Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 165 of 343
Found at i:54770433 original size:46 final size:47
Alignment explanation
Indices: 54770366--54770461 Score: 176
Period size: 47 Copynumber: 2.1 Consensus size: 47
54770356 GAAGAAGTGA
54770366 AAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
*
54770412 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
54770459 AAA
1 AAA
54770462 AGAGGCTAGG
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 23 0.48
47 25 0.52
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (47 bp):
AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
Found at i:54770444 original size:24 final size:24
Alignment explanation
Indices: 54770365--54770482 Score: 179
Period size: 23 Copynumber: 5.0 Consensus size: 24
54770355 GGAAGAAGTG
54770365 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
54770389 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
54770412 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
54770435 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
54770459 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
54770483 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
23 46 0.52
24 31 0.35
25 11 0.12
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:54770712 original size:31 final size:31
Alignment explanation
Indices: 54770674--54770737 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
54770664 CGTTTACAGT
54770674 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
54770705 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
54770736 AA
1 AA
54770738 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:54778307 original size:20 final size:20
Alignment explanation
Indices: 54778282--54778349 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
54778272 GATTTTGATA
*
54778282 AACATGGTATGTATGATATG
1 AACATGATATGTATGATATG
*
54778302 AACATGACATGTATGATATG
1 AACATGATATGTATGATATG
*
54778322 CACATGATATGTATGATATG
1 AACATGATATGTATGATATG
*
54778342 CACATGAT
1 AACATGAT
54778350 GTAATCAGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (20 bp):
AACATGATATGTATGATATG
Found at i:54778455 original size:24 final size:24
Alignment explanation
Indices: 54778399--54778493 Score: 122
Period size: 24 Copynumber: 4.0 Consensus size: 24
54778389 GAGGAAGTGA
54778399 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
54778423 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
54778446 AAAAGGGCTTTTGGCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
54778470 CAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
54778494 ATGATAAAGC
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
23 23 0.37
24 28 0.45
25 11 0.18
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:54778468 original size:47 final size:49
Alignment explanation
Indices: 54778399--54778493 Score: 133
Period size: 47 Copynumber: 2.0 Consensus size: 49
54778389 GAGGAAGTGA
*
54778399 AAAAGGGCTTATGCCCCAGTTATT-AAAG-GGCTTATGCC-CCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTCAAAGAGGC-TAGGCCTCCAGTTATT
* *
54778446 AAAAGGGCTTTTGGCCCAGTTATTCAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATTCAAAGAGGCTAGGCCTCCAGTTAT
54778494 ATGATAAAGC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
47 22 0.52
48 9 0.21
49 11 0.26
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (49 bp):
AAAAGGGCTTATGCCCCAGTTATTCAAAGAGGCTAGGCCTCCAGTTATT
Found at i:54778721 original size:31 final size:31
Alignment explanation
Indices: 54778686--54778749 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
54778676 CGTTTACAGT
54778686 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
54778717 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
54778748 AA
1 AA
54778750 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:54783862 original size:40 final size:40
Alignment explanation
Indices: 54783759--54783979 Score: 223
Period size: 40 Copynumber: 5.5 Consensus size: 40
54783749 TATTCGAATG
* * * *
54783759 ATATCCGGGTTAAGTCCCGAAGGCTTTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC-GAGTGACT
* * * *
54783800 ATATCCGGACTAAGATCTGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
* * * *
54783840 ATATCCGGGCCAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
* * ** *
54783880 ATATCCGGGCTAAGTCCCGAAGGCATTTATGTTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
* **
54783920 ATATCCGGGCTAAGACCCGAAGGC-CTTGTGCGAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
54783959 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGA-CCCGAAG
54783980 ATACTTGGGT
Statistics
Matches: 148, Mismatches: 31, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
37 1 0.01
38 13 0.09
39 14 0.09
40 94 0.64
41 26 0.18
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
Found at i:54791487 original size:53 final size:53
Alignment explanation
Indices: 54791288--54791510 Score: 171
Period size: 53 Copynumber: 4.2 Consensus size: 53
54791278 ATTAAGGTTT
* * * * * * *
54791288 AAGGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTACGTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGATAAG-TTCAAAAGGC
* * * * * *
54791342 AAAGATATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAA-GC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGAT-AAGTTC-A-AAAGGC
* * * ** * *
54791397 AAAGATCCCCTGTAAGACCATGCCAAGGTAAGGCAATGATGAGTTCAAAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGATAAGTTCAAAAGGC
* * * * *
54791450 AAGGATACCATGTAAGACCATGTCAAGACCTGGCAATGGTAAGTTAAAAAGGA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGATAAGTTCAAAAGGC
54791503 AAGG-TACC
1 AAGGATACC
54791511 TGTGTATCCC
Statistics
Matches: 131, Mismatches: 34, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
52 7 0.05
53 48 0.37
54 38 0.29
55 36 0.27
56 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGATAAGTTCAAAAGGC
Found at i:54795103 original size:24 final size:24
Alignment explanation
Indices: 54795067--54795113 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
54795057 AGCCAAATTC
*
54795067 TAGGAAGATATTATGAAGAGATTT
1 TAGGAAGATATTAAGAAGAGATTT
*
54795091 TAGGAGAGA-ATTAAGGAGAGATT
1 TAGGA-AGATATTAAGAAGAGATT
54795114 GAGGTGTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.28
Consensus pattern (24 bp):
TAGGAAGATATTAAGAAGAGATTT
Found at i:54799362 original size:15 final size:15
Alignment explanation
Indices: 54799342--54799371 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
54799332 GGGGGATGGG
54799342 TTTATTATGATTGGA
1 TTTATTATGATTGGA
54799357 TTTATTATGATTGGA
1 TTTATTATGATTGGA
54799372 GGAAGTGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (15 bp):
TTTATTATGATTGGA
Found at i:54801755 original size:85 final size:85
Alignment explanation
Indices: 54801612--54801792 Score: 308
Period size: 85 Copynumber: 2.1 Consensus size: 85
54801602 GCAACTTTTG
* *
54801612 TTTGAACCTTTTGAGCCTTTCAAGCCAACCTCGGTGAAATTTTATCCCTTGAAACCCAACTTTGA
1 TTTGAACCCTTTGAGCCTTTCAAGCCAACCTCGATGAAATTTTATCCCTTGAAACCCAACTTTGA
*
54801677 GACTATATGGCCTAATTTCA
66 GACTATATAGCCTAATTTCA
* *
54801697 TTTGAACCCTTTGAGTCTTTCAAGCCAACCTTGATGAAATTTTATCCCTTGAAACCCAACTTTGA
1 TTTGAACCCTTTGAGCCTTTCAAGCCAACCTCGATGAAATTTTATCCCTTGAAACCCAACTTTGA
*
54801762 GACTATATAGCCTAATTTTA
66 GACTATATAGCCTAATTTCA
54801782 TTTGAACCCTT
1 TTTGAACCCTT
54801793 GCAATATTTA
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 90 1.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.36
Consensus pattern (85 bp):
TTTGAACCCTTTGAGCCTTTCAAGCCAACCTCGATGAAATTTTATCCCTTGAAACCCAACTTTGA
GACTATATAGCCTAATTTCA
Found at i:54810348 original size:47 final size:47
Alignment explanation
Indices: 54810285--54810787 Score: 724
Period size: 47 Copynumber: 10.6 Consensus size: 47
54810275 CCCTTCGGGA
* * * *
54810285 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
54810332 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * * *
54810379 CTTATCTCATAAATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTAGGC
* *
54810426 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCA-GC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATT-AGGC
* *
54810473 CTTATCACATATATATACACTTTCACATTCATCACATTGACCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
54810522 CTTATCACATATATACACTTTCACACTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
54810569 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
54810618 CTTATCACATATATACACTTTCACATTCATCACATCGGCAATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
54810665 CTTATCACAGATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
54810712 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTAGGC
54810761 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
54810788 TATTCAAATA
Statistics
Matches: 420, Mismatches: 26, Indels: 20
0.90 0.06 0.04
Matches are distributed among these distances:
46 1 0.00
47 287 0.68
49 131 0.31
50 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:54810525 original size:96 final size:96
Alignment explanation
Indices: 54810285--54810787 Score: 731
Period size: 96 Copynumber: 5.3 Consensus size: 96
54810275 CCCTTCGGGA
* *
54810285 CTTATCACAT-T-TATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
*
54810348 ACTTTCACATTCATCACATTGGCCATTCGGC
66 ACTTTCACATTCATCACATTGGCCATTAGGC
* * * *
54810379 CTTATCTCATA-A-ATGCA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACA
1 CTTATCACATATATATACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATA
54810441 CA-TGTTCACATTCATCACATTGGCCATTCA-GC
65 CACT-TTCACATTCATCACATTGGCCATT-AGGC
*
54810473 CTTATCACATATATATACACTTTCACATTCATCACATTGACCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
* *
54810538 ACTTTCACACTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATTGGCCATTAGGC
* *
54810569 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
* *
54810634 ACTTTCACATTCATCACATCGGCAATTAGGC
66 ACTTTCACATTCATCACATTGGCCATTAGGC
* * *
54810665 CTTATCAC--AGATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATAT
54810728 ACACTTTCACATTCATCACATTGGCCATTAGGC
64 ACACTTTCACATTCATCACATTGGCCATTAGGC
54810761 CTTATCAC--ATATATACACTTTCACATT
1 CTTATCACATATATATACACTTTCACATT
54810788 TATTCAAATA
Statistics
Matches: 374, Mismatches: 23, Indels: 22
0.89 0.05 0.05
Matches are distributed among these distances:
93 2 0.01
94 136 0.36
95 2 0.01
96 232 0.62
97 2 0.01
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
ACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:54810545 original size:143 final size:142
Alignment explanation
Indices: 54810285--54810787 Score: 746
Period size: 143 Copynumber: 3.5 Consensus size: 142
54810275 CCCTTCGGGA
* * * *
54810285 CTTATCAC-ATTTATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACA
1 CTTATCACAATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACA
* * *
54810349 CTTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATAAATGCA-TGTTCACATTCATCACA
66 CTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACT-TTCACATTCATCACA
* *
54810413 TTGGCCATTCGGC
130 TCGGCCATTAGGC
* *
54810426 CTTATCAC-ACATACACA-TGTTCACATTCATCACATTGGCCATTCA-GCCTTATCACATATATA
1 CTTATCACAATATATACACT-TTCACATTCATCACATTGGCCATT-AGGCCTTATCAC--ATATA
* *
54810488 TACACTTTCACATTCATCACATTGACCATTCGGCCTTATCACATATATACACTTTCACACTCATC
62 TACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATC
54810553 ACATCGGCCATTAGGC
127 ACATCGGCCATTAGGC
*
54810569 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACA-ATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
* * * *
54810634 ACTTTCACATTCATCACATCGGCAATTAGGCCTTATCACAGATATACACTTTCACATTCATCACA
65 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
54810699 TCGGCCATTAGGC
130 TCGGCCATTAGGC
54810712 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACA-ATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
54810777 ACTTTCACATT
65 ACTTTCACATT
54810788 TATTCAAATA
Statistics
Matches: 330, Mismatches: 23, Indels: 16
0.89 0.06 0.04
Matches are distributed among these distances:
140 1 0.00
141 46 0.14
143 240 0.73
144 2 0.01
145 40 0.12
146 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (142 bp):
CTTATCACAATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACA
CTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACAT
CGGCCATTAGGC
Found at i:54813285 original size:30 final size:30
Alignment explanation
Indices: 54813229--54813286 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
54813219 CATGGCCAGG
* * *
54813229 ACACACGGGCGTGTGGTCTACTCGTGTGTC
1 ACACACGGGCATGTGATCTACCCGTGTGTC
54813259 ACACACGGGCATGTGAATC-ACCCGTGTG
1 ACACACGGGCATGTG-ATCTACCCGTGTG
54813287 GAAGTACCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.19, C:0.28, G:0.31, T:0.22
Consensus pattern (30 bp):
ACACACGGGCATGTGATCTACCCGTGTGTC
Found at i:54818249 original size:5 final size:5
Alignment explanation
Indices: 54818239--54818336 Score: 56
Period size: 6 Copynumber: 18.2 Consensus size: 5
54818229 TATGTCTTTC
* * * *
54818239 AAAAT AAAAT AATAAT AAATTT GAGAT GAAAAT AAAAAT CAAAAGA AAAAT
1 AAAAT AAAAT AA-AAT AAA-AT AAAAT -AAAAT -AAAAT -AAAA-T AAAAT
*
54818290 AAAAAT AAAAT -AAAG AAAAT AAAAAT AAGAAT -AAAT AAAAT AAAAT
1 -AAAAT AAAAT AAAAT AAAAT -AAAAT AA-AAT AAAAT AAAAT AAAAT
54818336 A
1 A
54818337 GGAGGATTCA
Statistics
Matches: 72, Mismatches: 12, Indels: 18
0.71 0.12 0.18
Matches are distributed among these distances:
4 6 0.08
5 30 0.42
6 36 0.50
ACGTcount: A:0.73, C:0.01, G:0.06, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:54818282 original size:6 final size:6
Alignment explanation
Indices: 54818267--54818324 Score: 62
Period size: 6 Copynumber: 9.3 Consensus size: 6
54818257 ATTTGAGATG
* * *
54818267 AAAATA AAAATC AAAAGA AAAATA AAAATA AAATAAA GAAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAA-ATA -AAAATA AAAATA
*
54818317 AGAATA AA
1 AAAATA AA
54818325 TAAAATAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
6 35 0.83
7 4 0.10
8 3 0.07
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:54818314 original size:26 final size:25
Alignment explanation
Indices: 54818279--54818328 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
54818269 AATAAAAATC
54818279 AAAAGAAAAATAAAAATAAAATAAAG
1 AAAAGAAAAATAAAAAT-AAATAAAG
* *
54818305 AAAATAAAAATAAGAATAAATAAA
1 AAAAGAAAAATAAAAATAAATAAA
54818329 ATAAAATAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (25 bp):
AAAAGAAAAATAAAAATAAATAAAG
Found at i:54818336 original size:20 final size:20
Alignment explanation
Indices: 54818266--54818334 Score: 88
Period size: 21 Copynumber: 3.5 Consensus size: 20
54818256 AATTTGAGAT
* *
54818266 GAAAATAAAAATCAAA-AGA
1 GAAAATAAAAATAAAATAAA
54818285 -AAAATAAAAATAAAATAAA
1 GAAAATAAAAATAAAATAAA
54818304 GAAAATAAAAATAAGAATAAA
1 GAAAATAAAAATAA-AATAAA
*
54818325 TAAAATAAAA
1 GAAAATAAAA
54818335 TAGGAGGATT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
18 14 0.32
19 2 0.05
20 13 0.30
21 15 0.34
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.14
Consensus pattern (20 bp):
GAAAATAAAAATAAAATAAA
Found at i:54822925 original size:29 final size:29
Alignment explanation
Indices: 54822890--54822963 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
54822880 GTTGTGAGAT
* *
54822890 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
54822919 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
54822948 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
54822964 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:54831284 original size:29 final size:29
Alignment explanation
Indices: 54831249--54831322 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
54831239 GTTGTGAGAT
* *
54831249 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
54831278 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
54831307 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
54831323 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:54838564 original size:5 final size:5
Alignment explanation
Indices: 54838554--54838650 Score: 56
Period size: 6 Copynumber: 18.2 Consensus size: 5
54838544 TATGTCTTTC
* * *
54838554 AAAAT AAAAT AAGAAT AAAATT GAAAT GAAAAT AAAAAT CAAAAGA AAAAGA
1 AAAAT AAAAT AA-AAT AAAA-T AAAAT -AAAAT -AAAAT -AAAA-T AAAA-T
*
54838606 AAAAT AAAAT -AAA- AAAAT AAAAA AATGAAT -AAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA--AAT AAAAT AAAAT AAAAT A
54838651 GGATGATTCA
Statistics
Matches: 75, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
4 9 0.12
5 31 0.41
6 33 0.44
7 2 0.03
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:54838603 original size:18 final size:19
Alignment explanation
Indices: 54838559--54838648 Score: 67
Period size: 18 Copynumber: 4.5 Consensus size: 19
54838549 CTTTCAAAAT
*
54838559 AAAATAAGAATAAAATTGAAA
1 AAAATAAAAATAAAA-T-AAA
* *
54838580 TGAAAATAAAAATCAAA-AGA
1 --AAAATAAAAATAAAATAAA
*
54838600 AAAAGAAAAATAAAATAAA
1 AAAATAAAAATAAAATAAA
54838619 AAAATAAAAA-AATGAATAAA
1 AAAATAAAAATAA--AATAAA
54838639 TAAAATAAAA
1 -AAAATAAAA
54838649 TAGGATGATT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
18 15 0.27
19 11 0.20
20 8 0.14
21 9 0.16
23 13 0.23
ACGTcount: A:0.77, C:0.01, G:0.07, T:0.16
Consensus pattern (19 bp):
AAAATAAAAATAAAATAAA
Found at i:54838614 original size:29 final size:29
Alignment explanation
Indices: 54838577--54838648 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 29
54838567 AATAAAATTG
54838577 AAATGAAAATAAAAATCAA-AAGAAAAA-GAA-
1 AAAT-AAAATAAAAA--AATAA-AAAAATGAAT
54838607 AAATAAAATAAAAAAATAAAAAAATGAAT
1 AAATAAAATAAAAAAATAAAAAAATGAAT
54838636 AAATAAAATAAAA
1 AAATAAAATAAAA
54838649 TAGGATGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
27 7 0.18
28 5 0.13
29 23 0.59
30 4 0.10
ACGTcount: A:0.79, C:0.01, G:0.06, T:0.14
Consensus pattern (29 bp):
AAATAAAATAAAAAAATAAAAAAATGAAT
Found at i:54838620 original size:17 final size:16
Alignment explanation
Indices: 54838554--54838650 Score: 70
Period size: 17 Copynumber: 5.7 Consensus size: 16
54838544 TATGTCTTTC
*
54838554 AAAATAAAATAAGAATA
1 AAAATAAAATAA-AAAA
* * *
54838571 AAATTGAAATGAAAATA
1 AAAATAAAAT-AAAAAA
*
54838588 AAAATCAAAAGAAAAAGA
1 AAAAT-AAAATAAAAA-A
54838606 AAAATAAAATAAAAAA
1 AAAATAAAATAAAAAA
*
54838622 ATAAA-AAAATGAATAAAT
1 A-AAATAAAAT-AA-AAAA
54838640 AAAATAAAATA
1 AAAATAAAATA
54838651 GGATGATTCA
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
16 7 0.11
17 38 0.58
18 20 0.31
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.16
Consensus pattern (16 bp):
AAAATAAAATAAAAAA
Found at i:54842547 original size:37 final size:37
Alignment explanation
Indices: 54842486--54842564 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
54842476 TTATTACGAA
* * *
54842486 GTCTTACCCGGACATAATCTCCACACGAAGTTATCAG
1 GTCTTACCCGGAAAAAATCTCCACACGAAGTCATCAG
* *
54842523 GTCTTACCCGGAAAAAAT-TCCCACACGTAGTCATCGG
1 GTCTTACCCGGAAAAAATCT-CCACACGAAGTCATCAG
54842560 GTCTT
1 GTCTT
54842565 TAGAGCTCGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
36 1 0.03
37 35 0.97
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGAAAAAATCTCCACACGAAGTCATCAG
Found at i:54842761 original size:47 final size:47
Alignment explanation
Indices: 54842683--54843363 Score: 1128
Period size: 47 Copynumber: 14.4 Consensus size: 47
54842673 CCCTTCGGGA
* * * * * * *
54842683 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54842730 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54842777 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54842824 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54842871 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54842918 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54842967 CTTATCACATATATACACTTTCACATTCATCACATCAGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54843014 CTTATAACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54843061 CTTATCACACATATAAACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54843108 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54843157 CTTATCACATATATACACTTTCACATTCATCGCATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54843204 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54843251 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54843298 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54843345 CTTATCACATATATACACT
1 CTTATCACATATATACACT
54843364 GTCTTGGCTG
Statistics
Matches: 598, Mismatches: 32, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
47 507 0.85
49 91 0.15
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54843010 original size:190 final size:188
Alignment explanation
Indices: 54842683--54843363 Score: 1173
Period size: 190 Copynumber: 3.6 Consensus size: 188
54842673 CCCTTCGGGA
** * * * * * * * *
54842683 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
54842748 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
*
54842813 GGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 GGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54842871 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
54842936 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
* *
54843001 TCAGCTATTAGGCCTTATAACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
129 TCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54843061 CTTATCACACATATAAACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
*
54843126 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCGCA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
*
54843191 TCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
129 TCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54843251 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
54843316 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACT
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
54843364 GTCTTGGCTG
Statistics
Matches: 471, Mismatches: 20, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
188 102 0.22
190 369 0.78
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (188 bp):
CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54851191 original size:17 final size:19
Alignment explanation
Indices: 54851149--54851197 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
54851139 ATGAAATTTT
*
54851149 AATTAGTATTATAAGATAA
1 AATTATTATTATAAGATAA
*
54851168 AATTATTATTATTAGA-AA
1 AATTATTATTATAAGATAA
*
54851186 AA-TATTACTATA
1 AATTATTATTATA
54851198 TGTATGTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 8 0.31
18 4 0.15
19 14 0.54
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (19 bp):
AATTATTATTATAAGATAA
Found at i:54858529 original size:27 final size:27
Alignment explanation
Indices: 54858492--54858696 Score: 223
Period size: 27 Copynumber: 7.6 Consensus size: 27
54858482 TAAATTGTAC
*
54858492 AGCACTAAGTGTGCGATTTGGCTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
54858519 AGCACTAAGTGTGCGATTTGACCATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** **
54858546 TGCACTAAGTGTGCGAAATGAAAATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
54858572 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
54858600 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
54858627 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * * *
54858655 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
54858682 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
54858697 GACTTAATAT
Statistics
Matches: 152, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
27 128 0.84
28 24 0.16
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:54858553 original size:54 final size:54
Alignment explanation
Indices: 54858493--54858696 Score: 257
Period size: 54 Copynumber: 3.8 Consensus size: 54
54858483 AAATTGTACA
* * *
54858493 GCACTAAGTGTGCGATTTGGCTATGTAGCACTAAGTGTGCGATTTGACCATGTT
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
** ** * *
54858547 GCACTAAGTGTGCGAAATGAAAATG-ATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGTTGACTATGTA-GCACTAAGTGTGCGATTTGACCATGTG
**
54858601 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGTG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGA-TTTGACCATGTG
* * *
54858656 GCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
54858697 GACTTAATAT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 80 0.62
55 47 0.37
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
Found at i:54866685 original size:27 final size:27
Alignment explanation
Indices: 54866648--54866852 Score: 223
Period size: 27 Copynumber: 7.6 Consensus size: 27
54866638 TAAATTGTAC
*
54866648 AGCACTAAGTGTGCGATTTGGCTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
54866675 AGCACTAAGTGTGCGATTTGACCATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** **
54866702 TGCACTAAGTGTGCGAAATGAAAATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
54866728 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
54866756 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
54866783 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * * *
54866811 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
54866838 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
54866853 GACTTAATAT
Statistics
Matches: 152, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
27 128 0.84
28 24 0.16
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:54866709 original size:54 final size:54
Alignment explanation
Indices: 54866649--54866852 Score: 257
Period size: 54 Copynumber: 3.8 Consensus size: 54
54866639 AAATTGTACA
* * *
54866649 GCACTAAGTGTGCGATTTGGCTATGTAGCACTAAGTGTGCGATTTGACCATGTT
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
** ** * *
54866703 GCACTAAGTGTGCGAAATGAAAATG-ATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGTTGACTATGTA-GCACTAAGTGTGCGATTTGACCATGTG
**
54866757 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGTG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGA-TTTGACCATGTG
* * *
54866812 GCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
54866853 GACTTAATAT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 80 0.62
55 47 0.37
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
Found at i:54873311 original size:108 final size:110
Alignment explanation
Indices: 54873191--54873397 Score: 301
Period size: 113 Copynumber: 1.9 Consensus size: 110
54873181 GTCTTTCCTT
* * * * *
54873191 GTGTGCTCAATTTTGAGCATTCTATTTTGC-ATTTAGGTGCAGGGGGCACACGGTCAGATCACAC
1 GTGTGCTCAATTTTGAGCATTCTATTTTGCAATTTAGGTGCAGGGGACACACAGCCAGAACACAA
*
54873255 GCCCAT-GGGCTGACCGTGTGTCACACACGCCTGTGTCTCTGCCC
66 GCCCATGGGGCTAACCGTGTGTCACACACGCCTGTGTCTCTGCCC
*
54873299 GTGTGCTCAATTTTGAGCATTCTGTTTTGCAAAAAATTTAGGTGCAGGGGACACACAGCCAGAAC
1 GTGTGCTCAATTTTGAGCATTCTATTTTGC----AATTTAGGTGCAGGGGACACACAGCCAGAAC
54873364 ACAAGCCCATGGGGCTAACCGTGTGTCACACACG
62 ACAAGCCCATGGGGCTAACCGTGTGTCACACACG
54873398 GCCTAGAAAC
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
108 29 0.34
113 35 0.41
114 22 0.26
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (110 bp):
GTGTGCTCAATTTTGAGCATTCTATTTTGCAATTTAGGTGCAGGGGACACACAGCCAGAACACAA
GCCCATGGGGCTAACCGTGTGTCACACACGCCTGTGTCTCTGCCC
Found at i:54874569 original size:68 final size:68
Alignment explanation
Indices: 54874460--54874595 Score: 227
Period size: 68 Copynumber: 2.0 Consensus size: 68
54874450 CTCACATCTC
* *
54874460 ATAAATCACAATTTGTGTGAATAAAACATACTATATTATAACTCAATTTGGCCCGAAATCCAATT
1 ATAAATCACAATTTGTGTGAATAAAACATACTATATCATAACTCAATTTGGCCCGAAAGCCAATT
54874525 ACA
66 ACA
* * *
54874528 ATAAATCACAATTTGTGTGAATAAAATATGCTATATCATAACTCAATTTGGCCTGAAAGCCAATT
1 ATAAATCACAATTTGTGTGAATAAAACATACTATATCATAACTCAATTTGGCCCGAAAGCCAATT
54874593 ACA
66 ACA
54874596 TGATCACCAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (68 bp):
ATAAATCACAATTTGTGTGAATAAAACATACTATATCATAACTCAATTTGGCCCGAAAGCCAATT
ACA
Found at i:54877995 original size:19 final size:20
Alignment explanation
Indices: 54877971--54878008 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
54877961 GGTACCACCA
54877971 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
54877990 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
54878009 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:54878816 original size:30 final size:30
Alignment explanation
Indices: 54878782--54878841 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
54878772 ATTTAATACG
54878782 AACTTTAAAAAAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
*** * *
54878812 AACTTTTGCATAATTACACTTTTTCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
54878842 GGCTCGGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.38
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGCCCCTA
Found at i:54885718 original size:34 final size:34
Alignment explanation
Indices: 54885680--54885754 Score: 141
Period size: 34 Copynumber: 2.2 Consensus size: 34
54885670 TCATTCAACT
54885680 TTTCATTTCCAAAATAACACTATCTCAATTATGC
1 TTTCATTTCCAAAATAACACTATCTCAATTATGC
54885714 TTTCATTTCCAAAATAACACTATCTCAATTATGC
1 TTTCATTTCCAAAATAACACTATCTCAATTATGC
*
54885748 TTACATT
1 TTTCATT
54885755 CAAACATATA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.40
Consensus pattern (34 bp):
TTTCATTTCCAAAATAACACTATCTCAATTATGC
Found at i:54885972 original size:35 final size:35
Alignment explanation
Indices: 54885907--54886086 Score: 207
Period size: 35 Copynumber: 5.1 Consensus size: 35
54885897 TACTTACTTC
* * *
54885907 TATGGCCAAATACACATAGTTCATTATATCATCACA
1 TATGGCCGAATATACA-AGTTCAATATATCATCACA
* *
54885943 TATGGCCGAATATACAAGTACAATATATCATCATA
1 TATGGCCGAATATACAAGTTCAATATATCATCACA
* * *
54885978 TATGACCGAATATACAAGTTCAATAAAACATCACA
1 TATGGCCGAATATACAAGTTCAATATATCATCACA
*** * * *
54886013 TGCAGTCGAATATTCAAGTTCAATATAACATCACA
1 TATGGCCGAATATACAAGTTCAATATATCATCACA
* *
54886048 TGTGGCCAAATATACAAGTTCAATATATCATCACA
1 TATGGCCGAATATACAAGTTCAATATATCATCACA
54886083 TATG
1 TATG
54886087 TACATATCTA
Statistics
Matches: 120, Mismatches: 24, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
35 106 0.88
36 14 0.12
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (35 bp):
TATGGCCGAATATACAAGTTCAATATATCATCACA
Found at i:54894415 original size:47 final size:47
Alignment explanation
Indices: 54894357--54894702 Score: 570
Period size: 47 Copynumber: 7.4 Consensus size: 47
54894347 CAGCCAAGAC
54894357 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
54894404 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
**
54894451 AGTGTATATATGTGATAAGGCCTAATAACCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
54894498 AGTGTATATATGTGATAAGGCCTAAT-GCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
54894544 AGTGTATATATGT-ATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
54894590 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * *
54894637 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
54894684 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
54894703 TCCCGAAGGG
Statistics
Matches: 283, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
45 12 0.04
46 65 0.23
47 206 0.73
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:54894597 original size:38 final size:40
Alignment explanation
Indices: 54894507--54894638 Score: 131
Period size: 46 Copynumber: 3.0 Consensus size: 40
54894497 AAGTGTATAT
54894507 ATGTGATAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTG
1 ATGT-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG-G
54894548 TATATATGTATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 -----ATGTATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG-G
54894594 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 -----ATGT-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
54894639 TGTATATATG
Statistics
Matches: 84, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
45 12 0.14
46 37 0.44
47 35 0.42
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (40 bp):
ATGTATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGG
Found at i:54894685 original size:186 final size:187
Alignment explanation
Indices: 54894357--54894702 Score: 577
Period size: 186 Copynumber: 1.9 Consensus size: 187
54894347 CAGCCAAGAC
54894357 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
* * * *
54894422 GGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAACCGATGTG
66 GGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATAACCAACGTG
* *
54894487 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGCCGATGTGATGAATGTGAA
131 ATGAATGTGAAAGTGCATAAATGTGATAAGGCCTAATGCCGATGTGATGAATGTGAA
54894544 AGTGTATATATGT-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
* * * **
54894608 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTG
66 GGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATAACCAACGTG
*
54894673 ATGGATGTGAAAGTGCATAAATGTGATAAG
131 ATGAATGTGAAAGTGCATAAATGTGATAAG
54894703 TCCCGAAGGG
Statistics
Matches: 147, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
186 134 0.91
187 13 0.09
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (187 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
GGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATAACCAACGTG
ATGAATGTGAAAGTGCATAAATGTGATAAGGCCTAATGCCGATGTGATGAATGTGAA
Found at i:54894876 original size:37 final size:37
Alignment explanation
Indices: 54894820--54894898 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
54894810 TCCAGCTCTA
* *
54894820 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
54894857 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
54894894 AAGAC
1 AAGAC
54894899 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:54900655 original size:12 final size:12
Alignment explanation
Indices: 54900618--54900656 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
54900608 TACACGCCCA
*
54900618 TGTGCCAAGCCG
1 TGTGCCAGGCCG
54900630 TGTGCCAGGCCG
1 TGTGCCAGGCCG
* *
54900642 TGTGCTAGGTCG
1 TGTGCCAGGCCG
54900654 TGT
1 TGT
54900657 AACAACCTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.10, C:0.26, G:0.38, T:0.26
Consensus pattern (12 bp):
TGTGCCAGGCCG
Found at i:54916091 original size:42 final size:41
Alignment explanation
Indices: 54916032--54916182 Score: 171
Period size: 42 Copynumber: 3.6 Consensus size: 41
54916022 GAGACTATGC
* *
54916032 GTAAGACCATATCTGGGTTATGGCATCAATATGGGACTTCGA
1 GTAAGACCATATCTGGGTTATGGCATCGATATGAGA-TTCGA
* * *
54916074 GTAAGACCATAACTGGGTTATGGCATCGATGTGAGATTTCGT
1 GTAAGACCATATCTGGGTTATGGCATCGATATGAGA-TTCGA
*
54916116 GTAAGACCATAGT-TGGGCTATTGGCATCGATATGAGATTAC-A
1 GTAAGACCATA-TCTGGGTTA-TGGCATCGATATGAGATT-CGA
*
54916158 TGTAAGACCATATCTGGGATATGGC
1 -GTAAGACCATATCTGGGTTATGGC
54916183 GTTGGTATGG
Statistics
Matches: 93, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
42 60 0.65
43 33 0.35
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (41 bp):
GTAAGACCATATCTGGGTTATGGCATCGATATGAGATTCGA
Found at i:54917343 original size:20 final size:20
Alignment explanation
Indices: 54917318--54917371 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
54917308 CATGGTCTGC
*
54917318 CCACACAGGCGTGTCCCAAG
1 CCACACGGGCGTGTCCCAAG
*
54917338 CCACACGGGCATGTCCCAAG
1 CCACACGGGCGTGTCCCAAG
54917358 CCACACGGGCGTGT
1 CCACACGGGCGTGT
54917372 GGCTCTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.22, C:0.39, G:0.28, T:0.11
Consensus pattern (20 bp):
CCACACGGGCGTGTCCCAAG
Found at i:54918892 original size:23 final size:23
Alignment explanation
Indices: 54918830--54918916 Score: 68
Period size: 25 Copynumber: 3.6 Consensus size: 23
54918820 GAAGAGTTAT
* *
54918830 TATCAGGGAGCTCATGATAGCCA
1 TATCAGGAAGCTCAAGATAGCCA
*
54918853 TATAACAGGAAGTTCAAGCA-AGCCA
1 TAT--CAGGAAGCTCAAG-ATAGCCA
* *
54918878 TATCAGGAAGCTCAAAAGGAGCCTA
1 TATCAGGAAGCTCAAGA-TAGCC-A
*
54918903 TACCAGGAAGCTCA
1 TATCAGGAAGCTCA
54918917 GAAAGAGCTA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
22 1 0.02
23 14 0.27
24 4 0.08
25 32 0.62
26 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (23 bp):
TATCAGGAAGCTCAAGATAGCCA
Found at i:54918910 original size:25 final size:25
Alignment explanation
Indices: 54918873--54918921 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
54918863 AGTTCAAGCA
*
54918873 AGCCATATCAGGAAGCTCA-AAAGG
1 AGCCATACCAGGAAGCTCAGAAAGG
54918897 AGCCTATACCAGGAAGCTCAGAAAG
1 AGCC-ATACCAGGAAGCTCAGAAAG
54918922 AGCTACATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.18
25 14 0.64
26 4 0.18
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.12
Consensus pattern (25 bp):
AGCCATACCAGGAAGCTCAGAAAGG
Found at i:54919675 original size:154 final size:155
Alignment explanation
Indices: 54919373--54919714 Score: 338
Period size: 154 Copynumber: 2.2 Consensus size: 155
54919363 TCGAGTATTA
* * * * *
54919373 GCGGCATTTTTTAAAATGCACCGCTAAAAAACTAAGCCGAAAGACGACGTTTACATTGAGCTTCA
1 GCGGCATTTTTTAAAA-ACATCGCTAAAAAATTAAACAGAAAGACGACGTTTACATTGAGCTTCA
* * * * *
54919438 GTGGCATCTGCGGCGCTTTATTAGAAATGCCGCAATAGATCGTGAACTAGTGGCGTTTCTAGTAA
65 GTGGCATCTGCAGCGCTTTATTAAAAACGCCGCAATAGATCGTGAACTAGCGGCGTTTCTAGGAA
* *
54919503 AGCGCCACTAAAGATCGACC-TA-TG
130 AACGCCACCAAAGATCGACCATAGTG
* * ***
54919527 GCGGCATTTTTTAAAAACATCGCTAAAAAATTAAACAGAATGACGTCGTTTTGTTTTGAGCTTCA
1 GCGGCATTTTTTAAAAACATCGCTAAAAAATTAAACAGAAAGACGACG-TTTACATTGAGCTTCA
* * * * *
54919592 GTGGCAT-TAGCAGCGCTTTTTTAAAAACGTCGCAATAGATCGAT-CATTAGCGGCGTTTTTAGG
65 GTGGCATCT-GCAGCGCTTTATTAAAAACGCCGCAATAGATCG-TGAACTAGCGGCGTTTCTAGG
* * *
54919655 AAAACGCCGCCATAGGTCGACCATTAGTG
128 AAAACGCCACCAAAGATCGACCA-TAGTG
* *
54919684 GC-GC-TTTTCTAAAAAC-TCCGCTAAAAGATTA
1 GCGGCATTTTTTAAAAACAT-CGCTAAAAAATTA
54919715 GGCAGAACAT
Statistics
Matches: 154, Mismatches: 27, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
153 26 0.17
154 96 0.62
155 24 0.16
156 4 0.03
157 4 0.03
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (155 bp):
GCGGCATTTTTTAAAAACATCGCTAAAAAATTAAACAGAAAGACGACGTTTACATTGAGCTTCAG
TGGCATCTGCAGCGCTTTATTAAAAACGCCGCAATAGATCGTGAACTAGCGGCGTTTCTAGGAAA
ACGCCACCAAAGATCGACCATAGTG
Found at i:54919699 original size:40 final size:39
Alignment explanation
Indices: 54919596--54919704 Score: 112
Period size: 40 Copynumber: 2.7 Consensus size: 39
54919586 GCTTCAGTGG
* * *
54919596 CATTAGCAGCGCTTTTTTAAAAACGTCGCAATAGATCGAT
1 CATTAGCGGCGC-TTTTTAAAAACGCCGCAATAGATCGAC
* *
54919636 CATTAGCGGCG-TTTTTAGGAAAACGCCGCCATAGGTCGAC
1 CATTAGCGGCGCTTTTTA--AAAACGCCGCAATAGATCGAC
* *
54919676 CATTAGTGGCGCTTTTCTAAAAACTCCGC
1 CATTAGCGGCGCTTTT-TAAAAACGCCGC
54919705 TAAAAGATTA
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
38 6 0.10
40 46 0.79
41 4 0.07
42 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (39 bp):
CATTAGCGGCGCTTTTTAAAAACGCCGCAATAGATCGAC
Found at i:54920575 original size:21 final size:21
Alignment explanation
Indices: 54920525--54920577 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
54920515 TATAAAACTT
* **
54920525 AAAACTATTAACCCTAAATCTT
1 AAAAC-ATAAACCCTAAATCCA
*
54920547 AAACCATAAACCCTAAATCCA
1 AAAACATAAACCCTAAATCCA
54920568 AAAACATAAA
1 AAAACATAAA
54920578 ACCTTAAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.55, C:0.25, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAACATAAACCCTAAATCCA
Found at i:54923469 original size:27 final size:27
Alignment explanation
Indices: 54923439--54923677 Score: 282
Period size: 27 Copynumber: 8.9 Consensus size: 27
54923429 ATTACCAAAG
* * *
54923439 TACCATCGATTTATAAAATTACTATTT
1 TACCCTCGATTTATAGAATTACTGTTT
*
54923466 TACCCTTGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
* * * *
54923493 TACCCTTGATTTACAAAATTATTGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
*
54923520 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
* *
54923547 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
* **
54923574 TACCATCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACTGTTT
54923601 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
* * *
54923628 TACCCTTGATTTACA-ATATTACCGTTT
1 TACCCTCGATTTATAGA-ATTACTGTTT
* * *
54923655 TAACCTCGATTTACAAAATTACT
1 TACCCTCGATTTATAGAATTACT
54923678 ACAATATCCT
Statistics
Matches: 185, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
26 1 0.01
27 183 0.99
28 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.43
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACTGTTT
Found at i:54923504 original size:54 final size:54
Alignment explanation
Indices: 54923439--54923677 Score: 318
Period size: 54 Copynumber: 4.4 Consensus size: 54
54923429 ATTACCAAAG
* * * * *
54923439 TACCATCGATTTATAAAATTACTATTTTACCCTTGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTATAGAATTACCGTTT
* *
54923493 TACCCTTGATTTACAAAATTATTGTTTTACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTATAGAATTACCGTTT
* * * *
54923547 TACCCTCGATTTACAGAATTACCGTTTTACCATCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTATAGAATTACCGTTT
* * * *
54923601 TACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACA-ATATTACCGTTT
1 TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTATAGA-ATTACCGTTT
*
54923655 TAACCTCGATTTACAAAATTACT
1 TACCCTCGATTTACAAAATTACT
54923678 ACAATATCCT
Statistics
Matches: 162, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
53 1 0.01
54 161 0.99
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.43
Consensus pattern (54 bp):
TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTATAGAATTACCGTTT
Found at i:54923541 original size:81 final size:81
Alignment explanation
Indices: 54923439--54923676 Score: 325
Period size: 81 Copynumber: 2.9 Consensus size: 81
54923429 ATTACCAAAG
* * * * * *
54923439 TACCATCGATTTATAAAATTACTATTTTACCCTTGATTTATAGAATTACTGTTTTACCCTTGATT
1 TACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACCGTTTTACCCTCGATT
***
54923504 TACAAAATTATTGTTT
66 TACAAAATTACCATTT
* * *
54923520 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCATCGATT
1 TACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACCGTTTTACCCTCGATT
* *
54923585 TATAGAATTACCATTT
66 TACAAAATTACCATTT
*
54923601 TACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACA-ATATTACCGTTTTAACCTCGAT
1 TACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGA-ATTACCGTTTTACCCTCGAT
54923665 TTACAAAATTAC
65 TTACAAAATTAC
54923677 TACAATATCC
Statistics
Matches: 136, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
80 1 0.01
81 135 0.99
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.42
Consensus pattern (81 bp):
TACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACCGTTTTACCCTCGATT
TACAAAATTACCATTT
Found at i:54923768 original size:27 final size:28
Alignment explanation
Indices: 54923696--54923792 Score: 101
Period size: 27 Copynumber: 3.6 Consensus size: 28
54923686 CTTGGTTTAC
* * *
54923696 AAAATTACCAAAATA-CCCTCGATCAGT
1 AAAATTACCAAAATACCCCTAGCTTAGT
54923723 AAAATTACCAAAATACCCCTAGCTTA-T
1 AAAATTACCAAAATACCCCTAGCTTAGT
* *
54923750 AAGATTACCAAAATACCCCTGGCTT-GT
1 AAAATTACCAAAATACCCCTAGCTTAGT
* * *
54923777 GAAATTATCGAAATAC
1 AAAATTACCAAAATAC
54923793 TCTCGATTTG
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
27 52 0.88
28 7 0.12
ACGTcount: A:0.42, C:0.24, G:0.09, T:0.25
Consensus pattern (28 bp):
AAAATTACCAAAATACCCCTAGCTTAGT
Found at i:54923850 original size:27 final size:27
Alignment explanation
Indices: 54923812--54924027 Score: 272
Period size: 27 Copynumber: 8.0 Consensus size: 27
54923802 GTAAAATATC
54923812 GAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACT
*
54923839 GAAATACCCCTGTAGGGTAGAATTTCT
1 GAAATACCCCTGTAGGGTAGAATTACT
* *
54923866 GAAATAACCCTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACT
* * *
54923893 GAAATACTCCTATAGGGTAAAATTA-T
1 GAAATACCCCTGTAGGGTAGAATTACT
*
54923919 CGAAATACCCCTGTAGGGTAGAATTACC
1 -GAAATACCCCTGTAGGGTAGAATTACT
* * * *
54923947 GAAATACCCTTGTAGGGTAAAAATACC
1 GAAATACCCCTGTAGGGTAGAATTACT
54923974 GAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACT
* * * *
54924001 GAGATACCCTTGTGGGGTGAAAATTAC
1 GAAATACCCCTGTAGGGT-AGAATTAC
54924028 CATTTTGCCC
Statistics
Matches: 162, Mismatches: 24, Indels: 5
0.85 0.13 0.03
Matches are distributed among these distances:
27 155 0.96
28 7 0.04
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (27 bp):
GAAATACCCCTGTAGGGTAGAATTACT
Found at i:54923917 original size:81 final size:81
Alignment explanation
Indices: 54923804--54924028 Score: 301
Period size: 81 Copynumber: 2.8 Consensus size: 81
54923794 CTCGATTTGT
* * *
54923804 AAAATATCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTTCTGAA
1 AAAATACCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTACCGAA
54923869 ATAACCC-TGTAGGGTA
66 AT-ACCCTTGTAGGGTA
* * * * *
54923885 GAATTACCGAAATACTCCTATAGGGTAAAATTA-TCGAAATACCCCTGTAGGGTAGAATTACCGA
1 AAAATACCGAAATACCCCTGTAGGGTAGAATTACT-GAAATACCCCTGTAGGGTAGAATTACCGA
54923949 AATACCCTTGTAGGGTA
65 AATACCCTTGTAGGGTA
* * * *
54923966 AAAATACCGAAATACCCCTGTAGGGTAGAATTACTGAGATACCCTTGTGGGGTGAAAATTACC
1 AAAATACCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGT-AGAATTACC
54924029 ATTTTGCCCC
Statistics
Matches: 123, Mismatches: 17, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
80 5 0.04
81 109 0.89
82 9 0.07
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (81 bp):
AAAATACCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTACCGAA
ATACCCTTGTAGGGTA
Found at i:54924264 original size:25 final size:25
Alignment explanation
Indices: 54924231--54924325 Score: 138
Period size: 25 Copynumber: 3.8 Consensus size: 25
54924221 AGGAAGTGCT
*
54924231 AAAAGGGCTATGCCCCAGTTTACCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
54924256 AAAAGGGCTTTGCCCCAGTTTATCGA
1 AAAAGGGCTTTGCCCCAGTTTA-CCA
* *
54924282 AAAA-GGCTTTGCCGCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
54924306 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
54924326 ATTAAAAGAG
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
24 5 0.08
25 51 0.82
26 6 0.10
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.25
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:54924308 original size:50 final size:50
Alignment explanation
Indices: 54924231--54924350 Score: 154
Period size: 50 Copynumber: 2.4 Consensus size: 50
54924221 AGGAAGTGCT
*
54924231 AAAAGGGCTATGCCCCAGTTTACCAAAAAGGGCTTTGCCCCAGTTTATCG
1 AAAAAGGCTATGCCCCAGTTTACCAAAAAGGGCTTTGCCCCAGTTTATCG
* * * *
54924281 AAAAAGGCTTTGCCGCAGTTTATCAAAAAGGGCTTTGCCCCAG-TTAT-T
1 AAAAAGGCTATGCCCCAGTTTACCAAAAAGGGCTTTGCCCCAGTTTATCG
*
54924329 AAAAGAGGCTAGGCCTCCAGTT
1 AAAA-AGGCTATGCC-CCAGTT
54924351 ATATGATAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
48 4 0.07
49 12 0.20
50 44 0.73
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (50 bp):
AAAAAGGCTATGCCCCAGTTTACCAAAAAGGGCTTTGCCCCAGTTTATCG
Found at i:54924338 original size:24 final size:24
Alignment explanation
Indices: 54924231--54924338 Score: 128
Period size: 25 Copynumber: 4.4 Consensus size: 24
54924221 AGGAAGTGCT
* * *
54924231 AAAAGGGCTATGCCCCAGTTTACC
1 AAAAAGGCTTTGCCCCAGTTTATC
54924255 AAAAAGGGCTTTGCCCCAGTTTATC
1 AAAAA-GGCTTTGCCCCAGTTTATC
*
54924280 GAAAAAGGCTTTGCCGCAGTTTATC
1 -AAAAAGGCTTTGCCCCAGTTTATC
*
54924305 AAAAAGGGCTTTGCCCCAG-TTATT
1 AAAAA-GGCTTTGCCCCAGTTTATC
54924329 AAAAGAGGCT
1 AAAA-AGGCT
54924339 AGGCCTCCAG
Statistics
Matches: 74, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
24 21 0.28
25 48 0.65
26 5 0.07
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (24 bp):
AAAAAGGCTTTGCCCCAGTTTATC
Found at i:54924595 original size:31 final size:30
Alignment explanation
Indices: 54924546--54924628 Score: 123
Period size: 31 Copynumber: 2.7 Consensus size: 30
54924536 CGCTTACAAT
*
54924546 AAAGGCTTCGGCCAGTGATATGATTTATGA
1 AAAGGCTTCGCCCAGTGATATGATTTATGA
*
54924576 AAAGGCTTCGACCCAGTGATGTGATTTATGA
1 AAAGGCTTCG-CCCAGTGATATGATTTATGA
54924607 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTC-GCCCAGTGATATG
54924629 TTGAGACTGA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
30 14 0.29
31 33 0.69
32 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.28
Consensus pattern (30 bp):
AAAGGCTTCGCCCAGTGATATGATTTATGA
Found at i:54928044 original size:40 final size:40
Alignment explanation
Indices: 54927985--54928199 Score: 269
Period size: 40 Copynumber: 5.4 Consensus size: 40
54927975 AAACCAAGTA
* * * *
54927985 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* **
54928024 CCTTCGAGACTTAGCCCGGATATAGTAGTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
54928064 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
54928104 CCTTCGGGACTTAGCCTGGA-ATTAGTAACTCGCA-ACAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACA-AATG
* *
54928144 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
54928184 CCTTCGGGACTTAGCC
1 CCTTCGGGACTTAGCC
54928200 TGGTTATCAT
Statistics
Matches: 157, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
39 14 0.09
40 142 0.90
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:54930114 original size:27 final size:27
Alignment explanation
Indices: 54930095--54930305 Score: 264
Period size: 27 Copynumber: 7.8 Consensus size: 27
54930085 ATTACCAAAG
*
54930095 TACCATCGATTTATAGAATTACTGTTT
1 TACCATCGATTTATAGAATTACCGTTT
* * * * *
54930122 TACCCTTGATTTACAAAATTACTGTTT
1 TACCATCGATTTATAGAATTACCGTTT
*
54930149 TACCCTCGATTTATAGAATTACCGTTT
1 TACCATCGATTTATAGAATTACCGTTT
54930176 TACCATCGATTTATAGAATTACCGTTT
1 TACCATCGATTTATAGAATTACCGTTT
*
54930203 TACCATCGATTTATAGAATTACCATTT
1 TACCATCGATTTATAGAATTACCGTTT
* *
54930230 TACCCTCGATTTATAGAATTACCATTT
1 TACCATCGATTTATAGAATTACCGTTT
* *
54930257 TACCCTCGATTTACA-ATATTACCGTTT
1 TACCATCGATTTATAGA-ATTACCGTTT
* *
54930284 TAACC-TCGATTTACAAAATTAC
1 T-ACCATCGATTTATAGAATTAC
54930306 TACAATATCC
Statistics
Matches: 168, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
26 1 0.01
27 163 0.97
28 4 0.02
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (27 bp):
TACCATCGATTTATAGAATTACCGTTT
Found at i:54930170 original size:81 final size:81
Alignment explanation
Indices: 54930095--54930307 Score: 311
Period size: 81 Copynumber: 2.6 Consensus size: 81
54930085 ATTACCAAAG
* * *
54930095 TACCATCGATTTATAGAATTACTGTTTTACCCTTGATTTACAAAATTACTGTTTTACCCTCGATT
1 TACCATCGATTTATAGAATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTCGATT
*
54930160 TATAGAATTACCGTTT
66 TATAGAATTACCATTT
* * * *
54930176 TACCATCGATTTATAGAATTACCGTTTTACCATCGATTTATAGAATTACCATTTTACCCTCGATT
1 TACCATCGATTTATAGAATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTCGATT
54930241 TATAGAATTACCATTT
66 TATAGAATTACCATTT
* * *
54930257 TACCCTCGATTTACA-ATATTACCGTTTTAACCTCGATTTACAAAATTACTA
1 TACCATCGATTTATAGA-ATTACCGTTTTACCCTCGATTTACAAAATTACTA
54930308 CAATATCCTT
Statistics
Matches: 116, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
80 1 0.01
81 115 0.99
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (81 bp):
TACCATCGATTTATAGAATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTCGATT
TATAGAATTACCATTT
Found at i:54930405 original size:27 final size:26
Alignment explanation
Indices: 54930326--54930449 Score: 106
Period size: 27 Copynumber: 4.7 Consensus size: 26
54930316 TTAGTTTACA
**
54930326 AAATTACCAAAATACCCTCGATCAGT
1 AAATTACCAAAATACCCTCGATTTGT
**
54930352 AAAATTACCAAAATACCC-CTGGCTTGT
1 -AAATTACCAAAATACCCTC-GATTTGT
*
54930379 AAGATTACCAAAATACCCTTGATTTGT
1 AA-ATTACCAAAATACCCTCGATTTGT
* * *
54930406 GAAATTATCGAAATACTCTCGATTTGT
1 -AAATTACCAAAATACCCTCGATTTGT
* * *
54930433 AAAATATCGAAATACCC
1 AAATTACCAAAATACCC
54930450 CTGTAGGGTA
Statistics
Matches: 80, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
26 18 0.22
27 60 0.75
28 2 0.03
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (26 bp):
AAATTACCAAAATACCCTCGATTTGT
Found at i:54930447 original size:26 final size:27
Alignment explanation
Indices: 54930389--54930449 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
54930379 AAGATTACCA
* *
54930389 AAATACCCTTGATTTGTGAAATTATCG
1 AAATACCCTCGATTTGTGAAAATATCG
*
54930416 AAATACTCTCGATTTGT-AAAATATCG
1 AAATACCCTCGATTTGTGAAAATATCG
54930442 AAATACCC
1 AAATACCC
54930450 CTGTAGGGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 15 0.50
27 15 0.50
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (27 bp):
AAATACCCTCGATTTGTGAAAATATCG
Found at i:54930479 original size:27 final size:27
Alignment explanation
Indices: 54930437--54930638 Score: 280
Period size: 27 Copynumber: 7.5 Consensus size: 27
54930427 ATTTGTAAAA
54930437 TATCGAAATACCCCTGTAGGGTAGAAT
1 TATCGAAATACCCCTGTAGGGTAGAAT
*
54930464 TATTGAAATACCCCTGTAGGGTAGAAT
1 TATCGAAATACCCCTGTAGGGTAGAAT
* *
54930491 TA-CTAAAATAACCCTGTAGGGTAGAAT
1 TATC-GAAATACCCCTGTAGGGTAGAAT
* * * *
54930518 TACCGAAATACTCCTATAGGGTAAAAT
1 TATCGAAATACCCCTGTAGGGTAGAAT
54930545 TATCGAAATACCCCTGTAGGGTAGAAT
1 TATCGAAATACCCCTGTAGGGTAGAAT
* * * *
54930572 TACCGAAATACCCTTGTAGGGTAAAAA
1 TATCGAAATACCCCTGTAGGGTAGAAT
54930599 TATCGAAATACCCCTGTAGGGTAGAAT
1 TATCGAAATACCCCTGTAGGGTAGAAT
*
54930626 TATCGAGATACCC
1 TATCGAAATACCC
54930639 TTGTGAGGTA
Statistics
Matches: 151, Mismatches: 22, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
27 150 0.99
28 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (27 bp):
TATCGAAATACCCCTGTAGGGTAGAAT
Found at i:54930893 original size:25 final size:25
Alignment explanation
Indices: 54930860--54930954 Score: 147
Period size: 25 Copynumber: 3.8 Consensus size: 25
54930850 AGGAAGTGCT
*
54930860 AAAAGGGCTATGCCCCAGTTTACCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
54930885 AAAAGGGCTTTGCCCCAGTTTACCGA
1 AAAAGGGCTTTGCCCCAGTTTACC-A
* *
54930911 AAAA-GGCTTTGCCGCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
54930935 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
54930955 ATTAAAAGAG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
24 5 0.08
25 54 0.84
26 5 0.08
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:54930967 original size:24 final size:24
Alignment explanation
Indices: 54930860--54930967 Score: 119
Period size: 25 Copynumber: 4.4 Consensus size: 24
54930850 AGGAAGTGCT
* * *
54930860 AAAAGGGCTATGCCCCAGTTTACC
1 AAAAAGGCTTTGCCCCAGTTTATC
*
54930884 AAAAAGGGCTTTGCCCCAGTTTACC
1 AAAAA-GGCTTTGCCCCAGTTTATC
*
54930909 GAAAAAGGCTTTGCCGCAGTTTATC
1 -AAAAAGGCTTTGCCCCAGTTTATC
*
54930934 AAAAAGGGCTTTGCCCCAG-TTATT
1 AAAAA-GGCTTTGCCCCAGTTTATC
54930958 AAAAGAGGCT
1 AAAA-AGGCT
54930968 AGGCCTCCAG
Statistics
Matches: 74, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
24 21 0.28
25 48 0.65
26 5 0.07
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (24 bp):
AAAAAGGCTTTGCCCCAGTTTATC
Found at i:54930979 original size:50 final size:51
Alignment explanation
Indices: 54930858--54930979 Score: 153
Period size: 50 Copynumber: 2.5 Consensus size: 51
54930848 GGAGGAAGTG
54930858 CTAAAAG-GGCTATGCCCCAGTTTACCAAAAAGGGCTTTGCCCCAGTTTAC
1 CTAAAAGAGGCTATGCCCCAGTTTACCAAAAAGGGCTTTGCCCCAGTTTAC
* * * *
54930908 CGAAAA-AGGCTTTGCCGCAGTTTATCAAAAAGGGCTTTGCCCCAG-TTA-
1 CTAAAAGAGGCTATGCCCCAGTTTACCAAAAAGGGCTTTGCCCCAGTTTAC
* *
54930956 TTAAAAGAGGCTAGGCCTCCAGTT
1 CTAAAAGAGGCTATGCC-CCAGTT
54930980 ATATGATAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
48 4 0.07
49 11 0.18
50 45 0.75
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (51 bp):
CTAAAAGAGGCTATGCCCCAGTTTACCAAAAAGGGCTTTGCCCCAGTTTAC
Found at i:54931209 original size:30 final size:29
Alignment explanation
Indices: 54931175--54931257 Score: 121
Period size: 31 Copynumber: 2.7 Consensus size: 29
54931165 CGCTTACAGT
54931175 AAAGGCTTCGGCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCAGT-ATATGATTTATGA
*
54931205 AAAGGCTTCGACCCAGTAATATGATTTATGA
1 AAAGGCTTCG-GCCAGT-ATATGATTTATGA
54931236 AAAGGCTTCGGCCTAGTATATG
1 AAAGGCTTCGGCC-AGTATATG
54931258 TCGAGACTGA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
30 17 0.35
31 31 0.65
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (29 bp):
AAAGGCTTCGGCCAGTATATGATTTATGA
Found at i:54933128 original size:24 final size:24
Alignment explanation
Indices: 54933101--54933147 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
54933091 AATATTATTG
* *
54933101 AAATATTCTCGTCCGTTTTATCAC
1 AAATATTATCGTCCATTTTATCAC
54933125 AAATATTATCGTCCATTTTATCA
1 AAATATTATCGTCCATTTTATCA
54933148 TTTAAGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (24 bp):
AAATATTATCGTCCATTTTATCAC
Found at i:54933384 original size:15 final size:13
Alignment explanation
Indices: 54933366--54933496 Score: 53
Period size: 14 Copynumber: 10.0 Consensus size: 13
54933356 TCTTATTTTA
54933366 ATTAATATAATTT
1 ATTAATATAATTT
*
54933379 GGATTAAT-TTATTT
1 --ATTAATATAATTT
*
54933393 A--AATATTATTT
1 ATTAATATAATTT
54933404 AATTAATATAA--T
1 -ATTAATATAATTT
54933416 ATTAATATAA-TT
1 ATTAATATAATTT
**
54933428 -TGGAT-TAATTT
1 ATTAATATAATTT
* *
54933439 ATCTAAATATTATTAA
1 AT-T-AATATAATT-T
54933455 ATTAATATAATTTTT
1 ATTAATATAA--TTT
*
54933470 ATAAATATAATTT
1 ATTAATATAATTT
*
54933483 AATTAAAATAATTT
1 -ATTAATATAATTT
54933497 TTTCCATGTG
Statistics
Matches: 89, Mismatches: 13, Indels: 29
0.68 0.10 0.22
Matches are distributed among these distances:
10 6 0.07
11 21 0.24
12 5 0.06
13 3 0.03
14 30 0.34
15 20 0.22
16 4 0.04
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (13 bp):
ATTAATATAATTT
Found at i:54933397 original size:25 final size:25
Alignment explanation
Indices: 54933369--54933448 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 25
54933359 TATTTTAATT
54933369 AATATAATTTGGATTAATTTATTTA
1 AATATAATTTGGATTAATTTATTTA
* * *
54933394 AATATTATTT-AATTAATATAATATT-
1 AATATAATTTGGATTAAT-TTAT-TTA
*
54933419 AATATAATTTGGATTAATTTATCTA
1 AATATAATTTGGATTAATTTATTTA
54933444 AATAT
1 AATAT
54933449 TATTAAATTA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
24 7 0.16
25 29 0.66
26 8 0.18
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (25 bp):
AATATAATTTGGATTAATTTATTTA
Found at i:54933418 original size:19 final size:19
Alignment explanation
Indices: 54933362--54933419 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
54933352 TCAATCTTAT
54933362 TTTAATTAATATAAT-TTGGA
1 TTTAATTAATATAATATT--A
* *
54933382 -TTAATTTATTTAAATATTA
1 TTTAATTAATAT-AATATTA
54933401 TTTAATTAATATAATATTA
1 TTTAATTAATATAATATTA
54933420 ATATAATTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
19 17 0.55
20 12 0.39
21 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTAATTAATATAATATTA
Found at i:54933422 original size:50 final size:50
Alignment explanation
Indices: 54933366--54933465 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
54933356 TCTTATTTTA
* *
54933366 ATTAATATAATTTGGATTAATTTATTTAAATATTATTTAATTAATATAAT
1 ATTAATATAATTTGGATTAATTTATCTAAATATTATTAAATTAATATAAT
54933416 ATTAATATAATTTGGATTAATTTATCTAAATATTATTAAATTAATATAAT
1 ATTAATATAATTTGGATTAATTTATCTAAATATTATTAAATTAATATAAT
54933466 TTTTATAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (50 bp):
ATTAATATAATTTGGATTAATTTATCTAAATATTATTAAATTAATATAAT
Found at i:54933471 original size:20 final size:20
Alignment explanation
Indices: 54933416--54933486 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 20
54933406 TTAATATAAT
**
54933416 ATTAATATAATTTGGATT-A
1 ATTAATATAATTTTTATTAA
* * * *
54933435 ATTTATCTAAATATTATTAA
1 ATTAATATAATTTTTATTAA
54933455 ATTAATATAATTTTTA-TAA
1 ATTAATATAATTTTTATTAA
*
54933474 ATATAATTTAATT
1 AT-TAATATAATT
54933487 AAAATAATTT
Statistics
Matches: 39, Mismatches: 11, Indels: 3
0.74 0.21 0.06
Matches are distributed among these distances:
19 17 0.44
20 22 0.56
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (20 bp):
ATTAATATAATTTTTATTAA
Found at i:54933475 original size:29 final size:29
Alignment explanation
Indices: 54933433--54933498 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
54933423 TAATTTGGAT
* * * *
54933433 TAATTTATCTAAATATTATTAAATTAATA
1 TAATTTTTATAAATATAATTAAATTAAAA
*
54933462 TAATTTTTATAAATATAATTTAATTAAAA
1 TAATTTTTATAAATATAATTAAATTAAAA
54933491 TAATTTTT
1 TAATTTTT
54933499 TCCATGTGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
TAATTTTTATAAATATAATTAAATTAAAA
Found at i:54933806 original size:9 final size:9
Alignment explanation
Indices: 54933767--54933797 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
54933757 TATATACTTG
*
54933767 AACTTACAT
1 AACTCACAT
54933776 AACTCACAT
1 AACTCACAT
54933785 AACTCACAT
1 AACTCACAT
54933794 AACT
1 AACT
54933798 GACAGAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (9 bp):
AACTCACAT
Found at i:54933813 original size:18 final size:18
Alignment explanation
Indices: 54933766--54933815 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
54933756 ATATATACTT
54933766 GAACTTACATAACTCACA
1 GAACTTACATAACTCACA
* * *
54933784 TAACTCACATAACTGACA
1 GAACTTACATAACTCACA
*
54933802 GAACTTATATAACT
1 GAACTTACATAACT
54933816 TTTATAACTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.44, C:0.24, G:0.06, T:0.26
Consensus pattern (18 bp):
GAACTTACATAACTCACA
Found at i:54938881 original size:13 final size:14
Alignment explanation
Indices: 54938865--54938893 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
54938855 CTATAAATAT
54938865 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
54938878 TTATAATGGTTTAA
1 TTATAATGGTTTAA
54938892 TT
1 TT
54938894 CGTCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:54939632 original size:33 final size:31
Alignment explanation
Indices: 54939590--54939675 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
54939580 TTAGATATAA
* * *
54939590 TGTTTTTGGTTATATTTTTTATGCTACATTTGT
1 TGTTTTTGGTTAGA--TTTCATGCTACATTTGC
* *
54939623 TGTTTTTGGTTGGATTTCATGCTATATTTGC
1 TGTTTTTGGTTAGATTTCATGCTACATTTGC
* *
54939654 TGTTTTTGGTTGGATTTAATGC
1 TGTTTTTGGTTAGATTTCATGC
54939676 AGGAAGGGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 35 0.74
33 12 0.26
ACGTcount: A:0.14, C:0.07, G:0.21, T:0.58
Consensus pattern (31 bp):
TGTTTTTGGTTAGATTTCATGCTACATTTGC
Found at i:54939652 original size:31 final size:31
Alignment explanation
Indices: 54939610--54939675 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
54939600 TATATTTTTT
* *
54939610 ATGCTACATTTGTTGTTTTTGGTTGGATTTC
1 ATGCTACATTTGCTGTTTTTGGTTGGATTTA
*
54939641 ATGCTATATTTGCTGTTTTTGGTTGGATTTA
1 ATGCTACATTTGCTGTTTTTGGTTGGATTTA
54939672 ATGC
1 ATGC
54939676 AGGAAGGGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.15, C:0.09, G:0.23, T:0.53
Consensus pattern (31 bp):
ATGCTACATTTGCTGTTTTTGGTTGGATTTA
Found at i:54939793 original size:43 final size:43
Alignment explanation
Indices: 54939745--54939951 Score: 171
Period size: 43 Copynumber: 4.7 Consensus size: 43
54939735 TGTGAAAAAA
* *
54939745 GCACTTTTCCCATAAACGCCGCTAAAATCCATGACCTTTAGCG
1 GCACTTTTCCCACAAACGCCGCTAAAAGCCATGACCTTTAGCG
* * *
54939788 GCACTTTTGCGCTTTTCCACAAACGACGCTAAAAGACTTGACCTTTAGCG
1 GCACTTTT---C----CCACAAACGCCGCTAAAAGCCATGACCTTTAGCG
* * * * *
54939838 ACACTTTTACCACAAATGCTGCTAAAAGCCTTGACCTTTAGCG
1 GCACTTTTCCCACAAACGCCGCTAAAAGCCATGACCTTTAGCG
** ** * *
54939881 GTGCTTTTCCCACAAATTCAGCTAAAAGCCATGACTTTTAGCG
1 GCACTTTTCCCACAAACGCCGCTAAAAGCCATGACCTTTAGCG
** * *
54939924 GTGCTTTTCCCACAAACTCCACTAAAAG
1 GCACTTTTCCCACAAACGCCGCTAAAAG
54939952 TCTTGATTTT
Statistics
Matches: 135, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
43 98 0.73
46 1 0.01
50 36 0.27
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (43 bp):
GCACTTTTCCCACAAACGCCGCTAAAAGCCATGACCTTTAGCG
Found at i:54939818 original size:50 final size:51
Alignment explanation
Indices: 54939748--54939845 Score: 135
Period size: 50 Copynumber: 1.9 Consensus size: 51
54939738 GAAAAAAGCA
* * ** *
54939748 CTTTTCCCATAAACGCCGCTAAAATCCATGACCTTTAGCGGCACTTTTGCG
1 CTTTTCCCACAAACGACGCTAAAAGACATGACCTTTAGCGACACTTTTGCG
*
54939799 CTTTT-CCACAAACGACGCTAAAAGACTTGACCTTTAGCGACACTTTT
1 CTTTTCCCACAAACGACGCTAAAAGACATGACCTTTAGCGACACTTTT
54939846 ACCACAAATG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
50 36 0.88
51 5 0.12
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.30
Consensus pattern (51 bp):
CTTTTCCCACAAACGACGCTAAAAGACATGACCTTTAGCGACACTTTTGCG
Found at i:54942456 original size:15 final size:15
Alignment explanation
Indices: 54942436--54942465 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54942426 CTTTTTTGGC
*
54942436 CGATTTGCTTTCTGT
1 CGATTTGCTCTCTGT
54942451 CGATTTGCTCTCTGT
1 CGATTTGCTCTCTGT
54942466 TTTACCCTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.23, G:0.20, T:0.50
Consensus pattern (15 bp):
CGATTTGCTCTCTGT
Found at i:54943519 original size:19 final size:19
Alignment explanation
Indices: 54943495--54943531 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
54943485 GCATGACCTC
54943495 TATATGCACCTGAACGATG
1 TATATGCACCTGAACGATG
*
54943514 TATATGTACCTGAACGAT
1 TATATGCACCTGAACGAT
54943532 AATATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (19 bp):
TATATGCACCTGAACGATG
Found at i:54945570 original size:18 final size:17
Alignment explanation
Indices: 54945544--54945578 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54945534 AATATTAAGA
*
54945544 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
54945561 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
54945579 TTAATAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:54945590 original size:120 final size:120
Alignment explanation
Indices: 54945437--54945720 Score: 446
Period size: 120 Copynumber: 2.4 Consensus size: 120
54945427 TAATTGAAAA
* * *
54945437 TATATATTTT-ATTAAATTATATTTAATAATAATTATGTTAAATTATATTTCATAGTATTATATA
1 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTCACAGTATCATATA
* *
54945501 TTATGATTTTAGAAAATTCATATAAGAATATTTAA-TATTAAGAATTTTATTAAAT
66 TTATGATTTCAGAAAATTAATATAAGAATA-TTAATTATTAAGAATTTTATTAAAT
* * *
54945556 TATATATTTTAATTAAAATATATTTAATAGTAATTATGTTAATTTATATTTTACAGTATCATATA
1 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTCACAGTATCATATA
*
54945621 TTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
66 TTATGATTTCAGAAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
*
54945676 TATATATTTTAATTAAAATATATTTAATAAAAATTATGTTTAAAT
1 TATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
54945721 ATGATTAAAT
Statistics
Matches: 150, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
119 14 0.09
120 131 0.87
121 5 0.03
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTCACAGTATCATATA
TTATGATTTCAGAAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
Found at i:54945692 original size:18 final size:17
Alignment explanation
Indices: 54945664--54945698 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54945654 ATTATTAAGA
*
54945664 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
54945681 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
54945699 TTAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:54945698 original size:16 final size:16
Alignment explanation
Indices: 54945664--54945718 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
54945654 ATTATTAAGA
54945664 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
54945681 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
54945697 A-TTTAATAAAAAT-T
1 ATTTTAATTAAAATAT
54945711 ATGTTTAA
1 AT-TTTAA
54945719 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:54945955 original size:16 final size:16
Alignment explanation
Indices: 54945934--54946001 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
54945924 GATTTGCTAT
54945934 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
54945950 TACACCTTTAATCCAA
1 TACACCTCTAATCCAA
54945966 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
54945982 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
54945998 TACA
1 TACA
54946002 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:54947347 original size:13 final size:13
Alignment explanation
Indices: 54947329--54947353 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54947319 TTGTTAGCCC
54947329 TTATTATTTATTA
1 TTATTATTTATTA
54947342 TTATTATTTATT
1 TTATTATTTATT
54947354 TCCCTTCAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTATTTATTA
Found at i:54955505 original size:11 final size:12
Alignment explanation
Indices: 54955478--54955544 Score: 91
Period size: 12 Copynumber: 5.6 Consensus size: 12
54955468 CAAGTAAGTA
54955478 AAAAAAAGTTTC
1 AAAAAAAGTTTC
*
54955490 GAAAAAAAGTTTA
1 -AAAAAAAGTTTC
54955503 AAAAAAAGTTTC
1 AAAAAAAGTTTC
*
54955515 GAAAAAAG-TTC
1 AAAAAAAGTTTC
*
54955526 AAAAAAAGTTTG
1 AAAAAAAGTTTC
54955538 AAAAAAA
1 AAAAAAA
54955545 TTAAAAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.21
12 27 0.56
13 11 0.23
ACGTcount: A:0.63, C:0.04, G:0.12, T:0.21
Consensus pattern (12 bp):
AAAAAAAGTTTC
Found at i:54956625 original size:12 final size:12
Alignment explanation
Indices: 54956605--54956658 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
54956595 GAAAAAGAAC
54956605 AAAAAGAGAGTG
1 AAAAAGAGAGTG
* *
54956617 AAAATGAGATTG
1 AAAAAGAGAGTG
* *
54956629 AAAAAGA-AATC
1 AAAAAGAGAGTG
*
54956640 AAAAAGAGAATG
1 AAAAAGAGAGTG
54956652 AAAAAGA
1 AAAAAGA
54956659 TTTTGAGAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 9 0.26
12 26 0.74
ACGTcount: A:0.65, C:0.02, G:0.22, T:0.11
Consensus pattern (12 bp):
AAAAAGAGAGTG
Found at i:54956645 original size:11 final size:12
Alignment explanation
Indices: 54956596--54956658 Score: 51
Period size: 12 Copynumber: 5.5 Consensus size: 12
54956586 GATGAAAAAG
54956596 AAAA-AGAA-CA
1 AAAAGAGAATCA
* *
54956606 AAAAGAGAGTGA
1 AAAAGAGAATCA
* * *
54956618 AAATGAGATTGA
1 AAAAGAGAATCA
54956630 AAAAGA-AATCA
1 AAAAGAGAATCA
*
54956641 AAAAGAGAATGA
1 AAAAGAGAATCA
54956653 AAAAGA
1 AAAAGA
54956659 TTTTGAGAGA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
10 4 0.10
11 12 0.29
12 26 0.62
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (12 bp):
AAAAGAGAATCA
Found at i:54956660 original size:33 final size:32
Alignment explanation
Indices: 54956595--54956660 Score: 89
Period size: 35 Copynumber: 2.0 Consensus size: 32
54956585 CGATGAAAAA
*
54956595 GAAAAAGAACAAAAAGAGAGTGAAAATGAGATT
1 GAAAAAGAACAAAAAGAGAATGAAAA-GAGATT
54956628 GAAAAAGAAATCAAAAAGAGAATGAAAA-AGATT
1 GAAAAAG-AA-CAAAAAGAGAATGAAAAGAGATT
54956661 TTGAGAGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 12 0.40
34 2 0.07
35 16 0.53
ACGTcount: A:0.64, C:0.03, G:0.21, T:0.12
Consensus pattern (32 bp):
GAAAAAGAACAAAAAGAGAATGAAAAGAGATT
Found at i:54963418 original size:9 final size:10
Alignment explanation
Indices: 54963398--54963426 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
54963388 ATATCGTGTT
54963398 TGAATAGAAA
1 TGAATAGAAA
54963408 TGAAT-GAAA
1 TGAATAGAAA
54963417 TGAATAGAAA
1 TGAATAGAAA
54963427 AATGGAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (10 bp):
TGAATAGAAA
Found at i:54967068 original size:46 final size:45
Alignment explanation
Indices: 54967018--54967189 Score: 177
Period size: 46 Copynumber: 3.7 Consensus size: 45
54967008 ATCTCATAGT
*
54967018 CGATGCATGCCCCAGACATGTCTTACACTAGCTTACGTCTCGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTT-CGTCTCGAGGC
* * * * *
54967064 CGATGCATGTCTCAGACATGTCTTACGCTAGCGCTCGTCTCAATG-
1 CGATGCATGTCCCAGACATGTCTTACACTAGC-TTCGTCTCGAGGC
* * * * *
54967109 CGATGCCATGTCCCAGATATGGTCTTACACTGGCTCTCATAAT-GTGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCT-TCGT-CTCGAGGC
54967157 CGATGCATGTCCCAGACATGTCTTACACTAGCT
1 CGATGCATGTCCCAGACATGTCTTACACTAGCT
54967190 CACACAAGTG
Statistics
Matches: 102, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
45 5 0.05
46 62 0.61
47 29 0.28
48 6 0.06
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (45 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCTTCGTCTCGAGGC
Found at i:54967346 original size:27 final size:26
Alignment explanation
Indices: 54967301--54967360 Score: 93
Period size: 27 Copynumber: 2.3 Consensus size: 26
54967291 CACAATCAAG
*
54967301 CAATTCATGCTATATTAATTTTAATA
1 CAATTCATGCTATAATAATTTTAATA
*
54967327 CAATTCATTGCTATAATAATTTTGATA
1 CAATTCA-TGCTATAATAATTTTAATA
54967354 CAATTCA
1 CAATTCA
54967361 ATCACATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 7 0.23
27 24 0.77
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.43
Consensus pattern (26 bp):
CAATTCATGCTATAATAATTTTAATA
Found at i:54969770 original size:19 final size:19
Alignment explanation
Indices: 54969746--54969783 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
54969736 CACAAACTCT
54969746 ATCTTTGAACATCAAACAC
1 ATCTTTGAACATCAAACAC
54969765 ATCTTTGAACATCAAACAC
1 ATCTTTGAACATCAAACAC
54969784 CCATCGATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.05, T:0.26
Consensus pattern (19 bp):
ATCTTTGAACATCAAACAC
Found at i:54974880 original size:46 final size:45
Alignment explanation
Indices: 54974824--54974992 Score: 134
Period size: 46 Copynumber: 3.7 Consensus size: 45
54974814 ACATCTCGTA
* * *
54974824 CCGATACATGTCCCAAACATGTCTAACACTGGCTTACGTCTCGAGG
1 CCGATGCATGTCCCAGACATGTCTAACACTGGCTT-CGTCTCAAGG
*
54974870 CCGATGCATGTCCCAGA-ATGT-TGAACACTAGCGC-TCGTCTCAATG
1 CCGATGCATGTCCCAGACATGTCT-AACACT-G-GCTTCGTCTCAAGG
* *
54974915 CCGATGCGATGTCCTAGACATGGTCTTACACTGGC-TC-TCAT-AATGTGG
1 CCGATGC-ATGTCCCAGACAT-GTCTAACACTGGCTTCGTC-TCAA---GG
* *
54974963 CTGATGCATGTCCCAGACATGTCTTACACT
1 CCGATGCATGTCCCAGACATGTCTAACACT
54974993 AGCTCACACA
Statistics
Matches: 103, Mismatches: 9, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
44 1 0.01
45 29 0.28
46 41 0.40
47 17 0.17
48 14 0.14
49 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (45 bp):
CCGATGCATGTCCCAGACATGTCTAACACTGGCTTCGTCTCAAGG
Found at i:54975559 original size:19 final size:19
Alignment explanation
Indices: 54975535--54975618 Score: 127
Period size: 19 Copynumber: 4.5 Consensus size: 19
54975525 AATCTTTAAG
54975535 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
54975554 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
54975573 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* *
54975590 GATATGCAATCTTTGATGT
1 GATATGCAATCTTAGATAT
54975609 GATATGCAAT
1 GATATGCAAT
54975619 ATTGAATATA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
17 16 0.27
19 43 0.73
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:54975564 original size:36 final size:36
Alignment explanation
Indices: 54975524--54975618 Score: 106
Period size: 36 Copynumber: 2.6 Consensus size: 36
54975514 TATGGAAATA
54975524 TAATCTTTAAGGATATGCAATCTTAGATATGATATG
1 TAATCTTTAAGGATATGCAATCTTAGATATGATATG
54975560 TAATC-TT-A-GATATGATACAATCTTAGATATGATATG
1 TAATCTTTAAGGATATG---CAATCTTAGATATGATATG
* *
54975596 CAATCTTTGATGTGATATGCAAT
1 TAATCTTT-AAG-GATATGCAAT
54975619 ATTGAATATA
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
33 6 0.12
34 1 0.02
35 2 0.04
36 28 0.57
37 2 0.04
38 4 0.08
41 6 0.12
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (36 bp):
TAATCTTTAAGGATATGCAATCTTAGATATGATATG
Found at i:54975571 original size:14 final size:16
Alignment explanation
Indices: 54975542--54975593 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 16
54975532 AAGGATATGC
54975542 AATCTTAGATATGATA
1 AATCTTAGATATGATA
54975558 TGTAATCTTAGATATGATA
1 ---AATCTTAGATATGATA
54975577 CAATCTTAGATATGATA
1 -AATCTTAGATATGATA
54975594 TGCAATCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 16 0.50
19 16 0.50
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.38
Consensus pattern (16 bp):
AATCTTAGATATGATA
Found at i:54985877 original size:47 final size:47
Alignment explanation
Indices: 54985826--54986288 Score: 759
Period size: 47 Copynumber: 9.7 Consensus size: 47
54985816 TTAGGATTCT
* *
54985826 ATGTGATGGATGTGAACA-TGCATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
54985873 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
54985920 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
54985969 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
54986016 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
54986065 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
54986112 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
54986161 ATGTGATGAATGTGAAAGT-TATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
54986207 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
54986254 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
54986289 TCCTGAAGGG
Statistics
Matches: 396, Mismatches: 12, Indels: 16
0.93 0.03 0.04
Matches are distributed among these distances:
46 47 0.12
47 209 0.53
49 140 0.35
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:54985956 original size:96 final size:96
Alignment explanation
Indices: 54985847--54986288 Score: 791
Period size: 96 Copynumber: 4.6 Consensus size: 96
54985837 GTGAACATGC
54985847 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
54985912 AATGGCCGATGTGATGAATGTGAAAGTGTAT
66 AATGGCCGATGTGATGAATGTGAAAGTGTAT
54985943 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
54986008 AATGGCCGATGTGATGAATGTGAAAGTGTAT
66 AATGGCCGATGTGATGAATGTGAAAGTGTAT
54986039 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
54986104 AATGGCCGATGTGATGAATGTGAAAGTGTAT
66 AATGGCCGATGTGATGAATGTGAAAGTGTAT
54986135 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT-TATATATGTGATAAGGCCT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
54986199 AATGGCCGATGTGATGAATGTGAAAGTG--T
66 AATGGCCGATGTGATGAATGTGAAAGTGTAT
* * * * * * * *
54986228 ATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
54986289 TCCTGAAGGG
Statistics
Matches: 337, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
93 39 0.12
94 14 0.04
95 47 0.14
96 237 0.70
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (96 bp):
ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
AATGGCCGATGTGATGAATGTGAAAGTGTAT
Found at i:54986463 original size:37 final size:37
Alignment explanation
Indices: 54986407--54986485 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
54986397 CCGAGCTCTA
* * *
54986407 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
54986444 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
54986481 AAGAC
1 AAGAC
54986486 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:54987939 original size:40 final size:40
Alignment explanation
Indices: 54987696--54987927 Score: 356
Period size: 40 Copynumber: 5.8 Consensus size: 40
54987686 GAGAATTGAG
54987696 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
54987736 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
54987776 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
54987816 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* ** **
54987856 AGAGATATATCCATGCTAAACCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
54987896 GGTGTTATATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCA
54987928 ATCATGCTGG
Statistics
Matches: 171, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 171 1.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Found at i:54988248 original size:44 final size:45
Alignment explanation
Indices: 54988199--54988554 Score: 261
Period size: 44 Copynumber: 8.0 Consensus size: 45
54988189 GATTTCAGCA
* *
54988199 TGGCATCCCTGTGTTTATAGGGAATAAG-TTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGATCGAAGATAGCAGATT
* *
54988243 TGGCATCCCTGTGTTTATAGGGAAC-AGATCGAAGATAGTAGATC
1 TGGCATCCCTGTGTTTATAGGGAACAAGATCGAAGATAGCAGATT
* * * * * ***
54988287 TGACA-CTCCTATGCTTACAGCGAAGC-AGATCGAAGATTTTAGCA--
1 TGGCATC-CCTGTGTTTATAGGGAA-CAAGATCGAAGATAGCAG-ATT
* * * ***
54988331 TGGTATCCCTGTGTCTATAGGGAACAAG-TTGAAGATAATTGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGATCGAAGATAGCAGATT
* *
54988375 TGGCATCCCTGTGTTTATAGGGAAC-AGATCAAAGATAGCAGATC
1 TGGCATCCCTGTGTTTATAGGGAACAAGATCGAAGATAGCAGATT
* * * * * * *** **
54988419 TGACAGT-CCTGTGCTTACA-GCAAAACAGATCAAAGATTTTA-ACA
1 TGGCA-TCCCTGTGTTTATAGGGAACA-AGATCGAAGATAGCAGATT
*
54988463 TGGCATCCCTGTGTTTATAGGGAACAAG-TTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGATCGAAGATAGCAGATT
*
54988507 TGTCATCCCTGTGTTTATAGGGAACAA-ATCGAAGACATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGATCGAAG--ATAGCAGATT
54988553 TG
1 TG
54988555 ACTTTCGGAT
Statistics
Matches: 240, Mismatches: 54, Indels: 34
0.73 0.16 0.10
Matches are distributed among these distances:
42 1 0.00
43 26 0.11
44 167 0.70
45 33 0.14
46 13 0.05
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (45 bp):
TGGCATCCCTGTGTTTATAGGGAACAAGATCGAAGATAGCAGATT
Found at i:54988375 original size:132 final size:132
Alignment explanation
Indices: 54988137--54988556 Score: 624
Period size: 132 Copynumber: 3.2 Consensus size: 132
54988127 GTGAATGAAT
* * * * *
54988137 GATCGAAGATAGCAAATCTGATACTCCCATGCTTACAGCGAAGTAGATCGAAGATTTCAGCATGG
1 GATCGAAGATAGCAGATCTGACACTCCTATGCTTACAGCGAAGCAGATCGAAGATTTTAGCATGG
*
54988202 CATCCCTGTGTTTATAGGGAATAAGTTGAAGATAGCAGATTTGGCATCCCTGTGTTTATAGGGAA
66 CATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGTTTATAGGGAA
54988267 CA
131 CA
*
54988269 GATCGAAGATAGTAGATCTGACACTCCTATGCTTACAGCGAAGCAGATCGAAGATTTTAGCATGG
1 GATCGAAGATAGCAGATCTGACACTCCTATGCTTACAGCGAAGCAGATCGAAGATTTTAGCATGG
* * ***
54988334 TATCCCTGTGTCTATAGGGAACAAGTTGAAGATAATTGATTTGGCATCCCTGTGTTTATAGGGAA
66 CATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGTTTATAGGGAA
54988399 CA
131 CA
* * * * * * *
54988401 GATCAAAGATAGCAGATCTGACAGTCCTGTGCTTACAGCAAAACAGATCAAAGATTTTAACATGG
1 GATCGAAGATAGCAGATCTGACACTCCTATGCTTACAGCGAAGCAGATCGAAGATTTTAGCATGG
*
54988466 CATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGTCATCCCTGTGTTTATAGGGAA
66 CATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGTTTATAGGGAA
54988531 CA
131 CA
* *
54988533 AATCGAAGACATAGCAGATTTGAC
1 GATCGAAG--ATAGCAGATCTGAC
54988557 TTTCGGATGT
Statistics
Matches: 257, Mismatches: 29, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
132 244 0.95
134 13 0.05
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27
Consensus pattern (132 bp):
GATCGAAGATAGCAGATCTGACACTCCTATGCTTACAGCGAAGCAGATCGAAGATTTTAGCATGG
CATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGTTTATAGGGAA
CA
Found at i:54988807 original size:175 final size:175
Alignment explanation
Indices: 54988503--54988910 Score: 672
Period size: 175 Copynumber: 2.3 Consensus size: 175
54988493 GAAGATAGCA
* * * *
54988503 GATTTGTCATCCCTGTGTTTATAGGGAACAAATCGAAGACATAGCAGATTTGACTTTCGGATGTT
1 GATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTCGGATGTT
54988568 CTCACACCAAAGCAGATCCAAGATAACAAATCTGGCATCTCCATTTCGACAGAAAGCAGATACAT
66 CTCACACCAAAGCAGATCCAAGATAACAAATCTGGCATCTCCATTTCGACAGAAAGCAGATACAT
*
54988633 AGCAGATCTAACCTTCAGATGATTTTACTGAAGCAGATCTAAGAT
131 AGCAGATCTAACCTTCAGATGATTTTACTGAAGCAGATCCAAGAT
*
54988678 GATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTTGGATGTT
1 GATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTCGGATGTT
* * * *
54988743 CTTACACCAAAGCAGATCCAAGATAACAGATCTGGCATCTCCATTTCGACGGAGAGCAGATACAT
66 CTCACACCAAAGCAGATCCAAGATAACAAATCTGGCATCTCCATTTCGACAGAAAGCAGATACAT
* *
54988808 AGTAGATCTAACCTTTAGATGATTTTACTGAAGCAGATCCAAGAT
131 AGCAGATCTAACCTTCAGATGATTTTACTGAAGCAGATCCAAGAT
* * * *
54988853 GATTTGGCATCCTTATGTTCACAAGGAGCAAATCGAAGACATAGCAGATTTGGCTTTC
1 GATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTC
54988911 ACGTGTTTAC
Statistics
Matches: 216, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
175 216 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (175 bp):
GATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTCGGATGTT
CTCACACCAAAGCAGATCCAAGATAACAAATCTGGCATCTCCATTTCGACAGAAAGCAGATACAT
AGCAGATCTAACCTTCAGATGATTTTACTGAAGCAGATCCAAGAT
Found at i:54989247 original size:8 final size:8
Alignment explanation
Indices: 54989234--54989261 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
54989224 AAATAAGTTC
54989234 AAAAAAAT
1 AAAAAAAT
54989242 AAAAAAAT
1 AAAAAAAT
54989250 AAAAAAAT
1 AAAAAAAT
54989258 AAAA
1 AAAA
54989262 CAAAGTCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAAAT
Found at i:54989403 original size:14 final size:15
Alignment explanation
Indices: 54989384--54989440 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
54989374 AATCTTTAAG
54989384 GATATG-CAATCTTA
1 GATATGACAATCTTA
54989398 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
54989415 GATATGATATGCAATCTTA
1 GATATG--A--CAATCTTA
54989434 GATATGA
1 GATATGA
54989441 TATGCAATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.16
17 18 0.47
19 14 0.37
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:54989457 original size:19 final size:19
Alignment explanation
Indices: 54989384--54989451 Score: 122
Period size: 19 Copynumber: 3.7 Consensus size: 19
54989374 AATCTTTAAG
54989384 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
54989403 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
54989420 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
54989439 GATATGCAATCTT
1 GATATGCAATCTT
54989452 GAATATATGA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
17 17 0.36
19 30 0.64
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:54992116 original size:22 final size:22
Alignment explanation
Indices: 54992077--54992119 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
54992067 ATCACTCTTC
* *
54992077 CTCTCCTTTTATTTTTCTTTTT
1 CTCTCCATTTATTATTCTTTTT
*
54992099 CTCTCCATTTGTTATTCTTTT
1 CTCTCCATTTATTATTCTTTT
54992120 CTTCTTCTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.07, C:0.23, G:0.02, T:0.67
Consensus pattern (22 bp):
CTCTCCATTTATTATTCTTTTT
Found at i:54993399 original size:27 final size:27
Alignment explanation
Indices: 54993359--54993470 Score: 129
Period size: 27 Copynumber: 4.1 Consensus size: 27
54993349 AGGAAGCGTC
* *
54993359 CTGGTGGCTATGCCATAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
54993386 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
*
54993413 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
54993441 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
54993467 CTGG
1 CTGG
54993471 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 8 0.11
27 48 0.65
28 18 0.24
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:54993465 original size:54 final size:54
Alignment explanation
Indices: 54993359--54993470 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
54993349 AGGAAGCGTC
* * *
54993359 CTGGTGGCTATGCCATAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
54993413 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
54993467 CTGG
1 CTGG
54993471 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 33 0.65
55 18 0.35
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:54994898 original size:16 final size:18
Alignment explanation
Indices: 54994877--54994909 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
54994867 CATACAAGCT
54994877 CCAAAAT-ATAG-TAGTA
1 CCAAAATGATAGATAGTA
54994893 CCAAAATGATAGATAGT
1 CCAAAATGATAGATAGT
54994910 GTGACGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.24
Consensus pattern (18 bp):
CCAAAATGATAGATAGTA
Done.