Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009579.1 Hibiscus syriacus cultivar Beakdansim tig00116951_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: 6215474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 29
Found at i:5349246 original size:31 final size:31
Alignment explanation
Indices: 5349208--5349269 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
5349198 CCTCGGCAAT
*
5349208 TGTCCATAAGTCCCG-AAGAACCTAGGTAAAC
1 TGTCCATAAGTCCCGAAAG-ACATAGGTAAAC
* *
5349239 TGTCCATATGTCTCGAAAGACATAGGTAAAC
1 TGTCCATAAGTCCCGAAAGACATAGGTAAAC
5349270 CCTTGACTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (31 bp):
TGTCCATAAGTCCCGAAAGACATAGGTAAAC
Found at i:5350360 original size:64 final size:63
Alignment explanation
Indices: 5350247--5350387 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 63
5350237 TCTTTAACAT
* * * *
5350247 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCAT-TTTAAGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCAATG-TTTCATCTTTAAAGA
* * * ** *
5350310 GATGCATCGATGCACT-CCTTATGCATCGATGCACCAATTGCATTCAATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACC-CATGCATCGATACACAAATCACATTCAATGTTTCATCTTTAAAGA
5350374 GTGCATCGATGCAC
1 GTGCATCGATGCAC
5350388 ATTGAATATG
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
63 21 0.32
64 44 0.68
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCAATGTTTCATCTTTAAAGA
Found at i:5351224 original size:21 final size:21
Alignment explanation
Indices: 5351200--5351240 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5351190 TTCTTGAAGA
*
5351200 CATTAGTTTTTTTTATTATTT
1 CATTAGTTTTATTTATTATTT
*
5351221 CATTTGTTTTATTTATTATT
1 CATTAGTTTTATTTATTATT
5351241 ATTTTGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.71
Consensus pattern (21 bp):
CATTAGTTTTATTTATTATTT
Found at i:5351268 original size:11 final size:11
Alignment explanation
Indices: 5351229--5351283 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
5351219 TTCATTTGTT
5351229 TTAT-TTATTA
1 TTATATTATTA
* *
5351239 TTATTTTGTT-
1 TTATATTATTA
5351249 TTAATATTATTA
1 TT-ATATTATTA
5351261 TTATATTATTA
1 TTATATTATTA
5351272 TTATTATTATTA
1 TTA-TATTATTA
5351284 AATAAATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
10 6 0.16
11 22 0.58
12 10 0.26
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (11 bp):
TTATATTATTA
Found at i:5351303 original size:3 final size:3
Alignment explanation
Indices: 5351233--5351283 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
5351223 TTTGTTTTAT
* *
5351233 TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5351278 TTA TTA
1 TTA TTA
5351284 AATAAATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 6 0.14
3 37 0.86
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5360345 original size:114 final size:114
Alignment explanation
Indices: 5360130--5360349 Score: 359
Period size: 114 Copynumber: 1.9 Consensus size: 114
5360120 CATATTCTCG
* *
5360130 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGATTC
* * * *
5360195 GGTATGAACCCCAAAACCAATCATTATATTTGAAAGATGAATTTGCTCA
66 GGTAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAATTTGCTCA
*
5360244 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGATTC
* *
5360309 GGTAGGAACCCCAGAACCAATCATTGGAATTAAAAGATGAA
66 GGTAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAA
5360350 CTGCATGATC
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 97 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGATTC
GGTAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAATTTGCTCA
Found at i:5362969 original size:22 final size:22
Alignment explanation
Indices: 5362938--5362990 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
5362928 ATCTACACTC
*
5362938 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
5362960 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
5362982 TTCAAAGAT
1 TTCAAAGAT
5362991 AAAAGCTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:5363631 original size:113 final size:113
Alignment explanation
Indices: 5363400--5364065 Score: 1050
Period size: 113 Copynumber: 5.9 Consensus size: 113
5363390 GTTCAAATCT
* * * **
5363400 ATCATTCAATGGATCAACATTTCTA-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTCGATGGATCAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
5363464 TAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTC
* * *
5363512 ACCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGATGGAA
1 ATCATTCGATGGATCAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
5363577 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTC
*
5363625 ATCATTCGATGGATCAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAA
1 ATCATTCGATGGATCAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
5363690 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTC
* *
5363738 ATTATTCGATGGATCAACATTACCAGGTCGAGTTCATAATGAGAAAAACTCATCTGAAGAAGGAA
1 ATCATTCGATGGATCAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
5363803 GAAGAAGTTCATAATGAGAAGAACTTGTTCAAATTTTCGCTTGAATTC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTC
* * * * ** * *
5363851 ATCATTTGATGGACCAGCATTACCATGTCGAGAAC-CAATGAGAAGAACTCATCTGAAGAAAGAA
1 ATCATTCGATGGATCAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
5363915 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATTC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTC
* * * *
5363963 ATCACTCGATGGATCAACTTTTCCAGAG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCATTCGATGGATCAACATTACCAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
5364027 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTT
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTT
5364066 GCATGATTCT
Statistics
Matches: 508, Mismatches: 42, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
112 114 0.22
113 389 0.77
114 5 0.01
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
ATCATTCGATGGATCAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTC
Found at i:5364403 original size:21 final size:21
Alignment explanation
Indices: 5364373--5364452 Score: 67
Period size: 21 Copynumber: 3.7 Consensus size: 21
5364363 GAAGACACTA
*
5364373 GTTTTTTTTATTATTTCA-TTT
1 GTTTTATTTATTATTT-ATTTT
5364394 GTTTTATTTATTA-TTATTTT
1 GTTTTATTTATTATTTATTTT
5364414 GTTTTAATATTATTATTATATTATT
1 GTTTT-AT-TTATTATT-TATT-TT
* *
5364439 ATATTA-TTATTATT
1 GTTTTATTTATTATT
5364453 ATTAATTAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
19 1 0.02
20 10 0.20
21 14 0.28
22 14 0.28
23 1 0.02
24 5 0.10
25 5 0.10
ACGTcount: A:0.25, C:0.01, G:0.04, T:0.70
Consensus pattern (21 bp):
GTTTTATTTATTATTTATTTT
Found at i:5364409 original size:3 final size:3
Alignment explanation
Indices: 5364401--5364478 Score: 67
Period size: 3 Copynumber: 27.0 Consensus size: 3
5364391 TTTGTTTTAT
* *
5364401 TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA TTA -TA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
5364445 TTA TTA TTA TTAA TTA -AA TAA TTTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA -TTA TTA TTA TTA
5364479 CAGGCCCAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
2 9 0.14
3 50 0.78
4 5 0.08
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:5364412 original size:19 final size:20
Alignment explanation
Indices: 5364376--5364452 Score: 79
Period size: 19 Copynumber: 3.9 Consensus size: 20
5364366 GACACTAGTT
* *
5364376 TTTTTTATTATT-TCATTTG
1 TTTTATATTATTATTATTTG
5364395 TTTTAT-TTATTATTATTTTG
1 TTTTATATTATTATTA-TTTG
*
5364415 TTTTAATATTATTATTATAT-
1 TTTT-ATATTATTATTATTTG
*
5364435 TATTATATTATTATTATT
1 TTTTATATTATTATTATT
5364453 ATTAATTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
18 5 0.10
19 20 0.41
20 11 0.22
21 4 0.08
22 9 0.18
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.70
Consensus pattern (20 bp):
TTTTATATTATTATTATTTG
Found at i:5364429 original size:22 final size:22
Alignment explanation
Indices: 5364391--5364455 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
5364381 TATTATTTCA
5364391 TTTGTTTT-AT-TTATTATTAT
1 TTTGTTTTAATATTATTATTAT
5364411 TTTGTTTTAATATTATTATTAT
1 TTTGTTTTAATATTATTATTAT
* * * *
5364433 ATTATTATATTATTATTATTAT
1 TTTGTTTTAATATTATTATTAT
5364455 T
1 T
5364456 AATTAAATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
20 8 0.21
21 2 0.05
22 28 0.74
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (22 bp):
TTTGTTTTAATATTATTATTAT
Found at i:5364437 original size:8 final size:8
Alignment explanation
Indices: 5364424--5364460 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
5364414 GTTTTAATAT
5364424 TATTATTA
1 TATTATTA
5364432 TATTATTA
1 TATTATTA
5364440 TATTATTA
1 TATTATTA
5364448 TTATTATTA
1 -TATTATTA
5364457 -ATTA
1 TATTA
5364461 AATAATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 4 0.14
8 16 0.57
9 8 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTATTA
Found at i:5364470 original size:22 final size:25
Alignment explanation
Indices: 5364421--5364478 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 25
5364411 TTTGTTTTAA
* *
5364421 TATTATTATTATATTATTATATTAT
1 TATTATTATTATATTATAATAATAT
5364446 TATTATTATTA-ATTA-AATAAT-T
1 TATTATTATTATATTATAATAATAT
5364468 TATTATTATTA
1 TATTATTATTA
5364479 CAGGCCCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 12 0.39
23 4 0.13
24 4 0.13
25 11 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TATTATTATTATATTATAATAATAT
Found at i:5367031 original size:21 final size:21
Alignment explanation
Indices: 5367002--5367041 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5366992 ACCAATCTTC
*
5367002 ATTGCATCCTCGTAACTTTAG
1 ATTGCATCCTCATAACTTTAG
*
5367023 ATTGGATCCTCATAACTTT
1 ATTGCATCCTCATAACTTT
5367042 GATAACCCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (21 bp):
ATTGCATCCTCATAACTTTAG
Found at i:5369285 original size:28 final size:28
Alignment explanation
Indices: 5369232--5369289 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
5369222 TATATCATAT
*
5369232 ATATTACATATGCATATAGATCATTTTC
1 ATATTACATATGCACATAGATCATTTTC
*
5369260 ATATTCACATA-GCACATA-ATCAATTT-
1 ATATT-ACATATGCACATAGATCATTTTC
5369286 ATAT
1 ATAT
5369290 AAACAAGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.15
27 7 0.26
28 11 0.41
29 5 0.19
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.40
Consensus pattern (28 bp):
ATATTACATATGCACATAGATCATTTTC
Found at i:5369669 original size:24 final size:20
Alignment explanation
Indices: 5369616--5369673 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
5369606 TTCCCCTTGA
*
5369616 AGTGCATCAATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
5369636 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
5369659 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
5369674 CCACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:5369748 original size:64 final size:63
Alignment explanation
Indices: 5369661--5369801 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 63
5369651 TCTTTAACAT
* * *
5369661 GTGCATCGATGCACCACCCATGCATCGATACAGAAATCACCTTCGATGTTTTCAT-TTTAAAGG
1 GTGCATCGATGCACCACCCATGCATCGATACACAAATCACATTCGATG-TTTCATCTTTAAAGA
** * * ** *
5369724 GATGCATCGATGCACTC-CTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCAC-CACCCATGCATCGATACACAAATCACATTCGATGTTTCATCTTTAAAGA
5369788 GTGCATCGATGCAC
1 GTGCATCGATGCAC
5369802 ATTGAATATG
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
63 19 0.29
64 45 0.69
65 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCACCACCCATGCATCGATACACAAATCACATTCGATGTTTCATCTTTAAAGA
Found at i:5378078 original size:15 final size:15
Alignment explanation
Indices: 5378058--5378092 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
5378048 TATTGCACGT
5378058 CCTCCTCTAAGCACA
1 CCTCCTCTAAGCACA
5378073 CCTCCTCTAAGCACA
1 CCTCCTCTAAGCACA
5378088 CCTCC
1 CCTCC
5378093 AGTAACATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.23, C:0.51, G:0.06, T:0.20
Consensus pattern (15 bp):
CCTCCTCTAAGCACA
Found at i:5378725 original size:198 final size:198
Alignment explanation
Indices: 5378288--5379149 Score: 1654
Period size: 198 Copynumber: 4.4 Consensus size: 198
5378278 GTGCAAGAGT
5378288 CCATTTCTGTGCATAAGCAGCCCGAATGCATCTGATAGAGGCTGTTGAAGTACATATATAATCAA
1 CCATTTCTGTGCATAAGCAGCCCGAATGCATCTGATAGAGGCTGTTGAAGTACATATATAATCAA
*
5378353 TCAAAACAGCATTTCACATCAGAAAACTGTTATTGTGTTATAGTTTAATGAAAAACATAAATTAC
66 TCAAAACAGCATCTCACATCAGAAAACTGTTATTGTGTTATAGTTTAATGAAAAACATAAATTAC
*
5378418 AGG-AACCGTAGCATGCTGGTACCTTGGTTAAGGGGAAACTCCAGGTGCAAGAGTCCATTCCCAT
131 AGGAAACTGTAGCATGCTGGTACCTTGGTTAAGGGGAAACTCCAGGTGCAAGAGTCCATTCCCAT
5378482 TGA
196 TGA
*
5378485 CCATTTCTGTGCATAAGCAGCCCGAATGCATCTGATAGAGGCTGCTGAAGTACATATATAATCAA
1 CCATTTCTGTGCATAAGCAGCCCGAATGCATCTGATAGAGGCTGTTGAAGTACATATATAATCAA
* *
5378550 TCAAAACAGCATCTCACATCAGAAAACTGCTATTGTGTTATGGTTTAATGAAAAACATAAATTAC
66 TCAAAACAGCATCTCACATCAGAAAACTGTTATTGTGTTATAGTTTAATGAAAAACATAAATTAC
5378615 AGGAAACTGTAGCATGCTGGTACCTTGGTTAAGGGGAAACTCCAGGTGCAAGAGTCCATTCCCAT
131 AGGAAACTGTAGCATGCTGGTACCTTGGTTAAGGGGAAACTCCAGGTGCAAGAGTCCATTCCCAT
5378680 TGA
196 TGA
5378683 CCATTTCTGTGCATAAGCAGCCCGAATGCATCTGATAGAGGCTGTTGAAGTACATATATAATCAA
1 CCATTTCTGTGCATAAGCAGCCCGAATGCATCTGATAGAGGCTGTTGAAGTACATATATAATCAA
*
5378748 TCAAAACAGCATTTCACATCAGAAAACTGTTATTGTGTTATAGTTTAATGAAAAACATAAATTAC
66 TCAAAACAGCATCTCACATCAGAAAACTGTTATTGTGTTATAGTTTAATGAAAAACATAAATTAC
5378813 AGGAAACTGTAGCATGCTGGTACCTTGGTTAAGGGGAAACTCCAGGTGCAAGAGTCCATTCCCAT
131 AGGAAACTGTAGCATGCTGGTACCTTGGTTAAGGGGAAACTCCAGGTGCAAGAGTCCATTCCCAT
5378878 TGA
196 TGA
5378881 CCATTTCTGTGCATAAGCAGCCCGAATGCATCTGATAGAGGCTGTTGAAGTACATATATAATCAA
1 CCATTTCTGTGCATAAGCAGCCCGAATGCATCTGATAGAGGCTGTTGAAGTACATATATAATCAA
*
5378946 TCAAAACAGCATCTCACATCAGAAAACTGTTATTGTGTTATGGTTTAATGAAAAACATAAATTAC
66 TCAAAACAGCATCTCACATCAGAAAACTGTTATTGTGTTATAGTTTAATGAAAAACATAAATTAC
5379011 AGGAAACTGTAGCATGCTGGTACCTTGGTTAAGGGGAAACTCCAGGTGCAAGAGTCCATTCCCAT
131 AGGAAACTGTAGCATGCTGGTACCTTGGTTAAGGGGAAACTCCAGGTGCAAGAGTCCATTCCCAT
5379076 TGA
196 TGA
5379079 CCATTTCTGTGCATAAGCAGCCCGAATGCATCTGATAGAGGCTGTTGAAGTACATATATAATCAA
1 CCATTTCTGTGCATAAGCAGCCCGAATGCATCTGATAGAGGCTGTTGAAGTACATATATAATCAA
5379144 TCAAAA
66 TCAAAA
5379150 TAGGTGCCTA
Statistics
Matches: 653, Mismatches: 11, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
197 129 0.20
198 524 0.80
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (198 bp):
CCATTTCTGTGCATAAGCAGCCCGAATGCATCTGATAGAGGCTGTTGAAGTACATATATAATCAA
TCAAAACAGCATCTCACATCAGAAAACTGTTATTGTGTTATAGTTTAATGAAAAACATAAATTAC
AGGAAACTGTAGCATGCTGGTACCTTGGTTAAGGGGAAACTCCAGGTGCAAGAGTCCATTCCCAT
TGA
Found at i:5384869 original size:122 final size:122
Alignment explanation
Indices: 5384652--5384896 Score: 411
Period size: 122 Copynumber: 2.0 Consensus size: 122
5384642 ATGCAAGGTT
*
5384652 TTTTTGACATGTCAAACTGATATTGAAGTTATTCACAATTCAGTTCGCTCCATCCACAATGTCAA
1 TTTTTGACATGTCAAACTGATATTGAAGTTATTCACAATTCAGTTCACTCCATCCACAATGTCAA
*
5384717 AATTTGAATCCCTAATCATATTTAAAGATTC-GATATTTCATCCCACTAGACCAATCA
66 AATTTGAATCCCTAATCATATTTAAAGATTCAG-TATTTCATCCCAATAGACCAATCA
* * * *
5384774 TTTTTGACATGTCAAGCTGATATTGAAGTTGTTCACAATTCAGTTTACTCCATTCACAATGTCAA
1 TTTTTGACATGTCAAACTGATATTGAAGTTATTCACAATTCAGTTCACTCCATCCACAATGTCAA
*
5384839 GATTTGAATCCCTAATCATATTTAAAGATTCAGTATTTCATCCCAATAGACCAATCA
66 AATTTGAATCCCTAATCATATTTAAAGATTCAGTATTTCATCCCAATAGACCAATCA
5384896 T
1 T
5384897 ATAAATTTTA
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
122 114 0.99
123 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.36
Consensus pattern (122 bp):
TTTTTGACATGTCAAACTGATATTGAAGTTATTCACAATTCAGTTCACTCCATCCACAATGTCAA
AATTTGAATCCCTAATCATATTTAAAGATTCAGTATTTCATCCCAATAGACCAATCA
Found at i:5385063 original size:2 final size:2
Alignment explanation
Indices: 5385052--5385115 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
5385042 AATGCTCGAT
5385052 TA TA -A 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 TA TA TA
5385093 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
5385116 CAATACCAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5401426 original size:18 final size:18
Alignment explanation
Indices: 5401405--5401446 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
5401395 TAATAATCAT
5401405 ACTATATATTCTCCTCAA
1 ACTATATATTCTCCTCAA
5401423 ACTATATATTCTCCTCAA
1 ACTATATATTCTCCTCAA
5401441 ACTATA
1 ACTATA
5401447 CTGCTCGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.26, G:0.00, T:0.38
Consensus pattern (18 bp):
ACTATATATTCTCCTCAA
Found at i:5405460 original size:22 final size:21
Alignment explanation
Indices: 5405435--5405477 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5405425 ACTATCCTAT
5405435 TATTTGTAGGTT-ATTAGTTTTA
1 TATTT-TAGGTTGATTA-TTTTA
*
5405457 TATTTTAGTTTGATTATTTTA
1 TATTTTAGGTTGATTATTTTA
5405478 AGAGAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (21 bp):
TATTTTAGGTTGATTATTTTA
Found at i:5405669 original size:21 final size:21
Alignment explanation
Indices: 5405645--5405814 Score: 136
Period size: 21 Copynumber: 7.9 Consensus size: 21
5405635 ACTTCGACTA
5405645 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* * *
5405666 TCGCGTTGCGAT-TTACATA-T
1 TCGCATTGCGATAGTCCA-AGT
5405686 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
5405707 TCGCGTTGCGATTTATTCCAAGT
1 TCGCATTGCGA--TAGTCCAAGT
*
5405730 TCG--TTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
5405749 TCGCGATTCGTTGCGATAGTCCAAGT
1 TCGC-A----TTGCGATAGTCCAAGT
* *
5405775 TCGCGTTGCGATTTATTCCAAGT
1 TCGCATTGCGA--TAGTCCAAGT
5405798 TCG--TTGCGATAGTCCAA
1 TCGCATTGCGATAGTCCAA
5405815 AATCGCAACG
Statistics
Matches: 121, Mismatches: 14, Indels: 30
0.73 0.08 0.18
Matches are distributed among these distances:
19 18 0.15
20 16 0.13
21 44 0.36
23 24 0.20
26 19 0.16
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:5405765 original size:26 final size:26
Alignment explanation
Indices: 5405729--5405779 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
5405719 TTATTCCAAG
*
5405729 TTCGTTGCGATAGTCGAAGTTCGCGA
1 TTCGTTGCGATAGTCCAAGTTCGCGA
5405755 TTCGTTGCGATAGTCCAAGTTCGCG
1 TTCGTTGCGATAGTCCAAGTTCGCG
5405780 TTGCGATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (26 bp):
TTCGTTGCGATAGTCCAAGTTCGCGA
Found at i:5406553 original size:21 final size:21
Alignment explanation
Indices: 5406527--5406566 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5406517 CGTTGCAATT
5406527 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
5406548 TTGGACTATCGCAATGCGA
1 TTGGACTATCGCAACGCGA
5406567 TTTACATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:5406698 original size:104 final size:104
Alignment explanation
Indices: 5406551--5406753 Score: 325
Period size: 104 Copynumber: 2.0 Consensus size: 104
5406541 CGCGAACTTG
* *
5406551 GACTATCGCAATGCGATTTACATATTCGTATTACGATAATCCAAGTTCGCATTGAGATAGTCGAA
1 GACTATCGCAATGCGATTTACATATTCGCATTACGATAATCCAAGTTCGCATTGAGATAGTCCAA
* * *
5406616 GTTCGCGTTGCGATAGTCCAAGTTGGCATTGCGATAGTC
66 GTTCGCATTGCGATAATCCAAGTTCGCATTGCGATAGTC
* * *
5406655 GACTATCGCAATGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAA
1 GACTATCGCAATGCGATTTACATATTCGCATTACGATAATCCAAGTTCGCATTGAGATAGTCCAA
*
5406720 GTTCGCATTGCGATAATCCAAGTTCGCGTTGCGA
66 GTTCGCATTGCGATAATCCAAGTTCGCATTGCGA
5406754 ATCTGGAAAC
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
104 90 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (104 bp):
GACTATCGCAATGCGATTTACATATTCGCATTACGATAATCCAAGTTCGCATTGAGATAGTCCAA
GTTCGCATTGCGATAATCCAAGTTCGCATTGCGATAGTC
Found at i:5406726 original size:62 final size:62
Alignment explanation
Indices: 5406617--5406733 Score: 173
Period size: 62 Copynumber: 1.9 Consensus size: 62
5406607 ATAGTCGAAG
* * *
5406617 TTCGCGTTGCGATAGTCCAAGTTGGCATTGCGATAGTCGACTATCGCAATGCGATTTACATA
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCAACTATCGCAATGCGATTTACATA
* *
5406679 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGT-TCGCATTGCGAT
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGT-CAACTATCGCAATGCGAT
5406734 AATCCAAGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
62 46 0.94
63 3 0.06
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (62 bp):
TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCAACTATCGCAATGCGATTTACATA
Found at i:5406751 original size:21 final size:21
Alignment explanation
Indices: 5406575--5406753 Score: 193
Period size: 21 Copynumber: 8.6 Consensus size: 21
5406565 GATTTACATA
* * *
5406575 TTCGTATTACGATAATCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
5406596 TTCGCATTGAGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
5406617 TTCGCGTTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
5406638 TTGGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* * *
5406658 TATCGCAATGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
5406679 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
5406700 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
5406721 TTCGCATTGCGATAATCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
5406742 TTCGCGTTGCGA
1 TTCGCATTGCGA
5406754 ATCTGGAAAC
Statistics
Matches: 132, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
20 16 0.12
21 115 0.87
22 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:5413017 original size:19 final size:19
Alignment explanation
Indices: 5412993--5413030 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5412983 TGATGGTCAC
5412993 CTTATTAAGATGTCGACAA
1 CTTATTAAGATGTCGACAA
5413012 CTTATTAAGATGTCGACAA
1 CTTATTAAGATGTCGACAA
5413031 TCAATACAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
CTTATTAAGATGTCGACAA
Found at i:5415708 original size:23 final size:23
Alignment explanation
Indices: 5415682--5415745 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
5415672 CAGCTTGTAT
5415682 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
5415705 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
5415728 AATTGCACCGTAA-TGCCA
1 AATTGCACCG-AAGTGCCA
5415746 TATAATAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:5421874 original size:2 final size:2
Alignment explanation
Indices: 5421869--5421895 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5421859 GAGAGAGTCG
5421869 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
5421896 ATTTTCCATT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:5432605 original size:20 final size:20
Alignment explanation
Indices: 5432582--5432633 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
5432572 AACGCGATCC
5432582 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
5432602 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
5432622 CCAAAATCGCAA
1 CCAGAATCGCAA
5432634 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:5432650 original size:21 final size:20
Alignment explanation
Indices: 5432623--5432721 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
5432613 AATCAGTTTC
5432623 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
5432644 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
5432665 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
5432685 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
5432706 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
5432722 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:5432750 original size:20 final size:20
Alignment explanation
Indices: 5432688--5432881 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
5432678 CGATTTTCCA
* ** *
5432688 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
5432708 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
5432728 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
5432748 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
5432768 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
5432788 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
5432808 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
5432828 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
5432848 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
5432869 AAATCGCAACGCG
1 AAATCGCAACGCG
5432882 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:5432772 original size:60 final size:60
Alignment explanation
Indices: 5432688--5432881 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
5432678 CGATTTTCCA
* ** * *
5432688 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
5432748 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
5432808 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
5432869 AAATCGCAACGCG
1 AAATCGCAACGCG
5432882 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:5433302 original size:33 final size:33
Alignment explanation
Indices: 5433263--5433333 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
5433253 TTCACTTAGA
*
5433263 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
5433296 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
5433329 TTTCA
1 TTTCA
5433334 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:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:5433473 original size:14 final size:14
Alignment explanation
Indices: 5433454--5433508 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
5433444 AGAATGACTG
5433454 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
5433468 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
5433487 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
5433501 TCGCAACG
1 TCGCAACG
5433509 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:5433521 original size:33 final size:33
Alignment explanation
Indices: 5433454--5433524 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
5433444 AGAATGACTG
***
5433454 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
5433487 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
5433520 TCGCA
1 TCGCA
5433525 TTGCGATTTT
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:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:5433542 original size:19 final size:19
Alignment explanation
Indices: 5433520--5433617 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
5433510 GAAACCAAAA
*
5433520 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5433539 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
5433553 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5433572 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
5433586 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
5433605 TCGCGTTGCGATT
1 TCGCGTTGCGATT
5433618 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5433561 original size:14 final size:14
Alignment explanation
Indices: 5433542--5433631 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
5433532 TTTCATTTCG
5433542 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5433556 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
5433575 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5433589 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
5433606 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
5433622 CGTTGCGATT
1 CGTTGCGATT
5433632 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:5433567 original size:33 final size:33
Alignment explanation
Indices: 5433525--5433639 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
5433515 CAAAATCGCA
5433525 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
5433558 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
5433591 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
5433624 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
5433640 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:5435568 original size:185 final size:186
Alignment explanation
Indices: 5435338--5435719 Score: 748
Period size: 185 Copynumber: 2.1 Consensus size: 186
5435328 TAGATTGCTT
5435338 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5435403 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
5435468 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
5435523 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5435588 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
5435653 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
5435709 AGTAAATTTAT
1 AGTAAATTTAT
5435720 CCATTCAAGT
Statistics
Matches: 194, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
185 154 0.79
186 40 0.21
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:5435652 original size:93 final size:93
Alignment explanation
Indices: 5435338--5435717 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
5435328 TAGATTGCTT
*
5435338 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5435403 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5435431 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5435495 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5435523 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5435588 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5435616 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5435681 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5435709 AGTAAATTT
1 AGTAAATTT
5435718 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 193 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:5435801 original size:19 final size:19
Alignment explanation
Indices: 5435761--5435889 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
5435751 TAGTTTACTT
* *
5435761 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
5435781 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
5435800 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
5435819 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
5435833 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
5435852 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
5435866 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
5435885 TCGCA
1 TCGCA
5435890 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:5435840 original size:33 final size:32
Alignment explanation
Indices: 5435797--5435889 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
5435787 CGCGAAACCA
**
5435797 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
5435829 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
5435862 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
5435890 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:5435887 original size:52 final size:52
Alignment explanation
Indices: 5435761--5435889 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
5435751 TAGTTTACTT
**
5435761 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
5435813 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
5435866 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
5435890 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:5435907 original size:19 final size:19
Alignment explanation
Indices: 5435885--5436019 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
5435875 GAAACCAAAA
*
5435885 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5435904 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
5435920 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
5435937 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
5435953 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
5435970 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
5435989 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
5436009 TCGTGTTGCGA
1 TCGCGTTGCGA
5436020 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5435926 original size:14 final size:14
Alignment explanation
Indices: 5435907--5435963 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5435897 TTTCATTTCG
5435907 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
5435921 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
5435938 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
5435954 CGTTGCGATT
1 CGTTGCGATT
5435964 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:5435932 original size:33 final size:33
Alignment explanation
Indices: 5435890--5435982 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
5435880 CAAAATCGCA
*
5435890 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
5435923 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
5435956 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
5435983 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:5437879 original size:38 final size:38
Alignment explanation
Indices: 5437836--5437908 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
5437826 AATTGATTGT
*
5437836 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
5437874 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
5437909 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:5437895 original size:19 final size:19
Alignment explanation
Indices: 5437831--5437895 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
5437821 AGTTTAATTG
*
5437831 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
5437850 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
5437868 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
5437888 ATTGATTT
1 ATTGATTT
5437896 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:5437909 original size:14 final size:14
Alignment explanation
Indices: 5437890--5437925 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
5437880 ATTGTTTAAT
5437890 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
5437904 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
5437918 TGATTTGT
1 TGATTTGT
5437926 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:5438048 original size:19 final size:19
Alignment explanation
Indices: 5438032--5438133 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
5438022 AAAAATGACT
5438032 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5438051 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
5438070 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
5438084 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5438103 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
5438123 ATCGCAATGCG
1 ATCGCAATGCG
5438134 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:5438186 original size:19 final size:19
Alignment explanation
Indices: 5438162--5438468 Score: 367
Period size: 19 Copynumber: 17.4 Consensus size: 19
5438152 GATTATCTCG
5438162 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5438181 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5438200 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
5438214 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5438233 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5438252 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
5438271 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
5438290 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5438309 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
5438323 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5438342 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
5438356 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5438375 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5438394 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
5438408 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
5438428 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
5438442 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
5438461 TTGCGATT
1 TTGCGATT
5438469 GTATTTTCCG
Statistics
Matches: 250, Mismatches: 12, Indels: 52
0.80 0.04 0.17
Matches are distributed among these distances:
14 35 0.14
16 31 0.12
17 28 0.11
18 3 0.01
19 141 0.56
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:5438202 original size:52 final size:52
Alignment explanation
Indices: 5438140--5438401 Score: 341
Period size: 52 Copynumber: 4.9 Consensus size: 52
5438130 TGCGTTTATA
5438140 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
5438192 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
5438244 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
5438301 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATT-T-TC
* * * * *
5438355 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATT
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATT
5438402 CTCTCGTTGC
Statistics
Matches: 190, Mismatches: 12, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
52 120 0.63
53 5 0.03
54 15 0.08
55 7 0.04
57 43 0.23
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:5438328 original size:14 final size:14
Alignment explanation
Indices: 5438309--5438363 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
5438299 TCATTTCGCA
5438309 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
5438323 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
5438340 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
5438356 TTGCGATT
1 TTGCGATT
5438364 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:5438402 original size:52 final size:52
Alignment explanation
Indices: 5438162--5438440 Score: 295
Period size: 52 Copynumber: 5.2 Consensus size: 52
5438152 GATTATCTCG
*
5438162 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
5438214 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * * * * *
5438271 TTGCGATTTTAATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
5438323 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
5438375 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
5438428 TTGCGATTTTCAT
1 TTGCGATTTTCAT
5438441 GTTGGGATTT
Statistics
Matches: 202, Mismatches: 13, Indels: 23
0.85 0.05 0.10
Matches are distributed among these distances:
50 7 0.03
51 4 0.02
52 125 0.62
53 23 0.11
54 12 0.06
55 7 0.03
57 24 0.12
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:5438433 original size:34 final size:33
Alignment explanation
Indices: 5438140--5438468 Score: 153
Period size: 33 Copynumber: 9.5 Consensus size: 33
5438130 TGCGTTTATA
*
5438140 ATTTCGCATTGCGATTATC-TCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCAT-GTTGCGATTTTC
*
5438173 ATTTCGCATTGCGATTTTCAT-TT-CGCATTGCGATTC
1 ATTTCGCATTGCGATTCTCATGTTGCG-ATT----TTC
*
5438209 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCA--T-G--TTGCGATTTTC
* *
5438244 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTA
1 ATTTCGCATTGCGATTCTCA--T-G--TTGCGATTTTC
* *
5438282 ATTTCGCATTGCGATTTTCAT-TT-CGCA-TTGC
1 ATTTCGCATTGCGATTCTCATGTTGCG-ATTTTC
* * * *
5438313 GATTCTCTCGTTGCGATTTTCAT-TT-CGCA-TTGC
1 -ATT-TCGCATTGCGATTCTCATGTTGCG-ATTTTC
* * *
5438346 GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 -ATT-TCGCATTGCGATTCTCA--T-G--TTGCGATTTTC
5438386 ATTTCGCATTGCGATTCTC-TCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCAT-GTTGCGATTTTC
* *
5438419 ATTTCCGCATTGCGATTTTCATGTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTCATGTTGCGATTTTC
*
5438453 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
5438469 GTATTTTCCG
Statistics
Matches: 253, Mismatches: 14, Indels: 58
0.78 0.04 0.18
Matches are distributed among these distances:
31 6 0.02
32 11 0.04
33 104 0.41
34 30 0.12
35 14 0.06
36 9 0.04
38 61 0.24
39 11 0.04
40 7 0.03
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCATGTTGCGATTTTC
Found at i:5440792 original size:12 final size:12
Alignment explanation
Indices: 5440775--5440799 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5440765 TCTTCGGGGA
5440775 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5440787 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5440799 C
1 C
5440800 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:5441008 original size:24 final size:24
Alignment explanation
Indices: 5440974--5441020 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5440964 CTGAAACATC
5440974 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
5440998 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
5441021 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
Found at i:5441722 original size:20 final size:20
Alignment explanation
Indices: 5441694--5442062 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
5441684 AAATTTCAGT
* * * *
5441694 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
5441714 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
5441734 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
5441754 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
5441774 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5441794 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
5441814 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
5441834 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5441854 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5441874 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
5441894 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
5441914 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5441934 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
5441954 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
5441974 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
5441994 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
5442014 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
5442034 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
5442054 GTTGCGATT
1 GTTGCGATT
5442063 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:5445848 original size:2 final size:2
Alignment explanation
Indices: 5445841--5445869 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5445831 GTAATTAAAG
5445841 AT 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 AT A
5445870 ATCAAATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5450934 original size:24 final size:23
Alignment explanation
Indices: 5450899--5450957 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 23
5450889 ACAAATTTAT
5450899 AAAATTTTATAAATTTTA-AGTACTG
1 AAAA-TTTATAAATTTTAGAG-AC-G
5450924 AAAATTTATAAAATTTTAGAGACG
1 AAAATTTAT-AAATTTTAGAGACG
*
5450948 AAAATATATA
1 AAAATTTATA
5450958 TATAATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
23 1 0.03
24 14 0.45
25 14 0.45
26 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.37
Consensus pattern (23 bp):
AAAATTTATAAATTTTAGAGACG
Found at i:5469105 original size:24 final size:24
Alignment explanation
Indices: 5469056--5469106 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
5469046 AAACTAATAA
* *
5469056 AAAATACTATCTTATAAATAATTT
1 AAAATACTATCTTACAAATAACTT
*
5469080 AAAATACTATCTTACAATTAACTT
1 AAAATACTATCTTACAAATAACTT
5469104 AAA
1 AAA
5469107 CTATTAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAATACTATCTTACAAATAACTT
Found at i:5472283 original size:18 final size:19
Alignment explanation
Indices: 5472260--5472299 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
5472250 TATTTGTTTG
*
5472260 TTTCA-TAATTTTTAAAAT
1 TTTCATTAAATTTTAAAAT
*
5472278 TTTCATTAAATTTTAATAT
1 TTTCATTAAATTTTAAAAT
5472297 TTT
1 TTT
5472300 TGAATAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTCATTAAATTTTAAAAT
Found at i:5484345 original size:19 final size:20
Alignment explanation
Indices: 5484296--5484338 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
5484286 GCTAATATTA
5484296 ATTATTATTA-TT-ACTACT
1 ATTATTATTATTTAACTACT
5484314 ATTATTATTATTTAACTA-T
1 ATTATTATTATTTAACTACT
5484333 ATTATT
1 ATTATT
5484339 TTAATTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.43
19 9 0.39
20 4 0.17
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTATTATTATTTAACTACT
Found at i:5485030 original size:29 final size:30
Alignment explanation
Indices: 5484985--5485045 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 30
5484975 CATTTTGAGT
5484985 AATGAAATGAAACGTTAGACACCAAACTAA
1 AATGAAATGAAACGTTAGACACCAAACTAA
*
5485015 AATGAAAT-AAACGTTAGACACTAAACTAA
1 AATGAAATGAAACGTTAGACACCAAACTAA
5485044 AA
1 AA
5485046 AAAAGAGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.56, C:0.15, G:0.11, T:0.18
Consensus pattern (30 bp):
AATGAAATGAAACGTTAGACACCAAACTAA
Found at i:5485248 original size:57 final size:58
Alignment explanation
Indices: 5485144--5485254 Score: 170
Period size: 57 Copynumber: 1.9 Consensus size: 58
5485134 TTGTTATTAC
*
5485144 TCATTCTCAAATTATGACTCACATTCTAAATTAGTCTTTAAATTTTGAATATTTTGATT
1 TCATTCTCAAATTATGACT-ACATTCTAAATTAGTCTTTAAACTTTGAATATTTTGATT
* * *
5485203 TCATTCTTAAATTATGACT-CATTTTAAATTGGTCTTTAAACTTTGAATATTT
1 TCATTCTCAAATTATGACTACATTCTAAATTAGTCTTTAAACTTTGAATATTT
5485255 CAAATACATC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
57 30 0.62
59 18 0.38
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.49
Consensus pattern (58 bp):
TCATTCTCAAATTATGACTACATTCTAAATTAGTCTTTAAACTTTGAATATTTTGATT
Found at i:5497516 original size:31 final size:31
Alignment explanation
Indices: 5497434--5497553 Score: 116
Period size: 31 Copynumber: 3.9 Consensus size: 31
5497424 TAAAGAGTTG
** **
5497434 CAAAATGATCATTAAACTTCCCAAACGGTTA
1 CAAAATGATCATTAAACTTATCAAAATGTTA
* * *
5497465 C-AAGTGGTCATTAAACCTTATCAAAATATTA
1 CAAAATGATCATTAAA-CTTATCAAAATGTTA
*
5497496 CAAAATGATCATTAAACTTATCAAATTGTTA
1 CAAAATGATCATTAAACTTATCAAAATGTTA
* * * *
5497527 CAAAAAGGTCCTTAAACTAATCAAAAT
1 CAAAATGATCATTAAACTTATCAAAAT
5497554 TTATAACTAT
Statistics
Matches: 71, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
30 12 0.17
31 47 0.66
32 12 0.17
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.29
Consensus pattern (31 bp):
CAAAATGATCATTAAACTTATCAAAATGTTA
Found at i:5497550 original size:62 final size:62
Alignment explanation
Indices: 5497434--5497553 Score: 152
Period size: 62 Copynumber: 1.9 Consensus size: 62
5497424 TAAAGAGTTG
* ** *
5497434 CAAAATGATCATTAAACTTCCCAAACGGTTACAAGTGGTCATTAAACCTTATCAAAATATTA
1 CAAAATGATCATTAAACTTACCAAACGGTTACAAAAGGTCATTAAACCTAATCAAAATATTA
* ** *
5497496 CAAAATGATCATTAAACTTATCAAATTGTTACAAAAAGGTCCTTAAA-CTAATCAAAAT
1 CAAAATGATCATTAAACTTACCAAACGGTTAC-AAAAGGTCATTAAACCTAATCAAAAT
5497554 TTATAACTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
62 38 0.78
63 11 0.22
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.29
Consensus pattern (62 bp):
CAAAATGATCATTAAACTTACCAAACGGTTACAAAAGGTCATTAAACCTAATCAAAATATTA
Found at i:5517878 original size:21 final size:21
Alignment explanation
Indices: 5517849--5517894 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5517839 CTCATCATCG
5517849 AAGAAGCCCCTCCCACCGTTC
1 AAGAAGCCCCTCCCACCGTTC
* ** *
5517870 AAGATGCCCCTGTCATCGTTC
1 AAGAAGCCCCTCCCACCGTTC
5517891 AAGA
1 AAGA
5517895 GGTCATGCCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.37, G:0.17, T:0.20
Consensus pattern (21 bp):
AAGAAGCCCCTCCCACCGTTC
Found at i:5519463 original size:20 final size:20
Alignment explanation
Indices: 5519425--5519463 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5519415 GATTTTCGGT
*
5519425 TTGCAAATTTCACTTTCGCG
1 TTGCAAATTTCACTATCGCG
* *
5519445 TTGCGAATTTGACTATCGC
1 TTGCAAATTTCACTATCGC
5519464 AACGCTTATT
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:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (20 bp):
TTGCAAATTTCACTATCGCG
Found at i:5520181 original size:24 final size:24
Alignment explanation
Indices: 5520147--5520200 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
5520137 CCATCACATC
**
5520147 ATCAAAATCCGAGTATTTTCCAAG
1 ATCAAAATCCGAGTATTGACCAAG
*
5520171 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
5520195 ATCAAA
1 ATCAAA
5520201 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:5520214 original size:24 final size:24
Alignment explanation
Indices: 5520166--5520214 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5520156 CGAGTATTTT
* *
5520166 CCAAGATCAAAGTCCGAGTATTGA
1 CCAAGATCAAAGTCCGAATACTGA
* *
5520190 CCAAGATCAAATTTCGAATACTGA
1 CCAAGATCAAAGTCCGAATACTGA
5520214 C
1 C
5520215 TAGTACTCAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.22
Consensus pattern (24 bp):
CCAAGATCAAAGTCCGAATACTGA
Found at i:5521120 original size:19 final size:19
Alignment explanation
Indices: 5521096--5521167 Score: 117
Period size: 19 Copynumber: 3.7 Consensus size: 19
5521086 ACTAAAATCT
5521096 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
5521115 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
5521134 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATT-C-A
5521155 GTTGCGAATTTGA
1 GTTGCGAATTTGA
5521168 CTATCGCGTT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 36 0.72
20 1 0.02
21 13 0.26
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:5521177 original size:20 final size:22
Alignment explanation
Indices: 5521134--5521189 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 22
5521124 TTGAAATTCA
*
5521134 GTTGCGAATTTGA-AATTCCGC
1 GTTGCGAATTTGACTATTCCGC
5521155 GTTGCGAATTTGACTA-T-CGC
1 GTTGCGAATTTGACTATTCCGC
*
5521175 GTTGTGAATTTGACT
1 GTTGCGAATTTGACT
5521190 TCTGTGTTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 17 0.53
21 14 0.44
22 1 0.03
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (22 bp):
GTTGCGAATTTGACTATTCCGC
Found at i:5522074 original size:13 final size:15
Alignment explanation
Indices: 5522044--5522080 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
5522034 ATAATAAAAA
*
5522044 TTTATAAAAGTTATT
1 TTTATAATAGTTATT
5522059 TTTATAATA-TTATT
1 TTTATAATAGTTATT
5522073 TTT-TAATA
1 TTTATAATA
5522081 CAAGAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 5 0.24
14 8 0.38
15 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
TTTATAATAGTTATT
Found at i:5525866 original size:24 final size:24
Alignment explanation
Indices: 5525839--5525897 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 24
5525829 CCATTTAATA
*
5525839 TTAAATTAT-TATTATTATTTTATT
1 TTAAATTATAAATT-TTATTTTATT
5525863 TTAATATT-TAAATTTTATTTTATT
1 TTAA-ATTATAAATTTTATTTTATT
5525887 TTAAAATTATA
1 TT-AAATTATA
5525898 CTTAACGTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
24 20 0.67
25 10 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TTAAATTATAAATTTTATTTTATT
Found at i:5525866 original size:30 final size:29
Alignment explanation
Indices: 5525832--5525889 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
5525822 AAATTACCCA
5525832 TTTAATA-TTAAATTATTATTATTATTTTAT
1 TTTAATATTTAAATT-TTATT-TTATTTTAT
5525862 TTTAATATTTAAATTTTATTTTATTTTA
1 TTTAATATTTAAATTTTATTTTATTTTA
5525890 AAATTATACT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 8 0.30
30 12 0.44
31 7 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (29 bp):
TTTAATATTTAAATTTTATTTTATTTTAT
Found at i:5525940 original size:12 final size:12
Alignment explanation
Indices: 5525925--5525949 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5525915 GTTTTAATTC
5525925 ATTAAAAAATAG
1 ATTAAAAAATAG
5525937 ATTAAAAAATAG
1 ATTAAAAAATAG
5525949 A
1 A
5525950 ATTTAAGATG
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
ATTAAAAAATAG
Found at i:5527808 original size:27 final size:27
Alignment explanation
Indices: 5527777--5527851 Score: 123
Period size: 27 Copynumber: 2.8 Consensus size: 27
5527767 CCACCGTTAC
*
5527777 TTTCAAGTATTGTCTCGACGAAAAATA
1 TTTCAAGCATTGTCTCGACGAAAAATA
5527804 TTTCAAGCATTGTCTCGACGAAAAATA
1 TTTCAAGCATTGTCTCGACGAAAAATA
* *
5527831 TTTCAAGCACTGACTCGACGA
1 TTTCAAGCATTGTCTCGACGA
5527852 CATAGTGTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (27 bp):
TTTCAAGCATTGTCTCGACGAAAAATA
Found at i:5528305 original size:2 final size:2
Alignment explanation
Indices: 5528298--5528400 Score: 67
Period size: 2 Copynumber: 55.0 Consensus size: 2
5528288 TCGGGTCGGG
* * * *
5528298 TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
5528338 TA TT TT TA -A TT TA -A TT TA AA TT TA T- TA -A TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5528375 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
5528401 ATTATTTTTA
Statistics
Matches: 76, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
1 7 0.09
2 69 0.91
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5528828 original size:23 final size:23
Alignment explanation
Indices: 5528797--5528840 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
5528787 TTTAGATGGT
5528797 GTGTATATATATTATTAATAAAG
1 GTGTATATATATTATTAATAAAG
*
5528820 GTGTGTATATATTATTAATAA
1 GTGTATATATATTATTAATAA
5528841 TTAATCATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (23 bp):
GTGTATATATATTATTAATAAAG
Found at i:5530668 original size:5 final size:5
Alignment explanation
Indices: 5530658--5530682 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5530648 TGTAGCCATC
5530658 GGAAT GGAAT GGAAT GGAAT GGAAT
1 GGAAT GGAAT GGAAT GGAAT GGAAT
5530683 ATATGATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (5 bp):
GGAAT
Found at i:5533258 original size:23 final size:23
Alignment explanation
Indices: 5533232--5533276 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5533222 CACCATAGCT
*
5533232 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
5533255 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
5533277 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:5533419 original size:25 final size:25
Alignment explanation
Indices: 5533391--5533484 Score: 161
Period size: 25 Copynumber: 3.8 Consensus size: 25
5533381 TATATATATA
*
5533391 TCCCGAAAGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
*
5533416 TCCCGAAGGACCGCGTAGAATATTA
1 TCCCGAAGGACCGCGTAGAATATTG
5533441 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
*
5533466 TCCTGAAGGACCGCGTAGA
1 TCCCGAAGGACCGCGTAGA
5533485 CCCTCTACTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 65 1.00
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (25 bp):
TCCCGAAGGACCGCGTAGAATATTG
Found at i:5535173 original size:21 final size:21
Alignment explanation
Indices: 5535149--5535193 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5535139 TTTTGTTCGT
* *
5535149 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
5535170 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
5535191 TTG
1 TTG
5535194 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:5536329 original size:7 final size:7
Alignment explanation
Indices: 5536317--5536341 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5536307 TTTCATTTCT
5536317 TTATTCC
1 TTATTCC
5536324 TTATTCC
1 TTATTCC
5536331 TTATTCC
1 TTATTCC
5536338 TTAT
1 TTAT
5536342 ACATAAATCA
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:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (7 bp):
TTATTCC
Found at i:5538513 original size:25 final size:25
Alignment explanation
Indices: 5538485--5538553 Score: 138
Period size: 25 Copynumber: 2.8 Consensus size: 25
5538475 TATATATATA
5538485 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
5538510 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
5538535 TCCCGAAGGACCGCGTAGA
1 TCCCGAAGGACCGCGTAGA
5538554 CCCTCTACTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.17
Consensus pattern (25 bp):
TCCCGAAGGACCGCGTAGAATATTG
Found at i:5539798 original size:16 final size:16
Alignment explanation
Indices: 5539777--5539807 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5539767 TGTAATACAG
*
5539777 ATAACCACATATAATT
1 ATAACCACACATAATT
5539793 ATAACCACACATAAT
1 ATAACCACACATAAT
5539808 CATGTCCATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAACCACACATAATT
Found at i:5540182 original size:21 final size:21
Alignment explanation
Indices: 5540158--5540202 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5540148 TTTTGTTCGT
* *
5540158 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
5540179 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
5540200 TTG
1 TTG
5540203 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:5544460 original size:15 final size:15
Alignment explanation
Indices: 5544440--5544469 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5544430 ACTTTTGTCA
5544440 TTTTGTAAATATATT
1 TTTTGTAAATATATT
*
5544455 TTTTGTAATTATATT
1 TTTTGTAAATATATT
5544470 AAAAATCATT
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:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (15 bp):
TTTTGTAAATATATT
Found at i:5544564 original size:22 final size:21
Alignment explanation
Indices: 5544526--5544580 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
5544516 TATAATTTCG
*
5544526 AATA-AAATTAATTATTATAA
1 AATATAAATAAATTATTATAA
*
5544546 TATATAAATAAATTGATTATAA
1 AATATAAATAAATT-ATTATAA
5544568 AATATAATATAAA
1 AATATAA-ATAAA
5544581 AATATTTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.10
21 8 0.28
22 13 0.45
23 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AATATAAATAAATTATTATAA
Found at i:5544795 original size:35 final size:35
Alignment explanation
Indices: 5544719--5544797 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
5544709 TATTTATTCA
* *
5544719 AAATTTTAATTTAACATCTATTTTTGTTAGATTTT
1 AAATTTTAATTTAACATCTATTATTATTAGATTTT
* * *
5544754 ATATTTTAATTTAATATTTATTATTATTA-ATATTT
1 AAATTTTAATTTAACATCTATTATTATTAGAT-TTT
5544789 AAATTTTAA
1 AAATTTTAA
5544798 CATCATGTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
34 2 0.05
35 35 0.95
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (35 bp):
AAATTTTAATTTAACATCTATTATTATTAGATTTT
Found at i:5544954 original size:2 final size:2
Alignment explanation
Indices: 5544947--5545006 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
5544937 TCACAATGAC
5544947 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
5544989 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
5545007 CGAATCGAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5548881 original size:2 final size:2
Alignment explanation
Indices: 5548874--5548900 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5548864 TAATTAAGTT
5548874 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 T
5548901 TAAAAGGCAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5557304 original size:23 final size:21
Alignment explanation
Indices: 5557250--5557324 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 21
5557240 AAAGAATAAT
5557250 AAATAAAT-AATATTATAAAA
1 AAATAAATAAATATTATAAAA
* * *
5557270 AAAAAAAAAAATATTCATTAACA
1 AAATAAATAAATATT-A-TAAAA
5557293 AAATAAATAAATAATATTATAAATA
1 AAATAAAT--A-AATATTATAAA-A
5557318 AAATAAA
1 AAATAAA
5557325 GTTTAGCTAC
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
20 6 0.14
21 6 0.14
22 1 0.02
23 10 0.24
24 3 0.07
25 10 0.24
26 6 0.14
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATAAATAAATATTATAAAA
Found at i:5557322 original size:25 final size:24
Alignment explanation
Indices: 5557230--5557324 Score: 106
Period size: 25 Copynumber: 3.8 Consensus size: 24
5557220 AAATTTTATT
5557230 TAATATATATAAAGAATAATAAATAAA
1 TAATAT-TATAAA-AA-AATAAATAAA
5557257 TAATATTATAAAAAAA-AAA-AAA
1 TAATATTATAAAAAAATAAATAAA
*
5557279 -AATATTCATTAACAAAATAAATAAA
1 TAATATT-A-TAAAAAAATAAATAAA
5557304 TAATATTATAAATAAAATAAA
1 TAATATTATAAA-AAAATAAA
5557325 GTTTAGCTAC
Statistics
Matches: 60, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
21 6 0.10
22 4 0.07
23 10 0.17
24 8 0.13
25 14 0.23
26 12 0.20
27 6 0.10
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.28
Consensus pattern (24 bp):
TAATATTATAAAAAAATAAATAAA
Found at i:5557323 original size:21 final size:21
Alignment explanation
Indices: 5557250--5557324 Score: 78
Period size: 21 Copynumber: 3.3 Consensus size: 21
5557240 AAAGAATAAT
5557250 AAATAAATAATATTATAAAAA
1 AAATAAATAATATTATAAAAA
* *
5557271 AAAAAAAAAATATTCATTAACAAAA
1 AAATAAATAATATT-A-T-A-AAAA
*
5557296 TAAATAAATAATATTATAAATA
1 -AAATAAATAATATTATAAAAA
5557318 AAATAAA
1 AAATAAA
5557325 GTTTAGCTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
21 19 0.43
22 4 0.09
23 2 0.05
24 2 0.05
25 5 0.11
26 12 0.27
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATAAATAATATTATAAAAA
Found at i:5557651 original size:22 final size:22
Alignment explanation
Indices: 5557609--5557653 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
5557599 AAAATATAGA
*
5557609 ATTTTTATATTTGTAGATATGT
1 ATTTTTATATTTCTAGATATGT
*
5557631 ATTTTT-TATTTCTAAGTTATGT
1 ATTTTTATATTTCT-AGATATGT
5557653 A
1 A
5557654 AAATGAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.60
Consensus pattern (22 bp):
ATTTTTATATTTCTAGATATGT
Found at i:5557834 original size:19 final size:20
Alignment explanation
Indices: 5557790--5557834 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
5557780 ATTTATTTTT
*
5557790 AATAAATTTTTATCTATGAA
1 AATAAATTTTTATCTATCAA
* *
5557810 ATTAAATTTTTAT-TTTCAA
1 AATAAATTTTTATCTATCAA
5557829 AATAAA
1 AATAAA
5557835 ATATTAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATCTATCAA
Found at i:5558196 original size:3 final size:3
Alignment explanation
Indices: 5558190--5558294 Score: 210
Period size: 3 Copynumber: 35.0 Consensus size: 3
5558180 ATTATTTTGA
5558190 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5558238 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5558286 AAT AAT AAT
1 AAT AAT AAT
5558295 TGAAAGAGAA
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 102 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5575573 original size:380 final size:380
Alignment explanation
Indices: 5574872--5575632 Score: 1360
Period size: 380 Copynumber: 2.0 Consensus size: 380
5574862 CATAGGACGG
*
5574872 TGAGCCATCAACATACCAGGAGGTAATAAACAGCTCAGATGCTTCACTATGGATGATGGCGATGC
1 TGAGCCATCAACATACCAGGAGGTAATAAACAGCTCAGATGCTTCACTATGGATGATGGCGATAC
*
5574937 AAGAGGAAATTGAAGCCCTTCATAAAAATAATACATGGAACCTTGTGCTACTACCACAAGGAAGG
66 AAGAGGAAATTGAAGCCCTTCATAAAAATAATACATGGAACCTTGTGCCACTACCACAAGGAAGG
* *
5575002 AAGCCAATTGGTAACAAATGGGTCTTCAAAATCAAGTGAAATTATGACGATCAAGTTGAGAGGTA
131 AAACCAATTGGTAACAAATGGGCCTTCAAAATCAAGTGAAATTATGACGATCAAGTTGAGAGGTA
* * *
5575067 TCGTGCAAGACTAGTGGTCAAAGGATATGTTCAAAAAGAATGTATTGATTTCAATGAAATATTTT
196 TCGTGCAAGACTAGTGGTCAAAGGATATGCTAAAAAAGAAGGTATTGATTTCAATGAAATATTTT
* * * * * *
5575132 CTCCTGTGGTTTGACTAACAATAGTTCGAGTAGTTTTGGCAATGTGTGCTATATTGAACTTACAT
261 ATCATGTGGTTCGACTAACAACAGTTCGAGTAGTTTTGGAAATGTGTGCTACATTGAACTTACAT
*
5575197 CTAGAGCAGCTAGATGTTAAAACAGCTTTTCTTCATGGAAATCTTGAAGAAGAGA
326 CTAGAGCAACTAGATGTTAAAACAGCTTTTCTTCATGGAAATCTTGAAGAAGAGA
5575252 TGAGCCATCAACATACCAGGAGGTAATAAACAGCTCAGATGCTTCACTATGGATGATGGCGATAC
1 TGAGCCATCAACATACCAGGAGGTAATAAACAGCTCAGATGCTTCACTATGGATGATGGCGATAC
*
5575317 AAGAGGAAATTGAAGCCCTTCATAAAAATAATACATGGGACCTTGTGCCACTACCACAAGGAAGG
66 AAGAGGAAATTGAAGCCCTTCATAAAAATAATACATGGAACCTTGTGCCACTACCACAAGGAAGG
*
5575382 AAACCAATTGGTAACAAATGGGCCTTCAAAATCAAGTGAAATTATTACGATCAAGTTGAGAGGTA
131 AAACCAATTGGTAACAAATGGGCCTTCAAAATCAAGTGAAATTATGACGATCAAGTTGAGAGGTA
* *
5575447 TCTTGCAAGACTGGTGGTCAAAGGATATGCTAAAAAAGAAGGTATTGATTTCAATGAAATATTTT
196 TCGTGCAAGACTAGTGGTCAAAGGATATGCTAAAAAAGAAGGTATTGATTTCAATGAAATATTTT
5575512 ATCATGTGGTTCGACTAACAACAGTTCGAGTAGTTTTGGAAATGTGTGCTACATTGAACTTACAT
261 ATCATGTGGTTCGACTAACAACAGTTCGAGTAGTTTTGGAAATGTGTGCTACATTGAACTTACAT
5575577 CTAGAGCAACTAGATGTTAAAACAGCTTTTCTTCATGGAAATCTTGAAGAAGAGA
326 CTAGAGCAACTAGATGTTAAAACAGCTTTTCTTCATGGAAATCTTGAAGAAGAGA
5575632 T
1 T
5575633 TTACATGCTC
Statistics
Matches: 363, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
380 363 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (380 bp):
TGAGCCATCAACATACCAGGAGGTAATAAACAGCTCAGATGCTTCACTATGGATGATGGCGATAC
AAGAGGAAATTGAAGCCCTTCATAAAAATAATACATGGAACCTTGTGCCACTACCACAAGGAAGG
AAACCAATTGGTAACAAATGGGCCTTCAAAATCAAGTGAAATTATGACGATCAAGTTGAGAGGTA
TCGTGCAAGACTAGTGGTCAAAGGATATGCTAAAAAAGAAGGTATTGATTTCAATGAAATATTTT
ATCATGTGGTTCGACTAACAACAGTTCGAGTAGTTTTGGAAATGTGTGCTACATTGAACTTACAT
CTAGAGCAACTAGATGTTAAAACAGCTTTTCTTCATGGAAATCTTGAAGAAGAGA
Found at i:5579603 original size:13 final size:14
Alignment explanation
Indices: 5579580--5579610 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
5579570 ATTTTAAAAT
5579580 TTAATTTTTATATA
1 TTAATTTTTATATA
5579594 TTAA-TTTTATATA
1 TTAATTTTTATATA
5579607 TTAA
1 TTAA
5579611 CGATGTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTAATTTTTATATA
Found at i:5580740 original size:24 final size:23
Alignment explanation
Indices: 5580711--5580762 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 23
5580701 AGTACATATA
5580711 TATATAACTAAATAAATATAATTATT
1 TATA-AACTAAAT-AATATAATT-TT
* *
5580737 TATAAATTTAATAATATAATTTT
1 TATAAACTAAATAATATAATTTT
5580760 TAT
1 TAT
5580763 TTATGTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.21
24 9 0.38
25 6 0.25
26 4 0.17
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TATAAACTAAATAATATAATTTT
Found at i:5617247 original size:21 final size:21
Alignment explanation
Indices: 5617203--5617248 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
5617193 GATTTCTGGG
* *
5617203 CAAGGGGAATCGATACCCATT
1 CAAGGGGAACCGATACCCACT
*
5617224 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
5617245 CAAG
1 CAAG
5617249 CGAACCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.30, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:5617320 original size:23 final size:22
Alignment explanation
Indices: 5617272--5617320 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
5617262 ACAGAATGTC
5617272 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
5617293 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
5617316 AAGGA
1 AAGGA
5617321 AAATTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:5618145 original size:31 final size:31
Alignment explanation
Indices: 5618107--5618289 Score: 259
Period size: 31 Copynumber: 6.0 Consensus size: 31
5618097 AGGGTCGAGG
5618107 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
5618138 GTTTACCTATGTTCTTCGGGAC--AT--ACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
5618165 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
5618196 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
5618227 GTTTATCTTTGTTCTTCGAGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
5618258 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
5618289 G
1 G
5618290 GTCCTTCGGG
Statistics
Matches: 136, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
27 25 0.18
29 4 0.03
31 106 0.78
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:5618159 original size:23 final size:23
Alignment explanation
Indices: 5618133--5618186 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 23
5618123 CGGGACATAT
5618133 GGACTGTTTACCTATGTTCTTCG
1 GGACTGTTTACCTATGTTCTTCG
5618156 GGACATACTGTTTACCTATGTTCTTCG
1 GG----ACTGTTTACCTATGTTCTTCG
5618183 GGAC
1 GGAC
5618187 ATATGGACTG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
23 4 0.15
27 23 0.85
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (23 bp):
GGACTGTTTACCTATGTTCTTCG
Found at i:5618172 original size:58 final size:60
Alignment explanation
Indices: 5618107--5618276 Score: 254
Period size: 58 Copynumber: 2.8 Consensus size: 60
5618097 AGGGTCGAGG
5618107 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGAC-AT-ACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACAATGACT
*
5618165 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACA-AT-GACT
* * * * *
5618227 GTTTATCTTTGTTCTTCGAGACATATGGACTGATTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGG
5618277 AATCTATGGA
Statistics
Matches: 102, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
58 53 0.52
60 2 0.02
62 47 0.46
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (60 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACAATGACT
Found at i:5621474 original size:21 final size:21
Alignment explanation
Indices: 5621430--5621475 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5621420 GATTTCTGGG
* * *
5621430 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
5621451 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
5621472 CAAG
1 CAAG
5621476 CGAACCAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:5621547 original size:23 final size:22
Alignment explanation
Indices: 5621499--5621547 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
5621489 ACAGAATGTC
5621499 AAGG-GGGAACCAATACCCCCA
1 AAGGAGGGAACCAATACCCCCA
* * *
5621520 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCAATACCCCC-A
5621543 AAGGA
1 AAGGA
5621548 AAATTGTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.14
22 14 0.64
23 5 0.23
ACGTcount: A:0.35, C:0.31, G:0.27, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCAATACCCCCA
Found at i:5622520 original size:31 final size:31
Alignment explanation
Indices: 5622334--5622505 Score: 317
Period size: 31 Copynumber: 5.5 Consensus size: 31
5622324 AGGGTCGAGG
5622334 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
5622365 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
5622396 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
5622427 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
5622458 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
5622489 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
5622506 AGAATCTATG
Statistics
Matches: 137, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 137 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:5634808 original size:11 final size:11
Alignment explanation
Indices: 5634792--5634817 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5634782 CTGGATTGCA
5634792 CGCCTATCACT
1 CGCCTATCACT
5634803 CGCCTATCACT
1 CGCCTATCACT
5634814 CGCC
1 CGCC
5634818 ATTAGGGGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.50, G:0.12, T:0.23
Consensus pattern (11 bp):
CGCCTATCACT
Found at i:5635459 original size:15 final size:16
Alignment explanation
Indices: 5635432--5635462 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5635422 GGGGGGAACA
5635432 AAGGAACGAAACAAAC
1 AAGGAACGAAACAAAC
5635448 AAGGAA-GAAACAAAC
1 AAGGAACGAAACAAAC
5635463 GTGGTTCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.65, C:0.16, G:0.19, T:0.00
Consensus pattern (16 bp):
AAGGAACGAAACAAAC
Found at i:5647778 original size:180 final size:180
Alignment explanation
Indices: 5647476--5647839 Score: 710
Period size: 180 Copynumber: 2.0 Consensus size: 180
5647466 TAAGCATCCG
5647476 ACAAGTCCATGAATTTGAGAAATAATAATGAAATGTTAATATTTACAGGTGTTTTATCACAGAAA
1 ACAAGTCCATGAATTTGAGAAATAATAATGAAATGTTAATATTTACAGGTGTTTTATCACAGAAA
5647541 TTACAACATTTTCTAAATCGAAACCCATTTCCCAAATGCTATCACTGACGTCATGTAAATTCATC
66 TTACAACATTTTCTAAATCGAAACCCATTTCCCAAATGCTATCACTGACGTCATGTAAATTCATC
5647606 CAATAAAGTAAACAACCACTTGATTTTTTTTCACAATGAAAAATAACAAA
131 CAATAAAGTAAACAACCACTTGATTTTTTTTCACAATGAAAAATAACAAA
* *
5647656 ACAAGTCCATTAATTTGAGAAATAATAATGAAATGTTAATATTTACAGGTGTTTTATCGCAGAAA
1 ACAAGTCCATGAATTTGAGAAATAATAATGAAATGTTAATATTTACAGGTGTTTTATCACAGAAA
5647721 TTACAACATTTTCTAAATCGAAACCCATTTCCCAAATGCTATCACTGACGTCATGTAAATTCATC
66 TTACAACATTTTCTAAATCGAAACCCATTTCCCAAATGCTATCACTGACGTCATGTAAATTCATC
5647786 CAATAAAGTAAACAACCACTTGATTTTTTTTCACAATGAAAAATAACAAA
131 CAATAAAGTAAACAACCACTTGATTTTTTTTCACAATGAAAAATAACAAA
5647836 ACAA
1 ACAA
5647840 ATCGGGAATA
Statistics
Matches: 182, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 182 1.00
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (180 bp):
ACAAGTCCATGAATTTGAGAAATAATAATGAAATGTTAATATTTACAGGTGTTTTATCACAGAAA
TTACAACATTTTCTAAATCGAAACCCATTTCCCAAATGCTATCACTGACGTCATGTAAATTCATC
CAATAAAGTAAACAACCACTTGATTTTTTTTCACAATGAAAAATAACAAA
Found at i:5658283 original size:12 final size:12
Alignment explanation
Indices: 5658266--5658290 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5658256 GTCAAATAAT
5658266 TTAGGCACCAAA
1 TTAGGCACCAAA
5658278 TTAGGCACCAAA
1 TTAGGCACCAAA
5658290 T
1 T
5658291 GGTGCTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:5664510 original size:75 final size:75
Alignment explanation
Indices: 5664371--5664510 Score: 183
Period size: 75 Copynumber: 1.9 Consensus size: 75
5664361 TCTATTGGCA
* * * * *
5664371 AAAGGGAGCCGAAGAAGATGACGACGAGTTGCAGCTTGTCAATTTATGGGACAGAATGATTGATT
1 AAAGGGAGCCGAAGAAGATGACCACGAGTCGCAGCTTGTCAATTTACGGGACAGAAAGACTGATT
5664436 TTGTCCAGTG
66 TTGTCCAGTG
* * * *
5664446 AAAGGGAGCCGAGGAAGATGACCATGAGTCGCAGCTTGTTC-GTTTACGGGACGGAAAGACTGAT
1 AAAGGGAGCCGAAGAAGATGACCACGAGTCGCAGCTTG-TCAATTTACGGGACAGAAAGACTGAT
5664510 T
65 T
5664511 GTGGCAGGTG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
75 53 0.96
76 2 0.04
ACGTcount: A:0.30, C:0.15, G:0.32, T:0.23
Consensus pattern (75 bp):
AAAGGGAGCCGAAGAAGATGACCACGAGTCGCAGCTTGTCAATTTACGGGACAGAAAGACTGATT
TTGTCCAGTG
Done.