Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007927.1 Hibiscus syriacus cultivar Beakdansim tig00110333_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: 706544
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:491322 original size:27 final size:27
Alignment explanation
Indices: 491252--491329 Score: 129
Period size: 27 Copynumber: 2.9 Consensus size: 27
491242 CTCACCCGCA
* * *
491252 ATTCGATCACCGGCCCACCCAGCAGCC
1 ATTCGAACACCGGCCTAGCCAGCAGCC
491279 ATTCGAACACCGGCCTAGCCAGCAGCC
1 ATTCGAACACCGGCCTAGCCAGCAGCC
491306 ATTCGAACACCGGCCTAGCCAGCA
1 ATTCGAACACCGGCCTAGCCAGCA
491330 TCAATTTGAG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.26, C:0.42, G:0.21, T:0.12
Consensus pattern (27 bp):
ATTCGAACACCGGCCTAGCCAGCAGCC
Found at i:493174 original size:2 final size:2
Alignment explanation
Indices: 493167--493194 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
493157 TTGTCATAAT
493167 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
493195 AAACAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:496720 original size:13 final size:13
Alignment explanation
Indices: 496703--496735 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
496693 CGCCCCGATT
496703 ACCCGATTACCCG
1 ACCCGATTACCCG
*
496716 CCCCGATTACCCG
1 ACCCGATTACCCG
496729 ACCCGAT
1 ACCCGAT
496736 AAATATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.21, C:0.48, G:0.15, T:0.15
Consensus pattern (13 bp):
ACCCGATTACCCG
Found at i:496796 original size:24 final size:26
Alignment explanation
Indices: 496769--496829 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 26
496759 ATATATATAT
*
496769 ATAATATTAATA-A-ATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
496793 ATAA-A-AAATATATATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
*
496817 AT-ATATATATATA
1 ATAATATAAATATA
496830 CCTGGTCCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
22 4 0.13
23 3 0.10
24 18 0.58
25 6 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATAATATAAATATATATTTAATTTAA
Found at i:496811 original size:19 final size:19
Alignment explanation
Indices: 496787--496826 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
496777 AATAAATTTA
496787 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
496806 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
496825 AT
1 AT
496827 ATACCTGGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:496871 original size:12 final size:12
Alignment explanation
Indices: 496847--496880 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
496837 CGATTCCCAG
496847 CCCAATA-CCGA
1 CCCAATACCCGA
496858 CCCAATACCCGA
1 CCCAATACCCGA
496870 CCCAATACCCG
1 CCCAATACCCG
496881 TTTAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.32, C:0.50, G:0.09, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:498304 original size:18 final size:18
Alignment explanation
Indices: 498280--498324 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
498270 GCTCTAACAG
498280 CATTATCCTCTAGATCAA
1 CATTATCCTCTAGATCAA
*
498298 GATTATCCTCTAGATCAA
1 CATTATCCTCTAGATCAA
498316 CATTATCCT
1 CATTATCCT
498325 AGGGTCGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.36
Consensus pattern (18 bp):
CATTATCCTCTAGATCAA
Found at i:500454 original size:16 final size:15
Alignment explanation
Indices: 500406--500465 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 15
500396 AAGAATTCAT
500406 ATATAATTTTGAAATTA
1 ATATAA-TTT-AAATTA
* *
500423 ATTTAA-GTATAATTA
1 ATATAATTTA-AATTA
500438 ATACTAATTTAAATTA
1 ATA-TAATTTAAATTA
*
500454 ATATTATTTAAA
1 ATATAATTTAAA
500466 AAAAAGTGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
14 1 0.03
15 16 0.46
16 11 0.31
17 7 0.20
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (15 bp):
ATATAATTTAAATTA
Found at i:506225 original size:18 final size:19
Alignment explanation
Indices: 506202--506248 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
506192 ATGTTAGACA
*
506202 TTGTACTATT-GCTTGTGT
1 TTGTACTATTAGCTTGAGT
*
506220 TTGTACTGCTTAGCTTGAGT
1 TTGTACT-ATTAGCTTGAGT
506240 TTGTACTAT
1 TTGTACTAT
506249 GAACATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 7 0.29
19 3 0.12
20 14 0.58
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (19 bp):
TTGTACTATTAGCTTGAGT
Found at i:507652 original size:23 final size:24
Alignment explanation
Indices: 507620--507664 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
507610 ATAAGAAAGA
*
507620 AAACAGAAAACGTGTTATAAAGGC
1 AAACAGAAAACGTGTTACAAAGGC
*
507644 AAACA-AAAATGTGTTACAAAG
1 AAACAGAAAACGTGTTACAAAG
507665 ATAATTATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.53, C:0.11, G:0.18, T:0.18
Consensus pattern (24 bp):
AAACAGAAAACGTGTTACAAAGGC
Found at i:509129 original size:25 final size:25
Alignment explanation
Indices: 509095--509145 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
509085 GTAATCCATT
509095 TTCTCATTTTGTTTAGTGAAGGAAA
1 TTCTCATTTTGTTTAGTGAAGGAAA
509120 TTCTCATTTTGTTTAGTGAAGGAAA
1 TTCTCATTTTGTTTAGTGAAGGAAA
509145 T
1 T
509146 AGGAGAAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (25 bp):
TTCTCATTTTGTTTAGTGAAGGAAA
Found at i:510903 original size:158 final size:158
Alignment explanation
Indices: 510605--510914 Score: 566
Period size: 158 Copynumber: 2.0 Consensus size: 158
510595 GGCATTTTGA
* *
510605 TCGATTGACTGTGTGTCGTACTGGTTTATGGTGTTACAGGAATTGAGCACTTTTTGTGTCCAAAT
1 TCGATTGACTGTGTGTCGTACTGATTTATGGTGTTACAGGAATTGAGCACTTTGTGTGTCCAAAT
510670 AACTCTATTGATCCTACTTGAAAAAAGTGGCACGCTTATAGGTTTATTTCTTATGCATATGACCA
66 AACTCTATTGATCCTACTTGAAAAAAGTGGCACGCTTATAGGTTTATTTCTTATGCATATGACCA
*
510735 ATAAGCAAATTGAAGTAGGTAATTCTGT
131 AGAAGCAAATTGAAGTAGGTAATTCTGT
510763 TCGATTGACTGTGTGTCGTACTGATTTATGGTGTTACAGGAATTGAGCACTTTGTGTGTCCAAAT
1 TCGATTGACTGTGTGTCGTACTGATTTATGGTGTTACAGGAATTGAGCACTTTGTGTGTCCAAAT
* *
510828 AACTCTATTGATGCTACTTGAAAAAAGTGGCACGCTTATAGGTTTATTTCTTATGCATATGAGCA
66 AACTCTATTGATCCTACTTGAAAAAAGTGGCACGCTTATAGGTTTATTTCTTATGCATATGACCA
*
510893 AGAAGTAAATTGAAGTAGGTAA
131 AGAAGCAAATTGAAGTAGGTAA
510915 CAAACTTTAT
Statistics
Matches: 146, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
158 146 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.36
Consensus pattern (158 bp):
TCGATTGACTGTGTGTCGTACTGATTTATGGTGTTACAGGAATTGAGCACTTTGTGTGTCCAAAT
AACTCTATTGATCCTACTTGAAAAAAGTGGCACGCTTATAGGTTTATTTCTTATGCATATGACCA
AGAAGCAAATTGAAGTAGGTAATTCTGT
Found at i:512483 original size:13 final size:13
Alignment explanation
Indices: 512483--512558 Score: 62
Period size: 13 Copynumber: 5.3 Consensus size: 13
512473 CCGTTGACCC
512483 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
512496 TACCTGACCCGTT
1 GACCCGACCCGTT
512509 GACTCGACCCGACCCGTT
1 G-----ACCCGACCCGTT
512527 GACCCGACCCGTT
1 GACCCGACCCGTT
*
512540 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
512555 GACC
1 GACC
512559 ATTGACCGGA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
13 27 0.53
15 12 0.24
18 12 0.24
ACGTcount: A:0.16, C:0.42, G:0.22, T:0.20
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:512484 original size:18 final size:18
Alignment explanation
Indices: 512461--512537 Score: 92
Period size: 18 Copynumber: 4.6 Consensus size: 18
512451 ACCGGTCACA
512461 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
512479 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
* *
512496 ----TACCTGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
512510 ACTCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
512528 ACCCGACCCG
1 ACCCGACCCG
512538 TTGACCGTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
13 11 0.22
18 38 0.78
ACGTcount: A:0.17, C:0.48, G:0.21, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:512508 original size:31 final size:31
Alignment explanation
Indices: 512465--512543 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
512455 GTCACAACCC
512465 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* * *
512496 TACCTGACCCGTTGACTCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
512527 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
512544 GTTGACCCGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:512530 original size:8 final size:8
Alignment explanation
Indices: 512519--512558 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
512509 GACTCGACCC
512519 GACCCGTT
1 GACCCGTT
512527 GACCC---
1 GACCCGTT
512532 GACCCGTT
1 GACCCGTT
512540 GA-CCGTT
1 GACCCGTT
512547 GACCCGTT
1 GACCCGTT
512555 GACC
1 GACC
512559 ATTGACCGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.18
7 7 0.25
8 16 0.57
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.20
Consensus pattern (8 bp):
GACCCGTT
Found at i:512552 original size:15 final size:14
Alignment explanation
Indices: 512519--512565 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
512509 GACTCGACCC
*
512519 GACCCGTTGACC-C
1 GACCCGTTGACCTT
512532 GACCCGTTGACCGTT
1 GACCCGTTGACC-TT
512547 GACCCGTTGACCATT
1 GACCCGTTGACC-TT
512562 GACC
1 GACC
512566 GGAGTTGACC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 12 0.40
15 18 0.60
ACGTcount: A:0.17, C:0.38, G:0.23, T:0.21
Consensus pattern (14 bp):
GACCCGTTGACCTT
Found at i:513874 original size:18 final size:18
Alignment explanation
Indices: 513848--513882 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
513838 TCGAAAGGAC
*
513848 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
513866 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
513883 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:516660 original size:13 final size:13
Alignment explanation
Indices: 516660--516717 Score: 80
Period size: 13 Copynumber: 4.3 Consensus size: 13
516650 CCGTTGACCC
516660 GACCCGACCCGTT
1 GACCCGACCCGTT
*
516673 TACCCGACCCGTT
1 GACCCGACCCGTT
516686 GACCCGACCCGTT
1 GACCCGACCCGTT
*
516699 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
516714 GACC
1 GACC
516718 ATTGACCGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
13 28 0.70
15 12 0.30
ACGTcount: A:0.16, C:0.43, G:0.22, T:0.19
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:516689 original size:8 final size:8
Alignment explanation
Indices: 516678--516717 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
516668 CCGTTTACCC
516678 GACCCGTT
1 GACCCGTT
516686 GACCC---
1 GACCCGTT
516691 GACCCGTT
1 GACCCGTT
516699 GA-CCGTT
1 GACCCGTT
516706 GACCCGTT
1 GACCCGTT
516714 GACC
1 GACC
516718 ATTGACCGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.18
7 7 0.25
8 16 0.57
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.20
Consensus pattern (8 bp):
GACCCGTT
Found at i:516696 original size:18 final size:18
Alignment explanation
Indices: 516638--516683 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
516628 ACCGGTCACA
516638 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
516656 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
516674 ACCCGACCCG
1 ACCCGACCCG
516684 TTGACCCGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.52, G:0.20, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:516711 original size:15 final size:14
Alignment explanation
Indices: 516665--516724 Score: 61
Period size: 13 Copynumber: 4.3 Consensus size: 14
516655 GACCCGACCC
* *
516665 GACCCGTTTACC-C
1 GACCCGTTGACCTT
*
516678 GACCCGTTGACC-C
1 GACCCGTTGACCTT
516691 GACCCGTTGACCGTT
1 GACCCGTTGACC-TT
516706 GACCCGTTGACCATT
1 GACCCGTTGACC-TT
516721 GACC
1 GACC
516725 GGAGTTGACC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
13 24 0.57
15 18 0.43
ACGTcount: A:0.17, C:0.40, G:0.22, T:0.22
Consensus pattern (14 bp):
GACCCGTTGACCTT
Found at i:518041 original size:18 final size:18
Alignment explanation
Indices: 518015--518049 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
518005 TCGAAAGGAC
*
518015 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
518033 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
518050 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:521155 original size:18 final size:19
Alignment explanation
Indices: 521132--521170 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
521122 AATTAACTCA
521132 AAATTATTT-AAAAAATTT
1 AAATTATTTGAAAAAATTT
*
521150 AAATTATTTGATAAAATTT
1 AAATTATTTGAAAAAATTT
521169 AA
1 AA
521171 CAACAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
AAATTATTTGAAAAAATTT
Found at i:523152 original size:12 final size:12
Alignment explanation
Indices: 523135--523159 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
523125 AAGAGGAGTG
523135 CATCATTGCCTC
1 CATCATTGCCTC
523147 CATCATTGCCTC
1 CATCATTGCCTC
523159 C
1 C
523160 TGGTGTGGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.44, G:0.08, T:0.32
Consensus pattern (12 bp):
CATCATTGCCTC
Found at i:524926 original size:18 final size:18
Alignment explanation
Indices: 524903--524938 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
524893 TTGATGTTAT
524903 CCTTTTATCTGCAGCCAG
1 CCTTTTATCTGCAGCCAG
524921 CCTTTTATCTGCAGCCAG
1 CCTTTTATCTGCAGCCAG
524939 TTGTGATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.33
Consensus pattern (18 bp):
CCTTTTATCTGCAGCCAG
Found at i:526935 original size:35 final size:35
Alignment explanation
Indices: 526889--526964 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
526879 AAAACAGTCC
* *
526889 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
526924 TCAATTTCATTCTCAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
526959 TCAATT
1 TCAATT
526965 AAATTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:527525 original size:130 final size:130
Alignment explanation
Indices: 527362--527609 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
527352 TATTTATATA
* ** *
527362 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* * *
527427 TTAGCACATGATCATGACACGTGTCATTGGTGACGCATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
527492 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* * *
527557 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
527610 GAAGAAAATT
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:527582 original size:23 final size:21
Alignment explanation
Indices: 527536--527582 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
527526 AATTAATCAT
527536 TTAACCAGGATCTGACATATG
1 TTAACCAGGATCTGACATATG
* *
527557 TTAACACATGATCATGATATATG
1 TTAAC-CAGGATC-TGACATATG
527580 TTA
1 TTA
527583 TTGGTGACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (21 bp):
TTAACCAGGATCTGACATATG
Found at i:527640 original size:130 final size:129
Alignment explanation
Indices: 527376--527640 Score: 291
Period size: 130 Copynumber: 2.0 Consensus size: 129
527366 ATTTGGTCCT
* ** * *
527376 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
* * *** * * **** *
527441 TGACACGTGTCATTGGTGACGCATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
527506 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
* * * *
527571 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
527635 -A
128 CA
527636 AAATT
1 AAATT
527641 TGGGTCTTGG
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
130 98 0.88
132 8 0.07
133 5 0.05
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:527972 original size:30 final size:28
Alignment explanation
Indices: 527936--527995 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
527926 AGTTGATACA
527936 ATATTTTAAAAGAATAAATTTAAGATTTAT
1 ATATTTT-AAA-AATAAATTTAAGATTTAT
* * *
527966 ATATTTTTAAACTAAATTTAATATTTAT
1 ATATTTTAAAAATAAATTTAAGATTTAT
527994 AT
1 AT
527996 TTTCATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 18 0.67
29 2 0.07
30 7 0.26
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (28 bp):
ATATTTTAAAAATAAATTTAAGATTTAT
Found at i:533434 original size:36 final size:36
Alignment explanation
Indices: 533393--533467 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
533383 TTAACAAAGA
533393 TAAATAACTTTACTGACCAAAGTTAAATATTTTCAG
1 TAAATAACTTTACTGACCAAAGTTAAATATTTTCAG
533429 TAAATAACTTTACTGACCAAAGTTAAATATTTTCAG
1 TAAATAACTTTACTGACCAAAGTTAAATATTTTCAG
533465 TAA
1 TAA
533468 GTACCTCTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (36 bp):
TAAATAACTTTACTGACCAAAGTTAAATATTTTCAG
Found at i:534729 original size:21 final size:20
Alignment explanation
Indices: 534643--534799 Score: 93
Period size: 20 Copynumber: 7.8 Consensus size: 20
534633 AAATGACCAA
**
534643 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
534662 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
534682 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
534702 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
534723 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
534743 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
534763 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
534784 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
534800 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 9
0.73 0.20 0.06
Matches are distributed among these distances:
19 16 0.15
20 56 0.54
21 32 0.31
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:534752 original size:41 final size:41
Alignment explanation
Indices: 534643--534799 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
534633 AAATGACCAA
* **
534643 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
534682 CAGAATCGCAAATC-AGTTTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
534723 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
534764 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
534800 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:534859 original size:20 final size:20
Alignment explanation
Indices: 534766--534975 Score: 192
Period size: 20 Copynumber: 10.5 Consensus size: 20
534756 CGATTTTCCA
* ** *
534766 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
534786 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
534806 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
534826 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
534846 AAATCGCAACGCGTTTCCGT
1 AAATCGCAACGCGTATCCGT
*
534866 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
534886 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
534906 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
534926 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
534946 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
534966 AAATCACAAC
1 AAATCGCAAC
534976 ACTGAAATTT
Statistics
Matches: 156, Mismatches: 28, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 152 0.97
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:535696 original size:24 final size:24
Alignment explanation
Indices: 535657--535703 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
535647 AAATTTGGTC
535657 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
535681 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
535704 GATGTTCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:535894 original size:12 final size:12
Alignment explanation
Indices: 535877--535901 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
535867 ATATAATCCT
535877 GAAGAAGAAAAA
1 GAAGAAGAAAAA
535889 GAAGAAGAAAAA
1 GAAGAAGAAAAA
535901 G
1 G
535902 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:538269 original size:33 final size:33
Alignment explanation
Indices: 538182--538379 Score: 192
Period size: 33 Copynumber: 5.8 Consensus size: 33
538172 CGGAAATTAC
* * *
538182 AATCGCAACGCAAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
538215 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
538249 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
538287 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
538320 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
538353 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
538380 TGCGAAATGA
Statistics
Matches: 145, Mismatches: 8, Indels: 24
0.82 0.05 0.14
Matches are distributed among these distances:
33 84 0.58
34 30 0.21
35 5 0.03
36 4 0.03
37 2 0.01
38 20 0.14
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:538273 original size:19 final size:19
Alignment explanation
Indices: 538210--538398 Score: 237
Period size: 19 Copynumber: 10.7 Consensus size: 19
538200 AAATCCCAAC
538210 ATGAAAATCGCAATGCGGAA
1 ATGAAAATCGCAATGC-GAA
538230 ATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAA
*
538245 A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
538263 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
538282 ATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAA
*
538297 A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
538315 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
538334 ATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAA
*
538349 A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
538367 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
538386 ATGAAAATCGCAA
1 ATGAAAATCGCAA
538399 CGAGAGAATC
Statistics
Matches: 148, Mismatches: 6, Indels: 31
0.80 0.03 0.17
Matches are distributed among these distances:
14 30 0.20
15 3 0.02
16 6 0.04
17 5 0.03
18 4 0.03
19 87 0.59
20 13 0.09
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
ATGAAAATCGCAATGCGAA
Found at i:538409 original size:33 final size:33
Alignment explanation
Indices: 538268--538420 Score: 159
Period size: 33 Copynumber: 4.5 Consensus size: 33
538258 GCGAAATGAA
538268 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
538301 AATCGCAATGCGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* * * *
538333 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAG
538372 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
538405 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
538421 TATAAACGCA
Statistics
Matches: 98, Mismatches: 11, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
31 7 0.07
32 7 0.07
33 56 0.57
34 1 0.01
35 1 0.01
36 2 0.02
38 10 0.10
39 7 0.07
40 7 0.07
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:538436 original size:52 final size:52
Alignment explanation
Indices: 538210--538420 Score: 413
Period size: 52 Copynumber: 4.0 Consensus size: 52
538200 AAATCCCAAC
538210 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
538263 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
538315 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
538367 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
538419 AT
1 AT
538421 TATAAACGCA
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 142 0.90
53 16 0.10
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:538539 original size:52 final size:53
Alignment explanation
Indices: 538427--538542 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
538417 AAATTATAAA
538427 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
538480 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
538532 CGCATTGCGAT
1 CGCATTGCGAT
538543 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
Found at i:538550 original size:19 final size:19
Alignment explanation
Indices: 538445--538542 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
538435 GATTCTCTCG
538445 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
538465 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
538484 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
538498 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
538517 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
538536 TTGCGAT
1 TTGCGAT
538543 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:540655 original size:19 final size:19
Alignment explanation
Indices: 540590--540718 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
540580 TAGTTTACTT
* *
540590 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
540610 TCGCAACACGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
540629 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
540648 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
540662 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
540681 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
540695 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
540714 TCGCA
1 TCGCA
540719 TTTGCGATTT
Statistics
Matches: 92, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.12
17 11 0.12
19 41 0.45
20 13 0.14
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:540665 original size:14 final size:14
Alignment explanation
Indices: 540646--540702 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
540636 GCGAAATGAA
*
540646 AATCGCAACGACAG
1 AATCGCAACGAAAG
540660 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
540677 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
540693 AATCGCAACG
1 AATCGCAACG
540703 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:540673 original size:33 final size:33
Alignment explanation
Indices: 540627--540718 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
540617 ACGAAACCAA
*
540627 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
540660 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
540693 AATCGCAACGCGAAATGAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
540719 TTTGCGATTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:540744 original size:19 final size:19
Alignment explanation
Indices: 540720--540816 Score: 105
Period size: 19 Copynumber: 5.3 Consensus size: 19
540710 AAAATCGCAT
540720 TTGCGATTTTGGTTTCGCG
1 TTGCGATTTTGGTTTCGCG
*
540739 TTGCGATTCT-G--T--CG
1 TTGCGATTTTGGTTTCGCG
**
540753 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTGGTTTCGCG
540772 TTGCGATTTTGGTTTCGCG
1 TTGCGATTTTGGTTTCGCG
* *
540791 TTGCGATTTTAAGTTTCGTG
1 TTGCGATTTT-GGTTTCGCG
540811 TTGCGA
1 TTGCGA
540817 AAGTAAACTA
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
14 11 0.17
16 1 0.02
17 1 0.02
18 1 0.02
19 38 0.58
20 13 0.20
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTGGTTTCGCG
Found at i:541152 original size:93 final size:93
Alignment explanation
Indices: 540864--541328 Score: 877
Period size: 91 Copynumber: 5.1 Consensus size: 93
540854 ATGGATTGCA
540864 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
540928 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
540956 TTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
541019 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
541047 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
541112 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
541140 TTACTTTCAACCAAAAGACAAAAC-AA-ACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
541203 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
541231 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
* *
541296 TAGCAGAATGGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
541324 TTACT
1 TTACT
541329 AAGCAATCTA
Statistics
Matches: 366, Mismatches: 2, Indels: 9
0.97 0.01 0.02
Matches are distributed among these distances:
91 162 0.44
92 44 0.12
93 160 0.44
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:541183 original size:184 final size:184
Alignment explanation
Indices: 540864--541328 Score: 873
Period size: 184 Copynumber: 2.5 Consensus size: 184
540854 ATGGATTGCA
540864 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
540928 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAACAAAGACAAATACTA
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAACAAAGACAAATACTA
540993 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
541047 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
541112 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAA-ACAA-ACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAACA-AAGACAAATACT
541175 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
130 A-TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
541231 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
* *
541296 TAGCAGAATGGGCAGCAACCGAATAAATTTACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACT
541329 AAGCAATCTA
Statistics
Matches: 277, Mismatches: 2, Indels: 5
0.98 0.01 0.02
Matches are distributed among these distances:
183 15 0.05
184 262 0.95
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (184 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAACAAAGACAAATACTA
TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:543045 original size:14 final size:14
Alignment explanation
Indices: 543026--543115 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
543016 TTGAAATGAA
543026 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
543040 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
543059 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
543073 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
543092 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
543106 AATCACAACG
1 AATCGCAACG
543116 CGAAATGAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
14 29 0.48
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 20 0.33
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:543063 original size:33 final size:33
Alignment explanation
Indices: 543018--543132 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
543008 TCTTTTGGTT
543018 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
543051 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
543084 GAAATGAAAATCGCAACGAGAGAATCACAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
543117 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
543133 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.47, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:543064 original size:19 final size:19
Alignment explanation
Indices: 543040--543137 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
543030 GCAACGAGAG
*
543040 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
543059 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
543073 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
543092 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
543106 AATCACAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
543125 AATCGCAATGCGA
1 AATCGCAACGCGA
543138 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:543168 original size:14 final size:14
Alignment explanation
Indices: 543149--543205 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
543139 TTTGGTTTCG
543149 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
543163 CGTTGCGATTTTCATAT
1 CGTTGCGA--TTC-TCT
543180 CGCTTTGCGATTCTCT
1 CG--TTGCGATTCTCT
543196 CGTTGCGATT
1 CGTTGCGATT
543206 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:543188 original size:33 final size:33
Alignment explanation
Indices: 543146--543210 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
543136 GATTTTGGTT
543146 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
*
543179 TCGCTTTGCGATTCTCTCGTTGCGATTTTCAT
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
543211 TTCTCTCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.45
Consensus pattern (33 bp):
TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
Found at i:543246 original size:41 final size:41
Alignment explanation
Indices: 543189--543266 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
543179 TCGCTTTGCG
*
543189 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
543230 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
543267 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:543251 original size:20 final size:21
Alignment explanation
Indices: 543190--543265 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
543180 CGCTTTGCGA
543190 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
543211 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
543231 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
543252 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
543266 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:543387 original size:33 final size:33
Alignment explanation
Indices: 543345--543415 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
543335 AATACTAACT
543345 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
543378 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
543411 TGAAA
1 TGAAA
543416 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:543649 original size:22 final size:22
Alignment explanation
Indices: 543597--543651 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
543587 TGGTTGTGAG
**
543597 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
* **
543619 TGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
543641 GGATTTCTTCG
1 GGATTTCTTCG
543652 CCGTAGAGAG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.20, C:0.16, G:0.38, T:0.25
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:543823 original size:20 final size:20
Alignment explanation
Indices: 543798--543971 Score: 208
Period size: 20 Copynumber: 8.7 Consensus size: 20
543788 CTTTAAATAT
543798 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
543818 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
543840 -TCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATA
*
543859 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
543879 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
543899 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
543919 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
543939 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
543959 CGCGTTGCGATTT
1 CGCGTTGCGATTT
543972 TCATATTCGC
Statistics
Matches: 130, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
19 2 0.02
20 111 0.85
21 15 0.12
22 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:543963 original size:60 final size:60
Alignment explanation
Indices: 543800--543971 Score: 236
Period size: 60 Copynumber: 2.9 Consensus size: 60
543790 TTAAATATCG
** *
543800 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACCGATACA
* * *** * *
543861 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
*
543921 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTT
543972 TCATATTCGC
Statistics
Matches: 94, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 68 0.72
61 26 0.28
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
Found at i:543980 original size:20 final size:19
Alignment explanation
Indices: 543939--543992 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
543929 TTTACGGATA
* *
543939 CGCGTTGCGATTTATGTGTT
1 CGCGTTGCGATTT-TATATT
543959 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTT-ATATT
*
543979 CGCGTTGTGATTTT
1 CGCGTTGCGATTTT
543993 GGAAAATCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.11, C:0.17, G:0.26, T:0.46
Consensus pattern (19 bp):
CGCGTTGCGATTTTATATT
Found at i:543985 original size:60 final size:60
Alignment explanation
Indices: 543798--543991 Score: 235
Period size: 60 Copynumber: 3.2 Consensus size: 60
543788 CTTTAAATAT
** *
543798 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACAGATA
* * *** * *
543859 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
* * * * *
543919 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
*
543979 CGCGTTGTGATTT
1 CGCGTTGCGATTT
543992 TGGAAAATCG
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 82 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
Found at i:553240 original size:31 final size:31
Alignment explanation
Indices: 553191--553252 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
553181 GGTCAAGGAT
* * * *
553191 CATATTGCAAATAGACTAAATGTTGAGAGAC
1 CATATTACAAACAAACTAAATATTGAGAGAC
*
553222 CATATTACAAACAAACTAAATATTGGGAGAC
1 CATATTACAAACAAACTAAATATTGAGAGAC
553253 TGTATTAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (31 bp):
CATATTACAAACAAACTAAATATTGAGAGAC
Found at i:559420 original size:21 final size:21
Alignment explanation
Indices: 559391--559440 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
559381 TTCTTGTTCC
*
559391 TATGTAATGCTTGCGCATCAT
1 TATGCAATGCTTGCGCATCAT
559412 TATGCAATGCTTGCGCATCAT
1 TATGCAATGCTTGCGCATCAT
559433 TATGCAAT
1 TATGCAAT
559441 TGATGTGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (21 bp):
TATGCAATGCTTGCGCATCAT
Found at i:568980 original size:33 final size:34
Alignment explanation
Indices: 568938--569006 Score: 113
Period size: 33 Copynumber: 2.0 Consensus size: 34
568928 AGAGTGTTAT
*
568938 TCTTCTTAAAAACACTC-TTTTTAAAAGTTTTAA
1 TCTTCTTAAAAACACTCTTTTTTAAAAGTATTAA
568971 TCTTCTTAAAAACACTCTTTTTTTAAAAGTATTAA
1 TCTTCTTAAAAACACTC-TTTTTTAAAAGTATTAA
569006 T
1 T
569007 TTAAACAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
33 17 0.52
35 16 0.48
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.46
Consensus pattern (34 bp):
TCTTCTTAAAAACACTCTTTTTTAAAAGTATTAA
Found at i:572167 original size:2 final size:2
Alignment explanation
Indices: 572158--572190 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
572148 TCTTAAAAAA
572158 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
572191 TTTATTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:574695 original size:114 final size:117
Alignment explanation
Indices: 574463--574685 Score: 292
Period size: 114 Copynumber: 1.9 Consensus size: 117
574453 TCCTACTTTA
* * * * * * *
574463 TTATACTTGTAATTAAGATCTCTAATTTTTATAATTTTATAAAGTTTTTAGCTTTTGATAATCTT
1 TTATACTTATAATTAAGATCCCTAATTTTTATAATTTCATAAAATGTTTAGCTTTTGA-AACCCT
*
574528 TTTCCATTTCTCCTATTAATTCATTAATTTTGAATTAAATTTAACTAATTTTT
65 TTCCCATTTCTCCTATTAATTCATTAATTTTGAATTAAATTTAACTAATTTTT
* *
574581 TTATATTTATAATTAAGA-CCCTAATTTTTATAATTTCATAAAATGTTTAG-TTTTG-ACCCCTT
1 TTATACTTATAATTAAGATCCCTAATTTTTATAATTTCATAAAATGTTTAGCTTTTGAAACCCTT
* *
574643 TCCCATTTCTCTTATTTATTCATTCAATTTT-AATTAAATTTAA
66 TCCCATTTCTCCTATTAATTCATT-AATTTTGAATTAAATTTAA
574686 TCATGTTTTT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
114 37 0.40
115 6 0.07
116 5 0.05
117 28 0.30
118 16 0.17
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.52
Consensus pattern (117 bp):
TTATACTTATAATTAAGATCCCTAATTTTTATAATTTCATAAAATGTTTAGCTTTTGAAACCCTT
TCCCATTTCTCCTATTAATTCATTAATTTTGAATTAAATTTAACTAATTTTT
Found at i:577218 original size:2 final size:2
Alignment explanation
Indices: 577211--577256 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
577201 AACTTACATA
577211 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
577253 AT AT
1 AT AT
577257 CATAAATAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:577916 original size:12 final size:12
Alignment explanation
Indices: 577899--577924 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
577889 ACAACGATGA
577899 GATTTTTAAAAT
1 GATTTTTAAAAT
577911 GATTTTTAAAAT
1 GATTTTTAAAAT
577923 GA
1 GA
577925 AATGTTGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (12 bp):
GATTTTTAAAAT
Found at i:579169 original size:31 final size:31
Alignment explanation
Indices: 579134--579194 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
579124 TCCATACATA
579134 TAAAATCAGGTTT-TCATATGAAAAATTAGGC
1 TAAAATCAGGTTTCT-ATATGAAAAATTAGGC
*
579165 TAAAATCTGGTTTCTATATGAAAAATTAGG
1 TAAAATCAGGTTTCTATATGAAAAATTAGG
579195 TTCCGACCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.34
Consensus pattern (31 bp):
TAAAATCAGGTTTCTATATGAAAAATTAGGC
Found at i:579294 original size:38 final size:39
Alignment explanation
Indices: 579166--579338 Score: 206
Period size: 39 Copynumber: 4.5 Consensus size: 39
579156 AAATTAGGCT
* * * * *
579166 AAAATCTGGTTTCTATATGAAAAATTAGGTTCCGACCTA
1 AAAATCTGGTTTCTAAATGAAAAATCAGGTTGCAACATA
*
579205 AAAATCTGATTTCTAAATGAAAAATCAGGTTGCAACATA
1 AAAATCTGGTTTCTAAATGAAAAATCAGGTTGCAACATA
* * * *
579244 AAACTCTAGTTTCTAAAT-AAAAACTCATGTTACAACA-A
1 AAAATCTGGTTTCTAAATGAAAAA-TCAGGTTGCAACATA
*
579282 AAAATTTGGTTTCTAAATGAAAAATCAGGTTGCAACATA
1 AAAATCTGGTTTCTAAATGAAAAATCAGGTTGCAACATA
* *
579321 AAAATCTAGTTCCTAAAT
1 AAAATCTGGTTTCTAAAT
579339 TGATTTTTGG
Statistics
Matches: 112, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
38 32 0.29
39 80 0.71
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (39 bp):
AAAATCTGGTTTCTAAATGAAAAATCAGGTTGCAACATA
Found at i:579312 original size:20 final size:19
Alignment explanation
Indices: 579166--579326 Score: 71
Period size: 19 Copynumber: 8.3 Consensus size: 19
579156 AAATTAGGCT
* *
579166 AAAATCTGGTTTCTATATGA
1 AAAATCAGGTTTCTAAAT-A
* * * **
579186 AAAATTAGGTTCCGACCTA
1 AAAATCAGGTTTCTAAATA
* *
579205 AAAATCTGATTTCTAAATGA
1 AAAATCAGGTTTCTAAAT-A
*
579225 AAAATCAGGTTGC-AACATA
1 AAAATCAGGTTTCTAA-ATA
*
579244 AAACTCTA-GTTTCTAAATA
1 AAAATC-AGGTTTCTAAATA
* *
579263 AAAACTCATGTTAC-AACA-A
1 AAAA-TCAGGTTTCTAA-ATA
**
579282 AAAATTTGGTTTCTAAATGA
1 AAAATCAGGTTTCTAAAT-A
*
579302 AAAATCAGGTTGC-AACATA
1 AAAATCAGGTTTCTAA-ATA
579321 AAAATC
1 AAAATC
579327 TAGTTCCTAA
Statistics
Matches: 103, Mismatches: 27, Indels: 23
0.67 0.18 0.15
Matches are distributed among these distances:
18 6 0.06
19 49 0.48
20 48 0.47
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (19 bp):
AAAATCAGGTTTCTAAATA
Found at i:591999 original size:15 final size:15
Alignment explanation
Indices: 591962--592010 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
591952 TGAGGTTAGG
591962 AAATTTTA--TAAGA
1 AAATTTTATTTAAGA
591975 ACAATATTTATTTAAGA
1 A-AAT-TTTATTTAAGA
591992 AAATTTTATTTAAGA
1 AAATTTTATTTAAGA
592007 AAAT
1 AAAT
592011 AATACTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
13 1 0.03
14 3 0.09
15 19 0.59
16 3 0.09
17 6 0.19
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (15 bp):
AAATTTTATTTAAGA
Found at i:594371 original size:2 final size:2
Alignment explanation
Indices: 594364--594395 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
594354 CCATTCAGTA
594364 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
594396 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:594400 original size:2 final size:2
Alignment explanation
Indices: 594395--594430 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
594385 TCTCTCTCTC
594395 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
594431 AAACTGCACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:597162 original size:2 final size:2
Alignment explanation
Indices: 597157--597186 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
597147 TGACAAATCG
597157 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
597187 CTAGCTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:597712 original size:28 final size:28
Alignment explanation
Indices: 597672--597725 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
597662 CGTCTCCTAT
*
597672 AATTTTATAAGTTCAAGTTTACCCCTGA
1 AATTTTATAAGTTCAAATTTACCCCTGA
597700 AATTTTATAAGTTCAAATTTACCCCT
1 AATTTTATAAGTTCAAATTTACCCCT
597726 AACATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (28 bp):
AATTTTATAAGTTCAAATTTACCCCTGA
Found at i:605487 original size:12 final size:12
Alignment explanation
Indices: 605470--605494 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
605460 GTCAAATAAT
605470 TTAGGCACCAAA
1 TTAGGCACCAAA
605482 TTAGGCACCAAA
1 TTAGGCACCAAA
605494 T
1 T
605495 GGTGCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:610120 original size:12 final size:12
Alignment explanation
Indices: 610103--610127 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
610093 GTCAAATAAT
610103 TTAGGCACCAAA
1 TTAGGCACCAAA
610115 TTAGGCACCAAA
1 TTAGGCACCAAA
610127 T
1 T
610128 GGTGCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:616167 original size:30 final size:27
Alignment explanation
Indices: 616103--616167 Score: 67
Period size: 30 Copynumber: 2.3 Consensus size: 27
616093 ATAAACACTC
616103 AAAATATTATTATTTTATATATTTAACA
1 AAAATA-TATTATTTTATATATTTAACA
** *
616131 TTAATATATTATTTTATTATCATTTTAATA
1 AAAATATATTATTTTA-TAT-A-TTTAACA
616161 AAAATAT
1 AAAATAT
616168 TAATTATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 10 0.34
28 7 0.24
29 1 0.03
30 11 0.38
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (27 bp):
AAAATATATTATTTTATATATTTAACA
Found at i:616392 original size:35 final size:34
Alignment explanation
Indices: 616353--616451 Score: 92
Period size: 39 Copynumber: 2.7 Consensus size: 34
616343 TTTTAATAGT
*
616353 TTAATAATATTATTATTTTAATAAGTAATTAATA
1 TTAATAATATTATTATTTTAATAAATAATTAATA
*
616387 CTTAATAATACATTATTTTATTTTAATAAATATTTAATA
1 -TTAATAAT--ATTA--TTATTTTAATAAATAATTAATA
* *
616426 TAATTATAATATTTTTA-TTTAATAAA
1 T--TAATAATATTATTATTTTAATAAA
616452 ATATAATTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
35 17 0.31
36 3 0.06
37 4 0.07
38 4 0.07
39 20 0.37
40 6 0.11
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (34 bp):
TTAATAATATTATTATTTTAATAAATAATTAATA
Found at i:616445 original size:24 final size:25
Alignment explanation
Indices: 616417--616470 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
616407 TTTTAATAAA
*
616417 TATTTAATATAATTATAA-TAT-TTT
1 TATTTAATA-AAATATAATTATATTT
616441 TATTTAATAAAATATAATTATATTT
1 TATTTAATAAAATATAATTATATTT
616466 TATTT
1 TATTT
616471 GCATTTGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 7 0.26
24 12 0.44
25 8 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TATTTAATAAAATATAATTATATTT
Found at i:631217 original size:3 final size:3
Alignment explanation
Indices: 631209--631234 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
631199 GGGTTCTAAC
631209 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
631235 TACATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:645263 original size:19 final size:19
Alignment explanation
Indices: 645214--645255 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
645204 CACGTTTGGA
645214 AGAAGAGAAG-AGTGAAGAAG
1 AGAAGA-AAGAAG-GAAGAAG
*
645234 ATAAGAAAGAAGGAAGAAG
1 AGAAGAAAGAAGGAAGAAG
645253 AGA
1 AGA
645256 TGAGAGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.36, T:0.05
Consensus pattern (19 bp):
AGAAGAAAGAAGGAAGAAG
Found at i:650828 original size:23 final size:23
Alignment explanation
Indices: 650802--650846 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
650792 CACCACAGCT
* *
650802 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATACACCGAAGTGCCG
* *
650825 CGTAGAATTACACCGTAGTGCC
1 CGTAGAAATACACCGAAGTGCC
650847 ATATAATAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCG
Found at i:652084 original size:19 final size:19
Alignment explanation
Indices: 652035--652076 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
652025 CACGTTTGGA
652035 AGAAGAGAAG-AGTGAAGAAG
1 AGAAGA-AAGAAG-GAAGAAG
*
652055 ATAAGAAAGAAGGAAGAAG
1 AGAAGAAAGAAGGAAGAAG
652074 AGA
1 AGA
652077 TGAGAGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.36, T:0.05
Consensus pattern (19 bp):
AGAAGAAAGAAGGAAGAAG
Found at i:653214 original size:2 final size:2
Alignment explanation
Indices: 653203--653231 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
653193 AAATTTATTA
653203 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
653232 TAATTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:653270 original size:12 final size:12
Alignment explanation
Indices: 653253--653287 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
653243 TTTTAATATT
653253 TATCGGGTCGGG
1 TATCGGGTCGGG
*
653265 TATCGGGCCGGG
1 TATCGGGTCGGG
653277 TAATCGGGTCG
1 T-ATCGGGTCG
653288 AGTAATTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.11, C:0.20, G:0.46, T:0.23
Consensus pattern (12 bp):
TATCGGGTCGGG
Found at i:653292 original size:13 final size:13
Alignment explanation
Indices: 653254--653293 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
653244 TTTAATATTT
653254 ATCGGGTCGGGT-
1 ATCGGGTCGGGTA
*
653266 ATCGGGCCGGGTA
1 ATCGGGTCGGGTA
*
653279 ATCGGGTCGAGTA
1 ATCGGGTCGGGTA
653292 AT
1 AT
653294 TGGGGCGGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.17, C:0.17, G:0.42, T:0.23
Consensus pattern (13 bp):
ATCGGGTCGGGTA
Found at i:662240 original size:20 final size:20
Alignment explanation
Indices: 662212--662251 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
662202 TAAAAGGTAT
* *
662212 AAAATTAATATTTTCGATAA
1 AAAAATAATATTTTAGATAA
662232 AAAAATAATATTTTAGATAA
1 AAAAATAATATTTTAGATAA
662252 CATTTTACTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAAATAATATTTTAGATAA
Found at i:663540 original size:3 final size:3
Alignment explanation
Indices: 663527--663582 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
663517 TTTTTTATCG
663527 TTA TT- TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
*
663571 TTA TTA ATA TTA
1 TTA TTA TTA TTA
663583 CATATTACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
2 4 0.08
3 41 0.85
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:663589 original size:16 final size:16
Alignment explanation
Indices: 663527--663589 Score: 76
Period size: 16 Copynumber: 4.0 Consensus size: 16
663517 TTTTTTATCG
663527 TTATT-TTAT-TATTA
1 TTATTATTATATATTA
*
663541 TTATTATTATTTATTA
1 TTATTATTATATATTA
663557 TTATTATTATTATATTA
1 TTATTATTA-TATATTA
* *
663574 TTAATATTACATATTA
1 TTATTATTATATATTA
663590 CAATTTTTGC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
14 5 0.12
15 4 0.09
16 20 0.47
17 14 0.33
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATTATTATATATTA
Found at i:663589 original size:33 final size:33
Alignment explanation
Indices: 663527--663589 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
663517 TTTTTTATCG
* **
663527 TTATTTTATTATTATTATTATTATTTATTATTA
1 TTATTTTATTATTATTAATATTACATATTATTA
663560 TTATTATTA-TATTATTAATATTACATATTA
1 TTATT-TTATTATTATTAATATTACATATTA
663590 CAATTTTTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 23 0.88
34 3 0.12
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (33 bp):
TTATTTTATTATTATTAATATTACATATTATTA
Found at i:663684 original size:25 final size:25
Alignment explanation
Indices: 663655--663703 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
663645 CCCAACCCAT
663655 CAGATTAGGGTTTCAAACCCTAAAC
1 CAGATTAGGGTTTCAAACCCTAAAC
663680 CAGATTAGGGTTTCAAACCCTAAA
1 CAGATTAGGGTTTCAAACCCTAAA
663704 TGTTCCAGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.24
Consensus pattern (25 bp):
CAGATTAGGGTTTCAAACCCTAAAC
Found at i:667163 original size:31 final size:32
Alignment explanation
Indices: 667127--667188 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
667117 ATTTTACATG
667127 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
667158 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
667189 CATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:669650 original size:26 final size:25
Alignment explanation
Indices: 669621--669698 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 25
669611 AATTTTTGAC
669621 ATTCTATCTCTTTGAGACCTTGAAAT
1 ATTCT-TCTCTTTGAGACCTTGAAAT
* *
669647 A---TTCT-TTT-CGACCTTGAAAC
1 ATTCTTCTCTTTGAGACCTTGAAAT
* *
669667 ATTCCCTCTCTTTGAGACCTTAAAAT
1 ATT-CTTCTCTTTGAGACCTTGAAAT
669693 ATTCTT
1 ATTCTT
669699 TCCACCTTGA
Statistics
Matches: 39, Mismatches: 7, Indels: 13
0.66 0.12 0.22
Matches are distributed among these distances:
20 11 0.28
21 3 0.08
22 3 0.08
23 1 0.03
24 3 0.08
25 5 0.13
26 13 0.33
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (25 bp):
ATTCTTCTCTTTGAGACCTTGAAAT
Found at i:672073 original size:36 final size:34
Alignment explanation
Indices: 672027--672096 Score: 86
Period size: 36 Copynumber: 2.0 Consensus size: 34
672017 ATTTTTCTAA
* * *
672027 AAAATAAATTTTGTCTCGCTTGAGACAATTTATTTC
1 AAAACAAATTTCGTCTCACTTGAGAC-ATTT-TTTC
*
672063 AAAACAAATTTCGTCTCATTTGAGACATTTTTTC
1 AAAACAAATTTCGTCTCACTTGAGACATTTTTTC
672097 CTTTGAGATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 4 0.13
35 4 0.13
36 22 0.73
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (34 bp):
AAAACAAATTTCGTCTCACTTGAGACATTTTTTC
Found at i:672237 original size:196 final size:197
Alignment explanation
Indices: 671887--672277 Score: 603
Period size: 196 Copynumber: 2.0 Consensus size: 197
671877 ATTCAGTCCC
671887 TTGAGACATTTTTCCTTTGAGATCCAAATTTTGAATTTGTTTCACATTAAACAAAGTTGATCTCA
1 TTGAGACATTTTTCCTTTGAGATCCAAATTTTGAATTTGTTTCACATTAAACAAAGTTGATCTCA
* * *
671952 TTTGAGATCGTATTTATTTCAAAACAAATTTTTGTCCCTTGAGACATTTTTCCACAAACTTTGAG
66 TTTGAGATCGTATCTATTTCAAAACAAATTTTTGTCCCTGGAGACAGTTTTCCACAAACTTTGAG
*
672017 ATTTTTCTAAAAAATAAATTTTGTCTC-GC-TTGAGACAATTTATTTCAAAACAAATTTCGTCTC
131 ATATTTCTAAAAAATAAATTTTGTCTCAGCTTTGAGACAATTTATTTCAAAACAAATTTCGTCTC
672080 AT
196 AT
672082 TTGAGACATTTTTTCCTTTGAGATCCAAATTTTGAATTTGTTTCACATTAAACAAAGTTGATCTC
1 TTGAGACA-TTTTTCCTTTGAGATCCAAATTTTGAATTTGTTTCACATTAAACAAAGTTGATCTC
* *
672147 ATTTGAGATCGTATCTATTTCAAAACAAAATTTTTGTCTCACTGGAGATAGTTTTCCACAAATTT
65 ATTTGAGATCGTATCTATTTCAAAAC-AAATTTTTGTC-C-CTGGAGACAGTTTTCCACAAACTT
* * * * * *
672212 TGAGA-ATTT-TAAAACA-AATTTTTGTCTCATCTTTGAGACAATTTCTTTCAAAGCAAATTTTG
127 TGAGATATTTCTAAAAAATAAATTTTGTCTCAGCTTTGAGACAATTTATTTCAAAACAAATTTCG
672274 TCTC
192 TCTC
672278 GATCGAGACA
Statistics
Matches: 178, Mismatches: 12, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
195 8 0.04
196 92 0.52
197 18 0.10
198 35 0.20
199 25 0.14
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (197 bp):
TTGAGACATTTTTCCTTTGAGATCCAAATTTTGAATTTGTTTCACATTAAACAAAGTTGATCTCA
TTTGAGATCGTATCTATTTCAAAACAAATTTTTGTCCCTGGAGACAGTTTTCCACAAACTTTGAG
ATATTTCTAAAAAATAAATTTTGTCTCAGCTTTGAGACAATTTATTTCAAAACAAATTTCGTCTC
AT
Found at i:672308 original size:35 final size:36
Alignment explanation
Indices: 672222--672341 Score: 120
Period size: 35 Copynumber: 3.3 Consensus size: 36
672212 TGAGAATTTT
**
672222 AAAACAAATTTTTGTCTC-ATCTTTGAGACAATTTCTTTC
1 AAAACAAA-TTTTGTCTCGATC---GAGACAATTTCTTGA
* *
672261 AAAGCAAATTTTGTCTCGATCGAGACAGCTTTC-T-A
1 AAAACAAATTTTGTCTCGATCGAGACA-ATTTCTTGA
* *
672296 AAAACAAATTTTGTCTCGTTTGAGACAATTTCTTGA
1 AAAACAAATTTTGTCTCGATCGAGACAATTTCTTGA
672332 AAAACAAATT
1 AAAACAAATT
672342 CCGCCTTACT
Statistics
Matches: 70, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
34 4 0.06
35 25 0.36
36 18 0.26
37 4 0.06
38 9 0.13
39 10 0.14
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGATCGAGACAATTTCTTGA
Found at i:672525 original size:36 final size:36
Alignment explanation
Indices: 672444--672525 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 36
672434 ATTTTGTTTT
* *
672444 GCTTGAGACAATTTCTTTAAAAACAAAGTTTGTATC
1 GCTTGAGACAAATTCTTTAAAAACAAAGTTCGTATC
* * *
672480 ACTTAAGACAAATTCTCTT-AAAACAAA-TTGCGTCTC
1 GCTTGAGACAAATTCT-TTAAAAACAAAGTT-CGTATC
672516 GCTTGAGACA
1 GCTTGAGACA
672526 TTTTTCCTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
35 2 0.05
36 33 0.89
37 2 0.05
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (36 bp):
GCTTGAGACAAATTCTTTAAAAACAAAGTTCGTATC
Found at i:673091 original size:29 final size:29
Alignment explanation
Indices: 673049--673155 Score: 141
Period size: 29 Copynumber: 3.8 Consensus size: 29
673039 TTTCTCTTGA
673049 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
*
673078 AAAAATCTTGGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
* * *
673107 AAATATCTTTGAG-TCGTTTCTTTTG---
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
*
673132 AAAAATCTTTGAGTTTGTTTCTTT
1 AAAAATCTTTGAGTTTGTTCCTTT
673156 GGAAACAAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
25 12 0.17
26 9 0.13
28 10 0.14
29 39 0.56
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (29 bp):
AAAAATCTTTGAGTTTGTTCCTTTTGAAT
Found at i:673190 original size:37 final size:36
Alignment explanation
Indices: 673148--673269 Score: 123
Period size: 37 Copynumber: 3.5 Consensus size: 36
673138 CTTTGAGTTT
*
673148 GTTTCTTTGGAAACAAAATTTTTTCTCTCTTAAGATA
1 GTTTCTTTTGAAACAAAA-TTTTTCTCTCTTAAGATA
* * *
673185 GTTTCTTTTGAAACAAAA-----ATCT-TTGAG-TCT
1 GTTTCTTTTGAAACAAAATTTTTCTCTCTTAAGAT-A
673215 GTTTCTTTTGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTTGAAACAAAATTTT-TCTCTCTTAAGATA
*
673252 ATTTCTTTTGAAACAAAA
1 GTTTCTTTTGAAACAAAA
673270 ATCTTTGAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
29 1 0.01
30 22 0.32
31 3 0.04
36 3 0.04
37 38 0.56
38 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (36 bp):
GTTTCTTTTGAAACAAAATTTTTCTCTCTTAAGATA
Found at i:673228 original size:67 final size:67
Alignment explanation
Indices: 673132--673287 Score: 267
Period size: 67 Copynumber: 2.3 Consensus size: 67
673122 GTTTCTTTTG
* * *
673132 AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTTTCTCTCTTAAGATAGTTTCTTTTGAA
1 AAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAA
673197 AC
66 AC
*
673199 AAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAA
1 AAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAA
673264 AC
66 AC
*
673266 AAAAATCTTTGAATCTGTTTCT
1 AAAAATCTTTGAGTCTGTTTCT
673288 CTTAAAATGA
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 84 1.00
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.46
Consensus pattern (67 bp):
AAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAA
AC
Found at i:673668 original size:28 final size:28
Alignment explanation
Indices: 673630--673696 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
673620 GACAATTTTG
*
673630 TGAAAAAAATCTTTGAGATTGTTTCTTT
1 TGAAAAAAATCTTTGAGATTGTTTCCTT
*
673658 TGAAAAAAATCTTTGAGTTTGTTTCCTT
1 TGAAAAAAATCTTTGAGATTGTTTCCTT
673686 TGAAACAAAAT
1 TGAAA-AAAAT
673697 TGTGTCTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 31 0.86
29 5 0.14
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (28 bp):
TGAAAAAAATCTTTGAGATTGTTTCCTT
Found at i:673813 original size:35 final size:36
Alignment explanation
Indices: 673747--673821 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
673737 TATTTCTTTG
* *
673747 GAAACAAAATTTACCATCTTTGAATCTGTTTCCCTT
1 GAAACAAAATTAAACATCTTTGAATCTGTTTCCCTT
*
673783 GAAACAAAA-TAAACATCTTTGAGATC-GTTTCTCTT
1 GAAACAAAATTAAACATCTTTGA-ATCTGTTTCCCTT
673818 GAAA
1 GAAA
673822 TGAATTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35
Consensus pattern (36 bp):
GAAACAAAATTAAACATCTTTGAATCTGTTTCCCTT
Found at i:674140 original size:28 final size:28
Alignment explanation
Indices: 674090--674143 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
674080 TCAAAATCCA
* *
674090 ATCTTTGAGTTTGTTTCTATTGAAACAC
1 ATCTTTGAGTTGGTTCCTATTGAAACAC
674118 ATCTTTGAGTTGGTCTCCT-TTGAAAC
1 ATCTTTGAGTTGGT-TCCTATTGAAAC
674144 CATTATCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (28 bp):
ATCTTTGAGTTGGTTCCTATTGAAACAC
Found at i:674306 original size:43 final size:43
Alignment explanation
Indices: 674207--674539 Score: 184
Period size: 43 Copynumber: 7.7 Consensus size: 43
674197 CTTTAGATGG
* * **
674207 CCAGAACTCTTCATCACGTATGAGCCGTGTCATTCC-CCG---A
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCA-ACCATAGATAA
*
674247 CCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAA
* * * * * **
674290 CCAG-CCGTCTTCATCACGTAGGAACCATGTTATCACCTTTAGATGG
1 CCAGAAC-TCTTCATCACGTAGGAGCCGTGTCA--ACC-ATAGATAA
* * * **
674336 CCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCAG---A
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAA
* *
674376 CCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAA
* * * * * * * **
674419 ACAG-CCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGG
1 CCAGAAC-TCTTCATCACGTAGGAGCCGTGTCA--ACC-ATAGATAA
* * *
674465 CCAAGAACTCTTCATCACGTAGGAGCCGTGTC-ACCTTTAGACGAC
1 CC-AGAACTCTTCATCACGTAGGAGCCGTGTCAACC-ATAGA-TAA
* *
674510 CCA-AACTCTTCATCACGTATGAGCAGTGTC
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTC
674540 GTCCCCAACA
Statistics
Matches: 226, Mismatches: 48, Indels: 35
0.73 0.16 0.11
Matches are distributed among these distances:
39 2 0.01
40 63 0.28
42 2 0.01
43 80 0.35
44 12 0.05
45 8 0.04
46 35 0.15
47 23 0.10
48 1 0.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (43 bp):
CCAGAACTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAA
Found at i:674390 original size:129 final size:129
Alignment explanation
Indices: 674155--674497 Score: 589
Period size: 129 Copynumber: 2.7 Consensus size: 129
674145 ATTATCCTAG
*
674155 AGATAACCAGCCGTCCTCGTCATGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
*
674220 TCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCAT
66 TCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
* * *
674284 AGATAACCAGCCGTCTTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
*
674349 TCACGTATGAGTCGTGTCA-TCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
66 TCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
*
674413 AGATAAACAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAAGAACTCTTC
1 AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCC-AGAACTCTTC
*
674478 ATCACGTAGGAGCCGTGTCA
65 ATCACGTATGAGCCGTGTCA
674498 CCTTTAGACG
Statistics
Matches: 200, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
128 5 0.03
129 167 0.83
130 28 0.14
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (129 bp):
AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
TCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
Found at i:674710 original size:3 final size:3
Alignment explanation
Indices: 674697--674742 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
674687 TTTTTTATCG
*
674697 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
674743 CATATTACAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:674844 original size:25 final size:25
Alignment explanation
Indices: 674815--674863 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
674805 CCCAACCCAT
674815 CAGATTAGGGTTTCAAACCCTAAAC
1 CAGATTAGGGTTTCAAACCCTAAAC
674840 CAGATTAGGGTTTCAAACCCTAAA
1 CAGATTAGGGTTTCAAACCCTAAA
674864 TGTTCCAGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.24
Consensus pattern (25 bp):
CAGATTAGGGTTTCAAACCCTAAAC
Found at i:679522 original size:18 final size:17
Alignment explanation
Indices: 679499--679545 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
679489 CAACCCCTCC
679499 ACAAGTGCCACCCCTAA
1 ACAAGTGCCACCCCTAA
*
679516 TACAAGT-CTCACCCCTCA
1 -ACAAGTGC-CACCCCTAA
679534 A-AAGTGCCACCC
1 ACAAGTGCCACCC
679546 TGGGGCTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 9 0.35
17 3 0.12
18 14 0.54
ACGTcount: A:0.32, C:0.43, G:0.11, T:0.15
Consensus pattern (17 bp):
ACAAGTGCCACCCCTAA
Found at i:681436 original size:33 final size:33
Alignment explanation
Indices: 681390--681453 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
681380 TGGACACTAC
* * *
681390 AAGTTGTCTGAACCATGTCTTGTTACCCTGATT
1 AAGTTGTCTGAACCATGCCCTGCTACCCTGATT
681423 AAGTTG-CTCGAACCATGCCCTGCTACCCTGA
1 AAGTTGTCT-GAACCATGCCCTGCTACCCTGA
681454 CACTACAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 25 0.93
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (33 bp):
AAGTTGTCTGAACCATGCCCTGCTACCCTGATT
Found at i:681548 original size:27 final size:27
Alignment explanation
Indices: 681498--681622 Score: 99
Period size: 27 Copynumber: 4.4 Consensus size: 27
681488 TTACTCGATT
** *
681498 CATGCCCTGTTACCAAGATTCTCGAAC
1 CATGCCCTGTTACCAATCTGCTCGAAC
681525 CATGCCCTGTTACCAATCTGCTCGAAC
1 CATGCCCTGTTACCAATCTGCTCGAAC
* *
681552 CATGCCCTATTTCCTTGATCAATCTGCTCGAAC
1 CATGCCC----T-GTT-ACCAATCTGCTCGAAC
** *
681585 CATGCCCTACTACCAAAT-TGCTCAAAC
1 CATGCCCTGTTACC-AATCTGCTCGAAC
*
681612 CATTCCCTGTT
1 CATGCCCTGTT
681623 GCTTGAACCA
Statistics
Matches: 79, Mismatches: 12, Indels: 14
0.75 0.11 0.13
Matches are distributed among these distances:
27 49 0.62
28 4 0.05
29 1 0.01
31 1 0.01
32 2 0.03
33 22 0.28
ACGTcount: A:0.24, C:0.35, G:0.12, T:0.29
Consensus pattern (27 bp):
CATGCCCTGTTACCAATCTGCTCGAAC
Found at i:681713 original size:27 final size:27
Alignment explanation
Indices: 681672--681727 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
681662 TGTAGTGTCA
* *
681672 TGGTAGCAAAGCATGGTTCGAGCAACT
1 TGGTAGAAAAACATGGTTCGAGCAACT
681699 TGGTAGAAAAACATGGTTCGAGCAACT
1 TGGTAGAAAAACATGGTTCGAGCAACT
681726 TG
1 TG
681728 ATTAGGGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (27 bp):
TGGTAGAAAAACATGGTTCGAGCAACT
Found at i:683459 original size:16 final size:17
Alignment explanation
Indices: 683426--683459 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
683416 CCTTTTATTT
*
683426 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
683443 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
683459 T
1 T
683460 AATAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:683595 original size:17 final size:19
Alignment explanation
Indices: 683573--683613 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
683563 AAGTATAATG
*
683573 AATAAAA-TAAG-AGAAAA
1 AATAAAATTAAGTAAAAAA
683590 AATAAAATTAAGTAAAAAA
1 AATAAAATTAAGTAAAAAA
683609 AATAA
1 AATAA
683614 GGGTAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 4 0.19
19 10 0.48
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (19 bp):
AATAAAATTAAGTAAAAAA
Found at i:689113 original size:19 final size:20
Alignment explanation
Indices: 689077--689115 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
689067 AATAAAGACA
*
689077 TATAAAATTAATAACTAATT
1 TATAAAAATAATAACTAATT
689097 TATAAAAATAA-AACTAATT
1 TATAAAAATAATAACTAATT
689116 ACTAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
TATAAAAATAATAACTAATT
Found at i:690437 original size:3 final size:3
Alignment explanation
Indices: 690429--690549 Score: 156
Period size: 3 Copynumber: 41.0 Consensus size: 3
690419 TTAATATATT
*
690429 TAA TAA TAA TAA TAA TAA TAA -AA -AA AAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
690475 TAA TAA AAA TAA TAA AAA TAA TAA TGA TAA TAA TAT TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
690523 TAA TAA TAT TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
690550 AATGGATAAA
Statistics
Matches: 102, Mismatches: 15, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
2 4 0.04
3 98 0.96
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:690557 original size:12 final size:11
Alignment explanation
Indices: 690462--690564 Score: 59
Period size: 12 Copynumber: 8.9 Consensus size: 11
690452 AAAAATAATA
*
690462 ATAATAATAATA
1 ATAATAA-AATG
690474 ATAATAAAA--
1 ATAATAAAATG
*
690483 ATAATAAAAATA
1 ATAAT-AAAATG
* *
690495 ATAATGATAATA
1 ATAAT-AAAATG
*
690507 ATATTAATAATG
1 ATAATAA-AATG
690519 ATAATAATAAT-
1 ATAATAA-AATG
690530 ATTAATAATAATG
1 A-TAATAA-AATG
690543 ATAATAAAATGG
1 ATAATAAAAT-G
*
690555 ATAAAAAAAT
1 ATAATAAAAT
690565 AGTATCTTCA
Statistics
Matches: 77, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
9 5 0.06
10 4 0.05
11 7 0.09
12 60 0.78
13 1 0.01
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (11 bp):
ATAATAAAATG
Found at i:691042 original size:119 final size:116
Alignment explanation
Indices: 690799--691325 Score: 841
Period size: 119 Copynumber: 4.5 Consensus size: 116
690789 GCTCTTGATG
* *
690799 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTAC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCC
* * * *
690863 -CTGGTAATG-TTGATCCATCAACTGATGAATTCAAGCAAAAGGTTGAACA
66 TCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
*
690912 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCT
* *
690977 TCCTCTGGAAATG-ATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
63 TCCTCTGGAAAAGAATGATCCATCAA-GTGATGAATTCAAGCAAAAGGTTGAACA
691031 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCT
691096 TCCTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
63 TCCTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
*
691150 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TT-C
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCC
691213 TCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
66 TCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
* *
691264 AGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTTATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT
691326 ACCTTGCAAT
Statistics
Matches: 393, Mismatches: 13, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
113 37 0.09
114 109 0.28
115 3 0.01
116 42 0.11
117 3 0.01
118 19 0.05
119 168 0.43
120 12 0.03
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (116 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCC
TCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
Done.