Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 178 of 279
Found at i:58638887 original size:3 final size:3
Alignment explanation
Indices: 58638825--58638877 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
58638815 TAAGGGTAGC
* *
58638825 ATA ATA A-A ATA A-A ATA A-A ATA ATA A-A ATA ATA ATA ATG GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
58638869 A-A ATA ATA A
1 ATA ATA ATA A
58638878 AGAAATAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
2 10 0.24
3 31 0.76
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (3 bp):
ATA
Found at i:58639188 original size:21 final size:22
Alignment explanation
Indices: 58639164--58639214 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
58639154 TATACAAAAC
*
58639164 AAAATATACACATAATATA-TT
1 AAAATATACACATAATATACGT
*
58639185 AAAATATATACATAATATACGT
1 AAAATATACACATAATATACGT
58639207 AAAATATA
1 AAAATATA
58639215 TGTAATGTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAATATACACATAATATACGT
Found at i:58639311 original size:11 final size:12
Alignment explanation
Indices: 58639289--58639321 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
58639279 TAATGTATAT
58639289 TAAAAGAATACA
1 TAAAAGAATACA
58639301 TAAAA-AATACA
1 TAAAAGAATACA
*
58639312 TAAAATAATA
1 TAAAAGAATA
58639322 ATATTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.70, C:0.06, G:0.03, T:0.21
Consensus pattern (12 bp):
TAAAAGAATACA
Found at i:58641170 original size:37 final size:37
Alignment explanation
Indices: 58641109--58641254 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
58641099 TACGTATGAT
* *
58641109 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
58641144 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
58641181 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
58641218 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
58641255 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:58641271 original size:46 final size:46
Alignment explanation
Indices: 58641218--58641486 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
58641208 TAAGTGTAGC
* **
58641218 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
58641264 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
58641310 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
58641362 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
58641408 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
58641460 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
58641487 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:58641337 original size:52 final size:52
Alignment explanation
Indices: 58641261--58641480 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
58641251 TAGCTAAAGC
* *
58641261 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
58641314 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
58641366 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
58641412 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
58641464 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
58641481 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:58641383 original size:98 final size:98
Alignment explanation
Indices: 58641218--58641486 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
58641208 TAAGTGTAGC
* * *
58641218 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
58641283 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
58641317 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
58641382 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
58641415 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
58641480 GATCAGA
66 GATCAGA
58641487 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:58644667 original size:49 final size:49
Alignment explanation
Indices: 58644612--58644757 Score: 229
Period size: 49 Copynumber: 3.0 Consensus size: 49
58644602 TTCGTTTTCT
* *
58644612 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACAAATCACATAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGAAATCACAAATCACATAC
* *
58644661 CGATGCCATAGCCCAACTATGGTCTTACACGAAATCACATATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGAAATCACAAATCACATAC
* *
58644710 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCACAT
1 CGATGCCATAGCCCAACTATGGTCTTACACGAAATCACA-AATCACAT
58644758 GTTCACATGT
Statistics
Matches: 88, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
49 82 0.93
50 6 0.07
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (49 bp):
CGATGCCATAGCCCAACTATGGTCTTACACGAAATCACAAATCACATAC
Found at i:58646071 original size:37 final size:37
Alignment explanation
Indices: 58646010--58646155 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
58646000 TACGTATGAT
* *
58646010 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
58646045 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
58646082 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
58646119 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
58646156 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:58646172 original size:46 final size:46
Alignment explanation
Indices: 58646119--58646387 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
58646109 TAAGTGTAGC
* **
58646119 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
58646165 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
58646211 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
58646263 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
58646309 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
58646361 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
58646388 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:58646238 original size:52 final size:52
Alignment explanation
Indices: 58646162--58646381 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
58646152 TAGCTAAAGC
* *
58646162 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
58646215 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
58646267 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
58646313 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
58646365 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
58646382 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:58646284 original size:98 final size:98
Alignment explanation
Indices: 58646119--58646387 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
58646109 TAAGTGTAGC
* * *
58646119 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
58646184 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
58646218 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
58646283 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
58646316 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
58646381 GATCAGA
66 GATCAGA
58646388 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:58648056 original size:21 final size:21
Alignment explanation
Indices: 58648032--58648073 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
58648022 CTTTTTGTTC
*
58648032 AATTAATTATCGGAACTTTAA
1 AATTAATTAACGGAACTTTAA
**
58648053 AATTTCTTAACGGAACTTTAA
1 AATTAATTAACGGAACTTTAA
58648074 TACTAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (21 bp):
AATTAATTAACGGAACTTTAA
Found at i:58648839 original size:26 final size:25
Alignment explanation
Indices: 58648779--58648841 Score: 108
Period size: 25 Copynumber: 2.5 Consensus size: 25
58648769 CCATTTACTT
58648779 TAAATCGTTTTTATAGTATCTATTC
1 TAAATCGTTTTTATAGTATCTATTC
58648804 TAAATCGTTTTTATAGTATCTATTC
1 TAAATCGTTTTTATAGTATCTATTC
*
58648829 TAAACTTGTTTTT
1 TAAA-TCGTTTTT
58648842 CCATACCTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 29 0.81
26 7 0.19
ACGTcount: A:0.27, C:0.11, G:0.08, T:0.54
Consensus pattern (25 bp):
TAAATCGTTTTTATAGTATCTATTC
Found at i:58649584 original size:255 final size:255
Alignment explanation
Indices: 58649129--58649587 Score: 686
Period size: 255 Copynumber: 1.8 Consensus size: 255
58649119 AAAATAAAGT
* * *
58649129 AATATTTCGTGTTTGAAAATTTTGAGAAATTGTGCCCTACGTGTTGGGTTTCGATTTGTCGTTTG
1 AATATTTCGTGTTTGAAAATTTCGAGAAATTGTGCCCTACGTGCTGGGTTTCGATTTATCGTTTG
* *
58649194 ACCGAACAACCAAATATCCTTTTTAAAATTTCAAAACATGAGTTTCAAAAATTATGAGATGATTT
66 ACCGAACAACCAAATATCCTTTTTAAAATTTCAAAACATAAATTTCAAAAATTATGAGATGATTT
* * * *
58649259 TGGTATCGAAGGTTTGAAATATCGTGTCCTACGTGTTGGATGTGATATTTTATTTCTTTGAAACA
131 TGATATCGAAGGTTTGAAATATCGTGTCCTACGTGCTGGATGTGATATTTTATTTATTCGAAACA
58649324 AGAGAATCTTAATCGTTTCATACTATTGCATTTTTATTCAAGACTTTTTTTTAACAAGGC
196 AGAGAATCTTAATCGTTTCATACTATTGCATTTTTATTCAAGACTTTTTTTTAACAAGGC
*
58649384 AATATTTCGTGTTTGGAAATTTCGAGAAATTGTGCCCTACGTGCTGGGTTTCGATTTATCGTTTG
1 AATATTTCGTGTTTGAAAATTTCGAGAAATTGTGCCCTACGTGCTGGGTTTCGATTTATCGTTTG
** * * ** ***
58649449 ACCGAATGACCGAATATCCTTTTTAAATTTTCAATGCATAAA-TTCTGGGAATTATGAGATGATT
66 ACCGAACAACCAAATATCCTTTTTAAAATTTCAAAACATAAATTTC-AAAAATTATGAGATGATT
* * * * *
58649513 TTGATATTGAAGGTTTGAAATGTTGTGTCCTACGTGCTGGATGTGATGTTTTATTTATTCGAAAT
130 TTGATATCGAAGGTTTGAAATATCGTGTCCTACGTGCTGGATGTGATATTTTATTTATTCGAAAC
58649578 AAGAGAATCT
195 AAGAGAATCT
58649588 CAATATTCAC
Statistics
Matches: 179, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
254 3 0.02
255 176 0.98
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.40
Consensus pattern (255 bp):
AATATTTCGTGTTTGAAAATTTCGAGAAATTGTGCCCTACGTGCTGGGTTTCGATTTATCGTTTG
ACCGAACAACCAAATATCCTTTTTAAAATTTCAAAACATAAATTTCAAAAATTATGAGATGATTT
TGATATCGAAGGTTTGAAATATCGTGTCCTACGTGCTGGATGTGATATTTTATTTATTCGAAACA
AGAGAATCTTAATCGTTTCATACTATTGCATTTTTATTCAAGACTTTTTTTTAACAAGGC
Found at i:58658704 original size:21 final size:21
Alignment explanation
Indices: 58658680--58658723 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
58658670 CCAATGAGAC
*
58658680 CCTTTAGTGGTATCACAATAT
1 CCTTTAGGGGTATCACAATAT
* * *
58658701 CCTTTTGGGGTATCGCGATAT
1 CCTTTAGGGGTATCACAATAT
58658722 CC
1 CC
58658724 ACCTTTCAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (21 bp):
CCTTTAGGGGTATCACAATAT
Found at i:58659271 original size:13 final size:13
Alignment explanation
Indices: 58659253--58659277 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58659243 TTAAAATTAA
58659253 AATTAACTAAATT
1 AATTAACTAAATT
58659266 AATTAACTAAAT
1 AATTAACTAAAT
58659278 AACACGACAA
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:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAACTAAATT
Found at i:58661891 original size:34 final size:35
Alignment explanation
Indices: 58661828--58661894 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
58661818 TAAGCTCACC
* * *
58661828 AAATGTATGAGCTCACCCAAGATTGCGAGCTTATA
1 AAATGTATGAGCTCACCCAAAACTACGAGCTTATA
*
58661863 AAATGTGTGAGCTC-CCCAAAACTACGAGCTTA
1 AAATGTATGAGCTCACCCAAAACTACGAGCTTA
58661895 CCAAGACTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 15 0.54
35 13 0.46
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (35 bp):
AAATGTATGAGCTCACCCAAAACTACGAGCTTATA
Found at i:58664261 original size:48 final size:48
Alignment explanation
Indices: 58664198--58664373 Score: 228
Period size: 48 Copynumber: 3.7 Consensus size: 48
58664188 CACACCCTAG
58664198 GTGCCAATATCATGGCCCAAAGCCAAATCAATGTAACTCGCACCCAAA
1 GTGCCAATATCATGGCCCAAAGCCAAATCAATGTAACTCGCACCCAAA
* * * **
58664246 GTGCTAATATCATGGCCCGAAGCCAAATCAATG-AAGCTCACACATAAA
1 GTGCCAATATCATGGCCCAAAGCCAAATCAATGTAA-CTCGCACCCAAA
* * * *
58664294 GTGCCAATATCATGGCTCGAAGCCAAATCAAAGTAACTCGCACCCGAA
1 GTGCCAATATCATGGCCCAAAGCCAAATCAATGTAACTCGCACCCAAA
* * *
58664342 GTGCTAATATCATGGCCCAAAACCAACTCAAT
1 GTGCCAATATCATGGCCCAAAGCCAAATCAAT
58664374 AAAGCTCCTA
Statistics
Matches: 108, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
47 2 0.02
48 104 0.96
49 2 0.02
ACGTcount: A:0.38, C:0.28, G:0.16, T:0.18
Consensus pattern (48 bp):
GTGCCAATATCATGGCCCAAAGCCAAATCAATGTAACTCGCACCCAAA
Found at i:58664350 original size:96 final size:96
Alignment explanation
Indices: 58664198--58664380 Score: 294
Period size: 96 Copynumber: 1.9 Consensus size: 96
58664188 CACACCCTAG
*
58664198 GTGCCAATATCATGGCCCAAAGCCAAATCAATGTAACTCGCACCCAAAGTGCTAATATCATGGCC
1 GTGCCAATATCATGGCCCAAAGCCAAATCAAAGTAACTCGCACCCAAAGTGCTAATATCATGGCC
* * *
58664263 CGAAGCCAAATCAATGAAGCTCACACATAAA
66 CAAAACCAAATCAATAAAGCTCACACATAAA
* * *
58664294 GTGCCAATATCATGGCTCGAAGCCAAATCAAAGTAACTCGCACCCGAAGTGCTAATATCATGGCC
1 GTGCCAATATCATGGCCCAAAGCCAAATCAAAGTAACTCGCACCCAAAGTGCTAATATCATGGCC
*
58664359 CAAAACCAACTCAATAAAGCTC
66 CAAAACCAAATCAATAAAGCTC
58664381 CTAATGACAT
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 79 1.00
ACGTcount: A:0.38, C:0.28, G:0.16, T:0.18
Consensus pattern (96 bp):
GTGCCAATATCATGGCCCAAAGCCAAATCAAAGTAACTCGCACCCAAAGTGCTAATATCATGGCC
CAAAACCAAATCAATAAAGCTCACACATAAA
Found at i:58671937 original size:48 final size:48
Alignment explanation
Indices: 58671877--58672106 Score: 284
Period size: 48 Copynumber: 4.8 Consensus size: 48
58671867 GCACCCTAGA
* *
58671877 TGCCCATATCATGGCCCGAAGCCAAATCAATGAAGCTCGCACTCGAAG
1 TGCCAATATCATGGCCCGAAGCCAAATCAATGAAGCTCGCACCCGAAG
* *
58671925 TGCCAATATCATGGCACAAAGCCAAATCAATGTAA-CTCGCACCCGAAG
1 TGCCAATATCATGGCCCGAAGCCAAATCAATG-AAGCTCGCACCCGAAG
* * * *
58671973 TGCTAATATCATGACCCGACGCCAAATCAATGAAGTTCGCACCCGAAG
1 TGCCAATATCATGGCCCGAAGCCAAATCAATGAAGCTCGCACCCGAAG
* * *
58672021 TGCCAATATCATGGTCCGAAGCCAAATCAATGTAA-CTTGCACCCAAAG
1 TGCCAATATCATGGCCCGAAGCCAAATCAATG-AAGCTCGCACCCGAAG
* * * * *
58672069 TGCTAATATCATGACCCGAAACCAACTTAATGAAGCTC
1 TGCCAATATCATGGCCCGAAGCCAAATCAATGAAGCTC
58672107 CTAATGACAT
Statistics
Matches: 154, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
47 4 0.03
48 146 0.95
49 4 0.03
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.19
Consensus pattern (48 bp):
TGCCAATATCATGGCCCGAAGCCAAATCAATGAAGCTCGCACCCGAAG
Found at i:58672029 original size:96 final size:96
Alignment explanation
Indices: 58671882--58672106 Score: 344
Period size: 96 Copynumber: 2.3 Consensus size: 96
58671872 CTAGATGCCC
* *
58671882 ATATCATGGCCCGAAGCCAAATCAATGAAGCTCGCACTCGAAGTGCCAATATCATGG-CACAAAG
1 ATATCATGACCCGAAGCCAAATCAATGAAGCTCGCACCCGAAGTGCCAATATCATGGTC-CAAAG
*
58671946 CCAAATCAATGTAACTCGCACCCGAAGTGCTA
65 CCAAATCAATGTAACTCGCACCCAAAGTGCTA
* * *
58671978 ATATCATGACCCGACGCCAAATCAATGAAGTTCGCACCCGAAGTGCCAATATCATGGTCCGAAGC
1 ATATCATGACCCGAAGCCAAATCAATGAAGCTCGCACCCGAAGTGCCAATATCATGGTCCAAAGC
*
58672043 CAAATCAATGTAACTTGCACCCAAAGTGCTA
66 CAAATCAATGTAACTCGCACCCAAAGTGCTA
* * *
58672074 ATATCATGACCCGAAACCAACTTAATGAAGCTC
1 ATATCATGACCCGAAGCCAAATCAATGAAGCTC
58672107 CTAATGACAT
Statistics
Matches: 116, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
96 115 0.99
97 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (96 bp):
ATATCATGACCCGAAGCCAAATCAATGAAGCTCGCACCCGAAGTGCCAATATCATGGTCCAAAGC
CAAATCAATGTAACTCGCACCCAAAGTGCTA
Found at i:58680450 original size:16 final size:16
Alignment explanation
Indices: 58680420--58680473 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 16
58680410 TTCCACACAT
*
58680420 ATATATAAAACATATAA
1 ATATA-AAAAAATATAA
58680437 ATATAAAAAAATAT-A
1 ATATAAAAAAATATAA
*
58680452 ATACAAAAAAA-ATAA
1 ATATAAAAAAATATAA
58680467 A-ATAAAA
1 ATATAAAA
58680474 TAAAATTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
14 7 0.21
15 13 0.39
16 8 0.24
17 5 0.15
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (16 bp):
ATATAAAAAAATATAA
Found at i:58680478 original size:16 final size:15
Alignment explanation
Indices: 58680435--58680479 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
58680425 TAAAACATAT
*
58680435 AAATATAAAAAAATA
1 AAATAAAAAAAAATA
*
58680450 TAATACAAAAAAAATA
1 AAATA-AAAAAAAATA
*
58680466 AAATAAAATAAAAT
1 AAATAAAAAAAAAT
58680480 TTTACTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (15 bp):
AAATAAAAAAAAATA
Found at i:58681404 original size:24 final size:24
Alignment explanation
Indices: 58681350--58681454 Score: 68
Period size: 24 Copynumber: 4.2 Consensus size: 24
58681340 TATTAGTTAC
** * *
58681350 ATATATTTCTTATGCTATTTTATGT
1 ATATATTT-TTATATTATCTTACGT
*
58681375 ACATATTTTTATATTATCTTACGT
1 ATATATTTTTATATTATCTTACGT
* *
58681399 ATATATTCTTAAATACTATTA-CATACAT
1 ATATATT-TT---TA-TATTATCTTACGT
* *
58681427 ATATATTTTTATATCATATTACGT
1 ATATATTTTTATATTATCTTACGT
58681451 ATAT
1 ATAT
58681455 TATTATATCT
Statistics
Matches: 62, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
23 4 0.06
24 28 0.45
25 9 0.15
27 2 0.03
28 14 0.23
29 5 0.08
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.52
Consensus pattern (24 bp):
ATATATTTTTATATTATCTTACGT
Found at i:58681532 original size:16 final size:17
Alignment explanation
Indices: 58681513--58681545 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
58681503 ATATTTTTTA
58681513 CATATAGTATTA-ATTT
1 CATATAGTATTATATTT
*
58681529 CATATATTATTATATTT
1 CATATAGTATTATATTT
58681546 ATTATTCTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (17 bp):
CATATAGTATTATATTT
Found at i:58681782 original size:17 final size:15
Alignment explanation
Indices: 58681746--58681775 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
58681736 ATGTGTATAT
58681746 TATGTTTTTTAATAC
1 TATGTTTTTTAATAC
58681761 TATGTTTTTTAATAC
1 TATGTTTTTTAATAC
58681776 CCTATGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.60
Consensus pattern (15 bp):
TATGTTTTTTAATAC
Found at i:58681810 original size:25 final size:26
Alignment explanation
Indices: 58681777--58681846 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
58681767 TTTTAATACC
*
58681777 CTATGTATTG-TGTATATTCTTAATA
1 CTATATATTGATGTATATTCTTAATA
*
58681802 CTATATATTGTATGTATTTTCTTAATA
1 CTATATATTG-ATGTATATTCTTAATA
* *
58681829 AT-TATATTATATGTATAT
1 CTATATATT-GATGTATAT
58681847 ATATACTATG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
25 9 0.24
26 13 0.35
27 15 0.41
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.54
Consensus pattern (26 bp):
CTATATATTGATGTATATTCTTAATA
Found at i:58681841 original size:26 final size:27
Alignment explanation
Indices: 58681787--58681846 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
58681777 CTATGTATTG
* *
58681787 TGTATATTCTTAATACTATATATTGTA
1 TGTATATTCTTAATAATATATATTATA
*
58681814 TGTATTTTCTTAATAAT-TATATTATA
1 TGTATATTCTTAATAATATATATTATA
58681840 TGTATAT
1 TGTATAT
58681847 ATATACTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 14 0.48
27 15 0.52
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (27 bp):
TGTATATTCTTAATAATATATATTATA
Found at i:58691687 original size:12 final size:12
Alignment explanation
Indices: 58691670--58691707 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
58691660 AATATCATTT
58691670 TAATTATAAAAA
1 TAATTATAAAAA
*
58691682 TAATTAAAAAAA
1 TAATTATAAAAA
*
58691694 TATTTATAAAAA
1 TAATTATAAAAA
58691706 TA
1 TA
58691708 TTAGGATAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TAATTATAAAAA
Found at i:58692806 original size:10 final size:10
Alignment explanation
Indices: 58692770--58692809 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
58692760 CAAATGCGGA
58692770 ATATGTTTAT
1 ATATGTTTAT
* *
58692780 ATCTATTTAT
1 ATATGTTTAT
*
58692790 ATCTGTTTAT
1 ATATGTTTAT
58692800 ATATGTTTAT
1 ATATGTTTAT
58692810 TTTGAGTGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (10 bp):
ATATGTTTAT
Found at i:58693418 original size:20 final size:19
Alignment explanation
Indices: 58693393--58693432 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
58693383 ATAAATACAT
*
58693393 ATATTATAAATACATAAAAA
1 ATATTA-AAAAACATAAAAA
*
58693413 ATATTAAAAAATATAAAAA
1 ATATTAAAAAACATAAAAA
58693432 A
1 A
58693433 AATTTTACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (19 bp):
ATATTAAAAAACATAAAAA
Found at i:58694007 original size:3 final size:3
Alignment explanation
Indices: 58693999--58694048 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
58693989 TACTTTTAAC
* * * *
58693999 ATT ATT ATT ATT A-T ATT A-T AAT AAT AAT AAT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
58694045 ATT A
1 ATT A
58694049 GTAGTAGTAG
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
2 4 0.09
3 40 0.91
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:58694162 original size:11 final size:11
Alignment explanation
Indices: 58694146--58694202 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
58694136 TTATTTCTAA
58694146 TATGTATATAT
1 TATGTATATAT
*
58694157 TATGTAAATAT
1 TATGTATATAT
* *
58694168 TTTAATACTATAT
1 TAT-GTA-TATAT
58694181 TATGTATATAT
1 TATGTATATAT
* *
58694192 TTTTTATATAT
1 TATGTATATAT
58694203 GTTATGTACA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
11 26 0.72
12 4 0.11
13 6 0.17
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (11 bp):
TATGTATATAT
Found at i:58694221 original size:26 final size:25
Alignment explanation
Indices: 58694150--58694256 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 25
58694140 TTCTAATATG
*
58694150 TATATATTATGTAA-ATA-TTTTAA
1 TATATATTATGTAATATATTTTTTA
58694173 TACTATATTATGT-ATATATTTTTTA
1 TA-TATATTATGTAATATATTTTTTA
*
58694198 TATATGTTATGTACATATATTTTTTAA
1 TATATATTATGTA-ATATATTTTTT-A
* * * *
58694225 TATTATATTTTTTAATATTATTATGTA
1 TA-TATATTATGTAATA-TATTTTTTA
58694252 TATAT
1 TATAT
58694257 TTTAATATCA
Statistics
Matches: 69, Mismatches: 7, Indels: 13
0.78 0.08 0.15
Matches are distributed among these distances:
23 3 0.04
24 22 0.32
25 7 0.10
26 14 0.20
27 9 0.13
28 14 0.20
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (25 bp):
TATATATTATGTAATATATTTTTTA
Found at i:58694248 original size:18 final size:15
Alignment explanation
Indices: 58694213--58694245 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
58694203 GTTATGTACA
58694213 TATATTTTTTAATAT
1 TATATTTTTTAATAT
58694228 TATATTTTTTAATAT
1 TATATTTTTTAATAT
58694243 TAT
1 TAT
58694246 TATGTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATATTTTTTAATAT
Found at i:58694312 original size:25 final size:25
Alignment explanation
Indices: 58694240--58694352 Score: 87
Period size: 25 Copynumber: 4.6 Consensus size: 25
58694230 TATTTTTTAA
58694240 TATTATTATGTATATATTT-TAATA-
1 TATT-TTATGTATATATTTCTAATAC
* *
58694264 TCA--TTA-GTTATATATTTTTTATAC
1 T-ATTTTATG-TATATATTTCTAATAC
58694288 TATTTTATGTATATATTTCTAATAC
1 TATTTTATGTATATATTTCTAATAC
* *
58694313 TA-TATAT-TGTATATTTCTAATAC
1 TATTTTATGTATATATTTCTAATAC
* *
58694336 CATTATTATTTATATAT
1 TATT-TTATGTATATAT
58694353 GTATATATGT
Statistics
Matches: 71, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.01
22 12 0.17
23 21 0.30
24 7 0.10
25 23 0.32
26 7 0.10
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.57
Consensus pattern (25 bp):
TATTTTATGTATATATTTCTAATAC
Found at i:58694504 original size:25 final size:24
Alignment explanation
Indices: 58694430--58694504 Score: 62
Period size: 25 Copynumber: 2.9 Consensus size: 24
58694420 ATATATCATG
58694430 TATATATGATTTTTTTTACATATAT
1 TATATAT-ATTTTTTTTACATATAT
* **
58694455 TATGTATATATCTTTAATACTATATAAT
1 TA--TATATATTTTTTTTAC-ATAT-AT
58694483 T-TATATATTTTTTCTTACATAT
1 TATATATATTTTTT-TTACATAT
58694505 TATCTTACGT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
25 16 0.41
26 11 0.28
27 9 0.23
28 3 0.08
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (24 bp):
TATATATATTTTTTTTACATATAT
Found at i:58694695 original size:22 final size:22
Alignment explanation
Indices: 58694642--58694695 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
58694632 ACATTTTTTA
*
58694642 AATACTATATTATATATATATT
1 AATACTATATTATATACATATT
* *
58694664 AATACCATATTATGTACATATT
1 AATACTATATTATATACATATT
* *
58694686 ATTATTATAT
1 AATACTATAT
58694696 CTATTTTTAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (22 bp):
AATACTATATTATATACATATT
Found at i:58694787 original size:18 final size:18
Alignment explanation
Indices: 58694764--58694821 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
58694754 GTATATATAC
*
58694764 TTTTATATATAGTATTAT
1 TTTTATATATATTATTAT
58694782 TTTTATATATCATTA-TAT
1 TTTTATATAT-ATTATTAT
58694800 TTATTAT-TATACTTATTAT
1 TT-TTATATATA-TTATTAT
58694819 TTT
1 TTT
58694822 CACTATTGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
17 1 0.03
18 22 0.63
19 12 0.34
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTATATATATTATTAT
Found at i:58698212 original size:22 final size:22
Alignment explanation
Indices: 58698187--58698231 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
58698177 ATTCATGACT
*
58698187 AACATTTATTCGTCATTTATTC
1 AACATTCATTCGTCATTTATTC
* *
58698209 AACATTCATTTGTGATTTATTC
1 AACATTCATTCGTCATTTATTC
58698231 A
1 A
58698232 TTCATCCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.49
Consensus pattern (22 bp):
AACATTCATTCGTCATTTATTC
Found at i:58705144 original size:28 final size:28
Alignment explanation
Indices: 58705112--58705166 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
58705102 CAAGGCTGAC
58705112 TTTT-ATCT-CTTGATTTCAATTTCAATCT
1 TTTTAATCTACTTG-TTT-AATTTCAATCT
*
58705140 TTTTAATTTACTTGTTTAATTTCAATC
1 TTTTAATCTACTTGTTTAATTTCAATC
58705167 ATTTACTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 14 0.58
29 6 0.25
30 4 0.17
ACGTcount: A:0.24, C:0.15, G:0.04, T:0.58
Consensus pattern (28 bp):
TTTTAATCTACTTGTTTAATTTCAATCT
Found at i:58709994 original size:75 final size:75
Alignment explanation
Indices: 58709854--58709994 Score: 246
Period size: 75 Copynumber: 1.9 Consensus size: 75
58709844 TTATTTTTGT
* *
58709854 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACTCCGAGGGATTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGACGGATTT
58709919 TCAATTTCAG
66 TCAATTTCAG
* *
58709929 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGACGTATTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGACGGATTT
58709994 T
66 T
58709995 TAGTTTCTAT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 62 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (75 bp):
TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGACGGATTT
TCAATTTCAG
Found at i:58710057 original size:64 final size:64
Alignment explanation
Indices: 58709939--58710058 Score: 188
Period size: 64 Copynumber: 1.9 Consensus size: 64
58709929 TTTTTCAAAA
* *
58709939 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGACGTATTTTTAGTTTCT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCCACACGCCGACGTATTTTTAGTTTCT
* *
58710003 ATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGCCACATGCCGA-GATATTTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCCACACGCCGACG-TATTTT
58710059 CAAGTTTTGT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
63 1 0.02
64 50 0.98
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (64 bp):
ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCCACACGCCGACGTATTTTTAGTTTCT
Found at i:58710211 original size:168 final size:165
Alignment explanation
Indices: 58710003--58710322 Score: 509
Period size: 168 Copynumber: 1.9 Consensus size: 165
58709993 TTTAGTTTCT
* *
58710003 ATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGCCACATGCCGAGATATTTTCAAGTTT-T
1 ATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGCCACATGCCGAGATATTTTCAA-TTTCT
* * *
58710067 GTTTTTTAATTTCTGCTTTTTCAAGAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGG
65 G-TTTTTAATTTCTGC-TTTTCAAG-AAAATCAACTCATATTGAGAGAGGGGAGTTGAGCCTCAG
*
58710132 GTCACACTCCGAGGTATT-TTCAATTTCAGTTTTTCAAAA
127 GTCACACACCGAGGTATTCTT-AATTTCAGTTTTTCAAAA
58710171 ATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGCCACATGCCGAGATATTTTCAATTTCTG
1 ATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGCCACATGCCGAGATATTTTCAATTTCTG
*
58710236 TTTTTAATTTTTGCTTTTCAAGAAAATCAACTCATATTGAGAGAGGGGAGTTGAGCCTCAGGTCA
66 TTTTTAATTTCTGCTTTTCAAGAAAATCAACTCATATTGAGAGAGGGGAGTTGAGCCTCAGGTCA
*
58710301 CACACTGAGGTATTCTTAATTT
131 CACACCGAGGTATTCTTAATTT
58710323 TTTTTTACTT
Statistics
Matches: 142, Mismatches: 8, Indels: 7
0.90 0.05 0.04
Matches are distributed among these distances:
165 57 0.40
166 10 0.07
167 16 0.11
168 59 0.42
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (165 bp):
ATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGCCACATGCCGAGATATTTTCAATTTCTG
TTTTTAATTTCTGCTTTTCAAGAAAATCAACTCATATTGAGAGAGGGGAGTTGAGCCTCAGGTCA
CACACCGAGGTATTCTTAATTTCAGTTTTTCAAAA
Found at i:58710219 original size:75 final size:75
Alignment explanation
Indices: 58710092--58710240 Score: 237
Period size: 75 Copynumber: 2.0 Consensus size: 75
58710082 CTTTTTCAAG
* * * *
58710092 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCACACTCCGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGCCACACTCCGAGATATTTTCAATT
58710157 TCAGTTTTTC
66 TCAGTTTTTC
58710167 AAAAATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGCCACA-TGCCGAGATATTTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGCCACACT-CCGAGATATTTTCAAT
*
58710231 TTCTGTTTTT
65 TTCAGTTTTT
58710241 AATTTTTGCT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
74 1 0.01
75 67 0.99
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (75 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGCCACACTCCGAGATATTTTCAATT
TCAGTTTTTC
Found at i:58712167 original size:24 final size:23
Alignment explanation
Indices: 58712136--58712206 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 23
58712126 TATATATATG
58712136 TATATATTATGTAAATATTTTAA
1 TATATATTATGTAAATATTTTAA
* *
58712159 TACTATATTATGTATATATTTTTTA
1 TA-TATATTATGTAAATA-TTTTAA
*
58712184 TATATGTTATGTACATATATTTT
1 TATATATTATGTA-A-ATATTTT
58712207 TTAATATTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 2 0.05
24 24 0.60
25 11 0.28
26 3 0.08
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (23 bp):
TATATATTATGTAAATATTTTAA
Found at i:58712226 original size:13 final size:15
Alignment explanation
Indices: 58712199--58712231 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
58712189 GTTATGTACA
58712199 TATATTTTTTAATAT
1 TATATTTTTTAATAT
58712214 TATA-TTTTTATATAT
1 TATATTTTTTA-ATAT
58712229 TAT
1 TAT
58712232 TATGTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATATTTTTTAATAT
Found at i:58712250 original size:14 final size:14
Alignment explanation
Indices: 58712164--58712243 Score: 55
Period size: 14 Copynumber: 6.1 Consensus size: 14
58712154 TTTAATACTA
58712164 TATTATGTATATAT
1 TATTATGTATATAT
58712178 T-TT-T-TATATA-
1 TATTATGTATATAT
* *
58712188 TGTTATGTACATA-
1 TATTATGTATATAT
* *
58712201 TATTTTTTA-ATAT
1 TATTATGTATATAT
* *
58712214 TATATTTTTATATAT
1 TAT-TATGTATATAT
58712229 TATTATGTATATAT
1 TATTATGTATATAT
58712243 T
1 T
58712244 TTAATGTCAT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
10 1 0.02
11 8 0.15
12 5 0.09
13 16 0.30
14 17 0.31
15 7 0.13
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.61
Consensus pattern (14 bp):
TATTATGTATATAT
Found at i:58712309 original size:25 final size:25
Alignment explanation
Indices: 58712258--58712338 Score: 71
Period size: 25 Copynumber: 3.3 Consensus size: 25
58712248 TGTCATTAGT
* * *
58712258 TATATATTTTTTATACTAT-TTTATG
1 TATATATTTCTAATACTATATAT-TG
58712283 TATATATTTCTAATACTATATATTG
1 TATATATTTCTAATACTATATATTG
*
58712308 --TATATTTCTAATACCATTATTATT-
1 TATATATTTCTAATACTA-TA-TATTG
58712332 TATATAT
1 TATATAT
58712339 GTATATATGT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
23 15 0.32
24 2 0.04
25 23 0.49
26 7 0.15
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.57
Consensus pattern (25 bp):
TATATATTTCTAATACTATATATTG
Found at i:58712461 original size:27 final size:27
Alignment explanation
Indices: 58712399--58712462 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
58712389 TTATTGTTGC
58712399 TAATATATATATCATGTATATATGATT
1 TAATATATATATCATGTATATATGATT
** * *
58712426 TTTTATATATATTATGTATATAT-CTT
1 TAATATATATATCATGTATATATGATT
58712452 TAATACTATAT
1 TAATA-TATAT
58712463 TGTTTTTATA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
26 5 0.17
27 25 0.83
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (27 bp):
TAATATATATATCATGTATATATGATT
Found at i:58712640 original size:27 final size:26
Alignment explanation
Indices: 58712610--58712668 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 26
58712600 TAATATATAA
* *
58712610 ATTATGTATACATTTTTTAAATACTAT
1 ATTATGTATACATATTTT-AATACCAT
*
58712637 ATTA--TATATATATTTTAATACCAT
1 ATTATGTATACATATTTTAATACCAT
58712661 ATTATGTA
1 ATTATGTA
58712669 CATATTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
24 11 0.41
25 10 0.37
26 2 0.07
27 4 0.15
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (26 bp):
ATTATGTATACATATTTTAATACCAT
Found at i:58712662 original size:24 final size:25
Alignment explanation
Indices: 58712616--58712674 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
58712606 ATAAATTATG
* *
58712616 TATACATTTTTTAAATACTATATTA
1 TATACATATTTTAAATACCATATTA
*
58712641 TATATATATTTT-AATACCATATTA
1 TATACATATTTTAAATACCATATTA
*
58712665 TGTACATATT
1 TATACATATT
58712675 ATTATATCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 19 0.66
25 10 0.34
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (25 bp):
TATACATATTTTAAATACCATATTA
Found at i:58712710 original size:12 final size:12
Alignment explanation
Indices: 58712695--58712808 Score: 53
Period size: 12 Copynumber: 9.3 Consensus size: 12
58712685 TTTTTACCCA
58712695 TATTATATTTAT
1 TATTATATTTAT
*
58712707 TATTA-ATATTAG
1 TATTATAT-TTAT
58712719 TA-TATATATT-T
1 TATTATAT-TTAT
*
58712730 TATTATACGTGTA-
1 TATTATA--TTTAT
58712743 TATATATACTTT-T
1 TAT-TATA-TTTAT
58712756 TATATATAGTATTAT
1 TAT-TATA-T-TTAT
*
58712771 T-TT-TATATAT
1 TATTATATTTAT
*
58712781 CATTATATTTAT
1 TATTATATTTAT
*
58712793 TATTATACTTAT
1 TATTATATTTAT
58712805 TATT
1 TATT
58712809 TTCACTATTG
Statistics
Matches: 79, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
10 3 0.04
11 9 0.11
12 41 0.52
13 16 0.20
14 8 0.10
15 2 0.03
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.59
Consensus pattern (12 bp):
TATTATATTTAT
Found at i:58712767 original size:24 final size:22
Alignment explanation
Indices: 58712698--58712798 Score: 61
Period size: 23 Copynumber: 4.5 Consensus size: 22
58712688 TTACCCATAT
58712698 TATAT-TTATTATTAATATTAGTA
1 TATATATT-TTATT-ATATTAGTA
58712721 TATATATTTTATTATACGTGTA-TA
1 TATATATTTTATTATA--T-TAGTA
*
58712745 TATATACTTT-TTATATATAGTA
1 TATATATTTTATTATAT-TAGTA
* *
58712767 T-TAT-TTTTA-TATATCATTA
1 TATATATTTTATTATATTAGTA
*
58712786 TATTTATTATTAT
1 TATATATT-TTAT
58712799 ACTTATTATT
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
19 4 0.06
20 10 0.16
21 8 0.13
22 9 0.15
23 15 0.24
24 14 0.23
25 2 0.03
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (22 bp):
TATATATTTTATTATATTAGTA
Found at i:58712775 original size:18 final size:18
Alignment explanation
Indices: 58712752--58712810 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 18
58712742 ATATATATAC
*
58712752 TTTTTATATATAGTATTA
1 TTTTTATATATATTATTA
58712770 TTTTTATATATCATTA-TA
1 TTTTTATATAT-ATTATTA
58712788 TTTATTAT-TATACTTATTA
1 TTT-TTATATATA-TTATTA
58712807 TTTT
1 TTTT
58712811 CACTATTGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
17 1 0.03
18 23 0.64
19 12 0.33
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTTATATATATTATTA
Found at i:58718225 original size:14 final size:14
Alignment explanation
Indices: 58718206--58718236 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
58718196 TGCTACTATT
58718206 TTACTATTATGTTG
1 TTACTATTATGTTG
*
58718220 TTACTATTTTGTTG
1 TTACTATTATGTTG
58718234 TTA
1 TTA
58718237 TTGTTTAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (14 bp):
TTACTATTATGTTG
Found at i:58724408 original size:18 final size:18
Alignment explanation
Indices: 58724372--58724409 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
58724362 TTTTTCTGCT
*
58724372 TCCCCTTCCCCATCCCCA
1 TCCCCTTCCCCATCACCA
*
58724390 TCCCCTTCCCCGTCACCA
1 TCCCCTTCCCCATCACCA
58724408 TC
1 TC
58724410 ACCGCCCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.63, G:0.03, T:0.24
Consensus pattern (18 bp):
TCCCCTTCCCCATCACCA
Found at i:58730214 original size:85 final size:85
Alignment explanation
Indices: 58730071--58730241 Score: 333
Period size: 85 Copynumber: 2.0 Consensus size: 85
58730061 GCATAGTGGA
58730071 AGATGAGGAGTGTCCACCTTCCTTTTTTTGTTTACAAGTGCTTTTTCTTATTTTTTTTATATTTA
1 AGATGAGGAGTGTCCACCTTCCTTTTTTTGTTTACAAGTGCTTTTTCTTATTTTTTTTATATTTA
58730136 AATAAAAATAATTAAATCTT
66 AATAAAAATAATTAAATCTT
*
58730156 AGATGAGGAGTGTCCCCCTTCCTTTTTTTGTTTACAAGTGCTTTTTCTTATTTTTTTTATATTTA
1 AGATGAGGAGTGTCCACCTTCCTTTTTTTGTTTACAAGTGCTTTTTCTTATTTTTTTTATATTTA
58730221 AATAAAAATAATTAAATCTT
66 AATAAAAATAATTAAATCTT
58730241 A
1 A
58730242 ATTTTATTCT
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (85 bp):
AGATGAGGAGTGTCCACCTTCCTTTTTTTGTTTACAAGTGCTTTTTCTTATTTTTTTTATATTTA
AATAAAAATAATTAAATCTT
Found at i:58737146 original size:42 final size:42
Alignment explanation
Indices: 58737060--58737202 Score: 162
Period size: 43 Copynumber: 3.3 Consensus size: 42
58737050 ATACCACATA
*
58737060 TGGGACGTTGGCATCG-ATTTGAGATTTACGTGTAAGACCATGTC
1 TGGGACATTGGCATCGTATTT--GATTT-CGTGTAAGACCATGTC
* *
58737104 TGGGACATTGGCATCGTATATGATTTCGTGTAAGACCTTGTC
1 TGGGACATTGGCATCGTATTTGATTTCGTGTAAGACCATGTC
* * * * *
58737146 TGAGACAGTGGCATCGATATTTGATTACATGTAAGACCACGTC
1 TGGGACATTGGCATCG-TATTTGATTTCGTGTAAGACCATGTC
*
58737189 TGGGACGTTGGCAT
1 TGGGACATTGGCAT
58737203 TATACGAGCT
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
42 29 0.35
43 37 0.44
44 15 0.18
45 3 0.04
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (42 bp):
TGGGACATTGGCATCGTATTTGATTTCGTGTAAGACCATGTC
Found at i:58737201 original size:43 final size:43
Alignment explanation
Indices: 58737031--58737202 Score: 165
Period size: 42 Copynumber: 4.0 Consensus size: 43
58737021 CATAGGATTT
* * *
58737031 TCGATA-TTG-TTATCGTGTAATACCACATATGGGACGTTGGCA
1 TCGATATTTGATTA-CGTGTAAGACCACGTCTGGGACGTTGGCA
* * *
58737073 TCGAT-TTGAGATTTACGTGTAAGACCATGTCTGGGACATTGGCA
1 TCGATATT-TGA-TTACGTGTAAGACCACGTCTGGGACGTTGGCA
* * ** *
58737117 TCG-TATATGATTTCGTGTAAGACCTTGTCTGAGACAG-TGGCA
1 TCGATATTTGATTACGTGTAAGACCACGTCTGGGAC-GTTGGCA
*
58737159 TCGATATTTGATTACATGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATTTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
58737202 T
1 T
58737203 TATACGAGCT
Statistics
Matches: 104, Mismatches: 18, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
42 37 0.36
43 36 0.35
44 28 0.27
45 3 0.03
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.33
Consensus pattern (43 bp):
TCGATATTTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
Found at i:58745928 original size:34 final size:34
Alignment explanation
Indices: 58745890--58745957 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
58745880 TTTCAACAGA
*
58745890 AAGCTTGCGAGGATGATTGCTCCTGTGGTGGAGC
1 AAGCTTGCGACGATGATTGCTCCTGTGGTGGAGC
58745924 AAGCTTGCGACGATGATTGCTCCTGTGGTGGAGC
1 AAGCTTGCGACGATGATTGCTCCTGTGGTGGAGC
58745958 TCTCTATAGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.18, C:0.19, G:0.37, T:0.26
Consensus pattern (34 bp):
AAGCTTGCGACGATGATTGCTCCTGTGGTGGAGC
Found at i:58749228 original size:85 final size:85
Alignment explanation
Indices: 58749125--58749284 Score: 293
Period size: 85 Copynumber: 1.9 Consensus size: 85
58749115 TTTATTGGAA
*
58749125 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGTGTTTGTGGAAAAAACGCCGCTAAAGGTCAAG
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGAAAAAACGCCGCTAAAGGTCAAG
58749190 GCTTTTAGCGCGTTTGTGAG
66 GCTTTTAGCGCGTTTGTGAG
* *
58749210 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAACGCCGCTAAAGGTCAAG
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGAAAAAACGCCGCTAAAGGTCAAG
58749275 GCTTTTAGCG
66 GCTTTTAGCG
58749285 GTGCTTTTTC
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 72 1.00
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (85 bp):
AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGAAAAAACGCCGCTAAAGGTCAAG
GCTTTTAGCGCGTTTGTGAG
Found at i:58749309 original size:43 final size:43
Alignment explanation
Indices: 58749125--58749285 Score: 279
Period size: 43 Copynumber: 3.8 Consensus size: 43
58749115 TTTATTGGAA
* *
58749125 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGTGTTTGTGGA
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
*
58749168 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGC-GCGTTTGTGAG
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
*
58749210 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
58749253 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGG
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGG
58749286 TGCTTTTTCT
Statistics
Matches: 111, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
42 38 0.34
43 73 0.66
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
Found at i:58749396 original size:31 final size:31
Alignment explanation
Indices: 58749361--58749443 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
58749351 CTTCCTGCAT
* *
58749361 TAAAATCCAACCAAATACAACAAATATAATA
1 TAAAATCCAACCAAAAACAACAAATATAACA
* * * *
58749392 TAAAATGCAGCCAAAAACAGCAAATTTAACA
1 TAAAATCCAACCAAAAACAACAAATATAACA
*
58749423 TAAAAAATACAACCAAAAACA
1 T--AAAATCCAACCAAAAACA
58749444 TTAATTCTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 26 0.62
33 16 0.38
ACGTcount: A:0.61, C:0.19, G:0.04, T:0.16
Consensus pattern (31 bp):
TAAAATCCAACCAAAAACAACAAATATAACA
Found at i:58750110 original size:75 final size:75
Alignment explanation
Indices: 58750024--58750172 Score: 271
Period size: 75 Copynumber: 2.0 Consensus size: 75
58750014 ATCACTTCAT
*
58750024 ATTCCGCCTTCTTCTCCTTTAGTTTCTCCTAAAAGATCAATTAAAGAGTTAGAAACGAAATATAT
1 ATTCCGCCTTCTTCTCCTTTAGTTTCTCCTAAAAAATCAATTAAAGAGTTAGAAACGAAATATAT
58750089 AATAAAAAGA
66 AATAAAAAGA
58750099 ATTCCGCCTTCTTCTCCTTTAGTTTCTCCTAAAAAATCAATTAAAGAGTTAGAAACGAAATATAT
1 ATTCCGCCTTCTTCTCCTTTAGTTTCTCCTAAAAAATCAATTAAAGAGTTAGAAACGAAATATAT
**
58750164 GGTAAAAAG
66 AATAAAAAG
58750173 GAATGCAACA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.32
Consensus pattern (75 bp):
ATTCCGCCTTCTTCTCCTTTAGTTTCTCCTAAAAAATCAATTAAAGAGTTAGAAACGAAATATAT
AATAAAAAGA
Found at i:58753542 original size:12 final size:12
Alignment explanation
Indices: 58753527--58753552 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
58753517 ATCATCCTCT
58753527 TCATCAGATTCA
1 TCATCAGATTCA
58753539 TCATCAGATTCA
1 TCATCAGATTCA
58753551 TC
1 TC
58753553 CCTCGATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (12 bp):
TCATCAGATTCA
Found at i:58755398 original size:9 final size:9
Alignment explanation
Indices: 58755384--58755500 Score: 99
Period size: 9 Copynumber: 12.3 Consensus size: 9
58755374 ATGTATTAGT
58755384 TAAGTTATG
1 TAAGTTATG
58755393 TAAGTTGTTATG
1 TAA---GTTATG
*
58755405 TACGTTATG
1 TAAGTTATG
* *
58755414 TGAGATATG
1 TAAGTTATG
*
58755423 TAAATTATG
1 TAAGTTATG
58755432 TAAGTTATG
1 TAAGTTATG
*
58755441 TGAGTTATG
1 TAAGTTATG
58755450 TAAGTTGTTATG
1 TAA---GTTATG
*
58755462 TAAATTATG
1 TAAGTTATG
*
58755471 TAAGTTATA
1 TAAGTTATG
*
58755480 TGAGTTATG
1 TAAGTTATG
*
58755489 TACGTTATG
1 TAAGTTATG
58755498 TAA
1 TAA
58755501 TTTCTTTAAG
Statistics
Matches: 84, Mismatches: 18, Indels: 12
0.74 0.16 0.11
Matches are distributed among these distances:
9 67 0.80
12 17 0.20
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.44
Consensus pattern (9 bp):
TAAGTTATG
Found at i:58755488 original size:57 final size:57
Alignment explanation
Indices: 58755386--58755498 Score: 154
Period size: 57 Copynumber: 2.0 Consensus size: 57
58755376 GTATTAGTTA
** * *
58755386 AGTTATGTAAGTTGTTATGTACGTTATGTGAGATATGTAAATTATGTAAGTTATGTG
1 AGTTATGTAAGTTGTTATGTAAATTATGTAAGATATATAAATTATGTAAGTTATGTG
* * * *
58755443 AGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATGAGTTATGTACGTTATGT
1 AGTTATGTAAGTTGTTATGTAAATTATGTAAGATATATAAATTATGTAAGTTATGT
58755499 AATTTCTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.45
Consensus pattern (57 bp):
AGTTATGTAAGTTGTTATGTAAATTATGTAAGATATATAAATTATGTAAGTTATGTG
Found at i:58755707 original size:9 final size:9
Alignment explanation
Indices: 58755693--58755809 Score: 99
Period size: 9 Copynumber: 12.3 Consensus size: 9
58755683 GAGTATTAGT
58755693 TAAGTTATG
1 TAAGTTATG
58755702 TAAGTTGTTATG
1 TAA---GTTATG
*
58755714 TACGTTATG
1 TAAGTTATG
* *
58755723 TGAGATATG
1 TAAGTTATG
*
58755732 TAAATTATG
1 TAAGTTATG
58755741 TAAGTTATG
1 TAAGTTATG
*
58755750 TGAGTTATG
1 TAAGTTATG
58755759 TAAGTTGTTATG
1 TAA---GTTATG
*
58755771 TAAATTATG
1 TAAGTTATG
*
58755780 TAAGTTATA
1 TAAGTTATG
*
58755789 TGAGTTATG
1 TAAGTTATG
*
58755798 TACGTTATG
1 TAAGTTATG
58755807 TAA
1 TAA
58755810 TTTCTTTAAG
Statistics
Matches: 84, Mismatches: 18, Indels: 12
0.74 0.16 0.11
Matches are distributed among these distances:
9 67 0.80
12 17 0.20
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.44
Consensus pattern (9 bp):
TAAGTTATG
Found at i:58755797 original size:57 final size:57
Alignment explanation
Indices: 58755695--58755807 Score: 154
Period size: 57 Copynumber: 2.0 Consensus size: 57
58755685 GTATTAGTTA
** * *
58755695 AGTTATGTAAGTTGTTATGTACGTTATGTGAGATATGTAAATTATGTAAGTTATGTG
1 AGTTATGTAAGTTGTTATGTAAATTATGTAAGATATATAAATTATGTAAGTTATGTG
* * * *
58755752 AGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATGAGTTATGTACGTTATGT
1 AGTTATGTAAGTTGTTATGTAAATTATGTAAGATATATAAATTATGTAAGTTATGT
58755808 AATTTCTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.45
Consensus pattern (57 bp):
AGTTATGTAAGTTGTTATGTAAATTATGTAAGATATATAAATTATGTAAGTTATGTG
Found at i:58755935 original size:309 final size:309
Alignment explanation
Indices: 58755376--58755997 Score: 1228
Period size: 309 Copynumber: 2.0 Consensus size: 309
58755366 TACACTACAT
58755376 GTATTAGTTAAGTTATGTAAGTTGTTATGTACGTTATGTGAGATATGTAAATTATGTAAGTTATG
1 GTATTAGTTAAGTTATGTAAGTTGTTATGTACGTTATGTGAGATATGTAAATTATGTAAGTTATG
58755441 TGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATGAGTTATGTACGTTATGTAATTTCT
66 TGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATGAGTTATGTACGTTATGTAATTTCT
58755506 TTAAGTAATGATCAATATCAGTATTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACA
131 TTAAGTAATGATCAATATCAGTATTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACA
58755571 CCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATA
196 CCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATA
*
58755636 TACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAATGTCAGA
261 TACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAAGGTCAGA
58755685 GTATTAGTTAAGTTATGTAAGTTGTTATGTACGTTATGTGAGATATGTAAATTATGTAAGTTATG
1 GTATTAGTTAAGTTATGTAAGTTGTTATGTACGTTATGTGAGATATGTAAATTATGTAAGTTATG
58755750 TGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATGAGTTATGTACGTTATGTAATTTCT
66 TGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATGAGTTATGTACGTTATGTAATTTCT
58755815 TTAAGTAATGATCAATATCAGTATTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACA
131 TTAAGTAATGATCAATATCAGTATTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACA
58755880 CCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATA
196 CCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATA
58755945 TACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAAGGTCAGA
261 TACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAAGGTCAGA
58755994 -TATT
1 GTATT
58755998 GTTGTCATTT
Statistics
Matches: 312, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
308 4 0.01
309 308 0.99
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (309 bp):
GTATTAGTTAAGTTATGTAAGTTGTTATGTACGTTATGTGAGATATGTAAATTATGTAAGTTATG
TGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATGAGTTATGTACGTTATGTAATTTCT
TTAAGTAATGATCAATATCAGTATTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACA
CCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATA
TACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAAGGTCAGA
Found at i:58759360 original size:13 final size:13
Alignment explanation
Indices: 58759339--58759369 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
58759329 TCGAATTGCT
58759339 GAAAATTTTAGGG
1 GAAAATTTTAGGG
*
58759352 GAAAGTTTTAGGG
1 GAAAATTTTAGGG
58759365 GAAAA
1 GAAAA
58759370 ACACTTAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.32, T:0.26
Consensus pattern (13 bp):
GAAAATTTTAGGG
Found at i:58759837 original size:18 final size:18
Alignment explanation
Indices: 58759803--58759837 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
58759793 TTGATTTATT
*
58759803 TAATATATAATTTAAAAA
1 TAATATATAATTAAAAAA
58759821 TAATATA-AATTAAAAAA
1 TAATATATAATTAAAAAA
58759838 CAATCAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAATATATAATTAAAAAA
Found at i:58759980 original size:26 final size:27
Alignment explanation
Indices: 58759951--58760025 Score: 109
Period size: 26 Copynumber: 2.9 Consensus size: 27
58759941 AAGAATTAGA
*
58759951 TAAAATTTGAAATATTGAAAATTATT-
1 TAAAATTTGAAATCTTGAAAATTATTC
*
58759977 TAAAATTTGAAATCTTGAAATTTATTC
1 TAAAATTTGAAATCTTGAAAATTATTC
*
58760004 T-AAATTTGAAATCTTTAAAATT
1 TAAAATTTGAAATCTTGAAAATT
58760026 TTAAATTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 43 0.98
27 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (27 bp):
TAAAATTTGAAATCTTGAAAATTATTC
Found at i:58760482 original size:29 final size:27
Alignment explanation
Indices: 58760416--58760505 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 27
58760406 TAATTAAACC
*
58760416 CCTT-AACCCCTAACCCATATCCCTTTAA
1 CCTTAAACCCATAACCCATA-CCC-TTAA
58760444 CCATTAAACCCATAACCCATGACCCTTAA
1 CC-TTAAACCCATAACCCAT-ACCCTTAA
*
58760473 TCCTTAAACCCATAATCCATAACCCTTAA
1 -CCTTAAACCCATAACCCAT-ACCCTTAA
58760502 CCTT
1 CCTT
58760506 TACCCACTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
28 6 0.11
29 30 0.55
30 18 0.33
31 1 0.02
ACGTcount: A:0.33, C:0.39, G:0.01, T:0.27
Consensus pattern (27 bp):
CCTTAAACCCATAACCCATACCCTTAA
Found at i:58760915 original size:28 final size:29
Alignment explanation
Indices: 58760875--58760929 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
58760865 AATAAATTGT
*
58760875 ATTTTAATCAATATAA-ATATAAATAAACC
1 ATTTAAATCAATA-AATATATAAATAAACC
*
58760904 ATTTAAAT-AATAAATATATACATAAA
1 ATTTAAATCAATAAATATATAAATAAA
58760930 ATACTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 2 0.09
28 14 0.61
29 7 0.30
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (29 bp):
ATTTAAATCAATAAATATATAAATAAACC
Found at i:58761144 original size:113 final size:115
Alignment explanation
Indices: 58760934--58761158 Score: 251
Period size: 113 Copynumber: 2.0 Consensus size: 115
58760924 CATAAAATAC
* * *
58760934 TTTTTGCGGCGTTTTTATAAGAAACGCCACTAATACTAGACCTATAGCGGCGTTTTTATAAAAAT
1 TTTTTGCGGCGTTTTCATAAGAAACGCCACTAATACTAGACCTATAGCGGCATTTTTATAAAAAC
** *** *
58760999 GCCGCTAATGTCACTAAGGTTTAAAACAAAACGACAGCGTCTTGCTGTTT
66 GCCGCTAATGAAACTAAGGGCCAAAACAAAACGACAGCATCTTGCTGTTT
* * * *
58761049 TTTTTGCGGCGTTTTCCA-AA-AAACGCCGCTAATACTTA-ACCTTTAGTGGCATTTTT-TGAAA
1 TTTTTGCGGCGTTTT-CATAAGAAACGCCACTAATAC-TAGACCTATAGCGGCATTTTTATAAAA
* ** *
58761110 ACGCCGCTAATGAAACTAAGGGCCGAAAGGAAACGACTGCATCTTGCTG
64 ACGCCGCTAATGAAACTAAGGGCCAAAACAAAACGACAGCATCTTGCTG
58761159 AAATTATTAG
Statistics
Matches: 91, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
113 42 0.46
114 29 0.32
115 19 0.21
116 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (115 bp):
TTTTTGCGGCGTTTTCATAAGAAACGCCACTAATACTAGACCTATAGCGGCATTTTTATAAAAAC
GCCGCTAATGAAACTAAGGGCCAAAACAAAACGACAGCATCTTGCTGTTT
Found at i:58761352 original size:40 final size:39
Alignment explanation
Indices: 58761208--58761339 Score: 149
Period size: 40 Copynumber: 3.3 Consensus size: 39
58761198 TAGGACATTT
*
58761208 GCGGCGTTTTTTATAAAAGCGCCGCTAATGCTCGATCTATA
1 GCGGCGTTTTTTA-AAAAACGCCGCTAATGCT-GATCTATA
* * *
58761249 GTGGCG-CTTTTAGAAAAACGCCGCTAATGTCTTATCTATA
1 GCGGCGTTTTTTA-AAAAACGCCGCTAATG-CTGATCTATA
* * * *
58761289 GTGGCGTTTGTTAAGAAACGCCGCTAATGCTGAACTATA
1 GCGGCGTTTTTTAAAAAACGCCGCTAATGCTGATCTATA
58761328 GCGGCGTTTTTT
1 GCGGCGTTTTTT
58761340 GTTTAAACGC
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
39 18 0.23
40 48 0.62
41 11 0.14
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (39 bp):
GCGGCGTTTTTTAAAAAACGCCGCTAATGCTGATCTATA
Found at i:58768805 original size:31 final size:30
Alignment explanation
Indices: 58768770--58768835 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
58768760 ATAATAAAGG
* *
58768770 TAAAATTGTATTTTAGTCCTTCTAAAAATGA
1 TAAAATTGTAATTTAAT-CTTCTAAAAATGA
* * *
58768801 TAAAATTTTAATTTAATCTTTTAAAAATTA
1 TAAAATTGTAATTTAATCTTCTAAAAATGA
58768831 TAAAA
1 TAAAA
58768836 ATATAAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (30 bp):
TAAAATTGTAATTTAATCTTCTAAAAATGA
Found at i:58775603 original size:23 final size:23
Alignment explanation
Indices: 58775573--58775624 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
58775563 TGCAACTTGG
58775573 TTTCATAATAATAGCTA-ATATGC
1 TTTCATAATAATAGCTATA-ATGC
*
58775596 TTTCATAATGATAGCTATAATGC
1 TTTCATAATAATAGCTATAATGC
58775619 TTTCAT
1 TTTCAT
58775625 CTTTTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (23 bp):
TTTCATAATAATAGCTATAATGC
Found at i:58779966 original size:9 final size:9
Alignment explanation
Indices: 58779952--58779983 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
58779942 AACTTGGTGC
58779952 ATTTTGTTT
1 ATTTTGTTT
58779961 ATTTTGTTT
1 ATTTTGTTT
58779970 ATTTTGTTT
1 ATTTTGTTT
58779979 ATTTT
1 ATTTT
58779984 TAATATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (9 bp):
ATTTTGTTT
Found at i:58780064 original size:23 final size:23
Alignment explanation
Indices: 58780034--58780085 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
58780024 TGCAACTTGG
58780034 TTTCATAATAATAGCTA-ATATGC
1 TTTCATAATAATAGCTATA-ATGC
*
58780057 TTTCATAATGATAGCTATAATGC
1 TTTCATAATAATAGCTATAATGC
58780080 TTTCAT
1 TTTCAT
58780086 CTTTTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (23 bp):
TTTCATAATAATAGCTATAATGC
Found at i:58782929 original size:35 final size:36
Alignment explanation
Indices: 58782889--58782960 Score: 128
Period size: 35 Copynumber: 2.0 Consensus size: 36
58782879 TCAATAAATG
*
58782889 TCATTAAGTTCCAAATGAAAATG-TTCCTTTTTTTT
1 TCATTAAGTTCCAAATGAAAATGTTTCATTTTTTTT
58782924 TCATTAAGTTCCAAATGAAAATGTTTCATTTTTTTT
1 TCATTAAGTTCCAAATGAAAATGTTTCATTTTTTTT
58782960 T
1 T
58782961 TCTTTACAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.50
Consensus pattern (36 bp):
TCATTAAGTTCCAAATGAAAATGTTTCATTTTTTTT
Found at i:58787214 original size:82 final size:82
Alignment explanation
Indices: 58787077--58787240 Score: 319
Period size: 82 Copynumber: 2.0 Consensus size: 82
58787067 GCCTCAGGGT
*
58787077 GTGGATATGATAAAATTTCATAGAACTCCGGTTGATAGAATTCGTAAACAAGGGGCCGAAGAATT
1 GTGGATATGATAAAATTTCACAGAACTCCGGTTGATAGAATTCGTAAACAAGGGGCCGAAGAATT
58787142 TAGGGCAAATATTGATG
66 TAGGGCAAATATTGATG
58787159 GTGGATATGATAAAATTTCACAGAACTCCGGTTGATAGAATTCGTAAACAAGGGGCCGAAGAATT
1 GTGGATATGATAAAATTTCACAGAACTCCGGTTGATAGAATTCGTAAACAAGGGGCCGAAGAATT
58787224 TAGGGCAAATATTGATG
66 TAGGGCAAATATTGATG
58787241 ACGGTGCCGA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.26
Consensus pattern (82 bp):
GTGGATATGATAAAATTTCACAGAACTCCGGTTGATAGAATTCGTAAACAAGGGGCCGAAGAATT
TAGGGCAAATATTGATG
Found at i:58792936 original size:46 final size:46
Alignment explanation
Indices: 58792886--58793058 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
58792876 TGGTTGAGCA
58792886 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
58792932 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
58792977 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
58793025 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
58793059 GGGGCGGGTT
Statistics
Matches: 108, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 60 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:58793042 original size:93 final size:93
Alignment explanation
Indices: 58792883--58793053 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
58792873 GGATGGTTGA
* * *
58792883 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
58792948 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
58792976 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
58793041 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
58793054 ACTTAGGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:58796661 original size:22 final size:22
Alignment explanation
Indices: 58796635--58796709 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
58796625 TATAAAATAG
*
58796635 ATATAAAAAAAATATGTACATA
1 ATATAAAAAAAATATATACATA
* *
58796657 ATATAGTGTAAAAAATACATACATA
1 ATATA---AAAAAAATATATACATA
**
58796682 ATATAATTAAAATATATACATA
1 ATATAAAAAAAATATATACATA
*
58796704 AGATAA
1 ATATAA
58796710 CATGTAGAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
22 23 0.55
25 19 0.45
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.29
Consensus pattern (22 bp):
ATATAAAAAAAATATATACATA
Found at i:58796679 original size:25 final size:24
Alignment explanation
Indices: 58796641--58796703 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
58796631 ATAGATATAA
** *
58796641 AAAAAATATGTACATAATATAGTGT
1 AAAAAATACATACATAATATAAT-T
58796666 AAAAAATACATACATAATATAATT
1 AAAAAATACATACATAATATAATT
58796690 AAAATATATACATA
1 AAAA-A-ATACATA
58796704 AGATAACATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.15
25 21 0.64
26 7 0.21
ACGTcount: A:0.59, C:0.06, G:0.05, T:0.30
Consensus pattern (24 bp):
AAAAAATACATACATAATATAATT
Found at i:58796754 original size:25 final size:25
Alignment explanation
Indices: 58796726--58796855 Score: 98
Period size: 23 Copynumber: 5.6 Consensus size: 25
58796716 GAAAAAATAT
*
58796726 ATATATAAATAATATAGTATTAAAG
1 ATATATACATAATATAGTATTAAAG
* *
58796751 ATATATACATAAAATAGTA-T-AAT
1 ATATATACATAATATAGTATTAAAG
* * *
58796774 ATATATACGTAATATAGAATT-TAG
1 ATATATACATAATATAGTATTAAAG
* *
58796798 A-ATATACCTAATATA-T-TAAAAG
1 ATATATACATAATATAGTATTAAAG
* *
58796820 A-ATATATATAATATAATATTAAA-
1 ATATATACATAATATAGTATTAAAG
*
58796843 AAATATA-ATAATA
1 ATATATACATAATA
58796856 ACAAAAAAAA
Statistics
Matches: 85, Mismatches: 15, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
21 1 0.01
22 15 0.18
23 39 0.46
24 13 0.15
25 17 0.20
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.35
Consensus pattern (25 bp):
ATATATACATAATATAGTATTAAAG
Found at i:58796754 original size:29 final size:28
Alignment explanation
Indices: 58796654--58796763 Score: 97
Period size: 29 Copynumber: 4.0 Consensus size: 28
58796644 AAATATGTAC
* *
58796654 ATAATATAGT-GTAAAA-A-ATACATAC
1 ATAATATAGTATTAAAATATATACATAA
58796679 ATAATATA--ATTAAAATATATACATAA
1 ATAATATAGTATTAAAATATATACATAA
* ** *
58796705 GATAACAT-GTAGAAAAAATATATATATAA
1 -ATAATATAGTA-TTAAAATATATACATAA
58796734 ATAATATAGTATTAAAGATATATACATAA
1 ATAATATAGTATTAAA-ATATATACATAA
58796763 A
1 A
58796764 ATAGTATAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
24 5 0.08
25 9 0.14
26 7 0.11
27 6 0.09
28 10 0.15
29 29 0.44
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.31
Consensus pattern (28 bp):
ATAATATAGTATTAAAATATATACATAA
Found at i:58796766 original size:27 final size:27
Alignment explanation
Indices: 58796654--58796787 Score: 81
Period size: 29 Copynumber: 5.1 Consensus size: 27
58796644 AAATATGTAC
*
58796654 ATAATATAGT-GTAAAA-A-ATACATA
1 ATAATATAGTATTAAAATATATACATA
58796678 CATAATATA--ATTAAAATATATACATAA
1 -ATAATATAGTATTAAAATATATACAT-A
* ** *
58796705 GATAACAT-GTAGAAAAAATATATATATAA
1 -ATAATATAGTA-TTAAAATATATACAT-A
58796734 ATAATATAGTATTAAAGATATATACAT-
1 ATAATATAGTATTAAA-ATATATACATA
* *
58796761 A-AA-ATAGTA-TAATATATATACGTA
1 ATAATATAGTATTAAAATATATACATA
58796785 ATA
1 ATA
58796788 TAGAATTTAG
Statistics
Matches: 86, Mismatches: 12, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
23 9 0.10
24 9 0.10
25 16 0.19
26 8 0.09
27 8 0.09
28 10 0.12
29 26 0.30
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (27 bp):
ATAATATAGTATTAAAATATATACATA
Found at i:58797178 original size:16 final size:16
Alignment explanation
Indices: 58797140--58797178 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
58797130 CTCCAAAAAA
*
58797140 AAAAACTAGCCTCTCC
1 AAAAACTAGCCTCTAC
*
58797156 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTCTAC
*
58797172 AATAACT
1 AAAAACT
58797179 CTTCTCCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAAACTAGCCTCTAC
Found at i:58797373 original size:30 final size:30
Alignment explanation
Indices: 58797336--58797434 Score: 180
Period size: 30 Copynumber: 3.3 Consensus size: 30
58797326 TAGGTACAAG
58797336 TGGTGGTGGAGCAAGTGTGGCTAATGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAATGGAGT
* *
58797366 AGGTGGTGGAGCAAATGTGGCTAATGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAATGGAGT
58797396 TGGTGGTGGAGCAAGTGTGGCTAATGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAATGGAGT
58797426 TGGTGGTGG
1 TGGTGGTGG
58797435 CAAAGGCTAG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.20, C:0.06, G:0.47, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAATGGAGT
Found at i:58797838 original size:21 final size:21
Alignment explanation
Indices: 58797812--58797853 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
58797802 GATATCCTCG
58797812 ATTAGCTCCACTGCAACTTCA
1 ATTAGCTCCACTGCAACTTCA
* *
58797833 ATTAGCTTCACTGTAACTTCA
1 ATTAGCTCCACTGCAACTTCA
58797854 GGGATATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.33
Consensus pattern (21 bp):
ATTAGCTCCACTGCAACTTCA
Found at i:58798095 original size:86 final size:89
Alignment explanation
Indices: 58797968--58798313 Score: 278
Period size: 86 Copynumber: 3.8 Consensus size: 89
58797958 ACTAGACATT
* * * * *
58797968 AAAAACATAAATTGAAAATA-ACTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATAA
1 AAAAACAT-AATTGAAAATACA-TCGGCATGTGACCCGAGGCTCAACTCACTTCTCGCAATATGA
**
58798032 GTTGATTTTTTTAAA-A-AAATTGTA
64 GTTGATTTTTTTAAACATAAATTAAA
* * * * * **
58798056 AAACAGAT-TTTGAAAATATC-TCGGTATGTGACCCGAGGCTCAACTCACCTCTCATAATATGAG
1 AAAAACATAATTGAAAATA-CATCGGCATGTGACCCGAGGCTCAACTCACTTCTCGCAATATGAG
*
58798119 TTGATTTTTGTAAAGCATAAATTAAA
65 TTGATTTTTTTAAA-CATAAATTAAA
* *
58798145 AAAAACATCAATTGAAAATACATCGGCGTGTGACCTGAGGCTCAACTCACCTT-TCGCAATATGA
1 AAAAACAT-AATTGAAAATACATCGGCATGTGACCCGAGGCTCAACTCA-CTTCTCGCAATATGA
58798209 GTTGATTTTTTTGACAAACATAAATTGAAAA
64 GTTGATTTTTTT---AAACATAAATT--AAA
* * * * * * * * *
58798240 AAAAAAAGAAATT-AAAA-ATATC-TCAGTGTGTCCTGAGGCTAAACTCACCTCTCGCAATATGC
1 AAAAACA-TAATTGAAAATACATCGGCA-TGTGACCCGAGGCTCAACTCACTTCTCGCAATATGA
58798302 GTTGATTTTTTT
64 GTTGATTTTTTT
58798314 TGGAAAAACA
Statistics
Matches: 207, Mismatches: 34, Indels: 29
0.77 0.13 0.11
Matches are distributed among these distances:
86 56 0.27
88 7 0.03
89 12 0.06
90 1 0.00
91 53 0.26
92 5 0.02
93 53 0.26
94 7 0.03
95 13 0.06
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (89 bp):
AAAAACATAATTGAAAATACATCGGCATGTGACCCGAGGCTCAACTCACTTCTCGCAATATGAGT
TGATTTTTTTAAACATAAATTAAA
Found at i:58798187 original size:91 final size:94
Alignment explanation
Indices: 58798065--58798311 Score: 292
Period size: 91 Copynumber: 2.7 Consensus size: 94
58798055 AAAACAGATT
* **
58798065 TTGAAAATATCTCGGTA-TGTGACCCGAGGCTCAACTCACCTCTCATAATATGAGTTGATTTTTG
1 TTGAAAATATCTCGG-AGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
* * **
58798129 T-A-AAGCATAAATT-AAAAAAAACATCAA
65 TGACAAACATAAATTAAAAAAAAAAAGAAA
* * *
58798156 TTGAAAATA-CATCGGCGTGTGACCTGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTT
1 TTGAAAATATC-TCGGAGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
58798220 TGACAAACATAAATTGAAAAAAAAAAAGAAA
65 TGACAAACATAAATT-AAAAAAAAAAAGAAA
* * * *
58798251 TTAAAAATATCTC--AGTGTGTCCTGAGGCTAAACTCACCTCTCGCAATATGCGTTGATTTTT
1 TTGAAAATATCTCGGAGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
58798312 TTTGGAAAAA
Statistics
Matches: 133, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
90 1 0.01
91 56 0.42
92 1 0.01
93 53 0.40
95 21 0.16
96 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (94 bp):
TTGAAAATATCTCGGAGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGT
GACAAACATAAATTAAAAAAAAAAAGAAA
Found at i:58798285 original size:93 final size:90
Alignment explanation
Indices: 58798005--58798313 Score: 276
Period size: 91 Copynumber: 3.4 Consensus size: 90
58797995 ACGTGAGCCA
* * ** * **
58798005 AGGCTCAACTCACTTCTCGCAATATAAGTTGATTTTTTT-AAA-A-AAATT--GTAAAACAGATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAACATAAATTAAAAAAAAAAGAAA
* *
58798065 TTGAAAATATC-TCG-GTATGTGACCCG
66 TTAAAAATA-CATCGAG--TGTGACCTG
** * * * **
58798091 AGGCTCAACTCACCTCTCATAATATGAGTTGATTTTTGTAAAGCATAAATTAAAAAAAACATCAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAACATAAATTAAAAAAAAAAGAAA
* *
58798156 TTGAAAATACATCGGCGTGTGACCTG
66 TTAAAAATACATC-GAGTGTGACCTG
*
58798182 AGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTTGACAAACATAAATTGAAAAAAAAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT-A-AAACATAAATT--AAAAAAAAAA
*
58798247 GAAATTAAAAATATC-TC-AGTGTGTCCTG
62 GAAATTAAAAATA-CATCGAGTGTGACCTG
* *
58798275 AGGCTAAACTCACCTCTCGCAATATGCGTTGATTTTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
58798314 TGGAAAAACA
Statistics
Matches: 183, Mismatches: 27, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
86 34 0.19
87 2 0.01
88 1 0.01
89 5 0.03
90 1 0.01
91 60 0.33
92 2 0.01
93 56 0.31
95 21 0.11
96 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (90 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAACATAAATTAAAAAAAAAAGAAA
TTAAAAATACATCGAGTGTGACCTG
Found at i:58798335 original size:15 final size:14
Alignment explanation
Indices: 58798316--58798348 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
58798306 ATTTTTTTTG
58798316 GAAAAACA-ATATTT
1 GAAAAACAGA-ATTT
58798330 GAAAAACAGAATTT
1 GAAAAACAGAATTT
58798344 GAAAA
1 GAAAA
58798349 TACCTCAGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.94
15 1 0.06
ACGTcount: A:0.61, C:0.06, G:0.12, T:0.21
Consensus pattern (14 bp):
GAAAAACAGAATTT
Found at i:58798362 original size:93 final size:92
Alignment explanation
Indices: 58797968--58798513 Score: 348
Period size: 93 Copynumber: 6.0 Consensus size: 92
58797958 ACTAGACATT
* * * * * *
58797968 AAAAACATAAATTGAAAATAACTCAGCACGTGAG-CC-AAGGCTCAACTCACTTCTCGCAATATA
1 AAAAACAGAAATTGAAAATACCTCAG--CGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
*
58798031 AGTTGA-TTTTTTT---AAA-AA-AATTG
64 AGCTGATTTTTTTTGAAAAACAATAATTG
* ** * * ** * * **
58798054 TAAAACAGATTTTGAAAATATCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCATAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
* * * *
58798119 TTGA---TTTTTGTAAAGC-ATAAATTAAA
66 CTGATTTTTTTTGAAAAACAAT-AATT--G
** * * * *
58798145 AAAAACATCAATTGAAAATACATCGGCGTGTGACCTGAGGCTCAACTCACCTTTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
* *
58798210 TTGA-TTTTTTTGACAAAC-ATAAATTG
66 CTGATTTTTTTTGAAAAACAAT-AATTG
* * * *
58798236 AAAAAAAAAAAGAAATTAAAAATATCTCA--GTGTGTCCTGAGGCTAAACTCACCTCTCGCAATA
1 ----AAAAACAGAAATTGAAAATACCTCAGCGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
* * *
58798299 TGCGTTGATTTTTTTTGGAAAAACAATATTTG
62 TGAGCTGATTTTTTTT-GAAAAACAATAATTG
* * * *
58798331 AAAAACAGAATTTGAAAATACCTCAGCGTGTGAGT-C-AAGGCTCAACTCACCACTCCCAATATG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGT--GTCCTGAGGCTCAACTCACCTCTCGCAATATG
*
58798394 AGCTGATTTTTTTTGAAACACAGA-AATTG
64 AGCTGATTTTTTTTGAAAAACA-ATAATTG
* * * * * *
58798423 AAGAACAGAAATGGAAAACACCTCAGC----GTCTTGAGGTTCAACTCACCTCTCACAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
* *
58798484 CTGA-TTTTTTTGAAAGACAAAAATTG
66 CTGATTTTTTTTGAAAAACAATAATTG
58798510 AAAA
1 AAAA
58798514 TACCTCAACG
Statistics
Matches: 364, Mismatches: 69, Indels: 53
0.75 0.14 0.11
Matches are distributed among these distances:
84 8 0.02
85 2 0.01
86 51 0.14
87 25 0.07
88 29 0.08
89 4 0.01
91 77 0.21
92 34 0.09
93 94 0.26
94 8 0.02
95 30 0.08
96 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (92 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
CTGATTTTTTTTGAAAAACAATAATTG
Found at i:58798579 original size:73 final size:74
Alignment explanation
Indices: 58798450--58799006 Score: 781
Period size: 73 Copynumber: 7.6 Consensus size: 74
58798440 ACACCTCAGC
* * * *
58798450 GTCTTGAGGTTCAACTCACCTCTCACAATATGAGCTGATTTTTTTGA-AAGACAAAAATTGAAAA
1 GTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGACAA-ACAAAAATTGAAAT
58798514 TACCTCAACGT
64 TACCTCAACGT
*
58798525 GTCTTGAGGCTCAACTCACCTCTTGCAATATGAGTTGA-TTTTTGACAAACAAAAATTGAAATTA
1 GTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGACAAACAAAAATTGAAATTA
*
58798589 CCTC-A-GC
66 CCTCAACGT
* * * *
58798596 GTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGA-AAGACAGAAATTGAAAA
1 GTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGACAA-ACAAAAATTGAAAT
58798660 TACCTCAACGT
64 TACCTCAACGT
58798671 GTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGACAAA-AAAAATTGAAATTA
1 GTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGACAAACAAAAATTGAAATTA
**
58798734 CCTCGGCGT
66 CCTCAACGT
* *
58798743 GTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTAACAAACAAAAATTGAAATTA
1 GTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGACAAACAAAAATTGAAATTA
*
58798807 CCTCAGCGT
66 CCTCAACGT
* * * * *
58798816 GTCCTGAGGCTCAACTCACCTATCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAT
1 GTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGACAAACAAAAATTGAAATT
58798881 ACCTCAACGT
65 ACCTCAACGT
* *
58798891 GTCTTGAGGCTCAACTCACCTCTTGCAATATGAGTTGAGTTTTT-ACAAACAAAAATTGAAATTA
1 GTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGACAAACAAAAATTGAAATTA
**
58798955 CCTCAGTGT
66 CCTCAACGT
*
58798964 GTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 GTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
58799007 GAAAAATAGA
Statistics
Matches: 433, Mismatches: 39, Indels: 22
0.88 0.08 0.04
Matches are distributed among these distances:
71 36 0.08
72 69 0.16
73 182 0.42
74 10 0.02
75 136 0.31
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (74 bp):
GTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGACAAACAAAAATTGAAATTA
CCTCAACGT
Found at i:58799045 original size:15 final size:14
Alignment explanation
Indices: 58799008--58799054 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
58798998 TTGATTTTTG
*
58799008 AAAAATAGAAATT-
1 AAAAAAAGAAATTA
**
58799021 AAAAGCAGAAATTGA
1 AAAAAAAGAAATT-A
58799036 AAAAAAAGAAATTA
1 AAAAAAAGAAATTA
58799050 AAAAA
1 AAAAA
58799055 TACCTCGCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
13 11 0.39
14 6 0.21
15 11 0.39
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (14 bp):
AAAAAAAGAAATTA
Found at i:58799147 original size:15 final size:14
Alignment explanation
Indices: 58799110--58799156 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
58799100 TTGATTTTTG
*
58799110 AAAAATAGAAATT-
1 AAAAAAAGAAATTA
**
58799123 AAAAGCAGAAATTGA
1 AAAAAAAGAAATT-A
58799138 AAAAAAAGAAATTA
1 AAAAAAAGAAATTA
58799152 AAAAA
1 AAAAA
58799157 TACCTCGCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
13 11 0.39
14 6 0.21
15 11 0.39
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (14 bp):
AAAAAAAGAAATTA
Found at i:58799217 original size:89 final size:90
Alignment explanation
Indices: 58799123--58799300 Score: 234
Period size: 90 Copynumber: 2.0 Consensus size: 90
58799113 AATAGAAATT
* * *
58799123 AAAAGCAGAAATTGAAAAAAAAGAAATTAAAAAATACCTC-GC-CATGCCCCAAGGCTCAGCTCA
1 AAAAGCAGAAATTGAAAAAAAAGAAATT-AAAAATACCTCAGCGCATGACCCAAGGCCCAACTCA
58799186 CCTCTCGCAATATGAGTTGATTTTTG
65 CCTCTCGCAATATGAGTTGATTTTTG
* ** * ** **
58799212 AAAAGCATAAATTGAAAAAACGGAAATTGAAAATACCTCAGCGTGTGACCTGAGGCCCAACTCAC
1 AAAAGCAGAAATTGAAAAAAAAGAAATTAAAAATACCTCAGCGCATGACCCAAGGCCCAACTCAC
58799277 CTCTCGCAATATGAGTTGATTTTT
66 CTCTCGCAATATGAGTTGATTTTT
58799301 TTGAAAGATA
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
88 10 0.13
89 27 0.36
90 39 0.51
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.24
Consensus pattern (90 bp):
AAAAGCAGAAATTGAAAAAAAAGAAATTAAAAATACCTCAGCGCATGACCCAAGGCCCAACTCAC
CTCTCGCAATATGAGTTGATTTTTG
Found at i:58799224 original size:102 final size:102
Alignment explanation
Indices: 58798970--58799215 Score: 483
Period size: 102 Copynumber: 2.4 Consensus size: 102
58798960 GTGTGTCCTG
*
58798970 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAAAAGCAGAAATTG
1 AGGCTCAGCTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAAAAGCAGAAATTG
58799035 AAAAAAAAGAAATTAAAAAATACCTCGCCATGCCCCA
66 AAAAAAAAGAAATTAAAAAATACCTCGCCATGCCCCA
58799072 AGGCTCAGCTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAAAAGCAGAAATTG
1 AGGCTCAGCTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAAAAGCAGAAATTG
58799137 AAAAAAAAGAAATTAAAAAATACCTCGCCATGCCCCA
66 AAAAAAAAGAAATTAAAAAATACCTCGCCATGCCCCA
58799174 AGGCTCAGCTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
1 AGGCTCAGCTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
58799216 GCATAAATTG
Statistics
Matches: 143, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 143 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (102 bp):
AGGCTCAGCTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAAAAGCAGAAATTG
AAAAAAAAGAAATTAAAAAATACCTCGCCATGCCCCA
Found at i:58800198 original size:17 final size:17
Alignment explanation
Indices: 58800176--58800208 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
58800166 CCCTCTCTCT
58800176 TTTTCT-TTTTTATTTTC
1 TTTTCTCTTTTT-TTTTC
58800193 TTTTCTCTTTTTTTTT
1 TTTTCTCTTTTTTTTT
58800209 AAGATGTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTCTCTTTTTTTTTC
Found at i:58810641 original size:25 final size:23
Alignment explanation
Indices: 58810589--58810643 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
58810579 TATAAATAGT
58810589 AATAGTGTTAGAAATATACTATA
1 AATAGTGTTAGAAATATACTATA
* *
58810612 TATAGTGTTTGAAGTATATAC-ATAA
1 AATAGTGTTAGAA--ATATACTAT-A
58810637 AATAGTG
1 AATAGTG
58810644 AAAATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 2 0.08
25 13 0.50
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
AATAGTGTTAGAAATATACTATA
Found at i:58810966 original size:16 final size:16
Alignment explanation
Indices: 58810928--58810966 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
58810918 TAGACCAAGA
*
58810928 AAAAACTAGCCTCTCC
1 AAAAACTAGCCTCTAC
*
58810944 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTCTAC
*
58810960 AATAACT
1 AAAAACT
58810967 CTTCTCCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAAACTAGCCTCTAC
Found at i:58811161 original size:30 final size:30
Alignment explanation
Indices: 58811125--58811252 Score: 211
Period size: 30 Copynumber: 4.3 Consensus size: 30
58811115 AGGTACAAGT
*
58811125 GGTGGTGGAGCAAGTGTGGCTAATGGAGTA
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
58811155 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
* *
58811185 GATGGTGGAGCAAGTGTGGCTAGTGGAGTT
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
* *
58811215 GGTGGTGGAGCAGGTGTGGCTAGTGGAGTT
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
58811245 GGTGGTGG
1 GGTGGTGG
58811253 CAAAGGCTAG
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 93 1.00
ACGTcount: A:0.18, C:0.06, G:0.51, T:0.25
Consensus pattern (30 bp):
GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
Found at i:58812655 original size:22 final size:22
Alignment explanation
Indices: 58812615--58812656 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
58812605 AAACATCCCT
*
58812615 TTATTATTATATCTTTTATCTC
1 TTATTATTATATCTATTATCTC
58812637 TTATTATTATTAT-TATTATC
1 TTATTATTA-TATCTATTATC
58812657 ATATTCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (22 bp):
TTATTATTATATCTATTATCTC
Found at i:58814211 original size:40 final size:40
Alignment explanation
Indices: 58814104--58814251 Score: 197
Period size: 41 Copynumber: 3.6 Consensus size: 40
58814094 AAATGCCGCT
* *
58814104 AAAAACTGAGCAATAGTGGCGTTTTCATTCAAAACGCTGCT
1 AAAAACTGAGAAATAGTGGCGTTTT-ATTCAAAACGCTGCA
* *
58814145 AAAAACTGAGTAATAGTGGCGTTTTTATACAAAACGCTGCA
1 AAAAACTGAGAAATAGTGGCG-TTTTATTCAAAACGCTGCA
* *
58814186 AAAAACTGAGAAATAGTGGCGTTTTATTCAAAATGCCGCA
1 AAAAACTGAGAAATAGTGGCGTTTTATTCAAAACGCTGCA
* * *
58814226 AAAAGCTGAGATATAGTGGCGCTTTA
1 AAAAACTGAGAAATAGTGGCGTTTTA
58814252 GGTCCAAACG
Statistics
Matches: 96, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
40 39 0.41
41 53 0.55
42 4 0.04
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (40 bp):
AAAAACTGAGAAATAGTGGCGTTTTATTCAAAACGCTGCA
Found at i:58814269 original size:81 final size:82
Alignment explanation
Indices: 58814104--58814269 Score: 198
Period size: 81 Copynumber: 2.0 Consensus size: 82
58814094 AAATGCCGCT
* * *
58814104 AAAAACTGAGCAATAGTGGCGTTTTCATTCAAAACGCTGCTAAAAACTGAGTAATAGTGGCGTTT
1 AAAAACTGAGAAATAGTGGCGTTTTCATTCAAAACGCCGCTAAAAACTGAGTAATAGTGGCGTCT
**
58814169 TTATACAAAACGCTGCA
66 TTATACAAAACGCCACA
*
58814186 AAAAACTGAGAAATAGTGGCGTTTT-ATTCAAAATGCCGC-AAAAAGCTGAG-ATATAGTGGCG-
1 AAAAACTGAGAAATAGTGGCGTTTTCATTCAAAACGCCGCTAAAAA-CTGAGTA-ATAGTGGCGT
*
58814247 CTTTAGGT-CCAAACGCCACA
64 CTTTA--TACAAAACGCCACA
58814267 AAA
1 AAA
58814270 GGTTGAGCTA
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
80 10 0.14
81 38 0.52
82 25 0.34
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.24
Consensus pattern (82 bp):
AAAAACTGAGAAATAGTGGCGTTTTCATTCAAAACGCCGCTAAAAACTGAGTAATAGTGGCGTCT
TTATACAAAACGCCACA
Found at i:58814270 original size:40 final size:40
Alignment explanation
Indices: 58814104--58814287 Score: 117
Period size: 41 Copynumber: 4.5 Consensus size: 40
58814094 AAATGCCGCT
* * **
58814104 AAAAA-CTGAGCA-ATAGTGGCGTTTTCATTCAAAACGCTGC
1 AAAAAGCTGAG-ATATAGTGGCGCTTT-AGTCAAAACGCCAC
* **
58814144 TAAAAA-CTGAG-TAATAGTGGCGTTTTTA-TACAAAACGCTGC
1 -AAAAAGCTGAGAT-ATAGTGGCG-CTTTAGT-CAAAACGCCAC
* * * * * *
58814185 AAAAAACTGAGAAATAGTGGCGTTTTATTCAAAATGCCGC
1 AAAAAGCTGAGATATAGTGGCGCTTTAGTCAAAACGCCAC
*
58814225 AAAAAGCTGAGATATAGTGGCGCTTTAGGTCCAAACGCCAC
1 AAAAAGCTGAGATATAGTGGCGCTTTA-GTCAAAACGCCAC
* * *
58814266 AAAAGGTTGAGCTATAGTGGCG
1 AAAAAGCTGAGATATAGTGGCG
58814288 TTTTTGTAAA
Statistics
Matches: 122, Mismatches: 13, Indels: 16
0.81 0.09 0.11
Matches are distributed among these distances:
40 44 0.36
41 74 0.61
42 4 0.03
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (40 bp):
AAAAAGCTGAGATATAGTGGCGCTTTAGTCAAAACGCCAC
Found at i:58814871 original size:29 final size:29
Alignment explanation
Indices: 58814832--58814887 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
58814822 AAAATATGAA
*
58814832 GCCTAACCCCTAAATCATAACCGATGACC
1 GCCTAACCCCTAAATCATAACCCATGACC
*
58814861 GCCTAATCCCTAAATCATAACCCATGA
1 GCCTAACCCCTAAATCATAACCCATGA
58814888 TCTAAACTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.36, G:0.09, T:0.20
Consensus pattern (29 bp):
GCCTAACCCCTAAATCATAACCCATGACC
Found at i:58815081 original size:14 final size:15
Alignment explanation
Indices: 58815055--58815098 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
58815045 CTTTAAACCC
58815055 TTATAATACCCTAAA-
1 TTATAA-ACCCTAAAT
58815070 TTATAAACCCTAAAT
1 TTATAAACCCTAAAT
*
58815085 TTGTAAACCCTAAA
1 TTATAAACCCTAAA
58815099 AATAAATTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 8 0.30
15 19 0.70
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.32
Consensus pattern (15 bp):
TTATAAACCCTAAAT
Found at i:58816228 original size:20 final size:20
Alignment explanation
Indices: 58816183--58816234 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
58816173 CCCCACCCAA
* *
58816183 ATTTCCCCAAATCCTTAACT
1 ATTTCCCCAAATCCCTAAAT
*
58816203 -TTTCCCCTAATCCCTAAAT
1 ATTTCCCCAAATCCCTAAAT
*
58816222 ATTTCCCCGAATC
1 ATTTCCCCAAATC
58816235 AAAATCGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.27, C:0.37, G:0.02, T:0.35
Consensus pattern (20 bp):
ATTTCCCCAAATCCCTAAAT
Found at i:58816276 original size:19 final size:19
Alignment explanation
Indices: 58816252--58816305 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
58816242 AAATATCCTT
58816252 CTGCCGTTGAAGACTCCGA
1 CTGCCGTTGAAGACTCCGA
58816271 CTGCCGTTGAAGACTCCGA
1 CTGCCGTTGAAGACTCCGA
*
58816290 CTGCCATTGAAGACTC
1 CTGCCGTTGAAGACTC
58816306 TGAGTGGACG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.22
Consensus pattern (19 bp):
CTGCCGTTGAAGACTCCGA
Found at i:58816677 original size:20 final size:19
Alignment explanation
Indices: 58816640--58816700 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 19
58816630 CATTTCATAT
* *
58816640 TTCAGTTTTAATTTTTTTTG
1 TTCAG-TTTAAATATTTTTG
58816660 TTCAGTTGTAAATA-TTTTG
1 TTCAGTT-TAAATATTTTTG
58816679 ATTCAG-TTAAAGTATTTTTG
1 -TTCAGTTTAAA-TATTTTTG
58816699 TT
1 TT
58816701 TTTGGGTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 4 0.11
19 12 0.34
20 19 0.54
ACGTcount: A:0.23, C:0.05, G:0.13, T:0.59
Consensus pattern (19 bp):
TTCAGTTTAAATATTTTTG
Found at i:58818376 original size:23 final size:23
Alignment explanation
Indices: 58818346--58818395 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
58818336 AACATTAATC
58818346 AAATGTATGAA-TTGCAGCCCTTT
1 AAATGTATGAATTTG-AGCCCTTT
58818369 AAATGTATGAATTTGAGCCCTTT
1 AAATGTATGAATTTGAGCCCTTT
58818392 AAAT
1 AAAT
58818396 AAACTTGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (23 bp):
AAATGTATGAATTTGAGCCCTTT
Found at i:58819025 original size:9 final size:9
Alignment explanation
Indices: 58819002--58819114 Score: 118
Period size: 9 Copynumber: 12.2 Consensus size: 9
58818992 ATTGATCATT
*
58819002 ACTTAAATA
1 ACTTACATA
*
58819011 AATTACATA
1 ACTTACATA
58819020 ACTTACATA
1 ACTTACATA
* *
58819029 ACTCATATA
1 ACTTACATA
*
58819038 ACTCACATA
1 ACTTACATA
58819047 ACTTACATAACA
1 ACTTACAT---A
58819059 ACTTACATA
1 ACTTACATA
*
58819068 ACTCACATA
1 ACTTACATA
58819077 ACTTACATA
1 ACTTACATA
*
58819086 ATTTACATA
1 ACTTACATA
*
58819095 ACTCACATA
1 ACTTACATA
*
58819104 ACGTACATA
1 ACTTACATA
58819113 AC
1 AC
58819115 AACTTACATA
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
9 78 0.90
12 9 0.10
ACGTcount: A:0.47, C:0.23, G:0.01, T:0.29
Consensus pattern (9 bp):
ACTTACATA
Done.