Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008724.1 Hibiscus syriacus cultivar Beakdansim tig00111783_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5289199
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 23
Found at i:527127 original size:21 final size:21
Alignment explanation
Indices: 527085--527123 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
527075 CATCAAGGTC
*
527085 TTTGTTGAGGCCATGAAATCT
1 TTTGTCGAGGCCATGAAATCT
527106 TTTGTCGAGGCCAT-AAAT
1 TTTGTCGAGGCCATGAAAT
527124 TCTTGCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (21 bp):
TTTGTCGAGGCCATGAAATCT
Found at i:528864 original size:26 final size:26
Alignment explanation
Indices: 528834--528883 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
528824 AATAACATAA
*
528834 TTTAATTTGATCCCTAAACATGTTTT
1 TTTAATTTGAACCCTAAACATGTTTT
528860 TTTAATTTGAACCCTAAACATGTT
1 TTTAATTTGAACCCTAAACATGTT
528884 GTTTGCATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (26 bp):
TTTAATTTGAACCCTAAACATGTTTT
Found at i:532241 original size:18 final size:20
Alignment explanation
Indices: 532218--532256 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
532208 AATCAGAATT
532218 AAAAGA-TCAAAA-TTTTAG
1 AAAAGATTCAAAACTTTTAG
*
532236 AAAAGATTTAAAACTTTTAG
1 AAAAGATTCAAAACTTTTAG
532256 A
1 A
532257 GTCGTCATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 5 0.28
20 7 0.39
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (20 bp):
AAAAGATTCAAAACTTTTAG
Found at i:538565 original size:16 final size:17
Alignment explanation
Indices: 538546--538578 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
538536 AACTTTTACC
538546 ATTT-CAACACTTTATT
1 ATTTCCAACACTTTATT
538562 ATTTCCAACACTTTATT
1 ATTTCCAACACTTTATT
538579 CAAATTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTTCCAACACTTTATT
Found at i:543107 original size:12 final size:12
Alignment explanation
Indices: 543092--543133 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
543082 TTGTGAAAAA
543092 TACCGTGAACAG
1 TACCGTGAACAG
543104 TACCGTGAACAG
1 TACCGTGAACAG
* *
543116 TACCCTGCTACAG
1 TACCGTG-AACAG
543129 TACCG
1 TACCG
543134 ATTACAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 18 0.69
13 8 0.31
ACGTcount: A:0.29, C:0.31, G:0.21, T:0.19
Consensus pattern (12 bp):
TACCGTGAACAG
Found at i:544140 original size:427 final size:424
Alignment explanation
Indices: 543348--544198 Score: 1639
Period size: 427 Copynumber: 2.0 Consensus size: 424
543338 TATATGATTT
543348 CTAAAGAGACAACATTTTACCGATTTTCAAATGTAGATTGTCTACAAATGTTTAGTGAAATCTCT
1 CTAAAGAGACAACATTTTACCGATTTTCAAATGTAGATTGTCTACAAATGTTTAGTGAAATCTCT
543413 GACTCATGTTCGGGGTCAGATACGGGAAAGGGGTTACATTTATTGGTGTAGAGCTTCAGGTTTAG
66 GACTCATGTTCGGGGTCAGATACGGGAAAGGGGTTACATTTATTGGTGTAGAGCTTCAGGTTTAG
543478 TCGATTCTAGGCATAAATTGAGTCTGTTTTGTGTCAAAAATAGTATACATGCCACAAGGATGTCA
131 TCGATTCTAGGCATAAATTGAGTCTGTTTTGTGTCAAAAATAGTATACATGCCACAAGGATGTCA
*
543543 TTATTACTAACATGATGTTTATATGATTTGATTTATGCAACTCCTTACTAATGAAAGTGAATAAG
196 TTATTACTAACATGATGTTTATATGATTTGATTGATGCAACTCCTTACTAATGAAAGTGAATAAG
543608 TGTAGTGTGTACATTTGATGTGTGTAATAGAGGGTTTAAAGCAAGTGACCAAATAAGATGTTCGA
261 TGTAGTGTGTACATTTGATGTGTGTAATAGAGGGTTTAAAGCAAGTGACCAAATAAGATGTTCGA
*
543673 GAATAAGTGAGTGGCAGTTGTAATGCAGTAATCATAATCCTCATATTATGATTAAAGTAATGTAC
326 GAATAAGTGAGTGGCAGTTGTAATGCAGTAATCATAATCCTCATATTATGATTAAAGTAATATAC
543738 CACCATGATGGGAAGTGCCAGTGTATGATTAAAG
391 CACCATGATGGGAAGTGCCAGTGTATGATTAAAG
543772 CTAAAGAGACAACATTTTACCGATTTTCAAATGTAGATTGTCTACAAATGTTTAGTGAAATCTCT
1 CTAAAGAGACAACATTTTACCGATTTTCAAATGTAGATTGTCTACAAATGTTTAGTGAAATCTCT
*
543837 GACTCATGTTTGGGGTCAGATACGGGAAAGGGGTGTTACATTTATTGGTGTTAGAGCTTCAGGTT
66 GACTCATGTTCGGGGTCAGATACGGGAAA-GGG-GTTACATTTATTGGTG-TAGAGCTTCAGGTT
543902 TAGTCGATTCTAGGCATAAATTGAGTCTGTTTTGTGTCAAAAATAGTATACATGCCACAAGGATG
128 TAGTCGATTCTAGGCATAAATTGAGTCTGTTTTGTGTCAAAAATAGTATACATGCCACAAGGATG
*
543967 TCATTATTACTAACATGATGTTTATATGATTTGGTTGATGCAACTCCTTACTAATGAAAGTGAAT
193 TCATTATTACTAACATGATGTTTATATGATTTGATTGATGCAACTCCTTACTAATGAAAGTGAAT
544032 AAGTGTAGTGTGTACATTTGATGTGTGTAATAGAGGGTTTAAAGCAAGTGACCAAATAAGATGTT
258 AAGTGTAGTGTGTACATTTGATGTGTGTAATAGAGGGTTTAAAGCAAGTGACCAAATAAGATGTT
544097 CGAGAATAAGTGAGTGGCAGTTGTAATGCAGTAATCATAATCCTCATATTATGATTAAAGTAATA
323 CGAGAATAAGTGAGTGGCAGTTGTAATGCAGTAATCATAATCCTCATATTATGATTAAAGTAATA
544162 TACCACCATGATGGGAAGTGCCAGTGTATGATTAAAG
388 TACCACCATGATGGGAAGTGCCAGTGTATGATTAAAG
544199 AAACCCTAGA
Statistics
Matches: 420, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
424 93 0.22
425 3 0.01
426 16 0.04
427 308 0.73
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.33
Consensus pattern (424 bp):
CTAAAGAGACAACATTTTACCGATTTTCAAATGTAGATTGTCTACAAATGTTTAGTGAAATCTCT
GACTCATGTTCGGGGTCAGATACGGGAAAGGGGTTACATTTATTGGTGTAGAGCTTCAGGTTTAG
TCGATTCTAGGCATAAATTGAGTCTGTTTTGTGTCAAAAATAGTATACATGCCACAAGGATGTCA
TTATTACTAACATGATGTTTATATGATTTGATTGATGCAACTCCTTACTAATGAAAGTGAATAAG
TGTAGTGTGTACATTTGATGTGTGTAATAGAGGGTTTAAAGCAAGTGACCAAATAAGATGTTCGA
GAATAAGTGAGTGGCAGTTGTAATGCAGTAATCATAATCCTCATATTATGATTAAAGTAATATAC
CACCATGATGGGAAGTGCCAGTGTATGATTAAAG
Found at i:558348 original size:31 final size:31
Alignment explanation
Indices: 558293--558351 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
558283 TTAGGTCCAT
*
558293 AAGGAATTACCAGTCAGTGCTGAACCTATAC
1 AAGGAATTACCAATCAGTGCTGAACCTATAC
*
558324 AAGGAATTACCAAT-AGTGAGTGAACCTA
1 AAGGAATTACCAATCAGTG-CTGAACCTA
558352 CAGAGTCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (31 bp):
AAGGAATTACCAATCAGTGCTGAACCTATAC
Found at i:577984 original size:23 final size:23
Alignment explanation
Indices: 577958--578009 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
577948 ATTTCATATT
577958 ATAAGTCAAGTTAGCATTATTGA
1 ATAAGTCAAGTTAGCATTATTGA
*
577981 ATAAGTCAGGTTAGCATTATTGA
1 ATAAGTCAAGTTAGCATTATTGA
578004 ATAAGT
1 ATAAGT
578010 AACTCCCACG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAAGTCAAGTTAGCATTATTGA
Found at i:581979 original size:16 final size:16
Alignment explanation
Indices: 581934--581986 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
581924 AAAAAAATTC
581934 AATAAATAATAAAATAGA
1 AATAAAT-ATAAAATA-A
*
581952 AA-AAA-CTAAAATAA
1 AATAAATATAAAATAA
*
581966 AATAAATATAAAATTA
1 AATAAATATAAAATAA
581982 AATAA
1 AATAA
581987 CCAAACTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 3 0.10
15 10 0.33
16 12 0.40
17 3 0.10
18 2 0.07
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (16 bp):
AATAAATATAAAATAA
Found at i:594516 original size:22 final size:21
Alignment explanation
Indices: 594474--594513 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
594464 GAGCTTATTT
*
594474 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
594495 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
594514 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:596524 original size:21 final size:20
Alignment explanation
Indices: 596477--596521 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
596467 AAACTTGCAT
596477 AGGGGTACCGGCACCCTATG
1 AGGGGTACCGGCACCCTATG
*
596497 AGGGGTACTGGCACCCTATG
1 AGGGGTACCGGCACCCTATG
596517 AGGGG
1 AGGGG
596522 GTATCGGTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (20 bp):
AGGGGTACCGGCACCCTATG
Found at i:600365 original size:15 final size:15
Alignment explanation
Indices: 600345--600385 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
600335 TAATAGTGAC
*
600345 AAAATTAGTTTTGAA
1 AAAATTAATTTTGAA
600360 AAAATTAATTTTGAA
1 AAAATTAATTTTGAA
600375 AAAATTAATTT
1 AAAATTAATTT
600386 CTTGTAGTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (15 bp):
AAAATTAATTTTGAA
Found at i:602412 original size:54 final size:54
Alignment explanation
Indices: 602343--602765 Score: 578
Period size: 54 Copynumber: 7.8 Consensus size: 54
602333 ACTTATTATG
* * *
602343 AACTTAAGAAGTTCATAATAAGTTTATGAATTTTCGCATTAGCACTGTGTGTGC
1 AACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTGTGTGTGC
* * ** *
602397 AACTTAAGAAGTTCATAATAAGTTTATGAATTTTTGTAACGACACTGTGTGTGC
1 AACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTGTGTGTGC
602451 AACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTGTGTGTGC
1 AACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTGTGTGTGC
* * * *
602505 AACTTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACTGTATGTGA
1 AACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTGTGTGTGC
* * * * *
602559 AACTTAATAAATTCATAATAAGTTTATGAATTTTAGTAATT-GCACCGTTTGTGA
1 AACTTAAGAAATTCATAATAAGTTTATGAATTTTCGT-ATTGGCACTGTGTGTGC
* *
602613 AACTTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACTGTGTGTGC
1 AACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTGTGTGTGC
* * * *
602667 AACTTAAGGAATTCATAATAAGTTTATGAATTTTTGTATTGGCATTGTGTGTAC
1 AACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTGTGTGTGC
* * * **
602721 AAATTAAGAAATTCAAAATAAGTTTTTGAATTACCGTATTGGCAC
1 AACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCAC
602766 CACGTGTGCA
Statistics
Matches: 325, Mismatches: 42, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
53 3 0.01
54 319 0.98
55 3 0.01
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.38
Consensus pattern (54 bp):
AACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTGTGTGTGC
Found at i:610474 original size:23 final size:22
Alignment explanation
Indices: 610419--610503 Score: 93
Period size: 22 Copynumber: 3.8 Consensus size: 22
610409 CCAGAACCCC
* *
610419 AGGGGGTATCGATTCCCTT-AC
1 AGGGGGAATCGATTCCCTTCAA
610440 AGGAGGGAATCGATTCCTCTTCAA
1 AGG-GGGAATCGATTCC-CTTCAA
*
610464 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGATT-CCCTTCAA
*
610486 AGGGGGTATCGATTCCCT
1 AGGGGGAATCGATTCCCT
610504 CTGCACTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
21 7 0.13
22 25 0.45
23 17 0.31
24 6 0.11
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCTTCAA
Found at i:613509 original size:60 final size:60
Alignment explanation
Indices: 613435--613550 Score: 205
Period size: 60 Copynumber: 1.9 Consensus size: 60
613425 CAACTAGGCA
*
613435 TAAATTAGTCATATCTATGAAATCTAAATGCACCATGTAAATGTTTCCTATTCTATGAAG
1 TAAATTAGTCATATCTATGAAATCTAAATGCACCATGTAAATGTTTCATATTCTATGAAG
* *
613495 TAAATTGGTCATATCTATGGAATCTAAATGCACCATGTAAATGTTTCATATTCTAT
1 TAAATTAGTCATATCTATGAAATCTAAATGCACCATGTAAATGTTTCATATTCTAT
613551 TACCAACAAG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (60 bp):
TAAATTAGTCATATCTATGAAATCTAAATGCACCATGTAAATGTTTCATATTCTATGAAG
Found at i:618024 original size:54 final size:54
Alignment explanation
Indices: 617965--618505 Score: 745
Period size: 54 Copynumber: 10.1 Consensus size: 54
617955 TTACCGAATG
* * *
617965 GGCACTATGTGTGTAACTTAA-AAAGTTCATAATAAGTTTATAAATTTTCGTATT
1 GGCACTGTGTGTGCAACTTAAGAAA-TTCATAATAAGTTTATGAATTTTCGTATT
*
618019 GGCACTGTGTGTGCAACTTAAGAAGTTCATAATAAGTTTATGAATTTTCGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * *
618073 GGCAGTGTGTGTGCAACTTAATAAATTCATAATAAGTTTATAAATTTTCGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* *
618127 GGCA-T-TGTGTGCAACTT-AGAAATTAATAATATA-TTTATGAA-TTTCTATATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATA-AGTTTATGAATTTTC-GTATT
* * * *
618178 GGCACTGTGTGTTCTACTTAAGAAGTTCATAATAAATTTATGAATTTTCGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * *
618232 GGCATTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTACGTGTT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * *
618286 GGCACTATGTGTGCAACTTAAGAAATTCATCATAAGTTTATGAATTTACGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* *
618340 GGCACTGTGTGTTCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * * * *
618394 GGGAATGTGTTTGTAACTTAAGAAATTCATAAT-AGTTTATGAATTTCCGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* **
618447 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTGTGAATTACCGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
618501 GGCAC
1 GGCAC
618506 CACGTGTGCA
Statistics
Matches: 435, Mismatches: 43, Indels: 18
0.88 0.09 0.04
Matches are distributed among these distances:
50 4 0.01
51 27 0.06
52 14 0.03
53 61 0.14
54 323 0.74
55 6 0.01
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (54 bp):
GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
Found at i:625248 original size:19 final size:19
Alignment explanation
Indices: 625224--625261 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
625214 AGATGTTTCA
625224 ATGTGTTGAAAAGTTAACT
1 ATGTGTTGAAAAGTTAACT
625243 ATGTGTTGAAAAGTTAACT
1 ATGTGTTGAAAAGTTAACT
625262 GAAAGACGAT
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:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (19 bp):
ATGTGTTGAAAAGTTAACT
Found at i:625506 original size:22 final size:22
Alignment explanation
Indices: 625464--625507 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
625454 GTAGTAGTAT
* *
625464 TACCATATAGTACCTACAATCA
1 TACCATATAGTACATAAAATCA
625486 TACCATATA-TATCATAAAATCA
1 TACCATATAGTA-CATAAAATCA
625508 ATTCATTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.45, C:0.23, G:0.02, T:0.30
Consensus pattern (22 bp):
TACCATATAGTACATAAAATCA
Found at i:625858 original size:31 final size:30
Alignment explanation
Indices: 625823--625887 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
625813 AACCAGTAAA
*
625823 GAACCGGCTAAAAACTGGCAAAAACCGGGGT
1 GAACCGGCTAAAAACCGGC-AAAACCGGGGT
* *
625854 GAACCGGCTGAAAACCGGCAAAACCGGTGT
1 GAACCGGCTAAAAACCGGCAAAACCGGGGT
625884 GAAC
1 GAAC
625888 TGTCGATTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 14 0.45
31 17 0.55
ACGTcount: A:0.37, C:0.25, G:0.29, T:0.09
Consensus pattern (30 bp):
GAACCGGCTAAAAACCGGCAAAACCGGGGT
Found at i:629098 original size:57 final size:58
Alignment explanation
Indices: 629022--629165 Score: 191
Period size: 59 Copynumber: 2.5 Consensus size: 58
629012 CTAAGATAGC
* ** *
629022 ACCTTGGGTCCATAAGGACTTACCCTAGT-CAAAGTGTAGGAGCCACTTGAGGGGTGT
1 ACCTTGGGTCCATAAGGACTTACCCTAGTACAAAATAAAGGAGCCACTTGAGAGGTGT
629079 ACCTTGGGTCCATAAGGACTTACCCTAAGTACAAAATAAAGGAGCCACTTGAGAGGTGT
1 ACCTTGGGTCCATAAGGACTTACCCT-AGTACAAAATAAAGGAGCCACTTGAGAGGTGT
* ** * *
629138 GCCTCAGGTTCATAAGGACTTACGCTAG
1 ACCTTGGGTCCATAAGGACTTACCCTAG
629166 GCACAAAGCA
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
57 26 0.34
58 5 0.07
59 45 0.59
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (58 bp):
ACCTTGGGTCCATAAGGACTTACCCTAGTACAAAATAAAGGAGCCACTTGAGAGGTGT
Found at i:629183 original size:59 final size:59
Alignment explanation
Indices: 629028--629224 Score: 157
Period size: 59 Copynumber: 3.4 Consensus size: 59
629018 TAGCACCTTG
* **** * **
629028 GGTCCATAAGGACTTACCCT-AG-TCAAAGTGTAGGAGCCACTTGAGGGGTGTACCTTG
1 GGTCCATAAGGACTTACCCTAAGCACAAAACAAAGGAGCCACTTGAGAGGTGTACCTCA
* * *
629085 GGTCCATAAGGACTTACCCTAAGTACAAAATAAAGGAGCCACTTGAGAGGTGTGCCTCA
1 GGTCCATAAGGACTTACCCTAAGCACAAAACAAAGGAGCCACTTGAGAGGTGTACCTCA
* * * * * * * * * *
629144 GGTTCATAAGGACTTACGCTAGGCACAAAGCAAATGAGCCATCCT-AAAGGAGTGCCTTA
1 GGTCCATAAGGACTTACCCTAAGCACAAAACAAAGGAGCCA-CTTGAGAGGTGTACCTCA
*
629203 GGATCCATAAGGTCTTACCCTA
1 GG-TCCATAAGGACTTACCCTA
629225 TGACCATTGG
Statistics
Matches: 114, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
57 20 0.18
58 2 0.02
59 74 0.65
60 18 0.16
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.22
Consensus pattern (59 bp):
GGTCCATAAGGACTTACCCTAAGCACAAAACAAAGGAGCCACTTGAGAGGTGTACCTCA
Found at i:631049 original size:20 final size:20
Alignment explanation
Indices: 631003--631049 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
630993 ACATTGCTGG
* *
631003 AATTTAATGTTAGAGAGTTA
1 AATTTGATGTTAGAGAGTGA
*
631023 AAATTGATGTTAGA-ATGTGA
1 AATTTGATGTTAGAGA-GTGA
631043 AATTTGA
1 AATTTGA
631050 CCACTTGGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.38
Consensus pattern (20 bp):
AATTTGATGTTAGAGAGTGA
Found at i:638790 original size:13 final size:13
Alignment explanation
Indices: 638772--638820 Score: 89
Period size: 13 Copynumber: 3.7 Consensus size: 13
638762 TTAAAAAATG
638772 AATGAAAATGAAA
1 AATGAAAATGAAA
638785 AATGAAAATGAAA
1 AATGAAAATGAAA
638798 AATGAAAAATGAAA
1 AATG-AAAATGAAA
638812 AATGAAAAT
1 AATGAAAAT
638821 TAAGGGCTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
13 22 0.63
14 13 0.37
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.16
Consensus pattern (13 bp):
AATGAAAATGAAA
Found at i:638820 original size:6 final size:7
Alignment explanation
Indices: 638772--638819 Score: 82
Period size: 7 Copynumber: 7.1 Consensus size: 7
638762 TTAAAAAATG
638772 AATG-AA
1 AATGAAA
638778 AATGAAA
1 AATGAAA
638785 AATG-AA
1 AATGAAA
638791 AATGAAA
1 AATGAAA
638798 AATGAAA
1 AATGAAA
638805 AATGAAA
1 AATGAAA
638812 AATGAAA
1 AATGAAA
638819 A
1 A
638820 TTAAGGGCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 10 0.25
7 30 0.75
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
AATGAAA
Found at i:644650 original size:32 final size:32
Alignment explanation
Indices: 644605--644679 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
644595 AACTAAATAA
* * *
644605 ATTTGTTACAATTTATTATTATGAAAAA-TATT
1 ATTT-TTATAATTTATTATTATAAAAAATTAAT
* *
644637 ATTTTTCATAATTTTTTATTTTAAAAAATTAAT
1 ATTTTT-ATAATTTATTATTATAAAAAATTAAT
644670 ATTTTTATAA
1 ATTTTTATAA
644680 ATATAAATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 2 0.06
32 25 0.69
33 9 0.25
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (32 bp):
ATTTTTATAATTTATTATTATAAAAAATTAAT
Found at i:648429 original size:43 final size:45
Alignment explanation
Indices: 648382--648492 Score: 127
Period size: 47 Copynumber: 2.5 Consensus size: 45
648372 GTAAGTATGC
648382 AAATAAGCTTATGAGCTTATGAA-T-AATGGCAAGTATATTGATA
1 AAATAAGCTTATGAGCTTATGAATTAAATGGCAAGTATATTGATA
* * * *
648425 AAATAAACTTATGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTATGAGCTTAT-GAA-TTAAATGGCAAGTATATTGATA
* * *
648472 AAATAAGTTTACGAGATTATG
1 AAATAAGCTTATGAGCTTATG
648493 GGATAAATGG
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
43 19 0.34
44 3 0.05
46 2 0.04
47 32 0.57
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.35
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGAATTAAATGGCAAGTATATTGATA
Found at i:655243 original size:22 final size:22
Alignment explanation
Indices: 655201--655243 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
655191 TCTTCATATC
**
655201 ATGAATTTCTTAAAGTTTGAGG
1 ATGAATTTCTTAAAGGGTGAGG
655223 ATGAATTTTCTT-AAGGGTGAG
1 ATGAA-TTTCTTAAAGGGTGAG
655244 AATTGTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.30, C:0.05, G:0.26, T:0.40
Consensus pattern (22 bp):
ATGAATTTCTTAAAGGGTGAGG
Found at i:656322 original size:18 final size:18
Alignment explanation
Indices: 656299--656339 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
656289 TGTATGGTAA
*
656299 GTGTAATAATGGATGCTT
1 GTGTAATAATGGATGCAT
656317 GTGTAATAATGGATGCAT
1 GTGTAATAATGGATGCAT
656335 GTGTA
1 GTGTA
656340 GATCGTAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.37
Consensus pattern (18 bp):
GTGTAATAATGGATGCAT
Found at i:656841 original size:111 final size:112
Alignment explanation
Indices: 656716--656942 Score: 314
Period size: 112 Copynumber: 2.0 Consensus size: 112
656706 GTACATTTTT
* * * * * *
656716 GACATACTTTGTGTATGATAG-TATCGATCGATTTTGT-TTAATGCATAACAGTACATTTTTGGC
1 GACATACTTCGTGTATGAAAGTTATCGATCAATTTT-TCTTAATGCACAACACTACATTTTCGGC
* * *
656779 ATTAAAGGTGCCACCCATGGTATTCAAAATGAGATGAATTACCATTTC
65 ATAAAAAGTGCCACCCATGGTATTCAAAATAAGATGAATTACCATTTC
* *
656827 GACATACTTCGTGTATGAAAGTTATCGATCAATTTTTCTTAATGCACAATACTGCATTTTCGGCA
1 GACATACTTCGTGTATGAAAGTTATCGATCAATTTTTCTTAATGCACAACACTACATTTTCGGCA
* *
656892 TAAAAAGTGCCACCCATGGTATTCATAATAAGGTGAATTACCATTTC
66 TAAAAAGTGCCACCCATGGTATTCAAAATAAGATGAATTACCATTTC
656939 GACA
1 GACA
656943 CTTCGGTGCA
Statistics
Matches: 101, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
111 20 0.20
112 81 0.80
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (112 bp):
GACATACTTCGTGTATGAAAGTTATCGATCAATTTTTCTTAATGCACAACACTACATTTTCGGCA
TAAAAAGTGCCACCCATGGTATTCAAAATAAGATGAATTACCATTTC
Found at i:658688 original size:3 final size:3
Alignment explanation
Indices: 658680--658735 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
658670 AAATCAAAGG
658680 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
658728 AAT AAT AA
1 AAT AAT AA
658736 AATCTAAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:661777 original size:30 final size:30
Alignment explanation
Indices: 661667--661844 Score: 85
Period size: 30 Copynumber: 5.9 Consensus size: 30
661657 AAAGTGTCTA
* * **
661667 TTTTTGCCATTTTAGCCTTTTAAATTTCAG
1 TTTTTGCTATTTTAGTCTTTTAAATTTTTG
* ** * * * *
661697 TTTGTAATA-TTTGGTCTTTAAAATTTCTA
1 TTTTTGCTATTTTAGTCTTTTAAATTTTTG
** *
661726 TTTTTATTATTCTAG-CTTTTTAAATTTTTG
1 TTTTTGCTATTTTAGTC-TTTTAAATTTTTG
* ***
661756 TTTGTGCTATTTTAGTCTTTT-AATTGTCCA
1 TTTTTGCTATTTTAGTCTTTTAAATT-TTTG
* *
661786 TTTTTGCTATTTTAATAC-TTTAAGTTTTTG
1 TTTTTGCTATTTTAGT-CTTTTAAATTTTTG
* *
661816 TTTTTCTCTATTTTGGTCTTTATAAATTT
1 TTTTT-GCTATTTTAGTCTTT-TAAATTT
661845 AAATACATAT
Statistics
Matches: 106, Mismatches: 33, Indels: 16
0.68 0.21 0.10
Matches are distributed among these distances:
29 27 0.25
30 58 0.55
31 15 0.14
32 6 0.06
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (30 bp):
TTTTTGCTATTTTAGTCTTTTAAATTTTTG
Found at i:662164 original size:16 final size:17
Alignment explanation
Indices: 662127--662164 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
662117 ACAGACCAGT
662127 TTTTTGTCTTAAAAATG
1 TTTTTGTCTTAAAAATG
* *
662144 ATTTT-TCTTAAAATTG
1 TTTTTGTCTTAAAAATG
662160 TTTTT
1 TTTTT
662165 AAAAGGCGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.61
Consensus pattern (17 bp):
TTTTTGTCTTAAAAATG
Found at i:665800 original size:11 final size:11
Alignment explanation
Indices: 665783--665832 Score: 68
Period size: 11 Copynumber: 4.5 Consensus size: 11
665773 TCAGAGAAGA
665783 AAAAAGAAAA-
1 AAAAAGAAAAG
665793 AGAAAAGAAAAAG
1 A-AAAAG-AAAAG
665806 AAAAAGAAAAG
1 AAAAAGAAAAG
665817 AAAAAG-AAAG
1 AAAAAGAAAAG
665827 AAAAAG
1 AAAAAG
665833 GAACGAGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
10 11 0.30
11 16 0.43
12 9 0.24
13 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:665805 original size:17 final size:17
Alignment explanation
Indices: 665783--665825 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
665773 TCAGAGAAGA
665783 AAAAAGAAAAAGAAAAG
1 AAAAAGAAAAAGAAAAG
665800 AAAAAGAAAAAGAAAAG
1 AAAAAGAAAAAGAAAAG
665817 AAAAAGAAA
1 AAAAAGAAA
665826 GAAAAAGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAGAAAAG
Found at i:665832 original size:6 final size:6
Alignment explanation
Indices: 665783--665825 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
665773 TCAGAGAAGA
665783 AAAAAG AAAAAG -AAAAG AAAAAG AAAAAG -AAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
665826 GAAAAAGGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 10 0.29
6 25 0.71
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:667248 original size:36 final size:35
Alignment explanation
Indices: 667201--667308 Score: 108
Period size: 36 Copynumber: 2.9 Consensus size: 35
667191 AATACAGAGG
667201 ATTTATCTCACTTGAGATTGTTTTTCTTAAAATAGA
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAAA-AGA
* * *
667237 ATTTGTCTCACTTGAGATAGTTTTTACTCGAAACAAGAA
1 ATTTATCTCACTTGAGATTGTTTTT-CT-TAAA-AAG-A
* **
667276 GATTTATTTCACTCAAGATTGTTTTTCTTAAAA
1 -ATTTATCTCACTTGAGATTGTTTTTCTTAAAA
667309 CAAAATTAGT
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
36 23 0.40
37 3 0.05
38 8 0.14
39 4 0.07
40 20 0.34
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (35 bp):
ATTTATCTCACTTGAGATTGTTTTTCTTAAAAAGA
Found at i:667288 original size:76 final size:76
Alignment explanation
Indices: 667200--667377 Score: 207
Period size: 76 Copynumber: 2.3 Consensus size: 76
667190 TAATACAGAG
** * * *
667200 GATTTATCTCACTTGAGATTGTTTTTCTTAAAATAGAATTTGTCTCACTTGAGATAG-TTTTTAC
1 GATTTATCTCACTCAAGATTGTTTTTCTTAAAACAAAATTAGTCTCACTTGAGA-AGATTTTTAC
667264 TCGAAACAAGAA
65 TCGAAACAAGAA
* * *
667276 GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAAATTAGTGTCACTTGAGACGATTTTTACT
1 GATTTATCTCACTCAAGATTGTTTTTCTTAAAACAAAATTAGTCTCACTTGAGAAGATTTTTACT
*
667341 CGAAAGAAG-A
66 CGAAACAAGAA
* * * *
667351 CATTTCATTTTACTCAAGATTATTTTT
1 GATTT-ATCTCACTCAAGATTGTTTTT
667378 AAAGAATATT
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
75 6 0.07
76 82 0.93
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (76 bp):
GATTTATCTCACTCAAGATTGTTTTTCTTAAAACAAAATTAGTCTCACTTGAGAAGATTTTTACT
CGAAACAAGAA
Found at i:667467 original size:39 final size:39
Alignment explanation
Indices: 667380--668050 Score: 930
Period size: 39 Copynumber: 17.2 Consensus size: 39
667370 TTATTTTTAA
* * * * *
667380 AGAATATTTTCTCTCTCTTAAGATAGTTTCCC-TAAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
* * * * *
667418 ATAATATTTTATCTCACTTGAGATAGTTTCCTTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
* *
667457 AGAAGATTTTATCTCGCTTGAGGTAGTTTCCCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
* * *
667496 AGATGATTTTGTCTCGCTTGAGATAGTTTCCATTAAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
* * * *
667535 ATAAGATTTTATATCGCTTGAGATAGTTTCCCTTGAAAT
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
* * * *
667574 AAAAGATTTTATCTCACTTGAGAGAGTTTCCCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
*
667613 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAT
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
* *
667652 AGAAGATTTTATCTCGCTTGAGATAATTTCCCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
* * *
667691 ATAAGATTTTATCTCGCTTGAGATAGTTTTCCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
* *
667730 AGAAGATTTTGTCTCTCTTAAGATAGTTTCCCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
* * *
667769 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTTAAAT
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
*
667808 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
* *
667847 AAAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
*
667886 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
**
667925 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCAAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
*
667964 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
* **
668003 AGAAGATTTTGTCTCGCTTGAGATAGTTTCTCTCAAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
*
668042 AAAAGATTT
1 AGAAGATTT
668051 AAGAAACTAA
Statistics
Matches: 572, Mismatches: 60, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
38 27 0.05
39 545 0.95
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.37
Consensus pattern (39 bp):
AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
Found at i:669929 original size:16 final size:17
Alignment explanation
Indices: 669891--669929 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
669881 ACACATACCG
669891 GTTTTTGTCTTAAAAAT
1 GTTTTTGTCTTAAAAAT
* *
669908 GATTTT-TCTTAAAATT
1 GTTTTTGTCTTAAAAAT
669924 GTTTTT
1 GTTTTT
669930 AAAAGACGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.59
Consensus pattern (17 bp):
GTTTTTGTCTTAAAAAT
Found at i:671232 original size:181 final size:178
Alignment explanation
Indices: 670777--671232 Score: 460
Period size: 181 Copynumber: 2.5 Consensus size: 178
670767 TAGTTCTGAC
* *
670777 AATACATTTTATCACTATAATTAAAATTTATAACTACAAATATAATTTGTCACAAAAAAAT-TGA
1 AATACATTTTGTCACTATAATTAAAATATATAACTACAAATATAATTTGTCAC--AAAAATCTGA
* * * * * * *
670841 ATATCATCATTTGTTGTGATAATATTTTTTGTAAGAATTATTAATAATTATAGTTACAAAACTTT
64 ATCTCATTATTTGTTGTGACAAT-TTTTTTGTAACAATTATTAATAATTACAGTAACAAAACTGT
* * **
670906 TCACTATATGACTTTTTTGGCACTAAAAATATGGAAGGAAATATTTATGAT
128 TCACTATATGACTTTTTTAGCACCAAAAATATGGAAAAAAATATTTATGAT
* * * * * * *
670957 AATATATTTAGTCATTATAATTAAAATCTATAACTACAAACATTATTTTTCACTAAAAA-CTTGA
1 AATACATTTTGTCACTATAATTAAAATATATAACTACAAATATAATTTGTCAC-AAAAATC-TGA
* *
671021 ATCTCATTATTT-TTAGTGACAACTTTTTTGTAACAATTATT-ATAGCTTACAGTAACAAAACAT
64 ATCTCATTATTTGTT-GTGACAATTTTTTTGTAACAATTATTAATA-ATTACAGTAACAAAAC-T
* *
671084 GTT-ACTATATGACTTTGTTTTTAG-ACCCAAAAT-TGGAAAAAAATCATTTGTGACT
126 GTTCACTATATGAC--T-TTTTTAGCACCAAAAATATGGAAAAAAAT-ATTTATGA-T
* * * * *
671139 -ATGCATTTTGTCACTATAATTAAAATATATAAATACAAATAAAATTTGTCACAACATATCTAAA
1 AATACATTTTGTCACTATAATTAAAATATATAACTACAAATATAATTTGTCACAA-AAATCTGAA
*
671203 TCTTATTATTTGTTGTGACAATTTTTTTGT
65 TCTCATTATTTGTTGTGACAATTTTTTTGT
671233 CATATTAACT
Statistics
Matches: 225, Mismatches: 38, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
178 3 0.01
179 47 0.21
180 78 0.35
181 87 0.39
182 10 0.04
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (178 bp):
AATACATTTTGTCACTATAATTAAAATATATAACTACAAATATAATTTGTCACAAAAATCTGAAT
CTCATTATTTGTTGTGACAATTTTTTTGTAACAATTATTAATAATTACAGTAACAAAACTGTTCA
CTATATGACTTTTTTAGCACCAAAAATATGGAAAAAAATATTTATGAT
Found at i:675502 original size:36 final size:36
Alignment explanation
Indices: 675436--675793 Score: 436
Period size: 36 Copynumber: 9.9 Consensus size: 36
675426 AAAACCAATT
*
675436 TTTTATCTCACTTGAGATT-TTTTTCTTAAAACATA
1 TTTTATCTCACTTGAGATTGTTTTTCTTAAAACAGA
*
675471 TTTTATCTCACTTGAGATTGTTTTTCTTAAAATAGA
1 TTTTATCTCACTTGAGATTGTTTTTCTTAAAACAGA
* * *
675507 TTTCATCTCACTTGAGATGGTTTTTCTTAAAATAGA
1 TTTTATCTCACTTGAGATTGTTTTTCTTAAAACAGA
* *
675543 --TTATCTCACTTGTGATTGTTTTTCTTAAACCAGA
1 TTTTATCTCACTTGAGATTGTTTTTCTTAAAACAGA
* *
675577 TTTTATCTCACCTGAGATTGTTTTTCTT-AACCAGA
1 TTTTATCTCACTTGAGATTGTTTTTCTTAAAACAGA
* *
675612 TTTTATCACACTTAAGATTGTTTTTCTTAAAACAGA
1 TTTTATCTCACTTGAGATTGTTTTTCTTAAAACAGA
* * *
675648 TTTTATCTCACTTGAGATTATTTTTTCTAAAAACAAA
1 TTTTATCTCACTTGAGATT-GTTTTTCTTAAAACAGA
* * *
675685 TTTTGTCTCACTTGAGATTGTTTCTTCCTCAAAACAAA
1 TTTTATCTCACTTGAGATTGTTT-TT-CTTAAAACAGA
* *
675723 TTTTTATCTCAATTGAGATTGTTTTTCTTCAAAACAAA
1 -TTTTATCTCACTTGAGATTGTTTTTCTT-AAAACAGA
* ** *
675761 TTTTGTCTCACTTGAGACAGTTTTCCTTAAAAC
1 TTTTATCTCACTTGAGATTGTTTTTCTTAAAAC
675794 TCAAACTTCA
Statistics
Matches: 283, Mismatches: 31, Indels: 17
0.85 0.09 0.05
Matches are distributed among these distances:
34 29 0.10
35 51 0.18
36 103 0.36
37 59 0.21
38 20 0.07
39 21 0.07
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (36 bp):
TTTTATCTCACTTGAGATTGTTTTTCTTAAAACAGA
Found at i:675648 original size:71 final size:72
Alignment explanation
Indices: 675436--675793 Score: 436
Period size: 71 Copynumber: 5.0 Consensus size: 72
675426 AAAACCAATT
*
675436 TTTTATCTCACTTGAGATT-TTTTTCTTAAAACATATTTTATCTCACTTGAGATTGTTTTTCTTA
1 TTTTATCTCACTTGAGATTGTTTTTCTTAAAACAGATTTTATCTCACTTGAGATTGTTTTTCTTA
*
675500 AAATAGA
66 AAACAGA
* * * *
675507 TTTCATCTCACTTGAGATGGTTTTTCTTAAAATAGA--TTATCTCACTTGTGATTGTTTTTCTTA
1 TTTTATCTCACTTGAGATTGTTTTTCTTAAAACAGATTTTATCTCACTTGAGATTGTTTTTCTTA
*
675570 AACCAGA
66 AAACAGA
* * * *
675577 TTTTATCTCACCTGAGATTGTTTTTCTT-AACCAGATTTTATCACACTTAAGATTGTTTTTCTTA
1 TTTTATCTCACTTGAGATTGTTTTTCTTAAAACAGATTTTATCTCACTTGAGATTGTTTTTCTTA
675641 AAACAGA
66 AAACAGA
* * * *
675648 TTTTATCTCACTTGAGATTATTTTTTCTAAAAACAAATTTTGTCTCACTTGAGATTGTTTCTTCC
1 TTTTATCTCACTTGAGATT-GTTTTTCTTAAAACAGATTTTATCTCACTTGAGATTGTTT-TT-C
* *
675713 TCAAAACAAA
63 TTAAAACAGA
* * * ** *
675723 TTTTTATCTCAATTGAGATTGTTTTTCTTCAAAACAAATTTTGTCTCACTTGAGACAGTTTTCCT
1 -TTTTATCTCACTTGAGATTGTTTTTCTT-AAAACAGATTTTATCTCACTTGAGATTGTTTTTCT
675788 TAAAAC
64 TAAAAC
675794 TCAAACTTCA
Statistics
Matches: 245, Mismatches: 33, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
69 5 0.02
70 56 0.23
71 65 0.27
72 21 0.09
73 25 0.10
74 9 0.04
75 17 0.07
76 47 0.19
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (72 bp):
TTTTATCTCACTTGAGATTGTTTTTCTTAAAACAGATTTTATCTCACTTGAGATTGTTTTTCTTA
AAACAGA
Found at i:675873 original size:36 final size:36
Alignment explanation
Indices: 675820--675897 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 36
675810 ATTTCACTCA
* *
675820 AGATTTTATCTCTCTTGAGATTGTTTTTCTTAAAAT
1 AGATTTTATCTCACTTGAGATTGTTTTCCTTAAAAT
*
675856 AGATTTTGTCTCACTTGAGATTGTTTTCCTTAAAAT
1 AGATTTTATCTCACTTGAGATTGTTTTCCTTAAAAT
*
675892 AAATTT
1 AGATTT
675898 GATCAATTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.50
Consensus pattern (36 bp):
AGATTTTATCTCACTTGAGATTGTTTTCCTTAAAAT
Found at i:676059 original size:3 final size:3
Alignment explanation
Indices: 676053--676133 Score: 162
Period size: 3 Copynumber: 27.0 Consensus size: 3
676043 TTGTTGTTGT
676053 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
676101 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
676134 ATGACATAAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:677525 original size:19 final size:20
Alignment explanation
Indices: 677501--677542 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
677491 GGGACGGAAA
677501 AATAAATAAAAA-TAAAAGG
1 AATAAATAAAAAGTAAAAGG
677520 AATAAATAAAAAGTTAAAAGG
1 AATAAATAAAAAG-TAAAAGG
677541 AA
1 AA
677543 AAAAGAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 12 0.57
21 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (20 bp):
AATAAATAAAAAGTAAAAGG
Found at i:677657 original size:31 final size:29
Alignment explanation
Indices: 677606--677682 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
677596 TTAAGAGAGG
* *
677606 AAAAAATA-A-AAAAAATATAATGATAAT
1 AAAAAATAGATAAAGAAAATAATGATAAT
* *
677633 AATGAAAATAGATAAATAAAATAATTATAAT
1 AA--AAAATAGATAAAGAAAATAATGATAAT
*
677664 AAAAAATATATAAAGAAAA
1 AAAAAATAGATAAAGAAAA
677683 AAAATAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
27 2 0.05
29 21 0.51
30 1 0.02
31 17 0.41
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.23
Consensus pattern (29 bp):
AAAAAATAGATAAAGAAAATAATGATAAT
Found at i:678702 original size:22 final size:21
Alignment explanation
Indices: 678676--678717 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
678666 AAACCATTCA
678676 GGGGGAATCGGTACCCCTTTGG
1 GGGGGAATCGGT-CCCCTTTGG
*
678698 GGGGGAATCGGTTCCCTTTG
1 GGGGGAATCGGTCCCCTTTG
678718 AGCAATCTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.12, C:0.21, G:0.40, T:0.26
Consensus pattern (21 bp):
GGGGGAATCGGTCCCCTTTGG
Found at i:684700 original size:23 final size:23
Alignment explanation
Indices: 684656--684701 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
684646 AAATAAAATG
* *
684656 AAAATAAAATTCATAAAAGATAA
1 AAAATAAAAATAATAAAAGATAA
* *
684679 AAAATAAAAATAATCAACGATAA
1 AAAATAAAAATAATAAAAGATAA
684702 TAATAAATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.70, C:0.07, G:0.04, T:0.20
Consensus pattern (23 bp):
AAAATAAAAATAATAAAAGATAA
Found at i:684745 original size:23 final size:24
Alignment explanation
Indices: 684719--684763 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
684709 TTTATTATTA
684719 TATACAA-A-ATATTTTCCAAAAAC
1 TATACAATATATATTTT-CAAAAAC
*
684742 TATATAATATATATTTTCAAAA
1 TATACAATATATATTTTCAAAA
684764 GTATTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 6 0.32
24 6 0.32
25 7 0.37
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (24 bp):
TATACAATATATATTTTCAAAAAC
Found at i:684780 original size:34 final size:35
Alignment explanation
Indices: 684742--684984 Score: 106
Period size: 34 Copynumber: 7.1 Consensus size: 35
684732 TTCCAAAAAC
*
684742 TATATAATATATATTTTCAAAA-GTATTT-AAATTA
1 TATATAATATATATTTTAAAAATGT-TTTAAAATTA
* * *
684776 TATATTATATATTTTTTAAAAATGTTTTCAAA--A
1 TATATAATATATATTTTAAAAATGTTTTAAAATTA
* * *
684809 T-TAT-ATA-GT-TTTCAAAAATGTTTTCAAAACTA
1 TATATAATATATATTTTAAAAATGTTTT-AAAATTA
* * *
684841 TATAT--TATA-AGTTTTCAAAATGATTTCAAAACTA
1 TATATAATATATA-TTTTAAAAATG-TTTTAAAATTA
* * *
684875 TATAATATATATATGTTTTTCAAAATGTTTTTAAA--A
1 TAT-ATA-ATATAT-ATTTTAAAAATGTTTTAAAATTA
* * * *
684911 -A-CT-ATATATATTTTCAAAATGTTTAAAAAGTA
1 TATATAATATATATTTTAAAAATGTTTTAAAATTA
* *
684943 TATA-ATATATATTTTTTCAAAAATGTTTTAAAAACTA
1 TATATA-ATATATATTTT-AAAAATGTTTT-AAAATTA
684980 TATAT
1 TATAT
684985 TATTTTTTTT
Statistics
Matches: 162, Mismatches: 22, Indels: 46
0.70 0.10 0.20
Matches are distributed among these distances:
29 14 0.09
30 21 0.13
31 9 0.06
32 8 0.05
33 7 0.04
34 41 0.25
35 21 0.13
36 10 0.06
37 10 0.06
38 10 0.06
39 11 0.07
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (35 bp):
TATATAATATATATTTTAAAAATGTTTTAAAATTA
Found at i:684820 original size:29 final size:29
Alignment explanation
Indices: 684779--684844 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
684769 TAAATTATAT
* *
684779 ATTATATATTTTTTAAAAATGTTTTCAAA
1 ATTATATAGTTTTCAAAAATGTTTTCAAA
684808 ATTATATAGTTTTCAAAAATGTTTTCAAA
1 ATTATATAGTTTTCAAAAATGTTTTCAAA
*
684837 ACTATATA
1 ATTATATA
684845 TTATAAGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (29 bp):
ATTATATAGTTTTCAAAAATGTTTTCAAA
Found at i:684855 original size:35 final size:34
Alignment explanation
Indices: 684808--684987 Score: 165
Period size: 34 Copynumber: 5.1 Consensus size: 34
684798 TGTTTTCAAA
*
684808 ATTATATAGTTTTCAAAAATGTTTTCAAAACTATAT
1 ATTATA-AGTTTTC-AAAATGTTTTAAAAACTATAT
* *
684844 ATTATAAGTTTTCAAAATGATTTCAAAACTATAT
1 ATTATAAGTTTTCAAAATGTTTTAAAAACTATAT
684878 AATATATATATGTTTTTCAAAATGTTTTTAAAAAC--TAT
1 -AT-TATA-A-G-TTTTCAAAATG-TTTTAAAAACTATAT
*
684916 A-TAT-A-TTTTCAAAATG-TTTAAAAAGTATAT
1 ATTATAAGTTTTCAAAATGTTTTAAAAACTATAT
**
684946 AATATATATTTTTTCAAAAATGTTTTAAAAACTATAT
1 -AT-TATAAGTTTTC-AAAATGTTTTAAAAACTATAT
684983 ATTAT
1 ATTAT
684988 TTTTTTTTTC
Statistics
Matches: 123, Mismatches: 6, Indels: 31
0.77 0.04 0.19
Matches are distributed among these distances:
28 8 0.07
30 14 0.11
31 1 0.01
33 4 0.03
34 20 0.16
35 20 0.16
36 18 0.15
37 15 0.12
38 4 0.03
39 11 0.09
40 8 0.07
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (34 bp):
ATTATAAGTTTTCAAAATGTTTTAAAAACTATAT
Found at i:684954 original size:37 final size:37
Alignment explanation
Indices: 684817--684997 Score: 154
Period size: 37 Copynumber: 5.1 Consensus size: 37
684807 AATTATATAG
* **
684817 TTTTCAAAAATGTTTTCAAAACTATAT-AT-TATAAG
1 TTTTCAAAAATGTTTTAAAAACTATATAATATATATT
* *
684852 TTTTC-AAAATGATTTCAAAACTATATAATATATATATGT
1 TTTTCAAAAATGTTTTAAAAACTATAT-A-ATATATAT-T
684891 TTTTC-AAAATGTTTTTAAAAAC----T-ATATATA--
1 TTTTCAAAAATG-TTTTAAAAACTATATAATATATATT
*
684921 TTTTC-AAAATG-TTTAAAAAGTATATAATATATATT
1 TTTTCAAAAATGTTTTAAAAACTATATAATATATATT
* * *
684956 TTTTCAAAAATGTTTTAAAAACTATATATTATTTTTT
1 TTTTCAAAAATGTTTTAAAAACTATATAATATATATT
684993 TTTTC
1 TTTTC
684998 CTCTCTTAAG
Statistics
Matches: 121, Mismatches: 10, Indels: 28
0.76 0.06 0.18
Matches are distributed among these distances:
28 8 0.07
30 11 0.09
32 1 0.01
33 14 0.12
34 20 0.17
35 10 0.08
36 7 0.06
37 27 0.22
38 4 0.03
39 11 0.09
40 8 0.07
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (37 bp):
TTTTCAAAAATGTTTTAAAAACTATATAATATATATT
Found at i:684993 original size:35 final size:34
Alignment explanation
Indices: 684808--684994 Score: 161
Period size: 35 Copynumber: 5.4 Consensus size: 34
684798 TGTTTTCAAA
* *
684808 ATTATATAGTTTTCAAAAATGTTTTCAAAACTATAT
1 ATTATAT-TTTTTC-AAAATGTTTTAAAAACTATAT
** * *
684844 ATTATAAGTTTTCAAAATGATTTCAAAACTATATAAT
1 ATTATATTTTTTCAAAATGTTTTAAAAAC--TAT-AT
684881 ATATATATGTTTTTCAAAATGTTTTTAAAAAC--TAT
1 AT-TATAT-TTTTTCAAAATG-TTTTAAAAACTATAT
*
684916 A-TATA--TTTTCAAAATG-TTTAAAAAGTATAT
1 ATTATATTTTTTCAAAATGTTTTAAAAACTATAT
684946 AATATATATTTTTTCAAAAATGTTTTAAAAACTATAT
1 -AT-TATATTTTTTC-AAAATGTTTTAAAAACTATAT
*
684983 ATTATTTTTTTT
1 ATTATATTTTTT
684995 TTCCTCTCTT
Statistics
Matches: 127, Mismatches: 9, Indels: 31
0.76 0.05 0.19
Matches are distributed among these distances:
28 8 0.06
30 14 0.11
31 1 0.01
33 8 0.06
34 15 0.12
35 23 0.18
36 18 0.14
37 17 0.13
38 4 0.03
39 11 0.09
40 8 0.06
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (34 bp):
ATTATATTTTTTCAAAATGTTTTAAAAACTATAT
Found at i:685101 original size:15 final size:16
Alignment explanation
Indices: 685077--685109 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
685067 TTTTTCCTTT
685077 TTCCTTTTTATTTTTA
1 TTCCTTTTTATTTTTA
685093 TTCC-TTTTATTTTTA
1 TTCCTTTTTATTTTTA
685108 TT
1 TT
685110 TATTTTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (16 bp):
TTCCTTTTTATTTTTA
Found at i:685115 original size:15 final size:15
Alignment explanation
Indices: 685082--685115 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
685072 CCTTTTTCCT
*
685082 TTTTATTTTTATTCC
1 TTTTATTTTTATTCA
*
685097 TTTTATTTTTATTTA
1 TTTTATTTTTATTCA
685112 TTTT
1 TTTT
685116 TCTATCCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTATTTTTATTCA
Found at i:686697 original size:110 final size:109
Alignment explanation
Indices: 686504--687104 Score: 775
Period size: 110 Copynumber: 5.5 Consensus size: 109
686494 TCTTTAAAGA
* **
686504 ACTGATTGTCAACAAACAACTTTTCAGAATCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
* *
686569 ATTGGACTCGAGACAACACAAGTTCAACTTCATAGCGAAAGGGTG
66 ATTGGACTCGAGACAACACAAGTTCAACTTCACAGCG-AAGGGCG
* **
686614 ACTGACTGTCAACAGACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGTGAAGGAT
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
* * *
686679 ATTGGACTCGAGATAACACAAGCTCCAA-TTCACAGCGAAGGGTTG
66 ATTGGACTCGAGACAACACAAG-TTCAACTTCACAGCGAAGGG-CG
* *
686724 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTTAACTTCACAGCGAAGGAT
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
* *
686789 ATTAGG-CTCGAGACAACACAAGCTT-AACTTCACAGTGGAGGGGCG
66 ATT-GGACTCGAGACAACACAAG-TTCAACTTCACAG-CGAAGGGCG
* * * * * *
686834 ACTGACTGTCAATAAATAAATTTTCAGTTTGATTCAGAGTCAATCTCAACTTCACAATGAAGGAT
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
* * * *
686899 ATTAGACTTGAGACAACACAAGCTCAACTTCACAGCGAAAGAGCG
66 ATTGGACTCGAGACAACACAAGTTCAACTTCACAGCG-AAGGGCG
* * * *
686944 ACTGACTGTCAATAAACAACTTTTCAGTTTCATTCAAAGTCAATTTTAAATTCACAACGAAGGAT
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
* *
687009 ATTGGACTCGAGACAACACAAGCTCAACTTCATAGCGAAGGGACG
66 ATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGG-CG
* * *
687054 ACTGGCTATCAACAAACAACTTTCCAG--T--TTCAGAGTCAATTTCAACTTCAC
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCAC
687105 GGTGAAGGAT
Statistics
Matches: 432, Mismatches: 50, Indels: 22
0.86 0.10 0.04
Matches are distributed among these distances:
106 20 0.05
108 1 0.00
109 14 0.03
110 386 0.89
111 11 0.03
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (109 bp):
ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
ATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGGCG
Found at i:686897 original size:220 final size:219
Alignment explanation
Indices: 686504--687135 Score: 855
Period size: 220 Copynumber: 2.9 Consensus size: 219
686494 TCTTTAAAGA
* ** *
686504 ACTGATTGTCAACAAACAACTTTTCAGAATCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTTAACTTCACAACGAAGGAT
* * *
686569 ATTGGACTCGAGACAACACAAG-TTCAACTTCATAGCGAAAGGGTGACTGACTGTCAACAGACAA
66 ATTGGACTCGAGACAACACAAGCTT-AACTTCATAGCGAAGGGGCGACTGACTGTCAACAAACAA
686633 CTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCGAGATAACAC
130 CTTTTCAGTTT-ATTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCGAGATAACAC
* *
686698 AAGCTCCAA-TTCACAGCG-AAGGGTTG
194 AAGCT-CAACTTCACAGCGAAAGAG-CG
*
686724 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTTAACTTCACAGCGAAGGAT
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTTAACTTCACAACGAAGGAT
* * * * *
686789 ATTAGG-CTCGAGACAACACAAGCTTAACTTCACAGTGGAGGGGCGACTGACTGTCAATAAATAA
66 ATT-GGACTCGAGACAACACAAGCTTAACTTCATAGCGAAGGGGCGACTGACTGTCAACAAACAA
* * * * * *
686853 ATTTTCAGTTTGATTCAGAGTCAATCTCAACTTCACAATGAAGGATATTAGACTTGAGACAACAC
130 CTTTTCAGTTT-ATTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCGAGATAACAC
686918 AAGCTCAACTTCACAGCGAAAGAGCG
194 AAGCTCAACTTCACAGCGAAAGAGCG
* * *
686944 ACTGACTGTCAATAAACAACTTTTCAGTTTCATTCAAAGTCAATTTTAAATTCACAACGAAGGAT
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTTAACTTCACAACGAAGGAT
* * * *
687009 ATTGGACTCGAGACAACACAAGCTCAACTTCATAGCGAAGGGACGACTGGCTATCAACAAACAAC
66 ATTGGACTCGAGACAACACAAGCTTAACTTCATAGCGAAGGGGCGACTGACTGTCAACAAACAAC
* * * ** *
687074 TTTCCAG--T-TTCAGAGTCAATTTCAACTTCACGGTGAAGGATTTTGTTCTCGAAATAACACAA
131 TTTTCAGTTTATTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCGAGATAACACAA
687136 ATGTTTGGAT
Statistics
Matches: 360, Mismatches: 47, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
216 44 0.12
218 1 0.00
219 5 0.01
220 302 0.84
221 8 0.02
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.26
Consensus pattern (219 bp):
ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTTAACTTCACAACGAAGGAT
ATTGGACTCGAGACAACACAAGCTTAACTTCATAGCGAAGGGGCGACTGACTGTCAACAAACAAC
TTTTCAGTTTATTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCGAGATAACACAA
GCTCAACTTCACAGCGAAAGAGCG
Found at i:687620 original size:165 final size:167
Alignment explanation
Indices: 687253--687857 Score: 582
Period size: 165 Copynumber: 3.6 Consensus size: 167
687243 CCAAACACCT
* * * * * *
687253 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAGCTTAAGTTGAGAAGGGCT
1 TCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTT
* * * * * * * * *
687318 ATCTGC---C-AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCCCATCATTTACAGAAT
66 ATCTGCTAACAAAAGACCTTCGAGTTTGACTACGCTCAAC-TCCAAGGCACATCATTTGCAGAAT
* * * * * * * *
687379 AACTCAAGGCTAGAAGGGTTATTTGTCACCAAATGACCT
130 AACTTAAGTCGAGAAGGGCTATCTGCCACTAAA-GACCC
* * * *
687418 TTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATATCTTAAGTCGAGAAGGGAT
1 TCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGG-T
* * *
687483 T-TCTGCTAACTAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTAT
65 TATCTGCTAACAAAAGACCTTCGAGTTTGACTACGCTCAACTCCAAGGCACATCATTTGCAGAAT
*
687547 AGCTTAAGTCGAGAAGGGCTATCTG-C-C-AAAGACCC
130 AACTTAAGTCGAGAAGGGCTATCTGCCACTAAAGACCC
* * * * * * * * * *
687582 TCGAGTTTGATTACACTCAGCTTCGAGGGCCCATCATTTACAGTATAACTCAAGGCTAGAAGGGT
1 TCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGT
* * * * *
687647 TATCTG-TGACCAAAAGACCTTTGTGTTTGACTACGCTCAACTCCAAGGCATATCATTTGTAGAA
65 TATCTGCT-AACAAAAGACCTTCGAGTTTGACTACGCTCAACTCCAAGGCACATCATTTGCAGAA
* * *
687711 TAACTTAAGTTGAGAAGGGTTATCTGCCAACTAAAGACCT
129 TAACTTAAGTCGAGAAGGGCTATCTGCC-ACTAAAGACCC
* *
687751 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTT
1 TCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTT
* * * *
687816 ATCTGCCAACCAAAA-ACCTTCGAGTTCGATTACACTCAACTC
66 ATCTGCTAA-CAAAAGACCTTCGAGTTTGACTACGCTCAACTC
687858 AGAGGCAAAC
Statistics
Matches: 358, Mismatches: 68, Indels: 25
0.79 0.15 0.06
Matches are distributed among these distances:
164 24 0.07
165 172 0.48
166 3 0.01
167 1 0.00
168 103 0.29
169 55 0.15
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.26
Consensus pattern (167 bp):
TCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTT
ATCTGCTAACAAAAGACCTTCGAGTTTGACTACGCTCAACTCCAAGGCACATCATTTGCAGAATA
ACTTAAGTCGAGAAGGGCTATCTGCCACTAAAGACCC
Found at i:687668 original size:249 final size:249
Alignment explanation
Indices: 687249--687853 Score: 969
Period size: 249 Copynumber: 2.4 Consensus size: 249
687239 CCCACCAAAC
* * *
687249 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAGCTTAAGTTGAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
687314 GGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCCCATCATTTACAGAAT
66 GGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCCCATCATTTACAGAAT
* * *
687379 AACTCAAGGCTAGAAGGGTTATTTGTCACCAAATGACCTTTGAGTTCGACTACGCTCAGCTCCAA
131 AACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACGCTCAACTCCAA
* * *
687444 GGCATATCATTTGCAGCATATCTTAAGTCGAGAAGGGATT-TCTGCTAACTAAAG
196 GGCATATCATTTGCAGAATAACTTAAGTCGAGAAGGG-TTATCTGCCAACTAAAG
* *
687498 ACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
* *
687563 GGCTATCTGCCAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCCCATCATTTACAGTAT
66 GGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCCCATCATTTACAGAAT
* * *
687628 AACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGTGTTTGACTACGCTCAACTCCAA
131 AACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACGCTCAACTCCAA
* *
687693 GGCATATCATTTGTAGAATAACTTAAGTTGAGAAGGGTTATCTGCCAACTAAAG
196 GGCATATCATTTGCAGAATAACTTAAGTCGAGAAGGGTTATCTGCCAACTAAAG
687747 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
* * *
687812 GGTTATCTGCCAACCAAAAACCTTCGAGTTCGATTACACTCA
66 GGCTATCTG----CCAAAGACCCTCGAGTTCGATTACACTCA
687854 ACTCAGAGGC
Statistics
Matches: 327, Mismatches: 24, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
248 2 0.01
249 299 0.91
253 26 0.08
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.26
Consensus pattern (249 bp):
ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
GGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCCCATCATTTACAGAAT
AACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACGCTCAACTCCAA
GGCATATCATTTGCAGAATAACTTAAGTCGAGAAGGGTTATCTGCCAACTAAAG
Found at i:687864 original size:84 final size:83
Alignment explanation
Indices: 687240--687853 Score: 612
Period size: 84 Copynumber: 7.4 Consensus size: 83
687230 GGAATCGTGC
* * * *
687240 CCACCAAACACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAGCTTAA
1 CCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAA
* *
687305 GTTGAGAAGGGCTATCTG
66 GTCGAGAAGGGTTATCTG
* * * * * * * * *
687323 ---CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCCCATCATTTACAGAATAACTCA
1 CCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTA
* * *
687385 AGGCTAGAAGGGTTATTTG
65 AGTCGAGAAGGGTTATCTG
* * * *
687404 TCACCAAATGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATATCTTA
1 CCACCAAA-GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTA
687469 AGTCGAGAAGGGATT-TCTG
65 AGTCGAGAAGGG-TTATCTG
* * * * *
687488 CTAACTAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTA
1 C-CACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTA
*
687553 AGTCGAGAAGGGCTATCTG
65 AGTCGAGAAGGGTTATCTG
* * * * * * * * * *
687572 ---CCAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCCCATCATTTACAGTATAACTCA
1 CCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTA
* *
687634 AGGCTAGAAGGGTTATCTG
65 AGTCGAGAAGGGTTATCTG
** * * * * * * *
687653 TGACCAAAAGACCTTTGTGTTTGACTACGCTCAACTCCAAGGCATATCATTTGTAGAATAACTTA
1 CCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTA
*
687718 AGTTGAGAAGGGTTATCTG
65 AGTCGAGAAGGGTTATCTG
* *
687737 CCAACTAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTA
1 CC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTA
687802 AGTCGAGAAGGGTTATCTG
65 AGTCGAGAAGGGTTATCTG
* * *
687821 CCAACCAAAAACCTTCGAGTTCGATTACACTCA
1 CC-ACCAAAGACCTTCGAGTTCGACTACGCTCA
687854 ACTCAGAGGC
Statistics
Matches: 431, Mismatches: 86, Indels: 27
0.79 0.16 0.05
Matches are distributed among these distances:
80 54 0.13
81 77 0.18
83 1 0.00
84 245 0.57
85 54 0.13
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (83 bp):
CCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAA
GTCGAGAAGGGTTATCTG
Found at i:688505 original size:39 final size:37
Alignment explanation
Indices: 688428--688561 Score: 164
Period size: 39 Copynumber: 3.6 Consensus size: 37
688418 TTCGTCATAT
*
688428 ATATATATATATATTATAG-TTTAAAAACATTTTTAAAC
1 ATATATATA-ATA-TATAGTTTTAAAAACATTTTGAAAC
*
688466 ATATATATAATATATAGTTTTCAAAACATGTTTGAAAAC
1 ATATATATAATATATAGTTTTAAAAACAT-TTTG-AAAC
* * *
688505 ATTTATATATTATATAGTTTTTAAAACATTTTGAAA-
1 ATATATATAATATATAGTTTTAAAAACATTTTGAAAC
*
688541 ATAAATATAATATATAGTTTT
1 ATATATATAATATATAGTTTT
688562 TAAATTGAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
36 23 0.27
37 16 0.19
38 16 0.19
39 30 0.35
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTAAAAACATTTTGAAAC
Found at i:689858 original size:29 final size:29
Alignment explanation
Indices: 689823--689922 Score: 76
Period size: 29 Copynumber: 3.3 Consensus size: 29
689813 AAAATTATAT
*
689823 ATTATATATATTTTTAAAATGTTTTCAAA
1 ATTATATATATTTTAAAAATGTTTTCAAA
* * *
689852 ATTATATAGT-TTTCAAAAATATTTTTAAA
1 ATTATATA-TATTTTAAAAATGTTTTCAAA
* *
689881 ACTATATATTATAAGTTTTCAAAATGATTTCAAA
1 A-T-TATA-TAT-A-TTTTAAAAATGTTTTCAAA
*
689915 ACTATATA
1 ATTATATA
689923 ATATATATAT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
29 24 0.44
30 2 0.04
31 7 0.13
32 6 0.11
34 15 0.28
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (29 bp):
ATTATATATATTTTAAAAATGTTTTCAAA
Found at i:689892 original size:36 final size:35
Alignment explanation
Indices: 689854--690218 Score: 297
Period size: 35 Copynumber: 10.2 Consensus size: 35
689844 TTTTCAAAAT
689854 TATATAGTTTTCAAAAATATTTTTAAAACTATATAT-
1 TATATA-TTTTC-AAAATATTTTTAAAACTATATATA
*
689890 TATA-AGTTTTCAAAATGA-TTTCAAAACTATATAATA
1 TATATA-TTTTCAAAAT-ATTTTTAAAACTATAT-ATA
* *
689926 TATATATGTTTTTCAAAATGTTTTT-AAA--A-A-CTA
1 TATATA---TTTTCAAAATATTTTTAAAACTATATATA
* * *
689959 TATATATTTT-AAAAT-GTTTAAAAAGTATATAATA
1 TATATATTTTCAAAATATTTTTAAAACTATAT-ATA
*
689993 TATATATTTTCAAAA-ATATTTAAAACTATATATTA
1 TATATATTTTCAAAATATTTTTAAAACTATATA-TA
* * * *
690028 TATTTATTTTCAAAATGTTTTAAAAATTATATAATA
1 TATATATTTTCAAAATATTTTTAAAACTATAT-ATA
* *
690064 TATATATTTTCAAAAT-TTTTAAAAAATATATATA
1 TATATATTTTCAAAATATTTTTAAAACTATATATA
* *
690098 CTATATTTATTTTTAAAATATTTTAAAAACTATATAATA
1 -TATA--TATTTTCAAAATATTTTTAAAACTATAT-ATA
*
690137 TATAAATATTTTCAAACATGTTTTTAAAACTATATATTA
1 TAT--ATATTTTCAAA-ATATTTTTAAAACTATATA-TA
*
690176 TATATATGTTTAAAAATATTTTT-AAACTATAATATA
1 TATATAT-TTTCAAAATATTTTTAAAACTAT-ATATA
690212 TATATAT
1 TATATAT
690219 ATATATATAT
Statistics
Matches: 274, Mismatches: 26, Indels: 58
0.77 0.07 0.16
Matches are distributed among these distances:
28 3 0.01
29 8 0.03
30 4 0.01
31 1 0.00
32 1 0.00
33 8 0.03
34 34 0.12
35 60 0.22
36 54 0.20
37 27 0.10
38 36 0.13
39 37 0.14
40 1 0.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.47
Consensus pattern (35 bp):
TATATATTTTCAAAATATTTTTAAAACTATATATA
Found at i:689950 original size:73 final size:70
Alignment explanation
Indices: 689854--690220 Score: 342
Period size: 73 Copynumber: 5.1 Consensus size: 70
689844 TTTTCAAAAT
*
689854 TATATAGTTTTCAAAAATATTTTTAAAACTATATATTATA-AGTTTTCAAAATGATTTCAAAACT
1 TATATA-TTTTC-AAAATATTTTTAAAACTATATATTATATA-TTTTCAAAATGATTTAAAAACT
689918 ATATAATA
63 ATATAATA
* * *
689926 TATATATGTTTTTCAAAATGTTTTTAAAA--A-CTA-TATATATTTT-AAAATG-TTTAAAAAGT
1 TATATA---TTTTCAAAATATTTTTAAAACTATATATTATATATTTTCAAAATGATTTAAAAACT
689985 ATATAATA
63 ATATAATA
* * *
689993 TATATATTTTCAAAA-ATATTTAAAACTATATATTATATTTATTTTCAAAATGTTTTAAAAATTA
1 TATATATTTTCAAAATATTTTTAAAACTATATATTATA--TATTTTCAAAATGATTTAAAAACTA
690057 TATAATA
64 TATAATA
* * *
690064 TATATATTTTCAAAAT-TTTTAAAAAATATATATACTATATTTATTTTTAAAAT-ATTTTAAAAA
1 TATATATTTTCAAAATATTTTTAAAACTATATAT--TATA--TATTTTCAAAATGA-TTTAAAAA
690127 CTATATAATA
61 CTATATAATA
* * **
690137 TATAAATATTTTCAAACATGTTTTTAAAACTATATATTATATATATGTTTAAAAAT-ATTTTTAA
1 TAT--ATATTTTCAAA-ATATTTTTAAAACTATATA-T-TATATAT-TTTCAAAATGATTTAAAA
690201 ACTATAATATATA
60 ACTAT-ATA-ATA
690214 TATATAT
1 TATATAT
690221 ATATATATAT
Statistics
Matches: 251, Mismatches: 21, Indels: 43
0.80 0.07 0.14
Matches are distributed among these distances:
63 8 0.03
64 9 0.04
65 1 0.00
66 2 0.01
67 26 0.10
68 6 0.02
69 14 0.06
70 9 0.04
71 47 0.19
72 6 0.02
73 51 0.20
74 5 0.02
75 28 0.11
76 14 0.06
77 24 0.10
78 1 0.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.47
Consensus pattern (70 bp):
TATATATTTTCAAAATATTTTTAAAACTATATATTATATATTTTCAAAATGATTTAAAAACTATA
TAATA
Found at i:689972 original size:29 final size:29
Alignment explanation
Indices: 689926--689989 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 29
689916 CTATATAATA
*
689926 TATATATGTTTTTCAAAATGTTTTTAAAAAC
1 TATATATGATTTTCAAAATG--TTTAAAAAC
*
689957 TATATAT-ATTTT-AAAATGTTTAAAAAG
1 TATATATGATTTTCAAAATGTTTAAAAAC
689984 TATATA
1 TATATA
689990 ATATATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 14 0.45
29 6 0.19
30 4 0.13
31 7 0.23
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (29 bp):
TATATATGATTTTCAAAATGTTTAAAAAC
Found at i:690214 original size:2 final size:2
Alignment explanation
Indices: 690203--690248 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
690193 ATTTTTAAAC
690203 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
690244 TA TA T
1 TA TA T
690249 GACGAAAATG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:691995 original size:32 final size:32
Alignment explanation
Indices: 691959--692026 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
691949 AATAAATTTA
691959 TTTATTACTATTTTCAATTGTACAATTAGATT
1 TTTATTACTATTTTCAATTGTACAATTAGATT
* * * * *
691991 TTTATTATTGTTTTTAATTTTATAATTAGATT
1 TTTATTACTATTTTCAATTGTACAATTAGATT
692023 TTTA
1 TTTA
692027 CTTTTATCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.60
Consensus pattern (32 bp):
TTTATTACTATTTTCAATTGTACAATTAGATT
Found at i:692208 original size:31 final size:32
Alignment explanation
Indices: 692158--692230 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
692148 TCTGTTTGAT
* *
692158 TTGCTTTCGGTTCGAGTTAAATTC-GTTCGGG
1 TTGCTTTCGGATCGAGTTAAATTCAGTTCAGG
* * *
692189 TTGCTTTTGGATCGGGTTAATTTCAGTTCAGG
1 TTGCTTTCGGATCGAGTTAAATTCAGTTCAGG
*
692221 TTACTTTCGG
1 TTGCTTTCGG
692231 TTGTGCTAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 20 0.59
32 14 0.41
ACGTcount: A:0.14, C:0.15, G:0.27, T:0.44
Consensus pattern (32 bp):
TTGCTTTCGGATCGAGTTAAATTCAGTTCAGG
Found at i:701472 original size:143 final size:144
Alignment explanation
Indices: 701210--701496 Score: 531
Period size: 143 Copynumber: 2.0 Consensus size: 144
701200 GTGCACATGA
*
701210 TAATTTAAAATATATATTTAAATTAGTAAGTACCATAAAAGGAACAAACCTAAAAAATGATCAAT
1 TAATTTAAAATATATATTTAAATTAGTAAGTACCATAAAAGGAACAAACCTAAAAAAGGATCAAT
*
701275 CTGGAAGGTCTACTAAGCACCAGCCTGGCTACGCTCTACAACAGCAGTCGAACCTAAACCATAAC
66 CTGGAAGGTCTACTAAGCACCAGCCTGGCTACGCTCTACAACAGCAGTCAAACCTAAACCATAAC
* *
701340 GAATTTGGGTTTCT
131 AAATTTGGATTTCT
701354 TAATTTAAAATATATATTTAAATTAGTAAGTACCATAAAAGGAACAAACCT-AAAAAGGATCAAT
1 TAATTTAAAATATATATTTAAATTAGTAAGTACCATAAAAGGAACAAACCTAAAAAAGGATCAAT
701418 CTGGAAGGTCTACTAAGCACCAGCCTGGCTACGCTCTACAACAGCAGTCAAACCTAAACCATAAC
66 CTGGAAGGTCTACTAAGCACCAGCCTGGCTACGCTCTACAACAGCAGTCAAACCTAAACCATAAC
701483 AAATTTGGATTTCT
131 AAATTTGGATTTCT
701497 ATTGAAGTAA
Statistics
Matches: 139, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
143 88 0.63
144 51 0.37
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (144 bp):
TAATTTAAAATATATATTTAAATTAGTAAGTACCATAAAAGGAACAAACCTAAAAAAGGATCAAT
CTGGAAGGTCTACTAAGCACCAGCCTGGCTACGCTCTACAACAGCAGTCAAACCTAAACCATAAC
AAATTTGGATTTCT
Found at i:702699 original size:5 final size:5
Alignment explanation
Indices: 702689--702715 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
702679 CTTCAAAATT
702689 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
702716 ATAATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:704317 original size:26 final size:26
Alignment explanation
Indices: 704288--704505 Score: 194
Period size: 26 Copynumber: 8.5 Consensus size: 26
704278 AGTCTTTGTT
* * *
704288 ATAAATAGCACATCCGAGTGGGAGTG
1 ATAAATAGCACTTTCGAGTGAGAGTG
*
704314 ATAAATTGCACTTTCGAGTGAGAGTG
1 ATAAATAGCACTTTCGAGTGAGAGTG
* *
704340 ATAAATAGAACTTT-GAGTGTGAGTG
1 ATAAATAGCACTTTCGAGTGAGAGTG
* *
704365 ATAAATAGCACTTTCGAATGCGAGTG
1 ATAAATAGCACTTTCGAGTGAGAGTG
* * *
704391 ATAAATATCACTTTGGAGTGCGAGTG
1 ATAAATAGCACTTTCGAGTGAGAGTG
* * * *
704417 AGAAATAACACTTTGGAGTGCGAGTG
1 ATAAATAGCACTTTCGAGTGAGAGTG
* * *
704443 AGAAAT-GACACTTTGGAGTGCGAGTG
1 ATAAATAG-CACTTTCGAGTGAGAGTG
*
704469 AGAAAT-GACACTTTCGAGT-ACGAGTG
1 ATAAATAG-CACTTTCGAGTGA-GAGTG
*
704495 A-AAATGGCACT
1 ATAAATAGCACT
704506 ATGTGTGCAT
Statistics
Matches: 170, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
25 31 0.18
26 139 0.82
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (26 bp):
ATAAATAGCACTTTCGAGTGAGAGTG
Found at i:704416 original size:77 final size:77
Alignment explanation
Indices: 704288--704499 Score: 236
Period size: 77 Copynumber: 2.7 Consensus size: 77
704278 AGTCTTTGTT
* * * *
704288 ATAAATAGCACATCCGAGTGGGAGTGATAAAT-TGCACTTTCGAGTGAGAGTGATAAATAGA-AC
1 ATAAATAGCACTTTCGAGTGCGAGTGATAAATAT-CACTTTCGAGTGCGAGTGA-AAATA-ACAC
*
704351 TTT-GAGTGTGAGTG
63 TTTGGAGTGCGAGTG
* *
704365 ATAAATAGCACTTTCGAATGCGAGTGATAAATATCACTTTGGAGTGCGAGTGAGAAATAACACTT
1 ATAAATAGCACTTTCGAGTGCGAGTGATAAATATCACTTTCGAGTGCGAGTGA-AAATAACACTT
704430 TGGAGTGCGAGTG
65 TGGAGTGCGAGTG
* * * *
704443 AGAAAT-GACACTTTGGAGTGCGAGTGAGAAATGA-CACTTTCGAGTACGAGTGAAAAT
1 ATAAATAG-CACTTTCGAGTGCGAGTGATAAAT-ATCACTTTCGAGTGCGAGTGAAAAT
704500 GGCACTATGT
Statistics
Matches: 116, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
76 1 0.01
77 60 0.52
78 54 0.47
79 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (77 bp):
ATAAATAGCACTTTCGAGTGCGAGTGATAAATATCACTTTCGAGTGCGAGTGAAAATAACACTTT
GGAGTGCGAGTG
Found at i:704439 original size:52 final size:51
Alignment explanation
Indices: 704303--704499 Score: 227
Period size: 52 Copynumber: 3.8 Consensus size: 51
704293 TAGCACATCC
* * ** * *
704303 GAGTGGGAGTGATAAATTGCACTTTCGAGTGAGAGTGATAAATAGAACTTT-
1 GAGTGCGAGTGAGAAATAACACTTTCGAGTGCGAGTGATAAATA-CACTTTG
* * * *
704354 GAGTGTGAGTGATAAATAGCACTTTCGAATGCGAGTGATAAATATCACTTTG
1 GAGTGCGAGTGAGAAATAACACTTTCGAGTGCGAGTGATAAATA-CACTTTG
* *
704406 GAGTGCGAGTGAGAAATAACACTTTGGAGTGCGAGTGAGAAATGACACTTTG
1 GAGTGCGAGTGAGAAATAACACTTTCGAGTGCGAGTGATAAAT-ACACTTTG
* *
704458 GAGTGCGAGTGAGAAATGACACTTTCGAGTACGAGTGA-AAAT
1 GAGTGCGAGTGAGAAATAACACTTTCGAGTGCGAGTGATAAAT
704500 GGCACTATGT
Statistics
Matches: 129, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
51 49 0.38
52 79 0.61
53 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (51 bp):
GAGTGCGAGTGAGAAATAACACTTTCGAGTGCGAGTGATAAATACACTTTG
Found at i:704746 original size:7 final size:7
Alignment explanation
Indices: 704736--704765 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
704726 CCGTGAATAG
704736 TGAACAA
1 TGAACAA
704743 TGAACAA
1 TGAACAA
*
704750 TGAACAG
1 TGAACAA
704757 TGAACAA
1 TGAACAA
704764 TG
1 TG
704766 TATCGATGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.50, C:0.13, G:0.20, T:0.17
Consensus pattern (7 bp):
TGAACAA
Found at i:705314 original size:47 final size:45
Alignment explanation
Indices: 705243--705368 Score: 157
Period size: 47 Copynumber: 2.8 Consensus size: 45
705233 TATAAAATCT
* *
705243 CTTACCATTTATCCCATATGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
705288 CTTACCATTTAAATTCCATAAGCTCGTAAGTTTATTTTATCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
705335 CTTGCCA-TTATT-CATAAGCTCATAAGCTTATTTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTT
705369 CATGCTTACC
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
43 20 0.28
44 3 0.04
45 10 0.14
46 2 0.03
47 36 0.51
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:709358 original size:24 final size:24
Alignment explanation
Indices: 709317--709367 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
709307 TTTATTCTCA
*
709317 CTTTTTTTTCTTCGTTTTCT-TTTT
1 CTTTTTATTCTTCGTTTT-TGTTTT
709341 CTTTTTATTCTTTC-TTTTTGTTTT
1 CTTTTTATTC-TTCGTTTTTGTTTT
709365 CTT
1 CTT
709368 CTTTTATGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 1 0.04
24 20 0.83
25 3 0.12
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.78
Consensus pattern (24 bp):
CTTTTTATTCTTCGTTTTTGTTTT
Found at i:709366 original size:15 final size:15
Alignment explanation
Indices: 709330--709380 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
709320 TTTTTTCTTC
709330 GTTTTCTTT-TTCTTT
1 GTTTTCTTTCTT-TTT
709345 -TTATTCTTTCTTTTT
1 GTT-TTCTTTCTTTTT
709360 GTTTTC-TTCTTTTAT
1 GTTTTCTTTCTTTT-T
709375 GTTTTC
1 GTTTTC
709381 CCCCATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 9 0.28
15 19 0.59
16 4 0.12
ACGTcount: A:0.04, C:0.14, G:0.06, T:0.76
Consensus pattern (15 bp):
GTTTTCTTTCTTTTT
Found at i:711745 original size:21 final size:21
Alignment explanation
Indices: 711715--711759 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
711705 AACAATACCT
*
711715 GTGAATAGTGAACAATGAATA
1 GTGAACAGTGAACAATGAATA
* *
711736 GTGAACAGTGAACAGTTAATA
1 GTGAACAGTGAACAATGAATA
711757 GTG
1 GTG
711760 TACCGATGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.07, G:0.27, T:0.24
Consensus pattern (21 bp):
GTGAACAGTGAACAATGAATA
Found at i:711759 original size:14 final size:14
Alignment explanation
Indices: 711716--711747 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
711706 ACAATACCTG
711716 TGAATAGTGAACAA
1 TGAATAGTGAACAA
*
711730 TGAATAGTGAACAG
1 TGAATAGTGAACAA
711744 TGAA
1 TGAA
711748 CAGTTAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.25, T:0.22
Consensus pattern (14 bp):
TGAATAGTGAACAA
Found at i:712211 original size:47 final size:44
Alignment explanation
Indices: 712136--712259 Score: 162
Period size: 47 Copynumber: 2.8 Consensus size: 44
712126 TATAAAATCT
*
712136 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACC-AAATA
* * *
712181 CTTACCATTTAAATTCCATAAGCTCATAAGCTTATTTTATCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAATA
*
712227 CTTGCCA-TTATT-CATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
712260 GCATACTTAC
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
42 20 0.28
43 3 0.04
45 12 0.17
46 10 0.14
47 26 0.37
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (44 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAATA
Found at i:717413 original size:23 final size:23
Alignment explanation
Indices: 717383--717430 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
717373 TGAGTTAAAA
717383 TAAAGGAAATGGATTGAATTCCT
1 TAAAGGAAATGGATTGAATTCCT
*
717406 TAAAGGAAATGGATTGAATTTCT
1 TAAAGGAAATGGATTGAATTCCT
717429 TA
1 TA
717431 GAGAGTAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (23 bp):
TAAAGGAAATGGATTGAATTCCT
Found at i:721316 original size:78 final size:78
Alignment explanation
Indices: 721143--721321 Score: 180
Period size: 78 Copynumber: 2.3 Consensus size: 78
721133 TATAAAAAGA
* ** * *
721143 ACTTTTGAATGCGAGTGATAAATAAAACTTTCGTGTGTGAATGATAAATAACACTTTCGAGTGTG
1 ACTTTTGAGTGCGAGTGATAAATAAAACTTTCAAGTGCGAATGATAAATAACACTTTCGAGTGCG
*
721208 GGTAATAAAATAC
66 AGTAATAAAATAC
* * ** * * * *
721221 ACTTTCGAGTGCAAGTGATAAATATCACTTTCAAGTGCGAGTGGTAAATAGCACTTTTGAGTGCG
1 ACTTTTGAGTGCGAGTGATAAATAAAACTTTCAAGTGCGAATGATAAATAACACTTTCGAGTGCG
* *
721286 AGTGA-CAAATGAC
66 AGTAATAAAAT-AC
* *
721299 ACTTTTGAGTGTGAGTGAAAAAT
1 ACTTTTGAGTGCGAGTGATAAAT
721322 GGCACTATGT
Statistics
Matches: 80, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
77 4 0.05
78 76 0.95
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.31
Consensus pattern (78 bp):
ACTTTTGAGTGCGAGTGATAAATAAAACTTTCAAGTGCGAATGATAAATAACACTTTCGAGTGCG
AGTAATAAAATAC
Found at i:721322 original size:26 final size:25
Alignment explanation
Indices: 721143--721321 Score: 151
Period size: 26 Copynumber: 6.9 Consensus size: 25
721133 TATAAAAAGA
* * *
721143 ACTTTTGAATGCGAGTGATAAATAAA
1 ACTTTCGAGTGCGAGTGATAAAT-AC
* * *
721169 ACTTTCGTGTGTGAATGATAAATAAC
1 ACTTTCGAGTGCGAGTGATAAAT-AC
* * *
721195 ACTTTCGAGTGTGGGTAATAAAATAC
1 ACTTTCGAGTGCGAGTGAT-AAATAC
*
721221 ACTTTCGAGTGCAAGTGATAAATATC
1 ACTTTCGAGTGCGAGTGATAAATA-C
* *
721247 ACTTTCAAGTGCGAGTGGTAAATAGC
1 ACTTTCGAGTGCGAGTGATAAATA-C
* *
721273 ACTTTTGAGTGCGAGTGACAAATGAC
1 ACTTTCGAGTGCGAGTGATAAAT-AC
* * *
721299 ACTTTTGAGTGTGAGTGAAAAAT
1 ACTTTCGAGTGCGAGTGATAAAT
721322 GGCACTATGT
Statistics
Matches: 126, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
25 5 0.04
26 116 0.92
27 5 0.04
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.31
Consensus pattern (25 bp):
ACTTTCGAGTGCGAGTGATAAATAC
Found at i:727557 original size:25 final size:26
Alignment explanation
Indices: 727505--727554 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
727495 AGTTTTATTA
727505 AAGTTTTCTCTTTTATTTTATTTTTC
1 AAGTTTTCTCTTTTATTTTATTTTTC
*
727531 AAGTTTTCAT-TTTTCTTTTATTTT
1 AAGTTTTC-TCTTTTATTTTATTTT
727555 CAATCTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.16, C:0.10, G:0.04, T:0.70
Consensus pattern (26 bp):
AAGTTTTCTCTTTTATTTTATTTTTC
Found at i:735376 original size:23 final size:22
Alignment explanation
Indices: 735344--735426 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 22
735334 TTAGTGCAGA
*
735344 GGGAATCGATACCCCCCTAGAAG
1 GGGAACCGATACCCCCCT-GAAG
* *
735367 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-CTGAAG
* *
735390 GGGAACCGAT-TCCCCCTGTAG
1 GGGAACCGATACCCCCCTGAAG
*
735411 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
735427 TGGAGGTTCT
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 13 0.26
22 8 0.16
23 28 0.56
24 1 0.02
ACGTcount: A:0.24, C:0.33, G:0.27, T:0.17
Consensus pattern (22 bp):
GGGAACCGATACCCCCCTGAAG
Found at i:735414 original size:21 final size:21
Alignment explanation
Indices: 735356--735428 Score: 92
Period size: 21 Copynumber: 3.3 Consensus size: 21
735346 GAATCGATAC
735356 CCCCCTAGAAGGGGAACCGATT
1 CCCCCT-GAAGGGGAACCGATT
735378 CCCCCTTTGAAGGGGAACCGATT
1 CCCCC--TGAAGGGGAACCGATT
* * *
735401 CCCCCTGTAGGGGAATCGATA
1 CCCCCTGAAGGGGAACCGATT
735422 CCCCCTG
1 CCCCCTG
735429 GAGGTTCTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
21 20 0.43
22 5 0.11
23 20 0.43
24 1 0.02
ACGTcount: A:0.22, C:0.34, G:0.26, T:0.18
Consensus pattern (21 bp):
CCCCCTGAAGGGGAACCGATT
Found at i:737335 original size:17 final size:18
Alignment explanation
Indices: 737297--737335 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
737287 TTTTAACATT
*
737297 TTGAATATTTTGGAATGT
1 TTGAATATTTTGGAATGA
*
737315 TTGAAT-TTTTGGATTGA
1 TTGAATATTTTGGAATGA
737332 TTGA
1 TTGA
737336 CTTTGAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (18 bp):
TTGAATATTTTGGAATGA
Found at i:745936 original size:26 final size:26
Alignment explanation
Indices: 745885--745936 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
745875 CAATCTGACA
* *
745885 TGGCAGTTTCTAGAAGGTCCAGTCAG
1 TGGCAGTTTCTAGAAGATCCACTCAG
* *
745911 TGGCGGTTTCTAGAAGATCTACTCAG
1 TGGCAGTTTCTAGAAGATCCACTCAG
745937 CGCGCCTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (26 bp):
TGGCAGTTTCTAGAAGATCCACTCAG
Found at i:746204 original size:25 final size:25
Alignment explanation
Indices: 746141--746205 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
746131 AGTTTTATTA
746141 AAGCTTTCTCTTTTATTTTATTTTTC
1 AAGCTTTCT-TTTTATTTTATTTTTC
* *
746167 AAGTTTTCATTTTATTTTATTTTTC
1 AAGCTTTCTTTTTATTTTATTTTTC
*
746192 AAGCTTTGTTTTTA
1 AAGCTTTCTTTTTA
746206 AATATGCTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 27 0.79
26 7 0.21
ACGTcount: A:0.18, C:0.11, G:0.06, T:0.65
Consensus pattern (25 bp):
AAGCTTTCTTTTTATTTTATTTTTC
Found at i:749630 original size:24 final size:25
Alignment explanation
Indices: 749588--749644 Score: 91
Period size: 24 Copynumber: 2.3 Consensus size: 25
749578 ACCGAAGTGC
749588 TAATACACATAAGGTCGTGCCCACCA
1 TAATACACA-AAGGTCGTGCCCACCA
749614 TAATACAC-AAGGTCGTGCCCACCA
1 TAATACACAAAGGTCGTGCCCACCA
749638 T-ATACAC
1 TAATACAC
749645 TTAGTGGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.19
24 17 0.55
26 8 0.26
ACGTcount: A:0.35, C:0.32, G:0.14, T:0.19
Consensus pattern (25 bp):
TAATACACAAAGGTCGTGCCCACCA
Found at i:752886 original size:22 final size:22
Alignment explanation
Indices: 752859--752901 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
752849 ATTTACAACA
752859 TTGCATCCAAAT-TTTTCAAATC
1 TTGCATCCAAATCTTTT-AAATC
*
752881 TTGCATCTAAATCTTTTAAAT
1 TTGCATCCAAATCTTTTAAAT
752902 TCCAAAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (22 bp):
TTGCATCCAAATCTTTTAAATC
Found at i:756421 original size:41 final size:43
Alignment explanation
Indices: 756343--756457 Score: 114
Period size: 41 Copynumber: 2.7 Consensus size: 43
756333 ATATGTATAT
*
756343 ATATATCTTTTGAAAATAT-ATA-ATA-TATATAACTTTTGAAA
1 ATATAACTTTT-AAAATATAATATATATTATATAACTTTTGAAA
**
756384 A-AT-ACTTTTAAAATATAATATATATTATATAGTTTTTGAAA
1 ATATAACTTTTAAAATATAATATATATTATATAACTTTTGAAA
* *
756425 ATATAGAGTTTTTAAATAGTATATATATATTAT
1 ATATA-ACTTTTAAAATA-TA-ATATATATTAT
756458 TACTATTTTC
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
38 7 0.11
39 8 0.13
40 5 0.08
41 16 0.26
42 2 0.03
44 10 0.16
45 2 0.03
46 11 0.18
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (43 bp):
ATATAACTTTTAAAATATAATATATATTATATAACTTTTGAAA
Found at i:758064 original size:26 final size:25
Alignment explanation
Indices: 758025--758079 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
758015 TTAGCATATT
* *
758025 TAAAAATAAAACTT-AAAAATAAAG
1 TAAAAATAAAACTTGAAAAACAAAA
758049 TAAAAATTGAAAACTTGAAAAACAAAA
1 TAAAAA-T-AAAACTTGAAAAACAAAA
758076 TAAA
1 TAAA
758080 GGGGAGAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 6 0.23
25 1 0.04
26 7 0.27
27 12 0.46
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.20
Consensus pattern (25 bp):
TAAAAATAAAACTTGAAAAACAAAA
Found at i:770094 original size:28 final size:29
Alignment explanation
Indices: 770057--770112 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
770047 TGTTCCAATT
*
770057 ACAATAATTTCAAAAATAAAACAAGATTG
1 ACAATAATTTCAAAAATAAAAAAAGATTG
* *
770086 ACAAT-ATTTTAAAATTAAAAAAAGATT
1 ACAATAATTTCAAAAATAAAAAAAGATT
770113 TTATAATATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.29
Consensus pattern (29 bp):
ACAATAATTTCAAAAATAAAAAAAGATTG
Found at i:770828 original size:29 final size:30
Alignment explanation
Indices: 770791--770867 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 30
770781 AAAATTTATC
* **
770791 TAGTGACTAAAATGTAAGTTTTG-AAAGTT
1 TAGTGACTAAAATATAAACTTTGAAAAGTT
*
770820 TAGTGACTAAAGTATAAACTTTGAAAAGTT
1 TAGTGACTAAAATATAAACTTTGAAAAGTT
* *
770850 TAGGGACCAAAATTATAA
1 TAGTGACTAAAA-TATAA
770868 TTTTTATAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 19 0.49
30 15 0.38
31 5 0.13
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.32
Consensus pattern (30 bp):
TAGTGACTAAAATATAAACTTTGAAAAGTT
Found at i:773406 original size:16 final size:16
Alignment explanation
Indices: 773385--773432 Score: 96
Period size: 16 Copynumber: 3.0 Consensus size: 16
773375 TCTGTTTTAA
773385 TCAAAATTTATACTTT
1 TCAAAATTTATACTTT
773401 TCAAAATTTATACTTT
1 TCAAAATTTATACTTT
773417 TCAAAATTTATACTTT
1 TCAAAATTTATACTTT
773433 AGCCACTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (16 bp):
TCAAAATTTATACTTT
Found at i:781100 original size:35 final size:34
Alignment explanation
Indices: 781015--781101 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
781005 AATATAATAT
*
781015 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
781049 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
781087 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
781102 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:781702 original size:18 final size:18
Alignment explanation
Indices: 781679--781713 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
781669 AGACGACGGG
*
781679 ATCATATATGGCTGCGGC
1 ATCATAAATGGCTGCGGC
781697 ATCATAAATGGCTGCGG
1 ATCATAAATGGCTGCGG
781714 TGGCTGCTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.26
Consensus pattern (18 bp):
ATCATAAATGGCTGCGGC
Found at i:783410 original size:17 final size:18
Alignment explanation
Indices: 783390--783430 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
783380 AAGTTATATT
783390 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
783407 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
783425 ATTAAA
1 AGTAAA
783431 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:789732 original size:45 final size:44
Alignment explanation
Indices: 789675--789885 Score: 242
Period size: 45 Copynumber: 4.7 Consensus size: 44
789665 ACTTTTATAT
* * * * * *
789675 CGATAATCCACCCATCTGCATTTCAACTGTGGTATCCTTTCATGC
1 CGATAATGCACCCATATGCATTT-TATTTTGGCATCCTTTCATGC
789720 CGATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGC
1 CGATAATGCACCCATATGCATT-TTATTTTGGCATCCTTTCATGC
* *
789765 CGATAATGCACCCATATGCAATATTATTTTGGCATCCGTTCATGC
1 CGATAATGCACCCATATGC-ATTTTATTTTGGCATCCTTTCATGC
* * *
789810 CAATAATGCACCCATATCCATTTTTATTTTGGCATCCTTTCATGT
1 CGATAATGCACCCATATGCA-TTTTATTTTGGCATCCTTTCATGC
** **
789855 TAATAATGCACCCATACACATTATTATTTTG
1 CGATAATGCACCCATATGCATT-TTATTTTG
789886 TTCATTCATT
Statistics
Matches: 146, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
44 3 0.02
45 140 0.96
46 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (44 bp):
CGATAATGCACCCATATGCATTTTATTTTGGCATCCTTTCATGC
Found at i:796327 original size:45 final size:45
Alignment explanation
Indices: 796262--796531 Score: 344
Period size: 45 Copynumber: 6.0 Consensus size: 45
796252 TTCAATTATA
* * * * * * *
796262 GCATACTTTTATGCTGATAATGCACCCATATGAATT-TCAACTATG
1 GCATCCTTTCATGCCGATAATGCACCCATATGCATTAT-TATTTTG
* * * * *
796307 GCATCATTTCATGCCAATAATACACTCGTATGCATTATTATTTTG
1 GCATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTTTG
* * *
796352 GCATCCTTTCAAGCCGATAATTCACCTATATGCATTATTATTTTG
1 GCATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTTTG
* *
796397 GCATCCTTTCATGCCGATAATGCACACATATACATTATTATTTTG
1 GCATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTTTG
* *
796442 GCATCCTTTCATGCCGATAACGCACCCATATGCATTGTTATTTTG
1 GCATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTTTG
*
796487 GCATCTTTTCATGCCGATAATGCACCCATATGCATTATTATTTTG
1 GCATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTTTG
796532 TTCATTCATT
Statistics
Matches: 193, Mismatches: 31, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
45 192 0.99
46 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (45 bp):
GCATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTTTG
Found at i:797072 original size:54 final size:54
Alignment explanation
Indices: 796988--797261 Score: 332
Period size: 54 Copynumber: 5.1 Consensus size: 54
796978 ATTACACCTA
* * * *
796988 AGTGCCGATATGAAAATTCACAAACTCATTATGATTTCCATGGATTGCACACAT
1 AGTGCCGATACGATAATTCACAAACTCATTATGAATTCCATGGGTTGCACACAT
* * *
797042 AGTGCCGATACGGTAATTCATAAACACATTATGAATTCCATGGGTTGCACACAT
1 AGTGCCGATACGATAATTCACAAACTCATTATGAATTCCATGGGTTGCACACAT
* * * * * *
797096 AGTACTGATACGATAATTTACAAACTCATTATGAATTCTATGGGTTCCACACAA
1 AGTGCCGATACGATAATTCACAAACTCATTATGAATTCCATGGGTTGCACACAT
* * * ** * *
797150 AGTGTCAATACGATAATTCACAAACTCACTATGAATTCTGTGGGTTCCACACAA
1 AGTGCCGATACGATAATTCACAAACTCATTATGAATTCCATGGGTTGCACACAT
* * * *
797204 AGTGTCGATATGGTAATTCACAAACTCATTATGAATTTCATGGGTTGCACACAT
1 AGTGCCGATACGATAATTCACAAACTCATTATGAATTCCATGGGTTGCACACAT
797258 AGTG
1 AGTG
797262 TTGATAGTAC
Statistics
Matches: 188, Mismatches: 32, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 188 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (54 bp):
AGTGCCGATACGATAATTCACAAACTCATTATGAATTCCATGGGTTGCACACAT
Found at i:797678 original size:20 final size:20
Alignment explanation
Indices: 797647--797700 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
797637 ACTAACTTAT
*
797647 ATCCATAAATCTCCCTATAAC
1 ATCCA-AAATCTCCCTAAAAC
797668 ATCCAAAATCTCCCTAAAAC
1 ATCCAAAATCTCCCTAAAAC
797688 ATCCAAAATCTCC
1 ATCCAAAATCTCC
797701 AAAGAACACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 27 0.84
21 5 0.16
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (20 bp):
ATCCAAAATCTCCCTAAAAC
Found at i:811328 original size:54 final size:54
Alignment explanation
Indices: 811261--811466 Score: 254
Period size: 54 Copynumber: 3.8 Consensus size: 54
811251 TCGATATTGA
* * *
811261 AATTCACGAACTCATTATG-ATTTCCATGGATTGCATACATAGTGTTGATACGGT
1 AATTCACAAACTCATTATGAATTT-CATGGGTTGCACACATAGTGTTGATACGGT
* * * ** *
811315 AATTCAAAAACTCATTATAAATTCCATGGGTTGCACACATAG-GACCGATATGGT
1 AATTCACAAACTCATTATGAATTTCATGGGTTGCACACATAGTG-TTGATACGGT
** * *
811369 AATTCACAAACTCATTATGAATTTTGTGGGTTGCACATATAGTGTTTATACGGT
1 AATTCACAAACTCATTATGAATTTCATGGGTTGCACACATAGTGTTGATACGGT
*
811423 AATTCACAAACTTATTATGAATTTCATGGGTTGCACACATAGTG
1 AATTCACAAACTCATTATGAATTTCATGGGTTGCACACATAGTG
811467 CCGATAGTAC
Statistics
Matches: 126, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
53 1 0.01
54 121 0.96
55 4 0.03
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (54 bp):
AATTCACAAACTCATTATGAATTTCATGGGTTGCACACATAGTGTTGATACGGT
Found at i:811451 original size:108 final size:108
Alignment explanation
Indices: 811246--811472 Score: 296
Period size: 108 Copynumber: 2.1 Consensus size: 108
811236 AATTATACCT
* * * *
811246 TAGTGTCGATATTGAAATTCACGAACTCATTATGATTTCCATGGATTGCATACATAGTGTTGATA
1 TAGTGCCGATATGGAAATTCACAAACTCATTATGATTTCCATGGATTGCACACATAGTGTTGATA
811311 CGGTAATTCAAAAACTCATTATAAATTCCATGGGTTGCACACA
66 CGGTAATTCAAAAACTCATTATAAATTCCATGGGTTGCACACA
* ** * * *
811354 TAG-GACCGATATGGTAATTCACAAACTCATTATGAATTT-TGTGGGTTGCACATATAGTGTTTA
1 TAGTG-CCGATATGGAAATTCACAAACTCATTATG-ATTTCCATGGATTGCACACATAGTGTTGA
* * * *
811417 TACGGTAATTCACAAACTTATTATGAATTTCATGGGTTGCACACA
64 TACGGTAATTCAAAAACTCATTATAAATTCCATGGGTTGCACACA
811462 TAGTGCCGATA
1 TAGTGCCGATA
811473 GTACAGAAGT
Statistics
Matches: 102, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
107 1 0.01
108 96 0.94
109 5 0.05
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (108 bp):
TAGTGCCGATATGGAAATTCACAAACTCATTATGATTTCCATGGATTGCACACATAGTGTTGATA
CGGTAATTCAAAAACTCATTATAAATTCCATGGGTTGCACACA
Found at i:816740 original size:75 final size:75
Alignment explanation
Indices: 816617--816761 Score: 256
Period size: 75 Copynumber: 1.9 Consensus size: 75
816607 GAGGTCCTGG
816617 GTTCGAGCCTCAGGAATATCAGAGATGTCAACGTTAAATGTCAAATAGTTGAGAGCTATCTTTTG
1 GTTCGAGCCTCAGGAATATCAGAGATGTCAACGTTAAATGTCAAATAGTTGAGAGCTATCTTTTG
816682 CCTTGTACTT
66 CCTTGTACTT
* *
816692 GTTCGAGCCTCAGGAATATCAGAGATGTCAGA-GTTCAATGTCAAATAGTTGAGAGTTATCTTTT
1 GTTCGAGCCTCAGGAATATCAGAGATGTCA-ACGTTAAATGTCAAATAGTTGAGAGCTATCTTTT
816756 GCCTTG
65 GCCTTG
816762 AGCTTACCCA
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
75 66 0.99
76 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (75 bp):
GTTCGAGCCTCAGGAATATCAGAGATGTCAACGTTAAATGTCAAATAGTTGAGAGCTATCTTTTG
CCTTGTACTT
Found at i:831773 original size:7 final size:7
Alignment explanation
Indices: 831746--831802 Score: 64
Period size: 7 Copynumber: 8.3 Consensus size: 7
831736 ATGAAAATGA
*
831746 ATAAAAT
1 ATAATAT
*
831753 ATAATAA
1 ATAATAT
831760 ATAATAT
1 ATAATAT
831767 ATAATATT
1 ATAATA-T
*
831775 ATACTAT
1 ATAATAT
831782 ATAATAT
1 ATAATAT
831789 AT-ATAT
1 ATAATAT
831795 AT-ATAT
1 ATAATAT
831801 AT
1 AT
831803 TCAAAAACTA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
6 12 0.27
7 26 0.59
8 6 0.14
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (7 bp):
ATAATAT
Found at i:831783 original size:17 final size:16
Alignment explanation
Indices: 831746--831801 Score: 64
Period size: 15 Copynumber: 3.6 Consensus size: 16
831736 ATGAAAATGA
*
831746 ATAAAATATAATA-A-
1 ATAATATATAATATAT
831760 ATAATATATAATAT-T
1 ATAATATATAATATAT
*
831775 ATACTATATAATATAT
1 ATAATATATAATATAT
831791 ATATATATATA
1 ATA-ATATATA
831802 TTCAAAAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 12 0.34
15 13 0.37
16 4 0.11
17 6 0.17
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAATATATAATATAT
Found at i:831784 original size:2 final size:2
Alignment explanation
Indices: 831751--831802 Score: 51
Period size: 2 Copynumber: 28.0 Consensus size: 2
831741 AATGAATAAA
*
831751 AT AT A- AT AA AT A- AT AT AT A- AT AT -T AT ACT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
831789 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
831803 TCAAAAACTA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
1 5 0.12
2 35 0.83
3 2 0.05
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:831802 original size:10 final size:10
Alignment explanation
Indices: 831751--831802 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 10
831741 AATGAATAAA
*
831751 ATATA-ATAA
1 ATATATATAT
831760 ATA-ATATAT
1 ATATATATAT
831769 A-ATAT-TAT
1 ATATATATAT
831777 ACTATATA-AT
1 A-TATATATAT
831787 ATATATATAT
1 ATATATATAT
831797 ATATAT
1 ATATAT
831803 TCAAAAACTA
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
8 6 0.17
9 15 0.42
10 15 0.42
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (10 bp):
ATATATATAT
Found at i:831851 original size:37 final size:37
Alignment explanation
Indices: 831797--832056 Score: 285
Period size: 37 Copynumber: 6.9 Consensus size: 37
831787 ATATATATAT
* *
831797 ATATATTCAAAAACTATATGTTATATATATATTCAAA
1 ATATTTTCAAAAACTATATATTATATATATATTCAAA
* *
831834 ATATTTTCAAAAGCTATATATTATATATATGTTTTCAAA
1 ATATTTTCAAAAACTATATATTATATATA--TATTCAAA
* *
831873 ATGTTTTCAAAAACTATATATTATATATAT-TTAGAAA
1 ATATTTTCAAAAACTATATATTATATATATATT-CAAA
* *
831910 ATATTTTCAAAAACTATATATTATATATATGTTTTTAAA
1 ATATTTTCAAAAACTATATATTATATATA--TATTCAAA
* *
831949 ATGTTCTT-AAAAACTATATATTATATATATATTAAAA
1 ATATT-TTCAAAAACTATATATTATATATATATTCAAA
* * *
831986 ATATTTTTAAAAATTATATATTATATATATGTTTTCAAA
1 ATATTTTCAAAAACTATATATTATATATA--TATTCAAA
832025 AT-TTTAT-AAAAACTATATATTATATACTATAT
1 ATATTT-TCAAAAACTATATATTATATA-TATAT
832057 ATATATACTA
Statistics
Matches: 193, Mismatches: 18, Indels: 24
0.82 0.08 0.10
Matches are distributed among these distances:
36 4 0.02
37 90 0.47
38 21 0.11
39 74 0.38
40 4 0.02
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (37 bp):
ATATTTTCAAAAACTATATATTATATATATATTCAAA
Found at i:831889 original size:76 final size:75
Alignment explanation
Indices: 831805--832056 Score: 391
Period size: 76 Copynumber: 3.3 Consensus size: 75
831795 ATATATATTC
* * *
831805 AAAAACTATATGTTATATATATATTCAAAATATTTTCAAAAGCTATATATTATATATATGTTTTC
1 AAAAACTATATATTATATATATATTAAAAATATTTTCAAAAACTATATATTATATATATGTTTTC
831870 AAAATGTTTT
66 AAAATGTTTT
831880 CAAAAACTATATATTATATATAT-TTAGAAAATATTTTCAAAAACTATATATTATATATATGTTT
1 -AAAAACTATATATTATATATATATTA-AAAATATTTTCAAAAACTATATATTATATATATGTTT
*
831944 TTAAAATGTTCTT
64 TCAAAATGTT-TT
* *
831957 AAAAACTATATATTATATATATATTAAAAATATTTTTAAAAATTATATATTATATATATGTTTTC
1 AAAAACTATATATTATATATATATTAAAAATATTTTCAAAAACTATATATTATATATATGTTTTC
832022 AAAAT-TTTAT
66 AAAATGTTT-T
832032 AAAAACTATATATTATATACTATAT
1 AAAAACTATATATTATATA-TATAT
832057 ATATATACTA
Statistics
Matches: 164, Mismatches: 7, Indels: 10
0.91 0.04 0.06
Matches are distributed among these distances:
74 1 0.01
75 24 0.15
76 134 0.82
77 5 0.03
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (75 bp):
AAAAACTATATATTATATATATATTAAAAATATTTTCAAAAACTATATATTATATATATGTTTTC
AAAATGTTTT
Found at i:832003 original size:26 final size:27
Alignment explanation
Indices: 831974--832032 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
831964 ATATATTATA
831974 TATATATTAAAAATAT-TTTTAAAAAT
1 TATATATTAAAAATATGTTTTAAAAAT
* * *
832000 TATATATTATATATATGTTTTCAAAAT
1 TATATATTAAAAATATGTTTTAAAAAT
*
832027 TTTATA
1 TATATA
832033 AAAACTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 14 0.50
27 14 0.50
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
TATATATTAAAAATATGTTTTAAAAAT
Found at i:834781 original size:54 final size:54
Alignment explanation
Indices: 834708--835314 Score: 697
Period size: 54 Copynumber: 11.3 Consensus size: 54
834698 TCTTTTGAGG
* * * * *
834708 TGCACACGTAGTG-TCGATACGGTCGTTCATAAACATATTATAAATTCCGCGGGT
1 TGCACACTTAGTGCT-GATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
** * * *
834762 TGCACACTTAGTATTGATACGGTCATTGATCAACATATGATGAATTCTGTGGGT
1 TGCACACTTAGTGCTGATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* * *
834816 TGTACACTTAGTGTCT-ATACTGTCGTTCATCAACATATGATGAATTCTGTGGGT
1 TGCACACTTAGTG-CTGATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* * * *
834870 TGCAAACTTAGTGCCT-ATACGATTGTTCATCAACATATGATGAATTCTGTGGGT
1 TGCACACTTAGTG-CTGATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
** * * **
834924 TGCACACTTAGTGCCAATACAGTCATTCATCAACATATGATGAATTTTGTGGGT
1 TGCACACTTAGTGCTGATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
** * *
834978 TGCACACTTAGTGCCAATATGGTCGTTCATCAATATATGATGAATTCCGTGGGT
1 TGCACACTTAGTGCTGATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* *
835032 TGCACACTTAGTGCCT-ATACGGTTGTTCATCAACATATGATGAATTACGTGGGT
1 TGCACACTTAGTG-CTGATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* * * *
835086 TGCACACTTAGTACCGATACGGTCATTCATCAACATATGATGAATTACGTGGGT
1 TGCACACTTAGTGCTGATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* * *
835140 TGCACACTTAGTGCAT-ATACGATCATTCATCAACATATGATGAATTTC-TGGGT
1 TGCACACTTAGTGC-TGATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* * * * * *
835193 TGCACACTCAGTGCCGATATGGTCGTTCATTAGCATATGATGAATTACGTGGGT
1 TGCACACTTAGTGCTGATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* * *
835247 TGCACACTTAGTGCATG-TACGATCGTTCGTCAACATATGATGAATTCCATGGGT
1 TGCACACTTAGTGC-TGATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
*
835301 TTCACACTTAGTGC
1 TGCACACTTAGTGC
835315 CTATAGTATA
Statistics
Matches: 479, Mismatches: 65, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
53 46 0.10
54 429 0.90
55 4 0.01
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (54 bp):
TGCACACTTAGTGCTGATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
Found at i:837155 original size:18 final size:18
Alignment explanation
Indices: 837129--837177 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
837119 GATGCAATTA
* * *
837129 GTATTGATACTGATGTAG
1 GTATCGATACTGAGGAAG
837147 GTATCGATACTATGAGGAAG
1 GTATCGATAC--TGAGGAAG
837167 GTATCGATACT
1 GTATCGATACT
837178 ATGGATTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.38
20 16 0.62
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.33
Consensus pattern (18 bp):
GTATCGATACTGAGGAAG
Found at i:837697 original size:46 final size:46
Alignment explanation
Indices: 837643--838157 Score: 762
Period size: 46 Copynumber: 11.2 Consensus size: 46
837633 TGCTCTAAAT
837643 GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
1 GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* * * * *
837689 AGTACATTATCGACATTAAAGGATGCCAAAAATGAAAATGCATAAC
1 GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* * * *
837735 GGTGCATTATCGACATGAAATGATGTCATAAATGAAAATGCATAAT
1 GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* *
837781 GGTGCATTATCGGCATGAAAGCATGCCATAAATGAAAAGGCATAAC
1 GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* *
837827 GGTGCATTATCGGCATGAAAGCATGCCATAAATGAAAAGGCATAAC
1 GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* *
837873 GGTACATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAT
1 GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* *
837919 GGTGCATTATCGGCATGAAAGCATGCCATAAATGAAAATACATAAC
1 GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* * *
837965 GGTGGATTATCGGCATGAAAGGATGTCATAAATGAAAATGTATAAC
1 GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* * *
838011 GATGCATTATCGGCATGAAAGGATGCCACAAATGAAAATACATAAC
1 GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* * * *
838057 GGTGGATTATGGGCAAT-AAAGGATGCCACAAATGAAAATGCATAAA
1 GGTGCATTATCGGC-ATGAAAGGATGCCATAAATGAAAATGCATAAC
*
838103 GGTGCATTATCGGCATGAAAGGATGCCACAAATGAAAATGCATAAC
1 GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
838149 GGTGCATTA
1 GGTGCATTA
838158 ACGACTTTTT
Statistics
Matches: 422, Mismatches: 45, Indels: 4
0.90 0.10 0.01
Matches are distributed among these distances:
45 2 0.00
46 418 0.99
47 2 0.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (46 bp):
GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
Found at i:840777 original size:12 final size:12
Alignment explanation
Indices: 840746--840780 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
840736 ATTTTATATA
*
840746 TATCTTAAACAC
1 TATCTTATACAC
840758 TATCTTATACAC
1 TATCTTATACAC
840770 TATCTTATACA
1 TATCTTATACA
840781 AGATTTCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (12 bp):
TATCTTATACAC
Found at i:840866 original size:21 final size:20
Alignment explanation
Indices: 840842--840937 Score: 71
Period size: 23 Copynumber: 4.9 Consensus size: 20
840832 TCTTGAACCT
840842 TATTTAAAAATATATGTTATA
1 TATTTAAAAATATA-GTTATA
840863 TATTTAAAAATATAGTTA-A
1 TATTTAAAAATATAGTTATA
* * *
840882 -A---ACAAGATTTA--AATA
1 TATTTA-AAAATATAGTTATA
840897 TATTTAAAAATATATGTTATATA
1 TATTTAAAAATATA-G-T-TATA
840920 TATTTAAAAATATAGTTA
1 TATTTAAAAATATAGTTA
840938 AAATAAAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 23
0.67 0.07 0.26
Matches are distributed among these distances:
14 1 0.02
15 2 0.03
16 7 0.12
18 7 0.12
19 2 0.03
20 6 0.10
21 15 0.26
22 1 0.02
23 17 0.29
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.43
Consensus pattern (20 bp):
TATTTAAAAATATAGTTATA
Found at i:840881 original size:12 final size:12
Alignment explanation
Indices: 840860--840940 Score: 55
Period size: 12 Copynumber: 7.0 Consensus size: 12
840850 AATATATGTT
*
840860 ATATATTTAAAA
1 ATATAGTTAAAA
840872 ATATAGTT-AAA
1 ATATAGTTAAAA
* *
840883 ACA-AGATT-TAA
1 ATATAG-TTAAAA
*
840894 ATATATTTAAAA
1 ATATAGTTAAAA
*
840906 ATATATGTT--AT
1 ATATA-GTTAAAA
*
840917 ATATATTTAAAA
1 ATATAGTTAAAA
840929 ATATAGTTAAAA
1 ATATAGTTAAAA
840941 TAAAAATAAA
Statistics
Matches: 52, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
10 4 0.08
11 19 0.37
12 27 0.52
13 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (12 bp):
ATATAGTTAAAA
Done.