Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008156.1 Hibiscus syriacus cultivar Beakdansim tig00110722_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 820393
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:323576 original size:27 final size:27
Alignment explanation
Indices: 323517--323576 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
323507 ATACACTATC
*
323517 ATATGATATTTTGATCTAACTATCGAT
1 ATATGATATTTTGATATAACTATCGAT
323544 AT-TGATATCTTTGATAT-ACTGAT-GAT
1 ATATGATAT-TTTGATATAACT-ATCGAT
323570 ATATGAT
1 ATATGAT
323577 TTTGATGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
26 14 0.48
27 15 0.52
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.45
Consensus pattern (27 bp):
ATATGATATTTTGATATAACTATCGAT
Found at i:328976 original size:25 final size:25
Alignment explanation
Indices: 328909--328976 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
328899 TTCAGTATCA
** *
328909 GTACCCTTTATCAGCGTCAGATTTG
1 GTACCCTTTCCCAGCGTTAGATTTG
328934 GTACCCTTTCCCAGCGTTAGATTTG
1 GTACCCTTTCCCAGCGTTAGATTTG
* **
328959 GTATCCTTTTGCAGCGTT
1 GTACCCTTTCCCAGCGTT
328977 GGAAAATGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.38
Consensus pattern (25 bp):
GTACCCTTTCCCAGCGTTAGATTTG
Found at i:331683 original size:36 final size:36
Alignment explanation
Indices: 331632--331786 Score: 202
Period size: 36 Copynumber: 4.3 Consensus size: 36
331622 GTGCGATATA
* * *
331632 TCCTTCCGTTTGACTTGAATCGGAAGTGTTGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCTGATGCT
* *
331668 TCCTTCCGTTCGACTTAAATCGGAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCTGATGCT
*
331704 TCCTTCCGTTTGACTTGAATCGGAAGTGCTGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCTGATGCT
* * * * *
331740 TCCTTCCGTTCAACGTGAATCGGAAGTCCCGATTCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCTGATGCT
*
331776 TCTTTCCGTTC
1 TCCTTCCGTTC
331787 TTCTTATTCA
Statistics
Matches: 104, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 104 1.00
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (36 bp):
TCCTTCCGTTCGACTTGAATCGGAAGTGCTGATGCT
Found at i:331714 original size:72 final size:72
Alignment explanation
Indices: 331632--331785 Score: 236
Period size: 72 Copynumber: 2.1 Consensus size: 72
331622 GTGCGATATA
* * * *
331632 TCCTTCCGTTTGACTTGAATCGGAAGTGTTGATGCCTCCTTCCGTTCGACTTAAATCGGAAGTGC
1 TCCTTCCGTTTGACTTGAATCGGAAGTGCTGATGCCTCCTTCCGTTCAACGTAAATCGGAAGTCC
331697 CGATGCT
66 CGATGCT
* *
331704 TCCTTCCGTTTGACTTGAATCGGAAGTGCTGATGCTTCCTTCCGTTCAACGTGAATCGGAAGTCC
1 TCCTTCCGTTTGACTTGAATCGGAAGTGCTGATGCCTCCTTCCGTTCAACGTAAATCGGAAGTCC
*
331769 CGATTCT
66 CGATGCT
*
331776 TCTTTCCGTT
1 TCCTTCCGTT
331786 CTTCTTATTC
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (72 bp):
TCCTTCCGTTTGACTTGAATCGGAAGTGCTGATGCCTCCTTCCGTTCAACGTAAATCGGAAGTCC
CGATGCT
Found at i:338496 original size:15 final size:14
Alignment explanation
Indices: 338453--338497 Score: 72
Period size: 14 Copynumber: 3.1 Consensus size: 14
338443 CAAACAATGT
*
338453 AAAATATTTTCTAA
1 AAAATATTTTCTGA
338467 AAAATATTTTCTGA
1 AAAATATTTTCTGA
338481 AAAATATTTTCATGA
1 AAAATATTTTC-TGA
338496 AA
1 AA
338498 TGTAATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 24 0.83
15 5 0.17
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (14 bp):
AAAATATTTTCTGA
Found at i:348644 original size:20 final size:20
Alignment explanation
Indices: 348616--348669 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
348606 TTACACTTAA
348616 GGAACCGATTCCCCATTAGG
1 GGAACCGATTCCCCATTAGG
*
348636 GGAATCGATTCCCCATTAGG
1 GGAACCGATTCCCCATTAGG
*
348656 GGTACCGATTCCCC
1 GGAACCGATTCCCC
348670 CCACGCTCCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.22
Consensus pattern (20 bp):
GGAACCGATTCCCCATTAGG
Found at i:351834 original size:132 final size:132
Alignment explanation
Indices: 351606--352106 Score: 530
Period size: 132 Copynumber: 3.8 Consensus size: 132
351596 TGCTCTTCAG
* * *
351606 GGAAGATCAAATCTGAAAACTTTGAATT-ATTTCACTACTCTTTTAAGGAAGATTGAATCGGGAT
1 GGAAGATCAGACCTGAAAACTTTG-ATTCACTTCACTACTC-TTTAAGGAAGATTGAATCGGGAT
* * * *
351670 GGATCTGCTTT-ACTGCTCTTCAGGGAAGATCAAATCTAGAAAAAAAG-GATATGCTTTGATACT
64 GGATCTG-TTTCACTGCTCTTCAGGGAAAATCAAATC-AGAAAGAAAGTGATCTGCTTTGCTACT
* *
351733 CTTTAG
127 CCTTAA
* * * *
351739 GGAAGATCAGACCTAAAAACTTTGACTCACTTCACTACTCTTTAGGGAAGATTGACTCGGGATGG
1 GGAAGATCAGACCTGAAAACTTTGATTCACTTCACTACTCTTTAAGGAAGATTGAATCGGGATGG
351804 ATCTGTTTCACTGCTCTTCAGGGAAAATCAAATCCAG-AAGAAAGTGATCTG-TTTCGCTACTCC
66 ATCTGTTTCACTGCTCTTCAGGGAAAATCAAAT-CAGAAAGAAAGTGATCTGCTTT-GCTACTCC
351867 TTAA
129 TTAA
* * * * **
351871 GGAAGATTAGACCTGAAAACTTTGATTAACTTCACTACTCTTTAAGGAAGATTAAATCAGGATTA
1 GGAAGATCAGACCTGAAAACTTTGATTCACTTCACTACTCTTTAAGGAAGATTGAATCGGGATGG
* * * * * *
351936 AT-TCGTTTCACTGCTCTTTAGGAAAAATAAAATCCGAAAGAAAGTGATCTACTTAGCTACTCCT
66 ATCT-GTTTCACTGCTCTTCAGGGAAAATCAAATCAGAAAGAAAGTGATCTGCTTTGCTACTCCT
352000 TAA
130 TAA
* * * * * * * ** *
352003 GGAAGATCAGACCTGGAAACTTTGATTCACTTCATTACTATTGAAGAAATAATGAATTAGGATTG
1 GGAAGATCAGACCTGAAAACTTTGATTCACTTCACTACTCTTTAAGGAAGATTGAATCGGGATGG
* * * *
352068 AT-TCGCTTCACTACTCTTCAGGGAAGATCAAATCGGAAA
66 ATCT-GTTTCACTGCTCTTCAGGGAAAATCAAATCAGAAA
352107 ATTCAACTAT
Statistics
Matches: 312, Mismatches: 48, Indels: 17
0.83 0.13 0.05
Matches are distributed among these distances:
131 15 0.05
132 262 0.84
133 35 0.11
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (132 bp):
GGAAGATCAGACCTGAAAACTTTGATTCACTTCACTACTCTTTAAGGAAGATTGAATCGGGATGG
ATCTGTTTCACTGCTCTTCAGGGAAAATCAAATCAGAAAGAAAGTGATCTGCTTTGCTACTCCTT
AA
Found at i:351873 original size:219 final size:218
Alignment explanation
Indices: 351372--351878 Score: 555
Period size: 219 Copynumber: 2.3 Consensus size: 218
351362 GTTGGTTCGC
* * * * *
351372 TTCACTGATCTTCAAGGAAGATCAAATCCGGAAAAAAGTGATCTACTTCACTACTCCTT-AGATA
1 TTCACTGCTCTTCAGGGAAGATCAAATCCAG-AAAAAGTGATCTATTTCACTACTCCTTAAG-GA
* * * *
351436 AGATAGAATCGGGATCGATTTGCTTCACTGCTCTTCAGGAAAGATCAAATCTTAAAGAAAATGAT
64 AGATTGAATCGGGATCGATCTGCTTCACTGCTCTTCAGGAAAGATCAAATCTTAAAAAAAAGGAT
*** *
351501 CAGCTTCACTACTTCTTAGGGAAGATCAGACCTGGGAACTTTGATTCACTTAACTACTCTCTAGA
129 CAGCTTCACTACTTCTTAGGGAAGATCAGACCTAAAAACTTTGACTCACTTAACTACTCTCTAGA
* *
351566 GAATATTGAATATGGGTAGATATTA
194 GAAGATTGAATACGGGTAGATATTA
* ** *
351591 TTCACTGCTCTTCAGGGAAGATCAAAT-CTGAAAACTTTGAAT-TATTTCACTACTCTTTTAAGG
1 TTCACTGCTCTTCAGGGAAGATCAAATCCAGAAAA-AGTG-ATCTATTTCACTACTC-CTTAAGG
* * *
351654 AAGATTGAATCGGGATGGATCTGCTTTACTGCTCTTCAGGGAAGATCAAATC-TAGAAAAAAAGG
63 AAGATTGAATCGGGATCGATCTGCTTCACTGCTCTTCAGGAAAGATCAAATCTTA-AAAAAAAGG
* *
351718 AT-ATGCTTTGA-TAC-TCTTTAGGGAAGATCAGACCTAAAAACTTTGACTCACTTCACTACTCT
127 ATCA-GC-TTCACTACTTC-TTAGGGAAGATCAGACCTAAAAACTTTGACTCACTTAACTACTCT
* * * * *
351780 TTAGGGAAGATTGACT-CGGGATGGATCTGT-
189 CTAGAGAAGATTGAATACGGG-TAGATAT-TA
* * *
351810 TTCACTGCTCTTCAGGGAAAATCAAATCCAGAAGAAAGTGATCTGTTTCGCTACTCCTTAAGGAA
1 TTCACTGCTCTTCAGGGAAGATCAAATCCAGAA-AAAGTGATCTATTTCACTACTCCTTAAGGAA
351875 GATT
65 GATT
351879 AGACCTGAAA
Statistics
Matches: 240, Mismatches: 35, Indels: 26
0.80 0.12 0.09
Matches are distributed among these distances:
217 4 0.02
218 24 0.10
219 187 0.78
220 23 0.10
221 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (218 bp):
TTCACTGCTCTTCAGGGAAGATCAAATCCAGAAAAAGTGATCTATTTCACTACTCCTTAAGGAAG
ATTGAATCGGGATCGATCTGCTTCACTGCTCTTCAGGAAAGATCAAATCTTAAAAAAAAGGATCA
GCTTCACTACTTCTTAGGGAAGATCAGACCTAAAAACTTTGACTCACTTAACTACTCTCTAGAGA
AGATTGAATACGGGTAGATATTA
Found at i:363211 original size:17 final size:17
Alignment explanation
Indices: 363189--363233 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
363179 CCATAGCAAA
363189 AGGAGTCAAAATTGCTT
1 AGGAGTCAAAATTGCTT
363206 AGGAGTCAAAATTGCTT
1 AGGAGTCAAAATTGCTT
*
363223 AGAAGTCAAAA
1 AGGAGTCAAAA
363234 GTTAACAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.24
Consensus pattern (17 bp):
AGGAGTCAAAATTGCTT
Found at i:369044 original size:27 final size:29
Alignment explanation
Indices: 368986--369044 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
368976 GCTCCTAAGG
*
368986 TGGTCAAAATAAATACCTAAAGTTATCTTTT
1 TGGTCAAAATAAATACATAAAGTTA--TTTT
*
369017 TGGTCAAAATAGATACATAAAG-TATTTT
1 TGGTCAAAATAAATACATAAAGTTATTTT
369045 ATGTCGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 4 0.15
30 2 0.08
31 20 0.77
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (29 bp):
TGGTCAAAATAAATACATAAAGTTATTTT
Found at i:370147 original size:60 final size:60
Alignment explanation
Indices: 370031--370157 Score: 134
Period size: 60 Copynumber: 2.1 Consensus size: 60
370021 GAACATATGA
* * ** * *
370031 ATAGTCAGATGACCATTTTGTAACTTTTAATAGTATGTGGATTCAAAAGAGTAACACCGT
1 ATAGTCAGAGGACCATTTTATAACTTTTAATAGTATGAAGATTCAAAAGAGCAACACCAT
*
370091 ATAGTCAGAGGATCATTTTATAACTTTTAATAGT-TGAAAGACTT-AACAA-AGCAACACCAT
1 ATAGTCAGAGGACCATTTTATAACTTTTAATAGTATG-AAGA-TTCAA-AAGAGCAACACCAT
*
370151 GTAGTCA
1 ATAGTCA
370158 AATGACGATT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
59 2 0.04
60 50 0.89
61 4 0.07
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (60 bp):
ATAGTCAGAGGACCATTTTATAACTTTTAATAGTATGAAGATTCAAAAGAGCAACACCAT
Found at i:372455 original size:18 final size:17
Alignment explanation
Indices: 372434--372470 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
372424 TTTCATCCAT
*
372434 ATTATTATTTTTATCTAA
1 ATTATTATTATTAT-TAA
372452 ATTATTATTATTATTAA
1 ATTATTATTATTATTAA
372469 AT
1 AT
372471 AATAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTATTATTATTATTAA
Found at i:373935 original size:28 final size:29
Alignment explanation
Indices: 373859--373935 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 29
373849 CCTTGATCTT
373859 TTATTAGT-TTTATAATTTAATCCCTAAAA
1 TTATTA-TATTTATAATTTAATCCCTAAAA
* *
373888 TTATTATATTTATTATTTTAA-CCCT-TAA
1 TTATTATATTTA-TAATTTAATCCCTAAAA
373916 TGTA-TATATTTATAAATTTA
1 T-TATTATATTTAT-AATTTA
373936 TTACTAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
27 1 0.02
28 17 0.41
29 16 0.39
30 7 0.17
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (29 bp):
TTATTATATTTATAATTTAATCCCTAAAA
Found at i:374058 original size:21 final size:20
Alignment explanation
Indices: 374033--374074 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
374023 TACTCGAATA
374033 AAATAATATTT-TTTATGTTTT
1 AAATAA-ATTTATTTAT-TTTT
374054 AAATAAATTTATTTATTTTT
1 AAATAAATTTATTTATTTTT
374074 A
1 A
374075 TCTATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
AAATAAATTTATTTATTTTT
Found at i:376730 original size:22 final size:22
Alignment explanation
Indices: 376666--376738 Score: 87
Period size: 21 Copynumber: 3.3 Consensus size: 22
376656 GGATTCTATG
*
376666 CATTCGAGACAGTTCTATGTGGT
1 CATTCGGGACA-TTCTATGTGGT
* *
376689 CCTTCGGGACA-TATATGTGGT
1 CATTCGGGACATTCTATGTGGT
376710 CATTCGGGACATTCTATGTGG-
1 CATTCGGGACATTCTATGTGGT
376731 CACTTCGG
1 CA-TTCGG
376739 TGCATTTCTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
21 21 0.49
22 13 0.30
23 9 0.21
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (22 bp):
CATTCGGGACATTCTATGTGGT
Found at i:376755 original size:23 final size:23
Alignment explanation
Indices: 376721--376768 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
376711 ATTCGGGACA
376721 TTCTATGTGGCACTTCGGTGCAT
1 TTCTATGTGGCACTTCGGTGCAT
*
376744 TTCTAT-TCGGCACTTCGGTGTAT
1 TTCTATGT-GGCACTTCGGTGCAT
376767 TT
1 TT
376769 TATACGAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (23 bp):
TTCTATGTGGCACTTCGGTGCAT
Found at i:376987 original size:23 final size:23
Alignment explanation
Indices: 376961--377005 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
376951 AGGTAAGTTC
*
376961 TGAAAGTATGTAATTGCATGTTA
1 TGAAAGTATGTAACTGCATGTTA
* *
376984 TGAAATTATTTAACTGCATGTT
1 TGAAAGTATGTAACTGCATGTT
377006 TCATTCGTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (23 bp):
TGAAAGTATGTAACTGCATGTTA
Found at i:388888 original size:55 final size:55
Alignment explanation
Indices: 388724--389387 Score: 838
Period size: 56 Copynumber: 12.0 Consensus size: 55
388714 AAGAGGGATG
* *
388724 TTCAAAGATTTCTCGAGTTTTATCTCCCCT-AAAGAATAGTGGAGCAGACCCGTCT
1 TTCAAAGATTTCTCGAGTCTTATCT-CCCTGAAAGAAGAGTGGAGCAGACCCGTCT
** * *
388779 ACCAAAAATTTCTCGAGTCTTATCTCCCT-AAAGAAGAATGGAGCAGACCCGTCT
1 TTCAAAGATTTCTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCT
* * * * * *
388833 TTCAAATATTTCTCGACTCTTATCTCTCCT-AAAGAAAAGTGGAGCAAATCAGTCT
1 TTCAAAGATTTCTCGAGTCTTATCTC-CCTGAAAGAAGAGTGGAGCAGACCCGTCT
* * * *
388888 TTCAAAAATTTCTCGAGTCTTATCTTTCCT-AAAGAAGAGTGGAGCTGACCCATCT
1 TTCAAAGATTTCTCGAGTCTTATC-TCCCTGAAAGAAGAGTGGAGCAGACCCGTCT
* * *
388943 TTCAAAGATTTCTTGAGTCTTATCTCCCCTGAAAGAAGAGTGGAGTAGACCCTTCT
1 TTCAAAGATTTCTCGAGTCTTATCT-CCCTGAAAGAAGAGTGGAGCAGACCCGTCT
* * * *
388999 TCCAAAGATTTCTTGAGTCTTATCTCCCTTGGAAGAAGAGTGGAGCAGACCCATC-
1 TTCAAAGATTTCTCGAGTCTTATCTCCC-TGAAAGAAGAGTGGAGCAGACCCGTCT
* *
389054 TTCTAAAGATTTCTTGAGTCTTATCTCCCTTGAAAGAAGAGTGGAGCAGACCCGACT
1 TTC-AAAGATTTCTCGAGTCTTATCTCCC-TGAAAGAAGAGTGGAGCAGACCCGTCT
* * *
389111 TTCAAAGATTTCTTGAGTCTTATCTGCCTGAAAGAAGAGTAGAGCAGACCCGTCT
1 TTCAAAGATTTCTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCT
* * **
389166 CTT-AAAGATTTCTTGAGTCTTATCTCCTATGAAAGAAGAGTGGAGCAGACATGTCT
1 -TTCAAAGATTTCTCGAGTCTTATCTCC-CTGAAAGAAGAGTGGAGCAGACCCGTCT
* *
389222 TTGAAAGATTTCTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCATACCCGTCT
1 TTCAAAGATTTCTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCT
*
389277 TCCAAAGATTTCTCGAGTCTTATCTCCCCTGAAAGAAGAGTGGAGCAGACCCGTCT
1 TTCAAAGATTTCTCGAGTCTTATCT-CCCTGAAAGAAGAGTGGAGCAGACCCGTCT
* * * *
389333 TCCAAAAATTTCTCGAGTCTTATC-CCCTGAAAGAAGAGTGGAGCATACCCATCT
1 TTCAAAGATTTCTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCT
389387 T
1 T
389388 CCTAAATTTA
Statistics
Matches: 541, Mismatches: 57, Indels: 23
0.87 0.09 0.04
Matches are distributed among these distances:
54 79 0.15
55 215 0.40
56 244 0.45
57 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (55 bp):
TTCAAAGATTTCTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCT
Found at i:389199 original size:111 final size:110
Alignment explanation
Indices: 388727--389387 Score: 846
Period size: 111 Copynumber: 6.0 Consensus size: 110
388717 AGGGATGTTC
* * *
388727 AAAGATTTCTCGAGTTTTATCTCCCCT-AAAGAATAGTGGAGCAGACCCGTCTACCAAAAATTTC
1 AAAGATTTCTCGAGTCTTATCTCCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAAATTTC
*
388791 TCGAGTCTTATCTCCCT-AAAGAAGAATGGAGCAGACCCGTCTTT
66 TCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTT
* * * * * * * *
388835 CAAATATTTCTCGACTCTTATCTCTCCT-AAAGAAAAGTGGAGCAAATCAGTCTTTCAAAAATTT
1 -AAAGATTTCTCGAGTCTTATCTCCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAAATTT
* * *
388899 CTCGAGTCTTATCTTTCCT-AAAGAAGAGTGGAGCTGACCCATCTTT
65 CTCGAGTCTTATC-TCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTT
* * * *
388945 CAAAGATTTCTTGAGTCTTATCTCCCCTGAAAGAAGAGTGGAGTAGACCCTTCTTCCAAAGATTT
1 -AAAGATTTCTCGAGTCTTATCTCCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAAATTT
* * *
389010 CTTGAGTCTTATCTCCCTTGGAAGAAGAGTGGAGCAGACCCATCTTCT
65 CTCGAGTCTTATCTCCC-TGAAAGAAGAGTGGAGCAGACCCGTCTT-T
* * * * *
389058 AAAGATTTCTTGAGTCTTATCTCCCTTGAAAGAAGAGTGGAGCAGACCCGACTTTCAAAGATTTC
1 AAAGATTTCTCGAGTCTTATCTCCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAAATTTC
* * *
389123 TTGAGTCTTATCTGCCTGAAAGAAGAGTAGAGCAGACCCGTCTCTT
66 TCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCT-TT
* ** ** ** *
389169 AAAGATTTCTTGAGTCTTATCTCCTATGAAAGAAGAGTGGAGCAGACATGTCTTTGAAAGATTTC
1 AAAGATTTCTCGAGTCTTATCTCCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAAATTTC
* *
389234 TCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCATACCCGTCTTCC
66 TCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTT-T
389280 AAAGATTTCTCGAGTCTTATCTCCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAAATTTC
1 AAAGATTTCTCGAGTCTTATCTCCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAAATTTC
* *
389345 TCGAGTCTTATC-CCCTGAAAGAAGAGTGGAGCATACCCATCTT
66 TCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTT
389388 CCTAAATTTA
Statistics
Matches: 486, Mismatches: 59, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
109 66 0.14
110 86 0.18
111 233 0.48
112 100 0.21
113 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (110 bp):
AAAGATTTCTCGAGTCTTATCTCCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAAATTTC
TCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTT
Found at i:389590 original size:3 final size:3
Alignment explanation
Indices: 389582--389652 Score: 70
Period size: 3 Copynumber: 22.7 Consensus size: 3
389572 TTTTCATCCA
* * * * *
389582 TAT TAT TAT TAT TAT CTAAGT TAT TAT TAT TAT GAT GAT GAT GAT GAT
1 TAT TAT TAT TAT TAT -T-A-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
389630 TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
389653 AATAATAAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
3 58 0.92
4 2 0.03
5 2 0.03
6 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.08, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:391064 original size:28 final size:29
Alignment explanation
Indices: 390988--391064 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 29
390978 CATTGATATT
390988 TTATTAGT-TTTATAATTTAATCCCTAAAA
1 TTATTA-TATTTATAATTTAATCCCTAAAA
* *
391017 TTATTATATTTATTATTTTAAT-CCT-TAA
1 TTATTATATTTA-TAATTTAATCCCTAAAA
391045 TGTA-TATATTTATAAATTTA
1 T-TATTATATTTAT-AATTTA
391065 TTACTAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
27 1 0.02
28 17 0.41
29 15 0.37
30 8 0.20
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (29 bp):
TTATTATATTTATAATTTAATCCCTAAAA
Found at i:391215 original size:23 final size:23
Alignment explanation
Indices: 391189--391232 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
391179 TTTACGTAAA
* * *
391189 TTTATTTATTTTTTTTATCTATT
1 TTTATATATTTATTGTATCTATT
391212 TTTATATATTTATTGTATCTA
1 TTTATATATTTATTGTATCTA
391233 AAATTCAAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (23 bp):
TTTATATATTTATTGTATCTATT
Found at i:391543 original size:17 final size:16
Alignment explanation
Indices: 391513--391554 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
391503 AAATGCAAAT
391513 AAATT-TTTTATCTTTTA
1 AAATTATTTTATC--TTA
391530 AAATTATTTT-TCTTA
1 AAATTATTTTATCTTA
391545 AAATTATTTT
1 AAATTATTTT
391555 GAAAGATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 13 0.54
17 7 0.29
18 4 0.17
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (16 bp):
AAATTATTTTATCTTA
Found at i:393324 original size:33 final size:34
Alignment explanation
Indices: 393271--393398 Score: 143
Period size: 34 Copynumber: 3.8 Consensus size: 34
393261 GAACCGACCT
* *
393271 CAAGCCCCCAGACCCAAAAAACCCAATCATAAAA
1 CAAGCCCCCATACCCAAAAAACCCAATCAGAAAA
* *
393305 CAAGCCCCCATATCCAAAAAAACCAATCAGAAAA
1 CAAGCCCCCATACCCAAAAAACCCAATCAGAAAA
* *
393339 -AAGCCCCCATGCCCCAAAAACCCAATCAGAAAA
1 CAAGCCCCCATACCCAAAAAACCCAATCAGAAAA
* * *
393372 TAAGACCCCA-ACTCAAATAAAACCCAA
1 CAAGCCCCCATAC-CCAA-AAAACCCAA
393399 ACCAAAGCCC
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
33 30 0.38
34 40 0.51
35 9 0.11
ACGTcount: A:0.50, C:0.36, G:0.06, T:0.08
Consensus pattern (34 bp):
CAAGCCCCCATACCCAAAAAACCCAATCAGAAAA
Found at i:400679 original size:55 final size:54
Alignment explanation
Indices: 400603--400876 Score: 261
Period size: 55 Copynumber: 5.0 Consensus size: 54
400593 TCCTTGATAG
* *
400603 GATGTTTTCAAATGAACTTTTAAATGAAGCTAAGCATAATTTTTAGGGGTTTCTT
1 GATGTTTTCAAATGAATTTTTAAA-GAAGCTAAGCCTAATTTTTAGGGGTTTCTT
* * * * *
400658 GATGTTTTCAAATGAGTTTTT--AGAAACAAAGCCTGATTTTCAGGGGTTTCTT
1 GATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTT
* *
400710 GATGATGATTTCTAATGAATTTTTAAAAGAATCTAAGCCTAATTTTTAGGGGTTTCTT
1 GATG-T--TTTCAAATGAATTTTT-AAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTT
* * * * * * *
400768 GATGTTTTCAATTGAGTTTTTAAA-AA-CAAATCTTAATTTTCAGGGGTTTCCT
1 GATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTT
* * *
400820 GACGATTATTTCCAAA-GAATTTTTAAAGAAGTTTAGCCTAATTTTTAGGGGTTTCTT
1 GATG--T-TTT-CAAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTT
400877 AATAATAACT
Statistics
Matches: 176, Mismatches: 31, Indels: 22
0.77 0.14 0.10
Matches are distributed among these distances:
52 53 0.30
53 4 0.02
54 4 0.02
55 59 0.34
56 5 0.03
57 20 0.11
58 31 0.18
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (54 bp):
GATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTT
Found at i:400713 original size:52 final size:52
Alignment explanation
Indices: 400634--400817 Score: 206
Period size: 52 Copynumber: 3.4 Consensus size: 52
400624 AAATGAAGCT
* *
400634 AAGCATAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAGTTTTTAGAAACA
1 AAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAGTTTTTAGAAACA
* * * * *
400686 AAGCCTGATTTTCAGGGGTTTCTTGATGATGATTTCTAATGAATTTTTAAAAGAATCT
1 AAGCCTAATTTTCAGGGGTTTCTTGATG-T--TTTCAAATGAGTTTTT---AGAAACA
* * *
400744 AAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAATTGAGTTTTTAAAAACA
1 AAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAGTTTTTAGAAACA
* *
400796 AATCTTAATTTTCAGGGGTTTC
1 AAGCCTAATTTTCAGGGGTTTC
400818 CTGACGATTA
Statistics
Matches: 108, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
52 48 0.44
53 1 0.01
55 27 0.25
57 1 0.01
58 31 0.29
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.43
Consensus pattern (52 bp):
AAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAGTTTTTAGAAACA
Found at i:400747 original size:110 final size:110
Alignment explanation
Indices: 400603--400876 Score: 374
Period size: 110 Copynumber: 2.5 Consensus size: 110
400593 TCCTTGATAG
* * * * *
400603 GATGTTTTCAAATGAACTTTTAAATGAAGCTAAGCATAATTTTTAGGGGTTTCTTGATGTTTTCA
1 GATGATTTCAAATGAATTTTTAAAAGAATCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCA
* * * *
400668 AATGAGTTTTTAGAAACAAAGCCTGATTTTCAGGGGTTTCTTGAT
66 AATGAGTTTTTAAAAACAAAGCCTAATTTTCAGGGGTTTCCTGAC
*
400713 GATGATTTCTAATGAATTTTTAAAAGAATCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCA
1 GATGATTTCAAATGAATTTTTAAAAGAATCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCA
* * *
400778 ATTGAGTTTTTAAAAACAAATCTTAATTTTCAGGGGTTTCCTGAC
66 AATGAGTTTTTAAAAACAAAGCCTAATTTTCAGGGGTTTCCTGAC
* *
400823 GATTATTTCCAAA-GAATTTTT-AAAGAAGT-TTAGCCTAATTTTTAGGGGTTTCTT
1 GATGATTT-CAAATGAATTTTTAAAAGAA-TCTAAGCCTAATTTTTAGGGGTTTCTT
400877 AATAATAACT
Statistics
Matches: 146, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
109 30 0.21
110 113 0.77
111 3 0.02
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (110 bp):
GATGATTTCAAATGAATTTTTAAAAGAATCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCA
AATGAGTTTTTAAAAACAAAGCCTAATTTTCAGGGGTTTCCTGAC
Found at i:401161 original size:59 final size:59
Alignment explanation
Indices: 401069--401224 Score: 258
Period size: 59 Copynumber: 2.6 Consensus size: 59
401059 TGATGTTTTC
*
401069 AACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACACCCCATCAAAGGGGTT
1 AACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACACCCCACCAAAGGGGTT
* *
401128 AACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTT
1 AACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACACCCCACCAAAGGGGTT
* *
401187 AACATTTCTTATTGCTTGATTCACAACACTTCGAATCA
1 AACATTTCCT-TTGCTCGATTCACAACACTTCGAATCA
401225 ACAAAAGTCC
Statistics
Matches: 91, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
59 65 0.71
60 26 0.29
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.28
Consensus pattern (59 bp):
AACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACACCCCACCAAAGGGGTT
Found at i:401333 original size:41 final size:41
Alignment explanation
Indices: 401239--401333 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
401229 AAGTCCTTTA
* * *
401239 GGCCAT-CAGTAAGTCTTTCGAGCATAATGCTTAAATCTTTG
1 GGCCATCCA-TAAGTCTTTCGAGCAAAATGCATAAATCTTCG
* * *
401280 GGTCATCTATAAGTCTTTCGAGCAAAATG-ATAAGTGCTTCG
1 GGCCATCCATAAGTCTTTCGAGCAAAATGCATAAAT-CTTCG
401321 GGCCATCCATAAG
1 GGCCATCCATAAG
401334 ACCTTCAGGT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
40 4 0.09
41 39 0.89
42 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (41 bp):
GGCCATCCATAAGTCTTTCGAGCAAAATGCATAAATCTTCG
Found at i:401869 original size:226 final size:225
Alignment explanation
Indices: 401129--401873 Score: 885
Period size: 226 Copynumber: 3.3 Consensus size: 225
401119 AAAGGGGTTA
* *
401129 ACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTT
1 ACATTTCCTTTACTCGATTCACAACACTTCGAATAAGCAACGCCCCACCAGAGGGGTTAACATTT
* * * *
401194 CTTATTGCTTGATTCACAACACTTCGAATCAACAAAAGTCCTTT-AGGCCATCAGTAAGTCTTTC
66 CCTATTGCTAGATTCACAACACTTCGAATCAGCTAAAGT--TTTCAGGCCATCAGTAAGTCTTTC
* *
401258 GAGCATAATGCTTAAAT-CTTTGGGTCATCTATAAGTCTTTCGAGCAAAATGATAAGTGC-TTCG
129 GAGCATGATGCTTAAATCCTTTGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGT-CATTC-
* * *
401321 GGCCATCCATAAGACCTTCAGGTAGGAGGTTTTC
192 GGCCATCCATAAGACCTTTAGGCAGGATGTTTTC
* * ** *
401355 AACATTTCCTTTACTCGATTGACAACACTTCGAATCAA-CAATGCTTCACCAGAGAGGTTAACAT
1 -ACATTTCCTTTACTCGATTCACAACACTTCGAAT-AAGCAACGCCCCACCAGAGGGGTTAACAT
* * * * ** * *
401419 TTCTTATTGCTCGATTAATAACACTTATAATCAGCTGAAGTCTTTCGGGCCATCAGTAAGTCTTT
64 TTCCTATTGCTAGATTCACAACACTTCGAATCAGCTAAAGT-TTTCAGGCCATCAGTAAGTCTTT
* * * *
401484 CGAGCACGATGCTTAAATCCTTCGGGTTATCTAT--GTCTTTCGAGTAAGATGATAAGTCATTCG
128 CGAGCATGATGCTTAAATCCTTTGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCATTCG
** * *
401547 GACCATTTATAAGACCTTTGGGCAAGATGTTTTC
193 G-CCATCCATAAGACCTTTAGGCAGGATGTTTTC
** * * * *
401581 ACATTTCCTTCGCTCGATTCACAAGACTTCGAATCAGTAATGCCCCACCAGAGGGGTTAACATTT
1 ACATTTCCTTTACTCGATTCACAACACTTCGAATAAGCAACGCCCCACCAGAGGGGTTAACATTT
* * **
401646 CCTATTGCTAGATTCACAACACTTCGAATCAGCTTAAGTTATTCAAGTTATCAGTAAGTCTTTCG
66 CCTATTGCTAGATTCACAACACTTCGAATCAGCTAAAGTT-TTCAGGCCATCAGTAAGTCTTTCG
*
401711 AG-ATGATACTTAAATCCTTTGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCATTCAGG
130 AGCATGATGCTTAAATCCTTTGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCATTC-GG
401775 CCATCCATAAGACCTTTAGGCAGGATGTTTTC
194 CCATCCATAAGACCTTTAGGCAGGATGTTTTC
*** * ** *
401807 ACATTTCCTTTACTATTTTCACAACACTTCAAATAAGCAACGCATCACTC-GAGGGATTAACATT
1 ACATTTCCTTTACTCGATTCACAACACTTCGAATAAGCAACGCCCCAC-CAGAGGGGTTAACATT
401871 TCC
65 TCC
401874 AGAGGAAAAA
Statistics
Matches: 436, Mismatches: 71, Indels: 23
0.82 0.13 0.04
Matches are distributed among these distances:
224 27 0.06
225 111 0.25
226 160 0.37
227 124 0.28
228 14 0.03
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.32
Consensus pattern (225 bp):
ACATTTCCTTTACTCGATTCACAACACTTCGAATAAGCAACGCCCCACCAGAGGGGTTAACATTT
CCTATTGCTAGATTCACAACACTTCGAATCAGCTAAAGTTTTCAGGCCATCAGTAAGTCTTTCGA
GCATGATGCTTAAATCCTTTGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCATTCGGCC
ATCCATAAGACCTTTAGGCAGGATGTTTTC
Found at i:402285 original size:22 final size:23
Alignment explanation
Indices: 402250--402299 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
402240 AATAAAACCA
*
402250 AAACCCAACCCAGA-CCTGAGTC
1 AAACCCAACCCAGATCCTAAGTC
* *
402272 AAACCCGACTCAGATCCTAAGTC
1 AAACCCAACCCAGATCCTAAGTC
*
402295 TAACC
1 AAACC
402300 TAAACCTACT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.36, C:0.38, G:0.12, T:0.14
Consensus pattern (23 bp):
AAACCCAACCCAGATCCTAAGTC
Found at i:403574 original size:7 final size:6
Alignment explanation
Indices: 403523--403580 Score: 57
Period size: 6 Copynumber: 9.5 Consensus size: 6
403513 TGTATTTGTG
* *
403523 TTTA-T TTTATT TTTATT TTTATA CTTATT TTTA-T TTTACTTT TTTATCT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTA--TT TTTAT-T
403572 TTTATT TTT
1 TTTATT TTT
403581 TTTAAATTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
5 9 0.20
6 24 0.55
7 6 0.14
8 5 0.11
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:403574 original size:15 final size:15
Alignment explanation
Indices: 403532--403581 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
403522 GTTTATTTTA
*
403532 TTTTTATTTTTATACT
1 TTTTTATATTT-TACT
403548 TATTTT-TATTTTACT
1 T-TTTTATATTTTACT
*
403563 TTTTTATCTTTTA-T
1 TTTTTATATTTTACT
403577 TTTTT
1 TTTTT
403582 TTAAATTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 10 0.33
15 11 0.37
16 5 0.17
17 4 0.13
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTATATTTTACT
Found at i:403582 original size:29 final size:28
Alignment explanation
Indices: 403523--403584 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 28
403513 TGTATTTGTG
403523 TTTATTTTATTTTTATTTTTATACTTATT
1 TTTATTTTATTTTTATTTTTATA-TTATT
403552 TTTATTTTACTTTTTTATCTTTTAT-TT-TT
1 TTTATTTTA--TTTTTAT-TTTTATATTATT
403581 TTTA
1 TTTA
403585 AATTAGATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 15 0.50
30 2 0.07
31 7 0.23
32 6 0.20
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTATTTTATTTTTATTTTTATATTATT
Found at i:406746 original size:24 final size:24
Alignment explanation
Indices: 406688--406755 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
406678 AGAAGGTAGT
406688 TTTTTAACTTTATTTTTTA-CTAAA
1 TTTTTAA-TTTATTTTTTATCTAAA
*
406712 TTTTTACATTTATTTTTTATCCTTAA
1 TTTTTA-ATTTATTTTTTAT-CTAAA
406738 TTTTT-ATTT-TTTATTTAT
1 TTTTTAATTTATTT-TTTAT
406756 TATAATGCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
23 3 0.08
24 26 0.67
25 1 0.03
26 9 0.23
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTTAATTTATTTTTTATCTAAA
Found at i:406753 original size:27 final size:25
Alignment explanation
Indices: 406688--406743 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 25
406678 AGAAGGTAGT
406688 TTTTTA-ACTTTATTTTTTA-CTAAA
1 TTTTTACA-TTTATTTTTTATCTAAA
*
406712 TTTTTACATTTATTTTTTATCCTTAA
1 TTTTTACATTTATTTTTTAT-CTAAA
406738 TTTTTA
1 TTTTTA
406744 TTTTTTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 17 0.61
25 1 0.04
26 10 0.36
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (25 bp):
TTTTTACATTTATTTTTTATCTAAA
Found at i:406925 original size:36 final size:37
Alignment explanation
Indices: 406863--406935 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
406853 GTGGTAAATA
* *
406863 TTTATTTATGTATTTATTTTAGTAATTTTT-TAATTT
1 TTTATTTATGTATTAATTTTACTAATTTTTATAATTT
*
406899 TTTATTTATTTA-TAATTTATACTAATTTTTATAATTT
1 TTTATTTATGTATTAATTT-TACTAATTTTTATAATTT
406936 AATTAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 5 0.16
36 21 0.66
37 6 0.19
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (37 bp):
TTTATTTATGTATTAATTTTACTAATTTTTATAATTT
Found at i:408562 original size:29 final size:29
Alignment explanation
Indices: 408522--408662 Score: 203
Period size: 29 Copynumber: 4.9 Consensus size: 29
408512 GAACCAGCAT
408522 AGGTCGCCATGCACGCCCGGCGTCCT-TA
1 AGGTCGCCATGCACGCCCGGCGTCCTATA
* *
408550 TAGGTCGCCATGCATGCCCGGCATCCTATA
1 -AGGTCGCCATGCACGCCCGGCGTCCTATA
*
408580 AGGTCGCCATGCACGCCCGACGTCCTATA
1 AGGTCGCCATGCACGCCCGGCGTCCTATA
* *
408609 AGGTCGTCATGCACGCCCGACGTCCTATA
1 AGGTCGCCATGCACGCCCGGCGTCCTATA
* *
408638 AGGACGCCATGCACACCCGGCGTCC
1 AGGTCGCCATGCACGCCCGGCGTCC
408663 AACGTTCTTT
Statistics
Matches: 101, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
29 99 0.98
30 2 0.02
ACGTcount: A:0.19, C:0.38, G:0.26, T:0.18
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGTCCTATA
Found at i:409207 original size:30 final size:29
Alignment explanation
Indices: 409165--409272 Score: 85
Period size: 29 Copynumber: 3.5 Consensus size: 29
409155 GGTTGTTGAA
409165 TTTATATTATATAAAAAATTAGTTAATTAG
1 TTTA-ATTATATAAAAAATTAGTTAATTAG
*
409195 TTTAAGTTATATAAAAGAATAATTATTTAAATTAG
1 TTTAA-TTATAT--AA-AA-AATTAGTT-AATTAG
* **
409230 TTT-ATTGTTATAAATTATTAGTTAATTAG
1 TTTAATT-ATATAAAAAATTAGTTAATTAG
409259 TTT-ATTATTATAAA
1 TTTAATTA-TATAAA
409273 TTAGGGTAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 17
0.74 0.07 0.20
Matches are distributed among these distances:
29 19 0.30
30 16 0.25
31 1 0.02
32 4 0.06
33 4 0.06
34 11 0.17
35 9 0.14
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (29 bp):
TTTAATTATATAAAAAATTAGTTAATTAG
Found at i:409245 original size:18 final size:18
Alignment explanation
Indices: 409222--409276 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
409212 AATAATTATT
409222 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
409240 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
409252 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
409269 TAAATTAG
1 TAAATTAG
409277 GGTAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 4 0.14
14 1 0.03
16 4 0.14
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAATTAGTTTATTGTTA
Found at i:409578 original size:29 final size:29
Alignment explanation
Indices: 409540--409617 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 29
409530 TAGTAATAAA
409540 TTATAATTAAAAATCA-TTTATTAGTTTAA-G
1 TTAT-ATTAAAAAT-AGTTTATTAG-TTAACG
409570 TTATATTAAAAAATAGTTTATTAGTTAACG
1 TTATATT-AAAAATAGTTTATTAGTTAACG
409600 TTATATTAAAGAATAGTT
1 TTATATTAAA-AATAGTT
409618 AAAGTTATGT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
29 11 0.25
30 33 0.75
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.45
Consensus pattern (29 bp):
TTATATTAAAAATAGTTTATTAGTTAACG
Found at i:409617 original size:22 final size:22
Alignment explanation
Indices: 409591--409636 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
409581 AATAGTTTAT
*
409591 TAGTTAACGTTATATTAAAGAA
1 TAGTTAAAGTTATATTAAAGAA
*
409613 TAGTTAAAGTTATGTTAAAGAA
1 TAGTTAAAGTTATATTAAAGAA
409635 TA
1 TA
409637 ATTTATTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.46, C:0.02, G:0.15, T:0.37
Consensus pattern (22 bp):
TAGTTAAAGTTATATTAAAGAA
Found at i:411921 original size:60 final size:60
Alignment explanation
Indices: 411853--411967 Score: 221
Period size: 60 Copynumber: 1.9 Consensus size: 60
411843 AATCATTACT
*
411853 AAATCATTAAATATTAATAATAATTTCATTATTATTAATCATTACTAAATCATTAATATC
1 AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATC
411913 AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA
1 AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA
411968 TTATAATTTC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (60 bp):
AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATC
Found at i:412113 original size:48 final size:49
Alignment explanation
Indices: 412042--412149 Score: 200
Period size: 48 Copynumber: 2.2 Consensus size: 49
412032 TCAAGTCGTA
412042 AATCATTACTATCAAATCATTAAATATTAATAATAAATT-ATTATTACT
1 AATCATTACTATCAAATCATTAAATATTAATAATAAATTCATTATTACT
*
412090 AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTATCAAATCATTAAATATTAATAATAAATTCATTATTACT
412139 AATCATTACTA
1 AATCATTACTA
412150 AATCATTAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
48 38 0.66
49 20 0.34
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (49 bp):
AATCATTACTATCAAATCATTAAATATTAATAATAAATTCATTATTACT
Found at i:412136 original size:25 final size:25
Alignment explanation
Indices: 412108--412196 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
412098 CTATCAAATC
412108 ATTAAATATTAATAATAATTTCATT
1 ATTAAATATTAATAATAATTTCATT
* * *
412133 ATTACTAATCATTACTAAATCATTAATATCAAATC
1 ATTA--AAT-A-T--T-AAT-AATAATTTC--ATT
412168 ATTAAATATTAATAATAATTTCATT
1 ATTAAATATTAATAATAATTTCATT
412193 ATTA
1 ATTA
412197 CTAATCATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 20
0.65 0.08 0.27
Matches are distributed among these distances:
25 10 0.21
27 10 0.21
28 4 0.08
29 2 0.04
31 2 0.04
32 4 0.08
33 10 0.21
35 6 0.12
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (25 bp):
ATTAAATATTAATAATAATTTCATT
Found at i:412163 original size:60 final size:60
Alignment explanation
Indices: 412084--412268 Score: 338
Period size: 60 Copynumber: 3.1 Consensus size: 60
412074 ATAAATTATT
412084 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
412143 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
412203 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAAATT-ATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
412262 ATTACTA
1 ATTACTA
412269 TCAAATCATT
Statistics
Matches: 122, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
59 26 0.21
60 96 0.79
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:412265 original size:48 final size:48
Alignment explanation
Indices: 412203--412375 Score: 220
Period size: 58 Copynumber: 3.4 Consensus size: 48
412193 ATTACTAATC
412203 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
1 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
412252 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAAT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAAT--A--A--ATTA-T--T
* *
412309 CATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 -ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATT-ATT
412359 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
412376 AATCATTAAT
Statistics
Matches: 111, Mismatches: 2, Indels: 22
0.82 0.01 0.16
Matches are distributed among these distances:
48 34 0.31
49 23 0.21
50 2 0.02
52 4 0.04
53 1 0.01
54 5 0.05
55 1 0.01
56 1 0.01
57 1 0.01
58 39 0.35
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (48 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
Found at i:412315 original size:10 final size:10
Alignment explanation
Indices: 412300--412326 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
412290 ATAAATTATT
412300 ATTACTAATC
1 ATTACTAATC
412310 ATTACTAATC
1 ATTACTAATC
412320 ATTACTA
1 ATTACTA
412327 TCAAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:412383 original size:21 final size:21
Alignment explanation
Indices: 412359--412446 Score: 51
Period size: 21 Copynumber: 4.3 Consensus size: 21
412349 TAATTTCATT
412359 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
* * *
412380 ATTAAT-ATCAAATCATTAAAT-
1 ATTACTAATC--ATTACTAAATC
* * * *
412401 ATTAATAATAATT--T-CATT
1 ATTACTAATCATTACTAAATC
*
412419 ATTACTAATCATTACTAAACC
1 ATTACTAATCATTACTAAATC
412440 ATTACTA
1 ATTACTA
412447 TCAAATCATT
Statistics
Matches: 49, Mismatches: 11, Indels: 14
0.66 0.15 0.19
Matches are distributed among these distances:
17 2 0.04
18 12 0.24
20 6 0.12
21 19 0.39
22 10 0.20
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTACTAATCATTACTAAATC
Found at i:412397 original size:60 final size:59
Alignment explanation
Indices: 412252--412457 Score: 351
Period size: 60 Copynumber: 3.5 Consensus size: 59
412242 ATAAATTATT
*
412252 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATT-ATTATTACTAATC
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
412310 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
412369 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
412429 ATTACTAAACCATTACTATCAAATCATTA
1 ATTACT-AATCATTACTATCAAATCATTA
412458 TTATTAAATC
Statistics
Matches: 140, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
58 43 0.31
59 19 0.14
60 78 0.56
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (59 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:412466 original size:14 final size:14
Alignment explanation
Indices: 412429--412475 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
412419 ATTACTAATC
* *
412429 ATTACTAAACCATT
1 ATTATTAAATCATT
* *
412443 ACTATCAAATCATT
1 ATTATTAAATCATT
412457 ATTATTAAATCATT
1 ATTATTAAATCATT
412471 ATTAT
1 ATTAT
412476 AATTGAAGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:412518 original size:3 final size:3
Alignment explanation
Indices: 412512--412585 Score: 85
Period size: 3 Copynumber: 24.0 Consensus size: 3
412502 TTTACTCATT
* * *
412512 TTA TTA TTA TTA TTA GTA TTA TTA TAA TTA TAA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
412560 TTA ATA TATA TTA TTTA TTA ATA TTA
1 TTA TTA T-TA TTA -TTA TTA TTA TTA
412586 CAAACAGGCC
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
3 53 0.90
4 6 0.10
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:414685 original size:22 final size:21
Alignment explanation
Indices: 414634--414698 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
414624 CATATACTTA
* *
414634 ATTTATA-ATTCTTTTTTTAT
1 ATTTATATATTATTTTTATAT
* *
414654 ATATACATATTATTTTTATAGT
1 ATTTATATATTATTTTTATA-T
*
414676 ATTTATATA-TATTATTA-AT
1 ATTTATATATTATTTTTATAT
414695 ATTT
1 ATTT
414699 CATTTTATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
19 5 0.14
20 6 0.17
21 17 0.47
22 8 0.22
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.62
Consensus pattern (21 bp):
ATTTATATATTATTTTTATAT
Found at i:418009 original size:15 final size:15
Alignment explanation
Indices: 417989--418020 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
417979 ATCAATACCT
417989 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
418004 TTTTGCATACATTCA
1 TTTTGCATACATGCA
418019 TT
1 TT
418021 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:425137 original size:13 final size:12
Alignment explanation
Indices: 425113--425146 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
425103 ATTATGCTTG
425113 AAGAAAAAAAAA
1 AAGAAAAAAAAA
*
425125 GAGAAAAAGAAAA
1 AAGAAAAA-AAAA
425138 AAGAAAAAA
1 AAGAAAAAA
425147 GGGGGGTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAA
Found at i:427354 original size:113 final size:113
Alignment explanation
Indices: 427158--427703 Score: 1006
Period size: 113 Copynumber: 4.8 Consensus size: 113
427148 GCAAAGATTT
427158 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
427223 GAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTT
66 GAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
*
427271 AAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
427336 GAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
66 GAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
*
427384 AAATCCATCACTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
427449 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
66 GAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
427497 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
427562 GAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
66 GAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
*
427610 AAATCCATCA-TTCAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTT-GATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
*
427674 GAAGGAAG-AGAAAGTTCATAATGAGAAGAA
65 GGAGGAAGAAGAAA-TTCATAATGAGAAGAA
427704 CTCATCTGAA
Statistics
Matches: 422, Mismatches: 9, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
112 7 0.02
113 415 0.98
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
GAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
Found at i:427695 original size:40 final size:40
Alignment explanation
Indices: 427640--427933 Score: 434
Period size: 40 Copynumber: 7.6 Consensus size: 40
427630 CAGCTTTTCC
427640 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
427680 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
427720 AGA-AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 AGAGA-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
427760 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
427800 AGA-AGAAGTTCATAATGAGAAGAATTCATCTGAAGAAGGA
1 AGAGA-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
427840 AGA-AGAAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-
1 AGAGA-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
427878 A-AG-AAGTTCATAATAAGAAGAACTCGTCTG-A-AA-GA
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
427913 AGAG--A-TTCATAATGAGAAGAA
1 AGAGAAAGTTCATAATGAGAAGAA
427934 TTTGTTCAAC
Statistics
Matches: 241, Mismatches: 7, Indels: 18
0.91 0.03 0.07
Matches are distributed among these distances:
34 18 0.07
35 3 0.01
36 27 0.11
37 1 0.00
38 1 0.00
39 3 0.01
40 187 0.78
41 1 0.00
ACGTcount: A:0.48, C:0.10, G:0.24, T:0.18
Consensus pattern (40 bp):
AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
Found at i:427836 original size:16 final size:18
Alignment explanation
Indices: 427798--427899 Score: 63
Period size: 17 Copynumber: 5.5 Consensus size: 18
427788 TCTGAAGAAG
427798 GAAGAAGAAGTTCATAAT
1 GAAGAAGAAGTTCATAAT
*
427816 G-AGAAGAA-TTCATCTGAAGAAG
1 GAAGAAGAAGTTCA--T----AAT
427838 GAAGAAGAAGTTCATAAT
1 GAAGAAGAAGTTCATAAT
*
427856 G-AGAAGAA-CTCATCTGAA-
1 GAAGAAGAAGTTCA--T-AAT
427874 GAAGAAGAAGTTCATAAT
1 GAAGAAGAAGTTCATAAT
427892 -AAGAAGAA
1 GAAGAAGAA
427900 CTCGTCTGAA
Statistics
Matches: 66, Mismatches: 4, Indels: 29
0.67 0.04 0.29
Matches are distributed among these distances:
16 7 0.11
17 24 0.36
18 8 0.12
19 9 0.14
20 3 0.05
22 4 0.06
23 7 0.11
24 4 0.06
ACGTcount: A:0.50, C:0.08, G:0.24, T:0.19
Consensus pattern (18 bp):
GAAGAAGAAGTTCATAAT
Found at i:427860 original size:24 final size:23
Alignment explanation
Indices: 427817--427861 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
427807 GTTCATAATG
*
427817 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
427840 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
427862 AACTCATCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:428294 original size:3 final size:3
Alignment explanation
Indices: 428288--428370 Score: 94
Period size: 3 Copynumber: 27.0 Consensus size: 3
428278 TTTACTCATT
* * * *
428288 TTA TTA TTA TTA TTA GTA TTA TTA TAA TTA TAA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
428336 TTA TTA TTA TTA ATA TATA TTA TTTA TTA ATA TTA
1 TTA TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA
428371 CAAACAGGCC
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
3 60 0.91
4 6 0.09
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:430369 original size:26 final size:26
Alignment explanation
Indices: 430333--430512 Score: 196
Period size: 26 Copynumber: 7.2 Consensus size: 26
430323 GACAATAATG
430333 ATTATTATAATGATTATTATTAAATC
1 ATTATTATAATGATTATTATTAAATC
*
430359 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATTAAATC
* * * *
430385 ATTACTA-AATCATCAAATCATT-AA--
1 ATTATTATAATGAT--TATTATTAAATC
*
430409 A-TATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATTAAATC
*
430431 ATTATTATAATGATTATTACTAAATC
1 ATTATTATAATGATTATTATTAAATC
*
430457 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATTAAATC
* *
430483 ATTATTATAATGATTATTATCATATC
1 ATTATTATAATGATTATTATTAAATC
430509 ATTA
1 ATTA
430513 CTAAATCATC
Statistics
Matches: 130, Mismatches: 14, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
19 5 0.04
20 2 0.02
21 2 0.02
22 1 0.01
23 9 0.07
24 4 0.03
25 5 0.04
26 98 0.75
27 4 0.03
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (26 bp):
ATTATTATAATGATTATTATTAAATC
Found at i:430470 original size:124 final size:124
Alignment explanation
Indices: 430333--430571 Score: 419
Period size: 124 Copynumber: 1.9 Consensus size: 124
430323 GACAATAATG
*
430333 ATTATTATAATGATTATTATTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCAT
1 ATTATTATAATGATTATTATCAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCAT
*
430398 CAAATCATTAAATATTTAAA-TCATTATTAAA-TCATTATTATAATGATTATTACTAAATC
66 CAAATCATTAAATA-TTAAATTCATTATTAAATTCATTATTA-AATCATTATTACTAAATC
*
430457 ATTATTATAATGATTATTATCAAATCATTATTATAATGATTATTATCATATCATTACTAAATCAT
1 ATTATTATAATGATTATTATCAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCAT
430522 CAAATCATTAAATATTAAATTCATTATTAAATTCATTATTAAATCATTAT
66 CAAATCATTAAATATTAAATTCATTATTAAATTCATTATTAAATCATTAT
430572 AATGATTATT
Statistics
Matches: 110, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
123 5 0.05
124 96 0.87
125 9 0.08
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (124 bp):
ATTATTATAATGATTATTATCAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCAT
CAAATCATTAAATATTAAATTCATTATTAAATTCATTATTAAATCATTATTACTAAATC
Found at i:430551 original size:12 final size:12
Alignment explanation
Indices: 430534--430571 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
430524 AATCATTAAA
430534 TATTAAATTCAT
1 TATTAAATTCAT
430546 TATTAAATTCAT
1 TATTAAATTCAT
430558 TATTAAA-TCAT
1 TATTAAATTCAT
430569 TAT
1 TAT
430572 AATGATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.27
12 19 0.73
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (12 bp):
TATTAAATTCAT
Found at i:430788 original size:17 final size:18
Alignment explanation
Indices: 430768--430802 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
430758 TATTAGTAAA
430768 TCATTATTATT-ATAATT
1 TCATTATTATTAATAATT
430785 TCATTATTATTAATAATT
1 TCATTATTATTAATAATT
430803 ACTAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TCATTATTATTAATAATT
Found at i:434142 original size:18 final size:17
Alignment explanation
Indices: 434117--434184 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 17
434107 ACAATATAAA
434117 TTAAACAAAATATTTTT
1 TTAAACAAAATATTTTT
* *
434134 TTAAAACAACACTAAGTATTT
1 TT-AAACAA-AAT-A-TTTTT
*
434155 TTAAACACAATATTTTTT
1 TTAAACAAAATA-TTTTT
434173 TTAAACAGAAAT
1 TTAAACA-AAAT
434185 TATCTCGCAC
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
17 2 0.05
18 18 0.46
19 7 0.18
20 6 0.15
21 6 0.15
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (17 bp):
TTAAACAAAATATTTTT
Found at i:434646 original size:8 final size:8
Alignment explanation
Indices: 434635--434659 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
434625 TTTAATAACT
434635 TAAACTAA
1 TAAACTAA
434643 TAAACTAA
1 TAAACTAA
434651 TAAACTAA
1 TAAACTAA
434659 T
1 T
434660 TTTTTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (8 bp):
TAAACTAA
Found at i:434712 original size:21 final size:21
Alignment explanation
Indices: 434679--434727 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
434669 AATATAATAT
434679 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
434700 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
434721 ATTAACT
1 A-TAACT
434728 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:435109 original size:21 final size:21
Alignment explanation
Indices: 435084--435154 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
435074 ACGCTGCAAT
435084 CATGCAGCTATGGATGCAACG
1 CATGCAGCTATGGATGCAACG
* *
435105 CATGCAGCTACGGATGC-AGG
1 CATGCAGCTATGGATGCAACG
* *
435125 AATCTCCCAGCTATGGATGCAACG
1 CA--T-GCAGCTATGGATGCAACG
435149 CATGCA
1 CATGCA
435155 TGAGTGATAG
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 3 0.08
21 18 0.47
22 2 0.05
23 12 0.32
24 3 0.08
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (21 bp):
CATGCAGCTATGGATGCAACG
Found at i:435234 original size:17 final size:17
Alignment explanation
Indices: 435212--435245 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
435202 ATGGATGCAT
435212 GATGAGGGATAGGGTTA
1 GATGAGGGATAGGGTTA
435229 GATGAGGGATAGGGTTA
1 GATGAGGGATAGGGTTA
435246 AAGTTTGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.47, T:0.24
Consensus pattern (17 bp):
GATGAGGGATAGGGTTA
Found at i:435356 original size:19 final size:20
Alignment explanation
Indices: 435334--435417 Score: 129
Period size: 19 Copynumber: 4.3 Consensus size: 20
435324 TACCTACACA
435334 CTCCCCATGCATGCA-CGAT
1 CTCCCCATGCATGCACCGAT
*
435353 CTCCCCATGCATGAACCGAT
1 CTCCCCATGCATGCACCGAT
435373 CTCCCCGA-GCATGCA-CGAT
1 CTCCCC-ATGCATGCACCGAT
435392 CTCCCCATGCATGCACCGAT
1 CTCCCCATGCATGCACCGAT
435412 CTCCCC
1 CTCCCC
435418 CCATGCGTGC
Statistics
Matches: 59, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
18 1 0.02
19 31 0.53
20 26 0.44
21 1 0.02
ACGTcount: A:0.20, C:0.45, G:0.15, T:0.19
Consensus pattern (20 bp):
CTCCCCATGCATGCACCGAT
Found at i:435377 original size:39 final size:39
Alignment explanation
Indices: 435334--435417 Score: 143
Period size: 39 Copynumber: 2.2 Consensus size: 39
435324 TACCTACACA
435334 CTCCCC-ATGCATGCACGATCTCCCCATGCATGAACCGAT
1 CTCCCCGA-GCATGCACGATCTCCCCATGCATGAACCGAT
*
435373 CTCCCCGAGCATGCACGATCTCCCCATGCATGCACCGAT
1 CTCCCCGAGCATGCACGATCTCCCCATGCATGAACCGAT
435412 CTCCCC
1 CTCCCC
435418 CCATGCGTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
39 42 0.98
40 1 0.02
ACGTcount: A:0.20, C:0.45, G:0.15, T:0.19
Consensus pattern (39 bp):
CTCCCCGAGCATGCACGATCTCCCCATGCATGAACCGAT
Found at i:435435 original size:26 final size:27
Alignment explanation
Indices: 435399--435450 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 27
435389 GATCTCCCCA
435399 TGCATGCACCGATCT-CCCCCCATGCG
1 TGCATGCACCGATCTCCCCCCCATGCG
435425 TGCATGCACCGATCTCCCCCCCATGC
1 TGCATGCACCGATCTCCCCCCCATGC
435451 ACACCATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.15, C:0.48, G:0.17, T:0.19
Consensus pattern (27 bp):
TGCATGCACCGATCTCCCCCCCATGCG
Found at i:435458 original size:28 final size:26
Alignment explanation
Indices: 435401--435460 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
435391 TCTCCCCATG
***
435401 CATGCACCGATCTCCCCCCATGCGTG
1 CATGCACCGATCTCCCCCCATGCCAC
435427 CATGCACCGATCTCCCCCCCATGCACAC
1 CATGCACCGATCT-CCCCCCATGC-CAC
435455 CATGCA
1 CATGCA
435461 GCTCCCGCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 13 0.45
27 10 0.34
28 6 0.21
ACGTcount: A:0.20, C:0.48, G:0.15, T:0.17
Consensus pattern (26 bp):
CATGCACCGATCTCCCCCCATGCCAC
Found at i:435517 original size:29 final size:29
Alignment explanation
Indices: 435485--435564 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
435475 GTCGCCCCGA
*
435485 GTGCATGGCGACCTCCTTGGTCGTTGGGC
1 GTGCATGGCGACCTCTTTGGTCGTTGGGC
*
435514 GTGCATGGTGACCTCTTTGGTCGTTGGGC
1 GTGCATGGCGACCTCTTTGGTCGTTGGGC
435543 GTGCATGGCGACCTCTTTGGTC
1 GTGCATGGCGACCTCTTTGGTC
435565 ACTGTAGAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.07, C:0.25, G:0.36, T:0.31
Consensus pattern (29 bp):
GTGCATGGCGACCTCTTTGGTCGTTGGGC
Found at i:440248 original size:27 final size:30
Alignment explanation
Indices: 440215--440284 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
440205 CACTAGGCGG
440215 TGATGATTGAATAA-AAAAT-TATTAAAT-T
1 TGATGATTGAATAATAAAATATA-TAAATAT
*
440243 T-ATGATTAAATTAATAAAATATATAAATAT
1 TGATGATTGAA-TAATAAAATATATAAATAT
*
440273 TGAGGATTGAAT
1 TGATGATTGAAT
440285 TTATAATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
27 8 0.24
28 4 0.12
29 10 0.29
30 5 0.15
31 7 0.21
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (30 bp):
TGATGATTGAATAATAAAATATATAAATAT
Found at i:442171 original size:29 final size:29
Alignment explanation
Indices: 442013--442163 Score: 178
Period size: 29 Copynumber: 5.2 Consensus size: 29
442003 CACATTCGAA
* **
442013 AATTACAAAAATATCACATTTTTTAAAAAT
1 AATTACCAAAATATCAC-CGTTTTAAAAAT
**
442043 AATTACCAAAATATCATTGTTTTAAAAAT
1 AATTACCAAAATATCACCGTTTTAAAAAT
* * *
442072 AATTACTAAAACATCACCGATTTAAAAAT
1 AATTACCAAAATATCACCGTTTTAAAAAT
*
442101 AATTACCGAAATATCACCGTTTTAAAAA-
1 AATTACCAAAATATCACCGTTTTAAAAAT
* * *
442129 AATTCCCAAAATGTCATCGTTTTAAAAAT
1 AATTACCAAAATATCACCGTTTTAAAAAT
442158 AATTAC
1 AATTAC
442164 TAGAATGTTA
Statistics
Matches: 103, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
28 24 0.23
29 64 0.62
30 15 0.15
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (29 bp):
AATTACCAAAATATCACCGTTTTAAAAAT
Found at i:442179 original size:29 final size:29
Alignment explanation
Indices: 442013--442228 Score: 174
Period size: 29 Copynumber: 7.4 Consensus size: 29
442003 CACATTCGAA
* *
442013 AATTACAAAAATATCACATTTTTTAAAAAT
1 AATTACCAAAATATCAC-TGTTTTAAAAAT
*
442043 AATTACCAAAATATCATTGTTTTAAAAAT
1 AATTACCAAAATATCACTGTTTTAAAAAT
* * * *
442072 AATTACTAAAACATCACCGATTTAAAAAT
1 AATTACCAAAATATCACTGTTTTAAAAAT
* *
442101 AATTACCGAAATATCACCGTTTTAAAAA-
1 AATTACCAAAATATCACTGTTTTAAAAAT
* *
442129 AATTCCCAAAATGTCA-TCGTTTTAAAAAT
1 AATTACCAAAATATCACT-GTTTTAAAAAT
* * * * *
442158 AATTACTAGAATGTTACTGTTTTTAAGAA-
1 AATTACCAAAATATCACTG-TTTTAAAAAT
* *
442187 AATTCCCAAAATGTCAGCT-TTTTCAAAAA-
1 AATTACCAAAATATCA-CTGTTTT-AAAAAT
442216 AATT-CTCAAAATA
1 AATTAC-CAAAATA
442229 CTATCGGGTC
Statistics
Matches: 152, Mismatches: 27, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
28 28 0.18
29 98 0.64
30 26 0.17
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (29 bp):
AATTACCAAAATATCACTGTTTTAAAAAT
Found at i:442215 original size:86 final size:86
Alignment explanation
Indices: 442013--442228 Score: 227
Period size: 86 Copynumber: 2.5 Consensus size: 86
442003 CACATTCGAA
* * * *
442013 AATTACAAAAATATCACATTTTTTAAAAATAATTACCAAAATATCATTGTTTTAAAAATAATTAC
1 AATTACCAAAATATCAC-CTTTTTAAAAA-AATTCCCAAAATATCATCGTTTTAAAAATAATTAC
442078 TAAAACATCACCGATTTAAAAAT
64 TAAAACATCACCGATTTAAAAAT
* * *
442101 AATTACCGAAATATCACCGTTTTAAAAAAATTCCCAAAATGTCATCGTTTTAAAAATAATTACTA
1 AATTACCAAAATATCACCTTTTTAAAAAAATTCCCAAAATATCATCGTTTTAAAAATAATTACTA
* ** * * * *
442166 GAATGTTACTGTTTTTAAGAA-
66 AAACATCACCG-ATTTAAAAAT
* * * *
442187 AATTCCCAAAATGTCAGCTTTTTCAAAAAAATTCTCAAAATA
1 AATTACCAAAATATCACCTTTTT-AAAAAAATTCCCAAAATA
442229 CTATCGGGTC
Statistics
Matches: 105, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
86 58 0.55
87 32 0.30
88 15 0.14
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (86 bp):
AATTACCAAAATATCACCTTTTTAAAAAAATTCCCAAAATATCATCGTTTTAAAAATAATTACTA
AAACATCACCGATTTAAAAAT
Found at i:448601 original size:31 final size:31
Alignment explanation
Indices: 448486--448608 Score: 90
Period size: 31 Copynumber: 3.9 Consensus size: 31
448476 CTAAGGGAAC
448486 ATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAG
1 ATCTTAGGGCC-GCAGAGCCTACCCAAGAAT-G
* * * * **
448517 ATTTTAGGGCCGTAAGGGCCTACCTAAGAACAC
1 ATCTTAGGGCCG-CAGAGCCTACCCAAGAA-TG
* * *
448550 ATCGTATGGCCGCA-AGGCCTACCCGAGAATG
1 ATCTTAGGGCCGCAGA-GCCTACCCAAGAATG
*
448581 ATCTTAGGGCCGCAGAGCCTACCTAAGA
1 ATCTTAGGGCCGCAGAGCCTACCCAAGA
448609 GTCATATTAG
Statistics
Matches: 68, Mismatches: 18, Indels: 12
0.69 0.18 0.12
Matches are distributed among these distances:
30 1 0.01
31 32 0.47
32 25 0.37
33 10 0.15
ACGTcount: A:0.28, C:0.27, G:0.26, T:0.19
Consensus pattern (31 bp):
ATCTTAGGGCCGCAGAGCCTACCCAAGAATG
Found at i:449533 original size:29 final size:29
Alignment explanation
Indices: 449494--449679 Score: 184
Period size: 29 Copynumber: 6.4 Consensus size: 29
449484 CACATTCAAA
*
449494 AATTACAAAAATATCAACTTTTTAAAAAT
1 AATTACCAAAATATCAACTTTTTAAAAAT
449523 AATTACCAAAATATC-ACTGTTTTAAAAAT
1 AATTACCAAAATATCAACT-TTTTAAAAAT
* *
449552 AATTACTAAAATATC-ACTGATTTAAAAAT
1 AATTACCAAAATATCAACT-TTTTAAAAAT
* *
449581 AATTACCAAAATATCATCGTTTTAAAAA-
1 AATTACCAAAATATCAACTTTTTAAAAAT
* * * *
449609 AATTCCCAAAATGTCATCGTTTTAAAAAT
1 AATTACCAAAATATCAACTTTTTAAAAAT
* * * *
449638 AATTACCAGAATGTCACAATTTTTAAGAA-
1 AATTACCAAAATATCA-ACTTTTTAAAAAT
449667 AATT-CTCAAAATA
1 AATTAC-CAAAATA
449680 CCATCGGGTT
Statistics
Matches: 135, Mismatches: 17, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
28 30 0.22
29 96 0.71
30 9 0.07
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.33
Consensus pattern (29 bp):
AATTACCAAAATATCAACTTTTTAAAAAT
Found at i:449578 original size:58 final size:58
Alignment explanation
Indices: 449491--449654 Score: 210
Period size: 58 Copynumber: 2.8 Consensus size: 58
449481 GTCCACATTC
449491 AAAAATTACAAAAATATCAACT-TTTTAAAAATAATTACCAAAATATCACT-GTTTTAA
1 AAAAATTACAAAAATATC-ACTGTTTTAAAAATAATTACCAAAATATCACTCGTTTTAA
* *
449548 AAATAATTACTAAAATATCACTGATTTAAAAATAATTACCAAAATATCA-TCGTTTTAA
1 AAA-AATTACAAAAATATCACTGTTTTAAAAATAATTACCAAAATATCACTCGTTTTAA
* * * * *
449606 AAAAATTCCCAAAATGTCA-TCGTTTTAAAAATAATTACCAGAATGTCAC
1 AAAAATTACAAAAATATCACT-GTTTTAAAAATAATTACCAAAATATCAC
449655 AATTTTTAAG
Statistics
Matches: 94, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
56 1 0.01
57 44 0.47
58 49 0.52
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.32
Consensus pattern (58 bp):
AAAAATTACAAAAATATCACTGTTTTAAAAATAATTACCAAAATATCACTCGTTTTAA
Found at i:449679 original size:86 final size:87
Alignment explanation
Indices: 449494--449654 Score: 227
Period size: 86 Copynumber: 1.9 Consensus size: 87
449484 CACATTCAAA
* * * *
449494 AATTACAAAAATATCAACTTTTTAAAAATAATTACCAAAATATCACTGTTTTAAAAATAATTACT
1 AATTACCAAAATATCATCGTTTTAAAAATAATTACCAAAATATCACTGTTTTAAAAATAATTACC
449559 AAAATATCACTGATTTAAAAAT
66 AAAATATCACTGATTTAAAAAT
* *
449581 AATTACCAAAATATCATCGTTTTAAAAA-AATTCCCAAAATGTCA-TCGTTTTAAAAATAATTAC
1 AATTACCAAAATATCATCGTTTTAAAAATAATTACCAAAATATCACT-GTTTTAAAAATAATTAC
* *
449644 CAGAATGTCAC
65 CAAAATATCAC
449655 AATTTTTAAG
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
85 1 0.02
86 39 0.60
87 25 0.38
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.33
Consensus pattern (87 bp):
AATTACCAAAATATCATCGTTTTAAAAATAATTACCAAAATATCACTGTTTTAAAAATAATTACC
AAAATATCACTGATTTAAAAAT
Found at i:449685 original size:58 final size:56
Alignment explanation
Indices: 449501--449685 Score: 203
Period size: 58 Copynumber: 3.2 Consensus size: 56
449491 AAAAATTACA
* *
449501 AAAATATCAACTTTTTAAAAATAATTACCAAAATATCACTGTTTTAAAAATAATTACT-
1 AAAATATCATCGTTTTAAAAATAATTACCAAAATATCACT-TTTTAAAAA-AATT-CTC
* * *
449559 AAAATATCA-CTGATTTAAAAATAATTACCAAAATATCATCGTTTTAAAAAAATTCCC
1 AAAATATCATC-GTTTTAAAAATAATTACCAAAATATCA-CTTTTTAAAAAAATTCTC
* * * *
449616 AAAATGTCATCGTTTTAAAAATAATTACCAGAATGTCACAATTTTTAAGAAAATTCTC
1 AAAATATCATCGTTTTAAAAATAATTACCAAAATATCAC--TTTTTAAAAAAATTCTC
*
449674 AAAATACCATCG
1 AAAATATCATCG
449686 GGTTGGTTCA
Statistics
Matches: 108, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
56 2 0.02
57 37 0.34
58 68 0.63
59 1 0.01
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.33
Consensus pattern (56 bp):
AAAATATCATCGTTTTAAAAATAATTACCAAAATATCACTTTTTAAAAAAATTCTC
Found at i:449848 original size:10 final size:12
Alignment explanation
Indices: 449821--449853 Score: 52
Period size: 10 Copynumber: 2.9 Consensus size: 12
449811 CTTCGGTCTC
449821 CAAAAATTCTTG
1 CAAAAATTCTTG
449833 CAAAAATT-TT-
1 CAAAAATTCTTG
449843 CAAAAATTCTT
1 CAAAAATTCTT
449854 TTAAGCGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.40
11 4 0.20
12 8 0.40
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.36
Consensus pattern (12 bp):
CAAAAATTCTTG
Found at i:451007 original size:21 final size:22
Alignment explanation
Indices: 450960--451016 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
450950 CAATTATTAT
450960 AAAATATTAAATTATTTATACA
1 AAAATATTAAATTATTTATACA
* *
450982 TAAATATT-AATTTTTTAATA-A
1 AAAATATTAAATTATTT-ATACA
*
451003 AAAATCTTATAATT
1 AAAATATTA-AATT
451017 CAAATAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 14 0.50
22 10 0.36
23 4 0.14
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (22 bp):
AAAATATTAAATTATTTATACA
Found at i:464656 original size:16 final size:16
Alignment explanation
Indices: 464603--464658 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
464593 ATTTAAACAT
464603 ATAAAATTAAAATATAA
1 ATAAAATTAAAAT-TAA
464620 ATAAACAATGAGTAAAA-TAA
1 AT-AA-AAT---TAAAATTAA
464640 ATAAAATTAAAATTAA
1 ATAAAATTAAAATTAA
464656 ATA
1 ATA
464659 TAAAAAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
15 5 0.15
16 6 0.18
17 2 0.06
18 5 0.15
19 5 0.15
20 5 0.15
22 5 0.15
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAATTAA
Found at i:464673 original size:37 final size:37
Alignment explanation
Indices: 464603--464673 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
464593 ATTTAAACAT
* *
464603 ATAAAATTAAAATATAAATAAACAATGAGTAAAATAA
1 ATAAAATTAAAATATAAATAAAAAATGAATAAAATAA
464640 ATAAAATTAAAAT-TAAATATAAAAA-GTAATAAAA
1 ATAAAATTAAAATATAAATA-AAAAATG-AATAAAA
464674 CTTATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 7 0.23
37 23 0.77
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (37 bp):
ATAAAATTAAAATATAAATAAAAAATGAATAAAATAA
Found at i:465889 original size:3 final size:3
Alignment explanation
Indices: 465883--465955 Score: 114
Period size: 3 Copynumber: 25.0 Consensus size: 3
465873 TTATTATTTT
465883 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
465929 TAA TAA TTA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
465956 ATAAATAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
2 4 0.06
3 62 0.94
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:465908 original size:20 final size:20
Alignment explanation
Indices: 465883--465955 Score: 123
Period size: 20 Copynumber: 3.8 Consensus size: 20
465873 TTATTATTTT
465883 TAATAATAATAATAATAATA
1 TAATAATAATAATAATAATA
465903 TAATAATAATAATAATAATA
1 TAATAATAATAATAATAATA
*
465923 TAATAATAATAAT--TATTA
1 TAATAATAATAATAATAATA
465941 TAATAATAATAATAA
1 TAATAATAATAATAA
465956 ATAAATAAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
18 17 0.34
20 33 0.66
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TAATAATAATAATAATAATA
Found at i:466221 original size:17 final size:17
Alignment explanation
Indices: 466199--466257 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
466189 TTGCACAAGC
466199 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
*
466216 TCTTCTTC-TTCAGATG-AGT
1 TCTTC-TCATT--G-TGAACT
466235 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
466252 TCTTCT
1 TCTTCT
466258 GGAAATGCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
16 2 0.06
17 16 0.47
18 4 0.12
19 10 0.29
20 2 0.06
ACGTcount: A:0.15, C:0.24, G:0.12, T:0.49
Consensus pattern (17 bp):
TCTTCTCATTGTGAACT
Found at i:466448 original size:113 final size:114
Alignment explanation
Indices: 466311--467067 Score: 924
Period size: 113 Copynumber: 6.6 Consensus size: 114
466301 GCAAAATGTC
*
466311 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
466376 CTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCGAGCGAAAA-GTT
66 CTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCGAGCGAAAAGGTT
* *
466424 GAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
* ** * * * *** *
466489 CTTTCACTGGGGATGCTGAT-GAT-GATAT-ATCTCCTTCTGTGATAGTGTTATGCAAAAGGTT
66 C--TCTCTGGAAAAGTTGATCCATCGA-ATGAT-GAATTC---G--A--G---CG-AAAAGGTT
* * *
466550 GAACAAGATCTTCTCATTATAAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
*
466615 CTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAA-GTT
66 CTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCGAGCGAAAAGGTT
* * *
466663 GAACAAGTTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
* * * * *
466728 TTCTTTGGAAAAGTTGATTCATC-AAGTGATGGATTTGAGC-AAAAGGTT
66 CTCTCTGGAAAAGTTGATCCATCGAA-TGATGAATTCGAGCGAAAAGGTT
466776 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
* * *
466841 TTCTCTGGAAAAGTTGATCCATC-AAGTGATGGATTTGAGC-AAAAGGTT
66 CTCTCTGGAAAAGTTGATCCATCGAA-TGATGAATTCGAGCGAAAAGGTT
*
466889 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
* * * * * *
466954 CGAC-CTGGTAATGCTGATCCATCAAATGATGAATTCAAGCGAAAA-GTT
66 C-TCTCTGGAAAAGTTGATCCATCGAATGATGAATTCGAGCGAAAAGGTT
** * *
467002 GAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTGAGATGAGTTTTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
467067 C
66 C
467068 GACCTGGAAA
Statistics
Matches: 565, Mismatches: 55, Indels: 48
0.85 0.08 0.07
Matches are distributed among these distances:
112 5 0.01
113 431 0.76
114 18 0.03
115 13 0.02
117 1 0.00
118 1 0.00
119 1 0.00
120 1 0.00
121 1 0.00
122 1 0.00
124 13 0.02
125 10 0.02
126 69 0.12
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (114 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
CTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCGAGCGAAAAGGTT
Found at i:466515 original size:239 final size:237
Alignment explanation
Indices: 466214--466971 Score: 1050
Period size: 239 Copynumber: 3.2 Consensus size: 237
466204 TCATTGTGAA
*
466214 CTTCTT-CTTCTTCAGATGAGTTCTTCTCATTGTGAACT-TCTT-CTGGAAATGCTGATGATGAT
1 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-TTCCTGGAAATGCTGATGATGAT
* *
466276 ATATCTCTTTCTGTGATAGAGTCATGCAAAATGTCGAACAAGCTCTTCTCATTATGAACTTCTTC
65 ATATCTC-TTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
466341 TTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAATGAT
129 TTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAATGAT
466406 GAATTCGAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTT
194 GAATTCGAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTT
**
466450 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCACTGGGGATGCTGATGATGAT
1 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTC-CTGGAAATGCTGATGATGAT
* * * *
466515 ATATCTCCTTCTGTGATAGTGTTATGCAAAAGGTTGAACAAGATCTTCTCATTATAAACTTCTTC
65 ATATCT-CTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
*
466580 TTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGAT
129 TTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAATGAT
466645 GAATTCGAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTT
194 GAATTCGAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTT
* * *
466689 CTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAA--CTTTCTTTGGAAAAG-T--TGAT--T
1 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTC-CTGGAAATGCTGATGATGAT
* ** * * *
466747 -CA--TC--AAGTGATGGATTTGA-GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
65 ATATCTCTTCTGTGATAGA-GTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
* *
466806 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATC-AAGTGA
129 TTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAA-TGA
* * * *
466870 TGGATTTGAGC-AAAAGGTTGAACAAGCTCTTCTCATTATGAACTT
193 TGAATTCGAGCGAAAA-GTTGAACAAGTTCTTCTTATTATGAACTT
* ** *
466915 CTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTC-GACCTGGTAATGCTGAT
1 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCCTGGAAATGCTGAT
466972 CCATCAAATG
Statistics
Matches: 470, Mismatches: 39, Indels: 33
0.87 0.07 0.06
Matches are distributed among these distances:
225 5 0.01
226 180 0.38
227 4 0.01
228 2 0.00
229 2 0.00
231 1 0.00
232 1 0.00
234 4 0.01
236 7 0.01
237 43 0.09
238 1 0.00
239 219 0.47
240 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (237 bp):
CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCCTGGAAATGCTGATGATGATA
TATCTCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT
CTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAATGATGA
ATTCGAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTT
Found at i:467906 original size:22 final size:22
Alignment explanation
Indices: 467872--467923 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
467862 CATAAAGCTT
* * *
467872 TCATATTTGAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAACCTA
467894 TCATCTTTAAAAAGAGAACCTA
1 TCATCTTTAAAAAGAGAACCTA
467916 TCATCTTT
1 TCATCTTT
467924 GAAGAGTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAACCTA
Found at i:470643 original size:114 final size:114
Alignment explanation
Indices: 470438--470657 Score: 395
Period size: 114 Copynumber: 1.9 Consensus size: 114
470428 GATCATGCAG
* * *
470438 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTTCATACCGAACCAGATCAGATAACTCAAAGA
*
470503 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAGCAAA
*
470552 TTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTTCATACCGAACCAGATCAGATAACTCAAAGA
470617 ACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTA
66 ACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTA
470658 CGAGAATGTG
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.32
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTTCATACCGAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:474832 original size:7 final size:7
Alignment explanation
Indices: 474798--474839 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
474788 ATAAGAGTAT
474798 AAATGCA
1 AAATGCA
* *
474805 TAATGAA
1 AAATGCA
474812 AAATGCA
1 AAATGCA
474819 AAGATGCA
1 AA-ATGCA
474827 AAATGC-
1 AAATGCA
474833 AAATGCA
1 AAATGCA
474840 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.12, G:0.17, T:0.17
Consensus pattern (7 bp):
AAATGCA
Found at i:477243 original size:16 final size:16
Alignment explanation
Indices: 477190--477245 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
477180 ATTTAAACAT
477190 ATAAAATTAAAATATAA
1 ATAAAATTAAAAT-TAA
477207 ATAAACAATGAGTAAAA-TAA
1 AT-AA-AAT---TAAAATTAA
477227 ATAAAATTAAAATTAA
1 ATAAAATTAAAATTAA
477243 ATA
1 ATA
477246 TAAAAAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
15 5 0.15
16 6 0.18
17 2 0.06
18 5 0.15
19 5 0.15
20 5 0.15
22 5 0.15
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAATTAA
Found at i:477260 original size:37 final size:37
Alignment explanation
Indices: 477190--477260 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
477180 ATTTAAACAT
* *
477190 ATAAAATTAAAATATAAATAAACAATGAGTAAAATAA
1 ATAAAATTAAAATATAAATAAAAAATGAATAAAATAA
477227 ATAAAATTAAAAT-TAAATATAAAAA-GTAATAAAA
1 ATAAAATTAAAATATAAATA-AAAAATG-AATAAAA
477261 CTTATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 7 0.23
37 23 0.77
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (37 bp):
ATAAAATTAAAATATAAATAAAAAATGAATAAAATAA
Found at i:478476 original size:3 final size:3
Alignment explanation
Indices: 478470--478507 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
478460 TTATTATTTT
478470 TAA TAA TAA TAA TAA T-A TATA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA
478508 TTATTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:480180 original size:83 final size:83
Alignment explanation
Indices: 480092--480367 Score: 265
Period size: 83 Copynumber: 3.3 Consensus size: 83
480082 CAAACATTGT
* * * * *
480092 AATAGGATTCATCTATAGTGGCGGTTTTTAAACAAACGCCGCAACAAAGTAGTACTTTAGCGGTG
1 AATAGGATTCATCTATAGTGGCGTTTTTTCAACAAACGCCACAACAGAGTAGTACTTTAGCGGCG
*
480157 TTTTTATATAAAT-GCCGC
66 TTCTTATA-AAATCGCCGC
* * ** * * * *
480175 AATAGGGTTTATCTATAGTATCATTTTTTCAACAAATGCTACAACAGAGTAGTACTTTAGAGGCG
1 AATAGGATTCATCTATAGTGGCGTTTTTTCAACAAACGCCACAACAGAGTAGTACTTTAGCGGCG
* *
480240 TTCTTATACAATCGCCTC
66 TTCTTATAAAATCGCCGC
* * *
480258 AATA-GAGTTCATCTATAGTGGTGTTTTTTCAACAAACGCCTCAACAGAGTAGTGCTTTAGCGGC
1 AATAGGA-TTCATCTATAGTGGCGTTTTTTCAACAAACGCCACAACAGAGTAGTACTTTAGCGGC
* *
480322 ATT-TTCATACAAA-CGTCGC
65 GTTCTT-ATA-AAATCGCCGC
* *
480341 AATAGTG-TTTATCTATAATGGCGTTTT
1 AATAG-GATTCATCTATAGTGGCGTTTT
480368 AAGCAAAAAT
Statistics
Matches: 153, Mismatches: 34, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
82 6 0.04
83 144 0.94
84 2 0.01
85 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (83 bp):
AATAGGATTCATCTATAGTGGCGTTTTTTCAACAAACGCCACAACAGAGTAGTACTTTAGCGGCG
TTCTTATAAAATCGCCGC
Found at i:487770 original size:26 final size:26
Alignment explanation
Indices: 487734--487792 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
487724 TGGCCGTGTT
* * * *
487734 ACCGATTCACTGGTTCAACCGATCGA
1 ACCGGTTCACTAGTTCAACAGATCAA
*
487760 ACCGGTTCACTAGTTCAACAGGTCAA
1 ACCGGTTCACTAGTTCAACAGATCAA
487786 ACCGGTT
1 ACCGGTT
487793 AAACCGGTCG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (26 bp):
ACCGGTTCACTAGTTCAACAGATCAA
Found at i:487806 original size:9 final size:9
Alignment explanation
Indices: 487780--487819 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
487770 TAGTTCAACA
487780 GGTCAAACC
1 GGTCAAACC
*
487789 GGTTAAACC
1 GGTCAAACC
*
487798 GGTCGAACC
1 GGTCAAACC
*
487807 GGTCAGACC
1 GGTCAAACC
487816 GGTC
1 GGTC
487820 GAAAGAACCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:487806 original size:18 final size:18
Alignment explanation
Indices: 487780--487822 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
487770 TAGTTCAACA
* *
487780 GGTCAAACCGGTTAAACC
1 GGTCGAACCGGTCAAACC
*
487798 GGTCGAACCGGTCAGACC
1 GGTCGAACCGGTCAAACC
487816 GGTCGAA
1 GGTCGAA
487823 AGAACCAGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.30, T:0.14
Consensus pattern (18 bp):
GGTCGAACCGGTCAAACC
Found at i:488788 original size:53 final size:53
Alignment explanation
Indices: 488708--488822 Score: 178
Period size: 53 Copynumber: 2.2 Consensus size: 53
488698 AACACTGTTC
* * *
488708 ACAGCTCAACATGGGCCAATTTTTTTTCAGTTGTAAAAGAAAAAATTGCATTT
1 ACAGCTCAACATGGACCAATTTTTTTTCAATTATAAAAGAAAAAATTGCATTT
*
488761 ACAGCTCAGCATGGACC-ATTTATTTTTCAATTATAAAAGAAAAAATTGCATTT
1 ACAGCTCAACATGGACCAATTT-TTTTTCAATTATAAAAGAAAAAATTGCATTT
488814 ACAGCTCAA
1 ACAGCTCAA
488823 ACAAATTGCA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
52 4 0.07
53 52 0.93
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (53 bp):
ACAGCTCAACATGGACCAATTTTTTTTCAATTATAAAAGAAAAAATTGCATTT
Found at i:490770 original size:10 final size:10
Alignment explanation
Indices: 490755--490792 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
490745 ATTTAAGGAT
*
490755 TAAATAATTA
1 TAAATAACTA
490765 TAAATAACTA
1 TAAATAACTA
490775 TAAATAACTA
1 TAAATAACTA
490785 TAAATAAC
1 TAAATAAC
490793 ATTTAGATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (10 bp):
TAAATAACTA
Found at i:492050 original size:28 final size:28
Alignment explanation
Indices: 492018--492076 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
492008 CATCTACTGG
492018 TTTATTTTTTTAATTTAAAAATGATTTA
1 TTTATTTTTTTAATTTAAAAATGATTTA
492046 TTTATTTTTTTAATTTAAAAATGATTTA
1 TTTATTTTTTTAATTTAAAAATGATTTA
492074 TTT
1 TTT
492077 TCGTCAATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (28 bp):
TTTATTTTTTTAATTTAAAAATGATTTA
Found at i:493500 original size:19 final size:20
Alignment explanation
Indices: 493476--493517 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
493466 TTAAATATTT
493476 TATA-TTTTTATTAAAAATA
1 TATATTTTTTATTAAAAATA
493495 TATATTTTTTATTAAAAATA
1 TATATTTTTTATTAAAAATA
493515 TAT
1 TAT
493518 TTGTATCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATTTTTTATTAAAAATA
Found at i:494193 original size:12 final size:12
Alignment explanation
Indices: 494161--494200 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
494151 TTCAAAGAAA
494161 TTAAAA-TTA-T
1 TTAAAATTTATT
*
494171 TT-AAATCTATT
1 TTAAAATTTATT
494182 TTAAAATTTATT
1 TTAAAATTTATT
494194 TTAAAAT
1 TTAAAAT
494201 ATGGATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 3 0.12
10 4 0.16
11 3 0.12
12 15 0.60
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:494212 original size:22 final size:22
Alignment explanation
Indices: 494187--494331 Score: 281
Period size: 22 Copynumber: 6.6 Consensus size: 22
494177 CTATTTTAAA
494187 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
494209 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
494231 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
494253 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
494275 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
494297 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
494319 ATTTATTTTAAAA
1 ATTTATTTTAAAA
494332 AATTTATTAT
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 121 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:494412 original size:31 final size:31
Alignment explanation
Indices: 494355--494413 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
494345 AGTTGTATGG
* *
494355 ATTATTTAAATTTCATTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
*
494386 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
494414 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:499787 original size:116 final size:115
Alignment explanation
Indices: 499501--499925 Score: 433
Period size: 116 Copynumber: 3.7 Consensus size: 115
499491 ATATTATATG
** ** * *
499501 AGCTCTCCTATATGAATTCTTTATTCTCCCATAAAGGCCATGATGAGGTCGATCAAGCTCTCCTA
1 AGCTCTCCTATAT-AATTCCCTATTCTCCCATAAAGATCATGTTGAGGTCGAACAAGCTCTCCTA
* * * * * * *
499566 TATGAACTTCTTCTCCCTTGATCACTTCCTACTATATGGAACGAGTACACG
65 TATGAACTTCTTCTTCCTTGGTCACTTCCTAATATCTGGAAAGAGTATACA
* ** * * *
499617 AG-TCACCTATATAATCTTTCTATTCTCCCATAAAGGTCATGTTGAGGTCGAACAAGCTCACCGA
1 AGCTCTCCTATATAAT-TCCCTATTCTCCCATAAAGATCATGTTGAGGTCGAACAAGCTCTCCTA
* * *
499681 TATGAACTTCTTCTTCTTTGGTCATTTCCTAATATCTAGAAAGAGTATACA
65 TATGAACTTCTTCTTCCTTGGTCACTTCCTAATATCTGGAAAGAGTATACA
* ** *
499732 AGCTCTCCTATATAAGTTCCCTATTCTCCCATAAAGATCATGTTTAGGTTAAACAAGCTCTTCTA
1 AGCTCTCCTATATAA-TTCCCTATTCTCCCATAAAGATCATGTTGAGGTCGAACAAGCTCTCCTA
* ** * *
499797 TATGAACTTCTTCTTCCTTAGTCACTTCCTCTTATCTGGAAATAAT-TGACA
65 TATGAACTTCTTCTTCCTTGGTCACTTCCTAATATCTGGAAAGAGTAT-ACA
* * * * * * *
499848 AGCTCTCTTATATAAGCTCCATATTCTCCCACAAA-AGTCATGTTAAGGTCGAACAAGCTTTCTT
1 AGCTCTCCTATATAA-TTCCCTATTCTCCCATAAAGA-TCATGTTGAGGTCGAACAAGCTCTCCT
499912 ATATGAACTTCTTC
64 ATATGAACTTCTTC
499926 CCTCTTTTTG
Statistics
Matches: 258, Mismatches: 46, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
114 3 0.01
115 95 0.37
116 159 0.62
117 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (115 bp):
AGCTCTCCTATATAATTCCCTATTCTCCCATAAAGATCATGTTGAGGTCGAACAAGCTCTCCTAT
ATGAACTTCTTCTTCCTTGGTCACTTCCTAATATCTGGAAAGAGTATACA
Found at i:500425 original size:42 final size:41
Alignment explanation
Indices: 500333--500435 Score: 100
Period size: 42 Copynumber: 2.5 Consensus size: 41
500323 AGTCTTATAA
*
500333 ATGGCCTGAATGACTTAATCACTATGCTCGAAAGACATACT
1 ATGGCCTGAATGACTTAATCACTATGCTCAAAAGACATACT
* * * * *
500374 AGTGACCTGATTGATTTAATCA-TAATGCTCAAAATACTTACT
1 A-TGGCCTGAATGACTTAATCACT-ATGCTCAAAAGACATACT
**
500416 GATGGCCTGAAAAACTTAAT
1 -ATGGCCTGAATGACTTAAT
500436 AGTTTTAAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
41 2 0.04
42 45 0.94
43 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (41 bp):
ATGGCCTGAATGACTTAATCACTATGCTCAAAAGACATACT
Found at i:500657 original size:42 final size:41
Alignment explanation
Indices: 500603--500693 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 41
500593 AAATGGCCTA
*
500603 AAGGACTTATCATCTTGCTCGAAAGATTGAC-AGATGACCCG
1 AAGGACTTATCATCATGCTCGAAAGATTGACGA-ATGACCCG
* * *
500644 AAGGATTTAATCATCATGCTTGAAAGATTTACGAATGACCCG
1 AAGGACTT-ATCATCATGCTCGAAAGATTGACGAATGACCCG
500686 AAGGACTT
1 AAGGACTT
500694 GTTAACTTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 7 0.16
42 35 0.81
43 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (41 bp):
AAGGACTTATCATCATGCTCGAAAGATTGACGAATGACCCG
Found at i:500913 original size:260 final size:261
Alignment explanation
Indices: 500443--500921 Score: 631
Period size: 260 Copynumber: 1.8 Consensus size: 261
500433 AATAGTTTTA
* * *
500443 AAAATAATCTACTAGGTAAGAAACGTTGGAAATCATTTTCTTACTTTTCAAAAATTTTATTTTCT
1 AAAATAATCTACTAGGTAAGAAACGTTGGAAATCACTTTCTTACTTTTCAAAAAGTTCATTTTCT
** *
500508 GAAATTATTAAATGAAAAACTTTGAAAATCACTTTCTCATTTTTTCATAAAATCATATGAAAACA
66 GAAAAAATTAAATGAAAAACTTTGAAAATCACTTTCTCATTTTTTCACAAAATCATATGAAAACA
* * * * * * * * * *
500573 TCTTGCTCGAATGTATTTATAAATGGCCTAAAGGACTTATCATCTTGCTCGAAAGATTGACAGAT
131 TCCTGCCCAAAGGTACTTATAAATGGCATAAAGAACTTATAATCTTACTCGAAAGACTGACAGAT
* *
500638 GACCCGAAGGATTTAATCATCATGCTTGAAAGATTTACGAATGACCCGAAGGACTTGTTAACTTT
196 GACCCAAAAGATTTAATCATCATGCTTGAAAGATTTACGAATGACCCGAAGGACTTGTTAACTTT
500703 G
261 G
* * * * * *
500704 AAAATAGTTTACTGGGTAAGAAACTTTTGAAATCACTTTCTTATTTTTC-AAAAGTTCATTTTCT
1 AAAATAATCTACTAGGTAAGAAACGTTGGAAATCACTTTCTTACTTTTCAAAAAGTTCATTTTCT
* * * * *
500768 GAAAAAATTAAATGAGAAATTTTGAAAATCATTTTCTCATTTTTTTCACAAAATTATATGAAAAT
66 GAAAAAATTAAATGAAAAACTTTGAAAATCACTTTCTCA-TTTTTTCACAAAATCATATGAAAAC
* * *
500833 ATCCTGCCCAAAGGT-CTTATAGATGGCATGAAGAACTTATAATCTTACTCGAAAGACTGATC-T
130 ATCCTGCCCAAAGGTACTTATAAATGGCATAAAGAACTTATAATCTTACTCGAAAGACTGA-CAG
500896 ATGACCCAAAAGATTTAATCATCATG
194 ATGACCCAAAAGATTTAATCATCATG
500922 TCCGAAAGAC
Statistics
Matches: 184, Mismatches: 32, Indels: 5
0.83 0.14 0.02
Matches are distributed among these distances:
260 108 0.59
261 76 0.41
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (261 bp):
AAAATAATCTACTAGGTAAGAAACGTTGGAAATCACTTTCTTACTTTTCAAAAAGTTCATTTTCT
GAAAAAATTAAATGAAAAACTTTGAAAATCACTTTCTCATTTTTTCACAAAATCATATGAAAACA
TCCTGCCCAAAGGTACTTATAAATGGCATAAAGAACTTATAATCTTACTCGAAAGACTGACAGAT
GACCCAAAAGATTTAATCATCATGCTTGAAAGATTTACGAATGACCCGAAGGACTTGTTAACTTT
G
Found at i:500967 original size:19 final size:20
Alignment explanation
Indices: 500925--500967 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
500915 CATCATGTCC
* * *
500925 GAAAGACTTAGTGATAGCAC
1 GAAAGACTTACTCATAGCAA
500945 GAAAGACTTACTCA-AGCAA
1 GAAAGACTTACTCATAGCAA
500964 GAAA
1 GAAA
500968 TTTTTAGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (20 bp):
GAAAGACTTACTCATAGCAA
Found at i:504233 original size:18 final size:19
Alignment explanation
Indices: 504210--504256 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
504200 GTTAATTTTG
*
504210 GTATCGGTA-CTCATGGGA
1 GTATCGATACCTCATGGGA
504228 GTATCGATACCCTCATGGGA
1 GTATCGATA-CCTCATGGGA
*
504248 GTATTGATA
1 GTATCGATA
504257 GTGAGGGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.32
20 17 0.68
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (19 bp):
GTATCGATACCTCATGGGA
Found at i:504244 original size:20 final size:20
Alignment explanation
Indices: 504219--504256 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
504209 GGTATCGGTA
504219 CTCATGGGAGTATCGATACC
1 CTCATGGGAGTATCGATACC
*
504239 CTCATGGGAGTATTGATA
1 CTCATGGGAGTATCGATA
504257 GTGAGGGTAG
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:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (20 bp):
CTCATGGGAGTATCGATACC
Found at i:509422 original size:16 final size:16
Alignment explanation
Indices: 509401--509432 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
509391 GTAAGCCAAT
509401 ATGCTAAATGGATATA
1 ATGCTAAATGGATATA
509417 ATGCTAAATGGATATA
1 ATGCTAAATGGATATA
509433 GTCAGGTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGCTAAATGGATATA
Found at i:510750 original size:36 final size:36
Alignment explanation
Indices: 510655--510937 Score: 168
Period size: 36 Copynumber: 7.9 Consensus size: 36
510645 TTTTAAAAAG
*
510655 AAAACA-TTTTGAAAA-TATGGGTAATATATAGTTTTTT
1 AAAACATTTTTGAAAATTAT--ATAATATATAG-TTTTT
* * * *
510692 AAAAATATTTTTGCAAACTATATAACATATAGTTTTT
1 -AAAACATTTTTGAAAATTATATAATATATAGTTTTT
*
510729 AAAACATTTTTGAAAATTATATAACATATA-TTTTT
1 AAAACATTTTTGAAAATTATATAATATATAGTTTTT
* * *
510764 GAAATCA-TTTTGAAAA--A-ATAATGTATAGTTTAAAATA
1 -AAAACATTTTTGAAAATTATATAATATATAGTTT----TT
*
510801 AAAACATTTTTTGAAAATTTTATATAATATATAGTTTTA
1 AAAACA-TTTTTGAAAA--TTATATAATATATAGTTTTT
* * * *
510840 AAAATATTTTGGAAAACT-CAT-ATA-ATA-TTTTT
1 AAAACATTTTTGAAAATTATATAATATATAGTTTTT
* * *
510872 AAAATCATTTTTGAAAACTATATGGA-ATATAGTTTTG
1 AAAA-CATTTTTGAAAATTATAT-AATATATAGTTTTT
510909 AAAACATTTTT---AA--ATATAATATATAGTTT
1 AAAACATTTTTGAAAATTATATAATATATAGTTT
510938 AAAAAATATT
Statistics
Matches: 200, Mismatches: 23, Indels: 51
0.73 0.08 0.19
Matches are distributed among these distances:
30 1 0.00
31 13 0.06
32 16 0.08
33 21 0.10
34 5 0.03
35 17 0.09
36 49 0.25
37 14 0.07
38 32 0.16
39 15 0.08
40 3 0.01
42 1 0.00
43 13 0.06
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.43
Consensus pattern (36 bp):
AAAACATTTTTGAAAATTATATAATATATAGTTTTT
Found at i:510901 original size:34 final size:33
Alignment explanation
Indices: 510827--510894 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 33
510817 ATTTTATATA
* *
510827 ATAT-ATAGTTTTAAAAAT-ATTTTGGAAAACTC
1 ATATAATA-TTTTTAAAATCATTTTTGAAAACTC
510859 ATATAATATTTTTAAAATCATTTTTGAAAACT-
1 ATATAATATTTTTAAAATCATTTTTGAAAACTC
510891 ATAT
1 ATAT
510895 GGAATATAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (33 bp):
ATATAATATTTTTAAAATCATTTTTGAAAACTC
Found at i:511027 original size:18 final size:18
Alignment explanation
Indices: 511006--511044 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
510996 ATTATTTCTT
*
511006 TTCATTTTA-TTCACTTTA
1 TTCATTTAATTTCA-TTTA
511024 TTCATTTAATTTCATTTA
1 TTCATTTAATTTCATTTA
511042 TTC
1 TTC
511045 TGTTTTATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCATTTAATTTCATTTA
Done.