Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007916.1 Hibiscus syriacus cultivar Beakdansim tig00110319_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3725575
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 16
Found at i:1468930 original size:15 final size:14
Alignment explanation
Indices: 1468904--1468934 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1468894 TAGATCATCA
1468904 TATTTTTTATTTAT
1 TATTTTTTATTTAT
1468918 TATTTTATTATTTAT
1 TATTTT-TTATTTAT
1468933 TA
1 TA
1468935 GTCGATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTTTTATTTAT
Found at i:1469705 original size:56 final size:56
Alignment explanation
Indices: 1469635--1469745 Score: 222
Period size: 56 Copynumber: 2.0 Consensus size: 56
1469625 AATAATTTGA
1469635 GGGGGGGGGGGGAATTGGCTCAGAATTTTTTTTTGTTAAAATATTATGAATGTTAG
1 GGGGGGGGGGGGAATTGGCTCAGAATTTTTTTTTGTTAAAATATTATGAATGTTAG
1469691 GGGGGGGGGGGGAATTGGCTCAGAATTTTTTTTTGTTAAAATATTATGAATGTTA
1 GGGGGGGGGGGGAATTGGCTCAGAATTTTTTTTTGTTAAAATATTATGAATGTTA
1469746 TAATGTTAGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.25, C:0.04, G:0.33, T:0.38
Consensus pattern (56 bp):
GGGGGGGGGGGGAATTGGCTCAGAATTTTTTTTTGTTAAAATATTATGAATGTTAG
Found at i:1470973 original size:60 final size:60
Alignment explanation
Indices: 1470909--1471021 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
1470899 GTCCTAAAAT
* * * * *
1470909 TTTTAAATATTTTAATTTCATTCTTAAACTATGTATCTT-ATTCTAAATTAGTCATTGAGC
1 TTTTAAACATTATAATTCCATCCCTAAACTATG-ATCTTCATTCTAAATTAGTCATTGAGC
* *
1470969 TTTTAAACATTATAATTCCATCCCTAAATTATGATCTTCTTTCTAAATTAGTC
1 TTTTAAACATTATAATTCCATCCCTAAACTATGATCTTCATTCTAAATTAGTC
1471022 CCCAAACTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
59 5 0.11
60 40 0.89
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.48
Consensus pattern (60 bp):
TTTTAAACATTATAATTCCATCCCTAAACTATGATCTTCATTCTAAATTAGTCATTGAGC
Found at i:1473851 original size:13 final size:15
Alignment explanation
Indices: 1473826--1473858 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1473816 TTATTTTTAG
1473826 TATTTTTATATTA-T
1 TATTTTTATATTATT
1473840 TATTTTTA-ATTATT
1 TATTTTTATATTATT
1473854 TATTT
1 TATTT
1473859 AAATATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTTTTATATTATT
Found at i:1473856 original size:17 final size:16
Alignment explanation
Indices: 1473813--1473857 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
1473803 TTTAATAAGT
*
1473813 TTTTTATT-TTTAGTA
1 TTTTTATTATTTATTA
1473828 TTTTTA-TA-TTATTA
1 TTTTTATTATTTATTA
1473842 TTTTTAATTATTTATT
1 TTTTT-ATTATTTATT
1473858 TAAATATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 11 0.44
15 7 0.28
16 2 0.08
17 5 0.20
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTTTATTATTTATTA
Found at i:1474332 original size:30 final size:30
Alignment explanation
Indices: 1474296--1474355 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1474286 TGTTATTTTA
1474296 GTTTAATATTAAAATTTGCTTATAGGATTC
1 GTTTAATATTAAAATTTGCTTATAGGATTC
*
1474326 GTTTAATATTAAAATTTTCTTATAGGATTC
1 GTTTAATATTAAAATTTGCTTATAGGATTC
1474356 ATGTTATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (30 bp):
GTTTAATATTAAAATTTGCTTATAGGATTC
Found at i:1474367 original size:2 final size:2
Alignment explanation
Indices: 1474360--1474395 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1474350 GGATTCATGT
1474360 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1474396 GCTAAAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1475446 original size:19 final size:19
Alignment explanation
Indices: 1475424--1475461 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1475414 AATAAAGAAC
1475424 TAAAGAAAAAT-TAAAAATA
1 TAAA-AAAAATATAAAAATA
*
1475443 TAAAAAATATATAAAAATA
1 TAAAAAAAATATAAAAATA
1475462 AAATAGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (19 bp):
TAAAAAAAATATAAAAATA
Found at i:1475474 original size:17 final size:17
Alignment explanation
Indices: 1475429--1475483 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 17
1475419 AGAACTAAAG
1475429 AAAAATTAAAAATATAA
1 AAAAATTAAAAATATAA
1475446 AAAATATATAAAAATA-AA
1 AAAA-AT-TAAAAATATAA
*
1475464 ATAGAATTAAATAA-ATAA
1 A-AAAATTAAA-AATATAA
1475482 AA
1 AA
1475484 GGAAATCTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
17 10 0.31
18 12 0.38
19 10 0.31
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
AAAAATTAAAAATATAA
Found at i:1476782 original size:189 final size:190
Alignment explanation
Indices: 1476436--1476790 Score: 482
Period size: 189 Copynumber: 1.9 Consensus size: 190
1476426 ATGGTTCAGT
* * *
1476436 CCAGGCATTCGACCGAAAAGTTTTGGCCAACTTGTTGGCGAGTGGTCTCCATGCGTGCTGCTTAC
1 CCAGGCATTCGACCGAAAAGTTTCGGCCAACTTGTTGGCGAGTGGCCTCCATGCGTGCTACTTAC
* * * * *
1476501 TTCCTCTCGTGCGACGCTTGGCTTTATATGATTAAGGTTTTGCAACTCTATTTTTCTTCGATCTC
66 TTCCTCTCGTACGACGCTTGGCTTCATATGATTAAGGGTTTGCAACCCTATTTTACTTCGATCTC
1476566 AGCCATTGATATGGTGCTACATTGAGCTTGATTTGTCCCTATTTTGCATATAGGCTGGTC
131 AGCCATTGATATGGTGCTACATTGAGCTTGATTTGTCCCTATTTTGCATATAGGCTGGTC
* * * *
1476626 CCAGGCGTTCGACCG-AAAGTTTCGGCCAACTTGTTGGCGCGTGGCCTTCACT-CGTGCTACTTG
1 CCAGGCATTCGACCGAAAAGTTTCGGCCAACTTGTTGGCGAGTGGCCTCCA-TGCGTGCTACTTA
* ** * *
1476689 CTTCCTTTCGTACGGTGTTTGGCTTCATATGATTAGGGGTTTGCAACCCTATTTTACTTCGATCT
65 CTTCCTCTCGTACGACGCTTGGCTTCATATGATTAAGGGTTTGCAACCCTATTTTACTTCGATCT
* * * *
1476754 CAGTCGTTGATCTGGTGC-AGCGTTGAGCTTGATTTGT
130 CAGCCATTGATATGGTGCTA-CATTGAGCTTGATTTGT
1476791 GAAACTCTAT
Statistics
Matches: 142, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
188 1 0.01
189 126 0.89
190 15 0.11
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.36
Consensus pattern (190 bp):
CCAGGCATTCGACCGAAAAGTTTCGGCCAACTTGTTGGCGAGTGGCCTCCATGCGTGCTACTTAC
TTCCTCTCGTACGACGCTTGGCTTCATATGATTAAGGGTTTGCAACCCTATTTTACTTCGATCTC
AGCCATTGATATGGTGCTACATTGAGCTTGATTTGTCCCTATTTTGCATATAGGCTGGTC
Found at i:1476927 original size:15 final size:15
Alignment explanation
Indices: 1476907--1476957 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
1476897 TGTTAAAATT
1476907 TAATAAATAAATAAA
1 TAATAAATAAATAAA
*
1476922 TAATAATATAACCTAAAA
1 TAATAA-ATAA-AT-AAA
1476940 TAAT-AATAAATAACA
1 TAATAAATAAATAA-A
1476955 TAA
1 TAA
1476958 ATAATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 2 0.07
15 11 0.37
16 8 0.27
17 2 0.07
18 7 0.23
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (15 bp):
TAATAAATAAATAAA
Found at i:1477058 original size:31 final size:31
Alignment explanation
Indices: 1476963--1477058 Score: 126
Period size: 31 Copynumber: 3.2 Consensus size: 31
1476953 CATAAATAAT
* *
1476963 AAAAATTATATAATATA-TATTATATTCCCG
1 AAAAACTATATAATATATTATTATATTCTCG
1476993 -AAAACTATATAATATATATATTATATTCTC-
1 AAAAACTATATAATATAT-TATTATATTCTCG
* *
1477023 AAAAACTATATAATATATTAATATATTTTCG
1 AAAAACTATATAATATATTATTATATTCTCG
1477054 AAAAA
1 AAAAA
1477059 AACTGTTTTC
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
29 15 0.26
30 10 0.17
31 33 0.57
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (31 bp):
AAAAACTATATAATATATTATTATATTCTCG
Found at i:1477195 original size:64 final size:63
Alignment explanation
Indices: 1477062--1477213 Score: 162
Period size: 64 Copynumber: 2.4 Consensus size: 63
1477052 CGAAAAAAAC
* * * * **
1477062 TGTTTTCAAAACCATTTTAAAAACTATATATTATACGTTTTCAAAACTGTTTTAAAGTTATACA
1 TGTTTTCAAAATCATTTTAAAAAC-ATATATTATAAGTGTTCAAAACTATTTTAAAACTATACA
* * * *
1477126 CGTTTTCAAAATTATTTTAAAAAC-TATATTATAAGTGTTCAAAATTATTTTAAAAAACTATATA
1 TGTTTTCAAAATCATTTTAAAAACATATATTATAAGTGTTCAAAACTATTTT--AAAACTATACA
*
1477190 TGTTTTCAAAATCGTTTTTAAAAA
1 TGTTTTCAAAATC-ATTTTAAAAA
1477214 ACACACGTTT
Statistics
Matches: 72, Mismatches: 13, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
62 23 0.32
64 40 0.56
65 9 0.12
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (63 bp):
TGTTTTCAAAATCATTTTAAAAACATATATTATAAGTGTTCAAAACTATTTTAAAACTATACA
Found at i:1477201 original size:31 final size:33
Alignment explanation
Indices: 1477127--1477215 Score: 114
Period size: 33 Copynumber: 2.7 Consensus size: 33
1477117 AGTTATACAC
1477127 GTTTTCAAAATTATTTT-AAAAACTATATTATAA
1 GTTTTCAAAATTATTTTAAAAAACTATATTAT-A
*
1477160 GTGTTCAAAATTATTTTAAAAAACTATA-TAT-
1 GTTTTCAAAATTATTTTAAAAAACTATATTATA
1477191 GTTTTCAAAATCGT-TTTTAAAAAAC
1 GTTTTCAAAAT--TATTTTAAAAAAC
1477216 ACACGTTTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
31 10 0.20
32 11 0.22
33 20 0.39
34 10 0.20
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.43
Consensus pattern (33 bp):
GTTTTCAAAATTATTTTAAAAAACTATATTATA
Found at i:1477288 original size:28 final size:27
Alignment explanation
Indices: 1477257--1477319 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
1477247 AACTATATAT
*
1477257 TATATATTTTCAAAATTATCTTAAAAA
1 TATATATTTTCAAAATCATCTTAAAAA
* * *
1477284 CTATATGTTTTCAAAATCGTTTTAAAAA
1 -TATATATTTTCAAAATCATCTTAAAAA
1477312 TATATATT
1 TATATATT
1477320 ATACGATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 7 0.23
28 23 0.77
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (27 bp):
TATATATTTTCAAAATCATCTTAAAAA
Found at i:1477700 original size:17 final size:17
Alignment explanation
Indices: 1477678--1477713 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1477668 CAAATTTTAA
1477678 AATATAATAAA-ATAATT
1 AATATAA-AAAGATAATT
1477695 AATATAAAAAGATAATT
1 AATATAAAAAGATAATT
1477712 AA
1 AA
1477714 AGTATATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
AATATAAAAAGATAATT
Found at i:1478797 original size:60 final size:59
Alignment explanation
Indices: 1478692--1478805 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 59
1478682 TTATAAGGTA
* *
1478692 TTACTTTGTTGAGTCTCTCGATTATTAAAAATTATAATGTAGTCATCTGACTATATGATG
1 TTACTTTGTTGAGTCTCACGATTATTAAAAATTATAATG-AGTCATCCGACTATATGATG
* *
1478752 TTACTTTGTTGAGTCTCACGATTATTAGAAGTTACTAACTG-GTCATCCGACTAT
1 TTACTTTGTTGAGTCTCACGATTATTAAAAATTA-TAA-TGAGTCATCCGACTAT
1478806 TCATATATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 43 0.90
61 3 0.06
62 2 0.04
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (59 bp):
TTACTTTGTTGAGTCTCACGATTATTAAAAATTATAATGAGTCATCCGACTATATGATG
Found at i:1487143 original size:21 final size:20
Alignment explanation
Indices: 1487028--1487163 Score: 60
Period size: 21 Copynumber: 6.7 Consensus size: 20
1487018 GCGTAATAAA
***
1487028 AATCGCAACGCGATCCCCAG
1 AATCGCAACGCGATTTTCAG
** *
1487048 AATCGCAAATC-AGTTTTCAA
1 AATCGCAACGCGA-TTTTCAG
* *
1487068 AATCGCAACGCGATTCTTGAC
1 AATCGCAACGCGATT-TTCAG
* * *
1487089 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGAT-TTTCAG
**
1487109 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTT-CAG
* * * *
1487131 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTTTCAG
1487151 AATCGCAACGCGA
1 AATCGCAACGCGA
1487164 ACACATAAAT
Statistics
Matches: 86, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
19 1 0.01
20 40 0.47
21 43 0.50
22 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGATTTTCAG
Found at i:1487205 original size:20 final size:20
Alignment explanation
Indices: 1487131--1487282 Score: 198
Period size: 20 Copynumber: 7.6 Consensus size: 20
1487121 GATTTTCCAG
* ** *
1487131 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1487151 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
*
1487171 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1487191 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1487211 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1487231 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1487251 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1487271 AATCGCAACGCG
1 AATCGCAACGCG
1487283 ATTTTTAAAG
Statistics
Matches: 115, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
19 1 0.01
20 112 0.97
21 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1487701 original size:33 final size:33
Alignment explanation
Indices: 1487662--1487732 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1487652 TTCACTTAGA
1487662 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1487695 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1487728 TTTCA
1 TTTCA
1487733 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1487838 original size:21 final size:20
Alignment explanation
Indices: 1487812--1487918 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
1487802 TGCAGAAGAG
1487812 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
1487833 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
1487853 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
1487875 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
1487889 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
1487908 TCGCAACGAGA
1 TCGCAACGAGA
1487919 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 9 0.13
21 25 0.36
22 10 0.14
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:1487892 original size:14 final size:14
Alignment explanation
Indices: 1487873--1487929 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1487863 GAAAAATGAA
1487873 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1487887 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1487906 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1487920 AATCGCAACG
1 AATCGCAACG
1487930 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1487904 original size:33 final size:33
Alignment explanation
Indices: 1487866--1487945 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
1487856 GCAACGAGAA
1487866 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1487899 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
1487932 AAACCAAAATCGCA
1 AAATGAAAATCGCA
1487946 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:1487963 original size:19 final size:19
Alignment explanation
Indices: 1487941--1488068 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
1487931 GAAACCAAAA
*
1487941 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1487960 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1487974 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1487993 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1488007 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
1488027 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
1488047 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1488067 TC
1 TC
1488069 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1487982 original size:14 final size:14
Alignment explanation
Indices: 1487963--1488019 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1487953 TTTCATTTCG
1487963 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1487977 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1487996 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1488010 CGTTGCGATT
1 CGTTGCGATT
1488020 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1487988 original size:33 final size:33
Alignment explanation
Indices: 1487946--1488068 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
1487936 CAAAATCGCA
1487946 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1487979 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1488012 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
1488053 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1488069 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1488030 original size:21 final size:21
Alignment explanation
Indices: 1488004--1488068 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1487994 CGCGTTGCGA
1488004 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1488025 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1488045 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
1488066 TTC
1 TTC
1488069 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1489632 original size:33 final size:33
Alignment explanation
Indices: 1489574--1489697 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
1489564 TAGTTTACTT
* * *
1489574 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACACGAAAC-CAAAATCGCAACGACAAAA
**
1489608 TCGCAACACGAAATGAAAATCGCAACGACAAAA
1 TCGCAACACGAAACCAAAATCGCAACGACAAAA
*
1489641 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACACGAAACCAAAATCGCAACGACAAAA
*
1489674 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACACGAAACCAAAATCGCA
1489698 TTGCGATTCT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 70 0.84
34 13 0.16
ACGTcount: A:0.48, C:0.27, G:0.16, T:0.09
Consensus pattern (33 bp):
TCGCAACACGAAACCAAAATCGCAACGACAAAA
Found at i:1489642 original size:14 final size:14
Alignment explanation
Indices: 1489623--1489681 Score: 73
Period size: 14 Copynumber: 3.9 Consensus size: 14
1489613 ACACGAAATG
1489623 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1489637 AAAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
1489656 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1489670 AAAATCGCAACG
1 AAAATCGCAACG
1489682 CGAAACCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
14 23 0.57
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 11 0.28
ACGTcount: A:0.49, C:0.29, G:0.15, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1489703 original size:19 final size:19
Alignment explanation
Indices: 1489636--1489697 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1489626 ATCGCAACGA
1489636 CAAAATCGCAACGCGAAAC
1 CAAAATCGCAACGCGAAAC
1489655 CAAAATCGCAA--CG--A-
1 CAAAATCGCAACGCGAAAC
1489669 CAAAATCGCAACGCGAAAC
1 CAAAATCGCAACGCGAAAC
1489688 CAAAATCGCA
1 CAAAATCGCA
1489698 TTGCGATTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 11 0.29
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 21 0.55
ACGTcount: A:0.48, C:0.31, G:0.15, T:0.06
Consensus pattern (19 bp):
CAAAATCGCAACGCGAAAC
Found at i:1489734 original size:19 final size:19
Alignment explanation
Indices: 1489710--1489813 Score: 127
Period size: 19 Copynumber: 5.4 Consensus size: 19
1489700 GCGATTCTGT
1489710 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
**
1489729 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTCATTTCG
** *
1489748 CGTTGCGATTTTGGTTTCT
1 CGTTGCGATTTTCATTTCG
*
1489767 CGTTGCGATTCTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1489786 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
1489806 TGTTGCGA
1 CGTTGCGA
1489814 AAGTAAACTA
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
19 62 0.84
20 12 0.16
ACGTcount: A:0.10, C:0.18, G:0.26, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1491754 original size:14 final size:14
Alignment explanation
Indices: 1491735--1491770 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1491725 ATTGTTTAAT
1491735 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1491749 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1491763 TGATTTGT
1 TGATTTGT
1491771 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1491972 original size:53 final size:52
Alignment explanation
Indices: 1491910--1492097 Score: 247
Period size: 53 Copynumber: 3.6 Consensus size: 52
1491900 AGAATCGCAA
1491910 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
1491963 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
* * * * *
1492015 TGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATTTTCATTT-CGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
*
1492068 TGCGATTTTCTTTTCCGCATTGCGATTTTC
1 TGCGATTTTCATTT-CGCATTGCGATTTTC
1492098 TTGTTGGGAT
Statistics
Matches: 125, Mismatches: 6, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
51 2 0.02
52 34 0.27
53 75 0.60
54 5 0.04
55 9 0.07
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1491986 original size:33 final size:33
Alignment explanation
Indices: 1491928--1492141 Score: 127
Period size: 34 Copynumber: 6.2 Consensus size: 33
1491918 TCATTTCGCA
1491928 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
1491962 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
1491998 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TC-CG
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
* * * * *
1492032 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
* * *
1492067 TTGCGATTTTCTTTTCCGCATTGCGATTTTCTTG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
1492101 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1492134 TTGCGATT
1 TTGCGATT
1492142 GTAATTTTCG
Statistics
Matches: 150, Mismatches: 17, Indels: 27
0.77 0.09 0.14
Matches are distributed among these distances:
31 4 0.03
32 6 0.04
33 45 0.30
34 64 0.43
35 5 0.03
36 4 0.03
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.06
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1492018 original size:86 final size:87
Alignment explanation
Indices: 1491928--1492141 Score: 378
Period size: 86 Copynumber: 2.5 Consensus size: 87
1491918 TCATTTCGCA
1491928 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
1491993 TTT-CGCATTGCGATTCTCTCG
66 TTTCCGCATTGCGATTCTCTCG
*
1492014 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCT
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
* *
1492079 TTTCCGCATTGCGATTTTCTTG
66 TTTCCGCATTGCGATTCTCTCG
*
1492101 TTGGGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
1492142 GTAATTTTCG
Statistics
Matches: 123, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
86 93 0.76
87 30 0.24
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.47
Consensus pattern (87 bp):
TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
TTTCCGCATTGCGATTCTCTCG
Found at i:1492109 original size:53 final size:53
Alignment explanation
Indices: 1491904--1492127 Score: 208
Period size: 53 Copynumber: 4.2 Consensus size: 53
1491894 AACGAGAGAA
* ** * *
1491904 TCGCAATGCGATTTTCATTT-CGCATTGCGATTTTCATT-TCCGCA-TTGCGATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC-TTGTTGGGATTTTC-ATT
* * * * * *
1491956 CTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCAT-TTCGCA-TTGCGATT
1 -TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCTTGTTGGGATTTTC-ATT
* * * * *
1492008 CTCTCGTTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 -TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCTTGTTGGGATTTTCATT
*
1492062 TCGCATTGCGATTTTCTTTTCCGCATTGCGATTTTCTTGTTGGGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCTTGTTGGGATTTTCATT
1492115 TCGCATTGCGATT
1 TCGCATTGCGATT
1492128 CTCTCGTTGC
Statistics
Matches: 150, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
52 35 0.23
53 106 0.71
54 6 0.04
55 3 0.02
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (53 bp):
TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCTTGTTGGGATTTTCATT
Found at i:1492149 original size:53 final size:53
Alignment explanation
Indices: 1492014--1492160 Score: 156
Period size: 53 Copynumber: 2.8 Consensus size: 53
1492004 GATTCTCTCG
* * *
1492014 TTGCGATTTTCAT-TTCCGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCA
1 TTGCGATTCTC-TGTTCCGCATTGCAATTTTCGT-GTTGCGATTTTCATTTCGCA
* * * * *
1492067 TTGCGATTTTCTTTTCCGCATTGCGATTTTCTTGTTGGGATTTTCATTTCGCA
1 TTGCGATTCTCTGTTCCGCATTGCAATTTTCGTGTTGCGATTTTCATTTCGCA
* *
1492120 TTGCGATTCTCTCGTTGCG-ATTGTAATTTTCGTGTTGCGAT
1 TTGCGATTCTCT-GTTCCGCATTGCAATTTTCGTGTTGCGAT
1492161 AATCAAATGC
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
52 1 0.01
53 76 0.93
54 5 0.06
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (53 bp):
TTGCGATTCTCTGTTCCGCATTGCAATTTTCGTGTTGCGATTTTCATTTCGCA
Found at i:1492160 original size:120 final size:118
Alignment explanation
Indices: 1491928--1492148 Score: 306
Period size: 120 Copynumber: 1.8 Consensus size: 118
1491918 TCATTTCGCA
1491928 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCA-TTCG-ATTGCGATTTTCA
* *
1491993 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
64 TTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTTCCGCATTGCGATTCTCTCG
* *
1492048 TTGCGATTTTCATTT-CGCATTGCGATTTTCTTTTCCGCATTGCGATTTTC-TT-G-TTGGGATT
1 TTGCGATTTTCATTTCCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATTCGATTGCGATT
1492109 TTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTT
60 TTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTT
1492149 TCGTGTTGCG
Statistics
Matches: 91, Mismatches: 4, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
119 10 0.11
120 60 0.66
121 3 0.03
122 3 0.03
123 4 0.04
125 11 0.12
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (118 bp):
TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTCGATTGCGATTTTCATT
TCGCATTGCGATTCTCTCGTTGCGATTGTAATTTCCGCATTGCGATTCTCTCG
Found at i:1494415 original size:12 final size:12
Alignment explanation
Indices: 1494398--1494422 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1494388 TCTTCGGGGA
1494398 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1494410 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1494422 C
1 C
1494423 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1494631 original size:24 final size:24
Alignment explanation
Indices: 1494597--1494650 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
1494587 CTGAAACATC
1494597 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1494621 ATCAAAGTCCGGATATTGACCAAT
1 ATCAAAATCCGGATATTGACCAAT
*
1494645 ACCAAA
1 ATCAAA
1494651 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1494664 original size:24 final size:24
Alignment explanation
Indices: 1494613--1494664 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1494603 ATCCGTGTAT
* * *
1494613 TGACCAATATCAAAGTCCGGATAT
1 TGACCAATACCAAAGTCCGAATAC
* *
1494637 TGACCAATACCAAATTTCGAATAC
1 TGACCAATACCAAAGTCCGAATAC
1494661 TGAC
1 TGAC
1494665 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (24 bp):
TGACCAATACCAAAGTCCGAATAC
Found at i:1495363 original size:20 final size:20
Alignment explanation
Indices: 1495335--1495563 Score: 235
Period size: 20 Copynumber: 11.4 Consensus size: 20
1495325 AAATTTCAGT
* * *
1495335 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1495355 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1495375 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1495395 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1495415 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1495435 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1495455 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
1495475 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
1495495 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1495515 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1495535 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1495555 GTTGCGATT
1 GTTGCGATT
1495564 CTTGAAAATC
Statistics
Matches: 181, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 180 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1495616 original size:21 final size:20
Alignment explanation
Indices: 1495531--1495628 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
1495521 ATTTATGTGT
* * *
1495531 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTCAAAA
* *
1495551 TCGCGTTGCGATTCTTGAAAA
1 TCGCATTGCGATT-TTCAAAA
* **
1495572 TCGCAATGCGAATTTGT-ACTA
1 TCGCATTGCG-ATTT-TCAAAA
1495593 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTCAA-AA
*
1495614 TCGCTTTGCGATTTT
1 TCGCATTGCGATTTT
1495629 GGAAACTAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTTCAAAA
Found at i:1502367 original size:34 final size:34
Alignment explanation
Indices: 1502322--1502392 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
1502312 TTAATCAAGG
*
1502322 AGGGTTAGAGTGTAATGCGTATCTTATGTAATTC
1 AGGGTTAGAGTGCAATGCGTATCTTATGTAATTC
* * **
1502356 AGGGTTTGAGTGCATTTTGTATCTTATGTAATTC
1 AGGGTTAGAGTGCAATGCGTATCTTATGTAATTC
1502390 AGG
1 AGG
1502393 TTAATTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.41
Consensus pattern (34 bp):
AGGGTTAGAGTGCAATGCGTATCTTATGTAATTC
Found at i:1506916 original size:29 final size:30
Alignment explanation
Indices: 1506883--1506943 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
1506873 TATGCCCGTT
* *
1506883 TTCCAGTTTAGTGTCTAACGTTT-ATTTCG
1 TTCCAGTTTAGTGCCTAACGTTTCATTCCG
*
1506912 TTCCAGTTTGGTGCCTAACGTTTCATTCCG
1 TTCCAGTTTAGTGCCTAACGTTTCATTCCG
1506942 TT
1 TT
1506944 ACTCGAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (30 bp):
TTCCAGTTTAGTGCCTAACGTTTCATTCCG
Found at i:1514041 original size:2 final size:2
Alignment explanation
Indices: 1514034--1514063 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1514024 TTATAAATTA
1514034 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
1514064 TTAAATTAAA
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:1526443 original size:30 final size:30
Alignment explanation
Indices: 1526407--1526465 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
1526397 TTACTTCGGG
** *
1526407 GACCATATTGTAAGCAGACTAAATGTTGGA
1 GACCATATTACAAACAGACTAAATGTTGGA
*
1526437 GACCATATTACAAACGGACTAAATGTTGG
1 GACCATATTACAAACAGACTAAATGTTGG
1526466 GGGACTGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.25
Consensus pattern (30 bp):
GACCATATTACAAACAGACTAAATGTTGGA
Found at i:1526955 original size:12 final size:12
Alignment explanation
Indices: 1526938--1526963 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1526928 CTAAGAGCCC
1526938 ATTTAGGATCAT
1 ATTTAGGATCAT
1526950 ATTTAGGATCAT
1 ATTTAGGATCAT
1526962 AT
1 AT
1526964 AGATGCATTT
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:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATTTAGGATCAT
Found at i:1526975 original size:20 final size:20
Alignment explanation
Indices: 1526950--1526991 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1526940 TTAGGATCAT
*
1526950 ATTTAGGATCATATAGATGC
1 ATTTAGGAGCATATAGATGC
*
1526970 ATTTAGGAGCATATAGTTGC
1 ATTTAGGAGCATATAGATGC
1526990 AT
1 AT
1526992 GTGGTGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (20 bp):
ATTTAGGAGCATATAGATGC
Found at i:1535497 original size:20 final size:20
Alignment explanation
Indices: 1535460--1535502 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1535450 ATTCCACCAC
*
1535460 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
1535480 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
1535500 ATG
1 ATG
1535503 TGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:1545900 original size:20 final size:20
Alignment explanation
Indices: 1545863--1545905 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1545853 ATTCCACCAC
*
1545863 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
1545883 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
1545903 ATG
1 ATG
1545906 TGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:1550686 original size:43 final size:43
Alignment explanation
Indices: 1550534--1550802 Score: 236
Period size: 43 Copynumber: 6.5 Consensus size: 43
1550524 AACAAAAAAT
* * * * *
1550534 GCCGCAATAGGTCAAGATCTATTGTGGCGTTTTCGGA-ACAAAC
1 GCCGCAAAAGGTC-AGATCTATAGCGGCATTTTTGGATACAAAC
* * * **
1550577 GCCGCAAAAGGTAGAGATCTATAGAGGCGTTTTAAGA-ACAAAC
1 GCCGCAAAAGGT-CAGATCTATAGCGGCATTTTTGGATACAAAC
*
1550620 GCCGCAAAAGGTCATATCTATAGCGGCATTTTTGGATACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCATTTTTGGATACAAAC
* *
1550663 GTCGCAAAAGGTCAGATCTATAGCGGTATTTTTGGAT----A-
1 GCCGCAAAAGGTCAGATCTATAGCGGCATTTTTGGATACAAAC
* * *
1550701 ----CAAAAGGTCAGTTCTATAGCGGCGTTTTTGCATACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCATTTTTGGATACAAAC
** * **
1550740 AACGCAAAATGTCAGATCTATAGCAACATTTTTGGATACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCATTTTTGGATACAAAC
* *
1550783 GTCGCAAAAAGTCAGATCTA
1 GCCGCAAAAGGTCAGATCTA
1550803 GCACTGTGTT
Statistics
Matches: 187, Mismatches: 28, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
34 29 0.16
38 1 0.01
39 1 0.01
42 18 0.10
43 138 0.74
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (43 bp):
GCCGCAAAAGGTCAGATCTATAGCGGCATTTTTGGATACAAAC
Found at i:1550710 original size:34 final size:34
Alignment explanation
Indices: 1550667--1550738 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
1550657 ACAAACGTCG
* *
1550667 CAAAAGGTCAGATCTATAGCGGTATTTTTGGATA
1 CAAAAGGTCAGATCTATAGCGGCATTTTTGCATA
* *
1550701 CAAAAGGTCAGTTCTATAGCGGCGTTTTTGCATA
1 CAAAAGGTCAGATCTATAGCGGCATTTTTGCATA
1550735 CAAA
1 CAAA
1550739 CAACGCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (34 bp):
CAAAAGGTCAGATCTATAGCGGCATTTTTGCATA
Found at i:1550754 original size:77 final size:77
Alignment explanation
Indices: 1550624--1550781 Score: 228
Period size: 77 Copynumber: 2.1 Consensus size: 77
1550614 ACAAACGCCG
* ** **
1550624 CAAAAGGTCATATCTATAGCGGCATTTTTGGATACAAACGTCGCAAAAGGTCAGATCTATAGCGG
1 CAAAAGGTCATATCTATAGCGGCATTTTTGCATACAAACAACGCAAAAGGTCAGATCTATAGCAA
*
1550689 TATTTTTGGATA
66 CATTTTTGGATA
* *
1550701 CAAAAGGTCAGT-TCTATAGCGGCGTTTTTGCATACAAACAACGCAAAATGTCAGATCTATAGCA
1 CAAAAGGTCA-TATCTATAGCGGCATTTTTGCATACAAACAACGCAAAAGGTCAGATCTATAGCA
1550765 ACATTTTTGGATA
65 ACATTTTTGGATA
1550778 CAAA
1 CAAA
1550782 CGTCGCAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
77 71 0.99
78 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (77 bp):
CAAAAGGTCATATCTATAGCGGCATTTTTGCATACAAACAACGCAAAAGGTCAGATCTATAGCAA
CATTTTTGGATA
Found at i:1553085 original size:41 final size:41
Alignment explanation
Indices: 1553022--1553259 Score: 235
Period size: 41 Copynumber: 5.8 Consensus size: 41
1553012 TTATAAATTT
* * * *
1553022 GCGGTGTTTGTAT-AAAACGCCACCAAAGTACAAGTGTATA
1 GCGGCGTTTATATAAAAACGCCACTAAAGTACAAGTCTATA
* * * *
1553062 GCGGCGTTTGTATATAAACGCCACTAAATTACAAGTCTTTA
1 GCGGCGTTTATATAAAAACGCCACTAAAGTACAAGTCTATA
* * * *
1553103 GCGGCGTTTATAAACACAAATGCCACTAAAGTACAATTATATA
1 GCGGCGTTTATATA-A-AAACGCCACTAAAGTACAAGTCTATA
* * ** **
1553146 ACGACGTTTATATAAAAATACCACTAAAGTATTAGTCTATA
1 GCGGCGTTTATATAAAAACGCCACTAAAGTACAAGTCTATA
** * *
1553187 GCGATGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATA
1 GCGGCGTTTATATAAAAACGCCACTAAAGTACAAGTCTATA
* *
1553228 GCGGTGTTTATATAAAAATGCCACTAAAGTAC
1 GCGGCGTTTATATAAAAACGCCACTAAAGTAC
1553260 TACTCTGTTG
Statistics
Matches: 163, Mismatches: 32, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
40 12 0.07
41 118 0.72
42 1 0.01
43 32 0.20
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (41 bp):
GCGGCGTTTATATAAAAACGCCACTAAAGTACAAGTCTATA
Found at i:1553183 original size:84 final size:82
Alignment explanation
Indices: 1553035--1553259 Score: 243
Period size: 84 Copynumber: 2.7 Consensus size: 82
1553025 GTGTTTGTAT
* * * * * *
1553035 AAAACGCCACCAAAGTACAAGTGTATAGCGGCGTTTGTATATAAACGCCACTAAATTACAAGTCT
1 AAAACGCCACTAAAGTACAAGTATATAGCGGCGTTTATATAAAAATGCCACTAAAGTACAAGTCT
* *
1553100 TTAGCGGCGTTTATAAA
66 ATAGCGACGTTTATAAA
* * * * * **
1553117 CACAAATGCCACTAAAGTACAATTATATAACGACGTTTATATAAAAATACCACTAAAGTATTAGT
1 -A-AAACGCCACTAAAGTACAAGTATATAGCGGCGTTTATATAAAAATGCCACTAAAGTACAAGT
* * *
1553182 CTATAGCGATGTTTGTATA
64 CTATAGCGACGTTTATAAA
* * *
1553201 AAAACGCCACTAAAGTACGAGTCTATAGCGGTGTTTATATAAAAATGCCACTAAAGTAC
1 AAAACGCCACTAAAGTACAAGTATATAGCGGCGTTTATATAAAAATGCCACTAAAGTAC
1553260 TACTCTGTTG
Statistics
Matches: 114, Mismatches: 27, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
82 49 0.43
83 2 0.02
84 63 0.55
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.27
Consensus pattern (82 bp):
AAAACGCCACTAAAGTACAAGTATATAGCGGCGTTTATATAAAAATGCCACTAAAGTACAAGTCT
ATAGCGACGTTTATAAA
Found at i:1553278 original size:82 final size:81
Alignment explanation
Indices: 1553019--1553347 Score: 270
Period size: 82 Copynumber: 4.0 Consensus size: 81
1553009 AAATTATAAA
* * * * * *
1553019 TTTGCGGTGTTTGTAT-AAAACGCCACCAAAGTACAAGTGTATAGCGGCGTTTGTATATAAACGC
1 TTTGCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTATATAAAAATGC
* * *
1553083 CACTAAATTACAAGTC
66 CACTAAAGTACTACTC
* * * * * * *
1553099 TTTAGCGGCGTTTATAAACACAAATGCCACTAAAGTACAATTATATAACGACGTTTATATAAAAA
1 TTT-GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTATATAAAAA
* * *
1553164 TACCACTAAAGTATTAGTC
63 TGCCACTAAAGTACTACTC
* ** * *
1553183 TATAGCGATGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGTGTTTATATAAAAATG
1 T-TTGCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTATATAAAAATG
1553248 CCACTAAAGTACTACTC
65 CCACTAAAGTACTACTC
* * * * * * *
1553265 TGTTGTGGCGTTTGT-TGAAAAAAAGCCACTATAAAT-GAA-CCTATTGCGGCGTTTGTATAAAA
1 T-TTGCGGCGTTTGTAT--AAAAACGCCACTA-AAGTACAAGTCTATAGCGGCGTTTATATAAAA
*
1553327 ATGCCGCTAAAGTACTACTC
62 ATGCCACTAAAGTACTACTC
1553347 T
1 T
1553348 ATATCGGCGT
Statistics
Matches: 196, Mismatches: 45, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
80 3 0.02
81 11 0.06
82 102 0.52
83 15 0.08
84 64 0.33
85 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (81 bp):
TTTGCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTATATAAAAATGC
CACTAAAGTACTACTC
Found at i:1553286 original size:41 final size:42
Alignment explanation
Indices: 1553020--1553359 Score: 186
Period size: 41 Copynumber: 8.3 Consensus size: 42
1553010 AATTATAAAT
* * * * * *
1553020 TTGCGGTGTTTGTAT--AAAACGCCACCAAAGTACAAGTGTA
1 TTGCGGCGTTTGTATAAAAAATGCCACTAAAGTACTACTCTA
* * * * * *
1553060 TAGCGGCGTTTGTAT-ATAAACGCCACTAAATTACAAGTCT-
1 TTGCGGCGTTTGTATAAAAAATGCCACTAAAGTACTACTCTA
* * * *
1553100 TTAGCGGCGTTTATA-AACACAAATGCCACTAAAGTACAATTATA
1 TT-GCGGCGTTTGTATAA-A-AAATGCCACTAAAGTACTACTCTA
** * * * * *
1553144 TAACGACGTTTATAT-AAAAATACCACTAAAGTATTAGTCTA
1 TTGCGGCGTTTGTATAAAAAATGCCACTAAAGTACTACTCTA
* ** * * *
1553185 TAGCGATGTTTGTAT-AAAAACGCCACTAAAGTACGAGTCTA
1 TTGCGGCGTTTGTATAAAAAATGCCACTAAAGTACTACTCTA
* * * *
1553226 TAGCGGTGTTTATAT-AAAAATGCCACTAAAGTACTACTCTG
1 TTGCGGCGTTTGTATAAAAAATGCCACTAAAGTACTACTCTA
* * *
1553267 TTGTGGCGTTTGT-TGAAAAAAAGCCACTATAAATGA--AC-CTA
1 TTGCGGCGTTTGTAT-AAAAAATGCCACTA-AAGT-ACTACTCTA
*
1553308 TTGCGGCGTTTGTAT-AAAAATGCCGCTAAAGTACTACTCTA
1 TTGCGGCGTTTGTATAAAAAATGCCACTAAAGTACTACTCTA
1553349 TAT-CGGCGTTT
1 T-TGCGGCGTTT
1553360 TAAAGAAAAA
Statistics
Matches: 239, Mismatches: 45, Indels: 31
0.76 0.14 0.10
Matches are distributed among these distances:
38 1 0.00
39 3 0.01
40 28 0.12
41 155 0.65
42 17 0.07
43 33 0.14
44 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (42 bp):
TTGCGGCGTTTGTATAAAAAATGCCACTAAAGTACTACTCTA
Found at i:1554256 original size:31 final size:31
Alignment explanation
Indices: 1554208--1554285 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
1554198 CTTTTAAAAC
* *
1554208 TTGCAATACAGTCCCCCAACATTTAGTCTGT
1 TTGCAATATAATCCCCCAACATTTAGTCTGT
* * *
1554239 TTGTAATATAATCCCCCAATATTTAGTTTGT
1 TTGCAATATAATCCCCCAACATTTAGTCTGT
*
1554270 TTGCAATATATTCCCC
1 TTGCAATATAATCCCC
1554286 GAAATAACTA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.38
Consensus pattern (31 bp):
TTGCAATATAATCCCCCAACATTTAGTCTGT
Found at i:1556473 original size:2 final size:2
Alignment explanation
Indices: 1556468--1556535 Score: 118
Period size: 2 Copynumber: 34.0 Consensus size: 2
1556458 CGATTTTTTG
* *
1556468 AT AT AT GT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1556510 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
1556536 GCATATCGTA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1558411 original size:14 final size:14
Alignment explanation
Indices: 1558392--1558424 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
1558382 ACGGTGCGAG
1558392 CGTCAGGTCTATGA
1 CGTCAGGTCTATGA
1558406 CGTCAGGTCTATGA
1 CGTCAGGTCTATGA
1558420 CGTCA
1 CGTCA
1558425 AGTTCATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.27
Consensus pattern (14 bp):
CGTCAGGTCTATGA
Found at i:1559675 original size:64 final size:63
Alignment explanation
Indices: 1559578--1559718 Score: 178
Period size: 64 Copynumber: 2.2 Consensus size: 63
1559568 CATATTCAAT
* * *
1559578 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGTAATTGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGTAATTGGTGCATCGATGCAT-AGGTA
* * * *
1559641 GTGCATCGATGCATCCCCTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGTA
1 GTGCATCGATGCA-CCCCTTAAAGAAG-AAACATCGAAGGTAATTGGTGCATCGATGCATAGGTA
1559705 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1559719 ATGTTAAAGA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
63 18 0.26
64 50 0.74
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGTAATTGGTGCATCGATGCATAGGTA
Found at i:1559751 original size:20 final size:22
Alignment explanation
Indices: 1559706--1559763 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
1559696 GCATGGGTAG
1559706 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
1559730 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
1559750 TGCATCGATGCACT
1 TGCATCGATGCACT
1559764 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:1567068 original size:15 final size:15
Alignment explanation
Indices: 1567044--1567075 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1567034 TGGCAGATCC
*
1567044 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
1567059 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
1567074 AA
1 AA
1567076 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:1579174 original size:23 final size:23
Alignment explanation
Indices: 1579148--1579191 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1579138 TTGTGACTTG
*
1579148 TTTATCTTTGCCTTTGTGACACA
1 TTTATCTTTGCCTTTATGACACA
* *
1579171 TTTATTTTTGTCTTTATGACA
1 TTTATCTTTGCCTTTATGACA
1579192 TGTTTTTCTC
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:0.18, C:0.16, G:0.11, T:0.55
Consensus pattern (23 bp):
TTTATCTTTGCCTTTATGACACA
Found at i:1580891 original size:15 final size:14
Alignment explanation
Indices: 1580853--1580892 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
1580843 TCGCCCATTT
1580853 TTTTTAATATTTTAA
1 TTTTTAATA-TTTAA
*
1580868 TTTTAAATATTTAA
1 TTTTTAATATTTAA
1580882 TTATTTAATAT
1 TT-TTTAATAT
1580893 ATATTATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTTAATATTTAA
Found at i:1582760 original size:35 final size:35
Alignment explanation
Indices: 1582714--1582783 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
1582704 TCTAAATATT
1582714 TTAAGAGAATGTACAATACTATCTTTAACCAATAA
1 TTAAGAGAATGTACAATACTATCTTTAACCAATAA
1582749 TTAAGAGAATGTACAATACTATCTTTAACCAATAA
1 TTAAGAGAATGTACAATACTATCTTTAACCAATAA
1582784 GACGTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (35 bp):
TTAAGAGAATGTACAATACTATCTTTAACCAATAA
Found at i:1583033 original size:26 final size:26
Alignment explanation
Indices: 1582983--1583034 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1582973 AAACAACATG
* * *
1582983 ATAATAATAATTATTATAATAATAAA
1 ATAACAATAATTATAACAATAATAAA
*
1583009 ATAACAATAATTATAACAATGATAAA
1 ATAACAATAATTATAACAATAATAAA
1583035 TAAGAAGATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (26 bp):
ATAACAATAATTATAACAATAATAAA
Found at i:1585995 original size:16 final size:16
Alignment explanation
Indices: 1585974--1586007 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1585964 TTACTATTCA
*
1585974 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
1585990 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
1586006 CG
1 CG
1586008 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:1592217 original size:18 final size:18
Alignment explanation
Indices: 1592194--1592229 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1592184 CACCAATCAT
1592194 CTCCTTGAACCAGCCAAC
1 CTCCTTGAACCAGCCAAC
1592212 CTCCTTGAACCAGCCAAC
1 CTCCTTGAACCAGCCAAC
1592230 GGCTATCATC
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:0.28, C:0.44, G:0.11, T:0.17
Consensus pattern (18 bp):
CTCCTTGAACCAGCCAAC
Found at i:1596594 original size:43 final size:43
Alignment explanation
Indices: 1596502--1596587 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
1596492 ACGTAATGAC
*
1596502 TCAAACCTATAACATTACTTAAGTGATCTAATATCTCATTCTA
1 TCAAACCTATAACATTACTTAAGTCATCTAATATCTCATTCTA
1596545 TCAAACCTATAACATTACTTAAGTCATCTAATATCTCATTCTA
1 TCAAACCTATAACATTACTTAAGTCATCTAATATCTCATTCTA
1596588 CTAAACCAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.37
Consensus pattern (43 bp):
TCAAACCTATAACATTACTTAAGTCATCTAATATCTCATTCTA
Found at i:1600766 original size:19 final size:19
Alignment explanation
Indices: 1600744--1600780 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1600734 GTTGACACTG
1600744 ACACAATCAGTTGTCCCAT
1 ACACAATCAGTTGTCCCAT
1600763 ACACAATCAGTTGTCCCA
1 ACACAATCAGTTGTCCCA
1600781 ACTCCTCTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.11, T:0.24
Consensus pattern (19 bp):
ACACAATCAGTTGTCCCAT
Found at i:1603949 original size:2 final size:2
Alignment explanation
Indices: 1603942--1603995 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1603932 AAGTTGAAGC
1603942 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1603984 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1603996 CTGATATGAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1604744 original size:11 final size:11
Alignment explanation
Indices: 1604728--1604768 Score: 82
Period size: 11 Copynumber: 3.7 Consensus size: 11
1604718 TATAAATCCC
1604728 CCAGTTTCTTT
1 CCAGTTTCTTT
1604739 CCAGTTTCTTT
1 CCAGTTTCTTT
1604750 CCAGTTTCTTT
1 CCAGTTTCTTT
1604761 CCAGTTTC
1 CCAGTTTC
1604769 CTTTGAACGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.10, C:0.29, G:0.10, T:0.51
Consensus pattern (11 bp):
CCAGTTTCTTT
Found at i:1610950 original size:3 final size:3
Alignment explanation
Indices: 1610942--1610981 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
1610932 ATTTTAAAAT
*
1610942 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
1610982 CAAAACCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1616322 original size:15 final size:15
Alignment explanation
Indices: 1616302--1616333 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1616292 ATCAATACCT
1616302 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
1616317 TTTTGCATACATTCA
1 TTTTGCATACATGCA
1616332 TT
1 TT
1616334 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:1623676 original size:13 final size:13
Alignment explanation
Indices: 1623658--1623696 Score: 69
Period size: 14 Copynumber: 2.9 Consensus size: 13
1623648 GCTTGAAGAG
1623658 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
1623671 AAAAAGAAAGAAAA
1 AAAAAGAAA-AAAA
1623685 AAAAAGAAAAAA
1 AAAAAGAAAAAA
1623697 GAAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAA
Found at i:1623682 original size:17 final size:17
Alignment explanation
Indices: 1623653--1623714 Score: 81
Period size: 17 Copynumber: 3.5 Consensus size: 17
1623643 ATTATGCTTG
1623653 AAGAGAAAAAGAAAAAAA
1 AAGA-AAAAAGAAAAAAA
1623671 AA-AAAGAAAGAAAAAAA
1 AAGAAA-AAAGAAAAAAA
1623688 AAGAAAAAAGAAAGAAAA
1 AAGAAAAAAGAAA-AAAA
*
1623706 AGGAAAAAA
1 AAGAAAAAA
1623715 ATGGGGGTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
16 2 0.05
17 21 0.52
18 17 0.43
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAGAAAAAAA
Found at i:1623688 original size:21 final size:21
Alignment explanation
Indices: 1623659--1623715 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
1623649 CTTGAAGAGA
1623659 AAAAGAAAAAAAAAAAAGAAAG
1 AAAA-AAAAAAAAAAAAGAAAG
*
1623681 AAAAAAAAAGAAAAAAGAAAG
1 AAAAAAAAAAAAAAAAGAAAG
**
1623702 AAAAAGGAAAAAAA
1 AAAAAAAAAAAAAA
1623716 TGGGGGTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAAAAAAAGAAAG
Found at i:1623693 original size:27 final size:27
Alignment explanation
Indices: 1623658--1623715 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
1623648 GCTTGAAGAG
1623658 AAAAAGAAAAAA-AAAAAAGAAAGAAAA
1 AAAAAGAAAAAAGAAAAAA-AAAGAAAA
* *
1623685 AAAAAGAAAAAAGAAAGAAAAAGGAAA
1 AAAAAGAAAAAAGAAAAAAAAAGAAAA
1623712 AAAA
1 AAAA
1623716 TGGGGGTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (27 bp):
AAAAAGAAAAAAGAAAAAAAAAGAAAA
Found at i:1625081 original size:83 final size:87
Alignment explanation
Indices: 1624942--1625170 Score: 299
Period size: 92 Copynumber: 2.6 Consensus size: 87
1624932 TGGAACAAAT
* *
1624942 AATGTTCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-AA-ATC-
1 AATGTGCTCATTGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACA-CA
1625004 A-A-TCATTGAATTTGGAAGAGG
65 ACAGTCATTGAATTTGGAAGAGG
1625025 AATGTGCTCATTGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
1 AATGTGCTCATTGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-GAA-CAC
*
1625090 AGAACCAGTTATTGAATTTGGAAGAGG
64 --AA-CAGTCATTGAATTTGGAAGAGG
* * *
1625117 AATGTGCTAATAT-CATCTTCTGGAAGTGTTCTTTGAGTTCTCTGATTTGGTTTG
1 AATGTGCTCAT-TGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
1625171 ATATAAAACC
Statistics
Matches: 129, Mismatches: 6, Indels: 13
0.87 0.04 0.09
Matches are distributed among these distances:
83 55 0.43
85 2 0.02
86 1 0.01
87 1 0.01
89 1 0.01
91 1 0.01
92 67 0.52
93 1 0.01
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (87 bp):
AATGTGCTCATTGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACACAA
CAGTCATTGAATTTGGAAGAGG
Found at i:1625659 original size:94 final size:95
Alignment explanation
Indices: 1625497--1625689 Score: 361
Period size: 94 Copynumber: 2.0 Consensus size: 95
1625487 TATTCTCCTC
*
1625497 ATCAGAATCATAATTCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATATTG
1 ATCAGAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATATTG
1625562 AAAGATCACTTCATAATCAGATGAGTTGTT
66 AAAGATCACTTCATAATCAGATGAGTTGTT
*
1625592 ATCAGAATCAGAATTCAAGATTTCTCGGTATT-AAAGAACTATCGATATCTGTGAAATCATCTTG
1 ATCAGAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATATTG
1625656 AAAGATCACTTCATAATCAGATGAGTTGTT
66 AAAGATCACTTCATAATCAGATGAGTTGTT
1625686 ATCA
1 ATCA
1625690 TAATTAACAT
Statistics
Matches: 96, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
94 65 0.68
95 31 0.32
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (95 bp):
ATCAGAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATATTG
AAAGATCACTTCATAATCAGATGAGTTGTT
Found at i:1626261 original size:113 final size:113
Alignment explanation
Indices: 1626028--1626675 Score: 766
Period size: 113 Copynumber: 5.7 Consensus size: 113
1626018 TGTCAGTTAG
* * * *
1626028 AGTTCATAATGAGAAGAACTCATCTG-AAGAGAGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
1 AGTTCATAATAAGAAGAACTCATCTGAAAAAG-GAAGAAGAAATTCATAATGAGAAGAACTTGTT
1626092 CAA-CTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAA
65 CAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAA
*
1626140 AGTTCATAATAAGAAGAACTCATCTGAAAAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAAAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
*
1626205 AACCTTTTGCTCAAATCCATCACTTGATAGATTAGCTTTGCCAGAGAA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAA
* * *
1626253 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAAAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
* * * * ** *
1626318 AACCTTATGCTCAAACCCATCACTTGATGGATCAGCTTTTCCAGTTAG
66 AACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAA
* * * * *
1626366 AGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAAAAATTCATAATGAGAAGAACTTGTTT
1 AGTTCATAATAAGAAGAACTCATCTGAAAAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
* * * *
1626431 AACCTTTTGTTCAAATTCATCACTTGATGGATCAACATTT-CCAGAGAA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATTAGC-TTTGCCAGAGAA
* * * * * *
1626479 AGTTCATAATAAGACGAACTTATTTG-AAGAGGAAGAAGAAATTCACAATGAGAAGAGCTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAAAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
* * * * *
1626543 AACCTTTTGCAT-AATTCTATCACAGAAGTAGATAGATTAGCATAAACCTTTCCAGAGAA
66 AACCTTTTGC-TCAAATCCATCAC-----TTGATGGATTAGC-T-----TTGCCAGAGAA
* * * * *
1626602 AGTTCATAATAAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCAAAATAAGAAGAACTTATTC
1 AGTTCATAATAAGAAGAACTCATCTGAAAAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
1626667 AACCTTTTG
66 AACCTTTTG
1626676 AATGACTCTA
Statistics
Matches: 463, Mismatches: 57, Indels: 20
0.86 0.11 0.04
Matches are distributed among these distances:
112 106 0.23
113 270 0.58
114 3 0.01
117 11 0.02
122 2 0.00
123 31 0.07
124 40 0.09
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.27
Consensus pattern (113 bp):
AGTTCATAATAAGAAGAACTCATCTGAAAAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
AACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAA
Found at i:1626687 original size:124 final size:123
Alignment explanation
Indices: 1626468--1626694 Score: 328
Period size: 124 Copynumber: 1.8 Consensus size: 123
1626458 TGGATCAACA
* * * * * * *
1626468 TTTCCAGAGAAAGTTCATAATAAGACGAACTTATTTGAAGAGGAAGAAGAAATTCACAATGAGAA
1 TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAAAGAAAGAAGAAATTCAAAATAAGAA
* * * *
1626533 GAGCTTGTTCAACCTTTTGCATAATTCTATCACAGAAGTAGATAGATTAGCATAAACC
66 GAACTTATTCAACCTTTTGAATAACTCTATCACAGAAGTAGATAGATTAGCATAAACC
*
1626591 TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCAAAATAAGA
1 TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTG-AAAAGAAAGAAGAAATTCAAAATAAGA
*
1626656 AGAACTTATTCAACCTTTTGAATGACTCTATCACAGAAG
65 AGAACTTATTCAACCTTTTGAATAACTCTATCACAGAAG
1626695 GAAATAGGTC
Statistics
Matches: 90, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
123 34 0.38
124 56 0.62
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (123 bp):
TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAAAGAAAGAAGAAATTCAAAATAAGAA
GAACTTATTCAACCTTTTGAATAACTCTATCACAGAAGTAGATAGATTAGCATAAACC
Found at i:1626901 original size:15 final size:16
Alignment explanation
Indices: 1626882--1626937 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 16
1626872 AGACATCAAT
1626882 TTATTTTATTTTATT-
1 TTATTTTATTTTATTA
*
1626897 TTATTTTAAAATTTATTA
1 TTATTTT--ATTTTATTA
1626915 TTATTATTATTATTATTA
1 TTATT-TTATT-TTATTA
1626933 TTATT
1 TTATT
1626938 AATATTACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
15 7 0.21
17 9 0.26
18 16 0.47
19 2 0.06
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTATTTTATTA
Found at i:1626917 original size:3 final size:3
Alignment explanation
Indices: 1626909--1626944 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1626899 ATTTTAAAAT
*
1626909 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1626945 CAAAACCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1629866 original size:16 final size:16
Alignment explanation
Indices: 1629845--1629876 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1629835 TATTATAAAG
*
1629845 ATTGTATAAGTATGAT
1 ATTGTAGAAGTATGAT
1629861 ATTGTAGAAGTATGAT
1 ATTGTAGAAGTATGAT
1629877 GTGACATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.41
Consensus pattern (16 bp):
ATTGTAGAAGTATGAT
Found at i:1632773 original size:14 final size:11
Alignment explanation
Indices: 1632744--1632774 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1632734 TACCTATCAT
1632744 GGGTGGTGGGC
1 GGGTGGTGGGC
1632755 GGGTGGTGGGC
1 GGGTGGTGGGC
*
1632766 GGATGGTGG
1 GGGTGGTGG
1632775 ATTGAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.03, C:0.06, G:0.71, T:0.19
Consensus pattern (11 bp):
GGGTGGTGGGC
Found at i:1633800 original size:2 final size:2
Alignment explanation
Indices: 1633793--1633819 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1633783 TTAATAGTCA
1633793 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
1633820 ACTGTAAAAA
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:1638733 original size:44 final size:44
Alignment explanation
Indices: 1638670--1638774 Score: 192
Period size: 44 Copynumber: 2.4 Consensus size: 44
1638660 CATTATGATT
1638670 GAGAAATATGAATTTTAGTTATCTAAAAGATTATATTAAAGATC
1 GAGAAATATGAATTTTAGTTATCTAAAAGATTATATTAAAGATC
* *
1638714 GAGAAATATGAATTTTAGTTATCTGAAAGATTATATTAAAGATT
1 GAGAAATATGAATTTTAGTTATCTAAAAGATTATATTAAAGATC
1638758 GAGAAATATGAATTTTA
1 GAGAAATATGAATTTTA
1638775 TAAGACGATA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.37
Consensus pattern (44 bp):
GAGAAATATGAATTTTAGTTATCTAAAAGATTATATTAAAGATC
Found at i:1639430 original size:60 final size:60
Alignment explanation
Indices: 1639366--1639490 Score: 137
Period size: 60 Copynumber: 2.1 Consensus size: 60
1639356 AAAGAGAATC
* * *
1639366 ATAGTGTAGGGATGAAATT-AGAATA-TTAAAAAATTGAAGGACTAATTTAAAATGAGATTT
1 ATAGTGTAGGGATGAAATTGA-AATATTTAAAAAATTAAAGG-CTAATTTAAAATGAAAATT
* ** ** *
1639426 ATAGTTTTTGGATGAAATTGAAATATTTAAAAGTTTAAAGGTTAATTTAAAATGAAAATT
1 ATAGTGTAGGGATGAAATTGAAATATTTAAAAAATTAAAGGCTAATTTAAAATGAAAATT
1639486 ATAGT
1 ATAGT
1639491 TTAAGGACCC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
60 41 0.76
61 13 0.24
ACGTcount: A:0.46, C:0.01, G:0.18, T:0.36
Consensus pattern (60 bp):
ATAGTGTAGGGATGAAATTGAAATATTTAAAAAATTAAAGGCTAATTTAAAATGAAAATT
Found at i:1647304 original size:16 final size:15
Alignment explanation
Indices: 1647264--1647306 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
1647254 AACTTAAAAA
1647264 TCAAATTATTAATTAT
1 TCAAATT-TTAATTAT
*
1647280 TAAAAATTTTGAATTAT
1 T-CAAATTTT-AATTAT
1647297 TCAAATTTTA
1 TCAAATTTTA
1647307 TTTTATAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 1 0.04
16 10 0.43
17 12 0.52
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (15 bp):
TCAAATTTTAATTAT
Found at i:1648628 original size:115 final size:119
Alignment explanation
Indices: 1648382--1648744 Score: 482
Period size: 125 Copynumber: 3.0 Consensus size: 119
1648372 TCCTGTTTAG
* * * *
1648382 GGAACATACACCATCAAAATATAGCAGCATGTTATGGTTTGCCGTGACTATCTGTACATGGTCAA
1 GGAACATAAACCATCAAAATATA--AGC----TATGGCTTGCCATGACTATCTGTACATGATCAA
* * *
1648447 TCAGTTTAATAGTTGATATTCTTGTGCATGCATGGACTTATTCATTCATGTGTGAGAAAA
60 TCAGTTTCATAGTTGACATTCTTGTGCATGCATGGACTAATTCATTCATGTGTGAGAAAA
* *
1648507 GGAACATACACCATCAGAATAT-AGC-A-GGCTT-CCATGACTATCTGTACATGATCAATCAGTT
1 GGAACATAAACCATCAAAATATAAGCTATGGCTTGCCATGACTATCTGTACATGATCAATCAGTT
*
1648568 TCGTAGTTGACATTCTTGTGCATGCATGGACTAATTCATTCATGTGTGAGAAAA
66 TCATAGTTGACATTCTTGTGCATGCATGGACTAATTCATTCATGTGTGAGAAAA
*
1648622 GGAACATAAACCATCAAAATATAGCAGCATGTTATGGTTTGCCATGACTATCTGTACATGATCAA
1 GGAACATAAACCATCAAAATATA--AGC----TATGGCTTGCCATGACTATCTGTACATGATCAA
*
1648687 TCAGTTTCATAGTTGACATTCTTGTGCATGCATTGACTAATTCATTCATGTGTGAGAA
60 TCAGTTTCATAGTTGACATTCTTGTGCATGCATGGACTAATTCATTCATGTGTGAGAA
1648745 CAGAAGTCCT
Statistics
Matches: 215, Mismatches: 13, Indels: 20
0.87 0.05 0.08
Matches are distributed among these distances:
115 98 0.46
116 4 0.02
117 1 0.00
118 3 0.01
122 3 0.01
123 1 0.00
124 4 0.02
125 101 0.47
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (119 bp):
GGAACATAAACCATCAAAATATAAGCTATGGCTTGCCATGACTATCTGTACATGATCAATCAGTT
TCATAGTTGACATTCTTGTGCATGCATGGACTAATTCATTCATGTGTGAGAAAA
Found at i:1650915 original size:31 final size:30
Alignment explanation
Indices: 1650873--1650938 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 30
1650863 ATTGAAATTT
*
1650873 AATTTTTTAATTTAATTACT-TAATTTTTA
1 AATTTTTTAATTTAATCACTCTAATTTTTA
*
1650902 AATTATTTCTAATTTAATCACTCTAATTTTTT
1 AATT-TTT-TAATTTAATCACTCTAATTTTTA
1650934 AATTT
1 AATTT
1650939 AATTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 4 0.12
30 3 0.09
31 13 0.41
32 12 0.38
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (30 bp):
AATTTTTTAATTTAATCACTCTAATTTTTA
Found at i:1650948 original size:15 final size:15
Alignment explanation
Indices: 1650928--1650957 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1650918 ATCACTCTAA
1650928 TTTTTTAATTTAATT
1 TTTTTTAATTTAATT
*
1650943 TTTTTTATTTTAATT
1 TTTTTTAATTTAATT
1650958 ATATATTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTAATTTAATT
Found at i:1652043 original size:2 final size:2
Alignment explanation
Indices: 1652036--1652063 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1652026 AGCCTCAGCA
1652036 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
1652064 TGATGACCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1660526 original size:46 final size:47
Alignment explanation
Indices: 1660426--1660532 Score: 173
Period size: 47 Copynumber: 2.3 Consensus size: 47
1660416 TTTCAATGAG
*
1660426 TATCAATATCCTACAAAAGATTATCGATATCACCCCTTAAGTATCAA
1 TATCAATGTCCTACAAAAGATTATCGATATCACCCCTTAAGTATCAA
* *
1660473 TATCAATGTCCTACAAAAGATTATTGATATCA-CCCTTAGGTATCAA
1 TATCAATGTCCTACAAAAGATTATCGATATCACCCCTTAAGTATCAA
1660519 TATCAATGT-CTACA
1 TATCAATGTCCTACA
1660533 TAAGCCTTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
45 5 0.09
46 22 0.39
47 30 0.53
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.32
Consensus pattern (47 bp):
TATCAATGTCCTACAAAAGATTATCGATATCACCCCTTAAGTATCAA
Found at i:1665065 original size:21 final size:20
Alignment explanation
Indices: 1664979--1665136 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1664969 AAATGACCAA
**
1664979 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1664998 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1665018 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1665038 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1665059 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1665080 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1665100 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1665121 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1665137 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1665152 original size:40 final size:40
Alignment explanation
Indices: 1665103--1665257 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
1665093 CGATTTTCCA
* ** *
1665103 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
1665143 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
1665183 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
1665223 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1665258 TATTTAAAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 62 0.65
41 33 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:1665165 original size:20 final size:20
Alignment explanation
Indices: 1665103--1665256 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
1665093 CGATTTTCCA
* ** *
1665103 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1665123 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1665143 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1665163 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1665183 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1665203 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1665223 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1665244 AAATCGCAACGCG
1 AAATCGCAACGCG
1665257 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.82
21 17 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1665678 original size:33 final size:33
Alignment explanation
Indices: 1665639--1665709 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1665629 TTCACTTAGA
*
1665639 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1665672 TTTCATTTCGCGTTCCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1665705 TTTCA
1 TTTCA
1665710 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1665833 original size:20 final size:20
Alignment explanation
Indices: 1665789--1665898 Score: 99
Period size: 21 Copynumber: 5.8 Consensus size: 20
1665779 TGCAGAAGAG
*
1665789 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
1665810 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
*
1665830 TCGCAACGTGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
1665851 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
1665865 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
1665884 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
1665899 CGCAACGCGA
Statistics
Matches: 72, Mismatches: 9, Indels: 17
0.73 0.09 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.06
17 2 0.03
19 15 0.21
20 19 0.26
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:1665846 original size:41 final size:37
Alignment explanation
Indices: 1665782--1665898 Score: 134
Period size: 41 Copynumber: 3.1 Consensus size: 37
1665772 TTCAATTTGC
* *
1665782 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACG-GAGAAATGAAAATCGCAACGAG
1665820 AGAATGACTGTCGCAACGTGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACG-GAGAAATGAAAATCGCAACGAG
*
1665861 AG-A-A-TCGCAAC-GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGGAGAAATGAAAATCGCAACGAG
1665894 AGAAT
1 AGAAT
1665899 CGCAACGCGA
Statistics
Matches: 70, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
33 23 0.33
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.12
Consensus pattern (37 bp):
AGAATAGTCGCAACGGAGAAATGAAAATCGCAACGAG
Found at i:1665868 original size:14 final size:14
Alignment explanation
Indices: 1665849--1665905 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1665839 GAGAAATGAA
1665849 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1665863 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1665882 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1665896 AATCGCAACG
1 AATCGCAACG
1665906 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1665881 original size:33 final size:33
Alignment explanation
Indices: 1665841--1665921 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
1665831 CGCAACGTGA
1665841 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1665874 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
1665907 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1665922 TTACGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1665947 original size:19 final size:19
Alignment explanation
Indices: 1665925--1666014 Score: 83
Period size: 19 Copynumber: 5.3 Consensus size: 19
1665915 AATCGCATTA
1665925 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
*
1665944 CGA--TTC---TCTCGTTG
1 CGATTTTCATTTCGCGTTG
1665958 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
**
1665977 CGA--TTC---TCTAGTTG
1 CGATTTTCATTTCGCGTTG
1665991 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
1666010 CGATT
1 CGATT
1666015 CTCTCGTTGC
Statistics
Matches: 55, Mismatches: 6, Indels: 20
0.68 0.07 0.25
Matches are distributed among these distances:
14 19 0.35
16 6 0.11
17 6 0.11
19 24 0.44
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.46
Consensus pattern (19 bp):
CGATTTTCATTTCGCGTTG
Found at i:1665958 original size:14 final size:14
Alignment explanation
Indices: 1665939--1666028 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
1665929 TTTCATTTCG
1665939 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1665953 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1665972 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
1665986 AGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1666005 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1666019 CGTTGCGATT
1 CGTTGCGATT
1666029 TTCATTTCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 29 0.48
16 6 0.10
17 6 0.10
19 19 0.32
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1665967 original size:33 final size:33
Alignment explanation
Indices: 1665925--1666036 Score: 215
Period size: 33 Copynumber: 3.4 Consensus size: 33
1665915 AATCGCATTA
1665925 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
*
1665958 CGATTTTCATTTCGCGTTGCGATTCTCTAGTTG
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
1665991 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
1666024 CGATTTTCATTTC
1 CGATTTTCATTTC
1666037 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (33 bp):
CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
Found at i:1667893 original size:93 final size:93
Alignment explanation
Indices: 1667734--1668388 Score: 1276
Period size: 93 Copynumber: 7.1 Consensus size: 93
1667724 TAGATTGCTT
* * *
1667734 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACATTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1667799 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1667827 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1667892 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1667920 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1667985 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1668013 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1668078 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1668106 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1668171 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1668199 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1668264 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1668292 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1668357 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1668384 AGTAA
1 AGTAA
1668389 TGCAATCCAT
Statistics
Matches: 559, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 6 0.01
93 553 0.99
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1668483 original size:19 final size:19
Alignment explanation
Indices: 1668459--1668588 Score: 118
Period size: 19 Copynumber: 7.3 Consensus size: 19
1668449 CTTAAAATCA
1668459 TTGCGATTTTGGTTTCGCG
1 TTGCGATTTTGGTTTCGCG
*
1668478 TTGCGATCTT-G--T--CG
1 TTGCGATTTTGGTTTCGCG
1668492 TTGCGATTTTGGTTTCGCG
1 TTGCGATTTTGGTTTCGCG
*
1668511 TTGCGATTCT-G--T--CG
1 TTGCGATTTTGGTTTCGCG
* **
1668525 TTTCGATTTTCATTTCGCG
1 TTGCGATTTTGGTTTCGCG
1668544 TTGCGATTTTGGTTTCGCG
1 TTGCGATTTTGGTTTCGCG
* *
1668563 TTGCGATTTTAAGTTTCGTG
1 TTGCGATTTT-GGTTTCGCG
1668583 TTGCGA
1 TTGCGA
1668589 AAGTAAACTA
Statistics
Matches: 89, Mismatches: 11, Indels: 21
0.74 0.09 0.17
Matches are distributed among these distances:
14 21 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.54
20 13 0.15
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTGGTTTCGCG
Found at i:1668497 original size:33 final size:33
Alignment explanation
Indices: 1668459--1668551 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 33
1668449 CTTAAAATCA
1668459 TTGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCG
1 TTGCGATTTTGGTTTCGCGTTGCGATTC-TGTCG
1668492 TTGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
* **
1668525 TTTCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTGGTTTCGCGTTGCGATT
1668552 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.27, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
Found at i:1670534 original size:14 final size:14
Alignment explanation
Indices: 1670515--1670550 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1670505 ATTGTTTAAT
1670515 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1670529 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1670543 TGATTTGT
1 TGATTTGT
1670551 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1670681 original size:19 final size:19
Alignment explanation
Indices: 1670657--1670754 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1670647 AAAATTGACT
1670657 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1670676 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1670695 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1670709 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1670728 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1670748 ATCGCAA
1 ATCGCAA
1670755 CGGGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1670786 original size:53 final size:53
Alignment explanation
Indices: 1670657--1670773 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
1670647 AAAATTGACT
1670657 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
1670709 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1670762 ATCGCAATGCGA
1 ATCGCAATGCGA
1670774 TTTTAATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:1670791 original size:19 final size:19
Alignment explanation
Indices: 1670763--1670932 Score: 181
Period size: 19 Copynumber: 9.7 Consensus size: 19
1670753 AACGGGAGAA
* *
1670763 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
1670782 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1670798 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1670815 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1670831 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1670848 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1670867 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1670886 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
1670904 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1670920 TCGCATTGCGATT
1 TCGCATTGCGATT
1670933 CTCTCGTTGC
Statistics
Matches: 127, Mismatches: 8, Indels: 32
0.76 0.05 0.19
Matches are distributed among these distances:
14 23 0.18
16 16 0.13
17 14 0.11
18 1 0.01
19 57 0.45
20 16 0.13
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1670806 original size:14 final size:14
Alignment explanation
Indices: 1670787--1670841 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1670777 TAATTTCGCA
1670787 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1670801 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1670818 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1670834 TTGCGATT
1 TTGCGATT
1670842 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1670914 original size:72 final size:68
Alignment explanation
Indices: 1670769--1670946 Score: 240
Period size: 72 Copynumber: 2.6 Consensus size: 68
1670759 AGAATCGCAA
*
1670769 TGCGATTTTAATTTCGCATTGCGA--TTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 TGCGATTTTCATTTCGCATTGCGATTTTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1670832 CGT
66 CGT
*
1670835 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTC-TCTCG--TTGCGATTTTCATTT-CGCATTGCGATT
*
1670900 TTCAT-GT
62 CTC-TCGT
*
1670907 TGGGATTTTCATTTCGCATTGCGA--TTCTCTCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCTCTCGTTGCGATT
1670947 GTAATTTCCG
Statistics
Matches: 100, Mismatches: 5, Indels: 13
0.85 0.04 0.11
Matches are distributed among these distances:
66 23 0.23
67 8 0.08
68 3 0.03
69 8 0.08
70 3 0.03
71 15 0.15
72 39 0.39
73 1 0.01
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (68 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCT
CGT
Found at i:1670954 original size:33 final size:33
Alignment explanation
Indices: 1670769--1670946 Score: 250
Period size: 33 Copynumber: 5.2 Consensus size: 33
1670759 AGAATCGCAA
*
1670769 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1670802 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
1670835 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
*
1670873 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
*
1670907 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1670940 TGCGATT
1 TGCGATT
1670947 GTAATTTCCG
Statistics
Matches: 130, Mismatches: 7, Indels: 16
0.85 0.05 0.10
Matches are distributed among these distances:
32 1 0.01
33 78 0.60
34 14 0.11
35 3 0.02
36 6 0.05
37 3 0.02
38 15 0.12
39 10 0.08
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1670954 original size:105 final size:104
Alignment explanation
Indices: 1670763--1670954 Score: 305
Period size: 105 Copynumber: 1.8 Consensus size: 104
1670753 AACGGGAGAA
1670763 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
* *
1670828 CTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
66 CTCTCGTTGCGATTGTAATTTCGCATTGCGATTTTCATT
* * * *
1670867 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCATTGCGA
1 TCGCAATGCGATTTTAATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCATTGCGA
1670931 TTCTCTCGTTGCGATTGTAATTTC
64 TTCTCTCGTTGCGATTGTAATTTC
1670955 CGTGTTGCGA
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
104 18 0.22
105 61 0.76
106 1 0.01
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.45
Consensus pattern (104 bp):
TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
CTCTCGTTGCGATTGTAATTTCGCATTGCGATTTTCATT
Found at i:1673410 original size:24 final size:24
Alignment explanation
Indices: 1673376--1673422 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1673366 CTGAAACATC
1673376 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1673400 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1673423 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Done.