Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold591
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1432801
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 160147 characters in sequence are not A, C, G, or T
File 5 of 4
Found at i:1140721 original size:114 final size:114
Alignment explanation
Indices: 1140582--1140952 Score: 629
Period size: 114 Copynumber: 3.3 Consensus size: 114
1140572 TCTGTAGATG
**
1140582 TTTACAGTCAACT-TATTTCTGTTTTACAGTCAGTGTGTACGCTGAGTACTGTTAAGACGAGCGG
1 TTTACAGTCAACTGTATTTCACTTTTACAGTCAGTGTGTACGCTGAGTACTGTTAAGACGAGCGG
1140646 GACTGCTCTATCACTATCTGTAGATGTTTACAGTCAGCTGTATTTCTGT
66 GACTGCTCTATCACTATCTGTAGATGTTTACAGTCAGCTGTATTTCTGT
*
1140695 TTTACAGTCAGCTGTATTTCACTTTTACAGTCAGTGTGTACGCTGAGTACTGTTAAGACGAGCGG
1 TTTACAGTCAACTGTATTTCACTTTTACAGTCAGTGTGTACGCTGAGTACTGTTAAGACGAGCGG
1140760 GACTGCTCTATCACTATCTGTAGATGTTTACAGTCAGCTGTATTTCTGT
66 GACTGCTCTATCACTATCTGTAGATGTTTACAGTCAGCTGTATTTCTGT
*
1140809 TTTACAGTCAGCTGTATTTCACTTTTACAGTCAGTGTGTACGCTGAGTACTGTTAAGACGAGCGG
1 TTTACAGTCAACTGTATTTCACTTTTACAGTCAGTGTGTACGCTGAGTACTGTTAAGACGAGCGG
* *
1140874 GACTGCTCTATCACTATCTGTAGATGTTTATAGTCAACT-TATTTCTGT
66 GACTGCTCTATCACTATCTGTAGATGTTTACAGTCAGCTGTATTTCTGT
* * * **
1140922 TTTAAAGACAAATGTATTTCTGTTTTACAGT
1 TTTACAGTCAACTGTATTTCACTTTTACAGT
1140953 TAGCTGTATT
Statistics
Matches: 246, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
113 46 0.19
114 200 0.81
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.38
Consensus pattern (114 bp):
TTTACAGTCAACTGTATTTCACTTTTACAGTCAGTGTGTACGCTGAGTACTGTTAAGACGAGCGG
GACTGCTCTATCACTATCTGTAGATGTTTACAGTCAGCTGTATTTCTGT
Found at i:1140813 original size:23 final size:23
Alignment explanation
Indices: 1140786--1140842 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
1140776 TCTGTAGATG
**
1140786 TTTACAGTCAGCTGTATTTCTGT
1 TTTACAGTCAGCTGTATTTCACT
1140809 TTTACAGTCAGCTGTATTTCACT
1 TTTACAGTCAGCTGTATTTCACT
1140832 TTTACAGTCAG
1 TTTACAGTCAG
1140843 TGTGTACGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (23 bp):
TTTACAGTCAGCTGTATTTCACT
Found at i:1140940 original size:23 final size:23
Alignment explanation
Indices: 1140913--1140971 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
1140903 ATAGTCAACT
1140913 TATTTCTGTTTTAAAGACAAATG
1 TATTTCTGTTTTAAAGACAAATG
* ** **
1140936 TATTTCTGTTTTACAGTTAGCTG
1 TATTTCTGTTTTAAAGACAAATG
1140959 TATTTCTGTTTTA
1 TATTTCTGTTTTA
1140972 CAGTCAGTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.53
Consensus pattern (23 bp):
TATTTCTGTTTTAAAGACAAATG
Found at i:1141295 original size:2 final size:2
Alignment explanation
Indices: 1141288--1141335 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
1141278 CAGATTTAAN
*
1141288 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT 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
1141330 -T AT AT A
1 AT AT AT A
1141336 GTGCTTTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1145145 original size:42 final size:44
Alignment explanation
Indices: 1145099--1145180 Score: 114
Period size: 42 Copynumber: 1.9 Consensus size: 44
1145089 CACAAGTAAT
* *
1145099 TTTTACACTAGGTTTGTTCTACATTAGTTT-T-TTTTACACATG
1 TTTTAAACTAGGTTTGTTCTACACTAGTTTCTGTTTTACACATG
**
1145141 TTTTAAACTATTTTTGTTCTACACTAGTTTCTGTTTTACA
1 TTTTAAACTAGGTTTGTTCTACACTAGTTTCTGTTTTACA
1145181 ATAGTGTGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 26 0.76
43 1 0.03
44 7 0.21
ACGTcount: A:0.22, C:0.15, G:0.10, T:0.54
Consensus pattern (44 bp):
TTTTAAACTAGGTTTGTTCTACACTAGTTTCTGTTTTACACATG
Found at i:1145180 original size:17 final size:17
Alignment explanation
Indices: 1145139--1145197 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
1145129 TTTTTACACA
* *
1145139 TGTTTTAAACTA-TTTT
1 TGTTTTACACTAGTTTC
*
1145155 TGTTCTACACTAGTTTC
1 TGTTTTACACTAGTTTC
* *
1145172 TGTTTTACAATAG--TG
1 TGTTTTACACTAGTTTC
1145187 TGTTTTACACT
1 TGTTTTACACT
1145198 TATGCCTAGT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
15 11 0.31
16 10 0.29
17 14 0.40
ACGTcount: A:0.22, C:0.14, G:0.12, T:0.53
Consensus pattern (17 bp):
TGTTTTACACTAGTTTC
Found at i:1145295 original size:18 final size:18
Alignment explanation
Indices: 1145272--1145317 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
1145262 TATACTTGTT
1145272 TTGTTCTACATAAGTTAA
1 TTGTTCTACATAAGTTAA
* * *
1145290 TTGTTCTACCTACGTTAT
1 TTGTTCTACATAAGTTAA
*
1145308 TTTTTCTACA
1 TTGTTCTACA
1145318 CTAGAGTTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.17, G:0.09, T:0.50
Consensus pattern (18 bp):
TTGTTCTACATAAGTTAA
Found at i:1147489 original size:161 final size:161
Alignment explanation
Indices: 1147265--1147692 Score: 669
Period size: 161 Copynumber: 2.6 Consensus size: 161
1147255 TTTGACAGTC
* * ** *
1147265 TGTACTGATATCACGGAATAAATCGTATAACTGATGATTTTTTAACAGCCTGACAGTGTATACTC
1 TGTACAGATATCACGGACTGTATCGTATAACTGATGATTTTTT-ACAGCCTGACAATGTATACTC
* *
1147330 AGATATCACGGATTGTATCATATAACTGATGATCTTTTAAAAGCCTGTAGACTCGGATATCACGG
65 AGATATCACGGATTGTATCATATAACTGATGATCTTTTAAAAGCCTGTACACTCAGATATCACGG
*
1147395 ACTGTATTATATAGTGTAATCC-TTTACAGCT
130 ACTGTATTATAAAGTGTAATCCTTTTACAGCT
* *
1147426 TTTACAGATATCACGGACTGTATCGTATAACTGATAATTGTTTTACAGCCTGACAATGTATACTC
1 TGTACAGATATCACGGACTGTATCGTATAACTGATGATT-TTTTACAGCCTGACAATGTATACTC
*
1147491 AGATATCACGGATTGTATCATATAACTGATGATCTTTTAACAGCCTGTACACTCAGATATCACGG
65 AGATATCACGGATTGTATCATATAACTGATGATCTTTTAAAAGCCTGTACACTCAGATATCACGG
1147556 ACTGTATTATAAAGTGTAATCCTTTTACAGCT
130 ACTGTATTATAAAGTGTAATCCTTTTACAGCT
* *
1147588 TGTACAGATATCACGGACTGTATCGTATAACTGACGATTTTTTACAGCCTGACAATGTATGCTCA
1 TGTACAGATATCACGGACTGTATCGTATAACTGATGATTTTTTACAGCCTGACAATGTATACTCA
* *
1147653 GATATCACGGATTGTATACTCATATAAATTATGATCTTTT
66 GATATCACGGATTG--TA-TCATATAACTGATGATCTTTT
1147693 TACAGCTTGT
Statistics
Matches: 245, Mismatches: 17, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
161 175 0.71
162 49 0.20
163 2 0.01
164 19 0.08
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (161 bp):
TGTACAGATATCACGGACTGTATCGTATAACTGATGATTTTTTACAGCCTGACAATGTATACTCA
GATATCACGGATTGTATCATATAACTGATGATCTTTTAAAAGCCTGTACACTCAGATATCACGGA
CTGTATTATAAAGTGTAATCCTTTTACAGCT
Found at i:1147534 original size:60 final size:56
Alignment explanation
Indices: 1147271--1147698 Score: 283
Period size: 60 Copynumber: 7.8 Consensus size: 56
1147261 AGTCTGTACT
* ** *
1147271 GATATCACGGAATAAATCGTATAACTGATGAT-TTTTTAACAGCCTGACAGTGTATACTCA
1 GATATCACGGACTGTATCATATAACTGATGATCTTTTT-ACAGCCT--C--TGTATACTCA
* * * * *
1147331 GATATCACGGATTGTATCATATAACTGATGATCTTTTAAAAG-C-CTGTAGACTCG
1 GATATCACGGACTGTATCATATAACTGATGATCTTTTTACAGCCTCTGTATACTCA
* * * *
1147385 GATATCACGGACTGTATTATAT-AGTG-TAATC-CTTTACAG-CT-T-T-TA--CA
1 GATATCACGGACTGTATCATATAACTGATGATCTTTTTACAGCCTCTGTATACTCA
* *
1147432 GATATCACGGACTGTATCGTATAACTGATAAT-TGTTTTACAGCCTGACAATGTATACTCA
1 GATATCACGGACTGTATCATATAACTGATGATCT-TTTTACAGCCT--C--TGTATACTCA
* * *
1147492 GATATCACGGATTGTATCATATAACTGATGATCTTTTAACAG-C-CTGTACACTCA
1 GATATCACGGACTGTATCATATAACTGATGATCTTTTTACAGCCTCTGTATACTCA
* * * *
1147546 GATATCACGGACTGTATTATA-AAGTG-TAATCCTTTTACAG-CT-TG--TA--CA
1 GATATCACGGACTGTATCATATAACTGATGATCTTTTTACAGCCTCTGTATACTCA
* * *
1147594 GATATCACGGACTGTATCGTATAACTGACGAT-TTTTTACAGCCTGACAATGTATGCTCA
1 GATATCACGGACTGTATCATATAACTGATGATCTTTTTACAGCCT--C--TGTATACTCA
* * *
1147653 GATATCACGGATTGTATACTCATATAAATTATGATCTTTTTACAGC
1 GATATCACGGACTG--TA-TCATATAACTGATGATCTTTTTACAGC
1147699 TTGTACATAT
Statistics
Matches: 289, Mismatches: 45, Indels: 65
0.72 0.11 0.16
Matches are distributed among these distances:
47 21 0.07
48 24 0.08
49 17 0.06
50 13 0.04
51 9 0.03
52 18 0.06
53 7 0.02
54 56 0.19
55 2 0.01
56 3 0.01
57 2 0.01
58 2 0.01
59 17 0.06
60 69 0.24
61 7 0.02
62 12 0.04
63 10 0.03
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (56 bp):
GATATCACGGACTGTATCATATAACTGATGATCTTTTTACAGCCTCTGTATACTCA
Found at i:1147793 original size:160 final size:159
Alignment explanation
Indices: 1147265--1147794 Score: 604
Period size: 161 Copynumber: 3.3 Consensus size: 159
1147255 TTTGACAGTC
* * ** * * *
1147265 TGTACTGATATCACGGAATAAATCGTATAACTGATGATTTTTTAACAGCCTGACAGTGTATACTC
1 TGTACAGATATCACGGACTGTATCGTATAACTGATAATCTTTT-ACAGCCTGACAATGTATACTC
* * * *
1147330 AGATATCACGGATTGTATCATATAACTGATGATCTTTTAAAAGCCTGTAGACTCGGATATCACGG
65 AGATATCACGGATTGTATCATATAAATGATGATCTTTTAACAGCCTGTACACT--AATATCACGG
*
1147395 ACTGTATTATATAGTGTAATCC-TTTACAGCT
128 ACTGTATTATAAAGTGTAATCCTTTTACAGCT
* *
1147426 TTTACAGATATCACGGACTGTATCGTATAACTGATAATTGTTTTACAGCCTGACAATGTATACTC
1 TGTACAGATATCACGGACTGTATCGTATAACTGATAA-TCTTTTACAGCCTGACAATGTATACTC
*
1147491 AGATATCACGGATTGTATCATATAACTGATGATCTTTTAACAGCCTGTACACTCAGATATCACGG
65 AGATATCACGGATTGTATCATATAAATGATGATCTTTTAACAGCCTGTACACT-A-ATATCACGG
1147556 ACTGTATTATAAAGTGTAATCCTTTTACAGCT
128 ACTGTATTATAAAGTGTAATCCTTTTACAGCT
** * *
1147588 TGTACAGATATCACGGACTGTATCGTATAACTGACGATTTTTTACAGCCTGACAATGTATGCTCA
1 TGTACAGATATCACGGACTGTATCGTATAACTGATAATCTTTTACAGCCTGACAATGTATACTCA
* * * * *
1147653 GATATCACGGATTGTATACTCATATAAATTATGATCTTTTTACAGCTTGTACA-T-ATTTGACGG
66 GATATCACGGATTG--TA-TCATATAAATGATGATCTTTTAACAGCCTGTACACTAATATCACGG
* *** * * *
1147716 ACT-T-TTTTTTCGTTGATGATCTTTTTACAGCC
128 ACTGTATTATAAAG-TG-TAATCCTTTTACAGCT
* * *
1147748 TGTACAGATACCACGGACTGTAGT-GTGTAACTGATTATCTTTTACAG
1 TGTACAGATATCACGGACTGTA-TCGTATAACTGATAATCTTTTACAG
1147795 TGTGTATAAA
Statistics
Matches: 324, Mismatches: 36, Indels: 19
0.85 0.09 0.05
Matches are distributed among these distances:
158 4 0.01
159 3 0.01
160 63 0.19
161 173 0.53
162 48 0.15
163 3 0.01
164 30 0.09
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.36
Consensus pattern (159 bp):
TGTACAGATATCACGGACTGTATCGTATAACTGATAATCTTTTACAGCCTGACAATGTATACTCA
GATATCACGGATTGTATCATATAAATGATGATCTTTTAACAGCCTGTACACTAATATCACGGACT
GTATTATAAAGTGTAATCCTTTTACAGCT
Found at i:1148647 original size:8 final size:8
Alignment explanation
Indices: 1148623--1148706 Score: 71
Period size: 8 Copynumber: 10.5 Consensus size: 8
1148613 ACCGACTATA
1148623 TGACCGAT
1 TGACCGAT
**
1148631 TGAGTGAT
1 TGACCGAT
*
1148639 TGTCCGAT
1 TGACCGAT
1148647 TGACCGAT
1 TGACCGAT
**
1148655 TGAGTGAT
1 TGACCGAT
**
1148663 TGACTTAT
1 TGACCGAT
1148671 TGACCGAT
1 TGACCGAT
1148679 TG-CCTGAT
1 TGACC-GAT
*
1148687 TTACCGAT
1 TGACCGAT
*
1148695 TGACTGAT
1 TGACCGAT
1148703 TGAC
1 TGAC
1148707 AGACCGACTG
Statistics
Matches: 59, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
7 2 0.03
8 55 0.93
9 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (8 bp):
TGACCGAT
Found at i:1148655 original size:16 final size:16
Alignment explanation
Indices: 1148623--1148769 Score: 114
Period size: 16 Copynumber: 9.2 Consensus size: 16
1148613 ACCGACTATA
*
1148623 TGACCGATTGAGTGAT
1 TGACCGATTGACTGAT
* *
1148639 TGTCCGATTGACCGAT
1 TGACCGATTGACTGAT
** *
1148655 TGAGTGATTGACTTAT
1 TGACCGATTGACTGAT
*
1148671 TGACCGATTGCCTGAT
1 TGACCGATTGACTGAT
*
1148687 TTACCGATTGACTGAT
1 TGACCGATTGACTGAT
* **
1148703 TGACAGACCGACTGAT
1 TGACCGATTGACTGAT
* * * *
1148719 CGAACGGTTAACTGAT
1 TGACCGATTGACTGAT
**
1148735 TGACTAATTGACTGAT
1 TGACCGATTGACTGAT
* * *
1148751 TGGCCAATTGTCTGAT
1 TGACCGATTGACTGAT
1148767 TGA
1 TGA
1148770 TTTTATGGAC
Statistics
Matches: 96, Mismatches: 35, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 96 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (16 bp):
TGACCGATTGACTGAT
Found at i:1148655 original size:24 final size:24
Alignment explanation
Indices: 1148623--1148705 Score: 96
Period size: 24 Copynumber: 3.5 Consensus size: 24
1148613 ACCGACTATA
1148623 TGACCGATTGAGTGATTGTCCGAT
1 TGACCGATTGAGTGATTGTCCGAT
* **
1148647 TGACCGATTGAGTGATTGACTTAT
1 TGACCGATTGAGTGATTGTCCGAT
**
1148671 TGACCGATTGCCTGATT-TACCGAT
1 TGACCGATTGAGTGATTGT-CCGAT
*
1148695 TGACTGATTGA
1 TGACCGATTGA
1148706 CAGACCGACT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (24 bp):
TGACCGATTGAGTGATTGTCCGAT
Found at i:1150305 original size:2 final size:2
Alignment explanation
Indices: 1150300--1150355 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1150290 ATATATATAT
1150300 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1150342 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
1150356 NNNNNNNNNN
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1153500 original size:13 final size:13
Alignment explanation
Indices: 1153482--1153507 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1153472 GGGGTAGAAG
1153482 GACGGTTATCATA
1 GACGGTTATCATA
1153495 GACGGTTATCATA
1 GACGGTTATCATA
1153508 ATAATACTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GACGGTTATCATA
Found at i:1158275 original size:17 final size:17
Alignment explanation
Indices: 1158250--1158284 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1158240 GATCATAAAT
1158250 TCATCAATTGAAATACA
1 TCATCAATTGAAATACA
* *
1158267 TCATTAATTGAGATACA
1 TCATCAATTGAAATACA
1158284 T
1 T
1158285 ATGTGTAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (17 bp):
TCATCAATTGAAATACA
Found at i:1158818 original size:16 final size:16
Alignment explanation
Indices: 1158794--1158846 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
1158784 ACTGTGAGGA
*
1158794 ACAGCGGGCTACTGCT
1 ACAGGGGGCTACTGCT
*
1158810 ACAGGGGGCTACTGAT
1 ACAGGGGGCTACTGCT
* * *
1158826 AGAGGCGGCTATTGCT
1 ACAGGGGGCTACTGCT
1158842 ACAGG
1 ACAGG
1158847 TATAGTGTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.23, C:0.23, G:0.36, T:0.19
Consensus pattern (16 bp):
ACAGGGGGCTACTGCT
Found at i:1161241 original size:1 final size:1
Alignment explanation
Indices: 1161231--1161274 Score: 70
Period size: 1 Copynumber: 44.0 Consensus size: 1
1161221 GAAAAGNGGT
* *
1161231 GGGGGTGGGGGGGGGGGGGGGGGGGGTGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1161275 CATTGATTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.95, T:0.05
Consensus pattern (1 bp):
G
Found at i:1161261 original size:20 final size:21
Alignment explanation
Indices: 1161231--1161274 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1161221 GAAAAGNGGT
1161231 GGGGGTGGGGGGGGGGGGGGG
1 GGGGGTGGGGGGGGGGGGGGG
1161252 GGGGGTGGGGGGGGGGGGGGG
1 GGGGGTGGGGGGGGGGGGGGG
1161273 GG
1 GG
1161275 CATTGATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.95, T:0.05
Consensus pattern (21 bp):
GGGGGTGGGGGGGGGGGGGGG
Found at i:1161602 original size:17 final size:18
Alignment explanation
Indices: 1161576--1161612 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1161566 TCTAATTTGT
1161576 AAAAAAAAACCAAAA-AC
1 AAAAAAAAACCAAAATAC
*
1161593 AAAAACAAACCAAAATAC
1 AAAAAAAAACCAAAATAC
1161611 AA
1 AA
1161613 GGCGTTGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.78, C:0.19, G:0.00, T:0.03
Consensus pattern (18 bp):
AAAAAAAAACCAAAATAC
Found at i:1164273 original size:33 final size:33
Alignment explanation
Indices: 1164153--1164421 Score: 188
Period size: 33 Copynumber: 8.2 Consensus size: 33
1164143 GTAAGTAAAG
*
1164153 CAGAAAAATCCTCACCAGAACCAGTTGGTGAAC
1 CAGAAAAATCCTTACCAGAACCAGTTGGTGAAC
** ** * * * *
1164186 CA-AAAGTGTCCCCACCTGGACTAGTTCGTGAAC
1 CAGAAA-AATCCTTACCAGAACCAGTTGGTGAAC
** *
1164219 CAGAAATGTTTCC-T-CCTGAACCAGTTGGTGAAC
1 CAGAAA--AATCCTTACCAGAACCAGTTGGTGAAC
* * * *
1164252 CAGAAGAATCCTCACCAGAACCACTTGCTGAAC
1 CAGAAAAATCCTTACCAGAACCAGTTGGTGAAC
* * * * * *
1164285 TAGAAAAATCGTTACCTGAGCCAGTTGATGAGC
1 CAGAAAAATCCTTACCAGAACCAGTTGGTGAAC
* *
1164318 CAGAAAAAAT-ATTTCCAGAACCAGTTGGTGAAC
1 CAG-AAAAATCCTTACCAGAACCAGTTGGTGAAC
* * *
1164351 C-GAAAAAATCCTTACTAGAACCACTTGGTGAGC
1 CAG-AAAAATCCTTACCAGAACCAGTTGGTGAAC
* * *
1164384 CAGAAGAATCTTTACAAGAACCAGTTGGTGAAC
1 CAGAAAAATCCTTACCAGAACCAGTTGGTGAAC
1164417 CAGAA
1 CAGAA
1164422 CCAGTTGGTG
Statistics
Matches: 183, Mismatches: 45, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
31 3 0.02
32 11 0.06
33 154 0.84
34 10 0.05
35 5 0.03
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (33 bp):
CAGAAAAATCCTTACCAGAACCAGTTGGTGAAC
Found at i:1164408 original size:99 final size:99
Alignment explanation
Indices: 1164236--1164421 Score: 239
Period size: 99 Copynumber: 1.9 Consensus size: 99
1164226 GTTTCCTCCT
* * *
1164236 GAACCAGTTGGTGAACCAGAAGAATCCTCACCAGAACCACTTGCTGAACTAGAAAAATCGTTACC
1 GAACCAGTTGGTGAACCAGAAAAATCCTCACCAGAACCACTTGCTGAACCAGAAAAATCGTTACA
* * *
1164301 TGAGCCAGTTGATGAGCCAGAAAAAATATTTCCA
66 AGAACCAGTTGATGAACCAGAAAAAATATTTCCA
* * * * * *
1164335 GAACCAGTTGGTGAACC-GAAAAAATCCTTACTAGAACCACTTGGTGAGCCAGAAGAATCTTTAC
1 GAACCAGTTGGTGAACCAG-AAAAATCCTCACCAGAACCACTTGCTGAACCAGAAAAATCGTTAC
*
1164399 AAGAACCAGTTGGTGAACCAGAA
65 AAGAACCAGTTGATGAACCAGAA
1164422 CCAGTTGGTG
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
98 1 0.01
99 72 0.99
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (99 bp):
GAACCAGTTGGTGAACCAGAAAAATCCTCACCAGAACCACTTGCTGAACCAGAAAAATCGTTACA
AGAACCAGTTGATGAACCAGAAAAAATATTTCCA
Found at i:1164422 original size:51 final size:51
Alignment explanation
Indices: 1164367--1164589 Score: 185
Period size: 51 Copynumber: 4.1 Consensus size: 51
1164357 AATCCTTACT
*
1164367 AGAACCACTTGGTGAGCCAGAAGAATCTTTACAAGAACCAGTTGGTGAACC
1 AGAACCACTTGGTGAGCCAGAAGAATCCTTACAAGAACCAGTTGGTGAACC
* *
1164418 AGAACCAGTTGGTGAGCCAGAAGAATCCTTACTAGAACCAGTTGGTGAACC
1 AGAACCACTTGGTGAGCCAGAAGAATCCTTACAAGAACCAGTTGGTGAACC
** * *
1164469 AGAAAAATCCTCATCAGAACCAGTTGGTGAGCCAGAAGAATCTTTACAAGAACCAGTTGTTGAAC
1 AG---AA----C--C---ACTTG---GTGAGCCAGAAGAATCCTTACAAGAACCAGTTGGTGAAC
1164534 C
51 C
* * * * ** *
1164535 AGAACCAGTTGGTGAACCAGAAAAATCCTCACCTGAACCAGCTGGTGAACC
1 AGAACCACTTGGTGAGCCAGAAGAATCCTTACAAGAACCAGTTGGTGAACC
1164586 AGAA
1 AGAA
1164590 AAATCCTTAT
Statistics
Matches: 137, Mismatches: 20, Indels: 30
0.73 0.11 0.16
Matches are distributed among these distances:
51 86 0.63
54 4 0.03
57 1 0.01
58 1 0.01
59 1 0.01
60 1 0.01
63 4 0.03
66 39 0.28
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.19
Consensus pattern (51 bp):
AGAACCACTTGGTGAGCCAGAAGAATCCTTACAAGAACCAGTTGGTGAACC
Found at i:1164423 original size:18 final size:18
Alignment explanation
Indices: 1164400--1164439 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1164390 AATCTTTACA
1164400 AGAACCAGTTGGTGAACC
1 AGAACCAGTTGGTGAACC
*
1164418 AGAACCAGTTGGTGAGCC
1 AGAACCAGTTGGTGAACC
1164436 AGAA
1 AGAA
1164440 GAATCCTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.35, C:0.20, G:0.30, T:0.15
Consensus pattern (18 bp):
AGAACCAGTTGGTGAACC
Found at i:1164430 original size:84 final size:84
Alignment explanation
Indices: 1164332--1164505 Score: 244
Period size: 84 Copynumber: 2.1 Consensus size: 84
1164322 AAAAATATTT
* * *
1164332 CCAGAACCAGTTGGTGAACC-GAAAAAATCCTTACTAGAACCACTTGGTGAGCCAGAAGAATCTT
1 CCAGAACCAGTTGGTGAACCAG-AAAAATCCTTACTAGAACCACTTGGTGAACCAGAAAAATCCT
*
1164396 TA-CAAGAACCAGTTGGTGAA
65 CATC-AGAACCAGTTGGTGAA
* * *
1164416 CCAGAACCAGTTGGTGAGCCAGAAGAATCCTTACTAGAACCAGTTGGTGAACCAGAAAAATCCTC
1 CCAGAACCAGTTGGTGAACCAGAAAAATCCTTACTAGAACCACTTGGTGAACCAGAAAAATCCTC
*
1164481 ATCAGAACCAGTTGGTGAG
66 ATCAGAACCAGTTGGTGAA
1164500 CCAGAA
1 CCAGAA
1164506 GAATCTTTAC
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
84 78 0.98
85 2 0.03
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.19
Consensus pattern (84 bp):
CCAGAACCAGTTGGTGAACCAGAAAAATCCTTACTAGAACCACTTGGTGAACCAGAAAAATCCTC
ATCAGAACCAGTTGGTGAA
Found at i:1164460 original size:33 final size:33
Alignment explanation
Indices: 1164418--1164538 Score: 163
Period size: 33 Copynumber: 3.7 Consensus size: 33
1164408 TTGGTGAACC
*
1164418 AGAACCAGTTGGTGAGCCAGAAGAATCCTTACT
1 AGAACCAGTTGGTGAACCAGAAGAATCCTTACT
* *
1164451 AGAACCAGTTGGTGAACCAGAAAAATCCTCA-T
1 AGAACCAGTTGGTGAACCAGAAGAATCCTTACT
* * *
1164483 CAGAACCAGTTGGTGAGCCAGAAGAATCTTTACA
1 -AGAACCAGTTGGTGAACCAGAAGAATCCTTACT
*
1164517 AGAACCAGTTGTTGAACCAGAA
1 AGAACCAGTTGGTGAACCAGAA
1164539 CCAGTTGGTG
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
32 1 0.01
33 75 0.99
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (33 bp):
AGAACCAGTTGGTGAACCAGAAGAATCCTTACT
Found at i:1164475 original size:117 final size:118
Alignment explanation
Indices: 1164334--1164618 Score: 461
Period size: 117 Copynumber: 2.4 Consensus size: 118
1164324 AAATATTTCC
*
1164334 AGAACCAGTTGGTGAACC-GAAAAAATCCTTA-CTAGAACCACTTGGTGAGCCAGAAGAATCTTT
1 AGAACCAGTTGGTGAACCAG-AAAAATCCTTATC-AGAACCAGTTGGTGAGCCAGAAGAATCTTT
* * *
1164397 ACAAGAACCAGTTGGTGAACCAGAACCAGTTGGTGAGCCAGAAGAATCCTTA-CT
64 ACAAGAACCAGTTGGTGAACCAGAACCAGTTGGTGAACCAGAAAAATCCTCACCT
*
1164451 AGAACCAGTTGGTGAACCAGAAAAATCCTCATCAGAACCAGTTGGTGAGCCAGAAGAATCTTTAC
1 AGAACCAGTTGGTGAACCAGAAAAATCCTTATCAGAACCAGTTGGTGAGCCAGAAGAATCTTTAC
*
1164516 AAGAACCAGTTGTTGAACCAGAACCAGTTGGTGAACCAGAAAAATCCTCACCT
66 AAGAACCAGTTGGTGAACCAGAACCAGTTGGTGAACCAGAAAAATCCTCACCT
*
1164569 -GAACCAGCTGGTGAACCAGAAAAATCCTTATCAGAACCAGTTGGTGAGCC
1 AGAACCAGTTGGTGAACCAGAAAAATCCTTATCAGAACCAGTTGGTGAGCC
1164619 GGAAACCTTG
Statistics
Matches: 157, Mismatches: 8, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
117 153 0.97
118 4 0.03
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (118 bp):
AGAACCAGTTGGTGAACCAGAAAAATCCTTATCAGAACCAGTTGGTGAGCCAGAAGAATCTTTAC
AAGAACCAGTTGGTGAACCAGAACCAGTTGGTGAACCAGAAAAATCCTCACCT
Found at i:1164539 original size:84 final size:84
Alignment explanation
Indices: 1164451--1164611 Score: 252
Period size: 84 Copynumber: 1.9 Consensus size: 84
1164441 AATCCTTACT
* * * * *
1164451 AGAACCAGTTGGTGAACCAGAAAAATCCTCATCAGAACCAGTTGGTGAGCCAGAAGAATCTTTA-
1 AGAACCAGTTGGTGAACCAGAAAAATCCTCACCAGAACCAGCTGGTGAACCAGAAAAATCCTTAT
1164515 CAAGAACCAGTTGTTGAACC
66 C-AGAACCAGTTGTTGAACC
*
1164535 AGAACCAGTTGGTGAACCAGAAAAATCCTCACCTGAACCAGCTGGTGAACCAGAAAAATCCTTAT
1 AGAACCAGTTGGTGAACCAGAAAAATCCTCACCAGAACCAGCTGGTGAACCAGAAAAATCCTTAT
1164600 CAGAACCAGTTG
66 CAGAACCAGTTG
1164612 GTGAGCCGGA
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
84 69 0.99
85 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.19
Consensus pattern (84 bp):
AGAACCAGTTGGTGAACCAGAAAAATCCTCACCAGAACCAGCTGGTGAACCAGAAAAATCCTTAT
CAGAACCAGTTGTTGAACC
Found at i:1164540 original size:18 final size:18
Alignment explanation
Indices: 1164517--1164556 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1164507 AATCTTTACA
*
1164517 AGAACCAGTTGTTGAACC
1 AGAACCAGTTGGTGAACC
1164535 AGAACCAGTTGGTGAACC
1 AGAACCAGTTGGTGAACC
1164553 AGAA
1 AGAA
1164557 AAATCCTCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (18 bp):
AGAACCAGTTGGTGAACC
Found at i:1164575 original size:33 final size:33
Alignment explanation
Indices: 1164532--1164615 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
1164522 CAGTTGTTGA
1164532 ACCAGAACCAGTTGGTGAACCAGAAAAATCCTC
1 ACCAGAACCAGTTGGTGAACCAGAAAAATCCTC
* * *
1164565 ACCTGAACCAGCTGGTGAACCAGAAAAATCCTT
1 ACCAGAACCAGTTGGTGAACCAGAAAAATCCTC
*
1164598 ATCAGAACCAGTTGGTGA
1 ACCAGAACCAGTTGGTGA
1164616 GCCGGAAACC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (33 bp):
ACCAGAACCAGTTGGTGAACCAGAAAAATCCTC
Found at i:1165123 original size:54 final size:54
Alignment explanation
Indices: 1165036--1165388 Score: 609
Period size: 54 Copynumber: 6.5 Consensus size: 54
1165026 GCTCCGCCCT
* * *
1165036 CTGTCGACAGACCCAGTGTAACTGTCGATACGACTAATGGGATAGACACATATA
1 CTGTAGACAGACCCAGTGTAACTGTCGATACGACTAATTGTATAGACACATATA
* *
1165090 CTGTAGACAGACCCAGTGTAACTGTCGATACGACTAATTATATAGATACATATA
1 CTGTAGACAGACCCAGTGTAACTGTCGATACGACTAATTGTATAGACACATATA
1165144 CTGTAGACAGACCCAGTGTAACTGTCGATACGACTAATTGTATAGACACATATA
1 CTGTAGACAGACCCAGTGTAACTGTCGATACGACTAATTGTATAGACACATATA
* * *
1165198 CTGAAGACAGACCCAGTGTAACTGTCGTTACGACTACTTGTATAGACACATATA
1 CTGTAGACAGACCCAGTGTAACTGTCGATACGACTAATTGTATAGACACATATA
*
1165252 CTGTAGACAGACCCAGCGTAACTGTCGATACGACTAATTGTATAGACACATATA
1 CTGTAGACAGACCCAGTGTAACTGTCGATACGACTAATTGTATAGACACATATA
1165306 CTGTAGACAGACCCAGTGTAACTGTCGATACGACTAATTGTATAGACACATATA
1 CTGTAGACAGACCCAGTGTAACTGTCGATACGACTAATTGTATAGACACATATA
1165360 CTGTAGACAGACCC-GTTGTAACTGTCGAT
1 CTGTAGACAGACCCAG-TGTAACTGTCGAT
1165389 GTTGTGCATT
Statistics
Matches: 283, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
53 1 0.00
54 282 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.25
Consensus pattern (54 bp):
CTGTAGACAGACCCAGTGTAACTGTCGATACGACTAATTGTATAGACACATATA
Found at i:1173085 original size:18 final size:18
Alignment explanation
Indices: 1173064--1173150 Score: 102
Period size: 18 Copynumber: 4.8 Consensus size: 18
1173054 TCTTGTGTCC
*
1173064 TACTGTGTACATTTACGG
1 TACTGTGTACATGTACGG
1173082 TACTGTGTACATGTACGG
1 TACTGTGTACATGTACGG
*
1173100 TACTGTGTACATGTACGT
1 TACTGTGTACATGTACGG
* * * *
1173118 TACTATGAAAATGTACGT
1 TACTGTGTACATGTACGG
* *
1173136 TGCTATGTACATGTA
1 TACTGTGTACATGTA
1173151 TGCCACTGTG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (18 bp):
TACTGTGTACATGTACGG
Found at i:1173194 original size:18 final size:18
Alignment explanation
Indices: 1173171--1173205 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1173161 TATAGATCTT
*
1173171 ATGTACATTACTGTGTAA
1 ATGTACATCACTGTGTAA
*
1173189 ATGTACGTCACTGTGTA
1 ATGTACATCACTGTGTA
1173206 CGTTTACGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (18 bp):
ATGTACATCACTGTGTAA
Found at i:1173353 original size:17 final size:17
Alignment explanation
Indices: 1173304--1173457 Score: 119
Period size: 17 Copynumber: 8.9 Consensus size: 17
1173294 AAGGTCCACT
* *
1173304 GTACGTCACTGTGTACA
1 GTACGTTACTGTGTATA
* * * *
1173321 TGCACATTACCGTGTACA
1 -GTACGTTACTGTGTATA
*
1173339 GTACGTTACTTTGTATA
1 GTACGTTACTGTGTATA
** * *
1173356 GTACGCAATTGTGTACA
1 GTACGTTACTGTGTATA
* *
1173373 TGGACGTTAGTGTGTATA
1 -GTACGTTACTGTGTATA
1173391 GTACGTTACTGTGTATA
1 GTACGTTACTGTGTATA
1173408 GTACGTTACTGTGTATA
1 GTACGTTACTGTGTATA
** * *
1173425 GTACGCAATTGTGTACA
1 GTACGTTACTGTGTATA
*
1173442 TGTACGTTATTGTGTA
1 -GTACGTTACTGTGTA
1173458 CTGGCACTTT
Statistics
Matches: 107, Mismatches: 27, Indels: 4
0.78 0.20 0.03
Matches are distributed among these distances:
17 69 0.64
18 38 0.36
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (17 bp):
GTACGTTACTGTGTATA
Found at i:1173360 original size:52 final size:52
Alignment explanation
Indices: 1173304--1173422 Score: 150
Period size: 52 Copynumber: 2.3 Consensus size: 52
1173294 AAGGTCCACT
*
1173304 GTACGTCACTGTGTACATGCACATTACCGTGTACAGTACGTTACTTTGTATA
1 GTACGTCACTGTGTACATGCACATTACCGTGTACAGTACGTTACTGTGTATA
* * * ** *
1173356 GTACG-CAATTGTGTACATGGACGTTAGTGTGTATAGTACGTTACTGTGTATA
1 GTACGTC-ACTGTGTACATGCACATTACCGTGTACAGTACGTTACTGTGTATA
*
1173408 GTACGTTACTGTGTA
1 GTACGTCACTGTGTA
1173423 TAGTACGCAA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
51 1 0.02
52 55 0.98
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (52 bp):
GTACGTCACTGTGTACATGCACATTACCGTGTACAGTACGTTACTGTGTATA
Found at i:1173411 original size:69 final size:69
Alignment explanation
Indices: 1173327--1173457 Score: 217
Period size: 69 Copynumber: 1.9 Consensus size: 69
1173317 TACATGCACA
*
1173327 TTACCGTGTACAGTACGTTACTTTGTATAGTACGCAATTGTGTACATGGACGTTAGTGTGTATAG
1 TTACCGTGTACAGTACGTTACTGTGTATAGTACGCAATTGTGTACATGGACGTTAGTGTGTATAG
1173392 TACG
66 TACG
* * * *
1173396 TTACTGTGTATAGTACGTTACTGTGTATAGTACGCAATTGTGTACATGTACGTTATTGTGTA
1 TTACCGTGTACAGTACGTTACTGTGTATAGTACGCAATTGTGTACATGGACGTTAGTGTGTA
1173458 CTGGCACTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 57 1.00
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (69 bp):
TTACCGTGTACAGTACGTTACTGTGTATAGTACGCAATTGTGTACATGGACGTTAGTGTGTATAG
TACG
Found at i:1173447 original size:52 final size:52
Alignment explanation
Indices: 1173332--1173457 Score: 137
Period size: 52 Copynumber: 2.4 Consensus size: 52
1173322 GCACATTACC
* * **
1173332 GTGTACAGTACGTTACTTTGTATAGTACGCAATTGTGTACATGGACGTTAGT
1 GTGTACAGTACGTTACTGTGTATAGTACGCAACTGTGTACATGGACGCAAGT
* ** * * *
1173384 GTGTATAGTACGTTACTGTGTATAGTACGTTACTGTGTATA-GTACGCAATT
1 GTGTACAGTACGTTACTGTGTATAGTACGCAACTGTGTACATGGACGCAAGT
*
1173435 GTGTACATGTACGTTATTGTGTA
1 GTGTACA-GTACGTTACTGTGTA
1173458 CTGGCACTTT
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
51 12 0.20
52 49 0.80
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.39
Consensus pattern (52 bp):
GTGTACAGTACGTTACTGTGTATAGTACGCAACTGTGTACATGGACGCAAGT
Found at i:1173895 original size:32 final size:32
Alignment explanation
Indices: 1173852--1174035 Score: 277
Period size: 32 Copynumber: 5.9 Consensus size: 32
1173842 TCTTTGGCTA
1173852 GCGTTTCTGCTCCAGTATTATAGCTATCAATG
1 GCGTTTCTGCTCCAGTATTATAGCTATCAATG
*
1173884 GTGTTTCTGCTCCAGTATTATAGCTATCAATG
1 GCGTTTCTGCTCCAGTATTATAGCTATCAATG
*
1173916 GCGTTTCTGCTCCAGTATTATCGCTATCAATG
1 GCGTTTCTGCTCCAGTATTATAGCTATCAATG
1173948 GCGTTTCTGCTCCAGTATTATAGCTATCAATG
1 GCGTTTCTGCTCCAGTATTATAGCTATCAATG
** * *
1173980 GCGTTTCTGCTTTAGTATTATAGTTATCAGT-
1 GCGTTTCTGCTCCAGTATTATAGCTATCAATG
*
1174011 G-G-TT-TGCTCTAGTATTATAGCTATC
1 GCGTTTCTGCTCCAGTATTATAGCTATC
1174036 GGTGTTTTTG
Statistics
Matches: 142, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
28 19 0.13
29 2 0.01
30 1 0.01
31 1 0.01
32 119 0.84
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.41
Consensus pattern (32 bp):
GCGTTTCTGCTCCAGTATTATAGCTATCAATG
Found at i:1174111 original size:32 final size:32
Alignment explanation
Indices: 1174069--1174184 Score: 223
Period size: 32 Copynumber: 3.6 Consensus size: 32
1174059 AATTGCCATC
*
1174069 AGTGTCGTTGCTGCTCTAGTGTTAAAACTACT
1 AGTGTTGTTGCTGCTCTAGTGTTAAAACTACT
1174101 AGTGTTGTTGCTGCTCTAGTGTTAAAACTACT
1 AGTGTTGTTGCTGCTCTAGTGTTAAAACTACT
1174133 AGTGTTGTTGCTGCTCTAGTGTTAAAACTACT
1 AGTGTTGTTGCTGCTCTAGTGTTAAAACTACT
1174165 AGTGTTGTTGCTGCTCTAGT
1 AGTGTTGTTGCTGCTCTAGT
1174185 ATTACAGCCA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 83 1.00
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (32 bp):
AGTGTTGTTGCTGCTCTAGTGTTAAAACTACT
Found at i:1174121 original size:17 final size:17
Alignment explanation
Indices: 1174099--1174155 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
1174089 GTTAAAACTA
1174099 CTAGTGTTGTTGCTGCT
1 CTAGTGTTGTTGCTGCT
**** *
1174116 CTAGTGTTAAAACT--A
1 CTAGTGTTGTTGCTGCT
1174131 CTAGTGTTGTTGCTGCT
1 CTAGTGTTGTTGCTGCT
1174148 CTAGTGTT
1 CTAGTGTT
1174156 AAAACTACTA
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
15 10 0.36
17 18 0.64
ACGTcount: A:0.16, C:0.16, G:0.25, T:0.44
Consensus pattern (17 bp):
CTAGTGTTGTTGCTGCT
Found at i:1174201 original size:64 final size:64
Alignment explanation
Indices: 1174037--1174207 Score: 236
Period size: 64 Copynumber: 2.7 Consensus size: 64
1174027 ATAGCTATCG
* * * * *
1174037 GTGTTTTTGTTGCTCTAGTATGAATTGCCATCAGTGTCGTTGCTGCTCTAGTGTTAAAACTACTA
1 GTGTTGTTGCTGCTCTAGTATTAA-AGCCATCAGTGTTGTTGCTGCTCTAGTGTTAAAACTACTA
* * *
1174102 GTGTTGTTGCTGCTCTAGTGTTAAAACTA-CTAGTGTTGTTGCTGCTCTAGTGTTAAAACTACTA
1 GTGTTGTTGCTGCTCTAGTATTAAAGCCATC-AGTGTTGTTGCTGCTCTAGTGTTAAAACTACTA
*
1174166 GTGTTGTTGCTGCTCTAGTATTACAGCCATCAGTGTTGTTGC
1 GTGTTGTTGCTGCTCTAGTATTAAAGCCATCAGTGTTGTTGC
1174208 CGCGGCCTTT
Statistics
Matches: 92, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 1 0.01
64 70 0.76
65 21 0.23
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.41
Consensus pattern (64 bp):
GTGTTGTTGCTGCTCTAGTATTAAAGCCATCAGTGTTGTTGCTGCTCTAGTGTTAAAACTACTA
Found at i:1178184 original size:2 final size:2
Alignment explanation
Indices: 1178177--1178223 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1178167 ATGACCAACC
1178177 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1178219 CT CT C
1 CT CT C
1178224 ATCCACACAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1180122 original size:1 final size:1
Alignment explanation
Indices: 1180116--1180141 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1180106 GTTCTCAATA
1180116 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
1180142 ATTCATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1187992 original size:4 final size:4
Alignment explanation
Indices: 1187983--1188038 Score: 53
Period size: 4 Copynumber: 14.5 Consensus size: 4
1187973 ATATAAACTT
* * * *
1187983 TCTC TCTC TCTC -CTC CCTC TCTC TCTC TTTC TCTC -CTC CCTC TCTT
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
*
1188029 TCTT TCTC TC
1 TCTC TCTC TC
1188039 ATTTTATTCT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
3 6 0.14
4 38 0.86
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (4 bp):
TCTC
Found at i:1188015 original size:23 final size:22
Alignment explanation
Indices: 1187982--1188038 Score: 89
Period size: 23 Copynumber: 2.6 Consensus size: 22
1187972 AATATAAACT
*
1187982 TTCTCTCTCTCTCCTCCCTCTC
1 TTCTCTTTCTCTCCTCCCTCTC
1188004 TCTCTCTTTCTCTCCTCCCTCTC
1 T-TCTCTTTCTCTCCTCCCTCTC
1188027 TT-TCTTTCTCTC
1 TTCTCTTTCTCTC
1188039 ATTTTATTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 10 0.30
22 2 0.06
23 21 0.64
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (22 bp):
TTCTCTTTCTCTCCTCCCTCTC
Found at i:1189857 original size:2 final size:2
Alignment explanation
Indices: 1189850--1189917 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
1189840 CTTTCGGATG
1189850 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1189892 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
1189918 ACTTACTGGA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1202474 original size:11 final size:12
Alignment explanation
Indices: 1202444--1202476 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1202434 TGCATGCCAA
1202444 AAAAAAAACACC
1 AAAAAAAACACC
*
1202456 AAACAAAACA-C
1 AAAAAAAACACC
1202467 AAAAAAAACA
1 AAAAAAAACA
1202477 AATTTTGCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAACACC
Found at i:1211561 original size:15 final size:15
Alignment explanation
Indices: 1211541--1211570 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1211531 AGTGGGGCCT
*
1211541 CAGATATCCGGACGC
1 CAGATAACCGGACGC
1211556 CAGATAACCGGACGC
1 CAGATAACCGGACGC
1211571 TTCAGTTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.33, G:0.27, T:0.10
Consensus pattern (15 bp):
CAGATAACCGGACGC
Found at i:1212376 original size:65 final size:65
Alignment explanation
Indices: 1212194--1212362 Score: 320
Period size: 65 Copynumber: 2.6 Consensus size: 65
1212184 AGGCTCCACT
*
1212194 GTACATGTACATATAGCAAACCCTGGGGGTAGAGAACAAGGGTGGGTTATAGCTCTGTCACAATG
1 GTACATGTACATATAGCAAACCCTGGGGGTAGAGAACAAGGGTAGGTTATAGCTCTGTCACAATG
1212259 GTACATGTACATATAGCAAACCCTGGGGGTAGAGAACAAGGGTAGGTTATAGCTCTGTCACAATG
1 GTACATGTACATATAGCAAACCCTGGGGGTAGAGAACAAGGGTAGGTTATAGCTCTGTCACAATG
*
1212324 GTGCATGTACATATAGCAAACCCTGGGGGTAGAGAACAA
1 GTACATGTACATATAGCAAACCCTGGGGGTAGAGAACAA
1212363 AGCTGTTATA
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 102 1.00
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (65 bp):
GTACATGTACATATAGCAAACCCTGGGGGTAGAGAACAAGGGTAGGTTATAGCTCTGTCACAATG
Found at i:1216350 original size:17 final size:17
Alignment explanation
Indices: 1216325--1216359 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1216315 CAAATTGCTT
1216325 TCTAAAGGGAAGTAATC
1 TCTAAAGGGAAGTAATC
* *
1216342 TCTACAGGGATGTAATC
1 TCTAAAGGGAAGTAATC
1216359 T
1 T
1216360 ACTCCACTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (17 bp):
TCTAAAGGGAAGTAATC
Found at i:1216937 original size:16 final size:16
Alignment explanation
Indices: 1216916--1216948 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1216906 TCGTTATCAT
1216916 TGGGCAAATTTAAGAC
1 TGGGCAAATTTAAGAC
1216932 TGGGCAAATTTAAGAC
1 TGGGCAAATTTAAGAC
1216948 T
1 T
1216949 TGCCGAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (16 bp):
TGGGCAAATTTAAGAC
Found at i:1253669 original size:2 final size:2
Alignment explanation
Indices: 1253664--1253707 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1253654 TTCACTCATC
*
1253664 GA GA GA GA GA GA GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1253706 GA
1 GA
1253708 ATTATATTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1255947 original size:21 final size:21
Alignment explanation
Indices: 1255919--1256103 Score: 209
Period size: 21 Copynumber: 9.0 Consensus size: 21
1255909 TGTTGGGAAT
*
1255919 GTCAGTTGGCCAGTTATAAGC
1 GTCAGTTGACCAGTTATAAGC
*
1255940 GGCAGTTGA-CA---ATAAGC
1 GTCAGTTGACCAGTTATAAGC
* * *
1255957 GTCAGCTGACAAGATATAAGC
1 GTCAGTTGACCAGTTATAAGC
*
1255978 GTCAGCTGACCAGTTATAAGC
1 GTCAGTTGACCAGTTATAAGC
* * *
1255999 GTCAGTTCACCAATTATGAGC
1 GTCAGTTGACCAGTTATAAGC
1256020 GTCAGTTGACCAGTTATAAGC
1 GTCAGTTGACCAGTTATAAGC
* *
1256041 GTCAGTTCACCAGTTA-CAGC
1 GTCAGTTGACCAGTTATAAGC
*
1256061 GTCAGTTGACCATTTATAAGC
1 GTCAGTTGACCAGTTATAAGC
* *
1256082 GTCAATTGACCAATTATAAGC
1 GTCAGTTGACCAGTTATAAGC
1256103 G
1 G
1256104 AGATGGTAAT
Statistics
Matches: 138, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
17 13 0.09
18 1 0.01
20 19 0.14
21 105 0.76
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (21 bp):
GTCAGTTGACCAGTTATAAGC
Found at i:1255956 original size:17 final size:17
Alignment explanation
Indices: 1255934--1255968 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1255924 TTGGCCAGTT
*
1255934 ATAAGCGGCAGTTGACA
1 ATAAGCGGCAGCTGACA
*
1255951 ATAAGCGTCAGCTGACA
1 ATAAGCGGCAGCTGACA
1255968 A
1 A
1255969 GATATAAGCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (17 bp):
ATAAGCGGCAGCTGACA
Found at i:1257642 original size:25 final size:25
Alignment explanation
Indices: 1257610--1257751 Score: 187
Period size: 25 Copynumber: 5.7 Consensus size: 25
1257600 TCATGAGTTC
*
1257610 TCTCCACAATTCGTAGGTCCTTAGT
1 TCTCCACAATCCGTAGGTCCTTAGT
**
1257635 TCTCCACAGCCCGTAGGT-CTTCAGT
1 TCTCCACAATCCGTAGGTCCTT-AGT
*
1257660 TCTCCACAATCCGTCGGTCCTTAGT
1 TCTCCACAATCCGTAGGTCCTTAGT
* *
1257685 TCTCCACAACCCGTCGGTCCTTAGT
1 TCTCCACAATCCGTAGGTCCTTAGT
* *
1257710 TCTCCACAATCCATAGGTTCTTAGT
1 TCTCCACAATCCGTAGGTCCTTAGT
*
1257735 TCTCCACAATCCATAGG
1 TCTCCACAATCCGTAGG
1257752 ATTTTAGTTA
Statistics
Matches: 104, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
24 3 0.03
25 98 0.94
26 3 0.03
ACGTcount: A:0.20, C:0.34, G:0.15, T:0.31
Consensus pattern (25 bp):
TCTCCACAATCCGTAGGTCCTTAGT
Found at i:1257758 original size:25 final size:25
Alignment explanation
Indices: 1257610--1257770 Score: 164
Period size: 25 Copynumber: 6.4 Consensus size: 25
1257600 TCATGAGTTC
* *
1257610 TCTCCACAATTCGTAGGTCCTTAGT
1 TCTCCACAATCCGTAGGTCTTTAGT
** *
1257635 TCTCCACAGCCCGTAGGTCTTCAGT
1 TCTCCACAATCCGTAGGTCTTTAGT
* *
1257660 TCTCCACAATCCGTCGGTCCTTAGT
1 TCTCCACAATCCGTAGGTCTTTAGT
* * *
1257685 TCTCCACAACCCGTCGGTCCTTAGT
1 TCTCCACAATCCGTAGGTCTTTAGT
*
1257710 TCTCCACAATCCATAGGT-TCTTAGT
1 TCTCCACAATCCGTAGGTCT-TTAGT
*
1257735 TCTCCACAATCCATAGGAT-TTTAGT
1 TCTCCACAATCCGTAGG-TCTTTAGT
* *
1257760 TATCCAGAATC
1 TCTCCACAATC
1257771 GACCAGCCTT
Statistics
Matches: 117, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
25 115 0.98
26 2 0.02
ACGTcount: A:0.21, C:0.32, G:0.15, T:0.32
Consensus pattern (25 bp):
TCTCCACAATCCGTAGGTCTTTAGT
Found at i:1257759 original size:50 final size:50
Alignment explanation
Indices: 1257610--1257770 Score: 198
Period size: 50 Copynumber: 3.2 Consensus size: 50
1257600 TCATGAGTTC
* * *
1257610 TCTCCACAATTCGTAGGTCCTTAGTTCTCCACAGCCCGTAGGTCTTCAGT
1 TCTCCACAATCCGTAGGTCCTTAGTTCTCCACAACCCGTAGGTCTTTAGT
* * *
1257660 TCTCCACAATCCGTCGGTCCTTAGTTCTCCACAACCCGTCGGTCCTTAGT
1 TCTCCACAATCCGTAGGTCCTTAGTTCTCCACAACCCGTAGGTCTTTAGT
* * * *
1257710 TCTCCACAATCCATAGGTTCTTAGTTCTCCACAATCCATAGGAT-TTTAGT
1 TCTCCACAATCCGTAGGTCCTTAGTTCTCCACAACCCGTAGG-TCTTTAGT
* *
1257760 TATCCAGAATC
1 TCTCCACAATC
1257771 GACCAGCCTT
Statistics
Matches: 95, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
50 94 0.99
51 1 0.01
ACGTcount: A:0.21, C:0.32, G:0.15, T:0.32
Consensus pattern (50 bp):
TCTCCACAATCCGTAGGTCCTTAGTTCTCCACAACCCGTAGGTCTTTAGT
Found at i:1258470 original size:43 final size:43
Alignment explanation
Indices: 1258423--1258526 Score: 181
Period size: 43 Copynumber: 2.4 Consensus size: 43
1258413 ATTAAGAAGG
*
1258423 CTGGATGGTCAACAAACTAACCATCATATCTACCTTAAGGAGA
1 CTGGATGGTCAACAAACTAACCATCACATCTACCTTAAGGAGA
*
1258466 CTGGATAGTCAACAAACTAACCATCACATCTACCTTAAGGAGA
1 CTGGATGGTCAACAAACTAACCATCACATCTACCTTAAGGAGA
*
1258509 CTGGGTGGTCAACAAACT
1 CTGGATGGTCAACAAACT
1258527 TTTTTTTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (43 bp):
CTGGATGGTCAACAAACTAACCATCACATCTACCTTAAGGAGA
Found at i:1258547 original size:12 final size:12
Alignment explanation
Indices: 1258526--1258557 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1258516 GTCAACAAAC
1258526 TTTT-TTTTTTT
1 TTTTATTTTTTT
1258537 TTTTATTTTTTT
1 TTTTATTTTTTT
1258549 TTTTATTTT
1 TTTTATTTT
1258558 CAAATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.06, C:0.00, G:0.00, T:0.94
Consensus pattern (12 bp):
TTTTATTTTTTT
Found at i:1272267 original size:43 final size:43
Alignment explanation
Indices: 1272206--1272924 Score: 1117
Period size: 43 Copynumber: 16.7 Consensus size: 43
1272196 TTTGGAATCC
* *
1272206 GGTCAACAAACTTACCATCAGATTTACCTTAAGGAGACTGGAT
1 GGTCAACAAACTAACCATCAGATCTACCTTAAGGAGACTGGAT
* * *
1272249 GGTCAACAAACTAACCATCATATCTACCTTAAGAAGGCTGGAT
1 GGTCAACAAACTAACCATCAGATCTACCTTAAGGAGACTGGAT
1272292 GGTCAACAAACTAACCATCAGATCTACCTTAAGGAGACTGGAT
1 GGTCAACAAACTAACCATCAGATCTACCTTAAGGAGACTGGAT
1272335 GGTCAACAAACTAACCATCAGATCTACCTTAAGGAGACTGGAT
1 GGTCAACAAACTAACCATCAGATCTACCTTAAGGAGACTGGAT
* * *
1272378 GGTCAACAAACTAACAATAACATCTACCTTAAGGATG-CTGGAT
1 GGTCAACAAACTAACCATCAGATCTACCTTAAGGA-GACTGGAT
*
1272421 GGTCAACAAACTAACCATCACATCTACCTTAAGGAGACTGGAT
1 GGTCAACAAACTAACCATCAGATCTACCTTAAGGAGACTGGAT
* *
1272464 GGTCAACAAACTAACCATCACATCTACTTTAAGGATG-CTGGAT
1 GGTCAACAAACTAACCATCAGATCTACCTTAAGGA-GACTGGAT
*
1272507 GGTCAACAAACTAACCATCATATCTACCTTAAGGAGACTGGAT
1 GGTCAACAAACTAACCATCAGATCTACCTTAAGGAGACTGGAT
1272550 GGTCAACAAACTAACCATCAGATCTACCTTAAGGAGACTGGAT
1 GGTCAACAAACTAACCATCAGATCTACCTTAAGGAGACTGGAT
1272593 GGTCAACAAACTAACCATCAGATCTACCTTAAGGAGACTGGAT
1 GGTCAACAAACTAACCATCAGATCTACCTTAAGGAGACTGGAT
* *
1272636 GGTCAACAAACTAACCATCACATCTACATTAAGGATG-CTGGAT
1 GGTCAACAAACTAACCATCAGATCTACCTTAAGGA-GACTGGAT
*
1272679 GGTCAACAAACTAACCATCATATCTACCTTAAGGATG-CTGGAT
1 GGTCAACAAACTAACCATCAGATCTACCTTAAGGA-GACTGGAT
* * *
1272722 GGTCAACAAACTAACCATCAGATTTACCTTAGGGAGACTCGAT
1 GGTCAACAAACTAACCATCAGATCTACCTTAAGGAGACTGGAT
* **
1272765 GGTCAACAAACCT-ACCATCATATCTACCTTAAGGAGGTTGGAT
1 GGTCAACAAA-CTAACCATCAGATCTACCTTAAGGAGACTGGAT
* * *
1272808 GGTCAACAAACTAACCATCAGATTTGCCTTAGGGAGACTGGAT
1 GGTCAACAAACTAACCATCAGATCTACCTTAAGGAGACTGGAT
*
1272851 GGTCAACAAACTAACCATCAGATCTACCTTAAGGAGGCTGGAT
1 GGTCAACAAACTAACCATCAGATCTACCTTAAGGAGACTGGAT
*
1272894 GGTC-ACAAACTAAACATCAGATCTACCTTAA
1 GGTCAACAAACTAACCATCAGATCTACCTTAA
1272925 ATCTTCAGAA
Statistics
Matches: 626, Mismatches: 42, Indels: 17
0.91 0.06 0.02
Matches are distributed among these distances:
42 31 0.05
43 590 0.94
44 5 0.01
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (43 bp):
GGTCAACAAACTAACCATCAGATCTACCTTAAGGAGACTGGAT
Found at i:1273919 original size:12 final size:12
Alignment explanation
Indices: 1273902--1273926 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1273892 CCATTGTCAT
1273902 TTCAGACGTATA
1 TTCAGACGTATA
1273914 TTCAGACGTATA
1 TTCAGACGTATA
1273926 T
1 T
1273927 GTACATGTCT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TTCAGACGTATA
Found at i:1273998 original size:22 final size:21
Alignment explanation
Indices: 1273968--1274046 Score: 113
Period size: 22 Copynumber: 3.6 Consensus size: 21
1273958 GATCTGAAAC
1273968 CCCACAGGCCGACCAATGAGA
1 CCCACAGGCCGACCAATGAGA
1273989 CCTCACAGGCCGACCAATGAGA
1 CC-CACAGGCCGACCAATGAGA
* *
1274011 CCCCACAGGCTGACCAATGAAAA
1 -CCCACAGGCCGACCAATG-AGA
1274034 CCCACAGGCCGAC
1 CCCACAGGCCGAC
1274047 GAAGCTCTAG
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
21 2 0.04
22 46 0.88
23 4 0.08
ACGTcount: A:0.33, C:0.39, G:0.22, T:0.06
Consensus pattern (21 bp):
CCCACAGGCCGACCAATGAGA
Found at i:1275834 original size:15 final size:14
Alignment explanation
Indices: 1275796--1275834 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1275786 AAATCCCAGC
**
1275796 ATTTTGTTGTTTTT
1 ATTTTGTTGAATTT
1275810 ATTTTGTTGAATTT
1 ATTTTGTTGAATTT
1275824 ATTTATGTTGA
1 ATTT-TGTTGA
1275835 CATCTTGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.67
Consensus pattern (14 bp):
ATTTTGTTGAATTT
Found at i:1275964 original size:23 final size:23
Alignment explanation
Indices: 1275932--1276095 Score: 175
Period size: 23 Copynumber: 6.9 Consensus size: 23
1275922 AATAGCACAT
* * * *
1275932 CACATCGTTTAGCGGGTGGATAG
1 CACATCGTTTAACAGGTAGATAA
*
1275955 CTCATCGTTTAACAGGTAGATAA
1 CACATCGTTTAACAGGTAGATAA
* *
1275978 CACATCGTTTAACACGTAGATAG
1 CACATCGTTTAACAGGTAGATAA
1276001 CACATCGTTTAACAGGTAGATAA
1 CACATCGTTTAACAGGTAGATAA
1276024 CACATCGTTTAACAGGTAGATAA
1 CACATCGTTTAACAGGTAGATAA
* *
1276047 CATACCGTTTACGTTTAACAGGTAAATAA
1 C--A-C--AT-CGTTTAACAGGTAGATAA
* *
1276076 CGCACCGTTTAACAGGTAGA
1 CACATCGTTTAACAGGTAGA
1276096 CCTTGTTTAC
Statistics
Matches: 119, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
23 97 0.82
25 1 0.01
26 2 0.02
28 1 0.01
29 18 0.15
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (23 bp):
CACATCGTTTAACAGGTAGATAA
Found at i:1276075 original size:29 final size:29
Alignment explanation
Indices: 1276029--1276086 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1276019 GATAACACAT
* *
1276029 CGTTTAACAGGTAGATAACATACCGTTTA
1 CGTTTAACAGGTAAATAACACACCGTTTA
*
1276058 CGTTTAACAGGTAAATAACGCACCGTTTA
1 CGTTTAACAGGTAAATAACACACCGTTTA
1276087 ACAGGTAGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (29 bp):
CGTTTAACAGGTAAATAACACACCGTTTA
Found at i:1280483 original size:2 final size:2
Alignment explanation
Indices: 1280476--1280507 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1280466 TTATCTGATT
1280476 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1280508 ATTTTACAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1282520 original size:90 final size:90
Alignment explanation
Indices: 1282367--1282533 Score: 316
Period size: 90 Copynumber: 1.9 Consensus size: 90
1282357 AATTTTGTTT
*
1282367 TATTTTCTGTTGGTTTTATCTCATGCTCTTATATAATATAATCATTGACACACAATGACGCATTT
1 TATTTTCTGTTGGTTTTATCTCATGCGCTTATATAATATAATCATTGACACACAATGACGCATTT
1282432 AATGCAAAAATAATGAAAAAAAAAA
66 AATGCAAAAATAATGAAAAAAAAAA
*
1282457 TATTTTCTGTTGGTTTTATCTCATGCGCTTATATAATATAATCATTGACACATAATGACGCATTT
1 TATTTTCTGTTGGTTTTATCTCATGCGCTTATATAATATAATCATTGACACACAATGACGCATTT
1282522 AATGCAAAAATA
66 AATGCAAAAATA
1282534 TTAAAAATAC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 75 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTTTCTGTTGGTTTTATCTCATGCGCTTATATAATATAATCATTGACACACAATGACGCATTT
AATGCAAAAATAATGAAAAAAAAAA
Found at i:1287322 original size:21 final size:21
Alignment explanation
Indices: 1287298--1287353 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
1287288 CAGCCTCTTT
1287298 TGCAAAACCAACAAACACCGA
1 TGCAAAACCAACAAACACCGA
* * * *
1287319 TGCAAAACAAACGATCACTGA
1 TGCAAAACCAACAAACACCGA
*
1287340 TGCAAACCCAACAA
1 TGCAAAACCAACAA
1287354 GCATGCACTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.50, C:0.30, G:0.11, T:0.09
Consensus pattern (21 bp):
TGCAAAACCAACAAACACCGA
Found at i:1289271 original size:23 final size:23
Alignment explanation
Indices: 1289234--1289300 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
1289224 ACAATACATT
1289234 ACACACC-TTTAAACAGGTAGATA
1 ACACACCATTT-AACAGGTAGATA
* * *
1289257 GCACATCATTTAACAGGTAAATA
1 ACACACCATTTAACAGGTAGATA
1289280 ACACACCATTTAACAGGTAGA
1 ACACACCATTTAACAGGTAGA
1289301 CCTTGTTTAC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
23 34 0.92
24 3 0.08
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.22
Consensus pattern (23 bp):
ACACACCATTTAACAGGTAGATA
Found at i:1291608 original size:18 final size:17
Alignment explanation
Indices: 1291573--1291606 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1291563 TCGTCCCCCC
1291573 CCCCAAAAAAAACCAAA
1 CCCCAAAAAAAACCAAA
* *
1291590 CCCCACAAAAAGCCAAA
1 CCCCAAAAAAAACCAAA
1291607 ACTAGATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.38, G:0.03, T:0.00
Consensus pattern (17 bp):
CCCCAAAAAAAACCAAA
Found at i:1294765 original size:40 final size:39
Alignment explanation
Indices: 1294720--1294800 Score: 144
Period size: 40 Copynumber: 2.1 Consensus size: 39
1294710 AGATATTTTA
1294720 ATGTAAATCAATGAAAAGTGGTACACCATAAAAAATTAT
1 ATGTAAATCAATGAAAAGTGGTACACCATAAAAAATTAT
*
1294759 NATGTAAATTAATGAAAAGTGGTACACCATAAAAAATTAT
1 -ATGTAAATCAATGAAAAGTGGTACACCATAAAAAATTAT
1294799 AT
1 AT
1294801 AGGATGAGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 2 0.05
40 38 0.95
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.27
Consensus pattern (39 bp):
ATGTAAATCAATGAAAAGTGGTACACCATAAAAAATTAT
Found at i:1299284 original size:29 final size:29
Alignment explanation
Indices: 1299242--1299316 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
1299232 AATGTATGGA
* *
1299242 AGTTACATAATACATCTGGAAGTTTTCTG
1 AGTTACGTAATACATCTGGAAGTTTACTG
1299271 AGTTACGTAATACATCTGGAAGTTTACTG
1 AGTTACGTAATACATCTGGAAGTTTACTG
*
1299300 AGTTAGGTAATACATCT
1 AGTTACGTAATACATCT
1299317 AAAGAAATGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (29 bp):
AGTTACGTAATACATCTGGAAGTTTACTG
Found at i:1300696 original size:27 final size:27
Alignment explanation
Indices: 1300658--1300711 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1300648 AACTACATGA
1300658 ACAGACAAGCCTTATTTGCATGTTTTT
1 ACAGACAAGCCTTATTTGCATGTTTTT
1300685 ACAGACAAGCCTTATTTGCATGTTTTT
1 ACAGACAAGCCTTATTTGCATGTTTTT
1300712 GCAATATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (27 bp):
ACAGACAAGCCTTATTTGCATGTTTTT
Found at i:1301022 original size:24 final size:23
Alignment explanation
Indices: 1300995--1301039 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1300985 CTACAGCTTT
* *
1300995 TTGTTTCTTCTTTCTTTTTCCTGC
1 TTGTTTCCT-TTTCCTTTTCCTGC
1301019 TTGTTTCCTTTTCCTTTTCCT
1 TTGTTTCCTTTTCCTTTTCCT
1301040 AGTGTCTCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.00, C:0.27, G:0.07, T:0.67
Consensus pattern (23 bp):
TTGTTTCCTTTTCCTTTTCCTGC
Found at i:1333240 original size:2 final size:2
Alignment explanation
Indices: 1333233--1333288 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1333223 TGCAGTTATA
1333233 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1333275 CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT
1333289 TACCGAGCTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1334248 original size:11 final size:11
Alignment explanation
Indices: 1334234--1334259 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1334224 TCTTATATTC
1334234 TTTTATTTATG
1 TTTTATTTATG
1334245 TTTTATTTATG
1 TTTTATTTATG
1334256 TTTT
1 TTTT
1334260 CTCTACTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (11 bp):
TTTTATTTATG
Found at i:1349949 original size:27 final size:27
Alignment explanation
Indices: 1349915--1349995 Score: 135
Period size: 27 Copynumber: 3.0 Consensus size: 27
1349905 TATAACAATA
*
1349915 TGGCCCGCCATACAATAATATGTATAT
1 TGGCCCGCCCTACAATAATATGTATAT
*
1349942 TGGCCCGCCCTACAATAATATGCATAT
1 TGGCCCGCCCTACAATAATATGTATAT
*
1349969 TGGCCCTCCCTACAATAATATGTATAT
1 TGGCCCGCCCTACAATAATATGTATAT
1349996 CGGAATTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.30
Consensus pattern (27 bp):
TGGCCCGCCCTACAATAATATGTATAT
Found at i:1350492 original size:2 final size:2
Alignment explanation
Indices: 1350485--1350529 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1350475 GCATATTGCA
1350485 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1350527 TC T
1 TC T
1350530 TACCGAGCTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1350755 original size:21 final size:21
Alignment explanation
Indices: 1350729--1350770 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1350719 AACGGCAAGG
1350729 GACTGCCAACTAGGCCACTCA
1 GACTGCCAACTAGGCCACTCA
*
1350750 GACTGCTAACTAGGCCACTCA
1 GACTGCCAACTAGGCCACTCA
1350771 ATAGTGTCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.36, G:0.19, T:0.17
Consensus pattern (21 bp):
GACTGCCAACTAGGCCACTCA
Found at i:1352756 original size:2 final size:2
Alignment explanation
Indices: 1352749--1352793 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
1352739 TGGACAAGGA
*
1352749 TG TG TG TG TG AG TG TG TG TG TG TG TG TG TG -G TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1352790 TG TG
1 TG TG
1352794 GGGGGGGGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.02, C:0.00, G:0.51, T:0.47
Consensus pattern (2 bp):
TG
Found at i:1355061 original size:37 final size:37
Alignment explanation
Indices: 1355012--1355209 Score: 222
Period size: 37 Copynumber: 5.4 Consensus size: 37
1355002 CCTAGTCTCA
* *
1355012 GTGTGTAATGTACACGTAACATACAGCTATTGTCACT
1 GTGTGTGATGTACATGTAACATACAGCTATTGTCACT
* * *
1355049 GTGCGTGATGTACAGGTAACATACAGGTA--GTCACT
1 GTGTGTGATGTACATGTAACATACAGCTATTGTCACT
* *
1355084 GTGTGTAATGTACATGTAACATAAAGGCTATTGTCACT
1 GTGTGTGATGTACATGTAACATACA-GCTATTGTCACT
* *
1355122 GTGTGTCATGTACATGT-ACATACAGCTTTTGTCACT
1 GTGTGTGATGTACATGTAACATACAGCTATTGTCACT
* * * ** *
1355158 GAGAGTGATTTACATGTAACATACAGCTATCATCAGT
1 GTGTGTGATGTACATGTAACATACAGCTATTGTCACT
*
1355195 GTGTGTAATGTACAT
1 GTGTGTGATGTACAT
1355210 ATTGTCACTG
Statistics
Matches: 133, Mismatches: 24, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
35 27 0.20
36 27 0.20
37 57 0.43
38 22 0.17
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (37 bp):
GTGTGTGATGTACATGTAACATACAGCTATTGTCACT
Found at i:1355095 original size:35 final size:35
Alignment explanation
Indices: 1354996--1355800 Score: 820
Period size: 35 Copynumber: 22.8 Consensus size: 35
1354986 TATTGTGTTC
* * * *
1354996 CATACACCTAGTCTCAGTGTGTAATGTACACGTAA
1 CATACAGCTAGTCACTGTGTGTAATGTACATGTAA
* * *
1355031 CATACAGCTATTGTCACTGTGCGTGATGTACAGGTAA
1 CATACAGCTA--GTCACTGTGTGTAATGTACATGTAA
*
1355068 CATACAGGTAGTCACTGTGTGTAATGTACATGTAA
1 CATACAGCTAGTCACTGTGTGTAATGTACATGTAA
* *
1355103 CATAAAGGCTATTGTCACTGTGTGTCATGTACATGT-A
1 CATACA-GCTA--GTCACTGTGTGTAATGTACATGTAA
* * * * *
1355140 CATACAGCTTTTGTCACTGAGAGTGATTTACATGTAA
1 CATACAGC--TAGTCACTGTGTGTAATGTACATGTAA
*
1355177 CATACAGCTA-TCATCAGTGTG---TGTA-ATGT-A
1 CATACAGCTAGTCA-CTGTGTGTAATGTACATGTAA
*
1355207 CAT--A--TTGTCACTGTGTAATGTACATGT--A----A
1 CATACAGCTAGTCACTGTG---TGTA-ATGTACATGTAA
* *
1355236 CATACAGGTAGTCACTGTGTGTGATGTACATGTAA
1 CATACAGCTAGTCACTGTGTGTAATGTACATGTAA
*
1355271 CATACAGCTAGTCTCTGTGTGTAATGTACATGTAA
1 CATACAGCTAGTCACTGTGTGTAATGTACATGTAA
*
1355306 CATACAGCTAGTCTCTGTGTGTAATGTACATGTAA
1 CATACAGCTAGTCACTGTGTGTAATGTACATGTAA
*
1355341 CATACAGCTAGTTACTGTGTGTAATGTACATGTAA
1 CATACAGCTAGTCACTGTGTGTAATGTACATGTAA
* * * *
1355376 CAAACATCTCTTGTTACTGTCTGTGATATACATGTACATGTAA
1 CATACA--GCTAGTCACTG--TGTG---TA-ATGTACATGTAA
* * *
1355419 CATACAGCTTTTGTCACTGTGTGTGATTTACATGTAA
1 CATACAGC--TAGTCACTGTGTGTAATGTACATGTAA
* * * *
1355456 CATACAGCTATTATCACTGTGCGTGATATACATGTAA
1 CATACAGCTA--GTCACTGTGTGTAATGTACATGTAA
*
1355493 CATACAGCTAGTCTCTGTGTGTAATGTACATGTAA
1 CATACAGCTAGTCACTGTGTGTAATGTACATGTAA
*
1355528 CATAAAGGCTATTGTCAC--TGTGTAATGTACATGTAA
1 CATACA-GCTA--GTCACTGTGTGTAATGTACATGTAA
* *
1355564 CATACAGCTAGTCTCTGTATGTAATGTACATGTAA
1 CATACAGCTAGTCACTGTGTGTAATGTACATGTAA
*
1355599 CATACAGCTAGTCTCTGTGTGTAATGTACATGTAA
1 CATACAGCTAGTCACTGTGTGTAATGTACATGTAA
* *
1355634 CATACAGCTAGTCTCTGTGTGTGATGTACATGTAA
1 CATACAGCTAGTCACTGTGTGTAATGTACATGTAA
*
1355669 CATACAGCTAGTCACTGTGTGTGATGTACATGTAA
1 CATACAGCTAGTCACTGTGTGTAATGTACATGTAA
*
1355704 CATACAGCTAGTCTCTGTGTGTAATGTACATGTAA
1 CATACAGCTAGTCACTGTGTGTAATGTACATGTAA
*
1355739 CATACAGCTAGTCTCTGTGTGTAATGTACATGTAA
1 CATACAGCTAGTCACTGTGTGTAATGTACATGTAA
* * *
1355774 CATACAGCTAGTCTCAGTGAGTAATGT
1 CATACAGCTAGTCACTGTGTGTAATGT
1355801 TCATCTTTTG
Statistics
Matches: 664, Mismatches: 62, Indels: 88
0.82 0.08 0.11
Matches are distributed among these distances:
26 5 0.01
27 3 0.00
28 1 0.00
29 10 0.02
30 7 0.01
31 6 0.01
32 4 0.01
33 17 0.03
34 3 0.00
35 389 0.59
36 51 0.08
37 104 0.16
38 28 0.04
39 4 0.01
41 5 0.01
42 2 0.00
43 25 0.04
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (35 bp):
CATACAGCTAGTCACTGTGTGTAATGTACATGTAA
Found at i:1355415 original size:43 final size:43
Alignment explanation
Indices: 1355364--1355454 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 43
1355354 ACTGTGTGTA
* *
1355364 ATGTACATGTAACAAACATCTCTTGTTACTGTCTGTGATATAC
1 ATGTACATGTAACAAACAGCTCTTGTCACTGTCTGTGATATAC
* * * *
1355407 ATGTACATGTAACATACAGCTTTTGTCACTGTGTGTGATTTAC
1 ATGTACATGTAACAAACAGCTCTTGTCACTGTCTGTGATATAC
1355450 ATGTA
1 ATGTA
1355455 ACATACAGCT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (43 bp):
ATGTACATGTAACAAACAGCTCTTGTCACTGTCTGTGATATAC
Found at i:1357538 original size:38 final size:38
Alignment explanation
Indices: 1357464--1357538 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
1357454 AAACTCAGTA
* **
1357464 AATCCACAGTCACTTGATAATAACTTACCACTTCACTC
1 AATCCACAGTCACTTGATAATAACTTACAAAATCACTC
1357502 AATCCACAGTCACTT-ATAAATAA-TCTACAAAATCACT
1 AATCCACAGTCACTTGAT-AATAACT-TACAAAATCACT
1357539 TAATTCTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 3 0.09
38 29 0.91
ACGTcount: A:0.40, C:0.28, G:0.04, T:0.28
Consensus pattern (38 bp):
AATCCACAGTCACTTGATAATAACTTACAAAATCACTC
Found at i:1357599 original size:19 final size:19
Alignment explanation
Indices: 1357566--1357621 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
1357556 CTTAATCTAC
* *
1357566 TGCCTCACTTCATCCTCAT
1 TGCCTCAATTAATCCTCAT
*
1357585 TGCCT-ATATTAATCCTCGT
1 TGCCTCA-ATTAATCCTCAT
*
1357604 TGCCTCACTTAATCCTCA
1 TGCCTCAATTAATCCTCA
1357622 ACACCTCACT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 1 0.03
19 28 0.93
20 1 0.03
ACGTcount: A:0.20, C:0.36, G:0.07, T:0.38
Consensus pattern (19 bp):
TGCCTCAATTAATCCTCAT
Found at i:1362084 original size:24 final size:24
Alignment explanation
Indices: 1362052--1362098 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1362042 CATAACATTT
1362052 CTGACATCAGCTACTAAAGCCACA
1 CTGACATCAGCTACTAAAGCCACA
*
1362076 CTGACATCAGCTACTAGAGCCAC
1 CTGACATCAGCTACTAAAGCCAC
1362099 CCCAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.34, G:0.15, T:0.17
Consensus pattern (24 bp):
CTGACATCAGCTACTAAAGCCACA
Found at i:1363711 original size:28 final size:28
Alignment explanation
Indices: 1363680--1363796 Score: 101
Period size: 28 Copynumber: 4.2 Consensus size: 28
1363670 AAAAATTCTT
* ** *
1363680 GACCCCTTGTGAATTCAAAATAATTTAG
1 GACCCCTTATGAACACAAAATAATTCAG
*
1363708 GACCTCTTATGAACACAAAATAATTCAG
1 GACCCCTTATGAACACAAAATAATTCAG
* **
1363736 GACCCCTTATGAACTCATTATAATTC-G
1 GACCCCTTATGAACACAAAATAATTCAG
* * * * *
1363763 TGACCTCTAATGAACTCCAAATAATTCAT
1 -GACCCCTTATGAACACAAAATAATTCAG
1363792 GACCC
1 GACCC
1363797 TCTTGAACTA
Statistics
Matches: 71, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
27 1 0.01
28 70 0.99
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (28 bp):
GACCCCTTATGAACACAAAATAATTCAG
Found at i:1363740 original size:56 final size:56
Alignment explanation
Indices: 1363680--1363801 Score: 138
Period size: 56 Copynumber: 2.2 Consensus size: 56
1363670 AAAAATTCTT
* *
1363680 GACCCCTTGTGAATTCAAAATAATTTAG-GACCTCTTATGAACACAAAATAATTCAG
1 GACCCCTTGTGAACTCAAAATAA-TTAGTGACCTCTAATGAACACAAAATAATTCAG
* ** * * * *
1363736 GACCCCTTATGAACTCATTATAATTCGTGACCTCTAATGAACTCCAAATAATTCAT
1 GACCCCTTGTGAACTCAAAATAATTAGTGACCTCTAATGAACACAAAATAATTCAG
1363792 GACCCTCTTG
1 GACCC-CTTG
1363802 AACTAAAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
55 3 0.06
56 48 0.89
57 3 0.06
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.30
Consensus pattern (56 bp):
GACCCCTTGTGAACTCAAAATAATTAGTGACCTCTAATGAACACAAAATAATTCAG
Found at i:1365167 original size:30 final size:30
Alignment explanation
Indices: 1364963--1365353 Score: 223
Period size: 30 Copynumber: 13.0 Consensus size: 30
1364953 AACCTCAAGT
* * * * *
1364963 ATAACCTCACCTGTGAGGTCAAACTCAGGT
1 ATAATCTCACCTGTGAGGTGACACTCATGC
* * *
1364993 ATAATCTCACCTTTGAGGTCACACTCATGT
1 ATAATCTCACCTGTGAGGTGACACTCATGC
* * * * * * *
1365023 ATTATCTCCCCTCTGAGATGA-ATCTGAAGT
1 ATAATCTCACCTGTGAGGTGACA-CTCATGC
* * *
1365053 ATTATCTCACCTGTGAGGTGACATTCATTTC
1 ATAATCTCACCTGTGAGGTGACACTCA-TGC
** *
1365084 -TAATCTCACCT-ACA-GT-ACACTCATGT
1 ATAATCTCACCTGTGAGGTGACACTCATGC
* * *
1365110 AAAATCTCATCTTGTGATGTGGA-ACTCATG-
1 ATAATCTCA-CCTGTGAGGT-GACACTCATGC
*
1365140 AGTAACCTCACCTGTGAGGTGACACTCATGC
1 A-TAATCTCACCTGTGAGGTGACACTCATGC
* * *
1365171 ATTATCTAACCTGTGAGGTGACACAT-ATTGT
1 ATAATCTCACCTGTGAGGTGACAC-TCA-TGC
* *
1365202 AAAATATCATCCTGTGAGGTAGA-ACTCATG-
1 ATAATCTCA-CCTGTGAGGT-GACACTCATGC
*
1365232 AGTAATCTCACCTGTGAGGTGACACTCACGC
1 A-TAATCTCACCTGTGAGGTGACACTCATGC
* * *
1365263 ATTATCTAACCTGTGAGGTGACACAT-ATTGT
1 ATAATCTCACCTGTGAGGTGACAC-TCA-TGC
* * *
1365294 AAAATATCATCCTGTGAGGTAGA-ACACATG-
1 ATAATCTCA-CCTGTGAGGT-GACACTCATGC
1365324 AGTAATCTCACCTGTGAGGTGACACTCATG
1 A-TAATCTCACCTGTGAGGTGACACTCATG
1365354 TATTATTTCA
Statistics
Matches: 278, Mismatches: 56, Indels: 54
0.72 0.14 0.14
Matches are distributed among these distances:
26 1 0.00
27 13 0.05
28 4 0.01
29 9 0.03
30 172 0.62
31 48 0.17
32 27 0.10
33 4 0.01
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.30
Consensus pattern (30 bp):
ATAATCTCACCTGTGAGGTGACACTCATGC
Found at i:1365218 original size:92 final size:92
Alignment explanation
Indices: 1365107--1365359 Score: 434
Period size: 92 Copynumber: 2.8 Consensus size: 92
1365097 AGTACACTCA
* * * * *
1365107 TGTAAAATCTCATCTTGTGATGTGGAACTCATGAGTAACCTCACCTGTGAGGTGACACTCATGCA
1 TGTAAAATATCATCCTGTGAGGTAGAACTCATGAGTAATCTCACCTGTGAGGTGACACTCATGCA
1365172 TTATCTAACCTGTGAGGTGACACATAT
66 TTATCTAACCTGTGAGGTGACACATAT
*
1365199 TGTAAAATATCATCCTGTGAGGTAGAACTCATGAGTAATCTCACCTGTGAGGTGACACTCACGCA
1 TGTAAAATATCATCCTGTGAGGTAGAACTCATGAGTAATCTCACCTGTGAGGTGACACTCATGCA
1365264 TTATCTAACCTGTGAGGTGACACATAT
66 TTATCTAACCTGTGAGGTGACACATAT
* *
1365291 TGTAAAATATCATCCTGTGAGGTAGAACACATGAGTAATCTCACCTGTGAGGTGACACTCATGTA
1 TGTAAAATATCATCCTGTGAGGTAGAACTCATGAGTAATCTCACCTGTGAGGTGACACTCATGCA
1365356 TTAT
66 TTAT
1365360 TTCACATGTA
Statistics
Matches: 152, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 152 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (92 bp):
TGTAAAATATCATCCTGTGAGGTAGAACTCATGAGTAATCTCACCTGTGAGGTGACACTCATGCA
TTATCTAACCTGTGAGGTGACACATAT
Found at i:1365389 original size:25 final size:26
Alignment explanation
Indices: 1365350--1365404 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
1365340 AGGTGACACT
** *
1365350 CATGTATTATTTCACATGTATAA-GA
1 CATGTATTAACTCACATGTAAAATGA
*
1365375 CATGTATTAACTCACCTGTAAAATGA
1 CATGTATTAACTCACATGTAAAATGA
1365401 CATG
1 CATG
1365405 ACTGTATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (26 bp):
CATGTATTAACTCACATGTAAAATGA
Found at i:1365432 original size:30 final size:29
Alignment explanation
Indices: 1365146--1365432 Score: 103
Period size: 30 Copynumber: 9.6 Consensus size: 29
1365136 CATGAGTAAC
* *
1365146 CTCACCTGTGAGGTGACACTCATGCATTAT
1 CTCACCTGTGAGGTGACA-TGATGTATTAT
* **
1365176 CTAACCTGTGAGGTGACACAT-ATTGTAAAAT
1 CTCACCTGTGAGGTG--ACATGA-TGTATTAT
*
1365207 ATCATCCTGTGAGGTAGAACTCATGA-GTA--AT
1 CTCA-CCTGTGAGGT-G-A--CATGATGTATTAT
* * *
1365238 CTCACCTGTGAGGTGACACTCACGCATTAT
1 CTCACCTGTGAGGTGACA-TGATGTATTAT
* **
1365268 CTAACCTGTGAGGTGACACAT-ATTGTAAAAT
1 CTCACCTGTGAGGTG--ACATGA-TGTATTAT
*
1365299 ATCATCCTGTGAGGTAGAACACATGA-GTA--AT
1 CTCA-CCTGTGAGGT-G---ACATGATGTATTAT
*
1365330 CTCACCTGTGAGGTGACACTCATGTATTAT
1 CTCACCTGTGAGGTGACA-TGATGTATTAT
* * * * * *
1365360 TTCACATGT-A--TAAGA-CATGTATTAA
1 CTCACCTGTGAGGTGACATGATGTATTAT
* **
1365385 CTCACCTGTAAAATGACATGACTGTATTAT
1 CTCACCTGTGAGGTGACATGA-TGTATTAT
1365415 CTCACCTGTGAGGTGACA
1 CTCACCTGTGAGGTGACA
1365433 CTCATGCTTC
Statistics
Matches: 196, Mismatches: 33, Indels: 56
0.69 0.12 0.20
Matches are distributed among these distances:
25 16 0.08
26 6 0.03
27 7 0.04
28 9 0.05
29 4 0.02
30 83 0.42
31 25 0.13
32 27 0.14
33 8 0.04
34 9 0.05
35 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (29 bp):
CTCACCTGTGAGGTGACATGATGTATTAT
Found at i:1368017 original size:17 final size:16
Alignment explanation
Indices: 1367990--1368024 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
1367980 ACGTCACAAT
1367990 GTACTGGCGAGAACTG
1 GTACTGGCGAGAACTG
1368006 GTACTCGGCGAGAACTG
1 GTACT-GGCGAGAACTG
1368023 GT
1 GT
1368025 CGCACGCCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.20
Consensus pattern (16 bp):
GTACTGGCGAGAACTG
Found at i:1369291 original size:45 final size:42
Alignment explanation
Indices: 1369208--1369342 Score: 166
Period size: 42 Copynumber: 3.1 Consensus size: 42
1369198 ATTATTTCTA
*
1369208 TCGACACGCAAC-TTATTTATGTTGACAAGCTAGATAAATATG
1 TCGACACGCAACATT-TTTATGTTGACATGCTAGATAAATATG
*
1369250 TC-ACACGCAACATTTTTATGTTAATTGACATGCTAGATAAATATA
1 TCGACACGCAACATTTTTATG----TTGACATGCTAGATAAATATG
* *
1369295 TCGACACGCAACTTTTTTATGTTGACATGCTAGACAAATATG
1 TCGACACGCAACATTTTTATGTTGACATGCTAGATAAATATG
*
1369337 TTGACA
1 TCGACA
1369343 TATCCATGCA
Statistics
Matches: 81, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
41 15 0.19
42 28 0.35
45 21 0.26
46 17 0.21
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (42 bp):
TCGACACGCAACATTTTTATGTTGACATGCTAGATAAATATG
Found at i:1369567 original size:20 final size:21
Alignment explanation
Indices: 1369542--1369588 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1369532 AGGTCTGTCA
*
1369542 ACATGCAACTTGT-TATCTTG
1 ACATGCAACTTATCTATCTTG
* *
1369562 ACATGCATCTTATCTATGTTG
1 ACATGCAACTTATCTATCTTG
1369583 ACATGC
1 ACATGC
1369589 GAGATAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (21 bp):
ACATGCAACTTATCTATCTTG
Found at i:1369688 original size:21 final size:20
Alignment explanation
Indices: 1369657--1369816 Score: 88
Period size: 21 Copynumber: 7.7 Consensus size: 20
1369647 TTTAACATAA
1369657 ATAATTAAGTTGCATGTTAAC
1 ATAA-TAAGTTGCATGTTAAC
* *
1369678 ATAGATAAGTTACATGTTAGC
1 ATA-ATAAGTTGCATGTTAAC
** *
1369699 AT-ATTTGTCTCGCATTTTAAC
1 ATAATAAGT-T-GCATGTTAAC
* * * *
1369720 ATAAATACGATGCATATCAAC
1 AT-AATAAGTTGCATGTTAAC
* *
1369741 ATAATAAATTGCATGTTGAC
1 ATAATAAGTTGCATGTTAAC
* *
1369761 ATAAATAAGTTACATGTTACC
1 AT-AATAAGTTGCATGTTAAC
* * *
1369782 ATAACTTAGTTGAATGTTGAC
1 ATAA-TAAGTTGCATGTTAAC
*
1369803 ATAAATAACTTGCA
1 AT-AATAAGTTGCA
1369817 CGCCAACATA
Statistics
Matches: 101, Mismatches: 30, Indels: 16
0.69 0.20 0.11
Matches are distributed among these distances:
19 4 0.04
20 17 0.17
21 73 0.72
22 4 0.04
23 3 0.03
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (20 bp):
ATAATAAGTTGCATGTTAAC
Found at i:1369915 original size:21 final size:21
Alignment explanation
Indices: 1369877--1369920 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1369867 CCAACTTATT
* *
1369877 TATCTCGCATGTTAACATTAA
1 TATCTCGCATGTCAACATAAA
* *
1369898 TATCTTGCATGTCGACATAAA
1 TATCTCGCATGTCAACATAAA
1369919 TA
1 TA
1369921 AGTAACTTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (21 bp):
TATCTCGCATGTCAACATAAA
Found at i:1370069 original size:42 final size:42
Alignment explanation
Indices: 1370012--1370091 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
1370002 ATTGCAATTT
* *
1370012 TCTTGCATGTCAACATAATTATGTTGCATGTTGACATAACTC
1 TCTTCCATGTCAACATAATTATCTTGCATGTTGACATAACTC
* *
1370054 TCTTCCATGTGAACATATTTATCTTGCATGTTGACATA
1 TCTTCCATGTCAACATAATTATCTTGCATGTTGACATA
1370092 TTTGATAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (42 bp):
TCTTCCATGTCAACATAATTATCTTGCATGTTGACATAACTC
Found at i:1370090 original size:21 final size:21
Alignment explanation
Indices: 1370008--1370094 Score: 79
Period size: 21 Copynumber: 4.2 Consensus size: 21
1369998 GTTGATTGCA
**
1370008 ATTT-TCTTGCATGTCAACAT
1 ATTTATCTTGCATGTTGACAT
* *
1370028 AATTATGTTGCATGTTGACAT
1 ATTTATCTTGCATGTTGACAT
** * *
1370049 AACTCTCTTCCATG-TGAACAT
1 ATTTATCTTGCATGTTG-ACAT
1370070 ATTTATCTTGCATGTTGACAT
1 ATTTATCTTGCATGTTGACAT
1370091 ATTT
1 ATTT
1370095 GATAGAAAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
20 5 0.10
21 45 0.87
22 2 0.04
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (21 bp):
ATTTATCTTGCATGTTGACAT
Found at i:1370960 original size:21 final size:21
Alignment explanation
Indices: 1370934--1371810 Score: 919
Period size: 21 Copynumber: 42.1 Consensus size: 21
1370924 GCTACTGACC
*
1370934 GCCGACAGTTAGCGAGGTCGT
1 GCCGACAGTTAGCTAGGTCGT
1370955 GCCGACAGTTAGCTAGGTCGT
1 GCCGACAGTTAGCTAGGTCGT
* *
1370976 GCCGACAGTTAGGTAGGCCGT
1 GCCGACAGTTAGCTAGGTCGT
* * * * * *
1370997 GCTGACTGTCAACTAGATCAT
1 GCCGACAGTTAGCTAGGTCGT
* *
1371018 GCCGACAGTTAGCTAGATCAT
1 GCCGACAGTTAGCTAGGTCGT
* *
1371039 GCCGACAGTTAGCTAGATCAT
1 GCCGACAGTTAGCTAGGTCGT
*
1371060 GCCGACAGTTAGCTAGATCGT
1 GCCGACAGTTAGCTAGGTCGT
* * * *
1371081 GCTGACAGTTAACTAGATCAT
1 GCCGACAGTTAGCTAGGTCGT
*
1371102 GCCGACAGTTACCTAGGTCGT
1 GCCGACAGTTAGCTAGGTCGT
*
1371123 GCCGACAGTAAGCTAGGTCGT
1 GCCGACAGTTAGCTAGGTCGT
* * *
1371144 GCCAACAGTTTA-CTAGATCAT
1 GCCGACAG-TTAGCTAGGTCGT
* *
1371165 ACCGACAATTAGCTAGGTCGT
1 GCCGACAGTTAGCTAGGTCGT
*
1371186 GCCGACAGTTAGTTAGGTCGT
1 GCCGACAGTTAGCTAGGTCGT
* * * *
1371207 GCTGACAGTTAACTAGATCAT
1 GCCGACAGTTAGCTAGGTCGT
* *
1371228 ACCGACAGTTAGCTAGGTTGT
1 GCCGACAGTTAGCTAGGTCGT
1371249 GCCGACAGTT---TAGGTCGT
1 GCCGACAGTTAGCTAGGTCGT
*
1371267 GCCGACAGTAAGCTAGGTCGT
1 GCCGACAGTTAGCTAGGTCGT
1371288 GCCGACCA-TTAGCTAGGTCGT
1 GCCGA-CAGTTAGCTAGGTCGT
* * *
1371309 GTCGACAGTTAGGTATGTCGT
1 GCCGACAGTTAGCTAGGTCGT
* *
1371330 GCCGACAGTTAGGTATGTCGT
1 GCCGACAGTTAGCTAGGTCGT
* *
1371351 GCCGACAGTTAGGTATGTCGT
1 GCCGACAGTTAGCTAGGTCGT
* * * *
1371372 CCCGACAGTTAGGTATGTAGT
1 GCCGACAGTTAGCTAGGTCGT
* * * *
1371393 GCCAACAGTTAGGTATGTAGT
1 GCCGACAGTTAGCTAGGTCGT
* *
1371414 GCCGACAGTTAGGTATGTCGT
1 GCCGACAGTTAGCTAGGTCGT
*
1371435 GCCGACAGTAAGCTAGGTCGT
1 GCCGACAGTTAGCTAGGTCGT
* * *
1371456 GCTGACAGTTAGCTAGATCAT
1 GCCGACAGTTAGCTAGGTCGT
1371477 GCCGACAGTTAGCTAGGTCGT
1 GCCGACAGTTAGCTAGGTCGT
*
1371498 GCCGACAGTTACCTAGGTCGT
1 GCCGACAGTTAGCTAGGTCGT
*
1371519 GCCGACAGTAAGCTAGGTCGT
1 GCCGACAGTTAGCTAGGTCGT
* * *
1371540 GCCAACAGTTTA-CTAGATCAT
1 GCCGACAG-TTAGCTAGGTCGT
*
1371561 GCCGACAATTAGCTAGGTCGT
1 GCCGACAGTTAGCTAGGTCGT
1371582 GCCGACAGTTAGCTAGGTCGT
1 GCCGACAGTTAGCTAGGTCGT
* * * *
1371603 GCTGACAGTTAACTAGATCAT
1 GCCGACAGTTAGCTAGGTCGT
* * *
1371624 ACCGACAGTTAGCTAAGTTGT
1 GCCGACAGTTAGCTAGGTCGT
1371645 GCCGACAGTT-G--AGGTCGT
1 GCCGACAGTTAGCTAGGTCGT
* * *
1371663 GCCGACAATTAGGTATGTCGT
1 GCCGACAGTTAGCTAGGTCGT
* *
1371684 GCC-ACAGTTAGGTATGTCGT
1 GCCGACAGTTAGCTAGGTCGT
* *
1371704 GCCGACAGTTAGGTATGTCGT
1 GCCGACAGTTAGCTAGGTCGT
* * *
1371725 GCCAACAGTTAGGTATGTCGT
1 GCCGACAGTTAGCTAGGTCGT
* *
1371746 GCCGACAGTTAGGTATGTCGT
1 GCCGACAGTTAGCTAGGTCGT
1371767 GCCGACAGTTAGCTAGGTCGT
1 GCCGACAGTTAGCTAGGTCGT
* * *
1371788 GTCGAGAGTTAGCTAGGTTGT
1 GCCGACAGTTAGCTAGGTCGT
1371809 GC
1 GC
1371811 TTTGGGTGTC
Statistics
Matches: 734, Mismatches: 109, Indels: 26
0.84 0.13 0.03
Matches are distributed among these distances:
18 30 0.04
19 1 0.00
20 28 0.04
21 669 0.91
22 6 0.01
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (21 bp):
GCCGACAGTTAGCTAGGTCGT
Found at i:1373673 original size:409 final size:400
Alignment explanation
Indices: 1372921--1373730 Score: 1530
Period size: 409 Copynumber: 2.0 Consensus size: 400
1372911 GAAATGATCT
1372921 TATGTATTATAGGCAATAGCTGTGTGCATAGTATGGTACACCCTTGTGGAACATTGCTTTGTCTT
1 TATGTATTATAGGCAATAGCTGTGTGCATAGTATGGTACACCCTTGTGGAACATTGCTTTGTCTT
1372986 CTGTGTTCAATATTTTGCATATAAAGTAACAATTTGTGTACATGTACAAACTATTTCCTAGGTGA
66 CTGTGTTCAATATTTTGCATATAAAGTAACAATTTGTGTACATGTACAAACTATTTCCTAGGTGA
1373051 CGTATGTGACGTTGTCGAGAAAAGTTACCCGGATCACGATTCCATCGAGTTTTGGAGAAGTATAG
131 CGTATGTGACGTTGTCGAGAAAAGTTACCCGGATCACGATTCCATCGAGTTTTGGAGAAGTATAG
1373116 AAGAATCCTCTGATTTCCGAACAAGGTGTCACAAAAAGGTCAGAGTTCAGACAATCTTTTTGTTT
196 AAGAATCCTCTGATTTCCGAACAAGGTGTCACAAAAAGGTCAGAGTTCAGACAATCTTTTTGTTT
1373181 CGGCATTGACCTAACTCAGAAATGTTTAATTTGACAGTTGCAATACATAAAAAGAACTGGAATTT
261 CGGCATTGACCTAACTCAGAAATGTTTAATTTGACAGTTGCAATACATAAAAAGAACTGGAATTT
1373246 GGTTCGAGCGTTGCAGCATTTAGTATTTGAAATTTTCAATTATATTGGTTTTGACAATGGTGTAT
326 GGTTCGAGCGTTGCAGCATTTAGTATTTGAAATTTTCAATTATATTGGTTTTGACAATGGTGTAT
1373311 GCGAATTCGG
391 GCGAATTCGG
1373321 TNATGTATTATAGGCAATAGCTGTGTGCATAGTATGGTACACCCTTGTGGAACATTGCTTTGTCT
1 T-ATGTATTATAGGCAATAGCTGTGTGCATAGTATGGTACACCCTTGTGGAACATTGCTTTGTCT
1373386 TCTGTGTTCAATATTTTGCATATAAAGTAACAATTTGTGTACATGCGGATATGTACAAACTATTT
65 TCTGTGTTCAATATTTTGCATATAAAGTAACAATTTGTGT--A--C----ATGTACAAACTATTT
1373451 CCTAGGTGACGTATGTGACGTTGTCGAGAAAAGTTACCCGGATCACGATTCCATCGAGTTTTGGA
122 CCTAGGTGACGTATGTGACGTTGTCGAGAAAAGTTACCCGGATCACGATTCCATCGAGTTTTGGA
1373516 GAAGTATAGAAGAATCCTCTGATTTCCGAACAAGGTGTCACAAAAAGGTCAGAGTTCAGACAATC
187 GAAGTATAGAAGAATCCTCTGATTTCCGAACAAGGTGTCACAAAAAGGTCAGAGTTCAGACAATC
*
1373581 TTTTTGTTTCGGCATTGACCTAACTTAGAAATGTTTAATTTGACAGTTGCAATACATAAAAAGAA
252 TTTTTGTTTCGGCATTGACCTAACTCAGAAATGTTTAATTTGACAGTTGCAATACATAAAAAGAA
1373646 CTGGAATTTGGTTCGAGCGTTGCAGCATTTAGTATTTGAAATTTTCAATTATATTGGTTTTGACA
317 CTGGAATTTGGTTCGAGCGTTGCAGCATTTAGTATTTGAAATTTTCAATTATATTGGTTTTGACA
1373711 ATGGTGTATGCGAATTCGG
382 ATGGTGTATGCGAATTCGG
1373730 T
1 T
1373731 CCATTGTTTT
Statistics
Matches: 400, Mismatches: 1, Indels: 9
0.98 0.00 0.02
Matches are distributed among these distances:
400 1 0.00
401 103 0.26
403 1 0.00
405 1 0.00
409 294 0.74
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.34
Consensus pattern (400 bp):
TATGTATTATAGGCAATAGCTGTGTGCATAGTATGGTACACCCTTGTGGAACATTGCTTTGTCTT
CTGTGTTCAATATTTTGCATATAAAGTAACAATTTGTGTACATGTACAAACTATTTCCTAGGTGA
CGTATGTGACGTTGTCGAGAAAAGTTACCCGGATCACGATTCCATCGAGTTTTGGAGAAGTATAG
AAGAATCCTCTGATTTCCGAACAAGGTGTCACAAAAAGGTCAGAGTTCAGACAATCTTTTTGTTT
CGGCATTGACCTAACTCAGAAATGTTTAATTTGACAGTTGCAATACATAAAAAGAACTGGAATTT
GGTTCGAGCGTTGCAGCATTTAGTATTTGAAATTTTCAATTATATTGGTTTTGACAATGGTGTAT
GCGAATTCGG
Found at i:1375644 original size:61 final size:61
Alignment explanation
Indices: 1375572--1375689 Score: 218
Period size: 61 Copynumber: 1.9 Consensus size: 61
1375562 CGGGCGTTGC
*
1375572 CCTCGGAAAATATGATTTTTCATGGGGGAATAAATCTTCATTTTTCCCTCACAATCAACGA
1 CCTCGGAAAATATGATTTTTCATGGGGGAATAAATCTTCATATTTCCCTCACAATCAACGA
*
1375633 CCTCGGTAAATATGATTTTTCATGGGGGAATAAATCTTCATATTTCCCTCACAATCA
1 CCTCGGAAAATATGATTTTTCATGGGGGAATAAATCTTCATATTTCCCTCACAATCA
1375690 TGCAATAGAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (61 bp):
CCTCGGAAAATATGATTTTTCATGGGGGAATAAATCTTCATATTTCCCTCACAATCAACGA
Found at i:1384481 original size:15 final size:14
Alignment explanation
Indices: 1384461--1384493 Score: 57
Period size: 14 Copynumber: 2.3 Consensus size: 14
1384451 GTTTAATATA
1384461 TTTTCATGGATTTTT
1 TTTTCATGG-TTTTT
1384476 TTTTCATGGTTTTT
1 TTTTCATGGTTTTT
1384490 TTTT
1 TTTT
1384494 AAAGAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.09, C:0.06, G:0.12, T:0.73
Consensus pattern (14 bp):
TTTTCATGGTTTTT
Found at i:1385179 original size:21 final size:21
Alignment explanation
Indices: 1385155--1385195 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1385145 TTTTCTATCA
1385155 AATATGTCGACATACAAGATG
1 AATATGTCGACATACAAGATG
* *
1385176 AATATGTTGACATGCAAGAT
1 AATATGTCGACATACAAGAT
1385196 AGTTATGTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (21 bp):
AATATGTCGACATACAAGATG
Found at i:1385393 original size:21 final size:21
Alignment explanation
Indices: 1385369--1385430 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
1385359 GCGAGATAAA
1385369 TATGTTGACATGCAACTTATT
1 TATGTTGACATGCAACTTATT
* * *
1385390 TATGTTAACATGCAACTAAGT
1 TATGTTGACATGCAACTTATT
*
1385411 TATGTTGACATGCAATTTAT
1 TATGTTGACATGCAACTTAT
1385431 AAGTTGCATC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (21 bp):
TATGTTGACATGCAACTTATT
Found at i:1385696 original size:21 final size:21
Alignment explanation
Indices: 1385672--1385725 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
1385662 CGTACTTATG
1385672 TTGCATGTTGACATAACTATC
1 TTGCATGTTGACATAACTATC
** *
1385693 TTGCATGTCAACATAATTATC
1 TTGCATGTTGACATAACTATC
1385714 TTGCATGTTGAC
1 TTGCATGTTGAC
1385726 CTATTTGATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (21 bp):
TTGCATGTTGACATAACTATC
Found at i:1389678 original size:36 final size:36
Alignment explanation
Indices: 1389650--1389723 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
1389640 ATATATACAC
*
1389650 ATAAAACCTATAATGAAAGTTAACAAATATGGAAAA
1 ATAAAACCTATAATGAAAGTTAACAAATATAGAAAA
* *
1389686 ATAAAACCTATCATGAAAGTTAACAAATATGGAAAA
1 ATAAAACCTATAATGAAAGTTAACAAATATAGAAAA
1389722 AT
1 AT
1389724 TGTTCTCTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.23
Consensus pattern (36 bp):
ATAAAACCTATAATGAAAGTTAACAAATATAGAAAA
Found at i:1390910 original size:30 final size:30
Alignment explanation
Indices: 1390876--1391249 Score: 336
Period size: 30 Copynumber: 12.4 Consensus size: 30
1390866 CGTATTTTAA
* *
1390876 TGGTTGATTGATCTGACTTTGATATTTGAT
1 TGGTTGATTGCTCTGACTCTGATATTTGAT
* *
1390906 TGGTT-AATGCTCTGACT-TTATATATTAAGAT
1 TGGTTGATTGCTCTGACTCTGATAT-TT--GAT
* * * *
1390937 TGGTTAATTG-TTTAGACTC-GTTATTT-AA
1 TGGTTGATTGCTCT-GACTCTGATATTTGAT
* * * *
1390965 TGGAATGGTTGCTCTAACT-T-ATGTTTGAT
1 TGG-TTGATTGCTCTGACTCTGATATTTGAT
*
1390994 TGGTTGATTGGTCTGACTCTGATATTTGAT
1 TGGTTGATTGCTCTGACTCTGATATTTGAT
* * *
1391024 TGGGTGATTGGTCTGACTCTGATATTCGAT
1 TGGTTGATTGCTCTGACTCTGATATTTGAT
* *
1391054 TGGGTGATTGTTCTGACTCTGATATTTGAT
1 TGGTTGATTGCTCTGACTCTGATATTTGAT
** *
1391084 TGGGGGATTGCCCTGACTCTGATATTT-AT
1 TGGTTGATTGCTCTGACTCTGATATTTGAT
*
1391113 TGGTTGATTGGTCTGACTCTGATATTTGAT
1 TGGTTGATTGCTCTGACTCTGATATTTGAT
*
1391143 TGGATGATTGCTCTG-CATCTGATATTTGAT
1 TGGTTGATTGCTCTGAC-TCTGATATTTGAT
* *
1391173 TGGGTGATTGCTCTGACTCTGTTATTTGAT
1 TGGTTGATTGCTCTGACTCTGATATTTGAT
* *
1391203 TGCCAGGGTGATTGCTCTGACTCTGATATATGAT
1 T----GGTTGATTGCTCTGACTCTGATATTTGAT
1391237 TCGG-TGATTGCTC
1 T-GGTTGATTGCTC
1391250 CTACCATTGT
Statistics
Matches: 286, Mismatches: 39, Indels: 38
0.79 0.11 0.10
Matches are distributed among these distances:
28 24 0.08
29 50 0.17
30 159 0.56
31 15 0.05
32 10 0.03
34 28 0.10
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.44
Consensus pattern (30 bp):
TGGTTGATTGCTCTGACTCTGATATTTGAT
Found at i:1391129 original size:119 final size:121
Alignment explanation
Indices: 1390992--1391231 Score: 378
Period size: 119 Copynumber: 2.0 Consensus size: 121
1390982 CTTATGTTTG
* *
1390992 ATTGGTTGATTGGTCTGACTCTGATATTTGATTGGGTGATTGGTCTG-ACTCTGATATTCGATTG
1 ATTGGTTGATTGGTCTGACTCTGATATTTGATTGGATGATTGCTCTGCA-TCTGATATTCGATTG
*
1391056 GGTGATTGTTCTGACTCTGATATTTGATTG-GGG-GATTGCCCTGACTCTGATATTT
65 GGTGATTGCTCTGACTCTGATATTTGATTGCGGGTGATTGCCCTGACTCTGATATTT
*
1391111 ATTGGTTGATTGGTCTGACTCTGATATTTGATTGGATGATTGCTCTGCATCTGATATTTGATTGG
1 ATTGGTTGATTGGTCTGACTCTGATATTTGATTGGATGATTGCTCTGCATCTGATATTCGATTGG
* *
1391176 GTGATTGCTCTGACTCTGTTATTTGATTGCCAGGGTGATTGCTCTGACTCTGATAT
66 GTGATTGCTCTGACTCTGATATTTGATTG-C-GGGTGATTGCCCTGACTCTGATAT
1391232 ATGATTCGGT
Statistics
Matches: 110, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
119 87 0.79
120 1 0.01
122 3 0.03
123 19 0.17
ACGTcount: A:0.17, C:0.13, G:0.27, T:0.43
Consensus pattern (121 bp):
ATTGGTTGATTGGTCTGACTCTGATATTTGATTGGATGATTGCTCTGCATCTGATATTCGATTGG
GTGATTGCTCTGACTCTGATATTTGATTGCGGGTGATTGCCCTGACTCTGATATTT
Found at i:1391144 original size:89 final size:90
Alignment explanation
Indices: 1391006--1391249 Score: 339
Period size: 89 Copynumber: 2.7 Consensus size: 90
1390996 GTTGATTGGT
* *
1391006 CTGACTCTGATATTTGATTGGGTGATTGGTCTGACTCTGATATTCGATTGGGTGATTGTTCTG-A
1 CTGACTCTGATATTTGATTGGGTGATTGGTCTGACTCTGATATTTGATTGGGTGATTGCTCTGCA
1391070 CTCTGATATTTGATTGGGGGATTGCC
66 -TCTGATATTTGATTGGGGGATTGCC
* *
1391096 CTGACTCTGATATTT-ATTGGTTGATTGGTCTGACTCTGATATTTGATTGGATGATTGCTCTGCA
1 CTGACTCTGATATTTGATTGGGTGATTGGTCTGACTCTGATATTTGATTGGGTGATTGCTCTGCA
* *
1391160 TCTGATATTTGATTGGGTGATTGCT
66 TCTGATATTTGATTGGGGGATTGCC
* * * *
1391185 CTGACTCTGTTATTTGATTGCCAGGGTGATTGCTCTGACTCTGATATATGATTCGGTGATTGCTC
1 CTGACTCTGATATTTGATT----GGGTGATTGGTCTGACTCTGATATTTGATTGGGTGATTGCTC
1391250 CTACCATTGT
Statistics
Matches: 136, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
89 80 0.59
90 19 0.14
94 37 0.27
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.42
Consensus pattern (90 bp):
CTGACTCTGATATTTGATTGGGTGATTGGTCTGACTCTGATATTTGATTGGGTGATTGCTCTGCA
TCTGATATTTGATTGGGGGATTGCC
Found at i:1391414 original size:3 final size:3
Alignment explanation
Indices: 1391406--1391454 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
1391396 TGGTTTATCG
* * *
1391406 GTT GTT GTT GTT GTT TTT GTT GTT GTT GTT GTT GTT TTT GCT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
1391454 G
1 G
1391455 AATTTGTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.02, G:0.31, T:0.67
Consensus pattern (3 bp):
GTT
Found at i:1391461 original size:21 final size:20
Alignment explanation
Indices: 1391406--1391472 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 20
1391396 TGGTTTATCG
*
1391406 GTTGTTGTTGTTGTTTTTGTT
1 GTTGTTGATGTTGTTTTTG-T
*
1391427 GTTGTTGTTGTTGTTTTTGCT
1 GTTGTTGATGTTGTTTTTG-T
1391448 GTTGTTGAAT-TTGTTATTTGT
1 GTTGTTG-ATGTTGTT-TTTGT
1391469 GTTG
1 GTTG
1391473 ACAGTGAACC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 37 0.88
22 5 0.12
ACGTcount: A:0.04, C:0.01, G:0.28, T:0.66
Consensus pattern (20 bp):
GTTGTTGATGTTGTTTTTGT
Found at i:1391684 original size:13 final size:13
Alignment explanation
Indices: 1391663--1391693 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1391653 TTCCATAAAT
*
1391663 TGTTTTGTATTTC
1 TGTTATGTATTTC
1391676 TGTTATGTATTTC
1 TGTTATGTATTTC
1391689 TGTTA
1 TGTTA
1391694 CAATCTCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.06, G:0.16, T:0.65
Consensus pattern (13 bp):
TGTTATGTATTTC
Found at i:1392267 original size:2 final size:2
Alignment explanation
Indices: 1392262--1392304 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1392252 AAAATAAAAT
* *
1392262 GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA AA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1392304 G
1 G
1392305 TATACCTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1393326 original size:22 final size:22
Alignment explanation
Indices: 1393298--1393344 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1393288 CTGTTCTTGT
1393298 TTACATAGGTTCAATTTACCAA
1 TTACATAGGTTCAATTTACCAA
1393320 TTACATAGGTTCAATTTACCAA
1 TTACATAGGTTCAATTTACCAA
1393342 TTA
1 TTA
1393345 AAAACTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (22 bp):
TTACATAGGTTCAATTTACCAA
Found at i:1410161 original size:2 final size:2
Alignment explanation
Indices: 1410154--1410218 Score: 112
Period size: 2 Copynumber: 32.5 Consensus size: 2
1410144 ATTAAAACAT
* *
1410154 GA GA GA GA GA AA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1410196 GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA G
1410219 CATATCAAGC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1412179 original size:2 final size:2
Alignment explanation
Indices: 1412174--1412213 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1412164 GTGTGTGTGC
1412174 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1412214 CCTGTAGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1412662 original size:30 final size:31
Alignment explanation
Indices: 1412596--1412726 Score: 90
Period size: 30 Copynumber: 4.2 Consensus size: 31
1412586 CTTTCACGGA
* * *
1412596 TATAACTGTCCCGCCCATACATATTCCCCTGT
1 TATAACTGT-CCGCCCATACACATTCCCCAGG
* *
1412628 TATAACTGT-CGCCCATACACCTTCTCCAGG
1 TATAACTGTCCGCCCATACACATTCCCCAGG
* * * * *
1412658 TATAACTGTTCCGTCTAAACAC-TTTCCCTGG
1 TATAACTG-TCCGCCCATACACATTCCCCAGG
* *
1412689 ATAAAACTG-CCGCCCATACACTTTCCCC-GG
1 -TATAACTGTCCGCCCATACACATTCCCCAGG
1412719 ATATAACT
1 -TATAACT
1412727 CTCGTCTGAT
Statistics
Matches: 78, Mismatches: 17, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
30 42 0.54
31 12 0.15
32 24 0.31
ACGTcount: A:0.25, C:0.34, G:0.11, T:0.29
Consensus pattern (31 bp):
TATAACTGTCCGCCCATACACATTCCCCAGG
Found at i:1422364 original size:90 final size:90
Alignment explanation
Indices: 1422210--1422389 Score: 351
Period size: 90 Copynumber: 2.0 Consensus size: 90
1422200 AACGGTTTGA
*
1422210 GAGATAATTTTGTATTAATTATTTTATTGGTTAATTAAATAAGTGTGAATTTTCCATTGTGGGGT
1 GAGATAATTTTGTATTAATTATTTTATTGGTTAATTAAATAAGTGTGAATTTTCCATTGGGGGGT
1422275 GGATCTGATCTCATTCTAGATCCGC
66 GGATCTGATCTCATTCTAGATCCGC
1422300 GAGATAATTTTGTATTAATTATTTTATTGGTTAATTAAATAAGTGTGAATTTTCCATTGGGGGGT
1 GAGATAATTTTGTATTAATTATTTTATTGGTTAATTAAATAAGTGTGAATTTTCCATTGGGGGGT
1422365 GGATCTGATCTCATTCTAGATCCGC
66 GGATCTGATCTCATTCTAGATCCGC
1422390 AATGCAATGT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.43
Consensus pattern (90 bp):
GAGATAATTTTGTATTAATTATTTTATTGGTTAATTAAATAAGTGTGAATTTTCCATTGGGGGGT
GGATCTGATCTCATTCTAGATCCGC
Found at i:1430606 original size:27 final size:27
Alignment explanation
Indices: 1430576--1430954 Score: 596
Period size: 27 Copynumber: 14.0 Consensus size: 27
1430566 AAAGTAAAAT
1430576 ATGTAATAAAGGTATACATTTCATAAC
1 ATGTAATAAAGGTATACATTTCATAAC
1430603 ATGTAATAAAGGTATACATTTCATAAC
1 ATGTAATAAAGGTATACATTTCATAAC
*
1430630 ATGTAATAAAGGTATAAATTTCATAAC
1 ATGTAATAAAGGTATACATTTCATAAC
*
1430657 ATCTAATAAAGGTATACATTTCATAAC
1 ATGTAATAAAGGTATACATTTCATAAC
* *
1430684 AAGTAATAAAAGTATACATTTCATAAC
1 ATGTAATAAAGGTATACATTTCATAAC
*
1430711 AGGTAATAAAGGTATACATTTCATAAC
1 ATGTAATAAAGGTATACATTTCATAAC
* *
1430738 AGGTAATAAAGGTATACATTTCGTAAC
1 ATGTAATAAAGGTATACATTTCATAAC
* *
1430765 AGGTAATAAAGTTATACATTTCATAAC
1 ATGTAATAAAGGTATACATTTCATAAC
*
1430792 AGGTAATAAAGGTATACATTTCATAAC
1 ATGTAATAAAGGTATACATTTCATAAC
*
1430819 AGGTAATAAAGGTATACATTTCATAAC
1 ATGTAATAAAGGTATACATTTCATAAC
* * *
1430846 ATGTGATAAGGGTATCCATTTCATAAC
1 ATGTAATAAAGGTATACATTTCATAAC
*
1430873 ATGTAATAATGGTATACATTTCATAAC
1 ATGTAATAAAGGTATACATTTCATAAC
* *
1430900 ATCTCATAAAGGTATACATTTCATAAC
1 ATGTAATAAAGGTATACATTTCATAAC
*
1430927 ATGTAATAAAAGTATACATTTCATAAC
1 ATGTAATAAAGGTATACATTTCATAAC
1430954 A
1 A
1430955 GTTAAGATCT
Statistics
Matches: 327, Mismatches: 25, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 327 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (27 bp):
ATGTAATAAAGGTATACATTTCATAAC
Done.