Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000989.1 Hibiscus syriacus cultivar Beakdansim tig00001980_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: 949177
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 3
Found at i:263788 original size:32 final size:33
Alignment explanation
Indices: 263724--263788 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
263714 TACTTATTAG
*
263724 TTTTAATTGATTTTTAAAACATTTAAAATTGAT
1 TTTTAATTGATTTTTAAAACATGTAAAATTGAT
263757 TTTTAATTGATTTTTAAAA-ATGTAAAATTGAT
1 TTTTAATTGATTTTTAAAACATGTAAAATTGAT
263789 ACTTTTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 12 0.39
33 19 0.61
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.51
Consensus pattern (33 bp):
TTTTAATTGATTTTTAAAACATGTAAAATTGAT
Found at i:265789 original size:2 final size:2
Alignment explanation
Indices: 265782--265832 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
265772 TTGTCAATCA
265782 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
265824 AT AT AT AT A
1 AT AT AT AT A
265833 ACTTATGAAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:266072 original size:83 final size:81
Alignment explanation
Indices: 265903--266122 Score: 235
Period size: 83 Copynumber: 2.6 Consensus size: 81
265893 CATTGACACG
* * *
265903 CAATGAAAGTCATACATGCGTGCCATAAATTTATGACACACAAATGTGAGTCAAGCAGATTTATG
1 CAATG-AAGTCATACATGCGTGTCATAAATTTATG--ACACAAATGTGTGTC-ATCAGATTTATG
** *
265968 ACGGGGGCTTCAATGACGCT
62 ACCAGGGCTTCAACGACGCT
*
265988 CAATGTAAGTCATACACGCGTGTCATAAATTTATGACACAAATGTGTGTCATCTTA-ATTTATGA
1 CAATG-AAGTCATACATGCGTGTCATAAATTTATGACACAAATGTGTGTCATC--AGATTTATGA
266052 CCAGGGCTTCAACGACGCT
63 CCAGGGCTTCAACGACGCT
* * * * * * *
266071 CAATGAACGTCATAAATGCGCGTCACAAATGTATGTCATAAATGAGTGTCAT
1 CAATGAA-GTCATACATGCGTGTCATAAATTTATGACACAAATGTGTGTCAT
266123 AAATGCGCGT
Statistics
Matches: 116, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
82 4 0.03
83 79 0.68
84 1 0.01
85 32 0.28
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (81 bp):
CAATGAAGTCATACATGCGTGTCATAAATTTATGACACAAATGTGTGTCATCAGATTTATGACCA
GGGCTTCAACGACGCT
Found at i:266094 original size:13 final size:13
Alignment explanation
Indices: 266078--266136 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
266068 GCTCAATGAA
266078 CGTCATAAATGCG
1 CGTCATAAATGCG
* **
266091 CGTCACAAATGTA
1 CGTCATAAATGCG
* *
266104 TGTCATAAATGAG
1 CGTCATAAATGCG
*
266117 TGTCATAAATGCG
1 CGTCATAAATGCG
266130 CGTCATA
1 CGTCATA
266137 GATTTATGAC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (13 bp):
CGTCATAAATGCG
Found at i:269511 original size:2 final size:2
Alignment explanation
Indices: 269504--269538 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
269494 TCATATTAAC
269504 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
269539 GAAAATAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:272255 original size:8 final size:8
Alignment explanation
Indices: 272242--272301 Score: 75
Period size: 8 Copynumber: 7.4 Consensus size: 8
272232 AATTCTATTC
272242 TTTTTCTT
1 TTTTTCTT
272250 TTTTTCTT
1 TTTTTCTT
*
272258 TTCTTCTT
1 TTTTTCTT
*
272266 TTCTTCTT
1 TTTTTCTT
*
272274 TTCTTCTT
1 TTTTTCTT
*
272282 TTTGTCTT
1 TTTTTCTT
272290 TTCTTTCTT
1 TT-TTTCTT
272299 TTT
1 TTT
272302 GCACTCCAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
8 40 0.85
9 7 0.15
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (8 bp):
TTTTTCTT
Found at i:272264 original size:16 final size:16
Alignment explanation
Indices: 272245--272301 Score: 87
Period size: 16 Copynumber: 3.5 Consensus size: 16
272235 TCTATTCTTT
272245 TTCTTTTTTTCTTTTC
1 TTCTTTTTTTCTTTTC
*
272261 TTCTTTTCTTCTTTTC
1 TTCTTTTTTTCTTTTC
*
272277 TTCTTTTTGTCTTTTC
1 TTCTTTTTTTCTTTTC
272293 TTTCTTTTT
1 -TTCTTTTT
272302 GCACTCCAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
16 29 0.78
17 8 0.22
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (16 bp):
TTCTTTTTTTCTTTTC
Found at i:276626 original size:2 final size:2
Alignment explanation
Indices: 276619--276650 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
276609 AGACTGAGTC
276619 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
276651 TCTTTTATGA
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):
AT
Found at i:284935 original size:96 final size:96
Alignment explanation
Indices: 284766--284967 Score: 341
Period size: 96 Copynumber: 2.1 Consensus size: 96
284756 TACAATTGAC
*
284766 CAGTAATTTCGATCATGCATTAATCAGTCACCAACATTAACCATAAAACATGCATAGGGTAGTAA
1 CAGTCATTTCGATCATGCATTAATCAGTCACCAACATTAACCATAAAACATGCATAGGGTAGTAA
* *
284831 AGTATTACCTCGAGTTTTGAGCTATATGCAT
66 AATATTACCTCGAGGTTTGAGCTATATGCAT
* * * *
284862 CAGTCATTTCGATCATGCATTAATCATTCACCAACATTAACCATGAAACATGCATATGTTAGTAA
1 CAGTCATTTCGATCATGCATTAATCAGTCACCAACATTAACCATAAAACATGCATAGGGTAGTAA
284927 AATATTACCTCGAGGTTTGAGCTATATGCAT
66 AATATTACCTCGAGGTTTGAGCTATATGCAT
284958 CAGTCATTTC
1 CAGTCATTTC
284968 AACTCCATTT
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 99 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (96 bp):
CAGTCATTTCGATCATGCATTAATCAGTCACCAACATTAACCATAAAACATGCATAGGGTAGTAA
AATATTACCTCGAGGTTTGAGCTATATGCAT
Found at i:286429 original size:33 final size:33
Alignment explanation
Indices: 286387--286453 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
286377 GAAAAGAGAA
286387 CCTTTGAAAATCATGTTGTCAAACACGTGAAGT
1 CCTTTGAAAATCATGTTGTCAAACACGTGAAGT
*
286420 CCTTTGAAAATCATGTTGTCAAACATGTGAAGT
1 CCTTTGAAAATCATGTTGTCAAACACGTGAAGT
286453 C
1 C
286454 TAAGAAAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (33 bp):
CCTTTGAAAATCATGTTGTCAAACACGTGAAGT
Found at i:290388 original size:26 final size:26
Alignment explanation
Indices: 290343--290394 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
290333 TATAATATAG
*
290343 TCATTTTACACTTCAAGGGTATTTTT
1 TCATTTTACACTTCAAGGGTAATTTT
* *
290369 TCATTTTACACTTTAGGGGTAATTTT
1 TCATTTTACACTTCAAGGGTAATTTT
290395 GTGATATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.50
Consensus pattern (26 bp):
TCATTTTACACTTCAAGGGTAATTTT
Found at i:290989 original size:22 final size:20
Alignment explanation
Indices: 290962--291033 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 20
290952 AAAGTCAATG
290962 GTCAACCGTCAGACTAGTCAAA
1 GTCAA-CGTCAGAC-AGTCAAA
*
290984 GTCAACGATCAGAACGGTCAAA
1 GTCAACG-TCAG-ACAGTCAAA
* *
291006 GTCAATGGTCAGACCGATCAACA
1 GTCAA-CGTCAGACAG-TCAA-A
291029 GTCAA
1 GTCAA
291034 AGGGTTAGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
21 5 0.12
22 28 0.67
23 9 0.21
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (20 bp):
GTCAACGTCAGACAGTCAAA
Found at i:292009 original size:13 final size:13
Alignment explanation
Indices: 291986--292023 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
291976 AGTCCATAAA
291986 ATTAAATAATTTAT
1 ATTAAA-AATTTAT
292000 -TTAATAAATTTAT
1 ATTAA-AAATTTAT
292013 ATTAAAAATTT
1 ATTAAAAATTT
292024 GGGTGTGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTAAAAATTTAT
Found at i:294669 original size:27 final size:27
Alignment explanation
Indices: 294612--294669 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
294602 TGTCATAGTC
** * *
294612 ATTTTACACTTCAAGGGTATTTAGGTT
1 ATTTTACACTTCAAGAATAATTAGGTG
**
294639 ATTTTACACTTCAAGAATAATTCTGTG
1 ATTTTACACTTCAAGAATAATTAGGTG
294666 ATTT
1 ATTT
294670 AATAATTAGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (27 bp):
ATTTTACACTTCAAGAATAATTAGGTG
Found at i:298136 original size:16 final size:16
Alignment explanation
Indices: 298115--298147 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
298105 TCTTTTAAAC
298115 ACATACCTCGTTCGAA
1 ACATACCTCGTTCGAA
298131 ACATACCTCGTTCGAA
1 ACATACCTCGTTCGAA
298147 A
1 A
298148 TTAATCTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.24
Consensus pattern (16 bp):
ACATACCTCGTTCGAA
Found at i:311983 original size:19 final size:19
Alignment explanation
Indices: 311938--311984 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
311928 CTTGTTTTAG
*
311938 GTTCATAACTTAATTTCAA
1 GTTCATAGCTTAATTTCAA
* *
311957 ATTCATAGCTTATTTTCAA
1 GTTCATAGCTTAATTTCAA
311976 GTTCATAGC
1 GTTCATAGC
311985 CCAATCCATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.43
Consensus pattern (19 bp):
GTTCATAGCTTAATTTCAA
Found at i:319756 original size:26 final size:26
Alignment explanation
Indices: 319720--319780 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
319710 AAAAAACCTG
319720 AAAAATCATAATCTTATGATTTTATT
1 AAAAATCATAATCTTATGATTTTATT
319746 AAAAATCATAATCTTATGATTTTATT
1 AAAAATCATAATCTTATGATTTTATT
319772 AAAAATCAT
1 AAAAATCAT
319781 GATAAACATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (26 bp):
AAAAATCATAATCTTATGATTTTATT
Found at i:319863 original size:49 final size:48
Alignment explanation
Indices: 319805--319911 Score: 119
Period size: 49 Copynumber: 2.2 Consensus size: 48
319795 AACAAAATAA
319805 TTATT-TCATATAATTTTCCTTTCAAACACATTT-CAAAACTTTCATAT
1 TTATTATCATATAATTTTCCTTTCAAACAC-TTTGCAAAACTTTCATAT
* * * * **
319852 TTCATTATCATATTATTTTCTTTTCAGATACTTTGCTTAACTTTCATAT
1 TT-ATTATCATATAATTTTCCTTTCAAACACTTTGCAAAACTTTCATAT
*
319901 TTATTTTCATA
1 TTATTATCATA
319912 GTTCACTGTA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
47 2 0.04
48 14 0.28
49 34 0.68
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.52
Consensus pattern (48 bp):
TTATTATCATATAATTTTCCTTTCAAACACTTTGCAAAACTTTCATAT
Found at i:322659 original size:20 final size:20
Alignment explanation
Indices: 322634--322687 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
322624 ATGAGTACTT
322634 ATGAGCTATGAAATAATATC
1 ATGAGCTATGAAATAATATC
322654 ATGAGCTATGAAATAATATC
1 ATGAGCTATGAAATAATATC
*
322674 ATGAGCTATAAAAT
1 ATGAGCTATGAAAT
322688 GGTATGAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (20 bp):
ATGAGCTATGAAATAATATC
Found at i:325262 original size:18 final size:19
Alignment explanation
Indices: 325231--325281 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
325221 ACTTAAATTT
*
325231 TTTTATGTGTTTTTAATCC
1 TTTTATGTGATTTTAATCC
* *
325250 TTTT-TGTGATTTTATTTC
1 TTTTATGTGATTTTAATCC
*
325268 TTTTCT-TGATTTTA
1 TTTTATGTGATTTTA
325282 CTTTTCTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.14, C:0.08, G:0.10, T:0.69
Consensus pattern (19 bp):
TTTTATGTGATTTTAATCC
Found at i:334838 original size:29 final size:30
Alignment explanation
Indices: 334791--334853 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
334781 AAAATTACAT
* *
334791 TTTAGTCTCTAAACTTTTCTAAATTTATAC
1 TTTAGTCTCTAAACTTTTCAAAACTTATAC
*
334821 TTTAGTCAT-TAAAC-TTTCAAAACTTATAT
1 TTTAGTC-TCTAAACTTTTCAAAACTTATAC
334850 TTTA
1 TTTA
334854 TTCACTAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 16 0.55
30 12 0.41
31 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.03, T:0.49
Consensus pattern (30 bp):
TTTAGTCTCTAAACTTTTCAAAACTTATAC
Found at i:337187 original size:17 final size:16
Alignment explanation
Indices: 337160--337193 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
337150 TACACATTAT
337160 TTAATCATATAATTCA
1 TTAATCATATAATTCA
*
337176 TTAATGCATATAGTTCA
1 TTAAT-CATATAATTCA
337193 T
1 T
337194 GTAGTTATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (16 bp):
TTAATCATATAATTCA
Found at i:340837 original size:15 final size:13
Alignment explanation
Indices: 340817--340864 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 13
340807 TGTCTAGGTT
340817 TTAATTAATTATTTA
1 TTAATT-ATTA-TTA
340832 TTAATTTATTATTA
1 TTAA-TTATTATTA
340846 TT-ATTATTATTA
1 TTAATTATTATTA
340858 TT-ATTAT
1 TTAATTAT
340865 CTTTTACATT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 16 0.50
13 1 0.03
14 5 0.16
15 8 0.25
16 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTAATTATTATTA
Found at i:340845 original size:3 final size:3
Alignment explanation
Indices: 340824--340864 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
340814 GTTTTAATTA
*
340824 ATT ATTT ATT AAT -TT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
340865 CTTTTACATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 30 0.88
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:343442 original size:43 final size:42
Alignment explanation
Indices: 343395--343683 Score: 303
Period size: 43 Copynumber: 6.8 Consensus size: 42
343385 ATAGGTAAAT
* *
343395 ATCTATTA-CGGCGTTTTTTGAACAAACGCCGCAAAAGGTCGAT
1 ATCTA-TAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC-AG
* * * *
343438 ATCTATAGCGGCATTTTTGGAATAAACGCCGCAAAAAGTTATG
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCA-G
* * * * * *
343481 ATATATAGCGGCGTTTCTAGAAAAAACGCCACAAAATGTCAG
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAG
* *
343523 ATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGATAAG
1 ATCTATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAGGTCAG
* * * *
343566 ACCTAT-GCTGGCATTTTTAGAACAAACGCCGTAAAAGGTCAG
1 ATCTATAGC-GGCGTTTTTGGAACAAACGCCGCAAAAGGTCAG
* * *
343608 ACCTATAGTGGCGTTTTTGGACACAAACGCCGCAAAAAGTCAG
1 ATCTATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAGGTCAG
*
343651 ACCTATAGCGGCGTTTTTGGATACAAACGCCGC
1 ATCTATAGCGGCGTTTTTGGA-ACAAACGCCGC
343684 TAATTACCTT
Statistics
Matches: 205, Mismatches: 35, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
42 58 0.28
43 147 0.72
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (42 bp):
ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAG
Found at i:343535 original size:128 final size:128
Alignment explanation
Indices: 343395--343683 Score: 343
Period size: 128 Copynumber: 2.3 Consensus size: 128
343385 ATAGGTAAAT
* * * * * *
343395 ATCTATTA-CGGCGTTTTTTGA-ACAAACGCCGCAAAAGGTCGATATCTATAGC-GGCATTTTTG
1 ATCTA-TAGCGGCGTTTTTGGATACAAACGCCGCAAAAGAT-AAGACCTAT-GCTGGCATTTTTA
* * * *
343457 GAATAAACGCCGCAAAAAGTTATGATATATAGCGGCGTTTCTAGA-AAAAACGCCACAAAATGTC
63 GAACAAACGCCGCAAAAAGTCA-GACATATAGCGGCGTTTCTAGACAAAAACGCCACAAAAAGTC
343521 AG
127 AG
343523 ATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGATAAGACCTATGCTGGCATTTTTAGAA
1 ATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGATAAGACCTATGCTGGCATTTTTAGAA
* * * * * * * *
343588 CAAACGCCGTAAAAGGTCAGACCTATAGTGGCGTTTTTGGACACAAACGCCGCAAAAAGTCAG
66 CAAACGCCGCAAAAAGTCAGACATATAGCGGCGTTTCTAGACAAAAACGCCACAAAAAGTCAG
*
343651 ACCTATAGCGGCGTTTTTGGATACAAACGCCGC
1 ATCTATAGCGGCGTTTTTGGATACAAACGCCGC
343684 TAATTACCTT
Statistics
Matches: 138, Mismatches: 19, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
127 21 0.15
128 100 0.72
129 17 0.12
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (128 bp):
ATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGATAAGACCTATGCTGGCATTTTTAGAA
CAAACGCCGCAAAAAGTCAGACATATAGCGGCGTTTCTAGACAAAAACGCCACAAAAAGTCAG
Found at i:343587 original size:85 final size:84
Alignment explanation
Indices: 343403--343683 Score: 296
Period size: 85 Copynumber: 3.3 Consensus size: 84
343393 ATATCTATTA
* * * * *
343403 CGGCGTTTTTTGAACAAACGCCGCAAAAGGTCGATATCTATAGCGGCATTTTTGGAATAAACGCC
1 CGGCATTTTTAGAACAAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAACGCC
* * *
343468 GCAAAAAGTTATGATATATAG
65 GC-AAAAGATAAGACATATAG
* * * * *
343489 CGGCGTTTCTAGAAAAAACGCCACAAAATGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCC
1 CGGCATTTTTAGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-ACAAACGCC
*
343554 GCAAAAGATAAGACCTAT-G
65 GCAAAAGATAAGACATATAG
* * *
343573 CTGGCATTTTTAGAACAAACGCCGTAAAAGGTCAGACCTATAGTGGCGTTTTTGGACACAAACGC
1 C-GGCATTTTTAGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-ACAAACGC
* *
343638 CGCAAAA-AGTCAGACCTATAG
64 CGCAAAAGA-TAAGACATATAG
* *
343659 CGGCGTTTTTGGATACAAACGCCGC
1 CGGCATTTTTAGA-ACAAACGCCGC
343684 TAATTACCTT
Statistics
Matches: 165, Mismatches: 25, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
84 3 0.02
85 113 0.68
86 49 0.30
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.23
Consensus pattern (84 bp):
CGGCATTTTTAGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAACGCCG
CAAAAGATAAGACATATAG
Found at i:347292 original size:41 final size:41
Alignment explanation
Indices: 347235--347742 Score: 500
Period size: 41 Copynumber: 12.3 Consensus size: 41
347225 TTGTAAACAC
* * * * * *
347235 AAACGCCACTATAGTACAAGTGTATAGCAGCGTTTGAATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
*
347276 AAACGCCACTAAAGTACGAGTCTTTAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* *
347317 ACAA-GTCAATAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 A-AACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * * *
347358 AAATGCCACTAAATTACGAGTCTTTAGCGACATTTGTAAACA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA-A
* * * * * * *
347400 CAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAA
1 -AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
347442 AAATGCCACTAAAGTACGCGTCTTTAGCGGAGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
*
347483 AAACGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * * * *
347524 AAATGCCTCTAAATTATGAGTCTTTAGCAGCGTTTGTAAACA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA-A
* * * * *
347566 TAAACGCCACTATAGTAC-ATGTGTATAACGACGTTTGTATAA
1 -AAACGCCACTAAAGTACGA-GTCTTTAGCGGCGTTTGTATAA
** * *
347608 AAACGCCACTAAAGTATAATTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* *
347649 AAATGCCACTAAATTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * * *
347690 AAACACCACTAAAATACTACTCTTTCGCGGCGTTTGCTGA-AA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTG-T-ATAA
347732 AAACGCCACTA
1 AAACGCCACTA
347743 TCGATGAACC
Statistics
Matches: 382, Mismatches: 75, Indels: 19
0.80 0.16 0.04
Matches are distributed among these distances:
40 2 0.01
41 301 0.79
42 21 0.05
43 58 0.15
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
Found at i:347575 original size:125 final size:123
Alignment explanation
Indices: 347235--347742 Score: 463
Period size: 125 Copynumber: 4.1 Consensus size: 123
347225 TTGTAAACAC
* * * *
347235 AAACGCCACTATAGTACAAGTGTATAGCAGCGTTTGAATAAAAACGCCACTAAAGTACGAGTCTT
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTT
* * * *
347300 TAGCGACGTTTGTATAAACAA-GTCAATAAAGTACGA-GTCTTTAGCGGCGTTTGTATAA
66 TAGCGACGTTTGTA-AAAAAACGCCACTAAAGTAC-ACGTCTTTAGCGGAGTTTGTATAA
* * * * * * * * * *
347358 AAATGCCACTAAATTACGAGTCTTTAGCGACATTTGTAAACACAAACGCCACTATAGTACAAGTG
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATA-A-AAACGCCACTAAAGTACGAGTC
* * * *
347423 TATAACGACGTTTG-AATAAAAATGCCACTAAAGTACGCGTCTTTAGCGGAGTTTGTATAA
64 TTTAGCGACGTTTGTAA-AAAAACGCCACTAAAGTACACGTCTTTAGCGGAGTTTGTATAA
** * * * * *
347483 AAACGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAAAAATGCCTCTAAATTATGAGTCTT
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTT
* * * * *
347548 TAGC-AGCGTTTGTAAACATAAACGCCACTATAGTACATGTGTATAAC-GACGTTTGTATAA
66 TAGCGA-CGTTTGTAAA-A-AAACGCCACTAAAGTACACGTCTTTAGCGGA-GTTTGTATAA
* * * *
347608 AAACGCCACTAAAGTATAATTCTATAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTT
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTT
* * * * * *
347673 TAGCGGCGTTTGTATAAAAACACCACTAAAATACTAC-TCTTTCGCGGCGTTTGCTGA-AA
66 TAGCGACGTTTGTAAAAAAACGCCACTAAAGTAC-ACGTCTTTAGCGGAGTTTG-T-ATAA
347732 AAACGCCACTA
1 AAACGCCACTA
347743 TCGATGAACC
Statistics
Matches: 311, Mismatches: 59, Indels: 29
0.78 0.15 0.07
Matches are distributed among these distances:
122 1 0.00
123 79 0.25
124 29 0.09
125 202 0.65
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (123 bp):
AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTT
TAGCGACGTTTGTAAAAAAACGCCACTAAAGTACACGTCTTTAGCGGAGTTTGTATAA
Found at i:347725 original size:166 final size:165
Alignment explanation
Indices: 347218--347743 Score: 718
Period size: 166 Copynumber: 3.2 Consensus size: 165
347208 TTGTAAACTT
*
347218 GCGGCATTTGTAAACACAAACGCCACTATAGTACAAGTGTATAGC-AGCGTTTGAATAAAAACGC
1 GCGGCATTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGA-CGTTTGAATAAAAACGC
* * *
347282 CACTAAAGTACGAGTCTTTAGCGACGTTTGTATAAACAAGTCAATAAAGTACGAGTCTTTAGCGG
65 CACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAA-AAGCCACTAAAGTACGAGTCTTTAGCGG
*
347347 CGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
129 CGTTTGTATAAAAATGCCACTAAATTACTAGTCTTTA
* *
347384 GCGACATTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAATGCC
1 GCGGCATTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAACGCC
* * *
347449 ACTAAAGTACGCGTCTTTAGCGGAGTTTGTATAAAAACGCCACTAAAGTATGAGTCTTTAGCGGC
66 ACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAA-GCCACTAAAGTACGAGTCTTTAGCGGC
*
347514 GTTTGTATAAAAATGCCTCTAAATTA-TGAGTCTTTA
130 GTTTGTATAAAAATGCCACTAAATTACT-AGTCTTTA
* * * * *
347550 GCAGCGTTTGTAAACATAAACGCCACTATAGTACATGTGTATAACGACGTTTGTATAAAAACGCC
1 GCGGCATTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAACGCC
** * * *
347615 ACTAAAGTATAATTCTATAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGC
66 ACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAA-GCCACTAAAGTACGAGTCTTTAGCGGC
** * * *
347680 GTTTGTATAAAAACACCACTAAAATACTACTCTTTC
130 GTTTGTATAAAAATGCCACTAAATTACTAGTCTTTA
* *
347716 GCGGCGTTTGCTGAA-A-AAACGCCACTAT
1 GCGGCATTTG-TAAACACAAACGCCACTAT
347744 CGATGAACCT
Statistics
Matches: 320, Mismatches: 35, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
165 14 0.04
166 301 0.94
167 5 0.02
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (165 bp):
GCGGCATTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAACGCC
ACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAGCCACTAAAGTACGAGTCTTTAGCGGCG
TTTGTATAAAAATGCCACTAAATTACTAGTCTTTA
Found at i:353016 original size:35 final size:35
Alignment explanation
Indices: 352942--353050 Score: 116
Period size: 38 Copynumber: 3.1 Consensus size: 35
352932 AGATTAAATC
*
352942 AAAGCAGAGAGAAAAGAAAAAAGCAGAGAGAAAAGAAA
1 AAAGCAGAGAGAGAA-AAAAAAGCA-A-AGAAAAGAAA
* *
352980 AAAGCAGAGAGAGAAAAACAAAGCAAAAAAACAAAAA
1 AAAGCAGAGAGAGAAAAA-AAAGCAAAGAAA-AGAAA
*
353017 AAAGCA-A-AGAG-AAAAAAAGCAAATAAAAGAAA
1 AAAGCAGAGAGAGAAAAAAAAGCAAAGAAAAGAAA
353049 AA
1 AA
353051 GAAGAAAGAG
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
32 6 0.09
33 11 0.17
34 4 0.06
35 4 0.06
36 5 0.08
37 14 0.22
38 20 0.31
ACGTcount: A:0.72, C:0.07, G:0.19, T:0.01
Consensus pattern (35 bp):
AAAGCAGAGAGAGAAAAAAAAGCAAAGAAAAGAAA
Found at i:353024 original size:23 final size:25
Alignment explanation
Indices: 352993--353045 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
352983 GCAGAGAGAG
352993 AAAAA-CAAAG-CAAAAAAA-CAAA
1 AAAAAGCAAAGACAAAAAAAGCAAA
*
353015 AAAAAGCAAAGAGAAAAAAAGCAAA
1 AAAAAGCAAAGACAAAAAAAGCAAA
*
353040 TAAAAG
1 AAAAAG
353046 AAAAAGAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 5 0.19
23 5 0.19
24 7 0.27
25 9 0.35
ACGTcount: A:0.77, C:0.09, G:0.11, T:0.02
Consensus pattern (25 bp):
AAAAAGCAAAGACAAAAAAAGCAAA
Found at i:353028 original size:37 final size:36
Alignment explanation
Indices: 352977--353061 Score: 97
Period size: 34 Copynumber: 2.4 Consensus size: 36
352967 GAGAGAAAAG
*
352977 AAAAAAGCAGAGAGAGAAAAACAAAGCAAA-AAAACAA
1 AAAAAAGCAAAGAGAG-AAAA-AAAGCAAATAAAACAA
*
353014 AAAAAAGC-AA-AGAGAAAAAAAGCAAATAAAAGAA
1 AAAAAAGCAAAGAGAGAAAAAAAGCAAATAAAACAA
*
353048 AAAGAAG-AAAGAGA
1 AAAAAAGCAAAGAGA
353062 ACAGATTGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
33 8 0.19
34 18 0.43
35 7 0.17
36 1 0.02
37 8 0.19
ACGTcount: A:0.74, C:0.07, G:0.18, T:0.01
Consensus pattern (36 bp):
AAAAAAGCAAAGAGAGAAAAAAAGCAAATAAAACAA
Found at i:353034 original size:19 final size:19
Alignment explanation
Indices: 352942--353034 Score: 109
Period size: 19 Copynumber: 4.9 Consensus size: 19
352932 AGATTAAATC
*
352942 AAAGCAGAGAGAAAAGAAA
1 AAAGCAGAGAGAAAAAAAA
*
352961 AAAGCAGAGAGAAAAGAAA
1 AAAGCAGAGAGAAAAAAAA
* *
352980 AAAGCAGAGAGAGAAAAAC
1 AAAGCAGAGAGAAAAAAAA
*
352999 AAAGCA-A-AAAAACAAAAA
1 AAAGCAGAGAGAAA-AAAAA
*
353017 AAAGCAAAGAGAAAAAAA
1 AAAGCAGAGAGAAAAAAA
353035 GCAAATAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
17 3 0.05
18 11 0.17
19 46 0.72
20 4 0.06
ACGTcount: A:0.72, C:0.08, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAGCAGAGAGAAAAAAAA
Found at i:353050 original size:33 final size:32
Alignment explanation
Indices: 352958--353062 Score: 97
Period size: 33 Copynumber: 3.0 Consensus size: 32
352948 GAGAGAAAAG
352958 AAAAAAGCAGAGAGAAAAG-AAAAAAGCAGAGAGAGAA
1 AAAAAAGCA-A-A-AAAAGAAAAAAAGCA-A-AGAG-A
*
352995 AAACAAAGCAAAAAAACAAAAAAAAGCAAAGAGA
1 AAA-AAAGCAAAAAAA-GAAAAAAAGCAAAGAGA
353029 AAAAAAGCAAATAAAAGAAAAAGAAG-AAAGAGA
1 AAAAAAGCAAA-AAAAGAAAAA-AAGCAAAGAGA
353062 A
1 A
353063 CAGATTGAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
33 21 0.34
34 11 0.18
35 8 0.13
36 2 0.03
37 13 0.21
38 6 0.10
ACGTcount: A:0.73, C:0.07, G:0.19, T:0.01
Consensus pattern (32 bp):
AAAAAAGCAAAAAAAGAAAAAAAGCAAAGAGA
Found at i:355751 original size:35 final size:36
Alignment explanation
Indices: 355710--355814 Score: 101
Period size: 37 Copynumber: 2.9 Consensus size: 36
355700 CTATAGACAT
355710 TTTTCTT-GAAACAAA-ATTGATCTCACTTGAGATTG
1 TTTTCTTAGAAACAAATATTG-TCTCACTTGAGATTG
* * **
355745 TTTTCTTAGAAACAAATTTTGTCTCGCTTGAGACAG
1 TTTTCTTAGAAACAAATATTGTCTCACTTGAGATTG
*
355781 TTATTCTTA-AGAAGAAAT-TGTGTCTCACTTGAGA
1 TT-TTCTTAGA-AACAAATAT-TGTCTCACTTGAGA
355815 CAGTCTTCCT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
35 7 0.12
36 24 0.41
37 28 0.47
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.39
Consensus pattern (36 bp):
TTTTCTTAGAAACAAATATTGTCTCACTTGAGATTG
Found at i:355827 original size:37 final size:37
Alignment explanation
Indices: 355758--355829 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
355748 TCTTAGAAAC
* * *
355758 AAATTTTGTCTCGCTTGAGACAGTTATTCTTAAGAAG
1 AAATTGTGTCTCACTTGAGACAGTTATCCTTAAGAAG
355795 AAATTGTGTCTCACTTGAGACAGTCT-TCCTTAAGA
1 AAATTGTGTCTCACTTGAGACAGT-TATCCTTAAGA
355830 CACAAACATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 30 0.97
38 1 0.03
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (37 bp):
AAATTGTGTCTCACTTGAGACAGTTATCCTTAAGAAG
Found at i:356097 original size:21 final size:21
Alignment explanation
Indices: 356073--356127 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
356063 ACAATTGAGA
*
356073 TTGTTTCACTTGAAAAAAAAT
1 TTGTCTCACTTGAAAAAAAAT
* *
356094 TTGTCTCTCTTGAAAAAAATT
1 TTGTCTCACTTGAAAAAAAAT
356115 TTGTCTCACTTGA
1 TTGTCTCACTTGA
356128 GACAGTTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.42
Consensus pattern (21 bp):
TTGTCTCACTTGAAAAAAAAT
Found at i:356164 original size:37 final size:37
Alignment explanation
Indices: 356099--356218 Score: 143
Period size: 37 Copynumber: 3.3 Consensus size: 37
356089 AAAATTTGTC
* *
356099 TCTCTTGAAA-AAAATTTTGTCTCACTTGAGACAGTT
1 TCTCTTGAAACAAAGTTTCGTCTCACTTGAGACAGTT
* *
356135 TCTCTCGAAACAAAGTTTCGTCTCGCTTGAGACAGTT
1 TCTCTTGAAACAAAGTTTCGTCTCACTTGAGACAGTT
* * ** * *
356172 TCTCTTGAAACAAAGTTTTGTCCCTGTTGAGGCAATT
1 TCTCTTGAAACAAAGTTTCGTCTCACTTGAGACAGTT
356209 TCTCTTGAAA
1 TCTCTTGAAA
356219 TATAAACAAT
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
36 9 0.12
37 63 0.88
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (37 bp):
TCTCTTGAAACAAAGTTTCGTCTCACTTGAGACAGTT
Found at i:356536 original size:139 final size:138
Alignment explanation
Indices: 356286--356710 Score: 566
Period size: 139 Copynumber: 3.1 Consensus size: 138
356276 CTATTGAAAA
* * *
356286 AAATTAACCCTAAAGACGGCTAGACGTCTTCATCACGTAGGAACAATGTCGTT-CACTGACTAGA
1 AAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAGGAACAATGTC-TTCCAC-GACCAGA
* * *
356350 TCTCCTCATCACGTAGGAGCAGTGTCGTCCTCAGATAACCAGACTTCCTCATCATGTAGGAACCA
64 TCTCCTCATCACGTAGGAGCAGTGTCATTCTCAGATAACCAGACTTCCTCATCACGTAGGAACCA
356415 TGTTGTCTCC
129 TGTTGTCTCC
* ** * *
356425 AAATTATCCCTAAAGATGATTAGACATCCTCATCACGTAGGAACAATATCTTCCATCGACCAGAT
1 AAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAGGAACAATGTCTTCCA-CGACCAGAT
* * * *
356490 CTCCTTATCACGTAGGAGCAGTGTCATTCTCATATAACCAGACTTCCTCATCACATAGAAACCAT
65 CTCCTCATCACGTAGGAGCAGTGTCATTCTCAGATAACCAGACTTCCTCATCACGTAGGAACCAT
356555 GTTGTCTCC
130 GTTGTCTCC
* *
356564 AAATTATCCCTAAAGAGGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCACCGACCAGAT
1 AAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAGGAACAATGTCTTCCA-CGACCAGAT
* * * * * *
356629 CTCCTCATCTA-GTAGGAACAGTGTCATTCTTAGACAATCAGACTTCTTCATCACGTAGGAACCG
65 CTCCTCATC-ACGTAGGAGCAGTGTCATTCTCAGATAACCAGACTTCCTCATCACGTAGGAACCA
*
356693 TGTTGTCACC
129 TGTTGTCTCC
*
356703 ATATTATC
1 AAATTATC
356711 TTCAAATTGA
Statistics
Matches: 249, Mismatches: 34, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
138 2 0.01
139 245 0.98
140 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (138 bp):
AAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAGGAACAATGTCTTCCACGACCAGATC
TCCTCATCACGTAGGAGCAGTGTCATTCTCAGATAACCAGACTTCCTCATCACGTAGGAACCATG
TTGTCTCC
Found at i:357479 original size:21 final size:20
Alignment explanation
Indices: 357453--357507 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
357443 ACATTCGAGG
357453 AAAAAACAAAAAAACCAGAGA
1 AAAAAACAAAAAAA-CAGAGA
* *
357474 AAAAAATAAAAAGAACTGAGA
1 AAAAAACAAAAA-AACAGAGA
357495 AAAAAACAAAAAA
1 AAAAAACAAAAAA
357508 TAAACAACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 27 0.90
22 2 0.07
ACGTcount: A:0.78, C:0.09, G:0.09, T:0.04
Consensus pattern (20 bp):
AAAAAACAAAAAAACAGAGA
Found at i:358591 original size:18 final size:19
Alignment explanation
Indices: 358568--358607 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
358558 TTTTTTCATA
358568 TTTGTT-TTATTTATTT-AT
1 TTTGTTCTTA-TTATTTGAT
358586 TTTGTTCTTATTATTTGAT
1 TTTGTTCTTATTATTTGAT
358605 TTT
1 TTT
358608 TTTATGCGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.15, C:0.03, G:0.07, T:0.75
Consensus pattern (19 bp):
TTTGTTCTTATTATTTGAT
Found at i:363319 original size:24 final size:24
Alignment explanation
Indices: 363292--363398 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
363282 AAACGGAGAT
*
363292 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
363316 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
363340 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
363364 ATCAGATGTCAAAATAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
363388 ATCAGAAATCA
1 ATCAGAAATCA
363399 GATAAAATAT
Statistics
Matches: 62, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:363398 original size:48 final size:48
Alignment explanation
Indices: 363292--363400 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
363282 AAACGGAGAT
* * * *
363292 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
363340 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAATAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
363388 ATCAGAAATCAGA
1 ATCAGAAATCAGA
363401 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:365900 original size:18 final size:18
Alignment explanation
Indices: 365877--365946 Score: 87
Period size: 18 Copynumber: 4.2 Consensus size: 18
365867 AACGGTCAAC
*
365877 GGTCAACGGGTGGGGTCG
1 GGTCAACGGGTCGGGTCG
365895 GGTCAA-----CGGGTCG
1 GGTCAACGGGTCGGGTCG
*
365908 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
365926 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
365944 GGT
1 GGT
365947 TGTGACCGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
13 11 0.25
18 33 0.75
ACGTcount: A:0.13, C:0.19, G:0.51, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:365924 original size:31 final size:31
Alignment explanation
Indices: 365881--365941 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
365871 GTCAACGGTC
*
365881 AACGGGTGGGGTCGGGTCAACGGGTCGGGTA
1 AACGGGTCGGGTCGGGTCAACGGGTCGGGTA
365912 AACGGGTCGGGTCGGGTCAACGGGTCGGGT
1 AACGGGTCGGGTCGGGTCAACGGGTCGGGT
365942 CGGGTTGTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.15, C:0.18, G:0.51, T:0.16
Consensus pattern (31 bp):
AACGGGTCGGGTCGGGTCAACGGGTCGGGTA
Found at i:365942 original size:13 final size:13
Alignment explanation
Indices: 365889--365924 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
365879 TCAACGGGTG
365889 GGGTCGGGTCAAC
1 GGGTCGGGTCAAC
*
365902 GGGTCGGGTAAAC
1 GGGTCGGGTCAAC
365915 GGGTCGGGTC
1 GGGTCGGGTC
365925 GGGTCAACGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.14, C:0.19, G:0.50, T:0.17
Consensus pattern (13 bp):
GGGTCGGGTCAAC
Found at i:367310 original size:13 final size:13
Alignment explanation
Indices: 367292--367321 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
367282 GTTCCAACCC
*
367292 GACCCGACCCGTT
1 GACCCGACCAGTT
367305 GACCCGACCAGTT
1 GACCCGACCAGTT
367318 GACC
1 GACC
367322 GGGTGATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.43, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCAGTT
Found at i:367370 original size:29 final size:30
Alignment explanation
Indices: 367323--367409 Score: 99
Period size: 29 Copynumber: 2.9 Consensus size: 30
367313 CAGTTGACCG
* *
367323 GGTGATATTTTCGTAATTATTTTTAAAAAT
1 GGTGTTATTTTCGAAATTATTTTTAAAAAT
*
367353 -GTGTTATTTTTGAAATTATTTTT-AAAAT
1 GGTGTTATTTTCGAAATTATTTTTAAAAAT
*
367381 GGTGTTGTTTTCGTAAA-TATTTCTTAAAA
1 GGTGTTATTTTCG-AAATTATTT-TTAAAA
367410 GGGTGATAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
28 5 0.10
29 35 0.73
30 5 0.10
31 3 0.06
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.52
Consensus pattern (30 bp):
GGTGTTATTTTCGAAATTATTTTTAAAAAT
Found at i:368539 original size:117 final size:117
Alignment explanation
Indices: 368330--368547 Score: 294
Period size: 117 Copynumber: 1.9 Consensus size: 117
368320 GGAAGTATTT
** *
368330 CAGGCTCCTTTGCTGTGGGCTCAGGGTAAGACCTTATTGGTGTGCAGGTAGGTGTATGGTTCTGG
1 CAGGCTCCTCAGCTGTGGGCTCAGGGTAAGACCTTACTGGTGTGCAGGTAGGTGTATGGTTCTGG
* * * * * * * *
368395 GGAACCTTCACATTTTGGTGATTGGAGTGATTGGATTGGGGAGTTATTACCG
66 AGAACATACAAATTCTAGTAATCGGAGTGATTGGATTGGGGAGTTATTACCG
* * *
368447 CAGGCTCCTCAGCTTTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGT-GGATGTATGGTTCTG
1 CAGGCTCCTCAGCTGTGGGCTCAGGGTAAGACCTTACTGGTGTGCAGGTAGG-TGTATGGTTCTG
368511 GAGAACATACAAATTCTAGTAATCGGAGTGATTGGAT
65 GAGAACATACAAATTCTAGTAATCGGAGTGATTGGAT
368548 GTAAATAGTG
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
116 2 0.02
117 84 0.98
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.32
Consensus pattern (117 bp):
CAGGCTCCTCAGCTGTGGGCTCAGGGTAAGACCTTACTGGTGTGCAGGTAGGTGTATGGTTCTGG
AGAACATACAAATTCTAGTAATCGGAGTGATTGGATTGGGGAGTTATTACCG
Found at i:374578 original size:13 final size:13
Alignment explanation
Indices: 374560--374603 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
374550 GGTTCTAACC
*
374560 TGACCCAACCCAT
1 TGACCCGACCCAT
374573 TGACCCGACCCAT
1 TGACCCGACCCAT
*
374586 TGACCCGACCCGT
1 TGACCCGACCCAT
374599 TGACC
1 TGACC
374604 GTTGATCGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.23, C:0.45, G:0.16, T:0.16
Consensus pattern (13 bp):
TGACCCGACCCAT
Found at i:374656 original size:29 final size:29
Alignment explanation
Indices: 374612--374703 Score: 121
Period size: 29 Copynumber: 3.1 Consensus size: 29
374602 CCGTTGATCG
* *
374612 GGTGATATATTCGTAATTATTTTTAAAAC
1 GGTGCTATTTTCGTAATTATTTTTAAAAC
* *
374641 GGTGCTATTTTTGTAATTATTTTTAAAAT
1 GGTGCTATTTTCGTAATTATTTTTAAAAC
* *
374670 GGTGCTATTTTCGTAAATATTTCTTAAAAG
1 GGTGCTATTTTCGTAATTATTT-TTAAAAC
374700 GGTG
1 GGTG
374704 ATAATTGTGT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 45 0.82
30 10 0.18
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (29 bp):
GGTGCTATTTTCGTAATTATTTTTAAAAC
Found at i:374716 original size:30 final size:29
Alignment explanation
Indices: 374611--374716 Score: 90
Period size: 29 Copynumber: 3.6 Consensus size: 29
374601 ACCGTTGATC
* *
374611 GGGTGAT-ATATTCGTAATTATTTTTAAAA
1 GGGTGATAAT-TTTGTAAATATTTTTAAAA
* * * *
374640 CGGTGCTATTTTTGTAATTATTTTTAAAA
1 GGGTGATAATTTTGTAAATATTTTTAAAA
* *
374669 TGGTGCT-ATTTTCGTAAATATTTCTTAAAA
1 GGGTGATAATTTT-GTAAATATTT-TTAAAA
*
374699 GGGTGATAATTGTGTAAA
1 GGGTGATAATTTTGTAAA
374717 ATGGACGATC
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
28 4 0.06
29 38 0.60
30 17 0.27
31 4 0.06
ACGTcount: A:0.31, C:0.06, G:0.18, T:0.45
Consensus pattern (29 bp):
GGGTGATAATTTTGTAAATATTTTTAAAA
Found at i:380226 original size:16 final size:16
Alignment explanation
Indices: 380205--380245 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
380195 AGAGCCCCTA
380205 AATCATTCAGCATTTG
1 AATCATTCAGCATTTG
380221 AATCATTCAGCATTTG
1 AATCATTCAGCATTTG
380237 AATCATTCA
1 AATCATTCA
380246 ACGCTTAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.37
Consensus pattern (16 bp):
AATCATTCAGCATTTG
Found at i:385892 original size:17 final size:18
Alignment explanation
Indices: 385860--385893 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
385850 TAACATATTA
385860 AAAACAAAACATGAAAAT
1 AAAACAAAACATGAAAAT
*
385878 AAAAGAAAA-ATGAAAA
1 AAAACAAAACATGAAAA
385894 ACTTGAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.76, C:0.06, G:0.09, T:0.09
Consensus pattern (18 bp):
AAAACAAAACATGAAAAT
Found at i:395543 original size:10 final size:10
Alignment explanation
Indices: 395528--395555 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
395518 AACTACTCTC
395528 CCAGCTACTT
1 CCAGCTACTT
395538 CCAGCTACTT
1 CCAGCTACTT
395548 CCAGCTAC
1 CCAGCTAC
395556 CTCTAGTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.43, G:0.11, T:0.25
Consensus pattern (10 bp):
CCAGCTACTT
Found at i:412330 original size:22 final size:20
Alignment explanation
Indices: 412305--412344 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
412295 ATGTTTGTTT
412305 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
412327 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
412345 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:416595 original size:22 final size:20
Alignment explanation
Indices: 416570--416609 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
416560 ATGTTTGTTT
416570 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
416592 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
416610 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:416847 original size:15 final size:15
Alignment explanation
Indices: 416824--416854 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
416814 TATTCTTTTC
*
416824 ATAATATATATTATA
1 ATAACATATATTATA
416839 ATAACATATATTATA
1 ATAACATATATTATA
416854 A
1 A
416855 AGCTAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAACATATATTATA
Found at i:424656 original size:10 final size:10
Alignment explanation
Indices: 424641--424715 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
424631 CATTTAATAA
424641 ATAAACGAAC
1 ATAAACGAAC
424651 ATAAACGAAC
1 ATAAACGAAC
424661 ----ACGAAC
1 ATAAACGAAC
*
424667 ATAAATGAAC
1 ATAAACGAAC
** *
424677 ACGAAC-ATAA
1 ATAAACGA-AC
424687 ATGAACACGAAC
1 AT-AA-ACGAAC
424699 ATAAACGAAC
1 ATAAACGAAC
424709 ATAAACG
1 ATAAACG
424716 TTGGAGACCC
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 33 0.67
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:424666 original size:16 final size:16
Alignment explanation
Indices: 424645--424709 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
424635 TAATAAATAA
424645 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
424661 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
424677 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
424693 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
424709 A
1 A
424710 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:424682 original size:32 final size:32
Alignment explanation
Indices: 424637--424709 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
424627 CGTTCATTTA
424637 ATAAAT-AA-ACGAACATAAACGAACACGAAC
1 ATAAATGAACACGAACATAAACGAACACGAAC
*
424667 ATAAATGAACACGAACATAAATGAACACGAAC
1 ATAAATGAACACGAACATAAACGAACACGAAC
*
424699 ATAAACGAACA
1 ATAAATGAACA
424710 TAAACGTTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
30 6 0.15
31 2 0.05
32 31 0.79
ACGTcount: A:0.59, C:0.19, G:0.11, T:0.11
Consensus pattern (32 bp):
ATAAATGAACACGAACATAAACGAACACGAAC
Found at i:425479 original size:14 final size:14
Alignment explanation
Indices: 425462--425517 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
425452 AATGAACATA
425462 AACGAACATAATCG
1 AACGAACATAATCG
425476 AACGAACAT-A---
1 AACGAACATAATCG
* *
425486 AACAAACATAACCG
1 AACGAACATAATCG
425500 AACGAACATAATCG
1 AACGAACATAATCG
425514 AACG
1 AACG
425518 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:425482 original size:24 final size:24
Alignment explanation
Indices: 425455--425516 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
425445 ATAAATGAAT
*
425455 GAACATAAACGAACATAATCGAAC
1 GAACATAAACGAACATAACCGAAC
*
425479 GAACATAAACAAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
*
425503 GAACATAATCGAAC
1 GAACATAAACGAAC
425517 GTTCACGAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.55, C:0.23, G:0.11, T:0.11
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:428243 original size:22 final size:23
Alignment explanation
Indices: 428216--428266 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 23
428206 AAATCCAGCA
428216 AAGAAATCGAAGCACTC-AAAAG
1 AAGAAATCGAAGCACTCAAAAAG
*
428238 AAGAAATTGAAGCACTCAAAAAG
1 AAGAAATCGAAGCACTCAAAAAG
428261 AAGAAA
1 AAGAAA
428267 AAGAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.59, C:0.14, G:0.18, T:0.10
Consensus pattern (23 bp):
AAGAAATCGAAGCACTCAAAAAG
Found at i:428280 original size:19 final size:19
Alignment explanation
Indices: 428256--428292 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
428246 GAAGCACTCA
428256 AAAAGAAGAA-AAAGAAAAT
1 AAAAGAA-AAGAAAGAAAAT
428275 AAAAGAAAAGAAAGAAAA
1 AAAAGAAAAGAAAGAAAA
428293 GTTGAACTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (19 bp):
AAAAGAAAAGAAAGAAAAT
Found at i:429521 original size:24 final size:21
Alignment explanation
Indices: 429487--429529 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
429477 TCCACAAGAC
*
429487 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
429509 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
429530 AGAATGTGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:431848 original size:4 final size:5
Alignment explanation
Indices: 431814--431851 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
431804 GAAGCACTCA
*
431814 AAAAG AAGA- AAAAG AAAAG AAAAG AAAAG -AAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
431852 TTGAAGCACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 7 0.24
5 22 0.76
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:433100 original size:24 final size:21
Alignment explanation
Indices: 433066--433108 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
433056 TCCACAAGAC
*
433066 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
433088 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
433109 AGAATGTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:439351 original size:11 final size:13
Alignment explanation
Indices: 439319--439348 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
439309 TGGCCAAAGA
439319 TGAAAAGGTATGT
1 TGAAAAGGTATGT
439332 TGAAAAGGTATG-
1 TGAAAAGGTATGT
439344 TGAAA
1 TGAAA
439349 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:442666 original size:32 final size:32
Alignment explanation
Indices: 442630--442692 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
442620 CACGACTAGG
442630 AAGCTTGGAGGAAGACCCGTGCACGCCCAAGT
1 AAGCTTGGAGGAAGACCCGTGCACGCCCAAGT
442662 AAGCTTGGAGGAAGACCCGTGCACGCCCAAG
1 AAGCTTGGAGGAAGACCCGTGCACGCCCAAG
442693 ATGATGCACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.29, C:0.29, G:0.32, T:0.11
Consensus pattern (32 bp):
AAGCTTGGAGGAAGACCCGTGCACGCCCAAGT
Found at i:443591 original size:11 final size:11
Alignment explanation
Indices: 443575--443600 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
443565 AATACAAAAA
443575 GAAGTGCAAGT
1 GAAGTGCAAGT
443586 GAAGTGCAAGT
1 GAAGTGCAAGT
443597 GAAG
1 GAAG
443601 AAATCAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.38, T:0.15
Consensus pattern (11 bp):
GAAGTGCAAGT
Found at i:443674 original size:4 final size:5
Alignment explanation
Indices: 443635--443677 Score: 54
Period size: 5 Copynumber: 9.0 Consensus size: 5
443625 GAAGCACTCA
* *
443635 AAAAG AAGA- AAAAC AAAAG AAAAG AAAAG AAAAG -AAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
443678 TTGAAGAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
4 7 0.21
5 26 0.79
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:443674 original size:9 final size:10
Alignment explanation
Indices: 443635--443677 Score: 54
Period size: 9 Copynumber: 4.5 Consensus size: 10
443625 GAAGCACTCA
*
443635 AAAAGAAGA-
1 AAAAGAAAAG
*
443644 AAAACAAAAG
1 AAAAGAAAAG
443654 AAAAGAAAAG
1 AAAAGAAAAG
443664 AAAAG-AAAG
1 AAAAGAAAAG
443673 AAAAG
1 AAAAG
443678 TTGAAGAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
9 16 0.53
10 14 0.47
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAG
Found at i:443677 original size:14 final size:14
Alignment explanation
Indices: 443635--443677 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
443625 GAAGCACTCA
*
443635 AAAAG-AAGAAAAAC
1 AAAAGAAAG-AAAAG
443649 AAAAGAAAAGAAAAG
1 AAAAG-AAAGAAAAG
443664 AAAAGAAAGAAAAG
1 AAAAGAAAGAAAAG
443678 TTGAAGAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 14 0.54
15 9 0.35
16 3 0.12
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAGAAAGAAAAG
Found at i:450148 original size:25 final size:25
Alignment explanation
Indices: 450101--450149 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
450091 ATAGGGTAAG
*
450101 GAAGAACTCCCATAGAAGCATCAAT
1 GAAGAACTCCCATAGAAGAATCAAT
*
450126 GAAGAACGT-CCATAGAATAATCAA
1 GAAGAAC-TCCCATAGAAGAATCAA
450150 GTTATGGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.16
Consensus pattern (25 bp):
GAAGAACTCCCATAGAAGAATCAAT
Found at i:451816 original size:24 final size:23
Alignment explanation
Indices: 451771--451816 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
451761 CTAACTTTTC
*
451771 TTATTTCATATGTTATACTATAG
1 TTATTTCATATATTATACTATAG
451794 TTATTATCATATATATATA-TATA
1 TTATT-TCATATAT-TATACTATA
451817 TATATATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 11 0.55
25 4 0.20
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (23 bp):
TTATTTCATATATTATACTATAG
Found at i:463777 original size:5 final size:5
Alignment explanation
Indices: 463763--463815 Score: 76
Period size: 5 Copynumber: 11.2 Consensus size: 5
463753 GTGCTTCAAC
*
463763 TTTC- TTTCT TTTCT TTTCT TTTC- TTTCT TTTCT TTTCT TCT-T TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
463810 TTTCT T
1 TTTCT T
463816 CTTTTGAGTG
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
4 11 0.25
5 33 0.75
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:463782 original size:14 final size:13
Alignment explanation
Indices: 463763--463820 Score: 80
Period size: 14 Copynumber: 4.2 Consensus size: 13
463753 GTGCTTCAAC
*
463763 TTTCTTTCTTTTCT
1 TTTCTTT-TCTTCT
463777 TTTCTTTTCTTTCT
1 TTTCTTTTC-TTCT
463791 TTTCTTTTCTTCTT
1 TTTCTTTTCTTC-T
463805 TTTCTTTTCTTCT
1 TTTCTTTTCTTCT
463818 TTT
1 TTT
463821 GAGTGCTTGC
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
13 8 0.20
14 33 0.80
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTCTTTTCTTCT
Found at i:463787 original size:19 final size:19
Alignment explanation
Indices: 463763--463815 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
463753 GTGCTTCAAC
463763 TTTCTTTCTTTTCTTTTCT
1 TTTCTTTCTTTTCTTTTCT
463782 TTTCTTTCTTTTCTTTTCT
1 TTTCTTTCTTTTCTTTTCT
463801 TCTT-TTTCTTTTCTT
1 T-TTCTTTCTTTTCTT
463816 CTTTTGAGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 31 0.94
20 2 0.06
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTCTTTCTTTTCTTTTCT
Found at i:467952 original size:19 final size:20
Alignment explanation
Indices: 467902--467952 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
467892 GAAACCCCTT
**
467902 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
*
467922 TGAAAATGCATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
467941 TGAATATACATG
1 TGAAAATACATG
467953 CTCTTGGCCG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:472785 original size:20 final size:20
Alignment explanation
Indices: 472756--472824 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
472746 TAATATAGTA
*
472756 GTATCAATACCATGGTAAGG
1 GTATCGATACCATGGTAAGG
472776 GTATCGATACC--GG-AAGGGG
1 GTATCGATACCATGGTAA--GG
* *
472795 GTATCTATACCATTGTAAGG
1 GTATCGATACCATGGTAAGG
472815 GTATCGATAC
1 GTATCGATAC
472825 TATAGAGCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
17 2 0.05
18 2 0.05
19 12 0.30
20 21 0.52
21 1 0.03
22 2 0.05
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (20 bp):
GTATCGATACCATGGTAAGG
Found at i:473370 original size:15 final size:15
Alignment explanation
Indices: 473352--473380 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
473342 ATTAAGAAAG
473352 GAAATGGAAAGAATT
1 GAAATGGAAAGAATT
473367 GAAATGGAAAGAAT
1 GAAATGGAAAGAAT
473381 AGTTATCAAA
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:0.55, C:0.00, G:0.28, T:0.17
Consensus pattern (15 bp):
GAAATGGAAAGAATT
Found at i:473569 original size:35 final size:37
Alignment explanation
Indices: 473523--473602 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
473513 TTTGAGAATT
*
473523 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
473558 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
473595 TGGTGATG
1 TGGTGATG
473603 GAAATAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:476092 original size:36 final size:36
Alignment explanation
Indices: 476018--476122 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
476008 ATTTATAAGT
* **
476018 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACCA
476053 TGGTGATGATATAGGCGTGATAATGGTGATGGACCA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACCA
476089 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
476123 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.29, C:0.06, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACCA
Found at i:480472 original size:13 final size:12
Alignment explanation
Indices: 480453--480538 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
480443 ATATAGGCGT
480453 GATATGGTGATG
1 GATATGGTGATG
480465 GAATATGGTGAT-
1 G-ATATGGTGATG
*
480477 GATATAGGCG-T-
1 GATAT-GGTGATG
480488 GATAATGGTGATG
1 GAT-ATGGTGATG
480501 GACTATGGTGAT-
1 GA-TATGGTGATG
*
480513 GATATAGGCG-T-
1 GATAT-GGTGATG
480524 GATAATGGTGATG
1 GAT-ATGGTGATG
480537 GA
1 GA
480539 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:480508 original size:36 final size:36
Alignment explanation
Indices: 480435--480539 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
480425 ATTTATAAGT
* *
480435 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
480470 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
480506 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
480540 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:483656 original size:35 final size:37
Alignment explanation
Indices: 483610--483689 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
483600 TTTGAGAATT
*
483610 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
483645 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
483682 TGGTGATG
1 TGGTGATG
483690 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:485095 original size:47 final size:48
Alignment explanation
Indices: 485016--485361 Score: 470
Period size: 47 Copynumber: 7.2 Consensus size: 48
485006 AAACAGAATA
485016 CATAACT-AAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* * *
485063 CATAACT-AAAAATGCATGAACGAATGCTTTAAGGCATGAAATGATGC
1 CATAACTAAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
*
485110 CATAACTAAAAACAATGCATGAACGGACGCATTAAGGCATGAAAGGATG-
1 CATAACT-AAAA-AATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* *
485159 CATAACT-AAAACTGCATGAACGGATGCATTAAGG-AAGAAAGGATGC
1 CATAACTAAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* * *
485205 CATAACTAAAAAAAATGCATGAACAGATACATTAAGGCATGAAAGGACGC
1 CATAACT--AAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* * * *
485255 TATAA-TCAAAAATGCATGAACGGATGGATTAAGGCATGATAGGATGC
1 CATAACTAAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* * *
485302 CATAACTAAAAAATGCATGAACCGATGCATTAAGGCATGAGAGGGTGC
1 CATAACTAAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
485350 CATAACTAAAAA
1 CATAACTAAAAA
485362 CGCATGTGAT
Statistics
Matches: 262, Mismatches: 28, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
45 10 0.04
46 29 0.11
47 93 0.35
48 49 0.19
49 35 0.13
50 46 0.18
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (48 bp):
CATAACTAAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
Found at i:485238 original size:95 final size:97
Alignment explanation
Indices: 485023--485367 Score: 493
Period size: 95 Copynumber: 3.6 Consensus size: 97
485013 ATACATAACT
*
485023 AAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAACGAAT
1 AAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAACGGAT
* *
485088 GCTTTAAGGCATGAAATGATGCCATAACTAAA
66 GCATTAAGGCATGAAAGGATGCCATAACTAAA
* * *
485120 AACAATGCATGAACGGACGCATTAAGGCATGAAAGGATG-CATAACTAAAACTGCATGAACGGAT
1 AAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAACGGAT
*
485184 GCATTAAGG-AAGAAAGGATGCCATAACTAAA
66 GCATTAAGGCATGAAAGGATGCCATAACTAAA
* * * *
485215 AAAAATGCATGAACAGATACATTAAGGCATGAAAGGACGCTATAA-TCAAAAATGCATGAACGGA
1 AAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACT-AAAAATGCATGAACGGA
* *
485279 TGGATTAAGGCATGATAGGATGCCATAACT--A
65 TGCATTAAGGCATGAAAGGATGCCATAACTAAA
* * * *
485310 AAAAATGCATGAACCGATGCATTAAGGCATGAGAGGGTGCCATAACTAAAAACGCATG
1 AAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATG
485368 TGATACGATC
Statistics
Matches: 220, Mismatches: 24, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
95 105 0.48
96 61 0.28
97 54 0.25
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (97 bp):
AAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAACGGAT
GCATTAAGGCATGAAAGGATGCCATAACTAAA
Found at i:489215 original size:24 final size:24
Alignment explanation
Indices: 489179--489286 Score: 101
Period size: 24 Copynumber: 4.5 Consensus size: 24
489169 AAATATTTTA
*
489179 TCTGATTTCTGACTTGAATTCTGT
1 TCTGATATCTGACTTGAATTCTGT
* * *
489203 TCTGATATATGACCTGAATTCTAT
1 TCTGATATCTGACTTGAATTCTGT
* * *
489227 TATGATTTCTGA-TATGGATTCTGT
1 TCTGATATCTGACT-TGAATTCTGT
**
489251 TCTGATATCTGTTTTGAATTCTGT
1 TCTGATATCTGACTTGAATTCTGT
* *
489275 TTTGATTTCTGA
1 TCTGATATCTGA
489287 TATCTCCGTT
Statistics
Matches: 65, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
24 64 0.98
25 1 0.02
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.50
Consensus pattern (24 bp):
TCTGATATCTGACTTGAATTCTGT
Found at i:489237 original size:48 final size:48
Alignment explanation
Indices: 489181--489289 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 48
489171 ATATTTTATC
489181 TGATTTCTGACT-TGAATTCTGTTCTGATATATGACCTGAATTCTATTA
1 TGATTTCTGA-TATGAATTCTGTTCTGATATATGACCTGAATTCTATTA
* * *** * *
489229 TGATTTCTGATATGGATTCTGTTCTGATATCTGTTTTGAATTCTGTTT
1 TGATTTCTGATATGAATTCTGTTCTGATATATGACCTGAATTCTATTA
489277 TGATTTCTGATAT
1 TGATTTCTGATAT
489290 CTCCGTTTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.50
Consensus pattern (48 bp):
TGATTTCTGATATGAATTCTGTTCTGATATATGACCTGAATTCTATTA
Found at i:489242 original size:12 final size:12
Alignment explanation
Indices: 489221--489285 Score: 51
Period size: 12 Copynumber: 5.4 Consensus size: 12
489211 ATGACCTGAA
*
489221 TTCTATTATGAT
1 TTCTGTTATGAT
*
489233 TTCTGATATGGA-
1 TTCTGTTAT-GAT
*
489245 TTCTGTTCTGAT
1 TTCTGTTATGAT
* * *
489257 ATCTGTTTTGAA
1 TTCTGTTATGAT
*
489269 TTCTGTTTTGAT
1 TTCTGTTATGAT
489281 TTCTG
1 TTCTG
489286 ATATCTCCGT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
11 2 0.05
12 38 0.90
13 2 0.05
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.55
Consensus pattern (12 bp):
TTCTGTTATGAT
Found at i:501610 original size:18 final size:19
Alignment explanation
Indices: 501589--501626 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
501579 GTATTTATTT
501589 TATACTAGTT-TAAT-CATA
1 TATACTA-TTATAATGCATA
501607 TATACTATTATAATGCATA
1 TATACTATTATAATGCATA
501626 T
1 T
501627 CATATTAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.11
18 11 0.61
19 5 0.28
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (19 bp):
TATACTATTATAATGCATA
Found at i:503414 original size:29 final size:28
Alignment explanation
Indices: 503378--503443 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
503368 AAAAATCAGC
** *
503378 AAAGAAAAGTCAAGCACTCCAAAAGAAG
1 AAAGAAAAAACAAGCACTCAAAAAGAAG
503406 -AAGAAAAAACAAGCACTCAAAAAGAAG
1 AAAGAAAAAACAAGCACTCAAAAAGAAG
503433 AAAAGAAAAAA
1 -AAAGAAAAAA
503444 AATAAAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 24 0.73
29 9 0.27
ACGTcount: A:0.67, C:0.14, G:0.15, T:0.05
Consensus pattern (28 bp):
AAAGAAAAAACAAGCACTCAAAAAGAAG
Found at i:516581 original size:23 final size:25
Alignment explanation
Indices: 516553--516603 Score: 88
Period size: 24 Copynumber: 2.1 Consensus size: 25
516543 ATATGCAAAG
516553 AAATTG-AAGCACTCAAAA-GAAGA
1 AAATTGTAAGCACTCAAAAGGAAGA
516576 AAATTGTAAGCACTCAAAAGGAAGA
1 AAATTGTAAGCACTCAAAAGGAAGA
516601 AAA
1 AAA
516604 AGAGAAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 6 0.23
24 12 0.46
25 8 0.31
ACGTcount: A:0.57, C:0.12, G:0.18, T:0.14
Consensus pattern (25 bp):
AAATTGTAAGCACTCAAAAGGAAGA
Found at i:550034 original size:13 final size:13
Alignment explanation
Indices: 550018--550057 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
550008 AGGAAACTAG
550018 AAAGTGAAAGTAA
1 AAAGTGAAAGTAA
* *
550031 AAAGAGAAAGTGA
1 AAAGTGAAAGTAA
550044 AAAGTGAAAAGTAA
1 AAAGTG-AAAGTAA
550058 GTGGGGTAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.25, T:0.12
Consensus pattern (13 bp):
AAAGTGAAAGTAA
Found at i:567660 original size:23 final size:23
Alignment explanation
Indices: 567618--567662 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
567608 TTTCCTTCCT
*
567618 TTTTGAGTGCTTTCAATTTCTTC
1 TTTTGAGTGATTTCAATTTCTTC
* *
567641 TTTTGAGTGATTTGATTTTCTT
1 TTTTGAGTGATTTCAATTTCTT
567663 TGCTGGATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.13, C:0.11, G:0.16, T:0.60
Consensus pattern (23 bp):
TTTTGAGTGATTTCAATTTCTTC
Found at i:568920 original size:14 final size:14
Alignment explanation
Indices: 568881--568922 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
568871 ATGGGCGTGA
*
568881 ATGGTGATGGAGA-
1 ATGGTGATGGAAAT
*
568894 ATGGTGATTGAAAT
1 ATGGTGATGGAAAT
*
568908 ATTGTGATGGAAAT
1 ATGGTGATGGAAAT
568922 A
1 A
568923 GATAGTATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.31
Consensus pattern (14 bp):
ATGGTGATGGAAAT
Found at i:572254 original size:16 final size:16
Alignment explanation
Indices: 572222--572269 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
572212 AAGGTAATGC
572222 AATAAGAATAGATGAAAG
1 AATAAGAA-A-ATGAAAG
*
572240 AATAAGAAAATGAAAT
1 AATAAGAAAATGAAAG
* *
572256 AGTAAGAAAGTGAA
1 AATAAGAAAATGAA
572270 GATAACTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 18 0.67
17 1 0.04
18 8 0.30
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (16 bp):
AATAAGAAAATGAAAG
Found at i:572909 original size:13 final size:13
Alignment explanation
Indices: 572891--572929 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
572881 ATGGACGTGA
*
572891 ATGGTGATGGAGG
1 ATGGTGATGGAAG
*
572904 ATGGTGATTGAAAG
1 ATGGTGA-TGGAAG
572918 ATGGTGATGGAA
1 ATGGTGATGGAA
572930 ATAGATAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.31, C:0.00, G:0.44, T:0.26
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:572922 original size:14 final size:14
Alignment explanation
Indices: 572891--572930 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
572881 ATGGACGTGA
*
572891 ATGGTGATGG-AGG
1 ATGGTGATGGAAAG
*
572904 ATGGTGATTGAAAG
1 ATGGTGATGGAAAG
572918 ATGGTGATGGAAA
1 ATGGTGATGGAAA
572931 TAGATAGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.33, C:0.00, G:0.42, T:0.25
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:584089 original size:26 final size:25
Alignment explanation
Indices: 584041--584090 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
584031 TTGATGGTCT
584041 TGATGGATGAAGATGATGGTGTTGA
1 TGATGGATGAAGATGATGGTGTTGA
* * *
584066 TGATGGAATGGAGATGGTGTTGTTG
1 TGATGG-ATGAAGATGATGGTGTTG
584091 TTGTATCACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.24, C:0.00, G:0.42, T:0.34
Consensus pattern (25 bp):
TGATGGATGAAGATGATGGTGTTGA
Found at i:585385 original size:30 final size:31
Alignment explanation
Indices: 585345--585404 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
585335 ACATGCTGCC
***
585345 ATGATATCTAAATGTTATGAAAACATAATAA
1 ATGATATCTAAAACATATGAAAACATAATAA
*
585376 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGAAAACATAATA
585405 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.30
Consensus pattern (31 bp):
ATGATATCTAAAACATATGAAAACATAATAA
Found at i:590968 original size:22 final size:20
Alignment explanation
Indices: 590943--590987 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
590933 GATGTGGAAT
590943 TGATGGTCTTGATAGATGAAGA
1 TGATGGTCTTGAT-GATGAA-A
*
590965 TGATGGTGTTGATGATGAAA
1 TGATGGTCTTGATGATGAAA
590985 TGA
1 TGA
590988 AGATGGTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 6 0.27
22 12 0.55
ACGTcount: A:0.31, C:0.02, G:0.33, T:0.33
Consensus pattern (20 bp):
TGATGGTCTTGATGATGAAA
Found at i:592287 original size:30 final size:31
Alignment explanation
Indices: 592247--592306 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
592237 ACATGCTGCC
* *
592247 ATGATATCTAAATGTTATACAAACATAATAA
1 ATGATATCTAAAAGATATACAAACATAATAA
*
592278 ATGA-ATCTAAAAGATATATAAACATAATA
1 ATGATATCTAAAAGATATACAAACATAATA
592307 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.55, C:0.08, G:0.07, T:0.30
Consensus pattern (31 bp):
ATGATATCTAAAAGATATACAAACATAATAA
Found at i:601300 original size:21 final size:22
Alignment explanation
Indices: 601271--601314 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
601261 CCCTATCTTA
601271 TATTATATCAT-GCATGCGTTC
1 TATTATATCATAGCATGCGTTC
*
601292 TATTCTATCATAAGCATGCGTTC
1 TATTATATCAT-AGCATGCGTTC
601315 ACATGTTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
23 10 0.50
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (22 bp):
TATTATATCATAGCATGCGTTC
Found at i:603329 original size:21 final size:20
Alignment explanation
Indices: 603273--603330 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
603263 ACATGTTATG
603273 ATATAAAATAA-TAATATATA
1 ATATAAAATAAGTAA-ATATA
*
603293 ATGCAT-AAATGAGTAAATATA
1 AT--ATAAAATAAGTAAATATA
603314 ATATAAAATAAGGTAAA
1 ATATAAAATAA-GTAAA
603331 ACTCCCTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
19 2 0.06
20 7 0.23
21 17 0.55
22 5 0.16
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (20 bp):
ATATAAAATAAGTAAATATA
Found at i:605464 original size:19 final size:20
Alignment explanation
Indices: 605427--605464 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
605417 TCTTCACTTT
*
605427 TTCTTTTGCTTTTGATTCTC
1 TTCTTTTGCTTTTCATTCTC
*
605447 TTCTTTT-CTTTTCTTTCT
1 TTCTTTTGCTTTTCATTCT
605465 TTTGCACTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.03, C:0.21, G:0.05, T:0.71
Consensus pattern (20 bp):
TTCTTTTGCTTTTCATTCTC
Found at i:615418 original size:14 final size:14
Alignment explanation
Indices: 615399--615426 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
615389 TAAGATACTA
615399 TTTCCATCACCATC
1 TTTCCATCACCATC
615413 TTTCCATCACCATC
1 TTTCCATCACCATC
615427 AATCCTTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:627927 original size:19 final size:18
Alignment explanation
Indices: 627895--627960 Score: 71
Period size: 19 Copynumber: 3.6 Consensus size: 18
627885 AAATTGGAGT
627895 ACAAAAAGAA-AGAAAAA
1 ACAAAAAGAAGAGAAAAA
627912 GACAAAAAGAAGAGAAAAA
1 -ACAAAAAGAAGAGAAAAA
* *
627931 TCAGAAAAGAAGAAAAGAAA
1 ACA-AAAAGAAGAGAA-AAA
*
627951 AGAAAAAGAA
1 ACAAAAAGAA
627961 TTCAAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
18 12 0.29
19 25 0.61
20 4 0.10
ACGTcount: A:0.76, C:0.05, G:0.18, T:0.02
Consensus pattern (18 bp):
ACAAAAAGAAGAGAAAAA
Found at i:630607 original size:20 final size:22
Alignment explanation
Indices: 630582--630624 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
630572 ATCATATTCA
630582 TACTAATGAAA-TTTT-TTTCT
1 TACTAATGAAAGTTTTCTTTCT
630602 TACTAATGAAAGTTTTCTTTCT
1 TACTAATGAAAGTTTTCTTTCT
630624 T
1 T
630625 TTCAGATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.52
21 4 0.19
22 6 0.29
ACGTcount: A:0.28, C:0.12, G:0.07, T:0.53
Consensus pattern (22 bp):
TACTAATGAAAGTTTTCTTTCT
Found at i:636522 original size:13 final size:12
Alignment explanation
Indices: 636485--636554 Score: 70
Period size: 13 Copynumber: 5.5 Consensus size: 12
636475 CTTTTTGAAC
636485 TTCTCTTTTTCTT
1 TTCT-TTTTTCTT
636498 TTCTTTTATTCTT
1 TTCTTTT-TTCTT
*
636511 TTCTTCTTTTCTGA
1 TTCTT-TTTTCT-T
*
636525 TT-TTTTTTCTC
1 TTCTTTTTTCTT
636536 TTCTTTTTGTCTT
1 TTCTTTTT-TCTT
636549 TTCTTT
1 TTCTTT
636555 CTTTTTGCAC
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
11 2 0.04
12 14 0.29
13 29 0.59
14 4 0.08
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.76
Consensus pattern (12 bp):
TTCTTTTTTCTT
Found at i:636560 original size:30 final size:29
Alignment explanation
Indices: 636484--636560 Score: 70
Period size: 30 Copynumber: 2.6 Consensus size: 29
636474 TCTTTTTGAA
*
636484 CTTCTCTT-TTTCTTTTCTTTTATTCTTTT
1 CTTCTTTTCTTTCTTTT-TTTTATTCTTTT
* *
636513 CTTCTTTTCTGATT-TTTTTTCTCTTCTTTT
1 CTTCTTTTCT--TTCTTTTTTTTATTCTTTT
636543 -TGTCTTTTCTTTCTTTTT
1 CT-TCTTTTCTTTCTTTTT
636561 GCACTCCAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
28 2 0.05
29 13 0.32
30 19 0.47
31 4 0.10
32 2 0.05
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (29 bp):
CTTCTTTTCTTTCTTTTTTTTATTCTTTT
Found at i:641048 original size:20 final size:19
Alignment explanation
Indices: 640991--641048 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 19
640981 TTCTCTTTTC
*
640991 TTTTCTTTCTTATTCAAACCT
1 TTTTCTTTCTT-TT-AATCCT
* *
641012 TTTTGTTTATTTCTAATCCT
1 TTTTCTTTCTTT-TAATCCT
641032 TTCTTCTTTCTTTTAAT
1 TT-TTCTTTCTTTTAAT
641049 TACATTTGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.16, C:0.19, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTCTTTCTTTTAATCCT
Found at i:644906 original size:24 final size:22
Alignment explanation
Indices: 644879--644933 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
644869 TTCAATTGGC
*
644879 ACATTCTTTCAAATTTCAAGAGG
1 ACATTCTTTCAAATGTCAA-AGG
* *
644902 TACATCCTTTGAAATGTCAAAGG
1 -ACATTCTTTCAAATGTCAAAGG
644925 ACATCTCTT
1 ACAT-TCTT
644934 GTGGATCACC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 4 0.15
23 6 0.23
24 16 0.62
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (22 bp):
ACATTCTTTCAAATGTCAAAGG
Found at i:646145 original size:27 final size:27
Alignment explanation
Indices: 646111--646167 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
646101 TTTCTTTGTT
* *
646111 TTTCTTCTTTTTGAATGC-TGAATTTC
1 TTTCTTCTTTTAGAATGCTTCAATTTC
*
646137 TTTCTTTCTTTTAGATTGCTTCAATTTC
1 TTTC-TTCTTTTAGAATGCTTCAATTTC
646165 TTT
1 TTT
646168 TCTGATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.15
27 12 0.46
28 10 0.38
ACGTcount: A:0.14, C:0.16, G:0.09, T:0.61
Consensus pattern (27 bp):
TTTCTTCTTTTAGAATGCTTCAATTTC
Found at i:648151 original size:11 final size:11
Alignment explanation
Indices: 648118--648201 Score: 73
Period size: 11 Copynumber: 7.2 Consensus size: 11
648108 ACAATCTGTC
648118 CATCACCATTAT
1 CATCACCA-TAT
*
648130 CA-CGCCTATAT
1 CATCACC-ATAT
648141 CATCACCATATT
1 CATCACCATA-T
648153 CCATCACCATAT
1 -CATCACCATAT
*
648165 CA-CGCCTATAT
1 CATCACC-ATAT
648176 CATCACCATATT
1 CATCACCATA-T
648188 CCATCACCATAT
1 -CATCACCATAT
648200 CA
1 CA
648202 CGCCAATAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
10 3 0.05
11 24 0.40
12 13 0.22
13 20 0.33
ACGTcount: A:0.32, C:0.37, G:0.02, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:648159 original size:13 final size:12
Alignment explanation
Indices: 648140--648199 Score: 63
Period size: 13 Copynumber: 5.0 Consensus size: 12
648130 CACGCCTATA
648140 TCATCACCATAT
1 TCATCACCATAT
648152 TCCATCACCATA-
1 T-CATCACCATAT
*
648164 TCA-CGCC-TAT
1 TCATCACCATAT
648174 ATCATCACCATAT
1 -TCATCACCATAT
648187 TCCATCACCATAT
1 T-CATCACCATAT
648200 CACGCCAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
9 2 0.05
10 3 0.08
11 5 0.12
12 6 0.15
13 24 0.60
ACGTcount: A:0.32, C:0.37, G:0.02, T:0.30
Consensus pattern (12 bp):
TCATCACCATAT
Found at i:648172 original size:35 final size:35
Alignment explanation
Indices: 648116--648215 Score: 173
Period size: 35 Copynumber: 2.8 Consensus size: 35
648106 ATACAATCTG
648116 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCA-TATCACGCCTATATCATCACCATAT
648152 TCCATCACCATATCACGCCTATATCATCACCATAT
1 TCCATCACCATATCACGCCTATATCATCACCATAT
* *
648187 TCCATCACCATATCACGCCAATAACATCA
1 TCCATCACCATATCACGCCTATATCATCA
648216 TCCTTCCATT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
35 52 0.84
36 10 0.16
ACGTcount: A:0.33, C:0.37, G:0.03, T:0.27
Consensus pattern (35 bp):
TCCATCACCATATCACGCCTATATCATCACCATAT
Done.