Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014498.1 Kokia drynarioides strain JFW-HI SEQ_129537, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 566721
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Warning! 27 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:457336 original size:43 final size:43
Alignment explanation
Indices: 457184--457457 Score: 301
Period size: 43 Copynumber: 6.4 Consensus size: 43
457174 AGTACATAAA
* * * * *
457184 TCTTCCTTTTTAAAC--AATCTTATGCTC-TACCGAGGCATAAG
1 TCTTCC-TTTTAAACATAATCTCATTCTCATCCCGAGACATGAG
* *
457225 TCTTCCTTTTTAAACATAATCTCACGT-TCATTCCGAGACATGAG
1 TCTTCC-TTTTAAACATAATCTCA-TTCTCATCCCGAGACATGAG
457269 TCTTCC-TTTAAACATAATCTCATTCTCATCCCGAGACATGAG
1 TCTTCCTTTTAAACATAATCTCATTCTCATCCCGAGACATGAG
*
457311 TCTTCCTTTTAAACATTATCTCATTCTCATCCCGAGACATGAG
1 TCTTCCTTTTAAACATAATCTCATTCTCATCCCGAGACATGAG
* *
457354 TCTTCC-TTTAAACATAATCTCAATCTCATCTCGAGACATGAG
1 TCTTCCTTTTAAACATAATCTCATTCTCATCCCGAGACATGAG
* * * * * *
457396 TCTTCCTTTTAAACATATTGC-CATGCTCATTCTGAGTCAAGAG
1 TCTTCCTTTTAAACATAAT-CTCATTCTCATCCCGAGACATGAG
*
457439 TCTTCCTTTTTATACATAA
1 TCTTCC-TTTTAAACATAA
457458 AGTGTTCAAG
Statistics
Matches: 202, Mismatches: 22, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
41 16 0.08
42 77 0.38
43 81 0.40
44 28 0.14
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.37
Consensus pattern (43 bp):
TCTTCCTTTTAAACATAATCTCATTCTCATCCCGAGACATGAG
Found at i:459130 original size:23 final size:23
Alignment explanation
Indices: 459096--459224 Score: 177
Period size: 23 Copynumber: 5.6 Consensus size: 23
459086 AATGTGTTAT
459096 ATATTAATGTGATTTATGCTTAA
1 ATATTAATGTGATTTATGCTTAA
* * *
459119 ATGTTAACGTGATTTGTGCTTAA
1 ATATTAATGTGATTTATGCTTAA
459142 ATATTAATGTGATTTATGCTTAA
1 ATATTAATGTGATTTATGCTTAA
* *
459165 ATATTCATGTGATTTATGTTTAA
1 ATATTAATGTGATTTATGCTTAA
* *
459188 ATGTTAATATGATTTATGCTTAA
1 ATATTAATGTGATTTATGCTTAA
* *
459211 ATATTCATTTGATT
1 ATATTAATGTGATT
459225 AAATGTGACT
Statistics
Matches: 91, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 91 1.00
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (23 bp):
ATATTAATGTGATTTATGCTTAA
Found at i:459175 original size:69 final size:69
Alignment explanation
Indices: 459096--459224 Score: 195
Period size: 69 Copynumber: 1.9 Consensus size: 69
459086 AATGTGTTAT
* *
459096 ATATTAATGTGATTTATGCTTAAATGTTAACGTGATTTGTGCTTAAATATTAATGTGATTTATGC
1 ATATTAATGTGATTTATGCTTAAATGTTAACATGATTTATGCTTAAATATTAATGTGATTTATGC
459161 TTAA
66 TTAA
* * * * *
459165 ATATTCATGTGATTTATGTTTAAATGTTAATATGATTTATGCTTAAATATTCATTTGATT
1 ATATTAATGTGATTTATGCTTAAATGTTAACATGATTTATGCTTAAATATTAATGTGATT
459225 AAATGTGACT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 53 1.00
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (69 bp):
ATATTAATGTGATTTATGCTTAAATGTTAACATGATTTATGCTTAAATATTAATGTGATTTATGC
TTAA
Found at i:459239 original size:10 final size:10
Alignment explanation
Indices: 459224--459326 Score: 91
Period size: 10 Copynumber: 9.9 Consensus size: 10
459214 TTCATTTGAT
459224 TAAATGTGAC
1 TAAATGTGAC
*
459234 TAAATGTGAT
1 TAAATGTGAC
*
459244 TAAATGTGAT
1 TAAATGTGAC
459254 TAATATGTGAC
1 TAA-ATGTGAC
*
459265 TAAATGTGAG
1 TAAATGTGAC
* *
459275 TAAATGTTAAAA
1 TAAATG-T-GAC
*
459287 TATTCATGTGAC
1 TA--AATGTGAC
*
459299 T-AATGTGAT
1 TAAATGTGAC
459308 TAAATGTGAC
1 TAAATGTGAC
459318 TAAATGTGA
1 TAAATGTGA
459327 TTAATTTGTG
Statistics
Matches: 76, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
9 7 0.09
10 50 0.66
11 10 0.13
12 5 0.07
13 1 0.01
14 3 0.04
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (10 bp):
TAAATGTGAC
Found at i:459368 original size:68 final size:70
Alignment explanation
Indices: 459209--459394 Score: 223
Period size: 68 Copynumber: 2.6 Consensus size: 70
459199 ATTTATGCTT
* * *
459209 AAATATTCATTTGATTAAATGTGACTAAATGTGATTAAATGTGATTAATATGTGACTAAATGTGA
1 AAATATTCATGTGACT-AATGTGATTAAATGTGATTAAATGTGATTAATATGTG----AATGTGA
459274 GTAAATGTTA
61 GTAAATGTTA
* *
459284 AAATATTCATGTGACTAATGTGATTAAATGTGACTAAATGTGATTAATTTGTG-ATGTGA-TAAA
1 AAATATTCATGTGACTAATGTGATTAAATGTGATTAAATGTGATTAATATGTGAATGTGAGTAAA
*
459347 TGTTG
66 TGTTA
* * *
459352 AAGTATTCATGTGACTATTGTGGTTAAATGTGATTAATATGTG
1 AAATATTCATGTGACTAATGTGATTAAATGTGATTAA-ATGTG
459395 CTGTGTTAAA
Statistics
Matches: 100, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
68 41 0.41
69 11 0.11
74 34 0.34
75 14 0.14
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.40
Consensus pattern (70 bp):
AAATATTCATGTGACTAATGTGATTAAATGTGATTAAATGTGATTAATATGTGAATGTGAGTAAA
TGTTA
Found at i:461705 original size:75 final size:75
Alignment explanation
Indices: 461575--461727 Score: 252
Period size: 75 Copynumber: 2.0 Consensus size: 75
461565 CACCGAGATA
*
461575 TTAGAATTTAAAGTTTCCTATGTTAAAGGTTTTGATTAAAAAGAGAATATAGCTTAAGTTATTGT
1 TTAGAATTTAAAGTTTCCTATGTTAAAGGTTTTGATTAAAAAGAGAACATAGCTTAAGTTATTGT
461640 TTGTGACTGT
66 TTGTGACTGT
* * **
461650 TTAGAATTTAAAGTTTCCTATGTTAAATGTTTTGATTAAAAAGAGAACATGGCTTATTTTATTGT
1 TTAGAATTTAAAGTTTCCTATGTTAAAGGTTTTGATTAAAAAGAGAACATAGCTTAAGTTATTGT
*
461715 TTGTGATTGT
66 TTGTGACTGT
461725 TTA
1 TTA
461728 AGATAAGTTA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (75 bp):
TTAGAATTTAAAGTTTCCTATGTTAAAGGTTTTGATTAAAAAGAGAACATAGCTTAAGTTATTGT
TTGTGACTGT
Found at i:462136 original size:36 final size:36
Alignment explanation
Indices: 462083--462273 Score: 229
Period size: 36 Copynumber: 5.3 Consensus size: 36
462073 CTGTTGTGAA
* * * *
462083 AGTAAATATCTGAGTATGTTATTCATACCATAAGAC
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
* * *
462119 ATTAAATATGTGGGTATGTTATTCATGTCATGTGAC
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
** *
462155 AGTAAATGCGTGGGTATGTTATTCATGCCATGAGAT
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
* * * *
462191 AGTAAATATGTGGGTATGTTATTCAGGTCATGTGAT
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
* *
462227 AGTAAATATGTGGGTATGTTATTCATGCCATGTGAT
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
*
462263 AGTGAATATGT
1 AGTAAATATGT
462274 TATGCTAAAT
Statistics
Matches: 134, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 134 1.00
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.37
Consensus pattern (36 bp):
AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
Found at i:462197 original size:72 final size:72
Alignment explanation
Indices: 462077--462273 Score: 270
Period size: 72 Copynumber: 2.7 Consensus size: 72
462067 TGATGACTGT
* * * * * *
462077 TGTGAAAGTAAATATC-TGAGTATGTTATTCATACCATAAGACATTAAATATGTGGGTATGTTAT
1 TGTGACAGTAAATA-CGTGGGTATGTTATTCATGCCATGAGATAGTAAATATGTGGGTATGTTAT
*
462141 TCATGTCA
65 TCAGGTCA
*
462149 TGTGACAGTAAATGCGTGGGTATGTTATTCATGCCATGAGATAGTAAATATGTGGGTATGTTATT
1 TGTGACAGTAAATACGTGGGTATGTTATTCATGCCATGAGATAGTAAATATGTGGGTATGTTATT
462214 CAGGTCA
66 CAGGTCA
* * * *
462221 TGTGATAGTAAATATGTGGGTATGTTATTCATGCCATGTGATAGTGAATATGT
1 TGTGACAGTAAATACGTGGGTATGTTATTCATGCCATGAGATAGTAAATATGT
462274 TATGCTAAAT
Statistics
Matches: 111, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
71 1 0.01
72 110 0.99
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.37
Consensus pattern (72 bp):
TGTGACAGTAAATACGTGGGTATGTTATTCATGCCATGAGATAGTAAATATGTGGGTATGTTATT
CAGGTCA
Found at i:462632 original size:66 final size:67
Alignment explanation
Indices: 462519--462657 Score: 208
Period size: 66 Copynumber: 2.1 Consensus size: 67
462509 GGGAAAATAA
* * * *
462519 GGAGAGTGTTAGCTATATGCTTCACTTTTGGGACATGTTTGATTCTATGAG-ATTTTTGGTGTTT
1 GGAGAGTGTTAGCTATATGCTTCACTTTTGGGACATGTTCGACTCTATGAGCATATTTGGTGTGT
462583 TT
66 TT
* *
462585 GGAGAGTGTTAGCTATATGCTTCAGTTTTGGGATATGTTCGACTCTATGAGTCATATTTGGTGTG
1 GGAGAGTGTTAGCTATATGCTTCACTTTTGGGACATGTTCGACTCTATGAG-CATATTTGGTGTG
462650 TTT
65 TTT
462653 GGAGA
1 GGAGA
462658 TCCACGTATC
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 47 0.72
68 18 0.28
ACGTcount: A:0.19, C:0.09, G:0.28, T:0.43
Consensus pattern (67 bp):
GGAGAGTGTTAGCTATATGCTTCACTTTTGGGACATGTTCGACTCTATGAGCATATTTGGTGTGT
TT
Found at i:462777 original size:23 final size:23
Alignment explanation
Indices: 462740--462941 Score: 307
Period size: 23 Copynumber: 8.8 Consensus size: 23
462730 TATTATTAAA
462740 TATG-TTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
462762 TATGCTTAAATGTTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
462785 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
462808 TGTGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
462831 TGTGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
462854 TATGCTTAAATGTTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
462877 TATGTTTAATTATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
462900 TATGCTTAAATGTTAATATGATT
1 TATGCTTAAATATTAATGTGATT
* *
462923 TTTGCTTAAATATTCATGT
1 TATGCTTAAATATTAATGT
462942 AATTAAATGT
Statistics
Matches: 163, Mismatches: 16, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
22 4 0.02
23 159 0.98
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.50
Consensus pattern (23 bp):
TATGCTTAAATATTAATGTGATT
Found at i:463020 original size:10 final size:10
Alignment explanation
Indices: 463005--463043 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
462995 TCATATGACT
463005 AATGTGATTA
1 AATGTGATTA
*
463015 AATGTGACTA
1 AATGTGATTA
*
463025 AATGTTATTA
1 AATGTGATTA
463035 ATATGTGAT
1 A-ATGTGAT
463044 GTGATAATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 18 0.75
11 6 0.25
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (10 bp):
AATGTGATTA
Found at i:463024 original size:19 final size:21
Alignment explanation
Indices: 463000--463042 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
462990 AATATTCATA
463000 TGACT-AATGTGATTAA-ATG
1 TGACTAAATGTGATTAATATG
*
463019 TGACTAAATGTTATTAATATG
1 TGACTAAATGTGATTAATATG
463040 TGA
1 TGA
463043 TGTGATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 10 0.48
21 6 0.29
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.40
Consensus pattern (21 bp):
TGACTAAATGTGATTAATATG
Found at i:463061 original size:68 final size:68
Alignment explanation
Indices: 462938--463099 Score: 225
Period size: 68 Copynumber: 2.4 Consensus size: 68
462928 TTAAATATTC
* * * *
462938 ATGTAATTAAATGTGACTAAATATGATTAATATGTGATGTGATAAATGTTGAAATATTCATATGA
1 ATGTGATTAAATGTGACTAAATATGATTAATATGTGATGTGATAAATGCTAAAATATTCACATGA
463003 CTA
66 CTA
* * * *
463006 ATGTGATTAAATGTGACTAAATGTTATTAATATGTGATGTGATAATTGCTAAAATATTCACGTGA
1 ATGTGATTAAATGTGACTAAATATGATTAATATGTGATGTGATAAATGCTAAAATATTCACATGA
463071 CTA
66 CTA
* *
463074 CTGTGATTAAATGTGATTAATATATG
1 ATGTGATTAAATGTGACTAA-ATATG
463100 TTGTGTTAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
68 78 0.96
69 3 0.04
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (68 bp):
ATGTGATTAAATGTGACTAAATATGATTAATATGTGATGTGATAAATGCTAAAATATTCACATGA
CTA
Found at i:463965 original size:38 final size:39
Alignment explanation
Indices: 463873--463976 Score: 129
Period size: 38 Copynumber: 2.7 Consensus size: 39
463863 AGCATATCGT
* *
463873 AGTGTTTATAATGTCACTGCCAGTTCAATAAGGTATTGC
1 AGTGTTTATAATGTCACTGCTAGTTCAATAAGGCATTGC
* * * *
463912 AGTGTTTACAGTGTCACTGCTAGTTTAAT-AGGCATTGT
1 AGTGTTTATAATGTCACTGCTAGTTCAATAAGGCATTGC
* *
463950 TGTGTTTATAATGTCACTACTAGTTCA
1 AGTGTTTATAATGTCACTGCTAGTTCA
463977 GTAATCCAGT
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
38 29 0.54
39 25 0.46
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.39
Consensus pattern (39 bp):
AGTGTTTATAATGTCACTGCTAGTTCAATAAGGCATTGC
Found at i:464335 original size:73 final size:72
Alignment explanation
Indices: 464097--464367 Score: 222
Period size: 73 Copynumber: 3.7 Consensus size: 72
464087 ATAGTATGCT
* * * * * * * **
464097 CACACGGTCTAGCTCACGCCCGTGTGTCCAGACCGTGTAACTCACTGTTTCCAATTTCACCCCTC
1 CACACAGTCTGGCACACGCCTGTGGGCCCAGACCGTGTAACTCACTATTTCCAATTTC-CCATTC
* ***
464162 AAATTTTT
65 AAAATAAC
* * * * *
464170 CACACTA-TCTGGCACATGCCCGTGGGCCTAGATCGTGTAACTCACTGTTTCCAATTTTTTCCCA
1 CACAC-AGTCTGGCACACGCCTGTGGGCCCAGACCGTGTAACTCACTATTTCCAA---TTTCCCA
* *
464234 TTTAACATAAC
62 TTCAAAATAAC
** ** *
464245 CACATGGTCTGGCACACGCCTGTGAACCCAGACCGTGTAACTCACTATTTCTAATTTCGCCATTC
1 CACACAGTCTGGCACACGCCTGTGGGCCCAGACCGTGTAACTCACTATTTCCAATTTC-CCATTC
464310 AAAATAAC
65 AAAATAAC
**
464318 CACACAGTCTGGCACACG-CTCGTGGGCCCAGTTCGTGTAACTCACTATTT
1 CACACAGTCTGGCACACGCCT-GTGGGCCCAGACCGTGTAACTCACTATTT
464368 TTGAATTCTC
Statistics
Matches: 157, Mismatches: 34, Indels: 14
0.77 0.17 0.07
Matches are distributed among these distances:
72 6 0.04
73 98 0.62
75 49 0.31
76 4 0.03
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (72 bp):
CACACAGTCTGGCACACGCCTGTGGGCCCAGACCGTGTAACTCACTATTTCCAATTTCCCATTCA
AAATAAC
Found at i:469253 original size:43 final size:43
Alignment explanation
Indices: 469191--469396 Score: 189
Period size: 43 Copynumber: 4.8 Consensus size: 43
469181 TTAACGACAC
* * * *
469191 TTTCCCACAAACACAGCTATAGAACATGGCCTTTAGCGGTGTT
1 TTTCCCACAAACGCCGCTATAGAACATGGTCTTTAGCAGTGTT
* * * **
469234 TTTCCCATAAATGCCGCTATAGAACATGGTCTTTAGCCGCATT
1 TTTCCCACAAACGCCGCTATAGAACATGGTCTTTAGCAGTGTT
* * * *
469277 TTTCCCACAAACGCTGTTATAGAACATGGTCTTTAACAGTGCT
1 TTTCCCACAAACGCCGCTATAGAACATGGTCTTTAGCAGTGTT
* * * * * * ** **
469320 TTTCCCACAAACACCACAATAGAGCATGATTTTTAGTGGCATT
1 TTTCCCACAAACGCCGCTATAGAACATGGTCTTTAGCAGTGTT
*
469363 TTTTCCACAAACGCCGCTATAGAACAT-GTCTTTA
1 TTTCCCACAAACGCCGCTATAGAACATGGTCTTTA
469397 AGTTGTAGCC
Statistics
Matches: 125, Mismatches: 38, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
42 5 0.04
43 120 0.96
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.31
Consensus pattern (43 bp):
TTTCCCACAAACGCCGCTATAGAACATGGTCTTTAGCAGTGTT
Found at i:469282 original size:86 final size:86
Alignment explanation
Indices: 469191--469390 Score: 229
Period size: 86 Copynumber: 2.3 Consensus size: 86
469181 TTAACGACAC
* * * * * ** * *
469191 TTTCCCACAAACACAGCTATAGAACATGGCCTTTAGCGGTGTTTTTCCCATAAATGCCGCTATAG
1 TTTCCCACAAACGCAGCTATAGAACATGGCCTTTAACAGTGCTTTTCCCACAAACACCACAATAG
*
469256 AACATGGTCTTTAGCCGCATT
66 AACATGATCTTTAGCCGCATT
* * *
469277 TTTCCCACAAACGCTGTTATAGAACATGGTCTTTAACAGTGCTTTTCCCACAAACACCACAATAG
1 TTTCCCACAAACGCAGCTATAGAACATGGCCTTTAACAGTGCTTTTCCCACAAACACCACAATAG
* * **
469342 AGCATGATTTTTAGTGGCATT
66 AACATGATCTTTAGCCGCATT
* *
469363 TTTTCCACAAACGCCGCTATAGAACATG
1 TTTCCCACAAACGCAGCTATAGAACATG
469391 TCTTTAAGTT
Statistics
Matches: 94, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
86 94 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (86 bp):
TTTCCCACAAACGCAGCTATAGAACATGGCCTTTAACAGTGCTTTTCCCACAAACACCACAATAG
AACATGATCTTTAGCCGCATT
Found at i:472706 original size:11 final size:11
Alignment explanation
Indices: 472690--472774 Score: 59
Period size: 11 Copynumber: 7.6 Consensus size: 11
472680 GCCCAACAAA
472690 TTTAAATTTAT
1 TTTAAATTTAT
* *
472701 TTTAAAGTTAAG
1 TTTAAA-TTTAT
*
472713 TTT-ATTTTAAT
1 TTTAAATTT-AT
472724 TTTAAATTTA-
1 TTTAAATTTAT
*
472734 TTTAAATTTGT
1 TTTAAATTTAT
*
472745 TATAAATTTAAAT
1 TTTAAATTT--AT
*
472758 TTAAAATTTA-
1 TTTAAATTTAT
472768 TTTAAAT
1 TTTAAAT
472775 AATGTCCAAG
Statistics
Matches: 56, Mismatches: 12, Indels: 13
0.69 0.15 0.16
Matches are distributed among these distances:
10 17 0.30
11 21 0.38
12 10 0.18
13 8 0.14
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:472738 original size:27 final size:27
Alignment explanation
Indices: 472708--472774 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
472698 TATTTTAAAG
* * *
472708 TTAAGTTTATTTTAATTTTAAATTTAT
1 TTAAATTTATTATAAATTTAAATTTAT
*
472735 TTAAATTTGTTATAAATTTAAATTTA-
1 TTAAATTTATTATAAATTTAAATTTAT
472761 --AAATTTATT-TAAAT
1 TTAAATTTATTATAAAT
472775 AATGTCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 5 0.14
24 8 0.23
27 22 0.63
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (27 bp):
TTAAATTTATTATAAATTTAAATTTAT
Found at i:472741 original size:17 final size:17
Alignment explanation
Indices: 472690--472774 Score: 75
Period size: 17 Copynumber: 5.0 Consensus size: 17
472680 GCCCAACAAA
472690 TTTAAATTTATTTTAAA-
1 TTTAAATTTA-TTTAAAT
* * *
472707 GTTAAGTTTATTTTAAT
1 TTTAAATTTATTTAAAT
472724 TTTAAATTTATTTAAAT
1 TTTAAATTTATTTAAAT
* **
472741 TTGT-TATAAATTTAAAT
1 TT-TAAATTTATTTAAAT
*
472758 TTAAAATTTATTTAAAT
1 TTTAAATTTATTTAAAT
472775 AATGTCCAAG
Statistics
Matches: 52, Mismatches: 13, Indels: 6
0.73 0.18 0.08
Matches are distributed among these distances:
16 5 0.10
17 46 0.88
18 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTAAAT
Found at i:474680 original size:29 final size:30
Alignment explanation
Indices: 474634--474876 Score: 155
Period size: 30 Copynumber: 8.2 Consensus size: 30
474624 TTGTTTTCAC
* *
474634 CCCCG-AACATCCAAAAAACCTATTTTTAA
1 CCCCGAAACTTCCAAAAATCCTATTTTTAA
** * *
474663 CCCCGAAACTTCTC-AAAATTTTGTTTTTAC
1 CCCCGAAACTTC-CAAAAATCCTATTTTTAA
*
474693 CCCCG-AACTTCCAAAAATCCCATTTTTAA
1 CCCCGAAACTTCCAAAAATCCTATTTTTAA
* * *
474722 CCACGAAACTTCAAAAAAAAT-CTATCTTT-A
1 CCCCGAAACTTC--CAAAAATCCTATTTTTAA
** * * *
474752 CCCTTAAACTTCCCAAAATCTTATTTTTGA
1 CCCCGAAACTTCCAAAAATCCTATTTTTAA
* *
474782 CCTCGAAACTTCCAAAAAT-TTCA-TTTT-A
1 CCCCGAAACTTCCAAAAATCCT-ATTTTTAA
* *
474810 CCCCTG-AACTTCCCAAAATCCCATTTTTAA
1 CCCC-GAAACTTCCAAAAATCCTATTTTTAA
*** *
474840 CCTTAAAACTTCCAAAAATCCCATTTTT-A
1 CCCCGAAACTTCCAAAAATCCTATTTTTAA
474869 CCCTCGAA
1 CCC-CGAA
474877 TGTCTAAAAA
Statistics
Matches: 162, Mismatches: 37, Indels: 29
0.71 0.16 0.13
Matches are distributed among these distances:
28 23 0.14
29 46 0.28
30 80 0.49
31 7 0.04
32 6 0.04
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.32
Consensus pattern (30 bp):
CCCCGAAACTTCCAAAAATCCTATTTTTAA
Found at i:474718 original size:59 final size:58
Alignment explanation
Indices: 474614--474905 Score: 235
Period size: 59 Copynumber: 4.9 Consensus size: 58
474604 CCCTAAATTG
* * * * *
474614 TCCAAAAATTTTGTTTTCACCCCCGAACATCCAAAAAACCTATTTTTAACCCCGAAACT
1 TCCAAAAA-TTTGTTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCACGAAACT
*
474673 TCTCAAAATTTTGTTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCACGAAACT
1 TC-CAAAAATTTGTTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCACGAAACT
* * * * *** * ** * *
474732 TCAAAAAAAATCTATCTTTACCCTTAAACTTCCCAAAATCTTATTTTTGACCTCGAAACT
1 TC--CAAAAATTTGTTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCACGAAACT
** * * ***
474792 TCCAAAAATTTCATTTTACCCCTGAACTTCCCAAAATCCCATTTTTAACCTTAAAACT
1 TCCAAAAATTTGTTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCACGAAACT
*** * * * *
474850 TCCAAAAATCCCATTTTTACCCTCGAA-TGTCTAAAAATCCCATTTTTTACCTCGAA
1 TCCAAAAAT-TTGTTTTTACCCCCGAACT-TCCAAAAATCCCATTTTTAACCACGAA
474906 TTTTCTCGAA
Statistics
Matches: 186, Mismatches: 43, Indels: 8
0.78 0.18 0.03
Matches are distributed among these distances:
58 54 0.29
59 82 0.44
60 50 0.27
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.33
Consensus pattern (58 bp):
TCCAAAAATTTGTTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCACGAAACT
Found at i:474770 original size:60 final size:58
Alignment explanation
Indices: 474687--474841 Score: 184
Period size: 60 Copynumber: 2.6 Consensus size: 58
474677 AAAATTTTGT
** *
474687 TTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCACGAAACTTCAAAAAAAATCTA
1 TTTTACCCCTAAACTTCCCAAAATCCCATTTTTAACCACGAAACTTCAAAAAAAATC-A
* ** * * * **
474746 TCTTTACCCTTAAACTTCCCAAAATCTTATTTTTGACCTCGAAACTTCCAAAAATTTCA
1 T-TTTACCCCTAAACTTCCCAAAATCCCATTTTTAACCACGAAACTTCAAAAAAAATCA
*
474805 TTTTACCCCTGAACTTCCCAAAATCCCATTTTTAACC
1 TTTTACCCCTAAACTTCCCAAAATCCCATTTTTAACC
474842 TTAAAACTTC
Statistics
Matches: 79, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
58 31 0.39
59 3 0.04
60 45 0.57
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (58 bp):
TTTTACCCCTAAACTTCCCAAAATCCCATTTTTAACCACGAAACTTCAAAAAAAATCA
Found at i:475803 original size:55 final size:55
Alignment explanation
Indices: 475719--475829 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
475709 TTTTCAAAAC
*
475719 AGTTTTTAAAACGTTTTGTGGTGATCCAATCACACCAAATAAAGGATTGGTGGCG
1 AGTTTTTAAAACGTTCTGTGGTGATCCAATCACACCAAATAAAGGATTGGTGGCG
*
475774 AGTTTTTAAAACGTTCTGTGGTGATCCAATCACACCGAATAAAGGATTGGTGGCG
1 AGTTTTTAAAACGTTCTGTGGTGATCCAATCACACCAAATAAAGGATTGGTGGCG
475829 A
1 A
475830 CTCCCATTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (55 bp):
AGTTTTTAAAACGTTCTGTGGTGATCCAATCACACCAAATAAAGGATTGGTGGCG
Found at i:480950 original size:205 final size:205
Alignment explanation
Indices: 480591--481257 Score: 809
Period size: 205 Copynumber: 3.3 Consensus size: 205
480581 GTGACCATCC
* * *
480591 ACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAAAAGACCAAATCAATCTCACGCTCGA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAGAAGACCAAATCAAACCCACGCTCGA
* * **
480656 TGTGAGTAAATCTTCGAATCCCAGCTTCCTGATGAGACACCGAGAAGCAGATAAAAGCAATAAAC
66 TGTGAGTAAATCTTCGAATCCCAGCTTCCTGATGAGACATCGAGAAGCAAATCGAAGCAATAAAC
* * *
480721 GGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGATGCAGAGAA
131 AGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAA
480786 GCGGATTGAA
196 GCGGATTGAA
* *
480796 ACAAACAACGCGGTCATCTTCCTGATGAGATACCGAGAAGAAGACCAAATCAAACCCATGCTCGA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAGAAGACCAAATCAAACCCACGCTCGA
* *
480861 TGTGAGTAGATCTTTGAATCCCAGCTTCCTGATGAGACATCGAGAAGCAAATCGAAGCAATAAAC
66 TGTGAGTAAATCTTCGAATCCCAGCTTCCTGATGAGACATCGAGAAGCAAATCGAAGCAATAAAC
* * *
480926 AGTTAGCTTCCCGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAA
131 AGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAA
480991 GCGGATTGAA
196 GCGGATTGAA
* * * *
481001 ACAAACGACGCGATCATCTTCCTGATGAGATACTGAGAGGAAGACCAATTCAAACCCACGCTCGA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAGAAGACCAAATCAAACCCACGCTCGA
** * * * * * * * *
481066 --TGAACAAATCTTCAAACCCCAGCTTCCTGATAAGATATTGATAAGCAAGTCGAAGTAATAAA-
66 TGTGAGTAAATCTTCGAATCCCAGCTTCCTGATGAGACATCGAGAAGCAAATCGAAGCAATAAAC
* * * * ** * * * *
481128 ATGGTTAGCTTCCTAATGAAATACAGGGAAGTAAACCAAAATCATCTTCCTAATGAAACACAGAG
131 A--GTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAG
* ***
481193 AAGTGGAACAAA
194 AAGCGGATTGAA
** *** * * * *
481205 ACAAGTGATATGGTCATCTTCCCGATGAGATACTGAGAAGAAGGCCAAGTCAA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAGAAGACCAAATCAA
481258 TGAAACCAGA
Statistics
Matches: 398, Mismatches: 62, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
202 1 0.00
203 50 0.13
204 100 0.25
205 247 0.62
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (205 bp):
ACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAGAAGACCAAATCAAACCCACGCTCGA
TGTGAGTAAATCTTCGAATCCCAGCTTCCTGATGAGACATCGAGAAGCAAATCGAAGCAATAAAC
AGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAA
GCGGATTGAA
Found at i:481609 original size:6 final size:6
Alignment explanation
Indices: 481569--481654 Score: 67
Period size: 6 Copynumber: 15.2 Consensus size: 6
481559 TGGGCCCAAC
* * * * *
481569 AAATTT AAA-TT CATTTT AAAGTT AAGTTT -ATTTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
481615 --GTTT AAATTT --ATTAT AAATTT AAATTT AAATTT AAATTT A
1 AAATTT AAATTT AAATT-T AAATTT AAATTT AAATTT AAATTT A
481655 TTTAAATAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
4 6 0.10
5 8 0.13
6 45 0.73
7 3 0.05
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:481620 original size:27 final size:27
Alignment explanation
Indices: 481590--481661 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 27
481580 CATTTTAAAG
* *
481590 TTAAGTTTATTTTAAATTTAAATTTGT
1 TTAAATTTATTATAAATTTAAATTTGT
*
481617 TTAAATTTATTATAAATTTAAATTTAAAT
1 TTAAATTTATTATAAATTTAAATTT--GT
481646 TTAAATTTATT-TAAAT
1 TTAAATTTATTATAAAT
481662 AATGTCCAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 23 0.57
28 5 0.12
29 12 0.30
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (27 bp):
TTAAATTTATTATAAATTTAAATTTGT
Found at i:481634 original size:11 final size:10
Alignment explanation
Indices: 481605--481648 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
481595 TTTATTTTAA
481605 ATTTAAATTT
1 ATTTAAATTT
*
481615 GTTTAAATTT
1 ATTTAAATTT
481625 ATTATAAATTT
1 ATT-TAAATTT
481636 AAATTTAAATTT
1 --ATTTAAATTT
481648 A
1 A
481649 AATTTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 12 0.41
11 7 0.24
12 7 0.24
13 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:481638 original size:17 final size:16
Alignment explanation
Indices: 481569--481648 Score: 70
Period size: 17 Copynumber: 4.8 Consensus size: 16
481559 TGGGCCCAAC
*
481569 AAATTTAAATTCATTTT
1 AAATTTAAATTTA-TTT
* *
481586 AAAGTTAAGTTTATTTT
1 AAATTTAAATTTA-TTT
*
481603 AAATTTAAATTTGTTT
1 AAATTTAAATTTATTT
* **
481619 AAATTTATTATAAATTT
1 AAATTTA-AATTTATTT
481636 AAATTTAAATTTA
1 AAATTTAAATTTA
481649 AATTTATTTA
Statistics
Matches: 49, Mismatches: 13, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
16 13 0.27
17 36 0.73
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (16 bp):
AAATTTAAATTTATTT
Found at i:482374 original size:3 final size:3
Alignment explanation
Indices: 482366--482452 Score: 70
Period size: 3 Copynumber: 29.0 Consensus size: 3
482356 TTAATAACAT
* ** * *
482366 TAA TAA TAA TAA TAA TAT TGT TAA TAT TAA TAA TAA -ATA TAA TAC
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
* * *
482411 TAA TGA CAT TAA TTAA TAA TAA TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
482453 GTAAAAAAAA
Statistics
Matches: 66, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
2 3 0.05
3 59 0.89
4 4 0.06
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:483630 original size:29 final size:28
Alignment explanation
Indices: 483567--483801 Score: 162
Period size: 30 Copynumber: 8.0 Consensus size: 28
483557 GGAGGTTCCT
*
483567 AAACTGTCCAAAAATTCC-ATTTTCACAGCCG
1 AAACT-TCCAAAAA-TCCTATTTTTAC--CCG
*
483598 -AACTTCAAAAAATCCTATTTTTGACCCG
1 AAACTTCCAAAAATCCTATTTTT-ACCCG
*
483626 AAACTTCTCAAAATTCC-ATTTTTACCCCCG
1 AAACTTC-CAAAAATCCTATTTTTA--CCCG
483656 -AACTTCCAAAAAT-CTCATTTTTTACCCTCG
1 AAACTTCCAAAAATCCT-A-TTTTTA-CC-CG
*
483686 -AACTTCCAAAAATCCCATTTTTAACCCG
1 AAACTTCCAAAAATCCTATTTTT-ACCCG
*
483714 AAAACTTCCAAAAATTTCC-ATTTTTACCCTC
1 -AAACTTCCAAAAA--TCCTATTTTTACCC-G
* *
483745 AAACTTCCCAAAAT-CTCATTTTTGACCCCA
1 AAACTTCCAAAAATCCT-ATTTTT-A-CCCG
*
483775 AAACTTCCAAAAATTCTATTTTTACCC
1 AAACTTCCAAAAATCCTATTTTTACCC
483802 TCGAATGTCT
Statistics
Matches: 172, Mismatches: 10, Indels: 47
0.75 0.04 0.21
Matches are distributed among these distances:
27 2 0.01
28 19 0.11
29 48 0.28
30 88 0.51
31 12 0.07
32 3 0.02
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (28 bp):
AAACTTCCAAAAATCCTATTTTTACCCG
Found at i:483678 original size:30 final size:30
Alignment explanation
Indices: 483595--483806 Score: 170
Period size: 30 Copynumber: 7.2 Consensus size: 30
483585 ATTTTCACAG
* *
483595 CCGAACTTCAAAAAATC-CTATTTTTGA--C
1 CCGAACTTCCAAAAATCTC-ATTTTTTACCC
*
483623 CCGAAACTTCTCAAAATTC-CA-TTTTTACCC
1 CCG-AACTTC-CAAAAATCTCATTTTTTACCC
483653 CCGAACTTCCAAAAATCTCATTTTTTACCC
1 CCGAACTTCCAAAAATCTCATTTTTTACCC
* * *
483683 TCGAACTTCCAAAAATCCCATTTTTAACCC
1 CCGAACTTCCAAAAATCTCATTTTTTACCC
*** *
483713 GAAAACTTCCAAAAATTTCCA-TTTTTACCC
1 CCGAACTTCCAAAAATCT-CATTTTTTACCC
* * * *
483743 TCAAACTTCCCAAAATCTCATTTTTGACCC
1 CCGAACTTCCAAAAATCTCATTTTTTACCC
**
483773 CAAAACTTCCAAAAAT-TC-TATTTTTACCC
1 CCGAACTTCCAAAAATCTCAT-TTTTTACCC
*
483802 TCGAA
1 CCGAA
483807 TGTCTAAAAA
Statistics
Matches: 150, Mismatches: 25, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
28 16 0.11
29 29 0.19
30 103 0.69
31 2 0.01
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (30 bp):
CCGAACTTCCAAAAATCTCATTTTTTACCC
Found at i:483740 original size:60 final size:60
Alignment explanation
Indices: 483627--483826 Score: 223
Period size: 60 Copynumber: 3.4 Consensus size: 60
483617 TTTGACCCGA
* * *
483627 AACTTCTC-AAAATTCCATTTTTACCCCCG--AACTTCCAAAAATCT-CATTTTTTACCCTCG
1 AACTTC-CAAAAATCCCATTTTTA-ACCCGAAAACTTCCAAAAATTTCCA-TTTTTACCCTCG
*
483686 AACTTCCAAAAATCCCATTTTTAACCCGAAAACTTCCAAAAATTTCCATTTTTACCCTCA
1 AACTTCCAAAAATCCCATTTTTAACCCGAAAACTTCCAAAAATTTCCATTTTTACCCTCG
* * * * *
483746 AACTTCCCAAAATCTCATTTTTGACCCCAAAACTTCCAAAAA-TTCTATTTTTACCCTCG
1 AACTTCCAAAAATCCCATTTTTAACCCGAAAACTTCCAAAAATTTCCATTTTTACCCTCG
* *
483805 AA-TGTCTAAAAATTCCATTTTT
1 AACT-TCCAAAAATCCCATTTTT
483827 GACCTCAAAT
Statistics
Matches: 122, Mismatches: 14, Indels: 10
0.84 0.10 0.07
Matches are distributed among these distances:
58 6 0.05
59 51 0.42
60 63 0.52
61 2 0.02
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (60 bp):
AACTTCCAAAAATCCCATTTTTAACCCGAAAACTTCCAAAAATTTCCATTTTTACCCTCG
Found at i:487500 original size:22 final size:19
Alignment explanation
Indices: 487473--487532 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 19
487463 ATTAGGGTTG
487473 TTTTAAATAATTAAATATT
1 TTTTAAATAATTAAATATT
* **
487492 TTGAATTAAATATTTGGAT-TT
1 TT---TTAAATAATTAAATATT
487513 TTTTAAATAATTAAATATT
1 TTTTAAATAATTAAATATT
487532 T
1 T
487533 AAATAATTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
18 11 0.35
19 5 0.16
21 4 0.13
22 11 0.35
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
TTTTAAATAATTAAATATT
Found at i:487528 original size:8 final size:8
Alignment explanation
Indices: 487515--487561 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
487505 TTGGATTTTT
487515 TTAAATAA
1 TTAAATAA
*
487523 TTAAATAT
1 TTAAATAA
487531 TTAAATAA
1 TTAAATAA
*
487539 TTGAATAA
1 TTAAATAA
*
487547 TTAATTAA
1 TTAAATAA
*
487555 TAAAATA
1 TTAAATA
487562 TTTGGATTGT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (8 bp):
TTAAATAA
Found at i:487535 original size:16 final size:16
Alignment explanation
Indices: 487514--487564 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
487504 TTTGGATTTT
487514 TTTAAATAATTAAATA
1 TTTAAATAATTAAATA
*
487530 TTTAAATAATTGAATA
1 TTTAAATAATTAAATA
* * *
487546 ATTAATTAATAAAATA
1 TTTAAATAATTAAATA
487562 TTT
1 TTT
487565 GGATTGTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
TTTAAATAATTAAATA
Found at i:487537 original size:34 final size:34
Alignment explanation
Indices: 487497--487626 Score: 120
Period size: 34 Copynumber: 4.1 Consensus size: 34
487487 ATATTTTGAA
487497 TTAAATATTTGGATT-TTTTTAAATAATTAAATAT
1 TTAAATATTTGGATTGTTTTT-AATAATTAAATAT
* *
487531 TTAAATA-----ATTG-----AATAATTAATTAA
1 TTAAATATTTGGATTGTTTTTAATAATTAAATAT
* *
487555 TAAAATATTTGGATTGTTTTTAATAATTAAATAA
1 TTAAATATTTGGATTGTTTTTAATAATTAAATAT
* *
487589 TTAAATATTTGGGTTGTTTTTAATAATTAAATTT
1 TTAAATATTTGGATTGTTTTTAATAATTAAATAT
487623 TTAA
1 TTAA
487627 TTAAATATAA
Statistics
Matches: 77, Mismatches: 8, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
24 17 0.22
29 7 0.09
34 53 0.69
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (34 bp):
TTAAATATTTGGATTGTTTTTAATAATTAAATAT
Found at i:487567 original size:58 final size:56
Alignment explanation
Indices: 487474--487595 Score: 167
Period size: 58 Copynumber: 2.1 Consensus size: 56
487464 TTAGGGTTGT
*
487474 TTTAAATAATTAAATATTTTGAATTAAATATTTGGATT-TTTTTAAATAATTAAATA
1 TTTAAATAATTAAATATTTTGAATAAAATATTTGGATTGTTTTT-AATAATTAAATA
*
487530 TTTAAATAATTGAATAATTAATT-AATAAAATATTTGGATTGTTTTTAATAATTAAATA
1 TTTAAATAATTAAAT-ATT--TTGAATAAAATATTTGGATTGTTTTTAATAATTAAATA
*
487588 ATTAAATA
1 TTTAAATA
487596 TTTGGGTTGT
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
56 14 0.24
57 3 0.05
58 35 0.59
59 7 0.12
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.48
Consensus pattern (56 bp):
TTTAAATAATTAAATATTTTGAATAAAATATTTGGATTGTTTTTAATAATTAAATA
Found at i:487643 original size:48 final size:47
Alignment explanation
Indices: 487585--487761 Score: 165
Period size: 48 Copynumber: 3.5 Consensus size: 47
487575 TAATAATTAA
*
487585 ATAATTAAATATTTGGGTTGTTTTTAATAATTAAATTTTTAATTAAATATAATT
1 ATAATTAAATATTTGGGTTGTTTTTAATAATTAAA----T-ATTTAA-ATAA-T
* * *
487639 AAATAATTAAATATTTGTGTTGTTTTTAATAATTAAATAATTAAATATT
1 --ATAATTAAATATTTGGGTTGTTTTTAATAATTAAATATTTAAATAAT
* * *
487688 TTGAATTAAATATTTAGATTGTTTTTAATAATTAAATATTTAAATAATT
1 AT-AATTAAATATTTGGGTTGTTTTTAATAATTAAATATTTAAATAA-T
*
487737 AAATAATTAAATATTTGGTTTGTTT
1 --ATAATTAAATATTTGGGTTGTTT
487762 CTAAAAAATA
Statistics
Matches: 104, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
47 1 0.01
48 39 0.38
49 2 0.02
50 22 0.21
51 5 0.05
52 1 0.01
56 34 0.33
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (47 bp):
ATAATTAAATATTTGGGTTGTTTTTAATAATTAAATATTTAAATAAT
Found at i:487645 original size:56 final size:52
Alignment explanation
Indices: 487577--487761 Score: 231
Period size: 56 Copynumber: 3.6 Consensus size: 52
487567 ATTGTTTTTA
487577 ATAATTAAATAATTAAATATTTGGGTTGTTTTTAATAATTAAATTTTTAATTAAAT
1 ATAATTAAATAATTAAATATTTGGGTTGTTTTTAATAATTAAA----TAATTAAAT
*
487633 ATAATTAAATAATTAAATATTTGTGTTGTTTTTAATAATTAAATAATTAAAT
1 ATAATTAAATAATTAAATATTTGGGTTGTTTTTAATAATTAAATAATTAAAT
* * *
487685 AT--TT---TGAATTAAATATTTAGATTGTTTTTAATAATTAAAT-ATTTAA-
1 ATAATTAAAT-AATTAAATATTTGGGTTGTTTTTAATAATTAAATAATTAAAT
*
487731 ATAATTAAATAATTAAATATTTGGTTTGTTT
1 ATAATTAAATAATTAAATATTTGGGTTGTTT
487762 CTAAAAAATA
Statistics
Matches: 116, Mismatches: 7, Indels: 18
0.82 0.05 0.13
Matches are distributed among these distances:
46 2 0.02
47 6 0.05
48 33 0.28
50 21 0.18
51 1 0.01
52 11 0.09
56 42 0.36
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (52 bp):
ATAATTAAATAATTAAATATTTGGGTTGTTTTTAATAATTAAATAATTAAAT
Found at i:487670 original size:90 final size:91
Alignment explanation
Indices: 487495--487688 Score: 286
Period size: 90 Copynumber: 2.1 Consensus size: 91
487485 AAATATTTTG
* *
487495 AATTAAATATTTGGATTTTTTTAAATAATTAAATATTTAAATAATTGAATAATTAATTAATAAAA
1 AATTAAATATTTGGATTTTTTTAAATAATTAAATATTTAAATAAAT-AATAATTAAATAATAAAA
487560 TATTTGGATTGTTTTTAATAATTAAAT
65 TATTTGGATTGTTTTTAATAATTAAAT
* * * *
487587 AATTAAATATTTGGGTTGTTTTT-AATAATTAAATTTTTAATTAAAT-ATAATTAAATAATTAAA
1 AATTAAATATTTGGATT-TTTTTAAATAATTAAATATTTAAATAAATAATAATTAAATAATAAAA
487650 TATTTGTG-TTGTTTTTAATAATTAAAT
65 TATTTG-GATTGTTTTTAATAATTAAAT
487677 AATTAAATATTT
1 AATTAAATATTT
487689 TGAATTAAAT
Statistics
Matches: 94, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
90 52 0.55
91 1 0.01
92 36 0.38
93 5 0.05
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (91 bp):
AATTAAATATTTGGATTTTTTTAAATAATTAAATATTTAAATAAATAATAATTAAATAATAAAAT
ATTTGGATTGTTTTTAATAATTAAAT
Found at i:487729 original size:26 final size:26
Alignment explanation
Indices: 487584--487729 Score: 106
Period size: 26 Copynumber: 5.6 Consensus size: 26
487574 TTAATAATTA
* *
487584 AATAATTAAATATTTGGGTTGTTTTT
1 AATAATTAAATATTTAGATTGTTTTT
* * *
487610 AATAATTAAATTTTTA-ATTAAATATAATTA
1 AATAATTAAATATTTAGATT--GT-T--TTT
*
487640 AATAATTAAATATTT-GTGTTGTTTTT
1 AATAATTAAATATTTAG-ATTGTTTTT
* * *
487666 AATAATTAAATAATTA-AAT-ATTTT
1 AATAATTAAATATTTAGATTGTTTTT
*
487690 --GAATTAAATATTTAGATTGTTTTT
1 AATAATTAAATATTTAGATTGTTTTT
487714 AATAATTAAATATTTA
1 AATAATTAAATATTTA
487730 AATAATTAAA
Statistics
Matches: 90, Mismatches: 18, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
22 12 0.13
23 2 0.02
24 8 0.09
25 3 0.03
26 43 0.48
27 1 0.01
28 2 0.02
29 1 0.01
30 16 0.18
31 2 0.02
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (26 bp):
AATAATTAAATATTTAGATTGTTTTT
Found at i:487730 original size:8 final size:8
Alignment explanation
Indices: 487714--487749 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
487704 GATTGTTTTT
487714 AATAATTA
1 AATAATTA
*
487722 AATATTTA
1 AATAATTA
487730 AATAATTA
1 AATAATTA
487738 AATAATTA
1 AATAATTA
487746 AATA
1 AATA
487750 TTTGGTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AATAATTA
Found at i:487731 original size:90 final size:88
Alignment explanation
Indices: 487515--487741 Score: 239
Period size: 90 Copynumber: 2.5 Consensus size: 88
487505 TTGGATTTTT
* * * *
487515 TTAAATAATTAAATATTTAAATAATTGAATAATTAATTAATAAAATATTTGGATTGTTTTTAATA
1 TTAAATAATTAAAT-TTT-AATAATTAAATATTTAAATAATTAAATATTTGGATTGTTTTTAATA
**
487580 ATTAAATAATTAAATATTTGGGTTGTT
64 ATTAAATAATTAAATATTT--GTTGAA
*
487607 TTTAATAATTAAATTTT--TAATTAAATATAATTAAATAATTAAATATTTGTG-TTGTTTTTAAT
1 TTAAATAATTAAATTTTAATAATTAAATAT--TTAAATAATTAAATATTTG-GATTGTTTTTAAT
487669 AATTAAATAATTAAATA-TT-TTGAA
63 AATTAAATAATTAAATATTTGTTGAA
* *
487693 TTAAATATTTAGATTGTTTTTAATAATTAAATATTTAAATAATTAAATA
1 TTAAATAATTA-A---ATTTTAATAATTAAATATTTAAATAATTAAATA
487742 ATTAAATATT
Statistics
Matches: 116, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
86 12 0.10
87 1 0.01
88 9 0.08
89 2 0.02
90 64 0.55
91 4 0.03
92 24 0.21
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (88 bp):
TTAAATAATTAAATTTTAATAATTAAATATTTAAATAATTAAATATTTGGATTGTTTTTAATAAT
TAAATAATTAAATATTTGTTGAA
Found at i:490355 original size:43 final size:42
Alignment explanation
Indices: 490268--490367 Score: 125
Period size: 43 Copynumber: 2.4 Consensus size: 42
490258 TTGCGGCATT
* * **
490268 TTGCTCTTTACCTTTTGCGGTGTTTTCCCATAAGCGTCGTTA
1 TTGCTCTTTACCTTTTGCGGTGTTTTCCCATAAACGCCACTA
490310 TTGCTCTTTACCTTTTGCTGCGT-TTTTCCCATAAACGCCACTA
1 TTGCTCTTTACCTTTTGC-G-GTGTTTTCCCATAAACGCCACTA
490353 TTG--CTTTACCTTTTG
1 TTGCTCTTTACCTTTTG
490368 TGTCGTTAGT
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
41 12 0.23
42 18 0.35
43 20 0.38
44 2 0.04
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.46
Consensus pattern (42 bp):
TTGCTCTTTACCTTTTGCGGTGTTTTCCCATAAACGCCACTA
Found at i:490750 original size:44 final size:44
Alignment explanation
Indices: 490702--490788 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
490692 TGCAAATTGA
490702 AAAATTAAATAATAATAATAAATAATTTGTGTATACAAAATAAG
1 AAAATTAAATAATAATAATAAATAATTTGTGTATACAAAATAAG
490746 AAAATTAAATAATAATAATAAATAATTTGTGTATACAAAATAA
1 AAAATTAAATAATAATAATAAATAATTTGTGTATACAAAATAA
490789 TAATAAATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (44 bp):
AAAATTAAATAATAATAATAAATAATTTGTGTATACAAAATAAG
Found at i:490789 original size:28 final size:28
Alignment explanation
Indices: 490756--490827 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
490746 AAAATTAAAT
490756 AATAATAATAAATAATTTGTGTATACAA
1 AATAATAATAAATAATTTGTGTATACAA
490784 AATAATAATAAATAATTTGTGTATACAA
1 AATAATAATAAATAATTTGTGTATACAA
*
490812 AATAA-AAAAAATAATT
1 AATAATAATAAATAATT
490828 AAAATTAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
27 10 0.23
28 33 0.77
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (28 bp):
AATAATAATAAATAATTTGTGTATACAA
Found at i:490855 original size:72 final size:71
Alignment explanation
Indices: 490712--490844 Score: 186
Period size: 72 Copynumber: 1.9 Consensus size: 71
490702 AAAATTAAAT
* *
490712 AATAATAATAAATAATTTGTGTATACAAAATAAGAAAATTAAATAATAATAATAAATAATTTGTG
1 AATAATAATAAATAATTTGTGTATACAAAATAAGAAAA-TAAATAATAATAATAAATAATTTCTA
490777 TATACAA
65 TATACAA
*
490784 AATAATAATAAATAATTTGTGTATACAAAAT-A-AAAA-AAATAATTAA-AATTAA-AATTTCTA
1 AATAATAATAAATAATTTGTGTATACAAAATAAGAAAATAAATAA-TAATAATAAATAATTTCTA
490844 T
65 T
490845 CCAAAGTACA
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
67 7 0.12
68 11 0.19
69 3 0.05
70 4 0.07
71 1 0.02
72 31 0.54
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (71 bp):
AATAATAATAAATAATTTGTGTATACAAAATAAGAAAATAAATAATAATAATAAATAATTTCTAT
ATACAA
Found at i:491818 original size:40 final size:41
Alignment explanation
Indices: 491707--491881 Score: 162
Period size: 40 Copynumber: 4.3 Consensus size: 41
491697 CGCTAATGCT
* *
491707 CTTTACCTTTTGCGGTGTTTTTTCCATAAACGCCGCTAT-TA
1 CTTTACCTTTTGCGGTG-TTTTCCCATAAACGCCGCTATCTG
* * ***
491748 CTTTACCTCTTGCAGTGTTTATGGTA-AAACGCCGCT-TCTG
1 CTTTACCTTTTGCGGTGTTT-TCCCATAAACGCCGCTATCTG
*
491788 CTTTAACTTTTGCGGTGTTTTCCCATAAACGCCGCTATC-G
1 CTTTACCTTTTGCGGTGTTTTCCCATAAACGCCGCTATCTG
* ** *
491828 CTCTTTACCTTTTACGACGTTTTCCCATAAACGCCCCTAT-TG
1 --CTTTACCTTTTGCGGTGTTTTCCCATAAACGCCGCTATCTG
*
491870 CTTTACCGTTTG
1 CTTTACCTTTTG
491882 TGATATTTTC
Statistics
Matches: 108, Mismatches: 19, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
39 3 0.03
40 52 0.48
41 19 0.18
42 34 0.31
ACGTcount: A:0.17, C:0.27, G:0.15, T:0.40
Consensus pattern (41 bp):
CTTTACCTTTTGCGGTGTTTTCCCATAAACGCCGCTATCTG
Found at i:493799 original size:20 final size:20
Alignment explanation
Indices: 493774--493814 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
493764 ACACGATCTG
493774 GGCCTACACCCGTGTGTCCA
1 GGCCTACACCCGTGTGTCCA
* *
493794 GGCCTACGCCTGTGTGTCCA
1 GGCCTACACCCGTGTGTCCA
493814 G
1 G
493815 ATCGTATAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.37, G:0.29, T:0.22
Consensus pattern (20 bp):
GGCCTACACCCGTGTGTCCA
Found at i:496317 original size:30 final size:29
Alignment explanation
Indices: 496281--496536 Score: 162
Period size: 30 Copynumber: 8.6 Consensus size: 29
496271 TGGAGGATTT
*
496281 AGGGTTAAAATGTAATTTTTGAAGAATTTA
1 AGGGTTAAAATGTAATTTTTGAA-AGTTTA
* *
496311 AGGGTTAAGATGCAATTTTATGAAAGTTT-
1 AGGGTTAAAATGTAATTTT-TGAAAGTTTA
* * * *
496340 AGGATCAAAATGTGATTTTGGAAAGGTTTA
1 AGGGTTAAAATGTAATTTTTGAAA-GTTTA
* * *
496370 AGGGTTAAAATGTGATTTTGGGAAAGTTTG
1 AGGGTTAAAATGTAATTTT-TGAAAGTTTA
* * **
496400 GGGGTCAAAACATAATTTTTGGAAAGTTTA
1 AGGGTTAAAATGTAATTTTT-GAAAGTTTA
* *
496430 AGGGTTAAAATGCAATTTTGGAAAAGTTT-
1 AGGGTTAAAATGTAATTTTTG-AAAGTTTA
* * * *
496459 -GGTTATCAAAATATAATTTTGGAGAAGTTTG
1 AGGGT-T-AAAATGTAATTTTTGA-AAGTTTA
* * *
496490 AGGATCAAAATGTAATTTAT-AGAAG-TTA
1 AGGGTTAAAATGTAATTTTTGA-AAGTTTA
*
496518 AGGTGTTAAAATGCAATTT
1 AGG-GTTAAAATGTAATTT
496537 AGAAAAGGTC
Statistics
Matches: 177, Mismatches: 37, Indels: 25
0.74 0.15 0.10
Matches are distributed among these distances:
28 12 0.07
29 38 0.21
30 115 0.65
31 9 0.05
32 3 0.02
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (29 bp):
AGGGTTAAAATGTAATTTTTGAAAGTTTA
Found at i:496436 original size:60 final size:59
Alignment explanation
Indices: 496293--496507 Score: 200
Period size: 60 Copynumber: 3.6 Consensus size: 59
496283 GGTTAAAATG
* * * * * * **
496293 TAATTTTTGAAGAATTTAAGGGTTAAGATGCAATTTTATG-AAAGTTT-AGGATCAAAATG
1 TAATTTTGGAA-AGTTTAAGGGTTAAAATGTAATTTT-GGAAAAGTTTGGGGATCAAAACA
* * * *
496352 TGATTTTGGAAAGGTTTAAGGGTTAAAATGTGATTTTGGGAAAGTTTGGGGGTCAAAACA
1 TAATTTTGGAAA-GTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTGGGGATCAAAACA
* ** *
496412 TAATTTTTGGAAAGTTTAAGGGTTAAAATGCAATTTTGGAAAAGTTTGGTTATCAAAATA
1 TAA-TTTTGGAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTGGGGATCAAAACA
* * *
496472 TAATTTTGGAGAAGTTTGAGGATCAAAATGTAATTT
1 TAATTTTGGA-AAGTTTAAGGGTTAAAATGTAATTT
496508 ATAGAAGTTA
Statistics
Matches: 128, Mismatches: 23, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
58 2 0.02
59 43 0.34
60 74 0.58
61 9 0.07
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (59 bp):
TAATTTTGGAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTGGGGATCAAAACA
Found at i:498943 original size:49 final size:49
Alignment explanation
Indices: 498878--498977 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
498868 AATAGAGCCA
498878 TCCCATCATGCAATTGCAAGCCTCCAAAATCTAAAGAAGGTTGAAATTT
1 TCCCATCATGCAATTGCAAGCCTCCAAAATCTAAAGAAGGTTGAAATTT
*
498927 TCCCATCATGCAATTGCAAGCCTCCAAAGTCTAAAGAAGGTTGAAATTT
1 TCCCATCATGCAATTGCAAGCCTCCAAAATCTAAAGAAGGTTGAAATTT
498976 TC
1 TC
498978 AATTGCAATA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (49 bp):
TCCCATCATGCAATTGCAAGCCTCCAAAATCTAAAGAAGGTTGAAATTT
Found at i:499893 original size:7 final size:7
Alignment explanation
Indices: 499881--499920 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
499871 TTATAATATT
499881 AAAATTA
1 AAAATTA
499888 AAAATTA
1 AAAATTA
499895 AAAATTA
1 AAAATTA
499902 AAAATTA
1 AAAATTA
499909 AAAATTA
1 AAAATTA
499916 AAAAT
1 AAAAT
499921 AAACAACTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAAATTA
Found at i:504869 original size:129 final size:128
Alignment explanation
Indices: 504723--504967 Score: 339
Period size: 128 Copynumber: 1.9 Consensus size: 128
504713 CACAAACATT
* * *
504723 GCTATAGAACATGGTCTTTAACGGTA-TTTTCCCCACAAACGTCGCTATAGAACATGGTTTTTAA
1 GCTATAGAACATAGTCTTTAACGGCACTTTT-CCCACAAACGTCGCTATAGAACAT-GTCTTTAA
* * *
504787 CGGCGCTTTTCCCACAAACGTCACTATAGAGCTTAGTATTTAGCAGCGTTTTTACCACAAATGCC
64 CGGCGCTTTTCCCACAAACGCCACTATAGAACATAGTATTTAGCAGCGTTTTTACCACAAATGCC
* * * *
504852 GCTATATAACATAGTCTTTAGCGGCACTTTTTCCACAAACGTCGCTATAGAACATGTCTTTAGCG
1 GCTATAGAACATAGTCTTTAACGGCACTTTTCCCACAAACGTCGCTATAGAACATGTCTTTAACG
* * * *
504917 GCGTTTTTCCCACAAACGCCGCTATAGAACATGGTCTTTAGCAGCGTTTTT
66 GCGCTTTTCCCACAAACGCCACTATAGAACATAGTATTTAGCAGCGTTTTT
504968 CCCAAAAACG
Statistics
Matches: 101, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
128 52 0.51
129 45 0.45
130 4 0.04
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.32
Consensus pattern (128 bp):
GCTATAGAACATAGTCTTTAACGGCACTTTTCCCACAAACGTCGCTATAGAACATGTCTTTAACG
GCGCTTTTCCCACAAACGCCACTATAGAACATAGTATTTAGCAGCGTTTTTACCACAAATGCC
Found at i:504978 original size:43 final size:43
Alignment explanation
Indices: 504673--504979 Score: 330
Period size: 43 Copynumber: 7.2 Consensus size: 43
504663 TTATGTGAGA
* **
504673 AAACGCCGCTATAGAACATGATCTTTAGCGGCACTTTTCCCAC
1 AAACGCCGCTATAGAACATGGTCTTTAGCGGCGTTTTTCCCAC
*** * ** *
504716 AAACATTGCTATAGAACATGGTCTTTAACGGTATTTTCCCCAC
1 AAACGCCGCTATAGAACATGGTCTTTAGCGGCGTTTTTCCCAC
* * * *
504759 AAACGTCGCTATAGAACATGGTTTTTAACGGCGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGGTCTTTAGCGGCGTTTTTCCCAC
* * * * * * * *
504802 AAACGTCACTATAGAGCTTAGTATTTAGCAGCGTTTTTACCAC
1 AAACGCCGCTATAGAACATGGTCTTTAGCGGCGTTTTTCCCAC
* * * *
504845 AAATGCCGCTATATAACATAGTCTTTAGCGGCACTTTTT-CCAC
1 AAACGCCGCTATAGAACATGGTCTTTAGCGGC-GTTTTTCCCAC
*
504888 AAACGTCGCTATAGAACAT-GTCTTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCTATAGAACATGGTCTTTAGCGGCGTTTTTCCCAC
* *
504930 AAACGCCGCTATAGAACATGGTCTTTAGCAGCGTTTTTCCCAA
1 AAACGCCGCTATAGAACATGGTCTTTAGCGGCGTTTTTCCCAC
504973 AAACGCC
1 AAACGCC
504980 ACTAACATAA
Statistics
Matches: 221, Mismatches: 40, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
41 5 0.02
42 34 0.15
43 177 0.80
44 5 0.02
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (43 bp):
AAACGCCGCTATAGAACATGGTCTTTAGCGGCGTTTTTCCCAC
Found at i:504991 original size:129 final size:129
Alignment explanation
Indices: 504673--504979 Score: 375
Period size: 129 Copynumber: 2.4 Consensus size: 129
504663 TTATGTGAGA
* * ** *** * *
504673 AAACGCCGCTATAGAACATGATCTTTAGCGGCACTTTTCCCACAAACATTGCTATAGAACATGGT
1 AAACGCCGCTATAGAACATGGTCTTTAGCAGCGTTTTTCCCACAAACGCCGCTATATAACATAGT
* *
504738 CTTTAACGGTATTTTCCCCACAAACGTCGCTATAGAACATGGTTTTTAACGGCGCTTTTCCCAC
66 CTTTAACGGCATTTTCCCCACAAACGTCGCTATAGAACATGGTCTTTAACGGCGCTTTTCCCAC
* * * * * * * *
504802 AAACGTCACTATAGAGCTTAGTATTTAGCAGCGTTTTTACCACAAATGCCGCTATATAACATAGT
1 AAACGCCGCTATAGAACATGGTCTTTAGCAGCGTTTTTCCCACAAACGCCGCTATATAACATAGT
* * * *
504867 CTTTAGCGGCACTTTT-TCCACAAACGTCGCTATAGAACAT-GTCTTTAGCGGCGTTTTTCCCAC
66 CTTTAACGGCA-TTTTCCCCACAAACGTCGCTATAGAACATGGTCTTTAACGGCGCTTTTCCCAC
*
504930 AAACGCCGCTATAGAACATGGTCTTTAGCAGCGTTTTTCCCAAAAACGCC
1 AAACGCCGCTATAGAACATGGTCTTTAGCAGCGTTTTTCCCACAAACGCC
504980 ACTAACATAA
Statistics
Matches: 145, Mismatches: 32, Indels: 3
0.81 0.18 0.02
Matches are distributed among these distances:
128 61 0.42
129 80 0.55
130 4 0.03
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (129 bp):
AAACGCCGCTATAGAACATGGTCTTTAGCAGCGTTTTTCCCACAAACGCCGCTATATAACATAGT
CTTTAACGGCATTTTCCCCACAAACGTCGCTATAGAACATGGTCTTTAACGGCGCTTTTCCCAC
Found at i:512445 original size:39 final size:40
Alignment explanation
Indices: 512393--512491 Score: 119
Period size: 39 Copynumber: 2.5 Consensus size: 40
512383 TACTATAGCT
**
512393 CTTTACCTTTTGCGGCGTTTCTTAAAAAATGCCGCTATT-G
1 CTTTA-CTTTTGCGGCGTTTCACAAAAAATGCCGCTATTGG
* * *
512433 CTTTAGTTTTGCGACGTTTCACCAAAAATGCCGCTATTGG
1 CTTTACTTTTGCGGCGTTTCACAAAAAATGCCGCTATTGG
* *
512473 TTTTTCTTTTGCGGCGTTT
1 CTTTACTTTTGCGGCGTTT
512492 TCCCATAAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
39 28 0.57
40 21 0.43
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.42
Consensus pattern (40 bp):
CTTTACTTTTGCGGCGTTTCACAAAAAATGCCGCTATTGG
Found at i:516359 original size:17 final size:17
Alignment explanation
Indices: 516337--516372 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
516327 CCTTCTATTT
516337 CCATTTCAAGTCATAAA
1 CCATTTCAAGTCATAAA
*
516354 CCATTTCAAGTTATAAA
1 CCATTTCAAGTCATAAA
516371 CC
1 CC
516373 TAACAACTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.39, C:0.25, G:0.06, T:0.31
Consensus pattern (17 bp):
CCATTTCAAGTCATAAA
Found at i:518273 original size:23 final size:23
Alignment explanation
Indices: 518243--518291 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
518233 CTCGTCCAAC
518243 TGGACGAGCTTTCCCCAAAAATT
1 TGGACGAGCTTTCCCCAAAAATT
518266 TGGACGAGCTTTCCCCAAAAATT
1 TGGACGAGCTTTCCCCAAAAATT
518289 TGG
1 TGG
518292 TCATATATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (23 bp):
TGGACGAGCTTTCCCCAAAAATT
Found at i:520679 original size:27 final size:27
Alignment explanation
Indices: 520649--520714 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
520639 TTAATAATAG
520649 TAAAATTATATTTTAA-CCTTTAAAAAA
1 TAAAATT-TATTTTAATCCTTTAAAAAA
* * * *
520676 TAAAGTTTTAATTTAATTCTTTAAAAAT
1 TAAA-ATTTATTTTAATCCTTTAAAAAA
520704 TAAAATTTATT
1 TAAAATTTATT
520715 AAATTATTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
27 16 0.52
28 15 0.48
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (27 bp):
TAAAATTTATTTTAATCCTTTAAAAAA
Found at i:522478 original size:81 final size:81
Alignment explanation
Indices: 522340--522502 Score: 263
Period size: 81 Copynumber: 2.0 Consensus size: 81
522330 AAACCCCTAC
* *
522340 TATCGCATTAACTAGTGCTATGGATTCTCCTATTAGATTTGGCTCTAATCTAATAGACTAATATC
1 TATCGCATTAACTAGTGCTACGGATTCTCCTATTAGATTTGACTCTAATCTAATAGACTAATATC
*
522405 GTCCTATTTCTATGAT
66 GTCCTATTTCTAGGAT
** * *
522421 TATCGCATTAACTAGTGCTACGGATTCTCCTATTAGATTTGACTCTAATCTGGTAGACTTATGTC
1 TATCGCATTAACTAGTGCTACGGATTCTCCTATTAGATTTGACTCTAATCTAATAGACTAATATC
522486 GTCCTATTTCTAGGAT
66 GTCCTATTTCTAGGAT
522502 T
1 T
522503 GCATGTAACT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (81 bp):
TATCGCATTAACTAGTGCTACGGATTCTCCTATTAGATTTGACTCTAATCTAATAGACTAATATC
GTCCTATTTCTAGGAT
Found at i:525973 original size:17 final size:17
Alignment explanation
Indices: 525943--525976 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
525933 ATTTTAACCC
**
525943 TTTAAATTTTTAAAAAT
1 TTTAAATTAGTAAAAAT
525960 TTTAAATTAGTAAAAAT
1 TTTAAATTAGTAAAAAT
525977 AAAATTACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTAAATTAGTAAAAAT
Found at i:527100 original size:21 final size:22
Alignment explanation
Indices: 527076--527122 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
527066 AAAATAAATT
527076 TTAAAAATAAAATTTGA-ATAA
1 TTAAAAATAAAATTTGACATAA
* *
527097 TTAAAATTTAAATTTGATCATAA
1 TTAAAAATAAAATTTGA-CATAA
527120 TTA
1 TTA
527123 TATGTACTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
23 7 0.32
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (22 bp):
TTAAAAATAAAATTTGACATAA
Found at i:533378 original size:16 final size:15
Alignment explanation
Indices: 533359--533393 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
533349 ATTTTCACTT
533359 CTTCGTTTCCTATCTC
1 CTTCGTTTCC-ATCTC
*
533375 CTTCGTTTTCATCTC
1 CTTCGTTTCCATCTC
533390 CTTC
1 CTTC
533394 ACATCTCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.06, C:0.37, G:0.06, T:0.51
Consensus pattern (15 bp):
CTTCGTTTCCATCTC
Found at i:533390 original size:15 final size:15
Alignment explanation
Indices: 533350--533393 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
533340 CATCTTTTCA
*
533350 TTTTCA-CTTCTTCG
1 TTTTCATCTCCTTCG
*
533364 TTTCCTATCTCCTTCG
1 TTTTC-ATCTCCTTCG
533380 TTTTCATCTCCTTC
1 TTTTCATCTCCTTC
533394 ACATCTCTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.07, C:0.34, G:0.05, T:0.55
Consensus pattern (15 bp):
TTTTCATCTCCTTCG
Found at i:534219 original size:27 final size:26
Alignment explanation
Indices: 534187--534268 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 26
534177 TCTGTCCATC
*
534187 AAAATAAAACCATCGAAATGATTCAAA
1 AAAATAAAACCATC-AAATGATCCAAA
*
534214 AAAATAAAATCATCCATCAAAATGATCCAAC
1 AAAAT-AAA--A-CCATC-AAATGATCCAAA
*
534245 AAAATAAAACCATCAAATTATCCA
1 AAAATAAAACCATCAAATGATCCA
534269 TCATATGTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
26 9 0.19
27 10 0.21
28 4 0.09
30 4 0.09
31 20 0.43
ACGTcount: A:0.57, C:0.20, G:0.04, T:0.20
Consensus pattern (26 bp):
AAAATAAAACCATCAAATGATCCAAA
Found at i:534237 original size:31 final size:31
Alignment explanation
Indices: 534196--534258 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
534186 CAAAATAAAA
* * *
534196 CCATCGAAATGATTCAAAAAAATAAAATCAT
1 CCATCAAAATGATCCAAAAAAATAAAACCAT
*
534227 CCATCAAAATGATCCAACAAAATAAAACCAT
1 CCATCAAAATGATCCAAAAAAATAAAACCAT
534258 C
1 C
534259 AAATTATCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.54, C:0.22, G:0.05, T:0.19
Consensus pattern (31 bp):
CCATCAAAATGATCCAAAAAAATAAAACCAT
Found at i:537701 original size:38 final size:39
Alignment explanation
Indices: 537650--537733 Score: 111
Period size: 38 Copynumber: 2.2 Consensus size: 39
537640 ATAGTGATAA
*
537650 ACATAACTTACATACATAGAT-AGTAATAAAC-ATAACAT
1 ACATAACTTACATACATA-ATCAATAATAAACAATAACAT
*
537688 ACATAA-TATACATACATAATCAATAATAAACAATAATAT
1 ACATAACT-TACATACATAATCAATAATAAACAATAACAT
537727 ACATAAC
1 ACATAAC
537734 AGACATAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
37 3 0.08
38 25 0.62
39 12 0.30
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.26
Consensus pattern (39 bp):
ACATAACTTACATACATAATCAATAATAAACAATAACAT
Found at i:539160 original size:21 final size:22
Alignment explanation
Indices: 539136--539176 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
539126 TATTTTAAAC
*
539136 ATAATGATATATTT-TTATTAT
1 ATAATGACATATTTATTATTAT
*
539157 ATAATTACATATTTATTATT
1 ATAATGACATATTTATTATT
539177 TAATTGTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
ATAATGACATATTTATTATTAT
Found at i:540175 original size:43 final size:43
Alignment explanation
Indices: 540128--540212 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
540118 TTAATTAGGT
* *
540128 TTTAGG-ATTTTTAAGTTAGGGTTTAGGGT-TTTTAAAATTAAAA
1 TTTAGGTA-TTTTAAATAAGGGTTTAGGGTATTTT-AAATTAAAA
540171 TTTAGGTATTTTAAATAAGGGTTTAGGGTATTTTAAATTAAA
1 TTTAGGTATTTTAAATAAGGGTTTAGGGTATTTTAAATTAAA
540213 GGTTTTGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
43 33 0.87
44 5 0.13
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (43 bp):
TTTAGGTATTTTAAATAAGGGTTTAGGGTATTTTAAATTAAAA
Found at i:540200 original size:22 final size:22
Alignment explanation
Indices: 540120--540217 Score: 80
Period size: 21 Copynumber: 4.5 Consensus size: 22
540110 TTTTTGGTTT
* *
540120 AATT-AGGTTTTAGGATTTTTA
1 AATTAAGGGTTTAGGGTTTTTA
*
540141 AGTT-AGGGTTTAGGGTTTTTAA
1 AATTAAGGGTTTAGGGTTTTT-A
**
540163 AATTAA-AATTTA-GGTATTTTA
1 AATTAAGGGTTTAGGGT-TTTTA
540184 AA-TAAGGGTTTAGGGTATTTTA
1 AATTAAGGGTTTAGGGT-TTTTA
*
540206 AATTAAAGGTTT
1 AATTAAGGGTTT
540218 TGAAAAATTG
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
20 3 0.05
21 27 0.44
22 23 0.37
23 9 0.15
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (22 bp):
AATTAAGGGTTTAGGGTTTTTA
Found at i:543060 original size:20 final size:20
Alignment explanation
Indices: 543035--543081 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
543025 GATAGAACTC
*
543035 CCTTAAGGTTTCTACCTAAA
1 CCTTAAGGTTTCTACCCAAA
*
543055 CCTTAAGGTTTTTACCCAAA
1 CCTTAAGGTTTCTACCCAAA
543075 CCTTAAG
1 CCTTAAG
543082 TATAAACCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.34
Consensus pattern (20 bp):
CCTTAAGGTTTCTACCCAAA
Found at i:543726 original size:20 final size:20
Alignment explanation
Indices: 543684--543732 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
543674 TAAAGGTATA
* **
543684 GGTAGAACTGAAGTTATGTC
1 GGTAGAAGTGAAGTTATACC
*
543704 GGTAGAAGTGAAGTTCTACC
1 GGTAGAAGTGAAGTTATACC
543724 GGTAGAAGT
1 GGTAGAAGT
543733 CCTAGGCCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.10, G:0.33, T:0.27
Consensus pattern (20 bp):
GGTAGAAGTGAAGTTATACC
Found at i:545486 original size:27 final size:27
Alignment explanation
Indices: 545448--545503 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
545438 GTGAGAAGAC
*
545448 TTATCTTTGATTTCTTGACTCTACTCG
1 TTATCTTTGATTCCTTGACTCTACTCG
*
545475 TTATCTTTGATTCCTTGACTTTACTCG
1 TTATCTTTGATTCCTTGACTCTACTCG
545502 TT
1 TT
545504 CCTTTATGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.14, C:0.21, G:0.11, T:0.54
Consensus pattern (27 bp):
TTATCTTTGATTCCTTGACTCTACTCG
Found at i:550317 original size:22 final size:22
Alignment explanation
Indices: 550289--550360 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 22
550279 AAAATAAAAT
550289 AAAATAATTAAATATTATTAAA
1 AAAATAATTAAATATTATTAAA
* *
550311 AAAATAATTAAATTATAAAAATAAA
1 AAAATAATTAAA-TAT--TATTAAA
*
550336 ATAAATAA-TAAATAATATTAAA
1 A-AAATAATTAAATATTATTAAA
550358 AAA
1 AAA
550361 TTAAAATTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
21 2 0.05
22 18 0.44
23 3 0.07
24 2 0.05
25 10 0.24
26 6 0.15
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATAATTAAATATTATTAAA
Found at i:550339 original size:11 final size:12
Alignment explanation
Indices: 550281--550347 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 12
550271 ATAAAAATAA
550281 AATAAAATAAAAT
1 AATAAAAT-AAAT
* *
550294 AATTAAAT-ATT
1 AATAAAATAAAT
*
550305 ATTAAAA-AAAT
1 AATAAAATAAAT
550316 AATTAAATTATAAA-
1 AA-TAAA--ATAAAT
550330 AATAAAATAAAT
1 AATAAAATAAAT
550342 AATAAA
1 AATAAA
550348 TAATATTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
11 15 0.36
12 10 0.24
13 11 0.26
14 3 0.07
15 3 0.07
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AATAAAATAAAT
Found at i:550340 original size:18 final size:18
Alignment explanation
Indices: 550246--550352 Score: 92
Period size: 18 Copynumber: 5.8 Consensus size: 18
550236 TATTCACATA
*
550246 AAATTATAAAAATATTAATT
1 AAATTATAAAAATA--AAAT
550266 AAATTATAAAAATAAAAT
1 AAATTATAAAAATAAAAT
* *
550284 AAAATA-AAATAATTAAAT
1 AAATTATAAA-AATAAAAT
* * *
550302 ATTATTAAAAAAAT-AATT
1 A-AATTATAAAAATAAAAT
550320 AAATTATAAAAATAAAAT
1 AAATTATAAAAATAAAAT
*
550338 AAATAATAAATAATA
1 AAATTATAAA-AATA
550353 TTAAAAAATT
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
17 13 0.18
18 32 0.44
19 10 0.14
20 17 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATTATAAAAATAAAAT
Found at i:550365 original size:18 final size:17
Alignment explanation
Indices: 550252--550366 Score: 79
Period size: 18 Copynumber: 6.3 Consensus size: 17
550242 CATAAAATTA
*
550252 TAAAAATATTAATTAAAT
1 TAAAAA-ATTAAATAAAT
* *
550270 TATAAAAATAAAATAAAA
1 TA-AAAAATTAAATAAAT
*
550288 TAAAATAATTAAATATTAT
1 TAAAA-AATTAAATA-AAT
* *
550307 TAAAAAAATAATTAAAT
1 TAAAAAATTAAATAAAT
*
550324 TATAAAAATAAAATAAAT
1 TA-AAAAATTAAATAAAT
550342 AATAAATAATATTAAA-AAAT
1 --TAAA-AA-ATTAAATAAAT
550362 TAAAA
1 TAAAA
550367 TTAACTCTTA
Statistics
Matches: 76, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
17 8 0.11
18 43 0.57
19 12 0.16
20 8 0.11
21 5 0.07
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAAATTAAATAAAT
Found at i:550528 original size:22 final size:22
Alignment explanation
Indices: 550503--550590 Score: 158
Period size: 22 Copynumber: 4.0 Consensus size: 22
550493 TTTTGAGAGC
*
550503 TTTAGAGAGAAATTGTGTGAAA
1 TTTAGAGAGAAATTGAGTGAAA
550525 TTTAGAGAGAAATTGAGTGAAA
1 TTTAGAGAGAAATTGAGTGAAA
550547 TTTAGAGAGAAATTGAGTGAAA
1 TTTAGAGAGAAATTGAGTGAAA
*
550569 TTTAGAGAGAAATTGAGAGAAA
1 TTTAGAGAGAAATTGAGTGAAA
550591 ATTGAGTGAA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 64 1.00
ACGTcount: A:0.45, C:0.00, G:0.27, T:0.27
Consensus pattern (22 bp):
TTTAGAGAGAAATTGAGTGAAA
Found at i:550603 original size:12 final size:10
Alignment explanation
Indices: 550507--550601 Score: 82
Period size: 10 Copynumber: 8.8 Consensus size: 10
550497 GAGAGCTTTA
550507 GAGAGAAATT
1 GAGAGAAATT
* *
550517 GTGTGAAATTT
1 GAGAGAAA-TT
550528 AGAGAGAAATT
1 -GAGAGAAATT
*
550539 GAGTGAAATTT
1 GAGAGAAA-TT
550550 AGAGAGAAATT
1 -GAGAGAAATT
*
550561 GAGTGAAATTT
1 GAGAGAAA-TT
550572 AGAGAGAAATT
1 -GAGAGAAATT
550583 GAGAGAAAATT
1 GAGAG-AAATT
*
550594 GAGTGAAA
1 GAGAGAAA
550602 AAGTAAAGGG
Statistics
Matches: 69, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
10 28 0.41
11 21 0.30
12 20 0.29
ACGTcount: A:0.46, C:0.00, G:0.28, T:0.25
Consensus pattern (10 bp):
GAGAGAAATT
Found at i:551301 original size:13 final size:13
Alignment explanation
Indices: 551283--551307 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
551273 GTTTCAAGTT
551283 TTTTTAATTAATG
1 TTTTTAATTAATG
551296 TTTTTAATTAAT
1 TTTTTAATTAAT
551308 AAATATATTG
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:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:561472 original size:10 final size:11
Alignment explanation
Indices: 561452--561476 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
561442 AATATAAATA
561452 TTTTTCTTTTT
1 TTTTTCTTTTT
561463 TTTTTCTTTTT
1 TTTTTCTTTTT
561474 TTT
1 TTT
561477 ATGTGAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTCTTTTT
Done.