Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 143 of 290
Found at i:45538533 original size:22 final size:24
Alignment explanation
Indices: 45538498--45538541 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
45538488 ATACGTATAA
*
45538498 ATAATATATAATATATGTAAAAAT
1 ATAATATATAATATATATAAAAAT
45538522 ATAATA-AT-ATATATATAAAA
1 ATAATATATAATATATATAAAA
45538542 TAATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 2 0.11
24 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
ATAATATATAATATATATAAAAAT
Found at i:45538546 original size:24 final size:25
Alignment explanation
Indices: 45538494--45538546 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
45538484 AATAATACGT
*
45538494 ATAA-ATAATATATAATATATGTAA
1 ATAATATAATATATAATATATGAAA
45538518 A-AATATAATA-ATATATATAT-AAA
1 ATAATATAATATATA-ATATATGAAA
45538541 ATAATA
1 ATAATA
45538547 ATTATGAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (25 bp):
ATAATATAATATATAATATATGAAA
Found at i:45538547 original size:22 final size:21
Alignment explanation
Indices: 45538496--45538548 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
45538486 TAATACGTAT
*
45538496 AAATAATATATAATATATGTAA
1 AAATAATA-ATAATATATATAA
45538518 AAAT-ATAATAATATATATATA
1 AAATAATAATAATATATATA-A
45538539 AAATAATAAT
1 AAATAATAAT
45538549 TATGAGAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 11 0.39
21 8 0.29
22 9 0.32
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AAATAATAATAATATATATAA
Found at i:45538663 original size:19 final size:20
Alignment explanation
Indices: 45538641--45538684 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
45538631 AAATAAAACA
45538641 AATAATAAAA-AATATATA-G
1 AATAATAAAATAA-ATATAGG
45538660 AATAATAAAATAAATATAGG
1 AATAATAAAATAAATATAGG
45538680 AATAA
1 AATAA
45538685 ATTTAGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (20 bp):
AATAATAAAATAAATATAGG
Found at i:45541065 original size:119 final size:119
Alignment explanation
Indices: 45540357--45541041 Score: 965
Period size: 119 Copynumber: 5.7 Consensus size: 119
45540347 TGAGTCTGTT
* * * *
45540357 TGAGAACATCTGAGAGTCAAATCTGCTATGTCCTTGATTTGTTTCTTGTAAACATAAGAATGTCA
1 TGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATATCA
* * * *
45540422 AATCATCTTGGACCTTGCTTCAGTATAAACCTCTGAAGGCTAGATCTGCCATGTC
66 AATCATCTTGGATC-TGCTTCAGTATAAACATCTGAAGGCTAGATCTGCTATATC
* * * * * *
45540477 TGAGAACATCTGAGAGTCAAATTTGCTATATCCTTGATTTGTTTCTTGTAAACATAAGAATGTCA
1 TGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATATCA
* * * * * *
45540542 AATCATCTTGGACCTTGCTTCAGTATAAACCTCTTAAGGCTAGATTTGCCATGTC
66 AATCATCTTGGATC-TGCTTCAGTATAAACATCTGAAGGCTAGATCTGCTATATC
* *
45540597 TGAGAACATCTGAGAGTCAAATCTGCTATGTCCTTGATTTGTTCCTTGTAAACACAAGAATATAA
1 TGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATATCA
* * *
45540662 AATCATCTTGGATCTGCTTTAGTATAAACATCTGAAAGCTAGATCTGCTATATT
66 AATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGCTAGATCTGCTATATC
* *
45540716 TGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCCTGTAAACACAAGAATACCA
1 TGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATATCA
* * *
45540781 AATCATCTTGGATTTGCTTCAGTATAAACATCTGAAAGCTAGATCTGCTATATT
66 AATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGCTAGATCTGCTATATC
* * *
45540835 TGAGAACATGTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATACCA
1 TGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATATCA
* * *
45540900 AATCATCTTGGATCTACTTCAGTATAAACATCTGAAGGTTAGATCTGTTATATC
66 AATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGCTAGATCTGCTATATC
* * * * * * *
45540954 TAAGAACGTTTGAGAGTCAAATCTGTTATGTCCTCGATTCGTTCCTTGTAAACACAAGAATGTGA
1 TGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATATCA
45541019 AATCATCTTGGATCTGCTTCAGT
66 AATCATCTTGGATCTGCTTCAGT
45541042 CTAATTGTAT
Statistics
Matches: 521, Mismatches: 44, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
119 333 0.64
120 188 0.36
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (119 bp):
TGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATATCA
AATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGCTAGATCTGCTATATC
Found at i:45553143 original size:21 final size:20
Alignment explanation
Indices: 45553117--45553176 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
45553107 AATTTTAAAT
45553117 AATATATATATAATATAATAA
1 AATATATATATAATATAAT-A
*
45553138 AATATATGGGAAATAATATAATA
1 AATATAT---ATATAATATAATA
*
45553161 AATATAGCATATAATA
1 AATATA-TATATAATA
45553177 ATGAAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
21 14 0.44
23 7 0.22
24 11 0.34
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (20 bp):
AATATATATATAATATAATA
Found at i:45553254 original size:22 final size:21
Alignment explanation
Indices: 45553196--45553310 Score: 77
Period size: 18 Copynumber: 5.8 Consensus size: 21
45553186 TATATGTAAA
* *
45553196 AATAATATGTATAAATAAATGT
1 AATAATATATATAAA-AAATAT
*
45553218 -ATAATATATGT-AAAAATAT
1 AATAATATATATAAAAAATAT
*
45553237 AATAATATATATAGAAAAAAAT
1 AATAATATATATA-AAAAATAT
* * *
45553259 AATAAT-TAT-GAGAGAAT-T
1 AATAATATATATAAAAAATAT
*
45553277 AAT-ATATA-ATAAACAAT-T
1 AATAATATATATAAAAAATAT
45553295 -ATAATATATATAAAAA
1 AATAATATATATAAAAA
45553311 TAACACTTAT
Statistics
Matches: 73, Mismatches: 13, Indels: 17
0.71 0.13 0.17
Matches are distributed among these distances:
17 4 0.05
18 17 0.23
19 14 0.19
20 13 0.18
21 12 0.16
22 13 0.18
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (21 bp):
AATAATATATATAAAAAATAT
Found at i:45553382 original size:19 final size:19
Alignment explanation
Indices: 45553358--45553394 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
45553348 AATAAAACAA
*
45553358 ATAATAAAATATATATAGC
1 ATAATAAAATAAATATAGC
45553377 ATAATAAAATAAATATAG
1 ATAATAAAATAAATATAG
45553395 GACTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (19 bp):
ATAATAAAATAAATATAGC
Found at i:45558281 original size:775 final size:787
Alignment explanation
Indices: 45557318--45558766 Score: 2279
Period size: 775 Copynumber: 1.8 Consensus size: 787
45557308 AATTTAAGTA
45557318 TTTAAAAGAATTAGATAAAATTTGAAATTTTTATATAATTTTTTATGTAAGAAAACAAAAACAAA
1 TTTAAAAGAATTAGATAAAATTTGAAATTTTTATATAATTTTTTATGTAAGAAAAC-AAAACAAA
*
45557383 AAATTTCAAAATATGAAAAAAAAAAACTAAAAAGCTTTAAAAAAATTCTCTTTTGTAGTTATATA
65 AAATTTCAAAATATGAAAAAAAAAAACTAAAAAGCTTTAAAAAAATTCTCTTTTGTAATTATATA
45557448 TTCTTTCAATATTTTAGGAAATTTAAATAACTTTTTTCAATATACTAATTAATTTTGTTTCTATA
130 TTCTTTCAATATTTTAGGAAATTTAAATAACTTTTTTCAATATACTAATTAATTTTGTTTCTATA
45557513 GAGATACATGGGTTAGCAA-TTATTTTAATTTTAATATATATAAAATTTATCTATTATCTCTTAA
195 GAGATACATGGGTTAGCAACTT-TTTTAATTTTAATATATATAAAATTTATCTATTATCTCTTAA
* * *
45557577 ATAATTTAAACTATAATGTTAATTTTAATATATTAAAATTAATATTATTTATTTTACAATTATAT
259 ATAATTTAAACTATAATGATAATTTTAATATATTAAAATTAATATTATCTATTTTAAAATTATAT
45557642 AAGAAATTAATTAATATAT-AA-AATAAAA-AA-A-TCA-AT-C-A-TTTAAATAATAGTATTTT
324 AAGAAATTAATTAATATATGAATAA-AAAACAACAGTCATATACAATTTTAAATAATAGTATTTT
* * *
45557698 AATTTTTTTCATTTTTAACGTATAT-T-TTTCTATGTTTTTACTTTCAATTTTTTTCTCTGTGTC
388 AA-TTTTTTCATTTTTAACATATATATATTTCTATGTTTTTACTTTCAAATTTTTTCTATGTGTC
*
45557761 ATTA-TTTTTTTGAAGATTTTAAATATTAAATTAAAAATAAATTTTATTTTAATTAATATAAAGA
452 ATTATTTTTTTTGAAGATTTTAAATATTAAATTAAAAATAAATTGTATTTTAATTAATATAAAGA
45557825 AAGTAGTTAAATAATAAATAGAAAAGGATGAAAGAGTACATGAGTTGTTGAAAAGAATACATGAT
517 AAGTAGTTAAATAATAAATAGAAAAGGATGAAAGAGTACATGAGTTGTTGAAAAGAATACATGAT
* *
45557890 GGACATTTGGATGATGGGTGAGAATATAGGGAGCAAAACAACG-CTATTTTGTTTAAAATAAAAT
582 GGACACTTGGATGATGGGTGAGAATACAGGGAGCAAAACAACGTC-ATTTTGTTTAAAATAAAAT
45557954 GATATTTTGCGGCGTTTTTGATAAAAACGCCGATATTGCTTACCTTTTGTGGTGTTTTTCTCATA
646 GATATTTTGCGGCGTTTTTGATAAAAACGCCGATATTGCTTACCTTTTGTGGTGTTTTTCTCATA
45558019 AACGCGGCTAATGCTTGACTTTTTTTAATAACATATGAGCAATTTTTATATTGAATTATTATATC
711 AACGCGGCTAATGCTTGACTTTTTTTAATAACATATGAGCAATTTTTATATTGAATTATTATATC
45558084 TTTCATATCAAT
776 TTTCATATCAAT
* *
45558096 TTTAAAAGAATTAGATAAAATTTGAATTTTTTATATAATTTTTTATGTAAGAAAAC-AAA-AAAG
1 TTTAAAAGAATTAGATAAAATTTGAAATTTTTATATAATTTTTTATGTAAGAAAACAAAACAAAA
45558159 AATTTCAAAATATG-AAAAAAAAAACTAAAAAGCTTTTAAAAAAAATTTCTCTTTTGTAATTATA
66 AATTTCAAAATATGAAAAAAAAAAACTAAAAAGC-TTT-AAAAAAA-TTCTCTTTTGTAATTATA
* *
45558223 TATTCTTTCAA-ATTTTAGGAAATTTAAATAAC-TTTTTCAATTTACTAATTAATTTTGTTTCTC
128 TATTCTTTCAATATTTTAGGAAATTTAAATAACTTTTTTCAATATACTAATTAATTTTGTTTCTA
** *
45558286 TAGAGATGTATGGGTTAGCAACTTTTTTAATTTTAATATATATAAAGTTTATCTATTATCTCTTA
193 TAGAGATACATGGGTTAGCAACTTTTTTAATTTTAATATATATAAAATTTATCTATTATCTCTTA
*
45558351 AATAATTTAAACTATAATGATAATTTTAATATATTAAAATTAATATTATCTCTTTTAAAATTATA
258 AATAATTTAAACTATAATGATAATTTTAATATATTAAAATTAATATTATCTATTTTAAAATTATA
*
45558416 TAATAAATTAATTAATATATGAATTAAAAAACAATCAGTCATATACCCAAAAAACTTTAAAATAA
323 TAAGAAATTAATTAATATATGAA-TAAAAAACAA-CAGTCATAT---------AC--------AA
*
45558481 TTTTAAATAATAGTATTTTAATTTTTTCATTTTTAACATATATATATTTTTATGTTTTTACTTTC
369 TTTTAAATAATAGTATTTTAATTTTTTCATTTTTAACATATATATATTTCTATGTTTTTACTTTC
45558546 AAATTTTTTCTATGTGTCATTATTTTTTTTGAAGATTTTAAATATTAAATTAAAAATAAATTGTA
434 AAATTTTTTCTATGTGTCATTATTTTTTTTGAAGATTTTAAATATTAAATTAAAAATAAATTGTA
* *
45558611 TTTTAATTAATATAAAGAAAGTAGTTAAATAATAAATAGAAGAGGATGAAAGAGTGCATGAGTTG
499 TTTTAATTAATATAAAGAAAGTAGTTAAATAATAAATAGAAAAGGATGAAAGAGTACATGAGTTG
* * * *
45558676 TTGAAAAGAATACATGATGGGCACTTGGATTATGGGTGAGAATACAGGGAGCAAAACAGCGTCGT
564 TTGAAAAGAATACATGATGGACACTTGGATGATGGGTGAGAATACAGGGAGCAAAACAACGTCAT
*
45558741 TTTGTTTAAAATAAAATGATTTTTTG
629 TTTGTTTAAAATAAAATGATATTTTG
45558767 TAGTGTGCTA
Statistics
Matches: 608, Mismatches: 27, Indels: 46
0.89 0.04 0.07
Matches are distributed among these distances:
774 19 0.03
775 188 0.31
776 35 0.06
777 32 0.05
778 59 0.10
780 1 0.00
781 3 0.00
782 2 0.00
792 1 0.00
801 22 0.04
802 21 0.03
803 38 0.06
804 186 0.31
805 1 0.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (787 bp):
TTTAAAAGAATTAGATAAAATTTGAAATTTTTATATAATTTTTTATGTAAGAAAACAAAACAAAA
AATTTCAAAATATGAAAAAAAAAAACTAAAAAGCTTTAAAAAAATTCTCTTTTGTAATTATATAT
TCTTTCAATATTTTAGGAAATTTAAATAACTTTTTTCAATATACTAATTAATTTTGTTTCTATAG
AGATACATGGGTTAGCAACTTTTTTAATTTTAATATATATAAAATTTATCTATTATCTCTTAAAT
AATTTAAACTATAATGATAATTTTAATATATTAAAATTAATATTATCTATTTTAAAATTATATAA
GAAATTAATTAATATATGAATAAAAAACAACAGTCATATACAATTTTAAATAATAGTATTTTAAT
TTTTTCATTTTTAACATATATATATTTCTATGTTTTTACTTTCAAATTTTTTCTATGTGTCATTA
TTTTTTTTGAAGATTTTAAATATTAAATTAAAAATAAATTGTATTTTAATTAATATAAAGAAAGT
AGTTAAATAATAAATAGAAAAGGATGAAAGAGTACATGAGTTGTTGAAAAGAATACATGATGGAC
ACTTGGATGATGGGTGAGAATACAGGGAGCAAAACAACGTCATTTTGTTTAAAATAAAATGATAT
TTTGCGGCGTTTTTGATAAAAACGCCGATATTGCTTACCTTTTGTGGTGTTTTTCTCATAAACGC
GGCTAATGCTTGACTTTTTTTAATAACATATGAGCAATTTTTATATTGAATTATTATATCTTTCA
TATCAAT
Found at i:45558530 original size:31 final size:31
Alignment explanation
Indices: 45558481--45558539 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
45558471 TTTAAAATAA
45558481 TTTTAAATAATAGTATTTTAAT-TTTTTCAT
1 TTTTAAATAATAGTATTTTAATGTTTTTCAT
*
45558511 TTTTAACATATATA-TATTTTTATGTTTTT
1 TTTTAA-ATA-ATAGTATTTTAATGTTTTT
45558540 ACTTTCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 6 0.24
31 11 0.44
32 8 0.32
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (31 bp):
TTTTAAATAATAGTATTTTAATGTTTTTCAT
Found at i:45565350 original size:23 final size:23
Alignment explanation
Indices: 45565308--45565351 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
45565298 AGGCATCACA
* **
45565308 GAATACGCCACACATTCTTTACT
1 GAATACGCCACAAAGGCTTTACT
45565331 GAATACGCCACAAAGGCTTTA
1 GAATACGCCACAAAGGCTTTA
45565352 TAGAAAATTA
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:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (23 bp):
GAATACGCCACAAAGGCTTTACT
Found at i:45567741 original size:28 final size:28
Alignment explanation
Indices: 45567683--45567752 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
45567673 CCTAATAGAT
* * *
45567683 TTCCACTTATAAGATAGTCCTACCGGGC
1 TTCCACATATAAGATAGTCCTACCAGAC
*
45567711 TTCCACATATAAGGTAGTCCTGA-CAGAC
1 TTCCACATATAAGATAGTCCT-ACCAGAC
**
45567739 TTCCATTTATAAGA
1 TTCCACATATAAGA
45567753 CAATCTTGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
28 33 0.97
29 1 0.03
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (28 bp):
TTCCACATATAAGATAGTCCTACCAGAC
Found at i:45569885 original size:29 final size:29
Alignment explanation
Indices: 45569851--45569924 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
45569841 TAATCAACCG
*
45569851 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
45569880 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
45569909 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
45569925 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:45578029 original size:29 final size:29
Alignment explanation
Indices: 45577995--45578068 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
45577985 TAATCAACCG
*
45577995 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
45578024 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
45578053 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
45578069 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:45583201 original size:43 final size:43
Alignment explanation
Indices: 45583139--45583224 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
45583129 GATTTATGTG
*
45583139 GCATCCGAGCTCGTCGAGTGGTCTGAGTTCATAATGGATGCGA
1 GCATCCGAGCTCATCGAGTGGTCTGAGTTCATAATGGATGCGA
*
45583182 GCATCCGAGCTCATTGAGTGGTCTGAGTTCATAATGGATGCGA
1 GCATCCGAGCTCATCGAGTGGTCTGAGTTCATAATGGATGCGA
45583225 TACATGTGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (43 bp):
GCATCCGAGCTCATCGAGTGGTCTGAGTTCATAATGGATGCGA
Found at i:45588911 original size:15 final size:15
Alignment explanation
Indices: 45588844--45588916 Score: 76
Period size: 15 Copynumber: 4.9 Consensus size: 15
45588834 TATGATATTG
45588844 TATCTTGGATTT-TT
1 TATCTTGGATTTCTT
*
45588858 GTACCTTGGATTTCTT
1 -TATCTTGGATTTCTT
*
45588874 TATCTAGGATTTCTT
1 TATCTTGGATTTCTT
* *
45588889 TGTCTTGGACTTCTT
1 TATCTTGGATTTCTT
* *
45588904 TATTTTGGTTTTC
1 TATCTTGGATTTC
45588917 ATGTCATCTC
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
15 45 0.96
16 2 0.04
ACGTcount: A:0.12, C:0.14, G:0.16, T:0.58
Consensus pattern (15 bp):
TATCTTGGATTTCTT
Found at i:45594883 original size:7 final size:7
Alignment explanation
Indices: 45594871--45594902 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
45594861 AAGTATAAGG
45594871 CCTAAAC
1 CCTAAAC
45594878 CCTAAAC
1 CCTAAAC
45594885 CCTAAAC
1 CCTAAAC
45594892 CCTAAAC
1 CCTAAAC
45594899 CCTA
1 CCTA
45594903 CATGCGGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.16
Consensus pattern (7 bp):
CCTAAAC
Found at i:45595745 original size:24 final size:25
Alignment explanation
Indices: 45595718--45595774 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 25
45595708 ATGAATACAA
*
45595718 ATATTTTTTTAAATA-TAATAAATT
1 ATATTTTTTTAAATATTAATAAAGT
*
45595742 ATATTTATTTAAATATTAATAAAGT
1 ATATTTTTTTAAATATTAATAAAGT
45595767 A-ATTTTTT
1 ATATTTTTT
45595775 CTCATACATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 20 0.69
25 9 0.31
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
ATATTTTTTTAAATATTAATAAAGT
Found at i:45611797 original size:44 final size:44
Alignment explanation
Indices: 45611734--45612320 Score: 946
Period size: 44 Copynumber: 13.3 Consensus size: 44
45611724 TTACCGATAG
* *
45611734 CAGATTTGGCATCTCTGTATTGACAGAGAGCAAATCAAAGATGA
1 CAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* *
45611778 CAGATTTGGCTTCTCTGTATTGACAGAGAGCAGATCAAAGATGA
1 CAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATGA
*
45611822 CAGATTTGGCATCTCTGTATTGACAGAGAGCAAATCGAAGATGA
1 CAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATGA
*
45611866 CAAATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATGA
1 CAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* * *
45611910 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCAAAGAT-A
1 CAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATGA
45611953 GCAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATGA
1 -CAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* *
45611998 TAGATTTGGCATATCTGTATTGACAGAGAGCAGATCGAAGATGA
1 CAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATGA
*
45612042 CAGATTTGACATCTCTGTATTGACAGAGAGCAGATCGAAGATGA
1 CAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* *
45612086 CAGATTTGACATCTCTGTATTGACAGAGAGCAGATCAAAGAT-A
1 CAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATGA
*
45612129 GCAGATTTGGCATCTCTGTATTGACAGAAAGCAGATCGAAGAT-A
1 -CAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATGA
*
45612173 GCAGATTTGGCATCTCTGTATTGACAGAAAGCAGATCGAAGATGA
1 -CAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATGA
45612218 CAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATGA
1 CAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* *
45612262 CAGATTTGGCATCTCTGTTTTGACAGAGAGCAGATCGAAGAGGA
1 CAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* *
45612306 TAGATTTGGCCTCTC
1 CAGATTTGGCATCTC
45612321 CGCATTAGGC
Statistics
Matches: 511, Mismatches: 28, Indels: 8
0.93 0.05 0.01
Matches are distributed among these distances:
43 2 0.00
44 507 0.99
45 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (44 bp):
CAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATGA
Found at i:45613918 original size:18 final size:17
Alignment explanation
Indices: 45613895--45613937 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
45613885 AGTATATATC
45613895 TTATTTTTATTCATTATA
1 TTATTTTTATT-ATTATA
*
45613913 TTATTTATATTATTATA
1 TTATTTTTATTATTATA
45613930 TATATTTT
1 T-TATTTT
45613938 CTTTATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTTTTATTATTATA
Found at i:45615948 original size:22 final size:22
Alignment explanation
Indices: 45615907--45615948 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
45615897 GTATTGGTAC
*
45615907 TTGCAAGCCAATAGTTAAGAAA
1 TTGCAAGCCAATAGTCAAGAAA
45615929 TTGCAAGCCAACTA-TCAAGA
1 TTGCAAGCCAA-TAGTCAAGA
45615949 CTTGCTCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (22 bp):
TTGCAAGCCAATAGTCAAGAAA
Found at i:45635993 original size:26 final size:26
Alignment explanation
Indices: 45635957--45636009 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
45635947 CCATGAGAAG
45635957 TTAACCAATCCATCCCAAGGATTACA
1 TTAACCAATCCATCCCAAGGATTACA
45635983 TTAACCAATCCATCCCAAGGATTACA
1 TTAACCAATCCATCCCAAGGATTACA
45636009 T
1 T
45636010 CAAATTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.30, G:0.08, T:0.25
Consensus pattern (26 bp):
TTAACCAATCCATCCCAAGGATTACA
Found at i:45642229 original size:46 final size:45
Alignment explanation
Indices: 45642135--45642343 Score: 154
Period size: 46 Copynumber: 4.5 Consensus size: 45
45642125 ATATCTGTGT
* * * *
45642135 CGATGCCATATCCCAGACATGGTCTTACACAGGC-ACCTCTCGTA-GC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTCGTCTCG-AGGC
*
45642181 CGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTTGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTT-CGTCTCGAGGC
** * * * *
45642227 CGAAACATGTCCCAGACATGTCTTACACTAGCACTCGTCTCAATGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGC-TTCGTCTCGAGGC
* * * * * * *
45642273 TGATGTTATGTCCCAAACATGGTCTTACATTGGCTCTCATAAT-GTGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TCGT-CTCGAGGC
45642321 CGATGCATGTCCCAGACATGTCT
1 CGATGCATGTCCCAGACATGTCT
45642344 AATTGCCCTT
Statistics
Matches: 127, Mismatches: 28, Indels: 16
0.74 0.16 0.09
Matches are distributed among these distances:
44 12 0.09
45 14 0.11
46 55 0.43
47 25 0.20
48 20 0.16
49 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.27
Consensus pattern (45 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCTTCGTCTCGAGGC
Found at i:45647590 original size:119 final size:120
Alignment explanation
Indices: 45647412--45647634 Score: 319
Period size: 119 Copynumber: 1.9 Consensus size: 120
45647402 TACTCGTTCA
* *
45647412 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGAGACATAGTCCGGTT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGAGACATAGTCCGGAT
*
45647477 ATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* *
45647532 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTCG-GATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGAGA-CATAGTCCGG
* * *
45647594 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
45647635 CATCATTCGA
Statistics
Matches: 92, Mismatches: 8, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
118 3 0.03
119 69 0.75
120 20 0.22
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGAGACATAGTCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:45647634 original size:40 final size:40
Alignment explanation
Indices: 45647391--45647634 Score: 282
Period size: 40 Copynumber: 6.1 Consensus size: 40
45647381 CAGAATTTAA
** *
45647391 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * * *
45647431 CCGGTTATAGTAACTCGCACAAATGCCTTCGAGACATAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
45647471 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
45647511 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
45647550 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
45647590 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
45647630 CCGGA
1 CCGGA
45647635 CATCATTCGA
Statistics
Matches: 177, Mismatches: 20, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
38 2 0.01
39 33 0.19
40 130 0.73
41 12 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:45648063 original size:23 final size:23
Alignment explanation
Indices: 45648012--45648068 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 23
45648002 AAAGGATGGA
45648012 CACATTTT-TTTTCTTTTGTTTT
1 CACATTTTCTTTTCTTTTGTTTT
*
45648034 CATCATTTTCTTTCTCTTTTTTTTT
1 CA-CATTTTCTTT-TCTTTTGTTTT
45648059 C-CA-TTTCTTT
1 CACATTTTCTTT
45648069 ATTACTAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
22 9 0.29
23 8 0.26
24 3 0.10
25 11 0.35
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (23 bp):
CACATTTTCTTTTCTTTTGTTTT
Found at i:45651257 original size:23 final size:23
Alignment explanation
Indices: 45651231--45651277 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
45651221 CAAACTCTAC
45651231 TCCCGAACAGGTGGTAAACCCGG
1 TCCCGAACAGGTGGTAAACCCGG
45651254 TCCCGAACAGGTGGTAAACCCGG
1 TCCCGAACAGGTGGTAAACCCGG
45651277 T
1 T
45651278 AATTCTTCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.15
Consensus pattern (23 bp):
TCCCGAACAGGTGGTAAACCCGG
Found at i:45654781 original size:119 final size:120
Alignment explanation
Indices: 45654603--45654818 Score: 305
Period size: 119 Copynumber: 1.8 Consensus size: 120
45654593 TACTCGTTCA
* *
45654603 AATGCCTTCAGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACATAGTCCGGTT
1 AATGCCTTCAGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACATAGTCCGGAT
*
45654668 ATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCTAGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCTAGATTTAGTAACTCGCACC
* * *
45654723 AATGCCTTC-GGGCTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCAGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CATAGTCCGG
* *
45654785 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTA
45654819 GCCCGGACAT
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
118 4 0.05
119 64 0.75
120 17 0.20
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.25
Consensus pattern (120 bp):
AATGCCTTCAGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACATAGTCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCTAGATTTAGTAACTCGCACC
Found at i:45654809 original size:79 final size:80
Alignment explanation
Indices: 45654627--45654825 Score: 219
Period size: 79 Copynumber: 2.5 Consensus size: 80
45654617 ATAGCCCGGT
* * * *
45654627 TATAGTAACTCGCACAAATGCCTTCGGGACATAGTCCGG-TTATAGTAACTCGCACAAATGCCTT
1 TATAGTAACTAGCACAAA-GCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTT
45654691 CGGGACTTAACCTAGA
65 CGGGACTTAACCTAGA
* * *
45654707 TTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTT
1 TATAGTAACTAGCA-CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTT
* *
45654770 C-GGATCTTAGTCC-GGA
65 CGGGA-CTTA-ACCTAGA
* *
45654786 TATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 TATAGTAAC-TAGCACAAAGCCTTCGGGACTTAGCCCGGA
45654826 CATCATTCGA
Statistics
Matches: 101, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
78 3 0.03
79 55 0.54
80 40 0.40
81 3 0.03
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (80 bp):
TATAGTAACTAGCACAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC
GGGACTTAACCTAGA
Found at i:45654825 original size:40 final size:40
Alignment explanation
Indices: 45654582--45654825 Score: 264
Period size: 40 Copynumber: 6.1 Consensus size: 40
45654572 CAGAATTTAA
** * *
45654582 CCGGATATAGCT-ACTCGTTCAAATGCCTTCAGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
45654622 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACATAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
45654662 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
** * *
45654702 CTAGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
45654741 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
45654781 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
45654821 CCGGA
1 CCGGA
45654826 CATCATTCGA
Statistics
Matches: 174, Mismatches: 23, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.01
39 31 0.18
40 129 0.74
41 12 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:45655255 original size:23 final size:24
Alignment explanation
Indices: 45655203--45655260 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
45655193 AAAGGATGGA
*
45655203 CACATTTT-TTTTTCTTTTGTTTT
1 CACATTTTCTTTCTCTTTTGTTTT
*
45655226 CATCATTTTCTTTCTCTTTTTTTTT
1 CA-CATTTTCTTTCTCTTTTGTTTT
45655251 C-CA-TTTCTTT
1 CACATTTTCTTT
45655261 ATTACTAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 7 0.23
23 4 0.13
24 6 0.19
25 14 0.45
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.71
Consensus pattern (24 bp):
CACATTTTCTTTCTCTTTTGTTTT
Found at i:45657707 original size:24 final size:24
Alignment explanation
Indices: 45657674--45657800 Score: 190
Period size: 23 Copynumber: 5.4 Consensus size: 24
45657664 CTAGAGGCCT
45657674 AGCCTCTTTTAATAACTGGGGCA-A
1 AGCC-CTTTTAATAACTGGGGCATA
45657698 AGCCCTTTTTAATAACTGGGGCATA
1 AGCCC-TTTTAATAACTGGGGCATA
*
45657723 AG-CCATTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
45657746 AG-CCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
45657769 AGCCC-TTTAATAACTAGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
45657792 AGCCCTTTT
1 AGCCCTTTT
45657801 GCACTTCCTC
Statistics
Matches: 96, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
23 65 0.68
24 28 0.29
25 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:45657874 original size:20 final size:20
Alignment explanation
Indices: 45657849--45657915 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
45657839 TTATAAATAC
45657849 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
45657869 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
45657889 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
45657909 ACCATGT
1 ATCATGT
45657916 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:45657880 original size:11 final size:11
Alignment explanation
Indices: 45657849--45657904 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
45657839 TTATAAATAC
45657849 ATCATGTGCAT
1 ATCATGTGCAT
*
45657860 ATCA--TACAT
1 ATCATGTGCAT
45657869 ATCATGTGCAT
1 ATCATGTGCAT
*
45657880 ATCA--TACAT
1 ATCATGTGCAT
*
45657889 GTCATGTGCAT
1 ATCATGTGCAT
45657900 ATCAT
1 ATCAT
45657905 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:45657984 original size:25 final size:25
Alignment explanation
Indices: 45657952--45657999 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
45657942 ATGTATAAAC
* * *
45657952 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
45657977 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
45658000 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:45660006 original size:45 final size:46
Alignment explanation
Indices: 45659923--45660010 Score: 115
Period size: 45 Copynumber: 1.9 Consensus size: 46
45659913 ATAAATGGTG
*
45659923 AAATAGAGAAATAGAAAACATATAGAAACGATTATGGTTTTCTCCA
1 AAATAGAGAAATAGAAAACATATAGAAACGAATATGGTTTTCTCCA
* * * * *
45659969 AAATGGAGAAAT-GAAATCATTTGGAAATGAATATGGTTTTCT
1 AAATAGAGAAATAGAAAACATATAGAAACGAATATGGTTTTCT
45660011 AAAAAAACAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 25 0.69
46 11 0.31
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (46 bp):
AAATAGAGAAATAGAAAACATATAGAAACGAATATGGTTTTCTCCA
Found at i:45665999 original size:17 final size:18
Alignment explanation
Indices: 45665972--45666005 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
45665962 ATATAATAAA
45665972 AGAATAAAGAAAGAAAAT
1 AGAATAAAGAAAGAAAAT
45665990 AGAA-AAAGAAAGAAAA
1 AGAATAAAGAAAGAAAA
45666006 AACAGACAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (18 bp):
AGAATAAAGAAAGAAAAT
Found at i:45673193 original size:17 final size:18
Alignment explanation
Indices: 45673166--45673199 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
45673156 ATATAATAAA
*
45673166 AGAATAAAGAAATAAAAT
1 AGAATAAAGAAAGAAAAT
45673184 AGAA-AAAGAAAGAAAA
1 AGAATAAAGAAAGAAAA
45673200 AACAGACAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (18 bp):
AGAATAAAGAAAGAAAAT
Found at i:45677397 original size:26 final size:26
Alignment explanation
Indices: 45677359--45677411 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
45677349 ATATAAATGC
* *
45677359 ATCCCCAATGATCATTTCTTGTACTA
1 ATCCCCAAGGATCATTTCTTCTACTA
45677385 ATCCCCAAGGATCATTTCTTCTACTA
1 ATCCCCAAGGATCATTTCTTCTACTA
45677411 A
1 A
45677412 CATGGAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (26 bp):
ATCCCCAAGGATCATTTCTTCTACTA
Found at i:45678394 original size:3 final size:3
Alignment explanation
Indices: 45678388--45678416 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
45678378 CACAACAATT
45678388 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
45678417 TTGTCAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:45679669 original size:5 final size:5
Alignment explanation
Indices: 45679656--45679727 Score: 74
Period size: 5 Copynumber: 14.4 Consensus size: 5
45679646 TTTCATATTG
* * *
45679656 TATCA TATCT TATCA TATCA TAACA TATCA TATCA TACCA TATCGA -ATCA
1 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATC-A TATCA
* * *
45679706 TAGCA TATCT TATCA TGTCA TA
1 TATCA TATCA TATCA TATCA TA
45679728 GAATGTCCTA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
4 1 0.02
5 51 0.96
6 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.38
Consensus pattern (5 bp):
TATCA
Found at i:45681931 original size:16 final size:16
Alignment explanation
Indices: 45681910--45681940 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
45681900 TTCAGACTTG
45681910 AATTTTCTCAAGCTTT
1 AATTTTCTCAAGCTTT
*
45681926 AATTTTTTCAAGCTT
1 AATTTTCTCAAGCTT
45681941 GGATTAGCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (16 bp):
AATTTTCTCAAGCTTT
Found at i:45687572 original size:26 final size:26
Alignment explanation
Indices: 45687541--45687641 Score: 108
Period size: 26 Copynumber: 4.2 Consensus size: 26
45687531 TGAAATGCCC
*
45687541 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
45687567 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
45687593 A--AT-----ATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
45687612 ACCATGGAGCATTTACCTAACCCATG
1 ATCATGGAACATTTACCTAACCCATT
45687638 ATCA
1 ATCA
45687642 ATTTGTACCA
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
19 16 0.25
21 2 0.03
24 2 0.03
26 43 0.68
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:45687611 original size:45 final size:45
Alignment explanation
Indices: 45687551--45687636 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
45687541 ATCATGGAAC
*
45687551 ATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATTAAT
1 ATTTACCTAAACCATTACCATGGAACATTTACCTAACCCATTAAT
* *
45687596 ATTTACCTAATCCATTACCATGGAGCATTTACCTAACCCAT
1 ATTTACCTAAACCATTACCATGGAACATTTACCTAACCCAT
45687637 GATCAATTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.33
Consensus pattern (45 bp):
ATTTACCTAAACCATTACCATGGAACATTTACCTAACCCATTAAT
Found at i:45689106 original size:7 final size:7
Alignment explanation
Indices: 45689073--45689205 Score: 82
Period size: 7 Copynumber: 19.7 Consensus size: 7
45689063 TACTTAGTAT
*
45689073 TCAATCC
1 TCAATTC
*
45689080 TCAATCC
1 TCAATTC
*
45689087 TAAATTC
1 TCAATTC
45689094 TCAATTC
1 TCAATTC
*
45689101 TCAATTT
1 TCAATTC
* * *
45689108 TTAGTCC
1 TCAATTC
*
45689115 TCAATTT
1 TCAATTC
45689122 TC-A-T-
1 TCAATTC
*
45689126 TCAATTG
1 TCAATTC
*
45689133 TCAATTG
1 TCAATTC
45689140 TCAATTC
1 TCAATTC
45689147 TCAA-TC
1 TCAATTC
45689153 TTCAA-TC
1 -TCAATTC
45689160 -CAATTC
1 TCAATTC
45689166 TCAATTC
1 TCAATTC
*
45689173 TGAA-TC
1 TCAATTC
*
45689179 ATCAATCC
1 -TCAATTC
*
45689187 TTAATTC
1 TCAATTC
45689194 TCAATTC
1 TCAATTC
45689201 TCAAT
1 TCAAT
45689206 CATCAATCAT
Statistics
Matches: 99, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
4 2 0.02
5 5 0.05
6 8 0.08
7 83 0.84
8 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.03, T:0.41
Consensus pattern (7 bp):
TCAATTC
Found at i:45689211 original size:7 final size:7
Alignment explanation
Indices: 45689175--45689247 Score: 96
Period size: 7 Copynumber: 10.4 Consensus size: 7
45689165 CTCAATTCTG
45689175 AATCATC
1 AATCATC
* *
45689182 AATCCTT
1 AATCATC
45689189 AATTC-TC
1 AA-TCATC
45689196 AATTC-TC
1 AA-TCATC
45689203 AATCATC
1 AATCATC
45689210 AATCATC
1 AATCATC
45689217 AATCATC
1 AATCATC
45689224 AATCATC
1 AATCATC
45689231 AATCATC
1 AATCATC
45689238 AATCATC
1 AATCATC
45689245 AAT
1 AAT
45689248 TTTCAATTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
6 2 0.03
7 57 0.93
8 2 0.03
ACGTcount: A:0.40, C:0.27, G:0.00, T:0.33
Consensus pattern (7 bp):
AATCATC
Found at i:45689211 original size:14 final size:14
Alignment explanation
Indices: 45689126--45689240 Score: 89
Period size: 14 Copynumber: 8.4 Consensus size: 14
45689116 CAATTTTCAT
* **
45689126 TCAATTGTCAATTG
1 TCAATTCTCAATCA
*
45689140 TCAATTCTCAATCT
1 TCAATTCTCAATCA
45689154 TCAA-TC-CAATTC-
1 TCAATTCTCAA-TCA
*
45689166 TCAATTCTGAATCA
1 TCAATTCTCAATCA
* *
45689180 TCAATCCTTAATTC-
1 TCAATTCTCAA-TCA
45689194 TCAATTCTCAATCA
1 TCAATTCTCAATCA
45689208 TCAA-TCATCAATCA
1 TCAATTC-TCAATCA
45689222 TCAA-TCATCAATCA
1 TCAATTC-TCAATCA
45689236 TCAAT
1 TCAAT
45689241 CATCAATTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
12 7 0.08
13 12 0.14
14 64 0.75
15 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.37
Consensus pattern (14 bp):
TCAATTCTCAATCA
Found at i:45689316 original size:20 final size:20
Alignment explanation
Indices: 45689279--45689316 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
45689269 TTTTTCTGAT
*
45689279 TTTTATTCTCTTAGATTTTA
1 TTTTATTCTCTTAAATTTTA
45689299 TTTTATTC-CTTATAATTT
1 TTTTATTCTCTTA-AATTT
45689317 GTAAAATTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.21, C:0.11, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTTATTCTCTTAAATTTTA
Found at i:45700829 original size:13 final size:13
Alignment explanation
Indices: 45700790--45700829 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
45700780 TGGTTCCCTC
45700790 TTATGGGCGTGTG
1 TTATGGGCGTGTG
*
45700803 CTATGGGCGTGTG
1 TTATGGGCGTGTG
*
45700816 TTATGGCCGTGTG
1 TTATGGGCGTGTG
45700829 T
1 T
45700830 CCCCTGCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.07, C:0.12, G:0.42, T:0.38
Consensus pattern (13 bp):
TTATGGGCGTGTG
Found at i:45702006 original size:18 final size:20
Alignment explanation
Indices: 45701983--45702024 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
45701973 AGCAAGATGA
45701983 AAATAATATT-AA-TAAAC-T
1 AAATAA-ATTGAATTAAACAT
45702001 AAATAAATTGAATTAAACAT
1 AAATAAATTGAATTAAACAT
45702021 AAAT
1 AAAT
45702025 CTACTCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.14
18 8 0.38
19 5 0.24
20 5 0.24
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (20 bp):
AAATAAATTGAATTAAACAT
Found at i:45707072 original size:55 final size:55
Alignment explanation
Indices: 45706962--45707072 Score: 143
Period size: 55 Copynumber: 2.0 Consensus size: 55
45706952 CAAGCCTGCC
* * *
45706962 AAAACAACACGGGCGTGCGACACGCCCGTGTGGAAGACCCGTGGTTGAACTTATT
1 AAAACAACACGGGCGTGCGACACGCCCGTGTCGAACACCCGTGGTTGAACCTATT
* * * *
45707017 AAAACAGCACGGGCGTGTGACACGCCCGTGTCTAACACCTGTGGTCT-AACCTATT
1 AAAACAACACGGGCGTGCGACACGCCCGTGTCGAACACCCGTGGT-TGAACCTATT
45707072 A
1 A
45707073 GATTGACACG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
55 47 0.98
56 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.26, T:0.20
Consensus pattern (55 bp):
AAAACAACACGGGCGTGCGACACGCCCGTGTCGAACACCCGTGGTTGAACCTATT
Found at i:45707493 original size:15 final size:15
Alignment explanation
Indices: 45707475--45707507 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
45707465 TTAAAACTAC
45707475 TTTTTATTTTTATTT
1 TTTTTATTTTTATTT
45707490 TTTTTATTTTTATTT
1 TTTTTATTTTTATTT
45707505 TTT
1 TTT
45707508 AGCAGATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTATTTTTATTT
Found at i:45711731 original size:39 final size:40
Alignment explanation
Indices: 45711654--45711800 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
45711644 TAGCTCCTCG
* * *
45711654 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
45711694 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
45711733 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
45711773 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
45711801 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:45711811 original size:80 final size:80
Alignment explanation
Indices: 45711700--45711880 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
45711690 CTCATTCAAT
* * *
45711700 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
45711763 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
45711779 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
45711843 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
45711860 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
45711881 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:45711840 original size:40 final size:40
Alignment explanation
Indices: 45711697--45711880 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
45711687 TAACTCATTC
* *
45711697 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
45711737 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
45711777 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
45711817 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
45711858 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
45711881 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:45719241 original size:39 final size:40
Alignment explanation
Indices: 45719164--45719270 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
45719154 TAGCTCCTCG
* * *
45719164 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATATTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATATAAACTCA
* *
45719204 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA
**
45719243 CACGAATGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
45719271 ATTAGTATCT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 25 0.43
40 33 0.57
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA
Found at i:45719269 original size:79 final size:80
Alignment explanation
Indices: 45719170--45719390 Score: 193
Period size: 80 Copynumber: 2.8 Consensus size: 80
45719160 CTCGTTCAAG
* * * ** * *
45719170 TGCCTTCGGGACATAGCCCGG-TTATATTAACTCATTC-AATGCCTTCGGGACTTAACCCGGATT
1 TGCCTTCGGGACATAACCCGGAAT-TAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGA-A
*
45719233 TTAA-AACTCGCACGAA
64 TTAATAACTCGCACAAA
* * *
45719249 TGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAGGCCTTCGGGACTTAACCCGGAATT
1 TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
45719314 AATAACTCGCACAAA
66 AATAACTCGCACAAA
* * ** * * *
45719329 TACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGA-CATAACCCGGAAT-TAGTAACTCA-CACAAAGGCCTTCGGGACTTAACCCGGA
45719391 CAGCATTCAA
Statistics
Matches: 117, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
79 36 0.31
80 75 0.64
81 6 0.05
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (80 bp):
TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
AATAACTCGCACAAA
Found at i:45719321 original size:80 final size:80
Alignment explanation
Indices: 45719210--45719390 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
45719200 CTCATTCAAT
* * *
45719210 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
45719273 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
45719289 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
45719353 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
45719370 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
45719391 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:45719350 original size:40 final size:40
Alignment explanation
Indices: 45719207--45719390 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
45719197 TAACTCATTC
* *
45719207 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
45719247 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
45719287 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
45719327 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
45719368 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
45719391 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:45722839 original size:52 final size:51
Alignment explanation
Indices: 45722711--45722885 Score: 203
Period size: 52 Copynumber: 3.5 Consensus size: 51
45722701 TGGATACTCG
* * * *
45722711 GTGGCCTACACATAGTACCACCCTTGT-AGTCAAAGCTACCTTATTCACAAA
1 GTGGCCTACACATAGTACCACACTTGTGA-CCAAAGCTACTTTCTTCACAAA
* * * *
45722762 GCGGCCTTCATATAGAACCACACTTGTGACCAAAGCTATCTTTCTTCACAAA
1 GTGGCCTACACATAGTACCACACTTGTGACCAAAGCTA-CTTTCTTCACAAA
* * *
45722814 GTGGCCTACACATAGTACCATACTTGTGACC-AAGCTA-TATCTTCTCAAA
1 GTGGCCTACACATAGTACCACACTTGTGACCAAAGCTACTTTCTTCACAAA
*
45722863 GTGGCCTTCACATAGTACCACAC
1 GTGGCCTACACATAGTACCACAC
45722886 CTGAGTCACT
Statistics
Matches: 105, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
49 31 0.30
51 36 0.34
52 38 0.36
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.26
Consensus pattern (51 bp):
GTGGCCTACACATAGTACCACACTTGTGACCAAAGCTACTTTCTTCACAAA
Found at i:45722875 original size:49 final size:51
Alignment explanation
Indices: 45722711--45722885 Score: 196
Period size: 51 Copynumber: 3.5 Consensus size: 51
45722701 TGGATACTCG
* * * *
45722711 GTGGCCTACACATAGTACCACCCTTGT-AGTCAAAGCTACCT-TATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGA-CCAAAGCTA-CTATCTTCACAAA
* * * *
45722762 GCGGCCTTCATATAGAACCACACTTGTGACCAAAGCTATCTTTCTTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTA-CTATCTTCACAAA
* * *
45722814 GTGGCCTACACATAGTACCATACTTGTGACC-AAGCTA-TATCTTCTCAAA
1 GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTACTATCTTCACAAA
45722863 GTGGCCTTCACATAGTACCACAC
1 GTGGCCTTCACATAGTACCACAC
45722886 CTGAGTCACT
Statistics
Matches: 105, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
49 31 0.30
51 38 0.36
52 36 0.34
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.26
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTACTATCTTCACAAA
Found at i:45729041 original size:42 final size:42
Alignment explanation
Indices: 45728944--45729049 Score: 131
Period size: 42 Copynumber: 2.5 Consensus size: 42
45728934 TTAGGGTTAC
* * *
45728944 CGAGGCTATGTGTAAGACCATATCTGGGATATGGCATCATTA
1 CGAGACTATGTGTAAGACCATATCTAGGATATGGCATCAATA
** * *
45728986 TTAGACTACGTGTAAAACCATATCTAGGATATGGCATCAATA
1 CGAGACTATGTGTAAGACCATATCTAGGATATGGCATCAATA
* *
45729028 CGAGATTTTGTGTAAGACCATA
1 CGAGACTATGTGTAAGACCATA
45729050 GCTGGGTTAT
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (42 bp):
CGAGACTATGTGTAAGACCATATCTAGGATATGGCATCAATA
Found at i:45734057 original size:45 final size:45
Alignment explanation
Indices: 45734007--45734097 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
45733997 CCAAAACATG
45734007 TGTCATATACATCATGAACTCAGACCACAACTCAATGAGTTCAGA
1 TGTCATATACATCATGAACTCAGACCACAACTCAATGAGTTCAGA
* *
45734052 TGTCATATATATCATGAACTCAGACCACAACTCGATGAGTTCAGA
1 TGTCATATACATCATGAACTCAGACCACAACTCAATGAGTTCAGA
45734097 T
1 T
45734098 CCCATAGTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.26
Consensus pattern (45 bp):
TGTCATATACATCATGAACTCAGACCACAACTCAATGAGTTCAGA
Found at i:45736543 original size:44 final size:44
Alignment explanation
Indices: 45736493--45736593 Score: 114
Period size: 44 Copynumber: 2.3 Consensus size: 44
45736483 AAGAACTCGT
* * * *
45736493 ACACTTAGTGCCAAAATGATT-AGCCTAAGTTATAACGATATCGC
1 ACACTTAGTGCCAAAA-CATTAAACCGAAGTTATAACAATATCGC
** **
45736537 ACACTTAGTGCCATCACATTAAACCGAAGTTATCTCAATATCGC
1 ACACTTAGTGCCAAAACATTAAACCGAAGTTATAACAATATCGC
45736581 ACACTTAGTGCCA
1 ACACTTAGTGCCA
45736594 GATATAGTCG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 3 0.06
44 45 0.94
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.27
Consensus pattern (44 bp):
ACACTTAGTGCCAAAACATTAAACCGAAGTTATAACAATATCGC
Found at i:45746708 original size:18 final size:19
Alignment explanation
Indices: 45746675--45746710 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
45746665 TATTATAATC
45746675 TATATGATAATAATATTTA
1 TATATGATAATAATATTTA
*
45746694 TATATG-TATTAATATTT
1 TATATGATAATAATATTT
45746711 TTAGTAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
TATATGATAATAATATTTA
Found at i:45766469 original size:29 final size:29
Alignment explanation
Indices: 45766419--45766533 Score: 135
Period size: 29 Copynumber: 4.0 Consensus size: 29
45766409 GCGTGAAAAT
* * *
45766419 AATATGATTTGGGCATAATGGGCCATATG
1 AATATGAATTGGGCCTAGTGGGCCATATG
* *
45766448 AATGTGAATTGGGCCTAGTGGGCCATAAG
1 AATATGAATTGGGCCTAGTGGGCCATATG
* *
45766477 AATATGAATTGGGTC-AGATGGGCCATTTG
1 AATATGAATTGGGCCTAG-TGGGCCATATG
*
45766506 AATAAG-ATTGGGCCTAGTGGGCCATATG
1 AATATGAATTGGGCCTAGTGGGCCATATG
45766534 CATGTATGTA
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
28 19 0.26
29 53 0.74
ACGTcount: A:0.29, C:0.12, G:0.31, T:0.28
Consensus pattern (29 bp):
AATATGAATTGGGCCTAGTGGGCCATATG
Found at i:45770957 original size:29 final size:28
Alignment explanation
Indices: 45770925--45771009 Score: 89
Period size: 29 Copynumber: 3.0 Consensus size: 28
45770915 TGGGATATAT
45770925 GAATGTGAATTGGGCCTAGTGGGCCATAA
1 GAAT-TGAATTGGGCCTAGTGGGCCATAA
* * * **
45770954 GAATATGAACTGGGCCAAATGGGCCATTT
1 GAAT-TGAATTGGGCCTAGTGGGCCATAA
**
45770983 GAATAAAATTGGGCCTAGTGGGCCATA
1 GAATTGAATTGGGCCTAGTGGGCCATA
45771010 TGCATGTATG
Statistics
Matches: 44, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
28 17 0.39
29 27 0.61
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.24
Consensus pattern (28 bp):
GAATTGAATTGGGCCTAGTGGGCCATAA
Found at i:45772078 original size:17 final size:18
Alignment explanation
Indices: 45772045--45772079 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
45772035 GTTTAAGAAG
45772045 GGTTTTCAATGAAAACAC
1 GGTTTTCAATGAAAACAC
*
45772063 GGTTTTCACT-AAAACAC
1 GGTTTTCAATGAAAACAC
45772080 TTCAATGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAC
Found at i:45775414 original size:37 final size:37
Alignment explanation
Indices: 45775373--45775447 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
45775363 GCACACTCAA
*
45775373 AGGTTTGAACACGTGACCTAAAGATACACTAATACAC
1 AGGTTCGAACACGTGACCTAAAGATACACTAATACAC
*
45775410 AGGTTCGAACATGTGACCTAAAGATACACTAATACAC
1 AGGTTCGAACACGTGACCTAAAGATACACTAATACAC
45775447 A
1 A
45775448 ACTAACCACC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.21
Consensus pattern (37 bp):
AGGTTCGAACACGTGACCTAAAGATACACTAATACAC
Found at i:45777204 original size:31 final size:31
Alignment explanation
Indices: 45777147--45777288 Score: 101
Period size: 31 Copynumber: 4.5 Consensus size: 31
45777137 ATAAAATATT
*
45777147 TTTAAA-AATTTAAATATAAT-ATTAAATAAGA
1 TTTAAATAATTT-AATATAATGA-TAAATAATA
* *
45777178 TTTAAATAATTTAATATAATGGTAAATGATA
1 TTTAAATAATTTAATATAATGATAAATAATA
* ** * *
45777209 TTTAAGTCGTTTAACATAACGATACGTAA-AATA
1 TTTAAATAATTTAATATAATGATA---AATAATA
* *
45777242 TTTAAATAATTTAATATAATGATATATAAAA
1 TTTAAATAATTTAATATAATGATAAATAATA
* *
45777273 TATAAATTAATCTAAT
1 TTTAAA-TAATTTAAT
45777289 TTTTTATACA
Statistics
Matches: 85, Mismatches: 19, Indels: 13
0.73 0.16 0.11
Matches are distributed among these distances:
30 1 0.01
31 47 0.55
32 13 0.15
33 22 0.26
34 2 0.02
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (31 bp):
TTTAAATAATTTAATATAATGATAAATAATA
Found at i:45777730 original size:19 final size:19
Alignment explanation
Indices: 45777686--45777732 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
45777676 GAAATTTTTC
45777686 TACTTATTTTAAAGAAATCT
1 TACTTA-TTTAAAGAAATCT
*
45777706 TA-TTATTTACAAG-AATTT
1 TACTTATTTA-AAGAAATCT
45777724 TACTTATTT
1 TACTTATTT
45777733 TTAATTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 10 0.42
19 12 0.50
20 2 0.08
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (19 bp):
TACTTATTTAAAGAAATCT
Found at i:45777749 original size:19 final size:21
Alignment explanation
Indices: 45777727--45777777 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
45777717 AGAATTTTAC
45777727 TTATTTTTA-ATTAA-ATATT
1 TTATTTTTATATTAATATATT
45777746 TTA-TTTTATATTAATTATATT
1 TTATTTTTATATTAA-TATATT
45777767 TTA-TTTTATAT
1 TTATTTTTATAT
45777778 CTAAGTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.17
19 8 0.28
21 16 0.55
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTATTTTTATATTAATATATT
Found at i:45778118 original size:23 final size:23
Alignment explanation
Indices: 45778069--45778118 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
45778059 TATCTGTTTG
* ** *
45778069 TATTTAGTTAGTATTTATTTTTT
1 TATTTAATTAGTATTTAAATTTA
45778092 TATTTAATTAGTATTTAAATTTA
1 TATTTAATTAGTATTTAAATTTA
45778115 TATT
1 TATT
45778119 CTATCACTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (23 bp):
TATTTAATTAGTATTTAAATTTA
Found at i:45778801 original size:3 final size:3
Alignment explanation
Indices: 45778793--45778829 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
45778783 TTAACTTCAA
* *
45778793 AAT AAT AAT AAT AAT AAT AAC AAA AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
45778830 TAAAAACTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:45778835 original size:18 final size:18
Alignment explanation
Indices: 45778799--45778853 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
45778789 TCAAAATAAT
45778799 AATAATAATAATA-ACAAA
1 AATAATAATAATATA-AAA
45778817 AATAATAATAATATAAAA
1 AATAATAATAATATAAAA
* *
45778835 ACTCAAT-ATATTATAAAA
1 AAT-AATAATAATATAAAA
45778853 A
1 A
45778854 TTTGAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 29 0.88
19 4 0.12
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.27
Consensus pattern (18 bp):
AATAATAATAATATAAAA
Found at i:45778954 original size:19 final size:19
Alignment explanation
Indices: 45778907--45778954 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
45778897 TGAAAGAATT
45778907 TATATTTTTTAAAATTTTCA
1 TATA-TTTTTAAAATTTTCA
* *
45778927 TATAATTTTAAATATTTTTA
1 TATATTTTTAAA-ATTTTCA
45778947 -ATATTTTT
1 TATATTTTT
45778955 GCCCGTGTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TATATTTTTAAAATTTTCA
Found at i:45779375 original size:15 final size:14
Alignment explanation
Indices: 45779345--45779386 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 14
45779335 CACTTTCTTG
*
45779345 AAAA-TATTTCAAA
1 AAAACTATTTAAAA
45779358 AAAACTATTTTAAAA
1 AAAACTA-TTTAAAA
45779373 AAAACTATTTAAAA
1 AAAACTATTTAAAA
45779387 TGAAACAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 4 0.15
14 9 0.35
15 13 0.50
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAACTATTTAAAA
Found at i:45780735 original size:19 final size:19
Alignment explanation
Indices: 45780711--45780750 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
45780701 TGTGTCATCA
*
45780711 TAAATTCATAGGCATAACT
1 TAAATTCATAGACATAACT
**
45780730 TAAATTTGTAGACATAACT
1 TAAATTCATAGACATAACT
45780749 TA
1 TA
45780751 CACATTTTCA
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:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (19 bp):
TAAATTCATAGACATAACT
Found at i:45782448 original size:35 final size:35
Alignment explanation
Indices: 45782386--45782471 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
45782376 TTTTATTTGT
*
45782386 TTTA-ATTATATAATTAATGATATTTAAA-TATAA
1 TTTATATTATATAATTAATGATAATTAAATTATAA
*
45782419 TTTATATTATATGAATTTATGATAATTAAATTATAA
1 TTTATATTATAT-AATTAATGATAATTAAATTATAA
* *
45782455 -TGATATTATATTATTAA
1 TTTATATTATATAATTAA
45782472 ATAAATCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 4 0.09
34 11 0.24
35 25 0.56
36 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (35 bp):
TTTATATTATATAATTAATGATAATTAAATTATAA
Found at i:45782457 original size:25 final size:23
Alignment explanation
Indices: 45782413--45782473 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
45782403 TGATATTTAA
*
45782413 ATATAATTTATATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
45782437 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
45782462 ATATTATTAAAT
1 ATATAATTAAAT
45782474 AAATCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:45783890 original size:45 final size:45
Alignment explanation
Indices: 45783839--45783949 Score: 170
Period size: 45 Copynumber: 2.5 Consensus size: 45
45783829 ATGTGCCGAC
*
45783839 TACTGTTACTGTTACTGTTACCGATT-AGACACTTTGTGTGTTGAA
1 TACTGTTACTGTTACTGTTACAGATTCAG-CACTTTGTGTGTTGAA
* *
45783884 TACTGTTACCGCTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACTGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
*
45783929 TATTGTTACTGTTACTGTTAC
1 TACTGTTACTGTTACTGTTAC
45783950 TGCTACCGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 57 0.97
46 2 0.03
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (45 bp):
TACTGTTACTGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
Found at i:45783943 original size:6 final size:6
Alignment explanation
Indices: 45783932--45783972 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
45783922 TGTTGAATAT
* *
45783932 TGTTAC TGTTAC TGTTAC TGCTAC CGTTAC TGATTAC TGTT
1 TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC TG-TTAC TGTT
45783973 TAGGTACTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (6 bp):
TGTTAC
Found at i:45785483 original size:29 final size:28
Alignment explanation
Indices: 45785417--45785531 Score: 113
Period size: 29 Copynumber: 4.0 Consensus size: 28
45785407 TACATACATG
*
45785417 CATATGGCCCACTAGGCCCAATCTTATT
1 CATATGGCCCACTAGGCCCAATCATATT
* * *
45785445 CATATGGCCCATTTGGCCCAGTTCATATT
1 CATATGGCCCACTAGGCCCA-ATCATATT
* * * *
45785474 CTTATGGCCCACTAGGCCTAATTCACATA
1 CATATGGCCCACTAGGCCCAA-TCATATT
* *
45785503 CATATGGCCTATTAGGCCCAAATCATATT
1 CATATGGCCCACTAGGCCC-AATCATATT
45785532 ATACTCATGC
Statistics
Matches: 67, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
28 18 0.27
29 47 0.70
30 2 0.03
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.30
Consensus pattern (28 bp):
CATATGGCCCACTAGGCCCAATCATATT
Found at i:45785529 original size:58 final size:57
Alignment explanation
Indices: 45785419--45785531 Score: 145
Period size: 58 Copynumber: 2.0 Consensus size: 57
45785409 CATACATGCA
** * * **
45785419 TATGGCCCACTAGGCCCAATCTTATTCATATGGCCCATTTGGCCCAGTTCATATTCT
1 TATGGCCCACTAGGCCCAATCACATACATATGGCCCATTAGGCCCAAATCATATTCT
* *
45785476 TATGGCCCACTAGGCCTAATTCACATACATATGGCCTATTAGGCCCAAATCATATT
1 TATGGCCCACTAGGCCCAA-TCACATACATATGGCCCATTAGGCCCAAATCATATT
45785532 ATACTCATGC
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
57 18 0.38
58 29 0.62
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (57 bp):
TATGGCCCACTAGGCCCAATCACATACATATGGCCCATTAGGCCCAAATCATATTCT
Found at i:45785637 original size:19 final size:18
Alignment explanation
Indices: 45785604--45785640 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
45785594 TGGGCCCAAC
45785604 AGCCCATTAGGCCCATTT
1 AGCCCATTAGGCCCATTT
*
45785622 AGCCCATTCCGGCCCATTT
1 AGCCCATT-AGGCCCATTT
45785641 GGCCAATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.19, C:0.38, G:0.16, T:0.27
Consensus pattern (18 bp):
AGCCCATTAGGCCCATTT
Found at i:45785649 original size:19 final size:19
Alignment explanation
Indices: 45785613--45785649 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
45785603 CAGCCCATTA
*
45785613 GGCCCATTTAGCCCATTCC
1 GGCCCATTTAGCCAATTCC
*
45785632 GGCCCATTTGGCCAATTC
1 GGCCCATTTAGCCAATTC
45785650 TCAACCCAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.38, G:0.19, T:0.27
Consensus pattern (19 bp):
GGCCCATTTAGCCAATTCC
Found at i:45785773 original size:16 final size:16
Alignment explanation
Indices: 45785751--45785804 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
45785741 CCAACTTTTA
*
45785751 GCTTTTCGACAATTCG
1 GCTTTTCGACATTTCG
* * *
45785767 ACTTTTCGACTTTTTG
1 GCTTTTCGACATTTCG
45785783 GCTTTTCGACATTTCG
1 GCTTTTCGACATTTCG
45785799 GCTTTT
1 GCTTTT
45785805 GCTGATTCAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.13, C:0.22, G:0.17, T:0.48
Consensus pattern (16 bp):
GCTTTTCGACATTTCG
Found at i:45785774 original size:8 final size:8
Alignment explanation
Indices: 45785752--45785804 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 8
45785742 CAACTTTTAG
45785752 CTTTTCGA
1 CTTTTCGA
**
45785760 CAATTCGA
1 CTTTTCGA
45785768 CTTTTCGA
1 CTTTTCGA
* *
45785776 CTTTTTGG
1 CTTTTCGA
45785784 CTTTTCGA
1 CTTTTCGA
* *
45785792 CATTTCGG
1 CTTTTCGA
45785800 CTTTT
1 CTTTT
45785805 GCTGATTCAT
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.13, C:0.23, G:0.15, T:0.49
Consensus pattern (8 bp):
CTTTTCGA
Found at i:45789206 original size:15 final size:16
Alignment explanation
Indices: 45789181--45789210 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
45789171 AACTAAAATT
45789181 ATCATTTTTTAAAAAA
1 ATCATTTTTTAAAAAA
45789197 ATCA-TTTTTAAAAA
1 ATCATTTTTTAAAAA
45789211 GATAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
ATCATTTTTTAAAAAA
Found at i:45790403 original size:29 final size:28
Alignment explanation
Indices: 45790362--45790422 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 28
45790352 CCTAAACAAG
*
45790362 TTTTATAGTAATTTTATATATTTTATGTTTT
1 TTTTATAG-AA-TTTATATA-TTTATATTTT
45790393 TTTTATA-AATTTATATATTTATATTTT
1 TTTTATAGAATTTATATATTTATATTTT
45790420 TTT
1 TTT
45790423 GTAAATTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 12 0.41
28 8 0.28
29 2 0.07
31 7 0.24
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (28 bp):
TTTTATAGAATTTATATATTTATATTTT
Found at i:45790406 original size:28 final size:30
Alignment explanation
Indices: 45790374--45790449 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 30
45790364 TTATAGTAAT
45790374 TTTATATATTTTATGTTTTT-T-TTATAAA
1 TTTATATATTTTATGTTTTTGTATTATAAA
*
45790402 TTTATATATTTATATTTTTTTGTAAATTATAAA
1 TTTATATATTT-TATGTTTTTGT--ATTATAAA
*
45790435 -TTATAAATTTTATGT
1 TTTATATATTTTATGT
45790450 ATTCTTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 11 0.28
29 8 0.20
30 1 0.03
31 4 0.10
32 9 0.22
33 7 0.17
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (30 bp):
TTTATATATTTTATGTTTTTGTATTATAAA
Found at i:45790419 original size:26 final size:28
Alignment explanation
Indices: 45790374--45790429 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
45790364 TTATAGTAAT
*
45790374 TTTATATATTTTATGTTTTTTTTATAAA
1 TTTATATATTTTATGATTTTTTTATAAA
*
45790402 TTTATATA-TTTAT-ATTTTTTTGTAAA
1 TTTATATATTTTATGATTTTTTTATAAA
45790428 TT
1 TT
45790430 ATAAATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 13 0.50
27 5 0.19
28 8 0.31
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (28 bp):
TTTATATATTTTATGATTTTTTTATAAA
Found at i:45790444 original size:26 final size:26
Alignment explanation
Indices: 45790390--45790445 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
45790380 TATTTTATGT
* *
45790390 TTTTTTTATAAATTTATATATTTATA
1 TTTTTTTATAAATTTATAAATTTAAA
*
45790416 TTTTTTTGTAAA-TTATAAATTATAAA
1 TTTTTTTATAAATTTATAAATT-TAAA
45790442 TTTT
1 TTTT
45790446 ATGTATTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTTTTTATAAATTTATAAATTTAAA
Found at i:45790445 original size:25 final size:26
Alignment explanation
Indices: 45790391--45790450 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 26
45790381 ATTTTATGTT
* * *
45790391 TTTTTTATAAATTTATATATTTATAT
1 TTTTTTGTAAATTTATAAATTTATAA
45790417 TTTTTTGTAAA-TTATAAA-TTATAAA
1 TTTTTTGTAAATTTATAAATTTAT-AA
*
45790442 TTTTATGTA
1 TTTTTTGTA
45790451 TTCTTCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 4 0.14
25 15 0.52
26 10 0.34
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (26 bp):
TTTTTTGTAAATTTATAAATTTATAA
Found at i:45793602 original size:28 final size:28
Alignment explanation
Indices: 45793561--45793629 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
45793551 TATAAAAATA
45793561 TCATTAAATTATTATTATTATTTTATTTTAG
1 TCATTAAATTATTA--ATTATTTTA-TTTAG
* *
45793592 TTATTAAATTATTAATTTTTTTATTTAG
1 TCATTAAATTATTAATTATTTTATTTAG
45793620 TCATTAAATT
1 TCATTAAATT
45793630 TTTTGAAATC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 14 0.40
29 8 0.23
31 13 0.37
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (28 bp):
TCATTAAATTATTAATTATTTTATTTAG
Found at i:45798378 original size:42 final size:43
Alignment explanation
Indices: 45798272--45798392 Score: 131
Period size: 44 Copynumber: 2.8 Consensus size: 43
45798262 CTAATATGTG
*
45798272 TTTTCGTGTAAGACCAC-GTCTGGGACGTTGGCATCGACTTATGA
1 TTTT-GTGTAAGACC-CTGTCTGGGACATTGGCATCGACTTATGA
** * *
45798316 TTTATGTGTAAGACTATGTCTAGGATATTGGCATCGTA-TT-TGA
1 TTT-TGTGTAAGACCCTGTCTGGGACATTGGCATCG-ACTTATGA
*
45798359 TTTTGTGTAAGACCCTGTCTGGGACAGTGGCATC
1 TTTTGTGTAAGACCCTGTCTGGGACATTGGCATC
45798393 AATATTCGAT
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
42 26 0.41
43 6 0.09
44 30 0.47
45 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (43 bp):
TTTTGTGTAAGACCCTGTCTGGGACATTGGCATCGACTTATGA
Found at i:45804122 original size:42 final size:43
Alignment explanation
Indices: 45804024--45804221 Score: 256
Period size: 43 Copynumber: 4.6 Consensus size: 43
45804014 CATTTATTTG
* *
45804024 AAAAACGCTGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCC
1 AAAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCCC
* *
45804067 AAAAATGCTGCTAAAGATCA-GTACCTTTAGCGGCGC-TTTCCC
1 AAAAACGCCGCTAAAGATCATG-ACCTTTAGCGGCGCTTTTCCC
**
45804109 ACCAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCCC
1 AAAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCCC
* * * * * *
45804152 ACAAACGCCACTAAAGATCACGACCTTTAGCAGCTCTTTTCTC
1 AAAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCCC
*
45804195 AAAAACGCCGCTAAAAATCATGACCTT
1 AAAAACGCCGCTAAAGATCATGACCTT
45804222 GAAAAAAATT
Statistics
Matches: 136, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
42 37 0.27
43 99 0.73
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCCC
Found at i:45804122 original size:85 final size:86
Alignment explanation
Indices: 45804024--45804221 Score: 258
Period size: 85 Copynumber: 2.3 Consensus size: 86
45804014 CATTTATTTG
* * **
45804024 AAAAACGCTGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAAAAATGCTGCTAAAGATCA-G
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAAAAACGCCACTAAAGATCACG
*
45804088 TACCTTTAGCGGCGC-TTTCCC
66 -ACCTTTAGCAGCGCTTTTCCC
** * *
45804109 ACCAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGATCACG
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAAAAACGCCACTAAAGATCACG
* *
45804174 ACCTTTAGCAGCTCTTTTCTC
66 ACCTTTAGCAGCGCTTTTCCC
45804195 AAAAACGCCGCTAAA-AATCATGACCTT
1 AAAAACGCCGCTAAAGAA-CATGACCTT
45804222 GAAAAAAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
85 68 0.71
86 28 0.29
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (86 bp):
AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAAAAACGCCACTAAAGATCACG
ACCTTTAGCAGCGCTTTTCCC
Found at i:45805695 original size:15 final size:16
Alignment explanation
Indices: 45805669--45805699 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
45805659 TCTCTCTTGC
45805669 TTTTAGATCATATATA
1 TTTTAGATCATATATA
45805685 TTTTA-ATCATATATA
1 TTTTAGATCATATATA
45805700 AGACAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (16 bp):
TTTTAGATCATATATA
Found at i:45808138 original size:43 final size:43
Alignment explanation
Indices: 45808054--45808320 Score: 349
Period size: 43 Copynumber: 6.2 Consensus size: 43
45808044 CTATATGTAG
*
45808054 CGCCGCTAAAGACCAGGACTTTTAGCGACGCTTATATAAAAAA
1 CGCCGCTAAAGACCAGGACTTTTAGCGGCGCTTATATAAAAAA
*
45808097 CGCCGC-AAAGACCAGGACTTATAGCGGCGCTTATATAAAAAA
1 CGCCGCTAAAGACCAGGACTTTTAGCGGCGCTTATATAAAAAA
* * * *
45808139 CGCCTCTAAAGACCAGGACTTTTAGTGGCGCTTTTCTAAAAAA
1 CGCCGCTAAAGACCAGGACTTTTAGCGGCGCTTATATAAAAAA
*
45808182 CGCTGCTAAAGACCAGGACTTTTAGCGGCGCTTATAT-AAAAA
1 CGCCGCTAAAGACCAGGACTTTTAGCGGCGCTTATATAAAAAA
* * * * * *
45808224 TGCCGCTAAAGACCAGGACTTATAGTGGCGTTTTTTTCAACAAAA
1 CGCCGCTAAAGACCAGGACTTTTAGCGGCGCTTATAT-AA-AAAA
* * *
45808269 CGCCGCTAAAGACCAGGACTTTTAGCGGCACTTTTTTAAAAAA
1 CGCCGCTAAAGACCAGGACTTTTAGCGGCGCTTATATAAAAAA
*
45808312 GGCCGCTAA
1 CGCCGCTAA
45808321 TTTGCCCAGT
Statistics
Matches: 195, Mismatches: 25, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
42 74 0.38
43 82 0.42
44 3 0.02
45 36 0.18
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (43 bp):
CGCCGCTAAAGACCAGGACTTTTAGCGGCGCTTATATAAAAAA
Found at i:45808156 original size:85 final size:86
Alignment explanation
Indices: 45808054--45808320 Score: 367
Period size: 85 Copynumber: 3.1 Consensus size: 86
45808044 CTATATGTAG
* * * *
45808054 CGCCGCTAAAGACCAGGACTTTTAGCGACGCTTATATAAAAAACGCCGC-AAAGACCAGGACTTA
1 CGCCGCTAAAGACCAGGACTTTTAGTGGCGCTTTTATAAAAAACGCCGCTAAAGACCAGGACTTT
45808118 TAGCGGCGCTTATATAAAAAA
66 TAGCGGCGCTTATATAAAAAA
* * *
45808139 CGCCTCTAAAGACCAGGACTTTTAGTGGCGCTTTTCTAAAAAACGCTGCTAAAGACCAGGACTTT
1 CGCCGCTAAAGACCAGGACTTTTAGTGGCGCTTTTATAAAAAACGCCGCTAAAGACCAGGACTTT
45808204 TAGCGGCGCTTATAT-AAAAA
66 TAGCGGCGCTTATATAAAAAA
* * * *
45808224 TGCCGCTAAAGACCAGGACTTATAGTGGCGTTTTTTTCAACAAAACGCCGCTAAAGACCAGGACT
1 CGCCGCTAAAGACCAGGACTTTTAGTGGCGCTTTTAT-AA-AAAACGCCGCTAAAGACCAGGACT
* * *
45808289 TTTAGCGGCACTTTTTTAAAAAA
64 TTTAGCGGCGCTTATATAAAAAA
*
45808312 GGCCGCTAA
1 CGCCGCTAA
45808321 TTTGCCCAGT
Statistics
Matches: 161, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
85 80 0.50
86 31 0.19
87 37 0.23
88 13 0.08
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (86 bp):
CGCCGCTAAAGACCAGGACTTTTAGTGGCGCTTTTATAAAAAACGCCGCTAAAGACCAGGACTTT
TAGCGGCGCTTATATAAAAAA
Found at i:45809037 original size:13 final size:14
Alignment explanation
Indices: 45809016--45809044 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
45809006 AAAAACGACG
45809016 AATTAAAATATTAT
1 AATTAAAATATTAT
45809030 AATT-AAATATTAT
1 AATTAAAATATTAT
45809043 AA
1 AA
45809045 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTAAAATATTAT
Found at i:45814198 original size:9 final size:9
Alignment explanation
Indices: 45814186--45814352 Score: 154
Period size: 9 Copynumber: 17.6 Consensus size: 9
45814176 ATGTACTAGT
45814186 TAAGTTATG
1 TAAGTTATG
45814195 TAAGTTGTTATG
1 TAA---GTTATG
*
45814207 TACGTTATG
1 TAAGTTATG
*
45814216 TGAGTTATG
1 TAAGTTATG
*
45814225 TAAATTATG
1 TAAGTTATG
45814234 TAAGTTATG
1 TAAGTTATG
*
45814243 TGAGTTATG
1 TAAGTTATG
45814252 TAAGTTGTTATG
1 TAA---GTTATG
*
45814264 TAAATTATG
1 TAAGTTATG
45814273 TAAGTTATG
1 TAAGTTATG
*
45814282 TGAGTTATG
1 TAAGTTATG
45814291 TAAGTTGTTATG
1 TAA---GTTATG
*
45814303 TAAATTATG
1 TAAGTTATG
*
45814312 TAAGTTATA
1 TAAGTTATG
*
45814321 TGAGTTATG
1 TAAGTTATG
45814330 TAAGTTATG
1 TAAGTTATG
* *
45814339 TAATTTATT
1 TAAGTTATG
45814348 TAAGT
1 TAAGT
45814353 AATGATCAAT
Statistics
Matches: 128, Mismatches: 21, Indels: 18
0.77 0.13 0.11
Matches are distributed among these distances:
9 102 0.80
12 26 0.20
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:45814233 original size:39 final size:40
Alignment explanation
Indices: 45814190--45814352 Score: 168
Period size: 39 Copynumber: 4.2 Consensus size: 40
45814180 ACTAGTTAAG
45814190 TTATGTAAGTTGTTATGT-ACGTTATGT-G-AGTTATGTAAA
1 TTATGTAAG-TGTTATGTGA-GTTATGTAGTAGTTATGTAAA
*
45814229 TTATGTAA--GTTATGTGAGTTATGTAAGTTGTTATGTAAA
1 TTATGTAAGTGTTATGTGAGTTATGT-AGTAGTTATGTAAA
*
45814268 TTATGTAA--GTTATGTGAGTTATGTAAGTTGTTATGTAAA
1 TTATGTAAGTGTTATGTGAGTTATGT-AGTAGTTATGTAAA
* *
45814307 TTATGTAA--GTTATATGAGTTATGTA--AGTTATGTAAT
1 TTATGTAAGTGTTATGTGAGTTATGTAGTAGTTATGTAAA
*
45814343 TTATTTAAGT
1 TTATGTAAGT
45814353 AATGATCAAT
Statistics
Matches: 113, Mismatches: 5, Indels: 13
0.86 0.04 0.10
Matches are distributed among these distances:
36 30 0.27
37 1 0.01
38 2 0.02
39 80 0.71
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (40 bp):
TTATGTAAGTGTTATGTGAGTTATGTAGTAGTTATGTAAA
Found at i:45814262 original size:48 final size:44
Alignment explanation
Indices: 45814201--45814340 Score: 183
Period size: 39 Copynumber: 3.4 Consensus size: 44
45814191 TATGTAAGTT
*
45814201 GTTATGTACGTTATGTGAGTTATGTAAATTATGTAAGTTATGTGA
1 GTTATGTAAGTTATGT-AGTTATGTAAATTATGTAAGTTATGTGA
45814246 GTTATGTAAG---T-T-GTTATGTAAATTATGTAAGTTATGTGA
1 GTTATGTAAGTTATGTAGTTATGTAAATTATGTAAGTTATGTGA
*
45814285 GTTATGTAAG---T-T-GTTATGTAAATTATGTAAGTTATATGA
1 GTTATGTAAGTTATGTAGTTATGTAAATTATGTAAGTTATGTGA
45814324 GTTATGTAAGTTATGTA
1 GTTATGTAAGTTATGTA
45814341 ATTTATTTAA
Statistics
Matches: 88, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
39 75 0.85
41 1 0.01
42 2 0.02
43 1 0.01
45 9 0.10
ACGTcount: A:0.31, C:0.01, G:0.23, T:0.46
Consensus pattern (44 bp):
GTTATGTAAGTTATGTAGTTATGTAAATTATGTAAGTTATGTGA
Found at i:45814279 original size:57 final size:57
Alignment explanation
Indices: 45814186--45814352 Score: 196
Period size: 57 Copynumber: 2.9 Consensus size: 57
45814176 ATGTACTAGT
* *
45814186 TAAGTTATGTAAGTTGTTATGTACGTTATGTGAGTTATGTAAATTATGTAAGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAATTATGTAAGTTATG
* * * *
45814243 TGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATGTGAGTTATGTAAGTTGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAATTATGTAA---GTTATG
* * * *
45814303 TAAATTATGTAAGTT-ATATG--AGTTATGTAAGTTATGTAATTTATTTAAGT
1 TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAATTATGTAAGT
45814353 AATGATCAAT
Statistics
Matches: 94, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
54 2 0.02
57 69 0.73
59 4 0.04
60 19 0.20
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.47
Consensus pattern (57 bp):
TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAATTATGTAAGTTATG
Found at i:45814341 original size:48 final size:48
Alignment explanation
Indices: 45814186--45814341 Score: 188
Period size: 48 Copynumber: 3.2 Consensus size: 48
45814176 ATGTACTAGT
* * *
45814186 TAAGTTATGTAAGTTGTTATGTACGTTATGTGAGTTATGTAAATTATG
1 TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAGTTATG
* * * * *
45814234 TAAGTTATGTGAGTTATGTAAGT-TGTTATGTAAATTATGTAAGTTATG
1 TAAGTTATGTAAGTTGT-TATGTAAGTTATGTAAGTTATGTAAGTTATG
* * * *
45814282 TGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATGAGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAGTTATG
45814330 TAAGTTATGTAA
1 TAAGTTATGTAA
45814342 TTTATTTAAG
Statistics
Matches: 89, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
47 4 0.04
48 81 0.91
49 4 0.04
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (48 bp):
TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAGTTATG
Found at i:45814937 original size:23 final size:23
Alignment explanation
Indices: 45814911--45814960 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
45814901 GTTCAAGTTT
45814911 ATTTAAAGGGCTGCAATTCATAC
1 ATTTAAAGGGCTGCAATTCATAC
45814934 ATTTAAAGGGCTGCAATTCATAC
1 ATTTAAAGGGCTGCAATTCATAC
45814957 ATTT
1 ATTT
45814961 GATTAATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (23 bp):
ATTTAAAGGGCTGCAATTCATAC
Found at i:45816948 original size:7 final size:7
Alignment explanation
Indices: 45816913--45816939 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
45816903 ATTGTTTAGA
45816913 TTAAAAT
1 TTAAAAT
45816920 TTAAAAT
1 TTAAAAT
45816927 TTAAAAT
1 TTAAAAT
45816934 TTAAAA
1 TTAAAA
45816940 AATATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TTAAAAT
Found at i:45817523 original size:19 final size:19
Alignment explanation
Indices: 45817484--45817535 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
45817474 TTTCGATTTT
*
45817484 GATTCGGGGAAATATTTAGG
1 GATTCGGGGAAA-AGTTAGG
45817504 GATTCGGGGAAAAGTTAGG
1 GATTCGGGGAAAAGTTAGG
*
45817523 GATTTGGGGAAAA
1 GATTCGGGGAAAA
45817536 TTGGGTGGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.33, C:0.04, G:0.38, T:0.25
Consensus pattern (19 bp):
GATTCGGGGAAAAGTTAGG
Found at i:45818648 original size:14 final size:15
Alignment explanation
Indices: 45818616--45818651 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
45818606 GAAATTTATT
45818616 TTTAGGGTTTACAAA
1 TTTAGGGTTTACAAA
*
45818631 TTTAGGGTTTA-TAA
1 TTTAGGGTTTACAAA
45818645 TTTAGGG
1 TTTAGGG
45818652 CATAAGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.28, C:0.03, G:0.25, T:0.44
Consensus pattern (15 bp):
TTTAGGGTTTACAAA
Found at i:45818860 original size:29 final size:29
Alignment explanation
Indices: 45818823--45818880 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
45818813 TTAGAGTTTA
* *
45818823 GATCATGGGTTATGATTTAGGGGTTAGGC
1 GATCATGGGTTATGATGTAAGGGTTAGGC
*
45818852 GATCGTGGGTTATGATGTAAGGGTTAGGC
1 GATCATGGGTTATGATGTAAGGGTTAGGC
45818881 TTGTAACACC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.07, G:0.40, T:0.33
Consensus pattern (29 bp):
GATCATGGGTTATGATGTAAGGGTTAGGC
Found at i:45819862 original size:27 final size:27
Alignment explanation
Indices: 45819800--45819938 Score: 165
Period size: 27 Copynumber: 5.1 Consensus size: 27
45819790 AGCATGGCTG
** *
45819800 CCAGAACAGATAA-TGTAACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
* *
45819826 CTAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAATTGTGGCAGAGCCA
45819854 CCAGAACAGA-AATATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* *
45819881 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
* *
45819908 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
45819935 CCAG
1 CCAG
45819939 GATGCTTCCT
Statistics
Matches: 100, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
26 7 0.07
27 77 0.77
28 16 0.16
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.17
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:45824287 original size:40 final size:40
Alignment explanation
Indices: 45824231--45824448 Score: 325
Period size: 40 Copynumber: 5.5 Consensus size: 40
45824221 CGGATGATAA
* *
45824231 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* *
45824271 TCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
45824311 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
45824351 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
45824391 CCGAGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
45824431 CC-GGCTAAATCTCGAAGG
1 CCGGGCTAAGTCCCGAAGG
45824449 TACTTGGTTT
Statistics
Matches: 165, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
39 15 0.09
40 149 0.90
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:45828390 original size:27 final size:27
Alignment explanation
Indices: 45828355--45828464 Score: 127
Period size: 27 Copynumber: 4.1 Consensus size: 27
45828345 AGCATGGCTG
* *
45828355 CCAGA-ACAGATAATGTGACAGAGTCA
1 CCAGATACAGATAATGTGGCAGAGCCA
*
45828381 CAAGATACAGATAATCGTGGCAGAGCCA
1 CCAGATACAGATAAT-GTGGCAGAGCCA
*
45828409 CCAGA-ACAGAAATATGTGGCAGAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
*
45828436 CCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGATACAGATAA-TGTGGCAGAGCCA
45828463 CC
1 CC
45828465 GGGGCGCTTC
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
26 5 0.07
27 51 0.71
28 16 0.22
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (27 bp):
CCAGATACAGATAATGTGGCAGAGCCA
Found at i:45828446 original size:54 final size:54
Alignment explanation
Indices: 45828355--45828464 Score: 150
Period size: 54 Copynumber: 2.0 Consensus size: 54
45828345 AGCATGGCTG
* *
45828355 CCAGAACAGATAATGTGACAGAGTCACAAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAAATGTGACAGAGCCACAAGATACAGATAATCGTGGCAGAGCCA
* * * *
45828409 CCAGAACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAA-ATGTGACAGAGCCACAAGATACAGATAATCGTGGCAGAGCCA
45828463 CC
1 CC
45828465 GGGGCGCTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
54 32 0.65
55 17 0.35
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGACAGAGCCACAAGATACAGATAATCGTGGCAGAGCCA
Found at i:45830954 original size:41 final size:41
Alignment explanation
Indices: 45830932--45831128 Score: 279
Period size: 41 Copynumber: 4.8 Consensus size: 41
45830922 GGACCTAAAG
*
45830932 CGCCACTA-TATCTCAGTTTTTTGCGGCGTTTTGCATGAAAA
1 CGCCACTATTA-CTCAGTTTTTAGCGGCGTTTTGCATGAAAA
45830973 CGCCACTATTACTCAGTTTTTAGCGGCGTTTTGCATGAAAA
1 CGCCACTATTACTCAGTTTTTAGCGGCGTTTTGCATGAAAA
*
45831014 CGCCACTATTGCTCAGTTTTTAGCGGCGTTTTGCATGAAAA
1 CGCCACTATTACTCAGTTTTTAGCGGCGTTTTGCATGAAAA
* * * ** *
45831055 CGCCGCTGTTGCTCAGTTTTTAATGGCGTTTTGCACGAAAA
1 CGCCACTATTACTCAGTTTTTAGCGGCGTTTTGCATGAAAA
* * *
45831096 TGCCACTATTGCTCAGTTTTTAGCGGTGTTTTG
1 CGCCACTATTACTCAGTTTTTAGCGGCGTTTTG
45831129 TTTCAAACGC
Statistics
Matches: 142, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
41 140 0.99
42 2 0.01
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (41 bp):
CGCCACTATTACTCAGTTTTTAGCGGCGTTTTGCATGAAAA
Found at i:45832747 original size:7 final size:7
Alignment explanation
Indices: 45832736--45832787 Score: 59
Period size: 7 Copynumber: 7.0 Consensus size: 7
45832726 TACATATTTA
45832736 AATTTTT
1 AATTTTT
*
45832743 TATTTTT
1 AATTTTT
*
45832750 TATTTTT
1 AATTTTT
45832757 AAAATTTTT
1 --AATTTTT
45832766 AATTTTT
1 AATTTTT
45832773 AATTTTT
1 AATTTTT
45832780 AAATTTTT
1 -AATTTTT
45832788 TTTGAAGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
7 27 0.68
8 7 0.17
9 6 0.15
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
AATTTTT
Found at i:45832757 original size:22 final size:22
Alignment explanation
Indices: 45832732--45832788 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 22
45832722 ATATTACATA
*
45832732 TTTAAATTTTTTATTTTTTATT
1 TTTAAATTTTTTATTTTTAATT
*
45832754 TTTAAAATTTTTAATTTTTAATT
1 TTT-AAATTTTTTATTTTTAATT
45832777 TTTAAATTTTTT
1 TTTAAATTTTTT
45832789 TTGAAGATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 11 0.35
23 20 0.65
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTAAATTTTTTATTTTTAATT
Found at i:45832763 original size:16 final size:16
Alignment explanation
Indices: 45832744--45832787 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
45832734 TAAATTTTTT
*
45832744 ATTTTTTATTTTTAAA
1 ATTTTTAATTTTTAAA
45832760 ATTTTTAATTTTT--A
1 ATTTTTAATTTTTAAA
45832774 ATTTTTAAATTTTT
1 ATTTTT-AATTTTT
45832788 TTTGAAGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 7 0.27
15 7 0.27
16 12 0.46
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTTTAATTTTTAAA
Done.