Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016255.1 Corchorus olitorius cultivar O-4 contig16288, whole genome shotgun sequence
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: 275281
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:24753 original size:31 final size:28
Alignment explanation
Indices: 24718--24779 Score: 97
Period size: 31 Copynumber: 2.1 Consensus size: 28
24708 ATTTCTTACT
24718 AAAGTAAAAACTCTCTTTGTGCCAAAAAAAA
1 AAAGTAAAAACTCTC-TTGT--CAAAAAAAA
24749 AAAGTAAAAACTCTCTTGTCAAAAAAAA
1 AAAGTAAAAACTCTCTTGTCAAAAAAAA
24777 AAA
1 AAA
24780 TAGAACTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 12 0.39
30 4 0.13
31 15 0.48
ACGTcount: A:0.56, C:0.15, G:0.08, T:0.21
Consensus pattern (28 bp):
AAAGTAAAAACTCTCTTGTCAAAAAAAA
Found at i:27319 original size:11 final size:11
Alignment explanation
Indices: 27295--27329 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
27285 TTTACAGCGC
27295 AACAAAAACAA
1 AACAAAAACAA
* *
27306 AACGAAAACGA
1 AACAAAAACAA
27317 AACAAAAACAA
1 AACAAAAACAA
27328 AA
1 AA
27330 AATAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:29949 original size:2 final size:2
Alignment explanation
Indices: 29942--29974 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29932 ATCTCATTAC
29942 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29975 GACACACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31673 original size:2 final size:2
Alignment explanation
Indices: 31668--31721 Score: 83
Period size: 2 Copynumber: 27.0 Consensus size: 2
31658 AGGTTGATAC
*
31668 TA TA TA GTA T- TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31710 TA TA TA TA TA TA
1 TA TA TA TA TA TA
31722 GTAGCTACCG
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 1 0.02
2 45 0.94
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:32013 original size:41 final size:41
Alignment explanation
Indices: 31968--32047 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
31958 AATTGTCCCT
* *
31968 CCTAATAATTAAGGAAATAAATTAAATCCAGGTTTAGCCAC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAAGTTTAGCCAC
* *
32009 CCTAATAATTAAGGTAAGAAATTAAATCCAATTTTAGCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAAGTTTAGCC
32048 CCTAGTTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (41 bp):
CCTAATAATTAAGGAAAGAAATTAAATCCAAGTTTAGCCAC
Found at i:32435 original size:2 final size:2
Alignment explanation
Indices: 32428--32458 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
32418 TATTTGCTAA
32428 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
32459 CATGGAGAGT
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:52005 original size:27 final size:27
Alignment explanation
Indices: 51967--52021 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
51957 ATAATATCCT
51967 TCCATTTAATTTAGCAGCGCCTTAGGA
1 TCCATTTAATTTAGCAGCGCCTTAGGA
51994 TCCATTTAATTTAGCAGCGCCTTAGGA
1 TCCATTTAATTTAGCAGCGCCTTAGGA
52021 T
1 T
52022 GACATAACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (27 bp):
TCCATTTAATTTAGCAGCGCCTTAGGA
Found at i:62320 original size:11 final size:11
Alignment explanation
Indices: 62304--62332 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
62294 TTAACAACGC
62304 AATAAAAACAA
1 AATAAAAACAA
62315 AATAAAAACAA
1 AATAAAAACAA
62326 AA-AAAAA
1 AATAAAAA
62333 GTGAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (11 bp):
AATAAAAACAA
Found at i:71831 original size:1 final size:1
Alignment explanation
Indices: 71825--71857 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
71815 TAATTACAAG
71825 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
71858 ATCTTATTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:78486 original size:6 final size:6
Alignment explanation
Indices: 78475--78514 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
78465 TTCAGGTATA
*
78475 TTTTCT TTTTCT TTTTCT TTTTC- TTTTCT CTGTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT -TTTTCT TTTT
78515 TTCCTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.17
6 20 0.67
7 5 0.17
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:94169 original size:28 final size:30
Alignment explanation
Indices: 94100--94175 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 30
94090 ATACTGTACA
* *
94100 GGTCCCTCTATTTACAAAAAGGGATCAATTT
1 GGTCCCTCTA-CTACAAAAACGGATCAATTT
* *
94131 GGTCCCCCTACTACAAAAACTG-TCAA-TT
1 GGTCCCTCTACTACAAAAACGGATCAATTT
94159 GGTCCCTCTACTTACAA
1 GGTCCCTCTAC-TACAA
94176 TTTGGTGTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
28 12 0.31
29 9 0.23
30 9 0.23
31 9 0.23
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (30 bp):
GGTCCCTCTACTACAAAAACGGATCAATTT
Found at i:94538 original size:30 final size:30
Alignment explanation
Indices: 94471--94543 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 30
94461 TACCAAATTG
94471 TAAGTAGAGGGACCAAATTGACAGTTTTTA
1 TAAGTAGAGGGACCAAATTGACAGTTTTTA
***
94501 T-AGTAGAGGGACCAAATTGATTTTTTTTA
1 TAAGTAGAGGGACCAAATTGACAGTTTTTA
94530 TAAGTAGAGGGACC
1 TAAGTAGAGGGACC
94544 TGTACGGTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
29 26 0.67
30 13 0.33
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.32
Consensus pattern (30 bp):
TAAGTAGAGGGACCAAATTGACAGTTTTTA
Found at i:97741 original size:3 final size:3
Alignment explanation
Indices: 97735--97769 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
97725 TTTTGAAAAA
97735 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
97770 AACATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:105246 original size:6 final size:6
Alignment explanation
Indices: 105237--105263 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
105227 GAAAATAGCG
105237 GTACTA GTACTA GTACTA GTACTA GTA
1 GTACTA GTACTA GTACTA GTACTA GTA
105264 TAAATTTGTC
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:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (6 bp):
GTACTA
Found at i:108385 original size:10 final size:10
Alignment explanation
Indices: 108372--108406 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
108362 CGAATATTAA
108372 TATATATAAT
1 TATATATAAT
108382 TATATATGATAT
1 TATATAT-A-AT
108394 TATATATAAT
1 TATATATAAT
108404 TAT
1 TAT
108407 TAAACGGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 12 0.52
11 2 0.09
12 9 0.39
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (10 bp):
TATATATAAT
Found at i:108388 original size:12 final size:11
Alignment explanation
Indices: 108365--108406 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
108355 AACCGGTCGA
108365 ATATTAATATAT
1 ATATT-ATATAT
108377 ATAATTATATAT
1 AT-ATTATATAT
108389 GATATTATATAT
1 -ATATTATATAT
108401 A-ATTAT
1 ATATTAT
108407 TAAACGGTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 5 0.18
11 1 0.04
12 17 0.61
13 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (11 bp):
ATATTATATAT
Found at i:128301 original size:74 final size:74
Alignment explanation
Indices: 128126--128637 Score: 885
Period size: 74 Copynumber: 7.0 Consensus size: 74
128116 ACCCTGAGTT
128126 TATGCAAAGTAGAATCATCTTGTCCTACATTTTATCTATTTTCTATCACCATTTCCTAC-----T
1 TATGCAAAGTAGAATCATCTTGTCCTACATTTTATCTATTTTCTATCACCATTTCCTACTTAGGT
128186 TAGAAGATA
66 TAGAAGATA
*
128195 TATGCAAAGTAGAATCATCTTGTCCTACATTTTATCTAATTTCTATCACCATTTCCTACTTAGGT
1 TATGCAAAGTAGAATCATCTTGTCCTACATTTTATCTATTTTCTATCACCATTTCCTACTTAGGT
128260 TAGAAGATA
66 TAGAAGATA
*
128269 TATGCAAAGTAGAATCATCTTGTCCTACATTTTATCTAATTTCTATCACCATTTCCTACTTAGGT
1 TATGCAAAGTAGAATCATCTTGTCCTACATTTTATCTATTTTCTATCACCATTTCCTACTTAGGT
128334 TAGAAGATA
66 TAGAAGATA
*
128343 TATGCAAAGTAGAATCATCTTGTCCTACATTTTATCTAATTTCTATCACCATTTCCTACTTAGGT
1 TATGCAAAGTAGAATCATCTTGTCCTACATTTTATCTATTTTCTATCACCATTTCCTACTTAGGT
128408 TAGAAGATA
66 TAGAAGATA
* *
128417 TGTGCAAAGTAGAATCATCTTGTCCTACATTTTATCTATTTTCTATTACCATTTCCTAC-TACGG
1 TATGCAAAGTAGAATCATCTTGTCCTACATTTTATCTATTTTCTATCACCATTTCCTACTTA-GG
128481 TTAGAAGATA
65 TTAGAAGATA
*
128491 TATGCAAAGTAGAATCATCTTGTCCTACATTTTACCTATTTTCTATCACCATTTCCTACTTAGGT
1 TATGCAAAGTAGAATCATCTTGTCCTACATTTTATCTATTTTCTATCACCATTTCCTACTTAGGT
128556 TAGAAGATA
66 TAGAAGATA
* *
128565 TATGCAAAGTAGAATCATCTTGTCCTACATTTTATCTATTTTCTATTACCA-TTCCTACTTAGCT
1 TATGCAAAGTAGAATCATCTTGTCCTACATTTTATCTATTTTCTATCACCATTTCCTACTTAGGT
*
128629 TAGTAGATA
66 TAGAAGATA
128638 CAGAGGGAAC
Statistics
Matches: 425, Mismatches: 11, Indels: 10
0.95 0.02 0.02
Matches are distributed among these distances:
69 58 0.14
73 22 0.05
74 343 0.81
75 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (74 bp):
TATGCAAAGTAGAATCATCTTGTCCTACATTTTATCTATTTTCTATCACCATTTCCTACTTAGGT
TAGAAGATA
Found at i:131137 original size:15 final size:15
Alignment explanation
Indices: 131117--131147 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
131107 AAATTACATC
131117 CGCTCAATAAAAGAA
1 CGCTCAATAAAAGAA
*
131132 CGCTCAATGAAAGAA
1 CGCTCAATAAAAGAA
131147 C
1 C
131148 TTTAACATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.23, G:0.16, T:0.13
Consensus pattern (15 bp):
CGCTCAATAAAAGAA
Found at i:146095 original size:16 final size:16
Alignment explanation
Indices: 146076--146110 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
146066 TCTTGCCATT
*
146076 TTCAATTCCCCCTCAA
1 TTCAATTACCCCTCAA
*
146092 TTCAATTACCCCTTAA
1 TTCAATTACCCCTCAA
146108 TTC
1 TTC
146111 CACCGAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.37, G:0.00, T:0.37
Consensus pattern (16 bp):
TTCAATTACCCCTCAA
Found at i:157430 original size:56 final size:56
Alignment explanation
Indices: 157334--157561 Score: 366
Period size: 56 Copynumber: 4.1 Consensus size: 56
157324 ATATTAAAGC
* * *
157334 ATGATCATGGTAGAAATTTGAAATTCCAATAACGAATAGCACAGCATTTATTCAAA
1 ATGATCATGGTAGAAATTTGAAATTCAAATAACGAGTAGCACAGCATTTAATCAAA
*
157390 ATGATCATGGTAGAAATTTGAAATTCAAATGACGAGTAGCACAGCATTTAATCAAA
1 ATGATCATGGTAGAAATTTGAAATTCAAATAACGAGTAGCACAGCATTTAATCAAA
*
157446 ATGATCATGGTAGAAATTTGAAATTCAAATAACGAGTAGCACAGAATTTAATCAAA
1 ATGATCATGGTAGAAATTTGAAATTCAAATAACGAGTAGCACAGCATTTAATCAAA
* * * * *
157502 ATGATCATGGTAGAAATTTGAAATTCAAATAATGAATAGCACAACGTATAATCAAA
1 ATGATCATGGTAGAAATTTGAAATTCAAATAACGAGTAGCACAGCATTTAATCAAA
157558 ATGA
1 ATGA
157562 CAAAGGAATA
Statistics
Matches: 160, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 160 1.00
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (56 bp):
ATGATCATGGTAGAAATTTGAAATTCAAATAACGAGTAGCACAGCATTTAATCAAA
Found at i:157475 original size:28 final size:29
Alignment explanation
Indices: 157383--157530 Score: 104
Period size: 28 Copynumber: 5.2 Consensus size: 29
157373 CACAGCATTT
157383 ATTCAAAATGATCATGGTAGAAATTTGAA
1 ATTCAAAATGATCATGGTAGAAATTTGAA
157412 ATTC-AAATGA-C--GAGTAGCACAGCATTT--A
1 ATTCAAAATGATCATG-GTAG-A-A--ATTTGAA
157440 A-TCAAAATGATCATGGTAGAAATTTGAA
1 ATTCAAAATGATCATGGTAGAAATTTGAA
* * * *
157468 ATTC-AAAT-AACGAGTAGCACAGAATTT--A
1 ATTCAAAATGATC-A-TGGTAGA-AATTTGAA
157496 A-TCAAAATGATCATGGTAGAAATTTGAA
1 ATTCAAAATGATCATGGTAGAAATTTGAA
157524 ATTCAAA
1 ATTCAAA
157531 TAATGAATAG
Statistics
Matches: 91, Mismatches: 8, Indels: 40
0.65 0.06 0.29
Matches are distributed among these distances:
25 1 0.01
26 13 0.14
27 12 0.13
28 32 0.35
29 19 0.21
30 13 0.14
31 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.28
Consensus pattern (29 bp):
ATTCAAAATGATCATGGTAGAAATTTGAA
Found at i:160942 original size:31 final size:31
Alignment explanation
Indices: 160901--160991 Score: 164
Period size: 31 Copynumber: 2.9 Consensus size: 31
160891 TTAGCTCCAG
*
160901 CCTACCTAGACCATGAGGCTTTGGGTTCAGT
1 CCTACTTAGACCATGAGGCTTTGGGTTCAGT
160932 CCTACTTAGACCATGAGGCTTTGGGTTCAGT
1 CCTACTTAGACCATGAGGCTTTGGGTTCAGT
*
160963 CCTACTTAGACCATGAGGTTTTGGGTTCA
1 CCTACTTAGACCATGAGGCTTTGGGTTCA
160992 ACTCTTACGG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (31 bp):
CCTACTTAGACCATGAGGCTTTGGGTTCAGT
Found at i:161137 original size:28 final size:28
Alignment explanation
Indices: 161103--161159 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
161093 AGATTTTGGG
*
161103 TTCAACTCTCACGGGATGTGAGTTTGTT
1 TTCAACTCTCACGGAATGTGAGTTTGTT
161131 TTCAACTCTCACGGAATGTGAGTTTGTT
1 TTCAACTCTCACGGAATGTGAGTTTGTT
161159 T
1 T
161160 GTAATTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (28 bp):
TTCAACTCTCACGGAATGTGAGTTTGTT
Found at i:161182 original size:32 final size:32
Alignment explanation
Indices: 161146--161265 Score: 160
Period size: 32 Copynumber: 3.9 Consensus size: 32
161136 CTCTCACGGA
161146 ATGTGAGTTTGTTTGTAATTTATTTGTTCGGG
1 ATGTGAGTTTGTTTGTAATTTATTTGTTCGGG
161178 ATGTGAGTTTGTTTGTAATTTATTTGTTCGGG
1 ATGTGAGTTTGTTTGTAATTTATTTGTTCGGG
* * * *
161210 ATGTGAGTTTGTTT-TCAA-CT-CTCG--CGGA
1 ATGTGAGTTTGTTTGT-AATTTATTTGTTCGGG
161238 ATGTGAGTTTGTTTGTAATTTATTTGTT
1 ATGTGAGTTTGTTTGTAATTTATTTGTT
161266 TATTTGGTAG
Statistics
Matches: 75, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
28 19 0.25
29 2 0.03
30 4 0.05
31 2 0.03
32 48 0.64
ACGTcount: A:0.17, C:0.06, G:0.26, T:0.52
Consensus pattern (32 bp):
ATGTGAGTTTGTTTGTAATTTATTTGTTCGGG
Found at i:161190 original size:17 final size:17
Alignment explanation
Indices: 161168--161222 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
161158 TTGTAATTTA
161168 TTTGTTCGGGATGTGAG
1 TTTGTTCGGGATGTGAG
* ** *
161185 TTTGTTTGTAAT-TTA-
1 TTTGTTCGGGATGTGAG
161200 TTTGTTCGGGATGTGAG
1 TTTGTTCGGGATGTGAG
161217 TTTGTT
1 TTTGTT
161223 TTCAACTCTC
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
15 9 0.32
16 4 0.14
17 15 0.54
ACGTcount: A:0.13, C:0.04, G:0.31, T:0.53
Consensus pattern (17 bp):
TTTGTTCGGGATGTGAG
Found at i:161342 original size:38 final size:38
Alignment explanation
Indices: 161300--161431 Score: 115
Period size: 38 Copynumber: 3.3 Consensus size: 38
161290 TATTGTATAA
161300 AATTTATTTGAATTTTAATGAGATTTCACTAGATTTGT
1 AATTTATTTGAATTTTAATGAGATTTCACTAGATTTGT
* * ** *
161338 AATTTATTTGTTTATTTGGTAGAT-AGATAGTTTA-TTTATTGTAT
1 AATTTATTTG--AATTT--TA-ATGAGAT--TTCACTAGATT-TGT
161382 AAAATTTATTTGAATTTTAATGAGATTTCACTAGATTTGT
1 --AATTTATTTGAATTTTAATGAGATTTCACTAGATTTGT
161422 AATTTATTTG
1 AATTTATTTG
161432 TTTATTTGGT
Statistics
Matches: 72, Mismatches: 10, Indels: 24
0.68 0.09 0.23
Matches are distributed among these distances:
38 20 0.28
40 9 0.12
41 6 0.08
42 12 0.17
43 6 0.08
44 9 0.12
46 10 0.14
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.52
Consensus pattern (38 bp):
AATTTATTTGAATTTTAATGAGATTTCACTAGATTTGT
Found at i:161351 original size:84 final size:84
Alignment explanation
Indices: 161249--161502 Score: 481
Period size: 84 Copynumber: 3.0 Consensus size: 84
161239 TGTGAGTTTG
161249 TTTGTAATTTATTTGTTTATTTGGTAGATAGATAGTTTATTTATTGTATAAAATTTATTTGAATT
1 TTTGTAATTTATTTGTTTATTTGGTAGATAGATAGTTTATTTATTGTATAAAATTTATTTGAATT
161314 TTAATGAGATTTCACTAGA
66 TTAATGAGATTTCACTAGA
161333 TTTGTAATTTATTTGTTTATTTGGTAGATAGATAGTTTATTTATTGTATAAAATTTATTTGAATT
1 TTTGTAATTTATTTGTTTATTTGGTAGATAGATAGTTTATTTATTGTATAAAATTTATTTGAATT
161398 TTAATGAGATTTCACTAGA
66 TTAATGAGATTTCACTAGA
* *
161417 TTTGTAATTTATTTGTTTATTTGGTAGATAGATAGTTTACTTATTGTATAAAATTTATTTGAATA
1 TTTGTAATTTATTTGTTTATTTGGTAGATAGATAGTTTATTTATTGTATAAAATTTATTTGAATT
*
161482 TTAATGAGATTTCACTGGA
66 TTAATGAGATTTCACTAGA
161501 TT
1 TT
161503 AGCGTTTTGG
Statistics
Matches: 167, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 167 1.00
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.52
Consensus pattern (84 bp):
TTTGTAATTTATTTGTTTATTTGGTAGATAGATAGTTTATTTATTGTATAAAATTTATTTGAATT
TTAATGAGATTTCACTAGA
Found at i:161352 original size:46 final size:46
Alignment explanation
Indices: 161302--161439 Score: 116
Period size: 46 Copynumber: 3.2 Consensus size: 46
161292 TTGTATAAAA
161302 TTTATTTGAATTTTAATGAGATTTCACTAGATTTGTAATTTATTTG
1 TTTATTTGAATTTTAATGAGATTTCACTAGATTTGTAATTTATTTG
* ** ** ***
161348 TTTATTTG-GTAGATAGAT-AG-TTT-A-TTTA-TTGT-A--TA-AAA
1 TTTATTTGAAT-TTTA-ATGAGATTTCACTAGATTTGTAATTTATTTG
161386 TTTATTTGAATTTTAATGAGATTTCACTAGATTTGTAATTTATTTG
1 TTTATTTGAATTTTAATGAGATTTCACTAGATTTGTAATTTATTTG
161432 TTTATTTG
1 TTTATTTG
161440 GTAGATAGAT
Statistics
Matches: 64, Mismatches: 16, Indels: 24
0.62 0.15 0.23
Matches are distributed among these distances:
37 2 0.03
38 12 0.19
39 6 0.09
40 1 0.02
41 3 0.05
42 8 0.12
43 3 0.05
44 1 0.02
45 6 0.09
46 20 0.31
47 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.54
Consensus pattern (46 bp):
TTTATTTGAATTTTAATGAGATTTCACTAGATTTGTAATTTATTTG
Found at i:165016 original size:69 final size:69
Alignment explanation
Indices: 164905--165042 Score: 267
Period size: 69 Copynumber: 2.0 Consensus size: 69
164895 GACTCCACAA
164905 GCGGGTTATGGAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAG
1 GCGGGTTATGGAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAG
164970 TTCC
66 TTCC
*
164974 GCGGGTTGTGGAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAG
1 GCGGGTTATGGAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAG
165039 TTCC
66 TTCC
165043 TAAAGGACAC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (69 bp):
GCGGGTTATGGAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAG
TTCC
Found at i:169745 original size:19 final size:18
Alignment explanation
Indices: 169717--169758 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
169707 AATTTATTGT
169717 TTTAATATTAAATTTTTA
1 TTTAATATTAAATTTTTA
*
169735 TTTATATATTATATTTTTA
1 TTTA-ATATTAAATTTTTA
*
169754 CTTAA
1 TTTAA
169759 AAATTACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAATATTAAATTTTTA
Found at i:170344 original size:22 final size:22
Alignment explanation
Indices: 170316--170360 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
170306 CTACTCCTTC
170316 TGTCCCTATATATCTGTCATCT
1 TGTCCCTATATATCTGTCATCT
* *
170338 TGTCCCTTTTTATCTGTCATCT
1 TGTCCCTATATATCTGTCATCT
170360 T
1 T
170361 CCAACATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.13, C:0.27, G:0.09, T:0.51
Consensus pattern (22 bp):
TGTCCCTATATATCTGTCATCT
Found at i:172778 original size:2 final size:2
Alignment explanation
Indices: 172771--172873 Score: 106
Period size: 2 Copynumber: 51.0 Consensus size: 2
172761 TATTTAGTAG
*
172771 TA TA TA TA TA TA TA TA TA TA TA CTA -A TA TG TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
*
172813 T- TA GTA TA TG TA TA TA TA CTA -A TA TA TA TA TA TA TA TA CTA
1 TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
*
172854 TT TA GT- TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA
172874 ACCTAATATG
Statistics
Matches: 86, Mismatches: 6, Indels: 18
0.78 0.05 0.16
Matches are distributed among these distances:
1 4 0.05
2 73 0.85
3 9 0.10
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:174168 original size:75 final size:75
Alignment explanation
Indices: 174045--174196 Score: 259
Period size: 75 Copynumber: 2.0 Consensus size: 75
174035 AATTAATATT
* * * *
174045 TTTATTTTCTTATAATTATTACATAAATTTGGATTCAACTTAATTTCTTAACATATCTTATGGGA
1 TTTATTTTCTTATAACTATTACATAAATTTGGATTCAACCTAATTTCTTAACATACCTTATCGGA
174110 TTAAATTACC
66 TTAAATTACC
*
174120 TTTATTTTCTTATTACTATTACATAAATTTGGATTCAACCTAATTTCTTAACATACCTTATCGGA
1 TTTATTTTCTTATAACTATTACATAAATTTGGATTCAACCTAATTTCTTAACATACCTTATCGGA
174185 TTAAATTACC
66 TTAAATTACC
174195 TT
1 TT
174197 CAGGTTGTAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.32, C:0.14, G:0.06, T:0.47
Consensus pattern (75 bp):
TTTATTTTCTTATAACTATTACATAAATTTGGATTCAACCTAATTTCTTAACATACCTTATCGGA
TTAAATTACC
Found at i:176967 original size:115 final size:117
Alignment explanation
Indices: 176812--177045 Score: 409
Period size: 116 Copynumber: 2.0 Consensus size: 117
176802 AAATTAGTAA
176812 AATGATAAAAATAAAATAGGGGTATAAGAATATTAGATTTAATTAAATAAAAATAGAG-TTTTTA
1 AATGATAAAAATAAAATAGGGGTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTTA
* * *
176876 GTTGAGTGAAACTGTAAAAGTATTTTAATTAAAATAGTAAAATGGTAAAAAT
66 GTTGAGTAAAACTATAAAAATATTTTAATTAAAATAGTAAAATGGTAAAAAT
*
176928 AATGATAAAAATAAAATA-GGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTTA
1 AATGATAAAAATAAAATAGGGGTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTTA
*
176992 GTTGAGTAAAACTATAAAAATATTTTGATTAAAATAGTAAAATGGTAAAAAT
66 GTTGAGTAAAACTATAAAAATATTTTAATTAAAATAGTAAAATGGTAAAAAT
177044 AA
1 AA
177046 AATAGTACTT
Statistics
Matches: 112, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
115 38 0.34
116 74 0.66
ACGTcount: A:0.52, C:0.01, G:0.15, T:0.33
Consensus pattern (117 bp):
AATGATAAAAATAAAATAGGGGTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTTA
GTTGAGTAAAACTATAAAAATATTTTAATTAAAATAGTAAAATGGTAAAAAT
Found at i:177081 original size:106 final size:103
Alignment explanation
Indices: 176928--177117 Score: 290
Period size: 106 Copynumber: 1.8 Consensus size: 103
176918 TGGTAAAAAT
* * * *
176928 AATGATAAAAATAAAATAGGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTTAG
1 AATGATAAAAATAAAATAGCGTATAAGGATACTAGATTCAATGAAATAAAAATAGAG-TTTTTAG
176993 TTGAGTAAAACTATAAAAATATTTTGATTAAAATAGTAA
65 TTGAGTAAAACTATAAAAATATTTTGATTAAAATAGTAA
* *
177032 AATGGTAAAAATAAAATAGTACTTATAAGGATACTAGATTCAATGAAATAAAAATAGAGTTTTTA
1 AATGATAAAAATAAAATAG--CGTATAAGGATACTAGATTCAATGAAATAAAAATAGAGTTTTTA
*
177097 GTTGAGTAAAATTATAAAAAT
64 GTTGAGTAAAACTATAAAAAT
177118 TTAAGCAATG
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
104 18 0.23
105 26 0.34
106 33 0.43
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.33
Consensus pattern (103 bp):
AATGATAAAAATAAAATAGCGTATAAGGATACTAGATTCAATGAAATAAAAATAGAGTTTTTAGT
TGAGTAAAACTATAAAAATATTTTGATTAAAATAGTAA
Found at i:177510 original size:89 final size:89
Alignment explanation
Indices: 177359--177528 Score: 340
Period size: 89 Copynumber: 1.9 Consensus size: 89
177349 TTCTTCAATC
177359 CTTCAAGAAAGATTCTCAAGTCTCCATCTTTACTTTCCTTTCCTTATTATAATAATAATAATATA
1 CTTCAAGAAAGATTCTCAAGTCTCCATCTTTACTTTCCTTTCCTTATTATAATAATAATAATATA
177424 ATAACAAGTGGTTCGACGCGCCAG
66 ATAACAAGTGGTTCGACGCGCCAG
177448 CTTCAAGAAAGATTCTCAAGTCTCCATCTTTACTTTCCTTTCCTTATTATAATAATAATAATATA
1 CTTCAAGAAAGATTCTCAAGTCTCCATCTTTACTTTCCTTTCCTTATTATAATAATAATAATATA
177513 ATAACAAGTGGTTCGA
66 ATAACAAGTGGTTCGA
177529 TTCGCGCTGG
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 81 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (89 bp):
CTTCAAGAAAGATTCTCAAGTCTCCATCTTTACTTTCCTTTCCTTATTATAATAATAATAATATA
ATAACAAGTGGTTCGACGCGCCAG
Found at i:178244 original size:5 final size:5
Alignment explanation
Indices: 178234--178293 Score: 120
Period size: 5 Copynumber: 12.0 Consensus size: 5
178224 ATATTTAGTA
178234 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
178284 ATAAT ATAAT
1 ATAAT ATAAT
178294 CCTATAAATC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 55 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:179069 original size:2 final size:2
Alignment explanation
Indices: 179062--179086 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
179052 TAATATTTAG
179062 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
179087 GATACGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:179396 original size:28 final size:28
Alignment explanation
Indices: 179356--179411 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
179346 GCAATGCACA
*
179356 TGGAAGTGAAAACTAGTCCATTAAAACG
1 TGGAAGTGAAAACTAATCCATTAAAACG
179384 TGGAAGTGAAAACTAATCCATTAAAACG
1 TGGAAGTGAAAACTAATCCATTAAAACG
179412 ACTCACAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.21
Consensus pattern (28 bp):
TGGAAGTGAAAACTAATCCATTAAAACG
Found at i:197972 original size:13 final size:13
Alignment explanation
Indices: 197954--197978 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
197944 GATTGACCAT
197954 AAGTATTAATTTG
1 AAGTATTAATTTG
197967 AAGTATTAATTT
1 AAGTATTAATTT
197979 TGCTAAAAAA
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:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
AAGTATTAATTTG
Found at i:199009 original size:149 final size:151
Alignment explanation
Indices: 198712--199009 Score: 413
Period size: 150 Copynumber: 2.0 Consensus size: 151
198702 AATCAAAATT
* *
198712 TTTAATATTAATACATATTCCTTATAAGGGGACACATGTCAACCCTTAAAACCTGCACGTACAGT
1 TTTAATATCAATACATATTCC-TATAAGGGGACACATGTCAACCCTTAAAACCCGCACGTACAGT
** * * *
198777 CTGCTAAATTCGACTAACGGTGTATAGTAGAAAATTTTCTTATAAGATTATTATACAATACACTG
65 CTGCTAAAACCCACTAACGATGTATAGTAGAAAATTTTCTTATAAGATTATTATACAACACACTG
198842 TCAGTGTAAATTTTGGACTCCA
130 TCAGTGTAAATTTTGGACTCCA
* * *
198864 TTTAATATCAATACATATTCC-CTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTC
1 TTTAATATCAATACATATTCCTATAAGGGGACACATGTCAACCCTTAAAACCCGCACGTACAGTC
* * * * **
198928 TGCTAAAACCCACTGACGATGTATTA-TA-TAATTTTTCTTATAGGATTATTATACAACACGTTG
66 TGCTAAAACCCACTAACGATGTA-TAGTAGAAAATTTTCTTATAAGATTATTATACAACACACTG
198991 TCAGTGTAAATTTTGGACT
130 TCAGTGTAAATTTTGGACT
199010 TTATAAGCGT
Statistics
Matches: 129, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
149 48 0.37
150 59 0.46
151 2 0.02
152 20 0.16
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (151 bp):
TTTAATATCAATACATATTCCTATAAGGGGACACATGTCAACCCTTAAAACCCGCACGTACAGTC
TGCTAAAACCCACTAACGATGTATAGTAGAAAATTTTCTTATAAGATTATTATACAACACACTGT
CAGTGTAAATTTTGGACTCCA
Found at i:199226 original size:199 final size:197
Alignment explanation
Indices: 198863--199522 Score: 961
Period size: 199 Copynumber: 3.3 Consensus size: 197
198853 TTTGGACTCC
*
198863 ATTTAATATCAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTC
1 ATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTC
*
198928 TGCTAAAAC-CCACTGACGATGTATTA-TATAATTTTTCTTATAGGATTATTATACA-ACACGTT
66 TGCT-AAACTCCACTGACGGTGTA-TAGTATAATTTTTCTTATAGGATTATTATACATACAC--T
* * *
198990 GTCAGTGTAAATTTTGGACTT-TATAAGCGTGTTAAGAAGTTGACACATACCTCATTTCATCATT
127 GTCAGTGTAAATTTTGGA-TTCCATAAACG-GTTAAGAAGTTGACACATACCTCATTTCATAATT
199054 AATTAAAT
190 AATTAAAT
* * * * *
199062 ATATAATATTAATACATATTCCCTAAGGAGACACATGTCAACCCTTAAACCCTGCACATGCAGTT
1 ATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTC
*
199127 TGCTAGACTCCACTGACGGTGTATAGTATAATTTTTCTTATAGGATTATTATACAGTACACTGTC
66 TGCTAAACTCCACTGACGGTGTATAGTATAATTTTTCTTATAGGATTATTATACA-TACACTGTC
*
199192 AGTGTAAATTTTGGATTCCATAAACGGATTAAGAAGTTGACACATACCTCATTTCATAATAAATT
130 AGTGTAAATTTTGGATTCCATAAACGG-TTAAGAAGTTGACACATACCTCATTTCATAATTAATT
199257 AAAT
194 AAAT
* * * * *
199261 ATTTAATATTAATACATATTCCTTAAGTGGATACATGTCAACCCTTAAACCCTGCACGTGCAATC
1 ATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTC
* * *
199326 TGCTAAACTCGACTGATGGTGTATAGTATAATTTTTCTTATAGGATTATTATACAATACACTTTC
66 TGCTAAACTCCACTGACGGTGTATAGTATAATTTTTCTTATAGGATTATTATAC-ATACACTGTC
* * *
199391 AGTGTAAATTTTGGACTCCATAAGCCGGTTAAGAAGTTGACACATATCC-CATTTTATAATTAAT
130 AGTGTAAATTTTGGATTCCATAA-ACGGTTAAGAAGTTGACACATA-CCTCATTTCATAATTAAT
*
199455 AAAAT
193 TAAAT
*
199460 ATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAATCCTTAAACCCCGCACGTGCAG
1 ATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAG
199523 CCTATCAACT
Statistics
Matches: 417, Mismatches: 35, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
198 8 0.02
199 399 0.96
200 6 0.01
201 4 0.01
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.33
Consensus pattern (197 bp):
ATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTC
TGCTAAACTCCACTGACGGTGTATAGTATAATTTTTCTTATAGGATTATTATACATACACTGTCA
GTGTAAATTTTGGATTCCATAAACGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAA
AT
Found at i:201317 original size:2 final size:2
Alignment explanation
Indices: 201310--201340 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
201300 ACTAATATTC
201310 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
201341 AAAGATACTT
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:201867 original size:16 final size:18
Alignment explanation
Indices: 201846--201879 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
201836 TCGCTAAGTT
201846 TAAGTAA-TAAG-TGATA
1 TAAGTAATTAAGATGATA
201862 TAAGTAATTAAGATGATA
1 TAAGTAATTAAGATGATA
201880 ATACTATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (18 bp):
TAAGTAATTAAGATGATA
Found at i:202076 original size:22 final size:24
Alignment explanation
Indices: 202050--202097 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
202040 ATACAAAATC
*
202050 AAATTCCT-AAACT-CGATTTCAA
1 AAATTCCTAAAACTCCAATTTCAA
202072 AAATTCCTAAAACTCCAATTTCAA
1 AAATTCCTAAAACTCCAATTTCAA
202096 AA
1 AA
202098 CTTCTCAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.35
23 5 0.22
24 10 0.43
ACGTcount: A:0.46, C:0.23, G:0.02, T:0.29
Consensus pattern (24 bp):
AAATTCCTAAAACTCCAATTTCAA
Found at i:202237 original size:29 final size:29
Alignment explanation
Indices: 202195--202254 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
202185 ATCCAATAGG
*
202195 ATTTGGGTAGGGAACAGTATGAAAAGAAT
1 ATTTGGGTAGGGAACAATATGAAAAGAAT
202224 ATTTGGGTAGGGAACAATATGAAAAGAAT
1 ATTTGGGTAGGGAACAATATGAAAAGAAT
202253 AT
1 AT
202255 AAAGTGTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.43, C:0.03, G:0.28, T:0.25
Consensus pattern (29 bp):
ATTTGGGTAGGGAACAATATGAAAAGAAT
Found at i:205008 original size:16 final size:16
Alignment explanation
Indices: 204987--205017 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
204977 TTAAAAAATA
204987 TTACTAAATTTTTATT
1 TTACTAAATTTTTATT
205003 TTACTAAATTTTTAT
1 TTACTAAATTTTTAT
205018 AATATGTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
TTACTAAATTTTTATT
Found at i:205829 original size:199 final size:199
Alignment explanation
Indices: 205355--205950 Score: 910
Period size: 198 Copynumber: 3.0 Consensus size: 199
205345 CTTTATAATA
* *
205355 AGGATTATTATACAAATATACTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGA
1 AGGATTATTATAC-AATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGA
* * *
205420 CACATACCCCATTTCATAATTAATTAAATATTTGATATTAATACGTATTACCTAAGGGGACACTT
65 CACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTACCTAAGGGGACACAT
* ** * * * *
205485 GTCAACCCTTAAATCTTGCATGTGCAGTCTGCTAAAATCCACTTACCG-GTATTGTATAATTTTT
130 GTCAACCCTTAAACCCCGAACGTGCAGTCTGCTAAAATCCACTGACGGTGTATTGTATAATTTTT
205549 CTTAT
195 CTTAT
205554 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
* * *
205619 ACATACCCCATTTTATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGATACATG
66 ACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTACCTAAGGGGACACATG
* *
205684 TCAACTCTTAAACCCCGAACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTC
131 TCAACCCTTAAACCCCGAACGTGCAGTCTGCTAAAATCCACTGACGGTGTATTGTATAATTTTTC
205749 TTAT
196 TTAT
* * * * * *
205753 GGGTTTATTATACAATACATTGTCAGTGTAAATTTTGTACTCTATAAGCGGGTTAAAAAGTTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
*
205818 ACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTTCCTAA-GGG-CACATG
66 ACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTACCTAAGGGGACACATG
* * * *
205881 TTAACCCTTAAACCCCAAACGTGCAGTCTGCTAAATTCCACTGACGGTGTCTTGTATAATTTTTC
131 TCAACCCTTAAACCCCGAACGTGCAGTCTGCTAAAATCCACTGACGGTGTATTGTATAATTTTTC
205946 TTAT
196 TTAT
205950 A
1 A
205951 ATAAACTTAT
Statistics
Matches: 364, Mismatches: 32, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
197 69 0.19
198 150 0.41
199 145 0.40
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (199 bp):
AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
ACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTACCTAAGGGGACACATG
TCAACCCTTAAACCCCGAACGTGCAGTCTGCTAAAATCCACTGACGGTGTATTGTATAATTTTTC
TTAT
Found at i:216650 original size:18 final size:17
Alignment explanation
Indices: 216614--216647 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
216604 GTACAGGGTG
216614 GAAGAGGTCCAATATTT
1 GAAGAGGTCCAATATTT
216631 GAAGATGGTCCAA-ATTT
1 GAAGA-GGTCCAATATTT
216648 TGATATGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (17 bp):
GAAGAGGTCCAATATTT
Found at i:224559 original size:30 final size:29
Alignment explanation
Indices: 224486--224562 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
224476 GGTATTCCTA
* *
224486 ACACGTGGCATGCCACGTGCCCTTTTTGT
1 ACACGTGGCATGCCATGTGCCATTTTTGT
* * *
224515 ACATGTGGCGTGCCATGTGTCATTTTTAGT
1 ACACGTGGCATGCCATGTGCCATTTTT-GT
*
224545 GCACGTGGCATGCCATGT
1 ACACGTGGCATGCCATGT
224563 CAGCCGCCGT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 22 0.56
30 17 0.44
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (29 bp):
ACACGTGGCATGCCATGTGCCATTTTTGT
Found at i:226148 original size:19 final size:19
Alignment explanation
Indices: 226126--226185 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
226116 ATTTAATACA
226126 ACTATAATAATATAGTAGT
1 ACTATAATAATATAGTAGT
226145 ACTATACATAA-ATA-TAAGT
1 ACTATA-ATAATATAGT-AGT
*
226164 A-TCT-AT-ATATAGTAGT
1 ACTATAATAATATAGTAGT
226180 ACTATA
1 ACTATA
226186 TAGTATATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
15 1 0.03
16 9 0.27
17 3 0.09
18 3 0.09
19 13 0.39
20 4 0.12
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (19 bp):
ACTATAATAATATAGTAGT
Found at i:233672 original size:18 final size:18
Alignment explanation
Indices: 233649--233686 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
233639 TTGTAAATAC
233649 GAATTACTTAAACAGAAG
1 GAATTACTTAAACAGAAG
233667 GAATTACTTAAACAGAAG
1 GAATTACTTAAACAGAAG
233685 GA
1 GA
233687 TTATTTGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.21
Consensus pattern (18 bp):
GAATTACTTAAACAGAAG
Found at i:236680 original size:17 final size:17
Alignment explanation
Indices: 236654--236687 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
236644 ATATACTCTC
236654 TTTTTCTTTTTCTTGTT
1 TTTTTCTTTTTCTTGTT
* *
236671 TTTTTTTTTTTGTTGTT
1 TTTTTCTTTTTCTTGTT
236688 GCAATCAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.85
Consensus pattern (17 bp):
TTTTTCTTTTTCTTGTT
Found at i:241083 original size:21 final size:21
Alignment explanation
Indices: 241051--241094 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
241041 GGACTTGGAC
*
241051 AAAACAAAACACGTGAAATAT
1 AAAACAAAACACGCGAAATAT
241072 AAAA-AAAGACACGCGAAATAT
1 AAAACAAA-ACACGCGAAATAT
241093 AA
1 AA
241095 TGAAATCGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.64, C:0.14, G:0.11, T:0.11
Consensus pattern (21 bp):
AAAACAAAACACGCGAAATAT
Found at i:242088 original size:22 final size:21
Alignment explanation
Indices: 242049--242089 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
242039 TTTTTTCCCC
242049 TTATTTTTCAATAAATTAAAT
1 TTATTTTTCAATAAATTAAAT
* *
242070 TTATTTATTTAATATATTAA
1 TTATTT-TTCAATAAATTAA
242090 CGGTTATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATTTTTCAATAAATTAAAT
Found at i:242556 original size:2 final size:2
Alignment explanation
Indices: 242549--242584 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
242539 CTTTACCAAA
242549 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
242585 GCTTGTTAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:262834 original size:46 final size:46
Alignment explanation
Indices: 262767--262862 Score: 174
Period size: 46 Copynumber: 2.1 Consensus size: 46
262757 TTACAACACA
* *
262767 AAAACCAAAATCCTTTTGGTCTTAATTACCAAAAGGCTAGAGGATT
1 AAAACCAAAATACTTTTGGTCTAAATTACCAAAAGGCTAGAGGATT
262813 AAAACCAAAATACTTTTGGTCTAAATTACCAAAAGGCTAGAGGATT
1 AAAACCAAAATACTTTTGGTCTAAATTACCAAAAGGCTAGAGGATT
262859 AAAA
1 AAAA
262863 TACTTTTAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.26
Consensus pattern (46 bp):
AAAACCAAAATACTTTTGGTCTAAATTACCAAAAGGCTAGAGGATT
Found at i:262861 original size:24 final size:24
Alignment explanation
Indices: 262790--262861 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
262780 TTTTGGTCTT
262790 AATTACCAAAAGGCTAGAGGATTA
1 AATTACCAAAAGGCTAGAGGATTA
** ***
262814 AA--ACCAAAATACTTTTGG-TCTA
1 AATTACCAAAAGGCTAGAGGAT-TA
262836 AATTACCAAAAGGCTAGAGGATTA
1 AATTACCAAAAGGCTAGAGGATTA
262860 AA
1 AA
262862 ATACTTTTAG
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
21 1 0.03
22 15 0.44
24 17 0.50
25 1 0.03
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.24
Consensus pattern (24 bp):
AATTACCAAAAGGCTAGAGGATTA
Found at i:262880 original size:40 final size:41
Alignment explanation
Indices: 262773--262886 Score: 149
Period size: 46 Copynumber: 2.7 Consensus size: 41
262763 CACAAAAACC
*
262773 AAAATCCTTTTGGTCTTAATTACCAAAAGGCTAGAGGATTAAAA
1 AAAATACTTTTGGTCTTAATTACCAAAAGGCTAGAGGATT---A
*
262817 CCAAAATACTTTTGGTCTAAATTACCAAAAGGCTAGAGGATT-
1 --AAAATACTTTTGGTCTTAATTACCAAAAGGCTAGAGGATTA
*
262859 AAAATACTTTTAGTCTTAATTACCAAAA
1 AAAATACTTTTGGTCTTAATTACCAAAA
262887 TACTTTAGGA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
40 26 0.41
46 38 0.59
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (41 bp):
AAAATACTTTTGGTCTTAATTACCAAAAGGCTAGAGGATTA
Found at i:270521 original size:28 final size:28
Alignment explanation
Indices: 270490--270544 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
270480 GCCCCTTGAA
*
270490 AATTTTG-ACGTTTTGCCCCTTAAACTTT
1 AATTTTGTAC-TTTTACCCCTTAAACTTT
*
270518 AATTTTGTACTTTTACTCCTTAAACTT
1 AATTTTGTACTTTTACCCCTTAAACTT
270545 GCAATTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.49
Consensus pattern (28 bp):
AATTTTGTACTTTTACCCCTTAAACTTT
Found at i:271864 original size:62 final size:62
Alignment explanation
Indices: 271767--271893 Score: 254
Period size: 62 Copynumber: 2.0 Consensus size: 62
271757 GACAAAATCA
271767 ATATAGATTTGTCATCAAATACTTGGAATTATAAGGTAACTCTTGAAAATGAAAGAATATTT
1 ATATAGATTTGTCATCAAATACTTGGAATTATAAGGTAACTCTTGAAAATGAAAGAATATTT
271829 ATATAGATTTGTCATCAAATACTTGGAATTATAAGGTAACTCTTGAAAATGAAAGAATATTT
1 ATATAGATTTGTCATCAAATACTTGGAATTATAAGGTAACTCTTGAAAATGAAAGAATATTT
271891 ATA
1 ATA
271894 GATTGAATGC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (62 bp):
ATATAGATTTGTCATCAAATACTTGGAATTATAAGGTAACTCTTGAAAATGAAAGAATATTT
Found at i:273172 original size:23 final size:23
Alignment explanation
Indices: 273144--273189 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
273134 TGGAACTTGA
273144 ATTCCTTTGATCTCCATTATTGT
1 ATTCCTTTGATCTCCATTATTGT
273167 ATTCCTTTGATCTCCATTATTGT
1 ATTCCTTTGATCTCCATTATTGT
273190 TGGCGACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.22, G:0.09, T:0.52
Consensus pattern (23 bp):
ATTCCTTTGATCTCCATTATTGT
Found at i:273635 original size:37 final size:37
Alignment explanation
Indices: 273585--273659 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
273575 TCGACCCATC
273585 TGTAATTTGCACACAAAAAATTTCAATATATAAGTTG
1 TGTAATTTGCACACAAAAAATTTCAATATATAAGTTG
* *
273622 TGTAATTTGCACACATAAAATTTCAATGTATAAGTTG
1 TGTAATTTGCACACAAAAAATTTCAATATATAAGTTG
273659 T
1 T
273660 AAATTAGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (37 bp):
TGTAATTTGCACACAAAAAATTTCAATATATAAGTTG
Done.