Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019951.1 Corchorus olitorius cultivar O-4 contig19984, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 154360
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:16096 original size:7 final size:7
Alignment explanation
Indices: 16084--16110 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
16074 AGATAAGCAA
16084 GCATATT
1 GCATATT
16091 GCATATT
1 GCATATT
16098 GCATATT
1 GCATATT
16105 GCATAT
1 GCATAT
16111 ATATGATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (7 bp):
GCATATT
Found at i:30304 original size:15 final size:15
Alignment explanation
Indices: 30266--30310 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
30256 TGTTTGGGAG
30266 GAAATGGGGAGGAAA
1 GAAATGGGGAGGAAA
30281 GAAGA-GGGGAGGAAA
1 GAA-ATGGGGAGGAAA
30296 GAAATGGGGAAGGAA
1 GAAATGGGG-AGGAA
30311 GGCAACGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.04
15 20 0.74
16 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.49, T:0.04
Consensus pattern (15 bp):
GAAATGGGGAGGAAA
Found at i:31427 original size:16 final size:16
Alignment explanation
Indices: 31384--31442 Score: 68
Period size: 16 Copynumber: 3.7 Consensus size: 16
31374 TGTGACTTCC
*
31384 TTTCCCTTCC-TCCTTA
1 TTTCCTTTCCTTCC-TA
*
31400 TTTCCTTTTCCTTGCTA
1 TTTCC-TTTCCTTCCTA
31417 TTTCCTTTCCTTCCTA
1 TTTCCTTTCCTTCCTA
31433 TTT-CTTTCCT
1 TTTCCTTTCCT
31443 CTCTACAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
15 7 0.18
16 18 0.47
17 11 0.29
18 2 0.05
ACGTcount: A:0.05, C:0.36, G:0.02, T:0.58
Consensus pattern (16 bp):
TTTCCTTTCCTTCCTA
Found at i:31941 original size:11 final size:11
Alignment explanation
Indices: 31919--31957 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
31909 TTTAAAAAAC
*
31919 TTCCTTTCCCT
1 TTCCTTTTCCT
*
31930 TCCCTTTTCCT
1 TTCCTTTTCCT
31941 TTCC-TTTCCT
1 TTCCTTTTCCT
31951 TTCCTTT
1 TTCCTTT
31958 AATGATTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (11 bp):
TTCCTTTTCCT
Found at i:31943 original size:5 final size:5
Alignment explanation
Indices: 31919--31957 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
31909 TTTAAAAAAC
*
31919 TTCCT TTCCCT TCCCTT TTCCT TTCCT TTCCT TTCCT TT
1 TTCCT TT-CCT TTCC-T TTCCT TTCCT TTCCT TTCCT TT
31958 AATGATTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 22 0.73
6 8 0.27
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (5 bp):
TTCCT
Found at i:35365 original size:2 final size:2
Alignment explanation
Indices: 35358--35428 Score: 76
Period size: 2 Copynumber: 36.5 Consensus size: 2
35348 CGACCGAATA
*
35358 AT AT AT AT AT AT AT AT A- AT A- AT AT AT AT TT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
35397 AT AT AT CT GAT AT TT AT AT TT AT AT AT AT AT A
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT A
35429 AATAATAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
1 3 0.05
2 53 0.93
3 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (2 bp):
AT
Found at i:36199 original size:70 final size:70
Alignment explanation
Indices: 36125--36285 Score: 322
Period size: 70 Copynumber: 2.3 Consensus size: 70
36115 GTGGCTGACC
36125 AATTTGTTTTCTTATTTTCTTATTTATGTTACTGAGTTGAATTTGTTTAAATCAGAAATCTTCAT
1 AATTTGTTTTCTTATTTTCTTATTTATGTTACTGAGTTGAATTTGTTTAAATCAGAAATCTTCAT
36190 GGTTG
66 GGTTG
36195 AATTTGTTTTCTTATTTTCTTATTTATGTTACTGAGTTGAATTTGTTTAAATCAGAAATCTTCAT
1 AATTTGTTTTCTTATTTTCTTATTTATGTTACTGAGTTGAATTTGTTTAAATCAGAAATCTTCAT
36260 GGTTG
66 GGTTG
36265 AATTTGTTTTCTTATTTTCTT
1 AATTTGTTTTCTTATTTTCTT
36286 CAATTCTCTG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 91 1.00
ACGTcount: A:0.23, C:0.09, G:0.13, T:0.55
Consensus pattern (70 bp):
AATTTGTTTTCTTATTTTCTTATTTATGTTACTGAGTTGAATTTGTTTAAATCAGAAATCTTCAT
GGTTG
Found at i:36836 original size:25 final size:27
Alignment explanation
Indices: 36796--36850 Score: 87
Period size: 25 Copynumber: 2.1 Consensus size: 27
36786 AAATGTTAAA
*
36796 TCAATTGTTATATTCTGAATTTCTT-T
1 TCAATTGTAATATTCTGAATTTCTTAT
36822 TCAATTG-AATATTCTGAATTTCTTAT
1 TCAATTGTAATATTCTGAATTTCTTAT
36848 TCA
1 TCA
36851 TTCTGAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (27 bp):
TCAATTGTAATATTCTGAATTTCTTAT
Found at i:57725 original size:49 final size:49
Alignment explanation
Indices: 57653--57750 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
57643 TCATTTTGAT
57653 CTTTTTTTAAATATAGACCTAAGGCCCATACAAAAAGCTAGGCAGGCAA
1 CTTTTTTTAAATATAGACCTAAGGCCCATACAAAAAGCTAGGCAGGCAA
57702 CTTTTTTTAAATATAGACCTAAGGCCCATACAAAAAGCTAGGCAGGCAA
1 CTTTTTTTAAATATAGACCTAAGGCCCATACAAAAAGCTAGGCAGGCAA
57751 ACAGGATGGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (49 bp):
CTTTTTTTAAATATAGACCTAAGGCCCATACAAAAAGCTAGGCAGGCAA
Found at i:59476 original size:30 final size:30
Alignment explanation
Indices: 59440--59498 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
59430 TTAATAAGCC
59440 ATTAAAATTTGAGGGTATAAGAGAAAAGTT
1 ATTAAAATTTGAGGGTATAAGAGAAAAGTT
*
59470 ATTAAAATTTGAGGGTATAAGAGGAAAGT
1 ATTAAAATTTGAGGGTATAAGAGAAAAGT
59499 CAAGATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.46, C:0.00, G:0.25, T:0.29
Consensus pattern (30 bp):
ATTAAAATTTGAGGGTATAAGAGAAAAGTT
Found at i:59812 original size:53 final size:52
Alignment explanation
Indices: 59730--59830 Score: 139
Period size: 53 Copynumber: 1.9 Consensus size: 52
59720 GGTGATCTTT
* * *
59730 GATCATCTGTGATGATCTTGGATGATGATCTCAGATCATCCTGTTTGGTTGG
1 GATCACCTGTGATGATATTGGATGATGATCTCAGATCACCCTGTTTGGTTGG
* * *
59782 GATCACCTGTTGATGATATTGGGTGGTGATCTCAGATTACCCTGTTTGG
1 GATCACCTG-TGATGATATTGGATGATGATCTCAGATCACCCTGTTTGG
59831 ATACACCTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
52 8 0.19
53 34 0.81
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.38
Consensus pattern (52 bp):
GATCACCTGTGATGATATTGGATGATGATCTCAGATCACCCTGTTTGGTTGG
Found at i:74975 original size:6 final size:6
Alignment explanation
Indices: 74964--75004 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
74954 ATTTGATAGG
*
74964 TTTTTA TTTTTA TTTTTA TTTTTA TTTATT- TATTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT-TTA TTTTTA TTTTT
75005 TAATTTTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 2 0.06
6 27 0.87
7 2 0.06
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:82715 original size:22 final size:21
Alignment explanation
Indices: 82667--82715 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
82657 TTACCCTTCT
* *
82667 TCTCTCTTCCCCCACTAACTC
1 TCTCTCCTCCCCCACTAACTA
* *
82688 TTTCTCCTCCTCCCACTCACTA
1 TCTCTCCTCC-CCCACTAACTA
82710 TCTCTC
1 TCTCTC
82716 TTCATAAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.12, C:0.51, G:0.00, T:0.37
Consensus pattern (21 bp):
TCTCTCCTCCCCCACTAACTA
Found at i:83904 original size:48 final size:48
Alignment explanation
Indices: 83847--83942 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
83837 ATTATAAACT
83847 TTTTTTTTAAGATAAGAATCATTTTCATTTCTTAAAAATTTTCATTTC
1 TTTTTTTTAAGATAAGAATCATTTTCATTTCTTAAAAATTTTCATTTC
83895 TTTTTTTTAAGATAAGAATCATTTTCATTTCTTAAAAATTTTCATTTC
1 TTTTTTTTAAGATAAGAATCATTTTCATTTCTTAAAAATTTTCATTTC
83943 ATAAAGAGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.54
Consensus pattern (48 bp):
TTTTTTTTAAGATAAGAATCATTTTCATTTCTTAAAAATTTTCATTTC
Found at i:83935 original size:17 final size:17
Alignment explanation
Indices: 83915--83947 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
83905 GATAAGAATC
*
83915 ATTTTCATTTCTTAAAA
1 ATTTTCATTTCATAAAA
83932 ATTTTCATTTCATAAA
1 ATTTTCATTTCATAAA
83948 GAGATTGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTTCATTTCATAAAA
Found at i:92835 original size:18 final size:18
Alignment explanation
Indices: 92790--92839 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
92780 GCCTCCACCC
*
92790 CCAAACCCACCTCCTGGG
1 CCAAACCCACCACCTGGG
* * *
92808 CCATAGCCACCACCTTGG
1 CCAAACCCACCACCTGGG
*
92826 CCAAATCCACCACC
1 CCAAACCCACCACC
92840 AAAGCCACCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.26, C:0.50, G:0.12, T:0.12
Consensus pattern (18 bp):
CCAAACCCACCACCTGGG
Found at i:92939 original size:63 final size:61
Alignment explanation
Indices: 92831--92975 Score: 193
Period size: 63 Copynumber: 2.4 Consensus size: 61
92821 CTTGGCCAAA
* * *
92831 TCCACCACCAAAGCCACCACC-GCCAGTTCCATAACCACCACCCCCAATGCCTACACCTCC
1 TCCACCGCCAAAACCACCACCAGCCAGGTCCATAACCACCACCCCCAATGCCTACACCTCC
* *
92891 TCCACCGCCAAAACCACCACCAGCACCAGGTCCATAACCACCACCCCCACTGCCTACGCCTCC
1 TCCACCGCCAAAACCACCACCAG--CCAGGTCCATAACCACCACCCCCAATGCCTACACCTCC
* * *
92954 TCCGCTGCCAAAACCGCCACCA
1 TCCACCGCCAAAACCACCACCA
92976 CGGCCATTGC
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
60 19 0.26
61 1 0.01
63 54 0.73
ACGTcount: A:0.28, C:0.53, G:0.09, T:0.10
Consensus pattern (61 bp):
TCCACCGCCAAAACCACCACCAGCCAGGTCCATAACCACCACCCCCAATGCCTACACCTCC
Found at i:93030 original size:27 final size:27
Alignment explanation
Indices: 92991--93125 Score: 189
Period size: 27 Copynumber: 5.0 Consensus size: 27
92981 ATTGCCTACG
* * *
92991 CCTCCCCCGCTGCCAAAACCACCACCT
1 CCTCCCCCACTGCCAATACCACCACCA
* *
93018 CCTCCTCCACTGCCAAAACCACCACCA
1 CCTCCCCCACTGCCAATACCACCACCA
*
93045 CCTCCTCCACTGCCAATACCACCACCA
1 CCTCCCCCACTGCCAATACCACCACCA
* *
93072 ACTCCCCCACTGCCAATACCACCACCG
1 CCTCCCCCACTGCCAATACCACCACCA
*
93099 CCTCCACCACTGCCAATACCACCACCA
1 CCTCCCCCACTGCCAATACCACCACCA
93126 GGTCCACCAC
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 98 1.00
ACGTcount: A:0.27, C:0.56, G:0.05, T:0.12
Consensus pattern (27 bp):
CCTCCCCCACTGCCAATACCACCACCA
Found at i:93069 original size:15 final size:15
Alignment explanation
Indices: 93051--93123 Score: 70
Period size: 15 Copynumber: 5.3 Consensus size: 15
93041 ACCACCTCCT
93051 CCACTGCCAATACCA
1 CCACTGCCAATACCA
*
93066 CCA---CCAACT-CCC
1 CCACTGCCAA-TACCA
93078 CCACTGCCAATACCA
1 CCACTGCCAATACCA
*
93093 CCACCGCC--T-CCA
1 CCACTGCCAATACCA
93105 CCACTGCCAATACCA
1 CCACTGCCAATACCA
93120 CCAC
1 CCAC
93124 CAGGTCCACC
Statistics
Matches: 46, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
12 19 0.41
13 2 0.04
14 2 0.04
15 23 0.50
ACGTcount: A:0.29, C:0.55, G:0.05, T:0.11
Consensus pattern (15 bp):
CCACTGCCAATACCA
Found at i:93133 original size:36 final size:36
Alignment explanation
Indices: 93093--93162 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
93083 GCCAATACCA
*
93093 CCACCGCCTCCACCACTGCCAATACCACCACCAGGT
1 CCACCACCTCCACCACTGCCAATACCACCACCAGGT
* * *
93129 CCACCACCTCCCCCCCTGCCAATTCCACCACCAG
1 CCACCACCTCCACCACTGCCAATACCACCACCAG
93163 AACCAGCCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.23, C:0.57, G:0.09, T:0.11
Consensus pattern (36 bp):
CCACCACCTCCACCACTGCCAATACCACCACCAGGT
Found at i:99745 original size:165 final size:167
Alignment explanation
Indices: 99235--99835 Score: 622
Period size: 165 Copynumber: 3.5 Consensus size: 167
99225 TCAGTGCAAA
* * *
99235 GGCGAATAACAACAGGGGAGGAACATGTGAAATCGGTGAAATTTGTAAGTTTATCAA-CTGAGAT
1 GGCGAATAACAACAGGGAAGGAACATGTGAAATCGGTGAAGTTTGTAAGTTTAGCAAGC-GAGAT
* * * * * *
99299 AACCCAAACTCGCAATCAGTGGCGAATTACATCAAGGGAGGAACACGTGAAATCGGT-AGCTTTG
65 AA-CCAAAATCACAATC-GCGGCGAATAACATC-AGTGAGGAACACGTGAAATCGGTGAACTTTG
* * * * *
99363 TACATTTATATTGGACAAGATACCGAAACTTGCAAATC-AA
127 TACATTTATATTGGACATGACACCCAAACCTGCAAATCGAT
* * * ** *
99403 GGCAATGGATAACAACAGGGGAGGAGCATGTGAAATCAATGAAAGTTTGTAAGTTTAGCAGGCGA
1 GGC---GAATAACAACAGGGAAGGAACATGTGAAATCGGTG-AAGTTTGTAAGTTTAGCAAGCGA
*
99468 GATAATCCAAAATCATAATCGGTGCAAAGGCGAATAACATCAGGTGAGGAACACGTGAAATCGGT
62 GATAA-CCAAAATCACAATC---GC---GGCGAATAACATCA-GTGAGGAACACGTGAAATCGGT
*
99533 GAACTTTGTACATTTATATTGGACATGACACCCAAAACTGCAAATCGAT
119 GAACTTTGTACATTTATATTGGACATGACACCCAAACCTGCAAATCGAT
*
99582 GGCGAATAACAACAGGGAAGGAACATGTGAAATCGGTGAAGTTTGTCAG-TTAGCAAGCGAGATA
1 GGCGAATAACAACAGGGAAGGAACATGTGAAATCGGTGAAGTTTGTAAGTTTAGCAAGCGAGATA
* *
99646 ACCAAAAATCACAA-C-CGACGAATAACATCATTGAGGAACACGTGAAATCGGTGAACTTTGTAC
66 ACC-AAAATCACAATCGCGGCGAATAACATCAGTGAGGAACACGTGAAATCGGTGAACTTTGTAC
* * **
99709 ATTTACATTGGACATGACACCTAAACCCACAAATCGATACAAT
130 ATTTATATTGGACATGACACCCAAACCTGCAAATCG-----AT
* * *
99752 GACGAATAACAACAGGGAAGGAACATGTGAAATCGGTGAAGTTTGTAA-TAAGTTAACAAACGAG
1 GGCGAATAACAACAGGGAAGGAACATGTGAAATCGGTGAAGTTTGTAAGT---TTAGCAAGCGAG
*
99816 ATAATCCAAAATCATAATCG
63 ATAA-CCAAAATCACAATCG
99836 ATGCAAAGGT
Statistics
Matches: 365, Mismatches: 42, Indels: 45
0.81 0.09 0.10
Matches are distributed among these distances:
165 63 0.17
166 13 0.04
168 3 0.01
169 1 0.00
170 48 0.13
171 31 0.08
172 34 0.09
173 27 0.07
174 28 0.08
175 10 0.03
176 31 0.08
177 33 0.09
178 39 0.11
179 4 0.01
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.21
Consensus pattern (167 bp):
GGCGAATAACAACAGGGAAGGAACATGTGAAATCGGTGAAGTTTGTAAGTTTAGCAAGCGAGATA
ACCAAAATCACAATCGCGGCGAATAACATCAGTGAGGAACACGTGAAATCGGTGAACTTTGTACA
TTTATATTGGACATGACACCCAAACCTGCAAATCGAT
Found at i:99826 original size:347 final size:346
Alignment explanation
Indices: 99235--99881 Score: 822
Period size: 347 Copynumber: 1.9 Consensus size: 346
99225 TCAGTGCAAA
* *
99235 GGCGAATAACAACAGGGGAGGAACATGTGAAATCGGTGAAATTTGTAAGTTTATCAACTGAGATA
1 GGCGAATAACAACAGGGAAGGAACATGTGAAATCGGTGAAATTTGTAAGTTTAGCAACTGAGATA
* * * * * * *
99300 ACCCAAACTCGCAATCAGTGGCGAATTACATCAAGGGAGGAACACGTGAAATCGGTAGCTTTGTA
66 ACCAAAAATCACAATCA-CGACGAATAACATCAAGGGAGGAACACGTGAAATCGGTAACTTTGTA
* * *** * * *
99365 CATTTATATTGGACAAGATACCGAAACTTGCAAATCAAGGCAATGGATAACAACAGGGGAGGAGC
130 CATTTACATTGGACAAGACACCGAAACCCACAAATCAAGACAATGGATAACAACAGGGAAGGAAC
* ** *
99430 ATGTGAAATCAATGAAAGTTTGTAAGTTTAGCAGGCGAGATAATCCAAAATCATAATCGGTGCAA
195 ATGTGAAATCAATGAAAGTTTGTAAGTTTAACAAACGAGATAATCCAAAATCATAATCGATGCAA
* * * * *
99495 AGGCGAATAACATCAGGTGAGGAACACGTGAAATCGGTGAACTTTGTACATTTATATTGGACATG
260 AGGCGAATAACATAAGGGGAGGAACAAGTAAAATCAGTGAACTTTGTACATTTATATTGGACATG
99560 ACACCCAAAACTGCAAATCGAT
325 ACACCCAAAACTGCAAATCGAT
* *
99582 GGCGAATAACAACAGGGAAGGAACATGTGAAATCGGTGAAGTTTGTCAG-TTAGCAAGC-GAGAT
1 GGCGAATAACAACAGGGAAGGAACATGTGAAATCGGTGAAATTTGTAAGTTTAGCAA-CTGAGAT
**
99645 AACCAAAAATCACAA-C-CGACGAATAACATC-ATTGAGGAACACGTGAAATCGGTGAACTTTGT
65 AACCAAAAATCACAATCACGACGAATAACATCAAGGGAGGAACACGTGAAATCGGT-AACTTTGT
* * * *
99707 ACATTTACATTGGACATGACACCTAAACCCACAAATCGATACAATGACGAATAACAACAGGGAAG
129 ACATTTACATTGGACAAGACACCGAAACCCACAAATCAAGACAATG--G-ATAACAACAGGGAAG
**
99772 GAACATGTGAAATCGGTG-AAGTTTGTAA-TAAGTTAACAAACGAGATAATCCAAAATCATAATC
191 GAACATGTGAAATCAATGAAAGTTTGTAAGT---TTAACAAACGAGATAATCCAAAATCATAATC
* *
99835 GATGCAAAGGTGAATAACGTAAGGGGAGGAACAAGTAAAATCAGTGA
253 GATGCAAAGGCGAATAACATAAGGGGAGGAACAAGTAAAATCAGTGA
99882 GTGAGATAAC
Statistics
Matches: 254, Mismatches: 38, Indels: 16
0.82 0.12 0.05
Matches are distributed among these distances:
342 21 0.08
343 54 0.21
344 1 0.00
345 12 0.05
346 52 0.20
347 114 0.45
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (346 bp):
GGCGAATAACAACAGGGAAGGAACATGTGAAATCGGTGAAATTTGTAAGTTTAGCAACTGAGATA
ACCAAAAATCACAATCACGACGAATAACATCAAGGGAGGAACACGTGAAATCGGTAACTTTGTAC
ATTTACATTGGACAAGACACCGAAACCCACAAATCAAGACAATGGATAACAACAGGGAAGGAACA
TGTGAAATCAATGAAAGTTTGTAAGTTTAACAAACGAGATAATCCAAAATCATAATCGATGCAAA
GGCGAATAACATAAGGGGAGGAACAAGTAAAATCAGTGAACTTTGTACATTTATATTGGACATGA
CACCCAAAACTGCAAATCGAT
Found at i:101971 original size:174 final size:175
Alignment explanation
Indices: 101683--103242 Score: 1883
Period size: 175 Copynumber: 9.0 Consensus size: 175
101673 TGTTGTTATT
* * * ** * *
101683 CACCTTTGCACCGATTGAGAGATAGAGTTATCTCGATCGCCGGCTAAACTTTATAAACTCCACGG
1 CACCTTTGCACCGATTGCGAGAT-GGGTTATCTCGACCGCTTGCTAAACTTTATAAACTTCACAG
* * * *
101748 ATTTCATGTGTTCCTCCCTTATTGTCATTTACCTTTGAACTCTTTCCAATTTTGGATTATATTGC
65 ATTTCATGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCGC
* *
101813 CCACTGAACTTACAAACCTCGGTCACCCATTGTTTTTCACAAAAGA
130 CCACTAAACTTACAAACCTCGGTCACCCACTGTTTTTCACAAAAGA
* * * *
101859 CACCTTTGCACCGATTGCGAGATGGGTTATCTCGATCGCTTGCCAAACTTT-TAAACTTAACATA
1 CACCTTTGCACCGATTGCGAGATGGGTTATCTCGACCGCTTGCTAAACTTTATAAACTTCACAGA
* * * *
101923 TTTCACGTGTTCCTTCCTTGTTGCCATTCACCTTTGAACTCCTTCCAATTTTGGATTATCTCGCC
66 TTTCATGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCGCC
** *
101988 CACTAAACTTACAAACCTCAATCACCCATTGTTTTTCACAAAAGA
131 CACTAAACTTACAAACCTCGGTCACCCACTGTTTTTCACAAAAGA
* * * *
102033 CACCTTTGCACCGATTGCGAGATGGGTTATCTCGACCACATGCTAAACTTCACAAACTT--C--A
1 CACCTTTGCACCGATTGCGAGATGGGTTATCTCGACCGCTTGCTAAACTTTATAAACTTCACAGA
* * * *
102094 ---C--GTGTTGCTCCCTTGTTGCCATTCACCTTTGAAATCCTTCCAATTTTGGATTATCTCGCC
66 TTTCATGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCGCC
* * * * *
102154 CACTAAACTTACAAACCTCAGTCGCCCACTGTTTTTAATAAAAAAA
131 CACTAAACTTACAAACCTCGGTCACCCACTGTTTTTCA-CAAAAGA
** * * * *
102200 CACCTTTGCACAAATTGCGAGATGGGTTATCTCAACCGCCTACTAAACTTTATAAACTTCACAGG
1 CACCTTTGCACCGATTGCGAGATGGGTTATCTCGACCGCTTGCTAAACTTTATAAACTTCACAGA
* * * *
102265 TTTCATGTGTTCCTCCCTTGTTGTCATTCAACTTTGAACTCTTTCCAATTCTGGATTGTCTTGCC
66 TTTCATGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCGCC
* * ** * * *
102330 CACTGAACTTATACGCCTCGGCCACCCACTGTTTTCCAAAAAAGA
131 CACTAAACTTACAAACCTCGGTCACCCACTGTTTTTCACAAAAGA
* * * * * *
102375 TACCTTTACACCGATTGCGAGGTGGGTTATCACCACCGCTTGCTAAGCTTTATAAACTTCACAGA
1 CACCTTTGCACCGATTGCGAGATGGGTTATCTCGACCGCTTGCTAAACTTTATAAACTTCACAGA
* * * *
102440 TTTCACGTGTTCCTACCTTGTTCTCATTAACCTTTGAACTCTTTCCAATTTTGGATTATCTCGCC
66 TTTCATGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCGCC
* * *
102505 CACTAAACTTACAAACCTCAGTCGCCCATTGTTTTTCACAAAAGA
131 CACTAAACTTACAAACCTCGGTCACCCACTGTTTTTCACAAAAGA
* * * * * * * * * *
102550 CACATTTGCACTGATTGTGAGATAGGTTATCCCAACTGCCTACTAAACTTTATAAACTTCACAGG
1 CACCTTTGCACCGATTGCGAGATGGGTTATCTCGACCGCTTGCTAAACTTTATAAACTTCACAGA
* * *
102615 TTTCATGTGTTCCTCCCTTGTTGTCATTCAACTTTGAACTCTTTCCAATTCTGGATTATCTTGCC
66 TTTCATGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCGCC
* *
102680 CACTGAACTTACAAACCTCGGTCACCCACTGTTTTTCAAAAAAGA
131 CACTAAACTTACAAACCTCGGTCACCCACTGTTTTTCACAAAAGA
* * * *
102725 TACCTTTGCACCGATTGCGAGGTGGGTTATCTCGACCACTTGCTAAGCTTTATAAACTTCACAGA
1 CACCTTTGCACCGATTGCGAGATGGGTTATCTCGACCGCTTGCTAAACTTTATAAACTTCACAGA
*
102790 TTTCACGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCGCC
66 TTTCATGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCGCC
* * * **
102855 CACTAAACTTTCAAATCTCAGT-TGCCACTGTTTTTCACAAAAGA
131 CACTAAACTTACAAACCTCGGTCACCCACTGTTTTTCACAAAAGA
* * * * *
102899 CACCTTTGCACTGATTGCGAGATGGGTTATCTCAACCGCATACTAAACTTTATAAACTTCACAGG
1 CACCTTTGCACCGATTGCGAGATGGGTTATCTCGACCGCTTGCTAAACTTTATAAACTTCACAGA
* * * *
102964 TTTCATGTCTTCCTCCCTCGTTGTCATTCAACTTTGAACTCTTTCCAATTTTGGATTATCTTGCC
66 TTTCATGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCGCC
* * * * *
103029 CACTGAACTTACAAACCTTGGCCGCCCA-TGTTTTT-AAATAAAGA
131 CACTAAACTTACAAACCTCGGTCACCCACTGTTTTTCACA-AAAGA
* * * * * *
103073 TACCTTTACACCAATTGCGAGGTGGGTTATCTCGACCGCTTGCTAAACTTTATAAAC-TCAATAT
1 CACCTTTGCACCGATTGCGAGATGGGTTATCTCGACCGCTTGCTAAACTTTATAAACTTC-ACAG
* * * * *
103137 ATTTCCATGTGTTCATCCCTTGTTGTCATTCACCTTAGAACTCTTTCCGATTTTGGGTTAGCTCG
65 ATTT-CATGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCG
** *
103202 CCCACTAAACTT--AAACCTCGGTTGCCTACTGTTTTTCACAA
129 CCCACTAAACTTACAAACCTCGGTCACCCACTGTTTTTCACAA
103243 TAGAAAGAAC
Statistics
Matches: 1176, Mismatches: 191, Indels: 36
0.84 0.14 0.03
Matches are distributed among these distances:
166 90 0.08
167 56 0.05
168 1 0.00
169 1 0.00
171 1 0.00
173 17 0.01
174 380 0.32
175 528 0.45
176 102 0.09
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (175 bp):
CACCTTTGCACCGATTGCGAGATGGGTTATCTCGACCGCTTGCTAAACTTTATAAACTTCACAGA
TTTCATGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCGCC
CACTAAACTTACAAACCTCGGTCACCCACTGTTTTTCACAAAAGA
Found at i:102667 original size:350 final size:350
Alignment explanation
Indices: 101684--103242 Score: 2079
Period size: 350 Copynumber: 4.5 Consensus size: 350
101674 GTTGTTATTC
* * * * * ** * * *
101684 ACCTTTGCACCGATTGAGAGATAGAGTTATCTCGATCGCCGGCTAAACTTTATAAACTCCACGGA
1 ACCTTTACACCGATTGCGAGGT-GGGTTATCTCGACCGCTTGCTAAGCTTTATAAACTTCACAGA
* * * * *
101749 TTTCATGTGTTCCTCCCTTATTGTCATTTACCTTTGAACTCTTTCCAATTTTGGATTATATTGCC
65 TTTCACGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCGCC
* * * * *
101814 CACTGAACTTACAAACCTCGGTCACCCATTGTTTTTCACAAAAGACACCTTTGCACCGATTGCGA
130 CACTAAACTTACAAACCTCAGTCGCCCACTGTTTTTCACAAAAGACACCTTTGCACTGATTGCGA
* * * * * * ** * *
101879 GATGGGTTATCTCGATCGCTTGCCAAACTTT-TAAACTTAACATATTTCACGTGTTCCTTCCTTG
195 GATGGGTTATCTCAACCGCCTACTAAACTTTATAAACTTCACAGGTTTCATGTGTTCCTCCCTTG
* * * * * * *
101943 TTGCCATTCACCTTTGAACTCCTTCCAATTTTGGATTATCTCGCCCACTAAACTTACAAACCTCA
260 TTGTCATTCAACTTTGAACTCTTTCCAATTCTGGATTATCTTGCCCACTGAACTTACAAACCTCG
** * * *
102008 ATCACCCATTGTTTTTCACAAAAGAC
325 GCCACCCACTGTTTTTCAAAAAAGAT
* * * * * *
102034 ACCTTTGCACCGATTGCGAGATGGGTTATCTCGA-C-C--AC-ATGC----TAAACTTCACAAAC
1 ACCTTTACACCGATTGCGAGGTGGGTTATCTCGACCGCTTGCTAAGCTTTATAAACTTCACAGAT
* * * *
102090 TTCACGTGTTGCTCCCTTGTTGCCATTCACCTTTGAAATCCTTCCAATTTTGGATTATCTCGCCC
66 TTCACGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCGCCC
* * * **
102155 ACTAAACTTACAAACCTCAGTCGCCCACTGTTTTTAATAAAAAAACACCTTTGCACAAATTGCGA
131 ACTAAACTTACAAACCTCAGTCGCCCACTGTTTTTCA-CAAAAGACACCTTTGCACTGATTGCGA
102220 GATGGGTTATCTCAACCGCCTACTAAACTTTATAAACTTCACAGGTTTCATGTGTTCCTCCCTTG
195 GATGGGTTATCTCAACCGCCTACTAAACTTTATAAACTTCACAGGTTTCATGTGTTCCTCCCTTG
* * **
102285 TTGTCATTCAACTTTGAACTCTTTCCAATTCTGGATTGTCTTGCCCACTGAACTTATACGCCTCG
260 TTGTCATTCAACTTTGAACTCTTTCCAATTCTGGATTATCTTGCCCACTGAACTTACAAACCTCG
*
102350 GCCACCCACTGTTTTCCAAAAAAGAT
325 GCCACCCACTGTTTTTCAAAAAAGAT
* *
102376 ACCTTTACACCGATTGCGAGGTGGGTTATCACCACCGCTTGCTAAGCTTTATAAACTTCACAGAT
1 ACCTTTACACCGATTGCGAGGTGGGTTATCTCGACCGCTTGCTAAGCTTTATAAACTTCACAGAT
* * *
102441 TTCACGTGTTCCTACCTTGTTCTCATTAACCTTTGAACTCTTTCCAATTTTGGATTATCTCGCCC
66 TTCACGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCGCCC
* * *
102506 ACTAAACTTACAAACCTCAGTCGCCCATTGTTTTTCACAAAAGACACATTTGCACTGATTGTGAG
131 ACTAAACTTACAAACCTCAGTCGCCCACTGTTTTTCACAAAAGACACCTTTGCACTGATTGCGAG
* * *
102571 ATAGGTTATCCCAACTGCCTACTAAACTTTATAAACTTCACAGGTTTCATGTGTTCCTCCCTTGT
196 ATGGGTTATCTCAACCGCCTACTAAACTTTATAAACTTCACAGGTTTCATGTGTTCCTCCCTTGT
102636 TGTCATTCAACTTTGAACTCTTTCCAATTCTGGATTATCTTGCCCACTGAACTTACAAACCTCGG
261 TGTCATTCAACTTTGAACTCTTTCCAATTCTGGATTATCTTGCCCACTGAACTTACAAACCTCGG
*
102701 TCACCCACTGTTTTTCAAAAAAGAT
326 CCACCCACTGTTTTTCAAAAAAGAT
* *
102726 ACCTTTGCACCGATTGCGAGGTGGGTTATCTCGACCACTTGCTAAGCTTTATAAACTTCACAGAT
1 ACCTTTACACCGATTGCGAGGTGGGTTATCTCGACCGCTTGCTAAGCTTTATAAACTTCACAGAT
102791 TTCACGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCGCCC
66 TTCACGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCGCCC
* * *
102856 ACTAAACTTTCAAATCTCAGTTG-CCACTGTTTTTCACAAAAGACACCTTTGCACTGATTGCGAG
131 ACTAAACTTACAAACCTCAGTCGCCCACTGTTTTTCACAAAAGACACCTTTGCACTGATTGCGAG
* * *
102920 ATGGGTTATCTCAACCGCATACTAAACTTTATAAACTTCACAGGTTTCATGTCTTCCTCCCTCGT
196 ATGGGTTATCTCAACCGCCTACTAAACTTTATAAACTTCACAGGTTTCATGTGTTCCTCCCTTGT
* *
102985 TGTCATTCAACTTTGAACTCTTTCCAATTTTGGATTATCTTGCCCACTGAACTTACAAACCTTGG
261 TGTCATTCAACTTTGAACTCTTTCCAATTCTGGATTATCTTGCCCACTGAACTTACAAACCTCGG
*
103050 CCGCCCA-TGTTTTT-AAATAAAGAT
326 CCACCCACTGTTTTTCAAA-AAAGAT
* * * *
103074 ACCTTTACACCAATTGCGAGGTGGGTTATCTCGACCGCTTGCTAAACTTTATAAAC-TCAATATA
1 ACCTTTACACCGATTGCGAGGTGGGTTATCTCGACCGCTTGCTAAGCTTTATAAACTTC-ACAGA
* * * * * *
103138 TTTCCATGTGTTCATCCCTTGTTGTCATTCACCTTAGAACTCTTTCCGATTTTGGGTTAGCTCGC
65 TTT-CACGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCGC
* * *
103203 CCACTAAACTT--AAACCTCGGTTGCCTACTGTTTTTCACAA
129 CCACTAAACTTACAAACCTCAGTCGCCCACTGTTTTTCACAA
103243 TAGAAAGAAC
Statistics
Matches: 1070, Mismatches: 124, Indels: 32
0.87 0.10 0.03
Matches are distributed among these distances:
340 98 0.09
341 49 0.05
342 132 0.12
343 1 0.00
344 3 0.00
345 1 0.00
346 1 0.00
347 19 0.02
348 87 0.08
349 242 0.23
350 332 0.31
351 105 0.10
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.35
Consensus pattern (350 bp):
ACCTTTACACCGATTGCGAGGTGGGTTATCTCGACCGCTTGCTAAGCTTTATAAACTTCACAGAT
TTCACGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCGCCC
ACTAAACTTACAAACCTCAGTCGCCCACTGTTTTTCACAAAAGACACCTTTGCACTGATTGCGAG
ATGGGTTATCTCAACCGCCTACTAAACTTTATAAACTTCACAGGTTTCATGTGTTCCTCCCTTGT
TGTCATTCAACTTTGAACTCTTTCCAATTCTGGATTATCTTGCCCACTGAACTTACAAACCTCGG
CCACCCACTGTTTTTCAAAAAAGAT
Found at i:117059 original size:21 final size:22
Alignment explanation
Indices: 117033--117076 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
117023 GCCAACCAAG
117033 TAATTGAATT-ATATTAATTTC
1 TAATTGAATTAATATTAATTTC
*
117054 TAATTGAATTAATATTCATTTC
1 TAATTGAATTAATATTAATTTC
117076 T
1 T
117077 CTTGTAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (22 bp):
TAATTGAATTAATATTAATTTC
Found at i:118061 original size:16 final size:16
Alignment explanation
Indices: 118040--118077 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
118030 ATATCGATGA
118040 TGTGACCCAATCAGAT
1 TGTGACCCAATCAGAT
118056 TGTGACCCAATCAGAT
1 TGTGACCCAATCAGAT
118072 TGTGAC
1 TGTGAC
118078 ACTTGCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (16 bp):
TGTGACCCAATCAGAT
Found at i:118521 original size:59 final size:59
Alignment explanation
Indices: 118458--118601 Score: 173
Period size: 60 Copynumber: 2.4 Consensus size: 59
118448 ATTGCTGGTT
* * *
118458 CAATGTTTGTAAAATGCTTAAATAAGGGCCCAAAGAAAAAAAAAGTTCAAATCAGGGCC
1 CAATGTTTGTAAAATGCTTAAATAAGGGCCCAAAGAAAAAAAAAGCTCAAATAAGAGCC
* * * * *
118517 CAATGTTTGCAAGAATGCTCAAATAAGGGCCTAGAGAAAAAAAATGCTCAAATAAGAGCC
1 CAATGTTTGTAA-AATGCTTAAATAAGGGCCCAAAGAAAAAAAAAGCTCAAATAAGAGCC
*
118577 TAATG-TTGTGAAAATTGCTTAAATA
1 CAATGTTTGT-AAAA-TGCTTAAATA
118602 GGCAGAGACT
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
59 16 0.23
60 55 0.77
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (59 bp):
CAATGTTTGTAAAATGCTTAAATAAGGGCCCAAAGAAAAAAAAAGCTCAAATAAGAGCC
Found at i:118647 original size:31 final size:30
Alignment explanation
Indices: 118609--118713 Score: 113
Period size: 30 Copynumber: 3.4 Consensus size: 30
118599 ATAGGCAGAG
*
118609 ACTTATTTGAGCAATTTTCGCAATGTTGGGC
1 ACTTATTTGAAC-ATTTTCGCAATGTTGGGC
* *
118640 ACTTATTTCAACATTTTCGTAATGTTGGGC
1 ACTTATTTGAACATTTTCGCAATGTTGGGC
* * *
118670 CCTTATTTGAGCATTTTCGCTAACT-TTGCGC
1 ACTTATTTGAACATTTTCGC-AA-TGTTGGGC
*
118701 CCTTATTTGAACA
1 ACTTATTTGAACA
118714 ATTAGCCAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
30 33 0.52
31 29 0.46
32 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (30 bp):
ACTTATTTGAACATTTTCGCAATGTTGGGC
Found at i:118991 original size:26 final size:26
Alignment explanation
Indices: 118935--118991 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
118925 GCCCGCCCAT
* *
118935 ATTT-ATTTTTTTAAAATAAAATAAT
1 ATTTAATTTTTTTAAAATAAAAAAAG
*
118960 AATTAATTTTTTTAAAGA-AAAAAAAG
1 ATTTAATTTTTTTAAA-ATAAAAAAAG
118986 ATTTAA
1 ATTTAA
118992 ACATTAAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 3 0.12
26 22 0.85
27 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (26 bp):
ATTTAATTTTTTTAAAATAAAAAAAG
Found at i:120792 original size:28 final size:29
Alignment explanation
Indices: 120741--120801 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
120731 GCTTTGAGTA
* *
120741 AGAGTTGAAGGAGAAGCGTTTGAGAGTTG
1 AGAGTTGAAAGAAAAGCGTTTGAGAGTTG
*
120770 AGAGTTGAAAGAAAAGTG-TTGAGAGTTG
1 AGAGTTGAAAGAAAAGCGTTTGAGAGTTG
120798 AGAG
1 AGAG
120802 AAGCGTACGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.36, C:0.02, G:0.39, T:0.23
Consensus pattern (29 bp):
AGAGTTGAAAGAAAAGCGTTTGAGAGTTG
Found at i:124960 original size:58 final size:59
Alignment explanation
Indices: 124888--125010 Score: 203
Period size: 58 Copynumber: 2.1 Consensus size: 59
124878 CTTCAATTTC
124888 AGCATTGCACTATTGACATAATTGGAAACATCTTTGCAGAGA-TTCCTTCCACTTTGCAA
1 AGCA-TGCACTATTGACATAATTGGAAACATCTTTGCAGAGACTTCCTTCCACTTTGCAA
* * *
124947 AGCATGCACTATTGATATAATTGGAAACATCTTTGCAGAGACTTCTTTCCACTTTGCAG
1 AGCATGCACTATTGACATAATTGGAAACATCTTTGCAGAGACTTCCTTCCACTTTGCAA
125006 AGCAT
1 AGCAT
125011 TATTTTCTCA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
58 36 0.60
59 24 0.40
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (59 bp):
AGCATGCACTATTGACATAATTGGAAACATCTTTGCAGAGACTTCCTTCCACTTTGCAA
Found at i:132314 original size:13 final size:13
Alignment explanation
Indices: 132296--132325 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
132286 ATAATTGAAT
132296 TTTTCTAACATTA
1 TTTTCTAACATTA
*
132309 TTTTCTAACTTTA
1 TTTTCTAACATTA
132322 TTTT
1 TTTT
132326 TATTACCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTCTAACATTA
Found at i:133528 original size:2 final size:2
Alignment explanation
Indices: 133521--133561 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
133511 ATAATTTCTC
133521 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
133562 GATCATACAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:134547 original size:27 final size:27
Alignment explanation
Indices: 134509--134562 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
134499 ATGAAGTGAC
*
134509 GCGCCTAGGACCATGATTGGAGTAACT
1 GCGCCTAGGACCATGATTGCAGTAACT
134536 GCGCCTAGGACCATGATTGCAGTAACT
1 GCGCCTAGGACCATGATTGCAGTAACT
134563 ATGCCTTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (27 bp):
GCGCCTAGGACCATGATTGCAGTAACT
Found at i:134568 original size:27 final size:27
Alignment explanation
Indices: 134510--134568 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
134500 TGAAGTGACG
* *
134510 CGCCTAGGACCATGATTGGAGTAACTG
1 CGCCTAGGACCATGATTGCAGTAACTA
134537 CGCCTAGGACCATGATTGCAGTAACTA
1 CGCCTAGGACCATGATTGCAGTAACTA
*
134564 TGCCT
1 CGCCT
134569 TGAATTTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.24
Consensus pattern (27 bp):
CGCCTAGGACCATGATTGCAGTAACTA
Found at i:136208 original size:643 final size:635
Alignment explanation
Indices: 134978--137008 Score: 1625
Period size: 643 Copynumber: 3.2 Consensus size: 635
134968 ATATTTTTTT
* *
134978 GAATTAATTTCTAATTAAATCGAAACAAGATTTAAATGCTCGTAAAAACAAATCCTTAAATAGAA
1 GAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAAT-CAA
* * * * * *
135043 TAT-GCATGAGATTTGATCAGATG-ATATAGATATTTTAAGGAGTCTTGACGCCAAAAATCATGC
65 TGTGGC-TAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGACACCAAAAATCATGC
* * ** **
135106 AAAACTAAGTCGGGGACCCGAAACGTCTTTTTTAGTTAAAATCCCATGATGGTAAAAATGACCCG
129 AAAACTGAGTCGGGGACCCGAAACGTCGTTTTTAGCCAAAATCCCAAAATGGTAAAAATGACCCG
* * *
135171 AAAGATTTTTCCTCATTTTTTGACGAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGT
194 AAAAATTTTTCCTCATTTCTAGACGAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGT
* ** * * * *
135236 TTGGAAGACTTTTCACGCTTTTAATATTGTTTTTCATTTTTTTTCTAAATTAATTTCTAATTAAA
259 ATAAAAGACTTTTCACGCTTCTAATATCGTTTTTCATTTTCTTTCCAAATTAATTTCTAATTAAA
* * ** * ** * *
135301 TCGATACAAGATTCAGATGCACATAAAAATAAATTGTTAAATCCAATGTGGCTGAGATTTTGTTA
324 TCAAAACAAGATTCAGAAACACATAAAAACAAATCCTTAAATACAATGTGGCTGAGATTTGGTTA
*** * **
135366 GATGAATAAAGATATTTCAAGGAGTCTCAGCGCCAAAAATCATGCAAAACAGAGTTGTGGCCTTG
389 GATGAATAAAGATATTTCAAGGAGTCTCAGCGCCAAAAATCATGCAAAACAGACAAGTGACCCCG
* * ** * *
135431 GAACGCGTTTTGAGCTAAAAACCGTGATGGTTAGTATACGATTTTGAATAAAATTTTGCAAAAAT
454 GAAAGCGTTTTGAGCAAAAAACAATGATGG-T-GTACACGATTTGGAATAAAATTTTGCAAAAAT
** * * * * *
135496 TGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATGATCCGATATC
517 CAACCCGAAAGATATTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATATATAATCCAACATC
* * * ** * *
135561 AAAAATATTGAAGGGCTTTTAAGGCTTTTAATATTGTTTTTCCTATTTCTTTCC
582 AAAAAGATTGAAGGGATTATAACACTTCTAATATCGTTTTTCCTATTTCTTTCC
* *
135615 GAATTAATTTCCAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAA
1 GAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATC-AA
* *
135680 TGTGGCTAAGATTTGGTTAGATGAATATATAGATATTTCAAGGAATCTTGGCACCAAAAATCATG
65 TGTGGCTAAGATTTGGTTAGATG-A-ATATAGATATTTCAAGGAGTCTTGACACCAAAAATCATG
* * * * * * **
135745 CAAAACTGAG-C-TGGACCCCGGAATG-CGTTTTTAGCCGAAATGCTAAAATTTTCCAAAAATTG
128 CAAAACTGAGTCGGGGA-CCCGAAACGTCGTTTTTAGCCAAAATCCCAAAATGGT--AAAAA-TG
*
135807 ACCC-AAAAATTTGTTTCCTTGATTTCTAG-CGAAAATACTCATAAAA-ATATATAATTCAACGC
189 ACCCGAAAAA-TT-TTTCC-TCATTTCTAGACGAAAATACTCATAAAATATATATAATTCAACGC
* *
135869 CAAAAA-TATAAAAGCCTTTTTCACGCTTCTAATATCGTTTTCCTTATTTTCTTTCCAAATTAAT
251 CAAAAAGTATAAAAGAC-TTTTCACGCTTCTAATATCGTTTT--TCATTTTCTTTCCAAATTAAT
* ** *
135933 TTCTAATTAAATCAAAACAAGATTTAGAAATTCGTAAAAACAAATCCTTAAATACAATGTGGCTG
313 TTCTAATTAAATCAAAACAAGATTCAGAAACACATAAAAACAAATCCTTAAATACAATGTGGCTG
* * ** *
135998 AGATTTGGTTAGATGAATATAGATATATTTTAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTG
378 AGATTTGGTTAGATGAATA-A-AGATATTTCAAGGAGTCTCAGCGCCAAAAATCATGCAAAACAG
* *
136063 ACCAAG-GACCCCGGAAAGCGTTTTTAGGCAAAAAAAACAATGAT-G-GTACACGATTTCGGCA-
441 A-CAAGTGACCCCGGAAAGCGTTTTGA-GC--AAAAAACAATGATGGTGTACACGATTT-GGAAT
* * * *
136124 AAAATTTTGCGAAAATCAACCCGAAATAT-TTTTCTCAATTTTTAGCCATAATACTCATAAAAAA
501 AAAATTTTGCAAAAATCAACCCGAAAGATATTTCCTCAATTTTTAGCCAAAATACTCATAAAAAA
* * * *
136188 TATATAATTCAACGTCAAAAAGATTGAAGGGATTATGACACTTCTAATATCGTTTTTCCTATTTT
566 TATATAATCCAACATCAAAAAGATTGAAGGGATTATAACACTTCTAATATCGTTTTTCCTATTTC
*
136253 TTTTC
631 TTTCC
* * * *
136258 AAATTAATTTCTAATTAAATCGAAACATGATTCAAATGCTTGCAAAAACAAATCCTTAAATCAAG
1 GAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCAA-
* * **
136323 TGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTTTGCCATAAAAAATCATGCA
65 TGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGACACCAAAAATCATGCA
** * * * *
136388 AAACTGACCCGGGG-CTTCGGAACG-CGTTTTTAGCC-AAA----AAACT-GT---GATG----G
130 AAACTGAGTCGGGGAC-CCGAAACGTCGTTTTTAGCCAAAATCCCAAAATGGTAAAAATGACCCG
* * * * * *
136438 -TACA------C-GACTTC--G--G------CTAATAAAATATATATAATTCAACACCAAAAAAG
194 AAAAATTTTTCCTCATTTCTAGACGAAAATACTCATAAAATATATATAATTCAACGCC-AAAAAG
** * * * **
136485 -ACTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATT-TTTCTGAATTAATTTCTAATTA
258 TA-TAAAAGACTTTTCACGCTTCTAATATCGTTTTTCATTTTCTTTCCAAATTAATTTCTAATTA
* ** * * * * * *
136548 AATCGAAACAAGATTCAGAGGCTCGTAAAAATAAATCCTTAAATTCAATGTGGCTAAGATTTGAT
322 AATCAAAACAAGATTCAGAAACACATAAAAACAAATCCTTAAATACAATGTGGCTGAGATTTGGT
* * * ** *
136613 TAGATGAATATAGATATTTCAAGAAGTCTCAGCGCAAAAAAATCATGCAAAACTA-AGCTTG-GG
387 TAGATGAATAAAGATATTTCAAGGAGTCTCAGCGC-CAAAAATCATGCAAAAC-AGA-CAAGTGA
* * * * * * *
136676 CCTC-GAAACGCGTTTTTAGC-CAAAAC---CA---TGTACACGATTT-CAGCTAAAATTTTGTA
449 CCCCGGAAA-GCGTTTTGAGCAAAAAACAATGATGGTGTACACGATTTGGA-ATAAAATTTTGCA
* * * ** * * * *
136732 AAAA-CTGACCCGAAAAATTTTTCAGACAATTTTTGGCTAAAATACTCATAAAATATATATAATT
512 AAAATC-AACCCGAAAGATATTTC-CTCAATTTTTAGCCAAAATACTCATAAAAAATATATAATC
* *** * ** * * * ** *
136796 TAATGCCAAAAAGATTGGAGAACATT-TCACGCTTTTAATATCGTTTTTATTATTT-TTT-T
575 CAACATCAAAAAGATTGAAG-GGATTATAACACTTCTAATATCGTTTTTCCTATTTCTTTCC
* * * * *
136855 GAATTAATTTTTAATTAAATCGAAATAAGATTCAGATGCTCATAAAAACAAATTCTTAAATCCAA
1 GAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAAT-CAA
* * * * * * * * * *
136920 TGTTGTTGATATTTGATTAGATGAATATGGATATCTCAAAGAGTCTTGGCGCCAAAAATCATGCA
65 TGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGACACCAAAAATCATGCA
* * * *
136985 AAACTAAGCCGGGGTCACGAAACG
130 AAACTGAGTCGGGGACCCGAAACG
137009 CGACTTTAGC
Statistics
Matches: 1149, Mismatches: 202, Indels: 126
0.78 0.14 0.09
Matches are distributed among these distances:
596 1 0.00
597 156 0.14
598 11 0.01
599 74 0.06
600 3 0.00
601 5 0.00
604 25 0.02
605 32 0.03
606 86 0.07
607 13 0.01
608 16 0.01
609 29 0.03
610 4 0.00
613 1 0.00
614 1 0.00
616 5 0.00
618 1 0.00
626 2 0.00
630 2 0.00
631 1 0.00
636 1 0.00
637 80 0.07
638 22 0.02
639 8 0.01
640 59 0.05
641 99 0.09
642 43 0.04
643 263 0.23
644 36 0.03
645 56 0.05
646 3 0.00
647 1 0.00
648 10 0.01
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (635 bp):
GAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCAAT
GTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGACACCAAAAATCATGCAA
AACTGAGTCGGGGACCCGAAACGTCGTTTTTAGCCAAAATCCCAAAATGGTAAAAATGACCCGAA
AAATTTTTCCTCATTTCTAGACGAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGTAT
AAAAGACTTTTCACGCTTCTAATATCGTTTTTCATTTTCTTTCCAAATTAATTTCTAATTAAATC
AAAACAAGATTCAGAAACACATAAAAACAAATCCTTAAATACAATGTGGCTGAGATTTGGTTAGA
TGAATAAAGATATTTCAAGGAGTCTCAGCGCCAAAAATCATGCAAAACAGACAAGTGACCCCGGA
AAGCGTTTTGAGCAAAAAACAATGATGGTGTACACGATTTGGAATAAAATTTTGCAAAAATCAAC
CCGAAAGATATTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATATATAATCCAACATCAAAA
AGATTGAAGGGATTATAACACTTCTAATATCGTTTTTCCTATTTCTTTCC
Found at i:138332 original size:332 final size:328
Alignment explanation
Indices: 136454--139610 Score: 2552
Period size: 332 Copynumber: 9.5 Consensus size: 328
136444 ACTTCGGCTA
* * * * *
136454 ATAAAATATATATAATTCAACACCAAAAAAGACTGGAGGACTTTTCACGCTTTTAATATCGTTTT
1 ATAAAAAATATATAATTCAACGCC-AAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTT
* *
136519 TCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGAGGCTCGTAAAAATAAAT
65 TCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT
* * * *
136584 CCTTAAATTCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCTCAGCGCA
130 CCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTAGCGC-
* * **
136649 AAAAAATCATGCAAAACTAAGCTTGGGCCTCGAAACGCGTTTTTAGCC-AAAACC---ATG----
194 CAAAAATCATGCAAAACTGA-CCGGGGCCT-GAAACGCGTTTTTAGCCAAAAACCGTGATGATTA
* * * ** *
136706 -TACACGATTTCAGCTAAAATTTTGTAAAAACTGACCCGAAAAATTTTTCAGACAATTTTTGGCT
257 TTACACGATTTCGGCTAAAATTTTGCAAAAATTGA-CCGAAAAATTTTTC-CTCAATTTTTGACT
136770 AAAATACTC
320 AAAATACTC
* * * * ** *
136779 ATAAAATATATATAATTTAATGCCAAAAAGATTGGAGAACATTTCACGCTTTTAATATCGTTTTT
1 ATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTT
* * * *
136844 -ATTATTTTTTTGAATTAATTTTTAATTAAATCGAAATAAGATTCAGATGCTCATAAAAACAAAT
66 CA-TATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT
* * * * * * * *
136908 TCTTAAATCCAATGTTGTTGATATTTGATTAGATGAATATGGATATCTCAAAGAGTCTTGGCGCC
130 CCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTAGCGCC
* ** *
136973 AAAAATCATGCAAAACTAAGCCGGGGTCAC-GAAACGCGACTTTAGCAAAAAACCGTGATGATTA
195 AAAAATCATGCAAAACTGA-CCGGGG-C-CTGAAACGCGTTTTTAGCCAAAAACCGTGATGATTA
* * ** * * ** * * *
137037 TCAAACGATTTCGG-TCAGTATTTTACAAAAATTGACTTGAAAGTTATTTTCTTAAATTTTAG-C
257 TTACACGATTTCGGCT-AAAATTTTGCAAAAATTGAC-CGAAAAAT-TTTTCCTCAATTTTTGAC
* * **
137100 CAGAGCACTC
319 TAAAATACTC
* * * * * *
137110 ATTAAAATTATATAATTCAACGCCAATAAGATTAAAGGGCTTTTCATGCTTCTAATATCGTTTTT
1 ATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTT
* * *** *
137175 ACTATTATTTTTC-GAATTAATTTCTGATTAAATCGAAACATGATTCAGATGC-CTGT-TTTAGA
66 -C-A-TATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC-GTAAAAACA
* * * * * *
137237 AATCCTTCAATCTAATGTGGCTGAGATTCGGTTAGATGAATATAAATATTTCAAGGAGTCTCAGC
127 AATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTAGC
* * ** * * * * * *
137302 GCAAAAAATCATG-AACACTGTACCAGGACCCCGGAACGCGTATTTAGCAAAAAAAACCATAATT
192 GCCAAAAATCATGCAAAACTG-ACC-GGGGCCTGAAACGCGTTTTTAGC--CAAAAACCGTGA--
* * * * **
137366 TCGACTAACATACACGATTTCGGCTAATATTTTGTAAAAATTGACCAGAAGTATTTTTCCTCAAT
251 T-GA-TTA-TTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC-GAAAAATTTTTCCTCAAT
*
137431 TTTTGTCTAAAATACTC
312 TTTTGACTAAAATACTC
* *
137448 ATAATATATATATATATATATATATATTTCAACGCCAAAAAGATTGCAGGACTTTTCACGCTTTT
1 -----ATA-A-A-A-A-ATATATA-A-TTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTT
** * * * *
137513 AATATTATTTTTCATATTTTTTCTGAATTAGTTTCAAATTACATCAAAACAAGATTCAGATGCTC
54 AATATCGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * * * * *
137578 GTAAAAACACATCCTTAAATGCAATTTGGCTGAGATTTGATTAGATAAATATATATTTTTCAAGG
118 GTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGG
* * * * * * * *
137643 AGTCTCAACGCCAAAAATCATGCAATACTAAGTCGGGGCCGGAAACGCGTTTTTCGCAAAAAAAA
183 AGTCTTAGCGCCAAAAATCATGCAAAACTGA-CCGGGGCCTGAAACGCGTTTTTAGC-------C
* * *
137708 AAAAAGCCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCAGAAAAATTT
240 AAAAA-CCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC-GAAAAATTT
*
137773 TTCCTCTATTTTTGACTAAAATACTC
303 TTCCTCAATTTTTGACTAAAATACTC
* * * * * * * *
137799 ATGAATATATATATAATTTAACGCCAAAAAGATTGGAGGACTTGTCACGCTTTTCATATCATTTT
1 AT-AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTT
* * * *
137864 TCATATTCTTTTTTTGAATTAATTTGTAATTAAATCGAAACAAGATACAAATGCTCGTAAAAACA
65 TCATA---TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
* * * * * * * *
137929 AATCATTAAATTCAATGTGGATGAGATTTGATTAGATTAATATGGATATCTCAAGGATTCTTAAC
127 AATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTAGC
* *
137994 GCCAAAAATCATGCAAAACTGACCTGGGGCCCTGGAACG-TTTTTTAGCCAAAAACCGTGATGAT
192 GCCAAAAATCATGCAAAACTGACC-GGGG-CCTGAAACGCGTTTTTAGCCAAAAACCGTGATGAT
* * * *
138058 TATTACACGATTTCGGCTACAATTTTGCAAAAATTGACCGAAAAAAATATGTCCTCAATTTTTAA
255 TATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCG--AAAAATTTTTCCTCAATTTTTGA
138123 CTAAAATACTC
318 CTAAAATACTC
* * * * * * * *
138134 ATAAAAAAATATATGATTCATCGCCAAAAATATTGAAGGGTTTTTTACACTTCTAATATCTTTTT
1 AT-AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTT
* * * * *
138199 TCCTACTTTTTCTAAATTAATTTTTAATTAAATCGAAACAAAATTTAGATGCTCGTAAAAA-AAA
65 TCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
* * * * * * *
138263 TCCTTAATTCCAATGTGGCTGAGATTTTATTAGATTAATATAGATATTTGC-ATGATTTTTGGCG
129 TCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTT-CAAGGAGTCTTAGCG
* * * * ** **
138327 CCAAAAATCATGCGAAACTGACCCGAGGCCTCGCAACGCAG-TTTTGGCCAAAAAAAGAAACCGT
193 CCAAAAATCATGCAAAACTGA-CCGGGGCCT-GAAACGC-GTTTTTAGCCAAAAACCGTGA---T
* ** * *
138391 GA-TGTTACACGATTTCAACTAATATTTTGCAAAAATTGACTC-AAAATGTTTTTCCTCAACTTT
252 GATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC-CGAAAA-ATTTTTCCTCAA-TTT
* *
138454 TAGAC-ACAATACTC
314 TTGACTAAAATACTC
* * * **
138468 ATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCATGCTTCTAATAGTTTTTTT
1 ATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATA-TCGTTTT
* * * * * * ** *
138533 TAAATTTTTTTCCGAATTAATTTCTATTTAAAACAAAACTCGATTCAGATGCTTGT-------AA
65 T-CATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
* * * ** *
138591 -----AAA--C-A-GTGGCTGGGATTTGGTTAGATGAATATAGGTATTTCAAGGAGTCTCGGCAC
129 TCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTAGCGC
* * * *
138647 CAAAAATTATTCAAAATTGAACC--GGCCTCGGAAACGAGTTTTTAGCCAAAAACCGTGATGATT
194 CAAAAATCATGCAAAACTG-ACCGGGGCCT--GAAACGCGTTTTTAGCCAAAAACCGTGATGATT
* * * * * *
138710 ATTATACAATTTCGACTAAAATTTTACAAAAATAGACCTGAAAGATATTTT-CTCAATTTTT-AG
256 ATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC-GAAAAAT-TTTTCCTCAATTTTTGA-
* *
138773 CCATAATACTC
318 CTAAAATACTC
* * *
138784 A-ATAAAATATATAATTCGATGCCAAAAAGATTGAAGGGCTTTTCGA-GCTTTTAATATCGTTTT
1 ATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTC-ACGCTTTTAATATCGTTTT
* *
138847 TCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG-GAAAAGAAA
65 TCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
** * ** * *
138911 TCCTTAAATGTAATGTGGCTAAGATTAAAATCAGATGAATATAGATATTTCAAGGAGTGTCTAG-
129 TCCTTAAATCCAATGTGGCTGAGATT-TGATTAGATGAATATAGATATTTCAAGGAGTCT-TAGC
*
138975 GCCAAAAATCATGCAAAACTAAGCCGGGGCCCTGAAACGCGTTTTTAGCCAAAAACCGTGATTG-
192 GCCAAAAATCATGCAAAACTGA-CCGGGG-CCTGAAACGCGTTTTTAGCCAAAAACCGTGA-TGA
* * * * * * *
139039 TTACTACACGATTTTGGCTAAAATTCTGCAAAAAATGACTTGAAAATTTTTTTCTCAATTTTTGG
254 TTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC-CGAAAAATTTTTCCTCAATTTTT-G
139104 A-TAAAATACTC
317 ACTAAAATACTC
* * * * * * **
139115 ATAAAATATATATAATTGAACCCCGAAACA-ATTGGAGGACTTTTCACGCTTTTAATATTATTTT
1 ATAAAAAATATATAATTCAACGCC-AAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTT
* * *
139179 TCATA-TTTTCTCAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAGCAAAT
65 TCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT
** * * * * * * *
139243 TTTTAAATCCAATGTGGCTGATATTTGATTAGAAGAATATGGATATCTCAATGAGTCTTGGCGGC
130 CCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTAGCGCC
* * * * * *
139308 AAAAATCAGGCAAAACTGAGCCGAGGTCCTAAAACGCATTTTTAGCCAAAAACAGTGATGGTTAT
195 AAAAATCATGCAAAACTGA-CCG-GGGCCTGAAACGCGTTTTTAGCCAAAAACCGTGATGATTAT
* * * * **
139373 TACACGATTTCGACTAAAATTTTGTAAAAATTGACTCGAAAGATGTTTCCTCAATTTTTGGTTAA
258 TACACGATTTCGGCTAAAATTTTGCAAAAATTGAC-CGAAAAATTTTTCCTCAATTTTTGACTAA
139438 AATACTC
322 AATACTC
* * * * * * *
139445 ATAAAAAATATATAATACAACTCCAAAAAGATTGAATGGCTTTTGAC-ATTTCTATTATCATTTT
1 ATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTT-TAATATCGTTTT
** * *
139509 TC-TAATTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCTTAAAAACAA
65 TCAT-A-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * * * * *
139573 ATTCATAAATCCAATGTTGCTAAGGTTTGGTTAGATGA
128 ATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGA
139611 TGTAAAGTAT
Statistics
Matches: 2258, Mismatches: 446, Indels: 249
0.76 0.15 0.08
Matches are distributed among these distances:
313 2 0.00
314 49 0.02
315 57 0.03
316 47 0.02
317 13 0.01
318 20 0.01
319 56 0.02
320 4 0.00
321 1 0.00
323 41 0.02
324 153 0.07
325 25 0.01
327 3 0.00
328 3 0.00
329 24 0.01
330 280 0.12
331 196 0.09
332 321 0.14
333 177 0.08
334 119 0.05
335 129 0.06
336 6 0.00
337 15 0.01
338 39 0.02
339 1 0.00
340 49 0.02
341 2 0.00
342 140 0.06
343 9 0.00
344 2 0.00
345 1 0.00
346 4 0.00
347 4 0.00
348 13 0.01
349 37 0.02
350 129 0.06
351 71 0.03
352 2 0.00
353 1 0.00
354 1 0.00
355 8 0.00
356 4 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (328 bp):
ATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTT
CATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATC
CTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTAGCGCCA
AAAATCATGCAAAACTGACCGGGGCCTGAAACGCGTTTTTAGCCAAAAACCGTGATGATTATTAC
ACGATTTCGGCTAAAATTTTGCAAAAATTGACCGAAAAATTTTTCCTCAATTTTTGACTAAAATA
CTC
Found at i:143727 original size:19 final size:19
Alignment explanation
Indices: 143703--143744 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
143693 AAACCAGAGT
*
143703 AAAACCAAGACAATCAATC
1 AAAACCAAGACAATAAATC
*
143722 AAAACCAAGATAATAAATC
1 AAAACCAAGACAATAAATC
143741 AAAA
1 AAAA
143745 TGCCAAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.64, C:0.19, G:0.05, T:0.12
Consensus pattern (19 bp):
AAAACCAAGACAATAAATC
Found at i:147433 original size:31 final size:31
Alignment explanation
Indices: 147398--147462 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
147388 TAAGTTTATT
147398 ATAGTTTGTTTATTTGATCATTTCTCATTGG
1 ATAGTTTGTTTATTTGATCATTTCTCATTGG
*
147429 ATAGTTTGTTTATTTGGTCATTTCTCATTGG
1 ATAGTTTGTTTATTTGATCATTTCTCATTGG
147460 ATA
1 ATA
147463 TATAAGGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.20, C:0.09, G:0.17, T:0.54
Consensus pattern (31 bp):
ATAGTTTGTTTATTTGATCATTTCTCATTGG
Found at i:151578 original size:22 final size:22
Alignment explanation
Indices: 151550--151640 Score: 85
Period size: 22 Copynumber: 3.9 Consensus size: 22
151540 TGCACTATTC
*
151550 TTTCCACTTTGCAGGGCATTAT
1 TTTCCACTTTGCAGAGCATTAT
151572 TTTCCACTTTGCAGAGCATT-T
1 TTTCCACTTTGCAGAGCATTAT
* *
151593 TCTTCAATCTTCTTGTTGCGGAGCATTAT
1 T-TTC---C-AC-T-TTGCAGAGCATTAT
151622 TTTCCACTTTGCAGAGCAT
1 TTTCCACTTTGCAGAGCAT
151641 GGTTTCTTTC
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
21 2 0.04
22 32 0.57
23 1 0.02
24 1 0.02
25 2 0.04
26 1 0.02
27 1 0.02
28 14 0.25
29 2 0.04
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (22 bp):
TTTCCACTTTGCAGAGCATTAT
Done.