Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 200 of 335
Found at i:59828673 original size:18 final size:19
Alignment explanation
Indices: 59828652--59828712 Score: 74
Period size: 18 Copynumber: 3.3 Consensus size: 19
59828642 ATACTCACTC
59828652 TCTTTTTCAATTTTC-TTT
1 TCTTTTTCAATTTTCTTTT
**
59828670 TCTTGATCAA-TTTCTTTT
1 TCTTTTTCAATTTTCTTTT
59828688 TCTTTTTCAA-TTTCATTTT
1 TCTTTTTCAATTTTC-TTTT
59828707 TCTTTT
1 TCTTTT
59828713 CCTTACTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
17 4 0.11
18 23 0.62
19 10 0.27
ACGTcount: A:0.13, C:0.16, G:0.02, T:0.69
Consensus pattern (19 bp):
TCTTTTTCAATTTTCTTTT
Found at i:59831136 original size:27 final size:27
Alignment explanation
Indices: 59831106--59831159 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
59831096 TCATACAACC
* *
59831106 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
59831133 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
59831160 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:59832359 original size:18 final size:17
Alignment explanation
Indices: 59832325--59832359 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
59832315 GGATATTACA
*
59832325 CTTTTTCTTTCATTTCT
1 CTTTTTCTTTCAATTCT
59832342 CTTTTTCTTTCAAATTCT
1 CTTTTTCTTTC-AATTCT
59832360 TTCTCACTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.11, C:0.23, G:0.00, T:0.66
Consensus pattern (17 bp):
CTTTTTCTTTCAATTCT
Found at i:59834272 original size:55 final size:53
Alignment explanation
Indices: 59834185--59834441 Score: 253
Period size: 55 Copynumber: 4.8 Consensus size: 53
59834175 ATTAGGGTTT
*
59834185 AAGGATACCATGTAAGACCAT-TCCAAGGCATGGCAATTGGTAAGGGTTCTAAGGC
1 AAGGATACCATGTAAGACCATGT-CAAGACATGGCAA-TGGTAA-GGTTCTAAGGC
* *
59834240 AAGGATATCATGTAAGACCATGTCAAGACATGGC-ATGGATAAGTTTCTATATGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGG-TAAGGTTCTA-A-GGC
* * * *
59834295 AAAGG-T-CTCATGTAAGACCATGCCAAGGCATGGCACTGGTGA-GTTCATAAGGC
1 -AAGGATAC-CATGTAAGACCATGTCAAGACATGGCAATGGTAAGGTTC-TAAGGC
* *
59834348 AAGGATACCATGTAAGACCATGTCGAGACATGGCAATGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGGTTCTAAGGC
* * * *
59834397 AAGGATACCACGTAAGACCATGACAAGTCATGGCAATGGTTAGGT
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGGT
59834442 ACCCGTGTAT
Statistics
Matches: 170, Mismatches: 21, Indels: 28
0.78 0.10 0.13
Matches are distributed among these distances:
49 39 0.23
52 6 0.04
53 42 0.25
54 13 0.08
55 62 0.36
56 8 0.05
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.23
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGGTTCTAAGGC
Found at i:59834391 original size:108 final size:109
Alignment explanation
Indices: 59834193--59834394 Score: 311
Period size: 108 Copynumber: 1.9 Consensus size: 109
59834183 TTAAGGATAC
* * * *
59834193 CATGTAAGACCATTCCAAGGCATGGCAATTGGTAAGGGTTCTAAGGCAAGGATATCATGTAAGAC
1 CATGTAAGACCATGCCAAGGCATGGCAACTGGT-AGAGTTCTAAGGCAAGGATACCATGTAAGAC
59834258 CATGTCAAGACATGGCATGGATAAGTTTCTATATGGCAAAGGTCT
65 CATGTCAAGACATGGCATGGATAAGTTTCTATATGGCAAAGGTCT
59834303 CATGTAAGACCATGCCAAGGCATGGC-ACTGGT-GAGTTCATAAGGCAAGGATACCATGTAAGAC
1 CATGTAAGACCATGCCAAGGCATGGCAACTGGTAGAGTTC-TAAGGCAAGGATACCATGTAAGAC
*
59834366 CATGTCGAGACATGGCAATGG-TAAGTTTC
65 CATGTCAAGACATGGC-ATGGATAAGTTTC
59834395 AAAAGGATAC
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
107 5 0.06
108 46 0.54
109 9 0.11
110 25 0.29
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (109 bp):
CATGTAAGACCATGCCAAGGCATGGCAACTGGTAGAGTTCTAAGGCAAGGATACCATGTAAGACC
ATGTCAAGACATGGCATGGATAAGTTTCTATATGGCAAAGGTCT
Found at i:59834508 original size:5 final size:5
Alignment explanation
Indices: 59834498--59834525 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
59834488 AGAGAATATC
59834498 AAGGT AAGGT AAGGT AAGGT AAGGT AAG
1 AAGGT AAGGT AAGGT AAGGT AAGGT AAG
59834526 ACGAGTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.39, T:0.18
Consensus pattern (5 bp):
AAGGT
Found at i:59835295 original size:19 final size:19
Alignment explanation
Indices: 59835271--59835310 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
59835261 AGCTCCCATG
59835271 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
59835290 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
59835309 TA
1 TA
59835311 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:59836063 original size:26 final size:26
Alignment explanation
Indices: 59836026--59836161 Score: 209
Period size: 26 Copynumber: 5.2 Consensus size: 26
59836016 TGATACAAAT
* *
59836026 TGATAATAGGTTAGGTAAATGTTCCT
1 TGATAATGGGTTAGGTAAATGTTCCA
*
59836052 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
59836078 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
59836104 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
59836130 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
59836156 TTATAA
1 TGATAA
59836162 GAATATCATG
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 102 1.00
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:59836088 original size:52 final size:52
Alignment explanation
Indices: 59836026--59836161 Score: 236
Period size: 52 Copynumber: 2.6 Consensus size: 52
59836016 TGATACAAAT
*
59836026 TGATAATAGGTTAGGTAAATGTTCCTTGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
59836078 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
* * *
59836130 TGATAATGGGTTAGGTAAATGTTTCATTATAA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAA
59836162 GAATATCATG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 80 1.00
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.38
Consensus pattern (52 bp):
TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
Found at i:59838188 original size:137 final size:137
Alignment explanation
Indices: 59837942--59838228 Score: 556
Period size: 137 Copynumber: 2.1 Consensus size: 137
59837932 GAGTAGTCTC
59837942 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
59838007 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
59838072 ACTGTTA
131 ACTGTTA
59838079 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
59838144 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
59838209 ACTGTTA
131 ACTGTTA
**
59838216 CCTGAATGGGCTT
1 CCCAAATGGGCTT
59838229 AGGCCCAATA
Statistics
Matches: 148, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 148 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:59841950 original size:26 final size:26
Alignment explanation
Indices: 59841913--59842048 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
59841903 TGATACAAAT
* *
59841913 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
59841939 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
59841965 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
59841991 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
59842017 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
59842043 TGATAA
1 TGATAA
59842049 GAATATCATG
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:59844071 original size:137 final size:136
Alignment explanation
Indices: 59843825--59844110 Score: 545
Period size: 137 Copynumber: 2.1 Consensus size: 136
59843815 GAGTAGTCTC
59843825 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
59843890 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
59843955 ACTGTTA
131 ACTG-TA
59843962 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
59844027 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
59844092 ACTGTA
131 ACTGTA
**
59844098 CCTGAATGGGCTT
1 CCCAAATGGGCTT
59844111 AGGCCCAATA
Statistics
Matches: 147, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
136 13 0.09
137 134 0.91
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (136 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTA
Found at i:59845653 original size:14 final size:14
Alignment explanation
Indices: 59845631--59845678 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
59845621 ACCTAAACCG
* *
59845631 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
59845645 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
59845659 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
59845673 ACCATT
1 ACCATT
59845679 CCATTTGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:59846047 original size:10 final size:10
Alignment explanation
Indices: 59846032--59846088 Score: 64
Period size: 10 Copynumber: 5.8 Consensus size: 10
59846022 TACAAGTTCA
59846032 AAAAAAAATT
1 AAAAAAAATT
59846042 AAAAAAAATT
1 AAAAAAAATT
* *
59846052 CAAAAAAATCG
1 AAAAAAAAT-T
59846063 AAAAAAAA-T
1 AAAAAAAATT
*
59846072 CAAAAAAA-T
1 AAAAAAAATT
59846081 AAAAAAAA
1 AAAAAAAA
59846089 GTGATTTATG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
9 15 0.38
10 18 0.45
11 7 0.17
ACGTcount: A:0.81, C:0.05, G:0.02, T:0.12
Consensus pattern (10 bp):
AAAAAAAATT
Found at i:59846047 original size:11 final size:10
Alignment explanation
Indices: 59846032--59846088 Score: 66
Period size: 9 Copynumber: 5.8 Consensus size: 10
59846022 TACAAGTTCA
*
59846032 AAAAAAAATT
1 AAAAAAAATC
59846042 AAAAAAAATTC
1 AAAAAAAA-TC
59846053 -AAAAAAATC
1 AAAAAAAATC
59846062 GAAAAAAAATC
1 -AAAAAAAATC
59846073 -AAAAAAAT-
1 AAAAAAAATC
59846081 AAAAAAAA
1 AAAAAAAA
59846089 GTGATTTATG
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
9 17 0.40
10 15 0.36
11 10 0.24
ACGTcount: A:0.81, C:0.05, G:0.02, T:0.12
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:59846056 original size:20 final size:19
Alignment explanation
Indices: 59846033--59846088 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 19
59846023 ACAAGTTCAA
59846033 AAAAAAATTAAAAAAAATTC
1 AAAAAAATTAAAAAAAA-TC
*
59846053 AAAAAAATCGAAAAAAAATC
1 AAAAAAAT-TAAAAAAAATC
59846073 AAAAAAA-TAAAAAAAA
1 AAAAAAATTAAAAAAAA
59846089 GTGATTTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.24
20 17 0.52
21 8 0.24
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.12
Consensus pattern (19 bp):
AAAAAAATTAAAAAAAATC
Found at i:59849493 original size:29 final size:29
Alignment explanation
Indices: 59849460--59849519 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
59849450 ATAACCAAAC
*
59849460 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
59849489 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
59849518 CT
1 CT
59849520 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:59849512 original size:15 final size:15
Alignment explanation
Indices: 59849466--59849513 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
59849456 AAACCTACAA
*
59849466 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
59849481 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
59849495 AAACTTCATATCCAT
1 AAACTTCATATCCAT
59849510 AAAC
1 AAAC
59849514 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:59852214 original size:46 final size:46
Alignment explanation
Indices: 59852161--59852336 Score: 234
Period size: 46 Copynumber: 3.8 Consensus size: 46
59852151 TATTTGGGCA
59852161 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
59852207 TCCGAACTCGTTGAGTTGAGTCCGAGTT--C-T-TGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATG---CGA-GCG
*
59852254 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
59852300 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
59852337 GCGGGTTACA
Statistics
Matches: 114, Mismatches: 7, Indels: 18
0.82 0.05 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
44 1 0.01
46 66 0.58
47 32 0.28
49 1 0.01
50 5 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:59852316 original size:93 final size:93
Alignment explanation
Indices: 59852157--59852328 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
59852147 GGGATATTTG
* *
59852157 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
59852222 TTGAGTCCGAGTTCTTGAGATGTAACTA
66 TTGAGTCCGAGTTCTTGAGATGTAACTA
*
59852250 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
59852315 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
59852329 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCTTGAGATGTAACTA
Found at i:59855078 original size:15 final size:15
Alignment explanation
Indices: 59855058--59855126 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
59855048 GTATCTTGGG
59855058 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
59855073 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
59855088 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
59855103 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
59855118 TTTCTTTAT
1 TTTCTTTAT
59855127 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:59855127 original size:30 final size:30
Alignment explanation
Indices: 59855049--59855136 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
59855039 CATAGTATTG
* * * *
59855049 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
59855079 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
59855109 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
59855137 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:59857548 original size:46 final size:46
Alignment explanation
Indices: 59857495--59857716 Score: 290
Period size: 46 Copynumber: 4.8 Consensus size: 46
59857485 TATTTGGGCA
*
59857495 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
59857541 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
*
59857586 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
59857634 CCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
59857680 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
59857717 GCGGGTTACA
Statistics
Matches: 157, Mismatches: 10, Indels: 18
0.85 0.05 0.10
Matches are distributed among these distances:
42 2 0.01
43 4 0.03
45 3 0.02
46 110 0.70
47 29 0.18
48 3 0.02
50 4 0.03
51 2 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:59857650 original size:93 final size:94
Alignment explanation
Indices: 59857491--59857716 Score: 320
Period size: 93 Copynumber: 2.4 Consensus size: 94
59857481 GGGATATTTG
* *
59857491 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
* *
59857556 TTGAGTCCGAGTTC-GTGA-GATG-TAACT
66 TTGAGTCCGAGTTCACTGAGGATGCGAA-T
*
59857583 AGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGA
1 -GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGA
*
59857648 GTTGAGTCCGAGTTCACTTATGGATGCGAAT
65 GTTGAGTCCGAGTTCACTGA-GGATGCGAAT
*
59857679 -GC--CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
59857717 GCGGGTTACA
Statistics
Matches: 122, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
92 35 0.29
93 76 0.62
94 4 0.03
96 5 0.04
97 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (94 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCACTGAGGATGCGAAT
Found at i:59860278 original size:14 final size:14
Alignment explanation
Indices: 59860259--59860303 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
59860249 AACTCATCTT
*
59860259 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
59860273 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
59860286 AATTTAATTTAATG
1 AGTTTAATTTAATG
59860300 AGTT
1 AGTT
59860304 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:59863600 original size:29 final size:29
Alignment explanation
Indices: 59863567--59863626 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
59863557 ATAACCAAAC
*
59863567 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
59863596 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
59863625 CT
1 CT
59863627 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:59863619 original size:15 final size:15
Alignment explanation
Indices: 59863573--59863620 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
59863563 AAACCTACAA
*
59863573 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
59863588 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
59863602 AAACTTCATATCCAT
1 AAACTTCATATCCAT
59863617 AAAC
1 AAAC
59863621 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:59868309 original size:14 final size:14
Alignment explanation
Indices: 59868287--59868334 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
59868277 ACCTAAACCG
* *
59868287 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
59868301 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
59868315 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
59868329 ACCATT
1 ACCATT
59868335 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:59871981 original size:30 final size:30
Alignment explanation
Indices: 59871947--59872044 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
59871937 AGCTCACTCC
59871947 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
59871977 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
59872007 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
59872037 TAGCTCAT
1 TAGCTCAT
59872045 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:59873711 original size:11 final size:11
Alignment explanation
Indices: 59873695--59873749 Score: 65
Period size: 11 Copynumber: 4.8 Consensus size: 11
59873685 TATACAAGTT
59873695 AAAAAAAAATC
1 AAAAAAAAATC
59873706 AAAAAAAAATTC
1 AAAAAAAAA-TC
* *
59873718 AAAAAAAATTG
1 AAAAAAAAATC
*
59873729 AAAAAAAATTC
1 AAAAAAAAATC
59873740 GAAAAAAAAA
1 -AAAAAAAAA
59873750 AAAAAGAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
11 20 0.53
12 18 0.47
ACGTcount: A:0.78, C:0.05, G:0.04, T:0.13
Consensus pattern (11 bp):
AAAAAAAAATC
Found at i:59873712 original size:12 final size:12
Alignment explanation
Indices: 59873695--59873725 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
59873685 TATACAAGTT
59873695 AAAAAAAAATCA
1 AAAAAAAAATCA
*
59873707 AAAAAAAATTCA
1 AAAAAAAAATCA
59873719 AAAAAAA
1 AAAAAAA
59873726 TTGAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.84, C:0.06, G:0.00, T:0.10
Consensus pattern (12 bp):
AAAAAAAAATCA
Found at i:59873721 original size:22 final size:23
Alignment explanation
Indices: 59873696--59873748 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
59873686 ATACAAGTTA
59873696 AAAAAAAATCAAAAAAAAATTC-
1 AAAAAAAATCAAAAAAAAATTCG
**
59873718 AAAAAAAATTGAAAAAAAATTCG
1 AAAAAAAATCAAAAAAAAATTCG
59873741 AAAAAAAA
1 AAAAAAAA
59873749 AAAAAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.77, C:0.06, G:0.04, T:0.13
Consensus pattern (23 bp):
AAAAAAAATCAAAAAAAAATTCG
Found at i:59874680 original size:9 final size:10
Alignment explanation
Indices: 59874673--59874728 Score: 62
Period size: 9 Copynumber: 5.5 Consensus size: 10
59874663 AAGAGAAAAC
59874673 AAAGAAAAGA
1 AAAGAAAAGA
59874683 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
59874695 AAAGAAGA-A
1 AAAGAAAAGA
59874704 AAAGAAAATGA
1 AAAGAAAA-GA
59874715 AAA-AAAAGA
1 AAAGAAAAGA
59874724 AAAGA
1 AAAGA
59874729 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 13 0.33
10 9 0.23
11 12 0.31
12 5 0.13
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:59874696 original size:21 final size:20
Alignment explanation
Indices: 59874662--59874728 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 20
59874652 ACATTCTTGT
59874662 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
59874683 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
59874704 AAAGAAAATGAAAAAAAAGA
1 AAAGAAAAAGCAAAAAAAGA
59874724 AAAGA
1 AAAGA
59874729 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.78, C:0.03, G:0.18, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:59874697 original size:6 final size:5
Alignment explanation
Indices: 59874673--59874728 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
59874663 AAGAGAAAAC
*
59874673 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AAA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AAAGA
59874719 AAAGA AAAGA
1 AAAGA AAAGA
59874729 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
4 7 0.16
5 22 0.50
6 15 0.34
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:59874805 original size:12 final size:12
Alignment explanation
Indices: 59874797--59874821 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59874787 TTTGAAAAGC
59874797 AAAAAGAAAATG
1 AAAAAGAAAATG
59874809 AAAAAGAAAATG
1 AAAAAGAAAATG
59874821 A
1 A
59874822 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:59874818 original size:18 final size:18
Alignment explanation
Indices: 59874791--59874846 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
59874781 AAAGCCTTTG
59874791 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
59874810 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
59874828 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
59874845 AA
1 AA
59874847 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:59874831 original size:30 final size:31
Alignment explanation
Indices: 59874797--59874878 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
59874787 TTTGAAAAGC
*
59874797 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
59874827 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
59874857 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
59874879 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:59874910 original size:20 final size:20
Alignment explanation
Indices: 59874885--59874922 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
59874875 AAATTGAAAC
59874885 AAAAGAAACGAGTGAGAAGA
1 AAAAGAAACGAGTGAGAAGA
*
59874905 AAAAGAATCGAGTGAGAA
1 AAAAGAAACGAGTGAGAA
59874923 AACAAGTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.05, G:0.29, T:0.08
Consensus pattern (20 bp):
AAAAGAAACGAGTGAGAAGA
Found at i:59877146 original size:30 final size:30
Alignment explanation
Indices: 59877112--59877209 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
59877102 AGCTCACTCC
59877112 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
59877142 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
59877172 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
59877202 TAGCTCAT
1 TAGCTCAT
59877210 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:59880674 original size:5 final size:5
Alignment explanation
Indices: 59880664--59880688 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
59880654 ATATCATTTT
59880664 CATTC CATTC CATTC CATTC CATTC
1 CATTC CATTC CATTC CATTC CATTC
59880689 TTTCGTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (5 bp):
CATTC
Found at i:59881051 original size:12 final size:11
Alignment explanation
Indices: 59881029--59881110 Score: 64
Period size: 12 Copynumber: 7.4 Consensus size: 11
59881019 CTTATCAAGT
59881029 AAGTT-AAAAA
1 AAGTTCAAAAA
59881039 AAGTTTCAAAAAA
1 AAG-TTC-AAAAA
59881052 AAGTTCAAAAAA
1 AAGTTC-AAAAA
*
59881064 AAGGTTAAAAAA
1 AA-GTTCAAAAA
**
59881076 AAGTTTTGAAAA
1 AAG-TTCAAAAA
59881088 AA-TTCAAAAA
1 AAGTTCAAAAA
59881098 AA-TT-AAAAA
1 AAGTTCAAAAA
59881107 AAGT
1 AAGT
59881111 GTGTTAAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
9 7 0.11
10 14 0.23
11 3 0.05
12 26 0.43
13 11 0.18
ACGTcount: A:0.65, C:0.04, G:0.10, T:0.22
Consensus pattern (11 bp):
AAGTTCAAAAA
Found at i:59881087 original size:13 final size:12
Alignment explanation
Indices: 59881034--59881099 Score: 73
Period size: 12 Copynumber: 5.5 Consensus size: 12
59881024 CAAGTAAGTT
59881034 AAAAAAAGTTTCA
1 AAAAAAAG-TTCA
59881047 AAAAAAAGTTCA
1 AAAAAAAGTTCA
59881059 AAAAAAAGGTT-A
1 AAAAAAA-GTTCA
**
59881071 AAAAAAAGTTTT
1 AAAAAAAGTTCA
*
59881083 GAAAAAA-TTCA
1 AAAAAAAGTTCA
59881094 AAAAAA
1 AAAAAA
59881100 TTAAAAAAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
11 10 0.22
12 25 0.54
13 11 0.24
ACGTcount: A:0.67, C:0.05, G:0.09, T:0.20
Consensus pattern (12 bp):
AAAAAAAGTTCA
Found at i:59881974 original size:19 final size:19
Alignment explanation
Indices: 59881950--59881989 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
59881940 AGCTCCCATG
59881950 TAGCTC-CACACCAGCTCAT
1 TAGCTCGCA-ACCAGCTCAT
*
59881969 TAGCTCGGAACCAGCTCAT
1 TAGCTCGCAACCAGCTCAT
59881988 TA
1 TA
59881990 TCAGCTCACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (19 bp):
TAGCTCGCAACCAGCTCAT
Found at i:59887403 original size:14 final size:14
Alignment explanation
Indices: 59887386--59887427 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
59887376 ACCGACCAAA
*
59887386 TTGTTCATACCATT
1 TTGTTCCTACCATT
*
59887400 TTGTTCCTACCCTT
1 TTGTTCCTACCATT
*
59887414 TCGTTCCTACCATT
1 TTGTTCCTACCATT
59887428 CCATTCGTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.14, C:0.31, G:0.07, T:0.48
Consensus pattern (14 bp):
TTGTTCCTACCATT
Found at i:59887637 original size:30 final size:30
Alignment explanation
Indices: 59887551--59887638 Score: 79
Period size: 30 Copynumber: 2.9 Consensus size: 30
59887541 TCGTATCACT
* *
59887551 TTCAACTCACGAGCTAAACCTTAGCTCAAC
1 TTCAGCTCACGAGCTAAAGCTTAGCTCAAC
* * * ** *
59887581 TTCATCTTAGGAG-TTTAGCCTCAGCTCAAC
1 TTCAGCTCACGAGCTAAAG-CTTAGCTCAAC
*
59887611 TTTAGCTCACGAGCTAAAGCTTAGCTCA
1 TTCAGCTCACGAGCTAAAGCTTAGCTCA
59887639 TTTTAGTTTA
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
29 2 0.05
30 37 0.88
31 3 0.07
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAAGCTTAGCTCAAC
Found at i:59890283 original size:15 final size:14
Alignment explanation
Indices: 59890265--59890318 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
59890255 AAGAGAAAAT
59890265 AAAGAAAGAAAAGAA
1 AAAGAAA-AAAAGAA
59890280 AAAGAAAAAGAAGAA
1 AAAGAAAAA-AAGAA
*
59890295 AAAGAAAATAAAATAA
1 AAAG-AAA-AAAAGAA
59890311 AAAGAAAA
1 AAAGAAAA
59890319 GAGAGGCAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
14 3 0.09
15 19 0.54
16 11 0.31
17 2 0.06
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (14 bp):
AAAGAAAAAAAGAA
Found at i:59890398 original size:11 final size:12
Alignment explanation
Indices: 59890367--59890397 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
59890357 TTGAGAGAAC
59890367 TTGAAAAAGCCT
1 TTGAAAAAGCCT
59890379 TTGAAAAAGCCT
1 TTGAAAAAGCCT
59890391 TTGAAAA
1 TTGAAAA
59890398 GAAAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:59890413 original size:12 final size:12
Alignment explanation
Indices: 59890393--59890423 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
59890383 AAAAGCCTTT
59890393 GAAAA-GAAAAA
1 GAAAATGAAAAA
59890404 GAAAATGAAAAA
1 GAAAATGAAAAA
59890416 GAAAATGA
1 GAAAATGA
59890424 GATTGAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (12 bp):
GAAAATGAAAAA
Found at i:59890432 original size:29 final size:31
Alignment explanation
Indices: 59890398--59890479 Score: 98
Period size: 29 Copynumber: 2.7 Consensus size: 31
59890388 CCTTTGAAAA
*
59890398 GAAAAAGAAAATGAAAAAGAAA-ATGAGATT
1 GAAAAAGAAAATGAAAAAGAAATATGAGAGT
* * *
59890428 G-AAAAGAGAACG-AAAAGAAATTTGAGAGT
1 GAAAAAGAAAATGAAAAAGAAATATGAGAGT
*
59890457 GAAAAAGAAGATGAAAAAGAAAT
1 GAAAAAGAAAATGAAAAAGAAAT
59890480 TGAAACAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
28 8 0.19
29 16 0.38
30 9 0.21
31 9 0.21
ACGTcount: A:0.63, C:0.01, G:0.23, T:0.12
Consensus pattern (31 bp):
GAAAAAGAAAATGAAAAAGAAATATGAGAGT
Found at i:59890465 original size:28 final size:28
Alignment explanation
Indices: 59890412--59890465 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
59890402 AAGAAAATGA
*
59890412 AAAAGAAAATGAGATTGAAAAGAGAACG
1 AAAAGAAAATGAGAGTGAAAAGAGAACG
*
59890440 AAAAGAAATTTGAGAGTGAAAA-AGAA
1 AAAAGAAA-ATGAGAGTGAAAAGAGAA
59890466 GATGAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.61, C:0.02, G:0.24, T:0.13
Consensus pattern (28 bp):
AAAAGAAAATGAGAGTGAAAAGAGAACG
Found at i:59890478 original size:18 final size:19
Alignment explanation
Indices: 59890394--59890478 Score: 52
Period size: 18 Copynumber: 4.4 Consensus size: 19
59890384 AAAGCCTTTG
*
59890394 AAAAGAAAAAGAA-AATGA
1 AAAAGAAAAAGAAGATTGA
*
59890412 AAAAGAAAATG-AGATTGA
1 AAAAGAAAAAGAAGATTGA
59890430 AAAGAGAACGAAAAGAA-ATTTGA
1 AAA-AG-A--AAAAGAAGA-TTGA
* **
59890453 GAGTGAAAAAGAAGA-TGA
1 AAAAGAAAAAGAAGATTGA
59890471 AAAAGAAA
1 AAAAGAAA
59890479 TTGAAACAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 16
0.67 0.12 0.21
Matches are distributed among these distances:
17 1 0.02
18 25 0.50
19 9 0.18
20 2 0.04
21 1 0.02
22 6 0.12
23 6 0.12
ACGTcount: A:0.66, C:0.01, G:0.22, T:0.11
Consensus pattern (19 bp):
AAAAGAAAAAGAAGATTGA
Found at i:59892613 original size:30 final size:31
Alignment explanation
Indices: 59892579--59892675 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
59892569 AGCTCACTCC
*
59892579 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
59892609 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
59892639 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
59892669 TAGCTCA
1 TAGCTCA
59892676 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:59894364 original size:12 final size:13
Alignment explanation
Indices: 59894338--59894394 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 13
59894328 ATACAAAGTC
59894338 AAAAAAATTCG--
1 AAAAAAATTCGAA
59894349 -AAAAAATTC-AA
1 AAAAAAATTCGAA
59894360 AAAAAAATTCGAAA
1 AAAAAAATTCG-AA
*
59894374 AGAAAAAAATCTGAA
1 A-AAAAAATTC-GAA
59894389 AAAAAA
1 AAAAAA
59894395 GTGTAGTCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
10 9 0.24
12 9 0.24
14 8 0.21
15 11 0.29
16 1 0.03
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAAAAATTCGAA
Found at i:59895528 original size:30 final size:30
Alignment explanation
Indices: 59895494--59895590 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
59895484 TAAACTAAAA
59895494 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
* * * * *
59895524 TGAGCTGAGGC-TAAACTCCTAAGCTAAAGT
1 TGAGCT-AAGCTTTAGCTCATGAGCTAAAGT
* * *
59895554 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCATGAGCT-AAAGT
59895584 TGAGCTA
1 TGAGCTA
59895591 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 2 0.04
30 43 0.83
31 7 0.13
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
Found at i:59897891 original size:30 final size:30
Alignment explanation
Indices: 59897820--59897902 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
59897810 CTTTTGTTTC
* *
59897820 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
59897851 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
59897880 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
59897903 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:59897902 original size:18 final size:18
Alignment explanation
Indices: 59897853--59897908 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
59897843 CACTCTCAAA
* *
59897853 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
59897870 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
59897888 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
59897907 TT
1 TT
59897909 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:59897909 original size:12 final size:12
Alignment explanation
Indices: 59897878--59897902 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59897868 TTTTTCAATC
59897878 TCATTTTCTTTT
1 TCATTTTCTTTT
59897890 TCATTTTCTTTT
1 TCATTTTCTTTT
59897902 T
1 T
59897903 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:59897981 original size:5 final size:5
Alignment explanation
Indices: 59897971--59898034 Score: 51
Period size: 5 Copynumber: 12.0 Consensus size: 5
59897961 CTCTTGCCTC
*
59897971 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TGCTTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT T-C-TTT
59898020 TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT
59898035 GTTTTCTCTT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
4 4 0.08
5 29 0.57
6 6 0.12
7 12 0.24
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:59898000 original size:22 final size:22
Alignment explanation
Indices: 59897973--59898025 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
59897963 CTTGCCTCTC
*
59897973 TTTTCTTTTTATTTCATTTT-CT
1 TTTTCTTTTT-TTGCATTTTGCT
* *
59897995 TTTTCTTCTTTTGCTTTTTGCT
1 TTTTCTTTTTTTGCATTTTGCT
59898017 TTTTCTTTT
1 TTTTCTTTT
59898026 CTTTTCTTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.77
Consensus pattern (22 bp):
TTTTCTTTTTTTGCATTTTGCT
Found at i:59900620 original size:30 final size:30
Alignment explanation
Indices: 59900586--59900682 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
59900576 AAAACTAAAA
59900586 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
59900616 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
59900646 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
59900676 TGAGCTA
1 TGAGCTA
59900683 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:59900735 original size:20 final size:21
Alignment explanation
Indices: 59900699--59900743 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
59900689 AGCTCGGTTT
59900699 AGCTCAGAAAAGATGGA-TTG
1 AGCTCAGAAAAGATGGATTTG
*
59900719 AGCTC-GAATAAGCTGGATTTG
1 AGCTCAGAA-AAGATGGATTTG
59900740 AGCT
1 AGCT
59900744 GGACAGAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 12 0.55
21 7 0.32
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.24
Consensus pattern (21 bp):
AGCTCAGAAAAGATGGATTTG
Found at i:59902689 original size:317 final size:318
Alignment explanation
Indices: 59902113--59902753 Score: 1257
Period size: 317 Copynumber: 2.0 Consensus size: 318
59902103 ATTTATGAAC
59902113 TATTTTAATACATTAGTGTGAACGTTTTTATTATTGTGTGAACACCTAGATGTCGAATTTGAAGG
1 TATTTTAATACATTAGTGTGAACGTTTTTATTATTGTGTGAACACCTAGATGTCGAATTTGAAGG
59902178 GTCATCTATGTGCCTATAAGTATTTGTTTTCTTTCAATTGTAAGGGACTTTTTGCCAAATTTTTT
66 GTCATCTATGTGCCTATAAGTATTTGTTTTCTTTCAATTGTAAGGGACTTTTTGCCAAATTTTTT
59902243 ATTGAATTTAATCTTGTGAGAATTTTCTTCTCTAAACTTTGTTTGAGACTTTGTTGACTTATCTA
131 ATTGAATTTAATCTTGTGAGAATTTTCTTCTCTAAACTTTGTTTGAGACTTTGTTGACTTATCTA
59902308 CCTAGTAGTGGCATCAACCCTGTTTCTTTCACCCTTATACCGAGGTTCCTACTTTGCTAAGTAGC
196 CCTAGTAGTGGCATCAACCCTGTTTCTTTCACCCTTATACCGAGGTTCCTACTTTGCTAAGTAGC
*
59902373 GGGTCGAGGTTCTATTATTTTCATTTTTGCCTTGAAAGCCTATAAGCATTTGGGTCGA
261 GGGTCGAGGTTCTATTATTTTCATTTTCGCCTTGAAAGCCTATAAGCATTTGGGTCGA
59902431 TATTTTAATACATTAGTGTGAACGTTTTTATTATTGTGTGAACACCTAGATGTCGAATTTGAAGG
1 TATTTTAATACATTAGTGTGAACGTTTTTATTATTGTGTGAACACCTAGATGTCGAATTTGAAGG
59902496 GTCATCTATGTGCCTATAAGTATTTGTTTTCTTTCAATTGTAAGGGACTTTTTGCCAAA-TTTTT
66 GTCATCTATGTGCCTATAAGTATTTGTTTTCTTTCAATTGTAAGGGACTTTTTGCCAAATTTTTT
59902560 ATTGAATTTAATCTTGTGAGAATTTTCTTCTCTAAACTTTGTTTGAGACTTTGTTGACTTATCTA
131 ATTGAATTTAATCTTGTGAGAATTTTCTTCTCTAAACTTTGTTTGAGACTTTGTTGACTTATCTA
*
59902625 CCTAGTAGTGGCGTCAACCCTGTTTCTTTCACCCTTATACCGAGGTTCCTACTTTGCTAAGTAGC
196 CCTAGTAGTGGCATCAACCCTGTTTCTTTCACCCTTATACCGAGGTTCCTACTTTGCTAAGTAGC
59902690 GGGTCGAGGTTCTATTATTTTCATTTTCGCCTTGAAAGCCTATAAGCATTTGGGTCGA
261 GGGTCGAGGTTCTATTATTTTCATTTTCGCCTTGAAAGCCTATAAGCATTTGGGTCGA
59902748 TATTTT
1 TATTTT
59902754 CTAATATTGG
Statistics
Matches: 321, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
317 197 0.61
318 124 0.39
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (318 bp):
TATTTTAATACATTAGTGTGAACGTTTTTATTATTGTGTGAACACCTAGATGTCGAATTTGAAGG
GTCATCTATGTGCCTATAAGTATTTGTTTTCTTTCAATTGTAAGGGACTTTTTGCCAAATTTTTT
ATTGAATTTAATCTTGTGAGAATTTTCTTCTCTAAACTTTGTTTGAGACTTTGTTGACTTATCTA
CCTAGTAGTGGCATCAACCCTGTTTCTTTCACCCTTATACCGAGGTTCCTACTTTGCTAAGTAGC
GGGTCGAGGTTCTATTATTTTCATTTTCGCCTTGAAAGCCTATAAGCATTTGGGTCGA
Found at i:59903208 original size:45 final size:45
Alignment explanation
Indices: 59903097--59903234 Score: 231
Period size: 45 Copynumber: 3.0 Consensus size: 45
59903087 CAAAAAAAAG
* * *
59903097 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAGGATGATAGGAACCTCGGTATA-AATGA
59903143 ACCTCGACCCACTATCAAGGATGATAGGAACCTCGGTATAAATGA
1 ACCTCGACCCACTATCAAGGATGATAGGAACCTCGGTATAAATGA
*
59903188 ACCTCGACCCACTATTAAGGATGATAGGAACCTCGGTATAAATGA
1 ACCTCGACCCACTATCAAGGATGATAGGAACCTCGGTATAAATGA
59903233 AC
1 AC
59903235 ACCACACTTT
Statistics
Matches: 88, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
45 50 0.57
46 38 0.43
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.22
Consensus pattern (45 bp):
ACCTCGACCCACTATCAAGGATGATAGGAACCTCGGTATAAATGA
Found at i:59904314 original size:50 final size:51
Alignment explanation
Indices: 59904217--59904314 Score: 135
Period size: 50 Copynumber: 1.9 Consensus size: 51
59904207 TTAATTTAAC
* **
59904217 GATGCAGACTTAAACTAACATGGTAGTTACATAATGCATGTCATTATTTAT
1 GATGCAGACTTAAACTAACATGGAAGTTACATAATGCATAACATTATTTAT
* * *
59904268 GATGCATACTT-AACTAGCATGGAAGTTACATAATGCATAACTTTATT
1 GATGCAGACTTAAACTAACATGGAAGTTACATAATGCATAACATTATT
59904315 AAATGCAGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
50 31 0.76
51 10 0.24
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (51 bp):
GATGCAGACTTAAACTAACATGGAAGTTACATAATGCATAACATTATTTAT
Found at i:59905755 original size:30 final size:30
Alignment explanation
Indices: 59905721--59905818 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
59905711 AGCTCACTCC
59905721 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
59905751 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
59905781 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
59905811 TAGCTCAT
1 TAGCTCAT
59905819 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:59907810 original size:8 final size:7
Alignment explanation
Indices: 59907793--59907843 Score: 59
Period size: 7 Copynumber: 7.0 Consensus size: 7
59907783 TTAAATTGAA
59907793 TTTTTAT
1 TTTTTAT
*
59907800 TTTTTAC
1 TTTTTAT
59907807 TTTTTATT
1 TTTTTA-T
59907815 TTTTTATT
1 TTTTTA-T
59907823 TTTTTAT
1 TTTTTAT
59907830 TTTTT-T
1 TTTTTAT
59907836 TATTTTAT
1 T-TTTTAT
59907844 CAGCATTGCA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
6 2 0.05
7 22 0.56
8 15 0.38
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTAT
Found at i:59907819 original size:9 final size:8
Alignment explanation
Indices: 59907793--59907841 Score: 66
Period size: 8 Copynumber: 6.2 Consensus size: 8
59907783 TTAAATTGAA
59907793 TTTTTA-T
1 TTTTTATT
*
59907800 TTTTTA-C
1 TTTTTATT
59907807 TTTTTATT
1 TTTTTATT
59907815 TTTTTATT
1 TTTTTATT
59907823 TTTTTATTT
1 TTTTTA-TT
59907832 TTTTTATT
1 TTTTTATT
59907840 TT
1 TT
59907842 ATCAGCATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
7 12 0.32
8 18 0.47
9 8 0.21
ACGTcount: A:0.12, C:0.02, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTATT
Found at i:59907820 original size:22 final size:20
Alignment explanation
Indices: 59907793--59907843 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 20
59907783 TTAAATTGAA
59907793 TTTTTATTTTTTACTTTTTATT
1 TTTTTATTTTTTA-TTTTT-TT
59907815 TTTTTATTTTTTTATTTTTTT
1 TTTTTA-TTTTTTATTTTTTT
59907836 TATTTTAT
1 T-TTTTAT
59907844 CAGCATTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.15
22 16 0.59
23 7 0.26
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTATTTTTTATTTTTTT
Found at i:59907841 original size:14 final size:14
Alignment explanation
Indices: 59907793--59907843 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 14
59907783 TTAAATTGAA
*
59907793 TTTTTATTTTTTAC
1 TTTTTATTTTTTAT
59907807 TTTTTATTTTTTTATT
1 TTTTTA-TTTTTTA-T
59907823 TTTTTATTTTTT-T
1 TTTTTATTTTTTAT
59907836 TATTTTAT
1 T-TTTTAT
59907844 CAGCATTGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 2 0.06
14 12 0.36
15 13 0.39
16 6 0.18
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTATTTTTTAT
Found at i:59910342 original size:15 final size:15
Alignment explanation
Indices: 59910304--59910361 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 15
59910294 ACCTTTTGTA
*
59910304 AAAAGAAAATGA--G
1 AAAAGAAAAAGAGTG
*
59910317 AAAATAAAAAGA-TG
1 AAAAGAAAAAGAGTG
59910331 AAAAGCAAAAAGAGGTG
1 AAAAG-AAAAAGA-GTG
59910348 AAAAGAAAAGAGAG
1 AAAAGAAAA-AGAG
59910362 GCAAGAAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 10 0.27
14 5 0.14
15 7 0.19
16 5 0.14
17 10 0.27
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.07
Consensus pattern (15 bp):
AAAAGAAAAAGAGTG
Found at i:59910351 original size:17 final size:17
Alignment explanation
Indices: 59910329--59910362 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
59910319 AATAAAAAGA
59910329 TGAAAAGCAAAA-AGAGG
1 TGAAAAG-AAAAGAGAGG
59910346 TGAAAAGAAAAGAGAGG
1 TGAAAAGAAAAGAGAGG
59910363 CAAGAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.59, C:0.03, G:0.32, T:0.06
Consensus pattern (17 bp):
TGAAAAGAAAAGAGAGG
Found at i:59910518 original size:18 final size:18
Alignment explanation
Indices: 59910465--59910519 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
59910455 AATGAGATTG
*
59910465 AAAAAGAGAATGAAAAAG-
1 AAAAAGAG-TTGAAAAAGA
**
59910483 AAAAAGAGTGTGTGAAAGA
1 AAAAAGAGT-TGAAAAAGA
59910502 AAAAAGAGTTGAAAAAGA
1 AAAAAGAGTTGAAAAAGA
59910520 GATTTAGATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 21 0.70
19 9 0.30
ACGTcount: A:0.64, C:0.00, G:0.25, T:0.11
Consensus pattern (18 bp):
AAAAAGAGTTGAAAAAGA
Found at i:59911999 original size:10 final size:10
Alignment explanation
Indices: 59911986--59912031 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
59911976 AGCTCACTTG
59911986 AGCTCGTTTT
1 AGCTCGTTTT
*
59911996 AGCTCGTTTG
1 AGCTCGTTTT
*
59912006 AGCTCGAATTT
1 AGCTCG-TTTT
*
59912017 AGCTCGTTTC
1 AGCTCGTTTT
59912027 AGCTC
1 AGCTC
59912032 ATTCCTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:59912019 original size:21 final size:20
Alignment explanation
Indices: 59911983--59912031 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
59911973 ATCAGCTCAC
*
59911983 TTGAGCTCGTTTTAGCTCGT
1 TTGAGCTCGATTTAGCTCGT
59912003 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAGCTCGT
*
59912024 TTCAGCTC
1 TTGAGCTC
59912032 ATTCCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:59915132 original size:10 final size:10
Alignment explanation
Indices: 59915119--59915220 Score: 60
Period size: 10 Copynumber: 9.1 Consensus size: 10
59915109 AAACTTTTGA
59915119 AAAAAAGTTC
1 AAAAAAGTTC
*
59915129 AAAAAAGTTTTGAA
1 AAAAAAG--TT--C
59915143 AAAAAAGTTC
1 AAAAAAGTTC
*
59915153 AAAAAAAAGTTTTG
1 --AAAAAAG--TTC
59915167 AAAAAAGTTTC
1 AAAAAAG-TTC
59915178 GAAAAAAAGTTC
1 --AAAAAAGTTC
*
59915190 AAAAAAATTC
1 AAAAAAGTTC
*
59915200 AAAAAAATTC
1 AAAAAAGTTC
*
59915210 AAAAAAATTC
1 AAAAAAGTTC
59915220 A
1 A
59915221 GAAATTTTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 20
0.75 0.05 0.20
Matches are distributed among these distances:
10 37 0.48
11 3 0.04
12 21 0.27
13 7 0.09
14 9 0.12
ACGTcount: A:0.62, C:0.07, G:0.09, T:0.23
Consensus pattern (10 bp):
AAAAAAGTTC
Found at i:59915132 original size:24 final size:25
Alignment explanation
Indices: 59915104--59915206 Score: 119
Period size: 24 Copynumber: 4.3 Consensus size: 25
59915094 CAAGTAAGTG
*
59915104 AAAAAAAACTTTTGAAAAAAAGTTC
1 AAAAAAAAGTTTTGAAAAAAAGTTC
59915129 --AAAAAAGTTTTGAAAAAAAAGTTC
1 AAAAAAAAGTTTTG-AAAAAAAGTTC
59915153 AAAAAAAAGTTTTG-AAAAAAGTTTC
1 AAAAAAAAGTTTTGAAAAAAAG-TTC
* *
59915178 GAAAAAAAG--TTCAAAAAAA-TTC
1 AAAAAAAAGTTTTGAAAAAAAGTTC
59915200 AAAAAAA
1 AAAAAAA
59915207 TTCAAAAAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
22 9 0.13
23 13 0.19
24 24 0.35
25 11 0.16
26 12 0.17
ACGTcount: A:0.62, C:0.06, G:0.10, T:0.22
Consensus pattern (25 bp):
AAAAAAAAGTTTTGAAAAAAAGTTC
Found at i:59915156 original size:12 final size:12
Alignment explanation
Indices: 59915118--59915216 Score: 89
Period size: 12 Copynumber: 8.5 Consensus size: 12
59915108 AAAACTTTTG
59915118 AAAAAAAGTTCA
1 AAAAAAAGTTCA
*** *
59915130 AAAAAGTTTTGA
1 AAAAAAAGTTCA
59915142 AAAAAAAGTTCA
1 AAAAAAAGTTCA
**
59915154 AAAAAAAGTTTT
1 AAAAAAAGTTCA
* *
59915166 GAAAAAAGTTTCG
1 AAAAAAAG-TTCA
59915179 AAAAAAAGTTC-
1 AAAAAAAGTTCA
59915190 AAAAAAA-TTC-
1 AAAAAAAGTTCA
59915200 AAAAAAA-TTCA
1 AAAAAAAGTTCA
59915211 AAAAAA
1 AAAAAA
59915217 TTCAGAAATT
Statistics
Matches: 71, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
10 13 0.18
11 13 0.18
12 36 0.51
13 9 0.13
ACGTcount: A:0.64, C:0.06, G:0.09, T:0.21
Consensus pattern (12 bp):
AAAAAAAGTTCA
Found at i:59915205 original size:20 final size:20
Alignment explanation
Indices: 59915179--59915220 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 20
59915169 AAAAGTTTCG
59915179 AAAAAAAGTTCAAAAAAATTC
1 AAAAAAA-TTCAAAAAAATTC
59915200 AAAAAAATTCAAAAAAATTC
1 AAAAAAATTCAAAAAAATTC
59915220 A
1 A
59915221 GAAATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.69, C:0.10, G:0.02, T:0.19
Consensus pattern (20 bp):
AAAAAAATTCAAAAAAATTC
Found at i:59916583 original size:46 final size:46
Alignment explanation
Indices: 59916530--59916702 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
59916520 TGGTTGAGCA
*
59916530 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
59916576 TCAGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* * *
59916623 TCCGAACTCGTTGAGTTGAGTCTGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*
59916669 CCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
59916703 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 60 0.58
47 27 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:59916686 original size:93 final size:93
Alignment explanation
Indices: 59916527--59916697 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
59916517 GGATGGTTGA
* *
59916527 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCAGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCAGAACTCGTTGAGT
59916592 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
59916620 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCATTTATGGATGCGAACGCCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCAGAACTCGTTGAGT
59916685 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
59916698 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCAGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:59920760 original size:30 final size:30
Alignment explanation
Indices: 59920726--59920822 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
59920716 TAAACTAAAA
* *
59920726 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * * *
59920756 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* *
59920786 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGATTTAGCTCGTGAGCT-AAAGT
59920816 TGAGCTA
1 TGAGCTA
59920823 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 47 0.94
31 3 0.06
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:59921955 original size:10 final size:10
Alignment explanation
Indices: 59921940--59921974 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
59921930 TTTGTACATA
*
59921940 ATATGCCACG
1 ATATGCCATG
59921950 ATATGCACATG
1 ATATGC-CATG
59921961 ATATGCCATG
1 ATATGCCATG
59921971 ATAT
1 ATAT
59921975 ATACATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (10 bp):
ATATGCCATG
Found at i:59921964 original size:21 final size:21
Alignment explanation
Indices: 59921935--59921974 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
59921925 ACTGATTTGT
59921935 ACATAATATGCCACGATATGC
1 ACATAATATGCCACGATATGC
* *
59921956 ACATGATATGCCATGATAT
1 ACATAATATGCCACGATAT
59921975 ATACATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (21 bp):
ACATAATATGCCACGATATGC
Found at i:59921980 original size:21 final size:20
Alignment explanation
Indices: 59921934--59921986 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
59921924 TACTGATTTG
*
59921934 TACATAATATGCCACGATATG
1 TACAT-ATATGCCACGATATA
* *
59921955 CACATGATATGCCATGATATA
1 TACAT-ATATGCCACGATATA
59921976 TACATATATGC
1 TACATATATGC
59921987 ATGGGTTGGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (20 bp):
TACATATATGCCACGATATA
Found at i:59922048 original size:25 final size:25
Alignment explanation
Indices: 59922020--59922086 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
59922010 GAGGAAGCGC
* * *
59922020 AAAACGGCTATGCCTCAGTATACCG
1 AAAAGGGCTTTGCCCCAGTATACCG
*
59922045 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTATACCG
59922070 AAAAGGGCTTTGCCCCA
1 AAAAGGGCTTTGCCCCA
59922087 ATTATTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.21
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTATACCG
Found at i:59922345 original size:31 final size:31
Alignment explanation
Indices: 59922310--59922393 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
59922300 CATTTACAGT
59922310 AAAGGCTTCGGCCCAGTGATATGAATAATGA
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
* *
59922341 AAAGGCTTCGGCCCAGTGGTATGAATAATGT
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
*
59922372 AAAGGCTTCAGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
59922394 CTGAGATTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 4 0.08
31 45 0.92
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATGA
Found at i:59924205 original size:30 final size:30
Alignment explanation
Indices: 59924171--59924237 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
59924161 TAAACTAAAA
59924171 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAG
1 TGAGCTAAGCTTTAGCTCGTGAGCTGAAAG
* *
59924200 TTGAGCTAAGGTTTAGCTCGTGAGTTGAAAG
1 -TGAGCTAAGCTTTAGCTCGTGAGCTGAAAG
59924231 TGAGCTA
1 TGAGCTA
59924238 GGAGTGAGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 30 0.88
31 4 0.12
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTGAAAG
Found at i:59924248 original size:30 final size:30
Alignment explanation
Indices: 59924184--59924249 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
59924174 GCTAAGCTTT
* *
59924184 AGCTCGTGAGCTAAAGTTGAGCTAAGGTTT
1 AGCTCGTGAGCTAAAGTTGAGCTAAGGGTG
*
59924214 AGCTCGTGAGTTGAAAG-TGAGCT-AGGAGTG
1 AGCTCGTGAGCT-AAAGTTGAGCTAAGG-GTG
59924244 AGCTCG
1 AGCTCG
59924250 GGTTAGCTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 3 0.10
30 24 0.77
31 4 0.13
ACGTcount: A:0.26, C:0.14, G:0.35, T:0.26
Consensus pattern (30 bp):
AGCTCGTGAGCTAAAGTTGAGCTAAGGGTG
Found at i:59926144 original size:30 final size:30
Alignment explanation
Indices: 59926073--59926155 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
59926063 CTTTTGTTTC
* *
59926073 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
*
59926104 AATTTC-TTTTCGTTCTCTTTTTTAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
59926133 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
59926156 GCTTTTCAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 5 0.11
30 31 0.70
31 8 0.18
ACGTcount: A:0.13, C:0.20, G:0.01, T:0.65
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:59926162 original size:12 final size:12
Alignment explanation
Indices: 59926131--59926155 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59926121 TTTTTTAATC
59926131 TCATTTTCTTTT
1 TCATTTTCTTTT
59926143 TCATTTTCTTTT
1 TCATTTTCTTTT
59926155 T
1 T
59926156 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:59926173 original size:12 final size:12
Alignment explanation
Indices: 59926158--59926188 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
59926148 TTCTTTTTGC
59926158 TTTTCAAAGGCT
1 TTTTCAAAGGCT
59926170 TTTTCAAAGGCT
1 TTTTCAAAGGCT
59926182 TTTTCAA
1 TTTTCAA
59926189 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:59926292 original size:21 final size:21
Alignment explanation
Indices: 59926236--59926302 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
59926226 CTCTTGCCTC
* *
59926236 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
59926257 TCTTTT-TCTTCCTTTGCTTTT
1 TCTTTTCT-TTTCTTTGCTTTT
59926278 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
59926298 CTCTT
1 -TCTT
59926303 CACAAGAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 5 0.13
21 31 0.82
22 2 0.05
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:59926302 original size:16 final size:16
Alignment explanation
Indices: 59926234--59926302 Score: 72
Period size: 16 Copynumber: 4.4 Consensus size: 16
59926224 GCCTCTTGCC
*
59926234 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
59926250 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
59926266 TC-CTTTGCTTTTTCT
1 TCTCTTTTCTTTTTCT
*
59926281 TTTCTTTTCTTTGTT-T
1 TCTCTTTTCTTT-TTCT
59926297 TCTCTT
1 TCTCTT
59926303 CACAAGAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
15 14 0.32
16 28 0.64
17 2 0.05
ACGTcount: A:0.03, C:0.20, G:0.03, T:0.74
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:59927244 original size:22 final size:19
Alignment explanation
Indices: 59927208--59927269 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 19
59927198 CATTAAACAC
59927208 TTTTTTTT-AGATTTTTTTT
1 TTTTTTTTGA-ATTTTTTTT
* *
59927227 TTCCTTTTCGAATTTTTTTGAAT
1 TT-TTTTTTGAATTTTTTT---T
59927250 TTTTTTTTGAATTTTTTTT
1 TTTTTTTTGAATTTTTTTT
59927269 T
1 T
59927270 GACTTGTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
19 4 0.12
20 12 0.35
21 1 0.03
22 14 0.41
23 3 0.09
ACGTcount: A:0.13, C:0.05, G:0.06, T:0.76
Consensus pattern (19 bp):
TTTTTTTTGAATTTTTTTT
Found at i:59927268 original size:11 final size:12
Alignment explanation
Indices: 59927239--59927271 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
59927229 CCTTTTCGAA
59927239 TTTTTTTGAATT
1 TTTTTTTGAATT
59927251 TTTTTTTGAATT
1 TTTTTTTGAATT
59927263 TTTTTTTGA
1 TTTTTTTGA
59927272 CTTGTATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:59929010 original size:30 final size:30
Alignment explanation
Indices: 59928976--59929042 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
59928966 TAAACTAAAA
59928976 TGAGCTAAGCTTTAACTCGTGAGCT-AAAG
1 TGAGCTAAGCTTTAACTCGTGAGCTGAAAG
* * *
59929005 TTGAGCTAAGGTTTAGCTCGTGAGTTGAAAG
1 -TGAGCTAAGCTTTAACTCGTGAGCTGAAAG
59929036 TGAGCTA
1 TGAGCTA
59929043 GGAGTGAGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 29 0.88
31 4 0.12
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGCTTTAACTCGTGAGCTGAAAG
Found at i:59929953 original size:20 final size:21
Alignment explanation
Indices: 59929930--59929982 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
59929920 TCCAGCTCAA
*
59929930 TTCAGCTCATTTGAGCTT-GT
1 TTCAGCTCATTCGAGCTTAGT
** *
59929950 TTCAGCTCAACCGAGCTTATT
1 TTCAGCTCATTCGAGCTTAGT
59929971 TTCAGCTCATTC
1 TTCAGCTCATTC
59929983 TTTATTTCAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.40
Consensus pattern (21 bp):
TTCAGCTCATTCGAGCTTAGT
Found at i:59932685 original size:35 final size:35
Alignment explanation
Indices: 59932639--59932708 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
59932629 ATCTTACACC
59932639 TTGATGTGATCCGGCCCGGGTAGATGAGTCGAGTT
1 TTGATGTGATCCGGCCCGGGTAGATGAGTCGAGTT
*
59932674 TTGATGTGATCCGGCTCGGGTAGATGAGTCGAGTT
1 TTGATGTGATCCGGCCCGGGTAGATGAGTCGAGTT
59932709 CACGTAGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.17, C:0.16, G:0.37, T:0.30
Consensus pattern (35 bp):
TTGATGTGATCCGGCCCGGGTAGATGAGTCGAGTT
Found at i:59933685 original size:16 final size:16
Alignment explanation
Indices: 59933666--59933712 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
59933656 CTGAACCAGG
59933666 CCGTTCATGAATCTTC
1 CCGTTCATGAATCTTC
59933682 CCGTTCATTGAA-CTTTC
1 CCGTTCA-TGAATC-TTC
*
59933699 CCGTTCATGCATCT
1 CCGTTCATGAATCT
59933713 CTTCATGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.17, C:0.32, G:0.13, T:0.38
Consensus pattern (16 bp):
CCGTTCATGAATCTTC
Found at i:59936149 original size:30 final size:28
Alignment explanation
Indices: 59936095--59936151 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
59936085 TTTCTTCCAC
* *
59936095 ACTTTCTTTTTGCTCACTCTCTTTTTCA
1 ACTTTCTTTTTGCACACACTCTTTTTCA
59936123 ACTTTACTTTCTTGCACACACTCTTTTTC
1 ACTTT-CTTT-TTGCACACACTCTTTTTC
59936152 TTTTTCGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.20
29 4 0.16
30 16 0.64
ACGTcount: A:0.14, C:0.30, G:0.04, T:0.53
Consensus pattern (28 bp):
ACTTTCTTTTTGCACACACTCTTTTTCA
Found at i:59936170 original size:19 final size:19
Alignment explanation
Indices: 59936146--59936207 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
59936136 GCACACACTC
59936146 TTTTTCTTTTTCGATTTCT
1 TTTTTCTTTTTCGATTTCT
* *
59936165 TTTTTCTTTTTCAACTTCT
1 TTTTTCTTTTTCGATTTCT
59936184 TTTTCTCTTCTCTT-GATTTCT
1 TTTT-TCTT-T-TTCGATTTCT
59936205 TTT
1 TTT
59936208 AGAATCTGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 21 0.58
20 4 0.11
21 9 0.25
22 2 0.06
ACGTcount: A:0.06, C:0.19, G:0.03, T:0.71
Consensus pattern (19 bp):
TTTTTCTTTTTCGATTTCT
Found at i:59940342 original size:50 final size:49
Alignment explanation
Indices: 59940227--59940347 Score: 129
Period size: 50 Copynumber: 2.4 Consensus size: 49
59940217 AATGAGTACT
* *
59940227 TAATGCA-AGACTTAATTTAATGATGCAAACTTAAAACATGGTAGTTACA
1 TAATGCATA-ACTTTATTTAATGATGCAAACTTAAAACATGGAAGTTACA
** * * *
59940276 TAATGCATGTCATTATTT-ATGATGCATACTTAACTAGCATGGAAGTTACA
1 TAATGCATAACTTTATTTAATGATGCAAACTTAA--AACATGGAAGTTACA
*
59940326 TAATGCATAACTTTATTAAATG
1 TAATGCATAACTTTATTTAATG
59940348 CAGAACACAC
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
48 14 0.25
49 13 0.23
50 27 0.47
51 3 0.05
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (49 bp):
TAATGCATAACTTTATTTAATGATGCAAACTTAAAACATGGAAGTTACA
Found at i:59940834 original size:17 final size:17
Alignment explanation
Indices: 59940812--59940846 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
59940802 GTACCAACGT
59940812 AAGTACCATCATTGGGA
1 AAGTACCATCATTGGGA
59940829 AAGTACCATCATTGGGA
1 AAGTACCATCATTGGGA
59940846 A
1 A
59940847 TAGTTTCGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (17 bp):
AAGTACCATCATTGGGA
Found at i:59941984 original size:15 final size:15
Alignment explanation
Indices: 59941945--59941988 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 15
59941935 TTGTAAAAAG
*
59941945 AAAAGAAAA-AGATG
1 AAAAGAAAAGAGATC
59941959 AAAAGCAAAAAGAGATC
1 AAAAG--AAAAGAGATC
59941976 AAAAGAAAAGAGA
1 AAAAGAAAAGAGA
59941989 GGTAAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 5 0.19
15 8 0.31
16 4 0.15
17 9 0.35
ACGTcount: A:0.70, C:0.05, G:0.20, T:0.05
Consensus pattern (15 bp):
AAAAGAAAAGAGATC
Found at i:59947889 original size:29 final size:30
Alignment explanation
Indices: 59947842--59947909 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
59947832 TGGCCCAAGA
* * * *
59947842 GTAAATACTCAAAATTTGAGGGATTAA-AGT
1 GTAAATA-TAAAAAGTTGAAGGACTAATAGT
59947872 GTAAATATAAAAAGTTGAAGGACTAATAGT
1 GTAAATATAAAAAGTTGAAGGACTAATAGT
*
59947902 GCAAATAT
1 GTAAATAT
59947910 TTTAAGGGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (30 bp):
GTAAATATAAAAAGTTGAAGGACTAATAGT
Found at i:59948170 original size:29 final size:31
Alignment explanation
Indices: 59948122--59948185 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
59948112 TTTATAGTTA
*
59948122 TTTAATTAGATAATTATTATT-TATTTAATAT
1 TTTAATAAGATAATTATTATTAT-TTTAATAT
*
59948153 TTTAATAAGAT-ATT-TTATTATTTTATTAT
1 TTTAATAAGATAATTATTATTATTTTAATAT
59948182 TTTA
1 TTTA
59948186 TTTAGTCCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 16 0.53
30 4 0.13
31 10 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (31 bp):
TTTAATAAGATAATTATTATTATTTTAATAT
Found at i:59948174 original size:8 final size:8
Alignment explanation
Indices: 59948163--59948187 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
59948153 TTTAATAAGA
59948163 TATTTTAT
1 TATTTTAT
59948171 TATTTTAT
1 TATTTTAT
59948179 TATTTTAT
1 TATTTTAT
59948187 T
1 T
59948188 TAGTCCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:59950987 original size:33 final size:33
Alignment explanation
Indices: 59950950--59951059 Score: 109
Period size: 33 Copynumber: 3.3 Consensus size: 33
59950940 AATATATATC
*
59950950 TAAGACCATAGCTAGGCTATGGCATCC-TGA-TG
1 TAAGACCATAGCTAGGCTATGGCA-CCACGAGTG
* *
59950982 ATAAGACCATATCTAGGATATGGCACCACGAGTG
1 -TAAGACCATAGCTAGGCTATGGCACCACGAGTG
* * **
59951016 TAAGACCATGGCTAGGCCATGGCAATAC-ACGTG
1 TAAGACCATAGCTAGGCTATGGCACCACGA-GTG
59951049 TAAGACCATAG
1 TAAGACCATAG
59951060 TCGGATTATG
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
32 3 0.05
33 59 0.92
34 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.21
Consensus pattern (33 bp):
TAAGACCATAGCTAGGCTATGGCACCACGAGTG
Found at i:59951135 original size:45 final size:45
Alignment explanation
Indices: 59951086--59951253 Score: 140
Period size: 45 Copynumber: 3.7 Consensus size: 45
59951076 TACCAAAAAT
* * *
59951086 GAGTAAGACCATAGCTGAAAGACACTATGGCATCAG-GATTCAGAC
1 GAGTAAGACCATAGCTGAAAGATACAATGGCATC-GCGATTCAAAC
* * *
59951131 GAGTAAGACCATAGCTAAAAGATGCAATGGCATCGCGATTCAAAT
1 GAGTAAGACCATAGCTGAAAGATACAATGGCATCGCGATTCAAAC
* * * * * ** * *
59951176 GTGTAAGACCATGGTTGAAAGATACCATGGCAACTTGATATGAAAT
1 GAGTAAGACCATAGCTGAAAGATACAATGGCATCGCGAT-TCAAAC
* * * *
59951222 GTGTAAGACCATGGTTGAAAGATACCATGGCA
1 GAGTAAGACCATAGCTGAAAGATACAATGGCA
59951254 ACGTGACATG
Statistics
Matches: 105, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
44 1 0.01
45 67 0.64
46 37 0.35
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (45 bp):
GAGTAAGACCATAGCTGAAAGATACAATGGCATCGCGATTCAAAC
Found at i:59951232 original size:46 final size:46
Alignment explanation
Indices: 59951082--59951382 Score: 282
Period size: 46 Copynumber: 6.6 Consensus size: 46
59951072 ATCATACCAA
* * * * * * *
59951082 AAATGAGTAAGACCATAGCTGAAAGACACTATGGCATCAGGAT-TC
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG
* * * * * * * * ** *
59951127 AGACGAGTAAGACCATAGCTAAAAGATGCAATGGCATCGCGAT-TC
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG
* *
59951172 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACTTGATATG
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG
* * *
59951218 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATG
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG
* * ***
59951264 AAATAAATAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGG
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGA-TATG
* * **
59951311 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACCTGATAAA
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG
*
59951357 AAATGAGTAAGACCATAGTTGAAAGA
1 AAATGAGTAAGACCATGGTTGAAAGA
59951383 CACTATGACA
Statistics
Matches: 217, Mismatches: 37, Indels: 3
0.84 0.14 0.01
Matches are distributed among these distances:
45 69 0.32
46 107 0.49
47 41 0.19
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (46 bp):
AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG
Found at i:59951342 original size:93 final size:92
Alignment explanation
Indices: 59951179--59951382 Score: 282
Period size: 93 Copynumber: 2.2 Consensus size: 92
59951169 TTCAAATGTG
* * * **
59951179 TAAGACCATGGTTGAAAGATACCATGGCAACTTGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGAGAGGAAATGAATAAGACCATGGTTGAAAGA
* **
59951244 TACCATGGCAACGTGACATGAAATAAA
66 TACCATGGCAACCTGACAAAAAATAAA
*
59951271 TAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGGAAATGAATAAGACCATGGTTGAAAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGA-GAGGAAATGAATAAGACCATGGTTGAAAG
* * *
59951336 ATACCATGGCAACCTGATAAAAAATGAG
65 ATACCATGGCAACCTGACAAAAAATAAA
*
59951364 TAAGACCATAGTTGAAAGA
1 TAAGACCATGGTTGAAAGA
59951383 CACTATGACA
Statistics
Matches: 98, Mismatches: 13, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
92 34 0.35
93 64 0.65
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.21
Consensus pattern (92 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGAGAGGAAATGAATAAGACCATGGTTGAAAGA
TACCATGGCAACCTGACAAAAAATAAA
Found at i:59952579 original size:27 final size:27
Alignment explanation
Indices: 59952549--59952608 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
59952539 CGACTTGTAA
59952549 AATTACCAAAGTACCCTCGATTTACAG
1 AATTACCAAAGTACCCTCGATTTACAG
**** *
59952576 AATTACCGTTTTACCCTCGATTTATAG
1 AATTACCAAAGTACCCTCGATTTACAG
59952603 AATTAC
1 AATTAC
59952609 TGTTTTACCC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (27 bp):
AATTACCAAAGTACCCTCGATTTACAG
Found at i:59952613 original size:27 final size:27
Alignment explanation
Indices: 59952560--59952624 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
59952550 ATTACCAAAG
59952560 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
59952587 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
59952614 TACCCTTGATT
1 TACCCTCGATT
59952625 GTGAAATTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:59952662 original size:80 final size:80
Alignment explanation
Indices: 59952587--59952751 Score: 269
Period size: 80 Copynumber: 2.1 Consensus size: 80
59952577 ATTACCGTTT
* * * * *
59952587 TACCCTCGATTTATAGAATTA-CTGTTTTACCCTTGATTGTGAAATTACTGAAATACCCTTGTAG
1 TACCCTCGATTTACAGAATTATC-ATTTTACCCTCGATTGCGAAATTACTAAAATACCCTTGTAG
59952651 GGTAGAATTACCAAAA
65 GGTAGAATTACCAAAA
59952667 TACCCTCGATTTACAGAATTATCATTTTACCCTCGATTGCGAAATTACTAAAATACCCTTGTAGG
1 TACCCTCGATTTACAGAATTATCATTTTACCCTCGATTGCGAAATTACTAAAATACCCTTGTAGG
59952732 GTAGAATTACCAAAA
66 GTAGAATTACCAAAA
59952747 TACCC
1 TACCC
59952752 CTAGTTTGTA
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
80 78 0.99
81 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (80 bp):
TACCCTCGATTTACAGAATTATCATTTTACCCTCGATTGCGAAATTACTAAAATACCCTTGTAGG
GTAGAATTACCAAAA
Found at i:59952684 original size:27 final size:27
Alignment explanation
Indices: 59952654--59952860 Score: 74
Period size: 27 Copynumber: 7.7 Consensus size: 27
59952644 CTTGTAGGGT
59952654 AGAATTACCAAAATACCCTCGATTTAC
1 AGAATTACCAAAATACCCTCGATTTAC
* *** *
59952681 AGAATTATCATTTTACCCTCGA-TTGC
1 AGAATTACCAAAATACCCTCGATTTAC
* * **
59952707 -GAAATTACTAAAATACCCTTGTAGGGT--
1 AG-AATTACCAAAATACCCTCG-A-TTTAC
* *
59952734 AGAATTACCAAAATACCCCTAGTTTGTA-
1 AGAATTACCAAAATA-CCCTCGATT-TAC
* *
59952762 A-AATTACCAAAATACCACT-GGTTT-G
1 AGAATTACCAAAATACC-CTCGATTTAC
* * * * **
59952787 TGAAATTACCGAAATACCCCCAATTTGT
1 AG-AATTACCAAAATACCCTCGATTTAC
*
59952815 AAAATTACCAAAATACCC-CTGATTTAC
1 AGAATTACCAAAATACCCTC-GATTTAC
*
59952842 AAAATTA-CAGAAATACCCT
1 AGAATTACCA-AAATACCCT
59952861 TGACTTTTTA
Statistics
Matches: 133, Mismatches: 30, Indels: 33
0.68 0.15 0.17
Matches are distributed among these distances:
25 2 0.02
26 25 0.19
27 98 0.74
28 7 0.05
29 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (27 bp):
AGAATTACCAAAATACCCTCGATTTAC
Found at i:59952740 original size:107 final size:107
Alignment explanation
Indices: 59952545--59952777 Score: 256
Period size: 107 Copynumber: 2.2 Consensus size: 107
59952535 CCCTCGACTT
* * * *
59952545 GTAAAATTACCAAAGTACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATTACT
1 GTAAAATTACCAAAATACCCTCGATTTACAGAATTACCATTTTACCCTCGATTGAGAGAATTACT
**** ** ** *
59952610 GTTTTACCCTTGATTGTGAAATTACTGAAATA-CCCTTGTAGG
66 AAAATACCCTTGAGGGTGAAATTACCAAAATACCCCTAGT-GG
* * *
59952652 GTAGAATTACCAAAATACCCTCGATTTACAGAATTATCATTTTACCCTCGATTGCGA-AATTACT
1 GTAAAATTACCAAAATACCCTCGATTTACAGAATTACCATTTTACCCTCGATTGAGAGAATTACT
**
59952716 AAAATACCCTTGTAGGGT-AGAATTACCAAAATACCCCTAGTTT
66 AAAATACCCTTG-AGGGTGA-AATTACCAAAATACCCCTAGTGG
59952759 GTAAAATTACCAAAATACC
1 GTAAAATTACCAAAATACC
59952778 ACTGGTTTGT
Statistics
Matches: 104, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
106 16 0.15
107 82 0.79
108 6 0.06
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (107 bp):
GTAAAATTACCAAAATACCCTCGATTTACAGAATTACCATTTTACCCTCGATTGAGAGAATTACT
AAAATACCCTTGAGGGTGAAATTACCAAAATACCCCTAGTGG
Found at i:59952847 original size:54 final size:54
Alignment explanation
Indices: 59952736--59952859 Score: 167
Period size: 54 Copynumber: 2.3 Consensus size: 54
59952726 TGTAGGGTAG
* * * * ***
59952736 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCACTGGTTTGTGA
1 AATTACCGAAATACCCCCAATTTGTAAAATTACCAAAATACCACTGATTTACAA
*
59952790 AATTACCGAAATACCCCCAATTTGTAAAATTACCAAAATACCCCTGATTTACAA
1 AATTACCGAAATACCCCCAATTTGTAAAATTACCAAAATACCACTGATTTACAA
*
59952844 AATTACAGAAATACCC
1 AATTACCGAAATACCC
59952860 TTGACTTTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (54 bp):
AATTACCGAAATACCCCCAATTTGTAAAATTACCAAAATACCACTGATTTACAA
Found at i:59952903 original size:26 final size:26
Alignment explanation
Indices: 59952867--59952922 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
59952857 CCCTTGACTT
*
59952867 TTTAAAAATTA-TATAAATACCATTGG
1 TTTAAAAATTACT-GAAATACCATTGG
* *
59952893 TTTACAAATTACTGAAATACCCTTGG
1 TTTAAAAATTACTGAAATACCATTGG
59952919 TTTA
1 TTTA
59952923 TAGATTTACC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 25 0.96
27 1 0.04
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (26 bp):
TTTAAAAATTACTGAAATACCATTGG
Found at i:59953748 original size:10 final size:10
Alignment explanation
Indices: 59953733--59953793 Score: 61
Period size: 10 Copynumber: 5.9 Consensus size: 10
59953723 ATATTGTTAT
59953733 ACATGATATG
1 ACATGATATG
59953743 ACATGATATG
1 ACATGATATG
59953753 CACATGATATG
1 -ACATGATATG
** *
59953764 TTATGAGATG
1 ACATGATATG
59953774 CACATGATATG
1 -ACATGATATG
59953785 -CTATGATAT
1 AC-ATGATAT
59953794 ACTCATTATA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 1 0.02
10 24 0.57
11 17 0.40
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (10 bp):
ACATGATATG
Done.