Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397275.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_34.0, 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: 2955990
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 53928 characters in sequence are not A, C, G, or T
File 3 of 8
Found at i:850998 original size:33 final size:33
Alignment explanation
Indices: 850935--850998 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
850925 ATTTTTAATG
* **
850935 TTATATATTTTATTTTTATTTTTTCTTATAACC
1 TTATAAATTTTATTTTTATTTTTTAATATAACC
850968 TTATAAATTTTATTTTTATTTTTTAATATAA
1 TTATAAATTTTATTTTTATTTTTTAATATAA
850999 TTTTTTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (33 bp):
TTATAAATTTTATTTTTATTTTTTAATATAACC
Found at i:851279 original size:13 final size:13
Alignment explanation
Indices: 851257--851307 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
851247 AATATCATTG
*
851257 TATTACAATATTA
1 TATTATAATATTA
851270 TATTATAATAATT-
1 TATTATAAT-ATTA
* *
851283 TATTATAAAATAAA
1 TATTATAATAT-TA
851297 TATTATAATAT
1 TATTATAATAT
851308 AATTTAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
12 2 0.06
13 16 0.52
14 13 0.42
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (13 bp):
TATTATAATATTA
Found at i:851559 original size:5 final size:5
Alignment explanation
Indices: 851549--851578 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
851539 GTGCCAATGG
851549 CTGCC CTGCC CTGCC CTGCC CTGCC CTGCC
1 CTGCC CTGCC CTGCC CTGCC CTGCC CTGCC
851579 TACCCGCGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.60, G:0.20, T:0.20
Consensus pattern (5 bp):
CTGCC
Found at i:857868 original size:15 final size:18
Alignment explanation
Indices: 857830--857869 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 18
857820 ATATTTTTTA
857830 ATTTTAATAGTATTGAAT
1 ATTTTAATAGTATTGAAT
*
857848 AATTTAA-A-TATT-AAT
1 ATTTTAATAGTATTGAAT
857863 ATTTTAA
1 ATTTTAA
857870 GTTAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 9 0.45
16 4 0.20
17 1 0.05
18 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
ATTTTAATAGTATTGAAT
Found at i:858512 original size:29 final size:29
Alignment explanation
Indices: 858478--858533 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
858468 TGGATATTCA
*
858478 GTATATCTTGCTTAGCTATTATAGATACT
1 GTATATCTTGCTTAACTATTATAGATACT
* *
858507 GTATATCTTGTTTAACTATTGTAGATA
1 GTATATCTTGCTTAACTATTATAGATA
858534 TTGCAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (29 bp):
GTATATCTTGCTTAACTATTATAGATACT
Found at i:871285 original size:21 final size:21
Alignment explanation
Indices: 871261--871302 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
871251 AATACCCATT
*
871261 ATTATAATATCTAATTTTTAA
1 ATTAAAATATCTAATTTTTAA
* *
871282 ATTAAAATATTTATTTTTTAA
1 ATTAAAATATCTAATTTTTAA
871303 TAATTTATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTAAAATATCTAATTTTTAA
Found at i:871698 original size:20 final size:20
Alignment explanation
Indices: 871642--871702 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
871632 AATGTTTATT
871642 ATTTTAATA-ATTTATTATAA
1 ATTTTAATATATTTATT-TAA
* *
871662 ATATTAATAAATTTTTATTTAA
1 ATTTTAAT--ATATTTATTTAA
*
871684 ATTTTAATATGTTTATTTA
1 ATTTTAATATATTTATTTA
871703 TTTTAATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 17 0.50
22 11 0.32
23 6 0.18
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTTTAATATATTTATTTAA
Found at i:871798 original size:12 final size:13
Alignment explanation
Indices: 871769--871802 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
871759 AATTAAAACA
*
871769 TTTATATTATTAC
1 TTTATTTTATTAC
871782 TTTATTTTATT-C
1 TTTATTTTATTAC
871794 TTTATTTTA
1 TTTATTTTA
871803 AAATATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATTTTATTAC
Found at i:881645 original size:6 final size:7
Alignment explanation
Indices: 881629--881653 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
881619 AGGTTTAGTG
881629 TTTTTCT
1 TTTTTCT
881636 TTTTTCT
1 TTTTTCT
881643 TTTTTCT
1 TTTTTCT
881650 TTTT
1 TTTT
881654 GGCCTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:883460 original size:32 final size:32
Alignment explanation
Indices: 883409--883470 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
883399 GTCTTTTAAT
* *
883409 TTTATGTTAACTTTCTTCATTATTTTTTCAAA
1 TTTATGTAAACTTTCTTCATTATTTCTTCAAA
* *
883441 TTTATGTAAATTTTTTTCATTATTTCTTCA
1 TTTATGTAAACTTTCTTCATTATTTCTTCA
883471 CCAAATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.24, C:0.11, G:0.03, T:0.61
Consensus pattern (32 bp):
TTTATGTAAACTTTCTTCATTATTTCTTCAAA
Found at i:892986 original size:468 final size:469
Alignment explanation
Indices: 891894--893104 Score: 1282
Period size: 468 Copynumber: 2.6 Consensus size: 469
891884 TGATTGATGG
* * * * * * * * * *
891894 TGATACAATTTAAATCATTATGCTTGATATTCTTAATCTATAGTACTACGCTTCCAAGCCTAACG
1 TGATACAATTCAAATCATTATACTTAATATCCATGATCTGTAATACTACACTTCCAAGCCTAATG
* ** * * * * ** * * * * * * *
891959 ATCGATATTCTTAATCTAGGGTACTATGGCTCTAAGCATAATATATGATATCATTGATACTGCTT
66 CTTAATATCCTTGATCTTGGATACTACAGTTCCAAACAGAATAGATGATATCTTTGATATTGCTT
* ** * * * *
892024 AATTATATCCTTGATTTGTAGTGCTATGCTTCCAAACATAGTACTTGATATCCTTGATCTGAGGT
131 AATTATATCCTTGATTTGTAGTGCTATGTTTCCAAGTATAATGCTTGATATCATTAATCTGAGGT
* * * *
892089 GCTACAATTTCAATTATAATGCTTGATATTCTTGATTTGTTGTGATATCTACTTGATATCTACTA
196 GTTACAATTTCAATTATAATGCTTGATA-TCTTAAATTGTTGTGATATCTACTTGATATCCACTA
* * * *
892154 CTTAATTATGCTTGATTGTAATGCTATGATTCTAAGTATAATGCTCGATATCATTGATTTAGGGT
260 CTTAATTATCCTTGATTGTAATGCTATGATTCCAAGCATAATGCTCAATATCATTGATTTAGGGT
*
892219 CTTATGGTACCAAGCATAATAGATAATATCTACTTGATATCTACAAAATATCCTTAATCTATAGC
325 CTTATGATACCAAG-ATAATAGATAATA--TAC-TGATATCTACAAAATATCCTTAA-CTATAGC
* * * * *
892284 ACTACAATTTCAAGCATAATAAATTATATCCTTAATATAAGGTGTTATGGTACCAAGCATAATGC
385 AATACAATTCCAAGCATAATAAATGATATCATTAATATAAGGTGTTATAGTACCAAGCATAATGC
892349 TTGATATCCTTGATCAATAA
450 TTGATATCCTTGATCAATAA
* **
892369 TGATACAATTCAAATCATTATACTTAATATCCATGATCTGTAGTGTTACACTTCCAAGCCTAATG
1 TGATACAATTCAAATCATTATACTTAATATCCATGATCTGTAATACTACACTTCCAAGCCTAATG
** * * *
892434 CTTAATATCCTTGATCTTGGATACTATGGTTCCAAGCAGAATAGATGATATCTTTGATGTTGTTT
66 CTTAATATCCTTGATCTTGGATACTACAGTTCCAAACAGAATAGATGATATCTTTGATATTGCTT
* * * * * * *
892499 AATTATATCCTTAATTTGTAGTGTTACGTTTCTAAGTATAATGCTCGATATCTTTCATCTGAGGT
131 AATTATATCCTTGATTTGTAGTGCTATGTTTCCAAGTATAATGCTTGATATCATTAATCTGAGGT
* * *
892564 GTTACAATTCCAATTATAATGCTTGATATCCTTAAATTGTTATGCTATCTACTTGATATCCACTA
196 GTTACAATTTCAATTATAATGCTTGATAT-CTTAAATTGTTGTGATATCTACTTGATATCCACTA
* * *
892629 CTTAATTATCCTTGATTTTGTAATGGTATGATTCCAAGCATAATGC-CTAATATCTTTGATTTGG
260 CTTAATTATCCTTGA--TTGTAATGCTATGATTCCAAGCATAATGCTC-AATATCATTGATTTAG
* *
892693 GGTCTTATGATATCAAG-T-ATA-AT-A-A-A-TGATATCTACTAAATATCCTTAA-TAT-GCAA
322 GGTCTTATGATACCAAGATAATAGATAATATACTGATATCTACAAAATATCCTTAACTATAGCAA
* *
892749 TACTGTAATTCCAAGCATAATAAATGATATCATTGATAT-GGAGTGTTATAGTACCAAGCATAAT
387 TAC---AATTCCAAGCATAATAAATGATATCATTAATATAAG-GTGTTATAGTACCAAGCAT-A-
** *
892813 ATGCTTGATAT-CTTGGATTTATAG
446 ATGCTTGATATCCTT-GATCAATAA
* * ** * * * *
892837 TGATACAATTCAAATCATTGTACTTGATATCTTTGCTCTGTAATACTACGCTTCGAAGCTTAATG
1 TGATACAATTCAAATCATTATACTTAATATCCATGATCTGTAATACTACACTTCCAAGCCTAATG
* * *
892902 CTTGATATCCTTGATC-TGGAATATTACAGTTCCAAAC-GTTATAGATGATAAT-TTTGATATTG
66 CTTAATATCCTTGATCTTGG-ATACTACAGTTCCAAACAG-AATAGATGAT-ATCTTTGATATTG
* * * *
892964 CTTAATTAGATCCTTGATTTGTAGTGCTATGTTTCCATGTATAATGTTTGATATCATTAATTTGA
128 CTTAATTATATCCTTGATTTGTAGTGCTATGTTTCCAAGTATAATGCTTGATATCATTAATCTGA
* * * *
893029 GGTGTTACAGTTTCAATTATAATGCTTGATATCTTTAATATATCGTGATATCTACTTGATATCCA
193 GGTGTTACAATTTCAATTATAATGCTTGATATCTTAAAT-TGTTGTGATATCTACTTGATATCCA
893094 CTACTTAATTA
257 CTACTTAATTA
893105 ATTATCTTTG
Statistics
Matches: 619, Mismatches: 102, Indels: 37
0.82 0.13 0.05
Matches are distributed among these distances:
463 6 0.01
464 3 0.00
465 1 0.00
466 69 0.11
467 14 0.02
468 233 0.38
469 2 0.00
471 1 0.00
472 1 0.00
473 2 0.00
474 4 0.01
475 228 0.37
476 1 0.00
477 54 0.09
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (469 bp):
TGATACAATTCAAATCATTATACTTAATATCCATGATCTGTAATACTACACTTCCAAGCCTAATG
CTTAATATCCTTGATCTTGGATACTACAGTTCCAAACAGAATAGATGATATCTTTGATATTGCTT
AATTATATCCTTGATTTGTAGTGCTATGTTTCCAAGTATAATGCTTGATATCATTAATCTGAGGT
GTTACAATTTCAATTATAATGCTTGATATCTTAAATTGTTGTGATATCTACTTGATATCCACTAC
TTAATTATCCTTGATTGTAATGCTATGATTCCAAGCATAATGCTCAATATCATTGATTTAGGGTC
TTATGATACCAAGATAATAGATAATATACTGATATCTACAAAATATCCTTAACTATAGCAATACA
ATTCCAAGCATAATAAATGATATCATTAATATAAGGTGTTATAGTACCAAGCATAATGCTTGATA
TCCTTGATCAATAA
Found at i:894572 original size:38 final size:39
Alignment explanation
Indices: 894505--894578 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 39
894495 AATTCTAGTT
* * *
894505 ATTATTATAAAAATTATTAGTTTTGAATATT-TATAAGC
1 ATTATTATAAAAATAAATAGTTTAGAATATTATATAAGC
894543 ATTATTATAAAAATAAAT-GTTTAGTAATATTATATA
1 ATTATTATAAAAATAAATAGTTTAG-AATATTATATA
894579 GTTTAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 5 0.16
38 22 0.71
39 4 0.13
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (39 bp):
ATTATTATAAAAATAAATAGTTTAGAATATTATATAAGC
Found at i:894599 original size:15 final size:15
Alignment explanation
Indices: 894581--894628 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 15
894571 ATTATATAGT
*
894581 TTAATATTTAAATAA
1 TTAATATTCAAATAA
894596 TTAATATTCAAATATTA
1 TTAATATTCAAATA--A
894613 TGTTAATATTCAAATA
1 --TTAATATTCAAATA
894629 TTTATAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 13 0.46
17 1 0.04
19 14 0.50
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (15 bp):
TTAATATTCAAATAA
Found at i:895954 original size:27 final size:26
Alignment explanation
Indices: 895862--895965 Score: 91
Period size: 27 Copynumber: 3.9 Consensus size: 26
895852 TGCTTCTGTC
* * **
895862 CTTAGAACACCCTTAAGCACTTATGCG
1 CTTAGAACACCCTT-GGCACTTCTATG
* * *
895889 CTTAGAACACCCTAGGCGCTTCCATG
1 CTTAGAACACCCTTGGCACTTCTATG
**
895915 CTTAGAATGCCCTTGGACACTTCTATG
1 CTTAGAACACCCTTGG-CACTTCTATG
*
895942 CTTGGAACACCCTTGGGCACTTCT
1 CTTAGAACACCCTT-GGCACTTCT
895966 TGGCTTGGAT
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
26 19 0.32
27 39 0.65
28 2 0.03
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (26 bp):
CTTAGAACACCCTTGGCACTTCTATG
Found at i:895971 original size:27 final size:27
Alignment explanation
Indices: 895924--895983 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
895914 GCTTAGAATG
895924 CCCTTGGACACTTCTATGCTTGGA-ACA
1 CCCTTGGACACTTCTATGCTTGGATA-A
*
895951 CCCTTGGGCACTTCT-TGGCTTGGATAA
1 CCCTTGGACACTTCTAT-GCTTGGATAA
895978 CCCTTG
1 CCCTTG
895984 ATGTAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 1 0.03
27 28 0.93
28 1 0.03
ACGTcount: A:0.17, C:0.30, G:0.22, T:0.32
Consensus pattern (27 bp):
CCCTTGGACACTTCTATGCTTGGATAA
Found at i:896331 original size:27 final size:27
Alignment explanation
Indices: 896280--896350 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
896270 CCTGGGCGAC
* *
896280 TCCACGCTAGGAACGCCTTTAGGTGCTT
1 TCCACTCTAGGAACGCCCTTAGGTG-TT
* *
896308 T-CACTCTAGGAATGCCCTTGGGTGTT
1 TCCACTCTAGGAACGCCCTTAGGTGTT
896334 TCCACTCTAGGAACGCC
1 TCCACTCTAGGAACGCC
896351 ATTTGGCACT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 3 0.08
27 33 0.89
28 1 0.03
ACGTcount: A:0.18, C:0.30, G:0.24, T:0.28
Consensus pattern (27 bp):
TCCACTCTAGGAACGCCCTTAGGTGTT
Found at i:897292 original size:27 final size:27
Alignment explanation
Indices: 897262--897319 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
897252 AACCCGAGAG
* *
897262 CTTCCGTGCTTGGAACATCCCTTAG-CA
1 CTTCCATGCTTGGAACAACCC-TAGACA
897289 CTTCCATGCTTGGAACAACCCTAGACA
1 CTTCCATGCTTGGAACAACCCTAGACA
897316 CTTC
1 CTTC
897320 TGCGTTTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.22, C:0.34, G:0.16, T:0.28
Consensus pattern (27 bp):
CTTCCATGCTTGGAACAACCCTAGACA
Found at i:897427 original size:27 final size:27
Alignment explanation
Indices: 897397--897469 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
897387 GCCTCTGGGA
* *
897397 GCTTCTGTACTTGGAACACTCCTAGGT
1 GCTTCTATACTTGGAACACTCCTAGGC
* * **
897424 GCTTCTACACTTGGAACGCTTTTAGGC
1 GCTTCTATACTTGGAACACTCCTAGGC
*
897451 ACTTCTATACTTGGAACAC
1 GCTTCTATACTTGGAACAC
897470 CCCTGGGCCC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (27 bp):
GCTTCTATACTTGGAACACTCCTAGGC
Found at i:898641 original size:19 final size:19
Alignment explanation
Indices: 898605--898642 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
898595 TAAAAGCACA
*
898605 TAAATAATAAAATTTAAAT
1 TAAATAATAAAATATAAAT
898624 TAAATAATCAAAA-ATAAAT
1 TAAATAAT-AAAATATAAAT
898643 ATCTCAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAATAATAAAATATAAAT
Found at i:898692 original size:34 final size:35
Alignment explanation
Indices: 898623--898696 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
898613 AAAATTTAAA
* * *
898623 TTAAATAATCAAAAATAAATATCTCAAATATCAAC
1 TTAAATAATCAAAAACAAATATCTCAAACAACAAC
*
898658 TTAAATAATTAAAAACAAATAT-TCAAACAACAAC
1 TTAAATAATCAAAAACAAATATCTCAAACAACAAC
898692 TTAAA
1 TTAAA
898697 CATTACAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
34 15 0.43
35 20 0.57
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (35 bp):
TTAAATAATCAAAAACAAATATCTCAAACAACAAC
Found at i:899343 original size:74 final size:75
Alignment explanation
Indices: 899212--899361 Score: 257
Period size: 74 Copynumber: 2.0 Consensus size: 75
899202 TTCGTATCCT
* * *
899212 ATAACAGGATATCCATTGACATCCATAAATAAACGTGTTAGGATTAGACATATATTTGTAAAAAT
1 ATAAAAGGATATCCATTGACATCCATAAATAAACATGCTAGGATTAGACATATATTTGTAAAAAT
899277 CGAAAAAAAA
66 CGAAAAAAAA
*
899287 ATAAAAGGA-ATCCATTGACATCCTTAAATAAACATGCTAGGATTAGACATATATTTGTAAAAAT
1 ATAAAAGGATATCCATTGACATCCATAAATAAACATGCTAGGATTAGACATATATTTGTAAAAAT
899351 CGAAAAAAAA
66 CGAAAAAAAA
899361 A
1 A
899362 AAAGAACAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
74 63 0.89
75 8 0.11
ACGTcount: A:0.49, C:0.12, G:0.13, T:0.26
Consensus pattern (75 bp):
ATAAAAGGATATCCATTGACATCCATAAATAAACATGCTAGGATTAGACATATATTTGTAAAAAT
CGAAAAAAAA
Found at i:905898 original size:19 final size:19
Alignment explanation
Indices: 905868--905914 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
905858 ACGAAAATTT
905868 ATTAATTAATTTATCA-ATAA
1 ATTAA-TAATTTAT-ATATAA
*
905888 ATTAATAATTTATATATTA
1 ATTAATAATTTATATATAA
905907 ATTAATAA
1 ATTAATAA
905915 AAAATTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 1 0.04
19 19 0.76
20 5 0.20
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTAATAATTTATATATAA
Found at i:905928 original size:23 final size:23
Alignment explanation
Indices: 905871--905930 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
905861 AAAATTTATT
* * *
905871 AATTAATTTATCAATAAATTAAT
1 AATTAATTTATTAATAAATAAAA
* * *
905894 AATTTATATATTAATTAATAAAA
1 AATTAATTTATTAATAAATAAAA
905917 AATTAATTTATTAA
1 AATTAATTTATTAA
905931 AATATTAAAC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTAATTTATTAATAAATAAAA
Found at i:910572 original size:19 final size:18
Alignment explanation
Indices: 910548--910586 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
910538 ATAAGTAGTC
910548 ATCCACATCTTGATGGGTT
1 ATCCACATC-TGATGGGTT
* *
910567 ATCCACTTCTGGTGGGTT
1 ATCCACATCTGATGGGTT
910585 AT
1 AT
910587 AAGTAATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (18 bp):
ATCCACATCTGATGGGTT
Found at i:910587 original size:47 final size:47
Alignment explanation
Indices: 910518--910629 Score: 206
Period size: 47 Copynumber: 2.4 Consensus size: 47
910508 TTTTCATTAT
*
910518 TTATCCACTTCTGGTGGGTTATAAGTAGTCATCCACATCTTGATGGG
1 TTATCCACTTCTGGTGGGTTATAAGTAATCATCCACATCTTGATGGG
910565 TTATCCACTTCTGGTGGGTTATAAGTAATCATCCACATCTTGATGGG
1 TTATCCACTTCTGGTGGGTTATAAGTAATCATCCACATCTTGATGGG
*
910612 TTATCCACTACTGGTGGG
1 TTATCCACTTCTGGTGGG
910630 CTAGTGTGTT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 63 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (47 bp):
TTATCCACTTCTGGTGGGTTATAAGTAATCATCCACATCTTGATGGG
Found at i:911066 original size:54 final size:56
Alignment explanation
Indices: 910959--911086 Score: 170
Period size: 54 Copynumber: 2.3 Consensus size: 56
910949 AATAATACCG
* * **
910959 CATTCACTTCAAAGAATGAACTAATTTATAATTTTTTATTAGTATCTTGTTTGTCA
1 CATTCACTTCAAAGAATGAACTAATTCATAATTTTTTATTAGTAGCTCATTTGTCA
* *
911015 CATTCACTTCAGAGAATG-AC-CATTCATAATTTTTTATTAGTAGCTCATTTGTCA
1 CATTCACTTCAAAGAATGAACTAATTCATAATTTTTTATTAGTAGCTCATTTGTCA
* *
911069 CATTCACTTTAAGGAATG
1 CATTCACTTCAAAGAATG
911087 GACATTCGTG
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 44 0.70
55 2 0.03
56 17 0.27
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (56 bp):
CATTCACTTCAAAGAATGAACTAATTCATAATTTTTTATTAGTAGCTCATTTGTCA
Found at i:911427 original size:15 final size:15
Alignment explanation
Indices: 911407--911444 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
911397 TATAAAGGAA
911407 AGAGAAAGTATTTAG
1 AGAGAAAGTATTTAG
911422 AGAGAAAGTATTTAG
1 AGAGAAAGTATTTAG
*
911437 AGAAAAAG
1 AGAGAAAG
911445 AAAATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.26, T:0.21
Consensus pattern (15 bp):
AGAGAAAGTATTTAG
Found at i:915656 original size:9 final size:9
Alignment explanation
Indices: 915642--915668 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
915632 GTTTTGTATA
915642 TTCTCATTT
1 TTCTCATTT
915651 TTCTCATTT
1 TTCTCATTT
915660 TTCTCATTT
1 TTCTCATTT
915669 CAAGTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (9 bp):
TTCTCATTT
Found at i:926444 original size:2 final size:2
Alignment explanation
Indices: 926437--926470 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
926427 TTAGGGTTGA
926437 AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
926471 TTTTGCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:934441 original size:22 final size:20
Alignment explanation
Indices: 934403--934451 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
934393 TTTTTTATTA
*
934403 TTTATTTTTTATTTTTCTTAGT
1 TTTATTTTTTATATTTC-TA-T
934425 TTTATTTTTTCA-ATTTCTAT
1 TTTATTTTTT-ATATTTCTAT
934445 TTTATTT
1 TTTATTT
934452 ATTTTTATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 8 0.32
21 2 0.08
22 14 0.56
23 1 0.04
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTATTTTTTATATTTCTAT
Found at i:934458 original size:30 final size:29
Alignment explanation
Indices: 934394--934459 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
934384 TTTGGGTTAT
* *
934394 TTTTTATTATTTATTTTTTATTTTTCTTA
1 TTTTTATTATTTAATTTCTATTTTTCTTA
* *
934423 GTTTTATTTTTTCAATTTCTATTTTAT-TTA
1 TTTTTATTATTT-AATTTCTATTTT-TCTTA
934453 TTTTTAT
1 TTTTTAT
934460 CATTAGAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 10 0.33
30 19 0.63
31 1 0.03
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.76
Consensus pattern (29 bp):
TTTTTATTATTTAATTTCTATTTTTCTTA
Found at i:947892 original size:19 final size:21
Alignment explanation
Indices: 947870--947925 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 21
947860 TTATAGGGGT
*
947870 AAAATTATAAAAT-TTTTA-A
1 AAAATTATAAAATATGTTAGA
*
947889 AAAAATA-AAAATATGTTAGA
1 AAAATTATAAAATATGTTAGA
*
947909 AAAATTTTAAAA-ATGTT
1 AAAATTATAAAATATGTT
947926 GTAGGGGTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 5 0.17
19 10 0.33
20 11 0.37
21 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (21 bp):
AAAATTATAAAATATGTTAGA
Found at i:949981 original size:2 final size:2
Alignment explanation
Indices: 949974--949998 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
949964 GGTTTAAGTA
949974 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
949999 GACATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:950198 original size:45 final size:44
Alignment explanation
Indices: 950116--950366 Score: 247
Period size: 45 Copynumber: 5.7 Consensus size: 44
950106 ACACGTCATG
* * * *
950116 ATGTTACACGTTATGGTTAGATTGTTACACGCTATGTATAAAAAC
1 ATGTGACACGTCATGGTTAGGTTGTTACACGC-ATGTACAAAAAC
* *
950161 ATGTGACATGTCATGGTTAGGTTGTTACACGTCATGTACAGAAAC
1 ATGTGACACGTCATGGTTAGGTTGTTACACG-CATGTACAAAAAC
* * * * *
950206 ATGTTACACGCCATGATTAGATTGTTACACGCTATGCACAAAAAC
1 ATGTGACACGTCATGGTTAGGTTGTTACACGC-ATGTACAAAAAC
* * *
950251 ATGTGACTCGCCATGGTTAGGTTGTTACATGTCATGTA-AAAAAC
1 ATGTGACACGTCATGGTTAGGTTGTTACACG-CATGTACAAAAAC
* * * * * *
950295 ATGTGACACATCAT-GTTAGTTTGTTACATGCCAGGTATAAAAAT
1 ATGTGACACGTCATGGTTAGGTTGTTACACG-CATGTACAAAAAC
*
950339 ATGTGACACATCAT-GTTAGGTTGTTACA
1 ATGTGACACGTCATGGTTAGGTTGTTACA
950367 AGTTATGGTT
Statistics
Matches: 175, Mismatches: 27, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
43 20 0.11
44 50 0.29
45 103 0.59
46 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (44 bp):
ATGTGACACGTCATGGTTAGGTTGTTACACGCATGTACAAAAAC
Found at i:950269 original size:90 final size:88
Alignment explanation
Indices: 950116--950366 Score: 308
Period size: 90 Copynumber: 2.8 Consensus size: 88
950106 ACACGTCATG
*
950116 ATGTTACACGTTATGGTTAGATTGTTACACGCTATGTATAAAAACATGTGACAT-GTCATGGTTA
1 ATGTTACACGTCAT-GTTAGATTGTTACACGCTATGTATAAAAACATGTGAC-TCGTCATGGTTA
*
950180 GGTTGTTACACGTCATGTACAGAAAC
64 GGTTGTTACACGTCATGTA-AAAAAC
* * * *
950206 ATGTTACACGCCATGATTAGATTGTTACACGCTATGCACAAAAACATGTGACTCGCCATGGTTAG
1 ATGTTACACGTCATG-TTAGATTGTTACACGCTATGTATAAAAACATGTGACTCGTCATGGTTAG
*
950271 GTTGTTACATGTCATGTAAAAAAC
65 GTTGTTACACGTCATGTAAAAAAC
* * * * * * * * *
950295 ATGTGACACATCATGTTAGTTTGTTACATGCCAGGTATAAAAATATGTGACACATCAT-GTTAGG
1 ATGTTACACGTCATGTTAGATTGTTACACGCTATGTATAAAAACATGTGACTCGTCATGGTTAGG
950359 TTGTTACA
66 TTGTTACA
950367 AGTTATGGTT
Statistics
Matches: 139, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
87 14 0.10
88 33 0.24
89 19 0.14
90 73 0.53
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (88 bp):
ATGTTACACGTCATGTTAGATTGTTACACGCTATGTATAAAAACATGTGACTCGTCATGGTTAGG
TTGTTACACGTCATGTAAAAAAC
Found at i:950565 original size:28 final size:28
Alignment explanation
Indices: 950534--950607 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
950524 CGCCTTGTTG
*
950534 AAAAAATATTGTTGTTACACGTTATAT-T
1 AAAAAATATTGTTGTTACACGTTA-ATGC
*
950562 AAAAAACTATT-TTGTTACACTTTAATGC
1 AAAAAA-TATTGTTGTTACACGTTAATGC
*
950590 AAAAACTATTGTTGTTAC
1 AAAAAATATTGTTGTTAC
950608 TTACAAACTA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 6 0.15
28 30 0.75
29 4 0.10
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (28 bp):
AAAAAATATTGTTGTTACACGTTAATGC
Found at i:962523 original size:2 final size:2
Alignment explanation
Indices: 962513--962546 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
962503 CTTTTTTTGT
962513 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
962547 TAGACTAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:971959 original size:2 final size:2
Alignment explanation
Indices: 971954--971988 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
971944 TGTGTGCAAC
* *
971954 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
971989 TATTAATTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1012676 original size:29 final size:29
Alignment explanation
Indices: 1012644--1012713 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
1012634 AGGGTGTCGA
*
1012644 AAATTGGGGAATTAGGGTTAAGGATATAG
1 AAATTGGGGAATTAAGGTTAAGGATATAG
* * *
1012673 AAATTGGGAAATTAAGGTTAGGGATCTAG
1 AAATTGGGGAATTAAGGTTAAGGATATAG
1012702 AAATT-GGGAATT
1 AAATTGGGGAATT
1012714 TAGAATTAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 6 0.17
29 30 0.83
ACGTcount: A:0.39, C:0.01, G:0.31, T:0.29
Consensus pattern (29 bp):
AAATTGGGGAATTAAGGTTAAGGATATAG
Found at i:1021115 original size:12 final size:12
Alignment explanation
Indices: 1021085--1021152 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
1021075 GAGGAAAAAG
1021085 AGAAAAAAAGAGGA
1 AGAAAAAAAGA--A
*
1021099 A-AAAATAAGAA
1 AGAAAAAAAGAA
1021110 AGAAAAAAAGATA
1 AGAAAAAAAGA-A
* *
1021123 AGAAAAGAACAA
1 AGAAAAAAAGAA
*
1021135 AGAAACAAAAGCA
1 AGAAA-AAAAGAA
1021148 AGAAA
1 AGAAA
1021153 CATTTAAAAG
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
11 2 0.05
12 14 0.32
13 27 0.61
14 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.03
Consensus pattern (12 bp):
AGAAAAAAAGAA
Found at i:1021128 original size:25 final size:25
Alignment explanation
Indices: 1021085--1021145 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
1021075 GAGGAAAAAG
* *
1021085 AGAAAAAAAGAGGAAAAAATAAGAA
1 AGAAAAAAAGAGGAAAAAAGAACAA
*
1021110 AGAAAAAAAGA-TAAGAAAAGAACAA
1 AGAAAAAAAGAGGAA-AAAAGAACAA
1021135 AGAAACAAAAG
1 AGAAA-AAAAG
1021146 CAAGAAACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.06
25 24 0.77
26 5 0.16
ACGTcount: A:0.75, C:0.03, G:0.18, T:0.03
Consensus pattern (25 bp):
AGAAAAAAAGAGGAAAAAAGAACAA
Found at i:1024565 original size:34 final size:34
Alignment explanation
Indices: 1024519--1024629 Score: 159
Period size: 35 Copynumber: 3.2 Consensus size: 34
1024509 TAGGGGCAAG
1024519 AATACCACTTGATTATAACCCATCATGGGGGTAA
1 AATACCACTTGATTATAACCCATCATGGGGGTAA
* * *
1024553 AATACCAGTTGATTATAACCCATCGTGAGGGTAAA
1 AATACCACTTGATTATAACCCATCATGGGGGT-AA
* *
1024588 AAAACCACTTGATTATAACCTATCATGGGGGTAA
1 AATACCACTTGATTATAACCCATCATGGGGGTAA
1024622 GAATACCA
1 -AATACCA
1024630 TATGAATAAC
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
34 31 0.47
35 35 0.53
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (34 bp):
AATACCACTTGATTATAACCCATCATGGGGGTAA
Found at i:1028597 original size:2 final size:2
Alignment explanation
Indices: 1028590--1028616 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1028580 TAATATTTAA
1028590 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1028617 CATTTTCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1036960 original size:28 final size:28
Alignment explanation
Indices: 1036898--1036961 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
1036888 ATGGACGTCC
* * *
1036898 ATGTTCATGAATATTTTTATGAATTTTT
1 ATGTTCTTAAATATTATTATGAATTTTT
1036926 ATGTTCTTAAATATTATTAT-AGATTTTT
1 ATGTTCTTAAATATTATTATGA-ATTTTT
*
1036954 GTGTTCTT
1 ATGTTCTT
1036962 CTTTAATATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 1 0.03
28 30 0.97
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.58
Consensus pattern (28 bp):
ATGTTCTTAAATATTATTATGAATTTTT
Found at i:1038383 original size:6 final size:6
Alignment explanation
Indices: 1038369--1038399 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1038359 TTTGAAATTT
*
1038369 TGGTCA TGGTTA TGGTCA TGGTCA TGGTCA T
1 TGGTCA TGGTCA TGGTCA TGGTCA TGGTCA T
1038400 AATCGTGGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.13, G:0.32, T:0.39
Consensus pattern (6 bp):
TGGTCA
Found at i:1041726 original size:219 final size:219
Alignment explanation
Indices: 1041342--1041780 Score: 842
Period size: 219 Copynumber: 2.0 Consensus size: 219
1041332 ATTCGATCAA
1041342 ATTAAATAAATTTTTATATGGATTAAAACAATCTGGATGCATATAGTATAATGGTCTTAATGAAT
1 ATTAAATAAATTTTTATATGGATTAAAACAATCTGGATGCATATAGTATAATGGTCTTAATGAAT
*
1041407 ATTTGTTGAAAGAATGCTATAAAAATAATCTTATATACCCACGTATTTTATAAAAAGGTTTAGAT
66 ATTTGTTGAAAGAATGCTATAAAAATAATCTTATATACCCACGTATTTTATAAAAAGATTTAGAT
*
1041472 ATGAATTTATCATAATTGTTGTTTATGTTGATGACTTGAACATTGTTGGAACTCTTGAAGAATTA
131 ATGAATTTATCATAATTGTTGTTTATGTCGATGACTTGAACATTGTTGGAACTCTTGAAGAATTA
1041537 TCAAAAACTATAGAATATTTAAAG
196 TCAAAAACTATAGAATATTTAAAG
1041561 ATTAAATAAATTTTTATATGGATTAAAACAATCTGGATGCATATAGTATAATGGTCTTAATGAAT
1 ATTAAATAAATTTTTATATGGATTAAAACAATCTGGATGCATATAGTATAATGGTCTTAATGAAT
1041626 ATTTGTTGAAAGAATGCTATAAAAATAATCTTATATACCCACGTATTTTATAAAAAGATTTAGAT
66 ATTTGTTGAAAGAATGCTATAAAAATAATCTTATATACCCACGTATTTTATAAAAAGATTTAGAT
1041691 ATGAATTTATCATAATTGTTGTTTATGTCGATGACTTGAACATTGTTGGAACTCTTGAAGAATTA
131 ATGAATTTATCATAATTGTTGTTTATGTCGATGACTTGAACATTGTTGGAACTCTTGAAGAATTA
* *
1041756 TCAAAAACTGTGGAATATTTAAAG
196 TCAAAAACTATAGAATATTTAAAG
1041780 A
1 A
1041781 GAGAATTTGA
Statistics
Matches: 216, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
219 216 1.00
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (219 bp):
ATTAAATAAATTTTTATATGGATTAAAACAATCTGGATGCATATAGTATAATGGTCTTAATGAAT
ATTTGTTGAAAGAATGCTATAAAAATAATCTTATATACCCACGTATTTTATAAAAAGATTTAGAT
ATGAATTTATCATAATTGTTGTTTATGTCGATGACTTGAACATTGTTGGAACTCTTGAAGAATTA
TCAAAAACTATAGAATATTTAAAG
Found at i:1043180 original size:23 final size:23
Alignment explanation
Indices: 1043152--1043198 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1043142 TTCTTTCTTC
1043152 TCTTTAATTATTCCTTCAAGTTA
1 TCTTTAATTATTCCTTCAAGTTA
* * * *
1043175 TCTTTATTTGTTCTTTTAAGTTA
1 TCTTTAATTATTCCTTCAAGTTA
1043198 T
1 T
1043199 AATTTCATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.21, C:0.13, G:0.06, T:0.60
Consensus pattern (23 bp):
TCTTTAATTATTCCTTCAAGTTA
Found at i:1044067 original size:17 final size:17
Alignment explanation
Indices: 1044027--1044060 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1044017 TTGAATCTTT
1044027 AATTT-TTAATATTTAA
1 AATTTATTAATATTTAA
*
1044043 AATTTATTAATTTTTAA
1 AATTTATTAATATTTAA
1044060 A
1 A
1044061 TATTATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTTATTAATATTTAA
Found at i:1059341 original size:68 final size:68
Alignment explanation
Indices: 1059153--1059343 Score: 224
Period size: 69 Copynumber: 2.8 Consensus size: 68
1059143 GCATGTAAGC
* * * *
1059153 TATGTTGTAATGTATGTGATGTTATTTGCACATACTATATGAGATGAGAATCAACATATGATGTA
1 TATGTTGTAATGTATGTGATGTTATTTCCACATACTATATGAGATGAGAATGAGCATATGATATA
1059218 TAT
66 TAT
** *
1059221 TATGTTGCCATGTATGTGATGCTTATTTTCACATACTATATGAGATGAGAATGAGCACT-TGATA
1 TATGTTGTAATGTATGTGATG-TTATTTCCACATACTATATGAGATGAGAATGAGCA-TATGATA
*
1059285 TGTAT
64 TATAT
* * * **
1059290 TATGTTGTAA-GTTATGTGATGTTAATACCACATCCTATATGAGACAAGAATGAG
1 TATGTTGTAATG-TATGTGATGTTATTTCCACATACTATATGAGATGAGAATGAG
1059344 ATTACCGTGA
Statistics
Matches: 105, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
68 47 0.45
69 57 0.54
70 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (68 bp):
TATGTTGTAATGTATGTGATGTTATTTCCACATACTATATGAGATGAGAATGAGCATATGATATA
TAT
Found at i:1063855 original size:20 final size:20
Alignment explanation
Indices: 1063805--1063859 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
1063795 TTATAATTTT
*
1063805 ATTAATTAATT-AA-TTTAA
1 ATTAATCAATTCAATTTTAA
*
1063823 ATGAATCATATTCAATTTTAA
1 ATTAATCA-ATTCAATTTTAA
*
1063844 ATTAATGAATTCAATT
1 ATTAATCAATTCAATT
1063860 CCATAGGCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 6 0.20
19 3 0.10
20 10 0.33
21 11 0.37
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (20 bp):
ATTAATCAATTCAATTTTAA
Found at i:1067427 original size:36 final size:36
Alignment explanation
Indices: 1067386--1067501 Score: 162
Period size: 36 Copynumber: 3.2 Consensus size: 36
1067376 GCTTCGCTTC
*
1067386 AAGGGTCTTCTGATATGATCTAGAACGATTGACCTT
1 AAGGGTCTTCTGATATGATCTAGAAAGATTGACCTT
*
1067422 AAGGGTCTTCTGATATGATCTAGAATGATTGACCTT
1 AAGGGTCTTCTGATATGATCTAGAAAGATTGACCTT
* * * *
1067458 AAGGGTCTTCTGACTA-GATTTTGAAAAATTAACCTT
1 AAGGGTCTTCTGA-TATGATCTAGAAAGATTGACCTT
1067494 AAGGGTCT
1 AAGGGTCT
1067502 CATGATTGAA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
36 71 0.97
37 2 0.03
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (36 bp):
AAGGGTCTTCTGATATGATCTAGAAAGATTGACCTT
Found at i:1067657 original size:70 final size:70
Alignment explanation
Indices: 1067517--1067650 Score: 187
Period size: 70 Copynumber: 1.9 Consensus size: 70
1067507 TTGAATCTTA
* * * *
1067517 ACCTCAAGGGTCTTATGAACAATTGGGAGGCTTTGCTTCAATGGTCTTCTAACTTAATCTTGAAC
1 ACCTCAAGGGTCTTATGAACAATTGGAAGGCTTCGCTTCAAGGGTCTTCTAACTTAATCTAGAAC
1067582 TATTG
66 TATTG
* * * * *
1067587 ACCTTAAGGGTCTTATGAACAATTTGAAGGCTTCGTTTCAAGGGTCTTCTGACTTGATCTAGAA
1 ACCTCAAGGGTCTTATGAACAATTGGAAGGCTTCGCTTCAAGGGTCTTCTAACTTAATCTAGAA
1067651 TAATTGATTT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
70 55 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (70 bp):
ACCTCAAGGGTCTTATGAACAATTGGAAGGCTTCGCTTCAAGGGTCTTCTAACTTAATCTAGAAC
TATTG
Found at i:1067680 original size:49 final size:49
Alignment explanation
Indices: 1067623--1067781 Score: 167
Period size: 49 Copynumber: 3.2 Consensus size: 49
1067613 AAGGCTTCGT
* ** *
1067623 TTCAAGGGTCTTCTGACTTGATCTAGAATAATTGATTTGGAAACTTTGC
1 TTCAAGGGTCTTCTGACTTGATCTTGAACGATTGATTTGGAGACTTTGC
* * * * *
1067672 TTCAAGGGTTTTTTGACTTGATCTTGAACGATTAATTTAGAGACTATGC
1 TTCAAGGGTCTTCTGACTTGATCTTGAACGATTGATTTGGAGACTTTGC
* * * * *
1067721 TTCAAGGGACTTGC-AACTTGATCTTGAACGATTGTTTTGGTGACTTCGC
1 TTCAAGGGTCTT-CTGACTTGATCTTGAACGATTGATTTGGAGACTTTGC
*
1067770 TTCAAGGATCTT
1 TTCAAGGGTCTT
1067782 GCAACTTAGT
Statistics
Matches: 88, Mismatches: 21, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
49 88 1.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.39
Consensus pattern (49 bp):
TTCAAGGGTCTTCTGACTTGATCTTGAACGATTGATTTGGAGACTTTGC
Found at i:1077853 original size:15 final size:16
Alignment explanation
Indices: 1077835--1077869 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1077825 GTAAATAAAG
1077835 TAAATGACATAAAAA-
1 TAAATGACATAAAAAC
*
1077850 TAAATGTCATAAAAAC
1 TAAATGACATAAAAAC
1077866 TAAA
1 TAAA
1077870 GTTGTTGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.63, C:0.09, G:0.06, T:0.23
Consensus pattern (16 bp):
TAAATGACATAAAAAC
Found at i:1081696 original size:14 final size:15
Alignment explanation
Indices: 1081677--1081707 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1081667 TATTGTTATA
1081677 ATTAAAATAAAA-AT
1 ATTAAAATAAAATAT
1081691 ATTAAAATAAAATAT
1 ATTAAAATAAAATAT
1081706 AT
1 AT
1081708 AATATAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
ATTAAAATAAAATAT
Found at i:1081729 original size:33 final size:34
Alignment explanation
Indices: 1081673--1081748 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 34
1081663 TTAGTATTGT
1081673 TATAAT-TAA-AATAAAAATATTAAAATAAAATA
1 TATAATATAAGAATAAAAATATTAAAATAAAATA
*
1081705 TATAATATAAGAATCAAAA-ATTAAAATAAAATA
1 TATAATATAAGAATAAAAATATTAAAATAAAATA
1081738 -A-AATATAAGAA
1 TATAATATAAGAA
1081749 ATTAAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
31 10 0.24
32 7 0.17
33 17 0.41
34 7 0.17
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (34 bp):
TATAATATAAGAATAAAAATATTAAAATAAAATA
Found at i:1083347 original size:14 final size:14
Alignment explanation
Indices: 1083328--1083354 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1083318 AAGGAAAAAA
1083328 GACCGAGAAAACTT
1 GACCGAGAAAACTT
1083342 GACCGAGAAAACT
1 GACCGAGAAAACT
1083355 AGCAGCCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.11
Consensus pattern (14 bp):
GACCGAGAAAACTT
Found at i:1087527 original size:18 final size:18
Alignment explanation
Indices: 1087504--1087539 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1087494 ATTAGGGATT
1087504 TGAAATAATATTTTTTGG
1 TGAAATAATATTTTTTGG
1087522 TGAAATAATATTTTTTGG
1 TGAAATAATATTTTTTGG
1087540 AAAAAAATAC
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:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (18 bp):
TGAAATAATATTTTTTGG
Found at i:1091607 original size:13 final size:13
Alignment explanation
Indices: 1091589--1091614 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1091579 ACTTGGCCAA
1091589 GTTACATCTCTAC
1 GTTACATCTCTAC
1091602 GTTACATCTCTAC
1 GTTACATCTCTAC
1091615 CATCTGTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (13 bp):
GTTACATCTCTAC
Found at i:1092981 original size:12 final size:12
Alignment explanation
Indices: 1092964--1092989 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1092954 CGTATCATGA
1092964 TAAGCAGTTCAT
1 TAAGCAGTTCAT
1092976 TAAGCAGTTCAT
1 TAAGCAGTTCAT
1092988 TA
1 TA
1092990 GATGGCATTG
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:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (12 bp):
TAAGCAGTTCAT
Found at i:1096354 original size:12 final size:12
Alignment explanation
Indices: 1096337--1096361 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1096327 GGACCTCAAC
1096337 TGAACTCCATAT
1 TGAACTCCATAT
1096349 TGAACTCCATAT
1 TGAACTCCATAT
1096361 T
1 T
1096362 ATGCTCCCTT
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:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (12 bp):
TGAACTCCATAT
Found at i:1113863 original size:21 final size:21
Alignment explanation
Indices: 1113837--1113876 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1113827 TACTAACTGA
1113837 TCTTAAATTATTTAAAAATAT
1 TCTTAAATTATTTAAAAATAT
1113858 TCTTAAATTATTTAAAAAT
1 TCTTAAATTATTTAAAAAT
1113877 CTAGATAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
TCTTAAATTATTTAAAAATAT
Found at i:1114138 original size:19 final size:18
Alignment explanation
Indices: 1114102--1114146 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1114092 ATTAATGTAG
* *
1114102 AAAAATAAATAAATAGAA
1 AAAAATAAAAAAAAAGAA
*
1114120 TAAAATAACAAAAAAAGAA
1 AAAAATAA-AAAAAAAGAA
1114139 AAAAATAA
1 AAAAATAA
1114147 GAGCTTCGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.13
Consensus pattern (18 bp):
AAAAATAAAAAAAAAGAA
Found at i:1121474 original size:25 final size:27
Alignment explanation
Indices: 1121446--1121501 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
1121436 TGGGTTGCTA
*
1121446 ACGGGC-T-ATTAGAAGTGGCTAGGCC
1 ACGGGCGTGATTAGAAGTGGCAAGGCC
* *
1121471 ACGGTCTGTGATTATAAGTGGCAAGGCC
1 ACGGGC-GTGATTAGAAGTGGCAAGGCC
1121499 ACG
1 ACG
1121502 AGTTGATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 5 0.20
27 1 0.04
28 19 0.76
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (27 bp):
ACGGGCGTGATTAGAAGTGGCAAGGCC
Found at i:1126645 original size:21 final size:21
Alignment explanation
Indices: 1126621--1126660 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1126611 AAAAGGACAA
1126621 GAAAAAGAAGA-TGAAGAAGTT
1 GAAAAAGAA-ATTGAAGAAGTT
*
1126642 GAAAAGGAAATTGAAGAAG
1 GAAAAAGAAATTGAAGAAG
1126661 AAGGCGAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.57, C:0.00, G:0.30, T:0.12
Consensus pattern (21 bp):
GAAAAAGAAATTGAAGAAGTT
Found at i:1158354 original size:3 final size:3
Alignment explanation
Indices: 1158346--1158384 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1158336 TATATACTTA
1158346 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1158385 CTTCTAATAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1159134 original size:27 final size:28
Alignment explanation
Indices: 1159090--1159149 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
1159080 ATTATGTTTG
* *
1159090 AAAAATAATATTGTTATATGTCATATTC
1 AAAAATAATATTGCTATACGTCATATTC
* * *
1159118 AAAAAT-ATGTTGCTATACGTCATGTTG
1 AAAAATAATATTGCTATACGTCATATTC
1159145 AAAAA
1 AAAAA
1159150 GAAAATGTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (28 bp):
AAAAATAATATTGCTATACGTCATATTC
Found at i:1159576 original size:34 final size:34
Alignment explanation
Indices: 1159506--1159631 Score: 126
Period size: 34 Copynumber: 3.7 Consensus size: 34
1159496 TGTTACACAC
* * *
1159506 CAAAACTTTAGCAACAGATATTACACGCTAAGGT
1 CAAAACTTCAGCACCAGATATTACATGCTAAGGT
* *
1159540 CAAAACTTCAGCACCAGATATTACATGTTAAAGT
1 CAAAACTTCAGCACCAGATATTACATGCTAAGGT
** * * * *
1159574 CAAAGTTTCAGTACCATATGTTACATGCCAAGGT
1 CAAAACTTCAGCACCAGATATTACATGCTAAGGT
* **
1159608 CAAAGCTTCAGCATTAGATATTAC
1 CAAAACTTCAGCACCAGATATTAC
1159632 TCACCAAACT
Statistics
Matches: 73, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
34 73 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (34 bp):
CAAAACTTCAGCACCAGATATTACATGCTAAGGT
Found at i:1159726 original size:34 final size:34
Alignment explanation
Indices: 1159688--1159785 Score: 83
Period size: 34 Copynumber: 2.9 Consensus size: 34
1159678 GCAACAGATA
1159688 TTACACGATAAGGTCAAAGCTTTAATACTAAATG
1 TTACACGATAAGGTCAAAGCTTTAATACTAAATG
* ** * * *
1159722 TTACACGTTAAAATCAAAGTTTTAGTAAC-AGATG
1 TTACACGATAAGGTCAAAGCTTTAAT-ACTAAATG
* * *
1159756 TTACA-TACCAAGGTCAAAGCTTTAACACTA
1 TTACACGA-TAAGGTCAAAGCTTTAATACTA
1159786 GATATTACTT
Statistics
Matches: 47, Mismatches: 14, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
33 2 0.04
34 43 0.91
35 2 0.04
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (34 bp):
TTACACGATAAGGTCAAAGCTTTAATACTAAATG
Found at i:1159761 original size:162 final size:162
Alignment explanation
Indices: 1159494--1159824 Score: 473
Period size: 162 Copynumber: 2.0 Consensus size: 162
1159484 AGCCTAAGTA
* * *
1159494 GATGTTACACACCAAAACTTTAGCAACAGATATTACACGCTAAGGTCAAAACTTCAGCACCAGAT
1 GATGTTACACACCAAAACTTTAGCAACAGATATTACACGATAAGGTCAAAACTTCAACACCAAAT
* * * * * * *
1159559 ATTACATGTTAAAGTCAAAGTTTCAGTACCATATGTTACATGCCAAGGTCAAAGCTTCAGCATTA
66 ATTACACGTTAAAATCAAAGTTTCAGTAACAGATGTTACATACCAAGGTCAAAGCTTCAACACTA
* *
1159624 GATATTACTCACCAAACTTTTTTCTTCCTACT
131 GATATTACTCACCAAACTTCTTTCTTCATACT
* * * * *
1159656 GATGTTACACACTAAAACTTTAGCAACAGATATTACACGATAAGGTCAAAGCTTTAATACTAAAT
1 GATGTTACACACCAAAACTTTAGCAACAGATATTACACGATAAGGTCAAAACTTCAACACCAAAT
* * *
1159721 GTTACACGTTAAAATCAAAGTTTTAGTAACAGATGTTACATACCAAGGTCAAAGCTTTAACACTA
66 ATTACACGTTAAAATCAAAGTTTCAGTAACAGATGTTACATACCAAGGTCAAAGCTTCAACACTA
*
1159786 GATATTACTTACCAAACTTCTTTCTTCATACT
131 GATATTACTCACCAAACTTCTTTCTTCATACT
1159818 GATGTTA
1 GATGTTA
1159825 TATGTCAAGG
Statistics
Matches: 148, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
162 148 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (162 bp):
GATGTTACACACCAAAACTTTAGCAACAGATATTACACGATAAGGTCAAAACTTCAACACCAAAT
ATTACACGTTAAAATCAAAGTTTCAGTAACAGATGTTACATACCAAGGTCAAAGCTTCAACACTA
GATATTACTCACCAAACTTCTTTCTTCATACT
Found at i:1160448 original size:2 final size:2
Alignment explanation
Indices: 1160441--1160470 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1160431 TTGATGCATA
1160441 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
1160471 GTATGTTAGT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1173750 original size:99 final size:99
Alignment explanation
Indices: 1173642--1173843 Score: 359
Period size: 99 Copynumber: 2.0 Consensus size: 99
1173632 CAAAGAAAAA
**
1173642 AAAAACTTAATAAAAAAAACTTTTCAAGAGATAAAGATTCACCAAGTCATGATTTCCTAATTTTT
1 AAAAACTTAATAAAAAAAACTTTTCAAGAGATAAAGATTCACCAAGTCACCATTTCCTAATTTTT
1173707 CCTCAAAAATTATTCAACAATCTCAACTAAAGGT
66 CCTCAAAAATTATTCAACAATCTCAACTAAAGGT
* *
1173741 AAAAACTTAATAAAAAAAACTTTTTAGGAGATAAAGATTCACCAAGTCACCATTTCCTAATTTTT
1 AAAAACTTAATAAAAAAAACTTTTCAAGAGATAAAGATTCACCAAGTCACCATTTCCTAATTTTT
*
1173806 CCTCAAAAATTATTCAACAATCTCAACTTAAGGT
66 CCTCAAAAATTATTCAACAATCTCAACTAAAGGT
1173840 AAAA
1 AAAA
1173844 TATAAATAAT
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
99 98 1.00
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (99 bp):
AAAAACTTAATAAAAAAAACTTTTCAAGAGATAAAGATTCACCAAGTCACCATTTCCTAATTTTT
CCTCAAAAATTATTCAACAATCTCAACTAAAGGT
Found at i:1175673 original size:12 final size:12
Alignment explanation
Indices: 1175656--1175690 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1175646 AGAATAGTTT
1175656 CTTGCTGCCTCC
1 CTTGCTGCCTCC
*
1175668 CTTGCTGCCTCT
1 CTTGCTGCCTCC
1175680 CTTGCTGCCTC
1 CTTGCTGCCTC
1175691 AAAAATCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.46, G:0.17, T:0.37
Consensus pattern (12 bp):
CTTGCTGCCTCC
Found at i:1176375 original size:21 final size:22
Alignment explanation
Indices: 1176340--1176383 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1176330 CTCTTAAAGT
1176340 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
1176362 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
1176383 A
1 A
1176384 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:1179244 original size:19 final size:19
Alignment explanation
Indices: 1179220--1179279 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
1179210 AATAATAGCT
*
1179220 AAATTAAAGTAAATAAATA
1 AAATTAAAATAAATAAATA
* *
1179239 AAATTAAAATAACTCAATA
1 AAATTAAAATAAATAAATA
* * *
1179258 AAAATAAACTAATTAAA-A
1 AAATTAAAATAAATAAATA
1179276 AAAT
1 AAAT
1179280 AATTAAATTC
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
18 4 0.12
19 29 0.88
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (19 bp):
AAATTAAAATAAATAAATA
Found at i:1179275 original size:14 final size:14
Alignment explanation
Indices: 1179240--1179286 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
1179230 AAATAAATAA
1179240 AATTAAAAT-AACT
1 AATTAAAATAAACT
*
1179253 CAATAAAAATAAACT
1 -AATTAAAATAAACT
1179268 AATTAAAA-AAA-T
1 AATTAAAATAAACT
1179280 AATTAAA
1 AATTAAA
1179287 TTCTAGTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 8 0.27
13 3 0.10
14 15 0.50
15 4 0.13
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (14 bp):
AATTAAAATAAACT
Found at i:1180920 original size:18 final size:19
Alignment explanation
Indices: 1180897--1180932 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1180887 TCATTAATTA
1180897 TTTAG-TTAAATAATCATT
1 TTTAGTTTAAATAATCATT
*
1180915 TTTAGTTTAATTAATCAT
1 TTTAGTTTAAATAATCAT
1180933 ATGAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.53
Consensus pattern (19 bp):
TTTAGTTTAAATAATCATT
Found at i:1191564 original size:23 final size:24
Alignment explanation
Indices: 1191520--1191624 Score: 67
Period size: 23 Copynumber: 4.5 Consensus size: 24
1191510 GAGATAGCCA
* *
1191520 TGGTGTGTAACATC-CAGTAGCTC
1 TGGTGTGTAACATCTTAGAAGCTC
*
1191543 TGGTGTGTAACATCTTA-AAGCTT
1 TGGTGTGTAACATCTTAGAAGCTC
* * * *
1191566 TGGCGTGTGACATCTT-GAATCTT
1 TGGTGTGTAACATCTTAGAAGCTC
* ** *
1191589 TGATGCATAACATCTT-GATGCGT-
1 TGGTGTGTAACATCTTAGAAGC-TC
1191612 TGGTGTGTAACAT
1 TGGTGTGTAACAT
1191625 TTAACAACAC
Statistics
Matches: 63, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
23 61 0.97
24 2 0.03
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (24 bp):
TGGTGTGTAACATCTTAGAAGCTC
Found at i:1192843 original size:20 final size:20
Alignment explanation
Indices: 1192806--1192844 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1192796 CATTAACTCA
**
1192806 TTTCTCTCACTAGTTTTATC
1 TTTCTCTCACTACCTTTATC
*
1192826 TTTCTCTCTCTACCTTTAT
1 TTTCTCTCACTACCTTTAT
1192845 TGTAAGTGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.28, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTCTCTCACTACCTTTATC
Found at i:1204361 original size:19 final size:19
Alignment explanation
Indices: 1204321--1204362 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1204311 AAAATTCTAG
** *
1204321 AATAAAATAATATTTTATT
1 AATAAAATAATATTAAAAT
1204340 AATAAAATAATATTAAAAT
1 AATAAAATAATATTAAAAT
1204359 AATA
1 AATA
1204363 CTGATGTCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATAAAATAATATTAAAAT
Found at i:1209924 original size:5 final size:5
Alignment explanation
Indices: 1209875--1209906 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1209865 TCCTTGCATG
*
1209875 TTTCT TTTCT TTTCT TTTCT TTTCT TTCCT TT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TT
1209907 CTCCCTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTCT
Found at i:1210041 original size:19 final size:19
Alignment explanation
Indices: 1210017--1210056 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
1210007 CCAAAGGTTA
1210017 TTTTCTTTT-TCTATTATTT
1 TTTTCTTTTCTCT-TTATTT
1210036 TTTTCTTTTCTCTTTATTT
1 TTTTCTTTTCTCTTTATTT
1210055 TT
1 TT
1210057 CTTTATTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTCTTTTCTCTTTATTT
Found at i:1210044 original size:18 final size:17
Alignment explanation
Indices: 1210017--1210060 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1210007 CCAAAGGTTA
*
1210017 TTTTCTTTTTCTATTATTT
1 TTTTC-TTTTCTATT-TAT
*
1210036 TTTTCTTTTCTCTTTAT
1 TTTTCTTTTCTATTTAT
1210053 TTTTCTTT
1 TTTTCTTT
1210061 ATTCATTCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 10 0.43
18 8 0.35
19 5 0.22
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTCTTTTCTATTTAT
Found at i:1219465 original size:106 final size:106
Alignment explanation
Indices: 1219280--1219478 Score: 258
Period size: 106 Copynumber: 1.9 Consensus size: 106
1219270 TTCTAGAAAA
* * * * *
1219280 TGGGTGCTGAAATCACTTTAACAAATGCAAGAATAGTTTTTCGGTGTTTGATGGTAGGTTTAGAA
1 TGGGTGCTCAAATCACTTTAACAAATGCAAGAACAATTTTTCAGTGTTTGATGGTAGCTTTAGAA
* * * *
1219345 CCATAATGATGATTGGCAATGGTGACTTGGCTGCTAGATAG
66 CAAAAATGATGATTGGAAATAGTGACTTGGCTGCTAGATAG
** *
1219386 TGGGTGCTCAAATCA-TTTAACTGGATGCAAGAACAATTTTTTAGTGTTTGATGGTAGCTTTAGA
1 TGGGTGCTCAAATCACTTTAAC-AAATGCAAGAACAATTTTTCAGTGTTTGATGGTAGCTTTAGA
1219450 ACAAAAATGGA-GATTGGAAATAGTGACTT
65 ACAAAAAT-GATGATTGGAAATAGTGACTT
1219479 TCTATTAATT
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
105 6 0.08
106 71 0.90
107 2 0.03
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.33
Consensus pattern (106 bp):
TGGGTGCTCAAATCACTTTAACAAATGCAAGAACAATTTTTCAGTGTTTGATGGTAGCTTTAGAA
CAAAAATGATGATTGGAAATAGTGACTTGGCTGCTAGATAG
Found at i:1226566 original size:34 final size:35
Alignment explanation
Indices: 1226528--1226609 Score: 123
Period size: 34 Copynumber: 2.4 Consensus size: 35
1226518 GGTTTTGTTA
*
1226528 GATCCCATGAAAAAGCT-TTGTAAGGGTT-TCACTT
1 GATCCCATGAAAAA-CTAGTGTAAGGGTTATCACTT
1226562 GATCCCATGAAAAACTAGTGTAAGGGTTATCACTT
1 GATCCCATGAAAAACTAGTGTAAGGGTTATCACTT
*
1226597 GATCCCATTAAAA
1 GATCCCATGAAAA
1226610 GGAAAAAATC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
33 2 0.05
34 24 0.55
35 18 0.41
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (35 bp):
GATCCCATGAAAAACTAGTGTAAGGGTTATCACTT
Found at i:1226714 original size:89 final size:89
Alignment explanation
Indices: 1226579--1226751 Score: 224
Period size: 89 Copynumber: 1.9 Consensus size: 89
1226569 TGAAAAACTA
* * *
1226579 GTGTAAGGGTTATCACTTGATCCCATTAAAAGGAAAAAATCTCTTTGTAAATTATGGAAGGGTTA
1 GTGTAAAGGTTATCACTTGATCCCATTAAAAAGAAAAAATCCCTTTGTAAATTATGGAAGGGTTA
*
1226644 TTGTTTGAT-TTGGTGAAAAAGCCG
66 TCGTTTGATCTT-GTGAAAAAGCCG
* * * * * *
1226668 GTGTAAAGGTTATCACTTGAT-CTAGTTAAAAAGCAAGAATCCCTTTGTACATTGTGTAAGGGTT
1 GTGTAAAGGTTATCACTTGATCCCA-TTAAAAAGAAAAAATCCCTTTGTAAATTATGGAAGGGTT
1226732 ATCGTTTGATCTTGTGAAAA
65 ATCGTTTGATCTTGTGAAAA
1226752 TGCCATTGTG
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
88 2 0.03
89 68 0.94
90 2 0.03
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.35
Consensus pattern (89 bp):
GTGTAAAGGTTATCACTTGATCCCATTAAAAAGAAAAAATCCCTTTGTAAATTATGGAAGGGTTA
TCGTTTGATCTTGTGAAAAAGCCG
Found at i:1227927 original size:44 final size:44
Alignment explanation
Indices: 1227835--1227927 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
1227825 CACTTGGATT
* * * *
1227835 AATCTCAGATGGGTGGCATCAAATACAAAGTTATCATCCAGAGT
1 AATCTCAAATGGGTAGCATCAAATACAAAGTAATCATCCAGAGC
* *
1227879 AATCTCAAATGGGTAGTATCAAATACAAAGTCAAT-ATCTAGAGC
1 AATCTCAAATGGGTAGCATCAAATACAAAGT-AATCATCCAGAGC
1227923 AATCT
1 AATCT
1227928 TAACGGATGA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 40 0.95
45 2 0.05
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (44 bp):
AATCTCAAATGGGTAGCATCAAATACAAAGTAATCATCCAGAGC
Found at i:1231308 original size:28 final size:28
Alignment explanation
Indices: 1231243--1231418 Score: 174
Period size: 28 Copynumber: 6.0 Consensus size: 28
1231233 TTTAAGATAA
* *
1231243 TTCTTGTCTTTAATTAAGACAAAAACATGTT
1 TTCTTGTC-TAAATTAAGAC--AAATATGTT
* *
1231274 ATCTTGTCTAAATTGAGACAAATATGTT
1 TTCTTGTCTAAATTAAGACAAATATGTT
* * *
1231302 TTATTGTCTAGATTAAGATAAAACATAT-TT
1 TTCTTGTCTAAATTAAG--ACAA-ATATGTT
* *
1231332 TTCTTGTCTTAAATTAAGACAAATATATG
1 TTCTTGTC-TAAATTAAGACAAATATGTT
*
1231361 TTCTTGTCTAAATTAAGACCAAACATGTT
1 TTCTTGTCTAAATTAAGA-CAAATATGTT
*
1231390 TTCTTGTCTAAATTAAGACAAACATGTT
1 TTCTTGTCTAAATTAAGACAAATATGTT
1231418 T
1 T
1231419 AAGCTGCTAT
Statistics
Matches: 123, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
28 46 0.37
29 37 0.30
30 21 0.17
31 19 0.15
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (28 bp):
TTCTTGTCTAAATTAAGACAAATATGTT
Found at i:1231352 original size:59 final size:57
Alignment explanation
Indices: 1231254--1231418 Score: 213
Period size: 59 Copynumber: 2.8 Consensus size: 57
1231244 TCTTGTCTTT
* *
1231254 AATTAAGACAAAAACATGTTATCTTGTCTAAATTGAGACAAATATGTTTTATTGTCTA
1 AATTAAGAC-AAAACATGTTTTCTTGTCTAAATTAAGACAAATATGTTTTATTGTCTA
* * * * * *
1231312 GATTAAGATAAAACATATTTTTCTTGTCTTAAATTAAGACAAATATATGTTCTTGTCTA
1 AATTAAGACAAAACAT-GTTTTCTTGTC-TAAATTAAGACAAATATGTTTTATTGTCTA
* *
1231371 AATTAAGACCAAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTT
1 AATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAATATGTTT
1231419 AAGCTGCTAT
Statistics
Matches: 90, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
57 25 0.28
58 26 0.29
59 39 0.43
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (57 bp):
AATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAATATGTTTTATTGTCTA
Found at i:1243145 original size:31 final size:31
Alignment explanation
Indices: 1243110--1243271 Score: 118
Period size: 31 Copynumber: 5.2 Consensus size: 31
1243100 CATAACTAAC
* *
1243110 CTTAAACATCTTGGATTCCAGCTAAATTGGG
1 CTTAAACATCTTCGATGCCAGCTAAATTGGG
* * * ***
1243141 CTTAAACTATTTTCG-TGCCAAC-ATAACTAAA
1 CTTAAAC-ATCTTCGATGCCAGCTA-AATTGGG
*
1243172 CTTAAACATCTTCGATGCTAGCTAAATTGGG
1 CTTAAACATCTTCGATGCCAGCTAAATTGGG
* * *
1243203 CTTAAA-ATCTTTTC-ATGCC-GATATAACTGGA
1 CTTAAACATC--TTCGATGCCAGCTA-AATTGGG
* *
1243234 CTTAAACATCTTGGATGCCAACTAAATTGGG
1 CTTAAACATCTTCGATGCCAGCTAAATTGGG
1243265 CTTAAAC
1 CTTAAAC
1243272 TCACTCTGTG
Statistics
Matches: 97, Mismatches: 24, Indels: 20
0.69 0.17 0.14
Matches are distributed among these distances:
30 15 0.15
31 68 0.70
32 14 0.14
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (31 bp):
CTTAAACATCTTCGATGCCAGCTAAATTGGG
Found at i:1243195 original size:62 final size:62
Alignment explanation
Indices: 1243110--1243408 Score: 325
Period size: 62 Copynumber: 4.8 Consensus size: 62
1243100 CATAACTAAC
* * **
1243110 CTTAAACATCTTGGATTCCAGCTAAATTGGGCTTAAACTATTTTCGTGCCAACATAACTAAA
1 CTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAACTATTTTCGTGCCAACATAACTGGA
* * * * * *
1243172 CTTAAACATCTTCGATGCTAGCTAAATTGGGCTTAAAATCTTTTCATGCCGATATAACTGGA
1 CTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAACTATTTTCGTGCCAACATAACTGGA
* * * * **
1243234 CTTAAACATCTTGGATGCCAACTAAATTGGGCTTAAACTCACTCT-GTGCCAACATAGTTGGA
1 CTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAACT-ATTTTCGTGCCAACATAACTGGA
* * ** * *
1243296 CTTAAACATCTTGAATGCTAGCTAAACTACGCTTAAACTCATTAT-GTGCAAACATAA-TGGA
1 CTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAACT-ATTTTCGTGCCAACATAACTGGA
* * * *
1243357 CTTAAATATCTTGGATGCTAACTAAATTGGGCTTAAACTTTTTTCATGCCAA
1 CTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAACTATTTTCGTGCCAA
1243409 GACAAGATGA
Statistics
Matches: 193, Mismatches: 42, Indels: 5
0.80 0.17 0.02
Matches are distributed among these distances:
60 3 0.02
61 42 0.22
62 146 0.76
63 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (62 bp):
CTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAACTATTTTCGTGCCAACATAACTGGA
Found at i:1243514 original size:107 final size:105
Alignment explanation
Indices: 1243314--1243515 Score: 233
Period size: 107 Copynumber: 1.9 Consensus size: 105
1243304 TCTTGAATGC
* * * *
1243314 TAGCTAAACTACGCTTAAACTCATTATGTGCAAACATAATGGACTTAAATATCTTGGATGCTAAC
1 TAGCTAAACTACGCTTAAACTCATTATATGCAAACACAATGGACTTAAACATCTTGGATGCTAAA
* * * *** *
1243379 TAAATTGGGCTTAAACTTTTTTCATGCCAAGACAAGATGA
66 AAAATTGGACATAAACTCAGTGCATGCCAAGACAAGATGA
* * * * *
1243419 TAGCTAAACTAGGCTTAAACTCTTTTTCATGCCAACACAACTGGCCTTAAACATCTTGGATGCTA
1 TAGCTAAACTACGCTTAAACTCATTAT-ATGCAAACACAA-TGGACTTAAACATCTTGGATGCTA
*
1243484 AAAAAATTGGACATAAACTCAGTGCGTGCCAA
64 AAAAAATTGGACATAAACTCAGTGCATGCCAA
1243516 CATAACGAGA
Statistics
Matches: 78, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
105 24 0.31
106 9 0.12
107 45 0.58
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (105 bp):
TAGCTAAACTACGCTTAAACTCATTATATGCAAACACAATGGACTTAAACATCTTGGATGCTAAA
AAAATTGGACATAAACTCAGTGCATGCCAAGACAAGATGA
Found at i:1243607 original size:31 final size:32
Alignment explanation
Indices: 1243572--1243832 Score: 186
Period size: 31 Copynumber: 8.3 Consensus size: 32
1243562 ACCCTTTTCG
* *
1243572 TGCCAACAT-AATTAGACTTAAATATC-TTGGA
1 TGCCAACATAAATTGGACTTAAA-ATCTTTGCA
* * *
1243603 TGCCAAC-TAAATTGGGCTTAAACTCTTTTCA
1 TGCCAACATAAATTGGACTTAAAATCTTTGCA
* * * *
1243634 TGTCAACATAAACTAGACTTAAACATC-TTGGA
1 TGCCAACATAAATTGGACTTAAA-ATCTTTGCA
* * *
1243666 TACCAAC-TAAATTGGGCTTAAAATCTTTTCA
1 TGCCAACATAAATTGGACTTAAAATCTTTGCA
*
1243697 TGCCAACATAAA-TGGACTTAAACATC-TTGAA
1 TGCCAACATAAATTGGACTTAAA-ATCTTTGCA
* * *
1243728 TGCCAAC-TAAAATGGGCTTAAAACTCATTGCA
1 TGCCAACATAAATTGGACTTAAAA-TCTTTGCA
**
1243760 TGCCAACAT-AATTGGACTTAAACAT-TTTATA
1 TGCCAACATAAATTGGACTTAAA-ATCTTTGCA
* * * *
1243791 TGCCAGC-TAAATTGGGC-TAAAGCTCTTTTCA
1 TGCCAACATAAATTGGACTTAAA-ATCTTTGCA
1243822 TGCCAACATAA
1 TGCCAACATAA
1243833 TTGTAACAAC
Statistics
Matches: 178, Mismatches: 37, Indels: 29
0.73 0.15 0.12
Matches are distributed among these distances:
30 17 0.10
31 104 0.58
32 53 0.30
33 4 0.02
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (32 bp):
TGCCAACATAAATTGGACTTAAAATCTTTGCA
Found at i:1243703 original size:125 final size:123
Alignment explanation
Indices: 1243442--1243835 Score: 448
Period size: 125 Copynumber: 3.2 Consensus size: 123
1243432 CTTAAACTCT
* * * * ** * * *
1243442 TTTTCATGCCAACACAACTGGCCTTAAACATCTTGGATGCTAAAAAAATTGGACATAAACTCAGT
1 TTTTCATGCCAACATAATTGGACTTAAACATCTTGGATGCCAACTAAATTGGGCTTAAACTCATT
* * * * *
1243507 GCGTGCCAACATAACGAGACTGAAACATTTTGGATGA-CAACTAAATTAGGCTAAAACCC
66 GCATGCCAACATAACTAGACTTAAACATTTTGGAT-ACCAACTAAATTGGGCTAAAA-TC
* * * *
1243566 TTTTCGTGCCAACATAATTAGACTTAAATATCTTGGATGCCAACTAAATTGGGCTTAAACTCTTT
1 TTTTCATGCCAACATAATTGGACTTAAACATCTTGGATGCCAACTAAATTGGGCTTAAACTCATT
* * *
1243631 TCATGTCAACATAAACTAGACTTAAACATCTTGGATACCAACTAAATTGGGCTTAAAATC
66 GCATGCCAACAT-AACTAGACTTAAACATTTTGGATACCAACTAAATTGGGC-TAAAATC
* * *
1243691 TTTTCATGCCAACATAAATGGACTTAAACATCTTGAATGCCAACTAAAATGGGCTTAAAACTCAT
1 TTTTCATGCCAACATAATTGGACTTAAACATCTTGGATGCCAACTAAATTGGGCTT-AAACTCAT
* * ** * * *
1243756 TGCATGCCAACATAATTGGACTTAAACATTTTATATGCCAGCTAAATTGGGCTAAAGCTC
65 TGCATGCCAACATAACTAGACTTAAACATTTTGGATACCAACTAAATTGGGCTAAA-ATC
1243816 TTTTCATGCCAACATAATTG
1 TTTTCATGCCAACATAATTG
1243836 TAACAACCCT
Statistics
Matches: 226, Mismatches: 39, Indels: 9
0.82 0.14 0.03
Matches are distributed among these distances:
124 66 0.29
125 137 0.61
126 23 0.10
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.29
Consensus pattern (123 bp):
TTTTCATGCCAACATAATTGGACTTAAACATCTTGGATGCCAACTAAATTGGGCTTAAACTCATT
GCATGCCAACATAACTAGACTTAAACATTTTGGATACCAACTAAATTGGGCTAAAATC
Found at i:1245143 original size:23 final size:23
Alignment explanation
Indices: 1245117--1245160 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1245107 TTGGTCGATA
1245117 TTGTGTGAGCCTAGACTATGACG
1 TTGTGTGAGCCTAGACTATGACG
1245140 TTGTGTGAGCCTAGACTATGA
1 TTGTGTGAGCCTAGACTATGA
1245161 AGTCAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.32
Consensus pattern (23 bp):
TTGTGTGAGCCTAGACTATGACG
Found at i:1253838 original size:28 final size:28
Alignment explanation
Indices: 1253805--1253859 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1253795 AGCTGTAGGA
1253805 CTAATATTGATAAGTTAGAAAGTAGACC
1 CTAATATTGATAAGTTAGAAAGTAGACC
1253833 CTAATATTGATAAGTTAGAAAGTAGAC
1 CTAATATTGATAAGTTAGAAAGTAGAC
1253860 ACCAAGCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (28 bp):
CTAATATTGATAAGTTAGAAAGTAGACC
Found at i:1256200 original size:17 final size:17
Alignment explanation
Indices: 1256170--1256202 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1256160 TTCTTGATAA
1256170 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
1256187 AATAATAACT-CTTATT
1 AATAA-AACTCCTTATT
1256203 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:1256393 original size:30 final size:29
Alignment explanation
Indices: 1256344--1256511 Score: 146
Period size: 29 Copynumber: 5.7 Consensus size: 29
1256334 TTAAGACAAC
1256344 TCTTGTCTTAAATTAAGACAAAAATATTTT
1 TCTTGTC-TAAATTAAGACAAAAATATTTT
* *
1256374 ATCTGGTCTAAATTGAGAC--AAATATGTTT
1 -TCTTGTCTAAATTAAGACAAAAATAT-TTT
* *
1256403 TCTTATCTAAATTAAGACAAAAAAAATTTT
1 TCTTGTCTAAATTAAGAC-AAAAATATTTT
* *
1256433 TCTTGTCTTAAATTAAAACAAACATA-TTT
1 TCTTGTC-TAAATTAAGACAAAAATATTTT
* * *
1256462 TCTTGTTTAAATTAAGATCAAACAT-GTTT
1 TCTTGTCTAAATTAAGA-CAAAAATATTTT
* * *
1256491 TCTTATCCAAATTAATACAAA
1 TCTTGTCTAAATTAAGACAAA
1256512 CATGTTAAAG
Statistics
Matches: 114, Mismatches: 16, Indels: 17
0.78 0.11 0.12
Matches are distributed among these distances:
28 34 0.30
29 35 0.31
30 24 0.21
31 21 0.18
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (29 bp):
TCTTGTCTAAATTAAGACAAAAATATTTT
Found at i:1256446 original size:59 final size:59
Alignment explanation
Indices: 1256352--1256483 Score: 160
Period size: 59 Copynumber: 2.2 Consensus size: 59
1256342 ACTCTTGTCT
* * * * *
1256352 TAAATTAAGAC-AAAAATATTTTATCTGGTCTAAATTGAGACAAATATGTTTTCTTATC
1 TAAATTAAGACAAAAAAAATTTTATCTGGTCTAAATTAAAACAAACATATTTTCTTATC
* * *
1256410 TAAATTAAGACAAAAAAAATTTT-TCTTGTCTTAAATTAAAACAAACATATTTTCTTGTT
1 TAAATTAAGACAAAAAAAATTTTATCTGGTC-TAAATTAAAACAAACATATTTTCTTATC
1256469 TAAATTAAGATCAAA
1 TAAATTAAGA-CAAA
1256484 CATGTTTTCT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
58 17 0.27
59 42 0.67
60 4 0.06
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.39
Consensus pattern (59 bp):
TAAATTAAGACAAAAAAAATTTTATCTGGTCTAAATTAAAACAAACATATTTTCTTATC
Found at i:1256502 original size:29 final size:28
Alignment explanation
Indices: 1256352--1256517 Score: 136
Period size: 28 Copynumber: 5.7 Consensus size: 28
1256342 ACTCTTGTCT
* * **
1256352 TAAATTAAGACAAAAATATTTTATCTGGTC
1 TAAATTAAGACAAACAT-GTTT-TCTTATC
* *
1256382 TAAATTGAGACAAATATGTTTTCTTATC
1 TAAATTAAGACAAACATGTTTTCTTATC
* *
1256410 TAAATTAAGACAAAAAAAAT-TTTTCTTGTC
1 TAAATTAAGAC---AAACATGTTTTCTTATC
* * * *
1256440 TTAAATTAAAACAAACATATTTTCTTGTT
1 -TAAATTAAGACAAACATGTTTTCTTATC
1256469 TAAATTAAGATCAAACATGTTTTCTTATC
1 TAAATTAAGA-CAAACATGTTTTCTTATC
* *
1256498 CAAATTAATACAAACATGTT
1 TAAATTAAGACAAACATGTT
1256518 AAAGTTGCCA
Statistics
Matches: 113, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
28 39 0.35
29 35 0.31
30 24 0.21
31 15 0.13
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.39
Consensus pattern (28 bp):
TAAATTAAGACAAACATGTTTTCTTATC
Found at i:1259624 original size:73 final size:73
Alignment explanation
Indices: 1259520--1259660 Score: 169
Period size: 73 Copynumber: 1.9 Consensus size: 73
1259510 ACTAAGTGAC
* * * * * *
1259520 ATTGTTAGTCGACTAAGAGCTTATTATCAAAAA-TTGAATTTAGAGATAAAAACGACTTAATCGA
1 ATTGTTAGTCGACTAAGAGCCTACTACCAAAAACTAG-ATTCAGAGACAAAAACGACTTAATCGA
1259584 CTAAAAAGT
65 CTAAAAAGT
* * *
1259593 ATTGTTAGTTGACT-AGAAGCCTACTACCAAAAACTAGGTTCAGAGACATAAACGACTTAATCGA
1 ATTGTTAGTCGACTAAG-AGCCTACTACCAAAAACTAGATTCAGAGACAAAAACGACTTAATCGA
1259657 CTAA
65 CTAA
1259661 GTAGCAATGT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
72 2 0.04
73 53 0.93
74 2 0.04
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.28
Consensus pattern (73 bp):
ATTGTTAGTCGACTAAGAGCCTACTACCAAAAACTAGATTCAGAGACAAAAACGACTTAATCGAC
TAAAAAGT
Found at i:1262729 original size:21 final size:21
Alignment explanation
Indices: 1262705--1262745 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1262695 AGATTTTTTT
*
1262705 ATATTATATAAATTTTTTAAA
1 ATATTATATAAATTTGTTAAA
* *
1262726 ATATTTTATATATTTGTTAA
1 ATATTATATAAATTTGTTAA
1262746 TAACCTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATATTATATAAATTTGTTAAA
Found at i:1273083 original size:45 final size:45
Alignment explanation
Indices: 1273032--1273133 Score: 125
Period size: 45 Copynumber: 2.3 Consensus size: 45
1273022 GTTGTTACAC
* * * * *
1273032 GTTACACGTCA-AATACAAAAATATGTTACATGTTATGGTTAGATT
1 GTTACACGCCATAA-ACAAAAATATATTACACGTCATGATTAGATT
* *
1273077 GTTACACGCCATGAACAAAAATATATTACACGTCATGATTAGGTT
1 GTTACACGCCATAAACAAAAATATATTACACGTCATGATTAGATT
1273122 GTTACACGCCAT
1 GTTACACGCCAT
1273134 GTTAAAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
45 48 0.98
46 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (45 bp):
GTTACACGCCATAAACAAAAATATATTACACGTCATGATTAGATT
Found at i:1273142 original size:45 final size:45
Alignment explanation
Indices: 1273046--1273134 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
1273036 CACGTCAAAT
* * * *
1273046 ACAAAAATATGTTACATGTTATGGTTAGATTGTTACACGCCATGA
1 ACAAAAATATATTACACGTCATGATTAGATTGTTACACGCCATGA
*
1273091 ACAAAAATATATTACACGTCATGATTAGGTTGTTACACGCCATG
1 ACAAAAATATATTACACGTCATGATTAGATTGTTACACGCCATG
1273135 TTAAAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (45 bp):
ACAAAAATATATTACACGTCATGATTAGATTGTTACACGCCATGA
Found at i:1285359 original size:20 final size:19
Alignment explanation
Indices: 1285305--1285359 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
1285295 AAAATTTATG
1285305 TATTTTAT-TTTTCTTAGTT
1 TATTTTATGTTTT-TTAGTT
* *
1285324 TAGTTTAAGTTATTTTAGTT
1 TATTTTATGTT-TTTTAGTT
1285344 TAATTTTATGTTTTTT
1 T-ATTTTATGTTTTTT
1285360 TACTTTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 6 0.21
20 13 0.45
21 10 0.34
ACGTcount: A:0.20, C:0.02, G:0.09, T:0.69
Consensus pattern (19 bp):
TATTTTATGTTTTTTAGTT
Found at i:1285360 original size:21 final size:21
Alignment explanation
Indices: 1285306--1285367 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
1285296 AAATTTATGT
*
1285306 ATTTTAT-TTTTCTTAGTTT-
1 ATTTTATGTTTTTTTAGTTTA
* * *
1285325 AGTTTAAGTTATTTTAGTTTA
1 ATTTTATGTTTTTTTAGTTTA
*
1285346 ATTTTATGTTTTTTTACTTTA
1 ATTTTATGTTTTTTTAGTTTA
1285367 A
1 A
1285368 ATTACTTTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
19 5 0.15
20 10 0.30
21 18 0.55
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.66
Consensus pattern (21 bp):
ATTTTATGTTTTTTTAGTTTA
Found at i:1286647 original size:25 final size:25
Alignment explanation
Indices: 1286619--1286667 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1286609 TCTAGTAAAC
1286619 TTTGTCA-TTTAATTATTAGTTTTAG
1 TTTGTCACTTTAATT-TTAGTTTTAG
* *
1286644 TTTGTTACTTTAATTTTATTTTTA
1 TTTGTCACTTTAATTTTAGTTTTA
1286668 ATTAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.22, C:0.04, G:0.08, T:0.65
Consensus pattern (25 bp):
TTTGTCACTTTAATTTTAGTTTTAG
Found at i:1294533 original size:40 final size:41
Alignment explanation
Indices: 1294475--1294551 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
1294465 TGAAAGACAA
*
1294475 CAATCATGGCGAGATTAG-AAACCCCACTAAGATGAACCAC
1 CAATCATGGCAAGATTAGAAAACCCCACTAAGATGAACCAC
* * * *
1294515 CAATCTTGGCAAGGTTAGAAAACCCCATTAAGGTGAA
1 CAATCATGGCAAGATTAGAAAACCCCACTAAGATGAA
1294552 GAATAGCTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 15 0.48
41 16 0.52
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.18
Consensus pattern (41 bp):
CAATCATGGCAAGATTAGAAAACCCCACTAAGATGAACCAC
Found at i:1306991 original size:33 final size:30
Alignment explanation
Indices: 1306954--1307065 Score: 116
Period size: 33 Copynumber: 3.5 Consensus size: 30
1306944 TTTTAACGTC
1306954 ATATATTTTATTTTCATTTATTATTATAATCTT
1 ATATATTTTATTTT-ATTT-TTATTATAAT-TT
*
1306987 ATATATTTTATTTTTATTTTTTTAATATAATTT
1 ATATATTTTA-TTTTA--TTTTTATTATAATTT
* * * *
1307020 TTTTATTTTATTTTATTTTTATTTTTATATT
1 ATATATTTTATTTTATTTTTATTATAAT-TT
1307051 ATATATTTTATTTTA
1 ATATATTTTATTTTA
1307066 ATATTTTTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
30 10 0.15
31 15 0.22
32 5 0.07
33 21 0.31
34 13 0.19
35 3 0.04
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (30 bp):
ATATATTTTATTTTATTTTTATTATAATTT
Found at i:1307000 original size:5 final size:5
Alignment explanation
Indices: 1306990--1307083 Score: 63
Period size: 5 Copynumber: 19.0 Consensus size: 5
1306980 TAATCTTATA
* * *
1306990 TATTT TATTT T-TATT T-TTT TAATA TAATT T-TTT TATTT TATTT TATTTT
1 TATTT TATTT TAT-TT TATTT TATTT TATTT TATTT TATTT TATTT TA-TTT
* * *
1307039 TATTTT TATAT TA-TA TATTT TATTT TAATAT T-TTT TATTT TATTT
1 TA-TTT TATTT TATTT TATTT TATTT T-ATTT TATTT TATTT TATTT
1307084 ATAATATCAT
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
4 12 0.17
5 45 0.62
6 15 0.21
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:1307032 original size:38 final size:36
Alignment explanation
Indices: 1306957--1307084 Score: 111
Period size: 38 Copynumber: 3.6 Consensus size: 36
1306947 TAACGTCATA
* * * * *
1306957 TATTTTATTTTCA-TTTATTATTATA-ATCTTA-TA
1 TATTTTATTTTTATTTTTTTAATATATATTTTATTT
*
1306990 TATTTTATTTTTATTTTTTTAATATAATTTTTTTATTT
1 TATTTTATTTTTATTTTTTTAATAT-A-TATTTTATTT
* *
1307028 TATTTTATTTTTATTTTTATATTATATATTTTATTT
1 TATTTTATTTTTATTTTTTTAATATATATTTTATTT
* *
1307064 TAATAT-TTTTTATTTTATTTA
1 TATTTTATTTTTATTTT-TTTA
1307085 TAATATCATA
Statistics
Matches: 77, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
33 12 0.16
34 9 0.12
35 11 0.14
36 16 0.21
37 5 0.06
38 24 0.31
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (36 bp):
TATTTTATTTTTATTTTTTTAATATATATTTTATTT
Found at i:1307672 original size:17 final size:18
Alignment explanation
Indices: 1307637--1307674 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1307627 TCCTAAATAA
* *
1307637 AAAAATTATATATATAAT
1 AAAAATTATATAAAAAAT
1307655 AAAAATTA-ATAAAAAAT
1 AAAAATTATATAAAAAAT
1307672 AAA
1 AAA
1307675 TAAATAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAATTATATAAAAAAT
Found at i:1308098 original size:7 final size:7
Alignment explanation
Indices: 1308088--1308129 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
1308078 AATCAAAAGG
1308088 AAAAACA
1 AAAAACA
*
1308095 AAAAGCACC
1 AAAA--ACA
1308104 AAAAACA
1 AAAAACA
1308111 AAAAA-A
1 AAAAACA
1308117 AAAAACA
1 AAAAACA
1308124 AAAAAC
1 AAAAAC
1308130 CATTGTTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
6 6 0.20
7 18 0.60
9 6 0.20
ACGTcount: A:0.81, C:0.17, G:0.02, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:1308122 original size:13 final size:13
Alignment explanation
Indices: 1308104--1308128 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1308094 AAAAAGCACC
1308104 AAAAACAAAAAAA
1 AAAAACAAAAAAA
1308117 AAAAACAAAAAA
1 AAAAACAAAAAA
1308129 CCATTGTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAAAA
Found at i:1309355 original size:3 final size:3
Alignment explanation
Indices: 1309347--1309377 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
1309337 GATAAATATG
1309347 ATA ATA ATA ATA ATA ATA ATA ATA ATGA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
1309378 CAACAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1309538 original size:2 final size:2
Alignment explanation
Indices: 1309531--1309559 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1309521 ATAAAGGCAA
1309531 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1309560 CACAAAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1311264 original size:66 final size:66
Alignment explanation
Indices: 1311150--1311273 Score: 187
Period size: 66 Copynumber: 1.9 Consensus size: 66
1311140 AATTACACGC
* *
1311150 CAAGATGTTATACACCGTGTACAGAAACATGTTACACGTCATGGTTAGGTTATTACACACCATGG
1 CAAGATGTTATACACCATGTACAGAAACATGTTACACGTCATGATTAGGTTATTACACACCATGG
1311215 T
66 T
* * *
1311216 CAAGTTGTTATACGCCATGTACAGAAACATGTTACACG-CTATGATTAGGTTGTTACAC
1 CAAGATGTTATACACCATGTACAGAAACATGTTACACGTC-ATGATTAGGTTATTACAC
1311274 GCTACGTATA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
65 1 0.02
66 51 0.98
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (66 bp):
CAAGATGTTATACACCATGTACAGAAACATGTTACACGTCATGATTAGGTTATTACACACCATGG
T
Found at i:1311411 original size:24 final size:24
Alignment explanation
Indices: 1311384--1311453 Score: 106
Period size: 24 Copynumber: 2.9 Consensus size: 24
1311374 AAAATATTAT
1311384 TGTTACATGCCATGTATAAAAAGA
1 TGTTACATGCCATGTATAAAAAGA
*
1311408 TGTTACATGCCATGTACAAAAAGA
1 TGTTACATGCCATGTATAAAAAGA
*
1311432 TGTTACACGCCATGGT-TAAAAA
1 TGTTACATGCCAT-GTATAAAAA
1311454 AAAATTATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
24 40 0.95
25 2 0.05
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (24 bp):
TGTTACATGCCATGTATAAAAAGA
Found at i:1313563 original size:11 final size:11
Alignment explanation
Indices: 1313547--1313571 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1313537 GATATTACTT
1313547 TTCTTTTTTTC
1 TTCTTTTTTTC
1313558 TTCTTTTTTTC
1 TTCTTTTTTTC
1313569 TTC
1 TTC
1313572 CTTAGATCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTCTTTTTTTC
Found at i:1313937 original size:254 final size:251
Alignment explanation
Indices: 1313479--1313964 Score: 712
Period size: 254 Copynumber: 1.9 Consensus size: 251
1313469 CCGAATGCCT
* * *
1313479 AATCCCTTCTAAGTCCAAATTTTGATATTTTTTTCTGGTTTTCCTTAGCTCAAATTTTGATATTA
1 AATCCCTTCTAAGTCCAAATTTTGATATTTTTTTCTGATGTTCCTTAGCTCAAATTTTGAAATTA
* * *
1313544 CTTTTCTTTTTTTCTTCTTTTTTTCTTCCTTAGATCTCTTGGTCCAAGTATTGGAATTATTTTGT
66 CTTTTCCTTTTTTCTTC-TGTTTTCTTCCTTAGATCTCTTGGCCCAAGTATTGGAATTATTTTGT
* * *
1313609 TTTTATTTTTTCTCTTTTATTTTTATTTTGTAAAAACTCAATTGTATATTTTCTCCTCGATTGTT
130 TTTTATTTTTTCTCTTTTATTTTTATTTTGCAAAAACTCAATTGAATATTTTCTCCTAGATTGTT
*
1313674 TAGTTGCATATGTGAAATATAAATTGGAGCATTTTGAACCATTGAGAATGCCTAGGTTC
195 TAATTGCATA--TGAAATATAAATTGGAGCATTTTGAACCATTGAGAATGCCTAGGTTC
*
1313733 AATCCCTTCTAAGTCCAAATTTTGAATTTTATTTTTCT-ATCGTTCCTTAGCTCAAATTTTGAAA
1 AATCCCTTCTAAGTCCAAATTTTG-ATATT-TTTTTCTGAT-GTTCCTTAGCTCAAATTTTGAAA
* * *
1313797 TTACTTTTCCTTTTTTCTTC-GTTTT-TTCCTTAGCTCATGTTGGCCCAAGTTTTGGAATTATTT
63 TTACTTTTCCTTTTTTCTTCTGTTTTCTTCCTTAGATC-TCTTGGCCCAAGTATTGGAATTATTT
* *
1313860 TGTTTTTATTTTTTTCTCTTTTATTTTTATTTTGCAAAAA-TTAATTGAATATTTTCTGCTAGA-
127 TGTTTTTA-TTTTTTCTCTTTTATTTTTATTTTGCAAAAACTCAATTGAATATTTTCTCCTAGAT
1313923 TGATTTAATTGCATATGAAATATAAATTGGAGCATTTTGAAC
191 TG-TTTAATTGCATATGAAATATAAATTGGAGCATTTTGAAC
1313965 TTGATATTAA
Statistics
Matches: 210, Mismatches: 16, Indels: 14
0.88 0.07 0.06
Matches are distributed among these distances:
252 27 0.13
253 12 0.06
254 89 0.42
255 35 0.17
256 47 0.22
ACGTcount: A:0.23, C:0.14, G:0.11, T:0.51
Consensus pattern (251 bp):
AATCCCTTCTAAGTCCAAATTTTGATATTTTTTTCTGATGTTCCTTAGCTCAAATTTTGAAATTA
CTTTTCCTTTTTTCTTCTGTTTTCTTCCTTAGATCTCTTGGCCCAAGTATTGGAATTATTTTGTT
TTTATTTTTTCTCTTTTATTTTTATTTTGCAAAAACTCAATTGAATATTTTCTCCTAGATTGTTT
AATTGCATATGAAATATAAATTGGAGCATTTTGAACCATTGAGAATGCCTAGGTTC
Done.