Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 170 of 195
Found at i:28377380 original size:24 final size:24
Alignment explanation
Indices: 28377352--28377410 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
28377342 ATCATTCAAC
*
28377352 TATAATATTA-ATCATGCAATAACA
1 TATAATATCATATCATGCAATAA-A
28377376 TATAATATCATATCATGCAATAAA
1 TATAATATCATATCATGCAATAAA
*
28377400 TATAAAATCAT
1 TATAATATCAT
28377411 GCAATAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 20 0.62
25 12 0.38
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.34
Consensus pattern (24 bp):
TATAATATCATATCATGCAATAAA
Found at i:28377426 original size:19 final size:19
Alignment explanation
Indices: 28377377--28377426 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
28377367 GCAATAACAT
*
28377377 ATAAT-ATCATATCATGCA
1 ATAATAATCAAATCATGCA
*
28377395 ATAA-ATATAAAATCATGCA
1 ATAATA-ATCAAATCATGCA
28377414 ATAATAATCAAAT
1 ATAATAATCAAAT
28377427 AAATATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 4 0.15
19 21 0.81
20 1 0.04
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.30
Consensus pattern (19 bp):
ATAATAATCAAATCATGCA
Found at i:28377615 original size:20 final size:22
Alignment explanation
Indices: 28377602--28377662 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
28377592 CATGCAATTA
28377602 AATATATAATCATGCAAATAAT
1 AATATATAATCATGCAAATAAT
*
28377624 AATATATAAATCATCCAAAT-AT
1 AATATAT-AATCATGCAAATAAT
*
28377646 AAT-T-TAGTCATGCAAAT
1 AATATATAATCATGCAAAT
28377663 TTGTGCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 10 0.29
20 1 0.03
21 1 0.03
22 12 0.34
23 11 0.31
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.33
Consensus pattern (22 bp):
AATATATAATCATGCAAATAAT
Found at i:28377630 original size:22 final size:21
Alignment explanation
Indices: 28377587--28377662 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 21
28377577 AACCAAGCAA
* *
28377587 ATAAACATGCAATTA-AATAT
1 ATAATCATGCAAATATAATAT
28377607 ATAATCATGCAAATAATAATAT
1 ATAATCATGCAAAT-ATAATAT
*
28377629 ATAAATCATCCAAATATAAT-T
1 AT-AATCATGCAAATATAATAT
*
28377650 -TAGTCATGCAAAT
1 ATAATCATGCAAAT
28377663 TTGTGCAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
19 10 0.21
20 13 0.27
21 2 0.04
22 12 0.25
23 11 0.23
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (21 bp):
ATAATCATGCAAATATAATAT
Found at i:28377643 original size:55 final size:55
Alignment explanation
Indices: 28377531--28377644 Score: 174
Period size: 55 Copynumber: 2.1 Consensus size: 55
28377521 ATAAACATGT
* * *
28377531 AATAAACATGCAATTTAATATATAATCATGCAAATAAAAATATGTAAACCAAGCA
1 AATAAACATGCAATTAAATATATAATCATGCAAATAAAAATATATAAACCAACCA
* * *
28377586 AATAAACATGCAATTAAATATATAATCATGCAAATAATAATATATAAATCATCCA
1 AATAAACATGCAATTAAATATATAATCATGCAAATAAAAATATATAAACCAACCA
28377641 AATA
1 AATA
28377645 TAATTTAGTC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.27
Consensus pattern (55 bp):
AATAAACATGCAATTAAATATATAATCATGCAAATAAAAATATATAAACCAACCA
Found at i:28377662 original size:19 final size:23
Alignment explanation
Indices: 28377587--28377648 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
28377577 AACCAAGCAA
*
28377587 ATAAA-CATGC-AATTA-AATAT
1 ATAAATCATGCAAATAATAATAT
28377607 AT-AATCATGCAAATAATAATAT
1 ATAAATCATGCAAATAATAATAT
*
28377629 ATAAATCATCCAAAT-ATAAT
1 ATAAATCATGCAAATAATAAT
28377649 TTAGTCATGC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
19 2 0.06
20 7 0.19
21 4 0.11
22 12 0.33
23 11 0.31
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.31
Consensus pattern (23 bp):
ATAAATCATGCAAATAATAATAT
Found at i:28378643 original size:42 final size:43
Alignment explanation
Indices: 28378567--28378774 Score: 273
Period size: 42 Copynumber: 5.0 Consensus size: 43
28378557 TTTAAATTGT
*
28378567 TCCCTCACAACTAAGGCTTTGAAACTTTTG-AAAATAAAATGC
1 TCCCCCACAACTAAGGCTTTGAAACTTTTGAAAAATAAAATGC
* * *
28378609 TCCCCCACAACT-AGGATTTGGACCTTTTGAAAAATAAAATGC
1 TCCCCCACAACTAAGGCTTTGAAACTTTTGAAAAATAAAATGC
* * * *
28378651 TCTCCCACAACTAAAGCTTTGAAA-ATTTG-AAAACAAAATGC
1 TCCCCCACAACTAAGGCTTTGAAACTTTTGAAAAATAAAATGC
*
28378692 TCCCCCACAACTGAGGCTTTGAAAC-TTTGAAAAATAAAATGC
1 TCCCCCACAACTAAGGCTTTGAAACTTTTGAAAAATAAAATGC
* * *
28378734 TTCCCCACAACTAAGGTTTTGAAATTTTTGAAAAATAAAAT
1 TCCCCCACAACTAAGGCTTTGAAACTTTTGAAAAATAAAAT
28378775 AAGATCATTC
Statistics
Matches: 142, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
41 50 0.35
42 70 0.49
43 22 0.15
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.27
Consensus pattern (43 bp):
TCCCCCACAACTAAGGCTTTGAAACTTTTGAAAAATAAAATGC
Found at i:28378700 original size:83 final size:84
Alignment explanation
Indices: 28378566--28378767 Score: 284
Period size: 83 Copynumber: 2.4 Consensus size: 84
28378556 TTTTAAATTG
* *
28378566 TTCCCTCACAACTAAGGCTTTGAAACTTTTGAAAATAAAATGCTCCCCCACAACT-AGGATTTGG
1 TTCCC-CACAACTAAGGCTTTGAAACTTTTGAAAACAAAATGCTCCCCCACAACTGAGGATTTGA
*
28378630 ACCTTTTGAAAAATAAAATGC
65 AAC-TTTGAAAAATAAAATGC
* * *
28378651 -TCTCCCACAACTAAAGCTTTGAAA-ATTTGAAAACAAAATGCTCCCCCACAACTGAGGCTTTGA
1 TTC-CCCACAACTAAGGCTTTGAAACTTTTGAAAACAAAATGCTCCCCCACAACTGAGGATTTGA
28378714 AACTTTGAAAAATAAAATGC
65 AACTTTGAAAAATAAAATGC
* *
28378734 TTCCCCACAACTAAGGTTTTGAAATTTTTGAAAA
1 TTCCCCACAACTAAGGCTTTGAAACTTTTGAAAA
28378768 ATAAAATAAG
Statistics
Matches: 104, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
83 63 0.61
84 39 0.38
85 2 0.02
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (84 bp):
TTCCCCACAACTAAGGCTTTGAAACTTTTGAAAACAAAATGCTCCCCCACAACTGAGGATTTGAA
ACTTTGAAAAATAAAATGC
Found at i:28380241 original size:17 final size:17
Alignment explanation
Indices: 28380216--28380259 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
28380206 TTAGTTTAAG
*
28380216 TTTTCATTTT-TTCATTT
1 TTTTTATTTTATT-ATTT
28380233 TTTTTATTTTATTATTT
1 TTTTTATTTTATTATTT
*
28380250 TTTTTGTTTT
1 TTTTTATTTT
28380260 GCTTTTTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 22 0.92
18 2 0.08
ACGTcount: A:0.11, C:0.05, G:0.02, T:0.82
Consensus pattern (17 bp):
TTTTTATTTTATTATTT
Found at i:28386601 original size:13 final size:13
Alignment explanation
Indices: 28386583--28386608 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28386573 TTTTTATTGA
28386583 TTTTTATTTTTAT
1 TTTTTATTTTTAT
28386596 TTTTTATTTTTAT
1 TTTTTATTTTTAT
28386609 GAAAACTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:28386746 original size:15 final size:15
Alignment explanation
Indices: 28386721--28386761 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
28386711 TTGTAGGGAT
28386721 TTTTATTTGAAAAAGA
1 TTTT-TTTGAAAAAGA
28386737 TTTTTTTG-AAAAGA
1 TTTTTTTGAAAAAGA
28386751 -TTTTTTGAAAA
1 TTTTTTTGAAAA
28386762 CTTAAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.29
14 9 0.38
15 4 0.17
16 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (15 bp):
TTTTTTTGAAAAAGA
Found at i:28386756 original size:13 final size:14
Alignment explanation
Indices: 28386721--28386761 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
28386711 TTGTAGGGAT
28386721 TTTTATTTGAAAAAGA
1 TTTT-TTTG-AAAAGA
28386737 TTTTTTTGAAAAGA
1 TTTTTTTGAAAAGA
28386751 -TTTTTTGAAAA
1 TTTTTTTGAAAA
28386762 CTTAAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 11 0.44
14 6 0.24
15 4 0.16
16 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (14 bp):
TTTTTTTGAAAAGA
Found at i:28386822 original size:24 final size:24
Alignment explanation
Indices: 28386795--28386840 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
28386785 TATTTTGAAA
28386795 ACTTATTTGAAAAGATTTTTTTTT
1 ACTTATTTGAAAAGATTTTTTTTT
*
28386819 ACTTATTTGAAAAGGTTTTTTT
1 ACTTATTTGAAAAGATTTTTTT
28386841 ATATATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.57
Consensus pattern (24 bp):
ACTTATTTGAAAAGATTTTTTTTT
Found at i:28386965 original size:19 final size:20
Alignment explanation
Indices: 28386941--28386982 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
28386931 AAATGAGCTA
28386941 AAAAATAAAATCAAAAAA-T
1 AAAAATAAAATCAAAAAAGT
*
28386960 AAAAATAAAATGAAAAAAGT
1 AAAAATAAAATCAAAAAAGT
28386980 AAA
1 AAA
28386983 CCTTTCGATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (20 bp):
AAAAATAAAATCAAAAAAGT
Found at i:28387692 original size:3 final size:3
Alignment explanation
Indices: 28387686--28387750 Score: 55
Period size: 3 Copynumber: 22.3 Consensus size: 3
28387676 AGAAAAAAAG
* * *
28387686 ATA ATA ATA AT- ATA ATA ATA ATA ATA ATG ATA CT- ATA AT- ATA TTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
28387731 TTA TATA ATA ATA AAA ATA A
1 ATA -ATA ATA ATA ATA ATA A
28387751 CCTTAAAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.86
4 2 0.04
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:28388668 original size:69 final size:68
Alignment explanation
Indices: 28388475--28388673 Score: 220
Period size: 69 Copynumber: 2.9 Consensus size: 68
28388465 AGATGTACGA
* * **
28388475 TTTGCAAGGACTTTT-AGATTTGTAAGAAAGAAAAATTCACACGATTCCAAGTTTCACAAAAATG
1 TTTGCAAGGA-TTTTCAGATTTGTAAGAAAG-AAAATTCACAAGATTTCAAGTTTCGTAAAAATG
*
28388539 CAAGG
64 CAAAG
** *** * **
28388544 TTCACAAGGATTTTCAGATTCACAAGAAAGAAAAGTTCATAAGATTTCAAGTTTCGTAAAGGTGC
1 TTTGCAAGGATTTTCAGATTTGTAAGAAAGAAAA-TTCACAAGATTTCAAGTTTCGTAAAAATGC
28388609 AAAG
65 AAAG
* *
28388613 TTTGTAAGGATTTTCAGATTTGTAAGAAAGAAAGATTTACAAGATTTCAAGTTTCGTAAAA
1 TTTGCAAGGATTTTCAGATTTGTAAGAAAGAAA-ATTCACAAGATTTCAAGTTTCGTAAAA
28388674 GTTCTAGATT
Statistics
Matches: 105, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
68 8 0.08
69 96 0.91
70 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (68 bp):
TTTGCAAGGATTTTCAGATTTGTAAGAAAGAAAATTCACAAGATTTCAAGTTTCGTAAAAATGCA
AAG
Found at i:28388699 original size:155 final size:155
Alignment explanation
Indices: 28388531--28388823 Score: 401
Period size: 155 Copynumber: 1.9 Consensus size: 155
28388521 CCAAGTTTCA
* * * *
28388531 CAAAAATGCAAGGTTCACAAGGATTTTCAGATTCACAAGAAAGAAA-AGTTCATAAGATTTCAAG
1 CAAAAATGAAAGGTTCACAAAGATTTTCAAATTCACAAGAAAGAAAGA-TTCACAAGATTTCAAG
** * * * *
28388595 TTTCGTAAAGGTGCAAAGTTTGTAAGGATTTTCAGATT-TGTAAGAAAGAAAGATTTACAAGATT
65 TTTCACAAAGGTGCAAAGTTTGCAAGGATTTTCAAATTCT-CAAGAAAGAAAGATTCACAAGATT
28388659 TCAAGTTTCGTAAAAGTTCTAGATTAG
129 TCAAGTTTCGTAAAAGTTCTAGATTAG
* * **
28388686 CAAAGATGAAAGGTTCACAAATATTTTCAAATTCGTAAGAAAGAAAGATTCACAAGATTTCAAGT
1 CAAAAATGAAAGGTTCACAAAGATTTTCAAATTCACAAGAAAGAAAGATTCACAAGATTTCAAGT
* **
28388751 TTCACAAAGGTGCAAGGTTTGCAAGGATTTTCAAATTCTCAAGAAAGAAAGATTCGTAAGATTTC
66 TTCACAAAGGTGCAAAGTTTGCAAGGATTTTCAAATTCTCAAGAAAGAAAGATTCACAAGATTTC
28388816 AAGTTTCG
131 AAGTTTCG
28388824 CAAAGGTGCA
Statistics
Matches: 119, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
155 117 0.98
156 2 0.02
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (155 bp):
CAAAAATGAAAGGTTCACAAAGATTTTCAAATTCACAAGAAAGAAAGATTCACAAGATTTCAAGT
TTCACAAAGGTGCAAAGTTTGCAAGGATTTTCAAATTCTCAAGAAAGAAAGATTCACAAGATTTC
AAGTTTCGTAAAAGTTCTAGATTAG
Found at i:28388767 original size:224 final size:224
Alignment explanation
Indices: 28388412--28388925 Score: 638
Period size: 224 Copynumber: 2.3 Consensus size: 224
28388402 ATTCCCAAGA
* * * * * *
28388412 AAGAAAGAAAAATTCACAAGATTTCAAGTTTTATAAAGGTTCTAAATTCA-CAAAGATGTACGAT
1 AAGAAAGAAAGATTCACAAGATTTCAAGTTTCATAAAGGTTCTAGATT-AGCAAAGATGAAAGGT
** * * * *
28388476 TTGCAAGGACTTTTAGATTTGTAAGAAAGAAAAATTCACACGATTCCAAGTTTCACAAAAATGCA
65 TCACAAAGACTTTTAAATTCGTAAGAAAGAAAAATTCACAAGATTCCAAGTTTCACAAAAATGCA
* *
28388541 AGGTTCACAAGGATTTTCAGATTCACAAGAAAGAAA-AGTTCATAAGATTTCAAGTTTCGTAAAG
130 AGGTTCACAAGGATTTTCAAATTCACAAGAAAGAAAGA-TTCATAAGATTTCAAGTTTCGCAAAG
* * * *
28388605 GTGCAAAGTTTGTAAGGATTTTCAGATTTGT
194 GTGCAAAGTTTGCAAGGATTTTCAAATTCGC
* * *
28388636 AAGAAAGAAAGATTTACAAGATTTCAAGTTTCGTAAAAGTTCTAGATTAGCAAAGATGAAAGGTT
1 AAGAAAGAAAGATTCACAAGATTTCAAGTTTCATAAAGGTTCTAGATTAGCAAAGATGAAAGGTT
* * * **
28388701 CACAAATA-TTTTCAAATTCGTAAGAAAGAAAGATTCACAAGATTTCAAGTTTCACAAAGGTGCA
66 CACAAAGACTTTT-AAATTCGTAAGAAAGAAAAATTCACAAGATTCCAAGTTTCACAAAAATGCA
** * *
28388765 AGGTTTGCAAGGATTTTCAAATTCTCAAGAAAGAAAGATTCGTAAGATTTCAAGTTTCGCAAAGG
130 AGGTTCACAAGGATTTTCAAATTCACAAGAAAGAAAGATTCATAAGATTTCAAGTTTCGCAAAGG
* *
28388830 TGCAAGGTTTGCAAGTATTTTCAAATTCGC
195 TGCAAAGTTTGCAAGGATTTTCAAATTCGC
** * * * *
28388860 AAGAAAGAAAGATTCGTAAGATTTCAAGTTTCACAAAGGTTCTAGATTTGCAAAAATGCAAGGTT
1 AAGAAAGAAAGATTCACAAGATTTCAAGTTTCATAAAGGTTCTAGATTAGCAAAGATGAAAGGTT
28388925 C
66 C
28388926 GCAAGCAGGG
Statistics
Matches: 246, Mismatches: 41, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
223 5 0.02
224 240 0.98
225 1 0.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (224 bp):
AAGAAAGAAAGATTCACAAGATTTCAAGTTTCATAAAGGTTCTAGATTAGCAAAGATGAAAGGTT
CACAAAGACTTTTAAATTCGTAAGAAAGAAAAATTCACAAGATTCCAAGTTTCACAAAAATGCAA
GGTTCACAAGGATTTTCAAATTCACAAGAAAGAAAGATTCATAAGATTTCAAGTTTCGCAAAGGT
GCAAAGTTTGCAAGGATTTTCAAATTCGC
Found at i:28388860 original size:35 final size:34
Alignment explanation
Indices: 28388738--28388861 Score: 92
Period size: 35 Copynumber: 3.6 Consensus size: 34
28388728 GAAAGATTCA
* *
28388738 CAAGA-TTTCAAGTTTCACAAAGGTGCAAGGTTTG
1 CAAGATTTTCAA-ATTCGCAAAGGTGCAAGGTTTG
* ** * * *
28388772 CAAGGATTTTCAAATTCTC-AAGAAAGAAAGATTCG
1 CAA-GATTTTCAAATTCGCAAAG-GTGCAAGGTTTG
* *
28388807 TAAGA-TTTCAAGTTTCGCAAAGGTGCAAGGTTTG
1 CAAGATTTTCAA-ATTCGCAAAGGTGCAAGGTTTG
28388841 CAAGTATTTTCAAATTCGCAA
1 CAAG-ATTTTCAAATTCGCAA
28388862 GAAAGAAAGA
Statistics
Matches: 66, Mismatches: 17, Indels: 13
0.69 0.18 0.14
Matches are distributed among these distances:
33 6 0.09
34 22 0.33
35 26 0.39
36 12 0.18
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (34 bp):
CAAGATTTTCAAATTCGCAAAGGTGCAAGGTTTG
Found at i:28388912 original size:69 final size:69
Alignment explanation
Indices: 28388707--28388899 Score: 332
Period size: 69 Copynumber: 2.8 Consensus size: 69
28388697 GGTTCACAAA
* **
28388707 TATTTTCAAATTCGTAAGAAAGAAAGATTCACAAGATTTCAAGTTTCACAAAGGTGCAAGGTTTG
1 TATTTTCAAATTCGCAAGAAAGAAAGATTCGTAAGATTTCAAGTTTCACAAAGGTGCAAGGTTTG
28388772 CAAG
66 CAAG
* * *
28388776 GATTTTCAAATTCTCAAGAAAGAAAGATTCGTAAGATTTCAAGTTTCGCAAAGGTGCAAGGTTTG
1 TATTTTCAAATTCGCAAGAAAGAAAGATTCGTAAGATTTCAAGTTTCACAAAGGTGCAAGGTTTG
28388841 CAAG
66 CAAG
28388845 TATTTTCAAATTCGCAAGAAAGAAAGATTCGTAAGATTTCAAGTTTCACAAAGGT
1 TATTTTCAAATTCGCAAGAAAGAAAGATTCGTAAGATTTCAAGTTTCACAAAGGT
28388900 TCTAGATTTG
Statistics
Matches: 115, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 115 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (69 bp):
TATTTTCAAATTCGCAAGAAAGAAAGATTCGTAAGATTTCAAGTTTCACAAAGGTGCAAGGTTTG
CAAG
Found at i:28389141 original size:10 final size:10
Alignment explanation
Indices: 28389104--28389147 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
28389094 ATATAAAAAA
28389104 TATATATTTT
1 TATATATTTT
28389114 TA-ATTATTTT
1 TATA-TATTTT
28389124 T-TA-A-TTT
1 TATATATTTT
28389131 TATATATTTT
1 TATATATTTT
28389141 TATATAT
1 TATATAT
28389148 ATCTAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
7 4 0.14
8 3 0.10
9 2 0.07
10 20 0.69
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TATATATTTT
Found at i:28390555 original size:14 final size:14
Alignment explanation
Indices: 28390536--28390613 Score: 57
Period size: 14 Copynumber: 5.4 Consensus size: 14
28390526 TTTTTGCTTC
28390536 TTTTTTTGTTTTTTT
1 TTTTTTTG-TTTTTT
** *
28390551 TTTTTTTGCATATT
1 TTTTTTTGTTTTTT
*
28390565 TTTTTTTGCTTTTT
1 TTTTTTTGTTTTTT
**
28390579 ACTTTTTGCTTTTTT
1 TTTTTTTG-TTTTTT
* * *
28390594 TCTTCTTCTTTTTT
1 TTTTTTTGTTTTTT
28390608 TTTTTT
1 TTTTTT
28390614 GCATGCCTTT
Statistics
Matches: 49, Mismatches: 13, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
14 31 0.63
15 18 0.37
ACGTcount: A:0.04, C:0.09, G:0.05, T:0.82
Consensus pattern (14 bp):
TTTTTTTGTTTTTT
Found at i:28390557 original size:28 final size:26
Alignment explanation
Indices: 28390526--28390615 Score: 92
Period size: 28 Copynumber: 3.3 Consensus size: 26
28390516 TTTTCATTCA
28390526 TTTTTGCTTCTTTTTTTGTT-TTTTTTT
1 TTTTTGCTT-TTTTTTT-TTCTTTTTTT
* **
28390553 TTTTTGCATATTTTTTTTTGCTTTTTAC
1 TTTTTGC-T-TTTTTTTTTTCTTTTTTT
28390581 TTTTTGCTTTTTTTCTTCTTCTTTTTTT
1 TTTTTGCTTTTTTT-TT-TTCTTTTTTT
28390609 TTTTTGC
1 TTTTTGC
28390616 ATGCCTTTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
26 6 0.12
27 11 0.21
28 34 0.65
29 1 0.02
ACGTcount: A:0.03, C:0.11, G:0.07, T:0.79
Consensus pattern (26 bp):
TTTTTGCTTTTTTTTTTTCTTTTTTT
Found at i:28390972 original size:11 final size:11
Alignment explanation
Indices: 28390943--28390972 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
28390933 CCCATCAAAA
28390943 TTTTTTTTCTT
1 TTTTTTTTCTT
*
28390954 TTTCTTTTCTT
1 TTTTTTTTCTT
28390965 TTTTTTTT
1 TTTTTTTT
28390973 GTGGATGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:28392019 original size:14 final size:13
Alignment explanation
Indices: 28392000--28392034 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
28391990 CTGTTGGTTA
28392000 TTTTATTTTATTGT
1 TTTTATTTTATT-T
28392014 TTTTATTTTTATTT
1 TTTTA-TTTTATTT
28392028 TTTTATT
1 TTTTATT
28392035 ATTTTAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 11 0.55
15 7 0.35
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (13 bp):
TTTTATTTTATTT
Found at i:28392355 original size:21 final size:21
Alignment explanation
Indices: 28392329--28392369 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28392319 GTAATCCTAA
28392329 AATTTTTAAGATTTTTTTTTG
1 AATTTTTAAGATTTTTTTTTG
* *
28392350 AATTTTTGATATTTTTTTTT
1 AATTTTTAAGATTTTTTTTT
28392370 TGAAAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (21 bp):
AATTTTTAAGATTTTTTTTTG
Found at i:28393708 original size:21 final size:21
Alignment explanation
Indices: 28393684--28394039 Score: 237
Period size: 21 Copynumber: 15.8 Consensus size: 21
28393674 TTAAGAAATC
28393684 TTTAAATGAGAATCTTTGAGT
1 TTTAAATGAGAATCTTTGAGT
28393705 TTTAAATGAGAAT-TCTTGAGT
1 TTTAAATGAGAATCT-TTGAGT
* * * *
28393726 CTTACATGAGAATCTATAAGACAT
1 TTTAAATGAGAATCT-T-TGA-GT
* * *
28393750 TTTCAAATGAAAATTTTTAAGT
1 TTT-AAATGAGAATCTTTGAGT
* *
28393772 TTCAAATAAGAATCTTTGAGT
1 TTTAAATGAGAATCTTTGAGT
* * *
28393793 CTTAAATGATAATCTTTAAGACATT
1 TTTAAATGAGAATCTTT--G--AGT
* *
28393818 TTTAAATGAGAATTTTTTAGT
1 TTTAAATGAGAATCTTTGAGT
*
28393839 TTCAAATGAGAATCTTTGAGT
1 TTTAAATGAGAATCTTTGAGT
* *
28393860 CTTAAATGAGAATCTTTAAGACAT
1 TTTAAATGAGAATCTTT--GA-GT
* *
28393884 TTTCGAATGAGAATCTTCGAGT
1 TTT-AAATGAGAATCTTTGAGT
28393906 TTTAAATGAGAATCTTTAAGACGTT
1 TTTAAATGAGAATCTTT--GA-G-T
** *
28393931 TTTAAAAAATAATCTTTAAGATGT
1 TTTAAATGAGAATCTTT--GA-GT
28393955 TTTCAAATGAGAATCTTTGAGT
1 TTT-AAATGAGAATCTTTGAGT
* *
28393977 TTTAAATGGGAATCTTTAAGACAT
1 TTTAAATGAGAATCTTT--GA-GT
* *
28394001 TTTCAAATGAAAATTTTTGAGT
1 TTT-AAATGAGAATCTTTGAGT
*
28394023 TTCAAATGAGAATCTTT
1 TTTAAATGAGAATCTTT
28394040 AATATGTGAA
Statistics
Matches: 258, Mismatches: 55, Indels: 44
0.72 0.15 0.12
Matches are distributed among these distances:
20 1 0.00
21 129 0.50
22 17 0.07
23 16 0.06
24 16 0.06
25 79 0.31
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (21 bp):
TTTAAATGAGAATCTTTGAGT
Found at i:28393758 original size:67 final size:67
Alignment explanation
Indices: 28393662--28393993 Score: 389
Period size: 67 Copynumber: 4.9 Consensus size: 67
28393652 ATTTTTTTAA
* *
28393662 AAATGAAAATCTTTAAGAAATCTTT-AAATGAGAATCTTTGAGTTTTAAATGAGAAT-TCTTGAG
1 AAATGAGAATCTTTAAGACAT-TTTCAAATGAGAATCTTTGAGTTTTAAATGAGAATCT-TTGAG
28393725 TCTT
64 TCTT
* * * * * * *
28393729 ACATGAGAATCTATAAGACATTTTCAAATGAAAATTTTTAAGTTTCAAATAAGAATCTTTGAGTC
1 AAATGAGAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTTTTAAATGAGAATCTTTGAGTC
28393794 TT
66 TT
* * * * *
28393796 AAATGATAATCTTTAAGACATTTTTAAATGAGAATTTTTTAGTTTCAAATGAGAATCTTTGAGTC
1 AAATGAGAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTTTTAAATGAGAATCTTTGAGTC
28393861 TT
66 TT
* *
28393863 AAATGAGAATCTTTAAGACATTTTCGAATGAGAATCTTCGAGTTTTAAATGAGAATCTTTAAGAC
1 AAATGAGAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTTTTAAATGAGAATCTTT--GA-
*
28393928 GTTTTT
63 G-TCTT
** * ** *
28393934 AAAAAATAATCTTTAAGATGTTTTCAAATGAGAATCTTTGAGTTTTAAATGGGAATCTTT
1 AAATGAGAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTTTTAAATGAGAATCTTT
28393994 AAGACATTTT
Statistics
Matches: 227, Mismatches: 32, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
66 3 0.01
67 165 0.73
68 1 0.00
69 2 0.01
70 1 0.00
71 55 0.24
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.39
Consensus pattern (67 bp):
AAATGAGAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTTTTAAATGAGAATCTTTGAGTC
TT
Found at i:28393853 original size:46 final size:45
Alignment explanation
Indices: 28393662--28394041 Score: 178
Period size: 46 Copynumber: 8.4 Consensus size: 45
28393652 ATTTTTTTAA
* * * *
28393662 AAATGAAAATCTTTAAGAAATCTTTAAATGAGAATCTTTGAGTTTT
1 AAATGAGAATCTTTAAG-AATTTTTAAATGAGAATTTTTGAGTTTC
* * * ** *
28393708 AAATGAGAAT-TCTT--G-AGTCTTACATGAGAATCTATAAGACATTTTC
1 AAATGAGAATCT-TTAAGAATTTTTAAATGAGAAT-T-TTTG--AGTTTC
* * * * *
28393754 AAATGAAAATTTTTAAG---TTTCAAATAAGAATCTTTGAGTCTT-
1 AAATGAGAATCTTTAAGAATTTTTAAATGAGAATTTTTGAGT-TTC
* *
28393796 AAATGATAATCTTTAAGACATTTTTAAATGAGAATTTTTTAGTTTC
1 AAATGAGAATCTTTAAGA-ATTTTTAAATGAGAATTTTTGAGTTTC
* * * *
28393842 AAATGAGAATCTTT--G-AGTCTTAAATGAGAATCTTTAAGACATTTTC
1 AAATGAGAATCTTTAAGAATTTTTAAATGAGAAT-TTT-TG--AGTTTC
* * * * *
28393888 GAATGAGAATC-TT-CG-AGTTTTAAATGAGAATCTTTAAGACGTTTTT
1 AAATGAGAATCTTTAAGAATTTTTAAATGAGAAT-TTT-TGA-G-TTTC
** * * *
28393934 AAAAAATAATCTTTAAG-ATGTTTTCAAATGAGAATCTTTGAGTTTT
1 AAATGAGAATCTTTAAGAAT-TTTT-AAATGAGAATTTTTGAGTTTC
* * *
28393980 AAATGGGAATCTTTAAGACATTTTCAAATGAAAATTTTTGAGTTTC
1 AAATGAGAATCTTTAAGA-ATTTTTAAATGAGAATTTTTGAGTTTC
28394026 AAATGAGAATCTTTAA
1 AAATGAGAATCTTTAA
28394042 TATGTGAAGC
Statistics
Matches: 255, Mismatches: 52, Indels: 54
0.71 0.14 0.15
Matches are distributed among these distances:
42 43 0.17
43 5 0.02
44 7 0.03
45 5 0.02
46 165 0.65
47 7 0.03
48 7 0.03
49 6 0.02
50 10 0.04
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.39
Consensus pattern (45 bp):
AAATGAGAATCTTTAAGAATTTTTAAATGAGAATTTTTGAGTTTC
Found at i:28393964 original size:71 final size:71
Alignment explanation
Indices: 28393870--28394003 Score: 214
Period size: 71 Copynumber: 1.9 Consensus size: 71
28393860 CTTAAATGAG
* *
28393870 AATCTTTAAGACATTTTCGAATGAGAATCTTCGAGTTTTAAATGAGAATCTTTAAGACGTTTTTA
1 AATCTTTAAGACATTTTCAAATGAGAATCTTCGAGTTTTAAATGAGAATCTTTAAGACATTTTTA
28393935 AAAAAT
66 AAAAAT
** * *
28393941 AATCTTTAAGATGTTTTCAAATGAGAATCTTTGAGTTTTAAATGGGAATCTTTAAGACATTTT
1 AATCTTTAAGACATTTTCAAATGAGAATCTTCGAGTTTTAAATGAGAATCTTTAAGACATTTT
28394004 CAAATGAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (71 bp):
AATCTTTAAGACATTTTCAAATGAGAATCTTCGAGTTTTAAATGAGAATCTTTAAGACATTTTTA
AAAAAT
Found at i:28394230 original size:65 final size:63
Alignment explanation
Indices: 28394122--28394248 Score: 166
Period size: 65 Copynumber: 2.0 Consensus size: 63
28394112 GAATCTCTAA
* * *
28394122 AATTCAAACAAAAAGCTTTAAACTTTTTGGATGTGAATCCCAAATTTATCAAATGTGAATCTTTG
1 AATTCAAACAAAAAGCTTTAAACTATTTGGATGTGAATCCCAAA-GT-TCAAATGAGAATCTTTG
* * *
28394187 AATTCAAATAAGAAGCTTTAAAC-ATTTGGGTGTGAATCTCCAAAGTTCAAATGAGAATCTTT
1 AATTCAAACAAAAAGCTTTAAACTATTTGGATGTGAATC-CCAAAGTTCAAATGAGAATCTTT
28394249 AAATAATGTA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
63 15 0.27
64 14 0.25
65 26 0.47
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (63 bp):
AATTCAAACAAAAAGCTTTAAACTATTTGGATGTGAATCCCAAAGTTCAAATGAGAATCTTTG
Found at i:28394735 original size:132 final size:132
Alignment explanation
Indices: 28394493--28394805 Score: 391
Period size: 132 Copynumber: 2.4 Consensus size: 132
28394483 AATTTATTTT
* * *
28394493 TTGTTTATTTTTTCAAAGTCGTT-AAGTCTCTGATTAGATGAGCTTTGTTTATTTTTTCAAAGTT
1 TTGTTTATTTTTTCAAAGTCGTTGAA-CCTCTGATTAGATGAGCCTTGTTTATTGTTTCAAAGTT
* ** * * *
28394557 GTTGAGCATCTGATTAAAGGAGCCTTGTTTATTTTTTTTAAGTTGTTGAA-CTTCTGTTTAGAGG
65 GTTGAGCATCTGATTAAAGAAGCCTTGTTTATTTTTTCAAACTTGTT-AAGCCTCTATTTAGAGG
28394621 AGCC
129 AGCC
* * * *
28394625 TTGTTTATTTTTTCGAAGTTGTTGAACCTTTGATTATATGAGCCTTGTTTATTGTTTCAAAGTTG
1 TTGTTTATTTTTTCAAAGTCGTTGAACCTCTGATTAGATGAGCCTTGTTTATTGTTTCAAAGTTG
* * *
28394690 TTGAGCCTCTGTTTAGAA-AAGTCTTGTTTATTTTTTCAAACTTGTTAAGCCTCTATTTAGAGGA
66 TTGAGCATCTGATTA-AAGAAGCCTTGTTTATTTTTTCAAACTTGTTAAGCCTCTATTTAGAGGA
28394754 GCC
130 GCC
* * *
28394757 TTGTTTATTTTTCTCAAAGTCATTGAACCTCTGTTTAGAAGAG-CTTGTT
1 TTGTTTATTTTT-TCAAAGTCGTTGAACCTCTGATTAGATGAGCCTTGTT
28394806 CTTAAAAAAA
Statistics
Matches: 154, Mismatches: 23, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
131 2 0.01
132 125 0.81
133 27 0.18
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (132 bp):
TTGTTTATTTTTTCAAAGTCGTTGAACCTCTGATTAGATGAGCCTTGTTTATTGTTTCAAAGTTG
TTGAGCATCTGATTAAAGAAGCCTTGTTTATTTTTTCAAACTTGTTAAGCCTCTATTTAGAGGAG
CC
Found at i:28394804 original size:44 final size:44
Alignment explanation
Indices: 28394493--28394805 Score: 328
Period size: 44 Copynumber: 7.1 Consensus size: 44
28394483 AATTTATTTT
* * * * *
28394493 TTGTTTATTTTTTCAAAGTCGTT-AAGTCTCTGATTAGATGAGCT
1 TTGTTTATTTTTTCAAAGTTGTTGAA-CCTCTGTTTAGAAGAGCC
* * *
28394537 TTGTTTATTTTTTCAAAGTTGTTGAGCATCTGATTA-AAGGAGCC
1 TTGTTTATTTTTTCAAAGTTGTTGAACCTCTGTTTAGAA-GAGCC
** * *
28394581 TTGTTTATTTTTTTTAAGTTGTTGAACTTCTGTTTAGAGGAGCC
1 TTGTTTATTTTTTCAAAGTTGTTGAACCTCTGTTTAGAAGAGCC
* * * * *
28394625 TTGTTTATTTTTTCGAAGTTGTTGAACCTTTGATTATATGAGCC
1 TTGTTTATTTTTTCAAAGTTGTTGAACCTCTGTTTAGAAGAGCC
* * * *
28394669 TTGTTTATTGTTTCAAAGTTGTTGAGCCTCTGTTTAGAAAAGTC
1 TTGTTTATTTTTTCAAAGTTGTTGAACCTCTGTTTAGAAGAGCC
* * *
28394713 TTGTTTATTTTTTCAAACTTGTT-AAGCCTCTATTTAGAGGAGCC
1 TTGTTTATTTTTTCAAAGTTGTTGAA-CCTCTGTTTAGAAGAGCC
**
28394757 TTGTTTATTTTTCTCAAAGTCATTGAACCTCTGTTTAGAAGAG-C
1 TTGTTTATTTTT-TCAAAGTTGTTGAACCTCTGTTTAGAAGAGCC
28394801 TTGTT
1 TTGTT
28394806 CTTAAAAAAA
Statistics
Matches: 223, Mismatches: 40, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
43 2 0.01
44 195 0.87
45 24 0.11
46 2 0.01
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (44 bp):
TTGTTTATTTTTTCAAAGTTGTTGAACCTCTGTTTAGAAGAGCC
Found at i:28395004 original size:36 final size:36
Alignment explanation
Indices: 28394936--28395009 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
28394926 AATTGATCTG
* *
28394936 AGCCTAAGCCCATTAGGCTTGATCCAACAGGGTTTA
1 AGCCTAAGCCCATTAGGCCTGATCCAACAGGGTCTA
* * *
28394972 AGCCTAAGCCCATTGGAGCCTGCT-CAATAGGGTCTA
1 AGCCTAAGCCCATTAG-GCCTGATCCAACAGGGTCTA
28395008 AG
1 AG
28395010 TATATAGGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
36 27 0.84
37 5 0.16
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23
Consensus pattern (36 bp):
AGCCTAAGCCCATTAGGCCTGATCCAACAGGGTCTA
Found at i:28395048 original size:13 final size:13
Alignment explanation
Indices: 28395030--28395098 Score: 60
Period size: 13 Copynumber: 5.6 Consensus size: 13
28395020 CAACTGTTGG
28395030 TTATTTTATTTTA
1 TTATTTTATTTTA
28395043 TTATTTTATTTTA
1 TTATTTTATTTTA
* *
28395056 TTCTTGT-TTTTA
1 TTATTTTATTTTA
28395068 TT-TTGATT-TTTT-
1 TTATT--TTATTTTA
28395080 TTATTTTA--TTA
1 TTATTTTATTTTA
28395091 TTATTTTA
1 TTATTTTA
28395099 AGATAATAGG
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
10 2 0.04
11 12 0.25
12 9 0.19
13 25 0.52
ACGTcount: A:0.19, C:0.01, G:0.03, T:0.77
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:28395076 original size:6 final size:5
Alignment explanation
Indices: 28395030--28395098 Score: 72
Period size: 5 Copynumber: 13.6 Consensus size: 5
28395020 CAACTGTTGG
*
28395030 TTATT TTATT TTA-- TTATT TTATT TTATT CTTGTTT TTATT TTGATT
1 TTATT TTATT TTATT TTATT TTATT TTATT -TT-ATT TTATT TT-ATT
28395076 TT-TT TTATT TTATT ATTATT TTA
1 TTATT TTATT TTATT -TTATT TTA
28395099 AGATAATAGG
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
3 3 0.05
4 4 0.07
5 32 0.58
6 14 0.25
7 2 0.04
ACGTcount: A:0.19, C:0.01, G:0.03, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:28395441 original size:23 final size:24
Alignment explanation
Indices: 28395406--28395458 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
28395396 AATCTTAGAA
*
28395406 TTTTTAAGATTTTTTTTT-CAAAT
1 TTTTTAAGATTTTTTTTTAAAAAT
28395429 TTTTTACAG-TTTTTTTTTAAAAAT
1 TTTTTA-AGATTTTTTTTTAAAAAT
28395453 TTTTTA
1 TTTTTA
28395459 GAAAATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (24 bp):
TTTTTAAGATTTTTTTTTAAAAAT
Found at i:28395442 original size:24 final size:23
Alignment explanation
Indices: 28395406--28395458 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
28395396 AATCTTAGAA
**
28395406 TTTTTAAGATTTTTTTTTCAAAT
1 TTTTTAAGATTTTTTTTAAAAAT
*
28395429 TTTTTACAGTTTTTTTTTAAAAAT
1 TTTTTA-AGATTTTTTTTAAAAAT
28395453 TTTTTA
1 TTTTTA
28395459 GAAAATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (23 bp):
TTTTTAAGATTTTTTTTAAAAAT
Found at i:28395953 original size:4 final size:4
Alignment explanation
Indices: 28395944--28396016 Score: 51
Period size: 4 Copynumber: 18.0 Consensus size: 4
28395934 ATTTTGGTAT
* *
28395944 TTTA TTTA TTTA TTTA TTTA TTGTT TTTA TTGTA TTT- TTTG TATT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TT-TA TTTA TTTA T-TTA TTTA
* * * *
28395993 TTTA TGTG TTTG TTTA TTTT TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA
28396017 AGAGTAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
3 5 0.09
4 42 0.75
5 9 0.16
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:28395985 original size:18 final size:18
Alignment explanation
Indices: 28395944--28395997 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
28395934 ATTTTGGTAT
28395944 TTTATT-TA-TTTATTTA
1 TTTATTGTATTTTATTTA
28395960 TTTATTGT-TTTTATTGTA
1 TTTATTGTATTTTATT-TA
*
28395978 TTTTTTGTATTTTTATTTA
1 TTTATTGTA-TTTTATTTA
28395997 T
1 T
28395998 GTGTTTGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
16 6 0.19
17 7 0.22
18 9 0.28
19 3 0.09
20 7 0.22
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.76
Consensus pattern (18 bp):
TTTATTGTATTTTATTTA
Found at i:28395988 original size:44 final size:45
Alignment explanation
Indices: 28395921--28396016 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 45
28395911 CCAACCGAGC
*
28395921 TGTTTTTATTTTTATTTTGGTA-TTTTATTTATTTATTTATTTAT
1 TGTTTTTATTTTTATTTTGGTATTTTTATTTATGTATTTATTTAT
* *
28395965 TGTTTTTATTGTATT-TTTT-GTATTTTTATTTATGTGTTTGTTTAT
1 TGTTTTTATT-T-TTATTTTGGTATTTTTATTTATGTATTTATTTAT
28396010 T-TTTTTA
1 TGTTTTTA
28396017 AGAGTAATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
44 19 0.41
45 25 0.54
46 2 0.04
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.75
Consensus pattern (45 bp):
TGTTTTTATTTTTATTTTGGTATTTTTATTTATGTATTTATTTAT
Found at i:28396028 original size:45 final size:44
Alignment explanation
Indices: 28395934--28396029 Score: 104
Period size: 45 Copynumber: 2.2 Consensus size: 44
28395924 TTTTATTTTT
* * **
28395934 ATTTTGGTATTTTATTTATTTATTTATTTATTGTTTTTATTGTA
1 ATTTTTGTATTTTATTTATGTATTTATTTATTGTTTTTAGAGTA
* * *
28395978 TTTTTTGTATTTTTATTTATGTGTTTGTTTATT-TTTTTAAGAGTA
1 ATTTTTGTA-TTTTATTTATGTATTTATTTATTGTTTTT-AGAGTA
28396023 ATTTTTG
1 ATTTTTG
28396030 CATTAATAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
44 12 0.29
45 30 0.71
ACGTcount: A:0.19, C:0.00, G:0.11, T:0.70
Consensus pattern (44 bp):
ATTTTTGTATTTTATTTATGTATTTATTTATTGTTTTTAGAGTA
Found at i:28399546 original size:16 final size:17
Alignment explanation
Indices: 28399517--28399554 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
28399507 TTTGTAGGAA
28399517 TTTTTATTTCAAAAT-T
1 TTTTTATTTCAAAATGT
* *
28399533 TTTTTTTTTGAAAATGT
1 TTTTTATTTCAAAATGT
28399550 TTTTT
1 TTTTT
28399555 GAAAACTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTTTATTTCAAAATGT
Found at i:28399612 original size:36 final size:36
Alignment explanation
Indices: 28399572--28399653 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 36
28399562 TAAAAAGATC
*
28399572 TTTTTTATTATTATTTTGAAAACTTATTTGAAAA-G
1 TTTTTTTTTATTATTTTGAAAACTTATTTGAAAAGG
* * ****
28399607 TTTTTTTTTGTTTTTTTTTTTACTTATTTGAAAAGG
1 TTTTTTTTTATTATTTTGAAAACTTATTTGAAAAGG
28399643 TTTTTTTTTAT
1 TTTTTTTTTAT
28399654 ATATAATTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
35 27 0.71
36 11 0.29
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.66
Consensus pattern (36 bp):
TTTTTTTTTATTATTTTGAAAACTTATTTGAAAAGG
Found at i:28400193 original size:20 final size:19
Alignment explanation
Indices: 28400170--28400216 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
28400160 ACATTCATCG
*
28400170 AAAAATTCATAT-TTTCTAGA
1 AAAAATTCAAATATTT-TA-A
*
28400190 AAAAATCCAAATATTTTAA
1 AAAAATTCAAATATTTTAA
28400209 AAAAATTC
1 AAAAATTC
28400217 TAGATTTTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 8 0.35
20 12 0.52
21 3 0.13
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAATATTTTAA
Found at i:28400945 original size:20 final size:20
Alignment explanation
Indices: 28400813--28400947 Score: 76
Period size: 18 Copynumber: 7.0 Consensus size: 20
28400803 CGCATGGATG
* *
28400813 TCATGCTAATATATTAATTAT
1 TCATGCAAATATA-TAATCAT
*
28400834 T-ATGC-AATA-ATAA-CAA
1 TCATGCAAATATATAATCAT
*
28400850 TCATGTAAATATATAAT-A-
1 TCATGCAAATATATAATCAT
*
28400868 TCATGCAAATATATTATCAT
1 TCATGCAAATATATAATCAT
*
28400888 TCA---ATAATATA-AATTA-
1 TCATGCA-AATATATAATCAT
*
28400904 CCATGCAAATATATTAATAATCAT
1 TCATGC-AA-ATA-T-ATAATCAT
28400928 TCATGCAAATATATAATCAT
1 TCATGCAAATATATAATCAT
28400948 GAAATCGAAT
Statistics
Matches: 88, Mismatches: 10, Indels: 33
0.67 0.08 0.25
Matches are distributed among these distances:
16 4 0.05
17 10 0.11
18 26 0.30
19 11 0.12
20 19 0.22
21 3 0.03
22 4 0.05
23 6 0.07
24 5 0.06
ACGTcount: A:0.47, C:0.12, G:0.04, T:0.37
Consensus pattern (20 bp):
TCATGCAAATATATAATCAT
Found at i:28400947 original size:16 final size:16
Alignment explanation
Indices: 28400928--28400975 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 16
28400918 TAATAATCAT
28400928 TCATGCAAATATATAA
1 TCATGCAAATATATAA
28400944 TCATG-AAATCGAATATAA
1 TCATGCAAAT---ATATAA
*
28400962 TCATACAAATATAT
1 TCATGCAAATATAT
28400976 TAGTAATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
15 4 0.15
16 9 0.33
18 10 0.37
19 4 0.15
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (16 bp):
TCATGCAAATATATAA
Found at i:28401082 original size:24 final size:24
Alignment explanation
Indices: 28401052--28401107 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 24
28401042 AATATCATTC
*
28401052 AAATATAATATTA-ATCATGCAAT
1 AAATATAATATCATATCATGCAAT
28401075 AACATATAATATCATATCATGCAAT
1 AA-ATATAATATCATATCATGCAAT
28401100 AAATATAA
1 AAATATAA
28401108 AATAATGCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 2 0.07
24 16 0.53
25 12 0.40
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.32
Consensus pattern (24 bp):
AAATATAATATCATATCATGCAAT
Found at i:28401131 original size:19 final size:19
Alignment explanation
Indices: 28401080--28401131 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
28401070 GCAATAACAT
*
28401080 ATAAT-ATCATATCATGCA
1 ATAATAATCATATAATGCA
* *
28401098 ATAA-ATATAAAATAATGCA
1 ATAATA-ATCATATAATGCA
28401117 ATAATAATCATATAA
1 ATAATAATCATATAA
28401132 ATATATAACC
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
18 4 0.15
19 21 0.81
20 1 0.04
ACGTcount: A:0.56, C:0.10, G:0.04, T:0.31
Consensus pattern (19 bp):
ATAATAATCATATAATGCA
Found at i:28401277 original size:23 final size:25
Alignment explanation
Indices: 28401251--28401301 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
28401241 ATGCAATTTA
* *
28401251 ATATAT-AATCATGCAAA-AAATAT
1 ATATATAAATCAAGCAAACAAACAT
28401274 ATATATAAATCAAGCAAACAAACAT
1 ATATATAAATCAAGCAAACAAACAT
28401299 ATA
1 ATA
28401302 ATTAAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.25
24 10 0.42
25 8 0.33
ACGTcount: A:0.59, C:0.12, G:0.04, T:0.25
Consensus pattern (25 bp):
ATATATAAATCAAGCAAACAAACAT
Found at i:28401343 original size:23 final size:21
Alignment explanation
Indices: 28401306--28401367 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 21
28401296 CATATAATTA
28401306 AATATATAATCATGCAAATAAT
1 AATATATAATCATGCAAAT-AT
28401328 AATATATAAATCATGCAAATAT
1 AATATAT-AATCATGCAAATAT
*
28401350 AATAT-TAGTCATGCAAAT
1 AATATATAATCATGCAAAT
28401368 TCATGCAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
20 11 0.29
21 1 0.03
22 14 0.37
23 12 0.32
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (21 bp):
AATATATAATCATGCAAATAT
Found at i:28401348 original size:20 final size:19
Alignment explanation
Indices: 28401306--28401367 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 19
28401296 CATATAATTA
28401306 AATATATAATCATGCAAATAAT
1 AATATATAATCATGC--A-AAT
28401328 AATATATAAATCATGCAAAT
1 AATATAT-AATCATGCAAAT
*
28401348 -ATAATATTAGTCATGCAAAT
1 AAT-ATA-TAATCATGCAAAT
28401368 TCATGCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 2 0.06
20 17 0.47
21 2 0.06
22 7 0.19
23 8 0.22
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (19 bp):
AATATATAATCATGCAAAT
Found at i:28408983 original size:30 final size:28
Alignment explanation
Indices: 28408949--28409041 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 28
28408939 CGGTAGTGAG
28408949 ATTGATCAGGAGGTGATCACCGATGATGA
1 ATTGATCAGGAGGTGATCA-CGATGATGA
* * * *
28408978 TATTGATCCGTAGTTGA-C-TGATGATGA
1 -ATTGATCAGGAGGTGATCACGATGATGA
*
28409005 GATTGATCAGGAGTTGA-CA-GATGATGA
1 -ATTGATCAGGAGGTGATCACGATGATGA
28409032 AGTTGATCAG
1 A-TTGATCAG
28409042 CTGTTGACTG
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
26 1 0.02
27 39 0.72
29 1 0.02
30 13 0.24
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.29
Consensus pattern (28 bp):
ATTGATCAGGAGGTGATCACGATGATGA
Found at i:28409050 original size:54 final size:54
Alignment explanation
Indices: 28408945--28409112 Score: 173
Period size: 54 Copynumber: 3.1 Consensus size: 54
28408935 TTACCGGTAG
*
28408945 TGAGATTGATCAGGAGGTGATCACCGATGATGATA-TTGATCCGTAGTTGACTGATGA
1 TGAGATTGATCAGGAGGTGA-CA--GATGATGA-AGTTGATCAGTAGTTGACTGATGA
*
28409002 TGAGATTGATCAGGAGTTGACAGATGATGAAGTTGATCAGCT-GTTGACTGATGA
1 TGAGATTGATCAGGAGGTGACAGATGATGAAGTTGATCAG-TAGTTGACTGATGA
* * * * * *
28409056 TGAGTTTGATCA-GATGGTAACCGATGATGAGGTTGATCAAG-AGCTGATTGATGA
1 TGAGATTGATCAGGA-GGTGACAGATGATGAAGTTGATC-AGTAGTTGACTGATGA
28409110 TGA
1 TGA
28409113 AGTTGGTTAG
Statistics
Matches: 97, Mismatches: 9, Indels: 13
0.82 0.08 0.11
Matches are distributed among these distances:
53 3 0.03
54 70 0.72
55 3 0.03
56 2 0.02
57 19 0.20
ACGTcount: A:0.29, C:0.10, G:0.31, T:0.30
Consensus pattern (54 bp):
TGAGATTGATCAGGAGGTGACAGATGATGAAGTTGATCAGTAGTTGACTGATGA
Found at i:28409108 original size:27 final size:26
Alignment explanation
Indices: 28408970--28409117 Score: 125
Period size: 27 Copynumber: 5.5 Consensus size: 26
28408960 GGTGATCACC
** *
28408970 GATGATGATATTGATCCGTAGTTGACT
1 GATGATGAGGTTGATCAG-AGTTGACT
* *
28408997 GATGATGAGATTGATCAGGAGTTGACA
1 GATGATGAGGTTGATCA-GAGTTGACT
* *
28409024 GATGATGAAGTTGATCAGCTGTTGACT
1 GATGATGAGGTTGATCAG-AGTTGACT
* * * *
28409051 GATGATGAGTTTGATCAGATGGTAACC
1 GATGATGAGGTTGATCAGA-GTTGACT
* *
28409078 GATGATGAGGTTGATCAAGAGCTGATT
1 GATGATGAGGTTGATC-AGAGTTGACT
*
28409105 GATGATGAAGTTG
1 GATGATGAGGTTG
28409118 GTTAGGCCAT
Statistics
Matches: 98, Mismatches: 19, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
26 1 0.01
27 93 0.95
28 4 0.04
ACGTcount: A:0.29, C:0.09, G:0.31, T:0.31
Consensus pattern (26 bp):
GATGATGAGGTTGATCAGAGTTGACT
Found at i:28413359 original size:32 final size:33
Alignment explanation
Indices: 28413304--28413386 Score: 98
Period size: 32 Copynumber: 2.5 Consensus size: 33
28413294 AGTTGTGATC
* * *
28413304 TTTAGAAGATTTT-TAAAAGCTTATATTATTA-T
1 TTTA-AAGATTTTCTAAAAACTTATACTATAATT
*
28413336 TTTAAAGATTTTCTAAAAACTTATGCTATAATT
1 TTTAAAGATTTTCTAAAAACTTATACTATAATT
*
28413369 TTTGAAGATTTTCTAAAA
1 TTTAAAGATTTTCTAAAA
28413387 TGTTAAATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
31 8 0.18
32 18 0.41
33 18 0.41
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (33 bp):
TTTAAAGATTTTCTAAAAACTTATACTATAATT
Found at i:28413382 original size:33 final size:32
Alignment explanation
Indices: 28413308--28413386 Score: 97
Period size: 33 Copynumber: 2.5 Consensus size: 32
28413298 GTGATCTTTA
* * *
28413308 GAAGATTTT-TAAAAGCTTATATTATTATTTT
1 GAAGATTTTCTAAAAACTTATACTATAATTTT
* *
28413339 AAAGATTTTCTAAAAACTTATGCTATAATTTTT
1 GAAGATTTTCTAAAAACTTATACTATAA-TTTT
28413372 GAAGATTTTCTAAAA
1 GAAGATTTTCTAAAA
28413387 TGTTAAATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
31 8 0.20
32 14 0.35
33 18 0.45
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (32 bp):
GAAGATTTTCTAAAAACTTATACTATAATTTT
Found at i:28416326 original size:9 final size:9
Alignment explanation
Indices: 28416302--28416343 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
28416292 CAATTTGTCC
*
28416302 TGTATTATTT
1 TGTATT-TTA
28416312 TGTATTTTA
1 TGTATTTTA
28416321 TGTATTTTA
1 TGTATTTTA
28416330 TGTATTTTA
1 TGTATTTTA
28416339 T-TATT
1 TGTATT
28416344 ATGTATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 4 0.13
9 21 0.68
10 6 0.19
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (9 bp):
TGTATTTTA
Found at i:28416335 original size:18 final size:19
Alignment explanation
Indices: 28416302--28416355 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
28416292 CAATTTGTCC
*
28416302 TGTATTATTTTGTATTTTA
1 TGTATTATTATGTATTTTA
28416321 TGTATT-TTATGTATTTTA
1 TGTATTATTATGTATTTTA
*
28416339 T-TATTATGTATATATTT
1 TGTATTAT-TATGTATTT
28416356 ATTTATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 4 0.13
18 13 0.42
19 14 0.45
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (19 bp):
TGTATTATTATGTATTTTA
Found at i:28416999 original size:20 final size:20
Alignment explanation
Indices: 28416974--28417011 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28416964 ACTTCCGGTG
*
28416974 AAATTTCCAGATTCCGGCGA
1 AAATTTCCAGAATCCGGCGA
28416994 AAATTTCCAGAATCCGGC
1 AAATTTCCAGAATCCGGC
28417012 ACCGGTGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
AAATTTCCAGAATCCGGCGA
Found at i:28417376 original size:27 final size:27
Alignment explanation
Indices: 28417338--28417411 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
28417328 CTCCAGGTTT
* * *
28417338 TTTTTTTTTTTTTTTTCTTTCTTTGAA
1 TTTTTTTATTTTATTTATTTCTTTGAA
28417365 TTTTTTTATTTTATTTATTTCTTTG--
1 TTTTTTTATTTTATTTATTTCTTTGAA
28417390 TTTATTTTAATTTTTATTTATT
1 TTT-TTTT-A-TTTTATTTATT
28417412 AGATTAGGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 3 0.07
26 4 0.10
27 23 0.56
28 11 0.27
ACGTcount: A:0.14, C:0.04, G:0.03, T:0.80
Consensus pattern (27 bp):
TTTTTTTATTTTATTTATTTCTTTGAA
Found at i:28417553 original size:60 final size:60
Alignment explanation
Indices: 28417488--28417834 Score: 472
Period size: 59 Copynumber: 5.7 Consensus size: 60
28417478 AAAAATTCCA
28417488 AAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 AAAAAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
* *
28417549 --AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAA-TTTC
1 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
* * *
28417606 AAAAAAAAAATATTTTTGGGGAAAAGTTGAAACTATCAATTTTCCTCAGAAATAAA-TTTC
1 -AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
* * *
28417666 GAAAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
1 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAAATTTTC
* *
28417731 AAAAAAAATATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAATTTTC
1 AAAAAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT-AAATTTTC
*
28417793 --CAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
28417835 CTACAAAAAA
Statistics
Matches: 259, Mismatches: 16, Indels: 24
0.87 0.05 0.08
Matches are distributed among these distances:
57 4 0.02
58 45 0.17
59 82 0.32
60 61 0.24
61 4 0.02
62 9 0.03
63 1 0.00
64 7 0.03
65 10 0.04
66 36 0.14
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.33
Consensus pattern (60 bp):
AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
Found at i:28417770 original size:125 final size:123
Alignment explanation
Indices: 28417483--28417848 Score: 537
Period size: 125 Copynumber: 3.0 Consensus size: 123
28417473 AAATAAAAAA
*
28417483 TTCCAAAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTT
1 TTCC-AAAAAAAATATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTT
* *
28417548 CAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT--CAG--AAATAAAT
65 CAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTAAAAGAAAAATAAAT
* * *
28417603 TT-CAAAAAAAAAATATTTTTGGGGAAAAGTTGAAACTATCAATTTTCCTCAGAAATAAA-TTTC
1 TTCCAAAAAAAATATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
*
28417666 GAAAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAAT
66 --AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC-TAAAAGAAAAATAAAT
*
28417727 TTCCAAAAAAAATATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAATTTT
1 TTCCAAAAAAAATATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT-AAATTTT
* *
28417792 CCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCCTACAAAAAAAAAT
65 CAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTT-CCTA-AAAGAAAAAT
28417849 CATTCTTTCC
Statistics
Matches: 220, Mismatches: 14, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
117 4 0.02
118 52 0.24
119 41 0.19
120 3 0.01
122 2 0.01
124 10 0.05
125 90 0.41
126 14 0.06
127 4 0.02
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (123 bp):
TTCCAAAAAAAATATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTAAAAGAAAAATAAAT
Found at i:28421682 original size:30 final size:29
Alignment explanation
Indices: 28421645--28421709 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
28421635 ATGAAAAAAA
28421645 AAAAAAAAAAAAGAAAAAAA-AGAAAAATG
1 AAAAAAAAAAAAGAAAAAAAGAG-AAAATG
* * *
28421674 AGAAAAAAAAGAAGGAAAAATGAGAAAATG
1 A-AAAAAAAAAAAGAAAAAAAGAGAAAATG
28421704 AAAAAA
1 AAAAAA
28421710 GAGATTCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 6 0.19
30 23 0.74
31 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (29 bp):
AAAAAAAAAAAAGAAAAAAAGAGAAAATG
Found at i:28421683 original size:1 final size:1
Alignment explanation
Indices: 28421638--28421671 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
28421628 ACAATGGATG
* *
28421638 AAAAAAAAAAAAAAAAAAAGAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
28421672 TGAGAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:28421683 original size:22 final size:22
Alignment explanation
Indices: 28421638--28421711 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
28421628 ACAATGGATG
28421638 AAAAAAAAAA-AAAAA--A-AA
1 AAAAAAAAAAGAAAAATGAGAA
*
28421656 AGAAAAAAAAGAAAAATGAGAA
1 AAAAAAAAAAGAAAAATGAGAA
* *
28421678 AAAAAAGAAGGAAAAATGAGAA
1 AAAAAAAAAAGAAAAATGAGAA
**
28421700 AATGAAAAAAGA
1 AAAAAAAAAAGA
28421712 GATTCAAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
18 9 0.20
19 5 0.11
21 1 0.02
22 29 0.66
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (22 bp):
AAAAAAAAAAGAAAAATGAGAA
Found at i:28421684 original size:18 final size:18
Alignment explanation
Indices: 28421635--28421686 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
28421625 TCAACAATGG
* *
28421635 ATGAAAAAAAAAAAAAAA
1 ATGAGAAAAAAAAGAAAA
**
28421653 AAAAGAAAAAAAAGAAAA
1 ATGAGAAAAAAAAGAAAA
28421671 ATGAGAAAAAAAAGAA
1 ATGAGAAAAAAAAGAA
28421687 GGAAAAATGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.04
Consensus pattern (18 bp):
ATGAGAAAAAAAAGAAAA
Found at i:28423079 original size:42 final size:40
Alignment explanation
Indices: 28422961--28423450 Score: 587
Period size: 40 Copynumber: 12.0 Consensus size: 40
28422951 TCTTTAGAGT
*
28422961 ATTTACTTTTCCAAAGTTCGTAGTACCTCTGTTTAGAGGA-CA
1 ATTTACTTTTCCAAAG-TCGT--TGCCTCTGTTTAGAGGAGCA
* *
28423003 A-TTAC-TTTCCAAAGTCCGGGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGT-C--GTTGCCTCTGTTTAGAGGAGCA
28423044 ATTTACTTTTCC-AAGTTCCGTTGCCTCTGTCTTAGAGGAGC-
1 ATTTACTTTTCCAAAG-T-CGTTGCCTCTGT-TTAGAGGAGCA
*
28423085 ATTTACTTTT-CAAAGTCAGTGGTACCTCTGTTTAGAGGAGCCA
1 ATTTACTTTTCCAAAGTC-GT--TGCCTCTGTTTAGAGGAG-CA
28423128 A-TTAC-TTT-C-AAGTTCGTTGCCTCTGTTTAGAGGAGCAA
1 ATTTACTTTTCCAAAG-TCGTTGCCTCTGTTTAGAGGAGC-A
28423166 TTTAGTTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ---A-TTTACTTTTCCAAAGTCGT--TGCCTCTGTTTAGAGGAGCA
28423211 ATTTACTTTT-CAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAG-TCGTTGCCTCTGTTTAGAGGAGCA
28423251 ATTTA-TTTTCCAAAGTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTTGCCTCTGTTTAGAGGAGCA
*
28423290 ATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGT--TGCCTCTGTTTAGAGGAGCA
28423332 ATTTACTTTTCCAAAGTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTTGCCTCTGTTTAGAGGAGCA
28423372 ATTTAC-TTTCCAAAGTCG-TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTTGCCTCTGTTTAGAGGAGCA
*
28423410 ATTTACTTTTCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
1 ATTTACTTTTCCAAAGTCGT--TGCCTCTGTTTAGAGGAGC
28423451 TTTGGTAAAA
Statistics
Matches: 406, Mismatches: 8, Indels: 68
0.84 0.02 0.14
Matches are distributed among these distances:
37 1 0.00
38 44 0.11
39 58 0.14
40 105 0.26
41 59 0.15
42 95 0.23
43 13 0.03
44 8 0.02
45 4 0.01
46 19 0.05
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (40 bp):
ATTTACTTTTCCAAAGTCGTTGCCTCTGTTTAGAGGAGCA
Found at i:28423168 original size:121 final size:120
Alignment explanation
Indices: 28422961--28423450 Score: 626
Period size: 121 Copynumber: 4.0 Consensus size: 120
28422951 TCTTTAGAGT
*
28422961 ATTTACTTTTCCAAAGTTCGTAGTACCTCTGTTTAGAGGA-CAA-TTACTTTCCAAAGTCCGGGG
1 ATTTACTTTTCCAAAGTTCGT--TACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGT-C--GT
* *
28423024 TACCTCTGTTTAGAGGAGCAATTTACTTTTCCAAGTTCCGT-TGCCTCTGTCTTAGAGGAGC-
61 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-T-CGTGTGCCTCTGT-TTAGAGGAGCA
28423085 ATTTACTTTT-CAAAG-TCAGTGGTACCTCTGTTTAGAGGAGCCAA-TTACTTT-C-AAGTTCGT
1 ATTTACTTTTCCAAAGTTC-GT--TACCTCTGTTTAGAGGAG-CAATTTACTTTCCAAAG-TCGT
28423145 TGCCTCTGTTTAGAGGAGCAATTTAGTTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
61 TGCCTCTGTTTAGAGGAGC-A---A-TTTACTTTTCAAAGTCGT-GTGCCTCTGTTTAGAGGAGC
28423210 A
120 A
* *
28423211 ATTTACTTTT-CAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTCCAAAGTCGTTGCCT
1 ATTTACTTTTCCAAAGTTCGTTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTTGCCT
*
28423275 CTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
66 CTGTTTAGAGGAGCAATTTACTTTT-CAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
*
28423332 ATTTACTTTTCCAAAG-TCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCG-TGCCT
1 ATTTACTTTTCCAAAGTTCGTTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTTGCCT
28423395 CTGTTTAGAGGAGCAATTTACTTTTCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
66 CTGTTTAGAGGAGCAATTTACTTTTC-AAAGTCGT-GTGCCTCTGTTTAGAGGAGC
28423451 TTTGGTAAAA
Statistics
Matches: 338, Mismatches: 9, Indels: 42
0.87 0.02 0.11
Matches are distributed among these distances:
119 1 0.00
120 67 0.20
121 101 0.30
122 8 0.02
123 32 0.09
124 39 0.12
125 46 0.14
126 42 0.12
127 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (120 bp):
ATTTACTTTTCCAAAGTTCGTTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTTGCCT
CTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGTGCCTCTGTTTAGAGGAGCA
Found at i:28423566 original size:1 final size:1
Alignment explanation
Indices: 28423457--28423559 Score: 152
Period size: 1 Copynumber: 103.0 Consensus size: 1
28423447 GAGCTTTGGT
* * *
28423457 AAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAAAAAACAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
28423522 CAAAAACAAAAAAAAAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
28423560 CCAAAAATGT
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 90 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:28423566 original size:27 final size:26
Alignment explanation
Indices: 28423457--28423559 Score: 172
Period size: 27 Copynumber: 3.9 Consensus size: 26
28423447 GAGCTTTGGT
*
28423457 AAAAAAAAAAAAA-AAAAAAAAAACA
1 AAAAAAAAAAAAACAAAAAAAAAAAA
28423482 AAAAAAAAAAAAACAAAAAAACAAAAA
1 AAAAAAAAAAAAACAAAAAAA-AAAAA
28423509 AAAAAAAAAAAAACAAAAACAAAAAAA
1 AAAAAAAAAAAAACAAAAA-AAAAAAA
28423536 AAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAACAAAAAAAAAA
28423560 CCAAAAATGT
Statistics
Matches: 74, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
25 13 0.18
26 12 0.16
27 47 0.64
28 2 0.03
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (26 bp):
AAAAAAAAAAAAACAAAAAAAAAAAA
Found at i:28429673 original size:54 final size:54
Alignment explanation
Indices: 28429571--28429737 Score: 180
Period size: 54 Copynumber: 3.1 Consensus size: 54
28429561 TTACCGGTAG
*
28429571 TGAGATTGATCAGGAGGTGATCACGATGATGATA-TTGATCCGTAGTTGACTGATGA
1 TGAGATTGATCAGGAGGTGA-CA-GATGATGA-AGTTGATCAGTAGTTGACTGATGA
*
28429627 TGAGATTGATCAGGAGTTGACAGATGATGAAGTTGATCAGCT-GTTGACTGATGA
1 TGAGATTGATCAGGAGGTGACAGATGATGAAGTTGATCAG-TAGTTGACTGATGA
* * * * * *
28429681 TGAGTTTGATCA-GATGGTAACCGATGATGAGGTTGATCAAG-AGCTGATTGATGA
1 TGAGATTGATCAGGA-GGTGACAGATGATGAAGTTGATC-AGTAGTTGACTGATGA
28429735 TGA
1 TGA
28429738 AGTTGGTTAG
Statistics
Matches: 97, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
53 3 0.03
54 70 0.72
55 5 0.05
56 19 0.20
ACGTcount: A:0.29, C:0.10, G:0.31, T:0.30
Consensus pattern (54 bp):
TGAGATTGATCAGGAGGTGACAGATGATGAAGTTGATCAGTAGTTGACTGATGA
Found at i:28429733 original size:27 final size:26
Alignment explanation
Indices: 28429595--28429742 Score: 125
Period size: 27 Copynumber: 5.5 Consensus size: 26
28429585 AGGTGATCAC
** *
28429595 GATGATGATATTGATCCGTAGTTGACT
1 GATGATGAGGTTGATCAG-AGTTGACT
* *
28429622 GATGATGAGATTGATCAGGAGTTGACA
1 GATGATGAGGTTGATCA-GAGTTGACT
* *
28429649 GATGATGAAGTTGATCAGCTGTTGACT
1 GATGATGAGGTTGATCAG-AGTTGACT
* * * *
28429676 GATGATGAGTTTGATCAGATGGTAACC
1 GATGATGAGGTTGATCAGA-GTTGACT
* *
28429703 GATGATGAGGTTGATCAAGAGCTGATT
1 GATGATGAGGTTGATC-AGAGTTGACT
*
28429730 GATGATGAAGTTG
1 GATGATGAGGTTG
28429743 GTTAGGCCAT
Statistics
Matches: 98, Mismatches: 19, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
26 1 0.01
27 93 0.95
28 4 0.04
ACGTcount: A:0.29, C:0.09, G:0.31, T:0.31
Consensus pattern (26 bp):
GATGATGAGGTTGATCAGAGTTGACT
Found at i:28433971 original size:32 final size:33
Alignment explanation
Indices: 28433916--28433998 Score: 98
Period size: 32 Copynumber: 2.5 Consensus size: 33
28433906 AGTTGTGATC
* * *
28433916 TTTAGAAGATTTT-TAAAAGCTTATATTATTA-T
1 TTTA-AAGATTTTCTAAAAACTTATACTATAATT
*
28433948 TTTAAAGATTTTCTAAAAACTTATGCTATAATT
1 TTTAAAGATTTTCTAAAAACTTATACTATAATT
*
28433981 TTTGAAGATTTTCTAAAA
1 TTTAAAGATTTTCTAAAA
28433999 TGTTAAATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
31 8 0.18
32 18 0.41
33 18 0.41
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (33 bp):
TTTAAAGATTTTCTAAAAACTTATACTATAATT
Found at i:28433994 original size:33 final size:32
Alignment explanation
Indices: 28433920--28433998 Score: 97
Period size: 33 Copynumber: 2.5 Consensus size: 32
28433910 GTGATCTTTA
* * *
28433920 GAAGATTTT-TAAAAGCTTATATTATTATTTT
1 GAAGATTTTCTAAAAACTTATACTATAATTTT
* *
28433951 AAAGATTTTCTAAAAACTTATGCTATAATTTTT
1 GAAGATTTTCTAAAAACTTATACTATAA-TTTT
28433984 GAAGATTTTCTAAAA
1 GAAGATTTTCTAAAA
28433999 TGTTAAATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
31 8 0.20
32 14 0.35
33 18 0.45
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (32 bp):
GAAGATTTTCTAAAAACTTATACTATAATTTT
Found at i:28436941 original size:9 final size:9
Alignment explanation
Indices: 28436917--28436958 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
28436907 CAATTTGTCC
*
28436917 TGTATTATTT
1 TGTATT-TTA
28436927 TGTATTTTA
1 TGTATTTTA
28436936 TGTATTTTA
1 TGTATTTTA
28436945 TGTATTTTA
1 TGTATTTTA
28436954 T-TATT
1 TGTATT
28436959 ATGTATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 4 0.13
9 21 0.68
10 6 0.19
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (9 bp):
TGTATTTTA
Found at i:28436950 original size:18 final size:19
Alignment explanation
Indices: 28436917--28436970 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
28436907 CAATTTGTCC
*
28436917 TGTATTATTTTGTATTTTA
1 TGTATTATTATGTATTTTA
28436936 TGTATT-TTATGTATTTTA
1 TGTATTATTATGTATTTTA
*
28436954 T-TATTATGTATATATTT
1 TGTATTAT-TATGTATTT
28436971 ATTTATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 4 0.13
18 13 0.42
19 14 0.45
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (19 bp):
TGTATTATTATGTATTTTA
Found at i:28437435 original size:26 final size:24
Alignment explanation
Indices: 28437393--28437446 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
28437383 CTGGGAGTGA
*
28437393 GAAAAATTTTTTAGAAATTTTTGG
1 GAAAAATTTTTTAGAAATTTCTGG
* *
28437417 CGAAAATTTTTTCTGGAAATTTCTGG
1 -GAAAAATTTTT-TAGAAATTTCTGG
28437443 GAAA
1 GAAA
28437447 TTTCCAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.41
Consensus pattern (24 bp):
GAAAAATTTTTTAGAAATTTCTGG
Found at i:28437514 original size:31 final size:31
Alignment explanation
Indices: 28437455--28437523 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
28437445 AATTTCCAGA
* ** *
28437455 TTCCGGCGAAAATTCCGGCGAAGTTTGAATT
1 TTCCGGCGAAAATTCCGGCCAACATTGAAGT
*
28437486 TTTCGGCGAAAATTCCGGCCAACATTGAAGT
1 TTCCGGCGAAAATTCCGGCCAACATTGAAGT
28437517 TTCCGGC
1 TTCCGGC
28437524 AACCTGCCCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (31 bp):
TTCCGGCGAAAATTCCGGCCAACATTGAAGT
Found at i:28437612 original size:20 final size:20
Alignment explanation
Indices: 28437587--28437624 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28437577 ACTTCCGGTG
*
28437587 AAATTTCCAGATTCCGGCGA
1 AAATTTCCAGAATCCGGCGA
28437607 AAATTTCCAGAATCCGGC
1 AAATTTCCAGAATCCGGC
28437625 ACCGGTGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
AAATTTCCAGAATCCGGCGA
Found at i:28437947 original size:25 final size:25
Alignment explanation
Indices: 28437904--28437951 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28437894 CAGGTTTTTT
* * *
28437904 TTTTTTTTTTTTTTCTTTCTTTGAA
1 TTTTTTATTTATTTATTTCTTTGAA
28437929 TTTTTTATTTATTTATTTCTTTG
1 TTTTTTATTTATTTATTTCTTTG
28437952 TTTATTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.10, C:0.06, G:0.04, T:0.79
Consensus pattern (25 bp):
TTTTTTATTTATTTATTTCTTTGAA
Found at i:28437971 original size:16 final size:16
Alignment explanation
Indices: 28437930--28437973 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
28437920 TTCTTTGAAT
*
28437930 TTTTTATTTA-TTTAT
1 TTTTTATTTATTTTAA
*
28437945 TTCTTTGTTTATTTTAA
1 TT-TTTATTTATTTTAA
28437962 TTTTTATTTATT
1 TTTTTATTTATT
28437974 AGATTAGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 2 0.08
16 16 0.67
17 6 0.25
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTTTATTTATTTTAA
Found at i:28438115 original size:61 final size:59
Alignment explanation
Indices: 28438050--28438395 Score: 400
Period size: 61 Copynumber: 5.7 Consensus size: 59
28438040 AAAAATTCCA
28438050 AAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 AAAAAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTC
* *
28438111 ---AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC
1 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
* * *
28438167 AAAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTCAGAAATAAATTTC
1 --AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
*
28438228 GAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTTC
1 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAAA-TTTC
*** * **
28438293 -AAAAAAAGGGTTTTT-GAGGAAAAGTTGAAAGTATCAATTTTTCTT-GAAGATCGAAATCGC
1 AAAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAGAA-AT--AAATTTC
*
28438353 -CAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
28438396 CTAAAAAAAA
Statistics
Matches: 251, Mismatches: 18, Indels: 33
0.83 0.06 0.11
Matches are distributed among these distances:
56 4 0.02
57 45 0.18
58 7 0.03
59 44 0.18
60 39 0.16
61 59 0.24
62 2 0.01
63 1 0.00
64 46 0.18
65 4 0.02
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (59 bp):
AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
Found at i:28438401 original size:124 final size:120
Alignment explanation
Indices: 28438042--28438408 Score: 415
Period size: 124 Copynumber: 3.0 Consensus size: 120
28438032 TAAAAATAAA
* * * *
28438042 AAATTCCAAAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAT
1 AAATTTCAAAAAAAAAGAT-TTTTGA-GGAAAAGTTGAAAGTATCAATTTTTCTT-GAAATAAA-
** * *
28438107 TTTC-AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT-CCT--CAG--AAAT
62 TCGCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCCTAAAAGAAAAAT
* * *
28438160 AAATTTCAAAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTCAGAAATAAAT
1 AAATTTC--AAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCT-TGAAATAAA-
* *
28438225 TTCGAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAAT
62 -TCGCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCCTAAAAGAAAAAT
* *
28438285 AAATTTTC-AAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAGATCGAAA
1 AAA-TTTCAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAA-AT--AAA
*
28438349 TCGCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCCTAAAAAAAAAAT
62 TCG-CAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCCTAAAAGAAAAAT
28438409 CATTCTTTCC
Statistics
Matches: 215, Mismatches: 19, Indels: 24
0.83 0.07 0.09
Matches are distributed among these distances:
118 40 0.19
119 6 0.03
120 50 0.23
121 2 0.01
122 3 0.01
123 47 0.22
124 53 0.25
125 10 0.05
126 4 0.02
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (120 bp):
AAATTTCAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAATAAATCGC
AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCCTAAAAGAAAAAT
Found at i:28442223 original size:10 final size:10
Alignment explanation
Indices: 28442208--28442255 Score: 71
Period size: 10 Copynumber: 4.9 Consensus size: 10
28442198 CAATGGATGA
28442208 AAAAAAAAAG
1 AAAAAAAAAG
28442218 AAAAAAAAAG
1 AAAAAAAAAG
28442228 -AAAAAAAAG
1 AAAAAAAAAG
**
28442237 AAAAAATGAG
1 AAAAAAAAAG
28442247 AAAAAAAAA
1 AAAAAAAAA
28442256 AGAAGGAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
9 9 0.27
10 24 0.73
ACGTcount: A:0.88, C:0.00, G:0.10, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:28442233 original size:19 final size:19
Alignment explanation
Indices: 28442209--28442254 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
28442199 AATGGATGAA
28442209 AAAAAAAAGAAAAAAAAAG
1 AAAAAAAAGAAAAAAAAAG
**
28442228 AAAAAAAAGAAAAAATGAG
1 AAAAAAAAGAAAAAAAAAG
28442247 AAAAAAAA
1 AAAAAAAA
28442255 AAGAAGGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (19 bp):
AAAAAAAAGAAAAAAAAAG
Found at i:28442250 original size:25 final size:25
Alignment explanation
Indices: 28442222--28442284 Score: 92
Period size: 25 Copynumber: 2.5 Consensus size: 25
28442212 AAAAAGAAAA
28442222 AAAAAGAAAAAAAAGAAAAAATGAG
1 AAAAAGAAAAAAAAGAAAAAATGAG
*
28442247 AAAAA-AAAAAGAAGGAAAAAATGAG
1 AAAAAGAAAAA-AAAGAAAAAATGAG
*
28442272 AAAATGAAAAAAA
1 AAAAAGAAAAAAA
28442285 GAGATTCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 5 0.15
25 24 0.71
26 5 0.15
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (25 bp):
AAAAAGAAAAAAAAGAAAAAATGAG
Found at i:28442266 original size:33 final size:31
Alignment explanation
Indices: 28442206--28442284 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 31
28442196 AACAATGGAT
28442206 GAAAAAA--AAAAGAAAAAAAAAGAAAAAAAA
1 GAAAAAATGAAAA-AAAAAAAAAGAAAAAAAA
* *
28442236 GAAAAAATGAGAAAAAAAAAAGAAGGAAAAAAT
1 GAAAAAATGA-AAAAAAAAAA-AAGAAAAAAAA
*
28442269 GAGAAAATGAAAAAAA
1 GAAAAAATGAAAAAAA
28442285 GAGATTCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 7 0.17
32 14 0.33
33 21 0.50
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (31 bp):
GAAAAAATGAAAAAAAAAAAAAGAAAAAAAA
Found at i:28442274 original size:10 final size:9
Alignment explanation
Indices: 28442211--28442288 Score: 60
Period size: 8 Copynumber: 9.1 Consensus size: 9
28442201 TGGATGAAAA
28442211 AAAAAAGA-
1 AAAAAAGAG
*
28442219 AAAAAAAAG
1 AAAAAAGAG
*
28442228 AAAAAAAAG
1 AAAAAAGAG
28442237 AAAAAATGAG
1 AAAAAA-GAG
28442247 AAAAAA-A-
1 AAAAAAGAG
*
28442254 AAAGAAG-G
1 AAAAAAGAG
28442262 AAAAAATGAG
1 AAAAAA-GAG
*
28442272 -AAAATGA-
1 AAAAAAGAG
28442279 AAAAAAGAG
1 AAAAAAGAG
28442288 A
1 A
28442289 TTCAAATTGA
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
7 5 0.09
8 21 0.38
9 21 0.38
10 9 0.16
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:28443651 original size:41 final size:40
Alignment explanation
Indices: 28443515--28443773 Score: 398
Period size: 41 Copynumber: 6.4 Consensus size: 40
28443505 GTCTAGGAGT
*
28443515 ATTTACCTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
28443555 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
*
28443595 ATTTACTTTTCCAAAG-TCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
*
28443637 ATTTACTTTTCAAAG-TCGTGGTGCCTTTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
*
28443678 ATTTACTTTTCAAAG-TCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
28443719 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
28443759 ATTTACTTTTCAAAG
1 ATTTACTTTTCAAAG
28443774 CAATTTACTT
Statistics
Matches: 208, Mismatches: 7, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
40 87 0.42
41 88 0.42
42 33 0.16
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (40 bp):
ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
Found at i:28443777 original size:17 final size:17
Alignment explanation
Indices: 28443755--28443790 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
28443745 TGTTTAGAGG
28443755 AGCAATTTACTTTTCAA
1 AGCAATTTACTTTTCAA
28443772 AGCAATTTACTTTTCAA
1 AGCAATTTACTTTTCAA
28443789 AG
1 AG
28443791 TCGTGGTGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (17 bp):
AGCAATTTACTTTTCAA
Found at i:28443816 original size:58 final size:57
Alignment explanation
Indices: 28443715--28443831 Score: 209
Period size: 58 Copynumber: 2.0 Consensus size: 57
28443705 TGTTTAGAGG
28443715 AGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAA
1 AGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAA
28443772 AGCAATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAA
1 AGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAA
28443830 AG
1 AG
28443832 TTCGTTGCCT
Statistics
Matches: 58, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
56 4 0.07
57 19 0.33
58 35 0.60
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.38
Consensus pattern (57 bp):
AGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAA
Found at i:28443843 original size:98 final size:97
Alignment explanation
Indices: 28443674--28443870 Score: 367
Period size: 98 Copynumber: 2.0 Consensus size: 97
28443664 TGTTTAGAGG
28443674 AGCAATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGT
1 AGCAATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGT
*
28443739 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAA
66 TGCCTCTGTTTAGAGGAGCAATTTA-TTTCCAA
*
28443772 AGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGT
1 AGCAATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGT
28443837 TGCCTCTGTTTAGAGGAGCAATTTATTTCCAA
66 TGCCTCTGTTTAGAGGAGCAATTTATTTCCAA
28443869 AG
1 AG
28443871 TCTGTTGCCT
Statistics
Matches: 97, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
97 8 0.08
98 89 0.92
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.38
Consensus pattern (97 bp):
AGCAATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGT
TGCCTCTGTTTAGAGGAGCAATTTATTTCCAA
Found at i:28443852 original size:40 final size:40
Alignment explanation
Indices: 28443772--28444056 Score: 377
Period size: 40 Copynumber: 7.1 Consensus size: 40
28443762 TACTTTTCAA
28443772 AGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGG
1 AGCAATTTACTTTTCAAAGTCGT-GTGCCTCTGTTTAGAGG
28443813 AGCAATTTACTTTTCAAAGTTCGT-TGCCTCTGTTTAGAGG
1 AGCAATTTACTTTTCAAAG-TCGTGTGCCTCTGTTTAGAGG
*
28443853 AGCAATTTA-TTTCCAAAGTC-TGTTGCCTCTGTTTAGAGG
1 AGCAATTTACTTTTCAAAGTCGTG-TGCCTCTGTTTAGAGG
* *
28443892 AGCAATTTACTTTCCAAAGTCGTGTACCTCTGTTTAGA-G
1 AGCAATTTACTTTTCAAAGTCGTGTGCCTCTGTTTAGAGG
*
28443931 AGCAA-TTAC-TTTCCAAGTTCGT-TGCCTCTGTTTAGAGG
1 AGCAATTTACTTTTCAAAG-TCGTGTGCCTCTGTTTAGAGG
* *
28443969 AGCAATTTACTTTCCAAAGTCGTGGTACCTCTGTTTAGAGG
1 AGCAATTTACTTTTCAAAGTCGT-GTGCCTCTGTTTAGAGG
*
28444010 AGCAATTTACTTTTTCAAAAAGTCGTGGTGCCTCTGTTTAGAAG
1 AGCAATTTAC-TTTTC--AAAGTCGT-GTGCCTCTGTTTAGAGG
28444054 AGC
1 AGC
28444057 TTTGGTTAAA
Statistics
Matches: 219, Mismatches: 11, Indels: 25
0.86 0.04 0.10
Matches are distributed among these distances:
37 20 0.09
38 16 0.07
39 47 0.21
40 55 0.25
41 46 0.21
42 8 0.04
44 27 0.12
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (40 bp):
AGCAATTTACTTTTCAAAGTCGTGTGCCTCTGTTTAGAGG
Found at i:28443910 original size:79 final size:81
Alignment explanation
Indices: 28443772--28444056 Score: 406
Period size: 79 Copynumber: 3.5 Consensus size: 81
28443762 TACTTTTCAA
* *
28443772 AGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGT
1 AGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAG-TCGT
*
28443837 -TGCCTCTGTTTAGAGG
65 GTACCTCTGTTTAGAGG
*
28443853 AGCAATTTA-TTTCCAAAGTC-TGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTG
1 AGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTG
28443916 TACCTCTGTTTAGA-G
66 TACCTCTGTTTAGAGG
28443931 AGCAA-TTACTTTCC-AAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGT
1 AGCAATTTACTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGT
28443992 GGTACCTCTGTTTAGAGG
65 -GTACCTCTGTTTAGAGG
* *
28444010 AGCAATTTACTTTTTCAAAAAGTCGTGGTGCCTCTGTTTAGAAGAGC
1 AGCAATTTAC--TTTC-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
28444057 TTTGGTTAAA
Statistics
Matches: 185, Mismatches: 6, Indels: 22
0.87 0.03 0.10
Matches are distributed among these distances:
77 45 0.24
78 32 0.17
79 56 0.30
80 14 0.08
81 9 0.05
82 4 0.02
83 4 0.02
84 3 0.02
85 18 0.10
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (81 bp):
AGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTG
TACCTCTGTTTAGAGG
Found at i:28444082 original size:13 final size:13
Alignment explanation
Indices: 28444064--28444092 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
28444054 AGCTTTGGTT
28444064 AAAAAAACAAAAA
1 AAAAAAACAAAAA
28444077 AAAAAAACAAAAA
1 AAAAAAACAAAAA
28444090 AAA
1 AAA
28444093 CCAAAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:28444279 original size:9 final size:9
Alignment explanation
Indices: 28444255--28444296 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
28444245 CAATTTGTCC
*
28444255 TGTATTATTT
1 TGTATT-TTA
28444265 TGTATTTTA
1 TGTATTTTA
28444274 TGTATTTTA
1 TGTATTTTA
28444283 TGTATTTTA
1 TGTATTTTA
28444292 T-TATT
1 TGTATT
28444297 ATGTATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 4 0.13
9 21 0.68
10 6 0.19
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (9 bp):
TGTATTTTA
Found at i:28444288 original size:18 final size:19
Alignment explanation
Indices: 28444255--28444308 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
28444245 CAATTTGTCC
*
28444255 TGTATTATTTTGTATTTTA
1 TGTATTATTATGTATTTTA
28444274 TGTATT-TTATGTATTTTA
1 TGTATTATTATGTATTTTA
*
28444292 T-TATTATGTATATATTT
1 TGTATTAT-TATGTATTT
28444309 ATTTATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 4 0.13
18 13 0.42
19 14 0.45
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (19 bp):
TGTATTATTATGTATTTTA
Found at i:28444828 original size:31 final size:31
Alignment explanation
Indices: 28444793--28444861 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
28444783 AATTTTCAGA
* ** *
28444793 TTCCGGCGAAAATTCCGGCGAAGTTTGAATT
1 TTCCGGCGAAAATTCCGGCCAACATTGAAGT
* *
28444824 TTCCGACGAAAATTCTGGCCAACATTGAAGT
1 TTCCGGCGAAAATTCCGGCCAACATTGAAGT
28444855 TTCCGGC
1 TTCCGGC
28444862 AACCTGCCCA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (31 bp):
TTCCGGCGAAAATTCCGGCCAACATTGAAGT
Found at i:28445346 original size:28 final size:27
Alignment explanation
Indices: 28445285--28445360 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
28445275 GCCGCTCCAG
* *
28445285 GTTTTTTTTT-TTTTTTTTCTTTCTTT
1 GTTTTTTTTTATTTTATTTATTTCTTT
**
28445311 GAATTTTTTTATTTTATTTATTTCTTT
1 GTTTTTTTTTATTTTATTTATTTCTTT
* *
28445338 GTTTATTTTAATTTTTATTTATT
1 GTTTTTTTTTA-TTTTATTTATT
28445361 AGATTAGGTT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 8 0.20
27 21 0.52
28 11 0.28
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.79
Consensus pattern (27 bp):
GTTTTTTTTTATTTTATTTATTTCTTT
Found at i:28445652 original size:59 final size:58
Alignment explanation
Indices: 28445439--28445784 Score: 437
Period size: 59 Copynumber: 5.7 Consensus size: 58
28445429 AAATTCCAAA
*
28445439 AAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 AAAAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAA-TTTC
*
28445499 --AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC
* *
28445555 AAAAAAAAAAATATTTTTGGGGAAAAGTTGAAACTATCAATTTTCCTCAGAAATAAATTTC
1 ---AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC
* *
28445616 GAAAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
1 -AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC-T--CAG--AAATAAATTT-C
* * *
28445681 AAAAAAAATATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTC
1 -AAAAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT--AAATTTC
*
28445743 -CAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
28445785 CTACAAAAAA
Statistics
Matches: 257, Mismatches: 15, Indels: 29
0.85 0.05 0.10
Matches are distributed among these distances:
56 4 0.02
57 45 0.18
58 5 0.02
59 75 0.29
60 6 0.02
61 59 0.23
62 3 0.01
63 7 0.03
64 10 0.04
65 9 0.04
66 34 0.13
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.33
Consensus pattern (58 bp):
AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC
Found at i:28445796 original size:125 final size:123
Alignment explanation
Indices: 28445420--28445796 Score: 525
Period size: 125 Copynumber: 3.1 Consensus size: 123
28445410 TTCTTTAAAT
* *
28445420 AAAAATAAA-AAATTCCAAAAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCT
1 AAAAA-AAATAAATTTC-AAAAAAAAATATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
* *
28445484 TAGAAATAAATTTTCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT-CCT-C
64 TAGAAATAAATTTCCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCCTAC
* * * *
28445542 ---AGAAATAAATTTCAAAAAAAAAAATATTTTTGGGGAAAAGTTGAAACTATCAATTTTCCTCA
1 AAAAAAAATAAATTTCAAAAAAAAATATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTA
* * *
28445604 GAAATAAATTTCGAAAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTA-
66 GAAATAAATTTC--CAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCCTAC
*
28445663 AAAGAAAAATAAATTTCCAAAAAAAATATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT
1 AAA-AAAAATAAATTTCAAAAAAAAATATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT
*
28445728 AAAAATCAAAATTTCCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCCTAC
65 AGAAAT--AAATTTCCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCCTAC
28445789 AAAAAAAA
1 AAAAAAAA
28445797 AATCATTCTT
Statistics
Matches: 223, Mismatches: 20, Indels: 21
0.84 0.08 0.08
Matches are distributed among these distances:
118 59 0.26
119 7 0.03
120 37 0.17
121 2 0.01
125 108 0.48
126 3 0.01
127 7 0.03
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.32
Consensus pattern (123 bp):
AAAAAAAATAAATTTCAAAAAAAAATATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTA
GAAATAAATTTCCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCCTAC
Found at i:28447490 original size:14 final size:14
Alignment explanation
Indices: 28447471--28447511 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
28447461 GCTAATAGGT
28447471 TATAGTAGTTAGTA
1 TATAGTAGTTAGTA
28447485 TATAGTAGTTAGTA
1 TATAGTAGTTAGTA
28447499 TATAGTAGTTAGT
1 TATAGTAGTTAGT
28447512 GTAAGGACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TATAGTAGTTAGTA
Found at i:28450727 original size:3 final size:3
Alignment explanation
Indices: 28450719--28450744 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28450709 AAATTTATTC
28450719 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
28450745 TTTAAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:28453918 original size:27 final size:27
Alignment explanation
Indices: 28453883--28454123 Score: 104
Period size: 27 Copynumber: 8.9 Consensus size: 27
28453873 GTGGTTGTCA
*
28453883 AGGTGACTGATAATGAGGTTGATCAAG
1 AGGTGACTGATAATGAGATTGATCAAG
* * *
28453910 AGGTTACTGATAGTGAGATTGATCAGG
1 AGGTGACTGATAATGAGATTGATCAAG
* *
28453937 AGGTGATCACTTATGATGAGATTGAT---G
1 AGGTG---ACTGATAATGAGATTGATCAAG
*** * * *
28453964 TCATGACTAATGATGAGATTGATCAGG
1 AGGTGACTGATAATGAGATTGATCAAG
* * * *
28453991 AGTTGACTGATGATGA-AGTTGATTATG
1 AGGTGACTGATAATGAGA-TTGATCAAG
* * *
28454018 AGTTGACTGATGATGA-AGTTGATCAGG
1 AGGTGACTGATAATGAGA-TTGATCAAG
*
28454045 A-GTAGACTGATGATGA-ATTTGATC-AG
1 AGGT-GACTGATAATGAGA-TTGATCAAG
* * *
28454071 ATGGTGACTGATGATGAGGTTGATCAGG
1 A-GGTGACTGATAATGAGATTGATCAAG
* * *
28454099 AGTTGATTGATGATGATG-TTGATCA
1 AGGTGACTGATAATGA-GATTGATCA
28454124 GGCCATTGAT
Statistics
Matches: 174, Mismatches: 27, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
24 17 0.10
26 4 0.02
27 133 0.76
28 5 0.03
30 15 0.09
ACGTcount: A:0.30, C:0.07, G:0.31, T:0.32
Consensus pattern (27 bp):
AGGTGACTGATAATGAGATTGATCAAG
Found at i:28453942 original size:54 final size:53
Alignment explanation
Indices: 28453883--28454123 Score: 181
Period size: 54 Copynumber: 4.5 Consensus size: 53
28453873 GTGGTTGTCA
* *
28453883 AGGTGACTGATAATGAGGTTGATCAAGAGGTTACTGAT-AGTGAGATTGATCAGG
1 AGGTGACTGATGATGAAGTTGATCAAGA-GTTACTGATGA-TGAGATTGATCAGG
* *** * *
28453937 AGGTGATCACTTATGATG-AGATTGAT-GTCA-TGACTAATGATGAGATTGATCAGG
1 AGGTG---ACTGATGATGAAG-TTGATCAAGAGTTACTGATGATGAGATTGATCAGG
* * *
28453991 AGTTGACTGATGATGAAGTTGATTATGAGTTGACTGATGATGA-AGTTGATCAGG
1 AGGTGACTGATGATGAAGTTGATCAAGAGTT-ACTGATGATGAGA-TTGATCAGG
* * *
28454045 A-GTAGACTGATGATGAATTTGATC-AGATGGTGACTGATGATGAGGTTGATCAGG
1 AGGT-GACTGATGATGAAGTTGATCAAGA--GTTACTGATGATGAGATTGATCAGG
* * *
28454099 AGTTGATTGATGATGATGTTGATCA
1 AGGTGACTGATGATGAAGTTGATCA
28454124 GGCCATTGAT
Statistics
Matches: 147, Mismatches: 24, Indels: 31
0.73 0.12 0.15
Matches are distributed among these distances:
51 14 0.10
52 4 0.03
53 5 0.03
54 105 0.71
55 4 0.03
56 2 0.01
57 13 0.09
ACGTcount: A:0.30, C:0.07, G:0.31, T:0.32
Consensus pattern (53 bp):
AGGTGACTGATGATGAAGTTGATCAAGAGTTACTGATGATGAGATTGATCAGG
Found at i:28454028 original size:15 final size:16
Alignment explanation
Indices: 28453991--28454039 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
28453981 ATTGATCAGG
28453991 AGTTGACTGATGATGA
1 AGTTGACTGATGATGA
28454007 AGTTGA-T--T-ATG-
1 AGTTGACTGATGATGA
28454018 AGTTGACTGATGATGA
1 AGTTGACTGATGATGA
28454034 AGTTGA
1 AGTTGA
28454040 TCAGGAGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
11 6 0.21
12 4 0.14
13 1 0.04
14 1 0.04
15 4 0.14
16 12 0.43
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.35
Consensus pattern (16 bp):
AGTTGACTGATGATGA
Found at i:28454124 original size:27 final size:27
Alignment explanation
Indices: 28453967--28454125 Score: 205
Period size: 27 Copynumber: 5.9 Consensus size: 27
28453957 ATTGATGTCA
*
28453967 TGACTAATGATG-AGATTGATCAGGAGT
1 TGACTGATGATGAAG-TTGATCAGGAGT
* *
28453994 TGACTGATGATGAAGTTGATTATGAGT
1 TGACTGATGATGAAGTTGATCAGGAGT
28454021 TGACTGATGATGAAGTTGATCAGGAGT
1 TGACTGATGATGAAGTTGATCAGGAGT
* * *
28454048 AGACTGATGATGAATTTGATCA-GATGG
1 TGACTGATGATGAAGTTGATCAGGA-GT
*
28454075 TGACTGATGATGAGGTTGATCAGGAGT
1 TGACTGATGATGAAGTTGATCAGGAGT
* *
28454102 TGATTGATGATGATGTTGATCAGG
1 TGACTGATGATGAAGTTGATCAGG
28454126 CCATTGATGA
Statistics
Matches: 115, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
26 2 0.02
27 109 0.95
28 4 0.03
ACGTcount: A:0.30, C:0.06, G:0.32, T:0.32
Consensus pattern (27 bp):
TGACTGATGATGAAGTTGATCAGGAGT
Found at i:28457333 original size:50 final size:50
Alignment explanation
Indices: 28457274--28457374 Score: 132
Period size: 50 Copynumber: 2.0 Consensus size: 50
28457264 ATTCTATCAC
* * * *
28457274 TTAGTTTTTCTTCCAAAATAATTAATGGCTTA-TTCAAGATAATTTCAACA
1 TTAGTTTTTCCTCCAAAATAATTAACGACCTACTT-AAGATAATTTCAACA
* *
28457324 TTAGTTTTTCCTCGAAAATAATTAACGACCTACTTAAGATCATTTCAACA
1 TTAGTTTTTCCTCCAAAATAATTAACGACCTACTTAAGATAATTTCAACA
28457374 T
1 T
28457375 AACATAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
50 42 0.95
51 2 0.05
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.40
Consensus pattern (50 bp):
TTAGTTTTTCCTCCAAAATAATTAACGACCTACTTAAGATAATTTCAACA
Found at i:28466902 original size:24 final size:25
Alignment explanation
Indices: 28466853--28466918 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 25
28466843 TTAGGAGTTC
*
28466853 ACTGATGATGAGGTTTATCAGGTGGTG
1 ACTGATGATGAGGTTAATC--GTGGTG
28466880 ACTGATGATGAGGTTAATC-TGGTG
1 ACTGATGATGAGGTTAATCGTGGTG
* *
28466904 ACTGATAATAAGGTT
1 ACTGATGATGAGGTT
28466919 GATCAGGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 18 0.50
27 18 0.50
ACGTcount: A:0.27, C:0.08, G:0.32, T:0.33
Consensus pattern (25 bp):
ACTGATGATGAGGTTAATCGTGGTG
Found at i:28466937 original size:27 final size:26
Alignment explanation
Indices: 28466826--28466952 Score: 105
Period size: 27 Copynumber: 4.8 Consensus size: 26
28466816 AGGTTGATTT
* *
28466826 ACTGATAATGAGGTTGATTAGGAGTTC
1 ACTGATAATGAGGTTGATCAGGAG-TG
* * *
28466853 ACTGATGATGAGGTTTATCAGGTGGTG
1 ACTGATAATGAGGTTGATCAGG-AGTG
* * *
28466880 ACTGATGATGAGGTTAATC-TG-GTG
1 ACTGATAATGAGGTTGATCAGGAGTG
*
28466904 ACTGATAATAAGGTTGATCAGGAGCTG
1 ACTGATAATGAGGTTGATCAGGAG-TG
* **
28466931 ACTGATACTGAAATTGATCAGG
1 ACTGATAATGAGGTTGATCAGG
28466953 CAATTAATGA
Statistics
Matches: 81, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
24 19 0.23
25 1 0.01
26 2 0.02
27 58 0.72
28 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.31, T:0.31
Consensus pattern (26 bp):
ACTGATAATGAGGTTGATCAGGAGTG
Found at i:28475733 original size:23 final size:25
Alignment explanation
Indices: 28475678--28475733 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
28475668 ATAATTTATT
* * *
28475678 CTATATATTTCTATAAAAAATTATA
1 CTATATATTTATAAAAAAAAATATA
28475703 CTACTATA-TTATAAAAAAAAATA-A
1 CTA-TATATTTATAAAAAAAAATATA
28475727 CTATATA
1 CTATATA
28475734 ACTAAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 4 0.15
24 4 0.15
25 15 0.56
26 4 0.15
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.38
Consensus pattern (25 bp):
CTATATATTTATAAAAAAAAATATA
Found at i:28475944 original size:2 final size:2
Alignment explanation
Indices: 28475939--28475979 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
28475929 TTTCCTTCTA
*
28475939 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TG TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
28475980 TCACTGTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.46, G:0.02, T:0.51
Consensus pattern (2 bp):
TC
Found at i:28478973 original size:18 final size:18
Alignment explanation
Indices: 28478952--28478988 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28478942 GATCACTCAA
28478952 AAAAAAAAAAAAGAAAAG
1 AAAAAAAAAAAAGAAAAG
* *
28478970 AAAAGAAAGAAAGAAAAG
1 AAAAAAAAAAAAGAAAAG
28478988 A
1 A
28478989 GAAGGGTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAGAAAAG
Found at i:28481372 original size:138 final size:138
Alignment explanation
Indices: 28481147--28481395 Score: 349
Period size: 138 Copynumber: 1.8 Consensus size: 138
28481137 ATGAAAATAA
* * *
28481147 CCTTTCCTTTTCAATTTCTGTTTCTAATGAATCAATCTTTGCAGACATCGTCTGGGCCACTGCTT
1 CCTTTCCTTTTCAATTTCCGCTTCTAATGAATCAATCTTTGCAGACATCGTCTCGGCCACTGCTT
*
28481212 CGATGCTAATGAGTTGAGACTCAAGAAGTTGCTTTG-ATTCATTTGCATTAACTGAAACTTGCTC
66 CCATGCTAATGAGTTGAGACTCAAGAAGTTGCTTTGCA-TCATTTGCATTAACTGAAACTTGCTC
28481276 TGACAAGGT
130 TGACAAGGT
* * * * * *
28481285 CCTTTCCTTTTCGATTTCCGCTTCTAATGAGTCAATCTTTGCTGACATTGTCTCTG-CATCTGTT
1 CCTTTCCTTTTCAATTTCCGCTTCTAATGAATCAATCTTTGCAGACATCGTCTCGGCCA-CTGCT
* **
28481349 TCCATGCTACTGAGTTGAGACTCAAGATTTTGCTTTGCATCATTTGC
65 TCCATGCTAATGAGTTGAGACTCAAGAAGTTGCTTTGCATCATTTGC
28481396 CATGCAAAGC
Statistics
Matches: 96, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
137 2 0.02
138 93 0.97
139 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.39
Consensus pattern (138 bp):
CCTTTCCTTTTCAATTTCCGCTTCTAATGAATCAATCTTTGCAGACATCGTCTCGGCCACTGCTT
CCATGCTAATGAGTTGAGACTCAAGAAGTTGCTTTGCATCATTTGCATTAACTGAAACTTGCTCT
GACAAGGT
Found at i:28487755 original size:20 final size:20
Alignment explanation
Indices: 28487730--28487770 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
28487720 CATAGTATTT
*
28487730 TTTTA-TTATTTTTTAATAAA
1 TTTTATTTATTATTT-ATAAA
28487750 TTTTATTTATTATTTATAAA
1 TTTTATTTATTATTTATAAA
28487770 T
1 T
28487771 ATAATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTATTTATTATTTATAAA
Found at i:28487763 original size:24 final size:24
Alignment explanation
Indices: 28487726--28487779 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
28487716 CTCCCATAGT
* *
28487726 ATTTTTTTATTATTTTTTAATA-A
1 ATTTTTTTATTATTTATAAATATA
28487749 ATTTTATTTATTATTTATAAATATA
1 ATTTT-TTTATTATTTATAAATATA
28487774 ATTTTT
1 ATTTTT
28487780 ACAATTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 5 0.19
24 16 0.59
25 6 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
ATTTTTTTATTATTTATAAATATA
Found at i:28487777 original size:20 final size:21
Alignment explanation
Indices: 28487735--28487777 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
28487725 TATTTTTTTA
* * *
28487735 TTATTTTTTAATAAATTTTAT
1 TTATTATTTAATAAATATAAT
28487756 TTATTATTT-ATAAATATAAT
1 TTATTATTTAATAAATATAAT
28487776 TT
1 TT
28487778 TTACAATTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATTATTTAATAAATATAAT
Found at i:28489056 original size:31 final size:31
Alignment explanation
Indices: 28488992--28489058 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
28488982 ATAATATATA
** *
28488992 ATTTAAAAGTTTAATATGTAAATTATCCATT
1 ATTTAAAAGTTTAATATAAAAATTATACATT
*
28489023 ATTTAAAAGTTTAA-ATAAAAATTATATATTT
1 ATTTAAAAGTTTAATATAAAAATTATACA-TT
28489054 ATTTA
1 ATTTA
28489059 TTTAAATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 10 0.32
31 21 0.68
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (31 bp):
ATTTAAAAGTTTAATATAAAAATTATACATT
Found at i:28489895 original size:26 final size:27
Alignment explanation
Indices: 28489866--28489923 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 27
28489856 ATTTTTATTT
28489866 TTATAAAAAATTTTAAAGT-AAATAAA
1 TTATAAAAAATTTTAAAGTAAAATAAA
* ** *
28489892 TTATTAAATTTTTTAAATTAAAATAAA
1 TTATAAAAAATTTTAAAGTAAAATAAA
*
28489919 ATATA
1 TTATA
28489924 TCATATCTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (27 bp):
TTATAAAAAATTTTAAAGTAAAATAAA
Done.