Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008756.1 Hibiscus syriacus cultivar Beakdansim tig00111848_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: 4584045
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 21
Found at i:2754825 original size:2 final size:2
Alignment explanation
Indices: 2754818--2754862 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
2754808 AGACAAAACG
* *
2754818 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2754860 TA T
1 TA T
2754863 GTAAGTAACG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2757126 original size:105 final size:105
Alignment explanation
Indices: 2756943--2757741 Score: 1327
Period size: 105 Copynumber: 7.6 Consensus size: 105
2756933 ACAACCAGCA
* * *
2756943 GTGAAGTTGAACTTGCGTTATCTAGAATCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
1 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
*
2757008 AACTGA-AACATGTTTGTTGACAACCAGCGGTCCCTTCGTC
66 AATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTC
* *
2757048 GTGAAGTTGAACTTGGGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAGATTGGCTCTG-
1 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
*
2757112 AATTGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCGTC
66 AATT-GAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTC
*
2757153 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTTGCTCTG-
1 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
*
2757217 AATTGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCGTC
66 AATT-GAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTC
2757258 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
1 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
* * *
2757323 AATTGAGAGATATTTGTCGACAACCAGCGGTCCCTTCGTC
66 AATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTC
* *
2757363 ATGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-
1 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
*
2757427 AATTGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCGTC
66 AATT-GAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTC
2757468 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
1 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
* * *
2757533 AATTGAGAGATATTTGTCGACAACCAGCGGTCCCTTCGTC
66 AATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTC
* * *
2757573 ATGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGTTGCGAAGTTGAAATTGGCTCTGA
1 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
2757638 AATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTC
66 AATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTC
* *
2757678 GTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTG
1 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
2757742 GGTAAAACCT
Statistics
Matches: 653, Mismatches: 36, Indels: 10
0.93 0.05 0.01
Matches are distributed among these distances:
104 7 0.01
105 636 0.97
106 10 0.02
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.32
Consensus pattern (105 bp):
GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
AATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTC
Found at i:2757370 original size:315 final size:315
Alignment explanation
Indices: 2756767--2757741 Score: 1548
Period size: 315 Copynumber: 3.1 Consensus size: 315
2756757 GTATTGTTCC
* * * **
2756767 GAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAATTGG-GAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAATTGGAGAAA-TGTTTGGTGACA
* *
2756831 ACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCATTGTGA
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
* * *
2756896 AGTTGAAATTGGCTCTGAAACTGAGAAATGTTTGTTGACAACCA---G------C--AGTGAAGT
129 AGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* * * *
2756950 TGAACTTGCGTTATCTAGAATCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGA-
194 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
* *
2757014 AACATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGGGTTGTCTG
259 AA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
*
2757072 GAGTCCAATATCCTTCGTTGTGAAGTTGAGATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
2757137 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
*
2757202 TTGAAATTTGCTCTG-AATTGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 TTGAAATTGGCTCTGAAATT-GAGAAATGTTTGGTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
2757266 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
195 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
* * * *
2757331 GATATTTGTCGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACATGCGTTGTCTG
260 AATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
2757387 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
2757452 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
* * *
2757517 TTGAAATTGGCTCTGAAATTGAGAGATATTT-GTCGACAACCAGCGGTCCCTTCGTCATGAAGTT
131 TTGAAATTGGCTCTGAAATTGAGAAATGTTTGGT-GACAACCAGCGGTCCCTTCGTCGTGAAGTT
* *
2757581 GAACATGCGTTGTCTGGAGTCCAATATCCTTCGTTGCGAAGTTGAAATTGGCTCTGAAATTGAGA
195 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
2757646 AATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
260 AATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
*
2757702 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
2757742 GGTAAAACCT
Statistics
Matches: 620, Mismatches: 34, Indels: 22
0.92 0.05 0.03
Matches are distributed among these distances:
303 3 0.00
304 117 0.19
305 39 0.06
307 1 0.00
313 1 0.00
314 2 0.00
315 452 0.73
316 5 0.01
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (315 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
TTGAAATTGGCTCTGAAATTGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA
ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
Found at i:2758515 original size:9 final size:8
Alignment explanation
Indices: 2758494--2758537 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
2758484 ACCCACCTTA
2758494 TTTTTCTTC
1 TTTTT-TTC
*
2758503 TTTTATTC
1 TTTTTTTC
*
2758511 TTTTTTCC
1 TTTTTTTC
2758519 TTTTTTTC
1 TTTTTTTC
2758527 -TTTTTTC
1 TTTTTTTC
2758534 TTTT
1 TTTT
2758538 CTCAATTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
7 7 0.23
8 19 0.63
9 4 0.13
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTTC
Found at i:2758521 original size:16 final size:15
Alignment explanation
Indices: 2758491--2758537 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
2758481 TGAACCCACC
*
2758491 TTATT-TTTCTTCTT
1 TTATTCTTTTTTCTT
2758505 TTATTCTTTTTTCCTT
1 TTATTCTTTTTT-CTT
*
2758521 TTTTTCTTTTTTCTT
1 TTATTCTTTTTTCTT
2758536 TT
1 TT
2758538 CTCAATTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 5 0.17
15 10 0.34
16 14 0.48
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (15 bp):
TTATTCTTTTTTCTT
Found at i:2758530 original size:7 final size:7
Alignment explanation
Indices: 2758495--2758537 Score: 50
Period size: 7 Copynumber: 5.6 Consensus size: 7
2758485 CCCACCTTAT
2758495 TTTTCTTC
1 TTTT-TTC
2758503 TTTTATTC
1 TTTT-TTC
2758511 TTTTTTCC
1 TTTTTT-C
2758519 TTTTTTTC
1 -TTTTTTC
2758527 TTTTTTC
1 TTTTTTC
2758534 TTTT
1 TTTT
2758538 CTCAATTTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
7 13 0.41
8 13 0.41
9 6 0.19
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTC
Found at i:2769319 original size:2 final size:2
Alignment explanation
Indices: 2769273--2769304 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2769263 AGACAAAACG
2769273 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
2769305 ATAAAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2769496 original size:2 final size:2
Alignment explanation
Indices: 2769489--2769521 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2769479 AAATAATAAA
*
2769489 AT AT AT AT AC 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 A
2769522 AATAAAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2772195 original size:22 final size:24
Alignment explanation
Indices: 2772152--2772195 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2772142 TGGGCTTTGA
2772152 TGTAATCTGGGTTTGGGGCTTCCT
1 TGTAATCTGGGTTTGGGGCTTCCT
2772176 TGTAATCT-GGTTT-GGGCTTC
1 TGTAATCTGGGTTTGGGGCTTC
2772196 ATTTGGCCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 5 0.25
24 8 0.40
ACGTcount: A:0.09, C:0.16, G:0.32, T:0.43
Consensus pattern (24 bp):
TGTAATCTGGGTTTGGGGCTTCCT
Found at i:2772224 original size:3 final size:3
Alignment explanation
Indices: 2772216--2772251 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2772206 CAAAAATGAA
2772216 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2772252 TTTTTTAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2775157 original size:13 final size:13
Alignment explanation
Indices: 2775139--2775165 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2775129 TTATGGGCTG
2775139 TAAATTAAAGAAA
1 TAAATTAAAGAAA
2775152 TAAATTAAAGAAA
1 TAAATTAAAGAAA
2775165 T
1 T
2775166 TGATTTAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (13 bp):
TAAATTAAAGAAA
Found at i:2775378 original size:2 final size:2
Alignment explanation
Indices: 2775371--2775463 Score: 141
Period size: 2 Copynumber: 46.5 Consensus size: 2
2775361 TCAATTTCAT
* * * *
2775371 TA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA CA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2775413 TA CA 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
2775455 TA TA TA TA T
1 TA TA TA TA T
2775464 TACTCATGTA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2781817 original size:29 final size:29
Alignment explanation
Indices: 2781775--2782020 Score: 126
Period size: 29 Copynumber: 7.8 Consensus size: 29
2781765 GAAAAAATTC
* *
2781775 GTTTCAAGGGAAACAATCTCAAAGATGAT
1 GTTTCAAGAGAAACGATCTCAAAGATGAT
2781804 GTTTCAAGAGAAACTG-TCTCAAGAGA-GACAAAATTT
1 GTTTCAAGAGAAAC-GATCTCAA-AGATG-----A--T
* *
2781840 GTTTTAAGGGAAACGATCTCAAAGATGAT
1 GTTTCAAGAGAAACGATCTCAAAGATGAT
**
2781869 GTTTCAAGAGAAACTG-TCTCAAGAAAGACAAAATT
1 GTTTCAAGAGAAAC-GATCTC---AAAG--ATGA-T
* *
2781904 CGTTTCAAGGGAAATGATCTCAAAGATGAT
1 -GTTTCAAGAGAAACGATCTCAAAGATGAT
2781934 GTTTCAAGAGAAACTG-TCTC-AAGATAGACAAAATT
1 GTTTCAAGAGAAAC-GATCTCAAAGAT-G-----A-T
*
2781969 CGTTTCAAGGGAAACGATCTCAAAGATGAT
1 -GTTTCAAGAGAAACGATCTCAAAGATGAT
2781999 GTTTCAAGAGAAACTG-TCTCAA
1 GTTTCAAGAGAAAC-GATCTCAA
2782021 GAGAGAAAAA
Statistics
Matches: 169, Mismatches: 16, Indels: 64
0.68 0.06 0.26
Matches are distributed among these distances:
28 5 0.03
29 73 0.43
30 8 0.05
31 4 0.02
32 4 0.02
33 4 0.02
34 4 0.02
35 8 0.05
36 54 0.32
37 5 0.03
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.25
Consensus pattern (29 bp):
GTTTCAAGAGAAACGATCTCAAAGATGAT
Found at i:2781849 original size:65 final size:65
Alignment explanation
Indices: 2781738--2782144 Score: 550
Period size: 65 Copynumber: 6.2 Consensus size: 65
2781728 TTTAGGGATT
*
2781738 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATTCGTTTCAAGGGAAACAATCTCAAAGATGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGATGA
* * *
2781803 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAACGATCTCAAAGATGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGATGA
* **
2781868 TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAATTCGTTTCAAGGGAAATGATCTCAAAGATGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGATGA
* *
2781933 TGTTTCAAGAGAAACTGTCTCAAGATAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGATGA
* * *
2781998 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-AAAATTCGTTTCAAGGGAAACAAACTCAAAGGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAA-GATG
*
2782062 T
65 A
* * * * **
2782063 TTTTTCAA-AAAAATATGTCTCAAGAGAGACAAAACTTTGTTTCAAGATAAA-AATACTCAAAGA
1 TGTTTCAAGAGAAA-CTGTCTCAAGAGAGACAAAA-TTCGTTTCAAGGGAAACAAT-CTCAAAGA
**
2782126 CTTT
63 -TGA
*
2782130 TGTTTCAAAAGAAAC
1 TGTTTCAAGAGAAAC
2782145 AAACTCAAAG
Statistics
Matches: 308, Mismatches: 27, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
64 32 0.10
65 236 0.77
66 7 0.02
67 29 0.09
68 4 0.01
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGATGA
Found at i:2782132 original size:30 final size:30
Alignment explanation
Indices: 2782098--2782238 Score: 110
Period size: 30 Copynumber: 4.5 Consensus size: 30
2782088 GAGACAAAAC
*
2782098 TTTGTTTCAAGATAAAAATACTCAAAGACT
1 TTTGTTTCAAGAGAAAAATACTCAAAGACT
*
2782128 TTTGTTTCAAAAGAAACAA-ACTCAAAGA-T
1 TTTGTTTCAAGAGAAA-AATACTCAAAGACT
* * *
2782157 TTT-TTTTAAGA-AAAACTATCTCAAGAGAGACAAAAC
1 TTTGTTTCAAGAGAAAAATA-CTC-A-A-AGAC----T
* *
2782193 TTTGTTTCAAGAGAAACATACTCAAGGACT
1 TTTGTTTCAAGAGAAAAATACTCAAAGACT
2782223 TTTGTTTCAAGAGAAA
1 TTTGTTTCAAGAGAAA
2782239 CAAATTCAGA
Statistics
Matches: 87, Mismatches: 11, Indels: 26
0.70 0.09 0.21
Matches are distributed among these distances:
26 1 0.01
27 4 0.05
28 9 0.10
29 5 0.06
30 40 0.46
31 5 0.06
34 3 0.03
35 1 0.01
36 4 0.05
37 10 0.11
38 5 0.06
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (30 bp):
TTTGTTTCAAGAGAAAAATACTCAAAGACT
Found at i:2782214 original size:95 final size:95
Alignment explanation
Indices: 2782034--2782295 Score: 323
Period size: 95 Copynumber: 2.7 Consensus size: 95
2782024 AGAAAAATTC
* *
2782034 GTTTCAAGGGAAACAAACTCAAAGGTTTTTTTTTCAA-AAAAA-TATGTCTCAAGAGAGACAAAA
1 GTTTCAAGAGAAACAAACTCAAA-GATTTTTTTT-AAGAAAAACTA--TCTCAAGAGAGACAAAA
*
2782097 CTTTGTTTCAAGATAAAAATACTCAAAGACTTTT
62 CTTTGTTTCAAGAGAAAAATACTCAAAGACTTTT
*
2782131 GTTTCAAAAGAAACAAACTCAAAGATTTTTTTTAAGAAAAACTATCTCAAGAGAGACAAAACTTT
1 GTTTCAAGAGAAACAAACTCAAAGATTTTTTTTAAGAAAAACTATCTCAAGAGAGACAAAACTTT
* *
2782196 GTTTCAAGAGAAACATACTCAAGGACTTTT
66 GTTTCAAGAGAAAAATACTCAAAGACTTTT
* * * * * * * *
2782226 GTTTCAAGAGAAACAAATTCAGAATATATGTTTTAAAGAAAAACTGTCTCCAGTGAGACGAAA-T
1 GTTTCAAGAGAAACAAACTCA-AAGAT-TTTTTTTAAGAAAAACTATCTCAAGAGAGACAAAACT
2782290 TTGTTT
64 TTGTTT
2782296 TGAGAGTAAT
Statistics
Matches: 146, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
95 69 0.47
96 25 0.17
97 52 0.36
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.30
Consensus pattern (95 bp):
GTTTCAAGAGAAACAAACTCAAAGATTTTTTTTAAGAAAAACTATCTCAAGAGAGACAAAACTTT
GTTTCAAGAGAAAAATACTCAAAGACTTTT
Found at i:2782347 original size:35 final size:36
Alignment explanation
Indices: 2782254--2782354 Score: 109
Period size: 36 Copynumber: 2.8 Consensus size: 36
2782244 TCAGAATATA
* * *
2782254 TGTTTTAAAGAAAAACTGTCTCCAGTGAGACGAAATT
1 TGTTTTAGAG-AAAACTGTCTCAAGCGAGACGAAATT
* *
2782291 TGTTTT-GAGAGTAATTGTCTCAAGCGAGAC-AATATT
1 TGTTTTAGAGA-AAACTGTCTCAAGCGAGACGAA-ATT
2782327 T-TTTTAGAGAAAACTGTCTCAAGCGAGA
1 TGTTTTAGAGAAAACTGTCTCAAGCGAGA
2782355 TAAAATTTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
35 23 0.43
36 25 0.46
37 6 0.11
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.32
Consensus pattern (36 bp):
TGTTTTAGAGAAAACTGTCTCAAGCGAGACGAAATT
Found at i:2783589 original size:12 final size:11
Alignment explanation
Indices: 2783572--2783627 Score: 67
Period size: 11 Copynumber: 5.0 Consensus size: 11
2783562 TCTTGTCCTC
2783572 TTTTTTTCTTT
1 TTTTTTTCTTT
2783583 TTTTTTTCTTT
1 TTTTTTTCTTT
* *
2783594 TTCTTTGCTTT
1 TTTTTTTCTTT
*
2783605 TTTCTTTCTTT
1 TTTTTTTCTTT
*
2783616 GCTTTTTTCTTT
1 -TTTTTTTCTTT
2783628 GTATTTTGAT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
11 28 0.76
12 9 0.24
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:2783596 original size:17 final size:18
Alignment explanation
Indices: 2783574--2783627 Score: 78
Period size: 16 Copynumber: 3.2 Consensus size: 18
2783564 TTGTCCTCTT
*
2783574 TTTTTCTTT-TTTTTTTC
1 TTTTTCTTTGCTTTTTTC
2783591 TTTTTCTTTGCTTTTTTC
1 TTTTTCTTTGCTTTTTTC
2783609 --TTTCTTTGCTTTTTTC
1 TTTTTCTTTGCTTTTTTC
2783625 TTT
1 TTT
2783628 GTATTTTGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 16 0.48
17 9 0.27
18 8 0.24
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (18 bp):
TTTTTCTTTGCTTTTTTC
Found at i:2783628 original size:12 final size:11
Alignment explanation
Indices: 2783572--2783615 Score: 56
Period size: 10 Copynumber: 4.1 Consensus size: 11
2783562 TCTTGTCCTC
2783572 TTTT-TTTCTT
1 TTTTCTTTCTT
*
2783582 TTTTTTTTC-T
1 TTTTCTTTCTT
2783592 TTTTCTTTGCTT
1 TTTTCTTT-CTT
2783604 TTTTCTTTCTT
1 TTTTCTTTCTT
2783615 T
1 T
2783616 GCTTTTTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 12 0.40
11 9 0.30
12 9 0.30
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:2785787 original size:18 final size:18
Alignment explanation
Indices: 2785764--2785834 Score: 124
Period size: 18 Copynumber: 3.9 Consensus size: 18
2785754 AGGGATTTAC
2785764 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
2785782 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
2785800 AGTGGTCCTTCGGGACAA
1 AGTGGTCCTTCGGGACAT
*
2785818 AATGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
2785835 AACATTCAGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 51 1.00
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.25
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:2789390 original size:19 final size:19
Alignment explanation
Indices: 2789355--2789391 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2789345 ACAAAAAATG
* *
2789355 CGGTTTTTTCGGTTTTTCC
1 CGGTTTTTTCCGATTTTCC
2789374 CGGTTTTTTCCGATTTTC
1 CGGTTTTTTCCGATTTTC
2789392 AGCTGGTTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.03, C:0.22, G:0.19, T:0.57
Consensus pattern (19 bp):
CGGTTTTTTCCGATTTTCC
Found at i:2790897 original size:13 final size:13
Alignment explanation
Indices: 2790879--2790905 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2790869 TTATGGGCTG
2790879 TAAATTAAAGAAA
1 TAAATTAAAGAAA
2790892 TAAATTAAAGAAA
1 TAAATTAAAGAAA
2790905 T
1 T
2790906 TGATTTAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (13 bp):
TAAATTAAAGAAA
Found at i:2791118 original size:2 final size:2
Alignment explanation
Indices: 2791111--2791250 Score: 244
Period size: 2 Copynumber: 70.0 Consensus size: 2
2791101 TCAATTTCAT
* *
2791111 TA TA TA TA CA TA CA 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
2791153 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
* *
2791195 TA TA CA TA CA 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
2791237 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
2791251 CTCATGTATT
Statistics
Matches: 130, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 130 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2799510 original size:17 final size:17
Alignment explanation
Indices: 2799485--2799530 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
2799475 TAACAATTGC
*
2799485 TGATATCACTTTAGTGA
1 TGATTTCACTTTAGTGA
2799502 TGATTTCACTTTAGTGA
1 TGATTTCACTTTAGTGA
2799519 TGATTTCACTTT
1 TGATTTCACTTT
2799531 TTCATCAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (17 bp):
TGATTTCACTTTAGTGA
Found at i:2802321 original size:135 final size:129
Alignment explanation
Indices: 2802050--2802384 Score: 476
Period size: 135 Copynumber: 2.5 Consensus size: 129
2802040 ATTTTGAAAA
* * *
2802050 AAAT-ATAATCAAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATTGGAAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAA-TAGTAGTTTAC
* * * * *
2802114 CCTAAATAAAATATATATGAATTATATTAGATAATTTATAAGTGACCAAATAGGTAGTTTACTCT
65 CCTAAATAAAATATACATAAATTAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCT
*
2802179 AAATAATAATCGAGTGACCGAAACATAAATTAGATAATATATAAGTGACCAAATAGTAGTTTACC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGTAGTTTACC
*
2802244 CTAAATAATAATCGAGTGACCA-AAACTTAAATTAGATAATATATATGTGACCAAATAGGTAGTT
66 CTAAATAA-AAT--A-T-A-CATAAA-TTAAATTAGATAATATATAAGTGACCAAATAGGTAGTT
2802308 TACCCT
124 TACCCT
*
2802314 AAATAATAATTGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATA-GTAGTTTAC
2802379 CCTAAA
65 CCTAAA
2802385 CAATTCCCTA
Statistics
Matches: 185, Mismatches: 12, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
129 22 0.12
130 49 0.26
132 1 0.01
133 1 0.01
134 3 0.02
135 94 0.51
136 15 0.08
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.29
Consensus pattern (129 bp):
AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGTAGTTTACC
CTAAATAAAATATACATAAATTAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCT
Found at i:2802332 original size:68 final size:68
Alignment explanation
Indices: 2802050--2802384 Score: 481
Period size: 68 Copynumber: 5.0 Consensus size: 68
2802040 ATTTTGAAAA
* * *
2802050 AAAT-ATAATCAAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATTGGAAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
2802114 CCT
66 CCT
* * * * *
2802117 AAATAA-AAT--A-T-A-TATGAA-TTATATTAGATAATTTATAAGTGACCAAATAGGTAGTTTA
1 AAATAATAATCGAGTGACCA-AAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTA
*
2802175 CTCT
65 CCCT
*
2802179 AAATAATAATCGAGTGACCGAAACATAAATTAGATAATATATAAGTGACCAAATA-GTAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
2802243 CCT
66 CCT
* *
2802246 AAATAATAATCGAGTGACCAAAACTTAAATTAGATAATATATATGTGACCAAATAGGTAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
2802311 CCT
66 CCT
*
2802314 AAATAATAATTGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
2802379 CCT
66 CCT
2802382 AAA
1 AAA
2802385 CAATTCCCTA
Statistics
Matches: 237, Mismatches: 21, Indels: 19
0.86 0.08 0.07
Matches are distributed among these distances:
62 45 0.19
63 6 0.03
64 1 0.00
65 2 0.01
66 1 0.00
67 73 0.31
68 109 0.46
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.29
Consensus pattern (68 bp):
AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
CCT
Found at i:2810435 original size:13 final size:13
Alignment explanation
Indices: 2810435--2810510 Score: 53
Period size: 13 Copynumber: 5.3 Consensus size: 13
2810425 CCGTTGACCC
2810435 GACCCGACCCGTT
1 GACCCGACCCGTT
* * *
2810448 TACCCAACCCATT
1 GACCCGACCCGTT
2810461 GACCCGACCCGACCCGTT
1 GACCCG-----ACCCGTT
2810479 GACCCGACCCGTT
1 GACCCGACCCGTT
*
2810492 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
2810507 GACC
1 GACC
2810511 GTTGACCGGA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
13 25 0.51
15 12 0.24
18 12 0.24
ACGTcount: A:0.18, C:0.45, G:0.20, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2810436 original size:18 final size:18
Alignment explanation
Indices: 2810413--2810489 Score: 101
Period size: 18 Copynumber: 4.6 Consensus size: 18
2810403 ACCGGTCACA
2810413 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
2810431 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
*
2810449 ACCC-A----ACCCATTG
1 ACCCGACCCGACCCGTTG
2810462 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
2810480 ACCCGACCCG
1 ACCCGACCCG
2810490 TTGACCGTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
13 10 0.20
14 1 0.02
17 1 0.02
18 38 0.76
ACGTcount: A:0.19, C:0.51, G:0.18, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:2810463 original size:31 final size:31
Alignment explanation
Indices: 2810417--2810495 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
2810407 GTCACAACCC
2810417 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* * *
2810448 TACCCAACCCATTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
2810479 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
2810496 GTTGACCCGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.19, C:0.48, G:0.19, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:2810482 original size:8 final size:8
Alignment explanation
Indices: 2810471--2810517 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
2810461 GACCCGACCC
2810471 GACCCGTT
1 GACCCGTT
2810479 GACCC---
1 GACCCGTT
2810484 GACCCGTT
1 GACCCGTT
2810492 GA-CCGTT
1 GACCCGTT
2810499 GACCCGTT
1 GACCCGTT
2810507 GA-CCGTT
1 GACCCGTT
2810514 GACC
1 GACC
2810518 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:2810499 original size:7 final size:7
Alignment explanation
Indices: 2810487--2810518 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
2810477 TTGACCCGAC
2810487 CCGTTGA
1 CCGTTGA
2810494 CCGTTGA
1 CCGTTGA
2810501 CCCGTTGA
1 -CCGTTGA
2810509 CCGTTGA
1 CCGTTGA
2810516 CCG
1 CCG
2810519 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:2810504 original size:15 final size:15
Alignment explanation
Indices: 2810471--2810517 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
2810461 GACCCGACCC
*
2810471 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
2810484 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
2810499 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
2810514 GACC
1 GACC
2810518 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:2813287 original size:51 final size:51
Alignment explanation
Indices: 2813193--2813293 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 51
2813183 GAAATAAATA
*
2813193 TTATCTGTATCTGCACGTTCATCAGCATCATCTGGTAGTTGTATTACTGAT
1 TTATATGTATCTGCACGTTCATCAGCATCATCTGGTAGTTGTATTACTGAT
2813244 TTATATGTATCTGCACG-TCATCAGCATCAT-TGGTAGTTCTGTATTACTGA
1 TTATATGTATCTGCACGTTCATCAGCATCATCTGGTAG-T-TGTATTACTGA
2813294 GCTTCCAAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
49 6 0.13
50 14 0.30
51 27 0.57
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.41
Consensus pattern (51 bp):
TTATATGTATCTGCACGTTCATCAGCATCATCTGGTAGTTGTATTACTGAT
Found at i:2815024 original size:13 final size:13
Alignment explanation
Indices: 2815024--2815084 Score: 59
Period size: 13 Copynumber: 4.3 Consensus size: 13
2815014 CCGTTGACCC
2815024 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
2815037 TACCCGACCCATT
1 GACCCGACCCGTT
2815050 GACCCGACCCGACCCGTT
1 G-----ACCCGACCCGTT
2815068 GACCCGACCCGTT
1 GACCCGACCCGTT
2815081 GACC
1 GACC
2815085 GTTGACACGT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
13 27 0.69
18 12 0.31
ACGTcount: A:0.18, C:0.48, G:0.20, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2815025 original size:18 final size:18
Alignment explanation
Indices: 2815002--2815078 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
2814992 ACCGGTCACA
2815002 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
2815020 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
2815038 ACCCGACCC-A----TTG
1 ACCCGACCCGACCCGTTG
2815051 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
2815069 ACCCGACCCG
1 ACCCGACCCG
2815079 TTGACCGTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 11 0.21
14 1 0.02
17 1 0.02
18 39 0.75
ACGTcount: A:0.18, C:0.51, G:0.19, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:2815045 original size:31 final size:31
Alignment explanation
Indices: 2815006--2815084 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
2814996 GTCACAACCC
2815006 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* *
2815037 TACCCGACCCATTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
2815068 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
2815085 GTTGACACGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.18, C:0.48, G:0.20, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:2815071 original size:8 final size:8
Alignment explanation
Indices: 2815060--2815106 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
2815050 GACCCGACCC
2815060 GACCCGTT
1 GACCCGTT
2815068 GACCC---
1 GACCCGTT
2815073 GACCCGTT
1 GACCCGTT
2815081 GA-CCGTT
1 GACCCGTT
*
2815088 GACACGTT
1 GACCCGTT
2815096 GA-CCGTT
1 GACCCGTT
2815103 GACC
1 GACC
2815107 GGAGTTGACC
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
5 5 0.16
7 13 0.41
8 14 0.44
ACGTcount: A:0.17, C:0.36, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:2815088 original size:7 final size:7
Alignment explanation
Indices: 2815076--2815107 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
2815066 TTGACCCGAC
2815076 CCGTTGA
1 CCGTTGA
2815083 CCGTTGA
1 CCGTTGA
2815090 CACGTTGA
1 C-CGTTGA
2815098 CCGTTGA
1 CCGTTGA
2815105 CCG
1 CCG
2815108 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.16, C:0.31, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:2815097 original size:15 final size:15
Alignment explanation
Indices: 2815077--2815105 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2815067 TGACCCGACC
2815077 CGTTGACCGTTGACA
1 CGTTGACCGTTGACA
2815092 CGTTGACCGTTGAC
1 CGTTGACCGTTGAC
2815106 CGGAGTTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (15 bp):
CGTTGACCGTTGACA
Found at i:2817656 original size:24 final size:24
Alignment explanation
Indices: 2817560--2817668 Score: 96
Period size: 24 Copynumber: 4.5 Consensus size: 24
2817550 GAATATTTTA
* *
2817560 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTCTGT
* *
2817584 T-TGGACATCTGATCTGAAATCTGT
1 TCT-GATATCTGATCTGAATTCTGT
* * *
2817608 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTCTGT
*
2817632 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTCTGT
* *
2817656 TTTGATTTCTGAT
1 TCTGATATCTGAT
2817669 ATCTCCGTTT
Statistics
Matches: 66, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
23 2 0.03
24 62 0.94
25 2 0.03
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.47
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTCTGT
Found at i:2818984 original size:2 final size:2
Alignment explanation
Indices: 2818977--2819016 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2818967 TTCATTAATA
2818977 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
2819017 TATTTTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2830532 original size:24 final size:22
Alignment explanation
Indices: 2830505--2830569 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
2830495 TATGCTTGAA
2830505 AAAAAGGAACAAATAAAAAGAAAG
1 AAAAAGGAA-AAATAAAAA-AAAG
* *
2830529 AAAAAAGAAAAA-AGAAAAAAG
1 AAAAAGGAAAAATAAAAAAAAG
* *
2830550 AAGAAGAAAAAAATAAAAAA
1 AAAAAG-GAAAAATAAAAAA
2830570 TGAAGAGAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
21 8 0.24
22 9 0.27
23 8 0.24
24 8 0.24
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.03
Consensus pattern (22 bp):
AAAAAGGAAAAATAAAAAAAAG
Found at i:2830562 original size:14 final size:14
Alignment explanation
Indices: 2830525--2830561 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
2830515 AAATAAAAAG
2830525 AAAGAAAAAAGAAA
1 AAAGAAAAAAGAAA
2830539 AAAGAAAAAAG-AA
1 AAAGAAAAAAGAAA
*
2830552 GAAGAAAAAA
1 AAAGAAAAAA
2830562 ATAAAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAGAAA
Found at i:2830562 original size:21 final size:19
Alignment explanation
Indices: 2830503--2830575 Score: 58
Period size: 20 Copynumber: 3.7 Consensus size: 19
2830493 ATTATGCTTG
* *
2830503 AAAAAAAGGAACAAATAAAA
1 AAAAAAAAGAAGAAA-AAAA
2830523 AGAAAGAAAA-AAGAAAAAAGA
1 A-AAA-AAAAGAAGAAAAAA-A
*
2830544 AAAAAGAAGAAGAAAAAAA
1 AAAAAAAAGAAGAAAAAAA
* *
2830563 TAAAAAATGAAGA
1 AAAAAAAAGAAGA
2830576 GAGAAAAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
19 14 0.33
20 16 0.37
21 10 0.23
22 3 0.07
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.04
Consensus pattern (19 bp):
AAAAAAAAGAAGAAAAAAA
Found at i:2830570 original size:7 final size:7
Alignment explanation
Indices: 2830525--2830561 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
2830515 AAATAAAAAG
2830525 AAAGAAA
1 AAAGAAA
2830532 AAAGAAA
1 AAAGAAA
2830539 AAAGAAA
1 AAAGAAA
2830546 AAAG-AA
1 AAAGAAA
*
2830552 GAAGAAA
1 AAAGAAA
2830559 AAA
1 AAA
2830562 ATAAAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:2830586 original size:21 final size:21
Alignment explanation
Indices: 2830536--2830583 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
2830526 AAGAAAAAAG
*
2830536 AAAAAAGAAAAAAGAAGAAGA
1 AAAAAATAAAAAAGAAGAAGA
2830557 AAAAAATAAAAAATGAAGAGAGA
1 AAAAAATAAAAAA-GAAGA-AGA
2830580 AAAA
1 AAAA
2830584 TAAGGGTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 12 0.50
22 5 0.21
23 7 0.29
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (21 bp):
AAAAAATAAAAAAGAAGAAGA
Found at i:2831854 original size:239 final size:240
Alignment explanation
Indices: 2831444--2832002 Score: 897
Period size: 240 Copynumber: 2.3 Consensus size: 240
2831434 AGGTGAACCG
* **
2831444 ACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAC-GAGGGAGAAGAAGTTCATAAT
* * * *
2831509 AAGAAGAGCTTGTTCGACCTATCACTCGATTCATGGTATTTTGAACCAGTGACACCTCGCTTAAG
65 AAGAAGAGCTTGTTCGACCTATAACTCGATTCACGGCATTTCGAACCAGTGACACCTCGCTTAAG
*
2831574 GGATTGACATTTTCAAAAGAGTTCATAATGAGAAGAACTCATCCTAAAAGAG-AAGTTCATAATG
130 GGATTGACATTTTCAAAAGAGTTCATAATGAGAAAAACTCATCCTAAAAGAGAAAGTTCATAATG
2831638 AGAAGAACTTGTTCATTTCAAGTCCATCACAGAAAGAGACT-GATCA
195 AGAAGAACTTGTTCATTTCAAGTCCATCACAGAAAGAGA-TGGATCA
* *
2831684 ACATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATA
* *
2831749 AGAAGAGCTTGTTCGACCTATAACTCGATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAGG
66 AGAAGAGCTTGTTCGACCTATAACTCGATTCACGGCATTTCGAACCAGTGACACCTCGCTTAAGG
* * * *
2831814 GATTGACATTTTCAAAAGAGTTTATAATGAGAAAAACTCATCCTAAAGGAGAAAGTTTATGATGA
131 GATTGACATTTTCAAAAGAGTTCATAATGAGAAAAACTCATCCTAAAAGAGAAAGTTCATAATGA
*
2831879 GAAGAACTTGTTCCTTTCAAGTCCATCACAGAAAGAGATGGATCA
196 GAAGAACTTGTTCATTTCAAGTCCATCACAGAAAGAGATGGATCA
* * *
2831924 ACATCTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATG
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATA
*
2831989 AGAAGAACTTGTTC
66 AGAAGAGCTTGTTC
2832003 AACTTCGCAT
Statistics
Matches: 295, Mismatches: 22, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
239 129 0.44
240 166 0.56
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.25
Consensus pattern (240 bp):
ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATA
AGAAGAGCTTGTTCGACCTATAACTCGATTCACGGCATTTCGAACCAGTGACACCTCGCTTAAGG
GATTGACATTTTCAAAAGAGTTCATAATGAGAAAAACTCATCCTAAAAGAGAAAGTTCATAATGA
GAAGAACTTGTTCATTTCAAGTCCATCACAGAAAGAGATGGATCA
Found at i:2832037 original size:91 final size:92
Alignment explanation
Indices: 2831920--2832094 Score: 246
Period size: 91 Copynumber: 1.9 Consensus size: 92
2831910 AAAGAGATGG
* * *
2831920 ATCAACATCTCCAATGGAGAGTTCATAATGAGAAGAACTCATCC-AACGAG-GAAGAAGAAGTTC
1 ATCAACATCTCCAATGGAAAGTTCATAATAAGAAGAACTCATCCAAAAGAGAG-AGAAGAAGTTC
2831983 ATAATGAGAAGAACTTGTTCAACTTCGC
65 ATAATGAGAAGAACTTGTTCAACTTCGC
* * * * *
2832011 ATCAACATTTTCAATTGAAAGTTCATAATAAGAAGAACTCATTCAAAAGAGAGAGAATAAGTTCA
1 ATCAACATCTCCAATGGAAAGTTCATAATAAGAAGAACTCATCCAAAAGAGAGAGAAGAAGTTCA
*
2832076 TAATGAGAAGAGCTTGTTC
66 TAATGAGAAGAACTTGTTC
2832095 GACCTATCAC
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
91 38 0.52
92 34 0.47
93 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (92 bp):
ATCAACATCTCCAATGGAAAGTTCATAATAAGAAGAACTCATCCAAAAGAGAGAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACTTCGC
Found at i:2832468 original size:3 final size:3
Alignment explanation
Indices: 2832460--2832509 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
2832450 GGTTAAAGAA
2832460 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2832508 TA
1 TA
2832510 AGTGTGTTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2844849 original size:22 final size:22
Alignment explanation
Indices: 2844821--2844864 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2844811 TTCCAATTTA
2844821 CACAAAATGGTCATTCAACATT
1 CACAAAATGGTCATTCAACATT
* *
2844843 CACAAAATGGTCCTTCACCATT
1 CACAAAATGGTCATTCAACATT
2844865 AACACTCCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.27
Consensus pattern (22 bp):
CACAAAATGGTCATTCAACATT
Found at i:2848102 original size:9 final size:9
Alignment explanation
Indices: 2848088--2848119 Score: 50
Period size: 8 Copynumber: 3.8 Consensus size: 9
2848078 TGACCATTAT
2848088 TATTTTAAA
1 TATTTTAAA
2848097 TATTTTAAA
1 TATTTTAAA
2848106 TA-TTTAAA
1 TATTTTAAA
2848114 T-TTTTA
1 TATTTTA
2848120 TAAAATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 11 0.50
9 11 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTTTAAA
Found at i:2849427 original size:25 final size:23
Alignment explanation
Indices: 2849380--2849441 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 23
2849370 GTTAAGAAAG
2849380 AATTTATAAAATTTTAGAAAAAATA
1 AATTTAT-AAATTTTAGAAAAAA-A
2849405 AATTTATAAATTTTAGGAGAAAAAA
1 AATTTATAAATTTTA-GA-AAAAAA
*
2849430 TATATTATAAAT
1 AAT-TTATAAAT
2849442 AAAAAATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 8 0.24
25 12 0.36
26 13 0.39
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.37
Consensus pattern (23 bp):
AATTTATAAATTTTAGAAAAAAA
Found at i:2849768 original size:23 final size:23
Alignment explanation
Indices: 2849740--2849790 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
2849730 TGAAAATAAA
2849740 AATATAATATCA-TATATTATTAT
1 AATATAAT-TCAGTATATTATTAT
*
2849763 AATATAATTGAGTATATTATTAT
1 AATATAATTCAGTATATTATTAT
2849786 AATAT
1 AATAT
2849791 TAAAAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (23 bp):
AATATAATTCAGTATATTATTAT
Found at i:2849799 original size:20 final size:20
Alignment explanation
Indices: 2849776--2849819 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
2849766 ATAATTGAGT
2849776 ATATTATTATAATATTAA-AA
1 ATATTA-TATAATATTAATAA
2849796 ATATTATATAATATTAATAA
1 ATATTATATAATATTAATAA
2849816 ATAT
1 ATAT
2849820 ATTTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATTATATAATATTAATAA
Found at i:2849802 original size:17 final size:19
Alignment explanation
Indices: 2849783--2849821 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2849773 AGTATATTAT
2849783 TATAATATTAA-AAATATTA
1 TATAATATTAATAAATA-TA
2849802 TATAATATTAATAAATATA
1 TATAATATTAATAAATATA
2849821 T
1 T
2849822 TTTAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TATAATATTAATAAATATA
Found at i:2849807 original size:19 final size:21
Alignment explanation
Indices: 2849753--2849846 Score: 79
Period size: 23 Copynumber: 4.4 Consensus size: 21
2849743 ATAATATCAT
*
2849753 ATATTATTATAATA-TAATTGAGT
1 ATATTATTATAATATTAA-T-A-A
2849776 ATATTATTATAATATTAA-AA
1 ATATTATTATAATATTAATAA
2849796 ATATTA-TATAATATTAATAA
1 ATATTATTATAATATTAATAA
*
2849816 ATA-TATTTTAAATATTTTAATAA
1 ATATTATTAT-AATA--TTAATAA
*
2849839 ATAATATT
1 ATATTATT
2849847 TTTGGTCAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 13
0.81 0.03 0.17
Matches are distributed among these distances:
19 13 0.21
20 13 0.21
21 5 0.08
23 24 0.39
24 7 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
ATATTATTATAATATTAATAA
Found at i:2849830 original size:40 final size:43
Alignment explanation
Indices: 2849753--2849831 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 43
2849743 ATAATATCAT
* *
2849753 ATATTATTATAATATAATTGAGTATATTATTATAATATTAAAA
1 ATATTATTATAATATAATTAAATATATTATTATAATATTAAAA
2849796 ATATTA-TATAATATTAA-TAAATATATT-TTA-AATATT
1 ATATTATTATAATA-TAATTAAATATATTATTATAATATT
2849832 TTAATAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
40 6 0.18
41 3 0.09
42 15 0.45
43 9 0.27
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (43 bp):
ATATTATTATAATATAATTAAATATATTATTATAATATTAAAA
Found at i:2858283 original size:29 final size:28
Alignment explanation
Indices: 2858237--2858351 Score: 124
Period size: 29 Copynumber: 4.0 Consensus size: 28
2858227 GATCCCAAAT
*
2858237 AGAATCATGACAGGGATATAATAC-CATGC
1 AGAATCAGGAC-GGGATATAAT-CTCATGC
* **
2858266 AAAATCAGGACGGTGATATAATCTCATAT
1 AGAATCAGGACGG-GATATAATCTCATGC
*
2858295 AGAATAAGGACGGAGATATAATCTCATGC
1 AGAATCAGGACGG-GATATAATCTCATGC
*
2858324 AGAATCAGGACGGGAATATAATCCCATG
1 AGAATCAGGACGGG-ATATAATCTCATG
2858352 TAGATGAAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
28 4 0.06
29 68 0.94
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (28 bp):
AGAATCAGGACGGGATATAATCTCATGC
Found at i:2867248 original size:2 final size:2
Alignment explanation
Indices: 2867241--2867267 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2867231 ATTCAAAAAT
2867241 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
2867268 TACTTTTTAC
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:2895887 original size:18 final size:17
Alignment explanation
Indices: 2895864--2895939 Score: 75
Period size: 18 Copynumber: 4.4 Consensus size: 17
2895854 GCACTCAAAG
* *
2895864 AAGAAAAGAGAAGAATAA
1 AAGAAAAGA-AAAAAGAA
*
2895882 AAGAAAAGAAAAGAGAA
1 AAGAAAAGAAAAAAGAA
2895899 GAAGAAAAG--AAAAGAA
1 -AAGAAAAGAAAAAAGAA
*
2895915 AAGATAAGAATAAAAGAA
1 AAGAAAAGAA-AAAAGAA
2895933 AAGAAAA
1 AAGAAAA
2895940 TTGCAAAGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
15 7 0.15
16 6 0.12
17 5 0.10
18 30 0.62
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (17 bp):
AAGAAAAGAAAAAAGAA
Found at i:2895892 original size:23 final size:23
Alignment explanation
Indices: 2895864--2895939 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
2895854 GCACTCAAAG
2895864 AAGAAAAGAGAAGAATAAAAGAA
1 AAGAAAAGAGAAGAATAAAAGAA
*
2895887 AAGAAAAGAGAAGAAGAAAAGAA
1 AAGAAAAGAGAAGAATAAAAGAA
*
2895910 AAGAAAAGATAAGAATAAAAGAA
1 AAGAAAAGAGAAGAATAAAAGAA
2895933 AAGAAAA
1 AAGAAAA
2895940 TTGCAAAGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (23 bp):
AAGAAAAGAGAAGAATAAAAGAA
Found at i:2895952 original size:5 final size:5
Alignment explanation
Indices: 2895880--2895939 Score: 65
Period size: 5 Copynumber: 12.8 Consensus size: 5
2895870 AGAGAAGAAT
* * *
2895880 AAAAG AAAAG AAAAG AGAAG --AAG AAAAG AAAAG AAAAG ATAAG --AAT
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
2895926 AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAA
2895940 TTGCAAAGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
3 5 0.11
5 42 0.89
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:2903718 original size:16 final size:18
Alignment explanation
Indices: 2903697--2903742 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
2903687 TATGGAATTG
*
2903697 GATTCCAATTTC-T-ACA
1 GATTCCAATTCCTTCACA
2903713 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
2903731 GATTCCAATTCC
1 GATTCCAATTCC
2903743 CTCATAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 11 0.41
17 1 0.04
18 15 0.56
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.35
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:2906605 original size:66 final size:66
Alignment explanation
Indices: 2906489--2906822 Score: 418
Period size: 66 Copynumber: 5.1 Consensus size: 66
2906479 CACTAGGTAA
* * ** * *
2906489 AGTGATTATTGAATATTGTATTGATCACTCGATGTGACTCATGTATCTTTGTGGTGCATGAGGTG
1 AGTGATAATTGAATAATGTACAGATCACTCGATGTGACTCGTGTACCTTTGTGGTGCATGAGGTG
2906554 G
66 G
* *
2906555 AGTGATAATTGAATAATGTACAGATCACTCGATATGACTCGTGTACCTTTGTGGTGCATAAGGTG
1 AGTGATAATTGAATAATGTACAGATCACTCGATGTGACTCGTGTACCTTTGTGGTGCATGAGGTG
2906620 G
66 G
* * **
2906621 AGTGATAATTGAATATTGTA-AGATCACTTGATGTGGTTCGTGTACCTTTGTGGTGCATGAGGTG
1 AGTGATAATTGAATAATGTACAGATCACTCGATGTGACTCGTGTACCTTTGTGGTGCATGAGGTG
*
2906685 A
66 G
* * * * * *
2906686 AATGATAATTGAATGATGTACAAGATCACTCGATGTGACTCATGTACATTTGTGGTGCATTAGAT
1 AGTGATAATTGAATAATGTAC-AGATCACTCGATGTGACTCGTGTACCTTTGTGGTGCATGAGGT
2906751 GG
65 GG
** * * * * *
2906753 AGTGATAATTGAATACCGTACATATCACTCGATGTGACTCGCGTACCTTAGTGGTACACGAGGTG
1 AGTGATAATTGAATAATGTACAGATCACTCGATGTGACTCGTGTACCTTTGTGGTGCATGAGGTG
2906818 G
66 G
2906819 AGTG
1 AGTG
2906823 TATCGAGTAC
Statistics
Matches: 227, Mismatches: 39, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
65 56 0.25
66 117 0.52
67 54 0.24
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.34
Consensus pattern (66 bp):
AGTGATAATTGAATAATGTACAGATCACTCGATGTGACTCGTGTACCTTTGTGGTGCATGAGGTG
G
Found at i:2907093 original size:17 final size:19
Alignment explanation
Indices: 2907071--2907108 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2907061 CGAAAAATAA
2907071 AAACAAT-AT-AAGAAAAG
1 AAACAATCATGAAGAAAAG
2907088 AAACAATGCATGAAGAAAAG
1 AAACAAT-CATGAAGAAAAG
2907108 A
1 A
2907109 TATTACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
19 2 0.11
20 9 0.50
ACGTcount: A:0.66, C:0.08, G:0.16, T:0.11
Consensus pattern (19 bp):
AAACAATCATGAAGAAAAG
Found at i:2909955 original size:31 final size:31
Alignment explanation
Indices: 2909917--2909976 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
2909907 TAAGAAAGGA
2909917 GATATGAATTTTATTAAACCTGTTAGTTGGG
1 GATATGAATTTTATTAAACCTGTTAGTTGGG
2909948 GATATGAATTTTATTAAACCTGTTAGTTG
1 GATATGAATTTTATTAAACCTGTTAGTTG
2909977 TGTCTACCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (31 bp):
GATATGAATTTTATTAAACCTGTTAGTTGGG
Found at i:2913703 original size:20 final size:20
Alignment explanation
Indices: 2913672--2913753 Score: 83
Period size: 20 Copynumber: 4.1 Consensus size: 20
2913662 GGTTGAACGC
*
2913672 CGCCGATAAACGGCGGTCGG
1 CGCCGATGAACGGCGGTCGG
* * *
2913692 CGTCGATGAACGGGGGTCGA
1 CGCCGATGAACGGCGGTCGG
* * *
2913712 TGCCGATGAACGGAGGTCAG
1 CGCCGATGAACGGCGGTCGG
* *
2913732 CGCCGATCAACGGCGGCCGG
1 CGCCGATGAACGGCGGTCGG
2913752 CG
1 CG
2913754 AGGCGACCAC
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.20, C:0.28, G:0.41, T:0.11
Consensus pattern (20 bp):
CGCCGATGAACGGCGGTCGG
Found at i:2914283 original size:24 final size:23
Alignment explanation
Indices: 2914256--2914336 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 23
2914246 CATTATTTTA
*
2914256 TTTTATTTTATTAGTTTTATTAGTT
1 TTTTATTTT-TTATTTTTATTAG-T
2914281 TTTTATTTTTTATTTTTTATTA-T
1 TTTTATTTTTTA-TTTTTATTAGT
* * *
2914304 TATATATTTTTTCTTTTTATAATGT
1 T-TTTATTTTTTATTTTTATTA-GT
2914329 TTTTATTT
1 TTTTATTT
2914337 ATATATGTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
23 10 0.21
24 18 0.38
25 19 0.40
ACGTcount: A:0.20, C:0.01, G:0.04, T:0.75
Consensus pattern (23 bp):
TTTTATTTTTTATTTTTATTAGT
Found at i:2914296 original size:6 final size:7
Alignment explanation
Indices: 2914256--2914336 Score: 63
Period size: 7 Copynumber: 10.1 Consensus size: 7
2914246 CATTATTTTA
2914256 TTTTATT
1 TTTTATT
2914263 TTATTAGTT
1 TT-TTA-TT
2914272 TTATTAGTT
1 TT-TTA-TT
2914281 TTTTATT
1 TTTTATT
2914288 TTTTATT
1 TTTTATT
2914295 TTTTATT
1 TTTTATT
2914302 ATTATATATT
1 -TT-T-TATT
*
2914312 TTTTCTT
1 TTTTATT
2914319 TTTATAATGT
1 TTT-T-AT-T
2914329 TTTTATT
1 TTTTATT
2914336 T
1 T
2914337 ATATATGTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 16
0.78 0.02 0.20
Matches are distributed among these distances:
7 26 0.41
8 12 0.19
9 18 0.28
10 8 0.12
ACGTcount: A:0.20, C:0.01, G:0.04, T:0.75
Consensus pattern (7 bp):
TTTTATT
Found at i:2914298 original size:25 final size:24
Alignment explanation
Indices: 2914248--2914336 Score: 76
Period size: 24 Copynumber: 3.7 Consensus size: 24
2914238 CTTAATTCCA
*
2914248 TTATT-TTATTTTATTTTATTA-GTT
1 TTATTATT-TTTTATTTT-TTATTTT
2914272 TTATTAGTTTTTTATTTTTTATTTT
1 TTATTA-TTTTTTATTTTTTATTTT
* * *
2914297 TTATTATTATATATTTTTT-CTTT
1 TTATTATTTTTTATTTTTTATTTT
*
2914320 TTATAATGTTTTTATTT
1 TTATTAT-TTTTTATTT
2914337 ATATATGTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
23 9 0.17
24 26 0.48
25 17 0.31
26 2 0.04
ACGTcount: A:0.20, C:0.01, G:0.03, T:0.75
Consensus pattern (24 bp):
TTATTATTTTTTATTTTTTATTTT
Found at i:2914323 original size:17 final size:16
Alignment explanation
Indices: 2914270--2914342 Score: 55
Period size: 15 Copynumber: 4.6 Consensus size: 16
2914260 ATTTTATTAG
2914270 TTTTAT-TAGTTTTTTAT
1 TTTTATATA-TTTTTT-T
*
2914287 TTTT-TAT-TTTTTAT
1 TTTTATATATTTTTTT
*
2914301 TATTATATATTTTTTCT
1 TTTTATATATTTTTT-T
*
2914318 TTTTATA-ATGTTTTT
1 TTTTATATATTTTTTT
*
2914333 ATTTATATAT
1 TTTTATATAT
2914343 GTTTCTTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
14 4 0.09
15 15 0.33
16 14 0.31
17 12 0.27
ACGTcount: A:0.22, C:0.01, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTATATATTTTTTT
Found at i:2914331 original size:16 final size:16
Alignment explanation
Indices: 2914280--2914352 Score: 62
Period size: 17 Copynumber: 4.5 Consensus size: 16
2914270 TTTTATTAGT
*
2914280 TTTTTATTT-TTTAT-
1 TTTTTATTTATATATG
2914294 TTTTTATTATTATATAT-
1 TTTTTA-T-TTATATATG
* *
2914311 TTTTTCTTTTTATAATG
1 TTTTTATTTATAT-ATG
2914328 TTTTTATTTATATATG
1 TTTTTATTTATATATG
2914344 TTTCTTATT
1 TTT-TTATT
2914353 ACTATTTTCC
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
14 6 0.12
15 6 0.12
16 11 0.23
17 25 0.52
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTTATTTATATATG
Found at i:2914339 original size:32 final size:30
Alignment explanation
Indices: 2914256--2914352 Score: 90
Period size: 32 Copynumber: 3.0 Consensus size: 30
2914246 CATTATTTTA
2914256 TTTTATTTTATTAGTTTTAT-TAGTTTTTTATT
1 TTTTATTTT-TTA-TTTTATATA-TTTTTTATT
*
2914288 TTTTATTTTTTATTATTATATATTTTTTCTT
1 TTTTATTTTTTATT-TTATATATTTTTTATT
2914319 TTTATAATGTTTTTA-TTTATATATGTTTCTTATT
1 TTT-T-AT-TTTTTATTTTATATAT-TTT-TTATT
2914353 ACTATTTTCC
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
30 2 0.04
31 18 0.32
32 20 0.36
33 6 0.11
34 10 0.18
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.73
Consensus pattern (30 bp):
TTTTATTTTTTATTTTATATATTTTTTATT
Found at i:2914351 original size:17 final size:17
Alignment explanation
Indices: 2914303--2914352 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 17
2914293 TTTTTTATTA
*
2914303 TTATATATTTTTTCTT-T
1 TTATATA-TGTTTCTTAT
2914320 TTATA-ATGTTT-TTAT
1 TTATATATGTTTCTTAT
2914335 TTATATATGTTTCTTAT
1 TTATATATGTTTCTTAT
2914352 T
1 T
2914353 ACTATTTTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 2 0.07
15 10 0.34
16 7 0.24
17 10 0.34
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (17 bp):
TTATATATGTTTCTTAT
Found at i:2920741 original size:81 final size:81
Alignment explanation
Indices: 2920601--2920757 Score: 242
Period size: 81 Copynumber: 1.9 Consensus size: 81
2920591 TAACCTTTCA
* * * * * *
2920601 TCTTTTAGTCAACGGTATCTCACCGTTCATCTAACTGGAATAATTGGTACCTTTCTACCAGTTGC
1 TCTTTTACTCAACGGTATCTAACCGTTCATCTAACTGGAATAATTGATACATTTATACCAATTGC
*
2920666 ATAGTTAGGCCATTCT
66 ACAGTTAGGCCATTCT
*
2920682 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGAATAATTGATACATTTATACCAATTGC
1 TCTTTTACTCAACGGTATCTAACCGTTCATCTAACTGGAATAATTGATACATTTATACCAATTGC
2920747 ACAGTTAGGCC
66 ACAGTTAGGCC
2920758 TTAAAGGCAC
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 68 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (81 bp):
TCTTTTACTCAACGGTATCTAACCGTTCATCTAACTGGAATAATTGATACATTTATACCAATTGC
ACAGTTAGGCCATTCT
Found at i:2920817 original size:68 final size:68
Alignment explanation
Indices: 2920745--2920895 Score: 241
Period size: 68 Copynumber: 2.2 Consensus size: 68
2920735 TATACCAATT
* *
2920745 GCACAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCT-AACTGGCTTATATGACACATTTCTGTC
1 GCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAAAC-GGCTTATATGAAACATTTCTGTC
2920809 ATAA
65 ATAA
* *
2920813 GCACAGTTAGGTCTCAAAGGCACTTAGCCTTTCATCTAAACGGCTTATATGAAACCTTTCTGTCA
1 GCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAAACGGCTTATATGAAACATTTCTGTCA
2920878 TAA
66 TAA
*
2920881 GCACAATTAGGCCTC
1 GCACAGTTAGGCCTC
2920896 TTAATCCATT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
68 73 0.96
69 3 0.04
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (68 bp):
GCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAAACGGCTTATATGAAACATTTCTGTCA
TAA
Found at i:2921170 original size:54 final size:54
Alignment explanation
Indices: 2921103--2921252 Score: 149
Period size: 59 Copynumber: 2.7 Consensus size: 54
2921093 ACATATATTT
** * * *
2921103 CCCATACAAAAATTCATACAATTGATATTAATTTCTTA-TTTCGCACACATAGTG
1 CCCATACGGAAATTCATACACTT-ATATGAATTTCTTATTTTCGCACACAAAGTG
* * * *
2921157 CCCATACGGAAATTCCTACACTTAGTAGGATTTTCTTAATATTTTTGCACACAAAGTG
1 CCCATACGGAAATTCATACACTTA-TATGAATTTC-T--TATTTTCGCACACAAAGTG
2921215 CCCAATACGGAAATTCATACACTTAATATGAATTTCTT
1 CCC-ATACGGAAATTCATACACTT-ATATGAATTTCTT
2921253 TACATTTTGT
Statistics
Matches: 77, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
53 1 0.01
54 26 0.34
55 1 0.01
56 1 0.01
57 2 0.03
58 18 0.23
59 27 0.35
60 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.35
Consensus pattern (54 bp):
CCCATACGGAAATTCATACACTTATATGAATTTCTTATTTTCGCACACAAAGTG
Found at i:2921217 original size:58 final size:58
Alignment explanation
Indices: 2921140--2921274 Score: 173
Period size: 58 Copynumber: 2.3 Consensus size: 58
2921130 TTAATTTCTT
* * * * *
2921140 ATTTCGCACACATAGTGCCC-ATACGGAAATTCCTACACTTAGTAGGATTTTCTTAAT
1 ATTTTGCACACATAGTGCCCAATACGGAAATTCATACACTTAATAGGAATTTCTTAAC
* * *
2921197 ATTTTTGCACACAAAGTGCCCAATACGGAAATTCATACACTTAATATGAATTTCTTTAC
1 A-TTTTGCACACATAGTGCCCAATACGGAAATTCATACACTTAATAGGAATTTCTTAAC
*
2921256 ATTTTGTACACATAGTGCC
1 ATTTTGCACACATAGTGCC
2921275 ATTTGGTAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
57 1 0.02
58 33 0.50
59 32 0.48
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (58 bp):
ATTTTGCACACATAGTGCCCAATACGGAAATTCATACACTTAATAGGAATTTCTTAAC
Found at i:2921615 original size:19 final size:19
Alignment explanation
Indices: 2921588--2921624 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2921578 ACATTTCTGG
*
2921588 CTCCATAGTATCGATACTA
1 CTCCATAGTACCGATACTA
*
2921607 CTCCCTAGTACCGATACT
1 CTCCATAGTACCGATACT
2921625 TCTAAACTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.32, G:0.11, T:0.30
Consensus pattern (19 bp):
CTCCATAGTACCGATACTA
Found at i:2921714 original size:20 final size:21
Alignment explanation
Indices: 2921689--2921733 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
2921679 ATGTTGCCTA
2921689 GTATCGATAC-CCTTACCATG
1 GTATCGATACACCTTACCATG
*
2921709 GTATCGATACTACCTTACTATG
1 GTATCGATAC-ACCTTACCATG
2921731 GTA
1 GTA
2921734 CTGATAACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (21 bp):
GTATCGATACACCTTACCATG
Found at i:2925541 original size:2 final size:2
Alignment explanation
Indices: 2925534--2925578 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
2925524 GTGAAAGTAC
*
2925534 TA TA TA TA TA AA 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
2925576 TA T
1 TA T
2925579 TTCACCAACG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 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):
TA
Found at i:2926017 original size:81 final size:81
Alignment explanation
Indices: 2925882--2926111 Score: 379
Period size: 81 Copynumber: 2.8 Consensus size: 81
2925872 CCTTTCATCA
* * *
2925882 TTTACTCAACTGTATCTCACTGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACA
1 TTTACTCAACAGTATTTAACTGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACA
2925947 GTTAGACCATTATTCT
66 GTTAGACCATTATTCT
* * *
2925963 TTTACTCAACAGTATTTAACCGTTCATCTAACTGGCAAAATTTGTACCTTTCTACCAATTGCACA
1 TTTACTCAACAGTATTTAACTGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACA
* *
2926028 GTCAGGCCATTATTCT
66 GTTAGACCATTATTCT
*
2926044 TTTACTCAACGGTATTTAACTGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACA
1 TTTACTCAACAGTATTTAACTGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACA
2926109 GTT
66 GTT
2926112 GGGCCTCAAA
Statistics
Matches: 136, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 136 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (81 bp):
TTTACTCAACAGTATTTAACTGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACA
GTTAGACCATTATTCT
Found at i:2926161 original size:68 final size:68
Alignment explanation
Indices: 2926048--2926254 Score: 222
Period size: 68 Copynumber: 3.0 Consensus size: 68
2926038 TATTCTTTTA
* * * ** *
2926048 CTCAACGGTATTTAA-CTGTTCATCTAACTGGCATA-ATTGGTACCTTTCTACCA-ATTGCACAG
1 CTCAAAGGTACTTAACCT-TTCATCTAACTGGCTTATA-TGACACCTTTCTACCATA-AGCACAG
*
2926110 TTGGGC
63 TTAGGC
**
2926116 CTCAAAGGTACTTAACCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCATAAGCACAGTTA
1 CTCAAAGGTACTTAACCTTTCATCTAACTGGCTTATATGACACCTTTCTACCATAAGCACAGTTA
*
2926181 GGT
66 GGC
* * * ** *
2926184 CTCAAAGGCACTTAGCCTTTCATCTAACCGGCTTATATGACACCTTTCTGTCATAAGCACAATTA
1 CTCAAAGGTACTTAACCTTTCATCTAACTGGCTTATATGACACCTTTCTACCATAAGCACAGTTA
2926249 GGC
66 GGC
2926252 CTC
1 CTC
2926255 TTAATCCATT
Statistics
Matches: 121, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
68 117 0.97
69 4 0.03
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (68 bp):
CTCAAAGGTACTTAACCTTTCATCTAACTGGCTTATATGACACCTTTCTACCATAAGCACAGTTA
GGC
Found at i:2926521 original size:54 final size:54
Alignment explanation
Indices: 2926462--2926611 Score: 158
Period size: 54 Copynumber: 2.7 Consensus size: 54
2926452 ACATATATTT
* * * *
2926462 CCCATACGAAAATTCATACAATTGATATTAATTTCTTA-TTTCGCACACATAGTG
1 CCCATACGGAAATTCATACACTT-ATATGAATTTCTTATTTTCGCACACAAAGTG
* * * *
2926516 CCCATACGGAAATTCCTACACTTAGTAGGATTTTCTTAATATTTTTGCACACAAAGTG
1 CCCATACGGAAATTCATACACTTA-TATGAATTTC-T--TATTTTCGCACACAAAGTG
2926574 CCCAATACGGAAATTCATACACTTAATATGAATTTCTT
1 CCC-ATACGGAAATTCATACACTT-ATATGAATTTCTT
2926612 TACATTTTGT
Statistics
Matches: 78, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
53 1 0.01
54 27 0.35
55 1 0.01
56 1 0.01
57 2 0.03
58 18 0.23
59 27 0.35
60 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.35
Consensus pattern (54 bp):
CCCATACGGAAATTCATACACTTATATGAATTTCTTATTTTCGCACACAAAGTG
Found at i:2926610 original size:59 final size:55
Alignment explanation
Indices: 2926462--2926613 Score: 171
Period size: 59 Copynumber: 2.7 Consensus size: 55
2926452 ACATATATTT
* * * * *
2926462 CCCATACGAAAATTCATACAATTGATATTAATTTC-TTATTTCGCACACATAGTG
1 CCCATACGGAAATTCATACACTTAATATGAATTTCTTTATTTCGCACACAAAGTG
* * * * *
2926516 CCCATACGGAAATTCCTACACTTAGTAGGATTTTCTTAATATTTTTGCACACAAAGTG
1 CCCATACGGAAATTCATACACTTAATATGAATTTCTT--TA-TTTCGCACACAAAGTG
2926574 CCCAATACGGAAATTCATACACTTAATATGAATTTCTTTA
1 CCC-ATACGGAAATTCATACACTTAATATGAATTTCTTTA
2926614 CATTTTGTAC
Statistics
Matches: 79, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
54 27 0.34
55 1 0.01
57 4 0.05
58 17 0.22
59 30 0.38
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (55 bp):
CCCATACGGAAATTCATACACTTAATATGAATTTCTTTATTTCGCACACAAAGTG
Found at i:2926620 original size:58 final size:56
Alignment explanation
Indices: 2926462--2926632 Score: 184
Period size: 58 Copynumber: 3.0 Consensus size: 56
2926452 ACATATATTT
* * * * *
2926462 CCCATACGAAAATTCATACAATTGATATTAATTTC-TT-ATTTCGCACACATAGTG
1 CCCATACGGAAATTCATACACTTAATATGAATTTCTTTAATTTTGCACACATAGTG
* * * * * *
2926516 CCCATACGGAAATTCCTACACTTAGTAGGATTTTCTTAATATTTTTGCACACAAAGTG
1 CCCATACGGAAATTCATACACTTAATATGAATTTCTT--TAATTTTGCACACATAGTG
*
2926574 CCCAATACGGAAATTCATACACTTAATATGAATTTCTTTACATTTTGTACACATAGTG
1 CCC-ATACGGAAATTCATACACTTAATATGAATTTCTTTA-ATTTTGCACACATAGTG
2926632 C
1 C
2926633 TATTTGGTAA
Statistics
Matches: 93, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
54 27 0.29
55 1 0.01
57 3 0.03
58 32 0.34
59 30 0.32
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.35
Consensus pattern (56 bp):
CCCATACGGAAATTCATACACTTAATATGAATTTCTTTAATTTTGCACACATAGTG
Found at i:2927147 original size:94 final size:96
Alignment explanation
Indices: 2926990--2927180 Score: 237
Period size: 95 Copynumber: 2.0 Consensus size: 96
2926980 ATACTTCTAT
* * ** *
2926990 ACTATGGTACCGATACCCCTTTCAGGTATTGATACCAAAAATAGGTTCGATGTTGCCTAGTATCG
1 ACTATGGTACCGATACCCCATACAGGTATCAATACCAAAAATAGATTCGATGTTGCCTAGTATCG
* *
2927055 ATA-CCCTTACCATGGTATCGATATTACCTC
66 ATACCCCTAACAATGGTATCGATATTACCTC
* *
2927085 ACTATGGTACCGATA-CCCATACCGGTATCAATACC-AAAATTGTATTCGATGTTG-CTAGGTAT
1 ACTATGGTACCGATACCCCATACAGGTATCAATACCAAAAATAG-ATTCGATGTTGCCTA-GTAT
* *
2927147 CGATACCCCTAATAATGGTATTGATATTACCTC
64 CGATACCCCTAACAATGGTATCGATATTACCTC
2927180 A
1 A
2927181 TCGATATCGA
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
93 9 0.11
94 34 0.41
95 39 0.48
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (96 bp):
ACTATGGTACCGATACCCCATACAGGTATCAATACCAAAAATAGATTCGATGTTGCCTAGTATCG
ATACCCCTAACAATGGTATCGATATTACCTC
Found at i:2933207 original size:23 final size:23
Alignment explanation
Indices: 2933165--2933224 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
2933155 CTAAATTGAA
*
2933165 AAAAATGAAAAGAA-AGAAAAGAG
1 AAAAATGAAAA-AAGAGAAAAAAG
*
2933188 AAAAATGAAAAAAGATAAAAAAG
1 AAAAATGAAAAAAGAGAAAAAAG
*
2933211 AAATA-GAAAAAAGA
1 AAAAATGAAAAAAGA
2933225 AATAAGGTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 11 0.33
23 22 0.67
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (23 bp):
AAAAATGAAAAAAGAGAAAAAAG
Found at i:2933222 original size:13 final size:13
Alignment explanation
Indices: 2933204--2933228 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2933194 GAAAAAAGAT
2933204 AAAAAAGAAATAG
1 AAAAAAGAAATAG
2933217 AAAAAAGAAATA
1 AAAAAAGAAATA
2933229 AGGTGGGTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (13 bp):
AAAAAAGAAATAG
Found at i:2933847 original size:21 final size:22
Alignment explanation
Indices: 2933823--2933863 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2933813 ACATTTGAAG
*
2933823 AATTCAAGA-TCGAGAATCAGA
1 AATTCAAGATTCAAGAATCAGA
2933844 AATTCAAGATTCAAGAATCA
1 AATTCAAGATTCAAGAATCA
2933864 AGAGTCACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.22
Consensus pattern (22 bp):
AATTCAAGATTCAAGAATCAGA
Found at i:2935188 original size:13 final size:13
Alignment explanation
Indices: 2935170--2935194 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2935160 CAAAAAACAA
2935170 AAGAAATATTGAC
1 AAGAAATATTGAC
2935183 AAGAAATATTGA
1 AAGAAATATTGA
2935195 GAAAAATACG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.16, T:0.24
Consensus pattern (13 bp):
AAGAAATATTGAC
Found at i:2935894 original size:9 final size:8
Alignment explanation
Indices: 2935850--2935920 Score: 58
Period size: 8 Copynumber: 8.8 Consensus size: 8
2935840 ACTTAATTCC
2935850 ATTTTTTT
1 ATTTTTTT
2935858 ATTTTGTTT
1 ATTTT-TTT
2935867 -TTGTTTTT
1 ATT-TTTTT
2935875 A-TTTTTT
1 ATTTTTTT
2935882 ATTTTTTT
1 ATTTTTTT
2935890 AATTTTTATT
1 -ATTTTT-TT
* *
2935900 A-TTATAT
1 ATTTTTTT
2935907 ATTTTTTT
1 ATTTTTTT
*
2935915 CTTTTT
1 ATTTTT
2935921 ATAGCGTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
7 8 0.16
8 29 0.57
9 12 0.24
10 2 0.04
ACGTcount: A:0.15, C:0.01, G:0.03, T:0.80
Consensus pattern (8 bp):
ATTTTTTT
Found at i:2936052 original size:20 final size:19
Alignment explanation
Indices: 2936019--2936073 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 19
2936009 TATGTATTAG
2936019 TATTT-TTTATTTTTATTATT
1 TATTTATTTA-TTTTATT-TT
2936039 TATTTATTTATTTTATTTT
1 TATTTATTTATTTTATTTT
2936058 TATGTTATTTGATTTT
1 TAT-TTATTT-ATTTT
2936074 TTTAATTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.16
20 18 0.56
21 9 0.28
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (19 bp):
TATTTATTTATTTTATTTT
Found at i:2936073 original size:15 final size:15
Alignment explanation
Indices: 2936019--2936074 Score: 52
Period size: 16 Copynumber: 4.1 Consensus size: 15
2936009 TATGTATTAG
2936019 TATTT-TTT-ATTTT
1 TATTTATTTGATTTT
2936032 TA-TTATTT-A--TT
1 TATTTATTTGATTTT
*
2936043 TATTTATTTTATTTT
1 TATTTATTTGATTTT
2936058 TATGTTATTTGATTTT
1 TAT-TTATTTGATTTT
2936074 T
1 T
2936075 TTAATTTAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
11 4 0.11
12 8 0.22
13 7 0.19
15 5 0.14
16 12 0.33
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.77
Consensus pattern (15 bp):
TATTTATTTGATTTT
Found at i:2936767 original size:13 final size:13
Alignment explanation
Indices: 2936749--2936775 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2936739 CACAAAAAAC
2936749 ACAAGAAATATTG
1 ACAAGAAATATTG
2936762 ACAAGAAATATTG
1 ACAAGAAATATTG
2936775 A
1 A
2936776 GAAAAATACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (13 bp):
ACAAGAAATATTG
Found at i:2937453 original size:18 final size:18
Alignment explanation
Indices: 2937430--2937480 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
2937420 TTAATTCCAT
*
2937430 TTTTTTATTTTTTATTTA
1 TTTTTTATTTTTTATATA
*
2937448 TTTTTTA-TTATTATATA
1 TTTTTTATTTTTTATATA
2937465 TTTTTT-TCTTTTTATA
1 TTTTTTAT-TTTTTATA
2937481 GCGTTTTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTATTTTTTATATA
Found at i:2937603 original size:17 final size:17
Alignment explanation
Indices: 2937581--2937639 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
2937571 ATTAGTATTC
2937581 TTTATTT-TTATTATTTA
1 TTTATTTATT-TTATTTA
2937598 TTTATTTATTTTA-TT-
1 TTTATTTATTTTATTTA
* *
2937613 TTTATGTTATTTGATTTT
1 TTTAT-TTATTTTATTTA
2937631 TTTAATTTA
1 TTT-ATTTA
2937640 GTTAACTTCC
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
15 5 0.14
16 9 0.25
17 12 0.33
18 8 0.22
19 2 0.06
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTATTTATTTTATTTA
Found at i:2937609 original size:20 final size:20
Alignment explanation
Indices: 2937581--2937630 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 20
2937571 ATTAGTATTC
2937581 TTTATTTTTATTATTTAT-TTA
1 TTTA-TTTTATT-TTTATGTTA
2937602 TTTATTTTATTTTTATGTTA
1 TTTATTTTATTTTTATGTTA
2937622 TTTGATTTT
1 TTT-ATTTT
2937631 TTTAATTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.19
20 13 0.48
21 9 0.33
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (20 bp):
TTTATTTTATTTTTATGTTA
Found at i:2937624 original size:16 final size:15
Alignment explanation
Indices: 2937598--2937631 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2937588 TTATTATTTA
*
2937598 TTTATTTATTTTATT
1 TTTATTTATTTGATT
2937613 TTTATGTTATTTGATT
1 TTTAT-TTATTTGATT
2937629 TTT
1 TTT
2937632 TTAATTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (15 bp):
TTTATTTATTTGATT
Found at i:2939320 original size:19 final size:19
Alignment explanation
Indices: 2939293--2939329 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2939283 ATGACCAACA
*
2939293 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
2939312 AAATTGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
2939330 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:2939437 original size:21 final size:21
Alignment explanation
Indices: 2939397--2939437 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2939387 TTTCTAAATA
** *
2939397 TTGCGATTTTCTAAATTCGCG
1 TTGCGATTTTAGAAAATCGCG
2939418 TTGCGATTTTAGAAAATCGC
1 TTGCGATTTTAGAAAATCGC
2939438 AATGCGAATA
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:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (21 bp):
TTGCGATTTTAGAAAATCGCG
Found at i:2939731 original size:19 final size:20
Alignment explanation
Indices: 2939707--2939747 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
2939697 AAATTTATGT
2939707 TAGTCCAAATT-CGTTGCGA
1 TAGTCCAAATTACGTTGCGA
*
2939726 TAGTCCAAGTTCACGTTGCGA
1 TAGTCCAAATT-ACGTTGCGA
2939747 T
1 T
2939748 TTCTTAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
21 9 0.47
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (20 bp):
TAGTCCAAATTACGTTGCGA
Found at i:2939818 original size:6 final size:6
Alignment explanation
Indices: 2939807--2939831 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2939797 GAGACGTATT
2939807 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
2939832 TCATGACCCG
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:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2940183 original size:22 final size:21
Alignment explanation
Indices: 2940158--2940214 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 21
2940148 ACTATCGCAA
*
2940158 CAACACGTTTTTCAAACTCTCG
1 CAACAC-TTTTTCAAACTATCG
*
2940180 CAACACATTTT--AACTATCG
1 CAACACTTTTTCAAACTATCG
*
2940199 CAACATATTTTTCAAA
1 CAACA-CTTTTTCAAA
2940215 ATCGTGTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 4 0.14
22 8 0.29
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.33
Consensus pattern (21 bp):
CAACACTTTTTCAAACTATCG
Found at i:2940199 original size:19 final size:19
Alignment explanation
Indices: 2940172--2940209 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2940162 ACGTTTTTCA
*
2940172 AACTCTCGCAACACATTTT
1 AACTATCGCAACACATTTT
*
2940191 AACTATCGCAACATATTTT
1 AACTATCGCAACACATTTT
2940210 TCAAAATCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.34
Consensus pattern (19 bp):
AACTATCGCAACACATTTT
Found at i:2941039 original size:3 final size:3
Alignment explanation
Indices: 2941026--2941065 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
2941016 AAACCTTTCG
*
2941026 AGA AAA AGA AGA AGA AGA AGA AGA AGA AGA AGAA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA
2941066 GGAGATTGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2945230 original size:3 final size:3
Alignment explanation
Indices: 2945214--2945313 Score: 112
Period size: 3 Copynumber: 32.7 Consensus size: 3
2945204 TTTGGGCTTG
* * *
2945214 TAA TAA TATT TAA TAA TAA TAT TAA TAA TAAA TAA TAA TAT TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* * *
2945261 TAA TAA TTA TAA TTA TAA TAA TTA TAA TAA TAA TAA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
2945309 TAA TA
1 TAA TA
2945314 TTTAAATGAA
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.02
3 72 0.89
4 7 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:2945671 original size:124 final size:121
Alignment explanation
Indices: 2945447--2945731 Score: 348
Period size: 124 Copynumber: 2.4 Consensus size: 121
2945437 ATGTTGAATA
* * *
2945447 AATTCTTCTCT-TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGTTGAC
1 AATTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGCTAAC
* * * *
2945511 CTATTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTT-ATTATG
66 CTATCTCCTTCTGTGATAGAATCATACAAAAGGTTGAACAAGCTCTT-TTCATTATG
* *
2945567 AACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCTGGAAAGGTTGATGC
1 AA-TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGG---GGATGATGC
* * * *
2945631 TAATCTATCTGCTTCTGTGATAGAATTATACAAAAGGTTGAACAAGCTCTTTTCATTGTG
62 TAACCTATCTCCTTCTGTGATAGAATCATACAAAAGGTTGAACAAGCTCTTTTCATTATG
* *
2945691 AA--CTT-ATTCTTCTTCAGATTAGTTCTTCTCATTATGAACTT
1 AATTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
2945732 CTTCTTCAGA
Statistics
Matches: 144, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
120 36 0.25
121 16 0.11
122 33 0.23
123 2 0.01
124 57 0.40
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.42
Consensus pattern (121 bp):
AATTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGCTAAC
CTATCTCCTTCTGTGATAGAATCATACAAAAGGTTGAACAAGCTCTTTTCATTATG
Found at i:2945718 original size:16 final size:16
Alignment explanation
Indices: 2945697--2945752 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
2945687 TGTGAACTTA
*
2945697 TTCTTCTTCAGATTAG
1 TTCTTCTTCAGATAAG
* *
2945713 TTCTTC-TCATTATGAAC
1 TTCTTCTTCA-GAT-AAG
*
2945730 TTCTTCTTCAGATGAG
1 TTCTTCTTCAGATAAG
2945746 TTCTTCT
1 TTCTTCT
2945753 CATTATGAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
15 3 0.10
16 16 0.52
17 9 0.29
18 3 0.10
ACGTcount: A:0.18, C:0.21, G:0.11, T:0.50
Consensus pattern (16 bp):
TTCTTCTTCAGATAAG
Found at i:2945730 original size:36 final size:35
Alignment explanation
Indices: 2945678--2945765 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 35
2945668 TTGAACAAGC
* * *
2945678 TCTTTTCATTGTGAACTTATTCTTCTTCAGATTAGT
1 TCTTCTCATTATGAACTT-TTCTTCTTCAGATGAGT
2945714 TCTTCTCATTATGAAC--TTCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTTTCTTCTTCAGATGAGT
2945747 TCTTCTCATTATGAACTTT
1 TCTTCTCATTATGAACTTT
2945766 CTCTAGAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
33 32 0.68
35 1 0.02
36 14 0.30
ACGTcount: A:0.20, C:0.19, G:0.10, T:0.50
Consensus pattern (35 bp):
TCTTCTCATTATGAACTTTTCTTCTTCAGATGAGT
Found at i:2945735 original size:17 final size:17
Alignment explanation
Indices: 2945713--2945764 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
2945703 TTCAGATTAG
2945713 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
* *
2945730 TTCTTCTTCA-GATG-AG
1 TTCTTC-TCATTATGAAC
2945746 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
2945763 TT
1 TT
2945765 TCTCTAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 3 0.11
16 10 0.36
17 12 0.43
18 3 0.11
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:2945739 original size:33 final size:33
Alignment explanation
Indices: 2945697--2945764 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
2945687 TGTGAACTTA
*
2945697 TTCTTCTTCAGATTAGTTCTTCTCATTATGAAC
1 TTCTTCTTCAGATGAGTTCTTCTCATTATGAAC
2945730 TTCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TTCTTCTTCAGATGAGTTCTTCTCATTATGAAC
2945763 TT
1 TT
2945765 TCTCTAGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.49
Consensus pattern (33 bp):
TTCTTCTTCAGATGAGTTCTTCTCATTATGAAC
Found at i:2945864 original size:116 final size:113
Alignment explanation
Indices: 2945732--2946633 Score: 1142
Period size: 113 Copynumber: 8.0 Consensus size: 113
2945722 TTATGAACTT
* *
2945732 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGCTGATCTATCAAGTGATGGA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGA
*
2945797 TTTGAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
66 TTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
* * * * *
2945845 CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGA
1 CTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAGTGA
* ** *
2945909 TGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
62 TGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
*
2945961 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCAAGTGATGGA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGA
* * * *
2946026 TTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTT
66 TTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
* * * * *
2946074 CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGA
1 CTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAGTGA
* ** *
2946138 TGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC
62 TGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
* * *
2946190 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACCGATCCATCAAGTGATGGT
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGA
* *
2946255 TTTGAACAAAAAGTTGAATAAATTCTTCTCATTATGAA--T-TTGTT-
66 TTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
**** * * * *
2946299 C-T-TTCAGATGAGTTCTTCTCATTATGAACTCGAACTAGAAATGTTGATCCATTGAA-TGAT-G
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCA-TCAAGTGATGG
* * *
2946360 AATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC
65 ATTTGAA-CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
* * * * * *
2946410 ATTCTTCAGATGAGTTCTTCTCATTATGAACTTGAC-CTGGTAATGCTGATCCATCAAATGATGA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTT-TCTCTGGAAAAGCTGATCCATCAAGTGATGG
** *
2946474 ATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC
65 ATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
2946523 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGA
* * *
2946588 TTTGAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTTTTCT
66 TTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
2946634 GGAAAAGCTG
Statistics
Matches: 679, Mismatches: 88, Indels: 44
0.84 0.11 0.05
Matches are distributed among these distances:
106 5 0.01
107 74 0.11
108 4 0.01
109 2 0.00
110 8 0.01
111 1 0.00
112 9 0.01
113 372 0.55
114 4 0.01
116 196 0.29
117 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGA
TTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
Found at i:2945991 original size:229 final size:226
Alignment explanation
Indices: 2945732--2946633 Score: 1307
Period size: 229 Copynumber: 4.0 Consensus size: 226
2945722 TTATGAACTT
* * *
2945732 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGCTGATCTATCAAGTGATGGA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCAAGTGATGGA
*
2945797 TTTGAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAG
66 TTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAG
* *
2945862 TTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGT
128 TTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGT
*
2945927 TGAACAAATTCTTCTCATTATGAACTTCTTCTTC
193 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTC
2945961 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCAAGTGATGGA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCAAGTGATGGA
* * * *
2946026 TTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGACGAG
66 TTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAG
*
2946091 TTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGT
128 TTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGT
2946156 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTC
193 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTC
* *
2946190 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACCGATCCATCAAGTGATGGT
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCAAGTGATGGA
* *
2946255 TTTGAACAAAAAGTTGAATAAATTCTTCTCATTATGAA--T-TTGTT-C-T-TTCAGATGAGTTC
66 TTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
* * * ** *
2946314 TTCTCATTATGAACTCGAACTAGAAATGTTGATCCATTGAATGATGAATTCAAGCAAAAAGTTGA
131 TTCTCATTATGAACTCTACCTGGAAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGA
2946379 ACAAGTTCTTCTCATTATGAACTTCTTCTTC
196 ACAAGTTCTTCTCATTATGAACTTCTTCTTC
* * * ** * *
2946410 ATTCTTCAGATGAGTTCTTCTCATTATGAACTTGAC-CTGGTAATGCTGATCCATCAAATGATGA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTT-TCTCTGGAAAAACTGATCCATCAAGTGATGG
** *
2946474 ATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT
65 ATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT
* * * * * ** *
2946539 CTTCTCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAAGTT
130 CTTCTCATTATGAACTCTAC-CTGGAAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTT
*
2946603 GAACAAGTTCTTCTCATTATGAACTTTTTCT
194 GAACAAGTTCTTCTCATTATGAACTTCTTCT
2946634 GGAAAAGCTG
Statistics
Matches: 617, Mismatches: 48, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
220 183 0.30
221 1 0.00
222 1 0.00
223 11 0.02
224 2 0.00
225 2 0.00
226 97 0.16
227 1 0.00
229 319 0.52
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (226 bp):
CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCAAGTGATGGA
TTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
TTCTCATTATGAACTCTACCTGGAAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGA
ACAAGTTCTTCTCATTATGAACTTCTTCTTC
Found at i:2947124 original size:22 final size:22
Alignment explanation
Indices: 2947045--2947121 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
2947035 CATAAAGCTT
2947045 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* * *
2947067 TCATATTTAAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATCTA
* *
2947089 TCATTTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
2947111 TCATCTTTGAA
1 TCATCTTTGAA
2947122 GAGTGTAGAT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2947599 original size:54 final size:53
Alignment explanation
Indices: 2947469--2947677 Score: 225
Period size: 54 Copynumber: 4.0 Consensus size: 53
2947459 ATCAGAATAG
* * *
2947469 CAGA-TTCGTAAAACATTTGACAATACATTCATCTTTTCCTGT-GTTATCTG-T
1 CAGAGTTCGTAAAACATTTGACAACACATTCATATTTTTCTGTGGTT-TCTGCT
* * *
2947520 C-GAGAT-GTAAAACACTTGACAACACATTCATATTTTTCTGTGGCTTCTGCT
1 CAGAGTTCGTAAAACATTTGACAACACATTCATATTTTTCTGTGGTTTCTGCT
**
2947571 CAGATGTTCGTAAAACATTTGACAACACATTCAT-CCTTTCTTGTGGTTTCTGCT
1 CAGA-GTTCGTAAAACATTTGACAACACATTCATATTTTTC-TGTGGTTTCTGCT
* * *
2947625 TAGACGTTCGTAAAGCGTTTGACAACACATTCATCA-TTTTCTGTGGTTTCTGC
1 CAGA-GTTCGTAAAACATTTGACAACACATTCAT-ATTTTTCTGTGGTTTCTGC
2947678 CAAGATTTCT
Statistics
Matches: 133, Mismatches: 16, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
50 37 0.28
51 6 0.05
52 2 0.02
53 6 0.05
54 78 0.59
55 4 0.03
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.38
Consensus pattern (53 bp):
CAGAGTTCGTAAAACATTTGACAACACATTCATATTTTTCTGTGGTTTCTGCT
Found at i:2947602 original size:104 final size:107
Alignment explanation
Indices: 2947473--2947677 Score: 267
Period size: 104 Copynumber: 1.9 Consensus size: 107
2947463 GAATAGCAGA
* * *
2947473 TTCGTAAAACATTTGACAATACATTCATCTTTTCCTGT-GTTATCTG-TCGA-GAT-GTAAAACA
1 TTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTT-TCTGCTAGACGATCGTAAAACA
2947534 CTTGACAACACATTCAT-ATTTTTCTGTGGCTTCTGCTCAGATG
65 CTTGACAACACATTCATCA-TTTTCTGTGGCTTCTGCTCAGATG
* * * *
2947577 TTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTCTGCTTAGACGTTCGTAAAGCG
1 TTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGC-TAGACGATCGTAAAACA
* *
2947642 TTTGACAACACATTCATCATTTTCTGTGGTTTCTGC
65 CTTGACAACACATTCATCATTTTCTGTGGCTTCTGC
2947678 CAAGATTTCT
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
104 39 0.45
105 3 0.03
106 3 0.03
107 2 0.02
108 38 0.44
109 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (107 bp):
TTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTAGACGATCGTAAAACAC
TTGACAACACATTCATCATTTTCTGTGGCTTCTGCTCAGATG
Found at i:2949864 original size:114 final size:114
Alignment explanation
Indices: 2949653--2949872 Score: 354
Period size: 114 Copynumber: 1.9 Consensus size: 114
2949643 GATCATGCAG
* * *
2949653 TTCATCTTTCAATTTCAATGATTGGTTATGGGATTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAATCTCAATGATTGGTTATGGGATTCATACCAAACCAGATCAGATAACTCAAAGA
*
2949718 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAACAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAACAAA
* *
2949767 TTCATCTTTCAAATCT-AATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTC-AATCTCAATGATTGGTTATGGGATTCATACCAAACCAGATCAGATAACTCAAAG
2949831 AACACTTCCAGAAGATGCTATTAGGG-CTCCTTATTTCTACTA
65 AACACTTCCAGAAGATGCTATT-GGGTCTCCTTATTTCTACTA
2949873 CGAGAATGTG
Statistics
Matches: 98, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
114 91 0.93
115 7 0.07
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAATCTCAATGATTGGTTATGGGATTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAACAAA
Found at i:2952134 original size:11 final size:11
Alignment explanation
Indices: 2952115--2952144 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2952105 CTTGATTCAA
*
2952115 TTTTCCTTTTT
1 TTTTTCTTTTT
2952126 TTTTTCTTTTT
1 TTTTTCTTTTT
2952137 TTTTTCTT
1 TTTTTCTT
2952145 CTTTCTTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTCTTTTT
Done.