Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009597.1 Hibiscus syriacus cultivar Beakdansim tig00116976_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1557931
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 5 of 7
Found at i:836429 original size:2 final size:2
Alignment explanation
Indices: 836422--836460 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
836412 GTTGAAAATA
836422 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
836461 ACTTCTCACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:836653 original size:2 final size:2
Alignment explanation
Indices: 836646--836696 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
836636 ACATACATAC
836646 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
836688 AT AT AT AT A
1 AT AT AT AT A
836697 CTTCTCACTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:838378 original size:20 final size:19
Alignment explanation
Indices: 838343--838380 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
838333 TTATTACAAA
*
838343 ATATATAACTAGAATATAT
1 ATATATAACTAAAATATAT
838362 ATATATAAACTAAAATATA
1 ATATAT-AACTAAAATATA
838381 ATTAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (19 bp):
ATATATAACTAAAATATAT
Found at i:853619 original size:24 final size:24
Alignment explanation
Indices: 853592--853766 Score: 248
Period size: 24 Copynumber: 7.4 Consensus size: 24
853582 TCAACAGCAG
*
853592 CAACAACAGCAGCAGCAGCAGCAA
1 CAACAACAGCAGCAGCAGCAACAA
853616 CAACAACA--A-CAGCAGCAACAA
1 CAACAACAGCAGCAGCAGCAACAA
* *
853637 CAGCAGCAGCAGCAGCAGCAACAA
1 CAACAACAGCAGCAGCAGCAACAA
*
853661 CAACAGCAGCAGCAGCAGCAACAA
1 CAACAACAGCAGCAGCAGCAACAA
*
853685 CAACAACAGCAGCAGCAGCAGCAA
1 CAACAACAGCAGCAGCAGCAACAA
* *
853709 CAACAACAACAGCAGCAGCAGCAA
1 CAACAACAGCAGCAGCAGCAACAA
* *
853733 CAACAACAGCAGCAGCAACAACAG
1 CAACAACAGCAGCAGCAGCAACAA
853757 CAACAACAGC
1 CAACAACAGC
853767 CTCAACAAAG
Statistics
Matches: 137, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
21 17 0.12
22 1 0.01
23 1 0.01
24 118 0.86
ACGTcount: A:0.48, C:0.34, G:0.18, T:0.00
Consensus pattern (24 bp):
CAACAACAGCAGCAGCAGCAACAA
Found at i:853764 original size:3 final size:3
Alignment explanation
Indices: 853586--853749 Score: 130
Period size: 3 Copynumber: 54.7 Consensus size: 3
853576 TGCTCATCAA
* * * * * * *
853586 CAG CAG CAA CAA CAG CAG CAG CAG CAG CAA CAA CAA CAA CAG CAG CAA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * * * *
853634 CAA CAG CAG CAG CAG CAG CAG CAA CAA CAA CAG CAG CAG CAG CAG CAA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * * * * * *
853682 CAA CAA CAA CAG CAG CAG CAG CAG CAA CAA CAA CAA CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * *
853730 CAA CAA CAA CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CA
853750 ACAACAGCAA
Statistics
Matches: 147, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 147 1.00
ACGTcount: A:0.47, C:0.34, G:0.20, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:853774 original size:21 final size:21
Alignment explanation
Indices: 853586--853766 Score: 200
Period size: 21 Copynumber: 8.2 Consensus size: 21
853576 TGCTCATCAA
* *
853586 CAGCAGCAACAACAGCAGCAG
1 CAGCAGCAACAACAACAACAG
853607 CAGCAGCAACAACAACAACAG
1 CAGCAGCAACAACAACAACAG
* * * *
853628 CAGCAACAACAGCAGCAGCAG
1 CAGCAGCAACAACAACAACAG
853649 CAGCAGCAACAACAACAGCAGCAG
1 CAGCAGCAACAACAACA--A-CAG
853673 CAGCAGCAACAACAACAACAGCAGCAG
1 CAGCAG---CAACAACAACA--A-CAG
853700 CAGCAGCAACAACAACAACAG
1 CAGCAGCAACAACAACAACAG
*
853721 CAGCAGCAGCAACAACAACAG
1 CAGCAGCAACAACAACAACAG
* *
853742 CAGCAGCAACAACAGCAACAA
1 CAGCAGCAACAACAACAACAG
853763 CAGC
1 CAGC
853767 CTCAACAAAG
Statistics
Matches: 140, Mismatches: 14, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
21 95 0.68
22 1 0.01
24 20 0.14
27 24 0.17
ACGTcount: A:0.48, C:0.34, G:0.19, T:0.00
Consensus pattern (21 bp):
CAGCAGCAACAACAACAACAG
Found at i:860223 original size:18 final size:18
Alignment explanation
Indices: 860196--860234 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
860186 CAAACTCGTG
*
860196 AAAATATTAA-TCATATA
1 AAAATATTAAGTCACATA
860213 AAAATTATTAAGTCACATA
1 AAAA-TATTAAGTCACATA
860232 AAA
1 AAA
860235 CAACCTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 6 0.32
19 9 0.47
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAATATTAAGTCACATA
Found at i:862608 original size:17 final size:17
Alignment explanation
Indices: 862567--862611 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
862557 CCCTACTTGA
862567 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** **
862584 TTTTATATTTTTTAAAT
1 TTAAATATTTAATAAAT
862601 TTAAATATTTA
1 TTAAATATTTA
862612 TTTTTACATG
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:868984 original size:2 final size:2
Alignment explanation
Indices: 868977--869057 Score: 153
Period size: 2 Copynumber: 40.5 Consensus size: 2
868967 AAAGAAGAGT
868977 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
*
869019 TC TC TC TC TC TC TC TC TC TC TC TA TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
869058 TTTTAAATGA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.01, C:0.48, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:882112 original size:2 final size:2
Alignment explanation
Indices: 882105--882131 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
882095 AGGTACCCCA
882105 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
882132 AGGTCCCCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:886203 original size:10 final size:10
Alignment explanation
Indices: 886188--886215 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
886178 AACTGAGATC
886188 GAAACTTGTT
1 GAAACTTGTT
886198 GAAACTTGTT
1 GAAACTTGTT
886208 GAAACTTG
1 GAAACTTG
886216 GCAAGAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (10 bp):
GAAACTTGTT
Found at i:893408 original size:208 final size:207
Alignment explanation
Indices: 893021--893409 Score: 496
Period size: 208 Copynumber: 1.9 Consensus size: 207
893011 ATAAGAGTTA
* * * *
893021 AAGGCCATACTATTACCAGGCCATCAGTCTATTTAGGTCCACGTCCTAAGCATTTTCAACAAAAG
1 AAGGCCATACTATTACCAGGCCATCAATCTATTTAGGTCCACATCCTAAGAATTCTCAACAAAAG
* *
893086 CAACACTTTCACAACTTCAACCCATGTTTTCTTTTCCCTTCCCTCCCATTGACACAATGAAAGAA
66 CAACACTTTCACAACTTCAACCCATGTCTTCTTTTCCCTTCCCTCCCATCGACACAATGAAAGAA
* * * *
893151 CATGATATTTTTAAACCCAAATATTATATTGTCTATATTGAATGAATTACTCACTTTGTCAGATA
131 AATAATATTTTTAAACCC--ATATAATATTGTCTATATTGAAGGAATTACTCACTTTGTCAGATA
893216 GACTATATGGGTTC
194 GACTATATGGGTTC
* * ** ** *
893230 AAGGCCATGCTATTACCAGG-CGTCAATCTATTTAGGTCCTTATTTTAAGAATTCTCAGCAAAAG
1 AAGGCCATACTATTACCAGGCCATCAATCTATTTAGGTCCACATCCTAAGAATTCTCAACAAAAG
* * * * *
893294 CAACATCCTTTCACAGCTTTAACCCATGTCTTCTTTTCCCTTTCCC-CCCCTCGACACGATGTAA
66 CAACA--CTTTCACAACTTCAACCCATGTCTTCTTTTCCC-TTCCCTCCCATCGACACAATGAAA
*
893358 GAAAATAATATTTTTAAACCTC-TATAATATTGTCTATATTGTAGGAATTACT
128 GAAAATAATATTTTTAAACC-CATATAATATTGTCTATATTGAAGGAATTACT
893410 GCAGACATTT
Statistics
Matches: 153, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
208 66 0.43
209 19 0.12
210 62 0.41
211 6 0.04
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.34
Consensus pattern (207 bp):
AAGGCCATACTATTACCAGGCCATCAATCTATTTAGGTCCACATCCTAAGAATTCTCAACAAAAG
CAACACTTTCACAACTTCAACCCATGTCTTCTTTTCCCTTCCCTCCCATCGACACAATGAAAGAA
AATAATATTTTTAAACCCATATAATATTGTCTATATTGAAGGAATTACTCACTTTGTCAGATAGA
CTATATGGGTTC
Found at i:895579 original size:18 final size:18
Alignment explanation
Indices: 895556--895591 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
895546 TAGAAAATTG
895556 GTGAAGAATAAAACATGT
1 GTGAAGAATAAAACATGT
895574 GTGAAGAATAAAACATGT
1 GTGAAGAATAAAACATGT
895592 TGCAAGTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (18 bp):
GTGAAGAATAAAACATGT
Found at i:902103 original size:160 final size:162
Alignment explanation
Indices: 901927--902249 Score: 607
Period size: 163 Copynumber: 2.0 Consensus size: 162
901917 AAGTAGGGGT
901927 TTCAGTTCTTTTACCTTCCATAGCATGATATAGCCCTTCCAA-AAACAAAATTGACAAAG-ATAG
1 TTCAGTTCTTTTACCTTCCATAGCATGATATAGCCCTTCCAATAAACAAAATTGACAAAGAATAG
901990 ATATAAACCAATCAGTACTTCAAGTTCTAGTATGTGTATTAGA-TTCCTTTTCCCTCTCTATAAG
66 ATATAAACCAATCAGTACTTCAAGTTCTAGTATGTGTATTAGATTTCCTTTT-CCTCTCTATAAG
902054 AGAACAACCAAAAAAATTGGTAGAATCTTTACC
130 AGAACAACCAAAAAAATTGGTAGAATCTTTACC
902087 TTCAGTTCTTTTACCTTCCATAGCATGATATAGCCCTTCCAATAAACAAAATTGACAAAGATATA
1 TTCAGTTCTTTTACCTTCCATAGCATGATATAGCCCTTCCAATAAACAAAATTGACAAAGA-ATA
902152 GATATAAACCAATCAGTACTTCAAGTTCTAGTATGTGTATTAGATTTCCTTTTCCTCTCTATAAG
65 GATATAAACCAATCAGTACTTCAAGTTCTAGTATGTGTATTAGATTTCCTTTTCCTCTCTATAAG
902217 AGAACAACCAAAAAAATTGGTAGAATCTTTACC
130 AGAACAACCAAAAAAATTGGTAGAATCTTTACC
902250 ACTTATTAAG
Statistics
Matches: 159, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
160 42 0.26
161 17 0.11
163 92 0.58
164 8 0.05
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (162 bp):
TTCAGTTCTTTTACCTTCCATAGCATGATATAGCCCTTCCAATAAACAAAATTGACAAAGAATAG
ATATAAACCAATCAGTACTTCAAGTTCTAGTATGTGTATTAGATTTCCTTTTCCTCTCTATAAGA
GAACAACCAAAAAAATTGGTAGAATCTTTACC
Found at i:906933 original size:314 final size:311
Alignment explanation
Indices: 906367--906991 Score: 1166
Period size: 314 Copynumber: 2.0 Consensus size: 311
906357 CAGAAGGCCT
906367 AAATAAACCGTCGGAAAGGAACCAATAGAGCAGCCAATGTCCTTAGCCCAATTTCCAATGATGTC
1 AAATAAACCGTCGGAAAGGAACCAATAGAGCAGCCAATGTCCTTAGCCCAATTTCCAATGATGTC
906432 CACATTAATACCATAAAGTTTGCTTTTAACTAAATTAAGATGAAGCACTGTCATAAAACTAAAGA
66 CACATTAATACCATAAAGTTTGCTTTTAACTAAATTAAGATGAAGCACTGTCATAAAACTAAAGA
906497 TCGTCAACACTCGTCTAACATTTTTAATTTGAGTGATGGAGGCTCGGCAAAAAATAATTAAGTCG
131 TCGTCAACACTCGTCTAACATTTTTAATTTGAGTGATGGAGGCTCGGCAAAAAATAATTAAGTCG
906562 TCAGCAAACTGGAGATGAGTCAAATTGAAACAGTTTTGACTCTTTCCAAAAGAAAATCCTTGGAA
196 TCAGCAAACTGGAGATGAGTCAAATTGAAACAGTTTTGACTCTTTCCAAAAGAAAATCCTTGGAA
906627 TAAGCCCGAATCCACAACTTTAGTTAACATCATATGAAGAAGTTCACCAAC
261 TAAGCCCGAATCCACAACTTTAGTTAACATCATATGAAGAAGTTCACCAAC
906678 AAATAAACCGTCGGAAAGGAACCAATAGAGCAGCCAATGTCCTTAGCCCAATTTCCAATGATGTC
1 AAATAAACCGTCGGAAAGGAACCAATAGAGCAGCCAATGTCCTTAGCCCAATTTCCAATGATG--
906743 CTCCTCCACATTAATACCATAAAGTTTGCTTTTAACTAAATTAAGATGAAGCACTGTCATAAAAC
64 ----TCCACATTAATACCATAAAGTTTGCTTTTAACTAAATTAAGATGAAGCACTGTCATAAAAC
906808 TAAAGATCGTC-A-ACTCGTCTAACA-TTTTAATTTGAGTGATGGAGGCTCGGCAAAAAATAATT
125 TAAAGATCGTCAACACTCGTCTAACATTTTTAATTTGAGTGATGGAGGCTCGGCAAAAAATAATT
*
906870 AAGTCGTCAGCAAACTGGAGATGAGTCAAATTGAAGCAGTTTTGACTCTTTCCAAAAGAAAATCC
190 AAGTCGTCAGCAAACTGGAGATGAGTCAAATTGAAACAGTTTTGACTCTTTCCAAAAGAAAATCC
906935 TTGGAATAAGCCCGAATCCACAACTTTAGTTAACATCATATGAAGAAGTTCACCAAC
255 TTGGAATAAGCCCGAATCCACAACTTTAGTTAACATCATATGAAGAAGTTCACCAAC
906992 CACGTTAAAC
Statistics
Matches: 307, Mismatches: 1, Indels: 9
0.97 0.00 0.03
Matches are distributed among these distances:
311 63 0.21
314 159 0.52
315 12 0.04
316 1 0.00
317 72 0.23
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (311 bp):
AAATAAACCGTCGGAAAGGAACCAATAGAGCAGCCAATGTCCTTAGCCCAATTTCCAATGATGTC
CACATTAATACCATAAAGTTTGCTTTTAACTAAATTAAGATGAAGCACTGTCATAAAACTAAAGA
TCGTCAACACTCGTCTAACATTTTTAATTTGAGTGATGGAGGCTCGGCAAAAAATAATTAAGTCG
TCAGCAAACTGGAGATGAGTCAAATTGAAACAGTTTTGACTCTTTCCAAAAGAAAATCCTTGGAA
TAAGCCCGAATCCACAACTTTAGTTAACATCATATGAAGAAGTTCACCAAC
Found at i:911732 original size:16 final size:16
Alignment explanation
Indices: 911713--911748 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
911703 TCTACGATTT
911713 GGTCTTTCATTCCAGG
1 GGTCTTTCATTCCAGG
911729 GGTCTTTCATTCCAGG
1 GGTCTTTCATTCCAGG
911745 GGTC
1 GGTC
911749 GTTCTTTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.11, C:0.25, G:0.28, T:0.36
Consensus pattern (16 bp):
GGTCTTTCATTCCAGG
Found at i:912565 original size:24 final size:24
Alignment explanation
Indices: 912538--912585 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
912528 GGCTCGATTT
912538 TCTTCCAACAGTCAGACCTTTTAA
1 TCTTCCAACAGTCAGACCTTTTAA
912562 TCTTCCAACAGTCAGACCTTTTAA
1 TCTTCCAACAGTCAGACCTTTTAA
912586 ATTCCAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (24 bp):
TCTTCCAACAGTCAGACCTTTTAA
Found at i:920371 original size:3 final size:3
Alignment explanation
Indices: 920352--920385 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
920342 ATATTATAAA
920352 TAT TAAT TAT ATAT TAT TAT TAT TAT TAT TAT TA
1 TAT T-AT TAT -TAT TAT TAT TAT TAT TAT TAT TA
920386 ATGTTACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 23 0.79
4 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:920510 original size:12 final size:12
Alignment explanation
Indices: 920493--920522 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
920483 TTCGAGCCCA
920493 AGACCCAGATCC
1 AGACCCAGATCC
920505 AGACCCAGATCC
1 AGACCCAGATCC
920517 AGACCC
1 AGACCC
920523 GGTTACAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.43, G:0.17, T:0.07
Consensus pattern (12 bp):
AGACCCAGATCC
Found at i:923845 original size:2 final size:2
Alignment explanation
Indices: 923840--923888 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
923830 TATCTCTCTT
923840 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
923882 TA TA TA T
1 TA TA TA T
923889 GCTAGTTACT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:932535 original size:38 final size:38
Alignment explanation
Indices: 932484--932591 Score: 152
Period size: 34 Copynumber: 2.9 Consensus size: 38
932474 AAAGTCAAGC
*
932484 CTTCACGGAAGAGTAGTGAAGCAAATCCATTTGTAAAA
1 CTTCACGGAAGAGTAGTGAAGCAAATCCATCTGTAAAA
* **
932522 CTTCACCGAAGAGTAGTGAAGC--A-CCATCT-TAAGC
1 CTTCACGGAAGAGTAGTGAAGCAAATCCATCTGTAAAA
932556 CTTCACGGAAGAGTAGTGAAGCAAATCCATCTGTAA
1 CTTCACGGAAGAGTAGTGAAGCAAATCCATCTGTAA
932592 GCCTTTAGAG
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
34 24 0.39
35 5 0.08
36 2 0.03
37 6 0.10
38 24 0.39
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.22
Consensus pattern (38 bp):
CTTCACGGAAGAGTAGTGAAGCAAATCCATCTGTAAAA
Found at i:932567 original size:34 final size:37
Alignment explanation
Indices: 932480--932596 Score: 159
Period size: 38 Copynumber: 3.2 Consensus size: 37
932470 GGGCAAAGTC
*
932480 AAGCCTTCACGGAAGAGTAGTGAAGCAAATCCATTTGT
1 AAGCCTTCACGGAAGAGTAGTGAAGC-AATCCATCTGT
** *
932518 AAAACTTCACCGAAGAGTAGTGAAGC-A-CCATCT-T
1 AAGCCTTCACGGAAGAGTAGTGAAGCAATCCATCTGT
932552 AAGCCTTCACGGAAGAGTAGTGAAGCAAATCCATCTGT
1 AAGCCTTCACGGAAGAGTAGTGAAGC-AATCCATCTGT
932590 AAGCCTT
1 AAGCCTT
932597 TAGAGCAAGA
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
34 24 0.35
35 5 0.07
36 2 0.03
37 6 0.09
38 31 0.46
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (37 bp):
AAGCCTTCACGGAAGAGTAGTGAAGCAATCCATCTGT
Found at i:932841 original size:41 final size:42
Alignment explanation
Indices: 932738--932845 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 42
932728 TTTCATAATT
* * * * * **
932738 TATAAGTCCGTCGGGCTATCAGTAAGTCTTTCGAGCTTGATG
1 TATAAGTCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATG
* * *
932780 TTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 TATAAGTCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATG
932822 -ATAAGTCCTTCGGGCCATCTGTAA
1 TATAAGTCCTTCGGGCCATCTGTAA
932846 AACCTTCGGG
Statistics
Matches: 53, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
41 21 0.40
42 32 0.60
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.32
Consensus pattern (42 bp):
TATAAGTCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATG
Found at i:933008 original size:215 final size:213
Alignment explanation
Indices: 932583--933024 Score: 715
Period size: 215 Copynumber: 2.1 Consensus size: 213
932573 GAAGCAAATC
932583 CATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGA
1 CATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGA
* ** * *
932648 TGTTTTTACATGAATTTGAAAATGAAAATTATGTTTTAAGAAGATGAAATTTTTGAAAACGAAGA
66 TGTTTTCACATGAATTTGAAAATGAAAACGATGTTTTAAGAAGATGAAACTTTTGAAAACAAAGA
* * * *
932713 ATGCGATTTTCAAAATTTCATAATTTATAAGTCCGTCGGGCTATCAGTAAGTCTTTCGAGCTTGA
131 ATACGATTTTCAAAATTTCACAATTTATAAGTCCGTCGGGCCATCAGTAAGTCTTTCGAGCATGA
*
932778 TGTTTAAATCCTTCGGGT
196 TGATTAAATCCTTCGGGT
**
932796 CATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCTGTAAAACCTTCGGGTAGGA
1 CATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGA
*
932861 TGTTTTCACATGAATTTGAAAATGAAAAAACGATGTTTTGAGAAGATGAAACTTTTGAAAACAAA
66 TGTTTTCACATGAATTTGAAAATG--AAAACGATGTTTTAAGAAGATGAAACTTTTGAAAACAAA
*
932926 GAATACGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
129 GAATACGATTTTCAAAATTTCACAATTTATAAGTCCGTCGGGCCATCAGTAAGTCTTTCGAGCAT
932991 GATGATTAAATCCTTCGGGT
194 GATGATTAAATCCTTCGGGT
*
933011 -AACTGGTAAGCCTT
1 CATCT-GTAAGCCTT
933025 CACGGAAGAG
Statistics
Matches: 211, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
213 86 0.41
214 3 0.01
215 122 0.58
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Consensus pattern (213 bp):
CATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGA
TGTTTTCACATGAATTTGAAAATGAAAACGATGTTTTAAGAAGATGAAACTTTTGAAAACAAAGA
ATACGATTTTCAAAATTTCACAATTTATAAGTCCGTCGGGCCATCAGTAAGTCTTTCGAGCATGA
TGATTAAATCCTTCGGGT
Found at i:933087 original size:22 final size:21
Alignment explanation
Indices: 933059--933129 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
933049 CATCAGTAAG
933059 TCTTTCGAGCATGATGATGAAA
1 TCTTTCGAGCATGATGAT-AAA
* * * *
933081 TCCTTCGGGTCATCA-G-TAAG
1 TCTTTCGAG-CATGATGATAAA
933101 TCTTTCGAGCATGATGATTAAA
1 TCTTTCGAGCATGATGA-TAAA
933123 TCTTTCG
1 TCTTTCG
933130 GCTCATTTGT
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 4 0.11
20 10 0.27
21 1 0.03
22 18 0.49
23 4 0.11
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.35
Consensus pattern (21 bp):
TCTTTCGAGCATGATGATAAA
Found at i:933095 original size:42 final size:42
Alignment explanation
Indices: 933048--933135 Score: 149
Period size: 42 Copynumber: 2.1 Consensus size: 42
933038 TGAAGCAAAT
*
933048 TCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
1 TCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGC
* *
933090 TCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGC
1 TCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGC
933132 TCAT
1 TCAT
933136 TTGTGAGTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.34
Consensus pattern (42 bp):
TCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGC
Found at i:934945 original size:2 final size:2
Alignment explanation
Indices: 934940--934968 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
934930 TATCTCTCTT
934940 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
934969 TGCTAGTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:936131 original size:2 final size:2
Alignment explanation
Indices: 936117--936157 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
936107 ATTGATGTAT
936117 TA TA TA T- TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
936157 T
1 T
936158 GGTATAACAC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:940538 original size:24 final size:24
Alignment explanation
Indices: 940511--940583 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
940501 GTAAACGGAG
940511 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
* * * * *
940535 ATATTAGATATCAGAACAAAATCC
1 ATATCAGAAATCAAAACAGAATTC
* *
940559 AGATCAGAAATCATAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
940583 A
1 A
940584 GGTAATGTAT
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.52, C:0.16, G:0.10, T:0.22
Consensus pattern (24 bp):
ATATCAGAAATCAAAACAGAATTC
Found at i:940617 original size:48 final size:48
Alignment explanation
Indices: 940513--940621 Score: 125
Period size: 48 Copynumber: 2.3 Consensus size: 48
940503 AAACGGAGAT
* * *
940513 ATCAGAAATCAAAACAGAATTCATATTAGATATCAGAACAAAATCCAG
1 ATCAGAAATCATAACAGAATTCATAATAGATATCAGAACAAAATCAAG
*
940561 ATCAGAAATCATAACAGAATTCAGGTAAT-G-TATCAGAACAGAATTCAAG
1 ATCAGAAATCATAACAGAATTCA--TAATAGATATCAGAACA-AAATCAAG
*
940610 -TCGGAAATCATA
1 ATCAGAAATCATA
940622 TAAAATATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
48 43 0.81
49 7 0.13
50 3 0.06
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCATAACAGAATTCATAATAGATATCAGAACAAAATCAAG
Found at i:957690 original size:36 final size:36
Alignment explanation
Indices: 957650--957727 Score: 131
Period size: 37 Copynumber: 2.2 Consensus size: 36
957640 TTTATTTTGT
957650 TCGGGTCGGG-TTTTTAAGTGTAATATTCGGGTCGAG
1 TCGGGTCGGGTTTTTTAAGTGTAATATTCGGGTC-AG
*
957686 TCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCAG
1 TCGGGTCGGGTTTTTTAAGTGTAATATTCGGGTCAG
957722 TCGGGT
1 TCGGGT
957728 TTAGGGTGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
36 18 0.45
37 22 0.55
ACGTcount: A:0.14, C:0.12, G:0.37, T:0.37
Consensus pattern (36 bp):
TCGGGTCGGGTTTTTTAAGTGTAATATTCGGGTCAG
Found at i:957877 original size:32 final size:32
Alignment explanation
Indices: 957799--957887 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 32
957789 CTTTATTTTG
* *
957799 TTCGGGTCGGGTCGGATTTTTTAAGTGTGATA
1 TTCGGGTCGGGTTGGGTTTTTTAAGTGTGATA
957831 TTCGGGTCGAGTCGGTTGGGTTTTTCTAAGTGTGATA
1 TTCGGGTC--G--GGTTGGGTTTTT-TAAGTGTGATA
957868 TTCGGGTCGGGTTCGGGTTT
1 TTCGGGTCGGGTT-GGGTTT
957888 AGGGTGAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
32 8 0.16
33 4 0.08
34 7 0.14
35 1 0.02
36 10 0.20
37 19 0.39
ACGTcount: A:0.11, C:0.11, G:0.37, T:0.40
Consensus pattern (32 bp):
TTCGGGTCGGGTTGGGTTTTTTAAGTGTGATA
Found at i:957922 original size:156 final size:150
Alignment explanation
Indices: 957613--957925 Score: 465
Period size: 156 Copynumber: 2.1 Consensus size: 150
957603 TTTCTAATTC
957613 ATAT-ATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTTTTTAAGTGTAATATT
1 ATATAATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTTTTTAAGTGTAATATT
957677 CGGGTCGAGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCAGTCGGGTTTAGGGTGAAAAAA
66 CGGGTCGAGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCAGTCGGGTTTAGGGTGAAAAAA
*
957742 TCGGACCGACCCGAAAATAT
131 CCGGACCGACCCGAAAATAT
957762 ATATAATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGATTTTTTAAGTGT
1 ATATAATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTC--G--GG--TTTTTAAGTGT
* * *
957827 GATATTCGGGTCGAGTC-GGTTGGGTTTTTCTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGG
60 AATATTCGGGTCGAGTCGGGTCGGGTTTTT-TAAGTGTGATATTCGGGTC-AG-TCGGGTTTAGG
957891 GTGAAAAAACCCGGACCGA-CCGAAAA-A-
122 GTGAAAAAA-CCGGACCGACCCGAAAATAT
957918 ATATAATT
1 ATATAATT
957926 TTACCTTATA
Statistics
Matches: 149, Mismatches: 4, Indels: 15
0.89 0.02 0.09
Matches are distributed among these distances:
149 4 0.03
150 40 0.27
152 1 0.01
154 2 0.01
155 11 0.07
156 54 0.36
157 2 0.01
158 27 0.18
159 8 0.05
ACGTcount: A:0.22, C:0.13, G:0.31, T:0.34
Consensus pattern (150 bp):
ATATAATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTTTTTAAGTGTAATATT
CGGGTCGAGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCAGTCGGGTTTAGGGTGAAAAAA
CCGGACCGACCCGAAAATAT
Found at i:971674 original size:16 final size:18
Alignment explanation
Indices: 971653--971685 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
971643 AAGAACGGGA
971653 GCAACC-AC-GAAACAAG
1 GCAACCAACAGAAACAAG
971669 GCAACCAACAGAAACAA
1 GCAACCAACAGAAACAA
971686 CAAACGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.55, C:0.30, G:0.15, T:0.00
Consensus pattern (18 bp):
GCAACCAACAGAAACAAG
Found at i:972537 original size:2 final size:2
Alignment explanation
Indices: 972530--972554 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
972520 TTTTTAAAAC
972530 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
972555 CCCCCATCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:972744 original size:24 final size:24
Alignment explanation
Indices: 972717--972816 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
972707 GATATCAAAA
*
972717 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
972741 ATCATAACAGAATCCAGTTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
** *
972765 ATCGGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
972789 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
972813 ATCA
1 ATCA
972817 GATAAAATAT
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 2 0.04
24 52 0.93
25 2 0.04
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:975318 original size:12 final size:13
Alignment explanation
Indices: 975286--975376 Score: 67
Period size: 13 Copynumber: 6.3 Consensus size: 13
975276 ATCCGTCAAC
*
975286 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
975301 GGTCAA-GGGTCG
1 GGTCAACGGGTCG
975313 GGTCAACGGGTCGGGTCG
1 GGTCAAC--G---GGTCG
975331 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
975344 GGTAAAGGTCGGGTCG
1 GGTCAA---CGGGTCG
975360 GGTCAACGGGTCG
1 GGTCAACGGGTCG
975373 GGTC
1 GGTC
975377 GGGTGTGACC
Statistics
Matches: 64, Mismatches: 3, Indels: 20
0.74 0.03 0.23
Matches are distributed among these distances:
12 6 0.09
13 21 0.33
14 5 0.08
15 7 0.11
16 13 0.20
18 12 0.19
ACGTcount: A:0.16, C:0.21, G:0.46, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:975325 original size:13 final size:13
Alignment explanation
Indices: 975324--975376 Score: 70
Period size: 13 Copynumber: 3.8 Consensus size: 13
975314 GTCAACGGGT
975324 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
975337 CGGGTCGGGTAAA
1 CGGGTCGGGTCAA
975350 GGTCGGGTCGGGTCAA
1 ---CGGGTCGGGTCAA
975366 CGGGTCGGGTC
1 CGGGTCGGGTC
975377 GGGTGTGACC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 23 0.66
16 12 0.34
ACGTcount: A:0.13, C:0.21, G:0.49, T:0.17
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:975330 original size:18 final size:17
Alignment explanation
Indices: 975292--975380 Score: 98
Period size: 18 Copynumber: 5.3 Consensus size: 17
975282 CAACGGTCAA
975292 CGGGTCAACGGTCAAGGGT
1 CGGGTCAACGGTC--GGGT
975311 CGGGTCAACGGGTCGGGT
1 CGGGTCAAC-GGTCGGGT
975329 CGGGTCAA----CGGGT
1 CGGGTCAACGGTCGGGT
*
975342 CGGGT-AAAGGTCGGGT
1 CGGGTCAACGGTCGGGT
975358 CGGGTCAACGGGTCGGGT
1 CGGGTCAAC-GGTCGGGT
975376 CGGGT
1 CGGGT
975381 GTGACCGGTC
Statistics
Matches: 62, Mismatches: 1, Indels: 15
0.79 0.01 0.19
Matches are distributed among these distances:
12 2 0.03
13 10 0.16
16 10 0.16
17 2 0.03
18 25 0.40
19 9 0.15
20 4 0.06
ACGTcount: A:0.15, C:0.20, G:0.48, T:0.17
Consensus pattern (17 bp):
CGGGTCAACGGTCGGGT
Found at i:975358 original size:29 final size:31
Alignment explanation
Indices: 975301--975376 Score: 122
Period size: 29 Copynumber: 2.5 Consensus size: 31
975291 ACGGGTCAAC
*
975301 GGTCAA-GGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACAGGTCGGGTCG
975331 GGTCAACGGGTCGGGT-AA-AGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACAGGTCGGGTCG
975360 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
975377 GGGTGTGACC
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
29 26 0.60
30 8 0.19
31 9 0.21
ACGTcount: A:0.14, C:0.20, G:0.49, T:0.17
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACAGGTCGGGTCG
Found at i:979329 original size:43 final size:42
Alignment explanation
Indices: 979265--979348 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 42
979255 GTCTTTGGAG
* ** * *
979265 AAGTTAGGAGTGAAATTTATCCTCTATATGTAAAGTTTTGTTA
1 AAGTTAAGAGTGAAAGCTATCC-CCATATATAAAGTTTTGTTA
*
979308 AAGTTAAGAGTGAAAGCTATCCCCATGTATAAAGTTTTGTT
1 AAGTTAAGAGTGAAAGCTATCCCCATATATAAAGTTTTGTT
979349 TGATGTACCA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
42 16 0.46
43 19 0.54
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (42 bp):
AAGTTAAGAGTGAAAGCTATCCCCATATATAAAGTTTTGTTA
Found at i:979458 original size:6 final size:7
Alignment explanation
Indices: 979428--979463 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
979418 CATACATTCA
979428 TTTGCAT
1 TTTGCAT
979435 TTTGCAT
1 TTTGCAT
979442 CTTTGCAT
1 -TTTGCAT
979450 TTT-CAT
1 TTTGCAT
979456 TTTGCAT
1 TTTGCAT
979463 T
1 T
979464 CGTACTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.22
7 14 0.52
8 7 0.26
ACGTcount: A:0.14, C:0.17, G:0.11, T:0.58
Consensus pattern (7 bp):
TTTGCAT
Found at i:979566 original size:20 final size:20
Alignment explanation
Indices: 979543--979580 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
979533 TTTCATGTAA
979543 ATTCACATATTTGCATTTGT
1 ATTCACATATTTGCATTTGT
* *
979563 ATTCGCATCTTTGCATTT
1 ATTCACATATTTGCATTT
979581 TTACATTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.11, T:0.50
Consensus pattern (20 bp):
ATTCACATATTTGCATTTGT
Found at i:981150 original size:22 final size:22
Alignment explanation
Indices: 981106--981150 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
981096 TTTAATCTTG
*
981106 AAATTTTTTTATCAAGTAGATT
1 AAATTTTTTTATCAAGAAGATT
*
981128 AAATATTTTTT-TCAAGAATATT
1 AAAT-TTTTTTATCAAGAAGATT
981150 A
1 A
981151 GATCTTTGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (22 bp):
AAATTTTTTTATCAAGAAGATT
Found at i:984397 original size:75 final size:75
Alignment explanation
Indices: 984307--984479 Score: 256
Period size: 75 Copynumber: 2.3 Consensus size: 75
984297 ATCAACAAGA
** *
984307 AGCAAATGTTGGGGCATGCTGAAAGCTTATTTCAATCAGAAATTGGAATATTGACACATTTTGAA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATAGGAATATTGACACATTTTGAA
*
984372 TGTTCGTATC
66 CGTTCGTATC
* *
984382 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATAGGAATGTTGACGCATTTTGAA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATAGGAATATTGACACATTTTGAA
* *
984447 CGTTTGTATT
66 CGTTCGTATC
* *
984457 AGCAAATATTGGGACATGCTGAA
1 AGCAAATGTTGGGGCATGCTGAA
984480 GACTCATACT
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 88 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (75 bp):
AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATAGGAATATTGACACATTTTGAA
CGTTCGTATC
Found at i:985828 original size:22 final size:22
Alignment explanation
Indices: 985803--985857 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
985793 ATCTACATTC
985803 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
985825 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
985847 TTCAAAAATGA
1 TTCAAAGATGA
985858 AAACTTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:986737 original size:115 final size:115
Alignment explanation
Indices: 986532--987128 Score: 701
Period size: 115 Copynumber: 5.0 Consensus size: 115
986522 CCCACATATG
* * * *
986532 TAAGACCTATAGTGCAGGATGTTTTCAAAAAGCATTCGGGAGCTTTTTGATATTTAAAACCTATG
1 TAAGACCTACAGTGCAGGATGTGTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCTG
*
986597 GGTCATCTGTAAGTCCTACAGTGCAAGATGATAAGACCTCAGGGCATCCA
66 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCATCCA
* *
986647 TAAGACCTACAGTGCAGGATGTGTTCAAAAAGCCTTCGGGTGCTTTTTGATATTTAAAGCCTCTG
1 TAAGACCTACAGTGCAGGATGTGTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCTG
* *
986712 GATCATCTGTAAGACCTACAATGCAAGATGATAAGACCTCAGGGCAATCCA
66 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC-ATCCA
* *
986763 TAAGACCTGCAGTGCAGGATGTGTTCAAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCA
1 TAAGACCTACAGTGCAGGATGTGTTC-AAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCT
* * *
986828 GGGTTATCTGTAAGACTTACAGTGCAAGATGATAAGATCTCAGGGCCATCCA
65 GGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGG-CATCCA
* * * ** ** * * *
986880 TAAGACCTCCAGTGCAGGATGTTTTCAAATGAGATTTTAAGAAACTGATTTTCAAAGGTTTCTTG
1 TAAGACCTACAGTGCAGGATGTGTTCAAA-AAG-CCTTCGGGAGCT--TTTT-----G----AT-
** * *
986945 ATCTTAAATATTTC-AGATCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATC
52 AT-TTAAA-ACCTCTGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGG-CATC
987009 CA
114 CA
*
987011 TAAGACCTATAGTGCAGGATGTGTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCTG
1 TAAGACCTACAGTGCAGGATGTGTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCTG
* * * * *
987076 GGTTATTTGTAAGACCTACAGTGCAAGATGATAAGACTTCAGGTCATTCA
66 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCATCCA
987126 TAA
1 TAA
987129 CCTTGGGCAG
Statistics
Matches: 407, Mismatches: 55, Indels: 40
0.81 0.11 0.08
Matches are distributed among these distances:
115 112 0.28
116 77 0.19
117 108 0.27
118 8 0.02
120 4 0.01
122 1 0.00
125 1 0.00
127 4 0.01
129 7 0.02
130 4 0.01
131 78 0.19
132 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (115 bp):
TAAGACCTACAGTGCAGGATGTGTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCTG
GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCATCCA
Found at i:986839 original size:117 final size:116
Alignment explanation
Indices: 986532--987118 Score: 703
Period size: 117 Copynumber: 4.9 Consensus size: 116
986522 CCCACATATG
* * *
986532 TAAGACCTATAGTGCAGGATGTTTTCAAAAAGCATTCGGGAGCTTTTTGATATTTAAAACCT-AT
1 TAAGACCTACAGTGCAGGATGTGTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCA-
*
986596 GGGTCATCTGTAAGTCCTACAGTGCAAGATGATAAGACCTCAGGG-CATCCA
65 GGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
* * *
986647 TAAGACCTACAGTGCAGGATGTGTTCAAAAAGCCTTCGGGTGCTTTTTGATATTTAAAGCCTCTG
1 TAAGACCTACAGTGCAGGATGTGTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCAG
* * *
986712 GATCATCTGTAAGACCTACAATGCAAGATGATAAGACCTCAGGGCAATCCA
66 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
*
986763 TAAGACCTGCAGTGCAGGATGTGTTCAAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCA
1 TAAGACCTACAGTGCAGGATGTGTTC-AAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCA
* * *
986828 GGGTTATCTGTAAGACTTACAGTGCAAGATGATAAGATCTCAGGGCCATCCA
65 GGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
* * * ** ** * * *
986880 TAAGACCTCCAGTGCAGGATGTTTTCAAATGAGATTTTAAGAAACTGATTTTCAAAGGTTTCTTG
1 TAAGACCTACAGTGCAGGATGTGTTCAAA-AAG-CCTTCGGGAGCT--TTTT-----G----AT-
** *
986945 ATCTTAAATATTTCA-GATCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATC
52 AT-TTAAA-ACCTCAGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATC
987009 CA
115 CA
* *
987011 TAAGACCTATAGTGCAGGATGTGTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCTG
1 TAAGACCTACAGTGCAGGATGTGTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCAG
* * *
987076 GGTTATTTGTAAGACCTACAGTGCAAGATGATAAGACTTCAGG
66 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGG
987119 TCATTCATAA
Statistics
Matches: 398, Mismatches: 54, Indels: 39
0.81 0.11 0.08
Matches are distributed among these distances:
115 102 0.26
116 77 0.19
117 109 0.27
118 7 0.02
120 4 0.01
122 1 0.00
125 1 0.00
127 4 0.01
129 7 0.02
130 4 0.01
131 78 0.20
132 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (116 bp):
TAAGACCTACAGTGCAGGATGTGTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCAG
GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
Found at i:987328 original size:3 final size:3
Alignment explanation
Indices: 987273--987319 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
987263 CATTTTACTT
*
987273 TTA TTA TTA TTA ATA -TA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
987319 T
1 T
987320 AAATTATTAC
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:987849 original size:85 final size:86
Alignment explanation
Indices: 987705--987876 Score: 321
Period size: 85 Copynumber: 2.0 Consensus size: 86
987695 AAAGAGAAGA
987705 CCACAGACAGCAACAGAAAAAAAACACAAACCAGCAGACAGAAACCAAACCATAGCAAAGACGAA
1 CCACAGACAGCAACAGAAAAAAAACACAAACCAGCAGACAGAAACCAAACCATAGCAAAGA-GAA
987770 TGATAGCAAG-ACGGGAACAAC
65 TGATAGCAAGAACGGGAACAAC
987791 CCACAGACAGCAACAGAAAAAAAACACAAA-CAGCAGACAGAAACCAAACCATAGCAAAGAGAAT
1 CCACAGACAGCAACAGAAAAAAAACACAAACCAGCAGACAGAAACCAAACCATAGCAAAGAGAAT
987855 GATAGCAAGAACGGGAACAAC
66 GATAGCAAGAACGGGAACAAC
987876 C
1 C
987877 ACGAAACAAG
Statistics
Matches: 85, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
84 13 0.15
85 42 0.49
86 30 0.35
ACGTcount: A:0.54, C:0.25, G:0.17, T:0.03
Consensus pattern (86 bp):
CCACAGACAGCAACAGAAAAAAAACACAAACCAGCAGACAGAAACCAAACCATAGCAAAGAGAAT
GATAGCAAGAACGGGAACAAC
Found at i:994908 original size:20 final size:20
Alignment explanation
Indices: 994883--994941 Score: 75
Period size: 22 Copynumber: 2.9 Consensus size: 20
994873 TAGGTAGCGC
994883 TTATATAATAAAATAGGCGA
1 TTATATAATAAAATAGGCGA
*
994903 TTATATAAT-AAATAGGTAGCGC
1 TTATATAATAAAATA-G--GCGA
994925 TTATATAATAAAATAGG
1 TTATATAATAAAATAGG
994942 TTAATTACTG
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 5 0.15
20 11 0.32
22 13 0.38
23 5 0.15
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.32
Consensus pattern (20 bp):
TTATATAATAAAATAGGCGA
Found at i:994910 original size:84 final size:84
Alignment explanation
Indices: 994692--994914 Score: 279
Period size: 84 Copynumber: 2.6 Consensus size: 84
994682 TATCAAGTAT
* *
994692 AATAACATATTAGGTACCACTTATATAATGTAATAGCTAGCGCTTATATAATAAAATATGTTAAT
1 AATAATATATTAGGTACCACTTATATAATGTAATAG---GCGATTATATAATAAAATATGTTAAT
*
994757 TACTGGAAACATTATCAAGCAC
63 TACTGGAAACATTATCAAACAC
** *
994779 AATAATATATTAGGTACCACTTATATAATGTAATA-GATATCACTATAATAAAATATGTTAATTA
1 AATAATATATTAGGTACCACTTATATAATGTAATAGGCGATTA-TATAATAAAATATGTTAATTA
* *
994843 -TCGTAAACATTATTAAACAC
65 CT-GGAAACATTATCAAACAC
* * **
994863 AATAATATATTAGGTAGCGCTTATATAATAAAATAGGCGATTATATAATAAA
1 AATAATATATTAGGTACCACTTATATAATGTAATAGGCGATTATATAATAAA
994915 TAGGTAGCGC
Statistics
Matches: 118, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
83 4 0.03
84 76 0.64
85 4 0.03
87 34 0.29
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (84 bp):
AATAATATATTAGGTACCACTTATATAATGTAATAGGCGATTATATAATAAAATATGTTAATTAC
TGGAAACATTATCAAACAC
Found at i:994942 original size:23 final size:23
Alignment explanation
Indices: 994864--994942 Score: 103
Period size: 23 Copynumber: 3.6 Consensus size: 23
994854 ATTAAACACA
* *
994864 ATAATATATTAGGTAGCGCTTAT
1 ATAATAAAATAGGTAGCGCTTAT
*
994887 ATAATAAAATA-G--GCGATTAT
1 ATAATAAAATAGGTAGCGCTTAT
994907 ATAAT-AAATAGGTAGCGCTTAT
1 ATAATAAAATAGGTAGCGCTTAT
994929 ATAATAAAATAGGT
1 ATAATAAAATAGGT
994943 TAATTACTGG
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
19 5 0.10
20 13 0.27
22 13 0.27
23 17 0.35
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.33
Consensus pattern (23 bp):
ATAATAAAATAGGTAGCGCTTAT
Found at i:995005 original size:23 final size:23
Alignment explanation
Indices: 994970--995029 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
994960 ATTAAGCACA
* *
994970 ATAATATATTAGGTACCGCTTAT
1 ATAATATAATAGGTACCACTTAT
* *
994993 ATAATGTAATAGGTATCACTTAT
1 ATAATATAATAGGTACCACTTAT
* *
995016 ATGATAAAATAGGT
1 ATAATATAATAGGT
995030 TAATTACTAG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (23 bp):
ATAATATAATAGGTACCACTTAT
Found at i:995017 original size:87 final size:87
Alignment explanation
Indices: 994903--995116 Score: 322
Period size: 87 Copynumber: 2.5 Consensus size: 87
994893 AAATAGGCGA
* * * * *
994903 TTATATAAT-AAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAATATTATTAAGC
1 TTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAAC
*
994967 ACAATAATATATTAGGTACCGC
66 ACAATAACATATTAGGTACCGC
* * *
994989 TTATATAATGTAATAGGTATCACTTATATGATAAAATAGGTTAATTACTAGAAACATTATCAAAC
1 TTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAAC
* *
995054 ACAATAACATATTAGGTATCGT
66 ACAATAACATATTAGGTACCGC
995076 TTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGT
1 TTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGT
995117 AACGCTTATA
Statistics
Matches: 113, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
86 9 0.08
87 104 0.92
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.35
Consensus pattern (87 bp):
TTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAAC
ACAATAACATATTAGGTACCGC
Found at i:995083 original size:23 final size:23
Alignment explanation
Indices: 995066--995156 Score: 137
Period size: 23 Copynumber: 4.0 Consensus size: 23
995056 AATAACATAT
* * **
995066 TAGGTATCGTTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
995089 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
*
995112 TAGGTAACGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
995135 TAGGTAGCGCTTATATAATAAA
1 TAGGTAGCGCTTATATAATAAA
995157 TAGATTAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 62 1.00
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:995212 original size:132 final size:133
Alignment explanation
Indices: 994970--995248 Score: 398
Period size: 132 Copynumber: 2.1 Consensus size: 133
994960 ATTAAGCACA
* * * ** * * *
994970 ATAATATATTAGGTACCGCTTATATAATGTAATAGGTATCACTTATATGATAAAATAGGTTAATT
1 ATAATAAAATAGGTAACGCTTATATAATAAAATAGGTAGCACTTATATAATAAAATAGATTAATT
* * ** * *
995035 ACTAGAAACATTATCAAACACAATAACATATTAGGTATCGTTTATATAATGTAATAGGTAGCGCT
66 ACTAGAAACATTATCAAACACAATAACATATTAGATACCACTTATATAATGTAATAGGTAACACT
995100 TAT
131 TAT
*
995103 ATAATAAAATAGGTAACGCTTATATAATAAAATAGGTAGCGCTTATATAAT-AAATAGATTAATT
1 ATAATAAAATAGGTAACGCTTATATAATAAAATAGGTAGCACTTATATAATAAAATAGATTAATT
* *
995167 ACTGGAAACATTATCAAGCACAATAACATATTAGATACCACTTATATAATGTAATAGGTAACACT
66 ACTAGAAACATTATCAAACACAATAACATATTAGATACCACTTATATAATGTAATAGGTAACACT
995232 TAT
131 TAT
995235 ATAATAAAATAGGT
1 ATAATAAAATAGGT
995249 TAATTACTAT
Statistics
Matches: 129, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
132 86 0.67
133 43 0.33
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (133 bp):
ATAATAAAATAGGTAACGCTTATATAATAAAATAGGTAGCACTTATATAATAAAATAGATTAATT
ACTAGAAACATTATCAAACACAATAACATATTAGATACCACTTATATAATGTAATAGGTAACACT
TAT
Found at i:995215 original size:23 final size:23
Alignment explanation
Indices: 995189--995238 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
995179 ATCAAGCACA
* *
995189 ATAACATATTAGATACCACTTAT
1 ATAACATAATAGATAACACTTAT
** *
995212 ATAATGTAATAGGTAACACTTAT
1 ATAACATAATAGATAACACTTAT
995235 ATAA
1 ATAA
995239 TAAAATAGGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.34
Consensus pattern (23 bp):
ATAACATAATAGATAACACTTAT
Found at i:995239 original size:23 final size:23
Alignment explanation
Indices: 995205--995248 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
995195 TATTAGATAC
**
995205 CACTTATATAATGTAATAGGTAA
1 CACTTATATAATAAAATAGGTAA
995228 CACTTATATAATAAAATAGGT
1 CACTTATATAATAAAATAGGT
995249 TAATTACTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.34
Consensus pattern (23 bp):
CACTTATATAATAAAATAGGTAA
Found at i:995249 original size:219 final size:217
Alignment explanation
Indices: 994864--995335 Score: 750
Period size: 219 Copynumber: 2.2 Consensus size: 217
994854 ATTAAACACA
* *
994864 ATAATATATTAGGTAGCGCTTATATAATAAAATAGG-CGATTATATAATAAATAGGTAGCGCTTA
1 ATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTCGATTATATAATAAATAGGTAGCGCTTA
* * * * * *
994928 TATAATAAAATAGGTTAATTACTGGAAATATTATTAAGCACAATAATATATTAGGTACCGCTTAT
66 TATAATAAAATAGATTAATTACTGGAAACATTATCAAGCACAATAACATATTAGATACCACTTAT
* *
994993 ATAATGTAATAGGTATCACTTATATGATAAAATAGGTTAATTACTAGAAACATTATCAAACACAA
131 ATAATGTAATAGGTAACACTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAACACAA
* *
995058 TAACATATTAGGTATCGTTTAT
196 TAACATATTAGGTAGCGCTTAT
*
995080 ATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTAACGCTTATATAATAAAATAGGTAGCGC
1 ATAATGTAATAGGTAGCGCTTATATAATAAAATAGGT--CGATTATATAAT-AAATAGGTAGCGC
995145 TTATATAAT-AAATAGATTAATTACTGGAAACATTATCAAGCACAATAACATATTAGATACCACT
63 TTATATAATAAAATAGATTAATTACTGGAAACATTATCAAGCACAATAACATATTAGATACCACT
* *
995209 TATATAATGTAATAGGTAACACTTATATAATAAAATAGGTTAATTACTATAAACATTATCAATCA
128 TATATAATGTAATAGGTAACACTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAACA
995274 CAATAACATATTAGGTAGCGCTTAT
193 CAATAACATATTAGGTAGCGCTTAT
* *
995299 ATAACGTAATAGGTAGCGTTTATATAATAAAATAGGT
1 ATAATGTAATAGGTAGCGCTTATATAATAAAATAGGT
995336 TAATTACTTA
Statistics
Matches: 235, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
216 34 0.14
219 179 0.76
220 22 0.09
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (217 bp):
ATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTCGATTATATAATAAATAGGTAGCGCTTA
TATAATAAAATAGATTAATTACTGGAAACATTATCAAGCACAATAACATATTAGATACCACTTAT
ATAATGTAATAGGTAACACTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAACACAA
TAACATATTAGGTAGCGCTTAT
Found at i:995276 original size:87 final size:87
Alignment explanation
Indices: 995121--995343 Score: 322
Period size: 87 Copynumber: 2.6 Consensus size: 87
995111 ATAGGTAACG
** * *
995121 CTTATATAATAAAATAGGTAGCGCTTATATAAT-AAATAGATTAATTACTGGAAACATTATCAAG
1 CTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAG
995185 CACAATAACATATTAGATACCA
66 CACAATAACATATTAGATACCA
* * * *
995207 CTTATATAATGTAATAGGTAACACTTATATAATAAAATAGGTTAATTACTATAAACATTATCAAT
1 CTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAG
* * *
995272 CACAATAACATATTAGGTAGCG
66 CACAATAACATATTAGATACCA
* *
995294 CTTATATAACGTAATAGGTAGCGTTTATATAATAAAATAGGTTAATTACT
1 CTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACT
995344 TAATTTGTTA
Statistics
Matches: 121, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
86 29 0.24
87 92 0.76
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (87 bp):
CTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAG
CACAATAACATATTAGATACCA
Found at i:995302 original size:23 final size:23
Alignment explanation
Indices: 995276--995335 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
995266 ATCAATCACA
*
995276 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
995299 ATAACGTAATAGGTAGCGTTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
995322 ATAATAAAATAGGT
1 ATAACATAATAGGT
995336 TAATTACTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:996320 original size:199 final size:196
Alignment explanation
Indices: 995911--996352 Score: 622
Period size: 199 Copynumber: 2.2 Consensus size: 196
995901 TTTAAAATAA
* * *
995911 ACATTGCAAATTTATCTATTACATTATAATTATCGGTTTTTTGATG-TTTTGGGATCGATACAAT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGG--TTTCGATGTTTTTGGGATCGATACAAT
* *
995975 TTTAAATGTATCAACACTTTGTGCGTGCACCTCGTTGGGCATTCATTTTGGAAAAAGTATCGACA
64 TTTAAATGTATCAACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGAAAAAGTATCGACA
* *
996040 CAAACTTAAAATGTGTCGATACATTATGTAGACCTATTTTCTCATAAAATCGGTATATTTATACT
129 C-AACTTAAAATGTGTCGATACATTATGTAGACCTATTCTCTCATAAAATCGGTATATTTATACC
996105 GAGT
193 GAGT
* * *
996109 ACATTGTAAATTTACCTTTTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATAC-TTTT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTT
* * *
996173 AATAAATGTATCGACACTTTATGTGTGCACCTCGTTTGGCATTCATTCTGGACAAAATGTATCGA
66 --TAAATGTATCAACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGA-AAAA-GTATCGA
* * *
996238 CAC-ATTTAAATTTGTGTCGATACATTATGTTGACCTATTCTCTCATAAAATCGGTATATTTATA
127 CACAACTTAAA-ATGTGTCGATACATTATGTAGACCTATTCTCTCATAAAATCGGTATATTTATA
996302 CCG-GTT
191 CCGAG-T
*
996308 ACATTGTAAATTTACCTATTATATTATAATTATCGGTTTCGATGT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGT
996353 AACATATGTG
Statistics
Matches: 218, Mismatches: 19, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
196 10 0.05
197 15 0.07
198 84 0.39
199 99 0.45
200 10 0.05
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (196 bp):
ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTT
TAAATGTATCAACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGAAAAAGTATCGACACA
ACTTAAAATGTGTCGATACATTATGTAGACCTATTCTCTCATAAAATCGGTATATTTATACCGAG
T
Found at i:996468 original size:31 final size:33
Alignment explanation
Indices: 996402--996468 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
996392 TGTGTTTCAC
*
996402 TATTCTCTCATTATAATATAATTAATGATATAT
1 TATTCTCTCATTATAATATAATAAATGATATAT
996435 TATTCT-T-ATTATAATAAATAATAAAT-ATA-AT
1 TATTCTCTCATTATAAT--ATAATAAATGATATAT
996466 TAT
1 TAT
996469 AATAATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
31 13 0.42
32 4 0.13
33 14 0.45
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (33 bp):
TATTCTCTCATTATAATATAATAAATGATATAT
Found at i:996480 original size:42 final size:42
Alignment explanation
Indices: 996416--996498 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
996406 CTCTCATTAT
* * *
996416 AATATAATTAATGATATATTATTCTTATTATAATA-AATAATA
1 AATATAATTAATAATATATTATT-TTAATAAAATATAATAATA
*
996458 AATATAATT-ATAATAATTTTATTTTAATAAAATATAATAAT
1 AATATAATTAATAAT-ATATTATTTTAATAAAATATAATAAT
996499 CATAATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
41 13 0.37
42 22 0.63
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (42 bp):
AATATAATTAATAATATATTATTTTAATAAAATATAATAATA
Found at i:996486 original size:36 final size:38
Alignment explanation
Indices: 996414--996495 Score: 93
Period size: 38 Copynumber: 2.3 Consensus size: 38
996404 TTCTCTCATT
*
996414 ATAATATAATTAATGATATATTATTCTTATTATAATAA
1 ATAATATAATTAATGATATATAATTCTTATTATAATAA
* *
996452 ATAATA-AATATAATTATA-ATAATT-TTATTTTAAT-A
1 ATAATATAAT-TAATGATATATAATTCTTATTATAATAA
996487 A-AATATAAT
1 ATAATATAAT
996496 AATCATAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
34 4 0.10
35 5 0.13
36 9 0.23
37 8 0.21
38 13 0.33
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (38 bp):
ATAATATAATTAATGATATATAATTCTTATTATAATAA
Found at i:996491 original size:30 final size:31
Alignment explanation
Indices: 996453--996547 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 31
996443 TTATAATAAA
996453 TAAT-AAATATAATTATAATAATTTTATT-T
1 TAATAAAATATAATTATAATAATTTTATTAT
* *
996482 TAATAAAATATAATAATCATAATTTT-TTAT
1 TAATAAAATATAATTATAATAATTTTATTAT
* * *
996512 TTATAAAATTATAGA-TATAAT-ATTTTAATAG
1 TAATAAAA-TATA-ATTATAATAATTTTATTAT
996543 TAATA
1 TAATA
996548 TTGACATAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
29 6 0.11
30 32 0.60
31 14 0.26
32 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (31 bp):
TAATAAAATATAATTATAATAATTTTATTAT
Found at i:996984 original size:32 final size:32
Alignment explanation
Indices: 996942--997003 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
996932 TATGCACAAT
* *
996942 AATAATAAAATCGGTACCACTTTTTTTTAGTC
1 AATAACAAAATCGGTACCACCTTTTTTTAGTC
*
996974 AATAACAAAATCGGTACCGCCTTTTTTTAG
1 AATAACAAAATCGGTACCACCTTTTTTTAG
997004 CCGTATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (32 bp):
AATAACAAAATCGGTACCACCTTTTTTTAGTC
Found at i:998210 original size:13 final size:13
Alignment explanation
Indices: 998192--998228 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
998182 AAGAAGGTTT
998192 AAATGAATTTGGA
1 AAATGAATTTGGA
998205 AAATGAATTTGGA
1 AAATGAATTTGGA
**
998218 GGATGAATTTG
1 AAATGAATTTG
998229 ATTTGACATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.32
Consensus pattern (13 bp):
AAATGAATTTGGA
Found at i:999633 original size:24 final size:23
Alignment explanation
Indices: 999582--999643 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 23
999572 CAATCTTATA
999582 TGGCACTAT-GGTGCATTTCTACG
1 TGGCACT-TCGGTGCATTTCTACG
*
999605 CGGCACTTCGGTGCATATTCTACG
1 TGGCACTTCGGTGCAT-TTCTACG
*
999629 TGGCACTACGGTGCA
1 TGGCACTTCGGTGCA
999644 AATTTATACG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.03
23 13 0.38
24 20 0.59
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:1003818 original size:2 final size:2
Alignment explanation
Indices: 1003811--1003840 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1003801 AGGCCTTTGA
1003811 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1003841 TCATAGATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1004980 original size:15 final size:15
Alignment explanation
Indices: 1004962--1004995 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1004952 TTAATATATT
1004962 AATAATA-AATACTAA
1 AATAATACAATA-TAA
1004977 AATAATACAATATAA
1 AATAATACAATATAA
1004992 AATA
1 AATA
1004996 CTAATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAATACAATATAA
Found at i:1010036 original size:60 final size:61
Alignment explanation
Indices: 1009921--1010041 Score: 147
Period size: 60 Copynumber: 2.0 Consensus size: 61
1009911 ATTATATATA
* * * * ** *
1009921 TTTAAATTATGATTTTTTATTTTAAATTGGTATTTTAATTTTTGAATGTTTTAATTTCATC
1 TTTAAATTATGATTTTTTATATAAAATTAGTACTTTAATTTTTGAACATTCTAATTTCATC
*
1009982 TTTAATTTATGA-TTTTTATATAAAATTAGT-CTTTAATTTTTAGAACATTCTAATTTCATC
1 TTTAAATTATGATTTTTTATATAAAATTAGTACTTTAATTTTT-GAACATTCTAATTTCATC
1010042 CTCAAACTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
59 10 0.20
60 30 0.59
61 11 0.22
ACGTcount: A:0.31, C:0.06, G:0.07, T:0.57
Consensus pattern (61 bp):
TTTAAATTATGATTTTTTATATAAAATTAGTACTTTAATTTTTGAACATTCTAATTTCATC
Found at i:1010196 original size:60 final size:60
Alignment explanation
Indices: 1010114--1010266 Score: 157
Period size: 60 Copynumber: 2.6 Consensus size: 60
1010104 CAAACTTTTG
* * * * * **
1010114 ATAG-TTTGAGATTAAATTGAAATGTTCAGAAGTCTGGA-GATTAATTTAGAATAAGGGTC
1 ATAGTTTTGGGATGAAATTGAAATATTCAAAAGT-TGGAGGACTAATTTAGAATAAAAGTC
* *
1010173 ATAGTTTTGGGATGAAATTGAAATATTTAAAAGTTTGAGGACTAATTTAGAATAAAAGTC
1 ATAGTTTTGGGATGAAATTGAAATATTCAAAAGTTGGAGGACTAATTTAGAATAAAAGTC
* * * * *
1010233 ATAATTTGGGGATGAAATTGGAACATTTAAAAGT
1 ATAGTTTTGGGATGAAATTGAAATATTCAAAAGT
1010267 ATAAGGATCA
Statistics
Matches: 79, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
59 7 0.09
60 72 0.91
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.34
Consensus pattern (60 bp):
ATAGTTTTGGGATGAAATTGAAATATTCAAAAGTTGGAGGACTAATTTAGAATAAAAGTC
Found at i:1010280 original size:60 final size:60
Alignment explanation
Indices: 1010155--1010286 Score: 176
Period size: 60 Copynumber: 2.2 Consensus size: 60
1010145 GTCTGGAGAT
** * * * * *
1010155 TAATTTAGAATAAGGGTCATAGTTTTGGGATGAAATTGAAATATTTAAAAGTTTGAGGAC
1 TAATTTAGAATAAAAGTCATAATTTGGGGATGAAATTGAAACATTTAAAAGTATAAGGAC
*
1010215 TAATTTAGAATAAAAGTCATAATTTGGGGATGAAATTGGAACATTTAAAAGTATAAGGA-
1 TAATTTAGAATAAAAGTCATAATTTGGGGATGAAATTGAAACATTTAAAAGTATAAGGAC
1010274 TCAATTTAGAATA
1 T-AATTTAGAATA
1010287 GGGATCATAG
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 1 0.02
60 62 0.98
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.33
Consensus pattern (60 bp):
TAATTTAGAATAAAAGTCATAATTTGGGGATGAAATTGAAACATTTAAAAGTATAAGGAC
Found at i:1020325 original size:168 final size:168
Alignment explanation
Indices: 1020129--1020467 Score: 532
Period size: 168 Copynumber: 2.0 Consensus size: 168
1020119 ACGCTTTTTT
1020129 TTCTGCAATATTTTATTTTTTTTATCATAA-TGGATTATGTAATAAGCTGATG-AGTTTT-AACT
1 TTCTGCAATA-TTTATTTTTTTTATCATAATTGGATTATGTAATAAGCTGATGAAGTTTTAAACT
1020191 TCTGCTGGTGTTGCTGTGGTCTGGTGCTGCTATTCGTAAAACACACCGTGCAG-TTATCTTGG-T
65 TCTGCTGGTGTTGCTGTGGTCT-G-G-TGCTATTCGT-AAACACACCGTGCAGTTTATCTTGGAT
1020254 GTTAAATACTACTCGGAGGGTTAATTTT-ATGCTAATTTTTGTGCTA
126 GTTAAA-A-TACTCGGAGGGTTAATTTTAATG--AATTTTTGTGCTA
1020300 TTCTGCAATA-TT-TTTTTTTTATCATAATTGGATTATGTAATAAGCTGATGAAGTTTTAAACTT
1 TTCTGCAATATTTATTTTTTTTATCATAATTGGATTATGTAATAAGCTGATGAAGTTTTAAACTT
1020363 CTGCTGGTGTTGCTGTGGTCTGGTGCTATTCGTAAACACACCGTGCAGTTTATCTTGGTATGTTA
66 CTGCTGGTGTTGCTGTGGTCTGGTGCTATTCGTAAACACACCGTGCAGTTTATCTTGG-ATGTTA
1020428 AAATACTCGGAGGGTTAATTTTAATGAATTTTTGTGCTA
130 AAATACTCGGAGGGTTAATTTTAATGAATTTTTGTGCTA
1020467 T
1 T
1020468 AAGGGATTGA
Statistics
Matches: 161, Mismatches: 0, Indels: 18
0.90 0.00 0.10
Matches are distributed among these distances:
167 29 0.18
168 53 0.33
169 29 0.18
170 14 0.09
171 36 0.22
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (168 bp):
TTCTGCAATATTTATTTTTTTTATCATAATTGGATTATGTAATAAGCTGATGAAGTTTTAAACTT
CTGCTGGTGTTGCTGTGGTCTGGTGCTATTCGTAAACACACCGTGCAGTTTATCTTGGATGTTAA
AATACTCGGAGGGTTAATTTTAATGAATTTTTGTGCTA
Found at i:1023066 original size:31 final size:31
Alignment explanation
Indices: 1023030--1023097 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 31
1023020 CAACGAGCTT
1023030 AACAAGCAAGCTTAACAAGTAACGAGTT-AGC
1 AACAAG-AAGCTTAACAAGTAACGAGTTAAGC
**
1023061 AACAAGTTGCTTAACAAGTAACGAGTTAAGC
1 AACAAGAAGCTTAACAAGTAACGAGTTAAGC
1023092 AACAAG
1 AACAAG
1023098 TTTTTTAACG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 19 0.56
31 15 0.44
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.18
Consensus pattern (31 bp):
AACAAGAAGCTTAACAAGTAACGAGTTAAGC
Found at i:1023074 original size:30 final size:31
Alignment explanation
Indices: 1023039--1023099 Score: 115
Period size: 30 Copynumber: 2.0 Consensus size: 31
1023029 TAACAAGCAA
1023039 GCTTAACAAGTAACGAGTT-AGCAACAAGTT
1 GCTTAACAAGTAACGAGTTAAGCAACAAGTT
1023069 GCTTAACAAGTAACGAGTTAAGCAACAAGTT
1 GCTTAACAAGTAACGAGTTAAGCAACAAGTT
1023100 TTTTAACGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (31 bp):
GCTTAACAAGTAACGAGTTAAGCAACAAGTT
Found at i:1027912 original size:31 final size:32
Alignment explanation
Indices: 1027855--1027918 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
1027845 AGTAACATTG
1027855 ATGAGAAAATGATGTATTGTTTATCAAATAAT
1 ATGAGAAAATGATGTATTGTTTATCAAATAAT
*
1027887 ATGAGGAAATGATGTATT-TTTATCAAATAAT
1 ATGAGAAAATGATGTATTGTTTATCAAATAAT
1027918 A
1 A
1027919 ATTATTACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 14 0.45
32 17 0.55
ACGTcount: A:0.44, C:0.03, G:0.16, T:0.38
Consensus pattern (32 bp):
ATGAGAAAATGATGTATTGTTTATCAAATAAT
Found at i:1029364 original size:64 final size:64
Alignment explanation
Indices: 1029263--1029391 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
1029253 GCCCCTCAAC
1029263 TCAGGTGGGATCACCACCCTCACATCATCAGTAGAATATGACACCCATTCAAACTAAAACAATA
1 TCAGGTGGGATCACCACCCTCACATCATCAGTAGAATATGACACCCATTCAAACTAAAACAATA
1029327 TCAGGTGGGATCACCACCCTCACATCATCAGTAGAATATGACACCCATTCAAACTAAAACAATA
1 TCAGGTGGGATCACCACCCTCACATCATCAGTAGAATATGACACCCATTCAAACTAAAACAATA
1029391 T
1 T
1029392 ATATAATTTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.39, C:0.28, G:0.12, T:0.21
Consensus pattern (64 bp):
TCAGGTGGGATCACCACCCTCACATCATCAGTAGAATATGACACCCATTCAAACTAAAACAATA
Found at i:1034359 original size:17 final size:17
Alignment explanation
Indices: 1034337--1034370 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1034327 CCAAGTGCGT
1034337 ACAATTTTACAGTACAC
1 ACAATTTTACAGTACAC
1034354 ACAATTTTACAGTACAC
1 ACAATTTTACAGTACAC
1034371 GCGTCTCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.29
Consensus pattern (17 bp):
ACAATTTTACAGTACAC
Found at i:1035922 original size:2 final size:2
Alignment explanation
Indices: 1035917--1035952 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1035907 GATTTTTTAA
1035917 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1035953 TTAGTTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1036931 original size:24 final size:23
Alignment explanation
Indices: 1036886--1036931 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1036876 TTTGCATTTT
*
1036886 TATTTTTGTTTCGTTGATGTTGA
1 TATTTTTGTTTCGTTGAGGTTGA
* *
1036909 TATTTTTTTTTTGTTGAAGGTTG
1 TATTTTTGTTTCGTTG-AGGTTG
1036932 CTGCAAAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.13, C:0.02, G:0.22, T:0.63
Consensus pattern (23 bp):
TATTTTTGTTTCGTTGAGGTTGA
Found at i:1048267 original size:5 final size:5
Alignment explanation
Indices: 1048257--1048288 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
1048247 AATGATTTGA
1048257 AGTCG AGTCG AGTCG AGTCG AGTCG AGTCG AG
1 AGTCG AGTCG AGTCG AGTCG AGTCG AGTCG AG
1048289 GAAGTGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.41, T:0.19
Consensus pattern (5 bp):
AGTCG
Found at i:1048596 original size:32 final size:32
Alignment explanation
Indices: 1048560--1048623 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
1048550 TATTTAATTG
1048560 TAAATATTTATAAAT-AATT-TAAATTTATTATT
1 TAAAT-TTT-TAAATCAATTATAAATTTATTATT
**
1048592 TAAATTTTTTTATCAATTATAAATTTATTATT
1 TAAATTTTTAAATCAATTATAAATTTATTATT
1048624 ATCGACTACC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 3 0.11
31 7 0.25
32 18 0.64
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (32 bp):
TAAATTTTTAAATCAATTATAAATTTATTATT
Found at i:1048700 original size:22 final size:22
Alignment explanation
Indices: 1048672--1048718 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1048662 AAATAACATA
*
1048672 GTGTATTTAGGTTTTTTTAAAC
1 GTGTATTTAGGGTTTTTTAAAC
1048694 GTGTATTTAGGGTTTTTTAAAC
1 GTGTATTTAGGGTTTTTTAAAC
1048716 GTG
1 GTG
1048719 GAGCTTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.04, G:0.23, T:0.51
Consensus pattern (22 bp):
GTGTATTTAGGGTTTTTTAAAC
Found at i:1049094 original size:79 final size:79
Alignment explanation
Indices: 1048963--1049125 Score: 281
Period size: 79 Copynumber: 2.1 Consensus size: 79
1048953 ACATTGAATG
*
1048963 ATATAAACAAGACAAATGAAACACAAAAACGTAGAGTTTTCATATTGAAAATTGAAACCGCTAAA
1 ATATAAACAAGACAAATGAAACACAAAAACGTAGAGTTTTCATATTGAAAATTGAAACCCCTAAA
1049028 TTACAAGAAGACAT
66 TTACAAGAAGACAT
* * *
1049042 ATATACACAAGATAAATGGAACACAAAAACGTAGAGTTTTCATATTGAAAATTGAAACCCCTAAA
1 ATATAAACAAGACAAATGAAACACAAAAACGTAGAGTTTTCATATTGAAAATTGAAACCCCTAAA
*
1049107 TTACAAGAAGATAT
66 TTACAAGAAGACAT
1049121 ATATA
1 ATATA
1049126 TATATATATA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.51, C:0.13, G:0.12, T:0.23
Consensus pattern (79 bp):
ATATAAACAAGACAAATGAAACACAAAAACGTAGAGTTTTCATATTGAAAATTGAAACCCCTAAA
TTACAAGAAGACAT
Found at i:1049124 original size:2 final size:2
Alignment explanation
Indices: 1049117--1049142 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1049107 TTACAAGAAG
1049117 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1049143 GGATGCGGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1052154 original size:18 final size:16
Alignment explanation
Indices: 1052122--1052156 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
1052112 TAATTTGTAG
1052122 AGAAAAAAAGAAGAAA
1 AGAAAAAAAGAAGAAA
1052138 AGAAAACAAATGAAGAAA
1 AGAAAA-AAA-GAAGAAA
1052156 A
1 A
1052157 AAAGGAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 3 0.18
18 8 0.47
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (16 bp):
AGAAAAAAAGAAGAAA
Found at i:1055139 original size:2 final size:2
Alignment explanation
Indices: 1055134--1055186 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1055124 TATATTTCAA
1055134 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1055176 AT AT AT A- AT AT
1 AT AT AT AT AT AT
1055187 TAATAAATCC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1055190 original size:6 final size:7
Alignment explanation
Indices: 1055133--1055191 Score: 63
Period size: 6 Copynumber: 8.6 Consensus size: 7
1055123 ATATATTTCA
1055133 AATATAT
1 AATATAT
1055140 -ATATAT
1 AATATAT
1055146 -ATATAT
1 AATATAT
1055152 -ATATAT
1 AATATAT
1055158 ATATATAT
1 A-ATATAT
1055166 ATATATAT
1 A-ATATAT
1055174 ATATATAT
1 A-ATATAT
1055182 AATAT-T
1 AATATAT
1055188 AATA
1 AATA
1055192 AATCCAAGAA
Statistics
Matches: 50, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
6 23 0.46
7 4 0.08
8 23 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
AATATAT
Found at i:1055639 original size:27 final size:26
Alignment explanation
Indices: 1055592--1055649 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
1055582 AAAATAAAGT
* *
1055592 TAATAAACGTATAGAACAAAATATAA
1 TAATAAACGTATAGAACAAAAAAGAA
*
1055618 TAATAAA-GTATAGTAAATAAAAAAGAA
1 TAATAAACGTATAG--AACAAAAAAGAA
1055645 TAATA
1 TAATA
1055650 CATTTACATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 6 0.22
26 7 0.26
27 14 0.52
ACGTcount: A:0.64, C:0.03, G:0.09, T:0.24
Consensus pattern (26 bp):
TAATAAACGTATAGAACAAAAAAGAA
Found at i:1055693 original size:17 final size:17
Alignment explanation
Indices: 1055671--1055705 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1055661 CTATGTATAA
* *
1055671 ATAATGACATGTAATAT
1 ATAATGAAATATAATAT
1055688 ATAATGAAATATAATAT
1 ATAATGAAATATAATAT
1055705 A
1 A
1055706 AATAATAATA
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:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (17 bp):
ATAATGAAATATAATAT
Found at i:1055976 original size:19 final size:21
Alignment explanation
Indices: 1055934--1055979 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
1055924 ATATTTATAT
1055934 AAAAGAATAATAAGATACTAAA
1 AAAAGAATAATAAGATAC-AAA
*
1055956 AAAAGTATAATAA-ATACAAA
1 AAAAGAATAATAAGATACAAA
1055976 AAAA
1 AAAA
1055980 CGGAAAGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.30
21 4 0.17
22 12 0.52
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.17
Consensus pattern (21 bp):
AAAAGAATAATAAGATACAAA
Found at i:1057772 original size:106 final size:106
Alignment explanation
Indices: 1057588--1058264 Score: 1036
Period size: 106 Copynumber: 6.4 Consensus size: 106
1057578 GTATTGTTCC
* * * * * * * * * * *
1057588 GAGTCCAATATCCTCCGCTGTGACGTTGGAACTGGTTCTGGAACTGGGAA-ATTGCTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGA-TGTTTATTGACA
* * *
1057652 ACCGGCGGTCCCTTCGTCGTGAAGTCGACCTTACGTTGTCTTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC-TG
* * **
1057695 GAGTCCAATATCCTTCGTTGGGAAGTTGAAATTGGCTCTGAAATGGAGAA-ATGTTTGGTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGATGTTTATTGACAA
*
1057759 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* *
1057800 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGATGTTTATTGACAA
1057865 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
*
1057906 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGATGTTTATTGACAA
* *
1057971 CCAGCGGTCTCTTCGTCTTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
1058012 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGA-TGTTTATTGACA
* *
1058076 ACCAGCGGTCCCTTCGTCTTAAAGTTGAACTTACGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* *
1058118 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGATGTTTATTGACAA
*
1058183 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
*
1058224 GAGTCCAATATCCTTCGTTGTGAAGTTGAGATTGGCTCTGA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
1058265 GTAAAACCTG
Statistics
Matches: 531, Mismatches: 36, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
105 49 0.09
106 442 0.83
107 40 0.08
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGATGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
Found at i:1068543 original size:10 final size:10
Alignment explanation
Indices: 1068518--1068551 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1068508 AAGGTTAGTA
*
1068518 AAATAGAAAT
1 AAATAAAAAT
*
1068528 AGATAAAAAT
1 AAATAAAAAT
1068538 AAATAAAAAT
1 AAATAAAAAT
1068548 AAAT
1 AAAT
1068552 GGTAAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:1069531 original size:2 final size:2
Alignment explanation
Indices: 1069526--1069598 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
1069516 ATATTTCAAA
1069526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1069568 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1069599 TAATAAATCC
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 69 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1070053 original size:27 final size:26
Alignment explanation
Indices: 1070006--1070063 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
1069996 AAAATAAAGT
* *
1070006 TAATAAACGTATAGAACAAAATATAA
1 TAATAAACGTATAGAACAAAAAAGAA
*
1070032 TAATAAA-GTATAGTAAATAAAAAAGAA
1 TAATAAACGTATAG--AACAAAAAAGAA
1070059 TAATA
1 TAATA
1070064 CATTTACATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 6 0.22
26 7 0.26
27 14 0.52
ACGTcount: A:0.64, C:0.03, G:0.09, T:0.24
Consensus pattern (26 bp):
TAATAAACGTATAGAACAAAAAAGAA
Found at i:1070126 original size:19 final size:19
Alignment explanation
Indices: 1070080--1070129 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
1070070 CATATCTATG
* * *
1070080 TATAAATAATGACATGTAA
1 TATAAATAATAAAATATAA
1070099 TAT--ATAATAAAATATAA
1 TATAAATAATAAAATATAA
1070116 TATAAATAATAAAA
1 TATAAATAATAAAA
1070130 CAAGGTAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 14 0.54
19 12 0.46
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (19 bp):
TATAAATAATAAAATATAA
Found at i:1070388 original size:19 final size:21
Alignment explanation
Indices: 1070346--1070391 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
1070336 ATATTTATAT
1070346 AAAAGAATAATAAGATACTAAA
1 AAAAGAATAATAAGATAC-AAA
*
1070368 AAAAGTATAATAA-ATACAAA
1 AAAAGAATAATAAGATACAAA
1070388 AAAA
1 AAAA
1070392 CGGAAAGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.30
21 4 0.17
22 12 0.52
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.17
Consensus pattern (21 bp):
AAAAGAATAATAAGATACAAA
Found at i:1071793 original size:11 final size:11
Alignment explanation
Indices: 1071779--1071805 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1071769 TTAAGATTAA
1071779 ATTTAAAAAAT
1 ATTTAAAAAAT
1071790 ATTTAAAAAAT
1 ATTTAAAAAAT
1071801 ATTTA
1 ATTTA
1071806 CTTTTATCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATTTAAAAAAT
Found at i:1079908 original size:46 final size:46
Alignment explanation
Indices: 1079855--1079946 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
1079845 ACGTTTTTTC
1079855 AAATAAAATTTAATTAATCATTAATTTTTATACAAAGATACAATTT
1 AAATAAAATTTAATTAATCATTAATTTTTATACAAAGATACAATTT
*
1079901 AAATAAAATTTAATTAATCATTAATTTTTATACAAAGATATAATTT
1 AAATAAAATTTAATTAATCATTAATTTTTATACAAAGATACAATTT
1079947 GATCCATGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.42
Consensus pattern (46 bp):
AAATAAAATTTAATTAATCATTAATTTTTATACAAAGATACAATTT
Found at i:1085210 original size:59 final size:60
Alignment explanation
Indices: 1085147--1085280 Score: 150
Period size: 60 Copynumber: 2.2 Consensus size: 60
1085137 TTTTTTATGG
* * *
1085147 TTAAAATTTATAAAAAGGTCA-TCCGATTA-TAGGTCGAT-ATTTTGTTGAGTCTCTG-ACTA
1 TTAAAAGTTATAAAAAGGTCACT-CGATTACAAGG-CGATGATTTTATTGAGTCTC-GAACTA
* * *
1085206 TTAAAAGTTATAAGACGGTCACTCGATTACAAGGCGATGTTTTTATTGAGTCTCGAACTA
1 TTAAAAGTTATAAAAAGGTCACTCGATTACAAGGCGATGATTTTATTGAGTCTCGAACTA
*
1085266 TTAAAAGTTACAAAA
1 TTAAAAGTTATAAAA
1085281 TGGCCACTTC
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
59 29 0.46
60 34 0.54
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (60 bp):
TTAAAAGTTATAAAAAGGTCACTCGATTACAAGGCGATGATTTTATTGAGTCTCGAACTA
Found at i:1090088 original size:60 final size:60
Alignment explanation
Indices: 1090015--1090153 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 60
1090005 TCCTTATTTT
* ** * * * * *
1090015 AATTATTCCTTAAACTTTTAAATGTTTCATTTTTATTCTCAAACTATGA-CTATGATTCTA
1 AATTAGTCCTTAAACTTTTAAACATTTCAATTTCATCCCCAAACTATGACCT-TCATTCTA
* *
1090075 AATTAGTCTTTAAACTTTTTAACATTTCAATTTCATCCCCAAACTATGACCTTCATTCTA
1 AATTAGTCCTTAAACTTTTAAACATTTCAATTTCATCCCCAAACTATGACCTTCATTCTA
*
1090135 AATTAGTCCCTAAACTTTT
1 AATTAGTCCTTAAACTTTT
1090154 TTGAACATTC
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 64 0.97
61 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (60 bp):
AATTAGTCCTTAAACTTTTAAACATTTCAATTTCATCCCCAAACTATGACCTTCATTCTA
Found at i:1090154 original size:60 final size:62
Alignment explanation
Indices: 1090054--1090175 Score: 169
Period size: 60 Copynumber: 2.0 Consensus size: 62
1090044 TTTTTATTCT
* ** *
1090054 CAAACTATGACTATGATTCTAAATTAGTCTTTAAAC-TTTTT-AACATTTCAATTTCATCCC
1 CAAACTATGACTATCATTCTAAATTAGTCCCTAAACTTTTTTGAACATTCCAATTTCATCCC
*
1090114 CAAACTATGACCT-TCATTCTAAATTAGTCCCTAAACTTTTTTGAACATTCCGATTTCATCCC
1 CAAACTATGA-CTATCATTCTAAATTAGTCCCTAAACTTTTTTGAACATTCCAATTTCATCCC
1090176 AAGTTATATG
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
60 30 0.56
61 7 0.13
62 17 0.31
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (62 bp):
CAAACTATGACTATCATTCTAAATTAGTCCCTAAACTTTTTTGAACATTCCAATTTCATCCC
Found at i:1091766 original size:17 final size:17
Alignment explanation
Indices: 1091725--1091769 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1091715 CCATACTTGA
1091725 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** **
1091742 TTTTATATTTTTTAAAT
1 TTAAATATTTAATAAAT
1091759 TTAAATATTTA
1 TTAAATATTTA
1091770 TTTTTACATA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:1100403 original size:36 final size:37
Alignment explanation
Indices: 1100338--1100420 Score: 98
Period size: 36 Copynumber: 2.2 Consensus size: 37
1100328 AACAAGTTGA
*
1100338 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAA-ATTTATATATTTTCTTTAAAAAATTTAAAAT-AT
* * *
1100377 -AAAATTTATA-ATTTTTTTTTACAAATTTAAAATAT
1 AAAAATTTATATATTTTCTTTAAAAAATTTAAAATAT
1100412 AAAAATTTA
1 AAAAATTTA
1100421 AAAGAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
35 2 0.05
36 27 0.69
37 7 0.18
38 3 0.08
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (37 bp):
AAAAATTTATATATTTTCTTTAAAAAATTTAAAATAT
Found at i:1111243 original size:20 final size:20
Alignment explanation
Indices: 1111170--1111531 Score: 273
Period size: 20 Copynumber: 18.5 Consensus size: 20
1111160 GCGATTTTCC
* **
1111170 AAATCGCAACGCGAATATG-
1 AAATCGCAACGCGTATCCGT
* *
1111189 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1111209 AAATCGCAAACGCGTATCCGT
1 AAATCGC-AACGCGTATCCGT
1111230 AAATCGCAACGCGTATCC--
1 AAATCGCAACGCGTATCCGT
* ** * *
1111248 --ATTG---CGATTTTCC-A
1 AAATCGCAACGCGTATCCGT
* ** *
1111262 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1111282 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1111302 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
1111322 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* **
1111342 AAATCGCAACGCATATGGGT
1 AAATCGCAACGCGTATCCGT
*
1111362 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1111382 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1111402 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
* *
1111422 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGTATCCGT
*
1111442 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1111462 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1111482 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1111502 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1111522 AAATCACAAC
1 AAATCGCAAC
1111532 ACTGAAATTT
Statistics
Matches: 276, Mismatches: 50, Indels: 33
0.77 0.14 0.09
Matches are distributed among these distances:
13 6 0.02
16 6 0.02
18 1 0.00
19 17 0.06
20 227 0.82
21 17 0.06
22 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1111278 original size:92 final size:91
Alignment explanation
Indices: 1111156--1111339 Score: 343
Period size: 92 Copynumber: 2.0 Consensus size: 91
1111146 TACAAATTCG
1111156 CATTGCGATTTTCCAAATCGCAACGCGAATATG-AAATCGCAACGCGAACACATAAATCGCAAAC
1 CATTGCGATTTTCCAAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGC-AAC
1111220 GCGTATCCGTAAATCGCAACGCGTATC
65 GCGTATCCGTAAATCGCAACGCGTATC
1111247 CATTGCGATTTTCCAAAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAAC
1 CATTGCGATTTTCC-AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAAC
1111312 GCGTATCCGTAAATCGCAACGCGTATC
65 GCGTATCCGTAAATCGCAACGCGTATC
1111339 C
1 C
1111340 GTAAATCGCA
Statistics
Matches: 91, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
91 14 0.15
92 50 0.55
93 27 0.30
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.20
Consensus pattern (91 bp):
CATTGCGATTTTCCAAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACG
CGTATCCGTAAATCGCAACGCGTATC
Found at i:1112450 original size:12 final size:12
Alignment explanation
Indices: 1112433--1112457 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1112423 ATATAATCCT
1112433 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1112445 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1112457 G
1 G
1112458 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1114811 original size:19 final size:19
Alignment explanation
Indices: 1114771--1114868 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1114761 GATTCTCTCG
1114771 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1114791 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1114810 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1114824 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1114843 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1114862 TTGCGAT
1 TTGCGAT
1114869 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1114865 original size:52 final size:53
Alignment explanation
Indices: 1114752--1114868 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
1114742 CGAAATGAAA
1114752 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1114805 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1114857 TCGCATTGCGAT
1 TCGCATTGCGAT
1114869 AGTCAATTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1114975 original size:31 final size:32
Alignment explanation
Indices: 1114927--1115016 Score: 146
Period size: 33 Copynumber: 2.8 Consensus size: 32
1114917 CCATTACATT
1114927 TCGCAATGCGGAAATGAAAATCGCAAC-GAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACAGAGAA
1114959 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAAC-AGAGAA
*
1114992 TCGCAATGCGAAATGAAAATTGCAA
1 TCGCAATGCGAAATGAAAATCGCAA
1115017 TGCGAAATGA
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
31 17 0.31
32 9 0.16
33 29 0.53
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.14
Consensus pattern (32 bp):
TCGCAATGCGAAATGAAAATCGCAACAGAGAA
Found at i:1114981 original size:19 final size:19
Alignment explanation
Indices: 1114927--1115073 Score: 121
Period size: 19 Copynumber: 8.6 Consensus size: 19
1114917 CCATTACATT
1114927 TCGCAATGCGGAAATGAAAA
1 TCGCAATGC-GAAATGAAAA
1114947 TCGCAA--CG--A-G--AA
1 TCGCAATGCGAAATGAAAA
1114959 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
1114978 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
1114992 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
1115011 TTGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
1115030 TCGCAA--CG--A-GATAA
1 TCGCAATGCGAAATGAAAA
*
1115044 TCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAA
*
1115063 TCGCATTGCGA
1 TCGCAATGCGA
1115074 TTCTCCCATT
Statistics
Matches: 102, Mismatches: 8, Indels: 35
0.70 0.06 0.24
Matches are distributed among these distances:
12 8 0.08
14 23 0.23
15 3 0.03
16 5 0.05
17 6 0.06
18 3 0.03
19 48 0.47
20 6 0.06
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:1115022 original size:52 final size:52
Alignment explanation
Indices: 1114957--1115073 Score: 198
Period size: 52 Copynumber: 2.2 Consensus size: 52
1114947 TCGCAACGAG
1114957 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
* * *
1115009 AATTGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
1115061 AATCGCATTGCGA
1 AATCGCAATGCGA
1115074 TTCTCCCATT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.17
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:1115122 original size:19 final size:19
Alignment explanation
Indices: 1115080--1115179 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
1115070 GCGATTCTCC
1115080 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
1115100 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
1115119 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
1115135 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
1115152 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
1115171 CATTGCGAT
1 CATTGCGAT
1115180 AGTCACTTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.49
20 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:1115176 original size:52 final size:53
Alignment explanation
Indices: 1115063--1115179 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
1115053 GAAATTAAAA
1115063 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* *
1115116 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1115168 TCGCATTGCGAT
1 TCGCATTGCGAT
1115180 AGTCACTTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1117309 original size:14 final size:14
Alignment explanation
Indices: 1117290--1117346 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1117280 GCGAAATGAA
*
1117290 AATCGCAACGACAG
1 AATCGCAACGAAAG
1117304 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1117321 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1117337 AATCGCAACG
1 AATCGCAACG
1117347 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1117317 original size:33 final size:33
Alignment explanation
Indices: 1117271--1117363 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1117261 GCGAAACCAA
*
1117271 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1117304 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1117337 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1117364 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1117328 original size:19 final size:19
Alignment explanation
Indices: 1117234--1117368 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1117224 TAGTTTACTT
* *
1117234 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1117254 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1117273 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1117292 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1117306 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1117325 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1117339 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1117358 TCGCAATGCGA
1 TCGCAACGCGA
1117369 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Done.