Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397258.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4.1, 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: 11097736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 71999 characters in sequence are not A, C, G, or T
File 9 of 22
Found at i:4618436 original size:13 final size:13
Alignment explanation
Indices: 4618418--4618442 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4618408 GTTTTTAAAA
4618418 TTTTTATTATAAT
1 TTTTTATTATAAT
4618431 TTTTTATTATAA
1 TTTTTATTATAA
4618443 ATATTGATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTATTATAAT
Found at i:4619712 original size:16 final size:16
Alignment explanation
Indices: 4619691--4619731 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
4619681 AATTTTATTT
4619691 TTATTAATTTTAAAAA
1 TTATTAATTTTAAAAA
* *
4619707 TTATTAA-TATATAAA
1 TTATTAATTTTAAAAA
4619722 TTA-TAATTTT
1 TTATTAATTTT
4619732 TTATTTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 3 0.14
15 11 0.52
16 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATTAATTTTAAAAA
Found at i:4649906 original size:22 final size:22
Alignment explanation
Indices: 4649862--4649906 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
4649852 GGGGTTTTCT
** *
4649862 AAATTTTTTTTATATTATTTTA
1 AAATTTTTAATATATTATCTTA
*
4649884 AAATTTTTAATATATTCTCTTA
1 AAATTTTTAATATATTATCTTA
4649906 A
1 A
4649907 TGACCCCCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
AAATTTTTAATATATTATCTTA
Found at i:4650506 original size:20 final size:22
Alignment explanation
Indices: 4650467--4650512 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
4650457 TATTTAACTA
*
4650467 TTTATATTTTATGCATTATAAT
1 TTTATATTTTATGCATTATAAG
*
4650489 TTTATA-TTTA-GTATTATAAG
1 TTTATATTTTATGCATTATAAG
4650509 TTTA
1 TTTA
4650513 AATAGAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 12 0.55
21 4 0.18
22 6 0.27
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.59
Consensus pattern (22 bp):
TTTATATTTTATGCATTATAAG
Found at i:4653125 original size:6 final size:6
Alignment explanation
Indices: 4653116--4653141 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4653106 CACACACATA
4653116 TATATG TATATG TATATG TATATG TA
1 TATATG TATATG TATATG TATATG TA
4653142 GGAAAAAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:4656758 original size:50 final size:50
Alignment explanation
Indices: 4656683--4656781 Score: 198
Period size: 50 Copynumber: 2.0 Consensus size: 50
4656673 GCCCAAACCA
4656683 AACCATTTTAGTTGGATCAACCTTAAATGTAAGCCCTACAAAGAAGCCCC
1 AACCATTTTAGTTGGATCAACCTTAAATGTAAGCCCTACAAAGAAGCCCC
4656733 AACCATTTTAGTTGGATCAACCTTAAATGTAAGCCCTACAAAGAAGCCC
1 AACCATTTTAGTTGGATCAACCTTAAATGTAAGCCCTACAAAGAAGCCC
4656782 TTTAAGGTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.24
Consensus pattern (50 bp):
AACCATTTTAGTTGGATCAACCTTAAATGTAAGCCCTACAAAGAAGCCCC
Found at i:4685562 original size:21 final size:21
Alignment explanation
Indices: 4685510--4685563 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
4685500 TAAAAACATA
*
4685510 TTACACGTTATGATTAAGTTG
1 TTACACGTTATAATTAAGTTG
* * *
4685531 TTATACATTATAATTAGGTTG
1 TTACACGTTATAATTAAGTTG
4685552 TTACACGTTATA
1 TTACACGTTATA
4685564 TTGAAAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.44
Consensus pattern (21 bp):
TTACACGTTATAATTAAGTTG
Found at i:4685710 original size:29 final size:27
Alignment explanation
Indices: 4685651--4685724 Score: 82
Period size: 26 Copynumber: 2.8 Consensus size: 27
4685641 TTATATTGAA
* *
4685651 AAAAAAATATTATTGTTACA-CATGTT
1 AAAAAAATATTATTATTACACCATATT
4685677 AAAAAAATATTATTATTACACGTCATATT
1 AAAAAAATATTATTATTACAC--CATATT
*
4685706 -TAAAAATATT-TTATTACAC
1 AAAAAAATATTATTATTACAC
4685725 TACTTAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 19 0.45
27 9 0.21
28 9 0.21
29 5 0.12
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.39
Consensus pattern (27 bp):
AAAAAAATATTATTATTACACCATATT
Found at i:4702175 original size:2 final size:2
Alignment explanation
Indices: 4702168--4702198 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4702158 CCAAAAGACA
*
4702168 AT AT AT AT CT 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 AT A
4702199 AAAGAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4702862 original size:139 final size:139
Alignment explanation
Indices: 4702612--4702885 Score: 494
Period size: 139 Copynumber: 2.0 Consensus size: 139
4702602 GATTATCCAG
4702612 ATCTTCAATCTGTACAATATTTGTACGGACGAATAAGGGGAAAGCATGGGAGTTTCCTCACCTCA
1 ATCTTCAATCTGTACAATATTTGTACGGACGAATAAGGGGAAAGCATGGGAGTTTCCTCACCTCA
* * *
4702677 AACTCAGAGGTGGCCAACCGTATAGATAATTTGCCATATTGAACAGCTTGTAAAACGTTATCAGG
66 AACTCAGAGGTGGCCAACCGTACAGATAATTAGCCATATTGAACAGCTTGCAAAACGTTATCAGG
4702742 AAAGGGGGA
131 AAAGGGGGA
* * *
4702751 ATCTTCAATCTGTACAATATTTGTAGGGACGAATAGGGGGAAAGCATGGGAGTTTCCTCACCTCC
1 ATCTTCAATCTGTACAATATTTGTACGGACGAATAAGGGGAAAGCATGGGAGTTTCCTCACCTCA
4702816 AACTCAGAGGTGGCCAACCGTACAGATAATTAGCCATATTGAACAGCTTGCAAAACGTTATCAGG
66 AACTCAGAGGTGGCCAACCGTACAGATAATTAGCCATATTGAACAGCTTGCAAAACGTTATCAGG
4702881 AAAGG
131 AAAGG
4702886 AAGAATCTCC
Statistics
Matches: 129, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
139 129 1.00
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (139 bp):
ATCTTCAATCTGTACAATATTTGTACGGACGAATAAGGGGAAAGCATGGGAGTTTCCTCACCTCA
AACTCAGAGGTGGCCAACCGTACAGATAATTAGCCATATTGAACAGCTTGCAAAACGTTATCAGG
AAAGGGGGA
Found at i:4706375 original size:12 final size:13
Alignment explanation
Indices: 4706358--4706398 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 13
4706348 AAGAGTTTTT
4706358 AAGAT-AAATAAA
1 AAGATAAAATAAA
4706370 AAGATAAAATATAA
1 AAGATAAAATA-AA
*
4706384 AAAATAAAATAAA
1 AAGATAAAATAAA
4706397 AA
1 AA
4706399 AAATAAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 5 0.19
13 9 0.35
14 12 0.46
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (13 bp):
AAGATAAAATAAA
Found at i:4706390 original size:14 final size:14
Alignment explanation
Indices: 4706365--4706406 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
4706355 TTTAAGATAA
4706365 ATAAAAAGATAAAAT
1 ATAAAAA-ATAAAAT
4706380 ATAAAAAATAAAAT
1 ATAAAAAATAAAAT
*
4706394 AAAAAAAATAAAA
1 ATAAAAAATAAAA
4706407 ACAAAACGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 19 0.73
15 7 0.27
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (14 bp):
ATAAAAAATAAAAT
Found at i:4706407 original size:7 final size:7
Alignment explanation
Indices: 4706363--4706407 Score: 56
Period size: 7 Copynumber: 6.3 Consensus size: 7
4706353 TTTTTAAGAT
4706363 AAATAAA
1 AAATAAA
4706370 AAGATAAA
1 AA-ATAAA
*
4706378 ATATAAA
1 AAATAAA
4706385 AAATAAA
1 AAATAAA
4706392 ATAA-AAA
1 A-AATAAA
4706399 AAATAAA
1 AAATAAA
4706406 AA
1 AA
4706408 CAAAACGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 2 0.06
7 23 0.70
8 8 0.24
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (7 bp):
AAATAAA
Found at i:4706576 original size:17 final size:17
Alignment explanation
Indices: 4706554--4706626 Score: 65
Period size: 17 Copynumber: 3.9 Consensus size: 17
4706544 AGGGAAGAGG
*
4706554 TATTTTTTTAGAAAAAA
1 TATTTTTTTAAAAAAAA
**
4706571 TATTTTTAGAAAAAAAA
1 TATTTTTTTAAAAAAAA
4706588 TAGTTTTTTTTAAAAAACTGACA
1 TA--TTTTTTTAAAAAA---A-A
4706611 TATTTTTTTAAAAAAA
1 TATTTTTTTAAAAAAA
4706627 GTTAAAACTC
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
17 16 0.36
18 1 0.02
19 11 0.24
21 13 0.29
22 1 0.02
23 3 0.07
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (17 bp):
TATTTTTTTAAAAAAAA
Found at i:4710141 original size:32 final size:32
Alignment explanation
Indices: 4710082--4710142 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
4710072 GATAAAAATA
* * *
4710082 TATTTTATTTTTTATGTATAATTATTTATTGT
1 TATTTTATTTTTAATATATAATAATTTATTGT
4710114 TATTTTATTTTTAA-ATATTAATAATTTAT
1 TATTTTATTTTTAATATA-TAATAATTTAT
4710143 AATTTGTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 2 0.08
32 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (32 bp):
TATTTTATTTTTAATATATAATAATTTATTGT
Found at i:4710255 original size:27 final size:27
Alignment explanation
Indices: 4710117--4710257 Score: 104
Period size: 27 Copynumber: 5.1 Consensus size: 27
4710107 TTATTGTTAT
4710117 TTTATTTTTAAATATTAATAATTTATAA
1 TTTA-TTTTAAATATTAATAATTTATAA
* * * *
4710145 TTTGTTTAAAATATTAATAATTGATAC
1 TTTATTTTAAATATTAATAATTTATAA
* ** * * * * *
4710172 TTTAAATATT-GTTATGATTATTTTTTAT
1 TTT--ATTTTAAATATTAATAATTTATAA
*
4710200 TTTATTTTTTAAATATTAGTAATTTATAA
1 TTTA--TTTTAAATATTAATAATTTATAA
*
4710229 TTTATTTTAAATATTAATAATTGATAA
1 TTTATTTTAAATATTAATAATTTATAA
4710256 TT
1 TT
4710258 AAAATAATAT
Statistics
Matches: 83, Mismatches: 25, Indels: 11
0.70 0.21 0.09
Matches are distributed among these distances:
26 1 0.01
27 46 0.55
28 19 0.23
29 17 0.20
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (27 bp):
TTTATTTTAAATATTAATAATTTATAA
Found at i:4710388 original size:19 final size:20
Alignment explanation
Indices: 4710359--4710396 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
4710349 TTTATTTTAT
*
4710359 TTTATAAATATTTATAATTA
1 TTTATAAATATTAATAATTA
4710379 TTTA-AAATATTAATAATT
1 TTTATAAATATTAATAATT
4710397 GATAGTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTATAAATATTAATAATTA
Found at i:4710439 original size:26 final size:25
Alignment explanation
Indices: 4710402--4710461 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 25
4710392 TAATTGATAG
*
4710402 TAATATTAATATTTTATGTATAATT
1 TAATATTAATATTTTATGTATAAGT
*
4710427 TAATCATTAATATTTTATTTATAAGT
1 TAAT-ATTAATATTTTATGTATAAGT
4710453 TAAATATTA
1 T-AATATTA
4710462 TATGATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 4 0.13
26 24 0.77
27 3 0.10
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (25 bp):
TAATATTAATATTTTATGTATAAGT
Found at i:4710506 original size:25 final size:24
Alignment explanation
Indices: 4710452--4710499 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
4710442 TATTTATAAG
4710452 TTAAATATTATATGATTATTAATTT
1 TTAAATATTATAT-ATTATTAATTT
4710477 TTAAATATTACTAT-TTA-TAATTT
1 TTAAATATTA-TATATTATTAATTT
4710500 ATTTAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 6 0.27
24 3 0.14
25 10 0.45
26 3 0.14
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
TTAAATATTATATATTATTAATTT
Found at i:4735145 original size:15 final size:16
Alignment explanation
Indices: 4735120--4735150 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
4735110 TCAAATTCAA
4735120 AACTCAACTTTTAAGT
1 AACTCAACTTTTAAGT
4735136 AACT-AACTTTTAAGT
1 AACTCAACTTTTAAGT
4735151 GAAAGCATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (16 bp):
AACTCAACTTTTAAGT
Found at i:4746099 original size:18 final size:18
Alignment explanation
Indices: 4746064--4746098 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
4746054 AAAATAGGAA
4746064 ATCTTGGAAATTATTTTT
1 ATCTTGGAAATTATTTTT
*
4746082 ATCTT-GAATTTATTTTT
1 ATCTTGGAAATTATTTTT
4746099 TGGTAGCAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.60
Consensus pattern (18 bp):
ATCTTGGAAATTATTTTT
Found at i:4753263 original size:18 final size:18
Alignment explanation
Indices: 4753240--4753296 Score: 114
Period size: 18 Copynumber: 3.2 Consensus size: 18
4753230 TTTGTAGGAG
4753240 TCTTGATTCACTTGAATT
1 TCTTGATTCACTTGAATT
4753258 TCTTGATTCACTTGAATT
1 TCTTGATTCACTTGAATT
4753276 TCTTGATTCACTTGAATT
1 TCTTGATTCACTTGAATT
4753294 TCT
1 TCT
4753297 AACTAAAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.21, C:0.18, G:0.11, T:0.51
Consensus pattern (18 bp):
TCTTGATTCACTTGAATT
Found at i:4753566 original size:81 final size:81
Alignment explanation
Indices: 4753431--4753592 Score: 324
Period size: 81 Copynumber: 2.0 Consensus size: 81
4753421 CAGTTGGCAT
4753431 TTGTTTAAGAAAAATGATAGGTGCGCTAAGGGTTAAACCATATGTATAAATAGATTCTACATAGA
1 TTGTTTAAGAAAAATGATAGGTGCGCTAAGGGTTAAACCATATGTATAAATAGATTCTACATAGA
4753496 TTTTTAGAAGTTTGAA
66 TTTTTAGAAGTTTGAA
4753512 TTGTTTAAGAAAAATGATAGGTGCGCTAAGGGTTAAACCATATGTATAAATAGATTCTACATAGA
1 TTGTTTAAGAAAAATGATAGGTGCGCTAAGGGTTAAACCATATGTATAAATAGATTCTACATAGA
4753577 TTTTTAGAAGTTTGAA
66 TTTTTAGAAGTTTGAA
4753593 AATTTTGATA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (81 bp):
TTGTTTAAGAAAAATGATAGGTGCGCTAAGGGTTAAACCATATGTATAAATAGATTCTACATAGA
TTTTTAGAAGTTTGAA
Found at i:4767106 original size:13 final size:13
Alignment explanation
Indices: 4767085--4767118 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
4767075 TGATTGTACA
4767085 CCCCC-CCCCCCC
1 CCCCCTCCCCCCC
*
4767097 CCCCCTCCCCTCC
1 CCCCCTCCCCCCC
4767110 CCCCCTCCC
1 CCCCCTCCC
4767119 TTGTTCTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.00, C:0.91, G:0.00, T:0.09
Consensus pattern (13 bp):
CCCCCTCCCCCCC
Found at i:4778807 original size:30 final size:29
Alignment explanation
Indices: 4778751--4778811 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
4778741 ATCTATATTT
* *
4778751 TTTTATTTTATATAATTAAGTTTTTATAA
1 TTTTATTTTAAATAATTAAATTTTTATAA
*
4778780 TTTTATTTTAAATTATATAAATTTTTATAA
1 TTTTATTTTAAATAAT-TAAATTTTTATAA
4778810 TT
1 TT
4778812 AATTATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (29 bp):
TTTTATTTTAAATAATTAAATTTTTATAA
Found at i:4779171 original size:31 final size:29
Alignment explanation
Indices: 4779133--4779200 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 29
4779123 AGTCTTTATA
4779133 TTTTTTTAAGTTCAAACAAATTTTTATAATT
1 TTTTTTTAAGTT-AAACAAATTTTT-TAATT
* *
4779164 TTTTTTTAAGTTAAATAAATTTTTTTATT
1 TTTTTTTAAGTTAAACAAATTTTTTAATT
4779193 TTTATTTT
1 TTT-TTTT
4779201 GAATTAAGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 7 0.21
30 15 0.44
31 12 0.35
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (29 bp):
TTTTTTTAAGTTAAACAAATTTTTTAATT
Found at i:4781434 original size:12 final size:12
Alignment explanation
Indices: 4781410--4781450 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
4781400 GGATCAGAGC
4781410 ATGGAATTGGATG
1 ATGGAA-TGGATG
4781423 ATGGAATGGATG
1 ATGGAATGGATG
4781435 ATGGAATGGATG
1 ATGGAATGGATG
4781447 -TGGA
1 ATGGA
4781451 GTGTGATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 4 0.14
12 18 0.64
13 6 0.21
ACGTcount: A:0.32, C:0.00, G:0.41, T:0.27
Consensus pattern (12 bp):
ATGGAATGGATG
Found at i:4781458 original size:24 final size:25
Alignment explanation
Indices: 4781410--4781459 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
4781400 GGATCAGAGC
4781410 ATGGAATTGGATGATGGAATGGATG
1 ATGGAATTGGATGATGGAATGGATG
*
4781435 ATGGAA-TGGATG-TGGAGTGTGATG
1 ATGGAATTGGATGATGGAATG-GATG
4781459 A
1 A
4781460 AGCAGAAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 6 0.26
24 11 0.48
25 6 0.26
ACGTcount: A:0.30, C:0.00, G:0.42, T:0.28
Consensus pattern (25 bp):
ATGGAATTGGATGATGGAATGGATG
Found at i:4797607 original size:35 final size:35
Alignment explanation
Indices: 4797529--4797656 Score: 125
Period size: 35 Copynumber: 3.7 Consensus size: 35
4797519 ATACTATTTT
* * *
4797529 ATACAGAGCAATTAAAACAAGTAAAGTGCTACTT-
1 ATACAGAACAATTAAAACAAGTGAAGCGCTACTTC
4797563 -TACGTAGAACAATTAAAACAAGTGAAGCGCTACTTC
1 ATAC--AGAACAATTAAAACAAGTGAAGCGCTACTTC
* * * * *
4797599 ATACAGAACAATTAGAATAAGTGGAGCACTACTCC
1 ATACAGAACAATTAAAACAAGTGAAGCGCTACTTC
* * *
4797634 ATATAGAACAACTAATACAAGTG
1 ATACAGAACAATTAAAACAAGTG
4797657 GAACAATTAC
Statistics
Matches: 77, Mismatches: 13, Indels: 7
0.79 0.13 0.07
Matches are distributed among these distances:
33 3 0.04
35 71 0.92
37 3 0.04
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (35 bp):
ATACAGAACAATTAAAACAAGTGAAGCGCTACTTC
Found at i:4813083 original size:1 final size:1
Alignment explanation
Indices: 4813077--4813102 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
4813067 AACCGGGGAC
4813077 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
4813103 ATCAAGCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:4815329 original size:27 final size:28
Alignment explanation
Indices: 4815290--4815344 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
4815280 TTATTAATTA
4815290 TTATAAATAAATTATAA-AATTTATTTT
1 TTATAAATAAATTATAATAATTTATTTT
* * *
4815317 TTATGAATTAATTTTAATTAATTTATTT
1 TTATAAATAAATTATAA-TAATTTATTT
4815345 AATTTTCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 14 0.61
29 9 0.39
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
TTATAAATAAATTATAATAATTTATTTT
Found at i:4840842 original size:13 final size:13
Alignment explanation
Indices: 4840824--4840848 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4840814 TGAAAATCAA
4840824 AGATTAAAGGTGG
1 AGATTAAAGGTGG
4840837 AGATTAAAGGTG
1 AGATTAAAGGTG
4840849 CGTTTGGTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.36, T:0.24
Consensus pattern (13 bp):
AGATTAAAGGTGG
Found at i:4851662 original size:2 final size:2
Alignment explanation
Indices: 4851655--4851680 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4851645 AAGAAAAGAC
4851655 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
4851681 GTTCATGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4855692 original size:14 final size:14
Alignment explanation
Indices: 4855673--4855704 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
4855663 TAGCCGAATA
*
4855673 GCAATTTGCAAAAT
1 GCAATTTCCAAAAT
4855687 GCAATTTCCAAAAT
1 GCAATTTCCAAAAT
4855701 GCAA
1 GCAA
4855705 AGGACTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (14 bp):
GCAATTTCCAAAAT
Found at i:4875730 original size:22 final size:22
Alignment explanation
Indices: 4875702--4875750 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
4875692 ATTATTTCAG
*
4875702 ATTTAAGCCATTGTCGTTTTAA
1 ATTTAAGCCACTGTCGTTTTAA
***
4875724 ATTTAAGTTGCTGTCGTTTTAA
1 ATTTAAGCCACTGTCGTTTTAA
4875746 ATTTA
1 ATTTA
4875751 GATAATTTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (22 bp):
ATTTAAGCCACTGTCGTTTTAA
Found at i:4884163 original size:32 final size:32
Alignment explanation
Indices: 4884116--4884193 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 32
4884106 GTAAGTAGTC
*
4884116 GTTTCTTTTCG-TAAGATAATTA-TTCAGAAGTT
1 GTTTCTTTT-GATAAGATAACTATTTCA-AAGTT
*
4884148 GTTTCTTTTGATAAGATAACTATTTTAAAGTT
1 GTTTCTTTTGATAAGATAACTATTTCAAAGTT
*
4884180 GTTTCTTTTTATAA
1 GTTTCTTTTGATAA
4884194 TACAGCTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 1 0.02
32 37 0.90
33 3 0.07
ACGTcount: A:0.28, C:0.08, G:0.13, T:0.51
Consensus pattern (32 bp):
GTTTCTTTTGATAAGATAACTATTTCAAAGTT
Found at i:4884203 original size:32 final size:33
Alignment explanation
Indices: 4884143--4884209 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 33
4884133 AATTATTCAG
*
4884143 AAGTTGTTTCTTTTGATAAGATAACTATTT-TA
1 AAGTTGTTTCTTTTGATAAGACAACTATTTATA
* * *
4884175 AAGTTGTTTCTTTTTATAATACAGCTATTTATA
1 AAGTTGTTTCTTTTGATAAGACAACTATTTATA
4884208 AA
1 AA
4884210 AATTATATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 26 0.87
33 4 0.13
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.49
Consensus pattern (33 bp):
AAGTTGTTTCTTTTGATAAGACAACTATTTATA
Found at i:4885294 original size:20 final size:22
Alignment explanation
Indices: 4885248--4885294 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
4885238 GTATTTATCT
* *
4885248 ATTTATATTTTATGTATTATAG
1 ATTTATATTTTATATATTATAA
*
4885270 TTTTATA-TTTA-ATATTATAA
1 ATTTATATTTTATATATTATAA
4885290 ATTTA
1 ATTTA
4885295 AATAAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 11 0.52
21 4 0.19
22 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
ATTTATATTTTATATATTATAA
Found at i:4892667 original size:27 final size:26
Alignment explanation
Indices: 4892627--4892683 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
4892617 TTTTTATTTT
*
4892627 ATTT-TTTAAATATTAATAATTTATA
1 ATTTATTTAAATATTAATAATTGATA
*
4892652 ATTTATTTAAATTATTAATAATTGATC
1 ATTTATTTAAA-TATTAATAATTGATA
4892679 ATTTA
1 ATTTA
4892684 AATATGAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 4 0.14
26 6 0.21
27 18 0.64
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
ATTTATTTAAATATTAATAATTGATA
Found at i:4892846 original size:224 final size:224
Alignment explanation
Indices: 4892593--4893252 Score: 996
Period size: 224 Copynumber: 3.0 Consensus size: 224
4892583 AAAAATATTG
* *
4892593 TTTATTATTATATATGATTATCAATTTTTATTTTATTTTTTAAATATTAATAATTTATAATTTAT
1 TTTATTATAATATATGATTATCTATTTTTATTTTATTTTTTAAATATTAATAATTTATAATTTAT
* *
4892658 TTAAATTATTAATAATTGATCATTTAAATATGAACATTTTAAGATATTAATATTTTATATATGCT
66 TTAAAATATTAATAATTGATCATTTAAATATGAACATTTTAAGATATTAATATTTTATATATGAT
*
4892723 CTAAATATTATCATGGTTAAATTATTTATAATTTTAATTAATTTTTAAATTTAAAGTATTATTTT
131 CTAAATATTATAATGGTTAAATTATTTATAATTTTAATTAATTTTTAAATTTAAAGTATTATTTT
* *
4892788 TTGTAATATATAAATAAAAGCTTAAATTT
196 TTATAATATATAAATAAAAGCTTAAACTT
4892817 TTTATTATAATATATGATTATCTATTTTTATTTTATTTTTTAAATATTAATAATTTATAATTTAT
1 TTTATTATAATATATGATTATCTATTTTTATTTTATTTTTTAAATATTAATAATTTATAATTTAT
*
4892882 TTAAAATATTAATAATTGATCATTTAAATATGAACATTTTAAGATATTAATATTTTATGTATGAT
66 TTAAAATATTAATAATTGATCATTTAAATATGAACATTTTAAGATATTAATATTTTATATATGAT
4892947 CTAAATATTATAATGGTTAAATTATTTATAATTTTAATTAATTTTTAAATTTAAAGTATTATTTT
131 CTAAATATTATAATGGTTAAATTATTTATAATTTTAATTAATTTTTAAATTTAAAGTATTATTTT
4893012 TTATAATATATAAATAAAAGCTTAAACTT
196 TTATAATATATAAATAAAAGCTTAAACTT
**
4893041 TTTATTATAATATATGATTATCTATTTTTATTTTATTTTTTAAATATTAATAATTTATCTTTTAT
1 TTTATTATAATATATGATTATCTATTTTTATTTTATTTTTTAAATATTAATAATTTATAATTTAT
* *
4893106 TTAAAATATCAATAATTGATAATTT-AA-ATG------TT-A-ATACTT--TA-TTTAT-TA--A
66 TTAAAATATTAATAATTGATCATTTAAATATGAACATTTTAAGATA-TTAATATTTTATATATGA
* * * * * *
4893155 T-TAAATGTTATTATGATTAAAATATTAATAATTTTAATTAATTTTAAAATTTTAAA-TATTAAT
130 TCTAAATATTATAATGGTTAAATTATTTATAATTTTAATTAATTTTTAAA-TTTAAAGTATT-AT
*
4893218 TTTTTATAATATATAATTAAAAGCTTAAACTT
193 TTTTTATAATATATAAATAAAAGCTTAAACTT
4893250 TTT
1 TTT
4893253 TTTTTAATTT
Statistics
Matches: 414, Mismatches: 19, Indels: 21
0.91 0.04 0.05
Matches are distributed among these distances:
208 46 0.11
209 44 0.11
211 2 0.00
212 5 0.01
213 2 0.00
214 3 0.01
215 3 0.01
216 2 0.00
222 3 0.01
223 2 0.00
224 302 0.73
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (224 bp):
TTTATTATAATATATGATTATCTATTTTTATTTTATTTTTTAAATATTAATAATTTATAATTTAT
TTAAAATATTAATAATTGATCATTTAAATATGAACATTTTAAGATATTAATATTTTATATATGAT
CTAAATATTATAATGGTTAAATTATTTATAATTTTAATTAATTTTTAAATTTAAAGTATTATTTT
TTATAATATATAAATAAAAGCTTAAACTT
Found at i:4892888 original size:27 final size:26
Alignment explanation
Indices: 4892851--4892907 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
4892841 TTTTTATTTT
*
4892851 ATTT-TTTAAATATTAATAATTTATA
1 ATTTATTTAAATATTAATAATTGATA
*
4892876 ATTTATTTAAAATATTAATAATTGATC
1 ATTTATTT-AAATATTAATAATTGATA
4892903 ATTTA
1 ATTTA
4892908 AATATGAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 4 0.14
26 3 0.11
27 21 0.75
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (26 bp):
ATTTATTTAAATATTAATAATTGATA
Found at i:4893097 original size:22 final size:22
Alignment explanation
Indices: 4893072--4893154 Score: 58
Period size: 22 Copynumber: 3.5 Consensus size: 22
4893062 CTATTTTTAT
4893072 TTTATTTTTTAAATATTAATAA
1 TTTATTTTTTAAATATTAATAA
*
4893094 TTTATCTTTTATTTAAAATATCAATAA
1 TTTA---TTT-TTT-AAATATTAATAA
* ** * *
4893121 TTGATAATTTAAATGTTAATAC
1 TTTATTTTTTAAATATTAATAA
*
4893143 TTTATTTATTAA
1 TTTATTTTTTAA
4893155 TTAAATGTTA
Statistics
Matches: 45, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
22 21 0.47
23 3 0.07
24 1 0.02
25 3 0.07
26 3 0.07
27 14 0.31
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTATTTTTTAAATATTAATAA
Found at i:4893131 original size:27 final size:26
Alignment explanation
Indices: 4893075--4893131 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
4893065 TTTTTATTTT
* * *
4893075 ATTT-TTTAAATATTAATAATTTATC
1 ATTTATTTAAATATCAATAATTGATA
*
4893100 TTTTATTTAAAATATCAATAATTGATA
1 ATTTATTT-AAATATCAATAATTGATA
4893127 ATTTA
1 ATTTA
4893132 AATGTTAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 3 0.12
26 3 0.12
27 19 0.76
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (26 bp):
ATTTATTTAAATATCAATAATTGATA
Found at i:4893700 original size:12 final size:12
Alignment explanation
Indices: 4893683--4893707 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4893673 CACACACCCG
4893683 TCTCTGTCTCTC
1 TCTCTGTCTCTC
4893695 TCTCTGTCTCTC
1 TCTCTGTCTCTC
4893707 T
1 T
4893708 AGGCATATTT
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:0.40, G:0.08, T:0.52
Consensus pattern (12 bp):
TCTCTGTCTCTC
Found at i:4899597 original size:14 final size:14
Alignment explanation
Indices: 4899574--4899604 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4899564 GTTATATAAA
4899574 AAATAATTAATTCT
1 AAATAATTAATTCT
*
4899588 AAATATTTAATTCT
1 AAATAATTAATTCT
4899602 AAA
1 AAA
4899605 AAAATAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATAATTAATTCT
Found at i:4929675 original size:2 final size:2
Alignment explanation
Indices: 4929668--4929698 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4929658 GTGAAAGTAA
4929668 CT CT CT CT CT CT CT CT CT CT CT CT -T CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4929699 GTGGATGCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:4932042 original size:47 final size:47
Alignment explanation
Indices: 4931985--4932079 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
4931975 AGGCTAGACT
*
4931985 ATTAATTATGGTGCCTGAGAGCTGAGTGTGTCTGAAATAGAATCATA
1 ATTAATTATGGTGCCTGAGAGCTGAGTGTGCCTGAAATAGAATCATA
* * *
4932032 ATTAATTATGGTGCTTGAGAGTTGAGTGTGCCTGAAATTGAATCATA
1 ATTAATTATGGTGCCTGAGAGCTGAGTGTGCCTGAAATAGAATCATA
4932079 A
1 A
4932080 ATAGAGATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.34
Consensus pattern (47 bp):
ATTAATTATGGTGCCTGAGAGCTGAGTGTGCCTGAAATAGAATCATA
Found at i:4939283 original size:15 final size:15
Alignment explanation
Indices: 4939263--4939294 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4939253 TATTGTTATA
4939263 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
4939278 ATTAAAATAAAATAT
1 ATTAAAATAAAAAAT
4939293 AT
1 AT
4939295 AATATAAGAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:4939402 original size:12 final size:14
Alignment explanation
Indices: 4939372--4939631 Score: 58
Period size: 14 Copynumber: 18.2 Consensus size: 14
4939362 ACAAATTAAA
*
4939372 ATAAAATATATAAT
1 ATAAAAAATATAAT
4939386 ATAAAAAATAT-AT
1 ATAAAAAATATAAT
*
4939399 -TAAAAAATA-AAA
1 ATAAAAAATATAAT
*
4939411 ATAAAATATATAAGATT
1 ATAAAAAATAT-A-A-T
*
4939428 ATAATAATAA-ATAAAA
1 ATAA-AA-AATAT-AAT
* * *
4939444 ATAAAATATATGAC
1 ATAAAAAATATAAT
*
4939458 ATTAAAAATAT-AT
1 ATAAAAAATATAAT
* * *
4939471 TTAAGAGATGATATTAT
1 ATAA-A-A-AATATAAT
*
4939488 ATAAAAATTAATAAT
1 ATAAAAAAT-ATAAT
4939503 ATAAATATAA-AT-AT
1 ATAAA-A-AATATAAT
* *
4939517 ATTAAAAATAAAAT
1 ATAAAAAATATAAT
* *
4939531 ATATAAGAT-T-AT
1 ATAAAAAATATAAT
* *
4939543 AATAATAAATA-AAA
1 -ATAAAAAATATAAT
* *
4939557 ATAAAATATATGAT
1 ATAAAAAATATAAT
*
4939571 ATTAAAAATAT-AT
1 ATAAAAAATATAAT
* * * *
4939584 TTAAGAGATGATATT
1 ATAAAAAAT-ATAAT
4939599 ATATAAAAAT-TAAT
1 ATA-AAAAATATAAT
4939613 AATAAAAAATATAAAT
1 -ATAAAAAATAT-AAT
4939629 ATA
1 ATA
4939632 TTAAACTTGT
Statistics
Matches: 173, Mismatches: 45, Indels: 55
0.63 0.16 0.20
Matches are distributed among these distances:
12 14 0.08
13 36 0.21
14 59 0.34
15 28 0.16
16 18 0.10
17 11 0.06
18 6 0.03
19 1 0.01
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (14 bp):
ATAAAAAATATAAT
Found at i:4939406 original size:33 final size:33
Alignment explanation
Indices: 4939369--4939454 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
4939359 ACAACAAATT
* *
4939369 AAAATAAAATATATAATATA-AAAAATATATTAA
1 AAAATAAAA-ATAAAATATATAAAAATATAATAA
* *
4939402 AAAATAAAAATAAAATATATAAGATTATAATAA
1 AAAATAAAAATAAAATATATAAAAATATAATAA
*
4939435 TAAATAAAAATAAAATATAT
1 AAAATAAAAATAAAATATAT
4939455 GACATTAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 9 0.19
33 38 0.81
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (33 bp):
AAAATAAAAATAAAATATATAAAAATATAATAA
Found at i:4939418 original size:39 final size:38
Alignment explanation
Indices: 4939364--4939471 Score: 109
Period size: 33 Copynumber: 2.9 Consensus size: 38
4939354 TGGGTACAAC
* *
4939364 AAATTAAAATAAAATATATAATATAAAAAATATATTAAA
1 AAATAAAAATAAAATATATAACAT-AAAAATATATTAAA
* * *
4939403 AAATAAAAATAAAATATATAAGAT-----TATAATAAT
1 AAATAAAAATAAAATATATAACATAAAAATATATTAAA
*
4939436 AAATAAAAATAAAATATATGACATTAAAAATATATT
1 AAATAAAAATAAAATATATAACA-TAAAAATATATT
4939472 TAAGAGATGA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
33 28 0.50
34 1 0.02
39 27 0.48
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.31
Consensus pattern (38 bp):
AAATAAAAATAAAATATATAACATAAAAATATATTAAA
Found at i:4939506 original size:15 final size:15
Alignment explanation
Indices: 4939486--4939551 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
4939476 AGATGATATT
4939486 ATATAAAAATTAATA
1 ATATAAAAATTAATA
* *
4939501 ATATAAATATAAAT-
1 ATATAAAAATTAATA
4939515 ATATTAAAAA-TAA-A
1 ATA-TAAAAATTAATA
*
4939529 ATATATAAGATT-ATA
1 ATATA-AAAATTAATA
4939544 ATAATAAA
1 AT-ATAAA
4939552 TAAAAATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
13 2 0.05
14 12 0.30
15 23 0.57
16 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (15 bp):
ATATAAAAATTAATA
Found at i:4939540 original size:113 final size:114
Alignment explanation
Indices: 4939372--4939636 Score: 437
Period size: 113 Copynumber: 2.3 Consensus size: 114
4939362 ACAAATTAAA
* *
4939372 ATAAAATATATAAT-ATAAAAAATATATTAA-AAAATAAAAATAAAATATATAAGATTATAATAA
1 ATAAAA-AT-TAATAATAAAAAATATA--AATATATTAAAAATAAAATATATAAGATTATAATAA
4939435 TAAATAAAAATAAAATATATGACATTAAAAATATATTTAAGAGATGATATTAT
62 TAAATAAAAATAAAATATATGACATTAAAAATATATTTAAGAGATGATATTAT
*
4939488 ATAAAAATTAATAAT-ATAAATATAAATATATTAAAAATAAAATATATAAGATTATAATAATAAA
1 ATAAAAATTAATAATAAAAAATATAAATATATTAAAAATAAAATATATAAGATTATAATAATAAA
*
4939552 TAAAAATAAAATATATGATATTAAAAATATATTTAAGAGATGATATTAT
66 TAAAAATAAAATATATGACATTAAAAATATATTTAAGAGATGATATTAT
4939601 ATAAAAATTAATAATAAAAAATATAAATATATTAAA
1 ATAAAAATTAATAATAAAAAATATAAATATATTAAA
4939637 CTTGTATTTT
Statistics
Matches: 141, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
112 2 0.01
113 98 0.70
114 31 0.22
115 4 0.03
116 6 0.04
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (114 bp):
ATAAAAATTAATAATAAAAAATATAAATATATTAAAAATAAAATATATAAGATTATAATAATAAA
TAAAAATAAAATATATGACATTAAAAATATATTTAAGAGATGATATTAT
Found at i:4939564 original size:15 final size:15
Alignment explanation
Indices: 4939488--4939564 Score: 50
Period size: 17 Copynumber: 4.9 Consensus size: 15
4939478 ATGATATTAT
*
4939488 ATAAAAAT-TAAT-A
1 ATAAAAATAAAATAA
*
4939501 ATATAAATATAAATATA
1 ATAAAAATA-AAATA-A
* *
4939518 TTAAAAATAAAATAT
1 ATAAAAATAAAATAA
*
4939533 ATAAGATTATAATAATAA
1 ATAA-A-AATAA-AATAA
4939551 ATAAAAATAAAATA
1 ATAAAAATAAAATA
4939565 TATGATATTA
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
13 7 0.15
15 10 0.21
16 10 0.21
17 13 0.27
18 8 0.17
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (15 bp):
ATAAAAATAAAATAA
Found at i:4939645 original size:60 final size:60
Alignment explanation
Indices: 4939458--4939645 Score: 182
Period size: 60 Copynumber: 3.2 Consensus size: 60
4939448 AATATATGAC
* *
4939458 ATTAAAAATATATTTAAGAGATGATATTATATAAAAATTAATAAT-ATAAATATAAATAT
1 ATTAAAATTATATTTAAGAGATGATATTATATAAAAATTAATAATAAAAAATATAAATAT
* * * *
4939517 ATTAAAAATAAAATATATA-AGAT--TA-TA-ATAATAAA-TAA-AA-ATAAAATAT--ATGAT
1 ATT-AAAATTATATTTA-AGAGATGATATTATATAA-AAATTAATAATAAAAAATATAAAT-AT
*
4939571 ATTAAAAATATATTTAAGAGATGATATTATATAAAAATTAATAATAAAAAATATAAATAT
1 ATTAAAATTATATTTAAGAGATGATATTATATAAAAATTAATAATAAAAAATATAAATAT
* *
4939631 ATTAAACTTGTATTT
1 ATTAAAATTATATTT
4939646 TAATAACTAA
Statistics
Matches: 100, Mismatches: 14, Indels: 29
0.70 0.10 0.20
Matches are distributed among these distances:
52 1 0.01
53 15 0.15
54 5 0.05
55 10 0.10
56 12 0.12
57 12 0.12
58 4 0.04
59 11 0.11
60 27 0.27
61 3 0.03
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.36
Consensus pattern (60 bp):
ATTAAAATTATATTTAAGAGATGATATTATATAAAAATTAATAATAAAAAATATAAATAT
Found at i:4946128 original size:21 final size:20
Alignment explanation
Indices: 4946091--4946130 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
4946081 TTTAAATTAA
*
4946091 ATAAATTTTTATAATTAATG
1 ATAAATTATTATAATTAATG
*
4946111 ATAAATTAATTATCATTAAT
1 ATAAATT-ATTATAATTAAT
4946131 CAAAATATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (20 bp):
ATAAATTATTATAATTAATG
Found at i:4946383 original size:29 final size:29
Alignment explanation
Indices: 4946351--4946412 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
4946341 ATTAATCATA
4946351 AAAATTTATTTGATTAAAAATAAAAATAT
1 AAAATTTATTTGATTAAAAATAAAAATAT
* * *
4946380 AAAATTTATTTGATTCAGAATAAAAGTAT
1 AAAATTTATTTGATTAAAAATAAAAATAT
4946409 AAAA
1 AAAA
4946413 GCTTGATTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.35
Consensus pattern (29 bp):
AAAATTTATTTGATTAAAAATAAAAATAT
Found at i:4946597 original size:26 final size:29
Alignment explanation
Indices: 4946545--4946609 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 29
4946535 TTATAAAAAT
*
4946545 TTAAAT-AATTTTTTATTATTTTATTATA
1 TTAAATCAAATTTTTATTATTTTATTATA
* *
4946573 TTCAATCAAATTTTTA-TA-TTT-TTATT
1 TTAAATCAAATTTTTATTATTTTATTATA
4946599 TTAAATCAAAT
1 TTAAATCAAAT
4946610 AAGTCCTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 14 0.44
27 3 0.09
28 7 0.22
29 8 0.25
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (29 bp):
TTAAATCAAATTTTTATTATTTTATTATA
Found at i:4947405 original size:21 final size:20
Alignment explanation
Indices: 4947381--4947451 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
4947371 CGTTTTTGAG
*
4947381 TTTATTTGATCTATTTTTTAT
1 TTTATTT-ATTTATTTTTTAT
* *
4947402 TTTACTTATTTTACTTTTCTAT
1 TTTATTTA-TTTA-TTTTTTAT
*
4947424 TTTATTTATTTATTTATTAAT
1 TTTATTTATTTATTT-TTTAT
4947445 TTTATTT
1 TTTATTT
4947452 CTATCATTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
20 4 0.10
21 23 0.56
22 14 0.34
ACGTcount: A:0.21, C:0.06, G:0.01, T:0.72
Consensus pattern (20 bp):
TTTATTTATTTATTTTTTAT
Found at i:4974377 original size:26 final size:28
Alignment explanation
Indices: 4974335--4974390 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 28
4974325 TGTTATAATT
*
4974335 AAAATAAAATTATAATATAAG-AATTAA
1 AAAATAAAATTAAAATATAAGAAATTAA
4974362 AAAATAAAA-TAAAATATAAGAAATTAA
1 AAAATAAAATTAAAATATAAGAAATTAA
4974389 AA
1 AA
4974391 TTTATGTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 10 0.37
27 17 0.63
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (28 bp):
AAAATAAAATTAAAATATAAGAAATTAA
Found at i:4974429 original size:26 final size:24
Alignment explanation
Indices: 4974331--4974429 Score: 81
Period size: 26 Copynumber: 3.7 Consensus size: 24
4974321 GTAGTGTTAT
4974331 AATTAAAATAAAATTATAATATAAG
1 AATTAAAATAAAA-TATAATATAAG
*
4974356 AATTAAAAAATAAAATAAAATATAAG
1 AATT--AAAATAAAATATAATATAAG
* *
4974382 AAATTAAAATTTATGTAATATAAGTAAAAG
1 -AATTAAAA--TA--AAATATAA-TATAAG
4974412 AAGTTAAAATAAAATATA
1 AA-TTAAAATAAAATATA
4974430 TAATATAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
25 8 0.13
26 16 0.27
27 15 0.25
28 2 0.03
29 8 0.13
30 11 0.18
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (24 bp):
AATTAAAATAAAATATAATATAAG
Found at i:4974460 original size:50 final size:46
Alignment explanation
Indices: 4974336--4974468 Score: 112
Period size: 50 Copynumber: 2.8 Consensus size: 46
4974326 GTTATAATTA
* *
4974336 AAAT-AAAATTATAATATAAGAATTAAAAAATAAAATAAAATATAAG
1 AAATAAAAATTATATTA-AAGAAATAAAAAATAAAATAAAATATAAG
* * *
4974382 AAATTAAAATT-TATGTAATATAAGTAAAAGAAGTTAAAATAAAATATATA-
1 AAATAAAAATTATAT-TAA-AGAAATAAAA-AA--TAAAATAAAATATA-AG
*
4974432 ATATAAAAAATTATATTAAAGAAAT-AAAAATAAAATA
1 AAAT-AAAAATTATATTAAAGAAATAAAAAATAAAATA
4974469 TATAAGATTA
Statistics
Matches: 71, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
46 14 0.20
47 16 0.23
48 4 0.06
49 3 0.04
50 21 0.30
51 10 0.14
52 3 0.04
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (46 bp):
AAATAAAAATTATATTAAAGAAATAAAAAATAAAATAAAATATAAG
Found at i:4974479 original size:34 final size:33
Alignment explanation
Indices: 4974418--4974504 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
4974408 AAAGAAGTTA
* *
4974418 AAATAAAATATATAATATAAAAAATTATATTA-AAG
1 AAATAAAA-ATAAAATATATAAAATTATA--ACAAG
*
4974453 AAATAAAAATAAAATATATAAGATTATAACAAG
1 AAATAAAAATAAAATATATAAAATTATAACAAG
* *
4974486 AAATGACAATAAAATATAT
1 AAATAAAAATAAAATATAT
4974505 GACATTAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
32 1 0.02
33 20 0.43
34 17 0.37
35 8 0.17
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (33 bp):
AAATAAAAATAAAATATATAAAATTATAACAAG
Found at i:4974508 original size:15 final size:16
Alignment explanation
Indices: 4974488--4974521 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4974478 ATAACAAGAA
4974488 ATGACAAT-AAAATAT
1 ATGACAATAAAAATAT
*
4974503 ATGACATTAAAAATAT
1 ATGACAATAAAAATAT
4974519 ATG
1 ATG
4974522 TAAGGGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (16 bp):
ATGACAATAAAAATAT
Found at i:4988298 original size:15 final size:15
Alignment explanation
Indices: 4988280--4988314 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
4988270 GCTTTCTCCT
4988280 CCACCGCCATCACCG
1 CCACCGCCATCACCG
4988295 CCACCGCCATCACCG
1 CCACCGCCATCACCG
4988310 CCACC
1 CCACC
4988315 ACCGATACCT
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:0.20, C:0.63, G:0.11, T:0.06
Consensus pattern (15 bp):
CCACCGCCATCACCG
Found at i:4988380 original size:21 final size:21
Alignment explanation
Indices: 4988350--4988396 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
4988340 CCGTGCCCCA
4988350 ATGCCCTCCACCATGCTCTGG
1 ATGCCCTCCACCATGCTCTGG
* * *
4988371 GTGCCGTCCACCCTGCTCTGG
1 ATGCCCTCCACCATGCTCTGG
4988392 ATGCC
1 ATGCC
4988397 TTCACCACCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.11, C:0.43, G:0.23, T:0.23
Consensus pattern (21 bp):
ATGCCCTCCACCATGCTCTGG
Found at i:5003076 original size:2 final size:2
Alignment explanation
Indices: 5003069--5003096 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5003059 CATATTTGCA
5003069 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
5003097 GTCATCTACT
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:5029839 original size:6 final size:6
Alignment explanation
Indices: 5029828--5029859 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
5029818 GAATTCACCA
5029828 TCATCT TCATCT TCATCT TCATCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TC
5029860 CCTTGTCCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.34, G:0.00, T:0.50
Consensus pattern (6 bp):
TCATCT
Found at i:5029842 original size:18 final size:18
Alignment explanation
Indices: 5029821--5029859 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5029811 CATCAGAGAA
5029821 TTCACCATCATCTTCATC
1 TTCACCATCATCTTCATC
* *
5029839 TTCATCTTCATCTTCATC
1 TTCACCATCATCTTCATC
5029857 TTC
1 TTC
5029860 CCTTGTCCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.36, G:0.00, T:0.46
Consensus pattern (18 bp):
TTCACCATCATCTTCATC
Found at i:5032677 original size:2 final size:2
Alignment explanation
Indices: 5032670--5032706 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5032660 ATAATGGTGA
5032670 AT AT AT AT 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 AT AT AT AT A
5032707 AACATGATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5051050 original size:33 final size:34
Alignment explanation
Indices: 5051013--5051099 Score: 99
Period size: 33 Copynumber: 2.6 Consensus size: 34
5051003 AGGTAAAAAT
* *
5051013 AAAAATAAAATATATAATATA-AAAATTATATTA
1 AAAAATAAAATATAAAATATATAAAATTATAATA
*
5051046 AAAAATAAAA-ATAAAATATATAAGATTATAATA
1 AAAAATAAAATATAAAATATATAAAATTATAATA
*
5051079 AGAAAAGAAAATA-AAACATAT
1 A-AAAATAAAATATAAA-ATAT
5051100 GACTTTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
32 9 0.20
33 21 0.46
34 11 0.24
35 5 0.11
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.26
Consensus pattern (34 bp):
AAAAATAAAATATAAAATATATAAAATTATAATA
Found at i:5051090 original size:39 final size:39
Alignment explanation
Indices: 5051007--5051094 Score: 106
Period size: 39 Copynumber: 2.3 Consensus size: 39
5050997 TAATATAGGT
* * * *
5051007 AAAAATAAAAATAAAATATATAATATAAAAATTATATTA
1 AAAAATAAAAATAAAATATATAAGATAAAAATAAGATAA
* *
5051046 AAAAATAAAAATAAAATATATAAGATTATAATAAGA-AA
1 AAAAATAAAAATAAAATATATAAGATAAAAATAAGATAA
5051084 AGAAAATAAAA
1 A-AAAATAAAA
5051095 CATATGACTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 2 0.05
39 40 0.95
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (39 bp):
AAAAATAAAAATAAAATATATAAGATAAAAATAAGATAA
Found at i:5052877 original size:43 final size:43
Alignment explanation
Indices: 5052829--5052914 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
5052819 TCCTTTAAGG
* *
5052829 TTCAAAATTTGAAATTATTTTTCCTTTTTCCTTCTAGAGTAAA
1 TTCAAAATTTAAAATTATTTTTCCTTTTTCCTTATAGAGTAAA
* * * *
5052872 TTCAAATTTTAAAATTATTTTTCTTTTTTTCTTATATAGTAAA
1 TTCAAAATTTAAAATTATTTTTCCTTTTTCCTTATAGAGTAAA
5052915 AGATGCATTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.53
Consensus pattern (43 bp):
TTCAAAATTTAAAATTATTTTTCCTTTTTCCTTATAGAGTAAA
Found at i:5055116 original size:22 final size:22
Alignment explanation
Indices: 5055083--5055169 Score: 88
Period size: 22 Copynumber: 4.0 Consensus size: 22
5055073 TGTAACTGGT
5055083 TTTTTGAA-TATTGCGTGACTAA
1 TTTTT-AAGTATTGCGTGACTAA
*
5055105 TTTTTAAGTATTGCGTGATTAA
1 TTTTTAAGTATTGCGTGACTAA
* * * *
5055127 TTTTT-AGATACTGCATGATTGA
1 TTTTTAAG-TATTGCGTGACTAA
*
5055149 TTTTTAAGTATTACGTGACTA
1 TTTTTAAGTATTGCGTGACTA
5055170 GTTGATATGG
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
21 4 0.08
22 47 0.89
23 2 0.04
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (22 bp):
TTTTTAAGTATTGCGTGACTAA
Found at i:5055331 original size:22 final size:22
Alignment explanation
Indices: 5055303--5055349 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5055293 ATGTCTAATT
*
5055303 CTAGTCACGCAAAGCTTAAAAA
1 CTAGTCACACAAAGCTTAAAAA
* * *
5055325 CTAGTCATATAATGCTTAAAAA
1 CTAGTCACACAAAGCTTAAAAA
5055347 CTA
1 CTA
5055350 AATATGCAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (22 bp):
CTAGTCACACAAAGCTTAAAAA
Found at i:5055416 original size:22 final size:22
Alignment explanation
Indices: 5055373--5055431 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
5055363 TAAATTACGT
* * *
5055373 AATACTTAAAAATCAGTCACAC
1 AATACTTAAAAATTAATAACAC
*
5055395 AGTACTTAAAAATTAATAACAC
1 AATACTTAAAAATTAATAACAC
**
5055417 AATGTTTAAAAATTA
1 AATACTTAAAAATTA
5055432 GTAATGCAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.29
Consensus pattern (22 bp):
AATACTTAAAAATTAATAACAC
Found at i:5055796 original size:10 final size:10
Alignment explanation
Indices: 5055781--5055810 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
5055771 TAAGTTATGT
5055781 TTAAAATTAA
1 TTAAAATTAA
5055791 TTAAAAATTAA
1 TT-AAAATTAA
5055802 TTAAAATTA
1 TTAAAATTA
5055811 TAGTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
TTAAAATTAA
Found at i:5087094 original size:28 final size:28
Alignment explanation
Indices: 5087053--5087112 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 28
5087043 ATTAGACTCA
*
5087053 AACTCTACTATGCTTACTAAGTTTTCTT
1 AACTCTACTATGCTGACTAAGTTTTCTT
5087081 AACTCTATCT-TGCTGACTAAGTTTTCTT
1 AACTCTA-CTATGCTGACTAAGTTTTCTT
5087109 AACT
1 AACT
5087113 TTCTTGATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 28 0.93
29 2 0.07
ACGTcount: A:0.25, C:0.22, G:0.08, T:0.45
Consensus pattern (28 bp):
AACTCTACTATGCTGACTAAGTTTTCTT
Found at i:5087287 original size:172 final size:171
Alignment explanation
Indices: 5086996--5087335 Score: 497
Period size: 172 Copynumber: 2.0 Consensus size: 171
5086986 TAGGCCCCAA
* * *
5086996 AGAGCTTTTTGTATCTTGATTTTATTTTTTTCTCAACTTTTGATTGAATTAGACTCAAACTCTAC
1 AGAGCTTTTTGTATCTTGACTTTATTTTTTTCTCAACTTCTGATTGAATTAGACTCAAACTCGAC
* * * * *
5087061 TATGCTTACTAAGTTTTCTTAACTCTATCTTGCTGACTAAGTTTTCTTAACTTTCTTGATTTTGT
66 TATGCTTACTAAGTTTTCTTAACTCTACCATGCTAACTAAGTCTTCTCAACTTTCTTGATTTTGT
* *
5087126 GTAATGTCTACCTA-ATTGCTGATTGGGTTTTTTCTCAACAG
131 GCAACGTCTACCTACA-TGCTGATTGGGTTTTTTCTCAACAG
*
5087167 AGAGCTTTTTGTATCTTGGCTTTATTTCTTTTCT-AAGCTTCTGATTGAATTAGACTCAAACTCG
1 AGAGCTTTTTGTATCTTGACTTTATTT-TTTTCTCAA-CTTCTGATTGAATTAGACTCAAACTCG
* * *
5087231 ACTATG-TTGATTAAGTTTTTTTAACTCTACCATGCTAACTATGTCTTCTCAACTTTCTTGATTT
64 ACTATGCTT-ACTAAGTTTTCTTAACTCTACCATGCTAACTAAGTCTTCTCAACTTTCTTGATTT
5087295 TGTGCAACGTCTACCTACATGCTGATTGGGTTTTTTCTCAA
128 TGTGCAACGTCTACCTACATGCTGATTGGGTTTTTTCTCAA
5087336 TTCCCCTGAT
Statistics
Matches: 151, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
171 29 0.19
172 121 0.80
173 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.47
Consensus pattern (171 bp):
AGAGCTTTTTGTATCTTGACTTTATTTTTTTCTCAACTTCTGATTGAATTAGACTCAAACTCGAC
TATGCTTACTAAGTTTTCTTAACTCTACCATGCTAACTAAGTCTTCTCAACTTTCTTGATTTTGT
GCAACGTCTACCTACATGCTGATTGGGTTTTTTCTCAACAG
Found at i:5087828 original size:18 final size:19
Alignment explanation
Indices: 5087805--5087848 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
5087795 TTGATAATGC
*
5087805 TGCCACCAT-TGTTCCTAT
1 TGCCACCATCTGTCCCTAT
*
5087823 TGCCA-CTTCTGTCCCTAT
1 TGCCACCATCTGTCCCTAT
5087841 TGCCACCA
1 TGCCACCA
5087849 CCACTGTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.10
18 18 0.86
19 1 0.05
ACGTcount: A:0.16, C:0.39, G:0.11, T:0.34
Consensus pattern (19 bp):
TGCCACCATCTGTCCCTAT
Found at i:5096916 original size:2 final size:2
Alignment explanation
Indices: 5096909--5096960 Score: 77
Period size: 2 Copynumber: 25.5 Consensus size: 2
5096899 GCACCTACAC
* *
5096909 TA TA TA TA TA TG TA TGG TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
5096952 TA TA TA TA T
1 TA TA TA TA T
5096961 TTAATGAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 44 0.98
3 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5105317 original size:10 final size:10
Alignment explanation
Indices: 5105288--5105317 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5105278 CTTGGTTTGC
*
5105288 TGTGTGTGTG
1 TGTGTGTGTT
5105298 TGTGTGTGTT
1 TGTGTGTGTT
5105308 TGTGTGTGTT
1 TGTGTGTGTT
5105318 AGAGATGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.43, T:0.57
Consensus pattern (10 bp):
TGTGTGTGTT
Found at i:5119874 original size:325 final size:314
Alignment explanation
Indices: 5119287--5119931 Score: 995
Period size: 325 Copynumber: 2.0 Consensus size: 314
5119277 ATTTTATAGA
*
5119287 AAGTGAAATCGAGGTAAGTTAAACATACAATTATAGGTTATAAGCATAACATTAAAAAAAAAATT
1 AAGTGAAATCGAGGTAAGTTAAACATACAATTATAGGTTACAAGCATAACATTAAAAAAAAAATT
* * * * * *
5119352 GTTCAAAAAATTTAAATAATTTTTTGTATTTTATTGAATTTAATACGATTTGTGTATTTTTATTT
66 ATTCAAAAAATTTAAATAAATTTTTATATTTTATTGAATGTAAGACAATTTGTGTATTTTTATTT
* *
5119417 TCCTTTAAACAAACTCTCATAATTAATTATTAATTAAAGTATCAAATATTATTTTATGTCACGTC
131 TCATTTAAACAAACTCTAATAATTAATTATTAATTAAAGTATCAAATATTATTTTATGTCACGTC
5119482 ATAACATATTAACATATTATAATAAATGATTATATGGTATGTCGATATAAATTGATGATATGATC
196 ATAACATATTAACATATTATAATAAATGATTATATGGTATGTCGATATAAATTGATGATATGATC
* *
5119547 ATGTGGTGATTTT-ATTTTTTATATCAACATTATGTTATGTGATATAACAAATGAG
261 ATGTGATG-TTTTCATTTTTT-TATCAACATTATGTTATGTGATATAACAAACGAG
*
5119602 AAGTGACATCGAGGTAAGTTAAACATACAATTATAGGTTAACAAGCATAACATTCAAAAAAAAAA
1 AAGTGAAATCGAGGTAAGTTAAACATACAATTATAGGTT-ACAAGCATAACATT-AAAAAAAAAA
5119667 GTTATTCAAAAAATTTAAATAAATTTTTATATTTTATTGAATGTAAGACAATTTGTGTATTTTTA
64 -TTATTCAAAAAATTTAAATAAATTTTTATATTTTATTGAATGTAAGACAATTTGTGTATTTTTA
5119732 TTTTCATTTAAACAAACTCTTATAATTAATTATTAATTATTAATTAAAGTATCAAATATTATTTT
128 TTTTCATTTAAACAAACTC---TAA-T-A--ATTAATTATTAATTAAAGTATCAAATATTATTTT
* * * * * *
5119797 ATGTCAGGTCATAACATATTAACATGTTATAATAAATGATTATGTTGTCTGTCGATATGAATTGA
186 ATGTCACGTCATAACATATTAACATATTATAATAAATGATTATATGGTATGTCGATATAAATTGA
* *
5119862 TGATATGATCATGTGATGTTTTCATTTTTTTATCAATATTATGTTATGTGATATAACAAACGAT
251 TGATATGATCATGTGATGTTTTCATTTTTTTATCAACATTATGTTATGTGATATAACAAACGAG
5119926 AAGTGA
1 AAGTGA
5119932 TATTTTAACT
Statistics
Matches: 299, Mismatches: 20, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
315 38 0.13
316 13 0.04
317 10 0.03
318 76 0.25
321 2 0.01
322 1 0.00
323 1 0.00
324 41 0.14
325 117 0.39
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (314 bp):
AAGTGAAATCGAGGTAAGTTAAACATACAATTATAGGTTACAAGCATAACATTAAAAAAAAAATT
ATTCAAAAAATTTAAATAAATTTTTATATTTTATTGAATGTAAGACAATTTGTGTATTTTTATTT
TCATTTAAACAAACTCTAATAATTAATTATTAATTAAAGTATCAAATATTATTTTATGTCACGTC
ATAACATATTAACATATTATAATAAATGATTATATGGTATGTCGATATAAATTGATGATATGATC
ATGTGATGTTTTCATTTTTTTATCAACATTATGTTATGTGATATAACAAACGAG
Found at i:5120398 original size:21 final size:22
Alignment explanation
Indices: 5120359--5120399 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
5120349 GTGATGATTT
5120359 TTAATACATTAAAAGAATATAA
1 TTAATACATTAAAAGAATATAA
5120381 TTAATA-ATTATAAA-AATAT
1 TTAATACATTA-AAAGAATAT
5120400 TTTTCAACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (22 bp):
TTAATACATTAAAAGAATATAA
Found at i:5121967 original size:14 final size:14
Alignment explanation
Indices: 5121948--5121979 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5121938 ATAAAATGAT
5121948 TAATTTTTAAAATA
1 TAATTTTTAAAATA
*
5121962 TAATTTTTAAAATT
1 TAATTTTTAAAATA
5121976 TAAT
1 TAAT
5121980 AAATAATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATTTTTAAAATA
Found at i:5123431 original size:2 final size:2
Alignment explanation
Indices: 5123426--5123456 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5123416 ACACACACAC
5123426 AT 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 AT A
5123457 AAAGAGAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5124205 original size:69 final size:69
Alignment explanation
Indices: 5124124--5124281 Score: 244
Period size: 69 Copynumber: 2.3 Consensus size: 69
5124114 CAGTAGACTC
* * *
5124124 AGAAAAGACTGATTATGGCAGAAAACGAATTTACCAAACACAGCCAGAAAAACCAGAGTCAGGAA
1 AGAAAAGCCTGATTATGGCAGAAAACCAATTTACCAAACACAGCCAGAAAAACCAGAGTCAGAAA
5124189 AGGA
66 AGGA
* * * *
5124193 AGAAAAGCCTGATTATGGGAGAAAACCAGTTTACCAACCACAGCCAGAAAAGCCAGAGTCAGAAA
1 AGAAAAGCCTGATTATGGCAGAAAACCAATTTACCAAACACAGCCAGAAAAACCAGAGTCAGAAA
5124258 AGGA
66 AGGA
*
5124262 AGAAAAGCCTGATAATGGCA
1 AGAAAAGCCTGATTATGGCA
5124282 CTAAACAGAA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 80 1.00
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.12
Consensus pattern (69 bp):
AGAAAAGCCTGATTATGGCAGAAAACCAATTTACCAAACACAGCCAGAAAAACCAGAGTCAGAAA
AGGA
Found at i:5124335 original size:81 final size:82
Alignment explanation
Indices: 5124237--5124415 Score: 274
Period size: 81 Copynumber: 2.2 Consensus size: 82
5124227 CAACCACAGC
*
5124237 CAGAAAAGCCAGAGTCAGAAAAGGAAGAAAAGCCTGATAATGGCACTAA-ACAGAACTTCTACAA
1 CAGAAAAGCCAGAGTCAGAAAAGGAAGAAAAGCCTGATAATAGCACTAAGACAG-ACTTCTACAA
*
5124301 ACCGCAGCCAGAAGAAAA
65 ACCACAGCCAGAAGAAAA
* * * *
5124319 -AGAAAAGCCAGAGTCAGAAGAGGAAGAGAAGCCTGATTATAGCACTAAGCCAGACTTCTACAAA
1 CAGAAAAGCCAGAGTCAGAAAAGGAAGAAAAGCCTGATAATAGCACTAAGACAGACTTCTACAAA
5124383 CCACAGCCAGAAGAAAA
66 CCACAGCCAGAAGAAAA
5124400 CA-AAAAGCCAGAGTCA
1 CAGAAAAGCCAGAGTCA
5124416 TCAGACGAGG
Statistics
Matches: 89, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
81 85 0.96
82 4 0.04
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.10
Consensus pattern (82 bp):
CAGAAAAGCCAGAGTCAGAAAAGGAAGAAAAGCCTGATAATAGCACTAAGACAGACTTCTACAAA
CCACAGCCAGAAGAAAA
Found at i:5127074 original size:15 final size:17
Alignment explanation
Indices: 5127037--5127076 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
5127027 CAGTAGACAT
*
5127037 ATATAGTAGATAATTAC
1 ATATAGTAGAAAATTAC
5127054 ATATAGTA-AAAATTA-
1 ATATAGTAGAAAATTAC
5127069 ATATAGTA
1 ATATAGTA
5127077 TATATTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 6 0.27
17 8 0.36
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.35
Consensus pattern (17 bp):
ATATAGTAGAAAATTAC
Found at i:5128132 original size:30 final size:30
Alignment explanation
Indices: 5128096--5128158 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 30
5128086 TCAAATGTGA
5128096 TAAAAAGAAAGAAAAATTTAGAAACTTACT
1 TAAAAAGAAAGAAAAATTTAGAAACTTACT
5128126 T---AA-AAAGAAAAATTTAGAAACTTACT
1 TAAAAAGAAAGAAAAATTTAGAAACTTACT
5128152 TAAAAAG
1 TAAAAAG
5128159 TTTTTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
26 24 0.83
27 2 0.07
29 2 0.07
30 1 0.03
ACGTcount: A:0.60, C:0.06, G:0.10, T:0.24
Consensus pattern (30 bp):
TAAAAAGAAAGAAAAATTTAGAAACTTACT
Found at i:5128156 original size:25 final size:26
Alignment explanation
Indices: 5128103--5128158 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
5128093 TGATAAAAAG
5128103 AAAGAAAAATTTAGAAACTTACTTAA
1 AAAGAAAAATTTAGAAACTTACTTAA
5128129 AAAGAAAAATTTAGAAACTTACTTAA
1 AAAGAAAAATTTAGAAACTTACTTAA
5128155 AAAG
1 AAAG
5128159 TTTTTAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.59, C:0.07, G:0.09, T:0.25
Consensus pattern (26 bp):
AAAGAAAAATTTAGAAACTTACTTAA
Found at i:5128509 original size:27 final size:25
Alignment explanation
Indices: 5128479--5128533 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
5128469 AATAAATAAT
*
5128479 TAAAAGATAAAACAATGAGAAAGAAAA
1 TAAAAGATAAAACAA-AAGAAA-AAAA
* *
5128506 TAAAATATAAAAGAAAAGAAAAAAA
1 TAAAAGATAAAACAAAAGAAAAAAA
5128531 TAA
1 TAA
5128534 GAGAGAATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.28
26 5 0.20
27 13 0.52
ACGTcount: A:0.75, C:0.02, G:0.11, T:0.13
Consensus pattern (25 bp):
TAAAAGATAAAACAAAAGAAAAAAA
Found at i:5130118 original size:69 final size:69
Alignment explanation
Indices: 5130038--5130195 Score: 237
Period size: 69 Copynumber: 2.3 Consensus size: 69
5130028 CGGTGGAGTC
* * *
5130038 AGAAAAGCCTGACTATGGTAGAAAACCAGTTTACCAAACACAGCCAGAACAGCCAGAGTCAGGAA
1 AGAAAAGCCTGACTATGGCAGAAAACCAGTTTACCAAACACAGCCAGAAAAGCCAGAGTCAGAAA
5130103 AGGA
66 AGGA
* * **
5130107 AGAAAAGCCTGATTATGGCAGAAAACCAGTTTACCAACCAGGGCCAGAAAAGCCAGAGTCAGAAA
1 AGAAAAGCCTGACTATGGCAGAAAACCAGTTTACCAAACACAGCCAGAAAAGCCAGAGTCAGAAA
5130172 AGGA
66 AGGA
5130176 AGAAAAGCCTGA-TAATGGCA
1 AGAAAAGCCTGACT-ATGGCA
5130196 CTAAACAGAA
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
68 1 0.01
69 80 0.99
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12
Consensus pattern (69 bp):
AGAAAAGCCTGACTATGGCAGAAAACCAGTTTACCAAACACAGCCAGAAAAGCCAGAGTCAGAAA
AGGA
Found at i:5130251 original size:81 final size:82
Alignment explanation
Indices: 5130151--5130329 Score: 247
Period size: 81 Copynumber: 2.2 Consensus size: 82
5130141 CAACCAGGGC
* *
5130151 CAGAAAAGCCAGAGTCAGAAAAGGAAGAAAAGCCTGATAATGGCACTAA-ACAGAACTTCTACAA
1 CAGAAAAGCCAGAGTCAGAAAAGGAAGAAAAGCCTGATAATAGCACTAAGACAG-ACGTCTACAA
5130215 ACCGCAGCCAGAAGAAAA
65 ACCGCAGCCAGAAGAAAA
* * * *
5130233 -AGAAAAGCCAGAGTCAGAAGAGGAAGAGAAGCCTGATTATAGCACTAAGCCAGACGTCTACAAA
1 CAGAAAAGCCAGAGTCAGAAAAGGAAGAAAAGCCTGATAATAGCACTAAGACAGACGTCTACAAA
* *
5130297 CCTCAGCCAGAGGAAAA
66 CCGCAGCCAGAAGAAAA
*
5130314 CA-AAAGGCCAGAGTCA
1 CAGAAAAGCCAGAGTCA
5130330 TCACAGGAGG
Statistics
Matches: 86, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
81 82 0.95
82 4 0.05
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (82 bp):
CAGAAAAGCCAGAGTCAGAAAAGGAAGAAAAGCCTGATAATAGCACTAAGACAGACGTCTACAAA
CCGCAGCCAGAAGAAAA
Found at i:5135693 original size:25 final size:22
Alignment explanation
Indices: 5135658--5135709 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 22
5135648 TTAATAAAAC
5135658 AATAATAGTAAATTAATAAAAATT
1 AATAATAGT-AATT-ATAAAAATT
*
5135682 ATATAATAGTAATTATTAAAATT
1 A-ATAATAGTAATTATAAAAATT
5135705 AATAA
1 AATAA
5135710 ATGATAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 4 0.15
23 9 0.35
24 5 0.19
25 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (22 bp):
AATAATAGTAATTATAAAAATT
Found at i:5136912 original size:57 final size:57
Alignment explanation
Indices: 5136848--5136991 Score: 150
Period size: 57 Copynumber: 2.5 Consensus size: 57
5136838 CGAGGTCGTC
* *
5136848 AAACCAAAGCCAGAAGGAAAAGAAAAGCCTAATTATGGCACAAAGCAAGAC-AT-CT
1 AAACCAAAGCCAGAAGGAAAAGAAAAGCCTAAGTATGGCACAAAACAAGACGATGCT
* * * * * * *
5136903 ACAAGCCAAAACCAGAA-GAAAAGGAAAGGCCTGAGTATGGCAGAAAACCATACGTTGCT
1 A-AA-CCAAAGCCAGAAGGAAAA-GAAAAGCCTAAGTATGGCACAAAACAAGACGATGCT
*
5136962 AAACCAAAGCCAGAAGGAGAAGAAAAGCCT
1 AAACCAAAGCCAGAAGGAAAAGAAAAGCCT
5136992 TACCATGACA
Statistics
Matches: 71, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
55 1 0.01
56 7 0.10
57 53 0.75
58 7 0.10
59 3 0.04
ACGTcount: A:0.49, C:0.20, G:0.22, T:0.10
Consensus pattern (57 bp):
AAACCAAAGCCAGAAGGAAAAGAAAAGCCTAAGTATGGCACAAAACAAGACGATGCT
Found at i:5139300 original size:23 final size:23
Alignment explanation
Indices: 5139252--5139311 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
5139242 TGTATCTTAC
5139252 AAGATTATTGAATACTATTGATT
1 AAGATTATTGAATACTATTGATT
*
5139275 AAGATTACTTAGAA-ACTATTTA-T
1 AAGATTA-TT-GAATACTATTGATT
*
5139298 AAGATTATTAAATA
1 AAGATTATTGAATA
5139312 ATAGATGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 2 0.06
22 3 0.09
23 15 0.47
24 9 0.28
25 3 0.09
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (23 bp):
AAGATTATTGAATACTATTGATT
Found at i:5144086 original size:54 final size:56
Alignment explanation
Indices: 5144051--5144516 Score: 376
Period size: 57 Copynumber: 8.2 Consensus size: 56
5144041 GTTCACCAAA
5144051 GCAATCATCATTTACAGCGGAGGAGAAAGAGGAAGAAGAAAAAGAAGAATATTCACTCAT
1 GCAATCATCATTTACAGCGGAGGAGAAAGAGGAAGAAG----AGAAGAATATTCACTCAT
* *
5144111 GCAATCAT--TTT-CAGCGGAGGAGGAAGAGGAGGAAGAAGAAGAATATTCACTCAT
1 GCAATCATCATTTACAGCGGAGGAGAAAGAGGAAGAAG-AGAAGAATATTCACTCAT
*
5144165 GCAATCATCATTTACAGCGGAGGAGGAAGAGGAAGAAGAAGAAGAATATTCACTCAT
1 GCAATCATCATTTACAGCGGAGGAGAAAGAGGAAGAAG-AGAAGAATATTCACTCAT
* *
5144222 GCAATCATCATTTTCAGCGGAGGAAGAGGAAGAAGAAGAAGAAGAAGAAGAAGAATATCCACTCA
1 GCAATCATCATTTACAGCGGA-G--GA-G-A-AAG-AG--GAAGAAG-AGAAGAATATTCACTCA
*
5144287 C
56 T
* * * *
5144288 GCAATCATCATTTTCAGCGGAGGAAGAGGAAGTAGAAGAAGAAGAAGAAGGATGTTCAGTCAT
1 GCAATCATCATTTACAGCGGAGG-AGA--AAG-AG--GAAGAAG-AGAAGAATATTCACTCAT
* * * *
5144351 GCAATCATCATTTTCAGC--A-GAGGAAGAAGAAG-A-AGAAGAATGTTCACTCAT
1 GCAATCATCATTTACAGCGGAGGAGAAAGAGGAAGAAGAGAAGAATATTCACTCAT
* * * *
5144402 GCAATCATCATTTTCA----A-CAG--A-A-GAAG-A-AGAAGAATGTTCAGTCAT
1 GCAATCATCATTTACAGCGGAGGAGAAAGAGGAAGAAGAGAAGAATATTCACTCAT
** * * *
5144447 GCAATCATCATTTTTAGCAGAGGAGGAAGAAGAAGAAGAAGAAGAATATTCACTCAT
1 GCAATCATCATTTACAGCGGAGGAGAAAGAGGAAGAAG-AGAAGAATATTCACTCAT
5144504 GCAATCATCATTT
1 GCAATCATCATTT
5144517 TCAACAGAAG
Statistics
Matches: 357, Mismatches: 23, Indels: 55
0.82 0.05 0.13
Matches are distributed among these distances:
45 37 0.10
46 1 0.00
47 1 0.00
49 4 0.01
50 2 0.01
51 32 0.09
52 1 0.00
53 2 0.01
54 35 0.10
55 1 0.00
56 4 0.01
57 116 0.32
58 4 0.01
59 2 0.01
60 11 0.03
61 2 0.01
62 1 0.00
63 52 0.15
64 3 0.01
65 1 0.00
66 45 0.13
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.19
Consensus pattern (56 bp):
GCAATCATCATTTACAGCGGAGGAGAAAGAGGAAGAAGAGAAGAATATTCACTCAT
Found at i:5144152 original size:66 final size:63
Alignment explanation
Indices: 5144051--5144390 Score: 268
Period size: 63 Copynumber: 5.7 Consensus size: 63
5144041 GTTCACCAAA
* * *
5144051 GCAATCATCATTTACAGC--GGAGGAGAAAGAGGAAGAAG-A-AAAAGAAGAATATTCACTCAT
1 GCAA-CATCATTTTCAGCGAGGAGGAGAGAGAAGAAGAAGAAGAAAAGAAGAATATTCACTCAT
5144111 GC-A-ATCATTTTCAGCGGAGGAGGA-AGAG--G-AG--GAAG--AAGAAGAATATTCACTCAT
1 GCAACATCATTTTCAGC-GAGGAGGAGAGAGAAGAAGAAGAAGAAAAGAAGAATATTCACTCAT
* *
5144165 GCAATCATCATTTACAGC--GGA-G-GAG-GAAGAGGAAGAAG--AAGAAGAATATTCACTCAT
1 GCAA-CATCATTTTCAGCGAGGAGGAGAGAGAAGAAGAAGAAGAAAAGAAGAATATTCACTCAT
* *
5144222 GCAATCATCATTTTCAGCGGAGGAAGAG-GAAGAAGAAGAAGAAGAAGAAGAAGAATATCCACTC
1 GCAA-CATCATTTTCAGC-GAGGAGGAGAG-AGAAGAAGAAGAAGAA-AAGAAGAATATTCACTC
*
5144286 AC
62 AT
* * * *
5144288 GCAATCATCATTTTCAGC--GGAGGA-AGAGGAAGTAGAAGAAGAAGAAGAAGGATGTTCAGTCA
1 GCAA-CATCATTTTCAGCGAGGAGGAGAGA-GAAGAAGAAGAAGAA-AAGAAGAATATTCACTCA
5144350 T
63 T
5144351 GCAATCATCATTTTCAGC-A-GAGGA-AGAAGAAGAAGAAGAA
1 GCAA-CATCATTTTCAGCGAGGAGGAGAG-AGAAGAAGAAGAA
5144391 TGTTCACTCA
Statistics
Matches: 236, Mismatches: 16, Indels: 53
0.77 0.05 0.17
Matches are distributed among these distances:
52 1 0.00
53 3 0.01
54 26 0.11
55 3 0.01
56 2 0.01
57 63 0.27
59 4 0.02
60 11 0.05
61 2 0.01
62 2 0.01
63 83 0.35
64 1 0.00
66 35 0.15
ACGTcount: A:0.43, C:0.13, G:0.27, T:0.17
Consensus pattern (63 bp):
GCAACATCATTTTCAGCGAGGAGGAGAGAGAAGAAGAAGAAGAAAAGAAGAATATTCACTCAT
Found at i:5144160 original size:114 final size:115
Alignment explanation
Indices: 5144051--5144516 Score: 451
Period size: 114 Copynumber: 4.1 Consensus size: 115
5144041 GTTCACCAAA
5144051 GCAATCATCATTTACAGCGGAGGAGAAAGAGGAAGAAGAAAAAGAAGAATATTCACTCATGC-A-
1 GCAATCATCATTTACAGCGGAGGAGAAAGAGGAAGAAG-AAAAGAAGAATATTCACTCATGCAAC
5144114 ATCATTTTCAGCGGAGGAGGAAGAGGAGGAAGAAGAAGAATATTCACTCAT
65 ATCATTTTCAGCGGAGGAGGAAGAGGAGGAAGAAGAAGAATATTCACTCAT
*
5144165 GCAATCATCATTTACAGCGGAGGAGGAAGAGGAAGAAG--AAGAAGAATATTCACTCATGCAATC
1 GCAATCATCATTTACAGCGGAGGAGAAAGAGGAAGAAGAAAAGAAGAATATTCACTCATGCAA-C
* *
5144228 ATCATTTTCAGCGGAGGAAGAGGAAGAAGAAGAAGAAGAAGAAGAAGAATATCCACTCAC
65 ATCATTTTCAGCGGA-G--GAGGAAG-AG--G-AG--GAAGAAGAAGAATATTCACTCAT
* * * *
5144288 GCAATCATCATTTTCAGCGGAGGAAGAGGAAGTA-GAAGAAGAAGAAGAAGGATGTTCAGTCATG
1 GCAATCATCATTTACAGCGGAGG-AGA--AAG-AGGAAGAAGAA-AAGAAGAATATTCACTCATG
*
5144352 CAATCATCATTTTCAGC--A-GAGGAAGA--A-GAAGAAGAAGAATGTTCACTCAT
61 CAA-CATCATTTTCAGCGGAGGAGGAAGAGGAGGAAGAAGAAGAATATTCACTCAT
* * * *
5144402 GCAATCATCATTT---TC--------AACA-GAAGAAG--AAGAAGAATGTTCAGTCATGCAATC
1 GCAATCATCATTTACAGCGGAGGAGAAAGAGGAAGAAGAAAAGAAGAATATTCACTCATGCAA-C
* * * *
5144453 ATCATTTTTAGCAGAGGAGGAAGAAGAAGAAGAAGAAGAATATTCACTCAT
65 ATCATTTTCAGCGGAGGAGGAAGAGGAGGAAGAAGAAGAATATTCACTCAT
5144504 GCAATCATCATTT
1 GCAATCATCATTT
5144517 TCAACAGAAG
Statistics
Matches: 311, Mismatches: 16, Indels: 62
0.80 0.04 0.16
Matches are distributed among these distances:
96 35 0.11
98 1 0.00
99 16 0.05
100 2 0.01
101 1 0.00
102 35 0.11
111 22 0.07
112 1 0.00
114 85 0.27
115 1 0.00
117 8 0.03
118 2 0.01
120 1 0.00
121 2 0.01
122 1 0.00
123 50 0.16
124 2 0.01
126 10 0.03
127 2 0.01
129 34 0.11
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.19
Consensus pattern (115 bp):
GCAATCATCATTTACAGCGGAGGAGAAAGAGGAAGAAGAAAAGAAGAATATTCACTCATGCAACA
TCATTTTCAGCGGAGGAGGAAGAGGAGGAAGAAGAAGAATATTCACTCAT
Found at i:5144258 original size:3 final size:3
Alignment explanation
Indices: 5144244--5144276 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
5144234 TTCAGCGGAG
*
5144244 GAA GAG GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
5144277 TATCCACTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5144527 original size:51 final size:51
Alignment explanation
Indices: 5144321--5144638 Score: 364
Period size: 51 Copynumber: 6.2 Consensus size: 51
5144311 AAGAGGAAGT
* * * *
5144321 AGAAGAAGAAGAAGAAGGATGTTCAGTCATGCAATCATCATTTTCAGCAGA
1 AGAAGAAGAAGAAGAAGAATATTCACTCATGCAATCATCATTTTCAACAGA
* *
5144372 GGAAGAAGAAGAAGAAGAATGTTCACTCATGCAATCATCATTTTCAAC---
1 AGAAGAAGAAGAAGAAGAATATTCACTCATGCAATCATCATTTTCAACAGA
* * *
5144420 ---AGAAGAAGAAGAAGAATGTTCAGTCATGCAATCATCATTTTTAGCAGAGGAGGA
1 AGAAGAAGAAGAAGAAGAATATTCACTCATGCAATCATCA-TTTT--CA-A-CA-GA
5144474 AGAAGAAGAAGAAGAAGAATATTCACTCATGCAATCATCATTTTCAACAGA
1 AGAAGAAGAAGAAGAAGAATATTCACTCATGCAATCATCATTTTCAACAGA
* * * * *
5144525 AGATGAAGATGACGAAGAATATTCAC-CAATGCTATCTTCATTTTCAACAGA
1 AGAAGAAGAAGAAGAAGAATATTCACTC-ATGCAATCATCATTTTCAACAGA
* *
5144576 AGAAGAAGAAGAAGAAGGATATTCAC-CAATGGAATCATCATTTTCAACAGA
1 AGAAGAAGAAGAAGAAGAATATTCACTC-ATGCAATCATCATTTTCAACAGA
5144627 AGAAGAAGAAGA
1 AGAAGAAGAAGA
5144639 CTCACCGTTG
Statistics
Matches: 233, Mismatches: 21, Indels: 26
0.83 0.08 0.09
Matches are distributed among these distances:
45 36 0.15
46 4 0.02
48 2 0.01
49 1 0.00
50 1 0.00
51 146 0.63
52 1 0.00
53 1 0.00
54 2 0.01
56 4 0.02
57 35 0.15
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.22
Consensus pattern (51 bp):
AGAAGAAGAAGAAGAAGAATATTCACTCATGCAATCATCATTTTCAACAGA
Found at i:5144550 original size:153 final size:157
Alignment explanation
Indices: 5144261--5144588 Score: 441
Period size: 153 Copynumber: 2.1 Consensus size: 157
5144251 AAGAAGAAGA
5144261 AGAAGAAGAAGAAGAATATCCACTCACGCAATCATCATTTTCAGCGGAGGAAGAGGAAGTAGAAG
1 AGAAGAAGAAGAAGAATATCCACTCACGCAATCATCATTTTCAGC-GAGGAAGAGGAAG-AGAAG
* * * * *
5144326 AAGAAGAAGAAGGATGTTCAGTCATGCAATCATCATTTTCAGCAGAGGAAGAAGAAGAAGAAGAA
64 AAGAAGAAGAAGAATATTCACTCATGCAATCATCATTTTCAACAGAAGAAGAAGAAGAAGAAGAA
*
5144391 TGTTCACTC-ATGCAATCATCATTTTCAAC
129 TATTCAC-CAATGCAATCATCATTTTCAAC
* * * * * *
5144420 AGAAGAAGAAGAAGAATGTTCAGTCATGCAATCATCATTTTTAGC-A-GAGGAGG-A-AGAAGAA
1 AGAAGAAGAAGAAGAATATCCACTCACGCAATCATCATTTTCAGCGAGGAAGAGGAAGAGAAGAA
* * *
5144481 GAAGAAGAAGAATATTCACTCATGCAATCATCATTTTCAACAGAAGATGAAGATGACGAAGAATA
66 GAAGAAGAAGAATATTCACTCATGCAATCATCATTTTCAACAGAAGAAGAAGAAGAAGAAGAATA
* *
5144546 TTCACCAATGCTATCTTCATTTTCAAC
131 TTCACCAATGCAATCATCATTTTCAAC
5144573 AGAAGAAGAAGAAGAA
1 AGAAGAAGAAGAAGAA
5144589 GAAGGATATT
Statistics
Matches: 151, Mismatches: 17, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
152 1 0.01
153 102 0.68
155 1 0.01
156 6 0.04
157 1 0.01
159 40 0.26
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.21
Consensus pattern (157 bp):
AGAAGAAGAAGAAGAATATCCACTCACGCAATCATCATTTTCAGCGAGGAAGAGGAAGAGAAGAA
GAAGAAGAAGAATATTCACTCATGCAATCATCATTTTCAACAGAAGAAGAAGAAGAAGAAGAATA
TTCACCAATGCAATCATCATTTTCAAC
Found at i:5144676 original size:102 final size:99
Alignment explanation
Indices: 5144368--5144676 Score: 276
Period size: 102 Copynumber: 3.0 Consensus size: 99
5144358 TCATTTTCAG
* *
5144368 CAGAGGAAGAAGAAGAAGAAGAATGTTCACTCATGCAATCATCATTTTCAACAGAAGAAGAAGAA
1 CAGAAGAAGAAGAAGAAGAAGAATATTCACTCATGCAATCATCATTTTCAACAGAAGAAGAAGAA
** *
5144433 GAATGTTCAGTCATGCAATCATCATTTTTAGCAGAGG-A
66 GAAT-CACCGT--TGCAATCATCA-TTTTA-CAGAGGAA
*
5144471 -GGAAGAAGAAGAAGAAGAAGAATATTCACTCATGCAATCATCATTTTCAACAGAAGATGAAGAT
1 CAGAAGAAGAAGAAGAAGAAGAATATTCACTCATGCAATCATCATTTTCAACAG-A-A-GAAGA-
** * *
5144535 GACGAAGAATATTCACCAATGCTATCTTCATTTT-C-----AA
62 -A-GAAG-A-A-TCACCGTTGCAATCATCATTTTACAGAGGAA
* *
5144572 CAGAAGAAGAAGAAGAAGAAGGATATTCAC-CAATGGAATCATCATTTTCAACAGAAGAAGAAGA
1 CAGAAGAAGAAGAAGAAGAAGAATATTCACTC-ATGCAATCATCATTTTCAACAGAAGAAGAAGA
*
5144636 AGACTCACCGTTGCAATCATCATTTTCGACAGAAGGAA
65 AGAATCACCGTTGCAATCATCATTTT--ACAG-AGGAA
5144674 CAG
1 CAG
5144677 GGAGCTCTTC
Statistics
Matches: 167, Mismatches: 18, Indels: 43
0.73 0.08 0.19
Matches are distributed among these distances:
93 18 0.11
95 1 0.01
96 5 0.03
97 1 0.01
99 5 0.03
100 1 0.01
101 3 0.02
102 103 0.62
103 1 0.01
104 1 0.01
105 6 0.04
107 5 0.03
108 13 0.08
109 1 0.01
110 2 0.01
111 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.22
Consensus pattern (99 bp):
CAGAAGAAGAAGAAGAAGAAGAATATTCACTCATGCAATCATCATTTTCAACAGAAGAAGAAGAA
GAATCACCGTTGCAATCATCATTTTACAGAGGAA
Found at i:5156086 original size:33 final size:33
Alignment explanation
Indices: 5156015--5156107 Score: 109
Period size: 33 Copynumber: 2.8 Consensus size: 33
5156005 TGATATTAAT
* * * * *
5156015 ATGATATGTTAATATATCATAATTAATGATGAT
1 ATGATATATTAATAAATCATAATTAATAATAAA
*
5156048 GTGATATATTAATAAATCATAATTAATAATAAA
1 ATGATATATTAATAAATCATAATTAATAATAAA
5156081 ATGATATATTAATTAAA-CATAA-TAATA
1 ATGATATATTAA-TAAATCATAATTAATA
5156108 TAATTATATA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
32 5 0.10
33 43 0.83
34 4 0.08
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.39
Consensus pattern (33 bp):
ATGATATATTAATAAATCATAATTAATAATAAA
Found at i:5156097 original size:17 final size:17
Alignment explanation
Indices: 5156049--5156097 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
5156039 AATGATGATG
5156049 TGATATATTAA-T-AAA
1 TGATATATTAATTAAAA
*
5156064 TCATA-ATTAATAATAAAA
1 TGATATATTAAT--TAAAA
5156082 TGATATATTAATTAAA
1 TGATATATTAATTAAA
5156098 CATAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 5 0.19
15 4 0.15
17 5 0.19
18 7 0.26
19 6 0.22
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (17 bp):
TGATATATTAATTAAAA
Found at i:5156543 original size:20 final size:20
Alignment explanation
Indices: 5156527--5156572 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
5156517 TGTAACCGAT
5156527 GGTTGTTTTTGCCAACCGTC
1 GGTTGTTTTTGCCAACCGTC
*
5156547 GGTTGTTTTTG-CAACTGTC
1 GGTTGTTTTTGCCAACCGTC
5156566 GGTTGTT
1 GGTTGTT
5156573 GCCGATCGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (20 bp):
GGTTGTTTTTGCCAACCGTC
Found at i:5156555 original size:19 final size:19
Alignment explanation
Indices: 5156514--5156572 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
5156504 GCAGCCGTCG
*
5156514 TTTTGTAACCGAT-GGTTGT
1 TTTTGCAACCG-TCGGTTGT
5156533 TTTTGCCAACCGTCGGTTGT
1 TTTTG-CAACCGTCGGTTGT
*
5156553 TTTTGCAACTGTCGGTTGT
1 TTTTGCAACCGTCGGTTGT
5156572 T
1 T
5156573 GCCGATCGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 20 0.56
20 16 0.44
ACGTcount: A:0.12, C:0.17, G:0.25, T:0.46
Consensus pattern (19 bp):
TTTTGCAACCGTCGGTTGT
Found at i:5156897 original size:31 final size:31
Alignment explanation
Indices: 5156825--5156898 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
5156815 TCCACTCCTA
* * * *
5156825 CCGATTCCCGCCGGCCCCCTTCCCACGAGTC
1 CCGATTCCCCCCTGCCCCCCTCCCAAGAGTC
*
5156856 CCAATT-CCCCCTGCCCCCCTCCCAAGAGTC
1 CCGATTCCCCCCTGCCCCCCTCCCAAGAGTC
5156886 CCGATTCCCCCCT
1 CCGATTCCCCCCT
5156899 CCCGGCCTGG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
30 25 0.69
31 11 0.31
ACGTcount: A:0.12, C:0.57, G:0.14, T:0.18
Consensus pattern (31 bp):
CCGATTCCCCCCTGCCCCCCTCCCAAGAGTC
Found at i:5158066 original size:4 final size:4
Alignment explanation
Indices: 5158038--5158097 Score: 88
Period size: 4 Copynumber: 15.0 Consensus size: 4
5158028 TTTTTTTTCA
5158038 ATTT ATATT ATTAT ATTT A--T ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT AT-TT ATT-T ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
5158086 ATTT ATTT ATTT
1 ATTT ATTT ATTT
5158098 CTATTCAACT
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.04
4 42 0.81
5 8 0.15
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:5166109 original size:9 final size:9
Alignment explanation
Indices: 5166095--5166150 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
5166085 TTTCAAAGTC
*
5166095 TAAAAAAGA
1 TAAAAAAAA
5166104 TAAAAAAAA
1 TAAAAAAAA
*
5166113 TAAAATAAA
1 TAAAAAAAA
*
5166122 -AAATAAAA
1 TAAAAAAAA
5166130 TAGAAAAAAA
1 TA-AAAAAAA
*
5166140 -AGAAAAAA
1 TAAAAAAAA
5166148 TAA
1 TAA
5166151 TACCTAAATG
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
8 12 0.32
9 19 0.51
10 6 0.16
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.12
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:5166122 original size:12 final size:12
Alignment explanation
Indices: 5166107--5166150 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
5166097 AAAAAGATAA
5166107 AAAAAATAAAAT
1 AAAAAATAAAAT
5166119 AAAAAATAAAAT
1 AAAAAATAAAAT
* *
5166131 AGAAAA-AAAAG
1 AAAAAATAAAAT
5166142 AAAAAATAA
1 AAAAAATAA
5166151 TACCTAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:5166140 original size:23 final size:21
Alignment explanation
Indices: 5166097--5166150 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
5166087 TCAAAGTCTA
* *
5166097 AAAAAGATAAAAAAAATAAAAT
1 AAAAA-ATAAAAAAAAAAAAAG
5166119 AAAAAATAAAATAGAAAAAAAAG
1 AAAAAATAAAA-A-AAAAAAAAG
5166142 AAAAAATAA
1 AAAAAATAA
5166151 TACCTAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 6 0.21
22 6 0.21
23 16 0.57
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (21 bp):
AAAAAATAAAAAAAAAAAAAG
Found at i:5167091 original size:15 final size:15
Alignment explanation
Indices: 5167073--5167120 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
5167063 ATAATTATTT
*
5167073 ATATTTTTTTATATA
1 ATATTTTTTTATAAA
* *
5167088 ATATTATATTATAAA
1 ATATTTTTTTATAAA
5167103 ATAATTTTTTTA-AAA
1 AT-ATTTTTTTATAAA
5167118 ATA
1 ATA
5167121 AATAATAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 1 0.04
15 19 0.70
16 7 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATATTTTTTTATAAA
Found at i:5169728 original size:21 final size:21
Alignment explanation
Indices: 5169704--5169748 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5169694 CGCAAACTCT
* *
5169704 AATACTACTAATTTTTACATA
1 AATACTACTAATTATTAAATA
* *
5169725 AATATTATTAATTATTAAATA
1 AATACTACTAATTATTAAATA
5169746 AAT
1 AAT
5169749 TTTTATTAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (21 bp):
AATACTACTAATTATTAAATA
Found at i:5169852 original size:53 final size:53
Alignment explanation
Indices: 5169725--5169852 Score: 179
Period size: 53 Copynumber: 2.4 Consensus size: 53
5169715 TTTTTACATA
*
5169725 AATATTATTAATTATTAAATAAATTTTTATTAACCGGTAACACTAATTCAAAC
1 AATATTTTTAATTATTAAATAAATTTTTATTAACCGGTAACACTAATTCAAAC
* * *
5169778 AATA-TTTT-ATATATGAGAATAAATTTTTATTAACTGGTGACACTAATTCAAAC
1 AATATTTTTAAT-TATTA-AATAAATTTTTATTAACCGGTAACACTAATTCAAAC
*
5169831 AGTATTTTTAATTATTAAATAA
1 AATATTTTTAATTATTAAATAA
5169853 TCCATATGCC
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
51 2 0.03
52 7 0.11
53 46 0.71
54 8 0.12
55 2 0.03
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (53 bp):
AATATTTTTAATTATTAAATAAATTTTTATTAACCGGTAACACTAATTCAAAC
Found at i:5171579 original size:21 final size:21
Alignment explanation
Indices: 5171546--5171606 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
5171536 AGTTAATGTA
**
5171546 TTTTTATTTTAAATTAAAAAT
1 TTTTTATAATAAATTAAAAAT
5171567 TTTTTATAATAAA-TAAATAAT
1 TTTTTATAATAAATTAAA-AAT
** * *
5171588 TAATTATCATTAATTAAAA
1 TTTTTATAATAAATTAAAA
5171607 TATCACTCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 4 0.12
21 24 0.75
22 4 0.12
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTTATAATAAATTAAAAAT
Found at i:5178656 original size:15 final size:16
Alignment explanation
Indices: 5178630--5178659 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5178620 TTTTTAATTT
5178630 TTAAAAATTAAAATCA
1 TTAAAAATTAAAATCA
5178646 TTAAAAA-TAAAATC
1 TTAAAAATTAAAATC
5178660 CACATAACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAAAAATTAAAATCA
Found at i:5178814 original size:25 final size:25
Alignment explanation
Indices: 5178778--5178835 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
5178768 ATATATGAGC
*
5178778 AAATAAAATATAATTA-AAAAACA-T
1 AAATAAAATATAAATAGAAAAA-ATT
5178802 AAATAATAATATAAATAGAAAAAATT
1 AAATAA-AATATAAATAGAAAAAATT
5178828 AAATAAAA
1 AAATAAAA
5178836 ACTTTACCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 6 0.20
25 12 0.40
26 12 0.40
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (25 bp):
AAATAAAATATAAATAGAAAAAATT
Found at i:5198320 original size:2 final size:2
Alignment explanation
Indices: 5198313--5198341 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5198303 TCACTGCTTT
5198313 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5198342 GATTGATTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.