Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005274.1 Hibiscus syriacus cultivar Beakdansim tig00011922_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: 315540
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:195405 original size:29 final size:30
Alignment explanation
Indices: 195345--195417 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 30
195335 CTGCATGGAT
*
195345 TGCATGGCGACCTACCTAGGTCGCTGGGCG
1 TGCATGGCGACCTACCTAAGTCGCTGGGCG
**
195375 TGCATGGCGACCT-GGTAAGTCGCTGGGCG
1 TGCATGGCGACCTACCTAAGTCGCTGGGCG
*
195404 TGCATGACGACCTA
1 TGCATGGCGACCTA
195418 TATGGGGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 25 0.66
30 13 0.34
ACGTcount: A:0.16, C:0.27, G:0.36, T:0.21
Consensus pattern (30 bp):
TGCATGGCGACCTACCTAAGTCGCTGGGCG
Found at i:196258 original size:12 final size:12
Alignment explanation
Indices: 196241--196268 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
196231 ATATTTAATA
196241 AATTAAATTTCT
1 AATTAAATTTCT
196253 AATTAAATTTCT
1 AATTAAATTTCT
196265 AATT
1 AATT
196269 TATTGTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTAAATTTCT
Found at i:196549 original size:51 final size:53
Alignment explanation
Indices: 196407--196554 Score: 158
Period size: 53 Copynumber: 2.8 Consensus size: 53
196397 GCATAAGTGC
* * * * * *
196407 TACATTTTTATTTTATTTTATCCACTTACCTTGATGTAAATATATATTAAGTGT
1 TACA-TTTTATTTTATTTTATTCACTTACATCGATGTAAGTATGTATTAAATGT
* ** *
196461 TACATTTTATTTTATTTTATTTACTTATGTCGATGTAAGTATGTGTTAAAT-T
1 TACATTTTATTTTATTTTATTCACTTACATCGATGTAAGTATGTATTAAATGT
*
196513 CTACA-TTT-TTTTATTTTATTCACTTACATCGTTGTAAGTATG
1 -TACATTTTATTTTATTTTATTCACTTACATCGATGTAAGTATG
196555 CGCTAAGTGA
Statistics
Matches: 80, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
51 30 0.38
52 4 0.05
53 42 0.52
54 4 0.05
ACGTcount: A:0.27, C:0.10, G:0.09, T:0.53
Consensus pattern (53 bp):
TACATTTTATTTTATTTTATTCACTTACATCGATGTAAGTATGTATTAAATGT
Found at i:196569 original size:51 final size:50
Alignment explanation
Indices: 196453--196627 Score: 181
Period size: 53 Copynumber: 3.4 Consensus size: 50
196443 TAAATATATA
* * *
196453 TTAAGTGTTACATTTTATTTTATTTTATTTACTTATGTCGATGTAAGTATGTG
1 TTAAGTGTTACA-TTT-TTTTATTTTATTCACTTATATCG-TGTAAGTATGCG
* *
196506 TTAAAT-TCTACATTTTTTTATTTTATTCACTTACATCGTTGTAAGTATGCG
1 TTAAGTGT-TACATTTTTTTATTTTATTCACTTATATCG-TGTAAGTATGCG
* * * * *
196557 CTAAGTGATACATTTTTTAAAATTTTACTCACTTATACCAGTGTAAGTATGCG
1 TTAAGTGTTACATTTTTT--TATTTTATTCACTTATATC-GTGTAAGTATGCG
196610 TTAAGTGTTACATTTTTT
1 TTAAGTGTTACATTTTTT
196628 AAGTATGAAT
Statistics
Matches: 102, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
51 45 0.44
52 4 0.04
53 52 0.51
54 1 0.01
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.50
Consensus pattern (50 bp):
TTAAGTGTTACATTTTTTTATTTTATTCACTTATATCGTGTAAGTATGCG
Found at i:199618 original size:27 final size:29
Alignment explanation
Indices: 199587--199649 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 29
199577 AAAATTTTAT
**
199587 TATTATTTTTAATATTTTTTGAT-AAAAA
1 TATTATTTAAAATATTTTTTGATCAAAAA
* *
199615 -ATTACTTAAAATATTTTTTTATCAAAAA
1 TATTATTTAAAATATTTTTTGATCAAAAA
199643 TATTATT
1 TATTATT
199650 ATTAGACGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 18 0.64
28 5 0.18
29 5 0.18
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (29 bp):
TATTATTTAAAATATTTTTTGATCAAAAA
Found at i:199703 original size:12 final size:12
Alignment explanation
Indices: 199686--199710 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
199676 ATATATCTGG
199686 TAAAAAATTATT
1 TAAAAAATTATT
199698 TAAAAAATTATT
1 TAAAAAATTATT
199710 T
1 T
199711 TTTTTCTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAAATTATT
Found at i:201375 original size:18 final size:18
Alignment explanation
Indices: 201354--201398 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
201344 TTTATTAATA
201354 AAAAATTGAGAGTGAACT
1 AAAAATTGAGAGTGAACT
*
201372 AAAAATTTTGAGAGTGAATT
1 AAAAA--TTGAGAGTGAACT
201392 AAAAATT
1 AAAAATT
201399 TTGAGATGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 7 0.29
20 17 0.71
ACGTcount: A:0.51, C:0.02, G:0.18, T:0.29
Consensus pattern (18 bp):
AAAAATTGAGAGTGAACT
Found at i:201409 original size:21 final size:20
Alignment explanation
Indices: 201359--201409 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
201349 TAATAAAAAA
201359 TTGAGAGTGAACTAAAAATT
1 TTGAGAGTGAACTAAAAATT
*
201379 TTGAGAGTGAATTAAAAATT
1 TTGAGAGTGAACTAAAAATT
201399 TTGAGATGTGA
1 TTGAGA-GTGA
201410 CGATTATTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 25 0.86
21 4 0.14
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (20 bp):
TTGAGAGTGAACTAAAAATT
Found at i:201533 original size:31 final size:30
Alignment explanation
Indices: 201498--201564 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 30
201488 AATTTAATGA
*
201498 TCAAATTGATATTTTATCTAAAGTTTAAAGG
1 TCAAATTAATATTTTATCT-AAGTTTAAAGG
* * *
201529 TCAAAATAATATTTTATCTAATTTTAACGG
1 TCAAATTAATATTTTATCTAAGTTTAAAGG
201559 TCAAAT
1 TCAAAT
201565 AAAAAATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 14 0.45
31 17 0.55
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (30 bp):
TCAAATTAATATTTTATCTAAGTTTAAAGG
Found at i:201561 original size:30 final size:31
Alignment explanation
Indices: 201506--201563 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
201496 GATCAAATTG
201506 ATATTTTATCTAAAGTTTAAAGGTCAAAATA
1 ATATTTTATCTAAAGTTTAAAGGTCAAAATA
* *
201537 ATATTTTATCT-AATTTTAACGGTCAAA
1 ATATTTTATCTAAAGTTTAAAGGTCAAA
201564 TAAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (31 bp):
ATATTTTATCTAAAGTTTAAAGGTCAAAATA
Found at i:220095 original size:20 final size:20
Alignment explanation
Indices: 220043--220113 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
220033 AAATGACTAA
*
220043 CAAATTCGCAACAC-GAACT
1 CAAATTCGCAACACAGAAGT
* **
220062 CCAATTTCATAACACAGAAGT
1 -CAAATTCGCAACACAGAAGT
*
220083 CAAATTCGCAACACATAAGT
1 CAAATTCGCAACACAGAAGT
220103 CAAATTCGCAA
1 CAAATTCGCAA
220114 AGTGCGTTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 38 0.90
21 4 0.10
ACGTcount: A:0.44, C:0.27, G:0.10, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACACAGAAGT
Found at i:220296 original size:22 final size:22
Alignment explanation
Indices: 220260--220313 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
220250 TCACTCTCTA
* *
220260 CGACGACATCCGTCCCCATCTC
1 CGACGAAATCTGTCCCCATCTC
*
220282 CGATGAAATCTGTCCCCATCTC
1 CGACGAAATCTGTCCCCATCTC
220304 CGACGAAATC
1 CGACGAAATC
220314 CGTCTCTCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.24, C:0.41, G:0.15, T:0.20
Consensus pattern (22 bp):
CGACGAAATCTGTCCCCATCTC
Found at i:222287 original size:21 final size:21
Alignment explanation
Indices: 222244--222293 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
222234 GTTAGGGGAG
*
222244 TTACGTGATGAGATCAGTGCT
1 TTACGTGATGAGATCAGTACT
* * *
222265 TTGCGTGATGAGGTCGGTACT
1 TTACGTGATGAGATCAGTACT
222286 TTACGTGA
1 TTACGTGA
222294 CGACAATGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGATCAGTACT
Found at i:222290 original size:42 final size:41
Alignment explanation
Indices: 222244--222339 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 41
222234 GTTAGGGGAG
* *
222244 TTACGTGATGAGATCAGTGCTTTGCGTGATGAGGT-CGGTACT
1 TTACGTGATGAGATCA-TGCATGGCGTGATGAGGTACGGT-CT
* * *
222286 TTACGTGACGACAATGATGCATGGCGTGATGAGGTACGGTCT
1 TTACGTGATGA-GATCATGCATGGCGTGATGAGGTACGGTCT
*
222328 TTATGTGATGAG
1 TTACGTGATGAG
222340 GTAGATGCTT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
42 37 0.84
43 7 0.16
ACGTcount: A:0.22, C:0.14, G:0.33, T:0.31
Consensus pattern (41 bp):
TTACGTGATGAGATCATGCATGGCGTGATGAGGTACGGTCT
Found at i:222350 original size:21 final size:21
Alignment explanation
Indices: 222311--222354 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
222301 GATGCATGGC
*
222311 GTGATGAGGTACGGTCTTTAT
1 GTGATGAGGTACGATCTTTAT
222332 GTGATGAGGTA-GATGCTTTAT
1 GTGATGAGGTACGAT-CTTTAT
222353 GT
1 GT
222355 CGAGTTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.20, C:0.07, G:0.34, T:0.39
Consensus pattern (21 bp):
GTGATGAGGTACGATCTTTAT
Found at i:222498 original size:21 final size:21
Alignment explanation
Indices: 222472--222543 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
222462 ACCTGTCATC
222472 ATTCAAGAGGCCCCTCCCACT
1 ATTCAAGAGGCCCCTCCCACT
* **
222493 ATTCAAGAGTCCCCTGTCA-T
1 ATTCAAGAGGCCCCTCCCACT
* *
222513 CGTTCAAGAGGTCCCTCCCACT
1 -ATTCAAGAGGCCCCTCCCACT
*
222535 GTTCAAGAG
1 ATTCAAGAG
222544 CCCGATTCAC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.02
21 39 0.95
22 1 0.02
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.24
Consensus pattern (21 bp):
ATTCAAGAGGCCCCTCCCACT
Found at i:222510 original size:42 final size:42
Alignment explanation
Indices: 222463--222543 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
222453 GCCTGATTCA
222463 CCTGTCATCATTCAAGAGGCCCCTCCCACTATTCAAGAGTCC
1 CCTGTCATCATTCAAGAGGCCCCTCCCACTATTCAAGAGTCC
* * *
222505 CCTGTCATCGTTCAAGAGGTCCCTCCCACTGTTCAAGAG
1 CCTGTCATCATTCAAGAGGCCCCTCCCACTATTCAAGAG
222544 CCCGATTCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (42 bp):
CCTGTCATCATTCAAGAGGCCCCTCCCACTATTCAAGAGTCC
Found at i:226665 original size:24 final size:24
Alignment explanation
Indices: 226631--226698 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
226621 CTGAAGCATC
226631 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
226655 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
226679 ATCAAATTTCGAATATTGAC
1 ATCAAAATCCGAGTATTGAC
226699 TAGTACTCAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:227657 original size:20 final size:20
Alignment explanation
Indices: 227632--227765 Score: 100
Period size: 20 Copynumber: 6.7 Consensus size: 20
227622 AAATAAAACC
227632 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
*
227652 TGTTGCG-AATTCAAAAATCG
1 TGTTGCGAAATT-AAAATTCG
* **
227672 AGTTGCGAAAACAAAATTCG
1 TGTTGCGAAATTAAAATTCG
227692 TGTTGCG-AATTCAGAAA-TCG
1 TGTTGCGAAATT-A-AAATTCG
* * *
227712 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAAATTAAAATTC-G
227733 TGTTGC-AAATTTGGAAAA-T-G
1 TGTTGCGAAA-TT--AAAATTCG
227753 TGTTGCGAAATTA
1 TGTTGCGAAATTA
227766 GAGTTTGCGT
Statistics
Matches: 89, Mismatches: 14, Indels: 24
0.70 0.11 0.19
Matches are distributed among these distances:
18 1 0.01
19 9 0.10
20 56 0.63
21 19 0.21
22 1 0.01
23 3 0.03
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.31
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:227678 original size:40 final size:40
Alignment explanation
Indices: 227633--227765 Score: 160
Period size: 40 Copynumber: 3.3 Consensus size: 40
227623 AATAAAACCT
227633 GTTGCGAAATTAAAATTCGTGTTGCGAATTCAAAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCAAAAATCGA
** *
227673 GTTGCGAAAACAAAATTCGTGTTGCGAATTCAGAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCAAAAATCGA
* * * ** *
227713 GTTGCGAATTTGAAATTCAGTGTTGCAAATTTGGAAAAT-GT
1 GTTGCGAAATTAAAATTC-GTGTTGCGAA-TTCAAAAATCGA
227754 GTTGCGAAATTA
1 GTTGCGAAATTA
227766 GAGTTTGCGT
Statistics
Matches: 77, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
40 51 0.66
41 20 0.26
42 6 0.08
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (40 bp):
GTTGCGAAATTAAAATTCGTGTTGCGAATTCAAAAATCGA
Found at i:229487 original size:2 final size:2
Alignment explanation
Indices: 229480--229506 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
229470 TTCATCACTT
229480 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
229507 TATCTTATTT
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:229820 original size:24 final size:24
Alignment explanation
Indices: 229771--229824 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
229761 GTTAATAAAC
229771 TTATTTTCTTTGCATTATTTTATTT
1 TTATTTTCTTTGCATTA-TTTATTT
229796 TTATTTCTCCTTTGCATTATTT-TTT
1 TTATTT-T-CTTTGCATTATTTATTT
229821 TTAT
1 TTAT
229825 GATTTTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 13 0.48
26 4 0.15
27 10 0.37
ACGTcount: A:0.15, C:0.11, G:0.04, T:0.70
Consensus pattern (24 bp):
TTATTTTCTTTGCATTATTTATTT
Found at i:229824 original size:25 final size:25
Alignment explanation
Indices: 229771--229822 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 25
229761 GTTAATAAAC
229771 TTATTTTCTTTGCATTATTTTATTT
1 TTATTTTCTTTGCATTATTTTATTT
229796 TTATTTCTCCTTTGCATTATTTT-TTT
1 TTATTT-T-CTTTGCATTATTTTATTT
229822 T
1 T
229823 ATGATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 14 0.56
ACGTcount: A:0.13, C:0.12, G:0.04, T:0.71
Consensus pattern (25 bp):
TTATTTTCTTTGCATTATTTTATTT
Found at i:234030 original size:95 final size:94
Alignment explanation
Indices: 233894--234137 Score: 260
Period size: 95 Copynumber: 2.7 Consensus size: 94
233884 TATAATATTA
*
233894 TATATATACAATAAAGCTTGAGTTTTCCCTCTAGAGAAATTGGTTAAACGCCCCGACATTATGGA
1 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGAAATTGGTTAAACGCCCCGACATTATGGA
* *
233959 TAATATTCGGCTAACCTAATAAAGGTGAT
66 TAAGATTCAGCTAACCTAATAAAGGTGAT
* * * * * *
233988 TATACTATACAATAAAGTTTGAGTTGTCCCTCTA-AGGCAATTGGTTAAACTCCCTGGCTTTATG
1 TATA-TATACAATAAAGCTTGAGTTGTCCCTCTAGA-GAAATTGGTTAAACGCCCCGACATTATG
* *
234052 GATAAGATTCAGTTAACCTGATAAAGGTG--
64 GATAAGATTCAGCTAACCTAATAAAGGTGAT
* * *
234081 --T-T-TA-GAT--A--TTGAGTTGTCCCTCTAGAGAAATTGGTTAAACGCCCCGTCTTTATGGA
1 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGAAATTGGTTAAACGCCCCGACATTATGGA
234137 T
66 T
234138 TCAACTAGCC
Statistics
Matches: 131, Mismatches: 16, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
83 43 0.33
84 1 0.01
85 1 0.01
87 2 0.02
88 2 0.02
89 1 0.01
91 1 0.01
94 5 0.04
95 75 0.57
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (94 bp):
TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGAAATTGGTTAAACGCCCCGACATTATGGA
TAAGATTCAGCTAACCTAATAAAGGTGAT
Found at i:234332 original size:47 final size:47
Alignment explanation
Indices: 234263--234356 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
234253 AGACCGATAT
234263 TTCTGCACTACCTTTGTTAGAGGAGCTTACAAAACTTGAACAAATGG
1 TTCTGCACTACCTTTGTTAGAGGAGCTTACAAAACTTGAACAAATGG
234310 TTCTGCACTACCTTTGTTAGAGGAGCTTACAAAACTTGAACAAATGG
1 TTCTGCACTACCTTTGTTAGAGGAGCTTACAAAACTTGAACAAATGG
234357 AAGATTTCAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (47 bp):
TTCTGCACTACCTTTGTTAGAGGAGCTTACAAAACTTGAACAAATGG
Found at i:236694 original size:21 final size:21
Alignment explanation
Indices: 236668--236712 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
236658 GATTTCTGGG
* *
236668 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
236689 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
236710 CAA
1 CAA
236713 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:237425 original size:31 final size:31
Alignment explanation
Indices: 237387--237540 Score: 274
Period size: 31 Copynumber: 5.0 Consensus size: 31
237377 GGGTCGAGGG
237387 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
237418 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
237449 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
237480 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
237511 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
237541 GTCCTTCGGG
Statistics
Matches: 120, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
31 119 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:241243 original size:21 final size:21
Alignment explanation
Indices: 241217--241261 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
241207 GATTTCTGGG
* *
241217 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
241238 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
241259 CAA
1 CAA
241262 ACGACATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:241331 original size:23 final size:22
Alignment explanation
Indices: 241287--241331 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
241277 AATGCCAGAG
*
241287 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
* *
241309 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
241332 AAATGTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.31, C:0.31, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:241974 original size:31 final size:31
Alignment explanation
Indices: 241936--242058 Score: 212
Period size: 31 Copynumber: 4.0 Consensus size: 31
241926 GGGTCGAGGG
241936 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
241967 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
241998 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
242029 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
242059 GTCCTTCGGG
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:245096 original size:18 final size:18
Alignment explanation
Indices: 245070--245127 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
245060 CTTCATTTTG
* *
245070 TTTTGTTATTTGTATTTA
1 TTTTATTATTTCTATTTA
* *
245088 TTTTATTATTTCTTTTTG
1 TTTTATTATTTCTATTTA
* *
245106 TTTT-TTGTTTTTATTTA
1 TTTTATTATTTCTATTTA
245123 TTTTA
1 TTTTA
245128 CCTTGTTTTC
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
17 13 0.42
18 18 0.58
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.78
Consensus pattern (18 bp):
TTTTATTATTTCTATTTA
Found at i:245133 original size:27 final size:28
Alignment explanation
Indices: 245103--245155 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
245093 TTATTTCTTT
*
245103 TTGTTTT-TTGTTTTTA-TTTATTTTACC
1 TTGTTTTCTT-TTATTATTTTATTTTACC
245130 TTGTTTTCTTTTATTATTTTATTTTA
1 TTGTTTTCTTTTATTATTTTATTTTA
245156 TTTCTTAGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.75
Consensus pattern (28 bp):
TTGTTTTCTTTTATTATTTTATTTTACC
Found at i:247219 original size:31 final size:31
Alignment explanation
Indices: 247181--247244 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
247171 GTACTAGTTT
247181 CTAAAATTATCGGTCCGTTCAATTTTAATAC
1 CTAAAATTATCGGTCCGTTCAATTTTAATAC
247212 CTAAAATTATCGGTCCGTTCAATTTTAATAC
1 CTAAAATTATCGGTCCGTTCAATTTTAATAC
247243 CT
1 CT
247245 CAACGGTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.39
Consensus pattern (31 bp):
CTAAAATTATCGGTCCGTTCAATTTTAATAC
Found at i:254396 original size:26 final size:26
Alignment explanation
Indices: 254361--254414 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
254351 AGCGGAGCTA
*
254361 AAAAAAATA-TCTTGGGTGTTAAATTT
1 AAAAAAATATTCTTGGG-GTCAAATTT
*
254387 AAAAAAATATTTTTGGGGTCAAATTT
1 AAAAAAATATTCTTGGGGTCAAATTT
254413 AA
1 AA
254415 GAATCATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.37
Consensus pattern (26 bp):
AAAAAAATATTCTTGGGGTCAAATTT
Found at i:255264 original size:24 final size:25
Alignment explanation
Indices: 255237--255293 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
255227 TACTAAATTA
255237 ATTTTACATCTTAAC-ATTAAAAAT
1 ATTTTACATCTTAACAATTAAAAAT
** *
255261 ATTTTTTTATCTTAACATATTAAATAT
1 A-TTTTACATCTTAACA-ATTAAAAAT
255288 ATTTTA
1 ATTTTA
255294 TTATTTTCGT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
24 1 0.04
25 12 0.46
26 4 0.15
27 9 0.35
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTTTACATCTTAACAATTAAAAAT
Found at i:255272 original size:25 final size:26
Alignment explanation
Indices: 255244--255297 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
255234 TTAATTTTAC
*
255244 ATCTTAAC-ATTAAAAATATTTTTTT
1 ATCTTAACAATTAAAAATATTTTATT
*
255269 ATCTTAACATATTAAATATATTTTATT
1 ATCTTAACA-ATTAAAAATATTTTATT
255296 AT
1 AT
255298 TTTCGTAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.32
27 17 0.68
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (26 bp):
ATCTTAACAATTAAAAATATTTTATT
Found at i:255350 original size:28 final size:28
Alignment explanation
Indices: 255310--255398 Score: 97
Period size: 28 Copynumber: 3.1 Consensus size: 28
255300 TCGTAACCTA
255310 AAAATATATTTTATTCTTATTTTAATTT
1 AAAATATATTTTATTCTTATTTTAATTT
* * *
255338 AAAATATATTTTAATCTTATCTTCAATTAA
1 AAAATATATTTTATTCTTAT-TTTAATT-T
* * * *
255368 AAAATGTAATTTATTCTTATCTTAACTT
1 AAAATATATTTTATTCTTATTTTAATTT
255396 AAA
1 AAA
255399 TATTTACATT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
28 22 0.45
29 10 0.20
30 17 0.35
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.51
Consensus pattern (28 bp):
AAAATATATTTTATTCTTATTTTAATTT
Found at i:255386 original size:30 final size:29
Alignment explanation
Indices: 255282--255398 Score: 112
Period size: 29 Copynumber: 4.0 Consensus size: 29
255272 TTAACATATT
* * * *
255282 AAATATATTTTATTATTTTCGTAACCT-AA
1 AAATATATTTTATTCTTATCTTAA-TTAAA
* *
255311 AAATATATTTTATTCTTATTTTAATT-TA
1 AAATATATTTTATTCTTATCTTAATTAAA
*
255339 AAATATATTTTAATCTTATCTTCAATTAAA
1 AAATATATTTTATTCTTATCTT-AATTAAA
* *
255369 AAATGTAATTTATTCTTATCTTAACTTAAA
1 AAATATATTTTATTCTTATCTTAA-TTAAA
255399 TATTTACATT
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
28 22 0.30
29 26 0.36
30 25 0.34
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (29 bp):
AAATATATTTTATTCTTATCTTAATTAAA
Found at i:255497 original size:19 final size:20
Alignment explanation
Indices: 255473--255514 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
255463 AAGATAAAAA
255473 TAAAAAATATATTTTT-AGT
1 TAAAAAATATATTTTTAAGT
255492 TAAAAAATATATTTTTAAGT
1 TAAAAAATATATTTTTAAGT
255512 TAA
1 TAA
255515 TATAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
TAAAAAATATATTTTTAAGT
Found at i:255579 original size:30 final size:31
Alignment explanation
Indices: 255539--255642 Score: 124
Period size: 30 Copynumber: 3.5 Consensus size: 31
255529 GTGTTTTAAG
* *
255539 TTAAAATAAGAATT-AATTATATTTAATAAT
1 TTAAGATAAGAATATAATTATATTTAATAAT
*
255569 TTAAGGTAAGAATATAA-TATATTTAATAAT
1 TTAAGATAAGAATATAATTATATTTAATAAT
** * *
255599 TTAATTTAAGAATATAATT-TATGTAATAAG
1 TTAAGATAAGAATATAATTATATTTAATAAT
255629 TTAAGATAAGAATA
1 TTAAGATAAGAATA
255643 AAGTAACTCC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
30 60 0.95
31 3 0.05
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (31 bp):
TTAAGATAAGAATATAATTATATTTAATAAT
Found at i:256693 original size:20 final size:21
Alignment explanation
Indices: 256630--256700 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 21
256620 TGGGCTAGAA
* *
256630 GTATCGATACTCATATAATGG
1 GTATCGATACTCATAGAGTGG
256651 GTATCGATACT-ATAG-GTAGG
1 GTATCGATACTCATAGAGT-GG
*
256671 GTATCGATACTCGTAGAGT-G
1 GTATCGATACTCATAGAGTGG
256691 GTATCGATAC
1 GTATCGATAC
256701 CAAGTTCAGT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 1 0.02
20 27 0.61
21 14 0.32
22 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (21 bp):
GTATCGATACTCATAGAGTGG
Found at i:256978 original size:20 final size:20
Alignment explanation
Indices: 256933--256972 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
256923 CAATAAGTCA
* *
256933 GTAGTATCGATACCCAGATG
1 GTAGTATCAATACCCAAATG
256953 GTAGTATCAATACCCAAATG
1 GTAGTATCAATACCCAAATG
256973 TCAGTAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (20 bp):
GTAGTATCAATACCCAAATG
Found at i:258004 original size:29 final size:28
Alignment explanation
Indices: 257935--258072 Score: 123
Period size: 29 Copynumber: 4.7 Consensus size: 28
257925 AGATAAAATG
*
257935 TATATTTTTTAAGTTAATATAAATACTAAAA
1 TATA-TTTTTAAGTTAAAATAAA-A-TAAAA
* *
257966 TATAATTTTAAGTTAAAATAAGAATAAAT
1 TATATTTTTAAGTTAAAATAA-AATAAAA
* * * * *
257995 TGTATTTTTAGGTTAAGACAAGATTAAAA
1 TATATTTTTAAGTTAAAATAA-AATAAAA
* *
258024 TATATTTAATAAGTTAATATAAAATAAAA
1 TATATTT-TTAAGTTAAAATAAAATAAAA
258053 TATATTTTTAATGTTAAAAT
1 TATATTTTTAA-GTTAAAAT
258073 GTAAAATTAA
Statistics
Matches: 86, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
28 3 0.03
29 52 0.60
30 26 0.30
31 5 0.06
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.42
Consensus pattern (28 bp):
TATATTTTTAAGTTAAAATAAAATAAAA
Found at i:259090 original size:13 final size:13
Alignment explanation
Indices: 259072--259098 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
259062 TTATCTTATG
259072 ACAACTTAATTTA
1 ACAACTTAATTTA
259085 ACAACTTAATTTA
1 ACAACTTAATTTA
259098 A
1 A
259099 GATTAAAGAA
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:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
ACAACTTAATTTA
Found at i:268331 original size:2 final size:2
Alignment explanation
Indices: 268324--268363 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
268314 GCCGACAATA
*
268324 AT AT AT AT AT AT AT AT AT GT 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
268364 TTCAAACGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:268754 original size:10 final size:10
Alignment explanation
Indices: 268739--268764 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
268729 AATTCAGTTT
268739 ATAAAATGAA
1 ATAAAATGAA
268749 ATAAAATGAA
1 ATAAAATGAA
268759 ATAAAA
1 ATAAAA
268765 CAAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (10 bp):
ATAAAATGAA
Found at i:275555 original size:18 final size:19
Alignment explanation
Indices: 275521--275556 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
275511 CTAGTTTGTT
275521 TTTTTTTTCTTTCTCTGTA
1 TTTTTTTTCTTTCTCTGTA
*
275540 TTTTTTTTGTTT-TCTGT
1 TTTTTTTTCTTTCTCTGT
275557 TTCTGTCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.03, C:0.11, G:0.08, T:0.78
Consensus pattern (19 bp):
TTTTTTTTCTTTCTCTGTA
Found at i:276066 original size:3 final size:3
Alignment explanation
Indices: 276058--276158 Score: 150
Period size: 3 Copynumber: 33.7 Consensus size: 3
276048 TAATATAAAT
*
276058 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** *
276106 TAA TGAA TAA TAA T-A TAA TAA TAA GGA TAA TAA TAA TAT TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
276151 TAA TAA TA
1 TAA TAA TA
276159 TGGATAAAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.02
3 83 0.94
4 3 0.03
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:276165 original size:15 final size:14
Alignment explanation
Indices: 276040--276159 Score: 115
Period size: 15 Copynumber: 8.4 Consensus size: 14
276030 ATTATGTATT
*
276040 TAATATATTAAT-A
1 TAATATAATAATAA
276053 TAA-ATTAATAATAA
1 TAATA-TAATAATAA
276067 TAATAATAATAATAA
1 TAAT-ATAATAATAA
*
276082 TAATAATAATAATAT
1 TAAT-ATAATAATAA
276097 TAATAATAATAATGAA
1 TAAT-ATAATAAT-AA
276113 TAATA-ATATAATAA
1 TAATATA-ATAATAA
*
276127 TAAGGATAATAATAA
1 TAA-TATAATAATAA
276142 T-AT-TAATAATAA
1 TAATATAATAATAA
276154 TAATAT
1 TAATAT
276160 GGATAAAAAA
Statistics
Matches: 92, Mismatches: 5, Indels: 19
0.79 0.04 0.16
Matches are distributed among these distances:
12 11 0.12
13 11 0.12
14 12 0.13
15 51 0.55
16 7 0.08
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (14 bp):
TAATATAATAATAA
Found at i:276607 original size:116 final size:112
Alignment explanation
Indices: 276406--277064 Score: 912
Period size: 113 Copynumber: 5.8 Consensus size: 112
276396 GCTCTTGATG
*
276406 AGTTCTTCTCATTATGAACTTTCTT-TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC
1 AGTTCTTCTCATTATGAAC-TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-CTAC
* * * *
276470 -CTGTCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGATTGAACA
64 TCTGGCAAAGATGATCCATCAAGTGATGAATTC-AGCAAAAGATTGAACA
*
276519 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CT
* *
276584 ACT-TGGCAAAGTTGATCCATCAAATGATGAATTCAAGCAAAAGATTGAACA
62 ACTCTGGCAAAGATGATCCATCAAGTGATGAATTC-AGCAAAAGATTGAACA
*
276635 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTACTC
* * *
276700 TGGCAAAAATAATCCATCAAGTGATGAATTCAGAAAAAGATTGAACA
66 TGGCAAAGATGATCCATCAAGTGATGAATTCAGCAAAAGATTGAACA
*
276747 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTACTC
* * * *
276812 TGGCAAAAATAATCCATCAAGTGATGAATTCAGAAAAAAGGTTGAACA
66 TGGCAAAGATGATCCATCAAGTGATGAATTCAG-CAAAAGATTGAACA
* *
276860 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTACTC
* * * * *
276925 TGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCTAAAGATTGAACA
66 TGGCAAAGATGATCCATCAAGTGAT-GAATTCAGCAAAAGATTGAACA
*
276973 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CT
* *
277038 AC-CTGGTAATGAATGATCCATCAAGTG
62 ACTCTGGCAAAG-ATGATCCATCAAGTG
277065 GATTTGAAAT
Statistics
Matches: 505, Mismatches: 28, Indels: 22
0.91 0.05 0.04
Matches are distributed among these distances:
112 122 0.24
113 225 0.45
114 6 0.01
116 135 0.27
117 17 0.03
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (112 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTACTC
TGGCAAAGATGATCCATCAAGTGATGAATTCAGCAAAAGATTGAACA
Found at i:277029 original size:341 final size:339
Alignment explanation
Indices: 276406--277034 Score: 962
Period size: 341 Copynumber: 1.8 Consensus size: 339
276396 GCTCTTGATG
*
276406 AGTTCTTCTCATTATGAACTTTCTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACC
1 AGTTCTTCTCATTATGAACTTTCTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTACC
* *** * * *
276471 TGTCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGA
66 TGGCAAAAATAATCCATCAAATGATGAATTCAAGAAAAAGATTGAACAAATTCTTCTCATTATGA
* * *
276536 ACTTCTTCTTCTTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACTTGGCAAAGTTGATC
131 ACTTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTCTACTTGGAAAAGCTGATC
276601 CATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTT
194 CATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTT
276666 CTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTC
259 CTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTC
276731 AGAAAAAGATTGAACA
324 AGAAAAAGATTGAACA
276747 AGTTCTTCTCATTATGAAC-TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTT-C
1 AGTTCTTCTCATTATGAACTTTCTT-TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTAC
* *
276810 TCTGGCAAAAATAATCCATCAAGTGATGAATTC-AGAAAAAAGGTTGAACAAATTCTTCTCATTA
65 -CTGGCAAAAATAATCCATCAAATGATGAATTCAAG-AAAAAGATTGAACAAATTCTTCTCATTA
*
276874 TGAACTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGCTGA
128 TGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTACT-TGGAAAAGCTGA
* * ** * *
276937 TCCATCAAGTGATGGATTTGAGCTAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCT
192 TCCATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
277002 TTCTTCAGATGACGAGTTCTTCTCATTATGAAC
257 TTCTTCAGAT---GAGTTCTTCTCATTATGAAC
277035 TCTACCTGGT
Statistics
Matches: 261, Mismatches: 20, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
337 4 0.02
338 99 0.38
340 8 0.03
341 150 0.57
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (339 bp):
AGTTCTTCTCATTATGAACTTTCTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTACC
TGGCAAAAATAATCCATCAAATGATGAATTCAAGAAAAAGATTGAACAAATTCTTCTCATTATGA
ACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTACTTGGAAAAGCTGATCCA
TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCT
TCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAG
AAAAAGATTGAACA
Found at i:277800 original size:50 final size:50
Alignment explanation
Indices: 277746--277842 Score: 160
Period size: 50 Copynumber: 1.9 Consensus size: 50
277736 TCAATGCTTG
*
277746 TTCTG-CTACACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATA
1 TTCTGTCTA-ACCAGATCAGATAAATCAAAGAACACTTCCAGAAGATGATA
*
277796 TTCTGTCTAATCAGATCAGATAAATCAAAGAACACTTCCAGAAGATG
1 TTCTGTCTAACCAGATCAGATAAATCAAAGAACACTTCCAGAAGATG
277843 CTTTTGTCTA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 41 0.93
51 3 0.07
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (50 bp):
TTCTGTCTAACCAGATCAGATAAATCAAAGAACACTTCCAGAAGATGATA
Found at i:277934 original size:133 final size:134
Alignment explanation
Indices: 277625--278123 Score: 808
Period size: 133 Copynumber: 3.7 Consensus size: 134
277615 TACATTTCTT
* *
277625 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAAATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
* * * * * * *
277690 AAAGAACACTTCCAGAAGATGCTATTGGT-AAATTCATATTCCAAATTCAATGCTT-GTTCTGCT
66 AAAGAACACTTCCAGAAGATGCTATTTGTCAAATCCATCTTCTAAATTCACTGATTGGTTCTGTT
*
277753 ACAC
131 AAAC
* *
277757 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTCTGTCTAATCAGATCAGATAAATC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
*
277822 AAAGAACACTTCCAGAAGATGCT-TTTGTCTAATCCATCTTCTAAATTCACTGATTGGTTCTGTT
66 AAAGAACACTTCCAGAAGATGCTATTTGTCAAATCCATCTTCTAAATTCACTGATTGGTTCTGTT
277886 AAAC
131 AAAC
277890 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
* *
277955 AAAGAACACTTCCAGAAGATGCTA-TTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTT
66 AAAGAACACTTCCAGAAGATGCTATTTGTCAAATCCATCTTCTAAATTCACTGATTGGTTCTGTT
*
278019 CAAC
131 AAAC
278023 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
*
278088 AAAGAACACTTCCAGAAGATGCTATTCTGTCTAATC
66 AAAGAACACTTCCAGAAGATGCTATT-TGTCAAATC
278124 AGATCAGATA
Statistics
Matches: 340, Mismatches: 22, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
131 4 0.01
132 104 0.31
133 225 0.66
134 1 0.00
135 6 0.02
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (134 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
AAAGAACACTTCCAGAAGATGCTATTTGTCAAATCCATCTTCTAAATTCACTGATTGGTTCTGTT
AAAC
Found at i:278079 original size:183 final size:183
Alignment explanation
Indices: 277890--278296 Score: 805
Period size: 183 Copynumber: 2.2 Consensus size: 183
277880 TCTGTTAAAC
277890 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
277955 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTC
66 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTC
*
278020 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
131 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTATAAT
278073 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
278138 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTC
66 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTC
278203 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTATAAT
131 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTATAAT
278256 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
278297 GGCAAATTCA
Statistics
Matches: 223, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
183 223 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (183 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTC
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTATAAT
Found at i:278087 original size:50 final size:50
Alignment explanation
Indices: 278023--278163 Score: 282
Period size: 50 Copynumber: 2.8 Consensus size: 50
278013 TCTGTTCAAC
278023 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
278073 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
278123 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
278164 GGCAAATTCA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 91 1.00
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (50 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
Found at i:279096 original size:16 final size:17
Alignment explanation
Indices: 279058--279102 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
279048 AATATAAAAG
*
279058 AATAAATTGAATTTCAAA
1 AATAAATTGAATCTC-AA
279076 AATAAATTGAATCTC-A
1 AATAAATTGAATCTCAA
279092 AATAAATTGAA
1 AATAAATTGAA
279103 CTTGAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (17 bp):
AATAAATTGAATCTCAA
Found at i:279439 original size:1 final size:1
Alignment explanation
Indices: 279433--279489 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
279423 TGACCTCCCC
* * * * * * *
279433 TTTTTTTTTTTCTTTTCTTTTTTTTCTTTTTTTCTTTTCTTTTTTCTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
279490 CTCTTCAAGC
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:279448 original size:7 final size:7
Alignment explanation
Indices: 279433--279494 Score: 76
Period size: 7 Copynumber: 9.1 Consensus size: 7
279423 TGACCTCCCC
279433 TTTTT-T
1 TTTTTCT
279439 TTTTTCT
1 TTTTTCT
279446 TTTCTT-T
1 TTT-TTCT
279453 TTTTTCT
1 TTTTTCT
279460 TTTTT-T
1 TTTTTCT
*
279466 CTTTTCT
1 TTTTTCT
279473 TTTTTCT
1 TTTTTCT
279480 TTTTTCT
1 TTTTTCT
*
279487 TTTCTCT
1 TTTTTCT
279494 T
1 T
279495 CAAGCATAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
6 12 0.24
7 35 0.71
8 2 0.04
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTCT
Found at i:279455 original size:14 final size:13
Alignment explanation
Indices: 279433--279489 Score: 87
Period size: 14 Copynumber: 4.2 Consensus size: 13
279423 TGACCTCCCC
279433 TTTTTTTTTTTCT
1 TTTTTTTTTTTCT
279446 TTTCTTTTTTTTCT
1 TTT-TTTTTTTTCT
*
279460 TTTTTTCTTTTCT
1 TTTTTTTTTTTCT
279473 TTTTTCTTTTTTCT
1 TTTTT-TTTTTTCT
279487 TTT
1 TTT
279490 CTCTTCAAGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
13 17 0.43
14 23 0.57
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTTCT
Found at i:279470 original size:27 final size:26
Alignment explanation
Indices: 279432--279489 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 26
279422 TTGACCTCCC
279432 CTTTTTTTTTTTCTTTTCTT-TTTTTT
1 CTTTTTTTTTTTCTTTT-TTCTTTTTT
279458 CTTTTTTTCTTTTCTTTTTTCTTTTTT
1 CTTTTTTT-TTTTCTTTTTTCTTTTTT
279485 CTTTT
1 CTTTT
279490 CTCTTCAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 10 0.33
27 20 0.67
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (26 bp):
CTTTTTTTTTTTCTTTTTTCTTTTTT
Found at i:279490 original size:5 final size:5
Alignment explanation
Indices: 279435--279491 Score: 61
Period size: 5 Copynumber: 12.2 Consensus size: 5
279425 ACCTCCCCTT
*
279435 TTTTT TTTTC TTTTC TTTT- TTTTC -TTT- TTTTC TTTTC TTTT- TTCTT-
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC
279481 TTTTC TTTTC T
1 TTTTC TTTTC T
279492 CTTCAAGCAT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
4 14 0.30
5 32 0.70
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (5 bp):
TTTTC
Found at i:291788 original size:18 final size:19
Alignment explanation
Indices: 291754--291789 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
291744 CTAGTTTGTT
291754 TTTTTTTTCTTTCTCTGTA
1 TTTTTTTTCTTTCTCTGTA
*
291773 TTTTTTTTGTTT-TCTGT
1 TTTTTTTTCTTTCTCTGT
291790 TTCTGTCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.03, C:0.11, G:0.08, T:0.78
Consensus pattern (19 bp):
TTTTTTTTCTTTCTCTGTA
Found at i:292300 original size:3 final size:3
Alignment explanation
Indices: 292292--292401 Score: 166
Period size: 3 Copynumber: 36.7 Consensus size: 3
292282 TAATATAAAT
*
292292 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * ** *
292340 TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA GGA TAA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
292388 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
292402 TGAATAAAAA
Statistics
Matches: 95, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 95 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:293425 original size:18 final size:18
Alignment explanation
Indices: 293402--293437 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
293392 ATGTACATAC
293402 TTACACCGGTATAAGTAT
1 TTACACCGGTATAAGTAT
293420 TTACACCGGTATAAGTAT
1 TTACACCGGTATAAGTAT
293438 GTGTTAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (18 bp):
TTACACCGGTATAAGTAT
Found at i:294704 original size:31 final size:30
Alignment explanation
Indices: 294582--294736 Score: 204
Period size: 30 Copynumber: 5.1 Consensus size: 30
294572 GAAGGACCTA
* * * *
294582 TCCAGAGGTCACAAAGA-CCCCAGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
294611 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
294641 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
294671 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
* * * * *
294702 TCCATAGGTCCTGAAGAACCTAGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
294733 TCCA
1 TCCA
294737 TATGTCTCGA
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
29 16 0.14
30 64 0.56
31 35 0.30
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.21
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:294757 original size:31 final size:31
Alignment explanation
Indices: 294666--294761 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 31
294656 GATCCTCGGT
* * * * * *
294666 AACTGTCCAGAGGTCATAAAGATCCTCGGTA
1 AACTGTCCATAGGTCCTGAAGAACATAGGTA
*
294697 AACTGTCCATAGGTCCTGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCTGAAGAACATAGGTA
*
294728 AACTGTCCATATGT-CTCGAA-AGACATAGGTA
1 AACTGTCCATAGGTCCT-GAAGA-ACATAGGTA
294759 AAC
1 AAC
294762 CCTCGACTCT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
30 3 0.05
31 53 0.95
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (31 bp):
AACTGTCCATAGGTCCTGAAGAACATAGGTA
Found at i:295781 original size:21 final size:21
Alignment explanation
Indices: 295751--295795 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
295741 ATTCTGTCGT
* *
295751 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
295772 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
295793 TTG
1 TTG
295796 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:299208 original size:31 final size:30
Alignment explanation
Indices: 299086--299215 Score: 208
Period size: 30 Copynumber: 4.3 Consensus size: 30
299076 GAAGGACCTA
* * *
299086 TCCAGAGGTCACAAAGA-CCCCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
299115 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
299145 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
299175 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
*
299206 TCCATAGGTC
1 TCCAGAGGTC
299216 CCGAAGAACC
Statistics
Matches: 95, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.17
30 65 0.68
31 14 0.15
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:299232 original size:31 final size:31
Alignment explanation
Indices: 299140--299265 Score: 103
Period size: 31 Copynumber: 4.1 Consensus size: 31
299130 GATCCTCGGT
* ** * *
299140 AACTGTCCAGAGGTCATAAAGATCCTCGGT-
1 AACTGTCCATAGGTCACGAAGAACCTAGGTA
* ** * *
299170 AACTGTCCAGAGGTCATAAAGATCCTCGGTA
1 AACTGTCCATAGGTCACGAAGAACCTAGGTA
*
299201 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCACGAAGAACCTAGGTA
* * *
299232 AACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTGTCCATAGGTCACGAAGA-ACCTAGGTA
299263 AAC
1 AAC
299266 CCTCGACTCT
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
30 31 0.36
31 54 0.64
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.22
Consensus pattern (31 bp):
AACTGTCCATAGGTCACGAAGAACCTAGGTA
Found at i:299766 original size:2 final size:2
Alignment explanation
Indices: 299759--299809 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
299749 ATACAATTCC
299759 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
299801 TA TA TA TA T
1 TA TA TA TA T
299810 CTAACTCATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:300313 original size:21 final size:21
Alignment explanation
Indices: 300283--300327 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
300273 ATTCTGTCGT
* *
300283 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
300304 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
300325 TTG
1 TTG
300328 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:305825 original size:26 final size:26
Alignment explanation
Indices: 305796--305878 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 26
305786 ACTCTAACTC
305796 ATTTAGCTTTAAAATCATCCCAAATA
1 ATTTAGCTTTAAAATCATCCCAAATA
* *
305822 ATTT--CTTAACTATAAAT-A-CCCTAACTC
1 ATTTAGCTT---TA-AAATCATCCC-AAATA
305849 ATTTAGCTTTAAAATCATCCCAAATA
1 ATTTAGCTTTAAAATCATCCCAAATA
305875 ATTT
1 ATTT
305879 CTTTCTCCCA
Statistics
Matches: 44, Mismatches: 4, Indels: 18
0.67 0.06 0.27
Matches are distributed among these distances:
24 3 0.07
25 4 0.09
26 17 0.39
27 13 0.30
28 4 0.09
29 3 0.07
ACGTcount: A:0.40, C:0.20, G:0.02, T:0.37
Consensus pattern (26 bp):
ATTTAGCTTTAAAATCATCCCAAATA
Found at i:305834 original size:53 final size:53
Alignment explanation
Indices: 305776--305881 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
305766 TTTATGCTTC
*
305776 AACTATAAATACTCTAACTCATTTAGCTTTAAAATCATCCCAAATAATTTCTT
1 AACTATAAATACCCTAACTCATTTAGCTTTAAAATCATCCCAAATAATTTCTT
305829 AACTATAAATACCCTAACTCATTTAGCTTTAAAATCATCCCAAATAATTTCTT
1 AACTATAAATACCCTAACTCATTTAGCTTTAAAATCATCCCAAATAATTTCTT
305882 TCTCCCAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.40, C:0.22, G:0.02, T:0.37
Consensus pattern (53 bp):
AACTATAAATACCCTAACTCATTTAGCTTTAAAATCATCCCAAATAATTTCTT
Found at i:305861 original size:24 final size:24
Alignment explanation
Indices: 305781--305861 Score: 56
Period size: 24 Copynumber: 3.2 Consensus size: 24
305771 GCTTCAACTA
*
305781 TAAATACTCTAACTCATTTAGCTT
1 TAAATACCCTAACTCATTTAGCTT
* * * *
305805 TAAAATCATCCC-AAATAATTTCTTAACTA
1 T-AAAT-A-CCCTAACTCA--T-TTAGCTT
305834 TAAATACCCTAACTCATTTAGCTT
1 TAAATACCCTAACTCATTTAGCTT
305858 TAAA
1 TAAA
305862 ATCATCCCAA
Statistics
Matches: 41, Mismatches: 9, Indels: 14
0.64 0.14 0.22
Matches are distributed among these distances:
24 10 0.24
25 5 0.12
26 8 0.20
27 7 0.17
28 5 0.12
29 6 0.15
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.37
Consensus pattern (24 bp):
TAAATACCCTAACTCATTTAGCTT
Found at i:308721 original size:36 final size:35
Alignment explanation
Indices: 308680--308779 Score: 91
Period size: 35 Copynumber: 2.9 Consensus size: 35
308670 TAAAAATAGT
308680 TATTATATTTTATTTATATTAATATAATTATATAAA
1 TATTATATTTTA-TTATATTAATATAATTATATAAA
* * * *
308716 TATTATTTTTTATTAAAATAATAT--TTATATAAT
1 TATTATATTTTATTATATTAATATAATTATATAAA
*
308749 TATTATTTATTTAAATT-TATTAAT-TAATTAT
1 TATTA--TATTT-TATTATATTAATATAATTAT
308780 TTTTTGTGCT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
33 13 0.25
34 1 0.02
35 19 0.37
36 18 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (35 bp):
TATTATATTTTATTATATTAATATAATTATATAAA
Found at i:308731 original size:30 final size:33
Alignment explanation
Indices: 308688--308761 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
308678 GTTATTATAT
*
308688 TTTATTTATATTAAT-ATAATTATATAAATATTA
1 TTTATTTAT-TAAATAATAATTATATAAATATTA
* *
308721 TTT-TTTATTAAAATAATATTTATATAATTATTA
1 TTTATTTATT-AAATAATAATTATATAAATATTA
308754 TTTATTTA
1 TTTATTTA
308762 AATTTATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 1 0.03
32 8 0.23
33 22 0.63
34 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
TTTATTTATTAAATAATAATTATATAAATATTA
Found at i:311902 original size:23 final size:23
Alignment explanation
Indices: 311876--311944 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
311866 CACCACAGCT
* *
311876 CGTATAAATGCACTGAAGTGCCA
1 CGTATAATTACACTGAAGTGCCA
* * * *
311899 CGTAGAATTTCACCGAAGTGCCG
1 CGTATAATTACACTGAAGTGCCA
*
311922 CGTATAATTACACTGTAGTGCCA
1 CGTATAATTACACTGAAGTGCCA
311945 TATAAGATTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (23 bp):
CGTATAATTACACTGAAGTGCCA
Found at i:312571 original size:20 final size:20
Alignment explanation
Indices: 312546--312594 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
312536 GAAAGTATGC
312546 ATCGATGCACTACACCATGT
1 ATCGATGCACTACACCATGT
312566 ATCGATGCACTACACCATGT
1 ATCGATGCACTACACCATGT
312586 ATCGATGCA
1 ATCGATGCA
312595 TCCCTTGACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (20 bp):
ATCGATGCACTACACCATGT
Found at i:312711 original size:62 final size:64
Alignment explanation
Indices: 312645--312763 Score: 170
Period size: 64 Copynumber: 1.9 Consensus size: 64
312635 CATAAATCCT
* * *
312645 ATTCGATGTTTGTA-TTT-AAGGGGTGCATCGATGCGCTACTTGTGCATCGATACACTGAAGGC
1 ATTCGATGTTTGTATTTTAAAAGAGTGCATCGATGCACTACTTGTGCATCGATACACTGAAGGC
* * *
312707 ATTCGATGTTTTTATTTTAAAATAGTGCATCGATGCACTTCTTGTGCATCGATACAC
1 ATTCGATGTTTGTATTTTAAAAGAGTGCATCGATGCACTACTTGTGCATCGATACAC
312764 CTTGAATAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
62 13 0.27
63 3 0.06
64 33 0.67
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (64 bp):
ATTCGATGTTTGTATTTTAAAAGAGTGCATCGATGCACTACTTGTGCATCGATACACTGAAGGC
Found at i:313512 original size:28 final size:30
Alignment explanation
Indices: 313472--313528 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
313462 TTCTTTGAAC
* * *
313472 TTTTTAATTTATC-TAATTTGGTCACTAAA
1 TTTTTAATATATCACAATTTGATCACTAAA
313501 TTTTTAA-ATATCACAATTTGATCACTAA
1 TTTTTAATATATCACAATTTGATCACTAA
313529 CCCGGTATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.47
Consensus pattern (30 bp):
TTTTTAATATATCACAATTTGATCACTAAA
Done.