Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008935.1 Hibiscus syriacus cultivar Beakdansim tig00112253_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1775090
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1325990 original size:38 final size:39
Alignment explanation
Indices: 1325935--1326037 Score: 138
Period size: 38 Copynumber: 2.7 Consensus size: 39
1325925 CATGTACTTC
*
1325935 TAGAGTCTTCTCCATTTGTTTGAAGATGTCATACAGTCG
1 TAGAGTCTTCTCTATTTGTTTGAAGATGTCATACAGTCG
* **
1325974 TGGA-TCTTCTCTATTTGCCTGAAGATGTCATACAGTCG
1 TAGAGTCTTCTCTATTTGTTTGAAGATGTCATACAGTCG
*
1326012 TAGAGTCTT-TATATTTGATTTGAAGA
1 TAGAGTCTTCTCTATTTG-TTTGAAGA
1326038 CAAACAGAAC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
38 41 0.76
39 13 0.24
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (39 bp):
TAGAGTCTTCTCTATTTGTTTGAAGATGTCATACAGTCG
Found at i:1333031 original size:30 final size:30
Alignment explanation
Indices: 1332988--1333068 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 30
1332978 GAACAAGGGG
1332988 TGATGGG-GTTGGTGTTGAAAAAAATGGGA
1 TGATGGGTGTTGGTGTTGAAAAAAATGGGA
*
1333017 TGATGGGTGTTGGTGTTG-AAAAAATGGGG
1 TGATGGGTGTTGGTGTTGAAAAAAATGGGA
* *
1333046 TGGTAGGTGTTGGTGTTGAAAAA
1 TGATGGGTGTTGGTGTTGAAAAA
1333069 TGGTGTTTAC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
29 33 0.70
30 14 0.30
ACGTcount: A:0.27, C:0.00, G:0.42, T:0.31
Consensus pattern (30 bp):
TGATGGGTGTTGGTGTTGAAAAAAATGGGA
Found at i:1333325 original size:50 final size:50
Alignment explanation
Indices: 1333250--1333401 Score: 259
Period size: 50 Copynumber: 3.0 Consensus size: 50
1333240 ATCGATCCAA
* *
1333250 CTCCTTTTGTGATGGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTT
1 CTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTT
*
1333300 CTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACTCTGATCCAACTCCTT
1 CTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTT
* *
1333350 CTCCTTCTGTGATAGAATCGAGAAAAAAGTTGACGATGATCCAACTCCTT
1 CTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTT
1333400 CT
1 CT
1333402 GCGATGGATT
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 96 1.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (50 bp):
CTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTT
Found at i:1333489 original size:44 final size:44
Alignment explanation
Indices: 1333428--1334168 Score: 281
Period size: 44 Copynumber: 16.8 Consensus size: 44
1333418 AAGATAAAAA
* * *
1333428 ATGTCGACCCACTTCCTTTTGTGATGGAATCGAACGAGATATCG
1 ATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATATCG
* * * * * * *
1333472 ATGTCGGTCTACCTCCTTCTGTGATAGAATCAAAC-AAAAAGTTG
1 ATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATA-TCG
* * * * * * ***
1333516 ACG-CTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAGATAAAA
1 ATGTC-GATCCACCTCCTTCTGTGATGGAATCGAACG-AGATATCG
*
1333561 ATGTCGATCCACCTCCTTTTGTGATGGAATCGAACGAGATATCG
1 ATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATATCG
* * * * * * *
1333605 ATGCCGGTCTACCTCCTTCTGTGATAGAATC-AA-GCAAAAAGTTG
1 ATGTCGATCCACCTCCTTCTGTGATGGAATCGAACG-AGATA-TCG
* * * * * * * ***
1333649 ACG-CTGATTCAACTCCTTCTGCGATGGATTTGAGCGAAGATAAAA
1 ATGTC-GATCCACCTCCTTCTGTGATGGAATCGAACG-AGATATCG
* * *
1333694 ATGTCGATCCACCTCCTTTTATGATGGAATCGAACGAGATGTCG
1 ATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATATCG
* * * * * *
1333738 ATG-CTGATCTACCTCCTTCTGTGATAGAATCGAGC-AAAAAGTTG
1 ATGTC-GATCCACCTCCTTCTGTGATGGAATCGAACGAGATA-TCG
* * * * * * * ***
1333782 ACG-CTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAATAAAA
1 ATGTC-GATCCACCTCCTTCTGTGATGGAATCGAACGAGATATCG
* * * * *
1333826 ATGTCGATCCACCTCCTTTTATGATGGAATCGAATGAGATGTTG
1 ATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATATCG
* * * * * * *
1333870 ATGCCGGTCTACCTCCTTCTGTGATAGAATC-AA-GCAAAAAGTTG
1 ATGTCGATCCACCTCCTTCTGTGATGGAATCGAACG-AGATA-TCG
* * * * * * ***
1333914 ACG-CTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAGATAAAA
1 ATGTC-GATCCACCTCCTTCTGTGATGGAATCGAACG-AGATATCG
* *
1333959 ATGTCGATCCACCTCATTTTGTGATGGAATCGAACGAGATATCG
1 ATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATATCG
* * * * *
1334003 ATG-CTGATCTACCTCCTTCTGTGATAGAATC-AA-GCAAAAAGTTG
1 ATGTC-GATCCACCTCCTTCTGTGATGGAATCGAACG-AGATA-TCG
* * * * * * * ***
1334047 ACG-CTGATCCAACTCCTACTGCGATGGATTTGAGCGAAGATAAAA
1 ATGTC-GATCCACCTCCTTCTGTGATGGAATCGAACG-AGATATCG
* * * * *
1334092 ATGTCAATCCACCTCATTCTGTGATAGAATCGAATGAGATGTCG
1 ATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATATCG
* *
1334136 ATG-CTGATCTACCTCCTTCTGTGATAGAATCGA
1 ATGTC-GATCCACCTCCTTCTGTGATGGAATCGA
1334169 GCTAAAAGTT
Statistics
Matches: 488, Mismatches: 181, Indels: 56
0.67 0.25 0.08
Matches are distributed among these distances:
42 3 0.01
43 25 0.05
44 332 0.68
45 109 0.22
46 19 0.04
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (44 bp):
ATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATATCG
Found at i:1333636 original size:133 final size:133
Alignment explanation
Indices: 1333350--1334180 Score: 1367
Period size: 133 Copynumber: 6.2 Consensus size: 133
1333340 CCAACTCCTT
* * *
1333350 CTCCTTCTGTGATAGAATCGAGAAAAAAGTTGACGATGATCCAACTCCTTCTGCGATGGATTTGA
1 CTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
* * * *
1333415 GCGAAGATAAAAAATGTCGACCCACTTCCTTTTGTGATGGAATCGAACGAGATATCGATGTCGGT
66 GCGAAGAT-AAAAATGTCGATCCACCTCCTTTTGTGATGGAATCGAACGAGATATCGATGCCGAT
1333480 CTAC
130 CTAC
*
1333484 CTCCTTCTGTGATAGAATCAAACAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
1 CTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
*
1333549 GCGAAGATAAAAATGTCGATCCACCTCCTTTTGTGATGGAATCGAACGAGATATCGATGCCGGTC
66 GCGAAGATAAAAATGTCGATCCACCTCCTTTTGTGATGGAATCGAACGAGATATCGATGCCGATC
1333614 TAC
131 TAC
*
1333617 CTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATTCAACTCCTTCTGCGATGGATTTGA
1 CTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
* * *
1333682 GCGAAGATAAAAATGTCGATCCACCTCCTTTTATGATGGAATCGAACGAGATGTCGATGCTGATC
66 GCGAAGATAAAAATGTCGATCCACCTCCTTTTGTGATGGAATCGAACGAGATATCGATGCCGATC
1333747 TAC
131 TAC
*
1333750 CTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
1 CTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
* * * * *
1333815 GCGAA-ATAAAAATGTCGATCCACCTCCTTTTATGATGGAATCGAATGAGATGTTGATGCCGGTC
66 GCGAAGATAAAAATGTCGATCCACCTCCTTTTGTGATGGAATCGAACGAGATATCGATGCCGATC
1333879 TAC
131 TAC
1333882 CTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
1 CTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
* *
1333947 GCGAAGATAAAAATGTCGATCCACCTCATTTTGTGATGGAATCGAACGAGATATCGATGCTGATC
66 GCGAAGATAAAAATGTCGATCCACCTCCTTTTGTGATGGAATCGAACGAGATATCGATGCCGATC
1334012 TAC
131 TAC
*
1334015 CTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTACTGCGATGGATTTGA
1 CTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
* * * * * * *
1334080 GCGAAGATAAAAATGTCAATCCACCTCATTCTGTGATAGAATCGAATGAGATGTCGATGCTGATC
66 GCGAAGATAAAAATGTCGATCCACCTCCTTTTGTGATGGAATCGAACGAGATATCGATGCCGATC
1334145 TAC
131 TAC
* *
1334148 CTCCTTCTGTGATAGAATCGAGCTAAAAGTTGA
1 CTCCTTCTGTGATAGAATCAAGCAAAAAGTTGA
1334181 ACAATCTCTT
Statistics
Matches: 661, Mismatches: 35, Indels: 3
0.95 0.05 0.00
Matches are distributed among these distances:
132 127 0.19
133 465 0.70
134 69 0.10
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (133 bp):
CTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
GCGAAGATAAAAATGTCGATCCACCTCCTTTTGTGATGGAATCGAACGAGATATCGATGCCGATC
TAC
Found at i:1333939 original size:265 final size:266
Alignment explanation
Indices: 1333350--1334180 Score: 1405
Period size: 265 Copynumber: 3.1 Consensus size: 266
1333340 CCAACTCCTT
* * *
1333350 CTCCTTCTGTGATAGAATCGAGAAAAAAGTTGACGATGATCCAACTCCTTCTGCGATGGATTTGA
1 CTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
* * *
1333415 GCGAAGATAAAAAATGTCGACCCACTTCCTTTTGTGATGGAATCGAACGAGATATCGATG-TCGG
66 GCGAAGAT-AAAAATGTCGATCCACCTCCTTTTGTGATGGAATCGAACGAGATATCGATGCT-GA
*
1333479 TCTACCTCCTTCTGTGATAGAATCAAACAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGA
129 TCTACCTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGA
* *
1333544 TTTGAGCGAAGATAAAAATGTCGATCCACCTCCTTTTGTGATGGAATCGAACGAGATATCGATGC
194 TTTGAGCGAAGATAAAAATGTCGATCCACCTCCTTTTGTGATGGAATCGAATGAGATGTCGATGC
1333609 CGGTCTAC
259 CGGTCTAC
*
1333617 CTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATTCAACTCCTTCTGCGATGGATTTGA
1 CTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
* *
1333682 GCGAAGATAAAAATGTCGATCCACCTCCTTTTATGATGGAATCGAACGAGATGTCGATGCTGATC
66 GCGAAGATAAAAATGTCGATCCACCTCCTTTTGTGATGGAATCGAACGAGATATCGATGCTGATC
*
1333747 TACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATT
131 TACCTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATT
* *
1333812 TGAGCGAA-ATAAAAATGTCGATCCACCTCCTTTTATGATGGAATCGAATGAGATGTTGATGCCG
196 TGAGCGAAGATAAAAATGTCGATCCACCTCCTTTTGTGATGGAATCGAATGAGATGTCGATGCCG
1333876 GTCTAC
261 GTCTAC
1333882 CTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
1 CTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
*
1333947 GCGAAGATAAAAATGTCGATCCACCTCATTTTGTGATGGAATCGAACGAGATATCGATGCTGATC
66 GCGAAGATAAAAATGTCGATCCACCTCCTTTTGTGATGGAATCGAACGAGATATCGATGCTGATC
*
1334012 TACCTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTACTGCGATGGATT
131 TACCTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATT
* * * * *
1334077 TGAGCGAAGATAAAAATGTCAATCCACCTCATTCTGTGATAGAATCGAATGAGATGTCGATGCTG
196 TGAGCGAAGATAAAAATGTCGATCCACCTCCTTTTGTGATGGAATCGAATGAGATGTCGATGCCG
*
1334142 ATCTAC
261 GTCTAC
* *
1334148 CTCCTTCTGTGATAGAATCGAGCTAAAAGTTGA
1 CTCCTTCTGTGATAGAATCAAGCAAAAAGTTGA
1334181 ACAATCTCTT
Statistics
Matches: 531, Mismatches: 31, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
265 255 0.48
266 206 0.39
267 70 0.13
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (266 bp):
CTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
GCGAAGATAAAAATGTCGATCCACCTCCTTTTGTGATGGAATCGAACGAGATATCGATGCTGATC
TACCTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATT
TGAGCGAAGATAAAAATGTCGATCCACCTCCTTTTGTGATGGAATCGAATGAGATGTCGATGCCG
GTCTAC
Found at i:1334088 original size:398 final size:400
Alignment explanation
Indices: 1333350--1334180 Score: 1450
Period size: 398 Copynumber: 2.1 Consensus size: 400
1333340 CCAACTCCTT
*
1333350 CTCCTTCTGTGATAGAATCGAGAAAAAAGTTGACGATGATCCAACTCCTTCTGCGATGGATTTGA
1 CTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGATGATCCAACTCCTTCTGCGATGGATTTGA
* * *
1333415 GCGAAGATAAAAAATGTCGACCCACTTCCTTTTGTGATGGAATCGAACGAGATATCGATGTCGGT
66 GCGAAGATAAAAAATGTCGACCCACCTCCTTTTATGATGGAATCGAACGAGATATCGATGCCGGT
1333480 CTACCTCCTTCTGTGATAGAATCAAACAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGAT
131 CTACCTCCTTCTGTGATAGAATCAAACAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGAT
*
1333545 TTGAGCGAAGATAAAAATGTCGATCCACCTCCTTTTGTGATGGAATCGAACGAGATATCGATGCC
196 TTGAGCGAAGATAAAAATGTCGATCCACCTCATTTTGTGATGGAATCGAACGAGATATCGATGCC
* * *
1333610 GGTCTACCTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATTCAACTCCTTCTGCGATG
261 GATCTACCTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTACTGCGATG
* * * *
1333675 GATTTGAGCGAAGATAAAAATGTCGATCCACCTCCTTTTATGATGGAATCGAACGAGATGTCGAT
326 GATTTGAGCGAAGATAAAAATGTCAATCCACCTCATTCTATGATAGAATCGAACGAGATGTCGAT
1333740 GCTGATCTAC
391 GCTGATCTAC
*
1333750 CTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
1 CTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGATGATCCAACTCCTTCTGCGATGGATTTGA
* * * *
1333815 GCGAA-AT-AAAAATGTCGATCCACCTCCTTTTATGATGGAATCGAATGAGATGTTGATGCCGGT
66 GCGAAGATAAAAAATGTCGACCCACCTCCTTTTATGATGGAATCGAACGAGATATCGATGCCGGT
*
1333878 CTACCTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGAT
131 CTACCTCCTTCTGTGATAGAATCAAACAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGAT
*
1333943 TTGAGCGAAGATAAAAATGTCGATCCACCTCATTTTGTGATGGAATCGAACGAGATATCGATGCT
196 TTGAGCGAAGATAAAAATGTCGATCCACCTCATTTTGTGATGGAATCGAACGAGATATCGATGCC
1334008 GATCTACCTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTACTGCGATG
261 GATCTACCTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTACTGCGATG
* *
1334073 GATTTGAGCGAAGATAAAAATGTCAATCCACCTCATTCTGTGATAGAATCGAATGAGATGTCGAT
326 GATTTGAGCGAAGATAAAAATGTCAATCCACCTCATTCTATGATAGAATCGAACGAGATGTCGAT
1334138 GCTGATCTAC
391 GCTGATCTAC
*
1334148 CTCCTTCTGTGATAGAATCGAGCTAAAAGTTGA
1 CTCCTTCTGTGATAGAATCGAGCAAAAAGTTGA
1334181 ACAATCTCTT
Statistics
Matches: 409, Mismatches: 22, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
398 339 0.83
399 2 0.00
400 68 0.17
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (400 bp):
CTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGATGATCCAACTCCTTCTGCGATGGATTTGA
GCGAAGATAAAAAATGTCGACCCACCTCCTTTTATGATGGAATCGAACGAGATATCGATGCCGGT
CTACCTCCTTCTGTGATAGAATCAAACAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGAT
TTGAGCGAAGATAAAAATGTCGATCCACCTCATTTTGTGATGGAATCGAACGAGATATCGATGCC
GATCTACCTCCTTCTGTGATAGAATCAAGCAAAAAGTTGACGCTGATCCAACTCCTACTGCGATG
GATTTGAGCGAAGATAAAAATGTCAATCCACCTCATTCTATGATAGAATCGAACGAGATGTCGAT
GCTGATCTAC
Found at i:1334995 original size:7 final size:7
Alignment explanation
Indices: 1334985--1335019 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
1334975 GAACCTATCA
1334985 TTTTCTT
1 TTTTCTT
1334992 TTTTC-T
1 TTTTCTT
1334998 TTTTCTT
1 TTTTCTT
1335005 TTTTC-T
1 TTTTCTT
1335011 TTTTCTT
1 TTTTCTT
1335018 TT
1 TT
1335020 CAGGCGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 12 0.46
7 14 0.54
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTCTT
Found at i:1335000 original size:6 final size:6
Alignment explanation
Indices: 1334985--1335019 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
1334975 GAACCTATCA
1334985 TTTTCTT TTTTCT TTTTCTT TTTTCT TTTTCT TTT
1 TTTTC-T TTTTCT TTTTC-T TTTTCT TTTTCT TTT
1335020 CAGGCGTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 16 0.59
7 11 0.41
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:1335003 original size:13 final size:13
Alignment explanation
Indices: 1334985--1335019 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
1334975 GAACCTATCA
1334985 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
1334998 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
1335011 TTTTCTTTT
1 TTTTCTTTT
1335020 CAGGCGTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTCTTTTTTCT
Found at i:1347784 original size:30 final size:30
Alignment explanation
Indices: 1347741--1347821 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 30
1347731 GAACAAGGGG
1347741 TGATGGG-GTTGGTGTTGAAAAAAATGGGA
1 TGATGGGTGTTGGTGTTGAAAAAAATGGGA
*
1347770 TGATGGGTGTTGGTGTTG-AAAAAATGGGG
1 TGATGGGTGTTGGTGTTGAAAAAAATGGGA
* *
1347799 TGGTAGGTGTTGGTGTTGAAAAA
1 TGATGGGTGTTGGTGTTGAAAAA
1347822 TGGTGTTTAC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
29 33 0.70
30 14 0.30
ACGTcount: A:0.27, C:0.00, G:0.42, T:0.31
Consensus pattern (30 bp):
TGATGGGTGTTGGTGTTGAAAAAAATGGGA
Found at i:1351866 original size:20 final size:20
Alignment explanation
Indices: 1351820--1351866 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1351810 GCGATTCCCA
* *
1351820 CTTC-CTTCTTTTTCTTGTT
1 CTTCTCTTCTTATTCTTATT
1351839 CTTCTCTTCTTATTCTTCATT
1 CTTCTCTTCTTATTCTT-ATT
1351860 CTT-TCTT
1 CTTCTCTT
1351867 TGGAGCTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.17
20 15 0.62
21 5 0.21
ACGTcount: A:0.04, C:0.28, G:0.02, T:0.66
Consensus pattern (20 bp):
CTTCTCTTCTTATTCTTATT
Found at i:1357749 original size:436 final size:434
Alignment explanation
Indices: 1356931--1357798 Score: 1276
Period size: 436 Copynumber: 2.0 Consensus size: 434
1356921 GACGAGTTAA
* *
1356931 ATGATACCTTTGAATCTTCTTGGATATCAATGAGACAAAGGTTGGCTAATTCTTCATTTTCATCA
1 ATGATACCTTTGAATCTTCTTAGATATCAATGAGACAAAGGTTGGCCAATTCTTCATTTTCATCA
* * *
1356996 TCGGTGACGTCTTCATCATTCCAAGCAGTAAAAAAAAGCCTTCTTCTTGCTTGATCCCTTCTTCT
66 TCGATGACGTCTTCATCACTCCAAGCAGTAAAAAAAAGCCTTCTTCTTACTTGATCCCTTCTTCT
* * * *
1357061 TTAGAAAAAGAAATTCATATTTGACATGTCATATTTTTTGGCATTCATAGCACAACGGGAAACCT
131 TTAGAAAAAGAAATTCATATTTGACATGTCATATTTTTTGGCATTAATAACACAACGAGAAACAT
* * *
1357126 TTCTTCTTGCTTGATTCATGCTTCTTGTCTTCTTTGGATGTCATGAATCGTTTGAATTTCTTGAA
196 TTATTCTTGCTTGATTCATGCTTCTTATCTTCTTTGGATGTCATGAATCATTTGAATTTCTTGAA
* * *
1357191 GAGTTTGACCATCTCTTCATCTTCATCCACTTCTTCACTTAAGTCATGATTACTCTCATTGGTGG
261 GAGCTTGACCATCTCTTCATCTTCATCCACATCTTCACTTAAGTCATGATTACCCTCATTGGTGG
* * * * *
1357256 ATTTCAAGGCGATTTCTACCTCCTTCTTTTTTTTGTTCTTCTCTTATTATTCTTCATTCTTT-TT
326 ATTTCAAGACGATTTCTACCTCCTTCTTTCTCTTGTTCTTATCTTATTATCCTTCATTCTTTCTT
**
1357320 TGGATTTTCACCTCATGAGTGAGTAAAGAACCGATGAGCTCATCG
391 TGGAGCTTCACCTCATGAGTGAGTAAAGAA-CGATGAGCTCATCG
* * *
1357365 ATGATACCTTTGAATCTTGTTAGATGTCAATGAGACAAAGGTTGGCCACTTCTTCATTTTCATCA
1 ATGATACCTTTGAATCTTCTTAGATATCAATGAGACAAAGGTTGGCCAATTCTTCATTTTCATCA
* *
1357430 TCGATGACGTCTTCATCACTCCAAGCAG-CAAAAAAAGCCTTCTTCTTACTTGATCTCTTCTTCT
66 TCGATGACGTCTTCATCACTCCAAGCAGTAAAAAAAAGCCTTCTTCTTACTTGATCCCTTCTTCT
* * * * * *
1357494 TTAGAAAAAGCAATTCATATTTGACATATTCCGTTTTTTTTTTGCATTAATAACACACCGAGAAA
131 TTAGAAAAAGAAATTCATATTTGACAT-GT-C-ATATTTTTTGGCATTAATAACACAACGAGAAA
*
1357559 CATTTATTCTTGTTTGATTCATGCTTCTTATCTTCTTTGGATGTCATGAATCATTTGAATTTCTT
193 CATTTATTCTTGCTTGATTCATGCTTCTTATCTTCTTTGGATGTCATGAATCATTTGAATTTCTT
*** *
1357624 GAAGAGCTTGGTTATCTCTTCATCTTCATCCACATCTTCACTTGAGTC-TCGATTACCCTCATTG
258 GAAGAGCTTGACCATCTCTTCATCTTCATCCACATCTTCACTTAAGTCAT-GATTACCCTCATTG
* * *
1357688 GTGGATTTCAAGACGA-TTCTCATCTCCTTCTTTCTCTTGTTCTTATCTTCTTCTCCTTCATTCT
322 GTGGATTTCAAGACGATTTCT-ACCTCCTTCTTTCTCTTGTTCTTATCTTATTATCCTTCATTCT
*
1357752 TTCTTTGGAGCTTCACCTTATGAGTGAGTAAAGAACGATGAGCTCAT
386 TTCTTTGGAGCTTCACCTCATGAGTGAGTAAAGAACGATGAGCTCAT
1357799 TGAGGGTGTA
Statistics
Matches: 386, Mismatches: 42, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
433 59 0.15
434 87 0.23
435 6 0.02
436 205 0.53
437 29 0.08
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (434 bp):
ATGATACCTTTGAATCTTCTTAGATATCAATGAGACAAAGGTTGGCCAATTCTTCATTTTCATCA
TCGATGACGTCTTCATCACTCCAAGCAGTAAAAAAAAGCCTTCTTCTTACTTGATCCCTTCTTCT
TTAGAAAAAGAAATTCATATTTGACATGTCATATTTTTTGGCATTAATAACACAACGAGAAACAT
TTATTCTTGCTTGATTCATGCTTCTTATCTTCTTTGGATGTCATGAATCATTTGAATTTCTTGAA
GAGCTTGACCATCTCTTCATCTTCATCCACATCTTCACTTAAGTCATGATTACCCTCATTGGTGG
ATTTCAAGACGATTTCTACCTCCTTCTTTCTCTTGTTCTTATCTTATTATCCTTCATTCTTTCTT
TGGAGCTTCACCTCATGAGTGAGTAAAGAACGATGAGCTCATCG
Found at i:1358248 original size:18 final size:18
Alignment explanation
Indices: 1358225--1358259 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1358215 GGAGGCACGG
*
1358225 GAGAACCATTGACGATGA
1 GAGAACCATTAACGATGA
*
1358243 GAGAACCGTTAACGATG
1 GAGAACCATTAACGATG
1358260 GCATCCCAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.17
Consensus pattern (18 bp):
GAGAACCATTAACGATGA
Found at i:1360009 original size:40 final size:40
Alignment explanation
Indices: 1359945--1360040 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
1359935 GGTTACGTAG
1359945 TACCGATAATGTTCTTACATTATCGATACTTCATGAACAA
1 TACCGATAATGTTCTTACATTATCGATACTTCATGAACAA
* * *
1359985 TACTGATACTGTTCTTACATTATCGATACTTCATGAATAA
1 TACCGATAATGTTCTTACATTATCGATACTTCATGAACAA
*
1360025 TACCGATATTGTTCTT
1 TACCGATAATGTTCTT
1360041 GTGGTACCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (40 bp):
TACCGATAATGTTCTTACATTATCGATACTTCATGAACAA
Found at i:1360012 original size:20 final size:20
Alignment explanation
Indices: 1359948--1360014 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
1359938 TACGTAGTAC
*
1359948 CGATAATGTTCTTACATTAT
1 CGATACTGTTCTTACATTAT
* *
1359968 CGATAC--TTCATGAACAATA-
1 CGATACTGTTC-T-TACATTAT
1359987 CTGATACTGTTCTTACATTAT
1 C-GATACTGTTCTTACATTAT
1360008 CGATACT
1 CGATACT
1360015 TCATGAATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 12
0.68 0.09 0.23
Matches are distributed among these distances:
18 3 0.08
19 2 0.06
20 26 0.72
21 2 0.06
22 3 0.08
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.39
Consensus pattern (20 bp):
CGATACTGTTCTTACATTAT
Found at i:1361846 original size:14 final size:14
Alignment explanation
Indices: 1361827--1361888 Score: 88
Period size: 14 Copynumber: 4.4 Consensus size: 14
1361817 CATTCAGTAA
1361827 TATGTTCGTTCATT
1 TATGTTCGTTCATT
*
1361841 TATGTTCATTCATT
1 TATGTTCGTTCATT
*
1361855 TATGTTCGTTCGTT
1 TATGTTCGTTCATT
* *
1361869 TATGTGCGTACATT
1 TATGTTCGTTCATT
1361883 TATGTT
1 TATGTT
1361889 TAGCCAATCT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.16, C:0.13, G:0.16, T:0.55
Consensus pattern (14 bp):
TATGTTCGTTCATT
Found at i:1362205 original size:24 final size:24
Alignment explanation
Indices: 1362143--1362206 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
1362133 GTTTATTGTA
*
1362143 TTCATTTATGTTCGCTTACATCCG
1 TTCATTTATGTTCGTTTACATCCG
* *
1362167 TTCGTTTATGTTCGTTTACATTCG
1 TTCATTTATGTTCGTTTACATCCG
1362191 TTCATTTATGTTCGTT
1 TTCATTTATGTTCGTT
1362207 CATTTGTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.14, C:0.19, G:0.14, T:0.53
Consensus pattern (24 bp):
TTCATTTATGTTCGTTTACATCCG
Found at i:1362222 original size:24 final size:23
Alignment explanation
Indices: 1362094--1362223 Score: 79
Period size: 24 Copynumber: 5.5 Consensus size: 23
1362084 ATATTTATTG
* *
1362094 TGTTT-GTTTACGTTCGTTCGTT
1 TGTTTCGTTTATGTTCGTTCATT
** *
1362116 TGTATTCGTTTACATTCGTTTA-T
1 TGT-TTCGTTTATGTTCGTTCATT
* *
1362139 TGTATTCATTTATGTTCGCTTACATC
1 TGT-TTCGTTTATGTTCG-TT-CATT
*
1362165 CG-TTCGTTTATGTTCGTTTACATT
1 TGTTTCGTTTATGTTCG-TT-CATT
* *
1362189 CG-TTCATTTATGTTCGTTCATT
1 TGTTTCGTTTATGTTCGTTCATT
1362211 TGTTTTCGTTTAT
1 TG-TTTCGTTTAT
1362224 CATTTAAATG
Statistics
Matches: 86, Mismatches: 15, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
22 8 0.09
23 20 0.23
24 56 0.65
25 1 0.01
26 1 0.01
ACGTcount: A:0.13, C:0.15, G:0.15, T:0.56
Consensus pattern (23 bp):
TGTTTCGTTTATGTTCGTTCATT
Found at i:1366029 original size:4 final size:4
Alignment explanation
Indices: 1366020--1366169 Score: 79
Period size: 4 Copynumber: 36.2 Consensus size: 4
1366010 AATCCAGAAG
** * *
1366020 TATT TATT TATT TATTT TATT TGGT TATG TATT TATT TATT TTTT TATT
1 TATT TATT TATT TA-TT TATT TATT TATT TATT TATT TATT TATT TATT
** * * * *
1366069 CGTA TATT TATTT TATT T-TGT CAGT TATT TATT TATT TCCTT TATT TAATT
1 TATT TATT TA-TT TATT TAT-T TATT TATT TATT TATT T-ATT TATT T-ATT
* * ** * *
1366120 GA-T TATT TATT TATT TTTT TCGGT TATT TTTT TATTT TAAT TATT TATT
1 TATT TATT TATT TATT TATT T-ATT TATT TATT TA-TT TATT TATT TATT
1366169 T
1 T
1366170 GAAGGGGTAT
Statistics
Matches: 106, Mismatches: 31, Indels: 18
0.68 0.20 0.12
Matches are distributed among these distances:
3 3 0.03
4 83 0.78
5 20 0.19
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.70
Consensus pattern (4 bp):
TATT
Found at i:1366058 original size:25 final size:25
Alignment explanation
Indices: 1366024--1366156 Score: 82
Period size: 25 Copynumber: 5.4 Consensus size: 25
1366014 CAGAAGTATT
1366024 TATTTATTTATTTTATTTGGTTATG
1 TATTTATTTATTTTATTTGGTTATG
* *
1366049 TATTTATTTATTTT-TTT-ATT-CG
1 TATTTATTTATTTTATTTGGTTATG
*
1366071 TA--TATTTATTTTATTTTGTCAGTTATT
1 TATTTATTTATTTTA-TTTG---GTTATG
** **
1366098 TATTTATTTCCTTTATTTAATTGAT-
1 TATTTATTTATTTTATTTGGTT-ATG
*
1366123 TATTTATTTATTTT-TTTCGGTTATT
1 TATTTATTTATTTTATTT-GGTTATG
*
1366148 TTTTTATTT
1 TATTTATTT
1366157 TAATTATTTA
Statistics
Matches: 82, Mismatches: 14, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
20 10 0.12
22 6 0.07
23 2 0.02
24 8 0.10
25 38 0.46
26 4 0.05
27 2 0.02
28 3 0.04
29 9 0.11
ACGTcount: A:0.20, C:0.04, G:0.07, T:0.70
Consensus pattern (25 bp):
TATTTATTTATTTTATTTGGTTATG
Found at i:1366105 original size:29 final size:27
Alignment explanation
Indices: 1366073--1366139 Score: 64
Period size: 29 Copynumber: 2.3 Consensus size: 27
1366063 TTTATTCGTA
1366073 TATTTATTTTATTT-TGTCAGTTATTTATT
1 TATTT-TTTTATTTAT-TCA-TTATTTATT
* *
1366102 TATTTCCTTTATTTAATTGATTATTTATT
1 TATTT-TTTTATTT-ATTCATTATTTATT
1366131 TATTTTTTT
1 TATTTTTTT
1366140 CGGTTATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
28 3 0.09
29 26 0.81
30 2 0.06
31 1 0.03
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.70
Consensus pattern (27 bp):
TATTTTTTTATTTATTCATTATTTATT
Found at i:1367652 original size:11 final size:11
Alignment explanation
Indices: 1367638--1367665 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1367628 GCACAATTCT
1367638 AGAACAAAGAA
1 AGAACAAAGAA
1367649 AGAACAAAGAA
1 AGAACAAAGAA
1367660 AGAACA
1 AGAACA
1367666 CTCAAGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.71, C:0.11, G:0.18, T:0.00
Consensus pattern (11 bp):
AGAACAAAGAA
Found at i:1374165 original size:21 final size:21
Alignment explanation
Indices: 1374139--1374180 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1374129 GAGCTTATTT
*
1374139 TCATTTTTCA-ATTTTGAAACA
1 TCATTTTT-ATATTTTAAAACA
1374160 TCATTTTTATATTTTAAAACA
1 TCATTTTTATATTTTAAAACA
1374181 ATTTCTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (21 bp):
TCATTTTTATATTTTAAAACA
Found at i:1376683 original size:22 final size:22
Alignment explanation
Indices: 1376618--1376688 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
1376608 ATGTCTGTGT
1376618 GCACGTTTATCTCTTA-TTGTGTC
1 GCACGTTTATCT-TTACTT-TGTC
* *
1376641 GCACATTTAT-TTTGTCTTTGTC
1 GCACGTTTATCTTT-ACTTTGTC
* *
1376663 GCACGTTTATCTTTACCTTGTG
1 GCACGTTTATCTTTACTTTGTC
1376685 GCAC
1 GCAC
1376689 TTTTTTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
21 2 0.05
22 23 0.59
23 14 0.36
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (22 bp):
GCACGTTTATCTTTACTTTGTC
Found at i:1378390 original size:14 final size:16
Alignment explanation
Indices: 1378373--1378410 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1378363 TAAAGTTTTA
1378373 TATATT-TGAT-GATT
1 TATATTATGATGGATT
*
1378387 TATATTATGTTGGATT
1 TATATTATGATGGATT
1378403 TATATTAT
1 TATATTAT
1378411 TAATAAAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 3 0.14
16 12 0.57
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (16 bp):
TATATTATGATGGATT
Found at i:1383987 original size:82 final size:81
Alignment explanation
Indices: 1383895--1384172 Score: 296
Period size: 82 Copynumber: 3.4 Consensus size: 81
1383885 ACACCGCAAT
* * *
1383895 ATAGTAGTACTTCAGCGGCGTTTTTATACAAATGCTGCAATAGGTTTATCCATAGTGGCATTTTT
1 ATAGTAGTACTTTAGCGGCGTTTTTATACAAACGC-GCAATAGGTTTATCTATAGTGGCATTTTT
*
1383960 TCAATAAACGCCTCAAC
65 TCAATAAACGCCACAAC
* * * *
1383977 ATAGTGGTACTTTAGCGGCGTTTTTATACAAACGCCGC-A-AGGGTCATCTATAGTGGC-GTTTT
1 ATAGTAGTACTTTAGCGGCGTTTTTATACAAACG-CGCAATAGGTTTATCTATAGTGGCATTTTT
* *
1384039 CCAACAAA-GCCACAAC
65 TCAATAAACGCCACAAC
1384055 ATAGTAGTACTTTAGCGGCGTTTTTATATACAAACGACGCAATAGGATTTATCTATAGTGG-ATT
1 ATAGTAGTACTTTAGCGGCG-TTTT-TATACAAACG-CGCAATAGG-TTTATCTATAGTGGCA--
** *
1384119 TTTTTTCAATAAACGCCGTAAT
60 TTTTTTCAATAAACGCCACAAC
* * * *
1384141 AGAGTAGTACTTTAGCAGCATTTTTTTACAAA
1 ATAGTAGTACTTTAGCGGCGTTTTTATACAAA
1384173 GACCACTATA
Statistics
Matches: 162, Mismatches: 24, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
78 26 0.16
79 14 0.09
80 28 0.17
81 2 0.01
82 36 0.22
83 13 0.08
84 7 0.04
85 14 0.09
86 22 0.14
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (81 bp):
ATAGTAGTACTTTAGCGGCGTTTTTATACAAACGCGCAATAGGTTTATCTATAGTGGCATTTTTT
CAATAAACGCCACAAC
Found at i:1384223 original size:41 final size:43
Alignment explanation
Indices: 1384182--1384414 Score: 260
Period size: 43 Copynumber: 5.5 Consensus size: 43
1384172 AGACCACTAT
* * * * *
1384182 AGACTCTTACTTTAGTGGCATTT-T-TATACAAACGCTGCTAT
1 AGACTCGTACTTTAGTGGCGTTTGTATTTACAAACGCAGCTAA
* *
1384223 AGACTCGTACTTTAGTGGCGCTTT-TA--TATAAACGCCGCTAA
1 AGACTCGTACTTTAGTGGCG-TTTGTATTTACAAACGCAGCTAA
* * *
1384264 AGACTCGTACTGTAGTGGCGTTTGTGTTTACAAATGCAGCTAA
1 AGACTCGTACTTTAGTGGCGTTTGTATTTACAAACGCAGCTAA
* **
1384307 AGACTCTTACTTTAGTGGCGTTTGTATTTACAAACGCAATTAA
1 AGACTCGTACTTTAGTGGCGTTTGTATTTACAAACGCAGCTAA
* **
1384350 AGACTCATACTTTAGTGGCGTTTGTATTTACAAACGCAATTAA
1 AGACTCGTACTTTAGTGGCGTTTGTATTTACAAACGCAGCTAA
* *
1384393 AGACTCATATTTTAGTGGCGTT
1 AGACTCGTACTTTAGTGGCGTT
1384415 CAAACACCGC
Statistics
Matches: 169, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
40 3 0.02
41 50 0.30
42 4 0.02
43 112 0.66
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (43 bp):
AGACTCGTACTTTAGTGGCGTTTGTATTTACAAACGCAGCTAA
Found at i:1389791 original size:21 final size:21
Alignment explanation
Indices: 1389761--1389831 Score: 133
Period size: 21 Copynumber: 3.4 Consensus size: 21
1389751 AAGAATAGAT
*
1389761 GTTTCTTTTTGAAGCGTTATG
1 GTTTCATTTTGAAGCGTTATG
1389782 GTTTCATTTTGAAGCGTTATG
1 GTTTCATTTTGAAGCGTTATG
1389803 GTTTCATTTTGAAGCGTTATG
1 GTTTCATTTTGAAGCGTTATG
1389824 GTTTCATT
1 GTTTCATT
1389832 AGCTAAAAGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.17, C:0.10, G:0.23, T:0.51
Consensus pattern (21 bp):
GTTTCATTTTGAAGCGTTATG
Found at i:1390408 original size:8 final size:8
Alignment explanation
Indices: 1390395--1390458 Score: 101
Period size: 8 Copynumber: 8.0 Consensus size: 8
1390385 TGCACCAATA
1390395 CATACATG
1 CATACATG
1390403 CATACATG
1 CATACATG
*
1390411 CATACATT
1 CATACATG
*
1390419 CATACATT
1 CATACATG
1390427 CATACATG
1 CATACATG
1390435 CATACATG
1 CATACATG
1390443 CATACATG
1 CATACATG
*
1390451 CATGCATG
1 CATACATG
1390459 TGCGTGTGTG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 53 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (8 bp):
CATACATG
Found at i:1396254 original size:20 final size:20
Alignment explanation
Indices: 1396229--1396578 Score: 339
Period size: 20 Copynumber: 17.5 Consensus size: 20
1396219 GATTTTCCAT
* * *
1396229 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATACGTA
* * *
1396249 AATCGCAACGCGAACACATA
1 AATCGCAACGCGTATACGTA
*
1396269 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATACGTA
* *
1396289 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATACGTA
**
1396309 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATACGTA
**
1396329 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATACGTA
* *
1396349 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATACGTA
*
1396369 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATACGTA
* * *
1396389 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATACGTA
*
1396409 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATACGTA
* *
1396429 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATACGTA
*
1396449 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATACGTA
* * *
1396469 AATCTCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATACGTA
*
1396489 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATACGTA
* *
1396509 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATACGTA
* *
1396529 AATCGCAACGAGAAT-CTGTA
1 AATCGCAACGCGTATAC-GTA
* *
1396549 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATACGTA
1396569 AATCGCAACG
1 AATCGCAACG
1396579 AGAATCTGTA
Statistics
Matches: 292, Mismatches: 31, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
19 3 0.01
20 287 0.98
21 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATACGTA
Found at i:1396312 original size:60 final size:60
Alignment explanation
Indices: 1396229--1396597 Score: 440
Period size: 60 Copynumber: 6.2 Consensus size: 60
1396219 GATTTTCCAT
* ** * * *
1396229 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATC-CGTAAATCGCAACGCGTATCCGTA
* ** **
1396289 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
* * *
1396349 AATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGTAAACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
*
1396409 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
* * *
1396469 AATCTCAACG-ATAATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGCGT-ATCCGTA
* * * * * * *
1396529 AATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGT-ATCCGTAAATCGCAACGCGTATCCGTA
*
1396589 AATCACAAC
1 AATCGCAAC
1396598 ACTGAAATTT
Statistics
Matches: 267, Mismatches: 36, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
59 3 0.01
60 263 0.99
61 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
Found at i:1396579 original size:20 final size:19
Alignment explanation
Indices: 1396267--1396597 Score: 374
Period size: 20 Copynumber: 16.6 Consensus size: 19
1396257 CGCGAACACA
1396267 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
1396287 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
**
1396307 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACG-GTATCCG
**
1396327 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACG-GTATCCG
*
1396347 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
1396367 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
1396387 TAAACCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
1396407 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
1396427 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
1396447 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
* *
1396467 TAAATCTCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
1396487 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
1396507 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
1396527 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
1396547 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
1396567 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
1396587 TAAATCACAAC
1 TAAATCGCAAC
1396598 ACTGAAATTT
Statistics
Matches: 276, Mismatches: 29, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
19 2 0.01
20 273 0.99
21 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (19 bp):
TAAATCGCAACGGTATCCG
Found at i:1397232 original size:24 final size:24
Alignment explanation
Indices: 1397193--1397239 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1397183 AAATTTGGTC
1397193 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1397217 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1397240 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1397429 original size:12 final size:12
Alignment explanation
Indices: 1397412--1397436 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1397402 ATATAATCCT
1397412 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1397424 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1397436 G
1 G
1397437 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1399758 original size:19 final size:19
Alignment explanation
Indices: 1399736--1400041 Score: 349
Period size: 19 Copynumber: 17.4 Consensus size: 19
1399726 CGGAAAATAC
*
1399736 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1399755 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1399769 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1399789 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1399803 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1399822 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1399841 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1399855 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1399874 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
* *
1399892 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
1399906 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
1399925 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
1399944 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1399963 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1399982 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1399996 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1400015 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1400034 AATCGCAA
1 AATCGCAA
1400042 CGAGATAATC
Statistics
Matches: 248, Mismatches: 13, Indels: 52
0.79 0.04 0.17
Matches are distributed among these distances:
14 45 0.18
15 4 0.02
16 21 0.08
17 12 0.05
18 9 0.04
19 144 0.58
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1399823 original size:33 final size:34
Alignment explanation
Indices: 1399736--1400063 Score: 274
Period size: 33 Copynumber: 9.5 Consensus size: 34
1399726 CGGAAAATAC
* *
1399736 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
1399769 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
1399803 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
1399841 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
* *
1399874 AATCGCAATGCGAAATG-AAATCG-AACCGA-CAT
1 AATCGCAATGCGAAATGAAAATCGCAA-CGATGAA
*
1399906 AATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGC-A-ACG--ATGAA
1399944 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
1399982 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
1400015 AATCGCAATGCGAAATGAAAATCGCAACGA-GAT
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
1400048 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
1400064 TATAAACGCA
Statistics
Matches: 255, Mismatches: 14, Indels: 52
0.79 0.04 0.16
Matches are distributed among these distances:
32 17 0.07
33 107 0.42
34 31 0.12
35 16 0.06
36 14 0.05
37 9 0.04
38 61 0.24
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:1399851 original size:52 final size:53
Alignment explanation
Indices: 1399764--1400041 Score: 349
Period size: 52 Copynumber: 5.2 Consensus size: 53
1399754 AAATCCCAAC
*
1399764 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
*
1399817 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* * *
1399869 ATGAAAATCGCAATGCGAAATG-AAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* *
1399920 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
1399977 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
1400029 ATGAAAATCGCAA
1 ATGAAAATCGCAA
1400042 CGAGATAATC
Statistics
Matches: 210, Mismatches: 8, Indels: 15
0.90 0.03 0.06
Matches are distributed among these distances:
50 2 0.01
51 44 0.21
52 110 0.52
53 18 0.09
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.13
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
Found at i:1400042 original size:52 final size:54
Alignment explanation
Indices: 1399736--1400063 Score: 308
Period size: 52 Copynumber: 6.3 Consensus size: 54
1399726 CGGAAAATAC
* *
1399736 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--C-GAAATG-A
*
1399789 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAATG-A
*
1399841 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAATGA
* * *
1399892 AATCG-AA-CCGACAT---AATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACGAAATG-A
1399944 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAA-G-
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAATGA
*
1399996 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAT--
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAATGA
1400048 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
1400064 TATAAACGCA
Statistics
Matches: 250, Mismatches: 7, Indels: 37
0.85 0.02 0.13
Matches are distributed among these distances:
48 9 0.04
49 1 0.00
50 3 0.01
51 41 0.16
52 131 0.52
53 28 0.11
54 6 0.02
55 6 0.02
56 1 0.00
57 24 0.10
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (54 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAATGA
Found at i:1400179 original size:19 final size:19
Alignment explanation
Indices: 1400070--1400171 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1400060 AAATTATAAA
1400070 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1400089 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1400109 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1400125 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1400142 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1400161 CGCATTGCGAT
1 CGCATTGCGAT
1400172 AGTCATTTTG
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1400304 original size:13 final size:14
Alignment explanation
Indices: 1400277--1400312 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1400267 CATCAATTAC
1400277 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1400291 ACAAATCATC-TTT
1 ACAAATCAACTTTT
1400304 ACAAATCAA
1 ACAAATCAA
1400313 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1400324 original size:12 final size:12
Alignment explanation
Indices: 1400307--1400379 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
1400297 CATCTTTACA
1400307 AATCAATTAAAC
1 AATCAATTAAAC
*
1400319 AATCAA--AAATTG
1 AATCAATTAAA--C
**
1400331 AATCAACTTTTAC
1 AATCAA-TTAAAC
1400344 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
1400357 AATCAA-AAAAC
1 AATCAATTAAAC
1400368 AATCAATTAAAC
1 AATCAATTAAAC
1400380 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:1402253 original size:14 final size:14
Alignment explanation
Indices: 1402234--1402290 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1402224 GCGAAATGAA
*
1402234 AATCGCAACGACAG
1 AATCGCAACGAAAG
1402248 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1402265 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1402281 AATCGCAACG
1 AATCGCAACG
1402291 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1402261 original size:33 final size:33
Alignment explanation
Indices: 1402215--1402307 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1402205 GCGAAACCAA
*
1402215 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1402248 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1402281 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1402308 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1402272 original size:19 final size:19
Alignment explanation
Indices: 1402178--1402312 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1402168 TAGTTTACTT
* *
1402178 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1402198 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1402217 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1402236 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1402250 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1402269 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1402283 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1402302 TCGCAATGCGA
1 TCGCAACGCGA
1402313 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1402330 original size:19 final size:19
Alignment explanation
Indices: 1402308--1402435 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1402298 AAAATCGCAA
1402308 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1402327 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1402341 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1402360 TGCGA-TCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1402373 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1402392 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1402411 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1402431 TGCGA
1 TGCGA
1402436 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
13 8 0.09
14 13 0.15
15 2 0.02
16 1 0.01
17 3 0.03
18 3 0.03
19 45 0.51
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1402376 original size:32 final size:33
Alignment explanation
Indices: 1402308--1402397 Score: 155
Period size: 32 Copynumber: 2.8 Consensus size: 33
1402298 AAAATCGCAA
1402308 TGCGATTTTGGTTTCGCGTTGCGATCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATCTTGTCGT
1402341 TGCGATTTTGGTTTCGCGTTGCGATC-TGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATCTTGTCGT
**
1402373 TGCGATTTTCATTTCGCGTTGCGAT
1 TGCGATTTTGGTTTCGCGTTGCGAT
1402398 TTTGGTTTCG
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 29 0.53
33 26 0.47
ACGTcount: A:0.08, C:0.19, G:0.29, T:0.44
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATCTTGTCGT
Found at i:1402820 original size:93 final size:93
Alignment explanation
Indices: 1402479--1402949 Score: 903
Period size: 92 Copynumber: 5.1 Consensus size: 93
1402469 TTGAATGGAT
1402479 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1402544 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1402572 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1402636 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1402664 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1402729 AGTTTAGCAG-ATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1402756 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1402820 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1402848 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1402913 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1402941 AAATTTACT
1 AAATTTACT
1402950 AAGCAATCTA
Statistics
Matches: 372, Mismatches: 3, Indels: 6
0.98 0.01 0.02
Matches are distributed among these distances:
91 34 0.09
92 204 0.55
93 134 0.36
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1404686 original size:19 final size:18
Alignment explanation
Indices: 1404647--1404757 Score: 102
Period size: 14 Copynumber: 6.8 Consensus size: 18
1404637 GTTGAAATGA
1404647 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1404662 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1404679 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1404695 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1404712 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
*
1404727 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1404744 AAATCGCAATGCGA
1 AAATCGCAACGCGA
1404758 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 23
0.75 0.04 0.22
Matches are distributed among these distances:
14 24 0.30
15 1 0.01
16 18 0.23
17 8 0.10
18 20 0.25
19 8 0.10
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1404722 original size:32 final size:32
Alignment explanation
Indices: 1404640--1404752 Score: 199
Period size: 32 Copynumber: 3.5 Consensus size: 32
1404630 TCTTTTGGTT
1404640 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATG-AAATCGCAACGAGAGAATCGCAACGC
*
1404673 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGA-AATCGCAACGAGAGAATCGCAACGC
1404706 GAAATGAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAATCGCAACGAGAGAATCGCAACGC
1404738 GAAATGAAATCGCAA
1 GAAATGAAATCGCAA
1404753 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
32 41 0.53
33 36 0.47
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (32 bp):
GAAATGAAATCGCAACGAGAGAATCGCAACGC
Found at i:1404788 original size:14 final size:14
Alignment explanation
Indices: 1404769--1404823 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1404759 TTTGGTTTCG
1404769 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1404783 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
1404802 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1404816 CGTTGCGA
1 CGTTGCGA
1404824 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1404986 original size:33 final size:33
Alignment explanation
Indices: 1404944--1405014 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1404934 AATACTAACT
*
1404944 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1404977 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1405010 TGAAA
1 TGAAA
1405015 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1405248 original size:22 final size:22
Alignment explanation
Indices: 1405196--1405250 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1405186 TGGTTGTGAG
**
1405196 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1405218 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1405240 GGATTTCTTCG
1 GGATTTCTTCG
1405251 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1405421 original size:20 final size:20
Alignment explanation
Indices: 1405396--1405589 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
1405386 CTTTAAATAT
1405396 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1405416 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1405438 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1405457 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* * **
1405477 TGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1405497 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1405517 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1405537 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1405557 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1405577 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1405590 TGGAAAATCG
Statistics
Matches: 145, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1405583 original size:60 final size:60
Alignment explanation
Indices: 1405396--1405589 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
1405386 CTTTAAATAT
**
1405396 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * * *** *
1405457 CGCGTTGCGATATACGGATATGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1405517 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1405577 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1405590 TGGAAAATCG
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 83 0.75
61 27 0.25
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1405606 original size:21 final size:20
Alignment explanation
Indices: 1405582--1405658 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
1405572 ATATTCGCGT
1405582 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
1405603 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
1405623 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
1405645 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
1405659 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:1405669 original size:20 final size:20
Alignment explanation
Indices: 1405644--1405695 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1405634 AAGAATCGCG
*
1405644 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1405664 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1405684 TTGCGATTCTGG
1 TTGCGATTCTGG
1405696 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:1406330 original size:18 final size:19
Alignment explanation
Indices: 1406295--1406331 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1406285 AAAAATCAGG
1406295 CTTAACAACCAAAACCAAC
1 CTTAACAACCAAAACCAAC
*
1406314 CTTAACAA-CATAACCAAC
1 CTTAACAACCAAAACCAAC
1406332 TTTGAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.51, C:0.35, G:0.00, T:0.14
Consensus pattern (19 bp):
CTTAACAACCAAAACCAAC
Found at i:1411459 original size:116 final size:115
Alignment explanation
Indices: 1411313--1411551 Score: 327
Period size: 116 Copynumber: 2.1 Consensus size: 115
1411303 AAAGAATAAG
*
1411313 AAAAACATGATTAAATTTAATTCAAAATTGAATGAATAAAGAAGAGAAACGA-AAAAAGAGGGTA
1 AAAAA-ATGATTAAATTTAATTCAAAATTGAATGAATAAAGAAGAGAAA-GAGAAAAAGAGGCTA
* * ** *
1411377 AAAATTAAACATTTTATGAAAATATAAAAATTAGGGGCCCTAATTATAAGTAT
64 AAAACTAAAAAAATTATGAAAATAT-AAAATTAGGGGCCCTAATTATAAATAT
* * * * * *
1411430 AAAAAATGGTTAAATTTAATTCAAAATTGAATGAATTAATAAGAGAAATAGAAAAAGATGCTCAA
1 AAAAAATGATTAAATTTAATTCAAAATTGAATGAATAAAGAAGAGAAAGAGAAAAAGAGGCTAAA
*
1411495 AACTAAAAAAATTATGAAATTATAAAATTAGGGGCCCTAATTATAAATAT
66 AACTAAAAAAATTATGAAAATATAAAATTAGGGGCCCTAATTATAAATAT
1411545 AAAAAAT
1 AAAAAAT
1411552 TGGGGATCCT
Statistics
Matches: 108, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
115 34 0.31
116 69 0.64
117 5 0.05
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.26
Consensus pattern (115 bp):
AAAAAATGATTAAATTTAATTCAAAATTGAATGAATAAAGAAGAGAAAGAGAAAAAGAGGCTAAA
AACTAAAAAAATTATGAAAATATAAAATTAGGGGCCCTAATTATAAATAT
Found at i:1412553 original size:2 final size:2
Alignment explanation
Indices: 1412546--1412572 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1412536 GTAATAAGTT
1412546 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1412573 TAACTACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1412817 original size:2 final size:2
Alignment explanation
Indices: 1412812--1412871 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1412802 ACACACACAC
1412812 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1412854 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1412872 CAAAAAGGTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1413477 original size:2 final size:2
Alignment explanation
Indices: 1413470--1413512 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1413460 GTTTCGGTCA
1413470 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1413512 A
1 A
1413513 ATTTACCTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1413557 original size:31 final size:31
Alignment explanation
Indices: 1413522--1413585 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
1413512 AATTTACCTT
** *
1413522 TTCAACTATTTTTAAAAGATTTAAGATCAAA
1 TTCAACTATTTCAAAAAGATTGAAGATCAAA
*
1413553 TTCAATTATTTCAAAAAGATTGAAGATCAAA
1 TTCAACTATTTCAAAAAGATTGAAGATCAAA
1413584 TT
1 TT
1413586 TAATAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (31 bp):
TTCAACTATTTCAAAAAGATTGAAGATCAAA
Found at i:1413911 original size:21 final size:21
Alignment explanation
Indices: 1413887--1413941 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
1413877 CGATTTTCCC
*
1413887 AATTCGCAATGCGAATAAGTA
1 AATTCGCAATGCGAATAAGGA
* **
1413908 AATT-GCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGGA
*
1413928 AAATCGCAATGCGA
1 AATTCGCAATGCGA
1413942 TACTGACTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (21 bp):
AATTCGCAATGCGAATAAGGA
Found at i:1413955 original size:20 final size:20
Alignment explanation
Indices: 1413930--1414044 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
1413920 AATTGGGAAA
1413930 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1413950 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* * **
1413970 ATCGCAATGCGATAATATAAA
1 ATCGCAATGCGATACT-GACT
* *
1413991 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
1414011 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
1414031 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
1414045 TTTCAAAGCG
Statistics
Matches: 77, Mismatches: 15, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
19 2 0.03
20 49 0.64
21 26 0.34
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1413992 original size:61 final size:62
Alignment explanation
Indices: 1413927--1414044 Score: 168
Period size: 61 Copynumber: 1.9 Consensus size: 62
1413917 GCGAATTGGG
* * * *
1413927 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTAC-T-ATCGCAATGCGATAATAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA-ATACATAATCGCAATGCGATAATAT
*
1413988 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATAATACATAATCGCAATGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATACATAATCGCAATGCGAT
1414045 TTTCAAAGCG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 3 0.06
61 34 0.68
62 13 0.26
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (62 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATACATAATCGCAATGCGATAATAT
Found at i:1414016 original size:41 final size:41
Alignment explanation
Indices: 1413950--1414038 Score: 115
Period size: 41 Copynumber: 2.2 Consensus size: 41
1413940 GATACTGACT
* * * * *
1413950 ATCGCAATGCGATACTTACTATCGCAATGCGATAATATAAA
1 ATCGCAACGAGATACTGACTATCGCAACGCGATAATACAAA
* *
1413991 ATCGCAACGAGATACTGACTTTCGCAACGCGATAATACATA
1 ATCGCAACGAGATACTGACTATCGCAACGCGATAATACAAA
1414032 ATCGCAA
1 ATCGCAA
1414039 TGCGATTTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (41 bp):
ATCGCAACGAGATACTGACTATCGCAACGCGATAATACAAA
Found at i:1414240 original size:22 final size:22
Alignment explanation
Indices: 1414212--1414255 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1414202 CACTCTCTCA
1414212 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1414234 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1414256 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1414557 original size:20 final size:20
Alignment explanation
Indices: 1414498--1414561 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
1414488 GCGATTTTAG
*
1414498 TTTCGCGTTGCGATTGTCAA
1 TTTCGCGTTGCGATTGTCAT
* *
1414518 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATTGTCAT
* *
1414538 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTGTCAT
1414558 TTTC
1 TTTC
1414562 AGAAACTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.45
Consensus pattern (20 bp):
TTTCGCGTTGCGATTGTCAT
Found at i:1414751 original size:25 final size:24
Alignment explanation
Indices: 1414697--1414751 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1414687 TGTTTATTAT
* *
1414697 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1414721 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1414747 TGTTT
1 TGTTT
1414752 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1416413 original size:20 final size:20
Alignment explanation
Indices: 1416388--1416433 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1416378 TAGTTTACTT
*
1416388 TCGCAACATGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
1416408 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
1416428 TCGCAA
1 TCGCAA
1416434 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1416442 original size:19 final size:20
Alignment explanation
Indices: 1416399--1416454 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1416389 CGCAACATGA
1416399 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
1416419 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
1416438 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
1416455 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:1416462 original size:14 final size:14
Alignment explanation
Indices: 1416443--1416500 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1416433 ATGCGAAATG
1416443 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1416457 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
*
1416473 ATGAAATCACAACGAC
1 A--AAATCGCAACGAC
1416489 AAAATCGCAACG
1 AAAATCGCAACG
1416501 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1416469 original size:33 final size:33
Alignment explanation
Indices: 1416427--1416517 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1416417 GGAAATGGCT
1416427 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1416460 ATCGCAATGCGAAATG-AAATCACAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1416492 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1416518 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1416553 original size:14 final size:14
Alignment explanation
Indices: 1416534--1416624 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 14
1416524 TTGTGTTTCG
*
1416534 CGTTGCTATTTTGT
1 CGTTGCGATTTTGT
*
1416548 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1416564 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
1416580 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
1416597 CGTATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1416613 CGTTGCGATTTT
1 CGTTGCGATTTT
1416625 CATTTCGCAT
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
14 26 0.41
15 3 0.05
16 12 0.19
17 4 0.06
18 12 0.19
19 6 0.10
ACGTcount: A:0.11, C:0.16, G:0.22, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1416598 original size:33 final size:33
Alignment explanation
Indices: 1416529--1416640 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
1416519 GCGATTTGTG
* *
1416529 TTTCGCGTTGCTATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1416561 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
1416594 TTTCGTATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1416627 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1416641 AGCCATTTCC
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 25 0.33
33 50 0.67
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.49
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1416659 original size:20 final size:19
Alignment explanation
Indices: 1416625--1416680 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1416615 TTGCGATTTT
*
1416625 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1416644 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1416664 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
1416681 TTTAAGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1417143 original size:42 final size:42
Alignment explanation
Indices: 1417046--1417134 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
1417036 GACTCACCTG
* * *
1417046 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
* * *
1417088 TCCTCCCTCAAGAGTCCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
1417130 TCATC
1 TCATC
1417135 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.21, C:0.44, G:0.15, T:0.20
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
Found at i:1418582 original size:14 final size:14
Alignment explanation
Indices: 1418548--1418586 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1418538 TTGATTGTTT
1418548 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
1418562 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
1418576 TGTTGATTTGT
1 AATTGATTTGT
1418587 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1418732 original size:14 final size:14
Alignment explanation
Indices: 1418713--1418766 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
1418703 GAAACTAACT
1418713 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1418727 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
1418746 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1418760 ATCGCAA
1 ATCGCAA
1418767 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:1418868 original size:20 final size:20
Alignment explanation
Indices: 1418843--1418881 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1418833 TTCGAATTGC
*
1418843 GATAGCCATTTTTGCGTTGT
1 GATAGCCATTTTCGCGTTGT
1418863 GATAGCCATTTTCGCGTTG
1 GATAGCCATTTTCGCGTTG
1418882 CGATTTCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.26, T:0.41
Consensus pattern (20 bp):
GATAGCCATTTTCGCGTTGT
Found at i:1419124 original size:20 final size:20
Alignment explanation
Indices: 1419098--1419168 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
1419088 TTTGAAGATG
*
1419098 ATTGCGATTTTCAGAATCTC
1 ATTGCGATTTTCAGAATCGC
* ** *
1419118 GTTGCGATAGTCAGTATCGC
1 ATTGCGATTTTCAGAATCGC
1419138 ATTGCGATTTTCCA-AATTCGC
1 ATTGCGATTTT-CAGAA-TCGC
*
1419159 ATTGTGATTT
1 ATTGCGATTT
1419169 ACTTATTCGC
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
20 24 0.62
21 15 0.38
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTGCGATTTTCAGAATCGC
Found at i:1419160 original size:21 final size:20
Alignment explanation
Indices: 1419134--1419185 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1419124 ATAGTCAGTA
*
1419134 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACAAAT
* **
1419155 TCGCATTGTGATTTACTTAT
1 TCGCATTGCGATTTACAAAT
1419175 TCGCATTGCGA
1 TCGCATTGCGA
1419186 ATTAGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAAT
Found at i:1419985 original size:24 final size:24
Alignment explanation
Indices: 1419958--1420011 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1419948 GTATTCGAAA
*
1419958 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1419982 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1420006 TTTGAT
1 TTTGAT
1420012 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1420203 original size:12 final size:12
Alignment explanation
Indices: 1420186--1420210 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1420176 ATATAATCCT
1420186 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1420198 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1420210 G
1 G
1420211 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1422547 original size:33 final size:33
Alignment explanation
Indices: 1422502--1422661 Score: 252
Period size: 33 Copynumber: 4.8 Consensus size: 33
1422492 GGAAATTACT
1422502 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1422535 ATTGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1422568 ATCGCAATGCGAAATGAAAATCGCAACGCGA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1422600 TTTCGCAATGCGAAATGAAAATCGCAACGA-AGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGA-GA
*
1422634 ATCGCAATGCGAAATGAAAATTGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1422662 CGAATTTAAT
Statistics
Matches: 117, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.02
33 114 0.97
34 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1422683 original size:19 final size:19
Alignment explanation
Indices: 1422661--1422702 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1422651 AAATTGCAAC
*
1422661 GCGAATTTAATTTCTCGTT
1 GCGAATTTAATTTCGCGTT
* *
1422680 GCGATTTTCATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
1422699 GCGA
1 GCGA
1422703 TTCTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (19 bp):
GCGAATTTAATTTCGCGTT
Found at i:1422703 original size:19 final size:19
Alignment explanation
Indices: 1422670--1422736 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
1422660 CGCGAATTTA
*
1422670 ATTTCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
1422689 ATTTCGCGTTGCGA--TTC
1 ATTTCGCGTTGCGATTTTC
*
1422706 ---TCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
1422722 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
1422737 AGTACTTTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
14 10 0.26
16 3 0.08
17 3 0.08
19 23 0.59
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:1422712 original size:33 final size:33
Alignment explanation
Indices: 1422673--1422736 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
1422663 GAATTTAATT
*
1422673 TCTCGTTGCGATTTTCATTTCGCGTTGCGATTC
1 TCTCGTTGCGATTTTCATTTCGCATTGCGATTC
1422706 TCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TCTCGTTGCGATTTTCATTTCGCATTGCGAT
1422737 AGTACTTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.45
Consensus pattern (33 bp):
TCTCGTTGCGATTTTCATTTCGCATTGCGATTC
Found at i:1422861 original size:14 final size:14
Alignment explanation
Indices: 1422842--1422878 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1422832 CATCAATTAA
1422842 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1422856 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1422870 ACAAATCAA
1 ACAAATCAA
1422879 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1424251 original size:21 final size:21
Alignment explanation
Indices: 1424185--1424251 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1424175 GTGAATCGGG
*
1424185 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1424205 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1424227 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1424248 CTCT
1 CTCT
1424252 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1424270 original size:42 final size:41
Alignment explanation
Indices: 1424185--1424307 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1424175 GTGAATCGGG
* * * *
1424185 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
1424227 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
1424269 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
1424308 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:1424700 original size:91 final size:90
Alignment explanation
Indices: 1424525--1424709 Score: 284
Period size: 91 Copynumber: 2.0 Consensus size: 90
1424515 ATTTCAAACT
*
1424525 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
1424590 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
1424618 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCATAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
1424682 -ATATTGGCAGCAACCGAATAAATTTAC
64 GA-ATTGGCAGCAACCGAATAAATTTAC
1424709 T
1 T
1424710 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
90 1 0.01
91 41 0.47
93 19 0.22
95 26 0.30
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:1425550 original size:21 final size:22
Alignment explanation
Indices: 1425508--1425550 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1425498 AATAACAAAC
*
1425508 ATTAGTAATTGTTAAATAATTA
1 ATTAGTAATTGTTAAAAAATTA
1425530 ATTA-TAATT-TTAAAAACATTA
1 ATTAGTAATTGTTAAAAA-ATTA
1425551 TATAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
ATTAGTAATTGTTAAAAAATTA
Found at i:1426427 original size:20 final size:19
Alignment explanation
Indices: 1426396--1426536 Score: 95
Period size: 19 Copynumber: 7.8 Consensus size: 19
1426386 TCTTTTGGTT
1426396 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1426415 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1426436 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1426455 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
1426469 GAAATGACTATCGCAAC--
1 GAAATGAAAATCGCAACGA
* * *
1426486 --AA-GAGAATCGTAACGC
1 GAAATGAAAATCGCAACGA
*
1426502 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
1426521 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1426537 TGCGATTTTG
Statistics
Matches: 97, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
14 19 0.20
15 2 0.02
16 2 0.02
17 2 0.02
18 2 0.02
19 39 0.40
20 29 0.30
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1426478 original size:33 final size:33
Alignment explanation
Indices: 1426421--1426519 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
1426411 ACGAGATAAT
1426421 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
1426455 GAGAATCGCAACGCGAAATGACTATCGCAACAA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
* **
1426488 GAGAATCGTAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
1426520 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 46 0.77
34 14 0.23
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:1426570 original size:19 final size:19
Alignment explanation
Indices: 1426537--1426581 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1426527 AAAATCGCAA
*
1426537 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
1426556 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
1426575 TGCGATT
1 TGCGATT
1426582 CTCTTGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:1427157 original size:20 final size:20
Alignment explanation
Indices: 1427132--1427184 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1427122 GCGCTATGTA
1427132 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1427152 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1427172 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1427185 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1427218 original size:20 final size:20
Alignment explanation
Indices: 1427193--1427246 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1427183 GATTTTGTAT
1427193 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1427213 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1427233 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1427247 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1427231 original size:61 final size:61
Alignment explanation
Indices: 1427133--1427249 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
1427123 CGCTATGTAA
* * * * *
1427133 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
1427194 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1427250 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1427265 original size:61 final size:61
Alignment explanation
Indices: 1427133--1427267 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
1427123 CGCTATGTAA
* * * * * ** *
1427133 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
1427194 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
1427256 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1427268 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:1427357 original size:21 final size:21
Alignment explanation
Indices: 1427317--1427357 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1427307 ACTGTAGACC
** *
1427317 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
1427338 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
1427358 GCGAATTTAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:1429055 original size:60 final size:60
Alignment explanation
Indices: 1428941--1429055 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
1428931 ACTATAGCAT
* * * * *
1428941 ATTGCTTTATTGAGTCCCTTGACTACTAAATGTTACAAAATGGTCCCTCGACTATAGGGA
1 ATTGCTTTATTGAGTCCCTCGACTACTAAAAGTTACAAAATGATCACTCAACTATAGGGA
* * *
1429001 ATTGCTTTGTTGAGTCTCTCGACTATTAAAAGTTACAAAATGATCACTCAACTAT
1 ATTGCTTTATTGAGTCCCTCGACTACTAAAAGTTACAAAATGATCACTCAACTAT
1429056 TCATTATGTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (60 bp):
ATTGCTTTATTGAGTCCCTCGACTACTAAAAGTTACAAAATGATCACTCAACTATAGGGA
Found at i:1431002 original size:228 final size:228
Alignment explanation
Indices: 1430575--1431035 Score: 610
Period size: 228 Copynumber: 2.0 Consensus size: 228
1430565 TATTAAATGT
*
1430575 AAATCTAATATTGCATTTCTTATTTTTATTTAAAGTGTCATGTCAACATCTATTATGACTAGGAT
1 AAATCTAATATTGCATTTCTTATTTTTATTTAAAGTGTCAGGTCAACATCTATTATGACT--GA-
* * ** *
1430640 TGTAAATGAGAAATGAATTACGAGCTATTTGAGATCGATTCGGATAAAGTTCAATCAACAATCAA
63 T-TAAATGAGAAATGAATTACAAGCTATTTGAGATCAATTCAAAAAAAGTTCAATCAACAATCAA
* * * * * * * *
1430705 ATCAGATGGACTCGACTCAAGCTAAGATTTGACTCAAATTCTTAAGGAGCCGAAACGAGCTACTT
127 ATCAAATGGACTCAACTCAAGCTAAGAATCGACTCAAATTCTTAACGAGCAGAAACAAACTACTT
1430770 GATACTCAAATCAAAAAGCTCGCAAGTTACTCGGAAAA
192 GATACTCAAATCAAAAAGCTCGCAAGTTACTC-GAAAA
*
1430808 AAATCTAATATTGCATTTCTTATTTTTATTTAGAGTGTCAGGTCAACATCTATTATG-CT-A-TA
1 AAATCTAATATTGCATTTCTTATTTTTATTTAAAGTGTCAGGTCAACATCTATTATGACTGATTA
* * *
1430870 AATGAGATAAATCG-ATTACAAGCTATTTGAGATTAATTCAAAAAAAGTTCAATCAACATTCATA
66 AATGAG--AAAT-GAATTACAAGCTATTTGAGATCAATTCAAAAAAAGTTCAATCAACAATCAAA
1430934 TCAAATGGACTCAACTCGAA-CTATA-AATCGACTCAAATTCTTAACGAGCAGAAACAAACTACT
128 TCAAATGGACTCAACTC-AAGCTA-AGAATCGACTCAAATTCTTAACGAGCAGAAACAAACTACT
* *
1430997 TGATACTCAAATCAAAAAGCTTGCAAGTTCCTCGAAAA
191 TGATACTCAAATCAAAAAGCTCGCAAGTTACTCGAAAA
1431035 A
1 A
1431036 TAATAATATT
Statistics
Matches: 203, Mismatches: 20, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
226 8 0.04
227 6 0.03
228 127 0.63
229 5 0.02
232 2 0.01
233 55 0.27
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (228 bp):
AAATCTAATATTGCATTTCTTATTTTTATTTAAAGTGTCAGGTCAACATCTATTATGACTGATTA
AATGAGAAATGAATTACAAGCTATTTGAGATCAATTCAAAAAAAGTTCAATCAACAATCAAATCA
AATGGACTCAACTCAAGCTAAGAATCGACTCAAATTCTTAACGAGCAGAAACAAACTACTTGATA
CTCAAATCAAAAAGCTCGCAAGTTACTCGAAAA
Found at i:1432186 original size:28 final size:28
Alignment explanation
Indices: 1432127--1432187 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1432117 TTTATAAAAT
* *
1432127 ATATATATTTTAATTTTTTATACGATTT
1 ATATTTATTTTAATTTTTTATACGATTG
1432155 ATATTTATTTTAATGATTTTTATA-G-TTG
1 ATATTTATTTTAAT--TTTTTATACGATTG
1432183 ATATT
1 ATATT
1432188 GTGATGCCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 20 0.69
29 1 0.03
30 8 0.28
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.61
Consensus pattern (28 bp):
ATATTTATTTTAATTTTTTATACGATTG
Found at i:1434381 original size:22 final size:22
Alignment explanation
Indices: 1434356--1434397 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1434346 AATATTTTTA
1434356 GTTAATTC-GATTAATTCGATCG
1 GTTAATTCAG-TTAATTCGATCG
1434378 GTTAATTCAGTTAATTCGAT
1 GTTAATTCAGTTAATTCGAT
1434398 TAAAACCGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.43
Consensus pattern (22 bp):
GTTAATTCAGTTAATTCGATCG
Found at i:1438815 original size:87 final size:87
Alignment explanation
Indices: 1438669--1438843 Score: 350
Period size: 87 Copynumber: 2.0 Consensus size: 87
1438659 GTCTCCCTCA
1438669 AGGGTTTGTTATACAAAAATTAATTCAGAGAAAGATGATTAAATTTAAGTTTGAAATAATTTGAT
1 AGGGTTTGTTATACAAAAATTAATTCAGAGAAAGATGATTAAATTTAAGTTTGAAATAATTTGAT
1438734 TTTAGAGTCAACCTCAATCTTT
66 TTTAGAGTCAACCTCAATCTTT
1438756 AGGGTTTGTTATACAAAAATTAATTCAGAGAAAGATGATTAAATTTAAGTTTGAAATAATTTGAT
1 AGGGTTTGTTATACAAAAATTAATTCAGAGAAAGATGATTAAATTTAAGTTTGAAATAATTTGAT
1438821 TTTAGAGTCAACCTCAATCTTT
66 TTTAGAGTCAACCTCAATCTTT
1438843 A
1 A
1438844 AAGTAAGTAG
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (87 bp):
AGGGTTTGTTATACAAAAATTAATTCAGAGAAAGATGATTAAATTTAAGTTTGAAATAATTTGAT
TTTAGAGTCAACCTCAATCTTT
Found at i:1438918 original size:8 final size:8
Alignment explanation
Indices: 1438905--1438940 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
1438895 TCATTATAAG
1438905 ATGGAAAA
1 ATGGAAAA
1438913 ATGGAAAA
1 ATGGAAAA
1438921 ATGGAAAA
1 ATGGAAAA
1438929 ATGGAAAA
1 ATGGAAAA
1438937 ATGG
1 ATGG
1438941 TATGTGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (8 bp):
ATGGAAAA
Found at i:1439085 original size:2 final size:2
Alignment explanation
Indices: 1439078--1439114 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1439068 ACAAACTCGA
1439078 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1439115 AATTACGATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1440202 original size:32 final size:31
Alignment explanation
Indices: 1440148--1440207 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
1440138 ATTAAATGTT
* **
1440148 GAAAATTAAAAGGGACTGAAATAAGAATGCAG
1 GAAAATTAAAAGGAACAAAAATAA-AATGCAG
*
1440180 GAAAATTAAAAGGAAGAAAAATAAAATG
1 GAAAATTAAAAGGAACAAAAATAAAATG
1440208 ATGGAATCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 4 0.17
32 20 0.83
ACGTcount: A:0.60, C:0.03, G:0.22, T:0.15
Consensus pattern (31 bp):
GAAAATTAAAAGGAACAAAAATAAAATGCAG
Found at i:1440446 original size:34 final size:34
Alignment explanation
Indices: 1440394--1440479 Score: 108
Period size: 34 Copynumber: 2.6 Consensus size: 34
1440384 TTAGTTTGTG
*
1440394 CAATAAAATAAAATGTTAGTAA-GTTAGTA-AAAA
1 CAATAAAATAAAAAGTTAG-AATGTTAGTAGAAAA
1440427 CAATAAAAATAAAAAGTTAGAATGTTAGTATGAAAA
1 CAAT-AAAATAAAAAGTTAGAATGTTAGTA-GAAAA
1440463 -AATAAAAT-AAAAGTTAG
1 CAATAAAATAAAAAGTTAG
1440480 GAGGTTGTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
33 15 0.31
34 26 0.54
35 3 0.06
36 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.13, T:0.26
Consensus pattern (34 bp):
CAATAAAATAAAAAGTTAGAATGTTAGTAGAAAA
Found at i:1440545 original size:202 final size:201
Alignment explanation
Indices: 1440268--1440683 Score: 634
Period size: 202 Copynumber: 2.1 Consensus size: 201
1440258 TGCATAAATT
*
1440268 TAAAAGTTAGGCAGTTGTTTTTAACCGTTTAACCCGGACCATAAATAATGTGGATCGTCCCACAA
1 TAAAAGTTAGG-AGTTGTTTTTAACCGTTTAACCCGGACCATAAATAATGCGGATCGTCCCACAA
* * * * *
1440333 GACGGGTCACCATAAGGTCGTTAAATATTCGAATGTTAGAAAATTAGCGGGTTAGTTTGTGCAAT
65 GACAGGTCACCACAAGGTCGTTAAATATTCGAATGTTAGAAAATTAGCGGGTTAATTTATACAAT
* *
1440398 AAAATAAAATGTTAGTAAGTTAGTAAAAACAATAAAAATAAAAAGTTAGAATGTTAGTATGAAAA
130 AAAATAAAATGTTAGCAAGTTAGTAAAAACAATAAAAATAAAAAGTAAGAATGTTAGTATGAAAA
1440463 AATAAAA
195 AATAAAA
* * * *
1440470 TAAAAGTTAGGAGGTTGTTTTTAATCGTTTAACCCGGATCATAAATAATGCGGATCGTCCCCCAG
1 TAAAAGTTAGGA-GTTGTTTTTAACCGTTTAACCCGGACCATAAATAATGCGGATCGTCCCACAA
* * * *
1440535 GGCAGGTCACCGCAAGGTCGTTGAATATTCGAATGTTAGAATATTAGCGGGTTAATTTATACAAT
65 GACAGGTCACCACAAGGTCGTTAAATATTCGAATGTTAGAAAATTAGCGGGTTAATTTATACAAT
* * * *
1440600 AAAATAAAATGTTAGCAAGTTAGTAAGAATAATAAAAATAAAAAGTAAGTATGTTAGTATGAACA
130 AAAATAAAATGTTAGCAAGTTAGTAAAAACAATAAAAATAAAAAGTAAGAATGTTAGTATGAAAA
1440665 AATAAAA
195 AATAAAA
1440672 TAAAAGTTAGGA
1 TAAAAGTTAGGA
1440684 TGTTAGTAAG
Statistics
Matches: 193, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
201 1 0.01
202 192 0.99
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.28
Consensus pattern (201 bp):
TAAAAGTTAGGAGTTGTTTTTAACCGTTTAACCCGGACCATAAATAATGCGGATCGTCCCACAAG
ACAGGTCACCACAAGGTCGTTAAATATTCGAATGTTAGAAAATTAGCGGGTTAATTTATACAATA
AAATAAAATGTTAGCAAGTTAGTAAAAACAATAAAAATAAAAAGTAAGAATGTTAGTATGAAAAA
ATAAAA
Found at i:1440656 original size:34 final size:34
Alignment explanation
Indices: 1440597--1440693 Score: 108
Period size: 34 Copynumber: 2.9 Consensus size: 34
1440587 TAATTTATAC
* * *
1440597 AATAAAATAAAATGTTAGCAAGTTAGTAAGAA-T
1 AATAAAATAAAAAGTTAGCATGTTAGTAAGAACA
* * *
1440630 AATAAAAATAAAAAGTAAGTATGTTAGTATGAACA
1 AAT-AAAATAAAAAGTTAGCATGTTAGTAAGAACA
*
1440665 AATAAAAT-AAAAGTTAGGATGTTAGTAAG
1 AATAAAATAAAAAGTTAGCATGTTAGTAAG
1440694 TTAGAAAAGT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
33 21 0.40
34 29 0.55
35 3 0.06
ACGTcount: A:0.55, C:0.02, G:0.16, T:0.27
Consensus pattern (34 bp):
AATAAAATAAAAAGTTAGCATGTTAGTAAGAACA
Found at i:1442883 original size:6 final size:6
Alignment explanation
Indices: 1442874--1442944 Score: 79
Period size: 6 Copynumber: 11.8 Consensus size: 6
1442864 TTCAGACTGG
* * * * * *
1442874 ATTTCA ATTTTA ATTTGA GTTTCA ATTTCA ATATCA ATTTTA ATTTGA
1 ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA
*
1442922 GTTTCA ATTTCA ATTTCA ATTTC
1 ATTTCA ATTTCA ATTTCA ATTTC
1442945 GACTCCACTA
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.52
Consensus pattern (6 bp):
ATTTCA
Found at i:1442897 original size:30 final size:30
Alignment explanation
Indices: 1442877--1442943 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
1442867 AGACTGGATT
*
1442877 TCAATTTTAATTTGAGTTTCAATTTCAATA
1 TCAATTTTAATTTGAGTTTCAATCTCAATA
* *
1442907 TCAATTTTAATTTGAGTTTCAATTTCAATT
1 TCAATTTTAATTTGAGTTTCAATCTCAATA
1442937 TCAATTT
1 TCAATTT
1442944 CGACTCCACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.52
Consensus pattern (30 bp):
TCAATTTTAATTTGAGTTTCAATCTCAATA
Found at i:1442901 original size:24 final size:24
Alignment explanation
Indices: 1442851--1442943 Score: 78
Period size: 24 Copynumber: 3.6 Consensus size: 24
1442841 TTTACGCATT
* ** **
1442851 TTTCAATTTTAATTTCAGACTGGA
1 TTTCAATTTTAATTTGAGTTTCAA
1442875 TTTCAATTTTAATTTGAGTTTCAA
1 TTTCAATTTTAATTTGAGTTTCAA
1442899 TTTCAATATCAATTTTAATTTGAGTTTCAA
1 --T---T-TCAATTTTAATTTGAGTTTCAA
*
1442929 TTTCAATTTCAATTT
1 TTTCAATTTTAATTT
1442944 CGACTCCACT
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
24 31 0.54
25 1 0.02
26 1 0.02
28 1 0.02
29 1 0.02
30 22 0.39
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.52
Consensus pattern (24 bp):
TTTCAATTTTAATTTGAGTTTCAA
Found at i:1444766 original size:21 final size:21
Alignment explanation
Indices: 1444740--1444801 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
1444730 CCTATATATA
1444740 TATTTAATTATATTTTTTATT
1 TATTTAATTATATTTTTTATT
* *
1444761 TATTT-ACTATATTCCTTT-TT
1 TATTTAATTATATT-TTTTATT
1444781 TA-TTATATTATATTTTTTATT
1 TATTTA-ATTATATTTTTTATT
1444802 ATATATATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
19 2 0.06
20 14 0.42
21 17 0.52
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (21 bp):
TATTTAATTATATTTTTTATT
Found at i:1444773 original size:20 final size:21
Alignment explanation
Indices: 1444748--1444801 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
1444738 TATATTTAAT
1444748 TATATTTTTTATTTATT-TAC
1 TATATTTTTTATTTATTATAC
* *
1444768 TATATTCCTTT-TTTATTATAT
1 TATATT-TTTTATTTATTATAC
1444789 TATATTTTTTATT
1 TATATTTTTTATT
1444802 ATATATATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (21 bp):
TATATTTTTTATTTATTATAC
Found at i:1444787 original size:16 final size:17
Alignment explanation
Indices: 1444758--1444805 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1444748 TATATTTTTT
*
1444758 ATTTATTTACTATATT-C
1 ATTT-TTTATTATATTAC
* *
1444775 CTTTTTTATTATATTAT
1 ATTTTTTATTATATTAC
1444792 ATTTTTTATTATAT
1 ATTTTTTATTATAT
1444806 ATATCTTATC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTTTATTATATTAC
Found at i:1444798 original size:17 final size:16
Alignment explanation
Indices: 1444776--1444809 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
1444766 ACTATATTCC
1444776 TTTTTTATTATATTATA
1 TTTTTTATTATA-TATA
1444793 TTTTTTATTATATATA
1 TTTTTTATTATATATA
1444809 T
1 T
1444810 CTTATCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTTATTATATATA
Done.