
1 TAACAAATTAATTTTATA
396659 CCCTTTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (18 bp):
TAACAAATTAATTTTATA
Found at i:398653 original size:21 final size:20
Alignment explanation
Indices: 398616--398674 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
398606 CCTTTCCTCA
398616 TTTTCTTT-TTTCCTTTTTGTC
1 TTTTCTTTCTTT-CTTTTT-TC
*
398637 TTTTCTTTCTTTTTTTTTTC
1 TTTTCTTTCTTTCTTTTTTC
*
398657 TTTCCTTTACTTTCTTTT
1 TTTTCTTT-CTTTCTTTT
398675 CTTACCTTCC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 9 0.27
21 21 0.64
22 3 0.09
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTCTTTCTTTCTTTTTTC
Found at i:398664 original size:25 final size:25
Alignment explanation
Indices: 398594--398674 Score: 71
Period size: 25 Copynumber: 3.3 Consensus size: 25
398584 ATATATATTT
* **
398594 TTTC-TTTTTTTTCCTTTCCTCAT-
1 TTTCTTTTTTTTTTCTTTCCTTTTC
*
398617 TTTCTTTTTTCCTTTT-TGT-CTTTTC
1 TTTCTTTTTT--TTTTCTTTCCTTTTC
*
398642 TTTCTTTTTTTTTTCTTTCCTTTAC
1 TTTCTTTTTTTTTTCTTTCCTTTTC
398667 TTTCTTTT
1 TTTCTTTT
398675 CTTACCTTCC
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
23 8 0.17
24 10 0.22
25 25 0.54
26 3 0.07
ACGTcount: A:0.02, C:0.21, G:0.01, T:0.75
Consensus pattern (25 bp):
TTTCTTTTTTTTTTCTTTCCTTTTC
Found at i:398675 original size:19 final size:17
Alignment explanation
Indices: 398598--398682 Score: 72
Period size: 17 Copynumber: 5.1 Consensus size: 17
398588 ATATTTTTTC
*
398598 TTTTT-TTTCCTTTCCT
1 TTTTTCTTTTCTTTCCT
*
398614 CATTTTC-TTT-TTTCCT
1 -TTTTTCTTTTCTTTCCT
398630 TTTTGTCTTTTCTTT-CT
1 TTTT-TCTTTTCTTTCCT
398647 TTTTT-TTTTCTTTCCT
1 TTTTTCTTTTCTTTCCT
*
398663 TTACTTTCTTTTCTTACCT
1 TT--TTTCTTTTCTTTCCT
398682 T
1 T
398683 CCTCATAATA
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
15 11 0.20
16 13 0.23
17 15 0.27
18 6 0.11
19 11 0.20
ACGTcount: A:0.04, C:0.22, G:0.01, T:0.73
Consensus pattern (17 bp):
TTTTTCTTTTCTTTCCT
Found at i:398695 original size:3 final size:3
Alignment explanation
Indices: 398687--398719 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
398677 TACCTTCCTC
398687 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
398720 CTTGCAAACA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:410028 original size:16 final size:16
Alignment explanation
Indices: 410009--410060 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
409999 TTTAAAATTT
410009 TATTTTATTAATATTA
1 TATTTTATTAATATTA
*
410025 TATTATTA-AAATATTA
1 TATT-TTATTAATATTA
410041 T-TTTATATTAATATTTA
1 TATTT-TATTAATA-TTA
410058 TAT
1 TAT
410061 AATTTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 1 0.03
15 4 0.14
16 16 0.55
17 7 0.24
18 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTTATTAATATTA
Found at i:410055 original size:32 final size:33
Alignment explanation
Indices: 410000--410077 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 33
409990 CCGAACCAAT
* *
410000 TTAAAATTTTA-TTT-TATTAATA-TTATATTA
1 TTAAAATATTATTTTATATTAATATTTATATAA
410030 TTAAAATATTATTTTATATTAATATTTATATAA
1 TTAAAATATTATTTTATATTAATATTTATATAA
**
410063 TTTTAA-ATTATTTTA
1 TTAAAATATTATTTTA
410078 AATAAAATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 10 0.24
31 3 0.07
32 17 0.41
33 11 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (33 bp):
TTAAAATATTATTTTATATTAATATTTATATAA
Found at i:410069 original size:35 final size:30
Alignment explanation
Indices: 409999--410074 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 30
409989 TCCGAACCAA
*
409999 TTTAAAATTTTATTTTATTAATATTATATT
1 TTTAAAATATTATTTTATTAATATTATATT
*
410029 ATTAAAATATTATTTTATATTAATATTTATATAAT
1 TTTAAAATATTA-TTT-TATTAATA-TTATAT--T
*
410064 TTTAAATTATT
1 TTTAAAATATT
410075 TTAAATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 10 0.27
31 3 0.08
32 8 0.22
33 6 0.16
35 10 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTAAAATATTATTTTATTAATATTATATT
Found at i:410236 original size:15 final size:15
Alignment explanation
Indices: 410213--410248 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
410203 TAATTTATTA
*
410213 TAAATATAATTATAAT
1 TAAA-ATAATTAAAAT
410229 TAAAATAATTAAAAT
1 TAAAATAATTAAAAT
410244 TAAAA
1 TAAAA
410249 ATTAATGGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAAATAATTAAAAT
Found at i:415397 original size:12 final size:12
Alignment explanation
Indices: 415376--415408 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
415366 TTCGATACAG
415376 ATTT-TAAATTA
1 ATTTATAAATTA
415387 ATTTATAAATTA
1 ATTTATAAATTA
*
415399 ATGTATAAAT
1 ATTTATAAAT
415409 CAATCACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (12 bp):
ATTTATAAATTA
Found at i:415572 original size:5 final size:6
Alignment explanation
Indices: 415556--415582 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
415546 ATACATCTTT
415556 TAAAAA TAAAAA TAAAAA TAAAAA TAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAA
415583 TTAAAAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:415802 original size:10 final size:10
Alignment explanation
Indices: 415772--415809 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
415762 TAAATAATTT
415772 TTAAAAATAA
1 TTAAAAATAA
*
415782 TTAATAA-AA
1 TTAAAAATAA
415791 TTAAAAATAA
1 TTAAAAATAA
415801 TTAATAAAT
1 TTAA-AAAT
415810 TAAAGTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.33
10 12 0.50
11 4 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
TTAAAAATAA
Found at i:415809 original size:18 final size:19
Alignment explanation
Indices: 415772--415813 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
415762 TAAATAATTT
415772 TTAAAAATAATTAATAAAA
1 TTAAAAATAATTAATAAAA
415791 TTAAAAATAATTAAT-AAA
1 TTAAAAATAATTAATAAAA
415809 TTAAA
1 TTAAA
415814 GTTATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TTAAAAATAATTAATAAAA
Found at i:415938 original size:24 final size:23
Alignment explanation
Indices: 415902--415948 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
415892 TTAAATAATT
*
415902 ATTTAAAAGTAAAATAAAATAAAA
1 ATTTAAAACTAAAA-AAAATAAAA
* *
415926 ATTTAAATCTAAAAAAATTAAAA
1 ATTTAAAACTAAAAAAAATAAAA
415949 TAAATAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (23 bp):
ATTTAAAACTAAAAAAAATAAAA
Found at i:416089 original size:19 final size:19
Alignment explanation
Indices: 416065--416108 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
416055 CTTTTAATTG
* *
416065 TTAATATTTTAATTATAAA
1 TTAATAATTTAATTAAAAA
*
416084 TTAATAATTTACTTAAAAA
1 TTAATAATTTAATTAAAAA
416103 TATAAT
1 T-TAAT
416109 TCAAAATATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAATAATTTAATTAAAAA
Found at i:416128 original size:23 final size:23
Alignment explanation
Indices: 416066--416130 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
416056 TTTTAATTGT
*
416066 TAATATTTTAATTATA-AATTAA
1 TAATATCTTAATTATATAATTAA
* **
416088 TAATTTACTTAAAAATATAATTCAA
1 TAATAT-CTTAATTATATAATT-AA
416113 -AATATCTTAATTATATAA
1 TAATATCTTAATTATATAA
416131 AATTGATTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
22 5 0.15
23 18 0.55
24 8 0.24
25 2 0.06
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.45
Consensus pattern (23 bp):
TAATATCTTAATTATATAATTAA
Found at i:416195 original size:18 final size:18
Alignment explanation
Indices: 416172--416260 Score: 53
Period size: 17 Copynumber: 5.2 Consensus size: 18
416162 AAAATATATT
*
416172 AAAAAATACTCAAATTC-
1 AAAAAATACTAAAATTCA
416189 AAAAAA-ACTTAAAATT-A
1 AAAAAATAC-TAAAATTCA
* * *
416206 AAAAAAAACTTAAACTCA
1 AAAAAATACTAAAATTCA
** *
416224 AAAAAATTTTAAACTT-A
1 AAAAAATACTAAAATTCA
* *
416241 AAAAAA-ATTAAAACTCA
1 AAAAAATACTAAAATTCA
416258 AAA
1 AAA
416261 GATCCACTGT
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
16 8 0.15
17 34 0.62
18 13 0.24
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.22
Consensus pattern (18 bp):
AAAAAATACTAAAATTCA
Found at i:416225 original size:34 final size:34
Alignment explanation
Indices: 416169--416260 Score: 107
Period size: 34 Copynumber: 2.7 Consensus size: 34
416159 TATAAAATAT
* * *
416169 ATTAAAAAATACTCAAATTCAAAAAAA-CTTAAA
1 ATTAAAAAAAACTTAAACTCAAAAAAATCTTAAA
*
416202 ATTAAAAAAAAACTTAAACTCAAAAAAATTTTAAA
1 ATT-AAAAAAAACTTAAACTCAAAAAAATCTTAAA
*
416237 CTTAAAAAAAA-TTAAAACTCAAAA
1 ATTAAAAAAAACTT-AAACTCAAAA
416261 GATCCACTGT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
33 5 0.10
34 39 0.76
35 7 0.14
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.24
Consensus pattern (34 bp):
ATTAAAAAAAACTTAAACTCAAAAAAATCTTAAA
Found at i:416235 original size:17 final size:17
Alignment explanation
Indices: 416187--416260 Score: 78
Period size: 17 Copynumber: 4.4 Consensus size: 17
416177 ATACTCAAAT
* *
416187 TCAAAAAAACTTAAAAT
1 TCAAAAAAAATTAAAAC
*
416204 TAAAAAAAAACTT-AAAC
1 TCAAAAAAAA-TTAAAAC
* *
416221 TCAAAAAAATTTTAAAC
1 TCAAAAAAAATTAAAAC
*
416238 TTAAAAAAAATTAAAAC
1 TCAAAAAAAATTAAAAC
416255 TCAAAA
1 TCAAAA
416261 GATCCACTGT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
16 2 0.04
17 42 0.91
18 2 0.04
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (17 bp):
TCAAAAAAAATTAAAAC
Done.