Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 201 of 202
Found at i:61479359 original size:31 final size:31
Alignment explanation
Indices: 61479282--61479362 Score: 135
Period size: 31 Copynumber: 2.6 Consensus size: 31
61479272 AAGAATGAAT
* *
61479282 TAAATTCAGTGCTTACTAAATCGTTGTAAAA
1 TAAATTCAGTGCTTATTAAAACGTTGTAAAA
*
61479313 TAAATTTAGTGCTTATTAAAACGTTGTAAAA
1 TAAATTCAGTGCTTATTAAAACGTTGTAAAA
61479344 TAAATTCAGTGCTTATTAA
1 TAAATTCAGTGCTTATTAA
61479363 TACCCAGCTC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (31 bp):
TAAATTCAGTGCTTATTAAAACGTTGTAAAA
Found at i:61482646 original size:218 final size:214
Alignment explanation
Indices: 61482272--61482705 Score: 814
Period size: 218 Copynumber: 2.0 Consensus size: 214
61482262 GAAAGCAGTT
61482272 TTTTATACACAAGACCATTAGGCTATCTGGACTGTCACATTAAAACAGTTAATTTTAAACCAACC
1 TTTTATACACAAGACCATTAGGCTATCTGGACTGTCACATTAAAACAGTTAATTTTAAACCAACC
61482337 AAAAGCATAAATTACAAACAAATCACTTTCTGAATCCTTAAAAGACGGAAAACACATTCAATTGA
66 AAAAGCATAAATTACAAACAAATCACTTTCTGAATCCTTAAAAGACGGAAAACACATTCAATTGA
61482402 ATACATAGATGATGTTAGACTACTATGGAATTTCTGTACCAGAATTTACTCCCTAAAACGAAAAT
131 ATACATAGATGATGTTAGACTACTATGGAATTTCTGTACCAGAATTTACTCCCTAAAACGAAAAT
61482467 ATTTACCACATATCCAAAG
196 ATTTACCACATATCCAAAG
* *
61482486 TTTTATACACGAGACCATTAGGCTATCTGGACTGTCACATTAAAATAGTTAAACTATTTTAAACC
1 TTTTATACACAAGACCATTAGGCTATCTGGACTGTCACATTAAAACAGTT--A--ATTTTAAACC
61482551 AACCAAAAGCATAAATTACAAACAAATCACTTTCTGAATCCTTAAAAGACGGAAAACACATTCAA
62 AACCAAAAGCATAAATTACAAACAAATCACTTTCTGAATCCTTAAAAGACGGAAAACACATTCAA
61482616 TTGAATACATAGATGATGTTAGACTACTATGGAATTTCTGTACCAGAATTTACTCCCTAAAACGA
127 TTGAATACATAGATGATGTTAGACTACTATGGAATTTCTGTACCAGAATTTACTCCCTAAAACGA
61482681 AAATATTTACCACATATCCAAAG
192 AAATATTTACCACATATCCAAAG
61482704 TT
1 TT
61482706 CTGTTAAGAA
Statistics
Matches: 214, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
214 48 0.22
216 1 0.00
218 165 0.77
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (214 bp):
TTTTATACACAAGACCATTAGGCTATCTGGACTGTCACATTAAAACAGTTAATTTTAAACCAACC
AAAAGCATAAATTACAAACAAATCACTTTCTGAATCCTTAAAAGACGGAAAACACATTCAATTGA
ATACATAGATGATGTTAGACTACTATGGAATTTCTGTACCAGAATTTACTCCCTAAAACGAAAAT
ATTTACCACATATCCAAAG
Found at i:61492501 original size:14 final size:14
Alignment explanation
Indices: 61492482--61492515 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
61492472 ATTTCATTTT
**
61492482 ATATTAATTGTATA
1 ATATTAATTAAATA
61492496 ATATTAATTAAATA
1 ATATTAATTAAATA
61492510 ATATTA
1 ATATTA
61492516 TAATTGCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
ATATTAATTAAATA
Found at i:61495554 original size:40 final size:40
Alignment explanation
Indices: 61495498--61495581 Score: 150
Period size: 40 Copynumber: 2.1 Consensus size: 40
61495488 CTACGTGCGT
*
61495498 CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
1 CACAACACCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
*
61495538 CACAACACCCATCGGGTTCCTAGAACCAAAATCAAGCCAA
1 CACAACACCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
61495578 CACA
1 CACA
61495582 GATGCAGTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.39, C:0.37, G:0.12, T:0.12
Consensus pattern (40 bp):
CACAACACCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
Found at i:61496871 original size:19 final size:19
Alignment explanation
Indices: 61496847--61496901 Score: 64
Period size: 15 Copynumber: 3.0 Consensus size: 19
61496837 TGTTAACTTT
61496847 TATTTCTTTCCTTACACTG
1 TATTTCTTTCCTTACACTG
61496866 TATTTC--T--TTACACTG
1 TATTTCTTTCCTTACACTG
61496881 TATTTCTTCCTCCTTACACTG
1 TATTTCTT--TCCTTACACTG
61496902 ATCCATCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
15 14 0.47
17 1 0.03
19 7 0.23
21 8 0.27
ACGTcount: A:0.16, C:0.27, G:0.05, T:0.51
Consensus pattern (19 bp):
TATTTCTTTCCTTACACTG
Found at i:61500068 original size:22 final size:23
Alignment explanation
Indices: 61500042--61500084 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
61500032 ATTTAGAATT
*
61500042 TAAAC-TAAAATGATAAATTTTG
1 TAAACATAAAAGGATAAATTTTG
*
61500064 TAAACATTAAAGGATAAATTT
1 TAAACATAAAAGGATAAATTT
61500085 GTTGAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (23 bp):
TAAACATAAAAGGATAAATTTTG
Found at i:61500508 original size:35 final size:35
Alignment explanation
Indices: 61500459--61500545 Score: 129
Period size: 35 Copynumber: 2.5 Consensus size: 35
61500449 ACTCAACCCT
** *
61500459 TGCAATCGACAGTCAGTCGTACGGCTCGCAAGCAG
1 TGCAATCGGTAGTCAGTCGCACGGCTCGCAAGCAG
*
61500494 TGCAATCGGTAGTCAGTCGCGCGGCTCGCAAGCAG
1 TGCAATCGGTAGTCAGTCGCACGGCTCGCAAGCAG
*
61500529 TGCAATCAGTAGTCAGT
1 TGCAATCGGTAGTCAGT
61500546 TGCGCAGCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.24, C:0.26, G:0.30, T:0.20
Consensus pattern (35 bp):
TGCAATCGGTAGTCAGTCGCACGGCTCGCAAGCAG
Found at i:61500560 original size:35 final size:35
Alignment explanation
Indices: 61500482--61500561 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
61500472 CAGTCGTACG
* *
61500482 GCTCGCAAGCAGTGCAATCGGTAGTCAGTCGCGCG
1 GCTCGCAAGCAGTGCAATCAGTAGTCAGTCGCGCA
*
61500517 GCTCGCAAGCAGTGCAATCAGTAGTCAGTTGCGCA
1 GCTCGCAAGCAGTGCAATCAGTAGTCAGTCGCGCA
*
61500552 GCTTGCAAGC
1 GCTCGCAAGC
61500562 GGCAAGTTCG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.23, C:0.28, G:0.31, T:0.19
Consensus pattern (35 bp):
GCTCGCAAGCAGTGCAATCAGTAGTCAGTCGCGCA
Found at i:61502461 original size:26 final size:26
Alignment explanation
Indices: 61502426--61502475 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
61502416 TATTCCGGCA
61502426 TTGGGCATATCCCATTCTTAGCATTC
1 TTGGGCATATCCCATTCTTAGCATTC
*
61502452 TTGGGTATATCCCATTCTTAGCAT
1 TTGGGCATATCCCATTCTTAGCAT
61502476 ATTCCGGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (26 bp):
TTGGGCATATCCCATTCTTAGCATTC
Found at i:61502745 original size:22 final size:23
Alignment explanation
Indices: 61502720--61502764 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
61502710 CTCTCATTCG
* *
61502720 TTCTCCCTCTTTTGTTTT-CTTT
1 TTCTCCCTCATTTCTTTTGCTTT
*
61502742 TTCTTCCTCATTTCTTTTGCTTT
1 TTCTCCCTCATTTCTTTTGCTTT
61502765 CATAACAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.02, C:0.27, G:0.04, T:0.67
Consensus pattern (23 bp):
TTCTCCCTCATTTCTTTTGCTTT
Found at i:61519877 original size:22 final size:22
Alignment explanation
Indices: 61519815--61519882 Score: 109
Period size: 22 Copynumber: 3.1 Consensus size: 22
61519805 ATTGTTCAAA
* **
61519815 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
61519837 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
61519859 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
61519881 CA
1 CA
61519883 GGGATTTCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:61547367 original size:26 final size:26
Alignment explanation
Indices: 61547331--61547384 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
61547321 TTGAAAATGT
61547331 ATATTTTTTAACCATGTTTCAACCCA
1 ATATTTTTTAACCATGTTTCAACCCA
61547357 ATATTTTTTAACCATGTTTCAACCCA
1 ATATTTTTTAACCATGTTTCAACCCA
61547383 AT
1 AT
61547385 TCGTTCCTCA
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:0.31, C:0.22, G:0.04, T:0.43
Consensus pattern (26 bp):
ATATTTTTTAACCATGTTTCAACCCA
Found at i:61556596 original size:11 final size:9
Alignment explanation
Indices: 61556570--61556615 Score: 65
Period size: 9 Copynumber: 4.8 Consensus size: 9
61556560 TATTTTTCTC
61556570 ATAAAAATT
1 ATAAAAATT
61556579 ATAAAAATT
1 ATAAAAATT
61556588 CATTAAAAATT
1 -A-TAAAAATT
61556599 ATAATAAATT
1 ATAA-AAATT
61556609 ATAAAAA
1 ATAAAAA
61556616 AATACTTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
9 15 0.44
10 11 0.32
11 8 0.24
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:61556615 original size:20 final size:20
Alignment explanation
Indices: 61556568--61556616 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
61556558 TCTATTTTTC
61556568 TCAT-AAAAATTATAAAAAT
1 TCATAAAAAATTATAAAAAT
*
61556587 TCATTAAAAATTATAATAAAT
1 TCATAAAAAATTATAA-AAAT
61556608 T-ATAAAAAA
1 TCATAAAAAA
61556617 ATACTTATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.15
20 18 0.67
21 5 0.19
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
TCATAAAAAATTATAAAAAT
Found at i:61563302 original size:96 final size:96
Alignment explanation
Indices: 61563131--61563322 Score: 312
Period size: 96 Copynumber: 2.0 Consensus size: 96
61563121 GATGGACTTC
* * * * *
61563131 AGTTGACTATATAAGATCAAGCAAAAGCACTTAATGGCGCAAGTTCAACTTCATTTGAACTTAAG
1 AGTTGACCATATAAGATCAAGAAAAAACACTTAATGGAGCAAGTTCAACTTCAATTGAACTTAAG
*
61563196 AACATTATGTCAAGTTCCATCTAAATAAAAA
66 AACATCATGTCAAGTTCCATCTAAATAAAAA
*
61563227 AGTTGACCATATATGATCAAGAAAAAACACTTAATGGAGCAAGTTCAACTTCAATTGAACTTAAG
1 AGTTGACCATATAAGATCAAGAAAAAACACTTAATGGAGCAAGTTCAACTTCAATTGAACTTAAG
*
61563292 AATATCATGTCAAGTTCCATCTAAATAAAAA
66 AACATCATGTCAAGTTCCATCTAAATAAAAA
61563323 TAAATGTGTA
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 88 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (96 bp):
AGTTGACCATATAAGATCAAGAAAAAACACTTAATGGAGCAAGTTCAACTTCAATTGAACTTAAG
AACATCATGTCAAGTTCCATCTAAATAAAAA
Found at i:61570394 original size:5 final size:5
Alignment explanation
Indices: 61570386--61570411 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
61570376 GAGAAAGAGG
61570386 AAAGC AAAGC AAAGC AAAGC AAAGC A
1 AAAGC AAAGC AAAGC AAAGC AAAGC A
61570412 TACCAGAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.19, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGC
Found at i:61571159 original size:14 final size:14
Alignment explanation
Indices: 61571124--61571163 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
61571114 ATAATGTTTA
61571124 ATATCAAT-AAAAT
1 ATATCAATAAAAAT
*
61571137 AT-T-ATTAAAAAT
1 ATATCAATAAAAAT
61571149 ATATCAATAAAAAT
1 ATATCAATAAAAAT
61571163 A
1 A
61571164 AATAAATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
11 2 0.09
12 8 0.36
13 3 0.14
14 9 0.41
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (14 bp):
ATATCAATAAAAAT
Found at i:61607146 original size:24 final size:24
Alignment explanation
Indices: 61607107--61607154 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
61607097 TTTTTGTGAT
* *
61607107 AATGATTTCTCTTTCTCTTCCTTG
1 AATGATTTATCCTTCTCTTCCTTG
61607131 AATGATTTATCCTTCTCTTCCTTG
1 AATGATTTATCCTTCTCTTCCTTG
61607155 GAAGACACGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.15, C:0.25, G:0.08, T:0.52
Consensus pattern (24 bp):
AATGATTTATCCTTCTCTTCCTTG
Found at i:61608615 original size:18 final size:19
Alignment explanation
Indices: 61608587--61608628 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
61608577 TTGATTTAAT
61608587 TTTTAGATAAAAATATCAA
1 TTTTAGATAAAAATATCAA
*
61608606 TTTT-GATAAAAATATCAG
1 TTTTAGATAAAAATATCAA
61608624 TTTTA
1 TTTTA
61608629 AAATTTTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (19 bp):
TTTTAGATAAAAATATCAA
Found at i:61608662 original size:25 final size:26
Alignment explanation
Indices: 61608632--61608681 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
61608622 AGTTTTAAAA
* *
61608632 TTTTTAGTGTTTCTATATAT-TATAT
1 TTTTTAATATTTCTATATATATATAT
*
61608657 TTTTTAATATTTTTATATATATATA
1 TTTTTAATATTTCTATATATATATA
61608682 ATATAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (26 bp):
TTTTTAATATTTCTATATATATATAT
Found at i:61610007 original size:31 final size:31
Alignment explanation
Indices: 61609969--61610028 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
61609959 CAGCCTAGTA
*
61609969 ACTTAAATAAAAACTTTTGAATAGTTCAGTG
1 ACTTAAATAAAAACTTTTGAATAATTCAGTG
* *
61610000 ACTTAAATGAAAATTTTTGAATAATTCAG
1 ACTTAAATAAAAACTTTTGAATAATTCAG
61610029 CGACCATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTTGAATAATTCAGTG
Found at i:61610253 original size:29 final size:29
Alignment explanation
Indices: 61610210--61610267 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
61610200 GCTGATGAAA
61610210 CTATAGCATTAGCTAAAAGTAGTGTTCTT
1 CTATAGCATTAGCTAAAAGTAGTGTTCTT
*
61610239 CTATAGCATTTGCTAAAAGTAGTGTTCTT
1 CTATAGCATTAGCTAAAAGTAGTGTTCTT
61610268 AGTTGCGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (29 bp):
CTATAGCATTAGCTAAAAGTAGTGTTCTT
Found at i:61611507 original size:196 final size:198
Alignment explanation
Indices: 61611151--61611542 Score: 614
Period size: 196 Copynumber: 2.0 Consensus size: 198
61611141 AACCTAATGA
* *
61611151 ATGTTACTGCAGCTAGTTACTATAAATATCGGCTATGGAAACTAGTTGAAACTGATAAATAGTGA
1 ATGTTACTGCAGCTAATTACTATAAATATCGGCTATGGAAACGAGTTGAAACTGATAAATAGTGA
* *
61611216 TTCTTAACACAGTGTTGTGGCTGCTATTTGAATCTCTTTATAATTTCTTAGTGCTATTCTCTCTT
66 CTCTTAACACAGTGTTGTGGCTGCTATTTGAATCTCTCTATAATTTCTTAGTGCTATTCTCTCTT
61611281 GACTGTATGCTTGGCTGCTAAATCCTGCTTACCCTGTTCTTGGTACCTTCTATCCAAATGGAATA
131 GACTGTATGCTTGGCTGCTAAATCCTGCTTACCCTGTTCTTGGTACCTTCTATCCAAATGGAATA
61611346 TTC
196 TTC
* * *
61611349 ATGTTACTGCAG-TCAATTGCTTTAAATATCGGCTATGGAAA-GAGTTGAAATTGA-AAATTTA-
1 ATGTTACTGCAGCT-AATTACTATAAATATCGGCTATGGAAACGAGTTGAAACTGATAAA--TAG
* * *
61611410 TGACTCTTAACACAGTGTTGTGGTTGCTATTTGAGTCTCTCTATAA-TTCTTATTGCTATTCTCT
63 TGACTCTTAACACAGTGTTGTGGCTGCTATTTGAATCTCTCTATAATTTCTTAGTGCTATTCTCT
* *
61611474 CTTGACTGTATGTTTGGCTGCTAAATCCTGCTTACCCTGTTCTTGTTACCTTCTATCCAAATGGA
128 CTTGACTGTATGCTTGGCTGCTAAATCCTGCTTACCCTGTTCTTGGTACCTTCTATCCAAATGGA
61611539 ATAT
193 ATAT
61611543 GCAATTTTTG
Statistics
Matches: 179, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
196 87 0.49
197 54 0.30
198 38 0.21
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (198 bp):
ATGTTACTGCAGCTAATTACTATAAATATCGGCTATGGAAACGAGTTGAAACTGATAAATAGTGA
CTCTTAACACAGTGTTGTGGCTGCTATTTGAATCTCTCTATAATTTCTTAGTGCTATTCTCTCTT
GACTGTATGCTTGGCTGCTAAATCCTGCTTACCCTGTTCTTGGTACCTTCTATCCAAATGGAATA
TTC
Found at i:61621254 original size:6 final size:6
Alignment explanation
Indices: 61621243--61621274 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
61621233 TATTAATTTA
61621243 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TT
61621275 AAATATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTCTTT
Found at i:61630179 original size:79 final size:79
Alignment explanation
Indices: 61630048--61630206 Score: 300
Period size: 79 Copynumber: 2.0 Consensus size: 79
61630038 AGATAATTTT
**
61630048 TCATTGGAGGGGCCAAGGTCCCTGCCGGCCTCTTAAATTCACCCTATAGGTTTGGACTAAAACTT
1 TCATTGGAGGGGCCAAACTCCCTGCCGGCCTCTTAAATTCACCCTATAGGTTTGGACTAAAACTT
61630113 CAAAATTCAAAAAG
66 CAAAATTCAAAAAG
61630127 TCATTGGAGGGGCCAAACTCCCTGCCGGCCTCTTAAATTCACCCTATAGGTTTGGACTAAAACTT
1 TCATTGGAGGGGCCAAACTCCCTGCCGGCCTCTTAAATTCACCCTATAGGTTTGGACTAAAACTT
61630192 CAAAATTCAAAAAG
66 CAAAATTCAAAAAG
61630206 T
1 T
61630207 AAAGGATTAA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.26
Consensus pattern (79 bp):
TCATTGGAGGGGCCAAACTCCCTGCCGGCCTCTTAAATTCACCCTATAGGTTTGGACTAAAACTT
CAAAATTCAAAAAG
Found at i:61659858 original size:31 final size:30
Alignment explanation
Indices: 61659795--61659873 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
61659785 TCTTAACAAC
*
61659795 TCAGTGACGTAAATAAACATTCCAAATAAT
1 TCAGTGACTTAAATAAACATTCCAAATAAT
* *
61659825 TCAGTGACTTAAATAGAAGC-TTTCAAATTAT
1 TCAGTGACTTAAATA-AA-CATTCCAAATAAT
*
61659856 TCAGTGATTTAAACTAAA
1 TCAGTGACTTAAA-TAAA
61659874 ATATTCAAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 14 0.33
31 25 0.60
32 3 0.07
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (30 bp):
TCAGTGACTTAAATAAACATTCCAAATAAT
Found at i:61660624 original size:23 final size:22
Alignment explanation
Indices: 61660594--61660641 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
61660584 TTGAAATCTG
61660594 AAAAATAAAAAGATCAAATTCCT
1 AAAAATAAAAAGATCAAATT-CT
* *
61660617 AAAAATAAAAGGATTAAATTCT
1 AAAAATAAAAAGATCAAATTCT
61660639 AAA
1 AAA
61660642 TTTGTGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.23
Consensus pattern (22 bp):
AAAAATAAAAAGATCAAATTCT
Found at i:61664780 original size:23 final size:23
Alignment explanation
Indices: 61664754--61664803 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
61664744 TGAAATTTAG
61664754 TTTTT-ATAATTTT-ATTTTAAAAA
1 TTTTTAAT-ATTTTAATTTT-AAAA
*
61664777 TTTTTAATTTTTTAATTTTAAAA
1 TTTTTAATATTTTAATTTTAAAA
61664800 TTTT
1 TTTT
61664804 AAAATTTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTTTAATATTTTAATTTTAAAA
Found at i:61664810 original size:24 final size:23
Alignment explanation
Indices: 61664763--61664806 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
61664753 GTTTTTATAA
*
61664763 TTTTATTTTAAAAATTTTTAATT
1 TTTTATTTTAAAAATTTTAAATT
61664786 TTTTAATTTT-AAAATTTTAAA
1 TTTT-ATTTTAAAAATTTTAAA
61664807 ATTTAAGTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTATTTTAAAAATTTTAAATT
Found at i:61670561 original size:16 final size:15
Alignment explanation
Indices: 61670540--61670580 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
61670530 AAATTTCTCG
61670540 AAAATAATTTTTGAAA
1 AAAATAATTTTT-AAA
61670556 AAAATAATTTTTAAA
1 AAAATAATTTTTAAA
61670571 AAAAT-ATTTT
1 AAAATAATTTT
61670581 ACACTGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.20
15 8 0.32
16 12 0.48
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
AAAATAATTTTTAAA
Found at i:61670566 original size:15 final size:15
Alignment explanation
Indices: 61670540--61670580 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
61670530 AAATTTCTCG
61670540 AAAATAATTTTTGAAA
1 AAAATAA-TTTTGAAA
*
61670556 AAAATAATTTTTAAA
1 AAAATAATTTTGAAA
61670571 AAAAT-ATTTT
1 AAAATAATTTT
61670581 ACACTGGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 5 0.21
15 12 0.50
16 7 0.29
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
AAAATAATTTTGAAA
Found at i:61670611 original size:20 final size:20
Alignment explanation
Indices: 61670588--61670625 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
61670578 TTTACACTGG
*
61670588 AAAAATA-ATATAAATGAAA
1 AAAAATACATAAAAATGAAA
61670607 AAAAATACATAAAAATGAA
1 AAAAATACATAAAAATGAA
61670626 CCATGTTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (20 bp):
AAAAATACATAAAAATGAAA
Found at i:61677256 original size:20 final size:20
Alignment explanation
Indices: 61677227--61677267 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
61677217 CAAATTTAAC
*
61677227 TAAAATATAAAAATTAAATT
1 TAAAAAATAAAAATTAAATT
*
61677247 TAAAAAATAAACATTAAATT
1 TAAAAAATAAAAATTAAATT
61677267 T
1 T
61677268 GATCTTATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAAATAAAAATTAAATT
Found at i:61677310 original size:29 final size:29
Alignment explanation
Indices: 61677278--61677339 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
61677268 GATCTTATGT
61677278 AAATTTTAAAATTCAAATTGAGCCAACCA
1 AAATTTTAAAATTCAAATTGAGCCAACCA
61677307 AAATTTTAAAATTCAAATTGAGCCAACCA
1 AAATTTTAAAATTCAAATTGAGCCAACCA
61677336 AAAT
1 AAAT
61677340 CCTTTCGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.27
Consensus pattern (29 bp):
AAATTTTAAAATTCAAATTGAGCCAACCA
Found at i:61679909 original size:2 final size:2
Alignment explanation
Indices: 61679902--61679928 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
61679892 ATTAAATGTT
61679902 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 T
61679929 TTTGCTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61681034 original size:31 final size:32
Alignment explanation
Indices: 61680965--61681034 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
61680955 AGTTAGTCTC
*
61680965 TAAATTTGACAATTATTCTCATATTTTGGGCT
1 TAAATTTGACAATTATTCTCATATTTGGGGCT
* *
61680997 TAAATTTGTCAATTATTTTCATA-TTGGGGCT
1 TAAATTTGACAATTATTCTCATATTTGGGGCT
*
61681028 TGAATTT
1 TAAATTT
61681035 TAAGTTTTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 13 0.38
32 21 0.62
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (32 bp):
TAAATTTGACAATTATTCTCATATTTGGGGCT
Found at i:61682464 original size:104 final size:104
Alignment explanation
Indices: 61682284--61682708 Score: 663
Period size: 104 Copynumber: 4.1 Consensus size: 104
61682274 TGTTGTAAAT
* * *
61682284 TTAGAGGCTTCAAGATTTTCTTGTAAGTAATGAATCAAAGCTCTTACATTGTAGAATGAGTTTGA
1 TTAGAGGTTTCAAGATTTTCATGTAAATAATGAATCAAAGCTCTTACATTGTAGAATGAGTTTGA
*
61682349 TTTTGATTCATCATTTTCGCTTAAACTTGAGTATTAAAC
66 TTTTGATTCATCATTTTCGCTTAAACTTGAGTATTTAAC
* *
61682388 TTAGAGGTTTAAAAATTTTCATGTAAATAATGAATCAAAGCTCTTACATTGTAGAATGAGTTTGA
1 TTAGAGGTTTCAAGATTTTCATGTAAATAATGAATCAAAGCTCTTACATTGTAGAATGAGTTTGA
*
61682453 TTTTGATTCATCATTTTCGCTTAAACTTGAATATTTAAC
66 TTTTGATTCATCATTTTCGCTTAAACTTGAGTATTTAAC
* *
61682492 TTAGAGGTTTCAAGATTTTCATGTAAACAAGGAATCAAAGCTCTTACATTGTAGAATGAGTTTGA
1 TTAGAGGTTTCAAGATTTTCATGTAAATAATGAATCAAAGCTCTTACATTGTAGAATGAGTTTGA
*
61682557 TTTTGATTCATCATTTTCTCTTAAACTTGAGTATTTAAC
66 TTTTGATTCATCATTTTCGCTTAAACTTGAGTATTTAAC
* * * *
61682596 TTAGAGGTTTCAAGATTTTTATGTAAATAATGAATCAAAGCTCTTACATTGTAGCAGGAGTTTGT
1 TTAGAGGTTTCAAGATTTTCATGTAAATAATGAATCAAAGCTCTTACATTGTAGAATGAGTTTGA
* * * *
61682661 TTTTGA-TCTGTAATTTTCGCATAAACTCGAGTATTTAAC
66 TTTTGATTC-ATCATTTTCGCTTAAACTTGAGTATTTAAC
*
61682700 TTAGTGGTT
1 TTAGAGGTT
61682709 GGTGCCTAAT
Statistics
Matches: 295, Mismatches: 25, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
103 2 0.01
104 293 0.99
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.41
Consensus pattern (104 bp):
TTAGAGGTTTCAAGATTTTCATGTAAATAATGAATCAAAGCTCTTACATTGTAGAATGAGTTTGA
TTTTGATTCATCATTTTCGCTTAAACTTGAGTATTTAAC
Found at i:61693738 original size:61 final size:60
Alignment explanation
Indices: 61693614--61693772 Score: 205
Period size: 61 Copynumber: 2.6 Consensus size: 60
61693604 TATTTTGGCC
* * * * **
61693614 CTATAGTGAAATTCTCACTTTGGTCCTTTTACTATTTTTTTTATCATTTTGTCCTTTGTA
1 CTATAATGAAATTCTCACATTGGCCCTTTTACTATTTTCTTTATCATTTTGTCCTTTACA
61693674 CTATAATGAAATTCTCACATTGGCCCTTTTACTAATTTTCTTTATCATTTTGTTCC-TTACA
1 CTATAATGAAATTCTCACATTGGCCCTTTTACT-ATTTTCTTTATCATTTTG-TCCTTTACA
* *
61693735 CTATAATGAAATTCTCAC-TTCGTCCCTCTTACTATTTT
1 CTATAATGAAATTCTCACATT-GGCCCTTTTACTATTTT
61693773 GTTCAGTTAC
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
60 37 0.42
61 48 0.55
62 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.08, T:0.50
Consensus pattern (60 bp):
CTATAATGAAATTCTCACATTGGCCCTTTTACTATTTTCTTTATCATTTTGTCCTTTACA
Found at i:61704669 original size:97 final size:96
Alignment explanation
Indices: 61704503--61704787 Score: 333
Period size: 97 Copynumber: 2.9 Consensus size: 96
61704493 CCTACTTTCG
*
61704503 AGTTTTCATTGCTTGGTTCGTGTTAGCAAGTTATGTCGATTTTCAAAATG-TTCAGGTTGCTTTT
1 AGTTTTCATTGCTTGGTTCGTGTTAGCAAGTTATATCGA-TTTCAAAATGTTTC-GGTTGCTTTT
*
61704567 TATTGGCTTTATGGTTCCATCTTCCTCCATACA
64 TATTGGATTTATGGTTCCATCTTCCTCCATACA
* * * *
61704600 AGTTTTCATTGCTTGGTTCGTGGTAGCAAGCTATATCGATTTCAAAATGTTTCTGTTGTTTTTTT
1 AGTTTTCATTGCTTGGTTCGTGTTAGCAAGTTATATCGATTTCAAAATGTTTCGGTTG-CTTTTT
* * * * *
61704665 ATTGGAATTACGGTTCCATCTTCCTACATTCG
65 ATTGGATTTATGGTTCCATCTTCCTCCATACA
* ** * *
61704697 AGTTTTCATTGCTCGGTTCGTGTTAGTGAGTTATATTGATCTTCAAAACGCTTT-GGTTGCTTTT
1 AGTTTTCATTGCTTGGTTCGTGTTAGCAAGTTATATCGAT-TTCAAAATG-TTTCGGTTGCTTTT
* *
61704761 T-TTGGTTTTATGGTTCAATCTTTCCTC
64 TATTGGATTTATGGTTCCATC-TTCCTC
61704788 ATTGTGTGCT
Statistics
Matches: 158, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
96 29 0.18
97 114 0.72
98 12 0.08
99 3 0.02
ACGTcount: A:0.18, C:0.16, G:0.19, T:0.47
Consensus pattern (96 bp):
AGTTTTCATTGCTTGGTTCGTGTTAGCAAGTTATATCGATTTCAAAATGTTTCGGTTGCTTTTTA
TTGGATTTATGGTTCCATCTTCCTCCATACA
Found at i:61707207 original size:13 final size:13
Alignment explanation
Indices: 61707170--61707199 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
61707160 ATATCTTTAT
61707170 TGTTTTTGAAAAG
1 TGTTTTTGAAAAG
61707183 TGTTTTTGAAAAG
1 TGTTTTTGAAAAG
61707196 TGTT
1 TGTT
61707200 GTTTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (13 bp):
TGTTTTTGAAAAG
Found at i:61708458 original size:20 final size:20
Alignment explanation
Indices: 61708433--61708470 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
61708423 TATATTTGAA
61708433 ATGTTA-CGTTTTGATTACTT
1 ATGTTATCGTTTTG-TTACTT
61708453 ATGTTATCGTTTTGTTAC
1 ATGTTATCGTTTTGTTAC
61708471 GAAATGACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.18, C:0.11, G:0.16, T:0.55
Consensus pattern (20 bp):
ATGTTATCGTTTTGTTACTT
Found at i:61709915 original size:7 final size:7
Alignment explanation
Indices: 61709903--61709959 Score: 55
Period size: 7 Copynumber: 8.0 Consensus size: 7
61709893 AATTTATTTT
61709903 AAAAATA
1 AAAAATA
61709910 AAAAAT-
1 AAAAATA
61709916 AAAAATA
1 AAAAATA
* *
61709923 AAAGTATTTT
1 AAA--A-ATA
61709933 AAAAATA
1 AAAAATA
61709940 AAAAAT-
1 AAAAATA
61709946 AAAAATA
1 AAAAATA
61709953 AAAAATA
1 AAAAATA
61709960 TATATTTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
6 12 0.29
7 23 0.56
8 1 0.02
9 1 0.02
10 4 0.10
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (7 bp):
AAAAATA
Found at i:61709918 original size:13 final size:13
Alignment explanation
Indices: 61709902--61709959 Score: 71
Period size: 13 Copynumber: 4.2 Consensus size: 13
61709892 AAATTTATTT
61709902 TAAAAATAAAAAA
1 TAAAAATAAAAAA
*
61709915 TAAAAATAAAAGTATTT
1 TAAAAATAAAA--A--A
61709932 TAAAAATAAAAAA
1 TAAAAATAAAAAA
61709945 TAAAAATAAAAAA
1 TAAAAATAAAAAA
61709958 TA
1 TA
61709960 TATATTTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
13 26 0.67
15 2 0.05
17 11 0.28
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:61709932 original size:30 final size:30
Alignment explanation
Indices: 61709897--61709955 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
61709887 ATTAAAAATT
61709897 TATTTTAAAAATAAAAAATAAAAATAAAAG
1 TATTTTAAAAATAAAAAATAAAAATAAAAG
61709927 TATTTTAAAAATAAAAAATAAAAATAAAA
1 TATTTTAAAAATAAAAAATAAAAATAAAA
61709956 AATATATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (30 bp):
TATTTTAAAAATAAAAAATAAAAATAAAAG
Found at i:61712647 original size:11 final size:10
Alignment explanation
Indices: 61712627--61712651 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
61712617 ATAATATGAT
61712627 AAAAACAAAA
1 AAAAACAAAA
61712637 AAAAACAAAA
1 AAAAACAAAA
61712647 AAAAA
1 AAAAA
61712652 TAATTACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:61712663 original size:32 final size:33
Alignment explanation
Indices: 61712604--61712665 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
61712594 TAACTTTCAT
* *
61712604 AAAAAAAAAACAAATAATATGATAAAAACAAAA
1 AAAAAAAAAAAAAATAATATGACAAAAACAAAA
61712637 AAAAACAAAAAAAAATAAT-T-ACAAAAACA
1 AAAAA-AAAAAAAAATAATATGACAAAAACA
61712666 CGTTCGGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 8 0.31
33 6 0.23
34 12 0.46
ACGTcount: A:0.79, C:0.08, G:0.02, T:0.11
Consensus pattern (33 bp):
AAAAAAAAAAAAAATAATATGACAAAAACAAAA
Found at i:61715411 original size:158 final size:157
Alignment explanation
Indices: 61715112--61715415 Score: 427
Period size: 158 Copynumber: 1.9 Consensus size: 157
61715102 TTCTTTGAGC
* * *
61715112 TCAATTTGGAGTTTATGTTTCGTTTTTTGTTCATAATTTATGATTTGGGAATATGGGTTAGCTCT
1 TCAATTTGAAGCTTATGGTTCGTTTTTTGTTCATAATTTATGATTTGGGAATATGGGTTAGCTCT
* * * * *
61715177 AAAATTAATAAAAATGTTGTTGTTGTTTTTTTTTTTTGTATTTATGTTTCTGATGATATCATATC
66 AAAAATAATAAAAATG-TGTTGTTGTTTTTTGTGTGTGTATTTATGTTTCTGATGAAATCATATC
*
61715242 ACCAACCTTTTTTTTTTTTTGTTTAAGT
130 AACAACCTTTTTTTTTTTTTGTTTAAGT
*
61715270 TCAATTTGAAGCTTATGGTTCGTTTTTTGTTCATAATTTATGATTTGGGAATTTGGGTTAGCTCT
1 TCAATTTGAAGCTTATGGTTCGTTTTTTGTTCATAATTTATGATTTGGGAATATGGGTTAGCTCT
* * * *
61715335 AAAAATAATCAAAATG-GTT-TT-TCTTTTTGTGTGTGTATTTGTGTTTTTTATGACAATCATAT
66 AAAAATAATAAAAATGTGTTGTTGT-TTTTTGTGTGTGTATTTATGTTTCTGATGA-AATCATAT
61715397 CAACAA-CTTTTTTTTTTTT
129 CAACAACCTTTTTTTTTTTT
61715416 GGTACTTTTG
Statistics
Matches: 130, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
154 1 0.01
155 39 0.30
156 15 0.12
158 75 0.58
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.53
Consensus pattern (157 bp):
TCAATTTGAAGCTTATGGTTCGTTTTTTGTTCATAATTTATGATTTGGGAATATGGGTTAGCTCT
AAAAATAATAAAAATGTGTTGTTGTTTTTTGTGTGTGTATTTATGTTTCTGATGAAATCATATCA
ACAACCTTTTTTTTTTTTTGTTTAAGT
Found at i:61732776 original size:19 final size:19
Alignment explanation
Indices: 61732729--61732790 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
61732719 AATTATGAGT
61732729 TTTTTATAATTTTTT-TTAA
1 TTTTTATAATTTTTTATT-A
* *
61732748 ATTTT-GAATTTTTTATTA
1 TTTTTATAATTTTTTATTA
*
61732766 TTTTTATAATTTTTAATTTA
1 TTTTTATAATTTTTTA-TTA
61732786 TTTTT
1 TTTTT
61732791 TTGACATAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 13 0.37
19 14 0.40
20 8 0.23
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTTATAATTTTTTATTA
Found at i:61735960 original size:2 final size:2
Alignment explanation
Indices: 61735955--61735981 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
61735945 TATAGCAAAA
61735955 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 A
61735982 GAATTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61741110 original size:3 final size:3
Alignment explanation
Indices: 61741102--61741127 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
61741092 TACCTTTTTC
61741102 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
61741128 AATTAGATTC
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:61741973 original size:14 final size:14
Alignment explanation
Indices: 61741954--61741993 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
61741944 TTGATTGGCA
61741954 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
61741968 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
61741982 GGAAAATGTTTT
1 GTAAAATGTTTT
61741994 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:61742002 original size:20 final size:20
Alignment explanation
Indices: 61741977--61742016 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
61741967 CGTAAAATGA
*
61741977 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
61741997 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
61742017 AGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:61742006 original size:34 final size:35
Alignment explanation
Indices: 61741962--61742028 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
61741952 CAGTAAAATG
* *
61741962 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
*
61741996 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
61742029 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:61742140 original size:20 final size:20
Alignment explanation
Indices: 61742115--61742153 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
61742105 GTTTTTACAT
61742115 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
61742135 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
61742154 TTTTAAATTA
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:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:61744543 original size:11 final size:11
Alignment explanation
Indices: 61744527--61744552 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
61744517 AACCATCTGT
61744527 ATATAACCAAA
1 ATATAACCAAA
61744538 ATATAACCAAA
1 ATATAACCAAA
61744549 ATAT
1 ATAT
61744553 CATCCAGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (11 bp):
ATATAACCAAA
Found at i:61744813 original size:25 final size:25
Alignment explanation
Indices: 61744785--61744841 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
61744775 GAATATGCTG
61744785 AGAAGAGAAG-ATGAAGAACAAAAGA
1 AGAAGA-AAGAATGAAGAACAAAAGA
**
61744810 AGAA-AAAGTAATGAAGAACGGAAGA
1 AGAAGAAAG-AATGAAGAACAAAAGA
61744835 AGAAGAA
1 AGAAGAA
61744842 GGAGCCTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 3 0.11
24 1 0.04
25 21 0.78
26 2 0.07
ACGTcount: A:0.63, C:0.04, G:0.28, T:0.05
Consensus pattern (25 bp):
AGAAGAAAGAATGAAGAACAAAAGA
Found at i:61745855 original size:20 final size:22
Alignment explanation
Indices: 61745816--61745857 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
61745806 TAGTTAATGA
61745816 ATTTGTTGGATACATTTATCCT
1 ATTTGTTGGATACATTTATCCT
*
61745838 ATTTGTT-G-TACGTTTATCCT
1 ATTTGTTGGATACATTTATCCT
61745858 TTTTTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 1 0.05
22 7 0.37
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.52
Consensus pattern (22 bp):
ATTTGTTGGATACATTTATCCT
Found at i:61749426 original size:3 final size:3
Alignment explanation
Indices: 61749418--61749455 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
61749408 TGTTAATCTG
61749418 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 TT
61749456 TGCTAAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:61753331 original size:2 final size:2
Alignment explanation
Indices: 61753324--61753353 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
61753314 CAGGTATATC
*
61753324 TG TG TG TG TG TG TG TG TG TG TG TT TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
61753354 CTAGCATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:61754826 original size:27 final size:27
Alignment explanation
Indices: 61754755--61754840 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
61754745 TCGTCCATAT
* * *
61754755 TATTTTTTAATTTTTTTAAAAGATATATTA
1 TATTTTTT-ATTTATTTAATA-ATTTA-TA
*
61754785 TATTATTTTA-ATATTTAATAATTTATA
1 TATT-TTTTATTTATTTAATAATTTATA
* **
61754812 TATTTTTTATTTATTGAATTTTTTATA
1 TATTTTTTATTTATTTAATAATTTATA
61754839 TA
1 TA
61754841 GTCTTCTAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
26 5 0.11
27 21 0.46
28 4 0.09
29 7 0.15
30 5 0.11
31 4 0.09
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
TATTTTTTATTTATTTAATAATTTATA
Found at i:61761833 original size:69 final size:70
Alignment explanation
Indices: 61761608--61761840 Score: 267
Period size: 69 Copynumber: 3.3 Consensus size: 70
61761598 TACTAATAAC
* * *
61761608 ATTCATGCTATCAGCAAAATCATCTTACTCGGACTCGGGTATGAGTATTGAATACAGATATATGA
1 ATTCATGCTATCAGCAAAATCATCTTATTCAGACTCGGGTATGAGTATTGAATACAGGTA-ATGA
* *
61761673 GTGTCTT
65 G-ATATT
* * *
61761680 ATTCATGCTATCAGCAAAATCAAGTATCTTATTCAGACTC-AGTACGAGTACTGAATACAGGT-A
1 ATTCATGCTATCAGCAAAATC----ATCTTATTCAGACTCGGGTATGAGTATTGAATACAGGTAA
*
61761743 TGAGCATCTT
62 TGAG-ATATT
* *
61761753 ATTCATTCTATCAGCAAAATCATCTTATTCAGACTCGGGTATGAGTATTGAATACTTGGTAAT-A
1 ATTCATGCTATCAGCAAAATCATCTTATTCAGACTCGGGTATGAGTATTGAATAC-AGGTAATGA
61761817 -ATATT
65 GATATT
61761822 ATTCATGCTATCAGCAAAA
1 ATTCATGCTATCAGCAAAA
61761841 CAGAAGTAAC
Statistics
Matches: 139, Mismatches: 15, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
69 37 0.27
70 15 0.11
71 4 0.03
72 23 0.17
73 29 0.21
75 18 0.13
76 13 0.09
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (70 bp):
ATTCATGCTATCAGCAAAATCATCTTATTCAGACTCGGGTATGAGTATTGAATACAGGTAATGAG
ATATT
Found at i:61766647 original size:2 final size:2
Alignment explanation
Indices: 61766640--61766664 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61766630 TGCCGGATTA
61766640 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 A
61766665 ATTTAATTTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61769390 original size:2 final size:2
Alignment explanation
Indices: 61769383--61769422 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
61769373 TTGCCATTCA
61769383 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61769423 GGTTCTTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61775949 original size:14 final size:14
Alignment explanation
Indices: 61775930--61775957 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
61775920 GATATCACAT
61775930 TACTCACCTAACAA
1 TACTCACCTAACAA
61775944 TACTCACCTAACAA
1 TACTCACCTAACAA
61775958 GGGATGATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.21
Consensus pattern (14 bp):
TACTCACCTAACAA
Found at i:61781694 original size:31 final size:31
Alignment explanation
Indices: 61781659--61781801 Score: 95
Period size: 31 Copynumber: 4.6 Consensus size: 31
61781649 ACTTAGCAGC
* *
61781659 TTAATAAGAATTTCCATAAATTTTGGAG-GGT
1 TTAATAAGAATTTTCA-AAATTTTGGAGAGGA
*
61781690 TTAATTAA-AATTTTTAAAAATTTT-GAGAGGA
1 TTAA-TAAGAA-TTTTCAAAATTTTGGAGAGGA
*
61781721 TTAATGAGAATTTTCAAAAGTTTTGGAGA-G-
1 TTAATAAGAATTTTCAAAA-TTTTGGAGAGGA
* *
61781751 TCTAATTAAAAATTTT-AAAACTTTTGGA-AGGC
1 T-TAA-TAAGAATTTTCAAAA-TTTTGGAGAGGA
*
61781783 TTAATTA-AATTTTCTAAAA
1 TTAATAAGAATTTTC-AAAA
61781802 AATTTGATGG
Statistics
Matches: 91, Mismatches: 9, Indels: 24
0.73 0.07 0.19
Matches are distributed among these distances:
29 6 0.07
30 17 0.19
31 48 0.53
32 20 0.22
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.40
Consensus pattern (31 bp):
TTAATAAGAATTTTCAAAATTTTGGAGAGGA
Found at i:61781765 original size:32 final size:31
Alignment explanation
Indices: 61781676--61781834 Score: 98
Period size: 31 Copynumber: 5.1 Consensus size: 31
61781666 GAATTTCCAT
* * *
61781676 AAATTTTGGAGGGTTTAATTAAAATTTTTAA
1 AAATTTTGGAGAGTCTAATTAAAAATTTTAA
* *
61781707 AAATTTT-GAGAGGAT-TAA-TGAGAATTTTCAA
1 AAATTTTGGAGA-G-TCTAATTAAAAATTTT-AA
*
61781738 AAGTTTTGGAGAGTCTAATTAAAAATTTTAA
1 AAATTTTGGAGAGTCTAATTAAAAATTTTAA
* * *
61781769 AACTTTTGGA-AGGCTTAATT-AAATTTTCTAA
1 AAATTTTGGAGAGTC-TAATTAAAAATTT-TAA
* * *
61781800 AAAATTT-GATG-GACCTAATTAAAATTTTTAA
1 AAATTTTGGA-GAG-TCTAATTAAAAATTTTAA
61781831 AAAT
1 AAAT
61781835 GAGTATAATA
Statistics
Matches: 102, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
30 22 0.22
31 59 0.58
32 21 0.21
ACGTcount: A:0.42, C:0.04, G:0.14, T:0.40
Consensus pattern (31 bp):
AAATTTTGGAGAGTCTAATTAAAAATTTTAA
Found at i:61781787 original size:62 final size:61
Alignment explanation
Indices: 61781657--61781801 Score: 168
Period size: 62 Copynumber: 2.3 Consensus size: 61
61781647 AAACTTAGCA
* * * *
61781657 GCTTAATAAGAATTTCCATAAATTTTGGAGGGTTTAATTAAAATTTTTAAAAATTTTGAGAG
1 GCTTAATAAGAATTTTCA-AAATTTTGGAGAGTCTAATTAAAAATTTTAAAAATTTTGAGAG
* * *
61781719 GATTAATGAGAATTTTCAAAAGTTTTGGAGAGTCTAATTAAAAATTTTAAAACTTTTG-GAAG
1 GCTTAATAAGAATTTTCAAAA-TTTTGGAGAGTCTAATTAAAAATTTTAAAAATTTTGAG-AG
*
61781781 GCTTAATTA-AATTTTCTAAAA
1 GCTTAATAAGAATTTTC-AAAA
61781802 AATTTGATGG
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
61 11 0.15
62 60 0.85
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.39
Consensus pattern (61 bp):
GCTTAATAAGAATTTTCAAAATTTTGGAGAGTCTAATTAAAAATTTTAAAAATTTTGAGAG
Found at i:61793459 original size:31 final size:31
Alignment explanation
Indices: 61793424--61793484 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
61793414 TATTCTAATT
* *
61793424 TGATCAATTTTAGTCTTTATACTTTTTAAAA
1 TGATCAATTTCAGTCCTTATACTTTTTAAAA
*
61793455 TGATCAATTTCAGTCCTTGTACTTTTTAAA
1 TGATCAATTTCAGTCCTTATACTTTTTAAA
61793485 TTTCAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (31 bp):
TGATCAATTTCAGTCCTTATACTTTTTAAAA
Found at i:61804042 original size:26 final size:26
Alignment explanation
Indices: 61804006--61804063 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
61803996 AAATAAATTT
61804006 AAATTGGATTGTCACATAGGACATCC
1 AAATTGGATTGTCACATAGGACATCC
*
61804032 AAATTGGATTGTCACATAGGACATCT
1 AAATTGGATTGTCACATAGGACATCC
61804058 AAATTG
1 AAATTG
61804064 ACATTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (26 bp):
AAATTGGATTGTCACATAGGACATCC
Found at i:61807662 original size:22 final size:23
Alignment explanation
Indices: 61807637--61807679 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
61807627 AAATTGGTCT
61807637 TTCAAAA-AAATTACAAAAATAA
1 TTCAAAATAAATTACAAAAATAA
* *
61807659 TTCAAAATAATTTTCAAAAAT
1 TTCAAAATAAATTACAAAAAT
61807680 TCAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.30
Consensus pattern (23 bp):
TTCAAAATAAATTACAAAAATAA
Found at i:61807696 original size:19 final size:20
Alignment explanation
Indices: 61807657--61807706 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
61807647 TTACAAAAAT
61807657 AATTCAAAATAATTTTCAAA
1 AATTCAAAATAATTTTCAAA
61807677 AATTCAAAAT-ATTTAT-AAA
1 AATTCAAAATAATTT-TCAAA
61807696 AATTTCAAAAT
1 AA-TTCAAAAT
61807707 TTATATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.32
20 19 0.68
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTCAAAATAATTTTCAAA
Found at i:61811292 original size:24 final size:24
Alignment explanation
Indices: 61811252--61811299 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
61811242 TAGCTGGCAT
61811252 TGAAGGAGGAGGAGGAGGTGGTGG
1 TGAAGGAGGAGGAGGAGGTGGTGG
*
61811276 TGAAGGCAGG-GGTGGAGGTGGTGG
1 TGAAGG-AGGAGGAGGAGGTGGTGG
61811300 AAATGGAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.21, C:0.02, G:0.62, T:0.15
Consensus pattern (24 bp):
TGAAGGAGGAGGAGGAGGTGGTGG
Found at i:61811420 original size:6 final size:6
Alignment explanation
Indices: 61811409--61811437 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
61811399 GGGATTTGGT
61811409 ATGGGA ATGGGA ATGGGA ATGGGA ATGGG
1 ATGGGA ATGGGA ATGGGA ATGGGA ATGGG
61811438 CATTGGGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.52, T:0.17
Consensus pattern (6 bp):
ATGGGA
Found at i:61811934 original size:2 final size:2
Alignment explanation
Indices: 61811927--61811957 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
61811917 CACATACAAC
61811927 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
61811958 CAAAATAAAA
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:61813978 original size:2 final size:2
Alignment explanation
Indices: 61813966--61814011 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
61813956 TAAAGAAGCC
* * * *
61813966 AT AT GT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61814008 AT AT
1 AT AT
61814012 GAAAAAAAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61840927 original size:22 final size:23
Alignment explanation
Indices: 61840901--61840943 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
61840891 GAAAAATATT
*
61840901 AAATAT-ATATTTTTTATTTTTA
1 AAATATAATAGTTTTTATTTTTA
61840923 AAATATAATAGTTTTTATTTT
1 AAATATAATAGTTTTTATTTT
61840944 AAGTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
AAATATAATAGTTTTTATTTTTA
Found at i:61841152 original size:16 final size:16
Alignment explanation
Indices: 61841131--61841172 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
61841121 AATAATTTGA
*
61841131 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
61841147 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
61841163 TAGTTTTAAT
1 TAATTTTAAT
61841173 TTTATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:61841156 original size:22 final size:23
Alignment explanation
Indices: 61841146--61841208 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
61841136 TTACTAACAA
* * *
61841146 TTAATTTTA-ATAACAATTAGTT
1 TTAATTTTATATAAAAAATAATT
*
61841168 TTAATTTTATTTAAAAAATAATT
1 TTAATTTTATATAAAAAATAATT
*
61841191 TTAATTTTA-ATTAAAAAT
1 TTAATTTTATATAAAAAAT
61841209 GGGCCGGGCC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 16 0.47
23 18 0.53
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
TTAATTTTATATAAAAAATAATT
Found at i:61846622 original size:38 final size:38
Alignment explanation
Indices: 61846577--61846652 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
61846567 TTTATTTTAA
* *
61846577 TTTTTATTTAAAGTTATATTAATTTGCGCCACTAATTT
1 TTTTTATTTAAAGTTATACTAATTTGAGCCACTAATTT
*
61846615 TTTTTATTTAAAGTTATACTAATTTTAGCCACTAATTT
1 TTTTTATTTAAAGTTATACTAATTTGAGCCACTAATTT
61846653 ATGCCAATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.53
Consensus pattern (38 bp):
TTTTTATTTAAAGTTATACTAATTTGAGCCACTAATTT
Found at i:61846864 original size:29 final size:29
Alignment explanation
Indices: 61846826--61846882 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
61846816 ACGTTTACTG
61846826 TTCAAAATAGGTCATTTACGTAAATAATT
1 TTCAAAATAGGTCATTTACGTAAATAATT
* **
61846855 TTCAAAATAGGTTATTTGTGTAAATAAT
1 TTCAAAATAGGTCATTTACGTAAATAAT
61846883 CAAAAGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (29 bp):
TTCAAAATAGGTCATTTACGTAAATAATT
Found at i:61847025 original size:30 final size:31
Alignment explanation
Indices: 61846977--61847034 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
61846967 TTCATTTCAG
*
61846977 TCACTCAACTTTTGAAAAA-TAACAAAACAA
1 TCACTCAACTTTTAAAAAAGTAACAAAACAA
61847007 TCACT-AACTTTATAAAAAAGTAACAAAA
1 TCACTCAACTTT-TAAAAAAGTAACAAAA
61847035 TAGTCACTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 6 0.24
30 11 0.44
31 8 0.32
ACGTcount: A:0.55, C:0.17, G:0.03, T:0.24
Consensus pattern (31 bp):
TCACTCAACTTTTAAAAAAGTAACAAAACAA
Found at i:61847042 original size:31 final size:30
Alignment explanation
Indices: 61846974--61847042 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 30
61846964 GGTTTCATTT
*
61846974 CAGTCACTCAACTTTTGAAAAATAACAAAA
1 CAGTCACTCAACTTTTAAAAAATAACAAAA
*
61847004 CAATCACT-AACTTTATAAAAAAGTAACAAAA
1 CAGTCACTCAACTTT-TAAAAAA-TAACAAAA
*
61847035 TAGTCACT
1 CAGTCACT
61847043 GATTAACAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 6 0.18
30 13 0.39
31 14 0.42
ACGTcount: A:0.51, C:0.19, G:0.06, T:0.25
Consensus pattern (30 bp):
CAGTCACTCAACTTTTAAAAAATAACAAAA
Found at i:61852589 original size:39 final size:39
Alignment explanation
Indices: 61852546--61852623 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
61852536 TACCAATCAA
61852546 AGCTCACATTCCCTTTTGTCCACAATTTAGTTTTTCCTT
1 AGCTCACATTCCCTTTTGTCCACAATTTAGTTTTTCCTT
61852585 AGCTCACATTCCCTTTTGTCCACAATTTAGTTTTTCCTT
1 AGCTCACATTCCCTTTTGTCCACAATTTAGTTTTTCCTT
61852624 TTATGAAACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.18, C:0.28, G:0.08, T:0.46
Consensus pattern (39 bp):
AGCTCACATTCCCTTTTGTCCACAATTTAGTTTTTCCTT
Found at i:61857419 original size:40 final size:40
Alignment explanation
Indices: 61857375--61857454 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
61857365 ACCGCACCGC
61857375 ACCGTGCACCTAATTGCCCATCTAAACCCACCCTTAATGT
1 ACCGTGCACCTAATTGCCCATCTAAACCCACCCTTAATGT
61857415 ACCGTGCACCTAATTGCCCATCTAAACCCACCCTTAATGT
1 ACCGTGCACCTAATTGCCCATCTAAACCCACCCTTAATGT
61857455 TCTCTTACAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.38, G:0.10, T:0.25
Consensus pattern (40 bp):
ACCGTGCACCTAATTGCCCATCTAAACCCACCCTTAATGT
Found at i:61864482 original size:23 final size:21
Alignment explanation
Indices: 61864440--61864482 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
61864430 TATACACTAC
* *
61864440 ATTTTAAATATTTTTTAAGTA
1 ATTTTAAATATTTGTAAAGTA
61864461 ATTTATAAATTATTTGTAAAGT
1 ATTT-TAAA-TATTTGTAAAGT
61864483 TAATGATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 4 0.22
23 10 0.56
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (21 bp):
ATTTTAAATATTTGTAAAGTA
Found at i:61876267 original size:27 final size:28
Alignment explanation
Indices: 61876213--61876267 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
61876203 ATGTTATCCT
*
61876213 TTTTTTTATTTACCAAAATATTATAAAA
1 TTTTTTTATTTACCAAAATATTACAAAA
61876241 TTTTTTTATTTACCAAAATA-TACAAAA
1 TTTTTTTATTTACCAAAATATTACAAAA
61876268 ACAAAAACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (28 bp):
TTTTTTTATTTACCAAAATATTACAAAA
Found at i:61876349 original size:27 final size:26
Alignment explanation
Indices: 61876319--61876378 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
61876309 GGCCAATCAC
*
61876319 ATTGGCGGCACCAAAGGCGCCAAAGTG
1 ATTGGCGG-ACCAAAGGCGCCAAAGAG
* *
61876346 ATTGGCCTGACCAAAGGTGCCAAAGAG
1 ATTGG-CGGACCAAAGGCGCCAAAGAG
61876373 ATTGGC
1 ATTGGC
61876379 CTGACCGGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 1 0.03
27 26 0.90
28 2 0.07
ACGTcount: A:0.30, C:0.23, G:0.32, T:0.15
Consensus pattern (26 bp):
ATTGGCGGACCAAAGGCGCCAAAGAG
Found at i:61876379 original size:27 final size:27
Alignment explanation
Indices: 61876328--61876384 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
61876318 CATTGGCGGC
*
61876328 ACCAAAGGCGCCAAAGTGATTGGCCTG
1 ACCAAAGGCGCCAAAGAGATTGGCCTG
*
61876355 ACCAAAGGTGCCAAAGAGATTGGCCTG
1 ACCAAAGGCGCCAAAGAGATTGGCCTG
61876382 ACC
1 ACC
61876385 GGATTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.32, C:0.26, G:0.28, T:0.14
Consensus pattern (27 bp):
ACCAAAGGCGCCAAAGAGATTGGCCTG
Found at i:61877318 original size:27 final size:27
Alignment explanation
Indices: 61877288--61877344 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
61877278 ATTTTAGTCC
* *
61877288 GGTCAGGCCAATCTCTTTTGCACCTTT
1 GGTCAGGCCAATCACTTTGGCACCTTT
61877315 GGTCAGGCCAATCACTTTGGCACCTTT
1 GGTCAGGCCAATCACTTTGGCACCTTT
61877342 GGT
1 GGT
61877345 GCCGCCAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.16, C:0.28, G:0.23, T:0.33
Consensus pattern (27 bp):
GGTCAGGCCAATCACTTTGGCACCTTT
Found at i:61877351 original size:27 final size:27
Alignment explanation
Indices: 61877288--61877353 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
61877278 ATTTTAGTCC
* * *
61877288 GGTCAGGCCAATCTCTTTTGCACCTTT
1 GGTCACGCCAATCACTTTGGCACCTTT
*
61877315 GGTCAGGCCAATCACTTTGGCACCTTT
1 GGTCACGCCAATCACTTTGGCACCTTT
61877342 GGTGC-CGCCAAT
1 GGT-CACGCCAAT
61877354 GTGATTGGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 34 0.97
28 1 0.03
ACGTcount: A:0.17, C:0.30, G:0.23, T:0.30
Consensus pattern (27 bp):
GGTCACGCCAATCACTTTGGCACCTTT
Found at i:61877451 original size:28 final size:28
Alignment explanation
Indices: 61877395--61877460 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
61877385 TTTTTTTGGT
* ***
61877395 ATATTTTGATAAATAAAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAAGGGATA
61877423 ATATTTTGGTAAATAAAAAAAAGGGATA
1 ATATTTTGGTAAATAAAAAAAAGGGATA
*
61877451 ACATTTTGGT
1 ATATTTTGGT
61877461 TATTTTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGGGATA
Found at i:61881183 original size:12 final size:11
Alignment explanation
Indices: 61881146--61881185 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
61881136 TTCACACACT
61881146 ATTTCT-TCAA
1 ATTTCTCTCAA
*
61881156 TTTTCTCTCAA
1 ATTTCTCTCAA
61881167 ATTTCTCTCTAA
1 ATTTCTCTC-AA
61881179 ATTTCTC
1 ATTTCTC
61881186 AAAGCTCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 5 0.19
11 12 0.46
12 9 0.35
ACGTcount: A:0.23, C:0.25, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTTCTCTCAA
Found at i:61883248 original size:24 final size:24
Alignment explanation
Indices: 61883221--61883276 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
61883211 CATTTAATAA
*
61883221 AATAAAAGTTGTTTTTCATA-TTTT
1 AATAAAAGTTATTTTT-ATATTTTT
* *
61883245 AATAGTAATTTATTTTTATATTTTT
1 AATA-AAAGTTATTTTTATATTTTT
61883270 AATAAAA
1 AATAAAA
61883277 TAAAAGTTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
24 9 0.35
25 17 0.65
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (24 bp):
AATAAAAGTTATTTTTATATTTTT
Found at i:61886695 original size:126 final size:126
Alignment explanation
Indices: 61886470--61887098 Score: 1010
Period size: 126 Copynumber: 5.0 Consensus size: 126
61886460 CTAGGGTCAA
*
61886470 TCAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTAGTAATTTTGCTGACAGTG
1 TCAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTG
*
61886535 CATCCTACTTGAAGCGTTTTTTACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTT
66 CATCCTACTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTT
* * * *
61886596 TCAGGAGCTACTGTAGAAAAACAGCATCCACGTGGGAGCTTTTTTCAGTAATTTTGCTAACAGTG
1 TCAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTG
** *
61886661 CATCCTGTTTGAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTT
66 CATCCTACTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTT
**
61886722 TCAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTATTGACAGTG
1 TCAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTG
* ** *
61886787 CATTCTACTTGAAATGTTTTTGACACTATTTGTTCATAACCGTCTTCTCAAAATTATTTTT
66 CATCCTACTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTT
* *
61886848 TTAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACATTG
1 TCAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTG
*
61886913 CATCCTACTTGAAGCGTTTTT-AAACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTT
66 CATCCTACTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTT
* * * *
61886973 TCAGGAACTACTATAGAAAAAGAGCATCCACGCGGGAGCTTTTTTCAGTAATTTTGCTAACAGTG
1 TCAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTG
* * *
61887038 CATCCTGCTTGAAGCGTTTTTTACATTATCTT-TTCAGAACCGTCTTCTCAAAATTATTTTT
66 CATCCTACTTGAAGCGTTTTTGACACTAT-TTGTTCAGAACCGTCTTCTCAAAATTATTTTT
61887099 CAGATACTAT
Statistics
Matches: 461, Mismatches: 40, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
125 116 0.25
126 343 0.74
127 2 0.00
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.37
Consensus pattern (126 bp):
TCAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTG
CATCCTACTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTT
Found at i:61887220 original size:34 final size:34
Alignment explanation
Indices: 61887182--61887246 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
61887172 TTAAAAAAAA
61887182 CTAAACTATAATTTAAATAATTT-TCTTAAAAACC
1 CTAAACTATAATTTAAATAATTTAT-TTAAAAACC
* *
61887216 CTAAACTCTAATTTAATTAATTTATTTAAAA
1 CTAAACTATAATTTAAATAATTTATTTAAAA
61887247 TTTCAAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.96
35 1 0.04
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (34 bp):
CTAAACTATAATTTAAATAATTTATTTAAAAACC
Found at i:61888810 original size:87 final size:87
Alignment explanation
Indices: 61888664--61888832 Score: 329
Period size: 87 Copynumber: 1.9 Consensus size: 87
61888654 AAGTGCTAAG
61888664 ATTGTAGTGAAGAGAGCTATGTTGGCATGGGACACCATGCTCATGCACACCCAAAGAGGATCGGA
1 ATTGTAGTGAAGAGAGCTATGTTGGCATGGGACACCATGCTCATGCACACCCAAAGAGGATCGGA
61888729 GTTTCGGAGTTCCGAGAGTTAA
66 GTTTCGGAGTTCCGAGAGTTAA
61888751 ATTGTAGTGAAGAGAGCTATGTTGGCATGGGACACCATGCTCATGCACACCCAAAGAGGATCGGA
1 ATTGTAGTGAAGAGAGCTATGTTGGCATGGGACACCATGCTCATGCACACCCAAAGAGGATCGGA
*
61888816 GTTTTGGAGTTCCGAGA
66 GTTTCGGAGTTCCGAGA
61888833 TGTTTAACTC
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.23
Consensus pattern (87 bp):
ATTGTAGTGAAGAGAGCTATGTTGGCATGGGACACCATGCTCATGCACACCCAAAGAGGATCGGA
GTTTCGGAGTTCCGAGAGTTAA
Found at i:61893164 original size:4 final size:4
Alignment explanation
Indices: 61893155--61893195 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
61893145 TTTCATCTCT
*
61893155 TACA TACA TACA TACA TGCA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T
61893196 TAAAATGGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.46, C:0.24, G:0.02, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:61896501 original size:31 final size:31
Alignment explanation
Indices: 61896466--61896533 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
61896456 TTACCATCGT
*
61896466 AGTGACTTAAATAAAAACTTTTGAATAGTTC
1 AGTGACTTAAATAAAAACTTCTGAATAGTTC
*
61896497 AGTGACTTAAATGAAAACTTCTGAATAGTTC
1 AGTGACTTAAATAAAAACTTCTGAATAGTTC
*
61896528 AATGAC
1 AGTGAC
61896534 CAAATTGCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (31 bp):
AGTGACTTAAATAAAAACTTCTGAATAGTTC
Found at i:61898189 original size:2 final size:2
Alignment explanation
Indices: 61898182--61898210 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
61898172 TGAAATTTTA
61898182 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
61898211 CCCAATATTA
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:61899253 original size:15 final size:15
Alignment explanation
Indices: 61899229--61899261 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
61899219 TTATTCTATA
61899229 AATTAGTATATTGAG
1 AATTAGTATATTGAG
*
61899244 AATTATTATATTGAG
1 AATTAGTATATTGAG
61899259 AAT
1 AAT
61899262 GCCTTTCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (15 bp):
AATTAGTATATTGAG
Found at i:61904250 original size:18 final size:17
Alignment explanation
Indices: 61904217--61904250 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
61904207 GTTATTAAAT
*
61904217 TTAAAACAATATATATC
1 TTAAAACAACATATATC
61904234 TTAAAACATACATATAT
1 TTAAAACA-ACATATAT
61904251 ATGATCTAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAACAACATATATC
Found at i:61904971 original size:2 final size:2
Alignment explanation
Indices: 61904964--61905000 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
61904954 CCTATATCAT
*
61904964 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
61905001 CGTTGTTCTA
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:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:61905272 original size:6 final size:6
Alignment explanation
Indices: 61905261--61905289 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
61905251 CAACCAACCC
61905261 CGCAAG CGCAAG CGCAAG CGCAAG CGCAA
1 CGCAAG CGCAAG CGCAAG CGCAAG CGCAA
61905290 CCTCAACCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.34, G:0.31, T:0.00
Consensus pattern (6 bp):
CGCAAG
Found at i:61908587 original size:22 final size:23
Alignment explanation
Indices: 61908535--61908579 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
61908525 TATCTTTATT
61908535 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAATTATAAAAATATA
61908557 TAAATATTAA-TATAAAAATATA
1 TAAATATTAATTATAAAAATATA
61908579 T
1 T
61908580 TTTTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAATATTAATTATAAAAATATA
Found at i:61914243 original size:24 final size:24
Alignment explanation
Indices: 61914216--61914262 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
61914206 TTGGCTATGC
61914216 AGGAAAAAGCAAGAACACATTGCA
1 AGGAAAAAGCAAGAACACATTGCA
61914240 AGGAAAAAGCAAGAACACATTGC
1 AGGAAAAAGCAAGAACACATTGC
61914263 CAATAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.53, C:0.17, G:0.21, T:0.09
Consensus pattern (24 bp):
AGGAAAAAGCAAGAACACATTGCA
Found at i:61919808 original size:12 final size:12
Alignment explanation
Indices: 61919791--61919817 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
61919781 AAAAGACACA
61919791 AGTGACTATTTG
1 AGTGACTATTTG
61919803 AGTGACTATTTG
1 AGTGACTATTTG
61919815 AGT
1 AGT
61919818 AGAGGTGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (12 bp):
AGTGACTATTTG
Found at i:61920031 original size:10 final size:11
Alignment explanation
Indices: 61920005--61920030 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
61919995 TTTAAAAATA
61920005 AAAAATATTTT
1 AAAAATATTTT
61920016 AAAAATATTTT
1 AAAAATATTTT
61920027 AAAA
1 AAAA
61920031 TTTAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:61936067 original size:30 final size:30
Alignment explanation
Indices: 61936033--61936139 Score: 130
Period size: 29 Copynumber: 3.6 Consensus size: 30
61936023 AATAAATACC
*
61936033 AAAAAATTATTTTAAAAATTAAAAAAAATT
1 AAAAAAGTATTTTAAAAATTAAAAAAAATT
*
61936063 AAAAAA-TATATTTTAAAATT-AAAAAAATT
1 AAAAAAGTAT-TTTAAAAATTAAAAAAAATT
**
61936092 -AAAAAGTATTTTAAAAAATTTAAAAAATTTT
1 AAAAAAGTATTTT-AAAAA-TTAAAAAAAATT
61936123 AAAAAAGTATTTTAAAA
1 AAAAAAGTATTTTAAAA
61936140 GTATTTTAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
28 8 0.12
29 19 0.28
30 17 0.25
31 11 0.16
32 12 0.18
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (30 bp):
AAAAAAGTATTTTAAAAATTAAAAAAAATT
Found at i:61936086 original size:29 final size:29
Alignment explanation
Indices: 61936033--61936139 Score: 112
Period size: 30 Copynumber: 3.6 Consensus size: 29
61936023 AATAAATACC
61936033 AAAAAAT-TATTTTAAAAATTAAAAAAAATT
1 AAAAAATATATTTT-AAAATT-AAAAAAATT
61936063 AAAAAATATATTTTAAAATTAAAAAAATT
1 AAAAAATATATTTTAAAATTAAAAAAATT
* * *
61936092 AAAAAGTAT-TTTAAAAAATTTAAAAAATTTT
1 AAAAAATATATTT-TAAAA-TTAAAAAA-ATT
*
61936123 AAAAAA-GTATTTTAAAA
1 AAAAAATATATTTTAAAA
61936140 GTATTTTAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
28 3 0.05
29 21 0.32
30 26 0.39
31 16 0.24
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAAAATATATTTTAAAATTAAAAAAATT
Found at i:61936107 original size:20 final size:19
Alignment explanation
Indices: 61936081--61936128 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 19
61936071 TATTTTAAAA
*
61936081 TTAAAAAAATTAAAAAGTATT
1 TTAAAAAATTTAAAAA--ATT
61936102 TTAAAAAATTTAAAAAATT
1 TTAAAAAATTTAAAAAATT
61936121 TTAAAAAA
1 TTAAAAAA
61936129 GTATTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 11 0.42
21 15 0.58
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
TTAAAAAATTTAAAAAATT
Found at i:61936121 original size:9 final size:9
Alignment explanation
Indices: 61936077--61936128 Score: 52
Period size: 9 Copynumber: 5.4 Consensus size: 9
61936067 AATATATTTT
61936077 AAAA-TTAA
1 AAAATTTAA
*
61936085 AAAAATTAA
1 AAAATTTAA
61936094 AAAGTATTTTAA
1 AAA--A-TTTAA
61936106 AAAATTTAA
1 AAAATTTAA
61936115 AAAATTTTAA
1 AAAA-TTTAA
61936125 AAAA
1 AAAA
61936129 GTATTTTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
8 4 0.11
9 16 0.42
10 10 0.26
11 1 0.03
12 7 0.18
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAATTTAA
Found at i:61936139 original size:11 final size:11
Alignment explanation
Indices: 61936093--61936150 Score: 59
Period size: 11 Copynumber: 5.4 Consensus size: 11
61936083 AAAAAAATTA
61936093 AAAAGTATTTT
1 AAAAGTATTTT
*
61936104 AAAA--AATTT
1 AAAAGTATTTT
*
61936113 AAAA-AATTTT
1 AAAAGTATTTT
61936123 AAAAAAGTATTTT
1 --AAAAGTATTTT
61936136 AAAAGTATTTT
1 AAAAGTATTTT
61936147 AAAA
1 AAAA
61936151 TAAAAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 8 0.20
10 4 0.10
11 19 0.47
12 4 0.10
13 5 0.12
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:61940624 original size:37 final size:38
Alignment explanation
Indices: 61940573--61940649 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 38
61940563 TTACCCACAT
* * *
61940573 AATACTCCGACATGTATACATCTCATTATTTCCCTTTG
1 AATACTCCCACATGTATACATCTCATTAATTCCCTCTG
*
61940611 AATAC-CCCACATGTATGCATCTCATTAATTCCCTCTG
1 AATACTCCCACATGTATACATCTCATTAATTCCCTCTG
61940648 AA
1 AA
61940650 AACTTGGATC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
37 30 0.86
38 5 0.14
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.35
Consensus pattern (38 bp):
AATACTCCCACATGTATACATCTCATTAATTCCCTCTG
Found at i:61941711 original size:2 final size:2
Alignment explanation
Indices: 61941704--61941737 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
61941694 TACTTGCTTG
61941704 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
61941738 TACAACGTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61945814 original size:24 final size:24
Alignment explanation
Indices: 61945753--61945801 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
61945743 TGAAAAGAAT
61945753 GGACAAAACCCACACAAGACATAA
1 GGACAAAACCCACACAAGACATAA
61945777 GGACAAAACCCACACAAGACATAA
1 GGACAAAACCCACACAAGACATAA
61945801 G
1 G
61945802 AGAAACCTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.29, G:0.14, T:0.04
Consensus pattern (24 bp):
GGACAAAACCCACACAAGACATAA
Found at i:61945987 original size:16 final size:16
Alignment explanation
Indices: 61945966--61946005 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
61945956 GTAAATATAT
61945966 TTGGGCCTTATTGGGC
1 TTGGGCCTTATTGGGC
*
61945982 TTGGGCCTTGTTGGGC
1 TTGGGCCTTATTGGGC
61945998 TTGGGCCT
1 TTGGGCCT
61946006 ATTAAGTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.03, C:0.20, G:0.40, T:0.38
Consensus pattern (16 bp):
TTGGGCCTTATTGGGC
Found at i:61946629 original size:37 final size:37
Alignment explanation
Indices: 61946588--61946661 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
61946578 TCATTATATT
* * * *
61946588 TCATCATTCGAATGTTAGATGATTTATTTTAGATTAA
1 TCATCATTAGAACGTCAAATGATTTATTTTAGATTAA
61946625 TCATCATTAGAACGTCAAATGATTTATTTTAGATTAA
1 TCATCATTAGAACGTCAAATGATTTATTTTAGATTAA
61946662 AATTTAATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.43
Consensus pattern (37 bp):
TCATCATTAGAACGTCAAATGATTTATTTTAGATTAA
Found at i:61947494 original size:68 final size:68
Alignment explanation
Indices: 61947385--61947522 Score: 276
Period size: 68 Copynumber: 2.0 Consensus size: 68
61947375 ACAAGACTCA
61947385 AACTCGTGACTTTACTTAAAGAAAATCAAGTTCCTTATCACTCGACGCAGCATTTTAAATTTACA
1 AACTCGTGACTTTACTTAAAGAAAATCAAGTTCCTTATCACTCGACGCAGCATTTTAAATTTACA
61947450 TCC
66 TCC
61947453 AACTCGTGACTTTACTTAAAGAAAATCAAGTTCCTTATCACTCGACGCAGCATTTTAAATTTACA
1 AACTCGTGACTTTACTTAAAGAAAATCAAGTTCCTTATCACTCGACGCAGCATTTTAAATTTACA
61947518 TCC
66 TCC
61947521 AA
1 AA
61947523 TTCATTCAAC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (68 bp):
AACTCGTGACTTTACTTAAAGAAAATCAAGTTCCTTATCACTCGACGCAGCATTTTAAATTTACA
TCC
Found at i:61952033 original size:31 final size:31
Alignment explanation
Indices: 61951938--61952036 Score: 96
Period size: 31 Copynumber: 3.2 Consensus size: 31
61951928 ATTAAGAGGA
*
61951938 TTAATAAATTTTGA-AGGATATAATTAAAATT
1 TTAA-AAATTTTGAGAGGACATAATTAAAATT
** * *
61951969 TTAAAACCTTTG-GAAGG-CGTAATTAGAATTT
1 TTAAAAATTTTGAG-AGGACATAATTA-AAATT
*
61952000 TTAAAAATTTTGAGAGGACCTAATTAAAATT
1 TTAAAAATTTTGAGAGGACATAATTAAAATT
61952031 TTAAAA
1 TTAAAA
61952037 TGCTTATTGT
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
30 12 0.22
31 34 0.63
32 8 0.15
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.37
Consensus pattern (31 bp):
TTAAAAATTTTGAGAGGACATAATTAAAATT
Found at i:61954634 original size:2 final size:2
Alignment explanation
Indices: 61954627--61954669 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
61954617 TTGCCTGTGA
*
61954627 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61954669 A
1 A
61954670 ATGCTTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.