Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold332
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: 2744988
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 17
Found at i:1026500 original size:5 final size:5
Alignment explanation
Indices: 1026479--1026518 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
1026469 TGTTCATATC
1026479 TTTTA TTGTTA -TTTA TTTTA TTTTA TTTTA TTTTTA TTTT
1 TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTT
1026519 TTTAGGTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 3 0.09
5 21 0.66
6 8 0.25
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:1027166 original size:11 final size:11
Alignment explanation
Indices: 1027150--1027194 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
1027140 TGGCAATTGG
*
1027150 AAAAAAA-AAT
1 AAAAAAAGAAA
*
1027160 AAAAAAATAAA
1 AAAAAAAGAAA
1027171 AAGAAAAAGAAA
1 AA-AAAAAGAAA
1027183 AAAAAAAGAAA
1 AAAAAAAGAAA
1027194 A
1 A
1027195 GTGAAGATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
10 7 0.23
11 14 0.45
12 10 0.32
ACGTcount: A:0.89, C:0.00, G:0.07, T:0.04
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:1027171 original size:6 final size:6
Alignment explanation
Indices: 1027149--1027194 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
1027139 ATGGCAATTG
* *
1027149 GAAAAA -AAAATA AAAAAA TAAAAA GAAAAA GAAAAA -AAAAA GAAAA
1 GAAAAA GAAAA-A GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
1027195 GTGAAGATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 9 0.26
6 22 0.63
7 4 0.11
ACGTcount: A:0.87, C:0.00, G:0.09, T:0.04
Consensus pattern (6 bp):
GAAAAA
Found at i:1033089 original size:4 final size:4
Alignment explanation
Indices: 1033075--1033123 Score: 50
Period size: 4 Copynumber: 13.0 Consensus size: 4
1033065 AGAAAAAAGG
* * *
1033075 GAAA AAAA GAAA GAAG GAAA G-AA -AAA GAGA GAAA GAAA G-AA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1033120 GAAA
1 GAAA
1033124 AAAAAGAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
3 7 0.19
4 29 0.81
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:1033126 original size:26 final size:26
Alignment explanation
Indices: 1033078--1033135 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
1033068 AAAAAGGGAA
*
1033078 AAAAAGAAAGAAGGAAAGAAAAAGAG
1 AAAAAGAAAGAAGGAAAGAAAAAAAG
*
1033104 AGAAAGAAAGAA-GAAAGAAAAAAAAG
1 AAAAAGAAAGAAGGAAAG-AAAAAAAG
1033130 AAAAAG
1 AAAAAG
1033136 GGGTGGCCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 5 0.18
26 23 0.82
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (26 bp):
AAAAAGAAAGAAGGAAAGAAAAAAAG
Found at i:1033403 original size:13 final size:13
Alignment explanation
Indices: 1033385--1033409 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1033375 TGGATTTGAG
1033385 TTATTTTATTTTA
1 TTATTTTATTTTA
1033398 TTATTTTATTTT
1 TTATTTTATTTT
1033410 TGTTTAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:1038951 original size:215 final size:214
Alignment explanation
Indices: 1038574--1039005 Score: 837
Period size: 215 Copynumber: 2.0 Consensus size: 214
1038564 TTTCCTATTT
1038574 TTGTTCCTTTTTCTCTCTTTTTTTCTATCTTTCTTTCCCCACTTGCTAAAGCTTTCTTTTGAAAT
1 TTGTTCCTTTTTCTCTCTTTTTTTCTATCTTTCTTTCCCCACTTGCTAAAGCTTTCTTTTGAAAT
*
1038639 AACCTTCCCCTACTTATAGGGGAAGGAATTGACCAAGGCTGAAGCAAATCAGCCTTAGCCGATTG
66 AACCTTCCCCTACTTATAGGGGAAGGAATTGACCAAGGCTGAAGCAAATCAACCTTAGCCGATTG
1038704 TCTCTAGTGTTTTCCGCAAATTTCTATTTTTTTTTTTGCCTTTTAGCTTGATTTTTTCATGCCAT
131 TCTCTAGTGTTTTCCGCAAATTTC-ATTTTTTTTTTTGCCTTTTAGCTTGATTTTTTCATGCCAT
1038769 TTATTGATGCATTAAATGAA
195 TTATTGATGCATTAAATGAA
1038789 TTGTTCCTTTTTCTCTCTTTTTTTCTATCTTTCTTTCCCCACTTGCTAAAGCTTTCTTTTGAAAT
1 TTGTTCCTTTTTCTCTCTTTTTTTCTATCTTTCTTTCCCCACTTGCTAAAGCTTTCTTTTGAAAT
1038854 AACCTTCCCCTACTTATAGGGGAAGGAATTGACCAAGGCTGAAGCAAATCAACCTTAGCCGATTG
66 AACCTTCCCCTACTTATAGGGGAAGGAATTGACCAAGGCTGAAGCAAATCAACCTTAGCCGATTG
*
1038919 TCTCTAGTGTTTTCCGCAAATTTCTTTTTTTTTTTTGCCTTTTAGCTTGATTTTTTCATGCCATT
131 TCTCTAGTGTTTTCCGCAAATTTCATTTTTTTTTTTGCCTTTTAGCTTGATTTTTTCATGCCATT
1038984 TATTGATGCATTAAATGAA
196 TATTGATGCATTAAATGAA
1039003 TTG
1 TTG
1039006 GCCAGCTTAC
Statistics
Matches: 215, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
214 62 0.29
215 153 0.71
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (214 bp):
TTGTTCCTTTTTCTCTCTTTTTTTCTATCTTTCTTTCCCCACTTGCTAAAGCTTTCTTTTGAAAT
AACCTTCCCCTACTTATAGGGGAAGGAATTGACCAAGGCTGAAGCAAATCAACCTTAGCCGATTG
TCTCTAGTGTTTTCCGCAAATTTCATTTTTTTTTTTGCCTTTTAGCTTGATTTTTTCATGCCATT
TATTGATGCATTAAATGAA
Found at i:1039288 original size:21 final size:21
Alignment explanation
Indices: 1039263--1039320 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
1039253 CCATATTTCG
1039263 AAAATAGAAAAATTTCAAGAA
1 AAAATAGAAAAATTTCAAGAA
*
1039284 AAAATA-AAAAA-TTCATGAA
1 AAAATAGAAAAATTTCAAGAA
*
1039303 ATAAA-AGGAAAATTTCAA
1 A-AAATAGAAAAATTTCAA
1039321 AACTAATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 9 0.29
20 12 0.39
21 10 0.32
ACGTcount: A:0.66, C:0.05, G:0.09, T:0.21
Consensus pattern (21 bp):
AAAATAGAAAAATTTCAAGAA
Found at i:1040418 original size:42 final size:42
Alignment explanation
Indices: 1040371--1040517 Score: 145
Period size: 42 Copynumber: 3.5 Consensus size: 42
1040361 AGACTAAGCT
* **
1040371 GACAAGTAAACAAAGGATAAAGAAGTTAACTAAGATTGAACC
1 GACAAGTAAACAAAGGATAAAGAAGTTAAATGGGATTGAACC
* * * ** *
1040413 GACAAGTAAACAAA-GATAAA-AGGATTTAGTCGGGGCTAAACC
1 GACAAGTAAACAAAGGATAAAGAAG-TTAAAT-GGGATTGAACC
* * *
1040455 GATAGGTAAACAAAGGATAAAGAACTTAAATGGGATTGAACC
1 GACAAGTAAACAAAGGATAAAGAAGTTAAATGGGATTGAACC
*
1040497 GACAAGTCAACAAAGGATAAA
1 GACAAGTAAACAAAGGATAAA
1040518 AGGATTAACC
Statistics
Matches: 81, Mismatches: 20, Indels: 8
0.74 0.18 0.07
Matches are distributed among these distances:
40 2 0.02
41 10 0.12
42 58 0.72
43 10 0.12
44 1 0.01
ACGTcount: A:0.50, C:0.12, G:0.22, T:0.16
Consensus pattern (42 bp):
GACAAGTAAACAAAGGATAAAGAAGTTAAATGGGATTGAACC
Found at i:1040476 original size:84 final size:85
Alignment explanation
Indices: 1040376--1040639 Score: 257
Period size: 85 Copynumber: 3.1 Consensus size: 85
1040366 AAGCTGACAA
* *
1040376 GTAAACAAAGGATAAAGAAGTTAACTAAGATTGAACCGACAAGTAAACAAA-GATAAAAGGATTT
1 GTAAACAAAGGATAAAGAAGTTAAATAAGATTGAACCGACAAGTAAACAAAGGATAAAAGGATTA
* * *
1040440 A-GTCGGGGCTAAACCGATAG
66 ACCT-AGGACTAAACCGATAG
* ** *
1040460 GTAAACAAAGGATAAAGAACTTAAATGGGATTGAACCGACAAGTCAACAAAGGATAAAAGGATTA
1 GTAAACAAAGGATAAAGAAGTTAAATAAGATTGAACCGACAAGTAAACAAAGGATAAAAGGATTA
* *
1040525 ACCTAGGACTAAGCCGATTG
66 ACCTAGGACTAAACCGATAG
* * * * * * * * *
1040545 GTAAACAAAGGATAAAAAAGTT-GATCGAGACTAAACTGATAAGTCAACAAAGGATAAAAGAATT
1 GTAAACAAAGGATAAAGAAGTTAAAT-AAGATTGAACCGACAAGTAAACAAAGGATAAAAGGATT
* * *
1040609 TACTTAGGACTAAGA-TGATAG
65 AACCTAGGACTAA-ACCGATAG
*
1040630 GTAAAGAAAG
1 GTAAACAAAG
1040640 TTGACCGAAA
Statistics
Matches: 150, Mismatches: 26, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
84 48 0.32
85 101 0.67
86 1 0.01
ACGTcount: A:0.48, C:0.11, G:0.22, T:0.19
Consensus pattern (85 bp):
GTAAACAAAGGATAAAGAAGTTAAATAAGATTGAACCGACAAGTAAACAAAGGATAAAAGGATTA
ACCTAGGACTAAACCGATAG
Found at i:1040755 original size:43 final size:42
Alignment explanation
Indices: 1040636--1040756 Score: 136
Period size: 43 Copynumber: 2.9 Consensus size: 42
1040626 ATAGGTAAAG
* *
1040636 AAAG-TTGACCGAAATTAAACCATCAAGTCAACAAAGGATAA
1 AAAGATTGACCGAGATTAAACCAACAAGTCAACAAAGGATAA
* * * * * *
1040677 AAAGATTTACCCAAGACTGAGCCAACAAGTAAACAAAGGATAA
1 AAAGATTGA-CCGAGATTAAACCAACAAGTCAACAAAGGATAA
*
1040720 AAAGATTGACCGGGATTAAACCAACAAAGTCAACAAA
1 AAAGATTGACCGAGATTAAACCAAC-AAGTCAACAAA
1040757 TTAAAAGGTT
Statistics
Matches: 62, Mismatches: 15, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
41 4 0.06
42 14 0.23
43 44 0.71
ACGTcount: A:0.51, C:0.18, G:0.16, T:0.15
Consensus pattern (42 bp):
AAAGATTGACCGAGATTAAACCAACAAGTCAACAAAGGATAA
Found at i:1040929 original size:81 final size:81
Alignment explanation
Indices: 1040737--1041217 Score: 482
Period size: 81 Copynumber: 6.0 Consensus size: 81
1040727 GACCGGGATT
* * * *
1040737 AAACCAACAAAGTCAACAAATTAAAAGGTTGGCCAAGGCAAAACCGATAAAGCCAACT-GGTTAA
1 AAACCAATAAAGTCAACCAATTAAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAA-TGGGTTAA
* * * *
1040801 AAAGGTTAACC-TGACA
65 AAAGGTTGACCAGGGCG
* * *
1040817 AAACCAAGAAAGTCAACCACTTAAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAATGGGTTATA
1 AAACCAATAAAGTCAACCAATTAAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAATGGGTTAAA
* *
1040882 AGGGTTGACCAGGGTG
66 AAGGTTGACCAGGGCG
*
1040898 AAACCAATAAAGTCAACCAATTAAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAATGGGTTAGA
1 AAACCAATAAAGTCAACCAATTAAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAATGGGTTAAA
* * *
1040963 AAGATTGACCAAGGCA
66 AAGGTTGACCAGGGCG
* * * **
1040979 AAATC-ATAAAGTCAACCTATTAAAAGGTTGGCTAGGGCAAAATCGATAAAGCCAACAGGTTAAA
1 AAACCAATAAAGTCAACCAATTAAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAATGGGTTAAA
* *
1041043 AAGGTTGACTAGGGTG
66 AAGGTTGACCAGGGCG
*** ** * * ** * ** *
1041059 AAATTGATAAAACCAACCAATTAAAAGGTTGGCAAAGGTGAAACCGATAAAGCCAACGATTTAGA
1 AAACCAATAAAGTCAACCAATTAAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAATGGGTTAAA
* * *
1041124 AGGGTTGACTAGAGCG
66 AAGGTTGACCAGGGCG
*** * * * ** *
1041140 AAATTGATAAACTAAACTAATTAAAAGGTTGGCTAGGGTGAAACTGATAAAGCCAATGGGTTAAA
1 AAACCAATAAAGTCAACCAATTAAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAATGGGTTAAA
*
1041205 AGGGTTGACCAGG
66 AAGGTTGACCAGG
1041218 ACAAAATTGA
Statistics
Matches: 338, Mismatches: 60, Indels: 5
0.84 0.15 0.01
Matches are distributed among these distances:
79 1 0.00
80 134 0.40
81 203 0.60
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.19
Consensus pattern (81 bp):
AAACCAATAAAGTCAACCAATTAAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAATGGGTTAAA
AAGGTTGACCAGGGCG
Found at i:1041004 original size:161 final size:160
Alignment explanation
Indices: 1040737--1041217 Score: 545
Period size: 161 Copynumber: 3.0 Consensus size: 160
1040727 GACCGGGATT
* * * *
1040737 AAACCAACAAAGTCAACAAATTAAAAGGTTGGCCAAGGCAAAACCGATAAAGCCAACT-GGTTAA
1 AAACCAATAAAGTCAACCAATTAAAAGGTTGGCAAAGGCAAAACCGATAAAGCCAA-TGGGTTAG
* * * * *
1040801 AAAGGTTAACCTGACAAAACCAAGAAAGTCAACC-ACTTAAAAGGTTGGCTAGGGCAAAACCGAT
65 AAAGGTTGACCAGGCAAAATC-ATAAAGTCAACCTA-TTAAAAGGTTGGCTAGGGCAAAACCGAT
*
1040865 AAAGCCAATGGGTTATAAGGGTTGACCAGGGTG
128 AAAGCCAATGGGTTAAAAGGGTTGACCAGGGTG
* *
1040898 AAACCAATAAAGTCAACCAATTAAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAATGGGTTAGA
1 AAACCAATAAAGTCAACCAATTAAAAGGTTGGCAAAGGCAAAACCGATAAAGCCAATGGGTTAGA
* *
1040963 AAGATTGACCAAGGCAAAATCATAAAGTCAACCTATTAAAAGGTTGGCTAGGGCAAAATCGATAA
66 AAGGTTGACC-AGGCAAAATCATAAAGTCAACCTATTAAAAGGTTGGCTAGGGCAAAACCGATAA
** * *
1041028 AGCCAACAGGTTAAAAAGGTTGACTAGGGTG
130 AGCCAATGGGTTAAAAGGGTTGACCAGGGTG
*** ** ** * **
1041059 AAATTGATAAAACCAACCAATTAAAAGGTTGGCAAAGGTGAAACCGATAAAGCCAACGATTTAGA
1 AAACCAATAAAGTCAACCAATTAAAAGGTTGGCAAAGGCAAAACCGATAAAGCCAATGGGTTAGA
* * * * * * ** *
1041124 AGGGTTGACTAGAGCGAAATTGATAAACT-AAACTAATTAAAAGGTTGGCTAGGGTGAAACTGAT
66 AAGGTTGACCAG-GC-AAAATCATAAAGTCAACCT-ATTAAAAGGTTGGCTAGGGCAAAACCGAT
1041188 AAAGCCAATGGGTTAAAAGGGTTGACCAGG
128 AAAGCCAATGGGTTAAAAGGGTTGACCAGG
1041218 ACAAAATTGA
Statistics
Matches: 270, Mismatches: 44, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
160 3 0.01
161 198 0.73
162 69 0.26
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.19
Consensus pattern (160 bp):
AAACCAATAAAGTCAACCAATTAAAAGGTTGGCAAAGGCAAAACCGATAAAGCCAATGGGTTAGA
AAGGTTGACCAGGCAAAATCATAAAGTCAACCTATTAAAAGGTTGGCTAGGGCAAAACCGATAAA
GCCAATGGGTTAAAAGGGTTGACCAGGGTG
Found at i:1041028 original size:40 final size:40
Alignment explanation
Indices: 1040756--1041195 Score: 244
Period size: 40 Copynumber: 10.9 Consensus size: 40
1040746 AAGTCAACAA
* * *
1040756 ATTAAAAGGTTGGCCAAGGCAAAACCGATAAAGCCAACTG
1 ATTAAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAACCG
* ** * * * *
1040796 GTTAAAAAGGTTAACCT--GACAAAACCAAGAAAGTCAACC-
1 ATT-AAAAGGTT-GGCTAGGGCAAAACCGATAAAGCCAACCG
**
1040835 ACTTAAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAATGG
1 A-TTAAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAACCG
* * * * ** * * *
1040876 GTTATAAGGGTTGACCAGGGTGAAACCAATAAAGTCAACCA
1 ATTA-AAAGGTTGGCTAGGGCAAAACCGATAAAGCCAACCG
**
1040917 ATTAAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAATGG
1 ATTAAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAACCG
* * * * * * * *
1040957 GTTAGAAAGATTGACCAAGGCAAAATC-ATAAAGTCAACCT
1 ATTA-AAAGGTTGGCTAGGGCAAAACCGATAAAGCCAACCG
* *
1040997 ATTAAAAGGTTGGCTAGGGCAAAATCGATAAAGCCAACAG
1 ATTAAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAACCG
* * ** ** * *
1041037 GTTAAAAAGGTTGACTAGGGTGAAATTGATAAAACCAACCA
1 ATT-AAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAACCG
* * **
1041078 ATTAAAAGGTTGGCAAAGGTGAAACCGATAAAGCCAA-CG
1 ATTAAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAACCG
* * * * ** * **
1041117 ATTTAGAAGGGTTGACTAGAGCGAAATTGATAAA-CTAAACTA
1 A-TTA-AAAGGTTGGCTAGGGCAAAACCGATAAAGC-CAACCG
** *
1041159 ATTAAAAGGTTGGCTAGGGTGAAACTGATAAAGCCAA
1 ATTAAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAA
1041196 TGGGTTAAAA
Statistics
Matches: 294, Mismatches: 91, Indels: 30
0.71 0.22 0.07
Matches are distributed among these distances:
38 2 0.01
39 28 0.10
40 150 0.51
41 112 0.38
42 2 0.01
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.19
Consensus pattern (40 bp):
ATTAAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAACCG
Found at i:1041068 original size:41 final size:41
Alignment explanation
Indices: 1040839--1041237 Score: 161
Period size: 41 Copynumber: 9.9 Consensus size: 41
1040829 TCAACCACTT
* * ** ** *
1040839 AAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAATGGGTTA
1 AAAAGGTTGACTAGGGCGAAATTGATAAAGCCAACAGATTA
* * * * *** *
1040880 TAAGGGTTGACCAGGGTGAAACCAATAAAGTCAACCA-ATT-
1 AAAAGGTTGACTAGGGCGAAATTGATAAAGCCAA-CAGATTA
* * ** ** *
1040920 AAAAGGTTGGCTAGGGCAAAACCGATAAAGCCAATGGGTTA
1 AAAAGGTTGACTAGGGCGAAATTGATAAAGCCAACAGATTA
* * * * * * * **
1040961 GAAAGATTGACCAAGGC-AAAATCATAAAGTCAACCTATT-
1 AAAAGGTTGACTAGGGCGAAATTGATAAAGCCAACAGATTA
* * * *
1041000 AAAAGGTTGGCTAGGGCAAAATCGATAAAGCCAACAGGTTA
1 AAAAGGTTGACTAGGGCGAAATTGATAAAGCCAACAGATTA
* *
1041041 AAAAGGTTGACTAGGGTGAAATTGATAAAACCAACCA-ATT-
1 AAAAGGTTGACTAGGGCGAAATTGATAAAGCCAA-CAGATTA
* * * * **
1041081 AAAAGGTTGGCAAAGGTGAAACCGATAAAGCCAAC-GATTTA
1 AAAAGGTTGACTAGGGCGAAATTGATAAAGCCAACAGA-TTA
* * * *
1041122 GAAGGGTTGACTAGAGCGAAATTGATAAA-CTAAACTA-ATT-
1 AAAAGGTTGACTAGGGCGAAATTGATAAAGC-CAAC-AGATTA
* * * ** *
1041162 AAAAGGTTGGCTAGGGTGAAACTGATAAAGCCAATGGGTTA
1 AAAAGGTTGACTAGGGCGAAATTGATAAAGCCAACAGATTA
* * * * *
1041203 AAAGGGTTGACCAGGACAAAATTGATAAAGTCAAC
1 AAAAGGTTGACTAGGGCGAAATTGATAAAGCCAAC
1041238 TAAGGATAAA
Statistics
Matches: 255, Mismatches: 88, Indels: 30
0.68 0.24 0.08
Matches are distributed among these distances:
39 14 0.05
40 115 0.45
41 123 0.48
42 3 0.01
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.20
Consensus pattern (41 bp):
AAAAGGTTGACTAGGGCGAAATTGATAAAGCCAACAGATTA
Found at i:1041434 original size:44 final size:44
Alignment explanation
Indices: 1041371--1041849 Score: 323
Period size: 44 Copynumber: 11.1 Consensus size: 44
1041361 AGCAAGAGAA
* *
1041371 GTTTGACCAGGGCAGAACCATCACGTCAAACGAAAACAAAAAGG
1 GTTTGACCAAGGCAAAACCATCACGTCAAACGAAAACAAAAAGG
* * * **
1041415 GTTTGACTAAGGTAAAACCATCACGTCAGACGAAAATGAAAAGG
1 GTTTGACCAAGGCAAAACCATCACGTCAAACGAAAACAAAAAGG
* * **
1041459 GTTTGACCAAGGCATAACCATCATGTCAAAC-AAAAGTGAAAA-G
1 GTTTGACCAAGGCAAAACCATCACGTCAAACGAAAA-CAAAAAGG
* * * *
1041502 GTTTGACCAGGGTAAAACCATCACGTTAAACGAAAAC-GAAAGG
1 GTTTGACCAAGGCAAAACCATCACGTCAAACGAAAACAAAAAGG
* * * *
1041545 AGTTTGACCAAGACAGAACCATCTCGTCAAATGAAAA-ATAAAA-G
1 -GTTTGACCAAGGCAAAACCATCACGTCAAACGAAAACA-AAAAGG
* * ** * * *
1041589 G--AGACC-A--C--CA-CATCAAAT-GAATGAAAGCAAGAGAA--
1 GTTTGACCAAGGCAAAACCATCACGTCAAACGAAAACAA-A-AAGG
* *
1041624 GTTTGACCAGGGCAGAACCATCACGTCAAACGAAAACAAAAAGG
1 GTTTGACCAAGGCAAAACCATCACGTCAAACGAAAACAAAAAGG
* * * **
1041668 GTTTGACTAAGGTAAAACCATCACGTCAGACGAAAATGAAAAGG
1 GTTTGACCAAGGCAAAACCATCACGTCAAACGAAAACAAAAAGG
* * **
1041712 GTTTGACCAAGGCATAACCATCATGTCAAAC-AAAAGTGAAAA-G
1 GTTTGACCAAGGCAAAACCATCACGTCAAACGAAAA-CAAAAAGG
* * * * *
1041755 GTTTGACCAGGGTATAACCATCACGTTAAACGAAAAC-GAAAGG
1 GTTTGACCAAGGCAAAACCATCACGTCAAACGAAAACAAAAAGG
* * * *
1041798 AGTTTGACCAAGACAGAACCATCTCGTCAAATGAAAA-ATAAAAGG
1 -GTTTGACCAAGGCAAAACCATCACGTCAAACGAAAACA-AAAAGG
1041843 AGTTTGA
1 -GTTTGA
1041850 TATCTAGGTC
Statistics
Matches: 341, Mismatches: 68, Indels: 51
0.74 0.15 0.11
Matches are distributed among these distances:
34 8 0.02
35 8 0.02
36 3 0.01
37 4 0.01
38 1 0.00
40 2 0.01
41 4 0.01
42 9 0.03
43 73 0.21
44 214 0.63
45 15 0.04
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (44 bp):
GTTTGACCAAGGCAAAACCATCACGTCAAACGAAAACAAAAAGG
Found at i:1041536 original size:87 final size:86
Alignment explanation
Indices: 1041371--1041828 Score: 388
Period size: 87 Copynumber: 5.3 Consensus size: 86
1041361 AGCAAGAGAA
* * * *
1041371 GTTTGACCAGGGCAGAACCATCACGTCAAACGAAAACAAAAAGGGTTTGACTAAGGTAAAACCAT
1 GTTTGACCAAGGCAGAACCATCATGTCAAAC-AAAATAAAAA-GGTTTGACCAAGGTAAAACCAT
* * *
1041436 CACGTCAGACGAAAATGAAAAGG
64 CACGTTAAACGAAAACGAAAAGG
* * *
1041459 GTTTGACCAAGGCATAACCATCATGTCAAACAAAAGTGAAAAGGTTTGACCAGGGTAAAACCATC
1 GTTTGACCAAGGCAGAACCATCATGTCAAACAAAA-TAAAAAGGTTTGACCAAGGTAAAACCATC
1041524 ACGTTAAACGAAAACG-AAAGG
65 ACGTTAAACGAAAACGAAAAGG
* * * **
1041545 AGTTTGACCAAGACAGAACCATC-TCGTCAAATGAAAA-ATAAAAGG--AGACC-----ACCA-C
1 -GTTTGACCAAGGCAGAACCATCAT-GTCAAA-CAAAATA-AAAAGGTTTGACCAAGGTAAAACC
** * * * * *
1041600 ATCA-AATGAATGAAAGC-AAGAGAA
62 ATCACGTTAAACGAAAACGAAAAG-G
* * * *
1041624 GTTTGACCAGGGCAGAACCATCACGTCAAACGAAAACAAAAAGGGTTTGACTAAGGTAAAACCAT
1 GTTTGACCAAGGCAGAACCATCATGTCAAAC-AAAATAAAAA-GGTTTGACCAAGGTAAAACCAT
* * *
1041689 CACGTCAGACGAAAATGAAAAGG
64 CACGTTAAACGAAAACGAAAAGG
* * * *
1041712 GTTTGACCAAGGCATAACCATCATGTCAAACAAAAGTGAAAAGGTTTGACCAGGGTATAACCATC
1 GTTTGACCAAGGCAGAACCATCATGTCAAACAAAA-TAAAAAGGTTTGACCAAGGTAAAACCATC
1041777 ACGTTAAACGAAAACG-AAAGG
65 ACGTTAAACGAAAACGAAAAGG
*
1041798 AGTTTGACCAAGACAGAACCATC-TCGTCAAA
1 -GTTTGACCAAGGCAGAACCATCAT-GTCAAA
1041829 TGAAAAATAA
Statistics
Matches: 291, Mismatches: 55, Indels: 49
0.74 0.14 0.12
Matches are distributed among these distances:
78 45 0.15
79 8 0.03
80 2 0.01
81 3 0.01
85 4 0.01
86 14 0.05
87 138 0.47
88 73 0.25
89 4 0.01
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (86 bp):
GTTTGACCAAGGCAGAACCATCATGTCAAACAAAATAAAAAGGTTTGACCAAGGTAAAACCATCA
CGTTAAACGAAAACGAAAAGG
Found at i:1041787 original size:253 final size:253
Alignment explanation
Indices: 1041339--1041844 Score: 1003
Period size: 253 Copynumber: 2.0 Consensus size: 253
1041329 CCGAGGTAGA
1041339 ACCACCACATCAAATGAATGAAAGCAAGAGAAGTTTGACCAGGGCAGAACCATCACGTCAAACGA
1 ACCACCACATCAAATGAATGAAAGCAAGAGAAGTTTGACCAGGGCAGAACCATCACGTCAAACGA
1041404 AAACAAAAAGGGTTTGACTAAGGTAAAACCATCACGTCAGACGAAAATGAAAAGGGTTTGACCAA
66 AAACAAAAAGGGTTTGACTAAGGTAAAACCATCACGTCAGACGAAAATGAAAAGGGTTTGACCAA
1041469 GGCATAACCATCATGTCAAACAAAAGTGAAAAGGTTTGACCAGGGTAAAACCATCACGTTAAACG
131 GGCATAACCATCATGTCAAACAAAAGTGAAAAGGTTTGACCAGGGTAAAACCATCACGTTAAACG
1041534 AAAACGAAAGGAGTTTGACCAAGACAGAACCATCTCGTCAAATGAAAAATAAAAGGAG
196 AAAACGAAAGGAGTTTGACCAAGACAGAACCATCTCGTCAAATGAAAAATAAAAGGAG
1041592 ACCACCACATCAAATGAATGAAAGCAAGAGAAGTTTGACCAGGGCAGAACCATCACGTCAAACGA
1 ACCACCACATCAAATGAATGAAAGCAAGAGAAGTTTGACCAGGGCAGAACCATCACGTCAAACGA
1041657 AAACAAAAAGGGTTTGACTAAGGTAAAACCATCACGTCAGACGAAAATGAAAAGGGTTTGACCAA
66 AAACAAAAAGGGTTTGACTAAGGTAAAACCATCACGTCAGACGAAAATGAAAAGGGTTTGACCAA
*
1041722 GGCATAACCATCATGTCAAACAAAAGTGAAAAGGTTTGACCAGGGTATAACCATCACGTTAAACG
131 GGCATAACCATCATGTCAAACAAAAGTGAAAAGGTTTGACCAGGGTAAAACCATCACGTTAAACG
1041787 AAAACGAAAGGAGTTTGACCAAGACAGAACCATCTCGTCAAATGAAAAATAAAAGGAG
196 AAAACGAAAGGAGTTTGACCAAGACAGAACCATCTCGTCAAATGAAAAATAAAAGGAG
1041845 TTTGATATCT
Statistics
Matches: 252, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
253 252 1.00
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.16
Consensus pattern (253 bp):
ACCACCACATCAAATGAATGAAAGCAAGAGAAGTTTGACCAGGGCAGAACCATCACGTCAAACGA
AAACAAAAAGGGTTTGACTAAGGTAAAACCATCACGTCAGACGAAAATGAAAAGGGTTTGACCAA
GGCATAACCATCATGTCAAACAAAAGTGAAAAGGTTTGACCAGGGTAAAACCATCACGTTAAACG
AAAACGAAAGGAGTTTGACCAAGACAGAACCATCTCGTCAAATGAAAAATAAAAGGAG
Found at i:1043004 original size:20 final size:20
Alignment explanation
Indices: 1042979--1043045 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
1042969 ACCCAGATGT
1042979 ATACATTTTTCAATGTATCG
1 ATACATTTTTCAATGTATCG
* * * *
1042999 ATACATGTATAAATGTATCA
1 ATACATTTTTCAATGTATCG
1043019 ATACATTTTTCAATGTATCG
1 ATACATTTTTCAATGTATCG
1043039 ATACATT
1 ATACATT
1043046 CTGTCTTTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (20 bp):
ATACATTTTTCAATGTATCG
Found at i:1043995 original size:20 final size:22
Alignment explanation
Indices: 1043955--1044002 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1043945 TAGCCTTTGA
*
1043955 CCATGCATTTTTTTACTATGTT
1 CCATGCATTTTTTAACTATGTT
1043977 CCATGCA-TTTTTAAC-ATG-T
1 CCATGCATTTTTTAACTATGTT
1043996 CCA-GCAT
1 CCATGCAT
1044003 CTCATTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 3 0.12
19 4 0.17
20 3 0.12
21 7 0.29
22 7 0.29
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (22 bp):
CCATGCATTTTTTAACTATGTT
Found at i:1048325 original size:162 final size:160
Alignment explanation
Indices: 1048033--1048354 Score: 538
Period size: 162 Copynumber: 2.0 Consensus size: 160
1048023 TATTTGTTTG
*
1048033 AAAATAAAAAATTTGGACCTCATTATCAAGATTCTAGACTTGGAAAATAAATTTTCCTAAAGGTT
1 AAAATAAAAAAATTGGACCTCATTATCAAGATTCTAGACTTGGAAAATAAATTTTCCTAAAGGTT
* * *
1048098 CTTGAATTAATCATAAAGAAAATGCTAAGTTCATGCTAGTACTCATTAGTTGAGGTTAGCATACT
66 ATTGAATTAATCATAAAGAAAATGCTAAGTTCATGCTAGTACTCATTAGTTAAGGTTAACATACT
1048163 TAGCTTGGAGAGATCTTTCAAAAACTATTTT
131 TAGCTTGGAGA-ATCTTTCAAAAACTATTTT
* *
1048194 AAAA-AAAAAAATTGGACCTCATTTGATCAAGATTCTAGACTTGGAAATTAAATTTTCCTCAAGG
1 AAAATAAAAAAATTGGACCTCA-TT-ATCAAGATTCTAGACTTGGAAAATAAATTTTCCTAAAGG
*
1048258 TTATTGAATTAATCATAAAGAAAATGCTAAGTTTATGCTAGTACTCATTAGTTAAGGTTAACATA
64 TTATTGAATTAATCATAAAGAAAATGCTAAGTTCATGCTAGTACTCATTAGTTAAGGTTAACATA
*
1048323 CTTAGCTTGGGGAATCTTTCAAAAACTATTTT
129 CTTAGCTTGGAGAATCTTTCAAAAACTATTTT
1048355 TGATAGCTTC
Statistics
Matches: 151, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
160 16 0.11
161 25 0.17
162 110 0.73
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (160 bp):
AAAATAAAAAAATTGGACCTCATTATCAAGATTCTAGACTTGGAAAATAAATTTTCCTAAAGGTT
ATTGAATTAATCATAAAGAAAATGCTAAGTTCATGCTAGTACTCATTAGTTAAGGTTAACATACT
TAGCTTGGAGAATCTTTCAAAAACTATTTT
Found at i:1049884 original size:92 final size:92
Alignment explanation
Indices: 1049727--1050183 Score: 502
Period size: 92 Copynumber: 5.0 Consensus size: 92
1049717 CAGAAATGAG
* * ** *
1049727 TGGTCAAGATATCCTTACCCCAAGGAAATCAAGCTTTGTGACACATCAATACCATCTAGTTGTTG
1 TGGTCAGGATATCCTTGCCCCAAGGAAATCAAGCTTTGTGATGCATCAATACCATCTAGTGGTTG
*
1049792 GATAAAGGGGATATGATTGGGAATGTG
66 GATAAAGGGGATATGATTGGGAATGTA
** * *
1049819 TGGTTGGGATATCCTTACCCCAAGAAAAAT-AAGCTTTGTGATGCATCAATACCATCTAGTGGTT
1 TGGTCAGGATATCCTTGCCCCAAG-GAAATCAAGCTTTGTGATGCATCAATACCATCTAGTGGTT
* *
1049883 GGATGAAGGGCATATGATTGGGAATGTA
65 GGATAAAGGGGATATGATTGGGAATGTA
* * * * * * * * *
1049911 TAGTCAGGATATCCTTGCCCCAAGGAAAACAGGCTTTATGATACATCAATATCATTTAGAGATTG
1 TGGTCAGGATATCCTTGCCCCAAGGAAATCAAGCTTTGTGATGCATCAATACCATCTAGTGGTTG
* * * *
1049976 GATAAAGTGGATATGATTAGGAATATG
66 GATAAAGGGGATATGATTGGGAATGTA
* ** * * * * *
1050003 TGATTGGGATATCCTTGCCCTAAGGAAATCAAGCTTTGTGATGCATCAATATCATCTAATGATAG
1 TGGTCAGGATATCCTTGCCCCAAGGAAATCAAGCTTTGTGATGCATCAATACCATCTAGTGGTTG
* *
1050068 GATTAAGGGGATATGATTGAGAATGTA
66 GATAAAGGGGATATGATTGGGAATGTA
* * * * *
1050095 TGGGCAGGATATCCTTGCCCCAAGGAAATCAAGCTTTGCGATGCATCAACACTATCTAGGGGTTG
1 TGGTCAGGATATCCTTGCCCCAAGGAAATCAAGCTTTGTGATGCATCAATACCATCTAGTGGTTG
*** *
1050160 GGCGAAGGGAATATGATTGGGAAT
66 GATAAAGGGGATATGATTGGGAAT
1050184 ATGTAGGCTG
Statistics
Matches: 297, Mismatches: 66, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
91 3 0.01
92 290 0.98
93 4 0.01
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (92 bp):
TGGTCAGGATATCCTTGCCCCAAGGAAATCAAGCTTTGTGATGCATCAATACCATCTAGTGGTTG
GATAAAGGGGATATGATTGGGAATGTA
Found at i:1050176 original size:184 final size:183
Alignment explanation
Indices: 1049734--1050187 Score: 561
Period size: 184 Copynumber: 2.5 Consensus size: 183
1049724 GAGTGGTCAA
* * * **
1049734 GATATCCTTACCCCAAGGAAATCAAGCTTTGTGACACATCAATACCATCTAGTTGTTGGATAAAG
1 GATATCCTTGCCCCAAGGAAATCAAGCTTTGTGATACATCAATACTATCTAGAGGTTGGATAAA-
* *
1049799 GGGATATGATTGGGAATGTGTGGTTGGGATATCCTTACCCCAAGAAAAATAAGCTTTGTGATGCA
65 GGGATATGATTGGGAATATGTGATTGGGATATCCTTACCCCAAGAAAAATAAGCTTTGTGATGCA
* * * * *
1049864 TCAATACCATCTAGTGGTTGGATGAAGGGCATATGATTGGGAATGTATAGTCAG
130 TCAATACCATCTAATGATAGGATGAAGGGCATATGATTGAGAATGTATAGGCAG
* * * * *
1049918 GATATCCTTGCCCCAAGGAAAACAGGCTTTATGATACATCAATA-TCATTTAGAGATTGGATAAA
1 GATATCCTTGCCCCAAGGAAATCAAGCTTTGTGATACATCAATACT-ATCTAGAGGTTGGATAAA
* * * *
1049982 GTGGATATGATTAGGAATATGTGATTGGGATATCCTTGCCCTAAG-GAAATCAAGCTTTGTGATG
65 G-GGATATGATTGGGAATATGTGATTGGGATATCCTTACCCCAAGAAAAAT-AAGCTTTGTGATG
* * * *
1050046 CATCAATATCATCTAATGATAGGATTAAGGGGATATGATTGAGAATGTATGGGCAG
128 CATCAATACCATCTAATGATAGGATGAAGGGCATATGATTGAGAATGTATAGGCAG
* * * * ***
1050102 GATATCCTTGCCCCAAGGAAATCAAGCTTTGCGATGCATCAACACTATCTAGGGGTTGGGCGAAG
1 GATATCCTTGCCCCAAGGAAATCAAGCTTTGTGATACATCAATACTATCTAGAGGTTGGATAAAG
1050167 GGAATATGATTGGGAATATGT
66 GG-ATATGATTGGGAATATGT
1050188 AGGCTGTACC
Statistics
Matches: 227, Mismatches: 38, Indels: 10
0.83 0.14 0.04
Matches are distributed among these distances:
183 7 0.03
184 219 0.96
185 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.29
Consensus pattern (183 bp):
GATATCCTTGCCCCAAGGAAATCAAGCTTTGTGATACATCAATACTATCTAGAGGTTGGATAAAG
GGATATGATTGGGAATATGTGATTGGGATATCCTTACCCCAAGAAAAATAAGCTTTGTGATGCAT
CAATACCATCTAATGATAGGATGAAGGGCATATGATTGAGAATGTATAGGCAG
Found at i:1053563 original size:22 final size:21
Alignment explanation
Indices: 1053528--1053577 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1053518 TTTGTTGATG
*
1053528 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
1053548 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
1053569 AATTTGAAG
1 ATTTTGAAG
1053578 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:1053574 original size:21 final size:22
Alignment explanation
Indices: 1053535--1053577 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1053525 ATGATTTTGA
* *
1053535 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1053557 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1053578 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:1058690 original size:13 final size:13
Alignment explanation
Indices: 1058672--1058697 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1058662 CAATTTTTTG
1058672 TGTATCGATACAT
1 TGTATCGATACAT
1058685 TGTATCGATACAT
1 TGTATCGATACAT
1058698 ACTTGCTGTA
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:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1059437 original size:21 final size:21
Alignment explanation
Indices: 1059396--1059439 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1059386 CTCCCCTTTA
* *
1059396 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1059417 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1059438 TC
1 TC
1059440 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1061257 original size:13 final size:13
Alignment explanation
Indices: 1061239--1061264 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1061229 ATAATCACCC
1061239 TGTATCGATACAA
1 TGTATCGATACAA
1061252 TGTATCGATACAA
1 TGTATCGATACAA
1061265 AGAAAAATGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1061321 original size:20 final size:20
Alignment explanation
Indices: 1061250--1061329 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1061240 GTATCGATAC
*
1061250 AATGTATCGATACAAAGAAA
1 AATGTATCGATACATAGAAA
*
1061270 AATGTATCGATACATTGAATTTCCA
1 AATGTATCGATACATAGAA-----A
*
1061295 GATGTATCGATACATAGAAA
1 AATGTATCGATACATAGAAA
*
1061315 CATGTATCGATACAT
1 AATGTATCGATACAT
1061330 TTTGGACATT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACATAGAAA
Found at i:1063362 original size:15 final size:15
Alignment explanation
Indices: 1063342--1063372 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1063332 ATTTCGTTTG
*
1063342 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1063357 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1063372 G
1 G
1063373 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1072232 original size:52 final size:51
Alignment explanation
Indices: 1072147--1072270 Score: 205
Period size: 52 Copynumber: 2.4 Consensus size: 51
1072137 ATATGAAAAG
* *
1072147 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
1072198 TTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACA-TTTAATAATGTATCGATACATCTGGGCAAA
1072250 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1072271 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 21 0.30
52 43 0.62
53 5 0.07
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:1072283 original size:51 final size:50
Alignment explanation
Indices: 1072147--1072290 Score: 177
Period size: 52 Copynumber: 2.8 Consensus size: 50
1072137 ATATGAAAAG
* *
1072147 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGCAAAT
1072199 TTGCCTGCATGTATCGATACATTTTAAA-A-TGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA----AAATAGTGTATCGATACATCTGGGCAAAT
1072250 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
1072291 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 2, Indels: 13
0.85 0.02 0.13
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
50 1 0.01
51 33 0.39
52 42 0.50
53 1 0.01
54 4 0.05
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (50 bp):
TTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1072297 original size:13 final size:13
Alignment explanation
Indices: 1072279--1072303 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1072269 CAAAGATCAG
1072279 TGTATCGATACAA
1 TGTATCGATACAA
1072292 TGTATCGATACA
1 TGTATCGATACA
1072304 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1073349 original size:10 final size:10
Alignment explanation
Indices: 1073334--1073362 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1073324 TTTACTGATT
1073334 CCGTTTATAG
1 CCGTTTATAG
1073344 CCGTTTATAG
1 CCGTTTATAG
1073354 CCGTTTATA
1 CCGTTTATA
1073363 CCTTTACGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (10 bp):
CCGTTTATAG
Found at i:1074726 original size:11 final size:13
Alignment explanation
Indices: 1074697--1074730 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1074687 CAATGGAATA
1074697 GTGTTTTTTTTTG
1 GTGTTTTTTTTTG
1074710 GTGTTTTTTTTTG
1 GTGTTTTTTTTTG
1074723 GT-TTTTTT
1 GTGTTTTTT
1074731 GCTAAAGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (13 bp):
GTGTTTTTTTTTG
Found at i:1075281 original size:33 final size:33
Alignment explanation
Indices: 1075243--1075309 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1075233 AAAATTTCCA
***
1075243 AATGTATCAATACAAAGATCCATGTATCGATAC
1 AATGTATCAATACAAAGAAAAATGTATCGATAC
* *
1075276 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCAATACAAAGAAAAATGTATCGATAC
1075309 A
1 A
1075310 TTTCCTTGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.25
Consensus pattern (33 bp):
AATGTATCAATACAAAGAAAAATGTATCGATAC
Found at i:1075282 original size:13 final size:13
Alignment explanation
Indices: 1075264--1075289 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1075254 ACAAAGATCC
1075264 ATGTATCGATACA
1 ATGTATCGATACA
1075277 ATGTATCGATACA
1 ATGTATCGATACA
1075290 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1075353 original size:19 final size:18
Alignment explanation
Indices: 1075329--1075396 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1075319 TAGTAGCTAA
1075329 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1075348 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1075363 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1075380 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1075397 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1075369 original size:13 final size:13
Alignment explanation
Indices: 1075351--1075375 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1075341 ACAATACTTA
1075351 TGTATCGATACAT
1 TGTATCGATACAT
1075364 TGTATCGATACA
1 TGTATCGATACA
1075376 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1075373 original size:32 final size:32
Alignment explanation
Indices: 1075332--1075394 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1075322 TAGCTAATTA
*
1075332 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1075364 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1075395 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1075459 original size:21 final size:21
Alignment explanation
Indices: 1075433--1075511 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
1075423 GTTGGGACCC
1075433 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGTAGAA
*
1075454 TGTATCGATACATTTGTGGAA
1 TGTATCGATACATTTGTAGAA
* *
1075475 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTA-GAA
1075496 TGTATCGATACATTTG
1 TGTATCGATACATTTG
1075512 GATAAATTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
20 3 0.06
21 46 0.90
22 2 0.04
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTGTAGAA
Found at i:1076555 original size:61 final size:60
Alignment explanation
Indices: 1076248--1076810 Score: 646
Period size: 55 Copynumber: 9.8 Consensus size: 60
1076238 GTATCCTACG
** * *
1076248 CTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT----GA-AAGGCGTCATGCT
1 CTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAGGCGTCCTGCT
* *
1076303 TTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT---A-AG-AGGTGTCCTGCT
1 CTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAGGCGTCCTGCT
* * *
1076358 CTTTGAGGACT-GAAAGGTGCCACCAAATTGTGTGGGCTTTAAAAGAAAAAGCGTCCTGCT
1 CTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAGGCGTCCTGCT
* *
1076418 CTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTT---A-A-AAGGCATCCTGCT
1 CTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAGGCGTCCTGCT
1076473 CTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTGCT
1 CTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTTAAAA-GAGAAGGCGTCCTGCT
* *
1076534 CTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTT---A-A-AAGGTGTCCTGCT
1 CTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAGGCGTCCTGCT
*
1076589 CTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTTAAGAGGAGAAGGCGTCCTGCT
1 CTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTTAA-AAGAGAAGGCGTCCTGCT
* *
1076650 CTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAGAAGGCGCCCTGCT
1 CTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG-AGAAGGCGTCCTGCT
* * *
1076711 CTTTGAGGACTGGGAAGTGCCACCAACTTGTATGGGCTTCAAAAG-G-A---GTCCTGCT
1 CTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAGGCGTCCTGCT
* * *
1076766 CTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGGTTTGAAAG
1 CTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAG
1076811 GAAAAAGCAT
Statistics
Matches: 449, Mismatches: 32, Indels: 54
0.84 0.06 0.10
Matches are distributed among these distances:
54 6 0.01
55 221 0.49
56 6 0.01
57 1 0.00
58 4 0.01
59 2 0.00
60 52 0.12
61 157 0.35
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (60 bp):
CTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAGGCGTCCTGCT
Found at i:1076574 original size:116 final size:115
Alignment explanation
Indices: 1076248--1076811 Score: 722
Period size: 116 Copynumber: 4.9 Consensus size: 115
1076238 GTATCCTACG
** * * *
1076248 CTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT----GA-AAGGCGTCATGCTTTTTG
1 CTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAGGCGTCCTGCTCTTTG
* *
1076308 AGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCT
66 AGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCT
* * * *
1076358 CTTTGAGGACT-GAAAGGTGCCACCAAATTGTGTGGGCTTTAAAAGAAAAAGCGTCCTGCTCTTT
1 CTTTGAGGACTAGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAGGCGTCCTGCTCTTT
* *
1076422 GAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCT
65 GAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCT
1076473 CTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTGCTCTTT
1 CTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAA-GAGAAGGCGTCCTGCTCTTT
* *
1076538 GAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCT
65 GAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCT
*
1076589 CTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGAGAAGGCGTCCTGCTCTTT
1 CTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAA-AAGAGAAGGCGTCCTGCTCTTT
* *
1076654 GAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAGAAGGCGCCCTGCT
65 GAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-----AA-AAGGCGTCCTGCT
* * *
1076711 CTTTGAGGACTGGGAAGTGCCACCAACTTGTATGGGCTTCAAAAG-G-A---GTCCTGCTCTTTG
1 CTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAGGCGTCCTGCTCTTTG
* * *
1076771 GGGACT-GAAAGGTGCCACCAACTTGTGTGGGGTTTGAAAGG
66 AGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGG
1076812 AAAAAGCATC
Statistics
Matches: 408, Mismatches: 29, Indels: 34
0.87 0.06 0.07
Matches are distributed among these distances:
109 3 0.01
110 37 0.09
111 1 0.00
114 2 0.00
115 99 0.24
116 209 0.51
117 1 0.00
119 1 0.00
120 1 0.00
121 4 0.01
122 50 0.12
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (115 bp):
CTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAGGCGTCCTGCTCTTTG
AGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCT
Found at i:1077841 original size:12 final size:12
Alignment explanation
Indices: 1077824--1077850 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1077814 TCTCTTTTTC
1077824 TTTGTTTTGTTT
1 TTTGTTTTGTTT
1077836 TTTGTTTTGTTT
1 TTTGTTTTGTTT
1077848 TTT
1 TTT
1077851 TCTTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (12 bp):
TTTGTTTTGTTT
Found at i:1077850 original size:29 final size:28
Alignment explanation
Indices: 1077818--1077877 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
1077808 CTTTTCTCTC
*
1077818 TTTTTCTTTGTT-TTGTTTTTTGTTTTGTT
1 TTTTTCTTT-TTATTGTTTTTTGCTTT-TT
*
1077847 TTTTTCTTTTTATTTTTTTTTGCTTTTT
1 TTTTTCTTTTTATTGTTTTTTGCTTTTT
1077875 TTT
1 TTT
1077878 GAAGAGAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.02, C:0.05, G:0.08, T:0.85
Consensus pattern (28 bp):
TTTTTCTTTTTATTGTTTTTTGCTTTTT
Found at i:1077874 original size:12 final size:11
Alignment explanation
Indices: 1077828--1077877 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 11
1077818 TTTTTCTTTG
1077828 TTTTGTTTTTT
1 TTTTGTTTTTT
1077839 GTTTTGTTTTTT
1 -TTTTGTTTTTT
*
1077851 TCTTTTTATTTTT
1 T-TTTGT-TTTTT
1077864 TTTTGCTTTTTT
1 TTTTG-TTTTTT
1077876 TT
1 TT
1077878 GAAGAGAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 1 0.03
12 25 0.76
13 7 0.21
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.86
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:1084320 original size:34 final size:34
Alignment explanation
Indices: 1084274--1084340 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
1084264 GAATGGCCTT
*
1084274 GTGCCCCGGCATGATATTCGCAGTAAGCACTCTC
1 GTGCCCCAGCATGATATTCGCAGTAAGCACTCTC
1084308 GTGCCCCAGCATGATATTCGCAGTAAGCACTCT
1 GTGCCCCAGCATGATATTCGCAGTAAGCACTCT
1084341 TGTCATACCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.24
Consensus pattern (34 bp):
GTGCCCCAGCATGATATTCGCAGTAAGCACTCTC
Found at i:1086811 original size:13 final size:13
Alignment explanation
Indices: 1086793--1086818 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1086783 TACAGCAAGT
1086793 ATGTATCGATACA
1 ATGTATCGATACA
1086806 ATGTATCGATACA
1 ATGTATCGATACA
1086819 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1089066 original size:21 final size:21
Alignment explanation
Indices: 1089033--1089077 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1089023 TTGCAAGTTG
*
1089033 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1089055 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1089075 AAA
1 AAA
1089078 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1090901 original size:15 final size:15
Alignment explanation
Indices: 1090881--1090911 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1090871 TAAAAATGTC
*
1090881 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1090896 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1090911 C
1 C
1090912 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1093158 original size:20 final size:20
Alignment explanation
Indices: 1093115--1093160 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1093105 AAATCTTTTG
1093115 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1093136 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1093156 CAAAA
1 CAAAA
1093161 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1095557 original size:13 final size:13
Alignment explanation
Indices: 1095539--1095564 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1095529 TACAGCAAGT
1095539 ATGTATCGATACA
1 ATGTATCGATACA
1095552 ATGTATCGATACA
1 ATGTATCGATACA
1095565 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1095649 original size:20 final size:21
Alignment explanation
Indices: 1095619--1095657 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1095609 CTATATTTTC
1095619 AAATATGTATCGATACATTAA
1 AAATATGTATCGATACATTAA
1095640 AAAT-TGTATCGATACATT
1 AAATATGTATCGATACATT
1095658 TACACGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (21 bp):
AAATATGTATCGATACATTAA
Found at i:1099990 original size:79 final size:79
Alignment explanation
Indices: 1099898--1100085 Score: 209
Period size: 79 Copynumber: 2.4 Consensus size: 79
1099888 TTGGAGCGTT
* ** * * *
1099898 CCCTTGAAAATAACGGGGTTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAGAAAAAAAA-A
1 CCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-ATTTAGAAAAAAAAGC
1099961 TCGGGATTGGAGTATC
65 T-GGGATTGGAGTATC
* * ** *
1099977 CCCTCGAAAATAACGGGGTTAGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCT
1 CCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTAGAAAAAAAAGCT
*
1100042 GGGGTTGGAGTATC
66 GGGATTGGAGTATC
* * *
1100056 CCTTCGGAAGTAACGGGGTTGGAGTATCCC
1 CCCTCGAAAATAACGGGGTTGGAGTATCCC
1100086 TGATGATTAA
Statistics
Matches: 91, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 1 0.01
79 89 0.98
80 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (79 bp):
CCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTAGAAAAAAAAGCT
GGGATTGGAGTATC
Found at i:1100104 original size:27 final size:28
Alignment explanation
Indices: 1100042--1100109 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 28
1100032 GAATAAAGCT
**
1100042 GGGGTTGGAGTATCCCTTCGGAAGTAAC
1 GGGGTTGGAGTATCCCTGAGGAAGTAAC
* *
1100070 GGGGTTGGAGTATCCCTGATG-ATTAAC
1 GGGGTTGGAGTATCCCTGAGGAAGTAAC
1100097 GGGGTTGGAGTAT
1 GGGGTTGGAGTAT
1100110 TCTCGATTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 18 0.50
28 18 0.50
ACGTcount: A:0.21, C:0.13, G:0.38, T:0.28
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCTGAGGAAGTAAC
Found at i:1102043 original size:11 final size:11
Alignment explanation
Indices: 1102026--1102054 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1102016 ATGGAATAGT
1102026 GTTTTTTTTT-
1 GTTTTTTTTTG
1102036 GTTTTTTTTTG
1 GTTTTTTTTTG
1102047 GTTTTTTT
1 GTTTTTTT
1102055 GCTAAAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (11 bp):
GTTTTTTTTTG
Found at i:1102673 original size:13 final size:13
Alignment explanation
Indices: 1102655--1102681 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1102645 TACAATGAAC
1102655 ATGTATCGATACA
1 ATGTATCGATACA
1102668 ATGTATCGATACA
1 ATGTATCGATACA
1102681 A
1 A
1102682 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1105084 original size:18 final size:18
Alignment explanation
Indices: 1105057--1105091 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1105047 TGCAACTGAA
1105057 TTTTTTTCTT-TTTTTTT
1 TTTTTTTCTTGTTTTTTT
1105074 TTTTGTTTCTTGTTTTTT
1 TTTT-TTTCTTGTTTTTT
1105092 GAAAATCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 6 0.38
19 6 0.38
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.89
Consensus pattern (18 bp):
TTTTTTTCTTGTTTTTTT
Found at i:1106664 original size:88 final size:88
Alignment explanation
Indices: 1106555--1106732 Score: 356
Period size: 88 Copynumber: 2.0 Consensus size: 88
1106545 AGAATAAATG
1106555 ACAACATCTTTTAAGTGAAATAAAATATTTTACAAAAAGTGATGACATTTGTTTATCGTTGTTCA
1 ACAACATCTTTTAAGTGAAATAAAATATTTTACAAAAAGTGATGACATTTGTTTATCGTTGTTCA
1106620 ATATTTAGATTAAAAAGGACCTT
66 ATATTTAGATTAAAAAGGACCTT
1106643 ACAACATCTTTTAAGTGAAATAAAATATTTTACAAAAAGTGATGACATTTGTTTATCGTTGTTCA
1 ACAACATCTTTTAAGTGAAATAAAATATTTTACAAAAAGTGATGACATTTGTTTATCGTTGTTCA
1106708 ATATTTAGATTAAAAAGGACCTT
66 ATATTTAGATTAAAAAGGACCTT
1106731 AC
1 AC
1106733 TACAAATGAT
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 90 1.00
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (88 bp):
ACAACATCTTTTAAGTGAAATAAAATATTTTACAAAAAGTGATGACATTTGTTTATCGTTGTTCA
ATATTTAGATTAAAAAGGACCTT
Found at i:1108892 original size:149 final size:149
Alignment explanation
Indices: 1108597--1108893 Score: 334
Period size: 149 Copynumber: 2.0 Consensus size: 149
1108587 TTGGAAAATA
* * * * * *
1108597 TAAAAGCAAGCCTACTCCTAATTCATACTTTCTGCGTAGAAGCGGACCCGGTAGTGTTATAAGAT
1 TAAAAGCAAACCTACTCCTAATTCATACATTCTGCATAGAAGCAGACCCGATAGTGTTATAAGAC
** * * *
1108662 TCGGTTTTAGGGAAAATGCTAAAATATCCCTAAGACCTACCATCGATATAGCAGTGCTCGGTGAT
66 TAAGTTTTAGAGAAAATGCTAAAATATCCCTAAGACCTACCATCGATATAGCAGTGCTCAGTAAT
**
1108727 CCTAAAGGACTTAAAAAGG
131 CCTAAAAAACTTAAAAAGG
*
1108746 TAAAAGCAAACCTACTCCTAATTCATACATTC-GTCATAGAAGCAGACCCGATAGTTTTATAAGA
1 TAAAAGCAAACCTACTCCTAATTCATACATTCTG-CATAGAAGCAGACCCGATAGTGTTATAAGA
* *** * *
1108810 CTAAG-TTTCGAGAAAAGTGCTAAAATATCCCTAAGGTTTA-CATC-ATCTTAGGAGTGC-CTAG
65 CTAAGTTTTAGAGAAAA-TGCTAAAATATCCCTAAGACCTACCATCGAT-ATAGCAGTGCTC-AG
1108871 TAATCCTAAAAAACTTGAAAAAG
127 TAATCCTAAAAAACTT-AAAAAG
1108894 ATTGCAAAGA
Statistics
Matches: 123, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
147 3 0.02
148 36 0.29
149 84 0.68
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (149 bp):
TAAAAGCAAACCTACTCCTAATTCATACATTCTGCATAGAAGCAGACCCGATAGTGTTATAAGAC
TAAGTTTTAGAGAAAATGCTAAAATATCCCTAAGACCTACCATCGATATAGCAGTGCTCAGTAAT
CCTAAAAAACTTAAAAAGG
Found at i:1111343 original size:161 final size:163
Alignment explanation
Indices: 1111130--1111547 Score: 468
Period size: 161 Copynumber: 2.6 Consensus size: 163
1111120 TGGTTTTTCA
* * *
1111130 AAAACAGAAAAATTTCAAGAAAAAAATGAAAAACTCATGAAAATAAATGAATTTTTTAAAACTGA
1 AAAATAGAAAAATTTCAAGAAAAAAATGAAAAACTCATG-AAATAAATGAATTTTTCAAAAATGA
* * *
1111195 TTTACTATGATTTAAATGAAGATATTTGATGAATATT-AAAATTTTGAACCGAG-AAACCCCCCG
65 TTTACTGTGATTTAAATGAAGATATTTGATAAATATTAAAAATTTTAAACCGAGAAAACCCCCCG
1111258 AAAACATTTATACAATAGAA-AACTTAAT-TTTTG
130 AAAACATTTATACAATA-AAGAACTTAATATTTTG
**** * * * *
1111291 AAAATAGGGGTATTTTAAGGAAAAAATGAAAAACTCATGAGAATATATGAATTTTTCAAAATTGA
1 AAAATAGAAAAATTTCAAGAAAAAAATGAAAAACTCATGA-AATAAATGAATTTTTCAAAAATGA
* * * * ***
1111356 TTTATTGTGATTTAAAT-AATGATATGTGGTAAATATTAAAAATTTTAAACTGAGAAAAACCTTT
65 TTTACTGTGATTTAAATGAA-GATATTTGATAAATATTAAAAATTTTAAACCGAG-AAAACCCCC
* ** *
1111420 TGAAAACATTTATGGAATAAAGAATTTAATATTTTG
128 CGAAAACATTTATACAATAAAGAACTTAATATTTTG
* * *
1111456 AAAATAGAAAAATTTCAAGAAAAAAATGAAAAATTCATGAAATAAAAGGAAATTTTCAAAAATGA
1 AAAATAGAAAAATTTCAAGAAAAAAATGAAAAACTCATGAAAT-AAATGAATTTTTCAAAAATGA
* * *
1111521 TTTAGTGTGAATTAAATGATGATATTT
65 TTTACTGTGATTTAAATGAAGATATTT
1111548 AAAGAATTTT
Statistics
Matches: 209, Mismatches: 39, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
160 3 0.01
161 82 0.39
162 14 0.07
163 2 0.01
164 31 0.15
165 76 0.36
166 1 0.00
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (163 bp):
AAAATAGAAAAATTTCAAGAAAAAAATGAAAAACTCATGAAATAAATGAATTTTTCAAAAATGAT
TTACTGTGATTTAAATGAAGATATTTGATAAATATTAAAAATTTTAAACCGAGAAAACCCCCCGA
AAACATTTATACAATAAAGAACTTAATATTTTG
Found at i:1111487 original size:20 final size:21
Alignment explanation
Indices: 1111464--1111518 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
1111454 TGAAAATAGA
*
1111464 AAAATTTCAAGAAA-AAAATG
1 AAAATTTCAAGAAATAAAAGG
* *
1111484 AAAAATTCATGAAATAAAAGG
1 AAAATTTCAAGAAATAAAAGG
*
1111505 AAATTTTCAA-AAAT
1 AAAATTTCAAGAAAT
1111519 GATTTAGTGT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.62, C:0.05, G:0.09, T:0.24
Consensus pattern (21 bp):
AAAATTTCAAGAAATAAAAGG
Found at i:1111502 original size:21 final size:21
Alignment explanation
Indices: 1111456--1111507 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
1111446 TAATATTTTG
1111456 AAAATAGAAAAATTTCAAGAAA
1 AAAAT-GAAAAATTTCAAGAAA
*
1111478 AAAATGAAAAA-TTCATGAAA
1 AAAATGAAAAATTTCAAGAAA
*
1111498 TAAAAGGAAA
1 -AAAATGAAA
1111508 TTTTCAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 8 0.30
21 14 0.52
22 5 0.19
ACGTcount: A:0.67, C:0.04, G:0.12, T:0.17
Consensus pattern (21 bp):
AAAATGAAAAATTTCAAGAAA
Found at i:1114349 original size:52 final size:52
Alignment explanation
Indices: 1114255--1114368 Score: 147
Period size: 52 Copynumber: 2.2 Consensus size: 52
1114245 TCTGGAAAGA
* * * *
1114255 AAATGTATCGATAAATTTTTTATTGTATTAATACATTATGGGTTTTTGACCT
1 AAATATATCGATAAATTTTTCATTGTATCAATACATTATGGGTTTTGGACCT
* * * *
1114307 AAATATATTGATACATTTTTCATTGTATCGATACATTCTGGGTTTTGGACCT
1 AAATATATCGATAAATTTTTCATTGTATCAATACATTATGGGTTTTGGACCT
*
1114359 AAATGTATCG
1 AAATATATCG
1114369 GTATATTCTT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.45
Consensus pattern (52 bp):
AAATATATCGATAAATTTTTCATTGTATCAATACATTATGGGTTTTGGACCT
Found at i:1115030 original size:47 final size:47
Alignment explanation
Indices: 1114976--1115069 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
1114966 ATTCCTTACA
*
1114976 CTTTCACCCTCAAACAGCCTCACCATCAACCATACCACTAAAAAACT
1 CTTTCACCCTCAAACAACCTCACCATCAACCATACCACTAAAAAACT
*
1115023 CTTTCACCCTCAAACAACCTCACCATCAACCATACCACTAGAAAACT
1 CTTTCACCCTCAAACAACCTCACCATCAACCATACCACTAAAAAACT
1115070 ACCTCCTTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.38, C:0.40, G:0.02, T:0.19
Consensus pattern (47 bp):
CTTTCACCCTCAAACAACCTCACCATCAACCATACCACTAAAAAACT
Found at i:1116921 original size:82 final size:80
Alignment explanation
Indices: 1116819--1117444 Score: 496
Period size: 81 Copynumber: 7.7 Consensus size: 80
1116809 TAAAACACCA
* * * *
1116819 AATTT-TTCGTCTCTAGGGATACTCCAACCCCCCCCATTTCCAAAGGGATACTCTAATCCCATTT
1 AATTTCTTCATCTCTAGGGATACTCCAA-CCCCACCATTTTCTAAGGGATACTCTAA-CCCATTT
1116883 TTACTTCTAAAACATTG
64 TTACTTCTAAAACATTG
* *
1116900 AATTTCTTCATCTCTAGGGATACTCCAACCCTACCA-TTTCTAAGGGAATACTCTAACCTCGTTT
1 AATTTCTTCATCTCTAGGGATACTCCAACCCCACCATTTTCTAAGGG-ATACTCTAACC-CATTT
1116964 TTACTTCTAAAACATTG
64 TTACTTCTAAAACATTG
* * * *
1116981 AATTTCTTCATCTCCAAGGATACTCTAA-CCCACCCATTTTCTAGGGGATACT-TCAACCCCATT
1 AATTTCTTCATCTCTAGGGATACTCCAACCCCA-CCATTTTCTAAGGGATACTCT-AA-CCCATT
1117044 TTTACTTCTAAAACATTG
63 TTTACTTCTAAAACATTG
* *
1117062 AATTTCTTCATCTCTGGGGATACTCCAACCCCACCATTTTCGAAGGGATACTCCAACCATTCCAA
1 AATTTCTTCATCTCTAGGGATACTCCAACCCCACCATTTTCTAAGGGATACT-----C--T--AA
* *
1117127 CCCCATTTTTACTTCTAAAACACTA
57 -CCCATTTTTACTTCTAAAACATTG
* * * ** * *
1117152 AAATT-TTCATCAC-AGGGGATA-TCCAATCCCACCATTTT-TAAGAAAATACTCCAACCTCGTT
1 AATTTCTTCATCTCTA-GGGATACTCCAACCCCACCATTTTCTAAG-GGATACTCTAACC-CATT
*
1117213 TTTATTTCCTAAAA-ATTG
63 TTTACTT-CTAAAACATTG
* * * * * * **
1117231 AATTT-TTTATCTTTGGGGATACTCCAACCCCATC-GTCTCCGAGGAGATACTCTAACCCTATTT
1 AATTTCTTCATCTCTAGGGATACTCCAACCCCACCATTTTCTAAGG-GATACTCTAACCC-ATTT
* *
1117294 TTACTT-TTAAA-A-TA
64 TTACTTCTAAAACATTG
* * * * * **
1117308 AAATT-TTCGTCTCAAGGGATACTCTAACCCCACCATTTTCGAAGGGATACT-TCAACACTGTTT
1 AATTTCTTCATCTCTAGGGATACTCCAACCCCACCATTTTCTAAGGGATACTCT-AAC-CCATTT
* *
1117371 TTACTTCCAAAGCATTG
64 TTACTTCTAAAACATTG
* * *
1117388 AATTT-TTCATCTCTAGAGATACTCCAACCCCACCATCTT-TAAGGGGATACTTTAACC
1 AATTTCTTCATCTCTAGGGATACTCCAACCCCACCATTTTCTAA-GGGATACTCTAACC
1117445 TCGATTTTCA
Statistics
Matches: 436, Mismatches: 75, Indels: 70
0.75 0.13 0.12
Matches are distributed among these distances:
76 1 0.00
77 45 0.10
78 16 0.04
79 35 0.08
80 95 0.22
81 139 0.32
82 36 0.08
83 1 0.00
87 3 0.01
88 21 0.05
89 14 0.03
90 30 0.07
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (80 bp):
AATTTCTTCATCTCTAGGGATACTCCAACCCCACCATTTTCTAAGGGATACTCTAACCCATTTTT
ACTTCTAAAACATTG
Found at i:1117205 original size:88 final size:90
Alignment explanation
Indices: 1117034--1117207 Score: 237
Period size: 90 Copynumber: 2.0 Consensus size: 90
1117024 GGGGATACTT
* * * * *
1117034 CAACCCCATTTTTACTTCTAAAACATTGAATTTCTTCATCTCTGGGGATACTCCAACCCCACCAT
1 CAACCCCATTTTTACTTCTAAAACACTAAAATTCTTCATCACAGGGGATACTCCAACCCCACCAT
**
1117099 TTTCGAAGGGATACTCCAACCATTC
66 TTTCGAAGAAATACTCCAACCATTC
*
1117124 CAACCCCATTTTTACTTCTAAAACACTAAAATT-TTCATCACAGGGGATA-TCCAATCCCACCAT
1 CAACCCCATTTTTACTTCTAAAACACTAAAATTCTTCATCACAGGGGATACTCCAACCCCACCAT
*
1117187 TTT-TAAGAAAATACTCCAACC
66 TTTCGAAG-AAATACTCCAACC
1117208 TCGTTTTTAT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
87 3 0.04
88 27 0.36
89 14 0.19
90 30 0.41
ACGTcount: A:0.32, C:0.30, G:0.08, T:0.30
Consensus pattern (90 bp):
CAACCCCATTTTTACTTCTAAAACACTAAAATTCTTCATCACAGGGGATACTCCAACCCCACCAT
TTTCGAAGAAATACTCCAACCATTC
Found at i:1117233 original size:250 final size:247
Alignment explanation
Indices: 1116876--1117363 Score: 567
Period size: 250 Copynumber: 2.0 Consensus size: 247
1116866 ATACTCTAAT
* * * *
1116876 CCCATTTTTACTTCTAAAACATTGAATTTCTTCATCTCTAGGGATACTCCAACCCTACCATTTCT
1 CCCATTTTTACTTCTAAAACACTAAAATTCTTCATCACTAGGGATACTCCAACCCTACCATTTCT
** *
1116941 AAGGGAATACTCTAACCTCGTTTTTACTTCTAAAACATTGAATTTCTTCATCTCCAAGGATACTC
66 AAGAAAATACTCCAACCTCGTTTTTACTTCTAAAACATTGAATTT-TTCATCTCCAAGGATACTC
* * * * * * *
1117006 TAA-CCCACCCATTTTCTAGGGGATACT-TCAACCCCATTTTTACTTCTAAAACATTGAATTTCT
130 CAACCCCA-CCATCTCCGAGGAGATACTCT-AACCCCATTTTTACTT-TAAAA-A-TAAAATT-T
**
1117069 TCATCTCTGGGGATACTCCAACCCCACCATTTTCGAAGGGATACTCCAACCATTCCAAC
189 TCATCTCAAGGGATACTCCAACCCCACCATTTTCGAAGGGATACTCCAACCATTCCAAC
1117128 CCCATTTTTACTTCTAAAACACTAAAATT-TTCATCAC-AGGGGATA-TCCAATCCC-ACCATTT
1 CCCATTTTTACTTCTAAAACACTAAAATTCTTCATCACTA-GGGATACTCCAA-CCCTACCATTT
* * * ****
1117189 TTAAGAAAATACTCCAACCTCGTTTTTATTTCCTAAAA-ATTGAATTTTTTATCTTTGGGGATAC
64 CTAAGAAAATACTCCAACCTCGTTTTTACTT-CTAAAACATTGAATTTTTCATCTCCAAGGATAC
* * * * *
1117253 TCCAACCCCATCGTCTCCGAGGAGATACTCTAACCCTATTTTTACTTTTAAAATAAAATTTTCGT
128 TCCAACCCCACCATCTCCGAGGAGATACTCTAACCCCATTTTTACTTTAAAAATAAAATTTTCAT
* *
1117318 CTCAAGGGATACTCTAACCCCACCATTTTCGAAGGGATACTTCAAC
193 CTCAAGGGATACTCCAACCCCACCATTTTCGAAGGGATACTCCAAC
1117364 ACTGTTTTTA
Statistics
Matches: 201, Mismatches: 30, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
245 46 0.23
246 5 0.02
247 1 0.00
248 4 0.02
249 44 0.22
250 53 0.26
251 22 0.11
252 26 0.13
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.34
Consensus pattern (247 bp):
CCCATTTTTACTTCTAAAACACTAAAATTCTTCATCACTAGGGATACTCCAACCCTACCATTTCT
AAGAAAATACTCCAACCTCGTTTTTACTTCTAAAACATTGAATTTTTCATCTCCAAGGATACTCC
AACCCCACCATCTCCGAGGAGATACTCTAACCCCATTTTTACTTTAAAAATAAAATTTTCATCTC
AAGGGATACTCCAACCCCACCATTTTCGAAGGGATACTCCAACCATTCCAAC
Found at i:1123646 original size:87 final size:87
Alignment explanation
Indices: 1123498--1123825 Score: 392
Period size: 87 Copynumber: 3.8 Consensus size: 87
1123488 ACAAAGGAAG
* * *** *
1123498 ATTTGAATTTTTGTTAGAGCGAGGTTGGAGTATCCTCTCGGAATAGTGGGGATGGAATTTCCCCA
1 ATTTGAATTTTTGTTAGAACGAGGTTGGAGTATCCCCTTAAAATAGTGGGGATGGAGTTTCCCCA
*
1123563 CAA-ATAAAATTTCATGAAGTAA
66 -AAGATAAAATTCCATGAAGTAA
* * * * * *
1123585 ATTTGAATTTTTGTTAAAACAAGTTTGGAGTATCCCCTTACAATAGTGGGGATAGAGTTTCCCTA
1 ATTTGAATTTTTGTTAGAACGAGGTTGGAGTATCCCCTTAAAATAGTGGGGATGGAGTTTCCCCA
*
1123650 AAGATAAAATACCATGAAGTAA
66 AAGATAAAATTCCATGAAGTAA
* *
1123672 ATTTGAATTTTTGTTAGAATGGGGTTGGAGTAT--CCTTCCAAAATAGTGGGGATGGAGTTTCCC
1 ATTTGAATTTTTGTTAGAACGAGGTTGGAGTATCCCCTT--AAAATAGTGGGGATGGAGTTTCCC
* **
1123735 CAAAGATATAATTCCAAAAAGTAA
64 CAAAGATAAAATTCCATGAAGTAA
* * ** *
1123759 ATTTGAATTTTTGTTAGAACGAGGTTGGAGTATCCCCTTAGAATGGTTAGGATGGAGTTTTCCCA
1 ATTTGAATTTTTGTTAGAACGAGGTTGGAGTATCCCCTTAAAATAGTGGGGATGGAGTTTCCCCA
1123824 AA
66 AA
1123826 AATTATATAA
Statistics
Matches: 204, Mismatches: 32, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
85 4 0.02
86 2 0.01
87 194 0.95
89 4 0.02
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (87 bp):
ATTTGAATTTTTGTTAGAACGAGGTTGGAGTATCCCCTTAAAATAGTGGGGATGGAGTTTCCCCA
AAGATAAAATTCCATGAAGTAA
Found at i:1130880 original size:16 final size:16
Alignment explanation
Indices: 1130859--1130889 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1130849 ATATGAAAAA
1130859 AAGCAAAAAAAATAAT
1 AAGCAAAAAAAATAAT
1130875 AAGCAAAAAAAATAA
1 AAGCAAAAAAAATAA
1130890 AAAATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.10
Consensus pattern (16 bp):
AAGCAAAAAAAATAAT
Found at i:1130898 original size:16 final size:16
Alignment explanation
Indices: 1130855--1130900 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1130845 TAAGATATGA
1130855 AAAAAAGCAAAAAAAAT
1 AAAAAA-CAAAAAAAAT
* *
1130872 AATAAGCAAAAAAAAT
1 AAAAAACAAAAAAAAT
*
1130888 AAAAAATAAAAAA
1 AAAAAACAAAAAA
1130901 GAGACAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.83, C:0.04, G:0.04, T:0.09
Consensus pattern (16 bp):
AAAAAACAAAAAAAAT
Found at i:1132199 original size:28 final size:27
Alignment explanation
Indices: 1132152--1132248 Score: 81
Period size: 28 Copynumber: 3.6 Consensus size: 27
1132142 ATTCACGTTA
* * *
1132152 AAGCCTACATTACCTGGCACACGAGTC
1 AAGCCTACACTAGCTAGCACACGAGTC
* * *
1132179 GAAGCCTGCACTAGTTAGCAC-CTAAGT-
1 -AAGCCTACACTAGCTAGCACAC-GAGTC
1132206 AAGCCTACACTAGCTAGCACACGAGTC
1 AAGCCTACACTAGCTAGCACACGAGTC
* *
1132233 AAAGCCCACATTAGCT
1 -AAGCCTACACTAGCT
1132249 GGCATTCGTG
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
26 21 0.39
27 2 0.04
28 31 0.57
ACGTcount: A:0.32, C:0.31, G:0.19, T:0.19
Consensus pattern (27 bp):
AAGCCTACACTAGCTAGCACACGAGTC
Found at i:1132545 original size:82 final size:82
Alignment explanation
Indices: 1132398--1132602 Score: 202
Period size: 82 Copynumber: 2.5 Consensus size: 82
1132388 GTATTCTCAT
* * * *
1132398 TAAAGCCCATATTAGTTGGCACATAAGTTG-AAGCCCACACTAGTTGACACCTTAGTCTAAGCCC
1 TAAAGCCCACACTAGTTGGCACATAAG-TGAAAGCCCACAATAGTTGACA-CTTAGTCTAAACCC
* *
1132462 ACACTAGTTGGTACCTAAG
64 ACACTAGTTGGCACATAAG
* *
1132481 T-AAGCCCACACTAGTTAGCACATAAGTGAAAGCCCACAATAGTTGGCA-TTCATGT-TAAAACC
1 TAAAGCCCACACTAGTTGGCACATAAGTGAAAGCCCACAATAGTTGACACTT-A-GTCT-AAACC
* *
1132543 CACATTAGTTGGCATATAAG
63 CACACTAGTTGGCACATAAG
* * * *
1132563 TCAAAGCCTACACTAGCTGGCACTTAAGTCAAAGCCCACA
1 T-AAAGCCCACACTAGTTGGCACATAAGTGAAAGCCCACA
1132603 CTAGCTAGTA
Statistics
Matches: 101, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
80 2 0.02
81 4 0.04
82 62 0.61
83 1 0.01
84 32 0.32
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (82 bp):
TAAAGCCCACACTAGTTGGCACATAAGTGAAAGCCCACAATAGTTGACACTTAGTCTAAACCCAC
ACTAGTTGGCACATAAG
Found at i:1132576 original size:138 final size:137
Alignment explanation
Indices: 1132187--1132606 Score: 461
Period size: 138 Copynumber: 3.0 Consensus size: 137
1132177 TCGAAGCCTG
* * *
1132187 CACTAGTTAGCACCTAAGTAAGCCTACACTAGCTAGCACACGAGTCAAAGCCCACATTAGCTGGC
1 CACTAGTTGGCACCTAAGTAAGCCCACACTAGCTAGCACACAAGTCAAAGCCCACATTAGCTGGC
* * * *
1132252 ATTCGTGTTCAAGCCCAAATTAGTTGGCACT-TGAA-TCGAAG-CTCACACCAATTGGTACCTTA
66 ATTC-TGTTAAAGCCCAAATTAGTTGGCA-TAT-AAGTCGAAGCCT-ACACTAGTTGGCACCTTA
* *
1132314 GGCCAAGCCCA
127 GTCAAAGCCCA
* * * ** *
1132325 CACTAGTTGGCATCTAAGTAAGCCCACACTAACTGGCACACAAGTCAAAGCCCATGTTAGCTGGT
1 CACTAGTTGGCACCTAAGTAAGCCCACACTAGCTAGCACACAAGTCAAAGCCCACATTAGCTGGC
* * * * * *
1132390 ATTCTCATTAAAGCCCATATTAGTTGGCACATAAGTTGAAGCCCACACTAGTTGACACCTTAGTC
66 ATTCT-GTTAAAGCCCAAATTAGTTGGCATATAAGTCGAAGCCTACACTAGTTGGCACCTTAGTC
*
1132455 TAAGCCCA
130 AAAGCCCA
* * * * * *
1132463 CACTAGTTGGTACCTAAGTAAGCCCACACTAGTTAGCACATAAGTGAAAGCCCACAATAGTTGGC
1 CACTAGTTGGCACCTAAGTAAGCCCACACTAGCTAGCACACAAGTCAAAGCCCACATTAGCTGGC
* * * *
1132528 ATTCATGTTAAAACCCACATTAGTTGGCATATAAGTCAAAGCCTACACTAGCTGGCA-CTTAAGT
66 ATTC-TGTTAAAGCCCAAATTAGTTGGCATATAAGTCGAAGCCTACACTAGTTGGCACCTT-AGT
1132592 CAAAGCCCA
129 CAAAGCCCA
1132601 CACTAG
1 CACTAG
1132607 CTAGTATCTA
Statistics
Matches: 233, Mismatches: 43, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
137 6 0.03
138 225 0.97
139 2 0.01
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (137 bp):
CACTAGTTGGCACCTAAGTAAGCCCACACTAGCTAGCACACAAGTCAAAGCCCACATTAGCTGGC
ATTCTGTTAAAGCCCAAATTAGTTGGCATATAAGTCGAAGCCTACACTAGTTGGCACCTTAGTCA
AAGCCCA
Found at i:1132601 original size:56 final size:56
Alignment explanation
Indices: 1132318--1132641 Score: 223
Period size: 56 Copynumber: 5.9 Consensus size: 56
1132308 ACCTTAGGCC
** *
1132318 AAGCCCACACTAGTTGGCATCTAAGT--AAGCCCACACTAACTGGCACACAAGTCA
1 AAGCCCACACTAGTTGGCATCTAAGTCAAAGCCCACACTAGTTGGCACATAAGTCA
*** * * * * * * **
1132372 AAGCCCATGTTAGCTGGTATTCTCA-TTAAAGCCCATATTAGTTGGCACATAAGTTG
1 AAGCCCACACTAGTTGGCA-TCTAAGTCAAAGCCCACACTAGTTGGCACATAAGTCA
* * * * * *
1132428 AAGCCCACACTAGTTGACACCTTAGTCTAAGCCCACACTAGTTGGTACCTAAGT--
1 AAGCCCACACTAGTTGGCATCTAAGTCAAAGCCCACACTAGTTGGCACATAAGTCA
* * * *
1132482 AAGCCCACACTAGTTAGCA-CATAAGTGAAAGCCCACAATAGTTGGCATTCAT--GTTA
1 AAGCCCACACTAGTTGGCATC-TAAGTCAAAGCCCACACTAGTTGGCA--CATAAGTCA
* * * * * *
1132538 AAACCCACATTAGTTGGCATATAAGTCAAAGCCTACACTAGCTGGCACTTAAGTCA
1 AAGCCCACACTAGTTGGCATCTAAGTCAAAGCCCACACTAGTTGGCACATAAGTCA
* * * * * * *
1132594 AAGCCCACACTAGCTAGTATCTAAGTTAAAACCCACACCAGCTGGCAC
1 AAGCCCACACTAGTTGGCATCTAAGTCAAAGCCCACACTAGTTGGCAC
1132642 CTCATAGGGA
Statistics
Matches: 203, Mismatches: 55, Indels: 22
0.73 0.20 0.08
Matches are distributed among these distances:
53 1 0.00
54 57 0.28
55 7 0.03
56 138 0.68
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (56 bp):
AAGCCCACACTAGTTGGCATCTAAGTCAAAGCCCACACTAGTTGGCACATAAGTCA
Found at i:1132608 original size:28 final size:28
Alignment explanation
Indices: 1132318--1132606 Score: 191
Period size: 28 Copynumber: 10.5 Consensus size: 28
1132308 ACCTTAGGCC
1132318 AAGCCCACACTAGTTGGCA-TCTAAGT--
1 AAGCCCACACTAGTTGGCACT-TAAGTCA
** **
1132344 AAGCCCACACTAACTGGCACACAAGTCA
1 AAGCCCACACTAGTTGGCACTTAAGTCA
*** * * * * *
1132372 AAGCCCATGTTAGCTGGTATTCTCA-TTA
1 AAGCCCACACTAGTTGGCACT-TAAGTCA
* * * **
1132400 AAGCCCATATTAGTTGGCACATAAGTTG
1 AAGCCCACACTAGTTGGCACTTAAGTCA
* *
1132428 AAGCCCACACTAGTTGACACCTT-AGTCT
1 AAGCCCACACTAGTTGGCA-CTTAAGTCA
* *
1132456 AAGCCCACACTAGTTGGTACCTAAGT--
1 AAGCCCACACTAGTTGGCACTTAAGTCA
* * *
1132482 AAGCCCACACTAGTTAGCACATAAGTGA
1 AAGCCCACACTAGTTGGCACTTAAGTCA
* * *
1132510 AAGCCCACAATAGTTGGCA-TTCATGTTA
1 AAGCCCACACTAGTTGGCACTT-AAGTCA
* *
1132538 AAACCCACATTAGTTGGCA-TATAAGTCA
1 AAGCCCACACTAGTTGGCACT-TAAGTCA
* *
1132566 AAGCCTACACTAGCTGGCACTTAAGTCA
1 AAGCCCACACTAGTTGGCACTTAAGTCA
1132594 AAGCCCACACTAG
1 AAGCCCACACTAG
1132607 CTAGTATCTA
Statistics
Matches: 204, Mismatches: 47, Indels: 22
0.75 0.17 0.08
Matches are distributed among these distances:
26 44 0.22
27 5 0.02
28 150 0.74
29 5 0.02
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.23
Consensus pattern (28 bp):
AAGCCCACACTAGTTGGCACTTAAGTCA
Found at i:1132618 original size:28 final size:28
Alignment explanation
Indices: 1132428--1132641 Score: 109
Period size: 28 Copynumber: 7.7 Consensus size: 28
1132418 ACATAAGTTG
* *
1132428 AAGCCCACACTAG-TTGACACCTT-AGTCT
1 AAGCCCACACTAGCTAG-CA-CTTAAGTCA
* * * *
1132456 AAGCCCACACTAGTTGGTACCTAAGT--
1 AAGCCCACACTAGCTAGCACTTAAGTCA
* * *
1132482 AAGCCCACACTAGTTAGCACATAAGTGA
1 AAGCCCACACTAGCTAGCACTTAAGTCA
* * * * *
1132510 AAGCCCACAATAGTTGGCA-TTCATGTTA
1 AAGCCCACACTAGCTAGCACTT-AAGTCA
* * * *
1132538 AAACCCACATTAGTTGGCA-TATAAGTCA
1 AAGCCCACACTAGCTAGCACT-TAAGTCA
* *
1132566 AAGCCTACACTAGCTGGCACTTAAGTCA
1 AAGCCCACACTAGCTAGCACTTAAGTCA
* *
1132594 AAGCCCACACTAGCTAGTA-TCTAAGTTA
1 AAGCCCACACTAGCTAGCACT-TAAGTCA
* * *
1132622 AAACCCACACCAGCTGGCAC
1 AAGCCCACACTAGCTAGCAC
1132642 CTCATAGGGA
Statistics
Matches: 150, Mismatches: 27, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
26 23 0.15
27 4 0.03
28 119 0.79
29 4 0.03
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (28 bp):
AAGCCCACACTAGCTAGCACTTAAGTCA
Found at i:1132619 original size:138 final size:137
Alignment explanation
Indices: 1132124--1132606 Score: 447
Period size: 138 Copynumber: 3.5 Consensus size: 137
1132114 CATCAAAAGG
* * * * * * **
1132124 AAGCCCACATTAGTTGGCATTCACGTTAAAGCCTACATTACCTGGCACAC-GAGTCGAAGCCTGC
1 AAGCCCACATTAGTTGGCATTCAAGTCAAAGCCTACACTAGCTGGCAC-CTTAGTCAAAGCCCAC
* *
1132188 ACTAGTTAGCACCTAAGTAAGCCTACACTAGCTAGCACACGAGTCAAAGCCCACATTAGCTGGCA
65 ACTAGTTAGCACCTAAGTAAGCCCACACTAGCTAGCACACAAGTCAAAGCCCACATTAGCTGGCA
*
1132253 TTCGTGTTC
130 TTC-TGTTA
* * * * ** * * *
1132262 AAGCCCAAATTAGTTGGCACTTGAA-TCGAAG-CTCACACCAATTGGTACCTTAGGCCAAGCCCA
1 AAGCCCACATTAGTTGGCA-TTCAAGTCAAAGCCT-ACACTAGCTGGCACCTTAGTCAAAGCCCA
* * * * ** *
1132325 CACTAGTTGGCATCTAAGTAAGCCCACACTAACTGGCACACAAGTCAAAGCCCATGTTAGCTGGT
64 CACTAGTTAGCACCTAAGTAAGCCCACACTAGCTAGCACACAAGTCAAAGCCCACATTAGCTGGC
*
1132390 ATTCTCATTA
129 ATTCT-GTTA
* * ** * * * *
1132400 AAGCCCATATTAGTTGGCACAT-AAGTTGAAGCCCACACTAGTTGACACCTTAGTCTAAGCCCAC
1 AAGCCCACATTAGTTGGCA-TTCAAGTCAAAGCCTACACTAGCTGGCACCTTAGTCAAAGCCCAC
* * * * * * *
1132464 ACTAGTTGGTACCTAAGTAAGCCCACACTAGTTAGCACATAAGTGAAAGCCCACAATAGTTGGCA
65 ACTAGTTAGCACCTAAGTAAGCCCACACTAGCTAGCACACAAGTCAAAGCCCACATTAGCTGGCA
1132529 TTCATGTTA
130 TTC-TGTTA
*
1132538 AAACCCACATTAGTTGGCATAT-AAGTCAAAGCCTACACTAGCTGGCA-CTTAAGTCAAAGCCCA
1 AAGCCCACATTAGTTGGCAT-TCAAGTCAAAGCCTACACTAGCTGGCACCTT-AGTCAAAGCCCA
1132601 CACTAG
64 CACTAG
1132607 CTAGTATCTA
Statistics
Matches: 278, Mismatches: 58, Indels: 18
0.79 0.16 0.05
Matches are distributed among these distances:
137 9 0.03
138 264 0.95
139 5 0.02
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (137 bp):
AAGCCCACATTAGTTGGCATTCAAGTCAAAGCCTACACTAGCTGGCACCTTAGTCAAAGCCCACA
CTAGTTAGCACCTAAGTAAGCCCACACTAGCTAGCACACAAGTCAAAGCCCACATTAGCTGGCAT
TCTGTTA
Found at i:1133544 original size:36 final size:31
Alignment explanation
Indices: 1133497--1133594 Score: 90
Period size: 36 Copynumber: 2.9 Consensus size: 31
1133487 ATAATGAACT
*
1133497 AGAAAAGAAAGATAAAAAAATAAGAGAAAGGAAGGG
1 AGAAAAAAAAGA-AAAAAAATAAGAGAAA--AA--G
* *
1133533 AGAAAAAAAAGAAAAAGAAAAAAGGGAAAAAG
1 AGAAAAAAAAGAAAAA-AAATAAGAGAAAAAG
1133565 AGAAAAAGAAAGAAGAAAAAATAAGA-AAAA
1 AGAAAAA-AAAGAA-AAAAAATAAGAGAAAA
1133595 TTGGTGGCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
32 12 0.22
33 12 0.22
34 5 0.09
35 4 0.07
36 21 0.39
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.03
Consensus pattern (31 bp):
AGAAAAAAAAGAAAAAAAATAAGAGAAAAAG
Found at i:1133553 original size:15 final size:15
Alignment explanation
Indices: 1133533--1133594 Score: 72
Period size: 15 Copynumber: 4.1 Consensus size: 15
1133523 AAAGGAAGGG
1133533 AGAAAAAAAAGAAAA
1 AGAAAAAAAAGAAAA
**
1133548 AGAAAAAAGGGAAAA
1 AGAAAAAAAAGAAAA
*
1133563 AG-AGAAAAAGAAAGA
1 AGAAAAAAAAGAAA-A
1133578 AGAAAAAATAAGAAAA
1 AGAAAAAA-AAGAAAA
1133594 A
1 A
1133595 TTGGTGGCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
14 8 0.21
15 18 0.47
16 6 0.16
17 6 0.16
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (15 bp):
AGAAAAAAAAGAAAA
Found at i:1133554 original size:7 final size:7
Alignment explanation
Indices: 1133537--1133585 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
1133527 GAAGGGAGAA
1133537 AAAAAAG
1 AAAAAAG
1133544 -AAAAAG
1 AAAAAAG
1133550 AAAAAAGG
1 AAAAAA-G
*
1133558 GAAAAAG
1 AAAAAAG
1133565 AGAAAAAG
1 A-AAAAAG
*
1133573 AAAGAAG
1 AAAAAAG
1133580 AAAAAA
1 AAAAAA
1133586 TAAGAAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 6 0.17
7 16 0.46
8 13 0.37
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1133562 original size:23 final size:22
Alignment explanation
Indices: 1133533--1133594 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 22
1133523 AAAGGAAGGG
1133533 AGAAAAAAAAGAAAAAGAAAAA
1 AGAAAAAAAAGAAAAAGAAAAA
* * *
1133555 AGGGAAAAAGAGAAAAAGAAAGA
1 A-GAAAAAAAAGAAAAAGAAAAA
1133578 AGAAAAAATAAGAAAAA
1 AGAAAAAA-AAGAAAAA
1133595 TTGGTGGCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 7 0.21
23 26 0.79
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (22 bp):
AGAAAAAAAAGAAAAAGAAAAA
Found at i:1138594 original size:20 final size:19
Alignment explanation
Indices: 1138545--1138594 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1138535 CCATTTTTGG
* *
1138545 TCAAAGTTAAAGTTAATAA
1 TCAAAGTCAAAGTCAATAA
*
1138564 TCAACGATCAAAGTCAATAGA
1 TCAAAG-TCAAAGTCAATA-A
1138585 TCAAAGTCAA
1 TCAAAGTCAA
1138595 CAATAAAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 5 0.20
20 14 0.56
21 6 0.24
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (19 bp):
TCAAAGTCAAAGTCAATAA
Found at i:1138994 original size:19 final size:19
Alignment explanation
Indices: 1138970--1139006 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1138960 AAATAATTTG
* *
1138970 AATTCATGGAGGATTCTTT
1 AATTCATGAAAGATTCTTT
1138989 AATTCATGAAAGATTCTT
1 AATTCATGAAAGATTCTT
1139007 AAACCTAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (19 bp):
AATTCATGAAAGATTCTTT
Found at i:1145673 original size:28 final size:28
Alignment explanation
Indices: 1145612--1145693 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
1145602 TTTTGGAGAT
*
1145612 AATAACGGGGTTGGAGTGTTCCCTCG--GA
1 AATAACGGGGTTGGAGT-ATCCC-CGATGA
*
1145640 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGGGGTTGGAGTATCCCCGATGA
* *
1145668 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGGGGTTGGAGTATCCCCGAT
1145694 TGTGAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.04
27 4 0.09
28 41 0.87
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.24
Consensus pattern (28 bp):
AATAACGGGGTTGGAGTATCCCCGATGA
Found at i:1145835 original size:51 final size:51
Alignment explanation
Indices: 1145673--1145844 Score: 202
Period size: 52 Copynumber: 3.3 Consensus size: 51
1145663 GATGAAATAA
* *
1145673 CGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAAT
1 CGAGGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGGAAATAAAAT
* * * * *
1145725 CG-GTGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAAC
1 CGAG-GTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTGGAAATAAAAT
* *** *
1145777 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGT
1 CGAGGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAAT
1145828 CGAGGTTGGAGTATCCC
1 CGAGGTTGGAGTATCCC
1145845 TTCGGAAATA
Statistics
Matches: 100, Mismatches: 17, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
51 37 0.37
52 52 0.52
53 11 0.11
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
CGAGGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAAT
Found at i:1145980 original size:211 final size:211
Alignment explanation
Indices: 1145620--1146009 Score: 554
Period size: 211 Copynumber: 1.8 Consensus size: 211
1145610 ATAATAACGG
* * *
1145620 GGTTGGAGTGTTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
1 GGTTGGAGTGATCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAAT
* *
1145685 ATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGTGTTGGAGTATCCCCGATTAAA
66 ATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA
** * * *
1145750 GGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATT
131 GGAAAATTAATGTTTTGAAAATAAAACCGGAGTTAGAATATCCCCGATTATGAAAAATCAATATT
1145815 TTGGAAATAAAGTCGA
196 TTGGAAATAAAGTCGA
* *
1145831 GGTTGGAGT-ATCCCTTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAA
1 GGTTGGAGTGATCCC-TCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAA
* *
1145894 TGTCCCCGATTGTGAAGAAATTGATGTTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGAT
65 TATCCCCGATTGTGAA-AAATTG--GTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGAT
* * * *
1145959 TATA-GAAAATTAATG-TTTGAAAGTAAAATCGGAGTTAGAATATCCTCGATT
127 TAAAGGAAAATTAATGTTTTGAAAATAAAACCGGAGTTAGAATATCCCCGATT
1146010 GTGGAGAATT
Statistics
Matches: 157, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
210 31 0.20
211 76 0.48
212 9 0.06
213 41 0.26
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.30
Consensus pattern (211 bp):
GGTTGGAGTGATCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAAT
ATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA
GGAAAATTAATGTTTTGAAAATAAAACCGGAGTTAGAATATCCCCGATTATGAAAAATCAATATT
TTGGAAATAAAGTCGA
Found at i:1148325 original size:20 final size:20
Alignment explanation
Indices: 1148300--1148350 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1148290 AAAATGCCTG
1148300 AATGTATCGATACATTGTAA
1 AATGTATCGATACATTGTAA
1148320 AATGTATCGATACATTGTAA
1 AATGTATCGATACATTGTAA
1148340 AATGTATCGAT
1 AATGTATCGAT
1148351 GCATCTGGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTGTAA
Found at i:1148410 original size:13 final size:13
Alignment explanation
Indices: 1148392--1148417 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1148382 ACAAAGATCC
1148392 ATGTATCGATACA
1 ATGTATCGATACA
1148405 ATGTATCGATACA
1 ATGTATCGATACA
1148418 CAAAAAATGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1148480 original size:19 final size:18
Alignment explanation
Indices: 1148456--1148523 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1148446 CAGTAGCTAA
1148456 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1148475 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1148490 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1148507 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1148524 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1148496 original size:13 final size:13
Alignment explanation
Indices: 1148478--1148502 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1148468 ACAATACTTA
1148478 TGTATCGATACAT
1 TGTATCGATACAT
1148491 TGTATCGATACA
1 TGTATCGATACA
1148503 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1148500 original size:32 final size:32
Alignment explanation
Indices: 1148459--1148521 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1148449 TAGCTAATTA
*
1148459 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1148491 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1148522 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1153147 original size:283 final size:284
Alignment explanation
Indices: 1152582--1153149 Score: 1030
Period size: 283 Copynumber: 2.0 Consensus size: 284
1152572 CATGTCGTGG
*
1152582 AGTAATTGGAAACATCACAATACTTCTTCAGATAGGCCCATGCACATATGAAGTTGACTTTCAAG
1 AGTAATTGGAAACATCACAATACTTCTTCAAATAGGCCCATGCACATATGAAGTTGACTTTCAAG
1152647 TAATGGATATCAATCTATCTTATAACTACCTATTAGGGAGGCCATGGATACACTCAGCCAGGACC
66 TAATGGATATCAATCTATCTTATAACTACCTATTAGGGAGGCCATGGATACACTCAGCCAGGACC
1152712 GTCCCATCTTCCCTCGATCAGAAGCTCAAATTTGTGGTAGATGACAAGGTAGTCACCATCGGGGC
131 GTCCCATCTTCCCTCGATCAGAAGCTCAAATTTGTGGTAGATGACAAGGTAGTCACCATCGGGGC
*
1152777 AAAAGAAGAAATGATTGCCACTGCTTTCACTGATGATGTCTACATAGAGCCAACTAAAAATGCAT
196 AAAAGAAGAAATGATTGCCACTGCTTTCACTGATGATGTCTACATAGAGCCAACTAAAAATGCAC
** * *
1152842 TGGAGTCGTCTTTCCAATCCTTCA
261 CAGAGCCATCTTTCCAATCCTTCA
1152866 AGTAATTGGAAACATCACAATACTTCTTCAAATAGGCCCATGCACATATGAAGTTGACTTTCAAG
1 AGTAATTGGAAACATCACAATACTTCTTCAAATAGGCCCATGCACATATGAAGTTGACTTTCAAG
*
1152931 TAATGGATATCAATCTATCTTATAACTACCTATTAGGGAGGCCATGGATACACTCAGCCGGGACC
66 TAATGGATATCAATCTATCTTATAACTACCTATTAGGGAGGCCATGGATACACTCAGCCAGGACC
* *
1152996 GT-CCATCTTCCCTCGATCAGAAGCTCAAATTTGTGGTAGATGATAAGGTGGTCACCATCGGGGC
131 GTCCCATCTTCCCTCGATCAGAAGCTCAAATTTGTGGTAGATGACAAGGTAGTCACCATCGGGGC
* *
1153060 AGAAGAAGAAATGATTGCCACTGCTTTCACTGATGATGTCTACATAGAGCCAACTGAAAATGCAC
196 AAAAGAAGAAATGATTGCCACTGCTTTCACTGATGATGTCTACATAGAGCCAACTAAAAATGCAC
1153125 CAGAGCCATCTTTCCAATCCTTCA
261 CAGAGCCATCTTTCCAATCCTTCA
1153149 A
1 A
1153150 ATTTGTTAAT
Statistics
Matches: 273, Mismatches: 11, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
283 143 0.52
284 130 0.48
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (284 bp):
AGTAATTGGAAACATCACAATACTTCTTCAAATAGGCCCATGCACATATGAAGTTGACTTTCAAG
TAATGGATATCAATCTATCTTATAACTACCTATTAGGGAGGCCATGGATACACTCAGCCAGGACC
GTCCCATCTTCCCTCGATCAGAAGCTCAAATTTGTGGTAGATGACAAGGTAGTCACCATCGGGGC
AAAAGAAGAAATGATTGCCACTGCTTTCACTGATGATGTCTACATAGAGCCAACTAAAAATGCAC
CAGAGCCATCTTTCCAATCCTTCA
Found at i:1158619 original size:15 final size:15
Alignment explanation
Indices: 1158599--1158633 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1158589 AGTCTTGATG
1158599 GAAGCCAAACTTGAA
1 GAAGCCAAACTTGAA
1158614 GAAGCCAAACTTGAA
1 GAAGCCAAACTTGAA
1158629 GAAGC
1 GAAGC
1158634 TGAATGGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (15 bp):
GAAGCCAAACTTGAA
Found at i:1159009 original size:9 final size:9
Alignment explanation
Indices: 1158995--1159085 Score: 86
Period size: 9 Copynumber: 10.6 Consensus size: 9
1158985 CTTTTGTTCT
1158995 AAAAAAAAC
1 AAAAAAAAC
1159004 --AAAAAAC
1 AAAAAAAAC
1159011 AAAAAAAAC
1 AAAAAAAAC
1159020 AAAAAAAAC
1 AAAAAAAAC
1159029 AAAAAAAAC
1 AAAAAAAAC
*
1159038 AGAAAAAAC
1 AAAAAAAAC
*
1159047 --CAAAAAC
1 AAAAAAAAC
*
1159054 -TAAAAAAC
1 AAAAAAAAC
1159062 AAATAAAAA-
1 AAA-AAAAAC
*
1159071 ACAAACAAAC
1 A-AAAAAAAC
1159081 AAAAA
1 AAAAA
1159086 GGGGTCTAGA
Statistics
Matches: 69, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
7 13 0.19
8 6 0.09
9 42 0.61
10 8 0.12
ACGTcount: A:0.84, C:0.13, G:0.01, T:0.02
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:1159018 original size:18 final size:18
Alignment explanation
Indices: 1158995--1159085 Score: 84
Period size: 16 Copynumber: 5.2 Consensus size: 18
1158985 CTTTTGTTCT
1158995 AAAAAAAACAAAAAAC--
1 AAAAAAAACAAAAAACAA
1159011 AAAAAAAACAAAAAA-AA
1 AAAAAAAACAAAAAACAA
*
1159028 CAAAAAAAAC-AGAAA-AA
1 -AAAAAAAACAAAAAACAA
**
1159045 ACCAAAAACTAAAAAACAA
1 AAAAAAAAC-AAAAAACAA
*
1159064 ATAAAAAACAAACAAACAA
1 AAAAAAAACAAA-AAACAA
1159083 AAA
1 AAA
1159086 GGGGTCTAGA
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
16 22 0.36
17 6 0.10
18 16 0.26
19 17 0.28
ACGTcount: A:0.84, C:0.13, G:0.01, T:0.02
Consensus pattern (18 bp):
AAAAAAAACAAAAAACAA
Found at i:1159034 original size:34 final size:35
Alignment explanation
Indices: 1158995--1159085 Score: 107
Period size: 35 Copynumber: 2.6 Consensus size: 35
1158985 CTTTTGTTCT
1158995 AAAAAAAACAAAAAACAAAAAAAAC-AAAAAA-AA
1 AAAAAAAACAAAAAACAAAAAAAACTAAAAAACAA
**
1159028 CAAAAAAAACAGAAAAA-ACCAAAAACTAAAAAACAA
1 -AAAAAAAACA-AAAAACAAAAAAAACTAAAAAACAA
*
1159064 ATAAAAAACAAACAAACAAAAA
1 AAAAAAAACAAA-AAACAAAAA
1159086 GGGGTCTAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
34 19 0.40
35 23 0.49
36 5 0.11
ACGTcount: A:0.84, C:0.13, G:0.01, T:0.02
Consensus pattern (35 bp):
AAAAAAAACAAAAAACAAAAAAAACTAAAAAACAA
Found at i:1159081 original size:43 final size:42
Alignment explanation
Indices: 1158996--1159085 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 42
1158986 TTTTGTTCTA
1158996 AAAAAAACAAAAAACAAAAAAAACAAAAAAAACAAAAAAAAC
1 AAAAAAACAAAAAACAAAAAAAACAAAAAAAACAAAAAAAAC
* * *
1159038 AGAAAAAACCAAAAAC-TAAAAAACAAATAAAAA-ACAAACAAAC
1 A-AAAAAACAAAAAACAAAAAAAACAAA-AAAAACA-AAAAAAAC
1159081 AAAAA
1 AAAAA
1159086 GGGGTCTAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
42 16 0.38
43 26 0.62
ACGTcount: A:0.83, C:0.13, G:0.01, T:0.02
Consensus pattern (42 bp):
AAAAAAACAAAAAACAAAAAAAACAAAAAAAACAAAAAAAAC
Found at i:1160299 original size:13 final size:14
Alignment explanation
Indices: 1160268--1160305 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1160258 TAATTTGCCA
1160268 TTTGTCAAGAAATT
1 TTTGTCAAGAAATT
*
1160282 ATTGTCAA-AAATT
1 TTTGTCAAGAAATT
*
1160295 TTTGTCTAGAA
1 TTTGTCAAGAA
1160306 TGTTCATCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (14 bp):
TTTGTCAAGAAATT
Found at i:1160347 original size:28 final size:28
Alignment explanation
Indices: 1160316--1160642 Score: 433
Period size: 28 Copynumber: 11.5 Consensus size: 28
1160306 TGTTCATCTC
*
1160316 TTCAAAGTCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1160344 TTCAAAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
1160372 TTCAAAGCCCATAAGTCAGTGACATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1160400 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
1160428 TTCAAAGCCCACAAGTCAGTGGCA-CTCT
1 TTCAAAGCCCACAAGTCAGTGGCATC-CT
* *
1160456 TTCAAAGCCCACAAATAAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1160484 TTCAAAGCCCATAAGTCAATGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1160511 CTTCAAAAGACCACAAGTCAGTGGCATCCT
1 -TTC-AAAGCCCACAAGTCAGTGGCATCCT
*
1160541 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
1160569 TTTAAAGCCCAAAAGTCAGTGGCATACCCC
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
*
1160599 TTCAAAGCCCACAAGTAAGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
1160629 TTCAAAGCCCACAA
1 TTCAAAGCCCACAA
1160643 AATTCGGTGG
Statistics
Matches: 264, Mismatches: 28, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
27 3 0.01
28 194 0.73
29 23 0.09
30 44 0.17
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:1160820 original size:45 final size:46
Alignment explanation
Indices: 1160769--1160900 Score: 158
Period size: 49 Copynumber: 2.8 Consensus size: 46
1160759 AAGTCTGATA
* *
1160769 TCGCTGGCATTGAATCAGCATATTGGCACCTTT-ATTAGCCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGGCACCTTTCATTAGCCCAATG
* * *
1160814 TCGCTGGCCTTGAATCAACACATTGGTCCACTTTTCCCTTAGCCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGG--CACCTTT-CATTAGCCCAATG
*
1160863 TCGCTGGCCTTGAATTAGCACATTGGCACTCTTCTCAT
1 TCGCTGGCCTTGAATCAGCACATTGGCAC-CTT-TCAT
1160901 CTCCAAGTCT
Statistics
Matches: 72, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
45 23 0.32
47 9 0.12
48 4 0.06
49 36 0.50
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (46 bp):
TCGCTGGCCTTGAATCAGCACATTGGCACCTTTCATTAGCCCAATG
Found at i:1164555 original size:15 final size:15
Alignment explanation
Indices: 1164535--1164565 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1164525 TAAAAATGTC
*
1164535 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1164550 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1164565 C
1 C
1164566 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1166654 original size:13 final size:13
Alignment explanation
Indices: 1166636--1166674 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1166626 ACATTTTTCC
1166636 TTGTATCGATACA
1 TTGTATCGATACA
1166649 TTGTATCGATACA
1 TTGTATCGATACA
*
1166662 CTGTATCGATACA
1 TTGTATCGATACA
1166675 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1168541 original size:37 final size:37
Alignment explanation
Indices: 1168468--1168566 Score: 170
Period size: 37 Copynumber: 2.8 Consensus size: 37
1168458 ATTTTGATAC
1168468 GAATTACTTGATTAAGGGGGAGA----TTTTTTTTTT
1 GAATTACTTGATTAAGGGGGAGATTTTTTTTTTTTTT
1168501 GAATTACTTGATTAAGGGGGAGATTTTTTTTTTTTTT
1 GAATTACTTGATTAAGGGGGAGATTTTTTTTTTTTTT
1168538 GAATTACTTGATTAAGGGGGAGATTTTTT
1 GAATTACTTGATTAAGGGGGAGATTTTTT
1168567 AATAAACGGG
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
33 23 0.37
37 39 0.63
ACGTcount: A:0.24, C:0.03, G:0.24, T:0.48
Consensus pattern (37 bp):
GAATTACTTGATTAAGGGGGAGATTTTTTTTTTTTTT
Found at i:1169210 original size:20 final size:20
Alignment explanation
Indices: 1169187--1169259 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1169177 ACAATTCAAA
1169187 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1169207 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
1169228 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1169248 GTATCGATACAT
1 GTATCGATACAT
1169260 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1169230 original size:21 final size:21
Alignment explanation
Indices: 1169204--1169280 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
1169194 TACATGTTGC
1169204 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
1169225 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
1169245 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
1169265 AGATGTATCGATACAT
1 A-ATGTATCGATACAT
1169281 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:1169238 original size:41 final size:41
Alignment explanation
Indices: 1169187--1169280 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
1169177 ACAATTCAAA
1169187 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAA-AT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAAGAT
1169228 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1169269 GTATCGATACAT
1 GTATCGATACAT
1169281 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 6 0.12
41 46 0.88
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1169337 original size:13 final size:13
Alignment explanation
Indices: 1169319--1169344 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1169309 TACAGCAAGT
1169319 ATGTATCGATACA
1 ATGTATCGATACA
1169332 ATGTATCGATACA
1 ATGTATCGATACA
1169345 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1171475 original size:22 final size:22
Alignment explanation
Indices: 1171447--1171489 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1171437 TTTCTTTGTT
*
1171447 TTTGCTTGTTGTTTCTTCTTTA
1 TTTGCTTGCTGTTTCTTCTTTA
1171469 TTTGCTTGCTGTTTCTTCTTT
1 TTTGCTTGCTGTTTCTTCTTT
1171490 CCTCAGTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.02, C:0.16, G:0.14, T:0.67
Consensus pattern (22 bp):
TTTGCTTGCTGTTTCTTCTTTA
Found at i:1171547 original size:47 final size:47
Alignment explanation
Indices: 1171473--1171563 Score: 114
Period size: 47 Copynumber: 1.9 Consensus size: 47
1171463 TCTTTATTTG
*
1171473 CTTGCTGTTTCTTCTTTCCTCAGTTGTTTT-TCTTCTTGCTATTTCAT
1 CTTGCTGTTTCTTCTTTCCTCAGTTGTTTTAT-TTCTTACTATTTCAT
* * *
1171520 CTTGCTGTTTCTTTTCTTGCTTA-TTGTTTTATTTCTTACTATTT
1 CTTGCTGTTTCTTCT-TTCCTCAGTTGTTTTATTTCTTACTATTT
1171564 TTGTTGCTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
47 32 0.84
48 6 0.16
ACGTcount: A:0.08, C:0.20, G:0.10, T:0.63
Consensus pattern (47 bp):
CTTGCTGTTTCTTCTTTCCTCAGTTGTTTTATTTCTTACTATTTCAT
Found at i:1171654 original size:25 final size:25
Alignment explanation
Indices: 1171623--1171691 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 25
1171613 TTGATGTTAC
* *
1171623 TGCTTCCTCCTCCATCAGCTGCTGT
1 TGCTTCCTCCACCATCAACTGCTGT
* *
1171648 TGCTTCCTCCACCATCAATTTCTGT
1 TGCTTCCTCCACCATCAACTGCTGT
*
1171673 TGCTTCTTCCACCATCAAC
1 TGCTTCCTCCACCATCAAC
1171692 AACTGTAGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.14, C:0.39, G:0.10, T:0.36
Consensus pattern (25 bp):
TGCTTCCTCCACCATCAACTGCTGT
Found at i:1173504 original size:20 final size:20
Alignment explanation
Indices: 1173479--1173522 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
1173469 GAGACAAAAT
1173479 TAAGTGTCTACATTATGAGA
1 TAAGTGTCTACATTATGAGA
1173499 TAAGTGTCTACATTATGAGA
1 TAAGTGTCTACATTATGAGA
1173519 TAAG
1 TAAG
1173523 ACACTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.34
Consensus pattern (20 bp):
TAAGTGTCTACATTATGAGA
Found at i:1174793 original size:21 final size:22
Alignment explanation
Indices: 1174759--1174799 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1174749 TTTCATGTTG
*
1174759 TTTTATTCCATTTTCTTTTATT
1 TTTTATTCCATTTTCATTTATT
*
1174781 TTTTA-TCCTTTTTCATTTA
1 TTTTATTCCATTTTCATTTA
1174800 ATTTCTCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTATTCCATTTTCATTTATT
Found at i:1174803 original size:22 final size:22
Alignment explanation
Indices: 1174759--1174803 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1174749 TTTCATGTTG
*
1174759 TTTTATTCCATTTTCTTTTATT
1 TTTTATTCCATTTTCTTTAATT
*
1174781 TTTTA-TCCTTTTTCATTTAATT
1 TTTTATTCCATTTTC-TTTAATT
1174803 T
1 T
1174804 CTCCTTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTATTCCATTTTCTTTAATT
Found at i:1175384 original size:164 final size:154
Alignment explanation
Indices: 1175158--1175502 Score: 397
Period size: 153 Copynumber: 2.2 Consensus size: 154
1175148 ATGTGAATTT
* * * ** **
1175158 AATAACAATATTAGATGAATTTTAAAATTTTAAACCAAGAAAAATCCCCTTGAAAACATTTACGG
1 AATAATAATATTTGATGAATTTTAAAATTTAAAACCAAGAAAAATCCCCCCGAAAACATTTACAA
*
1175223 AGTAAAAAACTCAATTTTTTGAAAATAGGAAAATTTCAAAGAAAAAATTTAAAACTCATGAAAAT
66 AG-AAAAAACTCAATTTTTAGAAAATAGG---A----AAA-AAAAAA---AAAACTCATGAAAAT
* *
1175288 AAATGAATTTTT-GAAAAATAATTTAATATGAATCA
119 AAATAAATTTTTAAAAAAATAATTTAATATGAATCA
*
1175323 AATAATAATATTTTATGAATTTTAAAA-TTAAAACCAAGAAAAATCCCCCCGAAAACATTTACAA
1 AATAATAATATTTGATGAATTTTAAAATTTAAAACCAAGAAAAATCCCCCCGAAAACATTTACAA
* *** *
1175387 AGCAAAAACTTTGTTTTTAGAAAATAGGAAAAAATAAAAAAACTCATGAAAATAAATAAATTTTT
66 AGAAAAAACTCAATTTTTAGAAAATAGGAAAAAAAAAAAAAACTCATGAAAATAAATAAATTTTT
* *
1175452 AAAAAAATGATTTAATATGAATTA
131 AAAAAAATAATTTAATATGAATCA
*
1175476 AATAATTATATTTGATGAATTTTAAAA
1 AATAATAATATTTGATGAATTTTAAAA
1175503 ATTTTAGATC
Statistics
Matches: 159, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
152 26 0.16
153 45 0.28
155 5 0.03
156 3 0.02
160 1 0.01
163 21 0.13
164 34 0.21
165 24 0.15
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.31
Consensus pattern (154 bp):
AATAATAATATTTGATGAATTTTAAAATTTAAAACCAAGAAAAATCCCCCCGAAAACATTTACAA
AGAAAAAACTCAATTTTTAGAAAATAGGAAAAAAAAAAAAAACTCATGAAAATAAATAAATTTTT
AAAAAAATAATTTAATATGAATCA
Found at i:1175803 original size:29 final size:29
Alignment explanation
Indices: 1175766--1175821 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1175756 ACCTCTTTTT
* *
1175766 AAATAAAA-TATTAATTTTCAAAATAAAGA
1 AAATAAAATTATCAAATTT-AAAATAAAGA
*
1175795 AAATGAAATTATCAAATTTAAAATAAA
1 AAATAAAATTATCAAATTTAAAATAAA
1175822 TTTAAAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 15 0.65
30 8 0.35
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (29 bp):
AAATAAAATTATCAAATTTAAAATAAAGA
Found at i:1176902 original size:44 final size:43
Alignment explanation
Indices: 1176852--1177366 Score: 290
Period size: 44 Copynumber: 11.6 Consensus size: 43
1176842 ATAAAGAATC
* **
1176852 TGACCAGGGCGGTAACCATATGTCAAACCAAAATGAGAAGAGTT
1 TGACCAGGGTGGTAACCATACATCAAACCAAAATGAGAAGA-TT
* *
1176896 TGACCAGGTTGGTAACCATACATCAAA-CAGAAAGGAGGCAA-ATT
1 TGACCAGGGTGGTAACCATACATCAAACCA-AAATGA-G-AAGATT
* * * * * * * *
1176940 TGATCAAGGTGATAACCATACATCAAATCAGAATAAAAAGAATC
1 TGACCAGGGTGGTAACCATACATCAAACCAAAATGAGAAG-ATT
* * * * * * * *
1176984 TGACTAGGGTGTTAACTATACGTTAGATCGAAATGAGCAAGAGTT
1 TGACCAGGGTGGTAACCATACATCAAACCAAAATGAG-AAGA-TT
1177029 TGACCAGGGTGGTAACCATACATCAAA-CAGGAAA-GAGACAGATT
1 TGACCAGGGTGGTAACCATACATCAAACCA--AAATGAGA-AGATT
* * * * * *
1177073 TGACCAAGGTGGTAGCCATACGTCAAACAGGAAAAAG-GCAGATT
1 TGACCAGGGTGGTAACCATACATCAAAC--CAAAATGAGAAGATT
* * * ** * * ** * * *
1177117 TGACCAAGATGATAACCATATGTTAAATCTGAATAAAAAAAAAATC
1 TGACCAGGGTGGTAACCATACATCAAA-C-CAA-AATGAGAAGATT
* * * * *
1177163 TAACCAAGGTGGTAACCATACATTAGACCAAAATGAGCAAAAGTT
1 TGACCAGGGTGGTAACCATACATCAAACCAAAATGAG-AAGA-TT
* * *
1177208 TGACTAGGGTGGTAACCATACATC-AACTAGGAAA-GAGGCAGATT
1 TGACCAGGGTGGTAACCATACATCAAACCA--AAATGA-GAAGATT
*
1177252 TGACCAGGGTGGTAACCATACATCAAATCAAAATGA-AAGAAATT
1 TGACCAGGGTGGTAACCATACATCAAACCAAAATGAGAAG--ATT
* * * *
1177296 TGACTAGGGTGGTAACCATACGTCAGACCGAAATGAGAAGAGTT
1 TGACCAGGGTGGTAACCATACATCAAACCAAAATGAGAAGA-TT
*
1177340 TGACTAGGGTGGTAACCATACATCAAA
1 TGACCAGGGTGGTAACCATACATCAAA
1177367 TAAGAATGAA
Statistics
Matches: 362, Mismatches: 80, Indels: 58
0.72 0.16 0.12
Matches are distributed among these distances:
42 4 0.01
43 9 0.02
44 239 0.66
45 75 0.21
46 34 0.09
47 1 0.00
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.20
Consensus pattern (43 bp):
TGACCAGGGTGGTAACCATACATCAAACCAAAATGAGAAGATT
Found at i:1177314 original size:179 final size:177
Alignment explanation
Indices: 1176852--1177316 Score: 514
Period size: 179 Copynumber: 2.6 Consensus size: 177
1176842 ATAAAGAATC
* ** *
1176852 TGACCAGGGCGGTAACCATATGTCAAACCA--AAATGAGA-AGAGTTTGACCAGGTTGGTAACCA
1 TGACCAGGGTGGTAACCATACATCAAA-CAGGAAA-GAGACAGA-TTTGACCAGGGTGGTAACCA
*
1176914 TACATCAAACAGAAAGGAGGCAAATTTGA-TCAAGGTGATAACCATACATCAAATCAGAATAAAA
63 TACATCAAACAGAAAGAAGGCAAATTTGACT-AAGGTGATAACCATACATCAAATCAGAATAAAA
* * * * * * * * * *
1176978 AGAATCTGACTAGGGTGTTAACTATACGTTAGATCGAAATGAGCAAGAGTT
127 AAAATCTAACCAAGGTGGTAACCATACATTAGACCAAAATGAGCAAAAGTT
* *
1177029 TGACCAGGGTGGTAACCATACATCAAACAGGAAAGAGACAGATTTGACCAAGGTGGTAGCCATAC
1 TGACCAGGGTGGTAACCATACATCAAACAGGAAAGAGACAGATTTGACCAGGGTGGTAACCATAC
* * * * ** * *
1177094 GTCAAACAGGAAA-AAGGCAGATTTGACCAAGATGATAACCATATGTTAAATCTGAATAAAAAAA
66 ATCAAACA-GAAAGAAGGCAAATTTGACTAAGGTGATAACCATACATCAAATCAGAAT--AAAAA
1177158 AAATCTAACCAAGGTGGTAACCATACATTAGACCAAAATGAGCAAAAGTT
128 AAATCTAACCAAGGTGGTAACCATACATTAGACCAAAATGAGCAAAAGTT
* *
1177208 TGACTAGGGTGGTAACCATACATC-AACTAGGAAAGAGGCAGATTTGACCAGGGTGGTAACCATA
1 TGACCAGGGTGGTAACCATACATCAAAC-AGGAAAGAGACAGATTTGACCAGGGTGGTAACCATA
* * *
1177272 CATCAAATCA-AAATGAAAG-AAATTTGACTAGGGTGGTAACCATAC
65 CATCAAA-CAGAAA-GAAGGCAAATTTGACTAAGGTGATAACCATAC
1177317 GTCAGACCGA
Statistics
Matches: 240, Mismatches: 37, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
176 2 0.01
177 90 0.38
178 16 0.07
179 127 0.53
180 5 0.02
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (177 bp):
TGACCAGGGTGGTAACCATACATCAAACAGGAAAGAGACAGATTTGACCAGGGTGGTAACCATAC
ATCAAACAGAAAGAAGGCAAATTTGACTAAGGTGATAACCATACATCAAATCAGAATAAAAAAAA
TCTAACCAAGGTGGTAACCATACATTAGACCAAAATGAGCAAAAGTT
Found at i:1179133 original size:22 final size:21
Alignment explanation
Indices: 1179094--1179152 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 21
1179084 CAATATGCCC
*
1179094 TTTTTCCTTTATTTTTTTCTTGA
1 TTTTT-CTTT-TTCTTTTCTTGA
* *
1179117 TTTTTCATTTTTCTTTTTTTGC
1 TTTTTC-TTTTTCTTTTCTTGA
1179139 TTTTTCTGTTTTCT
1 TTTTTCT-TTTTCT
1179153 GTCTTAATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 1 0.03
22 22 0.71
23 8 0.26
ACGTcount: A:0.05, C:0.14, G:0.05, T:0.76
Consensus pattern (21 bp):
TTTTTCTTTTTCTTTTCTTGA
Found at i:1180620 original size:16 final size:16
Alignment explanation
Indices: 1180599--1180629 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1180589 GTCAACTTTG
1180599 TCGACTTTCTATGATC
1 TCGACTTTCTATGATC
1180615 TCGACTTTCTATGAT
1 TCGACTTTCTATGAT
1180630 TAGGAGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (16 bp):
TCGACTTTCTATGATC
Done.