Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007173.1 Hibiscus syriacus cultivar Beakdansim tig00018827_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: 1357898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:394520 original size:36 final size:37
Alignment explanation
Indices: 394438--394520 Score: 114
Period size: 37 Copynumber: 2.3 Consensus size: 37
394428 TGTTTATGTC
* * * **
394438 TCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTT
1 TCAAGGGAAACTATCTCAAGAGAGACAAAATTTCATT
394475 TCAAGGGAAACTATCTCAAGAGAGACAAAA-TTCATT
1 TCAAGGGAAACTATCTCAAGAGAGACAAAATTTCATT
394511 TCAAGGGAAA
1 TCAAGGGAAA
394521 TGTTTTCAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
36 14 0.34
37 27 0.66
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.23
Consensus pattern (37 bp):
TCAAGGGAAACTATCTCAAGAGAGACAAAATTTCATT
Found at i:396118 original size:183 final size:183
Alignment explanation
Indices: 395810--396159 Score: 610
Period size: 183 Copynumber: 1.9 Consensus size: 183
395800 TGTTTAACTA
* * **
395810 AAGGGTTCATCTCATCGCAAAGTCTTTGGCCTGACAAAAGCAGTGGATCAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGAAAAAAGCAGTGGAGAAAACACCGAATTGCCA
* **
395875 AGTGTCCGAGCAATGTCATGGTTTGAATGTAATATATTCATAAAGCCAGGGCTTTCGAGTTTCCT
66 AGTGTCCGAGCAATGTCATAGTTTGAACATAATATATTCATAAAGCCAGGGCTTTCGAGTTTCCT
395940 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
*
395993 AAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGAAAAAAGCAGTGGAGAAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGAAAAAAGCAGTGGAGAAAACACCGAATTGCCA
* *
396058 AGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
66 AGTGTCCGAGCAATGTCATAGTTTGAACATAATATATTCATAAAGCCAGGGCTTTCGAGTTTCCT
396123 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
396160 CGGATTTAAT
Statistics
Matches: 157, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
183 157 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (183 bp):
AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGAAAAAAGCAGTGGAGAAAACACCGAATTGCCA
AGTGTCCGAGCAATGTCATAGTTTGAACATAATATATTCATAAAGCCAGGGCTTTCGAGTTTCCT
CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
Found at i:400195 original size:2 final size:2
Alignment explanation
Indices: 400185--400234 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
400175 AAAAGGAAAA
400185 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
400226 AT AT AT AT A
1 AT AT AT AT A
400235 ATAAAGTATA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:400363 original size:3 final size:3
Alignment explanation
Indices: 400357--400511 Score: 58
Period size: 3 Copynumber: 50.3 Consensus size: 3
400347 GGTTTAAAAA
*
400357 AAT AAT AAT AAT AAT AAT AAAT AA- AAA AAT AAT AAAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT -AAT AAT -AAT AAT
* * * * *
400404 AA- AGAT AAT ATAT ATGT AAAT AAA AAA AAT AAT AAAT AAA AAT ATT
1 AAT A-AT AAT A-AT A-AT -AAT AAT AAT AAT AAT -AAT AAT AAT AAT
400450 AA- AAT -AT AA- AA- AAT -AT ATAT AAAT AA- AAT AATT AA- AAT ATAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AA-T AAT AAT A-AT
* *
400492 GAT AGAT AAT AAT TAT AAT A
1 AAT A-AT AAT AAT AAT AAT A
400512 TAAAAGTATA
Statistics
Matches: 119, Mismatches: 13, Indels: 40
0.69 0.08 0.23
Matches are distributed among these distances:
2 17 0.14
3 69 0.58
4 31 0.26
5 2 0.02
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:400366 original size:29 final size:27
Alignment explanation
Indices: 400351--400406 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 27
400341 ATAATAGGTT
400351 TAAAAAAATAATAATAATAATAATAAA
1 TAAAAAAATAATAATAATAATAATAAA
400378 TAAAAAAATAATAAATAATAAATAATAAA
1 TAAAAAAATAAT-AATAAT-AATAATAAA
400407 GATAATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 12 0.44
28 6 0.22
29 9 0.33
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (27 bp):
TAAAAAAATAATAATAATAATAATAAA
Found at i:400412 original size:47 final size:47
Alignment explanation
Indices: 400361--400511 Score: 133
Period size: 45 Copynumber: 3.3 Consensus size: 47
400351 TAAAAAAATA
400361 ATAATAATAATAATAAATAAAAAAATAATAAATAATAAATAATAAAG
1 ATAATAATAATAATAAATAAAAAAATAATAAATAATAAATAATAAAG
* *
400408 ATAAT-AT-ATATGTAAATAAAAAAAATAATAAATAA-AAATATTAAA-
1 ATAATAATAATA-ATAAAT-AAAAAAATAATAAATAATAAATAATAAAG
* * *
400453 AT-ATAA-AA-AATATATATAAATAAAATAATTAA-AATATATGAT--AG
1 ATAATAATAATAATA-A-ATAAA-AAAATAATAAATAATAAATAATAAAG
*
400497 ATAATAATTATAATA
1 ATAATAATAATAATA
400512 TAAAAGTATA
Statistics
Matches: 84, Mismatches: 8, Indels: 24
0.72 0.07 0.21
Matches are distributed among these distances:
43 3 0.04
44 11 0.13
45 27 0.32
46 17 0.20
47 26 0.31
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (47 bp):
ATAATAATAATAATAAATAAAAAAATAATAAATAATAAATAATAAAG
Found at i:400462 original size:33 final size:33
Alignment explanation
Indices: 400423--400490 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
400413 ATATATGTAA
400423 ATAAAAAAAATA-ATAAATAAAA-ATATTAAAAT
1 ATAAAAAAAATATATAAATAAAATA-ATTAAAAT
*
400455 ATAAAAAATATATATAAATAAAATAATTAAAAT
1 ATAAAAAAAATATATAAATAAAATAATTAAAAT
400488 ATA
1 ATA
400491 TGATAGATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 11 0.33
33 21 0.64
34 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (33 bp):
ATAAAAAAAATATATAAATAAAATAATTAAAAT
Found at i:400506 original size:23 final size:23
Alignment explanation
Indices: 400459--400513 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
400449 TAAAATATAA
400459 AAAATATATATAAATAAAATAATT
1 AAAATATATATAAAT-AAATAATT
*
400483 AAAATATATGATAGAT-AATAATT
1 AAAATATAT-ATAAATAAATAATT
*
400506 ATAATATA
1 AAAATATA
400514 AAAGTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 14 0.50
24 9 0.32
25 5 0.18
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (23 bp):
AAAATATATATAAATAAATAATT
Found at i:400545 original size:2 final size:2
Alignment explanation
Indices: 400540--400627 Score: 58
Period size: 2 Copynumber: 44.5 Consensus size: 2
400530 TATGAAGAAA
*
400540 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AGT AT AT A- AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T
* * * * * *
400583 AA AA AT AA AT GA- AA AT A- AT TT A- AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
400623 AT AT A
1 AT AT A
400628 ATAATAATAA
Statistics
Matches: 68, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
1 4 0.06
2 60 0.88
3 4 0.06
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (2 bp):
AT
Found at i:400646 original size:18 final size:17
Alignment explanation
Indices: 400625--400667 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
400615 ATATATACAT
400625 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
400643 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
400660 ATAA-AATA
1 ATAATAATA
400668 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:400651 original size:65 final size:65
Alignment explanation
Indices: 400539--400660 Score: 169
Period size: 65 Copynumber: 1.9 Consensus size: 65
400529 ATATGAAGAA
* * *
400539 AATATATATATATATATATATATATATAAAGTATATAATATAGTAAAAATAAATGAAAATAATTT
1 AATATATATATATATATACATATATATAAAATACATAATATAGTAAAAATAAATGAAAATAATTT
400604 AATATATATATATATATACATATA-ATAATAATAACATGAATA-A-TAAAAATAAATGAA
1 AATATATATATATATATACATATATATAA-AAT-ACAT-AATATAGTAAAAATAAATGAA
400661 TAAAATATCC
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
64 4 0.08
65 39 0.76
66 4 0.08
67 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (65 bp):
AATATATATATATATATACATATATATAAAATACATAATATAGTAAAAATAAATGAAAATAATTT
Found at i:401124 original size:34 final size:34
Alignment explanation
Indices: 401081--401149 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
401071 GAATCCTAGC
401081 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
* *
401115 AAAATTCTATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
401149 A
1 A
401150 GTAGGACGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:409442 original size:18 final size:18
Alignment explanation
Indices: 409419--409459 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
409409 CCTCTGTGCT
409419 CAATGTTACGGTCAATGC
1 CAATGTTACGGTCAATGC
409437 CAATGTTACGGTCAATGC
1 CAATGTTACGGTCAATGC
409455 CAATG
1 CAATG
409460 AAGCAAGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (18 bp):
CAATGTTACGGTCAATGC
Found at i:410476 original size:53 final size:53
Alignment explanation
Indices: 410318--410523 Score: 235
Period size: 53 Copynumber: 4.0 Consensus size: 53
410308 AGATACTAAA
* * *
410318 ATATTGAGAGATGTACATACTTACACCGGTGTAAGTATGTGTTAATTGCTAAG
1 ATATTGAGAGATGTACATACTTACACCAGTATAAGTATGTGTTAATTGTTAAG
* * ** *
410371 ATATT--GAGA--TATATACATACACTTGTGA-AAGTATGTGTTAA-TGTCTAGG
1 ATATTGAGAGATGTACATACTTACACCAGT-ATAAGTATGTGTTAATTGT-TAAG
* *
410420 ATATTGAGAGATGCACATACTTGCACCAGTATAAGTATGTGTTAATTGTTAAG
1 ATATTGAGAGATGTACATACTTACACCAGTATAAGTATGTGTTAATTGTTAAG
* * *
410473 ATATTAAGAGATGTACAAACTTACACCAATATAAGTATGTGTTAATTGTTA
1 ATATTGAGAGATGTACATACTTACACCAGTATAAGTATGTGTTAATTGTTA
410524 GACTTTTTTA
Statistics
Matches: 126, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
48 2 0.02
49 34 0.27
51 8 0.06
52 1 0.01
53 78 0.62
54 3 0.02
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (53 bp):
ATATTGAGAGATGTACATACTTACACCAGTATAAGTATGTGTTAATTGTTAAG
Found at i:411532 original size:27 final size:28
Alignment explanation
Indices: 411485--411541 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
411475 ATAAAAATAT
* *
411485 AATTATTGAAAACAATATTTA-ATTTTA
1 AATTATTAAAAACAATATTTATATATTA
*
411512 AATTATTAAAAATAGAT-TTTATATATTA
1 AATTATTAAAAACA-ATATTTATATATTA
411540 AA
1 AA
411542 ATATAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (28 bp):
AATTATTAAAAACAATATTTATATATTA
Found at i:412676 original size:30 final size:30
Alignment explanation
Indices: 412640--412703 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 30
412630 ATTTAGTTGG
*
412640 GCGGGCGGATGTGGGGT-GGGTGGATGCGGT
1 GCGGGCGGATG-AGGGTCGGGTGGATGCGGT
412670 GCGGGCGGATGAGGGTCGGGTGGATGCGGT
1 GCGGGCGGATGAGGGTCGGGTGGATGCGGT
412700 GCGG
1 GCGG
412704 ATGCGGGGCG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.08, C:0.12, G:0.62, T:0.17
Consensus pattern (30 bp):
GCGGGCGGATGAGGGTCGGGTGGATGCGGT
Found at i:412679 original size:15 final size:15
Alignment explanation
Indices: 412640--412703 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
412630 ATTTAGTTGG
* *
412640 GCGGGCGGATGTGGG
1 GCGGGCGGATGCGGT
* *
412655 GTGGGTGGATGCGGT
1 GCGGGCGGATGCGGT
*
412670 GCGGGCGGATGAGG-
1 GCGGGCGGATGCGGT
*
412684 GTCGGGTGGATGCGGT
1 G-CGGGCGGATGCGGT
412700 GCGG
1 GCGG
412704 ATGCGGGGCG
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
14 1 0.03
15 36 0.95
16 1 0.03
ACGTcount: A:0.08, C:0.12, G:0.62, T:0.17
Consensus pattern (15 bp):
GCGGGCGGATGCGGT
Found at i:412715 original size:26 final size:26
Alignment explanation
Indices: 412640--412716 Score: 75
Period size: 30 Copynumber: 2.8 Consensus size: 26
412630 ATTTAGTTGG
* *
412640 GCGG-GCGGATGTGGGGTGGGTGGAT
1 GCGGTGCGGATGAGGGGCGGGTGGAT
*
412665 GCGGTGCGGGCGGATGAGGGTCGGGTGGAT
1 GCGGT----GCGGATGAGGGGCGGGTGGAT
*
412695 GCGGTGCGGATGCGGGGCGGGT
1 GCGGTGCGGATGAGGGGCGGGT
412717 AAGGTCTCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
25 4 0.10
26 15 0.36
30 23 0.55
ACGTcount: A:0.08, C:0.13, G:0.62, T:0.17
Consensus pattern (26 bp):
GCGGTGCGGATGAGGGGCGGGTGGAT
Found at i:418635 original size:7 final size:7
Alignment explanation
Indices: 418625--418670 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
418615 AAATAACAAA
418625 TTAGTGG
1 TTAGTGG
418632 TTAGTGG
1 TTAGTGG
418639 TTAGTGG
1 TTAGTGG
* *
418646 TTGGAGG
1 TTAGTGG
*
418653 TTAGAGG
1 TTAGTGG
418660 TTAGTGG
1 TTAGTGG
418667 TTAG
1 TTAG
418671 ATGTTAATAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.39
Consensus pattern (7 bp):
TTAGTGG
Found at i:418671 original size:14 final size:14
Alignment explanation
Indices: 418625--418676 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
418615 AAATAACAAA
*
418625 TTAGTGGTTAGTGG
1 TTAGAGGTTAGTGG
* * *
418639 TTAGTGGTTGGAGG
1 TTAGAGGTTAGTGG
418653 TTAGAGGTTAGTGG
1 TTAGAGGTTAGTGG
*
418667 TTAGATGTTA
1 TTAGAGGTTA
418677 ATAGAGTCTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.19, C:0.00, G:0.40, T:0.40
Consensus pattern (14 bp):
TTAGAGGTTAGTGG
Found at i:418676 original size:21 final size:21
Alignment explanation
Indices: 418625--418676 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
418615 AAATAACAAA
* *
418625 TTAGTGGTTAGTGGTTAGTGG
1 TTAGAGGTTAGAGGTTAGTGG
*
418646 TTGGAGGTTAGAGGTTAGTGG
1 TTAGAGGTTAGAGGTTAGTGG
*
418667 TTAGATGTTA
1 TTAGAGGTTA
418677 ATAGAGTCTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.40, T:0.40
Consensus pattern (21 bp):
TTAGAGGTTAGAGGTTAGTGG
Found at i:420915 original size:39 final size:38
Alignment explanation
Indices: 420855--420998 Score: 129
Period size: 39 Copynumber: 3.8 Consensus size: 38
420845 TAGCGTTCTT
*
420855 AAGAAAATAAATTCAATGATTTATTTCCTTTTACGAAAC
1 AAGAAAATAAATTCAACGATTTATTTCCTTTTAC-AAAC
* * *
420894 AAGAAAATAAATCCAACGA-TT-TTT--TTATA-AACC
1 AAGAAAATAAATTCAACGATTTATTTCCTTTTACAAAC
* * * *
420927 AGGAAAATAAATTCAATGATTTATTTTCTTTTTCAAA-
1 AAGAAAATAAATTCAACGATTTATTTCCTTTTACAAAC
*
420964 ATAGGAAAATAAAATTCAACGATTTATTTCTTTTT
1 A-A-GAAAAT-AAATTCAACGATTTATTTCCTTTT
420999 TTAAAAAATA
Statistics
Matches: 83, Mismatches: 14, Indels: 15
0.74 0.12 0.13
Matches are distributed among these distances:
33 19 0.23
34 2 0.02
35 7 0.08
37 7 0.08
38 4 0.05
39 23 0.28
40 21 0.25
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (38 bp):
AAGAAAATAAATTCAACGATTTATTTCCTTTTACAAAC
Found at i:420959 original size:40 final size:39
Alignment explanation
Indices: 420915--421003 Score: 110
Period size: 40 Copynumber: 2.3 Consensus size: 39
420905 TCCAACGATT
*
420915 TTTTTATAAACCAGGAAAAT-AAATTCAATGATTTATTTTC
1 TTTTTATAAA-CAGGAAAATAAAATTCAACGATTTA-TTTC
*
420955 TTTTTCA-AAATAGGAAAATAAAATTCAACGATTTATTTC
1 TTTTT-ATAAACAGGAAAATAAAATTCAACGATTTATTTC
*
420994 TTTTTTTAAA
1 TTTTTATAAA
421004 AAATAGAATC
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
39 20 0.47
40 22 0.51
41 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (39 bp):
TTTTTATAAACAGGAAAATAAAATTCAACGATTTATTTC
Found at i:421082 original size:60 final size:61
Alignment explanation
Indices: 420968--421083 Score: 141
Period size: 60 Copynumber: 1.9 Consensus size: 61
420958 TTCAAAATAG
* * *
420968 GAAAATAAAATTCAACGATTTATTTCTTTTTTTAAAAAATAGAATCATATAAGATTCTTAA
1 GAAAATAAAATTCAACAATTTATTTATTTTTATAAAAAATAGAATCATATAAGATTCTTAA
*
421029 GAAAAT-AAATTCAATAATTTATTTATTTTTAAATAAGAAAATA-AATCA-A-AAGATT
1 GAAAATAAAATTCAACAATTTATTTATTTTT--ATAA-AAAATAGAATCATATAAGATT
421084 TATTTCCTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
60 27 0.56
61 7 0.15
62 8 0.17
63 6 0.12
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (61 bp):
GAAAATAAAATTCAACAATTTATTTATTTTTATAAAAAATAGAATCATATAAGATTCTTAA
Found at i:421106 original size:136 final size:133
Alignment explanation
Indices: 420929--421175 Score: 286
Period size: 133 Copynumber: 1.8 Consensus size: 133
420919 TATAAACCAG
* * ** * *
420929 GAAAATAAATTCAATGATTTATTTTCTTTTTCAAAATAGGAAAATAAAAT-TCAACGATTTATTT
1 GAAAATAAATTCAAAGATTTATTTCCTTTCACAAAACAGGAAAAT-AAATCT-AACGACTTATTT
* *
420993 -CTTTTTTTAAAAAATAGAATCATATAA-GATTCTTAAGAAAATAAATTCAATAATTTATTTATT
64 AC---CTTTAAAAAATAGAATCAT-TAATGATTCATAAGAAAATAAATTCAATAATTTATTTATT
421056 TTTAAATAA
125 TTTAAATAA
* * *
421065 GAAAATAAA-TCAAAAGATTTATTTCCTTTCACAAACCAGGAAAATGAATCTGACGACTTATTTA
1 GAAAATAAATTC-AAAGATTTATTTCCTTTCACAAAACAGGAAAATAAATCTAACGACTTATTTA
* *
421129 CCTTTAAAAGATATAATCATTAATGATTCATAAGAAAATAAATTCAA
65 CCTTTAAAAAATAGAATCATTAATGATTCATAAGAAAATAAATTCAA
421176 AAATAAATTT
Statistics
Matches: 94, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
132 3 0.03
133 38 0.40
135 15 0.16
136 38 0.40
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (133 bp):
GAAAATAAATTCAAAGATTTATTTCCTTTCACAAAACAGGAAAATAAATCTAACGACTTATTTAC
CTTTAAAAAATAGAATCATTAATGATTCATAAGAAAATAAATTCAATAATTTATTTATTTTTAAA
TAA
Found at i:421319 original size:59 final size:59
Alignment explanation
Indices: 421195--421394 Score: 262
Period size: 60 Copynumber: 3.4 Consensus size: 59
421185 TCTTTATATT
* * * * *
421195 CAAGATTCCCGAGAAATTAAATTTAAC-ATTTTATTTC-TTTTAACAAAG-TAGAATCATT
1 CAAGATTCTCAAGAAAATAAATTTAACAATTTT-TTTCTTTTTAA-AAAGATATAATCATC
* *
421253 TAAGATTCTCAAGAAAATAAATTTAACAATTTTTTTCTTTTTAAAAAGATATAATCACC
1 CAAGATTCTCAAGAAAATAAATTTAACAATTTTTTTCTTTTTAAAAAGATATAATCATC
* *
421312 CACGATTCTCAAGAAAATAAATTTAATAATTTTTTTTCTTTTTAAAAAGATATAATCATC
1 CAAGATTCTCAAGAAAATAAATTTAACAA-TTTTTTTCTTTTTAAAAAGATATAATCATC
*
421372 CATGATTCTCAAGAAAATAAATT
1 CAAGATTCTCAAGAAAATAAATT
421395 CTACAAATTT
Statistics
Matches: 126, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
58 31 0.25
59 44 0.35
60 51 0.40
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (59 bp):
CAAGATTCTCAAGAAAATAAATTTAACAATTTTTTTCTTTTTAAAAAGATATAATCATC
Found at i:421452 original size:59 final size:58
Alignment explanation
Indices: 421192--421600 Score: 346
Period size: 58 Copynumber: 7.0 Consensus size: 58
421182 ATTTCTTTAT
* * * * *
421192 ATTCAAGATTCCCGAGAAATTAAATTTAAC-ATTT-TATTTCTTTTAACAAAG-TAGAATC
1 ATTCAAGATTCTCAAGAAAATAAATTCAACTATTTAT-TTTC-CTT-ACAAAGTTAGAATC
* * * * * * *
421250 ATTTAAGATTCTCAAGAAAATAAATTTAACAATTT-TTTTCTTTTTAAAAAGATATAATC
1 ATTCAAGATTCTCAAGAAAATAAATTCAACTATTTATTTTC--CTTACAAAGTTAGAATC
** * * * * * * *
421309 ACCCACGATTCTCAAGAAAATAAATTTAA-TAATTTTTTTTCTTTTTAAAAAGATATAATC
1 ATTCAAGATTCTCAAGAAAATAAATTCAACT-ATTTATTTTC--CTTACAAAGTTAGAATC
* * * * * * *
421369 ATCCATGATTCTCAAGAAAATAAATTCTACAAATTTATTTTCCTTGCGATGTTAGAATC
1 ATTCAAGATTCTCAAGAAAATAAATTCAAC-TATTTATTTTCCTTACAAAGTTAGAATC
* * *
421428 ATTCAAGATTTTCAAGAAAATAAATTCAACTATTTATTTTCATTACAAAGTTAGAATA
1 ATTCAAGATTCTCAAGAAAATAAATTCAACTATTTATTTTCCTTACAAAGTTAGAATC
* * * *
421486 ATTTAAGATTCTCAAGGAAATAAATTCAATTATTTATTTTCCTTACAAAGCTAGAATC
1 ATTCAAGATTCTCAAGAAAATAAATTCAACTATTTATTTTCCTTACAAAGTTAGAATC
*
421544 ATTTAAGATTCTCAA-AGAAATAAATTCAACTATTTATTTTCCTTA-AGAAGTTAGAAT
1 ATTCAAGATTCTCAAGA-AAATAAATTCAACTATTTATTTTCCTTACA-AAGTTAGAAT
421601 AAATGCAACA
Statistics
Matches: 298, Mismatches: 44, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
57 1 0.00
58 159 0.53
59 80 0.27
60 49 0.16
61 9 0.03
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (58 bp):
ATTCAAGATTCTCAAGAAAATAAATTCAACTATTTATTTTCCTTACAAAGTTAGAATC
Found at i:421875 original size:45 final size:45
Alignment explanation
Indices: 421763--421879 Score: 137
Period size: 45 Copynumber: 2.6 Consensus size: 45
421753 AAATTAATCC
* * * * *
421763 TTTAATTTTCGCAACTCAAAAATC-ACAAAGAACTAATCCTTTGAT
1 TTTAATTTTCACAACCCAATAATCGA-AAGGAACTAATCATTTGAT
** *
421808 TTTAATTTTCGTAATCCAATAATCGAAAGGAACTAATCATTTGAT
1 TTTAATTTTCACAACCCAATAATCGAAAGGAACTAATCATTTGAT
*
421853 TTTAATTTTCACAACCCGATAATCGAA
1 TTTAATTTTCACAACCCAATAATCGAA
421880 GCCGTGGATT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
45 60 0.98
46 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (45 bp):
TTTAATTTTCACAACCCAATAATCGAAAGGAACTAATCATTTGAT
Found at i:423402 original size:23 final size:26
Alignment explanation
Indices: 423375--423441 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 26
423365 TTTATTTTTC
423375 ATTATTTTATT-TATTATTGTA-A-T
1 ATTATTTTATTATATTATTGTATACT
* *
423398 ATTATTTTATTATTTTATTTTATACT
1 ATTATTTTATTATATTATTGTATACT
423424 ATTATTATTATTAATATT
1 ATTATT-TTATT-ATATT
423442 TTCATTATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 11 0.31
24 8 0.22
25 1 0.03
26 7 0.19
27 5 0.14
28 4 0.11
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (26 bp):
ATTATTTTATTATATTATTGTATACT
Found at i:423403 original size:3 final size:3
Alignment explanation
Indices: 423375--423453 Score: 55
Period size: 3 Copynumber: 28.0 Consensus size: 3
423365 TTTATTTTTC
* *
423375 ATT ATT -TT ATTT ATT ATT -GT AAT ATT ATT -TT ATT ATT -TT ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
423417 -TT A-T ACT ATT ATT ATT ATT AAT ATT -TT CATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
423454 TGTTTGTAGG
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
2 13 0.21
3 43 0.70
4 5 0.08
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:423420 original size:18 final size:19
Alignment explanation
Indices: 423365--423453 Score: 74
Period size: 19 Copynumber: 4.6 Consensus size: 19
423355 TTTGGCCGAG
*
423365 TTTATTTTTCATTATTTTA-
1 TTTATTATT-ATTATTTTAT
* * *
423384 TTTATTATTGTAATATTAT
1 TTTATTATTATTATTTTAT
423403 TTTATTATT-TTATTTTAT
1 TTTATTATTATTATTTTAT
** *
423421 ACTATTATTATTATTAATAT
1 TTTATTATTATTATT-TTAT
423441 TTTCATTATTATT
1 TTT-ATTATTATT
423454 TGTTTGTAGG
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
18 20 0.36
19 22 0.40
20 4 0.07
21 9 0.16
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (19 bp):
TTTATTATTATTATTTTAT
Found at i:425102 original size:10 final size:9
Alignment explanation
Indices: 425084--425133 Score: 55
Period size: 10 Copynumber: 5.2 Consensus size: 9
425074 TTTATTATTG
*
425084 TTTAGTTAT
1 TTTATTTAT
425093 TTTATTTTAT
1 TTTA-TTTAT
425103 TTTATTTAT
1 TTTATTTAT
*
425112 TTCTGTTTAGT
1 TT-TATTTA-T
425123 TTTATTTAT
1 TTTATTTAT
425132 TT
1 TT
425134 GTCATGGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 14 0.40
10 18 0.51
11 3 0.09
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.74
Consensus pattern (9 bp):
TTTATTTAT
Found at i:425108 original size:33 final size:34
Alignment explanation
Indices: 425070--425133 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
425060 TATGTATATA
425070 TTTATTTATTAT-TGTTTAGTTAT-TTTATTTTAT
1 TTTATTTATT-TCTGTTTAGTTATATTTATTTTAT
*
425103 TTTATTTATTTCTGTTTAGTTTTATTTATTT
1 TTTATTTATTTCTGTTTAGTTATATTTATTT
425134 GTCATGGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 1 0.04
33 20 0.71
34 7 0.25
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (34 bp):
TTTATTTATTTCTGTTTAGTTATATTTATTTTAT
Found at i:429412 original size:44 final size:43
Alignment explanation
Indices: 429323--429439 Score: 114
Period size: 44 Copynumber: 2.7 Consensus size: 43
429313 ATAGAATTTG
* * * *
429323 TCCTGAAAGACCACATATATGTCCCAAAGGACCACATAGAAATC
1 TCCT-AAAGACCACATATATATTCCAAAGGACAAAATAGAAATC
*
429367 TCCTTAAAGACCACATATATATTCCAAAGGACAAAATATG-TATC
1 TCC-TAAAGACCACATATATATTCCAAAGGACAAAATA-GAAATC
* *
429411 T-C-AAATAACCGCATATATATTCCAAAGGA
1 TCCTAAA-GACCACATATATATTCCAAAGGA
429440 TTACATATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
41 3 0.05
42 21 0.33
43 1 0.02
44 36 0.57
45 2 0.03
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.23
Consensus pattern (43 bp):
TCCTAAAGACCACATATATATTCCAAAGGACAAAATAGAAATC
Found at i:431576 original size:21 final size:21
Alignment explanation
Indices: 431512--431576 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
431502 TAGAATCTAC
* * *
431512 TGTGGTGGTATCTGATATGGA
1 TGTGGAGGCATCTGAAATGGA
* * *
431533 GGTGGTGGCATTTGAAA-GAGA
1 TGTGGAGGCATCTGAAATG-GA
*
431554 TGTGGAGTCATCTGAAATGGA
1 TGTGGAGGCATCTGAAATGGA
431575 TG
1 TG
431577 CATCCTCATC
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.06, G:0.38, T:0.31
Consensus pattern (21 bp):
TGTGGAGGCATCTGAAATGGA
Found at i:435418 original size:16 final size:15
Alignment explanation
Indices: 435397--435439 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
435387 CTATTTTTTC
435397 TTTTTCTTTTTTAAT
1 TTTTTCTTTTTTAAT
*
435412 ATTTTTCTTTAATTTTAT
1 -TTTTTCTTT--TTTAAT
435430 TTTTTCTTTT
1 TTTTTCTTTT
435440 AATAAATTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 1 0.04
16 9 0.38
17 9 0.38
18 5 0.21
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTCTTTTTTAAT
Found at i:436178 original size:19 final size:19
Alignment explanation
Indices: 436150--436218 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
436140 TATTGTTTCA
*
436150 TTTATTTTTTTAGTATTAG
1 TTTATATTTTTAGTATTAG
* * *
436169 TTTATATTTTAATTTTTA-
1 TTTATATTTTTAGTATTAG
*
436187 TATTAT-TTTTTAGTAATAG
1 T-TTATATTTTTAGTATTAG
436206 TTTATATTATTTA
1 TTTATATT-TTTA
436219 TTTAATTTGT
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
18 13 0.34
19 21 0.55
20 4 0.11
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (19 bp):
TTTATATTTTTAGTATTAG
Found at i:436235 original size:20 final size:20
Alignment explanation
Indices: 436212--436253 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
436202 ATAGTTTATA
*
436212 TTATTTATTTAATTTGTATT
1 TTATTTATTTAATTTATATT
436232 TTATTTATTTAATTTATATT
1 TTATTTATTTAATTTATATT
436252 TT
1 TT
436254 TACACTGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
TTATTTATTTAATTTATATT
Found at i:437006 original size:17 final size:17
Alignment explanation
Indices: 436962--437057 Score: 111
Period size: 17 Copynumber: 5.5 Consensus size: 17
436952 ATTTGATATT
*
436962 TGTAATTATCTAATAAC
1 TGTAAATATCTAATAAC
436979 TGTAAAAATATCTAATAAC
1 TGT--AAATATCTAATAAC
* *
436998 TGTAAATATCTGATAAT
1 TGTAAATATCTAATAAC
**
437015 TAAAAATCATCTAATAAC
1 TGTAAAT-ATCTAATAAC
*
437033 TGTAAATATCTTATAAC
1 TGTAAATATCTAATAAC
437050 TGTAAATA
1 TGTAAATA
437058 CCATAGTTGG
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
17 37 0.56
18 13 0.20
19 16 0.24
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.36
Consensus pattern (17 bp):
TGTAAATATCTAATAAC
Found at i:437032 original size:35 final size:36
Alignment explanation
Indices: 436939--437055 Score: 141
Period size: 35 Copynumber: 3.3 Consensus size: 36
436929 TATGTATATG
* * ** *
436939 ATAACTG-AAAAATATTTGATATTTGTAATTATCTA
1 ATAACTGTAAAAATATCTAATAACTGTAAATATCTA
*
436974 ATAACTGTAAAAATATCTAATAACTGTAAATATCTG
1 ATAACTGTAAAAATATCTAATAACTGTAAATATCTA
*
437010 ATAA-T-TAAAAATCATCTAATAACTGTAAATATCTT
1 ATAACTGTAAAAAT-ATCTAATAACTGTAAATATCTA
437045 ATAACTGTAAA
1 ATAACTGTAAA
437056 TACCATAGTT
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
34 7 0.10
35 33 0.46
36 27 0.38
37 4 0.06
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (36 bp):
ATAACTGTAAAAATATCTAATAACTGTAAATATCTA
Found at i:438126 original size:12 final size:12
Alignment explanation
Indices: 438109--438168 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
438099 TAATGGAGAT
*
438109 ATCAGAATAGAA
1 ATCAGAACAGAA
*
438121 ATCAGAGCAGAA
1 ATCAGAACAGAA
438133 ATCAGAACA-AA
1 ATCAGAACAGAA
* *
438144 ATTTAGAGCAGAA
1 A-TCAGAACAGAA
*
438157 ATCATAACAGAA
1 ATCAGAACAGAA
438169 TTTAGAGCAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
11 3 0.08
12 32 0.84
13 3 0.08
ACGTcount: A:0.55, C:0.13, G:0.17, T:0.15
Consensus pattern (12 bp):
ATCAGAACAGAA
Found at i:438185 original size:24 final size:24
Alignment explanation
Indices: 438124--438186 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
438114 AATAGAAATC
*
438124 AGAGCAGAAATCAGAACAAAATTT
1 AGAGCAGAAATCATAACAAAATTT
*
438148 AGAGCAGAAATCATAACAGAATTT
1 AGAGCAGAAATCATAACAAAATTT
*
438172 AGAGCATAAATCATA
1 AGAGCAGAAATCATA
438187 TAAAATATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.52, C:0.13, G:0.16, T:0.19
Consensus pattern (24 bp):
AGAGCAGAAATCATAACAAAATTT
Found at i:441652 original size:31 final size:31
Alignment explanation
Indices: 441617--441701 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 31
441607 TGAGTACCTT
* *
441617 GGGGCCTGCGAGCCTACCCAAGAATATTCTC
1 GGGGCCTGCGAGCCTACCCAAGAAAACTCTC
*
441648 GGGGCCAT-AGAGGCCTACCCAAGAAAACTCTC
1 GGGGCC-TGCGA-GCCTACCCAAGAAAACTCTC
*
441680 AGGGCC-GCAGAGCCTACCCAAG
1 GGGGCCTGC-GAGCCTACCCAAG
441702 GGTCGCCTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
31 19 0.42
32 26 0.58
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (31 bp):
GGGGCCTGCGAGCCTACCCAAGAAAACTCTC
Found at i:441665 original size:32 final size:31
Alignment explanation
Indices: 441626--441701 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 31
441616 TGGGGCCTGC
* * * *
441626 GAGCCTACCCAAGAATATTCTCGGGGCCATA
1 GAGCCTACCCAAGAAAACTCTCAGGGCCACA
*
441657 GAGGCCTACCCAAGAAAACTCTCAGGGCCGCA
1 GA-GCCTACCCAAGAAAACTCTCAGGGCCACA
441689 GAGCCTACCCAAG
1 GAGCCTACCCAAG
441702 GGTCGCCTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 13 0.33
32 26 0.67
ACGTcount: A:0.30, C:0.33, G:0.24, T:0.13
Consensus pattern (31 bp):
GAGCCTACCCAAGAAAACTCTCAGGGCCACA
Found at i:441871 original size:12 final size:12
Alignment explanation
Indices: 441856--441902 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
441846 TAAATTAGAA
441856 CAGAAATCAGAG
1 CAGAAATCAGAG
*
441868 CAGAAATCAGAA
1 CAGAAATCAGAG
*
441880 CAGAATTCAGAG
1 CAGAAATCAGAG
441892 CAGAAATCAGA
1 CAGAAATCAGA
441903 TAAAATATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.51, C:0.17, G:0.21, T:0.11
Consensus pattern (12 bp):
CAGAAATCAGAG
Found at i:441879 original size:24 final size:24
Alignment explanation
Indices: 441847--441902 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
441837 GAGATATCAT
*
441847 AAATTAGAACAGAAATCAGAGCAG
1 AAATCAGAACAGAAATCAGAGCAG
*
441871 AAATCAGAACAGAATTCAGAGCAG
1 AAATCAGAACAGAAATCAGAGCAG
441895 AAATCAGA
1 AAATCAGA
441903 TAAAATATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.54, C:0.14, G:0.20, T:0.12
Consensus pattern (24 bp):
AAATCAGAACAGAAATCAGAGCAG
Found at i:445797 original size:36 final size:35
Alignment explanation
Indices: 445685--445797 Score: 120
Period size: 36 Copynumber: 3.1 Consensus size: 35
445675 ATTGGTGCTA
* *
445685 AACCTATGTAAGGAATTACCAGTTTGATCAGAGTTG
1 AACCTATATAAGGAATTACCAG-TTGATCAGAGCTG
* *
445721 AACCTGCA-ATAAGGAATTACCAGTTGATCAGTGCTT
1 AACCT--ATATAAGGAATTACCAGTTGATCAGAGCTG
* * *
445757 AACCTATATAACGAATTACCAGCTTGATCAAAACTG
1 AACCTATATAAGGAATTACCAG-TTGATCAGAGCTG
445793 AACCT
1 AACCT
445798 GTAGAGACAT
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
34 1 0.02
35 14 0.22
36 34 0.53
37 14 0.22
38 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (35 bp):
AACCTATATAAGGAATTACCAGTTGATCAGAGCTG
Found at i:452195 original size:4 final size:4
Alignment explanation
Indices: 452186--452212 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
452176 AGACACTGTC
452186 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
452213 AGAAAGAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:455573 original size:20 final size:19
Alignment explanation
Indices: 455550--455596 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
455540 CGATATACCA
455550 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
455570 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
455590 GGTAAAA
1 GGTAAAA
455597 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:455698 original size:181 final size:182
Alignment explanation
Indices: 455338--455804 Score: 666
Period size: 181 Copynumber: 2.6 Consensus size: 182
455328 GATCCAAATT
* * * * **
455338 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCAGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * * * *
455403 AAACCGGTAAAGCGCTACCAGATACATTTAAAGTTTCGGTACTTTAATATAAAAATCAACACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAAAATCAACACTTT
* * *
455468 GTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCTATACTTTTA
131 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
* *
455520 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* ** *
455585 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAAAATCAACACTTT
** *
455649 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
* * *
455701 AAAAATATATCGATCCACAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
*
455766 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGA
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGA
455805 ACCTTTCGTA
Statistics
Matches: 254, Mismatches: 31, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
181 159 0.63
182 95 0.37
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAAAATCAACACTTT
GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:455779 original size:17 final size:19
Alignment explanation
Indices: 455740--455782 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
455730 ATGTAAAAAT
455740 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
455760 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
455777 ATGATA
1 ATGATA
455783 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:460409 original size:23 final size:23
Alignment explanation
Indices: 460350--460421 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
460340 ATAGGTAAAA
*
460350 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
460373 ATATAA-GTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
460395 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
460418 ATAT
1 ATAT
460422 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 21 0.48
23 23 0.52
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:460917 original size:24 final size:24
Alignment explanation
Indices: 460888--460939 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
460878 CCTTCCCAAG
460888 TTTTATACTATCAAACCGTAGAAA
1 TTTTATACTATCAAACCGTAGAAA
460912 TTTTATACTATCAAACCGTAGAAA
1 TTTTATACTATCAAACCGTAGAAA
460936 TTTT
1 TTTT
460940 GCCTTGTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (24 bp):
TTTTATACTATCAAACCGTAGAAA
Found at i:461608 original size:20 final size:20
Alignment explanation
Indices: 461583--461630 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
461573 TTATGTATGA
*
461583 TGTTCCACCAACCATGATGT
1 TGTTCCACCAACCATGATGC
*
461603 TGTTCCACCAATCATGATGC
1 TGTTCCACCAACCATGATGC
461623 TGTTCCAC
1 TGTTCCAC
461631 ATACCGACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (20 bp):
TGTTCCACCAACCATGATGC
Found at i:463552 original size:65 final size:67
Alignment explanation
Indices: 463475--463607 Score: 227
Period size: 69 Copynumber: 2.0 Consensus size: 67
463465 TGATTTGTTT
463475 AACTAAATGTGCTTAA-T-TTTTATTTATA-TGATAATTATGGGAAAGCAACTGAGTGCATAAAC
1 AACTAAATGTGCTTAATTCTTTTATTTATACTGATAATTATGGGAAAGCAACTGAGTGCATAAAC
463537 TC
66 TC
463539 AACTAAAATGTGCTTAATTTCTTTTATTTATACTGATAATTATGGGAAAGCAACTGAGTGCATAA
1 AACT-AAATGTGCTTAA-TTCTTTTATTTATACTGATAATTATGGGAAAGCAACTGAGTGCATAA
463604 ACTC
64 ACTC
463608 TTTGACACAC
Statistics
Matches: 64, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
64 4 0.06
65 12 0.19
67 1 0.02
68 11 0.17
69 36 0.56
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (67 bp):
AACTAAATGTGCTTAATTCTTTTATTTATACTGATAATTATGGGAAAGCAACTGAGTGCATAAAC
TC
Found at i:463745 original size:13 final size:13
Alignment explanation
Indices: 463729--463774 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
463719 GCTCAATGAA
463729 CGTCATAAATGTG
1 CGTCATAAATGTG
* *
463742 CGTCATAAATTTT
1 CGTCATAAATGTG
* *
463755 AGTCATAAATGCG
1 CGTCATAAATGTG
463768 CGTCATA
1 CGTCATA
463775 GATTTATGAC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (13 bp):
CGTCATAAATGTG
Found at i:463759 original size:26 final size:26
Alignment explanation
Indices: 463730--463779 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
463720 CTCAATGAAC
*
463730 GTCATAAATGTGCGTCATAAATTTTA
1 GTCATAAATGCGCGTCATAAATTTTA
*
463756 GTCATAAATGCGCGTCATAGATTT
1 GTCATAAATGCGCGTCATAAATTT
463780 ATGACACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (26 bp):
GTCATAAATGCGCGTCATAAATTTTA
Found at i:469051 original size:12 final size:12
Alignment explanation
Indices: 469031--469070 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
469021 GGAAAGAAAA
469031 AAAAT-AAAGGT
1 AAAATAAAAGGT
469042 AAAATAAAAGGT
1 AAAATAAAAGGT
*
469054 ATAATAAAA--T
1 AAAATAAAAGGT
469064 AAAATAA
1 AAAATAA
469071 TAAATAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 7 0.27
11 5 0.19
12 14 0.54
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (12 bp):
AAAATAAAAGGT
Found at i:469075 original size:12 final size:12
Alignment explanation
Indices: 469054--469099 Score: 65
Period size: 12 Copynumber: 3.7 Consensus size: 12
469044 AATAAAAGGT
469054 ATAATAAAATAAA
1 ATAAT-AAATAAA
469067 ATAATAAATAAA
1 ATAATAAATAAA
469079 ATAATAAATAATA
1 ATAATAAATAA-A
*
469092 GTAATAAA
1 ATAATAAA
469100 AATAAAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 18 0.58
13 13 0.42
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (12 bp):
ATAATAAATAAA
Found at i:471194 original size:21 final size:21
Alignment explanation
Indices: 471170--471224 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
471160 TCGCAACACA
*
471170 ATTTTCCTAATTCGCATTGCG
1 ATTTTCATAATTCGCATTGCG
* * *
471191 ATTTACGT-ATTCGCGTTGCG
1 ATTTTCATAATTCGCATTGCG
471211 ATTTTCATAATTCG
1 ATTTTCATAATTCG
471225 TAATGCGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (21 bp):
ATTTTCATAATTCGCATTGCG
Found at i:471284 original size:41 final size:41
Alignment explanation
Indices: 471226--471315 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
471216 CATAATTCGT
* *
471226 AATGCGAA-TACGTAAATCGC-ATCGCGATTAAGTAAATCGC
1 AATGCGAATTACGAAAATCGCAAT-GCGAATAAGTAAATCGC
* * *
471266 AATGCGAATTAGGAAAATCGCAATGCGAATACGTAAATCGT
1 AATGCGAATTACGAAAATCGCAATGCGAATAAGTAAATCGC
471307 AATGCGAAT
1 AATGCGAAT
471316 CTGACTATCG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
40 8 0.19
41 33 0.77
42 2 0.05
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (41 bp):
AATGCGAATTACGAAAATCGCAATGCGAATAAGTAAATCGC
Found at i:471314 original size:20 final size:20
Alignment explanation
Indices: 471226--471315 Score: 110
Period size: 20 Copynumber: 4.5 Consensus size: 20
471216 CATAATTCGT
471226 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
* *
471246 -ATCGCGATTAAGTAAATCGC
1 AAT-GCGAATACGTAAATCGC
* *
471266 AATGCGAATTAGGAAAATCGC
1 AATGCGAA-TACGTAAATCGC
*
471287 AATGCGAATACGTAAATCGT
1 AATGCGAATACGTAAATCGC
471307 AATGCGAAT
1 AATGCGAAT
471316 CTGACTATCG
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
19 2 0.03
20 37 0.63
21 20 0.34
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (20 bp):
AATGCGAATACGTAAATCGC
Found at i:471325 original size:20 final size:20
Alignment explanation
Indices: 471302--471353 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
471292 GAATACGTAA
*
471302 ATCGTAATGCGAATCTGACT
1 ATCGCAATGCGAATCTGACT
471322 ATCGCAATGCGAATCTGACT
1 ATCGCAATGCGAATCTGACT
471342 ATCGCAATGCGA
1 ATCGCAATGCGA
471354 TTTACATAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATCTGACT
Found at i:471904 original size:20 final size:19
Alignment explanation
Indices: 471879--471966 Score: 87
Period size: 19 Copynumber: 4.8 Consensus size: 19
471869 TAGTTTCGAG
*
471879 AATGACAATCGCAACGCGAA
1 AATGAAAATCGCAACGCG-A
**
471899 AATGACTATCGCAA--CGA
1 AATGAAAATCGCAACGCGA
*
471916 GA-G-A-ATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
471932 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
*
471951 AATGAAAATCACAACG
1 AATGAAAATCGCAACG
471967 AGATAATCGC
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
14 7 0.12
16 5 0.09
17 3 0.05
18 3 0.05
19 27 0.47
20 13 0.22
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:471966 original size:52 final size:53
Alignment explanation
Indices: 471879--471996 Score: 166
Period size: 52 Copynumber: 2.2 Consensus size: 53
471869 TAGTTTCGAG
* ** *
471879 AATGACAATCGCAACGCGAAAATGACTATCGCAACGAGAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGAAAATGAAAATCACAACGAGAGAATCGCAACGCGA
*
471932 AATGAAAATCGCAACGCG-AAATGAAAATCACAACGAGATAATCGCAACGCGA
1 AATGAAAATCGCAACGCGAAAATGAAAATCACAACGAGAGAATCGCAACGCGA
**
471984 AACCAAAATCGCA
1 AATGAAAATCGCA
471997 TTGCGATTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
52 41 0.71
53 17 0.29
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (53 bp):
AATGAAAATCGCAACGCGAAAATGAAAATCACAACGAGAGAATCGCAACGCGA
Found at i:472014 original size:19 final size:19
Alignment explanation
Indices: 471992--472104 Score: 119
Period size: 19 Copynumber: 6.1 Consensus size: 19
471982 GAAACCAAAA
*
471992 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
472011 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
472030 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
472044 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
472063 TCCGCGTTGCGATTGTCATT
1 T-CGCGTTGCGATTTTCATT
*
472083 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
472103 TC
1 TC
472105 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.12
16 2 0.03
17 3 0.04
19 32 0.40
20 32 0.40
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:472096 original size:20 final size:20
Alignment explanation
Indices: 472040--472102 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
472030 TCGCGTTGCG
*
472040 ATTCTCTCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATTGTC
*
472060 ATT-TCCGCGTTGCGATTGTC
1 ATTCT-CTCGTTGCGATTGTC
*
472080 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTGTC
472100 ATT
1 ATT
472103 TCAACCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTGTC
Found at i:473988 original size:94 final size:93
Alignment explanation
Indices: 473797--474101 Score: 501
Period size: 94 Copynumber: 3.3 Consensus size: 93
473787 TAGATTGCTT
* * *
473797 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACT-GT-TT-ATTAACACTATGAAGTTAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGGTATTCTTTAACACTGTGAAGTTAGTA
473859 TTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTC-TTTGTTTTGTCTTTTGGTTGAA
473887 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGCGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTG-GTATTCTTTAACACTGTGAAGTTAGT
473952 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
473981 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTG-GTATTCTTTAACACTGTGAAGTTAGT
474046 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
474075 AGTAAATTTGTTCGTTTGCTGCCAATT
1 AGTAAATTTATTCGGTTGCTGCCAATT
474102 GAAATTATTC
Statistics
Matches: 204, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
90 36 0.18
92 2 0.01
93 22 0.11
94 144 0.71
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGGTATTCTTTAACACTGTGAAGTTAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:474569 original size:21 final size:21
Alignment explanation
Indices: 474545--474611 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
474535 TCATTCCTCG
474545 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
474566 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
474587 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
474608 AGAG
1 AGAG
474612 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:474569 original size:42 final size:42
Alignment explanation
Indices: 474493--474611 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
474483 GAATCGCCTG
* * * * * * *
474493 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
474535 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
474577 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
474612 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:475981 original size:14 final size:14
Alignment explanation
Indices: 475962--475997 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
475952 ATTGTTTAAT
475962 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
475976 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
475990 TGATTTGT
1 TGATTTGT
475998 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:476136 original size:19 final size:19
Alignment explanation
Indices: 476114--476183 Score: 96
Period size: 19 Copynumber: 3.9 Consensus size: 19
476104 ATCACAATGT
476114 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
476133 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
476150 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
476166 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
476184 ACAAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
14 10 0.23
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 28 0.64
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:476164 original size:33 final size:33
Alignment explanation
Indices: 476120--476202 Score: 148
Period size: 33 Copynumber: 2.5 Consensus size: 33
476110 ATGTGAAATG
*
476120 AAAATCGCAACGCGAAATGAAAATCGCAACGAG
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
*
476153 AGAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
476186 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
476203 CTAAATTCGC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.48, C:0.23, G:0.20, T:0.08
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGAC
Found at i:476230 original size:19 final size:19
Alignment explanation
Indices: 476208--476358 Score: 89
Period size: 19 Copynumber: 8.7 Consensus size: 19
476198 CGAAACTAAA
476208 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
476227 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* * *
476242 -CCTCGTTGCAATTTTCAT
1 TTCGCGTTGCGATTTTCAT
476260 TTCGCGTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
476275 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
476293 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
476308 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
** **
476326 TTCGTATTGCGATAGTCATT
1 TTCGCGTTGCGATTTTCA-T
476346 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
476359 AGACATTAAG
Statistics
Matches: 96, Mismatches: 20, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 26 0.27
16 9 0.09
17 9 0.09
19 40 0.42
20 12 0.12
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:476256 original size:33 final size:33
Alignment explanation
Indices: 476212--476338 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
476202 ACTAAATTCG
*
476212 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCTTTGCGATTCTCT
* *
476245 CGTTGCAATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCTTTGCGATTCTCT
*
476278 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCTTTGCGATTCTCT
476311 CGTTGCGATTTTCATTTCG-TATTGCGAT
1 CGTTGCGATTTTCATTTCGCT-TTGCGAT
476339 AGTCATTTTC
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCTTTGCGATTCTCT
Found at i:476283 original size:14 final size:14
Alignment explanation
Indices: 476264--476320 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
476254 TTTCATTTCG
476264 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
476278 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
476295 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
476311 CGTTGCGATT
1 CGTTGCGATT
476321 TTCATTTCGT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:476355 original size:20 final size:20
Alignment explanation
Indices: 476312--476404 Score: 75
Period size: 20 Copynumber: 4.7 Consensus size: 20
476302 CGATTCTCTC
**
476312 GTTGCGATTTTCA-TTTCGT
1 GTTGCGATAGTCATTTTCGT
* *
476331 ATTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCATTTTCGT
* **
476351 GTTGCGATAGACA-TTAAGAT
1 GTTGCGATAGTCATTTTCG-T
476371 GATTGCGA-ACGTCATTTTCGT
1 G-TTGCGATA-GTCATTTTCGT
476392 GTTGCGATAGTCA
1 GTTGCGATAGTCA
476405 AATGATTGCC
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
19 13 0.23
20 28 0.50
21 12 0.21
22 3 0.05
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:478670 original size:12 final size:12
Alignment explanation
Indices: 478653--478677 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
478643 TCTTCGGGGA
478653 CTTTTTCTTCTT
1 CTTTTTCTTCTT
478665 CTTTTTCTTCTT
1 CTTTTTCTTCTT
478677 C
1 C
478678 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:479671 original size:20 final size:20
Alignment explanation
Indices: 479650--479797 Score: 233
Period size: 20 Copynumber: 7.4 Consensus size: 20
479640 TGTATTATCT
* *
479650 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
479670 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
479690 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
479710 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
479730 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
* *
479750 CGTTGCGAAAGTCAGTATTG
1 CGTTGCGAAAGTCAGAATCG
* * *
479770 CGTTGCAAAAGTAAGTATCG
1 CGTTGCGAAAGTCAGAATCG
479790 CGTTGCGA
1 CGTTGCGA
479798 TTTTGTATTA
Statistics
Matches: 120, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 120 1.00
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:479811 original size:21 final size:21
Alignment explanation
Indices: 479785--479878 Score: 77
Period size: 21 Copynumber: 4.5 Consensus size: 21
479775 CAAAAGTAAG
479785 TATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATTTTGTAT
* *
479806 TATCGCGTTGCGA--TAGTCAG
1 TATCGCGTTGCGATTTTGT-AT
* **
479826 TATCGCATTGCGATTTTCCA-
1 TATCGCGTTGCGATTTTGTAT
* **
479846 AATTCGTATTGCGATTTTGTAT
1 TA-TCGCGTTGCGATTTTGTAT
479868 TATCGCGTTGC
1 TATCGCGTTGC
479879 AATAGTCAGT
Statistics
Matches: 55, Mismatches: 13, Indels: 10
0.71 0.17 0.13
Matches are distributed among these distances:
19 3 0.05
20 14 0.25
21 36 0.65
22 2 0.04
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.41
Consensus pattern (21 bp):
TATCGCGTTGCGATTTTGTAT
Found at i:479839 original size:20 final size:20
Alignment explanation
Indices: 479645--479839 Score: 194
Period size: 20 Copynumber: 9.7 Consensus size: 20
479635 GATTATGTAT
*
479645 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
479665 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
479685 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
479705 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
479725 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
479745 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * * *
479765 TATTGCGTTGCAAAAGTAAG
1 TATCGCGTTGCGATAGTCAG
* *
479785 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
479806 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
479826 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
479840 TTTCCAAATT
Statistics
Matches: 157, Mismatches: 15, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
19 3 0.02
20 138 0.88
21 14 0.09
22 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:479874 original size:62 final size:62
Alignment explanation
Indices: 479787--479924 Score: 249
Period size: 62 Copynumber: 2.2 Consensus size: 62
479777 AAAGTAAGTA
* *
479787 TCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTGTATTATCGCGTTGCAATAGTCAGTATCGCATTGCGATTTTCCAAAT
*
479849 TCGTATTGCGATTTTGTATTATCGCGTTGCAATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTGTATTATCGCGTTGCAATAGTCAGTATCGCATTGCGATTTTCCAAAT
479911 TCGCATTGCGATTT
1 TCGCATTGCGATTT
479925 ACTTATTCGC
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 72 1.00
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (62 bp):
TCGCATTGCGATTTTGTATTATCGCGTTGCAATAGTCAGTATCGCATTGCGATTTTCCAAAT
Found at i:479955 original size:21 final size:21
Alignment explanation
Indices: 479931--479977 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
479921 ATTTACTTAT
*
479931 TCGCACCGCG-AATTGGGAAAA
1 TCGCAACGCGAAATT-GGAAAA
*
479952 TCGCAACGGGAAATTGGAAAA
1 TCGCAACGCGAAATTGGAAAA
479973 TCGCA
1 TCGCA
479978 TTGCGATAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.36, C:0.21, G:0.28, T:0.15
Consensus pattern (21 bp):
TCGCAACGCGAAATTGGAAAA
Found at i:485069 original size:67 final size:68
Alignment explanation
Indices: 484991--485142 Score: 243
Period size: 67 Copynumber: 2.2 Consensus size: 68
484981 ACCCATTCAA
* * *
484991 GGGGAACCGATACCCCCTCAACAAATATGAATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACAAATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCACA
485056 -GG
66 GGG
**
485058 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCACA
1 GGGGAACCGATACCCCCTCAACAAATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCACA
485123 GGG
66 GGG
*
485126 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
485143 ATGAGAAAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
67 60 0.77
68 18 0.23
ACGTcount: A:0.31, C:0.28, G:0.26, T:0.14
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACAAATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCACA
GGG
Found at i:485820 original size:23 final size:23
Alignment explanation
Indices: 485753--485812 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
485743 ATCATTATAT
*
485753 GGCACTACGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
485776 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
485799 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
485813 TTTATACGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:486464 original size:42 final size:42
Alignment explanation
Indices: 486401--486509 Score: 173
Period size: 42 Copynumber: 2.6 Consensus size: 42
486391 TATGGTATAA
* * * *
486401 AACCCTACGGGCTAGGCATGTAAGCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
486443 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
*
486485 AACCCTGCGGGCTCTGAATGTAACC
1 AACCCTGCGGGCTCGGAATGTAACC
486510 CTGCGGAGAT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.23, C:0.25, G:0.33, T:0.19
Consensus pattern (42 bp):
AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
Found at i:486510 original size:21 final size:21
Alignment explanation
Indices: 486401--486515 Score: 144
Period size: 21 Copynumber: 5.5 Consensus size: 21
486391 TATGGTATAA
* *
486401 AACCCTACGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
486422 AA-GCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
486443 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
486464 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
**
486485 AACCCTGCGGGCTCTGAATGT
1 AACCCTGCGGGCTAGGAATGT
486506 AACCCTGCGG
1 AACCCTGCGG
486516 AGATGGCATA
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.06
21 72 0.88
22 5 0.06
ACGTcount: A:0.22, C:0.25, G:0.34, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:486545 original size:21 final size:21
Alignment explanation
Indices: 486519--486566 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
486509 CCTGCGGAGA
*
486519 TGGCATATGAACTGGTGGGCT
1 TGGCATATGAACTGGAGGGCT
*
486540 TGGCATATGAAGTGGAGGGCT
1 TGGCATATGAACTGGAGGGCT
*
486561 GGGCAT
1 TGGCAT
486567 GTACCCCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.42, T:0.25
Consensus pattern (21 bp):
TGGCATATGAACTGGAGGGCT
Found at i:488081 original size:26 final size:27
Alignment explanation
Indices: 488052--488116 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
488042 GTATCCTAAA
*
488052 TAATATACATT-ATAAAAAATTAAAAT
1 TAATATAAATTCATAAAAAATTAAAAT
* * *
488078 TAATATAAATTCATAATAACTTTAAAT
1 TAATATAAATTCATAAAAAATTAAAAT
*
488105 TAAAAATAAATT
1 T-AATATAAATT
488117 TAAATATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 10 0.31
27 13 0.41
28 9 0.28
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (27 bp):
TAATATAAATTCATAAAAAATTAAAAT
Found at i:488105 original size:17 final size:17
Alignment explanation
Indices: 488068--488121 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
488058 ACATTATAAA
* *
488068 AAATT-AAAATTAATAT
1 AAATTAAAAATAAATTT
* * *
488084 AAATTCATAATAACTTT
1 AAATTAAAAATAAATTT
488101 AAATTAAAAATAAATTT
1 AAATTAAAAATAAATTT
488118 AAAT
1 AAAT
488122 ATTAACATTA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 5 0.17
17 25 0.83
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATTAAAAATAAATTT
Found at i:491899 original size:2 final size:2
Alignment explanation
Indices: 491883--491927 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
491873 AAGAATGTGA
*
491883 AT AT TT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
491924 AT AT
1 AT AT
491928 GCAATTGTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:496515 original size:2 final size:2
Alignment explanation
Indices: 496508--496548 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
496498 AATATTGATA
496508 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
496549 ATTGTTATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:499542 original size:16 final size:16
Alignment explanation
Indices: 499505--499552 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 16
499495 TAGTGTCCCA
*
499505 AAAATATTTAAACAAAAT
1 AAAATA-TT-AACTAAAT
499523 -AAATATTAACTAAAT
1 AAAATATTAACTAAAT
499538 AAAATATTAA-TAAAT
1 AAAATATTAACTAAAT
499553 GATTAATAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 12 0.43
16 11 0.39
17 5 0.18
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATATTAACTAAAT
Found at i:504097 original size:30 final size:30
Alignment explanation
Indices: 503994--504148 Score: 152
Period size: 30 Copynumber: 5.2 Consensus size: 30
503984 AACCAAACTC
*
503994 AAAGGGCTAAAATAGCTAAAATAG-AAGTTT
1 AAAGGACTAAAATAGCTAAAATAGAAAG-TT
* * * * * *
504024 AAAAGACTCAAAT-GACAAAAACATAAACTT
1 AAAGGACTAAAATAG-CTAAAATAGAAAGTT
*
504054 AATGGACTAAAATAGCTAAAATAGAAAGTT
1 AAAGGACTAAAATAGCTAAAATAGAAAGTT
* *** *
504084 AAAGGACTGAAATAAAAAAAATAGAAACTT
1 AAAGGACTAAAATAGCTAAAATAGAAAGTT
*
504114 AAAGGACTAAAATAGCTAAAACAGAAAGTT
1 AAAGGACTAAAATAGCTAAAATAGAAAGTT
504144 AAAGG
1 AAAGG
504149 GATGAACAGT
Statistics
Matches: 96, Mismatches: 26, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
29 1 0.01
30 92 0.96
31 3 0.03
ACGTcount: A:0.57, C:0.09, G:0.15, T:0.19
Consensus pattern (30 bp):
AAAGGACTAAAATAGCTAAAATAGAAAGTT
Found at i:504147 original size:60 final size:60
Alignment explanation
Indices: 503988--504148 Score: 216
Period size: 60 Copynumber: 2.7 Consensus size: 60
503978 TAATTTAACC
* * * * * *
503988 AAACTCAAAGGGCTAAAATAGCTAAAATAG-AAGTTTAAAAGACTCAAATGACAAAAACAT
1 AAACTTAAAGGACTAAAATAGCTAAAATAGAAAG-TTAAAGGACTCAAATAAAAAAAACAG
* * *
504048 AAACTTAATGGACTAAAATAGCTAAAATAGAAAGTTAAAGGACTGAAATAAAAAAAATAG
1 AAACTTAAAGGACTAAAATAGCTAAAATAGAAAGTTAAAGGACTCAAATAAAAAAAACAG
*
504108 AAACTTAAAGGACTAAAATAGCTAAAACAGAAAGTTAAAGG
1 AAACTTAAAGGACTAAAATAGCTAAAATAGAAAGTTAAAGG
504149 GATGAACAGT
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 86 0.97
61 3 0.03
ACGTcount: A:0.57, C:0.10, G:0.15, T:0.19
Consensus pattern (60 bp):
AAACTTAAAGGACTAAAATAGCTAAAATAGAAAGTTAAAGGACTCAAATAAAAAAAACAG
Found at i:505702 original size:3 final size:3
Alignment explanation
Indices: 505671--505720 Score: 55
Period size: 3 Copynumber: 15.7 Consensus size: 3
505661 ACAAAATATG
* *
505671 TAA TAA AAA TAA AAA TAA TAA GTATA TAA TAA TAA TAA TAA CTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TA-A TAA TAA TAA TAA TAA -TAA TAA
505719 TA
1 TA
505721 TTATTAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 32 0.80
4 7 0.17
5 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:505707 original size:20 final size:19
Alignment explanation
Indices: 505678--505720 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
505668 ATGTAATAAA
*
505678 AATAAAAATAATAAGTATAT
1 AATAAAAATAATAACTA-AT
*
505698 AATAATAATAATAACTAAT
1 AATAAAAATAATAACTAAT
505717 AATA
1 AATA
505721 TTATTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
AATAAAAATAATAACTAAT
Found at i:506225 original size:131 final size:131
Alignment explanation
Indices: 505927--506253 Score: 358
Period size: 131 Copynumber: 2.5 Consensus size: 131
505917 CGTCTAAGTT
* * * *
505927 TGACACGGTTCCTACGTGATGAGGAGATCTAGTCGGGGGATGACACTGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACGTGATGAGGAGGTATGGTCGGGGGATGACAC-GCTCATACGTGATGAAGA
* * *** *
505992 GTTCTTGGCCATCTTTAAGAATGGTGATAACTCGTTCCTGAGTGATGAGGATGGCTGATTATGTA
65 GTTCTTGGCCATATTTAAGAA--GTGATAACACGTTCCTGAGTGATGAGGACAACTGATTATCTA
*
506057 GGGG
128 AGGG
* * * * *
506061 TGACACGACTCTTAAGTGATGAGGAGGTTTGGTCGGTGGATGACACGACTCATACGTGATGAAGA
1 TGACACGGCTCCTACGTGATGAGGAGGTATGGTCGGGGGATGACACG-CTCATACGTGATGAAGA
*
506126 GTT-TTGGCCATATTT-AGCAA-TGATAACACAGTTCGT-ACGTGATGAGGACAACT-AGTTATC
65 GTTCTTGGCCATATTTAAG-AAGTGATAACAC-GTTCCTGA-GTGATGAGGACAACTGA-TTATC
506186 TAAGGG
126 TAAGGG
* * *
506192 TGACACGGCTCCTACGCGATGAGGAGGTATGGTCGGGGGATGACACGGTTCCTACGTGATGA
1 TGACACGGCTCCTACGTGATGAGGAGGTATGGTCGGGGGATGACAC-GCTCATACGTGATGA
506254 GGACGGCAGA
Statistics
Matches: 163, Mismatches: 24, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
130 10 0.06
131 78 0.48
132 3 0.02
133 14 0.09
134 58 0.36
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (131 bp):
TGACACGGCTCCTACGTGATGAGGAGGTATGGTCGGGGGATGACACGCTCATACGTGATGAAGAG
TTCTTGGCCATATTTAAGAAGTGATAACACGTTCCTGAGTGATGAGGACAACTGATTATCTAAGG
G
Found at i:506498 original size:29 final size:29
Alignment explanation
Indices: 506435--506511 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
506425 GAGAGATAAA
*
506435 ACTTTATTTCAAAAGAAACAGACTCAAAG
1 ACTTTTTTTCAAAAGAAACAGACTCAAAG
**
506464 TTTTTTGTTTCAAAAGAAACA-ACTCAAAG
1 ACTTTT-TTTCAAAAGAAACAGACTCAAAG
*
506493 ACTTTTCTTCAAAAGAAAC
1 ACTTTTTTTCAAAAGAAAC
506512 CGTCTCAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 12 0.29
29 15 0.37
30 14 0.34
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (29 bp):
ACTTTTTTTCAAAAGAAACAGACTCAAAG
Found at i:506518 original size:29 final size:30
Alignment explanation
Indices: 506442--506519 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 30
506432 AAAACTTTAT
* ** *
506442 TTCAAAAGAAACAGACTCAAAGTTTTTTGT
1 TTCAAAAGAAACCGACTCAAAGACTTTTGC
*
506472 TTCAAAAGAAA-CAACTCAAAGACTTTT-C
1 TTCAAAAGAAACCGACTCAAAGACTTTTGC
*
506500 TTCAAAAGAAACCGTCTCAA
1 TTCAAAAGAAACCGACTCAA
506520 TAGAGACAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 11 0.28
29 18 0.45
30 11 0.28
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (30 bp):
TTCAAAAGAAACCGACTCAAAGACTTTTGC
Found at i:506677 original size:33 final size:33
Alignment explanation
Indices: 506637--506704 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
506627 GTTGAATCCC
*
506637 CAAAGATGCCCCAACATTCGATGTTGATTGTTT
1 CAAAGATGCCCCAACATTCGATGTTGATTGATT
* *
506670 CAAAGATGCCCCAATATTTGATGTTGATTGATT
1 CAAAGATGCCCCAACATTCGATGTTGATTGATT
506703 CA
1 CA
506705 GCACTGATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (33 bp):
CAAAGATGCCCCAACATTCGATGTTGATTGATT
Found at i:506851 original size:24 final size:22
Alignment explanation
Indices: 506814--506875 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 22
506804 TGTATTTTCA
506814 AAAAGTTTGAAAATATCAATTC
1 AAAAGTTTGAAAATATCAATTC
**
506836 AAAGAGTTTTGAAAATGATTTA-TC
1 AAA-AG-TTTGAAAAT-ATCAATTC
506860 AAAAGTTTGAAAATAT
1 AAAAGTTTGAAAATAT
506876 TGCCCCTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
21 2 0.06
22 12 0.34
23 4 0.11
24 14 0.40
25 3 0.09
ACGTcount: A:0.48, C:0.05, G:0.13, T:0.34
Consensus pattern (22 bp):
AAAAGTTTGAAAATATCAATTC
Found at i:507764 original size:14 final size:14
Alignment explanation
Indices: 507747--507834 Score: 77
Period size: 14 Copynumber: 6.0 Consensus size: 14
507737 TCCTTCGTTT
507747 TTTTCTCTTTGCTC
1 TTTTCTCTTTGCTC
*
507761 TTTTTTCTTTGCTC
1 TTTTCTCTTTGCTC
* *
507775 TTTTTTCTTTGTTTC
1 TTTTCTCTTTG-CTC
* *
507790 TTTGTTTCTTTTCTC
1 TTT-TCTCTTTGCTC
* *
507805 TTTTTCTCTTTGATT
1 -TTTTCTCTTTGCTC
507820 TTTTCTTCTTTGCTC
1 TTTTC-TCTTTGCTC
507835 CTTATTTTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
14 29 0.48
15 21 0.35
16 10 0.17
ACGTcount: A:0.01, C:0.20, G:0.07, T:0.72
Consensus pattern (14 bp):
TTTTCTCTTTGCTC
Found at i:507783 original size:7 final size:7
Alignment explanation
Indices: 507745--507815 Score: 61
Period size: 8 Copynumber: 9.4 Consensus size: 7
507735 TTTCCTTCGT
507745 TTTTTTC
1 TTTTTTC
*
507752 TCTTTGCTC
1 T-TTT-TTC
507761 TTTTTTC
1 TTTTTTC
**
507768 TTTGCTC
1 TTTTTTC
507775 TTTTTTC
1 TTTTTTC
507782 TTTGTTTC
1 TTT-TTTC
507790 TTTGTTTC
1 TTT-TTTC
*
507798 TTTTCTC
1 TTTTTTC
507805 TTTTTCTC
1 TTTTT-TC
507813 TTT
1 TTT
507816 GATTTTTTCT
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
7 23 0.44
8 26 0.50
9 3 0.06
ACGTcount: A:0.00, C:0.20, G:0.06, T:0.75
Consensus pattern (7 bp):
TTTTTTC
Found at i:507791 original size:8 final size:8
Alignment explanation
Indices: 507759--507800 Score: 54
Period size: 7 Copynumber: 5.6 Consensus size: 8
507749 TTCTCTTTGC
507759 TCTTT-TT
1 TCTTTGTT
*
507766 TCTTTG-C
1 TCTTTGTT
507773 TCTTT-TT
1 TCTTTGTT
507780 TCTTTGTT
1 TCTTTGTT
507788 TCTTTGTT
1 TCTTTGTT
507796 TCTTT
1 TCTTT
507801 TCTCTTTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
7 15 0.50
8 15 0.50
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (8 bp):
TCTTTGTT
Found at i:507860 original size:50 final size:44
Alignment explanation
Indices: 507744--507866 Score: 120
Period size: 50 Copynumber: 2.6 Consensus size: 44
507734 TTTTCCTTCG
* * *
507744 TTTTTTTCTCTTTGCTCTTTTTTCTTTGCTCTTTTTTCTTTGTT
1 TTTTTTTTTCTTTGCTCTTTTCTCTTTGATCTTTTTTCTTTGTT
* * * *
507788 TCTTTGTTTCTTTTCTCTTTTTCTCTTTGATTTTTTCTTCTTTGCTCCT
1 TTTTTTTTTCTTTGCTC-TTTTCTCTTTGATCTTTT-TTCTTTG-T--T
507837 TATTTTTTTTCTTTGCTTCTTTTCTCTTTG
1 T-TTTTTTTTCTTTGC-TCTTTTCTCTTTG
507867 TTCTGATTTG
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
44 13 0.21
45 15 0.24
46 7 0.11
47 1 0.02
49 2 0.03
50 22 0.35
51 2 0.03
ACGTcount: A:0.02, C:0.20, G:0.07, T:0.72
Consensus pattern (44 bp):
TTTTTTTTTCTTTGCTCTTTTCTCTTTGATCTTTTTTCTTTGTT
Found at i:507870 original size:14 final size:14
Alignment explanation
Indices: 507752--507870 Score: 62
Period size: 14 Copynumber: 8.2 Consensus size: 14
507742 CGTTTTTTTC
* *
507752 TCTTTGCTCTTTTT
1 TCTTTTCTCTTTGT
* *
507766 TCTTTGCTCTTTTT
1 TCTTTTCTCTTTGT
*
507780 TCTTTGTTTCTTTGTT
1 TCTTT-TCTCTTTG-T
507796 TCTTTTCTCTTT-T
1 TCTTTTCTCTTTGT
* * *
507809 TCTCTTTGATTTTTTCT
1 TCT-TTT--CTCTTTGT
* * *
507826 TCTTTGCTCCTTAT
1 TCTTTTCTCTTTGT
*
507840 T-TTTTTTCTTTGCT
1 TCTTTTCTCTTTG-T
507854 TCTTTTCTCTTTGT
1 TCTTTTCTCTTTGT
507868 TCT
1 TCT
507871 GATTTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
13 11 0.14
14 33 0.41
15 21 0.26
16 12 0.15
17 4 0.05
ACGTcount: A:0.02, C:0.20, G:0.07, T:0.71
Consensus pattern (14 bp):
TCTTTTCTCTTTGT
Found at i:511880 original size:30 final size:30
Alignment explanation
Indices: 511759--511892 Score: 117
Period size: 30 Copynumber: 4.5 Consensus size: 30
511749 ACCAAACTCA
* * **
511759 AAAAG-CTGAAATAGCTAAAATAGAAGTTT
1 AAAAGACTGAAATAACAAAAATAGAAACTT
* * *
511788 AAAGGACTAAAATGACAAAAATAGAAACTT
1 AAAAGACTGAAATAACAAAAATAGAAACTT
** * * * * * *
511818 AATGGACTAAAATAGCTATAATTGAAAGTT
1 AAAAGACTGAAATAACAAAAATAGAAACTT
*
511848 AAAAGACTGAAATAACAAAAATAAAAACTT
1 AAAAGACTGAAATAACAAAAATAGAAACTT
511878 AAAAGACTGAAATAA
1 AAAAGACTGAAATAA
511893 TTAAACCAGA
Statistics
Matches: 81, Mismatches: 23, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
29 4 0.05
30 77 0.95
ACGTcount: A:0.57, C:0.08, G:0.13, T:0.21
Consensus pattern (30 bp):
AAAAGACTGAAATAACAAAAATAGAAACTT
Found at i:511891 original size:60 final size:60
Alignment explanation
Indices: 511759--511940 Score: 165
Period size: 60 Copynumber: 3.0 Consensus size: 60
511749 ACCAAACTCA
* * *
511759 AAAAG-CTGAAATAGCTAAAATAGAAGTTTAAAGGACTAAAATGACAAAAATAGAAACTT
1 AAAAGACTGAAATAGCTAAAATAGAAGTTTAAAAGACTAAAATAACAAAAATAAAAACTT
** * * * *
511818 AATGGACTAAAATAGCTATAATTGAAAG-TTAAAAGACTGAAATAACAAAAATAAAAACTT
1 AAAAGACTGAAATAGCTAAAATAG-AAGTTTAAAAGACTAAAATAACAAAAATAAAAACTT
** ** * * *
511878 AAAAGACTGAAATAATTAAACCAGAAAG-TTAAAGGACCAAAATAGA-AAAAATAAAAAGTT
1 AAAAGACTGAAATAGCTAAAATAG-AAGTTTAAAAGACTAAAATA-ACAAAAATAAAAACTT
511938 AAA
1 AAA
511941 GGGCTGAACA
Statistics
Matches: 98, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
59 3 0.03
60 91 0.93
61 4 0.04
ACGTcount: A:0.59, C:0.08, G:0.13, T:0.20
Consensus pattern (60 bp):
AAAAGACTGAAATAGCTAAAATAGAAGTTTAAAAGACTAAAATAACAAAAATAAAAACTT
Found at i:511910 original size:30 final size:30
Alignment explanation
Indices: 511841--511910 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
511831 AGCTATAATT
*
511841 GAAAGTTAAAAGACTGAAATAACAAAAATA
1 GAAAGTTAAAAGACTGAAATAACAAAAACA
* * ** *
511871 AAAACTTAAAAGACTGAAATAATTAAACCA
1 GAAAGTTAAAAGACTGAAATAACAAAAACA
511901 GAAAGTTAAA
1 GAAAGTTAAA
511911 GGACCAAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.19
Consensus pattern (30 bp):
GAAAGTTAAAAGACTGAAATAACAAAAACA
Found at i:513492 original size:20 final size:19
Alignment explanation
Indices: 513463--513508 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
513453 TAAAATATGA
* *
513463 AATAAAAATAAAAATAAGT
1 AATAATAATAAAAATAACT
*
513482 ATATAATAATAATAATAACT
1 A-ATAATAATAAAAATAACT
513502 AATAATA
1 AATAATA
513509 TTATTAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (19 bp):
AATAATAATAAAAATAACT
Found at i:522434 original size:49 final size:49
Alignment explanation
Indices: 522377--522474 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
522367 AAAACAACTT
*
522377 TCGTAAGTATTATCTTATCATAACATTATTGTCACTTTTAATTTTTTTA
1 TCGTAAGTATTATCTTATCATAACATTATTGTCACTGTTAATTTTTTTA
522426 TCGTAAGTATTATCTTATCATAACATTATTGTCACTGTTAATTTTTTTA
1 TCGTAAGTATTATCTTATCATAACATTATTGTCACTGTTAATTTTTTTA
522475 ATGATAGATG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.52
Consensus pattern (49 bp):
TCGTAAGTATTATCTTATCATAACATTATTGTCACTGTTAATTTTTTTA
Found at i:522626 original size:21 final size:23
Alignment explanation
Indices: 522600--522642 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
522590 TCTTATTGAT
*
522600 TAAATAATATT-TTA-AATTTTA
1 TAAATAACATTATTAGAATTTTA
522621 TAAATAACATTATTAGAATTTT
1 TAAATAACATTATTAGAATTTT
522643 TTATACTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 3 0.16
23 6 0.32
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAATAACATTATTAGAATTTTA
Found at i:525041 original size:22 final size:22
Alignment explanation
Indices: 525016--525064 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
525006 GGGACCCATG
525016 GACCCAATTTGGCCCACGTGTT
1 GACCCAATTTGGCCCACGTGTT
525038 GACCCAATTTGGCCCACGTGTT
1 GACCCAATTTGGCCCACGTGTT
525060 GACCC
1 GACCC
525065 GTTTCTCACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.18, C:0.35, G:0.22, T:0.24
Consensus pattern (22 bp):
GACCCAATTTGGCCCACGTGTT
Found at i:525312 original size:2 final size:2
Alignment explanation
Indices: 525307--525332 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
525297 CATTAGTATT
525307 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
525333 ATTATTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:525609 original size:17 final size:17
Alignment explanation
Indices: 525587--525631 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
525577 ATTTTATTTA
525587 CTTATTTTCTTTTTTCT
1 CTTATTTTCTTTTTTCT
*
525604 CTTA--TTCTTGTTTCT
1 CTTATTTTCTTTTTTCT
525619 C-TATTTTCATTTT
1 CTTATTTTC-TTTT
525632 GTTTATGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 3 0.13
17 7 0.30
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (17 bp):
CTTATTTTCTTTTTTCT
Found at i:527321 original size:44 final size:44
Alignment explanation
Indices: 527273--527364 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 44
527263 TACAAATATT
* * *
527273 GATACCAATGTGTAAAAATACACAACAATACCGCTACATGTATC
1 GATACCAATGTGTAAAAATACACAACAATACCGATACAGGTACC
* * * * *
527317 GATACTAGTGTGTAAAATTACACAATAGTACCGATACAGGTACC
1 GATACCAATGTGTAAAAATACACAACAATACCGATACAGGTACC
527361 GATA
1 GATA
527365 TTCCCTTTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (44 bp):
GATACCAATGTGTAAAAATACACAACAATACCGATACAGGTACC
Found at i:530747 original size:319 final size:317
Alignment explanation
Indices: 530125--531374 Score: 1879
Period size: 319 Copynumber: 4.0 Consensus size: 317
530115 GGTTGCAAAA
* * * * *
530125 TTGTTGACATTGCATCTAGTATGATTATGCTTGTTAGTCATAGAATAAGAAAAATTTACATGGTG
1 TTGTTGACATTGCATCTAATAGGATTATGCTTGTTGGTCATAAAATAAGAAACATTTACATGGTG
* * *
530190 CATTTAGATGACATTGTTTCCTCAAATGTATGCCTAGTAACTAAAGATGTAAGTGATTCATGGTT
66 CATTTAGATGATATTGTTTCCTCAAATGTATGCCTAGTAGCTAAAGATGAAAGTGATTCATGGTT
* *
530255 ATGTCATAG---A-TAGGTCATGCTAGCATGAGCATATTGGATAAACTTGTTAAAGGTGATCTAG
131 ATGGCATAGAAAACTAGGACATGCTAGCATGAGCATATTGGATAAACTTGTTAAAGGTGATCTAG
* * * * *
530316 TAAGAGGCTTACCGAAGCTAAAATTTAATTAAGACAAAATTTGTGATGCACGTGCAAAGAGTAAG
196 TAAGAGGCTTACCAAAGCTAAAATTTAATTTAGACAAAATTTGTGATGCATGTGTAAAGGGTAAG
*
530381 CATAAAAGAGTTTCCTTTAAATCC-TTAAATGATGTTTTCTCTAGTAAAGTATTATGC
261 CATAAAAGAGTTTCCTTTAAATCCATT-AATGATGTTTCCTCTAGTAAAGTATTATGC
* * * *
530438 TTGTTGACATTGCATCTAATAGGATTATGCTTGTTGGTCACAGAATAGGAAACATTTACATAGTG
1 TTGTTGACATTGCATCTAATAGGATTATGCTTGTTGGTCATAAAATAAGAAACATTTACATGGTG
*
530503 CATTTAGATGATATTGTTTCCTCATATGTATGCCTAGTAGCTAAAGATGAAAGTGATTCATGGTT
66 CATTTAGATGATATTGTTTCCTCAAATGTATGCCTAGTAGCTAAAGATGAAAGTGATTCATGGTT
* *
530568 ATAGCATAGAAAACTAGGACATGATAGCATGAGCATATTGGATATAAACTTGTTAAAGGTGATCT
131 ATGGCATAGAAAACTAGGACATGCTAGCATGAGCATATTGG--ATAAACTTGTTAAAGGTGATCT
* *
530633 AGTAAGAGGCTTATCAAAGCTATAATTTAATTTAGACAAAATTTGTGATGCATGTGTAAAGGGTA
194 AGTAAGAGGCTTACCAAAGCTAAAATTTAATTTAGACAAAATTTGTGATGCATGTGTAAAGGGTA
*
530698 AGCATAAAAGAGTTTCCTTTAAATCCATTAATGATGTTTCCTTTAGTAAAGTATTATGC
259 AGCATAAAAGAGTTTCCTTTAAATCCATTAATGATGTTTCCTCTAGTAAAGTATTATGC
* * * *
530757 TTGTTCACATTGCGTCTAATAGGATTATGCTTGTTGGTTATAAAATAAGAAA-AATTACATGGTG
1 TTGTTGACATTGCATCTAATAGGATTATGCTTGTTGGTCATAAAATAAGAAACATTTACATGGTG
* * *
530821 TATTTAGATGATATTGTTTTCTCAAATGTATTCCTAGTAGCTAAAGATGAAAGTGATTCATGGTT
66 CATTTAGATGATATTGTTTCCTCAAATGTATGCCTAGTAGCTAAAGATGAAAGTGATTCATGGTT
* * * ** *
530886 TTGGCATATAAAACTAAGACATGCTATTATGAGCATATTGGATAAACTTGTTAAAGCTGATCTAG
131 ATGGCATAGAAAACTAGGACATGCTAGCATGAGCATATTGGATAAACTTGTTAAAGGTGATCTAG
*
530951 TAAGAGGCTTGCCAAAGCTAAAATTTAATTTAG-----A----T-ATGCATGTGTAAAGGGTAAG
196 TAAGAGGCTTACCAAAGCTAAAATTTAATTTAGACAAAATTTGTGATGCATGTGTAAAGGGTAAG
* *
531006 CATAAAAGAGTTTTCTTTAAATCCATTAATGATGTTTCATCTAGTAAAGTATTATGC
261 CATAAAAGAGTTTCCTTTAAATCCATTAATGATGTTTCCTCTAGTAAAGTATTATGC
*
531063 TTGTTAACATTGCATCTAATAGGATTATGCTTGTTGGTCATAAAAT-AGAAAACATTTACATGGT
1 TTGTTGACATTGCATCTAATAGGATTATGCTTGTTGGTCATAAAATAAG-AAACATTTACATGGT
531127 GCATTTAGATGATATTGTTTCCTCAAATGTATGCCTAGTAGCTAAAGATGAAAGTGATTCATGGT
65 GCATTTAGATGATATTGTTTCCTCAAATGTATGCCTAGTAGCTAAAGATGAAAGTGATTCATGGT
**
531192 TATGGCATAGAAAACTAGGACATGCTAGCATGAGCATATTGGATAAACTTGTTAAAGACGATCTA
130 TATGGCATAGAAAACTAGGACATGCTAGCATGAGCATATTGGATAAACTTGTTAAAGGTGATCTA
* * *
531257 GTAAGAGGCTTACCAAAGCTAAAATTTAATTTAGACAAATTTTTTGATGCATGTGTAAA-GGAAA
195 GTAAGAGGCTTACCAAAGCTAAAATTTAATTTAGACAAAATTTGTGATGCATGTGTAAAGGGTAA
* * *
531321 GTATAAAAGAGTTTCCTTTAAATCCATTAATGATGTTTTCTCTAGTAAAATATT
260 GCATAAAAGAGTTTCCTTTAAATCCATTAATGATGTTTCCTCTAGTAAAGTATT
531375 GCAATTGATT
Statistics
Matches: 846, Mismatches: 72, Indels: 35
0.89 0.08 0.04
Matches are distributed among these distances:
305 2 0.00
306 120 0.14
307 164 0.19
311 1 0.00
313 126 0.15
316 108 0.13
317 38 0.04
318 105 0.12
319 180 0.21
320 2 0.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (317 bp):
TTGTTGACATTGCATCTAATAGGATTATGCTTGTTGGTCATAAAATAAGAAACATTTACATGGTG
CATTTAGATGATATTGTTTCCTCAAATGTATGCCTAGTAGCTAAAGATGAAAGTGATTCATGGTT
ATGGCATAGAAAACTAGGACATGCTAGCATGAGCATATTGGATAAACTTGTTAAAGGTGATCTAG
TAAGAGGCTTACCAAAGCTAAAATTTAATTTAGACAAAATTTGTGATGCATGTGTAAAGGGTAAG
CATAAAAGAGTTTCCTTTAAATCCATTAATGATGTTTCCTCTAGTAAAGTATTATGC
Found at i:536979 original size:55 final size:55
Alignment explanation
Indices: 536872--537140 Score: 332
Period size: 55 Copynumber: 4.9 Consensus size: 55
536862 CTATACGGAA
*
536872 ATTCATCAACTCATGATGAATTCTGTGGGTTT-CACACATAG-TGCCTGTACGGTG
1 ATTCATCAACTCATGATGAATTCTGTGGATTTGCACACA-AGATGCCTGTACGGTG
* * * *
536926 ATTCATCAACTCATGATAAACTCCGTGGATTTGCACACAAGATGCCTATACGGTG
1 ATTCATCAACTCATGATGAATTCTGTGGATTTGCACACAAGATGCCTGTACGGTG
* * * *
536981 ATTCATCAAATCATGATGAATTCTGTGAATATGCACACAA-AGTGCTTGTA-GGATG
1 ATTCATCAACTCATGATGAATTCTGTGGATTTGCACACAAGA-TGCCTGTACGG-TG
* *
537036 ATTCATCAACTCATGATGAATTCTGTGGATTTGTACACAAGGTGCCTGTACGGTG
1 ATTCATCAACTCATGATGAATTCTGTGGATTTGCACACAAGATGCCTGTACGGTG
** * *
537091 ATTCATCAACTCATGATGAATTCCATGAATATGCACACGAAG-TGCCTGTA
1 ATTCATCAACTCATGATGAATTCTGTGGATTTGCACAC-AAGATGCCTGTA
537141 GTACACATAG
Statistics
Matches: 184, Mismatches: 24, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
54 33 0.18
55 146 0.79
56 5 0.03
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (55 bp):
ATTCATCAACTCATGATGAATTCTGTGGATTTGCACACAAGATGCCTGTACGGTG
Found at i:537074 original size:110 final size:109
Alignment explanation
Indices: 536859--537141 Score: 388
Period size: 110 Copynumber: 2.6 Consensus size: 109
536849 GCACAATTAG
** ** * *
536859 TGCCTATACGGAAATTCATCAACTCATGATGAATTCTGTGGGT-TTCACACATAGTGCCTGTACG
1 TGCCTATACGGTGATTCATCAACTCATGATGAATTCTGTGAATATGCACACAAAGTGCCTGTA-G
536923 GTGATTCATCAACTCATGATAAACTCCGTGGATTTGCACACAAGA
65 GTGATTCATCAACTCATGATAAACTCCGTGGATTTGCACACAAGA
* *
536968 TGCCTATACGGTGATTCATCAAATCATGATGAATTCTGTGAATATGCACACAAAGTGCTTGTAGG
1 TGCCTATACGGTGATTCATCAACTCATGATGAATTCTGTGAATATGCACACAAAGTGCCTGTAGG
* * * * *
537033 ATGATTCATCAACTCATGATGAATTCTGTGGATTTGTACACAAGG
66 -TGATTCATCAACTCATGATAAACTCCGTGGATTTGCACACAAGA
* ** *
537078 TGCCTGTACGGTGATTCATCAACTCATGATGAATTCCATGAATATGCACACGAAGTGCCTGTAG
1 TGCCTATACGGTGATTCATCAACTCATGATGAATTCTGTGAATATGCACACAAAGTGCCTGTAG
537142 TACACATAGT
Statistics
Matches: 153, Mismatches: 19, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
109 40 0.26
110 113 0.74
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (109 bp):
TGCCTATACGGTGATTCATCAACTCATGATGAATTCTGTGAATATGCACACAAAGTGCCTGTAGG
TGATTCATCAACTCATGATAAACTCCGTGGATTTGCACACAAGA
Done.