Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008985.1 Hibiscus syriacus cultivar Beakdansim tig00112349_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: 1528252
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 8 of 9
Found at i:1300797 original size:25 final size:25
Alignment explanation
Indices: 1300769--1300848 Score: 64
Period size: 25 Copynumber: 3.3 Consensus size: 25
1300759 AATAAAGATT
1300769 TTAATTACAAAACTACTAAACAATA
1 TTAATTACAAAACTACTAAACAATA
* *
1300794 TTAATTA-ATATAA-TGGA-TAAA-GATT
1 TTAATTACA-A-AACT--ACTAAACAATA
1300819 TTAATTAC--AACTACTAAACAATA
1 TTAATTACAAAACTACTAAACAATA
1300842 TTAATTA
1 TTAATTA
1300849 TTAGGCTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
21 1 0.02
22 6 0.14
23 10 0.23
24 1 0.02
25 18 0.42
26 6 0.14
27 1 0.02
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35
Consensus pattern (25 bp):
TTAATTACAAAACTACTAAACAATA
Found at i:1300825 original size:50 final size:48
Alignment explanation
Indices: 1300750--1300848 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 48
1300740 CTCGACAGAG
1300750 AATATAATGAATAAAGATTTTAATTACAAAACTACTAAACAATATTAATT
1 AATATAATGAATAAAGATTTTAATTAC--AACTACTAAACAATATTAATT
*
1300800 AATATAATGGATAAAGATTTTAATTACAACTACTAAACAATATTAATT
1 AATATAATGAATAAAGATTTTAATTACAACTACTAAACAATATTAATT
1300848 A
1 A
1300849 TTAGGCTTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 22 0.46
50 26 0.54
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (48 bp):
AATATAATGAATAAAGATTTTAATTACAACTACTAAACAATATTAATT
Found at i:1303677 original size:60 final size:60
Alignment explanation
Indices: 1303516--1303693 Score: 193
Period size: 60 Copynumber: 3.0 Consensus size: 60
1303506 AAATTTGGGA
* * *
1303516 ATGAAATTAGAATATTCAAAAGTTT-GGGACCAATTTAGAAA-G-GGGTCATAGTTTAGGC
1 ATGAAATTAGAATATTCAAAAGTTTAGGGACTAATTTA-AAATGAGAGTCATAGTTTAGGG
* * * * * * * *
1303574 AT-AAATTTAAAATGTTCAAAATTTTAAGGACTATTTTACAATGAGAGACATATTTTAGGG
1 ATGAAA-TTAGAATATTCAAAAGTTTAGGGACTAATTTAAAATGAGAGTCATAGTTTAGGG
**
1303634 ATGAAATTAGAATATAAAAAAGTTTAGGGACTAATTTAAAATGAGAGTCATAGTTTAGGG
1 ATGAAATTAGAATATTCAAAAGTTTAGGGACTAATTTAAAATGAGAGTCATAGTTTAGGG
1303694 GCATATATGC
Statistics
Matches: 94, Mismatches: 21, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
57 3 0.03
58 20 0.21
59 10 0.11
60 58 0.62
61 3 0.03
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (60 bp):
ATGAAATTAGAATATTCAAAAGTTTAGGGACTAATTTAAAATGAGAGTCATAGTTTAGGG
Found at i:1304090 original size:18 final size:16
Alignment explanation
Indices: 1304058--1304107 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1304048 TTCATATTTC
1304058 ATATTTAATATTTTAA
1 ATATTTAATATTTTAA
1304074 ATATTTGAATAATTTT--
1 ATATTT-AAT-ATTTTAA
*
1304090 ATATTT-ATAATTTAA
1 ATATTTAATATTTTAA
1304105 ATA
1 ATA
1304108 ATTTTATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
13 4 0.14
14 2 0.07
15 3 0.10
16 12 0.41
17 3 0.10
18 5 0.17
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
ATATTTAATATTTTAA
Found at i:1304107 original size:23 final size:23
Alignment explanation
Indices: 1304076--1304120 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1304066 TATTTTAAAT
*
1304076 ATTTGAATAATTTTATATTTATA
1 ATTTAAATAATTTTATATTTATA
*
1304099 ATTTAAATAATTTTATTTTTAT
1 ATTTAAATAATTTTATATTTAT
1304121 TTAATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
ATTTAAATAATTTTATATTTATA
Found at i:1305598 original size:24 final size:24
Alignment explanation
Indices: 1305571--1305670 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
1305561 GATATCAAAA
*
1305571 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
1305595 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
1305619 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
1305643 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
1305667 ATCA
1 ATCA
1305671 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:1305670 original size:48 final size:48
Alignment explanation
Indices: 1305564--1305672 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
1305554 AAACGGAGAT
* * * * *
1305564 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
1305612 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
1305660 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1305673 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1308156 original size:8 final size:8
Alignment explanation
Indices: 1308123--1308177 Score: 67
Period size: 8 Copynumber: 6.5 Consensus size: 8
1308113 TCAAAGTTTT
1308123 GGTCAACAG
1 GGTCAAC-G
1308132 TGGTCAACG
1 -GGTCAACG
1308141 CCGGTCAACG
1 --GGTCAACG
1308151 GGTCAAC-
1 GGTCAACG
1308158 GGTCAACG
1 GGTCAACG
1308166 GGTCAACG
1 GGTCAACG
1308174 GGTC
1 GGTC
1308178 GGGTCGGGTA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
7 7 0.17
8 19 0.45
9 1 0.02
10 15 0.36
ACGTcount: A:0.24, C:0.27, G:0.35, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1308162 original size:15 final size:15
Alignment explanation
Indices: 1308142--1308174 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1308132 TGGTCAACGC
1308142 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
1308157 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
1308172 CGG
1 CGG
1308175 GTCGGGTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.36, T:0.12
Consensus pattern (15 bp):
CGGTCAACGGGTCAA
Found at i:1308182 original size:13 final size:13
Alignment explanation
Indices: 1308177--1308212 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1308167 GTCAACGGGT
1308177 CGGGTCGGGTACA
1 CGGGTCGGGTACA
* *
1308190 CTGGTCGGGTAAA
1 CGGGTCGGGTACA
1308203 CGGGTCGGGT
1 CGGGTCGGGT
1308213 CGGGTCGGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.47, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTACA
Found at i:1308213 original size:18 final size:18
Alignment explanation
Indices: 1308164--1308217 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
1308154 CAACGGTCAA
*
1308164 CGGGTCAACGGGTCGGGT
1 CGGGTAAACGGGTCGGGT
*
1308182 CGGGTACAC---T--GGT
1 CGGGTAAACGGGTCGGGT
1308195 CGGGTAAACGGGTCGGGT
1 CGGGTAAACGGGTCGGGT
1308213 CGGGT
1 CGGGT
1308218 CGGGTTATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 10
0.68 0.07 0.24
Matches are distributed among these distances:
13 11 0.39
15 1 0.04
16 1 0.04
18 15 0.54
ACGTcount: A:0.13, C:0.20, G:0.48, T:0.19
Consensus pattern (18 bp):
CGGGTAAACGGGTCGGGT
Found at i:1310310 original size:24 final size:24
Alignment explanation
Indices: 1310283--1310382 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
1310273 GATATCAAAA
*
1310283 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
1310307 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
1310331 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
1310355 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
1310379 ATCA
1 ATCA
1310383 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:1310382 original size:48 final size:48
Alignment explanation
Indices: 1310276--1310384 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
1310266 AAACGGAGAT
* * * * *
1310276 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
1310324 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
1310372 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1310385 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1312868 original size:8 final size:8
Alignment explanation
Indices: 1312835--1312882 Score: 60
Period size: 8 Copynumber: 5.5 Consensus size: 8
1312825 TCAAAGTTTT
1312835 GGTCAACAG
1 GGTCAAC-G
1312844 TGGTCAACG
1 -GGTCAACG
1312853 TCGGTCAACG
1 --GGTCAACG
1312863 GGTCAACG
1 GGTCAACG
1312871 GGTCAACG
1 GGTCAACG
1312879 GGTC
1 GGTC
1312883 GGGTCGGGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
8 20 0.56
9 1 0.03
10 15 0.42
ACGTcount: A:0.23, C:0.25, G:0.35, T:0.17
Consensus pattern (8 bp):
GGTCAACG
Found at i:1312900 original size:13 final size:13
Alignment explanation
Indices: 1312882--1312917 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1312872 GTCAACGGGT
*
1312882 CGGGTCGGGTACA
1 CGGGTCGGGTAAA
*
1312895 CTGGTCGGGTAAA
1 CGGGTCGGGTAAA
1312908 CGGGTCGGGT
1 CGGGTCGGGT
1312918 TGGGTCGGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.47, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:1315024 original size:24 final size:24
Alignment explanation
Indices: 1314997--1315096 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
1314987 GATATCAAAA
*
1314997 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
1315021 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
1315045 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
1315069 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
1315093 ATCA
1 ATCA
1315097 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:1315096 original size:48 final size:48
Alignment explanation
Indices: 1314990--1315098 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
1314980 AAACGGAGAT
* * * * *
1314990 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
1315038 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
1315086 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1315099 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1317582 original size:8 final size:8
Alignment explanation
Indices: 1317549--1317603 Score: 67
Period size: 8 Copynumber: 6.5 Consensus size: 8
1317539 TCAAAGTTTT
1317549 GGTCAACAG
1 GGTCAAC-G
1317558 TGGTCAACG
1 -GGTCAACG
1317567 CCGGTCAACG
1 --GGTCAACG
1317577 GGTCAAC-
1 GGTCAACG
1317584 GGTCAACG
1 GGTCAACG
1317592 GGTCAACG
1 GGTCAACG
1317600 GGTC
1 GGTC
1317604 GGGTCGGGTA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
7 7 0.17
8 19 0.45
9 1 0.02
10 15 0.36
ACGTcount: A:0.24, C:0.27, G:0.35, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1317588 original size:15 final size:15
Alignment explanation
Indices: 1317568--1317600 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1317558 TGGTCAACGC
1317568 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
1317583 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
1317598 CGG
1 CGG
1317601 GTCGGGTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.36, T:0.12
Consensus pattern (15 bp):
CGGTCAACGGGTCAA
Found at i:1317608 original size:13 final size:13
Alignment explanation
Indices: 1317603--1317638 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1317593 GTCAACGGGT
1317603 CGGGTCGGGTACA
1 CGGGTCGGGTACA
* *
1317616 CTGGTCGGGTAAA
1 CGGGTCGGGTACA
1317629 CGGGTCGGGT
1 CGGGTCGGGT
1317639 CGGGTCGGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.47, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTACA
Found at i:1317639 original size:18 final size:18
Alignment explanation
Indices: 1317590--1317643 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
1317580 CAACGGTCAA
*
1317590 CGGGTCAACGGGTCGGGT
1 CGGGTAAACGGGTCGGGT
*
1317608 CGGGTACAC---T--GGT
1 CGGGTAAACGGGTCGGGT
1317621 CGGGTAAACGGGTCGGGT
1 CGGGTAAACGGGTCGGGT
1317639 CGGGT
1 CGGGT
1317644 CGGGTTATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 10
0.68 0.07 0.24
Matches are distributed among these distances:
13 11 0.39
15 1 0.04
16 1 0.04
18 15 0.54
ACGTcount: A:0.13, C:0.20, G:0.48, T:0.19
Consensus pattern (18 bp):
CGGGTAAACGGGTCGGGT
Found at i:1319817 original size:48 final size:48
Alignment explanation
Indices: 1319711--1319819 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
1319701 AAACGGAGAT
* * * * * *
1319711 ATCAAAAATCAAAACATAATTCTGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
1319759 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
1319807 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1319820 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1322306 original size:15 final size:15
Alignment explanation
Indices: 1322286--1322318 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1322276 TGGTCAACGT
1322286 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
1322301 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
1322316 CGG
1 CGG
1322319 GTCGGGTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.36, T:0.12
Consensus pattern (15 bp):
CGGTCAACGGGTCAA
Found at i:1322326 original size:13 final size:13
Alignment explanation
Indices: 1322321--1322357 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1322311 GTCAACGGGT
1322321 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
* *
1322334 CTGGTCGGGTAAA
1 CGGGTCGGGTCAA
1322347 CGGGTCGGGTC
1 CGGGTCGGGTC
1322358 GGGTCGGGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.22, G:0.46, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:1322331 original size:18 final size:18
Alignment explanation
Indices: 1322308--1322362 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
1322298 CAACGGTCAA
1322308 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
1322326 CGGGTCAAC---T--GGT
1 CGGGTCAACGGGTCGGGT
*
1322339 CGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
1322357 CGGGTC
1 CGGGTC
1322363 GGGTTATGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
13 11 0.37
15 1 0.03
16 1 0.03
18 17 0.57
ACGTcount: A:0.13, C:0.22, G:0.47, T:0.18
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:1322339 original size:8 final size:8
Alignment explanation
Indices: 1322267--1322321 Score: 67
Period size: 8 Copynumber: 6.5 Consensus size: 8
1322257 TCAAAGTTTT
1322267 GGTCAACAG
1 GGTCAAC-G
1322276 TGGTCAACG
1 -GGTCAACG
1322285 TCGGTCAACG
1 --GGTCAACG
1322295 GGTCAAC-
1 GGTCAACG
1322302 GGTCAACG
1 GGTCAACG
1322310 GGTCAACG
1 GGTCAACG
1322318 GGTC
1 GGTC
1322322 GGGTCGGGTC
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
7 7 0.17
8 19 0.45
9 1 0.02
10 15 0.36
ACGTcount: A:0.24, C:0.25, G:0.35, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:1324467 original size:24 final size:24
Alignment explanation
Indices: 1324440--1324539 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
1324430 GATATCAAAA
*
1324440 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
1324464 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
1324488 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
1324512 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
1324536 ATCA
1 ATCA
1324540 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:1324539 original size:48 final size:48
Alignment explanation
Indices: 1324433--1324541 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
1324423 AAACGGAGAT
* * * * *
1324433 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
1324481 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
1324529 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1324542 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1327053 original size:13 final size:13
Alignment explanation
Indices: 1327048--1327084 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1327038 GTCAACGGGT
1327048 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
* *
1327061 CTGGTCGGGTAAA
1 CGGGTCGGGTCAA
1327074 CGGGTCGGGTC
1 CGGGTCGGGTC
1327085 GGGTCGGGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.22, G:0.46, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:1327056 original size:26 final size:27
Alignment explanation
Indices: 1327027--1327089 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 27
1327017 AACGGGTCAA
*
1327027 CGGGTCAA-CGGGTCAACGGGTCGGGT
1 CGGGTCAAGCGGGTAAACGGGTCGGGT
1327053 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAA---G-CGGGTAAACGGGTCGGGT
1327084 CGGGTC
1 CGGGTC
1327090 GGGTTATGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 8 0.26
31 23 0.74
ACGTcount: A:0.14, C:0.22, G:0.46, T:0.17
Consensus pattern (27 bp):
CGGGTCAAGCGGGTAAACGGGTCGGGT
Found at i:1327058 original size:18 final size:18
Alignment explanation
Indices: 1327035--1327089 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
1327025 AACGGGTCAA
1327035 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
1327053 CGGGTCAAC---T--GGT
1 CGGGTCAACGGGTCGGGT
*
1327066 CGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
1327084 CGGGTC
1 CGGGTC
1327090 GGGTTATGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
13 11 0.37
15 1 0.03
16 1 0.03
18 17 0.57
ACGTcount: A:0.13, C:0.22, G:0.47, T:0.18
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:1327066 original size:8 final size:8
Alignment explanation
Indices: 1326993--1327048 Score: 76
Period size: 8 Copynumber: 6.5 Consensus size: 8
1326983 TCAAAGTTTT
1326993 GGTCAACAG
1 GGTCAAC-G
1327002 TGGTCAACG
1 -GGTCAACG
1327011 CCGGTCAACG
1 --GGTCAACG
1327021 GGTCAACG
1 GGTCAACG
1327029 GGTCAACG
1 GGTCAACG
1327037 GGTCAACG
1 GGTCAACG
1327045 GGTC
1 GGTC
1327049 GGGTCGGGTC
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
8 28 0.64
9 1 0.02
10 15 0.34
ACGTcount: A:0.23, C:0.27, G:0.36, T:0.14
Consensus pattern (8 bp):
GGTCAACG
Found at i:1328824 original size:7 final size:7
Alignment explanation
Indices: 1328807--1328854 Score: 89
Period size: 7 Copynumber: 7.0 Consensus size: 7
1328797 CTCCAGAGAA
1328807 TTCTT-C
1 TTCTTCC
1328813 TTCTTCC
1 TTCTTCC
1328820 TTCTTCC
1 TTCTTCC
1328827 TTCTTCC
1 TTCTTCC
1328834 TTCTTCC
1 TTCTTCC
1328841 TTCTTCC
1 TTCTTCC
1328848 TTCTTCC
1 TTCTTCC
1328855 AACCGTGAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 5 0.12
7 36 0.88
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (7 bp):
TTCTTCC
Found at i:1329433 original size:35 final size:35
Alignment explanation
Indices: 1329380--1329446 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
1329370 GCATTCATGA
*
1329380 GGTATCGATACCTGAAGAATA-GTATCGATACCCAG
1 GGTACCGATACCTGAAGAA-AGGTATCGATACCCAG
*
1329415 GGTACCGATACCTTAAGAAAGGTATCGATACC
1 GGTACCGATACCTGAAGAAAGGTATCGATACC
1329447 ATCTTTGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 1 0.03
35 28 0.97
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.22
Consensus pattern (35 bp):
GGTACCGATACCTGAAGAAAGGTATCGATACCCAG
Found at i:1329443 original size:20 final size:19
Alignment explanation
Indices: 1329379--1329446 Score: 56
Period size: 20 Copynumber: 3.7 Consensus size: 19
1329369 GGCATTCATG
1329379 AGGTATCGATACCTGAAGAA
1 AGGTATCGATACCT-AAGAA
*
1329399 TA-GTATCGATACC-CAG--
1 -AGGTATCGATACCTAAGAA
*
1329415 -GGTACCGATACCTTAAGAA
1 AGGTATCGATACC-TAAGAA
1329434 AGGTATCGATACC
1 AGGTATCGATACC
1329447 ATCTTTGAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
15 10 0.27
17 2 0.05
18 2 0.05
20 22 0.59
21 1 0.03
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (19 bp):
AGGTATCGATACCTAAGAA
Found at i:1336522 original size:2 final size:2
Alignment explanation
Indices: 1336515--1336543 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1336505 TAGAATGTTG
1336515 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 A
1336544 ATTGTGTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1337324 original size:45 final size:45
Alignment explanation
Indices: 1337273--1337363 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
1337263 GACATGACTA
1337273 AATTATGATAAGATAAATACGATTGTATTGGAGTAACTAATATGC
1 AATTATGATAAGATAAATACGATTGTATTGGAGTAACTAATATGC
1337318 AATTATGATAAGATAAATACGATTGTATTGGAGTAACTAATATGC
1 AATTATGATAAGATAAATACGATTGTATTGGAGTAACTAATATGC
1337363 A
1 A
1337364 TGTTCATATC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.33
Consensus pattern (45 bp):
AATTATGATAAGATAAATACGATTGTATTGGAGTAACTAATATGC
Found at i:1340544 original size:14 final size:15
Alignment explanation
Indices: 1340525--1340553 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1340515 TCTAAACTAC
1340525 TAATTTAGGG-TTTA
1 TAATTTAGGGATTTA
1340539 TAATTTAGGGATTTA
1 TAATTTAGGGATTTA
1340554 AGTTAGGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (15 bp):
TAATTTAGGGATTTA
Found at i:1340809 original size:9 final size:10
Alignment explanation
Indices: 1340790--1340830 Score: 75
Period size: 10 Copynumber: 4.2 Consensus size: 10
1340780 CCATGTTATC
1340790 ATTGAAAAAA
1 ATTGAAAAAA
1340800 ATTG-AAAAA
1 ATTGAAAAAA
1340809 ATTGAAAAAA
1 ATTGAAAAAA
1340819 ATTGAAAAAA
1 ATTGAAAAAA
1340829 AT
1 AT
1340831 CCCATGTCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 9 0.30
10 21 0.70
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (10 bp):
ATTGAAAAAA
Found at i:1340814 original size:19 final size:19
Alignment explanation
Indices: 1340790--1340828 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1340780 CCATGTTATC
1340790 ATTGAAAAAAATTGAAAAA
1 ATTGAAAAAAATTGAAAAA
1340809 ATTGAAAAAAATTGAAAAA
1 ATTGAAAAAAATTGAAAAA
1340828 A
1 A
1340829 ATCCCATGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (19 bp):
ATTGAAAAAAATTGAAAAA
Found at i:1341885 original size:20 final size:19
Alignment explanation
Indices: 1341862--1341908 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1341852 AATTATAATC
*
1341862 AAAATAAGTATGATATATAA
1 AAAATAAG-ACGATATATAA
1341882 AAAATAAAGACGATATATAA
1 AAAAT-AAGACGATATATAA
1341902 AAAATAA
1 AAAATAA
1341909 AGGCTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AAAATAAGACGATATATAA
Found at i:1341909 original size:20 final size:20
Alignment explanation
Indices: 1341873--1341910 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1341863 AAATAAGTAT
1341873 GATATATAAAAAATAAAGAC
1 GATATATAAAAAATAAAGAC
1341893 GATATATAAAAAATAAAG
1 GATATATAAAAAATAAAG
1341911 GCTAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.66, C:0.03, G:0.11, T:0.21
Consensus pattern (20 bp):
GATATATAAAAAATAAAGAC
Found at i:1341919 original size:18 final size:19
Alignment explanation
Indices: 1341873--1341920 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1341863 AAATAAGTAT
*
1341873 GATATATAAAAAATAAAGA
1 GATAAATAAAAAATAAAGA
*
1341892 CGATATATAAAAAATAAAG-
1 -GATAAATAAAAAATAAAGA
*
1341911 GCTAAATAAA
1 GATAAATAAA
1341921 TTATCATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 8 0.31
20 18 0.69
ACGTcount: A:0.65, C:0.04, G:0.10, T:0.21
Consensus pattern (19 bp):
GATAAATAAAAAATAAAGA
Found at i:1342777 original size:18 final size:19
Alignment explanation
Indices: 1342754--1342790 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1342744 CCAGTAATCC
1342754 TATTCCC-TGATAATCTTT
1 TATTCCCATGATAATCTTT
1342772 TATTCCCATTGATAATCTT
1 TATTCCCA-TGATAATCTT
1342791 ACATTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (19 bp):
TATTCCCATGATAATCTTT
Found at i:1343007 original size:60 final size:60
Alignment explanation
Indices: 1342933--1343122 Score: 177
Period size: 60 Copynumber: 3.2 Consensus size: 60
1342923 CTGCACTAAA
* * * * * *
1342933 CATCCTTAAACTATG-ATCTTTATTTTAAATTGATCTTTAAATTTTTGAATATTTTAGTTT
1 CATCCCTAAACTATGAATC-TCATTCTAAATCGATCCTTAAACTTTTGAATATTTTAGTTT
* * *
1342993 CATCCCTAAGCTATGAATCTCATTCTAAATCGATCCTTAAACTTTTGAATATTTCAATTT
1 CATCCCTAAACTATGAATCTCATTCTAAATCGATCCTTAAACTTTTGAATATTTTAGTTT
* * * ** * ** *
1343053 TAACCCTAAAATATGACCCTCATTCTATAATAG-TCCCCAAACTTTTGAATGTTTTAGTTT
1 CATCCCTAAACTATGAATCTCATTCTA-AATCGATCCTTAAACTTTTGAATATTTTAGTTT
*
1343113 CAACCCTAAA
1 CATCCCTAAA
1343123 TTTTTAAGTG
Statistics
Matches: 106, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
60 99 0.93
61 7 0.07
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (60 bp):
CATCCCTAAACTATGAATCTCATTCTAAATCGATCCTTAAACTTTTGAATATTTTAGTTT
Found at i:1343296 original size:58 final size:59
Alignment explanation
Indices: 1343155--1343299 Score: 152
Period size: 58 Copynumber: 2.5 Consensus size: 59
1343145 TTATTGGAAC
* * *
1343155 GTTCAAAAGTTTTAGGACTAATTTAAAATTAGAATCATAGTTTGAGTATGAATTTAGAAT
1 GTTCAAAAGTTTAAGGACTAATTT-AGATTAGAATCATAATTTGAGTATGAATTTAGAAT
* ** * *
1343215 GTTCAAATGTTTAAAAACCAATTTAGATT-GAGTCATAATTTAGAG-ATAGAA-TTAGAAT
1 GTTCAAAAGTTTAAGGACTAATTTAGATTAGAATCATAATTT-GAGTAT-GAATTTAGAAT
* *
1343273 GTTCAAAAGTTTGAGGATTAATTTAGA
1 GTTCAAAAGTTTAAGGACTAATTTAGA
1343300 ATGGAAGACA
Statistics
Matches: 69, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
58 40 0.58
59 10 0.14
60 19 0.28
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.37
Consensus pattern (59 bp):
GTTCAAAAGTTTAAGGACTAATTTAGATTAGAATCATAATTTGAGTATGAATTTAGAAT
Found at i:1344690 original size:44 final size:44
Alignment explanation
Indices: 1344488--1344674 Score: 293
Period size: 44 Copynumber: 4.2 Consensus size: 44
1344478 GATTTCTTAT
* * *
1344488 CAATATACATATCATTTAATCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTAC
1344533 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
*
1344577 CAATATTCTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
* * *
1344621 CACTATACTTACCTTTATTCCATAAGCTCGTAAGCTTATTTTAT
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
*
1344665 CAATCTACTT
1 CAATATACTT
1344675 GCTATAATTT
Statistics
Matches: 132, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
44 120 0.91
45 12 0.09
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.40
Consensus pattern (44 bp):
CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
Found at i:1344934 original size:59 final size:59
Alignment explanation
Indices: 1344867--1345145 Score: 305
Period size: 59 Copynumber: 4.7 Consensus size: 59
1344857 TGTCCTAAGA
* * * * * *** * *
1344867 AAATCCATACTA-TTAGTATGATTTCCTTATCCTTGTAGCACCCTTAGTGCTTTTTCTAG
1 AAATCCATAC-ACTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGG
* * * *
1344926 AAATCCATACACTCAGTATGA-TTCCATTACCATTTTAGCACA-TATAATGC-CCTATCTGG
1 AAATCCATACACTCAGTATGATTTCC-TTATCATTTTAGCACACT-CAGTGCTCC-ATATGG
* * * *
1344985 AAATCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTTCATATGG
1 AAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGG
* * *
1345044 AAATTCATACACTCAATATGATTTCCTTATCTTTTTAGCACACTCAGTGCTCCATATGG
1 AAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGG
1345103 AAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACAC
1 AAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACAC
1345146 ATATAGTGCC
Statistics
Matches: 187, Mismatches: 26, Indels: 14
0.82 0.11 0.06
Matches are distributed among these distances:
58 6 0.03
59 175 0.94
60 6 0.03
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.37
Consensus pattern (59 bp):
AAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGG
Found at i:1345159 original size:118 final size:117
Alignment explanation
Indices: 1344735--1345166 Score: 337
Period size: 118 Copynumber: 3.7 Consensus size: 117
1344725 TTAGCACTCT
* * * * ** **
1344735 CAGTGCTCTATCTGGAATAT-CATATACTTAATATGATTTCCTCCTCATTTTAGCACACGAAGTG
1 CAGTGCTCCATATGGAA-ATCCATACACTCAATATGATTTCCTTATCATTTTAGCACACTTAGTG
* * * * *
1344799 C-CCTATGTGAGAATCCATAC-CATTAATATGATTCCTTTACTATTTTTAGCATATGA
65 CTCATATG-GA-AATCCATACAC-TCAATATGATTCCATTA-TCTTTTTAGCACAT-A
* * * * * * *
1344855 -AGTG-TCC-TAAGAAAATCCATACTA-TTAGTATGATTTCCTTATCCTTGTAGCACCCTTAGTG
1 CAGTGCTCCATATGGAAATCCATAC-ACTCAATATGATTTCCTTATCATTTTAGCACACTTAGTG
** * * * * *
1344916 CTTTTTCTAGAAATCCATACACTCAGTATGATTCCATTACCATTTTAGCACATA
65 C-TCATATGGAAATCCATACACTCAATATGATTCCATTATCTTTTTAGCACATA
* * * * * *
1344970 TAATGC-CCTATCTGGAAATCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTG
1 CAGTGCTCC-ATATGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACACTTAGTG
*
1345034 CTTCATATGGAAATTCATACACTCAATATGATTTCC-TTATCTTTTTAGCACACT-
65 C-TCATATGGAAATCCATACACTCAATATGA-TTCCATTATCTTTTTAGCACA-TA
*
1345088 CAGTGCTCCATATGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACACATATAGT
1 CAGTGCTCCATATGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACAC-T-TAGT
*
1345153 GC-CATATGGTAATC
64 GCTCATATGGAAATC
1345167 ACTATACATA
Statistics
Matches: 245, Mismatches: 52, Indels: 32
0.74 0.16 0.10
Matches are distributed among these distances:
115 1 0.00
116 17 0.07
117 62 0.25
118 146 0.60
119 14 0.06
120 5 0.02
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.37
Consensus pattern (117 bp):
CAGTGCTCCATATGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACACTTAGTGC
TCATATGGAAATCCATACACTCAATATGATTCCATTATCTTTTTAGCACATA
Found at i:1345161 original size:59 final size:58
Alignment explanation
Indices: 1344706--1345145 Score: 297
Period size: 59 Copynumber: 7.5 Consensus size: 58
1344696 TGTACAATTC
* * * * * * * * *
1344706 ATATAATTTTCTTATAATATTAGCACTCTCAGTGCTCTATCTGGAATAT-CATATACTTA
1 ATATGATTTCCTTATCATTTTAGCACACTCAGTGC-CCATATGGAA-ATCCATACACTCA
** ** *
1344765 ATATGATTTCCTCCTCATTTTAGCACACGAAGTGCCC-TATGTGAGAATCCATAC-CATTA
1 ATATGATTTCCTTATCATTTTAGCACACTCAGTGCCCATATG-GA-AATCCATACAC-TCA
* * * * * *
1344824 ATATGA-TTCCTT-TACTATTTTTAGCATA-TGAAGTGTCC-TAAGAAAATCCATACTA-TTA
1 ATATGATTTCCTTAT-C-A-TTTTAGCACACT-CAGTGCCCATATGGAAATCCATAC-ACTCA
* * * * * *** * *
1344882 GTATGATTTCCTTATCCTTGTAGCACCCTTAGTGCTTTTTCTAGAAATCCATACACTCA
1 ATATGATTTCCTTATCATTTTAGCACACTCAGTGC-CCATATGGAAATCCATACACTCA
* * * * * * *
1344941 GTATGA-TTCCATTACCATTTTAGCACA-TATAATGCCCTATCTGGAAATCCATATATTCA
1 ATATGATTTCC-TTATCATTTTAGCACACT-CAGTGCCC-ATATGGAAATCCATACACTCA
* *
1345000 ATATGATTTCCTTATCATTTTAGCACACTCAGTGCTTCATATGGAAATTCATACACTCA
1 ATATGATTTCCTTATCATTTTAGCACACTCAGTGC-CCATATGGAAATCCATACACTCA
*
1345059 ATATGATTTCCTTATCTTTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCA
1 ATATGATTTCCTTATCATTTTAGCACACTCAGTGC-CCATATGGAAATCCATACACTCA
*
1345118 GTATGATTTCCTTATCATTTTAGCACAC
1 ATATGATTTCCTTATCATTTTAGCACAC
1345146 ATATAGTGCC
Statistics
Matches: 302, Mismatches: 57, Indels: 44
0.75 0.14 0.11
Matches are distributed among these distances:
57 15 0.05
58 36 0.12
59 225 0.75
60 26 0.09
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (58 bp):
ATATGATTTCCTTATCATTTTAGCACACTCAGTGCCCATATGGAAATCCATACACTCA
Found at i:1345866 original size:13 final size:13
Alignment explanation
Indices: 1345848--1345883 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
1345838 TAGGTTCTTC
1345848 ATCAATTCTTACT
1 ATCAATTCTTACT
1345861 ATCAATTCTTACT
1 ATCAATTCTTACT
1345874 ATCAATTCTT
1 ATCAATTCTT
1345884 TAAAATCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.00, T:0.47
Consensus pattern (13 bp):
ATCAATTCTTACT
Found at i:1351192 original size:59 final size:59
Alignment explanation
Indices: 1351033--1351247 Score: 283
Period size: 59 Copynumber: 3.7 Consensus size: 59
1351023 ATGACACTAT
*
1351033 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATAGAGCACTGA
* *
1351092 --GTGCTAAAAAGATAAGGAAATCATACTGAGTGTATGAATTTCCATATAGAGCACTGA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATAGAGCACTGA
* * * * * *
1351149 GTGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCAGATAGGGCA-TTA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATAGAGCACTGA
* * * *
1351207 TATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTGTGGA
1 -GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGA
1351248 GAGTGTGTGG
Statistics
Matches: 135, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
57 54 0.40
58 2 0.01
59 79 0.59
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (59 bp):
GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATAGAGCACTGA
Found at i:1351441 original size:60 final size:60
Alignment explanation
Indices: 1351296--1351441 Score: 149
Period size: 60 Copynumber: 2.4 Consensus size: 60
1351286 CAAGGATAAG
* *
1351296 GAAATCATATTAATAGTATGGAT-TT-TCATATAGGGCACTTCATGTGCTAAAAATGGTAAA
1 GAAATCATATTAATA-TAT-GATATTCTCACATAGGACACTTCATGTGCTAAAAATGGTAAA
* * * * *
1351356 GGAATCATACTAATGATATGA-ATTCTCGCATAGGACACTTCGTGTGCT-AAAATGAG-GAA
1 GAAATCATATTAAT-ATATGATATTCTCACATAGGACACTTCATGTGCTAAAAATG-GTAAA
1351415 GAAATCATATTAAGTATATGATATTCT
1 GAAATCATATTAA-TATATGATATTCT
1351442 AGATAGAGTA
Statistics
Matches: 71, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
59 29 0.41
60 41 0.58
61 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (60 bp):
GAAATCATATTAATATATGATATTCTCACATAGGACACTTCATGTGCTAAAAATGGTAAA
Found at i:1351576 original size:44 final size:44
Alignment explanation
Indices: 1351513--1351687 Score: 278
Period size: 44 Copynumber: 4.0 Consensus size: 44
1351503 TGAAATTATA
* * *
1351513 GTAAGTAGATTGATAAAATAAACTTACGAGCTTATGGAATAAAG
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAAG
* *
1351557 GTAAGTATAGTGGTAAAATAAGCTTACGAGCTTATGGAATAATG
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAAG
* *
1351601 GTAAGAATATTGGTAAAATAAGCTTACGAGCTTATGGAATAATG
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAAG
*
1351645 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGATTAAA
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAA
1351688 TGATATGTTT
Statistics
Matches: 121, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 121 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (44 bp):
GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAAG
Found at i:1352049 original size:30 final size:30
Alignment explanation
Indices: 1352013--1352071 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
1352003 TGTTGAAATT
1352013 ACTGTAGCAGATAATGTAGCGTATCGATGC
1 ACTGTAGCAGATAATGTAGCGTATCGATGC
* * *
1352043 ACTGTAGCAGTTACTGTAGGGTATCGATG
1 ACTGTAGCAGATAATGTAGCGTATCGATG
1352072 AATAATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (30 bp):
ACTGTAGCAGATAATGTAGCGTATCGATGC
Found at i:1354019 original size:3 final size:3
Alignment explanation
Indices: 1354011--1354037 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1354001 GACATGATTC
1354011 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1354038 GTTTGAGTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1355150 original size:27 final size:28
Alignment explanation
Indices: 1355093--1355150 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
1355083 AGAGGTGCAC
*
1355093 AAAAAATCCGAATATCCGATTTTGGGTAA
1 AAAAAATACGAATATCCGATTTTGGG-AA
* *
1355122 AAAATATACGAA-ATCGGATTTT-GGAA
1 AAAAAATACGAATATCCGATTTTGGGAA
1355148 AAA
1 AAA
1355151 CCGGTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 5 0.19
27 2 0.08
28 9 0.35
29 10 0.38
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.26
Consensus pattern (28 bp):
AAAAAATACGAATATCCGATTTTGGGAA
Found at i:1355248 original size:24 final size:24
Alignment explanation
Indices: 1355221--1355308 Score: 106
Period size: 24 Copynumber: 3.5 Consensus size: 24
1355211 AAATTGAACG
*
1355221 ACCGGTTTTTTTACCGGATTAAAA
1 ACCGGTTTTTTTACCGGATAAAAA
1355245 ACCGGTTTTTTTCAAACCGGATAAAAA
1 ACCGGTTTTTTT---ACCGGATAAAAA
*
1355272 ACC-GATTTTTTATCCGGATAAAAA
1 ACCGGTTTTTTTA-CCGGATAAAAA
*
1355296 ACCGGGTTTTTTA
1 ACCGGTTTTTTTA
1355309 AAAAACTGGA
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
23 1 0.02
24 26 0.46
25 8 0.14
26 7 0.12
27 14 0.25
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (24 bp):
ACCGGTTTTTTTACCGGATAAAAA
Found at i:1355312 original size:17 final size:16
Alignment explanation
Indices: 1355290--1355362 Score: 56
Period size: 17 Copynumber: 4.1 Consensus size: 16
1355280 TTTATCCGGA
1355290 TAAAAAACCGGGTTTTT
1 TAAAAAACC-GGTTTTT
*
1355307 TAAAAAACTGGAATTTTAT
1 TAAAAAACCGG--TTTT-T
*
1355326 CCGAAAAAATCCGGTTTTT
1 --TAAAAAA-CCGGTTTTT
1355345 TAAAAAAACCGGTTTTT
1 T-AAAAAACCGGTTTTT
1355362 T
1 T
1355363 GCAAACCGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
16 2 0.04
17 18 0.40
18 10 0.22
19 2 0.04
20 4 0.09
21 6 0.13
22 3 0.07
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (16 bp):
TAAAAAACCGGTTTTT
Found at i:1355872 original size:31 final size:31
Alignment explanation
Indices: 1355836--1355895 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1355826 AACTTAAAAG
* *
1355836 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
1355867 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
1355896 CATACAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1356560 original size:20 final size:20
Alignment explanation
Indices: 1356512--1356573 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
1356502 AACTTAAATC
*
1356512 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
1356532 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
1356550 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
1356569 AAAAT
1 AAAAT
1356574 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:1356653 original size:63 final size:63
Alignment explanation
Indices: 1356568--1356788 Score: 388
Period size: 63 Copynumber: 3.5 Consensus size: 63
1356558 TTATATGATA
1356568 TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAATTAATAT
1 TAAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAATTAATAT
* * *
1356632 TAAAATTAATATCTATAATATAATATTAAAAAGTTAATATGTAATTTATTTAAAAAATTTATAT
1 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTT-AAAAATTAATAT
1356696 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAATTAATAT
1 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAATTAATAT
*
1356759 TAAAATTAATATCTATAATATAAAATTAAA
1 TAAAATTAATATCTATAATATAATATTAAA
1356789 TATAAAACCT
Statistics
Matches: 149, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
63 82 0.55
64 67 0.45
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (63 bp):
TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAATTAATAT
Found at i:1356728 original size:28 final size:26
Alignment explanation
Indices: 1356697--1356770 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 26
1356687 AATTTATATT
1356697 AAAATTAATATCTATAATATAATATTAA
1 AAAATTAATAT-TATAAT-TAATATTAA
*
1356725 AAAATTAATATT-TAATT--TATTTA
1 AAAATTAATATTATAATTAATATTAA
*
1356748 AAAATTAATATTAAAATTAATAT
1 AAAATTAATATTATAATTAATAT
1356771 CTATAATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
23 17 0.41
24 4 0.10
25 1 0.02
26 7 0.17
27 1 0.02
28 11 0.27
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (26 bp):
AAAATTAATATTATAATTAATATTAA
Found at i:1357723 original size:30 final size:31
Alignment explanation
Indices: 1357678--1357763 Score: 122
Period size: 31 Copynumber: 2.8 Consensus size: 31
1357668 TTATAAATTT
*
1357678 AATC-TTGGTTGGTGGCTAACTTATT-GAAA
1 AATCTTTGGTAGGTGGCTAACTTATTGGAAA
* * *
1357707 AATCTTTTGTAGGTGGCAAACTCATTGGAAA
1 AATCTTTGGTAGGTGGCTAACTTATTGGAAA
1357738 AATCTTTGGTAGGTGGCTAACTTATT
1 AATCTTTGGTAGGTGGCTAACTTATT
1357764 TTTCATGTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 4 0.08
30 17 0.35
31 27 0.56
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (31 bp):
AATCTTTGGTAGGTGGCTAACTTATTGGAAA
Found at i:1362448 original size:33 final size:34
Alignment explanation
Indices: 1362409--1362476 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 34
1362399 GATTAGAAAT
* *
1362409 TTAATCTTGGTTGGTGGATAACTTATT-GAAAAA
1 TTAATCTTGGTTGGTGGACAACTCATTGGAAAAA
*
1362442 TTAATCTTGGTTGGTGGCCAACTCATTGGAAAAA
1 TTAATCTTGGTTGGTGGACAACTCATTGGAAAAA
1362476 T
1 T
1362477 CTTTGGTAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (34 bp):
TTAATCTTGGTTGGTGGACAACTCATTGGAAAAA
Found at i:1363726 original size:90 final size:90
Alignment explanation
Indices: 1363572--1363747 Score: 255
Period size: 90 Copynumber: 2.0 Consensus size: 90
1363562 ATCCGCCACC
* * * *
1363572 TGCTGCAGCTTTCAAAAGAGCAGACAATGTAATAGAACTGAGTAGCTCTTTTGCTTCATATTCCC
1 TGCTGCAACTTTCAAAAGAGCAGACAATGCAACAGAACTGAGTAGCTCTTTAGCTTCATATTCCC
*
1363637 TCTCAGCTTCGGCTTCTTCATATCT
66 TCTCAGCTTCAGCTTCTTCATATCT
* * * *
1363662 TGCTGCAACTTTCAAAAGAGCAGCCAATGCAGCAGAATCT-AGTAGCTCTTTAGCTTCGTGTTCC
1 TGCTGCAACTTTCAAAAGAGCAGACAATGCAACAGAA-CTGAGTAGCTCTTTAGCTTCATATTCC
1363726 CTCTCAGCTTCAGCTTCTTCAT
65 CTCTCAGCTTCAGCTTCTTCAT
1363748 CTGAGTCTAC
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
90 74 0.97
91 2 0.03
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (90 bp):
TGCTGCAACTTTCAAAAGAGCAGACAATGCAACAGAACTGAGTAGCTCTTTAGCTTCATATTCCC
TCTCAGCTTCAGCTTCTTCATATCT
Found at i:1367676 original size:3 final size:3
Alignment explanation
Indices: 1367668--1367707 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
1367658 TGTAAAATAC
1367668 AAT AAT AAT AATT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1367708 TTAAAAGACG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1368228 original size:111 final size:111
Alignment explanation
Indices: 1367846--1368991 Score: 1574
Period size: 111 Copynumber: 10.3 Consensus size: 111
1367836 TATGATGAGG
* * * *
1367846 GATCTGTTCCGCTGTCACTC--AGGGAATATCAAATCT-GGAGATGTTGATTCATTGAATCAGAG
1 GATCTGTTCCGCT-TC-CTCTGAGGGAATATCAGATCTGGGA-AAGTTGATCCATTGAATCAGGG
*
1367908 TAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGAGA
63 TAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGA-A-AGA
* * * *
1367959 GATCTGTTCGGCTTCCTCTGAGGGAATATCAGATATGGGAGAGTTGATCCATTGAATC-GGGAAG
1 GATCTGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGTAG
*
1368023 ATTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGAGA
66 ACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGA-A-AGA
* * * * *
1368071 GATCTGTTCGGCTTCCTCTGAGGGAATATCAGATCTGGGAGAGTTGATCTATTGAATCGGGGCAG
1 GATCTGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGTAG
* *
1368136 ATTTGTTCCGCTGTCACTGAGGGAATATCAAATCTTGAAAGAAAGA
66 ACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAAAGA
* * *
1368182 GATCTGTTCCGCTTCCTCTGAGGGAATATCAGATATGGGAGAGTTGATCCATTGAATCGGGGTAG
1 GATCTGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGTAG
*
1368247 ATTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTG-AA-AAAGA
66 ACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAAAGA
* * * *
1368291 GGAATTTGTTCCGCTTCTTCTGATGGAATATCAGATCTGGGAAAGTTAATCCATTGAATCAGGGT
1 -G-ATCTGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGT
* * *
1368356 AGACTTATTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGG
64 AGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAAAGA
* * **
1368404 GATATGTTCTGCTTTTTCTGAGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGTAG
1 GATCTGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGTAG
** * * *
1368469 ACTTGTTATGCTGTCACTCAAGGAATATCAAATCTTGAAAGAGAGG
66 ACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAAAGA
* *
1368515 GATCTGTTCTGCTTTCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGTAG
1 GATCTGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGTAG
* * *
1368580 ACTTGTTCCGTTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGG
66 ACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAAAGA
* *
1368626 GATCTGTTCCGCTTCCTCTGAGGGAATATCAGTTCTGAGAAAGTTGATCCATTGAATCAGGGTAG
1 GATCTGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGTAG
* * * *
1368691 ACTTGTTCCGTTATCACTCAGGGAATATCGAATCTTGAAAGAGATG-
66 ACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGA-AAGA
* * * *
1368737 GATCTATTTCGCTTCCT-TGAGGGAATATCAGATCTGGGAAAGTTGATTCATTGAATCATGGTAG
1 GATCTGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGTAG
** * *
1368801 ACTTGTTCCATTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGG
66 ACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAAAGA
1368847 GATCTGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGTAG
1 GATCTGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGTAG
*
1368912 ACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTTAAA-AAA-A
66 ACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAAAGA
* * *
1368956 TGATATGTTCCACTTCTTCTGAAGGGAATATCAGAT
1 -GATCTGTTCCGCTTCCTCTG-AGGGAATATCAGAT
1368992 AGATGGATTT
Statistics
Matches: 944, Mismatches: 76, Indels: 28
0.90 0.07 0.03
Matches are distributed among these distances:
109 6 0.01
110 119 0.13
111 613 0.65
112 113 0.12
113 90 0.10
114 3 0.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (111 bp):
GATCTGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGTAG
ACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAAAGA
Found at i:1369160 original size:79 final size:80
Alignment explanation
Indices: 1368991--1369160 Score: 186
Period size: 79 Copynumber: 2.1 Consensus size: 80
1368981 GAATATCAGA
* ** * ** * *
1368991 TAGATGGATTTACTTCACTATTCTTCCGTGAAGGCTTAAAATGGCCCGGAGGACTTTATCGTCAT
1 TAGATGGATTTGCTTCACTACACTTCCGTGAAGGATTAAAATGGCCCAAAGGACTTTAGCATCAT
*
1369056 GCTCAGAAGGCTTAC
66 GCTCAGAAGACTTAC
* * *
1369071 TA-ATGAATTTGCTTCACTACACTTCGGTGAAGGATTAAGATGGCCCAAAGGA-TTTAAGCATCA
1 TAGATGGATTTGCTTCACTACACTTCCGTGAAGGATTAAAATGGCCCAAAGGACTTT-AGCATCA
1369134 TGCT-AGAAAGACTTAC
65 TGCTCAG-AAGACTTAC
1369150 -AGATGGATTTG
1 TAGATGGATTTG
1369161 ATCATTATGC
Statistics
Matches: 74, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
78 6 0.08
79 66 0.89
80 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (80 bp):
TAGATGGATTTGCTTCACTACACTTCCGTGAAGGATTAAAATGGCCCAAAGGACTTTAGCATCAT
GCTCAGAAGACTTAC
Found at i:1369171 original size:34 final size:34
Alignment explanation
Indices: 1369120--1369426 Score: 488
Period size: 34 Copynumber: 9.0 Consensus size: 34
1369110 ATGGCCCAAA
* * * * *
1369120 GGATTTAAGCATCATGCTAGAAAGACTTACAGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
* *
1369154 GGATTTGATCATTATGCTCGGAAGACTTACTAAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
*
1369188 GGATTTGATCATTATGCTCGGAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
1369222 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
*
1369256 GGTTTTGATCATCATGCTCGGAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
*
1369290 GGATTTGATCATCATGCTCGGAAGACTTATTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
** *
1369324 GGATTTGATCATCATGCTCATAAGACTTAATGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
1369358 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
*
1369392 GGATTTGATCATCATGCTCAGAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
1369426 G
1 G
1369427 ACCCGAAGGA
Statistics
Matches: 254, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 254 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (34 bp):
GGATTTGATCATCATGCTCGGAAGACTTACTGAT
Found at i:1375639 original size:13 final size:15
Alignment explanation
Indices: 1375616--1375647 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1375606 ATAAAAATAA
1375616 AATACTATT-AAAAC
1 AATACTATTAAAAAC
1375630 AATA-TATTAAAAAC
1 AATACTATTAAAAAC
1375644 AATA
1 AATA
1375648 AAATAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (15 bp):
AATACTATTAAAAAC
Found at i:1376515 original size:17 final size:17
Alignment explanation
Indices: 1376493--1376525 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1376483 GGTATTAGTT
1376493 TGTTTTTTTCTTTTCTC
1 TGTTTTTTTCTTTTCTC
*
1376510 TGTTTTTTTTTTTTCT
1 TGTTTTTTTCTTTTCT
1376526 GGTTCTGTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (17 bp):
TGTTTTTTTCTTTTCTC
Found at i:1376538 original size:6 final size:6
Alignment explanation
Indices: 1376529--1376555 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1376519 TTTTTCTGGT
1376529 TCTGTC TCTGTC TCTGTC TCTGTC TCT
1 TCTGTC TCTGTC TCTGTC TCTGTC TCT
1376556 TTTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.15, T:0.52
Consensus pattern (6 bp):
TCTGTC
Found at i:1377028 original size:3 final size:3
Alignment explanation
Indices: 1377020--1377116 Score: 151
Period size: 3 Copynumber: 32.7 Consensus size: 3
1377010 TTAATATATT
*
1377020 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1377067 TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1377115 TA
1 TA
1377117 TGGATAAAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
2 2 0.02
3 83 0.98
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1377478 original size:118 final size:118
Alignment explanation
Indices: 1377271--1377642 Score: 610
Period size: 118 Copynumber: 3.2 Consensus size: 118
1377261 TTCTCCAGAT
* ** *
1377271 GAGTTCTTCTCATTACGAA--CTTTCTGCTGGGGATGATGTTCCATCAAATGATGAATTCAAGCA
1 GAGTTCTTCTCATTATGAACTCTTTCT-CTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
* *
1377334 AAAGATTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAC
65 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
*
1377388 GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAA
1 GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCAA
1377453 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
66 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* *
1377506 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCA
1 GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAA-ATGATGAATTCAAGCA
1377571 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---
65 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
1377622 GAGTTCTTCTCATTATGAACT
1 GAGTTCTTCTCATTATGAACT
1377643 TCTTCTTCCT
Statistics
Matches: 243, Mismatches: 9, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
116 21 0.09
117 18 0.07
118 132 0.54
119 72 0.30
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.37
Consensus pattern (118 bp):
GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCAA
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
Found at i:1377627 original size:40 final size:40
Alignment explanation
Indices: 1377583--1377683 Score: 202
Period size: 40 Copynumber: 2.5 Consensus size: 40
1377573 AGGTTGAACA
1377583 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
1377623 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
1377663 AGTTCTTCTCATTATGAACTT
1 AGTTCTTCTCATTATGAACTT
1377684 TCTCTGGAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.19, C:0.24, G:0.10, T:0.48
Consensus pattern (40 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:1377749 original size:154 final size:157
Alignment explanation
Indices: 1377464--1377797 Score: 595
Period size: 154 Copynumber: 2.1 Consensus size: 157
1377454 AGGTTGAACA
1377464 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTCT
* *
1377529 TCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCA
64 TCCTCTGGAAAAGATGATCCATCAATGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCA
1377594 TTATGAACTTCTTCTTCCTTCTTCAGATG
129 TTATGAACTTCTTCTTCCTTCTTCAGATG
1377623 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGAACT-TT-
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTTC
1377685 CTCTGGAAAAGAATGATCCATCAA-GTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCAT
66 CTCTGGAAAAG-ATGATCCATCAATGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCAT
1377749 TATGAACTTCTTCTTCCTTCTTCAGATG
130 TATGAACTTCTTCTTCCTTCTTCAGATG
1377777 AGTTCTTCTCATTATGAACTT
1 AGTTCTTCTCATTATGAACTT
1377798 TCTCTGGAAA
Statistics
Matches: 172, Mismatches: 2, Indels: 7
0.95 0.01 0.04
Matches are distributed among these distances:
154 98 0.57
155 14 0.08
156 21 0.12
159 39 0.23
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (157 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTTC
CTCTGGAAAAGATGATCCATCAATGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATT
ATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:1377758 original size:114 final size:114
Alignment explanation
Indices: 1377623--1378053 Score: 844
Period size: 114 Copynumber: 3.8 Consensus size: 114
1377613 TCTTCAGATG
1377623 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1377688 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
1377737 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1377802 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
1377851 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
*
1377916 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGATTGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
*
1377965 AGTTCTTCTCATTATGATCTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1378030 TGGAAAAGAATGATCCATCAAGTG
66 TGGAAAAGAATGATCCATCAAGTG
1378054 GATTTGAAAT
Statistics
Matches: 315, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
114 315 1.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (114 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
Found at i:1378756 original size:52 final size:52
Alignment explanation
Indices: 1378678--1378988 Score: 586
Period size: 52 Copynumber: 6.0 Consensus size: 52
1378668 CAATACTTGA
*
1378678 TTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
*
1378730 TTCTGTCCAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
*
1378782 TTCTGTCCAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
*
1378834 TTCTGTCCAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1378886 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1378938 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1378989 AAGCACATTC
Statistics
Matches: 256, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 256 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (52 bp):
TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
Found at i:1380198 original size:18 final size:18
Alignment explanation
Indices: 1380131--1380216 Score: 70
Period size: 18 Copynumber: 4.8 Consensus size: 18
1380121 CCTTGACCCT
*
1380131 TTTCTTTTTCTATTATTT-
1 TTTCTTTTTCT-TTTTTTC
*
1380149 TTTCTTCTTCTTTTTTTC
1 TTTCTTTTTCTTTTTTTC
***
1380167 TTTTCCCCTT-TTTTTTTC
1 -TTTCTTTTTCTTTTTTTC
*
1380185 TTTCTTTTTCTTTTTCTC
1 TTTCTTTTTCTTTTTTTC
1380203 -TTCTTCTTTCTTTT
1 TTTCTT-TTTCTTTT
1380217 CTTCAAGCAT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
17 16 0.29
18 33 0.59
19 7 0.12
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTCTTTTTCTTTTTTTC
Found at i:1380217 original size:29 final size:29
Alignment explanation
Indices: 1380130--1380219 Score: 92
Period size: 28 Copynumber: 3.0 Consensus size: 29
1380120 ACCTTGACCC
*
1380130 TTTTCTTTTTCTATTATTTTTTCTTCTTCTTT
1 TTTTCTTTTTCTCTTATTTTTTCTT-TTC--T
* * *
1380162 TTTTCTTTTCCCCTTTTTTTTTC-TTTCT
1 TTTTCTTTTTCTCTTATTTTTTCTTTTCT
* *
1380190 TTTTCTTTTTCTCTTCTTCTTTCTTTTCT
1 TTTTCTTTTTCTCTTATTTTTTCTTTTCT
1380219 T
1 T
1380220 CAAGCATAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
28 20 0.41
29 6 0.12
30 3 0.06
31 1 0.02
32 19 0.39
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (29 bp):
TTTTCTTTTTCTCTTATTTTTTCTTTTCT
Found at i:1391554 original size:13 final size:15
Alignment explanation
Indices: 1391531--1391562 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1391521 TAAAAATAAA
1391531 AATACTATT-AAAAC
1 AATACTATTAAAAAC
1391545 AATA-TATTAAAAAC
1 AATACTATTAAAAAC
1391559 AATA
1 AATA
1391563 AAATAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (15 bp):
AATACTATTAAAAAC
Found at i:1392414 original size:15 final size:15
Alignment explanation
Indices: 1392394--1392425 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1392384 TGGTATTAGT
1392394 TGTTTTTTTTTTCTC
1 TGTTTTTTTTTTCTC
*
1392409 TGTTTTTTTTTTTTC
1 TGTTTTTTTTTTCTC
1392424 TG
1 TG
1392426 GTTGTCTCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.81
Consensus pattern (15 bp):
TGTTTTTTTTTTCTC
Found at i:1392437 original size:6 final size:6
Alignment explanation
Indices: 1392428--1392452 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1392418 TTTTTCTGGT
1392428 TGTCTC TGTCTC TGTCTC TGTCTC T
1 TGTCTC TGTCTC TGTCTC TGTCTC T
1392453 TTTTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.16, T:0.52
Consensus pattern (6 bp):
TGTCTC
Found at i:1392923 original size:3 final size:3
Alignment explanation
Indices: 1392915--1393014 Score: 148
Period size: 3 Copynumber: 33.7 Consensus size: 3
1392905 ATTTAATATT
* *
1392915 TAA TAA TAA -AA TAA TAA TAA TAA TAA AAA TAA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1392962 TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1393010 TAA TA
1 TAA TA
1393015 TGGATAAAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
2 2 0.02
3 84 0.98
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1397643 original size:3 final size:3
Alignment explanation
Indices: 1397635--1397696 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
1397625 TATGTAAAAT
1397635 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1397683 ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA
1397697 TTAAAAGACG
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1397831 original size:18 final size:18
Alignment explanation
Indices: 1397810--1397865 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 18
1397800 CTAAATTTAA
1397810 AATGTATAAAAAATCAAT
1 AATGTATAAAAAATCAAT
*
1397828 AATG-ATATAAATATCAAT
1 AATGTATA-AAAAATCAAT
1397846 AATTGTATAAAAAAATCAAT
1 AA-TGTAT-AAAAAATCAAT
1397866 GGTATATTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 3 0.09
18 15 0.47
19 2 0.06
20 11 0.34
21 1 0.03
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.30
Consensus pattern (18 bp):
AATGTATAAAAAATCAAT
Found at i:1399046 original size:2 final size:2
Alignment explanation
Indices: 1399041--1399071 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1399031 ATATTTTTGT
1399041 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1399072 TTATTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1402683 original size:63 final size:64
Alignment explanation
Indices: 1402598--1402756 Score: 180
Period size: 65 Copynumber: 2.5 Consensus size: 64
1402588 TGCACTAAGA
* * * * *
1402598 GTGCAGCGATGCATCAAGTGCATTCGATGTTTC--AAAATAGCTAGAGTGCATCGATGCATGG-C
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAAT-CCT-CAGTGCATCGATGCATGGTA
1402660 T
64 T
*
1402661 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAATCCTCAGTGCATCGATGCATGGTAT
* * * *
1402726 ATGCATCAATACATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
1402757 CAATTTATTT
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
63 27 0.33
64 22 0.27
65 28 0.34
66 5 0.06
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCTCAGTGCATCGATGCATGGTAT
Found at i:1403272 original size:2 final size:2
Alignment explanation
Indices: 1403265--1403322 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1403255 GCCAATTGAT
1403265 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1403307 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
1403323 ACTTAAGCTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1403896 original size:21 final size:21
Alignment explanation
Indices: 1403872--1403915 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1403862 GAGCTGGAGG
* *
1403872 AGGAGGAGCACGAGAGGAGCT
1 AGGAGCAGCACGAGAGGAACT
* *
1403893 AGGAGCAGCTCGTGAGGAACT
1 AGGAGCAGCACGAGAGGAACT
1403914 AG
1 AG
1403916 CTCCCGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.43, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAGGAACT
Found at i:1409369 original size:22 final size:21
Alignment explanation
Indices: 1409327--1409366 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1409317 GAGTTTATTT
*
1409327 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1409348 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1409367 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1411501 original size:65 final size:64
Alignment explanation
Indices: 1411308--1411513 Score: 213
Period size: 65 Copynumber: 3.2 Consensus size: 64
1411298 CTAAGAGTGA
* * ** * *
1411308 ATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGCCAGAGTGCATCGATGCATGGCTGGTGC
1 ATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCCTCAGTGCATCGATGCATGGTTTGTGC
* *
1411372 ATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTATGTGC
1 ATCGATGCATCAAATGCATTCGATG-TTTCATAAAATCCTCAGTGCATCGATGCATGGTTTGTGC
* ** *
1411437 ATCGATGCATGAAATGCATTCGATG-TTCA-ATTTAT-TTCATGGTGCATCGATGCATGGATTTG
1 ATCGATGCATCAAATGCATTCGATGTTTCATA-AAATCCTCA--GTGCATCGATGCATGG-TTTG
1411499 TGC
62 TGC
*
1411502 ATCGGTGCATCA
1 ATCGATGCATCA
1411514 CTATGAAAAA
Statistics
Matches: 120, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
62 4 0.03
63 6 0.05
64 39 0.32
65 68 0.57
66 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (64 bp):
ATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCTCAGTGCATCGATGCATGGTTTGTGC
Found at i:1411991 original size:2 final size:2
Alignment explanation
Indices: 1411984--1412022 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1411974 CATTGATTAA
1411984 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1412023 GCTTAAGCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1412599 original size:21 final size:21
Alignment explanation
Indices: 1412575--1412618 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1412565 GAGCTGGAGG
*
1412575 AGGAGGAGCACGAGAGGAGCT
1 AGGAGGAGCACGAGAGGAACT
* * *
1412596 AGGAGTAGCTCGTGAGGAACT
1 AGGAGGAGCACGAGAGGAACT
1412617 AG
1 AG
1412619 CTCTCGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.43, T:0.11
Consensus pattern (21 bp):
AGGAGGAGCACGAGAGGAACT
Found at i:1420202 original size:12 final size:12
Alignment explanation
Indices: 1420185--1420219 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1420175 AATAACACAA
1420185 AAAGAAAAACTT
1 AAAGAAAAACTT
1420197 AAAG-AAAACTT
1 AAAGAAAAACTT
*
1420208 AATGAAAAACTT
1 AAAGAAAAACTT
1420220 GATGTAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.63, C:0.09, G:0.09, T:0.20
Consensus pattern (12 bp):
AAAGAAAAACTT
Found at i:1420228 original size:12 final size:12
Alignment explanation
Indices: 1420188--1420230 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
1420178 AACACAAAAA
*
1420188 GAAAAACTTAAA
1 GAAAAACTTAAT
1420200 G-AAAACTTAAT
1 GAAAAACTTAAT
*
1420211 GAAAAACTTGAT
1 GAAAAACTTAAT
*
1420223 GTAAAACT
1 GAAAAACT
1420231 CATGCCCTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.23
Consensus pattern (12 bp):
GAAAAACTTAAT
Found at i:1421330 original size:13 final size:14
Alignment explanation
Indices: 1421312--1421344 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1421302 ATTTTGCTTC
1421312 TTTTTC-TTTTATT
1 TTTTTCGTTTTATT
*
1421325 TTTTTCGTTTTGTT
1 TTTTTCGTTTTATT
1421339 TTTTTC
1 TTTTTC
1421345 ATGAAAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.03, C:0.09, G:0.06, T:0.82
Consensus pattern (14 bp):
TTTTTCGTTTTATT
Found at i:1422559 original size:21 final size:22
Alignment explanation
Indices: 1422513--1422560 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
1422503 AATCAAGGAA
1422513 AAAAATAAAAATAAAAAGAATG
1 AAAAATAAAAATAAAAAGAATG
* **
1422535 -AAAATAGAAATTGAAA-AATG
1 AAAAATAAAAATAAAAAGAATG
1422555 AAAAAT
1 AAAAAT
1422561 TGGGTTGCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAATAAAAAGAATG
Found at i:1423945 original size:102 final size:102
Alignment explanation
Indices: 1423767--1423976 Score: 314
Period size: 102 Copynumber: 2.1 Consensus size: 102
1423757 CTCAAGAATT
*
1423767 TCTTTCTCTTCTGCTTCTTTATTGGACTTAGCGAATCTAGCGGGAAAAGAAGGATTTATGAAAAA
1 TCTTTCTCTTCTGCTTCTTTATTAGACTTAGCGAATCTAGCGGGAAAAGAAGGATTTATGAAAAA
1423832 TTCATTCGGTTTTTCACTTTTGAGTCCTTTAGGTTGG
66 TTCATTCGGTTTTTCACTTTTGAGTCCTTTAGGTTGG
* * * *
1423869 TCTTTCTCTTCTGCTTCTTTCTTAGACTTAGTGAATCTAGTGGGAAAATG-AGGATTTATGACAA
1 TCTTTCTCTTCTGCTTCTTTATTAGACTTAGCGAATCTAGCGGGAAAA-GAAGGATTTATGAAAA
* * ** *
1423933 ATTCCTTTGGTTTTTCGTTTTTGATTCCTTTAGGTTGG
65 ATTCATTCGGTTTTTCACTTTTGAGTCCTTTAGGTTGG
1423971 TCTTTC
1 TCTTTC
1423977 CGAGTCTGAG
Statistics
Matches: 97, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
102 96 0.99
103 1 0.01
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.45
Consensus pattern (102 bp):
TCTTTCTCTTCTGCTTCTTTATTAGACTTAGCGAATCTAGCGGGAAAAGAAGGATTTATGAAAAA
TTCATTCGGTTTTTCACTTTTGAGTCCTTTAGGTTGG
Found at i:1430012 original size:26 final size:26
Alignment explanation
Indices: 1429976--1430025 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
1429966 TAGTGCTACA
1429976 AAAGCATCCATGCTAAATCTAGAGAG
1 AAAGCATCCATGCTAAATCTAGAGAG
1430002 AAAGCATCCATGCTAAATCTAGAG
1 AAAGCATCCATGCTAAATCTAGAG
1430026 TTTATAGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (26 bp):
AAAGCATCCATGCTAAATCTAGAGAG
Found at i:1433452 original size:18 final size:16
Alignment explanation
Indices: 1433416--1433453 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 16
1433406 CCAAACTTTT
1433416 CTTCTTTTTTCATTTC
1 CTTCTTTTTTCATTTC
1433432 CTTCTTTTCTTCATCTTC
1 CTTCTTTT-TTCAT-TTC
1433450 CTTC
1 CTTC
1433454 ACCATCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 5 0.25
18 7 0.35
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.63
Consensus pattern (16 bp):
CTTCTTTTTTCATTTC
Found at i:1443504 original size:16 final size:16
Alignment explanation
Indices: 1443485--1443515 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1443475 TATGTTGGTT
*
1443485 TTAAATATATTTTTAA
1 TTAAATATAATTTTAA
1443501 TTAAATATAATTTTA
1 TTAAATATAATTTTA
1443516 CTTGATATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAAATATAATTTTAA
Found at i:1450788 original size:232 final size:232
Alignment explanation
Indices: 1450382--1450833 Score: 787
Period size: 232 Copynumber: 1.9 Consensus size: 232
1450372 CTAATTCCAT
* *
1450382 GGCCTAATCTCCGAAACTTGGTTGATTAAACAGGTATGGGACATCAAAAAGCAATCAGCCACGCT
1 GGCCTAATCTCCGAAACTCGGTTGATTAAACAGGTATGGGACATCAAAAAGCAATCAGCCACACT
*
1450447 GGTATGGGACGTGAAGGAGCGTAGGGACTCTGTGACATGCTTTGCACTCTTTGAACCAGGAGAGA
66 GGTATGGGACGTGAAGGAGCATAGGGACTCTGTGACATGCTTTGCACTCTTTGAACCAGGAGAGA
* *
1450512 CCCTTTTAAGTGGATCCACTGATAAGACCATTCGAGTAAGTTAAATCCGTGTCGTTCTTGCAGTC
131 CCCTTTTAAGTGGATCCACTGATAAGACCATTCGAGTAAGTTAAATCAGTGTCATTCTTGCAGTC
* *
1450577 TAAGTATCTTACGAGTCTTGTAACACTAGTGTCCCAA
196 TAAATATCTTACGAGTCTCGTAACACTAGTGTCCCAA
1450614 GGCCTAATCTCCGAAACTCGGTTGATTAAACAGGTATGGGACATCAAAAAGCAATCAGCCACACT
1 GGCCTAATCTCCGAAACTCGGTTGATTAAACAGGTATGGGACATCAAAAAGCAATCAGCCACACT
* *
1450679 GGTATGGGACGTGAAGTAGCATAGGGACTCTGTGACATGTTTTGCACTCTTTGAACCAGGAGAGA
66 GGTATGGGACGTGAAGGAGCATAGGGACTCTGTGACATGCTTTGCACTCTTTGAACCAGGAGAGA
* * *
1450744 CCCTTTTAAGTGGATCCGCTGATAAGACCATTCGAGTAAGTTAAATCATTGTCATTCTTGTAGTC
131 CCCTTTTAAGTGGATCCACTGATAAGACCATTCGAGTAAGTTAAATCAGTGTCATTCTTGCAGTC
*
1450809 TAAATATCTTACGAGTGTCGTAACA
196 TAAATATCTTACGAGTCTCGTAACA
1450834 GGAGTGTCTA
Statistics
Matches: 207, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
232 207 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (232 bp):
GGCCTAATCTCCGAAACTCGGTTGATTAAACAGGTATGGGACATCAAAAAGCAATCAGCCACACT
GGTATGGGACGTGAAGGAGCATAGGGACTCTGTGACATGCTTTGCACTCTTTGAACCAGGAGAGA
CCCTTTTAAGTGGATCCACTGATAAGACCATTCGAGTAAGTTAAATCAGTGTCATTCTTGCAGTC
TAAATATCTTACGAGTCTCGTAACACTAGTGTCCCAA
Found at i:1452850 original size:15 final size:15
Alignment explanation
Indices: 1452827--1452856 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1452817 ACGAGGCTGG
1452827 AATTACAACAATAAC
1 AATTACAACAATAAC
*
1452842 AATTCCAACAATAAC
1 AATTACAACAATAAC
1452857 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (15 bp):
AATTACAACAATAAC
Found at i:1458970 original size:16 final size:17
Alignment explanation
Indices: 1458943--1458975 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1458933 AAATATAAAA
1458943 ATAATAATTATAAATTT
1 ATAATAATTATAAATTT
*
1458960 ATAAT-ATTATATATTT
1 ATAATAATTATAAATTT
1458976 GATTGAACCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATAATAATTATAAATTT
Found at i:1460565 original size:25 final size:25
Alignment explanation
Indices: 1460519--1460567 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1460509 ATTTTTAATC
* *
1460519 ATAAGATGTTTAATTATTTAATATA
1 ATAAGATGTTTAATGATGTAATATA
1460544 ATAATGATGTTTAA-GATGTAATAT
1 ATAA-GATGTTTAATGATGTAATAT
1460568 TAAAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (25 bp):
ATAAGATGTTTAATGATGTAATATA
Found at i:1463558 original size:2 final size:2
Alignment explanation
Indices: 1463551--1463635 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
1463541 ATCCCCAAAG
1463551 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
1463593 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
1463635 A
1 A
1463636 AGATACTCAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1466475 original size:24 final size:24
Alignment explanation
Indices: 1466447--1466502 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
1466437 GGATGTGCAT
1466447 TTTCTTTCCCCATTGTCTTAGAAC
1 TTTCTTTCCCCATTGTCTTAGAAC
1466471 TTTCTTTCCCCATTGTCTTAGAAC
1 TTTCTTTCCCCATTGTCTTAGAAC
1466495 TTTCTTTC
1 TTTCTTTC
1466503 ACTTCCTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.14, C:0.29, G:0.07, T:0.50
Consensus pattern (24 bp):
TTTCTTTCCCCATTGTCTTAGAAC
Found at i:1470633 original size:23 final size:23
Alignment explanation
Indices: 1470606--1470668 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
1470596 TGCGGTACTC
1470606 CGGGACAATTCTATGTGGTCATT
1 CGGGACAATTCTATGTGGTCATT
* * ***
1470629 TGGGAGAATTCTACACGGTCATT
1 CGGGACAATTCTATGTGGTCATT
* *
1470652 CAGGACAAATCTATGTG
1 CGGGACAATTCTATGTG
1470669 ACACTTCAGT
Statistics
Matches: 28, Mismatches: 12, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (23 bp):
CGGGACAATTCTATGTGGTCATT
Found at i:1473165 original size:30 final size:30
Alignment explanation
Indices: 1473129--1473192 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1473119 GAATGACCTG
* *
1473129 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
1473159 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
1473189 TCCA
1 TCCA
1473193 TATGTTCATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:1473967 original size:64 final size:63
Alignment explanation
Indices: 1473871--1474094 Score: 263
Period size: 64 Copynumber: 3.5 Consensus size: 63
1473861 TAATGAAGGT
* * * * *
1473871 ATGCATCGATGCACTACTTGTGCATCGGTGCATTAAATGCATTCGATGTT-TCCTTATTAATGAG
1 ATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTTATTCTT-TTAA-AAG
* * *
1473935 ATGCATCGATGCACT-CCTTATGCATCGATGCATTGATTGCATTCGATGTTATTATTTTAAAAGG
1 ATGCATCGATGCACTACC-TATGCATCGATGCATTAAATGCATTCGATGTTATTCTTTTAAAA-G
* * * * *
1473999 ATGCATCGATGCATTAGCTATGCATCGATGCATCAAAGGCATTCGATGTTCTTCTTTTAAAAG
1 ATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTTATTCTTTTAAAAG
*
1474062 AGTGCATCGATGCACTACCAATGCATCGATGCA
1 A-TGCATCGATGCACTACCTATGCATCGATGCA
1474095 CATTCAAACA
Statistics
Matches: 136, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
63 4 0.03
64 128 0.94
65 4 0.03
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTTATTCTTTTAAAAG
Found at i:1478541 original size:64 final size:63
Alignment explanation
Indices: 1478445--1478668 Score: 263
Period size: 64 Copynumber: 3.5 Consensus size: 63
1478435 TAATGAAGGT
* * * * *
1478445 ATGCATCGATGCACTACTTGTGCATCGGTGCATTAAATGCATTCGATGTT-TCCTTATTAATGAG
1 ATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTTATTCTT-TTAA-AAG
* * *
1478509 ATGCATCGATGCACT-CCTTATGCATCGATGCATTGATTGCATTCGATGTTATTATTTTAAAAGG
1 ATGCATCGATGCACTACC-TATGCATCGATGCATTAAATGCATTCGATGTTATTCTTTTAAAA-G
* * * * *
1478573 ATGCATCGATGCATTAGCTATGCATCGATGCATCAAAGGCATTCGATGTTCTTCTTTTAAAAG
1 ATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTTATTCTTTTAAAAG
*
1478636 AGTGCATCGATGCACTACCAATGCATCGATGCA
1 A-TGCATCGATGCACTACCTATGCATCGATGCA
1478669 CATTCAAACA
Statistics
Matches: 136, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
63 4 0.03
64 128 0.94
65 4 0.03
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTTATTCTTTTAAAAG
Found at i:1482315 original size:30 final size:30
Alignment explanation
Indices: 1482279--1482342 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1482269 GAAGGACCTG
* *
1482279 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
1482309 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
1482339 TCCA
1 TCCA
1482343 TATATTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:1483117 original size:64 final size:63
Alignment explanation
Indices: 1483021--1483244 Score: 263
Period size: 64 Copynumber: 3.5 Consensus size: 63
1483011 TAATGAAGGT
* * * * *
1483021 ATGCATCGATGCACTACTTGTGCATCGGTGCATTAAATGCATTCGATGTT-TCCTTATTAATGAG
1 ATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTTATTCTT-TTAA-AAG
* * *
1483085 ATGCATCGATGCACT-CCTTATGCATCGATGCATTGATTGCATTCGATGTTATTATTTTAAAAGG
1 ATGCATCGATGCACTACC-TATGCATCGATGCATTAAATGCATTCGATGTTATTCTTTTAAAA-G
* * * * *
1483149 ATGCATCGATGCATTAGCTATGCATCGATGCATCAAAGGCATTCGATGTTCTTCTTTTAAAAG
1 ATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTTATTCTTTTAAAAG
*
1483212 AGTGCATCGATGCACTACCAATGCATCGATGCA
1 A-TGCATCGATGCACTACCTATGCATCGATGCA
1483245 CATTCAAACA
Statistics
Matches: 136, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
63 4 0.03
64 128 0.94
65 4 0.03
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTTATTCTTTTAAAAG
Found at i:1486882 original size:30 final size:30
Alignment explanation
Indices: 1486846--1486909 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1486836 GAAGGACCTG
* *
1486846 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
1486876 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
1486906 TCCA
1 TCCA
1486910 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:1487754 original size:64 final size:62
Alignment explanation
Indices: 1487584--1487803 Score: 214
Period size: 64 Copynumber: 3.5 Consensus size: 62
1487574 TAATGAAGGT
* * * * ** *
1487584 ATGCATCGATGCACTACTTGTGCATCGGTGCAT-TAATGCATTCGATGTT-TCCTTATTAATGAG
1 ATGCATCGATGCACTAC-TATGCATCGATGCATCAAAGGCATTCGATGTTATTATT-TTAA-AAG
** **
1487647 ATGCATCGATGCACT-CT-TGCATCGATGCATTGATTGCATTCGATGTTATTATTTTAAAAGG
1 ATGCATCGATGCACTACTATGCATCGATGCATCAAAGGCATTCGATGTTATTATTTTAAAA-G
* * *
1487708 ATGCATCGATGCATTAGCTATGCATCGATGCATCAAAGGCATTCGATGTTCTTCTTTTAAAAG
1 ATGCATCGATGCACTA-CTATGCATCGATGCATCAAAGGCATTCGATGTTATTATTTTAAAAG
*
1487771 AGTGCATCGATGCACTACCAATGCATCGATGCA
1 A-TGCATCGATGCACTA-CTATGCATCGATGCA
1487804 CATTCAAACA
Statistics
Matches: 134, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
60 13 0.10
61 34 0.25
62 4 0.03
63 19 0.14
64 64 0.48
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTACTATGCATCGATGCATCAAAGGCATTCGATGTTATTATTTTAAAAG
Found at i:1491417 original size:30 final size:30
Alignment explanation
Indices: 1491381--1491444 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1491371 GAAGGACCTG
* *
1491381 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
1491411 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
1491441 TCCA
1 TCCA
1491445 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:1492215 original size:64 final size:65
Alignment explanation
Indices: 1492106--1492341 Score: 250
Period size: 64 Copynumber: 3.7 Consensus size: 65
1492096 CCAATTTCCT
* * *
1492106 CTTTTAATGAGGTATGCATCGATGCACTACTTGTGCATCGGTGCATTAAATGCATTCGATGTT-T
1 CTTTTAATGAGG-ATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTTAT
1492170 C
65 C
* *
1492171 CTTATTAATGA-GATGCATCGATGCACT-CCTTATGCATCGATGCATTGATTGCATTCGATGTTA
1 CTT-TTAATGAGGATGCATCGATGCACTACC-TATGCATCGATGCATTAAATGCATTCGATGTTA
*
1492234 TT
64 TC
* * * * * * * *
1492236 ATTTTAA-AAGGATGCATCGATGCATTAGCTATGCATCGATGCATCAAAGGCATTCGATGTTCTT
1 CTTTTAATGAGGATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTTATC
* * *
1492300 CTTTAAAAGA-G-TGCATCGATGCACTACCAATGCATCGATGCA
1 CTTTTAATGAGGATGCATCGATGCACTACCTATGCATCGATGCA
1492342 CATTCAAACA
Statistics
Matches: 144, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
63 30 0.21
64 98 0.68
65 9 0.06
66 7 0.05
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (65 bp):
CTTTTAATGAGGATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTTATC
Found at i:1495356 original size:17 final size:17
Alignment explanation
Indices: 1495334--1495366 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1495324 GTACTTAATG
1495334 ACTTATTACAT-ACCAAC
1 ACTTA-TACATGACCAAC
1495351 ACTTATACATGACCAA
1 ACTTATACATGACCAA
1495367 ATACATACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.42, C:0.27, G:0.03, T:0.27
Consensus pattern (17 bp):
ACTTATACATGACCAAC
Done.