Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 111 of 153
Found at i:34818839 original size:39 final size:39
Alignment explanation
Indices: 34818752--34818844 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 39
34818742 CAACAACTTC
* * *
34818752 CCTCCGCAAAACCAACTTTGAAAATAAAGCATATACATT
1 CCTCCGCAAAGCCAACTTTCAAAATAAAACATATACATT
*
34818791 CCTCCGCAAAGCCAAC-TTCAAAAGTAAAACCTATACATT
1 CCTCCGCAAAGCCAACTTTCAAAA-TAAAACATATACATT
**
34818830 CCTTTGCAAAGCCAA
1 CCTCCGCAAAGCCAA
34818845 GGTTCTATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 6 0.13
39 41 0.87
ACGTcount: A:0.41, C:0.29, G:0.09, T:0.22
Consensus pattern (39 bp):
CCTCCGCAAAGCCAACTTTCAAAATAAAACATATACATT
Found at i:34822321 original size:33 final size:33
Alignment explanation
Indices: 34822279--34822367 Score: 108
Period size: 33 Copynumber: 2.7 Consensus size: 33
34822269 CTTACTCATA
* * *
34822279 TTTACTGTCCC-GATAGATTATCTCTATTTTATG
1 TTTACTGTCCCAG-TAGACTATCTATATTCTATG
* *
34822312 TTTACTGTCCCAGTAGACTATCTATGTTCTGTG
1 TTTACTGTCCCAGTAGACTATCTATATTCTATG
*
34822345 TTTACTGTCCCAGCAGACTATCT
1 TTTACTGTCCCAGTAGACTATCT
34822368 CTGTGGATGC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
33 48 0.98
34 1 0.02
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (33 bp):
TTTACTGTCCCAGTAGACTATCTATATTCTATG
Found at i:34827650 original size:21 final size:22
Alignment explanation
Indices: 34827626--34827666 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
34827616 AATTTAATCT
34827626 TTAAAAAATATAA-AAAAAATA
1 TTAAAAAATATAATAAAAAATA
**
34827647 TTAACTAATATAATAAAAAA
1 TTAAAAAATATAATAAAAAA
34827667 ATTTAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
TTAAAAAATATAATAAAAAATA
Found at i:34834414 original size:70 final size:67
Alignment explanation
Indices: 34834297--34834425 Score: 195
Period size: 70 Copynumber: 1.9 Consensus size: 67
34834287 ATAAACAATA
* **
34834297 TAATGGTTTTGCCTTTTAACTTAATGAGTAAACATTTATCAAAACGACATAGTTTTGCCCTTTAA
1 TAATGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAACGACATAGTTTTGCCCTTTAA
34834362 CT
66 CT
*
34834364 TAATGGTTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATCAAAACGACTTAGTTTTGCC
1 TAATGGTTTTGACTTTTAAC-TTA-AAAA-GTAAACATTTATCAAAACGACATAGTTTTGCC
34834426 TTTCCTTATT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
67 19 0.35
68 3 0.05
69 2 0.04
70 31 0.56
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (67 bp):
TAATGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAACGACATAGTTTTGCCCTTTAA
CT
Found at i:34838488 original size:28 final size:28
Alignment explanation
Indices: 34838456--34838527 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
34838446 TAATGAGATT
* *
34838456 AGCACTAAGTGTGCGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGAGATTAATTATAA
* *
34838484 AGCACTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGAGATTAATTATAA
34838512 AGCACTAAGTGTGCGA
1 AGCACTAAGTGTGCGA
34838528 ACTTATTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGATTAATTATAA
Found at i:34838533 original size:24 final size:24
Alignment explanation
Indices: 34838456--34838536 Score: 63
Period size: 28 Copynumber: 3.0 Consensus size: 24
34838446 TAATGAGATT
* *
34838456 AGCACTAAGTGTGCGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGA----AATTATTA
34838484 AGCACTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGA-A---ATTATTA
*
34838512 AGCACTAAGTGTGCGAACTTATTA
1 AGCACTAAGTGTGCGAAATTATTA
34838536 A
1 A
34838537 ATATTTTCGA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
24 7 0.15
25 1 0.02
27 1 0.02
28 37 0.80
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.31
Consensus pattern (24 bp):
AGCACTAAGTGTGCGAAATTATTA
Found at i:34840516 original size:28 final size:28
Alignment explanation
Indices: 34840473--34840544 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
34840463 TAATGAGATT
* *
34840473 AGCACTAAGTGTGCGAG-TTTAGTTGTAA
1 AGCACTAAGTGTGCGAGATTGA-TTATAA
* *
34840501 AGGACTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGAGATTGATTATAA
34840529 AGCACTAAGTGTGCGA
1 AGCACTAAGTGTGCGA
34840545 ACTTATTAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
28 35 0.92
29 3 0.08
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGATTGATTATAA
Found at i:34841628 original size:23 final size:23
Alignment explanation
Indices: 34841595--34842058 Score: 381
Period size: 23 Copynumber: 19.7 Consensus size: 23
34841585 AGATGCTTCA
* *
34841595 ATGCTGCCCAAATTGTTATATAT
1 ATGCTGCCCAATTTGTTGTATAT
* * * *
34841618 ATGCTGTCCAAATTTTGGTGTAAAA
1 ATGCTG-CCCAA-TTTGTTGTATAT
* * *
34841643 ATGCTGCTCAATTTGGTATATAT
1 ATGCTGCCCAATTTGTTGTATAT
**
34841666 ATGCTATCCAATTTGTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
* * * *
34841689 ATGCT-CTCCGATTTTTGGTGTAAAA
1 ATGCTGC-CC-A-ATTTGTTGTATAT
* *
34841714 ATGCTGCTCAATTTGTTGTATTT
1 ATGCTGCCCAATTTGTTGTATAT
*
34841737 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
* * * *
34841760 ATGCTGTCCAATTTTTGGTGTAAAA
1 ATGCTGCCCAA--TTTGTTGTATAT
* *
34841785 ATGCTGCTCAATTTGTTGTATTT
1 ATGCTGCCCAATTTGTTGTATAT
* *
34841808 ATGCTGCCCAAATAGTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
* * * *
34841831 ATGCTGTCCAATTTTGATGTAAAA
1 ATGCTGCCCAA-TTTGTTGTATAT
* * *
34841855 ATGCTGCTCAATTTGGTATATAT
1 ATGCTGCCCAATTTGTTGTATAT
34841878 ATGCTGCCCAATTTGTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
* * * * *
34841901 ATGTTGTCCAATTTTTGGTGTAAAA
1 ATGCTGCCCAA--TTTGTTGTATAT
* *
34841926 ATGCTGCTCAATTTGTTGTATTT
1 ATGCTGCCCAATTTGTTGTATAT
*
34841949 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
* * * *
34841972 ATGCTGTCCAATTTTGATGTAAAA
1 ATGCTGCCCAA-TTTGTTGTATAT
* * *
34841996 ATGCTGCTCAATTTGGTATATAT
1 ATGCTGCCCAATTTGTTGTATAT
34842019 ATGCTGCCCAATTTGTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
*
34842042 ATGCTGCCCAAATTGTT
1 ATGCTGCCCAATTTGTT
34842059 ACAGGGTAGA
Statistics
Matches: 339, Mismatches: 90, Indels: 24
0.75 0.20 0.05
Matches are distributed among these distances:
23 234 0.69
24 42 0.12
25 62 0.18
26 1 0.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.42
Consensus pattern (23 bp):
ATGCTGCCCAATTTGTTGTATAT
Found at i:34841665 original size:48 final size:47
Alignment explanation
Indices: 34841594--34842055 Score: 318
Period size: 48 Copynumber: 9.8 Consensus size: 47
34841584 GAGATGCTTC
* * * *
34841594 AATGCTGCCCAAATTGTTATATATATGCTGTCCAAATTTTGGTGTAAA
1 AATGCTGCTCAATTTGTTGTATATATGCTGTCCAAA-TTTGGTGTATA
* * * *
34841642 AATGCTGCTCAATTTGGTATATATATGCTATCC-AATTTGTTGTATA
1 AATGCTGCTCAATTTGTTGTATATATGCTGTCCAAATTTGGTGTATA
* * * * * * *
34841688 TATGCT-CTCCGATTTTTGGTGTAAAAATGCTG-CTC-AATTTGTTGTATT
1 AATGCTGCT-C-A-ATTTGTTGTATATATGCTGTC-CAAATTTGGTGTATA
* * * * *
34841736 TATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTTGGTGTAAA
1 AATGCTGCTCAATTTGTTGTATATATGCTGTCCAA-ATTTGGTGTATA
* * * *
34841784 AATGCTGCTCAATTTGTTGTATTTATGCTGCCCAAA-TAGTTGTATA
1 AATGCTGCTCAATTTGTTGTATATATGCTGTCCAAATTTGGTGTATA
* * * * *
34841830 TATGCTG-TCCAATTTTGATGTAAAAATGCTG-CTC-AATTTGGTATATA
1 AATGCTGCT-CAA-TTTGTTGTATATATGCTGTC-CAAATTTGGTGTATA
* * * * *
34841877 TATGCTGCCCAATTTGTTGTATATATGTTGTCCAATTTTTGGTGTAAA
1 AATGCTGCTCAATTTGTTGTATATATGCTGTCCAA-ATTTGGTGTATA
* * *
34841925 AATGCTGCTCAATTTGTTGTATTTATGCTGCCCAAA-TTGTTGTATA
1 AATGCTGCTCAATTTGTTGTATATATGCTGTCCAAATTTGGTGTATA
* * * * *
34841971 TATGCTG-TCCAATTTTGATGTAAAAATGCTG-CTC-AATTTGGTATATA
1 AATGCTGCT-CAA-TTTGTTGTATATATGCTGTC-CAAATTTGGTGTATA
* * *
34842018 TATGCTGCCCAATTTGTTGTATATATGCTGCCCAAATT
1 AATGCTGCTCAATTTGTTGTATATATGCTGTCCAAATT
34842056 GTTACAGGGT
Statistics
Matches: 324, Mismatches: 67, Indels: 47
0.74 0.15 0.11
Matches are distributed among these distances:
45 4 0.01
46 100 0.31
47 79 0.24
48 140 0.43
49 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (47 bp):
AATGCTGCTCAATTTGTTGTATATATGCTGTCCAAATTTGGTGTATA
Found at i:34841705 original size:71 final size:71
Alignment explanation
Indices: 34841595--34842055 Score: 683
Period size: 71 Copynumber: 6.5 Consensus size: 71
34841585 AGATGCTTCA
*
34841595 ATGCTGCCCAAATTGTTATATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
34841660 ATATAT
66 ATATAT
** * * * * *
34841666 ATGCTATCCAATTTGTTGTATATATGCTCTCCGATTTTTGGTGTAAAAATGCTGCTCAATTTGTT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
* *
34841731 GTATTT
66 ATATAT
* *
34841737 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
* *
34841802 GTATTT
66 ATATAT
* *
34841808 ATGCTGCCCAAATAGTTGTATATATGCTGTCC-AATTTTGATGTAAAAATGCTGCTCAATTTGGT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
34841872 ATATAT
66 ATATAT
* * * *
34841878 ATGCTGCCCAATTTGTTGTATATATGTTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
* *
34841943 GTATTT
66 ATATAT
*
34841949 ATGCTGCCCAAATTGTTGTATATATGCTGTCC-AATTTTGATGTAAAAATGCTGCTCAATTTGGT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
34842013 ATATAT
66 ATATAT
* *
34842019 ATGCTGCCCAATTTGTTGTATATATGCTGCCCAAATT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATT
34842056 GTTACAGGGT
Statistics
Matches: 350, Mismatches: 38, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
70 125 0.36
71 225 0.64
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (71 bp):
ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
ATATAT
Found at i:34841903 original size:141 final size:141
Alignment explanation
Indices: 34841595--34842052 Score: 736
Period size: 141 Copynumber: 3.2 Consensus size: 141
34841585 AGATGCTTCA
* * *
34841595 ATGCTGCCCAAATTGTTATATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTT
* * ** * * * *
34841660 ATATATATGCTATCCAATTTGTTGTATATATGCTCTCCGATTTTTGGTGTAAAAATGCTGCTCAA
66 GTATTTATGCTGCCCAAATTGTTGTATATATGCTGTCC-AATTTTGATGTAAAAATGCTGCTCAA
* * *
34841725 TTTGTTGTATTT
130 TTTGGTATATAT
34841737 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTT
*
34841802 GTATTTATGCTGCCCAAATAGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGCTGCTCAAT
66 GTATTTATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGCTGCTCAAT
34841867 TTGGTATATAT
131 TTGGTATATAT
* *
34841878 ATGCTGCCCAATTTGTTGTATATATGTTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTT
34841943 GTATTTATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGCTGCTCAAT
66 GTATTTATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGCTGCTCAAT
34842008 TTGGTATATAT
131 TTGGTATATAT
* *
34842019 ATGCTGCCCAATTTGTTGTATATATGCTGCCCAA
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAA
34842053 ATTGTTACAG
Statistics
Matches: 296, Mismatches: 20, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
141 203 0.69
142 93 0.31
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (141 bp):
ATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTT
GTATTTATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGCTGCTCAAT
TTGGTATATAT
Found at i:34842893 original size:106 final size:106
Alignment explanation
Indices: 34842764--34842978 Score: 360
Period size: 106 Copynumber: 2.0 Consensus size: 106
34842754 TGGATTGAGA
*
34842764 TTTAAGAGGATATTTGGCTATTTGATCAAACGAGAAATCAAAACCCAGCACGTTAGGGCACGATT
1 TTTAAAAGGATATTTGGCTATTTGATCAAACGAGAAATCAAAACCCAGCACGTTAGGGCACG-TT
* *
34842829 TT-TCGATTTTCCAAACGCAAAATATTACCCTATTTTGAAAT
65 TTCTCGATTTTCCAAACACAAAATATTACCCTACTTTGAAAT
*
34842870 TTTAAAAGGATATTTGGCTATTTGGTCAAACGAGAAATCAAAACCCAGCACGTTAGGGCACGTTT
1 TTTAAAAGGATATTTGGCTATTTGATCAAACGAGAAATCAAAACCCAGCACGTTAGGGCACGTTT
* *
34842935 TCTCGATTTTCCAAACACAAAATATTGCCTTACTTTGAAAT
66 TCTCGATTTTCCAAACACAAAATATTACCCTACTTTGAAAT
34842976 TTT
1 TTT
34842979 CCTTTTGAAG
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
105 4 0.04
106 98 0.96
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (106 bp):
TTTAAAAGGATATTTGGCTATTTGATCAAACGAGAAATCAAAACCCAGCACGTTAGGGCACGTTT
TCTCGATTTTCCAAACACAAAATATTACCCTACTTTGAAAT
Found at i:34848699 original size:16 final size:16
Alignment explanation
Indices: 34848678--34848711 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
34848668 ATTAAGTAAA
34848678 AATATATAAAA-TTTAT
1 AATATA-AAAATTTTAT
34848694 AATATAAAAATTTTAT
1 AATATAAAAATTTTAT
34848710 AA
1 AA
34848712 GTACTGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATAAAAATTTTAT
Found at i:34858183 original size:23 final size:25
Alignment explanation
Indices: 34858153--34858207 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 25
34858143 TAAAAATATT
34858153 AAATAAAATTCA-AAAA-TT-TTAAA
1 AAATAAAATT-ATAAAATTTATTAAA
34858176 AAATAAAAATTATAAAATTTATTAAA
1 AAAT-AAAATTATAAAATTTATTAAA
34858202 AAATAA
1 AAATAA
34858208 GTCCAGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 5 0.18
24 10 0.36
25 4 0.14
26 9 0.32
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
AAATAAAATTATAAAATTTATTAAA
Found at i:34858192 original size:24 final size:26
Alignment explanation
Indices: 34858153--34858207 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
34858143 TAAAAATATT
34858153 AAAT-AAAATTCAAAAA-TT-TTAAA
1 AAATAAAAATTCAAAAATTTATTAAA
34858176 AAATAAAAATT-ATAAAATTTATTAAA
1 AAATAAAAATTCA-AAAATTTATTAAA
34858202 AAATAA
1 AAATAA
34858208 GTCCAGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 5 0.18
24 10 0.36
25 2 0.07
26 11 0.39
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (26 bp):
AAATAAAAATTCAAAAATTTATTAAA
Found at i:34858817 original size:101 final size:99
Alignment explanation
Indices: 34858642--34858844 Score: 379
Period size: 101 Copynumber: 2.0 Consensus size: 99
34858632 TACAAGTTAT
34858642 TAAATTTAAAATAAATTTGCATAATGACAAAATTAGCCCTTAACGTTTGGGTGTTGGGTCACTTT
1 TAAATTTAAAATAAATTTGCATAATGACAAAATTAGCCCTTAACGTTTGGGTGTTGGGTCACTTT
34858707 GGCCTTTAAGGTTTTTTTTTGGAGCACTTTCATACA
66 GGCCTTTAAGG--TTTTTTTGGAGCACTTTCATACA
*
34858743 TAAATTTAAAATAAATTTGCATAATGACAAAATTAGCCCTTAATGTTTGGGTGTTGGGTCACTTT
1 TAAATTTAAAATAAATTTGCATAATGACAAAATTAGCCCTTAACGTTTGGGTGTTGGGTCACTTT
34858808 GGCCTTTAAGGTTTTTTTGGAGCACTTTCATACA
66 GGCCTTTAAGGTTTTTTTGGAGCACTTTCATACA
34858842 TAA
1 TAA
34858845 CCTTTTTTTT
Statistics
Matches: 101, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
99 26 0.26
101 75 0.74
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (99 bp):
TAAATTTAAAATAAATTTGCATAATGACAAAATTAGCCCTTAACGTTTGGGTGTTGGGTCACTTT
GGCCTTTAAGGTTTTTTTGGAGCACTTTCATACA
Found at i:34859103 original size:10 final size:9
Alignment explanation
Indices: 34859066--34859104 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
34859056 GGGGTTTACT
34859066 AACAATTAA
1 AACAATTAA
34859075 AACAATTAAA
1 AACAATT-AA
*
34859085 AAAAATTAA
1 AACAATTAA
34859094 AACAAGTTAA
1 AACAA-TTAA
34859104 A
1 A
34859105 CATTAACTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 13 0.50
10 13 0.50
ACGTcount: A:0.69, C:0.08, G:0.03, T:0.21
Consensus pattern (9 bp):
AACAATTAA
Found at i:34861378 original size:54 final size:54
Alignment explanation
Indices: 34861306--34861428 Score: 174
Period size: 54 Copynumber: 2.3 Consensus size: 54
34861296 TGAAGGTTTA
* * * * *
34861306 GGTAGGGAGGGTGATGATGTTGTTGTCAGTGAAGGTGGTGAGAGTGATAGAGGC
1 GGTAAGGAGGGGGTTGATGTTGCTGTCAATGAAGGTGGTGAGAGTGATAGAGGC
* * *
34861360 GGTGAGGAGGGGGTTGATGTTGCTGTCAATGAAGGTGGTGAGAGTGATGGAGGT
1 GGTAAGGAGGGGGTTGATGTTGCTGTCAATGAAGGTGGTGAGAGTGATAGAGGC
34861414 GGTAAGGAGGGGGTT
1 GGTAAGGAGGGGGTT
34861429 AGGGAAGTGG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 60 1.00
ACGTcount: A:0.21, C:0.03, G:0.50, T:0.25
Consensus pattern (54 bp):
GGTAAGGAGGGGGTTGATGTTGCTGTCAATGAAGGTGGTGAGAGTGATAGAGGC
Found at i:34862597 original size:160 final size:157
Alignment explanation
Indices: 34862295--34862685 Score: 500
Period size: 160 Copynumber: 2.5 Consensus size: 157
34862285 GGTGTCGTAA
* * * *
34862295 CACAGGTATATCGTAAACATTTTTTCATTGTCAATTCCAAAATATTAAAATCTAATTTGGGTTCT
1 CACAAGTATATCGTAAACATTTTTT-AATGTCAATTCAAAAATATTTAAATCTAATTTGGGTTCT
* *
34862360 GATTTTTTTGAAATTAGTCTAGTACGAGTACAAGAACTAGAAGCCCAAAAAATAACAATATAACA
65 GATTTTTTTGAAATTAGTCTAGTACGAGTACAAGAACTAGAAGCCCAAAAAAGAACAACATAACA
34862425 CCATGCATTCAGCATAATACAACTGGAT
130 CCATGCATTCAGCATAATACAACTGGAT
* * * *
34862453 CATAAGTATATCGTATACATTATTTTAATGTCAATTCAAAAATATTTTAATCTAATTTGGGATTT
1 CACAAGTATATCGTAAACATT-TTTTAATGTCAATTCAAAAATATTTAAATCTAATTTGGG-TTC
** *
34862518 TGACTTTTTTT-AGCCTTAGTCTGGTACGAGTACACA-AACTAGAAG-CCAAAAAGAGAACAACA
64 TGA-TTTTTTTGA-AATTAGTCTAGTACGAGTACA-AGAACTAGAAGCCCAAAAA-AGAACAACA
*
34862580 TAACACCATGCATTCAGCCTAATACAACTGGAT
125 TAACACCATGCATTCAGCATAATACAACTGGAT
* * * * * *
34862613 CACAGGTATATTGCAAACACTTTTTTAATCTCAATTCTAAATTATTTAAATCTAATTTAGGGTTC
1 CACAAGTATATCGTAAACA-TTTTTTAATGTCAATTCAAAAATATTTAAATCTAATTT-GGGTTC
34862678 TGATTTTT
64 TGATTTTT
34862686 GTTCTCAGTC
Statistics
Matches: 201, Mismatches: 24, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
158 49 0.24
159 22 0.11
160 124 0.62
161 6 0.03
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (157 bp):
CACAAGTATATCGTAAACATTTTTTAATGTCAATTCAAAAATATTTAAATCTAATTTGGGTTCTG
ATTTTTTTGAAATTAGTCTAGTACGAGTACAAGAACTAGAAGCCCAAAAAAGAACAACATAACAC
CATGCATTCAGCATAATACAACTGGAT
Found at i:34862946 original size:82 final size:78
Alignment explanation
Indices: 34862801--34862999 Score: 308
Period size: 82 Copynumber: 2.5 Consensus size: 78
34862791 TTGAGATAGT
*
34862801 TAACATATTTTGTTTGTTTTTTGAAATGATTTGTTGAAATGGTTAACATCTTACTGTTATAGGAT
1 TAACATATTTTGTTTGTTTTTTGAAATGATTTGTTGAAATGGTTAACATCTTACTGCTATAGGAT
34862866 CATTTTGTTAGCA
66 CATTTTGTTAGCA
34862879 TAACATATTTTGTTTGTTTTTTGAAATGATTTGTTGAAATGGTTGGTTAACATCTTACTGCTATA
1 TAACATATTTTGTTTGTTTTTTGAAATGATTTGTTGAAA----TGGTTAACATCTTACTGCTATA
* *
34862944 GGATTATTTTGTTAGTA
62 GGATCATTTTGTTAGCA
* * *
34862961 TAACGTATTTTGTTTGTTTTCTGAACTGATTTGTTGAAA
1 TAACATATTTTGTTTGTTTTTTGAAATGATTTGTTGAAA
34863000 AATGTATATT
Statistics
Matches: 111, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
78 39 0.35
82 72 0.65
ACGTcount: A:0.26, C:0.07, G:0.18, T:0.50
Consensus pattern (78 bp):
TAACATATTTTGTTTGTTTTTTGAAATGATTTGTTGAAATGGTTAACATCTTACTGCTATAGGAT
CATTTTGTTAGCA
Found at i:34865054 original size:18 final size:18
Alignment explanation
Indices: 34865031--34865073 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
34865021 TAATTACGGG
*
34865031 TTTTAAATGATTTTTTAA
1 TTTTAAATGATTTCTTAA
*
34865049 TTTT-AATTATTTCTTAA
1 TTTTAAATGATTTCTTAA
*
34865066 GTTTAAAT
1 TTTTAAAT
34865074 TCATTTGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (18 bp):
TTTTAAATGATTTCTTAA
Found at i:34869104 original size:18 final size:17
Alignment explanation
Indices: 34869064--34869096 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
34869054 AACATTAATT
34869064 TCAT-TATATGTTTTTA
1 TCATATATATGTTTTTA
34869080 TCATATATACTGTTTTT
1 TCATATATA-TGTTTTT
34869097 TTGATATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 4 0.27
18 7 0.47
ACGTcount: A:0.24, C:0.09, G:0.06, T:0.61
Consensus pattern (17 bp):
TCATATATATGTTTTTA
Found at i:34882573 original size:24 final size:23
Alignment explanation
Indices: 34882531--34882581 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
34882521 AATCAAAGTC
* *
34882531 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAAT-AATACT
*
34882555 AAATATATTATACTCATAATACT
1 AAATATATTATACTAATAATACT
34882578 AAAT
1 AAAT
34882582 CTTTTAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (23 bp):
AAATATATTATACTAATAATACT
Found at i:34885176 original size:13 final size:13
Alignment explanation
Indices: 34885149--34885185 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
34885139 AGTTCTTCAT
34885149 TGCTTTT-AAAAG
1 TGCTTTTGAAAAG
*
34885161 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
34885174 TGCTTTTGAAAA
1 TGCTTTTGAAAA
34885186 TTTTGGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.41
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:34890954 original size:170 final size:170
Alignment explanation
Indices: 34890672--34891012 Score: 673
Period size: 170 Copynumber: 2.0 Consensus size: 170
34890662 TTCTAAGTCC
34890672 ATCAATGATTTGTTTAATTTACTTGATGTTGAGGAAGATGAGTACTACCCTATGATAAACAACAT
1 ATCAATGATTTGTTTAATTTACTTGATGTTGAGGAAGATGAGTACTACCCTATGATAAACAACAT
*
34890737 CAATTGAGATTTTCTTCAATAAGTGCTTGATGTTGTGACAAATCTGGGATCCCAATGGATTATAA
66 CAATTGAGATTTTCTTCAATAAGTGCTTAATGTTGTGACAAATCTGGGATCCCAATGGATTATAA
34890802 GAAAGTATAGAAGCCATTCTTGTCGAAGAGAATATTTAAA
131 GAAAGTATAGAAGCCATTCTTGTCGAAGAGAATATTTAAA
34890842 ATCAATGATTTGTTTAATTTACTTGATGTTGAGGAAGATGAGTACTACCCTATGATAAACAACAT
1 ATCAATGATTTGTTTAATTTACTTGATGTTGAGGAAGATGAGTACTACCCTATGATAAACAACAT
34890907 CAATTGAGATTTTCTTCAATAAGTGCTTAATGTTGTGACAAATCTGGGATCCCAATGGATTATAA
66 CAATTGAGATTTTCTTCAATAAGTGCTTAATGTTGTGACAAATCTGGGATCCCAATGGATTATAA
34890972 GAAAGTATAGAAGCCATTCTTGTCGAAGAGAATATTTAAA
131 GAAAGTATAGAAGCCATTCTTGTCGAAGAGAATATTTAAA
34891012 A
1 A
34891013 CCAGTAGCAA
Statistics
Matches: 170, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 170 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (170 bp):
ATCAATGATTTGTTTAATTTACTTGATGTTGAGGAAGATGAGTACTACCCTATGATAAACAACAT
CAATTGAGATTTTCTTCAATAAGTGCTTAATGTTGTGACAAATCTGGGATCCCAATGGATTATAA
GAAAGTATAGAAGCCATTCTTGTCGAAGAGAATATTTAAA
Found at i:34897536 original size:40 final size:38
Alignment explanation
Indices: 34897478--34897589 Score: 117
Period size: 40 Copynumber: 2.9 Consensus size: 38
34897468 GCGCAATCAC
34897478 CGTTGGTTTATCCAACTAGAGCTGGGCTCACAATTATTAT
1 CGTTGGTTTATCCAACTAGAGCTGGGCTCA-AATTATT-T
* * *
34897518 CGTTGGTATATCCGACTAGCA-TTGGG-TGCAAA-TA-TT
1 CGTTGGTTTATCCAACTAG-AGCTGGGCT-CAAATTATTT
34897554 -GTTGGTTTATCCAACTAGAGCTGGGCTCAAAATTAT
1 CGTTGGTTTATCCAACTAGAGCTGGGCTC-AAATTAT
34897590 CATTGTCGGT
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
34 1 0.02
35 21 0.36
36 5 0.08
37 3 0.05
38 2 0.03
39 3 0.05
40 23 0.39
41 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (38 bp):
CGTTGGTTTATCCAACTAGAGCTGGGCTCAAATTATTT
Found at i:34900116 original size:24 final size:24
Alignment explanation
Indices: 34900088--34900139 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
34900078 TTTCTAGAAG
*
34900088 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGTATAATAT
*
34900112 ATTTAGCATTTATTAGTATAATTT
1 ATTTAGCATTTATTAGTATAATAT
34900136 ATTT
1 ATTT
34900140 GACCTACGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (24 bp):
ATTTAGCATTTATTAGTATAATAT
Found at i:34905827 original size:16 final size:18
Alignment explanation
Indices: 34905806--34905842 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
34905796 AGGGGGAGAA
34905806 AATAAAA-AATTGG-ATG
1 AATAAAATAATTGGAATG
*
34905822 AATAAAATATTTGGAATG
1 AATAAAATAATTGGAATG
34905840 AAT
1 AAT
34905843 TATCATTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 5 0.28
18 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.16, T:0.30
Consensus pattern (18 bp):
AATAAAATAATTGGAATG
Found at i:34908805 original size:9 final size:9
Alignment explanation
Indices: 34908788--34908818 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
34908778 TTATATATAA
*
34908788 AAAACATTT
1 AAAATATTT
34908797 AAAATATTT
1 AAAATATTT
34908806 AAAATATTT
1 AAAATATTT
34908815 AAAA
1 AAAA
34908819 AAAACTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAATATTT
Found at i:34912704 original size:53 final size:53
Alignment explanation
Indices: 34912602--34912704 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
34912592 GAATTTTCCC
* * *
34912602 ATATGATGCCATAACCCATCAGTTATGGTCTTACATGATATGATCTTCTTTCG
1 ATATGATGCCATAACCCACCAGTTACGGTCTTACATGATATGATATTCTTTCG
* *
34912655 ATATGATGTCATAACCCACCAGTTACGGTCTTACATGATATGGTATTCTT
1 ATATGATGCCATAACCCACCAGTTACGGTCTTACATGATATGATATTCTT
34912705 CCCATATAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (53 bp):
ATATGATGCCATAACCCACCAGTTACGGTCTTACATGATATGATATTCTTTCG
Found at i:34913030 original size:30 final size:30
Alignment explanation
Indices: 34912981--34913051 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
34912971 ACCAGTAGAT
* * *
34912981 TTCATGCATTACATGCTCTTATGTTCATCC
1 TTCATACATTAAATGCTCTTACGTTCATCC
* *
34913011 TTCGTACATTAAATTCTCTTACGTTCATCC
1 TTCATACATTAAATGCTCTTACGTTCATCC
34913041 TTCATACATTA
1 TTCATACATTA
34913052 CTTTTCTTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.24, C:0.25, G:0.07, T:0.44
Consensus pattern (30 bp):
TTCATACATTAAATGCTCTTACGTTCATCC
Found at i:34915405 original size:20 final size:20
Alignment explanation
Indices: 34915382--34915442 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
34915372 ATTTATCTGT
* *
34915382 ATTACTGGTAACTTGCCCAC
1 ATTACTGGTAGCTTGTCCAC
* **
34915402 ATTACTGGCAGCTTGTCTGC
1 ATTACTGGTAGCTTGTCCAC
34915422 ATTACTGGTAGCTTGTCCAC
1 ATTACTGGTAGCTTGTCCAC
34915442 A
1 A
34915443 AATTGGAGTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.33
Consensus pattern (20 bp):
ATTACTGGTAGCTTGTCCAC
Found at i:34918618 original size:21 final size:21
Alignment explanation
Indices: 34918594--34918664 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
34918584 TATCTCTGTA
* **
34918594 ACACGGGCGTGTTTCTCAGCC
1 ACACGGTCGTGTGCCTCAGCC
*
34918615 ACACGATCGTGTGCCTCAGCC
1 ACACGGTCGTGTGCCTCAGCC
* * *
34918636 ACACGGTCGTGTACCTCTGTC
1 ACACGGTCGTGTGCCTCAGCC
34918657 ACACGGTC
1 ACACGGTC
34918665 TGGACCCTTC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.17, C:0.35, G:0.25, T:0.23
Consensus pattern (21 bp):
ACACGGTCGTGTGCCTCAGCC
Found at i:34927966 original size:21 final size:21
Alignment explanation
Indices: 34927924--34927966 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
34927914 ATTTTATTTT
**
34927924 ATTTTCAAAATTTTAATTAAA
1 ATTTTCAAAATTTTAAAAAAA
34927945 ATTTT-AAATATTTTAAAAAAA
1 ATTTTCAAA-ATTTTAAAAAAA
34927966 A
1 A
34927967 AATTCAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTTTCAAAATTTTAAAAAAA
Found at i:34930912 original size:19 final size:19
Alignment explanation
Indices: 34930888--34930926 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
34930878 GTCTAATGTT
34930888 TTTAAGCTTAGGAAATATG
1 TTTAAGCTTAGGAAATATG
34930907 TTTAAGCTTAGGAAATATG
1 TTTAAGCTTAGGAAATATG
34930926 T
1 T
34930927 ATTGGTCGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (19 bp):
TTTAAGCTTAGGAAATATG
Found at i:34931042 original size:23 final size:22
Alignment explanation
Indices: 34931016--34931069 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
34931006 TAATTAAAAT
* *
34931016 TAAAATTAAAACTATTTTTTTAA
1 TAAAATTAAAACTA-ATTGTTAA
*
34931039 TAAAATTAAAACTAATTGTTAT
1 TAAAATTAAAACTAATTGTTAA
34931061 TAAAATTAA
1 TAAAATTAA
34931070 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAATTAAAACTAATTGTTAA
Found at i:34931067 original size:22 final size:23
Alignment explanation
Indices: 34931014--34931069 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
34931004 TTTAATTAAA
* *
34931014 ATTAAAATTAAAACTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
34931037 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
34931059 ATTAAAATTAA
1 ATTAAAATTAA
34931070 TTGTTAGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:34931082 original size:16 final size:16
Alignment explanation
Indices: 34931045--34931084 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
34931035 TTAATAAAAT
* *
34931045 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
34931061 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
34931077 TAAAATTA
1 TAAAATTA
34931085 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:34931154 original size:66 final size:59
Alignment explanation
Indices: 34931087--34931206 Score: 197
Period size: 59 Copynumber: 2.1 Consensus size: 59
34931077 TAAAATTATC
* * *
34931087 AAATTAT-TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
*
34931145 AATTTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
34931204 AAA
1 AAA
34931207 CAAACTTGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
58 6 0.11
59 50 0.89
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (59 bp):
AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
Found at i:34931312 original size:22 final size:24
Alignment explanation
Indices: 34931272--34931315 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
34931262 AAATAAACTT
34931272 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
34931296 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
34931316 AATATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:34935636 original size:45 final size:44
Alignment explanation
Indices: 34935452--34935822 Score: 273
Period size: 44 Copynumber: 8.3 Consensus size: 44
34935442 AATTTACTTG
** * *
34935452 ACTGCAACTTTGGGGAGATAAGATTAGTATCTTCAATCT-CTCC
1 ACTGCAACTTCAGAGAGATAAGATTTGTATCTTCAATCTGCTCC
* * * * *
34935495 ACTACATCTTCAGGGAGATAAGATTAGTAACTTC-ATCCTGCTCC
1 ACTGCAACTTCAGAGAGATAAGATTTGTATCTTCAAT-CTGCTCC
* * * * * * * *
34935539 ACTACATCTTCAGGGAGATAAGGTTTATAGT-TTTAATATGCTCT
1 ACTGCAACTTCAGAGAGATAAGATTTGTA-TCTTCAATCTGCTCC
* * * *
34935583 ACTACAACTTTAGAGAGATAGGATTTGTTATCTTCAGTCTGCTCC
1 ACTGCAACTTCAGAGAGATAAGATTTG-TATCTTCAATCTGCTCC
* * *
34935628 ACTGCAACTTTAGAGAGATAAGACTTGTATCTTCAATCTGCCCC
1 ACTGCAACTTCAGAGAGATAAGATTTGTATCTTCAATCTGCTCC
* * * *
34935672 ACTGCAACTTCAGGGAGATTCGATTGTAATTTGTAGCCTT-AATCTGTTCC
1 ACTGCAACTTCAGAGAGA-T--A-AG--ATTTGTA-TCTTCAATCTGCTCC
* * * * * *
34935722 ACTACAACTTCAGGGAAATAAGATTCGCTATCTTTAGTCTGCTCC
1 ACTGCAACTTCAGAGAGATAAGATTTG-TATCTTCAATCTGCTCC
* * * *
34935767 ACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCC
1 ACTGCAACTTCAGAGAGATAAGATTTGTATCTTCAATCTGCTCC
34935811 ACTGCAACTTCA
1 ACTGCAACTTCA
34935823 AGGGGATCTG
Statistics
Matches: 264, Mismatches: 49, Indels: 29
0.77 0.14 0.08
Matches are distributed among these distances:
42 2 0.01
43 31 0.12
44 122 0.46
45 71 0.27
46 1 0.00
47 2 0.01
48 1 0.00
49 1 0.00
50 30 0.11
51 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32
Consensus pattern (44 bp):
ACTGCAACTTCAGAGAGATAAGATTTGTATCTTCAATCTGCTCC
Found at i:34935680 original size:89 final size:87
Alignment explanation
Indices: 34935452--34935820 Score: 289
Period size: 89 Copynumber: 4.1 Consensus size: 87
34935442 AATTTACTTG
* *
34935452 ACTGCAACTTTGGGGAGATAAGATTAGTATCTTCAATCT-CTCCACTACATCTTCAGGGAGATAA
1 ACTGCAACTTTAGGGAGATAAGATT-GTATCTTCAATCTGCTCCACTACAACTTCAGGGAGATAA
34935516 GATTAGTAACTTCATCCTGCTCC
65 GATTAGTAACTTCATCCTGCTCC
* * * * * * * * * *
34935539 ACTACATCTTCAGGGAGATAAGGTT-TATAGTTTTAATATGCTCTACTACAACTTTAGAGAGATA
1 ACTGCAACTTTAGGGAGATAAGATTGTAT--CTTCAATCTGCTCCACTACAACTTCAGGGAGATA
* * *
34935603 GGATTTGTTATCTTCAGT-CTGCTCC
64 AGATTAG-TAACTTCA-TCCTGCTCC
* * *
34935628 ACTGCAACTTTAGAGAGATAAGACTTGTATCTTCAATCTGCCCCACTGCAACTTCAGGGAGATTC
1 ACTGCAACTTTAGGGAGATAAGA-TTGTATCTTCAATCTGCTCCACTACAACTTCAGGGAGA-T-
* * * * *
34935693 GATTGTAATTTGTAGCCTTAAT-CTGTTCC
63 -A-AG--ATTAGTA-ACTTCATCCTGCTCC
* * * * * *
34935722 ACTACAACTTCAGGGAAATAAGATTCGCTATCTTTAGTCTGCTCCACTGCAACTTCAGGGAGATA
1 ACTGCAACTTTAGGGAGATAAGATT-G-TATCTTCAATCTGCTCCACTACAACTTCAGGGAGATA
*
34935787 AGACTT-GTAACTTCAACCTGCTCC
64 AGA-TTAGTAACTTCATCCTGCTCC
34935811 ACTGCAACTT
1 ACTGCAACTT
34935821 CAAGGGGATC
Statistics
Matches: 219, Mismatches: 45, Indels: 34
0.73 0.15 0.11
Matches are distributed among these distances:
85 3 0.01
87 26 0.12
88 29 0.13
89 75 0.34
90 6 0.03
91 4 0.02
92 2 0.01
93 3 0.01
94 30 0.14
95 41 0.19
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32
Consensus pattern (87 bp):
ACTGCAACTTTAGGGAGATAAGATTGTATCTTCAATCTGCTCCACTACAACTTCAGGGAGATAAG
ATTAGTAACTTCATCCTGCTCC
Found at i:34935766 original size:139 final size:140
Alignment explanation
Indices: 34935583--34935891 Score: 462
Period size: 139 Copynumber: 2.2 Consensus size: 140
34935573 AATATGCTCT
* * * * * *
34935583 ACTACAACTTTAGAGAGATAGGATTTGTTATCTTCAGTCTGCTCCACTGCAACTTTAGAGAGATA
1 ACTACAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGAGAGATA
* * *
34935648 AGACTTGTATCTTCAATCTGCCCCACTGCAACTTC-AGGGAGAT-TCGA-TTGTAATTTGTAGCC
66 AGACTTGTAACTTCAACCTGCCCCACTGCAACTTCAAGGG-GATCT-GACTTGTAATTTATAGCC
34935710 TTAATCTGTTCC
129 TTAATCTGTTCC
* * *
34935722 ACTACAACTTCAGGGAAATAAGATTCGCTATCTTTAGTCTGCTCCACTGCAACTTCAGGGAGATA
1 ACTACAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGAGAGATA
*
34935787 AGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAAGGGGATCTGACTTGTAATTTATAGCCTT
66 AGACTTGTAACTTCAACCTGCCCCACTGCAACTTCAAGGGGATCTGACTTGTAATTTATAGCCTT
34935852 AATCTGTTCC
131 AATCTGTTCC
34935862 ACTACAACTTCAGGGAAATAAGATTTGCTA
1 ACTACAACTTCAGGGAAATAAGATTTGCTA
34935892 CGATGACTAT
Statistics
Matches: 153, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
139 93 0.61
140 60 0.39
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32
Consensus pattern (140 bp):
ACTACAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGAGAGATA
AGACTTGTAACTTCAACCTGCCCCACTGCAACTTCAAGGGGATCTGACTTGTAATTTATAGCCTT
AATCTGTTCC
Found at i:34947946 original size:18 final size:19
Alignment explanation
Indices: 34947915--34947951 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
34947905 GCAATTTGTA
34947915 ATAAAATAGATAATAATAG
1 ATAAAATAGATAATAATAG
34947934 ATAAAAT-GATAATAATAG
1 ATAAAATAGATAATAATAG
34947952 TGAGAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (19 bp):
ATAAAATAGATAATAATAG
Found at i:34949738 original size:39 final size:40
Alignment explanation
Indices: 34949611--34949745 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 40
34949601 GTTTGGATAC
* * **
34949611 AAAACGCCACCAAAAATCAAGCATTAGCGGCGCTTTAGGA
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTCGA
* * * * * * *
34949651 AAAACGCCGCTAAAGATCTAGTATTAGCGGTGTTTTTTGG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTCGA
*
34949691 AAAACGCCGCTAAAAAT-AAGCATTAGCGGCG-TTTTCCA
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTCGA
*
34949729 AAAAGCGCCGCAAAAAA
1 AAAA-CGCCGCTAAAAA
34949746 CCCAAGCACA
Statistics
Matches: 76, Mismatches: 18, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
38 8 0.11
39 22 0.29
40 46 0.61
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTCGA
Found at i:34950635 original size:14 final size:14
Alignment explanation
Indices: 34950595--34950637 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
34950585 AGGGATTATT
* *
34950595 GTTTATGGTTTACG
1 GTTTAAGGTTTAGG
*
34950609 GTTTAAGGGTTAGG
1 GTTTAAGGTTTAGG
34950623 GTTTAAGGTTTAGG
1 GTTTAAGGTTTAGG
34950637 G
1 G
34950638 CCGGGTTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.19, C:0.02, G:0.37, T:0.42
Consensus pattern (14 bp):
GTTTAAGGTTTAGG
Found at i:34957394 original size:22 final size:22
Alignment explanation
Indices: 34957354--34957395 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
34957344 TTTCCTCTAT
* *
34957354 TATTTAGATTTTATCATAATAA
1 TATTAAGATTTTATAATAATAA
*
34957376 TATTAAGATTTTCTAATAAT
1 TATTAAGATTTTATAATAAT
34957396 CTAATTAGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (22 bp):
TATTAAGATTTTATAATAATAA
Found at i:34957676 original size:28 final size:28
Alignment explanation
Indices: 34957636--34957691 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
34957626 TGGATAAGTT
34957636 CAATTTCTGAAATGTGTATAATGGACTA
1 CAATTTCTGAAATGTGTATAATGGACTA
34957664 CAATTTCTGAAATGTGTATAATGGACTA
1 CAATTTCTGAAATGTGTATAATGGACTA
34957692 TTAAATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (28 bp):
CAATTTCTGAAATGTGTATAATGGACTA
Found at i:34959068 original size:30 final size:31
Alignment explanation
Indices: 34959029--34959088 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
34959019 GGAGGTGAGA
*
34959029 TGGGAAGGGAATAAAATTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
34959060 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
34959089 TAAAAGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.22
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:34959236 original size:30 final size:31
Alignment explanation
Indices: 34959193--34959253 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
34959183 GGGTTGGGAG
* *
34959193 GGGAGAGGAGTAAAAGTTTTGGGGGGAAAGT
1 GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
*
34959224 GGGA-AGGTGTAAAAGTTTTGAGGGAAAAGT
1 GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
34959254 AAAAAGGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.44, T:0.21
Consensus pattern (31 bp):
GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
Found at i:34959261 original size:30 final size:30
Alignment explanation
Indices: 34959202--34959261 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
34959192 GGGGAGAGGA
* * ***
34959202 GTAAAAGTTTTGGGGGGAAAGTGGGAAGGT
1 GTAAAAGTTTTGAGGGAAAAGTAAAAAGGT
34959232 GTAAAAGTTTTGAGGGAAAAGTAAAAAGGT
1 GTAAAAGTTTTGAGGGAAAAGTAAAAAGGT
34959262 TTAGGAGTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (30 bp):
GTAAAAGTTTTGAGGGAAAAGTAAAAAGGT
Found at i:34959320 original size:9 final size:9
Alignment explanation
Indices: 34959302--34959338 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
34959292 TATAGTTTGA
34959302 TATTCGAAT
1 TATTCGAAT
*
34959311 TATTCAAAT
1 TATTCGAAT
*
34959320 TATTCGAGT
1 TATTCGAAT
34959329 TATTCGAAT
1 TATTCGAAT
34959338 T
1 T
34959339 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:34965893 original size:25 final size:25
Alignment explanation
Indices: 34965855--34965925 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
34965845 AGGCCTATTT
* *
34965855 TCACAACTCATGTGAGCATACTGAA
1 TCACAACTCGTGTGAGCATACCGAA
*
34965880 TCACAACTCGTGTGAGCATACCGAT
1 TCACAACTCGTGTGAGCATACCGAA
*
34965905 TCACAGCTCGTGTGAGCATAC
1 TCACAACTCGTGTGAGCATAC
34965926 ATGTACAAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.24
Consensus pattern (25 bp):
TCACAACTCGTGTGAGCATACCGAA
Found at i:34969131 original size:106 final size:106
Alignment explanation
Indices: 34968944--34969143 Score: 269
Period size: 106 Copynumber: 1.9 Consensus size: 106
34968934 ATATGATATG
* * * *
34968944 AAATGTTTATAGATATGTGTTCGTATGATTTAAAAACTTCGGTAATGCTCCATAACCCTGTTTCG
1 AAATGTTTATAAATATGTGTTCGTATGATTTAAAAACTCCGGAAATGCTCCATAACCCTGTTTCA
* *
34969009 GTGACAGATACAGGTTATGTGTGTTACATTTATTGGTATTA
66 GCGACAGATACAGGTTATGTGTCTTACATTTATTGGTATTA
* **
34969050 AAATGTTTATAAATATGTGTTCGTATGATTTGAAAACTCCGGAAATGCTTTATAA-CCT-TATTC
1 AAATGTTTATAAATATGTGTTCGTATGATTTAAAAACTCCGGAAATGCTCCATAACCCTGT-TTC
* *
34969113 TAGCGACGGATACGGGTTATGTGTCTTACAT
65 -AGCGACAGATACAGGTTATGTGTCTTACAT
34969144 AGGATGTGTG
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
104 1 0.01
105 6 0.07
106 74 0.91
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.39
Consensus pattern (106 bp):
AAATGTTTATAAATATGTGTTCGTATGATTTAAAAACTCCGGAAATGCTCCATAACCCTGTTTCA
GCGACAGATACAGGTTATGTGTCTTACATTTATTGGTATTA
Found at i:34972020 original size:50 final size:50
Alignment explanation
Indices: 34971945--34972086 Score: 194
Period size: 50 Copynumber: 2.8 Consensus size: 50
34971935 ATTTGGGTAA
34971945 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGATG
** * *
34971995 AGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGATG
** * * * *
34972045 AGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGCA
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCA
34972087 GTACAAAAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 79 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGATG
Found at i:34975946 original size:13 final size:13
Alignment explanation
Indices: 34975928--34975954 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
34975918 TAGTCAAAAC
34975928 ACCCTTATTAAGT
1 ACCCTTATTAAGT
34975941 ACCCTTATTAAGT
1 ACCCTTATTAAGT
34975954 A
1 A
34975955 ATATCTTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (13 bp):
ACCCTTATTAAGT
Found at i:34978922 original size:6 final size:6
Alignment explanation
Indices: 34978911--34978937 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
34978901 GAGTTTAGCT
34978911 AAAAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA
34978938 GAGAGAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:34983751 original size:46 final size:46
Alignment explanation
Indices: 34983676--34983763 Score: 110
Period size: 46 Copynumber: 1.9 Consensus size: 46
34983666 AATCTAATCT
* *
34983676 AATAATACATAAAAATTTATGATGTTAATAATAT-ATTGTAATTTAA
1 AATAATACATAAAAATTTATAATGCTAAT-ATATGATTGTAATTTAA
34983722 AATAATACATAATGAAA-TTA-AATGCTAATATATGATTGTAAT
1 AATAATACATAA--AAATTTATAATGCTAATATATGATTGTAAT
34983764 ATATTAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
45 4 0.11
46 27 0.73
47 3 0.08
48 3 0.08
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (46 bp):
AATAATACATAAAAATTTATAATGCTAATATATGATTGTAATTTAA
Found at i:34986385 original size:24 final size:26
Alignment explanation
Indices: 34986357--34986411 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
34986347 CACCCGGAAT
*
34986357 AATATA-A-ATCCTCCTTAACACACC
1 AATATACATATCCTCCTAAACACACC
*
34986381 AATATATCATATCCTCCTAAACACACT
1 AATATA-CATATCCTCCTAAACACACC
34986408 AATA
1 AATA
34986412 AGACATTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 6 0.23
26 1 0.04
27 19 0.73
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (26 bp):
AATATACATATCCTCCTAAACACACC
Found at i:34986986 original size:22 final size:24
Alignment explanation
Indices: 34986943--34986986 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
34986933 TAGCTAAGCT
34986943 TACTTACTTTTCTAGCTTAATTCA
1 TACTTACTTTTCTAGCTTAATTCA
34986967 TACTT-CTTTTCTA-CTTAATT
1 TACTTACTTTTCTAGCTTAATT
34986987 TCTTGCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.23, C:0.20, G:0.02, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAGCTTAATTCA
Found at i:34987856 original size:3 final size:3
Alignment explanation
Indices: 34987848--34987897 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
34987838 AACTTATTTC
*
34987848 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATTA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
34987893 ATA AT
1 ATA AT
34987898 TTATTTTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:34990234 original size:18 final size:17
Alignment explanation
Indices: 34990202--34990238 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
34990192 AAATTTATCA
*
34990202 TTATATTTTATTTATAT
1 TTATATTTTAATTATAT
34990219 TTATATTTTTAATTATAT
1 TTATA-TTTTAATTATAT
34990237 TT
1 TT
34990239 TGAAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATATTTTAATTATAT
Found at i:34995454 original size:3 final size:3
Alignment explanation
Indices: 34995448--34995526 Score: 142
Period size: 3 Copynumber: 26.3 Consensus size: 3
34995438 AAAAAACCAT
34995448 AGA AGA AGA AGA AGA ATG- AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA
34995493 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
34995527 AAAAAAGAAA
Statistics
Matches: 74, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 1 0.01
3 72 0.97
4 1 0.01
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (3 bp):
AGA
Found at i:34997271 original size:21 final size:21
Alignment explanation
Indices: 34997245--34997300 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
34997235 CGAGTTATTA
34997245 AGTTCAAGTGGTTTGACCCTG
1 AGTTCAAGTGGTTTGACCCTG
*
34997266 AGTTCAAGTGGTTTGACCTTG
1 AGTTCAAGTGGTTTGACCCTG
*
34997287 AGGTCAAGTGGTTT
1 AGTTCAAGTGGTTT
34997301 TAGAAAATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.14, G:0.30, T:0.36
Consensus pattern (21 bp):
AGTTCAAGTGGTTTGACCCTG
Found at i:34998578 original size:33 final size:33
Alignment explanation
Indices: 34998535--34998606 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
34998525 ACATGCTGTA
* *
34998535 ACAGTCTGGGCCTGAGCCCTAT-TCAGTAATAGT
1 ACAGTGTGGGCCTGAGCCCAATAT-AGTAATAGT
*
34998568 ACAGTGTGGGCCTTAGCCCAATATAGTAATAGT
1 ACAGTGTGGGCCTGAGCCCAATATAGTAATAGT
34998601 ACAGTG
1 ACAGTG
34998607 CAAAAATGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 34 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (33 bp):
ACAGTGTGGGCCTGAGCCCAATATAGTAATAGT
Found at i:34998756 original size:26 final size:26
Alignment explanation
Indices: 34998703--34998757 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
34998693 AACACACCGA
*
34998703 TATCACAGCAAAGCTGCCAAAAATAG
1 TATCACAGCAAAGCTGCCAAAAACAG
* **
34998729 TATCGCAGCAAAGCTGCCAGTAACAG
1 TATCACAGCAAAGCTGCCAAAAACAG
34998755 TAT
1 TAT
34998758 ATGTGACAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (26 bp):
TATCACAGCAAAGCTGCCAAAAACAG
Found at i:34999133 original size:29 final size:29
Alignment explanation
Indices: 34999076--34999144 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
34999066 ATAATAGTGT
*
34999076 AAATGGGCCCAATGCCCATTACTCGGCCC
1 AAATGGGCCCAATGCCCATTACTCAGCCC
34999105 AAATGGGCCCACATGGCCCA-T-CTCAGCCC
1 AAATGGGCCCA-AT-GCCCATTACTCAGCCC
34999134 AACAT-GGCCCA
1 AA-ATGGGCCCA
34999145 TTACTTCCCA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
29 26 0.72
30 5 0.14
31 5 0.14
ACGTcount: A:0.26, C:0.39, G:0.20, T:0.14
Consensus pattern (29 bp):
AAATGGGCCCAATGCCCATTACTCAGCCC
Found at i:34999154 original size:20 final size:20
Alignment explanation
Indices: 34999131--34999168 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
34999121 CCCATCTCAG
*
34999131 CCCAACATGGCCCATTACTT
1 CCCAACAGGGCCCATTACTT
*
34999151 CCCAATAGGGCCCATTAC
1 CCCAACAGGGCCCATTAC
34999169 GGCCCAAGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.39, G:0.13, T:0.21
Consensus pattern (20 bp):
CCCAACAGGGCCCATTACTT
Found at i:35002064 original size:7 final size:7
Alignment explanation
Indices: 35002054--35002113 Score: 120
Period size: 7 Copynumber: 8.6 Consensus size: 7
35002044 TTATTAAGCT
35002054 TATAATA
1 TATAATA
35002061 TATAATA
1 TATAATA
35002068 TATAATA
1 TATAATA
35002075 TATAATA
1 TATAATA
35002082 TATAATA
1 TATAATA
35002089 TATAATA
1 TATAATA
35002096 TATAATA
1 TATAATA
35002103 TATAATA
1 TATAATA
35002110 TATA
1 TATA
35002114 TTAGATGTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 53 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TATAATA
Found at i:35002148 original size:19 final size:22
Alignment explanation
Indices: 35002126--35002172 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 22
35002116 AGATGTTAGA
35002126 ATATTA-ATTCT-AT-TATATT
1 ATATTATATTCTAATATATATT
35002145 ATA-TATATTCTAATATATATT
1 ATATTATATTCTAATATATATT
35002166 AGTATTA
1 A-TATTA
35002173 GAATTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 2 0.09
19 8 0.35
20 2 0.09
21 7 0.30
22 2 0.09
23 2 0.09
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
ATATTATATTCTAATATATATT
Found at i:35002153 original size:14 final size:14
Alignment explanation
Indices: 35002058--35002255 Score: 69
Period size: 14 Copynumber: 14.4 Consensus size: 14
35002048 TAAGCTTATA
* *
35002058 ATATATAATATATA
1 ATATATATTATATT
* *
35002072 ATATATAATATATA
1 ATATATATTATATT
* *
35002086 ATATATAATATATA
1 ATATATATTATATT
35002100 ATATATAATATATATT
1 ATATAT-AT-TATATT
* * **
35002116 AGATGTTAGAATATT
1 ATAT-ATATTATATT
*
35002131 A-ATTCTATTATATT
1 ATA-TATATTATATT
*
35002145 ATATATATTCTA--
1 ATATATATTATATT
35002157 ATATATATTAGTATT
1 ATATATATTA-TATT
*
35002172 AGA-AT-TTAT-TT
1 ATATATATTATATT
*
35002183 ATATATTTTATTCATT
1 ATATATATTA-T-ATT
* *
35002199 -TATTTATCTATTTT
1 ATATATAT-TATATT
* *
35002213 ATTTATAATATATT
1 ATATATATTATATT
*
35002227 AGA-ATATTATATT
1 ATATATATTATATT
35002240 A-A-A-ATTATATT
1 ATATATATTATATT
35002251 A-ATAT
1 ATATAT
35002256 TATTTTTCTA
Statistics
Matches: 143, Mismatches: 24, Indels: 35
0.71 0.12 0.17
Matches are distributed among these distances:
11 14 0.10
12 15 0.10
13 18 0.13
14 61 0.43
15 21 0.15
16 13 0.09
17 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (14 bp):
ATATATATTATATT
Found at i:35002201 original size:21 final size:21
Alignment explanation
Indices: 35002175--35002215 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
35002165 TAGTATTAGA
35002175 ATTTATTTATATATTTTATTC
1 ATTTATTTATATATTTTATTC
*
35002196 ATTTATTTATCTATTTTATT
1 ATTTATTTATATATTTTATT
35002216 TATAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (21 bp):
ATTTATTTATATATTTTATTC
Found at i:35006105 original size:6 final size:6
Alignment explanation
Indices: 35006096--35006147 Score: 52
Period size: 6 Copynumber: 8.2 Consensus size: 6
35006086 TAATTTTAAC
*
35006096 TTTATT TTTATT TTTATT GGTTTATT TTTA-T TTTATTAT TTTATT ATTATT
1 TTTATT TTTATT TTTATT --TTTATT TTTATT TTTA-T-T TTTATT TTTATT
35006147 T
1 T
35006148 GGGAAAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
5 5 0.13
6 22 0.56
7 1 0.03
8 11 0.28
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:35006129 original size:19 final size:19
Alignment explanation
Indices: 35006096--35006147 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
35006086 TAATTTTAAC
*
35006096 TTTATTTTTATTTTTATTGG
1 TTTATTTTTA-TTTTATTAG
*
35006116 TTTATTTTTATTTTATTAT
1 TTTATTTTTATTTTATTAG
*
35006135 TTTATTATTATTT
1 TTTATTTTTATTT
35006148 GGGAAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (19 bp):
TTTATTTTTATTTTATTAG
Found at i:35006134 original size:14 final size:15
Alignment explanation
Indices: 35006097--35006146 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
35006087 AATTTTAACT
*
35006097 TTATTTTTATTTTTA
1 TTATTATTATTTTTA
**
35006112 TTGGT-TTATTTTTA
1 TTATTATTATTTTTA
35006126 TT-TTATTA-TTTTA
1 TTATTATTATTTTTA
35006139 TTATTATT
1 TTATTATT
35006147 TGGGAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 8 0.27
14 19 0.63
15 3 0.10
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (15 bp):
TTATTATTATTTTTA
Found at i:35013275 original size:138 final size:137
Alignment explanation
Indices: 35013032--35013292 Score: 357
Period size: 138 Copynumber: 1.9 Consensus size: 137
35013022 CCGTATTTTG
* * *
35013032 GGTGCTAGTCCTGAATGTCCTACCGGTGGCTAAGTTTCAGGCATATGTTGCGGTTACTTGACAAC
1 GGTGCTAGTCCTGAATGTCCTACCGATGGCTAAGTTT-AGGCATATGTTGCGGATACTCGACAAC
* *
35013097 TTGTCTGAGCAGCACCGTGTAGCTACGTTTTGACCTACAGCTTGTGTGAGCAGACCCAGGTTACC
65 TTGTCTGAGCAGCACCGTGTAGCTACATTCTGACCTACAGCTTGTGTGAGCAGACCCAGGTTACC
35013162 ATGTTTCA
130 ATGTTTCA
* * *
35013170 GGTGCTAGTCTTGAATGTCCTACCGATGGCTGAGGTTT-GGCAT-TAGTTGTGGATACTCGACAA
1 GGTGCTAGTCCTGAATGTCCTACCGATGGCT-AAGTTTAGGCATAT-GTTGCGGATACTCGACAA
* * *
35013233 CTTGTGTGAGTAGCATCGTGTAGCTTACATTCTGA-CTGACAGCTTGTGTGAGCAGACCCA
64 CTTGTCTGAGCAGCACCGTGTAGC-TACATTCTGACCT-ACAGCTTGTGTGAGCAGACCCA
35013293 TTTTATAGCT
Statistics
Matches: 108, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
136 1 0.01
137 43 0.40
138 59 0.55
139 5 0.05
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (137 bp):
GGTGCTAGTCCTGAATGTCCTACCGATGGCTAAGTTTAGGCATATGTTGCGGATACTCGACAACT
TGTCTGAGCAGCACCGTGTAGCTACATTCTGACCTACAGCTTGTGTGAGCAGACCCAGGTTACCA
TGTTTCA
Found at i:35017636 original size:48 final size:48
Alignment explanation
Indices: 35017581--35017714 Score: 180
Period size: 48 Copynumber: 2.8 Consensus size: 48
35017571 CTATTTATCT
* * * * *
35017581 TGTAGGTTCAACCCTAAAGGGTAACCAAAAACTATTACTCATTATTTG
1 TGTAGGTTTAACCCTAAATGGTAACCAGACACTATTACTCATTACTTG
* * * *
35017629 TGTAGGTTTAACCCTGACTGGTAACCAGACACTATTATTTATTACTTG
1 TGTAGGTTTAACCCTAAATGGTAACCAGACACTATTACTCATTACTTG
35017677 TGTAGGTTTAACCC-AAATGGTAACCAGACACTATTACT
1 TGTAGGTTTAACCCTAAATGGTAACCAGACACTATTACT
35017715 TTCACCTGTG
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
47 21 0.28
48 53 0.72
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (48 bp):
TGTAGGTTTAACCCTAAATGGTAACCAGACACTATTACTCATTACTTG
Found at i:35018695 original size:26 final size:26
Alignment explanation
Indices: 35018666--35018719 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
35018656 TTTTGATGAA
*
35018666 TTCTTGTTGTCTTTGGTGGTTAAAGC
1 TTCTTGTTGTCTTTAGTGGTTAAAGC
35018692 TTCTTGTTGTCTTTAGTGGTTAAAGC
1 TTCTTGTTGTCTTTAGTGGTTAAAGC
35018718 TT
1 TT
35018720 GCTCTCAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.13, C:0.11, G:0.24, T:0.52
Consensus pattern (26 bp):
TTCTTGTTGTCTTTAGTGGTTAAAGC
Found at i:35020215 original size:21 final size:22
Alignment explanation
Indices: 35020189--35020238 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
35020179 TTTAATGTTT
*
35020189 TAAATTTG-AAAAAAGAAAAAC
1 TAAATTTGTAAAAAACAAAAAC
* * *
35020210 TAAATTCGTAAAATACAAATAC
1 TAAATTTGTAAAAAACAAAAAC
35020232 TAAATTT
1 TAAATTT
35020239 CAAATTGCTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (22 bp):
TAAATTTGTAAAAAACAAAAAC
Found at i:35022854 original size:54 final size:54
Alignment explanation
Indices: 35022796--35022999 Score: 151
Period size: 54 Copynumber: 3.8 Consensus size: 54
35022786 CAAATCATAG
* * * *
35022796 GATTCTAAAAATCTTGGAAGAGCAAGGTTACGATCGTAAATTAGTGAA-CTAAAA
1 GATTCTAAAAATCTTGGAAGTGCAAGGTTACAATCGTAAATCAGCGAACCT-AAA
* * * * * *
35022850 GATTCTAAAAAACTTAGAAGTGCAAGGTTGCAATTGTAAATCGGCGAACCTCAA
1 GATTCTAAAAATCTTGGAAGTGCAAGGTTACAATCGTAAATCAGCGAACCTAAA
* * *** * * *
35022904 GATTCTAATAATCATGGAAGTGCAAGGTTGTGATTGTAAATCAACAAACC-AGAA
1 GATTCTAAAAATCTTGGAAGTGCAAGGTTACAATCGTAAATCAGCGAACCTA-AA
* * * * * * *
35022958 GTTTCTGAAAATCTTGTAAGTACAGGGTTGCAATTGTAAATC
1 GATTCTAAAAATCTTGGAAGTGCAAGGTTACAATCGTAAATC
35023000 GGCAAACTAT
Statistics
Matches: 119, Mismatches: 29, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
54 117 0.98
55 2 0.02
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (54 bp):
GATTCTAAAAATCTTGGAAGTGCAAGGTTACAATCGTAAATCAGCGAACCTAAA
Found at i:35027205 original size:25 final size:26
Alignment explanation
Indices: 35027175--35027291 Score: 85
Period size: 25 Copynumber: 4.5 Consensus size: 26
35027165 AAGTAGATTA
35027175 TAAATTATATTTAATAATAATTAT-T
1 TAAATTATATTTAATAATAATTATAT
* * *
35027200 TAAATTATATTTTATAGTATTATATAT
1 TAAATTATATTTAATAATAAT-TATAT
* * * * * *
35027227 TATGATTTTAGTAAATTATATATTTTAT
1 TA-AATTATATTTAATAATA-ATTATAT
** *
35027255 TAAATTA-AGATAATAATAATTATTT
1 TAAATTATATTTAATAATAATTATAT
35027280 TAAATTATATTT
1 TAAATTATATTT
35027292 TAGTATTATA
Statistics
Matches: 66, Mismatches: 21, Indels: 9
0.69 0.22 0.09
Matches are distributed among these distances:
25 30 0.45
26 13 0.20
27 6 0.09
28 16 0.24
29 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (26 bp):
TAAATTATATTTAATAATAATTATAT
Found at i:35027236 original size:23 final size:22
Alignment explanation
Indices: 35027203--35027255 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
35027193 AATTATTTAA
*
35027203 ATTATATTTTA-TAGTATTATAT
1 ATTATATTTTAGTA-AATTATAT
35027225 ATTATGATTTTAGTAAATTATAT
1 ATTAT-ATTTTAGTAAATTATAT
*
35027248 ATTTTATT
1 ATTATATT
35027256 AAATTAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 8 0.30
23 17 0.63
24 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (22 bp):
ATTATATTTTAGTAAATTATAT
Found at i:35027253 original size:17 final size:17
Alignment explanation
Indices: 35027200--35027261 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
35027190 AATAATTATT
35027200 TAAATTATAT-TTTATAG
1 TAAATTATATATTT-TAG
*
35027217 TATTATATATTATGATTTTAG
1 TA-AAT-TA-TAT-ATTTTAG
*
35027238 TAAATTATATATTTTAT
1 TAAATTATATATTTTAG
35027255 TAAATTA
1 TAAATTA
35027262 AGATAATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
17 15 0.41
18 5 0.14
19 4 0.11
20 5 0.14
21 5 0.14
22 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (17 bp):
TAAATTATATATTTTAG
Found at i:35027289 original size:40 final size:39
Alignment explanation
Indices: 35027186--35027293 Score: 98
Period size: 40 Copynumber: 2.7 Consensus size: 39
35027176 AAATTATATT
* *
35027186 TAATAATAATTA-TTTAAATTATATTTTATAGTATTATA
1 TAATAATAATTATTTTAAATTATATTTTATAGAATTAGA
* * *
35027224 T-ATTATGATT-TTAGTAAATTATATATTTTATTA-AATTAAGA
1 TAATAATAATTATT-TTAAA-T-TATATTTTA-TAGAATT-AGA
35027265 TAATAATAATTATTTTAAATTATATTTTA
1 TAATAATAATTATTTTAAATTATATTTTA
35027294 GTATTATATA
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
37 8 0.15
38 5 0.09
39 1 0.02
40 21 0.39
41 6 0.11
42 11 0.20
43 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (39 bp):
TAATAATAATTATTTTAAATTATATTTTATAGAATTAGA
Found at i:35027298 original size:20 final size:21
Alignment explanation
Indices: 35027275--35027314 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
35027265 TAATAATAAT
*
35027275 TATTTTAAATTAT-ATTTTAG
1 TATTATAAATTATGATTTTAG
*
35027295 TATTATATATTATGATTTTA
1 TATTATAAATTATGATTTTA
35027315 TTAGTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (21 bp):
TATTATAAATTATGATTTTAG
Found at i:35027385 original size:15 final size:17
Alignment explanation
Indices: 35027347--35027380 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
35027337 TTTATTAACA
35027347 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
35027364 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
35027381 TTTATAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:35027394 original size:16 final size:15
Alignment explanation
Indices: 35027347--35027394 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
35027337 TTTATTAACA
*
35027347 ATTTTATTAAATTATAT
1 ATTTTA-TAAAAT-TAT
*
35027364 ATTTTATTAAATTAT
1 ATTTTATAAAATTAT
35027379 ATTTTATAACAATTAT
1 ATTTTATAA-AATTAT
35027395 GTTAAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.41
16 10 0.37
17 6 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTATAAAATTAT
Found at i:35027414 original size:117 final size:117
Alignment explanation
Indices: 35027231--35027634 Score: 702
Period size: 117 Copynumber: 3.5 Consensus size: 117
35027221 ATATATTATG
* ** * *
35027231 ATTTTAGTAAATTATATATTTTATTAAATTA-AGATAATAATAATTATTTTAAATTATATTTTAG
1 ATTTTATTAAATTATATATTTTATTAAATTATATTTAATAACAATTATGTTAAATTATATTTTAG
35027295 TATTATATATTATGATTTTATTAGTAAATTCATATAAGAATATTTATTAACA
66 TATTATATATTATGATTTTATTAGTAAATTCATATAAGAATATTTATTAACA
*
35027347 ATTTTATTAAATTATATATTTTATTAAATTATATTTTATAACAATTATGTTAAATTATATTTTAG
1 ATTTTATTAAATTATATATTTTATTAAATTATATTTAATAACAATTATGTTAAATTATATTTTAG
35027412 TATTATATATTATGATTTTATTAGTAAATTCATATAAGAATATTTATTAACA
66 TATTATATATTATGATTTTATTAGTAAATTCATATAAGAATATTTATTAACA
* *
35027464 ATTTTATTAAATTATATATTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTAG
1 ATTTTATTAAATTATATATTTTATTAAATTATATTTAATAACAATTATGTTAAATTATATTTTAG
* *
35027529 TATCATATATTATGATTTTATTAGTAAATTCATATAAGAATATTTATTAAAA
66 TATTATATATTATGATTTTATTAGTAAATTCATATAAGAATATTTATTAACA
*
35027581 ATTTTATTAAATTATATATTTTATTAAATTATATTTTATAACAATTATGTTAAA
1 ATTTTATTAAATTATATATTTTATTAAATTATATTTAATAACAATTATGTTAAA
35027635 ATATGATTAA
Statistics
Matches: 273, Mismatches: 14, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
116 30 0.11
117 243 0.89
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (117 bp):
ATTTTATTAAATTATATATTTTATTAAATTATATTTAATAACAATTATGTTAAATTATATTTTAG
TATTATATATTATGATTTTATTAGTAAATTCATATAAGAATATTTATTAACA
Found at i:35027484 original size:17 final size:17
Alignment explanation
Indices: 35027464--35027497 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
35027454 TTTATTAACA
35027464 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
35027481 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
35027498 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:35027601 original size:17 final size:17
Alignment explanation
Indices: 35027581--35027614 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
35027571 TTTATTAAAA
35027581 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
35027598 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
35027615 TTTATAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:35027628 original size:16 final size:15
Alignment explanation
Indices: 35027581--35027628 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
35027571 TTTATTAAAA
*
35027581 ATTTTATTAAATTATAT
1 ATTTTA-TAAAAT-TAT
*
35027598 ATTTTATTAAATTAT
1 ATTTTATAAAATTAT
35027613 ATTTTATAACAATTAT
1 ATTTTATAA-AATTAT
35027629 GTTAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.41
16 10 0.37
17 6 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTATAAAATTAT
Found at i:35027805 original size:39 final size:41
Alignment explanation
Indices: 35027761--35027865 Score: 124
Period size: 44 Copynumber: 2.5 Consensus size: 41
35027751 TTCCTTATGT
* *
35027761 TATTACACCTCTATTCCATTCAACCAAACACAAGAA-TACC
1 TATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTACC
*
35027801 -ATTACGCCTATATTCCATTACATTCAACCAAACAAAAGAATTACC
1 TATTACGCCTCTATT-C----CATTCAACCAAACAAAAGAATTACC
35027846 TATTACGCCTCTATTCCATT
1 TATTACGCCTCTATTCCATT
35027866 ACGCCTCTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
39 12 0.22
40 1 0.02
41 4 0.07
44 19 0.35
45 5 0.09
46 13 0.24
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.30
Consensus pattern (41 bp):
TATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTACC
Found at i:35027840 original size:44 final size:46
Alignment explanation
Indices: 35027777--35027867 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
35027767 ACCTCTATTC
*
35027777 CATTCAACCAAACACAAGAA-TACC-ATTACGCCTATATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTATATTCCATTA
*
35027821 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTATATTCCATTA
35027867 C
1 C
35027868 GCCTCTATTC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 19 0.44
45 4 0.09
46 20 0.47
ACGTcount: A:0.40, C:0.30, G:0.04, T:0.26
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTATATTCCATTA
Found at i:35027868 original size:16 final size:16
Alignment explanation
Indices: 35027847--35027899 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
35027837 AGAATTACCT
35027847 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
35027863 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
35027879 ATTACGCCTCTATTCT
1 ATTACGCCTCTATTCC
35027895 ATTAC
1 ATTAC
35027900 AGCGAACCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:35031473 original size:22 final size:21
Alignment explanation
Indices: 35031448--35031513 Score: 70
Period size: 22 Copynumber: 3.3 Consensus size: 21
35031438 CACTAGCAAA
*
35031448 AAGCCCGAATAACACTGGCACT
1 AAGCCTGAATAACAC-GGCACT
35031470 AAGCCTG-ATAA-A---CACT
1 AAGCCTGAATAACACGGCACT
35031486 AAGCCTGAATAACACCGGCACT
1 AAGCCTGAATAACA-CGGCACT
35031508 AAGCCT
1 AAGCCT
35031514 TCTAAGCACT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
16 11 0.30
17 4 0.11
18 1 0.03
20 1 0.03
21 4 0.11
22 16 0.43
ACGTcount: A:0.38, C:0.30, G:0.17, T:0.15
Consensus pattern (21 bp):
AAGCCTGAATAACACGGCACT
Found at i:35031499 original size:38 final size:38
Alignment explanation
Indices: 35031448--35031540 Score: 132
Period size: 38 Copynumber: 2.4 Consensus size: 38
35031438 CACTAGCAAA
*
35031448 AAGCCCGAATAACACTGGCACTAAGCCTGATAAACACT
1 AAGCCTGAATAACACTGGCACTAAGCCTGATAAACACT
* ** *
35031486 AAGCCTGAATAACACCGGCACTAAGCCTTCTAAGCACT
1 AAGCCTGAATAACACTGGCACTAAGCCTGATAAACACT
*
35031524 AAACCTGAATAACACTG
1 AAGCCTGAATAACACTG
35031541 ATTCAACATT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.39, C:0.29, G:0.15, T:0.17
Consensus pattern (38 bp):
AAGCCTGAATAACACTGGCACTAAGCCTGATAAACACT
Found at i:35033767 original size:187 final size:187
Alignment explanation
Indices: 35033452--35033795 Score: 580
Period size: 187 Copynumber: 1.8 Consensus size: 187
35033442 TAGATGCGCT
* * * *
35033452 TTCCTTCCATGGTTAAAAAGTAACGGCTTTTTGAACGTTGCTGCGCTAACGGTAAAAGAAATTAA
1 TTCCTTCCATGGTAAAAAAGTAACGGCTTTTTGAACGTTGCTACGCCAACGGTAAAAAAAATTAA
*
35033517 AATTTCAAAGGTAAGCTTTTTTTACCCTATAAATATCCCTCTAATTTCATTTTTTTTCATTCACA
66 AATTTCAAAGGTAAGCTTTTTTTACCCTATAAATATCCCTCAAATTTCATTTTTTTTCATTCACA
35033582 TCCTTCTCTCAACTCTCTCATTTTGATTGTGTTGAAGCGTGTCCAACCAGACAAGCA
131 TCCTTCTCTCAACTCTCTCATTTTGATTGTGTTGAAGCGTGTCCAACCAGACAAGCA
* *
35033639 TTCCTTCCATGGTAAAAAAGTAACGGGTTTTTGAACGTTGCTATGCCAACGGTAAAAAAAATTAA
1 TTCCTTCCATGGTAAAAAAGTAACGGCTTTTTGAACGTTGCTACGCCAACGGTAAAAAAAATTAA
* * *
35033704 AATTTCAACGGTAAGTTTTTTTTACCCTATAATTATCCCTCAAATTTCATTTTTTTTCATTCACA
66 AATTTCAAAGGTAAGCTTTTTTTACCCTATAAATATCCCTCAAATTTCATTTTTTTTCATTCACA
* *
35033769 TTCTTCTCTCAACTCTTTCATTTTGAT
131 TCCTTCTCTCAACTCTCTCATTTTGAT
35033796 CATGTTTGAT
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
187 145 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (187 bp):
TTCCTTCCATGGTAAAAAAGTAACGGCTTTTTGAACGTTGCTACGCCAACGGTAAAAAAAATTAA
AATTTCAAAGGTAAGCTTTTTTTACCCTATAAATATCCCTCAAATTTCATTTTTTTTCATTCACA
TCCTTCTCTCAACTCTCTCATTTTGATTGTGTTGAAGCGTGTCCAACCAGACAAGCA
Found at i:35037494 original size:25 final size:25
Alignment explanation
Indices: 35037466--35037516 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
35037456 TAGAATGGCT
35037466 AAGGTTTCATCTTCCATCTTATTGG
1 AAGGTTTCATCTTCCATCTTATTGG
35037491 AAGGTTTCATCTTCCATCTTATTGG
1 AAGGTTTCATCTTCCATCTTATTGG
35037516 A
1 A
35037517 CAATTAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.43
Consensus pattern (25 bp):
AAGGTTTCATCTTCCATCTTATTGG
Found at i:35038587 original size:27 final size:26
Alignment explanation
Indices: 35038529--35038590 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
35038519 CCTTGAATTG
*
35038529 AATTGAACAAACCAATGTTGGGTGTT
1 AATTGAACAAAACAATGTTGGGTGTT
*
35038555 AATTGAACAAAACGATGTTGGGTGTT
1 AATTGAACAAAACAATGTTGGGTGTT
*
35038581 ATTTTGAACA
1 A-ATTGAACA
35038591 TGAATTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 25 0.78
27 7 0.22
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.32
Consensus pattern (26 bp):
AATTGAACAAAACAATGTTGGGTGTT
Found at i:35039172 original size:12 final size:12
Alignment explanation
Indices: 35039157--35039184 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
35039147 TTTTATTCAT
35039157 GTAATTATTATC
1 GTAATTATTATC
35039169 GTAATTATTATC
1 GTAATTATTATC
35039181 GTAA
1 GTAA
35039185 CTGCATACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (12 bp):
GTAATTATTATC
Found at i:35047120 original size:14 final size:14
Alignment explanation
Indices: 35047086--35047120 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
35047076 TATTTAGTAT
*
35047086 GTATAATCATTTTA
1 GTATAGTCATTTTA
35047100 GTATAGTCATTTTA
1 GTATAGTCATTTTA
*
35047114 GTTTAGT
1 GTATAGT
35047121 TGAATCTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.06, G:0.14, T:0.51
Consensus pattern (14 bp):
GTATAGTCATTTTA
Found at i:35053637 original size:26 final size:26
Alignment explanation
Indices: 35053601--35053654 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
35053591 AACTTTAAAA
35053601 TATAGATGATGGTAAGGGACTAACTT
1 TATAGATGATGGTAAGGGACTAACTT
*
35053627 TATAGGTGATGGTAAGGGACTAACTT
1 TATAGATGATGGTAAGGGACTAACTT
35053653 TA
1 TA
35053655 ATCCAAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.31
Consensus pattern (26 bp):
TATAGATGATGGTAAGGGACTAACTT
Found at i:35054376 original size:21 final size:22
Alignment explanation
Indices: 35054352--35054394 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
35054342 TTACATGTAA
*
35054352 TTATGTAG-TAAATTATATTTT
1 TTATGTAGTTAAATAATATTTT
35054373 TTATGTAGTTAAATAATATTTT
1 TTATGTAGTTAAATAATATTTT
35054395 ACTTCGTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (22 bp):
TTATGTAGTTAAATAATATTTT
Found at i:35055873 original size:85 final size:85
Alignment explanation
Indices: 35055732--35055967 Score: 332
Period size: 85 Copynumber: 2.8 Consensus size: 85
35055722 CCGTTACTCG
* * *
35055732 GTGGATTCAGTACTTAACAACCACC-TTAAATTCAGTGATACGGGGAATCAACACATAGCAACCC
1 GTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAACACATAGCAACCC
**
35055796 CTTTCACAATCAAAGATATG
66 CTTTCACAATCAAAGATACA
* *
35055816 GTGGAATCAGCGCTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAACACATAGCAACCC
1 GTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAACACATAGCAACCC
*
35055881 CTTTCACAATCAAATATACA
66 CTTTCACAATCAAAGATACA
* * * * *
35055901 GTGGAATCAGCACTTAGCAACCACCTTTAGAA-TCAATAATTCGGGGAATCATCACTTAGCAACC
1 GTGGAATCAGCACTTAGCAACCACCTTTA-AATTCAGTGATACGGGGAATCAACACATAGCAACC
35055965 CCT
65 CCT
35055968 CGAGGAATCT
Statistics
Matches: 135, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
84 21 0.16
85 113 0.84
86 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (85 bp):
GTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAACACATAGCAACCC
CTTTCACAATCAAAGATACA
Found at i:35055876 original size:42 final size:42
Alignment explanation
Indices: 35055743--35055964 Score: 202
Period size: 43 Copynumber: 5.3 Consensus size: 42
35055733 TGGATTCAGT
* *
35055743 ACTTAACAACCACC-TTA-AATTCAGTGATACGGGGAATCAAC
1 ACTTAGCAACCACCTTTACAA-TCAATGATACGGGGAATCAAC
* * * *
35055784 ACATAGCAACC-CCTTTCACAATCAAAGATATGGTGGAATCAGC
1 ACTTAGCAACCACCTTT-ACAATCAATGATACGG-GGAATCAAC
* * * *
35055827 GCTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAAC
1 ACTTAGCAACCACCTTTACAATCAATGATACGGGGAATCAAC
* * *
35055869 ACATAGCAACC-CCTTTCACAATCAAAT-ATACAGTGGAATCAGC
1 ACTTAGCAACCACCTTT-ACAATC-AATGATAC-GGGGAATCAAC
* * * *
35055912 ACTTAGCAACCACCTTTAGAATCAATAATTCGGGGAATCATC
1 ACTTAGCAACCACCTTTACAATCAATGATACGGGGAATCAAC
35055954 ACTTAGCAACC
1 ACTTAGCAACC
35055965 CCTCGAGGAA
Statistics
Matches: 145, Mismatches: 26, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
40 2 0.01
41 16 0.11
42 58 0.40
43 59 0.41
44 10 0.07
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (42 bp):
ACTTAGCAACCACCTTTACAATCAATGATACGGGGAATCAAC
Found at i:35067028 original size:17 final size:17
Alignment explanation
Indices: 35067006--35067039 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
35066996 GCAGAAAATC
35067006 AAAGTGAGCGGAATAGT
1 AAAGTGAGCGGAATAGT
35067023 AAAGTGAGCGGAATAGT
1 AAAGTGAGCGGAATAGT
35067040 CATTAGCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.35, T:0.18
Consensus pattern (17 bp):
AAAGTGAGCGGAATAGT
Found at i:35076638 original size:18 final size:18
Alignment explanation
Indices: 35076595--35076638 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
35076585 ACTTATTAAT
**
35076595 TTTTTATTTTCTTTGTTC
1 TTTTTATTTTCTTTGTGA
35076613 TTTTTATTTT-TTTGTGA
1 TTTTTATTTTCTTTGTGA
35076630 TTTTCTATT
1 TTTT-TATT
35076639 AAGGTCTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.09, C:0.07, G:0.07, T:0.77
Consensus pattern (18 bp):
TTTTTATTTTCTTTGTGA
Found at i:35079389 original size:206 final size:206
Alignment explanation
Indices: 35079035--35079448 Score: 632
Period size: 206 Copynumber: 2.0 Consensus size: 206
35079025 CATTCCCAAG
* * *
35079035 TATCCAATGTAATCCTAGATGGTTGAGCAGGTACGCAAAGGTTAATTGTCAAGGCATGTATAAAA
1 TATCCAATGTAATCCTAGATGGTTCAACAGGTACGCAAAGGTTAATTGGCAAGGCATGTATAAAA
* * * * *
35079100 TTTAACAATGGTTCATGATCCTATGAAATGTTAATGAGTTACATGATGTGCATATGAAATGTACT
66 TTGAACAATGGTTCATGATCCTATGAAATGTTAATAAGTTAAATGATGTGCATATGAAATCTACA
* * * * *
35079165 TATTATATAATTGAACTCATATGTATCTTGTATGAATTTACTAACTTGTGAGTTTGATGGTTCTT
131 TATGATATAATTGAACTCATATGTATCATATATGAACTTACTAACTTGTGAGTTTGATGGTGCTT
35079230 GTATAAGATTT
196 GTATAAGATTT
* *
35079241 TATCCAATGTAATCCTAGATGGTTCAACGGGTACGCAAAGGTTAA-TGGCAAGGCATGTATACAA
1 TATCCAATGTAATCCTAGATGGTTCAACAGGTACGCAAAGGTTAATTGGCAAGGCATGTATAAAA
* * * *
35079305 TTGAATAATTGTTTATGATCCTATGAAATGGTTAATAAGTTAAATGATGTGTATATGAAATCTAC
66 TTGAACAATGGTTCATGATCCTATGAAAT-GTTAATAAGTTAAATGATGTGCATATGAAATCTAC
35079370 ATATGATATAATTGAACTCATATGTATCATATATGAACTTACTAACTTGTGAGTTTGATGGTGCT
130 ATATGATATAATTGAACTCATATGTATCATATATGAACTTACTAACTTGTGAGTTTGATGGTGCT
*
35079435 TGTATAGGATTT
195 TGTATAAGATTT
35079447 TA
1 TA
35079449 CTATGCTTAT
Statistics
Matches: 187, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
205 42 0.22
206 145 0.78
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (206 bp):
TATCCAATGTAATCCTAGATGGTTCAACAGGTACGCAAAGGTTAATTGGCAAGGCATGTATAAAA
TTGAACAATGGTTCATGATCCTATGAAATGTTAATAAGTTAAATGATGTGCATATGAAATCTACA
TATGATATAATTGAACTCATATGTATCATATATGAACTTACTAACTTGTGAGTTTGATGGTGCTT
GTATAAGATTT
Found at i:35097604 original size:20 final size:21
Alignment explanation
Indices: 35097581--35097623 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
35097571 TTACAGTAGT
*
35097581 AATTTAGTAAATAAAAGA-AA
1 AATTAAGTAAATAAAAGACAA
35097601 AATTAAGTAAATAAAAGACAA
1 AATTAAGTAAATAAAAGACAA
35097622 AA
1 AA
35097624 GAAAGATGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.21
Consensus pattern (21 bp):
AATTAAGTAAATAAAAGACAA
Found at i:35099326 original size:40 final size:40
Alignment explanation
Indices: 35099025--35099331 Score: 308
Period size: 40 Copynumber: 7.7 Consensus size: 40
35099015 AAGAAAATTC
* * * * *
35099025 CCCTAAAAGCACATATGTTCCCCTTTTTGTACTTCGGTAC
1 CCCTAAATGCACATACGTGCCCCTGTTTGTACTTCGGTAT
* * **
35099065 CCCTAAATGTACATATGTGCCCCTGTTTGTACTTTAGTAT
1 CCCTAAATGCACATACGTGCCCCTGTTTGTACTTCGGTAT
* * * * *
35099105 ACCTAAATGCACATATGTGCCCCTGTTTTTACTTTGGTAA
1 CCCTAAATGCACATACGTGCCCCTGTTTGTACTTCGGTAT
* * * *
35099145 CCCTGAATGCATATACGTGCCCCTGTTTGTACATCGGTAC
1 CCCTAAATGCACATACGTGCCCCTGTTTGTACTTCGGTAT
* ** * * *
35099185 CCCTGAATGCACATATATGCCCTTGTTTATACTTTGGTAT
1 CCCTAAATGCACATACGTGCCCCTGTTTGTACTTCGGTAT
* *
35099225 CCCTGAATGCACATACGTGCCCCTATTTGTACTTCGGTAT
1 CCCTAAATGCACATACGTGCCCCTGTTTGTACTTCGGTAT
* * * *
35099265 CACTAAATGCACATGCATGCCCCTATTTGTACTTCGGTAT
1 CCCTAAATGCACATACGTGCCCCTGTTTGTACTTCGGTAT
** * *
35099305 CATTAAATGCACATGCGTGCCCTTGTT
1 CCCTAAATGCACATACGTGCCCCTGTT
35099332 CTGCATCCAC
Statistics
Matches: 225, Mismatches: 42, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 225 1.00
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.35
Consensus pattern (40 bp):
CCCTAAATGCACATACGTGCCCCTGTTTGTACTTCGGTAT
Found at i:35099326 original size:120 final size:120
Alignment explanation
Indices: 35099044--35099331 Score: 342
Period size: 120 Copynumber: 2.4 Consensus size: 120
35099034 CACATATGTT
* * * *
35099044 CCCCTTTTTGTACTTCGGTACCCCTAAATGTACATATGTGCCCCTGTTTGTACTTTAGTATACCT
1 CCCCTATTTGTACTTCGGTACCCCTAAATGCACATATGTGCCCTTGTTTATACTTTAGTATACCT
* * * * * * * *
35099109 AAATGCACATATGTGCCCCTGTTTTTACTTTGGTAACCCTGAATGCATATACGTG
66 AAATGCACATACGTGCCCCTATTTGTACTTCGGTAACACTAAATGCACATACATG
* * * * * *
35099164 CCCCTGTTTGTACATCGGTACCCCTGAATGCACATATATGCCCTTGTTTATACTTTGGTATCCCT
1 CCCCTATTTGTACTTCGGTACCCCTAAATGCACATATGTGCCCTTGTTTATACTTTAGTATACCT
* * *
35099229 GAATGCACATACGTGCCCCTATTTGTACTTCGGTATCACTAAATGCACATGCATG
66 AAATGCACATACGTGCCCCTATTTGTACTTCGGTAACACTAAATGCACATACATG
* ** **
35099284 CCCCTATTTGTACTTCGGTATCATTAAATGCACATGCGTGCCCTTGTT
1 CCCCTATTTGTACTTCGGTACCCCTAAATGCACATATGTGCCCTTGTT
35099332 CTGCATCCAC
Statistics
Matches: 139, Mismatches: 29, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
120 139 1.00
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (120 bp):
CCCCTATTTGTACTTCGGTACCCCTAAATGCACATATGTGCCCTTGTTTATACTTTAGTATACCT
AAATGCACATACGTGCCCCTATTTGTACTTCGGTAACACTAAATGCACATACATG
Found at i:35100745 original size:23 final size:24
Alignment explanation
Indices: 35100719--35100780 Score: 83
Period size: 23 Copynumber: 2.6 Consensus size: 24
35100709 ACCTAGATTT
35100719 AGTCAAAGTAATTCTCAAG-AAAA
1 AGTCAAAGTAATTCTCAAGAAAAA
*
35100742 AGTC-AAGCTAATTTTCAAGAAAAA
1 AGTCAAAG-TAATTCTCAAGAAAAA
*
35100766 AGTCAAAATAATTCT
1 AGTCAAAGTAATTCT
35100781 TGATTATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 3 0.09
23 14 0.42
24 14 0.42
25 2 0.06
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (24 bp):
AGTCAAAGTAATTCTCAAGAAAAA
Found at i:35107402 original size:24 final size:24
Alignment explanation
Indices: 35107370--35107417 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
35107360 CATGTGACCA
35107370 AGTTGTCTACGCTCCAAACGAGTT
1 AGTTGTCTACGCTCCAAACGAGTT
35107394 AGTTGTCTACGCTCCAAACGAGTT
1 AGTTGTCTACGCTCCAAACGAGTT
35107418 GACTTCGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (24 bp):
AGTTGTCTACGCTCCAAACGAGTT
Found at i:35110006 original size:17 final size:17
Alignment explanation
Indices: 35109986--35110022 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
35109976 TACTCATCCA
35109986 TTCATTTT-TTTCATTCT
1 TTCATTTTCTTTC-TTCT
35110003 TTCATTTTCTTTCTTCT
1 TTCATTTTCTTTCTTCT
35110020 TTC
1 TTC
35110023 CACACCTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.70
Consensus pattern (17 bp):
TTCATTTTCTTTCTTCT
Found at i:35111328 original size:23 final size:24
Alignment explanation
Indices: 35111280--35111328 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
35111270 ATCGGTGTAC
35111280 AAATAATCCAAGTGATAAATATTCA
1 AAATAATCCAAGTGAT-AATATTCA
**
35111305 AAATAATTTAAGTGAT-ATATTCA
1 AAATAATCCAAGTGATAATATTCA
35111328 A
1 A
35111329 TTTTTAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 8 0.36
25 14 0.64
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (24 bp):
AAATAATCCAAGTGATAATATTCA
Found at i:35115130 original size:17 final size:17
Alignment explanation
Indices: 35115108--35115140 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
35115098 AGGTTTGTGA
35115108 AGTATGCCAGCTAGGTT
1 AGTATGCCAGCTAGGTT
35115125 AGTATGCCAGCTAGGT
1 AGTATGCCAGCTAGGT
35115141 AAGCAAGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.27
Consensus pattern (17 bp):
AGTATGCCAGCTAGGTT
Found at i:35115150 original size:17 final size:17
Alignment explanation
Indices: 35115113--35115151 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
35115103 TGTGAAGTAT
* * *
35115113 GCCAGCTAGGTTAGTAT
1 GCCAGCTAGGTAAGCAA
35115130 GCCAGCTAGGTAAGCAA
1 GCCAGCTAGGTAAGCAA
35115147 GCCAG
1 GCCAG
35115152 GATCCCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.23, G:0.31, T:0.18
Consensus pattern (17 bp):
GCCAGCTAGGTAAGCAA
Found at i:35119540 original size:28 final size:28
Alignment explanation
Indices: 35119497--35119552 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
35119487 ACCTGTTAGG
35119497 CCCGGGGGACGCTGGACGGGTGCAACAA
1 CCCGGGGGACGCTGGACGGGTGCAACAA
*
35119525 CCCGGGGGACGTTGGACGGGTGCAACAA
1 CCCGGGGGACGCTGGACGGGTGCAACAA
35119553 TAAAGGTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.27, G:0.43, T:0.09
Consensus pattern (28 bp):
CCCGGGGGACGCTGGACGGGTGCAACAA
Found at i:35130436 original size:28 final size:28
Alignment explanation
Indices: 35130376--35130441 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
35130366 GGTTGTTGGA
* ***
35130376 CTGGCCTGCTGTGCTGCTGGGTTGGGTG
1 CTGGCCTGCTATGCTGCTGGGTCAAGTG
* *
35130404 TTGGCCTGCTATGCTGCTTGGTCAAGTG
1 CTGGCCTGCTATGCTGCTGGGTCAAGTG
35130432 CTGGCCTGCT
1 CTGGCCTGCT
35130442 GTTTGTTGGG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.05, C:0.24, G:0.38, T:0.33
Consensus pattern (28 bp):
CTGGCCTGCTATGCTGCTGGGTCAAGTG
Found at i:35130653 original size:11 final size:11
Alignment explanation
Indices: 35130639--35130696 Score: 57
Period size: 10 Copynumber: 5.4 Consensus size: 11
35130629 ATTTTTTATT
35130639 TTTCTTTTTTC
1 TTTCTTTTTTC
35130650 TTTCTTTTTTC
1 TTTCTTTTTTC
* *
35130661 -TTATTTTTCC
1 TTTCTTTTTTC
**
35130671 TTT-TTTCCTC
1 TTTCTTTTTTC
35130681 TTTCTTCTTTTC
1 TTTCTT-TTTTC
35130693 TTTC
1 TTTC
35130697 CCTCTTCTTC
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
10 15 0.41
11 15 0.41
12 7 0.19
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTCTTTTTTC
Done.